if s.startswith("keep:"):
return s
- #print("BBB", s, baseuri)
uri = urlexpander(s, baseuri)
- #print("CCC", uri)
if uri.startswith("keep:"):
return uri
fileuri = urllib.parse.urldefrag(baseuri)[0]
- #print("BBB", s, baseuri, uri)
-
for u in (baseuri, fileuri):
if u in merged_map:
replacements = merged_map[u].resolved
- #print("RRR", u, uri, replacements)
if uri in replacements:
return replacements[uri]
p2 = os.path.dirname(uri_file_path(uri))
p3 = os.path.basename(uri_file_path(uri))
- #print("PPP", p1, p2, p3)
-
r = os.path.relpath(p2, p1)
if r == ".":
r = ""
- #print("RRR", r)
-
return os.path.join(r, p3)
def is_basetype(tp):
else:
update_refs(s, baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix)
elif isinstance(d, MutableMapping):
+ for field in ("id", "name"):
+ if isinstance(d.get(field), str) and d[field].startswith("_:"):
+ # blank node reference, was added in automatically, can get rid of it.
+ del d[field]
+
if "id" in d:
baseuri = urlexpander(d["id"], baseuri, scoped_id=True)
elif "name" in d and isinstance(d["name"], str):
continue
if field in ("$include", "$import") and isinstance(d[field], str):
- d[field] = rel_ref(d[field], baseuri, urlexpander, {}, None)
+ d[field] = rel_ref(d[field], baseuri, urlexpander, {}, jobmapper)
continue
- if (field == "type" and
- isinstance(d["type"], str) and
- not is_basetype(d["type"])):
- d["type"] = rel_ref(d["type"], baseuri, urlexpander, merged_map, jobmapper)
- continue
+ for t in ("type", "items"):
+ if (field == t and
+ isinstance(d[t], str) and
+ not is_basetype(d[t])):
+ d[t] = rel_ref(d[t], baseuri, urlexpander, merged_map, jobmapper)
+ continue
if field == "inputs" and isinstance(d["inputs"], MutableMapping):
for inp in d["inputs"]:
update_refs(d[field], baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix)
-def fix_schemadef(req, baseuri, urlexpander, merged_map, pdh):
+def fix_schemadef(req, baseuri, urlexpander, merged_map, jobmapper, pdh):
req = copy.deepcopy(req)
for f in req["types"]:
r = f["name"]
path, frag = urllib.parse.urldefrag(r)
- rel = rel_ref(r, baseuri, urlexpander, merged_map)
+ rel = rel_ref(r, baseuri, urlexpander, merged_map, jobmapper)
merged_map.setdefault(path, FileUpdates({}, {}))
- #print("PPP", path, r, frag)
rename = "keep:%s/%s" %(pdh, rel)
- #rename = "#%s" % frag
for mm in merged_map:
merged_map[mm].resolved[r] = rename
return req
drop_ids(d[field])
-def new_upload_workflow(arvRunner, tool, job_order, project_uuid,
+def upload_workflow(arvRunner, tool, job_order, project_uuid,
runtimeContext,
uuid=None,
submit_runner_ram=0, name=None, merged_map=None,
col = arvados.collection.Collection(api_client=arvRunner.api)
- #print(merged_map)
-
for w in workflow_files | import_files:
# 1. load YAML
update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, set_block_style, runtimeContext, "", "")
with col.open(w[n+1:], "wt") as f:
- #print(yamlloader.dump(result, stream=sys.stdout))
+ # yamlloader.dump(result, stream=sys.stdout)
yamlloader.dump(result, stream=f)
+ with col.open(os.path.join("original", w[n+1:]), "wt") as f:
+ f.write(text)
+
+
for w in include_files:
with col.open(w[n+1:], "wb") as f1:
- with open(uri_file_path(w), "rb") as f2:
- dat = f2.read(65536)
- while dat:
- f1.write(dat)
+ with col.open(os.path.join("original", w[n+1:]), "wb") as f3:
+ with open(uri_file_path(w), "rb") as f2:
dat = f2.read(65536)
+ while dat:
+ f1.write(dat)
+ f3.write(dat)
+ dat = f2.read(65536)
+
toolname = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
if git_info and git_info.get("http://arvados.org/cwl#gitDescribe"):
p = g.split("#", 1)[1]
properties["arv:"+p] = git_info[g]
- col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties)
+ existing = arvRunner.api.collections().list(filters=[["portable_data_hash", "=", col.portable_data_hash()],
+ ["owner_uuid", "=", arvRunner.project_uuid]]).execute(num_retries=arvRunner.num_retries)
+ if len(existing["items"]) == 0:
+ col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties)
+ logger.info("Workflow uploaded to %s", col.manifest_locator())
+ else:
+ logger.info("Workflow uploaded to %s", existing["items"][0]["uuid"])
adjustDirObjs(job_order, trim_listing)
adjustFileObjs(job_order, trim_anonymous_location)
for g in git_info:
doc[g] = git_info[g]
- #print("MMM", main["id"])
- #print(yamlloader.dump(wrapper, stream=sys.stdout))
-
for i, r in enumerate(wrapper["requirements"]):
if r["class"] == "SchemaDefRequirement":
- wrapper["requirements"][i] = fix_schemadef(r, main["id"], tool.doc_loader.expand_url, merged_map, col.portable_data_hash())
-
- # print()
- # print("merrrrged maaap", merged_map)
- # print()
- #print("update_refs", main["id"], runfile)
-
- #print(yamlloader.dump(wrapper, stream=sys.stdout))
+ 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, False, runtimeContext, main["id"]+"#", "#main/")
# Remove any lingering file references.
drop_ids(wrapper)
- #print("HHH")
-
- #print(yamlloader.dump(wrapper, stream=sys.stdout))
-
return doc
return call.execute(num_retries=arvRunner.num_retries)["uuid"]
-def upload_workflow(arvRunner, tool, job_order, project_uuid,
- runtimeContext, uuid=None,
- submit_runner_ram=0, name=None, merged_map=None,
- submit_runner_image=None,
- git_info=None):
-
- packed = packed_workflow(arvRunner, tool, merged_map, runtimeContext, git_info)
-
- adjustDirObjs(job_order, trim_listing)
- adjustFileObjs(job_order, trim_anonymous_location)
- adjustDirObjs(job_order, trim_anonymous_location)
-
- main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
- for inp in main["inputs"]:
- sn = shortname(inp["id"])
- if sn in job_order:
- inp["default"] = job_order[sn]
-
- if not name:
- name = tool.tool.get("label", os.path.basename(tool.tool["id"]))
-
- upload_dependencies(arvRunner, name, tool.doc_loader,
- packed, tool.tool["id"],
- runtimeContext)
-
- wf_runner_resources = None
-
- hints = main.get("hints", [])
- found = False
- for h in hints:
- if h["class"] == "http://arvados.org/cwl#WorkflowRunnerResources":
- wf_runner_resources = h
- found = True
- break
- if not found:
- wf_runner_resources = {"class": "http://arvados.org/cwl#WorkflowRunnerResources"}
- hints.append(wf_runner_resources)
-
- wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner,
- submit_runner_image or "arvados/jobs:"+__version__,
- runtimeContext)
-
- if submit_runner_ram:
- wf_runner_resources["ramMin"] = submit_runner_ram
-
- main["hints"] = hints
-
- wrapper = make_wrapper_workflow(arvRunner, main, packed, project_uuid, name, git_info, tool)
-
- body = {
- "workflow": {
- "name": name,
- "description": tool.tool.get("doc", ""),
- "definition": wrapper
- }}
- if project_uuid:
- body["workflow"]["owner_uuid"] = project_uuid
-
- if uuid:
- call = arvRunner.api.workflows().update(uuid=uuid, body=body)
- else:
- call = arvRunner.api.workflows().create(body=body)
- return call.execute(num_retries=arvRunner.num_retries)["uuid"]
-
def dedup_reqs(reqs):
dedup = {}
for r in reversed(reqs):
projects / arvados.git / blobdiff