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'perspective' : perspective,
'rotation_angle' : rotation_angle,
'zoom' : zoom,
'imager_stage_vertical_position' : stage_position,
'camera_gain' : camera_gain,
'camera_exposure' : camera_exposure,
'image_id' : img_id,
'imagedate' : snap_details['timestamp'],
'species' : species,
'genotype' : genotype,
'treatment' : treatment,
'sample_id' : barcode['unique_id']
}
conn = Connector({}, mounted_paths={"/home/clowder/sites":"/home/clowder/sites"})
experiment_root = sys.argv[1]
experiment_name = os.path.basename(experiment_root)
if os.path.exists(experiment_root):
logger.debug("Searching for index files in %s" % experiment_root)
md_file = os.path.join(experiment_root, experiment_name+"_metadata.json")
csv_file = os.path.join(experiment_root, "SnapshotInfo.csv")
if not os.path.isfile(md_file):
logger.debug("%s not found" % md_file)
sys.exit(1)
if not os.path.isfile(csv_file):
logger.debug("%s not found" % csv_file)
sys.exit(1)
logger.debug("Found index files; loading %s" % md_file)
base_md = loadJsonFile(md_file)
from terrautils.sensors import Sensors
import utils
import counts
config = {}
app_dir = '/home/filecounter'
SCAN_LOCK = False
count_defs = counts.SENSOR_COUNT_DEFINITIONS
DEFAULT_COUNT_START = None
DEFAULT_COUNT_END = None
CLOWDER_HOST = "https://terraref.ncsa.illinois.edu/clowder/"
CLOWDER_KEY = os.getenv('CLOWDER_KEY', False)
CONN = Connector("", {}, mounted_paths={"/home/clowder/sites":"/home/clowder/sites"})
# UTILITIES ----------------------------
def update_nested_dict(existing, new):
"""Nested update of python dictionaries for config parsing
Adapted from http://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
"""
for k, v in new.iteritems():
if isinstance(existing, collections.Mapping):
if isinstance(v, collections.Mapping):
r = update_nested_dict(existing.get(k, {}), v)
existing[k] = r
else:
existing[k] = new[k]
else:
existing = {k: new[k]}
# Set to True to actually upload a dataset from each product then stop
test_one = True
# ---------------------------------
# Clowder instance configuration
# ---------------------------------
clowder_admin_key = "SECRET_KEY"
clowder_host = "https://terraref.ncsa.illinois.edu/clowder/"
# The following user will be shown as the creator and owner of uploaded datasets
clowder_user = "terrarefglobus+uamac@ncsa.illinois.edu"
clowder_pass = "PASSWORD"
clowder_userid = "57adcb81c0a7465986583df1"
# The following space in Clowder will contain all uploaded datasets and collections
clowder_space = "571fb3e1e4b032ce83d95ecf"
# Mapping of local files to the Clowder directory if mounts are different
conn = Connector("", {}, mounted_paths={"/home/clowder/sites":"/home/clowder/sites"})
# ---------------------------------
# Filesystem configuration
# ---------------------------------
root_path = "/home/clowder/sites/ua-mac"
# Defines which products to upload (i.e. remove raw_data key to only upload Level_1 data)
products_to_upload = {
"raw_data": ["stereoTop", "flirIrCamera", "VNIR", "SWIR", "EnvironmentLogger"],
"Level_1": ["scanner3DTop"]
}
# Products which only have a date level for each dataset
no_timestamps = ["EnvironmentLogger"]
# Defines start and end date to upload (inclusive)