galaxy-commits March 2013

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commit/galaxy-central: greg: Remove ~/tool_shed/util/shed_util.py
by commits-noreply＠bitbucket.org 15 Mar '13

15 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1cc6973069b5/ changeset: 1cc6973069b5 user: greg date: 2013-03-15 21:09:08 summary: Remove ~/tool_shed/util/shed_util.py affected #: 1 file diff -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 -r 1cc6973069b5e7afeb5c2d401c262b0d39efd24b lib/tool_shed/util/shed_util.py --- a/lib/tool_shed/util/shed_util.py +++ /dev/null @@ -1,24 +0,0 @@ -import os, tempfile, shutil, logging, urllib2, threading -from galaxy.datatypes import checkers -from galaxy.web import url_for -from galaxy import util -from galaxy.util import json -from galaxy.webapps.tool_shed.util import container_util -from tool_shed.galaxy_install.tool_dependencies.install_util import install_package, set_environment -from galaxy.model.orm import and_ -import tool_shed.util.shed_util_common as suc -from tool_shed.util import encoding_util, repository_dependency_util, tool_dependency_util - -from galaxy import eggs -import pkg_resources - -pkg_resources.require( 'mercurial' ) -from mercurial import hg, ui, commands - -pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude -from elementtree.ElementTree import Element, SubElement - -log = logging.getLogger( __name__ ) - - 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: Refactor shed_util and shed_util_common into appropriate tool shed Galaxy utilities components.
by commits-noreply＠bitbucket.org 15 Mar '13

15 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/320c9b7f08c4/ changeset: 320c9b7f08c4 user: greg date: 2013-03-15 21:01:09 summary: Refactor shed_util and shed_util_common into appropriate tool shed Galaxy utilities components. affected #: 24 files diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 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 @@ -5,10 +5,10 @@ from galaxy.web.framework.helpers import iff, grids from galaxy.util import json from galaxy.model.orm import or_ -import tool_shed.util.shed_util as shed_util import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util -from tool_shed.util import encoding_util +from tool_shed.util import common_install_util, data_manager_util, datatype_util, encoding_util, metadata_util +from tool_shed.util import repository_dependency_util, tool_dependency_util, tool_util +from tool_shed.galaxy_install import repository_util from galaxy.webapps.tool_shed.util import workflow_util import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids import pkg_resources @@ -36,7 +36,7 @@ repository_id = kwd[ 'id' ] repository = suc.get_installed_tool_shed_repository( trans, repository_id ) try: - shed_util.activate_repository( trans, repository ) + common_install_util.activate_repository( trans, repository ) except Exception, e: error_message = "Error activating repository %s: %s" % ( repository.name, str( e ) ) log.debug( error_message ) @@ -92,7 +92,7 @@ # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies # will be current. Only allow selecting a different section in the tool panel if the repository was uninstalled and it contained # tools that should be displayed in the tool panel. - changeset_revision_dict = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) + changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_changeset_revision and current_ctx_rev: @@ -142,7 +142,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - tool_dependency = shed_util.get_tool_dependency( trans, kwd[ 'id' ] ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, kwd[ 'id' ] ) if tool_dependency.in_error_state: message = "This tool dependency is not installed correctly (see the Tool dependency installation error below). " message += "Choose Uninstall this tool dependency from the Repository Actions menu, correct problems " @@ -217,16 +217,16 @@ if params.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle tool panel alterations. - shed_util.remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) + tool_util.remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_data_managers: - shed_util.remove_from_data_manager( trans.app, tool_shed_repository ) + data_manager_util.remove_from_data_manager( trans.app, tool_shed_repository ) if tool_shed_repository.includes_datatypes: # Deactivate proprietary datatypes. - installed_repository_dict = shed_util.load_installed_datatypes( trans.app, tool_shed_repository, repository_install_dir, deactivate=True ) + installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, tool_shed_repository, repository_install_dir, deactivate=True ) if installed_repository_dict and 'converter_path' in installed_repository_dict: - shed_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) + datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) if installed_repository_dict and 'display_path' in installed_repository_dict: - shed_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) + datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. @@ -244,7 +244,7 @@ tool_shed_repository.uninstalled = True # Remove all installed tool dependencies, but don't touch any repository dependencies.. for tool_dependency in tool_shed_repository.installed_tool_dependencies: - uninstalled, error_message = shed_util.remove_tool_dependency( trans, tool_dependency ) + uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans, tool_dependency ) if error_message: errors = '%s %s' % ( errors, error_message ) tool_shed_repository.deleted = True @@ -371,7 +371,7 @@ return repo_information_dict def get_versions_of_tool( self, app, guid ): - tool_version = shed_util.get_tool_version( app, guid ) + tool_version = tool_util.get_tool_version( app, guid ) return tool_version.get_version_ids( app, reverse=True ) def handle_repository_contents( self, trans, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir, tool_shed=None, @@ -395,26 +395,26 @@ trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() if 'tool_dependencies' in metadata_dict and not reinstalling: - tool_dependencies = shed_util.create_tool_dependency_objects( trans.app, tool_shed_repository, relative_install_dir, set_status=True ) + tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, tool_shed_repository, relative_install_dir, set_status=True ) if 'tools' in metadata_dict: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) + tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = shed_util.get_tool_index_sample_files( sample_files ) - shed_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) + tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) + tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = shed_util.handle_missing_data_table_entry( trans.app, relative_install_dir, tool_path, repository_tools_tups ) + repository_tools_tups = tool_util.handle_missing_data_table_entry( trans.app, relative_install_dir, tool_path, repository_tools_tups ) # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups, sample_files_copied = shed_util.handle_missing_index_file( trans.app, + repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups, sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - shed_util.copy_sample_files( trans.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - shed_util.add_to_tool_panel( app=trans.app, + tool_util.copy_sample_files( trans.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) + tool_util.add_to_tool_panel( app=trans.app, repository_name=tool_shed_repository.name, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.installed_changeset_revision, @@ -424,8 +424,13 @@ tool_panel_dict=tool_panel_dict, new_install=True ) if 'data_manager' in metadata_dict: - new_data_managers = shed_util.install_data_managers( trans.app, trans.app.config.shed_data_manager_config_file, metadata_dict, shed_config_dict, relative_install_dir, - tool_shed_repository, repository_tools_tups ) + new_data_managers = data_manager_util.install_data_managers( trans.app, + trans.app.config.shed_data_manager_config_file, + metadata_dict, + shed_config_dict, + relative_install_dir, + tool_shed_repository, + repository_tools_tups ) if 'datatypes' in metadata_dict: tool_shed_repository.status = trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -437,16 +442,16 @@ files_dir = os.path.join( shed_config_dict['tool_path'], files_dir ) datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', files_dir ) # Load data types required by tools. - converter_path, display_path = shed_util.alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, files_dir, override=False ) + converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, files_dir, override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. - repository_dict = shed_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, - name=tool_shed_repository.name, - owner=tool_shed_repository.owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) + repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, + name=tool_shed_repository.name, + owner=tool_shed_repository.owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters trans.app.datatypes_registry.load_datatype_converters( trans.app.toolbox, installed_repository_dict=repository_dict ) @@ -533,10 +538,10 @@ tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', tool_shed_repository.repo_path( trans.app ) ) - installed_tool_dependencies = shed_util.handle_tool_dependencies( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies ) + installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.model.ToolDependency.installation_status.ERROR: message += ' %s' % suc.to_safe_string( installed_tool_dependency.error_message ) @@ -564,7 +569,7 @@ tool_dependency_ids = util.listify( params.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) tool_dependencies.append( tool_dependency ) if kwd.get( 'install_tool_dependencies_button', False ): # Filter tool dependencies to only those that are installed. @@ -616,10 +621,10 @@ if isinstance( repo_info_dict, basestring ): 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 ) + suc.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 ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple - relative_clone_dir = shed_util.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision ) + relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision ) clone_dir = os.path.join( tool_path, relative_clone_dir ) relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name ) install_dir = os.path.join( tool_path, relative_install_dir ) @@ -627,12 +632,12 @@ if cloned_ok: if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. - changeset_revision_dict = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) + changeset_revision_dict = repository_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_ctx_rev != ctx_rev: repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) - shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) + repository_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) self.handle_repository_contents( trans, tool_shed_repository=tool_shed_repository, @@ -647,9 +652,9 @@ metadata = tool_shed_repository.metadata if 'tools' in metadata: # Get the tool_versions from the tool shed for each tool in the installed change set. - shed_util.update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + suc.update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) url = suc.url_join( tool_shed_url, '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ @@ -659,7 +664,7 @@ response.close() if text: tool_version_dicts = json.from_json_string( text ) - shed_util.handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository ) + tool_util.handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository ) else: message += "Version information for the tools included in the %s repository is missing. " % name message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions " @@ -668,20 +673,20 @@ if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: work_dir = tempfile.mkdtemp() # Install tool dependencies. - shed_util.update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + suc.update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir )#relative_install_dir ) - installed_tool_dependencies = shed_util.handle_tool_dependencies( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies ) + installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies ) try: shutil.rmtree( work_dir ) except: pass - shed_util.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) + suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. self.set_repository_attributes( trans, @@ -739,12 +744,12 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message = "The repository information has been updated." - containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - repository=repository, - reinstalling=False, - required_repo_info_dicts=None ) + containers_dict = metadata_util.populate_containers_dict_from_repository_metadata( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository=repository, + reinstalling=False, + required_repo_info_dicts=None ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, @@ -825,9 +830,9 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - tool_dependency_ids = shed_util.get_tool_dependency_ids( as_string=False, **kwd ) + tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) # We need a tool_shed_repository, so get it from one of the tool_dependencies. - tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) tool_shed_repository = tool_dependency.tool_shed_repository self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % tool_shed_repository.name self.tool_dependency_grid.global_actions = \ @@ -868,7 +873,7 @@ elif operation == 'uninstall': tool_dependencies_for_uninstallation = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) if tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLED, trans.model.ToolDependency.installation_status.ERROR ]: tool_dependencies_for_uninstallation.append( tool_dependency ) @@ -883,7 +888,7 @@ if trans.app.config.tool_dependency_dir: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, trans.model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) @@ -978,15 +983,15 @@ install_tool_dependencies = False tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ - shed_util.create_repository_dependency_objects( trans, - tool_path, - tool_shed_url, - repo_info_dicts, - reinstalling=False, - install_repository_dependencies=install_repository_dependencies, - no_changes_checked=False, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + repository_dependency_util.create_repository_dependency_objects( trans, + tool_path, + tool_shed_url, + repo_info_dicts, + reinstalling=False, + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=False, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if message and len( repo_info_dicts ) == 1: installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ] message+= 'Click <a href="%s">here</a> to manage the repository. ' % \ @@ -1069,39 +1074,39 @@ repo_info_dict = repo_info_dicts[ 0 ] name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ - shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) - readme_files_dict = shed_util.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ) + common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) + readme_files_dict = suc.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ) # We're handling 1 of 2 scenarios here: (1) we're installing a tool shed repository for the first time, so we've retrieved the list of installed # and missing repository dependencies from the database (2) we're handling the scenario where an error occurred during the installation process, # so we have a tool_shed_repository record in the database with associated repository dependency records. Since we have the repository # dependencies in either case, we'll merge the list of missing repository dependencies into the list of installed repository dependencies since # each displayed repository dependency will display a status, whether installed or missing. - containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies ) else: # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies. containers_dicts = [] for repo_info_dict in repo_info_dicts: name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ - shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) - containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=None, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) + containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=None, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies ) containers_dicts.append( containers_dict ) # Merge all containers into a single container. - containers_dict = shed_util.merge_containers_dicts_for_new_install( containers_dicts ) + containers_dict = repository_util.merge_containers_dicts_for_new_install( containers_dicts ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: @@ -1165,8 +1170,8 @@ install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) - clone_dir = os.path.join( tool_path, shed_util.generate_tool_shed_repository_install_dir( repository_clone_url, - tool_shed_repository.installed_changeset_revision ) ) + clone_dir = os.path.join( tool_path, suc.generate_tool_shed_repository_install_dir( repository_clone_url, + tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) tool_section = None @@ -1179,12 +1184,11 @@ includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle the selected tool panel location for loading tools included in the tool shed repository. - tool_section, new_tool_panel_section, tool_panel_section_key = \ - shed_util.handle_tool_panel_selection( trans=trans, - metadata=metadata, - no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + tool_section, new_tool_panel_section, tool_panel_section_key = tool_util.handle_tool_panel_selection( trans=trans, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) # The repository's status must be updated from 'Uninstall' to 'New' when initiating reinstall so the repository_installation_updater will function. tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app, tool_shed_repository.name, @@ -1217,28 +1221,28 @@ tool_dependencies = metadata.get( 'tool_dependencies', None ) else: tool_dependencies = None - repo_info_dict = suc.create_repo_info_dict( trans=trans, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - ctx_rev=ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - repository=None, - repository_metadata=None, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_util.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + ctx_rev=ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ - shed_util.create_repository_dependency_objects( trans=trans, - tool_path=tool_path, - tool_shed_url=tool_shed_url, - repo_info_dicts=repo_info_dicts, - reinstalling=True, - install_repository_dependencies=install_repository_dependencies, - no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + repository_dependency_util.create_repository_dependency_objects( trans=trans, + tool_path=tool_path, + tool_shed_url=tool_shed_url, + repo_info_dicts=repo_info_dicts, + reinstalling=True, + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) # Default the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location # selected for the repository selected for reinstallation. for index, tps_key in enumerate( tool_panel_section_keys ): @@ -1365,19 +1369,19 @@ repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, changeset_revision=tool_shed_repository.changeset_revision ) - repo_info_dict = suc.create_repo_info_dict( trans=trans, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - ctx_rev=tool_shed_repository.ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - repository=None, - repository_metadata=None, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_util.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + ctx_rev=tool_shed_repository.ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) repository_name, repository_owner, changeset_revision, includes_tool_dependencies, installed_repository_dependencies, \ missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies = \ - shed_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) + common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) if installed_repository_dependencies or missing_repository_dependencies: has_repository_dependencies = True else: @@ -1387,7 +1391,7 @@ if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if tool_panel_dict: - if shed_util.panel_entry_per_tool( tool_panel_dict ): + if tool_util.panel_entry_per_tool( tool_panel_dict ): # The following forces everything to be loaded into 1 section (or no section) in the tool panel. tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] tool_section_dict = tool_section_dicts[ 0 ] @@ -1415,17 +1419,17 @@ original_section_name = '' tool_panel_section_select_field = None shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans ) - containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed # repository dependency will display a status, whether installed or missing. - containers_dict = suc.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. @@ -1566,7 +1570,7 @@ response.close() if text: tool_version_dicts = json.from_json_string( text ) - shed_util.handle_tool_versions( trans.app, tool_version_dicts, repository ) + tool_util.handle_tool_versions( trans.app, tool_version_dicts, repository ) message = "Tool versions have been set for all included tools." status = 'done' else: @@ -1576,12 +1580,12 @@ status = 'error' shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) - containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - repository=repository, - reinstalling=False, - required_repo_info_dicts=None ) + containers_dict = metadata_util.populate_containers_dict_from_repository_metadata( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository=repository, + reinstalling=False, + required_repo_info_dicts=None ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=repository.description, @@ -1622,7 +1626,7 @@ tool_dependency_ids = util.listify( params.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = shed_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) tool_dependencies.append( tool_dependency ) tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository if kwd.get( 'uninstall_tool_dependencies_button', False ): @@ -1633,7 +1637,7 @@ if tool_dependency.can_uninstall: tool_dependencies_for_uninstallation.append( tool_dependency ) for tool_dependency in tool_dependencies_for_uninstallation: - uninstalled, error_message = shed_util.remove_tool_dependency( trans, tool_dependency ) + uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans, tool_dependency ) if error_message: errors = True message = '%s %s' % ( message, error_message ) @@ -1681,12 +1685,12 @@ repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) repo = hg.repository( suc.get_configured_ui(), path=repo_files_dir ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) - shed_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) + repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) suc.update_repository( repo, latest_ctx_rev ) tool_shed = suc.clean_tool_shed_url( tool_shed_url ) # Remove old Data Manager entries if repository.includes_data_managers: - shed_util.remove_from_data_manager( trans.app, repository ) + data_manager_util.remove_from_data_manager( trans.app, repository ) # Update the repository metadata. metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, @@ -1710,7 +1714,7 @@ if tool_panel_dict is None: tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) - shed_util.add_to_tool_panel( app=trans.app, + tool_util.add_to_tool_panel( app=trans.app, repository_name=repository.name, repository_clone_url=repository_clone_url, changeset_revision=repository.installed_changeset_revision, @@ -1721,12 +1725,16 @@ new_install=False ) # Add new Data Manager entries if 'data_manager' in metadata_dict: - new_data_managers = shed_util.install_data_managers( trans.app, trans.app.config.shed_data_manager_config_file, metadata_dict, - repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), - repository, repository_tools_tups ) + new_data_managers = data_manager_util.install_data_managers( trans.app, + trans.app.config.shed_data_manager_config_file, + metadata_dict, + repository.get_shed_config_dict( trans.app ), + os.path.join( relative_install_dir, name ), + repository, + repository_tools_tups ) # Create tool_dependency records if necessary. if 'tool_dependencies' in metadata_dict: - tool_dependencies = shed_util.create_tool_dependency_objects( trans.app, repository, relative_install_dir, set_status=False ) + tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, repository, relative_install_dir, set_status=False ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % ( name, latest_changeset_revision ) # See if any tool dependencies can be installed. shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) @@ -1829,10 +1837,6 @@ def can_select_tool_panel_section(): pass -def get_tool_dependency( trans, id ): - """Get a tool_dependency from the database via id""" - return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) - def have_shed_tool_conf_for_install( trans ): if not trans.app.toolbox.shed_tool_confs: return False diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/galaxy/webapps/tool_shed/api/repository_revision_contents.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revision_contents.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revision_contents.py @@ -1,6 +1,7 @@ import logging from galaxy.web.framework.helpers import time_ago import tool_shed.util.shed_util_common as suc +from tool_shed.util import metadata_util from galaxy import web from galaxy.web.base.controller import BaseAPIController @@ -29,7 +30,7 @@ rval = [] repository_metadata_id = kwd.get( 'repository_metadata_id', None ) try: - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_dict = repository_metadata.as_dict( value_mapper=default_value_mapper( trans, repository_metadata ) ) repository_dict[ 'url' ] = web.url_for( 'repository_revision_contents', repository_metadata_id=repository_metadata_id ) rval.append( repository_dict ) diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -1,6 +1,7 @@ import datetime from galaxy.web.framework.helpers import time_ago import tool_shed.util.shed_util_common as suc +from tool_shed.util import metadata_util from galaxy import web, util from galaxy.model.orm import and_, or_ from galaxy.web.base.controller import BaseAPIController @@ -73,7 +74,7 @@ Displays information about a repository_metadata record in the Tool Shed. """ try: - repository_metadata = suc.get_repository_metadata_by_id( trans, id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) repository_data = repository_metadata.get_api_value( view='element', value_mapper=default_value_mapper( trans, repository_metadata ) ) repository_data[ 'contents_url' ] = web.url_for( 'repository_revision_contents', repository_metadata_id=id ) @@ -91,7 +92,7 @@ """ repository_metadata_id = kwd.get( 'id', None ) try: - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) flush_needed = False for key, new_value in payload.items(): if hasattr( repository_metadata, key ): diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -106,7 +106,7 @@ # The received id is a RepositoryMetadata object id, so we need to get the # associated Repository and redirect to view_or_manage_repository with the # changeset_revision. - repository_metadata = suc.get_repository_metadata_by_id( trans, kwd[ 'id' ] ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, kwd[ 'id' ] ) repository = repository_metadata.repository kwd[ 'id' ] = trans.security.encode_id( repository.id ) kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision @@ -196,7 +196,7 @@ ids = util.listify( id ) count = 0 for repository_metadata_id in ids: - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() count += 1 @@ -332,7 +332,7 @@ for repository_metadata in repository.metadata_revisions: metadata = repository_metadata.metadata if metadata: - if suc.is_downloadable( metadata ): + if metadata_util.is_downloadable( metadata ): repository_metadata.downloadable = True trans.sa_session.add( repository_metadata ) repository.deleted = False diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 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 @@ -11,10 +11,9 @@ from galaxy.util import json from galaxy.model.orm import and_, or_ import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util -from tool_shed.util import encoding_util -from galaxy.webapps.tool_shed.util import workflow_util -from galaxy.webapps.tool_shed.util import common_util +from tool_shed.util import encoding_util, metadata_util, repository_dependency_util, tool_dependency_util +from tool_shed.galaxy_install import repository_util +from galaxy.webapps.tool_shed.util import common_util, workflow_util import galaxy.tools import tool_shed.grids.repository_grids as repository_grids import tool_shed.grids.util as grids_util @@ -85,7 +84,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd[ 'id' ] - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision new_kwd = dict( id=repository_id, @@ -266,7 +265,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd[ 'id' ] - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision new_kwd = dict( id=repository_id, @@ -287,7 +286,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd['id' ] - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision new_kwd = dict( id=repository_id, @@ -304,7 +303,7 @@ operation = kwd[ 'operation' ].lower() # The received id is a RepositoryMetadata id. repository_metadata_id = kwd[ 'id' ] - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision new_kwd = dict( id=repository_id, @@ -689,7 +688,7 @@ status = params.get( 'status', 'done' ) repository = suc.get_repository_by_id( trans, repository_id ) if repository: - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) changeset_revision = repository_metadata.changeset_revision if repository_metadata: metadata = repository_metadata.metadata @@ -757,7 +756,7 @@ is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = suc.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) kwd[ 'id' ] = repository_id @@ -774,7 +773,7 @@ encoded_repository_ids = [] changeset_revisions = [] for repository_metadata_id in util.listify( item_id ): - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) new_kwd = {} @@ -844,7 +843,7 @@ is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = suc.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) kwd[ 'id' ] = repository_id @@ -861,7 +860,7 @@ encoded_repository_ids = [] changeset_revisions = [] for repository_metadata_id in util.listify( item_id ): - repository_metadata = suc.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, item_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) new_kwd = {} @@ -1085,14 +1084,15 @@ if repository_metadata: metadata = repository_metadata.metadata if metadata: - repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None, - circular_repository_dependencies=None ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None, + circular_repository_dependencies=None ) if repository_dependencies: return encoding_util.tool_shed_encode( repository_dependencies ) return '' @@ -1144,16 +1144,16 @@ repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = suc.create_repo_info_dict( trans=trans, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - ctx_rev=str( ctx.rev() ), - repository_owner=repository.user.username, - repository_name=repository.name, - repository=repository, - repository_metadata=repository_metadata, - tool_dependencies=None, - repository_dependencies=None ) + repo_info_dict = repository_util.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) return dict( includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, @@ -1257,16 +1257,16 @@ repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = suc.create_repo_info_dict( trans=trans, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - ctx_rev=str( ctx.rev() ), - repository_owner=repository.user.username, - repository_name=repository.name, - repository=repository, - repository_metadata=repository_metadata, - tool_dependencies=None, - repository_dependencies=None ) + repo_info_dict = repository_util.create_repo_info_dict( trans=trans, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) includes_data_managers = False includes_datatypes = False includes_tools = False @@ -1686,15 +1686,16 @@ if repository_metadata: metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None ) # Handle messaging for orphan tool dependencies. - orphan_message = suc.generate_message_for_orphan_tool_dependencies( metadata ) + orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( metadata ) if orphan_message: message += orphan_message status = 'warning' @@ -1809,13 +1810,14 @@ repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None ) if metadata: if 'repository_dependencies' in metadata and not repository_dependencies: message += 'The repository dependency definitions for this repository are invalid and will be ignored.' @@ -2254,7 +2256,7 @@ repository = None if repository: repository_id = trans.security.encode_id( repository.id ) - repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) + repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) if not repository_metadata: # Get updates to the received changeset_revision if any exist. repo_dir = repository.repo_path( trans.app ) @@ -2262,7 +2264,7 @@ upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) if upper_bound_changeset_revision: changeset_revision = upper_bound_changeset_revision - repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) + repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: return trans.response.send_redirect( web.url_for( controller='repository', action='index', @@ -2471,15 +2473,16 @@ if repository_metadata: metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, - repository=repository, - repository_metadata=repository_metadata, - toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), - key_rd_dicts_to_be_processed=None, - all_repository_dependencies=None, - handled_key_rd_dicts=None ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None ) # Handle messaging for orphan tool dependencies. - orphan_message = suc.generate_message_for_orphan_tool_dependencies( metadata ) + orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( metadata ) if orphan_message: message += orphan_message status = 'warning' @@ -2621,7 +2624,7 @@ status = params.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 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 @@ -3,7 +3,7 @@ from galaxy import web, util from galaxy.datatypes import checkers import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util +from tool_shed.util import metadata_util, repository_dependency_util, tool_dependency_util from galaxy import eggs eggs.require('mercurial') @@ -198,17 +198,17 @@ # so warning messages are important because orphans are always valid. The repository owner must be warned in case they did not intend to define an # orphan dependency, but simply provided incorrect information (tool shed, name owner, changeset_revision) for the definition. # Handle messaging for orphan tool dependencies. - orphan_message = suc.generate_message_for_orphan_tool_dependencies( metadata_dict ) + orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( metadata_dict ) if orphan_message: message += orphan_message status = 'warning' # Handle messaging for invalid tool dependencies. - invalid_tool_dependencies_message = suc.generate_message_for_invalid_tool_dependencies( metadata_dict ) + invalid_tool_dependencies_message = tool_dependency_util.generate_message_for_invalid_tool_dependencies( metadata_dict ) if invalid_tool_dependencies_message: message += invalid_tool_dependencies_message status = 'error' # Handle messaging for invalid repository dependencies. - invalid_repository_dependencies_message = suc.generate_message_for_invalid_repository_dependencies( metadata_dict ) + invalid_repository_dependencies_message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict ) if invalid_repository_dependencies_message: message += invalid_repository_dependencies_message status = 'error' diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/galaxy/webapps/tool_shed/util/workflow_util.py --- a/lib/galaxy/webapps/tool_shed/util/workflow_util.py +++ b/lib/galaxy/webapps/tool_shed/util/workflow_util.py @@ -6,7 +6,7 @@ import logging, svgfig from galaxy.util import json import tool_shed.util.shed_util_common as suc -from tool_shed.util import encoding_util +from tool_shed.util import encoding_util, metadata_util from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory import galaxy.webapps.galaxy.controllers.workflow import galaxy.tools @@ -152,7 +152,7 @@ workflow_name = encoding_util.tool_shed_decode( workflow_name ) if trans.webapp.name == 'tool_shed': # We're in the tool shed. - repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/galaxy_install/__init__.py --- a/lib/tool_shed/galaxy_install/__init__.py +++ b/lib/tool_shed/galaxy_install/__init__.py @@ -2,8 +2,8 @@ Classes encapsulating the management of repositories installed from Galaxy tool sheds. """ import os, logging -import tool_shed.util.shed_util import tool_shed.util.shed_util_common +import tool_shed.util.datatype_util from galaxy.model.orm import and_ from galaxy import eggs @@ -51,13 +51,13 @@ .order_by( self.model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - installed_repository_dict = tool_shed.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = tool_shed.util.datatype_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) if installed_repository_dict: self.installed_repository_dicts.append( installed_repository_dict ) def load_proprietary_converters_and_display_applications( self, deactivate=False ): for installed_repository_dict in self.installed_repository_dicts: if installed_repository_dict[ 'converter_path' ]: - tool_shed.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + tool_shed.util.datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - tool_shed.util.shed_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + tool_shed.util.datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) \ No newline at end of file diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -3,7 +3,7 @@ from galaxy import model, util from galaxy.web.framework.helpers import iff, grids from galaxy.model.orm import or_ -import tool_shed.util.shed_util as shed_util +from tool_shed.util import tool_dependency_util log = logging.getLogger( __name__ ) @@ -345,7 +345,7 @@ ] def build_initial_query( self, trans, **kwd ): - tool_dependency_ids = shed_util.get_tool_dependency_ids( as_string=False, **kwd ) + tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) if tool_dependency_ids: clause_list = [] for tool_dependency_id in tool_dependency_ids: diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -6,11 +6,9 @@ from galaxy import util from galaxy.tools import ToolSection from galaxy.util.json import from_json_string, to_json_string -import tool_shed.util.shed_util as shed_util import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util +from tool_shed.util import common_install_util, common_util, datatype_util, metadata_util, tool_dependency_util, tool_util from galaxy.util.odict import odict -from tool_shed.util import common_util class InstallManager( object ): def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ): @@ -174,7 +172,7 @@ # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) if is_displayed: - tool_panel_dict_for_tool_config = shed_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) + tool_panel_dict_for_tool_config = tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v else: @@ -195,43 +193,43 @@ self.app.sa_session.flush() if 'tool_dependencies' in metadata_dict: # All tool_dependency objects must be created before the tools are processed even if no tool dependencies will be installed. - tool_dependencies = shed_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) + tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) else: tool_dependencies = None if 'tools' in metadata_dict: sample_files = metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] - tool_index_sample_files = shed_util.get_tool_index_sample_files( sample_files ) - shed_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) + tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) + tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = shed_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups ) + repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups ) # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups, sample_files_copied = shed_util.handle_missing_index_file( self.app, + repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app, self.tool_path, sample_files, repository_tools_tups, sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - shed_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied ) + tool_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied ) if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict: # Install tool dependencies. - shed_util.update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + suc.update_tool_shed_repository_status( self.app, + tool_shed_repository, + self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) - installed_tool_dependencies = shed_util.handle_tool_dependencies( app=self.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_dependencies ) + installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_dependencies ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == self.app.model.ToolDependency.installation_status.ERROR: print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - shed_util.add_to_tool_panel( self.app, + tool_util.add_to_tool_panel( self.app, tool_shed_repository.name, repository_clone_url, tool_shed_repository.installed_changeset_revision, @@ -250,16 +248,16 @@ datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', repo_install_dir ) # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started # after this installation completes. - converter_path, display_path = shed_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir + converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir if converter_path or display_path: # Create a dictionary of tool shed repository related information. - repository_dict = shed_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, - name=tool_shed_repository.name, - owner=self.repository_owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) + repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, + name=tool_shed_repository.name, + owner=self.repository_owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict ) @@ -297,7 +295,7 @@ current_changeset_revision=None, owner=self.repository_owner, dist_to_shed=True ) - shed_util.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) + suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, @@ -308,9 +306,9 @@ self.app.sa_session.refresh( tool_shed_repository ) metadata_dict = tool_shed_repository.metadata if 'tools' in metadata_dict: - shed_util.update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + suc.update_tool_shed_repository_status( self.app, + tool_shed_repository, + self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) # Get the tool_versions from the tool shed for each tool in the installed change set. url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) @@ -319,7 +317,7 @@ response.close() if text: tool_version_dicts = from_json_string( text ) - shed_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) + tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) else: # Set the tool versions since they seem to be missing for this repository in the tool shed. # CRITICAL NOTE: These default settings may not properly handle all parent/child associations. @@ -328,8 +326,8 @@ tool_id = tool_dict[ 'guid' ] old_tool_id = tool_dict[ 'id' ] tool_version = tool_dict[ 'version' ] - tool_version_using_old_id = shed_util.get_tool_version( self.app, old_tool_id ) - tool_version_using_guid = shed_util.get_tool_version( self.app, tool_id ) + tool_version_using_old_id = tool_util.get_tool_version( self.app, old_tool_id ) + tool_version_using_guid = tool_util.get_tool_version( self.app, tool_id ) if not tool_version_using_old_id: tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id, tool_shed_repository=tool_shed_repository ) @@ -341,7 +339,7 @@ self.app.sa_session.add( tool_version_using_guid ) self.app.sa_session.flush() # Associate the two versions as parent / child. - tool_version_association = shed_util.get_tool_version_association( self.app, + tool_version_association = tool_util.get_tool_version_association( self.app, tool_version_using_old_id, tool_version_using_guid ) if not tool_version_association: @@ -349,7 +347,7 @@ parent_id=tool_version_using_old_id.id ) self.app.sa_session.add( tool_version_association ) self.app.sa_session.flush() - shed_util.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED ) + suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED ) @property def non_shed_tool_panel_configs( self ): return common_util.get_non_shed_tool_panel_configs( self.app ) diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -1,89 +1,230 @@ -import tool_shed.util.shed_util as shed_util +import os, logging, threading, urllib2 +from galaxy.web import url_for +from galaxy.webapps.tool_shed.util import container_util import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util +from tool_shed.util import encoding_util, repository_dependency_util, tool_dependency_util, tool_util -def handle_repository_contents( app, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir, tool_shed=None, tool_section=None, - shed_tool_conf=None, reinstalling=False ): +from galaxy import eggs +import pkg_resources + +pkg_resources.require( 'mercurial' ) +from mercurial import hg, ui, commands + +log = logging.getLogger( __name__ ) + +def create_repo_info_dict( trans, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, repository=None, + repository_metadata=None, tool_dependencies=None, repository_dependencies=None ): """ - Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy (never the tool shed) - when an admin is installing a new repository or reinstalling an uninstalled repository. + Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance. The dictionary will also + contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. + + This method is called from Galaxy under three scenarios: + 1. During the tool shed repository installation process via the tool shed's get_repository_information() method. In this case both the received + repository and repository_metadata will be objects., but tool_dependencies and repository_dependencies will be None + 2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no updates available. In this case, both + repository and repository_metadata will be None, but tool_dependencies and repository_dependencies will be objects previously retrieved from the + tool shed if the repository includes definitions for them. + 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates available. In this case, this + method is reached via the tool shed's get_updated_repository_information() method, and both repository and repository_metadata will be objects + but tool_dependencies and repository_dependencies will be None. """ - sa_session = app.model.context.current - shed_config_dict = app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) - metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=app, - repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict - sa_session.add( tool_shed_repository ) - sa_session.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: - tool_dependencies = shed_util.create_tool_dependency_objects( app, tool_shed_repository, relative_install_dir, set_status=True ) - if 'tools' in metadata_dict: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = shed_util.get_tool_index_sample_files( sample_files ) - shed_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) - sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = suc.get_repository_tools_tups( app, metadata_dict ) - if repository_tools_tups: - # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = shed_util.handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ) - # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups, sample_files_copied = shed_util.handle_missing_index_file( app, - tool_path, - sample_files, - repository_tools_tups, - sample_files_copied ) - # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - shed_util.copy_sample_files( app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - shed_util.add_to_tool_panel( app=app, - repository_name=tool_shed_repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=tool_shed_repository.owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=True ) - if 'data_manager' in metadata_dict: - new_data_managers = shed_util.install_data_managers( app, - app.config.shed_data_manager_config_file, - metadata_dict, - shed_config_dict, - relative_install_dir, - tool_shed_repository, - repository_tools_tups ) - if 'datatypes' in metadata_dict: - tool_shed_repository.status = app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES - if not tool_shed_repository.includes_datatypes: - tool_shed_repository.includes_datatypes = True - sa_session.add( tool_shed_repository ) - sa_session.flush() - files_dir = relative_install_dir - if shed_config_dict.get( 'tool_path' ): - files_dir = os.path.join( shed_config_dict['tool_path'], files_dir ) - datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', files_dir ) - # Load data types required by tools. - converter_path, display_path = shed_util.alter_config_and_load_prorietary_datatypes( app, datatypes_config, files_dir, override=False ) - if converter_path or display_path: - # Create a dictionary of tool shed repository related information. - repository_dict = shed_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, - name=tool_shed_repository.name, - owner=tool_shed_repository.owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) - if converter_path: - # Load proprietary datatype converters - app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=repository_dict ) - if display_path: - # Load proprietary datatype display applications - app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) + repo_info_dict = {} + repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) + if trans.webapp.name == 'tool_shed': + # We're in the tool shed. + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) + 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 = \ + repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None, + circular_repository_dependencies=None ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + new_tool_dependencies = {} + for dependency_key, requirements_dict in tool_dependencies.items(): + if dependency_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + set_environment_dict[ 'repository_name' ] = repository_name + set_environment_dict[ 'repository_owner' ] = repository_owner + set_environment_dict[ 'changeset_revision' ] = changeset_revision + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list + else: + requirements_dict[ 'repository_name' ] = repository_name + requirements_dict[ 'repository_owner' ] = repository_owner + requirements_dict[ 'changeset_revision' ] = changeset_revision + new_tool_dependencies[ dependency_key ] = requirements_dict + tool_dependencies = new_tool_dependencies + # Cast unicode to string. + repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), + str( repository_clone_url ), + str( changeset_revision ), + str( ctx_rev ), + str( repository_owner ), + repository_dependencies, + tool_dependencies ) + return repo_info_dict + +def get_update_to_changeset_revision_and_ctx_rev( trans, repository ): + """Return the changeset revision hash to which the repository can be updated.""" + changeset_revision_dict = {} + tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + url = suc.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \ + ( repository.name, repository.owner, repository.installed_changeset_revision ) ) + try: + response = urllib2.urlopen( url ) + encoded_update_dict = response.read() + if encoded_update_dict: + update_dict = encoding_util.tool_shed_decode( encoded_update_dict ) + includes_data_managers = update_dict.get( 'includes_data_managers', False ) + includes_datatypes = update_dict.get( 'includes_datatypes', False ) + includes_tools = update_dict.get( 'includes_tools', False ) + includes_tools_for_display_in_tool_panel = update_dict.get( 'includes_tools_for_display_in_tool_panel', False ) + includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False ) + includes_workflows = update_dict.get( 'includes_workflows', False ) + has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) + changeset_revision = update_dict.get( 'changeset_revision', None ) + ctx_rev = update_dict.get( 'ctx_rev', None ) + response.close() + changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers + changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes + changeset_revision_dict[ 'includes_tools' ] = includes_tools + changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel + changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies + changeset_revision_dict[ 'includes_workflows' ] = includes_workflows + changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies + changeset_revision_dict[ 'changeset_revision' ] = changeset_revision + changeset_revision_dict[ 'ctx_rev' ] = ctx_rev + except Exception, e: + log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) ) + changeset_revision_dict[ 'includes_data_managers' ] = False + changeset_revision_dict[ 'includes_datatypes' ] = False + changeset_revision_dict[ 'includes_tools' ] = False + changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = False + changeset_revision_dict[ 'includes_tool_dependencies' ] = False + changeset_revision_dict[ 'includes_workflows' ] = False + changeset_revision_dict[ 'has_repository_dependencies' ] = False + changeset_revision_dict[ 'changeset_revision' ] = None + changeset_revision_dict[ 'ctx_rev' ] = None + return changeset_revision_dict + +def merge_containers_dicts_for_new_install( containers_dicts ): + """ + When installing one or more tool shed repositories for the first time, the received list of containers_dicts contains a containers_dict for + each repository being installed. Since the repositories are being installed for the first time, all entries are None except the repository + dependencies and tool dependencies. The entries for missing dependencies are all None since they have previously been merged into the installed + dependencies. This method will merge the dependencies entries into a single container and return it for display. + """ + new_containers_dict = dict( readme_files=None, + datatypes=None, + missing_repository_dependencies=None, + repository_dependencies=None, + missing_tool_dependencies=None, + tool_dependencies=None, + invalid_tools=None, + valid_tools=None, + workflows=None ) + if containers_dicts: + lock = threading.Lock() + lock.acquire( True ) + try: + repository_dependencies_root_folder = None + tool_dependencies_root_folder = None + # Use a unique folder id (hopefully the following is). + folder_id = 867 + for old_container_dict in containers_dicts: + # Merge repository_dependencies. + old_container_repository_dependencies_root = old_container_dict[ 'repository_dependencies' ] + if old_container_repository_dependencies_root: + if repository_dependencies_root_folder is None: + repository_dependencies_root_folder = container_util.Folder( id=folder_id, key='root', label='root', parent=None ) + folder_id += 1 + repository_dependencies_folder = container_util.Folder( id=folder_id, + key='merged', + label='Repository dependencies', + parent=repository_dependencies_root_folder ) + folder_id += 1 + # The old_container_repository_dependencies_root will be a root folder containing a single sub_folder. + old_container_repository_dependencies_folder = old_container_repository_dependencies_root.folders[ 0 ] + # Change the folder id so it won't confict with others being merged. + old_container_repository_dependencies_folder.id = folder_id + folder_id += 1 + # Generate the label by retrieving the repository name. + toolshed, name, owner, changeset_revision = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + old_container_repository_dependencies_folder.label = str( name ) + repository_dependencies_folder.folders.append( old_container_repository_dependencies_folder ) + # Merge tool_dependencies. + old_container_tool_dependencies_root = old_container_dict[ 'tool_dependencies' ] + if old_container_tool_dependencies_root: + if tool_dependencies_root_folder is None: + tool_dependencies_root_folder = container_util.Folder( id=folder_id, key='root', label='root', parent=None ) + folder_id += 1 + tool_dependencies_folder = container_util.Folder( id=folder_id, + key='merged', + label='Tool dependencies', + parent=tool_dependencies_root_folder ) + folder_id += 1 + else: + td_list = [ td.listify for td in tool_dependencies_folder.tool_dependencies ] + # The old_container_tool_dependencies_root will be a root folder containing a single sub_folder. + old_container_tool_dependencies_folder = old_container_tool_dependencies_root.folders[ 0 ] + for td in old_container_tool_dependencies_folder.tool_dependencies: + if td.listify not in td_list: + tool_dependencies_folder.tool_dependencies.append( td ) + if repository_dependencies_root_folder: + repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) + new_containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + if tool_dependencies_root_folder: + tool_dependencies_root_folder.folders.append( tool_dependencies_folder ) + new_containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + except Exception, e: + log.debug( "Exception in merge_containers_dicts_for_new_install: %s" % str( e ) ) + finally: + lock.release() + return new_containers_dict + +def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies, + installed_tool_dependencies, missing_tool_dependencies ): + """Return the populated containers for a repository being installed for the first time.""" + installed_tool_dependencies, missing_tool_dependencies = \ + tool_dependency_util.populate_tool_dependencies_dicts( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository_installed_tool_dependencies=installed_tool_dependencies, + repository_missing_tool_dependencies=missing_tool_dependencies, + required_repo_info_dicts=None ) + # Since we are installing a new repository, most of the repository contents are set to None since we don't yet know what they are. + containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, + repository=None, + datatypes=None, + invalid_tools=None, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None, + data_managers_errors=None, + new_install=True, + reinstalling=False ) + # Merge the missing_repository_dependencies container contents to the installed_repository_dependencies container. + containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container. + containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict ) + return containers_dict + +def pull_repository( repo, repository_clone_url, ctx_rev ): + """Pull changes from a remote repository to a local one.""" + commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] ) diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -1,7 +1,7 @@ import sys, os, subprocess, tempfile, urllib2 import common_util import fabric_util -from tool_shed.util import encoding_util +from tool_shed.util import encoding_util, tool_dependency_util from galaxy.model.orm import and_ from galaxy.web import url_for @@ -16,24 +16,6 @@ protocol, base = base_url.split( '://' ) return base.rstrip( '/' ) -def create_or_update_tool_dependency( app, tool_shed_repository, name, version, type, status, set_status=True ): - # Called from Galaxy (never the tool shed) when a new repository is being installed or when an uninstalled repository is being reinstalled. - sa_session = app.model.context.current - # First see if an appropriate tool_dependency record exists for the received tool_shed_repository. - if version: - tool_dependency = get_tool_dependency_by_name_version_type_repository( app, tool_shed_repository, name, version, type ) - else: - tool_dependency = get_tool_dependency_by_name_type_repository( app, tool_shed_repository, name, type ) - if tool_dependency: - if set_status: - tool_dependency.status = status - else: - # Create a new tool_dependency record for the tool_shed_repository. - tool_dependency = app.model.ToolDependency( tool_shed_repository.id, name, version, type, status ) - sa_session.add( tool_dependency ) - sa_session.flush() - return tool_dependency - def create_temporary_tool_dependencies_config( tool_shed_url, name, owner, changeset_revision ): """Make a call to the tool shed to get the required repository's tool_dependencies.xml file.""" url = url_join( tool_shed_url, @@ -95,23 +77,6 @@ return tool_shed_repository return None -def get_tool_dependency_by_name_type_repository( app, repository, name, type ): - sa_session = app.model.context.current - return sa_session.query( app.model.ToolDependency ) \ - .filter( and_( app.model.ToolDependency.table.c.tool_shed_repository_id == repository.id, - app.model.ToolDependency.table.c.name == name, - app.model.ToolDependency.table.c.type == type ) ) \ - .first() - -def get_tool_dependency_by_name_version_type_repository( app, repository, name, version, type ): - sa_session = app.model.context.current - return sa_session.query( app.model.ToolDependency ) \ - .filter( and_( app.model.ToolDependency.table.c.tool_shed_repository_id == repository.id, - app.model.ToolDependency.table.c.name == name, - app.model.ToolDependency.table.c.version == version, - app.model.ToolDependency.table.c.type == type ) ) \ - .first() - def get_tool_dependency_install_dir( app, repository_name, repository_owner, repository_changeset_revision, tool_dependency_type, tool_dependency_name, tool_dependency_version ): if tool_dependency_type == 'package': @@ -147,13 +112,13 @@ for package_elem in elem: if package_elem.tag == 'install': # Create the tool_dependency record in the database. - tool_dependency = create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.INSTALLING, - set_status=True ) + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.INSTALLING, + set_status=True ) # Get the installation method version from a tag like: <install version="1.0"> package_install_version = package_elem.get( 'version', '1.0' ) if package_install_version == '1.0': @@ -296,13 +261,13 @@ elif package_elem.tag == 'install': # <install version="1.0"> package_install_version = package_elem.get( 'version', '1.0' ) - tool_dependency = create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.model.ToolDependency.installation_status.INSTALLING, - set_status=True ) + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.model.ToolDependency.installation_status.INSTALLING, + set_status=True ) if package_install_version == '1.0': # Handle tool dependency installation using a fabric method included in the Galaxy framework. for actions_elem in package_elem: @@ -324,7 +289,11 @@ # print 'Installing tool dependencies via fabric script ', proprietary_fabfile_path else: print '\nSkipping installation of tool dependency', package_name, 'version', package_version, 'since it is installed in', install_dir, '\n' - tool_dependency = get_tool_dependency_by_name_version_type_repository( app, tool_shed_repository, package_name, package_version, 'package' ) + tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, + tool_shed_repository, + package_name, + package_version, + 'package' ) tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED sa_session.add( tool_dependency ) sa_session.flush() @@ -550,13 +519,13 @@ if env_var_dict: if not os.path.exists( install_dir ): os.makedirs( install_dir ) - tool_dependency = create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=env_var_name, - version=None, - type='set_environment', - status=app.model.ToolDependency.installation_status.INSTALLING, - set_status=True ) + tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=env_var_name, + version=None, + type='set_environment', + status=app.model.ToolDependency.installation_status.INSTALLING, + set_status=True ) cmd = common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) if env_var_version == '1.0': # Handle setting environment variables using a fabric method. diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/galaxy_install/update_manager.py --- a/lib/tool_shed/galaxy_install/update_manager.py +++ b/lib/tool_shed/galaxy_install/update_manager.py @@ -3,7 +3,6 @@ """ import threading, urllib2, logging from galaxy.util import string_as_bool -import tool_shed.util.shed_util as shed_util import tool_shed.util.shed_util_common as suc from galaxy.model.orm import and_ diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -5,6 +5,7 @@ from galaxy.util import json import tool_shed.util.shed_util_common as suc import tool_shed.grids.util as grids_util +from tool_shed.util import metadata_util from galaxy import eggs eggs.require('markupsafe') @@ -776,12 +777,16 @@ required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if required_repository: required_repository_id = trans.security.encode_id( required_repository.id ) - required_repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, changeset_revision ) + required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + required_repository_id, + changeset_revision ) if not required_repository_metadata: repo_dir = required_repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) updated_changeset_revision = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset_revision ) - required_repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, updated_changeset_revision ) + required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + required_repository_id, + updated_changeset_revision ) required_repository_metadata_id = trans.security.encode_id( required_repository_metadata.id ) rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s">' % ( required_repository_metadata_id ) rd_str += 'Repository %s revision %s owned by %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 3 ] ), escape_html( rd_tup[ 2 ] ) ) diff -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 -r 320c9b7f08c42c16ac942f05329c134dcdbb2770 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -4,7 +4,7 @@ from galaxy.model.orm import and_, or_ from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util +from tool_shed.util import metadata_util from galaxy import eggs eggs.require('mercurial') @@ -73,7 +73,7 @@ class WithoutReviewsRevisionColumn( grids.GridColumn ): def get_value( self, trans, grid, repository ): # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = suc.get_repository_metadata_revisions_for_review( repository, reviewed=False ) + repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review( repository, reviewed=False ) if repository_metadata_revisions: rval = '' for repository_metadata in repository_metadata_revisions: This diff is so big that we needed to truncate the remainder. 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: inithello: Also require and pass-through authentication for the 'pushkey' mercurial command when pushing changes to a tool shed repository.
by commits-noreply＠bitbucket.org 15 Mar '13

15 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/62bd6fe0e9aa/ changeset: 62bd6fe0e9aa user: inithello date: 2013-03-15 20:11:04 summary: Also require and pass-through authentication for the 'pushkey' mercurial command when pushing changes to a tool shed repository. affected #: 1 file diff -r 750222a21eff68b96069d853a4744d6e3682508c -r 62bd6fe0e9aa297b4448dfbcae32d27c8e313c38 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -56,12 +56,12 @@ times_downloaded += 1 connection.execute( "update repository set times_downloaded = %d where user_id = %d and name = '%s'" % ( times_downloaded, user_id, name.lower() ) ) connection.close() - if cmd == 'unbundle': + if cmd in [ 'unbundle', 'pushkey' ]: # This is an hg push from the command line. When doing this, the following commands, in order, # will be retrieved from environ (see the docs at http://mercurial.selenic.com/wiki/WireProtocol): - # # If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey + # # If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey -> listkeys # - # The mercurial API unbundle() ( i.e., hg push ) method ultimately requires authorization. + # The mercurial API unbundle() ( i.e., hg push ) and pushkey() methods ultimately require authorization. # We'll force password entry every time a change set is pushed. # # When a user executes hg commit, it is not guaranteed to succeed. Mercurial records your name 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: guerler: Fixed: No confirm on delete permanently (footer button), saved histories
by commits-noreply＠bitbucket.org 15 Mar '13

15 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/750222a21eff/ changeset: 750222a21eff user: guerler date: 2013-03-15 19:32:30 summary: Fixed: No confirm on delete permanently (footer button), saved histories affected #: 3 files diff -r f1bd817063e092711a9b13f60e569abbce877fba -r 750222a21eff68b96069d853a4744d6e3682508c static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -541,4 +541,28 @@ } } init_grid_elements(); +} + + +// confirmation/submission of operation request +function submit_operation(selected_button, confirmation_text) +{ + // verify in any item is selected + var number_of_checked_ids = $('input[name="id"]:checked').length; + if (!number_of_checked_ids > 0) + return false; + + // show confirmation box + if (confirmation_text != 'None' && confirmation_text != '') + if(!confirm(confirmation_text)) + return false; + + // set up hidden field to parse the command/operation to controller + $('#operation').val(selected_button.value); + + // submit form + selected_button.form.submit(); + + // return + return true; } \ No newline at end of file diff -r f1bd817063e092711a9b13f60e569abbce877fba -r 750222a21eff68b96069d853a4744d6e3682508c static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.keys(b.attributes.filters),function(c){a["f-"+c]=b.attributes.filters[c]});return a}});function init_operation_buttons(){$("input[name=operation]:submit").each(function(){$(this).click(function(){var b=$(this).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});do_operation(b,a)})})}function init_grid_controls(){init_operation_buttons();$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});$(".sort-link").each(function(){$(this).click(function(){set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var d=$(this).attr("column_key");var c=$("#input-"+d+"-filter");var e=c.val();c.val("");add_filter_condition(d,e,true);return false})});var a=$("#input-tags-filter");if(a.length){a.autocomplete(history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var b=$("#input-name-filter");if(b.length){b.autocomplete(history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})}function init_grid_elements(){$(".grid").each(function(){var b=$(this).find("input.grid-row-select-checkbox");var a=$(this).find("span.grid-selected-count");var c=function(){a.text($(b).filter(":checked").length)};$(b).each(function(){$(this).change(c)});c()});$(".label").each(function(){var a=$(this).attr("href");if(a!==undefined&&a.indexOf("operation=")!=-1){$(this).click(function(){do_operation_from_href($(this).attr("href"));return false})}});$(".community_rating_star").rating({});make_popup_menus()}function go_page_one(){var a=grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){grid.set("cur_page",1)}}function add_filter_condition(c,e,a){if(e===""){return false}grid.add_filter(c,e,a);var d=$(""+e+"<a href='javascript:void(0);'></a>");d.addClass("text-filter-val");d.click(function(){grid.remove_filter(c,e);$(this).remove();go_page_one();update_grid()});var b=$("#"+c+"-filtering-criteria");b.append(d);go_page_one();update_grid()}function add_tag_to_grid_filter(c,b){var a=c+(b!==undefined&&b!==""?":"+b:"");$("#advanced-search").show("fast");add_filter_condition("tags",a,true)}function set_sort_condition(f){var e=grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$(""+c+"").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();init_operation_buttons();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}; \ No newline at end of file +jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.keys(b.attributes.filters),function(c){a["f-"+c]=b.attributes.filters[c]});return a}});function init_operation_buttons(){$("input[name=operation]:submit").each(function(){$(this).click(function(){var b=$(this).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});do_operation(b,a)})})}function init_grid_controls(){init_operation_buttons();$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});$(".sort-link").each(function(){$(this).click(function(){set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var d=$(this).attr("column_key");var c=$("#input-"+d+"-filter");var e=c.val();c.val("");add_filter_condition(d,e,true);return false})});var a=$("#input-tags-filter");if(a.length){a.autocomplete(history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var b=$("#input-name-filter");if(b.length){b.autocomplete(history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})}function init_grid_elements(){$(".grid").each(function(){var b=$(this).find("input.grid-row-select-checkbox");var a=$(this).find("span.grid-selected-count");var c=function(){a.text($(b).filter(":checked").length)};$(b).each(function(){$(this).change(c)});c()});$(".label").each(function(){var a=$(this).attr("href");if(a!==undefined&&a.indexOf("operation=")!=-1){$(this).click(function(){do_operation_from_href($(this).attr("href"));return false})}});$(".community_rating_star").rating({});make_popup_menus()}function go_page_one(){var a=grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){grid.set("cur_page",1)}}function add_filter_condition(c,e,a){if(e===""){return false}grid.add_filter(c,e,a);var d=$(""+e+"<a href='javascript:void(0);'></a>");d.addClass("text-filter-val");d.click(function(){grid.remove_filter(c,e);$(this).remove();go_page_one();update_grid()});var b=$("#"+c+"-filtering-criteria");b.append(d);go_page_one();update_grid()}function add_tag_to_grid_filter(c,b){var a=c+(b!==undefined&&b!==""?":"+b:"");$("#advanced-search").show("fast");add_filter_condition("tags",a,true)}function set_sort_condition(f){var e=grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$(""+c+"").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();init_operation_buttons();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}function submit_operation(b,c){var a=$('input[name="id"]:checked').length;if(!a>0){return false}if(c!="None"&&c!=""){if(!confirm(c)){return false}}$("#operation").val(b.value);b.form.submit();return true}; \ No newline at end of file diff -r f1bd817063e092711a9b13f60e569abbce877fba -r 750222a21eff68b96069d853a4744d6e3682508c templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -459,12 +459,14 @@ ## Grid operations for multiple items. %if show_item_checkboxes: <tr> + ## place holder for multiple operation commands + <input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100"> For selected ${items_plural}: %for operation in grid.operations: %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> + <input type="button" value="${operation.label}" class="action-button" onclick="submit_operation(this, '${operation.confirm}')"> %endif %endfor </td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: browser tests: cleanup, unify datasource format, add more documentation
by commits-noreply＠bitbucket.org 13 Mar '13

13 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1bd817063e0/ changeset: f1bd817063e0 user: carlfeberhard date: 2013-03-13 23:58:42 summary: browser tests: cleanup, unify datasource format, add more documentation affected #: 7 files diff -r c2f310489973fc2ba42e5289ccec3ed88a42aabc -r f1bd817063e092711a9b13f60e569abbce877fba test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -39,12 +39,9 @@ spaceghost.info( 'Will use fixtureData.testUser: ' + email ); } -var tooltipSelector = '.bs-tooltip', - - editableTextClass = 'editable-text', - editableTextInputSelector = 'input#renaming-active', - - galaxyCookieName = 'galaxysession'; +var tooltipSelector = spaceghost.data.selectors.tooltipBalloon, + editableTextClass = spaceghost.data.selectors.editableText, + editableTextInput = spaceghost.data.selectors.editableTextInput, unnamedName = spaceghost.historypanel.data.text.history.newName, nameSelector = spaceghost.historypanel.data.selectors.history.name, @@ -57,6 +54,7 @@ anonNameTooltip = spaceghost.historypanel.data.text.anonymous.tooltips.name; var historyFrameInfo = {}, + filepathToUpload = '../../test-data/1.txt', testUploadInfo = {}; @@ -69,18 +67,6 @@ if( loggedInAs ){ this.logout(); } }); -// ------------------------------------------------------------------- check anon cookies -spaceghost.then( function testAnonCookies(){ - this.test.comment( 'session cookie for anon-user should be present and well formed' ); - var cookies = this.page.cookies; - this.debug( this.jsonStr( this.page.cookies ) ); - //??: what are 'well formed' values? - this.test.assert( cookies.length === 1, "Has one cookie" ); - var galaxyCookie = cookies[0]; - this.test.assert( galaxyCookie.name === galaxyCookieName, "Cookie named: " + galaxyCookieName ); - this.test.assert( !galaxyCookie.secure, "Cookie.secure is false" ); -}); - // ------------------------------------------------------------------- check the empty history for well formedness // grab the history frame bounds for mouse later tests spaceghost.then( function(){ @@ -90,7 +76,7 @@ spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ this.test.comment( 'history panel for anonymous user, new history' ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.test.comment( "frame should have proper url and title: 'History'" ); this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); @@ -118,33 +104,29 @@ this.test.comment( 'name should have a tooltip with info on anon-user name editing' ); // mouse over to find tooltip - //NOTE!!: bounds are returned relative to containing frame - need to adjust using historyFrameInfo - //TODO: into conv. fn - var nameInfo = this.getElementInfo( nameSelector ); - //this.debug( 'nameInfo:' + this.jsonStr( nameInfo ) ); - this.page.sendEvent( 'mousemove', - historyFrameInfo.x + nameInfo.x + 1, historyFrameInfo.y + nameInfo.y + 1 ); - this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); - this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); + this.historypanel.hoverOver( nameSelector, function testingHover(){ + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); + }, historyFrameInfo ); this.test.comment( 'name should NOT be editable when clicked by anon-user' ); - this.test.assert( nameInfo.attributes[ 'class' ].indexOf( editableTextClass ) === -1, - "Name field is not class for editable text" ); + this.assertDoesntHaveClass( nameSelector, editableTextClass, + "Name field is not classed as editable text" ); this.click( nameSelector ); - this.test.assertDoesntExist( editableTextInputSelector, "Clicking on name does not create an input" ); + this.test.assertDoesntExist( editableTextInput, "Clicking on name does not create an input" ); }); }); // ------------------------------------------------------------------- anon user can upload file spaceghost.then( function testAnonUpload(){ this.test.comment( 'anon-user should be able to upload files' ); - spaceghost.tools.uploadFile( '../../test-data/1.txt', function uploadCallback( _uploadInfo ){ + spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); var hasHda = _uploadInfo.hdaElement, hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'historyItem-ok' ) !== -1; this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); - uploadInfo = _uploadInfo; + testUploadInfo = _uploadInfo; }); }); spaceghost.then( function testAnonUpload(){ @@ -157,18 +139,17 @@ // ------------------------------------------------------------------- anon user registers/logs in -> same history spaceghost.user.loginOrRegisterUser( email, password ); -//??: why is a reload needed here? If we don't, loggedInAs === '' ... spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.test.comment( 'anon-user should login and be associated with previous history' ); var loggedInAs = spaceghost.user.loggedInAs(); this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); - this.withFrame( this.selectors.frames.history, function(){ - var hdaInfo = this.historypanel.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); + this.withFrame( spaceghost.data.selectors.frames.history, function(){ + var hdaInfo = this.historypanel.hdaElementInfoByTitle( testUploadInfo.name, testUploadInfo.hid ); this.test.assert( hdaInfo !== null, "After logging in - found a matching hda by name and hid" ); if( hdaInfo ){ - this.test.assert( uploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, + this.test.assert( testUploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, "After logging in - found a matching hda by hda view id: " + hdaInfo.attributes.id ); } }); @@ -177,8 +158,7 @@ spaceghost.user.logout(); spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.test.comment( 'logging out should create a new, anonymous history' ); - - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, 'Message contains "' + emptyMsgStr + '"' ); diff -r c2f310489973fc2ba42e5289ccec3ed88a42aabc -r f1bd817063e092711a9b13f60e569abbce877fba test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -40,7 +40,7 @@ spaceghost.info( 'Will use fixtureData.testUser: ' + email ); } -var tooltipSelector = '.bs-tooltip'; +var tooltipSelector = spaceghost.data.selectors.tooltipBalloon; var utils = require( 'utils' ), historyFrameInfo = {}, @@ -70,8 +70,7 @@ }); -// =================================================================== TESTS -// ------------------------------------------------------------------- helpers +// =================================================================== TEST HELPERS //NOTE: to be called with fn.call( spaceghost, ... ) function testTitle( hdaSelector, hid, name ){ @@ -238,19 +237,18 @@ testPeek.call( this, hdaSelector, peekShouldBeArray ); } +// =================================================================== TESTS // ------------------------------------------------------------------- ok state spaceghost.then( function checkOkState(){ this.test.comment( 'HDAs in the "ok" state should be well formed' ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.test.assertVisible( uploadSelector, 'HDA is visible' ); this.test.comment( 'should have the proper state class' ); - var okStateClass = this.historypanel.data.selectors.hda.wrapper.stateClasses.ok, - uploadElement = this.getElementInfo( uploadSelector ); - this.test.assert( uploadElement.attributes['class'].indexOf( okStateClass ) !== -1, - 'HDA has "ok" state class' ); + this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses.ok, + 'HDA has ok state class' ); // since we're using css there's no great way to test state icon (.state-icon is empty) @@ -273,11 +271,27 @@ }); }); -/* +// restore to collapsed +spaceghost.then( function collapseOkState(){ + this.test.comment( "Collapsing hda in 'ok' state should hide body again" ); + this.withFrame( spaceghost.data.selectors.frames.history, function(){ + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id, + hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; + body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; + + this.click( hdaTitle ); + this.wait( 500, function(){ + this.test.assertNotVisible( body, 'body is not visible' ); + }); + }); +}); + + +// ------------------------------------------------------------------- new state spaceghost.then( function checkNewState(){ this.test.comment( 'HDAs in the "new" state should be well formed' ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ // set state directly through model //TODO: not ideal this.evaluate( function(){ @@ -291,37 +305,45 @@ // should have proper title and hid testTitle.call( spaceghost, uploadSelector, testUploadInfo.hid, testUploadInfo.name ); - // should have the new state class - var newStateClass = this.historypanel.data.selectors.hda.wrapper.stateClasses['new']; - uploadElement = this.getElementInfo( uploadSelector ); - this.test.assert( uploadElement.attributes['class'].indexOf( newStateClass ) !== -1, + this.test.comment( 'new HDA should have the new state class' ); + this.assertHasClass( uploadSelector, this.historypanel.data.selectors.hda.wrapper.stateClasses['new'], 'HDA has new state class' ); - // since we're using css there's no great way to test this - //var stateIconSelector = uploadSelector + ' .state-icon'; - //this.test.assertVisible( stateIconSelector, 'HDA has proper hid' ); - - // should NOT have any of the three, main buttons + this.test.comment( 'new HDA should NOT have any of the three, main buttons' ); var buttonSelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons + ' a'; this.test.assertDoesntExist( buttonSelector, 'No display, edit, or delete buttons' ); - // expand and check the body - this.click( titleSelector ); + this.test.comment( 'clicking the title of the new HDA will expand the body' ); + var hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; + this.click( hdaTitle ); this.wait( 500, function(){ var bodySelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; this.test.assertVisible( bodySelector, 'HDA body is visible (after expanding)' ); var expectedBodyText = 'This is a new dataset'; + this.test.comment( 'the body should have the text: ' + expectedBodyText ); this.test.assertSelectorHasText( bodySelector, expectedBodyText, 'HDA body has text: ' + expectedBodyText ); // restore to collapsed - this.click( titleSelector ); + this.click( hdaTitle ); }); }); }); }); -*/ +// restore state, collapse +spaceghost.then( function revertStateAndCollapse(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ + this.evaluate( function(){ + return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'ok' ); + }); + this.wait( 500, function(){ + var hdaTitle = '#' + testUploadInfo.hdaElement.attributes.id + + ' ' + this.historypanel.data.selectors.hda.title; + this.click( hdaTitle ); + }); + }); +}); // =================================================================== diff -r c2f310489973fc2ba42e5289ccec3ed88a42aabc -r f1bd817063e092711a9b13f60e569abbce877fba test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -38,7 +38,11 @@ } // selectors and labels -var nameSelector = spaceghost.historypanel.data.selectors.history.name, +var tooltipSelector = spaceghost.data.selectors.tooltipBalloon, + editableTextClass = spaceghost.data.selectors.editableText, + editableTextInput = spaceghost.data.selectors.editableTextInput, + + nameSelector = spaceghost.historypanel.data.selectors.history.name, subtitleSelector = spaceghost.historypanel.data.selectors.history.subtitle, unnamedName = spaceghost.historypanel.data.text.history.newName, initialSizeStr = spaceghost.historypanel.data.text.history.newSize, @@ -51,14 +55,9 @@ annoAreaSelector = spaceghost.historypanel.data.selectors.history.annoArea, nameTooltip = spaceghost.historypanel.data.text.history.tooltips.name, - tooltipSelector = '.bs-tooltip', - - editableTextClass = 'editable-text', - editableTextInputSelector = 'input#renaming-active', - - refreshButtonSelector = 'a#history-refresh-button', - refreshButtonIconSelector = 'span.fa-icon-refresh', - refreshButtonHref = '/history', + refreshButtonSelector = 'a#history-refresh-button', + refreshButtonIconSelector = 'span.fa-icon-refresh', + refreshButtonHref = '/history', includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; @@ -66,7 +65,7 @@ var newHistoryName = "Test History", filepathToUpload = '../../test-data/1.txt', historyFrameInfo = {}, - uploadInfo = {}; + testUploadInfo = {}; // =================================================================== TESTS @@ -88,7 +87,7 @@ // ------------------------------------------------------------------- check structure of empty history spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ this.test.comment( 'history panel, new history' ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.test.comment( "frame should have proper url and title: 'History'" ); this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); @@ -98,7 +97,7 @@ this.test.assertVisible( nameSelector, 'History name is visible' ); this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); - this.test.comment( "history subtitle should display size and size should be 0 bytes" ); + this.test.comment( "history subtitle should display size and size should be: " + initialSizeStr ); this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, @@ -119,50 +118,46 @@ // ------------------------------------------------------------------- name editing spaceghost.then( function(){ this.test.comment( 'history panel, editing the history name' ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.test.comment( 'name should have a tooltip with proper info on name editing' ); var nameInfo = this.getElementInfo( nameSelector ); - this.page.sendEvent( 'mousemove', - historyFrameInfo.x + nameInfo.x + 1, historyFrameInfo.y + nameInfo.y + 1 ); + this.page.sendEvent( 'mousemove', historyFrameInfo.x + nameInfo.x + 1, historyFrameInfo.y + nameInfo.y + 1 ); this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); this.test.comment( 'name should be create an input when clicked' ); - this.test.assert( nameInfo.attributes[ 'class' ].indexOf( editableTextClass ) !== -1, - "Name field classed for editable text" ); + this.assertHasClass( nameSelector, editableTextClass, "Name field classed for editable text" ); this.click( nameSelector ); - this.test.assertExists( editableTextInputSelector, "Clicking on name creates an input" ); + this.test.assertExists( editableTextInput, "Clicking on name creates an input" ); this.test.comment( 'name should be editable by entering keys and pressing enter' ); //NOTE: casperjs.sendKeys adds a click before and a selector.blur after sending - won't work here - //TODO: to conv. fn this.page.sendEvent( 'keypress', newHistoryName ); this.page.sendEvent( 'keypress', this.page.event.key.Enter ); this.wait( 1000, function(){ this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInputSelector, "Input disappears after pressing enter" ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after pressing enter" ); }); }); }); spaceghost.then( function(){ - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.test.comment( 'name should revert if user clicks away while editing' ); this.click( nameSelector ); this.page.sendEvent( 'keypress', "Woodchipper metagenomics, Fargo, ND" ); // click above the name input element - var inputInfo = this.getElementInfo( editableTextInputSelector ); - this.page.sendEvent( 'mousedown', - historyFrameInfo.x + inputInfo.x + 1, historyFrameInfo.y + inputInfo.y - 5 ); + var inputInfo = this.getElementInfo( editableTextInput ); + this.page.sendEvent( 'mousedown', historyFrameInfo.x + inputInfo.x + 1, historyFrameInfo.y + inputInfo.y - 5 ); this.wait( 1000, function(){ this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInputSelector, "Input disappears after clicking away" ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after clicking away" ); }); }); }); spaceghost.then( function(){ - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.test.comment( 'name should revert if user hits ESC while editing' ); this.click( nameSelector ); this.page.sendEvent( 'keypress', "Arsenic Bacteria" ); @@ -170,7 +165,7 @@ this.page.sendEvent( 'keypress', this.page.event.key.Escape ); this.wait( 1000, function(){ this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); - this.test.assertDoesntExist( editableTextInputSelector, "Input disappears after hitting ESC" ); + this.test.assertDoesntExist( editableTextInput, "Input disappears after hitting ESC" ); }); }); }); @@ -185,14 +180,14 @@ hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); - uploadInfo = _uploadInfo; + testUploadInfo = _uploadInfo; }); }); spaceghost.then( function checkPanelStructure(){ this.test.comment( 'checking structure of non-empty panel' ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); this.test.assertExists( nameSelector, nameSelector + ' exists' ); this.test.assertVisible( nameSelector, 'History name is visible' ); @@ -221,8 +216,7 @@ //TODO: check tooltips spaceghost.then( function openTags(){ this.test.comment( 'tag area should open when the history panel tag icon is clicked' ); - this.withFrame( this.selectors.frames.history, function(){ - this.capture( 'tag-area.png' ); + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.mouseEvent( 'click', tagIconSelector ); this.wait( 1000, function(){ this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); @@ -235,7 +229,7 @@ //TODO: check tooltips spaceghost.then( function openAnnotation(){ this.test.comment( 'annotation area should open when the history panel annotation icon is clicked' ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.mouseEvent( 'click', annoIconSelector ); this.wait( 1000, function(){ this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); @@ -244,7 +238,7 @@ }); spaceghost.then( function closeAnnotation(){ this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); - this.withFrame( this.selectors.frames.history, function bler(){ + this.withFrame( spaceghost.data.selectors.frames.history, function bler(){ this.mouseEvent( 'click', annoIconSelector ); this.wait( 1000, function(){ this.test.assertNotVisible( annoAreaSelector, 'Tag area is now hidden' ); @@ -296,8 +290,9 @@ spaceghost.then( function(){ this.test.comment( 'deleted hdas shouldn\'t be in the history panel DOM' ); - this.historypanel.deleteHda( '#' + uploadInfo.hdaElement.attributes.id, function(){ - this.test.assertDoesntExist( '#' + uploadInfo.hdaElement.attributes.id, "Deleted HDA is not in the DOM" ); + this.historypanel.deleteHda( '#' + testUploadInfo.hdaElement.attributes.id, function(){ + this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, + "Deleted HDA is not in the DOM" ); }); }); @@ -306,11 +301,11 @@ this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' shows deleted datasets' ); this.historyoptions.includeDeleted(); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.waitForSelector( nameSelector, function(){ - this.test.assertExists( '#' + uploadInfo.hdaElement.attributes.id, + this.test.assertExists( '#' + testUploadInfo.hdaElement.attributes.id, "Deleted HDA is in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); - this.test.assertVisible( '#' + uploadInfo.hdaElement.attributes.id, + this.test.assertVisible( '#' + testUploadInfo.hdaElement.attributes.id, "Deleted HDA is visible again (using history options -> " + includeDeletedOptionsLabel + ")" ); }); }); @@ -320,9 +315,9 @@ this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' (again) re-hides deleted datasets' ); this.historyoptions.includeDeleted(); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.waitForSelector( nameSelector, function(){ - this.test.assertDoesntExist( '#' + uploadInfo.hdaElement.attributes.id, + this.test.assertDoesntExist( '#' + testUploadInfo.hdaElement.attributes.id, "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); }); }); @@ -331,10 +326,10 @@ // undelete the uploaded file spaceghost.then( function(){ this.historyoptions.includeDeleted(); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.waitForSelector( nameSelector, function(){ //TODO: to conv. fn - this.click( '#' + uploadInfo.hdaElement.attributes.id + this.click( '#' + testUploadInfo.hdaElement.attributes.id + ' ' + this.historypanel.data.selectors.history.undeleteLink ); }); }); @@ -348,16 +343,13 @@ // broken in webkit w/ jq 1.7 spaceghost.then( function(){ this.test.comment( 'HDAs can be expanded by clicking on the name' ); - var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.click( uploadedSelector + ' .historyItemTitle' ); - this.debug( 'title: ' + this.debugElement( uploadedSelector + ' .historyItemTitle' ) ); - this.debug( 'wrapper: ' + this.debugElement( uploadedSelector ) ); - this.wait( 1000, function(){ - this.test.assertExists( uploadedSelector + ' .historyItemBody', "Body for uploaded file is found" ); - this.test.assertVisible( uploadedSelector + ' .hda-summary', "hda-summary is visible" ); + this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is visible" ); }); }); }); @@ -365,13 +357,13 @@ // ------------------------------------------------------------------- expanded hdas are still expanded after a refresh spaceghost.then( function(){ this.test.comment( 'Expanded hdas are still expanded after a refresh' ); - var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.click( refreshButtonSelector ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.waitForSelector( nameSelector, function(){ - this.test.assertExists( uploadedSelector + ' .historyItemBody', "Body for uploaded file is found" ); - this.test.assertVisible( uploadedSelector + ' .hda-summary', "hda-summary is visible" ); + this.test.assertVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is visible" ); }); }); // this will break: webkit + jq 1.7 @@ -380,26 +372,27 @@ // ------------------------------------------------------------------- expanded hdas collapse by clicking name again spaceghost.then( function(){ this.test.comment( 'Expanded hdas collapse by clicking name again' ); - var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; - this.withFrame( this.selectors.frames.history, function(){ - this.click( uploadedSelector + ' .historyItemTitle' ); - + this.withFrame( spaceghost.data.selectors.frames.history, function(){ + this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); this.wait( 500, function(){ - this.test.assertNotVisible( uploadedSelector + ' .hda-summary', "hda-summary is not visible" ); + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); }); -// ------------------------------------------------------------------- collapsed hdas are still collapsed after a refresh +// ------------------------------------------------------------------- collapsed hdas still collapsed after a refresh spaceghost.then( function(){ - this.test.comment( 'Expanded hdas are still expanded after a refresh' ); - var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + this.test.comment( 'collapsed hdas still collapsed after a refresh' ); + var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.click( refreshButtonSelector ); - this.withFrame( this.selectors.frames.history, function(){ + this.withFrame( spaceghost.data.selectors.frames.history, function(){ this.waitForSelector( nameSelector, function(){ - this.test.assertNotVisible( uploadedSelector + ' .hda-summary', "hda-summary is not visible" ); + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); }); @@ -407,19 +400,20 @@ // ------------------------------------------------------------------- history options collapses all expanded hdas spaceghost.then( function(){ // expand again - this.withFrame( this.selectors.frames.history, function(){ - this.click( '#' + uploadInfo.hdaElement.attributes.id + ' .historyItemTitle' ); + this.withFrame( spaceghost.data.selectors.frames.history, function(){ + this.click( '#' + testUploadInfo.hdaElement.attributes.id + ' ' + this.historypanel.data.selectors.hda.title ); this.wait( 500, function(){}); }); }); spaceghost.then( function(){ this.test.comment( 'History option collapses all expanded hdas' ); - var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.historyoptions.collapseExpanded(); this.wait( 500, function(){ - this.withFrame( this.selectors.frames.history, function(){ - this.test.assertNotVisible( uploadedSelector + ' .hda-summary', "hda-summary is not visible" ); + this.withFrame( spaceghost.data.selectors.frames.history, function(){ + this.test.assertNotVisible( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.body, + "Body for uploaded file is not visible" ); }); }); }); diff -r c2f310489973fc2ba42e5289ccec3ed88a42aabc -r f1bd817063e092711a9b13f60e569abbce877fba test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -73,7 +73,7 @@ finalStateClass = '.historyItem-' + finalState; spaceghost.then( function(){ - spaceghost.withFrame( spaceghost.selectors.frames.history, function(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.history, function(){ // save the old time out var oldWaitTimeout = spaceghost.options.waitTimeout, @@ -157,7 +157,7 @@ whenDeletedFn = whenDeletedFn || function(){}; var spaceghost = this.spaceghost; - spaceghost.withFrame( spaceghost.selectors.frames.history, function deletingHda(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.history, function deletingHda(){ //precondition: historyItemWrapper's (hda dom elements) should have an id // we could use the selector directly, but better if it errors before an attempted delete var hdaId = spaceghost.getElementInfo( hdaSelector ).attributes.id; @@ -192,7 +192,7 @@ var spaceghost = this.spaceghost, historyFrameInfo = spaceghost.getElementInfo( 'iframe[name="galaxy_history"]' ); - spaceghost.withFrame( spaceghost.selectors.frames.history, function expandingHda(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.history, function expandingHda(){ var titleInfo = spaceghost.getElementInfo( hdaSelector + ' .historyItemTitle' ); spaceghost.page.sendEvent( 'mousedown', historyFrameInfo.x + titleInfo.x + 1, historyFrameInfo.y + titleInfo.y - 5 ); @@ -233,7 +233,7 @@ if( !historyFrameInfo ){ //TODO: move selector to data (use selectors.frames? ) historyFrameInfo = spaceghost.getElementInfo( 'iframe[name="galaxy_history"]' ); - spaceghost.withFrame( spaceghost.selectors.frames.history, function inHistoryPanel(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.history, function inHistoryPanel(){ hoverAndCallback.call( spaceghost, historyFrameInfo, selector, whenHovering ); }); diff -r c2f310489973fc2ba42e5289ccec3ed88a42aabc -r f1bd817063e092711a9b13f60e569abbce877fba test/casperjs/modules/tools.js --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -22,7 +22,11 @@ return this.spaceghost + '.Tools'; }; +// ------------------------------------------------------------------- +/* TODO: + move selectors from sg to here +*/ // =================================================================== INTERNAL /** Tests uploading a file. * NOTE: this version does NOT throw an error on a bad upload. @@ -35,52 +39,34 @@ uploadInfo = {}; //TODO: check file exists using phantom.fs //TODO: pull from test data - uploadInfo[ spaceghost.selectors.tools.upload.fileInput ] = filepath; + uploadInfo[ spaceghost.data.selectors.tools.upload.fileInput ] = filepath; spaceghost.debug( 'uploading file: ' + filepath ); spaceghost.then( function(){ - spaceghost.withFrame( spaceghost.selectors.frames.tools, function(){ - spaceghost.clickLabel( spaceghost.labels.tools.upload.panelLabel ); + spaceghost.withFrame( spaceghost.data.selectors.frames.tools, function(){ + spaceghost.clickLabel( spaceghost.data.labels.tools.upload.panelLabel ); }); }); spaceghost.then( function beginUpload(){ - spaceghost.withFrame( spaceghost.selectors.frames.main, function(){ - spaceghost.fill( spaceghost.selectors.tools.general.form, uploadInfo, false ); + spaceghost.withFrame( spaceghost.data.selectors.frames.main, function(){ + spaceghost.fill( spaceghost.data.selectors.tools.general.form, uploadInfo, false ); // the following throws: // [error] [remote] Failed dispatching clickmouse event on xpath selector: //input[@value="Execute"]: // PageError: TypeError: 'undefined' is not a function (evaluating '$(spaceghost).formSerialize()') // ...and yet the upload still seems to work - spaceghost.click( xpath( spaceghost.selectors.tools.general.executeButton_xpath ) ); + spaceghost.click( xpath( spaceghost.data.selectors.tools.general.executeButton_xpath ) ); }); }); // debugging - spaceghost.withFrame( spaceghost.selectors.frames.main, function afterUpload(){ - var messageInfo = spaceghost.elementInfoOrNull( spaceghost.selectors.messages.all ); + spaceghost.withFrame( spaceghost.data.selectors.frames.main, function afterUpload(){ + var messageInfo = spaceghost.elementInfoOrNull( spaceghost.data.selectors.messages.all ); spaceghost.debug( 'post upload message:\n' + spaceghost.jsonStr( messageInfo ) ); }); }; -/** Uploads a file. - * @param {String} filepath the local filesystem path of the file to upload (absolute (?)) - */ -//Tools.prototype.uploadFile = function uploadFile( filepath ){ -// this._uploadFile( filepath ); -// this.then( function(){ -// this.withFrame( this.selectors.frames.main, function mainAfterUpload(){ -// var messageInfo = this.elementInfoOrNull( this.selectors.messages.all ); -// if( ( !messageInfo ) -// || ( messageInfo.attributes[ 'class' ] !== 'donemessagelarge' ) -// || ( messageInfo.text.indexOf( this.text.upload.success ) === -1 ) ){ -// throw new GalaxyError( 'UploadError: ' + this.jsonStr( messageInfo ) ); -// } -// }); -// }); -// return this; -//}; - /** Parses the hid and name of a newly uploaded file from the tool execution donemessagelarge * @param {String} doneMsgText the text extracted from the donemessagelarge after a tool execution */ @@ -159,9 +145,9 @@ // upload the file erroring if a done message is not displayed, aggregate info about upload spaceghost.info( 'uploading file: ' + filepath + ' (timeout after ' + timeoutAfterMs + ')' ); this._uploadFile( filepath ); - spaceghost.withFrame( spaceghost.selectors.frames.main, function toolExecuted(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.main, function toolExecuted(){ spaceghost.debug( 'checking for done message' ); - var doneElementInfo = spaceghost.elementInfoOrNull( spaceghost.selectors.messages.donelarge ); + var doneElementInfo = spaceghost.elementInfoOrNull( spaceghost.data.selectors.messages.donelarge ); if( !doneElementInfo ){ throw new spaceghost.GalaxyError( 'Upload Error: no done message uploading "' + filepath + '"' ); } @@ -178,7 +164,7 @@ spaceghost.then( function getNewHda(){ spaceghost.debug( 'beginning wait for upload file\'s ok state' ); // get the hda view DOM element from the upload name and hid - spaceghost.withFrame( spaceghost.selectors.frames.history, function(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.history, function(){ spaceghost.waitForSelector( '#history-name', function(){ var hdaInfo = spaceghost.historypanel.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); if( hdaInfo === null ){ diff -r c2f310489973fc2ba42e5289ccec3ed88a42aabc -r f1bd817063e092711a9b13f60e569abbce877fba test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -43,19 +43,19 @@ spaceghost.debug( 'registering user:\n' + spaceghost.jsonStr( userInfo ) ); spaceghost.thenOpen( spaceghost.baseUrl, function(){ - spaceghost.clickLabel( spaceghost.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.labels.masthead.userMenu.register ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.register ); - spaceghost.withFrame( spaceghost.selectors.frames.main, function mainBeforeRegister(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainBeforeRegister(){ spaceghost.debug( 'submitting registration... ' + spaceghost.getCurrentUrl() ); - spaceghost.fill( spaceghost.selectors.registrationPage.form, userInfo, false ); + spaceghost.fill( spaceghost.data.selectors.registrationPage.form, userInfo, false ); // need manual submit (not a normal html form) - spaceghost.click( xpath( spaceghost.selectors.registrationPage.submit_xpath ) ); + spaceghost.click( xpath( spaceghost.data.selectors.registrationPage.submit_xpath ) ); }); //// debugging - //spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterRegister(){ - // var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterRegister(){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); // spaceghost.debug( 'post registration message:\n' + spaceghost.jsonStr( messageInfo ) ); //}); }); @@ -78,21 +78,21 @@ spaceghost.thenOpen( spaceghost.baseUrl, function(){ - spaceghost.clickLabel( spaceghost.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.labels.masthead.userMenu.login ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.login ); - spaceghost.withFrame( spaceghost.selectors.frames.main, function mainBeforeLogin(){ + spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainBeforeLogin(){ spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') logging in user:\n' + spaceghost.jsonStr( loginInfo ) ); - spaceghost.fill( spaceghost.selectors.loginPage.form, loginInfo, false ); - spaceghost.click( xpath( spaceghost.selectors.loginPage.submit_xpath ) ); + spaceghost.fill( spaceghost.data.selectors.loginPage.form, loginInfo, false ); + spaceghost.click( xpath( spaceghost.data.selectors.loginPage.submit_xpath ) ); }); //// debugging - //spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterLogin(){ + //spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterLogin(){ // //TODO: prob. could use a more generalized form of this for url breakdown/checking - // if( spaceghost.getCurrentUrl().search( spaceghost.selectors.loginPage.url_regex ) != -1 ){ - // var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + // if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); // } //}); @@ -111,8 +111,8 @@ var spaceghost = this.spaceghost; this._submitRegistration( email, password, username ); spaceghost.then( function(){ - spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterRegister(){ - var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterRegister(){ + var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); spaceghost.debug( 'post registration message:\n' + this.jsonStr( messageInfo ) ); if( messageInfo.attributes[ 'class' ] === 'errormessage' ){ @@ -132,9 +132,9 @@ var spaceghost = this.spaceghost; this._submitLogin( email, password ); spaceghost.then( function(){ - spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterLogin(){ - if( spaceghost.getCurrentUrl().search( spaceghost.selectors.loginPage.url_regex ) != -1 ){ - var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + spaceghost.withFrame( spaceghost.data.selectors.frames.main, function mainAfterLogin(){ + if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ + var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.html ); } @@ -154,7 +154,8 @@ var spaceghost = this.spaceghost, userEmail = ''; try { - var loggedInInfo = spaceghost.getElementInfo( xpath( spaceghost.selectors.masthead.userMenu.userEmail_xpath ) ); + var loggedInInfo = spaceghost.getElementInfo( + xpath( spaceghost.data.selectors.masthead.userMenu.userEmail_xpath ) ); userEmail = loggedInInfo.text; } catch( err ){ spaceghost.error( err ); @@ -170,8 +171,8 @@ var spaceghost = this.spaceghost; spaceghost.thenOpen( spaceghost.baseUrl, function(){ //TODO: handle already logged out - spaceghost.clickLabel( spaceghost.labels.masthead.menus.user ); - spaceghost.clickLabel( spaceghost.labels.masthead.userMenu.logout ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); }); return spaceghost; }; diff -r c2f310489973fc2ba42e5289ccec3ed88a42aabc -r f1bd817063e092711a9b13f60e569abbce877fba test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -64,11 +64,13 @@ var utils = require( 'utils' ); // ------------------------------------------------------------------- inheritance -/** +/** @class An extension of the Casper object with methods and overrides specifically + * for interacting with a Galaxy web page. + * @augments Casper */ function SpaceGhost(){ SpaceGhost.super_.apply( this, arguments ); - this.init.apply( this, arguments ); + this._init.apply( this, arguments ); } utils.inherits( SpaceGhost, Casper ); @@ -85,6 +87,9 @@ // ------------------------------------------------------------------- error types PageError.prototype = new CasperError(); PageError.prototype.constructor = CasperError; +/** @class Represents a javascript error on the page casper is browsing + * (as opposed to an error in the test script). + */ function PageError(){ CasperError.apply( this, arguments ); this.name = "PageError"; @@ -93,6 +98,7 @@ GalaxyError.prototype = new CasperError(); GalaxyError.prototype.constructor = CasperError; +/** @class Thrown when Galaxy has (gracefully?) indicated pilot error. */ function GalaxyError(){ CasperError.apply( this, arguments ); this.name = "GalaxyError"; @@ -101,6 +107,7 @@ AlertError.prototype = new CasperError(); AlertError.prototype.constructor = CasperError; +/** @class Thrown when Galaxy has displayed a javascript alert. */ function AlertError(){ CasperError.apply( this, arguments ); this.name = "AlertError"; @@ -111,14 +118,17 @@ // ------------------------------------------------------------------- set up /** More initialization: cli, event handlers, etc. * @param {Object} options option hash + * @private */ -SpaceGhost.prototype.init = function init( options ){ +SpaceGhost.prototype._init = function _init( options ){ //console.debug( 'init, options:', JSON.stringify( options, null, 2 ) ); //NOTE: cli will override in-script options this._setOptionsFromCli(); // save errors for later output (needs to go before process CLI) + /** cache of errors that have occurred + * @memberOf SpaceGhost */ this.errors = []; this.on( 'error', function pushErrorToStack( msg, backtrace ){ //this.debug( 'adding error to stack: ' + msg + ', trace:' + JSON.stringify( backtrace, null, 2 ) ); @@ -139,8 +149,9 @@ }; /** Allow CLI arguments to set options if the proper option name is used. - * @example: + * @example * casperjs myscript.js --verbose=true --logLevel=debug + * @private */ SpaceGhost.prototype._setOptionsFromCli = function setOptionsFromCli(){ // get and remove any casper options passed on the command line @@ -154,25 +165,8 @@ }; // ------------------------------------------------------------------- cli args and options -SpaceGhost.prototype._saveHtmlOnErrorHandler = function _saveHtmlOnErrorHandler( msg, backtrace ){ - // needs to output to a file in GALAXY_SAVE - //this.debugHTML(); -}; - -SpaceGhost.prototype._saveTextOnErrorHandler = function _saveTextOnErrorHandler( msg, backtrace ){ - // needs to output to a file in GALAXY_SAVE - //this.debugPage(); -}; - -SpaceGhost.prototype._saveScreenOnErrorHandler = function _saveScreenOnErrorHandler( msg, backtrace ){ - // needs to output to a pic in GALAXY_SAVE - //var filename = ...?? - //?? this.getCurrentUrl(), this.getCurrent - //this.capture( filename ); -}; - - /** Set up any SG specific options passed in on the cli. + * @private */ SpaceGhost.prototype._processCLIArguments = function _processCLIArguments(){ //this.debug( 'cli: ' + this.jsonStr( this.cli ) ); @@ -262,6 +256,7 @@ }; /** Suppress the normal output from the casper object (echo, errors) + * @private */ SpaceGhost.prototype._suppressOutput = function _suppressOutput(){ // currently (1.0) the only way to suppress test pass/fail messages @@ -274,6 +269,7 @@ }; /** Suppress the normal output from the casper object (echo, errors) + * @private */ SpaceGhost.prototype._redirectOutputToStderr = function _redirectOutputToStderr(){ // currently (1.0) the only way to suppress test pass/fail messages @@ -288,7 +284,7 @@ this.removeListener( 'error', this.listeners( 'error' )[1] ); }; -/** Outputs logs, test results and errors in a single JSON formatted object. +/** Outputs logs, test results and errors in a single JSON formatted object to the console. */ SpaceGhost.prototype.outputStateAsJson = function outputStateAsJson(){ var returnedJSON = { @@ -303,18 +299,20 @@ // ------------------------------------------------------------------- event handling //note: using non-anon fns to allow removal if needed -// most of these are stubs (w logging) for later expansion -/** Event handler for failed page loads +/** 'load failed' Event handler for failed page loads that only records to the log + * @private */ SpaceGhost.prototype._loadFailedHandler = function _loadFailedHandler( object ){ this.error( 'load.failed: ' + spaceghost.jsonStr( object ) ); //TODO: throw error? }; -/** Event handler for page errors (js) - throws test scope as PageError +/** 'page.error' Event handler that re-raises as PageError * NOTE: this has some special handling for DOM exc 12 which some casper selectors are throwing * (even tho the selector still works) + * @throws {PageError} (with original's msg and backtrace) + * @private */ SpaceGhost.prototype._pageErrorHandler = function _pageErrorHandler( msg, backtrace ){ // add a page error handler to catch page errors (what we're most interested with here) @@ -337,7 +335,9 @@ } }; -/** Event handler for step/casper timeouts - throws PageError +/** 'timeout' Event handler for step/casper timeouts - raises as PageError + * @throws {PageError} Timeout occurred + * @private */ SpaceGhost.prototype._timeoutHandler = function _timeoutHandler(){ console.debug( 'timeout' ); @@ -345,17 +345,13 @@ throw new PageError( 'Timeout occurred' ); }; -/** Event handler for console messages from the page. - */ -SpaceGhost.prototype._pageConsoleHandler = function _pageConsoleHandler(){ - // remote.message - var DELIM = '-'; - this.debug( this + '(page console) "' + Array.prototype.join.call( arguments, DELIM ) + '"' ); -}; - -/** Event handler for alerts +/** 'alert' Event handler that raises an AlertError with the alert message + * @throws {AlertError} (the alert message) + * @private */ SpaceGhost.prototype._alertHandler = function _alertHandler( message ){ + //TODO: this still isn't working well... + // casper info level already has outputs these //this.warning( this + '(page alert)\n"' + message + '"' ); var ALERT_MARKER = '(page alert) '; @@ -374,13 +370,34 @@ } }; -/** Event handler for navigation requested (loading of frames, redirects(?)) +/** 'error' Event handler that saves html from the errored page. + * @private */ -SpaceGhost.prototype._navHandler = function _navHandler( url, navigationType, navigationLocked, isMainFrame ){ - this.debug( 'navigation.requested: ' + url ); +SpaceGhost.prototype._saveHtmlOnErrorHandler = function _saveHtmlOnErrorHandler( msg, backtrace ){ + // needs to output to a file in GALAXY_SAVE + //this.debugHTML(); }; -/** Set up event handlers. +/** 'error' Event handler that saves text from the errored page. + * @private + */ +SpaceGhost.prototype._saveTextOnErrorHandler = function _saveTextOnErrorHandler( msg, backtrace ){ + // needs to output to a file in GALAXY_SAVE + //this.debugPage(); +}; + +/** 'error' Event handler that saves a screenshot of the errored page. + * @private + */ +SpaceGhost.prototype._saveScreenOnErrorHandler = function _saveScreenOnErrorHandler( msg, backtrace ){ + // needs to output to a pic in GALAXY_SAVE + //var filename = ...?? + //?? this.getCurrentUrl(), this.getCurrent + //this.capture( filename ); +}; + +/** Sets up event handlers. + * @private */ SpaceGhost.prototype._setUpEventHandlers = function _setUpEventHandlers(){ //console.debug( '_setUpEventHandlers' ); @@ -393,18 +410,17 @@ this.on( 'waitFor.timeout', this._timeoutHandler ); // ........................ page info/debugging - // these are already displayed at the casper info level - - //this.on( 'remote.message', this._pageConsoleHandler ); this.on( 'remote.alert', this._alertHandler ); - // these are already displayed at the casper debug level - //this.on( 'navigation.requested', this._navHandler ); - }; // ------------------------------------------------------------------- sub modules /** Load sub modules (similar to casperjs.test) + * @requires User modules/user.js + * @requires Tools modules/tools.js + * @requires HistoryPanel modules/historypanel.js + * @requires HistoryOptions modules/historyoptions.js + * @private */ SpaceGhost.prototype._loadModules = function _loadModules(){ this.user = require( this.options.scriptDir + 'modules/user' ).create( this ); @@ -416,6 +432,7 @@ // =================================================================== PAGE CONTROL /** An override of casper.start for additional set up. * (Currently only used to change viewport) + * @see Casper#start */ SpaceGhost.prototype.start = function start(){ var returned = Casper.prototype.start.apply( this, arguments ); @@ -423,8 +440,9 @@ return returned; }; -/** An override of casper.open specifically for Galaxy. +/** An override of casper.open for additional page control. * (Currently only used to change language headers) + * @see Casper#open */ SpaceGhost.prototype.open = function open(){ //TODO: this can be moved to start (I think...?) @@ -433,13 +451,13 @@ return Casper.prototype.open.apply( this, arguments ); }; -/** An override to provide json output and more informative error codes +/** An override to provide json output and more informative error codes. + * Exits with 2 if a test has failed. + * Exits with 1 if some error has occurred. + * Exits with 0 if all tests passed. + * @see Casper#run run, boy, run (doesn't he fly?) */ SpaceGhost.prototype.run = function run( onComplete, time ){ - // wrap the onComplete to: - // return code 2 on test failure - // 0 on success - // (1 on js error - in error handler) var new_onComplete = function(){ onComplete.call( this ); var returnCode = ( this.test.testResults.failed )?( 2 ):( 0 ); @@ -467,7 +485,6 @@ * @param {Function} catchFn some portion of the correct error msg */ SpaceGhost.prototype.tryStepsCatch = function tryStepsCatch( stepsFn, catchFn ){ - //TODO: * @param {Boolean} removeOtherListeners option to remove other listeners while this fires // create three steps: 1) set up new error handler, 2) try the fn, 3) check for errors and rem. handler var originalExitOnError, originalErrorHandlers = [], @@ -522,11 +539,10 @@ /** Casper has an (undocumented?) skip test feature. This is a conv. wrapper for that. */ SpaceGhost.prototype.skipTest = function(){ - //TODO: does this work? seems to... throw this.test.SKIP_MESSAGE; }; -/** test helper - within frame, assert selector, and assert text in selector +/** Test helper - within frame, assert selector, and assert text in selector * @param {CasperJS selector} selector what element in which to search for the text * @param {String} text what text to search for * @param {String} frame frame selector (gen. name) in which to search for selector (defaults to top) @@ -548,15 +564,17 @@ } } -/** test helper - within frame, assert errormessage, and assert text in errormessage +/** Test helper - within frame, assert errormessage, and assert text in errormessage * *message is a common UI feedback motif in Galaxy (often displayed in the main panel) - * @param {String} message what the message should contain - * @param {String} frame frame selector (gen. name) in which to search for selector (defaults to 'galaxy_main') - * @param {CasperJS selector} messageSelector what element in which to search for the text (defaults to '.errormessage') + * @param {String} message what the message should contain + * @param {String} frame frame selector (gen. name) in which to search for selector + * (defaults to 'galaxy_main') + * @param {CasperJS selector} messageSelector what element in which to search for the text + * (defaults to '.errormessage') */ SpaceGhost.prototype.assertErrorMessage = function assertSelectorAndTextInFrame( message, frame, messageSelector ){ - messageSelector = messageSelector || this.selectors.messages.error; - frame = frame || this.selectors.frames.main; + messageSelector = messageSelector || this.data.selectors.messages.error; + frame = frame || this.data.selectors.frames.main; this.assertSelectorAndTextInFrame( messageSelector, message, frame ); }; @@ -610,9 +628,32 @@ this.test.assert( toSearch.indexOf( searchFor ) !== -1, msg ); }; +/** Assert that a given element has a given class. + * @param {CasperJS selector} selector what element to test + * @param {String} className the class to test for (classes passed in with a leading '.' will have it trimmed) + */ +SpaceGhost.prototype.assertHasClass = function assertHasClass( selector, className, msg ){ + className = ( className[0] == '.' )?( className.slice( 1 ) ):( className ); + msg = msg || 'selector "' + selector + '" has class: "' + className + '"'; + var classes = this.getElementAttribute( selector, 'class' ); + this.test.assert( classes.indexOf( className ) !== -1, msg ); +}; + +/** Assert that a given element doesn't have a given class. + * @param {CasperJS selector} selector what element to test + * @param {String} className the class to test for (classes passed in with a leading '.' will have it trimmed) + */ +SpaceGhost.prototype.assertDoesntHaveClass = function assertDoesntHaveClass( selector, className, msg ){ + className = ( className[0] == '.' )?( className.slice( 1 ) ):( className ); + msg = msg || 'selector "' + selector + '" has class: "' + className + '"'; + var classes = this.getElementAttribute( selector, 'class' ); + this.test.assert( classes.indexOf( className ) === -1, msg ); +}; + // =================================================================== CONVENIENCE /** Wraps casper.getElementInfo in try, returning null if element not found instead of erroring. * @param {String} selector css or xpath selector for the element to find + * @returns {Object|null} element info if found, null if not */ SpaceGhost.prototype.elementInfoOrNull = function elementInfoOrNull( selector ){ var found = null; @@ -622,8 +663,9 @@ return found; }; -/** Wraps casper.click in try, returning true if element found and clicked, false if not instead of erroring. +/** Wraps casper.click in try to prevent error if element isn't found * @param {String} selector css or xpath selector for the element to find + * @returns {Boolean} true if element found and clicked, false if not instead of erroring */ SpaceGhost.prototype.tryClick = function tryClick( selector ){ var done = false; @@ -634,9 +676,9 @@ return done; }; +// =================================================================== GALAXY CONVENIENCE -// =================================================================== GALAXY CONVENIENCE // =================================================================== MISCELAIN /** Override capture to save to environ: GALAXY_TEST_SAVE (or passed in from CLI) * @param {String} filename the image filename @@ -651,6 +693,7 @@ /** Pop all handlers for eventName from casper and return them in order. * @param {String} eventName the name of the event from which to remove handlers + * @returns {Function[]} the array of functions no longer bound to the event */ SpaceGhost.prototype.popAllListeners = function popAllListeners( eventName ){ var returnedListeners = this.listeners( eventName ); @@ -660,7 +703,7 @@ /** Add the given list of handler functions to the listener for eventName in order. * @param {String} eventName the name of the event to which to add handlers - * @param {Array} handlerArray an array of event handler functions to add + * @param {Function[]} handlerArray an array of event handler functions to add */ SpaceGhost.prototype.addListeners = function addListeners( eventName, handlerArray ){ for( var i=0; i<handlerArray.length; i++ ){ @@ -668,14 +711,15 @@ } }; -/** Send message to stderr +/** Send message to stderr using the phantom fs module. + * @param {String} the msg to output */ SpaceGhost.prototype.stderr = function( msg ){ var fs = require( 'fs' ); fs.write( '/dev/stderr', msg + '\n', 'w' ); }; -// convenience logging funcs +// ------------------------------------------------------------------- convenience logging funcs /** log using level = 'debug' and default namespace = 'spaceghost' */ SpaceGhost.prototype.debug = function( msg, namespace ){ @@ -690,14 +734,14 @@ this.log( msg, 'info', namespace ); }; -/** log using level = 'info' and default namespace = 'spaceghost' +/** log using level = 'warning' and default namespace = 'spaceghost' */ SpaceGhost.prototype.warning = function( msg, namespace ){ namespace = namespace || 'spaceghost'; this.log( msg, 'warning', namespace ); }; -/** log using level = 'info' and default namespace = 'spaceghost' +/** log using level = 'error' and default namespace = 'spaceghost' */ SpaceGhost.prototype.error = function( msg, namespace ){ namespace = namespace || 'spaceghost'; @@ -707,6 +751,7 @@ /** log despite logLevel settings, unless returnJsonOnly is set */ SpaceGhost.prototype.out = function( msg, namespace ){ + namespace = namespace || 'spaceghost'; if( !this.options.returnJsonOnly ){ console.debug( msg ); } @@ -718,10 +763,10 @@ return JSON.stringify( obj, null, 2 ); }; -/** output to debug the JSON of the selector (or null if not found) +/** output the JSON of the selector (or null if not found) to debug level */ SpaceGhost.prototype.debugElement = function debugElement( selector ){ - this.debug( this.jsonStr( this.elementInfoOrNull( selector ) ) ); + this.debug( selector + ':\n' + this.jsonStr( this.elementInfoOrNull( selector ) ) ); }; /** Debug SG itself @@ -737,21 +782,6 @@ return this.errors[( this.errors.length - 1 )]; }; -/** Get the last error from an assertRaises test (gen. for the message) - */ -SpaceGhost.prototype.getLastAssertRaisesError = function(){ - // assuming the test passed here... - var testsThatPassed = this.test.testResults.passes; - var test = null; - for( var i=( testsThatPassed.length - 1 ); i>=0; i-- ){ - currTest = testsThatPassed[i]; - if( currTest.type === 'assertRaises' ){ - test = currTest; break; - } - } - return ( ( test && test.values )?( test.values.error ):( undefined ) ); -}; - /** String representation */ SpaceGhost.prototype.toString = function(){ @@ -762,12 +792,105 @@ return 'SpaceGhost(' + currentUrl + ')'; }; +/** Load and parse a JSON file into an object. + * @param filepath filepath relative to the current scriptDir + * @returns the object parsed + */ +SpaceGhost.prototype.loadJSONFile = function loadJSONFile( filepath ){ + //precondition: filepath is relative to script dir + filepath = this.options.scriptDir + filepath; + return JSON.parse( require( 'fs' ).read( filepath ) ); +}; + +/** Load and parse a JSON file into an object. + * @param filepath filepath relative to the current scriptDir + * @param object the object to write + * @param mode 'w' for a new file, 'a' for append + */ +SpaceGhost.prototype.writeJSONFile = function writeJSONFile( filepath, object, mode ){ + mode = mode || 'w'; + //precondition: filepath is relative to script dir + filepath = this.options.scriptDir + filepath; + return require( 'fs' ).write( filepath, this.jsonStr( object ), mode ); +}; + // =================================================================== TEST DATA -// maintain selectors, labels, text here in one central location +/** General use selectors, labels, and text. Kept here to allow a centralized location. + */ +SpaceGhost.prototype.data = { + selectors : { + tooltipBalloon : '.bs-tooltip', + editableText : '.editable-text', + editableTextInput : 'input#renaming-active', + masthead : { + userMenu : { + userEmail : 'a #user-email', + userEmail_xpath : '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' + } + }, + frames : { + main : 'galaxy_main', + tools : 'galaxy_tools', + history : 'galaxy_history' + }, + messages : { + all : '[class*="message"]', + error : '.errormessage', + done : '.donemessage', + donelarge : '.donemessagelarge' + }, + loginPage : { + form : 'form#login', + submit_xpath : "//input[@value='Login']", + url_regex : /\/user\/login/ + }, + registrationPage : { + form : 'form#registration', + submit_xpath : "//input[@value='Submit']" + }, + tools : { + general : { + form : 'form#tool_form', + executeButton_xpath : '//input[@value="Execute"]' + }, + upload : { + fileInput : 'files_0|file_data' // is this general? + } + } + }, + labels : { + masthead : { + menus : { + user : 'User' + }, + userMenu : { + register : 'Register', + login : 'Login', + logout : 'Logout' + } + }, + tools : { + upload : { + panelLabel : 'Upload File' + } + } + }, + text : { + registrationPage : { + badEmailError : 'Enter a real email address' + }, + upload : { + success : 'The following job has been successfully added to the queue' + } + } +}; -//TODO: to data +/* SpaceGhost.prototype.selectors = { + tooltipBalloon : '.bs-tooltip', + editableText : '.editable-text', + editableTextInput : 'input#renaming-active', masthead : { userMenu : { userEmail : 'a #user-email', @@ -832,28 +955,14 @@ success : 'The following job has been successfully added to the queue' } }; - -SpaceGhost.prototype.loadJSONFile = function loadJSONFile( filepath ){ - //precondition: filepath is relative to script dir - filepath = this.options.scriptDir + filepath; - return JSON.parse( require( 'fs' ).read( filepath ) ); -}; - -SpaceGhost.prototype.writeJSONFile = function writeJSONFile( filepath, object, mode ){ - mode = mode || 'w'; - //precondition: filepath is relative to script dir - filepath = this.options.scriptDir + filepath; - return require( 'fs' ).write( filepath, this.jsonStr( object ), mode ); -}; +*/ // =================================================================== EXPORTS -/** - */ exports.SpaceGhost = SpaceGhost; exports.PageError = PageError; exports.GalaxyError = GalaxyError; exports.AlertError = AlertError; -/** +/** creation function */ exports.create = function create(options) { "use strict"; 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: carlfeberhard: browser tests: add tests for structure of HDA in the 'ok' state
by commits-noreply＠bitbucket.org 13 Mar '13

13 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c2f310489973/ changeset: c2f310489973 user: carlfeberhard date: 2013-03-13 21:03:31 summary: browser tests: add tests for structure of HDA in the 'ok' state affected #: 4 files diff -r 4827bed265e7563c58346654f5a668f5de6d9d68 -r c2f310489973fc2ba42e5289ccec3ed88a42aabc test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -40,22 +40,22 @@ spaceghost.info( 'Will use fixtureData.testUser: ' + email ); } -var newHistoryName = "Test History", +var tooltipSelector = '.bs-tooltip'; + +var utils = require( 'utils' ), historyFrameInfo = {}, filepathToUpload = '../../test-data/1.txt', - possibleHDAStates = [], - testUploadInfo = {}; + testUploadInfo = {}, + //TODO: get from the api module - that doesn't exist yet + summaryShouldBeArray = [ '10 lines', 'format: txt' ], + infoShouldBe = 'uploaded txt file', + peekShouldBeArray = []; // ------------------------------------------------------------------- set up // start a new user spaceghost.user.loginOrRegisterUser( email, password ); -// ??: why is a reload needed here? If we don't, loggedInAs === '' ... -spaceghost.thenOpen( spaceghost.baseUrl, function(){ - var loggedInAs = spaceghost.user.loggedInAs(); - this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); -}); -// grab the history frame bounds for mouse later tests +// grab the history frame bounds for later mouse tests spaceghost.then( function(){ historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); @@ -69,15 +69,211 @@ }); }); -spaceghost.then( function getHDAStates(){ + +// =================================================================== TESTS +// ------------------------------------------------------------------- helpers +//NOTE: to be called with fn.call( spaceghost, ... ) + +function testTitle( hdaSelector, hid, name ){ + var titleSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.title, + titleShouldBe = hid + ': ' + name; + this.test.assertVisible( titleSelector, + 'HDA title is visible' ); + this.test.assertSelectorHasText( titleSelector, titleShouldBe, + 'HDA has proper hid and title' ); +} + +function testTitleButtonStructure( hdaSelector, shouldHaveTheseButtons ){ + // defaults to the current buttons most states should have + shouldHaveTheseButtons = shouldHaveTheseButtons || [ 'display', 'edit', 'delete' ]; + + var hdaDbId = this.getElementAttribute( hdaSelector, 'id' ).split( '-' )[1], + buttonsArea = hdaSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons, + buttons = { + // this seems backwards -> TODO: move buttonsArea concat into loop below, move this data to historypanel.data + display : { + nodeName : this.historypanel.data.text.hda.ok.nodeNames.displayButton, + selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.displayButton, + tooltip : this.historypanel.data.text.hda.ok.tooltips.displayButton, + hrefTpl : this.historypanel.data.text.hda.ok.hrefs.displayButton + }, + edit : { + nodeName : this.historypanel.data.text.hda.ok.nodeNames.editAttrButton, + selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.editAttrButton, + tooltip : this.historypanel.data.text.hda.ok.tooltips.editAttrButton, + hrefTpl : this.historypanel.data.text.hda.ok.hrefs.editAttrButton + }, + 'delete' : { + nodeName : this.historypanel.data.text.hda.ok.nodeNames.deleteButton, + selector : buttonsArea + ' ' + this.historypanel.data.selectors.hda.deleteButton, + tooltip : this.historypanel.data.text.hda.ok.tooltips.deleteButton, + hrefTpl : this.historypanel.data.text.hda.ok.hrefs.deleteButton + } + }; + this.test.assertVisible( buttonsArea, 'Button area is visible' ); + + for( var i=0; i<shouldHaveTheseButtons.length; i++ ){ + // don't use button names we don't have data for + var buttonName = shouldHaveTheseButtons[ i ]; + if( !buttons.hasOwnProperty( buttonName ) ){ continue; } + + this.test.comment( buttonName + ' should exist, be visible, and well formed' ); + var button = buttons[ buttonName ]; + this.debug( 'checking button "' + buttonName + '" on hda "' + hdaDbId + '":\n' + this.jsonStr( button ) ); + this.test.assertExists( button.selector, buttonName + ' button exists' ); + this.test.assertVisible( button.selector, buttonName + ' button is visible' ); + + var buttonElement = this.getElementInfo( button.selector ); + this.debug( 'buttonElement:' + this.jsonStr( buttonElement ) ); + + // should be an anchor + this.test.assert( buttonElement.nodeName === button.nodeName, + buttonName + ' is proper node type (' + button.nodeName + '): ' + buttonElement.nodeName ); + + // should have a proper href + var href = buttonElement.attributes.href, + hrefShouldBe = utils.format( button.hrefTpl, hdaDbId ); + this.assertTextContains( href, hrefShouldBe, + buttonName + ' has proper href (' + hrefShouldBe + '): ' + href ); + + this.historypanel.hoverOver( button.selector, function testingHover(){ + var tooltipText = button.tooltip; + this.test.assertVisible( tooltipSelector, buttonName + ' button tooltip is visible when hovering' ); + this.test.assertSelectorHasText( tooltipSelector, tooltipText, + buttonName + ' button has tooltip text: "' + tooltipText + '"' ); + }, historyFrameInfo ); + } +} + +function testDbkey( hdaSelector, dbkeySetTo ){ + var dbkeySelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.body + + ' ' + this.historypanel.data.selectors.hda.dbkey, + unspecifiedDbkeyText = '?', + unspecifiedDbkeyNodeName = 'a', + specifiedDbkeyNodeName = 'span', + editAttrHrefRegex = /\/datasets\/\w+\/edit/; + + this.test.assertExists( dbkeySelector, 'dbkey exists' ); + this.test.assertVisible( dbkeySelector, 'dbkey is visible' ); + var dbkey = this.elementInfoOrNull( dbkeySelector ); + if( !dbkey ){ return; } + + // dbkey is set, check text + if( dbkeySetTo ){ + this.test.comment( '(specified) dbkey should be displayed correctly' ); + this.test.assertSelectorHasText( dbkeySelector, dbkeySetTo, + 'dbkey is specified: ' + dbkey.text ); + this.test.assert( dbkey.nodeName === specifiedDbkeyNodeName, + 'dbkey has proper nodeName (' + specifiedDbkeyNodeName + '):' + dbkey.nodeName ); + + // dbkey expected to be not set + } else { + this.test.comment( '(unspecified) dbkey should be displayed correctly' ); + this.test.assertSelectorHasText( dbkeySelector, unspecifiedDbkeyText, + 'dbkey is not specified: ' + dbkey.text ); + this.test.assert( dbkey.nodeName === unspecifiedDbkeyNodeName, + 'dbkey has proper nodeName (' + unspecifiedDbkeyNodeName + '):' + dbkey.nodeName ); + + this.test.comment( '(unspecified) dbkey href should point to edit attributes' ); + this.test.assertMatch( dbkey.attributes.href, editAttrHrefRegex, + 'dbkey has a proper href: ' + dbkey.attributes.href ); + } +} + +function testPrimaryActionButtons( hdaSelector ){ + var buttonsSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.body + + ' ' + this.historypanel.data.selectors.hda.primaryActionButtons; + this.test.comment( 'Primary action buttons div should exist and be visible' ); + this.test.assertExists( buttonsSelector, 'Primary action buttons div exists' ); + this.test.assertVisible( buttonsSelector, 'Primary action buttons div is visible' ); +} + +function testSecondaryActionButtons( hdaSelector ){ + var buttonsSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.body + + ' ' + this.historypanel.data.selectors.hda.secondaryActionButtons; + this.test.comment( 'Secondary action buttons div should exist and be visible' ); + this.test.assertExists( buttonsSelector, 'Secondary action buttons div exists' ); + this.test.assertVisible( buttonsSelector, 'Secondary action buttons div is visible' ); +} + +function testPeek( hdaSelector, expectedPeekArray ){ + var peekSelector = hdaSelector + ' ' + this.historypanel.data.selectors.hda.body + + ' ' + this.historypanel.data.selectors.hda.peek; + this.test.comment( 'Peek div should exist and be visible' ); + this.test.assertExists( peekSelector, 'peek exists' ); + this.test.assertVisible( peekSelector, 'peek is visible' ); + expectedPeekArray.forEach( function( string, i ){ + spaceghost.test.assertSelectorHasText( peekSelector, string, 'peek has proper text (' + string + ')' ); + }); +} + +function testExpandedBody( hdaSelector, expectedSummaryTextArray, expectedInfoText, dbkeySetTo ){ + var body = hdaSelector + ' ' + this.historypanel.data.selectors.hda.body; + this.test.assertExists( body, 'body exists' ); + this.test.assertVisible( body, 'body is visible' ); + + //TODO: create api module, match with api history_contents + + this.test.comment( 'Summary should be displayed correctly' ); + var summary = body + ' ' + this.historypanel.data.selectors.hda.summary; + this.test.assertExists( summary, 'summary exists' ); + this.test.assertVisible( summary, 'summary is visible' ); + // summary text is broken up by whitespace making it inconv. to test in one go + expectedSummaryTextArray.forEach( function( string, i ){ + spaceghost.test.assertSelectorHasText( summary, string, 'summary has proper text (' + string + ')' ); + }); + this.debug( 'summary text: ' + this.fetchText( summary ) ); + + testDbkey.call( this, hdaSelector, dbkeySetTo ); + + this.test.comment( 'Info should be displayed correctly' ); + var info = body + ' ' + this.historypanel.data.selectors.hda.info; + this.test.assertExists( info, 'info exists' ); + this.test.assertVisible( info, 'info is visible' ); + this.test.assertSelectorHasText( info, expectedInfoText, + 'info has proper text (' + expectedInfoText + '): ' + this.fetchText( info ) ); + + testPrimaryActionButtons.call( this, hdaSelector ); + testSecondaryActionButtons.call( this, hdaSelector ); //TODO: isAnonymous + testPeek.call( this, hdaSelector, peekShouldBeArray ); +} + +// ------------------------------------------------------------------- ok state +spaceghost.then( function checkOkState(){ + this.test.comment( 'HDAs in the "ok" state should be well formed' ); + this.withFrame( this.selectors.frames.history, function(){ - var model = this.evaluate( function(){ - return Galaxy.currHistoryPanel.model.hdas.at( 0 ).attributes; + var uploadSelector = '#' + testUploadInfo.hdaElement.attributes.id; + this.test.assertVisible( uploadSelector, 'HDA is visible' ); + + this.test.comment( 'should have the proper state class' ); + var okStateClass = this.historypanel.data.selectors.hda.wrapper.stateClasses.ok, + uploadElement = this.getElementInfo( uploadSelector ); + this.test.assert( uploadElement.attributes['class'].indexOf( okStateClass ) !== -1, + 'HDA has "ok" state class' ); + + // since we're using css there's no great way to test state icon (.state-icon is empty) + + this.test.comment( 'should have proper title and hid' ); + testTitle.call( spaceghost, uploadSelector, testUploadInfo.hid, testUploadInfo.name ); + + this.test.comment( 'should have all of the three, main buttons' ); + testTitleButtonStructure.call( spaceghost, uploadSelector ); + + this.test.comment( 'body is not visible before clicking the hda title' ); + var body = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; + this.test.assertNotVisible( body, 'body is not visible' ); + + this.test.comment( 'clicking the hda title should expand its body' ); + var hdaTitle = uploadSelector + ' ' + this.historypanel.data.selectors.hda.title; + this.click( hdaTitle ); + this.wait( 500, function(){ + testExpandedBody.call( spaceghost, uploadSelector, summaryShouldBeArray, infoShouldBe, false ); }); - this.info( 'model:' + this.jsonStr( model ) ); }); }); +/* spaceghost.then( function checkNewState(){ this.test.comment( 'HDAs in the "new" state should be well formed' ); @@ -93,15 +289,10 @@ this.test.assertVisible( uploadSelector, 'HDA is visible' ); // should have proper title and hid - var titleSelector = uploadSelector + ' .historyItemTitle'; - this.test.assertVisible( titleSelector, 'HDA title is visible' ); - this.test.assertSelectorHasText( titleSelector, testUploadInfo.name, - 'HDA has proper title' ); - this.test.assertSelectorHasText( titleSelector, testUploadInfo.hid, - 'HDA has proper hid' ); + testTitle.call( spaceghost, uploadSelector, testUploadInfo.hid, testUploadInfo.name ); // should have the new state class - var newStateClass = 'historyItem-new', + var newStateClass = this.historypanel.data.selectors.hda.wrapper.stateClasses['new']; uploadElement = this.getElementInfo( uploadSelector ); this.test.assert( uploadElement.attributes['class'].indexOf( newStateClass ) !== -1, 'HDA has new state class' ); @@ -111,13 +302,13 @@ //this.test.assertVisible( stateIconSelector, 'HDA has proper hid' ); // should NOT have any of the three, main buttons - var buttonSelector = uploadSelector + ' .historyItemButtons a'; + var buttonSelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.titleButtons + ' a'; this.test.assertDoesntExist( buttonSelector, 'No display, edit, or delete buttons' ); // expand and check the body this.click( titleSelector ); this.wait( 500, function(){ - var bodySelector = uploadSelector + ' .historyItemBody'; + var bodySelector = uploadSelector + ' ' + this.historypanel.data.selectors.hda.body; this.test.assertVisible( bodySelector, 'HDA body is visible (after expanding)' ); var expectedBodyText = 'This is a new dataset'; @@ -130,8 +321,7 @@ }); }); }); - -// =================================================================== TESTS +*/ // =================================================================== diff -r 4827bed265e7563c58346654f5a668f5de6d9d68 -r c2f310489973fc2ba42e5289ccec3ed88a42aabc test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -79,7 +79,7 @@ this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); }); -// grab the history frame bounds for mouse later tests +// grab the history frame bounds for later mouse tests spaceghost.then( function(){ historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); diff -r 4827bed265e7563c58346654f5a668f5de6d9d68 -r c2f310489973fc2ba42e5289ccec3ed88a42aabc test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -136,12 +136,12 @@ }; //TODO!: this will break if the hda name has single or double quotes (which are permitted in names) -/** Find the id of the hda wrapper given the hda title and hid. +/** Find the DOM id of the hda wrapper given the hda title and hid. * @param {String} title the title of the hda * @param {Int} hid (optional) the hid of the hda to look for * @returns {String|null} DOM id of the historyItemWrapper found, null if not found */ -HistoryPanel.prototype.hdaIdByTitle = function hdaIdByTitle( title, hid ){ +HistoryPanel.prototype.hdaElementIdByTitle = function hdaElementIdByTitle( title, hid ){ var elementInfo = this.hdaElementInfoByTitle( title, hid ); return (( elementInfo && elementInfo.attributes && elementInfo.attributes.id )? ( elementInfo.attributes.id ):( null )); @@ -200,6 +200,49 @@ return spaceghost; }; +/** Hover over an element in the history panel. + * This is re-implemented here because element bounds in iframes are calc'd + * relative to the iframe - but mouse coords are not. Capture the iframe + * bounds first to re-calc for mouse coords + * @param {String} selector a css or xpath selector for an historyItemWrapper + * @param {Function} whenHovering a function to call after the hover (will be scoped to spaceghost) + * @param {ElementInfo} historyFrameInfo casper ElementInfo for the history iframe (optional) + * If undefined, hoverOver will use withFrame first and gather the information itself. + * Send in history iframe info if you're already in the frame when calling this. bleh. + */ +HistoryPanel.prototype.hoverOver = function hoverOver( selector, whenHovering, historyFrameInfo ){ + var spaceghost = this.spaceghost; + + // helper function + function hoverAndCallback( historyFrameInfo, selector, whenHovering ){ + // ...this suddenly started working when I upped the viewport size + //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); + var elementInfo = this.getElementInfo( selector ), + newCoords = { x: ( historyFrameInfo.x + elementInfo.x ), + y: ( historyFrameInfo.y + elementInfo.y ) }; + //this.debug( 'elementInfo:' + this.jsonStr( elementInfo ) ); + //this.debug( 'newCoords:' + this.jsonStr( newCoords ) ); + this.page.sendEvent( 'mousemove', newCoords.x + 1, newCoords.y + 1 ); + if( whenHovering ){ + whenHovering.call( this ); + } + } + + // complicated by iframes + // if no history frame info was passed - assume not in history frame already and move into using withFrame + if( !historyFrameInfo ){ + //TODO: move selector to data (use selectors.frames? ) + historyFrameInfo = spaceghost.getElementInfo( 'iframe[name="galaxy_history"]' ); + spaceghost.withFrame( spaceghost.selectors.frames.history, function inHistoryPanel(){ + hoverAndCallback.call( spaceghost, historyFrameInfo, selector, whenHovering ); + }); + + // otherwise, assume we're already 'in' the history frame and use the passed info + } else { + hoverAndCallback.call( spaceghost, historyFrameInfo, selector, whenHovering ); + } + //return spaceghost; +}; // =================================================================== SELECTORS //TODO: data is not a very good name @@ -219,9 +262,22 @@ wrapper : { stateClasses : { prefix : 'historyItem-', - ok : 'historyItem-ok' + ok : 'historyItem-ok', + 'new' : 'historyItem-new' } - } + }, + title : '.historyItemTitle', + titleButtons : '.historyItemButtons', + displayButton : '.icon-button.display', + editAttrButton : '.icon-button.edit', + deleteButton : '.icon-button.delete', + body : '.historyItemBody', + summary : '.hda-summary', + dbkey : '.metadata-dbkey', + info : '.hda-info', + primaryActionButtons : 'div[id^="primary-actions"]', + secondaryActionButtons : 'div[id^="secondary-actions"]', + peek : 'pre.peek' } }, labels : { @@ -247,6 +303,23 @@ emptyMsg : "Your history is empty. Click 'Get Data' on the left pane to start" }, hda : { + ok: { + tooltips : { + displayButton : 'Display data in browser', + editAttrButton : 'Edit Attributes', + deleteButton : 'Delete' + }, + hrefs : { + displayButton : '/datasets/%s/display', + editAttrButton : '/datasets/%s/edit', + deleteButton : '/datasets/%s/delete_async' + }, + nodeNames : { + displayButton : 'a', + editAttrButton : 'a', + deleteButton : 'a' + } + } } } }; diff -r 4827bed265e7563c58346654f5a668f5de6d9d68 -r c2f310489973fc2ba42e5289ccec3ed88a42aabc test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -136,7 +136,6 @@ this.debug( 'clientScripts:\n' + this.jsonStr( this.options.clientScripts ) ); this._loadModules(); - }; /** Allow CLI arguments to set options if the proper option name is used. @@ -415,6 +414,15 @@ }; // =================================================================== PAGE CONTROL +/** An override of casper.start for additional set up. + * (Currently only used to change viewport) + */ +SpaceGhost.prototype.start = function start(){ + var returned = Casper.prototype.start.apply( this, arguments ); + this.viewport( 1024, 728 ); + return returned; +}; + /** An override of casper.open specifically for Galaxy. * (Currently only used to change language headers) */ @@ -492,18 +500,20 @@ }); }; -/** Override capture to save to environ: GALAXY_TEST_SAVE (or passed in from CLI) - * @param {String} filename the image filename +/** Hover over an element. + * NOTE: not for use with iframes (main, tool, history) - they need to re-calc + * for the iframe bounds and should be implemented in their own modules + * @param {String} selector a css or xpath selector for an historyItemWrapper + * @param {Function} whenHovering a function to call after the hover (will be scoped to spaceghost) */ -SpaceGhost.prototype.capture = function capture( filename, clipRect_or_selector ){ - //TODO: override with saved output dir - if( clipRect_or_selector && ( !utils.isClipRect( clipRect_or_selector ) ) ){ - this.debug( "USING CAPTURE SELECTOR" ); - return this.captureSelector( filename, clipRect_or_selector ); - } - return Casper.prototype.capture.apply( this, arguments ); +SpaceGhost.prototype.hoverOver = function hoverOver( selector, whenHovering ){ + var elementInfo = this.getElementInfo( selector ); + this.page.sendEvent( 'mousemove', elementInfo.x + 1, elementInfo.y + 1 ); + whenHovering.call( this ); + return this; }; + // =================================================================== TESTING //TODO: form fill doesn't work as casperjs would want it - often a button -> controller url //TODO: saveScreenshot (to GALAXY_TEST_SAVE) @@ -591,6 +601,15 @@ }); }; +/** Assert that a given string (toSearch) contains some given string (searchFor). + * @param {String} toSearch the string to search + * @param {String} searchFor the string to search for + * @param {String} msg assertion msg to display + */ +SpaceGhost.prototype.assertTextContains = function assertTextContains( toSearch, searchFor, msg ){ + this.test.assert( toSearch.indexOf( searchFor ) !== -1, msg ); +}; + // =================================================================== CONVENIENCE /** Wraps casper.getElementInfo in try, returning null if element not found instead of erroring. * @param {String} selector css or xpath selector for the element to find @@ -619,6 +638,17 @@ // =================================================================== GALAXY CONVENIENCE // =================================================================== MISCELAIN +/** Override capture to save to environ: GALAXY_TEST_SAVE (or passed in from CLI) + * @param {String} filename the image filename + */ +SpaceGhost.prototype.capture = function capture( filename, clipRect_or_selector ){ + //TODO: override with saved output dir + if( clipRect_or_selector && ( !utils.isClipRect( clipRect_or_selector ) ) ){ + return this.captureSelector( filename, clipRect_or_selector ); + } + return Casper.prototype.capture.apply( this, arguments ); +}; + /** Pop all handlers for eventName from casper and return them in order. * @param {String} eventName the name of the event from which to remove handlers */ @@ -736,7 +766,7 @@ // =================================================================== TEST DATA // maintain selectors, labels, text here in one central location -//TODO: to separate file? +//TODO: to data SpaceGhost.prototype.selectors = { masthead : { userMenu : { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add a new ~/tool_shed/util/metadata_util.py component to contain all tool shed related repository metadata utility methods.
by commits-noreply＠bitbucket.org 13 Mar '13

13 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4827bed265e7/ changeset: 4827bed265e7 user: greg date: 2013-03-13 20:37:29 summary: Add a new ~/tool_shed/util/metadata_util.py component to contain all tool shed related repository metadata utility methods. affected #: 11 files diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 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 @@ -7,6 +7,7 @@ from galaxy.model.orm import or_ import tool_shed.util.shed_util as shed_util import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util from tool_shed.util import encoding_util from galaxy.webapps.tool_shed.util import workflow_util import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids @@ -380,16 +381,16 @@ when an admin is installing a new repository or reinstalling an uninstalled repository. """ shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, - repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) + metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=trans.app, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -1462,7 +1463,7 @@ @web.require_admin def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: - message, status = suc.reset_metadata_on_selected_repositories( trans, **kwd ) + message, status = metadata_util.reset_metadata_on_selected_repositories( trans, **kwd ) else: message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) @@ -1482,16 +1483,16 @@ tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) + metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: suc.update_in_shed_tool_config( trans.app, repository ) @@ -1687,16 +1688,16 @@ if repository.includes_data_managers: shed_util.remove_from_data_manager( trans.app, repository ) # Update the repository metadata. - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - changeset_revision=latest_changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) + metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + changeset_revision=latest_changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -3,6 +3,7 @@ from galaxy.web.base.controllers.admin import Admin from galaxy.util import inflector import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util import tool_shed.grids.admin_grids as admin_grids from galaxy import eggs @@ -301,7 +302,7 @@ @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: - message, status = suc.reset_metadata_on_selected_repositories( trans, **kwd ) + message, status = metadata_util.reset_metadata_on_selected_repositories( trans, **kwd ) else: message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -1,7 +1,8 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController -from tool_shed.util.shed_util_common import get_repository_by_name_and_owner, set_repository_metadata +from tool_shed.util.shed_util_common import get_repository_by_name_and_owner +from tool_shed.util.metadata_util import set_repository_metadata from galaxy import eggs eggs.require('mercurial') diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 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 @@ -11,6 +11,7 @@ from galaxy.util import json from galaxy.model.orm import and_, or_ import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util from tool_shed.util import encoding_util from galaxy.webapps.tool_shed.util import workflow_util from galaxy.webapps.tool_shed.util import common_util @@ -365,7 +366,7 @@ operation = kwd[ 'operation' ].lower() if operation == "preview_tools_in_changeset": repository = suc.get_repository_in_tool_shed( trans, repository_id ) - repository_metadata = suc.get_latest_repository_metadata( trans, repository.id ) + repository_metadata = metadata_util.get_latest_repository_metadata( trans, repository.id ) latest_installable_changeset_revision = repository_metadata.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', @@ -1914,7 +1915,7 @@ def reset_all_metadata( self, trans, id, **kwd ): # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. # It resets all metadata on the complete changelog for a single repository in the tool shed. - invalid_file_tups, metadata_dict = suc.reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) + invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) if invalid_file_tups: repository = suc.get_repository_in_tool_shed( trans, id ) message = suc.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict ) @@ -2082,7 +2083,7 @@ else: message += 'The selected files were deleted from the repository. ' kwd[ 'message' ] = message - suc.set_repository_metadata_due_to_new_tip( trans, repository, **kwd ) + metadata_util.set_repository_metadata_due_to_new_tip( trans, repository, **kwd ) else: message = "Select at least 1 file to delete from the repository before clicking Delete selected files." status = "error" diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 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 @@ -3,6 +3,7 @@ from galaxy import web, util from galaxy.datatypes import checkers import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util from galaxy import eggs eggs.require('mercurial') @@ -15,6 +16,26 @@ CHUNK_SIZE = 2**20 # 1Mb class UploadController( BaseUIController ): + def check_file_contents_for_email_alerts( self, trans ): + """ + See if any admin users have chosen to receive email alerts when a repository is updated. If so, the file contents of the update must be + checked for inappropriate content. + """ + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.email_alerts != None ): + email_alerts = json.from_json_string( repository.email_alerts ) + for user_email in email_alerts: + if user_email in admin_users: + return True + return False + def check_file_content_for_html_and_images( self, file_path ): + message = '' + if checkers.check_html( file_path ): + message = 'The file "%s" contains HTML content.\n' % str( file_path ) + elif checkers.check_image( file_path ): + message = 'The file "%s" contains image content.\n' % str( file_path ) + return message @web.expose @web.require_login( 'upload', use_panels=True ) def upload( self, trans, **kwd ): @@ -120,9 +141,9 @@ shutil.move( uploaded_file_name, full_path ) # See if any admin users have chosen to receive email alerts when a repository is # updated. If so, check every uploaded file to ensure content is appropriate. - check_contents = suc.check_file_contents( trans ) + check_contents = self.check_file_contents_for_email_alerts( trans ) if check_contents and os.path.isfile( full_path ): - content_alert_str = self.__check_file_content( full_path ) + content_alert_str = self.check_file_content_for_html_and_images( full_path ) else: content_alert_str = '' commands.add( repo.ui, repo, full_path ) @@ -166,7 +187,7 @@ else: message += " %d files were removed from the repository root. " % len( files_to_remove ) kwd[ 'message' ] = message - suc.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) + metadata_util.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) if repository.metadata_revisions: # A repository's metadata revisions are order descending by update_time, so the zeroth revision will be the tip just after an upload. metadata_dict = repository.metadata_revisions[0].metadata @@ -330,11 +351,11 @@ pass # See if any admin users have chosen to receive email alerts when a repository is # updated. If so, check every uploaded file to ensure content is appropriate. - check_contents = suc.check_file_contents( trans ) + check_contents = self.check_file_contents_for_email_alerts( trans ) for filename_in_archive in filenames_in_archive: # Check file content to ensure it is appropriate. if check_contents and os.path.isfile( filename_in_archive ): - content_alert_str += self.__check_file_content( filename_in_archive ) + content_alert_str += self.check_file_content_for_html_and_images( filename_in_archive ) commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ): # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries @@ -421,10 +442,3 @@ message = "Uploaded archives cannot contain hgrc files." return False, message return True, '' - def __check_file_content( self, file_path ): - message = '' - if checkers.check_html( file_path ): - message = 'The file "%s" contains HTML content.\n' % str( file_path ) - elif checkers.check_image( file_path ): - message = 'The file "%s" contains image content.\n' % str( file_path ) - return message diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -8,6 +8,7 @@ from galaxy.util.json import from_json_string, to_json_string import tool_shed.util.shed_util as shed_util import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util from galaxy.util.odict import odict from tool_shed.util import common_util @@ -179,16 +180,16 @@ else: print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=self.app, - repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) + metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=self.app, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -1,5 +1,6 @@ import tool_shed.util.shed_util as shed_util import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util def handle_repository_contents( app, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir, tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False ): @@ -9,16 +10,16 @@ """ sa_session = app.model.context.current shed_config_dict = app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=app, - repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) + metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=app, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict sa_session.add( tool_shed_repository ) sa_session.flush() diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 lib/tool_shed/grids/repository_review_grids.py --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -4,6 +4,7 @@ from galaxy.model.orm import and_, or_ from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util from galaxy import eggs eggs.require('mercurial') @@ -76,9 +77,9 @@ if repository_metadata_revisions: rval = '' for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + rev, label, changeset_revision = metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a> ' % \ ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval diff -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 -r 4827bed265e7563c58346654f5a668f5de6d9d68 lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -1,5 +1,6 @@ import os, logging import tool_shed.util.shed_util_common as suc +import tool_shed.util.metadata_util as metadata_util from galaxy.web.form_builder import SelectField def build_approved_select_field( trans, name, selected_value=None, for_component=True ): @@ -43,7 +44,7 @@ # Restrict the options to all revisions that have associated metadata. repository_metadata_revisions = repository.metadata_revisions for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) + rev, label, changeset_revision = metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, This diff is so big that we needed to truncate the remainder. 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: Comment out description for vcf to summary tree converter tool.
by commits-noreply＠bitbucket.org 13 Mar '13

13 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/185a0ed00d8f/ changeset: 185a0ed00d8f user: dan date: 2013-03-13 20:31:06 summary: Comment out description for vcf to summary tree converter tool. affected #: 1 file diff -r bdd46627880ce13479c49c065ee118952ba8e2f2 -r 185a0ed00d8f245aa4ec161ba134df38edf19f70 lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml +++ b/lib/galaxy/datatypes/converters/vcf_to_summary_tree_converter.xml @@ -1,5 +1,5 @@ <tool id="CONVERTER_vcf_to_summary_tree_0" name="Convert VCF to Summary Tree" version="1.0.0" hidden="true"> - <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> + <command interpreter="python">vcf_to_summary_tree_converter.py $input1 $output1</command><inputs><page> 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: Handle Updating Data Managers when installed from Tool Shed.
by commits-noreply＠bitbucket.org 13 Mar '13

13 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bdd46627880c/ changeset: bdd46627880c user: dan date: 2013-03-13 20:12:55 summary: Handle Updating Data Managers when installed from Tool Shed. affected #: 1 file diff -r 188400f16e5f997f16c2a31db99da55c37909d00 -r bdd46627880ce13479c49c065ee118952ba8e2f2 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 @@ -1683,6 +1683,9 @@ shed_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) suc.update_repository( repo, latest_ctx_rev ) tool_shed = suc.clean_tool_shed_url( tool_shed_url ) + # Remove old Data Manager entries + if repository.includes_data_managers: + shed_util.remove_from_data_manager( trans.app, repository ) # Update the repository metadata. metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, @@ -1715,6 +1718,11 @@ shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=False ) + # Add new Data Manager entries + if 'data_manager' in metadata_dict: + new_data_managers = shed_util.install_data_managers( trans.app, trans.app.config.shed_data_manager_config_file, metadata_dict, + repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), + repository, repository_tools_tups ) # Create tool_dependency records if necessary. if 'tool_dependencies' in metadata_dict: tool_dependencies = shed_util.create_tool_dependency_objects( trans.app, repository, relative_install_dir, set_status=False ) 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: Fix the json import in the new Galaxy bioatar controller.
by commits-noreply＠bitbucket.org 13 Mar '13

13 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/188400f16e5f/ changeset: 188400f16e5f user: greg date: 2013-03-13 19:52:42 summary: Fix the json import in the new Galaxy bioatar controller. affected #: 1 file diff -r 5a17ab5f5466eaf61e80d6efda90c394c601f4ad -r 188400f16e5f997f16c2a31db99da55c37909d00 lib/galaxy/webapps/galaxy/controllers/biostar.py --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -5,7 +5,7 @@ from galaxy.web.base.controller import BaseUIController, url_for, error, web import base64 -import json +from galaxy.util import json import hmac # Biostar requires all keys to be present, so we start with a template 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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galaxy-commits March 2013