galaxy-commits November 2012

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commit/galaxy-central: natefoo: Explicitly import galaxy.util.shed_util in galaxy.tool_shed that was causing a failure to start on test.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8420c9a0f730/ changeset: 8420c9a0f730 user: natefoo date: 2012-11-26 19:45:14 summary: Explicitly import galaxy.util.shed_util in galaxy.tool_shed that was causing a failure to start on test. affected #: 1 file diff -r f03725b8272bd13aa3fc693b9fcb20d2f0f4c28f -r 8420c9a0f7308bbbd79c0a0db29dab063ff9070a lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -2,7 +2,7 @@ Classes encapsulating the management of repositories installed from Galaxy tool sheds. """ import os -from galaxy.util.shed_util import * +import galaxy.util.shed_util from galaxy.model.orm import * from galaxy import eggs @@ -27,7 +27,7 @@ ElementInclude.include( root ) tool_path = root.get( 'tool_path', None ) if tool_path: - tool_shed = clean_tool_shed_url( tool_shed_repository.tool_shed ) + tool_shed = galaxy.util.shed_util.clean_tool_shed_url( tool_shed_repository.tool_shed ) relative_path = os.path.join( tool_path, tool_shed, 'repos', @@ -44,13 +44,13 @@ .order_by( self.model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - installed_repository_dict = load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = galaxy.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) if installed_repository_dict: self.installed_repository_dicts.append( installed_repository_dict ) def load_proprietary_converters_and_display_applications( self, deactivate=False ): for installed_repository_dict in self.installed_repository_dicts: if installed_repository_dict[ 'converter_path' ]: - load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + galaxy.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) - \ No newline at end of file + galaxy.util.shed_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + 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: 4 new changesets
by Bitbucket 26 Nov '12

26 Nov '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ec3b5956130f/ changeset: ec3b5956130f user: jmchilton date: 2012-10-31 18:18:55 summary: Fix small bug in exception handler in lib/galaxy/jobs/handler.py. The bug was preventing exceptions in dynamic job runner methods from being percolated up into the logs. affected #: 1 file diff -r 4ceab232dc02a5a99eca0b24c0038c490d49a392 -r ec3b5956130f767d6f5d9c07c6a64dafd128351f lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -397,6 +397,11 @@ def put( self, job_wrapper ): try: runner_name = self.__get_runner_name( job_wrapper ) + except Exception: + log.exception( 'Failed to generate job runner name' ) + job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) + return + try: if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and isinstance(job_wrapper, TaskWrapper): #DBTODO Refactor log.debug( "dispatching task %s, of job %d, to %s runner" %( job_wrapper.task_id, job_wrapper.job_id, runner_name ) ) https://bitbucket.org/galaxy/galaxy-central/changeset/0206d3a8a4d0/ changeset: 0206d3a8a4d0 user: jmchilton date: 2012-10-31 21:04:33 summary: Allow dynamic job runner rules to pass error messages back to users via job failure message. To do this simply raise galaxy.jobs.mapper.JobMappingException(user_messsage) from a rule method where user_message is the desired message. affected #: 2 files diff -r ec3b5956130f767d6f5d9c07c6a64dafd128351f -r 0206d3a8a4d03b2447ab1ef09cd2a2015ce4c3ae lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -17,6 +17,7 @@ # States for running a job. These are NOT the same as data states JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_READY, JOB_DELETED, JOB_ADMIN_DELETED = 'wait', 'error', 'input_error', 'input_deleted', 'ready', 'deleted', 'admin_deleted' +DEFAULT_JOB_PUT_FAILURE_MESSAGE = 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' class JobHandler( object ): """ @@ -41,6 +42,7 @@ a JobRunner. """ STOP_SIGNAL = object() + def __init__( self, app, dispatcher ): """Start the job manager""" self.app = app @@ -397,9 +399,13 @@ def put( self, job_wrapper ): try: runner_name = self.__get_runner_name( job_wrapper ) - except Exception: - log.exception( 'Failed to generate job runner name' ) - job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) + except Exception, e: + failure_message = getattr(e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE ) + if failure_message == DEFAULT_JOB_PUT_FAILURE_MESSAGE: + log.exception( 'Failed to generate job runner name' ) + else: + log.debug( "Intentionally failing job with message (%s)" % failure_message ) + job_wrapper.fail( failure_message ) return try: if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and isinstance(job_wrapper, TaskWrapper): @@ -410,7 +416,7 @@ self.job_runners[runner_name].put( job_wrapper ) except KeyError: log.error( 'put(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) - job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) + job_wrapper.fail( DEFAULT_JOB_PUT_FAILURE_MESSAGE ) def stop( self, job ): """ @@ -452,7 +458,7 @@ self.job_runners[runner_name].recover( job, job_wrapper ) except KeyError: log.error( 'recover(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) - job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) + job_wrapper.fail( DEFAULT_JOB_PUT_FAILURE_MESSAGE ) def shutdown( self ): for runner in self.job_runners.itervalues(): diff -r ec3b5956130f767d6f5d9c07c6a64dafd128351f -r 0206d3a8a4d03b2447ab1ef09cd2a2015ce4c3ae lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -8,6 +8,12 @@ DYNAMIC_RUNNER_PREFIX = "dynamic:///" +class JobMappingException( Exception ): + + def __init__( self, failure_message ): + self.failure_message = failure_message + + class JobRunnerMapper( object ): """ This class is responsible to managing the mapping of jobs https://bitbucket.org/galaxy/galaxy-central/changeset/6f3b4e88fc21/ changeset: 6f3b4e88fc21 user: jmchilton date: 2012-11-15 05:23:19 summary: Merge latest galaxy-central to resolve conflict introdcued with 73e05bc. affected #: 227 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/f03725b8272b/ changeset: f03725b8272b user: natefoo date: 2012-11-26 19:36:09 summary: Merged in jmchilton/galaxy-central-dynamic-job-runner-enhancements (pull request #82) affected #: 2 files diff -r d0e7bd064cf9a2b991f793c1dc7720430906174f -r f03725b8272bd13aa3fc693b9fcb20d2f0f4c28f lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -17,6 +17,7 @@ # States for running a job. These are NOT the same as data states JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_READY, JOB_DELETED, JOB_ADMIN_DELETED, JOB_USER_OVER_QUOTA = 'wait', 'error', 'input_error', 'input_deleted', 'ready', 'deleted', 'admin_deleted', 'user_over_quota' +DEFAULT_JOB_PUT_FAILURE_MESSAGE = 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' class JobHandler( object ): """ @@ -41,6 +42,7 @@ a JobRunner. """ STOP_SIGNAL = object() + def __init__( self, app, dispatcher ): """Start the job manager""" self.app = app @@ -462,6 +464,15 @@ def put( self, job_wrapper ): try: runner_name = self.__get_runner_name( job_wrapper ) + except Exception, e: + failure_message = getattr(e, 'failure_message', DEFAULT_JOB_PUT_FAILURE_MESSAGE ) + if failure_message == DEFAULT_JOB_PUT_FAILURE_MESSAGE: + log.exception( 'Failed to generate job runner name' ) + else: + log.debug( "Intentionally failing job with message (%s)" % failure_message ) + job_wrapper.fail( failure_message ) + return + try: if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and isinstance(job_wrapper, TaskWrapper): #DBTODO Refactor log.debug( "dispatching task %s, of job %d, to %s runner" %( job_wrapper.task_id, job_wrapper.job_id, runner_name ) ) @@ -470,7 +481,7 @@ self.job_runners[runner_name].put( job_wrapper ) except KeyError: log.error( 'put(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) - job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) + job_wrapper.fail( DEFAULT_JOB_PUT_FAILURE_MESSAGE ) def stop( self, job ): """ @@ -512,7 +523,7 @@ self.job_runners[runner_name].recover( job, job_wrapper ) except KeyError: log.error( 'recover(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) - job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) + job_wrapper.fail( DEFAULT_JOB_PUT_FAILURE_MESSAGE ) def shutdown( self ): for runner in self.job_runners.itervalues(): diff -r d0e7bd064cf9a2b991f793c1dc7720430906174f -r f03725b8272bd13aa3fc693b9fcb20d2f0f4c28f lib/galaxy/jobs/mapper.py --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -8,6 +8,12 @@ DYNAMIC_RUNNER_PREFIX = "dynamic:///" +class JobMappingException( Exception ): + + def __init__( self, failure_message ): + self.failure_message = failure_message + + class JobRunnerMapper( object ): """ This class is responsible to managing the mapping of jobs 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: Don't allow reviewing empty repositories in the tool shed.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d0e7bd064cf9/ changeset: d0e7bd064cf9 user: greg date: 2012-11-26 18:09:23 summary: Don't allow reviewing empty repositories in the tool shed. affected #: 3 files diff -r 593c0d6c3d447aaa79c61fea2688b6091b44dda5 -r d0e7bd064cf9a2b991f793c1dc7720430906174f templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -21,7 +21,7 @@ can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated can_reset_all_metadata = not is_deprecated and is_admin and len( repo ) > 0 has_readme = metadata and 'readme' in metadata - can_review_repository = not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) + can_review_repository = not is_new and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) reviewing_repository = cntrller and cntrller == 'repository_review' if can_push: diff -r 593c0d6c3d447aaa79c61fea2688b6091b44dda5 -r d0e7bd064cf9a2b991f793c1dc7720430906174f templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -20,7 +20,7 @@ browse_label = 'Browse repository tip files' has_readme = metadata and 'readme' in metadata reviewing_repository = cntrller and cntrller == 'repository_review' - can_review_repository = not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) + can_review_repository = not is_new and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) %><%! diff -r 593c0d6c3d447aaa79c61fea2688b6091b44dda5 -r d0e7bd064cf9a2b991f793c1dc7720430906174f templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -8,6 +8,7 @@ from urllib import quote_plus is_admin = trans.user_is_admin() is_new = repository.is_new( trans.app ) + is_deprecated = repository.deprecated can_contact_owner = trans.user and trans.user != repository.user can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push @@ -21,7 +22,7 @@ else: browse_label = 'Browse repository tip files' has_readme = metadata and 'readme' in metadata - can_review_repository = trans.app.security_agent.user_can_review_repositories( trans.user ) + can_review_repository = not is_new and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.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: greg: Fixes for tool shed functional tests.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/593c0d6c3d44/ changeset: 593c0d6c3d44 user: greg date: 2012-11-26 17:43:38 summary: Fixes for tool shed functional tests. affected #: 3 files diff -r 770580cf77ccd49f2a8c2aab2b559c45a318db51 -r 593c0d6c3d447aaa79c61fea2688b6091b44dda5 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -1,9 +1,6 @@ import galaxy.webapps.community.model as model from galaxy.model.orm import * from galaxy.webapps.community.model.mapping import context as sa_session -from base.twilltestcase import * -from sqlalchemy import desc -import sys def delete_obj( obj ): sa_session.delete( obj ) diff -r 770580cf77ccd49f2a8c2aab2b559c45a318db51 -r 593c0d6c3d447aaa79c61fea2688b6091b44dda5 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1,5 +1,4 @@ from base.twilltestcase import * -from tool_shed.base.test_db_util import * class ShedTwillTestCase( TwillTestCase ): def setUp( self ): @@ -37,7 +36,7 @@ self.check_for_strings( strings_displayed, strings_not_displayed ) def check_for_valid_tools( self, repository ): self.manage_repository( repository ) - self.check_page_for_string( '<b>Valid tools</b><i> - click the name to preview the tool' ) + self.check_page_for_string( 'Valid tools' ) def check_repository_changelog( self, repository, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) @@ -149,6 +148,6 @@ self.visit_url( '/upload/upload?repository_id=%s' % self.security.encode_id( repository.id ) ) for key in kwargs: tc.fv( "1", key, kwargs[ key ] ) - tc.formfile( "1", "file_data", filename ) + tc.formfile( "1", "file_data", self.get_filename( filename ) ) tc.submit( "upload_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) diff -r 770580cf77ccd49f2a8c2aab2b559c45a318db51 -r 593c0d6c3d447aaa79c61fea2688b6091b44dda5 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -1,8 +1,3 @@ -import tempfile, time, re, tempfile, os, shutil -import galaxy.webapps.community.model -from galaxy.util import parse_xml, string_as_bool -from galaxy.util.shed_util import clean_tool_shed_url -from galaxy.model.orm import * from tool_shed.base.twilltestcase import * from tool_shed.base.test_db_util import * @@ -19,8 +14,6 @@ repository_name = 'filter' repository_description = "Galaxy's filter tool" repository_long_description = "Long description of Galaxy's filter tool" -files_path = os.path.abspath( os.path.join( "test", "tool_shed", "test_data" ) ) -filter_filename = os.path.join( files_path, "filtering_1.1.0.tar" ) class TestCreateRepository( ShedTwillTestCase ): @@ -65,8 +58,9 @@ def test_0030_upload_tarball( self ): """Upload filtering_1.1.0.tar to the repository""" repository = get_repository_by_name( repository_name, admin_username ) - self.upload( repository, filter_filename, \ - strings_displayed=[ "The file '%s' has been successfully uploaded to the repository." % filter_filename ], \ + self.upload( repository, + 'filtering_1.1.0.tar', + strings_displayed=[ "has been successfully uploaded to the repository." ], commit_message="Uploaded filtering 1.1.0" ) self.check_for_valid_tools( repository ) latest_repository_metadata = self.get_latest_repository_metadata_for_repository( 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: greg: Change name of first tool shed functional test file.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/770580cf77cc/ changeset: 770580cf77cc user: greg date: 2012-11-26 17:24:39 summary: Change name of first tool shed functional test file. affected #: 2 files diff -r a27a0f7d3ac90dfabd1050e26b9216eeb9ebc46b -r 770580cf77ccd49f2a8c2aab2b559c45a318db51 test/tool_shed/functional/test_0000_basic_repository_features.py --- /dev/null +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -0,0 +1,94 @@ +import tempfile, time, re, tempfile, os, shutil +import galaxy.webapps.community.model +from galaxy.util import parse_xml, string_as_bool +from galaxy.util.shed_util import clean_tool_shed_url +from galaxy.model.orm import * +from tool_shed.base.twilltestcase import * +from tool_shed.base.test_db_util import * + +admin_user = None +admin_user_private_role = None +admin_email = 'test(a)bx.psu.edu' +admin_username = 'admin-user' + +regular_user = None +regular_user_private_role = None +regular_email = 'test-1(a)bx.psu.edu' +regular_username = 'user1' + +repository_name = 'filter' +repository_description = "Galaxy's filter tool" +repository_long_description = "Long description of Galaxy's filter tool" +files_path = os.path.abspath( os.path.join( "test", "tool_shed", "test_data" ) ) +filter_filename = os.path.join( files_path, "filtering_1.1.0.tar" ) + +class TestCreateRepository( ShedTwillTestCase ): + + def test_0000_initiate_users( self ): + """Create necessary users and login as an admin user.""" + self.login( email=regular_email, username=regular_username ) + regular_user = get_user( regular_email ) + assert regular_user is not None, 'Problem retrieving user with email %s from the database' % regular_email + regular_user_private_role = get_private_role( regular_user ) + self.logout() + self.login( email=admin_email, username=admin_username ) + admin_user = get_user( admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = get_private_role( admin_user ) + def test_0005_create_categories( self ): + """Create a category""" + self.create_category( 'Text Manipulation', 'Tools for manipulating text' ) + self.create_category( 'Text Analysis', 'Tools for analyzing text' ) + def test_0010_create_repository( self ): + """Create a repository""" + strings_displayed = [ '<div class="toolFormTitle">Repository %s</div>' % "'%s'" % repository_name, \ + 'Repository %s has been created' % "'%s'" % repository_name ] + self.create_repository( repository_name, repository_description, \ + repository_long_description=repository_long_description, \ + categories=[ 'Text Manipulation' ], \ + strings_displayed=strings_displayed ) + def test_0015_edit_repository( self ): + """Edit the repository name, description, and long description""" + repository = get_repository_by_name( repository_name, admin_username ) + new_name = "renamed_filter" + new_description = "Edited filter tool" + new_long_description = "Edited long description" + self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) + def test_0020_change_repository_category( self ): + """Change the category of a repository""" + repository = get_repository_by_name( repository_name, admin_username ) + self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] ) +# def test_0025_grant_write_access( self ): +# '''Grant write access to another user''' +# repository = get_repository_by_name( repository_name, admin_username ) +# self.grant_write_access( repository, usernames=[ regular_username ] ) + def test_0030_upload_tarball( self ): + """Upload filtering_1.1.0.tar to the repository""" + repository = get_repository_by_name( repository_name, admin_username ) + self.upload( repository, filter_filename, \ + strings_displayed=[ "The file '%s' has been successfully uploaded to the repository." % filter_filename ], \ + commit_message="Uploaded filtering 1.1.0" ) + self.check_for_valid_tools( repository ) + latest_repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) + changeset_revision = latest_repository_metadata.changeset_revision + self.check_repository_changelog( repository, strings_displayed=[ 'Repository metadata is associated with this change set.' ] ) + self.set_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) + self.unset_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) + self.load_display_tool_page( repository, tool_xml_filename='filtering.xml', \ + changeset_revision=changeset_revision, \ + strings_displayed=[ 'Filter (version 1.1.0)', "c1=='chr1'" ], \ + strings_not_displayed=[] ) + tool = latest_repository_metadata.metadata[ 'tools' ][0] + metadata_strings_displayed = [ tool[ 'guid' ], tool[ 'version' ], tool[ 'id' ], tool[ 'name' ], tool[ 'description' ], changeset_revision ] + self.check_for_tool_metadata( repository, changeset_revision, 'Filter1', strings_displayed=metadata_strings_displayed ) + def test_0035_repository_browse_page( self ): + '''Visit the repository browse page''' + repository = get_repository_by_name( repository_name, admin_username ) + self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) + def test_0040_visit_clone_url_via_hgweb( self ): + '''Visit the repository clone URL via hgweb''' + repository = get_repository_by_name( repository_name, admin_username ) + latest_changeset_revision = self.get_latest_repository_metadata_for_repository( repository ) + self.display_repository_clone_page( admin_username, \ + repository_name, \ + strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision.changeset_revision ] ) diff -r a27a0f7d3ac90dfabd1050e26b9216eeb9ebc46b -r 770580cf77ccd49f2a8c2aab2b559c45a318db51 test/tool_shed/functional/test_0000_create_repository.py --- a/test/tool_shed/functional/test_0000_create_repository.py +++ /dev/null @@ -1,94 +0,0 @@ -import tempfile, time, re, tempfile, os, shutil -import galaxy.webapps.community.model -from galaxy.util import parse_xml, string_as_bool -from galaxy.util.shed_util import clean_tool_shed_url -from galaxy.model.orm import * -from tool_shed.base.twilltestcase import * -from tool_shed.base.test_db_util import * - -admin_user = None -admin_user_private_role = None -admin_email = 'test(a)bx.psu.edu' -admin_username = 'admin-user' - -regular_user = None -regular_user_private_role = None -regular_email = 'test-1(a)bx.psu.edu' -regular_username = 'user1' - -repository_name = 'filter' -repository_description = "Galaxy's filter tool" -repository_long_description = "Long description of Galaxy's filter tool" -files_path = os.path.abspath( os.path.join( "test", "tool_shed", "test_data" ) ) -filter_filename = os.path.join( files_path, "filtering_1.1.0.tar" ) - -class TestCreateRepository( ShedTwillTestCase ): - - def test_0000_initiate_users( self ): - """Create necessary users and login as an admin user.""" - self.login( email=regular_email, username=regular_username ) - regular_user = get_user( regular_email ) - assert regular_user is not None, 'Problem retrieving user with email %s from the database' % regular_email - regular_user_private_role = get_private_role( regular_user ) - self.logout() - self.login( email=admin_email, username=admin_username ) - admin_user = get_user( admin_email ) - assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email - admin_user_private_role = get_private_role( admin_user ) - def test_0005_create_categories( self ): - """Create a category""" - self.create_category( 'Text Manipulation', 'Tools for manipulating text' ) - self.create_category( 'Text Analysis', 'Tools for analyzing text' ) - def test_0010_create_repository( self ): - """Create a repository""" - strings_displayed = [ '<div class="toolFormTitle">Repository %s</div>' % "'%s'" % repository_name, \ - 'Repository %s has been created' % "'%s'" % repository_name ] - self.create_repository( repository_name, repository_description, \ - repository_long_description=repository_long_description, \ - categories=[ 'Text Manipulation' ], \ - strings_displayed=strings_displayed ) - def test_0015_edit_repository( self ): - """Edit the repository name, description, and long description""" - repository = get_repository_by_name( repository_name, admin_username ) - new_name = "renamed_filter" - new_description = "Edited filter tool" - new_long_description = "Edited long description" - self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) - def test_0020_change_repository_category( self ): - """Change the category of a repository""" - repository = get_repository_by_name( repository_name, admin_username ) - self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] ) -# def test_0025_grant_write_access( self ): -# '''Grant write access to another user''' -# repository = get_repository_by_name( repository_name, admin_username ) -# self.grant_write_access( repository, usernames=[ regular_username ] ) - def test_0030_upload_tarball( self ): - """Upload filtering_1.1.0.tar to the repository""" - repository = get_repository_by_name( repository_name, admin_username ) - self.upload( repository, filter_filename, \ - strings_displayed=[ "The file '%s' has been successfully uploaded to the repository." % filter_filename ], \ - commit_message="Uploaded filtering 1.1.0" ) - self.check_for_valid_tools( repository ) - latest_repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) - changeset_revision = latest_repository_metadata.changeset_revision - self.check_repository_changelog( repository, strings_displayed=[ 'Repository metadata is associated with this change set.' ] ) - self.set_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) - self.unset_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) - self.load_display_tool_page( repository, tool_xml_filename='filtering.xml', \ - changeset_revision=changeset_revision, \ - strings_displayed=[ 'Filter (version 1.1.0)', "c1=='chr1'" ], \ - strings_not_displayed=[] ) - tool = latest_repository_metadata.metadata[ 'tools' ][0] - metadata_strings_displayed = [ tool[ 'guid' ], tool[ 'version' ], tool[ 'id' ], tool[ 'name' ], tool[ 'description' ], changeset_revision ] - self.check_for_tool_metadata( repository, changeset_revision, 'Filter1', strings_displayed=metadata_strings_displayed ) - def test_0035_repository_browse_page( self ): - '''Visit the repository browse page''' - repository = get_repository_by_name( repository_name, admin_username ) - self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) - def test_0040_visit_clone_url_via_hgweb( self ): - '''Visit the repository clone URL via hgweb''' - repository = get_repository_by_name( repository_name, admin_username ) - latest_changeset_revision = self.get_latest_repository_metadata_for_repository( repository ) - self.display_repository_clone_page( admin_username, \ - repository_name, \ - strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision.changeset_revision ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Style fix for rendering tool dependency information when installing tool shed repositories.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a27a0f7d3ac9/ changeset: a27a0f7d3ac9 user: greg date: 2012-11-26 16:44:32 summary: Style fix for rendering tool dependency information when installing tool shed repositories. affected #: 2 files diff -r a627f341d01ae4a9741164981ff2e5300353354f -r a27a0f7d3ac90dfabd1050e26b9216eeb9ebc46b lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -484,18 +484,6 @@ if ctx_file_name == config_file: return get_named_tmpfile_from_ctx( changeset_ctx, ctx_file, dir ) return None -def get_headers( fname, sep, count=60, is_multi_byte=False ): - """Returns a list with the first 'count' lines split by 'sep'.""" - headers = [] - for idx, line in enumerate( file( fname ) ): - line = line.rstrip( '\n\r' ) - if is_multi_byte: - line = unicode( line, 'utf-8' ) - sep = sep.encode( 'utf-8' ) - headers.append( line.split( sep ) ) - if idx == count: - break - return headers def get_converter_and_display_paths( registration_elem, relative_install_dir ): """Find the relative path to data type converters and display applications included in installed tool shed repositories.""" converter_path = None @@ -544,6 +532,18 @@ ctx_rev = response.read() response.close() return ctx_rev +def get_headers( fname, sep, count=60, is_multi_byte=False ): + """Returns a list with the first 'count' lines split by 'sep'.""" + headers = [] + for idx, line in enumerate( file( fname ) ): + line = line.rstrip( '\n\r' ) + if is_multi_byte: + line = unicode( line, 'utf-8' ) + sep = sep.encode( 'utf-8' ) + headers.append( line.split( sep ) ) + if idx == count: + break + return headers def get_installed_tool_shed_repository( trans, id ): """Get a repository on the Galaxy side from the database via id""" return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) diff -r a627f341d01ae4a9741164981ff2e5300353354f -r a27a0f7d3ac90dfabd1050e26b9216eeb9ebc46b templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -90,8 +90,18 @@ </div></div><div style="clear: both"></div> - <div class="form-row"> - <table class="grid"> + <div class="form-row"> + <style type="text/css"> + #dependency_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> + <table class="grid" id="dependency_table"><tr><td colspan="4" bgcolor="#D8D8D8"><b>Tool dependencies</b></td></tr><% env_settings_heaader_row_displayed = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Removed lastz and bowtie from tool_conf.xml.main
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a627f341d01a/ changeset: a627f341d01a user: inithello date: 2012-11-26 16:20:38 summary: Removed lastz and bowtie from tool_conf.xml.main affected #: 1 file diff -r 87828175dfe7475aa846f383a5038e5ca4f1e312 -r a627f341d01ae4a9741164981ff2e5300353354f tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -259,13 +259,10 @@ </section><section name="NGS: Mapping" id="ngs_mapping"><label text="Illumina" id="illumina"/> - <tool file="sr_mapping/bowtie_wrapper.xml" /><label text="Roche-454" id="roche_454"/> - <tool file="sr_mapping/lastz_wrapper.xml" /><tool file="metag_tools/megablast_wrapper.xml" /><tool file="metag_tools/megablast_xml_parser.xml" /><label text="AB-SOLiD" id="ab_solid"/> - <tool file="sr_mapping/bowtie_color_wrapper.xml" /></section><section name="NGS: SAM Tools" id="samtools"><tool file="samtools/sam_bitwise_flag_filter.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/87828175dfe7/ changeset: 87828175dfe7 user: inithello date: 2012-11-26 16:18:47 summary: Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process. affected #: 54 files Diff too large to display. 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: Improvements in the display of repository dependencies and contents in the tool shed.
by Bitbucket 26 Nov '12

26 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/519b7df6d72a/ changeset: 519b7df6d72a user: greg date: 2012-11-26 16:15:45 summary: Improvements in the display of repository dependencies and contents in the tool shed. affected #: 14 files diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1050,23 +1050,6 @@ trans.sa_session.add( tool_dependency ) trans.sa_session.flush() return removed, error_message -def to_html_str( text ): - """Translates the characters in text to an html string""" - translated = [] - for c in text: - if c in VALID_CHARS: - translated.append( c ) - elif c in MAPPED_CHARS: - translated.append( MAPPED_CHARS[ c ] ) - elif c == ' ': - translated.append( ' ' ) - elif c == '\t': - translated.append( '    ' ) - elif c == '\n': - translated.append( '<br/>' ) - elif c not in [ '\r' ]: - translated.append( '' ) - return ''.join( translated ) def tool_shed_from_repository_clone_url( repository_clone_url ): return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def translate_string( raw_text, to_html=True ): diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1331,6 +1331,23 @@ except: file_name = fpath return file_name +def to_html_str( text ): + """Translates the characters in text to an html string""" + translated = [] + for c in text: + if c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + elif c == ' ': + translated.append( ' ' ) + elif c == '\t': + translated.append( '    ' ) + elif c == '\n': + translated.append( '<br/>' ) + elif c not in [ '\r' ]: + translated.append( '' ) + return ''.join( translated ) def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ): """ Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,11 +1,13 @@ -import os, string, socket, logging, simplejson, binascii, tempfile, filecmp +import os, string, socket, logging, simplejson, binascii, tempfile, filecmp, threading from time import strftime from datetime import * from galaxy.datatypes.checkers import * from galaxy.tools import * +from galaxy.util.odict import odict from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * from galaxy.util.shed_util_common import * +from galaxy.webapps.community.util.container_util import * from galaxy.web.base.controller import * from galaxy.web.base.controllers.admin import * from galaxy.webapps.community import model @@ -73,9 +75,6 @@ '${host}' """ -# String separator -STRSEP = '__ESEP__' - # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" @@ -105,6 +104,62 @@ trans.sa_session.flush() return item_rating +def build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata ): + containers_dict = dict( datatypes=None, + invalid_tools=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) + if repository_metadata: + metadata = repository_metadata.metadata + lock = threading.Lock() + lock.acquire( True ) + try: + folder_id = 0 + # Datatypes container. + if metadata and 'datatypes' in metadata: + datatypes = metadata[ 'datatypes' ] + folder_id, datatypes_root_folder = build_datatypes_folder( folder_id, datatypes ) + containers_dict[ 'datatypes' ] = datatypes_root_folder + # Invalid tools container. + if metadata and 'invalid_tools' in metadata: + invalid_tool_configs = metadata[ 'invalid_tools' ] + folder_id, invalid_tools_root_folder = build_invalid_tools_folder( folder_id, + invalid_tool_configs, + repository, + changeset_revision, + label='Invalid tools' ) + containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder + # Repository dependencies container. + folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( repository, + changeset_revision, + folder_id, + repository_dependencies ) + if repository_dependencies_root_folder: + containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + # Tool dependencies container. + if metadata and 'tool_dependencies' in metadata: + tool_dependencies = metadata[ 'tool_dependencies' ] + folder_id, tool_dependencies_root_folder = build_tool_dependencies_folder( folder_id, tool_dependencies ) + containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + # Valid tools container. + if metadata and 'tools' in metadata: + valid_tools = metadata[ 'tools' ] + folder_id, valid_tools_root_folder = build_tools_folder( folder_id, valid_tools, repository, changeset_revision, label='Valid tools' ) + containers_dict[ 'valid_tools' ] = valid_tools_root_folder + # Workflows container. + if metadata and 'workflows' in metadata: + workflows = metadata[ 'workflows' ] + folder_id, workflows_root_folder = build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) + containers_dict[ 'workflows' ] = workflows_root_folder + except Exception, e: + repository_dependencies_root_folder = None + tool_dependencies_root_folder = None + log.debug( "Exception in build_repository_containers: %s" % str( e ) ) + finally: + lock.release() + return containers_dict def add_tool_versions( trans, id, repository_metadata, changeset_revisions ): # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata. metadata = repository_metadata.metadata @@ -183,18 +238,6 @@ else: tmp_filename = None return tmp_filename -def copy_file_from_manifest( repo, ctx, filename, dir ): - """Copy the latest version of the file named filename from the repository manifest to the directory to which dir refers.""" - for changeset in reversed_upper_bounded_changelog( repo, ctx ): - changeset_ctx = repo.changectx( changeset ) - fctx = get_file_context_from_ctx( changeset_ctx, filename ) - if fctx and fctx not in [ 'DELETED' ]: - file_path = os.path.join( dir, filename ) - fh = open( file_path, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return file_path - return None def generate_tool_guid( trans, repository, tool ): """ Generate a guid for the received tool. The form of the guid is @@ -285,11 +328,28 @@ fh.close() return tmp_filename return None -def get_previous_downloadable_changset_revision( repository, repo, before_changeset_revision ): +def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ): """ - Return the downloadable changeset_revision in the repository changelog just prior to the changeset to which before_changeset_revision - refers. If there isn't one, return the hash value of an empty repository changlog, INITIAL_CHANGELOG_HASH. + Return the installable changeset_revision in the repository changelog after to the changeset to which after_changeset_revision + refers. If there isn't one, return None. """ + changeset_revisions = get_ordered_downloadable_changeset_revisions( repository, repo ) + if len( changeset_revisions ) == 1: + changeset_revision = changeset_revisions[ 0 ] + if changeset_revision == after_changeset_revision: + return None + found_after_changeset_revision = False + for changeset in repo.changelog: + changeset_revision = str( repo.changectx( changeset ) ) + if found_after_changeset_revision: + if changeset_revision in downloadable_changeset_revisions: + return changeset_revision + elif not found_after_changeset_revision and changeset_revision == after_changeset_revision: + # We've found the changeset in the changelog for which we need to get the next downloadable changset. + found_after_changeset_revision = True + return None +def get_ordered_downloadable_changeset_revisions( repository, repo ): + """Return an ordered list of changeset_revisions defined by a repository changelog.""" changeset_tups = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision @@ -299,24 +359,30 @@ else: rev = '-1' changeset_tups.append( ( rev, changeset_revision ) ) - if len( changeset_tups ) == 1: - changeset_tup = changeset_tups[ 0 ] - current_changeset_revision = changeset_tup[ 1 ] - if current_changeset_revision == before_changeset_revision: + sorted_changeset_tups = sorted( changeset_tups ) + sorted_changeset_revisions = [ changeset_tup[ 1 ] for changeset_tup in sorted_changeset_tups ] + return sorted_changeset_revisions +def get_previous_downloadable_changset_revision( repository, repo, before_changeset_revision ): + """ + Return the installable changeset_revision in the repository changelog prior to the changeset to which before_changeset_revision + refers. If there isn't one, return the hash value of an empty repository changelog, INITIAL_CHANGELOG_HASH. + """ + changeset_revisions = get_ordered_downloadable_changeset_revisions( repository, repo ) + if len( changeset_revisions ) == 1: + changeset_revision = changeset_revisions[ 0 ] + if changeset_revision == before_changeset_revision: return INITIAL_CHANGELOG_HASH - return current_changeset_revision + return changeset_revision previous_changeset_revision = None - current_changeset_revision = None - for changeset_tup in sorted( changeset_tups ): - current_changeset_revision = changeset_tup[ 1 ] - if current_changeset_revision == before_changeset_revision: + for changeset_revision in changeset_revisions: + if changeset_revision == before_changeset_revision: if previous_changeset_revision: return previous_changeset_revision else: - # Return the hash value of an empty repository changlog - note that this will not be a valid changset revision. + # Return the hash value of an empty repository changelog - note that this will not be a valid changeset revision. return INITIAL_CHANGELOG_HASH else: - previous_changeset_revision = current_changeset_revision + previous_changeset_revision = changeset_revision def get_previous_repository_reviews( trans, repository, changeset_revision ): """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) @@ -332,6 +398,110 @@ previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, reviews=revision_reviews ) return previous_reviews_dict +def get_repository_by_name( trans, name ): + """Get a repository from the database via name""" + return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() +def get_repository_by_name_and_owner( trans, name, owner ): + """Get a repository from the database via name and owner""" + user = get_user_by_username( trans, owner ) + return trans.sa_session.query( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.name == name, + trans.model.Repository.table.c.user_id == user.id ) ) \ + .first() +def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, repository_dependencies=None, + all_repository_dependencies=None ): + """ + Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend. The dictionary keys + are name-spaced values consisting of tool_shed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of + repository_dependency tuples consisting of ( tool_shed_base_url, repository_name, repository_owner, changeset_revision ). This is a + recursive method, so it ensures that all required repositories to the nth degree are returned. + """ + if all_repository_dependencies is None: + all_repository_dependencies = odict() + if repository_dependencies is None: + repository_dependencies = [] + metadata = repository_metadata.metadata + if metadata and 'repository_dependencies' in metadata: + repository_dependencies_root_key = generate_repository_dependencies_key_for_repository( repository, repository_metadata.changeset_revision ) + for repository_dependency in metadata[ 'repository_dependencies' ]: + if repository_dependency not in repository_dependencies: + repository_dependencies.append( repository_dependency ) + else: + repository_dependencies_root_key = None + if repository_dependencies: + repository_dependency = repository_dependencies.pop( 0 ) + tool_shed, name, owner, changeset_revision = repository_dependency + if repository_dependencies_root_key: + if repository_dependencies_root_key in all_repository_dependencies: + # See if this repository_dependency is contained in the list associated with the repository_dependencies_root_key. + all_repository_dependencies_val = all_repository_dependencies[ repository_dependencies_root_key ] + if repository_dependency not in all_repository_dependencies_val: + all_repository_dependencies_val.append( repository_dependency ) + all_repository_dependencies[ repository_dependencies_root_key ] = all_repository_dependencies_val + else: + # Insert this repository_dependency. + all_repository_dependencies[ repository_dependencies_root_key ] = [ repository_dependency ] + if tool_shed_is_this_tool_shed( tool_shed ): + # The repository is in the current tool shed. + required_repository = get_repository_by_name_and_owner( trans, name, owner ) + required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( required_repository.id ), + changeset_revision ) + if required_repository_metadata: + required_repo_dir = required_repository.repo_path( trans.app ) + required_repo = hg.repository( get_configured_ui(), required_repo_dir ) + else: + # The repository changeset_revision is no longer installable, so see if there's been an update. + required_repo_dir = required_repository.repo_path( trans.app ) + required_repo = hg.repository( get_configured_ui(), required_repo_dir ) + required_repository_metadata = get_next_downloadable_changeset_revision( required_repository, required_repo, changeset_revision ) + if required_repository_metadata: + # The required_repository_metadata changeset_revision is installable. + required_metadata = required_repository_metadata.metadata + if required_metadata: + return get_repository_dependencies_for_changeset_revision( trans=trans, + repo=required_repo, + repository=required_repository, + repository_metadata=required_repository_metadata, + toolshed_base_url=tool_shed, + repository_dependencies=repository_dependencies, + all_repository_dependencies=all_repository_dependencies ) + else: + # The repository is in a different tool shed, so build an url and send a request. + raise Exception( "Repository dependencies that refer to repositories in other tool sheds is not yet supported." ) + return all_repository_dependencies +def get_repository_metadata_by_id( trans, id ): + """Get repository metadata from the database""" + return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) +def get_repository_metadata_by_repository_id( trans, id ): + """Get all metadata records for a specified repository.""" + return trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) +def get_repository_metadata_by_repository_id_changset_revision( trans, id, changeset_revision ): + """Get a specified metadata record for a specified repository.""" + return trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), + trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ + .first() +def get_repository_metadata_revisions_for_review( repository, reviewed=True ): + repository_metadata_revisions = [] + metadata_changeset_revision_hashes = [] + if reviewed: + for metadata_revision in repository.metadata_revisions: + metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision ) + for review in repository.reviews: + if review.changeset_revision in metadata_changeset_revision_hashes: + rmcr_hashes = [ rmr.changeset_revision for rmr in repository_metadata_revisions ] + if review.changeset_revision not in rmcr_hashes: + repository_metadata_revisions.append( review.repository_metadata ) + else: + for review in repository.reviews: + if review.changeset_revision not in metadata_changeset_revision_hashes: + metadata_changeset_revision_hashes.append( review.changeset_revision ) + for metadata_revision in repository.metadata_revisions: + if metadata_revision.changeset_revision not in metadata_changeset_revision_hashes: + repository_metadata_revisions.append( metadata_revision ) + return repository_metadata_revisions def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ): if repository is None: repository = repository_metadata.repository @@ -359,42 +529,6 @@ for changeset in repo.changelog: reversed_changelog.insert( 0, changeset ) return reversed_changelog -def get_repository_by_name( trans, name ): - """Get a repository from the database via name""" - return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() -def get_repository_by_name_and_owner( trans, name, owner ): - """Get a repository from the database via name and owner""" - user = get_user_by_username( trans, owner ) - return trans.sa_session.query( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.name == name, - trans.model.Repository.table.c.user_id == user.id ) ) \ - .first() -def get_repository_metadata_by_id( trans, id ): - """Get repository metadata from the database""" - return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) -def get_repository_metadata_by_repository_id( trans, id ): - """Get all metadata records for a specified repository.""" - return trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) -def get_repository_metadata_revisions_for_review( repository, reviewed=True ): - repository_metadata_revisions = [] - metadata_changeset_revision_hashes = [] - if reviewed: - for metadata_revision in repository.metadata_revisions: - metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision ) - for review in repository.reviews: - if review.changeset_revision in metadata_changeset_revision_hashes: - rmcr_hashes = [ rmr.changeset_revision for rmr in repository_metadata_revisions ] - if review.changeset_revision not in rmcr_hashes: - repository_metadata_revisions.append( review.repository_metadata ) - else: - for review in repository.reviews: - if review.changeset_revision not in metadata_changeset_revision_hashes: - metadata_changeset_revision_hashes.append( review.changeset_revision ) - for metadata_revision in repository.metadata_revisions: - if metadata_revision.changeset_revision not in metadata_changeset_revision_hashes: - repository_metadata_revisions.append( metadata_revision ) - return repository_metadata_revisions def get_review( trans, id ): """Get a repository_review from the database via id""" return trans.sa_session.query( trans.model.RepositoryReview ).get( trans.security.decode_id( id ) ) @@ -693,6 +827,8 @@ id=trans.security.encode_id( repository.id ), message=error_message, status='error' ) ) +def tool_shed_is_this_tool_shed( toolshed_base_url ): + return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' ) def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): # This method id deprecated, but we'll keep it around for a while in case we need it. The problem is that hg purge # is not supported by the mercurial API. diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1748,9 +1748,11 @@ add_id_to_name=False, downloadable=False ) revision_label = get_revision_label( trans, repository, repository.tip( trans.app ) ) + repository_metadata = None repository_metadata_id = None metadata = None is_malicious = False + repository_dependencies = [] if changeset_revision != INITIAL_CHANGELOG_HASH: repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -1768,6 +1770,15 @@ repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious + if repository_metadata: + # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, + repo, + repository, + repository_metadata, + str( url_for( '/', qualified=True ) ).rstrip( '/' ), + repository_dependencies=None, + all_repository_dependencies=None ) if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push @@ -1787,6 +1798,7 @@ review_id = trans.security.encode_id( review.id ) else: review_id = None + containers_dict = build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata ) return trans.fill_template( '/webapps/community/repository/manage_repository.mako', cntrller=cntrller, repo_name=repo_name, @@ -1796,6 +1808,7 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + containers_dict=containers_dict, repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, reviewed_by_user=reviewed_by_user, @@ -1865,22 +1878,35 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository_in_tool_shed( trans, repository_id ) + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_dir ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata + # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, + repo, + repository, + repository_metadata, + str( url_for( '/', qualified=True ) ).rstrip( '/' ), + repository_dependencies=None, + all_repository_dependencies=None ) else: repository_metadata_id = None metadata = None + repository_dependencies = None revision_label = get_revision_label( trans, repository, changeset_revision ) changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) + containers_dict = build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata ) return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', repository=repository, + containers_dict=containers_dict, repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, revision_label=revision_label, @@ -2408,6 +2434,7 @@ email_alerts = from_json_string( repository.email_alerts ) else: email_alerts = [] + repository_dependencies = [] user = trans.user if user and params.get( 'receive_email_alerts_button', False ): flush_needed = False @@ -2434,8 +2461,16 @@ revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: - repository_metadata_id = trans.security.encode_id( repository_metadata.id ), + repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata + # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, + repo, + repository, + repository_metadata, + str( url_for( '/', qualified=True ) ).rstrip( '/' ), + repository_dependencies=None, + all_repository_dependencies=None ) else: repository_metadata_id = None metadata = None @@ -2456,12 +2491,14 @@ review_id = trans.security.encode_id( review.id ) else: review_id = None + containers_dict = build_repository_containers( repository, changeset_revision, repository_dependencies, repository_metadata ) return trans.fill_template( '/webapps/community/repository/view_repository.mako', cntrller=cntrller, repo=repo, repository=repository, repository_metadata_id=repository_metadata_id, metadata=metadata, + containers_dict=containers_dict, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -7,6 +7,7 @@ from galaxy.model.orm import * from sqlalchemy.sql.expression import func from common import * +from galaxy.webapps.community.util.container_util import STRSEP from repository import RepositoryGrid from galaxy.util.shed_util_common import * from galaxy.util.odict import odict diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -151,7 +151,7 @@ changeset_revision=repository_metadata.changeset_revision, repository_metadata_id=repository_metadata_id, workflow_name=workflow_name, - metadata=repository_metadata, + metadata=repository_metadata.metadata, message=message, status=status ) @web.expose diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c lib/galaxy/webapps/community/util/container_util.py --- /dev/null +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -0,0 +1,314 @@ +import logging +from galaxy.web import url_for + +log = logging.getLogger( __name__ ) + +# String separator +STRSEP = '__ESEP__' + +class Folder( object ): + """Container object.""" + def __init__( self, id=None, key=None, label=None ): + self.id = id + self.key = key + self.label = label + self.datatypes = [] + self.folders = [] + self.invalid_tools = [] + self.valid_tools = [] + self.tool_dependencies = [] + self.repository_dependencies = [] + self.workflows = [] + def contains_folder( self, folder ): + for index, contained_folder in enumerate( self.folders ): + if folder == contained_folder: + return index, contained_folder + return 0, None + +class Datatype( object ): + """Datatype object""" + def __init__( self, id=None, extension=None, type=None, mimetype=None, subclass=None ): + self.id = id + self.extension = extension + self.type = type + self.mimetype = mimetype + self.subclass = subclass + +class InvalidTool( object ): + """Invalid tool object""" + def __init__( self, id=None, tool_config=None, repository_id=None, changeset_revision=None ): + self.id = id + self.tool_config = tool_config + self.repository_id = repository_id + self.changeset_revision = changeset_revision + +class RepositoryDependency( object ): + """Repository dependency object""" + def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None ): + self.id = id + self.toolshed = toolshed + self.repository_name = repository_name + self.repository_owner = repository_owner + self.changeset_revision = changeset_revision + +class Tool( object ): + """Tool object""" + def __init__( self, id=None, tool_config=None, tool_id=None, name=None, description=None, version=None, requirements=None, + repository_id=None, changeset_revision=None ): + self.id = id + self.tool_config = tool_config + self.tool_id = tool_id + self.name = name + self.description = description + self.version = version + self.requirements = requirements + self.repository_id = repository_id + self.changeset_revision = changeset_revision + +class ToolDependency( object ): + """Tool dependency object""" + def __init__( self, id=None, name=None, version=None, type=None ): + self.id = id + self.name = name + self.version = version + self.type = type + +class Workflow( object ): + """Workflow object""" + def __init__( self, id=None, repository_metadata_id=None, workflow_name=None, steps=None, format_version=None, annotation=None ): + self.id = id + self.repository_metadata_id = repository_metadata_id + self.workflow_name = workflow_name + self.steps = steps + self.format_version = format_version + self.annotation = annotation + +def build_datatypes_folder( folder_id, datatypes, label='Datatypes' ): + """Return a folder hierarchy containing datatypes.""" + if datatypes: + datatype_id = 0 + folder_id += 1 + datatypes_root_folder = Folder( id=folder_id, key='root', label='root' ) + folder_id += 1 + folder = Folder( id=folder_id, key='datatypes', label=label ) + datatypes_root_folder.folders.append( folder ) + # Insert a header row. + datatype_id += 1 + datatype = Datatype( id=datatype_id, + extension='extension', + type='type', + mimetype='mimetype', + subclass='subclass' ) + folder.datatypes.append( datatype ) + for datatypes_dict in datatypes: + datatype_id += 1 + datatype = Datatype( id=datatype_id, + extension=datatypes_dict.get( 'extension', '' ), + type=datatypes_dict.get( 'dtype', '' ), + mimetype=datatypes_dict.get( 'mimetype', '' ), + subclass=datatypes_dict.get( 'subclass', '' ) ) + folder.datatypes.append( datatype ) + else: + datatypes_root_folder = None + return folder_id, datatypes_root_folder +def build_invalid_tools_folder( folder_id, invalid_tool_configs, repository, changeset_revision, label='Invalid tools' ): + """Return a folder hierarchy containing invalid tools.""" + if invalid_tool_configs: + invalid_tool_id = 0 + folder_id += 1 + invalid_tools_root_folder = Folder( id=folder_id, key='root', label='root' ) + folder_id += 1 + folder = Folder( id=folder_id, key='invalid_tools', label=label ) + invalid_tools_root_folder.folders.append( folder ) + for invalid_tool_config in invalid_tool_configs: + invalid_tool_id += 1 + invalid_tool = InvalidTool( id=invalid_tool_id, + tool_config=invalid_tool_config, + repository_id=repository.id, + changeset_revision=changeset_revision ) + folder.invalid_tools.append( invalid_tool ) + else: + invalid_tools_root_folder = None + return folder_id, invalid_tools_root_folder +def build_repository_dependencies_folder( repository, changeset_revision, folder_id, repository_dependencies, label='Repository dependencies' ): + """Return a folder hierarchy containing repository dependencies.""" + if repository_dependencies: + repository_dependency_id = 0 + folder_id += 1 + # Create the root folder. + repository_dependencies_root_folder = Folder( id=folder_id, key='root', label='root' ) + folder_id += 1 + # Create the Repository dependencies folder and add it to the root folder. + key = generate_repository_dependencies_key_for_repository( repository, changeset_revision ) + repository_dependencies_folder = Folder( id=folder_id, key=key, label=label ) + repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) + # Process the repository dependencies. + for key, val in repository_dependencies.items(): + # Only create a new folder object if necessary. + folder = get_folder( repository_dependencies_root_folder, key ) + if not folder: + # Create a new folder. + folder_id += 1 + label = generate_repository_dependencies_folder_label_from_key( repository, changeset_revision, key ) + folder = Folder( id=folder_id, key=key, label=label ) + for repository_dependency_tup in val: + toolshed, name, owner, changeset_revision = repository_dependency_tup + if not is_folder( repository_dependencies.keys(), toolshed, name, owner, changeset_revision ): + # Create a new repository_dependency. + repository_dependency_id += 1 + repository_dependency = RepositoryDependency( id=repository_dependency_id, + toolshed=toolshed, + repository_name=name, + repository_owner=owner, + changeset_revision=changeset_revision ) + # Insert the repository_dependency into the folder. + folder.repository_dependencies.append( repository_dependency ) + if not get_folder( repository_dependencies_folder, key ): + # Insert the folder into the list. + repository_dependencies_folder.folders.append( folder ) + else: + repository_dependencies_root_folder = None + return folder_id, repository_dependencies_root_folder +def build_tools_folder( folder_id, tool_dicts, repository, changeset_revision, valid=True, label='Valid tools' ): + """Return a folder hierarchy containing valid tools.""" + if tool_dicts: + tool_id = 0 + folder_id += 1 + tools_root_folder = Folder( id=folder_id, key='root', label='root' ) + folder_id += 1 + folder = Folder( id=folder_id, key='tools', label=label ) + tools_root_folder.folders.append( folder ) + # Insert a header row. + tool_id += 1 + tool = Tool( id=tool_id, + tool_config='', + tool_id='', + name='Name', + description='Description', + version='Version', + requirements='', + repository_id='', + changeset_revision='' ) + folder.valid_tools.append( tool ) + for tool_dict in tool_dicts: + tool_id += 1 + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + requirements_str = '' + for requirement_dict in requirements: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + else: + requirements_str = 'none' + tool = Tool( id=tool_id, + tool_config=tool_dict[ 'tool_config' ], + tool_id=tool_dict[ 'id' ], + name=tool_dict[ 'name' ], + description=tool_dict[ 'description' ], + version=tool_dict[ 'version' ], + requirements=requirements_str, + repository_id=repository.id, + changeset_revision=changeset_revision ) + folder.valid_tools.append( tool ) + else: + tools_root_folder = None + return folder_id, tools_root_folder +def build_tool_dependencies_folder( folder_id, tool_dependencies, label='Tool dependencies' ): + """Return a folder hierarchy containing tool dependencies.""" + if tool_dependencies: + tool_dependency_id = 0 + folder_id += 1 + tool_dependencies_root_folder = Folder( id=folder_id, key='root', label='root' ) + folder_id += 1 + folder = Folder( id=folder_id, key='tool_dependencies', label=label ) + tool_dependencies_root_folder.folders.append( folder ) + # Insert a header row. + tool_dependency_id += 1 + tool_dependency = ToolDependency( id=tool_dependency_id, + name='Name', + version='Version', + type='Type' ) + folder.tool_dependencies.append( tool_dependency ) + for dependency_key, requirements_dict in tool_dependencies.items(): + tool_dependency_id += 1 + if dependency_key == 'set_environment': + version = None + else: + version = requirements_dict[ 'version' ] + tool_dependency = ToolDependency( id=tool_dependency_id, + name=requirements_dict[ 'name' ], + version=version, + type=requirements_dict[ 'type' ] ) + folder.tool_dependencies.append( tool_dependency ) + else: + tool_dependencies_root_folder = None + return folder_id, tool_dependencies_root_folder +def build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ): + """Return a folder hierarchy containing invalid tools.""" + if workflows: + workflow_id = 0 + folder_id += 1 + workflows_root_folder = Folder( id=folder_id, key='root', label='root' ) + folder_id += 1 + folder = Folder( id=folder_id, key='workflows', label=label ) + workflows_root_folder.folders.append( folder ) + # Insert a header row. + workflow_id += 1 + workflow = Workflow( id=workflow_id, + repository_metadata_id=None, + workflow_name='Name', + steps='steps', + format_version='format-version', + annotation='annotation' ) + folder.workflows.append( workflow ) + for workflow_tup in workflows: + workflow_dict=workflow_tup[ 1 ] + steps = workflow_dict.get( 'steps', [] ) + if steps: + steps = str( len( steps ) ) + else: + steps = 'unknown' + workflow_id += 1 + workflow = Workflow( id=workflow_id, + repository_metadata_id=repository_metadata.id, + workflow_name=workflow_dict[ 'name' ], + steps=steps, + format_version=workflow_dict[ 'format-version' ], + annotation=workflow_dict[ 'annotation' ] ) + folder.workflows.append( workflow ) + else: + workflows_root_folder = None + return folder_id, workflows_root_folder +def generate_repository_dependencies_folder_label_from_key( repository, changeset_revision, key ): + """Return a repository dependency label based on the repository dependency key.""" + if key_is_current_repositorys_key( repository, changeset_revision, key ): + label = 'Repository dependencies' + else: + toolshed_base_url, name, owner, revision = get_components_from_key( key ) + label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( name, revision, owner ) + return label +def generate_repository_dependencies_key_for_repository( repository, changeset_revision ): + # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported. + toolshed_base_url = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + return '%s%s%s%s%s%s%s' % ( toolshed_base_url, STRSEP, repository.name, STRSEP, repository.user.username, STRSEP, changeset_revision ) +def get_folder( folder, key ): + if folder and folder.key == key: + return folder + for sub_folder in folder.folders: + return get_folder( sub_folder, key ) + return None +def get_components_from_key( key ): + # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported. + items = key.split( STRSEP ) + toolshed_base_url = items[ 0 ] + repository_name = items[ 1 ] + repository_owner = items[ 2 ] + changeset_revision = items[ 3 ] + return toolshed_base_url, repository_name, repository_owner, changeset_revision +def is_folder( folder_keys, toolshed_base_url, repository_name, repository_owner, changeset_revision ): + key = '%s%s%s%s%s%s%s' % ( toolshed_base_url, STRSEP, repository_name, STRSEP, repository_owner, STRSEP, changeset_revision ) + return key in folder_keys +def key_is_current_repositorys_key( repository, changeset_revision, key ): + toolshed_base_url, repository_name, repository_owner, changeset_revision = get_components_from_key( key ) + return repository_name == repository.name and repository_owner == repository.user.username and repository_changeset_revision == changeset_revision + \ No newline at end of file diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -75,6 +75,93 @@ </script></%def> +<%def name="dependency_javascripts()"> + <script type="text/javascript"> + var init_dependencies = function() { + var storage_id = "library-expand-state-${trans.security.encode_id(10000)}"; + var restore_folder_state = function() { + var state = $.jStorage.get(storage_id); + if (state) { + for (var id in state) { + if (state[id] === true) { + var row = $("#" + id), + index = row.parent().children().index(row); + row.addClass("expanded").show(); + row.siblings().filter("tr[parent='" + index + "']").show(); + } + } + } + }; + var save_folder_state = function() { + var state = {}; + $("tr.folderRow").each( function() { + var folder = $(this); + state[folder.attr("id")] = folder.hasClass("expanded"); + }); + $.jStorage.set(storage_id, state); + }; + $(".container-table").each(function() { + //var container_id = this.id.split( "-" )[0]; + //alert( container_id ); + var child_of_parent_cache = {}; + // Recursively fill in children and descendants of each row + var process_row = function(q, parents) { + // Find my index + var parent = q.parent(), + this_level = child_of_parent_cache[parent] || (child_of_parent_cache[parent] = parent.children()); + var index = this_level.index(q); + // Find my immediate children + var children = $(par_child_dict[index]); + // Recursively handle them + var descendants = children; + children.each( function() { + child_descendants = process_row( $(this), parents.add(q) ); + descendants = descendants.add(child_descendants); + }); + // Set up expand / hide link + var expand_fn = function() { + if ( q.hasClass("expanded") ) { + descendants.hide(); + descendants.removeClass("expanded"); + q.removeClass("expanded"); + } else { + children.show(); + q.addClass("expanded"); + } + save_folder_state(); + }; + $("." + q.attr("id") + "-click").click(expand_fn); + // return descendants for use by parent + return descendants; + } + // Initialize dict[parent_id] = rows_which_have_that_parent_id_as_parent_attr + var par_child_dict = {}, + no_parent = []; + $(this).find("tbody tr").each( function() { + if ( $(this).attr("parent")) { + var parent = $(this).attr("parent"); + if (par_child_dict[parent] !== undefined) { + par_child_dict[parent].push(this); + } else { + par_child_dict[parent] = [this]; + } + } else { + no_parent.push(this); + } + }); + $(no_parent).each( function() { + descendants = process_row( $(this), $([]) ); + descendants.hide(); + }); + }); + restore_folder_state(); + }; + $(function() { + init_dependencies(); + }); + </script> +</%def> + <%def name="render_clone_str( repository )"><% from galaxy.util.shed_util_common import generate_clone_url_for_repository_in_tool_shed @@ -83,272 +170,337 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_items( repository_metadata_id, changeset_revision, metadata, can_set_metadata=False )"> - <% from galaxy.tool_shed.encoding_util import tool_shed_encode %> - %if metadata or can_set_metadata: +<%def name="render_folder( folder, folder_pad, parent=None, row_counter=None, is_root_folder=False )"> + <% + encoded_id = trans.security.encode_id( folder.id ) + + if is_root_folder: + pad = folder_pad + expander = h.url_for("/static/images/silk/resultset_bottom.png") + folder_img = h.url_for("/static/images/silk/folder_page.png") + else: + pad = folder_pad + 20 + expander = h.url_for("/static/images/silk/resultset_next.png") + folder_img = h.url_for("/static/images/silk/folder.png") + my_row = None + %> + %if not is_root_folder: + <% + if parent is None: + bg_str = 'bgcolor="#D8D8D8"' + else: + bg_str = '' + %> + <tr id="folder-${encoded_id}" ${bg_str} class="folderRow libraryOrFolderRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <% + col_span_str = '' + if folder.datatypes: + label = folder.label + col_span_str = 'colspan="4"' + elif folder.label == 'Repository dependencies': + label = "%s<i> - this repository requires installation of these additional repositories</i>" % folder.label + elif folder.repository_dependencies: + label = folder.label + elif folder.invalid_tools: + label = "%s<i> - click the tool config file name to see why the tool is invalid</i>" % folder.label + elif folder.tool_dependencies: + label = "%s<i> - this repository's tools require installation of these dependencies</i>" % folder.label + col_span_str = 'colspan="3"' + elif folder.valid_tools: + label = "%s<i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i>" % folder.label + col_span_str = 'colspan="3"' + elif folder.workflows: + label = folder.label + col_span_str = 'colspan="4"' + %> + <td ${col_span_str} style="padding-left: ${folder_pad}px;"> + <span class="expandLink folder-${encoded_id}-click"> + <div style="float: left; margin-left: 2px;" class="expandLink folder-${encoded_id}-click"> + <a class="folder-${encoded_id}-click" href="javascript:void(0);"> + ${label} + </a> + </div> + </span> + <td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> + %endif + %for sub_folder in folder.folders: + ${render_folder( sub_folder, pad, parent=my_row, row_counter=row_counter, is_root_folder=False )} + %endfor + %for repository_dependency in folder.repository_dependencies: + ${render_repository_dependency( repository_dependency, pad, my_row, row_counter )} + %endfor + %for index, tool_dependency in enumerate( folder.tool_dependencies ): + <% row_is_header = index == 0 %> + ${render_tool_dependency( tool_dependency, pad, my_row, row_counter, row_is_header )} + %endfor + %if folder.valid_tools: + %for index, tool in enumerate( folder.valid_tools ): + <% row_is_header = index == 0 %> + ${render_tool( tool, pad, my_row, row_counter, row_is_header )} + %endfor + %endif + %for invalid_tool in folder.invalid_tools: + ${render_invalid_tool( invalid_tool, pad, my_row, row_counter )} + %endfor + %if folder.workflows: + %for index, workflow in enumerate( folder.workflows ): + <% row_is_header = index == 0 %> + ${render_workflow( workflow, pad, my_row, row_counter, row_is_header )} + %endfor + %endif + %if folder.datatypes: + %for index, datatype in enumerate( folder.datatypes ): + <% row_is_header = index == 0 %> + ${render_datatype( datatype, pad, my_row, row_counter, row_is_header )} + %endfor + %endif +</%def> + +<%def name="render_datatype( datatype, pad, parent, row_counter, row_is_header=False )"> + <% + encoded_id = trans.security.encode_id( datatype.id ) + if row_is_header: + cell_type = 'th' + else: + cell_type = 'td' + %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <${cell_type} style="padding-left: ${pad+20}px;">${datatype.extension | h}</${cell_type}> + <${cell_type}>${datatype.type | h}</${cell_type}> + <${cell_type}>${datatype.mimetype | h}</${cell_type}> + <${cell_type}>${datatype.subclass | h}</${cell_type}> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_invalid_tool( invalid_tool, pad, parent, row_counter, valid=True )"> + <% encoded_id = trans.security.encode_id( invalid_tool.id ) %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision )}"> + ${invalid_tool.tool_config | h} + </a> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_repository_dependency( repository_dependency, pad, parent, row_counter )"> + + <% encoded_id = trans.security.encode_id( repository_dependency.id ) %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + ##<td style="padding-left: ${pad+20}px;">${repository_dependency.toolshed | h}</td> + <td style="padding-left: ${pad+20}px;">Repository <b>${repository_dependency.repository_name | h}</b> revision <b>${repository_dependency.changeset_revision | h}</b> owned by <b>${repository_dependency.repository_owner | h}</b></td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_tool( tool, pad, parent, row_counter, row_is_header )"> + <% + encoded_id = trans.security.encode_id( tool.id ) + if row_is_header: + cell_type = 'th' + else: + cell_type = 'td' + %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + %if row_is_header: + <th style="padding-left: ${pad+20}px;">${tool.name | h}</th> + %else: + <td style="padding-left: ${pad+20}px;"> + <div style="float:left;" class="menubutton split popup" id="tool-${encoded_id}-popup"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( tool.repository_id ), tool_config=tool.tool_config, changeset_revision=tool.changeset_revision )}">${tool.name | h}</a> + </div> + <div popupmenu="tool-${encoded_id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a> + </div> + </td> + %endif + <${cell_type}>${tool.description | h}</${cell_type}> + <${cell_type}>${tool.version | h}</${cell_type}> + ##<${cell_type}>${tool.requirements | h}</${cell_type}> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_tool_dependency( tool_dependency, pad, parent, row_counter, row_is_header )"> + <% + encoded_id = trans.security.encode_id( tool_dependency.id ) + if row_is_header: + cell_type = 'th' + else: + cell_type = 'td' + %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <${cell_type} style="padding-left: ${pad+20}px;">${tool_dependency.name | h}</${cell_type}> + <${cell_type}> + <% + if tool_dependency.version: + version_str = tool_dependency.version + else: + version_str = '' + %> + ${version_str | h} + </${cell_type}> + <${cell_type}>${tool_dependency.type | h}</${cell_type}> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_workflow( workflow, pad, parent, row_counter, row_is_header=False )"> + <% + from galaxy.tool_shed.encoding_util import tool_shed_encode + encoded_id = trans.security.encode_id( workflow.id ) + if row_is_header: + cell_type = 'th' + else: + cell_type = 'td' + %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <${cell_type} style="padding-left: ${pad+20}px;"> + %if row_is_header: + ${workflow.workflow_name | h} + %else: + <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=trans.security.encode_id( workflow.repository_metadata_id ), workflow_name=tool_shed_encode( workflow.workflow_name ) )}">${workflow.workflow_name | h}</a> + %endif + </${cell_type}> + <${cell_type}>${workflow.steps | h}</${cell_type}> + <${cell_type}>${workflow.format_version | h}</${cell_type}> + <${cell_type}>${workflow.annotation | h}</${cell_type}> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + +<%def name="render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=False )"> + <% + from galaxy.tool_shed.encoding_util import tool_shed_encode + + has_datatypes = metadata and 'datatypes' in metadata + has_readme = metadata and 'readme' in metadata + has_workflows = metadata and 'workflows' in metadata + + datatypes_root_folder = containers_dict[ 'datatypes' ] + invalid_tools_root_folder = containers_dict[ 'invalid_tools' ] + repository_dependencies_root_folder = containers_dict[ 'repository_dependencies' ] + tool_dependencies_root_folder = containers_dict[ 'tool_dependencies' ] + valid_tools_root_folder = containers_dict[ 'valid_tools' ] + workflows_root_folder = containers_dict[ 'workflows' ] + + has_contents = datatypes_root_folder, invalid_tools_root_folder or valid_tools_root_folder or workflows_root_folder + + class RowCounter( object ): + def __init__( self ): + self.count = 0 + def increment( self ): + self.count += 1 + def __str__( self ): + return str( self.count ) + %> + %if repository_dependencies_root_folder or tool_dependencies_root_folder: + <div class="toolForm"> + <div class="toolFormTitle">Dependencies of this repository</div> + <div class="toolFormBody"> + %if repository_dependencies_root_folder: + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="repository_dependencies"> + ${self.render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + %endif + %if tool_dependencies_root_folder: + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="tool_dependencies"> + ${self.render_folder( tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + %endif + </div> + </div> + %endif + %if has_contents: <p/><div class="toolForm"> - <div class="toolFormTitle">Preview tools and inspect metadata by tool version</div> + <div class="toolFormTitle">Contents of this repository</div><div class="toolFormBody"> - %if metadata: - %if 'repository_dependencies' in metadata: - <div class="form-row"> - <table class="grid"> - <tr> - <td><b>tool shed</b></td> - <td><b>name</b></td> - <td><b>version</b></td> - <td><b>type</b></td> - </tr> - %for repository_dependency_tup in metadata[ 'repository_dependencies' ]: - <% toolshed, name, owner, changeset_revision = repository_dependency_tup %> - <tr> - <td>${toolshed | h}</td> - <td>${name | h}</td> - <td>${owner | h}</td> - <td>${changeset_revision | h}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'tool_dependencies' in metadata: - <% - # See if tool dependencies are packages, environment settings or both. - tool_dependencies = metadata[ 'tool_dependencies' ] - contains_packages = False - for k in tool_dependencies.keys(): - if k != 'set_environment': - contains_packages = True - break - contains_env_settings = 'set_environment' in tool_dependencies.keys() - %> - %if contains_packages: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>The following tool dependencies can optionally be automatically installed</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>version</b></td> - <td><b>type</b></td> - </tr> - %for dependency_key, requirements_dict in tool_dependencies.items(): - %if dependency_key != 'set_environment': - <% - name = requirements_dict[ 'name' ] - version = requirements_dict[ 'version' ] - type = requirements_dict[ 'type' ] - %> - <tr> - <td>${name | h}</td> - <td>${version | h}</td> - <td>${type | h}</td> - </tr> - %endif - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if contains_env_settings: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>The following environment settings can optionally be handled as part of the installation</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>type</b></td> - </tr> - <% environment_settings = tool_dependencies[ 'set_environment' ] %> - %for requirements_dict in environment_settings: - <tr> - <td>${requirements_dict[ 'name' ] | h}</td> - <td>${requirements_dict[ 'type' ] | h}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %endif - %if 'tools' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Valid tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td> - </tr> - </table> - </div> - <div class="form-row"> - <% tool_dicts = metadata[ 'tools' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>description</b></td> - <td><b>version</b></td> - <td><b>requirements</b></td> - </tr> - %for index, tool_dict in enumerate( tool_dicts ): - <tr> - <td> - <div style="float:left;" class="menubutton split popup" id="tool-${index}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}">${tool_dict[ 'name' ]}</a> - </div> - <div popupmenu="tool-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a> - </div> - </td> - <td>${tool_dict[ 'description' ] | h}</td> - <td>${tool_dict[ 'version' ] | h}</td> - <td> - <% - if 'requirements' in tool_dict: - requirements = tool_dict[ 'requirements' ] - else: - requirements = None - %> - %if requirements: - <% - requirements_str = '' - for requirement_dict in tool_dict[ 'requirements' ]: - requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) - requirements_str = requirements_str.rstrip( ', ' ) - %> - ${requirements_str | h} - %else: - none - %endif - </td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'invalid_tools' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Invalid tools</b><i> - click the tool config file name to see why the tool is invalid</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% invalid_tool_configs = metadata[ 'invalid_tools' ] %> - <table class="grid"> - %for invalid_tool_config in invalid_tool_configs: - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> - ${invalid_tool_config | h} - </a> - </td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'workflows' in metadata: - ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is - ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Workflows</b></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% workflow_tups = metadata[ 'workflows' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>steps</b></td> - <td><b>format-version</b></td> - <td><b>annotation</b></td> - </tr> - %for workflow_tup in workflow_tups: - <% - relative_path = workflow_tup[0] - workflow_dict = workflow_tup[1] - workflow_name = workflow_dict[ 'name' ] - ## Initially steps were not stored in the metadata record. - steps = workflow_dict.get( 'steps', [] ) - format_version = workflow_dict[ 'format-version' ] - annotation = workflow_dict[ 'annotation' ] - %> - <tr> - <td> - <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">${workflow_name | h}</a> - </td> - <td> - %if steps: - ${len( steps )} - %else: - unknown - %endif - </td> - <td>${format_version | h}</td> - <td>${annotation | h}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'datatypes' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Data types</b></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% datatypes_dicts = metadata[ 'datatypes' ] %> - <table class="grid"> - <tr> - <td><b>extension</b></td> - <td><b>type</b></td> - <td><b>mimetype</b></td> - <td><b>subclass</b></td> - </tr> - %for datatypes_dict in datatypes_dicts: - <% - extension = datatypes_dict.get( 'extension', ' ' ) - dtype = datatypes_dict.get( 'dtype', ' ' ) - mimetype = datatypes_dict.get( 'mimetype', ' ' ) - subclass = datatypes_dict.get( 'subclass', ' ' ) - %> - <tr> - <td>${extension | h}</td> - <td>${dtype | h}</td> - <td>${mimetype | h}</td> - <td>${subclass | h}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif + %if valid_tools_root_folder: + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="valid_tools"> + ${self.render_folder( valid_tools_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + %endif + %if invalid_tools_root_folder: + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="invalid_tools"> + ${self.render_folder( invalid_tools_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + %endif + %if workflows_root_folder: + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="workflows"> + ${self.render_folder( workflows_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + %endif + %if datatypes_root_folder: + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="tables container-table" id="datatypes"> + ${self.render_folder( datatypes_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> %endif </div></div> diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -16,10 +16,6 @@ can_set_metadata = not is_new and not is_deprecated can_rate = not is_new and not is_deprecated and trans.user and repository.user != trans.user can_view_change_log = not is_new - if can_push: - browse_label = 'Browse or delete repository tip files' - else: - browse_label = 'Browse repository tip files' can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip( trans.app ) can_deprecate = not is_new and trans.user and ( is_admin or repository.user == trans.user ) and not is_deprecated can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated @@ -27,6 +23,11 @@ has_readme = metadata and 'readme' in metadata can_review_repository = not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) reviewing_repository = cntrller and cntrller == 'repository_review' + + if can_push: + browse_label = 'Browse or delete repository tip files' + else: + browse_label = 'Browse repository tip files' if changeset_revision == repository.tip( trans.app ): tip_str = 'repository tip' else: @@ -42,10 +43,15 @@ %><%inherit file="${inherit(context)}"/> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating" )} - ${common_javascripts(repository)} + ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )} + ${dependency_javascripts()} </%def><br/><br/> @@ -204,7 +210,7 @@ </form></div></div> -${render_repository_items( repository_metadata_id, changeset_revision, metadata, can_set_metadata=True )} +${render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=True )} <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div> diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -28,10 +28,15 @@ %><%inherit file="${inherit(context)}"/> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating" )} - ${common_javascripts(repository)} + ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )} + ${dependency_javascripts()} </%def><br/><br/> @@ -79,4 +84,4 @@ </div></div><p/> -${render_repository_items( repository_metadata_id, changeset_revision, metadata, can_set_metadata=False )} +${render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=False )} diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -32,10 +32,15 @@ %><%inherit file="${inherit(context)}"/> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating" )} - ${common_javascripts(repository)} + ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )} + ${dependency_javascripts()} </%def><br/><br/> @@ -181,7 +186,7 @@ %endif </div></div> -${render_repository_items( repository_metadata_id, changeset_revision, metadata, can_set_metadata=False )} +${render_repository_items( repository_metadata_id, changeset_revision, metadata, containers_dict, can_set_metadata=False )} %if repository.categories: <p/><div class="toolForm"> diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c templates/webapps/community/repository_review/browse_review.mako --- a/templates/webapps/community/repository_review/browse_review.mako +++ b/templates/webapps/community/repository_review/browse_review.mako @@ -4,7 +4,7 @@ <% from galaxy.web.form_builder import CheckboxField - from galaxy.webapps.community.controllers.common import STRSEP + from galaxy.webapps.community.util.container_util import STRSEP can_manage_repository = is_admin or repository.user == trans.user %> diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c templates/webapps/community/repository_review/edit_review.mako --- a/templates/webapps/community/repository_review/edit_review.mako +++ b/templates/webapps/community/repository_review/edit_review.mako @@ -5,7 +5,7 @@ <% from galaxy.web.form_builder import CheckboxField from galaxy.webapps.community.controllers.repository_review import build_approved_select_field - from galaxy.webapps.community.controllers.common import STRSEP + from galaxy.webapps.community.util.container_util import STRSEP can_manage_repository = is_admin or repository.user == trans.user %> diff -r eea034b7cc625fa294fdd1e071d99defb40f67d3 -r 519b7df6d72a28689582e02879026c04b2214f2c templates/webapps/community/repository_review/reviews_of_changeset_revision.mako --- a/templates/webapps/community/repository_review/reviews_of_changeset_revision.mako +++ b/templates/webapps/community/repository_review/reviews_of_changeset_revision.mako @@ -5,7 +5,7 @@ <% from galaxy.webapps.community.controllers.repository_review import build_approved_select_field - from galaxy.webapps.community.controllers.common import STRSEP + from galaxy.webapps.community.util.container_util import STRSEP is_admin = trans.user_is_admin() is_new = repository.is_new( trans.app ) can_browse_contents = not is_new 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 the tool migration process that was broken due to the recent changes in the imports to various Galaxy framework files, mostly the Galaxy model.
by Bitbucket 24 Nov '12

24 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/eea034b7cc62/ changeset: eea034b7cc62 user: greg date: 2012-11-24 16:21:48 summary: Fix the tool migration process that was broken due to the recent changes in the imports to various Galaxy framework files, mostly the Galaxy model. affected #: 4 files diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -2,7 +2,7 @@ Classes encapsulating the management of repositories installed from Galaxy tool sheds. """ import os -import galaxy.util.shed_util +from galaxy.util.shed_util import * from galaxy.model.orm import * from galaxy import eggs @@ -27,7 +27,7 @@ ElementInclude.include( root ) tool_path = root.get( 'tool_path', None ) if tool_path: - tool_shed = galaxy.util.shed_util.clean_tool_shed_url( tool_shed_repository.tool_shed ) + tool_shed = clean_tool_shed_url( tool_shed_repository.tool_shed ) relative_path = os.path.join( tool_path, tool_shed, 'repos', @@ -44,13 +44,13 @@ .order_by( self.model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - installed_repository_dict = galaxy.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) if installed_repository_dict: self.installed_repository_dicts.append( installed_repository_dict ) def load_proprietary_converters_and_display_applications( self, deactivate=False ): for installed_repository_dict in self.installed_repository_dicts: if installed_repository_dict[ 'converter_path' ]: - galaxy.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - galaxy.util.shed_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) \ No newline at end of file diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -2,6 +2,7 @@ import galaxy.config import galaxy.datatypes.registry from galaxy import tools +from galaxy.tools.data import * import galaxy.model.mapping import galaxy.tools.search from galaxy.objectstore import build_object_store_from_config @@ -42,8 +43,8 @@ # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( tool_data_path=self.config.tool_data_path, - config_filename=self.config.tool_data_table_config_path ) + self.tool_data_tables = ToolDataTableManager( tool_data_path=self.config.tool_data_path, + config_filename=self.config.tool_data_table_config_path ) # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, tool_data_path=self.tool_data_tables.tool_data_path, diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,7 +1,6 @@ import os, tempfile, shutil, logging, urllib2 from galaxy import util from galaxy.datatypes.checkers import * -from galaxy.datatypes.sniff import is_column_based from galaxy.util.json import * from galaxy.util.shed_util_common import * from galaxy.tools.search import ToolBoxSearch @@ -475,13 +474,6 @@ else: tool_section = None return tool_section -def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ): - """Update the received metadata_dict with changes that have been applied to the received exported_workflow_dict.""" - if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) ) - else: - metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] - return metadata_dict def get_config( config_file, repo, ctx, dir ): """Return the latest version of config_filename from the repository manifest.""" config_file = strip_path( config_file ) @@ -817,6 +809,24 @@ parent_id=tool_version_using_parent_id.id ) sa_session.add( tool_version_association ) sa_session.flush() +def is_column_based( fname, sep='\t', skip=0, is_multi_byte=False ): + """See if the file is column based with respect to a separator.""" + headers = get_headers( fname, sep, is_multi_byte=is_multi_byte ) + count = 0 + if not headers: + return False + for hdr in headers[ skip: ]: + if hdr and hdr[ 0 ] and not hdr[ 0 ].startswith( '#' ): + if len( hdr ) > 1: + count = len( hdr ) + break + if count < 2: + return False + for hdr in headers[ skip: ]: + if hdr and hdr[ 0 ] and not hdr[ 0 ].startswith( '#' ): + if len( hdr ) != count: + return False + return True def is_data_index_sample_file( file_path ): """ Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when a tool shed repository is being installed diff -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 -r eea034b7cc625fa294fdd1e071d99defb40f67d3 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -2,6 +2,7 @@ from galaxy import util from galaxy.tools import parameters from galaxy.util import inflector +from galaxy.util.json import * from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.datatypes.checkers import * @@ -724,6 +725,13 @@ else: metadata_dict[ 'tools' ] = [ tool_dict ] return metadata_dict +def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ): + """Update the received metadata_dict with changes that have been applied to the received exported_workflow_dict.""" + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) ) + else: + metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] + return metadata_dict def get_changectx_for_changeset( repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits November 2012