invalid json

Finally catching up to development. I initialized a test project to get pipelines going. I can run a PSII pipeline with one image pair. I ran

scripts/psii.py -i1 "data\psII\A1-SILK_dark-2018-12-10 20_01_50-PSII0_1_0_0.tif" -i2 "data\psII\A1-SILK_dark-2018-12-10 20_01_50-PSII0_2_0_0.tif" -o debug -D print -writeimg True -r results.json

which spit out results.json, but when i try to convert it to a csv i get an error:

(test-environment) 
Dominik Schneider@CPPC1 MINGW64 ~/Documents/phenomics/testpipeline (master)
$ plantcv-utils.py json2csv -j results.json -c result-table
Traceback (most recent call last):
  File "C:/Users/dominikschneider/Miniconda3/envs/test-environment/Scripts/plantcv-utils.py", line 4, in <module>
    __import__('pkg_resources').run_script('plantcv==3.5.0+16.g5b9908c.dirty', 'plantcv-utils.py')
  File "C:\Users\dominikschneider\Miniconda3\envs\test-environment\lib\site-packages\pkg_resources\__init__.py", line 666, in run_script    
    self.require(requires)[0].run_script(script_name, ns)
  File "C:\Users\dominikschneider\Miniconda3\envs\test-environment\lib\site-packages\pkg_resources\__init__.py", line 1453, in run_script   
    exec(code, namespace, namespace)
  File "c:\users\dominikschneider\miniconda3\envs\test-environment\lib\site-packages\plantcv-3.5.0+16.g5b9908c.dirty-py3.7.egg\EGG-INFO\scripts\plantcv-utils.py", line 74, in <module>
    main()
  File "c:\users\dominikschneider\miniconda3\envs\test-environment\lib\site-packages\plantcv-3.5.0+16.g5b9908c.dirty-py3.7.egg\EGG-INFO\scripts\plantcv-utils.py", line 69, in main
    options()
  File "c:\users\dominikschneider\miniconda3\envs\test-environment\lib\site-packages\plantcv-3.5.0+16.g5b9908c.dirty-py3.7.egg\EGG-INFO\scripts\plantcv-utils.py", line 44, in options
    args.func(args)
  File "c:\users\dominikschneider\miniconda3\envs\test-environment\lib\site-packages\plantcv-3.5.0+16.g5b9908c.dirty-py3.7.egg\EGG-INFO\scripts\plantcv-utils.py", line 52, in run_json2csv    plantcv.utils.json2csv(json_file=args.json, csv_file=args.csv)
  File "C:\Users\dominikschneider\Miniconda3\envs\test-environment\lib\site-packages\plantcv-3.5.0+16.g5b9908c.dirty-py3.7.egg\plantcv\utils\converters.py", line 12, in json2csv    raise ValueError("Invalid JSON file: {0}".format(json_file))ValueError: Invalid JSON file: results.json

I took a look at the parallel version for flat files and of course I’ve been labeling my files from lemnabase differently from you. I am using format code {0}-{3}-{1}-{6} which corresponds to plantid-measurement label-timestamp-camera label whereas you have it setup with measurement label and timestamp flipped. Anyway to work on making this more flexible?
Is this going to iterate through every timestamp?

here is my repo: https://github.com/dschneiderch/testpipeline

[HaleySchuhl]

I agree, it would be easier to have temp files saved as .json during parallelization. On my branch I’m working on I had if 'text/plain' in mimetypes.guess_type(filename) or 'application/json' in mimetypes.guess_type(filename): but this can certainly be simplified and ensure that .py scripts, git files, or anything else gets identified as plain text.

[nfahlgren]

Looks like we should name the files with the .json extension so that we can do:

if 'application/json' in mimetypes.guess_type(filename):

That should avoid the overlap with other text files at least.