Handle numerical data generated by PlantCV pipeline

terraref / computing-pipeline

Pipeline to Extract Plant Phenotypes from Reference Data

BSD 3-Clause "New" or "Revised" License

24 stars 13 forks source link

Handle numerical data generated by PlantCV pipeline #31

Closed dlebauer closed 8 years ago

dlebauer commented 8 years ago

[x] add normalization / correction step to plantcv scripts @nfahlgren
- generate plant-level phenotypes
- posted to danforthcenter/plantcv#19
[ ] Display in Clowder interface #119 @yanliu-chn
[ ] Insert traits into BETYdb #33 @gsrohde

yanliu-chn commented 8 years ago

@nfahlgren : is the new extractor code somewhere online?

nfahlgren commented 8 years ago

@yanliu-chn: https://github.com/terraref/computing-pipeline/blob/plantcv-clowder-extractor/scripts/plantcv/PlantcvClowderIndoorAnalysis.py

max-zilla commented 8 years ago

@nfahlgren can you try:

changing in_bounds: true to "True" - python likes capitalized True/False
post to /metadata as opposed to /metadata.jsonld - we want to use jsonld metadata eventually but your JSON object there does not have a @context entry which is expected in a JSON-LD standard: http://json-ld.org/

If posting to /metadata works we're in pretty good shape - we'll need to identify some context links that can point to metadata definitions (if you don't have something like that already).

nfahlgren commented 8 years ago

@max-zilla posting to metadata instead of metadata.jsonld did the trick. The in_bounds thing was converted to lowercase by the json.dumps function. It's working now though!

dlebauer commented 8 years ago

@nfahlgren and @max-zilla what is the status of this?

max-zilla commented 8 years ago

@dlebauer @nfahlgren Noah, I'll look at your pull request before our meeting tomorrow.

max-zilla commented 8 years ago

@caicai89- @robkooper is "terra" the correct exchange to use for this extractor config? as opposed to "clowder"?

@caicai89- we can sit down and try to figure this out tomorrow if you have time. something that would be worth doing is installing a local test instance of Clowder and RabbitMQ to test this on a local environment: https://opensource.ncsa.illinois.edu/confluence/display/CATS/Installing+Clowder

install MongoDB > in folder, ./bin/mongod
install RabbitMQ > in folder, ./sbin/rabbitmq-server
install Clowder > in folder, ./sbt run
https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/pyclowder/browse install PyClowder and try running wordcount

robkooper commented 8 years ago

yes for plantcv terra is the right one to use. clowder is good for generic extractors.

nfahlgren commented 8 years ago

The PlantCV analysis script was merged in #108. @gsrohde is working on inserting PlantCV traits into BETYdb in #33. The Clowder extractor that will run PlantCV is being developed in #119