Upgrade syntax to Python 3.7

using `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus`

Also more refactoring of Python files in `packages/` .

config/plugins/webhooks/demo/tour_generator/__init__.py

@@ -163,7 +163,7 @@ def _generate_tour(self):
                 if name in test_inputs:
                     hid = self._hids[name]
                     dataset = self._test.inputs[name][0]
-                    step["content"] = "Select dataset: <b>{}: {}</b>".format(hid, dataset)
+                    step["content"] = f"Select dataset: <b>{hid}: {dataset}</b>"
                 else:
                     step["content"] = "Select a dataset"
 
@@ -192,7 +192,7 @@ def _generate_tour(self):
                             if case_id in self._data_inputs.keys():
                                 hid = self._hids[case_id]
                                 dataset = self._test.inputs[tour_id][0]
-                                step_msg = "Select dataset: <b>%s: %s</b>" % (hid, dataset)
+                                step_msg = f"Select dataset: <b>{hid}: {dataset}</b>"
                             else:
                                 case_params = ", ".join(self._test.inputs[tour_id])
                                 step_msg = "Select parameter(s): " + "<b>%s</b>" % case_params

lib/galaxy/containers/docker_swarm.py

@@ -374,7 +374,7 @@ def node_ps(self, node_id):
     def node_update(self, node_id, **kwopts):
         return self._run_docker(
             subcommand="node update",
-            args="{kwopts} {node_id}".format(kwopts=self._stringify_kwopts(kwopts), node_id=node_id),
+            args=f"{self._stringify_kwopts(kwopts)} {node_id}",
         )
 
     @docker_json

lib/galaxy/datatypes/blast.py

@@ -102,7 +102,7 @@ def merge(split_files, output_file):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("Given no BLAST XML files, %r, to merge into %s" % (split_files, output_file))
+            raise ValueError(f"Given no BLAST XML files, {split_files!r}, to merge into {output_file}")
         with open(output_file, "w") as out:
             h = None
             old_header = None

lib/galaxy/datatypes/goldenpath.py

@@ -151,7 +151,7 @@ def _read_file(self):
 
         line_number = 0
         in_body = False
-        with open(self.fname, "r") as f:
+        with open(self.fname) as f:
             for line in f:
                 line_number += 1
                 line = line.rstrip("\n")
@@ -217,14 +217,12 @@ def num_lines(self):
 
     def iterate_objs(self):
         """Iterate over the objects of the AGP file."""
-        for obj in self._objects:
-            yield obj
+        yield from self._objects
 
     def iterate_lines(self):
         """Iterate over the non-comment lines of AGP file."""
         for obj in self.iterate_objs():
-            for j in obj.iterate_lines():
-                yield j
+            yield from obj.iterate_lines()
 
 
 class AGPObject:
@@ -302,11 +300,10 @@ def add_line(self, agp_line):
         self._agp_lines.append(agp_line)
 
     def iterate_lines(self):
-        for i in self._agp_lines:
-            yield i
+        yield from self._agp_lines
 
 
-class AGPLine(object, metaclass=abc.ABCMeta):
+class AGPLine(metaclass=abc.ABCMeta):
     """
     An abstract base class representing a single AGP file line. Inheriting subclasses should
     override or implement new methods to check the validity of a single AFP line. Validity
@@ -388,7 +385,7 @@ def __init__(
         self.orientation = orientation
 
         # Set the object attributes and perform superclass-defined validations
-        super(AGPSeqLine, self).__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
+        super().__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
 
         self.is_gap = False
         self.seqdict = dict(
@@ -509,7 +506,7 @@ def __init__(
         self.linkage_evidence = linkage_evidence
 
         # Set the object attributes and perform superclass-defined validations
-        super(AGPGapLine, self).__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
+        super().__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type)
 
         self.is_gap = True
         self.gapdict = dict(

lib/galaxy/datatypes/interval.py

@@ -315,9 +315,7 @@ def ucsc_links(self, dataset, type, app, base_url):
                 "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
                 % (base_url, app.url_for(controller="root"), dataset.id, type)
             )
-            redirect_url = quote_plus(
-                "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop)
-            )
+            redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
             link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
             ret_val.append((site_name, link))
         return ret_val
@@ -933,7 +931,7 @@ def ucsc_links(self, dataset, type, app, base_url):
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build("ucsc", dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites("ucsc"):
                     redirect_url = quote_plus(
-                        "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, seqid, start, stop)
+                        f"{site_url}db={dataset.dbkey}&position={seqid}:{start}-{stop}&hgt.customText=%s"
                     )
                     link = self._get_remote_call_url(redirect_url, site_name, dataset, type, app, base_url)
                     ret_val.append((site_name, link))

lib/galaxy/datatypes/molecules.py

@@ -360,7 +360,7 @@ def merge(split_files, output_file):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("No fps files given, %r, to merge into %s" % (split_files, output_file))
+            raise ValueError(f"No fps files given, {split_files!r}, to merge into {output_file}")
         with open(output_file, "w") as out:
             first = True
             for filename in split_files:
@@ -940,7 +940,7 @@ def merge(split_files, output_file):
             # For one file only, use base class method (move/copy)
             return Text.merge(split_files, output_file)
         if not split_files:
-            raise ValueError("Given no CML files, %r, to merge into %s" % (split_files, output_file))
+            raise ValueError(f"Given no CML files, {split_files!r}, to merge into {output_file}")
         with open(output_file, "w") as out:
             for filename in split_files:
                 with open(filename) as handle:

lib/galaxy/datatypes/neo4j.py

@@ -34,7 +34,7 @@ def generate_primary_file(self, dataset=None):
             opt_text = ""
             if composite_file.optional:
                 opt_text = " (optional)"
-            rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
+            rval.append(f'<li><a href="{composite_name}">{composite_name}</a>{opt_text}')
         rval.append("</ul></html>")
         return "\n".join(rval)
 

lib/galaxy/datatypes/spaln.py

@@ -64,7 +64,7 @@ def generate_primary_file(self, dataset=None):
                     % (fn, fn, composite_file.get("description"), opt_text)
                 )
             else:
-                rval.append('<li><a href="%s" type="application/binary">%s</a>%s</li>' % (fn, fn, opt_text))
+                rval.append(f'<li><a href="{fn}" type="application/binary">{fn}</a>{opt_text}</li>')
         rval.append("</ul></div></html>")
         return "\n".join(rval)
 
@@ -141,7 +141,7 @@ def display_data(self, trans, data, preview=False, filename=None, to_ext=None, s
             msg = title
         # Galaxy assumes HTML for the display of composite datatypes,
         return (
-            smart_str("<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg)),
+            smart_str(f"<html><head><title>{title}</title></head><body><pre>{msg}</pre></body></html>"),
             headers,
         )
 

lib/galaxy/datatypes/util/gff_util.py

@@ -121,7 +121,7 @@ def __init__(
         for interval in self.intervals:
             # Error checking. NOTE: intervals need not share the same strand.
             if interval.chrom != self.chrom:
-                raise ValueError("interval chrom does not match self chrom: %s != %s" % (interval.chrom, self.chrom))
+                raise ValueError(f"interval chrom does not match self chrom: {interval.chrom} != {self.chrom}")
             # Set start, end of interval.
             if interval.start < self.start:
                 self.start = interval.start

lib/galaxy/managers/base.py

@@ -173,11 +173,11 @@ def get_object(trans, id, class_name, check_ownership=False, check_accessible=Fa
         security_check(trans, item, check_ownership, check_accessible)
     if deleted is True and not item.deleted:
         raise exceptions.ItemDeletionException(
-            '%s "%s" is not deleted' % (class_name, getattr(item, "name", id)), type="warning"
+            '{} "{}" is not deleted'.format(class_name, getattr(item, "name", id)), type="warning"
         )
     elif deleted is False and item.deleted:
         raise exceptions.ItemDeletionException(
-            '%s "%s" is deleted' % (class_name, getattr(item, "name", id)), type="warning"
+            '{} "{}" is deleted'.format(class_name, getattr(item, "name", id)), type="warning"
         )
     return item
 

lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py

@@ -77,7 +77,7 @@ def upgrade(migrate_engine):
             # handle tool_version_associaions because we do not have the information we need to do so.
             tools = repository_metadata.get("tools", [])
             for tool_dict in tools:
-                cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % (
+                cmd = "INSERT INTO tool_version VALUES ({}, {}, {}, '{}', {})".format(
                     nextval(migrate_engine, "tool_version"),
                     localtimestamp(migrate_engine),
                     localtimestamp(migrate_engine),

lib/galaxy/objectstore/cloud.py

@@ -614,7 +614,7 @@ def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {str(obj)}, kwargs: {str(kwargs)}")
 
     def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
@@ -711,7 +711,7 @@ def _get_filename(self, obj, **kwargs):
         # even if it does not exist.
         # if dir_only:
         #     return cache_path
-        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {str(obj)}, kwargs: {str(kwargs)}")
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -737,7 +737,7 @@ def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
             self._push_to_os(rel_path, source_file)
         else:
             raise ObjectNotFound(
-                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
+                f"objectstore.update_from_file, object does not exist: {str(obj)}, kwargs: {str(kwargs)}"
             )
 
     def _get_object_url(self, obj, **kwargs):

lib/galaxy/objectstore/irods.py

@@ -542,7 +542,7 @@ def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {str(obj)}, kwargs: {str(kwargs)}")
 
     def _size(self, obj, **kwargs):
         ipt_timer = ExecutionTimer()
@@ -682,7 +682,7 @@ def _get_filename(self, obj, **kwargs):
         # if dir_only:
         #     return cache_path
         log.debug("irods_pt _get_filename: %s", ipt_timer)
-        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {str(obj)}, kwargs: {str(kwargs)}")
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -710,7 +710,7 @@ def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         else:
             log.debug("irods_pt _update_from_file: %s", ipt_timer)
             raise ObjectNotFound(
-                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
+                f"objectstore.update_from_file, object does not exist: {str(obj)}, kwargs: {str(kwargs)}"
             )
         log.debug("irods_pt _update_from_file: %s", ipt_timer)
 

lib/galaxy/objectstore/s3.py

@@ -626,7 +626,7 @@ def _empty(self, obj, **kwargs):
         if self._exists(obj, **kwargs):
             return bool(self._size(obj, **kwargs) > 0)
         else:
-            raise ObjectNotFound("objectstore.empty, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs)))
+            raise ObjectNotFound(f"objectstore.empty, object does not exist: {str(obj)}, kwargs: {str(kwargs)}")
 
     def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
@@ -723,7 +723,7 @@ def _get_filename(self, obj, **kwargs):
         # even if it does not exist.
         # if dir_only:
         #     return cache_path
-        raise ObjectNotFound("objectstore.get_filename, no cache_path: %s, kwargs: %s" % (str(obj), str(kwargs)))
+        raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {str(obj)}, kwargs: {str(kwargs)}")
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
     def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
@@ -749,7 +749,7 @@ def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
             self._push_to_os(rel_path, source_file)
         else:
             raise ObjectNotFound(
-                "objectstore.update_from_file, object does not exist: %s, kwargs: %s" % (str(obj), str(kwargs))
+                f"objectstore.update_from_file, object does not exist: {str(obj)}, kwargs: {str(kwargs)}"
             )
 
     def _get_object_url(self, obj, **kwargs):

lib/galaxy/queue_worker.py

@@ -299,7 +299,9 @@ def admin_job_lock(app, **kwargs):
     # point, so we're using the reference from the handler.
     app.job_manager.job_lock = job_lock
     log.info(
-        "Administrative Job Lock is now set to %s. Jobs will %s dispatch." % (job_lock, "not" if job_lock else "now")
+        "Administrative Job Lock is now set to {}. Jobs will {} dispatch.".format(
+            job_lock, "not" if job_lock else "now"
+        )
     )
 
 

lib/galaxy/security/vault.py

@@ -260,7 +260,7 @@ def list_secrets(self, key: str) -> List[str]:
         raise NotImplementedError()
 
 
-class VaultFactory(object):
+class VaultFactory:
     @staticmethod
     def load_vault_config(vault_conf_yml: str) -> Optional[dict]:
         if os.path.exists(vault_conf_yml):

lib/galaxy/tool_shed/galaxy_install/install_manager.py

@@ -228,7 +228,7 @@ def install_specified_tool_dependencies(self, tool_shed_repository, tool_depende
                                 elem, tool_shed_repository, tool_dependencies=tool_dependencies
                             )
                         except Exception as e:
-                            error_message = "Error installing tool dependency %s version %s: %s" % (
+                            error_message = "Error installing tool dependency {} version {}: {}".format(
                                 str(name),
                                 str(version),
                                 str(e),
@@ -553,7 +553,7 @@ def __get_install_info_from_tool_shed(self, tool_shed_url, name, owner, changese
             )
         except Exception:
             message = "Error attempting to retrieve installation information from tool shed "
-            message += "%s for revision %s of repository %s owned by %s" % (
+            message += "{} for revision {} of repository {} owned by {}".format(
                 tool_shed_url,
                 changeset_revision,
                 name,

lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py

@@ -874,7 +874,7 @@ def purge_repository(self, repository):
             # Purge the repository.
             sa_session.delete(repository)
             sa_session.flush()
-            message = "The repository named <b>%s</b> with status <b>%s</b> has been purged.<br/>" % (
+            message = "The repository named <b>{}</b> with status <b>{}</b> has been purged.<br/>".format(
                 str(repository.name),
                 str(repository.status),
             )
@@ -909,13 +909,13 @@ def remove_entry_from_installed_repository_dependencies_of_installed_repositorie
         altered_installed_dependent_repositories_of_installed_repositories = {}
         for r_tup, v_tups in self.installed_dependent_repositories_of_installed_repositories.items():
             if repository_tup in v_tups:
-                debug_msg = "Removing entry for revision %s of repository %s owned by %s " % (
+                debug_msg = "Removing entry for revision {} of repository {} owned by {} ".format(
                     installed_changeset_revision,
                     name,
                     owner,
                 )
                 r_tool_shed, r_name, r_owner, r_installed_changeset_revision = r_tup
-                debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % (
+                debug_msg += "from the dependent list for revision {} of repository {} owned by {} ".format(
                     r_installed_changeset_revision,
                     r_name,
                     r_owner,