diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/case_attributes.py | 69 |
1 files changed, 41 insertions, 28 deletions
diff --git a/gn3/api/case_attributes.py b/gn3/api/case_attributes.py index 536d74d..5662bfe 100644 --- a/gn3/api/case_attributes.py +++ b/gn3/api/case_attributes.py @@ -1,5 +1,6 @@ """Implement case-attribute manipulations.""" from typing import Union +from pathlib import Path from functools import reduce from urllib.parse import urljoin @@ -181,21 +182,22 @@ def inbredset_case_attribute_values(inbredset_id: int) -> Response: return jsonify(__case_attribute_values_by_inbred_set__(conn, inbredset_id)) +# pylint: disable=[too-many-locals] @caseattr.route("/<int:inbredset_id>/edit", methods=["POST"]) @require_token -def edit_case_attributes(inbredset_id: int, auth_token=None) -> Response: +def edit_case_attributes(inbredset_id: int, auth_token=None) -> tuple[Response, int]: """Edit the case attributes for `InbredSetId` based on data received. :inbredset_id: Identifier for the population that the case attribute belongs :auth_token: A validated JWT from the auth server """ with database_connection(current_app.config["SQL_URI"]) as conn, conn.cursor() as cursor: - data = request.json["edit-data"] + data = request.json["edit-data"] # type: ignore modified = { "inbredset_id": inbredset_id, "Modifications": {}, } - original, current = {}, {} + original, current = {}, {} # type: ignore for key, value in data.items(): strain, case_attribute = key.split(":") @@ -205,16 +207,18 @@ def edit_case_attributes(inbredset_id: int, auth_token=None) -> Response: if not original.get(strain): original[strain] = {} original[strain][case_attribute] = value["Original"] - modified["Modifications"]["Original"] = original - modified["Modifications"]["Current"] = current + modified["Modifications"]["Original"] = original # type: ignore + modified["Modifications"]["Current"] = current # type: ignore edit = CaseAttributeEdit( inbredset_id=inbredset_id, status=EditStatus.review, user_id=auth_token["jwt"]["sub"], changes=modified ) + directory = (Path(current_app.config["LMDB_DATA_PATH"]) / + "case-attributes" / str(inbredset_id)) _id = queue_edit(cursor=cursor, - directory=current_app.config["LMDB_DATA_PATH"], + directory=directory, edit=edit) try: required_access(auth_token, @@ -223,31 +227,31 @@ def edit_case_attributes(inbredset_id: int, auth_token=None) -> Response: "system:inbredset:apply-case-attribute-edit")) match apply_change( cursor, change_type=EditStatus.approved, - change_id=_id, - directory=current_app.config["LMDB_DATA_PATH"] + change_id=_id, # type: ignore + directory=directory ): case True: return jsonify({ "diff-status": "applied", "message": ("The changes to the case-attributes have been " "applied successfully.") - }) + }), 201 case _: return jsonify({ "diff-status": "no changes to be applied", "message": ("There were no changes to be made ") - }) + }), 200 except AuthorisationError as _auth_err: return jsonify({ "diff-status": "queued", "message": ("The changes to the case-attributes have been " "queued for approval."), - }), 401 + }), 201 @caseattr.route("/<int:inbredset_id>/diff/list", methods=["GET"]) @require_token -def list_diffs(inbredset_id: int, auth_token=None) -> Response: +def list_diffs(inbredset_id: int, auth_token=None) -> tuple[Response, int]: """List any changes that have not been approved/rejected.""" try: required_access(auth_token, @@ -256,9 +260,9 @@ def list_diffs(inbredset_id: int, auth_token=None) -> Response: "system:inbredset:apply-case-attribute-edit")) with (database_connection(current_app.config["SQL_URI"]) as conn, conn.cursor(cursorclass=DictCursor) as cursor): - changes = get_changes(cursor, inbredset_id=inbredset_id, - directory=current_app.config["LMDB_DATA_PATH"]) - current_app.logger.error(changes) + directory = (Path(current_app.config["LMDB_DATA_PATH"]) / + "case-attributes" / str(inbredset_id)) + changes = get_changes(cursor, directory=directory) return jsonify( changes ), 200 @@ -270,27 +274,32 @@ def list_diffs(inbredset_id: int, auth_token=None) -> Response: @caseattr.route("/<int:inbredset_id>/approve/<int:change_id>", methods=["POST"]) @require_token -def approve_case_attributes_diff(inbredset_id: int, change_id: int, auth_token=None) -> Response: +def approve_case_attributes_diff( + inbredset_id: int, + change_id: int, auth_token=None +) -> tuple[Response, int]: """Approve the changes to the case attributes in the diff.""" try: required_access(auth_token, inbredset_id, - ("system:inbredset:edit-case-attribute")) - with database_connection(current_app.config["SQL_URI"]) as conn, \ - conn.cursor() as cursor: + ("system:inbredset:edit-case-attribute",)) + with (database_connection(current_app.config["SQL_URI"]) as conn, + conn.cursor() as cursor): + directory = (Path(current_app.config["LMDB_DATA_PATH"]) / + "case-attributes" / str(inbredset_id)) match apply_change(cursor, change_type=EditStatus.rejected, change_id=change_id, - directory=current_app.config["LMDB_DATA_PATH"]): + directory=directory): case True: return jsonify({ "diff-status": "rejected", "message": (f"Successfully approved # {change_id}") - }) + }), 201 case _: return jsonify({ "diff-status": "queued", "message": (f"Was not able to successfully approve # {change_id}") - }) + }), 200 except AuthorisationError as __auth_err: return jsonify({ "diff-status": "queued", @@ -300,7 +309,9 @@ def approve_case_attributes_diff(inbredset_id: int, change_id: int, auth_token=N @caseattr.route("/<int:inbredset_id>/reject/<int:change_id>", methods=["POST"]) @require_token -def reject_case_attributes_diff(inbredset_id: int, change_id: int, auth_token=None) -> Response: +def reject_case_attributes_diff( + inbredset_id: int, change_id: int, auth_token=None +) -> tuple[Response, int]: """Reject the changes to the case attributes in the diff.""" try: required_access(auth_token, @@ -309,20 +320,22 @@ def reject_case_attributes_diff(inbredset_id: int, change_id: int, auth_token=No "system:inbredset:apply-case-attribute-edit")) with database_connection(current_app.config["SQL_URI"]) as conn, \ conn.cursor() as cursor: + directory = (Path(current_app.config["LMDB_DATA_PATH"]) / + "case-attributes" / str(inbredset_id)) match apply_change(cursor, change_type=EditStatus.rejected, change_id=change_id, - directory=current_app.config["LMDB_DATA_PATH"]): + directory=directory): case True: return jsonify({ "diff-status": "rejected", "message": ("The changes to the case-attributes have been " "rejected.") - }) + }), 201 case _: return jsonify({ "diff-status": "queued", "message": ("Failed to reject changes") - }) + }), 200 except AuthorisationError as __auth_err: return jsonify({ "message": ("You don't have the right privileges to edit this resource.") @@ -331,7 +344,7 @@ def reject_case_attributes_diff(inbredset_id: int, change_id: int, auth_token=No @caseattr.route("/<int:inbredset_id>/diff/<int:change_id>/view", methods=["GET"]) @require_token -def view_diff(inbredset_id: int, change_id: int, auth_token=None) -> Response: +def view_diff(inbredset_id: int, change_id: int, auth_token=None) -> tuple[Response, int]: """View a diff.""" try: required_access( @@ -340,7 +353,7 @@ def view_diff(inbredset_id: int, change_id: int, auth_token=None) -> Response: conn.cursor(cursorclass=DictCursor) as cursor): return jsonify( view_change(cursor, change_id) - ) + ), 200 except AuthorisationError as __auth_err: return jsonify({ "message": ("You don't have the right privileges to view the diffs.") |