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

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github terraref / computing-pipeline / scripts / plantcv / extractor / terra.plantcv.py View on Github external
vn_traits = pcia.process_sv_images_core(vis_id, img, nir_id, nir, nir2, traits)

        print "...uploading resulting metadata"
        # upload the individual file metadata
        metadata = {
            "@context": {
                "@vocab": "https://clowder.ncsa.illinois.edu/clowder/assets/docs/api/index.html#!/files/uploadToDataset"
            },
            "content": vn_traits[0],
            "agent": {
                "@type": "cat:extractor",
                "extractor_id": parameters['host'] + "/api/extractors/" + extractorName
            }
        }
        parameters["fileid"] = vis_id
        extractors.upload_file_metadata_jsonld(mdata=metadata, parameters=parameters)
        metadata = {
            "@context": {
                "@vocab": "https://clowder.ncsa.illinois.edu/clowder/assets/docs/api/index.html#!/files/uploadToDataset"
            },
            "content": vn_traits[1],
            "agent": {
                "@type": "cat:extractor",
                "extractor_id": parameters['host'] + "/api/extractors/" + extractorName
            }
        }
        parameters["fileid"] = nir_id
        extractors.upload_file_metadata_jsonld(mdata=metadata, parameters=parameters)

    # compose the summary traits
    trait_list = pcia.generate_traits_list(traits)
github terraref / computing-pipeline / scripts / plantcv / extractor_with_avg_traits / terra.plantcv.py View on Github external
}
        }
        parameters["fileid"] = vis_id
        extractors.upload_file_metadata_jsonld(mdata=metadata, parameters=parameters)
        metadata = {
            "@context": {
                "@vocab": "https://clowder.ncsa.illinois.edu/clowder/assets/docs/api/index.html#!/files/uploadToDataset"
            },
            "content": vn_traits[1],
            "agent": {
                "@type": "cat:extractor",
                "extractor_id": parameters['host'] + "/api/extractors/" + extractorName
            }
        }
        parameters["fileid"] = nir_id
        extractors.upload_file_metadata_jsonld(mdata=metadata, parameters=parameters)

    # compose the summary traits
    trait_list = [  traits['plant_barcode'], 
                    traits['genotype'], 
                    traits['treatment'], 
                    traits['imagedate'],
                    np.mean(traits['sv_area']), 
                    traits['tv_area'], 
                    np.mean(traits['hull_area']),
                    np.mean(traits['solidity']), 
                    np.mean(traits['height']),
                    np.mean(traits['perimeter'])]


    outfile = 'avg_traits.csv'
    with open(outfile, 'w') as csv:
github terraref / computing-pipeline / scripts / plantcv / extractor / terra.plantcv.py View on Github external
}
        }
        parameters["fileid"] = vis_id
        extractors.upload_file_metadata_jsonld(mdata=metadata, parameters=parameters)
        metadata = {
            "@context": {
                "@vocab": "https://clowder.ncsa.illinois.edu/clowder/assets/docs/api/index.html#!/files/uploadToDataset"
            },
            "content": vn_traits[1],
            "agent": {
                "@type": "cat:extractor",
                "extractor_id": parameters['host'] + "/api/extractors/" + extractorName
            }
        }
        parameters["fileid"] = nir_id
        extractors.upload_file_metadata_jsonld(mdata=metadata, parameters=parameters)

    # compose the summary traits
    trait_list = pcia.generate_traits_list(traits)

    # generate output CSV
    outfile = 'avg_traits.csv'
    pcia.generate_average_csv(outfile, fields, trait_list)
    extractors.upload_file_to_dataset(outfile, parameters)
    os.remove(outfile)
    metadata = {
        "@context": {
            "@vocab": "https://clowder.ncsa.illinois.edu/clowder/assets/docs/api/index.html#!/files/uploadToDataset"
        },
        "dataset_id": parameters["datasetId"],
        "content": {"status": "COMPLETED"},
        "agent": {