Spaces:
Runtime error
Runtime error
Yijun-Yang
commited on
Commit
·
3702bb5
1
Parent(s):
dbe9ffc
pythonversion
Browse files
.ipynb_checkpoints/app-checkpoint.py
ADDED
@@ -0,0 +1,644 @@
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1 |
+
import argparse
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2 |
+
import json
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3 |
+
import time
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4 |
+
import os
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5 |
+
import glob
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6 |
+
import random
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7 |
+
import shutil
|
8 |
+
from enum import Enum
|
9 |
+
from threading import Thread
|
10 |
+
from multiprocessing import Process, Value
|
11 |
+
|
12 |
+
import gradio as gr
|
13 |
+
import pytoml
|
14 |
+
from loguru import logger
|
15 |
+
import spaces
|
16 |
+
|
17 |
+
from huixiangdou.service import Worker, llm_serve, ArticleRetrieval, CacheRetriever, FeatureStore, FileOperation
|
18 |
+
|
19 |
+
class PARAM_CODE(Enum):
|
20 |
+
"""Parameter code."""
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21 |
+
SUCCESS = 0
|
22 |
+
FAILED = 1
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23 |
+
ERROR = 2
|
24 |
+
|
25 |
+
def parse_args():
|
26 |
+
"""Parse args."""
|
27 |
+
parser = argparse.ArgumentParser(description='Worker.')
|
28 |
+
parser.add_argument('--work_dir',
|
29 |
+
type=str,
|
30 |
+
default='workdir',
|
31 |
+
help='Working directory.')
|
32 |
+
parser.add_argument('--repo_dir',
|
33 |
+
type=str,
|
34 |
+
default='repodir',
|
35 |
+
help='Repository directory.')
|
36 |
+
parser.add_argument(
|
37 |
+
'--config_path',
|
38 |
+
default='config.ini',
|
39 |
+
type=str,
|
40 |
+
help='Worker configuration path. Default value is config.ini')
|
41 |
+
parser.add_argument('--standalone',
|
42 |
+
action='store_true',
|
43 |
+
default=True,
|
44 |
+
help='Auto deploy required Hybrid LLM Service.')
|
45 |
+
args = parser.parse_args()
|
46 |
+
return args
|
47 |
+
|
48 |
+
def update_remote_buttons(remote):
|
49 |
+
if remote:
|
50 |
+
return [
|
51 |
+
gr.Markdown("[如何配置API]('https://github.com/jabberwockyang/MedicalReviewAgent/blob/main/README.md')",
|
52 |
+
visible=True),
|
53 |
+
gr.Dropdown(["kimi", "deepseek", "zhipuai",'gpt'],
|
54 |
+
label="选择大模型提供商",
|
55 |
+
interactive=True,visible=True),
|
56 |
+
gr.Textbox(label="您的API",lines = 1,
|
57 |
+
interactive=True,visible=True),
|
58 |
+
gr.Dropdown([],label="选择模型",
|
59 |
+
interactive=True,visible=True)
|
60 |
+
]
|
61 |
+
else:
|
62 |
+
return [
|
63 |
+
gr.Markdown("[如何配置API]('https://github.com/jabberwockyang/MedicalReviewAgent/blob/main/README.md')",
|
64 |
+
visible=False),
|
65 |
+
gr.Dropdown(["kimi", "deepseek", "zhipuai",'gpt'],
|
66 |
+
label="选择大模型提供商",
|
67 |
+
interactive=False,visible=False),
|
68 |
+
gr.Textbox(label="您的API",lines = 1,
|
69 |
+
interactive=False,visible=False),
|
70 |
+
gr.Dropdown([],label="选择模型",
|
71 |
+
interactive=False,visible=False)
|
72 |
+
]
|
73 |
+
|
74 |
+
def udate_model_dropdown(remote_company):
|
75 |
+
model_choices = {
|
76 |
+
'kimi': ['moonshot-v1-128k'],
|
77 |
+
'deepseek': ['deepseek-chat'],
|
78 |
+
'zhipuai': ['glm-4'],
|
79 |
+
'gpt': ['gpt-4-32k-0613','gpt-3.5-turbo']
|
80 |
+
}
|
81 |
+
return gr.Dropdown(choices= model_choices[remote_company])
|
82 |
+
|
83 |
+
def update_remote_config(remote_ornot,remote_company = None,api = None,model = None):
|
84 |
+
with open(CONFIG_PATH, encoding='utf8') as f:
|
85 |
+
config = pytoml.load(f)
|
86 |
+
|
87 |
+
if remote_ornot:
|
88 |
+
if remote_company == None or api == None or model == None:
|
89 |
+
raise ValueError('remote_company, api, model not provided')
|
90 |
+
config['llm']['enable_local'] = 0
|
91 |
+
config['llm']['enable_remote'] = 1
|
92 |
+
config['llm']['server']['remote_type'] = remote_company
|
93 |
+
config['llm']['server']['remote_api_key'] = api
|
94 |
+
config['llm']['server']['remote_llm_model'] = model
|
95 |
+
else:
|
96 |
+
config['llm']['enable_local'] = 1
|
97 |
+
config['llm']['enable_remote'] = 0
|
98 |
+
with open(CONFIG_PATH, 'w') as f:
|
99 |
+
pytoml.dump(config, f)
|
100 |
+
return gr.Button("配置已保存")
|
101 |
+
|
102 |
+
@spaces.GPU
|
103 |
+
def get_ready(query:str,chunksize=None,k=None):
|
104 |
+
|
105 |
+
with open(CONFIG_PATH, encoding='utf8') as f:
|
106 |
+
config = pytoml.load(f)
|
107 |
+
workdir = config['feature_store']['work_dir']
|
108 |
+
repodir = config['feature_store']['repo_dir']
|
109 |
+
|
110 |
+
if query == 'repo_work': # no need to return assistant
|
111 |
+
return repodir, workdir, config
|
112 |
+
theme = ''
|
113 |
+
try:
|
114 |
+
with open(os.path.join(config['feature_store']['repo_dir'],'config.json'), 'r') as f:
|
115 |
+
repo_config = json.load(f)
|
116 |
+
theme = ' '.join(repo_config['keywords'])
|
117 |
+
except:
|
118 |
+
pass
|
119 |
+
|
120 |
+
if query == 'annotation':
|
121 |
+
if not chunksize or not k:
|
122 |
+
raise ValueError('chunksize or k not provided')
|
123 |
+
chunkdir = os.path.join(workdir, f'chunksize_{chunksize}')
|
124 |
+
clusterdir = os.path.join(chunkdir, 'cluster_features', f'cluster_features_{k}')
|
125 |
+
assistant = Worker(work_dir=chunkdir, config_path=CONFIG_PATH,language='en')
|
126 |
+
samples_json = os.path.join(clusterdir,'samples.json')
|
127 |
+
with open(samples_json, 'r') as f:
|
128 |
+
samples = json.load(f)
|
129 |
+
f.close()
|
130 |
+
return clusterdir, samples, assistant, theme
|
131 |
+
|
132 |
+
elif query == 'inspiration':
|
133 |
+
if not chunksize or not k:
|
134 |
+
raise ValueError('chunksize or k not provided')
|
135 |
+
|
136 |
+
chunkdir = os.path.join(workdir, f'chunksize_{chunksize}')
|
137 |
+
clusterdir = os.path.join(chunkdir, 'cluster_features', f'cluster_features_{k}')
|
138 |
+
assistant = Worker(work_dir=chunkdir, config_path=CONFIG_PATH,language='en')
|
139 |
+
annofile = os.path.join(clusterdir,'annotation.jsonl')
|
140 |
+
with open(annofile, 'r') as f:
|
141 |
+
annoresult = f.readlines()
|
142 |
+
|
143 |
+
f.close()
|
144 |
+
annoresult = [json.loads(obj) for obj in annoresult]
|
145 |
+
return clusterdir, annoresult, assistant, theme
|
146 |
+
elif query == 'summarize': # no need for params k
|
147 |
+
if not chunksize:
|
148 |
+
raise ValueError('chunksize not provided')
|
149 |
+
chunkdir = os.path.join(workdir, f'chunksize_{chunksize}')
|
150 |
+
assistant = Worker(work_dir=chunkdir, config_path=CONFIG_PATH,language='en')
|
151 |
+
return assistant,theme
|
152 |
+
|
153 |
+
else:
|
154 |
+
raise ValueError('query not recognized')
|
155 |
+
|
156 |
+
def update_repo_info():
|
157 |
+
with open(CONFIG_PATH, encoding='utf8') as f:
|
158 |
+
config = pytoml.load(f)
|
159 |
+
repodir = config['feature_store']['repo_dir']
|
160 |
+
if os.path.exists(repodir):
|
161 |
+
pdffiles = glob.glob(os.path.join(repodir, '*.pdf'))
|
162 |
+
number_of_pdf = len(pdffiles)
|
163 |
+
if os.path.exists(os.path.join(repodir,'config.json')):
|
164 |
+
|
165 |
+
with open(os.path.join(repodir,'config.json'), 'r') as f:
|
166 |
+
repo_config = json.load(f)
|
167 |
+
|
168 |
+
keywords = repo_config['keywords']
|
169 |
+
length = repo_config['len']
|
170 |
+
retmax = repo_config['retmax']
|
171 |
+
|
172 |
+
return keywords,length,retmax,number_of_pdf
|
173 |
+
else:
|
174 |
+
return None,None,None,number_of_pdf
|
175 |
+
else:
|
176 |
+
return None,None,None,None
|
177 |
+
|
178 |
+
def upload_file(files):
|
179 |
+
repodir, workdir, _ = get_ready('repo_work')
|
180 |
+
if not os.path.exists(repodir):
|
181 |
+
os.makedirs(repodir)
|
182 |
+
|
183 |
+
for file in files:
|
184 |
+
destination_path = os.path.join(repodir, os.path.basename(file.name))
|
185 |
+
|
186 |
+
shutil.copy(file.name, destination_path)
|
187 |
+
|
188 |
+
|
189 |
+
return files
|
190 |
+
|
191 |
+
def generate_articles_repo(keywords:str,retmax:int):
|
192 |
+
keys= [k.strip() for k in keywords.split('\n')]
|
193 |
+
repodir, _, _ = get_ready('repo_work')
|
194 |
+
|
195 |
+
articelfinder = ArticleRetrieval(keywords = keys,
|
196 |
+
repo_dir = repodir,
|
197 |
+
retmax = retmax)
|
198 |
+
articelfinder.initiallize()
|
199 |
+
return update_repo()
|
200 |
+
|
201 |
+
def delete_articles_repo():
|
202 |
+
# 在这里运行生成数据库的函数
|
203 |
+
repodir, workdir, _ = get_ready('repo_work')
|
204 |
+
if os.path.exists(repodir):
|
205 |
+
shutil.rmtree(repodir)
|
206 |
+
if os.path.exists(workdir):
|
207 |
+
shutil.rmtree(workdir)
|
208 |
+
|
209 |
+
return gr.Textbox(label="文献库概况",lines =3,
|
210 |
+
value = '文献库和相关数据库已删除',
|
211 |
+
visible = True)
|
212 |
+
|
213 |
+
def update_repo():
|
214 |
+
keys,len,retmax,pdflen = update_repo_info()
|
215 |
+
if keys:
|
216 |
+
newinfo = f"搜索得到文献:\n 关键词:{keys}\n 文献数量:{len}\n 获取上限:{retmax}\n\n上传文献:\n 数量:{pdflen}"
|
217 |
+
else:
|
218 |
+
if pdflen:
|
219 |
+
newinfo = f'搜索得到文献:无\n上传文献:\n 数量:{pdflen}'
|
220 |
+
else:
|
221 |
+
newinfo = '目前还没有文献库'
|
222 |
+
|
223 |
+
return gr.Textbox(label="文献库概况",lines =1,
|
224 |
+
value = newinfo,
|
225 |
+
visible = True)
|
226 |
+
|
227 |
+
def update_database_info():
|
228 |
+
with open(CONFIG_PATH, encoding='utf8') as f:
|
229 |
+
config = pytoml.load(f)
|
230 |
+
workdir = config['feature_store']['work_dir']
|
231 |
+
chunkdirs = glob.glob(os.path.join(workdir, 'chunksize_*'))
|
232 |
+
chunkdirs.sort()
|
233 |
+
list_of_chunksize = [int(chunkdir.split('_')[-1]) for chunkdir in chunkdirs]
|
234 |
+
# print(list_of_chunksize)
|
235 |
+
jsonobj = {}
|
236 |
+
for chunkdir in chunkdirs:
|
237 |
+
k_dir = glob.glob(os.path.join(chunkdir, 'cluster_features','cluster_features_*'))
|
238 |
+
k_dir.sort()
|
239 |
+
list_of_k = [int(k.split('_')[-1]) for k in k_dir]
|
240 |
+
jsonobj[int(chunkdir.split('_')[-1])] = list_of_k
|
241 |
+
|
242 |
+
|
243 |
+
new_options = [f"chunksize:{chunksize}, k:{k}" for chunksize in list_of_chunksize for k in jsonobj[chunksize]]
|
244 |
+
|
245 |
+
return new_options, jsonobj
|
246 |
+
|
247 |
+
@spaces.GPU
|
248 |
+
def generate_database(chunksize:int,nclusters:str|list[str]):
|
249 |
+
# 在这里运行生成数据库的函数
|
250 |
+
repodir, workdir, _ = get_ready('repo_work')
|
251 |
+
if not os.path.exists(repodir):
|
252 |
+
return gr.Textbox(label="数据库已生成",value = '请先生成文献库',visible = True)
|
253 |
+
nclusters = [int(i) for i in nclusters]
|
254 |
+
# 文献库和数据库的覆盖删除逻辑待定
|
255 |
+
# 理论上 文献库只能生成一次 所以每次生成文献库都要删除之前的文献库和数据库
|
256 |
+
# 数据库可以根据文献库多次生成 暂不做删除 目前没有节省算力的逻辑 重复计算后覆盖 以后优化
|
257 |
+
# 不同的chunksize和nclusters会放在不同的文件夹下 不会互相覆盖
|
258 |
+
# if os.path.exists(workdir):
|
259 |
+
# shutil.rmtree(workdir)
|
260 |
+
|
261 |
+
cache = CacheRetriever(config_path=CONFIG_PATH)
|
262 |
+
fs_init = FeatureStore(embeddings=cache.embeddings,
|
263 |
+
reranker=cache.reranker,
|
264 |
+
chunk_size=chunksize,
|
265 |
+
n_clusters=nclusters,
|
266 |
+
config_path=CONFIG_PATH)
|
267 |
+
|
268 |
+
# walk all files in repo dir
|
269 |
+
file_opr = FileOperation()
|
270 |
+
files = file_opr.scan_dir(repo_dir=repodir)
|
271 |
+
fs_init.initialize(files=files, work_dir=workdir,file_opr=file_opr)
|
272 |
+
file_opr.summarize(files)
|
273 |
+
del fs_init
|
274 |
+
cache.pop('default')
|
275 |
+
texts, _ = update_database_info()
|
276 |
+
return gr.Textbox(label="数据库概况",value = '\n'.join(texts) ,visible = True)
|
277 |
+
|
278 |
+
def delete_database():
|
279 |
+
_, workdir, _ = get_ready('repo_work')
|
280 |
+
if os.path.exists(workdir):
|
281 |
+
shutil.rmtree(workdir)
|
282 |
+
return gr.Textbox(label="数据库概况",lines =3,value = '数据库已删除',visible = True)
|
283 |
+
|
284 |
+
def update_database_textbox():
|
285 |
+
texts, _ = update_database_info()
|
286 |
+
if texts == []:
|
287 |
+
return gr.Textbox(label="数据库概况",value = '目前还没有数据库',visible = True)
|
288 |
+
else:
|
289 |
+
return gr.Textbox(label="数据库概况",value = '\n'.join(texts),visible = True)
|
290 |
+
|
291 |
+
def update_chunksize_dropdown():
|
292 |
+
_, jsonobj = update_database_info()
|
293 |
+
return gr.Dropdown(choices= jsonobj.keys())
|
294 |
+
|
295 |
+
def update_ncluster_dropdown(chunksize:int):
|
296 |
+
_, jsonobj = update_database_info()
|
297 |
+
nclusters = jsonobj[chunksize]
|
298 |
+
return gr.Dropdown(choices= nclusters)
|
299 |
+
|
300 |
+
@spaces.GPU
|
301 |
+
def annotation(n,chunksize:int,nclusters:int,remote_ornot:bool):
|
302 |
+
'''
|
303 |
+
use llm to annotate cluster
|
304 |
+
n: percentage of clusters to annotate
|
305 |
+
'''
|
306 |
+
query = 'annotation'
|
307 |
+
if remote_ornot:
|
308 |
+
backend = 'remote'
|
309 |
+
else:
|
310 |
+
backend = 'local'
|
311 |
+
|
312 |
+
clusterdir, samples, assistant, theme = get_ready('annotation',chunksize,nclusters)
|
313 |
+
new_obj_list = []
|
314 |
+
n = round(n * len(samples.keys()))
|
315 |
+
for cluster_no in random.sample(samples.keys(), n):
|
316 |
+
chunk = '\n'.join(samples[cluster_no]['samples'][:10])
|
317 |
+
|
318 |
+
code, reply, cluster_no = assistant.annotate_cluster(
|
319 |
+
theme = theme,
|
320 |
+
cluster_no=cluster_no,
|
321 |
+
chunk=chunk,
|
322 |
+
history=[],
|
323 |
+
groupname='',
|
324 |
+
backend=backend)
|
325 |
+
references = f"cluster_no: {cluster_no}"
|
326 |
+
new_obj = {
|
327 |
+
'cluster_no': cluster_no,
|
328 |
+
'chunk': chunk,
|
329 |
+
'annotation': reply
|
330 |
+
}
|
331 |
+
new_obj_list.append(new_obj)
|
332 |
+
logger.info(f'{code}, {query}, {reply}, {references}')
|
333 |
+
|
334 |
+
with open(os.path.join(clusterdir, 'annotation.jsonl'), 'a') as f:
|
335 |
+
json.dump(new_obj, f, ensure_ascii=False)
|
336 |
+
f.write('\n')
|
337 |
+
|
338 |
+
return '\n\n'.join([obj['annotation'] for obj in new_obj_list])
|
339 |
+
|
340 |
+
@spaces.GPU
|
341 |
+
def inspiration(annotation:str,chunksize:int,nclusters:int,remote_ornot:bool):
|
342 |
+
query = 'inspiration'
|
343 |
+
if remote_ornot:
|
344 |
+
backend = 'remote'
|
345 |
+
else:
|
346 |
+
backend = 'local'
|
347 |
+
|
348 |
+
clusterdir, annoresult, assistant, theme = get_ready('inspiration',chunksize,nclusters)
|
349 |
+
new_obj_list = []
|
350 |
+
|
351 |
+
if annotation is not None: # if the user wants to get inspiration from specific clusters only
|
352 |
+
annoresult = [obj for obj in annoresult if obj['annotation'] in [txt.strip() for txt in annotation.split('\n')]]
|
353 |
+
|
354 |
+
for index in random.sample(range(len(annoresult)), min(5, len(annoresult))):
|
355 |
+
cluster_no = annoresult[index]['cluster_no']
|
356 |
+
chunks = annoresult[index]['annotation']
|
357 |
+
|
358 |
+
code, reply = assistant.getinspiration(
|
359 |
+
theme = theme,
|
360 |
+
annotations = chunks,
|
361 |
+
history=[],
|
362 |
+
groupname='',backend=backend)
|
363 |
+
new_obj = {
|
364 |
+
'inspiration': reply,
|
365 |
+
'cluster_no': cluster_no
|
366 |
+
}
|
367 |
+
new_obj_list.append(new_obj)
|
368 |
+
logger.info(f'{code}, {query}, {cluster_no},{reply}')
|
369 |
+
|
370 |
+
with open(os.path.join(clusterdir, 'inspiration.jsonl'), 'a') as f:
|
371 |
+
json.dump(new_obj, f, ensure_ascii=False)
|
372 |
+
with open(os.path.join(clusterdir, 'inspiration.txt'), 'a') as f:
|
373 |
+
f.write(f'{reply}\n')
|
374 |
+
|
375 |
+
return '\n\n'.join(list(set([obj['inspiration'] for obj in new_obj_list])))
|
376 |
+
|
377 |
+
|
378 |
+
def getpmcurls(references):
|
379 |
+
urls = []
|
380 |
+
for ref in references:
|
381 |
+
if ref.startswith('PMC'):
|
382 |
+
|
383 |
+
refid = ref.replace('.txt','')
|
384 |
+
urls.append(f'https://www.ncbi.nlm.nih.gov/pmc/articles/{refid}/')
|
385 |
+
else:
|
386 |
+
urls.append(ref)
|
387 |
+
return urls
|
388 |
+
|
389 |
+
@spaces.GPU
|
390 |
+
def summarize_text(query,chunksize:int,remote_ornot:bool):
|
391 |
+
if remote_ornot:
|
392 |
+
backend = 'remote'
|
393 |
+
else:
|
394 |
+
backend = 'local'
|
395 |
+
|
396 |
+
assistant,_ = get_ready('summarize',chunksize=chunksize,k=None)
|
397 |
+
code, reply, references = assistant.generate(query=query,
|
398 |
+
history=[],
|
399 |
+
groupname='',backend = backend)
|
400 |
+
|
401 |
+
logger.info(f'{code}, {query}, {reply}, {references}')
|
402 |
+
urls = getpmcurls(references)
|
403 |
+
mds = '\n'.join([f'[{ref}]({url})' for ref,url in zip(references,urls)])
|
404 |
+
return reply, gr.Markdown(label="参考文献",value = mds)
|
405 |
+
|
406 |
+
def main_interface():
|
407 |
+
with gr.Blocks() as demo:
|
408 |
+
with gr.Row():
|
409 |
+
gr.Markdown(
|
410 |
+
"""
|
411 |
+
# 医学文献综述助手 (又名 不想看文献)
|
412 |
+
"""
|
413 |
+
)
|
414 |
+
|
415 |
+
with gr.Tab("模型服务配置"):
|
416 |
+
gr.Markdown("""
|
417 |
+
#### 配置模型服务 🛠️
|
418 |
+
|
419 |
+
1. **是否使用远程大模型**
|
420 |
+
- 勾选此项,如果你想使用远程的大模型服务。
|
421 |
+
- 如果不勾选,将默认使用本地模型服务。
|
422 |
+
|
423 |
+
2. **API配置**
|
424 |
+
- 配置大模型提供商和API,确保模型服务能够正常运行。
|
425 |
+
- 提供商选择:kimi、deepseek、zhipuai、gpt。
|
426 |
+
- 输入您的API密钥和选择对应模型。
|
427 |
+
- 点击“保存配置”按钮以保存您的设置。
|
428 |
+
|
429 |
+
📝 **备注**:请参考[如何使用]('https://github.com/jabberwockyang/MedicalReviewAgent/blob/main/README.md')获取更多信息。
|
430 |
+
|
431 |
+
""")
|
432 |
+
|
433 |
+
remote_ornot = gr.Checkbox(label="是否使用远程大模型")
|
434 |
+
with gr.Accordion("API配置", open=True):
|
435 |
+
apimd = gr.Markdown("[如何配置API]('https://github.com/jabberwockyang/MedicalReviewAgent/blob/main/README.md')",visible=False)
|
436 |
+
remote_company = gr.Dropdown(["kimi", "deepseek", "zhipuai",'gpt'],
|
437 |
+
label="选择大模型提供商",interactive=False,visible=False)
|
438 |
+
api = gr.Textbox(label="您的API",lines = 1,interactive=False,visible=False)
|
439 |
+
model = gr.Dropdown([],label="选择模型",interactive=False,visible=False)
|
440 |
+
|
441 |
+
confirm_button = gr.Button("保存配置")
|
442 |
+
|
443 |
+
remote_ornot.change(update_remote_buttons, inputs=[remote_ornot],outputs=[apimd,remote_company,api,model])
|
444 |
+
remote_company.change(udate_model_dropdown, inputs=[remote_company],outputs=[model])
|
445 |
+
confirm_button.click(update_remote_config, inputs=[remote_ornot,remote_company,api,model],outputs=[confirm_button])
|
446 |
+
|
447 |
+
|
448 |
+
with gr.Tab("文献查找+数据库生成"):
|
449 |
+
gr.Markdown("""
|
450 |
+
#### 查找文献 📚
|
451 |
+
|
452 |
+
1. **输入关键词批量PubMed PMC文献**
|
453 |
+
- 在“感兴趣的关键词”框中输入您感兴趣的关键词,每行一个。
|
454 |
+
- 设置查找数量(0-1000)。
|
455 |
+
- 点击“搜索PubMed PMC”按钮进行文献查找。
|
456 |
+
|
457 |
+
2. **上传PDF**
|
458 |
+
- 通过“上传PDF”按钮上传您已有的PDF文献文件。
|
459 |
+
|
460 |
+
3. **更新文献库情况 删除文献库**
|
461 |
+
- 点击“更新文献库情况”按钮,查看当前文献库的概况。
|
462 |
+
- 如果需要重置或删除现有文献库,点击“删除文献库”按钮。
|
463 |
+
|
464 |
+
|
465 |
+
#### 生成数据库 🗂️
|
466 |
+
|
467 |
+
1. **设置数据库构建参数 生成数据库**
|
468 |
+
- 选择块大小(Chunk Size)和聚类数(Number of Clusters)。
|
469 |
+
- 提供选项用于选择合适的块大小和聚类数。
|
470 |
+
- 点击“生成数据库”按钮开始数据库生成过程。
|
471 |
+
|
472 |
+
2. **更新数据库情况 删除数据库**
|
473 |
+
- 点击“更新数据库情况”按钮,查看当前数据库的概况。
|
474 |
+
- 点击“删除数据库”按钮移除现有数据库。
|
475 |
+
|
476 |
+
📝 **备注**:请参考[如何选择数据库构建参数]('https://github.com/jabberwockyang/MedicalReviewAgent/tree/main')获取更多信息。
|
477 |
+
""")
|
478 |
+
with gr.Row(equal_height=True):
|
479 |
+
with gr.Column(scale=1):
|
480 |
+
input_keys = gr.Textbox(label="感兴趣的关键词",
|
481 |
+
lines = 5)
|
482 |
+
retmax = gr.Slider(
|
483 |
+
minimum=0,
|
484 |
+
maximum=1000,
|
485 |
+
value=500,
|
486 |
+
interactive=True,
|
487 |
+
label="查多少",
|
488 |
+
)
|
489 |
+
generate_repo_button = gr.Button("搜索PubMed PMC")
|
490 |
+
with gr.Column(scale=2):
|
491 |
+
file_output = gr.File(scale=2)
|
492 |
+
upload_button = gr.UploadButton("上传PDF",
|
493 |
+
file_types=[".pdf",".csv",".doc"],
|
494 |
+
file_count="multiple",scale=0)
|
495 |
+
|
496 |
+
with gr.Row(equal_height=True):
|
497 |
+
with gr.Column(scale=0):
|
498 |
+
delete_repo_button = gr.Button("删除文献库")
|
499 |
+
update_repo_button = gr.Button("更新文献库情况")
|
500 |
+
with gr.Column(scale=2):
|
501 |
+
|
502 |
+
repo_summary =gr.Textbox(label= '文献库概况', value="目前还没有文献库")
|
503 |
+
|
504 |
+
generate_repo_button.click(generate_articles_repo,
|
505 |
+
inputs=[input_keys,retmax],
|
506 |
+
outputs = [repo_summary])
|
507 |
+
|
508 |
+
|
509 |
+
delete_repo_button.click(delete_articles_repo, inputs=None,
|
510 |
+
outputs = repo_summary)
|
511 |
+
update_repo_button.click(update_repo, inputs=None,
|
512 |
+
outputs = repo_summary)
|
513 |
+
upload_button.upload(upload_file, upload_button, file_output)
|
514 |
+
|
515 |
+
with gr.Accordion("数据库构建参数", open=True):
|
516 |
+
gr.Markdown("[如何选择数据库构建参数]('https://github.com/jabberwockyang/MedicalReviewAgent/tree/main')")
|
517 |
+
chunksize = gr.Slider(label="Chunk Size",
|
518 |
+
info= 'How long you want the chunk to be?',
|
519 |
+
minimum=128, maximum=4096,value=1024,step=1,
|
520 |
+
interactive=True)
|
521 |
+
ncluster = gr.CheckboxGroup(["10", "20", "50", '100','200','500','1000'],
|
522 |
+
# default=["20", "50", '100'],
|
523 |
+
label="Number of Clusters",
|
524 |
+
info="How many Clusters you want to generate")
|
525 |
+
|
526 |
+
with gr.Row():
|
527 |
+
gene_database_button = gr.Button("生成数据库")
|
528 |
+
delete_database_button = gr.Button("删除数据库")
|
529 |
+
update_database_button = gr.Button("更新数据库情况")
|
530 |
+
|
531 |
+
database_summary = gr.Textbox(label="数据库概况",lines = 1,value="目前还没有数据库")
|
532 |
+
|
533 |
+
|
534 |
+
gene_database_button.click(generate_database, inputs=[chunksize,ncluster],
|
535 |
+
outputs = database_summary)
|
536 |
+
|
537 |
+
update_database_button.click(update_database_textbox,inputs=None,
|
538 |
+
outputs = [database_summary])
|
539 |
+
|
540 |
+
delete_database_button.click(delete_database, inputs=None,
|
541 |
+
outputs = database_summary)
|
542 |
+
with gr.Tab("写综述"):
|
543 |
+
gr.Markdown("""
|
544 |
+
#### 写综述 ✍️
|
545 |
+
|
546 |
+
1. **更新数据库情况**
|
547 |
+
- 点击“更新数据库情况”按钮,确保使用最新的数据库信息。
|
548 |
+
|
549 |
+
2. **选择块大小和聚类数**
|
550 |
+
- 从下拉菜单中选择合适的块大小和聚类数。
|
551 |
+
|
552 |
+
3. **抽样标注文章聚类**
|
553 |
+
- 设置抽样标注比例(0-1)。
|
554 |
+
- 点击“抽样标注文章聚类”按钮开始标注过程。
|
555 |
+
|
556 |
+
4. **获取灵感**
|
557 |
+
- 如果不知道写什么,点击“获取灵感”按钮。
|
558 |
+
- 系统将基于标注的文章聚类提供相应的综述子问题。
|
559 |
+
|
560 |
+
5. **写综述**
|
561 |
+
- 输入您想写的内容或主题。
|
562 |
+
- 点击“写综述”按钮,生成综述文本。
|
563 |
+
|
564 |
+
6. **查看生成结果**
|
565 |
+
- 生成的综述文本将显示在“看看”文本框中。
|
566 |
+
- 参考文献将显示在“参考文献”框中。
|
567 |
+
|
568 |
+
📝 **备注**:可以尝试不同的参数进行标注和灵感获取,有助于提高综述的质量和相关性。
|
569 |
+
""")
|
570 |
+
|
571 |
+
with gr.Accordion("聚类标注相关参数", open=True):
|
572 |
+
with gr.Row():
|
573 |
+
update_options = gr.Button("更新数据库情况", scale=0)
|
574 |
+
chunksize = gr.Dropdown([], label="选择块大小", scale=0)
|
575 |
+
nclusters = gr.Dropdown([], label="选择聚类数", scale=0)
|
576 |
+
ntoread = gr.Slider(
|
577 |
+
minimum=0,maximum=1,value=0.5,
|
578 |
+
interactive=True,
|
579 |
+
label="抽样标注比例",
|
580 |
+
)
|
581 |
+
|
582 |
+
annotation_button = gr.Button("抽样标注文章聚类")
|
583 |
+
annotation_output = gr.Textbox(label="文章聚类标注/片段摘要",
|
584 |
+
lines = 5,
|
585 |
+
interactive= True,
|
586 |
+
show_copy_button=True)
|
587 |
+
inspiration_button = gr.Button("获取灵感")
|
588 |
+
inspiration_output = gr.Textbox(label="灵光一现",
|
589 |
+
lines = 5,
|
590 |
+
show_copy_button=True)
|
591 |
+
|
592 |
+
|
593 |
+
query = gr.Textbox(label="想写什么")
|
594 |
+
|
595 |
+
write_button = gr.Button("写综述")
|
596 |
+
output_text = gr.Textbox(label="看看",lines=10)
|
597 |
+
output_references = gr.Markdown(label="参考文献")
|
598 |
+
|
599 |
+
update_options.click(update_chunksize_dropdown,
|
600 |
+
outputs=[chunksize])
|
601 |
+
|
602 |
+
chunksize.change(update_ncluster_dropdown,
|
603 |
+
inputs=[chunksize],
|
604 |
+
outputs= [nclusters])
|
605 |
+
|
606 |
+
annotation_button.click(annotation,
|
607 |
+
inputs = [ntoread, chunksize, nclusters,remote_ornot],
|
608 |
+
outputs=[annotation_output])
|
609 |
+
|
610 |
+
inspiration_button.click(inspiration,
|
611 |
+
inputs= [annotation_output, chunksize, nclusters,remote_ornot],
|
612 |
+
outputs=[inspiration_output])
|
613 |
+
|
614 |
+
write_button.click(summarize_text,
|
615 |
+
inputs=[query, chunksize,remote_ornot],
|
616 |
+
outputs =[output_text,output_references])
|
617 |
+
|
618 |
+
demo.launch(share=False, server_name='0.0.0.0', debug=True,show_error=True,allowed_paths=['img_0.jpg'])
|
619 |
+
|
620 |
+
# start service
|
621 |
+
if __name__ == '__main__':
|
622 |
+
args = parse_args()
|
623 |
+
# copy config from config-bak
|
624 |
+
shutil.copy('config-bak.ini', args.config_path) # yyj
|
625 |
+
CONFIG_PATH = args.config_path
|
626 |
+
|
627 |
+
if args.standalone is True:
|
628 |
+
# hybrid llm serve
|
629 |
+
server_ready = Value('i', 0)
|
630 |
+
server_process = Process(target=llm_serve,
|
631 |
+
args=(args.config_path, server_ready))
|
632 |
+
server_process.start()
|
633 |
+
while True:
|
634 |
+
if server_ready.value == 0:
|
635 |
+
logger.info('waiting for server to be ready..')
|
636 |
+
time.sleep(3)
|
637 |
+
elif server_ready.value == 1:
|
638 |
+
break
|
639 |
+
else:
|
640 |
+
logger.error('start local LLM server failed, quit.')
|
641 |
+
raise Exception('local LLM path')
|
642 |
+
logger.info('Hybrid LLM Server start.')
|
643 |
+
|
644 |
+
main_interface()
|
.ipynb_checkpoints/config-bak-checkpoint.ini
ADDED
@@ -0,0 +1,63 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
[feature_store]
|
2 |
+
reject_throttle = 0
|
3 |
+
embedding_model_path = "maidalun1020/bce-embedding-base_v1"
|
4 |
+
reranker_model_path = "maidalun1020/bce-reranker-base_v1"
|
5 |
+
repo_dir = "repodir"
|
6 |
+
work_dir = "workdir"
|
7 |
+
n_clusters = [20, 50]
|
8 |
+
chunk_size = 1024
|
9 |
+
|
10 |
+
[web_search]
|
11 |
+
x_api_key = "${YOUR-API-KEY}"
|
12 |
+
domain_partial_order = ["openai.com", "pytorch.org", "readthedocs.io", "nvidia.com", "stackoverflow.com", "juejin.cn", "zhuanlan.zhihu.com", "www.cnblogs.com"]
|
13 |
+
save_dir = "logs/web_search_result"
|
14 |
+
|
15 |
+
[llm]
|
16 |
+
enable_local = 1
|
17 |
+
enable_remote = 1
|
18 |
+
client_url = "http://127.0.0.1:8888/inference"
|
19 |
+
|
20 |
+
[llm.server]
|
21 |
+
local_llm_path = "Qwen/Qwen1.5-7B-Chat"
|
22 |
+
local_llm_max_text_length = 32000
|
23 |
+
local_llm_bind_port = 8888
|
24 |
+
remote_type = ""
|
25 |
+
remote_api_key = ""
|
26 |
+
remote_llm_max_text_length = 32000
|
27 |
+
remote_llm_model = ""
|
28 |
+
rpm = 500
|
29 |
+
|
30 |
+
[worker]
|
31 |
+
enable_sg_search = 0
|
32 |
+
save_path = "logs/work.txt"
|
33 |
+
|
34 |
+
[worker.time]
|
35 |
+
start = "00:00:00"
|
36 |
+
end = "23:59:59"
|
37 |
+
has_weekday = 1
|
38 |
+
|
39 |
+
[sg_search]
|
40 |
+
binary_src_path = "/usr/local/bin/src"
|
41 |
+
src_access_token = "${YOUR-SRC-ACCESS-TOKEN}"
|
42 |
+
|
43 |
+
[sg_search.opencompass]
|
44 |
+
github_repo_id = "open-compass/opencompass"
|
45 |
+
introduction = "用于评测大型语言模型(LLM). 它提供了完整的开源可复现的评测框架,支持大语言模型、多模态模型的一站式评测,基于分布式技术,对大参数量模型亦能实现高效评测。评测方向汇总为知识、语言、理解、推理、考试五大能力维度,整合集纳了超过70个评测数据集,合计提供了超过40万个模型评测问题,并提供长文本、安全、代码3类大模型特色技术能力评测。"
|
46 |
+
|
47 |
+
[sg_search.lmdeploy]
|
48 |
+
github_repo_id = "internlm/lmdeploy"
|
49 |
+
introduction = "lmdeploy 是一个用于压缩、部署和服务 LLM(Large Language Model)的工具包。是一个服务端场景下,transformer 结构 LLM 部署工具,支持 GPU 服务端部署,速度有保障,支持 Tensor Parallel,多并发优化,功能全面,包括模型转换、缓存历史会话的 cache feature 等. 它还提供了 WebUI、命令行和 gRPC 客户端接入。"
|
50 |
+
|
51 |
+
[frontend]
|
52 |
+
type = "none"
|
53 |
+
webhook_url = "https://open.feishu.cn/open-apis/bot/v2/hook/xxxxxxxxxxxxxxx"
|
54 |
+
message_process_policy = "immediate"
|
55 |
+
|
56 |
+
[frontend.lark_group]
|
57 |
+
app_id = "cli_a53a34dcb778500e"
|
58 |
+
app_secret = "2ajhg1ixSvlNm1bJkH4tJhPfTCsGGHT1"
|
59 |
+
encrypt_key = "abc"
|
60 |
+
verification_token = "def"
|
61 |
+
|
62 |
+
[frontend.wechat_personal]
|
63 |
+
bind_port = 9527
|