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Closed
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mguidon opened this issue Jan 23, 2018 · 4 comments
Closed
6 tasks done

Cardiac model from Kember (Java code) #5

mguidon opened this issue Jan 23, 2018 · 4 comments
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@mguidon @sanderegg
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PO issue Created by Product owners [PLEASE use osparc-issue repo]

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@mguidon
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mguidon commented Jan 23, 2018 •
edited by drniiken
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User story

As a user I want to create a pipeline consisting of the cardiac model from Kember and a post-processing service that reproduces the plots in the official MVP use case. I am able to edit all necessary input settings directly in the frontend. Optionally, I would like to have the option to choose a compiler and compiler flags in case I want to build the kernel first.

Definition of done

  • The model is available in the list of services
  • The required pipeline can be created
  • The code is containerized as binary and as code only with compilation performed on the fly
  • For the second part of the pipeline, either python or octave/matlab will be used
  • check if there is a need/possibility to have settings (property window)
  • the results of the python postpro script should be mapped as time series to the outputs, such that they can be visualized with the 2d plot service (item was modified)

Use case

There is documentation/code example for this case in filesrv. In addition, the full workflow is available on MaG's VM.
@ITISFoundation ITISFoundation deleted a comment from esraneufeld Feb 1, 2018
@sanderegg sanderegg added this to the Leonis milestone Jun 29, 2018
@sanderegg
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  • dockerize java code as binary
  • make solver available on osparc platform
  • convert matlab code to python
  • make 2D graph analysis available on platform

@sanderegg sanderegg mentioned this issue Jul 4, 2018
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8 tasks
sanderegg added a commit that referenced this issue Jul 6, 2018
@sanderegg
#5 kember postprocessing (#157)
fdb10f5 
* added link def in configuration

* removed int from available types.
changed float to number

* refactoring get value

* changed type from int to integer

* added exception for invalid item type error
added exception for s3 transfer error

* typo

* nodeports now able to upload files and folders to S3

* pylint

* Makefile usable from Windows bash

* renamed methods

* fixed type

* fixed tests after renaming int to integer

* added default values for SIMCORE_NODE_UUID and SIMCORE_PIPELINE_ID

* moved environment variable inside init function

* typo

* added minio as a fixture

* added unit tests that use minio

* removed empty file

* renamed minio fixture, pylint

* fixed issue with converting booleans
added test with setters

* fixed conversions
added test for folderûrl

* pylint

* moved getting env variable in init function

* moved file to test folder
moved json encoding/decoding of db configuration in io module
removed unnecessary test_postgres module

* simplifications

* renamed io module to dbmanager

* removed unnecessary test

* get the ip directly from docker

* moved creation of env variables to a better location
use docker API to get the IP and port

* skip 2 tests that do not run on travis

* added Dockerfile for kember postpro case
extended docker-compose accordingly

* completed all graphs

* create dummy file

* fixed figure 7 and partly 6

* completed figure 1 with annotations

* all plots but figure 5 missing now

* autorun notebook
completeted heatmap code

* added button to show/hide raw code
added auto slicing of data with a max display of 50k points for now
all graphs are in now

* code cleanup

* added Makefile, docker-compose for jupyter notebook solo

* makefile similar to root makefile

* fix development dummy file

* use jupyter notebook 1.3

* make pylint happy

* fixed JS
added hide_input

* sort lines according to review @manuel
oetiker referenced this issue in oetiker/osparc-simcore Jul 10, 2018
@sanderegg @oetiker
#5 kember postprocessing (ITISFoundation#157)
ec9418e 
* added link def in configuration

* removed int from available types.
changed float to number

* refactoring get value

* changed type from int to integer

* added exception for invalid item type error
added exception for s3 transfer error

* typo

* nodeports now able to upload files and folders to S3

* pylint

* Makefile usable from Windows bash

* renamed methods

* fixed type

* fixed tests after renaming int to integer

* added default values for SIMCORE_NODE_UUID and SIMCORE_PIPELINE_ID

* moved environment variable inside init function

* typo

* added minio as a fixture

* added unit tests that use minio

* removed empty file

* renamed minio fixture, pylint

* fixed issue with converting booleans
added test with setters

* fixed conversions
added test for folderûrl

* pylint

* moved getting env variable in init function

* moved file to test folder
moved json encoding/decoding of db configuration in io module
removed unnecessary test_postgres module

* simplifications

* renamed io module to dbmanager

* removed unnecessary test

* get the ip directly from docker

* moved creation of env variables to a better location
use docker API to get the IP and port

* skip 2 tests that do not run on travis

* added Dockerfile for kember postpro case
extended docker-compose accordingly

* completed all graphs

* create dummy file

* fixed figure 7 and partly 6

* completed figure 1 with annotations

* all plots but figure 5 missing now

* autorun notebook
completeted heatmap code

* added button to show/hide raw code
added auto slicing of data with a max display of 50k points for now
all graphs are in now

* code cleanup

* added Makefile, docker-compose for jupyter notebook solo

* makefile similar to root makefile

* fix development dummy file

* use jupyter notebook 1.3

* make pylint happy

* fixed JS
added hide_input

* sort lines according to review @manuel
sanderegg referenced this issue in sanderegg/osparc-simcore Jul 10, 2018
@odeimaiz
Merge pull request #5 from sanderegg/odeimaiz-vtkjs
8e514f3 
added sample code to create a grid added sample code to display slice…
@drniiken
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REVIEW

SA

  • showing the service

  • java based solver

  • service, viewer

  • pipeline starting

  • progress bar working

  • made faster for demo

  • has only internal parameters

  • tomorrow:
    proactively ask which parameters to wire through

  • replaying a matlab project

  • do not show some of the heavy ones tomorrow

  • nice !

  • a raw data toggler

  • code of Jupyter script

  • now loading original file

  • showing the graph from the paper

@pcrespov pcrespov modified the milestones: Leonis, Libra Aug 15, 2018
@sanderegg sanderegg removed this from the Libra milestone Aug 29, 2018
@pcrespov pcrespov removed the review label Sep 11, 2018
@pcrespov pcrespov reopened this Sep 11, 2018
@pcrespov pcrespov removed the review label Sep 11, 2018
@pcrespov pcrespov reopened this Sep 11, 2018
@drniiken
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For the very moment, we are happy with the Jupyter based 2D plot visualization.

@pcrespov
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Would it be possible then to close this case and create a smaller one with the remaining issue? The latter could refer as a continuation of this

@mguidon mguidon added PO issue Created by Product owners [PLEASE use osparc-issue repo] and removed Deliverable: D5.1 labels Jan 10, 2019
@odeimaiz odeimaiz mentioned this issue Mar 15, 2019
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@ghost ghost removed the in progress label Apr 10, 2019
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