builder_job_order,
discovered)
- _jobloaderctx = jobloaderctx.copy()
- loader = schema_salad.ref_resolver.Loader(_jobloaderctx, fetcher_constructor=document_loader.fetcher_constructor)
-
- copied, _ = loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
+ copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
for d in list(discovered):
tool.tool["inputs"],
job_order)
+ _jobloaderctx = jobloaderctx.copy()
+ jobloader = schema_salad.ref_resolver.Loader(_jobloaderctx, fetcher_constructor=tool.doc_loader.fetcher_constructor)
+
jobmapper = upload_dependencies(arvrunner,
name,
- tool.doc_loader,
+ jobloader,
job_order,
job_order.get("id", "#"),
False,
merged_map = {}
tool_dep_cache = {}
+
+ todo = []
+
+ # Standard traversal is top down, we want to go bottom up, so use
+ # the visitor to accumalate a list of nodes to visit, then
+ # visit them in reverse order.
def upload_tool_deps(deptool):
if "id" in deptool:
- 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():
- toolmap[k] = v.resolved
- merged_map[deptool["id"]] = FileUpdates(toolmap, discovered_secondaryfiles)
+ todo.append(deptool)
tool.visit(upload_tool_deps)
+ for deptool in reversed(todo):
+ 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():
+ toolmap[k] = v.resolved
+ merged_map[deptool["id"]] = FileUpdates(toolmap, discovered_secondaryfiles)
+
return merged_map
def arvados_jobs_image(arvrunner, img, runtimeContext):
ADD cwl/cwltool_dist/$cwltool /tmp/
ADD cwl/dist/$runner /tmp/
+RUN $pipcmd install wheel
RUN cd /tmp/arvados-python-client-* && $pipcmd install .
RUN if test -d /tmp/schema-salad-* ; then cd /tmp/schema-salad-* && $pipcmd install . ; fi
RUN if test -d /tmp/cwltool-* ; then cd /tmp/cwltool-* && $pipcmd install . ; fi
RUN cd /tmp/arvados-cwl-runner-* && $pipcmd install .
+# Sometimes Python dependencies install successfully but don't
+# actually work. So run arvados-cwl-runner here to catch fun
+# dependency errors like pkg_resources.DistributionNotFound.
+RUN arvados-cwl-runner --version
+
# Install dependencies and set up system.
RUN /usr/sbin/adduser --disabled-password \
--gecos 'Crunch execution user' crunch && \