Merge branch '20933-arv-copy-cwl' refs #20933

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

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index cdce3d643a337bb28f43c7124233fbcb094853ea..3ad2c6419a2b9ce39c11b6471e3dac6555c317ef 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -42,6 +42,7 @@ from .pathmapper import ArvPathMapper, trim_listing
 from .arvtool import ArvadosCommandTool, set_cluster_target
 from ._version import __version__
 from .util import common_prefix
+from .arvdocker import arv_docker_get_image
 
 from .perf import Perf
 
@@ -178,14 +179,14 @@ def rel_ref(s, baseuri, urlexpander, merged_map, jobmapper):
 def is_basetype(tp):
     return _basetype_re.match(tp) is not None
 
-def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix):
+def update_refs(api, d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix):
     if isinstance(d, MutableSequence):
         for i, s in enumerate(d):
             if prefix and isinstance(s, str):
                 if s.startswith(prefix):
                     d[i] = replacePrefix+s[len(prefix):]
             else:
-                update_refs(s, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
+                update_refs(api, s, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
     elif isinstance(d, MutableMapping):
         for field in ("id", "name"):
             if isinstance(d.get(field), str) and d[field].startswith("_:"):
@@ -198,8 +199,8 @@ def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext,
             baseuri = urlexpander(d["name"], baseuri, scoped_id=True)
 
         if d.get("class") == "DockerRequirement":
-            dockerImageId = d.get("dockerImageId") or d.get("dockerPull")
-            d["http://arvados.org/cwl#dockerCollectionPDH"] = runtimeContext.cached_docker_lookups.get(dockerImageId)
+            d["http://arvados.org/cwl#dockerCollectionPDH"] = arv_docker_get_image(api, d, False,
+                                                                                   runtimeContext)
 
         for field in d:
             if field in ("location", "run", "name") and isinstance(d[field], str):
@@ -222,15 +223,21 @@ def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext,
                     if isinstance(d["inputs"][inp], str) and not is_basetype(d["inputs"][inp]):
                         d["inputs"][inp] = rel_ref(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper)
                     if isinstance(d["inputs"][inp], MutableMapping):
-                        update_refs(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
+                        update_refs(api, d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
                 continue
 
+            if field in ("requirements", "hints") and isinstance(d[field], MutableMapping):
+                dr = d[field].get("DockerRequirement")
+                if dr:
+                    dr["http://arvados.org/cwl#dockerCollectionPDH"] = arv_docker_get_image(api, dr, False,
+                                                                                            runtimeContext)
+
             if field == "$schemas":
                 for n, s in enumerate(d["$schemas"]):
                     d["$schemas"][n] = rel_ref(d["$schemas"][n], baseuri, urlexpander, merged_map, jobmapper)
                 continue
 
-            update_refs(d[field], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
+            update_refs(api, d[field], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
 
 
 def fix_schemadef(req, baseuri, urlexpander, merged_map, jobmapper, pdh):
@@ -327,7 +334,7 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid,
 
         # 2. find $import, $include, $schema, run, location
         # 3. update field value
-        update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, "", "")
+        update_refs(arvRunner.api, result, w, tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, "", "")
 
         # Write the updated file to the collection.
         with col.open(w[len(prefix):], "wt") as f:
@@ -485,7 +492,7 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid,
         if r["class"] == "SchemaDefRequirement":
             wrapper["requirements"][i] = fix_schemadef(r, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, col.portable_data_hash())
 
-    update_refs(wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, main["id"]+"#", "#main/")
+    update_refs(arvRunner.api, wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, main["id"]+"#", "#main/")
 
     doc = {"cwlVersion": "v1.2", "$graph": [wrapper]}