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

commit/galaxy-central: 2 new changesets
by Bitbucket 20 Feb '13

20 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9697f9fc92b1/ changeset: 9697f9fc92b1 user: inithello date: 2013-02-20 21:51:56 summary: Fix an import in the repository_revisions API controller. affected #: 1 file diff -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 -r 9697f9fc92b1bc8fbfaca72917eeff928c2cc4ac lib/galaxy/webapps/community/api/repository_revisions.py --- a/lib/galaxy/webapps/community/api/repository_revisions.py +++ b/lib/galaxy/webapps/community/api/repository_revisions.py @@ -1,10 +1,11 @@ -from galaxy import web, util, logging +from galaxy import web, util from galaxy.web.base.controller import BaseController, BaseAPIController from galaxy.web.framework.helpers import is_true import pkg_resources pkg_resources.require( "Routes" ) import routes +import logging log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/1adf6fdd9c49/ changeset: 1adf6fdd9c49 user: inithello date: 2013-02-20 21:52:10 summary: Add do_not_test, tools_functionally_correct, time_last_tested, and tool_test_errors columns to the repository_metadata table. affected #: 3 files diff -r 9697f9fc92b1bc8fbfaca72917eeff928c2cc4ac -r 1adf6fdd9c49bda204e5d90f70f10e7ef4ec06bd lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -170,13 +170,18 @@ class RepositoryMetadata( object, APIItem ): api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable' ) api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable' ) - def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False ): + def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, + tools_functionally_correct=False, do_not_test=False, time_last_tested=None, tool_test_errors=None ): self.repository_id = repository_id self.changeset_revision = changeset_revision self.metadata = metadata or dict() self.tool_versions = tool_versions or dict() self.malicious = malicious self.downloadable = downloadable + self.tools_functionally_correct = tools_functionally_correct + self.do_not_test = do_not_test + self.time_last_tested = time_last_tested + self.tool_test_errors = tool_test_errors def get_api_value( self, view='collection', value_mapper=None ): if value_mapper is None: value_mapper = {} diff -r 9697f9fc92b1bc8fbfaca72917eeff928c2cc4ac -r 1adf6fdd9c49bda204e5d90f70f10e7ef4ec06bd lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -130,7 +130,11 @@ Column( "metadata", JSONType, nullable=True ), Column( "tool_versions", JSONType, nullable=True ), Column( "malicious", Boolean, default=False ), - Column( "downloadable", Boolean, default=True ) ) + Column( "downloadable", Boolean, default=True ), + Column( "tools_functionally_correct", Boolean, default=False, index=True ), + Column( "do_not_test", Boolean, default=False, index=True ), + Column( "time_last_tested", DateTime, default=None, nullable=True ), + Column( "tool_test_errors", JSONType, nullable=True ) ) RepositoryReview.table = Table( "repository_review", metadata, Column( "id", Integer, primary_key=True ), diff -r 9697f9fc92b1bc8fbfaca72917eeff928c2cc4ac -r 1adf6fdd9c49bda204e5d90f70f10e7ef4ec06bd lib/galaxy/webapps/community/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py --- /dev/null +++ b/lib/galaxy/webapps/community/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py @@ -0,0 +1,99 @@ +""" +Migration script to add the tool_test_errors, do_not_test, tools_functionally_correct, and time_last_tested columns to the repository_metadata table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table. + RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) + c = Column( "tools_functionally_correct", Boolean, default=False, index=True ) + try: + # Create tools_functionally_correct column + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.tools_functionally_correct + # Initialize. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE repository_metadata SET tools_functionally_correct=%s" % default_false ) + except Exception, e: + print "Adding tools_functionally_correct column to the repository_metadata table failed: %s" % str( e ) + log.debug( "Adding tools_functionally_correct column to the repository_metadata table failed: %s" % str( e ) ) + c = Column( "do_not_test", Boolean, default=False, index=True ) + try: + # Create do_not_test column + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.do_not_test + # Initialize. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE repository_metadata SET do_not_test=%s" % default_false ) + except Exception, e: + print "Adding do_not_test column to the repository_metadata table failed: %s" % str( e ) + log.debug( "Adding do_not_test column to the repository_metadata table failed: %s" % str( e ) ) + c = Column( "time_last_tested", DateTime, default=None, nullable=True ) + try: + # Create time_last_tested column + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.time_last_tested + except Exception, e: + print "Adding time_last_tested column to the repository_metadata table failed: %s" % str( e ) + log.debug( "Adding time_last_tested column to the repository_metadata table failed: %s" % str( e ) ) + c = Column( "tool_test_errors", JSONType, nullable=True ) + try: + pass + # Create tool_test_errors column + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.tool_test_errors + except Exception, e: + print "Adding tool_test_errors column to the repository_metadata table failed: %s" % str( e ) + log.debug( "Adding tool_test_errors column to the repository_metadata table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + # Drop tool_test_errors, time_last_tested, do_not_test, and tools_functionally_correct columns from repository_metadata table. + RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) + try: + RepositoryMetadata_table.c.tool_test_errors.drop() + except Exception, e: + print "Dropping column tool_test_errors from the repository_metadata table failed: %s" % str( e ) + log.debug( "Dropping column tool_test_errors from the repository_metadata table failed: %s" % str( e ) ) + try: + RepositoryMetadata_table.c.time_last_tested.drop() + except Exception, e: + print "Dropping column time_last_tested from the repository_metadata table failed: %s" % str( e ) + log.debug( "Dropping column time_last_tested from the repository_metadata table failed: %s" % str( e ) ) + try: + RepositoryMetadata_table.c.do_not_test.drop() + except Exception, e: + print "Dropping column do_not_test from the repository_metadata table failed: %s" % str( e ) + log.debug( "Dropping column do_not_test from the repository_metadata table failed: %s" % str( e ) ) + try: + RepositoryMetadata_table.c.tools_functionally_correct.drop() + except Exception, e: + print "Dropping column tools_functionally_correct from the repository_metadata table failed: %s" % str( e ) + log.debug( "Dropping column tools_functionally_correct from the repository_metadata table failed: %s" % str( e ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add the API framework to the Galaxy Tool Shed.
by Bitbucket 20 Feb '13

20 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1bd67f03d4f1/ changeset: 1bd67f03d4f1 user: greg date: 2013-02-20 20:55:26 summary: Add the API framework to the Galaxy Tool Shed. affected #: 10 files diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 lib/galaxy/webapps/community/api/repository_revisions.py --- /dev/null +++ b/lib/galaxy/webapps/community/api/repository_revisions.py @@ -0,0 +1,34 @@ +from galaxy import web, util, logging +from galaxy.web.base.controller import BaseController, BaseAPIController +from galaxy.web.framework.helpers import is_true + +import pkg_resources +pkg_resources.require( "Routes" ) +import routes + +log = logging.getLogger( __name__ ) + +class RepositoryRevisionsController( BaseAPIController ): + """RESTful controller for interactions with tool shed repositories.""" + @web.expose_api + def index( self, trans, downloadable=True, **kwd ): + """ + GET /api/repository_revisions + Displays a collection (list) of repository revisions. + """ + rval = [] + downloadable = util.string_as_bool( downloadable ) + try: + query = trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ + .filter( trans.app.model.RepositoryMetadata.table.c.downloadable == downloadable ) \ + .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ + .all() + for repository_metadata in query: + item = repository_metadata.get_api_value( value_mapper={ 'id' : trans.security.encode_id } ) + item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) + rval.append( item ) + except Exception, e: + rval = "Error in repository_revisions API" + log.error( rval + ": %s" % str( e ) ) + trans.response.status = 500 + return rval diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 lib/galaxy/webapps/community/buildapp.py --- a/lib/galaxy/webapps/community/buildapp.py +++ b/lib/galaxy/webapps/community/buildapp.py @@ -69,6 +69,9 @@ webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='repository', action='index' ) webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) + # Add the web API + webapp.add_api_controllers( 'galaxy.webapps.community.api', app ) + webapp.api_mapper.resource( 'repository_revision', 'repository_revisions', path_prefix='/api' ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 lib/galaxy/webapps/community/framework/middleware/remoteuser.py --- a/lib/galaxy/webapps/community/framework/middleware/remoteuser.py +++ b/lib/galaxy/webapps/community/framework/middleware/remoteuser.py @@ -75,6 +75,9 @@ elif path_info.startswith( '/api/' ): # The API handles its own authentication via keys return self.app( environ, start_response ) + elif path_info.startswith( '/user/api_keys' ): + # api_keys can be managed when remote_user is in use. + pass else: title = "Access to this Galaxy tool shed is denied" message = """ diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -9,14 +9,20 @@ from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash from galaxy.web.form_builder import * +from galaxy.model.item_attrs import APIItem from galaxy import eggs eggs.require('mercurial') from mercurial import hg, ui log = logging.getLogger( __name__ ) - -class User( object ): + +class APIKeys( object ): + pass + +class User( object, APIItem ): + api_collection_visible_keys = ( 'id', 'email' ) + api_element_visible_keys = ( 'id', 'email', 'username' ) def __init__( self, email=None, password=None ): self.email = email self.password = password @@ -47,12 +53,16 @@ def nice_total_disk_usage( self ): return 0 -class Group( object ): +class Group( object, APIItem ): + api_collection_visible_keys = ( 'id', 'name' ) + api_element_visible_keys = ( 'id', 'name' ) def __init__( self, name = None ): self.name = name self.deleted = False -class Role( object ): +class Role( object, APIItem ): + api_collection_visible_keys = ( 'id', 'name' ) + api_element_visible_keys = ( 'id', 'name', 'description', 'type' ) private_id = None types = Bunch( PRIVATE = 'private', @@ -103,7 +113,9 @@ self.is_valid = is_valid self.prev_session_id = prev_session_id -class Repository( object ): +class Repository( object, APIItem ): + api_collection_visible_keys = ( 'id', 'name' ) + api_element_visible_keys = ( 'id', 'name', 'description' ) file_states = Bunch( NORMAL = 'n', NEEDS_MERGING = 'm', MARKED_FOR_REMOVAL = 'r', @@ -155,7 +167,9 @@ fp.write( line ) fp.close() -class RepositoryMetadata( object ): +class RepositoryMetadata( object, APIItem ): + api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable' ) + api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable' ) def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False ): self.repository_id = repository_id self.changeset_revision = changeset_revision @@ -163,8 +177,26 @@ self.tool_versions = tool_versions or dict() self.malicious = malicious self.downloadable = downloadable + def get_api_value( self, view='collection', value_mapper=None ): + if value_mapper is None: + value_mapper = {} + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[ key ] = self.__getattribute__( key ) + if key in value_mapper: + rval[ key ] = value_mapper.get( key )( rval[ key ] ) + except AttributeError: + rval[ key ] = None + return rval -class RepositoryReview( object ): +class RepositoryReview( object, APIItem ): + api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating' ) + api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating' ) approved_states = Bunch( NO='no', YES='yes' ) def __init__( self, repository_id=None, changeset_revision=None, user_id=None, rating=None, deleted=False ): self.repository_id = repository_id @@ -173,7 +205,9 @@ self.rating = rating self.deleted = deleted -class ComponentReview( object ): +class ComponentReview( object, APIItem ): + api_collection_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' ) + api_element_visible_keys = ( 'id', 'repository_review_id', 'component_id', 'private', 'approved', 'rating', 'deleted' ) approved_states = Bunch( NO='no', YES='yes', NA='not_applicable' ) def __init__( self, repository_review_id=None, component_id=None, comment=None, private=False, approved=False, rating=None, deleted=False ): self.repository_review_id = repository_review_id @@ -204,7 +238,9 @@ def set_item( self, repository ): self.repository = repository -class Category( object ): +class Category( object, APIItem ): + api_collection_visible_keys = ( 'id', 'name', 'description', 'deleted' ) + api_element_visible_keys = ( 'id', 'name', 'description', 'deleted' ) def __init__( self, name=None, description=None, deleted=False ): self.name = name self.description = description diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -39,6 +39,12 @@ # Return the current time in UTC without any timezone information now = datetime.datetime.utcnow +APIKeys.table = Table( "api_keys", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "key", TrimmedString( 32 ), index=True, unique=True ) ) + User.table = Table( "galaxy_user", metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), @@ -186,7 +192,11 @@ # With the tables defined we can define the mappers and setup the relationships between the model objects. assign_mapper( context, User, User.table, properties=dict( active_repositories=relation( Repository, primaryjoin=( ( Repository.table.c.user_id == User.table.c.id ) & ( not_( Repository.table.c.deleted ) ) ), order_by=( Repository.table.c.name ) ), - galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ) ) ) + galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ), + api_keys=relation( APIKeys, backref="user", order_by=desc( APIKeys.table.c.create_time ) ) ) ) + +assign_mapper( context, APIKeys, APIKeys.table, + properties = {} ) assign_mapper( context, Group, Group.table, properties=dict( users=relation( UserGroupAssociation ) ) ) diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 lib/galaxy/webapps/community/model/migrate/versions/0015_add_api_keys_table.py --- /dev/null +++ b/lib/galaxy/webapps/community/model/migrate/versions/0015_add_api_keys_table.py @@ -0,0 +1,46 @@ +""" +Migration script to add the api_keys table. +""" +import datetime, sys, logging +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import * + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +now = datetime.datetime.utcnow + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +metadata = MetaData( migrate_engine ) + +APIKeys_table = Table( "api_keys", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "key", TrimmedString( 32 ), index=True, unique=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + APIKeys_table.create() + except Exception, e: + log.debug( "Creating api_keys table failed: %s" % str( e ) ) + +def downgrade(): + # Load existing tables + metadata.reflect() + try: + APIKeys_table.drop() + except Exception, e: + log.debug( "Dropping api_keys table failed: %s" % str( e ) ) diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 templates/user/index.mako --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -25,6 +25,7 @@ %endif %else: <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li> + <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li><li><a href="${h.url_for( controller='repository', action='manage_email_alerts', cntrller=cntrller )}">${_('Manage your email alerts')}</a></li><li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li> %endif diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -105,6 +105,7 @@ menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) else: menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) + menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) diff -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 -r 1bd67f03d4f12d0f6cddacb57a6402cf306f8f55 templates/webapps/galaxy/user/api_keys.mako --- a/templates/webapps/galaxy/user/api_keys.mako +++ b/templates/webapps/galaxy/user/api_keys.mako @@ -30,11 +30,14 @@ (invalidates old key) %endif <div class="toolParamHelp" style="clear: both;"> - An API key will allow you to access Galaxy via its web - API (documentation forthcoming). Please note that - <strong>this key acts as an alternate means to access - your account, and should be treated with the same care - as your login password</strong>. + <% + if trans.webapp.name == 'galaxy': + webapp_str = 'Galaxy' + else: + webapp_str = 'the Tool Shed' + %> + An API key will allow you to access ${webapp_str} via its web API. Please note that <strong>this key acts as an alternate means + to access your account and should be treated with the same care as your login password</strong>. </div></div></form> 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: Tool shed functional test enhancement, made the grant_write_access method more robust, added functional test for contacting a repository's owner.
by Bitbucket 20 Feb '13

20 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0fb1af8ce741/ changeset: 0fb1af8ce741 user: inithello date: 2013-02-20 20:33:04 summary: Tool shed functional test enhancement, made the grant_write_access method more robust, added functional test for contacting a repository's owner. affected #: 3 files diff -r b9c93f559efa7a50cfa445b5f79c579690155589 -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -587,13 +587,20 @@ self.visit_url( url ) strings_displayed = [ "Role '%s' has been updated" % role.name ] self.check_for_strings( strings_displayed, strings_not_displayed ) - def grant_write_access( self, repository, usernames=[], strings_displayed=[], strings_not_displayed=[] ): + def grant_write_access( self, + repository, + usernames=[], + strings_displayed=[], + strings_not_displayed=[], + post_submit_strings_displayed=[], + post_submit_strings_not_displayed=[] ): self.display_manage_repository_page( repository ) - tc.fv( "3", "allow_push", '-Select one' ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + tc.fv( "user_access", "allow_push", '-Select one' ) for username in usernames: - tc.fv( "3", "allow_push", '+%s' % username ) + tc.fv( "user_access", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) - self.check_for_strings( strings_displayed, strings_not_displayed ) + self.check_for_strings( post_submit_strings_displayed, post_submit_strings_not_displayed ) def import_workflow( self, repository, workflow_name, strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/import_workflow?repository_id=%s&workflow_name=%s' % \ ( self.security.encode_id( repository.id ), tool_shed_encode( workflow_name ) ) @@ -847,6 +854,19 @@ tc.fv( "1", field_name, search_string ) tc.submit() self.check_for_strings( strings_displayed, strings_not_displayed ) + def send_message_to_repository_owner( self, + repository, + message, + strings_displayed=[], + strings_not_displayed=[], + post_submit_strings_displayed=[], + post_submit_strings_not_displayed=[] ): + url = '/repository/contact_owner?id=%s' % self.security.encode_id( repository.id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + tc.fv( 1, 'message', message ) + tc.submit() + self.check_for_strings( post_submit_strings_displayed, post_submit_strings_not_displayed ) def set_repository_deprecated( self, repository, set_deprecated=True, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/deprecate?id=%s&mark_deprecated=%s' % ( self.security.encode_id( repository.id ), set_deprecated ) self.visit_url( url ) diff -r b9c93f559efa7a50cfa445b5f79c579690155589 -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -9,11 +9,17 @@ '''Test core repository features.''' def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" + 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.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + 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 @@ -51,8 +57,8 @@ def test_0025_grant_write_access( self ): '''Grant write access to another user''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) - self.grant_write_access( repository, usernames=[ common.admin_username ] ) - self.revoke_write_access( repository, common.admin_username ) + self.grant_write_access( repository, usernames=[ common.test_user_2_name ] ) + self.revoke_write_access( repository, common.test_user_2_name ) def test_0030_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -214,3 +220,22 @@ assert test_user_1 is None, 'Creating user with public name "repos" succeeded.' error_message = 'The term <b>repos</b> is a reserved word in the tool shed, so it cannot be used as a public user name.' self.check_for_strings( strings_displayed=[ error_message ] ) + def test_0105_contact_repository_owner( self ): + '''Fill out and submit the form to contact the owner of a repository.''' + ''' + This test should not actually send the email, since functional tests are designed to function without + any external network connection. The embedded tool shed server these tests are running against has been configured + with an SMTP server address that will not and should not resolve correctly. However, since the successful sending of + the email is the last step in the process, this will verify functional correctness of all preceding steps. + ''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + message = 'This is a test message.' + strings_displayed = [ 'Contact the owner of the repository named', repository.name, 'streamline appropriate communication' ] + post_submit_strings_displayed = [ 'An error occurred sending your message by email' ] + self.send_message_to_repository_owner( repository=repository, + message=message, + strings_displayed=strings_displayed, + post_submit_strings_displayed=post_submit_strings_displayed ) + diff -r b9c93f559efa7a50cfa445b5f79c579690155589 -r 0fb1af8ce7410cd48c9259962a4e0da528ff4ef6 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -199,6 +199,8 @@ new_file_path = new_repos_path, running_functional_tests = True, shed_tool_data_table_config = shed_tool_data_table_conf_file, + smtp_server = 'smtp.dummy.string.tld', + email_from = 'functional@localhost', template_path = 'templates', tool_path=tool_path, tool_parse_help = False, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Extension of framework to automate the installation of a list of tool shed repositories to also run any functional tests in the tools contained within each repository.
by Bitbucket 20 Feb '13

20 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9c93f559efa/ changeset: b9c93f559efa user: inithello date: 2013-02-20 20:27:36 summary: Extension of framework to automate the installation of a list of tool shed repositories to also run any functional tests in the tools contained within each repository. affected #: 6 files diff -r efebd50fd708aa3af73f954e4da68e88f2bced9a -r b9c93f559efa7a50cfa445b5f79c579690155589 install_and_test_tool_shed_repositories.sh --- /dev/null +++ b/install_and_test_tool_shed_repositories.sh @@ -0,0 +1,7 @@ +#!/bin/sh + +# A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ +#rm -f ./test/tool_shed/run_functional_tests.log + +python test/install_and_test_tool_shed_repositories/functional_tests.py -v --with-nosehtml --html-report-file ./test/install_and_test_tool_shed_repositories/run_functional_tests.html test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py test/functional/test_toolbox.py + diff -r efebd50fd708aa3af73f954e4da68e88f2bced9a -r b9c93f559efa7a50cfa445b5f79c579690155589 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -4,10 +4,12 @@ # Assume we are run from the galaxy root directory, add lib to the python path cwd = os.getcwd() -new_path = [ os.path.join( cwd, "lib" ) ] +new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, "test" ) ] new_path.extend( sys.path[1:] ) sys.path = new_path +from base.util import parse_tool_panel_config + from galaxy import eggs eggs.require( "nose" ) @@ -85,73 +87,6 @@ global_conf.update( get_static_settings() ) return global_conf -def parse_tool_panel_config( config, shed_tools_dict ): - """ - Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. - """ - last_galaxy_test_file_dir = None - last_tested_repository_name = None - last_tested_changeset_revision = None - tool_path = None - tree = util.parse_xml( config ) - root = tree.getroot() - tool_path = root.get('tool_path') - for elem in root: - if elem.tag == 'tool': - galaxy_test_file_dir, \ - last_tested_repository_name, \ - last_tested_changeset_revision = get_installed_repository_info( elem, - last_galaxy_test_file_dir, - last_tested_repository_name, - last_tested_changeset_revision, - tool_path ) - if galaxy_test_file_dir: - if galaxy_test_file_dir != last_galaxy_test_file_dir: - if not os.path.isabs( galaxy_test_file_dir ): - galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) - guid = elem.get( 'guid' ) - shed_tools_dict[ guid ] = galaxy_test_file_dir - last_galaxy_test_file_dir = galaxy_test_file_dir - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - galaxy_test_file_dir, \ - last_tested_repository_name, \ - last_tested_changeset_revision = get_installed_repository_info( section_elem, - last_galaxy_test_file_dir, - last_tested_repository_name, - last_tested_changeset_revision, - tool_path ) - if galaxy_test_file_dir: - if galaxy_test_file_dir != last_galaxy_test_file_dir: - if not os.path.isabs( galaxy_test_file_dir ): - galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) - guid = section_elem.get( 'guid' ) - shed_tools_dict[ guid ] = galaxy_test_file_dir - last_galaxy_test_file_dir = galaxy_test_file_dir - return shed_tools_dict - -def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ): - """ - Return the GALAXY_TEST_FILE_DIR, the containing repository name and the change set revision for the tool elem. - This only happens when testing tools installed from the tool shed. - """ - tool_config_path = elem.get( 'file' ) - installed_tool_path_items = tool_config_path.split( '/repos/' ) - sans_shed = installed_tool_path_items[ 1 ] - path_items = sans_shed.split( '/' ) - repository_owner = path_items[ 0 ] - repository_name = path_items[ 1 ] - changeset_revision = path_items[ 2 ] - if repository_name != last_tested_repository_name or changeset_revision != last_tested_changeset_revision: - # Locate the test-data directory. - installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision ) - for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )): - if 'test-data' in dirs: - return os.path.join( root, 'test-data' ), repository_name, changeset_revision - return None, repository_name, changeset_revision - return last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision - def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) plug_loader = test_config.plugins.prepareTestLoader( loader ) diff -r efebd50fd708aa3af73f954e4da68e88f2bced9a -r b9c93f559efa7a50cfa445b5f79c579690155589 test/base/util.py --- /dev/null +++ b/test/base/util.py @@ -0,0 +1,80 @@ +import os, sys + +cwd = os.getcwd() +if cwd not in sys.path: + sys.path.append( cwd ) + +new_path = [ os.path.join( cwd, "lib" ) ] +if new_path not in sys.path: + new_path.extend( sys.path ) + sys.path = new_path + +from galaxy.util import parse_xml + +def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ): + """ + Return the GALAXY_TEST_FILE_DIR, the containing repository name and the change set revision for the tool elem. + This only happens when testing tools installed from the tool shed. + """ + tool_config_path = elem.get( 'file' ) + installed_tool_path_items = tool_config_path.split( '/repos/' ) + sans_shed = installed_tool_path_items[ 1 ] + path_items = sans_shed.split( '/' ) + repository_owner = path_items[ 0 ] + repository_name = path_items[ 1 ] + changeset_revision = path_items[ 2 ] + if repository_name != last_tested_repository_name or changeset_revision != last_tested_changeset_revision: + # Locate the test-data directory. + installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision ) + for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )): + if 'test-data' in dirs: + return os.path.join( root, 'test-data' ), repository_name, changeset_revision + return None, repository_name, changeset_revision + return last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision + +def parse_tool_panel_config( config, shed_tools_dict ): + """ + Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. + """ + last_galaxy_test_file_dir = None + last_tested_repository_name = None + last_tested_changeset_revision = None + tool_path = None + tree = parse_xml( config ) + root = tree.getroot() + tool_path = root.get('tool_path') + for elem in root: + if elem.tag == 'tool': + galaxy_test_file_dir, \ + last_tested_repository_name, \ + last_tested_changeset_revision = get_installed_repository_info( elem, + last_galaxy_test_file_dir, + last_tested_repository_name, + last_tested_changeset_revision, + tool_path ) + if galaxy_test_file_dir: + if galaxy_test_file_dir != last_galaxy_test_file_dir: + if not os.path.isabs( galaxy_test_file_dir ): + galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) + guid = elem.get( 'guid' ) + shed_tools_dict[ guid ] = galaxy_test_file_dir + last_galaxy_test_file_dir = galaxy_test_file_dir + elif elem.tag == 'section': + for section_elem in elem: + if section_elem.tag == 'tool': + galaxy_test_file_dir, \ + last_tested_repository_name, \ + last_tested_changeset_revision = get_installed_repository_info( section_elem, + last_galaxy_test_file_dir, + last_tested_repository_name, + last_tested_changeset_revision, + tool_path ) + if galaxy_test_file_dir: + if galaxy_test_file_dir != last_galaxy_test_file_dir: + if not os.path.isabs( galaxy_test_file_dir ): + galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) + guid = section_elem.get( 'guid' ) + shed_tools_dict[ guid ] = galaxy_test_file_dir + last_galaxy_test_file_dir = galaxy_test_file_dir + return shed_tools_dict + diff -r efebd50fd708aa3af73f954e4da68e88f2bced9a -r b9c93f559efa7a50cfa445b5f79c579690155589 test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -121,4 +121,12 @@ ( timeout_counter, repository.status ) ) break time.sleep( 1 ) + def uninstall_repository( self, installed_repository ): + url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( installed_repository.id ) + self.visit_url( url ) + tc.fv ( 1, "remove_from_disk", 'true' ) + tc.submit( 'deactivate_or_uninstall_repository_button' ) + strings_displayed = [ 'The repository named' ] + strings_displayed.append( 'has been uninstalled' ) + self.check_for_strings( strings_displayed, strings_not_displayed=[] ) diff -r efebd50fd708aa3af73f954e4da68e88f2bced9a -r b9c93f559efa7a50cfa445b5f79c579690155589 test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -1,18 +1,33 @@ -import new +import new, logging import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository +log = logging.getLogger(__name__) class TestInstallRepositories( InstallTestRepository ): - """Abstract test case that installs a predefined list of repositories.""" + """Abstract test case that installs and uninstalls a predefined list of repositories.""" def do_installation( self, repository_info_dict ): self.logout() self.login( email='test(a)bx.psu.edu', username='test' ) admin_user = test_db_util.get_user( 'test(a)bx.psu.edu' ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) + # Install the repository through the web interface using twill. self.install_repository( repository_info_dict ) -def build_tests( repository_dict=None ): + def do_uninstallation( self, repository_info_dict ): + self.logout() + self.login( email='test(a)bx.psu.edu', username='test' ) + admin_user = test_db_util.get_user( 'test(a)bx.psu.edu' ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + # Get the repository from the database. + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( repository_info_dict[ 'name' ], + repository_info_dict[ 'owner' ], + repository_info_dict[ 'changeset_revision' ] ) + admin_user_private_role = test_db_util.get_private_role( admin_user ) + # Uninstall the repository through the web interface using twill. + self.uninstall_repository( repository ) + +def generate_install_method( repository_dict=None ): """Generate abstract test cases for the defined list of repositories.""" if repository_dict is None: return @@ -20,7 +35,7 @@ G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): del G[ key ] # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. name = "TestInstallRepository_" + repository_dict[ 'name' ] @@ -37,3 +52,29 @@ # from baseclasses (which should be a tuple of classes) and with namespace dict. new_class_obj = new.classobj( name, baseclasses, namespace ) G[ name ] = new_class_obj + +def generate_uninstall_method( repository_dict=None ): + """Generate abstract test cases for the defined list of repositories.""" + if repository_dict is None: + return + # Push all the toolbox tests to module level + G = globals() + # Eliminate all previous tests from G. + for key, val in G.items(): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): + del G[ key ] + # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. + name = "TestUninstallRepository_" + repository_dict[ 'name' ] + baseclasses = ( TestInstallRepositories, ) + namespace = dict() + def make_uninstall_method( repository_dict ): + def test_install_repository( self ): + self.do_uninstallation( repository_dict ) + return test_install_repository + test_method = make_uninstall_method( repository_dict ) + test_method.__doc__ = "Uninstall the repository %s." % repository_dict[ 'name' ] + namespace[ 'install_repository_%s' % repository_dict[ 'name' ] ] = test_method + # The new.classobj function returns a new class object, with name name, derived + # from baseclasses (which should be a tuple of classes) and with namespace dict. + new_class_obj = new.classobj( name, baseclasses, namespace ) + G[ name ] = new_class_obj diff -r efebd50fd708aa3af73f954e4da68e88f2bced9a -r b9c93f559efa7a50cfa445b5f79c579690155589 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -1,5 +1,9 @@ #!/usr/bin/env python +# NOTE: This script cannot be run directly, because it needs to have test/functional/test_toolbox.py in sys.argv in +# order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh +# will execute this script with the appropriate parameters. + import os, sys, shutil, tempfile, re, string # Assume we are run from the galaxy root directory, add lib to the python path @@ -8,9 +12,9 @@ test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories' ) default_test_file_dir = os.path.join( test_home_directory, 'test_data' ) + # Here's the directory where everything happens. Temporary directories are created within this directory to contain -# the hgweb.config file, the database, new repositories, etc. Since the tool shed browses repository contents via HTTP, -# the full path to the temporary directroy wher eht repositories are located cannot contain invalid url characters. +# the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" @@ -43,12 +47,15 @@ import galaxy.app from galaxy.app import UniverseApplication from galaxy.web import buildapp +from galaxy.util import parse_xml import nose.core import nose.config import nose.loader import nose.plugins.manager +from base.util import parse_tool_panel_config + log = logging.getLogger( 'install_and_test_repositories' ) default_galaxy_test_port_min = 10000 @@ -66,11 +73,13 @@ </tool_sheds> ''' +# Create a blank shed_tool_conf.xml to hold the installed repositories. shed_tool_conf_xml_template = '''<?xml version="1.0"?><toolbox tool_path="${shed_tool_path}"></toolbox> ''' +# Since we will be running functional tests, we'll need the upload tool, but the rest can be omitted. tool_conf_xml = '''<?xml version="1.0"?><toolbox><section name="Get Data" id="getext"> @@ -79,11 +88,13 @@ </toolbox> ''' +# And set up a blank tool_data_table_conf.xml and shed_tool_data_table_conf.xml. tool_data_table_conf_xml_template = '''<?xml version="1.0"?><tables></tables> ''' +# Define a default location to find the list of repositories to check. galaxy_repository_list = os.environ.get( 'GALAXY_INSTALL_TEST_REPOSITORY_FILE', 'repository_list.json' ) if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: @@ -92,7 +103,7 @@ else: galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] -def get_repositories_to_install(): +def get_repositories_to_install( format='json' ): ''' Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: [ @@ -107,7 +118,10 @@ ] NOTE: If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. ''' - return simplejson.loads( file( galaxy_repository_list, 'r' ).read() ) + if format == 'json': + return simplejson.loads( file( galaxy_repository_list, 'r' ).read() ) + else: + raise AssertonError( 'Unknown format %s.' % format ) def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) @@ -126,7 +140,7 @@ def main(): # ---- Configuration ------------------------------------------------------ galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', default_galaxy_test_host ) - galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', None ) + galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( default_galaxy_test_port_max ) ) tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: @@ -134,28 +148,32 @@ galaxy_test_file_dir = os.environ.get( 'GALAXY_INSTALL_TEST_FILE_DIR', default_galaxy_test_file_dir ) if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.abspath( galaxy_test_file_dir ) + # Set up the tool dependency path for the Galaxy instance. tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_INSTALL_TEST_USE_DISTRIBUTED_OBJECT_STORE', False ) if not os.path.isdir( galaxy_test_tmp_dir ): os.mkdir( galaxy_test_tmp_dir ) galaxy_test_proxy_port = None + # Set up the configuration files for the Galaxy instance. shed_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_data_table_conf.xml' ) ) galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_data_table_conf.xml' ) ) galaxy_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_conf.xml' ) ) galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) - shed_tool_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) else: tool_data_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ] = tool_data_path + # Configure the database connection and path. if 'GALAXY_INSTALL_TEST_DBPATH' in os.environ: galaxy_db_path = os.environ[ 'GALAXY_INSTALL_TEST_DBPATH' ] else: tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) galaxy_db_path = os.path.join( tempdir, 'database' ) + # Configure the paths Galaxy needs to install and test tools. galaxy_file_path = os.path.join( galaxy_db_path, 'files' ) new_repos_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) @@ -239,6 +257,7 @@ static_enabled=False, app=app ) + # Serve the app on a specified or random port. if galaxy_test_port is not None: server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) else: @@ -260,9 +279,10 @@ os.environ[ 'GALAXY_INSTALL_TEST_PORT' ] = galaxy_test_proxy_port else: os.environ[ 'GALAXY_INSTALL_TEST_PORT' ] = galaxy_test_port + # Start the server. t = threading.Thread( target=server.serve_forever ) t.start() - # Test if the server is up + # Test if the server is up. for i in range( 10 ): # Directly test the app, not the proxy. conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) @@ -273,27 +293,71 @@ else: raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) log.info( "Embedded galaxy web server started" ) - # ---- Load the module to generate installation methods ------------------- + # ---- Load the modules to generate installation, testing, and uninstallation methods ------------------- import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories + import functional.test_toolbox as test_toolbox if galaxy_test_proxy_port: log.info( "Tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_proxy_port ) ) else: log.info( "Tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) success = False try: + # Iterate through a list of repository info dicts. for repository_dict in get_repositories_to_install(): - test_install_repositories.build_tests( repository_dict ) + # Generate the method that will install this repository into the running Galaxy instance. + test_install_repositories.generate_install_method( repository_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host + # Configure nose to run the install method as a test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) - # Run the tests. + # Run the configured install method as a test. This method uses the Galaxy web interface to install the specified + # repository, with tool and repository dependencies also selected for installation. result = run_tests( test_config ) success = result.wasSuccessful() + # If the installation succeeds, set up and run functional tests for this repository. This is equivalent to + # sh run_functional_tests.sh -installed + if success: + log.debug( 'Installation of %s succeeded, running any defined functional tests.' % repository_dict[ 'name' ] ) + # Parse the tool panel config to get the test-data path for this repository. + shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, {} ) + # Write this to a file, so the functional test framework can find it. + file( galaxy_shed_tools_dict, 'w' ).write( simplejson.dumps( shed_tools_dict ) ) + # Set up the environment so that test.functional.test_toolbox can find the Galaxy server we configured in this framework. + os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict + os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host + os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. + test_toolbox.toolbox = app.toolbox + # Generate the test methods for this installed repository. We need to pass in True here, or it will look + # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. + test_toolbox.build_tests( testing_shed_tools=True ) + # Set up nose to run the generated functional tests. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the configured tests. + result = run_tests( test_config ) + success = result.wasSuccessful() + if success: + log.debug( 'Repository %s installed and passed functional tests.' % repository_dict[ 'name' ] ) + else: + log.debug( 'Repository %s installed, but did not pass functional tests.' % repository_dict[ 'name' ] ) + # Generate an uninstall method for this repository, so that the next repository has a clean environment for testing. + test_install_repositories.generate_uninstall_method( repository_dict ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed + # repository and delete it from disk. + result = run_tests( test_config ) + success = result.wasSuccessful() + else: + log.debug( 'Repository %s failed to install correctly.' % repository_dict[ 'name' ] ) except: log.exception( "Failure running tests" ) log.info( "Shutting down" ) # ---- Tear down ----------------------------------------------------------- + # Gracefully shut down the embedded web server and UniverseApplication. if server: log.info( "Shutting down embedded galaxy web server" ) server.server_close() @@ -304,6 +368,7 @@ app.shutdown() app = None log.info( "Embedded galaxy application stopped" ) + # Clean up test files unless otherwise specified. if 'GALAXY_INSTALL_TEST_NO_CLEANUP' not in os.environ: try: for dir in [ galaxy_test_tmp_dir ]: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Move grid element initialization to main body to prevent it from happening too early. Pack scripts.
by Bitbucket 20 Feb '13

20 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c3df0bcbc22/ changeset: 7c3df0bcbc22 branch: stable user: jgoecks date: 2013-02-17 20:59:02 summary: Move grid element initialization to main body to prevent it from happening too early. Pack scripts. affected #: 4 files diff -r 5ac8d92a066edefa4ab63936372ec9bcc689cafc -r 7c3df0bcbc222f478b1e21886fbb384d3dc96f31 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -4,18 +4,6 @@ // not appended to the identifier of a nested array. jQuery.ajaxSettings.traditional = true; -// Initialize grid objects on load. -$(document).ready(function() { - init_grid_elements(); - init_grid_controls(); - - // Initialize text filters to select text on click and use normal font when user is typing. - $('input[type=text]').each(function() { - $(this).click(function() { $(this).select(); } ) - .keyup(function () { $(this).css("font-style", "normal"); }); - }); -}); - /** * A Galaxy grid. */ diff -r 5ac8d92a066edefa4ab63936372ec9bcc689cafc -r 7c3df0bcbc222f478b1e21886fbb384d3dc96f31 static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;$(document).ready(function(){init_grid_elements();init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})});var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.key,a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete 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b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();init_operation_buttons();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}; \ No newline at end of file diff -r 5ac8d92a066edefa4ab63936372ec9bcc689cafc -r 7c3df0bcbc222f478b1e21886fbb384d3dc96f31 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,p){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("isResolved" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_paths.attributes.image_path+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=x.indexOf(v);if(u!==-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=this.attributes.num_elements;if(!y[v]){if(z.length>=w){var u=z.shift();delete y[u]}z.push(v)}y[v]=x;return x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,init_data:null,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")=="raw_data"?"state":this.get("data_type")=="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(A,z,w,y){var B=this.get_elt(A);if(B&&(j(B)||this.get("data_mode_compatible")(B,z))){return B}var C=this.get("key_ary"),v=this.get("obj_cache"),D,u;for(var x=0;x<C.length;x++){D=C[x];u=new g({from_str:D});if(u.contains(A)){B=v[D];if(j(B)||(this.get("data_mode_compatible")(B,z)&&this.get("can_subset")(B))){this.move_key_to_end(D,x);return B}}}return this.load_data(A,z,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}else{if(u.dataset_type==="summary_tree"){w.level=Math.min(u.level-1,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},get_elt:function(u){return q.prototype.get_elt.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString(),u)}});var n=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,w,x,u,v)}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom==u});return new g({chrom:v.chrom,end:v.len})}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<=w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}return u},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=i.Dataset.extend({initialize:function(u){this.set("id",u.dataset_id);this.set("config",p.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var o=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=o.extend({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,ReferenceTrackDataManager:n,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,p){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("isResolved" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_paths.attributes.image_path+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=x.indexOf(v);if(u!==-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=this.attributes.num_elements;if(!y[v]){if(z.length>=w){var u=z.shift();delete y[u]}z.push(v)}y[v]=x;return x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,init_data:null,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(A,z,w,y){var B=this.get_elt(A);if(B&&(j(B)||this.get("data_mode_compatible")(B,z))){return B}var C=this.get("key_ary"),v=this.get("obj_cache"),D,u;for(var x=0;x<C.length;x++){D=C[x];u=new g({from_str:D});if(u.contains(A)){B=v[D];if(j(B)||(this.get("data_mode_compatible")(B,z)&&this.get("can_subset")(B))){this.move_key_to_end(D,x);return B}}}return this.load_data(A,z,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}else{if(u.dataset_type==="summary_tree"){w.level=Math.min(u.level-1,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},get_elt:function(u){return q.prototype.get_elt.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString(),u)}});var n=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,w,x,u,v)}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<=w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}return u},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=i.Dataset.extend({initialize:function(u){this.set("id",u.dataset_id);this.set("config",p.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var o=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=o.extend({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,ReferenceTrackDataManager:n,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file diff -r 5ac8d92a066edefa4ab63936372ec9bcc689cafc -r 7c3df0bcbc222f478b1e21886fbb384d3dc96f31 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -129,6 +129,19 @@ cur_page: ${cur_page_num}, num_pages: ${num_pages} }); + + // Initialize grid objects on load. + // FIXME: use a grid view object eventually. + $(document).ready(function() { + init_grid_elements(); + init_grid_controls(); + + // Initialize text filters to select text on click and use normal font when user is typing. + $('input[type=text]').each(function() { + $(this).click(function() { $(this).select(); } ) + .keyup(function () { $(this).css("font-style", "normal"); }); + }); + }); </script></%def> 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 Bitbucket 20 Feb '13

20 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5ac8d92a066e/ changeset: 5ac8d92a066e branch: stable user: inithello date: 2013-02-20 14:56:36 summary: Fix missing import in repository controller. affected #: 1 file diff -r d5896e8a60fa948f1713d4b5e30126a12a958679 -r 5ac8d92a066edefa4ab63936372ec9bcc689cafc lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1,4 +1,4 @@ -import os, logging, re, tempfile, shutil, ConfigParser +import os, logging, re, tempfile, shutil, ConfigParser, string from time import gmtime, strftime from datetime import date, datetime from galaxy import util, web https://bitbucket.org/galaxy/galaxy-central/commits/efebd50fd708/ changeset: efebd50fd708 user: inithello date: 2013-02-20 14:56:36 summary: Fix missing import in repository controller. affected #: 1 file diff -r 1895646e8ce0ed905f7fef8a8fc184ae1606a006 -r efebd50fd708aa3af73f954e4da68e88f2bced9a lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1,4 +1,4 @@ -import os, logging, re, tempfile, shutil, ConfigParser +import os, logging, re, tempfile, shutil, ConfigParser, string from time import gmtime, strftime from datetime import date, datetime from galaxy import util, web Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: More reporting for buildbot corrections
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1895646e8ce0/ changeset: 1895646e8ce0 user: carlfeberhard date: 2013-02-20 02:00:27 summary: More reporting for buildbot corrections affected #: 2 files diff -r bff6388644ba9b2b5ccb102ce01380778fdefdfe -r 1895646e8ce0ed905f7fef8a8fc184ae1606a006 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -20,6 +20,9 @@ from galaxy.openid.providers import OpenIDProviders from galaxy.tools.data_manager.manager import DataManagers +import logging +log = logging.getLogger( __name__ ) + class UniverseApplication( object ): """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): @@ -41,6 +44,8 @@ self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) else: self.tool_shed_registry = None + log.debug( 'self.config.tool_sheds_config: %s, self.tool_shed_registry: %s', + self.config.tool_sheds_config, self.tool_shed_registry ) # Initialize database / check for appropriate schema version. # If this # is a new installation, we'll restrict the tool migration messaging. from galaxy.model.migrate.check import create_or_verify_database diff -r bff6388644ba9b2b5ccb102ce01380778fdefdfe -r 1895646e8ce0ed905f7fef8a8fc184ae1606a006 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -277,7 +277,6 @@ os.makedirs( dir ) except OSError: pass - log.info( "Database connection:", database_connection ) # ---- Build Application -------------------------------------------------- app = None @@ -293,7 +292,7 @@ kwargs[ 'object_store' ] = 'distributed' kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample' # Build the Universe Application - log.debug( 'app.kwargs:\n%s', pprint.pformat( kwargs ) ) + print 'app.kwargs:\n%s' %( pprint.pformat( kwargs ) ) app = UniverseApplication( job_queue_workers = 5, id_secret = 'changethisinproductiontoo', template_path = "templates", @@ -321,6 +320,7 @@ running_functional_tests=True, **kwargs ) log.info( "Embedded Universe application started" ) + # ---- Run webserver ------------------------------------------------------ server = None 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: Fix for tool shed functional test 1060 failing when all tests are run.
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bff6388644ba/ changeset: bff6388644ba user: inithello date: 2013-02-19 23:04:04 summary: Fix for tool shed functional test 1060 failing when all tests are run. affected #: 1 file diff -r bc0114ce0f7b5224cd4ef58d1dd2ef8b30c77a69 -r bff6388644ba9b2b5ccb102ce01380778fdefdfe test/tool_shed/functional/test_0060_workflows.py --- a/test/tool_shed/functional/test_0060_workflows.py +++ b/test/tool_shed/functional/test_0060_workflows.py @@ -88,6 +88,8 @@ strings_displayed=[] ) workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read() workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) ) + workflow = workflow.replace( 'Workflow for 0060_filter_workflow_repository', + 'New workflow for 0060_filter_workflow_repository' ) workflow_filepath = self.generate_temp_path( 'test_0060', additional_paths=[ 'filtering_workflow_2' ] ) if not os.path.exists( workflow_filepath ): os.makedirs( workflow_filepath ) @@ -106,7 +108,7 @@ def test_0030_check_workflow_repository( self ): """Check for strings on the manage page for the filtering_workflow_0060 repository.""" repository = test_db_util.get_repository_by_name_and_owner( workflow_repository_name, common.test_user_1_name ) - strings_displayed = [ 'Workflows', 'Workflow for 0060_filter', '0.1' ] + strings_displayed = [ 'Workflows', 'New workflow for 0060_filter', '0.1' ] strings_not_displayed = [ 'Valid tools', 'Invalid tools' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) def test_0035_verify_repository_metadata( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: functional_tests: fix import
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc0114ce0f7b/ changeset: bc0114ce0f7b user: carlfeberhard date: 2013-02-19 22:21:16 summary: functional_tests: fix import affected #: 1 file diff -r 7bf93ff108fe4a62ee3084d84a77fa9b71c8b1f7 -r bc0114ce0f7b5224cd4ef58d1dd2ef8b30c77a69 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -40,6 +40,7 @@ import nose.loader import nose.plugins.manager +import pprint log = logging.getLogger( "functional_tests.py" ) default_galaxy_test_host = "localhost" 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: Enhancement to tool shed functional tests for repositories that only contain a workflow.
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7bf93ff108fe/ changeset: 7bf93ff108fe user: inithello date: 2013-02-19 22:01:18 summary: Enhancement to tool shed functional tests for repositories that only contain a workflow. affected #: 2 files diff -r 305680a482c3096b082daffa5ff665f5f60d1528 -r 7bf93ff108fe4a62ee3084d84a77fa9b71c8b1f7 test/tool_shed/functional/test_0060_workflows.py --- a/test/tool_shed/functional/test_0060_workflows.py +++ b/test/tool_shed/functional/test_0060_workflows.py @@ -4,11 +4,17 @@ repository_name = 'filtering_0060' repository_description="Galaxy's filtering tool for test 0060" repository_long_description="Long description of Galaxy's filtering tool for test 0060" + workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' + category_name = 'Test 0060 Workflow Features' category_description = 'Test 0060 for workflow features' +workflow_repository_name = 'filtering_workflow_0060' +workflow_repository_description="Workflow referencing the filtering tool for test 0060" +workflow_repository_long_description="Long description of the workflow for test 0060" + class TestToolShedWorkflowFeatures( ShedTwillTestCase ): '''Test valid and invalid workflows.''' def test_0000_initiate_users( self ): @@ -69,7 +75,41 @@ strings_displayed=[], strings_not_displayed=[] ) self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] ) - def test_0025_verify_repository_metadata( self ): + def test_0025_create_repository_with_only_workflow( self ): + """Create and populate the filtering_workflow_0060 repository""" + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.get_or_create_repository( name=workflow_repository_name, + description=workflow_repository_description, + long_description=workflow_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read() + workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) ) + workflow_filepath = self.generate_temp_path( 'test_0060', additional_paths=[ 'filtering_workflow_2' ] ) + if not os.path.exists( workflow_filepath ): + os.makedirs( workflow_filepath ) + file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow ) + repository = test_db_util.get_repository_by_name_and_owner( workflow_repository_name, common.test_user_1_name ) + self.upload_file( repository, + filename=workflow_filename, + filepath=workflow_filepath, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering workflow.', + strings_displayed=[], + strings_not_displayed=[] ) + self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_displayed=[ '#EBBCB2' ] ) + def test_0030_check_workflow_repository( self ): + """Check for strings on the manage page for the filtering_workflow_0060 repository.""" + repository = test_db_util.get_repository_by_name_and_owner( workflow_repository_name, common.test_user_1_name ) + strings_displayed = [ 'Workflows', 'Workflow for 0060_filter', '0.1' ] + strings_not_displayed = [ 'Valid tools', 'Invalid tools' ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + def test_0035_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.verify_unchanged_repository_metadata( repository ) diff -r 305680a482c3096b082daffa5ff665f5f60d1528 -r 7bf93ff108fe4a62ee3084d84a77fa9b71c8b1f7 test/tool_shed/functional/test_1060_install_repository_with_workflow.py --- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py +++ b/test/tool_shed/functional/test_1060_install_repository_with_workflow.py @@ -1,15 +1,21 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -import logging -log = logging.getLogger(__name__) + repository_name = 'filtering_0060' repository_description="Galaxy's filtering tool for test 0060" repository_long_description="Long description of Galaxy's filtering tool for test 0060" + workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' +second_workflow_name = 'New workflow for 0060_filter_workflow_repository' + category_name = 'Test 0060 Workflow Features' category_description = 'Test 0060 for workflow features' +workflow_repository_name = 'filtering_workflow_0060' +workflow_repository_description="Workflow referencing the filtering tool for test 0060" +workflow_repository_long_description="Long description of the workflow for test 0060" + class ToolWithRepositoryDependencies( ShedTwillTestCase ): '''Test installing a repository with repository dependencies.''' def test_0000_initiate_users( self ): @@ -87,3 +93,61 @@ self.display_all_workflows( strings_not_displayed=[ 'Workflow for 0060_filter_workflow_repository' ] ) self.import_workflow( installed_repository, workflow_name ) self.display_all_workflows( strings_displayed=[ 'Workflow for 0060_filter_workflow_repository' ] ) + def test_0020_create_filter_workflow_repository( self ): + '''Create, if necessary, a filtering repository with only a workflow.''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=workflow_repository_name, + description=workflow_repository_description, + long_description=workflow_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read() + workflow = workflow.replace( '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) ) + workflow = workflow.replace( 'Workflow for 0060_filter_workflow_repository', + 'New workflow for 0060_filter_workflow_repository' ) + workflow_filepath = self.generate_temp_path( 'test_0060', additional_paths=[ 'filtering_workflow_2' ] ) + if not os.path.exists( workflow_filepath ): + os.makedirs( workflow_filepath ) + file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow ) + self.upload_file( repository, + filename=workflow_filename, + filepath=workflow_filepath, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering workflow.', + strings_displayed=[], + strings_not_displayed=[] ) + self.load_workflow_image_in_tool_shed( repository, + 'New workflow for 0060_filter_workflow_repository', + strings_displayed=[ '#EBBCB2' ] ) + def test_0025_install_repository_with_workflow( self ): + """Browse the available tool sheds in this Galaxy instance and preview the filtering workflow repository.""" + self.preview_repository_in_tool_shed( workflow_repository_name, + common.test_user_1_name, + strings_displayed=[ 'filtering_workflow_0060', 'Workflows' ], + strings_not_displayed=[ 'Valid tools', 'Invalid tools' ] ) + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( workflow_repository_name, + common.test_user_1_name, + 'Test 0060 Workflow Features', + install_tool_dependencies=False, + includes_tools=False ) + def test_0030_import_workflow_from_installed_repository( self ): + '''Import the workflow from the installed repository and verify that it appears in the list of all workflows.''' + installed_repository = test_db_util.get_installed_repository_by_name_owner( workflow_repository_name, common.test_user_1_name ) + self.display_installed_workflow_image( installed_repository, + 'New workflow for 0060_filter_workflow_repository', + strings_displayed=[ '#EBD9B2' ], + strings_not_displayed=[ '#EBBCB2' ] ) + self.display_all_workflows( strings_not_displayed=[ 'New workflow for 0060_filter_workflow_repository' ] ) + self.import_workflow( installed_repository, + 'New workflow for 0060_filter_workflow_repository', + strings_displayed=[ 'New workflow for 0060_filter_workflow_repository' ] ) + self.display_all_workflows( strings_displayed=[ 'New workflow for 0060_filter_workflow_repository' ] ) + Repository URL: 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