Specimen File Manifest

Overview

Generates a JSON-LD file containing specimen file data using the BICAN Library Generation Schema.

The input file manifest must be in CSV format and contain the following columns:

Project ID

Specimen ID

File Name

Checksum

File Type

Archive

Archive URI

Command Line

`bkbit filemanifest2jsonld`

$ bkbit filemanifest2jsonld [OPTIONS] FILE_MANIFEST_CSV

Options

--list_library_aliquots
A boolean flag that, when provided, generates a list of unique library aliquots contained in the given file manifest and saves output in file called ‘file_manifest_library_aliquots.txt’. If this flag is not set (DEFAULT), then only the JSON-LD output will be generated.

Arguments

FILE_MANIFEST_CSV
Required argument

Examples

Example 1: Only generate JSON-LD output

# Run filemanifest2jsonld command
$ bkbit filemanifest2jsonld file_manifest.csv > output.jsonld

Example 2: Generate JSON-LD output and list of library aliquots

# Run filemanifest2jsonld command
$ bkbit filemanifest2jsonld --list_library_aliquots file_manifest.csv > output.jsonld

# Generated output files
$ ls .
output.jsonld
file_manifest_library_aliquots.txt

# Contents of file_manifest_library_aliquots.txt
$ cat file_manifest_library_aliquots.txt
LP-123
LP-345