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solr query in separate module
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async context manager for api key injection
download as image working (via solr)
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@vedina
vedina committed Sep 13, 2024
1 parent 251b86d commit b8c3c82
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Showing 6 changed files with 107 additions and 174 deletions.
41 changes: 17 additions & 24 deletions src/rcapi/api/convertor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,13 @@
import ramanchada2 as rc2
from pynanomapper.clients.datamodel_simple import StudyRaman
from numcompress import compress
from rcapi.services.convertor_service import empty_figure,dict2figure, image, thumbnail, knnquery, recursive_copy
from rcapi.services.kc import inject_api_key_h5pyd, inject_api_key_into_requests, get_api_key
from rcapi.services.convertor_service import empty_figure,dict2figure, solr2image, knnquery, recursive_copy
from rcapi.services.kc import inject_api_key_h5pyd, inject_api_key_into_httpx, get_api_key
import h5py, h5pyd
from rcapi.services.solr_query import SOLR_ROOT,SOLR_VECTOR,SOLR_COLLECTION

router = APIRouter()

solr_root = "https://solr-kc.ideaconsult.net/solr/"

@router.get("/download", )
async def convert_get(
Expand All @@ -33,7 +33,7 @@ async def convert_get(
#tr.set_error("missing domain")
raise HTTPException(status_code=400, detail=str("missing domain"))

solr_url = "{}charisma/select".format(solr_root)
solr_url = "{}{}/select".format(SOLR_ROOT,SOLR_COLLECTION)

width = w
height = h
Expand All @@ -47,37 +47,30 @@ async def convert_get(
FigureCanvas(fig).print_png(output)
return Response(content=output.getvalue(), media_type='image/png')

if what in ["dict","thumbnail"]: #solr query
if what in ["dict","thumbnail","b64png","image"]: #solr query
if what == "dict":
prm = dict(request.query_params)
prm["what"] = None
fig = dict2figure(prm, figsize)
output = io.BytesIO()
FigureCanvas(fig).print_png(output)
return Response(content=output.getvalue(), media_type='image/png')
if what == "thumbnail":
with inject_api_key_into_requests(api_key):
fig = thumbnail(solr_url, domain, figsize, extra)
else:
async with inject_api_key_into_httpx(api_key):
fig = await solr2image(solr_url, domain, figsize, extra)
output = io.BytesIO()
FigureCanvas(fig).print_png(output)
return Response(content=output.getvalue(), media_type='image/png')

if what == "b64png":
base64_bytes = base64.b64encode(output.getvalue())
return Response(content=base64_bytes, media_type='text/plain')
else:
return Response(content=output.getvalue(), media_type='image/png')


elif what in ["knnquery","h5","b64png","image"]: # h5 query
elif what in ["knnquery","h5"]: # h5 query
try:
with inject_api_key_h5pyd(api_key):
if what == "b64png":
fig = image(domain, dataset)
output = io.BytesIO()
FigureCanvas(fig).print_png(output)
base64_bytes = base64.b64encode(output.getvalue())
return Response(content=base64_bytes, media_type='text/plain')
elif what == "image":
fig = image(domain, dataset, figsize, extra)
output = io.BytesIO()
FigureCanvas(fig).print_png(output)
return Response(content=output.getvalue(), media_type='image/png')
elif what == "knnquery":
if what == "knnquery":
return knnquery(domain, dataset)
elif what == "h5":
try:
Expand All @@ -88,6 +81,7 @@ async def convert_get(
tmpfile.seek(0)
return Response(content=tmpfile.read(), media_type="application/x-hdf5", headers={"Content-Disposition": "attachment; filename=download.h5"})
except Exception as e:
print(traceback.format_exc())
raise HTTPException(status_code=400, detail=f" error: {str(e)}")
except Exception as e:
raise HTTPException(status_code=500, detail=f" error: {str(e)}")
Expand Down Expand Up @@ -121,7 +115,6 @@ async def convert_post(

if file_extension != ".cha":
x, y, _meta = rc2.spectrum.from_local_file(file=uf.file, f_name=f_name)
print(x)
if what == "knnquery":
_cdf, pdf = StudyRaman.xy2embedding(x, y, StudyRaman.x4search(dim=2048))
result_json = {"cdf": compress(pdf.tolist(), precision=6)}
Expand Down
9 changes: 4 additions & 5 deletions src/rcapi/api/query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,9 @@
from typing import Optional, Literal
from rcapi.services import query_service
import traceback
router = APIRouter()
from rcapi.services.solr_query import SOLR_ROOT,SOLR_VECTOR,SOLR_COLLECTION

solr_root = "https://solr-kc.ideaconsult.net/solr/"
solr_vector_field = "spectrum_p1024"
router = APIRouter()

@router.get("/query", )
async def get_query(
Expand All @@ -18,7 +17,7 @@ async def get_query(
page : Optional[int] = 0, pagesize : Optional[int] = 10,
img: Optional[Literal["embedded", "original", "thumbnail"]] = "thumbnail",
):
solr_url = "{}charisma/select".format(solr_root)
solr_url = "{}{}/select".format(SOLR_ROOT,SOLR_COLLECTION)

textQuery = q
textQuery = "*" if textQuery is None or textQuery=="" else textQuery
Expand All @@ -36,7 +35,7 @@ async def get_query(
page=page,
pagesize=pagesize,
img=img,
vector_field=solr_vector_field
vector_field=SOLR_VECTOR
)
return results
except Exception as err:
Expand Down
47 changes: 11 additions & 36 deletions src/rcapi/services/convertor_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,7 @@
from numcompress import compress
from pynanomapper.clients.datamodel_simple import StudyRaman
import h5py, h5pyd
import requests
from .kc import AuthenticatedRequest
from rcapi.services.solr_query import solr_query_post,solr_query_get,SOLR_ROOT,SOLR_COLLECTION,SOLR_VECTOR
import traceback

def empty_figure(figsize,title,label):
Expand Down Expand Up @@ -60,33 +59,6 @@ def dict2figure(pm,figsize):
axis.set_title(pm["domain"])
return fig

def image(domain,dataset="raw",figsize=(6,4),extraprm=""):
try:
with h5pyd.File(domain,mode="r") as h5:
x = h5[dataset][0]
y = h5[dataset][1]
try:
_sample = h5["annotation_sample"].attrs["sample"]
except:
_sample = None
try:
_provider = h5["annotation_study"].attrs["provider"]
except:
_provider = None
try:
_wavelength = h5["annotation_study"].attrs["wavelength"]
except:
_wavelength = None
fig = Figure(figsize=figsize)
axis = fig.add_subplot(1, 1, 1)
axis.plot(x, y, color='black')
axis.set_ylabel(h5[dataset].dims[1].label)
axis.set_xlabel(h5[dataset].dims[0].label)
axis.title.set_text("{} {} ({}) {}".format(extraprm,_sample,_provider,_wavelength))
#domain.split("/")[-1],dataset))
return fig
except Exception as err:
return empty_figure(figsize,"Error","{}".format(domain.split("/")[-1]))

def knnquery(domain,dataset="raw"):
try:
Expand Down Expand Up @@ -116,22 +88,25 @@ def knnquery(domain,dataset="raw"):
except Exception as err:
raise(err)

def thumbnail(solr_url,domain,figsize=(6,4),extraprm=""):
async def solr2image(solr_url,domain,figsize=(6,4),extraprm=None):
rs = None
try:
query="textValue_s:\"{}\"".format(domain.replace(" ","\ "))
params = {"q": query, "fq" : ["type_s:study"], "fl" : "name_s,textValue_s,reference_s,reference_owner_s,spectrum_p1024"}
rs = solrquery_get(solr_url, params = params)
params = {"q": query, "fq" : ["type_s:study"], "fl" : "name_s,textValue_s,reference_s,reference_owner_s,{}".format(SOLR_VECTOR)}
rs = await solr_query_get(solr_url, params)
if rs.status_code==200:
x = StudyRaman.x4search()
x = None
for doc in rs.json()["response"]["docs"]:
y = doc["spectrum_p1024"]
y = doc[SOLR_VECTOR]
if x is None:
x = StudyRaman.x4search(len(y))
fig = Figure(figsize=figsize)
axis = fig.add_subplot(1, 1, 1)
axis.plot(x, y)
axis.set_ylabel("a.u.")
axis.set_xlabel("Raman shift [1/cm]")
axis.title.set_text("{} {} {} ({})".format(extraprm,doc["name_s"],doc["reference_owner_s"],doc["reference_s"]))
axis.set_xlabel("Wavenumber [1/cm]")
axis.title.set_text("{} {} {} ({})".format("" if extraprm is None else extraprm,
doc["name_s"],doc["reference_owner_s"],doc["reference_s"]))
return fig
else:
return empty_figure(figsize,"{} {}".format(rs.status_code,rs.reason),"{}".format(domain.split("/")[-1]))
Expand Down
120 changes: 40 additions & 80 deletions src/rcapi/services/kc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
import logging
import threading
import h5pyd
import requests
from contextlib import contextmanager
import httpx
from contextlib import contextmanager, asynccontextmanager
from typing import Optional

# Thread-local storage for API key
Expand All @@ -23,84 +23,6 @@ def get_api_key(authorization: Optional[str] = Header(None)):
return None
# raise HTTPException(status_code=401, detail="Invalid or missing Authorization header")

class AuthenticatedRequest:
def __init__(self, get_token):
"""
Initialize the AuthenticatedRequest context manager.
Args:
get_token (callable): A function to retrieve the current token.
with AuthenticatedRequest(get_token):
requests.get()
...
"""
self.get_token = get_token
self.original_post = None

def __enter__(self):
# Save the original requests.post method
self.original_post = requests.post
# Override requests.post with our modified version
requests.post = self.modified_post

def __exit__(self, exc_type, exc_value, traceback):
# Restore the original requests.post method
requests.post = self.original_post


def modified_post(self, url, **kwargs):
# Retrieve the current token
token = self.get_token()
# Ensure the headers dictionary exists
headers = kwargs.setdefault('headers', {})
# Add the Authorization header, without overwriting other headers
if 'Authorization' not in headers:
headers['Authorization'] = f'Bearer {token}'
# Make the request with the modified headers
return self.original_post(url, **kwargs)


# Context manager to inject the API key into a thread-local session for all requests
@contextmanager
def inject_api_key_into_requests(api_key):
"""
Thread-safe context manager to inject the API key into the thread-local `requests.Session`
used for making HTTP requests.
Each thread will have its own independent `requests.Session`, ensuring that the
`Authorization: Bearer <api_key>` header is correctly applied without affecting other threads.
Parameters:
-----------
api_key : str
The API key to inject into the requests headers.
Yields:
-------
session : requests.Session
The thread-local session object, with the Authorization header pre-configured.
Example:
--------
>>> with inject_api_key_into_requests(api_key="your_api_key") as session:
>>> response = session.get("https://example.com/data")
>>> response = session.post("https://example.com/data", json={"key": "value"})
>>> # The Authorization header will automatically be included in both requests.
"""
if not hasattr(thread_local, "session"):
thread_local.session = requests.Session()

# Add Authorization header to the session for this thread
thread_local.session.headers.update({"Authorization": f"Bearer {api_key}"})

try:
yield thread_local.session # Provide the session for this thread's context
finally:
# Optional: Clean up if necessary (e.g., closing the session)
pass


# Context manager to temporarily patch h5pyd.File to inject the api_key
@contextmanager
Expand Down Expand Up @@ -163,3 +85,41 @@ def patched_h5pyd_folder(*args, **kwargs):
h5pyd.File = original_h5pyd_file
h5pyd.Folder = original_h5pyd_folder

@asynccontextmanager
async def inject_api_key_into_httpx(api_key: str):
"""
Thread-safe async context manager to inject the API key into the thread-local `httpx.AsyncClient`
used for making HTTP requests.
Each thread will have its own independent `httpx.AsyncClient`, ensuring that the
`Authorization: Bearer <api_key>` header is correctly applied without affecting other threads.
Parameters:
-----------
api_key : str
The API key to inject into the requests headers.
Yields:
-------
client : httpx.AsyncClient
The thread-local `AsyncClient` object, with the Authorization header pre-configured.
Example:
--------
>>> async with inject_api_key_into_requests(api_key="your_api_key") as client:
>>> response = await client.get("https://example.com/data")
>>> response = await client.post("https://example.com/data", json={"key": "value"})
>>> # The Authorization header will automatically be included in both requests.
"""
if not hasattr(thread_local, "client"):
thread_local.client = httpx.AsyncClient()

# Add Authorization header to the client for this thread
thread_local.client.headers.update({"Authorization": f"Bearer {api_key}"})

try:
yield thread_local.client # Provide the client for this thread's context
finally:
# Optionally close the client if required
await thread_local.client.aclose()
del thread_local.client # Clean up the client after use
30 changes: 1 addition & 29 deletions src/rcapi/services/query_service.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,36 +2,8 @@
from typing import Optional, Literal
from fastapi import Request, HTTPException
from numcompress import decompress
import httpx
import traceback
from rcapi.services.solr_query import solr_query_post,solr_query_get

async def solr_query_post(solr_url,query_params = None,post_param = None):
async with httpx.AsyncClient() as client:
try:
response = await client.post(
solr_url,
json=post_param,
params = query_params
)
response.raise_for_status() # Check for HTTP errors
return response
except httpx.HTTPStatusError as e:
print(traceback.format_exc())
raise HTTPException(status_code=e.response.status_code, detail="Error fetching data from external service")

async def solr_query_get(solr_url,query_params = None):
async with httpx.AsyncClient() as client:
try:
response = await client.get(
solr_url,
params = query_params
)
response.raise_for_status() # Check for HTTP errors
return response
except httpx.HTTPStatusError as e:
print(traceback.format_exc())
raise HTTPException(status_code=e.response.status_code, detail="Error fetching data from external service")

async def process(request: Request,
solr_url: str,
q: Optional[str] = "*",
Expand Down
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