1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/84baec18959c/
changeset: 84baec18959c
user: greg
date: 2012-02-03 22:30:30
summary: Correctly handle ToolPanelSection objects when presenting the tool panel sectin redio buttons for selecting a section to contain tools installed with a tool shed repostory into a local Galaxy instance.
affected #: 1 file
diff -r 86d9c5ddbafc3f54acd8398cf3f3d9c10a5ca54c -r 84baec18959cb7f48f450f9aa676aaa1882044c1 lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -797,8 +797,9 @@
def build_tool_panel_section_select_field( trans ):
"""Build a SelectField whose options are the sections of the current in-memory toolbox."""
options = []
- for k, tool_section in trans.app.toolbox.tool_panel.items():
- options.append( ( tool_section.name, tool_section.id ) )
+ for k, v in trans.app.toolbox.tool_panel.items():
+ if isinstance( v, tools.ToolSection ):
+ options.append( ( v.name, v.id ) )
select_field = SelectField( name='tool_panel_section', display='radio' )
for option_tup in options:
select_field.add_option( option_tup[0], option_tup[1] )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/86d9c5ddbafc/
changeset: 86d9c5ddbafc
user: greg
date: 2012-02-03 21:29:02
summary: Make sure a tool shed repository has metadata before setting versions for contained tools.
affected #: 2 files
diff -r e6464387ed3fce7f235cf5c9af1281da14a32811 -r 86d9c5ddbafc3f54acd8398cf3f3d9c10a5ca54c lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -559,23 +559,25 @@
for index, changeset_revision in enumerate( changeset_revisions ):
tool_versions_dict = {}
repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
- metadata = repository_metadata.metadata
- tool_dicts = metadata.get( 'tools', [] )
- if index == 0:
- # The first changset_revision is a special case because it will have no ancestor
- # changeset_revisions in which to match tools. The parent tool id for tools in
- # the first changeset_revision will be the "old_id" in the tool config.
- for tool_dict in tool_dicts:
- tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ]
- else:
- for tool_dict in tool_dicts:
- # We have at least 2 changeset revisions to compare tool guids and tool ids.
- parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] )
- tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id
- if tool_versions_dict:
- repository_metadata.tool_versions = tool_versions_dict
- trans.sa_session.add( repository_metadata )
- trans.sa_session.flush()
+ if repository_metadata:
+ metadata = repository_metadata.metadata
+ if metadata:
+ tool_dicts = metadata.get( 'tools', [] )
+ if index == 0:
+ # The first changset_revision is a special case because it will have no ancestor
+ # changeset_revisions in which to match tools. The parent tool id for tools in
+ # the first changeset_revision will be the "old_id" in the tool config.
+ for tool_dict in tool_dicts:
+ tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ]
+ else:
+ for tool_dict in tool_dicts:
+ # We have at least 2 changeset revisions to compare tool guids and tool ids.
+ parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] )
+ tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id
+ if tool_versions_dict:
+ repository_metadata.tool_versions = tool_versions_dict
+ trans.sa_session.add( repository_metadata )
+ trans.sa_session.flush()
def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ):
parent_id = None
# Compare from most recent to oldest.
diff -r e6464387ed3fce7f235cf5c9af1281da14a32811 -r 86d9c5ddbafc3f54acd8398cf3f3d9c10a5ca54c lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py
--- a/lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py
+++ b/lib/galaxy/webapps/community/model/migrate/versions/0011_add_tool_versions_column.py
@@ -1,5 +1,5 @@
"""
-Migration script to add the new_repo_alert column to the galaxy_user table.
+Migration script to add the tool_versions column to the repository_metadata table.
"""
from sqlalchemy import *
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8ba74c17e809/
changeset: 8ba74c17e809
branch: meme_requirement_on_fimo
user: jmchilton
date: 2012-02-03 04:29:30
summary: Specify meme requirement for fimo tool.
affected #: 1 file
diff -r 87d5491cc3fef55931c09eb6bd688d1b10e946f5 -r 8ba74c17e8091e448ea448c563d883bb35102283 tools/meme/fimo.xml
--- a/tools/meme/fimo.xml
+++ b/tools/meme/fimo.xml
@@ -1,4 +1,5 @@
<tool id="meme_fimo" name="FIMO" version="0.0.1">
+ <requirements><requirement type="package">meme</requirement></requirements><description>- Find Individual Motif Occurrences</description><command interpreter="python">fimo_wrapper.py 'fimo --o "${$html_outfile.files_path}" --verbosity "1"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/238207122b68/
changeset: 238207122b68
user: natefoo
date: 2012-02-02 19:25:59
summary: DRMAA runner no longer needs to clean up its stdout/stderr since they live in the working directory which is cleaned up by the job wrapper.
affected #: 1 file
diff -r 37e787787128662a1aba3c6c831f9dabc9de3289 -r 238207122b68e961dac14238fe1af0a585a9e903 lib/galaxy/jobs/runners/drmaa.py
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -196,7 +196,6 @@
if job_wrapper.get_state() == model.Job.states.DELETED:
log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() )
if self.app.config.cleanup_job in ( "always", "onsuccess" ):
- self.cleanup( ( ofile, efile, jt.remoteCommand ) )
job_wrapper.cleanup()
return
@@ -334,25 +333,12 @@
except:
log.exception("Job wrapper finish method failed")
- # clean up the drm files
- if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ):
- self.cleanup( ( ofile, efile, job_file ) )
-
def fail_job( self, drm_job_state ):
"""
Seperated out so we can use the worker threads for it.
"""
self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) )
drm_job_state.job_wrapper.fail( drm_job_state.fail_message )
- if self.app.config.cleanup_job == "always":
- self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file ) )
-
- def cleanup( self, files ):
- for file in files:
- try:
- os.unlink( file )
- except Exception, e:
- log.warning( "Unable to cleanup: %s" % str( e ) )
def put( self, job_wrapper ):
"""Add a job to the queue (by job identifier)"""
@@ -440,6 +426,6 @@
# The expected output is a single line containing a single numeric value:
# the DRMAA job-ID. If not the case, will throw an error.
jobId = stdoutdata
- return jobId;
+ return jobId
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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