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
|
"""The views/routes for the resources package"""
from uuid import UUID, uuid4
import json
import operator
import sqlite3
import time
from dataclasses import asdict
from functools import reduce
from werkzeug.exceptions import BadRequest
from authlib.jose import jwt
from authlib.integrations.flask_oauth2.errors import _HTTPException
from flask import (make_response, request, jsonify, Response,
Blueprint, current_app as app)
from gn_auth.auth.db import sqlite3 as db
from gn_auth.auth.db.sqlite3 import with_db_connection
from gn_auth.auth.authorisation.roles import Role
from gn_auth.auth.authorisation.roles.models import (
create_role,
user_resource_roles as _user_resource_roles)
from gn_auth.auth.errors import (
InvalidData,
InconsistencyError,
AuthorisationError)
from gn_auth.auth.authorisation.privileges import (
privilege_by_id,
privileges_by_ids)
from gn_auth.auth.authorisation.roles.models import (
role_by_id,
db_rows_to_roles,
delete_privilege_from_resource_role)
from gn_auth.auth.authentication.oauth2.resource_server import require_oauth
from gn_auth.auth.authentication.users import User, user_by_id, user_by_email
from .checks import authorised_for
from .models import (
Resource, resource_data, resource_by_id, public_resources,
resource_categories, assign_resource_user, link_data_to_resource,
unassign_resource_user, resource_category_by_id, user_roles_on_resources,
unlink_data_from_resource, create_resource as _create_resource,
get_resource_id)
from .groups.models import Group, resource_owner, group_role_by_id
resources = Blueprint("resources", __name__)
@resources.route("/categories", methods=["GET"])
@require_oauth("profile group resource")
def list_resource_categories() -> Response:
"""Retrieve all resource categories"""
db_uri = app.config["AUTH_DB"]
with db.connection(db_uri) as conn:
return jsonify(tuple(
asdict(category) for category in resource_categories(conn)))
@resources.route("/create", methods=["POST"])
@require_oauth("profile group resource")
def create_resource() -> Response:
"""Create a new resource"""
with require_oauth.acquire("profile group resource") as the_token:
form = request.json
resource_name = form.get("resource_name")
resource_category_id = UUID(form.get("resource_category"))
db_uri = app.config["AUTH_DB"]
with db.connection(db_uri) as conn:
try:
resource = _create_resource(
conn,
resource_name,
resource_category_by_id(conn, resource_category_id),
the_token.user,
(form.get("public") == "on"))
return jsonify(asdict(resource))
except sqlite3.IntegrityError as sql3ie:
if sql3ie.args[0] == ("UNIQUE constraint failed: "
"resources.resource_name"):
raise InconsistencyError(
"You cannot have duplicate resource names.") from sql3ie
app.logger.debug(
f"{type(sql3ie)=}: {sql3ie=}")
raise
@resources.route("/view/<uuid:resource_id>")
@require_oauth("profile group resource")
def view_resource(resource_id: UUID) -> Response:
"""View a particular resource's details."""
with require_oauth.acquire("profile group resource") as the_token:
db_uri = app.config["AUTH_DB"]
with db.connection(db_uri) as conn:
return jsonify(
asdict(
resource_by_id(conn, the_token.user, resource_id)
)
)
def __safe_get_requests_page__(key: str = "page") -> int:
"""Get the results page if it exists or default to the first page."""
try:
return abs(int(request.args.get(key, "1"), base=10))
except ValueError as _valerr:
return 1
def __safe_get_requests_count__(key: str = "count_per_page") -> int:
"""Get the results page if it exists or default to the first page."""
try:
count = request.args.get(key, "0")
if count != 0:
return abs(int(count, base=10))
return 0
except ValueError as _valerr:
return 0
@resources.route("/view/<uuid:resource_id>/data")
@require_oauth("profile group resource")
def view_resource_data(resource_id: UUID) -> Response:
"""Retrieve a particular resource's data."""
with require_oauth.acquire("profile group resource") as the_token:
db_uri = app.config["AUTH_DB"]
count_per_page = __safe_get_requests_count__("count_per_page")
offset = (__safe_get_requests_page__("page") - 1)
with db.connection(db_uri) as conn:
resource = resource_by_id(conn, the_token.user, resource_id)
return jsonify(resource_data(
conn,
resource,
((offset * count_per_page) if bool(count_per_page) else offset),
count_per_page))
@resources.route("/data/link", methods=["POST"])
@require_oauth("profile group resource")
def link_data():
"""Link group data to a specific resource."""
try:
form = request.json
assert "resource_id" in form, "Resource ID not provided."
assert "data_link_id" in form, "Data Link ID not provided."
assert "dataset_type" in form, "Dataset type not specified"
assert form["dataset_type"].lower() in (
"mrna", "genotype", "phenotype"), "Invalid dataset type provided."
with require_oauth.acquire("profile group resource") as the_token:
def __link__(conn: db.DbConnection):
return link_data_to_resource(
conn, the_token.user, UUID(form["resource_id"]),
form["dataset_type"], UUID(form["data_link_id"]))
return jsonify(with_db_connection(__link__))
except AssertionError as aserr:
raise InvalidData(aserr.args[0]) from aserr
@resources.route("/data/unlink", methods=["POST"])
@require_oauth("profile group resource")
def unlink_data():
"""Unlink data bound to a specific resource."""
try:
form = request.json
assert "resource_id" in form, "Resource ID not provided."
assert "data_link_id" in form, "Data Link ID not provided."
with require_oauth.acquire("profile group resource") as the_token:
def __unlink__(conn: db.DbConnection):
return unlink_data_from_resource(
conn, the_token.user, UUID(form["resource_id"]),
UUID(form["data_link_id"]))
return jsonify(with_db_connection(__unlink__))
except AssertionError as aserr:
raise InvalidData(aserr.args[0]) from aserr
@resources.route("<uuid:resource_id>/user/list", methods=["GET"])
@require_oauth("profile group resource")
def resource_users(resource_id: UUID):
"""Retrieve all users with access to the given resource."""
with require_oauth.acquire("profile group resource") as the_token:
def __the_users__(conn: db.DbConnection):
########## BEGIN: HACK ##########
# This hack gets the UI to work, but needs replacing.
# It resolves (albeit, temporarily) the bug introduced after a
# refactor that made the system itself, and the groups into
# resources.
grouplevelauth = authorised_for(
conn,
the_token.user,
("group:resource:view-resource",),
(resource_id,))
systemlevelauth = authorised_for(
conn,
the_token.user,
("system:user:list",),
(resource_id,))
authorised = {
key: (grouplevelauth.get(key, False)
or systemlevelauth.get(key, False))
for key in grouplevelauth.keys() | systemlevelauth.keys()
}
########## END: HACK ##########
if authorised.get(resource_id, False):
with db.cursor(conn) as cursor:
def __organise_users_n_roles__(users_n_roles, row):
user_id = UUID(row["user_id"])
user = users_n_roles.get(user_id, {}).get(
"user", User.from_sqlite3_row(row))
role = Role(
UUID(row["role_id"]), row["role_name"],
bool(int(row["user_editable"])), tuple())
return {
**users_n_roles,
user_id: {
"user": user,
"user_group": Group(
UUID(row["group_id"]), row["group_name"],
json.loads(row["group_metadata"])),
"roles": users_n_roles.get(
user_id, {}).get("roles", tuple()) + (role,)
}
}
cursor.execute(
"SELECT g.*, u.*, r.* "
"FROM groups AS g INNER JOIN group_users AS gu "
"ON g.group_id=gu.group_id INNER JOIN users AS u "
"ON gu.user_id=u.user_id INNER JOIN user_roles AS ur "
"ON u.user_id=ur.user_id INNER JOIN roles AS r "
"ON ur.role_id=r.role_id "
"WHERE ur.resource_id=?",
(str(resource_id),))
return reduce(__organise_users_n_roles__, cursor.fetchall(), {})
raise AuthorisationError(
"You do not have sufficient privileges to view the resource "
"users.")
results = (
{
"user": asdict(row["user"]),
"user_group": asdict(row["user_group"]),
"roles": tuple(asdict(role) for role in row["roles"])
} for row in (
user_row for user_id, user_row
in with_db_connection(__the_users__).items()))
return jsonify(tuple(results))
@resources.route("<uuid:resource_id>/user/assign", methods=["POST"])
@require_oauth("profile group resource role")
def assign_role_to_user(resource_id: UUID) -> Response:
"""Assign a role on the specified resource to a user."""
with require_oauth.acquire("profile group resource role") as the_token:
try:
form = request.json
group_role_id = form.get("group_role_id", "")
user_email = form.get("user_email", "")
assert bool(group_role_id), "The role must be provided."
assert bool(user_email), "The user email must be provided."
def __assign__(conn: db.DbConnection) -> dict:
resource = resource_by_id(conn, the_token.user, resource_id)
user = user_by_email(conn, user_email)
return assign_resource_user(
conn, resource, user,
group_role_by_id(conn,
resource_owner(conn, resource),
UUID(group_role_id)))
except AssertionError as aserr:
raise AuthorisationError(aserr.args[0]) from aserr
return jsonify(with_db_connection(__assign__))
@resources.route("<uuid:resource_id>/user/unassign", methods=["POST"])
@require_oauth("profile group resource role")
def unassign_role_to_user(resource_id: UUID) -> Response:
"""Unassign a role on the specified resource from a user."""
with require_oauth.acquire("profile group resource role") as the_token:
try:
form = request.json
group_role_id = form.get("group_role_id", "")
user_id = form.get("user_id", "")
assert bool(group_role_id), "The role must be provided."
assert bool(user_id), "The user id must be provided."
def __assign__(conn: db.DbConnection) -> dict:
resource = resource_by_id(conn, the_token.user, resource_id)
return unassign_resource_user(
conn, resource, user_by_id(conn, UUID(user_id)),
group_role_by_id(conn,
resource_owner(conn, resource),
UUID(group_role_id)))
except AssertionError as aserr:
raise AuthorisationError(aserr.args[0]) from aserr
return jsonify(with_db_connection(__assign__))
def __public_view_params__(cursor, user_id, resource_id):
ignore = (str(user_id),)
# sys admins
cursor.execute(
"SELECT ur.user_id FROM user_roles AS ur INNER JOIN roles AS r "
"ON ur.role_id=r.role_id WHERE r.role_name='system-administrator'")
ignore = ignore + tuple(
row["user_id"] for row in cursor.fetchall())
# group admins
cursor.execute(
"SELECT DISTINCT gu.user_id FROM resource_ownership AS ro "
"INNER JOIN groups AS g ON ro.group_id=g.group_id "
"INNER JOIN group_users AS gu ON g.group_id=gu.group_id "
"INNER JOIN user_roles AS ur ON gu.user_id=ur.user_id "
"INNER JOIN roles AS r ON ur.role_id=r.role_id "
"WHERE ro.resource_id=? AND r.role_name='group-leader'",
(str(resource_id),))
ignore = tuple(set(
ignore + tuple(row["user_id"] for row in cursor.fetchall())))
cursor.execute(
"SELECT user_id FROM users WHERE user_id NOT IN "
f"({', '.join(['?'] * len(ignore))})",
ignore)
user_ids = tuple(row["user_id"] for row in cursor.fetchall())
cursor.execute(
"SELECT role_id FROM roles WHERE role_name='public-view'")
role_id = cursor.fetchone()["role_id"]
return tuple({
"user_id": user_id,
"role_id": role_id,
"resource_id": str(resource_id)
} for user_id in user_ids)
def __assign_revoke_public_view__(cursor, user_id, resource_id, public):
if public:
cursor.executemany(
"INSERT INTO user_roles(user_id, role_id, resource_id) "
"VALUES(:user_id, :role_id, :resource_id) "
"ON CONFLICT (user_id, role_id, resource_id) "
"DO NOTHING",
__public_view_params__(cursor, user_id, resource_id))
return
cursor.executemany(
"DELETE FROM user_roles WHERE user_id=:user_id "
"AND role_id=:role_id AND resource_id=:resource_id",
__public_view_params__(cursor, user_id, resource_id))
@resources.route("<uuid:resource_id>/toggle-public", methods=["POST"])
@require_oauth("profile group resource role")
def toggle_public(resource_id: UUID) -> Response:
"""Make a resource public if it is private, or private if public."""
with require_oauth.acquire("profile group resource") as the_token:
def __toggle__(conn: db.DbConnection) -> Resource:
old_rsc = resource_by_id(conn, the_token.user, resource_id)
public = not old_rsc.public
new_resource = Resource(
old_rsc.resource_id, old_rsc.resource_name,
old_rsc.resource_category, public,
old_rsc.resource_data)
with db.cursor(conn) as cursor:
cursor.execute(
"UPDATE resources SET public=:public "
"WHERE resource_id=:resource_id",
{
"public": 1 if public else 0,
"resource_id": str(resource_id)
})
__assign_revoke_public_view__(
cursor, the_token.user.user_id, resource_id, public)
return new_resource
return new_resource
resource = with_db_connection(__toggle__)
return jsonify({
"resource": asdict(resource),
"description": (
"Made resource public" if resource.public
else "Made resource private")})
@resources.route("<uuid:resource_id>/roles", methods=["GET"])
@require_oauth("profile group resource role")
def resource_roles(resource_id: UUID) -> Response:
"""Return the roles the user has to act on a given resource."""
with require_oauth.acquire("profile group resource role") as _token:
def __roles__(conn: db.DbConnection) -> tuple[Role, ...]:
with db.cursor(conn) as cursor:
cursor.execute(
"SELECT r.*, p.* FROM resource_roles AS rr "
"INNER JOIN roles AS r ON rr.role_id=r.role_id "
"INNER JOIN role_privileges AS rp ON r.role_id=rp.role_id "
"INNER JOIN privileges AS p "
"ON rp.privilege_id=p.privilege_id "
"WHERE rr.resource_id=? AND rr.role_created_by=?",
(str(resource_id), str(_token.user.user_id)))
results = cursor.fetchall()
return db_rows_to_roles(results)
return jsonify(with_db_connection(__roles__))
@resources.route("/authorisation", methods=["POST"])
def resources_authorisation():
"""Get user authorisations for given resource(s):"""
try:
data = request.json
assert (data and "resource-ids" in data)
resource_ids = tuple(UUID(resid) for resid in data["resource-ids"])
pubres = tuple(
res.resource_id for res in with_db_connection(public_resources)
if res.resource_id in resource_ids)
with require_oauth.acquire("profile resource") as the_token:
the_resources = with_db_connection(lambda conn: user_roles_on_resources(
conn, the_token.user, resource_ids))
resp = jsonify({
str(resid): {
"public-read": resid in pubres,
"roles": tuple(
asdict(rol) for rol in
the_resources.get(resid, {}).get("roles", tuple()))
} for resid in resource_ids
})
except _HTTPException as _httpe:
err_msg = json.loads(_httpe.body)
if err_msg["error"] == "missing_authorization":
resp = jsonify({
str(resid): {
"public-read": resid in pubres
} for resid in resource_ids
})
except AssertionError as _aerr:
resp = jsonify({
"status": "bad-request",
"error_description": (
"Expected a JSON object with a 'resource-ids' key.")
})
resp.status_code = 400
return resp
@resources.route("/authorisation/<name>", methods=["GET"])
def get_user_roles_on_resource(name) -> Response:
"""Get user authorisation for a given resource given it's name"""
resid = with_db_connection(
lambda conn: get_resource_id(conn, name)
)
def _extract_privilege_id(privileges):
return tuple(
p_.privilege_id for p_ in privileges
)
with require_oauth.acquire("profile resource") as _token:
resources_ = with_db_connection(
lambda conn: user_roles_on_resources(
conn, _token.user, (resid,)
)
)
roles: list = reduce (operator.iconcat,
tuple(
_extract_privilege_id(role.privileges)
for role in
resources_.get(
UUID(resid), {}
).get("roles", tuple())), [])
response = make_response({
# Flatten this list
"roles": roles,
"silly": "ausah",
})
iat = int(time.time())
jose_header = {
"alg": "RS256",
"typ": "jwt",
"cty": "json",
}
payload = {
# Registered Claims
"iss": request.url, # Issuer Claim
"iat": iat, # Issued At
"sub": name, # Subject Claim
"aud": f"Edit {name}", # Audience Claim
"exp": iat + 300, # Expiration Time Claim
"jti": str(uuid4()), # Unique Identifier for this token
# Private Claims
"account-name": _token.user.name,
"email": _token.user.email,
"roles": roles,
}
token = jwt.encode(jose_header, payload, app.config["SSL_PRIVATE_KEY"])
response.headers["Authorization"] = f"Bearer {token.decode('utf-8')}"
return response
@resources.route("/<uuid:resource_id>/role/<uuid:role_id>", methods=["GET"])
@require_oauth("profile group resource")
def resource_role(resource_id: UUID, role_id: UUID):
"""Fetch details for resource."""
with (require_oauth.acquire("profile group resource") as _token,
db.connection(app.config["AUTH_DB"]) as conn,
db.cursor(conn) as cursor):
cursor.execute(
"SELECT rr.role_created_by, r.*, p.* FROM resource_roles AS rr "
"INNER JOIN roles AS r ON rr.role_id=r.role_id "
"INNER JOIN role_privileges AS rp ON r.role_id=rp.role_id "
"INNER JOIN privileges AS p ON rp.privilege_id=p.privilege_id "
"WHERE rr.resource_id=? AND rr.role_created_by=? AND rr.role_id=?",
(str(resource_id), str(_token.user.user_id), str(role_id)))
results = cursor.fetchall()
if not bool(results):
msg = f"Could not find role with ID '{role_id}'."
return jsonify({
"error": "RoleNotFound",
"error_description": msg,
"error_message": msg,
"message": msg
}), 404
_roles = db_rows_to_roles(results)
if len(_roles) > 1:
msg = "There is data corruption in the database."
return jsonify({
"error": "RoleNotFound",
"error_description": msg,
"error_message": msg,
"message": msg
}), 500
return asdict(_roles[0])
@resources.route("/<uuid:resource_id>/role/<uuid:role_id>/unassign-privilege",
methods=["POST"])
@require_oauth("profile group resource")
def unassign_resource_role_privilege(resource_id: UUID, role_id: UUID):
"""Unassign a privilege from a resource role."""
with (require_oauth.acquire("profile group resource") as _token,
db.connection(app.config["AUTH_DB"]) as conn,
db.cursor(conn) as cursor):
_role = role_by_id(conn, role_id)
_authorised = authorised_for(
conn,
_token.user,
privileges=("resource:role:edit-role",),
resource_ids=(resource_id,)).get(resource_id)
if not _authorised:
raise AuthorisationError(
"You are not authorised to edit/update this role.")
# Actually unassign the privilege from the role
privilege_id = request.json.get("privilege_id")
if not privilege_id:
raise AuthorisationError(
"You need to provide a privilege to unassign")
delete_privilege_from_resource_role(cursor,
_role,
privilege_by_id(conn, privilege_id))
return jsonify({
"status": "Success",
"message": "Privilege was unassigned."
}), 200
@resources.route("/<uuid:resource_id>/role/<uuid:role_id>/users",
methods=["GET"])
@require_oauth("profile group resource")
def resource_role_users(resource_id: UUID, role_id: UUID):
"""Retrieve users assigned role on resource."""
with (require_oauth.acquire("profile group resource") as _token,
db.connection(app.config["AUTH_DB"]) as conn,
db.cursor(conn) as cursor):
# MAYBE: check user has something like resource:role:view-users
cursor.execute(
"SELECT u.* FROM user_roles AS ur INNER JOIN users AS u "
"ON ur.user_id=u.user_id WHERE ur.resource_id=? AND ur.role_id=?",
(str(resource_id), str(role_id)))
results = cursor.fetchall() or []
return jsonify(tuple(User.from_sqlite3_row(row) for row in results)), 200
@resources.route("/<uuid:resource_id>/roles/create", methods=["POST"])
@require_oauth("profile group resource")
def create_resource_role(resource_id: UUID):
"""Create a role to act upon a specific resource."""
role_name = request.json.get("role_name", "").strip()
if not bool(role_name):
raise BadRequest("You must provide the name for the new role.")
with (require_oauth.acquire("profile group resource") as _token,
db.connection(app.config["AUTH_DB"]) as conn,
db.cursor(conn) as cursor):
resource = resource_by_id(conn, _token.user, resource_id)
if not bool(resource):
raise BadRequest("No resource with that ID exists.")
privileges = privileges_by_ids(conn, request.json.get("privileges", []))
if len(privileges) == 0:
raise BadRequest(
"You must provide at least one privilege for the new role.")
role = create_role(cursor,
f"{resource.resource_name}::{role_name}",
privileges)
cursor.execute(
"INSERT INTO resource_roles(resource_id, role_created_by, role_id) "
"VALUES (:resource_id, :user_id, :role_id)",
{
"resource_id": str(resource_id),
"user_id": str(_token.user.user_id),
"role_id": str(role.role_id)
})
return jsonify(asdict(role))
@resources.route("/<uuid:resource_id>/users/<uuid:user_id>/roles", methods=["GET"])
@require_oauth("profile group resource role")
def user_resource_roles(resource_id: UUID, user_id: UUID):
"""Get a specific user's roles on a particular resource."""
with (require_oauth.acquire("profile group resource") as _token,
db.connection(app.config["AUTH_DB"]) as conn):
if _token.user.user_id != user_id:
raise AuthorisationError(
"You are not authorised to view the roles this user has.")
_resource = resource_by_id(conn, _token.user, resource_id)
if not bool(_resource):
raise BadRequest("No resource was found with the given ID.")
return jsonify([asdict(role) for role in
_user_resource_roles(conn, _token.user, _resource)])
|