Merge branch '19109-upload-secondary' refs #19109

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

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 38e2c4d806f36ed80f9dac70da8cf37006f3de19..f232178c5d5400ab90aad300d2f1d2d70909b98d 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -39,6 +39,7 @@ from cwltool.builder import Builder
 import schema_salad.validate as validate
 
 import arvados.collection
 import schema_salad.validate as validate
 
 import arvados.collection

+import arvados.util

 from .util import collectionUUID
 from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from .util import collectionUUID
 from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap, CommentedSeq


@@ -128,6 +129,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
         return
 
             set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
         return
 

+    if inputschema == "File":
+        inputschema = {"type": "File"}
+

     if isinstance(inputschema, basestring):
         sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
         if sd:
     if isinstance(inputschema, basestring):
         sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
         if sd:


@@ -163,10 +167,13 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered)
 
     elif (inputschema["type"] == "File" and
             set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered)
 
     elif (inputschema["type"] == "File" and

-          secondaryspec and

           isinstance(primary, Mapping) and
           isinstance(primary, Mapping) and

-          primary.get("class") == "File" and
-          "secondaryFiles" not in primary):
+          primary.get("class") == "File"):
+
+        if "secondaryFiles" in primary or not secondaryspec:
+            # Nothing to do.
+            return
+

         #
         # Found a file, check for secondaryFiles
         #
         #
         # Found a file, check for secondaryFiles
         #


@@ -174,9 +181,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         primary["secondaryFiles"] = secondaryspec
         for i, sf in enumerate(aslist(secondaryspec)):
             if builder.cwlVersion == "v1.0":
         primary["secondaryFiles"] = secondaryspec
         for i, sf in enumerate(aslist(secondaryspec)):
             if builder.cwlVersion == "v1.0":

-                pattern = builder.do_eval(sf, context=primary)
+                pattern = sf

             else:
             else:

-                pattern = builder.do_eval(sf["pattern"], context=primary)
+                pattern = sf["pattern"]

             if pattern is None:
                 continue
             if isinstance(pattern, list):
             if pattern is None:
                 continue
             if isinstance(pattern, list):


@@ -213,7 +220,20 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
                     "Expression must return list, object, string or null")
 
             if pattern is not None:
                     "Expression must return list, object, string or null")
 
             if pattern is not None:

-                sfpath = substitute(primary["location"], pattern)
+                if "${" in pattern or "$(" in pattern:
+                    sfname = builder.do_eval(pattern, context=primary)
+                else:
+                    sfname = substitute(primary["basename"], pattern)
+
+                if sfname is None:
+                    continue
+
+                p_location = primary["location"]
+                if "/" in p_location:
+                    sfpath = (
+                        p_location[0 : p_location.rindex("/") + 1]
+                        + sfname
+                    )

 
             required = builder.do_eval(required, context=primary)
 
 
             required = builder.do_eval(required, context=primary)
 


@@ -239,7 +259,7 @@ def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=No
             set_secondary(fsaccess, builder, inputschema, None, primary, discovered)
 
 def upload_dependencies(arvrunner, name, document_loader,
             set_secondary(fsaccess, builder, inputschema, None, primary, discovered)
 
 def upload_dependencies(arvrunner, name, document_loader,

-                        workflowobj, uri, loadref_run,
+                        workflowobj, uri, loadref_run, runtimeContext,

                         include_primary=True, discovered_secondaryfiles=None):
     """Upload the dependencies of the workflowobj document to Keep.
 
                         include_primary=True, discovered_secondaryfiles=None):
     """Upload the dependencies of the workflowobj document to Keep.
 


@@ -285,10 +305,18 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     sc_result = scandeps(uri, scanobj,
                          loadref_fields,
 
     sc_result = scandeps(uri, scanobj,
                          loadref_fields,

-                         set(("$include", "$schemas", "location")),
+                         set(("$include", "location")),

                          loadref, urljoin=document_loader.fetcher.urljoin,
                          nestdirs=False)
 
                          loadref, urljoin=document_loader.fetcher.urljoin,
                          nestdirs=False)
 

+    optional_deps = scandeps(uri, scanobj,
+                                  loadref_fields,
+                                  set(("$schemas",)),
+                                  loadref, urljoin=document_loader.fetcher.urljoin,
+                                  nestdirs=False)
+
+    sc_result.extend(optional_deps)
+

     sc = []
     uuids = {}
 
     sc = []
     uuids = {}
 


@@ -345,24 +373,14 @@ def upload_dependencies(arvrunner, name, document_loader,
     if include_primary and "id" in workflowobj:
         sc.append({"class": "File", "location": workflowobj["id"]})
 
     if include_primary and "id" in workflowobj:
         sc.append({"class": "File", "location": workflowobj["id"]})
 

-    if "$schemas" in workflowobj:
-        for s in workflowobj["$schemas"]:
-            sc.append({"class": "File", "location": s})
-

     def visit_default(obj):
     def visit_default(obj):

-        remove = [False]
-        def ensure_default_location(f):
+        def defaults_are_optional(f):

             if "location" not in f and "path" in f:
                 f["location"] = f["path"]
                 del f["path"]
             if "location" not in f and "path" in f:
                 f["location"] = f["path"]
                 del f["path"]

-            if "location" in f and not arvrunner.fs_access.exists(f["location"]):
-                # Doesn't exist, remove from list of dependencies to upload
-                sc[:] = [x for x in sc if x["location"] != f["location"]]
-                # Delete "default" from workflowobj
-                remove[0] = True
-        visit_class(obj["default"], ("File", "Directory"), ensure_default_location)
-        if remove[0]:
-            del obj["default"]
+            normalizeFilesDirs(f)
+            optional_deps.append(f)
+        visit_class(obj["default"], ("File", "Directory"), defaults_are_optional)

 
     find_defaults(workflowobj, visit_default)
 
 
     find_defaults(workflowobj, visit_default)
 


@@ -398,12 +416,19 @@ def upload_dependencies(arvrunner, name, document_loader,
                            "keep:%s",
                            "keep:%s/%s",
                            name=name,
                            "keep:%s",
                            "keep:%s/%s",
                            name=name,

-                           single_collection=True)
+                           single_collection=True,
+                           optional_deps=optional_deps)
+
+    keeprefs = set()
+    def addkeepref(k):
+        if k.startswith("keep:"):
+            keeprefs.add(collection_pdh_pattern.match(k).group(1))

 
     def setloc(p):
         loc = p.get("location")
         if loc and (not loc.startswith("_:")) and (not loc.startswith("keep:")):
             p["location"] = mapper.mapper(p["location"]).resolved
 
     def setloc(p):
         loc = p.get("location")
         if loc and (not loc.startswith("_:")) and (not loc.startswith("keep:")):
             p["location"] = mapper.mapper(p["location"]).resolved

+            addkeepref(p["location"])

             return
 
         if not loc:
             return
 
         if not loc:


@@ -425,7 +450,10 @@ def upload_dependencies(arvrunner, name, document_loader,
 
         gp = collection_uuid_pattern.match(loc)
         if not gp:
 
         gp = collection_uuid_pattern.match(loc)
         if not gp:

+            # Not a uuid pattern (must be a pdh pattern)
+            addkeepref(p["location"])

             return
             return

+

         uuid = gp.groups()[0]
         if uuid not in uuid_map:
             raise SourceLine(p, "location", validate.ValidationException).makeError(
         uuid = gp.groups()[0]
         if uuid not in uuid_map:
             raise SourceLine(p, "location", validate.ValidationException).makeError(


@@ -440,6 +468,38 @@ def upload_dependencies(arvrunner, name, document_loader,
         for d in discovered:
             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 
         for d in discovered:
             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 

+    if runtimeContext.copy_deps:
+        # Find referenced collections and copy them into the
+        # destination project, for easy sharing.
+        already_present = list(arvados.util.keyset_list_all(arvrunner.api.collections().list,
+                                     filters=[["portable_data_hash", "in", list(keeprefs)],
+                                              ["owner_uuid", "=", runtimeContext.project_uuid]],
+                                     select=["uuid", "portable_data_hash", "created_at"]))
+
+        keeprefs = keeprefs - set(a["portable_data_hash"] for a in already_present)
+        for kr in keeprefs:
+            col = arvrunner.api.collections().list(filters=[["portable_data_hash", "=", kr]],
+                                                  order="created_at desc",
+                                                   select=["name", "description", "properties", "portable_data_hash", "manifest_text", "storage_classes_desired", "trash_at"],
+                                                   limit=1).execute()
+            if len(col["items"]) == 0:
+                logger.warning("Cannot find collection with portable data hash %s", kr)
+                continue
+            col = col["items"][0]
+            try:
+                arvrunner.api.collections().create(body={"collection": {
+                    "owner_uuid": runtimeContext.project_uuid,
+                    "name": col["name"],
+                    "description": col["description"],
+                    "properties": col["properties"],
+                    "portable_data_hash": col["portable_data_hash"],
+                    "manifest_text": col["manifest_text"],
+                    "storage_classes_desired": col["storage_classes_desired"],
+                    "trash_at": col["trash_at"]
+                }}, ensure_unique_name=True).execute()
+            except Exception as e:
+                logger.warning("Unable copy collection to destination: %s", e)
+

     if "$schemas" in workflowobj:
         sch = CommentedSeq()
         for s in workflowobj["$schemas"]:
     if "$schemas" in workflowobj:
         sch = CommentedSeq()
         for s in workflowobj["$schemas"]:


@@ -450,32 +510,36 @@ def upload_dependencies(arvrunner, name, document_loader,
     return mapper
 
 
     return mapper
 
 

-def upload_docker(arvrunner, tool):
+def upload_docker(arvrunner, tool, runtimeContext):

     """Uploads Docker images used in CommandLineTool objects."""
 
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = tool.get_requirement("DockerRequirement")
         if docker_req:
             if docker_req.get("dockerOutputDirectory") and arvrunner.work_api != "containers":
     """Uploads Docker images used in CommandLineTool objects."""
 
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = tool.get_requirement("DockerRequirement")
         if docker_req:
             if docker_req.get("dockerOutputDirectory") and arvrunner.work_api != "containers":

-                # TODO: can be supported by containers API, but not jobs API.

                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")

-            arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid,
-                                                       arvrunner.runtimeContext.force_docker_pull,
-                                                       arvrunner.runtimeContext.tmp_outdir_prefix,
-                                                       arvrunner.runtimeContext.match_local_docker)
+
+            arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, docker_req, True,
+                                                       runtimeContext.project_uuid,
+                                                       runtimeContext.force_docker_pull,
+                                                       runtimeContext.tmp_outdir_prefix,
+                                                       runtimeContext.match_local_docker,
+                                                       runtimeContext.copy_deps)

         else:
             arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": "arvados/jobs:"+__version__},
         else:
             arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": "arvados/jobs:"+__version__},

-                                                       True, arvrunner.project_uuid,
-                                                       arvrunner.runtimeContext.force_docker_pull,
-                                                       arvrunner.runtimeContext.tmp_outdir_prefix,
-                                                       arvrunner.runtimeContext.match_local_docker)
+                                                       True,
+                                                       runtimeContext.project_uuid,
+                                                       runtimeContext.force_docker_pull,
+                                                       runtimeContext.tmp_outdir_prefix,
+                                                       runtimeContext.match_local_docker,
+                                                       runtimeContext.copy_deps)

     elif isinstance(tool, cwltool.workflow.Workflow):
         for s in tool.steps:
     elif isinstance(tool, cwltool.workflow.Workflow):
         for s in tool.steps:

-            upload_docker(arvrunner, s.embedded_tool)
+            upload_docker(arvrunner, s.embedded_tool, runtimeContext)

 
 
 
 

-def packed_workflow(arvrunner, tool, merged_map):
+def packed_workflow(arvrunner, tool, merged_map, runtimeContext):

     """Create a packed workflow.
 
     A "packed" workflow is one where all the components have been combined into a single document."""
     """Create a packed workflow.
 
     A "packed" workflow is one where all the components have been combined into a single document."""


@@ -504,10 +568,11 @@ def packed_workflow(arvrunner, tool, merged_map):
                     v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
             if v.get("class") == "DockerRequirement":
                 v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True,
                     v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
             if v.get("class") == "DockerRequirement":
                 v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True,

-                                                                                                             arvrunner.project_uuid,
-                                                                                                             arvrunner.runtimeContext.force_docker_pull,
-                                                                                                             arvrunner.runtimeContext.tmp_outdir_prefix,
-                                                                                                             arvrunner.runtimeContext.match_local_docker)
+                                                                                                             runtimeContext.project_uuid,
+                                                                                                             runtimeContext.force_docker_pull,
+                                                                                                             runtimeContext.tmp_outdir_prefix,
+                                                                                                             runtimeContext.match_local_docker,
+                                                                                                             runtimeContext.copy_deps)

             for l in v:
                 visit(v[l], cur_id)
         if isinstance(v, list):
             for l in v:
                 visit(v[l], cur_id)
         if isinstance(v, list):


@@ -528,7 +593,7 @@ def tag_git_version(packed):
             packed["http://schema.org/version"] = githash
 
 
             packed["http://schema.org/version"] = githash
 
 

-def upload_job_order(arvrunner, name, tool, job_order):
+def upload_job_order(arvrunner, name, tool, job_order, runtimeContext):

     """Upload local files referenced in the input object and return updated input
     object with 'location' updated to the proper keep references.
     """
     """Upload local files referenced in the input object and return updated input
     object with 'location' updated to the proper keep references.
     """


@@ -564,7 +629,8 @@ def upload_job_order(arvrunner, name, tool, job_order):
                                     tool.doc_loader,
                                     job_order,
                                     job_order.get("id", "#"),
                                     tool.doc_loader,
                                     job_order,
                                     job_order.get("id", "#"),

-                                    False)
+                                    False,
+                                    runtimeContext)

 
     if "id" in job_order:
         del job_order["id"]
 
     if "id" in job_order:
         del job_order["id"]


@@ -578,10 +644,10 @@ def upload_job_order(arvrunner, name, tool, job_order):
 
 FileUpdates = namedtuple("FileUpdates", ["resolved", "secondaryFiles"])
 
 
 FileUpdates = namedtuple("FileUpdates", ["resolved", "secondaryFiles"])
 

-def upload_workflow_deps(arvrunner, tool):
+def upload_workflow_deps(arvrunner, tool, runtimeContext):

     # Ensure that Docker images needed by this workflow are available
 
     # Ensure that Docker images needed by this workflow are available
 

-    upload_docker(arvrunner, tool)
+    upload_docker(arvrunner, tool, runtimeContext)

 
     document_loader = tool.doc_loader
 
 
     document_loader = tool.doc_loader
 


@@ -596,6 +662,7 @@ def upload_workflow_deps(arvrunner, tool):
                                      deptool,
                                      deptool["id"],
                                      False,
                                      deptool,
                                      deptool["id"],
                                      False,

+                                     runtimeContext,

                                      include_primary=False,
                                      discovered_secondaryfiles=discovered_secondaryfiles)
             document_loader.idx[deptool["id"]] = deptool
                                      include_primary=False,
                                      discovered_secondaryfiles=discovered_secondaryfiles)
             document_loader.idx[deptool["id"]] = deptool


@@ -608,19 +675,22 @@ def upload_workflow_deps(arvrunner, tool):
 
     return merged_map
 
 
     return merged_map
 

-def arvados_jobs_image(arvrunner, img):
+def arvados_jobs_image(arvrunner, img, runtimeContext):

     """Determine if the right arvados/jobs image version is available.  If not, try to pull and upload it."""
 
     try:
     """Determine if the right arvados/jobs image version is available.  If not, try to pull and upload it."""
 
     try:

-        return arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": img}, True, arvrunner.project_uuid,
-                                                          arvrunner.runtimeContext.force_docker_pull,
-                                                          arvrunner.runtimeContext.tmp_outdir_prefix,
-                                                          arvrunner.runtimeContext.match_local_docker)
+        return arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": img},
+                                                          True,
+                                                          runtimeContext.project_uuid,
+                                                          runtimeContext.force_docker_pull,
+                                                          runtimeContext.tmp_outdir_prefix,
+                                                          runtimeContext.match_local_docker,
+                                                          runtimeContext.copy_deps)

     except Exception as e:
         raise Exception("Docker image %s is not available\n%s" % (img, e) )
 
 
     except Exception as e:
         raise Exception("Docker image %s is not available\n%s" % (img, e) )
 
 

-def upload_workflow_collection(arvrunner, name, packed):
+def upload_workflow_collection(arvrunner, name, packed, runtimeContext):

     collection = arvados.collection.Collection(api_client=arvrunner.api,
                                                keep_client=arvrunner.keep_client,
                                                num_retries=arvrunner.num_retries)
     collection = arvados.collection.Collection(api_client=arvrunner.api,
                                                keep_client=arvrunner.keep_client,
                                                num_retries=arvrunner.num_retries)


@@ -629,15 +699,15 @@ def upload_workflow_collection(arvrunner, name, packed):
 
     filters = [["portable_data_hash", "=", collection.portable_data_hash()],
                ["name", "like", name+"%"]]
 
     filters = [["portable_data_hash", "=", collection.portable_data_hash()],
                ["name", "like", name+"%"]]

-    if arvrunner.project_uuid:
-        filters.append(["owner_uuid", "=", arvrunner.project_uuid])
+    if runtimeContext.project_uuid:
+        filters.append(["owner_uuid", "=", runtimeContext.project_uuid])

     exists = arvrunner.api.collections().list(filters=filters).execute(num_retries=arvrunner.num_retries)
 
     if exists["items"]:
         logger.info("Using collection %s", exists["items"][0]["uuid"])
     else:
         collection.save_new(name=name,
     exists = arvrunner.api.collections().list(filters=filters).execute(num_retries=arvrunner.num_retries)
 
     if exists["items"]:
         logger.info("Using collection %s", exists["items"][0]["uuid"])
     else:
         collection.save_new(name=name,

-                            owner_uuid=arvrunner.project_uuid,
+                            owner_uuid=runtimeContext.project_uuid,

                             ensure_unique_name=True,
                             num_retries=arvrunner.num_retries)
         logger.info("Uploaded to %s", collection.manifest_locator())
                             ensure_unique_name=True,
                             num_retries=arvrunner.num_retries)
         logger.info("Uploaded to %s", collection.manifest_locator())