# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks jeremy.goecks@emory.edu # Date 1289568743 18000 # Node ID b5b6b92a71e960691bb514af32ba2e21a731bd4e # Parent a6cd0223a53b4f9498a0dde69dcef53387188e5f Refactored tracks/data function into multiple helper functions that can be reused as needed.
--- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -7,7 +7,7 @@ pkg_resources.require( "bx-python" )
from bx.seq.twobit import TwoBitFile from galaxy import model -from galaxy.util.json import to_json_string, from_json_string +from galaxy.util.json import from_json_string from galaxy.web.base.controller import * from galaxy.web.framework import simplejson from galaxy.web.framework.helpers import grids @@ -249,29 +249,21 @@ class TracksController( BaseController, """ Called by the browser to request a block of data """ + + # Parameter check. + if not chrom: + return messages.NO_DATA + + # Dataset check. dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) - if not dataset or not chrom: - return messages.NO_DATA - if dataset.state == trans.app.model.Job.states.ERROR: - return messages.ERROR - if dataset.state != trans.app.model.Job.states.OK: - return messages.PENDING - - track_type, data_sources = dataset.datatype.get_track_type() - for source_type, data_source in data_sources.iteritems(): - try: - converted_dataset = dataset.get_converted_dataset(trans, data_source) - except ValueError: - return messages.NO_CONVERTER - - # Need to check states again for the converted version - if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: - job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ).filter_by( dataset_id=converted_dataset.id ).first().job_id - job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) - return { 'kind': messages.ERROR, 'message': job.stderr } - - if not converted_dataset or converted_dataset.state != model.Dataset.states.OK: - return messages.PENDING + msg = self._check_dataset_state( trans, dataset ) + if msg: + return msg + + # Get converted datasets. + data_sources, message = self._get_converted_datasets( trans, dataset ) + if not data_sources: + return message
extra_info = None if 'index' in data_sources: @@ -365,4 +357,43 @@ class TracksController( BaseController, @web.expose def list_tracks( self, trans, **kwargs ): return self.tracks_grid( trans, **kwargs ) - + + + # + # Helper methods. + # + + def _check_dataset_state( self, trans, dataset ): + """ + Returns a message if dataset is not ready to be used in visualization. + """ + if not dataset: + return messages.NO_DATA + if dataset.state == trans.app.model.Job.states.ERROR: + return messages.ERROR + if dataset.state != trans.app.model.Job.states.OK: + return messages.PENDING + return None + + def _get_converted_datasets( self, trans, dataset ): + """ + Returns (a) converted datasets for a dataset and (b) dictionary of + any messages based on or derived from the conversion. + """ + track_type, data_sources = dataset.datatype.get_track_type() + for source_type, data_source in data_sources.iteritems(): + try: + converted_dataset = dataset.get_converted_dataset(trans, data_source) + except ValueError: + return None, messages.NO_CONVERTER + + # Need to check states again for the converted version + if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: + job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ).filter_by( dataset_id=converted_dataset.id ).first().job_id + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) + return None, { 'kind': messages.ERROR, 'message': job.stderr } + + if not converted_dataset or converted_dataset.state != model.Dataset.states.OK: + return None, messages.PENDING + + return data_sources, None