X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f98e0188777b3e2d229c968824b3e64307dae4e6..32d79def3a400de6fbe4cd02a8c71643238d867d:/sdk/cwl/arvados_cwl/runner.py diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py index bf0eb08129..8db3e61cf1 100644 --- a/sdk/cwl/arvados_cwl/runner.py +++ b/sdk/cwl/arvados_cwl/runner.py @@ -8,10 +8,11 @@ from functools import partial 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 from cwltool.command_line_tool import CommandLineTool import cwltool.workflow @@ -45,11 +46,13 @@ def trim_anonymous_location(obj): 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: @@ -61,8 +64,27 @@ def find_defaults(d, op): 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 @@ -116,22 +138,33 @@ def upload_dependencies(arvrunner, name, document_loader, for s in workflowobj["$schemas"]: sc.append({"class": "File", "location": s}) - def capture_default(obj): + def visit_default(obj): remove = [False] - def add_default(f): + def ensure_default_location(f): if "location" not in f and "path" in f: f["location"] = f["path"] del f["path"] if "location" in f and not arvrunner.fs_access.exists(f["location"]): - # Remove from sc + # Doesn't exist, remove from list of dependencies to upload sc[:] = [x for x in sc if x["location"] != f["location"]] # Delete "default" from workflowobj remove[0] = True - visit_class(obj["default"], ("File", "Directory"), add_default) + visit_class(obj["default"], ("File", "Directory"), ensure_default_location) if remove[0]: del obj["default"] - find_defaults(workflowobj, capture_default) + find_defaults(workflowobj, visit_default) + + discovered = {} + def discover_default_secondary_files(obj): + discover_secondary_files(obj["inputs"], + {shortname(t["id"]): t["default"] for t in obj["inputs"] if "default" in t}, + discovered) + + visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files) + + for d in discovered: + sc.extend(discovered[d]) mapper = ArvPathMapper(arvrunner, sc, "", "keep:%s", @@ -142,8 +175,13 @@ def upload_dependencies(arvrunner, name, document_loader, def setloc(p): if "location" in p and (not p["location"].startswith("_:")) and (not p["location"].startswith("keep:")): p["location"] = mapper.mapper(p["location"]).resolved - adjustFileObjs(workflowobj, setloc) - adjustDirObjs(workflowobj, setloc) + + visit_class(workflowobj, ("File", "Directory"), setloc) + visit_class(discovered, ("File", "Directory"), setloc) + + if discovered_secondaryfiles is not None: + for d in discovered: + discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d] if "$schemas" in workflowobj: sch = [] @@ -171,6 +209,7 @@ def upload_docker(arvrunner, tool): for s in tool.steps: upload_docker(arvrunner, s.embedded_tool) + def packed_workflow(arvrunner, tool, merged_map): """Create a packed workflow. @@ -189,7 +228,9 @@ def packed_workflow(arvrunner, tool, merged_map): 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): @@ -198,6 +239,7 @@ def packed_workflow(arvrunner, tool, merged_map): visit(packed, None) return packed + def tag_git_version(packed): if tool.tool["id"].startswith("file://"): path = os.path.dirname(tool.tool["id"][7:]) @@ -209,20 +251,6 @@ def tag_git_version(packed): 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. @@ -247,6 +275,8 @@ def upload_job_order(arvrunner, name, tool, job_order): return job_order +FileUpdates = namedtuple("FileUpdates", ["resolved", "secondaryFiles"]) + def upload_workflow_deps(arvrunner, tool): # Ensure that Docker images needed by this workflow are available @@ -258,18 +288,20 @@ def upload_workflow_deps(arvrunner, tool): 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) @@ -399,5 +431,3 @@ class Runner(object): self.arvrunner.output_callback({}, "permanentFail") else: self.arvrunner.output_callback(outputs, processStatus) - finally: - self.arvrunner.process_done(record["uuid"])