Opal 5.6.3 search

[Sean Hurley]

Greetings

If I select an entity search and put in a query, the results are never displayed. I suspect I'm missing something but I don't know what. Any help would be appreciated.

Thanks.

[Yannick Marcon]

Hi Sean,

What do you get using the opal python CLI, with an entity command similar to this one:

opal entity 1444 --opal https://opal-demo.obiba.org --user administrator --password password --tables --type Participant

If it fails you can add the --verbose option to get details of the http response.

Regards

Yannick

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[Sean Hurley]

Hi Yannick, 

The command hangs without any output beyond the initial python request:
send: b'GET /ws/entity/XXXXXXX/type/Participant/tables HTTP/1.1\r\nHost: opal-demo.obiba.org\r\nUser-Agent: python-requests/2.31.0\r\nAccept-Encoding: gzip, deflate\r\nAccept: application/json\r\nConnection: keep-alive\r\nAuthorization: Basic c2h1TYuupUnngxMDoxNw==\r\n\r\n'

Logs don't show any errors or information related.

Sean.

[Elson, Dwain]

Not sure if this helps but ctrl C out of the process.

^CTraceback (most recent call last):

  File "/usr/local/bin/opal", line 8, in <module>

    sys.exit(run())

  File "/usr/local/lib/python3.10/dist-packages/obiba_opal/console.py", line 184, in run

    args.func(args)

  File "/usr/local/lib/python3.10/dist-packages/obiba_opal/data.py", line 153, in do_command

    res = EntityService(client, args.verbose).get_entity_tables(args.id, args.type)

  File "/usr/local/lib/python3.10/dist-packages/obiba_opal/data.py", line 175, in get_entity_tables

    response = request.fail_on_error().accept_json().get().resource(self._make_ws(id, type, True)).send()

  File "/usr/local/lib/python3.10/dist-packages/obiba_opal/core.py", line 399, in send

    response = OpalResponse(self.client.session.send(request.prepare()))

  File "/usr/local/lib/python3.10/dist-packages/requests/sessions.py", line 703, in send

    r = adapter.send(request, **kwargs)

  File "/usr/local/lib/python3.10/dist-packages/requests/adapters.py", line 486, in send

    resp = conn.urlopen(

  File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 703, in urlopen

    httplib_response = self._make_request(

  File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 449, in _make_request

    six.raise_from(e, None)

  File "<string>", line 3, in raise_from

  File "/usr/local/lib/python3.10/dist-packages/urllib3/connectionpool.py", line 444, in _make_request

    httplib_response = conn.getresponse()

  File "/usr/lib/python3.10/http/client.py", line 1395, in getresponse

    response.begin()

  File "/usr/lib/python3.10/http/client.py", line 323, in begin

    version, status, reason = self._read_status()

  File "/usr/lib/python3.10/http/client.py", line 284, in _read_status

    line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")

  File "/usr/lib/python3.10/socket.py", line 705, in readinto

    return self._sock.recv_into(b)

KeyboardInterrupt

Dwain

---

From: obiba...@googlegroups.com <obiba...@googlegroups.com> on behalf of Sean Hurley <cyber...@gmail.com>
Sent: Tuesday, April 28, 2026 3:57 PM
To: obiba-users <obiba...@googlegroups.com>
Subject: Re: [OBiBa] Opal 5.6.3 search

 

  Caution: External email.

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[Yannick Marcon]

You did connect to opal-demo.obiba.org apparently, if there is no answer it is a network issue on your side.

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[Sean Hurley]

That's just a placeholder. It is not the URL. 

[Sean Hurley]

Hi Yannick

I misunderstood. You wanted me to use that URL. I had replaced it with my own. Please see below.

opal entity 1444 --opal https://opal-demo.obiba.org --user administrator --password password --tables --type Participant

[{"datasourceName": "CNSIM", "entityType": "Participant", "link": "/datasource/CNSIM/table/CNSIM1", "name": "CNSIM1", "status": "READY", "timestamps": {"created": "2026-04-28T06:29:57.248Z", "lastUpdate": "2026-04-28T06:29:58.370Z"}}, {
"datasourceName": "CNSIM", "entityType": "Participant", "link": "/datasource/CNSIM/table/CNSIM2", "name": "CNSIM2", "status": "READY", "timestamps": {"created": "2026-04-28T06:29:58.373Z", "lastUpdate": "2026-04-28T06:29:59.514Z"}}, {"d
atasourceName": "CNSIM", "entityType": "Participant", "link": "/datasource/CNSIM/table/CNSIM3", "name": "CNSIM3", "status": "READY", "timestamps": {"created": "2026-04-28T06:29:59.517Z", "lastUpdate": "2026-04-28T06:30:00.682Z"}}, {"dat
asourceName": "DASIM", "entityType": "Participant", "link": "/datasource/DASIM/table/DASIM1", "name": "DASIM1", "status": "READY", "timestamps": {"created": "2026-04-28T06:30:04.694Z", "lastUpdate": "2026-04-28T06:30:05.986Z"}}, {"datas
ourceName": "DASIM", "entityType": "Participant", "link": "/datasource/DASIM/table/DASIM2", "name": "DASIM2", "status": "READY", "timestamps": {"created": "2026-04-28T06:30:05.997Z", "lastUpdate": "2026-04-28T06:30:07.255Z"}}, {"datasou
rceName": "DASIM", "entityType": "Participant", "link": "/datasource/DASIM/table/DASIM3", "name": "DASIM3", "status": "READY", "timestamps": {"created": "2026-04-28T06:30:07.266Z", "lastUpdate": "2026-04-28T06:30:08.533Z"}}, {"datasourc
eName": "SURVIVAL", "entityType": "Participant", "link": "/datasource/SURVIVAL/table/EXPAND_WITH_MISSING1", "name": "EXPAND_WITH_MISSING1", "status": "READY", "timestamps": {"created": "2026-04-28T06:30:19.098Z", "lastUpdate": "2026-04-
28T06:30:20.204Z"}}, {"datasourceName": "SURVIVAL", "entityType": "Participant", "link": "/datasource/SURVIVAL/table/EXPAND_WITH_MISSING2", "name": "EXPAND_WITH_MISSING2", "status": "READY", "timestamps": {"created": "2026-04-28T06:30:2
0.210Z", "lastUpdate": "2026-04-28T06:30:21.284Z"}}, {"datasourceName": "SURVIVAL", "entityType": "Participant", "link": "/datasource/SURVIVAL/table/EXPAND_WITH_MISSING3", "name": "EXPAND_WITH_MISSING3", "status": "READY", "timestamps":
{"created": "2026-04-28T06:30:21.291Z", "lastUpdate": "2026-04-28T06:30:22.412Z"}}]

[Yannick Marcon]

No, I wanted you to test your Opal :)

* Do you still get a response after a while ?

* Would there be some projects that are in pending state? Check with: 

opal project --opal https://opal-demo.obiba.org --user administrator --password password --json | grep datasourceStatus

Y

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[Sean Hurley]

Hi Yannick

There is no response after a long period.
I have datasourceStatus that is either READY or NONE. There are no pending.

Sean.

[Sean Hurley]

Hi Yannick

I got the following:

reply: 'HTTP/1.1 400 Bad Request\r\n'
header: Date: Wed, 29 Apr 2026 23:42:15 GMT
header: Vary: Accept-Encoding
header: X-Opal-Version: 5.6.3
header: Set-Cookie: opalsid=7e360284-a35b-4060-b1a8-71a9e3f264b5;Version=1;Path=/;Max-Age=1800;Secure;HttpOnly;SameSite=Lax
header: Set-Cookie: XSRF-TOKEN=2353948c-f7e2-4b14-bb45-e8c68dd4c0b8;Version=1;Path=/;Secure;SameSite=Lax
header: Allow: GET, OPTIONS
header: Cache-Control: no-cache
header: Content-Type: application/x-protobuf+json
header: Expires: -1
header: Pragma: no-cache
header: Transfer-Encoding: chunked
{"arguments": ["CCT_ALZH_TRF1"], "code": 400, "status": "NoSuchVariable"}

[Sean Hurley]

P.S. This is after deleting the work folder. It still took a very long time. But now, it's very quick and gives me the same result each time. This is a different entity search:

eply: 'HTTP/1.1 400 Bad Request\r\n'

header: Date: Thu, 30 Apr 2026 01:23:38 GMT

header: Vary: Accept-Encoding
header: X-Opal-Version: 5.6.3

header: Set-Cookie: opalsid=a4469ff9-e5c5-4632-bdc3-1c9f948d622b;Version=1;Path=/;Max-Age=1800;Secure;HttpOnly;SameSite=Lax
header: Set-Cookie: XSRF-TOKEN=e8ceea1d-14c9-42ae-acc3-2c845515e01e;Version=1;Path=/;Secure;SameSite=Lax

header: Allow: GET, OPTIONS
header: Cache-Control: no-cache
header: Content-Type: application/x-protobuf+json
header: Expires: -1
header: Pragma: no-cache
header: Transfer-Encoding: chunked
{"arguments": ["CCT_ALZH_TRF1"], "code": 400, "status": "NoSuchVariable"}

[Yannick Marcon]

Hi,

Looks like it is an issue with a View, that has a broken script.

Y

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