def show(self, trans, id, hda_ldda='hda', data_type=None, provider=None, **kwd):
"""
GET /api/datasets/{encoded_dataset_id}
Displays information about and/or content of a dataset.
"""
# Get dataset.
dataset = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=id)
# Use data type to return particular type of data.
if data_type == 'state':
rval = self._dataset_state(trans, dataset)
elif data_type == 'converted_datasets_state':
rval = self._converted_datasets_state(trans, dataset, kwd.get('chrom', None),
is_true(kwd.get('retry', False)))
elif data_type == 'data':
rval = self._data(trans, dataset, **kwd)
elif data_type == 'features':
rval = self._search_features(trans, dataset, kwd.get('query'))
elif data_type == 'raw_data':
rval = self._raw_data(trans, dataset, provider, **kwd)
elif data_type == 'track_config':
rval = self.get_new_track_config(trans, dataset)
elif data_type == 'genome_data':
rval = self._get_genome_data(trans, dataset, kwd.get('dbkey', None))
else:
# Default: return dataset as dict.
if hda_ldda == 'hda':
return self.hda_serializer.serialize_to_view(dataset,
view=kwd.get('view', 'detailed'), user=trans.user, trans=trans)
else:
rval = dataset.to_dict()
return rval
def show(self,
trans,
id,
num=None,
chrom=None,
low=None,
high=None,
**kwd):
"""
GET /api/genomes/{id}
Returns information about build <id>
"""
# Process kwds.
id = get_id(id, kwd.get('format', None))
reference = is_true(kwd.get('reference', False))
# Return info.
rval = None
if reference:
region = self.app.genomes.reference(trans,
dbkey=id,
chrom=chrom,
low=low,
high=high)
rval = {'dataset_type': 'refseq', 'data': region.sequence}
else:
rval = self.app.genomes.chroms(trans,
dbkey=id,
num=num,
chrom=chrom,
low=low)
return rval
def show(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):
"""
GET /api/genomes/{id}
Returns information about build <id>
"""
id = get_id(id, kwd.get('format'))
reference = is_true(kwd.get('reference', False))
return self.manager.get_genome(trans, id, num, chrom, low, high, reference)
def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):
"""
GET /api/genomes/{id}/sequences
This is a wrapper for accepting sequence requests that
want a raw return, not json
"""
id = get_id(id, kwd.get('format', None))
reference = is_true(kwd.get('reference', False))
assert reference
region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
return region.sequence
def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd):
"""
GET /api/genomes/{id}/sequences
This is a wrapper for accepting sequence requests that
want a raw return, not json
"""
id = get_id(id, kwd.get('format', None))
reference = is_true(kwd.get('reference', False))
assert reference
region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high)
return region.sequence
def show(self,
trans,
id,
hda_ldda='hda',
data_type=None,
provider=None,
**kwd):
"""
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)
except Exception as e:
return str(e)
# Use data type to return particular type of data.
try:
if data_type == 'state':
rval = self._dataset_state(trans, dataset)
elif data_type == 'converted_datasets_state':
rval = self._converted_datasets_state(
trans, dataset, kwd.get('chrom', None),
is_true(kwd.get('retry', False)))
elif data_type == 'data':
rval = self._data(trans, dataset, **kwd)
elif data_type == 'features':
rval = self._search_features(trans, dataset, kwd.get('query'))
elif data_type == 'raw_data':
rval = self._raw_data(trans, dataset, provider, **kwd)
elif data_type == 'track_config':
rval = self.get_new_track_config(trans, dataset)
elif data_type == 'genome_data':
rval = self._get_genome_data(trans, dataset,
kwd.get('dbkey', None))
else:
# Default: return dataset as dict.
if hda_ldda == 'hda':
return self.hda_serializer.serialize_to_view(
trans, dataset, view=kwd.get('view', 'detailed'))
else:
rval = dataset.to_dict()
except Exception as e:
rval = "Error in dataset API at listing contents: " + str(e)
log.error(rval + ": %s" % str(e), exc_info=True)
trans.response.status = 500
return rval
class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
@web.expose_api
def index( self, trans, **kwd ):
"""
GET /api/datasets
Lists datasets.
"""
pass
@web.expose_api
def show( self, trans, id, hda_ldda='hda', data_type=None, **kwd ):
"""
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 )
except Exception, e:
return str( e )
# Use data type to return particular type of data.
try:
if data_type == 'state':
rval = self._dataset_state( trans, dataset )
elif data_type == 'converted_datasets_state':
rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ),
is_true( kwd.get( 'retry', False ) ) )
elif data_type == 'data':
rval = self._data( trans, dataset, **kwd )
elif data_type == 'features':
rval = self._search_features( trans, dataset, kwd.get( 'query' ) )
elif data_type == 'raw_data':
rval = self._raw_data( trans, dataset, **kwd )
elif data_type == 'track_config':
rval = self.get_new_track_config( trans, dataset )
elif data_type == 'genome_data':
rval = self._get_genome_data( trans, dataset, kwd.get('dbkey', None) )
else:
# Default: return dataset as API value.
rval = dataset.get_api_value()
except Exception, e:
rval = "Error in dataset API at listing contents: " + str( e )
log.error( rval + ": %s" % str(e), exc_info=True )
trans.response.status = 500
def show( self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ):
"""
GET /api/genomes/{id}
Returns information about build <id>
"""
# Process kwds.
id = get_id( id, kwd.get( 'format', None ) )
reference = is_true( kwd.get( 'reference', False ) )
# Return info.
rval = None
if reference:
rval = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high )
else:
rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low )
return rval
def show( self, trans, id, hda_ldda='hda', data_type=None, provider=None, **kwd ):
"""
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 )
except Exception as e:
return str( e )
# Use data type to return particular type of data.
try:
if data_type == 'state':
rval = self._dataset_state( trans, dataset )
elif data_type == 'converted_datasets_state':
rval = self._converted_datasets_state( trans, dataset, kwd.get( 'chrom', None ),
is_true( kwd.get( 'retry', False ) ) )
elif data_type == 'data':
rval = self._data( trans, dataset, **kwd )
elif data_type == 'features':
rval = self._search_features( trans, dataset, kwd.get( 'query' ) )
elif data_type == 'raw_data':
rval = self._raw_data( trans, dataset, provider, **kwd )
elif data_type == 'track_config':
rval = self.get_new_track_config( trans, dataset )
elif data_type == 'genome_data':
rval = self._get_genome_data( trans, dataset, kwd.get('dbkey', None) )
elif data_type == 'mzidentml':
rval = self._mzIdentMLProcess(**kwd)
else:
# Default: return dataset as dict.
if hda_ldda == 'hda':
return self.hda_serializer.serialize_to_view( dataset,
view=kwd.get( 'view', 'detailed' ), user=trans.user, trans=trans )
else:
rval = dataset.to_dict()
except Exception as e:
rval = "Error in dataset API at listing contents: " + str( e )
log.error( rval + ": %s" % str(e), exc_info=True )
trans.response.status = 500
return rval
