import uuid
import os
import urllib
+import datetime
import arvados.commands.run
import arvados.collection
from schema_salad.sourceline import SourceLine
+from arvados.errors import ApiError
from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
from cwltool.workflow import WorkflowException
+from .http import http_to_keep
+
logger = logging.getLogger('arvados.cwl-runner')
def trim_listing(obj):
raise WorkflowException("File literal '%s' is missing `contents`" % src)
if srcobj["class"] == "Directory" and "listing" not in srcobj:
raise WorkflowException("Directory literal '%s' is missing `listing`" % src)
+ elif src.startswith("http:") or src.startswith("https:"):
+ keepref = http_to_keep(self.arvrunner.api, self.arvrunner.project_uuid, src)
+ logger.info("%s is %s", src, keepref)
+ self._pathmap[src] = MapperEnt(keepref, keepref, srcobj["class"], True)
else:
self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True)
elif obj["location"].startswith("_:") and "contents" in obj:
with c.open(path + "/" + obj["basename"], "w") as f:
f.write(obj["contents"].encode("utf-8"))
+ remap.append((obj["location"], path + "/" + obj["basename"]))
else:
raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"])
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
- already_uploaded = self.arvrunner.get_uploaded()
- copied_files = set()
- for k in referenced_files:
- loc = k["location"]
- if loc in already_uploaded:
- v = already_uploaded[loc]
- self._pathmap[loc] = MapperEnt(v.resolved, self.collection_pattern % urllib.unquote(v.resolved[5:]), v.type, True)
- if self.single_collection:
- basename = k["basename"]
- if basename not in collection:
- self.addentry({"location": loc, "class": v.type, "basename": basename}, collection, ".", [])
- copied_files.add((loc, basename, v.type))
-
for srcobj in referenced_files:
self.visit(srcobj, uploadfiles)
fnPattern="keep:%s/%s",
name=self.name,
project=self.arvrunner.project_uuid,
- collection=collection)
+ collection=collection,
+ packed=False)
for src, ab, st in uploadfiles:
self._pathmap[src] = MapperEnt(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:],
"Directory" if os.path.isdir(ab) else "File", True)
- self.arvrunner.add_uploaded(src, self._pathmap[src])
-
- for loc, basename, cls in copied_files:
- fn = "keep:%s/%s" % (collection.portable_data_hash(), basename)
- self._pathmap[loc] = MapperEnt(urllib.quote(fn, "/:+@"), self.collection_pattern % fn[5:], cls, True)
for srcobj in referenced_files:
remap = []
for l in srcobj.get("listing", []):
self.addentry(l, c, ".", remap)
- check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
- if not check["items"]:
- c.save_new(owner_uuid=self.arvrunner.project_uuid)
+ trash_time, props = self.__get_collection_attributes()
+
+ c.save_new(name="Intermediate collection",
+ owner_uuid=self.arvrunner.project_uuid,
+ ensure_unique_name=True,
+ trash_at=trash_time,
+ properties=props)
ab = self.collection_pattern % c.portable_data_hash()
self._pathmap[srcobj["location"]] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
num_retries=self.arvrunner.num_retries )
self.addentry(srcobj, c, ".", remap)
- check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
- if not check["items"]:
- c.save_new(owner_uuid=self.arvrunner.project_uuid)
+ trash_time, props = self.__get_collection_attributes()
+
+ c.save_new(name="Intermediate collection",
+ owner_uuid=self.arvrunner.project_uuid,
+ ensure_unique_name=True,
+ trash_at=trash_time,
+ properties=props)
ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
self._pathmap[srcobj["location"]] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]),
else:
return None
+ def __get_collection_attributes(self):
+ trash_time = None
+ if self.arvrunner.intermediate_output_ttl > 0:
+ trash_time = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+
+ current_container_uuid = None
+ try:
+ current_container = self.arvrunner.api.containers().current().execute(num_retries=self.arvrunner.num_retries)
+ current_container_uuid = current_container['uuid']
+ except ApiError as e:
+ # Status code 404 just means we're not running in a container.
+ if e.resp.status != 404:
+ logger.info("Getting current container: %s", e)
+ properties = {"type": "Intermediate",
+ "container": current_container_uuid}
+
+ return (trash_time, properties)
+
+
class StagingPathMapper(PathMapper):
_follow_dirs = True
tgt = os.path.join(stagedir, obj["basename"])
basetgt, baseext = os.path.splitext(tgt)
n = 1
- while tgt in self.targets:
- n += 1
- tgt = "%s_%i%s" % (basetgt, n, baseext)
+ if tgt in self.targets and (self.reversemap(tgt)[0] != loc):
+ while tgt in self.targets:
+ n += 1
+ tgt = "%s_%i%s" % (basetgt, n, baseext)
self.targets.add(tgt)
if obj["class"] == "Directory":
if obj.get("writable"):
projects / arvados.git / blobdiff