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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 01 May '13

01 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47ddf167c9f1/ Changeset: 47ddf167c9f1 Branch: stable User: natefoo Date: 2013-05-01 15:50:31 Summary: Use Galaxy's ErrorMiddleware since Paste's doesn't return start_response. Fixes downloading tarballs from the Tool Shed when use_debug = false. Affected #: 1 file diff -r 6ab749e3563153f714fe0699435ae9215ebe4ba2 -r 47ddf167c9f11c903a438c0979e101fe7535f061 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -160,8 +160,8 @@ log.debug( "Enabling 'eval exceptions' middleware" ) else: # Not in interactive debug mode, just use the regular error middleware - from paste.exceptions import errormiddleware - app = errormiddleware.ErrorMiddleware( app, conf ) + import galaxy.web.framework.middleware.error + app = galaxy.web.framework.middleware.error.ErrorMiddleware( app, conf ) log.debug( "Enabling 'error' middleware" ) # Transaction logging (apache access.log style) if asbool( conf.get( 'use_translogger', True ) ): https://bitbucket.org/galaxy/galaxy-central/commits/cd6c9cc0079c/ Changeset: cd6c9cc0079c User: natefoo Date: 2013-05-01 16:06:21 Summary: Merge stable. Affected #: 2 files diff -r 56e7a8b0823434bd1458a31da4b35cec8acf88a8 -r cd6c9cc0079ce10685c04d003e735d6054a4a8c6 lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -161,8 +161,8 @@ log.debug( "Enabling 'eval exceptions' middleware" ) else: # Not in interactive debug mode, just use the regular error middleware - from paste.exceptions import errormiddleware - app = errormiddleware.ErrorMiddleware( app, conf ) + import galaxy.web.framework.middleware.error + app = galaxy.web.framework.middleware.error.ErrorMiddleware( app, conf ) log.debug( "Enabling 'error' middleware" ) # Transaction logging (apache access.log style) if asbool( conf.get( 'use_translogger', True ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Filter out deleted and deprecated repositories from the new tool shed lists for reviewing repositories with tool, and filter out repositories with missing tool components from the list that shows failing tool tests.
by commits-noreply＠bitbucket.org 01 May '13

01 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56e7a8b08234/ Changeset: 56e7a8b08234 User: greg Date: 2013-05-01 02:49:20 Summary: Filter out deleted and deprecated repositories from the new tool shed lists for reviewing repositories with tool, and filter out repositories with missing tool components from the list that shows failing tool tests. Affected #: 1 file diff -r 6dc37563b0b744d8b571b0075110da54fd120df4 -r 56e7a8b0823434bd1458a31da4b35cec8acf88a8 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -537,7 +537,9 @@ def build_initial_query( self, trans, **kwd ): # Filter by latest installable revisions that contain tools with missing tool test components. revision_clause_list = [] - for repository in trans.sa_session.query( model.Repository ): + for repository in trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deprecated == False, + model.Repository.table.c.deleted == False ) ): changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ) if changeset_revision: revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) @@ -614,7 +616,9 @@ def build_initial_query( self, trans, **kwd ): # Filter by latest installable revisions that contain tools with at least 1 failing tool test. revision_clause_list = [] - for repository in trans.sa_session.query( model.Repository ): + for repository in trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deprecated == False, + model.Repository.table.c.deleted == False ) ): changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( trans, repository ) if changeset_revision: revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) @@ -692,7 +696,9 @@ # We have the list of repositories that the current user is authorized to update, so filter further by latest installable revisions that contain # tools with at least 1 failing tool test. revision_clause_list = [] - for repository in trans.sa_session.query( model.Repository ): + for repository in trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deprecated == False, + model.Repository.table.c.deleted == False ) ): changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_no_failing_tool_tests( trans, repository ) if changeset_revision: revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) @@ -1345,7 +1351,7 @@ repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) - if repository_metadata and not repository_metadata.tools_functionally_correct: + if repository_metadata and not repository_metadata.missing_test_components and not repository_metadata.tools_functionally_correct: return repository_metadata.changeset_revision return 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: 2 new changesets
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6dc37563b0b7/ Changeset: 6dc37563b0b7 User: dan Date: 2013-04-30 23:19:11 Summary: Update GenomeSpace serverurl.properties file location. Should resolve network issues experienced with Jumbo Frames and the Broad. Affected #: 3 files diff -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 -r 6dc37563b0b744d8b571b0075110da54fd120df4 tools/genomespace/genomespace_exporter.py --- a/tools/genomespace/genomespace_exporter.py +++ b/tools/genomespace/genomespace_exporter.py @@ -11,7 +11,7 @@ log = logging.getLogger( "tools.genomespace.genomespace_exporter" )#( __name__ ) GENOMESPACE_API_VERSION_STRING = "v1.0" -GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.properti…" +GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb diff -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 -r 6dc37563b0b744d8b571b0075110da54fd120df4 tools/genomespace/genomespace_file_browser.py --- a/tools/genomespace/genomespace_file_browser.py +++ b/tools/genomespace/genomespace_file_browser.py @@ -9,7 +9,7 @@ import simplejson GENOMESPACE_API_VERSION_STRING = "v1.0" -GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.properti…" +GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb diff -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 -r 6dc37563b0b744d8b571b0075110da54fd120df4 tools/genomespace/genomespace_importer.py --- a/tools/genomespace/genomespace_importer.py +++ b/tools/genomespace/genomespace_importer.py @@ -13,7 +13,7 @@ from galaxy.datatypes.registry import Registry GENOMESPACE_API_VERSION_STRING = "v1.0" -GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.properti…" +GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb https://bitbucket.org/galaxy/galaxy-central/commits/6ab749e35631/ Changeset: 6ab749e35631 Branch: stable User: dan Date: 2013-04-30 23:19:11 Summary: Update GenomeSpace serverurl.properties file location. Should resolve network issues experienced with Jumbo Frames and the Broad. Affected #: 3 files diff -r b0ea9722b9dd8e0da63208b59be20b90eae0cea7 -r 6ab749e3563153f714fe0699435ae9215ebe4ba2 tools/genomespace/genomespace_exporter.py --- a/tools/genomespace/genomespace_exporter.py +++ b/tools/genomespace/genomespace_exporter.py @@ -11,7 +11,7 @@ log = logging.getLogger( "tools.genomespace.genomespace_exporter" )#( __name__ ) GENOMESPACE_API_VERSION_STRING = "v1.0" -GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.properti…" +GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb diff -r b0ea9722b9dd8e0da63208b59be20b90eae0cea7 -r 6ab749e3563153f714fe0699435ae9215ebe4ba2 tools/genomespace/genomespace_file_browser.py --- a/tools/genomespace/genomespace_file_browser.py +++ b/tools/genomespace/genomespace_file_browser.py @@ -9,7 +9,7 @@ import simplejson GENOMESPACE_API_VERSION_STRING = "v1.0" -GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.properti…" +GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb diff -r b0ea9722b9dd8e0da63208b59be20b90eae0cea7 -r 6ab749e3563153f714fe0699435ae9215ebe4ba2 tools/genomespace/genomespace_importer.py --- a/tools/genomespace/genomespace_importer.py +++ b/tools/genomespace/genomespace_importer.py @@ -13,7 +13,7 @@ from galaxy.datatypes.registry import Registry GENOMESPACE_API_VERSION_STRING = "v1.0" -GENOMESPACE_SERVER_URL_PROPERTIES = "http://www.genomespace.org/sites/genomespacefiles/config/serverurl.properti…" +GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix queries in the current user's lists of repositories that display the latest revision of each of their repositories with 1) missing tool test components 2) failing tool tests and 3) no failing tool tests. Add links for the same filtered lists for all users under the Review repositories with tools section in the tool shed menu.
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9a21a5156b2e/ Changeset: 9a21a5156b2e User: greg Date: 2013-04-30 22:40:06 Summary: Fix queries in the current user's lists of repositories that display the latest revision of each of their repositories with 1) missing tool test components 2) failing tool tests and 3) no failing tool tests. Add links for the same filtered lists for all users under the Review repositories with tools section in the tool shed menu. Affected #: 5 files diff -r f44f6beea3daf77bd48fdb8a657f7cb593b72b6f -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -65,6 +65,9 @@ repositories_by_user_grid = repository_grids.RepositoriesByUserGrid() repositories_i_own_grid = repository_grids.RepositoriesIOwnGrid() repositories_in_category_grid = repository_grids.RepositoriesInCategoryGrid() + repositories_missing_tool_test_components_grid = repository_grids.RepositoriesMissingToolTestComponentsGrid() + repositories_with_failing_tool_tests_grid = repository_grids.RepositoriesWithFailingToolTestsGrid() + repositories_with_no_failing_tool_tests_grid = repository_grids.RepositoriesWithNoFailingToolTestsGrid() repository_dependencies_grid = repository_grids.RepositoryDependenciesGrid() repository_grid = repository_grids.RepositoryGrid() # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. @@ -121,6 +124,23 @@ return self.datatypes_grid( trans, **kwd ) @web.expose + def browse_deprecated_repositories_i_own( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + if repository: + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=trans.security.encode_id( repository.id ), + changeset_revision=selected_changeset_revision ) ) + return self.deprecated_repositories_i_own_grid( trans, **kwd ) + + @web.expose def browse_invalid_tools( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -188,6 +208,34 @@ return self.my_writable_repositories_grid( trans, **kwd ) @web.expose + def browse_my_writable_repositories_missing_tool_test_components( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + elif operation == "repositories_by_user": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories_by_user', + **kwd ) ) + elif operation in [ 'mark as deprecated', 'mark as not deprecated' ]: + kwd[ 'mark_deprecated' ] = operation == 'mark as deprecated' + return trans.response.send_redirect( web.url_for( controller='repository', + action='deprecate', + **kwd ) ) + if 'message' not in kwd: + message = 'This list contains repositories that match the following criteria:<br>' + message += '<ul>' + message += '<li>you are authorized to update them</li>' + message += '<li>the latest installable revision contains at least 1 tool with no defined tests <b>OR</b>:</li>' + message += '<li>the latest installable revision contains at least 1 tool with a test that requires a missing test data file</li>' + message += '</ul>' + kwd[ 'message' ] = message + kwd[ 'status' ] = 'warning' + return self.my_writable_repositories_missing_tool_test_components_grid( trans, **kwd ) + + @web.expose def browse_my_writable_repositories_with_failing_tool_tests( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() @@ -246,44 +294,6 @@ return self.my_writable_repositories_with_no_failing_tool_tests_grid( trans, **kwd ) @web.expose - def browse_my_writable_repositories_missing_tool_test_components( self, trans, **kwd ): - if 'operation' in kwd: - operation = kwd[ 'operation' ].lower() - if operation == "view_or_manage_repository": - return trans.response.send_redirect( web.url_for( controller='repository', - action='view_or_manage_repository', - **kwd ) ) - elif operation == "repositories_by_user": - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories_by_user', - **kwd ) ) - elif operation in [ 'mark as deprecated', 'mark as not deprecated' ]: - kwd[ 'mark_deprecated' ] = operation == 'mark as deprecated' - return trans.response.send_redirect( web.url_for( controller='repository', - action='deprecate', - **kwd ) ) - if 'message' not in kwd: - message = 'This list contains repositories that match the following criteria:<br>' - message += '<ul>' - message += '<li>you are authorized to update them</li>' - message += '<li>the latest installable revision contains at least 1 tool with no defined tests <b>OR</b>:</li>' - message += '<li>the latest installable revision contains at least 1 tool with a test that requires a missing test data file</li>' - message += '</ul>' - kwd[ 'message' ] = message - kwd[ 'status' ] = 'warning' - return self.my_writable_repositories_missing_tool_test_components_grid( trans, **kwd ) - - @web.expose - def browse_deprecated_repositories_i_own( self, trans, **kwd ): - if 'operation' in kwd: - operation = kwd[ 'operation' ].lower() - if operation == "view_or_manage_repository": - return trans.response.send_redirect( web.url_for( controller='repository', - action='view_or_manage_repository', - **kwd ) ) - return self.deprecated_repositories_i_own_grid( trans, **kwd ) - - @web.expose def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search # link. We have to take this approach because the "-" character is illegal in HTTP requests. @@ -427,6 +437,89 @@ return self.repositories_in_category_grid( trans, **kwd ) @web.expose + def browse_repositories_missing_tool_test_components( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + elif operation == "repositories_by_user": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories_by_user', + **kwd ) ) + elif operation in [ 'mark as deprecated', 'mark as not deprecated' ]: + kwd[ 'mark_deprecated' ] = operation == 'mark as deprecated' + return trans.response.send_redirect( web.url_for( controller='repository', + action='deprecate', + **kwd ) ) + if 'message' not in kwd: + message = 'This list contains repositories that match the following criteria:<br>' + message += '<ul>' + message += '<li>the latest installable revision contains at least 1 tool with no defined tests <b>OR</b>:</li>' + message += '<li>the latest installable revision contains at least 1 tool with a test that requires a missing test data file</li>' + message += '</ul>' + kwd[ 'message' ] = message + kwd[ 'status' ] = 'warning' + return self.repositories_missing_tool_test_components_grid( trans, **kwd ) + + @web.expose + def browse_repositories_with_failing_tool_tests( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + elif operation == "repositories_by_user": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories_by_user', + **kwd ) ) + elif operation in [ 'mark as deprecated', 'mark as not deprecated' ]: + kwd[ 'mark_deprecated' ] = operation == 'mark as deprecated' + return trans.response.send_redirect( web.url_for( controller='repository', + action='deprecate', + **kwd ) ) + if 'message' not in kwd: + message = 'This list contains repositories that match the following criteria:<br>' + message += '<ul>' + message += '<li>the latest installable revision contains at least 1 tool</li>' + message += '<li>the latest installable revision is not missing any tool test components</li>' + message += '<li>the latest installable revision has at least 1 tool test that fails</li>' + message += '</ul>' + kwd[ 'message' ] = message + kwd[ 'status' ] = 'warning' + return self.repositories_with_failing_tool_tests_grid( trans, **kwd ) + + @web.expose + def browse_repositories_with_no_failing_tool_tests( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + elif operation == "repositories_by_user": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories_by_user', + **kwd ) ) + elif operation in [ 'mark as deprecated', 'mark as not deprecated' ]: + kwd[ 'mark_deprecated' ] = operation == 'mark as deprecated' + return trans.response.send_redirect( web.url_for( controller='repository', + action='deprecate', + **kwd ) ) + if 'message' not in kwd: + message = 'This list contains repositories that match the following criteria:<br>' + message += '<ul>' + message += '<li>the latest installable revision contains at least 1 tool</li>' + message += '<li>the latest installable revision is not missing any tool test components</li>' + message += '<li>the latest installable revision has no tool tests that fail</li>' + message += '</ul>' + kwd[ 'message' ] = message + kwd[ 'status' ] = 'warning' + return self.repositories_with_no_failing_tool_tests_grid( trans, **kwd ) + + @web.expose def browse_repository( self, trans, id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) diff -r f44f6beea3daf77bd48fdb8a657f7cb593b72b6f -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -1,17 +1,24 @@ -import os, logging +import logging +import os from galaxy.webapps.tool_shed import model from galaxy.web.framework.helpers import grids -from galaxy.model.orm import and_, or_ +from galaxy.model.orm import and_ +from galaxy.model.orm import or_ from galaxy.util import json import tool_shed.util.shed_util_common as suc import tool_shed.grids.util as grids_util from tool_shed.util import metadata_util from galaxy import eggs + eggs.require('markupsafe') from markupsafe import escape as escape_html + eggs.require('mercurial') -from mercurial import hg, ui, patch, commands +from mercurial import commands +from mercurial import hg +from mercurial import patch +from mercurial import ui log = logging.getLogger( __name__ ) @@ -462,7 +469,7 @@ class MyWritableRepositoriesGrid( RepositoryGrid ): # This grid filters out repositories that have been marked as either deprecated or deleted. - title = 'Repositories that I can change' + title = 'Repositories I can change' columns = [ RepositoryGrid.NameColumn( "Name", key="name", @@ -505,19 +512,19 @@ .filter( model.Repository.table.c.id < 0 ) -class MyWritableRepositoriesMissingToolTestComponentsGrid( MyWritableRepositoriesGrid ): - title = "Repositories that I can change with missing tool test components" +class RepositoriesMissingToolTestComponentsGrid( RepositoryGrid ): + title = "Repositories with missing tool test components" columns = [ - RepositoriesIOwnGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), + RepositoryGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=False ), RepositoryGrid.LatestInstallableRevisionColumn( "Latest Installable Revision" ), RepositoryGrid.UserColumn( "Owner", + key="User.username", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[0] ], @@ -528,6 +535,29 @@ use_paging = False def build_initial_query( self, trans, **kwd ): + # Filter by latest installable revisions that contain tools with missing tool test components. + revision_clause_list = [] + for repository in trans.sa_session.query( model.Repository ): + changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ) + if changeset_revision: + revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) + if revision_clause_list: + return trans.sa_session.query( model.Repository ) \ + .join( model.RepositoryMetadata ) \ + .filter( or_( *revision_clause_list ) ) \ + .join( model.User.table ) + # Return an empty query. + return trans.sa_session.query( model.Repository ) \ + .filter( model.Repository.table.c.id < 0 ) + + +class MyWritableRepositoriesMissingToolTestComponentsGrid( RepositoriesMissingToolTestComponentsGrid ): + title = "Repositories I can change with missing tool test components" + columns = [ col for col in RepositoriesMissingToolTestComponentsGrid.columns ] + operations = [] + use_paging = False + + def build_initial_query( self, trans, **kwd ): # First get all repositories that the current user is authorized to update. username = trans.user.username user_clause_list = [] @@ -545,8 +575,8 @@ revision_clause_list = [] for repository in trans.sa_session.query( model.Repository ) \ .filter( or_( *user_clause_list ) ): - changeset_revision = suc.filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ) - if changeset_revision not in [ None, suc.INITIAL_CHANGELOG_HASH ]: + changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ) + if changeset_revision: revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) if revision_clause_list: return trans.sa_session.query( model.Repository ) \ @@ -559,19 +589,19 @@ .filter( model.Repository.table.c.id < 0 ) -class MyWritableRepositoriesWithFailingToolTestsGrid( MyWritableRepositoriesMissingToolTestComponentsGrid ): - title = "Repositories that I can change with failing tool tests" +class RepositoriesWithFailingToolTestsGrid( RepositoryGrid ): + title = "Repositories with failing tool tests" columns = [ - RepositoriesIOwnGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), + RepositoryGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=False ), RepositoryGrid.LatestInstallableRevisionColumn( "Latest Installable Revision" ), RepositoryGrid.UserColumn( "Owner", + key="User.username", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[0] ], @@ -582,6 +612,29 @@ use_paging = False def build_initial_query( self, trans, **kwd ): + # Filter by latest installable revisions that contain tools with at least 1 failing tool test. + revision_clause_list = [] + for repository in trans.sa_session.query( model.Repository ): + changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( trans, repository ) + if changeset_revision: + revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) + if revision_clause_list: + return trans.sa_session.query( model.Repository ) \ + .join( model.RepositoryMetadata ) \ + .filter( or_( *revision_clause_list ) ) \ + .join( model.User.table ) + # Return an empty query. + return trans.sa_session.query( model.Repository ) \ + .filter( model.Repository.table.c.id < 0 ) + + +class MyWritableRepositoriesWithFailingToolTestsGrid( RepositoriesWithFailingToolTestsGrid ): + title = "Repositories I can change with failing tool tests" + columns = [ col for col in RepositoriesWithFailingToolTestsGrid.columns ] + operations = [] + use_paging = False + + def build_initial_query( self, trans, **kwd ): # First get all repositories that the current user is authorized to update. username = trans.user.username user_clause_list = [] @@ -595,38 +648,37 @@ user_clause_list.append( model.Repository.table.c.id == repository.id ) if user_clause_list: # We have the list of repositories that the current user is authorized to update, so filter further by latest installable revisions that contain - # tools with missing tool test components. + # tools with at least 1 failing tool test. revision_clause_list = [] for repository in trans.sa_session.query( model.Repository ) \ .filter( or_( *user_clause_list ) ): - changeset_revision = suc.filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ) - if changeset_revision not in [ None, suc.INITIAL_CHANGELOG_HASH ]: + changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( trans, repository ) + if changeset_revision: revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) if revision_clause_list: return trans.sa_session.query( model.Repository ) \ .join( model.User.table ) \ .filter( or_( *user_clause_list ) ) \ .join( model.RepositoryMetadata ) \ - .filter( or_( *revision_clause_list ) ) \ - .filter( model.RepositoryMetadata.table.c.tools_functionally_correct == False ) + .filter( or_( *revision_clause_list ) ) # Return an empty query. return trans.sa_session.query( model.Repository ) \ .filter( model.Repository.table.c.id < 0 ) -class MyWritableRepositoriesWithNoFailingToolTestsGrid( MyWritableRepositoriesMissingToolTestComponentsGrid ): - title = "Repositories that I can change with failing tool tests" +class RepositoriesWithNoFailingToolTestsGrid( RepositoryGrid ): + title = "Repositories with no failing tool tests" columns = [ - RepositoriesIOwnGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), + RepositoryGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=False ), RepositoryGrid.LatestInstallableRevisionColumn( "Latest Installable Revision" ), RepositoryGrid.UserColumn( "Owner", + key="User.username", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[0] ], @@ -637,6 +689,30 @@ use_paging = False def build_initial_query( self, trans, **kwd ): + # We have the list of repositories that the current user is authorized to update, so filter further by latest installable revisions that contain + # tools with at least 1 failing tool test. + revision_clause_list = [] + for repository in trans.sa_session.query( model.Repository ): + changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_no_failing_tool_tests( trans, repository ) + if changeset_revision: + revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) + if revision_clause_list: + return trans.sa_session.query( model.Repository ) \ + .join( model.RepositoryMetadata ) \ + .filter( or_( *revision_clause_list ) ) \ + .join( model.User.table ) + # Return an empty query. + return trans.sa_session.query( model.Repository ) \ + .filter( model.Repository.table.c.id < 0 ) + + +class MyWritableRepositoriesWithNoFailingToolTestsGrid( RepositoriesWithNoFailingToolTestsGrid ): + title = "Repositories I can change with no failing tool tests" + columns = [ col for col in RepositoriesWithNoFailingToolTestsGrid.columns ] + operations = [] + use_paging = False + + def build_initial_query( self, trans, **kwd ): # First get all repositories that the current user is authorized to update. username = trans.user.username user_clause_list = [] @@ -650,20 +726,19 @@ user_clause_list.append( model.Repository.table.c.id == repository.id ) if user_clause_list: # We have the list of repositories that the current user is authorized to update, so filter further by latest installable revisions that contain - # tools with missing tool test components. + # at least 1 tool, no missing tool test components, and no failing tool tests. revision_clause_list = [] for repository in trans.sa_session.query( model.Repository ) \ .filter( or_( *user_clause_list ) ): - changeset_revision = suc.filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ) - if changeset_revision not in [ None, suc.INITIAL_CHANGELOG_HASH ]: + changeset_revision = filter_by_latest_downloadable_changeset_revision_that_has_no_failing_tool_tests( trans, repository ) + if changeset_revision: revision_clause_list.append( model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) if revision_clause_list: return trans.sa_session.query( model.Repository ) \ .join( model.User.table ) \ .filter( or_( *user_clause_list ) ) \ .join( model.RepositoryMetadata ) \ - .filter( or_( *revision_clause_list ) ) \ - .filter( model.RepositoryMetadata.table.c.tools_functionally_correct == True ) + .filter( or_( *revision_clause_list ) ) # Return an empty query. return trans.sa_session.query( model.Repository ) \ .filter( model.Repository.table.c.id < 0 ) @@ -1259,3 +1334,62 @@ model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ .join( model.User.table ) + +# ------ utility methods ------------------- + +def filter_by_latest_downloadable_changeset_revision_that_has_failing_tool_tests( trans, repository ): + """ + Inspect the latest installable changeset revision for the received repository to see if it includes at least 1 tool that has at least 1 failing test. + """ + encoded_repository_id = trans.security.encode_id( repository.id ) + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) + repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) + if repository_metadata and not repository_metadata.tools_functionally_correct: + return repository_metadata.changeset_revision + return None + +def filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ): + """ + Inspect the latest installable changeset revision for the received repository to see if it includes tools that are either missing functional tests + or functional test data. If the changset revision includes tools, but is missing tool test components, return the changeset revision hash. + """ + encoded_repository_id = trans.security.encode_id( repository.id ) + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) + repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) + if repository_metadata and repository_metadata.missing_test_components: + return repository_metadata.changeset_revision + return None + +def filter_by_latest_downloadable_changeset_revision_that_has_no_failing_tool_tests( trans, repository ): + """ + Inspect the latest installable changeset revision for the received repository to see if it includes tools with no failing tests. + """ + encoded_repository_id = trans.security.encode_id( repository.id ) + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) + repository_metadata = get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ) + if repository_metadata and not repository_metadata.missing_test_components and repository_metadata.tools_functionally_correct: + return repository_metadata.changeset_revision + return None + +def get_latest_installable_repository_metadata_if_it_includes_tools( trans, repository ): + """Return the latest installable repository_metadata record for the received repository if one exists.""" + encoded_repository_id = trans.security.encode_id( repository.id ) + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) + repository_metadata = None + try: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx ) + if repository_metadata and repository_metadata.includes_tools and repository_metadata.downloadable: + return repository_metadata + return None + except: + latest_installable_revision = suc.get_previous_downloadable_changeset_revision( repository, repo, tip_ctx ) + if latest_installable_revision == suc.INITIAL_CHANGELOG_HASH: + return None + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, latest_installable_revision ) + if repository_metadata and repository_metadata.includes_tools and repository_metadata.downloadable: + return repository_metadata + return None diff -r f44f6beea3daf77bd48fdb8a657f7cb593b72b6f -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -255,29 +255,6 @@ sa_session.flush() return tool_shed_repository -def filter_by_latest_downloadable_changeset_revision_that_has_missing_tool_test_components( trans, repository ): - """ - Inspect the latest installable changeset revision for the received repository to see if it includes tool that are either missing functional tests - or functional test data. If the changset revision includes tools, but is missing tool test components, return the changeset revision hash. Otherwise - return the INITIAL_CHANGELOG_HASH. - """ - print_debug = repository.name == 'convert_chars' - encoded_repository_id = trans.security.encode_id( repository.id ) - repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) - tip_ctx = str( repo.changectx( repo.changelog.tip() ) ) - repository_metadata = None - try: - repository_metadata = get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, tip_ctx ) - except: - latest_installable_revision = get_previous_downloadable_changeset_revision( repository, repo, tip_ctx ) - if latest_installable_revision != INITIAL_CHANGELOG_HASH: - repository_metadata = get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, latest_installable_revision ) - else: - repository_metadata = None - if repository_metadata and repository_metadata.downloadable and repository_metadata.missing_test_components: - return repository_metadata.changeset_revision - return INITIAL_CHANGELOG_HASH - def generate_clone_url_for_installed_repository( app, repository ): """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" tool_shed_url = get_url_from_tool_shed( app, repository.tool_shed ) diff -r f44f6beea3daf77bd48fdb8a657f7cb593b72b6f -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 templates/webapps/tool_shed/admin/index.mako --- a/templates/webapps/tool_shed/admin/index.mako +++ b/templates/webapps/tool_shed/admin/index.mako @@ -96,9 +96,18 @@ Reviewing Repositories With Tools </div><div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_invalid_tests' )}">Repositories missing tests or data</a> + <div class="toolSectionPad"></div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_missing_tool_test_components' )}">Latest revision missing tool tests</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_with_failing_tool_tests' )}">Latest revision failing tool tests</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_with_no_failing_tool_tests' )}">Latest revision all tool tests pass</a> + </div></div></div></div> diff -r f44f6beea3daf77bd48fdb8a657f7cb593b72b6f -r 9a21a5156b2efd6b4a169a62bd663bf69fdadf79 templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -164,7 +164,13 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_invalid_tests' )}">Repositories missing tests or data</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_missing_tool_test_components' )}">Latest revision missing tool tests</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_with_failing_tool_tests' )}">Latest revision failing tool tests</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_with_no_failing_tool_tests' )}">Latest revision all tool tests pass</a></div></div></div> 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: Clean up for copying datasets to current history.
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f44f6beea3da/ Changeset: f44f6beea3da User: jgoecks Date: 2013-04-30 20:36:20 Summary: Clean up for copying datasets to current history. Affected #: 1 file diff -r 4c7b5f4d569d478fd83fbfa3bf8d2f0187a30c1a -r f44f6beea3daf77bd48fdb8a657f7cb593b72b6f lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -546,8 +546,14 @@ hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ] trans.template_context[ 'seek_hda_ids' ] = hda_ids elif operation == "copy to current history": - # Copy a dataset to the current history. + # + # Copy datasets to the current history. + # + target_histories = [ trans.get_history() ] + + # Reverse HDAs so that they appear in the history in the order they are provided. + hda_ids.reverse() status, message = self._copy_datasets( trans, hda_ids, target_histories ) # Current history changed, refresh history frame. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Clean up for inheritance chain display.
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4c7b5f4d569d/ Changeset: 4c7b5f4d569d User: jgoecks Date: 2013-04-30 20:15:27 Summary: Clean up for inheritance chain display. Affected #: 1 file diff -r 3a6d4a323e3ae7764a6a3704cf35b9dcb9b315f2 -r 4c7b5f4d569d478fd83fbfa3bf8d2f0187a30c1a templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -153,7 +153,9 @@ <div class="inherit" style="background-color: #fff; font-weight:bold;">${hda.name | h}</div> % for dep in inherit_chain: - <div style="font-size: 36px; text-align: center;">↑</div> - <div class="inherit">${dep[0].name | h}<br/>${dep[1]}</div> + <div style="font-size: 36px; text-align: center; position: relative; top: 3px">↑</div> + <div class="inherit"> + '${dep[0].name | h}' in ${dep[1]}<br/> + </div> % endfor 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: Datasets API: better error handling on api/datasets/display
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a6d4a323e3a/ Changeset: 3a6d4a323e3a User: carlfeberhard Date: 2013-04-30 20:06:12 Summary: Datasets API: better error handling on api/datasets/display Affected #: 1 file diff -r 746d59a574bbccdf5cedfbc7bd25a50b37d6667f -r 3a6d4a323e3ae7764a6a3704cf35b9dcb9b315f2 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -68,8 +68,9 @@ return rval def _dataset_state( self, trans, dataset, **kwargs ): - """ Returns state of dataset. """ - + """ + Returns state of dataset. + """ msg = self.check_dataset_state( trans, dataset ) if not msg: msg = dataset.conversion_messages.DATA @@ -216,7 +217,7 @@ Displays history content (dataset). """ # Huge amount of code overlap with lib/galaxy/webapps/galaxy/api/history_content:show here. - hda_dict = {} + rval = '' try: # for anon users: #TODO: check login_required? @@ -233,6 +234,13 @@ check_ownership=True, check_accessible=True, deleted=False ) hda = self.get_history_dataset_association( trans, history, history_content_id, check_ownership=True, check_accessible=True ) - except: - raise - return hda.datatype.display_data(trans, hda, preview, filename, to_ext, chunk, **kwd) + + rval = hda.datatype.display_data( trans, hda, preview, filename, to_ext, chunk, **kwd ) + + except Exception, exception: + log.error( "Error getting display data for dataset (%s) from history (%s): %s", + history_content_id, history_id, str( exception ), exc_info=True ) + trans.response.status = 500 + rval = ( "Could not get display data for dataset: " + str( exception ) ) + + return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Datasets API: import cleanup, misc. cleanup
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/746d59a574bb/ Changeset: 746d59a574bb User: carlfeberhard Date: 2013-04-30 19:56:11 Summary: Datasets API: import cleanup, misc. cleanup Affected #: 1 file diff -r 07f09e119bfcbe8e4cfda3400c8892f8fb3891d2 -r 746d59a574bbccdf5cedfbc7bd25a50b37d6667f lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,15 +1,17 @@ """ API operations on the contents of a dataset. """ -import logging, os, string, shutil, urllib, re, socket -from galaxy import util, datatypes, jobs, web, util +from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.framework.helpers import is_true +import logging log = logging.getLogger( __name__ ) -class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin ): +class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin, + UsesHistoryDatasetAssociationMixin ): @web.expose_api def index( self, trans, **kwd ): @@ -17,7 +19,8 @@ GET /api/datasets Lists datasets. """ - pass + trans.response.status = 501 + return 'not implemented' @web.expose_api def show( self, trans, id, hda_ldda='hda', data_type=None, **kwd ): @@ -25,7 +28,6 @@ GET /api/datasets/{encoded_dataset_id} Displays information about and/or content of a dataset. """ - # Get dataset. try: dataset = self.get_hda_or_ldda( trans, hda_ldda=hda_ldda, dataset_id=id ) @@ -98,7 +100,8 @@ # If there is a chrom, check for data on the chrom. if chrom: data_provider_registry = trans.app.data_provider_registry - data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, source='index' ) if not data_provider.has_data( chrom ): return dataset.conversion_messages.NO_DATA @@ -118,13 +121,11 @@ return data_provider.get_data( query ) return [] - def _data( self, trans, dataset, chrom, low, high, start_val=0, max_vals=None, **kwargs ): """ Provides a block of data from a dataset. """ - # Parameter check. if not chrom: return dataset.conversion_messages.NO_DATA @@ -151,7 +152,8 @@ summary = indexer.get_data( chrom, low, high, detail_cutoff=0, draw_cutoff=0, **kwargs ) if summary == "detail": # Use maximum level of detail--2--to get summary data no matter the resolution. - summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 ) + summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], + level=2, detail_cutoff=0, draw_cutoff=0 ) return summary if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto": @@ -207,7 +209,8 @@ return data @web.expose_api_raw - def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): + def display( self, trans, history_content_id, history_id, + preview=False, filename=None, to_ext=None, chunk=None, **kwd ): """ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display Displays history content (dataset). Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Update check strings in functional tests to reflect recent changes to the UI.
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/07f09e119bfc/ Changeset: 07f09e119bfc User: inithello Date: 2013-04-30 19:41:26 Summary: Update check strings in functional tests to reflect recent changes to the UI. Affected #: 1 file diff -r 6b996d66ce37e20de68d6f02f32355c026a5324b -r 07f09e119bfcbe8e4cfda3400c8892f8fb3891d2 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 @@ -118,14 +118,17 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) self.set_repository_deprecated( repository, - strings_displayed=[ 'has been marked as deprecated', 'Mark as not deprecated' ] ) + strings_displayed=[ 'has been marked as deprecated' ] ) + strings_displayed = [ 'This repository has been marked as deprecated', 'Mark repository as not deprecated' ] self.display_manage_repository_page( repository, - strings_displayed=[ 'This repository has been marked as deprecated' ], + strings_displayed=strings_displayed, strings_not_displayed=[ 'Upload files', 'Reset all repository metadata' ] ) self.browse_repository( repository, strings_not_displayed=[ 'Upload files' ] ) self.set_repository_deprecated( repository, - strings_displayed=[ 'has been marked as not deprecated', 'Mark as deprecated' ], + strings_displayed=[ 'has been marked as not deprecated' ], set_deprecated=False ) + strings_displayed = [ 'Mark repository as deprecated', 'Upload files', 'Reset all repository metadata' ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) def test_0045_display_repository_tip_file( self ): '''Display the contents of filtering.xml in the repository tip revision''' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Browser tests: first draft at running a workflow from the API, remove screen-caps from tools, fix POST method in API interface
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b996d66ce37/ Changeset: 6b996d66ce37 User: carlfeberhard Date: 2013-04-30 17:05:18 Summary: Browser tests: first draft at running a workflow from the API, remove screen-caps from tools, fix POST method in API interface Affected #: 3 files diff -r a27856f42a616378bf5b152a06707d1d8c24e66d -r 6b996d66ce37e20de68d6f02f32355c026a5324b test/casperjs/api-workflow-tests.js --- a/test/casperjs/api-workflow-tests.js +++ b/test/casperjs/api-workflow-tests.js @@ -43,57 +43,245 @@ return true; } -function compareObjs( obj1, where ){ - for( var key in where ){ - if( where.hasOwnProperty( key ) ){ - if( !obj1.hasOwnProperty( key ) ){ return false; } - if( obj1[ key ] !== where[ key ] ){ return false; } - } +function countKeys( object ){ + if( !utils.isObject( object ) ){ return 0; } + var count = 0; + for( var key in object ){ + if( object.hasOwnProperty( key ) ){ count += 1; } } - return true; -} - -function findObject( objectArray, where, start ){ - start = start || 0; - for( var i=start; i<objectArray.length; i += 1 ){ - if( compareObjs( objectArray[i], where ) ){ return objectArray[i]; } - } - return null; + return count; } // =================================================================== TESTS -var workflowSummaryKeys = [ +var workflowJSONFilepath = 'test-data/Bed_interval_lengths.ga', + workflowModelClass = 'StoredWorkflow', + workflowSummaryKeys = [ 'id', 'model_class', 'name', 'published', 'tags', 'url' ], workflowDetailKeys = workflowSummaryKeys.concat([ 'inputs', 'steps' - ]); + ]), + stepKeys = [ + 'id', 'input_steps', 'tool_id', 'type' + ], + simpleBedFilepath = 'test-data/simple.bed', + uploadedFile = null, + workflowCreateKeys = [ 'history', 'outputs' ]; spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + // ------------------------------------------------------------------------------------------- UPLOAD + // upload first or we have no data to test + this.test.comment( 'upload should allow importing a new workflow given in JSON form' ); + var workflowToUpload = this.loadJSONFile( workflowJSONFilepath ); + //this.debug( this.jsonStr( workflowToUpload ) ); + var returned = this.api.workflows.upload( workflowToUpload ); + + this.test.comment( 'upload should return a summary object of what we uploaded' ); + //this.debug( this.jsonStr( returned ) ); + this.test.assert( utils.isObject( returned ), "upload returned an object" ); + this.test.assert( hasKeys( returned, workflowSummaryKeys ), "upload's return has the proper keys" ); + this.test.assert( this.api.isEncodedId( returned.id ), + "id is of the proper form: " + returned.id ); + this.test.assert( returned.model_class === workflowModelClass, + "has the proper model_class: " + returned.model_class ); + this.test.assert( returned.name === workflowToUpload.name + ' ' + '(imported from API)', + "has the proper, modified name: " + returned.name ); + this.test.assert( !returned.published, + "uploaded workflow defaults to un-published: " + returned.published ); + this.test.assert( utils.isArray( returned.tags ) && returned.tags.length === 0, + "upload returned an empty tag array: " + this.jsonStr( returned.tags ) ); + this.test.assert( returned.url === '/' + utils.format( this.api.workflows.urlTpls.show, returned.id ), + "url matches the show url: " + returned.url ); + + // ------------------------------------------------------------------------------------------- INDEX this.test.comment( 'index should get a list of workflows' ); var workflowIndex = this.api.workflows.index(); this.debug( this.jsonStr( workflowIndex ) ); this.test.assert( utils.isArray( workflowIndex ), "index returned an array: length " + workflowIndex.length ); + this.test.assert( workflowIndex.length >= 1, "index returned at least one job" ); - // need a way to import/create a workflow here for testing - if( workflowIndex.length <= 0 ){ - log.warn( 'No workflows available' ); - return; - } - this.test.assert( workflowIndex.length >= 1, 'Has at least one workflow' ); + this.test.comment( 'index should have returned an object matching the workflow uploaded' ); + var firstWorkflow = workflowIndex[0]; + this.test.assert( hasKeys( firstWorkflow, workflowSummaryKeys ), "index has the proper keys" ); + this.test.assert( this.api.isEncodedId( firstWorkflow.id ), + "id is of the proper form: " + firstWorkflow.id ); + this.test.assert( firstWorkflow.model_class === workflowModelClass, + "has the proper model_class: " + firstWorkflow.model_class ); + this.test.assert( firstWorkflow.name === workflowToUpload.name + ' ' + '(imported from API)', + "has the proper, modified name: " + firstWorkflow.name ); + this.test.assert( !firstWorkflow.published, + "workflow is un-published: " + firstWorkflow.published ); + this.test.assert( utils.isArray( firstWorkflow.tags ) && firstWorkflow.tags.length === 0, + "tag array is empty: " + this.jsonStr( firstWorkflow.tags ) ); + this.test.assert( firstWorkflow.url === '/' + utils.format( this.api.workflows.urlTpls.show, firstWorkflow.id ), + "url matches the show url: " + firstWorkflow.url ); + // ------------------------------------------------------------------------------------------- SHOW this.test.comment( 'show should get detailed data about the workflow with the given id' ); - var workflowShow = this.api.workflows.show( workflowIndex[0].id ); + var workflowShow = this.api.workflows.show( firstWorkflow.id ); this.debug( this.jsonStr( workflowShow ) ); + this.test.assert( utils.isObject( workflowShow ), "show returned an object" ); + this.test.assert( hasKeys( workflowShow, workflowDetailKeys ), "show has the proper keys" ); + this.test.assert( this.api.isEncodedId( workflowShow.id ), + "id is of the proper form: " + workflowShow.id ); + this.test.assert( workflowShow.model_class === workflowModelClass, + "has the proper model_class: " + workflowShow.model_class ); + this.test.assert( workflowShow.name === workflowToUpload.name + ' ' + '(imported from API)', + "has the proper, modified name: " + workflowShow.name ); + this.test.assert( !workflowShow.published, + "workflow is un-published: " + workflowShow.published ); + this.test.assert( utils.isArray( workflowShow.tags ) && workflowShow.tags.length === 0, + "tag array is empty: " + this.jsonStr( workflowShow.tags ) ); + this.test.assert( workflowShow.url === '/' + utils.format( this.api.workflows.urlTpls.show, workflowShow.id ), + "url matches the show url: " + workflowShow.url ); + this.test.comment( 'inputs from show should be an object (and, in this case, empty)' ); + var inputs = workflowShow.inputs; + //this.debug( 'inputs:\n' + this.jsonStr( inputs ) ); + this.test.assert( utils.isObject( workflowShow.inputs ), "inputs is an object" ); + //for( var inputKey in inputs ){ + // if( inputs.hasOwnProperty( inputKey ) ){ + // } + //} + this.test.assert( countKeys( workflowShow.inputs ) === 0, "inputs is empty" ); + + this.test.comment( 'steps from show should be an object containing each tool defined as a step' ); + var steps = workflowShow.steps; + //this.debug( 'steps:\n' + this.jsonStr( steps ) ); + this.test.assert( utils.isObject( workflowShow.steps ), "steps is an object" ); + //! ids for steps (and the keys used) are un-encoded (and in strings) + for( var stepKey in steps ){ + if( steps.hasOwnProperty( stepKey ) ){ + // any way to match this up with the workflowToUpload? + + this.test.assert( utils.isString( stepKey ), "step key is a string: " + stepKey ); + var step = steps[ stepKey ]; + this.debug( 'step:\n' + this.jsonStr( step ) ); + this.test.assert( hasKeys( step, stepKeys ), "step has the proper keys" ); + + this.test.assert( utils.isNumber( step.id ), + "step id is a number: " + step.id ); + try { + this.test.assert( parseInt( stepKey, 10 ) === step.id, + "step id matches step key: " + step.id ); + } catch( err ){ + this.test.fail( 'couldnt parse stepKey: ' + stepKey + ',' + err ); + } + + this.test.assert( utils.isObject( step.input_steps ), "input_steps is an object" ); + if( countKeys( step.input_steps ) !== 0 ){ + this.test.assert( hasKeys( step.input_steps, [ 'input' ] ), "input_steps has the proper keys" ); + } + + this.test.assert( step.type === 'tool', + "step type is a tool: " + step.type ); + + // check for tools in this wf with the api + this.test.assert( utils.isString( step.tool_id ), + "step tool_id is a string: " + step.tool_id ); + var tool_used = this.api.tools.show( step.tool_id ); + //this.debug( this.jsonStr( tool_used ) ) + this.test.assert( countKeys( step.input_steps ) !== 0, "found tool in api.tools for: " + step.tool_id ); + + // trace the path through input_steps, source_steps + } + } + + + + // ------------------------------------------------------------------------------------------- MISC +}); + +// now run the uploaded workflow +spaceghost.tools.uploadFile( simpleBedFilepath, function( uploadInfo ){ + uploadedFile = uploadInfo; +}); +spaceghost.then( function(){ + var currentHistory = this.api.histories.index()[0], + firstWorkflow = this.api.workflows.show( this.api.workflows.index()[0].id ); + + //this.debug( this.jsonStr( uploadedFile ) ); + var uploadedFileId = uploadedFile.hdaElement.attributes.id.split( '-' )[1]; + this.debug( this.jsonStr( uploadedFileId ) ); + this.debug( this.jsonStr( this.api.hdas.show( currentHistory.id, uploadedFileId ) ) ); + + //this.debug( this.jsonStr( firstWorkflow ) ); + // find the input step by looking for a step where input_steps == {} + var input_step = null; + for( var stepKey in firstWorkflow.steps ){ + if( firstWorkflow.steps.hasOwnProperty( stepKey ) ){ + var step = firstWorkflow.steps[ stepKey ]; + if( countKeys( step.input_steps ) === 0 ){ + input_step = stepKey; + this.debug( 'input step: ' + this.jsonStr( step ) ) + break; + } + } + } // ------------------------------------------------------------------------------------------- CREATE + this.test.comment( 'create should allow running an existing workflow' ); + // needs workflow_id, history, ds_map + var executionData = { + workflow_id : firstWorkflow.id, + history : 'hist_id=' + currentHistory.id, + ds_map : {} + }; + executionData.ds_map[ input_step ] = { + src: 'hda', + id: uploadedFileId + }; + var returned = this.api.workflows.create( executionData ); + this.debug( this.jsonStr( returned ) ); + this.test.assert( utils.isObject( returned ), "create returned an object" ); + this.test.assert( hasKeys( returned, workflowCreateKeys ), "create returned the proper keys" ); + this.test.assert( this.api.isEncodedId( returned.history ), + "history id is proper: " + returned.history ); + this.test.assert( utils.isArray( returned.outputs ), + "create.outputs is an array: length " + returned.outputs.length ); + this.test.assert( returned.outputs.length >= 1, "there is at least one output" ); + for( var i=0; i<returned.outputs.length; i+=1 ){ + this.test.assert( this.api.isEncodedId( returned.outputs[i] ), + "output id is proper: " + returned.outputs[i] ); + } - // ------------------------------------------------------------------------------------------- MISC + var counter = 0; + this.waitFor( + function checkHdas(){ + if( counter % 4 !== 0 ){ + counter += 1; + return false; + } + counter += 1; + + var outputs = this.api.hdas.index( currentHistory.id, returned.outputs ); + //this.debug( 'outputs:\n' + this.jsonStr( outputs ) ); + for( var i=0; i<outputs.length; i+=1 ){ + var output = outputs[i]; + this.debug( utils.format( 'name: %s, state: %s', output.name, output.state ) ); + if( output.state === 'queued' || output.state === 'running' ){ + return false; + } + } + return true; + }, + function allDone(){ + this.debug( 'DONE' ); + var outputs = this.api.hdas.index( currentHistory.id, returned.outputs ); + this.debug( 'outputs:\n' + this.jsonStr( outputs ) ); + }, + function timeout(){ + this.debug( 'timeout' ); + + }, + 45 * 1000 + ); +/* +*/ }); // =================================================================== diff -r a27856f42a616378bf5b152a06707d1d8c24e66d -r 6b996d66ce37e20de68d6f02f32355c026a5324b test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -58,7 +58,8 @@ // PUT data needs to be stringified in jq.ajax and the content changed //TODO: server side handling could change this? - if( ( options.type && options.type === 'PUT' ) && ( options.data ) ){ + if( ( options.type && [ 'PUT', 'POST' ].indexOf( options.type ) !== -1 ) + && ( options.data ) ){ options.contentType = 'application/json'; options.data = JSON.stringify( options.data ); } @@ -384,39 +385,23 @@ }); }; -//WorkflowsAPI.prototype.create = function create( payload ){ -// this.api.spaceghost.info( 'workflows.create: ' + [ this.api.spaceghost.jsonStr( payload ) ] ); -// -// // py.payload <-> ajax.data -// payload = this.api.ensureObject( payload ); -// return this.api._ajax( utils.format( this.urlTpls.create ), { -// type : 'POST', -// data : payload -// }); -//}; -// -//WorkflowsAPI.prototype.update = function create( id, payload ){ -// this.api.spaceghost.info( 'workflows.update: ' + [ id, this.api.spaceghost.jsonStr( payload ) ] ); -// -// // py.payload <-> ajax.data -// historyId = this.api.ensureId( historyId ); -// id = this.api.ensureId( id ); -// payload = this.api.ensureObject( payload ); -// url = utils.format( this.urlTpls.update, id ); -// -// return this.api._ajax( url, { -// type : 'PUT', -// data : payload -// }); -//}; +WorkflowsAPI.prototype.create = function create( payload ){ + this.api.spaceghost.info( 'workflows.create: ' + [ this.api.spaceghost.jsonStr( payload ) ] ); -WorkflowsAPI.prototype.upload = function upload( filepath ){ - this.api.spaceghost.info( 'workflows.show: ' + [ id ] ); - var data = {}; + // py.payload <-> ajax.data + payload = this.api.ensureObject( payload ); + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : payload + }); +}; - id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); - return this.api._ajax( utils.format( this.urlTpls.show, this.api.ensureId( id ) ), { - data : data +WorkflowsAPI.prototype.upload = function create( workflowJSON ){ + this.api.spaceghost.info( 'workflows.upload: ' + [ this.api.spaceghost.jsonStr( workflowJSON ) ] ); + + return this.api._ajax( utils.format( this.urlTpls.upload ), { + type : 'POST', + data : { 'workflow': this.api.ensureObject( workflowJSON ) } }); }; diff -r a27856f42a616378bf5b152a06707d1d8c24e66d -r 6b996d66ce37e20de68d6f02f32355c026a5324b test/casperjs/modules/tools.js --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -118,7 +118,6 @@ }); }, function timeoutWaitingForUploadRefreshes( urlsStillWaitingOn ){ - this.capture( 'upload-error.png' ) throw new this.GalaxyError( 'Upload Error: ' + 'timeout waiting for upload "' + filepath + '" refreshes: ' + urlsStillWaitingOn ); }, @@ -178,7 +177,6 @@ // capture any other messages on the page var otherInfo = spaceghost.elementInfoOrNull( this.data.selectors.messages.all ), message = ( otherInfo && otherInfo.text )?( otherInfo.text ):( '' ); - this.capture( 'upload-error.png' ) throw new this.GalaxyError( 'Upload Error: no success message uploading "' + filepath + '": ' + message ); } }); @@ -191,7 +189,6 @@ if( hdaElement === null ){ var hdaContainer = this.historypanel.data.selectors.hdaContainer; this.warning( 'Upload Error: ' + hdaContainer + ':\n' + this.getHTML( hdaContainer ) ); - this.capture( 'upload-error.png' ) throw new this.GalaxyError( 'Upload Error: uploaded file HDA not found: ' + uploadInfo.filename ); } this.debug( 'uploaded HDA element: ' + this.jsonStr( this.quickInfo( hdaElement ) ) ); @@ -206,7 +203,6 @@ }, function timeoutFn( newHdaInfo ){ this.warning( 'timeout waiting for upload:\n' + this.jsonStr( this.quickInfo( newHdaInfo ) ) ); - this.capture( 'upload-error.png' ) throw new spaceghost.GalaxyError( 'Upload Error: timeout waiting for ok state: ' + '"' + uploadInfo.filepath + '" (waited ' + timeoutAfterMs + ' ms)' ); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: refactoring to use dataset attributes rather than .dataset_id and .hda_ldda
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a27856f42a61/ Changeset: a27856f42a61 User: jgoecks Date: 2013-04-30 15:12:18 Summary: Trackster: refactoring to use dataset attributes rather than .dataset_id and .hda_ldda Affected #: 1 file diff -r f8d07c98812903dc98de2665874a2c31b65b84da -r a27856f42a616378bf5b152a06707d1d8c24e66d static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1534,7 +1534,7 @@ if (this.overview_drawable) { // If drawable to be set as overview is already in overview, do nothing. // Otherwise, remove overview. - if (this.overview_drawable.dataset_id === drawable.dataset_id) { + if (this.overview_drawable.dataset.id === drawable.dataset.id) { return; } this.overview_viewport.find(".track").remove(); @@ -1712,7 +1712,7 @@ tool.run( // URL params. { - target_dataset_id: this.track.dataset_id, + target_dataset_id: this.track.dataset.id, action: 'rerun', tool_id: tool.id }, @@ -1741,7 +1741,7 @@ }), url_params = { - target_dataset_id: this.track.dataset_id, + target_dataset_id: this.track.dataset.id, action: 'rerun', tool_id: this.id, regions: [ @@ -2249,8 +2249,6 @@ // Attribute init. // this.dataset = new data.Dataset(obj_dict.dataset); - this.dataset_id = this.dataset.get('id'); - this.hda_ldda = this.dataset.get('hda_ldda'); this.dataset_check_type = 'converted_datasets_state'; this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); @@ -2395,8 +2393,8 @@ window.location.href = galaxy_paths.get('sweepster_url') + "?" + $.param({ - dataset_id: track.dataset_id, - hda_ldda: track.hda_ldda, + dataset_id: track.dataset.id, + hda_ldda: track.dataset.get('hda_ldda'), regions: JSON.stringify(new Backbone.Collection(regions).toJSON()) }); }, @@ -2420,7 +2418,7 @@ ], can_draw: function() { - if ( this.dataset_id && Drawable.prototype.can_draw.call(this) ) { + if ( this.dataset.id && Drawable.prototype.can_draw.call(this) ) { return true; } return false; @@ -2444,8 +2442,6 @@ set_dataset: function(dataset) { this.dataset = dataset; this.data_manager.set('dataset', dataset); - this.dataset_id = dataset.get('id'); - this.hda_ldda = dataset.get('hda_ldda'); }, /** @@ -2601,7 +2597,7 @@ // Tracks with no dataset id are handled differently. // FIXME: is this really necessary? // - if (!track.dataset_id) { + if (!track.dataset.id) { return; } @@ -2609,7 +2605,7 @@ // about track status. var init_deferred = $.Deferred(), params = { - hda_ldda: track.hda_ldda, + hda_ldda: track.dataset.get('hda_ldda'), data_type: this.dataset_check_type, chrom: track.view.chrom, retry: retry @@ -2771,8 +2767,8 @@ return { "track_type": this.get_type(), "name": this.name, - "hda_ldda": this.hda_ldda, - "dataset_id": this.dataset_id, + "hda_ldda": this.dataset.get('hda_ldda'), + "dataset_id": this.dataset.id, "prefs": this.prefs, "mode": this.mode, "filters": this.filters_manager.to_dict(), @@ -3200,7 +3196,7 @@ // Reset data URL when dataset indexing has completed/when not pending. var ss_deferred = new util.ServerStateDeferred({ url: self.dataset_state_url, - url_params: {dataset_id : self.dataset_id, hda_ldda: self.hda_ldda}, + url_params: {dataset_id : self.dataset.id, hda_ldda: self.dataset.get('hda_ldda')}, interval: self.data_query_wait, // Set up deferred to check dataset state until it is not pending. success_fn: function(result) { return result !== "pending"; } @@ -3651,7 +3647,7 @@ */ set_min_value: function(new_val) { this.prefs.min_value = new_val; - $('#linetrack_' + this.dataset_id + '_minval').text(this.prefs.min_value); + $('#linetrack_' + this.dataset.id + '_minval').text(this.prefs.min_value); this.tile_cache.clear(); this.request_draw(); }, @@ -3661,7 +3657,7 @@ */ set_max_value: function(new_val) { this.prefs.max_value = new_val; - $('#linetrack_' + this.dataset_id + '_maxval').text(this.prefs.max_value); + $('#linetrack_' + this.dataset.id + '_maxval').text(this.prefs.max_value); this.tile_cache.clear(); this.request_draw(); }, @@ -3671,7 +3667,7 @@ track.vertical_range = undefined; return $.getJSON( track.dataset.url(), { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, - high: track.view.max_high, hda_ldda: track.hda_ldda }, function(result) { + high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) { track.container_div.addClass( "line-track" ); var data = result.data; if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { @@ -3689,8 +3685,8 @@ // FIXME: we should probably only save this when the user explicately sets it // since we lose the ability to compute it on the fly (when changing // chromosomes for example). - $('#track_' + track.dataset_id + '_minval').val(track.prefs.min_value); - $('#track_' + track.dataset_id + '_maxval').val(track.prefs.max_value); + $('#track_' + track.dataset.id + '_minval').val(track.prefs.min_value); + $('#track_' + track.dataset.id + '_maxval').val(track.prefs.max_value); } track.vertical_range = track.prefs.max_value - track.prefs.min_value; track.total_frequency = data.total_frequency; @@ -3710,7 +3706,7 @@ } }, help_text: "Set min value" - }).addClass('yaxislabel bottom').attr("id", 'linetrack_' + track.dataset_id + '_minval') + }).addClass('yaxislabel bottom').attr("id", 'linetrack_' + track.dataset.id + '_minval') .prependTo(track.container_div), max_label = $("<div/>").text(round(track.prefs.max_value, 3)).make_text_editable({ num_cols: 6, @@ -3722,7 +3718,7 @@ } }, help_text: "Set max value" - }).addClass('yaxislabel top').attr("id", 'linetrack_' + track.dataset_id + '_maxval') + }).addClass('yaxislabel top').attr("id", 'linetrack_' + track.dataset.id + '_maxval') .prependTo(track.container_div); }); }, 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 more granular lists of writable repositories for the current user: repositories with missing tool test components, repositories with failing tool tests and repositories with no failing tool tests.
by commits-noreply＠bitbucket.org 29 Apr '13

29 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8d07c988129/ Changeset: f8d07c988129 User: greg Date: 2013-04-29 23:09:44 Summary: Add more granular lists of writable repositories for the current user: repositories with missing tool test components, repositories with failing tool tests and repositories with no failing tool tests. Affected #: 8 files diff -r 8264c77e4f07c0dee932add796f5ee7ce02245b3 -r f8d07c98812903dc98de2665874a2c31b65b84da lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -77,19 +77,19 @@ # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) webapp.mapper.resource( 'repository', - 'repositories', - controller='repositories', - collection={ 'get_repository_revision_install_info' : 'GET', - 'get_ordered_installable_revisions' : 'GET' }, - name_prefix='repository_', - path_prefix='/api', - parent_resources=dict( member_name='repository', collection_name='repositories' ) ) + 'repositories', + controller='repositories', + collection={ 'get_repository_revision_install_info' : 'GET', + 'get_ordered_installable_revisions' : 'GET' }, + name_prefix='repository_', + path_prefix='/api', + parent_resources=dict( member_name='repository', collection_name='repositories' ) ) webapp.mapper.resource( 'repository_revision', - 'repository_revisions', - controller='repository_revisions', - name_prefix='repository_revision_', - path_prefix='/api', - parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) ) + 'repository_revisions', + controller='repository_revisions', + name_prefix='repository_revision_', + path_prefix='/api', + parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix failing functional test for dataset features.
by commits-noreply＠bitbucket.org 28 Apr '13

28 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8264c77e4f07/ Changeset: 8264c77e4f07 User: inithello Date: 2013-04-28 17:03:41 Summary: Fix failing functional test for dataset features. Affected #: 2 files diff -r 6638dbca87d3c7dfc4e5b0522eb4a17f124b5040 -r 8264c77e4f07c0dee932add796f5ee7ce02245b3 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -255,6 +255,13 @@ def get_latest_history( self ): return self.json_from_url( '/api/histories' )[ 0 ] + + def find_hda_by_dataset_name( self, name, history=None ): + if history is None: + history = self.get_history_from_api() + for hda in history: + if hda[ 'name' ] == name: + return hda def check_history_for_errors( self ): """Raises an exception if there are errors in a history""" diff -r 6638dbca87d3c7dfc4e5b0522eb4a17f124b5040 -r 8264c77e4f07c0dee932add796f5ee7ce02245b3 test/functional/test_dataset_features.py --- a/test/functional/test_dataset_features.py +++ b/test/functional/test_dataset_features.py @@ -1,7 +1,9 @@ from base.twilltestcase import TwillTestCase import base.test_db_util as test_db_util + class TestDatasetFeatures( TwillTestCase ): + def test_0000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() @@ -16,14 +18,18 @@ self.new_history() latest_history = test_db_util.get_latest_history_for_user( admin_user ) assert latest_history is not None, "Problem retrieving latest_history from database" + def test_0005_initiate_data( self ): '''Ensure that data exists for this test suite.''' self.upload_file( '1.bed' ) + def test_0010_view_dataset_params( self ): '''Test viewing a dataset's parameters.''' - hda = test_db_util.get_latest_hda() - self.visit_url( '/datasets/%s/show_params' % self.security.encode_id( hda.hid ) ) + hda = self.find_hda_by_dataset_name( '1.bed' ) + assert hda is not None, 'Could not retrieve latest hda from history API.' + self.visit_url( '/datasets/%s/show_params' % hda[ 'id'] ) self.check_for_strings( strings_displayed=[ '1.bed', 'uploaded' ] ) + def test_0015_report_dataset_error( self ): '''Load and submit the report error form. This should show an error message, as the functional test instance should not be configured for email.''' hda = test_db_util.get_latest_hda() 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: Configuration API: include and standardize error handling, complete documentation
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6638dbca87d3/ Changeset: 6638dbca87d3 User: carlfeberhard Date: 2013-04-26 21:36:33 Summary: Configuration API: include and standardize error handling, complete documentation Affected #: 1 file diff -r a0877019caa1e1f6b4407d92eaa7c44f654d27df -r 6638dbca87d3c7dfc4e5b0522eb4a17f124b5040 lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -1,5 +1,6 @@ """ -API operations allowing clients to determine Galaxy instance's capabilities. +API operations allowing clients to determine Galaxy instance's capabilities +and configuration settings. """ from galaxy import web @@ -9,6 +10,7 @@ log = logging.getLogger( __name__ ) class ConfigurationController( BaseAPIController ): + # config attributes viewable by non-admin users EXPOSED_USER_OPTIONS = [ 'enable_unique_workflow_defaults', 'ftp_upload_site', @@ -19,6 +21,7 @@ 'terms_url', 'allow_user_dataset_purge', ] + # config attributes viewable by admin users EXPOSED_ADMIN_OPTIONS = [ 'library_import_dir', 'user_library_import_dir', @@ -30,12 +33,28 @@ @web.expose_api def index( self, trans, **kwd ): """ + GET /api/configuration + Return an object containing exposable configuration settings. + + Note: a more complete list is returned if the user is an admin. """ - config = trans.app.config - options = self._get_options( config, self.EXPOSED_USER_OPTIONS ) - if trans.user_is_admin(): - options.update( self._get_options( config, self.EXPOSED_ADMIN_OPTIONS ) ) - return options + try: + config = trans.app.config + options = self._get_options( config, self.EXPOSED_USER_OPTIONS ) + if trans.user_is_admin(): + options.update( self._get_options( config, self.EXPOSED_ADMIN_OPTIONS ) ) + return options + + except Exception, exception: + log.error( 'could not get configuration: %s', str( exception ), exc_info=True ) + trans.response.status = 500 + return { 'error': str( exception ) } def _get_options( self, config, keys ): + """ + Build and return a subset of the config dictionary restricted to the + list `keys`. + + The attribute value will default to None if not available. + """ return dict( [ (key, getattr( config, key, None ) ) for key in keys ] ) 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: update test_history_functions 060 to use the new json variable name in history.mako
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0877019caa1/ Changeset: a0877019caa1 User: carlfeberhard Date: 2013-04-26 21:26:33 Summary: Functional tests: update test_history_functions 060 to use the new json variable name in history.mako Affected #: 1 file diff -r 365d31607a569575ac666d142556403fe82d693a -r a0877019caa1e1f6b4407d92eaa7c44f654d27df test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -656,7 +656,7 @@ if hda[ 'id' ] == self.security.encode_id( hda_2_bed.id ): return ( not hda[ 'accessible' ] ) return False - self.check_history_json( r'\bhdas\s*=\s*(.*);', hda_2_bed_is_inaccessible ) + self.check_history_json( r'\bhdaJson\s*=\s*(.*);', hda_2_bed_is_inaccessible ) # Admin users can view all datasets ( using the history/view feature ), so make sure 2.bed is accessible to the admin self.logout() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Browser tests: allow for use of test admin user, test configuration API, begin tests of user API
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/365d31607a56/ Changeset: 365d31607a56 User: carlfeberhard Date: 2013-04-26 21:17:08 Summary: Browser tests: allow for use of test admin user, test configuration API, begin tests of user API Affected #: 7 files diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -48,9 +48,17 @@ global datatypes_registry datatypes_registry = d_registry + class User( object, APIItem ): + """ + Data for a Galaxy user or admin and relations to their + histories, credentials, and roles. + """ + # attributes that will be accessed and returned when calling get_api_value( view='collection' ) api_collection_visible_keys = ( 'id', 'email' ) + # attributes that will be accessed and returned when calling get_api_value( view='element' ) api_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' ) + def __init__( self, email=None, password=None ): self.email = email self.password = password @@ -61,45 +69,78 @@ # Relationships self.histories = [] self.credentials = [] + #? self.roles = [] def set_password_cleartext( self, cleartext ): - """Set 'self.password' to the digest of 'cleartext'.""" + """ + Set user password to the digest of `cleartext`. + """ self.password = new_secure_hash( text_type=cleartext ) + def check_password( self, cleartext ): - """Check if 'cleartext' matches 'self.password' when hashed.""" + """ + Check if `cleartext` matches user password when hashed. + """ return self.password == new_secure_hash( text_type=cleartext ) + def all_roles( self ): + """ + Return a unique list of Roles associated with this user or any of their groups. + """ roles = [ ura.role for ura in self.roles ] for group in [ uga.group for uga in self.groups ]: for role in [ gra.role for gra in group.roles ]: if role not in roles: roles.append( role ) return roles + def get_disk_usage( self, nice_size=False ): + """ + Return byte count of disk space used by user or a human-readable + string if `nice_size` is `True`. + """ rval = 0 if self.disk_usage is not None: rval = self.disk_usage if nice_size: rval = galaxy.datatypes.data.nice_size( rval ) return rval + def set_disk_usage( self, bytes ): + """ + Manually set the disk space used by a user to `bytes`. + """ self.disk_usage = bytes + total_disk_usage = property( get_disk_usage, set_disk_usage ) + @property def nice_total_disk_usage( self ): + """ + Return byte count of disk space used in a human-readable string. + """ return self.get_disk_usage( nice_size=True ) + def calculate_disk_usage( self ): + """ + Return byte count total of disk space used by all non-purged, non-library + HDAs in non-purged histories. + """ + # maintain a list so that we don't double count dataset_ids = [] total = 0 # this can be a huge number and can run out of memory, so we avoid the mappers db_session = object_session( self ) for history in db_session.query( History ).enable_eagerloads( False ).filter_by( user_id=self.id, purged=False ).yield_per( 1000 ): for hda in db_session.query( HistoryDatasetAssociation ).enable_eagerloads( False ).filter_by( history_id=history.id, purged=False ).yield_per( 1000 ): + #TODO: def hda.counts_toward_disk_usage(): + # return ( not self.dataset.purged and not self.dataset.library_associations ) if not hda.dataset.id in dataset_ids and not hda.dataset.purged and not hda.dataset.library_associations: dataset_ids.append( hda.dataset.id ) total += hda.dataset.get_total_size() return total + class Job( object ): """ A job represents a request to run a tool given input datasets, tool diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -2,30 +2,29 @@ API operations allowing clients to determine Galaxy instance's capabilities. """ -import logging from galaxy import web from galaxy.web.base.controller import BaseAPIController +import logging log = logging.getLogger( __name__ ) - class ConfigurationController( BaseAPIController ): EXPOSED_USER_OPTIONS = [ - 'enable_unique_workflow_defaults', - 'ftp_upload_site', - 'ftp_upload_dir', - 'wiki_url', - 'support_url', - 'logo_url', - 'terms_url', - 'allow_user_dataset_purge', + 'enable_unique_workflow_defaults', + 'ftp_upload_site', + 'ftp_upload_dir', + 'wiki_url', + 'support_url', + 'logo_url', + 'terms_url', + 'allow_user_dataset_purge', ] EXPOSED_ADMIN_OPTIONS = [ - 'library_import_dir', - 'user_library_import_dir', - 'allow_library_path_paste', - 'allow_user_creation', - 'allow_user_deletion', + 'library_import_dir', + 'user_library_import_dir', + 'allow_library_path_paste', + 'allow_user_creation', + 'allow_user_deletion', ] @web.expose_api diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/api-configuration-tests.js --- /dev/null +++ b/test/casperjs/api-configuration-tests.js @@ -0,0 +1,121 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +spaceghost.user.loginOrRegisterUser( email, password ); + +function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + spaceghost.debug( 'key not found: ' + keysArray[i] ); + return false; + } + } + return true; +} + +function compareObjs( obj1, where ){ + for( var key in where ){ + if( where.hasOwnProperty( key ) ){ + if( !obj1.hasOwnProperty( key ) ){ return false; } + if( obj1[ key ] !== where[ key ] ){ return false; } + } + } + return true; +} + +function findObject( objectArray, where, start ){ + start = start || 0; + for( var i=start; i<objectArray.length; i += 1 ){ + if( compareObjs( objectArray[i], where ) ){ return objectArray[i]; } + } + return null; +} + +// =================================================================== TESTS +var normKeys = [ + 'enable_unique_workflow_defaults', + 'ftp_upload_site', + 'ftp_upload_dir', + 'wiki_url', + 'support_url', + 'logo_url', + 'terms_url', + 'allow_user_dataset_purge' + ], + adminKeys = normKeys.concat([ + 'library_import_dir', + 'user_library_import_dir', + 'allow_library_path_paste', + 'allow_user_creation', + 'allow_user_deletion' + ]); + + +// ------------------------------------------------------------------------------------------- INDEX +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + this.test.comment( 'index should get a (shortened) list of configuration settings ' + + 'when requested by a normal user' ); + var configIndex = this.api.configuration.index(); + this.debug( this.jsonStr( configIndex ) ); + this.test.assert( utils.isObject( configIndex ), "index returned an object" ); + this.test.assert( hasKeys( configIndex, normKeys ), 'Has the proper keys' ); + +}); +spaceghost.user.logout(); + +// ------------------------------------------------------------------------------------------- INDEX (admin) +spaceghost.tryStepsCatch( function tryAdminLogin(){ + spaceghost.user.loginAdmin(); +}); + +//}, function failedLoginRegister(){ +// this.info( 'Admin level configuration API tests not run: no admin account available' ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + if( spaceghost.user.userIsAdmin() ){ + this.test.comment( 'index should get a (full) list of configuration settings ' + + 'when requested by an admin user' ); + configIndex = this.api.configuration.index(); + this.debug( this.jsonStr( configIndex ) ); + this.test.assert( utils.isObject( configIndex ), "index returned an object" ); + this.test.assert( hasKeys( configIndex, adminKeys ), 'Has the proper keys' ); + + } else { + this.info( 'Admin level configuration API tests not run: no admin account available' ); + } +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/api-user-tests.js --- /dev/null +++ b/test/casperjs/api-user-tests.js @@ -0,0 +1,105 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +spaceghost.user.loginOrRegisterUser( email, password ); + +function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + spaceghost.debug( 'key not found: ' + keysArray[i] ); + return false; + } + } + return true; +} + +function compareObjs( obj1, where ){ + for( var key in where ){ + if( where.hasOwnProperty( key ) ){ + if( !obj1.hasOwnProperty( key ) ){ return false; } + if( obj1[ key ] !== where[ key ] ){ return false; } + } + } + return true; +} + +function findObject( objectArray, where, start ){ + start = start || 0; + for( var i=start; i<objectArray.length; i += 1 ){ + if( compareObjs( objectArray[i], where ) ){ return objectArray[i]; } + } + return null; +} + +// =================================================================== TESTS +var workflowSummaryKeys = [ + 'id', 'model_class', 'name', 'published', 'tags', 'url' + ], + workflowDetailKeys = workflowSummaryKeys.concat([ + 'inputs', 'steps' + ]); + + +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + // ------------------------------------------------------------------------------------------- INDEX + this.test.comment( 'index should get a list of users' ); + var userIndex = this.api.users.index(); + this.debug( this.jsonStr( userIndex ) ); + this.test.assert( utils.isArray( userIndex ), "index returned an array: length " + userIndex.length ); + + // need a way to import/create a user here for testing + if( userIndex.length <= 0 ){ + log.warn( 'No users available' ); + return; + } + this.test.assert( userIndex.length >= 1, 'Has at least one user' ); + + //TODO: index( deleted ) + + // ------------------------------------------------------------------------------------------- SHOW + this.test.comment( 'show should get detailed data about the user with the given id' ); + var userShow = this.api.users.show( userIndex[0].id ); + this.debug( this.jsonStr( userShow ) ); + + //TODO: show( current ) + //TODO: show( deleted ) + + // ------------------------------------------------------------------------------------------- CREATE + + // ------------------------------------------------------------------------------------------- MISC +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -18,10 +18,12 @@ this.encodedIdExpectedLength = 16; this.jQueryLocation = '../../static/scripts/libs/jquery/jquery.js'; + this.configuration = new ConfigurationAPI( this ); this.histories = new HistoriesAPI( this ); this.hdas = new HDAAPI( this ); this.tools = new ToolsAPI( this ); this.workflows = new WorkflowsAPI( this ); + this.users = new UsersAPI( this ); }; exports.API = API; @@ -121,6 +123,28 @@ }; +// =================================================================== CONFIGURATION +var ConfigurationAPI = function ConfigurationAPI( api ){ + this.api = api; +}; +ConfigurationAPI.prototype.toString = function toString(){ + return this.api + '.ConfigurationAPI'; +}; + +// ------------------------------------------------------------------- +ConfigurationAPI.prototype.urlTpls = { + index : 'api/configuration' +}; + +ConfigurationAPI.prototype.index = function index( deleted ){ + this.api.spaceghost.info( 'configuration.index' ); + + return this.api._ajax( this.urlTpls.index, { + data : {} + }); +}; + + // =================================================================== HISTORIES var HistoriesAPI = function HistoriesAPI( api ){ this.api = api; @@ -140,7 +164,7 @@ }; HistoriesAPI.prototype.index = function index( deleted ){ - this.api.spaceghost.info( 'history.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); + this.api.spaceghost.info( 'histories.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); deleted = deleted || false; return this.api._ajax( this.urlTpls.index, { @@ -149,7 +173,7 @@ }; HistoriesAPI.prototype.show = function show( id, deleted ){ - this.api.spaceghost.info( 'history.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + this.api.spaceghost.info( 'histories.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; @@ -159,7 +183,7 @@ }; HistoriesAPI.prototype.create = function create( payload ){ - this.api.spaceghost.info( 'history.create: ' + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'histories.create: ' + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data payload = this.api.ensureObject( payload ); @@ -170,7 +194,7 @@ }; HistoriesAPI.prototype.delete_ = function delete_( id, purge ){ - this.api.spaceghost.info( 'history.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); + this.api.spaceghost.info( 'histories.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); // py.payload <-> ajax.data var payload = ( purge )?({ purge: true }):({}); @@ -182,7 +206,7 @@ HistoriesAPI.prototype.undelete = function undelete( id ){ //throw ( 'unimplemented' ); - this.api.spaceghost.info( 'history.undelete: ' + id ); + this.api.spaceghost.info( 'histories.undelete: ' + id ); return this.api._ajax( utils.format( this.urlTpls.undelete, this.api.ensureId( id ) ), { type : 'POST' @@ -190,7 +214,7 @@ }; HistoriesAPI.prototype.update = function create( id, payload ){ - this.api.spaceghost.info( 'history.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'histories.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data id = this.api.ensureId( id ); @@ -269,6 +293,7 @@ }); }; + // =================================================================== TOOLS var ToolsAPI = function HDAAPI( api ){ this.api = api; @@ -319,6 +344,7 @@ // }); //}; + // =================================================================== WORKFLOWS var WorkflowsAPI = function WorkflowsAPI( api ){ this.api = api; @@ -394,3 +420,88 @@ }); }; + +// =================================================================== USERS +var UsersAPI = function UsersAPI( api ){ + this.api = api; +}; +UsersAPI.prototype.toString = function toString(){ + return this.api + '.UsersAPI'; +}; + +// ------------------------------------------------------------------- +//NOTE: lots of admin only functionality in this section +UsersAPI.prototype.urlTpls = { + index : 'api/users', + show : 'api/users/%s', + create : 'api/users', + delete_ : 'api/users/%s', + undelete: 'api/users/deleted/%s/undelete', + update : 'api/users/%s' +}; + +UsersAPI.prototype.index = function index( deleted ){ + this.api.spaceghost.info( 'users.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); + + deleted = deleted || false; + return this.api._ajax( this.urlTpls.index, { + data : { deleted: deleted } + }); +}; + +UsersAPI.prototype.show = function show( id, deleted ){ + this.api.spaceghost.info( 'users.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + + id = ( id === 'current' )?( id ):( this.api.ensureId( id ) ); + deleted = deleted || false; + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : { deleted: deleted } + }); +}; + +UsersAPI.prototype.create = function create( payload ){ + this.api.spaceghost.info( 'users.create: ' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + payload = this.api.ensureObject( payload ); + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : payload + }); +}; + +UsersAPI.prototype.delete_ = function delete_( id, purge ){ + this.api.spaceghost.info( 'users.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); + + // py.payload <-> ajax.data + var payload = ( purge )?({ purge: true }):({}); + return this.api._ajax( utils.format( this.urlTpls.delete_, this.api.ensureId( id ) ), { + type : 'DELETE', + data : payload + }); +}; + +UsersAPI.prototype.undelete = function undelete( id ){ + //throw ( 'unimplemented' ); + this.api.spaceghost.info( 'users.undelete: ' + id ); + + return this.api._ajax( utils.format( this.urlTpls.undelete, this.api.ensureId( id ) ), { + type : 'POST' + }); +}; + +UsersAPI.prototype.update = function create( id, payload ){ + this.api.spaceghost.info( 'users.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + id = this.api.ensureId( id ); + payload = this.api.ensureObject( payload ); + url = utils.format( this.urlTpls.update, id ); + + return this.api._ajax( url, { + type : 'PUT', + data : payload + }); +}; + + diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -134,7 +134,7 @@ this._submitLogin( email, password ); spaceghost.withMainPanel( function mainAfterLogin(){ - if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ + if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ this.warning( 'Login failed: ' + messageInfo.text ); @@ -171,6 +171,7 @@ User.prototype.logout = function logout(){ var spaceghost = this.spaceghost; spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.info( 'user logging out' ); //TODO: handle already logged out spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); @@ -196,6 +197,63 @@ return spaceghost; }; +// ------------------------------------------------------------------- Admin +/** Gets the admin user data from spaceghost if set and checks the universe_wsgi.ini file for the email. + * @returns {Object|null} the admin data object (email, pasword, username) + * or null if no admin is set in both the universe_wsgi.ini and spaceghost. + */ +User.prototype.getAdminData = function getAdminData(){ + //TODO: this might be better inside sg + // check for the setting in sg and the universe_wsgi.ini file + var adminData = this.spaceghost.options.adminUser, + iniAdminEmails = this.spaceghost.getUniverseSetting( 'admin_users' ); + iniAdminEmails = ( iniAdminEmails )?( iniAdminEmails.split( ',' ) ):( null ); + + //TODO: seems like we only need the wsgi setting - that's the only thing we can't change + if( adminData ){ + if( iniAdminEmails.indexOf( adminData.email ) !== -1 ){ return adminData; } + + // if not set in options, but there are entries in the ini and a default admin pass: + // return the first email with the default pass + // Hopefully this is no less secure than the user/pwd in twilltestcase + } else if( iniAdminEmails.length && this.spaceghost.options.adminPassword ){ + return { email: iniAdminEmails[0], password: this.spaceghost.options.adminPassword }; + } + + return null; +}; + +/** Logs in the admin user (if available) as the current user. + * Note: logs out any other current users. + * @throws {GalaxyError} err if specified user is not admin or no admin found + * @returns {SpaceGhost} the spaceghost instance (for chaining) + */ +User.prototype.loginAdmin = function loginAdmin(){ + this.spaceghost.then( function(){ + var adminData = this.user.getAdminData(); + if( !adminData ){ + throw new this.GalaxyError( 'No admin users found' ); + } + this.info( 'logging in administrator' ); + return this.user.loginOrRegisterUser( adminData.email, adminData.password ); + }); +}; + +/** Is the currently logged in user an admin? + * @returns {Boolean} true if the currently logged in user is admin, false if not. + */ +User.prototype.userIsAdmin = function userIsAdmin(){ + // simple test of whether the Admin tab is displayed in the masthead + return this.spaceghost.jumpToTop( function(){ + if( this.visible( this.data.selectors.masthead.adminLink ) ){ + return true; + } + return false; + }); +}; + + +// ------------------------------------------------------------------- Utility /** Gets a psuedo-random (unique?) email based on the time stamp. * Helpful for testing registration. * @param {String} username email user (defaults to 'test') @@ -207,3 +265,4 @@ domain = domain || 'test.test'; return username + Date.now() + '@' + domain; }; + diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -47,7 +47,17 @@ } utils.inherits( SpaceGhost, Casper ); -//console.debug( 'CasperError:' + CasperError ); +/** String representation + * @returns {String} + */ +SpaceGhost.prototype.toString = function(){ + var currentUrl = ''; + try { + currentUrl = this.getCurrentUrl(); + } catch( err ){} + return 'SpaceGhost(' + currentUrl + ')'; +}; + // ------------------------------------------------------------------- included libs //??: can we require underscore, etc. from the ../../static/scripts/lib? @@ -157,9 +167,14 @@ //htmlOnError : { defaultsTo: false, flag: 'error-html', help: 'output page html on a page error' } //htmlOnFail : { defaultsTo: false, flag: 'fail-html', help: 'output page html on a test failure' }, //screenOnFail : { defaultsTo: false, flag: 'fail-screen', help: 'capture a screenshot on a test failure' } - logNamespace : { defaultsTo: false, flag: 'log-namespace', help: 'filter log messages to this namespace' } + logNamespace : { defaultsTo: false, flag: 'log-namespace', help: 'filter log messages to this namespace' }, + + adminUser : { defaultsTo: null, flag: 'admin', help: 'JSON string with email and password of admin' } }; + // no switches/hardcoded options: + this.options.adminPassword = 'testuser'; + // --url parameter required (the url of the server to test with) if( !this.cli.has( 'url' ) ){ this.die( 'Test server URL is required - ' + @@ -237,6 +252,13 @@ this._setLogNamespaceFilter( this.options.logNamespace ); } + /** email and password JSON string for admin user */ + this.options.adminUser = CLI_OPTIONS.adminUser.defaultsTo; + if( this.cli.has( CLI_OPTIONS.adminUser.flag ) ){ + this.options.adminUser = JSON.parse( this.cli.get( CLI_OPTIONS.adminUser.flag ) ); + this.warning( 'Using admin user from CLI: ' + this.jsonStr( this.options.adminUser ) ); + } + }; /** Suppress the normal output from the casper object (echo, errors) @@ -1002,6 +1024,7 @@ } }; +// ------------------------------------------------------------------- debugging /** JSON formatter */ SpaceGhost.prototype.jsonStr = function( obj ){ @@ -1036,17 +1059,7 @@ return this.errors[( this.errors.length - 1 )]; }; -/** String representation - * @returns {String} - */ -SpaceGhost.prototype.toString = function(){ - var currentUrl = ''; - try { - currentUrl = this.getCurrentUrl(); - } catch( err ){} - return 'SpaceGhost(' + currentUrl + ')'; -}; - +// ------------------------------------------------------------------- file system /** Load and parse a JSON file into an object. * @param {String} filepath filepath relative to the current scriptDir * @returns {Object} the object parsed @@ -1078,6 +1091,34 @@ return fs.write( filepath, this.getHTML( selector, outer ), 'w' ); }; +/** Read and search a file for the given regex. + * @param {String} filepath filepath relative to the current scriptDir + * @param {Regex} searchFor regex to search for + * @returns {Object} search results + */ +SpaceGhost.prototype.searchFile = function searchFile( filepath, regex ){ + //precondition: filepath is relative to script dir + filepath = this.options.scriptDir + filepath; + var read = fs.read( filepath ); + return read.match( regex ); +}; + +/** Read a configuration setting from the universe_wsgi.ini file. + * @param {String} iniKey the setting key to find + * @returns {String} value from file for iniKey (or null if not found or commented out) + */ +SpaceGhost.prototype.getUniverseSetting = function getUniverseSetting( iniKey ){ + var iniFilepath = '../../universe_wsgi.ini', + regex = new RegExp( '^([#]*)\\\s*' + iniKey + '\\\s*=\\\s*(.*)$', 'm' ), + match = this.searchFile( iniFilepath, regex ); + this.debug( 'regex: ' + regex ); + // if nothing found or found and first group (the ini comment char) is not empty + if( match === null || match[1] || !match[2] ){ + return null; + } + return match[2]; +}; + // =================================================================== TEST DATA /** General use selectors, labels, and text. Kept here to allow a centralized location. @@ -1105,6 +1146,7 @@ }, masthead : { + adminLink : '#masthead a[href="/admin"]', userMenu : { userEmail : 'a #user-email', userEmail_xpath : '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' 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: More compatibility with main tool shed.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/98cd1bcb36f1/ Changeset: 98cd1bcb36f1 User: inithello Date: 2013-04-26 21:01:21 Summary: More compatibility with main tool shed. Affected #: 1 file diff -r b16126d45099c38563e4372b4a7f781d30e44bde -r 98cd1bcb36f129e8fed213687deccd7701ab047a 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 @@ -269,9 +269,11 @@ api_path = [ 'api', 'repository_revisions', metadata_revision_id ] api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata = json_from_url( api_url ) - if repository_metadata[ 'tool_test_results' ] is None: - return {} - return repository_metadata[ 'tool_test_results' ] + tool_test_results = repository_metadata.get( 'tool_test_results', {} ) + # Compatibility code, remove before next release. + if not tool_test_results: + tool_test_results = repository_metadata.get( 'tool_test_errors', {} ) + return tool_test_results def json_from_url( url ): url_handle = urllib.urlopen( url ) 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: Remove stderr from passed test display.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b16126d45099/ Changeset: b16126d45099 User: inithello Date: 2013-04-26 17:22:27 Summary: Remove stderr from passed test display. Affected #: 2 files diff -r 4de773e06e148df80d85783b04408307ba277f00 -r b16126d45099c38563e4372b4a7f781d30e44bde lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -160,9 +160,8 @@ class PassedTest( object ): """Passed tool tests object""" - def __init__( self, id=None, stderr=None, test_id=None, tool_id=None, tool_version=None ): + def __init__( self, id=None, test_id=None, tool_id=None, tool_version=None ): self.id = id - self.stderr = stderr self.test_id = test_id self.tool_id = tool_id self.tool_version = tool_version @@ -1027,7 +1026,6 @@ for passed_tests_dict in passed_tests_dicts: passed_test_id += 1 passed_test = PassedTest( id=passed_test_id, - stderr=passed_tests_dict.get( 'stderr', '' ), test_id=passed_tests_dict.get( 'test_id' '' ), tool_id=passed_tests_dict.get( 'tool_id', '' ), tool_version=passed_tests_dict.get( 'tool_version', '' ) ) diff -r 4de773e06e148df80d85783b04408307ba277f00 -r b16126d45099c38563e4372b4a7f781d30e44bde templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -618,7 +618,6 @@ <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> - <tr><td><b>Stderr:</b><br/>${passed_test.stderr | h}</td></tr></table></td></tr> 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: Update rss feed per changes in tool test results dict.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4de773e06e14/ Changeset: 4de773e06e14 User: inithello Date: 2013-04-26 17:16:16 Summary: Update rss feed per changes in tool test results dict. Affected #: 1 file diff -r 3c9b47aca3a5d25f23fcccfbc8e42d897dd39743 -r 4de773e06e148df80d85783b04408307ba277f00 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1122,10 +1122,11 @@ # Generate a citable URL for this repository with owner and changeset revision. repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, metadata_row.changeset_revision ) title = 'Functional test results for changeset revision %s of %s' % ( metadata_row.changeset_revision, repository.name ) - tests_passed = len( metadata_row.tool_test_results.get( 'tests_passed', [] ) ) - tests_failed = len( metadata_row.tool_test_results.get( 'test_errors', [] ) ) - invalid_tests = len( metadata_row.tool_test_results.get( 'invalid_tests', [] ) ) - description = '%d tests passed, %d tests failed, %d tests determined to be invalid.' % ( tests_passed, tests_failed, invalid_tests ) + passed_tests = len( metadata_row.tool_test_results.get( 'passed_tests', [] ) ) + failed_tests = len( metadata_row.tool_test_results.get( 'failed_tests', [] ) ) + missing_test_components = len( metadata_row.tool_test_results.get( 'missing_test_components', [] ) ) + description = '%d tests passed, %d tests failed, %d tests missing test components.' % \ + ( passed_tests, failed_tests, missing_test_components ) # The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated # if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable # that behavior. 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 workflow display in tool shed.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3c9b47aca3a5/ Changeset: 3c9b47aca3a5 User: inithello Date: 2013-04-26 17:05:05 Summary: Fix workflow display in tool shed. Affected #: 1 file diff -r 01b7b48cc823a64f9ea9d35c144e9ac12b0d205b -r 3c9b47aca3a5d25f23fcccfbc8e42d897dd39743 templates/webapps/tool_shed/repository/view_workflow.mako --- a/templates/webapps/tool_shed/repository/view_workflow.mako +++ b/templates/webapps/tool_shed/repository/view_workflow.mako @@ -35,7 +35,7 @@ <%inherit file="${inherit(context)}"/><%def name="render_workflow( workflow_name, repository_metadata_id )"> - <% center_url = h.url_for( controller='repository', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_metadata_id=repository_metadata_id, repository_id=None ) %> + <% center_url = h.url_for( controller='repository', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_metadata_id=repository_metadata_id ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Browser tests: add skeleton for workflow API testing
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01b7b48cc823/ Changeset: 01b7b48cc823 User: carlfeberhard Date: 2013-04-26 14:59:05 Summary: Browser tests: add skeleton for workflow API testing Affected #: 2 files diff -r 3be9ecc2030b096dce14b6c8f91a347c88b39c64 -r 01b7b48cc823a64f9ea9d35c144e9ac12b0d205b test/casperjs/api-workflow-tests.js --- /dev/null +++ b/test/casperjs/api-workflow-tests.js @@ -0,0 +1,101 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +spaceghost.user.loginOrRegisterUser( email, password ); + +function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + spaceghost.debug( 'key not found: ' + keysArray[i] ); + return false; + } + } + return true; +} + +function compareObjs( obj1, where ){ + for( var key in where ){ + if( where.hasOwnProperty( key ) ){ + if( !obj1.hasOwnProperty( key ) ){ return false; } + if( obj1[ key ] !== where[ key ] ){ return false; } + } + } + return true; +} + +function findObject( objectArray, where, start ){ + start = start || 0; + for( var i=start; i<objectArray.length; i += 1 ){ + if( compareObjs( objectArray[i], where ) ){ return objectArray[i]; } + } + return null; +} + +// =================================================================== TESTS +var workflowSummaryKeys = [ + 'id', 'model_class', 'name', 'published', 'tags', 'url' + ], + workflowDetailKeys = workflowSummaryKeys.concat([ + 'inputs', 'steps' + ]); + + +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + // ------------------------------------------------------------------------------------------- INDEX + this.test.comment( 'index should get a list of workflows' ); + var workflowIndex = this.api.workflows.index(); + this.debug( this.jsonStr( workflowIndex ) ); + this.test.assert( utils.isArray( workflowIndex ), "index returned an array: length " + workflowIndex.length ); + + // need a way to import/create a workflow here for testing + if( workflowIndex.length <= 0 ){ + log.warn( 'No workflows available' ); + return; + } + this.test.assert( workflowIndex.length >= 1, 'Has at least one workflow' ); + + // ------------------------------------------------------------------------------------------- SHOW + this.test.comment( 'show should get detailed data about the workflow with the given id' ); + var workflowShow = this.api.workflows.show( workflowIndex[0].id ); + this.debug( this.jsonStr( workflowShow ) ); + + + // ------------------------------------------------------------------------------------------- CREATE + + // ------------------------------------------------------------------------------------------- MISC +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r 3be9ecc2030b096dce14b6c8f91a347c88b39c64 -r 01b7b48cc823a64f9ea9d35c144e9ac12b0d205b test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -21,6 +21,7 @@ this.histories = new HistoriesAPI( this ); this.hdas = new HDAAPI( this ); this.tools = new ToolsAPI( this ); + this.workflows = new WorkflowsAPI( this ); }; exports.API = API; @@ -318,3 +319,78 @@ // }); //}; +// =================================================================== WORKFLOWS +var WorkflowsAPI = function WorkflowsAPI( api ){ + this.api = api; +}; +WorkflowsAPI.prototype.toString = function toString(){ + return this.api + '.WorkflowsAPI'; +}; + +// ------------------------------------------------------------------- +WorkflowsAPI.prototype.urlTpls = { + index : 'api/workflows', + show : 'api/workflows/%s', + // run a workflow + create : 'api/workflows', + update : 'api/workflows/%s', + + upload : 'api/workflows/upload', // POST + download: 'api/workflows/download/%s' // GET +}; + +WorkflowsAPI.prototype.index = function index(){ + this.api.spaceghost.info( 'workflows.index: ' + [] ); + var data = {}; + + return this.api._ajax( utils.format( this.urlTpls.index ), { + data : data + }); +}; + +WorkflowsAPI.prototype.show = function show( id ){ + this.api.spaceghost.info( 'workflows.show: ' + [ id ] ); + var data = {}; + + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + return this.api._ajax( utils.format( this.urlTpls.show, this.api.ensureId( id ) ), { + data : data + }); +}; + +//WorkflowsAPI.prototype.create = function create( payload ){ +// this.api.spaceghost.info( 'workflows.create: ' + [ this.api.spaceghost.jsonStr( payload ) ] ); +// +// // py.payload <-> ajax.data +// payload = this.api.ensureObject( payload ); +// return this.api._ajax( utils.format( this.urlTpls.create ), { +// type : 'POST', +// data : payload +// }); +//}; +// +//WorkflowsAPI.prototype.update = function create( id, payload ){ +// this.api.spaceghost.info( 'workflows.update: ' + [ id, this.api.spaceghost.jsonStr( payload ) ] ); +// +// // py.payload <-> ajax.data +// historyId = this.api.ensureId( historyId ); +// id = this.api.ensureId( id ); +// payload = this.api.ensureObject( payload ); +// url = utils.format( this.urlTpls.update, id ); +// +// return this.api._ajax( url, { +// type : 'PUT', +// data : payload +// }); +//}; + +WorkflowsAPI.prototype.upload = function upload( filepath ){ + this.api.spaceghost.info( 'workflows.show: ' + [ id ] ); + var data = {}; + + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + return this.api._ajax( utils.format( this.urlTpls.show, this.api.ensureId( id ) ), { + data : data + }); +}; + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: More tool shed dict fixes.
by commits-noreply＠bitbucket.org 25 Apr '13

25 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3be9ecc2030b/ Changeset: 3be9ecc2030b User: greg Date: 2013-04-25 22:51:25 Summary: More tool shed dict fixes. Affected #: 1 file diff -r dc08c095b1a53fab468b21706889e3a87400648f -r 3be9ecc2030b096dce14b6c8f91a347c88b39c64 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -999,7 +999,7 @@ if tool_test_results_dict: folder_id += 1 tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) - test_environment_dict = tool_test_results_dict[ 'test_environment' ] + test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) if test_environment_dict: folder_id += 1 test_results_folder = Folder( id=folder_id, key='test_results', label=label, parent=tool_test_results_root_folder ) @@ -1008,17 +1008,17 @@ folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=test_results_folder ) test_results_folder.folders.append( folder ) test_environment = TestEnvironment( id=1, - architecture=test_environment_dict[ 'architecture' ], - galaxy_database_version=test_environment_dict[ 'galaxy_database_version' ], - galaxy_revision=test_environment_dict[ 'galaxy_revision' ], - python_version=test_environment_dict[ 'python_version' ], - system=test_environment_dict[ 'system' ], + architecture=test_environment_dict.get( 'architecture', '' ), + galaxy_database_version=test_environment_dict.get( 'galaxy_database_version', '' ), + galaxy_revision=test_environment_dict.get( 'galaxy_revision', '' ), + python_version=test_environment_dict.get( 'python_version', '' ), + system=test_environment_dict.get( 'system', '' ), time_last_tested=time_last_tested, - tool_shed_database_version=test_environment_dict[ 'tool_shed_database_version' ], - tool_shed_mercurial_version=test_environment_dict[ 'tool_shed_mercurial_version' ], - tool_shed_revision=test_environment_dict[ 'tool_shed_revision' ] ) + tool_shed_database_version=test_environment_dict.get( 'tool_shed_database_version', '' ), + tool_shed_mercurial_version=test_environment_dict.get( 'tool_shed_mercurial_version', '' ), + tool_shed_revision=test_environment_dict.get( 'tool_shed_revision', '' ) ) folder.test_environments.append( test_environment ) - passed_tests_dicts = tool_test_results_dict[ 'passed_tests' ] + passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) if passed_tests_dicts: folder_id += 1 folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=test_results_folder ) @@ -1032,7 +1032,7 @@ tool_id=passed_tests_dict.get( 'tool_id', '' ), tool_version=passed_tests_dict.get( 'tool_version', '' ) ) folder.passed_tests.append( passed_test ) - failed_tests_dicts = tool_test_results_dict[ 'failed_tests' ] + failed_tests_dicts = tool_test_results_dict.get( 'failed_tests', [] ) if failed_tests_dicts: folder_id += 1 folder = Folder( id=folder_id, key='failed_tests', label='Tests that failed', parent=test_results_folder ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: More tool shed dictionary fixes.
by commits-noreply＠bitbucket.org 25 Apr '13

25 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc08c095b1a5/ Changeset: dc08c095b1a5 User: greg Date: 2013-04-25 22:38:00 Summary: More tool shed dictionary fixes. Affected #: 1 file diff -r e3fae8e819f24eb43e555f857a15a77a1584b84e -r dc08c095b1a53fab468b21706889e3a87400648f lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -1027,10 +1027,10 @@ for passed_tests_dict in passed_tests_dicts: passed_test_id += 1 passed_test = PassedTest( id=passed_test_id, - stderr=passed_tests_dict[ 'stderr' ], - test_id=passed_tests_dict[ 'test_id' ], - tool_id=passed_tests_dict[ 'tool_id' ], - tool_version=passed_tests_dict[ 'tool_version' ] ) + stderr=passed_tests_dict.get( 'stderr', '' ), + test_id=passed_tests_dict.get( 'test_id' '' ), + tool_id=passed_tests_dict.get( 'tool_id', '' ), + tool_version=passed_tests_dict.get( 'tool_version', '' ) ) folder.passed_tests.append( passed_test ) failed_tests_dicts = tool_test_results_dict[ 'failed_tests' ] if failed_tests_dicts: @@ -1047,7 +1047,7 @@ tool_version=failed_tests_dict.get( 'tool_version', '' ), traceback=failed_tests_dict.get( 'traceback', '' ) ) folder.failed_tests.append( failed_test ) - missing_test_components_dicts = tool_test_results_dict[ 'missing_test_components' ] + missing_test_components_dicts = tool_test_results_dict.get( 'missing_test_components', [] ) if missing_test_components_dicts: folder_id += 1 folder = Folder( id=folder_id, key='missing_test_components', label='Tools missing tests or test data', parent=test_results_folder ) @@ -1056,10 +1056,10 @@ for missing_test_components_dict in missing_test_components_dicts: missing_test_component_id += 1 missing_test_component = MissingTestComponent( id=missing_test_component_id, - missing_components=missing_test_components_dict[ 'missing_components' ], - tool_guid=missing_test_components_dict[ 'tool_guid' ], - tool_id=missing_test_components_dict[ 'tool_id' ], - tool_version=missing_test_components_dict[ 'tool_version' ] ) + missing_components=missing_test_components_dict.get( 'missing_components', '' ), + tool_guid=missing_test_components_dict.get( 'tool_guid', '' ), + tool_id=missing_test_components_dict.get( 'tool_id', '' ), + tool_version=missing_test_components_dict.get( 'tool_version', '' ) ) folder.missing_test_components.append( missing_test_component ) else: tool_test_results_root_folder = None @@ -1098,10 +1098,10 @@ steps = 'unknown' workflow_id += 1 workflow = Workflow( id=workflow_id, - workflow_name=workflow_dict[ 'name' ], + workflow_name=workflow_dict.get( 'name', '' ), steps=steps, - format_version=workflow_dict[ 'format-version' ], - annotation=workflow_dict[ 'annotation' ], + format_version=workflow_dict.get( 'format-version', '' ), + annotation=workflow_dict.get( 'annotation', '' ), repository_metadata_id=repository_metadata_id, repository_id=repository_id ) folder.workflows.append( workflow ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle missing entries in the failed tests dictionary in the tool shed.
by commits-noreply＠bitbucket.org 25 Apr '13

25 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3fae8e819f2/ Changeset: e3fae8e819f2 User: greg Date: 2013-04-25 22:33:41 Summary: Handle missing entries in the failed tests dictionary in the tool shed. Affected #: 1 file diff -r 1d56c002d32e9116f9c6dc57587d9ffa00e24ca0 -r e3fae8e819f24eb43e555f857a15a77a1584b84e lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -1041,11 +1041,11 @@ for failed_tests_dict in failed_tests_dicts: failed_test_id += 1 failed_test = FailedTest( id=failed_test_id, - stderr=failed_tests_dict[ 'stderr' ], - test_id=failed_tests_dict[ 'test_id' ], - tool_id=failed_tests_dict[ 'tool_id' ], - tool_version=failed_tests_dict[ 'tool_version' ], - traceback=failed_tests_dict[ 'traceback' ] ) + stderr=failed_tests_dict.get( 'stderr', '' ), + test_id=failed_tests_dict.get( 'test_id', '' ), + tool_id=failed_tests_dict.get( 'tool_id', '' ), + tool_version=failed_tests_dict.get( 'tool_version', '' ), + traceback=failed_tests_dict.get( 'traceback', '' ) ) folder.failed_tests.append( failed_test ) missing_test_components_dicts = tool_test_results_dict[ 'missing_test_components' ] if missing_test_components_dicts: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Display automated tool test results in a container in the tool shed rather than a separate page.
by commits-noreply＠bitbucket.org 25 Apr '13

25 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d56c002d32e/ Changeset: 1d56c002d32e User: greg Date: 2013-04-25 22:17:23 Summary: Display automated tool test results in a container in the tool shed rather than a separate page. Affected #: 5 files diff -r 3d569f107f1d449b028fc4d5390dd8d07fdf26ce -r 1d56c002d32e9116f9c6dc57587d9ffa00e24ca0 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -734,50 +734,6 @@ status='error' ) ) @web.expose - def display_tool_functional_test_results( self, trans, repository_id, repository_metadata_id, **kwd ): - """ - The test framework in ~/test/install_and_test_tool_shed_repositories can be executed on a regularly defined schedule (e.g., via cron) to install appropriate - repositories from a tool shed into a Galaxy instance and run defined functional tests for the tools included in the repository. This process affects the values - if these columns in the repository_metadata table: do_not_test, missing_test_components, time_last_tested, tools_functionally_correct and tool_test_results. - """ - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository = suc.get_repository_by_id( trans, repository_id ) - if repository: - repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) - changeset_revision = repository_metadata.changeset_revision - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - revision_label = suc.get_revision_label( trans, repository, repository_metadata.changeset_revision ) - return trans.fill_template( '/webapps/tool_shed/repository/display_tool_functional_test_results.mako', - repository=repository, - repository_metadata=repository_metadata, - revision_label=revision_label, - message=message, - status=status ) - else: - message = 'Missing metadata for revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b>.' % \ - ( str( changeset_revision ), str( repository.name ), str( repository.user.username ) ) - else: - message = 'Invalid repository_metadata_id <b>%s</b> received for displaying functional test errors for repository <b>%s</b>.' % \ - ( str( repository_metadata_id ), str( repository.name ) ) - else: - message = 'Invalid repository_id received for displaying functional test errors.<b>%s</b>.' % str( repository_id ) - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - message=message, - status='error' ) ) - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - operation='view_or_manage_repository', - id=repository_id, - changeset_revision=changeset_revision, - message=message, - status='error' ) ) - - @web.expose def display_tool_help_image_in_repository( self, trans, **kwd ): repository_id = kwd.get( 'repository_id', None ) image_file = kwd.get( 'image_file', None ) @@ -2668,11 +2624,6 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ) - # TODO: Fix this when the install and test framework is completed. - # if repository_metadata.tool_test_results: - # tool_test_results = json.from_json_string( repository_metadata.tool_test_results ) - # else: - # tool_test_results = None metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: @@ -2708,7 +2659,6 @@ else: repository_metadata_id = None metadata = None - #tool_test_results = None is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, repository, @@ -2732,7 +2682,6 @@ tool=tool, tool_metadata_dict=tool_metadata_dict, tool_lineage=tool_lineage, - #tool_test_results=tool_test_results, changeset_revision=changeset_revision, revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, diff -r 3d569f107f1d449b028fc4d5390dd8d07fdf26ce -r 1d56c002d32e9116f9c6dc57587d9ffa00e24ca0 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -2,6 +2,7 @@ import os import threading from galaxy.util import asbool +from galaxy.web.framework.helpers import time_ago from tool_shed.util import readme_util import tool_shed.util.shed_util_common as suc @@ -29,6 +30,10 @@ self.valid_data_managers = [] self.invalid_data_managers = [] self.tool_dependencies = [] + self.failed_tests = [] + self.missing_test_components = [] + self.passed_tests = [] + self.test_environments = [] self.repository_dependencies = [] self.readme_files = [] self.workflows = [] @@ -85,6 +90,18 @@ self.display_app_containers = display_app_containers +class FailedTest( object ): + """Failed tool tests object""" + + def __init__( self, id=None, stderr=None, test_id=None, tool_id=None, tool_version=None, traceback=None ): + self.id = id + self.stderr = stderr + self.test_id = test_id + self.tool_id = tool_id + self.tool_version = tool_version + self.traceback = traceback + + class InvalidDataManager( object ): """Invalid data Manager object""" @@ -129,6 +146,28 @@ self.error = error +class MissingTestComponent( object ): + """Missing tool test components object""" + + def __init__( self, id=None, missing_components=None, tool_guid=None, tool_id=None, tool_version=None ): + self.id = id + self.missing_components = missing_components + self.tool_guid = tool_guid + self.tool_id = tool_id + self.tool_version = tool_version + + +class PassedTest( object ): + """Passed tool tests object""" + + def __init__( self, id=None, stderr=None, test_id=None, tool_id=None, tool_version=None ): + self.id = id + self.stderr = stderr + self.test_id = test_id + self.tool_id = tool_id + self.tool_version = tool_version + + class ReadMe( object ): """Readme text object""" @@ -157,6 +196,23 @@ return [ self.toolshed, self.repository_name, self.repository_owner, self.changeset_revision, asbool( str( self.prior_installation_required ) ) ] +class TestEnvironment( object ): + """Tool test environment object""" + + def __init__( self, id=None, architecture=None, galaxy_database_version=None, galaxy_revision=None, python_version=None, system=None, time_last_tested=None, + tool_shed_database_version=None, tool_shed_mercurial_version=None, tool_shed_revision=None ): + self.id = id + self.architecture = architecture + self.galaxy_database_version = galaxy_database_version + self.galaxy_revision = galaxy_revision + self.python_version = python_version + self.system = system + self.time_last_tested = time_last_tested + self.tool_shed_database_version = tool_shed_database_version + self.tool_shed_mercurial_version = tool_shed_mercurial_version + self.tool_shed_revision = tool_shed_revision + + class Tool( object ): """Tool object""" @@ -632,6 +688,11 @@ ) if repository_metadata: metadata = repository_metadata.metadata + tool_test_results = repository_metadata.tool_test_results + try: + time_last_tested = time_ago( repository_metadata.time_last_tested ) + except: + time_last_tested = None lock = threading.Lock() lock.acquire( True ) try: @@ -710,6 +771,10 @@ changeset_revision, label='Valid tools' ) containers_dict[ 'valid_tools' ] = valid_tools_root_folder + # Tool test results container. + if tool_test_results: + folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested ) + containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder # Workflows container. if metadata: if 'workflows' in metadata: @@ -928,6 +993,78 @@ tool_dependencies_root_folder = None return folder_id, tool_dependencies_root_folder +def build_tool_test_results_folder( trans, folder_id, tool_test_results_dict, label='Tool test results', time_last_tested=None ): + """Return a folder hierarchy containing tool dependencies.""" + # This container is displayed only in the tool shed. + if tool_test_results_dict: + folder_id += 1 + tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) + test_environment_dict = tool_test_results_dict[ 'test_environment' ] + if test_environment_dict: + folder_id += 1 + test_results_folder = Folder( id=folder_id, key='test_results', label=label, parent=tool_test_results_root_folder ) + tool_test_results_root_folder.folders.append( test_results_folder ) + folder_id += 1 + folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=test_results_folder ) + test_results_folder.folders.append( folder ) + test_environment = TestEnvironment( id=1, + architecture=test_environment_dict[ 'architecture' ], + galaxy_database_version=test_environment_dict[ 'galaxy_database_version' ], + galaxy_revision=test_environment_dict[ 'galaxy_revision' ], + python_version=test_environment_dict[ 'python_version' ], + system=test_environment_dict[ 'system' ], + time_last_tested=time_last_tested, + tool_shed_database_version=test_environment_dict[ 'tool_shed_database_version' ], + tool_shed_mercurial_version=test_environment_dict[ 'tool_shed_mercurial_version' ], + tool_shed_revision=test_environment_dict[ 'tool_shed_revision' ] ) + folder.test_environments.append( test_environment ) + passed_tests_dicts = tool_test_results_dict[ 'passed_tests' ] + if passed_tests_dicts: + folder_id += 1 + folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=test_results_folder ) + test_results_folder.folders.append( folder ) + passed_test_id = 0 + for passed_tests_dict in passed_tests_dicts: + passed_test_id += 1 + passed_test = PassedTest( id=passed_test_id, + stderr=passed_tests_dict[ 'stderr' ], + test_id=passed_tests_dict[ 'test_id' ], + tool_id=passed_tests_dict[ 'tool_id' ], + tool_version=passed_tests_dict[ 'tool_version' ] ) + folder.passed_tests.append( passed_test ) + failed_tests_dicts = tool_test_results_dict[ 'failed_tests' ] + if failed_tests_dicts: + folder_id += 1 + folder = Folder( id=folder_id, key='failed_tests', label='Tests that failed', parent=test_results_folder ) + test_results_folder.folders.append( folder ) + failed_test_id = 0 + for failed_tests_dict in failed_tests_dicts: + failed_test_id += 1 + failed_test = FailedTest( id=failed_test_id, + stderr=failed_tests_dict[ 'stderr' ], + test_id=failed_tests_dict[ 'test_id' ], + tool_id=failed_tests_dict[ 'tool_id' ], + tool_version=failed_tests_dict[ 'tool_version' ], + traceback=failed_tests_dict[ 'traceback' ] ) + folder.failed_tests.append( failed_test ) + missing_test_components_dicts = tool_test_results_dict[ 'missing_test_components' ] + if missing_test_components_dicts: + folder_id += 1 + folder = Folder( id=folder_id, key='missing_test_components', label='Tools missing tests or test data', parent=test_results_folder ) + test_results_folder.folders.append( folder ) + missing_test_component_id = 0 + for missing_test_components_dict in missing_test_components_dicts: + missing_test_component_id += 1 + missing_test_component = MissingTestComponent( id=missing_test_component_id, + missing_components=missing_test_components_dict[ 'missing_components' ], + tool_guid=missing_test_components_dict[ 'tool_guid' ], + tool_id=missing_test_components_dict[ 'tool_id' ], + tool_version=missing_test_components_dict[ 'tool_version' ] ) + folder.missing_test_components.append( missing_test_component ) + else: + tool_test_results_root_folder = None + return folder_id, tool_test_results_root_folder + def build_workflows_folder( trans, folder_id, workflows, repository_metadata_id=None, repository_id=None, label='Workflows' ): """ Return a folder hierarchy containing workflow objects for each workflow dictionary in the received workflows list. When diff -r 3d569f107f1d449b028fc4d5390dd8d07fdf26ce -r 1d56c002d32e9116f9c6dc57587d9ffa00e24ca0 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -325,6 +325,26 @@ ${render_invalid_data_manager( data_manager, pad, my_row, row_counter, row_is_header )} %endfor %endif + %if folder.test_environments: + %for test_environment in folder.test_environments: + ${render_test_environment( test_environment, pad, my_row, row_counter )} + %endfor + %endif + %if folder.failed_tests: + %for failed_test in folder.failed_tests: + ${render_failed_test( failed_test, pad, my_row, row_counter )} + %endfor + %endif + %if folder.passed_tests: + %for passed_test in folder.passed_tests: + ${render_passed_test( passed_test, pad, my_row, row_counter )} + %endfor + %endif + %if folder.missing_test_components: + %for missing_test_component in folder.missing_test_components: + ${render_missing_test_component( missing_test_component, pad, my_row, row_counter )} + %endfor + %endif </%def><%def name="render_datatype( datatype, pad, parent, row_counter, row_is_header=False )"> @@ -351,22 +371,22 @@ %></%def> -<%def name="render_valid_data_manager( data_manager, pad, parent, row_counter, row_is_header=False )"> - <% - encoded_id = trans.security.encode_id( data_manager.id ) - if row_is_header: - cell_type = 'th' - else: - cell_type = 'td' - %> +<%def name="render_failed_test( failed_test, pad, parent, row_counter, row_is_header=False )"> + <% encoded_id = trans.security.encode_id( failed_test.id ) %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <${cell_type} style="padding-left: ${pad+20}px;">${data_manager.name | h}</${cell_type}> - <${cell_type}>${data_manager.version | h}</${cell_type}> - <${cell_type}>${data_manager.data_tables | h}</${cell_type}> + <td style="padding-left: ${pad+20}px;"> + <table class="grid" id="readme_table"> + <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr> + <tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr> + <tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> + <tr><td><b>Stderr:</b><br/>${failed_test.stderr | h}</td></tr> + <tr><td><b>Traceback:</b><br/>${failed_test.traceback | h}</td></tr> + </table> + </td></tr><% my_row = row_counter.count @@ -467,6 +487,28 @@ %></%def> +<%def name="render_missing_test_component( missing_test_component, pad, parent, row_counter, row_is_header=False )"> + <% encoded_id = trans.security.encode_id( missing_test_component.id ) %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table class="grid" id="readme_table"> + <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr> + <tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr> + <tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr> + <tr><td><b>Missing components:</b><br/>${missing_test_component.missing_components | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_readme( readme, pad, parent, row_counter )"><% from tool_shed.util.shed_util_common import to_safe_string @@ -564,6 +606,28 @@ %></%def> +<%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"> + <% encoded_id = trans.security.encode_id( passed_test.id ) %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table class="grid" id="readme_table"> + <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr> + <tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr> + <tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> + <tr><td><b>Stderr:</b><br/>${passed_test.stderr | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_tool( tool, pad, parent, row_counter, row_is_header )"><% encoded_id = trans.security.encode_id( tool.id ) @@ -672,6 +736,56 @@ %></%def> +<%def name="render_test_environment( test_environment, pad, parent, row_counter, row_is_header=False )"> + <% encoded_id = trans.security.encode_id( test_environment.id ) %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table class="grid" id="readme_table"> + <tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr> + <tr><td><b>System:</b> ${test_environment.system | h}</td></tr> + <tr><td><b>Architecture:</b> ${test_environment.architecture | h}</td></tr> + <tr><td><b>Python version:</b> ${test_environment.python_version | h}</td></tr> + <tr><td><b>Galaxy revision:</b> ${test_environment.galaxy_revision | h}</td></tr> + <tr><td><b>Galaxy database version:</b> ${test_environment.galaxy_database_version | h}</td></tr> + <tr><td><b>Tool shed revision:</b> ${test_environment.tool_shed_revision | h}</td></tr> + <tr><td><b>Tool shed database version:</b> ${test_environment.tool_shed_database_version | h}</td></tr> + <tr><td><b>Tool shed mercurial version:</b> ${test_environment.tool_shed_mercurial_version | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_valid_data_manager( data_manager, pad, parent, row_counter, row_is_header=False )"> + <% + encoded_id = trans.security.encode_id( data_manager.id ) + if row_is_header: + cell_type = 'th' + else: + cell_type = 'td' + %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <${cell_type} style="padding-left: ${pad+20}px;">${data_manager.name | h}</${cell_type}> + <${cell_type}>${data_manager.version | h}</${cell_type}> + <${cell_type}>${data_manager.data_tables | h}</${cell_type}> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_workflow( workflow, pad, parent, row_counter, row_is_header=False )"><% from tool_shed.util.encoding_util import tool_shed_encode @@ -723,18 +837,20 @@ has_workflows = metadata and 'workflows' in metadata datatypes_root_folder = containers_dict.get( 'datatypes', None ) + invalid_data_managers_root_folder = containers_dict.get( 'invalid_data_managers', None ) + invalid_repository_dependencies_root_folder = containers_dict.get( 'invalid_repository_dependencies', None ) + invalid_tool_dependencies_root_folder = containers_dict.get( 'invalid_tool_dependencies', None ) invalid_tools_root_folder = containers_dict.get( 'invalid_tools', None ) - invalid_repository_dependencies_root_folder = containers_dict.get( 'invalid_repository_dependencies', None ) + missing_repository_dependencies_root_folder = containers_dict.get( 'missing_repository_dependencies', None ) + missing_tool_dependencies_root_folder = containers_dict.get( 'missing_tool_dependencies', None ) readme_files_root_folder = containers_dict.get( 'readme_files', None ) repository_dependencies_root_folder = containers_dict.get( 'repository_dependencies', None ) - missing_repository_dependencies_root_folder = containers_dict.get( 'missing_repository_dependencies', None ) - invalid_tool_dependencies_root_folder = containers_dict.get( 'invalid_tool_dependencies', None ) + test_environment_root_folder = containers_dict.get( 'test_environment', None ) tool_dependencies_root_folder = containers_dict.get( 'tool_dependencies', None ) - missing_tool_dependencies_root_folder = containers_dict.get( 'missing_tool_dependencies', None ) + tool_test_results_root_folder = containers_dict.get( 'tool_test_results', None ) + valid_data_managers_root_folder = containers_dict.get( 'valid_data_managers', None ) valid_tools_root_folder = containers_dict.get( 'valid_tools', None ) workflows_root_folder = containers_dict.get( 'workflows', None ) - valid_data_managers_root_folder = containers_dict.get( 'valid_data_managers', None ) - invalid_data_managers_root_folder = containers_dict.get( 'invalid_data_managers', None ) has_contents = datatypes_root_folder or invalid_tools_root_folder or valid_tools_root_folder or workflows_root_folder has_dependencies = \ @@ -864,4 +980,16 @@ </div></div> %endif + %if tool_test_results_root_folder: + <div class="toolForm"> + <div class="toolFormTitle">Automated tool test results</div> + <div class="toolFormBody"> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment"> + ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + </div> + </div> + %endif </%def> diff -r 3d569f107f1d449b028fc4d5390dd8d07fdf26ce -r 1d56c002d32e9116f9c6dc57587d9ffa00e24ca0 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -26,13 +26,6 @@ can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated can_upload = can_push can_view_change_log = not is_new - if repository_metadata: - if repository_metadata.includes_tools and repository_metadata.tool_test_results is not None: - can_display_tool_functional_test_results = True - else: - can_display_tool_functional_test_results = False - else: - can_display_tool_functional_test_results = False if can_push: browse_label = 'Browse or delete repository tip files' @@ -88,9 +81,6 @@ %if can_browse_repository_reviews: <a class="action-button" href="${h.url_for( controller='repository_review', action='manage_repository_reviews', id=trans.app.security.encode_id( repository.id ) )}">Browse reviews of this repository</a> %endif - %if can_display_tool_functional_test_results: - <a class="action-button" href="${h.url_for( controller='repository', action='display_tool_functional_test_results', repository_id=trans.security.encode_id( repository.id ), repository_metadata_id=trans.security.encode_id( repository_metadata.id ) )}">View tool functional test results</a> - %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif diff -r 3d569f107f1d449b028fc4d5390dd8d07fdf26ce -r 1d56c002d32e9116f9c6dc57587d9ffa00e24ca0 templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -25,14 +25,6 @@ can_view_change_log = trans.webapp.name == 'tool_shed' and not is_new changeset_revision_is_repository_tip = changeset_revision == repository.tip( trans.app ) - if repository_metadata: - if repository_metadata.includes_tools and repository_metadata.tool_test_results is not None: - can_display_tool_functional_test_results = True - else: - can_display_tool_functional_test_results = False - else: - can_display_tool_functional_test_results = False - if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -88,9 +80,6 @@ %if can_browse_repository_reviews: <a class="action-button" href="${h.url_for( controller='repository_review', action='manage_repository_reviews', id=trans.app.security.encode_id( repository.id ) )}">Browse reviews of this repository</a> %endif - %if can_display_tool_functional_test_results: - <a class="action-button" href="${h.url_for( controller='repository', action='display_tool_functional_test_results', repository_id=trans.security.encode_id( repository.id ), repository_metadata_id=trans.security.encode_id( repository_metadata.id ) )}">View tool functional test results</a> - %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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