From Brian.Chapman at utah.edu Tue Sep 8 15:38:33 2015 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Tue, 8 Sep 2015 19:38:33 +0000 Subject: [Girder-users] Access Control in Girder Message-ID: Hi, We have a local instance of girder running with two users. We are having problem with access control. User #1 has created a collection and is attempting to add User #2 to the collection. In the pop-up window User 1 proceeds to type User #2?s user name in the ?Grant access to another group or user.? An error message flashes: ?An error occurred while communicating with the server. Details have been logged to the console.? I?m assuming we?ve got some problem going on with Jqjuery or whatever the form is using. We are running girder in a docker container and I can?t seem to see how to access the console in Docker (versus creating a shell connection via docker exec). Nothing is being written to a log file under /girder/logs or /var/log, at least as I can see. Anyone seen anything similar? Is there a way to get Docker to log the error message rather than writing to console? Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: From zach.mullen at kitware.com Tue Sep 8 15:42:12 2015 From: zach.mullen at kitware.com (Zach Mullen) Date: Tue, 8 Sep 2015 15:42:12 -0400 Subject: [Girder-users] Access Control in Girder In-Reply-To: References: Message-ID: Hi Brian, When it says the console, it actually means the web developer console in your web browser that you can see if you use ctrl+alt+i and go to the "console" tab. If it's an unexpected exception, it will also be logged in the server logs. My guess is that full text search may not be enabled in your mongo database, but it could be something else. Thanks, Zach Mullen Kitware, Inc. 919-869-8858 On Tue, Sep 8, 2015 at 3:38 PM, Brian E Chapman wrote: > Hi, > > We have a local instance of girder running with two users. We are having > problem with access control. > > User #1 has created a collection and is attempting to add User #2 to the > collection. In the pop-up window User 1 proceeds to type User #2?s user > name in the ?Grant access to another group or user.? An error message > flashes: ?An error occurred while communicating with the server. Details > have been logged to the console.? I?m assuming we?ve got some problem going > on with Jqjuery or whatever the form is using. We are running girder in a > docker container and I can?t seem to see how to access the console in > Docker (versus creating a shell connection via docker exec). Nothing is > being written to a log file under /girder/logs or /var/log, at least as I > can see. > > Anyone seen anything similar? Is there a way to get Docker to log the > error message rather than writing to console? > > Brian > > > _______________________________________________ > Girder-users mailing list > Girder-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/girder-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.Chapman at utah.edu Tue Sep 8 15:51:38 2015 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Tue, 8 Sep 2015 19:51:38 +0000 Subject: [Girder-users] Access Control in Girder In-Reply-To: References: , Message-ID: <572AF30A-F768-4ADD-9309-02D4668153AF@utah.edu> Thanks. I'll check that Brian Sent from my mobile device On Sep 8, 2015, at 1:42 PM, Zach Mullen > wrote: Hi Brian, When it says the console, it actually means the web developer console in your web browser that you can see if you use ctrl+alt+i and go to the "console" tab. If it's an unexpected exception, it will also be logged in the server logs. My guess is that full text search may not be enabled in your mongo database, but it could be something else. Thanks, Zach Mullen Kitware, Inc. 919-869-8858 On Tue, Sep 8, 2015 at 3:38 PM, Brian E Chapman > wrote: Hi, We have a local instance of girder running with two users. We are having problem with access control. User #1 has created a collection and is attempting to add User #2 to the collection. In the pop-up window User 1 proceeds to type User #2?s user name in the ?Grant access to another group or user.? An error message flashes: ?An error occurred while communicating with the server. Details have been logged to the console.? I?m assuming we?ve got some problem going on with Jqjuery or whatever the form is using. We are running girder in a docker container and I can?t seem to see how to access the console in Docker (versus creating a shell connection via docker exec). Nothing is being written to a log file under /girder/logs or /var/log, at least as I can see. Anyone seen anything similar? Is there a way to get Docker to log the error message rather than writing to console? Brian _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.Chapman at utah.edu Wed Sep 9 18:24:23 2015 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Wed, 9 Sep 2015 22:24:23 +0000 Subject: [Girder-users] Access Control in Girder In-Reply-To: References: Message-ID: Thanks Zach, It was the MonoDB setting. Upgraded to a newer version where full text search is enabled by default (had been running MongoDB 2.4) and that all works fine. Brian From: Zach Mullen > Date: Tuesday, September 8, 2015 at 1:42 PM To: Brian Chapman > Cc: "girder-users at public.kitware.com" > Subject: Re: [Girder-users] Access Control in Girder Hi Brian, When it says the console, it actually means the web developer console in your web browser that you can see if you use ctrl+alt+i and go to the "console" tab. If it's an unexpected exception, it will also be logged in the server logs. My guess is that full text search may not be enabled in your mongo database, but it could be something else. Thanks, Zach Mullen Kitware, Inc. 919-869-8858 On Tue, Sep 8, 2015 at 3:38 PM, Brian E Chapman > wrote: Hi, We have a local instance of girder running with two users. We are having problem with access control. User #1 has created a collection and is attempting to add User #2 to the collection. In the pop-up window User 1 proceeds to type User #2?s user name in the ?Grant access to another group or user.? An error message flashes: ?An error occurred while communicating with the server. Details have been logged to the console.? I?m assuming we?ve got some problem going on with Jqjuery or whatever the form is using. We are running girder in a docker container and I can?t seem to see how to access the console in Docker (versus creating a shell connection via docker exec). Nothing is being written to a log file under /girder/logs or /var/log, at least as I can see. Anyone seen anything similar? Is there a way to get Docker to log the error message rather than writing to console? Brian _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zach.mullen at kitware.com Thu Sep 10 06:45:06 2015 From: zach.mullen at kitware.com (Zach Mullen) Date: Thu, 10 Sep 2015 06:45:06 -0400 Subject: [Girder-users] Access Control in Girder In-Reply-To: References: Message-ID: Great! Zach Mullen Kitware, Inc. 919-869-8858 On Wed, Sep 9, 2015 at 6:24 PM, Brian E Chapman wrote: > Thanks Zach, > > It was the MonoDB setting. Upgraded to a newer version where full text > search is enabled by default (had been running MongoDB 2.4) and that all > works fine. > > Brian > > > From: Zach Mullen > Date: Tuesday, September 8, 2015 at 1:42 PM > To: Brian Chapman > Cc: "girder-users at public.kitware.com" > Subject: Re: [Girder-users] Access Control in Girder > > Hi Brian, > > When it says the console, it actually means the web developer console in > your web browser that you can see if you use ctrl+alt+i and go to the > "console" tab. If it's an unexpected exception, it will also be logged in > the server logs. My guess is that full text search may not be enabled in > your mongo database, but it could be something else. > > Thanks, > > > Zach Mullen > Kitware, Inc. > 919-869-8858 > > On Tue, Sep 8, 2015 at 3:38 PM, Brian E Chapman > wrote: > >> Hi, >> >> We have a local instance of girder running with two users. We are having >> problem with access control. >> >> User #1 has created a collection and is attempting to add User #2 to the >> collection. In the pop-up window User 1 proceeds to type User #2?s user >> name in the ?Grant access to another group or user.? An error message >> flashes: ?An error occurred while communicating with the server. Details >> have been logged to the console.? I?m assuming we?ve got some problem going >> on with Jqjuery or whatever the form is using. We are running girder in a >> docker container and I can?t seem to see how to access the console in >> Docker (versus creating a shell connection via docker exec). Nothing is >> being written to a log file under /girder/logs or /var/log, at least as I >> can see. >> >> Anyone seen anything similar? Is there a way to get Docker to log the >> error message rather than writing to console? >> >> Brian >> >> >> _______________________________________________ >> Girder-users mailing list >> Girder-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/girder-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.Chapman at utah.edu Fri Sep 11 16:52:22 2015 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Fri, 11 Sep 2015 20:52:22 +0000 Subject: [Girder-users] Slicer interfacing with Girder Message-ID: Hi Everyone, I was wondering whether a Slicer extension for Girder (similar to ThingiverseBrowser or XNATSlicer) exists or is being developed to allow Slicer to interact directly with resources in Girder. Brian ? Brian E. Chapman, Ph.D. Associate Professor Department of Radiology University of Utah -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.reynolds at kitware.com Fri Sep 11 16:54:12 2015 From: patrick.reynolds at kitware.com (Patrick Reynolds) Date: Fri, 11 Sep 2015 16:54:12 -0400 Subject: [Girder-users] Slicer interfacing with Girder In-Reply-To: References: Message-ID: Hi Brian, This is certainly something we'd like to do. I believe we'll be doing some of this work sometime in the next few months, but JC (in copy) can probably better comment on that (he's our Slicer guy). Thanks, Patrick Reynolds Technical Leader Kitware, Inc. 919 869 8848 On Fri, Sep 11, 2015 at 4:52 PM, Brian E Chapman wrote: > Hi Everyone, > > I was wondering whether a Slicer extension for Girder (similar to > ThingiverseBrowser or XNATSlicer) exists or is being developed to allow > Slicer to interact directly with resources in Girder. > > Brian > ? > Brian E. Chapman, Ph.D. > Associate Professor > Department of Radiology > University of Utah > > > _______________________________________________ > Girder-users mailing list > Girder-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/girder-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From brian.helba at kitware.com Fri Sep 11 18:19:50 2015 From: brian.helba at kitware.com (Brian Helba) Date: Fri, 11 Sep 2015 18:19:50 -0400 Subject: [Girder-users] Slicer interfacing with Girder In-Reply-To: References: Message-ID: What a timely question! Today, at the DICOMweb 2025 hack session, JC and I worked on adding support for RESTful DICOM protocols (WADO first) into Girder. Steve Pieper, who was with us, worked on (and got a working demo for) adding similar support into Slicer. A goal that we discussed is to allow data exchange via this mechanism. If you're more interested in the Girder side, talk to me, JC, and Zack Mullen (but feel free to CC the list too). If you're more interested in the Slicer side, talk to JC and Steve. Hi Brian, This is certainly something we'd like to do. I believe we'll be doing some of this work sometime in the next few months, but JC (in copy) can probably better comment on that (he's our Slicer guy). Thanks, Patrick Reynolds Technical Leader Kitware, Inc. 919 869 8848 On Fri, Sep 11, 2015 at 4:52 PM, Brian E Chapman wrote: > Hi Everyone, > > I was wondering whether a Slicer extension for Girder (similar to > ThingiverseBrowser or XNATSlicer) exists or is being developed to allow > Slicer to interact directly with resources in Girder. > > Brian > ? > Brian E. Chapman, Ph.D. > Associate Professor > Department of Radiology > University of Utah > > > _______________________________________________ > Girder-users mailing list > Girder-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/girder-users > > _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brian.Chapman at utah.edu Fri Sep 25 11:32:05 2015 From: Brian.Chapman at utah.edu (Brian E Chapman) Date: Fri, 25 Sep 2015 15:32:05 +0000 Subject: [Girder-users] Slicer interfacing with Girder In-Reply-To: References: Message-ID: Hi Brian, I think I?m mostly interested in things from the Girder side as what I would like to do is be able to directly access images stored in Girder via a Jupyter notebook or Slicer (for two examples). Also more general than DICOM as we would tend to have as many jpeg, nifti, nrrd, or meta images as DICOM. This is something I struggled with in Midas and wrote some work-arounds for to get SimpleITK to read files from Midas (creating soft links with the correct file extension to the stored resource in Midas). I should delve into your dermatology code more as I imagine what you are doing in that is close to what I envision doing with volumetric medical images. Brian From: Brian Helba > Date: Friday, September 11, 2015 at 4:19 PM To: Patrick Reynolds > Cc: "girder-users at public.kitware.com" >, Brian Chapman >, Jean-Christophe Fillion-Robin >, "pieper at isomics.com" > Subject: Re: [Girder-users] Slicer interfacing with Girder What a timely question! Today, at the DICOMweb 2025 hack session, JC and I worked on adding support for RESTful DICOM protocols (WADO first) into Girder. Steve Pieper, who was with us, worked on (and got a working demo for) adding similar support into Slicer. A goal that we discussed is to allow data exchange via this mechanism. If you're more interested in the Girder side, talk to me, JC, and Zack Mullen (but feel free to CC the list too). If you're more interested in the Slicer side, talk to JC and Steve. Hi Brian, This is certainly something we'd like to do. I believe we'll be doing some of this work sometime in the next few months, but JC (in copy) can probably better comment on that (he's our Slicer guy). Thanks, Patrick Reynolds Technical Leader Kitware, Inc. 919 869 8848 On Fri, Sep 11, 2015 at 4:52 PM, Brian E Chapman > wrote: Hi Everyone, I was wondering whether a Slicer extension for Girder (similar to ThingiverseBrowser or XNATSlicer) exists or is being developed to allow Slicer to interact directly with resources in Girder. Brian ? Brian E. Chapman, Ph.D. Associate Professor Department of Radiology University of Utah _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users _______________________________________________ Girder-users mailing list Girder-users at public.kitware.com http://public.kitware.com/mailman/listinfo/girder-users -------------- next part -------------- An HTML attachment was scrubbed... URL: