1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
|
"""Implement case-attribute manipulations."""
import os
import csv
import json
import uuid
import tempfile
from typing import Union
from enum import Enum, auto
from pathlib import Path
from functools import reduce
from datetime import datetime
from urllib.parse import urljoin
import requests
from MySQLdb.cursors import DictCursor
from authlib.integrations.flask_oauth2.errors import _HTTPException
from flask import (
jsonify,
request,
Response,
Blueprint,
current_app,
make_response)
from gn3.commands import run_cmd
from gn3.db_utils import Connection, database_connection
from gn3.oauth2.authorisation import require_token
from gn3.auth.authorisation.errors import AuthorisationError
caseattr = Blueprint("case-attribute", __name__)
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__(
self, "No difference between existing data and sent data.")
class EditStatus(Enum):
"""Enumeration for the status of the edits."""
review = auto() # pylint: disable=[invalid-name]
approved = auto() # pylint: disable=[invalid-name]
rejected = auto() # pylint: disable=[invalid-name]
def __str__(self):
"""Print out human-readable form."""
return self.name
class CAJSONEncoder(json.JSONEncoder):
"""Encoder for CaseAttribute-specific data"""
def default(self, obj): # pylint: disable=[arguments-renamed]
"""Default encoder"""
if isinstance(obj, datetime):
return obj.isoformat()
if isinstance(obj, uuid.UUID):
return str(obj)
return json.JSONEncoder.default(self, obj)
def required_access(
token: dict,
inbredset_id: int,
access_levels: tuple[str, ...]
) -> Union[bool, tuple[str, ...]]:
"""Check whether the user has the appropriate access"""
def __species_id__(conn):
with conn.cursor() as cursor:
cursor.execute(
"SELECT SpeciesId FROM InbredSet WHERE InbredSetId=%s",
(inbredset_id,))
return cursor.fetchone()[0]
try:
with database_connection(current_app.config["SQL_URI"]) as conn:
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"
f"/{__species_id__(conn)}/{inbredset_id}"))
if result.status_code == 200:
resource_id = result.json()["resource-id"]
auth = requests.post(
# this section fetches the authorisations/privileges that
# the current user has on the resource we got above
urljoin(current_app.config["AUTH_SERVER_URL"],
"auth/resource/authorisation"),
json={"resource-ids": [resource_id]},
headers={"Authorization": f"Bearer {token['access_token']}"})
if auth.status_code == 200:
privs = tuple(priv["privilege_id"]
for role in auth.json()[resource_id]["roles"]
for priv in role["privileges"])
if all(lvl in privs for lvl in access_levels):
return privs
except _HTTPException as httpe:
raise AuthorisationError("You need to be logged in.") from httpe
raise AuthorisationError(
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:
cursor.execute(
"SELECT * FROM InbredSet WHERE InbredSetId=%(inbredset_id)s",
{"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:
cursor.execute(
"SELECT s.* FROM StrainXRef AS sxr INNER JOIN Strain AS s "
"ON sxr.StrainId=s.Id WHERE sxr.InbredSetId=%(inbredset_id)s "
"ORDER BY s.Name ASC",
{"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:
cursor.execute(
"SELECT * FROM CaseAttribute WHERE InbredSetId=%(inbredset_id)s",
{"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."""
with database_connection(current_app.config["SQL_URI"]) as conn:
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"]
if bool(accumulator.get(strain_name)):
return {
**accumulator,
strain_name: {
**accumulator[strain_name],
"case-attributes": {
**accumulator[strain_name]["case-attributes"],
**attr
}
}
}
return {
**accumulator,
strain_name: {
**{
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, ...]:
"""
Retrieve Case-Attributes by their InbredSet ID. Do not call this outside
this module.
"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT ca.Name AS CaseAttributeName, "
"caxrn.Value AS CaseAttributeValue, s.Name AS StrainName, "
"s.Name2 AS StrainName2, s.Symbol, s.Alias "
"FROM CaseAttribute AS ca "
"INNER JOIN CaseAttributeXRefNew AS caxrn "
"ON ca.CaseAttributeId=caxrn.CaseAttributeId "
"INNER JOIN Strain AS s "
"ON caxrn.StrainId=s.Id "
"WHERE ca.InbredSetId=%(inbredset_id)s "
"ORDER BY StrainName",
{"inbredset_id": inbredset_id})
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}
return tuple(
{
"Strain": strain["Name"],
**{
key: data.get(
strain["Name"], {}).get("case-attributes", {}).get(key, "")
for key in fieldnames[1:]
}
} 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 + ({
"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."""
fdesc, filepath = tempfile.mkstemp(".csv")
os.close(fdesc)
with open(filepath, "w", encoding="utf-8") as csvfile:
writer = csv.DictWriter(csvfile, fieldnames=fieldnames, dialect="unix")
writer.writeheader()
writer.writerows(data)
return filepath
def __compute_diff__(
fieldnames: tuple[str, ...],
original_data: tuple[dict, ...],
edit_data: tuple[dict, ...]):
"""Return the diff of the data."""
basefilename = __write_csv__(fieldnames, original_data)
deltafilename = __write_csv__(fieldnames, edit_data)
diff_results = run_cmd(json.dumps(
["csvdiff", basefilename, deltafilename, "--format", "json"]))
os.unlink(basefilename)
os.unlink(deltafilename)
if diff_results["code"] == 0:
return json.loads(diff_results["output"])
return {}
def __queue_diff__(conn: Connection, diff_data, diff_data_dir: Path) -> Path:
"""
Queue diff for future processing.
Returns: `diff`
On success, this will return the filename where the diff was saved.
On failure, it will raise a MySQL error.
"""
diff = diff_data["diff"]
if bool(diff["Additions"]) or bool(diff["Modifications"]) or bool(diff["Deletions"]):
diff_data_dir.mkdir(parents=True, exist_ok=True)
created = datetime.now()
filepath = Path(
diff_data_dir,
f"{diff_data['inbredset_id']}:::{diff_data['user_id']}:::"
f"{created.isoformat()}.json")
with open(filepath, "w", encoding="utf8") as diff_file:
# We want this to fail if the metadata items below are not provided.
the_diff = {**diff_data, "created": created}
insert_id = __save_diff__(conn, the_diff, EditStatus.review)
diff_file.write(json.dumps({**the_diff, "db_id": insert_id},
cls=CAJSONEncoder))
return filepath
raise NoDiffError
def __save_diff__(conn: Connection, diff_data: dict, status: EditStatus) -> int:
"""Save to the database."""
with conn.cursor() as cursor:
cursor.execute(
"INSERT INTO "
"caseattributes_audit(id, status, editor, json_diff_data, time_stamp) "
"VALUES(%(db_id)s, %(status)s, %(editor)s, %(diff)s, %(ts)s) "
"ON DUPLICATE KEY UPDATE status=%(status)s",
{
"db_id": diff_data.get("db_id"),
"status": str(status),
"editor": str(diff_data["user_id"]),
"diff": json.dumps(diff_data, cls=CAJSONEncoder),
"ts": diff_data["created"].isoformat()
})
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)
return {
**raw_diff,
"db_id": int(raw_diff["db_id"]) if raw_diff.get("db_id") else None,
"inbredset_id": (int(raw_diff["inbredset_id"])
if raw_diff.get("inbredset_id") else None),
"user_id": (uuid.UUID(raw_diff["user_id"])
if raw_diff.get("user_id") else None),
"created": (datetime.fromisoformat(raw_diff["created"])
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."""
# 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: tuple[dict, ...] = 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, auth_token, inbredset_id: int, 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.
"""
required_access(auth_token,
inbredset_id,
("system:inbredset:edit-case-attribute",
"system:inbredset:apply-case-attribute-edit"))
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,
auth_token: dict,
inbredset_id: int,
diff_filename: Path,
diff: dict) -> Path:
"""
Reject the changes in the diff at `diff_filename` to the data in the
database if the user has appropriate privileges.
"""
required_access(auth_token,
inbredset_id,
("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}")
os.rename(diff_filename, new_path)
return diff_filename
@caseattr.route("/<int:inbredset_id>/add", methods=["POST"])
@require_token
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]
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]
raise NotImplementedError
@caseattr.route("/<int:inbredset_id>/edit", methods=["POST"])
@require_token
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
:auth_token: A validated JWT from the auth server
"""
with database_connection(current_app.config["SQL_URI"]) as conn:
required_access(auth_token,
inbredset_id,
("system:inbredset:edit-case-attribute",))
fieldnames = tuple(["Strain"] + sorted(
attr["Name"] for attr in
__case_attribute_labels_by_inbred_set__(conn, inbredset_id)))
try:
diff_filename = __queue_diff__(
conn, {
"inbredset_id": inbredset_id,
"user_id": auth_token["jwt"]["sub"],
"fieldnames": fieldnames,
"diff": __compute_diff__(
fieldnames,
__process_orig_data__(
fieldnames,
__case_attribute_values_by_inbred_set__(
conn, inbredset_id),
__inbredset_strains__(conn, inbredset_id)),
__process_edit_data__(
fieldnames, request.json["edit-data"])) # type: ignore[index]
},
Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR))
except NoDiffError as _nde:
msg = "There were no changes to make from submitted data."
response = jsonify({
"diff-status": "error",
"error_description": msg
})
response.status_code = 400
return response
try:
__apply_diff__(conn,
auth_token,
inbredset_id,
diff_filename,
__load_diff__(diff_filename))
return jsonify({
"diff-status": "applied",
"message": ("The changes to the case-attributes have been "
"applied successfully.")
})
except AuthorisationError as _auth_err:
return jsonify({
"diff-status": "queued",
"message": ("The changes to the case-attributes have been "
"queued for approval."),
"diff-filename": str(diff_filename.name)
})
@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."""
Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR).mkdir(
parents=True, exist_ok=True)
def __generate_diff_files__(diffs):
diff_dir = Path(current_app.config["TMPDIR"], CATTR_DIFFS_DIR)
review_files = set(afile.name for afile in diff_dir.iterdir()
if ("-rejected" not in afile.name
and "-approved" not in afile.name))
for diff in diffs:
the_diff = diff["json_diff_data"]
diff_filepath = Path(
diff_dir,
f"{the_diff['inbredset_id']}:::{the_diff['user_id']}:::"
f"{the_diff['created'].isoformat()}.json")
if diff_filepath not in review_files:
with open(diff_filepath, "w", encoding="utf-8") as dfile:
dfile.write(json.dumps(
{**the_diff, "db_id": diff["id"]},
cls=CAJSONEncoder))
with (database_connection(current_app.config["SQL_URI"]) as conn,
conn.cursor(cursorclass=DictCursor) as cursor):
cursor.execute(
"SELECT * FROM caseattributes_audit WHERE status='review'")
diffs = tuple({
**row,
"json_diff_data": {
**__parse_diff_json__(row["json_diff_data"]),
"db_id": row["id"],
"created": row["time_stamp"],
"user_id": uuid.UUID(row["editor"])
}
} for row in cursor.fetchall())
__generate_diff_files__(diffs)
resp = make_response(json.dumps(
tuple({
**diff,
"filename": (
f"{diff['json_diff_data']['inbredset_id']}:::"
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),
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:
"""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)
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:
"""Reject 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:
__reject_diff__(conn,
auth_token,
the_diff["inbredset_id"],
diff_filename,
the_diff)
return jsonify({
"message": "Rejected diff successfully",
"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:
"""View a diff."""
with (database_connection(current_app.config["SQL_URI"]) as conn,
conn.cursor(cursorclass=DictCursor) as cursor):
required_access(
auth_token, inbredset_id, ("system:inbredset:view-case-attribute",))
cursor.execute(
"SELECT * FROM caseattributes_audit WHERE id=%s",
(diff_id,))
diff = cursor.fetchone()
if diff:
json_diff_data = __parse_diff_json__(diff["json_diff_data"])
if json_diff_data["inbredset_id"] != inbredset_id:
return jsonify({
"error": "Not Found",
"error_description": (
"Could not find diff with the given ID for the "
"InbredSet chosen.")
})
return jsonify({
**diff,
"json_diff_data": {
**json_diff_data,
"db_id": diff["id"],
"created": diff["time_stamp"].isoformat(),
"user_id": uuid.UUID(diff["editor"])
}
})
return jsonify({
"error": "Not Found",
"error_description": "Could not find diff with the given ID."
})
return jsonify({
"error": "Code Error",
"error_description": "The code should never run this."
}), 500
|