galaxy-commits November 2013

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commit/galaxy-central: greg: Fix for rendering Skip tool tests" form on the manage_repository page in the tool shed.
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/011df6fa309e/ Changeset: 011df6fa309e User: greg Date: 2013-11-25 22:53:40 Summary: Fix for rendering Skip tool tests" form on the manage_repository page in the tool shed. Affected #: 1 file diff -r 11eb2e028791aca01c206fa5e898e1feb28f4651 -r 011df6fa309e9b4a052d5342218e888deabd063f 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 @@ -209,7 +209,7 @@ <div class="toolFormTitle">Automated tool tests</div> %endif <div class="toolFormBody"> - <form name="skip_tool_tests" id="skip_tool_tests" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository_metadata.changeset_revision )}" method="post" > + <form name="skip_tool_tests" id="skip_tool_tests" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}" method="post" ><div class="form-row"> %if repository.type == TOOL_DEPENDENCY_DEFINITION: <label>Skip automated testing of this tool dependency recipe</label> 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: Minor fixes for the prep script for installing and testing tool shed repositories of type tool_dependency_definition.
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11eb2e028791/ Changeset: 11eb2e028791 User: greg Date: 2013-11-25 22:43:01 Summary: Minor fixes for the prep script for installing and testing tool shed repositories of type tool_dependency_definition. Affected #: 1 file diff -r ec2a03eea18ee82c71618d291394da81414cfb45 -r 11eb2e028791aca01c206fa5e898e1feb28f4651 lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py --- a/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py +++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py @@ -28,7 +28,9 @@ from base.util import get_database_version from base.util import get_repository_current_revision from base.util import get_test_environment -from galaxy.model.orm import and_, not_, select +from galaxy.model.orm import and_ +from galaxy.model.orm import not_ +from galaxy.model.orm import select from galaxy.web import url_for from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION @@ -138,21 +140,6 @@ app.model.RepositoryMetadata.table.c.repository_id.in_( tool_dependency_defintion_repository_ids ), not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): records_checked += 1 - # Create the repository_status dictionary, using the dictionary from the previous test run if available. - if repository_metadata.tool_test_results: - repository_status = repository_metadata.tool_test_results - else: - repository_status = {} - # Initialize the repository_status dictionary with the information about the current test environment. - last_test_environment = repository_status.get( 'test_environment', None ) - if last_test_environment is None: - test_environment = get_test_environment() - else: - test_environment = get_test_environment( last_test_environment ) - test_environment[ 'tool_shed_database_version' ] = get_database_version( app ) - test_environment[ 'tool_shed_mercurial_version' ] = __version__.version - test_environment[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) - repository_status[ 'test_environment' ] = test_environment # Check the next repository revision. changeset_revision = str( repository_metadata.changeset_revision ) name = repository.name @@ -174,7 +161,18 @@ print 'Revision %s of %s owned by %s has invalid metadata.' % ( changeset_revision, name, owner ) invalid_metadata += 1 if not info_only: - repository_metadata.tool_test_results = repository_status + # Create the tool_test_results_dict dictionary, using the dictionary from the previous test run if available. + if repository_metadata.tool_test_results: + tool_test_results_dict = repository_metadata.tool_test_results + else: + tool_test_results_dict = {} + # Initialize the tool_test_results_dict dictionary with the information about the current test environment. + test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) + test_environment_dict[ 'tool_shed_database_version' ] = get_database_version( app ) + test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version + test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) + tool_test_results_dict[ 'test_environment' ] = test_environment_dict + repository_metadata.tool_test_results = tool_test_results_dict app.sa_session.add( repository_metadata ) app.sa_session.flush() stop = time.time() 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 25 Nov '13

25 Nov '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8fc2bc86635/ Changeset: f8fc2bc86635 User: Dave Bouvier Date: 2013-11-25 22:23:51 Summary: Add API method to list datatype sniffers. Add functional tests for repositories defining datatype sniffers. Affected #: 1 file diff -r d0a3879c0708983fccb24b809bfe29d96a8dbb59 -r f8fc2bc8663593075a820157606cca11b905e0e9 test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar Binary file test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar has changed https://bitbucket.org/galaxy/galaxy-central/commits/ec2a03eea18e/ Changeset: ec2a03eea18e User: Dave Bouvier Date: 2013-11-25 22:29:41 Summary: Add API method to list datatype sniffers. Add functional tests for repositories defining datatype sniffers. Affected #: 4 files diff -r f8fc2bc8663593075a820157606cca11b905e0e9 -r ec2a03eea18ee82c71618d291394da81414cfb45 lib/galaxy/webapps/galaxy/api/datatypes.py --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -4,20 +4,45 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController +from galaxy.util import asbool import logging log = logging.getLogger( __name__ ) + class DatatypesController( BaseAPIController ): + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/datatypes - Return an object containing datatypes. + Return an object containing upload datatypes. """ + upload_only = asbool( kwd.get( 'upload_only', True ) ) try: - return trans.app.datatypes_registry.upload_file_formats + if upload_only: + return trans.app.datatypes_registry.upload_file_formats + else: + return [ ext for ext in trans.app.datatypes_registry.datatypes_by_extension ] except Exception, exception: log.error( 'could not get datatypes: %s', str( exception ), exc_info=True ) trans.response.status = 500 return { 'error': str( exception ) } + + @web.expose_api_anonymous + def sniffers( self, trans, **kwd ): + ''' + GET /api/datatypes/sniffers + Return a list of sniffers. + ''' + try: + rval = [] + for sniffer_elem in trans.app.datatypes_registry.sniffer_elems: + datatype = sniffer_elem.get( 'type' ) + if datatype is not None: + rval.append( datatype ) + return rval + except Exception, exception: + log.error( 'could not get datatypes: %s', str( exception ), exc_info=True ) + trans.response.status = 500 + return { 'error': str( exception ) } diff -r f8fc2bc8663593075a820157606cca11b905e0e9 -r ec2a03eea18ee82c71618d291394da81414cfb45 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -163,7 +163,11 @@ webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) - webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api' ) + webapp.mapper.resource( 'datatype', + 'datatypes', + path_prefix='/api', + collection={ 'sniffers': 'GET' }, + parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) diff -r f8fc2bc8663593075a820157606cca11b905e0e9 -r ec2a03eea18ee82c71618d291394da81414cfb45 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -618,13 +618,11 @@ return temp_path def get_datatypes_count( self ): - url = '/admin/view_datatypes_registry' + url = '/api/datatypes?upload_only=false' self.visit_galaxy_url( url ) html = self.last_page() - datatypes_count = re.search( 'registry contains (\d+) data types', html ) - if datatypes_count: - return datatypes_count.group( 1 ) - return None + datatypes = from_json_string( html ) + return len( datatypes ) def get_env_sh_path( self, tool_dependency_name, tool_dependency_version, repository ): '''Return the absolute path to an installed repository's env.sh file.''' @@ -735,6 +733,13 @@ repo = self.get_hg_repo( self.get_repo_path( repository ) ) return str( repo.changectx( repo.changelog.tip() ) ) + def get_sniffers_count( self ): + url = '/api/datatypes/sniffers' + self.visit_galaxy_url( url ) + html = self.last_page() + sniffers = from_json_string( html ) + return len( sniffers ) + def get_tools_from_repository_metadata( self, repository, include_invalid=False ): '''Get a list of valid and (optionally) invalid tool dicts from the repository metadata.''' valid_tools = [] diff -r f8fc2bc8663593075a820157606cca11b905e0e9 -r ec2a03eea18ee82c71618d291394da81414cfb45 test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py --- /dev/null +++ b/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py @@ -0,0 +1,191 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +repository_name = 'proteomics_datatypes_1450' +repository_description = "Proteomics datatypes" +repository_long_description = "Datatypes used in proteomics" + +category_name = 'Test 1450 Datatype Sniffers' +category_description = 'Test 1450 - Installing Datatype Sniffers' + + +''' +1. Get a count of datatypes and sniffers. +2. Install proteomics_datatypes_1450. +3. Verify the count of datatypes and sniffers is the previous count + the datatypes contained within proteomics_datatypes_1450. +4. Deactivate proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1. +5. Reactivate proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository. +6. Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1. +7. Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository. +''' + +base_datatypes_count = 0 +repository_datatypes_count = 0 +base_sniffers_count = 0 + + +class TestInstallDatatypesSniffers( ShedTwillTestCase ): + '''Test installing a repository that defines datatypes and datatype sniffers.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + global base_datatypes_count + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email ) + assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user ) + base_datatypes_count = self.get_datatypes_count() + base_sniffers_count = self.get_sniffers_count() + + def test_0005_ensure_repositories_and_categories_exist( self ): + '''Create the 1450 category and proteomics_datatypes_1450 repository.''' + global repository_datatypes_count + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + self.upload_file( repository, + filename='proteomics_datatypes/proteomics_datatypes.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded datatype and sniffer definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + repository_datatypes_count = self.get_repository_datatypes_count( repository ) + + def test_0010_install_datatypes_repository( self ): + '''Install the proteomics_datatypes_1450 repository into the Galaxy instance.''' + ''' + This includes steps 1 and 2 - Get a count of datatypes and sniffers. + Store a count of the current datatypes registry and sniffers in global variables, to compare with the updated count + after changing the installation status of the proteomics_datatypes_1450 repository. + ''' + global repository_datatypes_count + global base_datatypes_count + global base_sniffers_count + base_sniffers_count = self.get_sniffers_count() + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + strings_displayed = [ 'proteomics' ] + self.install_repository( 'proteomics_datatypes_1450', + common.test_user_1_name, + category_name, + strings_displayed=strings_displayed, + new_tool_panel_section='test_1450' ) + installed_repository = test_db_util.get_installed_repository_by_name_owner( 'proteomics_datatypes_1450', common.test_user_1_name ) + strings_displayed = [ 'user1', + self.url.replace( 'http://', '' ), + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + + def test_0015_verify_datatypes_count( self ): + '''Verify that datatypes were added in the previous step.''' + ''' + This is step 3 - Verify the count of datatypes and sniffers is the previous count + the datatypes + contained within proteomics_datatypes_1450. + Compare the current datatypes registry and sniffers with the values that were retrieved in the previous step. + ''' + current_datatypes = self.get_datatypes_count() + assert current_datatypes == base_datatypes_count + repository_datatypes_count, \ + 'Found %d datatypes, expected %d.' % ( current_datatypes, base_datatypes_count + repository_datatypes_count ) + current_sniffers = self.get_sniffers_count() + assert current_sniffers > base_sniffers_count, \ + 'Sniffer count after installing proteomics_datatypes_1450 is %d, which is not greater than %d' % \ + ( current_sniffers, base_sniffers_count ) + + def test_0020_deactivate_datatypes_repository( self ): + '''Deactivate the installed proteomics_datatypes_1450 repository.''' + ''' + This is step 4 - Deactivate proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to + the count determined in step 1. + Deactivate proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values + determined in the first step. + ''' + repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) + global repository_datatypes_count + global base_datatypes_count + global base_sniffers_count + self.uninstall_repository( repository, remove_from_disk=False ) + new_datatypes_count = self.get_datatypes_count() + assert new_datatypes_count == base_datatypes_count, 'Expected %d datatypes, got %d' % ( base_datatypes_count, new_datatypes_count ) + current_sniffers = self.get_sniffers_count() + assert current_sniffers == base_sniffers_count, \ + 'Sniffer count after deactivating proteomics_datatypes_1450 is %d, expected %d' % \ + ( current_sniffers, base_sniffers_count ) + + def test_0025_reactivate_datatypes_repository( self ): + '''Reactivate the deactivated proteomics_datatypes_1450 repository.''' + ''' + This is step 5 - Reactivate proteomics_datatypes, verify that the count of datatypes and sniffers has been + increased by the contents of the repository. + ''' + repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) + global repository_datatypes_count + global base_datatypes_count + global base_sniffers_count + self.reactivate_repository( repository ) + new_datatypes_count = self.get_datatypes_count() + assert new_datatypes_count == base_datatypes_count + repository_datatypes_count, \ + 'Found %d datatypes, expected %d.' % ( new_datatypes_count, base_datatypes_count + repository_datatypes_count ) + current_sniffers = self.get_sniffers_count() + assert current_sniffers > base_sniffers_count, \ + 'Sniffer count after reactivating proteomics_datatypes_1450 is %d, which is not greater than %d' % \ + ( current_sniffers, base_sniffers_count ) + + def test_0030_uninstall_datatypes_repository( self ): + '''Uninstall the installed proteomics_datatypes_1450 repository.''' + ''' + This is step 6 - Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal + to the count determined in step 1. + Uninstall proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values + determined in the first step. + ''' + repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) + global repository_datatypes_count + global base_datatypes_count + self.uninstall_repository( repository, remove_from_disk=True ) + new_datatypes_count = self.get_datatypes_count() + assert new_datatypes_count == base_datatypes_count, 'Expected %d datatypes, got %d' % ( base_datatypes_count, new_datatypes_count ) + current_sniffers = self.get_sniffers_count() + assert current_sniffers == base_sniffers_count, \ + 'Sniffer count after uninstalling proteomics_datatypes_1450 is %d, expected %d' % \ + ( current_sniffers, base_sniffers_count ) + + def test_0035_reinstall_datatypes_repository( self ): + '''Reinstall the uninstalled proteomics_datatypes_1450 repository.''' + ''' + This is step 7 - Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been + increased by the contents of the repository. + ''' + repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) + global repository_datatypes_count + global base_datatypes_count + self.reinstall_repository( repository ) + new_datatypes_count = self.get_datatypes_count() + assert new_datatypes_count == base_datatypes_count + repository_datatypes_count, \ + 'Found %d datatypes, expected %d.' % ( new_datatypes_count, base_datatypes_count + repository_datatypes_count ) + current_sniffers = self.get_sniffers_count() + assert current_sniffers > base_sniffers_count, \ + 'Sniffer count after reinstalling proteomics_datatypes_1450 is %d, which is not greater than %d' % \ + ( current_sniffers, base_sniffers_count ) + + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: UI: Refresh history on history switch
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d0a3879c0708/ Changeset: d0a3879c0708 User: guerler Date: 2013-11-25 21:37:46 Summary: UI: Refresh history on history switch Affected #: 1 file diff -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 -r d0a3879c0708983fccb24b809bfe29d96a8dbb59 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -221,8 +221,7 @@ <%def name="grid_javascripts()"> ${h.js("libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/jquery/jquery.rating" )} - ${handle_refresh_frames()} - + <script type="text/javascript"> var gridView = null; function add_tag_to_grid_filter (tag_name, tag_value) @@ -470,6 +469,8 @@ }); }); </script> + + ${handle_refresh_frames()} </%def> ## Render grid table footer contents. 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 fixes for the tool shed's install and test framework - the test environment including time last tested should now display correctly again (among other fixes).
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/61eacb9ce6d5/ Changeset: 61eacb9ce6d5 User: greg Date: 2013-11-25 21:09:50 Summary: More fixes for the tool shed's install and test framework - the test environment including time last tested should now display correctly again (among other fixes). Affected #: 5 files diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -170,6 +170,7 @@ if key in [ 'tools_functionally_correct', 'time_last_tested' ]: # Automatically update repository_metadata.time_last_tested. repository_metadata.time_last_tested = datetime.datetime.utcnow() + flush_needed = True flush_needed = True if flush_needed: trans.sa_session.add( repository_metadata ) diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -7,7 +7,6 @@ import tempfile import time -from datetime import datetime from optparse import OptionParser from time import strftime @@ -119,21 +118,11 @@ missing_test_components = [] repository = repository_metadata.repository records_checked += 1 - # Create the repository_status dictionary, using the dictionary from the previous test run if available. + # Create the tool_test_results_dict dictionary, using the dictionary from the previous test run if available. if repository_metadata.tool_test_results: - repository_status = repository_metadata.tool_test_results + tool_test_results_dict = repository_metadata.tool_test_results else: - repository_status = {} - # Initialize the repository_status dictionary with the information about the current test environment. - last_test_environment = repository_status.get( 'test_environment', None ) - if last_test_environment is None: - test_environment = get_test_environment() - else: - test_environment = get_test_environment( last_test_environment ) - test_environment[ 'tool_shed_database_version' ] = get_database_version( app ) - test_environment[ 'tool_shed_mercurial_version' ] = __version__.version - test_environment[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) - repository_status[ 'test_environment' ] = test_environment + tool_test_results_dict = {} # Check the next repository revision. changeset_revision = str( repository_metadata.changeset_revision ) name = repository.name @@ -262,6 +251,11 @@ if 'missing_components' in invalid_test: print '# %s' % invalid_test[ 'missing_components' ] if not info_only: + test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) + test_environment_dict[ 'tool_shed_database_version' ] = get_database_version( app ) + test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version + test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) + tool_test_results_dict[ 'test_environment' ] = test_environment_dict # The repository_metadata.time_last_tested column is not changed by this script since no testing is performed here. if missing_test_components: # If functional test definitions or test data are missing, set do_not_test = True if no tool with valid tests has been @@ -278,8 +272,8 @@ repository_metadata.do_not_test = True repository_metadata.tools_functionally_correct = False repository_metadata.missing_test_components = True - repository_status[ 'missing_test_components' ] = missing_test_components - repository_metadata.tool_test_results = repository_status + tool_test_results_dict[ 'missing_test_components' ] = missing_test_components + repository_metadata.tool_test_results = tool_test_results_dict app.sa_session.add( repository_metadata ) app.sa_session.flush() stop = time.time() diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -235,7 +235,7 @@ 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, + def __init__( self, id=None, architecture=None, galaxy_database_version=None, galaxy_revision=None, python_version=None, system=None, time_tested=None, tool_shed_database_version=None, tool_shed_mercurial_version=None, tool_shed_revision=None ): self.id = id self.architecture = architecture @@ -243,7 +243,7 @@ self.galaxy_revision = galaxy_revision self.python_version = python_version self.system = system - self.time_last_tested = time_last_tested + self.time_tested = time_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 @@ -743,11 +743,6 @@ ) 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: @@ -836,12 +831,17 @@ label='Valid tools' ) containers_dict[ 'valid_tools' ] = valid_tools_root_folder # Tool test results container. - if 'tool_test_results' not in exclude and tool_test_results and len( tool_test_results ) > 1: - # Only create and populate this folder if there are actual tool test results to display, since the display of the 'Test environment' - # folder by itself can be misleading. We check for more than a single entry in the tool_test_results dictionary because it may have - # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", "installation_errors", "missing_test_components" - # "skipped_tests", "not_tested" or any other entry that may be added in the future. - folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested ) + tool_test_results = repository_metadata.tool_test_results + # Only create and populate this folder if there are actual tool test results to display. + if can_display_tool_test_results( tool_test_results, exclude=exclude ): + time_tested = repository_metadata.time_last_tested + if time_tested is not None: + time_tested = time_ago( time_tested ) + folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, + folder_id, + tool_test_results, + time_tested, + label='Tool test results' ) containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder # Workflows container. if metadata: @@ -1052,30 +1052,39 @@ 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 ): +def build_tool_test_results_folder( trans, folder_id, tool_test_results_dict, time_tested, label='Tool test results' ): """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.get( 'test_environment', None ) - if test_environment_dict: + if test_environment_dict is not None: 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 ) + 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_tested = time_tested + 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', '' ) test_environment = TestEnvironment( id=1, - 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.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', '' ) ) + architecture=architecture, + galaxy_database_version=galaxy_database_version, + galaxy_revision=galaxy_revision, + python_version=python_version, + system=system, + time_tested=time_tested, + tool_shed_database_version=tool_shed_database_version, + tool_shed_mercurial_version=tool_shed_mercurial_version, + tool_shed_revision=tool_shed_revision ) folder.test_environments.append( test_environment ) not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) if not_tested_dict: @@ -1238,6 +1247,26 @@ workflows_root_folder = None return folder_id, workflows_root_folder +def can_display_tool_test_results( tool_test_results_dict, exclude=None ): + # Only create and populate the tool_test_results container if there are actual tool test results to display. + if exclude is None: + exclude = [] + if 'tool_test_results' in exclude: + return False + if tool_test_results_dict: + # We check for more than a single entry in the tool_test_results dictionary because it may have + # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", + # "installation_errors", "missing_test_components" "skipped_tests", "not_tested" or any other + # entry that may be added in the future. + display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', 'not_tested', 'passed_tests', 'skipped_tests' ] + for k, v in tool_test_results_dict.items(): + if k in display_entries: + # We've discovered an entry that can be displayed, so see if it has a value since displaying + # empty lists is not desired. + if v: + return True + return False + def cast_empty_repository_dependency_folders( folder, repository_dependency_id ): """ Change any empty folders contained within the repository dependencies container into a repository dependency since it has no repository dependencies diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -909,7 +909,7 @@ id="libraryItem-rte-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table class="grid" id="test_environment"> - <tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr> + <tr><td><b>Time tested:</b> ${test_environment.time_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> diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 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 @@ -21,7 +21,6 @@ import threading import unittest import urllib -import urllib2 from time import strftime # Assume we are run from the galaxy root directory, add lib to the python path @@ -42,8 +41,8 @@ sys.path = new_path from functional_tests import generate_config_file + from galaxy import eggs -from galaxy.util import unicodify eggs.require( "nose" ) eggs.require( "NoseHTML" ) @@ -53,10 +52,14 @@ eggs.require( "PasteDeploy" ) eggs.require( "Cheetah" ) eggs.require( "simplejson" ) +eggs.require( 'mercurial' ) import simplejson import twill +from datetime import datetime +from mercurial import __version__ + # This should not be required, but it is under certain conditions, thanks to this bug: http://code.google.com/p/python-nose/issues/detail?id=284 eggs.require( "pysqlite" ) @@ -76,13 +79,20 @@ import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_dependency_util +from galaxy.web.framework.helpers import time_ago + import nose.core import nose.config import nose.loader import nose.plugins.manager from nose.plugins import Plugin -from base.util import parse_tool_panel_config, get_database_version, get_test_environment, get_repository_current_revision +from base.util import get_database_version +from base.util import get_repository_current_revision +from base.util import get_test_environment +from base.util import parse_tool_panel_config + +from galaxy.util import unicodify from common import update @@ -472,29 +482,27 @@ return repository_dicts, error_message def get_tool_info_from_test_id( test_id ): - ''' - Test IDs come in the form test_tool_number (functional.test_toolbox.TestForTool_toolshed_url/repos/owner/repository_name/tool_id/tool_version) + """ + Test IDs come in the form test_tool_number + (functional.test_toolbox.TestForTool_toolshed_url/repos/owner/repository_name/tool_id/tool_version) We want the tool ID and tool version. - ''' + """ parts = test_id.replace( ')', '' ).split( '/' ) tool_version = parts[ -1 ] tool_id = parts[ -2 ] return tool_id, tool_version -def get_tool_test_results_from_api( tool_shed_url, metadata_revision_id ): +def get_tool_test_results_dict( tool_shed_url, encoded_repository_metadata_id ): error_message = '' - api_path = [ 'api', 'repository_revisions', metadata_revision_id ] + api_path = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata, error_message = json_from_url( api_url ) if error_message: return None, error_message tool_test_results = repository_metadata.get( 'tool_test_results', {} ) - # If, for some reason, the script that checks for functional tests has not run, tool_test_results will be None. - if tool_test_results is None: - return {}, error_message return tool_test_results, error_message -def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, repository_status_dict, results_dict ): +def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dict, results_dict ): """Handle missing repository or tool dependencies for an installed repository.""" # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed @@ -508,7 +516,7 @@ name=dependency.name, version=dependency.version, error_message=dependency.error_message ) - repository_status_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) for dependency in repository.missing_repository_dependencies: log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ ( str( dependency.name ), str( dependency.changeset_revision ), str( dependency.owner ), unicodify( dependency.error_message ) ) ) @@ -517,12 +525,12 @@ owner=dependency.owner, changeset_revision=dependency.changeset_revision, error_message=dependency.error_message ) - repository_status_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) # Record the status of this repository in the tool shed. params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=True ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES # is set to 'true'. @@ -629,27 +637,13 @@ # "tool_shed_url": "http://toolshed.local:10001", # "url": "/api/repository_revisions/529fd61ab1c6cc36", # "user_id": "529fd61ab1c6cc36" } - metadata_revision_id = repository_dict.get( 'id', None ) + encoded_repository_metadata_id = repository_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url # Get the name and owner out of the repository info dict. name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - # Populate the repository_status_dict. - repository_status_dict, error_message = get_tool_test_results_from_api( galaxy_tool_shed_url, metadata_revision_id ) - if error_message: - return None, error_message - if 'test_environment' not in repository_status_dict: - repository_status_dict[ 'test_environment' ] = {} - test_environment = get_test_environment( repository_status_dict[ 'test_environment' ] ) - test_environment[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) - repository_status_dict[ 'test_environment' ] = test_environment - repository_status_dict[ 'passed_tests' ] = [] - repository_status_dict[ 'failed_tests' ] = [] - repository_status_dict[ 'skip_reason' ] = None - repository_status_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) # See if this repository should be skipped for any reason. skip_this_repository = False skip_reason = None @@ -661,82 +655,104 @@ skip_reason = reason break if skip_this_repository: - repository_status_dict[ 'not_tested' ] = dict( reason=skip_reason ) + tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) params = dict( tools_functionally_correct=False, do_not_test=False ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) else: - repository, error_message = install_repository( app, repository_dict ) + # Populate the tool_test_results_dict. + tool_test_results_dict, error_message = get_tool_test_results_dict( galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: - repository_status_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - - # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) - try: - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except Exception, e: - error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) - log.exception( error_message ) - test_result = dict( tool_shed=galaxy_tool_shed_url, - name=name, - owner=owner, - changeset_revision=changeset_revision, - error_message=error_message ) - repository_status_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params = dict( tools_functionally_correct=False, - test_install_error=True, - do_not_test=False ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) - try: - if deactivate: - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) + log.debug( error_message ) + else: + # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered + # information in the 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories + # that are missing test components. We need to be careful to not lose this information. For all other repositories, + # no changes will have been made to this dictionary by the preparation script, and tool_test_results_dict will be None. + # Initialize the tool_test_results_dict dictionary with the information about the current test environment. + test_environment_dict = tool_test_results_dict.get( 'test_environent', None ) + test_environment_dict = get_test_environment( test_environment_dict ) + test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) + test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) + tool_test_results_dict[ 'test_environment' ] = test_environment_dict + tool_test_results_dict[ 'passed_tests' ] = [] + tool_test_results_dict[ 'failed_tests' ] = [] + tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) + repository, error_message = install_repository( app, repository_dict ) + if error_message: + tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message + # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. + log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) + try: + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + except Exception, e: + error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) + log.exception( error_message ) + test_result = dict( tool_shed=galaxy_tool_shed_url, + name=name, + owner=owner, + changeset_revision=changeset_revision, + error_message=error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + params = dict( tools_functionally_correct=False, + test_install_error=True, + do_not_test=False ) + + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + try: + if deactivate: + # We are deactivating this repository and all of its repository dependencies. + deactivate_repository( app, repository_dict ) + else: + # We are uninstalling this repository and all of its repository dependencies. + uninstall_repository( app, repository_dict ) + except: + log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) + results_dict[ 'repositories_failed_install' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + log.debug( 'Repository %s failed to install correctly.' % str( name ) ) + else: + # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed + remove_install_tests() + log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository + # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, + # and the tools_functionally_correct flag to False, as well as updating tool_test_results. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, + from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The + # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the + # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are + # missing test components. + if 'missing_test_components' not in tool_test_results_dict: + tool_test_results_dict[ 'missing_test_components' ] = [] + missing_tool_dependencies = get_missing_tool_dependencies( repository ) + if missing_tool_dependencies or repository.missing_repository_dependencies: + results_dict = handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dict, + results_dict ) else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository( app, repository_dict ) - except: - log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) - results_dict[ 'repositories_failed_install' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - log.debug( 'Repository %s failed to install correctly.' % str( name ) ) - else: - # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed - remove_install_tests() - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository - # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, - # and the tools_functionally_correct flag to False, as well as updating tool_test_results. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - if 'missing_test_components' not in repository_status_dict: - repository_status_dict[ 'missing_test_components' ] = [] - missing_tool_dependencies = get_missing_tool_dependencies( repository ) - if missing_tool_dependencies or repository.missing_repository_dependencies: - results_dict = handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - repository_status_dict, - results_dict ) - else: - # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional - # test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) - try: - results_dict = test_repository_tools( app, repository, repository_dict, repository_status_dict, results_dict ) - except Exception, e: - exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) - log.exception( exception_message ) - repository_status_dict[ 'failed_tests' ].append( exception_message ) - # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=False ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) - results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - total_repositories_tested += 1 + # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional + # test framework can find it. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) + log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) + try: + results_dict = test_repository_tools( app, repository, repository_dict, tool_test_results_dict, results_dict ) + except Exception, e: + exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) + log.exception( exception_message ) + tool_test_results_dict[ 'failed_tests' ].append( exception_message ) + # Record the status of this repository in the tool shed. + params = dict( tools_functionally_correct=False, + do_not_test=False, + test_install_error=False ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested return results_dict, error_message @@ -794,12 +810,20 @@ return exclude_list def register_test_result( url, test_results_dict, repository_dict, params ): - """Update the repository metadata tool_test_results and appropriate flags using the API.""" + """ + Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method + updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags + to the appropriate values and updates the time_last_tested field to the value of the received time_tested. + """ if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: return {} else: metadata_revision_id = repository_dict.get( 'id', None ) + log.debug("RRR In register_test_result, metadata_revision_id: %s" % str( metadata_revision_id )) if metadata_revision_id is not None: + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + time_tested = datetime.utcnow() + test_results_dict[ 'time_last_tested' ] = time_ago( time_tested ) params[ 'tool_test_results' ] = test_results_dict url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) try: @@ -876,7 +900,7 @@ for repository in repositories_by_owner[ owner ]: print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) -def test_repository_tools( app, repository, repository_dict, repository_status_dict, results_dict ): +def test_repository_tools( app, repository, repository_dict, tool_test_results_dict, results_dict ): """Test tools contained in the received repository.""" name = str( repository.name ) owner = str( repository.owner ) @@ -898,12 +922,12 @@ test_identifier = '%s/%s' % ( owner, name ) passed_tests = plugin.getTestStatus( test_identifier ) break - repository_status_dict[ 'passed_tests' ] = [] + tool_test_results_dict[ 'passed_tests' ] = [] for test_id in passed_tests: # Normalize the tool ID and version display. tool_id, tool_version = get_tool_info_from_test_id( test_id ) test_result = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) - repository_status_dict[ 'passed_tests' ].append( test_result ) + tool_test_results_dict[ 'passed_tests' ].append( test_result ) if success: # This repository's tools passed all functional tests. Update the repository_metadata table in the tool shed's database # to reflect that. Call the register_test_result method, which executes a PUT request to the repository_revisions API @@ -913,20 +937,16 @@ params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: - repository_status_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) - # Call the register_test_result method, which executes a PUT request to the repository_revisions API controller with the outcome - # of the tests, and updates tool_test_results with the relevant log data. - # This also sets the do_not_test and tools_functionally correct flags to the appropriate values, and updates the time_last_tested - # field to today's date. + tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ ( str( changeset_revision ), str( name ) ) ) # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the @@ -1256,7 +1276,7 @@ return 1 if __name__ == "__main__": - # The repository_status_dict should always have the following structure: + # The tool_test_results_dict should always have the following structure: # { # "test_environment": # { 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: UI: revert changes from 3f630f9 that broke links in PopupMenus
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1fbb0cb8dd58/ Changeset: 1fbb0cb8dd58 User: carlfeberhard Date: 2013-11-25 20:59:51 Summary: UI: revert changes from 3f630f9 that broke links in PopupMenus Affected #: 2 files diff -r 01b5a1a68ae6901936b6948769aa66b446e52e53 -r 1fbb0cb8dd5865185b186e609d747668510a25a8 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -232,7 +232,7 @@ // if the option has 'func', call that function when the anchor is clicked if( option.func ){ - $( this ).children( 'a.popupmenu-option' ).mousedown( function( event ){ + $( this ).children( 'a.popupmenu-option' ).click( function( event ){ option.func.call( menu, event, option ); // bubble up so that an option click will call the close behavior //return false; @@ -292,7 +292,7 @@ // function to close popup and unbind itself var menu = this; var closePopupWhenClicked = function( $elClicked ){ - $elClicked.one( "mousedown.close_popup", function(){ + $elClicked.one( "click.close_popup", function(){ menu.remove(); }); }; diff -r 01b5a1a68ae6901936b6948769aa66b446e52e53 -r 1fbb0cb8dd5865185b186e609d747668510a25a8 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").mousedown(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var b=this;var a=function(c){c.one("mousedown.close_popup",function(){b.remove()})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((a.target)?(' target="'+a.target+'"'):("")),' href="',((a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};var searchInput=function(k){var a=27,h=13,i=$("<div/>"),b={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onsearch:function(l){},minSearchLen:0,escWillClear:true,oninit:function(){}};if(jQuery.type(k)==="object"){k=jQuery.extend(true,b,k)}function d(l){var m=$(this).parent().children("input");m.val("");m.trigger("clear:searchInput");k.onclear()}function j(m,l){$(this).trigger("search:searchInput",l);k.onsearch(l)}function c(){return['<input type="text" name="',k.name,'" placeholder="',k.placeholder,'" ','class="search-query ',k.classes,'" ',"/>"].join("")}function g(){return $(c()).css({width:"100%","padding-right":"24px"}).focus(function(l){$(this).select()}).keyup(function(m){if(m.which===a&&k.escWillClear){d.call(this,m)}else{var l=$(this).val();if((m.which===h)||(k.minSearchLen&&l.length>=k.minSearchLen)){j.call(this,m,l)}else{if(!l.length){d.call(this,m)}}}}).val(k.initialVal)}function f(){return'<span class="search-clear fa fa-times-circle"></span>'}function e(){return $(f()).css({position:"absolute",right:"15px","font-size":"1.4em","line-height":"23px",color:"grey"}).click(function(l){d.call(this,l)})}return i.append([g(),e()])};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a 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commit/galaxy-central: carlfeberhard: History panel: use SessionStorageModel, remove PersistentStorage
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01b5a1a68ae6/ Changeset: 01b5a1a68ae6 User: carlfeberhard Date: 2013-11-25 20:24:14 Summary: History panel: use SessionStorageModel, remove PersistentStorage Affected #: 5 files diff -r 0e1d539dcfcb3246f144258514a43e07a514b52e -r 01b5a1a68ae6901936b6948769aa66b446e52e53 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -92,18 +92,30 @@ /** Backbone model that syncs to the browser's sessionStorage API. */ var SessionStorageModel = Backbone.Model.extend({ - initialize : function( hash, x, y, z ){ - if( !hash || !hash.hasOwnProperty( 'id' ) ){ - throw new Error( 'SessionStorageModel needs an id on init' ); - } - // immed. save the passed in model and save on any change to it - this.save(); + initialize : function( initialAttrs ){ + // create unique id if none provided + initialAttrs.id = ( !_.isString( initialAttrs.id ) )?( _.uniqueId() ):( initialAttrs.id ); + this.id = initialAttrs.id; + + // load existing from storage (if any), clear any attrs set by bbone before init is called, + // layer initial over existing and defaults, and save + var existing = ( !this.isNew() )?( this._read( this ) ):( {} ); + this.clear({ silent: true }); + this.save( _.extend( {}, this.defaults, existing, initialAttrs ), { silent: true }); + + // save on any change to it immediately this.on( 'change', function(){ this.save(); }); }, + + /** override of bbone sync to save to sessionStorage rather than REST + * bbone options (success, errror, etc.) should still apply + */ sync : function( method, model, options ){ - model.trigger('request', model, {}, options); + if( !options.silent ){ + model.trigger( 'request', model, {}, options ); + } var returned; switch( method ){ case 'create' : returned = this._create( model ); break; @@ -118,23 +130,41 @@ } return returned; }, + + /** set storage to the stringified item */ _create : function( model ){ var json = model.toJSON(), set = sessionStorage.setItem( model.id, JSON.stringify( json ) ); return ( set === null )?( set ):( json ); }, + + /** read and parse json from storage */ _read : function( model ){ - return JSON.parse( sessionStorage.getItem( model.id, JSON.stringify( model.toJSON() ) ) ); + return JSON.parse( sessionStorage.getItem( model.id ) ); }, + + /** set storage to the item (alias to create) */ _update : function( model ){ return model._create( model ); }, + + /** remove the item from storage */ _delete : function( model ){ return sessionStorage.removeItem( model.id ); }, + + /** T/F whether sessionStorage contains the model's id (data is present) */ isNew : function(){ return !sessionStorage.hasOwnProperty( this.id ); + }, + + _log : function(){ + return JSON.stringify( this.toJSON(), null, ' ' ); + }, + toString : function(){ + return 'SessionStorageModel(' + this.id + ')'; } + }); (function(){ SessionStorageModel.prototype = _.omit( SessionStorageModel.prototype, 'url', 'urlRoot' ); @@ -142,136 +172,6 @@ //============================================================================== -/** - * @class persistent storage adapter. - * Provides an easy interface to object based storage using method chaining. - * Allows easy change of the storage engine used (h5's local storage?). - * @augments StorageRecursionHelper - * - * @param {String} storageKey : the key the storage engine will place the storage object under - * @param {Object} storageDefaults : [optional] initial object to set up storage with - * - * @example - * // example of construction and use - * HistoryPanel.storage = new PersistanStorage( HistoryPanel.toString(), { visibleItems, {} }); - * itemView.bind( 'toggleBodyVisibility', function( id, visible ){ - * if( visible ){ - * HistoryPanel.storage.get( 'visibleItems' ).set( id, true ); - * } else { - * HistoryPanel.storage.get( 'visibleItems' ).deleteKey( id ); - * } - * }); - * @constructor - */ -var PersistentStorage = function( storageKey, storageDefaults ){ - if( !storageKey ){ - throw( "PersistentStorage needs storageKey argument" ); - } - storageDefaults = storageDefaults || {}; - - // ~constants for the current engine - var STORAGE_ENGINE = sessionStorage, - STORAGE_ENGINE_GETTER = function sessionStorageGet( key ){ - var item = this.getItem( key ); - return ( item !== null )?( JSON.parse( this.getItem( key ) ) ):( null ); - }, - STORAGE_ENGINE_SETTER = function sessionStorageSet( key, val ){ - return this.setItem( key, JSON.stringify( val ) ); - }, - STORAGE_ENGINE_KEY_DELETER = function sessionStorageDel( key ){ return this.removeItem( key ); }; - - /** Inner, recursive, private class for method chaining access. - * @name StorageRecursionHelper - * @constructor - */ - function StorageRecursionHelper( data, parent ){ - //console.debug( 'new StorageRecursionHelper. data:', data ); - data = data || {}; - parent = parent || null; - - return /** @lends StorageRecursionHelper.prototype */{ - /** get a value from the storage obj named 'key', - * if it's an object - return a new StorageRecursionHelper wrapped around it - * if it's something simpler - return the value - * if this isn't passed a key - return the data at this level of recursion - */ - get : function( key ){ - //console.debug( this + '.get', key ); - if( key === undefined ){ - return data; - } else if( data.hasOwnProperty( key ) ){ - return ( jQuery.type( data[ key ] ) === 'object' )? - ( new StorageRecursionHelper( data[ key ], this ) ) - :( data[ key ] ); - } - return undefined; - }, - /** get the underlying data based on this key */ - // set a value on the current data - then pass up to top to save current entire object in storage - set : function( key, value ){ - //TODO: add parameterless variation setting the data somehow - // ??: difficult bc of obj by ref, closure - //console.debug( this + '.set', key, value ); - data[ key ] = value; - this._save(); - return this; - }, - // remove a key at this level - then save entire (as 'set' above) - deleteKey : function( key ){ - //console.debug( this + '.deleteKey', key ); - delete data[ key ]; - this._save(); - return this; - }, - // pass up the recursion chain (see below for base case) - _save : function(){ - //console.debug( this + '.save', parent ); - return parent._save(); - }, - toString : function(){ - return ( 'StorageRecursionHelper(' + data + ')' ); - } - }; - } - - //??: more readable to make another class? - var returnedStorage = {}, - // attempt to get starting data from engine... - data = STORAGE_ENGINE_GETTER.call( STORAGE_ENGINE, storageKey ); - - // ...if that fails, use the defaults (and store them) - if( data === null || data === undefined ){ - data = jQuery.extend( true, {}, storageDefaults ); - STORAGE_ENGINE_SETTER.call( STORAGE_ENGINE, storageKey, data ); - } - - // the object returned by this constructor will be a modified StorageRecursionHelper - returnedStorage = new StorageRecursionHelper( data ); - jQuery.extend( returnedStorage, /** @lends PersistentStorage.prototype */{ - /** The base case for save()'s upward recursion - save everything to storage. - * @private - * @param {Any} newData data object to save to storage - */ - _save : function( newData ){ - //console.debug( returnedStorage, '._save:', JSON.stringify( returnedStorage.get() ) ); - return STORAGE_ENGINE_SETTER.call( STORAGE_ENGINE, storageKey, returnedStorage.get() ); - }, - /** Delete function to remove the entire base data object from the storageEngine. - */ - destroy : function(){ - //console.debug( returnedStorage, '.destroy:' ); - return STORAGE_ENGINE_KEY_DELETER.call( STORAGE_ENGINE, storageKey ); - }, - /** String representation. - */ - toString : function(){ return 'PersistentStorage(' + storageKey + ')'; } - }); - - return returnedStorage; -}; - - -//============================================================================== var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */{ /** */ diff -r 0e1d539dcfcb3246f144258514a43e07a514b52e -r 01b5a1a68ae6901936b6948769aa66b446e52e53 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -93,8 +93,8 @@ var $newRender = $( HDABaseView.templates.skeleton( this.model.toJSON() ) ); $newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() ); $newRender.children( '.dataset-body' ).replaceWith( this._render_body() ); + this._setUpBehaviors( $newRender ); //this._renderSelectable( $newRender ); - this._setUpBehaviors( $newRender ); // fade the old render out (if desired) if( fade ){ diff -r 0e1d539dcfcb3246f144258514a43e07a514b52e -r 01b5a1a68ae6901936b6948769aa66b446e52e53 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -3,6 +3,44 @@ "mvc/dataset/hda-base", "mvc/dataset/hda-edit" ], function( historyModel, hdaBase, hdaEdit ){ + + +// ============================================================================ +/** session storage for individual history preferences + */ +var HistoryPanelPrefs = SessionStorageModel.extend({ + defaults : { + //TODO:?? expandedHdas to array? + expandedHdas : {}, + //TODO:?? move to user? + show_deleted : false, + show_hidden : false + //TODO: add scroll position? + }, + /** add an hda id to the hash of expanded hdas */ + addExpandedHda : function( id ){ + this.save( 'expandedHdas', _.extend( this.get( 'expandedHdas' ), _.object([ id ], [ true ]) ) ); + }, + /** remove an hda id from the hash of expanded hdas */ + removeExpandedHda : function( id ){ + this.save( 'expandedHdas', _.omit( this.get( 'expandedHdas' ), id ) ); + }, + toString : function(){ + return 'HistoryPanelPrefs(' + this.id + ')'; + } +}); + +/** key string to store each histories settings under */ +HistoryPanelPrefs.historyStorageKey = function historyStorageKey( historyId ){ + // class lvl for access w/o instantiation + if( !historyId ){ + throw new Error( 'HistoryPanelPrefs.historyStorageKey needs valid id: ' + historyId ); + } + // single point of change + return ( 'history:' + historyId ); +}; + + /* ============================================================================= Backbone.js implementation of history panel @@ -216,8 +254,8 @@ // - hdas w/o details will have summary data only (name, hid, deleted, visible, state, etc.)) /** (re-)loads the user's current history & hdas w/ details */ - // implemented as a 'fresh start' or for when there is no model (intial panel render) loadCurrentHistory : function( attributes ){ + // implemented as a 'fresh start' or for when there is no model (intial panel render) var panel = this; return this.loadHistoryWithHDADetails( 'current', attributes ) .then(function( historyData, hdaData ){ @@ -334,7 +372,7 @@ return this; }, - // alias to the model. Updates the hda list only (not the history) + /** alias to the model. Updates the hda list only (not the history) */ refreshHdas : function( detailIds, options ){ if( this.model ){ return this.model.refresh( detailIds, options ); @@ -344,8 +382,6 @@ }, // ------------------------------------------------------------------------ browser stored prefs -//TODO: simplify - /** Set up client side storage. Currently PersistanStorage keyed under 'HistoryPanel.<id>' * @param {Object} initiallyExpanded * @param {Boolean} show_deleted whether to show deleted HDAs (overrides stored) @@ -353,55 +389,31 @@ * @see PersistentStorage */ _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){ - //this.log( '_setUpWebStorage, initiallyExpanded:', initiallyExpanded, - // 'show_deleted:', show_deleted, 'show_hidden', show_hidden ); + //console.debug( '_setUpWebStorage', initiallyExpanded, show_deleted, show_hidden ); + this.storage = new HistoryPanelPrefs({ + id: HistoryPanelPrefs.historyStorageKey( this.model.get( 'id' ) ) + }); - //TODO: add scroll position? - - // data that needs to be persistent over page refreshes - // (note the key function which uses the history id as well) - this.storage = new PersistentStorage( this._getStorageKey( this.model.get( 'id' ) ), { - expandedHdas : {}, - show_deleted : false, - show_hidden : false - }); - this.log( this + ' (prev) storage:', JSON.stringify( this.storage.get(), null, 2 ) ); - - // expanded Hdas is a map of hda.ids -> a boolean rep'ing whether this hda's body is expanded + // expanded Hdas is a map of hda.ids -> a boolean repr'ing whether this hda's body is already expanded // store any pre-expanded ids passed in - if( initiallyExpanded ){ + if( _.isObject( initiallyExpanded ) ){ this.storage.set( 'exandedHdas', initiallyExpanded ); } - //TODO: should be global pref? (not specific to each history) - - // get the show_deleted/hidden settings giving priority to values passed in, - // using web storage otherwise + // get the show_deleted/hidden settings giving priority to values passed in, using web storage otherwise // if the page has specifically requested show_deleted/hidden, these will be either true or false // (as opposed to undefined, null) - and we give priority to that setting - if( ( show_deleted === true ) || ( show_deleted === false ) ){ - // save them to web storage + if( _.isBoolean( show_deleted ) ){ this.storage.set( 'show_deleted', show_deleted ); } - if( ( show_hidden === true ) || ( show_hidden === false ) ){ + if( _.isBoolean( show_hidden ) ){ this.storage.set( 'show_hidden', show_hidden ); } - // if the page hasn't specified whether to show_deleted/hidden, pull show_deleted/hidden from the web storage - this.show_deleted = this.storage.get( 'show_deleted' ); - this.show_hidden = this.storage.get( 'show_hidden' ); - //this.log( 'this.show_deleted:', this.show_deleted, 'show_hidden', this.show_hidden ); + this.trigger( 'new-storage', this.storage, this ); this.log( this + ' (init\'d) storage:', this.storage.get() ); }, - /** key string to store each histories settings under */ - _getStorageKey : function( id ){ - if( !id ){ - throw new Error( '_getStorageKey needs valid id: ' + id ); - } - return ( 'history:' + id ); - }, - /** clear all stored history panel data */ clearWebStorage : function(){ for( var key in sessionStorage ){ @@ -417,11 +429,11 @@ return ( this.storage )?( this.storage.get() ):( {} ); } //TODO: make storage engine generic - var item = sessionStorage.getItem( this._getStorageKey( historyId ) ); + var item = sessionStorage.getItem( HistoryPanelPrefs.historyStorageKey( historyId ) ); return ( item === null )?( {} ):( JSON.parse( item ) ); }, - /** get all the map of expaneded hda ids for the given history id */ + /** get an array of expanded hda ids for the given history id */ getExpandedHdaIds : function( historyId ){ var expandedHdas = this.getStoredOptions( historyId ).expandedHdas; return (( _.isEmpty( expandedHdas ) )?( [] ):( _.keys( expandedHdas ) )); @@ -509,7 +521,7 @@ */ createHdaView : function( hda ){ var hdaId = hda.get( 'id' ), - expanded = this.storage.get( 'expandedHdas' ).get( hdaId ), + expanded = this.storage.get( 'expandedHdas' )[ hdaId ], hdaView = new this.HDAView({ model : hda, expanded : expanded, @@ -529,10 +541,10 @@ var historyView = this; // maintain a list of hdas whose bodies are expanded hdaView.on( 'body-expanded', function( id ){ - historyView.storage.get( 'expandedHdas' ).set( id, true ); + historyView.storage.addExpandedHda( id ); }); hdaView.on( 'body-collapsed', function( id ){ - historyView.storage.get( 'expandedHdas' ).deleteKey( id ); + historyView.storage.removeExpandedHda( id ); }); //TODO: remove? hdaView.on( 'error', function( model, xhr, options, msg ){ diff -r 0e1d539dcfcb3246f144258514a43e07a514b52e -r 01b5a1a68ae6901936b6948769aa66b446e52e53 static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b,a,d,c){if(!b||!b.hasOwnProperty("id")){throw new Error("SessionStorageModel needs an id on init")}this.save();this.on("change",function(){this.save()})},sync:function(d,b,a){b.trigger("request",b,{},a);var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id,JSON.stringify(a.toJSON())))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var PersistentStorage=function(k,g){if(!k){throw ("PersistentStorage needs storageKey argument")}g=g||{};var i=sessionStorage,c=function j(m){var n=this.getItem(m);return(n!==null)?(JSON.parse(this.getItem(m))):(null)},b=function e(m,n){return this.setItem(m,JSON.stringify(n))},d=function f(m){return this.removeItem(m)};function a(n,m){n=n||{};m=m||null;return{get:function(o){if(o===undefined){return n}else{if(n.hasOwnProperty(o)){return(jQuery.type(n[o])==="object")?(new a(n[o],this)):(n[o])}}return undefined},set:function(o,p){n[o]=p;this._save();return this},deleteKey:function(o){delete n[o];this._save();return this},_save:function(){return m._save()},toString:function(){return("StorageRecursionHelper("+n+")")}}}var l={},h=c.call(i,k);if(h===null||h===undefined){h=jQuery.extend(true,{},g);b.call(i,k,h)}l=new a(h);jQuery.extend(l,{_save:function(m){return b.call(i,k,l.get())},destroy:function(){return d.call(i,k)},toString:function(){return"PersistentStorage("+k+")"}});return l};var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},toggle:function(){if(this.HUAVOptions.$elementShown.is(":hidden")){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}else{if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}}}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},toggle:function(){if(this.HUAVOptions.$elementShown.is(":hidden")){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}else{if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}}}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file diff -r 0e1d539dcfcb3246f144258514a43e07a514b52e -r 01b5a1a68ae6901936b6948769aa66b446e52e53 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(d,b,a){var c=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(e){e=e||{};if(e.logger){this.logger=e.logger}this.log(this+".initialize:",e);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];if(this.model){this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden);this._setUpModelEventHandlers()}if(e.onready){e.onready.call(this)}},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(e){this.log(this+"",arguments)},this)}},errorHandler:function(g,j,f,i,h){var e=this._parseErrorMessage(g,j,f,i,h);if(j&&j.status===0&&j.readyState===0){}else{if(j&&j.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",e.message,e.details)})}else{this.displayMessage("error",e.message,e.details)}}}},_parseErrorMessage:function(h,l,g,k,j){var f=Galaxy.currUser,e={message:this._bePolite(k),details:{user:(f instanceof User)?(f.toJSON()):(f+""),source:(h instanceof Backbone.Model)?(h.toJSON()):(h+""),xhr:l,options:(l)?(_.omit(g,"xhr")):(g)}};_.extend(e.details,j||{});if(l&&_.isFunction(l.getAllResponseHeaders)){var i=l.getAllResponseHeaders();i=_.compact(i.split("\n"));i=_.map(i,function(m){return m.split(": ")});e.details.xhr.responseHeaders=_.object(i)}return e},_bePolite:function(e){e=e||_l("An error occurred while getting updates from the server");return e+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(f){var e=this;return this.loadHistoryWithHDADetails("current",f).then(function(h,g){e.trigger("current-history",e)})},switchToHistory:function(h,g){var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories/"+h+"/set_as_current")};return this.loadHistoryWithHDADetails(h,g,f).then(function(j,i){e.trigger("switched-history",e)})},createNewHistory:function(g){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,g,f).then(function(i,h){e.trigger("new-history",e)})},loadHistoryWithHDADetails:function(h,g,f,j){var e=this,i=function(k){return e.getExpandedHdaIds(k.id)};return this.loadHistory(h,g,f,j,i)},loadHistory:function(h,g,f,k,i){this.trigger("loading-history",this);g=g||{};var e=this;var j=d.History.getHistoryData(h,{historyFn:f,hdaFn:k,hdaDetailIds:g.initiallyExpanded||i});return this._loadHistoryFromXHR(j,g).fail(function(n,l,m){e.trigger("error",e,n,g,_l("An error was encountered while "+l),{historyId:h,history:m||{}})}).always(function(){e.trigger("loading-done",e)})},_loadHistoryFromXHR:function(g,f){var e=this;g.then(function(h,i){e.setModel(h,i,f)});g.fail(function(i,h){e.render()});return g},setModel:function(g,e,f){f=f||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){g.user=Galaxy.currUser.toJSON()}this.model=new d.History(g,e,f);this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(f,e){if(this.model){return this.model.refresh(f,e)}return $.when()},_setUpWebStorage:function(f,e,g){this.storage=new PersistentStorage(this._getStorageKey(this.model.get("id")),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(f){this.storage.set("exandedHdas",f)}if((e===true)||(e===false)){this.storage.set("show_deleted",e)}if((g===true)||(g===false)){this.storage.set("show_hidden",g)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},_getStorageKey:function(e){if(!e){throw new Error("_getStorageKey needs valid id: "+e)}return("history:"+e)},clearWebStorage:function(){for(var e in sessionStorage){if(e.indexOf("history:")===0){sessionStorage.removeItem(e)}}},getStoredOptions:function(f){if(!f||f==="current"){return(this.storage)?(this.storage.get()):({})}var e=sessionStorage.getItem(this._getStorageKey(f));return(e===null)?({}):(JSON.parse(e))},getExpandedHdaIds:function(e){var f=this.getStoredOptions(e).expandedHdas;return((_.isEmpty(f))?([]):(_.keys(f)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(f,h,e,g){this.errorHandler(f,h,e,g)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this);this.model.hdas.on("state:ready",function(f,g,e){if((!f.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[f.id])}},this)},addHdaView:function(h){this.log("add."+this,h);var f=this;if(!h.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function g(j){var i=f.$el.find(f.emptyMsgSelector);if(i.is(":visible")){i.fadeOut(f.fxSpeed,j)}else{j()}},function e(j){f.scrollToTop();var i=f.$el.find(f.datasetsSelector);f.createHdaView(h).$el.hide().prependTo(i).slideDown(f.fxSpeed)}])},createHdaView:function(g){var f=g.get("id"),e=this.storage.get("expandedHdas").get(f),h=new this.HDAView({model:g,expanded:e,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(h);this.hdaViews[f]=h;return h.render()},_setUpHdaListeners:function(f){var e=this;f.on("body-expanded",function(g){e.storage.get("expandedHdas").set(g,true)});f.on("body-collapsed",function(g){e.storage.get("expandedHdas").deleteKey(g)});f.on("error",function(h,j,g,i){e.errorHandler(h,j,g,i)})},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},render:function(g,h){g=(g===undefined)?(this.fxSpeed):(g);var e=this,f;if(this.model){f=this.renderModel()}else{f=this.renderWithoutModel()}$(e).queue("fx",[function(i){if(g&&e.$el.is(":visible")){e.$el.fadeOut(g,i)}else{i()}},function(i){e.$el.empty();if(f){e.$el.append(f.children())}i()},function(i){if(g&&!e.$el.is(":visible")){e.$el.fadeIn(g,i)}else{i()}},function(i){if(h){h.call(this)}e.trigger("rendered",this);i()}]);return this},renderWithoutModel:function(){var e=$("<div/>"),f=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return e.append(f)},renderModel:function(){var e=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){e.append(c.templates.anonHistoryPanel(this.model.toJSON()))}else{e.append(c.templates.historyPanel(this.model.toJSON()));this._renderTags(e);this._renderAnnotation(e)}this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var f=this;e.find(".history-name").make_text_editable({on_finish:function(g){e.find(".history-name").text(g);f.model.save({name:g}).fail(function(){e.find(".history-name").text(f.model.previous("name"))})}})},renderHdas:function(g){g=g||this.$el;this.hdaViews={};var f=this,e=g.find(this.datasetsSelector),h=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);e.empty();if(h.length){h.each(function(i){e.prepend(f.createHdaView(i).$el)});g.find(this.emptyMsgSelector).hide()}else{g.find(this.emptyMsgSelector).show()}return this.hdaViews},events:{"click .message-container":"clearMessages"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(e){e.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},renderSearchControls:function(){var e=this;e.model.hdas.fetchAllDetails({silent:true});function g(h){e.searchFor=h;e.filters=[function(i){return i.matchesAll(e.searchFor)}];e.trigger("search:searching",h,e);e.renderHdas()}function f(){e.searchFor="";e.filters=[];e.trigger("search:clear",e);e.renderHdas()}return searchInput({initialVal:e.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onsearch:g,onclear:f}).addClass("history-search-controls").css("padding","0px 0px 8px 0px")},toggleSearchControls:function(){var e=this.$el.find(".history-search-controls");if(!e.size()){e=this.renderSearchControls().hide();this.$el.find(".history-title").before(e)}e.slideToggle(this.fxSpeed)},showSelect:function(e){_.each(this.hdaViews,function(f){f.showSelect(e)})},hideSelect:function(e){_.each(this.hdaViews,function(f){f.hideSelect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},showLoadingIndicator:function(f,e,g){e=(e!==undefined)?(e):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,g)}else{this.$el.fadeOut(e);this.indicator.show(f,e,g)}},hideLoadingIndicator:function(e,f){e=(e!==undefined)?(e):(this.fxSpeed);if(this.indicator){this.indicator.hide(e,f)}},displayMessage:function(j,k,i){var g=this;this.scrollToTop();var h=this.$el.find(this.msgsSelector),e=$("<div/>").addClass(j+"message").html(k);if(!_.isEmpty(i)){var f=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(g.messageToModalOptions(j,k,i));return false});e.append(" ",f)}return h.html(e)},messageToModalOptions:function(i,k,h){var e=this,j=$("<div/>"),g={title:"Details"};function f(l){l=_.omit(l,_.functions(l));return["<table>",_.map(l,function(n,m){n=(_.isObject(n))?(f(n)):(n);return'<tr><td style="vertical-align: top; color: grey">'+m+'</td><td style="padding-left: 8px">'+n+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(h)){g.body=j.append(f(h))}else{g.body=j.html(h)}g.buttons={Ok:function(){Galaxy.modal.hide();e.clearMessages()}};return g},clearMessages:function(){var e=this.$el.find(this.msgsSelector);e.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(e){this.$el.parent().scrollTop(e)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(f,g){if(!g){this.$el.parent().parent().scrollTop(f);return this}var e=window,h=this.$el.parent().parent(),j=$(e).innerHeight(),i=(j/2)-(g/2);$(h).scrollTop(f-i);return this},scrollToId:function(f){if((!f)||(!this.hdaViews[f])){return this}var e=this.hdaViews[f].$el;this.scrollIntoView(e.offset().top,e.outerHeight());return this},scrollToHid:function(e){var f=this.model.hdas.getByHid(e);if(!f){return this}return this.scrollToId(f.id)},connectToQuotaMeter:function(e){if(!e){return this}this.listenTo(e,"quota:over",this.showQuotaMessage);this.listenTo(e,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(e&&e.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var e=this.$el.find(".quota-message");if(e.is(":hidden")){e.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var e=this.$el.find(".quota-message");if(!e.is(":hidden")){e.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(e){if(!e){return this}this.on("new-storage",function(g,f){if(e&&g){e.findItemByHtml(_l("Include Deleted Datasets")).checked=g.get("show_deleted");e.findItemByHtml(_l("Include Hidden Datasets")).checked=g.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});c.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:c}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(f,b,a){var c=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(g){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([g],[true])))},removeExpandedHda:function(g){this.save("expandedHdas",_.omit(this.get("expandedHdas"),g))},toString:function(){return"HistoryPanelPrefs("+this.id+")"}});c.historyStorageKey=function e(g){if(!g){throw new Error("HistoryPanelPrefs.historyStorageKey needs valid id: "+g)}return("history:"+g)};var d=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(g){g=g||{};if(g.logger){this.logger=g.logger}this.log(this+".initialize:",g);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];if(this.model){this._setUpWebStorage(g.initiallyExpanded,g.show_deleted,g.show_hidden);this._setUpModelEventHandlers()}if(g.onready){g.onready.call(this)}},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(g){this.log(this+"",arguments)},this)}},errorHandler:function(i,l,h,k,j){var g=this._parseErrorMessage(i,l,h,k,j);if(l&&l.status===0&&l.readyState===0){}else{if(l&&l.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",g.message,g.details)})}else{this.displayMessage("error",g.message,g.details)}}}},_parseErrorMessage:function(j,n,i,m,l){var h=Galaxy.currUser,g={message:this._bePolite(m),details:{user:(h instanceof User)?(h.toJSON()):(h+""),source:(j instanceof Backbone.Model)?(j.toJSON()):(j+""),xhr:n,options:(n)?(_.omit(i,"xhr")):(i)}};_.extend(g.details,l||{});if(n&&_.isFunction(n.getAllResponseHeaders)){var k=n.getAllResponseHeaders();k=_.compact(k.split("\n"));k=_.map(k,function(o){return o.split(": ")});g.details.xhr.responseHeaders=_.object(k)}return g},_bePolite:function(g){g=g||_l("An error occurred while getting updates from the server");return g+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories/"+j+"/set_as_current")};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},loadHistoryWithHDADetails:function(j,i,h,l){var g=this,k=function(m){return g.getExpandedHdaIds(m.id)};return this.loadHistory(j,i,h,l,k)},loadHistory:function(j,i,h,m,k){this.trigger("loading-history",this);i=i||{};var g=this;var l=f.History.getHistoryData(j,{historyFn:h,hdaFn:m,hdaDetailIds:i.initiallyExpanded||k});return this._loadHistoryFromXHR(l,i).fail(function(p,n,o){g.trigger("error",g,p,i,_l("An error was encountered while "+n),{historyId:j,history:o||{}})}).always(function(){g.trigger("loading-done",g)})},_loadHistoryFromXHR:function(i,h){var g=this;i.then(function(j,k){g.setModel(j,k,h)});i.fail(function(k,j){g.render()});return i},setModel:function(i,g,h){h=h||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){i.user=Galaxy.currUser.toJSON()}this.model=new f.History(i,g,h);this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(h,g){if(this.model){return this.model.refresh(h,g)}return $.when()},_setUpWebStorage:function(h,g,i){this.storage=new c({id:c.historyStorageKey(this.model.get("id"))});if(_.isObject(h)){this.storage.set("exandedHdas",h)}if(_.isBoolean(g)){this.storage.set("show_deleted",g)}if(_.isBoolean(i)){this.storage.set("show_hidden",i)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var g in sessionStorage){if(g.indexOf("history:")===0){sessionStorage.removeItem(g)}}},getStoredOptions:function(h){if(!h||h==="current"){return(this.storage)?(this.storage.get()):({})}var g=sessionStorage.getItem(c.historyStorageKey(h));return(g===null)?({}):(JSON.parse(g))},getExpandedHdaIds:function(g){var h=this.getStoredOptions(g).expandedHdas;return((_.isEmpty(h))?([]):(_.keys(h)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(h,j,g,i){this.errorHandler(h,j,g,i)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this);this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},addHdaView:function(j){this.log("add."+this,j);var h=this;if(!j.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function i(l){var k=h.$el.find(h.emptyMsgSelector);if(k.is(":visible")){k.fadeOut(h.fxSpeed,l)}else{l()}},function g(l){h.scrollToTop();var k=h.$el.find(h.datasetsSelector);h.createHdaView(j).$el.hide().prependTo(k).slideDown(h.fxSpeed)}])},createHdaView:function(i){var h=i.get("id"),g=this.storage.get("expandedHdas")[h],j=new this.HDAView({model:i,expanded:g,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(j);this.hdaViews[h]=j;return j.render()},_setUpHdaListeners:function(h){var g=this;h.on("body-expanded",function(i){g.storage.addExpandedHda(i)});h.on("body-collapsed",function(i){g.storage.removeExpandedHda(i)});h.on("error",function(j,l,i,k){g.errorHandler(j,l,i,k)})},handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$el.find(g.emptyMsgSelector).fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children())}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderWithoutModel:function(){var g=$("<div/>"),h=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return g.append(h)},renderModel:function(){var g=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){g.append(d.templates.anonHistoryPanel(this.model.toJSON()))}else{g.append(d.templates.historyPanel(this.model.toJSON()));this._renderTags(g);this._renderAnnotation(g)}this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_setUpBehaviours:function(g){g=g||this.$el;g.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var h=this;g.find(".history-name").make_text_editable({on_finish:function(i){g.find(".history-name").text(i);h.model.save({name:i}).fail(function(){g.find(".history-name").text(h.model.previous("name"))})}})},renderHdas:function(i){i=i||this.$el;this.hdaViews={};var h=this,g=i.find(this.datasetsSelector),j=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);g.empty();if(j.length){j.each(function(k){g.prepend(h.createHdaView(k).$el)});i.find(this.emptyMsgSelector).hide()}else{i.find(this.emptyMsgSelector).show()}return this.hdaViews},events:{"click .message-container":"clearMessages"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(g){g.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},renderSearchControls:function(){var g=this;g.model.hdas.fetchAllDetails({silent:true});function i(j){g.searchFor=j;g.filters=[function(k){return k.matchesAll(g.searchFor)}];g.trigger("search:searching",j,g);g.renderHdas()}function h(){g.searchFor="";g.filters=[];g.trigger("search:clear",g);g.renderHdas()}return searchInput({initialVal:g.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onsearch:i,onclear:h}).addClass("history-search-controls").css("padding","0px 0px 8px 0px")},toggleSearchControls:function(){var g=this.$el.find(".history-search-controls");if(!g.size()){g=this.renderSearchControls().hide();this.$el.find(".history-title").before(g)}g.slideToggle(this.fxSpeed)},showSelect:function(g){_.each(this.hdaViews,function(h){h.showSelect(g)})},hideSelect:function(g){_.each(this.hdaViews,function(h){h.hideSelect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},showLoadingIndicator:function(h,g,i){g=(g!==undefined)?(g):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,i)}else{this.$el.fadeOut(g);this.indicator.show(h,g,i)}},hideLoadingIndicator:function(g,h){g=(g!==undefined)?(g):(this.fxSpeed);if(this.indicator){this.indicator.hide(g,h)}},displayMessage:function(l,m,k){var i=this;this.scrollToTop();var j=this.$el.find(this.msgsSelector),g=$("<div/>").addClass(l+"message").html(m);if(!_.isEmpty(k)){var h=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(i.messageToModalOptions(l,m,k));return false});g.append(" ",h)}return j.html(g)},messageToModalOptions:function(k,m,j){var g=this,l=$("<div/>"),i={title:"Details"};function h(n){n=_.omit(n,_.functions(n));return["<table>",_.map(n,function(p,o){p=(_.isObject(p))?(h(p)):(p);return'<tr><td style="vertical-align: top; color: grey">'+o+'</td><td style="padding-left: 8px">'+p+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(j)){i.body=l.append(h(j))}else{i.body=l.html(j)}i.buttons={Ok:function(){Galaxy.modal.hide();g.clearMessages()}};return i},clearMessages:function(){var g=this.$el.find(this.msgsSelector);g.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(g){this.$el.parent().scrollTop(g)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(h,i){if(!i){this.$el.parent().parent().scrollTop(h);return this}var g=window,j=this.$el.parent().parent(),l=$(g).innerHeight(),k=(l/2)-(i/2);$(j).scrollTop(h-k);return this},scrollToId:function(h){if((!h)||(!this.hdaViews[h])){return this}var g=this.hdaViews[h].$el;this.scrollIntoView(g.offset().top,g.outerHeight());return this},scrollToHid:function(g){var h=this.model.hdas.getByHid(g);if(!h){return this}return this.scrollToId(h.id)},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file 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: Dave Bouvier: Fix the update manager functional test.
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0e1d539dcfcb/ Changeset: 0e1d539dcfcb User: Dave Bouvier Date: 2013-11-25 19:50:32 Summary: Fix the update manager functional test. Affected #: 1 file diff -r d37d6e711d671763d725ffb4931f0acc379964dc -r 0e1d539dcfcb3246f144258514a43e07a514b52e test/tool_shed/functional/test_1410_update_manager.py --- a/test/tool_shed/functional/test_1410_update_manager.py +++ b/test/tool_shed/functional/test_1410_update_manager.py @@ -123,6 +123,12 @@ self.galaxy_login( email=common.admin_email, username=common.admin_username ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.update_tool_shed_status() - strings_displayed = [ '"%s"><img src="/static/images/icon_warning_sml.gif"' % self.security.encode_id( repository.id ) ] + ok_icon = '/static/june_2007_style/blue/ok_small.png' + ok_title = 'This is the latest installable revision of this repository' + updates_icon = '/static/images/icon_warning_sml.gif' + repository_id = self.security.encode_id( repository.id ) + html = '<label id="%s" for="%s"><img src="%s" class="icon-button" title="%s"/><img src="%s' % \ + ( repository_id, repository_id, ok_icon, ok_title, updates_icon ) + strings_displayed = [ html ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) 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: 3 new changesets
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55d684093172/ Changeset: 55d684093172 User: Dave Bouvier Date: 2013-11-25 19:01:44 Summary: Fix for importing repositories. Affected #: 1 file diff -r 8ae8e19ea0762af833558f75b84fe19840c6e783 -r 55d684093172360d6329349337313da202e94108 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -164,7 +164,7 @@ # No repository with the specified name and owner currently exists, so make sure the current user can create one. if trans.user_is_admin(): repository_info_dict[ 'status' ] = None - elif trans.app.security_agent.user_can_import_repository_archive( trans.user, owner ): + elif trans.app.security_agent.user_can_import_repository_archive( trans.user, repository_info_dict[ 'owner' ] ): repository_info_dict[ 'status' ] = None else: repository_info_dict[ 'status' ] = 'Not authorized to import' https://bitbucket.org/galaxy/galaxy-central/commits/398287552d91/ Changeset: 398287552d91 User: Dave Bouvier Date: 2013-11-25 19:02:09 Summary: Functional tests for importing and exporting repositories. Affected #: 3 files diff -r 55d684093172360d6329349337313da202e94108 -r 398287552d91093721ea0de635ed6b0d7c7cd147 test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz Binary file test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz has changed diff -r 55d684093172360d6329349337313da202e94108 -r 398287552d91093721ea0de635ed6b0d7c7cd147 test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz Binary file test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz has changed diff -r 55d684093172360d6329349337313da202e94108 -r 398287552d91093721ea0de635ed6b0d7c7cd147 test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz Binary file test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz has changed https://bitbucket.org/galaxy/galaxy-central/commits/d37d6e711d67/ Changeset: d37d6e711d67 User: Dave Bouvier Date: 2013-11-25 19:02:09 Summary: Functional tests for importing and exporting repositories. Affected #: 5 files diff -r 398287552d91093721ea0de635ed6b0d7c7cd147 -r d37d6e711d671763d725ffb4931f0acc379964dc test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -4,6 +4,7 @@ import re import test_db_util import simplejson +import shutil import logging import time import tempfile @@ -12,6 +13,7 @@ import galaxy.model as galaxy_model import galaxy.util as util from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util from base.twilltestcase import tc, from_json_string, TwillTestCase, security, urllib from tool_shed.util.encoding_util import tool_shed_encode, tool_shed_decode @@ -98,6 +100,16 @@ self.check_repository_changelog( repository ) self.check_string_count_in_page( 'Repository metadata is associated with this change set.', metadata_count ) + def check_exported_repository_dependency( self, dependency_filename, repository_name, repository_owner ): + root, error_message = xml_util.parse_xml( dependency_filename ) + for elem in root.findall( 'repository' ): + if 'changeset_revision' in elem: + raise AssertionError( 'Exported repository %s with owner %s has a dependency with a defined changeset revision.' % \ + ( repository_name, repository_owner ) ) + if 'toolshed' in elem: + raise AssertionError( 'Exported repository %s with owner %s has a dependency with a defined tool shed.' % \ + ( repository_name, repository_owner ) ) + def check_for_valid_tools( self, repository, strings_displayed=[], strings_not_displayed=[] ): strings_displayed.append( 'Valid tools' ) self.display_manage_repository_page( repository, strings_displayed, strings_not_displayed ) @@ -144,6 +156,24 @@ self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def check_manifest( self, manifest_filepath, owner=None ): + root, error_message = xml_util.parse_xml( manifest_filepath ) + for elem in root.findall( 'repository' ): + repository_name = elem.get( 'name' ) + manifest_owner = elem.get( 'username' ) + if owner is not None: + assert manifest_owner == owner, 'Expected repository %s to be owned by %s, but found %s' % \ + ( elem.get( 'name' ), owner, manifest_owner ) + toolshed = elem.get( 'toolshed' ) + changeset_revision = elem.get( 'changeset_revision' ) + assert toolshed is None, 'Repository definition %s has a tool shed attribute %s.' % ( repository_name, toolshed ) + assert changeset_revision is None, 'Repository definition %s specifies a changeset revision %s.' % \ + ( repository_name, changeset_revision ) + repository_archive = elem.find( 'archive' ).text + filepath, filename = os.path.split( manifest_filepath ) + repository_path = os.path.join( filepath, repository_archive ) + self.verify_repository_in_capsule( repository_path, repository_name, owner ) + def check_repository_changelog( self, repository, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) @@ -1207,6 +1237,15 @@ tc.submit( "upload_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def verify_capsule_contents( self, capsule_filepath, owner ): + tar_object = tarfile.open( capsule_filepath, 'r:*' ) + extraction_path = tempfile.mkdtemp() + tar_object.extractall( extraction_path ) + for root, dirs, files in os.walk( extraction_path ): + if 'manifest.xml' in files: + self.check_manifest( os.path.join( root, 'manifest.xml' ), owner=owner ) + shutil.rmtree( extraction_path ) + def verify_installed_repositories( self, installed_repositories=[], uninstalled_repositories=[] ): for repository_name, repository_owner in installed_repositories: galaxy_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, repository_owner ) @@ -1279,6 +1318,17 @@ # or we know that the repository was not correctly installed! assert found, 'No entry for %s in %s.' % ( required_data_table_entry, self.shed_tool_data_table_conf ) + def verify_repository_in_capsule( self, repository_archive, repository_name, repository_owner ): + repository_extraction_dir = tempfile.mkdtemp() + repository_tar_object = tarfile.open( repository_archive, 'r:*' ) + repository_tar_object.extractall( repository_extraction_dir ) + for root, dirs, files in os.walk( repository_extraction_dir ): + for filename in files: + if filename in [ 'tool_dependencies.xml', 'repository_dependencies.xml' ]: + dependency_filepath = os.path.join( root, filename ) + self.check_exported_repository_dependency( dependency_filepath, repository_name, repository_owner ) + shutil.rmtree( repository_extraction_dir ) + def verify_repository_reviews( self, repository, reviewer=None, strings_displayed=[], strings_not_displayed=[] ): changeset_revision = self.get_repository_tip( repository ) # Verify that the currently logged in user has a repository review for the specified repository, reviewer, and changeset revision. diff -r 398287552d91093721ea0de635ed6b0d7c7cd147 -r d37d6e711d671763d725ffb4931f0acc379964dc test/tool_shed/functional/test_0490_export_import_repositories.py --- /dev/null +++ b/test/tool_shed/functional/test_0490_export_import_repositories.py @@ -0,0 +1,90 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +import logging +log = logging.getLogger( __name__ ) + +repository_name = 'filtering_0490' +repository_description = "Galaxy's filtering tool for test 0490" +repository_long_description = "Long description of Galaxy's filtering tool for test 0490" + +category_name = 'Test 0490 Repository Import Export' +category_description = 'Test script 0490 for importing and exporting single repositories.' + +''' +First test: + +1. Import a repository capsule containing a repository with no dependencies, e.g. filter1. +2. Check that the repository to be imported is not marked as preexisting. The word ' Exists' should not be displayed, but '<b>Exists</b>' will. +3. Export that repository. Check the capsule's contents, verify that changeset revision and tool shed are not set. +4. Import the capsule again. Check that the repository to be imported is marked as preexisting. The word ' Exists' should be + displayed, as will '<b>Exists</b>'. + +''' + +class TestExportImportRepository( ShedTwillTestCase ): + '''Test exporting and importing repositories.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_import_repository_capsule( self ): + """Import the filter_0490 repository capsule.""" + ''' + This is step 1 - Import a repository capsule containing a repository with no dependencies, e.g. filter1. + Check that the repository to be imported is not marked as preexisting. The string ' Exists' should not + be displayed, but '<b>Exists</b>' should. + ''' + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.import_capsule( self.get_filename( 'repository_capsules/0490_filtering.tar.gz' ), + strings_displayed=[ repository_name, '<b>Exists' ], + strings_not_displayed=[ ' Exists' ], + strings_displayed_after_submit=[ 'Repository <b>filtering_0490</b> has been created.' ], + strings_not_displayed_after_submit=[ 'Import not necessary' ] ) + + def test_0010_export_repository_capsule( self ): + '''Export the repository that was imported in the previous step.''' + ''' + This is step 2 - Export that repository. + Export the repository to a temporary location. + ''' + global capsule_filepath + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + capsule_filepath = self.export_capsule( repository ) + log.debug( os.path.exists( capsule_filepath ) ) + + def test_0015_verify_exported_capsule( self ): + '''Verify the exported capsule contents.''' + ''' + This is step 3 - Check the capsule's contents, verify that changeset revision and tool shed are not set. + Extract the exported capsule tarball to a temporary path, and confirm that the manifest does not specify + a tool shed or changeset revision. + ''' + global capsule_filepath + self.verify_capsule_contents( capsule_filepath, owner=common.test_user_1_name ) + + def test_0020_import_repository_capsule( self ): + '''Import the exported repository capsule.''' + ''' + This is step 4 - Import the capsule again. Check that the repository to be imported is marked as preexisting. + The string ' Exists' should be displayed, as should '<b>Exists</b>'. + ''' + global capsule_filepath + self.import_capsule( capsule_filepath, + strings_displayed=[ repository_name, ' Exists', self.url ], + strings_not_displayed_after_submit=[ 'Repository <b>filtering_0490</b> has been created.' ], + strings_displayed_after_submit=[ 'Import not necessary', 'Exists' ] ) diff -r 398287552d91093721ea0de635ed6b0d7c7cd147 -r d37d6e711d671763d725ffb4931f0acc379964dc test/tool_shed/functional/test_0500_export_repository_simple_dependency.py --- /dev/null +++ b/test/tool_shed/functional/test_0500_export_repository_simple_dependency.py @@ -0,0 +1,89 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +import logging +log = logging.getLogger( __name__ ) + +emboss_repository_name = 'emboss_5_0500' +emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools" +emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools" +datatypes_repository_name = 'emboss_datatypes_0500' +datatypes_repository_description = 'Galaxy applicable data formats used by Emboss tools.' +datatypes_repository_long_description = 'Galaxy applicable data formats used by Emboss tools. This repository contains no tools.' + +category_name = 'Test 0500 Repository Dependency Import Export' +category_description = 'Test script 0500 for importing and exporting repositories with simple repository dependencies.' + +''' +1. Export a repository with no dependencies, e.g. filter1. +2. Temporarily extract the repository capsule. +2a. For every owner in the manifest, set to a different user. +3. Import it into the same tool shed. +4. Check that the repository to be imported has no status in the status column. +5. Click the import button. +6. Verify the resulting page is correct. +''' + +class TestExportImportRepository( ShedTwillTestCase ): + '''Test exporting and importing repositories.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_category_and_repository( self ): + """Create categories for this test suite""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.import_capsule( self.get_filename( 'repository_capsules/0500_emboss_5.tar.gz' ), + strings_displayed=[ emboss_repository_name, datatypes_repository_name, '<b>Exists' ], + strings_not_displayed=[ ' Exists' ], + strings_displayed_after_submit=[ 'Repository <b>emboss_5_0500</b> has been created.', + 'Repository <b>emboss_datatypes_0500</b> has been created.' ], + strings_not_displayed_after_submit=[ 'Import not necessary' ] ) + + def test_0010_export_repository_capsule( self ): + '''Export the repository that was imported in the previous step.''' + ''' + This is step 2 - Export that repository. + Export the repository to a temporary location. + ''' + global capsule_filepath + repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + capsule_filepath = self.export_capsule( repository ) + log.debug( os.path.exists( capsule_filepath ) ) + + def test_0015_verify_exported_capsule( self ): + '''Verify the exported capsule contents.''' + ''' + This is step 3 - Check the capsule's contents, verify that changeset revision and tool shed are not set. + Extract the exported capsule tarball to a temporary path, and confirm that the manifest does not specify + a tool shed or changeset revision. + ''' + global capsule_filepath + self.verify_capsule_contents( capsule_filepath, owner=common.test_user_1_name ) + + def test_0020_import_repository_capsule( self ): + '''Import the exported repository capsule.''' + ''' + This is step 4 - Import the capsule again. Check that the repository to be imported is marked as preexisting. + The string ' Exists' should be displayed, as should '<b>Exists</b>'. + ''' + global capsule_filepath + self.import_capsule( capsule_filepath, + strings_displayed=[ emboss_repository_name, datatypes_repository_name, ' Exists', self.url ], + strings_not_displayed_after_submit=[ 'Repository <b>emboss_5_0500</b> has been created.', + 'Repository <b>emboss_datatypes_0500</b> has been created.' ], + strings_displayed_after_submit=[ 'Import not necessary', ' Exists' ] ) diff -r 398287552d91093721ea0de635ed6b0d7c7cd147 -r d37d6e711d671763d725ffb4931f0acc379964dc test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py @@ -0,0 +1,99 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +import logging +log = logging.getLogger( __name__ ) + +category_name = 'Test 0510 Import Export Complex Dependencies' +category_description = 'Test script 0510 for importing and exporting repositories with complex repository dependencies.' + +''' +Import a repository capsule with a complex repository dependency with trans_proteomic_pipeline and required repositories. +Check that the repository to be imported is not marked as preexisting. The word ' Exists' should not be displayed, but '<b>Exists</b>' will. +Click the import button. +Verify the resulting page is correct. +Verify the dependency structure that has been created. +Export the trans_proteomic_pipeline repository with dependencies. +Check the capsule's contents, verify that changeset revision and tool shed are not set. +''' + +class TestExportImportRepository( ShedTwillTestCase ): + '''Test exporting and importing repositories with complex dependencies.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_category_and_repositories( self ): + """Create categories for this test suite""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.import_capsule( self.get_filename( 'repository_capsules/0510_trans_proteomic_pipeline.tar.gz' ), + strings_displayed=[ 'package_trans_proteomic_pipeline_4_6_3', + 'package_perl_5_18', + 'package_libpng_1_2', + 'package_libgd_2_1', + 'package_expat_2_1', + '<b>Exists' ], + strings_not_displayed=[ ' Exists' ], + strings_displayed_after_submit=[ 'Repository <b>package_trans_proteomic_pipeline_4_6_3</b> has been created.', + 'Repository <b>package_perl_5_18</b> has been created.', + 'Repository <b>package_libpng_1_2</b> has been created.', + 'Repository <b>package_libgd_2_1</b> has been created.', + 'Repository <b>package_expat_2_1</b> has been created.' ], + strings_not_displayed_after_submit=[ 'Import not necessary' ] ) + + def test_0010_export_repository_capsule( self ): + '''Export the repository that was imported in the previous step.''' + ''' + This is step 2 - Export that repository. + Export the repository to a temporary location. + ''' + global capsule_filepath + repository = test_db_util.get_repository_by_name_and_owner( 'package_trans_proteomic_pipeline_4_6_3', common.test_user_1_name ) + capsule_filepath = self.export_capsule( repository ) + log.debug( os.path.exists( capsule_filepath ) ) + + def test_0015_verify_exported_capsule( self ): + '''Verify the exported capsule contents.''' + ''' + This is step 3 - Check the capsule's contents, verify that changeset revision and tool shed are not set. + Extract the exported capsule tarball to a temporary path, and confirm that the manifest does not specify + a tool shed or changeset revision. + ''' + global capsule_filepath + self.verify_capsule_contents( capsule_filepath, owner=common.test_user_1_name ) + + def test_0020_import_repository_capsule( self ): + '''Import the exported repository capsule.''' + ''' + This is step 4 - Import the capsule again. Check that the repository to be imported is marked as preexisting. + The string ' Exists' should be displayed, as should '<b>Exists</b>'. + ''' + global capsule_filepath + self.import_capsule( capsule_filepath, + strings_displayed=[ 'package_trans_proteomic_pipeline_4_6_3', + 'package_perl_5_18', + 'package_libpng_1_2', + 'package_libgd_2_1', + 'package_expat_2_1', + ' Exists', + self.url ], + strings_not_displayed_after_submit=[ 'Repository <b>package_trans_proteomic_pipeline_4_6_3</b> has been created.', + 'Repository <b>package_perl_5_18</b> has been created.', + 'Repository <b>package_libpng_1_2</b> has been created.', + 'Repository <b>package_libgd_2_1</b> has been created.', + 'Repository <b>package_expat_2_1</b> has been created.' ], + strings_displayed_after_submit=[ 'Import not necessary', ' Exists' ] ) diff -r 398287552d91093721ea0de635ed6b0d7c7cd147 -r d37d6e711d671763d725ffb4931f0acc379964dc test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -92,8 +92,9 @@ tool_sheds_conf_xml_template = '''<?xml version="1.0"?><tool_sheds> + <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> + <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/><tool_shed name="Embedded tool shed for functional tests" url="http://${shed_url}:${shed_port}/"/> - <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/></tool_sheds> ''' 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: Dave Bouvier: Handle cases where installed_repostory_dict has a converter_path or display_path set to None.
by commits-noreply＠bitbucket.org 25 Nov '13

25 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8ae8e19ea076/ Changeset: 8ae8e19ea076 User: Dave Bouvier Date: 2013-11-25 18:36:34 Summary: Handle cases where installed_repostory_dict has a converter_path or display_path set to None. Affected #: 2 files diff -r 6997fa059319b288877cf0728ac20fbb57e80dee -r 8ae8e19ea0762af833558f75b84fe19840c6e783 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -231,10 +231,13 @@ if tool_shed_repository.includes_datatypes: # Deactivate proprietary datatypes. installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, tool_shed_repository, repository_install_dir, deactivate=True ) - if installed_repository_dict and 'converter_path' in installed_repository_dict: - datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) - if installed_repository_dict and 'display_path' in installed_repository_dict: - datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) + if installed_repository_dict: + converter_path = installed_repository_dict.get( 'converter_path' ) + if converter_path is not None: + datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) + display_path = installed_repository_dict.get( 'display_path' ) + if display_path is not None: + datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. diff -r 6997fa059319b288877cf0728ac20fbb57e80dee -r 8ae8e19ea0762af833558f75b84fe19840c6e783 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -61,10 +61,13 @@ repository_install_dir = os.path.abspath( relative_install_dir ) # Activate proprietary datatypes. installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, repository, repository_install_dir, deactivate=False ) - if installed_repository_dict and 'converter_path' in installed_repository_dict: - datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=False ) - if installed_repository_dict and 'display_path' in installed_repository_dict: - datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False ) + if installed_repository_dict: + converter_path = installed_repository_dict.get( 'converter_path' ) + if converter_path is not None: + datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=False ) + display_path = installed_repository_dict.get( 'display_path' ) + if display_path is not None: + datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False ) def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits November 2013