Skip to content

Commit 9286f69

Browse files
amamd07amamd07
authored
Merge pull request #47 from rayyansys/tasks/8483
refactor and extend review.py endpoints
2 parents eccd29e + 8c61cc4 commit 9286f69

File tree

18 files changed

+670
-333
lines changed

18 files changed

+670
-333
lines changed

‎nb.ipynb‎

Lines changed: 325 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,325 @@
1+
{
2+
"cells": [
3+
{
4+
"cell_type": "markdown",
5+
"id": "24ac830c",
6+
"metadata": {},
7+
"source": [
8+
"## Initialize"
9+
]
10+
},
11+
{
12+
"cell_type": "code",
13+
"execution_count": null,
14+
"id": "841c00cd",
15+
"metadata": {
16+
"vscode": {
17+
"languageId": "plaintext"
18+
}
19+
},
20+
"outputs": [],
21+
"source": [
22+
"from rayyan import StatelessRayyan as client\n",
23+
"from rayyan.review import Review\n",
24+
"from rayyan.mylib import MyLib\n",
25+
"\n",
26+
"access_token = \"\"\n",
27+
"_client = client(access_token, url=\"https://rayyan.ai\")\n",
28+
"mylib_client = client(access_token, url=\"https://mylib.rayyan.ai\")\n",
29+
"\n",
30+
"_review = Review(_client)\n",
31+
"my_lib = MyLib(mylib_client)"
32+
]
33+
},
34+
{
35+
"cell_type": "code",
36+
"execution_count": null,
37+
"id": "d8675105",
38+
"metadata": {
39+
"vscode": {
40+
"languageId": "plaintext"
41+
}
42+
},
43+
"outputs": [],
44+
"source": [
45+
"# List articles in my library\n",
46+
"print(\"Listing a directory in my library\")\n",
47+
"resp = my_lib.list_directory(\"/\")\n",
48+
"print(resp)\n"
49+
]
50+
},
51+
{
52+
"cell_type": "code",
53+
"execution_count": null,
54+
"id": "8f18454f",
55+
"metadata": {
56+
"vscode": {
57+
"languageId": "plaintext"
58+
}
59+
},
60+
"outputs": [],
61+
"source": [
62+
"# Variables reused across tests\n",
63+
"review_id = 1646756\n",
64+
"stage_id = 177729 # Data Extraction\n",
65+
"sample_id = \"27989\"\n",
66+
"question_id = 20170\n",
67+
"criterion_id = 490407"
68+
]
69+
},
70+
{
71+
"cell_type": "code",
72+
"execution_count": null,
73+
"id": "e3e31a28",
74+
"metadata": {
75+
"vscode": {
76+
"languageId": "plaintext"
77+
}
78+
},
79+
"outputs": [],
80+
"source": [
81+
"# Import aricle from mylib\n",
82+
"file = {\n",
83+
" \"key\": \"pubmed-covid-set-22.txt\",\n",
84+
" \"size\": 40667022,\n",
85+
" \"metadata\": {\n",
86+
" \"metadata_signature\": \"dada04d571e3c2f3c3237c01a2e2de90c2b1068d83d4f95ec9eaf2e70707a81f\",\n",
87+
" \"total_articles\": \"10000\",\n",
88+
" \"type\": \"ref\"\n",
89+
" }\n",
90+
" }\n",
91+
"\n",
92+
"file = resp['items'][8]\n",
93+
"file_parsed = {\n",
94+
" \"key\": file[\"key\"],\n",
95+
" \"size\": file[\"file_size\"],\n",
96+
" \"metadata\": {\n",
97+
" \"metadata_signature\": file[\"metadata\"][\"metadata_signature\"],\n",
98+
" \"total_articles\": file[\"metadata\"][\"total_articles\"],\n",
99+
" \"type\": file[\"metadata\"][\"type\"]\n",
100+
" }\n",
101+
"}\n",
102+
"resp = _review.import_from_mylibrary_to_review(review_id=review_id, file=file_parsed)"
103+
]
104+
},
105+
{
106+
"cell_type": "code",
107+
"execution_count": null,
108+
"id": "cb0c1556",
109+
"metadata": {
110+
"vscode": {
111+
"languageId": "plaintext"
112+
}
113+
},
114+
"outputs": [],
115+
"source": [
116+
"# Full text\n",
117+
"print(\"Listing articles with full text\")\n",
118+
"resp = _review.list_articles_with_fulltext(review_id=review_id)\n",
119+
"print(resp)\n",
120+
"\n",
121+
"full_text_id = resp['data'][0]['fulltexts'][0]['id']\n",
122+
"resp = _review.get_fulltext_link(full_text_id)\n",
123+
"print(resp['url'])"
124+
]
125+
},
126+
{
127+
"cell_type": "markdown",
128+
"id": "c01a34b4",
129+
"metadata": {},
130+
"source": [
131+
"## Testing Questions, Criteria, MyLibrary Import and AI Screener endpoints"
132+
]
133+
},
134+
{
135+
"cell_type": "code",
136+
"execution_count": null,
137+
"id": "70fe0b60",
138+
"metadata": {
139+
"vscode": {
140+
"languageId": "plaintext"
141+
}
142+
},
143+
"outputs": [],
144+
"source": [
145+
"# --- Samples ---\n",
146+
"print(\"Creating sample...\")\n",
147+
"resp = _review.create_sample(\n",
148+
" review_id=review_id,\n",
149+
" samples=[{\"name\": \"created_by_python_sdk\", \"total\": 10}]\n",
150+
")\n",
151+
"print(resp)\n",
152+
"\n",
153+
"print(\"Listing samples...\")\n",
154+
"resp = _review.list_samples(review_id=review_id)\n",
155+
"print(resp)\n",
156+
"\n",
157+
"resp = _review.list_stages(review_id=review_id)\n",
158+
"print(resp)\n",
159+
"\n",
160+
"print(\"Updating sample...\")\n",
161+
"resp = _review.update_sample(\n",
162+
" review_id=review_id,\n",
163+
" sample_id=sample_id,\n",
164+
" sample={\"name\": \"Name Changed by python sdk\"}\n",
165+
")\n",
166+
"print(resp)\n",
167+
"\n",
168+
"print(\"Deleting sample...\")\n",
169+
"resp = _review.delete_sample(\n",
170+
" review_id=review_id,\n",
171+
" sample_id=sample_id\n",
172+
")\n",
173+
"print(resp)\n",
174+
"\n"
175+
]
176+
},
177+
{
178+
"cell_type": "markdown",
179+
"id": "b039c4ad",
180+
"metadata": {},
181+
"source": [
182+
"# --- Questions ---\n",
183+
"print(\"Creating question...\")\n",
184+
"resp = _review.create_question(\n",
185+
" review_id=review_id,\n",
186+
" stage_id=stage_id,\n",
187+
" question={\n",
188+
" \"type\": \"string\",\n",
189+
" \"title\": \"Added via Python SDK\",\n",
190+
" \"section_name\": \"Methods\",\n",
191+
" \"required\": True,\n",
192+
" \"body\": \"Describe your inclusion criteria\"\n",
193+
" }\n",
194+
")\n",
195+
"print(resp)\n",
196+
"\n",
197+
"print(\"Listing questions...\")\n",
198+
"resp = _review.list_questions(review_id=review_id, stage_id=stage_id)\n",
199+
"print(resp)\n",
200+
"\n",
201+
"print(\"Getting a specific question...\")\n",
202+
"resp = _review.get_question(review_id=review_id, stage_id=stage_id, question_id=question_id)\n",
203+
"print(resp)\n",
204+
"\n",
205+
"print(\"Updating question...\")\n",
206+
"resp = _review.update_question(\n",
207+
" review_id=review_id,\n",
208+
" stage_id=stage_id,\n",
209+
" question_id=question_id,\n",
210+
" question={\n",
211+
" \"type\": \"string\",\n",
212+
" \"title\": \"Updated Title by SDK\",\n",
213+
" \"section_name\": \"Results\",\n",
214+
" \"required\": False,\n",
215+
" \"body\": \"Updated body content\"\n",
216+
" }\n",
217+
")\n",
218+
"print(resp)\n",
219+
"\n",
220+
"print(\"Deleting question...\")\n",
221+
"resp = _review.delete_question(review_id=review_id, stage_id=stage_id, question_id=question_id)\n",
222+
"print(resp)\n"
223+
]
224+
},
225+
{
226+
"cell_type": "code",
227+
"execution_count": null,
228+
"id": "3e6407b4",
229+
"metadata": {
230+
"vscode": {
231+
"languageId": "plaintext"
232+
}
233+
},
234+
"outputs": [],
235+
"source": [
236+
"\n",
237+
"# --- Criteria ---\n",
238+
"print(\"Creating criterion...\")\n",
239+
"resp = _review.create_criterion(\n",
240+
" review_id=review_id,\n",
241+
" criterion={\"kind\": \"inclusion\", \"text\": \"Must include RCTs\"}\n",
242+
")\n",
243+
"print(resp)\n",
244+
"\n",
245+
"print(\"Listing criteria...\")\n",
246+
"resp = _review.list_criteria(review_id=review_id)\n",
247+
"print(resp)\n",
248+
"\n",
249+
"print(\"Updating criterion...\")\n",
250+
"resp = _review.update_criterion(\n",
251+
" review_id=review_id,\n",
252+
" criterion_id=criterion_id,\n",
253+
" criterion={\"kind\": \"exclusion\", \"text\": \"Exclude case reports\"}\n",
254+
")\n",
255+
"print(resp)\n",
256+
"\n",
257+
"print(\"Deleting criterion...\")\n",
258+
"resp = _review.delete_criterion(review_id=review_id, criterion_id=criterion_id)\n",
259+
"print(resp)\n"
260+
]
261+
},
262+
{
263+
"cell_type": "code",
264+
"execution_count": null,
265+
"id": "8ef8a2c5",
266+
"metadata": {
267+
"vscode": {
268+
"languageId": "plaintext"
269+
}
270+
},
271+
"outputs": [],
272+
"source": [
273+
"# --- MyLibrary Import ---\n",
274+
"print(\"Importing file to library...\")\n",
275+
"resp = _review.import_to_library(\n",
276+
" review_id=review_id,\n",
277+
" file={\n",
278+
" \"key\": \"/mnt/c/Users/amamd/Downloads/pubmed-covid-set-19.txt\",\n",
279+
" \"size\": 717,\n",
280+
" \"metadata\": {\n",
281+
" \"metadata_signature\": \"bea0cb4574d0a131bd0***\",\n",
282+
" \"total_articles\": \"3\",\n",
283+
" \"type\": \"ref\"\n",
284+
" }\n",
285+
" }\n",
286+
")\n",
287+
"print(resp)\n"
288+
]
289+
},
290+
{
291+
"cell_type": "code",
292+
"execution_count": null,
293+
"id": "3d21fa3b",
294+
"metadata": {
295+
"vscode": {
296+
"languageId": "plaintext"
297+
}
298+
},
299+
"outputs": [],
300+
"source": [
301+
"# --- AI Screener ---\n",
302+
"print(\"Creating AI screener...\")\n",
303+
"resp = _review.create_ai_screener(\n",
304+
" review_id=review_id,\n",
305+
" extra={\n",
306+
" }\n",
307+
")\n",
308+
"print(resp)"
309+
]
310+
}
311+
],
312+
"metadata": {
313+
"kernelspec": {
314+
"display_name": ".venv",
315+
"language": "python",
316+
"name": "python3"
317+
},
318+
"language_info": {
319+
"name": "python",
320+
"version": "3.12.3"
321+
}
322+
},
323+
"nbformat": 4,
324+
"nbformat_minor": 5
325+
}

‎rayyan/mylib.py‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
1+
2+
from rayyan.types import RayyanProtocol as Rayyan
3+
4+
5+
class MyLib:
6+
def __init__(self, rayyan: Rayyan):
7+
self.__rayyan__ = rayyan
8+
9+
def list_directory(self, path) -> dict:
10+
"""List all files in the user's My Library.
11+
12+
Returns:
13+
dict: A dictionary containing the list of files in My Library.
14+
"""
15+
return self.__rayyan__.request.request_handler(
16+
method="GET",
17+
path=f"/ls/{path}"
18+
)

‎rayyan/paths.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -9,5 +9,9 @@
99
THIRD_PARTY_AUTH = "/api/v1/third_party_auth"
1010
# ________review________
1111
REVIEWS_ROUTE = "/api/v1/reviews"
12+
# ________fulltext________
13+
FULLTEXT_ROUTE = "/api/v1/fulltexts"
14+
# ________my library________
15+
MYLIBRARY_ROUTE = "/api/v1/my_library/import"
1216
# ________admin________
1317
ADMIN_ROUTE = "/admin"

0 commit comments

Comments
 (0)