diff options
| -rw-r--r-- | gn3/case_attributes.py | 124 |
1 files changed, 116 insertions, 8 deletions
diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py index e3e6dc6..cec4850 100644 --- a/gn3/case_attributes.py +++ b/gn3/case_attributes.py @@ -305,8 +305,97 @@ def __load_diff__(diff_filename): with open(diff_filename, encoding="utf8") as diff_file: return __parse_diff_json__(diff_file.read()) +def __apply_additions__( + cursor, inbredset_id: int, additions_diff) -> None: + """Apply additions: creates new case attributes.""" + # TODO: Not tested... will probably fail. + cursor.execute( + "INSERT INTO CaseAttribute(InbredSetId, Name, Description) " + "VALUES (:inbredset_id, :name, :desc)", + tuple({ + "inbredset_id": inbredset_id, + "name": diff["name"], + "desc": diff["description"] + } for diff in additions_diff)) + +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") + + 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"], + cattr: new[cattr] + } for cattr in cattrs if new[cattr] != orig[cattr]) + + new_rows = reduce(__retrieve_changes__, modifications_diff, tuple()) + strain_names = tuple({row["Strain"] 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) + strain_ids = { + row["StrainName"]: int(row["StrainId"]) + for row in cursor.fetchall()} + + cursor.execute("SELECT CaseAttributeId, Name AS CaseAttributeName " + "FROM CaseAttribute WHERE InbredSetId=%s " + f"AND Name IN ({', '.join(['%s'] * len(cattrs))})", + (inbredset_id,) + cattrs) + cattr_ids = { + row["CaseAttributeName"]: row["CaseAttributeId"] + for row in cursor.fetchall() + } + + cursor.executemany( + "INSERT INTO CaseAttributeXRefNew" + "(InbredSetId, StrainId, CaseAttributeId, Value) " + "VALUES(%(isetid)s, %(strainid)s, %(cattrid)s, %(value)s) " + "ON DUPLICATE KEY UPDATE Value=VALUES(value)", + tuple( + { + "isetid": inbredset_id, + "strainid": strain_ids[row["Strain"]], + "cattrid": cattr_ids[cattr], + "value": row[cattr] + } + for cattr in cattrs for row in new_rows + if bool(row.get(cattr, "").strip()))) + cursor.executemany( + "DELETE FROM CaseAttributeXRefNew WHERE " + "InbredSetId=%(isetid)s AND StrainId=%(strainid)s " + "AND CaseAttributeId=%(cattrid)s", + tuple( + { + "isetid": inbredset_id, + "strainid": strain_ids[row["Strain"]], + "cattrid": cattr_ids[cattr] + } + for row in new_rows + for cattr in (key for key in row.keys() if key != "Strain") + if not bool(row[cattr].strip()))) + +def __apply_deletions__( + cursor, inbredset_id: int, deletions_diff) -> None: + """Apply deletions: delete existing case attributes and their values.""" + # TODO: Not tested... will probably fail. + params = tuple({ + "inbredset_id": inbredset_id, + "case_attribute_id": diff["case_attribute_id"] + } for diff in deletions_diff) + cursor.executemany( + "DELETE FROM CaseAttributeXRefNew WHERE " + "InbredSetId=:inbredset_id AND CaseAttributeId=:case_attribute_id", + params) + cursor.executemany( + "DELETE FROM CaseAttribute WHERE " + "InbredSetId=:inbredset_id AND CaseAttributeId=:case_attribute_id", + params) + def __apply_diff__( - conn: Connection, inbredset_id: int, user: User, diff_filename) -> None: + conn: Connection, inbredset_id: int, user: User, diff_filename, the_diff) -> None: """ Apply the changes in the diff at `diff_filename` to the data in the database if the user has appropriate privileges. @@ -314,7 +403,17 @@ def __apply_diff__( required_access( inbredset_id, ("system:inbredset:edit-case-attribute", "system:inbredset:apply-case-attribute-edit")) - raise NotImplementedError + diffs = the_diff["diff"] + with conn.cursor(cursorclass=DictCursor) as cursor: + # __apply_additions__(cursor, inbredset_id, diffs["Additions"]) + __apply_modifications__( + cursor, inbredset_id, diffs["Modifications"], the_diff["fieldnames"]) + # __apply_deletions__(cursor, inbredset_id, diffs["Deletions"]) + __save_diff__(conn, the_diff, EditStatus.approved) + new_path = Path( + diff_filename.parent, + f"{diff_filename.stem}-approved{diff_filename.suffix}") + os.rename(diff_filename, new_path) def __reject_diff__(conn: Connection, inbredset_id: int, @@ -370,9 +469,11 @@ def edit_case_attributes(inbredset_id: int) -> Response: fieldnames, __process_orig_data__( fieldnames, - __case_attribute_values_by_inbred_set__(conn, inbredset_id), + __case_attribute_values_by_inbred_set__( + conn, inbredset_id), __inbredset_strains__(conn, inbredset_id)), - __process_edit_data__(fieldnames, request.json["edit-data"])) + __process_edit_data__( + fieldnames, request.json["edit-data"])) }, Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR)) except NoDiffError as _nde: @@ -385,7 +486,8 @@ def edit_case_attributes(inbredset_id: int) -> Response: return response try: - __apply_diff__(conn, user, diff_filename) + __apply_diff__( + conn, inbredset_id, user, diff_filename, __load_diff__(diff_filename)) return jsonify({ "diff-status": "applied", "message": ("The changes to the case-attributes have been " @@ -451,12 +553,18 @@ def list_diffs(inbredset_id: int) -> Response: return resp @caseattr.route("/approve/<path:filename>", methods=["POST"]) -def approve_case_attributes_diff(inbredset_id: int) -> Response: +def approve_case_attributes_diff(filename: str) -> Response: """Approve the changes to the case attributes in the diff.""" + diff_dir = Path(current_app.config.get("TMPDIR"), CATTR_DIFFS_DIR) + diff_filename = Path(diff_dir, filename) + the_diff = __load_diff__(diff_filename) with (require_oauth.acquire("profile resource") as the_token, database_connection(current_app.config["SQL_URI"]) as conn): - __apply_diff__(conn, inbredset_id, the_token.user, diff_filename) - raise NotImplementedError + __apply_diff__(conn, the_diff["inbredset_id"], the_token.user, diff_filename, the_diff) + return jsonify({ + "message": "Applied the diff successfully.", + "diff_filename": diff_filename.name + }) @caseattr.route("/reject/<path:filename>", methods=["POST"]) def reject_case_attributes_diff(filename: str) -> Response: |