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logger.debug("Uploading %s" % img_file)
img_path = os.path.join(experiment_root, snap_dir, img_file)
img_md = formatImageMetadata(img_file, experiment_md['metadata'], snap_details)
file_md = {
"@context": ["https://clowder.ncsa.illinois.edu/contexts/metadata.jsonld"],
"content": img_md,
"agent": {
"@type": "cat:user",
"user_id": "%sapi/users/%s" % (clowder_host, clowder_uid)
}
}
if not dry_run:
file_id = upload_to_dataset(conn, clowder_host, clowder_user, clowder_pass, snap_dataset, img_path)
logger.debug("Created file %s [%s]" % (img_file, file_id))
file_md["file_id"] = file_id
upload_file_metadata(conn, clowder_host, clowder_key, file_id, file_md)
logger.debug("Uploaded metadata to [%s]" % file_id)
else:
logger.debug("Skipping file %s [%s]" % (img_file, "DRY RUN"))
# Submit new dataset for extraction to plantCV extractor
if not dry_run:
extractor = "terra.lemnatec.plantcv"
logger.debug("Submitting dataset [%s] to %s" % (snap_dataset, extractor))
submit_extraction(conn, clowder_host, clowder_key, snap_dataset, extractor)
logger.debug("Experiment uploading complete.")
else:
logger.debug("%s does not exist" % experiment_root)
sys.exit(1)
"source": row['source'],
"value": row['value']
}
trait = row['trait']
create_datapoint_with_dependencies(connector, host, secret_key, trait,
(centroid_lonlat[1], centroid_lonlat[0]), time_fmt, time_fmt,
dpmetadata, timestamp)
successful_plots += 1
# Add metadata to original dataset indicating this was run
self.log_info(resource, "updating file metadata (%s)" % resource['id'])
ext_meta = build_metadata(host, self.extractor_info, resource['id'], {
"plots_processed": successful_plots,
}, 'file')
upload_metadata(connector, host, secret_key, resource['id'], ext_meta)
self.end_message(resource)
def process_message(self, connector, host, secret_key, resource, parameters):
self.start_message(resource)
# submit CSV to BETY
self.log_info(resource, "submitting CSV to bety")
submit_traits(resource['local_paths'][0], betykey=self.bety_key)
# Add metadata to original dataset indicating this was run
self.log_info(resource, "updating file metadata (%s)" % resource['id'])
ext_meta = build_metadata(host, self.extractor_info, resource['id'], {
"betydb_link": "https://terraref.ncsa.illinois.edu/bety/api/v1/variables?name=canopy_cover"
}, 'file')
upload_metadata(connector, host, secret_key, resource['id'], ext_meta)
self.end_message(resource)