How to use the pyclowder.extractors.download_dataset_metadata_jsonld function in pyclowder

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github terraref / computing-pipeline / scripts / stereoImager / extractor / terra.demosaic.py View on Github external
def check_message(parameters):
    # TODO: re-enable once this is merged into Clowder: https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/clowder/pull-requests/883/overview
    # fetch metadata from dataset to check if we should remove existing entry for this extractor first
    md = extractors.download_dataset_metadata_jsonld(parameters['host'], parameters['secretKey'], parameters['datasetId'], extractorName)
    for m in md:
        if 'agent' in m and 'name' in m['agent']:
            if m['agent']['name'].find(extractorName) > -1:
                print("skipping, already done")
                return False
                #extractors.remove_dataset_metadata_jsonld(parameters['host'], parameters['secretKey'], parameters['datasetId'], extractorName)

    # Check for a left and right file before beginning processing
    found_left = False
    found_right = False
    for f in parameters['filelist']:
        if 'filename' in f and f['filename'].endswith('_left.bin'):
            found_left = True
        elif 'filename' in f and f['filename'].endswith('_right.bin'):
            found_right = True
github terraref / computing-pipeline / scripts / plantcv / extractor / terra.plantcv.py View on Github external
def check_message(parameters):
    # For now if the dataset already has metadata from this extractor, don't recreate
    md = extractors.download_dataset_metadata_jsonld(parameters['host'], parameters['secretKey'], parameters['datasetId'], extractorName)
    if len(md) > 0:
        for m in md:
            if 'agent' in m and 'name' in m['agent']:
                if m['agent']['name'].find(extractorName) > -1:
                    print("skipping dataset %s, already processed" % parameters['datasetId'])
                    return False

    # Expect at least 10 relevant files to execute this processing
    relevantFiles = 0
    for f in parameters['filelist']:
        raw_name = re.findall(r"(VIS|NIR|vis|nir)_(SV|TV|sv|tv)(_\d+)*" , f["filename"])
        if raw_name != []:
            relevantFiles += 1

    if relevantFiles >= 10:
        return True
github terraref / computing-pipeline / scripts / plantcv / extractor_with_avg_traits / terra.plantcv.py View on Github external
def process_dataset(parameters):
    # TODO: re-enable once this is merged into Clowder: https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/clowder/pull-requests/883/overview
    # fetch metadata from dataset to check if we should remove existing entry for this extractor first
    md = extractors.download_dataset_metadata_jsonld(parameters['host'], parameters['secretKey'], parameters['datasetId'], extractorName)
    if len(md) > 0:
        for m in md:
            if 'agent' in m and 'name' in m['agent']:
                if m['agent']['name'].find(extractorName) > -1:
                    print("skipping, already done")
                    return
        #extractors.remove_dataset_metadata_jsonld(parameters['host'], parameters['secretKey'], parameters['datasetId'], extractorName)
    #    pass


    # Compiled traits table
    fields = ('plant_barcode', 'genotype', 'treatment', 'imagedate', 'sv_area', 'tv_area', 'hull_area',
              'solidity', 'height', 'perimeter')
    traits = {'plant_barcode' : '',
              'genotype' : '',
              'treatment' : '',