diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/case_attributes.py | 49 |
1 files changed, 31 insertions, 18 deletions
diff --git a/gn3/case_attributes.py b/gn3/case_attributes.py index 89b3c63..04472c9 100644 --- a/gn3/case_attributes.py +++ b/gn3/case_attributes.py @@ -1,11 +1,12 @@ """Implement case-attribute manipulations.""" import os import csv +import json import tempfile from functools import reduce from MySQLdb.cursors import DictCursor -from flask import jsonify, Response, Blueprint, current_app +from flask import jsonify, request, Response, Blueprint, current_app from gn3.commands import run_cmd @@ -26,7 +27,7 @@ def __inbredset_group__(conn, inbredset_id): {"inbredset_id": inbredset_id}) return dict(cursor.fetchone()) -def __inbred_set_strains__(conn, inbredset_id): +def __inbredset_strains__(conn, inbredset_id): """Return all samples/strains for given InbredSet group.""" with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( @@ -54,7 +55,7 @@ def inbredset_group(inbredset_id: int) -> Response: 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(__inbred_set_strains__(conn, inbredset_id)) + return jsonify(__inbredset_strains__(conn, inbredset_id)) @caseattr.route("/<int:inbredset_id>/names", methods=["GET"]) def inbredset_case_attribute_names(inbredset_id: int) -> Response: @@ -115,35 +116,44 @@ def inbredset_case_attribute_values(inbredset_id: int) -> Response: 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__(data) -> tuple[dict, ...]: +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} return tuple( { - "Strain": row["StrainName"], + "Strain": strain["Name"], **{ - key: row["case-attributes"][key] - for key in sorted(row["case-attributes"].keys()) + key: data.get( + strain["Name"], {}).get("case-attributes", {}).get(key, "") + for key in fieldnames[1:] } - } for row in data) + } for strain in strains) -def __process_edit_data__(form_data) -> tuple[dict, ...]: +def __process_edit_data__(fieldnames, form_data) -> tuple[dict, ...]: """Process data from form and return tuple of dicts.""" - raise NotImplementedError + def __process__(acc, strain_cattrs): + strain, cattrs = strain_cattrs + return acc + ({ + "Strain": strain, **{ + 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.""" fd, filepath = tempfile.mkstemp(".csv") os.close(fd) with open(filepath, "w", encoding="utf-8") as csvfile: - writer = csv.DictWriter(filename, fieldnames=fieldnames, dialect="unix") + writer = csv.DictWriter(csvfile, fieldnames=fieldnames, dialect="unix") writer.writeheader() writer.writerows(data) return filepath -def __compute_diff__(calabels: tuple[str, ...], original_data: tuple[dict, ...], edit_data: tuple[dict, ...]): +def __compute_diff__(fieldnames: tuple[str, ...], original_data: tuple[dict, ...], edit_data: tuple[dict, ...]): """Return the diff of the data.""" - fieldnames = ["Strain"] + sorted(calabels) # Make first column the strain. basefilename = __write_csv__(fieldnames, original_data) deltafilename = __write_csv__(fieldnames, edit_data) diff_results = run_cmd(json.dumps( @@ -207,13 +217,16 @@ def edit_case_attributes(inbredset_id: int) -> Response: database_connection(current_app.config["SQL_URI"]) as conn): # TODO: Check user has "edit case attribute privileges" user = the_token.user + fieldnames = (["Strain"] + sorted( + attr["Name"] for attr in + __case_attribute_labels_by_inbred_set__(conn, inbredset_id))) diff_filename = __queue_diff__(conn, user, __compute_diff__( - (["Strain"] + sorted( - attr["Name"] for attr in - __case_attribute_labels_by_inbred_set__(conn, inbredset_id))), + fieldnames, __process_orig_data__( - __case_attribute_values_by_inbred_set__(conn, inbredset_id)), - __process_edit_data__(request.form))) + fieldnames, + __case_attribute_values_by_inbred_set__(conn, inbredset_id), + __inbredset_strains__(conn, inbredset_id)), + __process_edit_data__(fieldnames, request.json["edit-data"]))) try: __apply_diff__(conn, user, diff_filename) return jsonify({ |