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SBU-BMI / quip_distro

BSD 3-Clause "New" or "Revised" License
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Dynamic services not picking up UI parameters #17

Closed sharmaashish closed 7 years ago

sharmaashish commented 7 years ago

It appears that Dynamic service is stuck w/ default parameters. See here

sharmaashish commented 7 years ago

@tkurc Can you check the DynamicService log and confirm if the clumping parameter is showing up as False/0

tkurc commented 7 years ago

The output I sent in email was from the dynamic services log. See below. Look at the Process command line.

loc json: [{ "file-location" : "/data/images/TCGA-14-1396-01Z-00-DX1.ce29c5a9-6823-41be-9d07-f482a4539dad.svs"}] file-location:/data/images/TCGA-14-1396-01Z-00-DX1.ce29c5a9-6823-41be-9d07-f482a4539dad.svs

Image source: image_server

ImageURL: quip-oss:5000/data/images/TCGA-14-1396-01Z-00-DX1.ce29c5a9-6823-41be-9d07-f482a4539dad.svs/58836,18693,270,263/full/0/default.jpg Process command: mainSegmentFeatures -i images/27/27.JPEG -z images/27/output.zip -o images/27 -t img -c TCGA-14-1396-01Z-00-DX1 -p TCGA-14-1396-01Z-00-DX1 -a seg:r1.5:w8:l3:u10:k21.5 -s 58836,18693 -b 270,263 -d 270,263 post: curl -X POST -F case_id=TCGA-14-1396-01Z-00-DX1 -F zip=@images/27/output.zip quip-loader:3001/submitZipOrder % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 36631 100 304 100 36327 17425 2033k --:--:-- --:--:-- --:--:-- 2086k

command:curl -X POST -F case_id=TCGA-14-1396-01Z-00-DX1 -F zip=@images/27/output.zip quip-loader:3001/submitZipOrder Response from annotation server: {"Status":"Queued","Job":{"id":15,"type":"ZipOrder","data":{"case_id":"TCGA-14-1396-01Z-00-DX1","zipFilePath":"/root/731795ec4bfd3ff837d1dd8443d81850"},"priority":0,"progress":0,"state":"inactive","created_at":1485627188652,"promote_at":1485627188652,"attempts":{"made":0,"remaining":1,"max":1}},"id":15}

sharmaashish commented 7 years ago

@tkurc Since you are familiar with the expected parameters, can you check https://github.com/camicroscope/DynamicServices and the docker image: sbubmi/test_segmentation:latest for any hard coded values? I've looked through DynamicServices and I don't see anything hardcoded.

lastlegion commented 7 years ago

I went through the logs,

  1. The job is registered properly in Kue.
  2. I looked at dynamic services logs and it was running with default parameters.
  3. I dug up the dynamic services source code and found out it was expecting parameters in data.order.parameters (as provided in the sample order) json field instead of data.order.execution.parameters.
  4. I changed the order to provide parameters in data.order.parameters but it doesn't seem to work.
sharmaashish commented 7 years ago

@lastlegion Yes, that appears to be the case, but I find it odd that after you provided the order in data.order.parameter, you still did not get the desired behavior.

Take a look at this Print out the command that is being issued here.

lastlegion commented 7 years ago
  1. Modified dynamic services to pick parameters for this algorithm. I've pushed it on a seperate branch here: https://github.com/camicroscope/DynamicServices/tree/quip-distro. We need to use this branch while distributing
  2. Modified camicroscope viewer docker container to create the new order: (https://github.com/camicroscope/ViewerDockerContainer/commit/d03825aa44889664b642a218cf1826d03c8f1c36)
sharmaashish commented 7 years ago

I think @lastlegion worked on this and fixed it. Closing