Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Sep 20 08:51
    boucaud edited #3128
  • Sep 18 15:22
    boucaud commented #3128
  • Sep 18 15:19
    boucaud synchronize #3128
  • Sep 18 15:01
    boucaud synchronize #3128
  • Sep 18 14:47
    boucaud synchronize #3128
  • Sep 16 12:56
    zachmullen commented #3128
  • Sep 16 11:31
    boucaud commented #3128
  • Sep 12 07:31
    boucaud commented #3128
  • Sep 11 12:45
    zachmullen commented #3128
  • Sep 11 12:17
    boucaud opened #3128
  • Sep 11 09:49
  • Sep 07 03:20
    manthey synchronize #3127
  • Sep 07 03:20

    manthey on update-pytest-cov

    Update to handle newer pytest-c… (compare)

  • Sep 07 01:06
    manthey synchronize #3127
  • Sep 07 01:06

    manthey on update-pytest-cov

    Update to handle newer pytest-c… (compare)

  • Sep 06 21:42
    manthey synchronize #3127
  • Sep 06 21:42

    manthey on update-pytest-cov

    Update to handle newer pytest-c… (compare)

  • Sep 06 21:29
    manthey synchronize #3127
  • Sep 06 21:29

    manthey on update-pytest-cov

    Update to handle newer pytest-c… (compare)

  • Sep 06 17:18
    manthey opened #3127
Khai
@khairulslt
i can see a girder folder
but doing something like
"sudo service girder restart"
or "girder serve"
triggers a "girder: command not found"
using vagrant 2.0 and virtualbox 5.1
David Manthey
@manthey
@MmmaAlex_twitter: When you build the web assets for girder, did it print any errors? That is, in Girder 2.x when you do "girder-install web" or in Girder 3.0 with "girder build", sometimes there is an error that scrolls off screen. Can you tell more about your configuration? What OS are you using; what version of Girder?
Ghost
@ghost~599aeac8d73408ce4f7250bf
@manthey Thanks for response. After uninstalling exiting girder, clean cache and clean database I reinstall everything, now it works well. I install girder times ago, and I may probably not install everything correctly.
AndreasDavour
@AndreasDavour
Hi. I have installed a girder in a container and want to use ldap for authentication. I don't find any clear information about where and how to configure bindDN and server name. https://girder.readthedocs.io/en/stable/plugins.html#ldap-authentication talks about a "configuration page", but where do I find that? Looking at the Plugins tab of the Admin Console shows nothing, but 'pip install girder[ldap]' claims it's installed.
AndreasDavour
@AndreasDavour
Not that much action here, eh?
Kacper Kowalik
@Xarthisius
@AndreasDavour in the Admin Console > Plugins, there's a cog icon next to plugin name
alternatively you can access plugin's config page directly by going to http://<your_girder>/#plugins/ldap/config
make sure UI component for that plugin is actually built
girder-install web --dev --plugins=...,ldap
AndreasDavour
@AndreasDavour
Sorry. No cogs available, and that URL goes nowhere. I guess as you say some UI component is not built, as I'm using a container. I actually tried to run girder-install from within the container, and there's no such command.
docker.io/girder/girder Looks official enough, but maybe I've gotten a badly built image?
Kacper Kowalik
@Xarthisius
@AndreasDavour AFAICT girder/girder:latest is using master branch. There's been a lot of changes related to how plugins are handled and I don't see that they're being installed by default now. I'd suggest to use 2.x image for now, e.g. girder/girder:2.x-maintenance or girder/girder:2.5.0
ParinitaChowdhry
@ParinitaChowdhry
is admin console same as localhost:8080/api/v1 route??
i'm very new to girder..that's why very naive question
Kacper Kowalik
@Xarthisius
@ParinitaChowdhry no, it's an entry in the left panel visible if you log in to Girder using admin account. It goes to http://localhost:8080/#admin
AndreasDavour
@AndreasDavour
@Xarthisius thanks. Sounds like I should have looked for a girder:stable or something. Would be very good if that's on the official docs site.
Curtis Lisle
@curtislisle
A girder worker question: I am using a girder plugin that lets me create girder-worker jobs. I added a new method to the plugin. Each time I I run the new method through the Girder swagger interface, I see a new girder jobs entry, but it always says "Inactive" and nothing happens. There is no new entry in girder's error.log or info.log . Any suggestions on where I look for errors. Does girder worker have a separate log?
Curtis Lisle
@curtislisle
I already checked that girder-worker and rabbitmq are running. Other jobs seem to work, so I am assuming I declared my new job wrong, but can't find the girder-worker logs.
David Manthey
@manthey
When you started girder-worker, it outputs some information to stdout and stderr. Do you know where it is running and does that show anything? Are you calling scheduleJob? In some other code, I create a job model, save it, then call scheduleJob.
Asmaa Aljuhani
@aaljuhani
I am new to Girder.. Trying to setup an application. When I run girder serve I am getting girder.exceptions.ValidationException: Routes must be unique.
David Manthey
@manthey
If you are adding routes via a Resource and self.route, each route needs to be unique -- different resource name, different method, or different path. Either you've included the same resource multiple times (reused a resource name, for instance), or your routes will have some repetition.
Asmaa Aljuhani
@aaljuhani
Thanks @manthey .
tymiao1220
@tymiao1220

Ctest runs well previously until an error appears.

phantomjs://code/specRunner.js:153 in onError
228: Created error screenshot: build/test/artifacts/screenshot_cats_widgetSpec_error.png
228: Retrying test
228: ERROR: SyntaxError: Unexpected token '>'
228: TRACE:
228:  -> http://localhost:30044/static/built/testing/testEnv.html: 1985 (in function "appendChild")
228:  -> http://localhost:30044/static/built/girder_lib.min.js: 1360 (in function "DOMEval")
228:  -> http://localhost:30044/static/built/girder_lib.min.js: 1624 (in function "globalEval")
228:  -> http://localhost:30044/static/built/girder_lib.min.js: 10884 (in function "text script")
228:  -> http://localhost:30044/static/built/girder_lib.min.js: 10032 (in function "ajaxConvert")
228:  -> http://localhost:30044/static/built/girder_lib.min.js: 10500 (in function "done")
228:  -> http://localhost:30044/static/built/girder_lib.min.js: 10792

Could you give me a help, thanks

David Manthey
@manthey
When the girder web client was built, did it report an error?
tymiao1220
@tymiao1220
When I do 'girder-install web' and 'girder-install web -dev' they are all going well.
Melody
@Melody89057335_twitter
Hi,
I am wondering is it possible to use webpack 4 for plugin instead of 2.7 that girder provided, and if possible where should I work on? Thanks
Melody
@Melody89057335_twitter
The reason I am asking it because my plugin supported by typescript package, and ts-loader 5.2.1 typescript 3.1.1 are used to load and compile it, but ts-loader higher version will need webpack 4.
Brian Northan
@bnorthan
Hi. I recently attended the Girder tutorials at Kitware. I wanted to try large_image on a .tif file I have but get 'no available tile source'. The image loads into Fiji (ImageJ) and appears to be a multiresolution .tif. I've attached a screen shot of the error (and the preview of the image in Fiji) in case it's useful...
image.png
Any tips?? Is it possible I am missing a dependency?? I installed large_image and openslide using pip. Anything else I need??
David Manthey
@manthey
A couple of possibilities: It is possible that the file isn't one that the large_image plugin can read. For instance, if it is only tiles at the highest resolution, it won't read directly. For such files, there is a fall-back to convert the file to a fully-populated pyramidal tiff.
I assume you are using Girder 3. When you installed large_image, did you install the openslide tile source? The tile sources are all plugins. Did you do pip install large-image-source-openslide or pip install large-image[sources]?
Did you install the openslide library (via apt-get, for instance)? This isn't necessary if you used the large-image-wheels (adding "-f https://manthey.github.io/large_image_wheels" to your pip install command, for instance).
Brian Northan
@bnorthan
I just did pip install large-image
then pip install openslide-python, after that it complained about not finding one of the openslide dependencies, so I did apt-get install openslide-tools
David Manthey
@manthey
Try "pip install large-image-source-openslide" to get the openslide tile source. Or "pip install large-image[sources] -f https://manthey.github.io/large_image_wheels" to get all tile sources with prebuilt libraries (for linux).
Brian Northan
@bnorthan
"pip install large-image-source-openslide" did the trick, thanks a lot.
David Manthey
@manthey
Great. Is there a change to some documentation I could have done to have made this clearer?
Brian Northan
@bnorthan
I ended up on this page https://pypi.org/project/large-image/ and it wasn't entirely clear to me which modules I had to install in addition to large-image.
Asmaa Aljuhani
@aaljuhani
Hi. How can I wrap an existing girder client app in a Docker container ?
David Manthey
@manthey
There are many ways to do this. I find the easiest is to use docker-compose to set up a docker with Mongo and a docker with Girder. See the core repo for an example (https://github.com/girder/girder/blob/master/docker-compose.yml)
Asmaa Aljuhani
@aaljuhani
When I run docker-compose in girder/ I am getting this error:
ERROR: Service 'girder' failed to build: The command '/bin/sh -c girder-install web --all-plugins' returned a non-zero code: 1
David Manthey
@manthey
@aaljuhani Are you trying to use Girder 2 or Girder 3? Girder 3 uses "girder build"; Girder 2 uses "girder-install web".
David Manthey
@manthey
The GET /system/version endpoint should show the start date. Is this date before or after when you think the script restarted it? Are you sure you are waiting long enough for girder to restart? One way to ensure the restart is complete would be to poll system/version until it responds (for instance, apiVersion is in the output).
Once the server restarts, there should be anything that can reply to the old connection (and requests shouldn't hang on to such a connection unless you are using a session).