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

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Jun '13

06 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2a1459ef5bc4/ Changeset: 2a1459ef5bc4 Branch: stable User: natefoo Date: 2013-06-05 21:25:19 Summary: Fix a couple bugs in job recovery in the Condor runner found by Branden Timm. Affected #: 1 file diff -r 47b86d6a9077facb54804576be49ca545d18bd4e -r 2a1459ef5bc402c585f24c904e0d5ad82a7326db lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -232,6 +232,7 @@ """Recovers jobs stuck in the queued/running state when Galaxy started""" # TODO Check if we need any changes here job_id = job.get_job_runner_external_id() + galaxy_id_tag = job_wrapper.get_id_tag() if job_id is None: self.put( job_wrapper ) return @@ -252,7 +253,7 @@ cjs.running = False self.monitor_queue.put( cjs ) - def __old_state_paths( self, cjs, job ): + def __old_state_paths( self, cjs ): """For recovery of jobs started prior to standardizing the naming of files in the AsychronousJobState object """ https://bitbucket.org/galaxy/galaxy-central/commits/af91c734dbb7/ Changeset: af91c734dbb7 User: natefoo Date: 2013-06-05 21:25:30 Summary: Merge stable Affected #: 1 file diff -r 89d391f23c1bfb9a745b03095dbcf0459b830e19 -r af91c734dbb76b8c0e3166c7471370f9ba8260b5 lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -232,6 +232,7 @@ """Recovers jobs stuck in the queued/running state when Galaxy started""" # TODO Check if we need any changes here job_id = job.get_job_runner_external_id() + galaxy_id_tag = job_wrapper.get_id_tag() if job_id is None: self.put( job_wrapper ) return @@ -252,7 +253,7 @@ cjs.running = False self.monitor_queue.put( cjs ) - def __old_state_paths( self, cjs, job ): + def __old_state_paths( self, cjs ): """For recovery of jobs started prior to standardizing the naming of files in the AsychronousJobState object """ 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 05 Jun '13

05 Jun '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/81a20de198df/ Changeset: 81a20de198df User: dannon Date: 2013-06-05 17:24:55 Summary: Require decorator in manage_db.py -- resolves decorator not found for particular deployments Affected #: 1 file diff -r 4612c80302918943c3b4375613554a4f4960e8c8 -r 81a20de198df2480ef9ba4dfb87201ba14e048cc scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -6,6 +6,7 @@ from galaxy import eggs +eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) eggs.require( "sqlalchemy_migrate" ) https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077/ Changeset: 47b86d6a9077 Branch: stable User: dannon Date: 2013-06-05 17:24:55 Summary: Require decorator in manage_db.py -- resolves decorator not found for particular deployments Affected #: 1 file diff -r c4096b030f10eb346b24da98ce16b72d23672f03 -r 47b86d6a9077facb54804576be49ca545d18bd4e scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -6,6 +6,7 @@ from galaxy import eggs +eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) eggs.require( "sqlalchemy_migrate" ) https://bitbucket.org/galaxy/galaxy-central/commits/89d391f23c1b/ Changeset: 89d391f23c1b User: dannon Date: 2013-06-05 17:25:24 Summary: Merge with stable Affected #: 0 files 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 05 Jun '13

05 Jun '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4c31bdad50d2/ Changeset: 4c31bdad50d2 User: dannon Date: 2013-06-05 16:13:40 Summary: Strip select2 behavior from quota, role, and group creation in the admin panel Affected #: 3 files diff -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c templates/admin/dataset_security/group/group_create.mako --- a/templates/admin/dataset_security/group/group_create.mako +++ b/templates/admin/dataset_security/group/group_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c templates/admin/dataset_security/role/role_create.mako --- a/templates/admin/dataset_security/role/role_create.mako +++ b/templates/admin/dataset_security/role/role_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c templates/admin/quota/quota_create.mako --- a/templates/admin/quota/quota_create.mako +++ b/templates/admin/quota/quota_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> https://bitbucket.org/galaxy/galaxy-central/commits/c4096b030f10/ Changeset: c4096b030f10 Branch: stable User: dannon Date: 2013-06-05 16:13:40 Summary: Strip select2 behavior from quota, role, and group creation in the admin panel Affected #: 3 files diff -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 -r c4096b030f10eb346b24da98ce16b72d23672f03 templates/admin/dataset_security/group/group_create.mako --- a/templates/admin/dataset_security/group/group_create.mako +++ b/templates/admin/dataset_security/group/group_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 -r c4096b030f10eb346b24da98ce16b72d23672f03 templates/admin/dataset_security/role/role_create.mako --- a/templates/admin/dataset_security/role/role_create.mako +++ b/templates/admin/dataset_security/role/role_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 -r c4096b030f10eb346b24da98ce16b72d23672f03 templates/admin/quota/quota_create.mako --- a/templates/admin/quota/quota_create.mako +++ b/templates/admin/quota/quota_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> https://bitbucket.org/galaxy/galaxy-central/commits/4612c8030291/ Changeset: 4612c8030291 User: dannon Date: 2013-06-05 16:14:37 Summary: Merge w/ stable Affected #: 4 files diff -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c -r 4612c80302918943c3b4375613554a4f4960e8c8 .hgtags --- a/.hgtags +++ b/.hgtags @@ -2,3 +2,4 @@ 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 +524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 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: 2 new changesets
by commits-noreply＠bitbucket.org 05 Jun '13

05 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a6e2e099e89a/ Changeset: a6e2e099e89a User: greg Date: 2013-06-05 15:58:11 Summary: Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories. Affected #: 1 file diff -r 583f5edfc5977d92f884d86eb9f1af22294fe4c7 -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e 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 @@ -252,6 +252,8 @@ # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. required_repository_tups = [] for repo_info_dict in repo_info_dicts: + if repo_info_dict not in all_repo_info_dicts: + all_repo_info_dicts.append( repo_info_dict ) for repository_name, repo_info_tup in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tup ) https://bitbucket.org/galaxy/galaxy-central/commits/7f26e0efb93b/ Changeset: 7f26e0efb93b Branch: stable User: greg Date: 2013-06-05 15:58:11 Summary: Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories. Affected #: 1 file diff -r 2dd18c7198ad7ff1c354dbefa0715b2344360487 -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 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 @@ -252,6 +252,8 @@ # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. required_repository_tups = [] for repo_info_dict in repo_info_dicts: + if repo_info_dict not in all_repo_info_dicts: + all_repo_info_dicts.append( repo_info_dict ) for repository_name, repo_info_tup in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tup ) 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: Dave Bouvier: Add information on why a repository was not tested, if it has been configured not to be tested.
by commits-noreply＠bitbucket.org 05 Jun '13

05 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/583f5edfc597/ Changeset: 583f5edfc597 User: Dave Bouvier Date: 2013-06-04 21:54:28 Summary: Add information on why a repository was not tested, if it has been configured not to be tested. Affected #: 1 file diff -r 393b3d86fbf1b8c1471faef828de31110d3a90f5 -r 583f5edfc5977d92f884d86eb9f1af22294fe4c7 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 @@ -743,6 +743,10 @@ skip_because = reason break if skip_this_repository: + repository_status[ 'not_tested' ] = dict( reason=skip_because ) + params[ 'tools_functionally_correct' ] = False + params[ 'do_not_test' ] = False + register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, repository_info_dict, params ) log.info( "Not testing revision %s of repository %s owned by %s.", changeset_revision, name, owner ) continue else: @@ -854,6 +858,10 @@ # "missing_components": "Which components are missing, e.g. the test data filename, or the test-data directory." # }, # ] + # "not_tested": + # { + # "reason": "The Galaxy development team has determined that this repository should not be installed and tested by the automated framework." + # } # } failed_tool_dependencies = repository.includes_tool_dependencies and repository.tool_dependencies_with_installation_errors failed_repository_dependencies = repository.repository_dependencies_with_installation_errors Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Add a not tested container for the automated tool test results in the tool shed.
by commits-noreply＠bitbucket.org 05 Jun '13

05 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/393b3d86fbf1/ Changeset: 393b3d86fbf1 User: greg Date: 2013-06-04 21:50:25 Summary: Add a not tested container for the automated tool test results in the tool shed. Affected #: 2 files diff -r 4466b12313cc7e22e941c1255ba989e3adbbadf1 -r 393b3d86fbf1b8c1471faef828de31110d3a90f5 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -36,6 +36,7 @@ self.tool_dependencies = [] self.failed_tests = [] self.missing_test_components = [] + self.not_tested = [] self.passed_tests = [] self.test_environments = [] self.repository_dependencies = [] @@ -161,6 +162,14 @@ self.tool_version = tool_version +class NotTested( object ): + """NotTested object""" + + def __init__( self, id=None, reason=None ): + self.id = id + self.reason = reason + + class PassedTest( object ): """Passed tool tests object""" @@ -1048,6 +1057,15 @@ tool_shed_mercurial_version=test_environment_dict.get( 'tool_shed_mercurial_version', '' ), tool_shed_revision=test_environment_dict.get( 'tool_shed_revision', '' ) ) folder.test_environments.append( test_environment ) + not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) + if not_tested_dict: + folder_id += 1 + folder = Folder( id=folder_id, key='not_tested', label='Not tested', parent=test_results_folder ) + test_results_folder.folders.append( folder ) + not_tested_id = 0 + not_tested = NotTested( id=not_tested_id, + reason=not_tested_dict.get( 'reason', '' ) ) + folder.not_tested.append( not_tested ) passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) if passed_tests_dicts: folder_id += 1 diff -r 4466b12313cc7e22e941c1255ba989e3adbbadf1 -r 393b3d86fbf1b8c1471faef828de31110d3a90f5 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -337,6 +337,11 @@ ${render_failed_test( failed_test, pad, my_row, row_counter )} %endfor %endif + %if folder.not_tested: + %for not_tested in folder.not_tested: + ${render_not_tested( not_tested, pad, my_row, row_counter )} + %endfor + %endif %if folder.passed_tests: %for passed_test in folder.passed_tests: ${render_passed_test( passed_test, pad, my_row, row_counter )} @@ -731,6 +736,35 @@ %></%def> +<%def name="render_not_tested( not_tested, pad, parent, row_counter, row_is_header=False )"> + <% encoded_id = trans.security.encode_id( not_tested.id ) %> + <style type="text/css"> + #not_tested_table{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table id="not_tested_table"> + <tr><td>${not_tested.reason | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( passed_test.id ) %><style type="text/css"> 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: afgane: Add tabindex to cloudlaunch and set the width for select boxes
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4466b12313cc/ Changeset: 4466b12313cc User: afgane Date: 2013-06-04 20:24:10 Summary: Add tabindex to cloudlaunch and set the width for select boxes Affected #: 1 file diff -r a28faa6ac188594a60cd495327661a15efd37ea5 -r 4466b12313cc7e22e941c1255ba989e3adbbadf1 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -186,16 +186,16 @@ <div class="form-row"><label for="id_key_id">Key ID</label> - <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value=""/><br/> + <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value="" tabindex="1"/><br/><div class="toolParamHelp"> - This is the text string that uniquely identifies your account, found in the + This is the text string that uniquely identifies your account, found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>. </div></div><div class="form-row"><label for="id_secret">Secret Key</label> - <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value=""/><br/> + <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value="" tabindex="2"/><br/><div class="toolParamHelp"> This is your AWS Secret Key, also found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>. </div> @@ -205,7 +205,7 @@ %if not share_string: <div id='existing_instance_wrapper' style="display:none;" class="form-row"><label for="id_existing_instance">Instances in your account</label> - <select name="existing_instance" id="id_existing_instance"> + <select name="existing_instance" id="id_existing_instance" style="min-width: 228px"></select><input id='id_zone' type='hidden' name='zone' value=''/></div> @@ -231,7 +231,7 @@ <div class="form-row"><label for="id_keypair">Key Pair</label> - <select name="keypair" id="id_keypair"> + <select name="keypair" id="id_keypair" style="min-width: 228px"><option name="Create" value="cloudman_keypair">cloudman_keypair</option></select></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Data Managers: allow multiple value translations to be specifed per column and also allow multiple types of value translations.
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a28faa6ac188/ Changeset: a28faa6ac188 User: dan Date: 2013-06-04 20:05:20 Summary: Data Managers: allow multiple value translations to be specifed per column and also allow multiple types of value translations. Affected #: 1 file diff -r df488dbd5bdb22dc78549118834788992e5cabcb -r a28faa6ac188594a60cd495327661a15efd37ea5 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -16,6 +16,8 @@ log = logging.getLogger( __name__ ) SUPPORTED_DATA_TABLE_TYPES = ( TabularToolDataTable ) +VALUE_TRANSLATION_FUNCTIONS = dict( abspath=os.path.abspath ) +DEFAULT_VALUE_TRANSLATION_TYPE = 'template' class DataManagers( object ): def __init__( self, app, xml_filename=None ): @@ -160,15 +162,24 @@ if data_table_name not in self.output_ref_by_data_table: self.output_ref_by_data_table[ data_table_name ] = {} self.output_ref_by_data_table[ data_table_name ][ data_table_coumn_name ] = output_ref - value_translation_elem = column_elem.find( 'value_translation' ) - if value_translation_elem is not None: - value_translation = value_translation_elem.text - else: - value_translation = None - if value_translation is not None: - if data_table_name not in self.value_translation_by_data_table_column: - self.value_translation_by_data_table_column[ data_table_name ] = {} - self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = value_translation + value_translation_elems = column_elem.findall( 'value_translation' ) + if value_translation_elems is not None: + for value_translation_elem in value_translation_elems: + value_translation = value_translation_elem.text + if value_translation is not None: + value_translation_type = value_translation_elem.get( 'type', DEFAULT_VALUE_TRANSLATION_TYPE ) + if data_table_name not in self.value_translation_by_data_table_column: + self.value_translation_by_data_table_column[ data_table_name ] = {} + if data_table_coumn_name not in self.value_translation_by_data_table_column[ data_table_name ]: + self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = [] + if value_translation_type == 'function': + if value_translation in VALUE_TRANSLATION_FUNCTIONS: + value_translation = VALUE_TRANSLATION_FUNCTIONS[ value_translation ] + else: + raise ValueError( "Unsupported value translation function: '%s'" % ( value_translation ) ) + else: + assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError( "Unsupported value translation type: '%s'" % ( value_translation_type ) ) + self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ].append( value_translation ) for move_elem in column_elem.findall( 'move' ): move_type = move_elem.get( 'type', 'directory' ) @@ -290,8 +301,11 @@ def process_value_translation( self, data_table_name, column_name, **kwd ): value = kwd.get( column_name ) if data_table_name in self.value_translation_by_data_table_column and column_name in self.value_translation_by_data_table_column[ data_table_name ]: - value_translation = self.value_translation_by_data_table_column[ data_table_name ][ column_name ] - value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) + for value_translation in self.value_translation_by_data_table_column[ data_table_name ][ column_name ]: + if isinstance( value_translation, basestring ): + value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) + else: + value = value_translation( value ) return value def get_tool_shed_repository_info_dict( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Eliminate the use of util.Params in tool shed controller methods.
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df488dbd5bdb/ Changeset: df488dbd5bdb User: greg Date: 2013-06-04 19:36:14 Summary: Eliminate the use of util.Params in tool shed controller methods. Affected #: 3 files diff -r f3cfd3936759aa70f3a3b772ecf469e1a059d7cb -r df488dbd5bdb22dc78549118834788992e5cabcb lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -31,7 +31,7 @@ # with an "f-" prefix, simulating filtering by clicking a search link. We have # to take this approach because the "-" character is illegal in HTTP requests. if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -119,12 +119,11 @@ @web.expose @web.require_admin def create_category( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - name = util.restore_text( params.get( 'name', '' ) ).strip() - description = util.restore_text( params.get( 'description', '' ) ).strip() - if params.get( 'create_category_button', False ): + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + name = kwd.get( 'name', '' ).strip() + description = kwd.get( 'description', '' ).strip() + if kwd.get( 'create_category_button', False ): if not name or not description: message = 'Enter a valid name and a description' status = 'error' @@ -151,9 +150,8 @@ @web.expose @web.require_admin def delete_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. @@ -188,9 +186,8 @@ @web.expose @web.require_admin def delete_repository_metadata( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: ids = util.listify( id ) @@ -213,10 +210,9 @@ @web.expose @web.require_admin def edit_category( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = params.get( 'id', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + id = kwd.get( 'id', None ) if not id: message = "No category ids received for editing" trans.response.send_redirect( web.url_for( controller='admin', @@ -224,9 +220,9 @@ message=message, status='error' ) ) category = suc.get_category( trans, id ) - if params.get( 'edit_category_button', False ): - new_name = util.restore_text( params.get( 'name', '' ) ).strip() - new_description = util.restore_text( params.get( 'description', '' ) ).strip() + if kwd.get( 'edit_category_button', False ): + new_name = kwd.get( 'name', '' ).strip() + new_description = kwd.get( 'description', '' ).strip() if category.name != new_name or category.description != new_description: if not new_name: message = 'Enter a valid name' @@ -288,9 +284,8 @@ @web.expose @web.require_admin def regenerate_statistics( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if 'regenerate_statistics_button' in kwd: trans.app.shed_counter.generate_statistics() message = "Successfully regenerated statistics" @@ -315,9 +310,8 @@ @web.expose @web.require_admin def undelete_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. @@ -358,9 +352,8 @@ # TODO: We should probably eliminate the Category.deleted column since it really makes no # sense to mark a category as deleted (category names and descriptions can be changed instead). # If we do this, and the following 2 methods can be eliminated. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: ids = util.listify( id ) @@ -385,9 +378,8 @@ # This method should only be called for a Category that has previously been deleted. # Purging a deleted Category deletes all of the following from the database: # - RepoitoryCategoryAssociations where category_id == Category.id - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: ids = util.listify( id ) @@ -414,9 +406,8 @@ @web.expose @web.require_admin def undelete_category( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: ids = util.listify( id ) diff -r f3cfd3936759aa70f3a3b772ecf469e1a059d7cb -r df488dbd5bdb22dc78549118834788992e5cabcb lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -657,10 +657,9 @@ @web.expose def browse_repository( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. @@ -833,14 +832,13 @@ @web.expose def check_for_updates( self, trans, **kwd ): """Handle a request from a local Galaxy instance.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) # If the request originated with the UpdateManager, it will not include a galaxy_url. galaxy_url = suc.handle_galaxy_url( trans, **kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -913,9 +911,8 @@ @web.expose def contact_owner( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) if trans.user and trans.user.email: @@ -948,9 +945,8 @@ @web.expose def create_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) categories = suc.get_categories( trans ) if not categories: message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + \ @@ -960,12 +956,12 @@ action='browse_repositories', message=message, status=status ) ) - name = util.restore_text( params.get( 'name', '' ) ) - description = util.restore_text( params.get( 'description', '' ) ) - long_description = util.restore_text( params.get( 'long_description', '' ) ) - category_ids = util.listify( params.get( 'category_id', '' ) ) + name = kwd.get( 'name', '' ) + description = kwd.get( 'description', '' ) + long_description = kwd.get( 'long_description', '' ) + category_ids = util.listify( kwd.get( 'category_id', '' ) ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] - if params.get( 'create_repository_button', False ): + if kwd.get( 'create_repository_button', False ): error = False message = self.__validate_repository_name( name, trans.user ) if message: @@ -1031,12 +1027,11 @@ """Mark a repository in the tool shed as deprecated or not deprecated.""" # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset revisions that may be associated with the # repository. Revisions are not marked as not downlaodable because those that have installed the repository must be allowed to get updates. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository_id = params.get( 'id', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_id = kwd.get( 'id', None ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) - mark_deprecated = util.string_as_bool( params.get( 'mark_deprecated', False ) ) + mark_deprecated = util.string_as_bool( kwd.get( 'mark_deprecated', False ) ) repository.deprecated = mark_deprecated trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1052,9 +1047,8 @@ @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository, tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) if message: status = 'error' @@ -1105,7 +1099,6 @@ @web.expose def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. - params = util.Params( kwd ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) # Allow hgweb to handle the download. This requires the tool shed # server account's .hgrc file to include the following setting: @@ -1125,9 +1118,8 @@ @web.expose def find_tools( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) @@ -1169,7 +1161,7 @@ tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] - exact_matches = params.get( 'exact_matches', '' ) + exact_matches = kwd.get( 'exact_matches', '' ) exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] ok = True @@ -1210,9 +1202,8 @@ @web.expose def find_workflows( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if 'operation' in kwd: item_id = kwd.get( 'id', '' ) @@ -1253,7 +1244,7 @@ return trans.show_error_message( "No items were selected." ) if 'find_workflows_button' in kwd: workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ] - exact_matches = params.get( 'exact_matches', '' ) + exact_matches = kwd.get( 'exact_matches', '' ) exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] ok = True @@ -1327,12 +1318,11 @@ if 'workflows' in metadata: includes_workflows = True return includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), @@ -1532,10 +1522,9 @@ @web.json def get_repository_dependencies( self, trans, **kwd ): """Return an encoded dictionary of all repositories upon which the contents of the received repository depends.""" - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_id = trans.security.encode_id( repository.id ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -1629,10 +1618,9 @@ @web.expose def get_tool_dependencies( self, trans, **kwd ): """Handle a request from a Galaxy instance to get the tool_dependencies entry from the metadata for a specified changeset revision.""" - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) for downloadable_revision in repository.downloadable_revisions: if downloadable_revision.changeset_revision == changeset_revision: @@ -1646,10 +1634,9 @@ @web.expose def get_tool_dependencies_config_contents( self, trans, **kwd ): """Handle a request from a Galaxy instance to get the tool_dependencies.xml file contents for a specified changeset revision.""" - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) # TODO: We're currently returning the tool_dependencies.xml file that is available on disk. We need to enhance this process # to retrieve older versions of the tool-dependencies.xml file from the repository manafest. @@ -1786,9 +1773,8 @@ @web.expose def help( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): @@ -1840,9 +1826,8 @@ @web.expose def index( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) # See if there are any RepositoryMetadata records since menu items require them. repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first() current_user = trans.user @@ -1861,9 +1846,9 @@ break # Route in may have been from a sharable URL, in whcih case we'll have a user_id and possibly a name # The received user_id will be the id of the repository owner. - user_id = params.get( 'user_id', None ) - repository_id = params.get( 'repository_id', None ) - changeset_revision = params.get( 'changeset_revision', None ) + user_id = kwd.get( 'user_id', None ) + repository_id = kwd.get( 'repository_id', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) return trans.fill_template( '/webapps/tool_shed/index.mako', repository_metadata=repository_metadata, has_reviewed_repositories=has_reviewed_repositories, @@ -1904,9 +1889,8 @@ @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'error' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'error' ) repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) invalid_file_tups = [] @@ -1958,13 +1942,12 @@ @web.expose @web.require_login( "manage email alerts" ) def manage_email_alerts( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - new_repo_alert = params.get( 'new_repo_alert', '' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + new_repo_alert = kwd.get( 'new_repo_alert', '' ) new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert ) user = trans.user - if params.get( 'new_repo_alert_button', False ): + if kwd.get( 'new_repo_alert_button', False ): user.new_repo_alert = new_repo_alert_checked trans.sa_session.add( user ) trans.sa_session.flush() @@ -1990,15 +1973,15 @@ @web.expose @web.require_login( "manage repository" ) def manage_repository( self, trans, id, **kwd ): - message = util.restore_text( kwd.get( 'message', '' ) ) + message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - repo_name = util.restore_text( kwd.get( 'repo_name', repository.name ) ) - changeset_revision = util.restore_text( kwd.get( 'changeset_revision', repository.tip( trans.app ) ) ) - description = util.restore_text( kwd.get( 'description', repository.description ) ) - long_description = util.restore_text( kwd.get( 'long_description', repository.long_description ) ) + repo_name = kwd.get( 'repo_name', repository.name ) + changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) + description = kwd.get( 'description', repository.description ) + long_description = kwd.get( 'long_description', repository.long_description ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) alerts = kwd.get( 'alerts', '' ) @@ -2223,9 +2206,8 @@ @web.expose @web.require_login( "multi select email alerts" ) def multi_select_email_alerts( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "receive email alerts": @@ -2263,13 +2245,12 @@ @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) + changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ), @@ -2316,12 +2297,11 @@ older changeset_revsion, but later the repository was updated in the tool shed and the Galaxy admin is trying to install the latest changeset revision of the same repository instead of updating the one that was previously installed. """ - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -2340,10 +2320,9 @@ @web.require_login( "rate repositories" ) def rate_repository( self, trans, **kwd ): """ Rate a repository and return updated rating data. """ - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = params.get( 'id', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + id = kwd.get( 'id', None ) if not id: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -2356,12 +2335,12 @@ action='browse_repositories', message="You are not allowed to rate your own repository", status='error' ) ) - if params.get( 'rate_button', False ): - rating = int( params.get( 'rating', '0' ) ) - comment = util.restore_text( params.get( 'comment', '' ) ) + if kwd.get( 'rate_button', False ): + rating = int( kwd.get( 'rating', '0' ) ) + comment = kwd.get( 'comment', '' ) rating = self.rate_item( trans, trans.user, repository, rating, comment ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) + display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', @@ -2397,7 +2376,7 @@ if 'reset_metadata_on_selected_repositories_button' in kwd: message, status = metadata_util.reset_metadata_on_selected_repositories( trans, **kwd ) else: - message = util.restore_text( kwd.get( 'message', '' ) ) + message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repositories_select_field = suc.build_repository_ids_select_field( trans, my_writable=True ) return trans.fill_template( '/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako', @@ -2507,15 +2486,14 @@ @web.expose def select_files_to_delete( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + commit_message = kwd.get( 'commit_message', 'Deleted selected files' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) - if params.get( 'select_files_to_delete_button', False ): + selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' ) + if kwd.get( 'select_files_to_delete_button', False ): if selected_files_to_delete: selected_files_to_delete = selected_files_to_delete.split( ',' ) # Get the current repository tip. @@ -2771,10 +2749,9 @@ revision for the required repository, making it impossible to discover the repository without knowledge of revisions to which it could have been updated. """ - params = util.Params( kwd ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -2811,9 +2788,8 @@ @web.expose def view_changelog( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) changesets = [] @@ -2847,9 +2823,8 @@ @web.expose def view_changeset( self, trans, id, ctx_str, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) ctx = suc.get_changectx_for_changeset( repo, ctx_str ) @@ -2925,15 +2900,14 @@ @web.expose def view_repository( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) - display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) - alerts = params.get( 'alerts', '' ) + changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) + display_reviews = kwd.get( 'display_reviews', False ) + alerts = kwd.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) if repository.email_alerts: email_alerts = json.from_json_string( repository.email_alerts ) @@ -2941,7 +2915,7 @@ email_alerts = [] repository_dependencies = None user = trans.user - if user and params.get( 'receive_email_alerts_button', False ): + if user and kwd.get( 'receive_email_alerts_button', False ): flush_needed = False if alerts_checked: if user.email not in email_alerts: @@ -3009,9 +2983,8 @@ @web.expose def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) repo_files_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) @@ -3081,9 +3054,8 @@ @web.expose def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ): """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) diff -r f3cfd3936759aa70f3a3b772ecf469e1a059d7cb -r df488dbd5bdb22dc78549118834788992e5cabcb lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -34,9 +34,8 @@ @web.require_login( "approve repository review" ) def approve_repository_review( self, trans, **kwd ): # The value of the received id is the encoded review id. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) encoded_review_id = kwd[ 'id' ] review = review_util.get_review( trans, encoded_review_id ) if kwd.get( 'approve_repository_review_button', False ): @@ -69,9 +68,8 @@ @web.expose @web.require_login( "browse review" ) def browse_review( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) review = review_util.get_review( trans, kwd[ 'id' ] ) repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) @@ -101,12 +99,11 @@ @web.expose @web.require_login( "create component" ) def create_component( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - name = util.restore_text( params.get( 'name', '' ) ) - description = util.restore_text( params.get( 'description', '' ) ) - if params.get( 'create_component_button', False ): + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + name = kwd.get( 'name', '' ) + description = kwd.get( 'description', '' ) + if kwd.get( 'create_component_button', False ): if not name or not description: message = 'Enter a valid name and a description' status = 'error' @@ -133,9 +130,8 @@ @web.require_login( "create review" ) def create_review( self, trans, **kwd ): # The value of the received id is the encoded repository id. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) changeset_revision = kwd.get( 'changeset_revision', None ) previous_review_id = kwd.get( 'previous_review_id', None ) @@ -197,10 +193,9 @@ @web.expose @web.require_login( "edit component" ) def edit_component( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = params.get( 'id', None ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + id = kwd.get( 'id', None ) if not id: message = "No component ids received for editing" trans.response.send_redirect( web.url_for( controller='admin', @@ -208,8 +203,8 @@ message=message, status='error' ) ) component = review_util.get_component( trans, id ) - if params.get( 'edit_component_button', False ): - new_description = util.restore_text( params.get( 'description', '' ) ).strip() + if kwd.get( 'edit_component_button', False ): + new_description = kwd.get( 'description', '' ).strip() if component.description != new_description: component.description = new_description trans.sa_session.add( component ) @@ -229,9 +224,8 @@ @web.require_login( "edit review" ) def edit_review( self, trans, **kwd ): # The value of the received id is the encoded review id. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) review_id = kwd.get( 'id', None ) review = review_util.get_review( trans, review_id ) components_dict = odict() @@ -403,9 +397,8 @@ @web.require_login( "manage repositories reviewed by me" ) def manage_repositories_reviewed_by_me( self, trans, **kwd ): # The value of the received id is the encoded repository id. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if 'operation' in kwd: kwd[ 'mine' ] = True return trans.response.send_redirect( web.url_for( controller='repository_review', @@ -471,9 +464,8 @@ @web.require_login( "manage repository reviews" ) def manage_repository_reviews( self, trans, mine=False, **kwd ): # The value of the received id is the encoded repository id. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id: repository = suc.get_repository_in_tool_shed( trans, repository_id ) @@ -519,9 +511,8 @@ @web.require_login( "manage repository reviews of revision" ) def manage_repository_reviews_of_revision( self, trans, **kwd ): # The value of the received id is the encoded repository id. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) @@ -542,9 +533,8 @@ @web.expose @web.require_login( "repository reviews by user" ) def repository_reviews_by_user( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if 'operation' in kwd: operation = kwd['operation'].lower() @@ -569,9 +559,8 @@ @web.expose @web.require_login( "reviewed repositories i own" ) def reviewed_repositories_i_own( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) # The value of the received id is the encoded repository id. if 'operation' in kwd: operation = kwd['operation'].lower() @@ -589,9 +578,8 @@ @web.require_login( "select previous review" ) def select_previous_review( self, trans, **kwd ): # The value of the received id is the encoded repository id. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) 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: 2 new changesets
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2dd18c7198ad/ Changeset: 2dd18c7198ad Branch: stable User: Dave Bouvier Date: 2013-06-04 18:02:55 Summary: Fix missing import. Affected #: 1 file diff -r 2a116647d7d75d5088c43fe3ac1d10bd9e66a08c -r 2dd18c7198ad7ff1c354dbefa0715b2344360487 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -8,6 +8,7 @@ from time import strftime from galaxy import util from galaxy.util import json +from galaxy.util import unicodify from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.datatypes import checkers https://bitbucket.org/galaxy/galaxy-central/commits/f3cfd3936759/ Changeset: f3cfd3936759 User: Dave Bouvier Date: 2013-06-04 18:02:55 Summary: Fix missing import. Affected #: 1 file diff -r ef3816ca5e0cc88616c34144af00b4fcce5bf0d0 -r f3cfd3936759aa70f3a3b772ecf469e1a059d7cb lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -8,6 +8,7 @@ from time import strftime from galaxy import util from galaxy.util import json +from galaxy.util import unicodify from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.datatypes import checkers 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