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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 May '13

23 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3370974992f3/ Changeset: 3370974992f3 Branch: next-stable User: carlfeberhard Date: 2013-05-23 19:47:03 Summary: Controllers.dataset: add exception string to log msg in _delete Affected #: 1 file diff -r 0acfbcd4235b989f81c580c434471f1e657f298a -r 3370974992f38c9f1de1527982adb362ba644fd9 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -826,7 +826,7 @@ trans.sa_session.flush() except Exception, e: msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) - log.exception( msg ) + log.exception( msg + ': ' + str( e ) ) trans.log_event( msg ) message = 'Dataset deletion failed' status = 'error' https://bitbucket.org/galaxy/galaxy-central/commits/ff4cf806bf1e/ Changeset: ff4cf806bf1e User: carlfeberhard Date: 2013-05-23 19:50:10 Summary: merge next-stable Affected #: 1 file diff -r 1e006b5275f5d3fce99f98b3e6cb00454d5e3c3d -r ff4cf806bf1e6e3bfcd29a539b842f3398a1455c lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -826,7 +826,7 @@ trans.sa_session.flush() except Exception, e: msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) - log.exception( msg ) + log.exception( msg + ': ' + str( e ) ) trans.log_event( msg ) message = 'Dataset deletion failed' status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 May '13

23 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0acfbcd4235b/ Changeset: 0acfbcd4235b Branch: next-stable User: greg Date: 2013-05-23 17:49:52 Summary: Keep all contents of dependency definition files when re-writing them to include missing toolshed and changeset_revision attributes. Affected #: 3 files diff -r 966fbc93c483970092b677f17886e86060941093 -r 0acfbcd4235b989f81c580c434471f1e657f298a lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -129,18 +129,18 @@ # Move some version of the uploaded file to the load_point within the repository hierarchy. if uploaded_file_filename in [ '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 ) + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) elif uploaded_file_filename in [ 'tool_dependencies.xml' ]: # Inspect the contents of the file to see if it defines a complex repository dependency definition whose changeset_revision values # are missing and if so, set them appropriately. - altered, root = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) @@ -266,15 +266,15 @@ 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 ) + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) 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 ) + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) if ok: repo_path = os.path.join( full_path, relative_path ) @@ -328,15 +328,15 @@ 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 ) + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) 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 ) + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) return commit_util.handle_directory_changes( trans, repository, diff -r 966fbc93c483970092b677f17886e86060941093 -r 0acfbcd4235b989f81c580c434471f1e657f298a lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -9,7 +9,7 @@ from galaxy.web import url_for import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_util - +import xml.etree.ElementTree from galaxy import eggs eggs.require( 'mercurial' ) @@ -17,9 +17,6 @@ from mercurial import hg from mercurial import ui -pkg_resources.require( 'elementtree' ) -from elementtree.ElementTree import tostring - log = logging.getLogger( __name__ ) UNDESIRABLE_DIRS = [ '.hg', '.svn', '.git', '.cvs' ] @@ -64,12 +61,13 @@ return message def create_and_write_tmp_file( root ): + tmp_str = '%s\n' % xml.etree.ElementTree.tostring( root, encoding='utf-8' ) fh = tempfile.NamedTemporaryFile( 'wb' ) tmp_filename = fh.name fh.close() fh = open( tmp_filename, 'wb' ) fh.write( '<?xml version="1.0"?>\n' ) - fh.write( tostring( root, 'utf-8' ) ) + fh.write( tmp_str ) fh.close() return tmp_filename @@ -200,7 +198,7 @@ altered = False try: # Make sure we're looking at a valid repository_dependencies.xml file. - tree = util.parse_xml( repository_dependencies_config ) + tree = suc.parse_xml( repository_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_repository_dependencies_definition: " % str( repository_dependencies_config ) @@ -247,7 +245,7 @@ altered = False try: # Make sure we're looking at a valid tool_dependencies.xml file. - tree = util.parse_xml( tool_dependencies_config ) + tree = suc.parse_xml( tool_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_tool_dependencies_definition: " % str( tool_dependencies_config ) diff -r 966fbc93c483970092b677f17886e86060941093 -r 0acfbcd4235b989f81c580c434471f1e657f298a 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 @@ -14,6 +14,7 @@ from galaxy.model.orm import and_ import sqlalchemy.orm.exc from tool_shed.util import common_util +from xml.etree import ElementTree as XmlET from galaxy import eggs import pkg_resources @@ -36,6 +37,17 @@ MAX_DISPLAY_SIZE = 32768 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) + +class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ): + def __init__ ( self, html=0, target=None ): + XmlET.XMLTreeBuilder.__init__( self, html, target ) + self._parser.CommentHandler = self.handle_comment + + def handle_comment ( self, data ): + self._target.start( XmlET.Comment, {} ) + self._target.data( data ) + self._target.end( XmlET.Comment ) + new_repo_email_alert_template = """ Sharable link: ${sharable_link} Repository name: ${repository_name} @@ -1072,6 +1084,13 @@ prior_installation_required = util.asbool( str( prior_installation_required ) ) return tool_shed, name, owner, changeset_revision, prior_installation_required +def parse_xml( fname ): + """Returns a parsed xml tree with comments in tact.""" + fobj = open( fname, 'r' ) + tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() ) + fobj.close() + return tree + def pretty_print( dict=None ): if dict: return json.to_json_string( dict, sort_keys=True, indent=4 * ' ' ) https://bitbucket.org/galaxy/galaxy-central/commits/1e006b5275f5/ Changeset: 1e006b5275f5 User: greg Date: 2013-05-23 17:50:16 Summary: Merged from next-stable Affected #: 3 files diff -r 1e601ee269763ebc51a42b757f5bd6d93b9f8fc4 -r 1e006b5275f5d3fce99f98b3e6cb00454d5e3c3d lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -129,18 +129,18 @@ # Move some version of the uploaded file to the load_point within the repository hierarchy. if uploaded_file_filename in [ '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 ) + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) elif uploaded_file_filename in [ 'tool_dependencies.xml' ]: # Inspect the contents of the file to see if it defines a complex repository dependency definition whose changeset_revision values # are missing and if so, set them appropriately. - altered, root = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) @@ -266,15 +266,15 @@ 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 ) + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) 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 ) + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) if ok: repo_path = os.path.join( full_path, relative_path ) @@ -328,15 +328,15 @@ 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 ) + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) 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 ) + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: - tmp_filename = commit_util.create_and_write_tmp_file( root ) + tmp_filename = commit_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) return commit_util.handle_directory_changes( trans, repository, diff -r 1e601ee269763ebc51a42b757f5bd6d93b9f8fc4 -r 1e006b5275f5d3fce99f98b3e6cb00454d5e3c3d lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -9,7 +9,7 @@ from galaxy.web import url_for import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_util - +import xml.etree.ElementTree from galaxy import eggs eggs.require( 'mercurial' ) @@ -17,9 +17,6 @@ from mercurial import hg from mercurial import ui -pkg_resources.require( 'elementtree' ) -from elementtree.ElementTree import tostring - log = logging.getLogger( __name__ ) UNDESIRABLE_DIRS = [ '.hg', '.svn', '.git', '.cvs' ] @@ -64,12 +61,13 @@ return message def create_and_write_tmp_file( root ): + tmp_str = '%s\n' % xml.etree.ElementTree.tostring( root, encoding='utf-8' ) fh = tempfile.NamedTemporaryFile( 'wb' ) tmp_filename = fh.name fh.close() fh = open( tmp_filename, 'wb' ) fh.write( '<?xml version="1.0"?>\n' ) - fh.write( tostring( root, 'utf-8' ) ) + fh.write( tmp_str ) fh.close() return tmp_filename @@ -200,7 +198,7 @@ altered = False try: # Make sure we're looking at a valid repository_dependencies.xml file. - tree = util.parse_xml( repository_dependencies_config ) + tree = suc.parse_xml( repository_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_repository_dependencies_definition: " % str( repository_dependencies_config ) @@ -247,7 +245,7 @@ altered = False try: # Make sure we're looking at a valid tool_dependencies.xml file. - tree = util.parse_xml( tool_dependencies_config ) + tree = suc.parse_xml( tool_dependencies_config ) root = tree.getroot() except Exception, e: error_message = "Error parsing %s in handle_tool_dependencies_definition: " % str( tool_dependencies_config ) diff -r 1e601ee269763ebc51a42b757f5bd6d93b9f8fc4 -r 1e006b5275f5d3fce99f98b3e6cb00454d5e3c3d 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 @@ -14,6 +14,7 @@ from galaxy.model.orm import and_ import sqlalchemy.orm.exc from tool_shed.util import common_util +from xml.etree import ElementTree as XmlET from galaxy import eggs import pkg_resources @@ -36,6 +37,17 @@ MAX_DISPLAY_SIZE = 32768 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) + +class CommentedTreeBuilder ( XmlET.XMLTreeBuilder ): + def __init__ ( self, html=0, target=None ): + XmlET.XMLTreeBuilder.__init__( self, html, target ) + self._parser.CommentHandler = self.handle_comment + + def handle_comment ( self, data ): + self._target.start( XmlET.Comment, {} ) + self._target.data( data ) + self._target.end( XmlET.Comment ) + new_repo_email_alert_template = """ Sharable link: ${sharable_link} Repository name: ${repository_name} @@ -1072,6 +1084,13 @@ prior_installation_required = util.asbool( str( prior_installation_required ) ) return tool_shed, name, owner, changeset_revision, prior_installation_required +def parse_xml( fname ): + """Returns a parsed xml tree with comments in tact.""" + fobj = open( fname, 'r' ) + tree = XmlET.parse( fobj, parser=CommentedTreeBuilder() ) + fobj.close() + return tree + def pretty_print( dict=None ): if dict: return json.to_json_string( dict, sort_keys=True, indent=4 * ' ' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Dave Bouvier: Merged next-stable into default.
by commits-noreply＠bitbucket.org 23 May '13

23 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e601ee26976/ Changeset: 1e601ee26976 User: Dave Bouvier Date: 2013-05-23 17:48:03 Summary: Merged next-stable into default. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name.
by commits-noreply＠bitbucket.org 23 May '13

23 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/966fbc93c483/ Changeset: 966fbc93c483 Branch: next-stable User: dan Date: 2013-05-23 17:11:37 Summary: Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. Affected #: 1 file diff -r 064ea784eae74cdb7b4ac0319ec0aa13ee55fcbd -r 966fbc93c483970092b677f17886e86060941093 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -297,9 +297,12 @@ found_column = False for name, index in self.columns.iteritems(): if index == i: - rval.append( name ) + if not found_column: + rval.append( name ) + elif name == 'value': + #the column named 'value' always has priority over other named columns + rval[ -1 ] = name found_column = True - break if not found_column: rval.append( None ) return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 May '13

23 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/014548c6843c/ Changeset: 014548c6843c User: dan Date: 2013-05-23 17:11:37 Summary: Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. Affected #: 1 file diff -r 23dcf647ab620a032be9cbc3805707dff75f63b5 -r 014548c6843c8aa507719e4831f982ac967c5d4c lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -297,9 +297,12 @@ found_column = False for name, index in self.columns.iteritems(): if index == i: - rval.append( name ) + if not found_column: + rval.append( name ) + elif name == 'value': + #the column named 'value' always has priority over other named columns + rval[ -1 ] = name found_column = True - break if not found_column: rval.append( None ) return rval https://bitbucket.org/galaxy/galaxy-central/commits/03ebba1d1de6/ Changeset: 03ebba1d1de6 Branch: stable User: dan Date: 2013-05-23 17:11:37 Summary: Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. Affected #: 1 file diff -r 0f51ae4f1c84c5bab6cd1c93ae837696be9565e1 -r 03ebba1d1de6f14ccb00e08795ef2f1896135bae lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -273,9 +273,12 @@ found_column = False for name, index in self.columns.iteritems(): if index == i: - rval.append( name ) + if not found_column: + rval.append( name ) + elif name == 'value': + #the column named 'value' always has priority over other named columns + rval[ -1 ] = name found_column = True - break if not found_column: rval.append( None ) return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 May '13

23 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/064ea784eae7/ Changeset: 064ea784eae7 Branch: next-stable User: Dave Bouvier Date: 2013-05-23 15:45:24 Summary: Fix for missing tool test results display on manage repository page. Affected #: 1 file diff -r 252027d00b441db33005080860970c3441399a77 -r 064ea784eae74cdb7b4ac0319ec0aa13ee55fcbd lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -801,7 +801,7 @@ if tool_test_results: # Only create and populate this folder if there are actual tool test results to display, since the # display of the 'Test environment' folder by itself can be misleading. - if 'passed_tests' in tool_test_results or 'failed_tests' in tool_test_results or 'installation_errors' in tool_test_results: + if len( tool_test_results ) > 1: folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested ) containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder # Workflows container. https://bitbucket.org/galaxy/galaxy-central/commits/23dcf647ab62/ Changeset: 23dcf647ab62 User: Dave Bouvier Date: 2013-05-23 15:45:50 Summary: Merge in fix from next-stable. Affected #: 1 file diff -r ee040d59779808ec5d748f3df04377b333b74a54 -r 23dcf647ab620a032be9cbc3805707dff75f63b5 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -801,7 +801,7 @@ if tool_test_results: # Only create and populate this folder if there are actual tool test results to display, since the # display of the 'Test environment' folder by itself can be misleading. - if 'passed_tests' in tool_test_results or 'failed_tests' in tool_test_results or 'installation_errors' in tool_test_results: + if len( tool_test_results ) > 1: folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested ) containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder # Workflows container. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 22 May '13

22 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/252027d00b44/ Changeset: 252027d00b44 Branch: next-stable User: greg Date: 2013-05-22 22:11:55 Summary: Populate the toolshed attribute when it is missing from the repository tag in dependency definitions with the current tool shed url. Affected #: 1 file diff -r 2aea26f69ba8c39d726adc32c6163e806ba33817 -r 252027d00b441db33005080860970c3441399a77 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -6,6 +6,7 @@ from galaxy import util from galaxy.datatypes import checkers from galaxy.util import json +from galaxy.web import url_for import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_util @@ -219,6 +220,12 @@ def handle_repository_dependency_elem( trans, elem ): # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> populated = False + toolshed = elem.get( 'toolshed' ) + if not toolshed: + # Default the setting to the current tool shed. + toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + elem.attrib[ 'toolshed' ] = toolshed + populated = True name = elem.get( 'name' ) owner = elem.get( 'owner' ) changeset_revision = elem.get( 'changeset_revision' ) https://bitbucket.org/galaxy/galaxy-central/commits/ee040d597798/ Changeset: ee040d597798 User: greg Date: 2013-05-22 22:12:30 Summary: Merged from next-stable Affected #: 1 file diff -r f5b320301daa6e2cd74c54ab0bdd7a2145f92ba1 -r ee040d59779808ec5d748f3df04377b333b74a54 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -6,6 +6,7 @@ from galaxy import util from galaxy.datatypes import checkers from galaxy.util import json +from galaxy.web import url_for import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_util @@ -219,6 +220,12 @@ def handle_repository_dependency_elem( trans, elem ): # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> populated = False + toolshed = elem.get( 'toolshed' ) + if not toolshed: + # Default the setting to the current tool shed. + toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + elem.attrib[ 'toolshed' ] = toolshed + populated = True name = elem.get( 'name' ) owner = elem.get( 'owner' ) changeset_revision = elem.get( 'changeset_revision' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: White space fixes in the tool shed registry code.
by commits-noreply＠bitbucket.org 22 May '13

22 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f5b320301daa/ Changeset: f5b320301daa User: greg Date: 2013-05-22 22:09:52 Summary: White space fixes in the tool shed registry code. Affected #: 1 file diff -r c9d7d174492e530c8b9384391f9b3cf6c7d09e7e -r f5b320301daa6e2cd74c54ab0bdd7a2145f92ba1 lib/tool_shed/tool_shed_registry.py --- a/lib/tool_shed/tool_shed_registry.py +++ b/lib/tool_shed/tool_shed_registry.py @@ -11,7 +11,7 @@ class Registry( object ): def __init__( self, root_dir=None, config=None ): - self.tool_sheds = odict() + self.tool_sheds = odict() self.tool_sheds_auth = odict() if root_dir and config: # Parse tool_sheds_conf.xml @@ -20,17 +20,17 @@ log.debug( 'Loading references to tool sheds from %s' % config ) for elem in root.findall( 'tool_shed' ): try: - name = elem.get( 'name', None ) - url = elem.get( 'url', None ) + name = elem.get( 'name', None ) + url = elem.get( 'url', None ) username = elem.get( 'user', None ) password = elem.get( 'pass', None ) if name and url: - self.tool_sheds[ name ] = url + self.tool_sheds[ name ] = url self.tool_sheds_auth[ name ] = None log.debug( 'Loaded reference to tool shed: %s' % name ) if name and url and username and password: pass_mgr = urllib2.HTTPPasswordMgrWithDefaultRealm() - pass_mgr.add_password(None, url, username, password) + pass_mgr.add_password( None, url, username, password ) self.tool_sheds_auth[ name ] = pass_mgr except Exception, e: log.warning( 'Error loading reference to tool shed "%s", problem: %s' % ( name, str( e ) ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Eliminate the use of util.Params from the tool shed's repository controller.
by commits-noreply＠bitbucket.org 22 May '13

22 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c9d7d174492e/ Changeset: c9d7d174492e User: greg Date: 2013-05-22 22:08:38 Summary: Eliminate the use of util.Params from the tool shed's repository controller. Affected #: 1 file diff -r 1021adf470168815b1066c4c9022cb4136edf84c -r c9d7d174492e530c8b9384391f9b3cf6c7d09e7e 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 @@ -657,10 +657,9 @@ @web.expose def browse_repository( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. @@ -833,14 +832,13 @@ @web.expose def check_for_updates( self, trans, **kwd ): """Handle a request from a local Galaxy instance.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) # If the request originated with the UpdateManager, it will not include a galaxy_url. galaxy_url = suc.handle_galaxy_url( trans, **kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -913,9 +911,8 @@ @web.expose def contact_owner( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) if trans.user and trans.user.email: @@ -948,9 +945,8 @@ @web.expose def create_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) categories = suc.get_categories( trans ) if not categories: message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + \ @@ -960,12 +956,12 @@ action='browse_repositories', message=message, status=status ) ) - name = util.restore_text( params.get( 'name', '' ) ) - description = util.restore_text( params.get( 'description', '' ) ) - long_description = util.restore_text( params.get( 'long_description', '' ) ) - category_ids = util.listify( params.get( 'category_id', '' ) ) + name = kwd.get( 'name', '' ) + description = kwd.get( 'description', '' ) + long_description = kwd.get( 'long_description', '' ) + category_ids = util.listify( kwd.get( 'category_id', '' ) ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] - if params.get( 'create_repository_button', False ): + if kwd.get( 'create_repository_button', False ): error = False message = self.__validate_repository_name( name, trans.user ) if message: @@ -1031,12 +1027,11 @@ """Mark a repository in the tool shed as deprecated or not deprecated.""" # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset revisions that may be associated with the # repository. Revisions are not marked as not downlaodable because those that have installed the repository must be allowed to get updates. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository_id = params.get( 'id', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_id = kwd.get( 'id', None ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) - mark_deprecated = util.string_as_bool( params.get( 'mark_deprecated', False ) ) + mark_deprecated = util.string_as_bool( kwd.get( 'mark_deprecated', False ) ) repository.deprecated = mark_deprecated trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1052,9 +1047,8 @@ @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository, tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) if message: status = 'error' @@ -1105,7 +1099,6 @@ @web.expose def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. - params = util.Params( kwd ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) # Allow hgweb to handle the download. This requires the tool shed # server account's .hgrc file to include the following setting: @@ -1125,9 +1118,8 @@ @web.expose def find_tools( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) @@ -1169,7 +1161,7 @@ tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] - exact_matches = params.get( 'exact_matches', '' ) + exact_matches = kwd.get( 'exact_matches', '' ) exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] ok = True @@ -1210,9 +1202,8 @@ @web.expose def find_workflows( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) @@ -1253,7 +1244,7 @@ return trans.show_error_message( "No items were selected." ) if 'find_workflows_button' in kwd: workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ] - exact_matches = params.get( 'exact_matches', '' ) + exact_matches = kwd.get( 'exact_matches', '' ) exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] ok = True @@ -1327,12 +1318,11 @@ if 'workflows' in metadata: includes_workflows = True return includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), @@ -1518,10 +1508,9 @@ @web.json def get_repository_dependencies( self, trans, **kwd ): """Return an encoded dictionary of all repositories upon which the contents of the received repository depends.""" - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_id = trans.security.encode_id( repository.id ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -1615,10 +1604,9 @@ @web.expose def get_tool_dependencies( self, trans, **kwd ): """Handle a request from a Galaxy instance to get the tool_dependencies entry from the metadata for a specified changeset revision.""" - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) for downloadable_revision in repository.downloadable_revisions: if downloadable_revision.changeset_revision == changeset_revision: @@ -1632,10 +1620,9 @@ @web.expose def get_tool_dependencies_config_contents( self, trans, **kwd ): """Handle a request from a Galaxy instance to get the tool_dependencies.xml file contents for a specified changeset revision.""" - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) # TODO: We're currently returning the tool_dependencies.xml file that is available on disk. We need to enhance this process # to retrieve older versions of the tool-dependencies.xml file from the repository manafest. @@ -1772,9 +1759,8 @@ @web.expose def help( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = util.restore_text( kwd.get( 'message', '' ) ) + status = kwd.get( 'status', 'done' ) return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): @@ -1826,9 +1812,8 @@ @web.expose def index( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) # See if there are any RepositoryMetadata records since menu items require them. repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first() current_user = trans.user @@ -1847,9 +1832,9 @@ break # Route in may have been from a sharable URL, in whcih case we'll have a user_id and possibly a name # The received user_id will be the id of the repository owner. - user_id = params.get( 'user_id', None ) - repository_id = params.get( 'repository_id', None ) - changeset_revision = params.get( 'changeset_revision', None ) + user_id = kwd.get( 'user_id', None ) + repository_id = kwd.get( 'repository_id', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) return trans.fill_template( '/webapps/tool_shed/index.mako', repository_metadata=repository_metadata, has_reviewed_repositories=has_reviewed_repositories, @@ -1890,9 +1875,8 @@ @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'error' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'error' ) repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) invalid_file_tups = [] @@ -1944,13 +1928,12 @@ @web.expose @web.require_login( "manage email alerts" ) def manage_email_alerts( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - new_repo_alert = params.get( 'new_repo_alert', '' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + new_repo_alert = kwd.get( 'new_repo_alert', '' ) new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert ) user = trans.user - if params.get( 'new_repo_alert_button', False ): + if kwd.get( 'new_repo_alert_button', False ): user.new_repo_alert = new_repo_alert_checked trans.sa_session.add( user ) trans.sa_session.flush() @@ -2209,9 +2192,8 @@ @web.expose @web.require_login( "multi select email alerts" ) def multi_select_email_alerts( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "receive email alerts": @@ -2249,13 +2231,12 @@ @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) + changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ), @@ -2302,12 +2283,11 @@ older changeset_revsion, but later the repository was updated in the tool shed and the Galaxy admin is trying to install the latest changeset revision of the same repository instead of updating the one that was previously installed. """ - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -2326,10 +2306,9 @@ @web.require_login( "rate repositories" ) def rate_repository( self, trans, **kwd ): """ Rate a repository and return updated rating data. """ - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = params.get( 'id', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + id = kwd.get( 'id', None ) if not id: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -2342,12 +2321,12 @@ action='browse_repositories', message="You are not allowed to rate your own repository", status='error' ) ) - if params.get( 'rate_button', False ): - rating = int( params.get( 'rating', '0' ) ) - comment = util.restore_text( params.get( 'comment', '' ) ) + if kwd.get( 'rate_button', False ): + rating = int( kwd.get( 'rating', '0' ) ) + comment = kwd.get( 'comment', '' ) rating = self.rate_item( trans, trans.user, repository, rating, comment ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) + display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', @@ -2480,15 +2459,14 @@ @web.expose def select_files_to_delete( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) - if params.get( 'select_files_to_delete_button', False ): + selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' ) + if kwd.get( 'select_files_to_delete_button', False ): if selected_files_to_delete: selected_files_to_delete = selected_files_to_delete.split( ',' ) # Get the current repository tip. @@ -2744,10 +2722,9 @@ revision for the required repository, making it impossible to discover the repository without knowledge of revisions to which it could have been updated. """ - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -2784,9 +2761,8 @@ @web.expose def view_changelog( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) changesets = [] @@ -2820,9 +2796,8 @@ @web.expose def view_changeset( self, trans, id, ctx_str, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) ctx = suc.get_changectx_for_changeset( repo, ctx_str ) @@ -2898,15 +2873,14 @@ @web.expose def view_repository( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) - display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) - alerts = params.get( 'alerts', '' ) + changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) + display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) + alerts = kwd.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) if repository.email_alerts: email_alerts = json.from_json_string( repository.email_alerts ) @@ -2914,7 +2888,7 @@ email_alerts = [] repository_dependencies = None user = trans.user - if user and params.get( 'receive_email_alerts_button', False ): + if user and kwd.get( 'receive_email_alerts_button', False ): flush_needed = False if alerts_checked: if user.email not in email_alerts: @@ -2982,9 +2956,8 @@ @web.expose def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) @@ -3054,9 +3027,8 @@ @web.expose def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ): """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix recent changes to the tool shed menu to allow a logged in user to create a new repository.
by commits-noreply＠bitbucket.org 22 May '13

22 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1021adf47016/ Changeset: 1021adf47016 User: greg Date: 2013-05-22 21:28:40 Summary: Fix recent changes to the tool shed menu to allow a logged in user to create a new repository. Affected #: 1 file diff -r 901cf978cef1199ed230790b2837854c66ab7f79 -r 1021adf470168815b1066c4c9022cb4136edf84c templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -131,15 +131,14 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_my_writable_repositories_with_invalid_tools' )}">Latest revision: invalid tools</a></div> - %else: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Available Actions - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a> - </div> %endif + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Available Actions + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a> + </div> %if can_review_repositories: <div class="toolSectionPad"></div><div class="toolSectionTitle"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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