[ARVADOS] created: 1.1.4-177-g2074c17
Git user
git at public.curoverse.com
Wed May 9 05:13:24 EDT 2018
at 2074c175da359e754699baa2c9e9cc52468b1dd0 (commit)
commit 2074c175da359e754699baa2c9e9cc52468b1dd0
Author: Fuad Muhic <muhic.fuad at gmail.com>
Date: Tue May 8 16:38:55 2018 +0200
Added datetime import to arvjob.py
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index bde9700..eb6921c 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -7,6 +7,7 @@ import re
import copy
import json
import time
+import datetime
from cwltool.process import get_feature, shortname, UnsupportedRequirement
from cwltool.errors import WorkflowException
@@ -68,7 +69,7 @@ class ArvadosJob(object):
if vwd:
trash_time = None
if self.arvrunner.intermediate_output_ttl > 0:
- t = datetime.now() + timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+ t = datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
trash_time = t.strftime("%Y-%m-%dT%H:%M:%S.%f000Z")
current_container_uuid = None
commit f5ba876c9e637afcd90e4754346694bcea234fc7
Author: Fuad Muhic <muhic.fuad at gmail.com>
Date: Tue May 8 16:31:42 2018 +0200
Updated name, trash_at and properties field of intermediate collections.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic at capeannenterprises.com>
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index afcf2db..72efb60 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -5,14 +5,16 @@
import logging
import json
import os
+import datetime
import urllib
import time
-import datetime
import ciso8601
import uuid
+
import ruamel.yaml as yaml
+from arvados.errors import ApiError
from cwltool.errors import WorkflowException
from cwltool.process import get_feature, UnsupportedRequirement, shortname
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
@@ -154,8 +156,33 @@ class ArvadosContainer(object):
keepemptydirs(vwd)
+ trash_time = None
+ if self.arvrunner.intermediate_output_ttl > 0:
+ t = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+ trash_time = t.strftime("%Y-%m-%dT%H:%M:%S.%f000Z")
+
+ 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)
+ props = {"type": "Intermediate",
+ "container": current_container_uuid}
+
with Perf(metrics, "generatefiles.save_new %s" % self.name):
- vwd.save_new()
+ vwd.save_new(name="Intermediate collection",
+ ensure_unique_name=True,
+ trash_at=trash_time,
+ properties=props)
+
+ logger.debug("Intermediate: arvcontainer")
+ logger.debug("Intermediate: uuid = %s" % vwd._api_response["uuid"])
+ logger.debug("Intermediate: name = %s" % vwd._api_response["name"])
+ logger.debug("Intermediate: trash_at = %s" % vwd._api_response["trash_at"])
+ logger.debug("Intermediate: props = " + str(vwd._api_response["properties"]))
prev = None
for f, p in sorteditems:
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index decd692..bde9700 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -66,8 +66,34 @@ class ArvadosJob(object):
n.write(p.resolved.encode("utf-8"))
if vwd:
+ trash_time = None
+ if self.arvrunner.intermediate_output_ttl > 0:
+ t = datetime.now() + timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+ trash_time = t.strftime("%Y-%m-%dT%H:%M:%S.%f000Z")
+
+ 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)
+
+ props = {"type": "Intermediate",
+ "container": current_container_uuid}
+
with Perf(metrics, "generatefiles.save_new %s" % self.name):
- vwd.save_new()
+ vwd.save_new(name="Intermediate collection",
+ ensure_unique_name=True,
+ trash_at=trash_time,
+ properties=props)
+
+ logger.debug("Intermediate: arvjob")
+ logger.debug("Intermediate: uuid = %s" % vwd._api_response["uuid"])
+ logger.debug("Intermediate: name = %s" % vwd._api_response["name"])
+ logger.debug("Intermediate: trash_at = %s" % vwd._api_response["trash_at"])
+ logger.debug("Intermediate: props = " + str(vwd._api_response["properties"]))
for f, p in generatemapper.items():
if p.type == "File":
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 6fedb12..d786b9d 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -6,11 +6,14 @@ import re
import logging
import uuid
import os
+import datetime
import urllib
+
import arvados.commands.run
import arvados.collection
+from arvados.errors import ApiError
from schema_salad.sourceline import SourceLine
from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
@@ -164,9 +167,33 @@ class ArvPathMapper(PathMapper):
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 = None
+ if self.arvrunner.intermediate_output_ttl > 0:
+ t = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+ trash_time = t.strftime("%Y-%m-%dT%H:%M:%S.%f000Z")
+
+ 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)
+
+ props = {"type": "Intermediate",
+ "container": current_container_uuid}
+ c.save_new(name="Intermediate collection",
+ owner_uuid=self.arvrunner.project_uuid,
+ ensure_unique_name=True,
+ trash_at=trash_time,
+ properties=props)
+
+ logger.debug("Intermediate: pathmapper")
+ logger.debug("Intermediate: uuid = %s" % c._api_response["uuid"])
+ logger.debug("Intermediate: name = %s" % c._api_response["name"])
+ logger.debug("Intermediate: trash_at = %s" % c._api_response["trash_at"])
+ logger.debug("Intermediate: props = " + str(c._api_response["properties"]))
ab = self.collection_pattern % c.portable_data_hash()
self._pathmap[srcobj["location"]] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True)
@@ -178,9 +205,33 @@ class ArvPathMapper(PathMapper):
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 = None
+ if self.arvrunner.intermediate_output_ttl > 0:
+ t = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl)
+ trash_time = t.strftime("%Y-%m-%dT%H:%M:%S.%f000Z")
+
+ 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)
+
+ props = {"type": "Intermediate",
+ "container": current_container_uuid}
+ c.save_new(name="Intermediate collection",
+ owner_uuid=self.arvrunner.project_uuid,
+ ensure_unique_name=True,
+ trash_at=trash_time,
+ properties=props)
+
+ logger.debug("Intermediate: pathmapper")
+ logger.debug("Intermediate: uuid = %s" % c._api_response["uuid"])
+ logger.debug("Intermediate: name = %s" % c._api_response["name"])
+ logger.debug("Intermediate: trash_at = %s" % c._api_response["trash_at"])
+ logger.debug("Intermediate: props = " + str(c._api_response["properties"]))
ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
self._pathmap[srcobj["location"]] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]),
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