April 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: carlfeberhard: HDA model: add UsesAnnotations mixin; HDA API: add update method and allow name, deleted, visible, genome_build, dbkey, info, and annotation to be updated; History & HDA API: don't error on allowed but uneditable keys; Browser tests: test hda api
by commits-noreply＠bitbucket.org 24 Apr '13

24 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b9ca63f9128/ Changeset: 8b9ca63f9128 User: carlfeberhard Date: 2013-04-24 22:24:41 Summary: HDA model: add UsesAnnotations mixin; HDA API: add update method and allow name, deleted, visible, genome_build, dbkey, info, and annotation to be updated; History & HDA API: don't error on allowed but uneditable keys; Browser tests: test hda api Affected #: 9 files diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -727,6 +727,7 @@ """ # precondition: keys are proper, values are parsed and validated changed = {} + # unknown keys are ignored here for key in [ k for k in new_data.keys() if k in self.api_element_visible_keys ]: new_val = new_data[ key ] old_val = self.__getattribute__( key ) @@ -1428,7 +1429,11 @@ return msg -class HistoryDatasetAssociation( DatasetInstance ): +class HistoryDatasetAssociation( DatasetInstance, UsesAnnotations ): + """ + Resource class that creates a relation between a dataset and a user history. + """ + def __init__( self, hid = None, history = None, @@ -1436,6 +1441,9 @@ copied_from_library_dataset_dataset_association = None, sa_session = None, **kwd ): + """ + Create a a new HDA and associate it with the given history. + """ # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset # parameter is True so that the new object can be flushed. Is there a better way? DatasetInstance.__init__( self, sa_session=sa_session, **kwd ) @@ -1444,7 +1452,11 @@ self.history = history self.copied_from_history_dataset_association = copied_from_history_dataset_association self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association + def copy( self, copy_children = False, parent_id = None ): + """ + Create a copy of this HDA. + """ hda = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, @@ -1471,13 +1483,20 @@ hda.set_peek() object_session( self ).flush() return hda - def to_library_dataset_dataset_association( self, trans, target_folder, replace_dataset=None, parent_id=None, user=None, roles=[], ldda_message='' ): + + def to_library_dataset_dataset_association( self, trans, target_folder, + replace_dataset=None, parent_id=None, user=None, roles=[], ldda_message='' ): + """ + Copy this HDA to a library optionally replacing an existing LDDA. + """ if replace_dataset: - # The replace_dataset param ( when not None ) refers to a LibraryDataset that is being replaced with a new version. + # The replace_dataset param ( when not None ) refers to a LibraryDataset that + # is being replaced with a new version. library_dataset = replace_dataset else: - # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new - # LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset. + # If replace_dataset is None, the Library level permissions will be taken from the folder and + # applied to the new LibraryDataset, and the current user's DefaultUserPermissions will be applied + # to the associated Dataset. library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info ) object_session( self ).add( library_dataset ) object_session( self ).flush() @@ -1502,7 +1521,8 @@ object_session( self ).flush() # If roles were selected on the upload form, restrict access to the Dataset to those roles for role in roles: - dp = trans.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, ldda.dataset, role ) + dp = trans.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, + ldda.dataset, role ) trans.sa_session.add( dp ) trans.sa_session.flush() # Must set metadata after ldda flushed, as MetadataFiles require ldda.id @@ -1527,30 +1547,47 @@ ldda.set_peek() object_session( self ).flush() return ldda + def clear_associated_files( self, metadata_safe = False, purge = False ): + """ + """ # metadata_safe = True means to only clear when assoc.metadata_safe == False for assoc in self.implicitly_converted_datasets: if not assoc.deleted and ( not metadata_safe or not assoc.metadata_safe ): assoc.clear( purge = purge ) for assoc in self.implicitly_converted_parent_datasets: assoc.clear( purge = purge, delete_dataset = False ) + def get_display_name( self ): - ## Name can be either a string or a unicode object. If string, convert to unicode object assuming 'utf-8' format. + """ + Return the name of this HDA in either ascii or utf-8 encoding. + """ + # Name can be either a string or a unicode object. + # If string, convert to unicode object assuming 'utf-8' format. hda_name = self.name if isinstance(hda_name, str): hda_name = unicode(hda_name, 'utf-8') return hda_name + def get_access_roles( self, trans ): + """ + Return The access roles associated with this HDA's dataset. + """ return self.dataset.get_access_roles( trans ) + def quota_amount( self, user ): """ - If the user has multiple instances of this dataset, it will not affect their disk usage statistic. + Return the disk space used for this HDA relevant to user quotas. + + If the user has multiple instances of this dataset, it will not affect their + disk usage statistic. """ rval = 0 # Anon users are handled just by their single history size. if not user: return rval - # Gets an HDA and its children's disk usage, if the user does not already have an association of the same dataset + # Gets an HDA and its children's disk usage, if the user does not already + # have an association of the same dataset if not self.dataset.library_associations and not self.purged and not self.dataset.purged: for hda in self.dataset.history_associations: if hda.id == self.id: @@ -1562,7 +1599,11 @@ for child in self.children: rval += child.get_disk_usage( user ) return rval + def get_api_value( self, view='collection' ): + """ + Return attributes of this HDA that are exposed using the API. + """ # Since this class is a proxy to rather complex attributes we want to # display in other objects, we can't use the simpler method used by # other model classes. @@ -1598,6 +1639,33 @@ rval['metadata_' + name] = val return rval + def set_from_dict( self, new_data ): + #AKA: set_api_value + """ + Set object attributes to the values in dictionary new_data limiting + to only the following keys: name, deleted, visible, genome_build, + info, and blurb. + + Returns a dictionary of the keys, values that have been changed. + """ + # precondition: keys are proper, values are parsed and validated + #NOTE!: does not handle metadata + editable_keys = ( 'name', 'deleted', 'visible', 'dbkey', 'info', 'blurb' ) + + changed = {} + # unknown keys are ignored here + for key in [ k for k in new_data.keys() if k in editable_keys ]: + new_val = new_data[ key ] + old_val = self.__getattribute__( key ) + if new_val == old_val: + continue + + self.__setattr__( key, new_val ) + changed[ key ] = new_val + + return changed + + class HistoryDatasetAssociationDisplayAtAuthorization( object ): def __init__( self, hda=None, user=None, site=None ): self.history_dataset_association = hda diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -427,10 +427,15 @@ class UsesHistoryDatasetAssociationMixin: - """ Mixin for controllers that use HistoryDatasetAssociation objects. """ + """ + Mixin for controllers that use HistoryDatasetAssociation objects. + """ def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True ): - """ Get an HDA object by id. """ + """ + Get an HDA object by id performing security checks using + the current transaction. + """ # DEPRECATION: We still support unencoded ids for backward compatibility try: # encoded id? @@ -466,7 +471,10 @@ def get_history_dataset_association( self, trans, history, dataset_id, check_ownership=True, check_accessible=False, check_state=False ): - """Get a HistoryDatasetAssociation from the database by id, verifying ownership.""" + """ + Get a HistoryDatasetAssociation from the database by id, verifying ownership. + """ + #TODO: duplicate of above? alias to above (or vis-versa) self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible ) hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False ) @@ -479,8 +487,9 @@ return hda def get_data( self, dataset, preview=True ): - """ Gets a dataset's data. """ - + """ + Gets a dataset's data. + """ # Get data from file, truncating if necessary. truncated = False dataset_data = None @@ -610,6 +619,27 @@ return display_apps + def set_hda_from_dict( self, trans, hda, new_data ): + """ + Changes HDA data using the given dictionary new_data. + """ + # precondition: access of the hda has already been checked + + # send what we can down into the model + changed = hda.set_from_dict( new_data ) + # the rest (often involving the trans) - do here + if 'annotation' in new_data.keys() and trans.get_user(): + hda.add_item_annotation( trans.sa_session, trans.get_user(), hda, new_data[ 'annotation' ] ) + changed[ 'annotation' ] = new_data[ 'annotation' ] + # tags + # sharing/permissions? + # purged + + if changed.keys(): + trans.sa_session.flush() + + return changed + class UsesLibraryMixin: diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -2,15 +2,10 @@ API operations on a history. """ -import pkg_resources -pkg_resources.require("Paste") -from paste.httpexceptions import HTTPBadRequest - from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from galaxy.web import url_for from galaxy.model.orm import desc -from galaxy.util.bunch import Bunch import logging log = logging.getLogger( __name__ ) @@ -197,28 +192,39 @@ # - protection against bad data form/type # - protection against malicious data content # all other conversions and processing (such as permissions, etc.) should happen down the line + + # keys listed here don't error when attempting to set, but fail silently + # this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs + valid_but_uneditable_keys = ( + 'id', 'model_class', 'nice_size', 'contents_url', 'purged', 'tags', + 'state', 'state_details', 'state_ids' + ) + + validated_payload = {} for key, val in payload.items(): # TODO: lots of boilerplate here, but overhead on abstraction is equally onerous if key == 'name': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): raise ValueError( 'name must be a string or unicode: %s' %( str( type( val ) ) ) ) - payload[ 'name' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + validated_payload[ 'name' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) #TODO:?? if sanitized != val: log.warn( 'script kiddie' ) elif key == 'deleted': if not isinstance( val, bool ): raise ValueError( 'deleted must be a boolean: %s' %( str( type( val ) ) ) ) + validated_payload[ 'deleted' ] = val elif key == 'published': - if not isinstance( payload[ 'published' ], bool ): + if not isinstance( val, bool ): raise ValueError( 'published must be a boolean: %s' %( str( type( val ) ) ) ) + validated_payload[ 'published' ] = val elif key == 'genome_build': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): raise ValueError( 'genome_build must be a string: %s' %( str( type( val ) ) ) ) - payload[ 'genome_build' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + validated_payload[ 'genome_build' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) elif key == 'annotation': if not ( isinstance( val, str ) or isinstance( val, unicode ) ): raise ValueError( 'annotation must be a string or unicode: %s' %( str( type( val ) ) ) ) - payload[ 'annotation' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) - else: + validated_payload[ 'annotation' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + elif key not in valid_but_uneditable_keys: raise AttributeError( 'unknown key: %s' %( str( key ) ) ) - return payload + return validated_payload diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -1,13 +1,13 @@ """ API operations on the contents of a history. """ -import logging -from galaxy import web +from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, url_for from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin, UsesHistoryMixin from galaxy.web.base.controller import UsesLibraryMixin, UsesLibraryMixinItems +import logging log = logging.getLogger( __name__ ) class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, @@ -138,11 +138,14 @@ POST /api/histories/{encoded_history_id}/contents Creates a new history content item (file, aka HistoryDatasetAssociation). """ + #TODO: copy existing, accessible hda - dataset controller, copy_datasets + #TODO: convert existing, accessible hda - model.DatasetInstance(or hda.datatype).get_converter_types from_ld_id = payload.get( 'from_ld_id', None ) - try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) except Exception, e: + #TODO: no way to tell if it failed bc of perms or other (all MessageExceptions) + trans.response.status = 500 return str( e ) if from_ld_id: @@ -164,6 +167,90 @@ else: # TODO: implement other "upload" methods here. - trans.response.status = 403 + trans.response.status = 501 return "Not implemented." + @web.expose_api + def update( self, trans, history_id, id, payload, **kwd ): + """ + PUT /api/histories/{encoded_history_id}/contents/{encoded_content_id} + Changes an existing history dataset. + """ + #TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks) + changed = {} + try: + hda = self.get_dataset( trans, id, + check_ownership=True, check_accessible=True, check_state=True ) + # validation handled here and some parsing, processing, and conversion + payload = self._validate_and_parse_update_payload( payload ) + # additional checks here (security, etc.) + changed = self.set_hda_from_dict( trans, hda, payload ) + + except Exception, exception: + log.error( 'Update of history (%s), HDA (%s) failed: %s', + history_id, id, str( exception ), exc_info=True ) + # convert to appropo HTTP code + if( isinstance( exception, ValueError ) + or isinstance( exception, AttributeError ) ): + # bad syntax from the validater/parser + trans.response.status = 400 + else: + trans.response.status = 500 + return { 'error': str( exception ) } + + return changed + + def _validate_and_parse_update_payload( self, payload ): + """ + Validate and parse incomming data payload for an HDA. + """ + # This layer handles (most of the stricter idiot proofing): + # - unknown/unallowed keys + # - changing data keys from api key to attribute name + # - protection against bad data form/type + # - protection against malicious data content + # all other conversions and processing (such as permissions, etc.) should happen down the line + + # keys listed here don't error when attempting to set, but fail silently + # this allows PUT'ing an entire model back to the server without attribute errors on uneditable attrs + valid_but_uneditable_keys = ( + 'id', 'name', 'type', 'api_type', 'model_class', 'history_id', 'hid', + 'accessible', 'purged', 'state', 'data_type', 'file_ext', 'file_size', 'misc_blurb', + 'download_url', 'visualizations', 'display_apps', 'display_types', + 'metadata_dbkey', 'metadata_column_names', 'metadata_column_types', 'metadata_columns', + 'metadata_comment_lines', 'metadata_data_lines' + ) + + validated_payload = {} + for key, val in payload.items(): + # TODO: lots of boilerplate here, but overhead on abstraction is equally onerous + # typecheck, parse, remap key + if key == 'name': + if not ( isinstance( val, str ) or isinstance( val, unicode ) ): + raise ValueError( 'name must be a string or unicode: %s' %( str( type( val ) ) ) ) + validated_payload[ 'name' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + #TODO:?? if sanitized != val: log.warn( 'script kiddie' ) + elif key == 'deleted': + if not isinstance( val, bool ): + raise ValueError( 'deleted must be a boolean: %s' %( str( type( val ) ) ) ) + validated_payload[ 'deleted' ] = val + elif key == 'visible': + if not isinstance( val, bool ): + raise ValueError( 'visible must be a boolean: %s' %( str( type( val ) ) ) ) + validated_payload[ 'visible' ] = val + elif key == 'genome_build': + if not ( isinstance( val, str ) or isinstance( val, unicode ) ): + raise ValueError( 'genome_build must be a string: %s' %( str( type( val ) ) ) ) + validated_payload[ 'dbkey' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + elif key == 'annotation': + if not ( isinstance( val, str ) or isinstance( val, unicode ) ): + raise ValueError( 'annotation must be a string or unicode: %s' %( str( type( val ) ) ) ) + validated_payload[ 'annotation' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + elif key == 'misc_info': + if not ( isinstance( val, str ) or isinstance( val, unicode ) ): + raise ValueError( 'misc_info must be a string or unicode: %s' %( str( type( val ) ) ) ) + validated_payload[ 'info' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + elif key not in valid_but_uneditable_keys: + raise AttributeError( 'unknown key: %s' %( str( key ) ) ) + return validated_payload + diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 test/casperjs/api-hda-tests.js --- /dev/null +++ b/test/casperjs/api-hda-tests.js @@ -0,0 +1,406 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +spaceghost.user.loginOrRegisterUser( email, password ); + +var uploadFilename = '1.sam', + uploadFilepath = '../../test-data/' + uploadFilename, + upload = {}; +spaceghost.thenOpen( spaceghost.baseUrl ).tools.uploadFile( uploadFilepath, function( uploadInfo ){ + upload = uploadInfo; +}); + +function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + spaceghost.debug( 'object missing key: ' + keysArray[i] ); + return false; + } + } + return true; +} + +function countKeys( object ){ + if( !utils.isObject( object ) ){ return 0; } + var count = 0; + for( var key in object ){ + if( object.hasOwnProperty( key ) ){ count += 1; } + } + return count; +} + +// =================================================================== TESTS +var summaryKeys = [ 'id', 'name', 'type', 'url' ], + detailKeys = [ + // the following are always present regardless of datatype + 'id', 'name', 'api_type', 'model_class', + 'history_id', 'hid', + 'accessible', 'deleted', 'visible', 'purged', + 'state', 'data_type', 'file_ext', 'file_size', + 'misc_info', 'misc_blurb', + 'download_url', 'visualizations', 'display_apps', 'display_types', + 'genome_build', + // the following are NOT always present DEPENDING ON datatype + 'metadata_dbkey', + 'metadata_column_names', 'metadata_column_types', 'metadata_columns', + 'metadata_comment_lines', 'metadata_data_lines' + ]; + +spaceghost.historypanel.waitForHdas().then( function(){ + + var uploaded = this.historypanel.hdaElementInfoByTitle( uploadFilename ); + this.info( 'found uploaded hda: ' + uploaded.attributes.id ); + this.debug( 'uploaded hda: ' + this.jsonStr( uploaded ) ); + // ------------------------------------------------------------------------------------------- INDEX + this.test.comment( 'index should return a list of summary data for each hda' ); + var histories = this.api.histories.index(), + lastHistory = histories[0], + hdaIndex = this.api.hdas.index( lastHistory.id ); + //this.debug( 'hdaIndex:' + this.jsonStr( hdaIndex ) ); + + this.test.assert( utils.isArray( hdaIndex ), "index returned an array: length " + hdaIndex.length ); + this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' ); + + var firstHda = hdaIndex[0]; + this.test.assert( hasKeys( firstHda, summaryKeys ), 'Has the proper keys' ); + + this.test.assert( this.api.isEncodedId( firstHda.id ), 'Id appears well-formed: ' + firstHda.id ); + this.test.assert( uploaded.text.indexOf( firstHda.name ) !== -1, 'Title matches: ' + firstHda.name ); + // not caring about type or url here + + + // ------------------------------------------------------------------------------------------- SHOW + this.test.comment( 'show should get an HDA details object' ); + var hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + //this.debug( this.jsonStr( hdaShow ) ); + this.test.assert( hasKeys( hdaShow, detailKeys ), 'Has the proper keys' ); + + //TODO: validate data in each hdaShow attribute... + + + // ------------------------------------------------------------------------------------------- INDEX (detailed) + this.test.comment( 'index should return a list of detailed data for each hda in "ids" when passed' ); + hdaIndex = this.api.hdas.index( lastHistory.id, [ firstHda.id ] ); + this.debug( 'hdaIndex:' + this.jsonStr( hdaIndex ) ); + + this.test.assert( utils.isArray( hdaIndex ), "index returned an array: length " + hdaIndex.length ); + this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' ); + + firstHda = hdaIndex[0]; + this.test.assert( hasKeys( firstHda, detailKeys ), 'Has the proper keys' ); + + //TODO??: validate data in firstHda attribute? we ASSUME it's from a common method as show... + + + // ------------------------------------------------------------------------------------------- CREATE + //TODO: create from_ld_id + + + // ------------------------------------------------------------------------------------------- UPDATE + // ........................................................................................... idiot proofing + this.test.comment( 'updating to the current value should return no value (no change)' ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + var returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + name : hdaShow.name + }); + this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + + this.test.comment( 'updating using a nonsense key should fail with an error' ); + var err = {}; + try { + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + konamiCode : 'uuddlrlrba' + }); + } catch( error ){ + err = error; + //this.debug( this.jsonStr( err ) ); + } + this.test.assert( !!err.message, "Error occurred: " + err.message ); + this.test.assert( err.status === 400, "Error status is 400: " + err.status ); + + this.test.comment( 'updating by attempting to change type should cause an error' ); + err = {}; + try { + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + //name : false + deleted : 'sure why not' + }); + } catch( error ){ + err = error; + //this.debug( this.jsonStr( err ) ); + } + this.test.assert( !!err.message, "Error occurred: " + err.message ); + this.test.assert( err.status === 400, "Error status is 400: " + err.status ); + //TODO??: other type checks? + + + // ........................................................................................... name + this.test.comment( 'update should allow changing the name' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + name : 'New name' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.name === 'New name', "Name successfully set via update: " + hdaShow.name ); + + this.test.comment( 'update should sanitize any new name' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + name : 'New name<script type="text/javascript" src="bler">alert("blah");</script>' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.name === 'New name', "Update sanitized name: " + hdaShow.name ); + + //NOTE!: this fails on sqlite3 (with default setup) + try { + this.test.comment( 'update should allow unicode in names' ); + var unicodeName = 'Ржевский сапоги'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + name : unicodeName + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.name === unicodeName, "Update accepted unicode name: " + hdaShow.name ); + } catch( err ){ + //this.debug( this.jsonStr( err ) ); + if( ( err instanceof this.api.APIError ) + && ( err.status === 500 ) + && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ + this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } + } + + this.test.comment( 'update should allow escaped quotations in names' ); + var quotedName = '"Bler"'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + name : quotedName + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.name === quotedName, + "Update accepted escaped quotations in name: " + hdaShow.name ); + + + // ........................................................................................... deleted + this.test.comment( 'update should allow changing the deleted flag' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + deleted: true + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.deleted === true, "Update set the deleted flag: " + hdaShow.deleted ); + + this.test.comment( 'update should allow changing the deleted flag back' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + deleted: false + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.deleted === false, "Update set the deleted flag: " + hdaShow.deleted ); + + + // ........................................................................................... visible/hidden + this.test.comment( 'update should allow changing the visible flag' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + visible: false + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.visible === false, "Update set the visible flag: " + hdaShow.visible ); + + + // ........................................................................................... genome_build/dbkey + this.test.comment( 'update should allow changing the genome_build' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + genome_build : 'hg18' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.genome_build === 'hg18', + "genome_build successfully set via update: " + hdaShow.genome_build ); + this.test.assert( hdaShow.metadata_dbkey === 'hg18', + "metadata_dbkey successfully set via the same update: " + hdaShow.metadata_dbkey ); + + this.test.comment( 'update should sanitize any genome_build' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + genome_build : 'hg18<script type="text/javascript" src="bler">alert("blah");</script>' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.genome_build === 'hg18', + "Update sanitized genome_build: " + hdaShow.genome_build ); + this.test.assert( hdaShow.metadata_dbkey === 'hg18', + "metadata_dbkey successfully set via the same update: " + hdaShow.metadata_dbkey ); + + this.test.comment( 'update should allow unicode in genome builds' ); + var unicodeBuild = 'Ржевский18'; + //NOTE!: this fails on sqlite3 (with default setup) + try { + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + name : unicodeBuild + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.genome_build === unicodeBuild, + "Update accepted unicode genome_build: " + hdaShow.name ); + } catch( err ){ + //this.debug( this.jsonStr( err ) ); + if( ( err instanceof this.api.APIError ) + && ( err.status === 500 ) + && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ + this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } + } + + // ........................................................................................... misc_info/info + this.test.comment( 'update should allow changing the misc_info' ); + var newInfo = 'I\'ve made a huge mistake.'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + misc_info : newInfo + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.misc_info === newInfo, + "misc_info successfully set via update: " + hdaShow.misc_info ); + + this.test.comment( 'update should sanitize any misc_info' ); + var newInfo = 'You\'re going to get hop-ons.'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + misc_info : newInfo + '<script type="text/javascript" src="bler">alert("blah");</script>' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.misc_info === newInfo, + "Update sanitized misc_info: " + hdaShow.misc_info ); + + this.test.comment( 'update should allow unicode in misc_info' ); + var unicodeInfo = '여보!'; + //NOTE!: this fails on sqlite3 (with default setup) + try { + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + misc_info : unicodeInfo + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.misc_info === unicodeInfo, + "Update accepted unicode misc_info: " + hdaShow.misc_info ); + } catch( err ){ + //this.debug( this.jsonStr( err ) ); + if( ( err instanceof this.api.APIError ) + && ( err.status === 500 ) + && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ + this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } + } + +/* + // ........................................................................................... annotation + // currently fails because no annotation is returned in details + this.test.comment( 'update should allow changing the annotation' ); + var newAnnotation = 'Found this sample on a movie theatre floor'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + annotation : newAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.annotation === newAnnotation, + "Annotation successfully set via update: " + hdaShow.annotation ); + + this.test.comment( 'update should sanitize any new annotation' ); + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + annotation : 'New annotation<script type="text/javascript" src="bler">alert("blah");</script>' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.annotation === 'New annotation', + "Update sanitized annotation: " + hdaShow.annotation ); + + //NOTE!: this fails on sqlite3 (with default setup) + try { + this.test.comment( 'update should allow unicode in annotations' ); + var unicodeAnnotation = 'お願いは、それが落下させない'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + annotation : unicodeAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.annotation === unicodeAnnotation, + "Update accepted unicode annotation: " + hdaShow.annotation ); + } catch( err ){ + //this.debug( this.jsonStr( err ) ); + if( ( err instanceof this.api.APIError ) + && ( err.status === 500 ) + && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ + this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } + } + + this.test.comment( 'update should allow escaped quotations in annotations' ); + var quotedAnnotation = '"Bler"'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + annotation : quotedAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.annotation === quotedAnnotation, + "Update accepted escaped quotations in annotation: " + hdaShow.annotation ); +*/ + + + // ------------------------------------------------------------------------------------------- ERRORS + this.test.comment( 'create should error with "not implemented" when the param "from_ld_id" is not used' ); + var errored = false; + try { + // sending an empty object won't work + var created = this.api.hdas.create( lastHistory.id, { bler: 'bler' } ); + + } catch( err ){ + errored = true; + this.test.assert( err.message.indexOf( 'Not implemented' ) !== -1, + 'Error has the proper message: ' + err.message ); + this.test.assert( err.status === 501, 'Error has the proper status code: ' + err.status ); + } + if( !errored ){ + this.test.fail( 'create without "from_ld_id" did not cause error' ); + } + + + //var returned = this.api.hdas.update( lastHistory.id, hdaIndex[0].id, { deleted: true, blerp: 'blerp' }); + //var returned = this.api.hdas.update( lastHistory.id, { deleted: true, blerp: 'blerp' }); + //this.debug( 'returned:' + this.jsonStr( returned ) ); + //this.debug( 'page:' + this.jsonStr( this.page ) ); +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 test/casperjs/api-history-tests.js --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -36,7 +36,10 @@ function hasKeys( object, keysArray ){ if( !utils.isObject( object ) ){ return false; } for( var i=0; i<keysArray.length; i += 1 ){ - if( !object.hasOwnProperty( keysArray[i] ) ){ return false; } + if( !object.hasOwnProperty( keysArray[i] ) ){ + spaceghost.debug( 'object missing key: ' + keysArray[i] ); + return false; + } } return true; } @@ -362,6 +365,10 @@ "Update accepted escaped quotations in annotation: " + historyShow.annotation ); + // ------------------------------------------------------------------------------------------- ERRORS + //TODO: make sure expected errors are being passed back (but no permissions checks here - different suite) + // bad ids: index, show, update, delete, undelete + /* */ //this.debug( this.jsonStr( historyShow ) ); diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -232,7 +232,7 @@ }; HDAAPI.prototype.show = function show( historyId, id, deleted ){ - this.api.spaceghost.info( 'hda.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + this.api.spaceghost.info( 'hda.show: ' + [ historyId, id, (( deleted )?( 'w deleted' ):( '' )) ] ); id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; @@ -242,7 +242,7 @@ }; HDAAPI.prototype.create = function create( historyId, payload ){ - this.api.spaceghost.info( 'hda.create: ' + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'hda.create: ' + [ historyId, this.api.spaceghost.jsonStr( payload ) ] ); // py.payload <-> ajax.data payload = this.api.ensureObject( payload ); @@ -253,8 +253,7 @@ }; HDAAPI.prototype.update = function create( historyId, id, payload ){ - this.api.spaceghost.info( 'hda.update: ' + historyId + ',' + id + ',' - + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'hda.update: ' + [ historyId, id, this.api.spaceghost.jsonStr( payload ) ] ); // py.payload <-> ajax.data historyId = this.api.ensureId( historyId ); diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 test/casperjs/modules/tools.js --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -13,7 +13,7 @@ //??: circ ref? this.options = {}; /** Default amount of ms to wait for upload to finish */ - this.options.defaultUploadWait = ( 30 * 1000 ); + this.options.defaultUploadWait = ( 45 * 1000 ); this.spaceghost = spaceghost; }; exports.Tools = Tools; @@ -108,14 +108,22 @@ // wait for main panel, history reload ////NOTE!: assumes tool execution reloads the history panel - this.waitForMultipleNavigation( [ 'tool_runner/upload_async_message', 'history' ], function(){ - // debugging - this.jumpToMain( function(){ - var messageInfo = this.elementInfoOrNull( this.data.selectors.messages.all ); - this.debug( ( messageInfo )?( messageInfo.attributes['class'] + ':\n' + messageInfo.text ) - :( 'NO post upload message' ) ); - }); - }); + this.waitForMultipleNavigation( [ 'tool_runner/upload_async_message', 'history' ], + function thenAfterUploadRefreshes(){ + // debugging + this.jumpToMain( function(){ + var messageInfo = this.elementInfoOrNull( this.data.selectors.messages.all ); + this.debug( ( messageInfo )?( messageInfo.attributes['class'] + ':\n' + messageInfo.text ) + :( 'NO post upload message' ) ); + }); + }, + function timeoutWaitingForUploadRefreshes( urlsStillWaitingOn ){ + this.capture( 'upload-error.png' ) + throw new this.GalaxyError( 'Upload Error: ' + + 'timeout waiting for upload "' + filepath + '" refreshes: ' + urlsStillWaitingOn ); + }, + this.tools.options.defaultUploadWait + ); }); }; @@ -160,13 +168,19 @@ // error if an info message wasn't found spaceghost.withMainPanel( function checkUploadMessage(){ var infoInfo = spaceghost.elementInfoOrNull( this.data.selectors.messages.infolarge ); - if( ( !infoInfo ) - || ( infoInfo.text.indexOf( this.data.text.upload.success ) === -1 ) ){ - throw new this.GalaxyError( 'Upload Error: no info message uploading "' + filepath + '"' ); + if( ( infoInfo ) + && ( infoInfo.text.indexOf( this.data.text.upload.success ) !== -1 ) ){ + // safe to store these + uploadInfo.filename = filename; + uploadInfo.filepath = filepath; + + } else { + // capture any other messages on the page + var otherInfo = spaceghost.elementInfoOrNull( this.data.selectors.messages.all ), + message = ( otherInfo && otherInfo.text )?( otherInfo.text ):( '' ); + this.capture( 'upload-error.png' ) + throw new this.GalaxyError( 'Upload Error: no success message uploading "' + filepath + '": ' + message ); } - // safe to store these - uploadInfo.filename = filename; - uploadInfo.filepath = filepath; }); // the hpanel should refresh and display the uploading file, wait for that to go into the ok state @@ -177,6 +191,7 @@ if( hdaElement === null ){ var hdaContainer = this.historypanel.data.selectors.hdaContainer; this.warning( 'Upload Error: ' + hdaContainer + ':\n' + this.getHTML( hdaContainer ) ); + this.capture( 'upload-error.png' ) throw new this.GalaxyError( 'Upload Error: uploaded file HDA not found: ' + uploadInfo.filename ); } this.debug( 'uploaded HDA element: ' + this.jsonStr( this.quickInfo( hdaElement ) ) ); @@ -191,6 +206,7 @@ }, function timeoutFn( newHdaInfo ){ this.warning( 'timeout waiting for upload:\n' + this.jsonStr( this.quickInfo( newHdaInfo ) ) ); + this.capture( 'upload-error.png' ) throw new spaceghost.GalaxyError( 'Upload Error: timeout waiting for ok state: ' + '"' + uploadInfo.filepath + '" (waited ' + timeoutAfterMs + ' ms)' ); diff -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 -r 8b9ca63f9128fbe9c7f01805db64da3ec2916332 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -546,9 +546,10 @@ * @param {String} urlToWaitFor the url to wait for (rel. to spaceghost.baseUrl) * @param {Function} then the function to call after the nav request * @param {Function} timeoutFn the function to call on timeout (optional) + * @param {Integer} waitMs manual setting of ms to wait (optional) */ -SpaceGhost.prototype.waitForNavigation = function waitForNavigation( urlToWaitFor, then, timeoutFn ){ - return this.waitForMultipleNavigation( [ urlToWaitFor ], then, timeoutFn ); +SpaceGhost.prototype.waitForNavigation = function waitForNavigation( urlToWaitFor, then, timeoutFn, waitMs ){ + return this.waitForMultipleNavigation( [ urlToWaitFor ], then, timeoutFn, waitMs ); }; /** Wait for a multiple navigation requests then call a function. @@ -557,9 +558,13 @@ * @param {String[]} urlsToWaitFor the relative urls to wait for * @param {Function} then the function to call after the nav request * @param {Function} timeoutFn the function to call on timeout (optional) + * @param {Integer} waitMs manual setting of ms to wait (optional) */ -SpaceGhost.prototype.waitForMultipleNavigation = function waitForMultipleNavigation( urlsToWaitFor, then, timeoutFn ){ - this.info( 'waiting for navigation: ' + this.jsonStr( urlsToWaitFor ) ); +SpaceGhost.prototype.waitForMultipleNavigation = function waitForMultipleNavigation( urlsToWaitFor, + then, timeoutFn, waitMs ){ + waitMs = waitMs || ( this.options.waitTimeout * urlsToWaitFor.length ); + + this.info( 'waiting for navigation: ' + this.jsonStr( urlsToWaitFor ) + ', timeout after: ' + waitMs ); function urlMatches( urlToMatch, url ){ return ( url.indexOf( spaceghost.baseUrl + '/' + urlToMatch ) !== -1 ); } @@ -589,9 +594,10 @@ if( utils.isFunction( then ) ){ then.call( this ); } }, function timeout(){ - if( utils.isFunction( timeoutFn ) ){ timeoutFn.call( this ); } + this.removeListener( 'navigation.requested', catchNavReq ); + if( utils.isFunction( timeoutFn ) ){ timeoutFn.call( this, urlsToWaitFor ); } }, - this.options.waitTimeout * urlsToWaitFor.length + waitMs ); return this; }; 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: inithello: Account for the scenario where a test status is not present in the tool_test_errors dict.
by commits-noreply＠bitbucket.org 24 Apr '13

24 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2df57338a595/ Changeset: 2df57338a595 User: inithello Date: 2013-04-24 20:55:53 Summary: Account for the scenario where a test status is not present in the tool_test_errors dict. Affected #: 1 file diff -r 1a915a754396da8ac986dd410ee99bed12668235 -r 2df57338a595ab96f3f54af2b0e4c2e382198a40 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 @@ -1171,9 +1171,9 @@ # Generate a citable URL for this repository with owner and changeset revision. repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, metadata_row.changeset_revision ) title = 'Functional test results for changeset revision %s of %s' % ( metadata_row.changeset_revision, repository.name ) - tests_passed = len( metadata_row.tool_test_errors[ 'tests_passed' ] ) - tests_failed = len( metadata_row.tool_test_errors[ 'invalid_tests' ] ) - invalid_tests = len( metadata_row.tool_test_errors[ 'test_errors' ] ) + tests_passed = len( metadata_row.tool_test_errors.get( 'tests_passed', [] ) ) + tests_failed = len( metadata_row.tool_test_errors.get( 'test_errors', [] ) ) + invalid_tests = len( metadata_row.tool_test_errors.get( 'invalid_tests', [] ) ) description = '%d tests passed, %d tests failed, %d tests determined to be invalid.' % ( tests_passed, tests_failed, invalid_tests ) # The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated # if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Add support for a new <action type="set_environmnet_for_install"> tag in tool_dependencies.xml files included in tool shed repositories. This tag currently can include any number of <repository> tags, each of which will contain any number of tool dependency tags (i.e., <package> or <set_environmnet> tags). The settings in the env.sh file for each of the tool dependency tags will be injected into the environment for all following shell commands defined in the too
by commits-noreply＠bitbucket.org 24 Apr '13

24 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1a915a754396/ Changeset: 1a915a754396 User: greg Date: 2013-04-24 20:46:54 Summary: Add support for a new <action type="set_environmnet_for_install"> tag in tool_dependencies.xml files included in tool shed repositories. This tag currently can include any number of <repository> tags, each of which will contain any number of tool dependency tags (i.e., <package> or <set_environmnet> tags). The settings in the env.sh file for each of the tool dependency tags will be injected into the environment for all following shell commands defined in the tool_dependencies.xml file, ensuring that the required tool dependencies are sued when compiling the current dependency. I'm sure this will make no sense to anyone reading this commit message. Affected #: 7 files diff -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c -r 1a915a754396da8ac986dd410ee99bed12668235 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3443,7 +3443,7 @@ """Return the repository's tool dependencies that are currently installed.""" installed_dependencies = [] for tool_dependency in self.tool_dependencies: - if tool_dependency.status == ToolDependency.installation_status.INSTALLED: + if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, ToolDependency.installation_status.ERROR ]: installed_dependencies.append( tool_dependency ) return installed_dependencies @property diff -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c -r 1a915a754396da8ac986dd410ee99bed12668235 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 @@ -478,7 +478,7 @@ 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 ) + tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir ) installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, diff -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c -r 1a915a754396da8ac986dd410ee99bed12668235 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -1,6 +1,14 @@ -import os, shutil, tarfile, urllib2, zipfile +import logging +import os +import shutil +import tarfile +import urllib2 +import zipfile +import tool_shed.util.shed_util_common as suc from galaxy.datatypes import checkers +log = logging.getLogger( __name__ ) + def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ): env_var_name = elem.get( 'name', 'PATH' ) env_var_action = elem.get( 'action', 'prepend_to' ) @@ -76,6 +84,67 @@ zip_archive.close() return True +def get_env_shell_file_path( installation_directory ): + env_shell_file_name = 'env.sh' + default_location = os.path.abspath( os.path.join( installation_directory, env_shell_file_name ) ) + if os.path.exists( default_location ): + return default_location + for root, dirs, files in os.walk( installation_directory ): + for name in files: + if name == env_shell_file_name: + return os.path.abspath( os.path.join( root, name ) ) + return None + +def get_env_shell_file_paths( app, elem ): + # Currently only the following tag set is supported. + # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> + # <package name="numpy" version="1.7.1" /> + # </repository> + env_shell_file_paths = [] + toolshed = elem.get( 'toolshed', None ) + repository_name = elem.get( 'name', None ) + repository_owner = elem.get( 'owner', None ) + changeset_revision = elem.get( 'changeset_revision', None ) + if toolshed and repository_name and repository_owner and changeset_revision: + repository = suc.get_repository_for_dependency_relationship( app, toolshed, repository_name, repository_owner, changeset_revision ) + if repository: + for sub_elem in elem: + tool_dependency_type = sub_elem.tag + tool_dependency_name = sub_elem.get( 'name' ) + tool_dependency_version = sub_elem.get( 'version' ) + if tool_dependency_type and tool_dependency_name and tool_dependency_version: + # Get the tool_dependency so we can get it's installation directory. + tool_dependency = None + for tool_dependency in repository.tool_dependencies: + if tool_dependency.type == tool_dependency_type and tool_dependency.name == tool_dependency_name and tool_dependency.version == tool_dependency_version: + break + if tool_dependency: + tool_dependency_key = '%s/%s' % ( tool_dependency_name, tool_dependency_version ) + installation_directory = tool_dependency.installation_directory( app ) + env_shell_file_path = get_env_shell_file_path( installation_directory ) + env_shell_file_paths.append( env_shell_file_path ) + else: + error_message = "Skipping tool dependency definition because unable to locate tool dependency " + error_message += "type %s, name %s, version %s for repository %s" % \ + ( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ), str( repository.name ) ) + log.debug( error_message ) + continue + else: + error_message = "Skipping invalid tool dependency definition: type %s, name %s, version %s." % \ + ( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ) ) + log.debug( error_message ) + continue + else: + error_message = "Skipping set_environment_for_install definition because unable to locate required installed tool shed repository: " + error_message += "toolshed %s, name %s, owner %s, changeset_revision %s." % \ + ( str( toolshed ), str( repository_name ), str( repository_owner ), str( changeset_revision ) ) + log.debug( error_message ) + else: + error_message = "Skipping invalid set_environment_for_install definition: toolshed %s, name %s, owner %s, changeset_revision %s." % \ + ( str( toolshed ), str( repository_name ), str( repository_owner ), str( changeset_revision ) ) + log.debug( error_message ) + return env_shell_file_paths + def isbz2( file_path ): return checkers.is_bz2( file_path ) diff -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c -r 1a915a754396da8ac986dd410ee99bed12668235 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -28,30 +28,18 @@ if int( version.split( "." )[ 0 ] ) < 1: raise NotImplementedError( "Install Fabric version 1.0 or later." ) -def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): - """General Galaxy environment configuration""" - env.user = galaxy_user - env.install_dir = tool_dependency_dir - env.host_string = host - env.shell = shell - env.use_sudo = False - env.safe_cmd = local - return env - -@contextmanager -def make_tmp_dir(): - work_dir = tempfile.mkdtemp() - yield work_dir - if os.path.exists( work_dir ): - local( 'rm -rf %s' % work_dir ) - def handle_command( app, tool_dependency, install_dir, cmd ): sa_session = app.model.context.current output = local( cmd, capture=True ) log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) if output.return_code: tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = str( output.stderr ) + if output.stderr: + tool_dependency.error_message = str( output.stderr )[ :32768 ] + elif output.stdout: + tool_dependency.error_message = str( output.stdout )[ :32768 ] + else: + tool_dependency.error_message = "Unknown error occurred executing shell command %s, return_code: %s" % ( str( cmd ), str( output.return_code ) ) sa_session.add( tool_dependency ) sa_session.flush() return output.return_code @@ -63,6 +51,7 @@ package_name = actions_dict[ 'package_name' ] actions = actions_dict.get( 'actions', None ) filtered_actions = [] + env_shell_file_paths = [] if actions: with make_tmp_dir() as work_dir: with lcd( work_dir ): @@ -133,9 +122,19 @@ return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return + elif action_type == 'set_environment_for_install': + # Currently the only action supported in this category is a list of paths to one or more tool dependency env.sh files, + # the environment setting in each of which will be injected into the environment for all <action type="shell_command"> + # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. + env_shell_file_paths = action_dict[ 'env_shell_file_paths' ] elif action_type == 'shell_command': with settings( warn_only=True ): - return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] ) + cmd = '' + for env_shell_file_path in env_shell_file_paths: + for i, env_setting in enumerate( open( env_shell_file_path ) ): + cmd += '%s\n' % env_setting + cmd += action_dict[ 'command' ] + return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return @@ -157,3 +156,20 @@ logfile.write( str( fabric_AttributeString.stderr ) ) logfile.write( "\n#############################################\n" ) logfile.close() + +@contextmanager +def make_tmp_dir(): + work_dir = tempfile.mkdtemp() + yield work_dir + if os.path.exists( work_dir ): + local( 'rm -rf %s' % work_dir ) + +def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): + """General Galaxy environment configuration. This method is not currently used.""" + env.user = galaxy_user + env.install_dir = tool_dependency_dir + env.host_string = host + env.shell = shell + env.use_sudo = False + env.safe_cmd = local + return env diff -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c -r 1a915a754396da8ac986dd410ee99bed12668235 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 @@ -282,9 +282,6 @@ tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED sa_session.add( tool_dependency ) sa_session.flush() - - - else: package_install_version = package_elem.get( 'version', '1.0' ) tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, @@ -378,7 +375,28 @@ action_dict[ env_elem.tag ] = env_var_dicts else: continue + elif action_type == 'set_environment_for_install': + # <action type="set_environment_for_install"> + # <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056"> + # <package name="numpy" version="1.7.1" /> + # </repository> + # </action> + # This action type allows for defining an environment that will properly compile a tool dependency. Currently, tag set definitions like + # that above are supported, but in the future other approaches to setting environment variables or other environment attributes can be + # supported. The above tag set will result in the installed and compiled numpy version 1.7.1 binary to be used when compiling the current + # tool dependency package. See the package_matplotlib_1_2 repository in the test tool shed for a real-world example. + all_env_shell_file_paths = [] + for env_elem in action_elem: + if env_elem.tag == 'repository': + env_shell_file_paths = common_util.get_env_shell_file_paths( app, env_elem ) + if env_shell_file_paths: + all_env_shell_file_paths.extend( env_shell_file_paths ) + if all_env_shell_file_paths: + action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths + else: + continue else: + log.debug( "Skipping unsupported action type '%s'." % str( action_type ) ) continue actions.append( ( action_type, action_dict ) ) if actions: diff -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c -r 1a915a754396da8ac986dd410ee99bed12668235 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -307,6 +307,7 @@ will be installed in: ~/<app.config.tool_dependency_dir>/<package_name>/<package_version>/<repo_owner>/<repo_name>/<repo_installed_changeset_revision> """ + sa_session = app.model.context.current installed_tool_dependencies = [] # Parse the tool_dependencies.xml config. try: @@ -327,12 +328,30 @@ if tool_dependency.name==package_name and tool_dependency.version==package_version: break if tool_dependency.can_install: - tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) + try: + tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) + except Exception, e: + error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) + log.debug( error_message ) + if tool_dependency: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + sa_session.add( tool_dependency ) + sa_session.flush() if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) elif elem.tag == 'set_environment': - tool_dependency = set_environment( app, elem, tool_shed_repository ) + try: + tool_dependency = set_environment( app, elem, tool_shed_repository ) + except Exception, e: + error_message = "Error setting environment for tool dependency: %s" % str( e ) + log.debug( error_message ) + if tool_dependency: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + sa_session.add( tool_dependency ) + sa_session.flush() if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) diff -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c -r 1a915a754396da8ac986dd410ee99bed12668235 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -32,7 +32,8 @@ log = logging.getLogger( __name__ ) INITIAL_CHANGELOG_HASH = '000000000000' -MAX_CONTENT_SIZE = 32768 +MAX_CONTENT_SIZE = 1048576 +MAX_DISPLAY_SIZE = 32768 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) new_repo_email_alert_template = """ @@ -667,10 +668,17 @@ safe_str = '' for i, line in enumerate( open( file_path ) ): safe_str = '%s%s' % ( safe_str, to_safe_string( line ) ) + # Stop reading after string is larger than MAX_CONTENT_SIZE. if len( safe_str ) > MAX_CONTENT_SIZE: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) - safe_str = '%s%s' % ( safe_str, to_safe_string( large_str ) ) + large_str = \ + to_safe_string( '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) ) + safe_str = '%s%s' % ( safe_str, large_str ) break + if len( safe_str ) > MAX_DISPLAY_SIZE: + # Eliminate the middle of the file to display a file no larger than MAX_DISPLAY_SIZE. This may not be ideal if the file is larger than MAX_CONTENT_SIZE. + join_by_str = \ + to_safe_string( "\n\n...some text eliminated here because file size is larger than maximum viewing size of %s...\n\n" % util.nice_size( MAX_DISPLAY_SIZE ) ) + safe_str = util.shrink_string_by_size( safe_str, MAX_DISPLAY_SIZE, join_by=join_by_str, left_larger=True, beginning_on_size_error=True ) return safe_str def get_repository_files( trans, folder_path ): @@ -787,9 +795,8 @@ This method assumes all repository tools are defined in a single shed-related tool panel config. """ tool_shed = clean_tool_shed_url( repository.tool_shed ) - partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision ) + relative_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision ) # Get the relative tool installation paths from each of the shed tool configs. - relative_install_dir = None shed_config_dict = repository.get_shed_config_dict( app ) if not shed_config_dict: # Just pick a semi-random shed config. @@ -799,7 +806,6 @@ break shed_tool_conf = shed_config_dict[ 'config_filename' ] tool_path = shed_config_dict[ 'tool_path' ] - relative_install_dir = partial_install_dir return shed_tool_conf, tool_path, relative_install_dir def get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ): @@ -1188,13 +1194,13 @@ return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' ) def translate_string( raw_text, to_html=True ): - """Return a subset of a string (up to MAX_CONTENT_SIZE) translated to a safe string for display in a browser.""" + """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text: - if len( raw_text ) <= MAX_CONTENT_SIZE: + if len( raw_text ) <= MAX_DISPLAY_SIZE: translated_string = to_safe_string( raw_text, to_html=to_html ) else: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) - translated_string = to_safe_string( '%s%s' % ( raw_text[ 0:MAX_CONTENT_SIZE ], large_str ), to_html=to_html ) + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_DISPLAY_SIZE ) + translated_string = to_safe_string( '%s%s' % ( raw_text[ 0:MAX_DISPLAY_SIZE ], large_str ), to_html=to_html ) else: translated_string = '' return translated_string Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Retrieve functional test results by owner's username instead of user ID.
by commits-noreply＠bitbucket.org 24 Apr '13

24 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/333dfc42a868/ Changeset: 333dfc42a868 User: inithello Date: 2013-04-24 20:41:16 Summary: Retrieve functional test results by owner's username instead of user ID. Affected #: 1 file diff -r 322d7ae99729ac4235e3f6becc6707c9f0c359d1 -r 333dfc42a8688ec81627ae1164e3be9ba2aa864c 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 @@ -1127,14 +1127,17 @@ @web.expose def get_functional_test_rss( self, trans, **kwd ): - '''Return an RSS feed of the functional test results for the provided user ID, optionally filtered by the 'status' parameter.''' - encoded_user_id = kwd.get( 'user_id', None ) - if encoded_user_id: - user_id = trans.security.decode_id( encoded_user_id ) + '''Return an RSS feed of the functional test results for the provided user, optionally filtered by the 'status' parameter.''' + owner = kwd.get( 'owner', None ) + status = kwd.get( 'status', 'all' ) + if owner: + user = suc.get_user_by_username( trans.app, owner ) else: trans.response.status = 404 - return 'Unknown or missing user ID.' - status = kwd.get( 'status', 'all' ) + return 'Missing owner parameter.' + if user is None: + trans.response.status = 404 + return 'No user found with username %s.' % owner if status == 'passed': # Return only metadata revisions where tools_functionally_correct is set to True. metadata_filter = and_( trans.model.RepositoryMetadata.table.c.includes_tools == True, @@ -1150,6 +1153,7 @@ metadata_filter = and_( trans.model.RepositoryMetadata.table.c.includes_tools == True, trans.model.RepositoryMetadata.table.c.time_last_tested is not None ) + tool_shed_url = web.url_for( '/', qualified=True ) functional_test_results = [] for metadata_row in trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( metadata_filter ) \ @@ -1157,17 +1161,15 @@ .filter( and_( trans.model.Repository.table.c.deleted == False, trans.model.Repository.table.c.private == False, trans.model.Repository.table.c.deprecated == False, - trans.model.Repository.table.c.user_id == user_id ) ): + trans.model.Repository.table.c.user_id == user.id ) ): if not metadata_row.tool_test_errors: continue # Per the RSS 2.0 specification, all dates in RSS feeds must be formatted as specified in RFC 822 # section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT time_tested = metadata_row.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' ) - link = web.url_for( '/', qualified=True ) repository = metadata_row.repository - user = repository.user # Generate a citable URL for this repository with owner and changeset revision. - repository_citable_url = suc.url_join( link, 'view', user.username, repository.name, metadata_row.changeset_revision ) + repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, metadata_row.changeset_revision ) title = 'Functional test results for changeset revision %s of %s' % ( metadata_row.changeset_revision, repository.name ) tests_passed = len( metadata_row.tool_test_errors[ 'tests_passed' ] ) tests_failed = len( metadata_row.tool_test_errors[ 'invalid_tests' ] ) @@ -1184,7 +1186,7 @@ trans.response.set_content_type( 'application/rss+xml' ) return trans.fill_template( '/rss.mako', title='Tool functional test results', - link=link, + link=tool_shed_url, description='Functional test results for repositories owned by %s.' % user.username, pubdate=strftime( '%a, %d %b %Y %H:%M:%S UT', gmtime() ), items=functional_test_results ) 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: inithello: Basic rss feed for tool functional test results for repositories owned by a specific user.
by commits-noreply＠bitbucket.org 24 Apr '13

24 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/322d7ae99729/ Changeset: 322d7ae99729 User: inithello Date: 2013-04-24 20:14:15 Summary: Basic rss feed for tool functional test results for repositories owned by a specific user. Affected #: 2 files diff -r 4126ec15fd614dff9d5a0b555623626fa947197c -r 322d7ae99729ac4235e3f6becc6707c9f0c359d1 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 @@ -1125,6 +1125,70 @@ named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir ) return named_tmp_file + @web.expose + def get_functional_test_rss( self, trans, **kwd ): + '''Return an RSS feed of the functional test results for the provided user ID, optionally filtered by the 'status' parameter.''' + encoded_user_id = kwd.get( 'user_id', None ) + if encoded_user_id: + user_id = trans.security.decode_id( encoded_user_id ) + else: + trans.response.status = 404 + return 'Unknown or missing user ID.' + status = kwd.get( 'status', 'all' ) + if status == 'passed': + # Return only metadata revisions where tools_functionally_correct is set to True. + metadata_filter = and_( trans.model.RepositoryMetadata.table.c.includes_tools == True, + trans.model.RepositoryMetadata.table.c.tools_functionally_correct == True, + trans.model.RepositoryMetadata.table.c.time_last_tested is not None ) + elif status == 'failed': + # Return only metadata revisions where tools_functionally_correct is set to False. + metadata_filter = and_( trans.model.RepositoryMetadata.table.c.includes_tools == True, + trans.model.RepositoryMetadata.table.c.tools_functionally_correct == False, + trans.model.RepositoryMetadata.table.c.time_last_tested is not None ) + else: + # Return all metadata entries for this user's repositories. + metadata_filter = and_( trans.model.RepositoryMetadata.table.c.includes_tools == True, + trans.model.RepositoryMetadata.table.c.time_last_tested is not None ) + + functional_test_results = [] + for metadata_row in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( metadata_filter ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.private == False, + trans.model.Repository.table.c.deprecated == False, + trans.model.Repository.table.c.user_id == user_id ) ): + if not metadata_row.tool_test_errors: + continue + # Per the RSS 2.0 specification, all dates in RSS feeds must be formatted as specified in RFC 822 + # section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT + time_tested = metadata_row.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' ) + link = web.url_for( '/', qualified=True ) + repository = metadata_row.repository + user = repository.user + # Generate a citable URL for this repository with owner and changeset revision. + repository_citable_url = suc.url_join( link, 'view', user.username, repository.name, metadata_row.changeset_revision ) + title = 'Functional test results for changeset revision %s of %s' % ( metadata_row.changeset_revision, repository.name ) + tests_passed = len( metadata_row.tool_test_errors[ 'tests_passed' ] ) + tests_failed = len( metadata_row.tool_test_errors[ 'invalid_tests' ] ) + invalid_tests = len( metadata_row.tool_test_errors[ 'test_errors' ] ) + description = '%d tests passed, %d tests failed, %d tests determined to be invalid.' % ( tests_passed, tests_failed, invalid_tests ) + # The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated + # if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable + # that behavior. + functional_test_results.append( dict( title=title, + guid=repository_citable_url, + link=repository_citable_url, + description=description, + pubdate=time_tested ) ) + trans.response.set_content_type( 'application/rss+xml' ) + return trans.fill_template( '/rss.mako', + title='Tool functional test results', + link=link, + description='Functional test results for repositories owned by %s.' % user.username, + pubdate=strftime( '%a, %d %b %Y %H:%M:%S UT', gmtime() ), + items=functional_test_results ) + def get_metadata( self, trans, repository_id, changeset_revision ): repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata and repository_metadata.metadata: diff -r 4126ec15fd614dff9d5a0b555623626fa947197c -r 322d7ae99729ac4235e3f6becc6707c9f0c359d1 templates/rss.mako --- /dev/null +++ b/templates/rss.mako @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<rss version="2.0"> + <channel> + <title>${title}</title> + <link>${link}</link> + <pubDate>${pubdate}</pubDate> + <description>${description}</description> + <language>en-US</language> + <ttl>60</ttl> + <docs>http://cyber.law.harvard.edu/rss/rss.html</docs> + %for item in items: + <item> + <pubDate>${item['pubdate']}</pubDate> + <title>${item['title']}</title> + <link>${item['link']}</link> + <guid>${item['guid']}</guid> + <description> + ${item['description']} + </description> + </item> + %endfor + </channel> +</rss> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Apr '13

24 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4126ec15fd61/ Changeset: 4126ec15fd61 User: inithello Date: 2013-04-24 15:52:40 Summary: Fix functional test issue with forms having refresh_on_change. Affected #: 1 file diff -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 -r 4126ec15fd614dff9d5a0b555623626fa947197c test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1180,9 +1180,16 @@ # Check for refresh_on_change attribute, submit a change if required if hasattr( control, 'attrs' ) and 'refresh_on_change' in control.attrs.keys(): changed = False - item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] #For DataToolParameter, control.value is the HDA id, but kwd contains the filename. This loop gets the filename/label for the selected values. + # For DataToolParameter, control.value is the HDA id, but kwd contains the filename. + # This loop gets the filename/label for the selected values. + item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] for value in kwd[ control.name ]: - if value not in control.value and True not in [ value in item_label for item_label in item_labels ]: + # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py + if len( value ) > 30 and control.is_of_kind( 'singlelist' ): + field_value = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + field_value = value + if field_value not in control.value and True not in [ field_value in item_label for item_label in item_labels ]: changed = True break if changed: @@ -1190,7 +1197,11 @@ control.clear() # kwd[control.name] should be a singlelist for elem in kwd[ control.name ]: - tc.fv( f.name, control.name, str( elem ) ) + if len( elem ) > 30 and control.is_of_kind( 'singlelist' ): + elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + elem_name = elem + tc.fv( f.name, control.name, str( elem_name ) ) # Create a new submit control, allows form to refresh, instead of going to next page control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} ) control.add_to_form( f ) @@ -1241,7 +1252,7 @@ tc.fv( f.name, control.name, str( elem ) ) except Exception, e2: print "Attempting to set control '", control.name, "' to value '", elem, "' threw exception: ", e2 - # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py + # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py if len( elem ) > 30: elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) else: https://bitbucket.org/galaxy/galaxy-central/commits/b0ea9722b9dd/ Changeset: b0ea9722b9dd Branch: stable User: inithello Date: 2013-04-24 15:52:40 Summary: Fix functional test issue with forms having refresh_on_change. Affected #: 1 file diff -r ae53deed05b68f6febfcf3472c2a11514c12eb0c -r b0ea9722b9dd8e0da63208b59be20b90eae0cea7 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1180,9 +1180,16 @@ # Check for refresh_on_change attribute, submit a change if required if hasattr( control, 'attrs' ) and 'refresh_on_change' in control.attrs.keys(): changed = False - item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] #For DataToolParameter, control.value is the HDA id, but kwd contains the filename. This loop gets the filename/label for the selected values. + # For DataToolParameter, control.value is the HDA id, but kwd contains the filename. + # This loop gets the filename/label for the selected values. + item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] for value in kwd[ control.name ]: - if value not in control.value and True not in [ value in item_label for item_label in item_labels ]: + # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py + if len( value ) > 30 and control.is_of_kind( 'singlelist' ): + field_value = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + field_value = value + if field_value not in control.value and True not in [ field_value in item_label for item_label in item_labels ]: changed = True break if changed: @@ -1190,7 +1197,11 @@ control.clear() # kwd[control.name] should be a singlelist for elem in kwd[ control.name ]: - tc.fv( f.name, control.name, str( elem ) ) + if len( elem ) > 30 and control.is_of_kind( 'singlelist' ): + elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + elem_name = elem + tc.fv( f.name, control.name, str( elem_name ) ) # Create a new submit control, allows form to refresh, instead of going to next page control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} ) control.add_to_form( f ) @@ -1241,7 +1252,7 @@ tc.fv( f.name, control.name, str( elem ) ) except Exception, e2: print "Attempting to set control '", control.name, "' to value '", elem, "' threw exception: ", e2 - # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py + # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py if len( elem ) > 30: elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History API: add update method and allow name, genome_build, annotation, deleted, and published as updatable fields; browser tests: test history api; root/history: fix error handling when user is anonymous
by commits-noreply＠bitbucket.org 23 Apr '13

23 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fb28ceb83c37/ Changeset: fb28ceb83c37 User: carlfeberhard Date: 2013-04-23 23:38:00 Summary: History API: add update method and allow name, genome_build, annotation, deleted, and published as updatable fields; browser tests: test history api; root/history: fix error handling when user is anonymous Affected #: 9 files diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -575,8 +575,10 @@ self.group = group class History( object, UsesAnnotations ): + api_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' ) - api_element_visible_keys = ( 'id', 'name', 'published', 'deleted' ) + api_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged' ) + def __init__( self, id=None, name=None, user=None ): self.id = id self.name = name or "Unnamed history" @@ -589,6 +591,7 @@ self.user = user self.datasets = [] self.galaxy_sessions = [] + def _next_hid( self ): # TODO: override this with something in the database that ensures # better integrity @@ -600,18 +603,21 @@ if dataset.hid > last_hid: last_hid = dataset.hid return last_hid + 1 + def add_galaxy_session( self, galaxy_session, association=None ): if association is None: self.galaxy_sessions.append( GalaxySessionToHistoryAssociation( galaxy_session, self ) ) else: self.galaxy_sessions.append( association ) + def add_dataset( self, dataset, parent_id=None, genome_build=None, set_hid=True, quota=True ): if isinstance( dataset, Dataset ): dataset = HistoryDatasetAssociation(dataset=dataset) object_session( self ).add( dataset ) object_session( self ).flush() elif not isinstance( dataset, HistoryDatasetAssociation ): - raise TypeError, "You can only add Dataset and HistoryDatasetAssociation instances to a history ( you tried to add %s )." % str( dataset ) + raise TypeError, ( "You can only add Dataset and HistoryDatasetAssociation instances to a history" + + " ( you tried to add %s )." % str( dataset ) ) if parent_id: for data in self.datasets: if data.id == parent_id: @@ -630,6 +636,7 @@ self.genome_build = genome_build self.datasets.append( dataset ) return dataset + def copy( self, name=None, target_user=None, activatable=False ): # Create new history. if not name: @@ -647,7 +654,7 @@ # Copy annotation. self.copy_item_annotation( db_session, self.user, self, target_user, new_history ) - #Copy Tags + # Copy Tags new_history.copy_tags_from(target_user=target_user, source_history=self) # Copy HDAs. @@ -667,12 +674,17 @@ db_session.add( new_history ) db_session.flush() return new_history + @property def activatable_datasets( self ): # This needs to be a list return [ hda for hda in self.datasets if not hda.dataset.deleted ] + def get_display_name( self ): - """ History name can be either a string or a unicode object. If string, convert to unicode object assuming 'utf-8' format. """ + """ + History name can be either a string or a unicode object. + If string, convert to unicode object assuming 'utf-8' format. + """ history_name = self.name if isinstance(history_name, str): history_name = unicode(history_name, 'utf-8') @@ -682,6 +694,7 @@ if value_mapper is None: value_mapper = {} rval = {} + try: visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) except AttributeError: @@ -693,6 +706,7 @@ rval[key] = value_mapper.get( key )( rval[key] ) except AttributeError: rval[key] = None + tags_str_list = [] for tag in self.tags: tag_str = tag.user_tname @@ -702,25 +716,51 @@ rval['tags'] = tags_str_list rval['model_class'] = self.__class__.__name__ return rval + + def set_from_dict( self, new_data ): + #AKA: set_api_value + """ + Set object attributes to the values in dictionary new_data limiting + to only those keys in api_element_visible_keys. + + Returns a dictionary of the keys, values that have been changed. + """ + # precondition: keys are proper, values are parsed and validated + changed = {} + for key in [ k for k in new_data.keys() if k in self.api_element_visible_keys ]: + new_val = new_data[ key ] + old_val = self.__getattribute__( key ) + if new_val == old_val: + continue + + self.__setattr__( key, new_val ) + changed[ key ] = new_val + + return changed + @property def get_disk_size_bytes( self ): return self.get_disk_size( nice_size=False ) + def unhide_datasets( self ): for dataset in self.datasets: dataset.mark_unhidden() + def resume_paused_jobs( self ): for dataset in self.datasets: job = dataset.creating_job if job is not None and job.state == Job.states.PAUSED: job.set_state(Job.states.NEW) + def get_disk_size( self, nice_size=False ): # unique datasets only db_session = object_session( self ) - rval = db_session.query( func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset ) - .filter( HistoryDatasetAssociation.table.c.history_id == self.id ) - .filter( HistoryDatasetAssociation.purged != True ) - .filter( Dataset.purged != True ) - .distinct().subquery().c.total_size ) ).first()[0] + rval = db_session.query( + func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset ) + .filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + .filter( HistoryDatasetAssociation.purged != True ) + .filter( Dataset.purged != True ) + .distinct().subquery().c.total_size ) ).first()[0] if rval is None: rval = 0 if nice_size: @@ -733,6 +773,7 @@ new_shta.user = target_user self.tags.append(new_shta) + class HistoryUserShareAssociation( object ): def __init__( self ): self.history = None diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -245,6 +245,187 @@ return item +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.""" + history = self.get_object( trans, id, 'History', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) + return self.security_check( trans, history, check_ownership, check_accessible ) + + def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False, show_purged=False ): + """ Returns history's datasets. """ + query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ + .filter( trans.model.HistoryDatasetAssociation.history == history ) \ + .options( eagerload( "children" ) ) \ + .join( "dataset" ) \ + .options( eagerload_all( "dataset.actions" ) ) \ + .order_by( trans.model.HistoryDatasetAssociation.hid ) + if not show_deleted: + query = query.filter( trans.model.HistoryDatasetAssociation.deleted == False ) + if not show_purged: + query = query.filter( trans.model.Dataset.purged == False ) + return query.all() + + def get_hda_state_counts( self, trans, history, include_deleted=False, include_hidden=False ): + """ + Returns a dictionary with state counts for history's HDAs. Key is a + dataset state, value is the number of states in that count. + """ + # Build query to get (state, count) pairs. + cols_to_select = [ trans.app.model.Dataset.table.c.state, func.count( '*' ) ] + from_obj = trans.app.model.HistoryDatasetAssociation.table.join( trans.app.model.Dataset.table ) + + conditions = [ trans.app.model.HistoryDatasetAssociation.table.c.history_id == history.id ] + if not include_deleted: + # Only count datasets that have not been deleted. + conditions.append( trans.app.model.HistoryDatasetAssociation.table.c.deleted == False ) + if not include_hidden: + # Only count datasets that are visible. + conditions.append( trans.app.model.HistoryDatasetAssociation.table.c.visible == True ) + + group_by = trans.app.model.Dataset.table.c.state + query = select( columns=cols_to_select, + from_obj=from_obj, + whereclause=and_( *conditions ), + group_by=group_by ) + + # Initialize count dict with all states. + state_count_dict = {} + for k, state in trans.app.model.Dataset.states.items(): + state_count_dict[ state ] = 0 + + # Process query results, adding to count dict. + for row in trans.sa_session.execute( query ): + state, count = row + state_count_dict[ state ] = count + + return state_count_dict + + def get_hda_summary_dicts( self, trans, history ): + """Returns a list of dictionaries containing summary information + for each HDA in the given history. + """ + hda_model = trans.model.HistoryDatasetAssociation + + # get state, name, etc. + columns = ( hda_model.name, hda_model.hid, hda_model.id, hda_model.deleted, + trans.model.Dataset.state ) + column_keys = [ "name", "hid", "id", "deleted", "state" ] + + query = ( trans.sa_session.query( *columns ) + .enable_eagerloads( False ) + .filter( hda_model.history == history ) + .join( trans.model.Dataset ) + .order_by( hda_model.hid ) ) + + # build dictionaries, adding history id and encoding all ids + hda_dicts = [] + for hda_tuple in query.all(): + hda_dict = dict( zip( column_keys, hda_tuple ) ) + hda_dict[ 'history_id' ] = history.id + trans.security.encode_dict_ids( hda_dict ) + hda_dicts.append( hda_dict ) + return hda_dicts + + def _get_hda_state_summaries( self, trans, hda_dict_list ): + """Returns two dictionaries (in a tuple): state_counts and state_ids. + Each is keyed according to the possible hda states: + _counts contains a sum of the datasets in each state + _ids contains a list of the encoded ids for each hda in that state + + hda_dict_list should be a list of hda data in dictionary form. + """ + #TODO: doc to rst + # init counts, ids for each state + state_counts = {} + state_ids = {} + for key, state in trans.app.model.Dataset.states.items(): + state_counts[ state ] = 0 + state_ids[ state ] = [] + + for hda_dict in hda_dict_list: + item_state = hda_dict['state'] + if not hda_dict['deleted']: + state_counts[ item_state ] = state_counts[ item_state ] + 1 + # needs to return all ids (no deleted check) + state_ids[ item_state ].append( hda_dict['id'] ) + + return ( state_counts, state_ids ) + + def _get_history_state_from_hdas( self, trans, history, hda_state_counts ): + """Returns the history state based on the states of the HDAs it contains. + """ + states = trans.app.model.Dataset.states + + num_hdas = sum( hda_state_counts.values() ) + # (default to ERROR) + state = states.ERROR + if num_hdas == 0: + state = states.NEW + + else: + if( ( hda_state_counts[ states.RUNNING ] > 0 ) + or ( hda_state_counts[ states.SETTING_METADATA ] > 0 ) + or ( hda_state_counts[ states.UPLOAD ] > 0 ) ): + state = states.RUNNING + + elif hda_state_counts[ states.QUEUED ] > 0: + state = states.QUEUED + + elif( ( hda_state_counts[ states.ERROR ] > 0 ) + or ( hda_state_counts[ states.FAILED_METADATA ] > 0 ) ): + state = states.ERROR + + elif hda_state_counts[ states.OK ] == num_hdas: + state = states.OK + + return state + + def get_history_dict( self, trans, history, hda_dictionaries=None ): + """Returns history data in the form of a dictionary. + """ + history_dict = history.get_api_value( view='element', value_mapper={ 'id':trans.security.encode_id }) + + history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True ) + history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, history ) + if not history_dict[ 'annotation' ]: + history_dict[ 'annotation' ] = '' + #TODO: item_slug url + + hda_summaries = hda_dictionaries if hda_dictionaries else self.get_hda_summary_dicts( trans, history ) + #TODO remove the following in v2 + ( state_counts, state_ids ) = self._get_hda_state_summaries( trans, hda_summaries ) + history_dict[ 'state_details' ] = state_counts + history_dict[ 'state_ids' ] = state_ids + history_dict[ 'state' ] = self._get_history_state_from_hdas( trans, history, state_counts ) + + return history_dict + + def set_history_from_dict( self, trans, history, new_data ): + """ + Changes history data using the given dictionary new_data. + """ + # precondition: access of the history has already been checked + + # send what we can down into the model + changed = history.set_from_dict( new_data ) + # the rest (often involving the trans) - do here + if 'annotation' in new_data.keys() and trans.get_user(): + history.add_item_annotation( trans.sa_session, trans.get_user(), history, new_data[ 'annotation' ] ) + changed[ 'annotation' ] = new_data[ 'annotation' ] + # tags + # importable (ctrl.history.set_accessible_async) + # sharing/permissions? + # slugs? + # purged - duh duh duhhhhhhnnnnnnnnnn + + if changed.keys(): + trans.sa_session.flush() + + return changed + + class UsesHistoryDatasetAssociationMixin: """ Mixin for controllers that use HistoryDatasetAssociation objects. """ @@ -817,165 +998,6 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) -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.""" - history = self.get_object( trans, id, 'History', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) - return self.security_check( trans, history, check_ownership, check_accessible ) - - def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False, show_purged=False ): - """ Returns history's datasets. """ - query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ - .filter( trans.model.HistoryDatasetAssociation.history == history ) \ - .options( eagerload( "children" ) ) \ - .join( "dataset" ) \ - .options( eagerload_all( "dataset.actions" ) ) \ - .order_by( trans.model.HistoryDatasetAssociation.hid ) - if not show_deleted: - query = query.filter( trans.model.HistoryDatasetAssociation.deleted == False ) - if not show_purged: - query = query.filter( trans.model.Dataset.purged == False ) - return query.all() - - def get_hda_state_counts( self, trans, history, include_deleted=False, include_hidden=False ): - """ - Returns a dictionary with state counts for history's HDAs. Key is a - dataset state, value is the number of states in that count. - """ - # Build query to get (state, count) pairs. - cols_to_select = [ trans.app.model.Dataset.table.c.state, func.count( '*' ) ] - from_obj = trans.app.model.HistoryDatasetAssociation.table.join( trans.app.model.Dataset.table ) - - conditions = [ trans.app.model.HistoryDatasetAssociation.table.c.history_id == history.id ] - if not include_deleted: - # Only count datasets that have not been deleted. - conditions.append( trans.app.model.HistoryDatasetAssociation.table.c.deleted == False ) - if not include_hidden: - # Only count datasets that are visible. - conditions.append( trans.app.model.HistoryDatasetAssociation.table.c.visible == True ) - - group_by = trans.app.model.Dataset.table.c.state - query = select( columns=cols_to_select, - from_obj=from_obj, - whereclause=and_( *conditions ), - group_by=group_by ) - - # Initialize count dict with all states. - state_count_dict = {} - for k, state in trans.app.model.Dataset.states.items(): - state_count_dict[ state ] = 0 - - # Process query results, adding to count dict. - for row in trans.sa_session.execute( query ): - state, count = row - state_count_dict[ state ] = count - - return state_count_dict - - def get_hda_summary_dicts( self, trans, history ): - """Returns a list of dictionaries containing summary information - for each HDA in the given history. - """ - hda_model = trans.model.HistoryDatasetAssociation - - # get state, name, etc. - columns = ( hda_model.name, hda_model.hid, hda_model.id, hda_model.deleted, - trans.model.Dataset.state ) - column_keys = [ "name", "hid", "id", "deleted", "state" ] - - query = ( trans.sa_session.query( *columns ) - .enable_eagerloads( False ) - .filter( hda_model.history == history ) - .join( trans.model.Dataset ) - .order_by( hda_model.hid ) ) - - # build dictionaries, adding history id and encoding all ids - hda_dicts = [] - for hda_tuple in query.all(): - hda_dict = dict( zip( column_keys, hda_tuple ) ) - hda_dict[ 'history_id' ] = history.id - trans.security.encode_dict_ids( hda_dict ) - hda_dicts.append( hda_dict ) - return hda_dicts - - def _get_hda_state_summaries( self, trans, hda_dict_list ): - """Returns two dictionaries (in a tuple): state_counts and state_ids. - Each is keyed according to the possible hda states: - _counts contains a sum of the datasets in each state - _ids contains a list of the encoded ids for each hda in that state - - hda_dict_list should be a list of hda data in dictionary form. - """ - #TODO: doc to rst - # init counts, ids for each state - state_counts = {} - state_ids = {} - for key, state in trans.app.model.Dataset.states.items(): - state_counts[ state ] = 0 - state_ids[ state ] = [] - - for hda_dict in hda_dict_list: - item_state = hda_dict['state'] - if not hda_dict['deleted']: - state_counts[ item_state ] = state_counts[ item_state ] + 1 - # needs to return all ids (no deleted check) - state_ids[ item_state ].append( hda_dict['id'] ) - - return ( state_counts, state_ids ) - - def _get_history_state_from_hdas( self, trans, history, hda_state_counts ): - """Returns the history state based on the states of the HDAs it contains. - """ - states = trans.app.model.Dataset.states - - num_hdas = sum( hda_state_counts.values() ) - # (default to ERROR) - state = states.ERROR - if num_hdas == 0: - state = states.NEW - - else: - if( ( hda_state_counts[ states.RUNNING ] > 0 ) - or ( hda_state_counts[ states.SETTING_METADATA ] > 0 ) - or ( hda_state_counts[ states.UPLOAD ] > 0 ) ): - state = states.RUNNING - - elif hda_state_counts[ states.QUEUED ] > 0: - state = states.QUEUED - - elif( ( hda_state_counts[ states.ERROR ] > 0 ) - or ( hda_state_counts[ states.FAILED_METADATA ] > 0 ) ): - state = states.ERROR - - elif hda_state_counts[ states.OK ] == num_hdas: - state = states.OK - - return state - - def get_history_dict( self, trans, history, hda_dictionaries=None ): - """Returns history data in the form of a dictionary. - """ - history_dict = history.get_api_value( view='element', value_mapper={ 'id':trans.security.encode_id }) - - history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True ) - - #TODO: separate, move to annotation api, fill on the client - history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, history ) - if not history_dict[ 'annotation' ]: - history_dict[ 'annotation' ] = '' - - hda_summaries = hda_dictionaries if hda_dictionaries else self.get_hda_summary_dicts( trans, history ) - #TODO remove the following in v2 - ( state_counts, state_ids ) = self._get_hda_state_summaries( trans, hda_summaries ) - history_dict[ 'state_details' ] = state_counts - history_dict[ 'state_ids' ] = state_ids - history_dict[ 'state' ] = self._get_history_state_from_hdas( trans, history, state_counts ) - - return history_dict - - class UsesFormDefinitionsMixin: """Mixin for controllers that use Galaxy form objects.""" diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -1,12 +1,18 @@ """ API operations on a history. """ -import logging + +import pkg_resources +pkg_resources.require("Paste") +from paste.httpexceptions import HTTPBadRequest + from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from galaxy.web import url_for from galaxy.model.orm import desc +from galaxy.util.bunch import Bunch +import logging log = logging.getLogger( __name__ ) class HistoriesController( BaseAPIController, UsesHistoryMixin ): @@ -18,6 +24,7 @@ GET /api/histories/deleted Displays a collection (list) of histories. """ + #TODO: query (by name, date, etc.) rval = [] deleted = util.string_as_bool( deleted ) try: @@ -50,6 +57,8 @@ GET /api/histories/most_recently_used Displays information about a history. """ + #TODO: GET /api/histories/{encoded_history_id}?as_archive=True + #TODO: GET /api/histories/s/{username}/{slug} history_id = id deleted = util.string_as_bool( deleted ) @@ -92,6 +101,10 @@ trans.sa_session.flush() item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) item['url'] = url_for( 'history', id=item['id'] ) + + #TODO: copy own history + #TODO: import an importable history + #TODO: import from archive return item @web.expose_api @@ -146,3 +159,66 @@ trans.sa_session.add( history ) trans.sa_session.flush() return 'OK' + + @web.expose_api + def update( self, trans, id, payload, **kwd ): + """ + PUT /api/histories/{encoded_history_id} + Changes an existing history. + """ + #TODO: PUT /api/histories/{encoded_history_id} payload = { rating: rating } (w/ no security checks) + try: + history = self.get_history( trans, id, check_ownership=True, check_accessible=True, deleted=True ) + # validation handled here and some parsing, processing, and conversion + payload = self._validate_and_parse_update_payload( payload ) + # additional checks here (security, etc.) + changed = self.set_history_from_dict( trans, history, payload ) + + except Exception, exception: + log.error( 'Update of history (%s) failed: %s', id, str( exception ), exc_info=True ) + # convert to appropo HTTP code + if( isinstance( exception, ValueError ) + or isinstance( exception, AttributeError ) ): + # bad syntax from the validater/parser + trans.response.status = 400 + else: + trans.response.status = 500 + return { 'error': str( exception ) } + + return changed + + def _validate_and_parse_update_payload( self, payload ): + """ + Validate and parse incomming data payload for a history. + """ + # This layer handles (most of the stricter idiot proofing): + # - unknown/unallowed keys + # - changing data keys from api key to attribute name + # - protection against bad data form/type + # - protection against malicious data content + # all other conversions and processing (such as permissions, etc.) should happen down the line + for key, val in payload.items(): + # TODO: lots of boilerplate here, but overhead on abstraction is equally onerous + if key == 'name': + if not ( isinstance( val, str ) or isinstance( val, unicode ) ): + raise ValueError( 'name must be a string or unicode: %s' %( str( type( val ) ) ) ) + payload[ 'name' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + #TODO:?? if sanitized != val: log.warn( 'script kiddie' ) + elif key == 'deleted': + if not isinstance( val, bool ): + raise ValueError( 'deleted must be a boolean: %s' %( str( type( val ) ) ) ) + elif key == 'published': + if not isinstance( payload[ 'published' ], bool ): + raise ValueError( 'published must be a boolean: %s' %( str( type( val ) ) ) ) + elif key == 'genome_build': + if not ( isinstance( val, str ) or isinstance( val, unicode ) ): + raise ValueError( 'genome_build must be a string: %s' %( str( type( val ) ) ) ) + payload[ 'genome_build' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + elif key == 'annotation': + if not ( isinstance( val, str ) or isinstance( val, unicode ) ): + raise ValueError( 'annotation must be a string or unicode: %s' %( str( type( val ) ) ) ) + payload[ 'annotation' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) + else: + raise AttributeError( 'unknown key: %s' %( str( key ) ) ) + return payload + diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -724,10 +724,10 @@ 'include_hidden' : include_hidden, 'include_deleted' : include_deleted } history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) + url = url_for( controller='history', action="export_archive", id=id, qualified=True ) return trans.show_message( "Exporting History '%(n)s'. Use this link to download \ the archive or import it to another Galaxy server: \ - <a href='%(u)s'>%(u)s</a>" \ - % ( { 'n' : history.name, 'u' : url_for(controller='history', action="export_archive", id=id, qualified=True ) } ) ) + <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) ) @web.expose @web.json @@ -739,7 +739,8 @@ trans.sa_session.flush() return_dict = { "name" : history.name, - "link" : url_for(controller='history', action="display_by_username_and_slug", username=history.user.username, slug=history.slug ) } + "link" : url_for(controller='history', action="display_by_username_and_slug", + username=history.user.username, slug=history.slug ) } return return_dict @web.expose diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -167,7 +167,8 @@ history_dictionary = self.get_history_dict( trans, history, hda_dictionaries=hda_dictionaries ) except Exception, exc: - log.error( 'Error bootstrapping history for user %d: %s', trans.user.id, str( exc ), exc_info=True ) + user_id = str( trans.user.id ) if trans.user else '(anonymous)' + log.error( 'Error bootstrapping history for user %s: %s', user_id, str( exc ), exc_info=True ) message, status = err_msg() history_dictionary[ 'error' ] = message diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 test/casperjs/api-history-tests.js --- /dev/null +++ b/test/casperjs/api-history-tests.js @@ -0,0 +1,372 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +spaceghost.user.loginOrRegisterUser( email, password ); + +function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ return false; } + } + return true; +} + +function countKeys( object ){ + if( !utils.isObject( object ) ){ return 0; } + var count = 0; + for( var key in object ){ + if( object.hasOwnProperty( key ) ){ count += 1; } + } + return count; +} + +// =================================================================== TESTS +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + // ------------------------------------------------------------------------------------------- INDEX + this.test.comment( 'index should get a list of histories' ); + var historyIndex = this.api.histories.index(); + //this.debug( this.jsonStr( historyIndex ) ); + this.test.assert( utils.isArray( historyIndex ), "index returned an array: length " + historyIndex.length ); + this.test.assert( historyIndex.length >= 1, 'Has at least one history' ); + + var firstHistory = historyIndex[0]; + this.test.assert( hasKeys( firstHistory, [ 'id', 'name', 'url' ] ), 'Has the proper keys' ); + this.test.assert( this.api.isEncodedId( firstHistory.id ), 'Id appears well-formed' ); + + + // ------------------------------------------------------------------------------------------- SHOW + this.test.comment( 'show should get a history details object' ); + var historyShow = this.api.histories.show( firstHistory.id ); + //this.debug( this.jsonStr( historyShow ) ); + this.test.assert( hasKeys( historyShow, [ + 'id', 'name', 'annotation', 'nice_size', 'contents_url', + 'state', 'state_details', 'state_ids' ]), + 'Has the proper keys' ); + + this.test.comment( 'a history details object should contain two objects named state_details and state_ids' ); + var states = [ + 'discarded', 'empty', 'error', 'failed_metadata', 'new', + 'ok', 'paused', 'queued', 'running', 'setting_metadata', 'upload' ], + state_details = historyShow.state_details, + state_ids = historyShow.state_ids; + this.test.assert( hasKeys( state_details, states ), 'state_details has the proper keys' ); + this.test.assert( hasKeys( state_ids, states ), 'state_ids has the proper keys' ); + var state_detailsAreNumbers = true; + state_idsAreArrays = true; + states.forEach( function( state ){ + if( !utils.isArray( state_ids[ state ] ) ){ state_idsAreArrays = false; } + if( !utils.isNumber( state_details[ state ] ) ){ state_detailsAreNumbers = false; } + }); + this.test.assert( state_idsAreArrays, 'state_ids values are arrays' ); + this.test.assert( state_detailsAreNumbers, 'state_details values are numbers' ); + + this.test.comment( 'calling show with "most_recently_used" should return the first history' ); + historyShow = this.api.histories.show( 'most_recently_used' ); + //this.debug( this.jsonStr( historyShow ) ); + this.test.assert( historyShow.id === firstHistory.id, 'Is the first history' ); + + this.test.comment( 'Should be able to combine calls' ); + this.test.assert( this.api.histories.show( this.api.histories.index()[0].id ).id === firstHistory.id, + 'combining function calls works' ); + + // test server bad id protection + this.test.comment( 'A bad id to show should throw an error' ); + this.assertRaises( function(){ + this.api.histories.show( '1234123412341234' ); + }, 'Error in history API at showing history detail: 400 Bad Request', 'Raises an exception' ); + + + // ------------------------------------------------------------------------------------------- CREATE + this.test.comment( 'Calling create should create a new history and allow setting the name' ); + var newHistoryName = 'Created History', + createdHistory = this.api.histories.create({ name: newHistoryName }); + //this.debug( 'returned from create:\n' + this.jsonStr( createdHistory ) ); + this.test.assert( createdHistory.name === newHistoryName, + "Name of created history (from create) is correct: " + createdHistory.name ); + + // check the index + var newFirstHistory = this.api.histories.index()[0]; + //this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); + this.test.assert( newFirstHistory.name === newHistoryName, + "Name of last history (from index) is correct: " + newFirstHistory.name ); + this.test.assert( newFirstHistory.id === createdHistory.id, + "Id of last history (from index) is correct: " + newFirstHistory.id ); + + + // ------------------------------------------------------------------------------------------- DELETE + this.test.comment( 'calling delete should delete the given history and remove it from the standard index' ); + var deletedHistory = this.api.histories.delete_( createdHistory.id ); + //this.debug( 'returned from delete:\n' + this.jsonStr( deletedHistory ) ); + this.test.assert( deletedHistory === 'OK', + "Deletion returned 'OK' - even though that's not a great, informative response: " + deletedHistory ); + + newFirstHistory = this.api.histories.index()[0]; + //this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); + this.test.assert( newFirstHistory.id !== createdHistory.id, + "Id of last history (from index) DOES NOT appear: " + newFirstHistory.id ); + + this.test.comment( 'calling index with delete=true should include the deleted history' ); + newFirstHistory = this.api.histories.index( true )[0]; + //this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); + this.test.assert( newFirstHistory.id === createdHistory.id, + "Id of last history (from index) DOES appear using index( deleted=true ): " + newFirstHistory.id ); + + + // ------------------------------------------------------------------------------------------- UNDELETE + this.test.comment( 'calling undelete should undelete the given history and re-include it in index' ); + var undeletedHistory = this.api.histories.undelete( createdHistory.id ); + //this.debug( 'returned from undelete:\n' + this.jsonStr( undeletedHistory ) ); + this.test.assert( undeletedHistory === 'OK', + "Undeletion returned 'OK' - even though that's not a great, informative response: " + undeletedHistory ); + + newFirstHistory = this.api.histories.index()[0]; + this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); + this.test.assert( newFirstHistory.id === createdHistory.id, + "Id of last history (from index) DOES appear after undeletion: " + newFirstHistory.id ); + + + //TODO: show, deleted flag + //TODO: delete, purge flag + // ------------------------------------------------------------------------------------------- UPDATE + // ........................................................................................... idiot proofing + this.test.comment( 'updating to the current value should return no value (no change)' ); + historyShow = this.api.histories.show( newFirstHistory.id ); + var returned = this.api.histories.update( newFirstHistory.id, { + name : historyShow.name + }); + this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + + this.test.comment( 'updating using a nonsense key should fail with an error' ); + var err = {}; + try { + returned = this.api.histories.update( newFirstHistory.id, { + konamiCode : 'uuddlrlrba' + }); + } catch( error ){ + err = error; + //this.debug( this.jsonStr( err ) ); + } + this.test.assert( !!err.message, "Error occurred: " + err.message ); + this.test.assert( err.status === 400, "Error status is 400: " + err.status ); + + this.test.comment( 'updating by attempting to change type should cause an error' ); + err = {}; + try { + returned = this.api.histories.update( newFirstHistory.id, { + //name : false + deleted : 'sure why not' + }); + } catch( error ){ + err = error; + //this.debug( this.jsonStr( err ) ); + } + this.test.assert( !!err.message, "Error occurred: " + err.message ); + this.test.assert( err.status === 400, "Error status is 400: " + err.status ); + //TODO??: other type checks? + + + // ........................................................................................... name + this.test.comment( 'update should allow changing the name' ); + returned = this.api.histories.update( newFirstHistory.id, { + name : 'New name' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.name === 'New name', "Name successfully set via update: " + historyShow.name ); + + this.test.comment( 'update should sanitize any new name' ); + returned = this.api.histories.update( newFirstHistory.id, { + name : 'New name<script type="text/javascript" src="bler">alert("blah");</script>' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.name === 'New name', "Update sanitized name: " + historyShow.name ); + + //NOTE!: this fails on sqlite3 (with default setup) + try { + this.test.comment( 'update should allow unicode in names' ); + var unicodeName = '桜ゲノム'; + returned = this.api.histories.update( newFirstHistory.id, { + name : unicodeName + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.name === unicodeName, "Update accepted unicode name: " + historyShow.name ); + } catch( err ){ + //this.debug( this.jsonStr( err ) ); + if( ( err instanceof this.api.APIError ) + && ( err.status === 500 ) + && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ + this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } + } + + this.test.comment( 'update should allow escaped quotations in names' ); + var quotedName = '"Bler"'; + returned = this.api.histories.update( newFirstHistory.id, { + name : quotedName + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.name === quotedName, + "Update accepted escaped quotations in name: " + historyShow.name ); + + + // ........................................................................................... deleted + this.test.comment( 'update should allow changing the deleted flag' ); + returned = this.api.histories.update( newFirstHistory.id, { + deleted: true + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.deleted === true, "Update set the deleted flag: " + historyShow.deleted ); + + this.test.comment( 'update should allow changing the deleted flag back' ); + returned = this.api.histories.update( newFirstHistory.id, { + deleted: false + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.deleted === false, "Update set the deleted flag: " + historyShow.deleted ); + + + // ........................................................................................... published + this.test.comment( 'update should allow changing the published flag' ); + returned = this.api.histories.update( newFirstHistory.id, { + published: true + }); + this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.published === true, "Update set the published flag: " + historyShow.published ); + + + // ........................................................................................... genome_build + this.test.comment( 'update should allow changing the genome_build' ); + returned = this.api.histories.update( newFirstHistory.id, { + genome_build : 'hg18' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.genome_build === 'hg18', + "genome_build successfully set via update: " + historyShow.genome_build ); + + this.test.comment( 'update should sanitize any genome_build' ); + returned = this.api.histories.update( newFirstHistory.id, { + genome_build : 'hg18<script type="text/javascript" src="bler">alert("blah");</script>' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.genome_build === 'hg18', + "Update sanitized genome_build: " + historyShow.genome_build ); + + this.test.comment( 'update should allow unicode in genome builds' ); + var unicodeBuild = '桜12'; + //NOTE!: this fails on sqlite3 (with default setup) + try { + returned = this.api.histories.update( newFirstHistory.id, { + name : unicodeBuild + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.genome_build === unicodeBuild, + "Update accepted unicode genome_build: " + historyShow.name ); + } catch( err ){ + //this.debug( this.jsonStr( err ) ); + if( ( err instanceof this.api.APIError ) + && ( err.status === 500 ) + && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ + this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } + } + + + // ........................................................................................... annotation + this.test.comment( 'update should allow changing the annotation' ); + var newAnnotation = 'Here are some notes that I stole from the person next to me'; + returned = this.api.histories.update( newFirstHistory.id, { + annotation : newAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.annotation === newAnnotation, + "Annotation successfully set via update: " + historyShow.annotation ); + + this.test.comment( 'update should sanitize any new annotation' ); + returned = this.api.histories.update( newFirstHistory.id, { + annotation : 'New annotation<script type="text/javascript" src="bler">alert("blah");</script>' + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.annotation === 'New annotation', + "Update sanitized annotation: " + historyShow.annotation ); + + //NOTE!: this fails on sqlite3 (with default setup) + try { + this.test.comment( 'update should allow unicode in annotations' ); + var unicodeAnnotation = 'お願いは、それが落下させない'; + returned = this.api.histories.update( newFirstHistory.id, { + annotation : unicodeAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.annotation === unicodeAnnotation, + "Update accepted unicode annotation: " + historyShow.annotation ); + } catch( err ){ + //this.debug( this.jsonStr( err ) ); + if( ( err instanceof this.api.APIError ) + && ( err.status === 500 ) + && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ + this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); + } + } + + this.test.comment( 'update should allow escaped quotations in annotations' ); + var quotedAnnotation = '"Bler"'; + returned = this.api.histories.update( newFirstHistory.id, { + annotation : quotedAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.annotation === quotedAnnotation, + "Update accepted escaped quotations in annotation: " + historyShow.annotation ); + + +/* +*/ + //this.debug( this.jsonStr( historyShow ) ); +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -361,6 +361,14 @@ self.run_js_script( 'hda-state-tests.js' ) +class Test_05_API( CasperJSTestCase ): + """Tests for API functionality and security. + """ + def test_00_history_api( self ): + """Test history API. + """ + self.run_js_script( 'api-history-tests.js' ) + # ==================================================================== MAIN if __name__ == '__main__': diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -32,11 +32,13 @@ APIError.prototype = new Error(); APIError.prototype.constructor = Error; /** @class Thrown when Galaxy the API returns an error from a request */ -function APIError( msg ){ +function APIError( msg, status ){ Error.apply( this, arguments ); this.name = "APIError"; this.message = msg; + this.status = status; } +API.prototype.APIError = APIError; exports.APIError = APIError; /* ------------------------------------------------------------------- TODO: @@ -65,7 +67,8 @@ if( resp.status !== 200 ){ // grrr... this doesn't lose the \n\r\t - throw new APIError( resp.responseText.replace( /[\s\n\r\t]+/gm, ' ' ).replace( /"/, '' ) ); + //throw new APIError( resp.responseText.replace( /[\s\n\r\t]+/gm, ' ' ).replace( /"/, '' ) ); + throw new APIError( resp.responseText, resp.status ); } return JSON.parse( resp.responseText ); }; @@ -130,7 +133,8 @@ show : 'api/histories/%s', create : 'api/histories', delete_ : 'api/histories/%s', - undelete: 'api/histories/deleted/%s/undelete' + undelete: 'api/histories/deleted/%s/undelete', + update : 'api/histories/%s' }; HistoriesAPI.prototype.index = function index( deleted ){ @@ -183,6 +187,20 @@ }); }; +HistoriesAPI.prototype.update = function create( id, payload ){ + this.api.spaceghost.info( 'history.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + id = this.api.ensureId( id ); + payload = this.api.ensureObject( payload ); + url = utils.format( this.urlTpls.update, id ); + + return this.api._ajax( url, { + type : 'PUT', + data : payload + }); +}; + // =================================================================== HDAS var HDAAPI = function HDAAPI( api ){ @@ -201,7 +219,7 @@ }; HDAAPI.prototype.index = function index( historyId, ids ){ - this.api.spaceghost.info( 'history.index: ' + [ historyId, ids ] ); + this.api.spaceghost.info( 'hda.index: ' + [ historyId, ids ] ); var data = {}; if( ids ){ ids = ( utils.isArray( ids ) )?( ids.join( ',' ) ):( ids ); @@ -214,7 +232,7 @@ }; HDAAPI.prototype.show = function show( historyId, id, deleted ){ - this.api.spaceghost.info( 'history.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + this.api.spaceghost.info( 'hda.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; @@ -224,7 +242,7 @@ }; HDAAPI.prototype.create = function create( historyId, payload ){ - this.api.spaceghost.info( 'history.create: ' + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'hda.create: ' + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data payload = this.api.ensureObject( payload ); @@ -235,7 +253,8 @@ }; HDAAPI.prototype.update = function create( historyId, id, payload ){ - this.api.spaceghost.info( 'history.update: ' + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'hda.update: ' + historyId + ',' + id + ',' + + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data historyId = this.api.ensureId( historyId ); diff -r 7c59121055516595937b83d51eaf98b60723b622 -r fb28ceb83c379e1d792f622f9b2cbc8c3e050f37 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -545,9 +545,10 @@ * NOTE: uses string indexOf - doesn't play well with urls like [ 'history', 'history/bler' ] * @param {String} urlToWaitFor the url to wait for (rel. to spaceghost.baseUrl) * @param {Function} then the function to call after the nav request + * @param {Function} timeoutFn the function to call on timeout (optional) */ -SpaceGhost.prototype.waitForNavigation = function waitForNavigation( urlToWaitFor, then ){ - return this.waitForMultipleNavigation( [ urlToWaitFor ], then ); +SpaceGhost.prototype.waitForNavigation = function waitForNavigation( urlToWaitFor, then, timeoutFn ){ + return this.waitForMultipleNavigation( [ urlToWaitFor ], then, timeoutFn ); }; /** Wait for a multiple navigation requests then call a function. @@ -555,8 +556,9 @@ * NOTE: uses string indexOf - doesn't play well with urls like [ 'history', 'history/bler' ] * @param {String[]} urlsToWaitFor the relative urls to wait for * @param {Function} then the function to call after the nav request + * @param {Function} timeoutFn the function to call on timeout (optional) */ -SpaceGhost.prototype.waitForMultipleNavigation = function waitForMultipleNavigation( urlsToWaitFor, then ){ +SpaceGhost.prototype.waitForMultipleNavigation = function waitForMultipleNavigation( urlsToWaitFor, then, timeoutFn ){ this.info( 'waiting for navigation: ' + this.jsonStr( urlsToWaitFor ) ); function urlMatches( urlToMatch, url ){ return ( url.indexOf( spaceghost.baseUrl + '/' + urlToMatch ) !== -1 ); @@ -586,6 +588,9 @@ function callThen(){ if( utils.isFunction( then ) ){ then.call( this ); } }, + function timeout(){ + if( utils.isFunction( timeoutFn ) ){ timeoutFn.call( this ); } + }, this.options.waitTimeout * urlsToWaitFor.length ); return this; @@ -731,8 +736,9 @@ /** Casper has an (undocumented?) skip test feature. This is a conv. wrapper for that. */ -SpaceGhost.prototype.skipTest = function skipTest(){ - throw this.test.SKIP_MESSAGE; +SpaceGhost.prototype.skipTest = function skipTest( msg ){ + this.warn( 'Skipping test. ' + msg ); + //throw this.test.SKIP_MESSAGE; }; /** Test helper - within frame, assert selector, and assert text in selector 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: Functional tests to verify correct setting of metadata when dependency definitions are deleted.
by commits-noreply＠bitbucket.org 23 Apr '13

23 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c5912105551/ Changeset: 7c5912105551 User: inithello Date: 2013-04-23 20:46:53 Summary: Functional tests to verify correct setting of metadata when dependency definitions are deleted. Affected #: 1 file diff -r 1e3d92ec22b2794bfa2294edb74695c580791406 -r 7c59121055516595937b83d51eaf98b60723b622 test/tool_shed/functional/test_0440_deleting_dependency_definitions.py --- /dev/null +++ b/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py @@ -0,0 +1,365 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +column_repository_name = 'column_maker_0440' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_0440' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +bwa_package_repository_name = 'bwa_package_0440' +bwa_package_repository_description = "BWA Package Repository" +bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." + +bwa_base_repository_name = 'bwa_base_0440' +bwa_base_repository_description = "BWA Base" +bwa_base_repository_long_description = "NT space mapping with BWA" + +bwa_tool_dependency_repository_name = 'bwa_tool_dependency_0440' +bwa_tool_dependency_repository_description = "BWA Base" +bwa_tool_dependency_repository_long_description = "NT space mapping with BWA" + +''' +Simple repository dependencies: +1. Create and populate column_maker_0440 so that it has an installable revision 0. +2. Create and populate convert_chars_0440 so that it has an installable revision 0. +3. Add a valid simple repository_dependencies.xml to convert_chars_0440 that points to the installable revision of column_maker_0440. +4. Make sure the installable revision of convert_chars_0440 is now revision 1 instead of revision 0. +5. Delete repository_dependencies.xml from convert_chars_0440, and make sure convert_chars_0440 now has two installable revisions: 1 and 2 + +Complex repository dependencies: +1. Create and populate bwa_package_0440 so that it has a valid orphan tool dependency definition and an installable revision 0. +2. Create and populate bwa_base_0440 so that it has an installable revision 0. +3. Add a valid complex repository dependency tool_dependencies.xml to bwa_base_0440 that points to the installable revision 0 of bwa_package_0440. +4. Make sure that bwa_base_0440 installable revision is now revision 1 instead of revision 0. +5. Delete tool_dependencies.xml from bwa_base_0440, and make sure bwa_base_0440 now has two installable revisions: 1 and 2 + +Tool dependencies: +1. Create and populate bwa_tool_dependency_0440 so that it has a valid orphan tool dependency definition and an installable revision 0. +2. Delete tool_dependencies.xml from bwa_tool_dependency_0440, and make sure that bwa_tool_dependency_0440 still has + a single installable revision 0. +3. Add the same tool_dependencies.xml file to bwa_tool_dependency_0440, and make sure that bwa_tool_dependency_0440 + still has a single installable revision 0. +''' + + +class TestDeletedDependencies( ShedTwillTestCase ): + '''Test metadata setting when dependency definitions are deleted.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + """ + Create all the user accounts that are needed for this test script to run independently of other tests. + Previously created accounts will not be re-created. + """ + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_column_maker_repository( self ): + '''Create and populate a repository named column_maker_0440.''' + ''' + We are at simple repository dependencies, step 1 - Create and populate column_maker_0440 so that it has an installable revision 0. + ''' + category = self.create_category( name='Test 0440 Deleted Dependency Definitions', + description='Description of Deleted Dependency Definitions category for test 0440' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'column_maker_0440' has been created" ] + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='column_maker/column_maker.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded column maker tool tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_convert_chars_repository( self ): + '''Create and populate a repository named convert_chars_0440.''' + ''' + We are at simple repository dependencies, step 2 - Create and populate convert_chars_0440 so that it has an installable revision 0. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'convert_chars_0440' has been created" ] + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='convert_chars/convert_chars.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded convert chars tool tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_dependency_on_convert_chars( self ): + '''Create a dependency definition file that specifies column_maker_0440 and upload it to convert_chars_0440.''' + ''' + We are at simple repository dependencies, step 3 - Add a valid simple repository_dependencies.xml to + convert_chars_0440 that points to the installable revision of column_maker_0440. + ''' + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0440', additional_paths=[ 'dependencies' ] ) + column_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) ) + # After this, convert_chars_0440 should depend on column_maker_0440. + self.create_repository_dependency( repository=convert_repository, + repository_tuples=[ column_tuple ], + filepath=dependency_xml_path, + prior_installation_required=True ) + self.check_repository_dependency( convert_repository, column_repository ) + + def test_0020_verify_dependency_metadata( self ): + '''Verify that uploading the dependency moved metadata to the tip.''' + ''' + We are at simple repository dependencies, step 4 - Make sure the installable revision of convert_chars_0440 is now + revision 1 (the tip) instead of revision 0. + ''' + repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + tip = self.get_repository_tip( repository ) + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, tip ) + # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions. + assert metadata_record.downloadable, 'Tip is not downloadable.' + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0025_delete_repository_dependency( self ): + '''Delete the repository_dependencies.xml from convert_chars_0440.''' + ''' + We are at simple repository dependencies, steps 5 and 6 - Delete repository_dependencies.xml from convert_chars_0440. + Make sure convert_chars_0440 now has two installable revisions: 1 and 2 + ''' + repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml + # is deleted and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.delete_files_from_repository( repository, filenames=[ 'repository_dependencies.xml' ] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains repository_dependencies.xml is no longer downloadable.' % \ + repository.name + # Check that the new tip is also downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that does not contain repository_dependencies.xml is not downloadable.' % \ + repository.name + # Explicitly reload the repository instance from the database, to avoid potential caching issues. + test_db_util.refresh( repository ) + # Verify that there are only two downloadable revisions. + assert len( repository.downloadable_revisions ) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0030_create_bwa_package_repository( self ): + '''Create and populate the bwa_package_0440 repository.''' + ''' + We are at complex repository dependencies, step 1 - Create and populate bwa_package_0440 so that it has a valid orphan + tool dependency definition and an installable revision 0. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'bwa_package_0440' has been created" ] + repository = self.get_or_create_repository( name=bwa_package_repository_name, + description=bwa_package_repository_description, + long_description=bwa_package_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='bwa/complex/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded package tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0035_create_bwa_base_repository( self ): + '''Create and populate the bwa_base_0440 repository.''' + ''' + We are at complex repository dependencies, step 2 - Create and populate bwa_base_0440 so that it has an installable revision 0. + This repository should contain a tool with a defined dependency that will be satisfied by the tool dependency defined in bwa_package_0440. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'bwa_base_0440' has been created" ] + repository = self.get_or_create_repository( name=bwa_base_repository_name, + description=bwa_base_repository_description, + long_description=bwa_base_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='bwa/complex/bwa_base.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded BWA nucleotide space mapping tool tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0040_create_dependency_on_bwa_package_repository( self ): + '''Create a complex repository dependency on bwa_package_0440 and upload it to bwa_tool_0440.''' + ''' + We are at complex repository dependencies, step 3 - Add a valid complex repository dependency tool_dependencies.xml to + bwa_base_0440 that points to the installable revision 0 of bwa_package_0440. + ''' + bwa_package_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) + bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + dependency_path = self.generate_temp_path( 'test_0440', additional_paths=[ 'complex' ] ) + changeset_revision = self.get_repository_tip( bwa_package_repository ) + bwa_tuple = ( self.url, bwa_package_repository.name, bwa_package_repository.user.username, changeset_revision ) + self.create_repository_dependency( repository=bwa_base_repository, + repository_tuples=[ bwa_tuple ], + filepath=dependency_path, + prior_installation_required=True, + complex=True, + package='bwa', + version='0.5.9' ) + + def test_0045_verify_dependency_metadata( self ): + '''Verify that uploading the dependency moved metadata to the tip.''' + ''' + We are at complex repository dependencies, step 4 - Make sure that bwa_base_0440 installable revision is now revision 1 + instead of revision 0. + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tip = self.get_repository_tip( repository ) + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, tip ) + # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions. + assert metadata_record.downloadable, 'Tip is not downloadable.' + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0050_delete_complex_repository_dependency( self ): + '''Delete the tool_dependencies.xml from bwa_base_0440.''' + ''' + We are at complex repository dependencies, step 5 - Delete tool_dependencies.xml from bwa_base_0440, + and make sure bwa_base_0440 now has two installable revisions: 1 and 2 + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still a downloadable revision after tool_dependencies.xml + # is deleted and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.delete_files_from_repository( repository, filenames=[ 'tool_dependencies.xml' ] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is no longer downloadable.' % \ + repository.name + # Check that the new tip is also downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that does not contain tool_dependencies.xml is not downloadable.' % \ + repository.name + # Verify that there are only two downloadable revisions. + assert len( repository.downloadable_revisions ) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0055_create_bwa_tool_dependency_repository( self ): + '''Create and populate the bwa_tool_dependency_0440 repository.''' + ''' + We are at tool dependencies, step 1 - Create and populate bwa_tool_dependency_0440 so that it has a valid orphan tool + dependency definition and an installable revision 0. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'bwa_tool_dependency_0440' has been created" ] + repository = self.get_or_create_repository( name=bwa_tool_dependency_repository_name, + description=bwa_tool_dependency_repository_description, + long_description=bwa_tool_dependency_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='bwa/complex/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded package tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0060_delete_bwa_tool_dependency_definition( self ): + '''Delete the tool_dependencies.xml file from bwa_tool_dependency_0440.''' + ''' + We are at tool dependencies, step 2 - Delete tool_dependencies.xml from bwa_tool_dependency_0440. + Make sure bwa_tool_dependency_0440 still has a downloadable changeset revision at the old tip. + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_dependency_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml + # is deleted and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.delete_files_from_repository( repository, filenames=[ 'tool_dependencies.xml' ] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is no longer downloadable.' % \ + repository.name + # Check that the new tip does not have a metadata revision. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + # If a changeset revision does not have metadata, the above method will return None. + assert metadata_record is None, 'The tip revision of %s should not have metadata, but metadata was found.' % repository.name + # Verify that the new changeset revision is not downloadable. + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0065_reupload_bwa_tool_dependency_definition( self ): + '''Reupload the tool_dependencies.xml file to bwa_tool_dependency_0440.''' + ''' + We are at tool dependencies, step 3 - Add the same tool_dependencies.xml file to bwa_tool_dependency_0440, and make sure + that bwa_tool_dependency_0440 still has a single installable revision 0. + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_dependency_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still not a downloadable revision after tool_dependencies.xml + # is re-uploaded and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.upload_file( repository, + filename='bwa/complex/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded package tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record is None, 'The revision of %s that does not contain tool_dependencies.xml should not be downloadable, but is.' % \ + repository.name + # Check that the new tip is also downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is not downloadable.' % \ + repository.name + # Verify that there are only two downloadable revisions. + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Have data source tools display the provided 'name' parameter as the initial dataset name.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e3d92ec22b2/ Changeset: 1e3d92ec22b2 User: dan Date: 2013-04-22 22:58:49 Summary: Have data source tools display the provided 'name' parameter as the initial dataset name. Affected #: 3 files diff -r ea0b7ca55aec1552718132227d80b0ae82ca2913 -r 1e3d92ec22b2794bfa2294edb74695c580791406 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -36,6 +36,7 @@ from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.jobs import ParallelismInfo from galaxy.tools.actions import DefaultToolAction +from galaxy.tools.actions.data_source import DataSourceToolAction from galaxy.tools.actions.data_manager import DataManagerToolAction from galaxy.tools.deps import DependencyManager from galaxy.tools.parameters import check_param, params_from_strings, params_to_strings @@ -3028,6 +3029,7 @@ allow the user to query and extract data from another web site. """ tool_type = 'data_source' + default_tool_action = DataSourceToolAction def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=%s" />' % self.id ) ) diff -r ea0b7ca55aec1552718132227d80b0ae82ca2913 -r 1e3d92ec22b2794bfa2294edb74695c580791406 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -342,9 +342,10 @@ params['on_string'] = on_text data.name = fill_template( output.label, context=params ) else: - data.name = tool.name - if on_text: - data.name += ( " on " + on_text ) + if params is None: + params = make_dict_copy( incoming ) + wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values ) + data.name = self._get_default_data_name( data, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params ) # Store output out_data[ name ] = data if output.actions: @@ -430,3 +431,9 @@ trans.app.job_queue.put( job.id, job.tool_id ) trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) return job, out_data + + def _get_default_data_name( self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd ): + name = tool.name + if on_text: + name += ( " on " + on_text ) + return name diff -r ea0b7ca55aec1552718132227d80b0ae82ca2913 -r 1e3d92ec22b2794bfa2294edb74695c580791406 lib/galaxy/tools/actions/data_source.py --- /dev/null +++ b/lib/galaxy/tools/actions/data_source.py @@ -0,0 +1,12 @@ +from __init__ import DefaultToolAction + +import logging +log = logging.getLogger( __name__ ) + +class DataSourceToolAction( DefaultToolAction ): + """Tool action used for Data Source Tools""" + + def _get_default_data_name( self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd ): + if incoming and 'name' in incoming: + return incoming[ 'name' ] + return super( DataSourceToolAction, self )._get_default_data_name( dataset, tool, on_text=on_text, trans=trans, incoming=incoming, history=history, params=params, job_params=job_params ) 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: Raise exceptions when tool dependency definition <install> and <set_environment> tags define an unsupported version attribute.
by commits-noreply＠bitbucket.org 22 Apr '13

22 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ea0b7ca55aec/ Changeset: ea0b7ca55aec User: greg Date: 2013-04-22 20:51:48 Summary: Raise exceptions when tool dependency definition <install> and <set_environment> tags define an unsupported version attribute. Affected #: 1 file diff -r 42632cc2a166e8933fe29496a6087309769b8987 -r ea0b7ca55aec1552718132227d80b0ae82ca2913 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 @@ -151,6 +151,8 @@ action_dict[ env_elem.tag ] = env_var_dicts actions.append( ( action_type, action_dict ) ) return tool_dependency, actions + else: + raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) return None, actions def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): @@ -299,6 +301,8 @@ sa_session.refresh( tool_dependency ) if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: print package_name, 'version', package_version, 'installed in', install_dir + else: + raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) elif package_elem.tag == 'readme': # Nothing to be done. continue @@ -550,6 +554,8 @@ sa_session.add( tool_dependency ) sa_session.flush() print 'Environment variable ', env_var_name, 'set in', install_dir + else: + raise NotImplementedError( 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' ) def strip_path( fpath ): if not fpath: 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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