def glds_summary(accession):
"""Report factors, assays, and/or raw JSON"""
rargs = parse_rargs(request.args)
try:
glds = GLDS(accession)
except GeneLabJSONException as e:
raise FileNotFoundError(e)
if rargs.display_rargs["fmt"] == "raw":
return display_object([glds._json], {"fmt": "json"})
else:
return display_object(glds.summary_dataframe, rargs.display_rargs)
def get_data(accession, assay_name, rargs=None):
"""Serve any kind of data"""
if rargs is None:
rargs = parse_rargs(request.args)
assay, message, status = get_assay(accession, assay_name, rargs)
if assay is None:
return message, status
filename = resolve_file_name(assay, rargs)
table_data = try_sqlite(accession,
assay.name,
rargs.data_rargs,
expect_date=assay.glds_file_dates.get(
filename, -1))
if table_data is None:
table_data = retrieve_table_data(assay, filename, rargs.data_rargs)
dump_to_sqlite(accession,
assay.name,
rargs.data_rargs,
table_data,
set_date=assay.glds_file_dates.get(filename, -1))
if rargs.display_rargs["fmt"] in {"tsv", "json"}:
return display_object(filter_table_data(table_data,
rargs.data_filter_rargs),
rargs.display_rargs,
index="auto")
else:
raise NotImplementedError("fmt={}".format(rargs.display_rargs["fmt"]))
def assay_metadata(accession, assay_name):
"""DataFrame view of metadata, optionally queried"""
rargs = parse_rargs(request.args)
assay, message, status = get_assay(accession, assay_name, rargs)
if assay is None:
return message, status
subset, _ = subset_metadata(assay.metadata, rargs)
return display_object(subset, rargs.display_rargs, index=True)
def assay_factors(accession, assay_name):
"""DataFrame of samples and factors in human-readable form"""
rargs = parse_rargs(request.args)
assay, message, status = get_assay(accession, assay_name, rargs)
if assay is None:
return message, status
else:
if rargs.non_data_rargs["cls"]:
if rargs.display_rargs["fmt"] != "tsv":
error_mask = "{} format is unsuitable for CLS (use tsv)"
raise GeneLabException(
error_mask.format(rargs.display_rargs["fmt"]))
else:
obj = assay.factors(
cls=rargs.non_data_rargs["cls"],
continuous=rargs.non_data_rargs["continuous"])
return display_object(obj, {"fmt": "raw"})
else:
return display_object(assay.factors(),
rargs.display_rargs,
index=True)
def get_gct(accession, assay_name, rargs):
"""Get GCT formatted processed data; needs to be refactored!"""
assay, message, status = get_assay(accession, assay_name, rargs)
if assay is None:
return message, status
pdata = try_sqlite(accession, assay.name, rargs.data_rargs)
if pdata is None:
pdata = get_data(accession, assay.name, rargs=rargs)
gct_header = "#1.2\n{}\t{}\n".format(*pdata.shape)
pdata.columns = ["Description"] + list(pdata.columns)[1:]
pdata.insert(loc=0, column="Name", value=pdata["Description"])
gct_data = gct_header + pdata.to_csv(sep="\t", index=False)
return display_object(gct_data, {"fmt": "raw"})