def get_current_user(db: Session = Depends(get_db),
token: str = Security(reusable_oauth2)):
# try:
# payload = jwt.decode(token, config.SECRET_KEY, algorithms=[ALGORITHM])
# token_data = TokenPayload(**payload)
# except PyJWTError:
# raise HTTPException(
# status_code=HTTP_403_FORBIDDEN, detail="Could not validate credentials"
# )
# user = crud.user.get(db, user_id=token_data.user_id)
# if not user:
# raise HTTPException(status_code=404, detail="User not found")
# return user
# get the kid from the headers prior to verification
headers = jwt.get_unverified_headers(token)
kid = headers['kid']
# search for the kid in the downloaded public keys
key_index = -1
for i in range(len(keys)):
if kid == keys[i]['kid']:
key_index = i
break
if key_index == -1:
logger.info('Public key not found in jwks.json')
return False
# construct the public key
public_key = jwk.construct(keys[key_index])
# get the last two sections of the token,
# message and signature (encoded in base64)
message, encoded_signature = str(token).rsplit('.', 1)
# decode the signature
decoded_signature = base64url_decode(encoded_signature.encode('utf-8'))
# verify the signature
if not public_key.verify(message.encode("utf8"), decoded_signature):
logger.info('Signature verification failed')
return False
logger.info('Signature successfully verified')
# since we passed the verification, we can now safely
# use the unverified claims
claims = jwt.get_unverified_claims(token)
# additionally we can verify the token expiration
if time.time() > claims['exp']:
logger.info('Token is expired')
raise HTTPException(status_code=404, detail="Sessions has expired.")
# and the Audience (use claims['client_id'] if verifying an access token)
if claims['client_id'] != app_client_id:
logger.info('Token was not issued for this audience')
raise HTTPException(status_code=404,
detail="Unauthorized access. Access denied")
# now we can use the claims
# print(claims)
user = crud.user.get(db, cognito_user_id=claims["sub"])
if not user:
raise HTTPException(status_code=404, detail="User not found")
return user
async def faceted_search(
*,
db: Session = Depends(get_db),
start: int = 0,
limit: int = 25,
file_id: int,
category: str,
current_user: DBUser = Depends(get_current_active_user)):
confirm_case_id_with_biz_id = get_by_file_ids(db,
ids=[file_id],
user_details=current_user)
if not confirm_case_id_with_biz_id:
logger.info(
f"Invalid file_id of value {file_id} found for business_id {current_user.business_id}"
)
raise HTTPException(
status_code=400,
detail="Invalid details passed.",
)
cat = None
if category:
if category.__eq__("Body Part/Organ"):
cat = "t023"
else:
for k, v in all_categories.items():
if category.__eq__(v):
cat = k
break
else:
logger.info(
f"No category found for variable {category} and business_id {current_user.business_id}"
)
raise HTTPException(
status_code=400,
detail="Invalid details passed.",
)
params = {
"fq":
f"business_id%3A{current_user.business_id}%20AND%20file_id%3A{file_id}",
"q": f"tui%3A{cat}",
"rows": min(limit, 500),
"start": start
}
local_session = await get_session()
resp = await local_session.get(url, params=params)
res = json.loads(await resp.text())
result = res["response"]
return result
def confirm_case_id_with_biz_id_helper_func(db, case_id, current_user):
confirm_case_id_with_biz_id = get_by_case_id(db,
id=case_id,
user_details=current_user)
if not confirm_case_id_with_biz_id:
logger.info(
f"Invalid case_id of value {case_id} found for business_id {current_user.business_id}"
)
raise HTTPException(
status_code=400,
detail="Invalid details passed.",
)
async def preset_cat_filters(
*,
db: Session = Depends(get_db),
case_id: int,
category: str,
# txt: Optional[str],
# start: int = 0,
# limit: int = 25,
current_user: DBUser = Depends(get_current_active_user),
response: Response):
confirm_case_id_with_biz_id_helper_func(db, case_id, current_user)
f_pivot = "category,text,confirmed_visit_date,id"
params = {
"q": "*:*",
"fq":
f"category:\"{category}\" AND business_id:{current_user.business_id} AND case_id:{case_id}",
"facet.pivot": f_pivot,
"facet": "true",
"rows": "0",
"facet.pivot.mincount": "1",
"facet.limit": "-1"
}
local_session = await get_session()
resp = await local_session.get(url, params=urllib.parse.urlencode(params))
res = json.loads(await resp.text())
if "error" in res:
logger.info(
f"Exception occurred for business_id: {current_user.business_id} while fetching file_id: {case_id} "
f"with below exception. \n {res['error']['trace']}")
raise HTTPException(
status_code=res["error"]["code"],
detail="Invalid details passed.",
)
d: PresetCatFiltersSearchResults = PresetCatFiltersSearchResults(
field=None, value=None, count=None, pivot=None)
if len(res["facet_counts"]["facet_pivot"][f_pivot]) > 0:
d = res["facet_counts"]["facet_pivot"][f_pivot][0]
# response.headers["cache-control"] = f"private, max-age={int(86400)}"
return d
def delete_by_file_id(db_session, *, file_id: list, user_details=None):
# this is a cascade delete. It will delete from following tables:
# select * from file;
# select * from file_state;
# select * from sf_ctakes_mentions;
# select * from mentions_rel_text;
try:
deleted_objects = File.__table__.delete().where(File.id.in_(file_id))
db_session.execute(deleted_objects)
db_session.commit()
except Exception as e:
logger.info(
f"Exception for business_id: {user_details.business_id} and user: {user_details.id} "
f"{e}")
traceback.print_exc(file=sys.stdout)
raise HTTPException(
status_code=400,
detail="Exception occurred while deleting file(s).",
)
return True
async def get_pdf_cords(
*,
db: Session = Depends(get_db),
case_id: int,
m_id: int,
current_user: DBUser = Depends(get_current_active_user),
response: Response):
confirm_case_id_with_biz_id_helper_func(db, case_id, current_user)
params = {
"q": "*:*",
"fq":
f"id:{m_id} AND business_id:{current_user.business_id} AND case_id:{case_id}",
"fl": "full_text_bbox, page_number"
}
local_session = await get_session()
resp = await local_session.get(url, params=urllib.parse.urlencode(params))
res = json.loads(await resp.text())
if "error" in res:
logger.info(
f"Exception occurred for business_id: {current_user.business_id} while fetching file_id: {case_id} "
f"with below exception. \n {res['error']['trace']}")
raise HTTPException(
status_code=res["error"]["code"],
detail="Invalid details passed.",
)
obj_to_return = {}
if len(res["response"]["docs"]) > 0:
obj_to_return = res["response"]["docs"][0]
else:
obj_to_return["full_text_bbox"] = ""
obj_to_return["page_number"] = 0
# Cache-Control:public, max-age=31536000
# response.headers["cache-control"] = f"private, max-age={int(86400)}"
return obj_to_return
def delete_file(*,
db: Session = Depends(get_db),
file_id: list = Body(None),
current_user: DBUser = Depends(get_current_active_user)):
f_id = [(int(i["id"]), ) for i in file_id if "id" in i]
# confirm_file_for_user = crud.file.get_by_file_ids(db, ids=f_id, user_details=current_user)
try:
result = crud.file.get_filestate_files(db,
ids=f_id,
user_details=current_user)
# extract unique and all s3 files to delete
s3_files_delete = ()
for r in result:
s3_files_delete = s3_files_delete + r
final_s3_files_delete = list(set(s3_files_delete))
# delete from database first
crud.file.delete_by_file_id(db,
file_id=f_id,
user_details=current_user)
# delete from s3 next
crud.file.delete_s3_file(final_s3_files_delete)
except Exception as e:
logger.info(
f'Exception occurred while deleting file with id: {file_id} for '
f"business_id: {current_user.business_id}. Exception is: ")
logger.info(e)
raise HTTPException(
status_code=400,
detail="There was a problem while deleting file.",
)
return FileDelete(response="success")
async def faceted_search(
*,
db: Session = Depends(get_db),
case_id: int,
current_user: DBUser = Depends(get_current_active_user),
response: Response):
# confirm_case_id_with_biz_id = get_by_case_id(db, id=case_id, user_details=current_user)
#
# if not confirm_case_id_with_biz_id:
# logger.info(f"Invalid case_id of value {case_id} found for business_id {current_user.business_id}")
# raise HTTPException(
# status_code=400,
# detail="Invalid details passed.",
# )
confirm_case_id_with_biz_id_helper_func(db, case_id, current_user)
params = {
"q": "%2A:%2A",
"fq":
f"business_id:{current_user.business_id}%20AND%20case_id:{case_id}",
# %20AND%20"
# f"concept_attributes:%28t037%20OR%20t047%20OR%20t184%20OR%20t190%20OR%20t017%29",
"facet": "true",
# "facet.field": "tui",
"facet.field": "category",
"rows": "0",
"facet.mincount": "1"
}
local_session = await get_session()
resp = await local_session.get(url, params=params)
res = json.loads(await resp.text())
if "error" in res:
logger.info(
f"Exception occurred for business_id: {current_user.business_id} while fetching file_id: {case_id} "
f"with below exception. \n {res['error']['trace']}")
raise HTTPException(
status_code=res["error"]["code"],
detail="Invalid details passed.",
)
result = res["facet_counts"]["facet_fields"]["category"]
return_list = []
for i in range(0, len(result), 2):
# if we were faceting by TUI or CUI then we would need line
# obj = {str(all_categories[result[i]]): result[i + 1]}
# but we are faceting by Category for easy viewing for end user
if str(result[i]) in [
'Sign Or Symptom', 'Medication', 'Body Site',
'Medical Procedure', 'Disease Disorder'
]:
obj = {str(result[i]): result[i + 1]}
return_list.append(obj)
# response.headers["cache-control"] = f"private, max-age={int(86400)}"
return return_list
async def search_text_for_visit_date(
*,
db: Session = Depends(get_db),
file_id: int,
cvd: Optional[str],
txt: Optional[str],
start: int = 0,
limit: int = 25,
current_user: DBUser = Depends(get_current_active_user)):
if not cvd and not txt:
logger.info(
f"Visit Date and Text passed was Blank for file_id of value {file_id} and"
f" business_id {current_user.business_id}")
raise HTTPException(
status_code=400,
detail="Invalid details passed.",
)
main_str = f"business_id:{current_user.business_id} AND file_id:{file_id} "
if cvd:
cvd = cvd.split(",")
str_h = " AND ("
cvd_str = f"confirmed_visit_date:"
for i, c in enumerate(cvd):
if i > 0:
str_h = str_h + " OR "
str_h = str_h + cvd_str + c
str_h += ")"
main_str += str_h
if txt:
main_str += f" AND (text:{txt} OR full_text:{txt})"
confirm_case_id_with_biz_id = get_by_file_ids(db,
ids=[file_id],
user_details=current_user)
if not confirm_case_id_with_biz_id:
logger.info(
f"Invalid file_id of value {file_id} found for business_id {current_user.business_id}"
)
raise HTTPException(
status_code=400,
detail="Invalid details passed.",
)
# in case someone ever tries to temper with frontend payload and try to get other business' details:
if main_str.count("business_id") > 1:
logger.warn(
f"Looks like someone tried to temper with frontend payload and added business_id twice: "
f"\nmain_str: {main_str}")
raise HTTPException(
status_code=400,
detail="Invalid details passed.",
)
params = {"fq": main_str, "q": "%2A%3A%2A", "rows": limit, "start": start}
local_session = await get_session()
resp = await local_session.get(url, params=params)
res = json.loads(await resp.text())
distinct_full_text = []
result = res["response"]
for i, r in enumerate(result["docs"]):
if r["full_text"] + r["confirmed_visit_date"] not in distinct_full_text:
distinct_full_text.append(r["full_text"] +
r["confirmed_visit_date"])
else:
result["docs"].pop(i)
# numfound etc etc
return result