[ARVADOS] created: b810854ddeccc8fff3ac718e8085a4cafb7f6b86
Git user
git at public.curoverse.com
Mon Sep 19 09:14:18 EDT 2016
at b810854ddeccc8fff3ac718e8085a4cafb7f6b86 (commit)
commit b810854ddeccc8fff3ac718e8085a4cafb7f6b86
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Sat Sep 17 21:26:36 2016 -0400
10088: Bump cwltool dependency for bugfix to scandeps.
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index efc6056..6922b90 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160913171024',
+ 'cwltool==1.0.20160918012352',
'arvados-python-client>=0.1.20160826210445'
],
data_files=[
commit d63f3ade27bb506da049164789679f9fed171005
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Sep 16 17:37:13 2016 -0400
10088: upload_dependencies reads raw files to find actual dependencies
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index e17264b..40a64ff 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -58,6 +58,8 @@ class ArvPathMapper(PathMapper):
def addentry(self, obj, c, path, subdirs):
if obj["location"] in self._pathmap:
src, srcpath = self.arvrunner.fs_access.get_collection(self._pathmap[obj["location"]].resolved)
+ if srcpath == "":
+ srcpath = "."
c.copy(srcpath, path + "/" + obj["basename"], source_collection=src, overwrite=True)
for l in obj.get("secondaryFiles", []):
self.addentry(l, c, path, subdirs)
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 72f347e..570675b 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -4,6 +4,7 @@ from functools import partial
import logging
import json
import re
+from cStringIO import StringIO
import cwltool.draft2tool
from cwltool.draft2tool import CommandLineTool
@@ -13,6 +14,7 @@ from cwltool.load_tool import fetch_document
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
import arvados.collection
+import ruamel.yaml as yaml
from .arvdocker import arv_docker_get_image
from .pathmapper import ArvPathMapper
@@ -26,9 +28,16 @@ def upload_dependencies(arvrunner, name, document_loader,
loaded = set()
def loadref(b, u):
joined = urlparse.urljoin(b, u)
- if joined not in loaded:
- loaded.add(joined)
- return document_loader.fetch(urlparse.urljoin(b, u))
+ defrg, _ = urlparse.urldefrag(joined)
+ if defrg not in loaded:
+ loaded.add(defrg)
+ # Use fetch_text to get raw file (before preprocessing).
+ text = document_loader.fetch_text(defrg)
+ if isinstance(text, bytes):
+ textIO = StringIO(text.decode('utf-8'))
+ else:
+ textIO = StringIO(text)
+ return yaml.safe_load(textIO)
else:
return {}
@@ -37,9 +46,15 @@ def upload_dependencies(arvrunner, name, document_loader,
else:
loadref_fields = set(("$import",))
- sc = scandeps(uri, workflowobj,
+ scanobj = workflowobj
+ if "id" in workflowobj:
+ # Need raw file content (before preprocessing) to ensure
+ # that external references in $include and $mixin are captured.
+ scanobj = loadref("", workflowobj["id"])
+
+ sc = scandeps(uri, scanobj,
loadref_fields,
- set(("$include", "$schemas", "path", "location")),
+ set(("$include", "$schemas")),
loadref)
files = []
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