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 generate_table_records(profile_id=str(), component=str()):
# function generates component records for building an UI table - please note that for effective tabular display,
# all array and object-type fields (e.g., characteristics) are deferred to sub-table display.
# please define such in the schema as "show_in_table": false and "show_as_attribute": true
columns = list()
data_set = list()
# instantiate data access object
da_object = DAComponent(profile_id, 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_in_table", True)]
# build db column projection
projection = [(x["id"].split(".")[-1], 1) for x in schema]
# retrieve and process records
if component == "submission":
records = da_object.get_all_records_columns(sort_by="date_created", sort_direction=1,
projection=dict(projection))
else:
records = da_object.get_all_records_columns(projection=dict(projection))
if len(records):
df = pd.DataFrame(records)
df['s_n'] = df.index
df['record_id'] = df._id.astype(str)
df["DT_RowId"] = df.record_id
df.DT_RowId = 'row_' + df.DT_RowId
df = df.drop('_id', axis='columns')
if component == "submission":
df["special_repositories"] = df["repository"]
columns.append(dict(data="special_repositories", visible=False))
columns.append(dict(data="record_id", visible=False))
detail_dict = dict(className='summary-details-control detail-hover-message', orderable=False, data=None,
title='', defaultContent='', width="5%")
columns.insert(0, detail_dict)
df_columns = list(df.columns)
for x in schema:
x["id"] = x["id"].split(".")[-1]
columns.append(dict(data=x["id"], title=x["label"]))
if x["id"] not in df_columns:
df[x["id"]] = str()
df[x["id"]] = df[x["id"]].fillna('')
df[x["id"]] = df[x["id"]].apply(resolve_control_output_apply, args=(x,))
data_set = df.to_dict('records')
return_dict = dict(dataSet=data_set,
columns=columns
)
# do check for custom repos here
if component == "submission":
correct_repos = list()
user = ThreadLocal.get_current_user()
repo_ids = user.userdetails.repo_submitter
all_repos = Repository().get_by_ids(repo_ids)
for repo in all_repos:
for r_id in repo_ids:
if r_id == str(repo["_id"]):
correct_repos.append(repo)
for repo in correct_repos:
repo["_id"] = str(repo["_id"])
return_dict["repos"] = correct_repos
return return_dict
