1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/fbfa0c78ea29/ changeset: fbfa0c78ea29 user: greg date: 2012-12-17 21:02:54 summary: Add the framework for discovering and installing simple repository dependencies. affected #: 9 files
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/tool_shed/common_util.py --- a/lib/galaxy/tool_shed/common_util.py +++ b/lib/galaxy/tool_shed/common_util.py @@ -1,7 +1,7 @@ import os, urllib2 from galaxy import util from galaxy.util.odict import odict -from galaxy.tool_shed.encoding_util import tool_shed_decode +from galaxy.tool_shed import encoding_util
REPOSITORY_OWNER = 'devteam'
@@ -36,7 +36,7 @@ print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) ) if tool_shed_accessible: if text: - tool_dependencies_dict = tool_shed_decode( text ) + tool_dependencies_dict = encoding_util.tool_shed_decode( text ) for dependency_key, requirements_dict in tool_dependencies_dict.items(): tool_dependency_name = requirements_dict[ 'name' ] tool_dependency_version = requirements_dict[ 'version' ]
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/tool_shed/encoding_util.py --- a/lib/galaxy/tool_shed/encoding_util.py +++ b/lib/galaxy/tool_shed/encoding_util.py @@ -11,6 +11,7 @@ log = logging.getLogger( __name__ )
encoding_sep = '__esep__' +encoding_sep2 = '__esepii__'
def tool_shed_decode( value ): # Extract and verify hash @@ -23,12 +24,12 @@ try: values = simplejson.loads( value ) except Exception, e: - log.debug( "Decoding json value from tool shed threw exception: %s" % str( e ) ) + log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) ) if values is not None: try: return json_fix( values ) except Exception, e: - log.debug( "Fixing decoded json value from tool shed threw exception: %s" % str( e ) ) + log.debug( "Fixing decoded json values '%s' from tool shed threw exception: %s" % ( str( values ), str( e ) ) ) fixed_values = values if values is None: values = value
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -1,7 +1,7 @@ import sys, os, subprocess, tempfile import common_util import fabric_util -from galaxy.tool_shed.encoding_util import encoding_sep, tool_shed_encode, tool_shed_decode +from galaxy.tool_shed import encoding_util from galaxy.model.orm import and_
from galaxy import eggs @@ -214,10 +214,10 @@ for action_elem in param_elem: actions.append( action_elem.text.replace( '$INSTALL_DIR', install_dir ) ) if actions: - params_str += 'actions=%s,' % tool_shed_encode( encoding_sep.join( actions ) ) + params_str += 'actions=%s,' % encoding_util.tool_shed_encode( encoding_util.encoding_sep.join( actions ) ) else: if param_elem.text: - param_value = tool_shed_encode( param_elem.text ) + param_value = encoding_util.tool_shed_encode( param_elem.text ) params_str += '%s=%s,' % ( param_name, param_value ) if package_name: params_str += 'package_name=%s' % package_name
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1279,6 +1279,14 @@ valid_filenames.append( '%s.txt' % r ) valid_filenames.append( '%s.txt' % repository_name ) return valid_filenames +def get_repo_info_tuple_contents( repo_info_tuple ): + # Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced. + if len( repo_info_tuple ) == 6: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple + repository_dependencies = None + elif len( repo_info_tuple ) == 7: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies def get_repository_by_name_and_owner( trans, name, owner ): """Get a repository from the database via name and owner""" if trans.webapp.name == 'galaxy':
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -11,7 +11,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import and_ import galaxy.util.shed_util_common as suc -from galaxy.tool_shed.encoding_util import tool_shed_encode +from galaxy.tool_shed import encoding_util import common
from galaxy import eggs @@ -1264,14 +1264,14 @@ update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. - return tool_shed_encode( update_dict ) + return encoding_util.tool_shed_encode( update_dict ) else: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. - return tool_shed_encode( update_dict ) + return encoding_util.tool_shed_encode( update_dict ) else: # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the # repository was installed. We need to find the changeset_revision to which we need to update. @@ -1295,7 +1295,7 @@ update_to_changeset_hash = changeset_hash update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) - return tool_shed_encode( update_dict ) + return encoding_util.tool_shed_encode( update_dict ) @web.expose def get_ctx_rev( self, trans, **kwd ): """Given a repository and changeset_revision, return the correct ctx.rev() value.""" @@ -1328,7 +1328,20 @@ return repository_metadata.metadata return None @web.json + def get_readme_files( self, trans, **kwd ): + """ + This method is called when installing or re-installing a single repository into a Galaxy instance. If the received changeset_revision + includes one or more readme files, return them in a dictionary. + """ + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] + changeset_revision = kwd[ 'changeset_revision' ] + repository = suc.get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) + return suc.build_readme_files_dict( repository_metadata ) + @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 ) @@ -1339,7 +1352,6 @@ if repository_metadata: metadata = repository_metadata.metadata if metadata: - # Get a dictionary of all repositories upon which the contents of the received repository depends. repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, repository=repository, repository_metadata=repository_metadata, @@ -1349,7 +1361,7 @@ handled_key_rd_dicts=None, circular_repository_dependencies=None ) if repository_dependencies: - return tool_shed_encode( repository_dependencies ) + return encoding_util.tool_shed_encode( repository_dependencies ) return '' @web.json def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ): @@ -1385,26 +1397,34 @@ repository=repository, metadata=None, repository_metadata=repository_metadata ) - repo_info_dicts.append( tool_shed_encode( repo_info_dict ) ) + repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) return dict( includes_tools=includes_tools, includes_repository_dependencies=includes_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts ) @web.json - def get_readme_files( self, trans, **kwd ): - """ - This method is called when installing or re-installing a single repository into a Galaxy instance. If the received changeset_revision - includes one or more readme files, return them in a dictionary. - """ - repository_name = kwd[ 'name' ] - repository_owner = kwd[ 'owner' ] - changeset_revision = kwd[ 'changeset_revision' ] - repository = suc.get_repository_by_name_and_owner( trans, repository_name, repository_owner ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) - return suc.build_readme_files_dict( repository_metadata ) + def get_required_repo_info_dict( self, trans, encoded_str ): + """Retrive a list of dictionaries that each contain all of the information needed to install the list of repositories defined by encoded_str.""" + encoded_required_repository_str = encoding_util.tool_shed_decode( encoded_str ) + encoded_required_repository_tups = encoded_required_repository_str.split( encoding_util.encoding_sep2 ) + decoded_required_repository_tups = [] + for encoded_required_repository_tup in encoded_required_repository_tups: + decoded_required_repository_tups.append( encoded_required_repository_tup.split( encoding_util.encoding_sep ) ) + encoded_repository_ids = [] + changeset_revisions = [] + for required_repository_tup in decoded_required_repository_tups: + tool_shed, name, owner, changeset_revision = required_repository_tup + repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + encoded_repository_ids.append( trans.security.encode_id( repository.id ) ) + changeset_revisions.append( changeset_revision ) + if encoded_repository_ids and changeset_revisions: + repo_info_dict = from_json_string( self.get_repository_information( trans, encoded_repository_ids, changeset_revisions ) ) + else: + repo_info_dict = {} + return repo_info_dict @web.expose def get_tool_dependencies( self, trans, **kwd ): - """Handle a request from a local Galaxy instance.""" + """Handle a request from the InstallManager of a local Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1422,9 +1442,8 @@ from_install_manager = kwd.get( 'from_install_manager', False ) if from_install_manager: if tool_dependencies: - return tool_shed_encode( tool_dependencies ) - return '' - # TODO: future handler where request comes from some Galaxy admin feature. + return encoding_util.tool_shed_encode( tool_dependencies ) + return '' @web.expose def get_tool_versions( self, trans, **kwd ): """
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -11,7 +11,7 @@ from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps import common import galaxy.util.shed_util_common as suc -from galaxy.tool_shed.encoding_util import tool_shed_encode, tool_shed_decode +from galaxy.tool_shed import encoding_util
class RepoInputDataModule( InputDataModule ):
@@ -141,7 +141,7 @@ repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: - workflow_name = tool_shed_decode( workflow_name ) + workflow_name = encoding_util.tool_shed_decode( workflow_name ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -160,7 +160,7 @@ repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata - workflow_name = tool_shed_decode( workflow_name ) + workflow_name = encoding_util.tool_shed_decode( workflow_name ) # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] for workflow_tup in metadata[ 'workflows' ]: @@ -386,7 +386,7 @@ repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: - workflow_name = tool_shed_decode( workflow_name ) + workflow_name = encoding_util.tool_shed_decode( workflow_name ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -403,7 +403,7 @@ return open( tmp_fname ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s' % \ - ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ) ) + ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, encoding_util.tool_shed_encode( workflow_name ) ) return trans.response.send_redirect( url ) return trans.response.send_redirect( web.url_for( controller='workflow', action='view_workflow',
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -10,7 +10,7 @@ from galaxy.web.params import QuotaParamParser from galaxy.exceptions import * from galaxy.util.odict import * -from galaxy.tool_shed.encoding_util import tool_shed_decode +from galaxy.tool_shed import encoding_util import galaxy.datatypes.registry import logging, imp, subprocess, urllib2
@@ -717,7 +717,7 @@ text = response.read() response.close() if text: - tool_dependencies_dict = tool_shed_decode( text ) + tool_dependencies_dict = encoding_util.tool_shed_decode( text ) for dependency_key, requirements_dict in tool_dependencies_dict.items(): tool_dependency_name = requirements_dict[ 'name' ] tool_dependency_version = requirements_dict[ 'version' ]
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -3,7 +3,8 @@ from galaxy.util.json import from_json_string, to_json_string import galaxy.util.shed_util as shed_util import galaxy.util.shed_util_common as suc -from galaxy.tool_shed.encoding_util import tool_shed_encode, tool_shed_decode +from galaxy.tool_shed import encoding_util +from galaxy.webapps.community.util import container_util from galaxy import eggs, tools
eggs.require( 'mercurial' ) @@ -584,11 +585,59 @@ raw_text = response.read() response.close() if len( raw_text ) > 2: - text = json.from_json_string( tool_shed_decode( raw_text ) ) + text = json.from_json_string( encoding_util.tool_shed_decode( raw_text ) ) log.debug( text ) else: text = '' return text + def get_required_repo_info_dicts( self, tool_shed_url, repo_info_dicts ): + """ + Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of them to the list. All + repository_dependencies entries in each of the received repo_info_dicts includes all required repositories, so only one pass through + this methid is required to retrieve all repository dependencies. + """ + if repo_info_dicts: + all_repo_info_dicts = [ rid for rid in repo_info_dicts ] + # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. + required_repository_tups = [] + for repo_info_dict in repo_info_dicts: + for repository_name, repo_info_tup in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tup ) + if repository_dependencies: + for key, val in repository_dependencies.items(): + if key in [ 'root_key', 'description' ]: + continue + toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key ) + components_list = [ toolshed, name, owner, changeset_revision ] + if components_list not in required_repository_tups: + required_repository_tups.append( components_list ) + for components_list in val: + if components_list not in required_repository_tups: + required_repository_tups.append( components_list ) + if required_repository_tups: + # The value of required_repository_tups is a list of tuples, so we need to encode it. + encoded_required_repository_tups = [] + for required_repository_tup in required_repository_tups: + encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) ) + encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups ) + encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str ) + url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_str=%s' % encoded_required_repository_str ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + required_repo_info_dict = from_json_string( text ) + required_repo_info_dicts = [] + encoded_dict_strings = required_repo_info_dict[ 'repo_info_dicts' ] + for encoded_dict_str in encoded_dict_strings: + decoded_dict = encoding_util.tool_shed_decode( encoded_dict_str ) + required_repo_info_dicts.append( decoded_dict ) + if required_repo_info_dicts: + for required_repo_info_dict in required_repo_info_dicts: + if required_repo_info_dict not in all_repo_info_dicts: + all_repo_info_dicts.append( required_repo_info_dict ) + return all_repo_info_dicts def get_versions_of_tool( self, app, guid ): tool_version = shed_util.get_tool_version( app, guid ) return tool_version.get_version_ids( app, reverse=True ) @@ -694,7 +743,7 @@ tool_section = None for tup in zip( tool_shed_repositories, repo_info_dicts ): tool_shed_repository, repo_info_dict = tup - repo_info_dict = tool_shed_decode( repo_info_dict ) + repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) # Clone each repository to the configured location. shed_util.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING ) repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] @@ -939,7 +988,7 @@ elif operation == "install": reinstalling = util.string_as_bool( params.get( 'reinstalling', False ) ) encoded_kwd = kwd[ 'encoded_kwd' ] - decoded_kwd = tool_shed_decode( encoded_kwd ) + decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ] repositories_for_installation = [] for tsr_id in tsr_ids: @@ -1095,7 +1144,7 @@ includes_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_repository_dependencies', False ) ) includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) - repo_info_dicts = [ tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] + repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] if ( not includes_tools and not includes_repository_dependencies ) or \ ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) @@ -1122,14 +1171,12 @@ created_or_updated_tool_shed_repositories = [] # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly. filtered_repo_info_dicts = [] + # Disciver all repository dependencies and retrieve information for installing them. + repo_info_dicts = self.get_required_repo_info_dicts( tool_shed_url, repo_info_dicts ) for repo_info_dict in repo_info_dicts: for name, repo_info_tuple in repo_info_dict.items(): - # Take care in handling the repo_info_tuple as it evolves over time as new features are introduced. - if len( repo_info_tuple ) == 6: - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple - repository_dependencies = None - elif len( repo_info_tuple ) == 7: - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, name ) # Make sure the repository was not already installed. @@ -1173,7 +1220,7 @@ owner=repository_owner, dist_to_shed=False ) created_or_updated_tool_shed_repositories.append( tool_shed_repository ) - filtered_repo_info_dicts.append( tool_shed_encode( repo_info_dict ) ) + filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) if created_or_updated_tool_shed_repositories: if includes_tools and ( new_tool_panel_section or tool_panel_section ): if new_tool_panel_section: @@ -1201,6 +1248,7 @@ tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tools=includes_tools, includes_repository_dependencies=includes_repository_dependencies, + install_repository_dependencies=install_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies=install_tool_dependencies, message=message, @@ -1211,7 +1259,7 @@ tool_panel_section_key=tool_panel_section_key, tool_shed_repository_ids=tsrids_list, tool_shed_url=tool_shed_url ) - encoded_kwd = tool_shed_encode( new_kwd ) + encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) tsrids_str = ','.join( tsrids_list ) return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='initiate_repository_installation', @@ -1391,7 +1439,7 @@ repository_metadata=None, metadata=metadata, repository_dependencies=repository_dependencies ) - repo_info_dict = tool_shed_encode( repo_info_dict ) + repo_info_dict = encoding_util.tool_shed_encode( repo_info_dict ) new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, install_tool_dependencies=install_tool_dependencies, @@ -1405,7 +1453,7 @@ tool_panel_section_key=tool_panel_section_key, tool_shed_repository_ids=[ repository_id ], tool_shed_url=tool_shed_url ) - encoded_kwd = tool_shed_encode( new_kwd ) + encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='initiate_repository_installation', shed_repository_ids=repository_id, @@ -1437,11 +1485,8 @@ # Handle case where the repository was previously installed using an older changeset_revsion, but later the repository was updated # in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one # that was previously installed. We'll look in the database instead of on disk since the repository may be uninstalled. - if len( repo_info_tuple ) == 6: - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple - repository_dependencies = None - elif len( repo_info_tuple ) == 7: - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url ) # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. @@ -1553,7 +1598,7 @@ install_tool_dependencies_check_box=install_tool_dependencies_check_box, containers_dict=containers_dict, tool_panel_section_select_field=tool_panel_section_select_field, - encoded_repo_info_dict=tool_shed_encode( repo_info_dict ), + encoded_repo_info_dict=encoding_util.tool_shed_encode( repo_info_dict ), repo_info_dict=repo_info_dict, message=message, status=status )
diff -r a3ecba6f3e0c1ecc719a42b6bccfa0b32746ba27 -r fbfa0c78ea29b1e8d1ad339ab2d7d6ababb17e2a lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -14,7 +14,7 @@ from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html from galaxy.util.topsort import topsort, topsort_levels, CycleError -from galaxy.tool_shed.encoding_util import tool_shed_encode, tool_shed_decode +from galaxy.tool_shed import encoding_util from galaxy.workflow.modules import * from galaxy import model from galaxy import util @@ -1044,7 +1044,7 @@ # from a Galaxy tool shed, in which case the value was encoded. workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: - workflow_name = tool_shed_decode( workflow_name ) + workflow_name = encoding_util.tool_shed_decode( workflow_name ) # The following parameters will have a value only if the import originated # from a tool shed repository installed locally or from the API. installed_repository_file = kwd.get( 'installed_repository_file', '' ) @@ -1057,7 +1057,7 @@ if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&open_for_url=true' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ) ) + ( tool_shed_url, repository_metadata_id, encoding_util.tool_shed_encode( workflow_name ) ) response = urllib2.urlopen( workflow_url ) workflow_text = response.read() response.close() @@ -1164,7 +1164,7 @@ # We've received the textual representation of a workflow from a Galaxy tool shed. message = "Workflow <b>%s</b> imported successfully." % workflow.name url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&message=%s' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), message ) + ( tool_shed_url, repository_metadata_id, encoding_util.tool_shed_encode( workflow_name ), message ) return trans.response.send_redirect( url ) elif installed_repository_file: # The workflow was read from a file included with an installed tool shed repository.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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