1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0b8c0fda4f85/
changeset: 0b8c0fda4f85
user: greg
date: 2012-04-16 20:12:57
summary: Handle exceptions caused by invalid tool configs when setting repository metadata in the tool shed.
affected #: 1 file
diff -r ec624a7e04b124d0f6341ea7a545060a9cd10d0b -r 0b8c0fda4f852199d12e67cbd7bcdda9a99ac444 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -456,10 +456,14 @@
# Create a new repository_metadata table row.
repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
trans.sa_session.add( repository_metadata )
- trans.sa_session.flush()
- # If this is the first record stored for this repository, see if we need to send any email alerts.
- if len( repository.downloadable_revisions ) == 1:
- handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
+ try:
+ trans.sa_session.flush()
+ # If this is the first record stored for this repository, see if we need to send any email alerts.
+ if len( repository.downloadable_revisions ) == 1:
+ handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
+ except TypeError, e:
+ message = "Unable to save metadata for this repository probably due to a tool config file that doesn't conform to the Cheetah template syntax."
+ status = 'error'
else:
repository_metadata = get_latest_repository_metadata( trans, id )
if repository_metadata:
@@ -467,9 +471,13 @@
repository_metadata.changeset_revision = changeset_revision
repository_metadata.metadata = metadata_dict
trans.sa_session.add( repository_metadata )
- trans.sa_session.flush()
+ try:
+ trans.sa_session.flush()
+ except TypeError, e:
+ message = "Unable to save metadata for this repository probably due to a tool config file that doesn't conform to the Cheetah template syntax."
+ status = 'error'
else:
- # There are no tools in the repository, and we're setting metadat on the repository tip.
+ # There are no tools in the repository, and we're setting metadata on the repository tip.
repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
trans.sa_session.add( repository_metadata )
trans.sa_session.flush()
@@ -739,12 +747,12 @@
# Currently the only way to differentiate datatypes is by name.
ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ]
ancestor_datatype_extension = ancestor_datatype[ 'extension' ]
- ancestor_datatype_mimetype = ancestor_datatype[ 'mimetype' ]
+ ancestor_datatype_mimetype = ancestor_datatype.get( 'mimetype', None )
found_in_current = False
for current_datatype in current_datatypes:
if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \
current_datatype[ 'extension' ] == ancestor_datatype_extension and \
- current_datatype[ 'mimetype' ] == ancestor_datatype_mimetype:
+ current_datatype.get( 'mimetype', None ) == ancestor_datatype_mimetype:
found_in_current = True
break
if not found_in_current:
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/c1b6636c96aa/
changeset: c1b6636c96aa
user: greg
date: 2012-04-16 19:09:06
summary: Eliminate duplicate galaxy.datatypes.images:Xpm sniffer entry from datatypes_conf.xml.sample.
affected #: 1 file
diff -r 5b1ba14edd15720509b8842e7b5ea78823af3f07 -r c1b6636c96aa01e4d70b61d9454f42372338cb2e datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -267,7 +267,6 @@
<sniffer type="galaxy.datatypes.images:Ppm"/><sniffer type="galaxy.datatypes.images:Psd"/><sniffer type="galaxy.datatypes.images:Xbm"/>
- <sniffer type="galaxy.datatypes.images:Xpm"/><sniffer type="galaxy.datatypes.images:Rgb"/><sniffer type="galaxy.datatypes.images:Pbm"/><sniffer type="galaxy.datatypes.images:Pgm"/>
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/5b1ba14edd15/
changeset: 5b1ba14edd15
user: jgoecks
date: 2012-04-16 18:28:52
summary: Fix for displaying tools outside of a section.
affected #: 1 file
diff -r a471c61f91dc98d1c668e3718b3843422f5e77aa -r 5b1ba14edd15720509b8842e7b5ea78823af3f07 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -565,7 +565,7 @@
# Produce panel.
rval = []
for elt in panel_elts:
- rval.append( elt.to_dict( trans ) )
+ rval.append( elt.to_dict( trans, for_link=True ) )
else:
tools = []
for id, tool in self.app.toolbox.tools_by_id.items():
@@ -594,11 +594,11 @@
copy.elems = self.elems.copy()
return copy
- def to_dict( self, trans ):
+ def to_dict( self, trans, for_link=False ):
""" Return a dict that includes section's attributes. """
section_elts = []
for key, val in self.elems.items():
- section_elts.append( val.to_dict( trans, for_link=True ) )
+ section_elts.append( val.to_dict( trans, for_link=for_link ) )
return { 'type': 'section', 'id': self.id, 'name': self.name, 'version': self.version, 'elems': section_elts }
class ToolSectionLabel( object ):
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/96fb46cedf21/
changeset: 96fb46cedf21
user: natefoo
date: 2012-04-16 16:07:10
summary: Fix for cleanup_datasets.py when database_connection is the uncommented default in the config file.
affected #: 1 file
diff -r 1fdcce63a06fa62ef5789967d929dc78d46c3eb4 -r 96fb46cedf2120cd7c2e873985939c92392d40c2 scripts/cleanup_datasets/cleanup_datasets.py
--- a/scripts/cleanup_datasets/cleanup_datasets.py
+++ b/scripts/cleanup_datasets/cleanup_datasets.py
@@ -505,7 +505,7 @@
class CleanupDatasetsApplication( object ):
"""Encapsulates the state of a Universe application"""
def __init__( self, config ):
- if config.database_connection is None:
+ if config.database_connection is False:
config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database
self.object_store = build_object_store_from_config( config )
# Setup the database engine and ORM
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/1fdcce63a06f/
changeset: 1fdcce63a06f
user: dan
date: 2012-04-15 14:37:00
summary: Fix for workflow module.__get_tool_version.
affected #: 1 file
diff -r ac82d151373366b0b6f1a6a6e32642eb9d01dfd0 -r 1fdcce63a06fa62ef5789967d929dc78d46c3eb4 lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -199,7 +199,7 @@
# TODO: If workflows are ever enhanced to use tool version
# in addition to tool id, enhance the selection process here
# to retrieve the correct version of the tool.
- tool_version = self.__get_tool_version( trans, tool_id )
+ tool_version = Class.__get_tool_version( trans, tool_id )
if tool_version:
tool_version_ids = tool_version.get_version_ids( trans.app )
for tool_version_id in tool_version_ids:
@@ -219,7 +219,8 @@
module.post_job_actions = pjadict
return module
return None
- def __get_tool_version( self, trans, tool_id ):
+ @classmethod
+ def __get_tool_version( cls, trans, tool_id ):
# Return a ToolVersion if one exists for tool_id.
return trans.sa_session.query( trans.app.model.ToolVersion ) \
.filter( trans.app.model.ToolVersion.table.c.tool_id == tool_id ) \
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/52c03c6b8f29/
changeset: 52c03c6b8f29
user: dan
date: 2012-04-13 21:07:07
summary: Allow GenomeSpace OpenID provider for log in.
affected #: 1 file
diff -r 6fb1b84b81c3bb146674a3387d1358aa753bad31 -r 52c03c6b8f29a919a7bb19d7c414e65f611b9907 openid/genomespace.xml
--- a/openid/genomespace.xml
+++ b/openid/genomespace.xml
@@ -1,5 +1,5 @@
<?xml version="1.0"?>
-<provider id="genomespace" name="GenomeSpace" never_associate_with_user="True">
+<provider id="genomespace" name="GenomeSpace"><op_endpoint_url>https://identity.genomespace.org/identityServer/xrd.jsp</op_endpoint_url><sreg><field name="nickname" required="True">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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