import logging
import json
import subprocess
+from collections import namedtuple
from StringIO import StringIO
-from schema_salad.sourceline import SourceLine
+from schema_salad.sourceline import SourceLine, cmap
-import cwltool.draft2tool
-from cwltool.draft2tool import CommandLineTool
+from cwltool.command_line_tool import CommandLineTool
import cwltool.workflow
from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
from cwltool.load_tool import fetch_document
if obj.get("location", "").startswith("_:"):
del obj["location"]
+
def remove_redundant_fields(obj):
for field in ("path", "nameext", "nameroot", "dirname"):
if field in obj:
del obj[field]
+
def find_defaults(d, op):
if isinstance(d, list):
for i in d:
for i in d.itervalues():
find_defaults(i, op)
+
+def discover_secondary_files(inputs, job_order, discovered=None):
+ for t in inputs:
+ def setSecondary(fileobj):
+ if isinstance(fileobj, dict) and fileobj.get("class") == "File":
+ if "secondaryFiles" not in fileobj:
+ fileobj["secondaryFiles"] = cmap([{"location": substitute(fileobj["location"], sf), "class": "File"} for sf in t["secondaryFiles"]])
+ if discovered is not None:
+ discovered[fileobj["location"]] = fileobj["secondaryFiles"]
+
+ if isinstance(fileobj, list):
+ for e in fileobj:
+ setSecondary(e)
+
+ if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
+ setSecondary(job_order[shortname(t["id"])])
+
+
def upload_dependencies(arvrunner, name, document_loader,
- workflowobj, uri, loadref_run, include_primary=True):
+ workflowobj, uri, loadref_run,
+ include_primary=True, discovered_secondaryfiles=None):
"""Upload the dependencies of the workflowobj document to Keep.
Returns a pathmapper object mapping local paths to keep references. Also
for s in workflowobj["$schemas"]:
sc.append({"class": "File", "location": s})
- def capture_default(obj):
+ def visit_default(obj):
remove = [False]
- def add_default(f):
+ def ensure_default_location(f):
if "location" not in f and "path" in f:
f["location"] = f["path"]
del f["path"]
if "location" in f and not arvrunner.fs_access.exists(f["location"]):
- # Remove from sc
+ # Doesn't exist, remove from list of dependencies to upload
sc[:] = [x for x in sc if x["location"] != f["location"]]
# Delete "default" from workflowobj
remove[0] = True
- visit_class(obj["default"], ("File", "Directory"), add_default)
+ visit_class(obj["default"], ("File", "Directory"), ensure_default_location)
if remove[0]:
del obj["default"]
- find_defaults(workflowobj, capture_default)
+ find_defaults(workflowobj, visit_default)
+
+ discovered = {}
+ def discover_default_secondary_files(obj):
+ discover_secondary_files(obj["inputs"],
+ {shortname(t["id"]): t["default"] for t in obj["inputs"] if "default" in t},
+ discovered)
+
+ visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
+
+ for d in discovered:
+ sc.extend(discovered[d])
mapper = ArvPathMapper(arvrunner, sc, "",
"keep:%s",
def setloc(p):
if "location" in p and (not p["location"].startswith("_:")) and (not p["location"].startswith("keep:")):
p["location"] = mapper.mapper(p["location"]).resolved
- adjustFileObjs(workflowobj, setloc)
- adjustDirObjs(workflowobj, setloc)
+
+ visit_class(workflowobj, ("File", "Directory"), setloc)
+ visit_class(discovered, ("File", "Directory"), setloc)
+
+ if discovered_secondaryfiles is not None:
+ for d in discovered:
+ discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
if "$schemas" in workflowobj:
sch = []
for s in tool.steps:
upload_docker(arvrunner, s.embedded_tool)
+
def packed_workflow(arvrunner, tool, merged_map):
"""Create a packed workflow.
if v.get("class") in ("CommandLineTool", "Workflow"):
cur_id = rewrite_to_orig.get(v["id"], v["id"])
if "location" in v and not v["location"].startswith("keep:"):
- v["location"] = merged_map[cur_id][v["location"]]
+ 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"]]
for l in v:
visit(v[l], cur_id)
if isinstance(v, list):
visit(packed, None)
return packed
+
def tag_git_version(packed):
if tool.tool["id"].startswith("file://"):
path = os.path.dirname(tool.tool["id"][7:])
packed["http://schema.org/version"] = githash
-def discover_secondary_files(inputs, job_order):
- for t in inputs:
- def setSecondary(fileobj):
- if isinstance(fileobj, dict) and fileobj.get("class") == "File":
- if "secondaryFiles" not in fileobj:
- fileobj["secondaryFiles"] = [{"location": substitute(fileobj["location"], sf), "class": "File"} for sf in t["secondaryFiles"]]
-
- if isinstance(fileobj, list):
- for e in fileobj:
- setSecondary(e)
-
- if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
- setSecondary(job_order[shortname(t["id"])])
-
def upload_job_order(arvrunner, name, tool, job_order):
"""Upload local files referenced in the input object and return updated input
object with 'location' updated to the proper keep references.
return job_order
+FileUpdates = namedtuple("FileUpdates", ["resolved", "secondaryFiles"])
+
def upload_workflow_deps(arvrunner, tool):
# Ensure that Docker images needed by this workflow are available
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)
+ "%s dependencies" % (shortname(deptool["id"])),
+ document_loader,
+ deptool,
+ deptool["id"],
+ False,
+ include_primary=False,
+ discovered_secondaryfiles=discovered_secondaryfiles)
document_loader.idx[deptool["id"]] = deptool
toolmap = {}
for k,v in pm.items():
toolmap[k] = v.resolved
- merged_map[deptool["id"]] = toolmap
+ merged_map[deptool["id"]] = FileUpdates(toolmap, discovered_secondaryfiles)
tool.visit(upload_tool_deps)
def __init__(self, runner, tool, job_order, enable_reuse,
output_name, output_tags, submit_runner_ram=0,
name=None, on_error=None, submit_runner_image=None,
- intermediate_output_ttl=0, merged_map=None):
+ intermediate_output_ttl=0, merged_map=None, priority=None,
+ secret_store=None):
self.arvrunner = runner
self.tool = tool
self.job_order = job_order
self.on_error = on_error
self.jobs_image = submit_runner_image or "arvados/jobs:"+__version__
self.intermediate_output_ttl = intermediate_output_ttl
+ self.priority = priority
+ self.secret_store = secret_store
if submit_runner_ram:
self.submit_runner_ram = submit_runner_ram
self.arvrunner.output_callback({}, "permanentFail")
else:
self.arvrunner.output_callback(outputs, processStatus)
- finally:
- if record["uuid"] in self.arvrunner.processes:
- del self.arvrunner.processes[record["uuid"]]
projects / arvados.git / blobdiff