From 4db9dc48784a8dbf90aa70fe30b195937ad9e314 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Wed, 22 May 2024 15:03:49 -0700
Subject: [PATCH 01/46] tighten the axt format sniffer

e.g. it would incorrectly sniff chain as axt since the comment line starts with "##matrix=axtChain"
---
 lib/galaxy/datatypes/sequence.py | 35 ++++++++++++++++----------------
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index c88abfcde5cd..4e4982bb07a4 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -1206,25 +1206,24 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> Axt().sniff( fname )
         False
         """
-        headers = get_headers(file_prefix, None)
-        if len(headers) < 4:
+        headers = get_headers(file_prefix, None, count=4, comment_designator="#")
+        if not (
+            len(headers) == 4
+            and len(headers[0]) == 9
+            and headers[0][0].isdigit()
+            and headers[0][2].isdigit()
+            and headers[0][3].isdigit()
+            and headers[0][5].isdigit()
+            and headers[0][6].isdigit()
+            and headers[0][7] in data.valid_strand
+            and headers[0][8].isdigit()
+            and len(headers[1]) == 1
+            and len(headers[2]) == 1
+            and headers[3] == []
+        ):
             return False
-        for hdr in headers:
-            if len(hdr) > 0 and hdr[0].startswith("##matrix=axt"):
-                return True
-            if len(hdr) > 0 and not hdr[0].startswith("#"):
-                if len(hdr) != 9:
-                    return False
-                try:
-                    for _ in (hdr[0], hdr[2], hdr[3], hdr[5], hdr[6], hdr[8]):
-                        int(_)
-                except ValueError:
-                    return False
-                if hdr[7] not in data.valid_strand:
-                    return False
-                else:
-                    return True
-        return False
+        else:
+            return True
 
 
 @build_sniff_from_prefix

From 9ed4eda4b09a8f9fc626bb1ddcaa41ebf3885beb Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 23 May 2024 11:45:11 -0700
Subject: [PATCH 02/46] add unit test to sniffer, minor improvements

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample |  2 +-
 lib/galaxy/datatypes/sequence.py                   |  9 +++++++--
 lib/galaxy/datatypes/test/2.chain                  | 10 ++++++++++
 3 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 lib/galaxy/datatypes/test/2.chain

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 6ab652435950..f0f96237e80b 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -32,7 +32,7 @@
     <datatype extension="gfa2" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa2" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
+    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="A pairwise alignment format." description_url="https://genome.ucsc.edu/goldenPath/help/axt.html"/>
     <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
       <converter file="bam_to_bai.xml" target_datatype="bai"/>
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 4e4982bb07a4..3aae50344d3e 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -1205,10 +1205,13 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> fname = get_test_fname( 'alignment.lav' )
         >>> Axt().sniff( fname )
         False
+        >>> fname = get_test_fname( '2.chain' )
+        >>> Axt().sniff( fname )
+        False
         """
         headers = get_headers(file_prefix, None, count=4, comment_designator="#")
         if not (
-            len(headers) == 4
+            len(headers) >= 3
             and len(headers[0]) == 9
             and headers[0][0].isdigit()
             and headers[0][2].isdigit()
@@ -1219,9 +1222,11 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             and headers[0][8].isdigit()
             and len(headers[1]) == 1
             and len(headers[2]) == 1
-            and headers[3] == []
         ):
             return False
+        # the optional fourth non-comment line has to be empty
+        if len(headers) == 4 and not headers[3] == []:
+            return False
         else:
             return True
 
diff --git a/lib/galaxy/datatypes/test/2.chain b/lib/galaxy/datatypes/test/2.chain
new file mode 100644
index 000000000000..822a4ff7b052
--- /dev/null
+++ b/lib/galaxy/datatypes/test/2.chain
@@ -0,0 +1,10 @@
+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+##gapPenalties=axtChain O=400 E=30
+chain 67224 chr22 50818468 + 26560645 26561468 chr19 61431566 - 54838449 54839272 1
+823
+
+chain 48985 chr22 50818468 + 26560497 26561116 chr19 61431566 + 29160089 29160708 2
+619
+
+chain 46902 chr22 50818468 + 19792341 19793000 chr19 61431566 + 59180700 59181359 3
+659

From ce801e7d8ecdc707d574231772998b74b57b5082 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Thu, 23 May 2024 20:51:26 +0200
Subject: [PATCH 03/46] tighten more!

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/datatypes/sequence.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 3aae50344d3e..6bf58bacf4b0 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -1213,7 +1213,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         if not (
             len(headers) >= 3
             and len(headers[0]) == 9
-            and headers[0][0].isdigit()
+            and headers[0][0] == "0"
             and headers[0][2].isdigit()
             and headers[0][3].isdigit()
             and headers[0][5].isdigit()

From 6ac51e5a9b5d8fb8265770349b181149f267bdc2 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 23 May 2024 11:53:55 -0700
Subject: [PATCH 04/46] switch from isdigit to isdecimal

---
 lib/galaxy/datatypes/sequence.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 6bf58bacf4b0..911a1a2db31a 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -1214,12 +1214,12 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             len(headers) >= 3
             and len(headers[0]) == 9
             and headers[0][0] == "0"
-            and headers[0][2].isdigit()
-            and headers[0][3].isdigit()
-            and headers[0][5].isdigit()
-            and headers[0][6].isdigit()
+            and headers[0][2].isdecimal()
+            and headers[0][3].isdecimal()
+            and headers[0][5].isdecimal()
+            and headers[0][6].isdecimal()
             and headers[0][7] in data.valid_strand
-            and headers[0][8].isdigit()
+            and headers[0][8].isdecimal()
             and len(headers[1]) == 1
             and len(headers[2]) == 1
         ):

From 7819c9a3e9d8964d5e33a21b95e52de339cbae69 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Fri, 24 May 2024 10:14:49 -0700
Subject: [PATCH 05/46] switch to isdecimal

---
 lib/galaxy/datatypes/chain.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/datatypes/chain.py b/lib/galaxy/datatypes/chain.py
index acf451ce85c8..56e3b14e0e6f 100644
--- a/lib/galaxy/datatypes/chain.py
+++ b/lib/galaxy/datatypes/chain.py
@@ -103,9 +103,9 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
                         len(tokens) in [12, 13]
                         and tokens[4] in self.strands
                         and tokens[9] in self.strands
-                        and tokens[3].isdigit()
-                        and tokens[5].isdigit()
-                        and tokens[6].isdigit()
+                        and tokens[3].isdecimal()
+                        and tokens[5].isdecimal()
+                        and tokens[6].isdecimal()
                     ):
                         return False
                     prior_token_len = 0
@@ -118,7 +118,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
                             return False
                         if len(tokens) not in [1, 3]:
                             return False
-                        if not all(token.isdigit() for token in tokens):
+                        if not all(token.isdecimal() for token in tokens):
                             return False
                         prior_token_len = len(tokens)
                     if prior_token_len == 1:
@@ -167,7 +167,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             if line:  # first non-empty line
                 if line.startswith("net"):
                     tokens = line.split()
-                    if not (len(tokens) == 3 and tokens[2].isdigit()):
+                    if not (len(tokens) == 3 and tokens[2].isdecimal()):
                         return False
                     for line in fh:
                         if line[0] != " ":  # children are indented one space
@@ -180,11 +180,11 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
                             len(tokens) >= 7  # seven fixed fields
                             and len(tokens) <= 41  # plus seventeen optional name/value pairs
                             and tokens[0] in allowed_classes
-                            and tokens[1].isdigit()
-                            and tokens[2].isdigit()
+                            and tokens[1].isdecimal()
+                            and tokens[2].isdecimal()
                             and tokens[4] in strands
-                            and tokens[5].isdigit()
-                            and tokens[6].isdigit()
+                            and tokens[5].isdecimal()
+                            and tokens[6].isdecimal()
                         ):
                             return False
                         else:

From cae34c843a983219e45c10ec98aef293a8176ef3 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Fri, 24 May 2024 10:50:47 -0700
Subject: [PATCH 06/46] refactor chain and ucsc.net sniffing

properly ignore comments
do not read the dataset unbounded, I think we have enough info from the headers and the first data line
---
 lib/galaxy/datatypes/chain.py | 110 +++++++++++++---------------------
 1 file changed, 42 insertions(+), 68 deletions(-)

diff --git a/lib/galaxy/datatypes/chain.py b/lib/galaxy/datatypes/chain.py
index 56e3b14e0e6f..40fd847d4454 100644
--- a/lib/galaxy/datatypes/chain.py
+++ b/lib/galaxy/datatypes/chain.py
@@ -6,10 +6,7 @@
 
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.protocols import DatasetProtocol
-from galaxy.datatypes.sniff import (
-    build_sniff_from_prefix,
-    FilePrefix,
-)
+from galaxy.datatypes.sniff import build_sniff_from_prefix, FilePrefix, get_headers
 from galaxy.util import (
     commaify,
     compression_utils,
@@ -91,41 +88,31 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> fname = get_test_fname( '1.chain' )
         >>> Chain().sniff( fname )
         True
+        >>> fname = get_test_fname( '2.chain' )
+        >>> Chain().sniff( fname )
+        True
         >>>
         """
-        fh = file_prefix.string_io()
-        for line in fh:
-            line = line.strip()
-            if line:  # first non-empty line
-                if line.startswith("chain"):
-                    tokens = line.split()
-                    if not (
-                        len(tokens) in [12, 13]
-                        and tokens[4] in self.strands
-                        and tokens[9] in self.strands
-                        and tokens[3].isdecimal()
-                        and tokens[5].isdecimal()
-                        and tokens[6].isdecimal()
-                    ):
-                        return False
-                    prior_token_len = 0
-                    for line in fh:
-                        line = line.strip()
-                        if line == "":
-                            break
-                        tokens = line.split()
-                        if prior_token_len == 1:
-                            return False
-                        if len(tokens) not in [1, 3]:
-                            return False
-                        if not all(token.isdecimal() for token in tokens):
-                            return False
-                        prior_token_len = len(tokens)
-                    if prior_token_len == 1:
-                        return True
-                else:
-                    return False
-        return False
+        headers = get_headers(file_prefix, None, count=2, comment_designator="#")
+        if not (
+            len(headers) == 2
+            and len(headers[0]) in [12, 13]
+            and headers[0][0] == "chain"
+            and headers[0][1].isdecimal()
+            and headers[0][3].isdecimal()
+            and headers[0][4] in self.strands
+            and headers[0][5].isdecimal()
+            and headers[0][6].isdecimal()
+            and headers[0][8].isdecimal()
+            and headers[0][9] in self.strands
+            and headers[0][10].isdecimal()
+            and headers[0][11].isdecimal()
+            and headers[1][0].isdecimal()
+            and len(headers[1]) in [1, 3]
+        ):
+            return False
+        else:
+            return True
 
 
 @build_sniff_from_prefix
@@ -161,34 +148,21 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         allowed_classes = ["fill", "gap"]
         strands = ["+", "-"]
 
-        fh = file_prefix.string_io()
-        for line in fh:
-            line = line.strip()
-            if line:  # first non-empty line
-                if line.startswith("net"):
-                    tokens = line.split()
-                    if not (len(tokens) == 3 and tokens[2].isdecimal()):
-                        return False
-                    for line in fh:
-                        if line[0] != " ":  # children are indented one space
-                            return False
-                        line = line.strip()
-                        if line == "":
-                            break
-                        tokens = line.split()
-                        if not (
-                            len(tokens) >= 7  # seven fixed fields
-                            and len(tokens) <= 41  # plus seventeen optional name/value pairs
-                            and tokens[0] in allowed_classes
-                            and tokens[1].isdecimal()
-                            and tokens[2].isdecimal()
-                            and tokens[4] in strands
-                            and tokens[5].isdecimal()
-                            and tokens[6].isdecimal()
-                        ):
-                            return False
-                        else:
-                            return True
-                else:
-                    return False
-        return False
+        headers = get_headers(file_prefix, None, count=2, comment_designator="#")
+        if not (
+            len(headers) == 2
+            and len(headers[0]) == 3
+            and headers[0][0] == "net"
+            and headers[0][2].isdecimal()
+            and len(headers[1]) >= 7  # seven fixed fields
+            and len(headers[1]) <= 41  # plus seventeen optional name/value pairs
+            and headers[1][0] in allowed_classes
+            and headers[1][1].isdecimal()
+            and headers[1][2].isdecimal()
+            and headers[1][4] in strands
+            and headers[1][5].isdecimal()
+            and headers[1][6].isdecimal()
+        ):
+            return False
+        else:
+            return True

From 706ae5fab1b839b549d64c12259a6863c3f8cde8 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Fri, 24 May 2024 14:17:57 -0700
Subject: [PATCH 07/46] sorty sort

---
 lib/galaxy/datatypes/chain.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/chain.py b/lib/galaxy/datatypes/chain.py
index 40fd847d4454..4e853865d042 100644
--- a/lib/galaxy/datatypes/chain.py
+++ b/lib/galaxy/datatypes/chain.py
@@ -6,7 +6,11 @@
 
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.protocols import DatasetProtocol
-from galaxy.datatypes.sniff import build_sniff_from_prefix, FilePrefix, get_headers
+from galaxy.datatypes.sniff import (
+    build_sniff_from_prefix,
+    FilePrefix,
+    get_headers,
+)
 from galaxy.util import (
     commaify,
     compression_utils,

From cdbd5e32ce83021e0f7812362cbc21416bc1cf41 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:05:16 +0200
Subject: [PATCH 08/46] Drop backend restrictions to switch to immutable
 histories

---
 lib/galaxy/webapps/base/webapp.py                | 4 ++--
 lib/galaxy/webapps/galaxy/controllers/history.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 0cd502606613..7874de2ef77b 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -914,7 +914,7 @@ def get_history(self, create=False, most_recent=False):
         return history
 
     def set_history(self, history):
-        if history and not history.deleted:
+        if history:
             self.galaxy_session.current_history = history
         self.sa_session.add(self.galaxy_session)
         with transaction(self.sa_session):
@@ -932,7 +932,7 @@ def get_or_create_default_history(self):
 
         # Just return the current history if one exists and is not deleted.
         history = self.galaxy_session.current_history
-        if history and not history.deleted:
+        if history:
             return history
 
         # Look for an existing history that has the default name, is not
diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
index 3db60f29ad2a..a50a7b35c52f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -325,7 +325,7 @@ def history_data(self, trans, history):
     def set_as_current(self, trans, id, **kwargs):
         """Change the current user's current history to one with `id`."""
         try:
-            history = self.history_manager.get_mutable(self.decode_id(id), trans.user, current_history=trans.history)
+            history = self.history_manager.get_owned(self.decode_id(id), trans.user, current_history=trans.history)
             trans.set_history(history)
             return self.history_data(trans, history)
         except exceptions.MessageException as msg_exc:

From ead71fd8b4be7e1001f83d069221f781edbd6d24 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:15:42 +0200
Subject: [PATCH 09/46] Move immutability restriction check from HistoryView to
 HistoryPanel

---
 .../History/CurrentHistory/HistoryPanel.vue    | 14 +++++++++++---
 client/src/components/History/HistoryView.vue  | 18 ++----------------
 2 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryPanel.vue b/client/src/components/History/CurrentHistory/HistoryPanel.vue
index 759efea9a90b..8268153099f3 100644
--- a/client/src/components/History/CurrentHistory/HistoryPanel.vue
+++ b/client/src/components/History/CurrentHistory/HistoryPanel.vue
@@ -3,7 +3,7 @@ import { BAlert } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, onMounted, type Ref, ref, set as VueSet, unref, watch } from "vue";
 
-import type { HistoryItemSummary, HistorySummaryExtended } from "@/api";
+import { type HistoryItemSummary, type HistorySummaryExtended, userOwnsHistory } from "@/api";
 import { copyDataset } from "@/api/datasets";
 import ExpandedItems from "@/components/History/Content/ExpandedItems";
 import SelectedItems from "@/components/History/Content/SelectedItems";
@@ -15,6 +15,7 @@ import { startWatchingHistory } from "@/store/historyStore/model/watchHistory";
 import { useEventStore } from "@/stores/eventStore";
 import { useHistoryItemsStore } from "@/stores/historyItemsStore";
 import { useHistoryStore } from "@/stores/historyStore";
+import { useUserStore } from "@/stores/userStore";
 import { type Alias, getOperatorForAlias } from "@/utils/filtering";
 import { setDrag } from "@/utils/setDrag";
 
@@ -49,7 +50,6 @@ interface Props {
     listOffset?: number;
     history: HistorySummaryExtended;
     filter?: string;
-    canEditHistory?: boolean;
     filterable?: boolean;
     isMultiViewItem?: boolean;
 }
@@ -59,7 +59,6 @@ type ContentItemRef = Record<string, Ref<InstanceType<typeof ContentItem> | null
 const props = withDefaults(defineProps<Props>(), {
     listOffset: 0,
     filter: "",
-    canEditHistory: true,
     filterable: false,
     isMultiViewItem: false,
 });
@@ -90,6 +89,14 @@ const { lastCheckedTime, totalMatchesCount, isWatching } = storeToRefs(useHistor
 
 const historyStore = useHistoryStore();
 const historyItemsStore = useHistoryItemsStore();
+const { currentUser } = storeToRefs(useUserStore());
+
+const currentUserOwnsHistory = computed(() => {
+    return userOwnsHistory(currentUser.value, props.history);
+});
+const canEditHistory = computed(() => {
+    return currentUserOwnsHistory.value && !props.history.deleted && !props.history.archived;
+});
 
 const historyUpdateTime = computed(() => {
     return props.history.update_time;
@@ -542,6 +549,7 @@ function setItemDragstart(
                         :is-watching="isWatching"
                         :last-checked="lastCheckedTime"
                         :show-controls="canEditHistory"
+                        :owned-by-current-user="userOwnsHistory(currentUser, history)"
                         :filter-text.sync="filterText"
                         :hide-reload="isMultiViewItem"
                         @reloadContents="reloadContents" />
diff --git a/client/src/components/History/HistoryView.vue b/client/src/components/History/HistoryView.vue
index e185e7517147..23ccb4f62202 100644
--- a/client/src/components/History/HistoryView.vue
+++ b/client/src/components/History/HistoryView.vue
@@ -35,12 +35,7 @@
             :selected-collections.sync="selectedCollections"
             :show-controls="false"
             @view-collection="onViewCollection" />
-        <HistoryPanel
-            v-else
-            :history="history"
-            :can-edit-history="canEditHistory"
-            filterable
-            @view-collection="onViewCollection" />
+        <HistoryPanel v-else :history="history" filterable @view-collection="onViewCollection" />
 
         <CopyModal id="copy-history-modal" :history="history" @ok="copyOkay" />
     </div>
@@ -87,23 +82,14 @@ export default {
             return this.currentHistory?.id == this.history?.id;
         },
         isSetAsCurrentDisabled() {
-            return this.isCurrentHistory || this.history.archived || this.history.purged;
+            return this.isCurrentHistory;
         },
         setAsCurrentTitle() {
             if (this.isCurrentHistory) {
                 return "This history is already your current history.";
             }
-            if (this.history.archived) {
-                return "This history has been archived and cannot be set as your current history. Unarchive it first.";
-            }
-            if (this.history.purged) {
-                return "This history has been purged and cannot be set as your current history.";
-            }
             return "Switch to this history";
         },
-        canEditHistory() {
-            return this.userOwnsHistory && !this.history.archived && !this.history.purged;
-        },
         showHistoryArchived() {
             return this.history.archived && this.userOwnsHistory;
         },

From ade613ab5ded00c7651f19c42c346803b4693a52 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:18:11 +0200
Subject: [PATCH 10/46] Display history status in Panel

---
 .../CurrentHistory/HistoryMessages.vue        | 23 +++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryMessages.vue b/client/src/components/History/CurrentHistory/HistoryMessages.vue
index 91e06beb75fc..3d97f80dd24a 100644
--- a/client/src/components/History/CurrentHistory/HistoryMessages.vue
+++ b/client/src/components/History/CurrentHistory/HistoryMessages.vue
@@ -1,10 +1,15 @@
 <script setup lang="ts">
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faArchive, faBurn, faTrash } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
 import type { HistorySummary } from "@/api";
 import localize from "@/utils/localization";
 
+library.add(faArchive, faBurn, faTrash);
+
 interface Props {
     history: HistorySummary;
 }
@@ -14,14 +19,24 @@ const props = defineProps<Props>();
 const userOverQuota = ref(false);
 
 const hasMessages = computed(() => {
-    return userOverQuota.value || props.history.deleted;
+    return userOverQuota.value || props.history.deleted || props.history.archived;
 });
 </script>
 
 <template>
-    <div v-if="hasMessages" class="mx-3 my-2">
-        <BAlert :show="history.deleted" variant="warning">
-            {{ localize("This history has been deleted") }}
+    <div v-if="hasMessages" class="mx-3 mt-2">
+        <BAlert v-if="history.purged" :show="history.purged" variant="warning">
+            <FontAwesomeIcon :icon="faBurn" fixed-width />
+            {{ localize("History has been purged") }}
+        </BAlert>
+        <BAlert v-else-if="history.deleted" :show="history.deleted" variant="warning">
+            <FontAwesomeIcon :icon="faTrash" fixed-width />
+            {{ localize("History has been deleted") }}
+        </BAlert>
+
+        <BAlert :show="history.archived" variant="warning">
+            <FontAwesomeIcon :icon="faArchive" fixed-width />
+            {{ localize("History has been archived") }}
         </BAlert>
 
         <BAlert :show="userOverQuota" variant="warning">

From 0cd4ef17c62f51aa62ae1719d2bb81cdd65994a8 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:19:01 +0200
Subject: [PATCH 11/46] Add button to set archived histories as current

---
 .../History/Archiving/ArchivedHistoryCard.vue  | 18 ++++++++++++++++--
 .../History/Archiving/HistoryArchive.vue       |  5 +++++
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/client/src/components/History/Archiving/ArchivedHistoryCard.vue b/client/src/components/History/Archiving/ArchivedHistoryCard.vue
index 3da5cf613ef6..15ca422fce17 100644
--- a/client/src/components/History/Archiving/ArchivedHistoryCard.vue
+++ b/client/src/components/History/Archiving/ArchivedHistoryCard.vue
@@ -1,6 +1,6 @@
 <script setup lang="ts">
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faCopy, faEye, faUndo } from "@fortawesome/free-solid-svg-icons";
+import { faCopy, faExchangeAlt, faEye, faUndo } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BBadge, BButton, BButtonGroup } from "bootstrap-vue";
 import { computed } from "vue";
@@ -23,16 +23,21 @@ const canImportCopy = computed(() => props.history.export_record_data?.target_ur
 
 const emit = defineEmits<{
     (e: "onView", history: ArchivedHistorySummary): void;
+    (e: "onSwitch", history: ArchivedHistorySummary): void;
     (e: "onRestore", history: ArchivedHistorySummary): void;
     (e: "onImportCopy", history: ArchivedHistorySummary): void;
 }>();
 
-library.add(faUndo, faCopy, faEye);
+library.add(faExchangeAlt, faUndo, faCopy, faEye);
 
 function onViewHistoryInCenterPanel() {
     emit("onView", props.history);
 }
 
+function onSetAsCurrentHistory() {
+    emit("onSwitch", props.history);
+}
+
 async function onRestoreHistory() {
     emit("onRestore", props.history);
 }
@@ -84,6 +89,15 @@ async function onImportCopy() {
                     <FontAwesomeIcon :icon="faEye" size="lg" />
                     View
                 </BButton>
+                <BButton
+                    v-b-tooltip
+                    :title="localize('Set as current history')"
+                    variant="link"
+                    class="p-0 px-1"
+                    @click.stop="onSetAsCurrentHistory">
+                    <FontAwesomeIcon :icon="faExchangeAlt" size="lg" />
+                    Switch
+                </BButton>
                 <BButton
                     v-b-tooltip
                     :title="localize('Unarchive this history and move it back to your active histories')"
diff --git a/client/src/components/History/Archiving/HistoryArchive.vue b/client/src/components/History/Archiving/HistoryArchive.vue
index 9e20f99e8fbe..24c3cd4ed417 100644
--- a/client/src/components/History/Archiving/HistoryArchive.vue
+++ b/client/src/components/History/Archiving/HistoryArchive.vue
@@ -66,6 +66,10 @@ function onViewHistoryInCenterPanel(history: ArchivedHistorySummary) {
     router.push(`/histories/view?id=${history.id}`);
 }
 
+function onSetAsCurrentHistory(history: ArchivedHistorySummary) {
+    historyStore.setCurrentHistory(history.id);
+}
+
 async function onRestoreHistory(history: ArchivedHistorySummary) {
     const confirmTitle = localize(`Unarchive '${history.name}'?`);
     const confirmMessage =
@@ -145,6 +149,7 @@ async function onImportCopy(history: ArchivedHistorySummary) {
                     <ArchivedHistoryCard
                         :history="history"
                         @onView="onViewHistoryInCenterPanel"
+                        @onSwitch="onSetAsCurrentHistory"
                         @onRestore="onRestoreHistory"
                         @onImportCopy="onImportCopy" />
                 </BListGroupItem>

From 0f8d412843d1511de43346a3efa9f0407743213e Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:25:58 +0200
Subject: [PATCH 12/46] Drop redundant history state info in HistoryView

The state will be displayed in all history panels
---
 client/src/components/History/HistoryView.vue | 20 -------------------
 1 file changed, 20 deletions(-)

diff --git a/client/src/components/History/HistoryView.vue b/client/src/components/History/HistoryView.vue
index 23ccb4f62202..3a39909559bb 100644
--- a/client/src/components/History/HistoryView.vue
+++ b/client/src/components/History/HistoryView.vue
@@ -1,9 +1,5 @@
 <template>
     <div v-if="currentUser && history" class="d-flex flex-column h-100">
-        <b-alert v-if="showHistoryStateInfo" variant="info" show data-description="history state info">
-            {{ historyStateInfoMessage }}
-        </b-alert>
-
         <div class="flex-row flex-grow-0 pb-3">
             <b-button
                 v-if="userOwnsHistory"
@@ -90,22 +86,6 @@ export default {
             }
             return "Switch to this history";
         },
-        showHistoryArchived() {
-            return this.history.archived && this.userOwnsHistory;
-        },
-        showHistoryStateInfo() {
-            return this.showHistoryArchived || this.history.purged;
-        },
-        historyStateInfoMessage() {
-            if (this.showHistoryArchived && this.history.purged) {
-                return "This history has been archived and purged.";
-            } else if (this.showHistoryArchived) {
-                return "This history has been archived.";
-            } else if (this.history.purged) {
-                return "This history has been purged.";
-            }
-            return "";
-        },
         canImportHistory() {
             return !this.userOwnsHistory && !this.history.purged;
         },

From c3ab81876891413bb4de37a7fb42bbf828db3fad Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:28:24 +0200
Subject: [PATCH 13/46] Allow to set any owned history as current

---
 client/src/components/Grid/configs/histories.ts | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/components/Grid/configs/histories.ts b/client/src/components/Grid/configs/histories.ts
index 3a6479b3975e..70a865c21f1e 100644
--- a/client/src/components/Grid/configs/histories.ts
+++ b/client/src/components/Grid/configs/histories.ts
@@ -142,7 +142,6 @@ const fields: FieldArray = [
             {
                 title: "Switch",
                 icon: faExchangeAlt,
-                condition: (data: HistoryEntry) => !data.deleted,
                 handler: (data: HistoryEntry) => {
                     const historyStore = useHistoryStore();
                     historyStore.setCurrentHistory(String(data.id));

From 58fbd25aab9e052d0e78c2f4fb7ea591dabb1d80 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:29:05 +0200
Subject: [PATCH 14/46] Disable collection editing for immutable histories

---
 client/src/api/index.ts                                    | 4 ++++
 .../History/CurrentCollection/CollectionPanel.vue          | 7 ++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/client/src/api/index.ts b/client/src/api/index.ts
index 1b1aa6f66c93..949180cfa817 100644
--- a/client/src/api/index.ts
+++ b/client/src/api/index.ts
@@ -237,6 +237,10 @@ function hasOwner(history: AnyHistory): history is HistorySummaryExtended {
     return "user_id" in history && history.user_id !== null;
 }
 
+export function canMutateHistory(history: AnyHistory): boolean {
+    return !history.purged && !history.archived;
+}
+
 export type DatasetHash = components["schemas"]["DatasetHash"];
 
 export type DatasetTransform = {
diff --git a/client/src/components/History/CurrentCollection/CollectionPanel.vue b/client/src/components/History/CurrentCollection/CollectionPanel.vue
index 9ace9e6ba5d3..0744005e7f90 100644
--- a/client/src/components/History/CurrentCollection/CollectionPanel.vue
+++ b/client/src/components/History/CurrentCollection/CollectionPanel.vue
@@ -4,7 +4,7 @@
 import { computed, ref, watch } from "vue";
 
 import type { CollectionEntry, DCESummary, HistorySummary, SubCollection } from "@/api";
-import { isCollectionElement, isHDCA } from "@/api";
+import { canMutateHistory, isCollectionElement, isHDCA } from "@/api";
 import ExpandedItems from "@/components/History/Content/ExpandedItems";
 import { updateContentFields } from "@/components/History/model/queries";
 import { useCollectionElementsStore } from "@/stores/collectionElementsStore";
@@ -66,6 +66,7 @@ const rootCollection = computed(() => {
     }
 });
 const isRoot = computed(() => dsc.value == rootCollection.value);
+const canEdit = computed(() => isRoot.value && canMutateHistory(props.history));
 
 function updateDsc(collection: any, fields: Object | undefined) {
     updateContentFields(collection, fields).then((response) => {
@@ -124,8 +125,8 @@ watch(
                     :history-name="history.name"
                     :selected-collections="selectedCollections"
                     v-on="$listeners" />
-                <CollectionDetails :dsc="dsc" :writeable="isRoot" @update:dsc="updateDsc(dsc, $event)" />
-                <CollectionOperations v-if="isRoot && showControls" :dsc="dsc" />
+                <CollectionDetails :dsc="dsc" :writeable="canEdit" @update:dsc="updateDsc(dsc, $event)" />
+                <CollectionOperations v-if="canEdit && showControls" :dsc="dsc" />
             </section>
             <section class="position-relative flex-grow-1 scroller">
                 <div>

From fbf7b5d99d73024fd40b0c6847cf4cddabfe57d2 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:31:28 +0200
Subject: [PATCH 15/46] Allow to go to storage overview for immutable histories

And handle the controls visibility to avoid history mutation by deleting datasets, etc.
---
 .../History/CurrentHistory/HistoryCounter.vue          |  4 ++--
 .../Visualizations/HistoriesStorageOverview.vue        |  1 +
 .../Visualizations/HistoryStorageOverview.vue          | 10 ++++++++--
 .../DiskUsage/Visualizations/SelectedItemActions.vue   |  9 +++++----
 4 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryCounter.vue b/client/src/components/History/CurrentHistory/HistoryCounter.vue
index ce02cca585b4..84873949ca8c 100644
--- a/client/src/components/History/CurrentHistory/HistoryCounter.vue
+++ b/client/src/components/History/CurrentHistory/HistoryCounter.vue
@@ -9,7 +9,7 @@ import prettyBytes from "pretty-bytes";
 import { computed, onMounted, ref, toRef } from "vue";
 import { useRouter } from "vue-router/composables";
 
-import type { HistorySummaryExtended } from "@/api";
+import { type HistorySummaryExtended, userOwnsHistory } from "@/api";
 import { HistoryFilters } from "@/components/History/HistoryFilters.js";
 import { useConfig } from "@/composables/config";
 import { useHistoryContentStats } from "@/composables/historyContentStats";
@@ -137,7 +137,7 @@ onMounted(() => {
             variant="link"
             size="sm"
             class="rounded-0 text-decoration-none history-storage-overview-button"
-            :disabled="!showControls"
+            :disabled="!userOwnsHistory(currentUser, props.history)"
             data-description="storage dashboard button"
             @click="onDashboard">
             <FontAwesomeIcon :icon="faDatabase" />
diff --git a/client/src/components/User/DiskUsage/Visualizations/HistoriesStorageOverview.vue b/client/src/components/User/DiskUsage/Visualizations/HistoriesStorageOverview.vue
index 770c274e4740..5c9e98f04201 100644
--- a/client/src/components/User/DiskUsage/Visualizations/HistoriesStorageOverview.vue
+++ b/client/src/components/User/DiskUsage/Visualizations/HistoriesStorageOverview.vue
@@ -196,6 +196,7 @@ async function onPermanentlyDeleteHistory(historyId: string) {
                         item-type="history"
                         :is-recoverable="isRecoverableDataPoint(data)"
                         :is-archived="isArchivedDataPoint(data)"
+                        :can-edit="!isArchivedDataPoint(data)"
                         @set-current-history="onSetCurrentHistory"
                         @view-item="onViewHistory"
                         @undelete-item="onUndeleteHistory"
diff --git a/client/src/components/User/DiskUsage/Visualizations/HistoryStorageOverview.vue b/client/src/components/User/DiskUsage/Visualizations/HistoryStorageOverview.vue
index e6a6dd35431b..d3ca05932077 100644
--- a/client/src/components/User/DiskUsage/Visualizations/HistoryStorageOverview.vue
+++ b/client/src/components/User/DiskUsage/Visualizations/HistoryStorageOverview.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton, BForm, BFormGroup, BFormSelect, BInputGroup } from "bootstrap-vue";
-import { ref } from "vue";
+import { computed, ref } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { useSelectableObjectStores } from "@/composables/useObjectStores";
@@ -27,7 +27,7 @@ import FilterObjectStoreLink from "@/components/Common/FilterObjectStoreLink.vue
 import LoadingSpan from "@/components/LoadingSpan.vue";
 
 const router = useRouter();
-const { getHistoryNameById } = useHistoryStore();
+const { getHistoryNameById, getHistoryById } = useHistoryStore();
 
 interface Props {
     historyId: string;
@@ -53,6 +53,11 @@ const { selectableObjectStores, hasSelectableObjectStores } = useSelectableObjec
 
 const objectStore = ref<string | null>(null);
 
+const canEditHistory = computed(() => {
+    const history = getHistoryById(props.historyId);
+    return (history && !history.purged && !history.archived) ?? false;
+});
+
 function onChangeObjectStore(value: string | null) {
     objectStore.value = value;
     reloadDataFromServer();
@@ -209,6 +214,7 @@ function onUndelete(datasetId: string) {
                         :data="data"
                         item-type="dataset"
                         :is-recoverable="isRecoverableDataPoint(data)"
+                        :can-edit="canEditHistory"
                         @view-item="onViewDataset"
                         @undelete-item="onUndelete"
                         @permanently-delete-item="onPermDelete" />
diff --git a/client/src/components/User/DiskUsage/Visualizations/SelectedItemActions.vue b/client/src/components/User/DiskUsage/Visualizations/SelectedItemActions.vue
index 04b5b02604d3..070001525c0e 100644
--- a/client/src/components/User/DiskUsage/Visualizations/SelectedItemActions.vue
+++ b/client/src/components/User/DiskUsage/Visualizations/SelectedItemActions.vue
@@ -25,12 +25,14 @@ interface SelectedItemActionsProps {
     isRecoverable: boolean;
     itemType: ItemTypes;
     isArchived?: boolean;
+    canEdit?: boolean;
 }
 
 const { currentHistoryId } = useHistoryStore();
 
 const props = withDefaults(defineProps<SelectedItemActionsProps>(), {
     isArchived: false,
+    canEdit: false,
 });
 
 library.add(faArchive, faChartBar, faInfoCircle, faLocationArrow, faTrash, faUndo);
@@ -38,9 +40,7 @@ library.add(faArchive, faChartBar, faInfoCircle, faLocationArrow, faTrash, faUnd
 const label = computed(() => props.data?.label ?? "No data");
 const prettySize = computed(() => bytesToString(props.data?.value ?? 0));
 const viewDetailsIcon = computed(() => (props.itemType === "history" ? "chart-bar" : "info-circle"));
-const canSetAsCurrent = computed(
-    () => props.itemType === "history" && !props.isArchived && props.data.id !== currentHistoryId
-);
+const canSetAsCurrent = computed(() => props.itemType === "history" && props.data.id !== currentHistoryId);
 
 const emit = defineEmits<{
     (e: "set-current-history", historyId: string): void;
@@ -99,7 +99,7 @@ function onPermanentlyDeleteItem() {
                 <FontAwesomeIcon :icon="viewDetailsIcon" />
             </BButton>
             <BButton
-                v-if="isRecoverable"
+                v-if="isRecoverable && canEdit"
                 variant="outline-primary"
                 size="sm"
                 class="mx-2"
@@ -108,6 +108,7 @@ function onPermanentlyDeleteItem() {
                 <FontAwesomeIcon icon="undo" />
             </BButton>
             <BButton
+                v-if="canEdit"
                 variant="outline-danger"
                 size="sm"
                 class="mx-2"

From 9ae4870e5bd01e370a0d844f7374e4e204b084fa Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:32:21 +0200
Subject: [PATCH 16/46] Disable unavailable elements in History menu for
 immutable histories

---
 .../CurrentHistory/HistoryNavigation.vue        | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index e433f5a5738a..7b31df06ecfe 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -30,9 +30,9 @@ import {
     BSpinner,
 } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
-import { ref } from "vue";
+import { computed, ref } from "vue";
 
-import type { HistorySummary } from "@/api";
+import { canMutateHistory, type HistorySummary } from "@/api";
 import { iframeRedirect } from "@/components/plugins/legacyNavigation";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
@@ -80,6 +80,10 @@ const historyStore = useHistoryStore();
 const { isAnonymous } = storeToRefs(userStore);
 const { totalHistoryCount } = storeToRefs(historyStore);
 
+const canEditHistory = computed(() => {
+    return canMutateHistory(props.history);
+});
+
 function onDelete() {
     if (purgeHistory.value) {
         historyStore.deleteHistory(props.history.id, true);
@@ -161,6 +165,7 @@ function userTitle(title: string) {
                     <BDropdownDivider />
 
                     <BDropdownItem
+                        :disabled="!canEditHistory"
                         :title="localize('Resume all Paused Jobs in this History')"
                         @click="iframeRedirect('/history/resume_paused_jobs?current=True')">
                         <FontAwesomeIcon fixed-width :icon="faPlay" class="mr-1" />
@@ -198,7 +203,7 @@ function userTitle(title: string) {
                     </BDropdownItem>
 
                     <BDropdownItem
-                        :disabled="isAnonymous"
+                        :disabled="isAnonymous || history.archived"
                         data-description="archive history"
                         :title="userTitle('Archive this History')"
                         @click="$router.push(`/histories/${history.id}/archive`)">
@@ -225,7 +230,7 @@ function userTitle(title: string) {
                     <BDropdownDivider />
 
                     <BDropdownItem
-                        :disabled="isAnonymous"
+                        :disabled="isAnonymous || !canEditHistory"
                         :title="userTitle('Share or Publish this History')"
                         data-description="share or publish"
                         @click="$router.push(`/histories/sharing?id=${history.id}`)">
@@ -234,7 +239,7 @@ function userTitle(title: string) {
                     </BDropdownItem>
 
                     <BDropdownItem
-                        :disabled="isAnonymous"
+                        :disabled="isAnonymous || !canEditHistory"
                         :title="userTitle('Set who can View or Edit this History')"
                         @click="$router.push(`/histories/permissions?id=${history.id}`)">
                         <FontAwesomeIcon fixed-width :icon="faUserLock" class="mr-1" />
@@ -243,7 +248,7 @@ function userTitle(title: string) {
 
                     <BDropdownItem
                         v-b-modal:history-privacy-modal
-                        :disabled="isAnonymous"
+                        :disabled="isAnonymous || !canEditHistory"
                         :title="userTitle('Make this History Private')">
                         <FontAwesomeIcon fixed-width :icon="faLock" class="mr-1" />
                         <span v-localize>Make Private</span>

From 28015972de33616eff5a0ff0a775026e1247eae5 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 10:50:56 +0200
Subject: [PATCH 17/46] Inform users why some actions for histories might be
 disabled

---
 .../CurrentHistory/HistoryNavigation.vue      | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 7b31df06ecfe..6610ded47c94 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -84,6 +84,18 @@ const canEditHistory = computed(() => {
     return canMutateHistory(props.history);
 });
 
+const historyState = computed(() => {
+    if (props.history.purged) {
+        return "purged";
+    } else if (props.history.deleted) {
+        return "deleted";
+    } else if (props.history.archived) {
+        return "archived";
+    } else {
+        return "active";
+    }
+});
+
 function onDelete() {
     if (purgeHistory.value) {
         historyStore.deleteHistory(props.history.id, true);
@@ -164,6 +176,14 @@ function userTitle(title: string) {
 
                     <BDropdownDivider />
 
+                    <BDropdownText v-if="!canEditHistory">
+                        This history has been <span class="font-weight-bold">{{ historyState }}</span
+                        >.
+                        <span v-localize>Some actions might not be available.</span>
+                    </BDropdownText>
+
+                    <BDropdownDivider v-if="!canEditHistory" />
+
                     <BDropdownItem
                         :disabled="!canEditHistory"
                         :title="localize('Resume all Paused Jobs in this History')"

From 3aa4db55d1b6fb8aa58dd44921138de193d4edcf Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 11:46:29 +0200
Subject: [PATCH 18/46] Avoid running tools on immutable histories

---
 client/src/components/Tool/ToolForm.vue | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index d075ae597d93..33e430d1a1a8 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -3,6 +3,9 @@
         <b-alert :show="messageShow" :variant="messageVariant">
             {{ messageText }}
         </b-alert>
+        <b-alert v-if="!showLoading && !canMutateHistory" show variant="warning">
+            {{ immutableHistoryMessage }}
+        </b-alert>
         <LoadingSpan v-if="showLoading" message="Loading Tool" />
         <div v-if="showEntryPoints">
             <ToolEntryPoints v-for="job in entryPoints" :key="job.id" :job-id="job.id" />
@@ -87,6 +90,7 @@
                 <ButtonSpinner
                     id="execute"
                     title="Run Tool"
+                    :disabled="!canMutateHistory"
                     class="btn-sm"
                     :wait="showExecuting"
                     :tooltip="tooltip"
@@ -96,6 +100,7 @@
                 <ButtonSpinner
                     title="Run Tool"
                     class="mt-3 mb-3"
+                    :disabled="!canMutateHistory"
                     :wait="showExecuting"
                     :tooltip="tooltip"
                     @onClick="onExecute(config, currentHistoryId)" />
@@ -117,6 +122,7 @@ import { useHistoryItemsStore } from "stores/historyItemsStore";
 import { useJobStore } from "stores/jobStore";
 import { refreshContentsWrapper } from "utils/data";
 
+import { canMutateHistory } from "@/api";
 import { useConfigStore } from "@/stores/configurationStore";
 import { useHistoryStore } from "@/stores/historyStore";
 import { useUserStore } from "@/stores/userStore";
@@ -196,11 +202,13 @@ export default {
                 { label: "populate", value: "populate" },
                 { label: "bundle", value: "bundle" },
             ],
+            immutableHistoryMessage:
+                "This history is immutable and you cannot run tools in it. Please switch to a different history.",
         };
     },
     computed: {
         ...mapState(useUserStore, ["currentUser"]),
-        ...mapState(useHistoryStore, ["currentHistoryId"]),
+        ...mapState(useHistoryStore, ["currentHistoryId", "currentHistory"]),
         ...mapState(useHistoryItemsStore, ["lastUpdateTime"]),
         toolName() {
             return this.formConfig.name;
@@ -212,6 +220,9 @@ export default {
             return id.endsWith(version) ? id : `${id}/${version}`;
         },
         tooltip() {
+            if (!this.canMutateHistory) {
+                return this.immutableHistoryMessage;
+            }
             return `Run tool: ${this.formConfig.name} (${this.formConfig.version})`;
         },
         errorContentPretty() {
@@ -234,6 +245,9 @@ export default {
         initialized() {
             return this.formData !== undefined;
         },
+        canMutateHistory() {
+            return this.currentHistory && canMutateHistory(this.currentHistory);
+        },
     },
     watch: {
         currentHistoryId() {

From c3d99740762cd4f96b5f49f942883cba5e2eb0ad Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 12:15:18 +0200
Subject: [PATCH 19/46] Restrict some more options in history menu

---
 .../History/CurrentHistory/HistoryNavigation.vue          | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 6610ded47c94..316e10fe5982 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -202,7 +202,10 @@ function userTitle(title: string) {
                         <span v-localize>Copy this History</span>
                     </BDropdownItem>
 
-                    <BDropdownItem v-b-modal:delete-history-modal :title="localize('Permanently Delete History')">
+                    <BDropdownItem
+                        v-b-modal:delete-history-modal
+                        :disabled="!canEditHistory"
+                        :title="localize('Permanently Delete History')">
                         <FontAwesomeIcon fixed-width :icon="faTrash" class="mr-1" />
                         <span v-localize>Delete this History</span>
                     </BDropdownItem>
@@ -216,6 +219,7 @@ function userTitle(title: string) {
 
                     <BDropdownItem
                         data-description="export to file"
+                        :disabled="history.purged"
                         :title="localize('Export and Download History as a File')"
                         @click="$router.push(`/histories/${history.id}/export`)">
                         <FontAwesomeIcon fixed-width :icon="faFileArchive" class="mr-1" />
@@ -223,7 +227,7 @@ function userTitle(title: string) {
                     </BDropdownItem>
 
                     <BDropdownItem
-                        :disabled="isAnonymous || history.archived"
+                        :disabled="isAnonymous || history.archived || history.purged"
                         data-description="archive history"
                         :title="userTitle('Archive this History')"
                         @click="$router.push(`/histories/${history.id}/archive`)">

From 31e14a9f5862f30d2899d4b4e8231d70a596a6bd Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 16:38:29 +0200
Subject: [PATCH 20/46] Avoid workflow run on immutable histories

---
 .../components/Workflow/Run/WorkflowRun.vue   | 10 ++++++++++
 .../Workflow/Run/WorkflowRunForm.vue          | 19 +++++++++++++++++++
 .../Workflow/Run/WorkflowRunFormSimple.vue    | 15 ++++++++++++++-
 3 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Run/WorkflowRun.vue b/client/src/components/Workflow/Run/WorkflowRun.vue
index cce942b988b4..91b338323ad9 100644
--- a/client/src/components/Workflow/Run/WorkflowRun.vue
+++ b/client/src/components/Workflow/Run/WorkflowRun.vue
@@ -5,6 +5,7 @@ import { computed, onMounted, ref, watch } from "vue";
 import { RouterLink } from "vue-router";
 import { useRouter } from "vue-router/composables";
 
+import { canMutateHistory } from "@/api";
 import { copyWorkflow } from "@/components/Workflow/workflows.services";
 import { useHistoryItemsStore } from "@/stores/historyItemsStore";
 import { useHistoryStore } from "@/stores/historyStore";
@@ -52,6 +53,13 @@ const editorLink = computed(() => `/workflows/edit?id=${props.workflowId}`);
 const historyStatusKey = computed(() => `${currentHistoryId.value}_${lastUpdateTime.value}`);
 const isOwner = computed(() => currentUser.value?.username === workflowModel.value.runData.owner);
 const lastUpdateTime = computed(() => historyItemsStore.lastUpdateTime);
+const canRunOnHistory = computed(() => {
+    if (!currentHistoryId.value) {
+        return false;
+    }
+    const history = historyStore.getHistoryById(currentHistoryId.value);
+    return (history && canMutateHistory(history)) ?? false;
+});
 
 function handleInvocations(incomingInvocations: any) {
     invocations.value = incomingInvocations;
@@ -177,12 +185,14 @@ defineExpose({
                         :model="workflowModel"
                         :target-history="simpleFormTargetHistory"
                         :use-job-cache="simpleFormUseJobCache"
+                        :can-mutate-current-history="canRunOnHistory"
                         @submissionSuccess="handleInvocations"
                         @submissionError="handleSubmissionError"
                         @showAdvanced="showAdvanced" />
                     <WorkflowRunForm
                         v-else
                         :model="workflowModel"
+                        :can-mutate-current-history="canRunOnHistory"
                         @submissionSuccess="handleInvocations"
                         @submissionError="handleSubmissionError" />
                 </div>
diff --git a/client/src/components/Workflow/Run/WorkflowRunForm.vue b/client/src/components/Workflow/Run/WorkflowRunForm.vue
index ba312d74d6d3..2627554e526f 100644
--- a/client/src/components/Workflow/Run/WorkflowRunForm.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunForm.vue
@@ -1,11 +1,18 @@
 <template>
     <div v-if="currentUser && currentHistoryId" class="workflow-expanded-form">
+        <BAlert v-if="!canRunOnHistory" variant="warning" show>
+            <span v-localize>
+                The workflow cannot run because the current history is immutable. Please select a different history or
+                send the results to a new one.
+            </span>
+        </BAlert>
         <div class="h4 clearfix mb-3">
             <b>Workflow: {{ model.name }}</b>
             <ButtonSpinner
                 id="run-workflow"
                 class="float-right"
                 title="Run Workflow"
+                :disabled="!canRunOnHistory"
                 :wait="showExecuting"
                 @onClick="onExecute" />
         </div>
@@ -53,6 +60,7 @@
 </template>
 
 <script>
+import { BAlert } from "bootstrap-vue";
 import ButtonSpinner from "components/Common/ButtonSpinner";
 import FormCard from "components/Form/FormCard";
 import FormDisplay from "components/Form/FormDisplay";
@@ -70,6 +78,7 @@ import WorkflowRunInputStep from "./WorkflowRunInputStep";
 
 export default {
     components: {
+        BAlert,
         ButtonSpinner,
         FormDisplay,
         FormCard,
@@ -82,6 +91,10 @@ export default {
             type: Object,
             required: true,
         },
+        canMutateCurrentHistory: {
+            type: Boolean,
+            required: true,
+        },
     },
     data() {
         return {
@@ -140,6 +153,12 @@ export default {
         wpInputs() {
             return this.toArray(this.model.wpInputs);
         },
+        shouldRunOnNewHistory() {
+            return Boolean(this.historyData["new_history|name"]);
+        },
+        canRunOnHistory() {
+            return this.shouldRunOnNewHistory || this.canMutateCurrentHistory;
+        },
     },
     methods: {
         reuseAllowed(user) {
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index b74700c7abe2..8296b9b7faa3 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -1,11 +1,17 @@
 <template>
     <div>
         <div v-if="isConfigLoaded" class="h4 clearfix mb-3">
+            <BAlert v-if="!canRunOnHistory" variant="warning" show>
+                <span v-localize>
+                    The workflow cannot run because the current history is immutable. Please select a different history
+                    or send the results to a new one using the run settings ⚙️
+                </span>
+            </BAlert>
             <b>Workflow: {{ model.name }}</b>
             <ButtonSpinner
                 id="run-workflow"
                 :wait="waitingForRequest"
-                :disabled="hasValidationErrors"
+                :disabled="hasValidationErrors || !canRunOnHistory"
                 class="float-right"
                 title="Run Workflow"
                 @onClick="onExecute" />
@@ -89,6 +95,10 @@ export default {
             type: Boolean,
             default: false,
         },
+        canMutateCurrentHistory: {
+            type: Boolean,
+            required: true,
+        },
     },
     setup() {
         const { config, isConfigLoaded } = useConfig(true);
@@ -143,6 +153,9 @@ export default {
         hasValidationErrors() {
             return Boolean(Object.values(this.stepValidations).find((value) => value !== null && value !== undefined));
         },
+        canRunOnHistory() {
+            return this.canMutateCurrentHistory || this.sendToNewHistory;
+        },
     },
     methods: {
         onValidation(validation) {

From 0b4c0b23bbe4c59a87f305abea332d3739509b71 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 16:57:27 +0200
Subject: [PATCH 21/46] Avoid upload data to immutable histories

---
 client/src/components/Upload/UploadContainer.vue | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Upload/UploadContainer.vue b/client/src/components/Upload/UploadContainer.vue
index 9c7fe5a742dc..329e9b92315f 100644
--- a/client/src/components/Upload/UploadContainer.vue
+++ b/client/src/components/Upload/UploadContainer.vue
@@ -1,5 +1,5 @@
 <script setup>
-import { BTab, BTabs } from "bootstrap-vue";
+import { BAlert, BTab, BTabs } from "bootstrap-vue";
 import { getDatatypesMapper } from "components/Datatypes";
 import LoadingSpan from "components/LoadingSpan";
 import {
@@ -12,6 +12,8 @@ import {
 import { storeToRefs } from "pinia";
 import { computed, onMounted, ref } from "vue";
 
+import { canMutateHistory } from "@/api";
+import { useHistoryStore } from "@/stores/historyStore";
 import { useUploadStore } from "@/stores/uploadStore";
 import { uploadPayload } from "@/utils/upload-payload.js";
 
@@ -82,6 +84,8 @@ const regular = ref(null);
 
 const { percentage, status } = storeToRefs(useUploadStore());
 
+const { currentHistory } = storeToRefs(useHistoryStore());
+
 const effectiveExtensions = computed(() => {
     if (props.formats === null || !datatypesMapperReady.value) {
         return listExtensions.value;
@@ -106,6 +110,7 @@ const historyAvailable = computed(() => Boolean(props.currentHistoryId));
 const ready = computed(
     () => dbKeysSet.value && extensionsSet.value && historyAvailable.value && datatypesMapperReady.value
 );
+const canUploadToHistory = computed(() => currentHistory.value && canMutateHistory(currentHistory.value));
 const showCollection = computed(() => !props.formats && props.multiple);
 const showComposite = computed(() => !props.formats || hasCompositeExtension);
 const showRegular = computed(() => !props.formats || hasRegularExtension);
@@ -160,7 +165,13 @@ defineExpose({
 </script>
 
 <template>
-    <BTabs v-if="ready">
+    <BAlert v-if="!canUploadToHistory" variant="warning" show>
+        <span v-localize>
+            The current history is immutable and you cannot upload data to it. Please select a different history or
+            create a new one.
+        </span>
+    </BAlert>
+    <BTabs v-else-if="ready">
         <BTab v-if="showRegular" id="regular" title="Regular" button-id="tab-title-link-regular">
             <DefaultBox
                 ref="regular"

From a9de12285a794bd9f7e49d833847612334405826 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 17:55:39 +0200
Subject: [PATCH 22/46] Support extract workflow from any history in client
 controller

---
 .../History/CurrentHistory/HistoryNavigation.vue |  2 +-
 .../webapps/galaxy/controllers/workflow.py       | 16 ++++++++++++++--
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryNavigation.vue b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
index 316e10fe5982..1dd671f0e6a0 100644
--- a/client/src/components/History/CurrentHistory/HistoryNavigation.vue
+++ b/client/src/components/History/CurrentHistory/HistoryNavigation.vue
@@ -238,7 +238,7 @@ function userTitle(title: string) {
                     <BDropdownItem
                         :disabled="isAnonymous"
                         :title="userTitle('Convert History to Workflow')"
-                        @click="iframeRedirect('/workflow/build_from_current_history')">
+                        @click="iframeRedirect(`/workflow/build_from_current_history?history_id=${history.id}`)">
                         <FontAwesomeIcon fixed-width :icon="faFileExport" class="mr-1" />
                         <span v-localize>Extract Workflow</span>
                     </BDropdownItem>
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 0b073c65e0c6..ca0cb88b4c3c 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -9,8 +9,10 @@
     util,
     web,
 )
+from galaxy.managers.histories import HistoryManager
 from galaxy.managers.sharable import SlugBuilder
 from galaxy.model.item_attrs import UsesItemRatings
+from galaxy.structured_app import StructuredApp
 from galaxy.tools.parameters.workflow_utils import workflow_building_modes
 from galaxy.util import FILENAME_VALID_CHARS
 from galaxy.web import url_for
@@ -24,13 +26,18 @@
     summarize,
 )
 from galaxy.workflow.modules import load_module_sections
+from ..api import depends
 
 log = logging.getLogger(__name__)
 
 
 class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesItemRatings):
+    history_manager: HistoryManager = depends(HistoryManager)
     slug_builder = SlugBuilder()
 
+    def __init__(self, app: StructuredApp):
+        super().__init__(app)
+
     @web.expose
     def display_by_username_and_slug(self, trans, username, slug, format="html", **kwargs):
         """
@@ -304,14 +311,18 @@ def build_from_current_history(
         workflow_name=None,
         dataset_names=None,
         dataset_collection_names=None,
+        history_id=None,
         **kwargs,
     ):
         user = trans.get_user()
-        history = trans.get_history()
+        history = trans.history
+        if history_id:
+            # Optionally target a different history than the current one.
+            history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=history)
         if not user:
             return trans.show_error_message("Must be logged in to create workflows")
         if (job_ids is None and dataset_ids is None) or workflow_name is None:
-            jobs, warnings = summarize(trans)
+            jobs, warnings = summarize(trans, history)
             # Render
             return trans.fill_template(
                 "workflow/build_from_current_history.mako", jobs=jobs, warnings=warnings, history=history
@@ -324,6 +335,7 @@ def build_from_current_history(
             stored_workflow = extract_workflow(
                 trans,
                 user=user,
+                history=history,
                 job_ids=job_ids,
                 dataset_ids=dataset_ids,
                 dataset_collection_ids=dataset_collection_ids,

From 3bcc1717d05bcd01fba934cda179146e474ffc78 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 17:57:42 +0200
Subject: [PATCH 23/46] Restore back condition to set current history in
 backend

The effect of this is that we can switch to any owned history in the UI, but if the history has been deleted it will not change the current history in the backend and a browser refresh will bring back the real current history.
---
 lib/galaxy/webapps/base/webapp.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
index 7874de2ef77b..0cd502606613 100644
--- a/lib/galaxy/webapps/base/webapp.py
+++ b/lib/galaxy/webapps/base/webapp.py
@@ -914,7 +914,7 @@ def get_history(self, create=False, most_recent=False):
         return history
 
     def set_history(self, history):
-        if history:
+        if history and not history.deleted:
             self.galaxy_session.current_history = history
         self.sa_session.add(self.galaxy_session)
         with transaction(self.sa_session):
@@ -932,7 +932,7 @@ def get_or_create_default_history(self):
 
         # Just return the current history if one exists and is not deleted.
         history = self.galaxy_session.current_history
-        if history:
+        if history and not history.deleted:
             return history
 
         # Look for an existing history that has the default name, is not

From e41293de005d1d53706e07b297f6ceb37e39bae9 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 18:46:18 +0200
Subject: [PATCH 24/46] Display archived message only to the owner

---
 .../History/CurrentHistory/HistoryMessages.vue        | 11 ++++++++---
 .../History/CurrentHistory/HistoryPanel.vue           |  2 +-
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryMessages.vue b/client/src/components/History/CurrentHistory/HistoryMessages.vue
index 3d97f80dd24a..ab5b6c1180cc 100644
--- a/client/src/components/History/CurrentHistory/HistoryMessages.vue
+++ b/client/src/components/History/CurrentHistory/HistoryMessages.vue
@@ -5,13 +5,14 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
-import type { HistorySummary } from "@/api";
+import { type GenericUser, type HistorySummary, userOwnsHistory } from "@/api";
 import localize from "@/utils/localization";
 
 library.add(faArchive, faBurn, faTrash);
 
 interface Props {
     history: HistorySummary;
+    currentUser: GenericUser | null;
 }
 
 const props = defineProps<Props>();
@@ -21,10 +22,14 @@ const userOverQuota = ref(false);
 const hasMessages = computed(() => {
     return userOverQuota.value || props.history.deleted || props.history.archived;
 });
+
+const currentUserOwnsHistory = computed(() => {
+    return userOwnsHistory(props.currentUser, props.history);
+});
 </script>
 
 <template>
-    <div v-if="hasMessages" class="mx-3 mt-2">
+    <div v-if="hasMessages" class="mx-3 mt-2" data-description="history messages">
         <BAlert v-if="history.purged" :show="history.purged" variant="warning">
             <FontAwesomeIcon :icon="faBurn" fixed-width />
             {{ localize("History has been purged") }}
@@ -34,7 +39,7 @@ const hasMessages = computed(() => {
             {{ localize("History has been deleted") }}
         </BAlert>
 
-        <BAlert :show="history.archived" variant="warning">
+        <BAlert :show="history.archived && currentUserOwnsHistory" variant="warning">
             <FontAwesomeIcon :icon="faArchive" fixed-width />
             {{ localize("History has been archived") }}
         </BAlert>
diff --git a/client/src/components/History/CurrentHistory/HistoryPanel.vue b/client/src/components/History/CurrentHistory/HistoryPanel.vue
index 8268153099f3..8d1a54de8453 100644
--- a/client/src/components/History/CurrentHistory/HistoryPanel.vue
+++ b/client/src/components/History/CurrentHistory/HistoryPanel.vue
@@ -542,7 +542,7 @@ function setItemDragstart(
                         :summarized="isMultiViewItem"
                         @update:history="historyStore.updateHistory($event)" />
 
-                    <HistoryMessages :history="history" />
+                    <HistoryMessages :history="history" :current-user="currentUser" />
 
                     <HistoryCounter
                         :history="history"

From 562129f5619a03b08556f9599e2e034902aac7ed Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 27 May 2024 19:07:22 +0200
Subject: [PATCH 25/46] Adapt HistoryView tests

---
 .../components/History/HistoryView.test.js    | 21 ++++++++++---------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/client/src/components/History/HistoryView.test.js b/client/src/components/History/HistoryView.test.js
index f87a3324f5b8..c37f4306b124 100644
--- a/client/src/components/History/HistoryView.test.js
+++ b/client/src/components/History/HistoryView.test.js
@@ -22,6 +22,7 @@ function create_history(historyId, userId, purged = false, archived = false) {
         name: historyName,
         purged: purged,
         archived: archived,
+        deleted: purged,
         count: 10,
         annotation: "This is a history",
         tags: ["tag_1", "tag_2"],
@@ -174,17 +175,17 @@ describe("History center panel View", () => {
         const wrapper = await createWrapper(localVue, "user_1", history);
         expect(wrapper.vm.history).toEqual(history);
 
-        // history purged, not switchable and not importable
+        // history purged, is switchable but not importable
         const switchButton = wrapper.find("[data-description='switch to history button']");
         const importButton = wrapper.find("[data-description='import history button']");
-        expect(switchButton.attributes("disabled")).toBeTruthy();
+        expect(switchButton.attributes("disabled")).toBeFalsy();
         expect(importButton.exists()).toBe(false);
 
-        // storage dashboard button should be disabled
-        expect(storageDashboardButtonDisabled(wrapper)).toBeTruthy();
+        // storage dashboard button can be accessed
+        expect(storageDashboardButtonDisabled(wrapper)).toBeFalsy();
 
         // instead we have an alert
-        expect(wrapper.find("[data-description='history state info']").text()).toBe("This history has been purged.");
+        expect(wrapper.find("[data-description='history messages']").text()).toBe("History has been purged");
     });
 
     it("should not display archived message and should be importable when user is not owner and history is archived", async () => {
@@ -202,7 +203,8 @@ describe("History center panel View", () => {
         expect(storageDashboardButtonDisabled(wrapper)).toBeTruthy();
 
         expectCorrectLayout(wrapper);
-        expect(wrapper.find("[data-description='history state info']").exists()).toBe(false);
+        // There is no message about the history status
+        expect(wrapper.find("[data-description='history messages']").text()).toBe("");
     });
 
     it("should display archived message and should not be importable when user is owner and history is archived", async () => {
@@ -213,13 +215,12 @@ describe("History center panel View", () => {
         const switchButton = wrapper.find("[data-description='switch to history button']");
         const importButton = wrapper.find("[data-description='import history button']");
         expect(switchButton.exists()).toBe(true);
-        expect(switchButton.attributes("disabled")).toBeTruthy();
         expect(importButton.exists()).toBe(false);
 
-        // storage dashboard button should be disabled
-        expect(storageDashboardButtonDisabled(wrapper)).toBeTruthy();
+        // storage dashboard button can be accessed
+        expect(storageDashboardButtonDisabled(wrapper)).toBeFalsy();
 
         expectCorrectLayout(wrapper);
-        expect(wrapper.find("[data-description='history state info']").text()).toBe("This history has been archived.");
+        expect(wrapper.find("[data-description='history messages']").text()).toBe("History has been archived");
     });
 });

From 0359063816ada6d31f5b75bfd85d673907452aef Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 28 May 2024 08:15:10 +0200
Subject: [PATCH 26/46] Fix element serialization for collections that aren't
 populated yet

Fixes
https://github.com/galaxyproject/galaxy/pull/17818#issuecomment-2134060961:
```
AttributeError
'NoneType' object has no attribute 'dataset'
```
---
 lib/galaxy/webapps/galaxy/services/dataset_collections.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
index 40d32be49e7e..52b3a37fa7f3 100644
--- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py
+++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py
@@ -273,7 +273,7 @@ def serialize_element(dsc_element) -> DCESummary:
                     hdca_id=self.encode_id(hdca.id),
                     parent_id=self.encode_id(result["object"]["id"]),
                 )
-            else:
+            elif result["element_type"] == DCEType.hda:
                 result["object"]["accessible"] = self.hda_manager.is_accessible(dsc_element.element_object, trans.user)
             return result
 

From 6f38f5b7fe9dbe163893e93a7b0870b529cfb8fe Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 28 May 2024 13:31:19 +0200
Subject: [PATCH 27/46] Fix conditions for userOwnsHistory and isRegisteredUser

---
 client/src/api/index.test.ts | 113 +++++++++++++++++++++++++++++++++++
 client/src/api/index.ts      |  24 ++++++--
 2 files changed, 132 insertions(+), 5 deletions(-)
 create mode 100644 client/src/api/index.test.ts

diff --git a/client/src/api/index.test.ts b/client/src/api/index.test.ts
new file mode 100644
index 000000000000..42b666b2f03f
--- /dev/null
+++ b/client/src/api/index.test.ts
@@ -0,0 +1,113 @@
+import {
+    type AnonymousUser,
+    type AnyHistory,
+    type HistorySummary,
+    type HistorySummaryExtended,
+    isRegisteredUser,
+    type User,
+    userOwnsHistory,
+} from ".";
+
+const REGISTERED_USER_ID = "fake-user-id";
+const ANOTHER_USER_ID = "another-fake-user-id";
+const ANONYMOUS_USER_ID = null;
+
+const REGISTERED_USER: User = {
+    id: REGISTERED_USER_ID,
+    email: "test@mail.test",
+    tags_used: [],
+    isAnonymous: false,
+    total_disk_usage: 0,
+};
+
+const ANONYMOUS_USER: AnonymousUser = {
+    isAnonymous: true,
+};
+
+const SESSIONLESS_USER = null;
+
+function createFakeHistory<T>(historyId: string = "fake-id", user_id?: string | null): T {
+    const history: AnyHistory = {
+        id: historyId,
+        name: "test",
+        model_class: "History",
+        deleted: false,
+        archived: false,
+        purged: false,
+        published: false,
+        annotation: null,
+        update_time: "2021-09-01T00:00:00.000Z",
+        tags: [],
+        url: `/history/${historyId}`,
+        contents_active: { active: 0, deleted: 0, hidden: 0 },
+        count: 0,
+        size: 0,
+    };
+    if (user_id !== undefined) {
+        (history as HistorySummaryExtended).user_id = user_id;
+    }
+    return history as T;
+}
+
+const HISTORY_OWNED_BY_REGISTERED_USER = createFakeHistory<HistorySummaryExtended>("1234", REGISTERED_USER_ID);
+const HISTORY_OWNED_BY_ANOTHER_USER = createFakeHistory<HistorySummaryExtended>("5678", ANOTHER_USER_ID);
+const HISTORY_OWNED_BY_ANONYMOUS_USER = createFakeHistory<HistorySummaryExtended>("1234", ANONYMOUS_USER_ID);
+const HISTORY_SUMMARY_WITHOUT_USER_ID = createFakeHistory<HistorySummary>("1234");
+
+describe("API Types Helpers", () => {
+    describe("isRegisteredUser", () => {
+        it("should return true for a registered user", () => {
+            expect(isRegisteredUser(REGISTERED_USER)).toBe(true);
+        });
+
+        it("should return false for an anonymous user", () => {
+            expect(isRegisteredUser(ANONYMOUS_USER)).toBe(false);
+        });
+
+        it("should return false for sessionless users", () => {
+            expect(isRegisteredUser(SESSIONLESS_USER)).toBe(false);
+        });
+    });
+
+    describe("isAnonymousUser", () => {
+        it("should return true for an anonymous user", () => {
+            expect(isRegisteredUser(ANONYMOUS_USER)).toBe(false);
+        });
+
+        it("should return false for a registered user", () => {
+            expect(isRegisteredUser(REGISTERED_USER)).toBe(true);
+        });
+
+        it("should return false for sessionless users", () => {
+            expect(isRegisteredUser(SESSIONLESS_USER)).toBe(false);
+        });
+    });
+
+    describe("userOwnsHistory", () => {
+        it("should return true for a registered user owning the history", () => {
+            expect(userOwnsHistory(REGISTERED_USER, HISTORY_OWNED_BY_REGISTERED_USER)).toBe(true);
+        });
+
+        it("should return false for a registered user not owning the history", () => {
+            expect(userOwnsHistory(REGISTERED_USER, HISTORY_OWNED_BY_ANOTHER_USER)).toBe(false);
+        });
+
+        it("should return true for a registered user owning a history without user_id", () => {
+            expect(userOwnsHistory(REGISTERED_USER, HISTORY_SUMMARY_WITHOUT_USER_ID)).toBe(true);
+        });
+
+        it("should return true for an anonymous user owning a history with null user_id", () => {
+            expect(userOwnsHistory(ANONYMOUS_USER, HISTORY_OWNED_BY_ANONYMOUS_USER)).toBe(true);
+        });
+
+        it("should return false for an anonymous user not owning a history", () => {
+            expect(userOwnsHistory(ANONYMOUS_USER, HISTORY_OWNED_BY_REGISTERED_USER)).toBe(false);
+        });
+
+        it("should return false for sessionless users", () => {
+            expect(userOwnsHistory(SESSIONLESS_USER, HISTORY_OWNED_BY_REGISTERED_USER)).toBe(false);
+            expect(userOwnsHistory(SESSIONLESS_USER, HISTORY_SUMMARY_WITHOUT_USER_ID)).toBe(false);
+            expect(userOwnsHistory(SESSIONLESS_USER, HISTORY_OWNED_BY_ANONYMOUS_USER)).toBe(false);
+        });
+    });
+});
diff --git a/client/src/api/index.ts b/client/src/api/index.ts
index 949180cfa817..cf68f63223d2 100644
--- a/client/src/api/index.ts
+++ b/client/src/api/index.ts
@@ -26,7 +26,8 @@ export interface HistoryContentsStats {
  * Data returned by the API when requesting `?view=summary&keys=size,contents_active,user_id`.
  */
 export interface HistorySummaryExtended extends HistorySummary, HistoryContentsStats {
-    user_id: string;
+    /** The ID of the user that owns the history. Null if the history is owned by an anonymous user. */
+    user_id: string | null;
 }
 
 type HistoryDetailedModel = components["schemas"]["HistoryDetailed"];
@@ -203,6 +204,7 @@ export function isHistorySummaryExtended(history: AnyHistory): history is Histor
 
 type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
 
+/** Represents a registered user.**/
 export interface User extends QuotaUsageResponse {
     id: string;
     email: string;
@@ -221,15 +223,23 @@ export interface AnonymousUser {
 
 export type GenericUser = User | AnonymousUser;
 
-export function isRegisteredUser(user: User | AnonymousUser | null): user is User {
-    return !user?.isAnonymous;
+/** Represents any user, including anonymous users or session-less (null) users.**/
+export type AnyUser = GenericUser | null;
+
+export function isRegisteredUser(user: AnyUser): user is User {
+    return user !== null && !user?.isAnonymous;
+}
+
+export function isAnonymousUser(user: AnyUser): user is AnonymousUser {
+    return user !== null && user.isAnonymous;
 }
 
-export function userOwnsHistory(user: User | AnonymousUser | null, history: AnyHistory) {
+export function userOwnsHistory(user: AnyUser, history: AnyHistory) {
     return (
         // Assuming histories without user_id are owned by the current user
         (isRegisteredUser(user) && !hasOwner(history)) ||
-        (isRegisteredUser(user) && hasOwner(history) && user.id === history.user_id)
+        (isRegisteredUser(user) && hasOwner(history) && user.id === history.user_id) ||
+        (isAnonymousUser(user) && hasAnonymousOwner(history))
     );
 }
 
@@ -237,6 +247,10 @@ function hasOwner(history: AnyHistory): history is HistorySummaryExtended {
     return "user_id" in history && history.user_id !== null;
 }
 
+function hasAnonymousOwner(history: AnyHistory): history is HistorySummaryExtended {
+    return "user_id" in history && history.user_id === null;
+}
+
 export function canMutateHistory(history: AnyHistory): boolean {
     return !history.purged && !history.archived;
 }

From 9d662f5e4903a224bc2474abdb7d2bdb7fc9c839 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 28 May 2024 14:30:19 +0200
Subject: [PATCH 28/46] Adapt History SelectorModal test

---
 .../History/Modals/SelectorModal.test.js           | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/client/src/components/History/Modals/SelectorModal.test.js b/client/src/components/History/Modals/SelectorModal.test.js
index e6c4e708b1f9..a78afe094f7b 100644
--- a/client/src/components/History/Modals/SelectorModal.test.js
+++ b/client/src/components/History/Modals/SelectorModal.test.js
@@ -7,6 +7,8 @@ import { createPinia } from "pinia";
 import { useHistoryStore } from "stores/historyStore";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { useUserStore } from "@/stores/userStore";
+
 import SelectorModal from "./SelectorModal";
 
 const localVue = getLocalVue();
@@ -35,6 +37,14 @@ const PROPS_FOR_MODAL_MULTIPLE_SELECT = {
 
 const CURRENT_HISTORY_INDICATION_TEXT = "(Current)";
 
+const CURRENT_USER = {
+    email: "email",
+    id: "user_id",
+    tags_used: [],
+    isAnonymous: false,
+    total_disk_usage: 0,
+};
+
 describe("History SelectorModal.vue", () => {
     let wrapper;
     let axiosMock;
@@ -60,6 +70,10 @@ describe("History SelectorModal.vue", () => {
                 icon: { template: "<div></div>" },
             },
         });
+
+        const userStore = useUserStore();
+        userStore.setCurrentUser(CURRENT_USER);
+
         historyStore = useHistoryStore();
         axiosMock = new MockAdapter(axios);
         getUpdatedAxiosMock();

From fa73f2e9f41aaf042db52502322686d73caddca1 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 28 May 2024 13:31:19 +0200
Subject: [PATCH 29/46] Fix conditions for userOwnsHistory and isRegisteredUser

---
 client/src/api/index.test.ts | 113 +++++++++++++++++++++++++++++++++++
 client/src/api/index.ts      |  24 ++++++--
 2 files changed, 132 insertions(+), 5 deletions(-)
 create mode 100644 client/src/api/index.test.ts

diff --git a/client/src/api/index.test.ts b/client/src/api/index.test.ts
new file mode 100644
index 000000000000..42b666b2f03f
--- /dev/null
+++ b/client/src/api/index.test.ts
@@ -0,0 +1,113 @@
+import {
+    type AnonymousUser,
+    type AnyHistory,
+    type HistorySummary,
+    type HistorySummaryExtended,
+    isRegisteredUser,
+    type User,
+    userOwnsHistory,
+} from ".";
+
+const REGISTERED_USER_ID = "fake-user-id";
+const ANOTHER_USER_ID = "another-fake-user-id";
+const ANONYMOUS_USER_ID = null;
+
+const REGISTERED_USER: User = {
+    id: REGISTERED_USER_ID,
+    email: "test@mail.test",
+    tags_used: [],
+    isAnonymous: false,
+    total_disk_usage: 0,
+};
+
+const ANONYMOUS_USER: AnonymousUser = {
+    isAnonymous: true,
+};
+
+const SESSIONLESS_USER = null;
+
+function createFakeHistory<T>(historyId: string = "fake-id", user_id?: string | null): T {
+    const history: AnyHistory = {
+        id: historyId,
+        name: "test",
+        model_class: "History",
+        deleted: false,
+        archived: false,
+        purged: false,
+        published: false,
+        annotation: null,
+        update_time: "2021-09-01T00:00:00.000Z",
+        tags: [],
+        url: `/history/${historyId}`,
+        contents_active: { active: 0, deleted: 0, hidden: 0 },
+        count: 0,
+        size: 0,
+    };
+    if (user_id !== undefined) {
+        (history as HistorySummaryExtended).user_id = user_id;
+    }
+    return history as T;
+}
+
+const HISTORY_OWNED_BY_REGISTERED_USER = createFakeHistory<HistorySummaryExtended>("1234", REGISTERED_USER_ID);
+const HISTORY_OWNED_BY_ANOTHER_USER = createFakeHistory<HistorySummaryExtended>("5678", ANOTHER_USER_ID);
+const HISTORY_OWNED_BY_ANONYMOUS_USER = createFakeHistory<HistorySummaryExtended>("1234", ANONYMOUS_USER_ID);
+const HISTORY_SUMMARY_WITHOUT_USER_ID = createFakeHistory<HistorySummary>("1234");
+
+describe("API Types Helpers", () => {
+    describe("isRegisteredUser", () => {
+        it("should return true for a registered user", () => {
+            expect(isRegisteredUser(REGISTERED_USER)).toBe(true);
+        });
+
+        it("should return false for an anonymous user", () => {
+            expect(isRegisteredUser(ANONYMOUS_USER)).toBe(false);
+        });
+
+        it("should return false for sessionless users", () => {
+            expect(isRegisteredUser(SESSIONLESS_USER)).toBe(false);
+        });
+    });
+
+    describe("isAnonymousUser", () => {
+        it("should return true for an anonymous user", () => {
+            expect(isRegisteredUser(ANONYMOUS_USER)).toBe(false);
+        });
+
+        it("should return false for a registered user", () => {
+            expect(isRegisteredUser(REGISTERED_USER)).toBe(true);
+        });
+
+        it("should return false for sessionless users", () => {
+            expect(isRegisteredUser(SESSIONLESS_USER)).toBe(false);
+        });
+    });
+
+    describe("userOwnsHistory", () => {
+        it("should return true for a registered user owning the history", () => {
+            expect(userOwnsHistory(REGISTERED_USER, HISTORY_OWNED_BY_REGISTERED_USER)).toBe(true);
+        });
+
+        it("should return false for a registered user not owning the history", () => {
+            expect(userOwnsHistory(REGISTERED_USER, HISTORY_OWNED_BY_ANOTHER_USER)).toBe(false);
+        });
+
+        it("should return true for a registered user owning a history without user_id", () => {
+            expect(userOwnsHistory(REGISTERED_USER, HISTORY_SUMMARY_WITHOUT_USER_ID)).toBe(true);
+        });
+
+        it("should return true for an anonymous user owning a history with null user_id", () => {
+            expect(userOwnsHistory(ANONYMOUS_USER, HISTORY_OWNED_BY_ANONYMOUS_USER)).toBe(true);
+        });
+
+        it("should return false for an anonymous user not owning a history", () => {
+            expect(userOwnsHistory(ANONYMOUS_USER, HISTORY_OWNED_BY_REGISTERED_USER)).toBe(false);
+        });
+
+        it("should return false for sessionless users", () => {
+            expect(userOwnsHistory(SESSIONLESS_USER, HISTORY_OWNED_BY_REGISTERED_USER)).toBe(false);
+            expect(userOwnsHistory(SESSIONLESS_USER, HISTORY_SUMMARY_WITHOUT_USER_ID)).toBe(false);
+            expect(userOwnsHistory(SESSIONLESS_USER, HISTORY_OWNED_BY_ANONYMOUS_USER)).toBe(false);
+        });
+    });
+});
diff --git a/client/src/api/index.ts b/client/src/api/index.ts
index 730f03f5ddec..304573a4c81c 100644
--- a/client/src/api/index.ts
+++ b/client/src/api/index.ts
@@ -26,7 +26,8 @@ export interface HistoryContentsStats {
  * Data returned by the API when requesting `?view=summary&keys=size,contents_active,user_id`.
  */
 export interface HistorySummaryExtended extends HistorySummary, HistoryContentsStats {
-    user_id: string;
+    /** The ID of the user that owns the history. Null if the history is owned by an anonymous user. */
+    user_id: string | null;
 }
 
 type HistoryDetailedModel = components["schemas"]["HistoryDetailed"];
@@ -207,6 +208,7 @@ export function isHistorySummaryExtended(history: AnyHistory): history is Histor
 
 type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
 
+/** Represents a registered user.**/
 export interface User extends QuotaUsageResponse {
     id: string;
     email: string;
@@ -224,18 +226,30 @@ export interface AnonymousUser {
 
 export type GenericUser = User | AnonymousUser;
 
-export function isRegisteredUser(user: User | AnonymousUser | null): user is User {
-    return !user?.isAnonymous;
+/** Represents any user, including anonymous users or session-less (null) users.**/
+export type AnyUser = GenericUser | null;
+
+export function isRegisteredUser(user: AnyUser): user is User {
+    return user !== null && !user?.isAnonymous;
+}
+
+export function isAnonymousUser(user: AnyUser): user is AnonymousUser {
+    return user !== null && user.isAnonymous;
 }
 
-export function userOwnsHistory(user: User | AnonymousUser | null, history: AnyHistory) {
+export function userOwnsHistory(user: AnyUser, history: AnyHistory) {
     return (
         // Assuming histories without user_id are owned by the current user
         (isRegisteredUser(user) && !hasOwner(history)) ||
-        (isRegisteredUser(user) && hasOwner(history) && user.id === history.user_id)
+        (isRegisteredUser(user) && hasOwner(history) && user.id === history.user_id) ||
+        (isAnonymousUser(user) && hasAnonymousOwner(history))
     );
 }
 
 function hasOwner(history: AnyHistory): history is HistorySummaryExtended {
     return "user_id" in history && history.user_id !== null;
 }
+
+function hasAnonymousOwner(history: AnyHistory): history is HistorySummaryExtended {
+    return "user_id" in history && history.user_id === null;
+}

From 1637e202e5073b9a4ddd4fe54dde0b3dc2ca7fcc Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 28 May 2024 14:30:19 +0200
Subject: [PATCH 30/46] Adapt History SelectorModal test

---
 .../History/Modals/SelectorModal.test.js           | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/client/src/components/History/Modals/SelectorModal.test.js b/client/src/components/History/Modals/SelectorModal.test.js
index e6c4e708b1f9..a78afe094f7b 100644
--- a/client/src/components/History/Modals/SelectorModal.test.js
+++ b/client/src/components/History/Modals/SelectorModal.test.js
@@ -7,6 +7,8 @@ import { createPinia } from "pinia";
 import { useHistoryStore } from "stores/historyStore";
 import { getLocalVue } from "tests/jest/helpers";
 
+import { useUserStore } from "@/stores/userStore";
+
 import SelectorModal from "./SelectorModal";
 
 const localVue = getLocalVue();
@@ -35,6 +37,14 @@ const PROPS_FOR_MODAL_MULTIPLE_SELECT = {
 
 const CURRENT_HISTORY_INDICATION_TEXT = "(Current)";
 
+const CURRENT_USER = {
+    email: "email",
+    id: "user_id",
+    tags_used: [],
+    isAnonymous: false,
+    total_disk_usage: 0,
+};
+
 describe("History SelectorModal.vue", () => {
     let wrapper;
     let axiosMock;
@@ -60,6 +70,10 @@ describe("History SelectorModal.vue", () => {
                 icon: { template: "<div></div>" },
             },
         });
+
+        const userStore = useUserStore();
+        userStore.setCurrentUser(CURRENT_USER);
+
         historyStore = useHistoryStore();
         axiosMock = new MockAdapter(axios);
         getUpdatedAxiosMock();

From ad328169ff7dc69c0e2db100234f256f24552386 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Tue, 28 May 2024 09:39:13 -0500
Subject: [PATCH 31/46] [24.1] Change `ActivityPanel` go to button to primary

Tiny change that reverts the button's color to primary.

Co-authored-by: Alireza Heidari <itisalirh@gmail.com>
---
 client/src/components/Panels/ActivityPanel.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Panels/ActivityPanel.vue b/client/src/components/Panels/ActivityPanel.vue
index 753c0fc20a6b..df4d58a6de64 100644
--- a/client/src/components/Panels/ActivityPanel.vue
+++ b/client/src/components/Panels/ActivityPanel.vue
@@ -39,6 +39,7 @@ const hasGoToAll = computed(
             <BButton
                 v-if="hasGoToAll"
                 class="activity-panel-footer"
+                variant="primary"
                 :data-description="`props.mainButtonText button`"
                 :to="props.href"
                 size="sm"

From 067f6df3efce95392a459d4fe61ae2bc82ad8f08 Mon Sep 17 00:00:00 2001
From: Alireza Heidari <itisalirh@gmail.com>
Date: Tue, 28 May 2024 18:38:34 +0200
Subject: [PATCH 32/46] =?UTF-8?q?=E2=9C=A8:=20allow=20bookmarking=20public?=
 =?UTF-8?q?=20workflows?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 client/src/components/Workflow/WorkflowActions.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/Workflow/WorkflowActions.vue b/client/src/components/Workflow/WorkflowActions.vue
index 7c709b27aea8..c7422119e868 100644
--- a/client/src/components/Workflow/WorkflowActions.vue
+++ b/client/src/components/Workflow/WorkflowActions.vue
@@ -126,7 +126,7 @@ async function onDelete() {
 const actions: ComputedRef<(AAction | BAction)[]> = computed(() => {
     return [
         {
-            condition: !props.workflow.deleted && !shared.value && !props.workflow.show_in_tool_panel,
+            condition: !props.workflow.deleted && !props.workflow.show_in_tool_panel,
             class: "workflow-bookmark-button-add",
             component: "async",
             title: "Add bookmarks",
@@ -137,7 +137,7 @@ const actions: ComputedRef<(AAction | BAction)[]> = computed(() => {
             action: () => onToggleBookmark(true),
         },
         {
-            condition: !props.workflow.deleted && !shared.value && props.workflow.show_in_tool_panel,
+            condition: !props.workflow.deleted && props.workflow.show_in_tool_panel,
             class: "workflow-bookmark-button-remove",
             component: "async",
             title: "Remove bookmark",

From 229b1c5bcbd3985bf6247d7736407b151a68b2f6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 13:29:17 +0200
Subject: [PATCH 33/46] Skip doi unit test if request fails

---
 lib/galaxy/managers/citations.py                 |  1 +
 .../app/managers/test_CitationsManager_db.py     | 16 +++++++++++-----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/citations.py b/lib/galaxy/managers/citations.py
index 09a4e137cbee..958617289ebb 100644
--- a/lib/galaxy/managers/citations.py
+++ b/lib/galaxy/managers/citations.py
@@ -55,6 +55,7 @@ def _raw_get_bibtex(self, doi):
         # content encoding from the Content-Type header (res.encoding), and if
         # that fails, falls back to guessing from the content itself (res.apparent_encoding).
         # The guessed encoding is sometimes wrong, better to default to utf-8.
+        res.raise_for_status()
         if res.encoding is None:
             res.encoding = "utf-8"
         return res.text
diff --git a/test/unit/app/managers/test_CitationsManager_db.py b/test/unit/app/managers/test_CitationsManager_db.py
index 8c7b8f8eb29c..96d39a89135d 100644
--- a/test/unit/app/managers/test_CitationsManager_db.py
+++ b/test/unit/app/managers/test_CitationsManager_db.py
@@ -1,3 +1,6 @@
+from unittest import SkipTest
+
+import requests
 from beaker.cache import CacheManager
 from beaker.util import parse_cache_config_options
 
@@ -29,8 +32,11 @@ def test_DoiCache(url_factory):  # noqa: F811
     with create_and_drop_database(db_url):
         doi_cache = MockDoiCache(galaxy.config.GalaxyAppConfiguration(override_tempdir=False), db_url)
         assert is_cache_empty(db_url, "doi")
-        assert "Jörg" in doi_cache.get_bibtex("10.1093/bioinformatics/bts252")
-        assert "Özkurt" in doi_cache.get_bibtex("10.1101/2021.12.24.474111")
-        assert not is_cache_empty(db_url, "doi")
-        doi_cache._cache.clear()
-        assert is_cache_empty(db_url, "doi")
+        try:
+            assert "Jörg" in doi_cache.get_bibtex("10.1093/bioinformatics/bts252")
+            assert "Özkurt" in doi_cache.get_bibtex("10.1101/2021.12.24.474111")
+            assert not is_cache_empty(db_url, "doi")
+            doi_cache._cache.clear()
+            assert is_cache_empty(db_url, "doi")
+        except requests.exceptions.RequestException as e:
+            raise SkipTest(f"dx.doi failed to respond: {e}")

From 5f1ec2b06fe6f5d013ea68b1535b4ab715368d12 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 13:29:58 +0200
Subject: [PATCH 34/46] Skip tests that require toolshed to be up if toolshed
 down

---
 lib/galaxy_test/driver/uses_shed.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/lib/galaxy_test/driver/uses_shed.py b/lib/galaxy_test/driver/uses_shed.py
index e592de25aefd..b8db5296848e 100644
--- a/lib/galaxy_test/driver/uses_shed.py
+++ b/lib/galaxy_test/driver/uses_shed.py
@@ -5,7 +5,10 @@
 import tempfile
 from typing import ClassVar
 
+from unittest import SkipTest
+
 from galaxy.app import UniverseApplication
+from galaxy.util.unittest_utils import is_site_up
 from galaxy.model.base import transaction
 from galaxy_test.base.populators import DEFAULT_TIMEOUT
 from galaxy_test.base.uses_shed_api import UsesShedApi
@@ -34,6 +37,8 @@
 <tables>
 </tables>"""
 
+TOOLSHED_URL = "https://toolshed.g2.bx.psu.edu/"
+
 
 class UsesShed(UsesShedApi):
     @property
@@ -47,6 +52,8 @@ def _app(self) -> UniverseApplication: ...
 
     @classmethod
     def configure_shed(cls, config):
+        if not is_site_up(TOOLSHED_URL):
+            raise SkipTest("Test depends on [{TOOLSHED_URL}] being up and it appears to be down.")
         cls.shed_tools_dir = tempfile.mkdtemp()
         cls.shed_tool_data_dir = tempfile.mkdtemp()
         cls._test_driver.temp_directories.extend([cls.shed_tool_data_dir, cls.shed_tools_dir])

From 74e8d3257b56b8fa876426cd1c14136503d5a2c8 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 13:35:52 +0200
Subject: [PATCH 35/46] Make it an f-string

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy_test/driver/uses_shed.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy_test/driver/uses_shed.py b/lib/galaxy_test/driver/uses_shed.py
index b8db5296848e..bbfb4c247544 100644
--- a/lib/galaxy_test/driver/uses_shed.py
+++ b/lib/galaxy_test/driver/uses_shed.py
@@ -53,7 +53,7 @@ def _app(self) -> UniverseApplication: ...
     @classmethod
     def configure_shed(cls, config):
         if not is_site_up(TOOLSHED_URL):
-            raise SkipTest("Test depends on [{TOOLSHED_URL}] being up and it appears to be down.")
+            raise SkipTest(f"Test depends on [{TOOLSHED_URL}] being up and it appears to be down.")
         cls.shed_tools_dir = tempfile.mkdtemp()
         cls.shed_tool_data_dir = tempfile.mkdtemp()
         cls._test_driver.temp_directories.extend([cls.shed_tool_data_dir, cls.shed_tools_dir])

From d8379a79a102a73a70523d942c86aaf31d6b2a12 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 13:39:05 +0200
Subject: [PATCH 36/46] Also skip unit test

---
 test/unit/app/test_galaxy_install.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/unit/app/test_galaxy_install.py b/test/unit/app/test_galaxy_install.py
index 1695e8faebc2..6d6a2fffe823 100644
--- a/test/unit/app/test_galaxy_install.py
+++ b/test/unit/app/test_galaxy_install.py
@@ -17,8 +17,10 @@
 from galaxy.tool_shed.unittest_utils import StandaloneInstallationTarget
 from galaxy.tool_shed.util.repository_util import check_for_updates
 from galaxy.util.tool_shed.tool_shed_registry import DEFAULT_TOOL_SHED_URL
+from galaxy.util.unittest_utils import skip_if_site_down
 
 
+@skip_if_site_down("toolshed.g2.bx.psu.edu")
 def test_against_production_shed(tmp_path: Path):
     repo_owner = "iuc"
     repo_name = "featurecounts"

From 5d2ccdfbe79461a9df8a56d5c3f156232a6956f1 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 13:49:10 +0200
Subject: [PATCH 37/46] Use variable

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 test/unit/app/test_galaxy_install.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/app/test_galaxy_install.py b/test/unit/app/test_galaxy_install.py
index 6d6a2fffe823..a44fc823ad5e 100644
--- a/test/unit/app/test_galaxy_install.py
+++ b/test/unit/app/test_galaxy_install.py
@@ -20,7 +20,7 @@
 from galaxy.util.unittest_utils import skip_if_site_down
 
 
-@skip_if_site_down("toolshed.g2.bx.psu.edu")
+@skip_if_site_down(DEFAULT_TOOL_SHED_URL)
 def test_against_production_shed(tmp_path: Path):
     repo_owner = "iuc"
     repo_name = "featurecounts"

From ce1582f46a0e42aff8c42c36d07970cf29775525 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 13:50:29 +0200
Subject: [PATCH 38/46] Move assertions out request error handling

---
 test/unit/app/managers/test_CitationsManager_db.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/unit/app/managers/test_CitationsManager_db.py b/test/unit/app/managers/test_CitationsManager_db.py
index 96d39a89135d..d159015949a9 100644
--- a/test/unit/app/managers/test_CitationsManager_db.py
+++ b/test/unit/app/managers/test_CitationsManager_db.py
@@ -35,8 +35,8 @@ def test_DoiCache(url_factory):  # noqa: F811
         try:
             assert "Jörg" in doi_cache.get_bibtex("10.1093/bioinformatics/bts252")
             assert "Özkurt" in doi_cache.get_bibtex("10.1101/2021.12.24.474111")
-            assert not is_cache_empty(db_url, "doi")
-            doi_cache._cache.clear()
-            assert is_cache_empty(db_url, "doi")
         except requests.exceptions.RequestException as e:
             raise SkipTest(f"dx.doi failed to respond: {e}")
+        assert not is_cache_empty(db_url, "doi")
+        doi_cache._cache.clear()
+        assert is_cache_empty(db_url, "doi")

From b0ea69e4185dd83875181431491f271d3e520b8a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 13:58:00 +0200
Subject: [PATCH 39/46] Fix import order

---
 lib/galaxy_test/driver/uses_shed.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy_test/driver/uses_shed.py b/lib/galaxy_test/driver/uses_shed.py
index bbfb4c247544..e31237d5f166 100644
--- a/lib/galaxy_test/driver/uses_shed.py
+++ b/lib/galaxy_test/driver/uses_shed.py
@@ -4,12 +4,11 @@
 import string
 import tempfile
 from typing import ClassVar
-
 from unittest import SkipTest
 
 from galaxy.app import UniverseApplication
-from galaxy.util.unittest_utils import is_site_up
 from galaxy.model.base import transaction
+from galaxy.util.unittest_utils import is_site_up
 from galaxy_test.base.populators import DEFAULT_TIMEOUT
 from galaxy_test.base.uses_shed_api import UsesShedApi
 from galaxy_test.driver.driver_util import (

From 2ea3d342cc6e855eba2292a8ad77c63d11753571 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 15:29:39 +0200
Subject: [PATCH 40/46] Import tool shed url

---
 lib/galaxy_test/driver/uses_shed.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy_test/driver/uses_shed.py b/lib/galaxy_test/driver/uses_shed.py
index e31237d5f166..f563d516d5a6 100644
--- a/lib/galaxy_test/driver/uses_shed.py
+++ b/lib/galaxy_test/driver/uses_shed.py
@@ -8,6 +8,7 @@
 
 from galaxy.app import UniverseApplication
 from galaxy.model.base import transaction
+from galaxy.util.tool_shed.tool_shed_registry import DEFAULT_TOOL_SHED_URL
 from galaxy.util.unittest_utils import is_site_up
 from galaxy_test.base.populators import DEFAULT_TIMEOUT
 from galaxy_test.base.uses_shed_api import UsesShedApi
@@ -36,8 +37,6 @@
 <tables>
 </tables>"""
 
-TOOLSHED_URL = "https://toolshed.g2.bx.psu.edu/"
-
 
 class UsesShed(UsesShedApi):
     @property
@@ -51,8 +50,8 @@ def _app(self) -> UniverseApplication: ...
 
     @classmethod
     def configure_shed(cls, config):
-        if not is_site_up(TOOLSHED_URL):
-            raise SkipTest(f"Test depends on [{TOOLSHED_URL}] being up and it appears to be down.")
+        if not is_site_up(DEFAULT_TOOL_SHED_URL):
+            raise SkipTest(f"Test depends on [{DEFAULT_TOOL_SHED_URL}] being up and it appears to be down.")
         cls.shed_tools_dir = tempfile.mkdtemp()
         cls.shed_tool_data_dir = tempfile.mkdtemp()
         cls._test_driver.temp_directories.extend([cls.shed_tool_data_dir, cls.shed_tools_dir])

From b00beec3d26b7dff76b32d56078bf7c90eff915b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 17:44:55 +0200
Subject: [PATCH 41/46] Allow configuring hgweb repo prefix

---
 lib/galaxy/config/sample/tool_shed.yml.sample         | 4 ++++
 lib/galaxy/config/schemas/tool_shed_config_schema.yml | 8 ++++++++
 lib/tool_shed/util/repository_util.py                 | 2 +-
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample
index 3b04d57f94a7..e909ec253575 100644
--- a/lib/galaxy/config/sample/tool_shed.yml.sample
+++ b/lib/galaxy/config/sample/tool_shed.yml.sample
@@ -15,6 +15,10 @@ tool_shed:
   # installation directory.
   #hgweb_config_dir: null
 
+  # Default URL prefix for repositories served via hgweb. If running an
+  # external hgweb server you should set this to an empty string.
+  #hgweb_repo_prefix: repos/
+
   # Where Tool Shed repositories are stored.
   #file_path: database/community_files
 
diff --git a/lib/galaxy/config/schemas/tool_shed_config_schema.yml b/lib/galaxy/config/schemas/tool_shed_config_schema.yml
index 116f0521f483..47f97b1253c5 100644
--- a/lib/galaxy/config/schemas/tool_shed_config_schema.yml
+++ b/lib/galaxy/config/schemas/tool_shed_config_schema.yml
@@ -31,6 +31,14 @@ mapping:
           Where the hgweb.config file is stored.
           The default is the Galaxy installation directory.
 
+      hgweb_repo_prefix:
+        type: str
+        required: false
+        default: repos/
+        desc: |
+          Default URL prefix for repositories served via hgweb.
+          If running an external hgweb server you should set this to an empty string.
+
       file_path:
         type: str
         default: database/community_files
diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py
index 9d9e805ae669..c84b182ae993 100644
--- a/lib/tool_shed/util/repository_util.py
+++ b/lib/tool_shed/util/repository_util.py
@@ -218,7 +218,7 @@ def create_repository(
     # Create the local repository.
     init_repository(repo_path=repository_path)
     # Add an entry in the hgweb.config file for the local repository.
-    lhs = f"repos/{repository.user.username}/{repository.name}"
+    lhs = f"{app.config.hgweb_repo_prefix}{repository.user.username}/{repository.name}"
     app.hgweb_config_manager.add_entry(lhs, repository_path)
     # Create a .hg/hgrc file for the local repository.
     create_hgrc_file(app, repository)

From 410ccb9ab2218678e2ad878264812a2c4d3e155d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 May 2024 17:45:23 +0200
Subject: [PATCH 42/46] Fix up lock handling in hgweb_config_manager

---
 lib/tool_shed/util/hgweb_config.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/lib/tool_shed/util/hgweb_config.py b/lib/tool_shed/util/hgweb_config.py
index f39d9abcc3d3..8c1656406b0f 100644
--- a/lib/tool_shed/util/hgweb_config.py
+++ b/lib/tool_shed/util/hgweb_config.py
@@ -19,11 +19,11 @@ class HgWebConfigManager:
     def __init__(self):
         self.hgweb_config_dir = None
         self.in_memory_config = None
+        self.lock = threading.Lock()
 
     def add_entry(self, lhs, rhs):
         """Add an entry in the hgweb.config file for a new repository."""
-        lock = threading.Lock()
-        lock.acquire(True)
+        self.lock.acquire(True)
         try:
             # Since we're changing the config, make sure the latest is loaded into memory.
             self.read_config(force_read=True)
@@ -38,12 +38,11 @@ def add_entry(self, lhs, rhs):
         except Exception as e:
             log.debug("Exception in HgWebConfigManager.add_entry(): %s", unicodify(e))
         finally:
-            lock.release()
+            self.lock.release()
 
     def change_entry(self, old_lhs, new_lhs, new_rhs):
         """Change an entry in the hgweb.config file for a repository - this only happens when the owner changes the name of the repository."""
-        lock = threading.Lock()
-        lock.acquire(True)
+        self.lock.acquire(True)
         try:
             self.make_backup()
             # Remove the old entry.
@@ -55,7 +54,7 @@ def change_entry(self, old_lhs, new_lhs, new_rhs):
         except Exception as e:
             log.debug("Exception in HgWebConfigManager.change_entry(): %s", unicodify(e))
         finally:
-            lock.release()
+            self.lock.release()
 
     def get_entry(self, lhs):
         """Return an entry in the hgweb.config file for a repository"""

From a774c9234c4ff2cde49400d7d559b9962ee7bd65 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 29 May 2024 22:18:26 -0400
Subject: [PATCH 43/46] Add ts db migration: deleted column to api_keys tbl

---
 ...add_non_nullable_column_deleted_to_api_.py | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py

diff --git a/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
new file mode 100644
index 000000000000..6eefd98ff4b3
--- /dev/null
+++ b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
@@ -0,0 +1,43 @@
+"""add non-nullable column deleted to API keys
+
+Revision ID: 1b5bf427db25
+Revises: 969bbf7bcc29
+Create Date: 2024-05-29 21:53:53.516506
+
+"""
+import sqlalchemy as sa
+from sqlalchemy import (
+    Boolean,
+    Column,
+)
+
+from galaxy.model.database_object_names import build_index_name
+from galaxy.model.migrations.util import (
+    add_column,
+    drop_column,
+    drop_index,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "1b5bf427db25"
+down_revision = "969bbf7bcc29"
+branch_labels = None
+depends_on = None
+
+# database object names used in this revision
+table_name = "api_keys"
+column_name = "deleted"
+index_name = build_index_name(table_name, column_name)
+
+
+def upgrade():
+    add_column(
+        table_name, Column(column_name, Boolean(), default=False, index=True, nullable=False, server_default=sa.false())
+    )
+
+
+def downgrade():
+    with transaction():
+        drop_index(index_name, table_name)
+        drop_column(table_name, column_name)

From 4099fcc15ac3821f202dbde829ec10dc16349bd8 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 30 May 2024 11:45:12 +0200
Subject: [PATCH 44/46] Set all old keys to deleted

---
 ...add_non_nullable_column_deleted_to_api_.py | 27 ++++++++++++++++---
 1 file changed, 24 insertions(+), 3 deletions(-)

diff --git a/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
index 6eefd98ff4b3..4feafbffe2db 100644
--- a/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
+++ b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
@@ -6,14 +6,21 @@
 
 """
 import sqlalchemy as sa
+from alembic import op
 from sqlalchemy import (
     Boolean,
     Column,
+    ForeignKey,
+    Integer,
+    false,
+    select,
 )
+from sqlalchemy import func
 
 from galaxy.model.database_object_names import build_index_name
 from galaxy.model.migrations.util import (
     add_column,
+    alter_column,
     drop_column,
     drop_index,
     transaction,
@@ -32,9 +39,23 @@
 
 
 def upgrade():
-    add_column(
-        table_name, Column(column_name, Boolean(), default=False, index=True, nullable=False, server_default=sa.false())
-    )
+    with transaction():
+        # Add a nullable deleted column
+        add_column(table_name, Column(column_name, Boolean(), nullable=True, index=True))
+        table = sa.sql.table(
+            table_name,
+            Column("id", Integer, primary_key=True),
+            Column("user_id", ForeignKey("galaxy_user.id"), index=True),
+            Column(column_name, Boolean, index=True, default=False),
+        )
+        # Set everything to deleted
+        op.execute(table.update().where(table.c.deleted.is_(None)).values(deleted=True))
+        # Select the latest api keys
+        s = select(func.max(table.c.id)).group_by(table.c.user_id)
+        # Set all of these api keys to not deleted
+        op.execute(table.update().where(table.c.id.in_(s)).values(deleted=False))
+        # Make column not nullable and default to false
+        alter_column(table_name, column_name, existing_type=Boolean(), nullable=False, server_default=false())
 
 
 def downgrade():

From 063d9856506694da633cc34f588a9b53dad3b44f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 30 May 2024 11:50:43 +0200
Subject: [PATCH 45/46] Also set model to nullable=False

---
 lib/tool_shed/webapp/model/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index 1a6761156dd6..a62bb52e39f7 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -92,7 +92,7 @@ class APIKeys(Base):
     user_id = Column(ForeignKey("galaxy_user.id"), index=True)
     key = Column(TrimmedString(32), index=True, unique=True)
     user = relationship("User", back_populates="api_keys")
-    deleted = Column(Boolean, index=True, default=False)
+    deleted = Column(Boolean, index=True, default=False, nullable=False)
 
 
 class User(Base, Dictifiable):

From d0d16ebf49f73f62ad5b242048313a8986161dae Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 30 May 2024 09:34:38 -0400
Subject: [PATCH 46/46] Make column non-nullable

---
 ...7db25_add_non_nullable_column_deleted_to_api_.py | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
index 4feafbffe2db..390402f37b53 100644
--- a/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
+++ b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
@@ -10,17 +10,16 @@
 from sqlalchemy import (
     Boolean,
     Column,
+    false,
     ForeignKey,
+    func,
     Integer,
-    false,
     select,
 )
-from sqlalchemy import func
 
 from galaxy.model.database_object_names import build_index_name
 from galaxy.model.migrations.util import (
     add_column,
-    alter_column,
     drop_column,
     drop_index,
     transaction,
@@ -40,8 +39,8 @@
 
 def upgrade():
     with transaction():
-        # Add a nullable deleted column
-        add_column(table_name, Column(column_name, Boolean(), nullable=True, index=True))
+        # Add a deleted column
+        add_column(table_name, Column(column_name, Boolean(), nullable=False, index=True, server_default=false()))
         table = sa.sql.table(
             table_name,
             Column("id", Integer, primary_key=True),
@@ -49,13 +48,11 @@ def upgrade():
             Column(column_name, Boolean, index=True, default=False),
         )
         # Set everything to deleted
-        op.execute(table.update().where(table.c.deleted.is_(None)).values(deleted=True))
+        op.execute(table.update().values(deleted=True))
         # Select the latest api keys
         s = select(func.max(table.c.id)).group_by(table.c.user_id)
         # Set all of these api keys to not deleted
         op.execute(table.update().where(table.c.id.in_(s)).values(deleted=False))
-        # Make column not nullable and default to false
-        alter_column(table_name, column_name, existing_type=Boolean(), nullable=False, server_default=false())
 
 
 def downgrade():