WIP: handle mapped over jobs in workflows.

jmchilton · Nov 30, 2023 · b84b494 · b84b494
1 parent 2d7b0d6
commit b84b494
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Showing 2 changed files with 12 additions and 8 deletions.
diff --git a/lib/galaxy/managers/markdown_parse.py b/lib/galaxy/managers/markdown_parse.py
@@ -50,10 +50,10 @@ class DynamicArguments:
     "workflow_display": ["workflow_id", "workflow_checkpoint"],
     "workflow_license": ["workflow_id"],
     "workflow_image": ["workflow_id", "size", "workflow_checkpoint"],
-    "job_metrics": ["step", "job_id"],
-    "job_parameters": ["step", "job_id"],
-    "tool_stderr": ["step", "job_id"],
-    "tool_stdout": ["step", "job_id"],
+    "job_metrics": ["step", "job_id", "implicit_collection_jobs_id"],
+    "job_parameters": ["step", "job_id", "implicit_collection_jobs_id"],
+    "tool_stderr": ["step", "job_id", "implicit_collection_jobs_id"],
+    "tool_stdout": ["step", "job_id", "implicit_collection_jobs_id"],
     "generate_galaxy_version": [],
     "generate_time": [],
     "instance_access_link": [],

diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
@@ -72,10 +72,10 @@
 SIZE_PATTERN = re.compile(r"size=\s*%s\s*" % ARG_VAL_CAPTURED_REGEX)
 # STEP_OUTPUT_LABEL_PATTERN = re.compile(r'step_output=([\w_\-]+)/([\w_\-]+)')
 UNENCODED_ID_PATTERN = re.compile(
-    r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([\d]+)"
+    r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|implicit_collection_jobs|invocation_id)=([\d]+)"
 )
 ENCODED_ID_PATTERN = re.compile(
-    r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|invocation_id)=([a-z0-9]+)"
+    r"(history_id|workflow_id|history_dataset_id|history_dataset_collection_id|job_id|implicit_collection_jobs|invocation_id)=([a-z0-9]+)"
 )
 INVOCATION_SECTION_MARKDOWN_CONTAINER_LINE_PATTERN = re.compile(r"```\s*galaxy\s*")
 GALAXY_FENCED_BLOCK = re.compile(r"^```\s*galaxy\s*(.*?)^```", re.MULTILINE ^ re.DOTALL)
@@ -933,9 +933,13 @@ def find_non_empty_group(match):
         elif step_match:
             target_match = step_match
             name = find_non_empty_group(target_match)
-            ref_object_type = "job"
             invocation_step = invocation.step_invocation_for_label(name)
-            ref_object = invocation_step and invocation_step.job
+            if invocation_step and invocation_step.job:
+                ref_object_type = "job"
+                ref_object = invocation_step.job
+            elif invocation_step and invocation_step.implicit_collection_jobs:
+                ref_object_type = "implicit_collection_jobs"
+                ref_object = invocation_step.implicit_collection_jobs
         else:
             target_match = None
             ref_object = None