galaxy-commits July 2011

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commit/galaxy-central: greg: Change tool shed repository version to be revision, and some fixes for generating and saving repository metadata.
by Bitbucket 14 Jul '11

14 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e43c31f9e64c/ changeset: e43c31f9e64c user: greg date: 2011-07-14 20:25:29 summary: Change tool shed repository version to be revision, and some fixes for generating and saving repository metadata. affected #: 6 files (984 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Thu Jul 14 12:12:55 2011 +0200 +++ b/lib/galaxy/webapps/community/controllers/common.py Thu Jul 14 14:25:29 2011 -0400 @@ -75,14 +75,14 @@ .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 set_repository_metadata( trans, id, ctx_str, **kwd ): +def set_repository_metadata( trans, id, change_set_revision, **kwd ): """Set repository metadata""" message = '' status = 'done' repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) - change_set = get_change_set( trans, repo, ctx_str ) + change_set = get_change_set( trans, repo, change_set_revision ) invalid_files = [] flush_needed = False if change_set is not None: @@ -103,7 +103,6 @@ full_path = os.path.abspath( os.path.join( root, name ) ) tool = load_tool( trans, full_path ) if tool is not None: - repository_metadata = get_repository_metadata( trans, id, repository.tip ) tool_requirements = [] for tr in tool.requirements: requirement_dict = dict( name=tr.name, @@ -126,6 +125,7 @@ tool_config=os.path.join( root, name ), requirements=tool_requirements, tests=tool_tests ) + repository_metadata = get_repository_metadata( trans, id, change_set_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata and 'tools' in metadata: @@ -161,32 +161,39 @@ # Find all exported workflows elif name.endswith( '.ga' ): try: - repository_metadata = get_repository_metadata( trans, id, repository.tip ) full_path = os.path.abspath( os.path.join( root, name ) ) # Convert workflow data from json fp = open( full_path, 'rb' ) workflow_text = fp.read() fp.close() - workflow_dict = from_json_string( workflow_text ) + exported_workflow_dict = from_json_string( workflow_text ) + # We'll store everything except the workflow steps in the database. + workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], + 'name' :exported_workflow_dict[ 'name' ], + 'annotation' : exported_workflow_dict[ 'annotation' ], + 'format-version' : exported_workflow_dict[ 'format-version' ] } + repository_metadata = get_repository_metadata( trans, id, change_set_revision ) if repository_metadata: metadata = repository_metadata.metadata - old_metadata_workflows = metadata[ 'workflows' ] - new_metadata_workflows = [] - for workflow_metadata_dict in old_metadata_workflows: - # TODO: what if 2 exported galaxy workflows have the same name, annotation, format-version? - if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ - 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == workflow_dict[ 'name' ] and \ - 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == workflow_dict[ 'annotation' ] and \ - 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == workflow_dict[ 'format-version' ]: - new_metadata_workflows.append( workflow_dict ) - else: - new_metadata_workflows.append( workflow_metadata_dict ) - if metadata is None: - repository_metadata.metadata = {} - repository_metadata.metadata[ 'workflows' ] = new_metadata_workflows - trans.sa_session.add( repository_metadata ) - if not flush_needed: - flush_needed = True + if metadata and 'workflows' in metadata: + metadata_workflows = metadata[ 'workflows' ] + found = False + for workflow_metadata_dict in metadata_workflows: + if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ + 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == exported_workflow_dict[ 'name' ] and \ + 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == exported_workflow_dict[ 'annotation' ] and \ + 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == exported_workflow_dict[ 'format-version' ]: + found = True + break + if not found: + metadata_workflows.append( workflow_dict ) + else: + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'workflows' ] = workflow_dict + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True else: if 'workflows' in metadata_dict: metadata_dict[ 'workflows' ].append( workflow_dict ) @@ -202,10 +209,10 @@ if not flush_needed: flush_needed = True else: - message = "Repository does not include changeset revision '%s'." % str( ctx_str ) + message = "Repository does not include changeset revision '%s'." % str( change_set_revision ) status = 'error' if invalid_files: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( ctx_str ) + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( change_set_revision ) for itc_tup in invalid_files: message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) status = 'error' @@ -217,11 +224,11 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() -def get_change_set( trans, repo, ctx_str, **kwd ): +def get_change_set( trans, repo, change_set_revision, **kwd ): """Retrieve a specified change set from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) - if str( ctx ) == ctx_str: + if str( ctx ) == change_set_revision: return ctx return None def get_user( trans, id ): --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 14 12:12:55 2011 +0200 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Jul 14 14:25:29 2011 -0400 @@ -74,9 +74,9 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.name - class VersionColumn( grids.TextColumn ): + class RevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): - return repository.version + return repository.revision class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.description @@ -126,8 +126,8 @@ DescriptionColumn( "Synopsis", key="description", attach_popup=False ), - VersionColumn( "Version", - attach_popup=False ), + RevisionColumn( "Revision", + attach_popup=False ), CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -878,7 +878,6 @@ folder_contents.append( node ) return folder_contents def __get_files( self, trans, repository, folder_path ): - ok = True def print_ticks( d ): pass cmd = "ls -p '%s'" % folder_path @@ -887,17 +886,22 @@ events={ pexpect.TIMEOUT : print_ticks }, timeout=10 ) if 'No such file or directory' in output: - status = 'error' - message = "No folder named (%s) exists." % folder_path - ok = False - if ok: - return output.split() - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - operation="view_or_manage_repository", - id=trans.security.encode_id( repository.id ), - status=status, - message=message ) ) + if 'root' in output: + # The repository is empty + return [] + else: + # Some strange error occurred, the selected file was displayed, but + # does not exist in the sub-directory from which it was displayed. + # This should not happen... + status = 'error' + message = "No folder named (%s) exists." % folder_path + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation="view_or_manage_repository", + id=trans.security.encode_id( repository.id ), + status=status, + message=message ) ) + return output.split() @web.json def get_file_contents( self, trans, file_path ): # Avoid caching --- a/lib/galaxy/webapps/community/model/__init__.py Thu Jul 14 12:12:55 2011 +0200 +++ b/lib/galaxy/webapps/community/model/__init__.py Thu Jul 14 14:25:29 2011 -0400 @@ -114,7 +114,7 @@ return config.get( "paths", option ) raise Exception( "Entry for repository %s missing in %s/hgweb.config file." % ( lhs, os.getcwd() ) ) @property - def version( self ): + def revision( self ): repo = hg.repository( ui.ui(), self.repo_path ) tip_ctx = repo.changectx( repo.changelog.tip() ) return "%s:%s" % ( str( tip_ctx.rev() ), str( repo.changectx( repo.changelog.tip() ) ) ) --- a/templates/webapps/community/repository/manage_repository.mako Thu Jul 14 12:12:55 2011 +0200 +++ b/templates/webapps/community/repository/manage_repository.mako Thu Jul 14 14:25:29 2011 -0400 @@ -122,9 +122,9 @@ <div class="form-row"><label>Version:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.version}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> %else: - ${repository.version} + ${repository.revision} %endif </div><div class="form-row"> --- a/templates/webapps/community/repository/rate_repository.mako Thu Jul 14 12:12:55 2011 +0200 +++ b/templates/webapps/community/repository/rate_repository.mako Thu Jul 14 14:25:29 2011 -0400 @@ -104,7 +104,7 @@ </div><div class="form-row"><label>Version:</label> - ${repository.version} + ${repository.revision} <div style="clear: both"></div></div><div class="form-row"> --- a/templates/webapps/community/repository/view_repository.mako Thu Jul 14 12:12:55 2011 +0200 +++ b/templates/webapps/community/repository/view_repository.mako Thu Jul 14 14:25:29 2011 -0400 @@ -120,9 +120,9 @@ <div class="form-row"><label>Version:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.version}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.revision}</a> %else: - ${repository.version} + ${repository.revision} %endif </div><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: document FeaturePainter object and methods as abstract.
by Bitbucket 14 Jul '11

14 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fd53d9688eb3/ changeset: fd53d9688eb3 user: jgoecks date: 2011-07-14 12:12:55 summary: Trackster: document FeaturePainter object and methods as abstract. affected #: 1 file (377 bytes) --- a/static/scripts/trackster.js Wed Jul 13 16:51:51 2011 -0400 +++ b/static/scripts/trackster.js Thu Jul 14 12:12:55 2011 +0200 @@ -3307,6 +3307,9 @@ ctx.restore(); } +/** + * Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work. + */ var FeaturePainter = function( data, view_start, view_end, prefs, mode ) { Painter.call( this, data, view_start, view_end, prefs, mode ); } @@ -3327,7 +3330,6 @@ }, draw: function( ctx, width, height, slots ) { - var data = this.data, view_start = this.view_start, view_end = this.view_end; ctx.save(); @@ -3356,7 +3358,12 @@ } ctx.restore(); - } + }, + + /** + * Abstract function for drawing an individual feature. NOTE: this method must be implemented by subclasses for drawing to work. + */ + draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {} }); // Constants specific to feature tracks moved here (HACKING, these should Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add support for exproted Galaxy workflows when generating metadata for a tool shed repository.
by Bitbucket 13 Jul '11

13 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/31dda910849a/ changeset: 31dda910849a user: greg date: 2011-07-13 22:51:51 summary: Add support for exproted Galaxy workflows when generating metadata for a tool shed repository. affected #: 4 files (6.6 KB) --- a/lib/galaxy/webapps/community/controllers/common.py Wed Jul 13 09:39:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Wed Jul 13 16:51:51 2011 -0400 @@ -83,7 +83,7 @@ repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) change_set = get_change_set( trans, repo, ctx_str ) - invalid_tool_configs = [] + invalid_files = [] flush_needed = False if change_set is not None: metadata_dict = {} @@ -110,12 +110,22 @@ type=tr.type, version=tr.version ) tool_requirements.append( requirement_dict ) - tool_dict = dict( id = tool.id, - name = tool.name, - version = tool.version, - description = tool.description, - tool_config = os.path.join( root, name ), - requirements = tool_requirements ) + tool_tests = [] + if tool.tests: + for ttb in tool.tests: + test_dict = dict( name=ttb.name, + required_files=ttb.required_files, + inputs=ttb.inputs, + outputs=ttb.outputs ) + tool_tests.append( test_dict ) + tool_dict = dict( id=tool.id, + name=tool.name, + version=tool.version, + description=tool.description, + version_string_cmd = tool.version_string_cmd, + tool_config=os.path.join( root, name ), + requirements=tool_requirements, + tests=tool_tests ) if repository_metadata: metadata = repository_metadata.metadata if metadata and 'tools' in metadata: @@ -127,8 +137,10 @@ found = True tool_metadata_dict[ 'name' ] = tool.name tool_metadata_dict[ 'description' ] = tool.description + tool_metadata_dict[ 'version_string_cmd' ] = tool.version_string_cmd tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) tool_metadata_dict[ 'requirements' ] = tool_requirements + tool_metadata_dict[ 'tests' ] = tool_tests flush_needed = True if not found: metadata_tools.append( tool_dict ) @@ -145,7 +157,43 @@ else: metadata_dict[ 'tools' ] = [ tool_dict ] except Exception, e: - invalid_tool_configs.append( ( name, str( e ) ) ) + invalid_files.append( ( name, str( e ) ) ) + # Find all exported workflows + elif name.endswith( '.ga' ): + try: + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + full_path = os.path.abspath( os.path.join( root, name ) ) + # Convert workflow data from json + fp = open( full_path, 'rb' ) + workflow_text = fp.read() + fp.close() + workflow_dict = from_json_string( workflow_text ) + if repository_metadata: + metadata = repository_metadata.metadata + old_metadata_workflows = metadata[ 'workflows' ] + new_metadata_workflows = [] + for workflow_metadata_dict in old_metadata_workflows: + # TODO: what if 2 exported galaxy workflows have the same name, annotation, format-version? + if 'a_galaxy_workflow' in workflow_metadata_dict and util.string_as_bool( workflow_metadata_dict[ 'a_galaxy_workflow' ] ) and \ + 'name' in workflow_metadata_dict and workflow_metadata_dict[ 'name' ] == workflow_dict[ 'name' ] and \ + 'annotation' in workflow_metadata_dict and workflow_metadata_dict[ 'annotation' ] == workflow_dict[ 'annotation' ] and \ + 'format-version' in workflow_metadata_dict and workflow_metadata_dict[ 'format-version' ] == workflow_dict[ 'format-version' ]: + new_metadata_workflows.append( workflow_dict ) + else: + new_metadata_workflows.append( workflow_metadata_dict ) + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'workflows' ] = new_metadata_workflows + trans.sa_session.add( repository_metadata ) + if not flush_needed: + flush_needed = True + else: + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( workflow_dict ) + else: + metadata_dict[ 'workflows' ] = [ workflow_dict ] + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) if metadata_dict: # The metadata_dict dictionary will contain items only # if the repository did not already have metadata set. @@ -156,9 +204,9 @@ else: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' - if invalid_tool_configs: + if invalid_files: message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( ctx_str ) - for itc_tup in invalid_tool_configs: + for itc_tup in invalid_files: message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) status = 'error' elif flush_needed: --- a/templates/webapps/community/repository/manage_repository.mako Wed Jul 13 09:39:02 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Wed Jul 13 16:51:51 2011 -0400 @@ -187,7 +187,13 @@ %if metadata: %if 'tools' in metadata: <div class="form-row"> - <label>Tools:</label> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Tools:</label></td> + </tr> + </table> + </div> + <div class="form-row"><% tool_dicts = metadata[ 'tools' ] %><table class="grid"><tr> @@ -226,6 +232,34 @@ </div><div style="clear: both"></div> %endif + %if 'workflows' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Workflows:</label></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% workflow_dicts = metadata[ 'workflows' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + %for workflow_dict in workflow_dicts: + <tr> + <td>${workflow_dict[ 'name' ]}</td> + <td>${workflow_dict[ 'format-version' ]}</td> + <td>${workflow_dict[ 'annotation' ]}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif %endif <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"><div class="form-row"> --- a/templates/webapps/community/repository/view_changelog.mako Wed Jul 13 09:39:02 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Wed Jul 13 16:51:51 2011 -0400 @@ -94,7 +94,7 @@ %><% display_date = changeset[ 'display_date' ] %> %if test_date != display_date: - <tr colspan="2"><td bgcolor="#D8D8D8 ">${display_date}</td></tr> + <tr colspan="2"><td bgcolor="#D8D8D8">${display_date}</td></tr> %endif <tr><td> --- a/templates/webapps/community/repository/view_repository.mako Wed Jul 13 09:39:02 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Wed Jul 13 16:51:51 2011 -0400 @@ -166,7 +166,13 @@ <div class="toolFormBody"> %if 'tools' in metadata: <div class="form-row"> - <label>Tools:</label> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Tools:</label></td> + </tr> + </table> + </div> + <div class="form-row"><% tool_dicts = metadata[ 'tools' ] %><table class="grid"><tr> @@ -205,6 +211,34 @@ </div><div style="clear: both"></div> %endif + %if 'workflows' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><label>Workflows:</label></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% workflow_dicts = metadata[ 'workflows' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + %for workflow_dict in workflow_dicts: + <tr> + <td>${workflow_dict[ 'name' ]}</td> + <td>${workflow_dict[ 'format-version' ]}</td> + <td>${workflow_dict[ 'annotation' ]}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif </div></div> %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are:
by Bitbucket 13 Jul '11

13 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b2f7abd50f6a/ changeset: b2f7abd50f6a user: greg date: 2011-07-13 15:39:02 summary: Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are: 1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all. 2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed. 3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags. 4. The final summary message is slightly changed. affected #: 1 file (514 bytes) --- a/scripts/cleanup_datasets/cleanup_datasets.py Tue Jul 12 18:14:56 2011 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Jul 13 09:39:02 2011 -0400 @@ -310,17 +310,21 @@ dataset_ids.extend( [ row.id for row in history_dataset_ids_query.execute() ] ) # Process each of the Dataset objects for dataset_id in dataset_ids: + dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id ) + if dataset.id in skip: + continue + skip.append( dataset.id ) print "######### Processing dataset id:", dataset_id - dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id ) - if dataset.id not in skip and _dataset_is_deletable( dataset ): - deleted_dataset_count += 1 - for dataset_instance in dataset.history_associations + dataset.library_associations: - # Mark each associated HDA as deleted - _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True ) - deleted_instance_count += 1 - skip.append( dataset.id ) + if not _dataset_is_deletable( dataset ): + print "Dataset is not deletable (shared between multiple histories/libraries, at least one is not deleted)" + continue + deleted_dataset_count += 1 + for dataset_instance in dataset.history_associations + dataset.library_associations: + # Mark each associated HDA as deleted + _purge_dataset_instance( dataset_instance, app, remove_from_disk, include_children=True, info_only=info_only, is_deletable=True ) + deleted_instance_count += 1 stop = time.time() - print "Examined %d datasets, marked %d as deleted and purged %d dataset instances" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) + print "Examined %d datasets, marked %d datasets and %d dataset instances (HDA) as deleted" % ( len( skip ), deleted_dataset_count, deleted_instance_count ) print "Total elapsed time: ", stop - start print "##########################################" @@ -396,8 +400,13 @@ .filter( app.model.MetadataFile.table.c.lda_id==ldda.id ): metadata_files.append( metadata_file ) for metadata_file in metadata_files: - print "The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id - if not info_only: + op_description = "marked as deleted" + if remove_from_disk: + op_description = op_description + " and purged from disk" + if info_only: + print "The following metadata files attached to associations of Dataset '%s' will be %s (without 'info_only' mode):" % ( dataset.id, op_description ) + else: + print "The following metadata files attached to associations of Dataset '%s' have been %s:" % ( dataset.id, op_description ) if remove_from_disk: try: print "Removing disk file ", metadata_file.file_name 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: kanwei: Improve BLAST parser tool error handling, and improve elementtree import as well.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/26bffb1b7d57/ changeset: 26bffb1b7d57 user: kanwei date: 2011-07-13 00:14:56 summary: Improve BLAST parser tool error handling, and improve elementtree import as well. affected #: 3 files (260 bytes) --- a/tools/metag_tools/megablast_xml_parser.py Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.py Tue Jul 12 18:14:56 2011 -0400 @@ -2,12 +2,12 @@ import sys, os, re -assert sys.version_info[:2] >= ( 2, 4 ) - if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as cElementTree + import xml.etree.cElementTree as ElementTree else: - import cElementTree + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -34,7 +34,7 @@ # get an iterable try: - context = cElementTree.iterparse( source, events=( "start", "end" ) ) + context = ElementTree.iterparse( source, events=( "start", "end" ) ) except: stop_err( "Invalid data format." ) # turn it into an iterator @@ -46,7 +46,7 @@ stop_err( "Invalid data format." ) outfile = open( sys.argv[2], 'w' ) - try: + try: for event, elem in context: # for every <Iteration> tag if event == "end" and elem.tag == "Iteration": @@ -71,7 +71,7 @@ elem.clear() except: outfile.close() - stop_err( "The input data contains tags that are not recognizable by the tool." ) + stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] ) outfile.close() --- a/tools/metag_tools/megablast_xml_parser.xml Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.xml Tue Jul 12 18:14:56 2011 -0400 @@ -2,26 +2,23 @@ <description></description><command interpreter="python">megablast_xml_parser.py $input1 $output1</command><inputs> - <param name="input1" type="data" format="blastxml" label="Megablast XML output" /> + <param name="input1" type="data" format="blastxml" label="Megablast XML output" /></inputs><outputs> - <data name="output1" format="tabular"/> + <data name="output1" format="tabular"/></outputs> -<requirements> - <requirement type="python-module">cElementTree</requirement> -</requirements><tests> - <test> - <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" /> - <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" /> - </test> + <test> + <param name="input1" value="megablast_xml_parser_test1.gz" ftype="blastxml" /> + <output name="output1" file="megablast_xml_parser_test1_out.tabular" ftype="tabular" /> + </test></tests><help> **What it does** This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). - + ----- **Output fields** --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jul 12 17:04:16 2011 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Jul 12 18:14:56 2011 -0400 @@ -5,7 +5,7 @@ BLAST filename, output format (std for standard 12 columns, or ext for the extended 24 columns offered in the BLAST+ wrappers). -The 12 colums output are 'qseqid sseqid pident length mismatch gapopen qstart +The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which mean: @@ -51,22 +51,23 @@ Be aware that the sequence in the extended tabular output or XML direct from BLAST+ may or may not use XXXX masking on regions of low complexity. This can throw the off the calculation of percentage identity and gap openings. -[In fact, both BLAST 2.2.24+ and 2.2.25+ have a sutle bug in this regard, +[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard, with these numbers changing depending on whether or not the low complexity filter is used.] -This script attempts to produce idential output to what BLAST+ would have done. +This script attempts to produce identical output to what BLAST+ would have done. However, check this with "diff -b ..." since BLAST+ sometimes includes an extra space character (probably a bug). """ import sys import re -assert sys.version_info[:2] >= ( 2, 4 ) if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as cElementTree + import xml.etree.cElementTree as ElementTree else: - import cElementTree + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree def stop_err( msg ): sys.stderr.write("%s\n" % msg) @@ -90,7 +91,7 @@ # get an iterable try: - context = cElementTree.iterparse(in_file, events=("start", "end")) + context = ElementTree.iterparse(in_file, events=("start", "end")) except: stop_err("Invalid data format.") # turn it into an iterator 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: kanwei: Rename version_string -> version_command, update wrappers
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/12cb939a8147/ changeset: 12cb939a8147 user: kanwei date: 2011-07-12 23:04:16 summary: Rename version_string -> version_command, update wrappers affected #: 7 files (31 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jul 07 11:19:33 2011 +0100 +++ b/lib/galaxy/tools/__init__.py Tue Jul 12 17:04:16 2011 -0400 @@ -397,8 +397,9 @@ self.description = util.xml_text(root, "description") # Versioning for tools self.version_string_cmd = None - if root.find("version_string") is not None: - self.version_string_cmd = root.find("version_string").text + version_cmd = root.find("version_command") + if version_cmd is not None: + self.version_string_cmd = version_cmd.text # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> - <version_string>blastn -version</version_string> + <version_command>blastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> - <version_string>blastp -version</version_string> + <version_command>blastp -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> - <version_string>blastx -version</version_string> + <version_command>blastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> - <version_string>tblastn -version</version_string> + <version_command>tblastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> - <version_string>tblastx -version</version_string> + <version_command>tblastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ngs_rna/tophat_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ngs_rna/tophat_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="tophat" name="Tophat for Illumina" version="1.5.0"><description>Find splice junctions using RNA-seq data</description> - <version_string>tophat --version</version_string> + <version_command>tophat --version</version_command><requirements><requirement type="package">tophat</requirement></requirements> 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: peterjc: Support new tool version tag in NCBI BLAST+ wrappers
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/632d4c48d97c/ changeset: 632d4c48d97c user: peterjc date: 2011-07-07 12:19:33 summary: Support new tool version tag in NCBI BLAST+ wrappers affected #: 5 files (267 bytes) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.10"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> + <version_string>blastn -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.10"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> + <version_string>blastp -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.10"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> + <version_string>blastx -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.10"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> + <version_string>tblastn -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Jul 12 15:02:37 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 @@ -1,5 +1,6 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.10"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> + <version_string>tblastx -version</version_string><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for displaying tools.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/661aca672402/ changeset: 661aca672402 user: greg date: 2011-07-12 21:02:37 summary: Fix for displaying tools. affected #: 1 file (14 bytes) --- a/templates/webapps/community/repository/tool_form.mako Tue Jul 12 13:51:28 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Jul 12 15:02:37 2011 -0400 @@ -84,7 +84,7 @@ field = SelectField( param.name ) field.add_option( param.name, param.name ) field_html = field.get_html() - elif isinstance( param, SelectToolParameter ) and param.data_ref: + elif isinstance( param, SelectToolParameter ) and hasattr( param, 'data_ref' ): field = SelectField( param.name, display=param.display ) field.add_option( param.data_ref, param.data_ref ) field_html = field.get_html( prefix ) 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: Make a backup copy of the tool shed's hgweb.config file just before changes are made to it. Add the ability for a repository owner to change categories associated with their repository.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/af9b19b57969/ changeset: af9b19b57969 user: greg date: 2011-07-12 19:51:28 summary: Make a backup copy of the tool shed's hgweb.config file just before changes are made to it. Add the ability for a repository owner to change categories associated with their repository. affected #: 4 files (3.8 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 10:07:15 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 13:51:28 2011 -0400 @@ -356,11 +356,19 @@ if not( VALID_REPOSITORYNAME_RE.match( name ) ): return "Repository names must contain only lower-case letters, numbers and underscore '_'." return '' + def __make_hgweb_config_copy( self, trans, hgweb_config ): + # Make a backup of the hgweb.config file + today = date.today() + backup_date = today.strftime( "%Y_%m_%d" ) + hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) + shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) def __add_hgweb_config_entry( self, trans, repository, repository_path ): # Add an entry in the hgweb.config file for a new repository. # An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) ) if os.path.exists( hgweb_config ): output = open( hgweb_config, 'a' ) @@ -374,6 +382,8 @@ # the owner changes the name of the repository. An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) repo_dir = repository.repo_path old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) old_entry = "%s = %s" % ( old_lhs, repo_dir ) @@ -537,6 +547,7 @@ display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) alerts = params.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) + category_ids = util.listify( params.get( 'category_id', '' ) ) if repository.email_alerts: email_alerts = from_json_string( repository.email_alerts ) else: @@ -572,7 +583,21 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() - message = "The repository information has been updated." + message = "The repository information has been updated." + elif params.get( 'manage_categories_button', False ): + flush_needed = False + # Delete all currently existing categories. + for rca in repository.categories: + trans.sa_session.delete( rca ) + trans.sa_session.flush() + if category_ids: + # Create category associations + for category_id in category_ids: + category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) + rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) + trans.sa_session.add( rca ) + trans.sa_session.flush() + message = "The repository information has been updated." elif params.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: remove_auth = params.get( 'remove_auth', '' ) @@ -586,6 +611,7 @@ usernames.append( user.username ) usernames = ','.join( usernames ) repository.set_allow_push( usernames, remove_auth=remove_auth ) + message = "The repository information has been updated." elif params.get( 'receive_email_alerts_button', False ): flush_needed = False if alerts_checked: @@ -601,6 +627,7 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() + message = "The repository information has been updated." if error: status = 'error' if repository.allow_push: @@ -615,6 +642,8 @@ metadata = repository_metadata.metadata else: metadata = None + categories = get_categories( trans ) + selected_categories = [ rca.category_id for rca in repository.categories ] return trans.fill_template( '/webapps/community/repository/manage_repository.mako', repo_name=repo_name, description=description, @@ -623,6 +652,8 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + selected_categories=selected_categories, + categories=categories, metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, --- a/templates/webapps/community/repository/create_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/create_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -38,7 +38,7 @@ <div style="clear: both"></div></div><div class="form-row"> - <label>Category</label> + <label>Categories</label><div class="form-row"><select name="category_id" multiple> %for category in categories: @@ -50,6 +50,9 @@ %endfor </select></div> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple categories. + </div><div style="clear: both"></div></div><div class="form-row"> --- a/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -151,6 +151,34 @@ </form></div></div> +<p/> +<div class="toolForm"> + <div class="toolFormTitle">Manage categories</div> + <div class="toolFormBody"> + <form name="categories" id="categories" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Categories</label> + <select name="category_id" multiple> + %for category in categories: + %if category.id in selected_categories: + <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> + %else: + <option value="${trans.security.encode_id( category.id )}">${category.name}</option> + %endif + %endfor + </select> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple categories. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="manage_categories_button" value="Save"/> + </div> + </form> + </div> +</div> +<p/> %if can_set_metadata: <p/><div class="toolForm"> @@ -215,7 +243,7 @@ %if trans.app.config.smtp_server: <p/><div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormTitle">Notification on update</div><div class="toolFormBody"><form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"> --- a/templates/webapps/community/repository/view_repository.mako Tue Jul 12 10:07:15 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jul 12 13:51:28 2011 -0400 @@ -145,6 +145,20 @@ %endif </div></div> +%if repository.categories: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Categories</div> + <div class="toolFormBody"> + %for rca in repository.categories: + <div class="form-row"> + ${rca.category.name} + </div> + %endfor + <div style="clear: both"></div> + </div> + </div> +%endif %if metadata: <p/><div class="toolForm"> @@ -197,7 +211,7 @@ %if trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormTitle">Notification on update</div><div class="toolFormBody"><form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for renaming a tool shed repository, and aother fix for displaying a tool that includes a SelectToolParameter with a data_ref.
by Bitbucket 12 Jul '11

12 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7c7d01c511d0/ changeset: 7c7d01c511d0 user: greg date: 2011-07-12 16:07:15 summary: Fix for renaming a tool shed repository, and aother fix for displaying a tool that includes a SelectToolParameter with a data_ref. affected #: 5 files (2.0 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jul 11 14:48:12 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jul 12 10:07:15 2011 -0400 @@ -369,6 +369,23 @@ output.write( '[paths]\n' ) output.write( "%s\n" % entry ) output.close() + def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): + # Change an entry in the hgweb.config file for a repository. This only happens when + # the owner changes the name of the repository. An entry looks something like: + # repos/test/mira_assembler = database/community_files/000/repo_123. + hgweb_config = "%s/hgweb.config" % trans.app.config.root + repo_dir = repository.repo_path + old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) + old_entry = "%s = %s" % ( old_lhs, repo_dir ) + new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) + tmp_fd, tmp_fname = tempfile.mkstemp() + new_hgweb_config = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( hgweb_config ) ): + if line.startswith( old_lhs ): + new_hgweb_config.write( new_entry ) + else: + new_hgweb_config.write( line ) + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __create_hgrc_file( self, repository ): # At this point, an entry for the repository is required to be in the hgweb.config # file so we can call repository.repo_path. @@ -511,7 +528,8 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) - repo = hg.repository( ui.ui(), repository.repo_path ) + repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) description = util.restore_text( params.get( 'description', repository.description ) ) long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) @@ -528,6 +546,7 @@ user = trans.user if params.get( 'edit_repository_button', False ): flush_needed = False + # TODO: add a can_manage in the security agent. if user != repository.user: message = "You are not the owner of this repository, so you cannot manage it." status = error @@ -541,6 +560,7 @@ if message: error = True else: + self.__change_hgweb_config_entry( trans, repository, repository.name, repo_name ) repository.name = repo_name flush_needed = True if description != repository.description: @@ -552,6 +572,7 @@ if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() + message = "The repository information has been updated." elif params.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: remove_auth = params.get( 'remove_auth', '' ) --- a/lib/galaxy/webapps/community/model/__init__.py Mon Jul 11 14:48:12 2011 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Tue Jul 12 10:07:15 2011 -0400 @@ -4,7 +4,7 @@ Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno, sys, codecs, operator, tempfile, logging, tarfile, mimetypes, ConfigParser +import os.path, os, errno, sys, codecs, operator, logging, tarfile, mimetypes, ConfigParser from galaxy import util from galaxy.util.bunch import Bunch from galaxy.util.hash_util import * --- a/templates/webapps/community/repository/manage_repository.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jul 12 10:07:15 2011 -0400 @@ -9,6 +9,7 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_browse_contents = not is_new + can_set_metadata = not is_new can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: @@ -79,10 +80,10 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> @@ -150,65 +151,67 @@ </form></div></div> -<p/> -<div class="toolForm"> - <div class="toolFormTitle">Repository metadata</div> - <div class="toolFormBody"> - %if metadata: - %if 'tools' in metadata: +%if can_set_metadata: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Repository metadata</div> + <div class="toolFormBody"> + %if metadata: + %if 'tools' in metadata: + <div class="form-row"> + <label>Tools:</label> + <% 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 tool_dict in tool_dicts: + <tr> + <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> + <td>${tool_dict[ 'description' ]}</td> + <td>${tool_dict[ 'version' ]}</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( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %endif + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"><div class="form-row"> - <label>Tools:</label> - <% 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 tool_dict in tool_dicts: - <tr> - <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> - <td>${tool_dict[ 'description' ]}</td> - <td>${tool_dict[ 'version' ]}</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( ', ' ) - %> - ${requirements_str} - %else: - none - %endif - </td> - </tr> - %endfor - </table> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div></div> - <div style="clear: both"></div> - %endif - %endif - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes for the repository tip. - </div> - </div> - </form> + </form> + </div></div> -</div> +%endif %if trans.app.config.smtp_server: <p/><div class="toolForm"> --- a/templates/webapps/community/repository/tool_form.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Tue Jul 12 10:07:15 2011 -0400 @@ -4,7 +4,7 @@ <% from galaxy.util.expressions import ExpressionContext from galaxy import util - from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter + from galaxy.tools.parameters.basic import DataToolParameter, ColumnListParameter, SelectToolParameter from galaxy.web.form_builder import SelectField is_admin = trans.user_is_admin() @@ -84,6 +84,10 @@ field = SelectField( param.name ) field.add_option( param.name, param.name ) field_html = field.get_html() + elif isinstance( param, SelectToolParameter ) and param.data_ref: + field = SelectField( param.name, display=param.display ) + field.add_option( param.data_ref, param.data_ref ) + field_html = field.get_html( prefix ) else: field = param.get_html_field( trans, None, other_values ) field_html = field.get_html( prefix ) --- a/templates/webapps/community/repository/view_repository.mako Mon Jul 11 14:48:12 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jul 12 10:07:15 2011 -0400 @@ -79,10 +79,10 @@ %endif %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits July 2011