1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/74da2fbf0963/ changeset: 74da2fbf0963 user: greg date: 2013-03-16 16:25:43 summary: Extract repository review methods from shed_util_comman and put them into the new tool shed review_util component. affected #: 4 files

diff -r e40606362e962b4c452960c7c5f9b33b5b13f96c -r 74da2fbf09633268e1e6b6043bfd7e0515bd8422 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 @@ -11,7 +11,7 @@ from galaxy.util import json from galaxy.model.orm import and_, or_ import tool_shed.util.shed_util_common as suc -from tool_shed.util import encoding_util, metadata_util, readme_util, repository_dependency_util, tool_dependency_util, tool_util +from tool_shed.util import encoding_util, metadata_util, readme_util, repository_dependency_util, review_util, tool_dependency_util, tool_util from tool_shed.galaxy_install import repository_util from galaxy.webapps.tool_shed.util import common_util, container_util, workflow_util import galaxy.tools @@ -1709,16 +1709,16 @@ categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] # Determine if the current changeset revision has been reviewed by the current user. - reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) + reviewed_by_user = review_util.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: - review = suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ) + review = review_util.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ) review_id = trans.security.encode_id( review.id ) else: review_id = None - can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) + can_browse_repository_reviews = review_util.can_browse_repository_reviews( trans, repository ) containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, @@ -2496,17 +2496,17 @@ message += malicious_error status = 'error' # Determine if the current changeset revision has been reviewed by the current user. - reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) + reviewed_by_user = review_util.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: - review = suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ) + review = review_util.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ) review_id = trans.security.encode_id( review.id ) else: review_id = None containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) + can_browse_repository_reviews = review_util.can_browse_repository_reviews( trans, repository ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, repository=repository, @@ -2590,12 +2590,12 @@ add_id_to_name=False, downloadable=False ) trans.app.config.tool_data_path = original_tool_data_path - reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) + reviewed_by_user = review_util.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: - review = suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=repository_id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ) + review = review_util.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=repository_id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ) review_id = trans.security.encode_id( review.id ) else: review_id = None

diff -r e40606362e962b4c452960c7c5f9b33b5b13f96c -r 74da2fbf09633268e1e6b6043bfd7e0515bd8422 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -6,6 +6,7 @@ from galaxy.webapps.tool_shed.util import common_util from galaxy.webapps.tool_shed.util.container_util import STRSEP import tool_shed.util.shed_util_common as suc +from tool_shed.util import review_util from galaxy.util.odict import odict import tool_shed.grids.repository_review_grids as repository_review_grids import tool_shed.grids.util as grids_util @@ -36,7 +37,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) encoded_review_id = kwd[ 'id' ] - review = suc.get_review( trans, encoded_review_id ) + review = review_util.get_review( trans, encoded_review_id ) if kwd.get( 'approve_repository_review_button', False ): approved_select_field_name = '%s%sapproved' % ( encoded_review_id, STRSEP ) approved_select_field_value = str( kwd[ approved_select_field_name ] ) @@ -70,7 +71,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - review = suc.get_review( trans, kwd[ 'id' ] ) + review = review_util.get_review( trans, kwd[ 'id' ] ) repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) @@ -108,7 +109,7 @@ if not name or not description: message = 'Enter a valid name and a description' status = 'error' - elif suc.get_component_by_name( trans, name ): + elif review_util.get_component_by_name( trans, name ): message = 'A component with that name already exists' status = 'error' else: @@ -142,15 +143,15 @@ if changeset_revision: # Make sure there is not already a review of the revision by the user. repository = suc.get_repository_in_tool_shed( trans, repository_id ) - if suc.get_review_by_repository_id_changeset_revision_user_id( trans=trans, - repository_id=repository_id, - changeset_revision=changeset_revision, - user_id=trans.security.encode_id( trans.user.id ) ): + if review_util.get_review_by_repository_id_changeset_revision_user_id( trans=trans, + repository_id=repository_id, + changeset_revision=changeset_revision, + user_id=trans.security.encode_id( trans.user.id ) ): message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, repository.name ) status = "error" else: # See if there are any reviews for previous changeset revisions that the user can copy. - if not create_without_copying and not previous_review_id and suc.has_previous_repository_reviews( trans, repository, changeset_revision ): + if not create_without_copying and not previous_review_id and review_util.has_previous_repository_reviews( trans, repository, changeset_revision ): return trans.response.send_redirect( web.url_for( controller='repository_review', action='select_previous_review', **kwd ) ) @@ -168,7 +169,7 @@ trans.sa_session.add( review ) trans.sa_session.flush() if previous_review_id: - review_to_copy = suc.get_review( trans, previous_review_id ) + review_to_copy = review_util.get_review( trans, previous_review_id ) self.copy_review( trans, review_to_copy, review ) review_id = trans.security.encode_id( review.id ) message = "Begin your review of revision <b>%s</b> of repository <b>%s</b>." \ @@ -205,7 +206,7 @@ action='manage_categories', message=message, status='error' ) ) - component = suc.get_component( trans, id ) + component = review_util.get_component( trans, id ) if params.get( 'edit_component_button', False ): new_description = util.restore_text( params.get( 'description', '' ) ).strip() if component.description != new_description: @@ -231,9 +232,9 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) review_id = kwd.get( 'id', None ) - review = suc.get_review( trans, review_id ) + review = review_util.get_review( trans, review_id ) components_dict = odict() - for component in suc.get_components( trans ): + for component in review_util.get_components( trans ): components_dict[ component.name ] = dict( component=component, component_review=None ) repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) @@ -283,8 +284,8 @@ approved = str( v ) elif component_review_attr == 'rating': rating = int( str( v ) ) - component = suc.get_component( trans, component_id ) - component_review = suc.get_component_review_by_repository_review_id_component_id( trans, review_id, component_id ) + component = review_util.get_component( trans, component_id ) + component_review = review_util.get_component_review_by_repository_review_id_component_id( trans, review_id, component_id ) if component_review: # See if the existing component review should be updated. if component_review.comment != comment or \ @@ -481,7 +482,7 @@ rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) if changeset_revision in reviewed_revision_hashes: # Find the review for this changeset_revision - repository_reviews = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) + repository_reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) # Determine if the current user can add a review to this revision. can_add_review = trans.user not in [ repository_review.user for repository_review in repository_reviews ] repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -521,7 +522,7 @@ repo = hg.repository( suc.get_configured_ui(), repo_dir ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) - reviews = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) + reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako', repository=repository, changeset_revision=changeset_revision, @@ -541,7 +542,7 @@ if 'operation' in kwd: operation = kwd['operation'].lower() # The value of the received id is the encoded review id. - review = suc.get_review( trans, kwd[ 'id' ] ) + review = review_util.get_review( trans, kwd[ 'id' ] ) repository = review.repository kwd[ 'id' ] = trans.security.encode_id( repository.id ) if operation == "inspect repository revisions": @@ -587,7 +588,7 @@ repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - previous_reviews_dict = suc.get_previous_repository_reviews( trans, repository, changeset_revision ) + previous_reviews_dict = review_util.get_previous_repository_reviews( trans, repository, changeset_revision ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako', repository=repository,

diff -r e40606362e962b4c452960c7c5f9b33b5b13f96c -r 74da2fbf09633268e1e6b6043bfd7e0515bd8422 lib/tool_shed/util/review_util.py --- /dev/null +++ b/lib/tool_shed/util/review_util.py @@ -0,0 +1,100 @@ +import os, logging +from galaxy.util.odict import odict +import tool_shed.util.shed_util_common as suc +from galaxy.model.orm import and_ + +from galaxy import eggs +import pkg_resources + +pkg_resources.require( 'mercurial' ) +from mercurial import hg, ui, commands + +log = logging.getLogger( __name__ ) + +def can_browse_repository_reviews( trans, repository ): + """Determine if there are any reviews of the received repository for which the current user has permission to browse any component reviews.""" + user = trans.user + if user: + for review in repository.reviews: + for component_review in review.component_reviews: + if trans.app.security_agent.user_can_browse_component_review( trans.app, repository, component_review, user ): + return True + return False + +def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ): + """Determine if the current changeset revision has been reviewed by the current user.""" + for review in repository.reviews: + if review.changeset_revision == changeset_revision and review.user == user: + return True + return False + +def get_component( trans, id ): + """Get a component from the database.""" + return trans.sa_session.query( trans.model.Component ).get( trans.security.decode_id( id ) ) + +def get_component_review( trans, id ): + """Get a component_review from the database""" + return trans.sa_session.query( trans.model.ComponentReview ).get( trans.security.decode_id( id ) ) + +def get_component_by_name( trans, name ): + """Get a component from the database via a name.""" + return trans.sa_session.query( trans.app.model.Component ) \ + .filter( trans.app.model.Component.table.c.name==name ) \ + .first() + +def get_component_review_by_repository_review_id_component_id( trans, repository_review_id, component_id ): + """Get a component_review from the database via repository_review_id and component_id.""" + return trans.sa_session.query( trans.model.ComponentReview ) \ + .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == trans.security.decode_id( repository_review_id ), + trans.model.ComponentReview.table.c.component_id == trans.security.decode_id( component_id ) ) ) \ + .first() + +def get_components( trans ): + return trans.sa_session.query( trans.app.model.Component ) \ + .order_by( trans.app.model.Component.name ) \ + .all() + +def get_previous_repository_reviews( trans, repository, changeset_revision ): + """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] + previous_reviews_dict = odict() + for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): + previous_changeset_revision = str( repo.changectx( changeset ) ) + if previous_changeset_revision in reviewed_revision_hashes: + previous_rev, previous_changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) + revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, + trans.security.encode_id( repository.id ), + previous_changeset_revision ) + previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, + reviews=revision_reviews ) + return previous_reviews_dict + +def get_review( trans, id ): + """Get a repository_review from the database via id.""" + return trans.sa_session.query( trans.model.RepositoryReview ).get( trans.security.decode_id( id ) ) + +def get_review_by_repository_id_changeset_revision_user_id( trans, repository_id, changeset_revision, user_id ): + """Get a repository_review from the database via repository id, changeset_revision and user_id.""" + return trans.sa_session.query( trans.model.RepositoryReview ) \ + .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), + trans.model.RepositoryReview.changeset_revision == changeset_revision, + trans.model.RepositoryReview.user_id == trans.security.decode_id( user_id ) ) ) \ + .first() + +def get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ): + """Get all repository_reviews from the database via repository id and changeset_revision.""" + return trans.sa_session.query( trans.model.RepositoryReview ) \ + .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), + trans.model.RepositoryReview.changeset_revision == changeset_revision ) ) \ + .all() + +def has_previous_repository_reviews( trans, repository, changeset_revision ): + """Determine if a repository has a changeset revision review prior to the received changeset revision.""" + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] + for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ): + previous_changeset_revision = str( repo.changectx( changeset ) ) + if previous_changeset_revision in reviewed_revision_hashes: + return True + return False

diff -r e40606362e962b4c452960c7c5f9b33b5b13f96c -r 74da2fbf09633268e1e6b6043bfd7e0515bd8422 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 @@ -3,7 +3,6 @@ from time import gmtime, strftime from galaxy import util from galaxy.util import json -from galaxy.util.odict import odict from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.datatypes import checkers @@ -108,15 +107,6 @@ option_value = trans.security.encode_id( repository.id ) repositories_select_field.add_option( option_label, option_value ) return repositories_select_field -def can_browse_repository_reviews( trans, repository ): - """Determine if there are any reviews of the received repository for which the current user has permission to browse any component reviews.""" - user = trans.user - if user: - for review in repository.reviews: - for component_review in review.component_reviews: - if trans.app.security_agent.user_can_browse_component_review( trans.app, repository, component_review, user ): - return True - return False def changeset_is_malicious( trans, id, changeset_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -130,12 +120,6 @@ if changeset_revision == changeset_hash: return True return False -def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ): - """Determine if the current changeset revision has been reviewed by the current user.""" - for review in repository.reviews: - if review.changeset_revision == changeset_revision and review.user == user: - return True - return False def clean_repository_clone_url( repository_clone_url ): if repository_clone_url.find( '@' ) > 0: # We have an url that includes an authenticated user, something like: @@ -393,27 +377,6 @@ if str( ctx ) == changeset_revision: return ctx return None -def get_component( trans, id ): - """Get a component from the database.""" - return trans.sa_session.query( trans.model.Component ).get( trans.security.decode_id( id ) ) -def get_component_by_name( trans, name ): - """Get a component from the database via a name.""" - return trans.sa_session.query( trans.app.model.Component ) \ - .filter( trans.app.model.Component.table.c.name==name ) \ - .first() -def get_component_review( trans, id ): - """Get a component_review from the database""" - return trans.sa_session.query( trans.model.ComponentReview ).get( trans.security.decode_id( id ) ) -def get_component_review_by_repository_review_id_component_id( trans, repository_review_id, component_id ): - """Get a component_review from the database via repository_review_id and component_id.""" - return trans.sa_session.query( trans.model.ComponentReview ) \ - .filter( and_( trans.model.ComponentReview.table.c.repository_review_id == trans.security.decode_id( repository_review_id ), - trans.model.ComponentReview.table.c.component_id == trans.security.decode_id( component_id ) ) ) \ - .first() -def get_components( trans ): - return trans.sa_session.query( trans.app.model.Component ) \ - .order_by( trans.app.model.Component.name ) \ - .all() def get_config( config_file, repo, ctx, dir ): """Return the latest version of config_filename from the repository manifest.""" config_file = strip_path( config_file ) @@ -574,21 +537,6 @@ return INITIAL_CHANGELOG_HASH else: previous_changeset_revision = changeset_revision -def get_previous_repository_reviews( trans, repository, changeset_revision ): - """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" - repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) - reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] - previous_reviews_dict = odict() - for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): - previous_changeset_revision = str( repo.changectx( changeset ) ) - if previous_changeset_revision in reviewed_revision_hashes: - previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) - revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, - trans.security.encode_id( repository.id ), - previous_changeset_revision ) - previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, - reviews=revision_reviews ) - return previous_reviews_dict def get_repo_info_tuple_contents( repo_info_tuple ): # Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced. if len( repo_info_tuple ) == 6: @@ -723,22 +671,6 @@ for changeset in repo.changelog: reversed_changelog.insert( 0, changeset ) return reversed_changelog -def get_review( trans, id ): - """Get a repository_review from the database via id.""" - return trans.sa_session.query( trans.model.RepositoryReview ).get( trans.security.decode_id( id ) ) -def get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ): - """Get all repository_reviews from the database via repository id and changeset_revision.""" - return trans.sa_session.query( trans.model.RepositoryReview ) \ - .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), - trans.model.RepositoryReview.changeset_revision == changeset_revision ) ) \ - .all() -def get_review_by_repository_id_changeset_revision_user_id( trans, repository_id, changeset_revision, user_id ): - """Get a repository_review from the database via repository id, changeset_revision and user_id.""" - return trans.sa_session.query( trans.model.RepositoryReview ) \ - .filter( and_( trans.model.RepositoryReview.repository_id == trans.security.decode_id( repository_id ), - trans.model.RepositoryReview.changeset_revision == changeset_revision, - trans.model.RepositoryReview.user_id == trans.security.decode_id( user_id ) ) ) \ - .first() def get_revision_label( trans, repository, changeset_revision ): """Return a string consisting of the human read-able changeset rev and the changeset revision string.""" repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) @@ -954,15 +886,6 @@ util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) -def has_previous_repository_reviews( trans, repository, changeset_revision ): - """Determine if a repository has a changeset revision review prior to the received changeset revision.""" - repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) - reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] - for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): - previous_changeset_revision = str( repo.changectx( changeset ) ) - if previous_changeset_revision in reviewed_revision_hashes: - return True - return False def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path )

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