From 24ed7fcc0de95d0ac739119ac83d962ba8da2d36 Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Thu, 24 Sep 2020 18:04:11 +0300
Subject: [PATCH 01/13] fix folder path

---
 client/src/mvc/library/library-libraryrow-view.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/mvc/library/library-libraryrow-view.js b/client/src/mvc/library/library-libraryrow-view.js
index 279bb590d0a..f895bb4f163 100644
--- a/client/src/mvc/library/library-libraryrow-view.js
+++ b/client/src/mvc/library/library-libraryrow-view.js
@@ -243,7 +243,7 @@ var LibraryRowView = Backbone.View.extend({
                         <td style="color:grey;"><%- library.get("name") %></td>
                     <% } else { %>
                         <td>
-                            <a href="folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a>
+                            <a href="/library/folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a>
                         </td>
                     <% } %>
                     <% if(library.get("description")) { %>

From da59a4cbe8e5db5d758f21aa84ee62d914fa749f Mon Sep 17 00:00:00 2001
From: Oleg Zharkov <oleg.zharkov22@gmail.com>
Date: Fri, 25 Sep 2020 13:39:53 +0300
Subject: [PATCH 02/13] use getAppRoot()

---
 client/src/mvc/library/library-folder-view.js     | 4 ++--
 client/src/mvc/library/library-libraryrow-view.js | 4 +++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/client/src/mvc/library/library-folder-view.js b/client/src/mvc/library/library-folder-view.js
index 961374b8041..2a9c8719504 100644
--- a/client/src/mvc/library/library-folder-view.js
+++ b/client/src/mvc/library/library-folder-view.js
@@ -66,7 +66,7 @@ var FolderView = Backbone.View.extend({
             is_admin = Galaxy.user.isAdmin();
         }
         var template = this.templateFolderPermissions();
-        this.$el.html(template({ folder: this.model, is_admin: is_admin }));
+        this.$el.html(template({ folder: this.model, is_admin: is_admin, root_path: getAppRoot() }));
 
         var self = this;
         $.get(`${getAppRoot()}api/folders/${self.id}/permissions?scope=current`)
@@ -204,7 +204,7 @@ var FolderView = Backbone.View.extend({
         return _.template(
             `<div class="library_style_container">
                 <div>
-                    <a href="/library/folders/<%= folder.get("parent_id") %>">
+                    <a href="<%- root_path %>library/folders/<%= folder.get("parent_id") %>">
                         <button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder"
                             class="btn btn-secondary primary-button" type="button">
                             <span class="fa fa-caret-left fa-lg"/>
diff --git a/client/src/mvc/library/library-libraryrow-view.js b/client/src/mvc/library/library-libraryrow-view.js
index f895bb4f163..f405f6aa07d 100644
--- a/client/src/mvc/library/library-libraryrow-view.js
+++ b/client/src/mvc/library/library-libraryrow-view.js
@@ -4,6 +4,7 @@ import Backbone from "backbone";
 import { Toast } from "ui/toast";
 import { getGalaxyInstance } from "app";
 import { linkifyHtmlElements } from "mvc/library/library-util";
+import { getAppRoot } from "onload/loadConfig";
 
 // galaxy library row view
 var LibraryRowView = Backbone.View.extend({
@@ -44,6 +45,7 @@ var LibraryRowView = Backbone.View.extend({
                 library: library,
                 button_config: this.element_visibility_config,
                 edit_mode: this.edit_mode,
+                root_path: getAppRoot(),
             })
         );
         this.$el.show();
@@ -243,7 +245,7 @@ var LibraryRowView = Backbone.View.extend({
                         <td style="color:grey;"><%- library.get("name") %></td>
                     <% } else { %>
                         <td>
-                            <a href="/library/folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a>
+                            <a href="<%- root_path %>library/folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a>
                         </td>
                     <% } %>
                     <% if(library.get("description")) { %>

From 04186715e93a9ad25a10c3164ee585ea2e02c11e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 1 Oct 2020 20:17:36 +0200
Subject: [PATCH 03/13] Drop unused models

---
 lib/galaxy/model/__init__.py | 17 -----------------
 lib/galaxy/model/mapping.py  | 24 ------------------------
 2 files changed, 41 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index e211956bb0b..3af02e0c4b6 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3898,19 +3898,6 @@ class LibraryDatasetDatasetInfoAssociation(RepresentById):
         return True  # always allow inheriting, used for replacement
 
 
-class ValidationError(RepresentById):
-    def __init__(self, message=None, err_type=None, attributes=None):
-        self.message = message
-        self.err_type = err_type
-        self.attributes = attributes
-
-
-class DatasetToValidationErrorAssociation:
-    def __init__(self, dataset, validation_error):
-        self.dataset = dataset
-        self.validation_error = validation_error
-
-
 class ImplicitlyConvertedDatasetAssociation(RepresentById):
 
     def __init__(self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True):
@@ -6159,10 +6146,6 @@ class HistoryTagAssociation(ItemTagAssociation, RepresentById):
     pass
 
 
-class DatasetTagAssociation(ItemTagAssociation, RepresentById):
-    pass
-
-
 class HistoryDatasetAssociationTagAssociation(ItemTagAssociation, RepresentById):
     pass
 
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index d6dc167fcd1..11e84951eca 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -333,14 +333,6 @@ model.ImplicitlyConvertedDatasetAssociation.table = Table(
     Column("metadata_safe", Boolean, index=True, default=True),
     Column("type", TrimmedString(255)))
 
-model.ValidationError.table = Table(
-    "validation_error", metadata,
-    Column("id", Integer, primary_key=True),
-    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
-    Column("message", TrimmedString(255)),
-    Column("err_type", TrimmedString(64)),
-    Column("attributes", TEXT))
-
 model.Group.table = Table(
     "galaxy_group", metadata,
     Column("id", Integer, primary_key=True),
@@ -1342,16 +1334,6 @@ model.HistoryTagAssociation.table = Table(
     Column("value", TrimmedString(255), index=True),
     Column("user_value", TrimmedString(255), index=True))
 
-model.DatasetTagAssociation.table = Table(
-    "dataset_tag_association", metadata,
-    Column("id", Integer, primary_key=True),
-    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
-    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
-    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
-    Column("user_tname", TrimmedString(255), index=True),
-    Column("value", TrimmedString(255), index=True),
-    Column("user_value", TrimmedString(255), index=True))
-
 model.HistoryDatasetAssociationTagAssociation.table = Table(
     "history_dataset_association_tag_association", metadata,
     Column("id", Integer, primary_key=True),
@@ -1720,8 +1702,6 @@ mapper(model.CloudAuthz, model.CloudAuthz.table, properties=dict(
                    backref='cloudauthz')
 ))
 
-mapper(model.ValidationError, model.ValidationError.table)
-
 simple_mapping(model.DynamicTool)
 
 simple_mapping(model.HistoryDatasetAssociation,
@@ -1785,9 +1765,6 @@ simple_mapping(model.Dataset,
         primaryjoin=(
             (model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id) &
             (model.LibraryDatasetDatasetAssociation.table.c.deleted == false()))),
-    tags=relation(model.DatasetTagAssociation,
-        order_by=model.DatasetTagAssociation.table.c.id,
-        backref='datasets')
 )
 
 mapper(model.DatasetHash, model.DatasetHash.table, properties=dict(
@@ -2752,7 +2729,6 @@ def tag_mapping(tag_association_class, backref_name):
 
 
 tag_mapping(model.HistoryTagAssociation, "tagged_histories")
-tag_mapping(model.DatasetTagAssociation, "tagged_datasets")
 tag_mapping(model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations")
 tag_mapping(model.LibraryDatasetDatasetAssociationTagAssociation, "tagged_library_dataset_dataset_associations")
 tag_mapping(model.PageTagAssociation, "tagged_pages")

From d97606186c5986c20fcde2b38c6e2bd490db3d6c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 1 Oct 2020 20:20:05 +0200
Subject: [PATCH 04/13] Add missing indexes

---
 .../versions/0169_add_missing_indexes.py      | 130 ++++++++++++++++++
 lib/galaxy/model/migrate/versions/util.py     |  14 ++
 2 files changed, 144 insertions(+)
 create mode 100644 lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py

diff --git a/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py b/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py
new file mode 100644
index 00000000000..a9b56294e59
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0169_add_missing_indexes.py
@@ -0,0 +1,130 @@
+"""
+Migration script to create missing indexes.  Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True.
+"""
+
+import logging
+
+from sqlalchemy import MetaData
+
+from galaxy.model.migrate.versions.util import (
+    add_index,
+    drop_index
+)
+
+log = logging.getLogger(__name__)
+metadata = MetaData()
+
+indexes = [
+    [
+        "ix_galaxy_user_activation_token",
+        "galaxy_user",
+        "activation_token"
+    ],
+    [
+        "ix_workflow_step_dynamic_tool_id",
+        "workflow_step",
+        "dynamic_tool_id"
+    ],
+    [
+        "ix_history_dataset_association_version",
+        "history_dataset_association",
+        "version"
+    ],
+    [
+        "ix_workflow_invocation_scheduler",
+        "workflow_invocation",
+        "scheduler"
+    ],
+    [
+        "ix_page_slug",
+        "page",
+        "slug"
+    ],
+    [
+        "ix_workflow_invocation_state",
+        "workflow_invocation",
+        "state"
+    ],
+    [
+        "ix_history_dataset_collection_association_implicit_collection_jobs_id",
+        "history_dataset_collection_association",
+        "implicit_collection_jobs_id"
+    ],
+    [
+        "ix_workflow_step_subworkflow_id",
+        "workflow_step",
+        "subworkflow_id"
+    ],
+    [
+        "ix_dynamic_tool_update_time",
+        "dynamic_tool",
+        "update_time"
+    ],
+    [
+        "ix_library_dataset_dataset_association_extended_metadata_id",
+        "library_dataset_dataset_association",
+        "extended_metadata_id"
+    ],
+    [
+        "ix_workflow_invocation_step_implicit_collection_jobs_id",
+        "workflow_invocation_step",
+        "implicit_collection_jobs_id"
+    ],
+    [
+        "ix_workflow_invocation_step_state",
+        "workflow_invocation_step",
+        "state"
+    ],
+    [
+        "ix_workflow_invocation_history_id",
+        "workflow_invocation",
+        "history_id"
+    ],
+    [
+        "ix_workflow_parent_workflow_id",
+        "workflow",
+        "parent_workflow_id"
+    ],
+    [
+        "ix_metadata_file_uuid",
+        "metadata_file",
+        "uuid"
+    ],
+    [
+        "ix_history_dataset_collection_association_job_id",
+        "history_dataset_collection_association",
+        "job_id"
+    ],
+    [
+        "ix_galaxy_user_active",
+        "galaxy_user",
+        "active"
+    ],
+    [
+        "ix_job_dynamic_tool_id",
+        "job",
+        "dynamic_tool_id"
+    ],
+    [
+        "ix_history_dataset_association_extended_metadata_id",
+        "history_dataset_association",
+        "extended_metadata_id"
+    ]
+]
+
+
+def upgrade(migrate_engine):
+    print(__doc__)
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    for ix, table, col in indexes:
+        add_index(ix, table, col, metadata)
+
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    for ix, table, col in indexes:
+        drop_index(ix, table, col, metadata)
diff --git a/lib/galaxy/model/migrate/versions/util.py b/lib/galaxy/model/migrate/versions/util.py
index 273939147b2..9b9334ba9e9 100644
--- a/lib/galaxy/model/migrate/versions/util.py
+++ b/lib/galaxy/model/migrate/versions/util.py
@@ -1,3 +1,4 @@
+import hashlib
 import logging
 
 from sqlalchemy import (
@@ -47,6 +48,14 @@ def localtimestamp(migrate_engine):
         raise Exception('Unable to convert data for unknown database type: %s' % migrate_engine.name)
 
 
+def truncate_index_name(index_name, engine):
+    # does what sqlalchemy does, see https://github.com/sqlalchemy/sqlalchemy/blob/8455a11bcc23e97afe666873cd872b0f204848d8/lib/sqlalchemy/sql/compiler.py#L4696
+    max_index_name_length = engine.dialect.max_index_name_length or engine.dialect.max_identifier_length
+    if len(index_name) > max_index_name_length:
+        suffix = hashlib.md5(index_name.encode('utf-8')).hexdigest()[-4:]
+        index_name = "{trunc}_{suffix}".format(trunc=index_name[0 : max_index_name_length - 8], suffix=suffix)
+    return index_name
+
 def create_table(table):
     try:
         table.create()
@@ -135,10 +144,14 @@ def add_index(index_name, table, column_name, metadata=None, **kwds):
     :param metadata: Needed only if ``table`` is a table name
     :type metadata: :class:`Metadata`
     """
+    if len(index_name) > 63 and metadata.bind.name in ('postgres', 'postgresql'):
+        suffix = hashlib.md5(index_name.encode('utf-8')).hexdigest()[-4:]
+
     try:
         if not isinstance(table, Table):
             assert metadata is not None
             table = Table(table, metadata, autoload=True)
+        index_name = truncate_index_name(index_name, table.metadata.bind)
         if index_name not in [ix.name for ix in table.indexes]:
             column = table.c[column_name]
             # MySQL cannot index a TEXT/BLOB column without specifying mysql_length
@@ -168,6 +181,7 @@ def drop_index(index, table, column_name=None, metadata=None):
             if not isinstance(table, Table):
                 assert metadata is not None
                 table = Table(table, metadata, autoload=True)
+            index = truncate_index_name(index, table.metadata.bind)
             if index in [ix.name for ix in table.indexes]:
                 index = Index(index, table.c[column_name])
             else:

From 3af877573aeb170c75bfe94d8e8dbffbf9fdd8fd Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 2 Oct 2020 10:47:19 +0200
Subject: [PATCH 05/13] Cleanup add_index/drop_index

---
 lib/galaxy/model/migrate/versions/util.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/model/migrate/versions/util.py b/lib/galaxy/model/migrate/versions/util.py
index 9b9334ba9e9..feb36210150 100644
--- a/lib/galaxy/model/migrate/versions/util.py
+++ b/lib/galaxy/model/migrate/versions/util.py
@@ -56,6 +56,7 @@ def truncate_index_name(index_name, engine):
         index_name = "{trunc}_{suffix}".format(trunc=index_name[0 : max_index_name_length - 8], suffix=suffix)
     return index_name
 
+
 def create_table(table):
     try:
         table.create()
@@ -144,9 +145,6 @@ def add_index(index_name, table, column_name, metadata=None, **kwds):
     :param metadata: Needed only if ``table`` is a table name
     :type metadata: :class:`Metadata`
     """
-    if len(index_name) > 63 and metadata.bind.name in ('postgres', 'postgresql'):
-        suffix = hashlib.md5(index_name.encode('utf-8')).hexdigest()[-4:]
-
     try:
         if not isinstance(table, Table):
             assert metadata is not None
@@ -181,9 +179,9 @@ def drop_index(index, table, column_name=None, metadata=None):
             if not isinstance(table, Table):
                 assert metadata is not None
                 table = Table(table, metadata, autoload=True)
-            index = truncate_index_name(index, table.metadata.bind)
-            if index in [ix.name for ix in table.indexes]:
-                index = Index(index, table.c[column_name])
+            index_name = truncate_index_name(index, table.metadata.bind)
+            if index_name in [ix.name for ix in table.indexes]:
+                index = Index(index_name, table.c[column_name])
             else:
                 log.debug("Index '%s' in table '%s' does not exist.", index, table)
                 return

From ecf34f3b3754573ebc04961989069d9b7c28c2b0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 5 Oct 2020 15:55:46 +0200
Subject: [PATCH 06/13] Don't use subquery to update workflow invocation step
 update time

Thanks Nate, I don't think the subqeury was needed.
---
 lib/galaxy/model/__init__.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 3af02e0c4b6..e72b09b6ca7 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1158,10 +1158,7 @@ class Job(JobLike, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
         ''', '''
             UPDATE workflow_invocation_step
             SET update_time = :update_time
-            WHERE id in (
-                SELECT workflow_invocation_step.id
-                FROM workflow_invocation_step wis
-                WHERE wis.job_id = :job_id
+            WHERE job_id = :job_id
             );
         ''']
         sa_session = object_session(self)

From 1c76fbd18d17b35652361cc12f0aa930cab87f30 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Mon, 5 Oct 2020 17:18:12 +0200
Subject: [PATCH 07/13] Drop parens

Thanks Dannon!

Co-authored-by: Dannon <dannon.baker@gmail.com>
---
 lib/galaxy/model/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index e72b09b6ca7..bbe4367172f 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1158,8 +1158,7 @@ class Job(JobLike, UsesCreateAndUpdateTime, Dictifiable, RepresentById):
         ''', '''
             UPDATE workflow_invocation_step
             SET update_time = :update_time
-            WHERE job_id = :job_id
-            );
+            WHERE job_id = :job_id;
         ''']
         sa_session = object_session(self)
         params = {

From a681ebfa3fbb8b5266ff1c7300ed22ff73ef7a3c Mon Sep 17 00:00:00 2001
From: Helena Rasche <hxr@hx42.org>
Date: Tue, 6 Oct 2020 10:45:35 +0200
Subject: [PATCH 08/13] Fix chrome-only scrolling bug with GTN webhook

Content is reflown upon display changes, meaning that in chrome the iframe fails to retain it's original scroll offset. This fixes it by using visibility in place of display, thus preventing a content reflow.
---
 config/plugins/webhooks/gtn/script.js | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index b70527daec7..4702c1b4a45 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -1,7 +1,11 @@
 var gtnWebhookLoaded = false;
 
 function removeOverlay() {
-    document.getElementById("gtn-container").classList.add("d-none");
+    document.getElementById("gtn-container").style.visibility = 'hidden';
+}
+
+function showOverlay() {
+    document.getElementById("gtn-container").style.visibility = 'visible';
 }
 
 function addIframe() {
@@ -105,7 +109,7 @@ elementReady("#gtn a").then((el) => {
         if (!gtnWebhookLoaded) {
             addIframe();
         } else {
-            document.getElementById("gtn-container").classList.toggle("d-none");
+            showOverlay();
         }
     });
 });

From f7697a06cd2a92392552d061ccd7a4871d79867f Mon Sep 17 00:00:00 2001
From: cat-bro <cathjb@gmail.com>
Date: Thu, 1 Oct 2020 14:41:25 +1000
Subject: [PATCH 09/13] sort installed tools by ctx_rev prior to selecting the
 first from each name/owner

sort installed tools by ctx_rev prior to selecting the first from each name/owner

add some ;;;;;

prettier --write

another prettier file
---
 .../components/Toolshed/InstalledList/Index.vue  | 10 +++-------
 client/src/components/Toolshed/services.js       | 16 ++++++++++++++--
 client/src/components/Toolshed/services.test.js  |  7 ++++++-
 3 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/client/src/components/Toolshed/InstalledList/Index.vue b/client/src/components/Toolshed/InstalledList/Index.vue
index 5cd31cedf64..5f61b916b61 100644
--- a/client/src/components/Toolshed/InstalledList/Index.vue
+++ b/client/src/components/Toolshed/InstalledList/Index.vue
@@ -33,9 +33,7 @@
                     <template v-slot:cell(name)="row">
                         <b-link href="#" role="button" class="font-weight-bold" @click="row.toggleDetails">
                             <div v-if="!isLatest(row.item)">
-                                <b-badge variant="danger" class="mb-2">
-                                    Newer version available!
-                                </b-badge>
+                                <b-badge variant="danger" class="mb-2"> Newer version available! </b-badge>
                             </div>
                             <div class="name">{{ row.item.name }}</div>
                         </b-link>
@@ -49,9 +47,7 @@
                     No matching entries found for: <span class="font-weight-bold">{{ this.filter }}</span
                     >.
                 </div>
-                <div v-if="showNotAvailable">
-                    No installed repositories found.
-                </div>
+                <div v-if="showNotAvailable">No installed repositories found.</div>
             </div>
         </div>
     </div>
@@ -123,7 +119,7 @@ export default {
         load() {
             this.loading = true;
             this.services
-                .getInstalledRepositories()
+                .getInstalledRepositories({ selectLatest: true })
                 .then((repositories) => {
                     this.repositories = repositories;
                     this.nRepositories = repositories.length;
diff --git a/client/src/components/Toolshed/services.js b/client/src/components/Toolshed/services.js
index 0aab5f52fc9..0c78f080134 100644
--- a/client/src/components/Toolshed/services.js
+++ b/client/src/components/Toolshed/services.js
@@ -78,7 +78,7 @@ export class Services {
         const url = `${getAppRoot()}api/tool_shed_repositories/?uninstalled=False`;
         try {
             const response = await axios.get(url);
-            const repositories = this._groupByNameOwner(response.data, options.filter);
+            const repositories = this._groupByNameOwner(response.data, options.filter, options.selectLatest);
             this._fixToolshedUrls(repositories, Galaxy.config.tool_shed_urls);
             return repositories;
         } catch (e) {
@@ -125,7 +125,19 @@ export class Services {
             rethrowSimple(e);
         }
     }
-    _groupByNameOwner(incoming, filter) {
+    _groupByNameOwner(incoming, filter, selectLatest) {
+        if (selectLatest) {
+            const getSortValue = (x, y) => {
+                return x == y ? 0 : x < y ? -1 : 1;
+            };
+            incoming = incoming.sort((a, b) => {
+                return (
+                    getSortValue(a.name, b.name) ||
+                    getSortValue(a.owner, b.owner) ||
+                    getSortValue(parseInt(b.ctx_rev), parseInt(a.ctx_rev))
+                );
+            });
+        }
         const hash = {};
         const repositories = [];
         incoming.forEach((x) => {
diff --git a/client/src/components/Toolshed/services.test.js b/client/src/components/Toolshed/services.test.js
index ba17d54b19a..ed3d573bffd 100644
--- a/client/src/components/Toolshed/services.test.js
+++ b/client/src/components/Toolshed/services.test.js
@@ -8,6 +8,7 @@ describe("Toolshed service helpers", () => {
             status: "status_0_0",
             description: "description_0_0",
             tool_shed: "url_1",
+            ctx_rev: "1",
         },
         {
             name: "name_0",
@@ -15,6 +16,7 @@ describe("Toolshed service helpers", () => {
             status: "status_0_1",
             description: "description_0_1",
             tool_shed: "url_1",
+            ctx_rev: "3",
         },
         {
             name: "name_1",
@@ -22,6 +24,7 @@ describe("Toolshed service helpers", () => {
             status: "status_1",
             description: "description_1",
             tool_shed: "url_2",
+            ctx_rev: "42",
         },
         {
             name: "name_2",
@@ -29,6 +32,7 @@ describe("Toolshed service helpers", () => {
             status: "Installed",
             description: "description_2",
             tool_shed: "url_2",
+            ctx_rev: "1",
         },
     ];
     const urls = ["http://url_1.com", "http://url_2.com"];
@@ -36,11 +40,12 @@ describe("Toolshed service helpers", () => {
     it("test fix toolshed helper", () => {
         const services = new Services();
         const filter = (x) => x.status !== "Installed";
-        const grouped = services._groupByNameOwner(incoming, filter);
+        const grouped = services._groupByNameOwner(incoming, filter, true);
         services._fixToolshedUrls(grouped, urls);
         expect(grouped.length).toBe(2);
         expect(grouped[0].name).toBe("name_0");
         expect(grouped[0].tool_shed_url).toBe("http://url_1.com");
+        expect(grouped[0].ctx_rev).toBe("3");
         expect(grouped[1].name === "name_1");
         expect(grouped[1].tool_shed_url).toBe("http://url_2.com");
     });

From 60a83c446d34eb75c3c2b3565716a0b61c173d75 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 6 Oct 2020 10:03:24 +0200
Subject: [PATCH 10/13] Also order repository revisions on the backend

---
 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
index ba5b5a99966..8755ccdc863 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
@@ -6,7 +6,11 @@ from paste.httpexceptions import (
     HTTPBadRequest,
     HTTPForbidden
 )
-from sqlalchemy import and_
+from sqlalchemy import (
+    and_,
+    cast,
+    Integer,
+)
 
 from galaxy import (
     exceptions,
@@ -82,7 +86,8 @@ class ToolShedRepositoriesController(BaseAPIController):
             clause_list.append(self.app.install_model.ToolShedRepository.table.c.uninstalled == util.asbool(kwd.get('uninstalled')))
         tool_shed_repository_dicts = []
         query = trans.install_model.context.query(self.app.install_model.ToolShedRepository) \
-                                           .order_by(self.app.install_model.ToolShedRepository.table.c.name)
+                                           .order_by(self.app.install_model.ToolShedRepository.table.c.name) \
+                                           .order_by(cast(self.app.install_model.ToolShedRepository.ctx_rev, Integer).desc())
         if len(clause_list) > 0:
             query = query.filter(and_(*clause_list))
         for tool_shed_repository in query.all():

From fe4f81ef6636bcf553816e04492f3a7fa7a1bf8b Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 6 Oct 2020 10:33:03 -0400
Subject: [PATCH 11/13] Standard quotes

---
 config/plugins/webhooks/gtn/script.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/plugins/webhooks/gtn/script.js b/config/plugins/webhooks/gtn/script.js
index 4702c1b4a45..0d98fdaac03 100644
--- a/config/plugins/webhooks/gtn/script.js
+++ b/config/plugins/webhooks/gtn/script.js
@@ -1,11 +1,11 @@
 var gtnWebhookLoaded = false;
 
 function removeOverlay() {
-    document.getElementById("gtn-container").style.visibility = 'hidden';
+    document.getElementById("gtn-container").style.visibility = "hidden";
 }
 
 function showOverlay() {
-    document.getElementById("gtn-container").style.visibility = 'visible';
+    document.getElementById("gtn-container").style.visibility = "visible";
 }
 
 function addIframe() {

From 1f4dafbc77d335345bdc47ebccde82c44b7cac7d Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 6 Oct 2020 14:02:27 -0400
Subject: [PATCH 12/13] Defer metadata strategy resolution in job wrapper.

---
 lib/galaxy/jobs/__init__.py | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 2487ca94c57..46a543374c8 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -911,19 +911,26 @@ class JobWrapper(HasResourceParameters):
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination(from_job=job)
         # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
-        try:
-            metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
-        except JobMappingException:
-            metadata_strategy_override = None
-        if job.tasks:
-            metadata_strategy_override = "directory"
-        self.external_output_metadata = get_metadata_compute_strategy(self.app.config, job.id, metadata_strategy_override=metadata_strategy_override, tool_id=job.tool_id)
+        self.__external_output_metadata = None
+        self.__has_tasks = bool(job.tasks)
 
         self.__commands_in_new_shell = True
         self.__user_system_pwent = None
         self.__galaxy_system_pwent = None
         self.__working_directory = None
 
+    @property
+    def external_output_metadata(self):
+        if self.__external_output_metadata is None:
+            try:
+                metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
+            except JobMappingException:
+                metadata_strategy_override = None
+            if self.__has_tasks:
+                metadata_strategy_override = "directory"
+            self.__external_output_metadata = get_metadata_compute_strategy(self.app.config, self.job_id, metadata_strategy_override=metadata_strategy_override, tool_id=self.tool.id)
+        return self.__external_output_metadata
+
     @property
     def _job_dataset_path_rewriter(self):
         if self._dataset_path_rewriter is None:

From a1e95411beae1648694965cbce4fd6a54f0e20af Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 7 Oct 2020 15:42:57 +0200
Subject: [PATCH 13/13] Fixes data_source tools

tool_ids may be a list, so need to strip `'/'` in `get_tool_components`
instead.

Broken in https://github.com/galaxyproject/galaxy/pull/10332
---
 lib/galaxy/tools/__init__.py                         | 3 +++
 lib/galaxy/webapps/galaxy/controllers/tool_runner.py | 3 ---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 8b61dfe8137..44c2632ed2b 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -372,6 +372,9 @@ class ToolBox(BaseGalaxyToolBox):
         # are now using only GALAXY_URL.
         tool_ids = listify(tool_id)
         for tool_id in tool_ids:
+            if tool_id.endswith('/'):
+                # Some data sources send back redirects ending with `/`, this takes care of that case
+                tool_id = tool_id[:-1]
             if get_loaded_tools_by_lineage:
                 tools = toolbox.get_loaded_tools_by_lineage(tool_id)
             else:
diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
index 51f77266c40..d7df059f86e 100644
--- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
+++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py
@@ -47,9 +47,6 @@ class ToolRunner(BaseUIController):
         # tool id not available, redirect to main page
         if tool_id is None:
             return trans.response.send_redirect(url_for(controller='root', action='welcome'))
-        if tool_id.endswith('/'):
-            # Probably caused by a redirect
-            tool_id = tool_id[:-1]
         tool = self.__get_tool(tool_id)
         # tool id is not matching, display an error
         if not tool: