1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/746d59a574bb/ Changeset: 746d59a574bb User: carlfeberhard Date: 2013-04-30 19:56:11 Summary: Datasets API: import cleanup, misc. cleanup Affected #: 1 file
diff -r 07f09e119bfcbe8e4cfda3400c8892f8fb3891d2 -r 746d59a574bbccdf5cedfbc7bd25a50b37d6667f lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,15 +1,17 @@ """ API operations on the contents of a dataset. """ -import logging, os, string, shutil, urllib, re, socket -from galaxy import util, datatypes, jobs, web, util +from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.framework.helpers import is_true
+import logging log = logging.getLogger( __name__ )
-class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin ): +class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin, + UsesHistoryDatasetAssociationMixin ):
@web.expose_api def index( self, trans, **kwd ): @@ -17,7 +19,8 @@ GET /api/datasets Lists datasets. """ - pass + trans.response.status = 501 + return 'not implemented'
@web.expose_api def show( self, trans, id, hda_ldda='hda', data_type=None, **kwd ): @@ -25,7 +28,6 @@ GET /api/datasets/{encoded_dataset_id} Displays information about and/or content of a dataset. """ - # Get dataset. try: dataset = self.get_hda_or_ldda( trans, hda_ldda=hda_ldda, dataset_id=id ) @@ -98,7 +100,8 @@ # If there is a chrom, check for data on the chrom. if chrom: data_provider_registry = trans.app.data_provider_registry - data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, source='index' ) if not data_provider.has_data( chrom ): return dataset.conversion_messages.NO_DATA
@@ -118,13 +121,11 @@ return data_provider.get_data( query )
return [] -
def _data( self, trans, dataset, chrom, low, high, start_val=0, max_vals=None, **kwargs ): """ Provides a block of data from a dataset. """ - # Parameter check. if not chrom: return dataset.conversion_messages.NO_DATA @@ -151,7 +152,8 @@ summary = indexer.get_data( chrom, low, high, detail_cutoff=0, draw_cutoff=0, **kwargs ) if summary == "detail": # Use maximum level of detail--2--to get summary data no matter the resolution. - summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], level=2, detail_cutoff=0, draw_cutoff=0 ) + summary = indexer.get_data( chrom, low, high, resolution=kwargs[ 'resolution' ], + level=2, detail_cutoff=0, draw_cutoff=0 ) return summary
if 'index' in data_sources and data_sources['index']['name'] == "summary_tree" and mode == "Auto": @@ -207,7 +209,8 @@ return data
@web.expose_api_raw - def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): + def display( self, trans, history_content_id, history_id, + preview=False, filename=None, to_ext=None, chunk=None, **kwd ): """ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display Displays history content (dataset).
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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