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