[ARVADOS] created: bdfd1e9f8bc2a3933f6b0bc7afd5cfebd815fd90
Git user
git at public.curoverse.com
Thu Mar 10 09:42:46 EST 2016
at bdfd1e9f8bc2a3933f6b0bc7afd5cfebd815fd90 (commit)
commit bdfd1e9f8bc2a3933f6b0bc7afd5cfebd815fd90
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 10 09:42:40 2016 -0500
Add Dockerfile & update sources.list
diff --git a/docker/jobs/Dockerfile b/docker/jobs/Dockerfile
index 30ceea9..8366349 100644
--- a/docker/jobs/Dockerfile
+++ b/docker/jobs/Dockerfile
@@ -1,5 +1,5 @@
-# Based on Debian Wheezy
-FROM arvados/debian:wheezy
+# Based on Debian Jessie
+FROM debian:jessie
MAINTAINER Ward Vandewege <ward at curoverse.com>
ENV DEBIAN_FRONTEND noninteractive
@@ -8,7 +8,8 @@ ADD apt.arvados.org.list /etc/apt/sources.list.d/
RUN apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7
RUN apt-get update -q
-RUN apt-get install -qy git python-pip python-virtualenv python-arvados-python-client python-dev libcurl4-gnutls-dev arvados-cwl-runner
+RUN apt-get install -qy git python-pip python-virtualenv python-arvados-python-client python-dev libcurl4-gnutls-dev nodejs
+RUN pip install arvados-cwl-runner
RUN gpg --keyserver pool.sks-keyservers.net --recv-keys D39DC0E3
diff --git a/docker/jobs/apt.arvados.org.list b/docker/jobs/apt.arvados.org.list
index 7eb8716..3ae6df4 100644
--- a/docker/jobs/apt.arvados.org.list
+++ b/docker/jobs/apt.arvados.org.list
@@ -1,2 +1,2 @@
# apt.arvados.org
-deb http://apt.arvados.org/ wheezy main
+deb http://apt.arvados.org/ jessie main
commit 86865a741f902ac008e11d1dec90b87b89822025
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 10 08:28:58 2016 -0500
Fixes
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 3142fab..8cbf4d8 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -6,15 +6,20 @@ import arvados.collection
import arvados.util
from cwltool.process import shortname
import cwltool.main
+import logging
+import os
+from arvados.api import OrderedJsonModel
api = arvados.api("v1")
try:
job_order_object = arvados.current_job()['script_parameters']
+ print job_order_object
+
for k,v in job_order_object.items():
if arvados.util.keep_locator_pattern.match(v):
- job_order_object[k] = "%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+ job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
@@ -32,7 +37,8 @@ try:
'success': True,
'progress':1.0
}).execute()
-except:
+except Exception as e:
+ logging.exception("Unhandled exception")
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': None,
commit 4d5e04d4998d2fe6c33a98bb93e7ec05e559bcbd
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 10 08:03:39 2016 -0500
Stuff
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index a5e8ac7..3142fab 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -22,7 +22,7 @@ try:
outputObj = runner.arvExecutor(t, job_order_object, "", None)
- c = arvados.collection.Collection():
+ c = arvados.collection.Collection()
with c.open("cwl.output.json") as f:
json.dump(f, indent=4)
commit 30443c31bf020b6f558c4b7d954599b24c1a98ce
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Mar 9 17:44:36 2016 -0500
8654: cwl-runner crunch script
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 66a887e..a5e8ac7 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -1,5 +1,41 @@
#!/usr/bin/env python
+import arvados
import arvados_cwl
+import arvados.collection
+import arvados.util
+from cwltool.process import shortname
+import cwltool.main
-print "Hello world"
+api = arvados.api("v1")
+
+try:
+ job_order_object = arvados.current_job()['script_parameters']
+
+ for k,v in job_order_object.items():
+ if arvados.util.keep_locator_pattern.match(v):
+ job_order_object[k] = "%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+
+ runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+
+ t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
+
+ outputObj = runner.arvExecutor(t, job_order_object, "", None)
+
+ c = arvados.collection.Collection():
+ with c.open("cwl.output.json") as f:
+ json.dump(f, indent=4)
+
+ api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output': c.save_new(create_collection_record=False),
+ 'success': True,
+ 'progress':1.0
+ }).execute()
+except:
+ api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output': None,
+ 'success': False,
+ 'progress':1.0
+ }).execute()
commit 83645e26981cf9a01c72096298fd9f8dd0f5309e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Mar 9 17:02:05 2016 -0500
8654: cwl-runner crunch stub.
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
new file mode 100755
index 0000000..66a887e
--- /dev/null
+++ b/crunch_scripts/cwl-runner
@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+
+import arvados_cwl
+
+print "Hello world"
commit ca4958ad27277b1d4ae0226382e214fb2b1f2fec
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 7 16:35:33 2016 -0500
8654: arvados/jobs image install arvados-cwl-runner package
diff --git a/docker/jobs/Dockerfile b/docker/jobs/Dockerfile
index 0d72958..30ceea9 100644
--- a/docker/jobs/Dockerfile
+++ b/docker/jobs/Dockerfile
@@ -8,7 +8,7 @@ ADD apt.arvados.org.list /etc/apt/sources.list.d/
RUN apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7
RUN apt-get update -q
-RUN apt-get install -qy git python-pip python-virtualenv python-arvados-python-client python-dev libcurl4-gnutls-dev
+RUN apt-get install -qy git python-pip python-virtualenv python-arvados-python-client python-dev libcurl4-gnutls-dev arvados-cwl-runner
RUN gpg --keyserver pool.sks-keyservers.net --recv-keys D39DC0E3
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