def get_reagent_columns(dataset_id):
col_field_info = {}
for fi in FieldInformation.objects.all().filter(
table__in=['smallmolecule','protein','cell','antibody','otherreagent',
'smallmoleculebatch','proteinbatch','cellbatch','antibodybatch','otherreagentbatch']):
col_field_info[fi.get_camel_case_dwg_name()] = {
'reagentType': fi.table,
'dwgName': fi.dwg_field_name,
'description': fi.description
}
data_columns = ( DataColumn.objects.filter(dataset_id=dataset_id)
.filter(data_type__in=[
'small_molecule','cell','protein','antibody','otherreagent']) )
reagent_fields = OrderedDict()
meta_field_info = get_listing(DataColumn(),['datacolumn'])
for dc in data_columns.order_by('display_order'):
specific_name = dc.name
field_schema = {}
for item in meta_field_info.items():
meta_fi_attr = item[0]
meta_fi = item[1]['fieldinformation']
field_schema[meta_fi.get_camel_case_dwg_name()] = (
getattr(dc,meta_fi_attr) )
reagent_fields[specific_name] = field_schema
reagent_fields[specific_name]['columns'] = {}
for dwg_name in DataSetDataResource2.datapoint_cols[dc.data_type]:
col_name = '%s_%s' % (specific_name,dwg_name)
reagent_fields[specific_name]['columns'][col_name] = col_field_info.get(dwg_name, {})
return reagent_fields
def get_datapoint_fields(dataset_id):
data_columns = ( DataColumn.objects.filter(dataset_id=dataset_id)
.exclude(data_type__in=[
'small_molecule','cell','protein','antibody','otherreagent',
'omero_image'])
.exclude(unit__in=['day','hour','minute','second']) )
datapoint_fields = OrderedDict()
meta_field_info = get_listing(DataColumn(),['datacolumn'])
for dc in data_columns.order_by('display_order'):
specific_name = dc.name
field_schema = {}
for item in meta_field_info.items():
meta_fi_attr = item[0]
meta_fi = item[1]['fieldinformation']
field_schema[meta_fi.get_camel_case_dwg_name()] = (
getattr(dc,meta_fi_attr) )
datapoint_fields[specific_name] = field_schema
return datapoint_fields
def build_schema(self):
schema = super(DataSetResource,self).build_schema()
original_dict = schema['fields'] # TODO: reincorporate this information (this default information is about the DB schema definition)
fields = get_detail_schema(DataSet(), 'dataset', lambda x: x.show_in_detail )
# Custom fields for SAF: TODO: generate the names here from the fieldinformation
fields['datapointFile'] = get_schema_fieldinformation('datapoint_file','')
fields['safVersion'] = get_schema_fieldinformation('saf_version','')
fields['screeningFacility'] = get_schema_fieldinformation('screening_facility','')
schema['fields'] = OrderedDict(sorted(fields.items(), key=lambda x: x[0])) # sort alpha, todo sort on fi.order
ds_fieldinformation = DataSetDataResource.get_datasetdata_column_fieldinformation()
ds_fieldinformation.append(('datapoint_value',get_fieldinformation('datapoint_value',[''])) )
ds_fieldinformation.append(('timepoint',get_fieldinformation('timepoint',[''])) )
ds_fieldinformation.append(('timepoint_unit',get_fieldinformation('timepoint_unit',[''])) )
ds_fieldinformation.append(('timepoint_description',get_fieldinformation('timepoint_description',[''])) )
meta_field_info = get_listing(FieldInformation(),['fieldinformation'])
fields = {}
for field,fi in ds_fieldinformation:
field_schema_info = {}
for item in meta_field_info.items():
meta_fi_attr = item[0]
meta_fi = item[1]['fieldinformation']
field_schema_info[meta_fi.get_camel_case_dwg_name()] = getattr(fi,meta_fi_attr)
fields[fi.get_camel_case_dwg_name()]= field_schema_info
schema['datasetDataFile'] = OrderedDict(sorted(fields.items(), key=lambda x: x[0])) # sort alpha, todo sort on fi.order
dc_fieldinformation = FieldInformation.objects.all().filter(table='datacolumn', show_in_detail=True)
datapoint_fields = {}
for fi in dc_fieldinformation:
field_schema_info = {}
for item in meta_field_info.items():
meta_fi_attr = item[0]
meta_fi = item[1]['fieldinformation']
field_schema_info[meta_fi.get_camel_case_dwg_name()] = getattr(fi,meta_fi_attr)
datapoint_fields[fi.get_camel_case_dwg_name()]= field_schema_info
schema['datapointInformation'] = OrderedDict(sorted(datapoint_fields.items(), key=lambda x: x[0])) # sort alpha, todo sort on fi.order
return schema
def build_schema(self):
schema = super(DataSetDataResource,self).build_schema()
original_dict = schema['fields'] # TODO: reincorporate this information (this default information is about the DB schema definition)
ds_fieldinformation = DataSetDataResource.get_datasetdata_column_fieldinformation()
ds_fieldinformation.append(('datapoint_value',get_fieldinformation('datapoint_value',[''])) )
ds_fieldinformation.append(('timepoint',get_fieldinformation('timepoint',[''])) )
ds_fieldinformation.append(('timepoint_unit',get_fieldinformation('timepoint_unit',[''])) )
ds_fieldinformation.append(('timepoint_description',get_fieldinformation('timepoint_description',[''])) )
meta_field_info = get_listing(FieldInformation(),['fieldinformation'])
fields = {}
for __,fi in ds_fieldinformation:
field_schema_info = {}
for item in meta_field_info.items():
meta_fi_attr = item[0]
meta_fi = item[1]['fieldinformation']
field_schema_info[meta_fi.get_camel_case_dwg_name()] = getattr(fi,meta_fi_attr)
fields[fi.get_camel_case_dwg_name()]= field_schema_info
schema['fields'] = OrderedDict(sorted(fields.items(), key=lambda x: x[0])) # TODO, use the fieldinformation order
return schema
