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  • Aug 21 18:49

    brianhelba on audit-index

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  • Aug 21 18:49

    brianhelba on master

    Add indices to audit logs Merge pull request #3122 from g… (compare)

  • Aug 21 18:49
    brianhelba closed #3122
  • Aug 21 08:54
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  • Aug 21 02:03
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    brianhelba opened #3122
  • Aug 21 02:03

    brianhelba on audit-index

    Add indices to audit logs (compare)

  • Aug 20 18:33
    bpaniagua commented #3121
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    bpaniagua opened #3121
  • Aug 20 15:11
    zachmullen commented #3102
Khai
@khairulslt
hey guys, new to girder, i followed the instructions at https://girder.readthedocs.io/en/latest/dev-installation.html to the dot
after ssh-ing into vagrant
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".