May 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by Bitbucket 27 May '12

27 May '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c5ba3065b82e/ changeset: c5ba3065b82e user: jgoecks date: 2012-05-27 21:54:32 summary: Support for saving and validating different visualization types. affected #: 3 files diff -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -305,60 +305,64 @@ decoded_id = trans.security.decode_id( id ) vis = session.query( trans.model.Visualization ).get( decoded_id ) - # Decode the payload - decoded_payload = config # Create new VisualizationRevision that will be attached to the viz vis_rev = trans.model.VisualizationRevision() vis_rev.visualization = vis vis_rev.title = vis.title vis_rev.dbkey = dbkey + + # -- Validate config. -- + + if vis.type == 'trackster': + def unpack_track( track_json ): + """ Unpack a track from its json. """ + return { + "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), + "hda_ldda": track_json.get('hda_ldda', 'hda'), + "name": track_json['name'], + "track_type": track_json['track_type'], + "prefs": track_json['prefs'], + "mode": track_json['mode'], + "filters": track_json['filters'], + "tool_state": track_json['tool_state'] + } - def unpack_track( track_json ): - """ Unpack a track from its json. """ - return { - "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), - "hda_ldda": track_json.get('hda_ldda', 'hda'), - "name": track_json['name'], - "track_type": track_json['track_type'], - "prefs": track_json['prefs'], - "mode": track_json['mode'], - "filters": track_json['filters'], - "tool_state": track_json['tool_state'] - } + def unpack_collection( collection_json ): + """ Unpack a collection from its json. """ + unpacked_drawables = [] + drawables = collection_json[ 'drawables' ] + for drawable_json in drawables: + if 'track_type' in drawable_json: + drawable = unpack_track( drawable_json ) + else: + drawable = unpack_collection( drawable_json ) + unpacked_drawables.append( drawable ) + return { + "name": collection_json.get( 'name', '' ), + "obj_type": collection_json[ 'obj_type' ], + "drawables": unpacked_drawables, + "prefs": collection_json.get( 'prefs' , [] ), + "filters": collection_json.get( 'filters', None ) + } - def unpack_collection( collection_json ): - """ Unpack a collection from its json. """ - unpacked_drawables = [] - drawables = collection_json[ 'drawables' ] - for drawable_json in drawables: - if 'track_type' in drawable_json: - drawable = unpack_track( drawable_json ) - else: - drawable = unpack_collection( drawable_json ) - unpacked_drawables.append( drawable ) - return { - "name": collection_json.get( 'name', '' ), - "obj_type": collection_json[ 'obj_type' ], - "drawables": unpacked_drawables, - "prefs": collection_json.get( 'prefs' , [] ), - "filters": collection_json.get( 'filters', None ) - } + # TODO: unpack and validate bookmarks: + def unpack_bookmarks( bookmarks_json ): + return bookmarks_json - # TODO: unpack and validate bookmarks: - def unpack_bookmarks( bookmarks_json ): - return bookmarks_json - - # Unpack and validate view content. - view_content = unpack_collection( decoded_payload[ 'view' ] ) - bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] ) - vis_rev.config = { "view": view_content, "bookmarks": bookmarks } - # Viewport from payload - if 'viewport' in decoded_payload: - chrom = decoded_payload['viewport']['chrom'] - start = decoded_payload['viewport']['start'] - end = decoded_payload['viewport']['end'] - overview = decoded_payload['viewport']['overview'] - vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } + # Unpack and validate view content. + view_content = unpack_collection( config[ 'view' ] ) + bookmarks = unpack_bookmarks( config[ 'bookmarks' ] ) + vis_rev.config = { "view": view_content, "bookmarks": bookmarks } + # Viewport from payload + if 'viewport' in config: + chrom = config['viewport']['chrom'] + start = config['viewport']['start'] + end = config['viewport']['end'] + overview = config['viewport']['overview'] + vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } + elif type == 'circos': + # TODO. + pass vis.latest_revision = vis_rev session.add( vis_rev ) diff -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -234,6 +234,15 @@ rows.append( [location, name] ) return { 'data': rows } + # TODO: this is duplicated from visualization controller; remove it once + # routing incompatibilities have been resolved. + @web.json + def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): + """ + Save a visualization; if visualization does not have an ID, a new + visualization is created. Returns JSON of visualization. + """ + return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) @web.expose @web.require_login() @@ -409,11 +418,7 @@ result = data_provider.get_data( chrom, low, high, int( start_val ), int( max_vals ), **kwargs ) result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) return result - - @web.json - def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): - return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) - + @web.expose @web.require_login( "see all available libraries" ) def list_libraries( self, trans, **kwargs ): diff -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -349,7 +349,7 @@ def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="", visualization_type="" ): """ - Create a new visualization + Creates a new visualization or returns a form for creating visualization. """ visualization_title_err = visualization_slug_err = visualization_annotation_err = "" if trans.request.method == "POST": @@ -381,6 +381,14 @@ .add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err, help="A description of the visualization; annotation is shown alongside published visualizations."), template="visualization/create.mako" ) + + @web.json + def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): + """ + Save a visualization; if visualization does not have an ID, a new + visualization is created. Returns JSON of visualization. + """ + return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) @web.expose @web.require_login( "edit visualizations" ) https://bitbucket.org/galaxy/galaxy-central/changeset/03cb8ee86726/ changeset: 03cb8ee86726 user: jgoecks date: 2012-05-27 22:09:16 summary: Include 'mixin' in names of many common controller mixins. affected #: 22 files diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/tools/genome_index/__init__.py --- a/lib/galaxy/tools/genome_index/__init__.py +++ b/lib/galaxy/tools/genome_index/__init__.py @@ -3,7 +3,7 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.json import * -from galaxy.web.base.controller import UsesHistory +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.tools.data import ToolDataTableManager log = logging.getLogger(__name__) @@ -63,8 +63,6 @@ if gitd: destination = None - alldone = True - indexjobs = gitd.deferred.params[ 'indexjobs' ] tdtman = ToolDataTableManager() xmltree = tdtman.load_from_config_file(app.config.tool_data_table_config_path) for node in xmltree: @@ -165,14 +163,6 @@ self._check_link( fasta, target ) for line in location: self._add_line( line[ 'file' ], line[ 'line' ] ) - for indexjob in indexjobs: - js = sa_session.query( model.Job ).filter_by( id=indexjob ).first() - if js.state not in [ 'ok', 'done', 'error' ]: - alldone = False - if alldone: - gitd.deferred.state = 'ok' - sa_session.add( gitd.deferred ) - sa_session.flush() def _check_link( self, targetfile, symlink ): target = os.path.relpath( targetfile, os.path.dirname( symlink ) ) diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/tools/imp_exp/__init__.py --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -4,7 +4,7 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.json import * -from galaxy.web.base.controller import UsesHistory +from galaxy.web.base.controller import UsesHistoryMixin log = logging.getLogger(__name__) @@ -42,7 +42,7 @@ toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool log.debug( "Loaded history import tool: %s", history_imp_tool.id ) -class JobImportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): +class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that import a history from an archive. @@ -263,7 +263,7 @@ jiha.job.stderr += "Error cleaning up history import job: %s" % e db_session.flush() -class JobExportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): +class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that export a history to an archive. diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -10,7 +10,7 @@ log = logging.getLogger( __name__ ) -class DatasetsController( BaseAPIController, UsesHistoryDatasetAssociation ): +class DatasetsController( BaseAPIController, UsesHistoryMixinDatasetAssociationMixin ): @web.expose_api def index( self, trans, hda_id, **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -12,7 +12,7 @@ log = logging.getLogger( __name__ ) -class HistoriesController( BaseAPIController, UsesHistory ): +class HistoriesController( BaseAPIController, UsesHistoryMixin ): @web.expose_api def index( self, trans, deleted='False', **kwd ): @@ -153,7 +153,7 @@ POST /api/histories/deleted/{encoded_quota_id}/undelete Undeletes a quota """ - history = self.get_history( trans, id, check_ownership=True, check_accessible=False, deleted=True ) + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False, deleted=True ) history.deleted = False trans.sa_session.add( history ) trans.sa_session.flush() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -12,7 +12,7 @@ log = logging.getLogger( __name__ ) -class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory, UsesLibrary, UsesLibraryItems ): +class HistoryContentsController( BaseAPIController, UsesHistoryMixinDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems ): @web.expose_api def index( self, trans, history_id, **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/library_contents.py --- a/lib/galaxy/web/api/library_contents.py +++ b/lib/galaxy/web/api/library_contents.py @@ -10,7 +10,7 @@ log = logging.getLogger( __name__ ) -class LibraryContentsController( BaseAPIController, UsesLibrary, UsesLibraryItems ): +class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @web.expose_api def index( self, trans, library_id, **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/quotas.py --- a/lib/galaxy/web/api/quotas.py +++ b/lib/galaxy/web/api/quotas.py @@ -2,7 +2,7 @@ API operations on Quota objects. """ import logging -from galaxy.web.base.controller import BaseAPIController, Admin, UsesQuota, url_for +from galaxy.web.base.controller import BaseAPIController, Admin, UsesQuotaMixin, url_for from galaxy import web, util from elementtree.ElementTree import XML @@ -14,7 +14,7 @@ log = logging.getLogger( __name__ ) -class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): +class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ): @web.expose_api @web.require_admin def index( self, trans, deleted='False', **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -177,7 +177,11 @@ def not_implemented( self, trans, **kwd ): raise HTTPNotImplemented() -class SharableItemSecurity: +# +# -- Mixins for working with Galaxy objects. -- +# + +class SharableItemSecurityMixin: """ Mixin for handling security for sharable items. """ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ @@ -197,11 +201,7 @@ raise ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' ) return item -# -# TODO: need to move UsesHistory, etc. mixins to better location - perhaps lib/galaxy/model/XXX ? -# - -class UsesHistoryDatasetAssociation: +class UsesHistoryMixinDatasetAssociationMixin: """ Mixin for controllers that use HistoryDatasetAssociation objects. """ def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False ): """ Get an HDA object by id. """ @@ -259,14 +259,14 @@ truncated = False return truncated, dataset_data -class UsesLibrary: +class UsesLibraryMixin: def get_library( self, trans, id, check_ownership=False, check_accessible=True ): l = self.get_object( trans, id, 'Library' ) if check_accessible and not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), l ) ): error( "LibraryFolder is not accessible to the current user" ) return l -class UsesLibraryItems( SharableItemSecurity ): +class UsesLibraryMixinItems( SharableItemSecurityMixin ): def get_library_folder( self, trans, id, check_ownership=False, check_accessible=True ): return self.get_object( trans, id, 'LibraryFolder', check_ownership=False, check_accessible=check_accessible ) def get_library_dataset_dataset_association( self, trans, id, check_ownership=False, check_accessible=True ): @@ -274,7 +274,7 @@ def get_library_dataset( self, trans, id, check_ownership=False, check_accessible=True ): return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible ) -class UsesVisualization( SharableItemSecurity ): +class UsesVisualizationMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use Visualization objects. """ viz_types = [ "trackster", "circos" ] @@ -522,7 +522,7 @@ return visualization -class UsesStoredWorkflow( SharableItemSecurity ): +class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a StoredWorkflow from the database by id, verifying ownership. """ @@ -560,7 +560,7 @@ # Connections by input name step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) -class UsesHistory( SharableItemSecurity ): +class UsesHistoryMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use History objects. """ def get_history( self, trans, id, check_ownership=True, check_accessible=False, deleted=None ): """Get a History from the database by id, verifying ownership.""" @@ -580,7 +580,7 @@ query = query.filter( trans.model.Dataset.purged == False ) return query.all() -class UsesFormDefinitions: +class UsesFormDefinitionsMixin: """Mixin for controllers that use Galaxy form objects.""" def get_all_forms( self, trans, all_versions=False, filter=None, form_type='All' ): """ @@ -1342,7 +1342,7 @@ selected_value=selected_value, refresh_on_change=True ) -class Sharable: +class SharableMixin: """ Mixin for a controller that manages an item that can be shared. """ # -- Implemented methods. -- @@ -1433,7 +1433,7 @@ """ Return item based on id. """ raise "Unimplemented Method" -class UsesQuota( object ): +class UsesQuotaMixin( object ): def get_quota( self, trans, id, check_ownership=False, check_accessible=False, deleted=None ): return self.get_object( trans, id, 'Quota', check_ownership=False, check_accessible=False, deleted=deleted ) diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -428,7 +428,7 @@ def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ) -class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): +class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -150,7 +150,7 @@ .filter( model.History.deleted==False ) \ .filter( self.model_class.visible==True ) -class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHistoryDatasetAssociation, UsesItemRatings ): +class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryMixinDatasetAssociationMixin, UsesItemRatings ): stored_list_grid = HistoryDatasetAssociationListGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/external_service.py --- a/lib/galaxy/web/controllers/external_service.py +++ b/lib/galaxy/web/controllers/external_service.py @@ -63,7 +63,7 @@ grids.GridAction( "Create new external service", dict( controller='external_service', action='create_external_service' ) ) ] -class ExternalService( BaseUIController, UsesFormDefinitions ): +class ExternalService( BaseUIController, UsesFormDefinitionsMixin ): external_service_grid = ExternalServiceGrid() @web.expose diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -190,7 +190,7 @@ # A public history is published, has a slug, and is not deleted. return query.filter( self.model_class.published == True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) -class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRatings, UsesHistory ): +class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, UsesHistoryMixin ): @web.expose def index( self, trans ): return "" diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -68,7 +68,7 @@ pass os.rmdir( tmpd ) -class LibraryCommon( BaseUIController, UsesFormDefinitions ): +class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin ): @web.json def library_item_updates( self, trans, ids=None, states=None ): # Avoid caching diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -272,8 +272,8 @@ # Default behavior: _BaseHTMLProcessor.unknown_endtag( self, tag ) -class PageController( BaseUIController, Sharable, UsesAnnotations, UsesHistory, - UsesStoredWorkflow, UsesHistoryDatasetAssociation, UsesVisualization, UsesItemRatings ): +class PageController( BaseUIController, SharableMixin, UsesAnnotations, UsesHistoryMixin, + UsesStoredWorkflowMixin, UsesHistoryMixinDatasetAssociationMixin, UsesVisualizationMixin, UsesItemRatings ): _page_list = PageListGrid() _all_published_list = PageAllPublishedGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/request_type.py --- a/lib/galaxy/web/controllers/request_type.py +++ b/lib/galaxy/web/controllers/request_type.py @@ -72,7 +72,7 @@ grids.GridAction( "Create new request type", dict( controller='request_type', action='create_request_type' ) ) ] -class RequestType( BaseUIController, UsesFormDefinitions ): +class RequestType( BaseUIController, UsesFormDefinitionsMixin ): request_type_grid = RequestTypeGrid() @web.expose diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -94,7 +94,7 @@ return query return query.filter_by( sample_id=trans.security.decode_id( sample_id ) ) -class RequestsAdmin( BaseUIController, UsesFormDefinitions ): +class RequestsAdmin( BaseUIController, UsesFormDefinitionsMixin ): request_grid = AdminRequestsGrid() datatx_grid = DataTransferGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/requests_common.py --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -93,7 +93,7 @@ confirm="Samples cannot be added to this request after it is submitted. Click OK to submit." ) ] -class RequestsCommon( BaseUIController, UsesFormDefinitions ): +class RequestsCommon( BaseUIController, UsesFormDefinitionsMixin ): @web.json def sample_state_updates( self, trans, ids=None, states=None ): # Avoid caching diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -11,7 +11,7 @@ log = logging.getLogger( __name__ ) -class RootController( BaseUIController, UsesHistory, UsesAnnotations ): +class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ): @web.expose def default(self, trans, target1=None, target2=None, **kwd): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -163,7 +163,7 @@ def apply_query_filter( self, trans, query, **kwargs ): return query.filter( self.model_class.user_id == trans.user.id ) -class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetAssociation, Sharable ): +class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryMixinDatasetAssociationMixin, SharableMixin ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -38,7 +38,7 @@ def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) -class User( BaseUIController, UsesFormDefinitions ): +class User( BaseUIController, UsesFormDefinitionsMixin ): user_openid_grid = UserOpenIDGrid() installed_len_files = None diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -68,8 +68,8 @@ return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) -class VisualizationController( BaseUIController, Sharable, UsesAnnotations, - UsesHistoryDatasetAssociation, UsesVisualization, +class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations, + UsesHistoryMixinDatasetAssociationMixin, UsesVisualizationMixin, UsesItemRatings ): _user_list_grid = VisualizationListGrid() _published_list_grid = VisualizationAllPublishedGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -105,7 +105,7 @@ if self.cur_tag == self.target_tag: self.tag_content += text -class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAnnotations, UsesItemRatings ): +class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesAnnotations, UsesItemRatings ): stored_list_grid = StoredWorkflowListGrid() published_list_grid = StoredWorkflowAllPublishedGrid() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Provide generic support for saving visualizations.
by Bitbucket 27 May '12

27 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fdc3f20a46d3/ changeset: fdc3f20a46d3 user: jgoecks date: 2012-05-27 18:34:52 summary: Provide generic support for saving visualizations. affected #: 3 files diff -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -280,41 +280,91 @@ viz_types = [ "trackster", "circos" ] len_files = None - + def create_visualization( self, trans, title, slug, type, dbkey, annotation=None, config={} ): - user = trans.get_user() + """ Create visualiation and first revision. """ + visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation ) - # Error checking. - title_err = slug_err = "" - if not title: - title_err = "visualization name is required" - elif not slug: - slug_err = "visualization id is required" - elif not VALID_SLUG_RE.match( slug ): - slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" - elif trans.sa_session.query( trans.model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first(): - slug_err = "visualization id must be unique" - - if title_err or slug_err: - return { 'title_err': title_err, 'slug_err': slug_err } - - # Create visualization - visualization = trans.model.Visualization( user=user, title=title, slug=slug, dbkey=dbkey, type=type ) - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) - - # And the first visualization revision - revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config={}, dbkey=dbkey ) + # Create and save first visualization revision + revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config=config, dbkey=dbkey ) visualization.latest_revision = revision - - # Persist session = trans.sa_session - session.add(visualization) - session.add(revision) + session.add( revision ) session.flush() return visualization + + def save_visualization( self, trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None ): + session = trans.sa_session + + # Create/get visualization. + if not id: + # Create new visualization. + vis = self._create_visualization( trans, title, type, dbkey, slug, annotation ) + else: + decoded_id = trans.security.decode_id( id ) + vis = session.query( trans.model.Visualization ).get( decoded_id ) + + # Decode the payload + decoded_payload = config + # Create new VisualizationRevision that will be attached to the viz + vis_rev = trans.model.VisualizationRevision() + vis_rev.visualization = vis + vis_rev.title = vis.title + vis_rev.dbkey = dbkey + + def unpack_track( track_json ): + """ Unpack a track from its json. """ + return { + "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), + "hda_ldda": track_json.get('hda_ldda', 'hda'), + "name": track_json['name'], + "track_type": track_json['track_type'], + "prefs": track_json['prefs'], + "mode": track_json['mode'], + "filters": track_json['filters'], + "tool_state": track_json['tool_state'] + } + + def unpack_collection( collection_json ): + """ Unpack a collection from its json. """ + unpacked_drawables = [] + drawables = collection_json[ 'drawables' ] + for drawable_json in drawables: + if 'track_type' in drawable_json: + drawable = unpack_track( drawable_json ) + else: + drawable = unpack_collection( drawable_json ) + unpacked_drawables.append( drawable ) + return { + "name": collection_json.get( 'name', '' ), + "obj_type": collection_json[ 'obj_type' ], + "drawables": unpacked_drawables, + "prefs": collection_json.get( 'prefs' , [] ), + "filters": collection_json.get( 'filters', None ) + } + + # TODO: unpack and validate bookmarks: + def unpack_bookmarks( bookmarks_json ): + return bookmarks_json + + # Unpack and validate view content. + view_content = unpack_collection( decoded_payload[ 'view' ] ) + bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] ) + vis_rev.config = { "view": view_content, "bookmarks": bookmarks } + # Viewport from payload + if 'viewport' in decoded_payload: + chrom = decoded_payload['viewport']['chrom'] + start = decoded_payload['viewport']['start'] + end = decoded_payload['viewport']['end'] + overview = decoded_payload['viewport']['overview'] + vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } + + vis.latest_revision = vis_rev + session.add( vis_rev ) + session.flush() + encoded_id = trans.security.encode_id( vis.id ) + return { "vis_id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } def _get_dbkeys( self, trans ): """ Returns all valid dbkeys that a user can use in a visualization. """ @@ -432,6 +482,41 @@ config['viewport'] = latest_revision.config['viewport'] return config + + # -- Helper functions -- + + def _create_visualization( self, trans, title, type, dbkey, slug=None, annotation=None ): + """ Create visualization but not first revision. Returns Visualization object. """ + user = trans.get_user() + + # Error checking. + title_err = slug_err = "" + if not title: + title_err = "visualization name is required" + elif slug and not VALID_SLUG_RE.match( slug ): + slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" + elif slug and trans.sa_session.query( trans.model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first(): + slug_err = "visualization identifier must be unique" + + if title_err or slug_err: + return { 'title_err': title_err, 'slug_err': slug_err } + + + # Create visualization + visualization = trans.model.Visualization( user=user, title=title, dbkey=dbkey, type=type ) + if slug: + visualization.slug = slug + else: + self.create_item_slug( trans.sa_session, visualization ) + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) + + session = trans.sa_session + session.add( visualization ) + session.flush() + + return visualization class UsesStoredWorkflow( SharableItemSecurity ): """ Mixin for controllers that use StoredWorkflow objects. """ @@ -1255,7 +1340,9 @@ class Sharable: """ Mixin for a controller that manages an item that can be shared. """ - # Implemented methods. + + # -- Implemented methods. -- + @web.expose @web.require_login( "share Galaxy items" ) def set_public_username( self, trans, id, username, **kwargs ): @@ -1268,42 +1355,50 @@ trans.sa_session.flush return self.sharing( trans, id, **kwargs ) - # Abstract methods. + # -- Abstract methods. -- + @web.expose @web.require_login( "modify Galaxy items" ) def set_slug_async( self, trans, id, new_slug ): """ Set item slug asynchronously. """ raise "Unimplemented Method" + @web.expose @web.require_login( "share Galaxy items" ) def sharing( self, trans, id, **kwargs ): """ Handle item sharing. """ raise "Unimplemented Method" + @web.expose @web.require_login( "share Galaxy items" ) def share( self, trans, id=None, email="", **kwd ): """ Handle sharing an item with a particular user. """ raise "Unimplemented Method" + @web.expose def display_by_username_and_slug( self, trans, username, slug ): """ Display item by username and slug. """ raise "Unimplemented Method" - @web.expose + @web.json @web.require_login( "get item name and link" ) def get_name_and_link_async( self, trans, id=None ): """ Returns item's name and link. """ raise "Unimplemented Method" + @web.expose @web.require_login("get item content asynchronously") def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ raise "Unimplemented Method" - # Helper methods. + + # -- Helper methods. -- + def _make_item_accessible( self, sa_session, item ): """ Makes item accessible--viewable and importable--and sets item's slug. Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes. """ item.importable = True self.create_item_slug( sa_session, item ) + def create_item_slug( self, sa_session, item ): """ Create item slug. Slug is unique among user's importable items for item's class. Returns true if item's slug was set; false otherwise. """ if item.slug is None or item.slug == "": @@ -1323,12 +1418,13 @@ slug = slug_base count = 1 while sa_session.query( item.__class__ ).filter_by( user=item.user, slug=slug, importable=True ).count() != 0: - # Slug taken; choose a new slug based on count. This approach can handle numerous histories with the same name gracefully. + # Slug taken; choose a new slug based on count. This approach can handle numerous items with the same name gracefully. slug = '%s-%i' % ( slug_base, count ) count += 1 item.slug = slug return True return False + def get_item( self, trans, id ): """ Return item based on id. """ raise "Unimplemented Method" diff -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -163,7 +163,7 @@ def apply_query_filter( self, trans, query, **kwargs ): return query.filter( self.model_class.user_id == trans.user.id ) -class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetAssociation ): +class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetAssociation, Sharable ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. @@ -411,83 +411,8 @@ return result @web.json - def save( self, trans, **kwargs ): - session = trans.sa_session - vis_id = "undefined" - if 'vis_id' in kwargs: - vis_id = kwargs['vis_id'].strip('"') - dbkey = kwargs['dbkey'] - # Lookup or create Visualization object - if vis_id == "undefined": # new vis - vis = model.Visualization() - vis.user = trans.user - vis.title = kwargs['title'] - vis.type = "trackster" - vis.dbkey = dbkey - session.add( vis ) - else: - decoded_id = trans.security.decode_id( vis_id ) - vis = session.query( model.Visualization ).get( decoded_id ) - # Decode the payload - decoded_payload = simplejson.loads( kwargs['payload'] ) - # Create new VisualizationRevision that will be attached to the viz - vis_rev = model.VisualizationRevision() - vis_rev.visualization = vis - vis_rev.title = vis.title - vis_rev.dbkey = dbkey - - def unpack_track( track_json ): - """ Unpack a track from its json. """ - return { - "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), - "hda_ldda": track_json.get('hda_ldda', "hda"), - "name": track_json['name'], - "track_type": track_json['track_type'], - "prefs": track_json['prefs'], - "mode": track_json['mode'], - "filters": track_json['filters'], - "tool_state": track_json['tool_state'] - } - - def unpack_collection( collection_json ): - """ Unpack a collection from its json. """ - unpacked_drawables = [] - drawables = collection_json[ 'drawables' ] - for drawable_json in drawables: - if 'track_type' in drawable_json: - drawable = unpack_track( drawable_json ) - else: - drawable = unpack_collection( drawable_json ) - unpacked_drawables.append( drawable ) - return { - "name": collection_json.get( 'name', '' ), - "obj_type": collection_json[ 'obj_type' ], - "drawables": unpacked_drawables, - "prefs": collection_json.get( 'prefs' , [] ), - "filters": collection_json.get( 'filters', None ) - } - - # TODO: unpack and validate bookmarks: - def unpack_bookmarks( bookmarks_json ): - return bookmarks_json - - # Unpack and validate view content. - view_content = unpack_collection( decoded_payload[ 'view' ] ) - bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] ) - vis_rev.config = { "view": view_content, "bookmarks": bookmarks } - # Viewport from payload - if 'viewport' in decoded_payload: - chrom = decoded_payload['viewport']['chrom'] - start = decoded_payload['viewport']['start'] - end = decoded_payload['viewport']['end'] - overview = decoded_payload['viewport']['overview'] - vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } - - vis.latest_revision = vis_rev - session.add( vis_rev ) - session.flush() - encoded_id = trans.security.encode_id(vis.id) - return { "vis_id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } + def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): + return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) @web.expose @web.require_login( "see all available libraries" ) diff -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -209,10 +209,11 @@ url: "${h.url_for( action='save' )}", type: "POST", data: { - 'vis_id': view.vis_id, + 'id': view.vis_id, 'title': view.name, 'dbkey': view.dbkey, - 'payload': JSON.stringify(payload) + 'type': 'trackster', + 'config': JSON.stringify(payload) }, dataType: "json", success: function(vis_info) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Provide a modified check_galaxy.py that is suitable for use with nagios.
by Bitbucket 26 May '12

26 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f4c4ba7be3d1/ changeset: f4c4ba7be3d1 user: natefoo date: 2012-05-26 21:00:36 summary: Provide a modified check_galaxy.py that is suitable for use with nagios. affected #: 3 files diff -r 62bdb265d3007d4f761a1defa82a44d888c30bfd -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 contrib/nagios/README --- /dev/null +++ b/contrib/nagios/README @@ -0,0 +1,1 @@ +Nagios checks for Galaxy. check_galaxy is used to call check_galaxy.py. diff -r 62bdb265d3007d4f761a1defa82a44d888c30bfd -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 contrib/nagios/check_galaxy --- /dev/null +++ b/contrib/nagios/check_galaxy @@ -0,0 +1,40 @@ +#!/bin/sh + +if [ -z "$3" ]; then + echo "usage: check_galaxy <server><username><password>" + exit 3 +fi + +here=`dirname $0` +var="$HOME/.check_galaxy/$1" + +touch $var/iterations +iterations=`cat $var/iterations` +if [ -z "$iterations" ]; then + iterations=0 +fi + +new_history='' +if [ $iterations -gt 96 ]; then + new_history='-n' + echo 0 > $var/iterations +else + echo `expr $iterations + 1` > $var/iterations +fi + +date >> $var/log +status=`python $here/check_galaxy.py $new_history $1 $2 $3 2>&1 | tee -a $var/log | tail -n 1` + +echo "$status" + +case "$status" in + "Exception: Tool never finished") + exit 1 + ;; + "OK") + exit 0 + ;; + *) + exit 2 + ;; +esac diff -r 62bdb265d3007d4f761a1defa82a44d888c30bfd -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 contrib/nagios/check_galaxy.py --- /dev/null +++ b/contrib/nagios/check_galaxy.py @@ -0,0 +1,393 @@ +#!/usr/bin/env python +""" +check_galaxy can be run by hand, although it is meant to run from cron +via the check_galaxy.sh script in Galaxy's cron/ directory. +""" + +import socket, sys, os, time, tempfile, filecmp, htmllib, formatter, getopt +from user import home + +import warnings +with warnings.catch_warnings(): + warnings.simplefilter('ignore') + import twill + import twill.commands as tc + +# options +if os.environ.has_key( "DEBUG" ): + debug = os.environ["DEBUG"] +else: + debug = False + +test_data_dir = os.path.join( os.path.dirname( __file__ ), 'check_galaxy_data' ) +# what tools to run - not so pretty +tools = { + "Extract+genomic+DNA+1" : + [ + { + "inputs" : + ( + { + "file_path" : os.path.join( test_data_dir, "1.bed" ), + "dbkey" : "hg17", + }, + + ) + }, + { "check_file" : os.path.join( test_data_dir, "extract_genomic_dna_out1.fasta" ) }, + { + "tool_run_options" : + { + "input" : "1.bed", + "interpret_features" : "yes", + "index_source" : "cached", + "out_format" : "fasta" + } + } + ] +} + +# handle arg(s) +def usage(): + print "usage: check_galaxy.py <server><username><password>" + sys.exit(1) + +try: + opts, args = getopt.getopt( sys.argv[1:], 'n' ) +except getopt.GetoptError, e: + print str(e) + usage() +if len( args ) < 1: + usage() +server = args[0] +username = args[1] +password = args[2] + +if server.endswith(".g2.bx.psu.edu"): + if debug: + print "Checking a PSU Galaxy server, using maint file" + maint = "/errordocument/502/%s/maint" % args[0].split('.', 1)[0] +else: + maint = None + +new_history = False +for o, a in opts: + if o == "-n": + if debug: + print "Specified -n, will create a new history" + new_history = True + else: + usage() + +# state information +var_dir = os.path.join( home, ".check_galaxy", server ) +if not os.access( var_dir, os.F_OK ): + os.makedirs( var_dir, 0700 ) + +# default timeout for twill browser is never +socket.setdefaulttimeout(300) + +# user-agent +tc.agent("Mozilla/5.0 (compatible; check_galaxy/0.1)") +tc.config('use_tidy', 0) + +class Browser: + + def __init__(self): + self.server = server + self.maint = maint + self.tool = None + self.tool_opts = None + self.id = None + self.status = None + self.check_file = None + self.hid = None + self.cookie_jar = os.path.join( var_dir, "cookie_jar" ) + dprint("cookie jar path: %s" % self.cookie_jar) + if not os.access(self.cookie_jar, os.R_OK): + dprint("no cookie jar at above path, creating") + tc.save_cookies(self.cookie_jar) + tc.load_cookies(self.cookie_jar) + + def get(self, path): + tc.go("http://%s%s" % (self.server, path)) + tc.code(200) + + def reset(self): + self.tool = None + self.tool_opts = None + self.id = None + self.status = None + self.check_file = None + self.delete_datasets() + self.get("/root/history") + p = didParser() + p.feed(tc.browser.get_html()) + if len(p.dids) > 0: + print "Remaining datasets ids:", " ".join( p.dids ) + raise Exception, "History still contains datasets after attempting to delete them" + if new_history: + self.get("/history/delete_current") + tc.save_cookies(self.cookie_jar) + + def check_redir(self, url): + try: + tc.get_browser()._browser.set_handle_redirect(False) + tc.go(url) + tc.code(302) + tc.get_browser()._browser.set_handle_redirect(True) + dprint( "%s is returning redirect (302)" % url ) + return(True) + except twill.errors.TwillAssertionError, e: + tc.get_browser()._browser.set_handle_redirect(True) + dprint( "%s is not returning redirect (302): %s" % (url, e) ) + code = tc.browser.get_code() + if code == 502: + is_maint = self.check_maint() + if is_maint: + dprint( "Galaxy is down, but a maint file was found, so not sending alert" ) + sys.exit(0) + else: + print "Galaxy is down (code 502)" + sys.exit(1) + return(False) + + # checks for a maint file + def check_maint(self): + if self.maint is None: + #dprint( "Warning: unable to check maint file for %s" % self.server ) + return(False) + try: + self.get(self.maint) + return(True) + except twill.errors.TwillAssertionError, e: + return(False) + + def login(self, user, pw): + self.get("/user/login") + tc.fv("1", "email", user) + tc.fv("1", "password", pw) + tc.submit("Login") + tc.code(200) + if len(tc.get_browser().get_all_forms()) > 0: + # uh ohs, fail + p = userParser() + p.feed(tc.browser.get_html()) + if p.no_user: + dprint("user does not exist, will try creating") + self.create_user(user, pw) + elif p.bad_pw: + raise Exception, "Password is incorrect" + else: + raise Exception, "Unknown error logging in" + tc.save_cookies(self.cookie_jar) + + def create_user(self, user, pw): + self.get("/user/create") + tc.fv("1", "email", user) + tc.fv("1", "password", pw) + tc.fv("1", "confirm", pw) + tc.submit("Submit") + tc.code(200) + if len(tc.get_browser().get_all_forms()) > 0: + p = userParser() + p.feed(tc.browser.get_html()) + if p.already_exists: + raise Exception, 'The user you were trying to create already exists' + + def upload(self, input): + self.get("/tool_runner/index?tool_id=upload1") + tc.fv("1","file_type", "bed") + tc.fv("1","dbkey", input.get('dbkey', '?')) + tc.formfile("1","file_data", input['file_path']) + tc.submit("runtool_btn") + tc.code(200) + + def runtool(self): + self.get("/tool_runner/index?tool_id=%s" % self.tool) + for k, v in self.tool_opts.items(): + tc.fv("1", k, v) + tc.submit("runtool_btn") + tc.code(200) + + def wait(self): + sleep_amount = 1 + count = 0 + maxiter = 16 + while count < maxiter: + count += 1 + self.get("/root/history") + page = tc.browser.get_html() + if page.find( '' ) > -1: + time.sleep( sleep_amount ) + sleep_amount += 1 + else: + break + if count == maxiter: + raise Exception, "Tool never finished" + + def check_status(self): + self.get("/root/history") + p = historyParser() + p.feed(tc.browser.get_html()) + if p.status != "ok": + self.get("/datasets/%s/stderr" % p.id) + print tc.browser.get_html() + raise Exception, "HDA %s NOT OK: %s" % (p.id, p.status) + self.id = p.id + self.status = p.status + #return((p.id, p.status)) + + def diff(self): + self.get("/datasets/%s/display?to_ext=%s" % (self.id, self.tool_opts.get('out_format', 'fasta'))) + data = tc.browser.get_html() + tmp = tempfile.mkstemp() + dprint("tmp file: %s" % tmp[1]) + tmpfh = os.fdopen(tmp[0], 'w') + tmpfh.write(data) + tmpfh.close() + if filecmp.cmp(tmp[1], self.check_file): + dprint("Tool output is as expected") + else: + if not debug: + os.remove(tmp[1]) + raise Exception, "Tool output differs from expected" + if not debug: + os.remove(tmp[1]) + + def delete_datasets(self): + self.get("/root/history") + p = didParser() + p.feed(tc.browser.get_html()) + dids = p.dids + for did in dids: + self.get("/datasets/%s/delete" % did) + + def check_if_logged_in(self): + self.get("/user?cntrller=user") + p = loggedinParser() + p.feed(tc.browser.get_html()) + return p.logged_in + +class userParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.in_span = False + self.in_div = False + self.no_user = False + self.bad_pw = False + self.already_exists = False + def start_span(self, attrs): + self.in_span = True + def start_div(self, attrs): + self.in_div = True + def end_span(self): + self.in_span = False + def end_div(self): + self.in_div = False + def handle_data(self, data): + if self.in_span or self.in_div: + if data == "No such user (please note that login is case sensitive)": + self.no_user = True + elif data == "Invalid password": + self.bad_pw = True + elif data == "User with that email already exists": + self.already_exists = True + +class historyParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.status = None + self.id = None + def start_div(self, attrs): + # find the top history item + for i in attrs: + if i[0] == "class" and i[1].startswith("historyItemWrapper historyItem historyItem-"): + self.status = i[1].rsplit("historyItemWrapper historyItem historyItem-", 1)[1] + dprint("status: %s" % self.status) + if i[0] == "id" and i[1].startswith("historyItem-"): + self.id = i[1].rsplit("historyItem-", 1)[1] + dprint("id: %s" % self.id) + if self.status is not None: + self.reset() + +class didParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.dids = [] + def start_div(self, attrs): + for i in attrs: + if i[0] == "id" and i[1].startswith("historyItemContainer-"): + self.dids.append( i[1].rsplit("historyItemContainer-", 1)[1] ) + dprint("got a dataset id: %s" % self.dids[-1]) + +class loggedinParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.in_p = False + self.logged_in = False + def start_p(self, attrs): + self.in_p = True + def end_p(self): + self.in_p = False + def handle_data(self, data): + if self.in_p: + if data == "You are currently not logged in.": + self.logged_in = False + elif data.startswith( "You are currently logged in as " ): + self.logged_in = True + +def dprint(str): + if debug: + print str + +# do stuff here +if __name__ == "__main__": + + dprint("checking %s" % server) + + b = Browser() + + # login (or not) + if b.check_if_logged_in(): + dprint("we are already logged in (via cookies), hooray!") + else: + dprint("not logged in... logging in") + b.login(username, password) + + for tool, params in tools.iteritems(): + + check_file = "" + + # make sure history and state is clean + b.reset() + b.tool = tool + + # get all the tool run conditions + for dict in params: + for k, v in dict.items(): + if k == 'inputs': + for input in v: + b.upload(input) + b.wait() + elif k == 'check_file': + b.check_file = v + elif k == 'tool_run_options': + b.tool_opts = v + else: + raise Exception, "Unknown key in tools dict: %s" % k + + b.runtool() + b.wait() + b.check_status() + b.diff() + b.delete_datasets() + + # by this point, everything else has succeeded. there should be no maint. + is_maint = b.check_maint() + if is_maint: + print "Galaxy is up and fully functional, but a maint file is in place." + sys.exit(1) + + print "OK" + sys.exit(0) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Infrastructure for managing visualizations: (a) support for creating multiple types of visualizations; (b) a placeholder visualization API controller; (c) abstract visualization creation so that it can be reused in multiple controllers.
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/62bdb265d300/ changeset: 62bdb265d300 user: jgoecks date: 2012-05-26 00:23:43 summary: Infrastructure for managing visualizations: (a) support for creating multiple types of visualizations; (b) a placeholder visualization API controller; (c) abstract visualization creation so that it can be reused in multiple controllers. affected #: 6 files diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2445,12 +2445,13 @@ self.user = None class Visualization( object ): - def __init__( self, user=None, type=None, title=None, dbkey=None, latest_revision=None ): + def __init__( self, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None ): self.id = None self.user = user self.type = type self.title = title self.dbkey = dbkey + self.slug = slug self.latest_revision = latest_revision self.revisions = [] if self.latest_revision: diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/visualization/__init__.py --- a/lib/galaxy/visualization/__init__.py +++ b/lib/galaxy/visualization/__init__.py @@ -1,3 +1,3 @@ """ Package for Galaxy visualization plugins. -""" \ No newline at end of file +""" diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/api/visualizations.py --- /dev/null +++ b/lib/galaxy/web/api/visualizations.py @@ -0,0 +1,28 @@ +from galaxy import web +from galaxy.web.base.controller import BaseController, BaseAPIController + +class VisualizationsController( BaseAPIController ): + """ + RESTful controller for interactions with visualizations. + """ + + @web.expose_api + def index( self, trans, **kwds ): + """ + GET /api/visualizations: + """ + pass + + @web.json + def show( self, trans, id, **kwd ): + """ + GET /api/visualizations/{viz_id} + """ + pass + + @web.expose_api + def create( self, trans, payload, **kwd ): + """ + POST /api/visualizations + """ + pass \ No newline at end of file diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -7,6 +7,7 @@ from galaxy import config, tools, web, util from galaxy.util import inflector from galaxy.util.hash_util import * +from galaxy.util.sanitize_html import sanitize_html from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.workflow.modules import * @@ -275,8 +276,45 @@ class UsesVisualization( SharableItemSecurity ): """ Mixin for controllers that use Visualization objects. """ + + viz_types = [ "trackster", "circos" ] len_files = None + + def create_visualization( self, trans, title, slug, type, dbkey, annotation=None, config={} ): + user = trans.get_user() + + # Error checking. + title_err = slug_err = "" + if not title: + title_err = "visualization name is required" + elif not slug: + slug_err = "visualization id is required" + elif not VALID_SLUG_RE.match( slug ): + slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" + elif trans.sa_session.query( trans.model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first(): + slug_err = "visualization id must be unique" + + if title_err or slug_err: + return { 'title_err': title_err, 'slug_err': slug_err } + + # Create visualization + visualization = trans.model.Visualization( user=user, title=title, slug=slug, dbkey=dbkey, type=type ) + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) + + # And the first visualization revision + revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config={}, dbkey=dbkey ) + visualization.latest_revision = revision + + # Persist + session = trans.sa_session + session.add(visualization) + session.add(revision) + session.flush() + + return visualization def _get_dbkeys( self, trans ): """ Returns all valid dbkeys that a user can use in a visualization. """ diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -132,6 +132,7 @@ webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) + webapp.api_mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -4,7 +4,6 @@ from galaxy.web.framework.helpers import time_ago, grids, iff from galaxy.util.sanitize_html import sanitize_html - class VisualizationListGrid( grids.Grid ): # Grid definition title = "Saved Visualizations" @@ -14,6 +13,7 @@ columns = [ grids.TextColumn( "Title", key="title", attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), + grids.TextColumn( "Type", key="type" ), grids.TextColumn( "Dbkey", key="dbkey" ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), @@ -346,51 +346,31 @@ @web.expose @web.require_login( "create visualizations" ) - def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="" ): + def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="", + visualization_type="" ): """ Create a new visualization """ - user = trans.get_user() visualization_title_err = visualization_slug_err = visualization_annotation_err = "" if trans.request.method == "POST": - if not visualization_title: - visualization_title_err = "visualization name is required" - elif not visualization_slug: - visualization_slug_err = "visualization id is required" - elif not VALID_SLUG_RE.match( visualization_slug ): - visualization_slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" - elif trans.sa_session.query( model.Visualization ).filter_by( user=user, slug=visualization_slug, deleted=False ).first(): - visualization_slug_err = "visualization id must be unique" + rval = self.create_visualization( trans, title=visualization_title, + slug=visualization_slug, + annotation=visualization_annotation, + dbkey=visualization_dbkey, + type=visualization_type ) + if isinstance( rval, dict ): + # Found error creating viz. + visualization_title_err = rval[ 'title_err' ] + visualization_slug_err = rval[ 'slug_err' ] else: - # Create the new stored visualization - visualization = model.Visualization() - visualization.title = visualization_title - visualization.slug = visualization_slug - visualization.dbkey = visualization_dbkey - visualization.type = 'trackster' # HACK: set visualization type to trackster since it's the only viz - visualization_annotation = sanitize_html( visualization_annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), visualization, visualization_annotation ) - visualization.user = user - - # And the first (empty) visualization revision - visualization_revision = model.VisualizationRevision() - visualization_revision.title = visualization_title - visualization_revision.config = {} - visualization_revision.dbkey = visualization_dbkey - visualization_revision.visualization = visualization - visualization.latest_revision = visualization_revision - - # Persist - session = trans.sa_session - session.add(visualization) - session.add(visualization_revision) - session.flush() - + # Successfully created viz. return trans.response.send_redirect( web.url_for( action='list' ) ) - + + viz_type_options = [ ( t, t ) for t in self.viz_types ] return trans.show_form( web.FormBuilder( web.url_for(), "Create new visualization", submit_text="Submit" ) .add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err ) + .add_select( "visualization_type", "Type", options=viz_type_options, error=None ) .add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err, help="""A unique identifier that will be used for public links to this visualization. A default is generated 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: jgoecks: Partial implementation of Circos visualization using D3.
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4288ffb1bd16/ changeset: 4288ffb1bd16 user: jgoecks date: 2012-05-25 21:13:25 summary: Partial implementation of Circos visualization using D3. affected #: 7 files Diff too large to display. 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: guru: Suppressed R package-loading messages which were previously being written into stderr
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8cbbb813f286/ changeset: 8cbbb813f286 user: guru date: 2012-05-25 16:54:03 summary: Suppressed R package-loading messages which were previously being written into stderr affected #: 1 file diff -r 8335baa6881520cabfd3eb41986d7df203dc3183 -r 8cbbb813f2865de22ff671c980816cde5e225be5 tools/regVariation/logistic_regression_vif.py --- a/tools/regVariation/logistic_regression_vif.py +++ b/tools/regVariation/logistic_regression_vif.py @@ -5,16 +5,10 @@ from rpy import * import numpy -#export PYTHONPATH=~/galaxy/lib/ - def stop_err(msg): sys.stderr.write(msg) sys.exit() -#infile = 'logreg_inp.tab' -#y_col=3 -#x_cols=[1,2,3] -#outfile='logreg_out.txt' -#python logistic_regression_vif.py logreg_inp.tab 4 1,2,3 logreg_out2.tabular # running test + infile = sys.argv[1] y_col = int(sys.argv[2])-1 x_cols = sys.argv[3].split(',') @@ -84,17 +78,11 @@ set_default_mode(NO_CONVERSION) try: linear_model = r.glm(r("y ~ x"), data = r.na_exclude(dat),family="binomial") - #r('library(car)') - #r.assign('dat',dat) - #r.assign('ncols',len(x_cols)) - #r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')).as_py() - except RException, rex: stop_err("Error performing logistic regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.") if len(x_cols)>1: try: - - r('library(car)') + r('suppressPackageStartupMessages(library(car))') r.assign('dat',dat) r.assign('ncols',len(x_cols)) vif=r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')) @@ -163,9 +151,6 @@ rsq= r.round(float((null_deviance-residual_deviance)/null_deviance), digits=5) null_deviance= r.round(float(null_deviance), digits=5) residual_deviance= r.round(float(residual_deviance), digits=5) - - #rsq = r.round(float(rsq), digits=5) - except: pass 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: fubar: Reverse order of job manager and instance in warning
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8335baa68815/ changeset: 8335baa68815 user: fubar date: 2012-05-25 07:48:49 summary: Reverse order of job manager and instance in warning affected #: 1 file diff -r 3f1150fee33c6d7270549e0760fd84b7c35fdb50 -r 8335baa6881520cabfd3eb41986d7df203dc3183 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2380,7 +2380,7 @@ msg = None status = None if self.app.config.job_manager != self.app.config.server_name: - return trans.show_error_message( 'This Galaxy instance (%s) is not the job manager (%s). If using multiple servers, please directly access the job manager instance to manage jobs.' % ( self.app.config.job_manager,self.app.config.server_name) ) + return trans.show_error_message( 'This Galaxy instance (%s) is not the job manager (%s). If using multiple servers, please directly access the job manager instance to manage jobs.' % (self.app.config.server_name, self.app.config.job_manager) ) job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated' 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: fubar: Fix for bogus double negative compare - allows job management from admin screen when only one job manager running
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f1150fee33c/ changeset: 3f1150fee33c user: fubar date: 2012-05-25 07:40:44 summary: Fix for bogus double negative compare - allows job management from admin screen when only one job manager running affected #: 1 file diff -r 3fa05d052e820d21f1a6e5ae206d90edcc1a8782 -r 3f1150fee33c6d7270549e0760fd84b7c35fdb50 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2379,8 +2379,8 @@ deleted = [] msg = None status = None - if not self.app.config.job_manager != self.app.config.server_name: - return trans.show_error_message( 'This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs.' ) + if self.app.config.job_manager != self.app.config.server_name: + return trans.show_error_message( 'This Galaxy instance (%s) is not the job manager (%s). If using multiple servers, please directly access the job manager instance to manage jobs.' % ( self.app.config.job_manager,self.app.config.server_name) ) job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated' 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 a typo in the community common cntroller.
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fa05d052e82/ changeset: 3fa05d052e82 user: greg date: 2012-05-24 22:47:25 summary: Fix a typo in the community common cntroller. affected #: 1 file diff -r 676546e7038ae833e524bbc4b4b26c81c71954bd -r 3fa05d052e820d21f1a6e5ae206d90edcc1a8782 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -774,7 +774,7 @@ break if in_ctx: tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, dir=work_dir ) - element_tree = util.parse_xml( tmp_config ) + element_tree = util.parse_xml( tmp_tool_config ) element_tree_root = element_tree.getroot() # Look for code files required by the tool config. tmp_code_files = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhance setting metadata on tool shed repositories tha tinclude tools that require entries in the tool_data_table_conf.xml file.
by Bitbucket 24 May '12

24 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/676546e7038a/ changeset: 676546e7038a user: greg date: 2012-05-24 22:36:32 summary: Enhance setting metadata on tool shed repositories tha tinclude tools that require entries in the tool_data_table_conf.xml file. affected #: 5 files diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -8,6 +8,7 @@ from galaxy import eggs import pkg_resources +pkg_resources.require('ssh' ) pkg_resources.require( 'Fabric' ) from fabric.api import env, lcd, local diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,4 +1,5 @@ import sys, os, tempfile, shutil, logging, string, urllib2 +import galaxy.tools.data from datetime import date, datetime, timedelta from time import strftime, gmtime from galaxy import util @@ -528,10 +529,11 @@ exported_workflow_dict = from_json_string( workflow_text ) if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) - # This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + if 'tools' in metadata_dict: + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) + if tool_dependencies_config: + metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) return metadata_dict def generate_tool_guid( repository_clone_url, tool ): """ @@ -1026,6 +1028,8 @@ # Reload the tool into the local list of repository_tools_tups. repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( app ) return repository_tools_tups def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ): """ @@ -1398,6 +1402,9 @@ if uninstall: # Write the current in-memory version of the integrated_tool_panel.xml file to disk. trans.app.toolbox.write_integrated_tool_panel_config_file() +def reset_tool_data_tables( app ): + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + app.tool_data_tables = galaxy.tools.data.ToolDataTableManager( app.config.tool_data_table_config_path ) def strip_path( fpath ): file_path, file_name = os.path.split( fpath ) return file_name diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -7,7 +7,7 @@ from galaxy.util.hash_util import * from galaxy.util.shed_util import copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, handle_sample_tool_data_table_conf_file -from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, strip_path, to_html_escaped, to_html_str, update_repository +from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, strip_path, to_html_escaped, to_html_str, update_repository from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -245,6 +245,8 @@ correction_msg = "This file refers to a file named %s. " % str( index_file ) correction_msg += "Upload a file named %s.sample to the repository to correct this error." % str( index_file_name ) invalid_files.append( ( xml_file_in_ctx, correction_msg ) ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return sample_files_copied, can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata reecords associated with the repository that have a changeset_revision that is not in changeset_revisions. @@ -437,16 +439,20 @@ work_dir = make_tmp_directory() datatypes_config = get_config( 'datatypes_conf.xml', repo, repo_dir, ctx, work_dir ) if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) sample_files = get_sample_files( repo, repo_dir, dir=work_dir ) + # Handle the tool_data_table_conf.xml.sample file if it is included in the repository. + if 'tool_data_table_conf.xml.sample' in sample_files: + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) if sample_files: trans.app.config.tool_data_path = work_dir for filename in ctx: # Find all tool configs. ctx_file_name = strip_path( filename ) if ctx_file_name not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - valid, tool = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) - if valid and tool is not None: + is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) + if is_tool_config and valid and tool is not None: sample_files_copied, can_set_metadata, invalid_files = check_tool_input_params( trans, repo, repo_dir, @@ -484,9 +490,11 @@ os.unlink( os.path.join( original_tool_data_path, copied_file ) ) except: pass - elif tool is not None: - # We have a tool config but it is invalid. - invalid_files.append( ( ctx_file_name, 'Problems loading tool.' ) ) + elif is_tool_config: + if not error_message: + error_message = 'Unknown problems loading tool.' + # We have a tool config but it is invalid or the tool does not properly load. + invalid_files.append( ( ctx_file_name, error_message ) ) invalid_tool_configs.append( ctx_file_name ) # Find all exported workflows. elif filename.endswith( '.ga' ): @@ -498,15 +506,18 @@ metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( ctx_file_name, str( e ) ) ) - # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + if 'tools' in metadata_dict: + # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir ) + if tool_dependencies_config: + metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs if sample_files: # Don't forget to reset the value of trans.app.config.tool_data_path! trans.app.config.tool_data_path = original_tool_data_path + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) try: shutil.rmtree( work_dir ) except: @@ -737,9 +748,14 @@ repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) tool = None message = '' work_dir = make_tmp_directory() + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) + if tool_data_table_config: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) if changeset_revision == repository.tip: try: copied_tool_config = copy_file_from_disk( tool_config, repo_files_dir, work_dir ) @@ -750,7 +766,6 @@ else: # Get the tool config file name from the hgweb url, something like: /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( repo, changeset_revision ) in_ctx = False for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) @@ -784,14 +799,18 @@ pass else: tool = None + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) try: shutil.rmtree( work_dir ) except: pass return tool, message def load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, dir ): + is_tool_config = False tool = None valid = False + error_message = '' tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir=dir ) if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): @@ -799,11 +818,15 @@ # Make sure we're looking at a tool config and not a display application config or something else. element_tree = util.parse_xml( tmp_config ) element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' + is_tool_config = element_tree_root.tag == 'tool' except Exception, e: log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) - is_tool = False - if is_tool: + is_tool_config = False + if is_tool_config: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) + if tool_data_table_config: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) # Look for code files required by the tool config. The directory to which dir refers should be removed by the caller. for code_elem in element_tree_root.findall( 'code' ): code_file_name = code_elem.get( 'file' ) @@ -814,9 +837,17 @@ try: tool = load_tool( trans, tmp_config ) valid = True - except: + except KeyError, e: valid = False - return valid, tool + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + except Exception, e: + valid = False + error_message = str( e ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) + return is_tool_config, valid, tool, error_message def new_tool_metadata_required( trans, id, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata @@ -1049,13 +1080,11 @@ error_message, status = reset_all_metadata_on_repository( trans, id, **kwd ) if error_message: # If there is an error, display it. - message += '%s %s ' % ( message, error_message ) - status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, - message=message, - status=status ) ) + message=error_message, + status='error' ) ) def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): # This method id deprecated, but we'll keep it around for a while in case we need it. The problem is that hg purge # is not supported by the mercurial API. diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -950,7 +950,12 @@ for filename in ctx: # Find all tool configs in this repository changeset_revision. if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - valid, tool = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) + is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, + repo, + repo_dir, + ctx, + filename, + work_dir ) if valid and tool is not None: tool_guids.append( generate_tool_guid( trans, repository, tool ) ) tool_guids.sort() diff -r 95c05fcbbceb69e9100d8689694c22cc13d16b23 -r 676546e7038ae833e524bbc4b4b26c81c71954bd lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -3,7 +3,7 @@ from galaxy.model.orm import * from galaxy.datatypes.checkers import * from common import * -from galaxy.util.shed_util import get_configured_ui, handle_sample_tool_data_table_conf_file +from galaxy.util.shed_util import get_configured_ui, reset_tool_data_tables, handle_sample_tool_data_table_conf_file from galaxy import eggs eggs.require('mercurial') @@ -168,6 +168,8 @@ status=status ) ) else: status = 'error' + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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