pyushkevich / alfabis_server

RESTful API for the ALFABIS distributed image segmentation server
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Error while creating a User and/or adding a Provider. #3

Closed StuSerious closed 3 years ago

StuSerious commented 3 years ago

Context

Hey there ITK-SNAP team! 👋🏼 I'm Steve from the team over at University of Pavia, as a follow-up to our recent email chain, here is our official report on the issue! I have made a quick issue template since there isn't one preconfigured in this repo! I hope it's correct and suits your guidelines. Here we go:

Expected Behavior

While issuing the itksnap-wt -dssa-providers-users-add testlab test@example.com command, the user is correctly added.

Current Behavior

Both alfabis_server and console return an error, here is what git bash says: this is what cmd returns

..and here is what docker says: this is what docker returns

Possible Solution

I really have no idea, I don't know if I'm missing something blaringly obvious, but it seems like I tried everything I could!

Useful Links:

https://github.com/StuSerious/my_little_dss_test.git | git@github.com:StuSerious/my_little_dss_test.git I don't have any logs I can provide, but please do point me in the right direction to help you with anything!

Steps to Reproduce

I have reproduced this across multiple platforms and hardware configurations, but as a sanity check, here are the steps I take, following your guide to the letter:

  1. Run itksnap-wt -dss-auth http://localhost:8080 and use the generated key to log in as test@example;
  2. Run itksnap-wt -dssa-providers-add testlab to add a new environment, succeeding;
  3. And finally, run itksnap-wt -dssa-providers-users-add testlab test@example.com to get the error;
  4. You could try and continue with the guide and run itksnap-wt -dssa-providers-services-add testlab https://github.com/StuSerious/my_little_dss_test, but it just fails spitting this back: repo error

This has now left me confused on and off for about 6 months, and I'm really eager to make progress, so I really hope I'm missing something here, and that we can resolve it quickly without bothering you too much😆 Thanks in advance for your time and effort!

pyushkevich commented 3 years ago

Hi Stu,

I just tried to go through the tutorial. I had to make a small change to the requirements.txt file that I am going to push to git now for the command docker-compose up to work.

After that I had no problems.

[image: image.png]

If it complains about the email account, it means that the user you are trying to add has not yet registered with the system. The user test@example.com is automatically registered with the system in the "sandbox" docker container. When you navigate to http://localhost:8080/adminservices you should see the user under the list of users:

[image: image.png]

My suggestion is to run the tutorial once again from scratch. If it still fails at this point, let's talk.

Paul

On Mon, Feb 15, 2021 at 11:23 AM Ste notifications@github.com wrote:

Context

Hey there ITK-SNAP team! 👋🏼 I'm Steve from the team over at University of Pavia, as a follow-up to our recent email chain, here is our official report on the issue! I have made a quick issue template since there isn't one preconfigured in this repo! I hope it's correct and suits your guidelines. Here we go: Expected Behavior

While issuing the itksnap-wt -dssa-providers-users-add testlab test@example.com command, the user is correctly added. Current Behavior

Both alfabis_server and console return an error, here is what git bash says: [image: this is what cmd returns] https://user-images.githubusercontent.com/53015230/107968694-f75d1f80-6fae-11eb-8326-a872070f6037.png

..and here is what docker says: [image: this is what docker returns] https://user-images.githubusercontent.com/53015230/107968825-2378a080-6faf-11eb-9d4b-66f406b45568.png Possible Solution

I really have no idea, I don't know if I'm missing something blaringly obvious, but it seems like I tried everything I could, as described later in the context section. Useful Links:

https://github.com/StuSerious/my_little_dss_test.git | git@github.com :StuSerious/my_little_dss_test.git I don't have any logs I can provibe, but please do point me in the right direction to help you with anything! Steps to Reproduce

I have reproduced this across multiple platforms and hardware configurations, but as a sanity check, here are the steps I take, following your guide https://alfabis-server.readthedocs.io/en/latest/service_quick_start.html#our-example-service to the line:

  1. Run itksnap-wt -dss-auth http://localhost:8080 and use the generated key to log in as test@example;
  2. Run itksnap-wt -dssa-providers-add testlab to add a new environment, succeeding;
  3. And finally, run itksnap-wt -dssa-providers-users-add testlab test@example.com to get the error;
  4. You could try and continue with the guide and run itksnap-wt -dssa-providers-services-add testlab https://github.com/StuSerious/my_little_dss_test, but it just fails spitting this back: [image: repo error] https://user-images.githubusercontent.com/53015230/107969785-874f9900-6fb0-11eb-8612-0cc9e0e9827d.png

This has now left me confused on and off for about 6 months, and I'm really eager to make progress, so I really hope I'm missing something here, and that we can resolve it quickly without bothering you too much😆 Thanks in advance for your time and effort!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/pyushkevich/alfabis_server/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW2FZMZLCIM632N3AK3S7FC7HANCNFSM4XU6SSZQ .

-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

StuSerious commented 3 years ago

Hey there Paul! Thanks for your quick reply ❤️ docker-compose up always worked fine for me.

I am however still running into the same error even after starting again from scratch, take a look: 2 - logs

I really have no idea if I'm doing something wrong here, let me know how I can give you more logs or info, but maybe this could point us in the right direction: image As you can see there don't seem to be users added, even after running the command from terminal!

If I try to add it from GUI, it does add it though! image and here is the console output: image

In a similar way, in the next step if I try to add a service with command line it outputs: image image

But if I do it from the GUI it goes through no problem: image image

Also, sorry for the frequent updates on this comment, I prefer having one comment rather that 50 different ones :D

pyushkevich commented 3 years ago

Could you try downloading the most recent version of ITK-SNAP and using the itksnap-wt command that comes with it? You can run "Help->Install Command line Tools" to do that after the ITK-SNAP installl.

The reason I think this might work is that the output you get after the problematic command is different for you and me. For me, I have POST ... email=test@example.com and for you, POST ... email=testlab

Sounds like there might be an error in itksnap-wt

Paul

On Thu, Feb 18, 2021 at 4:50 AM Ste notifications@github.com wrote:

Hey there Paul! Thanks for your quick reply ❤️

docker-compose up always worked fine for me. I am however still running into the same error even after starting again from scratch, take a look: [image: 2 - logs] https://user-images.githubusercontent.com/53015230/108338579-b5162700-71d6-11eb-9c5f-00460b4195fb.png

I really have no idea if I'm doing something wrong here, let me know how I can give you more logs or info!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pyushkevich/alfabis_server/issues/3#issuecomment-781222008, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW7DPMQWRB52WD6HLPLS7TPHNANCNFSM4XU6SSZQ .

-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

StuSerious commented 3 years ago

I just noticed I can't see that menu in neither the most recent release nor in the nightly build..

image image

I do have ITK-SNAP's bin folder added to PATH.

pyushkevich commented 3 years ago

Are you using Windows? I'll have to check why it's not there.

But yes, it should be in the PATH

If that still doesn't work please try https://sourceforge.net/projects/itk-snap/files/itk-snap/Experimental/, the build marked most recent

Thanks Paul

On Thu, Feb 18, 2021 at 7:37 AM Ste notifications@github.com wrote:

I just noticed I can't see that menu in neither the most recent release nor in the nightly build.. [image: image] https://user-images.githubusercontent.com/53015230/108357290-83f52100-71ed-11eb-933b-f2e54b484dfe.png [image: image] https://user-images.githubusercontent.com/53015230/108357474-c4ed3580-71ed-11eb-9943-1f776411081b.png

I do have itksnap-wt added to path

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-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

StuSerious commented 3 years ago

Are you using Windows?

Yes sir, I am. Windows 10 Pro 20H2


I tried the experimental build from SourceForge but these error come up: image image image image

I uninstalled every instance of ITK-SNAP and reinstalled, but the errors persist..

Let me know if there is anything more I can do to help diagnose, and thanks a lot for your time

pyushkevich commented 3 years ago

Sorry about that...

It occurred to me that the @ symbol might cause problems on windows shell. Could you try putting the email in quotes, i.e., "test@example.com"

Thanks! Paul

On Thu, Feb 18, 2021 at 9:07 AM Ste notifications@github.com wrote:

Are you using Windows?

Yes sir, I am.

I tried the experimental build but these error come up: [image: image] https://user-images.githubusercontent.com/53015230/108368023-49de4c00-71fa-11eb-8cf0-ca2aaa6edcf1.png [image: image] https://user-images.githubusercontent.com/53015230/108368059-55317780-71fa-11eb-9feb-3996ce3f186f.png [image: image] https://user-images.githubusercontent.com/53015230/108368086-5c588580-71fa-11eb-874f-25128b991aed.png [image: image] https://user-images.githubusercontent.com/53015230/108368122-637f9380-71fa-11eb-9bce-3f42cb24dce1.png

I uninstalled every instance of ITK-SNAP and reinstalled, but the errors persist..

Let me know if there is anything more I can do to help diagnose, and thanks a lot for your time

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pyushkevich/alfabis_server/issues/3#issuecomment-781367515, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEWZ5GZGKOXBIS4QRYT3S7UNJDANCNFSM4XU6SSZQ .

-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

StuSerious commented 3 years ago

Test with email in quotes still comes back with errors :/

Here is the input: image And here is the console: image

pyushkevich commented 3 years ago

Steve,

It turned out to be an error in itksnap-wt related to different libraries on Mac, Linux and Windows.

I am compiling a new version of ITK-SNAP and hopefully it will work smoothly

Paul

On Thu, Feb 18, 2021 at 9:27 AM Ste notifications@github.com wrote:

Test with email in quotes still comes back with errors :/

Here is the input: [image: image] https://user-images.githubusercontent.com/53015230/108370860-6b8d0280-71fd-11eb-9ed9-d36510691cc9.png And here is the console: [image: image] https://user-images.githubusercontent.com/53015230/108371081-ab53ea00-71fd-11eb-86cf-f391ecf2dac7.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pyushkevich/alfabis_server/issues/3#issuecomment-781380925, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW2SNKAPS6FC56VP6L3S7UPTZANCNFSM4XU6SSZQ .

-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

pyushkevich commented 3 years ago

Steve,

Please look for itksnap-3.8.2-20210219-win64-AMD64.exe in the Experimental folder above. This should have the corrected itksnap-wt code.

Thanks! Paul

On Thu, Feb 18, 2021 at 2:33 PM Paul Yushkevich pyushkevich@gmail.com wrote:

Steve,

It turned out to be an error in itksnap-wt related to different libraries on Mac, Linux and Windows.

I am compiling a new version of ITK-SNAP and hopefully it will work smoothly

Paul

On Thu, Feb 18, 2021 at 9:27 AM Ste notifications@github.com wrote:

Test with email in quotes still comes back with errors :/

Here is the input: [image: image] https://user-images.githubusercontent.com/53015230/108370860-6b8d0280-71fd-11eb-9ed9-d36510691cc9.png And here is the console: [image: image] https://user-images.githubusercontent.com/53015230/108371081-ab53ea00-71fd-11eb-86cf-f391ecf2dac7.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pyushkevich/alfabis_server/issues/3#issuecomment-781380925, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW2SNKAPS6FC56VP6L3S7UPTZANCNFSM4XU6SSZQ .

-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

-- Paul A. Yushkevich, Ph.D. Professor of Radiology Penn Image Computing and Science Laboratory University of Pennsylvania Perelman School of Medicine

StuSerious commented 3 years ago

It worked Paul! Should I close the Issue?

image

Thank you so much for your help and patience! I can't wait to get this thing running and take it for a spin!

StuSerious commented 3 years ago

Seeing as this is resolved on my end and it's been a while, I will go ahead and close the issue.

Thanks again for the feedback!