10497: Add source line reporting to errors and fix tests to work with CommentedMap...

[arvados.git] / sdk / cwl / arvados_cwl / arvdocker.py

diff --git a/sdk/cwl/arvados_cwl/arvdocker.py b/sdk/cwl/arvados_cwl/arvdocker.py
index 7f6ab587d323a7dc65e39c00e8e1b38d019f009d..88c5dd2d4f428e946602c4eaeb5c59c1e4e4a2e6 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvdocker.py
+++ b/sdk/cwl/arvados_cwl/arvdocker.py
@@ -2,6 +2,8 @@ import logging
 import sys
 import threading
 
+from schema_salad.sourceline import SourceLine
+
 import cwltool.docker
 from cwltool.errors import WorkflowException
 import arvados.commands.keepdocker
@@ -16,6 +18,8 @@ def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid
 
     if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
         dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
+        if hasattr(dockerRequirement, 'lc'):
+            dockerRequirement.lc.data["dockerImageId"] = dockerRequirement.lc.data["dockerPull"]
 
     global cached_lookups
     global cached_lookups_lock
@@ -23,45 +27,46 @@ def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid
         if dockerRequirement["dockerImageId"] in cached_lookups:
             return cached_lookups[dockerRequirement["dockerImageId"]]
 
-    sp = dockerRequirement["dockerImageId"].split(":")
-    image_name = sp[0]
-    image_tag = sp[1] if len(sp) > 1 else None
-
-    images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
-                                                            image_name=image_name,
-                                                            image_tag=image_tag)
-
-    if not images:
-        # Fetch Docker image if necessary.
-        cwltool.docker.get_image(dockerRequirement, pull_image)
-
-        # Upload image to Arvados
-        args = []
-        if project_uuid:
-            args.append("--project-uuid="+project_uuid)
-        args.append(image_name)
-        if image_tag:
-            args.append(image_tag)
-        logger.info("Uploading Docker image %s", ":".join(args[1:]))
-        try:
-            arvados.commands.keepdocker.main(args, stdout=sys.stderr)
-        except SystemExit as e:
-            if e.code:
-                raise WorkflowException("keepdocker exited with code %s" % e.code)
+    with SourceLine(dockerRequirement, "dockerImageId", WorkflowException):
+        sp = dockerRequirement["dockerImageId"].split(":")
+        image_name = sp[0]
+        image_tag = sp[1] if len(sp) > 1 else None
 
         images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
                                                                 image_name=image_name,
                                                                 image_tag=image_tag)
 
-    if not images:
-        raise WorkflowException("Could not find Docker image %s:%s" % (image_name, image_tag))
-
-    pdh = api_client.collections().get(uuid=images[0][0]).execute()["portable_data_hash"]
-
-    with cached_lookups_lock:
-        cached_lookups[dockerRequirement["dockerImageId"]] = pdh
-
-    return pdh
+        if not images:
+            # Fetch Docker image if necessary.
+            cwltool.docker.get_image(dockerRequirement, pull_image)
+
+            # Upload image to Arvados
+            args = []
+            if project_uuid:
+                args.append("--project-uuid="+project_uuid)
+            args.append(image_name)
+            if image_tag:
+                args.append(image_tag)
+            logger.info("Uploading Docker image %s", ":".join(args[1:]))
+            try:
+                arvados.commands.keepdocker.main(args, stdout=sys.stderr)
+            except SystemExit as e:
+                if e.code:
+                    raise WorkflowException("keepdocker exited with code %s" % e.code)
+
+            images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3,
+                                                                    image_name=image_name,
+                                                                    image_tag=image_tag)
+
+        if not images:
+            raise WorkflowException("Could not find Docker image %s:%s" % (image_name, image_tag))
+
+        pdh = api_client.collections().get(uuid=images[0][0]).execute()["portable_data_hash"]
+
+        with cached_lookups_lock:
+            cached_lookups[dockerRequirement["dockerImageId"]] = pdh
+
+        return pdh
 
 def arv_docker_clear_cache():
     global cached_lookups