2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/719201cb28d3/
Changeset: 719201cb28d3
User: Dave Bouvier
Date: 2013-06-19 21:03:26
Summary: Fix for tool dependency installation when tarballs raise non-fatal errors, for example if the tarball contains a symlink to a file that does not exist on the local syste.
Affected #: 1 file
diff -r ae5a239a811224a898267e38ab5255d9bf7170f5 -r 719201cb28d3f89b31e6d52f12f1c6f0cc1c0fef lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
@@ -74,9 +74,9 @@
def extract_tar( file_name, file_path ):
if isgzip( file_name ) or isbz2( file_name ):
# Open for reading with transparent compression.
- tar = tarfile.open( file_name, 'r:*' )
+ tar = tarfile.open( file_name, 'r:*', errorlevel=0 )
else:
- tar = tarfile.open( file_name )
+ tar = tarfile.open( file_name, errorlevel=0 )
tar.extractall( path=file_path )
tar.close()
https://bitbucket.org/galaxy/galaxy-central/commits/adee6fc31991/
Changeset: adee6fc31991
Branch: stable
User: Dave Bouvier
Date: 2013-06-19 21:03:26
Summary: Fix for tool dependency installation when tarballs raise non-fatal errors, for example if the tarball contains a symlink to a file that does not exist on the local syste.
Affected #: 1 file
diff -r 1dd854e7d590eb4a6b7b756008288705532323d6 -r adee6fc31991ee4291a28e4e209ef9583ba811ab lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py
@@ -74,9 +74,9 @@
def extract_tar( file_name, file_path ):
if isgzip( file_name ) or isbz2( file_name ):
# Open for reading with transparent compression.
- tar = tarfile.open( file_name, 'r:*' )
+ tar = tarfile.open( file_name, 'r:*', errorlevel=0 )
else:
- tar = tarfile.open( file_name )
+ tar = tarfile.open( file_name, errorlevel=0 )
tar.extractall( path=file_path )
tar.close()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1dd854e7d590/
Changeset: 1dd854e7d590
Branch: stable
User: dan
Date: 2013-06-19 20:53:43
Summary: Fix for loading workflows with complex ToolShed Repositories dependencies.
Affected #: 1 file
diff -r ddeb0084587994c3a0b9d1504950b4639ab7e7e8 -r 1dd854e7d590eb4a6b7b756008288705532323d6 lib/tool_shed/util/workflow_util.py
--- a/lib/tool_shed/util/workflow_util.py
+++ b/lib/tool_shed/util/workflow_util.py
@@ -57,19 +57,19 @@
self.tool_id = tool_id
self.tool = None
self.errors = None
- for tool_dict in tools_metadata:
- if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
- if trans.webapp.name == 'tool_shed':
- # We're in the tool shed.
+ if trans.webapp.name == 'tool_shed':
+ # We're in the tool shed.
+ for tool_dict in tools_metadata:
+ if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
repository, self.tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] )
if message and self.tool is None:
self.errors = 'unavailable'
break
- else:
- # We're in Galaxy.
- self.tool = trans.app.toolbox.tools_by_id.get( self.tool_id, None )
- if self.tool is None:
- self.errors = 'unavailable'
+ else:
+ # We're in Galaxy.
+ self.tool = trans.app.toolbox.get_tool( self.tool_id )
+ if self.tool is None:
+ self.errors = 'unavailable'
self.post_job_actions = {}
self.workflow_outputs = []
self.state = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ae5a239a8112/
Changeset: ae5a239a8112
User: dan
Date: 2013-06-19 20:53:43
Summary: Fix for loading workflows with complex ToolShed Repositories dependencies.
Affected #: 1 file
diff -r fca2e3683ca13269db0c39fa9407f784508da0b5 -r ae5a239a811224a898267e38ab5255d9bf7170f5 lib/tool_shed/util/workflow_util.py
--- a/lib/tool_shed/util/workflow_util.py
+++ b/lib/tool_shed/util/workflow_util.py
@@ -56,19 +56,19 @@
self.tool_id = tool_id
self.tool = None
self.errors = None
- for tool_dict in tools_metadata:
- if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
- if trans.webapp.name == 'tool_shed':
- # We're in the tool shed.
+ if trans.webapp.name == 'tool_shed':
+ # We're in the tool shed.
+ for tool_dict in tools_metadata:
+ if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]:
repository, self.tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] )
if message and self.tool is None:
self.errors = 'unavailable'
break
- else:
- # We're in Galaxy.
- self.tool = trans.app.toolbox.tools_by_id.get( self.tool_id, None )
- if self.tool is None:
- self.errors = 'unavailable'
+ else:
+ # We're in Galaxy.
+ self.tool = trans.app.toolbox.get_tool( self.tool_id )
+ if self.tool is None:
+ self.errors = 'unavailable'
self.post_job_actions = {}
self.workflow_outputs = []
self.state = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fca2e3683ca1/
Changeset: fca2e3683ca1
User: Dave Bouvier
Date: 2013-06-19 19:48:04
Summary: Fix failing functional test.
Affected #: 1 file
diff -r c69a8a921b4100a1c6b12305945941cc6c7577e0 -r fca2e3683ca13269db0c39fa9407f784508da0b5 test/tool_shed/functional/test_0000_basic_repository_features.py
--- a/test/tool_shed/functional/test_0000_basic_repository_features.py
+++ b/test/tool_shed/functional/test_0000_basic_repository_features.py
@@ -353,5 +353,5 @@
# Check for the changeset revision, repository name, owner username, 'repos' in the clone url, and the captured
# unicode decoding error message.
strings_displayed = [ 'Changeset %d:%s' % ( revision_number, revision_hash ), 'filtering_0000', 'user1', 'repos', 'added:',
- 'Error decoding string:', "codec can't decode byte" ]
+ '+These characters should not' ]
self.load_changeset_in_tool_shed( repository_id, changeset_revision, strings_displayed=strings_displayed )
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fce9396b9a81/
Changeset: fce9396b9a81
Branch: search
User: dannon
Date: 2013-06-18 23:22:52
Summary: Close search branch
Affected #: 1 file
diff -r fd3a82d33bb6896ba6395a5e83add5c6ac7f7fbf -r fce9396b9a812aae5356206261d2e67cecd03542 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1045,6 +1045,11 @@
Import a workflow by reading an url, uploading a file, opening and reading the contents
of a local file, or receiving the textual representation of a workflow via http.
"""
+
+
+
+ print "\n\n\n\nIMPORT WORKFLOW\n\n"
+
url = kwd.get( 'url', '' )
workflow_text = kwd.get( 'workflow_text', '' )
message = kwd.get( 'message', '' )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/af1a9f44b529/
Changeset: af1a9f44b529
User: dannon
Date: 2013-06-18 20:27:34
Summary: Missed a file in the previous commit, continuation of StoredWorkflowAnnotation for toolshed-imported workflows.
Affected #: 1 file
diff -r f720e8e003f750a8c1f9c4f72ac4acadae9e761d -r af1a9f44b529bf8e46a5baf4ee693c0c4b7a390d lib/tool_shed/util/workflow_util.py
--- a/lib/tool_shed/util/workflow_util.py
+++ b/lib/tool_shed/util/workflow_util.py
@@ -4,6 +4,7 @@
import galaxy.webapps.galaxy.controllers.workflow
from galaxy import eggs
from galaxy.util import json
+from galaxy.util.sanitize_html import sanitize_html
from galaxy.workflow.modules import InputDataModule
from galaxy.workflow.modules import ToolModule
from galaxy.workflow.modules import WorkflowModuleFactory
@@ -390,7 +391,7 @@
# that's not possible here. This entire module
# needs to die and get replaced with the regular
# galaxy/workflow methods.
- from galaxy.util.sanitize_html import sanitize_html
+ # See WORKFLOW_REFACTOR below.
annotation = step_dict.get( 'annotation', '')
if annotation:
annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
@@ -436,13 +437,25 @@
break
return module_name
-def save_workflow( trans, workflow ):
+def save_workflow( trans, workflow, workflow_dict = None):
"""Use the received in-memory Workflow object for saving to the Galaxy database."""
stored = trans.model.StoredWorkflow()
stored.name = workflow.name
workflow.stored_workflow = stored
stored.latest_workflow = workflow
stored.user = trans.user
+
+ # One more temporary hack like above to support workflow level annotations.
+ # Same caveats.
+ # WORKFLOW_REFACTOR
+ if workflow_dict and workflow_dict.get('annotation',''):
+ annotation = sanitize_html( workflow_dict['annotation'], 'utf-8', 'text/html' )
+ new_annotation = trans.model.StoredWorkflowAnnotationAssociation()
+ new_annotation.annotation = annotation
+ new_annotation.user = trans.user
+ stored.annotations.append(new_annotation)
+ # End temporary hack
+
trans.sa_session.add( stored )
trans.sa_session.flush()
# Add a new entry to the Workflows menu.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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