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Modify the upload_directory and upload_tar methods to handle complex and simple repository dependencies without changeset revisions specified.

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This commit is contained in:
Dave Bouvier
2013-05-17 12:50:47 -04:00
parent 2ac57c4d6f
commit 936df8d89e
1 changed files with 28 additions and 1 deletions
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lib/galaxy/webapps/tool_shed/controllers/upload.py
+28 -1
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@@ -117,7 +117,7 @@ class UploadController( BaseUIController ):
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
self.upload_tar( trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
elif uploaded_directory:
ok,message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
self.upload_directory( trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
else:
if ( isgzip or isbz2 ) and uncompress_file:
@@ -263,6 +263,19 @@ class UploadController( BaseUIController ):
break
else:
undesirable_files_removed += 1
uploaded_file_name = os.path.abspath( os.path.join( root, uploaded_file ) )
if os.path.split( uploaded_file_name )[ -1 ] == 'repository_dependencies.xml':
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
shutil.move( tmp_filename, uploaded_file_name )
elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml':
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
shutil.move( tmp_filename, uploaded_file_name )
if ok:
repo_path = os.path.join( full_path, relative_path )
repo_basedir = os.path.normpath( os.path.join( repo_path, os.path.pardir ) )
@@ -311,6 +324,20 @@ class UploadController( BaseUIController ):
tar.extractall( path=full_path )
tar.close()
uploaded_file.close()
for filename in filenames_in_archive:
uploaded_file_name = os.path.join( full_path, filename )
if os.path.split( uploaded_file_name )[ -1 ] == 'repository_dependencies.xml':
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
shutil.move( tmp_filename, uploaded_file_name )
elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml':
# Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately.
altered, root = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name )
if altered:
tmp_filename = commit_util.create_and_write_tmp_file( util.xml_to_string( root, pretty=True ) )
shutil.move( tmp_filename, uploaded_file_name )
return commit_util.handle_directory_changes( trans,
repository,
full_path,