Closed fepegar closed 2 years ago
I addded girder-client
to the list of pip installs in minimal/Dockerfile
. I guess I misunderstood the meaning of dsarchive/dsa_minimal
(I'm still learning Docker). Would you like a PR?
The error is gone, but 8080 is still not reachable.
Actually, there seems to be something important in the console:
mongodb_1 | 2022-02-23T14:58:48.217+0000 I NETWORK [conn24] end connection 172.25.0.3:55508 (1 connection now open)
mongodb_1 | 2022-02-23T14:58:48.218+0000 I NETWORK [conn23] end connection 172.25.0.3:55506 (0 connections now open)
minimal_girder_1 exited with code 1
girder_1 | Running in mode: production
mongodb_1 | 2022-02-23T14:59:49.671+0000 I NETWORK [listener] connection accepted from 172.25.0.3:55528 #25 (1 connection now open)
mongodb_1 | 2022-02-23T14:59:49.671+0000 I NETWORK [conn25] received client metadata from 172.25.0.3:55528 conn25: { driver: { name: "PyMongo", version: "3.12.3" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "4.18.0-20-generic" }, platform: "CPython 3.9.10.final.0" }
girder_1 | Connecting to MongoDB: mongodb://mongodb:27017/girder?socketTimeoutMS=3600000
mongodb_1 | 2022-02-23T14:59:49.674+0000 I NETWORK [listener] connection accepted from 172.25.0.3:55530 #26 (2 connections now open)
mongodb_1 | 2022-02-23T14:59:49.674+0000 I NETWORK [conn26] received client metadata from 172.25.0.3:55530 conn26: { driver: { name: "PyMongo", version: "3.12.3" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "4.18.0-20-generic" }, platform: "CPython 3.9.10.final.0" }
girder_1 | Loaded plugin "jobs"
girder_1 | Loaded plugin "slicer_cli_web"
girder_1 | Loaded tile source multi
girder_1 | Loaded tile source tiff
girder_1 | Loaded tile source openjpeg
girder_1 | Loaded tile source bioformats
girder_1 | Loaded tile source nd2
girder_1 | Loaded tile source mapnik
girder_1 | Loaded tile source test
girder_1 | Loaded tile source deepzoom
girder_1 | Loaded tile source ometiff
girder_1 | Loaded tile source openslide
girder_1 | Loaded tile source pil
girder_1 | Loaded tile source gdal
girder_1 | Loaded plugin "large_image"
girder_1 | Loaded plugin "large_image_annotation"
girder_1 | Loaded plugin "histomicsui"
girder_1 | Loaded plugin "homepage"
girder_1 | Traceback (most recent call last):
girder_1 | File "//provision.py", line 312, in <module>
girder_1 | provision(opts)
girder_1 | File "//provision.py", line 197, in provision
girder_1 | Setting().set(key, value)
girder_1 | File "/usr/local/lib/python3.9/site-packages/girder/models/setting.py", line 125, in set
girder_1 | setting = self.save(setting)
girder_1 | File "/usr/local/lib/python3.9/site-packages/girder/models/model_base.py", line 479, in save
girder_1 | document = self.validate(document)
girder_1 | File "/usr/local/lib/python3.9/site-packages/girder/models/setting.py", line 76, in validate
girder_1 | raise ValidationException('Invalid setting key "%s".' % key, 'key')
girder_1 | girder.exceptions.ValidationException: Invalid setting key "worker.broker".
I've modified provision.py
to ignore exceptions from line 197, and things seem to be working as expected. I will leave this issue open, in case you'd like to track these problems.
It looks like it is the code for fetching sample data that is the problem, since that does need girder_client.
Hello again. I'm trying to deploy the minimal example using
docker-compose up
. I couldn't connect to8080
, so I checked the console and saw a lot of messages like this:Is a
pip
install forgirder-client
missing from thedsarchive/dsa_minimal
Dockerfile? I couldn't find the image on thedsarchive
repos on the Docker hub.