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

commit/galaxy-central: inithello: Correctly handle repository dependencies when running the automated install and test script.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb923432a1ac/ Changeset: eb923432a1ac User: inithello Date: 2013-04-18 21:16:47 Summary: Correctly handle repository dependencies when running the automated install and test script. Affected #: 1 file diff -r 02a467df84a365dde3084370a097a0859e6a45d3 -r eb923432a1ac56dd7a2e5a3b640a79487acea1b3 test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -88,7 +88,15 @@ checkbox.selected = False kwd[ 'install_tool_dependencies' ] = 'False' if 'install_repository_dependencies' in self.last_page(): - kwd[ 'install_repository_dependencies' ] = str( install_repository_dependencies ).lower() + form = tc.browser.get_form( 'select_tool_panel_section' ) + checkbox = form.find_control( id="install_repository_dependencies" ) + checkbox.disabled = False + if install_repository_dependencies: + checkbox.selected = True + kwd[ 'install_repository_dependencies' ] = 'True' + else: + checkbox.selected = False + kwd[ 'install_repository_dependencies' ] = 'False' if 'shed_tool_conf' not in kwd: kwd[ 'shed_tool_conf' ] = self.shed_tool_conf if new_tool_panel_section: 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: dan: Auto Focus on first item on forms.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/02a467df84a3/ Changeset: 02a467df84a3 User: dan Date: 2013-04-18 19:14:14 Summary: Auto Focus on first item on forms. Affected #: 2 files diff -r 18b23ed8de5b384f142db349e7379c03567758df -r 02a467df84a365dde3084370a097a0859e6a45d3 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -705,4 +705,9 @@ return anchor; }); + // Auto Focus on first item on form + if ( $("*:focus").html() == null ) { + $(":input:not([type=hidden]):visible:enabled:first").focus(); + } + }); diff -r 18b23ed8de5b384f142db349e7379c03567758df -r 02a467df84a365dde3084370a097a0859e6a45d3 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var 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b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".tooltip").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b});if($("*:focus").html()==null){$(":input:not([type=hidden]):visible:enabled:first").focus()}}); \ 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: greg: Add support for ordering installation of tool shed repositories into Galaxy via the Galaxy API.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/18b23ed8de5b/ Changeset: 18b23ed8de5b User: greg Date: 2013-04-18 17:07:25 Summary: Add support for ordering installation of tool shed repositories into Galaxy via the Galaxy API. Affected #: 1 file diff -r aaf9f60d8be28a1a3a896c51a5d4895563c8c0a3 -r 18b23ed8de5b384f142db349e7379c03567758df lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -240,10 +240,16 @@ # changeset_revision, there may be multiple repositories for installation at this point because repository dependencies may have added # additional repositories for installation along with the single specified repository. encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = repository_util.initiate_repository_installation( trans, installation_dict ) + # Some repositories may have repository dependencies that are required to be installed before the dependent repository, so we'll + # order the list of tsr_ids to ensure all repositories install in the required order. + tsr_ids = [ trans.security.encode_id( tool_shed_repository.id ) for tool_shed_repository in tool_shed_repositories ] + ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ + repository_util.order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys ) # Install the repositories, keeping track of each one for later display. - for index, tool_shed_repository in enumerate( tool_shed_repositories ): - repo_info_dict = repo_info_dicts[ index ] - tool_panel_section_key = tool_panel_section_keys[ index ] + for index, tsr_id in enumerate( ordered_tsr_ids ): + tool_shed_repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) + repo_info_dict = ordered_repo_info_dicts[ index ] + tool_panel_section_key = ordered_tool_panel_section_keys[ index ] repository_util.install_tool_shed_repository( trans, tool_shed_repository, repo_info_dict, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for displaying the appropriate page when installing tool shed repositories into Galxy.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aaf9f60d8be2/ Changeset: aaf9f60d8be2 User: greg Date: 2013-04-18 16:19:39 Summary: Fix for displaying the appropriate page when installing tool shed repositories into Galxy. Affected #: 2 files diff -r 56e9d6fb4201122a7545abf417b908b944aeab4e -r aaf9f60d8be28a1a3a896c51a5d4895563c8c0a3 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 @@ -830,8 +830,8 @@ includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] - if ( ( not includes_tools_for_display_in_tool_panel and not has_repository_dependencies ) and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \ - ( ( includes_tools_for_display_in_tool_panel or has_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): + if ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \ + ( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ): install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) @@ -938,7 +938,7 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) - if includes_tools_for_display_in_tool_panel or has_repository_dependencies: + if includes_tools_for_display_in_tool_panel: return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, diff -r 56e9d6fb4201122a7545abf417b908b944aeab4e -r aaf9f60d8be28a1a3a896c51a5d4895563c8c0a3 lib/tool_shed/util/encoding_util.py --- a/lib/tool_shed/util/encoding_util.py +++ b/lib/tool_shed/util/encoding_util.py @@ -25,7 +25,8 @@ try: values = simplejson.loads( value ) except Exception, e: - log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) ) + #log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) ) + pass if values is not None: try: return json_fix( values ) 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: dan: Remove leading slash from generation of tool_runner URL when a tool requires user log in, and still needs to.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56e9d6fb4201/ Changeset: 56e9d6fb4201 User: dan Date: 2013-04-18 15:56:13 Summary: Remove leading slash from generation of tool_runner URL when a tool requires user log in, and still needs to. Affected #: 1 file diff -r eba52974bfaf93806b5177363a1d731190e28d8b -r 56e9d6fb4201122a7545abf417b908b944aeab4e lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -65,7 +65,7 @@ if tool.require_login and not trans.user: message = "You must be logged in to use this tool." status = "info" - redirect = url_for( controller='/tool_runner', action='index', tool_id=tool_id, **kwd ) + redirect = url_for( controller='tool_runner', action='index', tool_id=tool_id, **kwd ) return trans.response.send_redirect( url_for( controller='user', action='login', cntrller='user', 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: dan: Fix for old style display application link generation broken by recent route changes.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eba52974bfaf/ Changeset: eba52974bfaf User: dan Date: 2013-04-18 15:50:27 Summary: Fix for old style display application link generation broken by recent route changes. Affected #: 1 file diff -r 781431663eb1c18bb9ab32eb8f3eff59e0848efb -r eba52974bfaf93806b5177363a1d731190e28d8b lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -244,7 +244,7 @@ # Accumulate links for valid sites ret_val = [] for site_name, site_url in valid_sites: - internal_url = url_for( controller='/dataset', dataset_id=dataset.id, + internal_url = url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) 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: dan: Fix for display application link generation broken by recent route changes.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/781431663eb1/ Changeset: 781431663eb1 User: dan Date: 2013-04-18 15:39:22 Summary: Fix for display application link generation broken by recent route changes. Affected #: 2 files diff -r 7d5a1290587ccd49ad06d7a85adc571410cc305c -r 781431663eb1c18bb9ab32eb8f3eff59e0848efb lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -12,7 +12,7 @@ log = logging.getLogger( __name__ ) #Any basic functions that we want to provide as a basic part of parameter dict should be added to this dict -BASE_PARAMS = { 'qp': quote_plus, 'url_for':url_for } #url_for has route memory... +BASE_PARAMS = { 'qp': quote_plus, 'url_for':url_for } class DisplayApplicationLink( object ): @classmethod @@ -40,7 +40,7 @@ self.name = None def get_display_url( self, data, trans ): dataset_hash, user_hash = encode_dataset_user( trans, data, None ) - return url_for( controller='/dataset', + return url_for( controller='dataset', action="display_application", dataset_id=dataset_hash, user_id=user_hash, diff -r 7d5a1290587ccd49ad06d7a85adc571410cc305c -r 781431663eb1c18bb9ab32eb8f3eff59e0848efb lib/galaxy/datatypes/display_applications/parameters.py --- a/lib/galaxy/datatypes/display_applications/parameters.py +++ b/lib/galaxy/datatypes/display_applications/parameters.py @@ -163,7 +163,7 @@ if self.parameter.strip_https and base_url[ : 5].lower() == 'https': base_url = "http%s" % base_url[ 5: ] return "%s%s" % ( base_url, - url_for( controller='/dataset', + url_for( controller='dataset', action="display_application", dataset_id=self._dataset_hash, user_id=self._user_hash, 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 18 Apr '13

18 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d056556a1e63/ Changeset: d056556a1e63 Branch: stable User: inithello Date: 2013-04-17 20:31:27 Summary: Improve recording of invalid tests. Check for the existence each file required by functional tests. Affected #: 1 file diff -r c6d032ef7e420b158248aeb71c65914799a78122 -r d056556a1e632d7f0fd7f9d195538c8e5c6d917b 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 @@ -167,21 +167,22 @@ no_tools = 0 valid_revisions = 0 invalid_revisions = 0 - # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test - # or tools_functionally_correct. Also filter out changeset revisions that are not downloadable, because it's redundant to test a revision that - # a user can't install. - # Initialize the repository_status dict with the test environment, but leave the test_errors empty. - repository_status = {} - repository_status[ 'invalid_tests' ] = [] + # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test, + # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable, + # because it's redundant to test a revision that a user can't install. metadata_records_to_check = app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, app.model.RepositoryMetadata.table.c.includes_tools == True, - app.model.RepositoryMetadata.table.c.do_not_test == False, - app.model.RepositoryMetadata.table.c.tools_functionally_correct == False ) ) \ + app.model.RepositoryMetadata.table.c.do_not_test == False ) ) \ .all() for metadata_record in metadata_records_to_check: + # Initialize the repository_status dict with the test environment, but leave the test_errors empty. + repository_status = {} if metadata_record.tool_test_errors: repository_status = metadata_record.tool_test_errors + # Clear any old invalid tests for this metadata revision, since this could lead to duplication of invalid test rows, + # or tests incorrectly labeled as invalid. + repository_status[ 'invalid_tests' ] = [] if 'test_environment' in repository_status: repository_status[ 'test_environment' ] = get_test_environment( repository_status[ 'test_environment' ] ) else: @@ -192,7 +193,6 @@ name = metadata_record.repository.name owner = metadata_record.repository.user.username changeset_revision = str( metadata_record.changeset_revision ) - repository_status[ 'invalid_tests' ] = [] if metadata_record.repository.id not in checked_repository_ids: checked_repository_ids.append( metadata_record.repository.id ) if verbosity >= 1: @@ -218,15 +218,13 @@ dirs.remove( '.hg' ) if 'test-data' in dirs: has_test_data = True + test_data_path = os.path.join( root, dirs[ dirs.index( 'test-data' ) ] ) break - # Remove the cloned repository path. - if os.path.exists( work_dir ): - shutil.rmtree( work_dir ) if verbosity >= 1: if not has_test_data: - print '# Test data missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# Test data directory missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) else: - print '# Test data found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# Test data directory found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) print '# Checking for functional tests in changeset revision %s of %s, owned by %s.' % \ ( changeset_revision, name, owner ) # Loop through all the tools in this metadata record, checking each one for defined functional tests. @@ -255,12 +253,22 @@ has_tests += 1 failure_reason = '' problem_found = False + missing_test_files = [] + if tool_has_tests and has_test_data: + missing_test_files = check_for_missing_test_files( tool_metadata[ 'tests' ], test_data_path ) + if missing_test_files: + if verbosity >= 2: + print "# Tool ID '%s' in changeset revision %s of %s is missing one or more required test files: %s" % \ + ( tool_id, changeset_revision, name, ', '.join( missing_test_files ) ) if not has_test_data: failure_reason += 'Repository does not have a test-data directory. ' problem_found = True if not tool_has_tests: failure_reason += 'Functional test definitions missing for %s. ' % tool_id problem_found = True + if missing_test_files: + failure_reason += 'One or more test files are missing for tool %s: %s' % ( tool_id, ', '.join( missing_test_files ) ) + problem_found = True test_errors = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid, reason_test_is_invalid=failure_reason ) # The repository_metadata.tool_test_errors attribute should always have the following structure: @@ -312,6 +320,9 @@ if problem_found: if test_errors not in repository_status[ 'invalid_tests' ]: repository_status[ 'invalid_tests' ].append( test_errors ) + # Remove the cloned repository path. This has to be done after the check for required test files, for obvious reasons. + if os.path.exists( work_dir ): + shutil.rmtree( work_dir ) if not repository_status[ 'invalid_tests' ]: valid_revisions += 1 if verbosity >= 1: @@ -319,17 +330,21 @@ else: invalid_revisions += 1 if verbosity >= 1: - print '# Some tools missing functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + print '# Some tools have problematic functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + if verbosity >= 2: + for invalid_test in repository_status[ 'invalid_tests' ]: + if 'reason_test_is_invalid' in invalid_test: + print '# %s' % invalid_test[ 'reason_test_is_invalid' ] if not info_only: # If repository_status[ 'test_errors' ] is empty, no issues were found, and we can just update time_last_tested with the platform # on which this script was run. if repository_status[ 'invalid_tests' ]: # If functional test definitions or test data are missing, set do_not_test = True if and only if: - # a) There are multiple downloadable revisions, and the revision being tested is not the most recent downloadable revision. In this case, - # the revision will never be updated with correct data, and re-testing it would be redundant. - # b) There are one or more downloadable revisions, and the revision being tested is the most recent downloadable revision. In this case, if - # the repository is updated with test data or functional tests, the downloadable changeset revision that was tested will be replaced - # with the new changeset revision, which will be automatically tested. + # a) There are multiple downloadable revisions, and the revision being tested is not the most recent downloadable revision. + # In this case, the revision will never be updated with correct data, and re-testing it would be redundant. + # b) There are one or more downloadable revisions, and the revision being tested is the most recent downloadable revision. + # In this case, if the repository is updated with test data or functional tests, the downloadable changeset revision + # that was tested will be replaced with the new changeset revision, which will be automatically tested. if should_set_do_not_test_flag( app, metadata_record.repository, changeset_revision ): metadata_record.do_not_test = True metadata_record.tools_functionally_correct = False @@ -357,6 +372,25 @@ changelog_tuples.append( ( ctx.rev(), str( ctx ) ) ) return changelog_tuples +def check_for_missing_test_files( test_definition, test_data_path ): + '''Process the tool's functional test definitions and check for each file specified as an input or output.''' + missing_test_files = [] + required_test_files = [] + for test_dict in test_definition: + for input_file in test_dict[ 'required_files' ]: + if input_file not in required_test_files: + required_test_files.append( input_file ) + for output in test_dict[ 'outputs' ]: + fieldname, filename = output + if filename not in required_test_files: + required_test_files.append( filename ) + # Make sure each specified file actually does exist in the test data path of the cloned repository. + for required_file in required_test_files: + required_file_full_path = os.path.join( test_data_path, required_file ) + if not os.path.exists( required_file_full_path ): + missing_test_files.append( required_file ) + return missing_test_files + def is_most_recent_downloadable_revision( app, repository, changeset_revision, downloadable_revisions ): # Get a list of ( numeric revision, changeset hash ) tuples from the changelog. changelog = get_repo_changelog_tuples( repository.repo_path( app ) ) @@ -376,8 +410,10 @@ a) There are multiple downloadable revisions, and the provided changeset revision is not the most recent downloadable revision. In this case, the revision will never be updated with correct data, and re-testing it would be redundant. b) There are one or more downloadable revisions, and the provided changeset revision is the most recent downloadable revision. In this case, if - the repository is updated with test data or functional tests, the downloadable changeset revision that was tested will be replaced - with the new changeset revision, which will be automatically tested. + the repository is updated with test data or functional tests, the downloadable changeset revision that was tested will either be replaced + with the new changeset revision, or a new downloadable changeset revision will be created, either of which will be automatically checked and + flagged as appropriate. In the install and test script, this behavior is slightly different, since we do want to always run functional tests + on the most recent downloadable changeset revision. ''' metadata_records = app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, https://bitbucket.org/galaxy/galaxy-central/commits/ae53deed05b6/ Changeset: ae53deed05b6 Branch: stable User: inithello Date: 2013-04-17 22:11:20 Summary: Account for condition where output filename is not defined. Affected #: 1 file diff -r d056556a1e632d7f0fd7f9d195538c8e5c6d917b -r ae53deed05b68f6febfcf3472c2a11514c12eb0c 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 @@ -382,6 +382,9 @@ required_test_files.append( input_file ) for output in test_dict[ 'outputs' ]: fieldname, filename = output + # In rare cases, the filename may be None. If that is the case, skip that output definition. + if filename is None: + continue if filename not in required_test_files: required_test_files.append( filename ) # Make sure each specified file actually does exist in the test data path of the cloned repository. 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: dan: Fix for generating stderr/stdout links in hda show_params.
by commits-noreply＠bitbucket.org 18 Apr '13

18 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c6d032ef7e42/ Changeset: c6d032ef7e42 Branch: stable User: dan Date: 2013-04-09 18:26:05 Summary: Fix for generating stderr/stdout links in hda show_params. Affected #: 1 file diff -r acf3193e027bbf6f71193c69e3796056e9d7dcdd -r c6d032ef7e420b158248aeb71c65914799a78122 templates/show_params.mako --- a/templates/show_params.mako +++ b/templates/show_params.mako @@ -105,6 +105,9 @@ </th></tr></thead><tbody> + <% + encoded_hda_id = trans.security.encode_id( hda.id ) + %><tr><td>Name:</td><td>${hda.name | h}</td></tr><tr><td>Created:</td><td>${hda.create_time.strftime("%b %d, %Y")}</td></tr> ## <tr><td>Copied from another history?</td><td>${hda.source_library_dataset}</td></tr> @@ -113,9 +116,10 @@ <tr><td>Format:</td><td>${hda.ext | h}</td></tr><tr><td>Galaxy Tool Version:</td><td>${job.tool_version | h}</td></tr><tr><td>Tool Version:</td><td>${hda.tool_version | h}</td></tr> - <tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout')}">stdout</a></td></tr> - <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr')}">stderr</a></td></tr> + <tr><td>Tool Standard Output:</td><td><a href="${h.url_for( controller='dataset', action='stdout', dataset_id=encoded_hda_id )}">stdout</a></td></tr> + <tr><td>Tool Standard Error:</td><td><a href="${h.url_for( controller='dataset', action='stderr', dataset_id=encoded_hda_id )}">stderr</a></td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr> + <tr><td>API ID:</td><td>${encoded_hda_id}</td></tr> %if trans.user_is_admin() or trans.app.config.expose_dataset_path: <tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr> %endif 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: dannon: Web Framework: Adjust logic for creating new sessions in the case of use_remote_user -- was preventing some display applications from functioning correctly
by commits-noreply＠bitbucket.org 17 Apr '13

17 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7d5a1290587c/ Changeset: 7d5a1290587c User: dannon Date: 2013-04-18 04:28:09 Summary: Web Framework: Adjust logic for creating new sessions in the case of use_remote_user -- was preventing some display applications from functioning correctly Affected #: 1 file diff -r 6d84efb087eb040bef8d388d1ca9c29da3f48725 -r 7d5a1290587ccd49ad06d7a85adc571410cc305c lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -539,27 +539,29 @@ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, self.app.model.GalaxySession.table.c.is_valid==True ) ) \ .first() - # If remote user is in use it can invalidate the session, so we need to to check some things now. - if self.app.config.use_remote_user: - #If this is an api request, and they've passed a key, we let this go. - assert "HTTP_REMOTE_USER" in self.environ, \ - "use_remote_user is set but no HTTP_REMOTE_USER variable" - remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] - if galaxy_session: - # An existing session, make sure correct association exists - if galaxy_session.user is None: - # No user, associate - galaxy_session.user = self.get_or_create_remote_user( remote_user_email ) - galaxy_session_requires_flush = True - elif galaxy_session.user.email != remote_user_email: - # Session exists but is not associated with the correct remote user - invalidate_existing_session = True - user_for_new_session = self.get_or_create_remote_user( remote_user_email ) - log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, galaxy_session.user.email ) - else: - # No session exists, get/create user for new session + # If remote user is in use it can invalidate the session and in some + # cases won't have a cookie set above, so we need to to check some + # things now. + if self.app.config.use_remote_user: + #If this is an api request, and they've passed a key, we let this go. + assert "HTTP_REMOTE_USER" in self.environ, \ + "use_remote_user is set but no HTTP_REMOTE_USER variable" + remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] + if galaxy_session: + # An existing session, make sure correct association exists + if galaxy_session.user is None: + # No user, associate + galaxy_session.user = self.get_or_create_remote_user( remote_user_email ) + galaxy_session_requires_flush = True + elif galaxy_session.user.email != remote_user_email: + # Session exists but is not associated with the correct remote user + invalidate_existing_session = True user_for_new_session = self.get_or_create_remote_user( remote_user_email ) + log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", + remote_user_email, galaxy_session.user.email ) + else: + # No session exists, get/create user for new session + user_for_new_session = self.get_or_create_remote_user( remote_user_email ) else: if galaxy_session is not None and galaxy_session.user and galaxy_session.user.external: # Remote user support is not enabled, but there is an existing 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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