diff options
| -rw-r--r-- | gn3/api/case_attributes.py (renamed from gn3/case_attributes.py) | 62 | ||||
| -rw-r--r-- | gn3/app.py | 2 |
2 files changed, 47 insertions, 17 deletions
diff --git a/gn3/case_attributes.py b/gn3/api/case_attributes.py index 7646c92..7053e6a 100644 --- a/gn3/case_attributes.py +++ b/gn3/api/case_attributes.py @@ -5,7 +5,6 @@ import json import uuid import tempfile import lmdb -import pickle from typing import Union from pathlib import Path @@ -42,6 +41,7 @@ CATTR_DIFFS_DIR = "case-attribute-diffs" class NoDiffError(ValueError): """Raised if there is no difference between the old and new data.""" + def __init__(self): """Initialise exception.""" super().__init__( @@ -50,7 +50,8 @@ class NoDiffError(ValueError): class CAJSONEncoder(json.JSONEncoder): """Encoder for CaseAttribute-specific data""" - def default(self, obj): # pylint: disable=[arguments-renamed] + + def default(self, obj): # pylint: disable=[arguments-renamed] """Default encoder""" if isinstance(obj, datetime): return obj.isoformat() @@ -58,6 +59,7 @@ class CAJSONEncoder(json.JSONEncoder): return str(obj) return json.JSONEncoder.default(self, obj) + def required_access( token: dict, inbredset_id: int, @@ -86,7 +88,8 @@ def required_access( urljoin(current_app.config["AUTH_SERVER_URL"], "auth/resource/authorisation"), json={"resource-ids": [resource_id]}, - headers={"Authorization": f"Bearer {token['access_token']}"}, + headers={ + "Authorization": f"Bearer {token['access_token']}"}, timeout=300) if auth.status_code == 200: privs = tuple(priv["privilege_id"] @@ -101,8 +104,6 @@ def required_access( f"User does not have the privileges {access_levels}") - - def __inbredset_group__(conn, inbredset_id): """Return InbredSet group's top-level details.""" with conn.cursor(cursorclass=DictCursor) as cursor: @@ -111,6 +112,7 @@ def __inbredset_group__(conn, inbredset_id): {"inbredset_id": inbredset_id}) return dict(cursor.fetchone()) + def __inbredset_strains__(conn, inbredset_id): """Return all samples/strains for given InbredSet group.""" with conn.cursor(cursorclass=DictCursor) as cursor: @@ -121,6 +123,7 @@ def __inbredset_strains__(conn, inbredset_id): {"inbredset_id": inbredset_id}) return tuple(dict(row) for row in cursor.fetchall()) + def __case_attribute_labels_by_inbred_set__(conn, inbredset_id): """Return the case-attribute labels/names for the given InbredSet group.""" with conn.cursor(cursorclass=DictCursor) as cursor: @@ -129,18 +132,21 @@ def __case_attribute_labels_by_inbred_set__(conn, inbredset_id): {"inbredset_id": inbredset_id}) return tuple(dict(row) for row in cursor.fetchall()) + @caseattr.route("/<int:inbredset_id>", methods=["GET"]) def inbredset_group(inbredset_id: int) -> Response: """Retrieve InbredSet group's details.""" with database_connection(current_app.config["SQL_URI"]) as conn: return jsonify(__inbredset_group__(conn, inbredset_id)) + @caseattr.route("/<int:inbredset_id>/strains", methods=["GET"]) def inbredset_strains(inbredset_id: int) -> Response: """Retrieve ALL strains/samples relating to a specific InbredSet group.""" with database_connection(current_app.config["SQL_URI"]) as conn: return jsonify(__inbredset_strains__(conn, inbredset_id)) + @caseattr.route("/<int:inbredset_id>/names", methods=["GET"]) def inbredset_case_attribute_names(inbredset_id: int) -> Response: """Retrieve ALL case-attributes for a specific InbredSet group.""" @@ -148,6 +154,7 @@ def inbredset_case_attribute_names(inbredset_id: int) -> Response: return jsonify( __case_attribute_labels_by_inbred_set__(conn, inbredset_id)) + def __by_strain__(accumulator, item): attr = {item["CaseAttributeName"]: item["CaseAttributeValue"]} strain_name = item["StrainName"] @@ -166,13 +173,14 @@ def __by_strain__(accumulator, item): **accumulator, strain_name: { **{ - key: value for key,value in item.items() + key: value for key, value in item.items() if key in ("StrainName", "StrainName2", "Symbol", "Alias") }, "case-attributes": attr } } + def __case_attribute_values_by_inbred_set__( conn: Connection, inbredset_id: int) -> tuple[dict, ...]: """ @@ -195,12 +203,14 @@ def __case_attribute_values_by_inbred_set__( return tuple( reduce(__by_strain__, cursor.fetchall(), {}).values()) + @caseattr.route("/<int:inbredset_id>/values", methods=["GET"]) def inbredset_case_attribute_values(inbredset_id: int) -> Response: """Retrieve the group's (InbredSet's) case-attribute values.""" with database_connection(current_app.config["SQL_URI"]) as conn: return jsonify(__case_attribute_values_by_inbred_set__(conn, inbredset_id)) + def __process_orig_data__(fieldnames, cadata, strains) -> tuple[dict, ...]: """Process data from database and return tuple of dicts.""" data = {item["StrainName"]: item for item in cadata} @@ -214,18 +224,20 @@ def __process_orig_data__(fieldnames, cadata, strains) -> tuple[dict, ...]: } } for strain in strains) + def __process_edit_data__(fieldnames, form_data) -> tuple[dict, ...]: """Process data from form and return tuple of dicts.""" def __process__(acc, strain_cattrs): strain, cattrs = strain_cattrs return acc + ({ "Sample": strain, **{ - field: cattrs["case-attributes"].get(field, "") - for field in fieldnames[1:] + field: cattrs["case-attributes"].get(field, "") + for field in fieldnames[1:] } },) return reduce(__process__, form_data.items(), tuple()) + def __write_csv__(fieldnames, data): """Write the given `data` to a csv file and return the path to the file.""" fdesc, filepath = tempfile.mkstemp(".csv") @@ -237,6 +249,7 @@ def __write_csv__(fieldnames, data): return filepath + def __compute_diff__( fieldnames: tuple[str, ...], original_data: tuple[dict, ...], @@ -252,6 +265,7 @@ def __compute_diff__( return json.loads(diff_results["output"]) return {} + def __queue_diff__(conn: Connection, diff_data, diff_data_dir: Path) -> Path: """ Queue diff for future processing. @@ -278,6 +292,7 @@ def __queue_diff__(conn: Connection, diff_data, diff_data_dir: Path) -> Path: return filepath raise NoDiffError + def __save_diff__(conn: Connection, diff_data: dict, status: EditStatus) -> int: """Save to the database.""" with conn.cursor() as cursor: @@ -295,6 +310,7 @@ def __save_diff__(conn: Connection, diff_data: dict, status: EditStatus) -> int: }) return diff_data.get("db_id") or cursor.lastrowid + def __parse_diff_json__(json_str): """Parse the json string to python objects.""" raw_diff = json.loads(json_str) @@ -309,11 +325,13 @@ def __parse_diff_json__(json_str): if raw_diff.get("created") else None) } + def __load_diff__(diff_filename): """Load the diff.""" 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.""" @@ -327,6 +345,7 @@ def __apply_additions__( "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.""" @@ -387,6 +406,7 @@ def __apply_modifications__( for cattr in (key for key in row.keys() if key != "Sample") 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.""" @@ -404,6 +424,7 @@ def __apply_deletions__( "InbredSetId=:inbredset_id AND CaseAttributeId=:case_attribute_id", params) + def __apply_diff__( conn: Connection, auth_token, inbredset_id: int, diff_filename, the_diff) -> None: """ @@ -426,6 +447,7 @@ def __apply_diff__( f"{diff_filename.stem}-approved{diff_filename.suffix}") os.rename(diff_filename, new_path) + def __reject_diff__(conn: Connection, auth_token: dict, inbredset_id: int, @@ -440,13 +462,14 @@ def __reject_diff__(conn: Connection, ("system:inbredset:edit-case-attribute", "system:inbredset:apply-case-attribute-edit")) __save_diff__(conn, diff, EditStatus.rejected) - new_path = Path(diff_filename.parent, f"{diff_filename.stem}-rejected{diff_filename.suffix}") + new_path = Path(diff_filename.parent, + f"{diff_filename.stem}-rejected{diff_filename.suffix}") os.rename(diff_filename, new_path) return diff_filename def __update_case_attributes__( - cursor, inbredset_id: int, modifications) -> None: + cursor, inbredset_id: int, modifications) -> None: for strain, changes in modifications.items(): for case_attribute, value in changes.items(): value = value.strip() @@ -474,21 +497,23 @@ def add_case_attributes(inbredset_id: int, auth_token=None) -> Response: """Add a new case attribute for `InbredSetId`.""" required_access( auth_token, inbredset_id, ("system:inbredset:create-case-attribute",)) - with database_connection(current_app.config["SQL_URI"]) as conn: # pylint: disable=[unused-variable] + with database_connection(current_app.config["SQL_URI"]) as conn: # pylint: disable=[unused-variable] raise NotImplementedError + @caseattr.route("/<int:inbredset_id>/delete", methods=["POST"]) @require_token def delete_case_attributes(inbredset_id: int, auth_token=None) -> Response: """Delete a case attribute from `InbredSetId`.""" required_access( auth_token, inbredset_id, ("system:inbredset:delete-case-attribute",)) - with database_connection(current_app.config["SQL_URI"]) as conn: # pylint: disable=[unused-variable] + with database_connection(current_app.config["SQL_URI"]) as conn: # pylint: disable=[unused-variable] raise NotImplementedError + @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) -> Response: """Edit the case attributes for `InbredSetId` based on data received. :inbredset_id: Identifier for the population that the case attribute belongs @@ -538,6 +563,7 @@ def edit_case_attributes(inbredset_id: int, auth_token = None) -> Response: "queued for approval."), }) + @caseattr.route("/<int:inbredset_id>/diff/list", methods=["GET"]) def list_diffs(inbredset_id: int) -> Response: """List any changes that have not been approved/rejected.""" @@ -584,25 +610,28 @@ def list_diffs(inbredset_id: int) -> Response: f"{diff['json_diff_data']['user_id']}:::" f"{diff['time_stamp'].isoformat()}") } for diff in diffs - if diff["json_diff_data"].get("inbredset_id") == inbredset_id), + if diff["json_diff_data"].get("inbredset_id") == inbredset_id), cls=CAJSONEncoder)) resp.headers["Content-Type"] = "application/json" return resp + @caseattr.route("/approve/<path:filename>", methods=["POST"]) @require_token -def approve_case_attributes_diff(filename: str, auth_token = None) -> Response: +def approve_case_attributes_diff(filename: str, auth_token=None) -> Response: """Approve the changes to the case attributes in the diff.""" diff_dir = Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR) diff_filename = Path(diff_dir, filename) the_diff = __load_diff__(diff_filename) with database_connection(current_app.config["SQL_URI"]) as conn: - __apply_diff__(conn, auth_token, the_diff["inbredset_id"], diff_filename, the_diff) + __apply_diff__(conn, auth_token, + the_diff["inbredset_id"], diff_filename, the_diff) return jsonify({ "message": "Applied the diff successfully.", "diff_filename": diff_filename.name }) + @caseattr.route("/reject/<path:filename>", methods=["POST"]) @require_token def reject_case_attributes_diff(filename: str, auth_token=None) -> Response: @@ -621,6 +650,7 @@ def reject_case_attributes_diff(filename: str, auth_token=None) -> Response: "diff_filename": diff_filename.name }) + @caseattr.route("/<int:inbredset_id>/diff/<int:diff_id>/view", methods=["GET"]) @require_token def view_diff(inbredset_id: int, diff_id: int, auth_token=None) -> Response: diff --git a/gn3/app.py b/gn3/app.py index 74bb5ab..6b5efa4 100644 --- a/gn3/app.py +++ b/gn3/app.py @@ -29,7 +29,7 @@ from gn3.api.sampledata import sampledata from gn3.api.llm import gnqa from gn3.api.rqtl2 import rqtl2 from gn3.api.streaming import streaming -from gn3.case_attributes import caseattr +from gn3.api.case_attributes import caseattr from gn3.api.lmdb_sample_data import lmdb_sample_data |