/ingestion-csvs

A definitive collection of calibration and ingestion parameter data for all platforms.

Primary LanguagePython

ingestion-csvs

A definitive collection of calibration and ingestion parameter data for all platforms.

The repository is organized by platform. Each platform directory contains two types of data files.

  • Calibration sheets in Excel format.
  • Ingestion parameter sheets in CSV format.

Filenames adhere to the following conventions:

  • Calibration sheets are named Omaha_Cal_Info_PLATFORM_XXXXX.xlsx, where:
    • PLATFORM is the platform name (e.g. CP02PMCI).
    • XXXXX is the five digit deployment number (e.g. 00001).
  • Ingestion parameter sheets are named PLATFORM_SXXXXX_ingest.csv, where:
    • PLATFORM is the platform name.
    • S is the source of data (e.g. D for telemetered, R for recovered).
    • XXXXX is the five-digit deployment number (e.g. 00001).

A Platform Parameters Checklist Excel spreadsheet is also included in the repository to help keep track of the sheets that are available and the sheets that still need to be created.

Ingestion Parameter Sheets (CSV Files)

The ingestion parameter sheets require 4 columns of data:

Column Name Description
uframe_route The name of the ingestion queue that the EDEX application will pull the files from.
filename_mask A filename mask that points to the files to be ingested. Can include UNIX style wildcards (*, ?).
reference_designator The reference designator associated with the files to be ingested.
data_source An indication of whether the data is telemetered or recovered.

Lines can be commented out in the CSV file by placing a pound sign # at the beginning of the line, or at the beginning of any cell in the line. It's recommended to place the pound sign # in the uframe_route column. When a line in the CSV file is commented out, the ingestion script will ignore that line completely.

Extra columns, such as "notes" or "status," can be included in the CSV files. The ingestion script will ignore these columns completely. Feel free to annotate CSV files with extra columns of data as necessary, but entries in the "status" column should use a standard set of codes, using the definitions below:

Status Description
Not Deployed Instrument was not integrated onto the platform for this deployment.
Not Expected Data are not available for a known reason (e.g. instrument failed, files were corrupted, instrument was lost).
Missing No data in raw data archive, although the instrument was deployed and operational.
Expected Data are scheduled for upload to the raw data archive.
Pending Data are on the raw data archive but not yet able to be ingested (e.g. parser needs to be developed or modified).
Available Data are on the raw data archive and ready for ingestion.

Utilities

ingest_csv.py

Ingest all files described in one or more ingestion csv files.

This allows a simple way to ingest a large amount of uncabled data by simply providing the list of ingestion CSV files.

Usage: ingest_csv.py csv_glob

For example, to ingest all the uncabled data from the CE02SHSP mooring:

./ingest_csv.py CE02SHSP/*

This uses ingest_file.py to process each file glob as defined in the ingestion csv file.

ingest_file.py

Ingest a set of files for a given reference designator.

This tool is designed to test ingestion for a particular uncabled instrument stream. It can also be used to patch ingestion on production, however Large or continual ingestion should be managed by the ingestion tool currently under design by Mark Steiner.

Usage: ingest_file.py uframe_route reference_designator data_source deployment number filename_mask

Example:

./ingest_file.py Ingest.flort-dj-cspp_recovered CE02SHSP-SP002-07-FLORTJ000 telemetered 2 /omc_data/whoi/OMC/CE02SHSP/R00002/extract/*TRIP.txt

ingest_missing.py

Ingest set of cabled files that have been missed during a previous ingestions. It will scrape all missing dates and then it will perform the playback command.

written by Phil Tran

Usage: ingest_missing.py event_url particle_url server

Example: python ingest_missing.py qpid://guest/guest@uframe-test?queue=Ingest.instrument_events qpid://guest/guest@uframe-test?queue=Ingest.instrument_particles uframe-test

find_raw_cabled_files

Find files associated with the specified cabled reference designator.

written by Phil Tran

find_raw_cabled_files.py reference_designator find_raw_cabled_files.py [-l] reference_designator

The optional -l option will provide the list of files associated with the provided reference designator.

Example:

python find_raw_cabled_files.py CE04OSPS-SF01B-4B-VELPTD106

python find_raw_cabled_files.py -l CE04OSPS-SF01B-4B-VELPTD106

Monitoring

The file ingest queue can be monitored using the qpid_stat.py utility in the ooi-tools repository: