1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b5c08cc6adbb/
Changeset: b5c08cc6adbb
User: dannon
Date: 2013-09-17 23:31:16
Summary: Typo in toolshed util common.
Affected #: 1 file
diff -r 1e664910d749be12d6f0ece29028f18b820476a1 -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 lib/tool_shed/util/shed_util_common.py
--- a/lib/tool_shed/util/shed_util_common.py
+++ b/lib/tool_shed/util/shed_util_common.py
@@ -1186,7 +1186,7 @@
encoded_tool_shed_status_dict = common_util.tool_shed_get( app, tool_shed_url, url )
tool_shed_status_dict = encoding_util.tool_shed_decode( encoded_tool_shed_status_dict )
except Exception, e:
- log.exception( "Error attemtping to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) )
+ log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) )
return {}
return tool_shed_status_dict
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1c9adf19f128/
Changeset: 1c9adf19f128
User: mdshw5
Date: 2013-09-04 16:42:56
Summary: fixed it's > its typos
Affected #: 1 file
diff -r b9da077a79c3ce0323bd8f8e5aed3e311d1fd8ae -r 1c9adf19f12813b9802e84bbde73ca1e7758a498 templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -1,4 +1,3 @@
-
<%def name="common_javascripts(repository)"><script type="text/javascript">
$(function(){
@@ -180,7 +179,7 @@
${repository_type | h}
%if render_help:
<div class="toolParamHelp" style="clear: both;">
- This repository's type cannot be changed because it's contents are valid only for it's current type or it has been cloned.
+ This repository's type cannot be changed because its contents are valid only for its current type or it has been cloned.
</div>
%endif
%else:
https://bitbucket.org/galaxy/galaxy-central/commits/1e664910d749/
Changeset: 1e664910d749
User: dannon
Date: 2013-09-17 22:46:32
Summary: Merged in mdshw5/galaxy-central-toolshed-typos (pull request #210)
fixed it's > its typos
Affected #: 1 file
diff -r 47798b37aed096b344c43c6796b7aae27ef11e90 -r 1e664910d749be12d6f0ece29028f18b820476a1 templates/webapps/tool_shed/repository/common.mako
--- a/templates/webapps/tool_shed/repository/common.mako
+++ b/templates/webapps/tool_shed/repository/common.mako
@@ -1,4 +1,3 @@
-
<%def name="common_javascripts(repository)"><script type="text/javascript">
$(function(){
@@ -180,7 +179,7 @@
${repository_type | h}
%if render_help:
<div class="toolParamHelp" style="clear: both;">
- This repository's type cannot be changed because it's contents are valid only for it's current type or it has been cloned.
+ This repository's type cannot be changed because its contents are valid only for its current type or it has been cloned.
</div>
%endif
%else:
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/6cf5d0cbaf96/
Changeset: 6cf5d0cbaf96
User: dannon
Date: 2013-09-17 20:56:56
Summary: MetadataFile shouldn't attempt to create by default without checking exists() first.
Affected #: 1 file
diff -r 96a2ab47b882690df5a2a962d3689474e4312e3a -r 6cf5d0cbaf96c9910b7e72a83f16d5c6a9f2f34a lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2416,7 +2416,8 @@
da = self.history_dataset or self.library_dataset
if self.object_store_id is None and da is not None:
self.object_store_id = da.dataset.object_store_id
- da.dataset.object_store.create( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
+ if not da.dataset.object_store.exists( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ):
+ da.dataset.object_store.create( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
path = da.dataset.object_store.get_filename( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id )
return path
except AttributeError:
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/96a2ab47b882/
Changeset: 96a2ab47b882
User: Richard Burhans
Date: 2013-09-17 20:37:36
Summary: Fix integrated_tool_panel dictionary before writing integrated_tool_panel.xml to keep tools/workflows in multiple sections
Affected #: 1 file
diff -r 48fad71361b3075c85c7d365dd52c106cabad73a -r 96a2ab47b882690df5a2a962d3689474e4312e3a lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -154,8 +154,24 @@
# This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
# config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel
# will be False when things like functional tests are the caller.
+ self.fix_integrated_tool_panel_dict()
self.write_integrated_tool_panel_config_file()
+ def fix_integrated_tool_panel_dict( self ):
+ # HACK: instead of fixing after the fact, I suggest some combination of:
+ # 1) adjusting init_tools() and called methods to get this right
+ # 2) redesigning the code and/or data structure used to read/write integrated_tool_panel.xml
+ for key, value in self.integrated_tool_panel.iteritems():
+ if key.startswith( 'section_' ):
+ for section_key, section_value in value.elems.iteritems():
+ if section_value is None:
+ if section_key.startswith( 'tool_' ):
+ tool_id = section_key[5:]
+ value.elems[section_key] = self.tools_by_id.get( tool_id )
+ elif section_key.startswith( 'workflow_' ):
+ workflow_id = section_key[9:]
+ value.elems[section_key] = self.workflows_by_id.get( workflow_id )
+
def init_tools( self, config_filename ):
"""
Read the configuration file and load each tool. The following tags are currently supported:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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