commit/galaxy-central: 4 new changesets

12 Feb 2015

4 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/852e7e14fab2/
Changeset:   852e7e14fab2
Branch:      stable
User:        dan
Date:        2015-02-11 21:50:25+00:00
Summary:     Fix for resetting repository metadata in the toolshed via UI (pass resetting_all_metadata_on_repository=True flag).
Affected #:  1 file

diff -r ca653e8d044d29e15d4ff3266e333aa75c09e5d7 -r 852e7e14fab21ac9bb2c4aa40840d054dddb6d91 lib/galaxy/webapps/tool_shed/controllers/repository.py

--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -2763,7 +2763,8 @@
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
                                                                      user=trans.user,
-                                                                     repository=repository )
+                                                                     repository=repository,
+                                                                     resetting_all_metadata_on_repository=True )
         rmm.reset_all_metadata_on_repository_in_tool_shed()
         rmm_metadata_dict = rmm.get_metadata_dict()
         rmm_invalid_file_tups = rmm.get_invalid_file_tups()
@@ -2784,7 +2785,7 @@
 
     @web.expose
     def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ):
-        rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user )
+        rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user, resetting_all_metadata_on_repository=True )
         if 'reset_metadata_on_selected_repositories_button' in kwd:
             message, status = rmm.reset_metadata_on_selected_repositories( **kwd )
         else:


https://bitbucket.org/galaxy/galaxy-central/commits/8e264f9103b5/
Changeset:   8e264f9103b5
Branch:      stable
User:        dan
Date:        2015-02-11 22:31:49+00:00
Summary:     Always add sample file info to metadata, not only during initial creation..
Affected #:  1 file

diff -r 852e7e14fab21ac9bb2c4aa40840d054dddb6d91 -r 8e264f9103b568eed5c7df899f749443b18e0954 lib/tool_shed/metadata/metadata_generator.py
--- a/lib/tool_shed/metadata/metadata_generator.py
+++ b/lib/tool_shed/metadata/metadata_generator.py
@@ -853,7 +853,7 @@
                             if tool_path and relative_install_dir:
                                 if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ):
                                     relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :]
-                            sample_file_metadata_paths.append( relative_path_to_sample_file )
+                        sample_file_metadata_paths.append( relative_path_to_sample_file )
         return sample_file_metadata_paths, sample_file_copy_paths
 
     def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ):


https://bitbucket.org/galaxy/galaxy-central/commits/81fc2eddcad8/
Changeset:   81fc2eddcad8
Branch:      stable
User:        dan
Date:        2015-02-11 22:36:05+00:00
Summary:     When resetting repository metadata in the toolshed, don't overwrite the already set relative_install_dir.
Affected #:  1 file

diff -r 8e264f9103b568eed5c7df899f749443b18e0954 -r 81fc2eddcad807ef6eac5e9eb42e2cb8b9e39b22 lib/tool_shed/metadata/repository_metadata_manager.py
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -834,7 +834,6 @@
             if cloned_ok:
                 log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) )
                 self.set_changeset_revision( str( repo.changectx( changeset ) ) )
-                self.set_relative_install_dir( work_dir )
                 self.set_repository_files_dir( work_dir )
                 self.generate_metadata_for_changeset_revision()
                 if self.metadata_dict:


https://bitbucket.org/galaxy/galaxy-central/commits/71054665755b/
Changeset:   71054665755b
Branch:      stable
User:        martenson
Date:        2015-02-12 16:42:29+00:00
Summary:     Merged in dan/galaxy-central-prs/stable (pull request #667)

[STABLE] Fixes for resetting metadata on ToolShed Repositories.
Affected #:  3 files

diff -r f1c89c016624edd48edf604b14745d2a85b8402a -r 71054665755b0b6c6348aedb56222b954fea3e7b lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -2766,7 +2766,8 @@
         repository = suc.get_repository_in_tool_shed( trans.app, id )
         rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
                                                                      user=trans.user,
-                                                                     repository=repository )
+                                                                     repository=repository,
+                                                                     resetting_all_metadata_on_repository=True )
         rmm.reset_all_metadata_on_repository_in_tool_shed()
         rmm_metadata_dict = rmm.get_metadata_dict()
         rmm_invalid_file_tups = rmm.get_invalid_file_tups()
@@ -2787,7 +2788,7 @@
 
     @web.expose
     def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ):
-        rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user )
+        rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user, resetting_all_metadata_on_repository=True )
         if 'reset_metadata_on_selected_repositories_button' in kwd:
             message, status = rmm.reset_metadata_on_selected_repositories( **kwd )
         else:

diff -r f1c89c016624edd48edf604b14745d2a85b8402a -r 71054665755b0b6c6348aedb56222b954fea3e7b lib/tool_shed/metadata/metadata_generator.py
--- a/lib/tool_shed/metadata/metadata_generator.py
+++ b/lib/tool_shed/metadata/metadata_generator.py
@@ -853,7 +853,7 @@
                             if tool_path and relative_install_dir:
                                 if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ):
                                     relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :]
-                            sample_file_metadata_paths.append( relative_path_to_sample_file )
+                        sample_file_metadata_paths.append( relative_path_to_sample_file )
         return sample_file_metadata_paths, sample_file_copy_paths
 
     def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ):

diff -r f1c89c016624edd48edf604b14745d2a85b8402a -r 71054665755b0b6c6348aedb56222b954fea3e7b lib/tool_shed/metadata/repository_metadata_manager.py
--- a/lib/tool_shed/metadata/repository_metadata_manager.py
+++ b/lib/tool_shed/metadata/repository_metadata_manager.py
@@ -834,7 +834,6 @@
             if cloned_ok:
                 log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) )
                 self.set_changeset_revision( str( repo.changectx( changeset ) ) )
-                self.set_relative_install_dir( work_dir )
                 self.set_repository_files_dir( work_dir )
                 self.generate_metadata_for_changeset_revision()
                 if self.metadata_dict:

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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