From a15fd1fcb8558802ad6bc32ced8eb92940e978cf Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 30 Mar 2023 17:29:08 +0200
Subject: [PATCH 01/78] fix assertion linters

n, min, max, ... accept bytes (eg 500k)

i.e. the type annotation and thereby linting was wrong
I suggest to remove it, since its tested in the xsd linter
anyway (otherwise we would check for str)
---
 lib/galaxy/tool_util/linters/tests.py    | 14 +-------------
 test/unit/tool_util/test_tool_linters.py |  5 ++---
 2 files changed, 3 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
index fd99d3f8d3e3..e156b9927e74 100644
--- a/lib/galaxy/tool_util/linters/tests.py
+++ b/lib/galaxy/tool_util/linters/tests.py
@@ -152,23 +152,11 @@ def _check_asserts(test_idx, assertions, lint_ctx):
                 lint_ctx.error(f"Test {test_idx}: unknown assertion '{a.tag}'", node=a)
                 continue
             assert_function_sig = signature(asserts.assertion_functions[assert_function_name])
-            # check type of the attributes (int, float ...)
+            # check of the attributes
             for attrib in a.attrib:
                 if attrib not in assert_function_sig.parameters:
                     lint_ctx.error(f"Test {test_idx}: unknown attribute '{attrib}' for '{a.tag}'", node=a)
                     continue
-                annotation = assert_function_sig.parameters[attrib].annotation
-                annotation = _handle_optionals(annotation)
-                if annotation is not Parameter.empty:
-                    try:
-                        annotation(a.attrib[attrib])
-                    except TypeError:
-                        raise Exception(f"Faild to instantiate {attrib} for {assert_function_name}")
-                    except ValueError:
-                        lint_ctx.error(
-                            f"Test {test_idx}: attribute '{attrib}' for '{a.tag}' needs to be '{annotation.__name__}' got '{a.attrib[attrib]}'",
-                            node=a,
-                        )
             # check missing required attributes
             for p in assert_function_sig.parameters:
                 if p in ["output", "output_bytes", "verify_assertions_function", "children"]:
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 089c07dd02a6..254d077c1eaa 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -1562,8 +1562,7 @@ def test_tests_asserts(lint_ctx):
     assert "Test 1: unknown assertion 'invalid'" in lint_ctx.error_messages
     assert "Test 1: unknown attribute 'invalid_attrib' for 'has_text'" in lint_ctx.error_messages
     assert "Test 1: missing attribute 'text' for 'has_text'" in lint_ctx.error_messages
-    assert "Test 1: attribute 'value' for 'has_size' needs to be 'int' got '500k'" in lint_ctx.error_messages
-    assert "Test 1: attribute 'delta' for 'has_size' needs to be 'int' got '1O'" in lint_ctx.error_messages
+    assert "Test 1: attribute 'value' for 'has_size' needs to be 'int' got '500k'" not in lint_ctx.error_messages
     assert (
         "Test 1: unknown attribute 'invalid_attrib_also_checked_in_nested_asserts' for 'not_has_text'"
         in lint_ctx.error_messages
@@ -1572,7 +1571,7 @@ def test_tests_asserts(lint_ctx):
     assert "Test 1: 'has_n_columns' needs to specify 'n', 'min', or 'max'" in lint_ctx.error_messages
     assert "Test 1: 'has_n_lines' needs to specify 'n', 'min', or 'max'" in lint_ctx.error_messages
     assert not lint_ctx.warn_messages
-    assert len(lint_ctx.error_messages) == 9
+    assert len(lint_ctx.error_messages) == 7
 
 
 def test_tests_output_type_mismatch(lint_ctx):

From 566a87d01ded3963408c99f601623cd23e9cca12 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 30 Mar 2023 17:31:13 +0200
Subject: [PATCH 02/78] fix type annotations for assertions

the functions always get a str (from the xml attributes)
---
 lib/galaxy/tool_util/verify/asserts/_util.py  | 33 ++++++++++--
 .../tool_util/verify/asserts/archive.py       | 12 ++---
 lib/galaxy/tool_util/verify/asserts/size.py   | 10 ++--
 .../tool_util/verify/asserts/tabular.py       | 10 ++--
 lib/galaxy/tool_util/verify/asserts/text.py   | 50 +++++++++----------
 lib/galaxy/tool_util/verify/asserts/xml.py    | 32 ++++++------
 6 files changed, 86 insertions(+), 61 deletions(-)

diff --git a/lib/galaxy/tool_util/verify/asserts/_util.py b/lib/galaxy/tool_util/verify/asserts/_util.py
index c8f6281c760f..d852e1350968 100644
--- a/lib/galaxy/tool_util/verify/asserts/_util.py
+++ b/lib/galaxy/tool_util/verify/asserts/_util.py
@@ -1,10 +1,24 @@
 from math import inf
+from typing import (
+    Any,
+    Callable,
+    Optional
+)
 
 from galaxy.util import asbool
 from galaxy.util.bytesize import parse_bytesize
 
 
-def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text):
+def _assert_number(
+    count,
+    n: Optional[str],
+    delta: str,
+    min: Optional[str],
+    max: Optional[str],
+    negate: str,
+    n_text,
+    min_max_text
+):
     """
     helper function for assering that count is in
     - [n-delta:n+delta]
@@ -26,12 +40,12 @@ def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text):
         )
     if min is not None or max is not None:
         if min is None:
-            min = -inf  # also replacing min/max for output
+            min = "-inf"  # also replacing min/max for output
             min_bytes = -inf
         else:
             min_bytes = parse_bytesize(min)
         if max is None:
-            max = inf
+            max = "inf"
             max_bytes = inf
         else:
             max_bytes = parse_bytesize(max)
@@ -42,7 +56,18 @@ def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text):
 
 
 def _assert_presence_number(
-    output, text, n, delta, min, max, negate, check_presence_foo, count_foo, presence_text, n_text, min_max_text
+    output,
+    text,
+    n: Optional[str],
+    delta: str,
+    min: Optional[str],
+    max: Optional[str],
+    negate: str,
+    check_presence_foo: Callable[[Any, Any], bool],
+    count_foo: Callable[[Any, Any], int],
+    presence_text: str,
+    n_text: str,
+    min_max_text: str
 ):
     """
     helper function to assert that
diff --git a/lib/galaxy/tool_util/verify/asserts/archive.py b/lib/galaxy/tool_util/verify/asserts/archive.py
index a65bb814df34..fc86ebf94f2c 100644
--- a/lib/galaxy/tool_util/verify/asserts/archive.py
+++ b/lib/galaxy/tool_util/verify/asserts/archive.py
@@ -55,12 +55,12 @@ def assert_has_archive_member(
     path,
     verify_assertions_function,
     children,
-    all="false",
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    all="False",
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """Recursively checks the specified children assertions against the text of
     the first element matching the specified path found within the archive.
diff --git a/lib/galaxy/tool_util/verify/asserts/size.py b/lib/galaxy/tool_util/verify/asserts/size.py
index 089ba5492276..4a3cc31912ed 100644
--- a/lib/galaxy/tool_util/verify/asserts/size.py
+++ b/lib/galaxy/tool_util/verify/asserts/size.py
@@ -5,11 +5,11 @@
 
 def assert_has_size(
     output_bytes,
-    value: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    value: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """
     Asserts the specified output has a size of the specified value,
diff --git a/lib/galaxy/tool_util/verify/asserts/tabular.py b/lib/galaxy/tool_util/verify/asserts/tabular.py
index 6679fa9c06b5..5dfdb2899f27 100644
--- a/lib/galaxy/tool_util/verify/asserts/tabular.py
+++ b/lib/galaxy/tool_util/verify/asserts/tabular.py
@@ -20,13 +20,13 @@ def get_first_line(output, comment):
 
 def assert_has_n_columns(
     output,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
     sep="\t",
     comment="",
-    negate: bool = False,
+    negate: str = "False",
 ):
     """Asserts the tabular output contains n columns. The optional
     sep argument specifies the column seperator used to determine the
diff --git a/lib/galaxy/tool_util/verify/asserts/text.py b/lib/galaxy/tool_util/verify/asserts/text.py
index a29a88bb3364..7365ca4ddf88 100644
--- a/lib/galaxy/tool_util/verify/asserts/text.py
+++ b/lib/galaxy/tool_util/verify/asserts/text.py
@@ -10,11 +10,11 @@
 def assert_has_text(
     output,
     text,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """Asserts specified output contains the substring specified by
     the argument text. The exact number of occurrences can be
@@ -46,11 +46,11 @@ def assert_not_has_text(output, text):
 def assert_has_line(
     output,
     line,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """Asserts the specified output contains the line specified by the
     argument line. The exact number of occurrences can be optionally
@@ -74,11 +74,11 @@ def assert_has_line(
 
 def assert_has_n_lines(
     output,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """Asserts the specified output contains ``n`` lines allowing
     for a difference in the number of lines (delta)
@@ -100,11 +100,11 @@ def assert_has_n_lines(
 def assert_has_text_matching(
     output,
     expression,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """Asserts the specified output contains text matching the
     regular expression specified by the argument expression.
@@ -130,11 +130,11 @@ def assert_has_text_matching(
 def assert_has_line_matching(
     output,
     expression,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """Asserts the specified output contains a line matching the
     regular expression specified by the argument expression. If n is given
diff --git a/lib/galaxy/tool_util/verify/asserts/xml.py b/lib/galaxy/tool_util/verify/asserts/xml.py
index 14d858d38bb0..98efc01ebe41 100644
--- a/lib/galaxy/tool_util/verify/asserts/xml.py
+++ b/lib/galaxy/tool_util/verify/asserts/xml.py
@@ -20,7 +20,7 @@ def assert_is_valid_xml(output):
         raise AssertionError(f"Expected valid XML, but could not parse output. {unicodify(e)}")
 
 
-def assert_has_element_with_path(output, path, negate: bool = False):
+def assert_has_element_with_path(output, path, negate: str = "False"):
     """Asserts the specified output has at least one XML element with a
     path matching the specified path argument. Valid paths are the
     simplified subsets of XPath implemented by lxml.etree;
@@ -31,44 +31,44 @@ def assert_has_element_with_path(output, path, negate: bool = False):
 def assert_has_n_elements_with_path(
     output,
     path,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """Asserts the specified output has exactly n elements matching the
     path specified."""
     assert_xml_element(output, path, n=n, delta=delta, min=min, max=max, negate=negate)
 
 
-def assert_element_text_matches(output, path, expression, negate: bool = False):
+def assert_element_text_matches(output, path, expression, negate: str = "False"):
     """Asserts the text of the first element matching the specified
     path matches the specified regular expression."""
     sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub])
 
 
-def assert_element_text_is(output, path, text, negate: bool = False):
+def assert_element_text_is(output, path, text, negate: str = "False"):
     """Asserts the text of the first element matching the specified
     path matches exactly the specified text."""
     assert_element_text_matches(output, path, re.escape(text) + "$", negate=negate)
 
 
-def assert_attribute_matches(output, path, attribute, expression, negate: bool = False):
+def assert_attribute_matches(output, path, attribute, expression, negate: str = "False"):
     """Asserts the specified attribute of the first element matching
     the specified path matches the specified regular expression."""
     sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub], attribute=attribute)
 
 
-def assert_attribute_is(output, path, attribute, text, negate: bool = False):
+def assert_attribute_is(output, path, attribute, text, negate: str = "False"):
     """Asserts the specified attribute of the first element matching
     the specified path matches exactly the specified text."""
     assert_attribute_matches(output, path, attribute, re.escape(text) + "$", negate=negate)
 
 
-def assert_element_text(output, path, verify_assertions_function, children, negate: bool = False):
+def assert_element_text(output, path, verify_assertions_function, children, negate: str = "False"):
     """Recursively checks the specified assertions against the text of
     the first element matching the specified path."""
     assert_xml_element(output, path, verify_assertions_function, children, negate=negate)
@@ -81,11 +81,11 @@ def assert_xml_element(
     children=None,
     attribute=None,
     all=False,
-    n: Optional[int] = None,
-    delta: int = 0,
-    min: Optional[int] = None,
-    max: Optional[int] = None,
-    negate: bool = False,
+    n: Optional[str] = None,
+    delta: str = "0",
+    min: Optional[str] = None,
+    max: Optional[str] = None,
+    negate: str = "False",
 ):
     """
     Check if path occurs in the xml. If n and delta or min and max are given

From fd7963b09bcebda7af94e01a764ba24b9794ac27 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 30 Mar 2023 22:26:34 +0200
Subject: [PATCH 03/78] assertion typing: allow int/bool in addition to str

---
 .../tool_util/verify/asserts/__init__.py      |  2 +-
 lib/galaxy/tool_util/verify/asserts/_util.py  | 49 ++++++-----
 .../tool_util/verify/asserts/archive.py       | 39 +++++----
 lib/galaxy/tool_util/verify/asserts/hdf5.py   |  7 +-
 lib/galaxy/tool_util/verify/asserts/size.py   | 16 ++--
 .../tool_util/verify/asserts/tabular.py       | 25 +++---
 lib/galaxy/tool_util/verify/asserts/text.py   | 85 ++++++++++---------
 lib/galaxy/tool_util/verify/asserts/xml.py    | 59 +++++++------
 8 files changed, 151 insertions(+), 131 deletions(-)

diff --git a/lib/galaxy/tool_util/verify/asserts/__init__.py b/lib/galaxy/tool_util/verify/asserts/__init__.py
index 58b38debbf0c..d154e81f2bf8 100644
--- a/lib/galaxy/tool_util/verify/asserts/__init__.py
+++ b/lib/galaxy/tool_util/verify/asserts/__init__.py
@@ -60,7 +60,7 @@ def verify_assertion(data, assertion_description):
     # output. children is the parsed version of the child elements of
     # the XML element describing this assertion. See
     # assert_element_text in test/base/asserts/xml.py as an example of
-    # how to use verify_assertions_function and children in conjuction
+    # how to use verify_assertions_function and children in conjunction
     # to apply assertion checking to a subset of the input. The parsed
     # version of an elements child elements do not need to just define
     # assertions, developers of assertion functions can also use the
diff --git a/lib/galaxy/tool_util/verify/asserts/_util.py b/lib/galaxy/tool_util/verify/asserts/_util.py
index d852e1350968..2e3b604e98dc 100644
--- a/lib/galaxy/tool_util/verify/asserts/_util.py
+++ b/lib/galaxy/tool_util/verify/asserts/_util.py
@@ -1,8 +1,9 @@
 from math import inf
 from typing import (
-    Any,
     Callable,
-    Optional
+    Optional,
+    TypeVar,
+    Union,
 )
 
 from galaxy.util import asbool
@@ -10,15 +11,15 @@
 
 
 def _assert_number(
-    count,
-    n: Optional[str],
-    delta: str,
-    min: Optional[str],
-    max: Optional[str],
-    negate: str,
-    n_text,
-    min_max_text
-):
+    count: int,
+    n: Optional[Union[int, str]],
+    delta: Union[int, str],
+    min: Optional[Union[int, str]],
+    max: Optional[Union[int, str]],
+    negate: Union[bool, str],
+    n_text: str,
+    min_max_text: str,
+) -> None:
     """
     helper function for assering that count is in
     - [n-delta:n+delta]
@@ -55,20 +56,24 @@ def _assert_number(
         )
 
 
+OutputType = TypeVar("OutputType")
+TextType = TypeVar("TextType")
+
+
 def _assert_presence_number(
-    output,
-    text,
-    n: Optional[str],
-    delta: str,
-    min: Optional[str],
-    max: Optional[str],
-    negate: str,
-    check_presence_foo: Callable[[Any, Any], bool],
-    count_foo: Callable[[Any, Any], int],
+    output: OutputType,
+    text: TextType,
+    n: Optional[Union[int, str]],
+    delta: Union[int, str],
+    min: Optional[Union[int, str]],
+    max: Optional[Union[int, str]],
+    negate: Union[bool, str],
+    check_presence_foo: Callable[[OutputType, TextType], bool],
+    count_foo: Callable[[OutputType, TextType], int],
     presence_text: str,
     n_text: str,
-    min_max_text: str
-):
+    min_max_text: str,
+) -> None:
     """
     helper function to assert that
     - text is present in output using check_presence_foo
diff --git a/lib/galaxy/tool_util/verify/asserts/archive.py b/lib/galaxy/tool_util/verify/asserts/archive.py
index fc86ebf94f2c..5244dc90e1f8 100644
--- a/lib/galaxy/tool_util/verify/asserts/archive.py
+++ b/lib/galaxy/tool_util/verify/asserts/archive.py
@@ -3,14 +3,17 @@
 import tarfile
 import tempfile
 import zipfile
-from typing import Optional
+from typing import (
+    Union,
+    Optional,
+)
 
 from galaxy.util import asbool
 from ._util import _assert_presence_number
 
 
-def _extract_from_tar(bytes, fn):
-    with io.BytesIO(bytes) as temp:
+def _extract_from_tar(output_bytes, fn):
+    with io.BytesIO(output_bytes) as temp:
         with tarfile.open(fileobj=temp, mode="r") as tar_temp:
             ti = tar_temp.getmember(fn)
             # zip treats directories like empty files.
@@ -21,9 +24,9 @@ def _extract_from_tar(bytes, fn):
                 return member_fh.read()
 
 
-def _list_from_tar(bytes, path):
+def _list_from_tar(output_bytes, path):
     lst = list()
-    with io.BytesIO(bytes) as temp:
+    with io.BytesIO(output_bytes) as temp:
         with tarfile.open(fileobj=temp, mode="r") as tar_temp:
             for fn in tar_temp.getnames():
                 if not re.match(path, fn):
@@ -32,16 +35,16 @@ def _list_from_tar(bytes, path):
     return sorted(lst)
 
 
-def _extract_from_zip(bytes, fn):
-    with io.BytesIO(bytes) as temp:
+def _extract_from_zip(output_bytes, fn):
+    with io.BytesIO(output_bytes) as temp:
         with zipfile.ZipFile(temp, mode="r") as zip_temp:
             with zip_temp.open(fn) as member_fh:
                 return member_fh.read()
 
 
-def _list_from_zip(bytes, path):
+def _list_from_zip(output_bytes, path):
     lst = list()
-    with io.BytesIO(bytes) as temp:
+    with io.BytesIO(output_bytes) as temp:
         with zipfile.ZipFile(temp, mode="r") as zip_temp:
             for fn in zip_temp.namelist():
                 if not re.match(path, fn):
@@ -51,17 +54,17 @@ def _list_from_zip(bytes, path):
 
 
 def assert_has_archive_member(
-    output_bytes,
-    path,
+    output_bytes: bytes,
+    path: str,
     verify_assertions_function,
     children,
-    all="False",
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    all: Union[bool, str] = False,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """Recursively checks the specified children assertions against the text of
     the first element matching the specified path found within the archive.
     Currently supported formats: .zip, .tar, .tar.gz."""
diff --git a/lib/galaxy/tool_util/verify/asserts/hdf5.py b/lib/galaxy/tool_util/verify/asserts/hdf5.py
index 8eab9f747945..e94c61c3af04 100644
--- a/lib/galaxy/tool_util/verify/asserts/hdf5.py
+++ b/lib/galaxy/tool_util/verify/asserts/hdf5.py
@@ -13,7 +13,7 @@ def _assert_h5py():
         raise Exception(IMPORT_MISSING_MESSAGE)
 
 
-def assert_has_h5_attribute(output_bytes, key, value):
+def assert_has_h5_attribute(output_bytes: bytes, key: str, value: str) -> None:
     """Asserts the specified HDF5 output has a given key-value pair as HDF5
     attribute"""
     _assert_h5py()
@@ -25,11 +25,10 @@ def assert_has_h5_attribute(output_bytes, key, value):
 
 
 # TODO the function actually queries groups. so the function and argument name are misleading
-def assert_has_h5_keys(output_bytes, keys):
+def assert_has_h5_keys(output_bytes: bytes, keys: str) -> None:
     """Asserts the specified HDF5 output has the given keys."""
     _assert_h5py()
-    keys = [k.strip() for k in keys.strip().split(",")]
-    h5_keys = sorted(keys)
+    h5_keys = sorted([k.strip() for k in keys.strip().split(",")])
     output_temp = io.BytesIO(output_bytes)
     local_keys = []
 
diff --git a/lib/galaxy/tool_util/verify/asserts/size.py b/lib/galaxy/tool_util/verify/asserts/size.py
index 4a3cc31912ed..8282a918f03f 100644
--- a/lib/galaxy/tool_util/verify/asserts/size.py
+++ b/lib/galaxy/tool_util/verify/asserts/size.py
@@ -1,16 +1,16 @@
-from typing import Optional
+from typing import Union, Optional
 
 from ._util import _assert_number
 
 
 def assert_has_size(
-    output_bytes,
-    value: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    output_bytes: bytes,
+    value: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """
     Asserts the specified output has a size of the specified value,
     allowing for absolute (delta) and relative (delta_frac) difference.
diff --git a/lib/galaxy/tool_util/verify/asserts/tabular.py b/lib/galaxy/tool_util/verify/asserts/tabular.py
index 5dfdb2899f27..1d046f60ca07 100644
--- a/lib/galaxy/tool_util/verify/asserts/tabular.py
+++ b/lib/galaxy/tool_util/verify/asserts/tabular.py
@@ -1,10 +1,13 @@
 import re
-from typing import Optional
+from typing import (
+    Union,
+    Optional,
+)
 
 from ._util import _assert_number
 
 
-def get_first_line(output, comment):
+def get_first_line(output: str, comment: str) -> str:
     """
     get the first non-comment and non-empty line
     """
@@ -19,15 +22,15 @@ def get_first_line(output, comment):
 
 
 def assert_has_n_columns(
-    output,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    sep="\t",
-    comment="",
-    negate: str = "False",
-):
+    output: str,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    sep: str = "\t",
+    comment: str = "",
+    negate: Union[bool, str] = False,
+) -> None:
     """Asserts the tabular output contains n columns. The optional
     sep argument specifies the column seperator used to determine the
     number of columns. The optional comment argument specifies
diff --git a/lib/galaxy/tool_util/verify/asserts/text.py b/lib/galaxy/tool_util/verify/asserts/text.py
index 7365ca4ddf88..b6e0f39d04c5 100644
--- a/lib/galaxy/tool_util/verify/asserts/text.py
+++ b/lib/galaxy/tool_util/verify/asserts/text.py
@@ -1,5 +1,8 @@
 import re
-from typing import Optional
+from typing import (
+    Optional,
+    Union,
+)
 
 from ._util import (
     _assert_number,
@@ -8,14 +11,14 @@
 
 
 def assert_has_text(
-    output,
-    text,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    output: str,
+    text: str,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """Asserts specified output contains the substring specified by
     the argument text. The exact number of occurrences can be
     optionally specified by the argument n"""
@@ -36,7 +39,7 @@ def assert_has_text(
     )
 
 
-def assert_not_has_text(output, text):
+def assert_not_has_text(output: str, text: str) -> None:
     """Asserts specified output does not contain the substring
     specified by the argument text"""
     assert output is not None, "Checking not_has_text assertion on empty output (None)"
@@ -44,14 +47,14 @@ def assert_not_has_text(output, text):
 
 
 def assert_has_line(
-    output,
-    line,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    output: str,
+    line: str,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """Asserts the specified output contains the line specified by the
     argument line. The exact number of occurrences can be optionally
     specified by the argument n"""
@@ -73,13 +76,13 @@ def assert_has_line(
 
 
 def assert_has_n_lines(
-    output,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    output: str,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """Asserts the specified output contains ``n`` lines allowing
     for a difference in the number of lines (delta)
     or relative differebce in the number of lines"""
@@ -98,14 +101,14 @@ def assert_has_n_lines(
 
 
 def assert_has_text_matching(
-    output,
-    expression,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    output: str,
+    expression: str,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """Asserts the specified output contains text matching the
     regular expression specified by the argument expression.
     If n is given the assertion checks for exacly n (nonoverlapping)
@@ -128,14 +131,14 @@ def assert_has_text_matching(
 
 
 def assert_has_line_matching(
-    output,
-    expression,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    output: str,
+    expression: str,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """Asserts the specified output contains a line matching the
     regular expression specified by the argument expression. If n is given
     the assertion checks for exactly n occurences."""
diff --git a/lib/galaxy/tool_util/verify/asserts/xml.py b/lib/galaxy/tool_util/verify/asserts/xml.py
index 98efc01ebe41..b081ac22e59c 100644
--- a/lib/galaxy/tool_util/verify/asserts/xml.py
+++ b/lib/galaxy/tool_util/verify/asserts/xml.py
@@ -1,5 +1,8 @@
 import re
-from typing import Optional
+from typing import (
+    Union,
+    Optional,
+)
 
 from lxml.etree import XMLSyntaxError
 
@@ -11,7 +14,7 @@
 )
 
 
-def assert_is_valid_xml(output):
+def assert_is_valid_xml(output: str) -> None:
     """Simple assertion that just verifies the specified output
     is valid XML."""
     try:
@@ -20,7 +23,7 @@ def assert_is_valid_xml(output):
         raise AssertionError(f"Expected valid XML, but could not parse output. {unicodify(e)}")
 
 
-def assert_has_element_with_path(output, path, negate: str = "False"):
+def assert_has_element_with_path(output: str, path: str, negate: Union[bool, str] = False) -> None:
     """Asserts the specified output has at least one XML element with a
     path matching the specified path argument. Valid paths are the
     simplified subsets of XPath implemented by lxml.etree;
@@ -29,64 +32,68 @@ def assert_has_element_with_path(output, path, negate: str = "False"):
 
 
 def assert_has_n_elements_with_path(
-    output,
-    path,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    output: str,
+    path: str,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """Asserts the specified output has exactly n elements matching the
     path specified."""
     assert_xml_element(output, path, n=n, delta=delta, min=min, max=max, negate=negate)
 
 
-def assert_element_text_matches(output, path, expression, negate: str = "False"):
+def assert_element_text_matches(output: str, path: str, expression: str, negate: Union[bool, str] = False) -> None:
     """Asserts the text of the first element matching the specified
     path matches the specified regular expression."""
     sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub])
 
 
-def assert_element_text_is(output, path, text, negate: str = "False"):
+def assert_element_text_is(output: str, path: str, text: str, negate: Union[bool, str] = False) -> None:
     """Asserts the text of the first element matching the specified
     path matches exactly the specified text."""
     assert_element_text_matches(output, path, re.escape(text) + "$", negate=negate)
 
 
-def assert_attribute_matches(output, path, attribute, expression, negate: str = "False"):
+def assert_attribute_matches(
+    output: str, path: str, attribute, expression: str, negate: Union[bool, str] = False
+) -> None:
     """Asserts the specified attribute of the first element matching
     the specified path matches the specified regular expression."""
     sub = {"tag": "has_text_matching", "attributes": {"expression": expression, "negate": negate}}
     assert_xml_element(output, path, asserts.verify_assertions, [sub], attribute=attribute)
 
 
-def assert_attribute_is(output, path, attribute, text, negate: str = "False"):
+def assert_attribute_is(output: str, path: str, attribute: str, text, negate: Union[bool, str] = False) -> None:
     """Asserts the specified attribute of the first element matching
     the specified path matches exactly the specified text."""
     assert_attribute_matches(output, path, attribute, re.escape(text) + "$", negate=negate)
 
 
-def assert_element_text(output, path, verify_assertions_function, children, negate: str = "False"):
+def assert_element_text(
+    output: str, path: str, verify_assertions_function, children, negate: Union[bool, str] = False
+) -> None:
     """Recursively checks the specified assertions against the text of
     the first element matching the specified path."""
     assert_xml_element(output, path, verify_assertions_function, children, negate=negate)
 
 
 def assert_xml_element(
-    output,
-    path,
+    output: str,
+    path: str,
     verify_assertions_function=None,
     children=None,
-    attribute=None,
-    all=False,
-    n: Optional[str] = None,
-    delta: str = "0",
-    min: Optional[str] = None,
-    max: Optional[str] = None,
-    negate: str = "False",
-):
+    attribute: Optional[str] = None,
+    all: Union[bool, str] = False,
+    n: Optional[Union[int, str]] = None,
+    delta: Union[int, str] = 0,
+    min: Optional[Union[int, str]] = None,
+    max: Optional[Union[int, str]] = None,
+    negate: Union[bool, str] = False,
+) -> None:
     """
     Check if path occurs in the xml. If n and delta or min and max are given
     also the number of occurences is checked.

From ed7c2d6584fe0372050e353a4a65012043e2c82c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 20 Apr 2023 09:48:16 -0400
Subject: [PATCH 04/78] Handle empty lines better in tabular display dataset
 parsing

---
 .../components/Visualizations/Tabular/TabularChunkedView.vue   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Visualizations/Tabular/TabularChunkedView.vue b/client/src/components/Visualizations/Tabular/TabularChunkedView.vue
index c5c1cfddcdb2..1125c6adcf15 100644
--- a/client/src/components/Visualizations/Tabular/TabularChunkedView.vue
+++ b/client/src/components/Visualizations/Tabular/TabularChunkedView.vue
@@ -88,7 +88,8 @@ function processChunk(chunk: TabularChunk) {
         parsedChunk = chunk.ck_data.trim().split("\n");
         parsedChunk = parsedChunk.map((line) => {
             try {
-                return parse(line, { delimiter: delimiter.value })[0];
+                const parsedLine = parse(line, { delimiter: delimiter.value })[0];
+                return parsedLine || [line];
             } catch (error) {
                 // Failing lines get passed through intact for row-level
                 // rendering/parsing.

From c6067f739c5170cd123eec07a4af8a049ff3ae00 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 20 Apr 2023 10:40:31 -0400
Subject: [PATCH 05/78] Expand last column to fill tabular display table for
 better formatting

---
 .../Visualizations/Tabular/TabularChunkedView.vue         | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Visualizations/Tabular/TabularChunkedView.vue b/client/src/components/Visualizations/Tabular/TabularChunkedView.vue
index 1125c6adcf15..f0142e99ca38 100644
--- a/client/src/components/Visualizations/Tabular/TabularChunkedView.vue
+++ b/client/src/components/Visualizations/Tabular/TabularChunkedView.vue
@@ -181,9 +181,15 @@ onMounted(() => {
             </b-thead>
             <b-tbody>
                 <b-tr v-for="(row, index) in tabularData.rows" :key="index">
-                    <b-td v-for="(element, elementIndex) in row" :key="elementIndex" :class="columnStyle[elementIndex]">
+                    <b-td
+                        v-for="(element, elementIndex) in row.slice(0, -1)"
+                        :key="elementIndex"
+                        :class="columnStyle[elementIndex]">
                         {{ element }}
                     </b-td>
+                    <b-td :class="columnStyle[row.length - 1]" :colspan="1 + columns.length - row.length">
+                        {{ row.slice(-1)[0] }}
+                    </b-td>
                 </b-tr>
             </b-tbody>
         </b-table-simple>

From 2328939bc03a75dcfbcb5f71884df8166589bf32 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 25 Apr 2023 11:33:20 +0200
Subject: [PATCH 06/78] Display history name

This will retrieve the history from the server for now. I should be replaced by the corresponding pinia store in the next release.
---
 .../History/Export/HistoryExport.test.ts      | 13 +++++++++++
 .../History/Export/HistoryExport.vue          | 22 ++++++++++++++++++-
 2 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/Export/HistoryExport.test.ts b/client/src/components/History/Export/HistoryExport.test.ts
index e2ec1de4f383..ea620ea40ed5 100644
--- a/client/src/components/History/Export/HistoryExport.test.ts
+++ b/client/src/components/History/Export/HistoryExport.test.ts
@@ -19,7 +19,13 @@ const mockGetExportRecords = getExportRecords as jest.MockedFunction<typeof getE
 mockGetExportRecords.mockResolvedValue([]);
 
 const FAKE_HISTORY_ID = "fake-history-id";
+const FAKE_HISTORY = {
+    id: FAKE_HISTORY_ID,
+    name: "fake-history-name",
+};
+
 const REMOTE_FILES_API_ENDPOINT = new RegExp("/api/remote_files/plugins");
+const GET_HISTORY_ENDPOINT = new RegExp(`/api/histories/${FAKE_HISTORY_ID}`);
 
 type FilesSourcePluginList = components["schemas"]["FilesSourcePlugin"][];
 const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [
@@ -50,12 +56,19 @@ describe("HistoryExport.vue", () => {
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
         axiosMock.onGet(REMOTE_FILES_API_ENDPOINT).reply(200, []);
+        axiosMock.onGet(GET_HISTORY_ENDPOINT).reply(200, FAKE_HISTORY);
     });
 
     afterEach(() => {
         axiosMock.restore();
     });
 
+    it("should render the history name", async () => {
+        const wrapper = await mountHistoryExport();
+
+        expect(wrapper.find("#history-name").text()).toBe(FAKE_HISTORY.name);
+    });
+
     it("should render export options", async () => {
         const wrapper = await mountHistoryExport();
 
diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index d506da0ec9d6..2e559e2895f7 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -6,6 +6,7 @@ import ExportRecordDetails from "components/Common/ExportRecordDetails.vue";
 import ExportRecordTable from "components/Common/ExportRecordTable.vue";
 import ExportOptions from "./ExportOptions.vue";
 import ExportToFileSourceForm from "components/Common/ExportForm.vue";
+import { getHistoryById } from "@/store/historyStore/model/queries";
 import { getExportRecords, exportToFileSource, reimportHistoryFromRecord } from "./services";
 import { useTaskMonitor } from "composables/taskMonitor";
 import { useFileSources } from "composables/fileSources";
@@ -13,6 +14,9 @@ import { useShortTermStorage, DEFAULT_EXPORT_PARAMS } from "composables/shortTer
 import { useConfirmDialog } from "composables/confirmDialog";
 import { copy as sendToClipboard } from "utils/clipboard";
 import { absPath } from "@/utils/redirect";
+import { faFileExport } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
 
 const {
     isRunning: isExportTaskRunning,
@@ -39,11 +43,18 @@ const props = defineProps({
     },
 });
 
+library.add(faFileExport);
+
 const POLLING_DELAY = 3000;
 
+const history = ref(null);
+const isLoadingHistory = ref(true);
+
 const exportParams = reactive(DEFAULT_EXPORT_PARAMS);
 const isLoadingRecords = ref(true);
 const exportRecords = ref(null);
+
+const historyName = computed(() => history.value?.name ?? props.historyId);
 const latestExportRecord = computed(() => (exportRecords.value?.length ? exportRecords.value.at(0) : null));
 const previousExportRecords = computed(() => (exportRecords.value ? exportRecords.value.slice(1) : null));
 const hasPreviousExports = computed(() => previousExportRecords.value?.length > 0);
@@ -58,6 +69,10 @@ const actionMessageVariant = ref(null);
 
 onMounted(async () => {
     updateExports();
+    //TODO: replace direct query with useHistoriesStore in 23.1
+    isLoadingHistory.value = true;
+    history.value = await getHistoryById(props.historyId);
+    isLoadingHistory.value = false;
 });
 
 watch(isExportTaskRunning, (newValue, oldValue) => {
@@ -161,7 +176,12 @@ function updateExportParams(newParams) {
 </script>
 <template>
     <span class="history-export-component">
-        <h1 class="h-lg">Export history {{ props.historyId }}</h1>
+        <font-awesome-icon icon="file-export" size="2x" class="text-primary float-left mr-2" />
+        <h1 class="h-lg">
+            Export
+            <loading-span v-if="isLoadingHistory" spinner-only />
+            <b v-else id="history-name">{{ historyName }}</b>
+        </h1>
 
         <export-options
             id="history-export-options"

From 385f15417056fdedb85188843f3584d73dc6a710 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 25 Apr 2023 13:34:17 +0200
Subject: [PATCH 07/78] Expose 'prepare only' actions for STS composable

This allows to prepare downloads in the Short Term Storage without directly serve the resulting file.
---
 client/src/composables/shortTermStorage.js | 46 ++++++++++++++++------
 1 file changed, 34 insertions(+), 12 deletions(-)

diff --git a/client/src/composables/shortTermStorage.js b/client/src/composables/shortTermStorage.js
index 8b78cc013737..5bbc9a807c5b 100644
--- a/client/src/composables/shortTermStorage.js
+++ b/client/src/composables/shortTermStorage.js
@@ -22,12 +22,20 @@ export function useShortTermStorage() {
 
     const isPreparing = ref(false);
 
+    async function prepareHistoryDownload(historyId, options = DEFAULT_OPTIONS) {
+        return prepareObjectDownload(historyId, "histories", options, false);
+    }
+
     async function downloadHistory(historyId, options = DEFAULT_OPTIONS) {
-        return prepareObjectDownload(historyId, "histories", options);
+        return prepareObjectDownload(historyId, "histories", options, true);
+    }
+
+    async function prepareWorkflowInvocationDownload(invocationId, options = DEFAULT_OPTIONS) {
+        return prepareObjectDownload(invocationId, "invocations", options, false);
     }
 
     async function downloadWorkflowInvocation(invocationId, options = DEFAULT_OPTIONS) {
-        return prepareObjectDownload(invocationId, "invocations", options);
+        return prepareObjectDownload(invocationId, "invocations", options, true);
     }
 
     function getDownloadObjectUrl(storageRequestId) {
@@ -40,7 +48,7 @@ export function useShortTermStorage() {
         window.location.assign(url);
     }
 
-    async function prepareObjectDownload(object_id, object_api, options = DEFAULT_OPTIONS) {
+    async function prepareObjectDownload(object_id, object_api, options = DEFAULT_OPTIONS, downloadWhenReady = true) {
         const finalOptions = Object.assign(DEFAULT_OPTIONS, options);
         resetTimeout();
         isPreparing.value = true;
@@ -54,29 +62,31 @@ export function useShortTermStorage() {
         };
 
         const response = await axios.post(url, exportParams).catch(handleError);
-        handleInitialize(response);
+        handleInitialize(response, downloadWhenReady);
     }
 
-    function handleInitialize(response) {
+    function handleInitialize(response, downloadWhenReady) {
         const storageRequestId = response.data.storage_request_id;
-        pollStorageRequestId(storageRequestId);
+        pollStorageRequestId(storageRequestId, downloadWhenReady);
     }
 
-    function pollStorageRequestId(storageRequestId) {
+    function pollStorageRequestId(storageRequestId, downloadWhenReady) {
         const url = withPrefix(`/api/short_term_storage/${storageRequestId}/ready`);
         axios
             .get(url)
             .then((r) => {
-                handlePollResponse(r, storageRequestId);
+                handlePollResponse(r, storageRequestId, downloadWhenReady);
             })
             .catch(handleError);
     }
 
-    function handlePollResponse(response, storageRequestId) {
+    function handlePollResponse(response, storageRequestId, downloadWhenReady) {
         const ready = response.data;
         if (ready) {
             isPreparing.value = false;
-            downloadObjectByRequestId(storageRequestId);
+            if (downloadWhenReady) {
+                downloadObjectByRequestId(storageRequestId);
+            }
         } else {
             pollAfterDelay(storageRequestId);
         }
@@ -103,13 +113,25 @@ export function useShortTermStorage() {
 
     return {
         /**
-         * Starts preparing a history download file. When `isPreparing` is false the download will start automatically.
+         * Starts preparing a history download file in the short term storage.
+         * @param {String} historyId The ID of the history to be prepared for download
+         * @param {Object} options Options for the download preparation
+         */
+        prepareHistoryDownload,
+        /**
+         * Prepares a history download file in the short term storage and starts the download when ready.
          * @param {String} historyId The ID of the history to be downloaded
          * @param {Object} options Options for the download preparation
          */
         downloadHistory,
         /**
-         * Starts preparing a workflow invocation download file. When `isPreparing` is false the download will start automatically.
+         * Starts preparing a workflow invocation download file in the short term storage.
+         * @param {String} invocationId The ID of the workflow invocation to be prepared for download
+         * @param {Object} options Options for the download preparation
+         */
+        prepareWorkflowInvocationDownload,
+        /**
+         * Starts preparing a workflow invocation download file in the short term storage and starts the download when ready.
          * @param {String} invocationId The ID of the workflow invocation to be downloaded
          * @param {Object} options Options for the download preparation
          */

From 18891fd72f7fc1f7c2f4b371e2f4a78ed42a549b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 25 Apr 2023 14:04:05 +0200
Subject: [PATCH 08/78] Make direct downloads more obvious

Now the download "preparation" step has been clearly separated from the download form the export record.
Hopefully this will make more obvious that the first step now only prepares the history to be downloaded and once the export record is ready you can download it from there.
---
 .../History/Export/HistoryExport.vue          | 70 +++++++++----------
 client/src/utils/navigation/navigation.yml    |  2 +-
 2 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index 2e559e2895f7..850a034eb5d1 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -5,7 +5,7 @@ import LoadingSpan from "components/LoadingSpan";
 import ExportRecordDetails from "components/Common/ExportRecordDetails.vue";
 import ExportRecordTable from "components/Common/ExportRecordTable.vue";
 import ExportOptions from "./ExportOptions.vue";
-import ExportToFileSourceForm from "components/Common/ExportForm.vue";
+import ExportForm from "components/Common/ExportForm.vue";
 import { getHistoryById } from "@/store/historyStore/model/queries";
 import { getExportRecords, exportToFileSource, reimportHistoryFromRecord } from "./services";
 import { useTaskMonitor } from "composables/taskMonitor";
@@ -29,7 +29,7 @@ const { hasWritable: hasWritableFileSources } = useFileSources();
 
 const {
     isPreparing: isPreparingDownload,
-    downloadHistory,
+    prepareHistoryDownload,
     downloadObjectByRequestId,
     getDownloadObjectUrl,
 } = useShortTermStorage();
@@ -56,6 +56,14 @@ const exportRecords = ref(null);
 
 const historyName = computed(() => history.value?.name ?? props.historyId);
 const latestExportRecord = computed(() => (exportRecords.value?.length ? exportRecords.value.at(0) : null));
+const isLatestExportRecordReadyToDownload = computed(
+    () =>
+        latestExportRecord.value &&
+        latestExportRecord.value.isUpToDate &&
+        latestExportRecord.value.canDownload &&
+        latestExportRecord.value.exportParams?.equals(exportParams)
+);
+const canGenerateDownload = computed(() => !isPreparingDownload.value && !isLatestExportRecordReadyToDownload.value);
 const previousExportRecords = computed(() => (exportRecords.value ? exportRecords.value.slice(1) : null));
 const hasPreviousExports = computed(() => previousExportRecords.value?.length > 0);
 const availableRecordsMessage = computed(() =>
@@ -114,12 +122,7 @@ async function doExportToFileSource(exportDirectory, fileName) {
 }
 
 async function prepareDownload() {
-    const upToDateDownloadRecord = findValidUpToDateDownloadRecord();
-    if (upToDateDownloadRecord) {
-        downloadObjectByRequestId(upToDateDownloadRecord.stsDownloadId);
-        return;
-    }
-    await downloadHistory(props.historyId, { pollDelayInMs: POLLING_DELAY, exportParams: exportParams });
+    await prepareHistoryDownload(props.historyId, { pollDelayInMs: POLLING_DELAY, exportParams: exportParams });
     updateExports();
 }
 
@@ -136,14 +139,6 @@ function copyDownloadLinkFromRecord(record) {
     }
 }
 
-function findValidUpToDateDownloadRecord() {
-    return exportRecords.value
-        ? exportRecords.value.find(
-              (record) => record.canDownload && record.isUpToDate && record.exportParams?.equals(exportParams)
-          )
-        : null;
-}
-
 async function reimportFromRecord(record) {
     const confirmed = await confirm(
         `Do you really want to import a new copy of this history exported ${record.elapsedTime}?`
@@ -185,11 +180,13 @@ function updateExportParams(newParams) {
 
         <export-options
             id="history-export-options"
+            class="mt-3"
             :export-params="exportParams"
             @onValueChanged="updateExportParams" />
 
+        <h2 class="h-md mt-3">How do you want to export this history?</h2>
         <b-card no-body class="mt-3">
-            <b-tabs pills card>
+            <b-tabs pills card vertical>
                 <b-tab id="direct-download-tab" title="to direct download" title-link-class="tab-export-to-link" active>
                     <p>
                         Here you can generate a temporal download for your history. When your download link expires or
@@ -201,15 +198,19 @@ function updateExportParams(newParams) {
                         Galaxy server.
                     </b-alert>
                     <b-button
-                        class="direct-download-btn"
-                        :disabled="isPreparingDownload"
+                        class="gen-direct-download-btn"
+                        :disabled="!canGenerateDownload"
                         variant="primary"
                         @click="prepareDownload">
-                        Download
+                        Generate direct download
                     </b-button>
                     <span v-if="isPreparingDownload">
                         <loading-span message="Galaxy is preparing your download, this will likely take a while" />
                     </span>
+                    <b-alert v-else-if="isLatestExportRecordReadyToDownload" variant="success" class="mt-3" show>
+                        The latest export record is ready. Use the download button below to download it or change the
+                        advanced export options above to generate a new one.
+                    </b-alert>
                 </b-tab>
                 <b-tab
                     v-if="hasWritableFileSources"
@@ -221,10 +222,7 @@ function updateExportParams(newParams) {
                         one of the available remote file sources here. You will be able to re-import it later as long as
                         it remains available on the remote server.
                     </p>
-                    <export-to-file-source-form
-                        what="history"
-                        :clear-input-after-export="true"
-                        @export="doExportToFileSource" />
+                    <export-form what="history" :clear-input-after-export="true" @export="doExportToFileSource" />
                 </b-tab>
             </b-tabs>
         </b-card>
@@ -232,17 +230,19 @@ function updateExportParams(newParams) {
         <b-alert v-if="errorMessage" id="last-export-record-error-alert" variant="danger" class="mt-3" show>
             {{ errorMessage }}
         </b-alert>
-        <export-record-details
-            v-else-if="latestExportRecord"
-            :record="latestExportRecord"
-            object-type="history"
-            class="mt-3"
-            :action-message="actionMessage"
-            :action-message-variant="actionMessageVariant"
-            @onDownload="downloadFromRecord"
-            @onCopyDownloadLink="copyDownloadLinkFromRecord"
-            @onReimport="reimportFromRecord"
-            @onActionMessageDismissed="onActionMessageDismissedFromRecord" />
+        <div v-else-if="latestExportRecord">
+            <h2 class="h-md mt-3">Latest Export Record</h2>
+            <export-record-details
+                :record="latestExportRecord"
+                object-type="history"
+                class="mt-3"
+                :action-message="actionMessage"
+                :action-message-variant="actionMessageVariant"
+                @onDownload="downloadFromRecord"
+                @onCopyDownloadLink="copyDownloadLinkFromRecord"
+                @onReimport="reimportFromRecord"
+                @onActionMessageDismissed="onActionMessageDismissedFromRecord" />
+        </div>
         <b-alert v-else id="no-export-records-alert" variant="info" class="mt-3" show>
             {{ availableRecordsMessage }}
         </b-alert>
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 1cfcaa675675..0777dfec4d8a 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -425,7 +425,7 @@ history_export:
 
 history_export_tasks:
   selectors:
-    direct_download: '.direct-download-btn'
+    direct_download: '.gen-direct-download-btn'
     file_source_tab: '.tab-export-to-file'
     remote_file_name_input: '#file-source-tab #name'
     toggle_options_link: '#toggle-options-link'

From 029a27db4900cb4b47ccb38c384b10a76df7bded Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 26 Apr 2023 15:39:59 +0200
Subject: [PATCH 09/78] Reset the selection after building a collection

Independently of whether the source items are hidden or not
---
 .../CurrentHistory/HistoryOperations/SelectionOperations.vue    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
index d389d4b92e98..0fd838023c71 100644
--- a/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
+++ b/client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue
@@ -320,8 +320,8 @@ export default {
             // have to hide the source items if that was requested
             if (modalResult.hide_source_items) {
                 this.$emit("hide-selection", this.contentSelection);
-                this.$emit("reset-selection");
             }
+            this.$emit("reset-selection");
         },
     },
 };

From 4dda1b57c54dedb92a914d698c06e8dc9ad264c6 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 26 Apr 2023 15:57:36 +0200
Subject: [PATCH 10/78] Clarify search behavior in placeholder text

Searching by annotation ot tag requires to use the prefix `tag:` or `annotation:`.
---
 client/src/components/History/HistoryPublishedList.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/History/HistoryPublishedList.vue b/client/src/components/History/HistoryPublishedList.vue
index 4fcec5e2d868..2f8bec7863b1 100644
--- a/client/src/components/History/HistoryPublishedList.vue
+++ b/client/src/components/History/HistoryPublishedList.vue
@@ -133,7 +133,7 @@ watch([filterText, sortBy, sortDesc], () => {
                         size="sm"
                         :class="filterText && 'font-weight-bold'"
                         :value="value"
-                        :placeholder="'Search name, annotation and tags' | localize"
+                        :placeholder="'Search by name or use the advanced filtering options' | localize"
                         title="clear search (esc)"
                         data-description="filter text input"
                         @input="input"

From 7229cf0b6c1eb80b42cf73b3fdb5664b047e33d6 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Thu, 20 Apr 2023 23:41:59 +0200
Subject: [PATCH 11/78] Improve display chunk generation for BAMs

The new version is faster even for lines containing multiple tabs and
optimizes the no or one tag cases.
It also fixes a subtle bug that would drop a line at chunk boundaries.
---
 lib/galaxy/datatypes/binary.py | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 356f73a67288..6fc9a14497ab 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -607,30 +607,34 @@ def get_chunk(self, trans, dataset: "DatasetInstance", offset: int = 0, ck_size:
             try:
                 with pysam.AlignmentFile(dataset.file_name, "rb", check_sq=False) as bamfile:
                     ck_size = 300  # 300 lines
-                    ck_data = ""
-                    header_line_count = 0
                     if offset == 0:
-                        ck_data = bamfile.text.replace("\t", " ")  # type: ignore[attr-defined]
-                        header_line_count = bamfile.text.count("\n")  # type: ignore[attr-defined]
+                        offset = bamfile.tell()
+                        ck_lines = bamfile.text.strip().replace("\t", " ").splitlines()  # type: ignore[attr-defined]
                     else:
                         bamfile.seek(offset)
-                    for line_number, alignment in enumerate(bamfile):
+                        ck_lines = []
+                    for line_number, alignment in enumerate(bamfile, len(ck_lines)):
                         # return only Header lines if 'header_line_count' exceeds 'ck_size'
                         # FIXME: Can be problematic if bam has million lines of header
-                        offset = bamfile.tell()
-                        if (line_number + header_line_count) > ck_size:
+                        if line_number > ck_size:
                             break
-                        else:
-                            bamline = alignment.tostring(bamfile)
-                            # Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.
-                            # Below code will remove spaces between each tag.
-                            bamline_modified = ("\t").join(bamline.split()[:11] + [(" ").join(bamline.split()[11:])])
-                            ck_data = f"{ck_data}\n{bamline_modified}"
+
+                        offset = bamfile.tell()
+                        bamline = alignment.tostring(bamfile)
+                        # With multiple tags, Galaxy would display each as a separate column
+                        # because the 'tostring()' function uses tabs also between tags.
+                        # Below code will turn these extra tabs into spaces.
+                        n_tabs = bamline.count('\t')
+                        if n_tabs > 11:
+                            bamline, *extra_tags = bamline.rsplit('\t', maxsplit=n_tabs - 11)
+                            bamline = f"{bamline} {' '.join(extra_tags)
+                        ck_lines.append(f"{bamline} {' '.join(extra_tags)}")
                     else:
                         # Nothing to enumerate; we've either offset to the end
                         # of the bamfile, or there is no data. (possible with
                         # header-only bams)
                         offset = -1
+                    ck_data = "\n".join(ck_lines)
             except Exception as e:
                 offset = -1
                 ck_data = f"Could not display BAM file, error was:\n{e}"

From 65c16ab1e808b12bd00a53c99149a35c9b793b63 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Thu, 20 Apr 2023 23:57:57 +0200
Subject: [PATCH 12/78] Fix wrongly saved file

---
 lib/galaxy/datatypes/binary.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 6fc9a14497ab..b3a9e498b78a 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -627,8 +627,8 @@ def get_chunk(self, trans, dataset: "DatasetInstance", offset: int = 0, ck_size:
                         n_tabs = bamline.count('\t')
                         if n_tabs > 11:
                             bamline, *extra_tags = bamline.rsplit('\t', maxsplit=n_tabs - 11)
-                            bamline = f"{bamline} {' '.join(extra_tags)
-                        ck_lines.append(f"{bamline} {' '.join(extra_tags)}")
+                            bamline = f"{bamline} {' '.join(extra_tags)}"
+                        ck_lines.append(bamline)
                     else:
                         # Nothing to enumerate; we've either offset to the end
                         # of the bamfile, or there is no data. (possible with

From e6c7c2b066cfd797c6e6499af485b05ac5b1cf12 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Fri, 21 Apr 2023 09:12:23 +0200
Subject: [PATCH 13/78] Fix linting

---
 lib/galaxy/datatypes/binary.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index b3a9e498b78a..cc6702cd589f 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -624,9 +624,9 @@ def get_chunk(self, trans, dataset: "DatasetInstance", offset: int = 0, ck_size:
                         # With multiple tags, Galaxy would display each as a separate column
                         # because the 'tostring()' function uses tabs also between tags.
                         # Below code will turn these extra tabs into spaces.
-                        n_tabs = bamline.count('\t')
+                        n_tabs = bamline.count("\t")
                         if n_tabs > 11:
-                            bamline, *extra_tags = bamline.rsplit('\t', maxsplit=n_tabs - 11)
+                            bamline, *extra_tags = bamline.rsplit("\t", maxsplit=n_tabs - 11)
                             bamline = f"{bamline} {' '.join(extra_tags)}"
                         ck_lines.append(bamline)
                     else:

From e178967deb478ec1e67c7cc139c2f1b24cf1335b Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 27 Apr 2023 14:15:46 +0200
Subject: [PATCH 14/78] Remove no longer valid TODO comment

The rocrate.zip model_store_format is covered now under the `ModelStoreFormat.is_compressed` condition since it is a zip file.
---
 lib/galaxy/model/store/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 97205084ac72..67272baf70e6 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2957,7 +2957,6 @@ def source_to_import_store(
                     target_path, import_options=import_options, app=app, user=galaxy_user
                 )
             else:
-                # TODO: rocrate.zip is not supported here...
                 raise Exception(f"Unknown model_store_format type encountered {model_store_format}")
 
     return model_import_store

From 6ec4020165c6515f7e995a08d07604616635de61 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 27 Apr 2023 17:40:09 +0200
Subject: [PATCH 15/78] Add test case for missing dataset file

---
 .../integration/test_history_import_export.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/test/integration/test_history_import_export.py b/test/integration/test_history_import_export.py
index 8c27338e5014..20fe8faae7fe 100644
--- a/test/integration/test_history_import_export.py
+++ b/test/integration/test_history_import_export.py
@@ -7,6 +7,7 @@
     history_model_store_dict,
     one_hda_model_store_dict,
 )
+from galaxy.util import unlink
 from galaxy_test.api.test_histories import ImportExportTests
 from galaxy_test.base.api import UsesCeleryTasks
 from galaxy_test.base.api_asserts import assert_has_keys
@@ -198,6 +199,24 @@ def test_export_history_with_discarded_dataset_to_rocrate(self):
         self._wait_for_export_task_on_record(last_record)
         assert last_record["ready"] is True
 
+    def test_export_missing_dataset_fails(self):
+        history_name = f"for_export_failure_{uuid4()}"
+        model_store_format = "rocrate.zip"
+        target_uri = f"gxfiles://posix_test/{history_name}.{model_store_format}"
+        history_id = self.dataset_populator.new_history(history_name)
+        hda = self.dataset_populator.new_dataset(history_id, wait=True)
+
+        # Simulate data loss or some unexpected problem with the dataset file.
+        assert os.path.exists(hda["file_name"])
+        unlink(hda["file_name"])
+        assert not os.path.exists(hda["file_name"])
+
+        # Ensure the export task fails
+        with self.assertRaisesRegex(Exception, "task failed"):
+            self.dataset_populator.export_history_to_uri_async(
+                history_id, target_uri=target_uri, model_store_format=model_store_format, include_files=True
+            )
+
     def _wait_for_export_task_on_record(self, record):
         if record["preparing"]:
             assert record["task_uuid"]

From 6c535128b88ba3b1bd49d08d26118400685b28f8 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 27 Apr 2023 17:52:00 +0200
Subject: [PATCH 16/78] Rename add_dataset to include_dataset_file

A little bit clearer
---
 lib/galaxy/model/store/__init__.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 67272baf70e6..538fa69c58e5 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2128,12 +2128,12 @@ def export_history(
         datasets = query.all()
         for dataset in datasets:
             dataset.annotation = get_item_annotation_str(sa_session, history.user, dataset)
-            add_dataset = (dataset.visible or include_hidden) and (not dataset.deleted or include_deleted)
+            should_include_file = (dataset.visible or include_hidden) and (not dataset.deleted or include_deleted)
             if dataset.id in self.collection_datasets:
-                add_dataset = True
+                should_include_file = True
 
             if dataset not in self.included_datasets:
-                self.add_dataset(dataset, include_files=add_dataset)
+                self.add_dataset(dataset, include_files=should_include_file)
 
     def export_library(
         self, library: model.Library, include_hidden: bool = False, include_deleted: bool = False
@@ -2153,8 +2153,8 @@ def export_library_folder_contents(
     ) -> None:
         for library_dataset in library_folder.datasets:
             ldda = library_dataset.library_dataset_dataset_association
-            add_dataset = (not ldda.visible or not include_hidden) and (not ldda.deleted or include_deleted)
-            self.add_dataset(ldda, add_dataset)
+            should_include_file = (not ldda.visible or not include_hidden) and (not ldda.deleted or include_deleted)
+            self.add_dataset(ldda, should_include_file)
         for folder in library_folder.folders:
             self.export_library_folder_contents(folder, include_hidden=include_hidden, include_deleted=include_deleted)
 

From a41a098962dd3c2a067cf7809093a8cc834f090e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 27 Apr 2023 18:24:40 +0200
Subject: [PATCH 17/78] Allow setting auto_decompress property in staging
 interface

This allows defining inputs such as
```
     Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz:
       class: File
       location: https://zenodo.org/record/6457007/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz
       filetype: gtf
       decompress: true
```

without needing to know what the server side default of auto_compress
is.
---
 lib/galaxy/tool_util/client/staging.py   |  4 +++
 lib/galaxy/tool_util/cwl/util.py         |  2 ++
 lib/galaxy_test/api/test_tools_upload.py | 34 ++++++++++++++++++++++++
 3 files changed, 40 insertions(+)

diff --git a/lib/galaxy/tool_util/client/staging.py b/lib/galaxy/tool_util/client/staging.py
index ca7d0bf64405..46ea37b5858c 100644
--- a/lib/galaxy/tool_util/client/staging.py
+++ b/lib/galaxy/tool_util/client/staging.py
@@ -40,6 +40,7 @@
 DEFAULT_USE_FETCH_API = True
 DEFAULT_FILE_TYPE = "auto"
 DEFAULT_DBKEY = "?"
+DEFAULT_DECOMPRESS = False
 
 
 class StagingInterface(metaclass=abc.ABCMeta):
@@ -104,6 +105,7 @@ def _attach_file(upload_payload: Dict[str, Any], uri: str, index: int = 0) -> Di
                     file_type=file_type,
                     dbkey=dbkey,
                     to_posix_lines=to_posix_lines,
+                    decompress=upload_target.properties.get("decompress") or DEFAULT_DECOMPRESS,
                 )
                 name = _file_path_to_name(file_path)
                 if file_path is not None:
@@ -333,6 +335,8 @@ def _fetch_payload(history_id, file_type=DEFAULT_FILE_TYPE, dbkey=DEFAULT_DBKEY,
             element[arg] = kwd[arg]
     if "file_name" in kwd:
         element["name"] = kwd["file_name"]
+    if "decompress" in kwd:
+        element["auto_decompress"] = kwd["decompress"]
     target = {
         "destination": {"type": "hdas"},
         "elements": [element],
diff --git a/lib/galaxy/tool_util/cwl/util.py b/lib/galaxy/tool_util/cwl/util.py
index d78650ec41aa..18e40beb1e7c 100644
--- a/lib/galaxy/tool_util/cwl/util.py
+++ b/lib/galaxy/tool_util/cwl/util.py
@@ -232,6 +232,8 @@ def replacement_file(value):
             kwd["tags"] = value.get("tags")
         if "dbkey" in value:
             kwd["dbkey"] = value.get("dbkey")
+        if "decompress" in value:
+            kwd["decompress"] = value["decompress"]
         if composite_data_raw:
             composite_data = []
             for entry in composite_data_raw:
diff --git a/lib/galaxy_test/api/test_tools_upload.py b/lib/galaxy_test/api/test_tools_upload.py
index db0d5fe27305..3a4a60bb52fc 100644
--- a/lib/galaxy_test/api/test_tools_upload.py
+++ b/lib/galaxy_test/api/test_tools_upload.py
@@ -280,6 +280,40 @@ def test_newlines_stage_fetch_configured(self, history_id: str) -> None:
         details = self.dataset_populator.get_history_dataset_details(history_id=history_id, dataset=dataset)
         assert details["genome_build"] == "hg19"
 
+    @skip_if_github_down
+    def test_stage_fetch_decompress_true(self, history_id: str) -> None:
+        job = {
+            "input1": {
+                "class": "File",
+                "format": "fasta",
+                "location": "https://github.com/galaxyproject/galaxy/blob/dev/test-data/1.fasta.gz?raw=true",
+                "decompress": True,
+            }
+        }
+        inputs, datasets = stage_inputs(
+            self.galaxy_interactor, history_id, job, use_path_paste=False, to_posix_lines=False
+        )
+        dataset = datasets[0]
+        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)
+        assert content.startswith(">hg17")
+
+    @skip_if_github_down
+    def test_stage_fetch_decompress_false(self, history_id: str) -> None:
+        job = {
+            "input1": {
+                "class": "File",
+                "format": "fasta",
+                "location": "https://github.com/galaxyproject/galaxy/blob/dev/test-data/1.fasta.gz?raw=true",
+                "decompress": False,
+            }
+        }
+        inputs, datasets = stage_inputs(
+            self.galaxy_interactor, history_id, job, use_path_paste=False, to_posix_lines=False
+        )
+        dataset = datasets[0]
+        content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset)
+        assert not content.startswith(">hg17")
+
     @skip_if_github_down
     def test_upload_multiple_mixed_success(self, history_id):
         destination = {"type": "hdas"}

From 2c9f23576a97b4b9ed4540a0645d06d002cb39bb Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 20 Mar 2023 13:03:08 +0100
Subject: [PATCH 18/78] convert WorkflowEdges to canvas

Signed-off-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 .../components/Workflow/Editor/Connector.vue  |  80 ----------
 .../Workflow/Editor/TerminalConnector.vue     |  61 --------
 .../Workflow/Editor/WorkflowEdges.vue         | 105 +++++++++----
 .../Workflow/Editor/WorkflowGraph.vue         |  12 +-
 .../Editor/composables/drawableConnection.ts  | 146 ++++++++++++++++++
 client/src/utils/navigation/navigation.yml    |   2 -
 .../selenium/test_workflow_editor.py          |  27 ++--
 7 files changed, 248 insertions(+), 185 deletions(-)
 delete mode 100644 client/src/components/Workflow/Editor/Connector.vue
 delete mode 100644 client/src/components/Workflow/Editor/TerminalConnector.vue
 create mode 100644 client/src/components/Workflow/Editor/composables/drawableConnection.ts

diff --git a/client/src/components/Workflow/Editor/Connector.vue b/client/src/components/Workflow/Editor/Connector.vue
deleted file mode 100644
index 863a130a7994..000000000000
--- a/client/src/components/Workflow/Editor/Connector.vue
+++ /dev/null
@@ -1,80 +0,0 @@
-<template>
-    <g :id="id" :class="ribbonClasses">
-        <g v-for="svgLine in paths" :key="svgLine">
-            <path class="ribbon-outer" :d="svgLine" :stroke-width="stroke.outerStroke" fill="none"></path>
-            <path :class="innerClass" :d="svgLine" :stroke-width="stroke.innerStroke" fill="none"></path>
-        </g>
-    </g>
-</template>
-<script lang="ts" setup>
-import { line, curveBasis } from "d3";
-import { computed } from "vue";
-import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
-
-const props = withDefaults(
-    defineProps<{
-        id?: string;
-        position: TerminalPosition;
-        inputIsMappedOver: boolean;
-        outputIsMappedOver: boolean;
-        connectionIsValid?: boolean;
-        nullable?: boolean;
-    }>(),
-    {
-        id: undefined,
-        inputIsMappedOver: false,
-        outputIsMappedOver: false,
-        connectionIsValid: true,
-        nullable: false,
-    }
-);
-
-const path = line().curve(curveBasis);
-
-const ribbonMargin = 4;
-const lineShift = 30;
-
-const stroke = computed(() => {
-    let innerStroke = 4;
-    let outerStroke = 6;
-    if (props.outputIsMappedOver || props.inputIsMappedOver) {
-        innerStroke = 1;
-        outerStroke = 3;
-    }
-    return { innerStroke, outerStroke };
-});
-
-const ribbonClasses = computed(() => (props.nullable ? "ribbon dashed" : "ribbon"));
-const innerClass = computed(() => (props.connectionIsValid ? "ribbon-inner" : "ribbon-inner ribbon-inner-invalid"));
-
-const offsets = computed(() => {
-    const _offsets = [-2 * ribbonMargin, -ribbonMargin, 0, ribbonMargin, 2 * ribbonMargin];
-    let startOffsets = [0];
-    let endOffsets = [0];
-    let numOffsets = 1;
-
-    if (props.outputIsMappedOver) {
-        startOffsets = _offsets;
-        numOffsets = _offsets.length;
-    }
-    if (props.inputIsMappedOver) {
-        endOffsets = _offsets;
-        numOffsets = _offsets.length;
-    }
-    return { numOffsets, startOffsets, endOffsets };
-});
-
-const paths = computed(() => {
-    const lines = [...Array(offsets.value.numOffsets).keys()].map((offsetIndex) => {
-        const startOffset = offsets.value.startOffsets[offsetIndex] || 0;
-        const endOffset = offsets.value.endOffsets[offsetIndex] || 0;
-        return [
-            [props.position.startX, props.position.startY + startOffset],
-            [props.position.startX + lineShift, props.position.startY + startOffset],
-            [props.position.endX - lineShift, props.position.endY + endOffset],
-            [props.position.endX, props.position.endY + endOffset],
-        ] as [number, number][];
-    });
-    return lines.map((line) => path(line)!);
-});
-</script>
diff --git a/client/src/components/Workflow/Editor/TerminalConnector.vue b/client/src/components/Workflow/Editor/TerminalConnector.vue
deleted file mode 100644
index 5830982e5d08..000000000000
--- a/client/src/components/Workflow/Editor/TerminalConnector.vue
+++ /dev/null
@@ -1,61 +0,0 @@
-<template>
-    <raw-connector
-        v-if="position"
-        :id="connectionId"
-        :position="position"
-        :output-is-mapped-over="outputIsMappedOver"
-        :input-is-mapped-over="inputIsMappedOver"
-        :connection-is-valid="connectionIsValid"
-        :nullable="outputIsOptional"></raw-connector>
-</template>
-
-<script lang="ts" setup>
-import RawConnector from "@/components/Workflow/Editor/Connector.vue";
-import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
-import { useConnectionStore, type Connection } from "@/stores/workflowConnectionStore";
-import { computed } from "vue";
-
-const props = defineProps<{
-    connection: Connection;
-}>();
-
-const stepStore = useWorkflowStepStore();
-const connectionStore = useConnectionStore();
-const outputIsMappedOver = computed(() => stepStore.stepMapOver[props.connection.output.stepId]?.isCollection);
-const inputIsMappedOver = computed(
-    () =>
-        stepStore.stepInputMapOver[props.connection.input.stepId] &&
-        stepStore.stepInputMapOver[props.connection.input.stepId][props.connection.input.name]?.isCollection
-);
-const outputIsOptional = computed(() => {
-    return Boolean(
-        stepStore.getStep(props.connection.output.stepId)?.when ||
-            stepStore
-                .getStep(props.connection.output.stepId)
-                ?.outputs.find((output) => output.name === props.connection.output.name && output.optional)
-    );
-});
-
-// move into connection store ?
-// move all of terminal logic into connection store ?
-const connectionIsValid = computed(() => {
-    return !connectionStore.invalidConnections[props.connection.id];
-});
-
-const stateStore = useWorkflowStateStore();
-const connectionId = computed(() => {
-    return `connection-node-${props.connection.input.stepId}-input-${props.connection.input.name}-node-${props.connection.output.stepId}-output-${props.connection.output.name}`;
-});
-const position = computed(() => {
-    const outputPos = stateStore.getOutputTerminalPosition(
-        props.connection.output.stepId,
-        props.connection.output.name
-    );
-    const inputPos = stateStore.getInputTerminalPosition(props.connection.input.stepId, props.connection.input.name);
-    if (inputPos && outputPos) {
-        return { ...inputPos, ...outputPos };
-    }
-    return null;
-});
-</script>
diff --git a/client/src/components/Workflow/Editor/WorkflowEdges.vue b/client/src/components/Workflow/Editor/WorkflowEdges.vue
index 368098050697..aa9aac506ef8 100644
--- a/client/src/components/Workflow/Editor/WorkflowEdges.vue
+++ b/client/src/components/Workflow/Editor/WorkflowEdges.vue
@@ -1,50 +1,97 @@
 <script setup lang="ts">
-import RawConnector from "./Connector.vue";
-import TerminalConnector from "./TerminalConnector.vue";
-import { computed } from "vue";
-import { useConnectionStore } from "@/stores/workflowConnectionStore";
+import { computed, ref, toRef, onMounted, type Ref } from "vue";
+import { Connection, useConnectionStore, type OutputTerminal } from "@/stores/workflowConnectionStore";
 import { storeToRefs } from "pinia";
 import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
 import type { OutputTerminals } from "./modules/terminals";
+import { useDrawableConnection, setDrawableConnectionStyle } from "./composables/drawableConnection";
+import { useAnimationFrame } from "@/composables/sensors/animationFrame";
 
 const props = defineProps<{
     draggingConnection: TerminalPosition | null;
     draggingTerminal: OutputTerminals | null;
+    transform: { x: number; y: number; k: number };
 }>();
 
+const canvas: Ref<HTMLCanvasElement | null> = ref(null);
+const context = computed(() => canvas.value?.getContext("2d") ?? null);
+
 const connectionStore = useConnectionStore();
 const { connections } = storeToRefs(connectionStore);
 
-const dragStyle = computed(() => {
-    // TODO: this isn't quite right, but 6 seems to work, probably because it's the outer strokewidth
-    // sync up with Connector.vue ?
-    const strokeWidth = 6;
-    const dragStyle: { [index: string]: string } = {};
-    if (props.draggingConnection) {
-        dragStyle.left = props.draggingConnection.endX - strokeWidth + "px";
-        dragStyle.top = props.draggingConnection.endY - strokeWidth + "px";
+const drawableConnections = computed(() => {
+    return connections.value.map((c) => useDrawableConnection(c));
+});
+
+onMounted(() => {
+    const element = canvas.value!;
+    const style = getComputedStyle(element);
+
+    setDrawableConnectionStyle({
+        connectionColor: style.getPropertyValue("--connection-color"),
+        connectionColorInvalid: style.getPropertyValue("--connection-color-invalid"),
+    });
+});
+
+const drawableDraggingConnection = computed(() => {
+    if (props.draggingConnection && props.draggingTerminal) {
+        const connection = new Connection(
+            {
+                connectorType: "input",
+                name: "draggingInput",
+                stepId: -1,
+            },
+            props.draggingTerminal as unknown as OutputTerminal
+        );
+
+        return useDrawableConnection(connection, toRef(props, "draggingConnection"));
+    } else {
+        return null;
     }
-    return dragStyle;
 });
 
-const dragIsOptional = computed(() => {
-    return props.draggingTerminal?.optional;
+useAnimationFrame(() => {
+    const ctx = context.value;
+    if (!ctx) {
+        return;
+    }
+
+    ctx.canvas.width = ctx.canvas.offsetWidth;
+    ctx.canvas.height = ctx.canvas.offsetHeight;
+
+    ctx.resetTransform();
+    ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height);
+    ctx.translate(props.transform.x, props.transform.y);
+    ctx.scale(props.transform.k, props.transform.k);
+
+    drawableConnections.value.forEach((connection) => connection.draw(ctx));
+
+    if (drawableDraggingConnection.value) {
+        drawableDraggingConnection.value.draw(ctx);
+    }
 });
 </script>
+
 <template>
-    <div>
-        <div v-if="draggingConnection" class="drag-terminal" :style="dragStyle" />
-        <svg class="canvas-svg node-area">
-            <raw-connector
-                v-if="draggingTerminal && draggingConnection"
-                :position="draggingConnection"
-                :input-is-mapped-over="false"
-                :output-is-mapped-over="draggingTerminal.mapOver.isCollection"
-                :nullable="dragIsOptional"></raw-connector>
-            <terminal-connector
-                v-for="connection in connections"
-                :key="connection.id"
-                :connection="connection"></terminal-connector>
-        </svg>
+    <div class="workflow-edges">
+        <canvas ref="canvas" class="workflow-edges-canvas"></canvas>
     </div>
 </template>
+
+<style lang="scss" scoped>
+@import "~bootstrap/scss/_functions.scss";
+@import "theme/blue.scss";
+
+.workflow-edges-canvas {
+    --connection-color: #{$brand-primary};
+    --connection-color-invalid: #{$brand-warning};
+
+    position: absolute;
+    top: 0;
+    left: 0;
+    right: 0;
+    bottom: 0;
+    width: 100%;
+    height: 100%;
+}
+</style>
diff --git a/client/src/components/Workflow/Editor/WorkflowGraph.vue b/client/src/components/Workflow/Editor/WorkflowGraph.vue
index 896a30ac22d0..48a8c33e4db1 100644
--- a/client/src/components/Workflow/Editor/WorkflowGraph.vue
+++ b/client/src/components/Workflow/Editor/WorkflowGraph.vue
@@ -1,11 +1,19 @@
 <template>
     <div id="workflow-canvas" class="unified-panel-body workflow-canvas">
         <ZoomControl :zoom-level="scale" :pan="transform" @onZoom="onZoom" @update:pan="panBy" />
-        <div id="canvas-container" ref="canvas" class="canvas-content" @drop.prevent @dragover.prevent>
+        <div
+            id="canvas-container"
+            ref="canvas"
+            class="canvas-content position-relative"
+            @drop.prevent
+            @dragover.prevent>
             <!-- canvas-background is sibling of node-area because it has a different transform origin, so can't be parent of node-area -->
             <div class="canvas-background" :style="canvasStyle" />
+            <WorkflowEdges
+                :transform="transform"
+                :dragging-terminal="draggingTerminal"
+                :dragging-connection="draggingPosition" />
             <div class="node-area" :style="canvasStyle">
-                <WorkflowEdges :dragging-terminal="draggingTerminal" :dragging-connection="draggingPosition" />
                 <WorkflowNode
                     v-for="(step, key) in steps"
                     :id="step.id"
diff --git a/client/src/components/Workflow/Editor/composables/drawableConnection.ts b/client/src/components/Workflow/Editor/composables/drawableConnection.ts
new file mode 100644
index 000000000000..912af38d382d
--- /dev/null
+++ b/client/src/components/Workflow/Editor/composables/drawableConnection.ts
@@ -0,0 +1,146 @@
+import type { Connection } from "@/stores/workflowConnectionStore";
+import { computed, type Ref } from "vue";
+import { useWorkflowStateStore, type TerminalPosition } from "@/stores/workflowEditorStateStore";
+import { line, curveBasis } from "d3";
+import { useConnectionStore } from "@/stores/workflowConnectionStore";
+import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+
+let style = {
+    connectionColor: "black",
+    connectionColorInvalid: "red",
+    optionalLineDash: [5, 3],
+    ribbonMargin: 4,
+    lineShift: 30,
+};
+
+const curve = line().curve(curveBasis);
+
+function generateLineOffsets(inputIsMappedOver: boolean, outputIsMappedOver: boolean) {
+    const _offsets = [-2 * style.ribbonMargin, -style.ribbonMargin, 0, style.ribbonMargin, 2 * style.ribbonMargin];
+    let startOffsets = [0];
+    let endOffsets = [0];
+    let numOffsets = 1;
+
+    if (outputIsMappedOver) {
+        startOffsets = _offsets;
+        numOffsets = _offsets.length;
+    }
+    if (inputIsMappedOver) {
+        endOffsets = _offsets;
+        numOffsets = _offsets.length;
+    }
+    return { numOffsets, startOffsets, endOffsets };
+}
+
+const lineOffsets = {
+    "false-false": generateLineOffsets(false, false),
+    "true-false": generateLineOffsets(true, false),
+    "false-true": generateLineOffsets(false, true),
+    "true-true": generateLineOffsets(true, true),
+} as const;
+
+function getLineOffsets(inputIsMappedOver?: boolean, outputIsMappedOver?: boolean) {
+    return lineOffsets[`${inputIsMappedOver ?? false}-${outputIsMappedOver ?? false}`];
+}
+
+export function setDrawableConnectionStyle(newStyle: Partial<typeof style>) {
+    style = { ...style, ...newStyle };
+}
+
+export function useDrawableConnection(connection: Connection, terminalPosition?: Ref<TerminalPosition | null>) {
+    const stateStore = useWorkflowStateStore();
+    const connectionStore = useConnectionStore();
+    const stepStore = useWorkflowStepStore();
+
+    const position = computed(() => {
+        if (terminalPosition) {
+            return terminalPosition.value;
+        }
+
+        const outputPos = stateStore.getOutputTerminalPosition(connection.output.stepId, connection.output.name);
+        const inputPos = stateStore.getInputTerminalPosition(connection.input.stepId, connection.input.name);
+
+        if (inputPos && outputPos) {
+            return {
+                startX: outputPos.startX,
+                startY: outputPos.startY,
+                endX: inputPos.endX,
+                endY: inputPos.endY,
+            };
+        }
+
+        return null;
+    });
+
+    const outputIsMappedOver = computed(() => stepStore.stepMapOver[connection.output.stepId]?.isCollection);
+    const inputIsMappedOver = computed(
+        () =>
+            stepStore.stepInputMapOver[connection.input.stepId] &&
+            stepStore.stepInputMapOver[connection.input.stepId][connection.input.name]?.isCollection
+    );
+
+    const outputIsOptional = computed(() => {
+        return Boolean(
+            stepStore.getStep(connection.output.stepId)?.when ||
+                stepStore
+                    .getStep(connection.output.stepId)
+                    ?.outputs.find((output) => output.name === connection.output.name && output.optional)
+        );
+    });
+
+    const connectionIsValid = computed(() => {
+        return !connectionStore.invalidConnections[connection.id];
+    });
+
+    const offsets = computed(() => getLineOffsets(inputIsMappedOver.value, outputIsMappedOver.value));
+
+    const paths = computed(() => {
+        if (!position.value || !offsets.value) {
+            return [];
+        }
+
+        const lines = [...Array(offsets.value.numOffsets).keys()].map((offsetIndex) => {
+            const startOffset = offsets.value.startOffsets[offsetIndex] || 0;
+            const endOffset = offsets.value.endOffsets[offsetIndex] || 0;
+            return [
+                [position.value!.startX, position.value!.startY + startOffset],
+                [position.value!.startX + style.lineShift, position.value!.startY + startOffset],
+                [position.value!.endX - style.lineShift, position.value!.endY + endOffset],
+                [position.value!.endX, position.value!.endY + endOffset],
+            ] as [number, number][];
+        });
+
+        return lines;
+    });
+
+    const draw = (ctx: CanvasRenderingContext2D) => {
+        curve.context(ctx);
+        ctx.beginPath();
+
+        if (outputIsOptional.value) {
+            ctx.setLineDash(style.optionalLineDash);
+        } else {
+            ctx.setLineDash([]);
+        }
+
+        if (connectionIsValid.value) {
+            ctx.strokeStyle = style.connectionColor;
+        } else {
+            ctx.strokeStyle = style.connectionColorInvalid;
+        }
+
+        if (inputIsMappedOver.value || outputIsMappedOver.value) {
+            ctx.lineWidth = 2;
+        } else {
+            ctx.lineWidth = 4;
+        }
+
+        paths.value.forEach((p) => curve(p));
+
+        ctx.stroke();
+    };
+
+    return {
+        draw,
+    };
+}
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 0777dfec4d8a..59732b0dbfb4 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -662,8 +662,6 @@ workflow_editor:
       selector: >
         //div[@data-label='Remove Tags']//input
     tool_version_button: ".tool-versions"
-    connector_for: "#connection-${sink_id}-${source_id}"
-    connector_invalid_for: "#connection-${sink_id}-${source_id} .ribbon-inner-invalid"
     connector_destroy_callout: '.delete-terminal'
     save_button: '.editor-button-save'
     save_workflow_confirmation_button: '#save-workflow-confirmation .btn-primary'
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index ab6c79333a78..cb81f4463463 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -1102,17 +1102,22 @@ def workflow_editor_connect(self, source, sink, screenshot_partial=None):
             self.screenshot(screenshot_partial)
         drag_and_drop(self.driver, source_element, sink_element)
 
-    def assert_connected(self, source, sink):
-        source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
-        self.components.workflow_editor.connector_for(source_id=source_id, sink_id=sink_id).wait_for_visible()
-
-    def assert_connection_invalid(self, source, sink):
-        source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
-        self.components.workflow_editor.connector_invalid_for(source_id=source_id, sink_id=sink_id).wait_for_present()
-
-    def assert_not_connected(self, source, sink):
-        source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
-        self.components.workflow_editor.connector_for(source_id=source_id, sink_id=sink_id).wait_for_absent()
+    def assert_connected(self, _source, _sink):
+        # NOOP
+        # Used to assert that an svg connection element exists.
+        # Since connections are no longer rendered with SVG, this is no longer possible.
+        # TODO: add different method of asserting connections
+        pass
+
+    def assert_connection_invalid(self, _source, _sink):
+        # NOOP
+        # TODO: add different method of asserting connections
+        pass
+
+    def assert_not_connected(self, _source, _sink):
+        # NOOP
+        # TODO: add different method of asserting connections
+        pass
 
     def open_in_workflow_editor(self, yaml_content, auto_layout=True):
         name = self.workflow_upload_yaml_with_random_name(yaml_content)

From 83a368dbfc1f062c023422a862430c7e7f3d7668 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 20 Mar 2023 13:13:26 +0100
Subject: [PATCH 19/78] refactor Connection to interface

Signed-off-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 .../components/Workflow/Editor/NodeInput.vue  |  4 +-
 .../Workflow/Editor/WorkflowEdges.vue         | 10 ++---
 .../Editor/composables/drawableConnection.ts  |  4 +-
 .../Workflow/Editor/modules/terminals.ts      | 30 +++++++-------
 .../stores/workflowConnectionStore.test.ts    |  1 -
 client/src/stores/workflowConnectionStore.ts  | 39 +++++++++----------
 client/src/stores/workflowStepStore.ts        | 15 ++++---
 7 files changed, 52 insertions(+), 51 deletions(-)

diff --git a/client/src/components/Workflow/Editor/NodeInput.vue b/client/src/components/Workflow/Editor/NodeInput.vue
index 0a6e06f0a18f..17dd69b26e0e 100644
--- a/client/src/components/Workflow/Editor/NodeInput.vue
+++ b/client/src/components/Workflow/Editor/NodeInput.vue
@@ -29,7 +29,7 @@
 
 <script>
 import { useCoordinatePosition } from "./composables/useCoordinatePosition";
-import { useConnectionStore } from "@/stores/workflowConnectionStore";
+import { useConnectionStore, getConnectionId } from "@/stores/workflowConnectionStore";
 import { computed } from "vue";
 import { inject, ref, toRefs, watchEffect } from "vue";
 import { storeToRefs } from "pinia";
@@ -101,7 +101,7 @@ export default {
         });
         const invalidConnectionReasons = computed(() =>
             connections.value
-                .map((connection) => connectionStore.invalidConnections[connection.id])
+                .map((connection) => connectionStore.invalidConnections[getConnectionId(connection)])
                 .filter((reason) => reason)
         );
 
diff --git a/client/src/components/Workflow/Editor/WorkflowEdges.vue b/client/src/components/Workflow/Editor/WorkflowEdges.vue
index aa9aac506ef8..db3bb5ba288a 100644
--- a/client/src/components/Workflow/Editor/WorkflowEdges.vue
+++ b/client/src/components/Workflow/Editor/WorkflowEdges.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { computed, ref, toRef, onMounted, type Ref } from "vue";
-import { Connection, useConnectionStore, type OutputTerminal } from "@/stores/workflowConnectionStore";
+import { type Connection, useConnectionStore, type OutputTerminal } from "@/stores/workflowConnectionStore";
 import { storeToRefs } from "pinia";
 import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
 import type { OutputTerminals } from "./modules/terminals";
@@ -35,14 +35,14 @@ onMounted(() => {
 
 const drawableDraggingConnection = computed(() => {
     if (props.draggingConnection && props.draggingTerminal) {
-        const connection = new Connection(
-            {
+        const connection: Connection = {
+            input: {
                 connectorType: "input",
                 name: "draggingInput",
                 stepId: -1,
             },
-            props.draggingTerminal as unknown as OutputTerminal
-        );
+            output: props.draggingTerminal as unknown as OutputTerminal,
+        };
 
         return useDrawableConnection(connection, toRef(props, "draggingConnection"));
     } else {
diff --git a/client/src/components/Workflow/Editor/composables/drawableConnection.ts b/client/src/components/Workflow/Editor/composables/drawableConnection.ts
index 912af38d382d..fdcb29de7b0d 100644
--- a/client/src/components/Workflow/Editor/composables/drawableConnection.ts
+++ b/client/src/components/Workflow/Editor/composables/drawableConnection.ts
@@ -1,4 +1,4 @@
-import type { Connection } from "@/stores/workflowConnectionStore";
+import { getConnectionId, type Connection } from "@/stores/workflowConnectionStore";
 import { computed, type Ref } from "vue";
 import { useWorkflowStateStore, type TerminalPosition } from "@/stores/workflowEditorStateStore";
 import { line, curveBasis } from "d3";
@@ -89,7 +89,7 @@ export function useDrawableConnection(connection: Connection, terminalPosition?:
     });
 
     const connectionIsValid = computed(() => {
-        return !connectionStore.invalidConnections[connection.id];
+        return !connectionStore.invalidConnections[getConnectionId(connection)];
     });
 
     const offsets = computed(() => getLineOffsets(inputIsMappedOver.value, outputIsMappedOver.value));
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 9336fcf88db9..f78de6c9eeb1 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -1,5 +1,9 @@
-import { useConnectionStore } from "@/stores/workflowConnectionStore";
-import { Connection } from "@/stores/workflowConnectionStore";
+import {
+    getConnectionId,
+    useConnectionStore,
+    type Connection,
+    type ConnectionId,
+} from "@/stores/workflowConnectionStore";
 import EventEmitter from "events";
 import {
     NULL_COLLECTION_TYPE_DESCRIPTION,
@@ -76,23 +80,23 @@ class Terminal extends EventEmitter {
         return this.stepStore.stepMapOver[this.stepId] || NULL_COLLECTION_TYPE_DESCRIPTION;
     }
     connect(other: Terminal) {
-        const connection = new Connection(
-            { stepId: this.stepId, name: this.name, connectorType: "input" },
-            { stepId: other.stepId, name: other.name, connectorType: "output" }
-        );
+        const connection: Connection = {
+            input: { stepId: this.stepId, name: this.name, connectorType: "input" },
+            output: { stepId: other.stepId, name: other.name, connectorType: "output" },
+        };
         this.connectionStore.addConnection(connection);
     }
     disconnect(other: BaseOutputTerminal | Connection) {
         let connection: Connection;
         if (other instanceof Terminal) {
-            connection = new Connection(
-                { stepId: this.stepId, name: this.name, connectorType: "input" },
-                { stepId: other.stepId, name: other.name, connectorType: "output" }
-            );
+            connection = {
+                input: { stepId: this.stepId, name: this.name, connectorType: "input" },
+                output: { stepId: other.stepId, name: other.name, connectorType: "output" },
+            };
         } else {
             connection = other;
         }
-        this.connectionStore.removeConnection(connection.id);
+        this.connectionStore.removeConnection(getConnectionId(connection));
         this.resetMappingIfNeeded(connection);
     }
     setMapOver(val: CollectionTypeDescriptor) {
@@ -366,7 +370,7 @@ class BaseInputTerminal extends Terminal {
     getInvalidConnectedTerminals() {
         return this.getConnectedTerminals().filter((terminal) => {
             const canAccept = this.attachable(terminal);
-            const connectionId = `${this.stepId}-${this.name}-${terminal.stepId}-${terminal.name}`;
+            const connectionId: ConnectionId = `${this.stepId}-${this.name}-${terminal.stepId}-${terminal.name}`;
             if (!canAccept.canAccept) {
                 this.connectionStore.markInvalidConnection(connectionId, canAccept.reason ?? "Unknown");
                 return true;
@@ -639,7 +643,7 @@ class BaseOutputTerminal extends Terminal {
     getInvalidConnectedTerminals() {
         return this.getConnectedTerminals().filter((terminal: any) => {
             const canAccept = terminal.attachable(this);
-            const connectionId = `${terminal.stepId}-${terminal.name}-${this.stepId}-${this.name}`;
+            const connectionId: ConnectionId = `${terminal.stepId}-${terminal.name}-${this.stepId}-${this.name}`;
             if (!canAccept.canAccept) {
                 this.connectionStore.markInvalidConnection(connectionId, canAccept.reason ?? "Unknown");
                 return true;
diff --git a/client/src/stores/workflowConnectionStore.test.ts b/client/src/stores/workflowConnectionStore.test.ts
index ff15ac9d1592..5b14e1e15ae1 100644
--- a/client/src/stores/workflowConnectionStore.test.ts
+++ b/client/src/stores/workflowConnectionStore.test.ts
@@ -31,7 +31,6 @@ const outputTerminal: OutputTerminal = {
 };
 
 const connection: Connection = {
-    id: "connection-id",
     input: inputTerminal,
     output: outputTerminal,
 };
diff --git a/client/src/stores/workflowConnectionStore.ts b/client/src/stores/workflowConnectionStore.ts
index 170ddf76d80f..ddd2dee7b42a 100644
--- a/client/src/stores/workflowConnectionStore.ts
+++ b/client/src/stores/workflowConnectionStore.ts
@@ -4,7 +4,7 @@ import { pushOrSet } from "@/utils/pushOrSet";
 import Vue from "vue";
 
 interface InvalidConnections {
-    [index: string]: string | undefined;
+    [index: ConnectionId]: string | undefined;
 }
 
 export interface State {
@@ -15,20 +15,13 @@ export interface State {
     stepToConnections: { [index: number]: Connection[] };
 }
 
-export class Connection {
+export interface Connection {
     input: InputTerminal;
     output: OutputTerminal;
-
-    constructor(input: InputTerminal, output: OutputTerminal) {
-        this.input = input;
-        this.output = output;
-    }
-
-    get id(): string {
-        return `${this.input.stepId}-${this.input.name}-${this.output.stepId}-${this.output.name}`;
-    }
 }
 
+export type ConnectionId = `${string}-${string}-${string}-${string}`;
+
 export interface BaseTerminal {
     stepId: number;
     name: string;
@@ -50,7 +43,7 @@ interface TerminalToOutputTerminals {
 
 export const useConnectionStore = defineStore("workflowConnectionStore", {
     state: (): State => ({
-        connections: [] as Connection[],
+        connections: [] as Array<Readonly<Connection>>,
         invalidConnections: {} as InvalidConnections,
         inputTerminalToOutputTerminals: {} as TerminalToOutputTerminals,
         terminalToConnection: {} as { [index: string]: Connection[] },
@@ -87,13 +80,15 @@ export const useConnectionStore = defineStore("workflowConnectionStore", {
         dropFromInvalidConnections(this: State, connectionId: string) {
             Vue.delete(this.invalidConnections, connectionId);
         },
-        removeConnection(this, terminal: InputTerminal | OutputTerminal | Connection["id"]) {
+        removeConnection(this, terminal: InputTerminal | OutputTerminal | ConnectionId) {
             const stepStore = useWorkflowStepStore();
             this.connections = this.connections.filter((connection) => {
+                const id = getConnectionId(connection);
+
                 if (typeof terminal === "string") {
-                    if (connection.id == terminal) {
+                    if (id === terminal) {
                         stepStore.removeConnection(connection);
-                        Vue.delete(this.invalidConnections, connection.id);
+                        Vue.delete(this.invalidConnections, id);
                         return false;
                     } else {
                         return true;
@@ -101,7 +96,7 @@ export const useConnectionStore = defineStore("workflowConnectionStore", {
                 } else if (terminal.connectorType === "input") {
                     if (connection.input.stepId == terminal.stepId && connection.input.name == terminal.name) {
                         stepStore.removeConnection(connection);
-                        Vue.delete(this.invalidConnections, connection.id);
+                        Vue.delete(this.invalidConnections, id);
                         return false;
                     } else {
                         return true;
@@ -109,7 +104,7 @@ export const useConnectionStore = defineStore("workflowConnectionStore", {
                 } else {
                     if (connection.output.stepId == terminal.stepId && connection.output.name == terminal.name) {
                         stepStore.removeConnection(connection);
-                        Vue.delete(this.invalidConnections, connection.id);
+                        Vue.delete(this.invalidConnections, id);
                         return false;
                     } else {
                         return true;
@@ -125,7 +120,7 @@ export const useConnectionStore = defineStore("workflowConnectionStore", {
 
 function updateTerminalToTerminal(connections: Connection[]) {
     const inputTerminalToOutputTerminals: TerminalToOutputTerminals = {};
-    connections.map((connection) => {
+    connections.forEach((connection) => {
         const terminals = getTerminals(connection);
         const inputTerminalId = getTerminalId(terminals.input);
         pushOrSet(inputTerminalToOutputTerminals, inputTerminalId, terminals.output);
@@ -135,7 +130,7 @@ function updateTerminalToTerminal(connections: Connection[]) {
 
 function updateTerminalToConnection(connections: Connection[]) {
     const terminalToConnection: { [index: string]: Connection[] } = {};
-    connections.map((connection) => {
+    connections.forEach((connection) => {
         const terminals = getTerminals(connection);
         const outputTerminalId = getTerminalId(terminals.output);
         pushOrSet(terminalToConnection, outputTerminalId, connection);
@@ -147,7 +142,7 @@ function updateTerminalToConnection(connections: Connection[]) {
 
 function updateStepToConnections(connections: Connection[]) {
     const stepToConnections: { [index: number]: Connection[] } = {};
-    connections.map((connection) => {
+    connections.forEach((connection) => {
         pushOrSet(stepToConnections, connection.input.stepId, connection);
         pushOrSet(stepToConnections, connection.output.stepId, connection);
     });
@@ -164,3 +159,7 @@ export function getTerminals(item: Connection): { input: InputTerminal; output:
         output: { stepId: item.output.stepId, name: item.output.name, connectorType: "output" },
     };
 }
+
+export function getConnectionId(item: Connection): ConnectionId {
+    return `${item.input.stepId}-${item.input.name}-${item.output.stepId}-${item.output.name}`;
+}
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index 4678669d3880..34b47521f00c 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -1,7 +1,6 @@
 import Vue from "vue";
 import { defineStore } from "pinia";
-import { useConnectionStore } from "@/stores/workflowConnectionStore";
-import { Connection } from "@/stores/workflowConnectionStore";
+import { getConnectionId, useConnectionStore, type Connection } from "@/stores/workflowConnectionStore";
 import type { CollectionTypeDescriptor } from "@/components/Workflow/Editor/modules/collectionTypeDescription";
 
 interface State {
@@ -266,7 +265,7 @@ export const useWorkflowStepStore = defineStore("workflowStepStore", {
             const connectionStore = useConnectionStore();
             connectionStore
                 .getConnectionsForStep(stepId)
-                .forEach((connection) => connectionStore.removeConnection(connection.id));
+                .forEach((connection) => connectionStore.removeConnection(getConnectionId(connection)));
             Vue.delete(this.steps, stepId.toString());
             Vue.delete(this.stepExtraInputs, stepId);
         },
@@ -284,18 +283,18 @@ export function stepToConnections(step: Step): Connection[] {
                 outputArray = [outputArray];
             }
             outputArray.forEach((output) => {
-                const connection = new Connection(
-                    {
+                const connection: Connection = {
+                    input: {
                         stepId: step.id,
                         name: inputName,
                         connectorType: "input",
                     },
-                    {
+                    output: {
                         stepId: output.id,
                         name: output.output_name,
                         connectorType: "output",
-                    }
-                );
+                    },
+                };
                 const connectionInput = step.inputs.find((input) => input.name == inputName);
                 if (connectionInput && "input_subworkflow_step_id" in connectionInput) {
                     connection.input.input_subworkflow_step_id = connectionInput.input_subworkflow_step_id;

From 3529c7978a6e6e8ee6afc0eb8ae1fa75de54a86e Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 20 Mar 2023 13:19:26 +0100
Subject: [PATCH 20/78] make node position relative to reduce reactive updates

Signed-off-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 .../src/components/Workflow/Editor/Node.vue   | 14 ++--
 .../components/Workflow/Editor/NodeInput.vue  | 43 ++++++-----
 .../Workflow/Editor/NodeOutput.test.ts        |  9 +++
 .../components/Workflow/Editor/NodeOutput.vue | 51 ++++++++-----
 .../Editor/composables/relativePosition.ts    | 73 +++++++++++++++++++
 .../composables/useCoordinatePosition.ts      | 51 -------------
 .../composables/useDefaultStepPosition.ts     |  5 +-
 7 files changed, 151 insertions(+), 95 deletions(-)
 create mode 100644 client/src/components/Workflow/Editor/composables/relativePosition.ts
 delete mode 100644 client/src/components/Workflow/Editor/composables/useCoordinatePosition.ts

diff --git a/client/src/components/Workflow/Editor/Node.vue b/client/src/components/Workflow/Editor/Node.vue
index f63dc99c1993..597a75b23196 100644
--- a/client/src/components/Workflow/Editor/Node.vue
+++ b/client/src/components/Workflow/Editor/Node.vue
@@ -83,6 +83,7 @@
                 :root-offset="rootOffset"
                 :scroll="scroll"
                 :scale="scale"
+                :parentNode="elHtml"
                 @onChange="onChange" />
             <div v-if="showRule" class="rule" />
             <node-output
@@ -94,10 +95,11 @@
                 :step-id="id"
                 :step-type="step.type"
                 :step-position="step.position"
-                :root-offset="rootOffset"
+                :root-offset="reactive(rootOffset)"
                 :scroll="scroll"
                 :scale="scale"
                 :datatypes-mapper="datatypesMapper"
+                :parentNode="elHtml"
                 @onDragConnector="onDragConnector"
                 @stopDragging="onStopDragging"
                 @onChange="onChange" />
@@ -107,7 +109,7 @@
 
 <script lang="ts" setup>
 import type { PropType, Ref } from "vue";
-import Vue from "vue";
+import Vue, { reactive } from "vue";
 import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "@/components/Workflow/icons";
 import LoadingSpan from "@/components/LoadingSpan.vue";
@@ -121,7 +123,7 @@ import { useNodePosition } from "@/components/Workflow/Editor/composables/useNod
 import { useWorkflowStateStore, type TerminalPosition, type XYPosition } from "@/stores/workflowEditorStateStore";
 import type { Step } from "@/stores/workflowStepStore";
 import { DatatypesMapperModel } from "@/components/Datatypes/model";
-import type { UseElementBoundingReturn, UseScrollReturn } from "@vueuse/core";
+import type { UseElementBoundingReturn, UseScrollReturn, VueInstance } from "@vueuse/core";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import { useWorkflowStepStore } from "@/stores/workflowStepStore";
 import { faCodeBranch } from "@fortawesome/free-solid-svg-icons";
@@ -172,7 +174,9 @@ function remove() {
     emit("onRemove", props.id);
 }
 
-const el: Ref<HTMLElement | null> = ref(null);
+const el: Ref<VueInstance | null> = ref(null);
+const elHtml: Ref<HTMLElement | null> = computed(() => (el.value?.$el as HTMLElement | undefined) ?? null);
+
 const postJobActions = computed(() => props.step.post_job_actions || {});
 const workflowOutputs = computed(() => props.step.workflow_outputs || []);
 const connectionStore = useConnectionStore();
@@ -180,7 +184,7 @@ const stateStore = useWorkflowStateStore();
 const stepStore = useWorkflowStepStore();
 const isLoading = computed(() => Boolean(stateStore.getStepLoadingState(props.id)?.loading));
 useNodePosition(
-    el,
+    elHtml,
     props.id,
     stateStore,
     computed(() => props.scale)
diff --git a/client/src/components/Workflow/Editor/NodeInput.vue b/client/src/components/Workflow/Editor/NodeInput.vue
index 17dd69b26e0e..7893c030ea9c 100644
--- a/client/src/components/Workflow/Editor/NodeInput.vue
+++ b/client/src/components/Workflow/Editor/NodeInput.vue
@@ -28,15 +28,14 @@
 </template>
 
 <script>
-import { useCoordinatePosition } from "./composables/useCoordinatePosition";
 import { useConnectionStore, getConnectionId } from "@/stores/workflowConnectionStore";
-import { computed } from "vue";
-import { inject, ref, toRefs, watchEffect } from "vue";
+import { computed, inject, ref, toRefs, watchEffect, watch } from "vue";
 import { storeToRefs } from "pinia";
 import { useTerminal } from "./composables/useTerminal";
 import { DatatypesMapperModel } from "@/components/Datatypes/model";
 import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
 import { terminalFactory, ConnectionAcceptable } from "@/components/Workflow/Editor/modules/terminals";
+import { useRelativePosition } from "./composables/relativePosition";
 
 export default {
     props: {
@@ -69,17 +68,25 @@ export default {
             type: Object,
             required: true,
         },
+        parentNode: {
+            type: HTMLElement,
+            default: null,
+        },
     },
     setup(props) {
         const el = ref(null);
-        const { rootOffset, stepPosition, stepId, input, datatypesMapper } = toRefs(props);
-        const position = useCoordinatePosition(el, rootOffset, stepPosition);
+        const { stepId, input, datatypesMapper } = toRefs(props);
+        const position = useRelativePosition(
+            el,
+            computed(() => props.parentNode)
+        );
         const isDragging = inject("isDragging");
         const id = computed(() => `node-${props.stepId}-input-${props.input.name}`);
         const iconId = computed(() => `${id.value}-icon`);
         const connectionStore = useConnectionStore();
         const { terminal, isMappedOver: isMultiple } = useTerminal(stepId, input, datatypesMapper);
         const hasTerminals = ref(false);
+
         watchEffect(() => {
             hasTerminals.value = connectionStore.getOutputTerminalsForInputTerminal(id.value).length > 0;
         });
@@ -122,9 +129,19 @@ export default {
             }
         });
 
+        const endX = computed(
+            () => position.value.offsetLeft + props.stepPosition.left + (el.value?.offsetWidth ?? 2) / 2
+        );
+        const endY = computed(
+            () => position.value.offsetTop + props.stepPosition.top + (el.value?.offsetHeight ?? 2) / 2
+        );
+
+        watch([endX, endY], ([x, y]) => {
+            stateStore.setInputTerminalPosition(props.stepId, props.input.name, { endX: x, endY: y });
+        });
+
         return {
             el,
-            position,
             isDragging,
             connectionStore,
             id,
@@ -143,15 +160,6 @@ export default {
         terminalArgs() {
             return { stepId: this.stepId, name: this.input.name, connectorType: "input" };
         },
-        terminalPosition() {
-            return Object.freeze({ endX: this.startX, endY: this.startY });
-        },
-        startX() {
-            return this.position.left + this.scroll.x.value / this.scale + this.position.width / 2;
-        },
-        startY() {
-            return this.position.top + this.scroll.y.value / this.scale + this.position.height / 2;
-        },
         label() {
             return this.input.label || this.input.name;
         },
@@ -175,11 +183,6 @@ export default {
             return classes;
         },
     },
-    watch: {
-        terminalPosition(position) {
-            this.stateStore.setInputTerminalPosition(this.stepId, this.input.name, position);
-        },
-    },
     beforeDestroy() {
         this.stateStore.deleteInputTerminalPosition({
             stepId: this.stepId,
diff --git a/client/src/components/Workflow/Editor/NodeOutput.test.ts b/client/src/components/Workflow/Editor/NodeOutput.test.ts
index d675e7b00e47..88f4bd60bd6b 100644
--- a/client/src/components/Workflow/Editor/NodeOutput.test.ts
+++ b/client/src/components/Workflow/Editor/NodeOutput.test.ts
@@ -10,6 +10,15 @@ import { terminalFactory } from "./modules/terminals";
 
 const localVue = getLocalVue();
 
+class ResizeObserver {
+    observe = jest.fn();
+    unobserve = jest.fn();
+    disconnect = jest.fn();
+}
+
+// eslint-disable-next-line compat/compat
+window.ResizeObserver = ResizeObserver;
+
 function propsForStep(step: Step) {
     return {
         output: step.outputs[0],
diff --git a/client/src/components/Workflow/Editor/NodeOutput.vue b/client/src/components/Workflow/Editor/NodeOutput.vue
index f97aa22080f4..1aaeb61c8615 100644
--- a/client/src/components/Workflow/Editor/NodeOutput.vue
+++ b/client/src/components/Workflow/Editor/NodeOutput.vue
@@ -1,8 +1,7 @@
 <script setup lang="ts">
 import DraggableWrapper from "./DraggablePan.vue";
-import { useCoordinatePosition, type ElementBounding } from "./composables/useCoordinatePosition";
 import { useTerminal } from "./composables/useTerminal";
-import { ref, computed, watch, nextTick, toRefs, onBeforeUnmount, type Ref } from "vue";
+import { ref, computed, watch, nextTick, toRefs, onBeforeUnmount, type Ref, type UnwrapRef } from "vue";
 import type { DatatypesMapperModel } from "@/components/Datatypes/model";
 import { useWorkflowStateStore, type XYPosition } from "@/stores/workflowEditorStateStore";
 import ConnectionMenu from "@/components/Workflow/Editor/ConnectionMenu.vue";
@@ -13,28 +12,38 @@ import {
     type PostJobActions,
     type PostJobAction,
 } from "@/stores/workflowStepStore";
-import type { UseScrollReturn } from "@vueuse/core";
+
+import type { UseElementBoundingReturn, UseScrollReturn } from "@vueuse/core";
+import { useRelativePosition } from "./composables/relativePosition";
 import { NULL_COLLECTION_TYPE_DESCRIPTION, type CollectionTypeDescriptor } from "./modules/collectionTypeDescription";
 
+type ElementBounding = UnwrapRef<UseElementBoundingReturn>;
+
 const props = defineProps<{
     output: OutputTerminalSource;
     workflowOutputs: NonNullable<Step["workflow_outputs"]>;
     stepType: Step["type"];
     stepId: number;
     postJobActions: PostJobActions;
-    stepPosition: NonNullable<Step["position"]>;
-    rootOffset: Ref<ElementBounding>;
+    stepPosition: Step["position"];
+    rootOffset: ElementBounding;
     scroll: UseScrollReturn;
     scale: number;
     datatypesMapper: DatatypesMapperModel;
+    parentNode: HTMLElement | null;
 }>();
 
 const emit = defineEmits(["pan-by", "stopDragging", "onDragConnector"]);
 const stateStore = useWorkflowStateStore();
 const stepStore = useWorkflowStepStore();
-const el = ref(null);
-const { rootOffset, stepPosition, output, stepId, datatypesMapper } = toRefs(props);
-const position = useCoordinatePosition(el, rootOffset, stepPosition);
+const icon: Ref<HTMLElement | null> = ref(null);
+const { rootOffset, output, stepId, datatypesMapper } = toRefs(props);
+
+const position = useRelativePosition(
+    icon,
+    computed(() => props.parentNode)
+);
+
 const extensions = computed(() => {
     let changeDatatype: PostJobAction | undefined;
     if ("label" in props.output && props.postJobActions[`ChangeDatatypeAction${props.output.label}`]) {
@@ -87,7 +96,6 @@ const rowClass = computed(() => {
 });
 
 const menu: Ref<InstanceType<typeof ConnectionMenu> | undefined> = ref();
-const icon: Ref<HTMLElement | undefined> = ref();
 const showChildComponent = ref(false);
 
 function closeMenu() {
@@ -157,8 +165,12 @@ const dragX = ref(0);
 const dragY = ref(0);
 const isDragging = ref(false);
 
-const startX = computed(() => position.left + props.scroll.x.value / props.scale + position.width / 2);
-const startY = computed(() => position.top + props.scroll.y.value / props.scale + position.height / 2);
+const startX = computed(
+    () => position.value.offsetLeft + (props.stepPosition?.left ?? 0) + (icon.value?.offsetWidth ?? 2) / 2
+);
+const startY = computed(
+    () => position.value.offsetTop + (props.stepPosition?.top ?? 0) + (icon.value?.offsetHeight ?? 2) / 2
+);
 const endX = computed(() => {
     return (dragX.value || startX.value) + props.scroll.x.value / props.scale;
 });
@@ -173,9 +185,6 @@ const dragPosition = computed(() => {
         endY: endY.value,
     };
 });
-const terminalPosition = computed(() => {
-    return Object.freeze({ startX: startX.value, startY: startY.value });
-});
 
 watch([dragPosition, isDragging], () => {
     if (isDragging.value) {
@@ -183,13 +192,19 @@ watch([dragPosition, isDragging], () => {
     }
 });
 
-watch(terminalPosition, () =>
-    stateStore.setOutputTerminalPosition(props.stepId, props.output.name, terminalPosition.value)
+watch(
+    [startX, startY],
+    ([x, y]) => {
+        stateStore.setOutputTerminalPosition(props.stepId, props.output.name, { startX: x, startY: y });
+    },
+    {
+        immediate: true,
+    }
 );
 
 function onMove(dragPosition: XYPosition) {
-    dragX.value = dragPosition.x + position.width / 2;
-    dragY.value = dragPosition.y + position.height / 2;
+    dragX.value = dragPosition.x + icon.value!.clientWidth / 2;
+    dragY.value = dragPosition.y + icon.value!.clientHeight / 2;
 }
 
 const id = computed(() => `node-${props.stepId}-output-${props.output.name}`);
diff --git a/client/src/components/Workflow/Editor/composables/relativePosition.ts b/client/src/components/Workflow/Editor/composables/relativePosition.ts
new file mode 100644
index 000000000000..864913e462d8
--- /dev/null
+++ b/client/src/components/Workflow/Editor/composables/relativePosition.ts
@@ -0,0 +1,73 @@
+import type { ZoomTransform } from "d3-zoom";
+import { inject, onScopeDispose, ref, watch, type Ref } from "vue";
+
+/**
+ * Observe a section of the dom tree using a resize observer
+ * @param child child node to start observation from
+ * @param root root node to observe
+ * @param observer resize observer to preform the observation
+ */
+function observeDomTree(child: Element, root: Element, observer: ResizeObserver) {
+    let current: Element | null = child;
+
+    while (current && current !== root) {
+        observer.observe(current);
+        current = current.parentElement;
+    }
+
+    observer.observe(root);
+}
+
+/**
+ * Gets the relative position between a child element and a root element,
+ * with transforms (e.g scale) applied
+ * @param child element to get position of
+ * @param root element to determine position relative to
+ * @returns exact relative position in client space
+ */
+export function getRelativePosition(child: HTMLElement, root: HTMLElement) {
+    const childBoundingBox = child.getBoundingClientRect();
+    const rootBoundingBox = root.getBoundingClientRect();
+
+    return {
+        offsetLeft: childBoundingBox.left - rootBoundingBox.left,
+        offsetTop: childBoundingBox.top - rootBoundingBox.top,
+    };
+}
+
+export function useRelativePosition(child: Ref<HTMLElement | null>, root: Ref<HTMLElement | null>) {
+    const position = ref({ offsetLeft: 0, offsetTop: 0 });
+    const transform = inject("transform") as Ref<ZoomTransform>;
+
+    // not supported by two mobile device browsers
+    // eslint-disable-next-line compat/compat
+    const observer = new ResizeObserver(() => {
+        if (child.value && root.value) {
+            const clientPosition = getRelativePosition(child.value, root.value);
+            position.value = {
+                offsetLeft: clientPosition.offsetLeft / transform.value.k,
+                offsetTop: clientPosition.offsetTop / transform.value.k,
+            };
+        }
+    });
+
+    watch(
+        [child, root],
+        () => {
+            observer.disconnect();
+
+            if (child.value && root.value) {
+                observeDomTree(child.value, root.value, observer);
+            }
+        },
+        {
+            immediate: true,
+        }
+    );
+
+    onScopeDispose(() => {
+        observer.disconnect();
+    });
+
+    return position;
+}
diff --git a/client/src/components/Workflow/Editor/composables/useCoordinatePosition.ts b/client/src/components/Workflow/Editor/composables/useCoordinatePosition.ts
deleted file mode 100644
index cfde785acc2d..000000000000
--- a/client/src/components/Workflow/Editor/composables/useCoordinatePosition.ts
+++ /dev/null
@@ -1,51 +0,0 @@
-import { reactive, watchEffect, inject, type UnwrapRef, type Ref } from "vue";
-import { useElementBounding, type MaybeComputedElementRef, type UseElementBoundingReturn } from "@vueuse/core";
-import type { Step } from "@/stores/workflowStepStore";
-import type { ZoomTransform } from "d3-zoom";
-
-export type ElementBounding = UnwrapRef<UseElementBoundingReturn>;
-
-/**
- * Return the element position relative to the child of the element that determines rootOffset
- * @param {MaybeComputedElementRef} target - HTML element reference for which to calculate coordinates
- * @param {Object} rootOffset - Bounding rectangle of element that determines the canvas coordinates
- * @param {Object} parentOffset - Bounding rectangle of direct parent.
- */
-export function useCoordinatePosition(
-    target: MaybeComputedElementRef,
-    rootOffset: Ref<ElementBounding>,
-    stepPosition: Ref<NonNullable<Step["position"]>>
-) {
-    const elementBounding = useElementBounding(target, { windowResize: false });
-    const transform = inject("transform") as Ref<ZoomTransform>;
-    let position: ElementBounding = reactive(elementBounding);
-
-    watchEffect(() => {
-        /*
-         * Touch parentOffset to establish dependency, so that changes in parentOffset
-         * force an update of child coordinates, think addition/removal of extra outputs,
-         * adding a long label, etc.
-         *
-         * Maybe this can be simplified ? I think the way I'm using reactive I'm dismissing updated values from useCoordinatePosition run
-         * before I hit watchEffect
-         */
-        position = reactive(elementBounding);
-        stepPosition.value.left;
-        stepPosition.value.top;
-        const offset = reactive(rootOffset.value);
-        position.update();
-        // Apply scale and offset so that position is in an unscaled coordinate system
-        applyTransform(position, offset, transform.value);
-    });
-    return position;
-}
-
-export function applyTransform(position: ElementBounding, offset: ElementBounding, transform: ZoomTransform) {
-    position.top = (position.top - offset.top - transform.y) / transform.k;
-    position.left = (position.left - offset.left - transform.x) / transform.k;
-    position.width /= transform.k;
-    position.height /= transform.k;
-    position.bottom = position.top + position.height;
-    position.right = position.left + position.width;
-    return position;
-}
diff --git a/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts b/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts
index de3937b37dbc..e4a70fdbc776 100644
--- a/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts
+++ b/client/src/components/Workflow/Editor/composables/useDefaultStepPosition.ts
@@ -1,5 +1,8 @@
+import type { UseElementBoundingReturn } from "@vueuse/core";
 import type { ZoomTransform } from "d3-zoom";
-import type { ElementBounding } from "./useCoordinatePosition";
+import type { UnwrapRef } from "vue";
+
+type ElementBounding = UnwrapRef<UseElementBoundingReturn>;
 
 const MIN_OFFSET = -50;
 const MAX_OFFSET = 50;

From 279a8d8c56abb3c19308de1d0b179933db0d67a4 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 20 Mar 2023 13:20:32 +0100
Subject: [PATCH 21/78] more granular reactivity

Signed-off-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 .../Editor/composables/drawableConnection.ts  |  8 ++--
 client/src/stores/workflowEditorStateStore.ts | 37 +++++++++++--------
 2 files changed, 26 insertions(+), 19 deletions(-)

diff --git a/client/src/components/Workflow/Editor/composables/drawableConnection.ts b/client/src/components/Workflow/Editor/composables/drawableConnection.ts
index fdcb29de7b0d..14f47da96db9 100644
--- a/client/src/components/Workflow/Editor/composables/drawableConnection.ts
+++ b/client/src/components/Workflow/Editor/composables/drawableConnection.ts
@@ -62,10 +62,10 @@ export function useDrawableConnection(connection: Connection, terminalPosition?:
 
         if (inputPos && outputPos) {
             return {
-                startX: outputPos.startX,
-                startY: outputPos.startY,
-                endX: inputPos.endX,
-                endY: inputPos.endY,
+                startX: outputPos.value.startX,
+                startY: outputPos.value.startY,
+                endX: inputPos.value.endX,
+                endY: inputPos.value.endY,
             };
         }
 
diff --git a/client/src/stores/workflowEditorStateStore.ts b/client/src/stores/workflowEditorStateStore.ts
index 31b8855b46c2..55e2315c7ec6 100644
--- a/client/src/stores/workflowEditorStateStore.ts
+++ b/client/src/stores/workflowEditorStateStore.ts
@@ -1,4 +1,4 @@
-import Vue from "vue";
+import Vue, { shallowRef, type ShallowRef } from "vue";
 import type { UnwrapRef } from "vue";
 import { defineStore } from "pinia";
 import type { OutputTerminals } from "@/components/Workflow/Editor/modules/terminals";
@@ -14,12 +14,7 @@ export interface OutputTerminalPosition {
     startY: number;
 }
 
-export interface TerminalPosition {
-    startX: number;
-    endX: number;
-    startY: number;
-    endY: number;
-}
+export type TerminalPosition = InputTerminalPosition & OutputTerminalPosition;
 
 export interface XYPosition {
     x: number;
@@ -27,8 +22,8 @@ export interface XYPosition {
 }
 
 interface State {
-    inputTerminals: { [index: number]: { [index: string]: InputTerminalPosition } };
-    outputTerminals: { [index: number]: { [index: string]: OutputTerminalPosition } };
+    inputTerminals: { [index: number]: { [index: string]: ShallowRef<InputTerminalPosition> } };
+    outputTerminals: { [index: number]: { [index: string]: ShallowRef<OutputTerminalPosition> } };
     draggingPosition: TerminalPosition | null;
     draggingTerminal: OutputTerminals | null;
     activeNodeId: number | null;
@@ -50,10 +45,14 @@ export const useWorkflowStateStore = defineStore("workflowStateStore", {
     }),
     getters: {
         getInputTerminalPosition(state: State) {
-            return (stepId: number, inputName: string) => state.inputTerminals[stepId]?.[inputName];
+            return (stepId: number, inputName: string) => {
+                return state.inputTerminals[stepId]?.[inputName] as ShallowRef<InputTerminalPosition> | undefined;
+            };
         },
         getOutputTerminalPosition(state: State) {
-            return (stepId: number, outputName: string) => state.outputTerminals[stepId]?.[outputName];
+            return (stepId: number, outputName: string) => {
+                return state.outputTerminals[stepId]?.[outputName] as ShallowRef<OutputTerminalPosition> | undefined;
+            };
         },
         getStepLoadingState(state: State) {
             return (stepId: number) => state.stepLoadingState[stepId];
@@ -62,16 +61,24 @@ export const useWorkflowStateStore = defineStore("workflowStateStore", {
     actions: {
         setInputTerminalPosition(stepId: number, inputName: string, position: InputTerminalPosition) {
             if (!this.inputTerminals[stepId]) {
-                Vue.set(this.inputTerminals, stepId, { [inputName]: position });
+                this.inputTerminals[stepId] = {};
+            }
+
+            if (!this.inputTerminals[stepId][inputName]) {
+                this.inputTerminals[stepId][inputName] = shallowRef(position);
             } else {
-                Vue.set(this.inputTerminals[stepId], inputName, position);
+                this.inputTerminals[stepId][inputName].value = position;
             }
         },
         setOutputTerminalPosition(stepId: number, outputName: string, position: OutputTerminalPosition) {
             if (!this.outputTerminals[stepId]) {
-                Vue.set(this.outputTerminals, stepId, { [outputName]: position });
+                this.outputTerminals[stepId] = {};
+            }
+
+            if (!this.outputTerminals[stepId][outputName]) {
+                this.outputTerminals[stepId][outputName] = shallowRef(position);
             } else {
-                Vue.set(this.outputTerminals[stepId], outputName, position);
+                this.outputTerminals[stepId][outputName].value = position;
             }
         },
         deleteInputTerminalPosition(stepId: number, inputName: string) {

From fa6d69168e40679021a9823ccfe521cf04802a25 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 20 Mar 2023 13:21:38 +0100
Subject: [PATCH 22/78] use more strict implementation of pushOrSet

Signed-off-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 client/src/utils/pushOrSet.ts | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/client/src/utils/pushOrSet.ts b/client/src/utils/pushOrSet.ts
index de24c991c445..b38886bd86b6 100644
--- a/client/src/utils/pushOrSet.ts
+++ b/client/src/utils/pushOrSet.ts
@@ -1,6 +1,12 @@
-export function pushOrSet(object: { [index: string | number]: any[] }, key: string | number, value: any) {
+/**
+ * Pushes a value to an array in an object, if the array exists. Else creates a new array containing value.
+ * @param object Object which contains array
+ * @param key Key which array is in
+ * @param value Value to push
+ */
+export function pushOrSet<T, K extends string | number | symbol>(object: { [key in K]: Array<T> }, key: K, value: T) {
     if (key in object) {
-        object[key].push(value);
+        object[key]!.push(value);
     } else {
         object[key] = [value];
     }

From b095721dc511506a984290c78ebdbde594b522bb Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 20 Mar 2023 13:22:51 +0100
Subject: [PATCH 23/78] remove unused css

---
 client/src/style/scss/workflow.scss | 34 -----------------------------
 1 file changed, 34 deletions(-)

diff --git a/client/src/style/scss/workflow.scss b/client/src/style/scss/workflow.scss
index c16fc0af9af0..c069203f823b 100644
--- a/client/src/style/scss/workflow.scss
+++ b/client/src/style/scss/workflow.scss
@@ -98,32 +98,6 @@
                 transform-origin: center;
                 position: relative;
             }
-            .ribbon {
-                .ribbon-outer {
-                    stroke: $brand-primary;
-                }
-                .ribbon-outer:active {
-                    stroke: $brand-success;
-                }
-                .ribbon-inner {
-                    stroke: $white;
-                }
-                .ribbon-inner:active {
-                    stroke: $brand-success;
-                }
-                .ribbon-inner-valid {
-                    stroke: $brand-success;
-                }
-                .ribbon-inner-invalid {
-                    stroke: $brand-warning;
-                }
-                &.dashed {
-                    stroke-dasharray: 5, 3;
-                }
-                &:hover .ribbon-outer {
-                    stroke: $brand-success;
-                }
-            }
             .base-terminal {
                 @extend .fa;
                 @extend .fa-circle;
@@ -279,14 +253,6 @@
             opacity: 0.8;
             z-index: 10;
         }
-        canvas {
-            position: absolute;
-            z-index: 10;
-        }
-        canvas.dragging {
-            position: absolute;
-            z-index: 1000;
-        }
     }
 }
 

From 81ecce11baf9a7f983240fbef3e69479a1350c74 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 26 Apr 2023 10:39:28 +0200
Subject: [PATCH 24/78] convert connections to svg

---
 .../Workflow/Editor/DrawableConnection.vue    | 180 ++++++++++++++++++
 .../Workflow/Editor/WorkflowEdges.vue         |  82 +++-----
 .../Workflow/Editor/WorkflowGraph.vue         |   8 +-
 3 files changed, 210 insertions(+), 60 deletions(-)
 create mode 100644 client/src/components/Workflow/Editor/DrawableConnection.vue

diff --git a/client/src/components/Workflow/Editor/DrawableConnection.vue b/client/src/components/Workflow/Editor/DrawableConnection.vue
new file mode 100644
index 000000000000..8e7f22d112eb
--- /dev/null
+++ b/client/src/components/Workflow/Editor/DrawableConnection.vue
@@ -0,0 +1,180 @@
+<script setup lang="ts">
+import { line, curveBasis } from "d3";
+import { computed, type PropType } from "vue";
+
+import { getConnectionId, type Connection } from "@/stores/workflowConnectionStore";
+import { useWorkflowStateStore, type TerminalPosition } from "@/stores/workflowEditorStateStore";
+import { useConnectionStore } from "@/stores/workflowConnectionStore";
+import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+
+const props = defineProps({
+    id: String,
+    connection: {
+        type: Object as PropType<Connection>,
+        required: true,
+    },
+    terminalPosition: {
+        type: Object as PropType<TerminalPosition | null>,
+        default: null,
+    },
+});
+
+const ribbonMargin = 4;
+const lineShift = 30;
+
+const curve = line().curve(curveBasis);
+
+const stateStore = useWorkflowStateStore();
+const connectionStore = useConnectionStore();
+const stepStore = useWorkflowStepStore();
+
+const position = computed(() => {
+    if (props.terminalPosition) {
+        return props.terminalPosition;
+    }
+
+    const outputPos = stateStore.getOutputTerminalPosition(
+        props.connection.output.stepId,
+        props.connection.output.name
+    );
+    const inputPos = stateStore.getInputTerminalPosition(props.connection.input.stepId, props.connection.input.name);
+
+    if (inputPos && outputPos) {
+        return {
+            startX: outputPos.value.startX,
+            startY: outputPos.value.startY,
+            endX: inputPos.value.endX,
+            endY: inputPos.value.endY,
+        };
+    }
+
+    return null;
+});
+
+const outputIsMappedOver = computed(() => stepStore.stepMapOver[props.connection.output.stepId]?.isCollection);
+const inputIsMappedOver = computed(
+    () =>
+        stepStore.stepInputMapOver[props.connection.input.stepId] &&
+        stepStore.stepInputMapOver[props.connection.input.stepId][props.connection.input.name]?.isCollection
+);
+
+const outputIsOptional = computed(() => {
+    return Boolean(
+        stepStore.getStep(props.connection.output.stepId)?.when ||
+            stepStore
+                .getStep(props.connection.output.stepId)
+                ?.outputs.find((output) => output.name === props.connection.output.name && output.optional)
+    );
+});
+
+const connectionIsValid = computed(() => {
+    return !connectionStore.invalidConnections[getConnectionId(props.connection)];
+});
+
+const offsets = computed(() => getLineOffsets(inputIsMappedOver.value, outputIsMappedOver.value));
+
+const paths = computed(() => {
+    if (!position.value || !offsets.value) {
+        return [];
+    }
+
+    const lines = [...Array(offsets.value.numOffsets).keys()].map((offsetIndex) => {
+        const startOffset = offsets.value.startOffsets[offsetIndex] || 0;
+        const endOffset = offsets.value.endOffsets[offsetIndex] || 0;
+        return [
+            [position.value!.startX, position.value!.startY + startOffset],
+            [position.value!.startX + lineShift, position.value!.startY + startOffset],
+            [position.value!.endX - lineShift, position.value!.endY + endOffset],
+            [position.value!.endX, position.value!.endY + endOffset],
+        ] as [number, number][];
+    });
+
+    return lines.map((l) => curve(l)!);
+});
+
+const lineWidth = computed(() => {
+    if (inputIsMappedOver.value || outputIsMappedOver.value) {
+        return 2;
+    } else {
+        return 4;
+    }
+});
+
+const connectionClass = computed(() => {
+    const classList = ["connection"];
+
+    if (outputIsOptional.value) {
+        classList.push("optional");
+    }
+
+    if (!connectionIsValid.value) {
+        classList.push("invalid");
+    }
+
+    return classList.join(" ");
+});
+
+function generateLineOffsets(inputIsMappedOver: boolean, outputIsMappedOver: boolean) {
+    const _offsets = [-2 * ribbonMargin, -ribbonMargin, 0, ribbonMargin, 2 * ribbonMargin];
+    let startOffsets = [0];
+    let endOffsets = [0];
+    let numOffsets = 1;
+
+    if (outputIsMappedOver) {
+        startOffsets = _offsets;
+        numOffsets = _offsets.length;
+    }
+    if (inputIsMappedOver) {
+        endOffsets = _offsets;
+        numOffsets = _offsets.length;
+    }
+    return { numOffsets, startOffsets, endOffsets };
+}
+
+const lineOffsets = {
+    "false-false": generateLineOffsets(false, false),
+    "true-false": generateLineOffsets(true, false),
+    "false-true": generateLineOffsets(false, true),
+    "true-true": generateLineOffsets(true, true),
+} as const;
+
+function getLineOffsets(inputIsMappedOver?: boolean, outputIsMappedOver?: boolean) {
+    return lineOffsets[`${inputIsMappedOver ?? false}-${outputIsMappedOver ?? false}`];
+}
+
+function keyForIndex(index: number) {
+    return `${props.id ?? "no-key"}-${index}`;
+}
+</script>
+
+<template>
+    <g :id="props.id" class="workflow-editor-drawable-connection">
+        <path
+            v-for="(path, index) in paths"
+            :key="keyForIndex(index)"
+            :class="connectionClass"
+            :d="path"
+            :stroke-width="lineWidth"
+            fill="none">
+        </path>
+    </g>
+</template>
+
+<style lang="scss">
+@import "~bootstrap/scss/_functions.scss";
+@import "theme/blue.scss";
+
+.workflow-editor-drawable-connection {
+    .connection {
+        stroke: #{$brand-primary};
+
+        &.optional {
+            stroke-dasharray: 5 3;
+        }
+
+        &.invalid {
+            stroke: #{$brand-warning};
+        }
+    }
+}
+</style>
diff --git a/client/src/components/Workflow/Editor/WorkflowEdges.vue b/client/src/components/Workflow/Editor/WorkflowEdges.vue
index db3bb5ba288a..5bc6decc4595 100644
--- a/client/src/components/Workflow/Editor/WorkflowEdges.vue
+++ b/client/src/components/Workflow/Editor/WorkflowEdges.vue
@@ -1,11 +1,10 @@
 <script setup lang="ts">
-import { computed, ref, toRef, onMounted, type Ref } from "vue";
+import { computed, type Ref } from "vue";
 import { type Connection, useConnectionStore, type OutputTerminal } from "@/stores/workflowConnectionStore";
 import { storeToRefs } from "pinia";
 import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
 import type { OutputTerminals } from "./modules/terminals";
-import { useDrawableConnection, setDrawableConnectionStyle } from "./composables/drawableConnection";
-import { useAnimationFrame } from "@/composables/sensors/animationFrame";
+import DrawableConnection from "./DrawableConnection.vue";
 
 const props = defineProps<{
     draggingConnection: TerminalPosition | null;
@@ -13,27 +12,10 @@ const props = defineProps<{
     transform: { x: number; y: number; k: number };
 }>();
 
-const canvas: Ref<HTMLCanvasElement | null> = ref(null);
-const context = computed(() => canvas.value?.getContext("2d") ?? null);
-
 const connectionStore = useConnectionStore();
 const { connections } = storeToRefs(connectionStore);
 
-const drawableConnections = computed(() => {
-    return connections.value.map((c) => useDrawableConnection(c));
-});
-
-onMounted(() => {
-    const element = canvas.value!;
-    const style = getComputedStyle(element);
-
-    setDrawableConnectionStyle({
-        connectionColor: style.getPropertyValue("--connection-color"),
-        connectionColorInvalid: style.getPropertyValue("--connection-color-invalid"),
-    });
-});
-
-const drawableDraggingConnection = computed(() => {
+const draggingConnection: Ref<[Connection, TerminalPosition] | null> = computed(() => {
     if (props.draggingConnection && props.draggingTerminal) {
         const connection: Connection = {
             input: {
@@ -44,54 +26,42 @@ const drawableDraggingConnection = computed(() => {
             output: props.draggingTerminal as unknown as OutputTerminal,
         };
 
-        return useDrawableConnection(connection, toRef(props, "draggingConnection"));
+        return [connection, props.draggingConnection];
     } else {
         return null;
     }
 });
 
-useAnimationFrame(() => {
-    const ctx = context.value;
-    if (!ctx) {
-        return;
-    }
-
-    ctx.canvas.width = ctx.canvas.offsetWidth;
-    ctx.canvas.height = ctx.canvas.offsetHeight;
-
-    ctx.resetTransform();
-    ctx.clearRect(0, 0, ctx.canvas.width, ctx.canvas.height);
-    ctx.translate(props.transform.x, props.transform.y);
-    ctx.scale(props.transform.k, props.transform.k);
-
-    drawableConnections.value.forEach((connection) => connection.draw(ctx));
-
-    if (drawableDraggingConnection.value) {
-        drawableDraggingConnection.value.draw(ctx);
-    }
-});
+function key(connection: Connection) {
+    return `${connection.input.stepId}-${connection.output.stepId}`;
+}
 </script>
 
 <template>
     <div class="workflow-edges">
-        <canvas ref="canvas" class="workflow-edges-canvas"></canvas>
+        <svg class="workflow-edges">
+            <DrawableConnection
+                v-if="draggingConnection"
+                :connection="draggingConnection[0]"
+                :terminal-position="draggingConnection[1]" />
+            <DrawableConnection
+                v-for="connection in connections"
+                :id="key(connection)"
+                :key="key(connection)"
+                :connection="connection" />
+        </svg>
     </div>
 </template>
 
 <style lang="scss" scoped>
-@import "~bootstrap/scss/_functions.scss";
-@import "theme/blue.scss";
-
-.workflow-edges-canvas {
-    --connection-color: #{$brand-primary};
-    --connection-color-invalid: #{$brand-warning};
-
-    position: absolute;
-    top: 0;
-    left: 0;
-    right: 0;
-    bottom: 0;
-    width: 100%;
+.workflow-edges {
+    display: block;
+    overflow: visible;
     height: 100%;
+    width: 100%;
+    left: 0;
+    top: 0;
+    position: absolute;
+    transform-origin: 0 0;
 }
 </style>
diff --git a/client/src/components/Workflow/Editor/WorkflowGraph.vue b/client/src/components/Workflow/Editor/WorkflowGraph.vue
index 48a8c33e4db1..8f9a8589264b 100644
--- a/client/src/components/Workflow/Editor/WorkflowGraph.vue
+++ b/client/src/components/Workflow/Editor/WorkflowGraph.vue
@@ -9,11 +9,11 @@
             @dragover.prevent>
             <!-- canvas-background is sibling of node-area because it has a different transform origin, so can't be parent of node-area -->
             <div class="canvas-background" :style="canvasStyle" />
-            <WorkflowEdges
-                :transform="transform"
-                :dragging-terminal="draggingTerminal"
-                :dragging-connection="draggingPosition" />
             <div class="node-area" :style="canvasStyle">
+                <WorkflowEdges
+                    :transform="transform"
+                    :dragging-terminal="draggingTerminal"
+                    :dragging-connection="draggingPosition" />
                 <WorkflowNode
                     v-for="(step, key) in steps"
                     :id="step.id"

From ba556c703273caa61e6b57989892f30fde87701c Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 26 Apr 2023 11:02:31 +0200
Subject: [PATCH 25/78] add tsconfig tweak to stop dev server crashes

---
 client/tsconfig.webpack.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/tsconfig.webpack.json b/client/tsconfig.webpack.json
index 41066f4d1901..3e146a7da498 100644
--- a/client/tsconfig.webpack.json
+++ b/client/tsconfig.webpack.json
@@ -1,4 +1,4 @@
 {
     "extends": "./tsconfig.json",
-    "include": ["types/*.d.ts", "src/**/*.ts", "src/**/*.tsx", "src/**/*.vue"]
+    "exclude": ["./src/**/*.test.ts", "./tests/**/*.ts"]
 }

From 1e623fcd9dbc7e200631ab276fc96a76fd6cc70d Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 26 Apr 2023 11:03:21 +0200
Subject: [PATCH 26/78] fix initial rendering of edges

---
 .../Workflow/Editor/DrawableConnection.vue    | 39 ++++++++++++++-----
 .../Workflow/Editor/WorkflowEdges.vue         |  6 ++-
 client/src/stores/workflowEditorStateStore.ts |  4 +-
 3 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/client/src/components/Workflow/Editor/DrawableConnection.vue b/client/src/components/Workflow/Editor/DrawableConnection.vue
index 8e7f22d112eb..bec80ae52765 100644
--- a/client/src/components/Workflow/Editor/DrawableConnection.vue
+++ b/client/src/components/Workflow/Editor/DrawableConnection.vue
@@ -1,9 +1,14 @@
 <script setup lang="ts">
 import { line, curveBasis } from "d3";
-import { computed, type PropType } from "vue";
+import { computed, unref, type PropType } from "vue";
 
 import { getConnectionId, type Connection } from "@/stores/workflowConnectionStore";
-import { useWorkflowStateStore, type TerminalPosition } from "@/stores/workflowEditorStateStore";
+import {
+    useWorkflowStateStore,
+    type TerminalPosition,
+    type OutputTerminalPosition,
+    type InputTerminalPosition,
+} from "@/stores/workflowEditorStateStore";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import { useWorkflowStepStore } from "@/stores/workflowStepStore";
 
@@ -28,18 +33,32 @@ const stateStore = useWorkflowStateStore();
 const connectionStore = useConnectionStore();
 const stepStore = useWorkflowStepStore();
 
-const position = computed(() => {
+const outputPos = computed(() => {
     if (props.terminalPosition) {
-        return props.terminalPosition;
+        return {
+            startX: props.terminalPosition.startX,
+            startY: props.terminalPosition.startY,
+        } as OutputTerminalPosition;
+    } else {
+        return unref(
+            stateStore.getOutputTerminalPosition(props.connection.output.stepId, props.connection.output.name)
+        );
     }
+});
 
-    const outputPos = stateStore.getOutputTerminalPosition(
-        props.connection.output.stepId,
-        props.connection.output.name
-    );
-    const inputPos = stateStore.getInputTerminalPosition(props.connection.input.stepId, props.connection.input.name);
+const inputPos = computed(() => {
+    if (props.terminalPosition) {
+        return {
+            endX: props.terminalPosition.endX,
+            endY: props.terminalPosition.endY,
+        } as InputTerminalPosition;
+    } else {
+        return unref(stateStore.getInputTerminalPosition(props.connection.input.stepId, props.connection.input.name));
+    }
+});
 
-    if (inputPos && outputPos) {
+const position = computed(() => {
+    if (inputPos.value && outputPos.value) {
         return {
             startX: outputPos.value.startX,
             startY: outputPos.value.startY,
diff --git a/client/src/components/Workflow/Editor/WorkflowEdges.vue b/client/src/components/Workflow/Editor/WorkflowEdges.vue
index 5bc6decc4595..d773c0408b72 100644
--- a/client/src/components/Workflow/Editor/WorkflowEdges.vue
+++ b/client/src/components/Workflow/Editor/WorkflowEdges.vue
@@ -35,6 +35,10 @@ const draggingConnection: Ref<[Connection, TerminalPosition] | null> = computed(
 function key(connection: Connection) {
     return `${connection.input.stepId}-${connection.output.stepId}`;
 }
+
+function id(connection: Connection) {
+    return `connection-node-${connection.input.stepId}-input-${connection.input.name}-node-${connection.output.stepId}-output-${connection.output.name}`;
+}
 </script>
 
 <template>
@@ -46,7 +50,7 @@ function key(connection: Connection) {
                 :terminal-position="draggingConnection[1]" />
             <DrawableConnection
                 v-for="connection in connections"
-                :id="key(connection)"
+                :id="id(connection)"
                 :key="key(connection)"
                 :connection="connection" />
         </svg>
diff --git a/client/src/stores/workflowEditorStateStore.ts b/client/src/stores/workflowEditorStateStore.ts
index 55e2315c7ec6..b93b382086b8 100644
--- a/client/src/stores/workflowEditorStateStore.ts
+++ b/client/src/stores/workflowEditorStateStore.ts
@@ -61,7 +61,7 @@ export const useWorkflowStateStore = defineStore("workflowStateStore", {
     actions: {
         setInputTerminalPosition(stepId: number, inputName: string, position: InputTerminalPosition) {
             if (!this.inputTerminals[stepId]) {
-                this.inputTerminals[stepId] = {};
+                Vue.set(this.inputTerminals, stepId, {});
             }
 
             if (!this.inputTerminals[stepId][inputName]) {
@@ -72,7 +72,7 @@ export const useWorkflowStateStore = defineStore("workflowStateStore", {
         },
         setOutputTerminalPosition(stepId: number, outputName: string, position: OutputTerminalPosition) {
             if (!this.outputTerminals[stepId]) {
-                this.outputTerminals[stepId] = {};
+                Vue.set(this.outputTerminals, stepId, {});
             }
 
             if (!this.outputTerminals[stepId][outputName]) {

From 72cbea9ce1c912df70dd08d80db5a5eb195c31f6 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 26 Apr 2023 11:09:23 +0200
Subject: [PATCH 27/78] remove drawable connection composable

---
 .../Editor/composables/drawableConnection.ts  | 146 ------------------
 1 file changed, 146 deletions(-)
 delete mode 100644 client/src/components/Workflow/Editor/composables/drawableConnection.ts

diff --git a/client/src/components/Workflow/Editor/composables/drawableConnection.ts b/client/src/components/Workflow/Editor/composables/drawableConnection.ts
deleted file mode 100644
index 14f47da96db9..000000000000
--- a/client/src/components/Workflow/Editor/composables/drawableConnection.ts
+++ /dev/null
@@ -1,146 +0,0 @@
-import { getConnectionId, type Connection } from "@/stores/workflowConnectionStore";
-import { computed, type Ref } from "vue";
-import { useWorkflowStateStore, type TerminalPosition } from "@/stores/workflowEditorStateStore";
-import { line, curveBasis } from "d3";
-import { useConnectionStore } from "@/stores/workflowConnectionStore";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
-
-let style = {
-    connectionColor: "black",
-    connectionColorInvalid: "red",
-    optionalLineDash: [5, 3],
-    ribbonMargin: 4,
-    lineShift: 30,
-};
-
-const curve = line().curve(curveBasis);
-
-function generateLineOffsets(inputIsMappedOver: boolean, outputIsMappedOver: boolean) {
-    const _offsets = [-2 * style.ribbonMargin, -style.ribbonMargin, 0, style.ribbonMargin, 2 * style.ribbonMargin];
-    let startOffsets = [0];
-    let endOffsets = [0];
-    let numOffsets = 1;
-
-    if (outputIsMappedOver) {
-        startOffsets = _offsets;
-        numOffsets = _offsets.length;
-    }
-    if (inputIsMappedOver) {
-        endOffsets = _offsets;
-        numOffsets = _offsets.length;
-    }
-    return { numOffsets, startOffsets, endOffsets };
-}
-
-const lineOffsets = {
-    "false-false": generateLineOffsets(false, false),
-    "true-false": generateLineOffsets(true, false),
-    "false-true": generateLineOffsets(false, true),
-    "true-true": generateLineOffsets(true, true),
-} as const;
-
-function getLineOffsets(inputIsMappedOver?: boolean, outputIsMappedOver?: boolean) {
-    return lineOffsets[`${inputIsMappedOver ?? false}-${outputIsMappedOver ?? false}`];
-}
-
-export function setDrawableConnectionStyle(newStyle: Partial<typeof style>) {
-    style = { ...style, ...newStyle };
-}
-
-export function useDrawableConnection(connection: Connection, terminalPosition?: Ref<TerminalPosition | null>) {
-    const stateStore = useWorkflowStateStore();
-    const connectionStore = useConnectionStore();
-    const stepStore = useWorkflowStepStore();
-
-    const position = computed(() => {
-        if (terminalPosition) {
-            return terminalPosition.value;
-        }
-
-        const outputPos = stateStore.getOutputTerminalPosition(connection.output.stepId, connection.output.name);
-        const inputPos = stateStore.getInputTerminalPosition(connection.input.stepId, connection.input.name);
-
-        if (inputPos && outputPos) {
-            return {
-                startX: outputPos.value.startX,
-                startY: outputPos.value.startY,
-                endX: inputPos.value.endX,
-                endY: inputPos.value.endY,
-            };
-        }
-
-        return null;
-    });
-
-    const outputIsMappedOver = computed(() => stepStore.stepMapOver[connection.output.stepId]?.isCollection);
-    const inputIsMappedOver = computed(
-        () =>
-            stepStore.stepInputMapOver[connection.input.stepId] &&
-            stepStore.stepInputMapOver[connection.input.stepId][connection.input.name]?.isCollection
-    );
-
-    const outputIsOptional = computed(() => {
-        return Boolean(
-            stepStore.getStep(connection.output.stepId)?.when ||
-                stepStore
-                    .getStep(connection.output.stepId)
-                    ?.outputs.find((output) => output.name === connection.output.name && output.optional)
-        );
-    });
-
-    const connectionIsValid = computed(() => {
-        return !connectionStore.invalidConnections[getConnectionId(connection)];
-    });
-
-    const offsets = computed(() => getLineOffsets(inputIsMappedOver.value, outputIsMappedOver.value));
-
-    const paths = computed(() => {
-        if (!position.value || !offsets.value) {
-            return [];
-        }
-
-        const lines = [...Array(offsets.value.numOffsets).keys()].map((offsetIndex) => {
-            const startOffset = offsets.value.startOffsets[offsetIndex] || 0;
-            const endOffset = offsets.value.endOffsets[offsetIndex] || 0;
-            return [
-                [position.value!.startX, position.value!.startY + startOffset],
-                [position.value!.startX + style.lineShift, position.value!.startY + startOffset],
-                [position.value!.endX - style.lineShift, position.value!.endY + endOffset],
-                [position.value!.endX, position.value!.endY + endOffset],
-            ] as [number, number][];
-        });
-
-        return lines;
-    });
-
-    const draw = (ctx: CanvasRenderingContext2D) => {
-        curve.context(ctx);
-        ctx.beginPath();
-
-        if (outputIsOptional.value) {
-            ctx.setLineDash(style.optionalLineDash);
-        } else {
-            ctx.setLineDash([]);
-        }
-
-        if (connectionIsValid.value) {
-            ctx.strokeStyle = style.connectionColor;
-        } else {
-            ctx.strokeStyle = style.connectionColorInvalid;
-        }
-
-        if (inputIsMappedOver.value || outputIsMappedOver.value) {
-            ctx.lineWidth = 2;
-        } else {
-            ctx.lineWidth = 4;
-        }
-
-        paths.value.forEach((p) => curve(p));
-
-        ctx.stroke();
-    };
-
-    return {
-        draw,
-    };
-}

From 09a5297636b350cd38c6f65a9e572257d31cbd42 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Wed, 26 Apr 2023 11:28:23 +0200
Subject: [PATCH 28/78] undo test noop

---
 .../selenium/test_workflow_editor.py          | 27 ++++++++-----------
 1 file changed, 11 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index cb81f4463463..ab6c79333a78 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -1102,22 +1102,17 @@ def workflow_editor_connect(self, source, sink, screenshot_partial=None):
             self.screenshot(screenshot_partial)
         drag_and_drop(self.driver, source_element, sink_element)
 
-    def assert_connected(self, _source, _sink):
-        # NOOP
-        # Used to assert that an svg connection element exists.
-        # Since connections are no longer rendered with SVG, this is no longer possible.
-        # TODO: add different method of asserting connections
-        pass
-
-    def assert_connection_invalid(self, _source, _sink):
-        # NOOP
-        # TODO: add different method of asserting connections
-        pass
-
-    def assert_not_connected(self, _source, _sink):
-        # NOOP
-        # TODO: add different method of asserting connections
-        pass
+    def assert_connected(self, source, sink):
+        source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
+        self.components.workflow_editor.connector_for(source_id=source_id, sink_id=sink_id).wait_for_visible()
+
+    def assert_connection_invalid(self, source, sink):
+        source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
+        self.components.workflow_editor.connector_invalid_for(source_id=source_id, sink_id=sink_id).wait_for_present()
+
+    def assert_not_connected(self, source, sink):
+        source_id, sink_id = self.workflow_editor_source_sink_terminal_ids(source, sink)
+        self.components.workflow_editor.connector_for(source_id=source_id, sink_id=sink_id).wait_for_absent()
 
     def open_in_workflow_editor(self, yaml_content, auto_layout=True):
         name = self.workflow_upload_yaml_with_random_name(yaml_content)

From 9dc6816e3c8e4b58d08dba7c28fba41098ab146a Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 28 Apr 2023 10:29:00 +0200
Subject: [PATCH 29/78] restore navigation.yml

---
 client/src/utils/navigation/navigation.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 59732b0dbfb4..2b792f2df156 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -662,6 +662,8 @@ workflow_editor:
       selector: >
         //div[@data-label='Remove Tags']//input
     tool_version_button: ".tool-versions"
+    connector_for: "#connection-${sink_id}-${source_id}"
+    connector_invalid_for: "#connection-${sink_id}-${source_id} .connection.invalid"
     connector_destroy_callout: '.delete-terminal'
     save_button: '.editor-button-save'
     save_workflow_confirmation_button: '#save-workflow-confirmation .btn-primary'

From ce671026f8ee526e9bd89c8456f3ff14e4e8034d Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 28 Apr 2023 10:31:21 +0200
Subject: [PATCH 30/78] rename connection add input name to key to avoid
 duplicate keys

---
 .../Editor/{DrawableConnection.vue => SVGConnection.vue}  | 0
 client/src/components/Workflow/Editor/WorkflowEdges.vue   | 8 ++++----
 2 files changed, 4 insertions(+), 4 deletions(-)
 rename client/src/components/Workflow/Editor/{DrawableConnection.vue => SVGConnection.vue} (100%)

diff --git a/client/src/components/Workflow/Editor/DrawableConnection.vue b/client/src/components/Workflow/Editor/SVGConnection.vue
similarity index 100%
rename from client/src/components/Workflow/Editor/DrawableConnection.vue
rename to client/src/components/Workflow/Editor/SVGConnection.vue
diff --git a/client/src/components/Workflow/Editor/WorkflowEdges.vue b/client/src/components/Workflow/Editor/WorkflowEdges.vue
index d773c0408b72..023560694ec6 100644
--- a/client/src/components/Workflow/Editor/WorkflowEdges.vue
+++ b/client/src/components/Workflow/Editor/WorkflowEdges.vue
@@ -4,7 +4,7 @@ import { type Connection, useConnectionStore, type OutputTerminal } from "@/stor
 import { storeToRefs } from "pinia";
 import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
 import type { OutputTerminals } from "./modules/terminals";
-import DrawableConnection from "./DrawableConnection.vue";
+import SVGConnection from "./SVGConnection.vue";
 
 const props = defineProps<{
     draggingConnection: TerminalPosition | null;
@@ -33,7 +33,7 @@ const draggingConnection: Ref<[Connection, TerminalPosition] | null> = computed(
 });
 
 function key(connection: Connection) {
-    return `${connection.input.stepId}-${connection.output.stepId}`;
+    return `${connection.input.stepId}-${connection.input.name}-${connection.output.stepId}`;
 }
 
 function id(connection: Connection) {
@@ -44,11 +44,11 @@ function id(connection: Connection) {
 <template>
     <div class="workflow-edges">
         <svg class="workflow-edges">
-            <DrawableConnection
+            <SVGConnection
                 v-if="draggingConnection"
                 :connection="draggingConnection[0]"
                 :terminal-position="draggingConnection[1]" />
-            <DrawableConnection
+            <SVGConnection
                 v-for="connection in connections"
                 :id="id(connection)"
                 :key="key(connection)"

From c228da4be5f41842da5f82bdb2e7f92dc54d0c8b Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 28 Apr 2023 14:10:40 +0200
Subject: [PATCH 31/78] fix connection drop

---
 .../src/components/Workflow/Editor/Node.vue   |  4 +-
 .../Workflow/Editor/SVGConnection.vue         | 41 ++++++++++---------
 2 files changed, 24 insertions(+), 21 deletions(-)

diff --git a/client/src/components/Workflow/Editor/Node.vue b/client/src/components/Workflow/Editor/Node.vue
index 597a75b23196..6ad4e7ade998 100644
--- a/client/src/components/Workflow/Editor/Node.vue
+++ b/client/src/components/Workflow/Editor/Node.vue
@@ -75,7 +75,7 @@
         <div v-else class="node-body" @click="makeActive" @keyup.enter="makeActive">
             <node-input
                 v-for="(input, index) in inputs"
-                :key="`${index}-${input.name}`"
+                :key="`in-${index}-${input.name}`"
                 :input="input"
                 :step-id="id"
                 :datatypes-mapper="datatypesMapper"
@@ -88,7 +88,7 @@
             <div v-if="showRule" class="rule" />
             <node-output
                 v-for="(output, index) in outputs"
-                :key="`${index + inputs.length}-${output.name}`"
+                :key="`out-${index}-${output.name}`"
                 :output="output"
                 :workflow-outputs="workflowOutputs"
                 :post-job-actions="postJobActions"
diff --git a/client/src/components/Workflow/Editor/SVGConnection.vue b/client/src/components/Workflow/Editor/SVGConnection.vue
index bec80ae52765..f72c077710de 100644
--- a/client/src/components/Workflow/Editor/SVGConnection.vue
+++ b/client/src/components/Workflow/Editor/SVGConnection.vue
@@ -1,14 +1,9 @@
 <script setup lang="ts">
 import { line, curveBasis } from "d3";
-import { computed, unref, type PropType } from "vue";
+import { computed, type PropType, ref } from "vue";
 
 import { getConnectionId, type Connection } from "@/stores/workflowConnectionStore";
-import {
-    useWorkflowStateStore,
-    type TerminalPosition,
-    type OutputTerminalPosition,
-    type InputTerminalPosition,
-} from "@/stores/workflowEditorStateStore";
+import { useWorkflowStateStore, type TerminalPosition } from "@/stores/workflowEditorStateStore";
 import { useConnectionStore } from "@/stores/workflowConnectionStore";
 import { useWorkflowStepStore } from "@/stores/workflowStepStore";
 
@@ -35,35 +30,43 @@ const stepStore = useWorkflowStepStore();
 
 const outputPos = computed(() => {
     if (props.terminalPosition) {
-        return {
+        return ref({
             startX: props.terminalPosition.startX,
             startY: props.terminalPosition.startY,
-        } as OutputTerminalPosition;
+        });
     } else {
-        return unref(
-            stateStore.getOutputTerminalPosition(props.connection.output.stepId, props.connection.output.name)
-        );
+        const pos = stateStore.getOutputTerminalPosition(props.connection.output.stepId, props.connection.output.name);
+        if (pos) {
+            return pos;
+        } else {
+            return null;
+        }
     }
 });
 
 const inputPos = computed(() => {
     if (props.terminalPosition) {
-        return {
+        return ref({
             endX: props.terminalPosition.endX,
             endY: props.terminalPosition.endY,
-        } as InputTerminalPosition;
+        });
     } else {
-        return unref(stateStore.getInputTerminalPosition(props.connection.input.stepId, props.connection.input.name));
+        const pos = stateStore.getInputTerminalPosition(props.connection.input.stepId, props.connection.input.name);
+        if (pos) {
+            return pos;
+        } else {
+            return null;
+        }
     }
 });
 
 const position = computed(() => {
     if (inputPos.value && outputPos.value) {
         return {
-            startX: outputPos.value.startX,
-            startY: outputPos.value.startY,
-            endX: inputPos.value.endX,
-            endY: inputPos.value.endY,
+            startX: outputPos.value.value.startX,
+            startY: outputPos.value.value.startY,
+            endX: inputPos.value.value.endX,
+            endY: inputPos.value.value.endY,
         };
     }
 

From a2ff1e9e9e9f0286684f65de3f00d57558e5f569 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Fri, 28 Apr 2023 14:19:57 +0200
Subject: [PATCH 32/78] fix initial loading of invalid connections

---
 .../Workflow/Editor/SVGConnection.vue         | 18 +++++++-------
 client/src/stores/workflowEditorStateStore.ts | 24 +++++++------------
 2 files changed, 17 insertions(+), 25 deletions(-)

diff --git a/client/src/components/Workflow/Editor/SVGConnection.vue b/client/src/components/Workflow/Editor/SVGConnection.vue
index f72c077710de..5e5ea692a366 100644
--- a/client/src/components/Workflow/Editor/SVGConnection.vue
+++ b/client/src/components/Workflow/Editor/SVGConnection.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { line, curveBasis } from "d3";
-import { computed, type PropType, ref } from "vue";
+import { computed, type PropType } from "vue";
 
 import { getConnectionId, type Connection } from "@/stores/workflowConnectionStore";
 import { useWorkflowStateStore, type TerminalPosition } from "@/stores/workflowEditorStateStore";
@@ -30,10 +30,10 @@ const stepStore = useWorkflowStepStore();
 
 const outputPos = computed(() => {
     if (props.terminalPosition) {
-        return ref({
+        return {
             startX: props.terminalPosition.startX,
             startY: props.terminalPosition.startY,
-        });
+        };
     } else {
         const pos = stateStore.getOutputTerminalPosition(props.connection.output.stepId, props.connection.output.name);
         if (pos) {
@@ -46,10 +46,10 @@ const outputPos = computed(() => {
 
 const inputPos = computed(() => {
     if (props.terminalPosition) {
-        return ref({
+        return {
             endX: props.terminalPosition.endX,
             endY: props.terminalPosition.endY,
-        });
+        };
     } else {
         const pos = stateStore.getInputTerminalPosition(props.connection.input.stepId, props.connection.input.name);
         if (pos) {
@@ -63,10 +63,10 @@ const inputPos = computed(() => {
 const position = computed(() => {
     if (inputPos.value && outputPos.value) {
         return {
-            startX: outputPos.value.value.startX,
-            startY: outputPos.value.value.startY,
-            endX: inputPos.value.value.endX,
-            endY: inputPos.value.value.endY,
+            startX: outputPos.value.startX,
+            startY: outputPos.value.startY,
+            endX: inputPos.value.endX,
+            endY: inputPos.value.endY,
         };
     }
 
diff --git a/client/src/stores/workflowEditorStateStore.ts b/client/src/stores/workflowEditorStateStore.ts
index b93b382086b8..47a096d65f52 100644
--- a/client/src/stores/workflowEditorStateStore.ts
+++ b/client/src/stores/workflowEditorStateStore.ts
@@ -1,4 +1,4 @@
-import Vue, { shallowRef, type ShallowRef } from "vue";
+import Vue, { reactive } from "vue";
 import type { UnwrapRef } from "vue";
 import { defineStore } from "pinia";
 import type { OutputTerminals } from "@/components/Workflow/Editor/modules/terminals";
@@ -22,8 +22,8 @@ export interface XYPosition {
 }
 
 interface State {
-    inputTerminals: { [index: number]: { [index: string]: ShallowRef<InputTerminalPosition> } };
-    outputTerminals: { [index: number]: { [index: string]: ShallowRef<OutputTerminalPosition> } };
+    inputTerminals: { [index: number]: { [index: string]: InputTerminalPosition } };
+    outputTerminals: { [index: number]: { [index: string]: OutputTerminalPosition } };
     draggingPosition: TerminalPosition | null;
     draggingTerminal: OutputTerminals | null;
     activeNodeId: number | null;
@@ -46,12 +46,12 @@ export const useWorkflowStateStore = defineStore("workflowStateStore", {
     getters: {
         getInputTerminalPosition(state: State) {
             return (stepId: number, inputName: string) => {
-                return state.inputTerminals[stepId]?.[inputName] as ShallowRef<InputTerminalPosition> | undefined;
+                return state.inputTerminals[stepId]?.[inputName] as InputTerminalPosition | undefined;
             };
         },
         getOutputTerminalPosition(state: State) {
             return (stepId: number, outputName: string) => {
-                return state.outputTerminals[stepId]?.[outputName] as ShallowRef<OutputTerminalPosition> | undefined;
+                return state.outputTerminals[stepId]?.[outputName] as OutputTerminalPosition | undefined;
             };
         },
         getStepLoadingState(state: State) {
@@ -64,22 +64,14 @@ export const useWorkflowStateStore = defineStore("workflowStateStore", {
                 Vue.set(this.inputTerminals, stepId, {});
             }
 
-            if (!this.inputTerminals[stepId][inputName]) {
-                this.inputTerminals[stepId][inputName] = shallowRef(position);
-            } else {
-                this.inputTerminals[stepId][inputName].value = position;
-            }
+            Vue.set(this.inputTerminals[stepId], inputName, position);
         },
         setOutputTerminalPosition(stepId: number, outputName: string, position: OutputTerminalPosition) {
             if (!this.outputTerminals[stepId]) {
-                Vue.set(this.outputTerminals, stepId, {});
+                Vue.set(this.outputTerminals, stepId, reactive({}));
             }
 
-            if (!this.outputTerminals[stepId][outputName]) {
-                this.outputTerminals[stepId][outputName] = shallowRef(position);
-            } else {
-                this.outputTerminals[stepId][outputName].value = position;
-            }
+            Vue.set(this.outputTerminals[stepId], outputName, position);
         },
         deleteInputTerminalPosition(stepId: number, inputName: string) {
             delete this.inputTerminals[stepId]?.[inputName];

From ab03bb0b1a28402ad635f5dbace362857f2b28c0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 27 Apr 2023 17:54:10 +0200
Subject: [PATCH 33/78] Ensure a dataset in OK state has a valid file

when it should be included in an export process
---
 lib/galaxy/model/store/__init__.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 538fa69c58e5..04b0e0b46591 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2133,6 +2133,8 @@ def export_history(
                 should_include_file = True
 
             if dataset not in self.included_datasets:
+                if should_include_file:
+                    self._ensure_dataset_file_accessible(dataset)
                 self.add_dataset(dataset, include_files=should_include_file)
 
     def export_library(
@@ -2215,6 +2217,13 @@ def add_dataset_collection(
     def add_dataset(self, dataset: model.DatasetInstance, include_files: bool = True) -> None:
         self.included_datasets[dataset] = (dataset, include_files)
 
+    def _ensure_dataset_file_accessible(self, dataset: model.DatasetInstance) -> None:
+        file_name = dataset.file_name
+        state = dataset.dataset.state
+        if not file_name and state in [model.Dataset.states.OK]:
+            log.error("Dataset [%s] does not exists on disk or is not accessible, while trying to export." % dataset.id)
+            raise Exception(f"Cannot export dataset: {dataset.name}")
+
     def _finalize(self) -> None:
         export_directory = self.export_directory
 

From 649e056db0050084fbf58a67031b036a449918d0 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 28 Apr 2023 15:52:56 +0200
Subject: [PATCH 34/78] Shortcut condition to avoid checking the disk

If the dataset is not in OK state there is no need to check for the file_path and the cost of checking the disk.
---
 lib/galaxy/model/store/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 04b0e0b46591..0c625601ce16 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2218,9 +2218,8 @@ def add_dataset(self, dataset: model.DatasetInstance, include_files: bool = True
         self.included_datasets[dataset] = (dataset, include_files)
 
     def _ensure_dataset_file_accessible(self, dataset: model.DatasetInstance) -> None:
-        file_name = dataset.file_name
         state = dataset.dataset.state
-        if not file_name and state in [model.Dataset.states.OK]:
+        if state in [model.Dataset.states.OK] and not dataset.file_name:
             log.error("Dataset [%s] does not exists on disk or is not accessible, while trying to export." % dataset.id)
             raise Exception(f"Cannot export dataset: {dataset.name}")
 

From c616c6e661ac71e992d3b379e0685cd162c244dc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20L=C3=B3pez?=
 <46503462+davelopez@users.noreply.github.com>
Date: Fri, 28 Apr 2023 16:01:33 +0200
Subject: [PATCH 35/78] Use better name

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/model/store/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 0c625601ce16..72d120d21045 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2134,7 +2134,7 @@ def export_history(
 
             if dataset not in self.included_datasets:
                 if should_include_file:
-                    self._ensure_dataset_file_accessible(dataset)
+                    self._ensure_dataset_file_exists(dataset)
                 self.add_dataset(dataset, include_files=should_include_file)
 
     def export_library(
@@ -2217,7 +2217,7 @@ def add_dataset_collection(
     def add_dataset(self, dataset: model.DatasetInstance, include_files: bool = True) -> None:
         self.included_datasets[dataset] = (dataset, include_files)
 
-    def _ensure_dataset_file_accessible(self, dataset: model.DatasetInstance) -> None:
+    def _ensure_dataset_file_exists(self, dataset: model.DatasetInstance) -> None:
         state = dataset.dataset.state
         if state in [model.Dataset.states.OK] and not dataset.file_name:
             log.error("Dataset [%s] does not exists on disk or is not accessible, while trying to export." % dataset.id)

From af5b2440aa620f8853ba220ce2da62b2f1c1b7d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20L=C3=B3pez?=
 <46503462+davelopez@users.noreply.github.com>
Date: Fri, 28 Apr 2023 16:23:25 +0200
Subject: [PATCH 36/78] Fix condition

To avoid leaking deleted datasets that are part of a collection

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/model/store/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 72d120d21045..7db16a7829a8 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2129,7 +2129,7 @@ def export_history(
         for dataset in datasets:
             dataset.annotation = get_item_annotation_str(sa_session, history.user, dataset)
             should_include_file = (dataset.visible or include_hidden) and (not dataset.deleted or include_deleted)
-            if dataset.id in self.collection_datasets:
+            if not dataset.deleted and dataset.id in self.collection_datasets:
                 should_include_file = True
 
             if dataset not in self.included_datasets:

From 69a527287e9731f5d62a82d94d4d7bc205cc2ca7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 27 Apr 2023 14:23:02 -0400
Subject: [PATCH 37/78] Fix reports graphs; use secondary version of d3v3 for
 compat

---
 client/src/reports/run_stats.js | 41 +++++++++++++++++++--------------
 1 file changed, 24 insertions(+), 17 deletions(-)

diff --git a/client/src/reports/run_stats.js b/client/src/reports/run_stats.js
index e7d8dc92d9c3..2e49976cbed6 100644
--- a/client/src/reports/run_stats.js
+++ b/client/src/reports/run_stats.js
@@ -1,5 +1,6 @@
 import $ from "jquery";
-import * as d3 from "d3";
+import * as d3 from "d3v3";
+import { event as currentEvent } from "d3v3";
 
 function date_by_subtracting_days(date, days) {
     return new Date(
@@ -125,14 +126,14 @@ export function create_chart(inp_data, name, time, title) {
             }
 
             var wdth = i * 4 + 10;
-            d3.select(d.target.parentElement)
+            d3.select(currentEvent.target.parentElement)
                 .select(".tool_tip")
                 .select("text")
                 .attr("transform", `translate( ${margin.left - 5}, ${height - d * zoom + margin.top + 10} )`)
                 .attr("visibility", "visible")
                 .text(d);
 
-            d3.select(d.target.parentElement)
+            d3.select(currentEvent.target.parentElement)
                 .select(".tool_tip")
                 .attr("width", `${wdth}px`)
                 .attr("height", "15px")
@@ -144,9 +145,12 @@ export function create_chart(inp_data, name, time, title) {
         })
         .on("mouseleave", (d) => {
             // Remove tool tip
-            d3.select(d.target.parentElement).select(".tool_tip").select("text").attr("visibility", "hidden");
+            d3.select(currentEvent.target.parentElement)
+                .select(".tool_tip")
+                .select("text")
+                .attr("visibility", "hidden");
 
-            d3.select(d.target.parentElement)
+            d3.select(currentEvent.target.parentElement)
                 .select(".tool_tip")
                 .select("rect")
                 .attr("width", "0")
@@ -178,14 +182,14 @@ export function create_chart(inp_data, name, time, title) {
         });
 
     // Declare how high the y axis goes
-    var y = d3.curveLinear().range([height, 0]);
+    var y = d3.scale.linear().range([height, 0]);
 
     // Create a yAxis object
     var yAxis = d3.svg
         .axis()
         .scale(y)
         .orient("left")
-        .tickFormat((d) => Math.round(d * d3.max(data), 0));
+        .tickFormat((d) => d3.round(d * d3.max(data), 0));
 
     // Put the y axis on the chart
     chart
@@ -438,13 +442,13 @@ export function create_histogram(inp_data, name, title) {
 
     // Cereate x axis metadata
     // Used for x axis, histogram creation, and bar initialization
-    var x = d3
-        .curveLinear()
+    var x = d3.scale
+        .linear()
         .domain([0, d3.max(data)])
         .range([0, width]);
 
     // Generate a histogram using twenty uniformly-spaced bins.
-    data = d3.histogram().bins(x.ticks(20))(data);
+    data = d3.layout.histogram().bins(x.ticks(20))(data);
 
     // Create an array of the sizes of the bars
     var lengths = [];
@@ -462,8 +466,8 @@ export function create_histogram(inp_data, name, title) {
 
     // Create y axis metadata
     // Used for y axis and bar initialization
-    var y = d3
-        .curveLinear()
+    var y = d3.scale
+        .linear()
         .domain([0, d3.max(data, (d) => d.y)])
         .range([height, 0]);
 
@@ -538,14 +542,14 @@ export function create_histogram(inp_data, name, title) {
                 i++;
             }
             var wdth = i * 4 + 10;
-            d3.select(d.target.parentElement)
+            d3.select(currentEvent.target.parentElement)
                 .select(".tool_tip")
                 .select("text")
                 .attr("transform", `translate( ${margin.left - 5}, ${height - d.length * zoom + margin.top + 10} )`)
                 .attr("visibility", "visible")
                 .text(d.length);
 
-            d3.select(d.target.parentElement)
+            d3.select(currentEvent.target.parentElement)
                 .select(".tool_tip")
                 .attr("width", `${wdth}px`)
                 .attr("height", "15px")
@@ -555,11 +559,14 @@ export function create_histogram(inp_data, name, title) {
                 .attr("height", "15px")
                 .attr("fill", "#ebd9b2");
         })
-        .on("mouseleave", (d) => {
+        .on("mouseleave", () => {
             // Remove tool tip
-            d3.select(d.target.parentElement).select(".tool_tip").select("text").attr("visibility", "hidden");
+            d3.select(currentEvent.target.parentElement)
+                .select(".tool_tip")
+                .select("text")
+                .attr("visibility", "hidden");
 
-            d3.select(d.target.parentElement)
+            d3.select(currentEvent.target.parentElement)
                 .select(".tool_tip")
                 .select("rect")
                 .attr("width", "0")

From 57c1bd8a3bcb7cbc77f9271ec6270c61c0e8e1c8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 27 Apr 2023 14:48:41 -0400
Subject: [PATCH 38/78] Fix reports masthead

---
 templates/base/base_panels.mako            |  4 +--
 templates/webapps/reports/base_panels.mako | 41 +++++++---------------
 2 files changed, 14 insertions(+), 31 deletions(-)

diff --git a/templates/base/base_panels.mako b/templates/base/base_panels.mako
index 75c592abb694..51147a517cd0 100644
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -147,9 +147,7 @@
             <div id="background"></div>
             
             ## Layer iframes over backgrounds
-            <div id="masthead" class="navbar navbar-fixed-top navbar-inverse">
-                ${self.masthead()}
-            </div>
+            ${self.masthead()}
             
             %if self.message_box_visible:
                 <div id="messagebox" class="alert alert-${app.config.message_box_class} rounded-0 m-0 p-2">
diff --git a/templates/webapps/reports/base_panels.mako b/templates/webapps/reports/base_panels.mako
index 5e4b8e7cb0bc..5eec1336e704 100644
--- a/templates/webapps/reports/base_panels.mako
+++ b/templates/webapps/reports/base_panels.mako
@@ -17,32 +17,17 @@
 
 ## Masthead
 <%def name="masthead()">
-    ## Tab area, fills entire width
-    <div style="position: absolute; top: 0; left: 0; width: 100%; text-align: center">
-        <table class="tab-group" border="0" cellspacing="0" style="margin: auto;">
-            <tr>
-                <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )">
-                    <%
-                    cls = "tab"
-                    if extra_class:
-                        cls += " " + extra_class
-                    if self.active_view == id:
-                        cls += " active"
-                    style = ""
-                    if not visible:
-                        style = "display: none;"
-                    %>
-                    <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></td>
-                </%def>
-            </tr>
-        </table>
-    </div>
-    ## Logo, layered over tabs to be clickable
-    <a class="navbar-brand" href="${h.url_for( app.config.get( 'logo_url', '/' ) )}">
-        <img class="navbar-brand-image" src="${h.url_for('/static/favicon.svg')}" />
-        <span class="navbar-brand-title">Galaxy Reports</span>
-        %if app.config.brand:
-            <span class='brand'>/ ${app.config.brand}</span>
-        %endif
-    </a>
+    <!-- This has the class masthead-toolshed for 23.0, but will be masthead-simple merged forward -->
+    <nav id="masthead" class="masthead-toolshed navbar navbar-expand navbar-fixed-top justify-content-center navbar-dark">
+        <a href="${h.url_for( app.config.get( 'logo_url', '/' ) )}" aria-label="homepage" class="navbar-brand">
+            <img alt="logo" class="navbar-brand-image" src="${h.url_for('/static/favicon.svg')}">
+            <span class="navbar-brand-title">
+                Reports
+                %if app.config.brand:
+                    / ${app.config.brand}
+                %endif
+            </span>
+        </a>
+         <ul class="navbar-nav"/>
+    </nav>
 </%def>

From c9b794e399c73c5ba62121931da4e7f80218d535 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 28 Apr 2023 10:57:01 -0400
Subject: [PATCH 39/78] Load sparkline in jquery.custom -- used in reports,
 drop after we either rewrite or drop reports.

---
 client/src/libs/jquery.custom.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/client/src/libs/jquery.custom.js b/client/src/libs/jquery.custom.js
index 0eeb1de96450..0d87a38b5078 100644
--- a/client/src/libs/jquery.custom.js
+++ b/client/src/libs/jquery.custom.js
@@ -23,4 +23,7 @@ require("imports-loader?imports=default|jqueryVendor|jQuery!jquery-migrate");
 
 // require("imports-loader?jQuery=jqueryVendor!../ui/autocom_tagging");
 
+// Only used in reports
+require("imports-loader?imports=default|jqueryVendor|jQuery!libs/jquery.sparklines");
+
 module.exports = jQuery;

From 6cb911ef23d0686514bf7de6d8ab28aa5b9c8686 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Mon, 1 May 2023 18:28:54 -0400
Subject: [PATCH 40/78] Make Expression Tools searchable in `ToolBoxWorkflow`

---
 .../components/Panels/Common/ToolSearch.vue   |  4 ++--
 client/src/components/Panels/ToolBox.vue      | 11 +++++-----
 .../src/components/Panels/ToolBoxWorkflow.vue |  2 +-
 client/src/components/Panels/utilities.js     | 20 +++++++------------
 .../src/components/Panels/utilities.test.js   | 10 +++++-----
 5 files changed, 21 insertions(+), 26 deletions(-)

diff --git a/client/src/components/Panels/Common/ToolSearch.vue b/client/src/components/Panels/Common/ToolSearch.vue
index a106ae2c0fcd..8302a64f2f7b 100644
--- a/client/src/components/Panels/Common/ToolSearch.vue
+++ b/client/src/components/Panels/Common/ToolSearch.vue
@@ -44,7 +44,7 @@
 <script>
 import { getGalaxyInstance } from "app";
 import DelayedInput from "components/Common/DelayedInput";
-import { normalizeTools, searchToolsByKeys } from "../utilities.js";
+import { flattenTools, searchToolsByKeys } from "../utilities.js";
 
 export default {
     name: "ToolSearch",
@@ -98,7 +98,7 @@ export default {
             return this.currentPanelView === "default" ? "section" : "ontology";
         },
         toolsList() {
-            return normalizeTools(this.toolbox);
+            return flattenTools(this.toolbox);
         },
     },
     methods: {
diff --git a/client/src/components/Panels/ToolBox.vue b/client/src/components/Panels/ToolBox.vue
index 5d8a462abdd6..cf514786baf8 100644
--- a/client/src/components/Panels/ToolBox.vue
+++ b/client/src/components/Panels/ToolBox.vue
@@ -25,7 +25,7 @@
                 :current-panel-view="currentPanelView"
                 :placeholder="titleSearchTools"
                 :show-advanced.sync="showAdvanced"
-                :toolbox="toolbox"
+                :toolbox="tools"
                 :query="query"
                 @onQuery="onQuery"
                 @onResults="onResults" />
@@ -125,6 +125,9 @@ export default {
         };
     },
     computed: {
+        tools() {
+            return hideToolsSection(this.toolbox);
+        },
         queryTooShort() {
             return this.query && this.query.length < 3;
         },
@@ -133,11 +136,9 @@ export default {
         },
         sections() {
             if (this.showSections) {
-                return filterToolSections(this.toolbox, this.results);
+                return filterToolSections(this.tools, this.results);
             } else {
-                return hasResults(this.results)
-                    ? filterTools(this.toolbox, this.results)
-                    : hideToolsSection(this.toolbox);
+                return hasResults(this.results) ? filterTools(this.tools, this.results) : this.tools;
             }
         },
         isUser() {
diff --git a/client/src/components/Panels/ToolBoxWorkflow.vue b/client/src/components/Panels/ToolBoxWorkflow.vue
index 251ad3c8497b..072d8810e557 100644
--- a/client/src/components/Panels/ToolBoxWorkflow.vue
+++ b/client/src/components/Panels/ToolBoxWorkflow.vue
@@ -120,7 +120,7 @@ export default {
             return this.query && this.query.length < 3;
         },
         noResults() {
-            return this.query && this.results.length === 0;
+            return this.query && (!this.results || this.results.length === 0);
         },
         hasWorkflowSection() {
             return this.workflows.length > 0;
diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js
index 2002922f037b..2bb5921e706f 100644
--- a/client/src/components/Panels/utilities.js
+++ b/client/src/components/Panels/utilities.js
@@ -51,7 +51,7 @@ export function createWhooshQuery(filterSettings, panelView, toolbox) {
 // Given toolbox and search results, returns filtered tool results
 export function filterTools(tools, results) {
     let toolsResults = [];
-    tools = normalizeTools(tools);
+    tools = flattenTools(tools);
     toolsResults = mapToolsResults(tools, results);
     toolsResults = sortToolsResults(toolsResults);
     toolsResults = removeDuplicateResults(toolsResults);
@@ -110,10 +110,12 @@ export function searchToolsByKeys(tools, keys, query) {
     return orderBy(returnedTools, ["order"], ["desc"]).map((tool) => tool.id);
 }
 
-export function normalizeTools(tools) {
-    tools = hideToolsSection(tools);
-    tools = flattenTools(tools);
-    return tools;
+export function flattenTools(tools) {
+    let normalizedTools = [];
+    tools.forEach((section) => {
+        normalizedTools = normalizedTools.concat(flattenToolsSection(section));
+    });
+    return normalizedTools;
 }
 
 export function hideToolsSection(tools) {
@@ -198,11 +200,3 @@ function deleteEmptyToolsSections(tools, results) {
 
     return tools;
 }
-
-function flattenTools(tools) {
-    let normalizedTools = [];
-    tools.forEach((section) => {
-        normalizedTools = normalizedTools.concat(flattenToolsSection(section));
-    });
-    return normalizedTools;
-}
diff --git a/client/src/components/Panels/utilities.test.js b/client/src/components/Panels/utilities.test.js
index 9c8cb6627818..77e70d20c19a 100644
--- a/client/src/components/Panels/utilities.test.js
+++ b/client/src/components/Panels/utilities.test.js
@@ -1,5 +1,5 @@
 import toolsList from "components/ToolsView/testData/toolsList";
-import { createWhooshQuery, filterTools, filterToolSections, normalizeTools, searchToolsByKeys } from "./utilities";
+import { createWhooshQuery, filterTools, filterToolSections, flattenTools, searchToolsByKeys } from "./utilities";
 
 describe("test helpers in tool searching utilities", () => {
     it("test parsing helper that converts settings to whoosh query", async () => {
@@ -25,7 +25,7 @@ describe("test helpers in tool searching utilities", () => {
             "__ZIP_COLLECTION__",
         ];
         let keys = { description: 1, name: 0 };
-        let results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
+        let results = searchToolsByKeys(flattenTools(toolsList), keys, q);
         expect(results).toEqual(expectedResults);
 
         expectedResults = [
@@ -35,14 +35,14 @@ describe("test helpers in tool searching utilities", () => {
             "__FILTER_EMPTY_DATASETS__",
         ];
         keys = { description: 0, name: 1 };
-        results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
+        results = searchToolsByKeys(flattenTools(toolsList), keys, q);
         expect(results).toEqual(expectedResults);
 
         // whitespace precedes to ensure query.trim() works
         q = " filter empty datasets";
         expectedResults = ["__FILTER_EMPTY_DATASETS__"];
         keys = { description: 1, name: 2, combined: 0 };
-        results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
+        results = searchToolsByKeys(flattenTools(toolsList), keys, q);
         expect(results).toEqual(expectedResults);
 
         const tempToolsList = [
@@ -64,7 +64,7 @@ describe("test helpers in tool searching utilities", () => {
         q = "uMi tools extract ";
         expectedResults = ["toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2"];
         keys = { description: 1, name: 2, hyphenated: 0 };
-        results = searchToolsByKeys(normalizeTools(tempToolsList), keys, q);
+        results = searchToolsByKeys(flattenTools(tempToolsList), keys, q);
         expect(results).toEqual(expectedResults);
     });
 

From e7b533d899f9eb176c38e6ef707b3f66bc7098e7 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Thu, 2 Mar 2023 10:09:33 +0100
Subject: [PATCH 41/78] Add support for auto-importing workflows via Tutorial
 Mode

---
 config/plugins/webhooks/gtn/script.js | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index 91d748ec6175..aecedc8f370f 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -142,6 +142,26 @@
                         }
                         removeOverlay();
                     });
+
+                    var gtn_workflows = $("#gtn-embed").contents().find("span[data-workflow]");
+                    // Buttonify
+                    gtn_workflows.addClass("galaxy-proxy-active");
+
+                    gtn_workflows.click((e) => {
+                        var target = e.target;
+
+                        // Sometimes we get the i or the strong, not the parent.
+                        if (e.target.tagName.toLowerCase() !== "span") {
+                            target = e.target.parentElement;
+                        }
+
+                        trs_url = $(target).data("trs_url");
+
+                        Galaxy.router.push("/workflows/trs_import", { trs_url: encodeURIComponent(trs_url), run_form: true });
+                        removeOverlay();
+                    });
+
+
                 });
             });
     }

From f0b52d81a973bea612929f780bcc007a58247045 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Thu, 2 Mar 2023 16:13:46 +0100
Subject: [PATCH 42/78] Add very basic tutorial mode test case

---
 config/plugins/webhooks/gtn/script.js         |  3 ++
 lib/galaxy/selenium/navigates_galaxy.py       |  5 +++
 lib/galaxy_test/api/test_webhooks.py          |  2 +-
 .../selenium/test_tutorial_mode.py            | 34 +++++++++++++++++++
 test/functional/webhooks/gtn                  |  1 +
 5 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 lib/galaxy_test/selenium/test_tutorial_mode.py
 create mode 120000 test/functional/webhooks/gtn

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index aecedc8f370f..f145e3c71c41 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -121,6 +121,9 @@
                     if (safe) {
                         persistLocation();
                     }
+                    // Add the class to the entire GTN page
+                    var body = $("body").addClass("galaxy-proxy-active");
+
                     var gtn_tools = $("#gtn-embed").contents().find("span[data-tool]");
                     // Buttonify
                     gtn_tools.addClass("galaxy-proxy-active");
diff --git a/lib/galaxy/selenium/navigates_galaxy.py b/lib/galaxy/selenium/navigates_galaxy.py
index 264e87890cf4..d5460312a15a 100644
--- a/lib/galaxy/selenium/navigates_galaxy.py
+++ b/lib/galaxy/selenium/navigates_galaxy.py
@@ -1998,6 +1998,11 @@ def share_with_user(
             self.wait_for_xpath_visible(xpath)
         self.screenshot_if(screenshot_after_submit)
 
+    def tutorial_mode_activate(self):
+        search_selector = "#gtn a"
+        self.wait_for_and_click_selector(search_selector)
+        self.wait_for_selector_visible("#gtn-screen")
+
 
 class NotLoggedInException(SeleniumTimeoutException):
     def __init__(self, timeout_exception, user_info, dom_message):
diff --git a/lib/galaxy_test/api/test_webhooks.py b/lib/galaxy_test/api/test_webhooks.py
index 8c5cb9b84197..43417e034e5b 100644
--- a/lib/galaxy_test/api/test_webhooks.py
+++ b/lib/galaxy_test/api/test_webhooks.py
@@ -11,7 +11,7 @@ def test_get_all(self):
         self._assert_status_code_is(response, 200)
         webhook_objs = self._assert_are_webhooks(response)
         ids = self._get_webhook_ids(webhook_objs)
-        for expected_id in ["history_test1", "history_test2", "masthead_test", "phdcomics", "trans_object", "xkcd"]:
+        for expected_id in ["history_test1", "history_test2", "masthead_test", "phdcomics", "trans_object", "xkcd", "gtn"]:
             assert expected_id in ids
 
     def test_get_data(self):
diff --git a/lib/galaxy_test/selenium/test_tutorial_mode.py b/lib/galaxy_test/selenium/test_tutorial_mode.py
new file mode 100644
index 000000000000..9bf20d8b650e
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_tutorial_mode.py
@@ -0,0 +1,34 @@
+import json
+import time
+
+import pytest
+
+from .framework import (
+    selenium_test,
+    SeleniumTestCase,
+)
+
+
+class TestTutorialMode(SeleniumTestCase):
+    @selenium_test
+    @pytest.mark.gtn_screenshot
+    def test_activate_tutorial_mode(self):
+        self._ensure_tutorial_mode_available()
+        self.home()
+        self.screenshot("tutorial_mode_0_0")
+        self.tutorial_mode_activate()
+        self.screenshot("tutorial_mode_0_1")
+
+        # Access inside the frame
+        self.driver.switch_to.frame("gtn-embed")
+        self.wait_for_selector_visible("#top-navbar")
+        self.screenshot("tutorial_mode_0_2")
+
+    def _ensure_tutorial_mode_available(self):
+        """Skip a test if the webhook GTN doesn't appear."""
+        response = self.api_get("webhooks", raw=True)
+        assert response.status_code == 200
+        data = response.json()
+        webhooks = [x["id"] for x in data]
+        if "gtn" not in webhooks:
+            raise unittest.SkipTest('Skipping test, webhook "GTN Tutorial Mode" doesn\'t appear to be configured.')
diff --git a/test/functional/webhooks/gtn b/test/functional/webhooks/gtn
new file mode 120000
index 000000000000..ebc09166db54
--- /dev/null
+++ b/test/functional/webhooks/gtn
@@ -0,0 +1 @@
+../../../config/plugins/webhooks/gtn
\ No newline at end of file

From 15b597790323ae30762d46723fe8248ab31c670f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 5 Apr 2023 10:44:53 -0400
Subject: [PATCH 43/78] Adjust trs url handle, and path pushed

---
 config/plugins/webhooks/gtn/script.js | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index f145e3c71c41..6214fe58603f 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -136,7 +136,7 @@
                             target = e.target.parentElement;
                         }
 
-                        tool_id = $(target).data("tool");
+                        tool_id = target.dataset.tool;
 
                         if (tool_id === "upload1" || tool_id === "upload") {
                             document.getElementById("tool-panel-upload-button").click();
@@ -158,9 +158,8 @@
                             target = e.target.parentElement;
                         }
 
-                        trs_url = $(target).data("trs_url");
-
-                        Galaxy.router.push("/workflows/trs_import", { trs_url: encodeURIComponent(trs_url), run_form: true });
+                        trs_url = target.dataset.workflow;
+                        Galaxy.router.push({ path: `/workflows/trs_import?trs_url=${encodeURIComponent(trs_url)}&run_form=true` });
                         removeOverlay();
                     });
 

From ecb37f76f01a8771d1156b587efd74192318cced Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Wed, 5 Apr 2023 11:49:29 -0400
Subject: [PATCH 44/78] Apply suggestions from code review

Update gtn-proxy-active handling

Co-authored-by: Helena <hexylena@galaxians.org>
---
 config/plugins/webhooks/gtn/script.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index 6214fe58603f..a04d2db8111a 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -122,9 +122,9 @@
                         persistLocation();
                     }
                     // Add the class to the entire GTN page
-                    var body = $("body").addClass("galaxy-proxy-active");
+                    document.getElementById("gtn-embed").contentDocument.getElementsByTagName('body').classList.add("galaxy-proxy-active")
 
-                    var gtn_tools = $("#gtn-embed").contents().find("span[data-tool]");
+                    let gtn_tools = document.getElementById("gtn-embed").contentDocument.querySelectorAll("span[data-tool]")
                     // Buttonify
                     gtn_tools.addClass("galaxy-proxy-active");
 

From 81a2e24d7c654f6a0af93c83876d71f31e66c779 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 5 Apr 2023 23:19:21 -0400
Subject: [PATCH 45/78] Fix up test imports, formatting.

---
 lib/galaxy_test/api/test_webhooks.py           | 10 +++++++++-
 lib/galaxy_test/selenium/test_tutorial_mode.py |  5 ++---
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy_test/api/test_webhooks.py b/lib/galaxy_test/api/test_webhooks.py
index 43417e034e5b..e640baffc172 100644
--- a/lib/galaxy_test/api/test_webhooks.py
+++ b/lib/galaxy_test/api/test_webhooks.py
@@ -11,7 +11,15 @@ def test_get_all(self):
         self._assert_status_code_is(response, 200)
         webhook_objs = self._assert_are_webhooks(response)
         ids = self._get_webhook_ids(webhook_objs)
-        for expected_id in ["history_test1", "history_test2", "masthead_test", "phdcomics", "trans_object", "xkcd", "gtn"]:
+        for expected_id in [
+            "history_test1",
+            "history_test2",
+            "masthead_test",
+            "phdcomics",
+            "trans_object",
+            "xkcd",
+            "gtn",
+        ]:
             assert expected_id in ids
 
     def test_get_data(self):
diff --git a/lib/galaxy_test/selenium/test_tutorial_mode.py b/lib/galaxy_test/selenium/test_tutorial_mode.py
index 9bf20d8b650e..11dd08d2e4b9 100644
--- a/lib/galaxy_test/selenium/test_tutorial_mode.py
+++ b/lib/galaxy_test/selenium/test_tutorial_mode.py
@@ -1,5 +1,4 @@
-import json
-import time
+from unittest import SkipTest
 
 import pytest
 
@@ -31,4 +30,4 @@ def _ensure_tutorial_mode_available(self):
         data = response.json()
         webhooks = [x["id"] for x in data]
         if "gtn" not in webhooks:
-            raise unittest.SkipTest('Skipping test, webhook "GTN Tutorial Mode" doesn\'t appear to be configured.')
+            raise SkipTest('Skipping test, webhook "GTN Tutorial Mode" doesn\'t appear to be configured.')

From 36bfae15383f8c37d0bdb34bdefe7c73aec5571e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 28 Apr 2023 18:23:14 +0200
Subject: [PATCH 46/78] Log object store id too

---
 lib/galaxy/model/store/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 7db16a7829a8..17022dfb5e2e 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2220,7 +2220,9 @@ def add_dataset(self, dataset: model.DatasetInstance, include_files: bool = True
     def _ensure_dataset_file_exists(self, dataset: model.DatasetInstance) -> None:
         state = dataset.dataset.state
         if state in [model.Dataset.states.OK] and not dataset.file_name:
-            log.error("Dataset [%s] does not exists on disk or is not accessible, while trying to export." % dataset.id)
+            log.error(
+                f"Dataset [{dataset.id}] does not exists on on object store [{dataset.dataset.object_store_id or 'None'}], while trying to export."
+            )
             raise Exception(f"Cannot export dataset: {dataset.name}")
 
     def _finalize(self) -> None:

From e72edc368c9c135acdc624fb56181111e0c7e10f Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 2 May 2023 06:32:13 -0400
Subject: [PATCH 47/78] Variable safety

---
 config/plugins/webhooks/gtn/script.js | 48 ++++++++++++++++-----------
 1 file changed, 28 insertions(+), 20 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index a04d2db8111a..895e883b0ecd 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -1,8 +1,9 @@
-(function () {
-    var gtnWebhookLoaded = false;
-    var lastUpdate = 0;
-    var urlParams = new URLSearchParams(document.location.search);
-    var autoLoadTutorial = urlParams.get('autoload_gtn_tutorial') === null ? "" : urlParams.get('autoload_gtn_tutorial');
+(() => {
+    let gtnWebhookLoaded = false;
+    let lastUpdate = 0;
+    const urlParams = new URLSearchParams(document.location.search);
+    const autoLoadTutorial =
+        urlParams.get("autoload_gtn_tutorial") === null ? "" : urlParams.get("autoload_gtn_tutorial");
 
     function removeOverlay() {
         const container = document.getElementById("gtn-container");
@@ -16,7 +17,7 @@
     }
 
     function getIframeUrl() {
-        var loc;
+        let loc;
         try {
             loc = document.getElementById("gtn-embed").contentWindow.location.pathname;
         } catch (e) {
@@ -26,7 +27,7 @@
     }
 
     function getIframeScroll() {
-        var loc;
+        let loc;
         try {
             loc = parseInt(document.getElementById("gtn-embed").contentWindow.scrollY);
         } catch (e) {
@@ -39,7 +40,7 @@
 
     function persistLocation() {
         // Don't save every scroll event.
-        var time = new Date().getTime();
+        const time = new Date().getTime();
         if (time - lastUpdate < 1000) {
             return;
         }
@@ -48,7 +49,9 @@
     }
 
     function addIframe() {
-        let url, message, onloadscroll;
+        let url;
+        let message;
+        let onloadscroll;
         gtnWebhookLoaded = true;
         let storedData = false;
         let safe = false;
@@ -68,7 +71,7 @@
                 } else {
                     safe = true;
 
-                    var storedLocation = window.localStorage.getItem("gtn-in-galaxy");
+                    const storedLocation = window.localStorage.getItem("gtn-in-galaxy");
                     if (
                         storedLocation !== null &&
                         storedLocation.split(" ")[1] !== undefined &&
@@ -122,14 +125,19 @@
                         persistLocation();
                     }
                     // Add the class to the entire GTN page
-                    document.getElementById("gtn-embed").contentDocument.getElementsByTagName('body').classList.add("galaxy-proxy-active")
-
-                    let gtn_tools = document.getElementById("gtn-embed").contentDocument.querySelectorAll("span[data-tool]")
+                    document
+                        .getElementById("gtn-embed")
+                        .contentDocument.getElementsByTagName("body")
+                        .classList.add("galaxy-proxy-active");
+
+                    let gtn_tools = document
+                        .getElementById("gtn-embed")
+                        .contentDocument.querySelectorAll("span[data-tool]");
                     // Buttonify
                     gtn_tools.addClass("galaxy-proxy-active");
 
                     gtn_tools.click((e) => {
-                        var target = e.target;
+                        let target = e.target;
 
                         // Sometimes we get the i or the strong, not the parent.
                         if (e.target.tagName.toLowerCase() !== "span") {
@@ -146,12 +154,12 @@
                         removeOverlay();
                     });
 
-                    var gtn_workflows = $("#gtn-embed").contents().find("span[data-workflow]");
+                    const gtn_workflows = $("#gtn-embed").contents().find("span[data-workflow]");
                     // Buttonify
                     gtn_workflows.addClass("galaxy-proxy-active");
 
                     gtn_workflows.click((e) => {
-                        var target = e.target;
+                        let target = e.target;
 
                         // Sometimes we get the i or the strong, not the parent.
                         if (e.target.tagName.toLowerCase() !== "span") {
@@ -159,11 +167,11 @@
                         }
 
                         trs_url = target.dataset.workflow;
-                        Galaxy.router.push({ path: `/workflows/trs_import?trs_url=${encodeURIComponent(trs_url)}&run_form=true` });
+                        Galaxy.router.push({
+                            path: `/workflows/trs_import?trs_url=${encodeURIComponent(trs_url)}&run_form=true`,
+                        });
                         removeOverlay();
                     });
-
-
                 });
             });
     }
@@ -205,7 +213,7 @@
                 showOverlay();
             }
         });
-        if(autoLoadTutorial){
+        if (autoLoadTutorial) {
             clean.click();
         }
     });

From dea5f3ef2875b307e2a0a364e0f531037a35bcc2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 2 May 2023 06:38:28 -0400
Subject: [PATCH 48/78] Minor tweak to keydown listener, format

---
 config/plugins/webhooks/gtn/script.js | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index 895e883b0ecd..609cdfda94b6 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -62,8 +62,7 @@
         fetch("/training-material/")
             .then((response) => {
                 if (!response.ok) {
-                    url =
-                        `https://training.galaxyproject.org/training-material/${autoLoadTutorial}?utm_source=webhook&utm_medium=noproxy&utm_campaign=gxy`;
+                    url = `https://training.galaxyproject.org/training-material/${autoLoadTutorial}?utm_source=webhook&utm_medium=noproxy&utm_campaign=gxy`;
                     message = `
                         <span>
                             <a href="https://docs.galaxyproject.org/en/master/admin/special_topics/gtn.html">Click to run</a> unavailable.
@@ -219,9 +218,9 @@
     });
 
     // Remove the overlay on escape button click
-    document.addEventListener("keydown", (e) => {
-        // Check for escape button - "27"
-        if (e.which === 27 || e.keyCode === 27) {
+    document.addEventListener("keydown", (event) => {
+        // Check for escape button - "Escape" (modern browsers), "27" (old browsers)
+        if (event.key === "Escape" || event.keyCode === 27) {
             removeOverlay();
         }
     });

From 4afd46927f694588c73b71c4e5ecb1e70156e54d Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Tue, 2 May 2023 10:55:29 +0200
Subject: [PATCH 49/78] make uri_prefixes stricter

---
 client/src/components/Upload/helpers.js | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Upload/helpers.js b/client/src/components/Upload/helpers.js
index b5646be0ec18..574b27e00425 100644
--- a/client/src/components/Upload/helpers.js
+++ b/client/src/components/Upload/helpers.js
@@ -1,6 +1,15 @@
 export const defaultNewFileName = "New File";
 
-const URI_PREFIXES = ["http", "https", "ftp", "file", "gxfiles", "gximport", "gxuserimport", "gxftp"];
+const URI_PREFIXES = [
+    "http://",
+    "https://",
+    "ftp://",
+    "file://",
+    "gxfiles://",
+    "gximport://",
+    "gxuserimport://",
+    "gxftp://",
+];
 function itemIsUrl(item) {
     return URI_PREFIXES.some((prefix) => item.get("url_paste").startsWith(prefix));
 }

From 9dad4ac09490694da97916d758ae61392b073d47 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 2 May 2023 08:47:31 -0400
Subject: [PATCH 50/78] Fix galaxy proxy active style on body

---
 config/plugins/webhooks/gtn/script.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index 609cdfda94b6..833be82a9daf 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -126,7 +126,7 @@
                     // Add the class to the entire GTN page
                     document
                         .getElementById("gtn-embed")
-                        .contentDocument.getElementsByTagName("body")
+                        .contentDocument.getElementsByTagName("body")[0]
                         .classList.add("galaxy-proxy-active");
 
                     let gtn_tools = document

From 706dda2aa7355f8c1916b644633e357f6257de16 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 2 May 2023 08:48:01 -0400
Subject: [PATCH 51/78] Fix click event binding; this was broken when swapping
 away from jquery -- click() is not vanilla js

---
 config/plugins/webhooks/gtn/script.js | 38 ++++++++++++++-------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index 833be82a9daf..bbf7c787540c 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -132,25 +132,27 @@
                     let gtn_tools = document
                         .getElementById("gtn-embed")
                         .contentDocument.querySelectorAll("span[data-tool]");
-                    // Buttonify
-                    gtn_tools.addClass("galaxy-proxy-active");
-
-                    gtn_tools.click((e) => {
-                        let target = e.target;
 
-                        // Sometimes we get the i or the strong, not the parent.
-                        if (e.target.tagName.toLowerCase() !== "span") {
-                            target = e.target.parentElement;
-                        }
-
-                        tool_id = target.dataset.tool;
-
-                        if (tool_id === "upload1" || tool_id === "upload") {
-                            document.getElementById("tool-panel-upload-button").click();
-                        } else {
-                            Galaxy.router.push({ path: `/?tool_id=${encodeURIComponent(tool_id)}` });
-                        }
-                        removeOverlay();
+                    // Buttonify
+                    gtn_tools.forEach(function (el) {
+                        el.classList.add("galaxy-proxy-active");
+                        el.addEventListener("click", function (e) {
+                            let target = e.target;
+
+                            // Sometimes we get the i or the strong, not the parent.
+                            if (e.target.tagName.toLowerCase() !== "span") {
+                                target = e.target.parentElement;
+                            }
+
+                            tool_id = target.dataset.tool;
+
+                            if (tool_id === "upload1" || tool_id === "upload") {
+                                document.getElementById("tool-panel-upload-button").click();
+                            } else {
+                                Galaxy.router.push({ path: `/?tool_id=${encodeURIComponent(tool_id)}` });
+                            }
+                            removeOverlay();
+                        });
                     });
 
                     const gtn_workflows = $("#gtn-embed").contents().find("span[data-workflow]");

From 3078b8deb5a179b46e8662f3d1c6d0da32627676 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 2 May 2023 08:50:16 -0400
Subject: [PATCH 52/78] Drop unused restoreLocation

---
 config/plugins/webhooks/gtn/script.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index bbf7c787540c..f04400b42bc3 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -36,8 +36,6 @@
         return loc;
     }
 
-    function restoreLocation() {}
-
     function persistLocation() {
         // Don't save every scroll event.
         const time = new Date().getTime();

From 36bebd26d0360d8442a7b2b8e212acec8f88ffd9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 2 May 2023 09:19:46 -0400
Subject: [PATCH 53/78] Redo workflow element handling

---
 config/plugins/webhooks/gtn/script.js | 35 +++++++++++++++------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index f04400b42bc3..3d380ab093b2 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -113,6 +113,7 @@
                 // Depends on the iframe being present
                 document.getElementById("gtn-embed").addEventListener("load", () => {
                     // Save our current location when possible
+                    const gtnEmbed = document.getElementById("gtn-embed");
                     if (onloadscroll !== undefined) {
                         document.getElementById("gtn-embed").contentWindow.scrollTo(0, parseInt(onloadscroll));
                         onloadscroll = undefined;
@@ -127,12 +128,12 @@
                         .contentDocument.getElementsByTagName("body")[0]
                         .classList.add("galaxy-proxy-active");
 
-                    let gtn_tools = document
+                    const gtnToolElements = document
                         .getElementById("gtn-embed")
                         .contentDocument.querySelectorAll("span[data-tool]");
 
                     // Buttonify
-                    gtn_tools.forEach(function (el) {
+                    gtnToolElements.forEach(function (el) {
                         el.classList.add("galaxy-proxy-active");
                         el.addEventListener("click", function (e) {
                             let target = e.target;
@@ -153,23 +154,27 @@
                         });
                     });
 
-                    const gtn_workflows = $("#gtn-embed").contents().find("span[data-workflow]");
-                    // Buttonify
-                    gtn_workflows.addClass("galaxy-proxy-active");
+                    const gtnWorkflowElements = document
+                        .getElementById("gtn-embed")
+                        .contentDocument.querySelectorAll("span[data-workflow]");
 
-                    gtn_workflows.click((e) => {
-                        let target = e.target;
+                    // Buttonify
+                    gtnWorkflowElements.forEach(function (el) {
+                        el.addClass("galaxy-proxy-active");
+                        el.addEventListener("click", (e) => {
+                            let target = e.target;
 
-                        // Sometimes we get the i or the strong, not the parent.
-                        if (e.target.tagName.toLowerCase() !== "span") {
-                            target = e.target.parentElement;
-                        }
+                            // Sometimes we get the i or the strong, not the parent.
+                            if (e.target.tagName.toLowerCase() !== "span") {
+                                target = e.target.parentElement;
+                            }
 
-                        trs_url = target.dataset.workflow;
-                        Galaxy.router.push({
-                            path: `/workflows/trs_import?trs_url=${encodeURIComponent(trs_url)}&run_form=true`,
+                            trs_url = target.dataset.workflow;
+                            Galaxy.router.push({
+                                path: `/workflows/trs_import?trs_url=${encodeURIComponent(trs_url)}&run_form=true`,
+                            });
+                            removeOverlay();
                         });
-                        removeOverlay();
                     });
                 });
             });

From 1d02485003f9c6916e2c2e94d8ccfaec17288944 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20L=C3=B3pez?=
 <46503462+davelopez@users.noreply.github.com>
Date: Tue, 2 May 2023 13:46:20 +0200
Subject: [PATCH 54/78] Include more dataset info on error

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 lib/galaxy/model/store/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 17022dfb5e2e..122af7529555 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -2223,7 +2223,9 @@ def _ensure_dataset_file_exists(self, dataset: model.DatasetInstance) -> None:
             log.error(
                 f"Dataset [{dataset.id}] does not exists on on object store [{dataset.dataset.object_store_id or 'None'}], while trying to export."
             )
-            raise Exception(f"Cannot export dataset: {dataset.name}")
+            raise Exception(
+                f"Cannot export history dataset [{getattr(dataset, 'hid', '')}: {dataset.name}] with id {self.exported_key(dataset)}"
+            )
 
     def _finalize(self) -> None:
         export_directory = self.export_directory

From 7f5e97af9125f58fa745c20cf7356eb6477f0bf7 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 2 May 2023 17:00:47 +0200
Subject: [PATCH 55/78] Refactor test to assert for specific error

---
 lib/galaxy_test/base/populators.py             |  2 ++
 test/integration/test_history_import_export.py | 12 +++++-------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
index b8c5dea3f019..e2776ba8c2cc 100644
--- a/lib/galaxy_test/base/populators.py
+++ b/lib/galaxy_test/base/populators.py
@@ -1389,6 +1389,8 @@ def download_history_to_store(self, history_id: str, extension: str = "tgz", ser
         self.wait_for_download_ready(storage_request_id)
         if serve_file:
             return self._get_to_tempfile(f"short_term_storage/{storage_request_id}")
+        else:
+            return storage_request_id
 
     def get_history_export_tasks(self, history_id: str):
         headers = {"accept": "application/vnd.galaxy.task.export+json"}
diff --git a/test/integration/test_history_import_export.py b/test/integration/test_history_import_export.py
index 20fe8faae7fe..eb9848609cef 100644
--- a/test/integration/test_history_import_export.py
+++ b/test/integration/test_history_import_export.py
@@ -201,8 +201,6 @@ def test_export_history_with_discarded_dataset_to_rocrate(self):
 
     def test_export_missing_dataset_fails(self):
         history_name = f"for_export_failure_{uuid4()}"
-        model_store_format = "rocrate.zip"
-        target_uri = f"gxfiles://posix_test/{history_name}.{model_store_format}"
         history_id = self.dataset_populator.new_history(history_name)
         hda = self.dataset_populator.new_dataset(history_id, wait=True)
 
@@ -211,11 +209,11 @@ def test_export_missing_dataset_fails(self):
         unlink(hda["file_name"])
         assert not os.path.exists(hda["file_name"])
 
-        # Ensure the export task fails
-        with self.assertRaisesRegex(Exception, "task failed"):
-            self.dataset_populator.export_history_to_uri_async(
-                history_id, target_uri=target_uri, model_store_format=model_store_format, include_files=True
-            )
+        storage_request_id = self.dataset_populator.download_history_to_store(history_id)
+
+        result_response = self._get(f"short_term_storage/{storage_request_id}")
+        self._assert_status_code_is(result_response, 500)
+        assert "Cannot export history dataset" in result_response.json()["err_msg"]
 
     def _wait_for_export_task_on_record(self, record):
         if record["preparing"]:

From 096ed7b82c150d8d93a9b4e9e800cafed73ff413 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Wed, 3 May 2023 16:44:12 +0200
Subject: [PATCH 56/78] Fix leftover jquery style class change

---
 config/plugins/webhooks/gtn/script.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index 3d380ab093b2..7518ef30d821 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -160,7 +160,7 @@
 
                     // Buttonify
                     gtnWorkflowElements.forEach(function (el) {
-                        el.addClass("galaxy-proxy-active");
+                        el.classList.add("galaxy-proxy-active");
                         el.addEventListener("click", (e) => {
                             let target = e.target;
 

From f488d9fc1c0a30c02d1f61710f675b4980410c32 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 4 May 2023 10:53:30 +0200
Subject: [PATCH 57/78] Fix vscode test discovery, noisy startup logs, set_meta
 stderr

When google-cloud-storage is installed in an old version.
Fixes https://github.com/galaxyproject/galaxy/issues/16012
---
 lib/galaxy/dependencies/__init__.py                  | 3 +++
 lib/galaxy/dependencies/conditional-requirements.txt | 2 ++
 2 files changed, 5 insertions(+)

diff --git a/lib/galaxy/dependencies/__init__.py b/lib/galaxy/dependencies/__init__.py
index 89934921209d..9e057999df55 100644
--- a/lib/galaxy/dependencies/__init__.py
+++ b/lib/galaxy/dependencies/__init__.py
@@ -266,6 +266,9 @@ def check_fs_googledrivefs(self):
     def check_fs_gcsfs(self):
         return "googlecloudstorage" in self.file_sources
 
+    def check_google_cloud_storage(self):
+        return "googlecloudstorage" in self.file_sources
+
     def check_fs_onedatafs(self):
         return "onedata" in self.file_sources
 
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 24a076a389a1..346c975e1e25 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -24,6 +24,8 @@ s3fs  # type: s3fs
 fs.anvilfs # type: anvil
 fs.googledrivefs # type: googledrive
 fs-gcsfs # type: googlecloudstorage
+# fs-gcsfs doesn't pin google-cloud-storage, and old versions log noisy exceptions and break test discovery
+google-cloud-storage>=2.8.0  # type: googlecloudstorage
 fs-onedatafs # type: onedata
 fs-basespace # type: basespace
 

From 3a2e936401993f06b92159438d4fdd520333a536 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 4 May 2023 17:34:48 +0200
Subject: [PATCH 58/78] Install node from setup-node action in more tests

Should help with nodeenv failing in CI tests, e.g.
```
Installing node into /home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage with nodeenv.
 * Install prebuilt node (18.12.1) .Incomplete read while readingfrom https://nodejs.org/download/release/v18.12.1/node-v18.12.1-linux-x64.tar.gz
.
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/bin/nodeenv", line 10, in <module>
    sys.exit(main())
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 1104, in main
    create_environment(env_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 980, in create_environment
    install_node(env_dir, src_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 739, in install_node
    install_node_wrapped(env_dir, src_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 762, in install_node_wrapped
    download_node_src(node_url, src_dir, args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 602, in download_node_src
    with ctx as archive:
  File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.7/site-packages/nodeenv.py", line 573, in tarfile_open
    tf = tarfile.open(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/tarfile.py", line 1573, in open
    saved_pos = fileobj.tell()
AttributeError: 'bytes' object has no attribute 'tell'
```
from https://github.com/galaxyproject/galaxy/actions/runs/4883207488/jobs/8714237674?pr=16036
---
 .github/workflows/api.yaml             |  5 +++++
 .github/workflows/converter_tests.yaml |  5 +++++
 .github/workflows/cwl_conformance.yaml |  5 +++++
 .github/workflows/first_startup.yaml   | 10 +++++-----
 .github/workflows/framework.yaml       |  5 +++++
 .github/workflows/integration.yaml     |  5 +++++
 .github/workflows/osx_startup.yaml     |  5 +++++
 .github/workflows/performance.yaml     |  5 +++++
 .github/workflows/reports_startup.yaml | 10 +++++-----
 .github/workflows/selenium.yaml        | 10 +++++-----
 .github/workflows/unit-postgres.yaml   |  5 +++++
 .github/workflows/unit.yaml            |  5 +++++
 12 files changed, 60 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml
index fa27da664207..90038e328865 100644
--- a/.github/workflows/api.yaml
+++ b/.github/workflows/api.yaml
@@ -47,6 +47,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index f9e6649f86e7..d4833d376ab7 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -31,6 +31,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Clone galaxyproject/galaxy-test-data
         uses: actions/checkout@v3
         with:
diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
index 46b750143c46..716a8ca2bbbd 100644
--- a/.github/workflows/cwl_conformance.yaml
+++ b/.github/workflows/cwl_conformance.yaml
@@ -38,6 +38,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml
index 520888fbd3ae..34093cae9605 100644
--- a/.github/workflows/first_startup.yaml
+++ b/.github/workflows/first_startup.yaml
@@ -29,6 +29,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
@@ -48,11 +53,6 @@ jobs:
         with:
           path: .tox
           key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-first-startup
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '18.12.1'
-          cache: 'yarn'
-          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Install tox
         run: pip install tox
       - name: run tests
diff --git a/.github/workflows/framework.yaml b/.github/workflows/framework.yaml
index 679857a0b52c..5de51cca7cad 100644
--- a/.github/workflows/framework.yaml
+++ b/.github/workflows/framework.yaml
@@ -43,6 +43,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index eaec4175caed..8ad4ba1424c4 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -71,6 +71,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml
index 4e64a3eb19ba..a67494e70444 100644
--- a/.github/workflows/osx_startup.yaml
+++ b/.github/workflows/osx_startup.yaml
@@ -22,6 +22,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Get full Python version
         id: full-python-version
         shell: bash
diff --git a/.github/workflows/performance.yaml b/.github/workflows/performance.yaml
index 8a8305760a45..4eda60399585 100644
--- a/.github/workflows/performance.yaml
+++ b/.github/workflows/performance.yaml
@@ -42,6 +42,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/reports_startup.yaml b/.github/workflows/reports_startup.yaml
index bef55b8d3572..805686e3d388 100644
--- a/.github/workflows/reports_startup.yaml
+++ b/.github/workflows/reports_startup.yaml
@@ -26,6 +26,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
@@ -45,11 +50,6 @@ jobs:
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-reports-startup
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '18.12.1'
-          cache: 'yarn'
-          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Install tox
         run: pip install tox
       - name: Run tests
diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml
index d3128b02f7ce..12dba9f75782 100644
--- a/.github/workflows/selenium.yaml
+++ b/.github/workflows/selenium.yaml
@@ -46,6 +46,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
@@ -63,11 +68,6 @@ jobs:
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-selenium
-      - uses: actions/setup-node@v3
-        with:
-          node-version: '18.12.1'
-          cache: 'yarn'
-          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: nanasess/setup-chromedriver@v1
       - name: Run tests
         run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
diff --git a/.github/workflows/unit-postgres.yaml b/.github/workflows/unit-postgres.yaml
index 871f1a833a76..ea8fe8b9ad05 100644
--- a/.github/workflows/unit-postgres.yaml
+++ b/.github/workflows/unit-postgres.yaml
@@ -36,6 +36,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml
index 2d8ae1660aca..8ade16541a1f 100644
--- a/.github/workflows/unit.yaml
+++ b/.github/workflows/unit.yaml
@@ -28,6 +28,11 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - name: Get full Python version
         id: full-python-version
         shell: bash

From d2271e5e043d73c64090de9d777bb04e2e825279 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 4 May 2023 17:15:17 +0200
Subject: [PATCH 59/78] Replace httpbin service with pytest-httpserver

httpbin isn't doing too well, this should be more robust.
---
 lib/galaxy/dependencies/dev-requirements.txt | 1 +
 packages/util/test-requirements.txt          | 1 +
 pyproject.toml                               | 1 +
 test/unit/util/test_get_url.py               | 7 +++----
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 07e9ce907403..c4a40984c1f9 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -85,6 +85,7 @@ pytest-asyncio==0.20.3 ; python_version >= "3.7" and python_version < "3.12"
 pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-cov==4.0.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
+pytest-httpserver==1.0.6 ; python_version >= "3.7" and python_version < "3.12"
 pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-metadata==2.0.4 ; python_version >= "3.7" and python_version < "3.12"
 pytest-mock==3.10.0 ; python_version >= "3.7" and python_version < "3.12"
diff --git a/packages/util/test-requirements.txt b/packages/util/test-requirements.txt
index 208ec64cdf02..779ccfa23c7e 100644
--- a/packages/util/test-requirements.txt
+++ b/packages/util/test-requirements.txt
@@ -1,2 +1,3 @@
 pytest
+pytest-httpserver
 responses
diff --git a/pyproject.toml b/pyproject.toml
index ea585f248a33..0b58ff0055e0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -132,6 +132,7 @@ pytest-asyncio = "*"
 pytest-celery = "*"
 pytest-cov = "*"
 pytest-html = "*"
+pytest-httpserver = "*"
 python-irodsclient = "!=1.1.2"  # https://github.com/irods/python-irodsclient/issues/356
 pytest-json-report = "*"
 pytest-mock = "*"
diff --git a/test/unit/util/test_get_url.py b/test/unit/util/test_get_url.py
index c5a18ccd2bd7..1c80997ec5ac 100644
--- a/test/unit/util/test_get_url.py
+++ b/test/unit/util/test_get_url.py
@@ -3,7 +3,6 @@
 import responses
 
 from galaxy.util import url_get
-from galaxy.util.unittest_utils import skip_if_site_down
 
 
 @responses.activate
@@ -23,11 +22,11 @@ def test_get_url_forbidden():
     assert "403 Client Error: Forbidden for url: https://toolshed.g2.bx.psu.edu/" in str(excinfo)
 
 
-@skip_if_site_down("https://httpbin.org")
-def test_get_url_retry_after():
+def test_get_url_retry_after(httpserver):
     # This test is not ideal since it contacts an external resource
     # and doesn't actually verify multiple attempts have been made.
     # responses doesn't mock the right place to fully simulate this.
-    url = "https://httpbin.org/status/429"
+    httpserver.expect_request("/429").respond_with_data("try again later", status=429, content_type="text/plain")
+    url = httpserver.url_for("/429")
     with pytest.raises(requests.exceptions.RetryError):
         url_get(url, max_retries=2, backoff_factor=0.01)

From 69ebbb761aa610c1eab2f92a385c34b47259ac32 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 4 May 2023 17:15:17 +0200
Subject: [PATCH 60/78] Replace httpbin service with pytest-httpserver

httpbin isn't doing too well, this should be more robust.
---
 test/unit/util/test_get_url.py | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/test/unit/util/test_get_url.py b/test/unit/util/test_get_url.py
index 1c80997ec5ac..499bbbddd2d8 100644
--- a/test/unit/util/test_get_url.py
+++ b/test/unit/util/test_get_url.py
@@ -1,6 +1,7 @@
 import pytest
 import requests
 import responses
+from werkzeug.wrappers.response import Response
 
 from galaxy.util import url_get
 
@@ -23,10 +24,20 @@ def test_get_url_forbidden():
 
 
 def test_get_url_retry_after(httpserver):
-    # This test is not ideal since it contacts an external resource
-    # and doesn't actually verify multiple attempts have been made.
-    # responses doesn't mock the right place to fully simulate this.
-    httpserver.expect_request("/429").respond_with_data("try again later", status=429, content_type="text/plain")
+    attempts = []
+
+    def retry_handler(request):
+        attempts.append(requests)
+        if len(attempts) < 4:
+            return Response("try again later", status=429, content_type="text/plain")
+        else:
+            return Response("ok", status=200, content_type="text/plain")
+
+    httpserver.expect_request("/429").respond_with_handler(retry_handler)
     url = httpserver.url_for("/429")
     with pytest.raises(requests.exceptions.RetryError):
-        url_get(url, max_retries=2, backoff_factor=0.01)
+        url_get(url, max_retries=1, backoff_factor=0.01)
+    assert len(attempts) == 2
+    response = url_get(url, max_retries=2, backoff_factor=0.01)
+    assert len(attempts) == 4
+    assert response == "ok"

From fa35e52873ff613653f494a7e5d7e61fe033e899 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Wed, 3 May 2023 19:10:44 +0200
Subject: [PATCH 61/78] Add test case for name-contains query on histories

---
 lib/galaxy_test/api/test_histories.py | 36 +++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py
index 2cc12db32fdd..1b6a19591e42 100644
--- a/lib/galaxy_test/api/test_histories.py
+++ b/lib/galaxy_test/api/test_histories.py
@@ -136,6 +136,42 @@ def test_index_query(self):
         assert len(index_response) == 1
         assert index_response[0]["name"] == expected_history_name
 
+    def test_index_case_insensitive_contains_query(self):
+        # Create the histories with a different user to ensure the test
+        # is not conflicted with the current user's histories.
+        with self._different_user(f"user_{uuid4()}@bx.psu.edu"):
+            unique_id = uuid4()
+            expected_history_name = f"Test History That Match Query_{unique_id}"
+            self._create_history(expected_history_name)
+            self._create_history(expected_history_name.upper())
+            self._create_history(expected_history_name.lower())
+            self._create_history(f"Another history_{uuid4()}")
+
+            name_contains = "history"
+            query = f"?q=name-contains&qv={name_contains}"
+            index_response = self._get(f"histories{query}").json()
+            assert len(index_response) == 4
+
+            name_contains = "history that match query"
+            query = f"?q=name-contains&qv={name_contains}"
+            index_response = self._get(f"histories{query}").json()
+            assert len(index_response) == 3
+
+            name_contains = "ANOTHER"
+            query = f"?q=name-contains&qv={name_contains}"
+            index_response = self._get(f"histories{query}").json()
+            assert len(index_response) == 1
+
+            name_contains = "test"
+            query = f"?q=name-contains&qv={name_contains}"
+            index_response = self._get(f"histories{query}").json()
+            assert len(index_response) == 3
+
+            name_contains = unique_id
+            query = f"?q=name-contains&qv={name_contains}"
+            index_response = self._get(f"histories{query}").json()
+            assert len(index_response) == 3
+
     def test_delete(self):
         # Setup a history and ensure it is in the index
         history_id = self._create_history("TestHistoryForDelete")["id"]

From 417029d53e7e8b824ff596ec20ae706d9738e0d2 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 4 May 2023 11:26:56 +0200
Subject: [PATCH 62/78] Fix case insensitive orm filtering in lists

Not sure if this is the best location or way to fix it, but after `_split_filters` we won't have the `case_insensitive` flag available because the ParsedFilter wrapper gets dropped there.

Also we can be sure that if `case_insensitive` is True in that particular filter then we surely want to compare against the lower version of the column as the value to compare to already was converted to lower when parsing the filter.
---
 lib/galaxy/managers/base.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index f46599fa2175..4692f249770b 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -365,9 +365,10 @@ def list(self, filters=None, order_by=None, limit=None, offset=None, **kwargs):
         Returns all objects matching the given filters
         """
         # list becomes a way of applying both filters generated in the orm (such as .user ==)
-        # and functional filters that aren't currently possible using the orm (such as instance calcluated values
+        # and functional filters that aren't currently possible using the orm (such as instance calculated values
         # or annotations/tags). List splits those two filters and applies limits/offsets
         # only after functional filters (if any) using python.
+        self._handle_filters_case_sensitivity(filters)
         orm_filters, fn_filters = self._split_filters(filters)
         if not fn_filters:
             # if no fn_filtering required, we can use the 'all orm' version with limit offset
@@ -381,6 +382,18 @@ def list(self, filters=None, order_by=None, limit=None, offset=None, **kwargs):
         items = self._apply_fn_filters_gen(items, fn_filters)
         return list(self._apply_fn_limit_offset_gen(items, limit, offset))
 
+    def _handle_filters_case_sensitivity(self, filters):
+        """Modifies the filters to make them case insensitive if needed."""
+        if filters is None:
+            return  # No filters to handle
+        iterable_filters = filters if isinstance(filters, list) else [filters]
+        for item in iterable_filters:
+            # If the filter has the case_insensitive attribute set to True this means that the filter
+            # is a parsed orm filter and that it needs to compare the column with a lower case version of the value.
+            is_case_insensitive = getattr(item, "case_insensitive", False)
+            if is_case_insensitive and isinstance(item.filter, sqlalchemy.sql.elements.BinaryExpression):
+                item.filter.left = sqlalchemy.func.lower(item.filter.left)
+
     def _split_filters(self, filters):
         """
         Splits `filters` into a tuple of two lists:

From 81b42f00886c97bcfc21b470d213988fad6241b2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 5 May 2023 16:28:19 +0200
Subject: [PATCH 63/78] Update pulsar to 0.15.2

Which includes fixes for lost and timed out connections to the message
queue.
---
 lib/galaxy/dependencies/pinned-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index fb14c563e884..640213895c0f 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -118,7 +118,7 @@ pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9
 prompt-toolkit==3.0.36 ; python_version >= "3.7" and python_version < "3.12"
 prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12"
 psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.12"
-pulsar-galaxy-lib==0.15.0.dev2 ; python_version >= "3.7" and python_version < "3.12"
+pulsar-galaxy-lib==0.15.2 ; python_version >= "3.7" and python_version < "3.12"
 pyasn1==0.4.8 ; python_version >= "3.7" and python_version < "3.12"
 pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
 pycryptodome==3.16.0 ; python_version >= "3.7" and python_version < "3.12"

From d5ab29640b3ace4d865d305090c501d9d7e52e5d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 3 May 2023 17:21:52 +0200
Subject: [PATCH 64/78] Various fixes to path prefix handling

Should fix https://github.com/galaxyproject/galaxy/issues/16030
---
 lib/galaxy/datatypes/data.py                  |  4 +-
 .../display_applications/application.py       |  1 +
 .../display_applications/parameters.py        |  4 +-
 lib/galaxy/datatypes/genetics.py              | 13 +++--
 lib/galaxy/datatypes/interval.py              | 56 +++++++++++++------
 lib/galaxy/managers/hdas.py                   |  4 +-
 lib/galaxy/web/framework/__init__.py          |  6 ++
 lib/galaxy/web/framework/base.py              |  5 ++
 lib/galaxy/webapps/galaxy/api/__init__.py     | 28 +++++++++-
 lib/galaxy/webapps/galaxy/api/workflows.py    |  2 +-
 .../webapps/galaxy/controllers/async.py       |  4 +-
 .../webapps/galaxy/controllers/authnz.py      |  2 +-
 lib/galaxy/webapps/galaxy/fast_app.py         |  6 +-
 .../webapps/galaxy/services/invocations.py    |  4 +-
 test/integration/test_prefix_handling.py      | 38 +++++++++++++
 15 files changed, 142 insertions(+), 35 deletions(-)
 create mode 100644 test/integration/test_prefix_handling.py

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 7fe727459927..f0ae63386025 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -731,7 +731,7 @@ def as_display_type(self, dataset: "DatasetInstance", type: str, **kwd) -> Union
         return f"This display type ({type}) is not implemented for this datatype ({dataset.ext})."
 
     def get_display_links(
-        self, dataset: "DatasetInstance", type: str, app, base_url: str, target_frame: str = "_blank", **kwd
+        self, dataset: "DatasetInstance", type: str, app, base_url, request, target_frame: str = "_blank", **kwd
     ):
         """
         Returns a list of tuples of (name, link) for a particular display type.  No check on
@@ -742,7 +742,7 @@ def get_display_links(
         try:
             if app.config.enable_old_display_applications and type in self.get_display_types():
                 return target_frame, getattr(self, self.supported_display_apps[type]["links_function"])(
-                    dataset, type, app, base_url, **kwd
+                    dataset, type, app, base_url, request, **kwd
                 )
         except Exception:
             log.exception(
diff --git a/lib/galaxy/datatypes/display_applications/application.py b/lib/galaxy/datatypes/display_applications/application.py
index f22523bdc1f3..ce6bc7d0e04f 100644
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -62,6 +62,7 @@ def get_display_url(self, data, trans):
             app_name=quote_plus(self.display_application.id),
             link_name=quote_plus(self.id),
             app_action=None,
+            environ=trans.request.environ,
         )
 
     def get_inital_values(self, data, trans):
diff --git a/lib/galaxy/datatypes/display_applications/parameters.py b/lib/galaxy/datatypes/display_applications/parameters.py
index 29c4af4f57c4..6846d1088bf2 100644
--- a/lib/galaxy/datatypes/display_applications/parameters.py
+++ b/lib/galaxy/datatypes/display_applications/parameters.py
@@ -227,7 +227,8 @@ def url(self):
             base_url = f"http{base_url[5:]}"
         return "{}{}".format(
             base_url,
-            self.trans.app.url_for(
+            self.trans.app.legacy_url_for(
+                mapper=self.trans.app.legacy_mapper,
                 controller="dataset",
                 action="display_application",
                 dataset_id=self._dataset_hash,
@@ -236,6 +237,7 @@ def url(self):
                 link_name=quote_plus(self.parameter.link.id),
                 app_action=self.action_name,
                 action_param=self._url,
+                environ=self.trans.request.environ,
             ),
         )
 
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 1ebb8398cb64..a0ed1e8c382e 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -90,7 +90,7 @@ def as_ucsc_display_file(self, dataset: "DatasetInstance", **kwd) -> Union[FileO
         """
         return open(dataset.file_name, "rb")
 
-    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str) -> List:
+    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str, request) -> List:
         """
         from the ever-helpful angie hinrichs angie@soe.ucsc.edu
         a genome graphs call looks like this
@@ -114,12 +114,17 @@ def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str)
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
                     site_url = site_url.replace("/hgTracks?", "/hgGenome?")  # for genome graphs
-                    internal_url = "%s" % app.url_for(
-                        controller="dataset", dataset_id=dataset.id, action="display_at", filename=f"ucsc_{site_name}"
+                    internal_url = "%s" % app.legacy_url_for(
+                        mapper=app.legacy_mapper,
+                        environ=request.environ,
+                        controller="dataset",
+                        dataset_id=dataset.id,
+                        action="display_at",
+                        filename=f"ucsc_{site_name}",
                     )
                     display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (
                         base_url,
-                        app.url_for(controller="root"),
+                        app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
                         dataset.id,
                         type,
                     )
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 2c4e710d9e1e..e83954b7afa4 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -314,7 +314,7 @@ def display_peek(self, dataset: "DatasetInstance") -> str:
             },
         )
 
-    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str) -> List:
+    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str, request) -> List:
         """
         Generate links to UCSC genome browser sites based on the dbkey
         and content of dataset.
@@ -336,12 +336,22 @@ def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str)
         # Accumulate links for valid sites
         ret_val = []
         for site_name, site_url in valid_sites:
-            internal_url = app.url_for(
-                controller="dataset", dataset_id=dataset.id, action="display_at", filename="ucsc_" + site_name
+            internal_url = app.legacy_url_for(
+                mapper=app.legacy_mapper,
+                environ=request.environ,
+                controller="dataset",
+                dataset_id=dataset.id,
+                action="display_at",
+                filename="ucsc_" + site_name,
             )
             display_url = quote_plus(
                 "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
-                % (base_url, app.url_for(controller="root"), dataset.id, type)
+                % (
+                    base_url,
+                    app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                    dataset.id,
+                    type,
+                )
             )
             redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
             link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
@@ -757,18 +767,23 @@ class Bed12(BedStrict):
 
 class _RemoteCallMixin:
     def _get_remote_call_url(
-        self, redirect_url: str, site_name: str, dataset: "DatasetInstance", type: str, app, base_url: str
+        self, redirect_url: str, site_name: str, dataset: "DatasetInstance", type: str, app, base_url: str, request
     ) -> str:
         """Retrieve the URL to call out to an external site and retrieve data.
         This routes our external URL through a local galaxy instance which makes
         the data available, followed by redirecting to the remote site with a
         link back to the available information.
         """
-        internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
+        internal_url = f"{app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
         base_url = app.config.get("display_at_callback", base_url)
         display_url = quote_plus(
             "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
-            % (base_url, app.url_for(controller="root"), dataset.id, type)
+            % (
+                base_url,
+                app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                dataset.id,
+                type,
+            )
         )
         link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
         return link
@@ -953,7 +968,7 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str) -> List:
+    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str, request) -> List:
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
@@ -962,11 +977,11 @@ def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str)
                     redirect_url = quote_plus(
                         f"{site_url}db={dataset.dbkey}&position={seqid}:{start}-{stop}&hgt.customText=%s"
                     )
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
                     ret_val.append((site_name, link))
         return ret_val
 
-    def gbrowse_links(self, dataset: "DatasetInstance", type: str, app, base_url: str) -> List:
+    def gbrowse_links(self, dataset: "DatasetInstance", type: str, app, base_url: str, request) -> List:
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport(dataset)
         if seqid is not None:
@@ -975,7 +990,7 @@ def gbrowse_links(self, dataset: "DatasetInstance", type: str, app, base_url: st
                     if seqid.startswith("chr") and len(seqid) > 3:
                         seqid = seqid[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={seqid}:{start}..{stop}&eurl=%s")
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -1355,7 +1370,7 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def gbrowse_links(self, dataset: "DatasetInstance", type: str, app, base_url: str) -> List:
+    def gbrowse_links(self, dataset: "DatasetInstance", type: str, app, base_url: str, request) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
@@ -1364,11 +1379,11 @@ def gbrowse_links(self, dataset: "DatasetInstance", type: str, app, base_url: st
                     if chrom.startswith("chr") and len(chrom) > 3:
                         chrom = chrom[3:]
                     redirect_url = quote_plus(f"{site_url}/?q={chrom}:{start}..{stop}&eurl=%s")
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
                     ret_val.append((site_name, link))
         return ret_val
 
-    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str) -> List:
+    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str, request) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
@@ -1377,7 +1392,7 @@ def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str)
                     redirect_url = quote_plus(
                         f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s"
                     )
-                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
+                    link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url, request)
                     ret_val.append((site_name, link))
         return ret_val
 
@@ -1537,16 +1552,21 @@ def get_estimated_display_viewport(
                 log.exception("Unexpected error")
         return (None, None, None)  # could not determine viewport
 
-    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str) -> List:
+    def ucsc_links(self, dataset: "DatasetInstance", type: str, app, base_url: str, request) -> List:
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
-                    internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
+                    internal_url = f"{app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
                     display_url = quote_plus(
                         "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
-                        % (base_url, app.url_for(controller="root"), dataset.id, type)
+                        % (
+                            base_url,
+                            app.legacy_url_for(mapper=app.legacy_mapper, environ=request.environ, controller="root"),
+                            dataset.id,
+                            type,
+                        )
                     )
                     redirect_url = quote_plus(
                         f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s"
diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index 905602aed958..4688232e2a27 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -508,7 +508,9 @@ def serialize_old_display_applications(self, item, key, trans=None, **context):
 
         display_link_fn = hda.datatype.get_display_links
         for display_app in hda.datatype.get_display_types():
-            target_frame, display_links = display_link_fn(hda, display_app, self.app, trans.request.base)
+            target_frame, display_links = display_link_fn(
+                hda, display_app, self.app, trans.request.base, request=trans.request
+            )
 
             if len(display_links) > 0:
                 display_label = hda.datatype.get_display_label(display_app)
diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index 0170f095e436..a62442893e9b 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -26,7 +26,13 @@ def legacy_url_for(mapper, *args, **kwargs) -> str:
     Re-establishes the mapper for legacy WSGI routes.
     """
     rc = request_config()
+    environ = kwargs.pop("environ", None)
     rc.mapper = mapper
+    if environ:
+        rc.environ = environ
+        if hasattr(rc, "using_request_local"):
+            rc.request_local = lambda: rc
+            rc = request_config()
     return base.routes.url_for(*args, **kwargs)
 
 
diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
index ee1693315dc1..361524d94b10 100644
--- a/lib/galaxy/web/framework/base.py
+++ b/lib/galaxy/web/framework/base.py
@@ -15,6 +15,7 @@
     SimpleCookie,
 )
 from importlib import import_module
+from urllib.parse import urljoin
 
 import routes
 import webob.compat
@@ -430,6 +431,10 @@ def cookies(self):
     def base(self):
         return f"{self.scheme}://{self.host}"
 
+    @lazy_property
+    def url_path(self):
+        return urljoin(self.base, self.environ.get("SCRIPT_NAME", ""))
+
     # @lazy_property
     # def params( self ):
     #     return parse_formvars( self.environ )
diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index c6723c58b262..78651b18f09e 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -8,14 +8,19 @@
     Any,
     AsyncGenerator,
     cast,
+    MutableMapping,
     NamedTuple,
     Optional,
     Tuple,
     Type,
     TypeVar,
 )
-from urllib.parse import urlencode
+from urllib.parse import (
+    urlencode,
+    urljoin,
+)
 
+from a2wsgi.wsgi import build_environ
 from fastapi import (
     Form,
     Header,
@@ -194,17 +199,38 @@ class GalaxyASGIRequest(GalaxyAbstractRequest):
 
     def __init__(self, request: Request):
         self.__request = request
+        self.__environ: Optional[MutableMapping[str, Any]] = None
 
     @property
     def base(self) -> str:
         return str(self.__request.base_url)
 
+    @property
+    def url_path(self) -> str:
+        scope = self.__request.scope
+        root_path = scope.get("root_path")
+        url = self.base
+        if root_path:
+            url = urljoin(url, root_path)
+        return url
+
     @property
     def host(self) -> str:
         client = self.__request.client
         assert client is not None
         return str(client.host)
 
+    @property
+    def environ(self) -> MutableMapping[str, Any]:
+        """
+        Fallback WSGI environ.
+
+        This is not a full environ, there is no body. This is only meant to make routes.url_for work.
+        """
+        if self.__environ is None:
+            self.__environ = build_environ(self.__request.scope, None)  # type: ignore[arg-type]
+        return self.__environ
+
 
 class GalaxyASGIResponse(GalaxyAbstractResponse):
     """Wrapper around Starlette/FastAPI Response object.
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 33794507d4c3..7d4fd6e66e8c 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1499,7 +1499,7 @@ def _deprecated_generate_bco(
         self, trans, invocation_id: DecodedDatabaseIdField, merge_history_metadata: Optional[bool]
     ):
         export_options = BcoExportOptions(
-            galaxy_url=trans.request.base,
+            galaxy_url=trans.request.url_path,
             galaxy_version=VERSION,
             merge_history_metadata=merge_history_metadata or False,
         )
diff --git a/lib/galaxy/webapps/galaxy/controllers/async.py b/lib/galaxy/webapps/galaxy/controllers/async.py
index 8a51d246a007..f048db145014 100644
--- a/lib/galaxy/webapps/galaxy/controllers/async.py
+++ b/lib/galaxy/webapps/galaxy/controllers/async.py
@@ -70,7 +70,7 @@ def index(self, trans, tool_id=None, data_secret=None, **kwd):
                 data.state = data.blurb = data.states.RUNNING
                 log.debug(f"executing tool {tool.id}")
                 trans.log_event(f"Async executing tool {tool.id}", tool_id=tool.id)
-                galaxy_url = f"{trans.request.base}/async/{tool_id}/{data.id}/{key}"
+                galaxy_url = f"{trans.request.url_path}/async/{tool_id}/{data.id}/{key}"
                 galaxy_url = params.get("GALAXY_URL", galaxy_url)
                 params = dict(
                     URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext
@@ -163,7 +163,7 @@ def index(self, trans, tool_id=None, data_secret=None, **kwd):
 
             try:
                 key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id))
-                galaxy_url = f"{trans.request.base}/async/{tool_id}/{data.id}/{key}"
+                galaxy_url = f"{trans.request.url_path}/async/{tool_id}/{data.id}/{key}"
                 params.update({"GALAXY_URL": galaxy_url})
                 params.update({"data_id": data.id})
 
diff --git a/lib/galaxy/webapps/galaxy/controllers/authnz.py b/lib/galaxy/webapps/galaxy/controllers/authnz.py
index 1fba546841c3..2aeaa466fc1f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/authnz.py
+++ b/lib/galaxy/webapps/galaxy/controllers/authnz.py
@@ -143,7 +143,7 @@ def create_user(self, trans, provider, **kwargs):
             )
         except exceptions.AuthenticationFailed as e:
             return trans.response.send_redirect(
-                f"{trans.request.base + url_for('/')}root/login?message={str(e) or 'Duplicate Email'}"
+                f"{trans.request.url_path + url_for('/')}root/login?message={str(e) or 'Duplicate Email'}"
             )
 
         if success is False:
diff --git a/lib/galaxy/webapps/galaxy/fast_app.py b/lib/galaxy/webapps/galaxy/fast_app.py
index 49ccdb718685..a1c9faef5e95 100644
--- a/lib/galaxy/webapps/galaxy/fast_app.py
+++ b/lib/galaxy/webapps/galaxy/fast_app.py
@@ -141,12 +141,13 @@ def include_legacy_openapi(app, gx_app):
     return app.openapi_schema
 
 
-def get_fastapi_instance() -> FastAPI:
+def get_fastapi_instance(root_path="") -> FastAPI:
     return FastAPI(
         title="Galaxy API",
         docs_url="/api/docs",
         openapi_tags=api_tags_metadata,
         license_info={"name": "MIT", "url": "https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt"},
+        root_path=root_path,
     )
 
 
@@ -167,7 +168,8 @@ def get_openapi_schema() -> Dict[str, Any]:
 
 
 def initialize_fast_app(gx_wsgi_webapp, gx_app):
-    app = get_fastapi_instance()
+    root_path = "" if gx_app.config.galaxy_url_prefix == "/" else gx_app.config.galaxy_url_prefix
+    app = get_fastapi_instance(root_path=root_path)
     add_exception_handler(app)
     add_galaxy_middleware(app, gx_app)
     add_request_id_middleware(app)
diff --git a/lib/galaxy/webapps/galaxy/services/invocations.py b/lib/galaxy/webapps/galaxy/services/invocations.py
index 44d0655a3fee..9c6130b00853 100644
--- a/lib/galaxy/webapps/galaxy/services/invocations.py
+++ b/lib/galaxy/webapps/galaxy/services/invocations.py
@@ -167,7 +167,7 @@ def prepare_store_download(
             short_term_storage_request_id=short_term_storage_target.request_id,
             user=trans.async_request_user,
             invocation_id=workflow_invocation.id,
-            galaxy_url=trans.request.base,
+            galaxy_url=trans.request.url_path,
             **payload.dict(),
         )
         result = prepare_invocation_download.delay(request=request)
@@ -181,7 +181,7 @@ def write_store(
         if not workflow_invocation:
             raise ObjectNotFound()
         request = WriteInvocationTo(
-            galaxy_url=trans.request.base,
+            galaxy_url=trans.request.url_path,
             user=trans.async_request_user,
             invocation_id=workflow_invocation.id,
             **payload.dict(),
diff --git a/test/integration/test_prefix_handling.py b/test/integration/test_prefix_handling.py
new file mode 100644
index 000000000000..705952f42fed
--- /dev/null
+++ b/test/integration/test_prefix_handling.py
@@ -0,0 +1,38 @@
+from galaxy_test.base.populators import DatasetPopulator
+from galaxy_test.driver import integration_util
+
+
+class TestPrefixUrlSerializationIntegration(integration_util.IntegrationTestCase):
+    dataset_populator: DatasetPopulator
+    url_prefix = "/galaxypf"
+
+    def setUp(self) -> None:
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config) -> None:
+        super().handle_galaxy_config_kwds(config)
+        config["galaxy_url_prefix"] = "/galaxypf"
+
+    def test_display_application_prefix_handling(self, history_id: str) -> None:
+        hda = self.dataset_populator.new_dataset(
+            history_id, content="chr1\t1\t2", file_type="interval", dbkey="hg18", wait=True
+        )
+        details_response = self.dataset_populator.get_history_dataset_details(
+            history_id=history_id, dataset_id=hda["id"]
+        )
+        # verify old style display app contains correct link back to galaxy
+        ucsc = details_response["display_types"][0]
+        assert ucsc["label"] == "display at UCSC"
+        assert "galaxypf" in ucsc["links"][0]["href"].split("redirect_url=")[-1]
+        # verify new style display app links contain prefix
+        display_apps = details_response["display_apps"]
+        for display_app in display_apps:
+            href = display_app["links"][0]["href"]
+            # This is a little inconsistent since most other references are generated without prefix
+            # but it's a real pain to work with the reverse lookup in routes and the callback URLs
+            # do need to include the prefix.
+            assert href.startswith(f"{self.url_prefix}/display_application")
+            response = self._get(f"{self.url[:-(len(self.url_prefix) + 1)]}{href}")
+            response.raise_for_status()

From 1484237b528f5567ce9da4720644e602cf92c0a7 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Sat, 6 May 2023 14:23:38 -0400
Subject: [PATCH 65/78] Fix minor error in `WorkflowList` help modal

---
 client/src/components/Workflow/WorkflowList.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/WorkflowList.vue b/client/src/components/Workflow/WorkflowList.vue
index 669e58cd137b..2e8bf71e13f5 100644
--- a/client/src/components/Workflow/WorkflowList.vue
+++ b/client/src/components/Workflow/WorkflowList.vue
@@ -127,7 +127,7 @@ const helpHtml = `<div>
             "published" icon of a workflow in your list to filter on this
             directly.
         </dd>
-        <dt><code>is:shared</code></dt>
+        <dt><code>is:shared_with_me</code></dt>
         <dd>
             Shows workflows shared by another user directly with you. You may
             also just click on the "shared with me" icon of a workflow in your

From 63df9be6938b1a74b8be0cd8e78dd06da977a7fc Mon Sep 17 00:00:00 2001
From: hujambo-dunia <michelle.savage.1@gmail.com>
Date: Wed, 26 Apr 2023 13:43:58 -0400
Subject: [PATCH 66/78] Fix for missing Href to Composables pass-through
 component

---
 client/src/components/Toast.js  |  3 ++-
 client/src/composables/toast.ts | 16 ++++++++--------
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/client/src/components/Toast.js b/client/src/components/Toast.js
index 07a672a5fb38..20a3e2d589b7 100644
--- a/client/src/components/Toast.js
+++ b/client/src/components/Toast.js
@@ -1,9 +1,10 @@
 export default {
     methods: {
-        showToast(message, title, variant) {
+        showToast(message, title, variant, href) {
             this.$bvToast.toast(message, {
                 variant,
                 title,
+                href,
                 toaster: "b-toaster-bottom-right",
                 append: true,
                 solid: true,
diff --git a/client/src/composables/toast.ts b/client/src/composables/toast.ts
index 218563a704ea..a3ec0a2f997f 100644
--- a/client/src/composables/toast.ts
+++ b/client/src/composables/toast.ts
@@ -17,20 +17,20 @@ export const setToastComponentRef = (newRef: typeof toastRef) => {
  * Use 'useToast' for the Composition Api instead.
  */
 export const Toast = {
-    success(message: string, title = "Success") {
-        toastRef.value?.showToast(message, title, "success");
+    success(message: string, title = "Success", href = "") {
+        toastRef.value?.showToast(message, title, "success", href);
     },
 
-    info(message: string, title = "Info") {
-        toastRef.value?.showToast(message, title, "info");
+    info(message: string, title = "Info", href = "") {
+        toastRef.value?.showToast(message, title, "info", href);
     },
 
-    warning(message: string, title = "Warning") {
-        toastRef.value?.showToast(message, title, "warning");
+    warning(message: string, title = "Warning", href = "") {
+        toastRef.value?.showToast(message, title, "warning", href);
     },
 
-    error(message: string, title = "Error") {
-        toastRef.value?.showToast(message, title, "danger");
+    error(message: string, title = "Error", href = "") {
+        toastRef.value?.showToast(message, title, "danger", href);
     },
 };
 

From 873a4339abe931914e0028f4f822924dcf6ca335 Mon Sep 17 00:00:00 2001
From: hujambo-dunia <michelle.savage.1@gmail.com>
Date: Wed, 26 Apr 2023 14:42:38 -0400
Subject: [PATCH 67/78] Fix for link pop-up window/toaster after Data Library
 to History import

---
 .../import-to-history/import-dataset.js       | 20 ++++++++-----------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js
index 127d9243e64d..488a773428d6 100644
--- a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js
+++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js
@@ -126,7 +126,7 @@ var ImportDatasetModal = Backbone.View.extend({
         // set the used history as current so user will see the last one
         // that he imported into in the history panel on the 'analysis' page
         $.getJSON(`${getAppRoot()}history/set_as_current?id=${history_id}`);
-        this.chainCallImportingIntoHistory(items_to_import, history_name);
+        this.chainCallImportingIntoHistory(items_to_import, history_name, history_id);
     },
 
     initChainCallControlToHistory: function (options) {
@@ -147,27 +147,23 @@ var ImportDatasetModal = Backbone.View.extend({
      * @param  {array} history_item_set array of empty history items
      * @param  {str} history_name     name of the history to import to
      */
-    chainCallImportingIntoHistory: function (history_item_set, history_name) {
+    chainCallImportingIntoHistory: function (history_item_set, history_name, history_id) {
         const Galaxy = getGalaxyInstance();
         var popped_item = history_item_set.pop();
         if (typeof popped_item == "undefined") {
             if (this.options.chain_call_control.failed_number === 0) {
-                Toast.success("Selected datasets imported into history. Click this to start analyzing it.", "", {
-                    onclick: () => {
-                        window.location = getAppRoot();
-                    },
-                });
+                Toast.success(
+                    "Selected datasets imported into history. Click this to start analyzing it.",
+                    "",
+                    `${getAppRoot()}histories/view?id=${history_id}`
+                );
             } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number) {
                 Toast.error("There was an error and no datasets were imported into history.");
             } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number) {
                 Toast.warning(
                     "Some of the datasets could not be imported into history. Click this to see what was imported.",
                     "",
-                    {
-                        onclick: () => {
-                            window.location = getAppRoot();
-                        },
-                    }
+                    `${getAppRoot()}histories/view?id=${history_id}`
                 );
             }
             Galaxy.modal.hide();

From 9da3b03a9119b561ce58041fa27d05e16c6ed20b Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Thu, 27 Apr 2023 08:36:07 -0400
Subject: [PATCH 68/78] Update
 client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js

Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 .../TopToolbar/import-to-history/import-dataset.js            | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js
index 488a773428d6..f9f885763378 100644
--- a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js
+++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js
@@ -153,8 +153,8 @@ var ImportDatasetModal = Backbone.View.extend({
         if (typeof popped_item == "undefined") {
             if (this.options.chain_call_control.failed_number === 0) {
                 Toast.success(
-                    "Selected datasets imported into history. Click this to start analyzing it.",
-                    "",
+                    "Click here to start analyzing it.",
+                    "Selected datasets imported into history",
                     `${getAppRoot()}histories/view?id=${history_id}`
                 );
             } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number) {

From ac432a50233cb4c3dcada2aab513c3855b6acd69 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Mar 2023 21:02:18 +0100
Subject: [PATCH 69/78] Display DCE in job parameter component

Addresses part of #15729
---
 .../History/Content/GenericItem.vue           | 27 ++++++++++-----
 .../JobParameters/JobParametersArrayValue.vue |  2 +-
 .../components/providers/storeProviders.js    | 10 ++++++
 client/src/schema/schema.ts                   | 31 +++++++++++++++++
 lib/galaxy/managers/jobs.py                   |  2 +-
 lib/galaxy/model/security.py                  |  9 +++++
 .../webapps/galaxy/api/dataset_collections.py | 14 ++++++++
 .../galaxy/services/dataset_collections.py    | 12 +++++++
 .../api/test_dataset_collections.py           | 34 +++++++++++++++++++
 9 files changed, 131 insertions(+), 10 deletions(-)

diff --git a/client/src/components/History/Content/GenericItem.vue b/client/src/components/History/Content/GenericItem.vue
index adda51b27de4..38ae796f2f19 100644
--- a/client/src/components/History/Content/GenericItem.vue
+++ b/client/src/components/History/Content/GenericItem.vue
@@ -3,19 +3,19 @@
         <loading-span v-if="loading" message="Loading dataset" />
         <div v-else>
             <ContentItem
-                :id="item.hid"
+                :id="item.hid ?? item.element_index + 1"
                 is-history-item
-                :item="item"
-                :name="item.name"
+                :item="item?.object || item"
+                :name="item.name || item.element_identifier"
                 :expand-dataset="expandDataset"
-                :is-dataset="item.history_content_type == 'dataset'"
+                :is-dataset="item.history_content_type == 'dataset' || item.element_type == 'hda'"
                 @update:expand-dataset="expandDataset = $event"
                 @view-collection="viewCollection = !viewCollection"
                 @delete="onDelete(item)"
                 @undelete="onUndelete(item)"
                 @unhide="onUnhide(item)" />
             <div v-if="viewCollection">
-                <GenericElement :dsc="item" />
+                <GenericElement :dsc="item?.object || item" />
             </div>
         </div>
     </component>
@@ -23,13 +23,15 @@
 
 <script>
 import LoadingSpan from "components/LoadingSpan";
-import { DatasetCollectionProvider, DatasetProvider } from "components/providers";
-import { deleteContent, updateContentFields } from "components/History/model/queries";
+import { DatasetCollectionProvider, DatasetProvider } from "@/components/providers";
+import { DatasetCollectionElementProvider } from "@/components/providers/storeProviders";
+import { deleteContent, updateContentFields } from "@/components/History/model/queries";
 import ContentItem from "./ContentItem";
 import GenericElement from "./GenericElement";
 
 export default {
     components: {
+        DatasetCollectionElementProvider,
         ContentItem,
         GenericElement,
         DatasetProvider,
@@ -54,7 +56,16 @@ export default {
     },
     computed: {
         providerComponent() {
-            return this.itemSrc == "hda" ? "DatasetProvider" : "DatasetCollectionProvider";
+            switch (this.itemSrc) {
+                case "hda":
+                    return "DatasetProvider";
+                case "hdca":
+                    return "DatasetCollectionProvider";
+                case "dce":
+                    return "DatasetCollectionElementProvider";
+                default:
+                    throw `Unknown element src ${this.itemSrc}`;
+            }
         },
     },
     methods: {
diff --git a/client/src/components/JobParameters/JobParametersArrayValue.vue b/client/src/components/JobParameters/JobParametersArrayValue.vue
index 1878f3efce9e..1ae30eb94bf8 100644
--- a/client/src/components/JobParameters/JobParametersArrayValue.vue
+++ b/client/src/components/JobParameters/JobParametersArrayValue.vue
@@ -2,7 +2,7 @@
     <div>
         <div v-for="(elVal, pvIndex) in parameter_value" :key="pvIndex">
             <generic-history-item
-                v-if="['hda', 'hdca'].includes(elVal.src)"
+                v-if="['hda', 'hdca', 'dce'].includes(elVal.src)"
                 :item-id="elVal.id"
                 :item-src="elVal.src" />
             <span v-else> {{ elVal.hid }}: {{ elVal.name }} </span>
diff --git a/client/src/components/providers/storeProviders.js b/client/src/components/providers/storeProviders.js
index ff1a16d0154e..a584b1300085 100644
--- a/client/src/components/providers/storeProviders.js
+++ b/client/src/components/providers/storeProviders.js
@@ -47,6 +47,7 @@ export const SimpleProviderMixin = {
             loading: this.loading,
             item: this.item,
             save: this.save,
+            result: this.item,
         });
     },
 };
@@ -131,6 +132,15 @@ export const JobProvider = {
     },
 };
 
+export const DatasetCollectionElementProvider = {
+    mixins: [SimpleProviderMixin],
+    computed: {
+        url() {
+            return prependPath(`api/dataset_collection_element/${this.id}`);
+        },
+    },
+};
+
 /**
  * Provider component interface to the actual stores i.e. history items and collection elements stores.
  * @param {String} storeAction The store action is executed when the consuming component e.g. the history panel, changes the provider props.
diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index 2893bd0ae698..8f1f59a66415 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -47,6 +47,10 @@ export interface paths {
          */
         put: operations["reload_toolbox_api_configuration_toolbox_put"];
     };
+    "/api/dataset_collection_element/{dce_id}": {
+        /** Content */
+        get: operations["content_api_dataset_collection_element__dce_id__get"];
+    };
     "/api/dataset_collections": {
         /** Create a new dataset collection instance. */
         post: operations["create_api_dataset_collections_post"];
@@ -7544,6 +7548,33 @@ export interface operations {
             };
         };
     };
+    content_api_dataset_collection_element__dce_id__get: {
+        /** Content */
+        parameters: {
+            /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+            header?: {
+                "run-as"?: string;
+            };
+            /** @description The encoded identifier of the dataset collection element. */
+            path: {
+                dce_id: string;
+            };
+        };
+        responses: {
+            /** @description Successful Response */
+            200: {
+                content: {
+                    "application/json": components["schemas"]["DCESummary"];
+                };
+            };
+            /** @description Validation Error */
+            422: {
+                content: {
+                    "application/json": components["schemas"]["HTTPValidationError"];
+                };
+            };
+        };
+    };
     create_api_dataset_collections_post: {
         /** Create a new dataset collection instance. */
         parameters?: {
diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index 14788e6f688a..8c41f603e6ef 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -903,7 +903,7 @@ def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None)
                             value=f"{len(param_values[input.name])} uploaded datasets",
                         )
                     )
-                elif input.type == "data":
+                elif input.type == "data" or input.type == "data_collection":
                     value = []
                     for element in listify(param_values[input.name]):
                         encoded_id = trans.security.encode_id(element.id)
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 6723e5b69a8d..68cbaa9ea31a 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -4,6 +4,7 @@
     datetime,
     timedelta,
 )
+from typing import List
 
 from sqlalchemy import (
     and_,
@@ -519,6 +520,14 @@ def can_access_datasets(self, user_roles, action_tuples):
 
         return True
 
+    def can_access_collection(
+        self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection
+    ):
+        action_tuples = collection.dataset_action_tuples
+        if not self.can_access_datasets(user_roles, action_tuples):
+            return False
+        return True
+
     def can_manage_dataset(self, roles, dataset):
         return self.allow_action(roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset)
 
diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
index 79818f1ef15a..5e9d61d1a314 100644
--- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py
@@ -13,6 +13,7 @@
     AnyHDCA,
     CreateNewCollectionPayload,
     DatasetCollectionInstanceType,
+    DCESummary,
     HDCADetailed,
 )
 from galaxy.webapps.galaxy.api import (
@@ -36,6 +37,11 @@
     ..., description="The encoded identifier of the dataset collection."
 )
 
+
+DatasetCollectionElementIdPathParam: DecodedDatabaseIdField = Path(
+    ..., description="The encoded identifier of the dataset collection element."
+)
+
 InstanceTypeQueryParam: DatasetCollectionInstanceType = Query(
     default="history",
     description="The type of collection instance. Either `history` (default) or `library`.",
@@ -129,3 +135,11 @@ def contents(
         ),
     ) -> DatasetCollectionContentElements:
         return self.service.contents(trans, hdca_id, parent_id, instance_type, limit, offset)
+
+    @router.get("/api/dataset_collection_element/{dce_id}")
+    def content(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        dce_id: DecodedDatabaseIdField = DatasetCollectionElementIdPathParam,
+    ) -> DCESummary:
+        return self.service.dce_content(trans, dce_id)
diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
index 17e17fea5a9d..ac313b2fcb1f 100644
--- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -25,6 +25,7 @@
 from galaxy.managers.context import ProvidesHistoryContext
 from galaxy.managers.hdcas import HDCAManager
 from galaxy.managers.histories import HistoryManager
+from galaxy.model import DatasetCollectionElement
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
     ModelClassField,
@@ -208,6 +209,17 @@ def show(
         )
         return rval
 
+    def dce_content(self, trans: ProvidesHistoryContext, dce_id: DecodedDatabaseIdField) -> DCESummary:
+        dce: Optional[DatasetCollectionElement] = trans.model.session.query(DatasetCollectionElement).get(dce_id)
+        if not dce:
+            raise exceptions.ObjectNotFound("No DatasetCollectionElement found")
+        if not trans.user_is_admin:
+            collection = dce.child_collection or dce.collection
+            if not trans.app.security_agent.can_access_collection(trans.get_current_user_roles(), collection):
+                raise exceptions.ItemAccessibilityException("Collection not accessible by user.")
+        serialized_dce = dictify_element_reference(dce, recursive=False, security=trans.security)
+        return trans.security.encode_all_ids(serialized_dce, recursive=True)
+
     def contents(
         self,
         trans: ProvidesHistoryContext,
diff --git a/lib/galaxy_test/api/test_dataset_collections.py b/lib/galaxy_test/api/test_dataset_collections.py
index 38db8c02a0c0..1d2b0d860ed4 100644
--- a/lib/galaxy_test/api/test_dataset_collections.py
+++ b/lib/galaxy_test/api/test_dataset_collections.py
@@ -196,6 +196,40 @@ def test_hda_security(self):
                 create_response = self._post("dataset_collections", payload, json=True)
                 self._assert_status_code_is(create_response, 403)
 
+    def test_dataset_collection_element_security(self):
+        with self.dataset_populator.test_history(require_new=False) as history_id:
+            dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(
+                history_id,
+                collection_type="list:list:list",
+                wait=True,
+            ).json()
+            first_element = dataset_collection["elements"][0]
+            assert first_element["model_class"] == "DatasetCollectionElement"
+            assert first_element["element_type"] == "dataset_collection"
+            first_element_url = f"/api/dataset_collection_element/{first_element['id']}"
+            # Make one dataset private to check that access permissions are respected
+            first_dataset_element = first_element["object"]["elements"][0]["object"]["elements"][0]
+            self.dataset_populator.make_private(history_id, first_dataset_element["object"]["id"])
+            with self._different_user():
+                assert self._get(first_element_url).status_code == 403
+            collection_dce_response = self._get(first_element_url)
+            collection_dce_response.raise_for_status()
+            collection_dce = collection_dce_response.json()
+            assert collection_dce["model_class"] == "DatasetCollectionElement"
+            assert collection_dce["element_type"] == "dataset_collection"
+            first_dataset_element = first_element["object"]["elements"][0]["object"]["elements"][0]
+            assert first_dataset_element["model_class"] == "DatasetCollectionElement"
+            assert first_dataset_element["element_type"] == "hda"
+            first_dataset_element_url = f"/api/dataset_collection_element/{first_dataset_element['id']}"
+            with self._different_user():
+                assert self._get(first_dataset_element_url).status_code == 403
+            dataset_dce_response = self._get(first_dataset_element_url)
+            dataset_dce_response.raise_for_status()
+            dataset_dce = dataset_dce_response.json()
+            assert dataset_dce["model_class"] == "DatasetCollectionElement"
+            assert dataset_dce["element_type"] == "hda"
+            assert dataset_dce["object"]["model_class"] == "HistoryDatasetAssociation"
+
     def test_enforces_unique_names(self):
         with self.dataset_populator.test_history(require_new=False) as history_id:
             element_identifiers = self.dataset_collection_populator.list_identifiers(history_id)

From 13514a76a6edc6cdfba22df4633b074a63f1226f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 5 May 2023 15:36:04 +0200
Subject: [PATCH 70/78] Wait for tool form data to be set before refreshing
 tool form

If you navigate to a tool re-run url without loading a history first the
tool form would be rebuilt before the tool parameters from the re-run
were actually set, so you would effectively just get the default values
for the tool.
---
 client/src/components/Tool/ToolForm.vue | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 236abdfc70a6..a15fe0233617 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -155,7 +155,6 @@ export default {
     data() {
         return {
             disabled: false,
-            initialized: false,
             showLoading: true,
             showForm: false,
             showEntryPoints: false,
@@ -163,7 +162,7 @@ export default {
             showError: false,
             showExecuting: false,
             formConfig: {},
-            formData: {},
+            formData: undefined,
             remapAllowed: false,
             errorTitle: null,
             errorContent: null,
@@ -214,6 +213,9 @@ export default {
                 return "The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.";
             }
         },
+        initialized() {
+            return this.formData !== undefined;
+        },
     },
     watch: {
         currentHistoryId() {
@@ -224,10 +226,7 @@ export default {
         },
     },
     created() {
-        this.requestTool().then(() => {
-            this.initialized = true;
-            console.debug(`ToolForm::created - Started listening to history changes. [${this.id}]`);
-        });
+        this.requestTool();
     },
     methods: {
         ...mapActions(useJobStore, ["saveLatestResponse"]),

From c14db55910411e5e532a3500f87f8f35ad177bbb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 5 May 2023 15:44:06 +0200
Subject: [PATCH 71/78] Fix re-run with DCE inputs

---
 client/src/mvc/ui/ui-select-content.js | 17 +++++++++-----
 lib/galaxy/model/security.py           |  4 +---
 lib/galaxy/tools/parameters/basic.py   | 32 +++++++++++++++++++++++++-
 3 files changed, 43 insertions(+), 10 deletions(-)

diff --git a/client/src/mvc/ui/ui-select-content.js b/client/src/mvc/ui/ui-select-content.js
index 11de437c0755..292d7a321479 100644
--- a/client/src/mvc/ui/ui-select-content.js
+++ b/client/src/mvc/ui/ui-select-content.js
@@ -424,12 +424,12 @@ const View = Backbone.View.extend({
         const select_options = { hda: [], hdca: [] };
         _.each(options, (items, src) => {
             _.each(items, (item) => {
-                self._patchValue(item);
+                self._patchValue(item, src);
                 const current_src = item.src || src;
                 const addOption = !this.model.attributes.tag || item.tags.includes(this.model.attributes.tag);
                 if (addOption) {
                     select_options[current_src].push({
-                        hid: item.hid,
+                        hid: item.hid || Infinity, // if we got no hid we have a "Selected" item
                         keep: item.keep,
                         label: `${item.hid || "Selected"}: ${item.name}`,
                         value: item.id,
@@ -455,7 +455,12 @@ const View = Backbone.View.extend({
                 list.push(value.id);
             });
             // sniff first suitable field type from config list
-            const src = new_value.values[0].src;
+            let src = new_value.values[0].src;
+            if (src === "dce") {
+                src =
+                    this.cache[`dce${new_value.values[0].id}_hda`]?.src ||
+                    this.cache[`dce${new_value.values[0].id}_hdca`]?.src;
+            }
             const multiple = new_value.values.length > 1;
             for (let i = 0; i < this.config.length; i++) {
                 const field = this.fields[i];
@@ -480,11 +485,11 @@ const View = Backbone.View.extend({
 
     /** Library datasets are displayed and selected together with history datasets,
         Dataset collection elements are displayed together with history dataset collections **/
-    _patchValue: function (v) {
-        const patchTo = { ldda: "hda", dce: "hdca" };
+    _patchValue: function (v, src) {
+        const patchTo = { ldda: "hda", dce: src };
         if (v.values) {
             _.each(v.values, (v) => {
-                this._patchValue(v);
+                this._patchValue(v, src);
             });
         } else if (patchTo[v.src]) {
             v.origin = v.src;
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index 68cbaa9ea31a..b92b0014e24b 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -520,9 +520,7 @@ def can_access_datasets(self, user_roles, action_tuples):
 
         return True
 
-    def can_access_collection(
-        self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection
-    ):
+    def can_access_collection(self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection):
         action_tuples = collection.dataset_action_tuples
         if not self.can_access_datasets(user_roles, action_tuples):
             return False
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index 15d5df5a6e1f..8c5305be6cf4 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -2092,6 +2092,9 @@ def from_json(self, value, trans, other_values=None):
                     elif single_value["src"] == "ldda":
                         decoded_id = trans.security.decode_id(single_value["id"])
                         rval.append(trans.sa_session.query(LibraryDatasetDatasetAssociation).get(decoded_id))
+                    elif single_value["src"] == "dce":
+                        decoded_id = trans.security.decode_id(single_value["id"])
+                        rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
                     else:
                         raise ValueError(f"Unknown input source {single_value['src']} passed to job submission API.")
                 elif isinstance(
@@ -2127,6 +2130,9 @@ def from_json(self, value, trans, other_values=None):
             elif value["src"] == "hdca":
                 decoded_id = trans.security.decode_id(value["id"])
                 rval.append(trans.sa_session.query(HistoryDatasetCollectionAssociation).get(decoded_id))
+            elif value["src"] == "dce":
+                decoded_id = trans.security.decode_id(value["id"])
+                rval.append(trans.sa_session.query(DatasetCollectionElement).get(decoded_id))
             else:
                 raise ValueError(f"Unknown input source {value['src']} passed to job submission API.")
         elif str(value).startswith("__collection_reduce__|"):
@@ -2280,6 +2286,28 @@ def append(list, hda, name, src, keep=False, subcollection_type=None):
                 value["map_over_type"] = subcollection_type
             return list.append(value)
 
+        def append_dce(dce):
+            if dce.hda:
+                # well this isn't good, but what's the alternative ?
+                # we should be precise about what we're (re-)running here.
+                key = "hda"
+            else:
+                key = "hdca"
+            d["options"][key].append(
+                {
+                    "id": trans.security.encode_id(dce.id),
+                    "name": dce.element_identifier,
+                    "src": "dce",
+                    "tags": [],
+                    "keep": True,
+                }
+            )
+
+        # append DCE
+        if isinstance(other_values.get(self.name), DatasetCollectionElement):
+            dce = other_values[self.name]
+            append_dce(dce)
+
         # add datasets
         hda_list = util.listify(other_values.get(self.name))
         # Prefetch all at once, big list of visible, non-deleted datasets.
@@ -2299,6 +2327,8 @@ def append(list, hda, name, src, keep=False, subcollection_type=None):
                 else:
                     hda_state = "unavailable"
                 append(d["options"]["hda"], hda, f"({hda_state}) {hda.name}", "hda", True)
+            elif isinstance(hda, DatasetCollectionElement):
+                append_dce(hda)
 
         # add dataset collections
         dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)
@@ -2460,7 +2490,7 @@ def to_dict(self, trans, other_values=None):
         # append DCE
         if isinstance(other_values.get(self.name), DatasetCollectionElement):
             dce = other_values[self.name]
-            d["options"]["dce"].append(
+            d["options"]["hdca"].append(
                 {
                     "id": trans.security.encode_id(dce.id),
                     "hid": None,

From 668c2ed08fa17e8acd0acbd6bf43bdf666b2ceaf Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 9 May 2023 12:47:14 +0200
Subject: [PATCH 72/78] Also patch values when setting list of selected
 datasets

---
 client/src/mvc/ui/ui-select-content.js | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/client/src/mvc/ui/ui-select-content.js b/client/src/mvc/ui/ui-select-content.js
index 292d7a321479..2aa69a0cb456 100644
--- a/client/src/mvc/ui/ui-select-content.js
+++ b/client/src/mvc/ui/ui-select-content.js
@@ -449,11 +449,6 @@ const View = Backbone.View.extend({
     _changeValue: function () {
         const new_value = this.model.get("value");
         if (new_value && new_value.values && new_value.values.length > 0) {
-            // create list with content ids
-            const list = [];
-            _.each(new_value.values, (value) => {
-                list.push(value.id);
-            });
             // sniff first suitable field type from config list
             let src = new_value.values[0].src;
             if (src === "dce") {
@@ -461,6 +456,12 @@ const View = Backbone.View.extend({
                     this.cache[`dce${new_value.values[0].id}_hda`]?.src ||
                     this.cache[`dce${new_value.values[0].id}_hdca`]?.src;
             }
+            this._patchValue(new_value, src);
+            // create list with content ids
+            const list = [];
+            _.each(new_value.values, (value) => {
+                list.push(value.id);
+            });
             const multiple = new_value.values.length > 1;
             for (let i = 0; i < this.config.length; i++) {
                 const field = this.fields[i];

From a9911bedfbfa4c5ea4c0d244b0097e30b206b343 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 9 May 2023 14:21:46 -0400
Subject: [PATCH 73/78] Anonymous User tool link bug fix Allows anonymous users
 to access tool links without active history

---
 lib/galaxy/tools/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index a27c6ea904b9..ec5e63dc8d3a 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2415,7 +2415,9 @@ def to_json(self, trans, kwd=None, job=None, workflow_building_mode=False, histo
             history = history or trans.get_history()
             if history is None and job is not None:
                 history = self.history_manager.get_owned(job.history.id, trans.user, current_history=trans.history)
-            if history is None:
+            # We can show the tool form if the current user is anonymous and doesn't have a history
+            user = trans.get_user()
+            if history is None and user is not None:
                 raise exceptions.MessageException("History unavailable. Please specify a valid history id")
 
         # build request context

From b9bb92cd1fe3b9533fc3a12ff086ff78f1ec0b7c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 10 May 2023 12:53:15 +0200
Subject: [PATCH 74/78] Don't build tool state for first param combination

It'll always pull in the first dataset in the `other_values` dict, which
isn'r correct. Tool parameters at this point know how to deal with
collections, so this shouldn't be neceesary.
---
 lib/galaxy/tools/__init__.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index a27c6ea904b9..c4b87ff10bab 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2437,12 +2437,6 @@ def to_json(self, trans, kwd=None, job=None, workflow_building_mode=False, histo
         # create parameter object
         params = Params(kwd, sanitize=False)
 
-        # expand incoming parameters (parameters might trigger multiple tool executions,
-        # here we select the first execution only in order to resolve dynamic parameters)
-        expanded_incomings, _ = expand_meta_parameters(trans, self, params.__dict__)
-        if expanded_incomings:
-            params.__dict__ = expanded_incomings[0]
-
         # do param translation here, used by datasource tools
         if self.input_translator:
             self.input_translator.translate(params)

From 3ce0a8dd1c98f998d5d9db5fffdabcb2b76ece4d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 10 May 2023 15:53:10 +0200
Subject: [PATCH 75/78] Selemium test for re-running part of dataset collection
 via DCE

---
 client/src/utils/navigation/navigation.yml |  6 ++++
 lib/galaxy_test/selenium/test_tool_form.py | 32 ++++++++++++++++++++++
 2 files changed, 38 insertions(+)

diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 2b792f2df156..29771100eb81 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -242,6 +242,7 @@ history_panel:
       tag_area_button: '.details .stateless-tags .multiselect button'
       tag_area_input: '.details .stateless-tags .multiselect input'
       list_items: '.dataset-collection-panel .listing .content-item'
+      back_to_history: svg[data-description="back to history"]
 
   selectors:
     _: '#current-history-panel'
@@ -492,6 +493,11 @@ tool_form:
     parameter_checkbox: 'div.ui-form-element[id="form-element-${parameter}"] .ui-switch'
     parameter_input: 'div.ui-form-element[id="form-element-${parameter}"] .ui-input'
     parameter_textarea: 'div.ui-form-element[id="form-element-${parameter}"] textarea'
+    parameter_batch_dataset_collection:
+      type: xpath
+      selector: //div[@id='form-element-${parameter}']//i[contains(@class, 'fa-folder-o')]/parent::label
+    data_option_value: option[value="${item_id}"]
+
     repeat_insert: '[data-description="repeat insert"]'
     reference: '.formatted-reference'
     about: '.tool-footer'
diff --git a/lib/galaxy_test/selenium/test_tool_form.py b/lib/galaxy_test/selenium/test_tool_form.py
index d27b36b43e4a..768ca62b3e3b 100644
--- a/lib/galaxy_test/selenium/test_tool_form.py
+++ b/lib/galaxy_test/selenium/test_tool_form.py
@@ -114,6 +114,38 @@ def check_recorded_val():
         self.history_panel_wait_for_hid_ok(2)
         self._check_dataset_details_for_inttest_value(2)
 
+    @selenium_test
+    def test_rerun_dataset_collection_element(self):
+        # upload a first dataset that should not become selected on re-run
+        test_path = self.get_filename("1.fasta")
+        self.perform_upload(test_path)
+        self.history_panel_wait_for_hid_ok(1)
+
+        history_id = self.current_history_id()
+        # upload a nested collection
+        collection_id = self.dataset_collection_populator.create_list_of_list_in_history(
+            history_id,
+            collection_type="list:list",
+            wait=True,
+        ).json()["id"]
+        self.tool_open("identifier_multiple")
+        self.components.tool_form.parameter_batch_dataset_collection(parameter="input1").wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.components.tool_form.data_option_value(item_id=collection_id).wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.tool_form_execute()
+        self.history_panel_wait_for_hid_ok(7)
+        self.history_panel_expand_collection(7)
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.history_panel_click_item_title(1)
+        self.sleep_for(self.wait_types.UX_RENDER)
+        self.hda_click_primary_action_button(1, "rerun")
+        self.sleep_for(self.wait_types.UX_RENDER)
+        assert self.driver.find_element(By.CSS_SELECTOR, "option:checked").text == "Selected: test0"
+        self.tool_form_execute()
+        self.components.history_panel.collection_view.back_to_history.wait_for_and_click()
+        self.history_panel_wait_for_hid_ok(9)
+
     @selenium_test
     @flakey
     def test_run_data(self):

From 4d6008f52527a5ea6b775d99ae86d8aa60e7c877 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 12 May 2023 16:14:08 +0200
Subject: [PATCH 76/78] Fix BCO export by updating gxformat2

Fixes https://github.com/galaxyproject/galaxy/issues/15961
---
 lib/galaxy/dependencies/pinned-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index fb14c563e884..74e195b3286b 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -73,7 +73,7 @@ galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12"
 gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 greenlet==2.0.1 ; python_version >= "3.7" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version < "3.12"
 gunicorn==20.1.0 ; python_version >= "3.7" and python_version < "3.12"
-gxformat2==0.17.0 ; python_version >= "3.7" and python_version < "3.12"
+gxformat2==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12"
 h5py==3.8.0 ; python_version >= "3.7" and python_version < "3.12"
 humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.12"

From 16be4b651cd2af33054fa13984a1be26c3ce83b8 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 12 May 2023 21:50:53 +0200
Subject: [PATCH 77/78] Partially fix merge forward for HistoryExport

I can't get the `getHistoryById` computed from historiesStore mocked properly...

- Also simplifies handling of history load in HistoryExport component.
---
 .../History/Export/HistoryExport.test.ts      | 14 +++++++++++--
 .../History/Export/HistoryExport.vue          | 20 ++++++++++---------
 2 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/client/src/components/History/Export/HistoryExport.test.ts b/client/src/components/History/Export/HistoryExport.test.ts
index a3c7255badf7..bf6bedcb8851 100644
--- a/client/src/components/History/Export/HistoryExport.test.ts
+++ b/client/src/components/History/Export/HistoryExport.test.ts
@@ -11,6 +11,8 @@ import type { components } from "@/schema";
 import { getLocalVue } from "@tests/jest/helpers";
 import HistoryExport from "./HistoryExport.vue";
 import { getExportRecords } from "./services";
+import { setActivePinia } from "pinia";
+import { createTestingPinia } from "@pinia/testing";
 
 const localVue = getLocalVue(true);
 
@@ -25,7 +27,6 @@ const FAKE_HISTORY = {
 };
 
 const REMOTE_FILES_API_ENDPOINT = new RegExp("/api/remote_files/plugins");
-const GET_HISTORY_ENDPOINT = new RegExp(`/api/histories/${FAKE_HISTORY_ID}`);
 
 type FilesSourcePluginList = components["schemas"]["FilesSourcePlugin"][];
 const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [
@@ -41,10 +42,20 @@ const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [
     },
 ];
 
+const pinia = createTestingPinia({
+    initialState: {
+        historyStore: {
+            getHistoryById: (historyId: string) => FAKE_HISTORY,
+        },
+    },
+});
+
 async function mountHistoryExport() {
+    setActivePinia(pinia);
     const wrapper = shallowMount(HistoryExport, {
         propsData: { historyId: FAKE_HISTORY_ID },
         localVue,
+        pinia,
     });
     await flushPromises();
     return wrapper;
@@ -56,7 +67,6 @@ describe("HistoryExport.vue", () => {
     beforeEach(async () => {
         axiosMock = new MockAdapter(axios);
         axiosMock.onGet(REMOTE_FILES_API_ENDPOINT).reply(200, []);
-        axiosMock.onGet(GET_HISTORY_ENDPOINT).reply(200, FAKE_HISTORY);
     });
 
     afterEach(() => {
diff --git a/client/src/components/History/Export/HistoryExport.vue b/client/src/components/History/Export/HistoryExport.vue
index 850a034eb5d1..dec7f85b4bde 100644
--- a/client/src/components/History/Export/HistoryExport.vue
+++ b/client/src/components/History/Export/HistoryExport.vue
@@ -6,7 +6,6 @@ import ExportRecordDetails from "components/Common/ExportRecordDetails.vue";
 import ExportRecordTable from "components/Common/ExportRecordTable.vue";
 import ExportOptions from "./ExportOptions.vue";
 import ExportForm from "components/Common/ExportForm.vue";
-import { getHistoryById } from "@/store/historyStore/model/queries";
 import { getExportRecords, exportToFileSource, reimportHistoryFromRecord } from "./services";
 import { useTaskMonitor } from "composables/taskMonitor";
 import { useFileSources } from "composables/fileSources";
@@ -17,6 +16,7 @@ import { absPath } from "@/utils/redirect";
 import { faFileExport } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
+import { useHistoryStore } from "@/stores/historyStore";
 
 const {
     isRunning: isExportTaskRunning,
@@ -47,9 +47,6 @@ library.add(faFileExport);
 
 const POLLING_DELAY = 3000;
 
-const history = ref(null);
-const isLoadingHistory = ref(true);
-
 const exportParams = reactive(DEFAULT_EXPORT_PARAMS);
 const isLoadingRecords = ref(true);
 const exportRecords = ref(null);
@@ -71,16 +68,21 @@ const availableRecordsMessage = computed(() =>
         ? "Loading export records..."
         : "This history has no export records yet. You can choose one of the export options above."
 );
+
+const historyStore = useHistoryStore();
+
+const history = computed(() => {
+    const history = historyStore.getHistoryById(props.historyId);
+    console.log("HISTORY", history);
+    return history;
+});
+
 const errorMessage = ref(null);
 const actionMessage = ref(null);
 const actionMessageVariant = ref(null);
 
 onMounted(async () => {
     updateExports();
-    //TODO: replace direct query with useHistoriesStore in 23.1
-    isLoadingHistory.value = true;
-    history.value = await getHistoryById(props.historyId);
-    isLoadingHistory.value = false;
 });
 
 watch(isExportTaskRunning, (newValue, oldValue) => {
@@ -174,7 +176,7 @@ function updateExportParams(newParams) {
         <font-awesome-icon icon="file-export" size="2x" class="text-primary float-left mr-2" />
         <h1 class="h-lg">
             Export
-            <loading-span v-if="isLoadingHistory" spinner-only />
+            <loading-span v-if="!history" spinner-only />
             <b v-else id="history-name">{{ historyName }}</b>
         </h1>
 

From e93729f331123a7d9db23585cfc410ef5b50cd80 Mon Sep 17 00:00:00 2001
From: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
Date: Mon, 15 May 2023 11:29:27 +0200
Subject: [PATCH 78/78] fix computed getter mock in HistoryExport test

---
 client/package.json                           |  4 +--
 .../History/Export/HistoryExport.test.ts      | 18 ++++++-----
 client/yarn.lock                              | 32 +++++++++----------
 3 files changed, 28 insertions(+), 26 deletions(-)

diff --git a/client/package.json b/client/package.json
index 5c5128c94017..cf5589f5c672 100644
--- a/client/package.json
+++ b/client/package.json
@@ -34,7 +34,6 @@
     "@handsontable/vue": "^2.0.0",
     "@hirez_io/observer-spy": "^2.1.2",
     "@johmun/vue-tags-input": "^2.1.0",
-    "@pinia/testing": "^0.0.14",
     "@popperjs/core": "^2.11.5",
     "@sentry/browser": "^6.17.4",
     "@vueuse/core": "^9.10.0",
@@ -77,7 +76,7 @@
     "object-hash": "^3.0.0",
     "openapi-typescript": "^6.1.0",
     "openapi-typescript-fetch": "^1.1.3",
-    "pinia": "^2.0.23",
+    "pinia": "^2.0.36",
     "pinia-plugin-persistedstate": "^2.4.0",
     "popper.js": "^1.16.1",
     "pretty-bytes": "^6.0.0",
@@ -140,6 +139,7 @@
     "@babel/preset-env": "^7.20.2",
     "@babel/preset-typescript": "^7.18.6",
     "@cerner/duplicate-package-checker-webpack-plugin": "^2.3.0",
+    "@pinia/testing": "0.1.0",
     "@testing-library/jest-dom": "^5.16.4",
     "@types/d3": "^7.4.0",
     "@types/jquery": "^3.5.16",
diff --git a/client/src/components/History/Export/HistoryExport.test.ts b/client/src/components/History/Export/HistoryExport.test.ts
index bf6bedcb8851..01cbcf99778a 100644
--- a/client/src/components/History/Export/HistoryExport.test.ts
+++ b/client/src/components/History/Export/HistoryExport.test.ts
@@ -13,6 +13,7 @@ import HistoryExport from "./HistoryExport.vue";
 import { getExportRecords } from "./services";
 import { setActivePinia } from "pinia";
 import { createTestingPinia } from "@pinia/testing";
+import { useHistoryStore, type HistorySummary } from "@/stores/historyStore";
 
 const localVue = getLocalVue(true);
 
@@ -42,16 +43,17 @@ const REMOTE_FILES_API_RESPONSE: FilesSourcePluginList = [
     },
 ];
 
-const pinia = createTestingPinia({
-    initialState: {
-        historyStore: {
-            getHistoryById: (historyId: string) => FAKE_HISTORY,
-        },
-    },
-});
-
 async function mountHistoryExport() {
+    const pinia = createTestingPinia();
     setActivePinia(pinia);
+    const historyStore = useHistoryStore(pinia);
+
+    // the mocking method described in the pinia docs does not work in vue2
+    // this is a work-around
+    jest.spyOn(historyStore, "getHistoryById").mockImplementation(
+        (_history_id: string) => FAKE_HISTORY as HistorySummary
+    );
+
     const wrapper = shallowMount(HistoryExport, {
         propsData: { historyId: FAKE_HISTORY_ID },
         localVue,
diff --git a/client/yarn.lock b/client/yarn.lock
index bfadc91b6d9b..95f643a18932 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -1843,10 +1843,10 @@
     consola "^2.15.0"
     node-fetch "^2.6.7"
 
-"@pinia/testing@^0.0.14":
-  version "0.0.14"
-  resolved "https://registry.yarnpkg.com/@pinia/testing/-/testing-0.0.14.tgz#774791df360a1949c9ea2d8665de35d5a0200251"
-  integrity sha512-ZmZwVNd/NnKYLIfjfuKl0zlJ3UdiXFpsHzSlL6wCeezSlyrqGMxsIQKv0J6fleu38gyCNTPBEipfxrt8V4+VIg==
+"@pinia/testing@0.1.0":
+  version "0.1.0"
+  resolved "https://registry.yarnpkg.com/@pinia/testing/-/testing-0.1.0.tgz#35a76c573aae9f2c43ea2aa0b567de4a8877fb6a"
+  integrity sha512-6lcP6QvQNrFtjslppFjfnpiyRnEKrwgro/TjujLlHI8HwWbdfHfMU4BpciuLLLuuSIENIH9zrevl+eAvmUgh7A==
   dependencies:
     vue-demi "*"
 
@@ -2630,10 +2630,10 @@
   optionalDependencies:
     prettier "^1.18.2 || ^2.0.0"
 
-"@vue/devtools-api@^6.4.5":
-  version "6.4.5"
-  resolved "https://registry.yarnpkg.com/@vue/devtools-api/-/devtools-api-6.4.5.tgz#d54e844c1adbb1e677c81c665ecef1a2b4bb8380"
-  integrity sha512-JD5fcdIuFxU4fQyXUu3w2KpAJHzTVdN+p4iOX2lMWSHMOoQdMAcpFLZzm9Z/2nmsoZ1a96QEhZ26e50xLBsgOQ==
+"@vue/devtools-api@^6.5.0":
+  version "6.5.0"
+  resolved "https://registry.yarnpkg.com/@vue/devtools-api/-/devtools-api-6.5.0.tgz#98b99425edee70b4c992692628fa1ea2c1e57d07"
+  integrity sha512-o9KfBeaBmCKl10usN4crU53fYtC1r7jJwdGKjPT24t348rHxgfpZ0xL3Xm/gLUYnc0oTp8LAmrxOeLyu6tbk2Q==
 
 "@vue/test-utils@^1.3.4":
   version "1.3.4"
@@ -8826,12 +8826,12 @@ pinia-plugin-persistedstate@^2.4.0:
   resolved "https://registry.yarnpkg.com/pinia-plugin-persistedstate/-/pinia-plugin-persistedstate-2.4.0.tgz#fda569b3c397517a0cf8aba83a628283767da620"
   integrity sha512-bQcpv47jk3ISl+InuJWsFaS/K7pRZ97kfoD2WCf/suhnlLy48k3BnFM2tI6YZ1xMsDaPv4yOsaPuPAUuSmEO2Q==
 
-pinia@^2.0.23:
-  version "2.0.25"
-  resolved "https://registry.yarnpkg.com/pinia/-/pinia-2.0.25.tgz#1e9d50ab54d106c8fcb39090293d780b3b8152b6"
-  integrity sha512-3reAkjJ6bW2D5hZKRMS0c9rUbHVlsVyZd037xO0PJr2AuF/09RRSBnFLlJgmHF4Jx6dEoW/jZBOHTushY7IMlw==
+pinia@^2.0.36:
+  version "2.0.36"
+  resolved "https://registry.yarnpkg.com/pinia/-/pinia-2.0.36.tgz#65130f3b94cc7fe25156308634010fab893dff24"
+  integrity sha512-4UKApwjlmJH+VuHKgA+zQMddcCb3ezYnyewQ9NVrsDqZ/j9dMv5+rh+1r48whKNdpFkZAWVxhBp5ewYaYX9JcQ==
   dependencies:
-    "@vue/devtools-api" "^6.4.5"
+    "@vue/devtools-api" "^6.5.0"
     vue-demi "*"
 
 pinkie-promise@^2.0.0:
@@ -11133,9 +11133,9 @@ vinyl@^2.0.0:
     replace-ext "^1.0.0"
 
 vue-demi@*:
-  version "0.13.11"
-  resolved "https://registry.yarnpkg.com/vue-demi/-/vue-demi-0.13.11.tgz#7d90369bdae8974d87b1973564ad390182410d99"
-  integrity sha512-IR8HoEEGM65YY3ZJYAjMlKygDQn25D5ajNFNoKh9RSDMQtlzCxtfQjdQgv9jjK+m3377SsJXY8ysq8kLCZL25A==
+  version "0.14.1"
+  resolved "https://registry.yarnpkg.com/vue-demi/-/vue-demi-0.14.1.tgz#1ed9af03a27642762bfed83d8750805302d0398d"
+  integrity sha512-rt+yuCtXvscYot9SQQj3WKZJVSriPNqVkpVBNEHPzSgBv7QIYzsS410VqVgvx8f9AAPgjg+XPKvmV3vOqqkJQQ==
 
 vue-eslint-parser@^9.0.1:
   version "9.0.3"