Cyl

bloom cyl #

Manage cylinder scans.

bloom cyl download DIR #

Download cylinder scans.

USAGE
  $ bloom cyl download DIR --experiment_id <value> -p staging|prod|local [--plant_age_min <value>]
    [--plant_age_max <value>] [--plant_qr_code <value>] [--dry_run] [--limit <value>] [-n <value>]

ARGUMENTS
  DIR  output directory to download cylinder scans to

FLAGS
  -n, --n_workers=<value>  [default: 16] number of workers to use for downloading
  -p, --profile=<option>   (required) Bloom database profile
                           <options: staging|prod|local>
  --dry_run                only print what would be downloaded
  --experiment_id=<value>  (required) experiment ID (run 'bloom cyl experiments list' for options)
  --limit=<value>          [default: 100000] limit the number of scans to download
  --plant_age_max=<value>  [default: 1000] maximum plant age in days
  --plant_age_min=<value>  minimum plant age in days
  --plant_qr_code=<value>  return only scans matching this cylinder QR code

DESCRIPTION
  Download cylinder scans.

  Downloads metadata and image files for cylinder scans from Bloom.

  Creates scans in the directory specified by DIR. If DIR does not exist, it
  will be created.

  Metadata is saved to "<DIR>/scans.csv". Scans are saved to
  "<DIR>/images/Wave<wave_number>/Day<plant_age_days>_<date_scanned>/<plant_qr_code>".


EXAMPLES
  $ bloom cyl download /path/to/download/directory --experiment_id 1

  $ bloom cyl download /path/to/download/directory --experiment_id 1 --plant_age_min 10 --plant_age_max 13

  $ bloom cyl download /path/to/download/directory --experiment_id 1 --plant_qr_code ABC123

bloom cyl experiments list #

List cylinder experiments.

USAGE
  $ bloom cyl experiments list -p staging|prod|local

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  List cylinder experiments.

bloom cyl init DIR #

Initialize a cylinder experiment.

USAGE
  $ bloom cyl init DIR -p staging|prod|local

ARGUMENTS
  DIR  directory of cylinder scans

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  Initialize a cylinder experiment.

  Will create a 'cyl-metadata.yml' file in the specified directory that
  describes the metadata for the cylinder scans below that directory. It must
  be edited to reflect the correct metadata format.


EXAMPLES
  $ bloom cyl init /path/to/cylinder/experiment

bloom cyl preview DIR #

Preview cylinder scans before uploading.

USAGE
  $ bloom cyl preview DIR -p staging|prod|local

ARGUMENTS
  DIR  directory of cylinder scans

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  Preview cylinder scans before uploading.

  Expects the directory or one of its ancestors to contain a file named
  'cyl-metadata.yml' that describes the metadata for the scans.

  The 'cyl-metadata.yml' file can be created with the 'bloom cyl init DIR'
  command. It must be edited to reflect the correct metadata format.


EXAMPLES
  $ bloom cyl preview /path/to/cylinder/experiment

bloom cyl scanners add SCANNER_NAME #

Add a cylinder scanner.

USAGE
  $ bloom cyl scanners add SCANNER_NAME -p staging|prod|local

ARGUMENTS
  SCANNER_NAME  name of the scanner to add

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  Add a cylinder scanner.

bloom cyl scanners delete SCANNER_NAME #

Delete a cylinder scanner.

USAGE
  $ bloom cyl scanners delete SCANNER_NAME -p staging|prod|local

ARGUMENTS
  SCANNER_NAME  name of the scanner to delete

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  Delete a cylinder scanner.

bloom cyl scanners list #

List cylinder scanners.

USAGE
  $ bloom cyl scanners list -p staging|prod|local

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  List cylinder scanners.

bloom cyl traits list-sources #

List cylinder trait sources.

USAGE
  $ bloom cyl traits list-sources -p staging|prod|local

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  List cylinder trait sources.

  Lists all the sources of cylinder traits in the Bloom database.


EXAMPLES
  $ bloom cyl traits list-sources

bloom cyl traits upload CSV_FILE SOURCE_NAME [BATCH_SIZE] #

Upload cylinder scan traits.

USAGE
  $ bloom cyl traits upload CSV_FILE SOURCE_NAME [BATCH_SIZE] -p staging|prod|local

ARGUMENTS
  CSV_FILE     traits CSV file to upload
  SOURCE_NAME  source of the traits (run 'bloom cyl traits list-sources' for options)
  BATCH_SIZE   [default: 25] number of scans to upload at a time

FLAGS
  -p, --profile=<option>  (required) Bloom database profile
                          <options: staging|prod|local>

DESCRIPTION
  Upload cylinder scan traits.

  Uploads cylinder scan traits to the Bloom server.

  Expects a CSV file with one row per scan and the following column names:
  - scan_id: scan ID number
  - plant_name: plant ID string (the last non-trait column)
  - [...trait columns]: the remaining columns are different traits


EXAMPLES
  $ bloom cyl traits upload /path/to/traits.csv

bloom cyl upload DIR #

Upload cylinder scans.

USAGE
  $ bloom cyl upload DIR -p staging|prod|local [-n <value>] [-c <value>]

ARGUMENTS
  DIR  directory of cylinder scans

FLAGS
  -c, --pngCompression=<value>  [default: 9] PNG compression level (0-9)
  -n, --nWorkers=<value>        [default: 4] number of workers to use for uploading
  -p, --profile=<option>        (required) Bloom database profile
                                <options: staging|prod|local>

DESCRIPTION
  Upload cylinder scans.

  Uploads metadata and image files for cylinder scans to the Bloom server.

  Expects the directory or one of its ancestors to contain a file named
  'cyl-metadata.yml' that describes the metadata for the scans.

  The 'cyl-metadata.yml' file can be created with the 'bloom cyl init DIR'
  command. It must be edited to reflect the correct metadata format.


EXAMPLES
  $ bloom cyl upload /path/to/cylinder/experiment