1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/317d2d4b1f7d/ changeset: 317d2d4b1f7d user: John Duddy date: 2011-08-22 21:29:49 summary: APIs to add histories, add items to histories, and list the status of datasets within a history affected #: 2 files (4.1 KB)

--- a/lib/galaxy/web/api/histories.py Mon Aug 22 10:45:22 2011 -0400 +++ b/lib/galaxy/web/api/histories.py Mon Aug 22 12:29:49 2011 -0700 @@ -7,6 +7,9 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from galaxy.model import Dataset +import galaxy.datatypes +from galaxy.util.bunch import Bunch

log = logging.getLogger( __name__ )

@@ -17,20 +20,19 @@ """ GET /api/histories Displays a collection (list) of histories. - """ - try: - query = trans.sa_session.query( trans.app.model.History ).filter( trans.app.model.History.table.c.deleted == False ) - current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] - user = trans.get_user() - query = query.filter_by( user=user, deleted=False ) + """ + try: + query = trans.sa_session.query( trans.app.model.History ).filter_by( user=trans.user, deleted=False ).order_by( + desc(trans.app.model.History.table.c.update_time)).all() except Exception, e: log.debug("Error in history API: %s" % str(e)) + rval = [] try: for history in query: - item = history.get_api_value() + item = history.get_api_value(value_mapper={'id':trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + # item['id'] = trans.security.encode_id( item['id'] ) rval.append( item ) except Exception, e: log.debug("Error in history API at constructing return list: %s" % str(e)) @@ -39,26 +41,63 @@ @web.expose_api def show( self, trans, id, **kwd ): """ - GET /api/histories/{encoded_library_id} + GET /api/histories/{encoded_history_id} Displays information about a history. """ history_id = id params = util.Params( kwd ) + + def traverse( datasets ): + rval = {} + states = Dataset.states + for key, state in states.items(): + rval[state] = 0 + #log.debug("History API: Init rval %s" % rval) + for dataset in datasets: + item = dataset.get_api_value( view='element' ) + #log.debug("History API: Set rval %s" % item['state']) + if not item['deleted']: + rval[item['state']] = rval[item['state']] + 1 + return rval + try: decoded_history_id = trans.security.decode_id( history_id ) except TypeError: trans.response.status = 400 - return "Malformed history id ( %s ) specified, unable to decode." % str( library_id ) + return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) try: - history = trans.sa_session.query( trans.app.model.History ).get( decoded_history_id ) + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + if history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") except: - history = None + trans.response.status = 400 + return "That history does not exist." + try: - if not history or not ( trans.user_is_admin() or trans.app.security_agent.can_access_history( trans.get_current_user_roles(), history ) ): - trans.response.status = 400 - return "Invalid history id ( %s ) specified." % str( history_id ) - item = history.get_api_value( view='element' ) + item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + num_sets = len( [hda.id for hda in history.datasets if not hda.deleted] ) + states = Dataset.states + state = states.ERROR + if num_sets == 0: + state = states.NEW + else: + summary = traverse(history.datasets) + #log.debug("History API: Status summary %s" % summary) + if summary[states.ERROR] > 0 or summary[states.FAILED_METADATA] > 0: + state = states.ERROR + elif summary[states.RUNNING] > 0 or summary[states.SETTING_METADATA] > 0: + state = states.RUNNING + elif summary[states.QUEUED] > 0: + state = states.QUEUED + elif summary[states.OK] == num_sets: + state = states.OK + #item['user'] = item['user'].username item['contents_url'] = url_for( 'history_contents', history_id=history_id ) + #item['datasets'] = len( item['datasets'] ) + item['state'] = state + #log.debug("History API: State %s for %d datasets" % (state, num_sets)) except Exception, e: log.debug("Error in history API at showing history detail: %s" % str(e)) return item @@ -69,5 +108,48 @@ POST /api/histories Creates a new history. """ - trans.response.status = 403 - return "Not implemented." + params = util.Params( payload ) + hist_name = util.restore_text( params.get( 'name', None ) ) + new_history = trans.app.model.History( user=trans.user, name=hist_name ) + + trans.sa_session.add( new_history ) + trans.sa_session.flush() + item = new_history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) + return item + @web.expose_api + def delete( self, trans, id, **kwd ): + """ + DELETE /api/histories/{encoded_history_id} + Deletes a history + """ + history_id = id + params = util.Params( kwd ) + + try: + decoded_history_id = trans.security.decode_id( history_id ) + except TypeError: + trans.response.status = 400 + return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) + try: + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + if history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") + except: + trans.response.status = 400 + return "That history does not exist." + history.deleted = True + # If deleting the current history, make a new current. + if history == trans.get_history(): + trans.new_history() + if trans.app.config.allow_user_dataset_purge: + for hda in history.datasets: + hda.purged = True + trans.sa_session.add( hda ) + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.sa_session.add( hda.dataset ) + except: + trans.sa_session.flush()

--- a/lib/galaxy/web/api/history_contents.py Mon Aug 22 10:45:22 2011 -0400 +++ b/lib/galaxy/web/api/history_contents.py Mon Aug 22 12:29:49 2011 -0700 @@ -21,42 +21,23 @@ """ GET /api/histories/{encoded_history_id}/contents Displays a collection (list) of history contents - """ - rval = [] - current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_path = folder.api_path + '/' + subfolder.name - subfolder.api_type = 'folder' - rval.append( subfolder ) - rval.extend( traverse( subfolder ) ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_path = folder.api_path + '/' + ld.name - ld.api_type = 'file' - rval.append( ld ) - return rval - #log.debug("Entering Content API for history with %s" % str(history_id)) + """ try: decoded_history_id = trans.security.decode_id( history_id ) except TypeError: trans.response.status = 400 return "Malformed history id ( %s ) specified, unable to decode." % str( history_id ) try: - history = trans.sa_session.query( trans.app.model.History ).get( decoded_history_id ) + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + if history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") except: - history = None - if not history or not ( trans.user_is_admin() or trans.app.security_agent.can_access_history( current_user_roles, history ) ): trans.response.status = 400 - return "Invalid history id ( %s ) specified." % str( history_id ) - #log.debug("History item %s" % str(history)) + return "That history does not exist." + + rval = [] try: for dataset in history.datasets: api_type = "file" @@ -93,10 +74,12 @@ try: content = trans.sa_session.query( model_class ).get( decoded_content_id ) except: - content = None - if not content or ( not trans.user_is_admin() and not trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), content, trans.user ) ): trans.response.status = 400 return "Invalid %s id ( %s ) specified." % ( content_type, str( content_id ) ) + if content.history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + trans.response.status = 400 + return("History is not owned by or shared with current user") item = content.get_api_value( view='element' ) if not item['deleted']: # Problem: Method url_for cannot use the dataset controller @@ -106,14 +89,21 @@ # url_for is being phased out, so new applications should use url item['download_url'] = url(controller='dataset', action='display', dataset_id=trans.security.encode_id(decoded_content_id), to_ext=content.ext) except Exception, e: - log.debug("Error in history API at listing dataset: %s" % str(e)) + log.debug("Error in history API at listing dataset: %s" % str(e)) return item

@web.expose_api def create( self, trans, history_id, payload, **kwd ): """ - POST /api/libraries/{encoded_library_id}/contents - Creates a new history content item (file or folder). - """ - trans.response.status = 403 - return "Not implemented." + POST /api/libraries/{encoded_history_id}/contents + Creates a new history content item. """ + params = util.Params( payload ) + history_id = util.restore_text( params.get( 'history_id', None ) ) + ldda_id = util.restore_text( params.get( 'ldda_id', None ) ) + add_to_history = True + decoded_history_id = trans.security.decode_id( history_id ) + ld_t, ld_id = trans.security.decode_string_id(ldda_id).split('.') + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get(ld_id) + hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + history.add_dataset(hda)

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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