def dehydrate(self, bundle):
_filter = (
lambda field_information:
( not bundle.obj.is_restricted
or field_information.is_unrestricted ) )
bundle.data = get_detail_bundle(bundle.obj, ['smallmolecule',''], _filter=_filter)
smbs = SmallMoleculeBatch.objects.filter(smallmolecule=bundle.obj)
bundle.data['batches'] = []
for smb in smbs:
bundle.data['batches'].append(
get_detail_bundle(smb, ['smallmoleculebatch',''], _filter=_filter))
return bundle
def dehydrate(self, bundle):
def _filter(field_information):
return (not bundle.obj.is_restricted
or field_information.is_unrestricted )
bundle.data = get_detail_bundle(bundle.obj, ['cell',''], _filter=_filter)
batches = ( CellBatch.objects.filter(reagent=bundle.obj)
.exclude(batch_id=0) )
bundle.data['batches'] = []
for batch in batches:
bundle.data['batches'].append(
get_detail_bundle(batch, ['cellbatch',''], _filter=_filter))
return bundle
def dehydrate(self, bundle):
def _filter(field_information):
return (not bundle.obj.is_restricted
or field_information.is_unrestricted )
bundle.data = get_detail_bundle(bundle.obj, ['smallmolecule',''], _filter=_filter)
smbs = ( SmallMoleculeBatch.objects.filter(reagent=bundle.obj)
.exclude(batch_id=0) )
bundle.data['batches'] = []
for smb in smbs:
bundle.data['batches'].append(
get_detail_bundle(smb, ['smallmoleculebatch',''], _filter=_filter))
return bundle
def dehydrate(self, bundle):
_facility_id =str(bundle.data['facility_id'])
dataset_id = bundle.data['id']
datasetDataColumns = DataSetDataResource.get_datasetdata_camel_case_columns(dataset_id)
bundle.data = get_detail_bundle(
bundle.obj, ['dataset',''],
_override_filter=lambda x: x.show_in_detail or x.field=='bioassay' )
saf_uri = self.absolute_uri.replace('dataset','datasetdata')
saf_uri = saf_uri.replace('json','csv');
datacolumns = list( DataColumn.objects.all().filter(dataset_id=dataset_id) )
# TODO: drive the columns to show here from fieldinformation inputs
dc_fieldinformation = FieldInformation.objects.all().filter(table='datacolumn', show_in_detail=True)
dc_field_names = [fi.get_camel_case_dwg_name() for fi in dc_fieldinformation]
datapoints = [ dict(zip(dc_field_names, [ getattr(x,fi.field) for fi in dc_fieldinformation ] )) for x in datacolumns ]
# Custom fields for SAF: TODO: generate the names here from the fieldinformation
bundle.data['datapointFile'] = {'uri': saf_uri,
'noCols':len(datasetDataColumns),
'cols':datasetDataColumns,
'noDatapoints': len(datapoints),
'datapoints': datapoints
}
bundle.data['safVersion'] = '0.1' # TODO: drive this from data
bundle.data['screeningFacility'] = 'HMS' #TODO: drive this from data
return bundle
def dehydrate(self, bundle):
def _filter(field_information):
return (not bundle.obj.is_restricted
or field_information.is_unrestricted )
bundle.data = get_detail_bundle(
bundle.obj, ['primarycell',''], _filter=_filter,
extra_properties=self._meta.extra_properties)
batches = (
PrimaryCellBatch.objects.filter(reagent=bundle.obj)
.exclude(batch_id=0).order_by('batch_id') )
bundle.data['batches'] = []
for batch in batches:
bundle.data['batches'].append(
get_detail_bundle(
batch, ['primarycellbatch',''], _filter=_filter))
return bundle
def dehydrate(self, bundle):
# TODO: the following call executes the query *just* to get the column names
_facility_id =str(bundle.data['facility_id'])
visibleColumns = get_visible_columns(views.DataSetManager(bundle.obj).get_table())
bundle.data = get_detail_bundle(bundle.obj, ['dataset',''])
# TODO: this is a kludge to deal with issue #103 db: api: URI for datasetdata is incorrect
bundle.data['endpointFile'] = {'uri':'http://lincs.hms.harvard.edu/db/api/v1/datasetdata/'+ _facility_id + "/?format=csv",
'noCols':len(visibleColumns),
'cols':visibleColumns.values()
}
return bundle
def dehydrate(self, bundle):
# TODO: the following call executes the query *just* to get the column names
_facility_id =str(bundle.data['facility_id'])
visibleColumns = get_visible_columns(views.DataSetManager(bundle.obj).get_table())
bundle.data = get_detail_bundle(bundle.obj, ['dataset',''])
saf_uri = self.absolute_uri.replace('dataset','datasetdata')
saf_uri = saf_uri.replace('json','csv');
bundle.data['datapointFile'] = {'uri': saf_uri,
'noCols':len(visibleColumns),
'cols':visibleColumns.values()
}
return bundle
def dehydrate(self, bundle):
dataset_id = bundle.data['id']
bundle.data = get_detail_bundle(
bundle.obj, ['dataset',''],
_override_filter=lambda x: x.show_in_detail or x.field=='bioassay')
if bundle.obj.datarecord_set.exists():
datapointFileSchema = DataSetDataResource2.generate_schema(dataset_id)
_uri = self.get_resource_uri(bundle)
saf_uri = _uri.replace('dataset','datasetdata')
saf_uri = saf_uri + '?format=csv'
datapointFileSchema['uri'] = bundle.request.build_absolute_uri(saf_uri)
bundle.data['datapointFile'] = datapointFileSchema
bundle.data['safVersion'] = '0.1'
if bundle.obj.dataset_data_url:
bundle.data['data_url'] = bundle.obj.dataset_data_url
bundle.data['screeningFacility'] = 'HMS'
bundle.data['reagents_studied'] = {
'antibodies': [
x.facility_batch for x in
bundle.obj.antibodies.all().order_by(
'reagent__facility_id', 'batch_id')],
'cells': [
x.facility_batch for x in
bundle.obj.cells.all().order_by(
'reagent__facility_id', 'batch_id')],
'other_reagents': [
x.facility_batch for x in
bundle.obj.other_reagents.all().order_by(
'reagent__facility_id', 'batch_id')],
'primary_cells': [
x.facility_batch for x in
bundle.obj.primary_cells.all().order_by(
'reagent__facility_id', 'batch_id')],
'proteins': [
x.facility_batch for x in
bundle.obj.proteins.all().order_by(
'reagent__facility_id', 'batch_id')],
'small_molecules': [
x.facility_salt_batch for x in
bundle.obj.small_molecules.all().order_by(
'reagent__facility_id', 'reagent__salt_id', 'batch_id')]
}
return bundle
def dehydrate(self, bundle):
dataset_id = bundle.data['id']
bundle.data = get_detail_bundle(
bundle.obj, ['dataset',''],
_override_filter=lambda x: x.show_in_detail or x.field=='bioassay')
datapointFileSchema = DataSetDataResource2.generate_schema(dataset_id)
_uri = self.get_resource_uri(bundle)
saf_uri = _uri.replace('dataset','datasetdata')
saf_uri = saf_uri + '?format=csv'
datapointFileSchema['uri'] = bundle.request.build_absolute_uri(saf_uri)
bundle.data['datapointFile'] = datapointFileSchema
bundle.data['safVersion'] = '0.1'
bundle.data['screeningFacility'] = 'HMS'
return bundle
def dehydrate(self, bundle):
bundle.data = get_detail_bundle(bundle.obj, ['library',''])
return bundle
def dehydrate(self, bundle):
bundle.data = get_detail_bundle(bundle.obj, ['library',''])
return bundle
def dehydrate(self, bundle):
bundle.data = get_detail_bundle(bundle.obj, ['protein',''])
return bundle
def dehydrate(self, bundle):
bundle.data = get_detail_bundle(bundle.obj, ['otherreagent',''])
return bundle
def dehydrate(self, bundle):
bundle.data = get_detail_bundle(bundle.obj, ['antibody',''])
return bundle
def dehydrate(self, bundle):
bundle.data = get_detail_bundle(bundle.obj, ['smallmolecule',''])
return bundle