19280: More metrics

[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 7664abef7c52ffe95f3c114ac1ba1ee9d833f8f9..2582c0a3a3e3fd88c464b58a23c5d74b0281b92e 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -39,8 +39,9 @@ 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 .util import collectionUUID

-import ruamel.yaml as yaml
+from ruamel.yaml import YAML

 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 import arvados_cwl.arvdocker
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 import arvados_cwl.arvdocker


@@ -48,8 +49,10 @@ from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, col
 from ._version import __version__
 from . import done
 from . context import ArvRuntimeContext
 from ._version import __version__
 from . import done
 from . context import ArvRuntimeContext

+from .perf import Perf

 
 logger = logging.getLogger('arvados.cwl-runner')
 
 logger = logging.getLogger('arvados.cwl-runner')

+metrics = logging.getLogger('arvados.cwl-runner.metrics')

 
 def trim_anonymous_location(obj):
     """Remove 'location' field from File and Directory literals.
 
 def trim_anonymous_location(obj):
     """Remove 'location' field from File and Directory literals.


@@ -105,7 +108,8 @@ def make_builder(joborder, hints, requirements, runtimeContext, metadata):
                  outdir="",              # type: Text
                  tmpdir="",              # type: Text
                  stagedir="",            # type: Text
                  outdir="",              # type: Text
                  tmpdir="",              # type: Text
                  stagedir="",            # type: Text

-                 cwlVersion=metadata.get("http://commonwl.org/cwltool#original_cwlVersion") or metadata.get("cwlVersion")
+                 cwlVersion=metadata.get("http://commonwl.org/cwltool#original_cwlVersion") or metadata.get("cwlVersion"),
+                 container_engine="docker"

                 )
 
 def search_schemadef(name, reqs):
                 )
 
 def search_schemadef(name, reqs):


@@ -127,6 +131,9 @@ 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:


@@ -162,10 +169,13 @@ 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
         #


@@ -173,9 +183,9 @@ 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):


@@ -183,7 +193,10 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             elif isinstance(pattern, dict):
                 specs.append(pattern)
             elif isinstance(pattern, str):
             elif isinstance(pattern, dict):
                 specs.append(pattern)
             elif isinstance(pattern, str):

-                specs.append({"pattern": pattern})
+                if builder.cwlVersion == "v1.0":
+                    specs.append({"pattern": pattern, "required": True})
+                else:
+                    specs.append({"pattern": pattern, "required": sf.get("required")})

             else:
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Expression must return list, object, string or null")
             else:
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Expression must return list, object, string or null")


@@ -192,7 +205,12 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         for i, sf in enumerate(specs):
             if isinstance(sf, dict):
                 if sf.get("class") == "File":
         for i, sf in enumerate(specs):
             if isinstance(sf, dict):
                 if sf.get("class") == "File":

-                    pattern = sf["basename"]
+                    pattern = None
+                    if sf.get("location") is None:
+                        raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
+                            "File object is missing 'location': %s" % sf)
+                    sfpath = sf["location"]
+                    required = True

                 else:
                     pattern = sf["pattern"]
                     required = sf.get("required")
                 else:
                     pattern = sf["pattern"]
                     required = sf.get("required")


@@ -203,11 +221,29 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Expression must return list, object, string or null")
 
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Expression must return list, object, string or null")
 

-            sfpath = substitute(primary["location"], pattern)
+            if pattern is not None:
+                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)
 
             if fsaccess.exists(sfpath):
             required = builder.do_eval(required, context=primary)
 
             if fsaccess.exists(sfpath):

-                found.append({"location": sfpath, "class": "File"})
+                if pattern is not None:
+                    found.append({"location": sfpath, "class": "File"})
+                else:
+                    found.append(sf)

             elif required:
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Required secondary file '%s' does not exist" % sfpath)
             elif required:
                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
                     "Required secondary file '%s' does not exist" % sfpath)


@@ -215,7 +251,7 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         primary["secondaryFiles"] = cmap(found)
         if discovered is not None:
             discovered[primary["location"]] = primary["secondaryFiles"]
         primary["secondaryFiles"] = cmap(found)
         if discovered is not None:
             discovered[primary["location"]] = primary["secondaryFiles"]

-    elif inputschema["type"] not in primitive_types_set:
+    elif inputschema["type"] not in primitive_types_set and inputschema["type"] not in ("File", "Directory"):

         set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered)
 
 def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=None):
         set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered)
 
 def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=None):


@@ -225,8 +261,9 @@ 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,
-                        include_primary=True, discovered_secondaryfiles=None):
+                        workflowobj, uri, loadref_run, runtimeContext,
+                        include_primary=True, discovered_secondaryfiles=None,
+                        cache=None):

     """Upload the dependencies of the workflowobj document to Keep.
 
     Returns a pathmapper object mapping local paths to keep references.  Also
     """Upload the dependencies of the workflowobj document to Keep.
 
     Returns a pathmapper object mapping local paths to keep references.  Also


@@ -245,13 +282,19 @@ def upload_dependencies(arvrunner, name, document_loader,
         defrg, _ = urllib.parse.urldefrag(joined)
         if defrg not in loaded:
             loaded.add(defrg)
         defrg, _ = urllib.parse.urldefrag(joined)
         if defrg not in loaded:
             loaded.add(defrg)

+            if cache is not None and defrg in cache:
+                return cache[defrg]

             # Use fetch_text to get raw file (before preprocessing).
             text = document_loader.fetch_text(defrg)
             if isinstance(text, bytes):
                 textIO = StringIO(text.decode('utf-8'))
             else:
                 textIO = StringIO(text)
             # Use fetch_text to get raw file (before preprocessing).
             text = document_loader.fetch_text(defrg)
             if isinstance(text, bytes):
                 textIO = StringIO(text.decode('utf-8'))
             else:
                 textIO = StringIO(text)

-            return yaml.safe_load(textIO)
+            yamlloader = YAML(typ='safe', pure=True)
+            result = yamlloader.load(textIO)
+            if cache is not None:
+                cache[defrg] = result
+            return result

         else:
             return {}
 
         else:
             return {}
 


@@ -268,10 +311,21 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     metadata = scanobj
 
 
     metadata = scanobj
 

-    sc_result = scandeps(uri, scanobj,
-                  loadref_fields,
-                  set(("$include", "$schemas", "location")),
-                  loadref, urljoin=document_loader.fetcher.urljoin)
+    with Perf(metrics, "scandeps include, location"):
+        sc_result = scandeps(uri, scanobj,
+                             loadref_fields,
+                             set(("$include", "location")),
+                             loadref, urljoin=document_loader.fetcher.urljoin,
+                             nestdirs=False)
+
+    with Perf(metrics, "scandeps $schemas"):
+        optional_deps = scandeps(uri, scanobj,
+                                      loadref_fields,
+                                      set(("$schemas",)),
+                                      loadref, urljoin=document_loader.fetcher.urljoin,
+                                      nestdirs=False)
+
+    sc_result.extend(optional_deps)

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


@@ -299,54 +353,48 @@ def upload_dependencies(arvrunner, name, document_loader,
             sc.append(obj)
         collect_uuids(obj)
 
             sc.append(obj)
         collect_uuids(obj)
 

-    visit_class(workflowobj, ("File", "Directory"), collect_uuids)
-    visit_class(sc_result, ("File", "Directory"), collect_uploads)
+    with Perf(metrics, "collect uuids"):
+        visit_class(workflowobj, ("File", "Directory"), collect_uuids)
+
+    with Perf(metrics, "collect uploads"):
+        visit_class(sc_result, ("File", "Directory"), collect_uploads)

 
     # Resolve any collection uuids we found to portable data hashes
     # and assign them to uuid_map
     uuid_map = {}
     fetch_uuids = list(uuids.keys())
 
     # Resolve any collection uuids we found to portable data hashes
     # and assign them to uuid_map
     uuid_map = {}
     fetch_uuids = list(uuids.keys())

-    while fetch_uuids:
-        # For a large number of fetch_uuids, API server may limit
-        # response size, so keep fetching from API server has nothing
-        # more to give us.
-        lookups = arvrunner.api.collections().list(
-            filters=[["uuid", "in", fetch_uuids]],
-            count="none",
-            select=["uuid", "portable_data_hash"]).execute(
-                num_retries=arvrunner.num_retries)
+    with Perf(metrics, "fetch_uuids"):
+        while fetch_uuids:
+            # For a large number of fetch_uuids, API server may limit
+            # response size, so keep fetching from API server has nothing
+            # more to give us.
+            lookups = arvrunner.api.collections().list(
+                filters=[["uuid", "in", fetch_uuids]],
+                count="none",
+                select=["uuid", "portable_data_hash"]).execute(
+                    num_retries=arvrunner.num_retries)

 
 

-        if not lookups["items"]:
-            break
+            if not lookups["items"]:
+                break

 
 

-        for l in lookups["items"]:
-            uuid_map[l["uuid"]] = l["portable_data_hash"]
+            for l in lookups["items"]:
+                uuid_map[l["uuid"]] = l["portable_data_hash"]

 
 

-        fetch_uuids = [u for u in fetch_uuids if u not in uuid_map]
+            fetch_uuids = [u for u in fetch_uuids if u not in uuid_map]

 
     normalizeFilesDirs(sc)
 
     if include_primary and "id" in workflowobj:
         sc.append({"class": "File", "location": workflowobj["id"]})
 
 
     normalizeFilesDirs(sc)
 
     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)
 


@@ -378,16 +426,24 @@ def upload_dependencies(arvrunner, name, document_loader,
         else:
             del discovered[d]
 
         else:
             del discovered[d]
 

-    mapper = ArvPathMapper(arvrunner, sc, "",
-                           "keep:%s",
-                           "keep:%s/%s",
-                           name=name,
-                           single_collection=True)
+    with Perf(metrics, "mapper"):
+        mapper = ArvPathMapper(arvrunner, sc, "",
+                               "keep:%s",
+                               "keep:%s/%s",
+                               name=name,
+                               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:


@@ -409,7 +465,10 @@ 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(


@@ -417,13 +476,46 @@ def upload_dependencies(arvrunner, name, document_loader,
         p["location"] = "keep:%s%s" % (uuid_map[uuid], gp.groups()[1] if gp.groups()[1] else "")
         p[collectionUUID] = uuid
 
         p["location"] = "keep:%s%s" % (uuid_map[uuid], gp.groups()[1] if gp.groups()[1] else "")
         p[collectionUUID] = uuid
 

-    visit_class(workflowobj, ("File", "Directory"), setloc)
-    visit_class(discovered, ("File", "Directory"), setloc)
+    with Perf(metrics, "setloc"):
+        visit_class(workflowobj, ("File", "Directory"), setloc)
+        visit_class(discovered, ("File", "Directory"), setloc)

 
     if discovered_secondaryfiles is not None:
         for d in discovered:
             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 
 
     if discovered_secondaryfiles is not None:
         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"]:


@@ -434,30 +526,36 @@ 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)
+
+            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)
+                                                       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."""


@@ -471,7 +569,7 @@ def packed_workflow(arvrunner, tool, merged_map):
 
     def visit(v, cur_id):
         if isinstance(v, dict):
 
     def visit(v, cur_id):
         if isinstance(v, dict):

-            if v.get("class") in ("CommandLineTool", "Workflow"):
+            if v.get("class") in ("CommandLineTool", "Workflow", "ExpressionTool"):

                 if tool.metadata["cwlVersion"] == "v1.0" and "id" not in v:
                     raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field, add an 'id' or use to cwlVersion: v1.1")
                 if "id" in v:
                 if tool.metadata["cwlVersion"] == "v1.0" and "id" not in v:
                     raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field, add an 'id' or use to cwlVersion: v1.1")
                 if "id" in v:


@@ -479,15 +577,18 @@ def packed_workflow(arvrunner, tool, merged_map):
             if "path" in v and "location" not in v:
                 v["location"] = v["path"]
                 del v["path"]
             if "path" in v and "location" not in v:
                 v["location"] = v["path"]
                 del v["path"]

-            if "location" in v and not v["location"].startswith("keep:"):
-                v["location"] = merged_map[cur_id].resolved[v["location"]]
-            if "location" in v and v["location"] in merged_map[cur_id].secondaryFiles:
-                v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
+            if "location" in v and cur_id in merged_map:
+                if v["location"] in merged_map[cur_id].resolved:
+                    v["location"] = merged_map[cur_id].resolved[v["location"]]
+                if v["location"] in merged_map[cur_id].secondaryFiles:
+                    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,
             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)
+                                                                                                             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):


@@ -508,7 +609,7 @@ 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.
     """


@@ -544,7 +645,8 @@ 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"]


@@ -558,26 +660,30 @@ 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)
+    with Perf(metrics, "upload_docker"):
+        upload_docker(arvrunner, tool, runtimeContext)

 
     document_loader = tool.doc_loader
 
     merged_map = {}
 
     document_loader = tool.doc_loader
 
     merged_map = {}

-
+    tool_dep_cache = {}

     def upload_tool_deps(deptool):
         if "id" in deptool:
             discovered_secondaryfiles = {}
     def upload_tool_deps(deptool):
         if "id" in deptool:
             discovered_secondaryfiles = {}

-            pm = upload_dependencies(arvrunner,
-                                     "%s dependencies" % (shortname(deptool["id"])),
-                                     document_loader,
-                                     deptool,
-                                     deptool["id"],
-                                     False,
-                                     include_primary=False,
-                                     discovered_secondaryfiles=discovered_secondaryfiles)
+            with Perf(metrics, "upload_dependencies %s" % shortname(deptool["id"])):
+                pm = upload_dependencies(arvrunner,
+                                         "%s dependencies" % (shortname(deptool["id"])),
+                                         document_loader,
+                                         deptool,
+                                         deptool["id"],
+                                         False,
+                                         runtimeContext,
+                                         include_primary=False,
+                                         discovered_secondaryfiles=discovered_secondaryfiles,
+                                         cache=tool_dep_cache)

             document_loader.idx[deptool["id"]] = deptool
             toolmap = {}
             for k,v in pm.items():
             document_loader.idx[deptool["id"]] = deptool
             toolmap = {}
             for k,v in pm.items():


@@ -588,18 +694,22 @@ 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)
+        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)


@@ -608,15 +718,15 @@ 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())