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commit/galaxy-central: greg: Fixes for determining if a new metadata revision is required when inspecting tool shed repository dependency definitions.
by commits-noreply＠bitbucket.org 16 May '13

16 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/477979aa944f/ Changeset: 477979aa944f User: greg Date: 2013-05-16 17:55:41 Summary: Fixes for determining if a new metadata revision is required when inspecting tool shed repository dependency definitions. Affected #: 2 files diff -r 311cf2ae1623289551b0b568975e9840d46097a2 -r 477979aa944f14ab7189aa51e67168da333f0840 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -1,15 +1,27 @@ -import sys, os, shutil, logging, tarfile, tempfile, urllib +import logging +import os +import shutil +import sys +import tarfile +import tempfile +import urllib from galaxy.web.base.controller import BaseUIController -from galaxy import web, util +from galaxy import util +from galaxy import web from galaxy.datatypes import checkers from galaxy.util import json import tool_shed.util.shed_util_common as suc -from tool_shed.util import metadata_util, repository_dependency_util, tool_dependency_util, tool_util +from tool_shed.util import metadata_util +from tool_shed.util import repository_dependency_util +from tool_shed.util import tool_dependency_util +from tool_shed.util import tool_util from galaxy import eggs -eggs.require('mercurial') -from mercurial import hg, ui, commands +eggs.require( 'mercurial' ) +from mercurial import commands +from mercurial import hg +from mercurial import ui log = logging.getLogger( __name__ ) @@ -17,7 +29,9 @@ undesirable_files = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] CHUNK_SIZE = 2**20 # 1Mb + class UploadController( BaseUIController ): + def check_file_contents_for_email_alerts( self, trans ): """ See if any admin users have chosen to receive email alerts when a repository is updated. If so, the file contents of the update must be @@ -31,6 +45,7 @@ if user_email in admin_users: return True return False + def check_file_content_for_html_and_images( self, file_path ): message = '' if checkers.check_html( file_path ): @@ -38,6 +53,7 @@ elif checkers.check_image( file_path ): message = 'The file "%s" contains image content.\n' % str( file_path ) return message + @web.expose @web.require_login( 'upload', use_panels=True ) def upload( self, trans, **kwd ): @@ -235,6 +251,7 @@ remove_repo_files_not_in_tar=remove_repo_files_not_in_tar, message=message, status=status ) + def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) @@ -269,7 +286,9 @@ os.remove(repo_path) shutil.move(os.path.join(uploaded_directory, relative_path), repo_path) filenames_in_archive.append( relative_path ) - return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed) + return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, + undesirable_dirs_removed, undesirable_files_removed) + def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path( trans.app ) @@ -303,8 +322,18 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() - return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed) - def __handle_directory_changes( self, trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): + return self.__handle_directory_changes( trans, + repository, + full_path, + filenames_in_archive, + remove_repo_files_not_in_tar, + new_repo_alert, + commit_message, + undesirable_dirs_removed, + undesirable_files_removed ) + + def __handle_directory_changes( self, trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, + undesirable_dirs_removed, undesirable_files_removed ): repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) content_alert_str = '' @@ -369,6 +398,7 @@ admin_only = len( repository.downloadable_revisions ) != 1 suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed + def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: self.__handle_gzip( repository, uploaded_file_name ) @@ -376,6 +406,7 @@ if isbz2: self.__handle_bz2( repository, uploaded_file_name ) return uploaded_file_filename.rstrip( '.bz2' ) + def __handle_gzip( self, repository, uploaded_file_name ): fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) @@ -393,6 +424,7 @@ os.close( fd ) gzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) + def __handle_bz2( self, repository, uploaded_file_name ): fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_bunzip2_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) @@ -410,6 +442,7 @@ os.close( fd ) bzipped_file.close() shutil.move( uncompressed, uploaded_file_name ) + def __get_upload_point( self, repository, **kwd ): upload_point = kwd.get( 'upload_point', None ) if upload_point is not None: @@ -430,6 +463,7 @@ # Must have been an error selecting something that didn't exist, so default to repository root upload_point = None return upload_point + def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only diff -r 311cf2ae1623289551b0b568975e9840d46097a2 -r 477979aa944f14ab7189aa51e67168da333f0840 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1088,7 +1088,7 @@ owner = repository_elem.get( 'owner' ) changeset_revision = repository_elem.get( 'changeset_revision' ) prior_installation_required = repository_elem.get( 'prior_installation_required', False ) - repository_dependency_tup = ( toolshed, name, owner, changeset_revision, prior_installation_required ) + repository_dependency_tup = [ toolshed, name, owner, changeset_revision, prior_installation_required ] user = None repository = None if app.name == 'galaxy': @@ -1284,11 +1284,8 @@ if new_repository_dependencies_metadata: new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # The saved metadata must be a subset of the new metadata. - for new_repository_dependency in new_repository_dependencies: - if new_repository_dependency not in saved_repository_dependencies: - return True - for saved_repository_dependency_metadata in saved_repository_dependencies: - if saved_repository_dependency_metadata not in new_repository_dependencies: + for saved_repository_dependency in saved_repository_dependencies: + if saved_repository_dependency not in new_repository_dependencies: return True return False else: @@ -1318,9 +1315,6 @@ new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # The saved metadata must be a subset of the new metadata. - for new_tool_dependency in new_tool_dependencies: - if new_tool_dependency not in saved_tool_dependencies: - return True for saved_tool_dependency in saved_tool_dependencies: if saved_tool_dependency not in new_tool_dependencies: return True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Dave Bouvier: Add exception handling for edge case when a repository record is not created by the install method.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/311cf2ae1623/ Changeset: 311cf2ae1623 User: Dave Bouvier Date: 2013-05-16 05:51:39 Summary: Add exception handling for edge case when a repository record is not created by the install method. Affected #: 1 file diff -r 53d3c967d373c3b0589a31a4e400b01786cea091 -r 311cf2ae1623289551b0b568975e9840d46097a2 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -646,7 +646,11 @@ repository_status[ 'passed_tests' ] = [] repository_status[ 'failed_tests' ] = [] repository_status[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + try: + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + except: + log.exception( 'Error getting installed repository.' ) + continue # If the installation succeeds, configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed if success: 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 the ability for a repository owner to check a "Skip automated testing of tools in this revision" checkbox on the Manage repository page. If checked, the tool shed automated test framework will skip testing the tools in that revision.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/53d3c967d373/ Changeset: 53d3c967d373 User: greg Date: 2013-05-16 02:15:11 Summary: Add the ability for a repository owner to check a "Skip automated testing of tools in this revision" checkbox on the Manage repository page. If checked, the tool shed automated test framework will skip testing the tools in that revision. Affected #: 2 files diff -r f2e183a522d8b1d08ff293f23cce254cc4597721 -r 53d3c967d373c3b0589a31a4e400b01786cea091 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -341,7 +341,7 @@ message += '<ul>' message += '<li>you are authorized to update them</li>' message += '<li>the latest installable revision contains at least 1 tool</li>' - message += '<li>the latest installable revision has <b>Skip tool tests</b> checked</li>' + message += '<li>the latest installable revision has <b>Skip automated testing of tools in this revision</b> checked</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' @@ -649,7 +649,7 @@ message = 'This list contains repositories that match the following criteria:<br>' message += '<ul>' message += '<li>the latest installable revision contains at least 1 tool</li>' - message += '<li>the latest installable revision has <b>Skip tool tests</b> checked</li>' + message += '<li>the latest installable revision has <b>Skip automated testing of tools in this revision</b> checked</li>' message += '</ul>' kwd[ 'message' ] = message kwd[ 'status' ] = 'warning' @@ -1976,29 +1976,31 @@ @web.expose @web.require_login( "manage repository" ) def manage_repository( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = util.restore_text( kwd.get( 'message', '' ) ) + status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) - repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) - description = util.restore_text( params.get( 'description', repository.description ) ) - long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) + repo_name = util.restore_text( kwd.get( 'repo_name', repository.name ) ) + changeset_revision = util.restore_text( kwd.get( 'changeset_revision', repository.tip( trans.app ) ) ) + description = util.restore_text( kwd.get( 'description', repository.description ) ) + long_description = util.restore_text( kwd.get( 'long_description', repository.long_description ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) - alerts = params.get( 'alerts', '' ) + display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) + alerts = kwd.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) - category_ids = util.listify( params.get( 'category_id', '' ) ) + skip_tool_tests = kwd.get( 'skip_tool_tests', '' ) + skip_tool_tests_checked = CheckboxField.is_checked( skip_tool_tests ) + skip_tool_tests_comment = kwd.get( 'skip_tool_tests_comment', '' ) + category_ids = util.listify( kwd.get( 'category_id', '' ) ) if repository.email_alerts: email_alerts = json.from_json_string( repository.email_alerts ) else: email_alerts = [] - allow_push = params.get( 'allow_push', '' ) + allow_push = kwd.get( 'allow_push', '' ) error = False user = trans.user - if params.get( 'edit_repository_button', False ): + if kwd.get( 'edit_repository_button', False ): flush_needed = False # TODO: add a can_manage in the security agent. if not ( user.email == repository.user.email or trans.user_is_admin() ): @@ -2034,7 +2036,32 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message += "The repository information has been updated." - elif params.get( 'manage_categories_button', False ): + elif kwd.get( 'skip_tool_tests_button', False ): + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + skip_tool_test = repository_metadata.skip_tool_tests + if skip_tool_test: + # Handle the mapper behavior. + skip_tool_test = skip_tool_test[ 0 ] + if skip_tool_tests_checked: + if skip_tool_test: + comment = skip_tool_test.comment + if comment != skip_tool_tests_comment: + skip_tool_test.comment = skip_tool_tests_comment + trans.sa_session.add( skip_tool_test ) + trans.sa_session.flush() + else: + skip_tool_test = trans.model.SkipToolTest( repository_metadata_id=repository_metadata.id, + initial_changeset_revision=changeset_revision, + comment=skip_tool_tests_comment ) + trans.sa_session.add( skip_tool_test ) + trans.sa_session.flush() + message = "Tools in this revision will be tested by the automated test framework." + else: + if skip_tool_test: + trans.sa_session.delete( skip_tool_test ) + trans.sa_session.flush() + message = "Tools in this revision will not be tested by the automated test framework." + elif kwd.get( 'manage_categories_button', False ): flush_needed = False # Delete all currently existing categories. for rca in repository.categories: @@ -2043,14 +2070,14 @@ if category_ids: # Create category associations for category_id in category_ids: - category = trans.sa_session.query(model.Category).get( trans.security.decode_id( category_id ) ) + category = trans.sa_session.query( trans.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 ): + elif kwd.get( 'user_access_button', False ): if allow_push not in [ 'none' ]: - remove_auth = params.get( 'remove_auth', '' ) + remove_auth = kwd.get( 'remove_auth', '' ) if remove_auth: usernames = '' else: @@ -2062,7 +2089,7 @@ usernames = ','.join( usernames ) repository.set_allow_push( trans.app, usernames, remove_auth=remove_auth ) message = "The repository information has been updated." - elif params.get( 'receive_email_alerts_button', False ): + elif kwd.get( 'receive_email_alerts_button', False ): flush_needed = False if alerts_checked: if user.email not in email_alerts: @@ -2097,6 +2124,7 @@ repository_metadata = None metadata = None is_malicious = False + skip_tool_test = None repository_dependencies = None if changeset_revision != suc.INITIAL_CHANGELOG_HASH: repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -2114,6 +2142,11 @@ metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious if repository_metadata: + skip_tool_test = repository_metadata.skip_tool_tests + if skip_tool_test: + # Handle the mapper behavior. + skip_tool_test = skip_tool_test[ 0 ] + skip_tool_tests_checked = True metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = \ @@ -2136,6 +2169,7 @@ message += malicious_error status = 'error' malicious_check_box = CheckboxField( 'malicious', checked=is_malicious ) + skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) @@ -2159,6 +2193,8 @@ display_reviews=display_reviews, num_ratings=num_ratings, alerts_check_box=alerts_check_box, + skip_tool_tests_check_box=skip_tool_tests_check_box, + skip_tool_test=skip_tool_test, malicious_check_box=malicious_check_box, message=message, status=status ) diff -r f2e183a522d8b1d08ff293f23cce254cc4597721 -r 53d3c967d373c3b0589a31a4e400b01786cea091 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -58,6 +58,11 @@ can_view_change_log = not is_new + if repository_metadata and repository_metadata.includes_tools: + includes_tools = True + else: + includes_tools = False + if changeset_revision_is_repository_tip: tip_str = 'repository tip' sharable_link_label = 'Sharable link to this repository:' @@ -193,6 +198,36 @@ </div></div> ${render_repository_items( metadata, containers_dict, can_set_metadata=True )} +%if includes_tools: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Automated tool tests</div> + <div class="toolFormBody"> + <form name="skip_tool_tests" id="skip_tool_tests" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository_metadata.changeset_revision )}" method="post" > + <div class="form-row"> + <label>Skip automated testing of tools in this revision:</label> + ${skip_tool_tests_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box and click <b>Save</b> to skip automated testing of the tools in this revision. + </div> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Reason for skipping automated testing:</label> + %if skip_tool_test: + <pre><textarea name="skip_tool_tests_comment" rows="3" cols="80">${skip_tool_test.comment | h}</textarea></pre> + %else: + <textarea name="skip_tool_tests_comment" rows="3" cols="80"></textarea> + %endif + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="skip_tool_tests_button" value="Save"/> + </div> + </form> + </div> + </div> +%endif <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fixes for determing if a new repository_metadata record is required for a tool shed repository.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f2e183a522d8/ Changeset: f2e183a522d8 User: greg Date: 2013-05-16 02:06:44 Summary: Fixes for determing if a new repository_metadata record is required for a tool shed repository. Affected #: 2 files diff -r 590f27390d0dca446fe804a99ba819663653207e -r f2e183a522d8b1d08ff293f23cce254cc4597721 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -300,18 +300,17 @@ skip_tool_test = suc.get_skip_tool_test_by_changeset_revision( trans, changeset_hash ) if skip_tool_test: # We found a skip_tool_test record associated with the changeset_revision, so see if it has a valid repository_revision. - try: - repository_revision = skip_tool_test.repository_revision + repository_revision = suc.get_repository_metadata_by_id( trans, trans.security.encode_id( repository_metadata.id ) ) + if repository_revision: # The skip_tool_test record is associated with a valid repository_metadata record, so proceed. continue - except: - # We found a skip_tool_test record that is associated with an invalid repository_metadata record, so update it to point to - # the newly created repository_metadata record. In some special cases there may be multiple skip_tool_test records that - # require updating, so we won't break here, we'll continue to inspect the rest of the changelog up to the received - # changeset_revision. - skip_tool_test.repository_revision = repository_metadata - trans.sa_session.add( skip_tool_test ) - trans.sa_session.flush() + # We found a skip_tool_test record that is associated with an invalid repository_metadata record, so update it to point to + # the newly created repository_metadata record. In some special cases there may be multiple skip_tool_test records that + # require updating, so we won't break here, we'll continue to inspect the rest of the changelog up to the received + # changeset_revision. + skip_tool_test.repository_metadata_id = repository_metadata.id + trans.sa_session.add( skip_tool_test ) + trans.sa_session.flush() if changeset_hash == changeset_revision: # Proceed no further than the received changeset_revision. break @@ -1285,16 +1284,19 @@ if new_repository_dependencies_metadata: new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # The saved metadata must be a subset of the new metadata. - for new_repository_dependency_metadata in new_repository_dependencies: - if new_repository_dependency_metadata not in saved_repository_dependencies: + for new_repository_dependency in new_repository_dependencies: + if new_repository_dependency not in saved_repository_dependencies: return True for saved_repository_dependency_metadata in saved_repository_dependencies: if saved_repository_dependency_metadata not in new_repository_dependencies: return True + return False else: # The repository_dependencies.xml file must have been deleted, so create a new repository_metadata record so we always have # access to the deleted file. return True + else: + return False else: if 'repository_dependencies' in metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata record. @@ -1316,16 +1318,19 @@ new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # The saved metadata must be a subset of the new metadata. - for new_repository_dependency_metadata in new_tool_dependencies: - if new_repository_dependency_metadata not in saved_tool_dependencies: + for new_tool_dependency in new_tool_dependencies: + if new_tool_dependency not in saved_tool_dependencies: return True - for saved_repository_dependency_metadata in saved_tool_dependencies: - if saved_repository_dependency_metadata not in new_tool_dependencies: + for saved_tool_dependency in saved_tool_dependencies: + if saved_tool_dependency not in new_tool_dependencies: return True + return False else: # The tool_dependencies.xml file must have been deleted, so create a new repository_metadata record so we always have # access to the deleted file. return True + else: + return False else: # We have repository metadata that does not include metadata for any tool dependencies in the repository, so we can update # the existing repository metadata. @@ -1367,6 +1372,7 @@ for new_tool_metadata_dict in metadata_dict[ 'tools' ]: if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: return True + return False else: # The new metadata includes tools, but the stored metadata does not, so we can update the stored metadata. return False diff -r 590f27390d0dca446fe804a99ba819663653207e -r f2e183a522d8b1d08ff293f23cce254cc4597721 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -724,6 +724,9 @@ return all_metadata_records[ 0 ] return None +def get_repository_metadata_by_id( trans, id ): + return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) + def get_repository_owner( cleaned_repository_url ): """Gvien a "cleaned" repository clone URL, return the owner of the repository.""" items = cleaned_repository_url.split( '/repos/' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/582a0194b5c5/ Changeset: 582a0194b5c5 User: dannon Date: 2013-05-16 00:47:30 Summary: Library API: import cleanup (fixes incorrect util import) Affected #: 1 file diff -r a87623b5f358a570718afc07d7a714269220db61 -r 582a0194b5c55994e0f961da7b762d0a8779ce2f lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -1,13 +1,12 @@ """ API operations on a library. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * -from paste.httpexceptions import * +import logging +from galaxy import util +from galaxy import web +from galaxy.model.orm import and_, not_, or_ +from galaxy.web.base.controller import BaseAPIController, url_for +from paste.httpexceptions import HTTPBadRequest, HTTPForbidden log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/f301a34b2ca6/ Changeset: f301a34b2ca6 User: dannon Date: 2013-05-16 00:47:52 Summary: Remove unused params from library.show Affected #: 1 file diff -r 582a0194b5c55994e0f961da7b762d0a8779ce2f -r f301a34b2ca6ae3c8ab842161e32a5c2d6dd458b lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -56,7 +56,6 @@ log.debug( "LibraryContentsController.show: enter" ) library_id = id deleted = util.string_as_bool( deleted ) - params = util.Params( kwd ) try: decoded_library_id = trans.security.decode_id( library_id ) except TypeError: https://bitbucket.org/galaxy/galaxy-central/commits/590f27390d0d/ Changeset: 590f27390d0d User: dannon Date: 2013-05-16 00:48:44 Summary: Library Contents API: import cleanup, remove import *'s. Affected #: 1 file diff -r f301a34b2ca6ae3c8ab842161e32a5c2d6dd458b -r 590f27390d0dca446fe804a99ba819663653207e lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -1,13 +1,10 @@ """ API operations on the contents of a library. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * +import logging +from galaxy import web from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex +from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest, url_for, UsesLibraryMixin, UsesLibraryMixinItems log = logging.getLogger( __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: jgoecks: Viz framework: (a) add sam-to-bigwig converter and (b) Trackster bug fixes.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a87623b5f358/ Changeset: a87623b5f358 User: jgoecks Date: 2013-05-15 22:15:12 Summary: Viz framework: (a) add sam-to-bigwig converter and (b) Trackster bug fixes. Affected #: 2 files diff -r 00ecd6a50591b108d3af3a2c6fd6f9389217d363 -r a87623b5f358a570718afc07d7a714269220db61 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml @@ -0,0 +1,20 @@ +<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true"> + <command> + samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output + </command> + <inputs> + <param format="bam" name="input" type="data" label="Choose BAM file"/> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r 00ecd6a50591b108d3af3a2c6fd6f9389217d363 -r a87623b5f358a570718afc07d7a714269220db61 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3026,7 +3026,7 @@ num_cols: 12, on_finish: function(new_val) { $(".bs-tooltip").remove(); - var new_val = parseFloat(new_val); + var new_val = round(parseFloat(new_val), 3); track.prefs[ pref_name ] = (!isNaN(new_val) ? new_val : null); on_change(); }, @@ -3134,14 +3134,14 @@ track.tile_cache.set_elt(key, tile_drawn); $.when.apply($, get_tile_data()).then( function() { var tile_data = get_tile_data(), - tracks_data = tile_data.slice(0, tile_data.length - 1), - seq_data = tile_data[tile_data.length - 1]; - + tracks_data = tile_data, + seq_data; + // If sequence data is available, subset to get only data in region. - if (seq_data) { - seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); + if (view.reference_track) { + seq_data = view.reference_track.data_manager.subset_entry(tile_data.pop(), region); } - + // Get drawing modes, heights for all tracks. var drawing_modes = [], drawing_heights = []; @@ -3733,8 +3733,8 @@ */ postdraw_actions: function(tiles, width, w_scale, clear_after) { // Add min, max labels. - this._add_yaxis_label('max', round(this.prefs.max_value, 3), 'max_value'); - this._add_yaxis_label('min', round(this.prefs.min_value, 3), 'min_value'); + this._add_yaxis_label('max'); + this._add_yaxis_label('min'); } }); 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: 5 new changesets
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d97d7e9e50b/ Changeset: 8d97d7e9e50b User: dan Date: 2013-05-15 22:03:48 Summary: Fix imports in lib/galaxy/webapps/reports/controllers/root.py Affected #: 1 file diff -r 2c3d59e8341e42117537a6d81760801191240a92 -r 8d97d7e9e50b5d2e0d3cbd62b9bf92d4217f562c lib/galaxy/webapps/reports/controllers/root.py --- a/lib/galaxy/webapps/reports/controllers/root.py +++ b/lib/galaxy/webapps/reports/controllers/root.py @@ -1,4 +1,4 @@ -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController, web import logging log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/87b4c2c7b04c/ Changeset: 87b4c2c7b04c User: dan Date: 2013-05-15 22:04:04 Summary: Fix imports in lib/galaxy/webapps/reports/controllers/sample_tracking.py Affected #: 1 file diff -r 8d97d7e9e50b5d2e0d3cbd62b9bf92d4217f562c -r 87b4c2c7b04c33fa0d89c6b9ca1d799e18df5efc lib/galaxy/webapps/reports/controllers/sample_tracking.py --- a/lib/galaxy/webapps/reports/controllers/sample_tracking.py +++ b/lib/galaxy/webapps/reports/controllers/sample_tracking.py @@ -1,10 +1,10 @@ import calendar, operator, os, socket -from datetime import * +from datetime import datetime, date, timedelta from time import mktime, strftime, localtime -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.model.orm import * +from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa https://bitbucket.org/galaxy/galaxy-central/commits/2f18df41a411/ Changeset: 2f18df41a411 User: dan Date: 2013-05-15 22:05:38 Summary: Fix imports in lib/galaxy/webapps/reports/controllers/workflows.py Affected #: 1 file diff -r 87b4c2c7b04c33fa0d89c6b9ca1d799e18df5efc -r 2f18df41a411db2cfa876135b1e2cbeee063b73f lib/galaxy/webapps/reports/controllers/workflows.py --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -1,10 +1,10 @@ import calendar, operator, os, socket -from datetime import * +from datetime import datetime, date, timedelta from time import mktime, strftime, localtime -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.model.orm import * +from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa https://bitbucket.org/galaxy/galaxy-central/commits/c75d043c9d4b/ Changeset: c75d043c9d4b User: dan Date: 2013-05-15 22:08:07 Summary: Fix imports in lib/galaxy/webapps/reports/controllers/users.py Affected #: 1 file diff -r 2f18df41a411db2cfa876135b1e2cbeee063b73f -r c75d043c9d4bcdf006f4e0b69387e0ee35e354ea lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/lib/galaxy/webapps/reports/controllers/users.py @@ -1,9 +1,10 @@ -from datetime import * +from datetime import datetime, date, timedelta from time import strftime import calendar, operator -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController, web import galaxy.model -from galaxy.model.orm import * +from galaxy import util +from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa https://bitbucket.org/galaxy/galaxy-central/commits/00ecd6a50591/ Changeset: 00ecd6a50591 User: dan Date: 2013-05-15 22:10:07 Summary: Fix imports in lib/galaxy/webapps/reports/controllers/system.py Affected #: 1 file diff -r c75d043c9d4bcdf006f4e0b69387e0ee35e354ea -r 00ecd6a50591b108d3af3a2c6fd6f9389217d363 lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -1,8 +1,8 @@ import operator, os from datetime import datetime, timedelta -from galaxy.web.base.controller import * -from galaxy import model -from galaxy.model.orm import * +from galaxy.web.base.controller import BaseUIController, web +from galaxy import model, util +from galaxy.model.orm import and_, not_, or_, desc import logging log = logging.getLogger( __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: dan: Fix import * in webapps/reports/controllers/jobs.py. Was causing util from galaxy to be overwritten with util from galaxy.model.orm.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c3d59e8341e/ Changeset: 2c3d59e8341e User: dan Date: 2013-05-15 21:59:44 Summary: Fix import * in webapps/reports/controllers/jobs.py. Was causing util from galaxy to be overwritten with util from galaxy.model.orm. Affected #: 1 file diff -r b8c951a4e56b7e0cdc8cd176dd96521c2e0eb764 -r 2c3d59e8341e42117537a6d81760801191240a92 lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -1,10 +1,10 @@ import calendar, operator, os, socket -from datetime import * +from datetime import datetime, date, timedelta from time import mktime, strftime, localtime -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController, web from galaxy import model, util from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.model.orm import * +from galaxy.model.orm import and_, not_, or_ import pkg_resources pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add missing message_box_* config elements to Reports app. Broken in cb0432cfcc8a.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8c951a4e56b/ Changeset: b8c951a4e56b User: dan Date: 2013-05-15 21:44:58 Summary: Add missing message_box_* config elements to Reports app. Broken in cb0432cfcc8a. Affected #: 1 file diff -r 52b6923d713b0c205cdc8c970e49f4b606710056 -r b8c951a4e56b7e0cdc8cd176dd96521c2e0eb764 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -35,6 +35,10 @@ self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) + # Configuration for the message box directly below the masthead. + self.message_box_visible = kwargs.get( 'message_box_visible', False ) + self.message_box_content = kwargs.get( 'message_box_content', None ) + self.message_box_class = kwargs.get( 'message_box_class', 'info' ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Fix incorrect setting of the do_not_test flag when a repository has installation errors.
by commits-noreply＠bitbucket.org 15 May '13

15 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/52b6923d713b/ Changeset: 52b6923d713b User: Dave Bouvier Date: 2013-05-15 21:25:48 Summary: Fix incorrect setting of the do_not_test flag when a repository has installation errors. Affected #: 1 file diff -r 89b5f6866eeb2fcb955d4e773d5b5328dd214610 -r 52b6923d713b0c205cdc8c970e49f4b606710056 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -790,9 +790,8 @@ error_message=dependency.error_message ) repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) # Record the status of this repository in the tool shed. - set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_info_dict ) params[ 'tools_functionally_correct' ] = 'false' - params[ 'do_not_test' ] = str( set_do_not_test ) + params[ 'do_not_test' ] = 'false' params[ 'test_install_error' ] = 'true' register_test_result( galaxy_tool_shed_url, metadata_revision_id, @@ -925,10 +924,9 @@ changeset_revision=repository.changeset_revision, error_message=repository.error_message ) repository_status[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_info_dict ) params[ 'tools_functionally_correct' ] = 'false' params[ 'test_install_error' ] = 'true' - params[ 'do_not_test' ] = str( set_do_not_test ) + params[ 'do_not_test' ] = 'false' register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, 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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