diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/traits.py | 28 |
1 files changed, 26 insertions, 2 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 5013844..3827c34 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -99,12 +99,36 @@ def get_trait_csv_sample_data(conn: Any, "cxref.StrainId = st.Id) " "LEFT JOIN CaseAttribute ca ON ca.Id = cxref.CaseAttributeId" "WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name") + case_attr_columns = set() + csv_data = {} with conn.cursor() as cursor: cursor.execute(__query, (trait_name, phenotype_id)) - return ("Strain Name,Value,SE,Count\n" + - "\n".join(map(lambda x:x[0], cursor.fetchall()))) + for data in cursor.fetchall(): + if data[1] == "x": + csv_data[data[0]] = None + else: + sample, case_attr, value = data[0], data[1], data[2] + if not csv_data.get(sample): + csv_data[sample] = {} + csv_data[sample][case_attr] = None if value == "x" else value + case_attr_columns.add(case_attr) + if not case_attr_columns: + return ("Strain Name,Value,SE,Count\n" + + "\n".join(csv_data.keys())) + else: + columns = sorted(case_attr_columns) + csv = ("Strain Name,Value,SE,Count," + + ",".join(columns) + "\n") + for key, value in csv_data.items(): + if not value: + csv += (key + (len(case_attr_columns) * ",x") + "\n") + else: + vals = [str(value.get(column, "x")) for column in columns] + csv += (key + "," + ",".join(vals) + "\n") + return csv return "No Sample Data Found" + def update_sample_data(conn: Any, #pylint: disable=[R0913] trait_name: str, strain_name: str, |