Merge branch 'release_24.1' into dev

galaxyproject · Aug 7, 2024 · 5f635a3 · 5f635a3
2 parents 203573a + dfea749
commit 5f635a3
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diff --git a/client/src/components/Workflow/Invocation/Graph/InvocationGraph.vue b/client/src/components/Workflow/Invocation/Graph/InvocationGraph.vue
@@ -226,6 +226,7 @@ function toggleActiveStep(stepId: number) {
                 <div v-if="!hideGraph" class="position-relative w-100">
                     <BCard no-body>
                         <WorkflowGraph
+                            class="invocation-graph"
                             :steps="steps"
                             :datatypes-mapper="datatypesMapper"
                             :initial-position="initialPosition"
@@ -341,9 +342,15 @@ function toggleActiveStep(stepId: number) {
 
 .graph-steps-aside {
     overflow-y: scroll;
-    scroll-behavior: smooth;
     &.steps-fixed-height {
         max-height: 60vh;
     }
 }
+
+.invocation-graph {
+    &:deep(.workflow-overview),
+    &:deep(.zoom-control) {
+        z-index: 100;
+    }
+}
 </style>
diff --git a/client/src/components/Workflow/Invocation/Graph/WorkflowInvocationSteps.vue b/client/src/components/Workflow/Invocation/Graph/WorkflowInvocationSteps.vue
@@ -2,7 +2,7 @@
 import { library } from "@fortawesome/fontawesome-svg-core";
 import { faChevronDown, faChevronUp, faSignInAlt } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { computed, ref, watch } from "vue";
+import { computed, nextTick, ref, watch } from "vue";
 
 import type { WorkflowInvocationElementView } from "@/api/invocations";
 import { isWorkflowInput } from "@/components/Workflow/constants";
@@ -43,28 +43,28 @@ const props = withDefaults(defineProps<Props>(), {
 });
 
 const stepsDiv = ref<HTMLDivElement>();
-const expandInvocationInputs = ref(false);
 
 const workflowInputSteps = Object.values(props.workflow.steps).filter((step) => isWorkflowInput(step.type));
-const hasSingularInput = computed(() => workflowInputSteps.length === 1);
-const workflowRemainingSteps = hasSingularInput.value
-    ? Object.values(props.workflow.steps)
-    : Object.values(props.workflow.steps).filter((step) => !isWorkflowInput(step.type));
+const oneOrNoInput = computed(() => workflowInputSteps.length <= 1);
+const expandInvocationInputs = ref(oneOrNoInput.value);
 
 watch(
     () => [props.activeNodeId, stepsDiv.value],
     async ([nodeId, card]) => {
-        // if the active node id is an input step, expand the inputs section, else, collapse it
-        const isAnInput = workflowInputSteps.findIndex((step) => step.id === props.activeNodeId) !== -1;
-        expandInvocationInputs.value = isAnInput;
+        // if the active node id is an input step, expand the inputs section if not already expanded
+        if (!expandInvocationInputs.value) {
+            const isAnInput = workflowInputSteps.findIndex((step) => step.id === props.activeNodeId) !== -1;
+            expandInvocationInputs.value = isAnInput;
+        }
+
+        await nextTick();
 
         // on full page view, scroll to the active step card in the steps section
         if (props.isFullPage) {
             if (nodeId !== undefined && card) {
                 // scroll to the active step card
                 const stepCard = stepsDiv.value?.querySelector(`[data-index="${props.activeNodeId}"]`);
-                const portletHeaderDiv = stepCard?.querySelector(".portlet-header");
-                stepsDiv.value?.scrollTo({ top: portletHeaderDiv?.getBoundingClientRect().top });
+                stepCard?.scrollIntoView({ block: "nearest", inline: "start" });
             }
         }
         // clear any job being shown
@@ -81,7 +81,7 @@ function showJob(jobId: string | undefined) {
 <template>
     <div ref="stepsDiv" class="d-flex flex-column w-100">
         <!-- Input Steps grouped in a separate portlet -->
-        <div v-if="workflowInputSteps.length > 1" class="ui-portlet-section w-100">
+        <div v-if="!oneOrNoInput" class="ui-portlet-section w-100">
             <div
                 class="portlet-header portlet-operations"
                 role="button"
@@ -96,36 +96,21 @@ function showJob(jobId: string | undefined) {
                 </span>
                 <FontAwesomeIcon class="float-right" :icon="expandInvocationInputs ? faChevronUp : faChevronDown" />
             </div>
-
-            <div v-if="expandInvocationInputs" class="portlet-content m-1">
-                <WorkflowInvocationStep
-                    v-for="step in workflowInputSteps"
-                    :key="step.id"
-                    :data-index="step.id"
-                    :invocation="props.invocation"
-                    :workflow="props.workflow"
-                    :workflow-step="step"
-                    :in-graph-view="!props.hideGraph"
-                    :graph-step="steps[step.id]"
-                    :expanded="props.hideGraph ? undefined : props.activeNodeId === step.id"
-                    :showing-job-id="props.showingJobId"
-                    @show-job="showJob"
-                    @update:expanded="emit('focus-on-step', step.id)" />
-            </div>
         </div>
-        <!-- Non-Input (Tool/Subworkflow) Steps -->
-        <WorkflowInvocationStep
-            v-for="step in workflowRemainingSteps"
-            :key="step.id"
-            :data-index="step.id"
-            :invocation="props.invocation"
-            :workflow="props.workflow"
-            :workflow-step="step"
-            :in-graph-view="!props.hideGraph"
-            :graph-step="steps[step.id]"
-            :expanded="props.hideGraph ? undefined : props.activeNodeId === step.id"
-            :showing-job-id="props.showingJobId"
-            @show-job="showJob"
-            @update:expanded="emit('focus-on-step', step.id)" />
+        <div v-for="step in props.workflow.steps" :key="step.id">
+            <WorkflowInvocationStep
+                v-if="!isWorkflowInput(step.type) || (isWorkflowInput(step.type) && expandInvocationInputs)"
+                :class="{ 'mx-1': !oneOrNoInput && isWorkflowInput(step.type) }"
+                :data-index="step.id"
+                :invocation="props.invocation"
+                :workflow="props.workflow"
+                :workflow-step="step"
+                :in-graph-view="!props.hideGraph"
+                :graph-step="steps[step.id]"
+                :expanded="props.hideGraph ? undefined : props.activeNodeId === step.id"
+                :showing-job-id="props.showingJobId"
+                @show-job="showJob"
+                @update:expanded="emit('focus-on-step', step.id)" />
+        </div>
     </div>
 </template>
diff --git a/config/plugins/visualizations/h5web/package.json b/config/plugins/visualizations/h5web/package.json
@@ -8,16 +8,17 @@
     ],
     "license": "AFL-3.0",
     "dependencies": {
-        "@h5web/app": "^8.0.0",
+        "@h5web/app": "^12.0.1",
         "buffer": "^6.0.3",
         "normalize.css": "^8.0.1",
-        "react": "18.2.0",
-        "react-dom": "18.2.0"
+        "react": "18.3.1",
+        "react-dom": "18.3.1"
     },
     "scripts": {
         "build": "parcel build src/script.js --dist-dir static"
     },
     "devDependencies": {
-        "parcel": "^2.12.0"
+        "parcel": "^2.12.0",
+        "process": "^0.11.10"
     }
 }
diff --git a/doc/schema_template.md b/doc/schema_template.md
@@ -82,7 +82,7 @@ $tag:tool|outputs|data|actions|action://complexType[@name='Action']
 $tag:tool|outputs|data|actions|action|option://complexType[@name='ActionsOption']
 $tag:tool|outputs|data|discover_datasets://complexType[@name='OutputDiscoverDatasets']
 $tag:tool|outputs|collection://complexType[@name='OutputCollection']
-$tag:tool|outputs|collection|data://complexType[@name='OutputCollectionDataElement']
+$tag:tool|outputs|collection|data://complexType[@name='OutputCollectionData']
 $tag:tool|outputs|collection|filter://complexType[@name='OutputFilter']
 $tag:tool|outputs|collection|discover_datasets://complexType[@name='OutputCollectionDiscoverDatasets']
 $tag:tool|tests://complexType[@name='Tests']

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -4382,8 +4382,6 @@ def full_delete(self):
         # TODO: purge metadata files
         self.deleted = True
         self.purged = True
-        self.file_size = 0
-        self.total_size = 0
 
     def get_access_roles(self, security_agent):
         roles = []

diff --git a/lib/galaxy/schema/invocation.py b/lib/galaxy/schema/invocation.py
@@ -78,6 +78,21 @@ class FailureReason(str, Enum):
     unexpected_failure = "unexpected_failure"
 
 
+# The reasons below are attached to the invocation and user-actionable.
+# Not included are `unexpected_failure` and `expression_evaluation_failed`.
+# If expression evaluation fails we're not attaching the templated
+# expression to the invocation, as it could contain secrets.
+# If the failure reason is not in `FAILURE_REASONS_EXPECTED` we should
+# log an exception so admins can debug and/or submit bug reports.
+FAILURE_REASONS_EXPECTED = (
+    FailureReason.dataset_failed,
+    FailureReason.collection_failed,
+    FailureReason.job_failed,
+    FailureReason.output_not_found,
+    FailureReason.when_not_boolean,
+)
+
+
 class CancelReason(str, Enum):
     """Possible reasons for a cancelled workflow."""
 

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -5827,15 +5827,24 @@ on Human (hg18)``.
     <xs:attributeGroup ref="OutputDataAttributes"/>
   </xs:complexType>
 
+  <!-- Allowed tags included in collection-data -->
+  <xs:group name="OutputCollectionDataElement">
+    <xs:choice>
+      <xs:element name="actions" type="Actions" />
+      <xs:element name="change_format" type="ChangeFormat" />
+    </xs:choice>
+  </xs:group>
+
+  <!-- Allowed tags included in collection -->
   <xs:group name="OutputCollectionElement">
     <xs:choice>
-      <xs:element name="data" type="OutputCollectionDataElement" />
+      <xs:element name="data" type="OutputCollectionData" />
       <xs:element name="discover_datasets" type="OutputCollectionDiscoverDatasets" />
       <xs:element name="filter" type="OutputFilter" />
     </xs:choice>
   </xs:group>
 
-  <xs:complexType name="OutputCollectionDataElement">
+  <xs:complexType name="OutputCollectionData">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
 
@@ -5844,7 +5853,7 @@ define the elements of a collection statically. See also [Planemo's documentatio
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
+      <xs:group ref="OutputCollectionDataElement" minOccurs="0" maxOccurs="unbounded" />
     </xs:sequence>
     <xs:attributeGroup ref="OutputCommon" />
     <xs:attributeGroup ref="OutputDataAttributes" />
@@ -6002,23 +6011,7 @@ Therefore a filter for such a variable looks like the following example.
     </xs:simpleContent>
   </xs:complexType>
 
-  <xs:complexType name="OutputDiscoverDatasets">
-     <xs:annotation>
-      <xs:documentation xml:lang="en"><![CDATA[
-
-Describe datasets to dynamically collect after the job complete.
-
-There are many simple tools with examples of this element distributed with
-Galaxy, including:
-
-* [multi_output.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output.xml)
-* [multi_output_assign_primary.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_assign_primary.xml)
-* [multi_output_configured.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_configured.xml)
-
-More information can be found on Planemo's documentation for
-[multiple output files](https://planemo.readthedocs.io/en/latest/writing_advanced.html#multiple-output-files).
-]]></xs:documentation>
-    </xs:annotation>
+  <xs:attributeGroup name="OutputDiscoverDatasetsCommon">
     <xs:attribute name="from_provided_metadata" type="xs:boolean" use="optional">
       <xs:annotation>
         <xs:documentation xml:lang="en">Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort must not be set.</xs:documentation>
@@ -6069,6 +6062,26 @@ More information can be found on Planemo's documentation for
         <xs:documentation xml:lang="en">Indication if this dataset is visible in output history. This defaults to ``false``, but probably shouldn't - be sure to set to ``true`` if that is your intention.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
+  </xs:attributeGroup>
+
+  <xs:complexType name="OutputDiscoverDatasets">
+     <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[
+
+Describe datasets to dynamically collect after the job complete.
+
+There are many simple tools with examples of this element distributed with
+Galaxy, including:
+
+* [multi_output.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output.xml)
+* [multi_output_assign_primary.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_assign_primary.xml)
+* [multi_output_configured.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/multi_output_configured.xml)
+
+More information can be found on Planemo's documentation for
+[multiple output files](https://planemo.readthedocs.io/en/latest/writing_advanced.html#multiple-output-files).
+]]></xs:documentation>
+    </xs:annotation>
+    <xs:attributeGroup ref="OutputDiscoverDatasetsCommon"/>
     <xs:attribute name="assign_primary_output" type="xs:boolean" use="optional">
       <xs:annotation>
         <xs:documentation xml:lang="en">Replace the primary dataset described by the parameter ``data`` parameter with the first output discovered.</xs:documentation>
@@ -6092,51 +6105,7 @@ Galaxy, including:
 
 ]]></xs:documentation>
     </xs:annotation>
-    <xs:attribute name="from_provided_metadata" type="xs:boolean" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Indicate that dataset filenames should simply be read from the provided metadata file (e.g. galaxy.json). If this is set - pattern and sort_by must not be set.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="pattern" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Regular expression used to find filenames and parse dynamic properties.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="directory" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Directory (relative to working directory) to search for files.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="recurse" type="xs:boolean" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Indicates that the specified directory should be searched recursively for matching files.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="match_relative_path" type="xs:boolean" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Indicates that the entire path of the discovered dataset relative to the specified directory should be available for matching patterns.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="format" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``ext``).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="ext" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Format (or datatype) of discovered datasets (an alias with ``format``).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="sort_by" type="xs:string" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">A string `[reverse_][SORT_COMP_]SORTBY` describing the desired sort order of the collection elements. `SORTBY` can be `filename`, `name`, `designation`, `dbkey` and the optional `SORT_COMP` can be either `lexical` or `numeric`. Default is lexical sorting by filename.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="visible" type="xs:boolean" use="optional">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Indication if this dataset is visible in the history. This defaults to ``false``, but probably shouldn't - be sure to set to ``true`` if that is your intention.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
+    <xs:attributeGroup ref="OutputDiscoverDatasetsCommon"/>
   </xs:complexType>
   <xs:complexType name="Actions">
     <xs:annotation>

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -3867,8 +3867,14 @@ def add_copied_value_to_new_elements(new_label, dce_object):
         if how_type == "tabular":
             # We have a tabular file, where the first column is an existing element identifier,
             # and the second column is the new element identifier.
+            new_labels_dict = {}
             source_new_label = (line.strip().split("\t") for line in new_labels)
-            new_labels_dict = dict(source_new_label)
+            for i, label_pair in enumerate(source_new_label):
+                if not len(label_pair) == 2:
+                    raise exceptions.MessageException(
+                        f"Relabel mapping file line {i + 1} contains {len(label_pair)} columns, but 2 are required"
+                    )
+                new_labels_dict[label_pair[0]] = label_pair[1]
             for dce in hdca.collection.elements:
                 dce_object = dce.element_object
                 element_identifier = dce.element_identifier

diff --git a/lib/galaxy/web/framework/base.py b/lib/galaxy/web/framework/base.py
@@ -104,6 +104,7 @@ def __init__(self):
         self.transaction_factory = DefaultWebTransaction
         # Set if trace logging is enabled
         self.trace_logger = None
+        self.session_factories = []
 
     def add_ui_controller(self, controller_name, controller):
         """
@@ -170,10 +171,12 @@ def __call__(self, environ, start_response):
         path_info = environ.get("PATH_INFO", "")
 
         try:
-            self._model.set_request_id(request_id)  # Start SQLAlchemy session scope
+            for session_factory in self.session_factories:
+                session_factory.set_request_id(request_id)  # Start SQLAlchemy session scope
             return self.handle_request(request_id, path_info, environ, start_response)
         finally:
-            self._model.unset_request_id(request_id)  # End SQLAlchemy session scope
+            for session_factory in self.session_factories:
+                session_factory.unset_request_id(request_id)  # End SQLAlchemy session scope
             self.trace(message="Handle request finished")
             if self.trace_logger:
                 self.trace_logger.context_remove("request_id")

diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py
@@ -119,7 +119,7 @@ def __init__(
 
         # We need this to set the REQUEST_ID contextvar in model.base *BEFORE* a GalaxyWebTransaction is created.
         # This will ensure a SQLAlchemy session is request-scoped for legacy (non-fastapi) endpoints.
-        self._model = galaxy_app.model
+        self.session_factories.append(galaxy_app.model)
 
     def build_apispec(self):
         """