ProteinsWebTeam / interpro7-api / 1

Committed 18 Jun 2024 09:19AM UTC coverage: 25.541% (-68.5%) from 94.023%

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push

github

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web-flow

Commit Message

Merge pull request #147 from ProteinsWebTeam/set-sortable

sort by in sets

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20.74

/webfront/tests/tests_modifiers.py

1	import unittest	2✔
2	import gzip	2✔
3	import json	2✔
4	from webfront.tests.InterproRESTTestCase import InterproRESTTestCase	2✔
5	from rest_framework import status	2✔
6	import ssl	2✔
7
8	ssl._create_default_https_context = ssl._create_unverified_context	2✔
9
10
11	class GroupByModifierTest(InterproRESTTestCase):	2✔
12	def test_can_get_the_entry_type_groups(self):	2✔
UNCOV 13	response = self.client.get("/api/entry?group_by=type")	×
UNCOV 14	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 15	self.assertIn("domain", response.data)	×
UNCOV 16	self.assertIn("family", response.data)	×
17
18	def test_can_get_the_entry_type_groups_of_entries_with_proteins(self):	2✔
UNCOV 19	response = self.client.get("/api/entry/protein?group_by=type")	×
UNCOV 20	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 21	self.assertIn("domain", response.data)	×
UNCOV 22	self.assertNotIn("family", response.data)	×
23
24	def test_can_get_the_entry_type_groups_proteins_by_tax_id(self):	2✔
UNCOV 25	response = self.client.get("/api/protein?group_by=tax_id")	×
UNCOV 26	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
27	# Only Mus musculus is a key species
UNCOV 28	self.assertEqual(	×
29	{"10090": {"value": 1, "title": "Mus musculus"}}, response.data
30	)
31
32	def test_can_group_interpro_entries_with_member_databases(self):	2✔
UNCOV 33	response = self.client.get("/api/entry/interpro?group_by=member_databases")	×
UNCOV 34	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 35	self.assertIn("pfam", response.data)	×
UNCOV 36	self.assertIn("smart", response.data)	×
UNCOV 37	self.assertIn("profile", response.data)	×
38
39	def test_wrong_field_for_group_by_should_fail(self):	2✔
UNCOV 40	self._check_HTTP_response_code(	×
41	"/api/entry?group_by=entry_type", code=status.HTTP_404_NOT_FOUND
42	)
43
44	def test_can_get_the_match_presence_groups(self):	2✔
UNCOV 45	response = self.client.get("/api/protein?group_by=match_presence")	×
UNCOV 46	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 47	self.assertIn("match_presence", response.data)	×
UNCOV 48	self.assertIn("true", response.data["match_presence"])	×
UNCOV 49	self.assertIn("false", response.data["match_presence"])	×
UNCOV 50	self.assertEqual(response.data["match_presence"]["true"], 3)	×
UNCOV 51	self.assertEqual(response.data["match_presence"]["false"], 2)	×
52
53	def test_can_get_the_fragment_groups(self):	2✔
UNCOV 54	response = self.client.get("/api/protein?group_by=is_fragment")	×
UNCOV 55	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 56	self.assertIn("is_fragment", response.data)	×
UNCOV 57	self.assertIn("true", response.data["is_fragment"])	×
UNCOV 58	self.assertIn("false", response.data["is_fragment"])	×
UNCOV 59	self.assertEqual(response.data["is_fragment"]["true"], 1)	×
UNCOV 60	self.assertEqual(response.data["is_fragment"]["false"], 2)	×
61
62	def test_can_group_proteomes_by_is_reference(self):	2✔
UNCOV 63	response = self.client.get(	×
64	"/api/proteome/uniprot?group_by=proteome_is_reference"
65	)
UNCOV 66	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 67	self.assertIn("proteome_is_reference", response.data)	×
UNCOV 68	self.assertIn("true", response.data["proteome_is_reference"])	×
UNCOV 69	self.assertIn("false", response.data["proteome_is_reference"])	×
UNCOV 70	self.assertEqual(response.data["proteome_is_reference"]["true"], 2)	×
UNCOV 71	self.assertEqual(response.data["proteome_is_reference"]["false"], 1)	×
72
73
74	class FilterByFieldModifierTest(InterproRESTTestCase):	2✔
75	def test_can_filter_pfam_by_integrated(self):	2✔
UNCOV 76	acc = "IPR003165"	×
UNCOV 77	response = self.client.get("/api/entry/pfam?integrated=" + acc)	×
UNCOV 78	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 79	self.assertIn("count", response.data)	×
UNCOV 80	self.assertEqual(response.data["count"], 1)	×
UNCOV 81	self.assertIn("results", response.data)	×
UNCOV 82	for result in response.data["results"]:	×
UNCOV 83	self.assertEqual(result["metadata"]["integrated"].lower(), acc.lower())	×
84
85	def test_fails_filtering_interpro_by_integrated(self):	2✔
UNCOV 86	self._check_HTTP_response_code(	×
87	"/api/entry/interpro?integrated=IPR003165", code=status.HTTP_204_NO_CONTENT
88	)
89
90	def test_can_filter_smart_by_type(self):	2✔
UNCOV 91	entry_types = ["family", "domain"]	×
UNCOV 92	for entry_type in entry_types:	×
UNCOV 93	response = self.client.get("/api/entry/smart?type=" + entry_type)	×
UNCOV 94	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 95	self.assertIn("count", response.data)	×
UNCOV 96	self.assertEqual(response.data["count"], 1)	×
UNCOV 97	self.assertIn("results", response.data)	×
UNCOV 98	for result in response.data["results"]:	×
UNCOV 99	self.assertEqual(result["metadata"]["type"], entry_type)	×
100
101	def test_can_filter_proteins_by_match_presence(self):	2✔
UNCOV 102	options = ["true", "false"]	×
UNCOV 103	for option in options:	×
UNCOV 104	response = self.client.get(	×
105	"/api/protein/uniprot?extra_fields=counters&match_presence=" + option
106	)
UNCOV 107	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 108	self.assertIn("results", response.data)	×
UNCOV 109	for result in response.data["results"]:	×
UNCOV 110	entries = result["extra_fields"]["counters"]["entries"]	×
UNCOV 111	if option == "true":	×
UNCOV 112	self.assertGreater(entries, 0)	×
113	else:
UNCOV 114	self.assertEqual(entries, 0)	×
115
116	def test_can_filter_proteins_by_is_fragment(self):	2✔
UNCOV 117	urls = ["protein/uniprot", "protein/uniprot/entry"]	×
UNCOV 118	for url in urls:	×
UNCOV 119	options = [True, False]	×
UNCOV 120	for option in options:	×
UNCOV 121	response = self.client.get(	×
122	"/api/{}?extra_fields=is_fragment&is_fragment={}".format(
123	url, option
124	)
125	)
UNCOV 126	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 127	self.assertIn("results", response.data)	×
UNCOV 128	for result in response.data["results"]:	×
UNCOV 129	is_fragment = result["extra_fields"]["is_fragment"]	×
UNCOV 130	self.assertEqual(is_fragment, option)	×
131
132
133	class FilterByContainsFieldModifierTest(InterproRESTTestCase):	2✔
134	def test_can_filter_pfam_by_signature_in(self):	2✔
UNCOV 135	db = "pfam"	×
UNCOV 136	response = self.client.get("/api/entry/interpro?signature_in=" + db)	×
UNCOV 137	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 138	self.assertIn("count", response.data)	×
UNCOV 139	self.assertEqual(response.data["count"], 1)	×
UNCOV 140	self.assertIn("results", response.data)	×
UNCOV 141	for result in response.data["results"]:	×
UNCOV 142	self.assertIn(db, result["metadata"]["member_databases"])	×
143
144
145	@unittest.skip	2✔
146	class SortByModifierTest(InterproRESTTestCase):	2✔
147	def test_can_sort_pfam_by_accession(self):	2✔
148	response = self.client.get("/api/entry/pfam?sort_by=accession")	×
149	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
150	self.assertIn("results", response.data)	×
151	payload_accs = [r["metadata"]["accession"] for r in response.data["results"]]	×
152	self.assertEqual(payload_accs, sorted(payload_accs))	×
153
154	def test_can_sort_pfam_by_integrated_and_reverse_sorting(self):	2✔
155	response = self.client.get("/api/entry/pfam?sort_by=integrated")	×
156	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
157	self.assertIn("results", response.data)	×
158	payload_accs = [r["metadata"]["integrated"] for r in response.data["results"]]	×
159	response = self.client.get("/api/entry/pfam?sort_by=-integrated")	×
160	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
161	self.assertIn("results", response.data)	×
162	payload_accs_rev = [	×
163	r["metadata"]["integrated"] for r in response.data["results"]
164	]
165	self.assertEqual(payload_accs_rev, list(reversed(payload_accs)))	×
166
167
168	class InterProStatusModifierTest(InterproRESTTestCase):	2✔
169	def test_can_apply_interpro_status(self):	2✔
UNCOV 170	mdbs = ["profile", "smart", "pfam"]	×
UNCOV 171	for db in mdbs:	×
UNCOV 172	response = self.client.get("/api/entry/" + db)	×
UNCOV 173	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 174	self.assertIn("results", response.data)	×
UNCOV 175	unintegrated = len(	×
176	[
177	r["metadata"]["integrated"]
178	for r in response.data["results"]
179	if r["metadata"]["integrated"] is None
180	]
181	)
UNCOV 182	response2 = self.client.get("/api/entry/" + db + "?interpro_status")	×
UNCOV 183	self.assertEqual(response2.status_code, status.HTTP_200_OK)	×
UNCOV 184	self.assertEqual(response2.data["unintegrated"], unintegrated)	×
UNCOV 185	self.assertEqual(	×
186	response2.data["integrated"],
187	len(response.data["results"]) - unintegrated,
188	)
189
190
191	class IDAModifiersTest(InterproRESTTestCase):	2✔
192	def test_ida_modifier(self):	2✔
UNCOV 193	response = self.client.get("/api/entry/interpro/IPR001165?ida")	×
UNCOV 194	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 195	self.assertIn("results", response.data)	×
UNCOV 196	self.assertIn("count", response.data)	×
UNCOV 197	self.assertEqual(response.data["count"], len(response.data["results"]))	×
198
199	def test_filter_by_ida_modifier(self):	2✔
UNCOV 200	response = self.client.get("/api/protein/uniprot?ida=50134")	×
UNCOV 201	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 202	self.assertIn("results", response.data)	×
UNCOV 203	self.assertIn("count", response.data)	×
UNCOV 204	self.assertEqual(response.data["count"], 1)	×
UNCOV 205	self.assertEqual(	×
206	"a1cuj5", response.data["results"][0]["metadata"]["accession"].lower()
207	)
208
209
210	class ExtraFieldsModifierTest(InterproRESTTestCase):	2✔
211	fields = {	2✔
212	"entry": [
213	"entry_id",
214	"accession",
215	"type",
216	"name",
217	"short_name",
218	"source_database",
219	"member_databases",
220	"go_terms",
221	"description",
222	"wikipedia",
223	"literature",
224	"hierarchy",
225	"cross_references",
226	"entry_date",
227	],
228	"protein": [
229	"accession",
230	"identifier",
231	"organism",
232	"name",
233	"description",
234	"sequence",
235	"length",
236	"proteome",
237	"gene",
238	"go_terms",
239	"evidence_code",
240	"source_database",
241	"structure",
242	"is_fragment",
243	"tax_id",
244	],
245	"structure": [
246	"accession",
247	"name",
248	"experiment_type",
249	"release_date",
250	"literature",
251	"chains",
252	"source_database",
253	"resolution",
254	],
255	"taxonomy": [
256	"accession",
257	"scientific_name",
258	"full_name",
259	"lineage",
260	"rank",
261	"children",
262	],
263	"proteome": ["accession", "strain", "is_reference", "assembly"],
264	"set": ["accession", "name", "description", "source_database", "relationships"],
265	}
266	list_url = {	2✔
267	"entry": "/entry/interpro",
268	"protein": "/protein/uniprot",
269	"structure": "/structure/pdb",
270	"taxonomy": "/taxonomy/uniprot",
271	"proteome": "/proteome/uniprot",
272	"set": "/set/pfam",
273	}
274
275	def test_extra_fields(self):	2✔
UNCOV 276	for endpoint in self.fields:	×
UNCOV 277	for field in self.fields[endpoint]:	×
UNCOV 278	url = "/api{}?extra_fields={}".format(self.list_url[endpoint], field)	×
UNCOV 279	response = self.client.get(url)	×
UNCOV 280	self.assertEqual(response.status_code, status.HTTP_200_OK, url)	×
UNCOV 281	self.assertIn("results", response.data)	×
UNCOV 282	for result in response.data["results"]:	×
UNCOV 283	self.assertIn("extra_fields", result)	×
UNCOV 284	self.assertIn(field, result["extra_fields"])	×
UNCOV 285	url = "/api{}?extra_fields=ERROR".format(self.list_url[endpoint])	×
UNCOV 286	response = self.client.get(url)	×
UNCOV 287	self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND)	×
288
289	def test_extra_fields_together(self):	2✔
UNCOV 290	for endpoint in self.fields:	×
UNCOV 291	url = "/api{}?extra_fields={}".format(	×
292	self.list_url[endpoint], ",".join(self.fields[endpoint])
293	)
UNCOV 294	response = self.client.get(url)	×
UNCOV 295	self.assertEqual(response.status_code, status.HTTP_200_OK, url)	×
UNCOV 296	self.assertIn("results", response.data)	×
UNCOV 297	for field in self.fields[endpoint]:	×
UNCOV 298	for result in response.data["results"]:	×
UNCOV 299	self.assertIn("extra_fields", result)	×
UNCOV 300	self.assertIn(field, result["extra_fields"])	×
UNCOV 301	url = "/api{}?extra_fields=name,ERROR".format(self.list_url[endpoint])	×
UNCOV 302	response = self.client.get(url)	×
UNCOV 303	self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND)	×
304
305	def test_extra_fields_with_other_endpoint(self):	2✔
UNCOV 306	for endpoint in self.fields:	×
UNCOV 307	other_ep = [ep for ep in self.fields if ep != endpoint]	×
UNCOV 308	for ep in other_ep:	×
UNCOV 309	for field in self.fields[endpoint]:	×
UNCOV 310	url = "/api{}/{}?extra_fields={}".format(	×
311	self.list_url[endpoint], ep, field
312	)
UNCOV 313	response = self.client.get(url)	×
UNCOV 314	if response.status_code == status.HTTP_200_OK:	×
UNCOV 315	self.assertIn("results", response.data)	×
UNCOV 316	for result in response.data["results"]:	×
UNCOV 317	self.assertIn("extra_fields", result)	×
UNCOV 318	self.assertIn(field, result["extra_fields"])	×
319	else:
UNCOV 320	self.assertEqual(	×
321	response.status_code, status.HTTP_204_NO_CONTENT
322	)
UNCOV 323	url = "/api{}/{}?extra_fields=name,ERROR".format(	×
324	self.list_url[endpoint], ep
325	)
UNCOV 326	response = self.client.get(url)	×
UNCOV 327	self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND)	×
328
329	accession = {	2✔
330	"entry": "IPR003165",
331	"protein": "a1cuj5",
332	"structure": "1jm7",
333	"taxonomy": "2579",
334	"proteome": "up000006701",
335	"set": "cl0001",
336	}
337
338	def test_counters_as_extra_fields(self):	2✔
UNCOV 339	for endpoint1, path1 in self.list_url.items():	×
UNCOV 340	for endpoint2, path2 in self.list_url.items():	×
UNCOV 341	if endpoint1 == endpoint2:	×
UNCOV 342	continue	×
UNCOV 343	url = f"/api{path1}{path2}/{self.accession[endpoint2]}?extra_fields=counters"	×
UNCOV 344	response = self.client.get(url)	×
UNCOV 345	if response.status_code == status.HTTP_200_OK:	×
UNCOV 346	self.assertIn("results", response.data)	×
UNCOV 347	for result in response.data["results"]:	×
UNCOV 348	self.assertIn("extra_fields", result)	×
UNCOV 349	self.assertIn("counters", result["extra_fields"])	×
UNCOV 350	self.assertGreater(	×
351	len(result["extra_fields"]["counters"].keys()), 1
352	)
353	else:
UNCOV 354	self.assertEqual(	×
355	response.status_code,
356	status.HTTP_204_NO_CONTENT,
357	f"ERROR CODE [{response.status_code}]: {url}",
358	)
359
360	def test_granular_counters_as_extra_fields(self):	2✔
UNCOV 361	counters_to_ask = [	×
362	["entry"],
363	["protein"],
364	["entry", "protein"],
365	]
UNCOV 366	for endpoint1, path1 in self.list_url.items():	×
UNCOV 367	for endpoint2, path2 in self.list_url.items():	×
UNCOV 368	for counters in counters_to_ask:	×
UNCOV 369	if (	×
370	endpoint1 == endpoint2
371	or endpoint1 in counters
372	or endpoint2 in counters
373	):
UNCOV 374	continue	×
UNCOV 375	url = f"/api{path1}{path2}/{self.accession[endpoint2]}?extra_fields=counters:{'-'.join(counters)}"	×
UNCOV 376	response = self.client.get(url)	×
UNCOV 377	if response.status_code == status.HTTP_200_OK:	×
UNCOV 378	self.assertIn("results", response.data)	×
UNCOV 379	for result in response.data["results"]:	×
UNCOV 380	self.assertIn("extra_fields", result)	×
UNCOV 381	self.assertIn("counters", result["extra_fields"])	×
382	# It should be equal to the counters requested
UNCOV 383	self.assertEqual(	×
384	len(result["extra_fields"]["counters"].keys()),
385	len(counters),
386	)
387	else:
UNCOV 388	self.assertEqual(	×
389	response.status_code,
390	status.HTTP_204_NO_CONTENT,
391	f"ERROR CODE [{response.status_code}]: {url}",
392	)
393
394
395	class ExtraFeaturesModifierTest(InterproRESTTestCase):	2✔
396	def test_extra_features_modifier_is_different_than_acc_protein(self):	2✔
UNCOV 397	response1 = self.client.get("/api/protein/uniprot/a1cuj5")	×
UNCOV 398	self.assertEqual(response1.status_code, status.HTTP_200_OK)	×
UNCOV 399	response2 = self.client.get("/api/protein/uniprot/a1cuj5?extra_features")	×
UNCOV 400	self.assertEqual(response2.status_code, status.HTTP_200_OK)	×
UNCOV 401	self.assertNotEquals(response1.data, response2.data)	×
402
403	def test_extra_features_modifier(self):	2✔
UNCOV 404	response2 = self.client.get("/api/protein/uniprot/a1cuj5?extra_features")	×
UNCOV 405	self.assertEqual(response2.status_code, status.HTTP_200_OK)	×
UNCOV 406	self.assertIn("TMhelix", response2.data)	×
UNCOV 407	self.assertIn("locations", response2.data["TMhelix"])	×
408
409
410	class IsoformsModifiersTest(InterproRESTTestCase):	2✔
411	def test_isoform_modifier(self):	2✔
UNCOV 412	response = self.client.get("/api/protein/uniprot/a1cuj5?isoforms")	×
UNCOV 413	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 414	self.assertIn("results", response.data)	×
UNCOV 415	self.assertIn("count", response.data)	×
UNCOV 416	self.assertEqual(response.data["count"], len(response.data["results"]))	×
UNCOV 417	self.assertGreater(response.data["count"], 0)	×
418
419	def test_isoform_detail_modifier(self):	2✔
UNCOV 420	response = self.client.get("/api/protein/uniprot/a1cuj5?isoforms=a1cuj5-2")	×
UNCOV 421	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 422	self.assertIn("accession", response.data)	×
UNCOV 423	self.assertIn("features", response.data)	×
424
425	def test_isoform_detail_wrong_acc_modifier(self):	2✔
UNCOV 426	response = self.client.get("/api/protein/uniprot/a1cuj5?isoforms=wrong")	×
UNCOV 427	self.assertEqual(response.status_code, status.HTTP_204_NO_CONTENT)	×
428
429
430	class LatestEntriesModifiersTest(InterproRESTTestCase):	2✔
431	def test_can_read_entry_interpro_new_entries(self):	2✔
UNCOV 432	response = self.client.get("/api/entry/interpro?latest_entries")	×
UNCOV 433	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 434	self.assertEqual(len(response.data["results"]), 1)	×
UNCOV 435	self._check_is_list_of_objects_with_key(response.data["results"], "metadata")	×
UNCOV 436	self.assertEqual(	×
437	response.data["results"][0]["metadata"]["accession"], "IPR003165"
438	)
439
440
441	class EntryAnnotationModifiersTest(InterproRESTTestCase):	2✔
442	def test_annotation_modifier_hmm(self):	2✔
UNCOV 443	response = self.client.get("/api/entry/pfam/pf02171?annotation=hmm")	×
UNCOV 444	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 445	self.assertEqual(response["content-type"], "application/gzip")	×
446
447	def test_annotation_modifier_logo(self):	2✔
UNCOV 448	response = self.client.get("/api/entry/pfam/pf02171?annotation=logo")	×
UNCOV 449	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 450	self.assertEqual(response["content-type"], "application/json")	×
UNCOV 451	data = json.loads(response.content)	×
UNCOV 452	self.assertIn("ali_map", data)	×
UNCOV 453	self.assertEqual(302, len(data["ali_map"]))	×
454
455	def test_annotation_modifier_pfam_alignment(self):	2✔
UNCOV 456	response = self.client.get("/api/entry/pfam/pf02171?annotation=alignment:seed")	×
UNCOV 457	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 458	self.assertEqual(response["content-type"], "text/plain")	×
459
460	def test_annotation_modifier_interpro_alignment(self):	2✔
UNCOV 461	response = self.client.get(	×
462	"/api/entry/interpro/ipr003165?annotation=alignment:seed"
463	)
UNCOV 464	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 465	self.assertEqual(response["content-type"], "text/plain")	×
466
467	# TODO This test should fail but doesn't
468	# def test_annotation_wrong_acc_modifier(self):
469	# response = self.client.get("/api/entry/pfam/pf00001?annotation=hmm")
470	# self.assertEqual(response.status_code, status.HTTP_204_NO_CONTENT)
471
472
473	class ValueForFieldModifiersTest(InterproRESTTestCase):	2✔
474	def test_interactions_modifier(self):	2✔
UNCOV 475	response = self.client.get("/api/entry/interpro/IPR001165?interactions")	×
UNCOV 476	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 477	self.assertIn("interactions", response.data)	×
UNCOV 478	self.assertIsInstance(response.data["interactions"], list)	×
UNCOV 479	self.assertEqual(1, len(response.data["interactions"]))	×
480
481	def test_no_interactions_modifier(self):	2✔
UNCOV 482	response = self.client.get("/api/entry/interpro/IPR003165?interactions")	×
UNCOV 483	self.assertEqual(response.status_code, status.HTTP_204_NO_CONTENT)	×
484
485	def test_pathways_modifier(self):	2✔
UNCOV 486	response = self.client.get("/api/entry/interpro/IPR001165?pathways")	×
UNCOV 487	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 488	self.assertIn("pathways", response.data)	×
UNCOV 489	self.assertIsInstance(response.data["pathways"], object)	×
UNCOV 490	self.assertIn("reactome", response.data["pathways"])	×
UNCOV 491	self.assertEqual(2, len(response.data["pathways"]["reactome"]))	×
492
493	def test_no_pathways_modifier(self):	2✔
UNCOV 494	response = self.client.get("/api/entry/interpro/IPR003165?pathways")	×
UNCOV 495	self.assertEqual(response.status_code, status.HTTP_204_NO_CONTENT)	×
496
497	def test_taxa_modifier(self):	2✔
UNCOV 498	response = self.client.get("/api/entry/interpro/IPR003165?taxa")	×
UNCOV 499	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 500	self.assertIn("taxa", response.data)	×
UNCOV 501	self.assertIsInstance(response.data["taxa"], object)	×
UNCOV 502	self.assertIn("children", response.data["taxa"])	×
UNCOV 503	self.assertEqual(1, len(response.data["taxa"]["children"]))	×
504
505	def test_no_taxa_modifier(self):	2✔
UNCOV 506	response = self.client.get("/api/entry/interpro/IPR001165?taxa")	×
UNCOV 507	self.assertEqual(response.status_code, status.HTTP_204_NO_CONTENT)	×
508
509
510	class TaxonomyScientificNameModifierTest(InterproRESTTestCase):	2✔
511	def test_scientific_name_modifier(self):	2✔
UNCOV 512	response = self.client.get("/api/taxonomy/uniprot/?scientific_name=Bacteria")	×
UNCOV 513	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 514	self.assertIn("metadata", response.data)	×
UNCOV 515	self.assertIn("accession", response.data["metadata"])	×
UNCOV 516	self.assertIn("counters", response.data["metadata"])	×
UNCOV 517	self.assertEqual("2", response.data["metadata"]["accession"])	×
UNCOV 518	self.assertEqual(2, response.data["metadata"]["counters"]["entries"])	×
UNCOV 519	self.assertEqual(2, response.data["metadata"]["counters"]["proteins"])	×
520
521	def test_scientific_name_modifier_member_database_filter(self):	2✔
UNCOV 522	response = self.client.get(	×
523	"/api/taxonomy/uniprot/entry/interpro?scientific_name=Bacteria"
524	)
UNCOV 525	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 526	self.assertIn("metadata", response.data)	×
UNCOV 527	self.assertIn("accession", response.data["metadata"])	×
UNCOV 528	self.assertIn("counters", response.data["metadata"])	×
UNCOV 529	self.assertEqual("2", response.data["metadata"]["accession"])	×
UNCOV 530	self.assertEqual(5, response.data["metadata"]["counters"]["entries"])	×
UNCOV 531	self.assertEqual(10, response.data["metadata"]["counters"]["proteins"])	×
532
533
534	class ResidueModifierTest(InterproRESTTestCase):	2✔
535	def test_residue_modifier_is_different_than_acc_protein(self):	2✔
UNCOV 536	response1 = self.client.get("/api/protein/uniprot/a1cuj5")	×
UNCOV 537	self.assertEqual(response1.status_code, status.HTTP_200_OK)	×
UNCOV 538	response2 = self.client.get("/api/protein/uniprot/a1cuj5?residues")	×
UNCOV 539	self.assertEqual(response2.status_code, status.HTTP_200_OK)	×
UNCOV 540	self.assertNotEquals(response1.data, response2.data)	×
541
542	def test_residue_modifier(self):	2✔
UNCOV 543	response2 = self.client.get("/api/protein/uniprot/a1cuj5?residues")	×
UNCOV 544	self.assertEqual(response2.status_code, status.HTTP_200_OK)	×
UNCOV 545	self.assertIn("residue", response2.data)	×
UNCOV 546	self.assertIn("locations", response2.data["residue"])	×
547
548
549	class StructuralModelTest(InterproRESTTestCase):	2✔
550	def test_model_structure_modifier(self):	2✔
UNCOV 551	response = self.client.get("/api/entry/pfam/PF17176?model:structure")	×
UNCOV 552	self.assertEqual(response.status_code, status.HTTP_410_GONE)	×
553
554	def test_model_contacts_modifier(self):	2✔
UNCOV 555	response = self.client.get("/api/entry/pfam/PF17176?model:contacts")	×
UNCOV 556	self.assertEqual(response.status_code, status.HTTP_410_GONE)	×
557
558	def test_model_lddt_modifier(self):	2✔
UNCOV 559	response = self.client.get("/api/entry/pfam/PF17176?model:lddt")	×
UNCOV 560	self.assertEqual(response.status_code, status.HTTP_410_GONE)	×
561
562
563	class SubfamiliesTest(InterproRESTTestCase):	2✔
564	entries = [	2✔
565	{"db": "panther", "acc": "PTHR43214", "sf": "PTHR43214:sf24"},
566	{"db": "cathgene3d", "acc": "G3DSA:1.10.10.10", "sf": "G3DSA:1.10.10.10:1"},
567	]
568
569	def test_subfamilies_counter(self):	2✔
UNCOV 570	for entry in self.entries:	×
UNCOV 571	response = self.client.get(f"/api/entry/{entry['db']}/{entry['acc']}")	×
UNCOV 572	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 573	self.assertIn("counters", response.data["metadata"])	×
UNCOV 574	self.assertEqual(response.data["metadata"]["counters"]["subfamilies"], 1)	×
575
576	def test_panther_subfamilies(self):	2✔
UNCOV 577	for entry in self.entries:	×
UNCOV 578	response = self.client.get(	×
579	f"/api/entry/{entry['db']}/{entry['acc']}?subfamilies"
580	)
UNCOV 581	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 582	self.assertEqual(len(response.data["results"]), 1)	×
UNCOV 583	self.assertEqual(	×
584	response.data["results"][0]["metadata"]["accession"], entry["sf"]
585	)
UNCOV 586	self.assertEqual(	×
587	response.data["results"][0]["metadata"]["integrated"], entry["acc"]
588	)
589
590	def test_no_subfamilies_in_pfam(self):	2✔
UNCOV 591	response = self.client.get(f"/api/entry/pfam/PF02171")	×
UNCOV 592	self.assertEqual(response.status_code, status.HTTP_200_OK)	×
UNCOV 593	self.assertIn("counters", response.data["metadata"])	×
UNCOV 594	self.assertNotIn("subfamilies", response.data["metadata"]["counters"])	×
UNCOV 595	response2 = self.client.get(f"/api/entry/pfam/PF02171?subfamilies")	×
UNCOV 596	self.assertEqual(response2.status_code, status.HTTP_204_NO_CONTENT)	×

ProteinsWebTeam / interpro7-api / 1

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