def generate_stage_items(self):
sample_types = list()
for s_t in d_utils.get_sample_type_options():
sample_types.append(s_t["value"])
wizard_stages = dict()
# get start stages
start = d_utils.json_to_pytype(lkup.WIZARD_FILES["sample_start"])['properties']
wizard_stages['start'] = start
# if required, resolve data source for select-type controls,
# i.e., if a callback is defined on the 'option_values' field
for stage in wizard_stages['start']:
if "items" in stage:
for st in stage['items']:
if "option_values" in st:
st["option_values"] = htags.get_control_options(st)
# get sample types
for s_t in sample_types:
s_stages = d_utils.json_to_pytype(lkup.WIZARD_FILES["sample_attributes"])['properties']
form_schema = list()
for f in self.schema:
# get relevant attributes based on sample type
if f.get("show_in_form", True) and s_t in f.get("specifications", sample_types):
# if required, resolve data source for select-type controls,
# i.e., if a callback is defined on the 'option_values' field
if "option_values" in f:
f["option_values"] = htags.get_control_options(f)
# change sample-source control to wizard-compliant version
if f.get("control", str()) == "copo-sample-source":
f["control"] = "copo-sample-source-2"
# get short-form id
f["id"] = f["id"].split(".")[-1]
# might not need to include name
if f["id"] == "name":
continue
form_schema.append(f)
for p in s_stages:
if p["ref"] == "sample_attributes":
p["items"] = form_schema
wizard_stages[s_t] = s_stages
return wizard_stages
def generate_attributes(component, target_id):
da_object = DAComponent(component=component)
if component in da_dict:
da_object = da_dict[component]()
# get and filter schema elements based on displayable columns
schema = [x for x in da_object.get_schema().get("schema_dict") if x.get("show_as_attribute", False)]
# build db column projection
projection = [(x["id"].split(".")[-1], 1) for x in schema]
# account for description metadata in datafiles
if component == "datafile":
projection.append(('description', 1))
filter_by = dict(_id=ObjectId(target_id))
record = da_object.get_all_records_columns(projection=dict(projection), filter_by=filter_by)
result = dict()
if len(record):
record = record[0]
if component == "sample": # filter based on sample type
sample_types = [s_t['value'] for s_t in d_utils.get_sample_type_options()]
sample_type = record.get("sample_type", str())
schema = [x for x in schema if sample_type in x.get("specifications", sample_types)]
for x in schema:
x['id'] = x["id"].split(".")[-1]
if component == "datafile":
key_split = "___0___"
attributes = record.get("description", dict()).get("attributes", dict())
stages = record.get("description", dict()).get("stages", list())
datafile_attributes = dict()
datafile_items = list()
for st in stages:
for item in st.get("items", list()):
if str(item.get("hidden", False)).lower() == "false":
atrib_val = attributes.get(st["ref"], dict()).get(item["id"], str())
item["id"] = st["ref"] + key_split + item["id"]
datafile_attributes[item["id"]] = atrib_val
datafile_items.append(item)
record.update(datafile_attributes)
schema = schema + datafile_items
result = resolve_display_data(schema, record)
return result
def filter_sample_type(form_value, elem):
# filters UI elements based on sample type
allowable = True
default_type = "biosample"
sample_types = list()
for s_t in d_utils.get_sample_type_options():
sample_types.append(s_t["value"])
if "sample_type" in form_value:
default_type = form_value["sample_type"]
if default_type not in elem.get("specifications", sample_types):
allowable = False
return allowable
def filter_sample_type(form_value, elem):
# filters UI elements based on sample type
allowable = True
default_type = "biosample"
sample_types = list()
for s_t in d_utils.get_sample_type_options():
sample_types.append(s_t["value"])
if "sample_type" in form_value:
default_type = form_value["sample_type"]
if default_type not in elem.get("specifications", sample_types):
allowable = False
return allowable
def generate_attributes(self, target_id):
sample_attributes = dict()
record = Sample().get_record(target_id)
sample_attributes["record"] = record
table_schema = list()
sample_types = list()
for s_t in d_utils.get_sample_type_options():
sample_types.append(s_t["value"])
sample_type = str()
if "sample_type" in record:
sample_type = record["sample_type"]
for f in self.schema:
# get relevant attributes based on sample type
if f.get("show_in_sub_table", False) and sample_type in f.get("specifications", sample_types):
# if required, resolve data source for select-type controls,
# i.e., if a callback is defined on the 'option_values' field
if "option_values" in f:
f["option_values"] = htags.get_control_options(f)
# change sample-source control to wizard-compliant version
if f.get("control", str()) == "copo-sample-source":
f["control"] = "copo-sample-source-2"
# get short-form id
f["id"] = f["id"].split(".")[-1]
# might not need to include name
if f["id"] == "name":
continue
table_schema.append(f)
sample_attributes["schema"] = table_schema
return sample_attributes
