Fix workflow report to target right workflow version.

There was a past jmchilton todo in the code base about it. Directives that might target particular versions of a workflow (so workflow_display and workflow_image) now can take a workflow_version attribute and when these things are auto-populated for workflow invocations - they are populated with the right version for the invocation.

client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue

@@ -10,11 +10,13 @@ import LoadingSpan from "@/components/LoadingSpan.vue";
 
 interface WorkflowDisplayProps {
     workflowId: string;
+    workflowVersion?: string;
     embedded?: boolean;
     expanded?: boolean;
 }
 
 const props = withDefaults(defineProps<WorkflowDisplayProps>(), {
+    workflowVersion: null,
     embedded: false,
     expanded: false,
 });
@@ -31,7 +33,13 @@ const loading = ref(true);
 const workflowName = computed(() => (itemContent.value ? itemContent.value.name : "..."));
 const downloadUrl = computed(() => withPrefix(`/api/workflows/${props.workflowId}/download?format=json-download`));
 const importUrl = computed(() => withPrefix(`/workflow/imp?id=${props.workflowId}`));
-const itemUrl = computed(() => withPrefix(`/api/workflows/${props.workflowId}/download?style=preview`));
+const itemUrl = computed(() => {
+    let extra = "";
+    if (props.workflowVersion) {
+        extra = `&version=${props.workflowVersion}`;
+    }
+    return withPrefix(`/api/workflows/${props.workflowId}/download?style=preview${extra}`);
+});
 
 onMounted(async () => {
     axios

client/src/components/Markdown/Elements/Workflow/WorkflowImage.vue

@@ -5,15 +5,21 @@ import { getAppRoot } from "@/onload/loadConfig";
 
 interface WorkflowImageProps {
     workflowId: string;
+    workflowVersion?: string;
     size?: string;
 }
 
 const props = withDefaults(defineProps<WorkflowImageProps>(), {
     size: "lg",
+    workflowVersion: null,
 });
 
 const src = computed(() => {
-    return `${getAppRoot()}workflow/gen_image?id=${props.workflowId}&embed=true`;
+    let extraArgs = "";
+    if (props.workflowVersion) {
+        extraArgs = `&version=${props.workflowVersion}`;
+    }
+    return `${getAppRoot()}workflow/gen_image?id=${props.workflowId}&embed=true${extraArgs}`;
 });
 const width = computed(() => {
     const size = props.size;

client/src/components/Markdown/MarkdownContainer.vue

@@ -83,7 +83,10 @@ const isVisible = computed(() => !isCollapsible.value || toggle.value);
                 <pre><code>{{ time }}</code></pre>
             </div>
             <div v-else-if="name == 'workflow_image'" class="workflow-image" style="text-align: center">
-                <WorkflowImage :workflow-id="args.workflow_id" :size="args.size || 'lg'" />
+                <WorkflowImage
+                    :workflow-id="args.workflow_id"
+                    :size="args.size || 'lg'"
+                    :workflow-version="args.workflow_checkpoint || undefined" />
             </div>
             <div v-else-if="name == 'workflow_license'" class="workflow-license">
                 <WorkflowLicense :license-id="workflows[args.workflow_id]['license']" />
@@ -131,6 +134,7 @@ const isVisible = computed(() => !isCollapsible.value || toggle.value);
             <WorkflowDisplay
                 v-else-if="name == 'workflow_display'"
                 :workflow-id="args.workflow_id"
+                :workflow-version="args.workflow_checkpoint"
                 :workflows="workflows" />
             <Visualization v-else-if="name == 'visualization'" :args="args" />
             <HistoryDatasetCollectionDisplay

lib/galaxy/managers/markdown_parse.py

@@ -37,9 +37,9 @@ class DynamicArguments:
     "history_dataset_name": ["input", "output", "history_dataset_id"],
     "history_dataset_type": ["input", "output", "history_dataset_id"],
     "history_dataset_collection_display": ["input", "output", "history_dataset_collection_id"],
-    "workflow_display": ["workflow_id"],
+    "workflow_display": ["workflow_id", "workflow_checkpoint"],
     "workflow_license": ["workflow_id"],
-    "workflow_image": ["workflow_id", "size"],
+    "workflow_image": ["workflow_id", "size", "workflow_checkpoint"],
     "job_metrics": ["step", "job_id"],
     "job_parameters": ["step", "job_id"],
     "tool_stderr": ["step", "job_id"],

lib/galaxy/managers/markdown_util.py

@@ -156,10 +156,14 @@ def _remap(container, line):
                 rval = self.handle_dataset_name(line, hda)
             elif container == "workflow_display":
                 stored_workflow = workflow_manager.get_stored_accessible_workflow(trans, encoded_id)
-                rval = self.handle_workflow_display(line, stored_workflow)
+                workflow_version_str = _parse_directive_argument_value("workflow_checkpoint", line)
+                workflow_version = None if not workflow_version_str else int(workflow_version_str)
+                rval = self.handle_workflow_display(line, stored_workflow, workflow_version)
             elif container == "workflow_image":
                 stored_workflow = workflow_manager.get_stored_accessible_workflow(trans, encoded_id)
-                rval = self.handle_workflow_image(line, stored_workflow)
+                workflow_version_str = _parse_directive_argument_value("workflow_checkpoint", line)
+                workflow_version = None if not workflow_version_str else int(workflow_version_str)
+                rval = self.handle_workflow_image(line, stored_workflow, workflow_version)
             elif container == "workflow_license":
                 stored_workflow = workflow_manager.get_stored_accessible_workflow(trans, encoded_id)
                 rval = self.handle_workflow_license(line, stored_workflow)
@@ -270,11 +274,11 @@ def handle_dataset_type(self, line, hda):
         pass
 
     @abc.abstractmethod
-    def handle_workflow_display(self, line, stored_workflow):
+    def handle_workflow_display(self, line, stored_workflow, workflow_version: Optional[int]):
         pass
 
     @abc.abstractmethod
-    def handle_workflow_image(self, line, stored_workflow):
+    def handle_workflow_image(self, line, stored_workflow, workflow_version: Optional[int]):
         pass
 
     @abc.abstractmethod
@@ -377,10 +381,10 @@ def handle_dataset_peek(self, line, hda):
     def handle_dataset_info(self, line, hda):
         self.extend_history_dataset_rendering_data(hda, "info", hda.info, "*No Dataset Info Available*")
 
-    def handle_workflow_display(self, line, stored_workflow):
+    def handle_workflow_display(self, line, stored_workflow, workflow_version: Optional[int]):
         self.ensure_rendering_data_for("workflows", stored_workflow)["name"] = stored_workflow.name
 
-    def handle_workflow_image(self, line, stored_workflow):
+    def handle_workflow_image(self, line, stored_workflow, workflow_version: Optional[int]):
         pass
 
     def handle_workflow_license(self, line, stored_workflow):
@@ -558,7 +562,7 @@ def handle_dataset_info(self, line, hda):
             content = "*No Dataset Info Available*"
         return (content, True)
 
-    def handle_workflow_display(self, line, stored_workflow):
+    def handle_workflow_display(self, line, stored_workflow, workflow_version: Optional[int]):
         # simple markdown
         markdown = "---\n"
         markdown += f"**Workflow:** {stored_workflow.name}\n\n"
@@ -567,7 +571,8 @@ def handle_workflow_display(self, line, stored_workflow):
         markdown += "|----|----------|\n"
         # Pass two should add tool information, labels, etc.. but
         # it requires module_injector and such.
-        for order_index, step in enumerate(stored_workflow.latest_workflow.steps):
+        workflow = stored_workflow.get_internal_version(workflow_version)
+        for order_index, step in enumerate(workflow.steps):
             annotation = get_item_annotation_str(self.trans.sa_session, self.trans.user, step) or ""
             markdown += "|{}|{}|\n".format(step.label or "Step %d" % (order_index + 1), annotation)
         markdown += "\n---\n"
@@ -586,9 +591,10 @@ def handle_workflow_license(self, line, stored_workflow):
                 markdown = f"Unknown license ({license_id})"
         return (f"\n\n{markdown}\n\n", True)
 
-    def handle_workflow_image(self, line, stored_workflow):
+    def handle_workflow_image(self, line, stored_workflow, workflow_version: Optional[int]):
         workflow_manager = self.trans.app.workflow_manager
-        image_data = workflow_manager.get_workflow_svg(self.trans, stored_workflow.latest_workflow, for_embed=True)
+        workflow = stored_workflow.get_internal_version(workflow_version)
+        image_data = workflow_manager.get_workflow_svg(self.trans, workflow, for_embed=True)
         rval = (self._embed_image("Workflow", "svg+xml", image_data), True)
         return rval
 
@@ -868,9 +874,12 @@ def _section_remap(container, line):
 
     def _remap(container, line):
         if container == "workflow_display":
-            # TODO: this really should be workflow id not stored workflow id but the API
-            # it consumes wants the stored id.
-            return (f"workflow_display(workflow_id={invocation.workflow.stored_workflow.id})\n", False)
+            stored_workflow_id = invocation.workflow.stored_workflow.id
+            workflow_version = invocation.workflow.version
+            return (
+                f"workflow_display(workflow_id={stored_workflow_id},workflow_checkpoint={workflow_version})\n",
+                False,
+            )
         if container == "history_link":
             return (f"history_link(history_id={invocation.history.id})\n", False)
         if container == "invocation_time":
@@ -948,6 +957,15 @@ def _remap_galaxy_markdown_containers(func, markdown):
     return new_markdown
 
 
+def _parse_directive_argument_value(arg_name: str, line: str) -> Optional[str]:
+    arg_pattern = re.compile(rf"{arg_name}=\s*{ARG_VAL_CAPTURED_REGEX}\s*")
+    match = re.search(arg_pattern, line)
+    if not match:
+        return None
+    value = match.group(1)
+    return value
+
+
 def _remap_galaxy_markdown_calls(func, markdown):
     def _remap_container(container):
         matching_line = None

lib/galaxy/managers/workflows.py

@@ -361,9 +361,10 @@ def check_security(self, trans, has_workflow, check_ownership=True, check_access
 
         return True
 
-    def get_workflow_svg_from_id(self, trans, id, for_embed=False) -> bytes:
+    def get_workflow_svg_from_id(self, trans, id, version=None, for_embed=False) -> bytes:
         stored = self.get_stored_accessible_workflow(trans, id)
-        return self.get_workflow_svg(trans, stored.latest_workflow, for_embed=for_embed)
+        workflow = stored.get_internal_version(version)
+        return self.get_workflow_svg(trans, workflow, for_embed=for_embed)
 
     def get_workflow_svg(self, trans, workflow, for_embed=False) -> bytes:
         try:

lib/galaxy/model/__init__.py

@@ -7358,6 +7358,12 @@ def get_internal_version(self, version):
             raise Exception("Version does not exist")
         return list(reversed(self.workflows))[version]
 
+    def version_of(self, workflow):
+        for version, workflow_instance in enumerate(reversed(self.workflows)):
+            if workflow_instance.id == workflow.id:
+                return version
+        raise KeyError("Failed to find a version of target workflow instance in stored workflow.")
+
     def show_in_tool_panel(self, user_id):
         sa_session = object_session(self)
         stmt = (
@@ -7552,6 +7558,10 @@ def copy(self, user=None):
         copied_workflow.steps = copied_steps
         return copied_workflow
 
+    @property
+    def version(self):
+        return self.stored_workflow.version_of(self)
+
     def log_str(self):
         extra = ""
         if self.stored_workflow:

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -326,10 +326,16 @@ def annotate_async(self, trans, id, new_annotation=None, **kwargs):
 
     @web.expose
     @web.require_login("use Galaxy workflows")
-    def gen_image(self, trans, id, embed="false", **kwargs):
+    def gen_image(self, trans, id, embed="false", version="", **kwargs):
         embed = util.asbool(embed)
+        if version:
+            version_int_or_none = int(version)
+        else:
+            version_int_or_none = None
         try:
-            s = trans.app.workflow_manager.get_workflow_svg_from_id(trans, id, for_embed=embed)
+            s = trans.app.workflow_manager.get_workflow_svg_from_id(
+                trans, id, version=version_int_or_none, for_embed=embed
+            )
             trans.response.set_content_type("image/svg+xml")
             return s
         except Exception as e:

test/unit/workflows/test_workflow_markdown.py

@@ -17,7 +17,7 @@ def test_workflow_section_expansion():
 """
     galaxy_markdown = resolved_markdown(workflow_markdown)
     assert "## Workflow\n" in galaxy_markdown
-    assert "```galaxy\nworkflow_display(workflow_id=342)\n```\n" in galaxy_markdown
+    assert "```galaxy\nworkflow_display(workflow_id=342,workflow_checkpoint=0)\n```\n" in galaxy_markdown
 
 
 def test_inputs_section_expansion():