import cwltool.draft2tool
from cwltool.draft2tool import CommandLineTool
import cwltool.workflow
-from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs
+from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
from cwltool.load_tool import fetch_document
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.utils import aslist
+from cwltool.builder import substitute
import arvados.collection
import ruamel.yaml as yaml
from .arvdocker import arv_docker_get_image
from .pathmapper import ArvPathMapper
+from ._version import __version__
logger = logging.getLogger('arvados.cwl-runner')
def upload_instance(arvrunner, name, tool, job_order):
upload_docker(arvrunner, tool)
+ for t in tool.tool["inputs"]:
+ def setSecondary(fileobj):
+ if "__norecurse" in fileobj:
+ del fileobj["__norecurse"]
+ return
+ if "secondaryFiles" not in fileobj:
+ fileobj["secondaryFiles"] = [{"location": substitute(fileobj["location"], sf), "class": "File", "__norecurse": True} for sf in t["secondaryFiles"]]
+
+ if shortname(t["id"]) in job_order and t.get("secondaryFiles"):
+ adjustFileObjs(job_order, setSecondary)
+
workflowmapper = upload_dependencies(arvrunner,
name,
tool.doc_loader,
tool.tool,
tool.tool["id"],
True)
-
jobmapper = upload_dependencies(arvrunner,
os.path.basename(job_order.get("id", "#")),
tool.doc_loader,
return workflowmapper
+def arvados_jobs_image(arvrunner):
+ img = "arvados/jobs:"+__version__
+ try:
+ arv_docker_get_image(arvrunner.api, {"dockerPull": img}, True, arvrunner.project_uuid)
+ except Exception as e:
+ raise Exception("Docker image %s is not available\n%s" % (img, e) )
+ return img
class Runner(object):
def __init__(self, runner, tool, job_order, enable_reuse, output_name):