Specimen Digital File Manifest

Overview

Generates a JSON-LD file containing digital asset objects using the BICAN Library Generation Schema.

Retrieve Specimen File Manifest from Brain Knowledge Platform

  • Step 1: Go to Brain Knowledge Platform

  • Step 2: Navigate to ‘Data/Projects’ tab on the top right menu

  • Step 3: Filter by ‘Specimen Type’ specifically “Library Aliquot”

  • Step 4: Click on specific project i.e. “BICAN Rapid Release Inventory: Single cell transcriptomics and epigenomics”

  • Step 5: Click on ‘BROWSE SPECIMENS’ button

  • Step 6: Click on download icon (arrow pointing down) on top menu bar and select ‘File Manifest’

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

-l, --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
LA-123
LA-345