teffalump / beren Goto Github PK

Hi,

I tried to send dicom with Orthanc's store_modality function. I got 400 bad request error. This function takes dcm and data
properties. I didn't fully understand the data parameter. Can you provide an example

Thanks

Thank you very much for this developpement. I am struggling to get it work properly though.

What is the id you are referring to ?
this snippet

query_pat = {'Level': 'Patient',
            'Query': {'PatientName': 'test*'},
        }

id = orthanc.find(query_pat)
print(id)
orthanc.get_patient_series(id[0])

gives me a keyword error message. KeyError: 'id'
and some warnings

... site-packages\orthanc_rest_client\orthanc.py:33: RuntimeWarning: An unknown path kwarg was supplied to patients/{id}/series/. kwargs supplied: {'path_kwargs': {'id': 'cf74b893-0c49f5f4-c491da1d-b7485ee8-9a3ea1e1'}}
return function(self, *args, **kwargs)

when i try to obtain all patients from orthanc, i get a timeout error.
the orthanc server hosts quite a large number of patients, and orthanc is running on a single-core VM, so it might take much more than the 3 seconds default timeout.
how to increase the timeout?
(sorry, i am still not an REST expert, if this issue is a simple extra argument somewhere)

Hi, I am using your library when uploading DICOM file to OrthanC server. Previously, I used HTTP client like this:

class OrthancClient:
    def __init__(self, url=None, username=None, password=None):
        self.url = url
        self.client = httpx.AsyncClient(verify=False)

    def init(self, url):
        self.url = url

    async def get_simplified_tags(self, level, uuid):
        res = await self.client.get(f"{self.url}/{level}/{uuid}/simplified-tags")
        res.raise_for_status()
        return res.json()

    async def find(self, body):
        res = await self.client.post(f"{self.url}/tools/find", json=body)
        res.raise_for_status()
        return res.json()

    async def retrieve(self, level, uuid, asset=None):
        if asset is None:
            res = await self.client.get(f"f{self.url}/{level}/{uuid}")
        else:
            res = await self.client.get(f"f{self.url}/{level}/{uuid}/{asset}")
        res.raise_for_status()
        return res

    async def upload(self, data):
        res = await self.client.post(f"{self.url}/instances", content=data)
        res.raise_for_status()
        return res.json()

    async def get(self, path: str):
        res = await self.client.get(f"{self.url}{path}")
        res.raise_for_status()
        return res.json()

As you see, I've set self.client = httpx.AsyncClient(verify=False). But when I used oc2 = Orthanc(settings.ORTHANC_API_URI), I dont know how to configure like it before.

Please help me!

hi, thanks for the package.

i want to communicate with a personal, "off-the-internet" server which unfortunately has no kind of SSL certificate, but still communicates with https. i get a handshake error:

Error Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/urllib3/contrib/pyopenssl.py in wrap_socket(self, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname)
452 try:
--> 453 cnx.do_handshake()
454 except OpenSSL.SSL.WantReadError:

/usr/lib/python3/dist-packages/OpenSSL/SSL.py in do_handshake(self)
1807 result = _lib.SSL_do_handshake(self._ssl)
-> 1808 self._raise_ssl_error(self._ssl, result)
1809

/usr/lib/python3/dist-packages/OpenSSL/SSL.py in _raise_ssl_error(self, ssl, result)
1547 else:
-> 1548 _raise_current_error()
1549

/usr/lib/python3/dist-packages/OpenSSL/_util.py in exception_from_error_queue(exception_type)
53
---> 54 raise exception_type(errors)
55

Error: [('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')]

During handling of the above exception, another exception occurred:

SSLError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
599 body=body, headers=headers,
--> 600 chunked=chunked)
601

/usr/local/lib/python3.6/dist-packages/urllib3/connectionpool.py in _make_request(self, conn, method, url, timeout, chunked, **httplib_request_kw)
342 try:
--> 343 self._validate_conn(conn)
344 except (SocketTimeout, BaseSSLError) as e:

/usr/local/lib/python3.6/dist-packages/urllib3/connectionpool.py in _validate_conn(self, conn)
838 if not getattr(conn, 'sock', None): # AppEngine might not have .sock
--> 839 conn.connect()
840

/usr/local/lib/python3.6/dist-packages/urllib3/connection.py in connect(self)
343 server_hostname=server_hostname,
--> 344 ssl_context=context)
345

/usr/local/lib/python3.6/dist-packages/urllib3/util/ssl_.py in ssl_wrap_socket(sock, keyfile, certfile, cert_reqs, ca_certs, server_hostname, ssl_version, ciphers, ssl_context, ca_cert_dir)
356
--> 357 return context.wrap_socket(sock)
358

/usr/local/lib/python3.6/dist-packages/urllib3/contrib/pyopenssl.py in wrap_socket(self, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname)
458 except OpenSSL.SSL.Error as e:
--> 459 raise ssl.SSLError('bad handshake: %r' % e)
460 break

SSLError: ("bad handshake: Error([('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')],)",)

During handling of the above exception, another exception occurred:

MaxRetryError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies)
448 retries=self.max_retries,
--> 449 timeout=timeout
450 )

/usr/local/lib/python3.6/dist-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
666 release_conn=release_conn, body_pos=body_pos,
--> 667 **response_kw)
668

/usr/local/lib/python3.6/dist-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
637 retries = retries.increment(method, url, error=e, _pool=self,
--> 638 _stacktrace=sys.exc_info()[2])
639 retries.sleep()

/usr/local/lib/python3.6/dist-packages/urllib3/util/retry.py in increment(self, method, url, response, error, _pool, _stacktrace)
397 if new_retry.is_exhausted():
--> 398 raise MaxRetryError(_pool, url, error or ResponseError(cause))
399

MaxRetryError: HTTPSConnectionPool(host='X.X.X.X, port=8042): Max retries exceeded with url: /patients/ (Caused by SSLError(SSLError("bad handshake: Error([('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')],)",),))

During handling of the above exception, another exception occurred:

SSLError Traceback (most recent call last)
in ()
----> 1 orthanc.get_patients()

/usr/local/lib/python3.6/dist-packages/beren/orthanc.py in get_patients(self, expand, since, limit, params, **kwargs)
490 kwargs["params"] = params
491 kwargs["auth"] = kwargs.get("auth", self.auth)
--> 492 return self.patients.patients(**kwargs)
493
494 def get_patient(self, id, **kwargs):

/usr/local/lib/python3.6/dist-packages/apiron/client.py in call(service, endpoint, method, session, params, data, files, json, headers, cookies, auth, encoding, retry_spec, timeout_spec, logger, allow_redirects, return_raw_response_object, **kwargs)
246 timeout=(timeout_spec.connection_timeout, timeout_spec.read_timeout),
247 stream=getattr(endpoint, "streaming", False),
--> 248 allow_redirects=allow_redirects,
249 )
250

/usr/local/lib/python3.6/dist-packages/requests/sessions.py in send(self, request, **kwargs)
641
642 # Send the request
--> 643 r = adapter.send(request, **kwargs)
644
645 # Total elapsed time of the request (approximately)

/usr/local/lib/python3.6/dist-packages/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies)
512 if isinstance(e.reason, _SSLError):
513 # This branch is for urllib3 v1.22 and later.
--> 514 raise SSLError(e, request=request)
515
516 raise ConnectionError(e, request=request)

SSLError: HTTPSConnectionPool(host='X.X.X.X', port=8042): Max retries exceeded with url: /patients/ (Caused by SSLError(SSLError("bad handshake: Error([('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')],)",),))

is there a way to go around this problem? or is it possible to add a "verify" argument to Orthanc? (possibly aprion needs the corresponding change)

thanks

Thoughts:

• More robust examples.
• Document every method
• Doxygen/Sphinx (eventually)

Hi,

is there any support for performing finds?

Thanks,
Joshy

Hello,

Is there any way to convert an instance into a .dcm file? I am trying to do the code below but 'get_file()' doesn't exist.

    query = {'Level': 'Instance',
                'Query': {'PatientName': data.get('case')},
            }
    for id in orthanc.find(query):
        dicom = orthanc.get_instance(id)
        # orthanc.get_file(dicom) - then convert to a file locally using OS or something

In other words, I am trying to do this as mentioned in https://book.orthanc-server.com/users/rest.html#accessing-the-dicom-fields-of-an-instance-as-a-json-file

$ curl http://localhost:8042/instances/e668dcbf-8829a100-c0bd203b-41e404d9-c533f3d4/file > Instance.dcm

How to config a new timeout? I can not find slow_endpoint in the source code.