Moving from Sp6 to Docker Sp7 Any query fails

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1

I’m on the test phase of migrating NOU collection from Specify 6 to Specify 7, using so far docker composition “just-specify-7”.

Any query, existing or new one (even the dumbest one based on catalog number), systematically fails with same error message:

Error occurred fetching from `http://localhost/stored_query/ephemeral/`
Invalid response code 500. Expected 200.
## ParseError
*not well-formed (invalid token): line 179, column 29
* Content
"None"

I tried on local machine and distant server, with exactly same issue. It feels like I’m missing a simple point.
Thanks for any clue !

2

Hi @pverley,

Can you provide the docker-compose.yml file you are using so we can investigate further?
Have you tried other versions of Specify 7 as well?

3

Please find attached the docker compose file (I’ve just hidden the password). I barely modified it from original github version, except that I commented out the attachment server.
My local mariadb server is configured such as ITUserName and MasterUsername have been granting permissions from any host (I have not mastered docker yet so I do not control how IP is assigned to just-specify7 container, so for testing purpose I opened everything).

MariaDB [virot]> SELECT User, Host FROM mysql.user;
+----------------+-----------+
| User           | Host      |
+----------------+-----------+
| ITUserName     | %         |
| MasterUsername | %         |
| ITUserName     | *         |
| mariadb.sys    | localhost |
| mysql          | localhost |
| root           | localhost |
+----------------+-----------+

Which user is running the queries in Sp7 ?

I have not yet tried any other Docker recipe. I will try asap all-in-one and keep you posted whether it solves the issue.

Thanks for helping out.
Regards
docker-compose_just-specify7.yml (2.3 KB)

1 Like
4

I just gave it a try with docker compose from all-in-one and I’ve got the very same issue with every query.

To initialize all-in-one container I had copied an extract of the NOU database (schema 2.10) in folder all-in-one/seed-database.

5

Hey,

Can you attach the crash report that you get when the query fails?

6

Hi @pverley,

Can you try to deploy version 7.9.0 and inform us if the issue persists?

To do this, replace the image: for the specify7 and specify7-worker sections in the docker-compose.yml file with the following:

    image: specifyconsortium/specify7-service:v7.9.0

Once you have made this change, pull the image and rebuild the containers. If you are still encountering the issue after using this version, please let us know!

7

@pverley,

Could you please download and send us the DataObjFormatters app resource(s) from the App Resources viewer in Specify?

8

Thank you so much for your assistance.

I did update specify7 and specify7-worker services to v7.9.0 as suggested, but the issue persists. Specify 7 Crash Report - Query - 2023-11-29T22 19 43.440Z.txt (1.2 MB)

Interestingly when I tried to open the DataObjFormatters app resource(s), it also crashed with the following StackTrace:

Traceback (most recent call last):
  File "/opt/specify7/ve/lib/python3.8/site-packages/django/core/handlers/base.py", line 181, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/opt/specify7/specifyweb/specify/views.py", line 40, in wrapped
    return view(request, *args, **kwargs)
  File "/opt/specify7/ve/lib/python3.8/site-packages/django/views/decorators/cache.py", line 31, in _cache_controlled
    response = viewfunc(request, *args, **kw)
  File "/opt/specify7/specifyweb/specify/views.py", line 73, in view
    return dispatch_func(request, *args, **kwargs)
  File "/opt/specify7/specifyweb/specify/api.py", line 202, in collection_dispatch
    resp = HttpResponse(toJson(data), content_type='application/json')
  File "/opt/specify7/specifyweb/specify/api.py", line 61, in toJson
    return json.dumps(obj, cls=JsonEncoder)
  File "/usr/lib/python3.8/json/__init__.py", line 234, in dumps
    return cls(
  File "/usr/lib/python3.8/json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib/python3.8/json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)
  File "/opt/specify7/specifyweb/specify/api.py", line 57, in default
    return obj.decode()
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 5027: invalid continuation byte

Specify 7 Crash Report - DataObjFormatters - 2023-11-29T22 21 48.742Z.txt (531.9 KB)

Error message reminded my of similar issue on the forum, with special characters encoding issue.

And a quick search on SO confirm that the root of the problem might be accentuated letters (é, è, à, etc., sorry for our French !) in the database ? It feels that we have a lead.