diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/sample_data.py | 40 |
1 files changed, 7 insertions, 33 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index 4d8a14f..4062705 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -1,7 +1,6 @@ """Module containing functions that work with sample data""" from typing import Any, Tuple, Dict, Callable -import re import MySQLdb from gn3.csvcmp import extract_strain_name @@ -63,45 +62,20 @@ def get_trait_csv_sample_data( conn: Any, trait_name: int, phenotype_id: int ) -> str: """Fetch a trait and return it as a csv string""" - case_attr_columns = set() - csv_data: Dict = {} with conn.cursor() as cursor: cursor.execute(""" SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',', -ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) AS 'Data', -ifnull(ca.Name, 'x') AS 'CaseAttr', ifnull(cxref.value, 'x') AS 'Value' +ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) AS 'Data' FROM PublishFreeze pf JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId JOIN PublishData pd ON pd.Id = px.DataId JOIN Strain st ON pd.StrainId = st.Id LEFT JOIN PublishSE ps ON ps.DataId = pd.Id AND ps.StrainId = pd.StrainId LEFT JOIN NStrain ns ON ns.DataId = pd.Id AND ns.StrainId = pd.StrainId -LEFT JOIN CaseAttributeXRefNew cxref ON (cxref.InbredSetId = px.InbredSetId -AND 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""", (trait_name, phenotype_id)) - for data in cursor.fetchall(): - if data[1] == "x": - csv_data[data[0]] = None - else: - sample, case_attr, value = [ - re.sub(r"(\\n|\\r|\\t|\\)", "", x).strip() - for x in [data[0], data[1], data[2]] - ] - if not csv_data.get(sample): - csv_data[sample] = {} - csv_data[sample][case_attr] = value - case_attr_columns.add(case_attr) - if not case_attr_columns: - return "Strain Name,Value,SE,Count\n" + "\n".join(csv_data.keys()) - 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" +WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name""", + (trait_name, phenotype_id)) + if not (data := cursor.fetchall()): + return "No Sample Data Found" + return "Strain Name,Value,SE,Count\n" + \ + "\n".join([el[0] for el in data]) def get_sample_data_ids( |