Specimen Metadata

Overview

Generate JSON-LD files for specimens, subjects, and their repective ancestors or descendants. Data is retrieved from the BICAN Specimen Portal.

Command Line

`bkbit specimen2jsonld`

$ bkbit specimen2jsonld [OPTIONS] NHASH_ID_OR_FILE

Options

-d, --decendants
A boolean flag that, when provided, generates BICAN objects for the given NHASH_ID and all of its descendants. If this flag is not set (DEFAULT), then the ancestors will be processed.

Arguments

NHASH_ID_OR_FILE
The NHASH_ID of the specimen or a file containing a list of NHASH_IDs. If a file is provided, the file should contain one NHASH_ID per line.

Environment Variables

jwt_token

Token is used to authenticate with the Specimen Portal API and retrieve the specimen metadata.

Note

You must set the Specimen Portal Personal API Token as an environment variable before running bkbit specimen2jsonld.

$ export jwt_token=specimen_portal_personal_api_token

Examples

Example 1: Parse a single record and its ancestors

# If first time running specimen2jsonld or if token is expired, set jwt_token environment variable
$ export jwt_token=specimen_portal_personal_api_token

# Run specimen2jsonld command
$ bkbit specimen2jsonld 'LP-CVFLMQ819998' > output.jsonld

Example 2: Parse a single record and its descendants

# If first time running specimen2jsonld or if token is expired, set jwt_token environment variable
$ export jwt_token=specimen_portal_personal_api_token

# Run specimen2jsonld command. Important: include '--descendants' flag
$ bkbit specimen2jsonld -d 'DO-GICE7463' > output.jsonld

Example 3: Parse a file containing record(s) and their respective ancestors

# If first time running specimen2jsonld or if token is expired, set jwt_token environment variable
$ export jwt_token=specimen_portal_personal_api_token

# Contents of input file
$ cat input_nhash_ids.txt
LA-TZWCWB265559FVVNTS329147
LA-IAXCCV360563HBFKKM103455
LA-JFCEST535498UIPMOH349083

# Run specimen2jsonld command
$ bkbit specimen2jsonld input_nhash_ids.txt

# Expected output
$ ls .
LA-TZWCWB265559FVVNTS329147.jsonld
LA-IAXCCV360563HBFKKM103455.jsonld
LA-JFCEST535498UIPMOH349083.jsonld

Example 4: Parse a file containing record(s) and their respective descendants

# If first time running specimen2jsonld or if token is expired, set jwt_token environment variable
$ export jwt_token=specimen_portal_personal_api_token

# Contents of input file
$ cat input_nhash_ids.txt
DO-XIQQ6047
DO-WFFF3774
DO-RMRL6873

# Run specimenjsonld command. Important: include '--descendants' flag
$ bkbit specimen2jsonld -d input_nhash_ids.txt

# Expected output
$ ls .
DO-XIQQ6047.jsonld
DO-WFFF3774.jsonld
DO-RMRL6873.jsonld