diff options
Diffstat (limited to 'gn3/case_attributes.py')
| -rw-r--r-- | gn3/case_attributes.py | 22 |
1 files changed, 11 insertions, 11 deletions
diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py index 9baff1e..2c878d2 100644 --- a/gn3/case_attributes.py +++ b/gn3/case_attributes.py @@ -77,7 +77,7 @@ def required_access( result = requests.get( # this section fetches the resource ID from the auth server urljoin(current_app.config["AUTH_SERVER_URL"], - "auth/resource/inbredset/resource-id" + "auth/resource/populations/resource-id" f"/{__species_id__(conn)}/{inbredset_id}")) if result.status_code == 200: resource_id = result.json()["resource-id"] @@ -186,7 +186,7 @@ def __case_attribute_values_by_inbred_set__( "ON ca.CaseAttributeId=caxrn.CaseAttributeId " "INNER JOIN Strain AS s " "ON caxrn.StrainId=s.Id " - "WHERE ca.InbredSetId=%(inbredset_id)s " + "WHERE caxrn.InbredSetId=%(inbredset_id)s " "ORDER BY StrainName", {"inbredset_id": inbredset_id}) return tuple( @@ -203,7 +203,7 @@ def __process_orig_data__(fieldnames, cadata, strains) -> tuple[dict, ...]: data = {item["StrainName"]: item for item in cadata} return tuple( { - "Strain": strain["Name"], + "Sample": strain["Name"], **{ key: data.get( strain["Name"], {}).get("case-attributes", {}).get(key, "") @@ -216,7 +216,7 @@ def __process_edit_data__(fieldnames, form_data) -> tuple[dict, ...]: def __process__(acc, strain_cattrs): strain, cattrs = strain_cattrs return acc + ({ - "Strain": strain, **{ + "Sample": strain, **{ field: cattrs["case-attributes"].get(field, "") for field in fieldnames[1:] } @@ -327,19 +327,19 @@ def __apply_additions__( def __apply_modifications__( cursor, inbredset_id: int, modifications_diff, fieldnames) -> None: """Apply modifications: changes values of existing case attributes.""" - cattrs = tuple(field for field in fieldnames if field != "Strain") + cattrs = tuple(field for field in fieldnames if field != "Sample") def __retrieve_changes__(acc, row): orig = dict(zip(fieldnames, row["Original"].split(","))) new = dict(zip(fieldnames, row["Current"].split(","))) return acc + tuple({ - "Strain": new["Strain"], + "Sample": new["Sample"], cattr: new[cattr] } for cattr in cattrs if new[cattr] != orig[cattr]) new_rows: tuple[dict, ...] = reduce( __retrieve_changes__, modifications_diff, tuple()) - strain_names = tuple({row["Strain"] for row in new_rows}) + strain_names = tuple({row["Sample"] for row in new_rows}) cursor.execute("SELECT Id AS StrainId, Name AS StrainName FROM Strain " f"WHERE Name IN ({', '.join(['%s'] * len(strain_names))})", strain_names) @@ -364,7 +364,7 @@ def __apply_modifications__( tuple( { "isetid": inbredset_id, - "strainid": strain_ids[row["Strain"]], + "strainid": strain_ids[row["Sample"]], "cattrid": cattr_ids[cattr], "value": row[cattr] } @@ -377,11 +377,11 @@ def __apply_modifications__( tuple( { "isetid": inbredset_id, - "strainid": strain_ids[row["Strain"]], + "strainid": strain_ids[row["Sample"]], "cattrid": cattr_ids[cattr] } for row in new_rows - for cattr in (key for key in row.keys() if key != "Strain") + for cattr in (key for key in row.keys() if key != "Sample") if not bool(row[cattr].strip()))) def __apply_deletions__( @@ -471,7 +471,7 @@ def edit_case_attributes(inbredset_id: int, auth_token = None) -> Response: required_access(auth_token, inbredset_id, ("system:inbredset:edit-case-attribute",)) - fieldnames = tuple(["Strain"] + sorted( + fieldnames = tuple(["Sample"] + sorted( attr["Name"] for attr in __case_attribute_labels_by_inbred_set__(conn, inbredset_id))) try: |