Export Labarchives to ro-crate packages

This is a work-in-progress script to create data packages conforming to the RO-Crate Research Data packaging standard from LabArchives notebooks.

Audience

This is for experienced node developers only at the moment.

Status

This is a proof of concept.

TODO:

• More extensive testing than "that looks about right"
• Review the modeling of notebooks in RO-Crate
• Export comments
• Refine the way HTML is generated

Install

• Download the code using git.

• From the commandline type:

  npm install . --local

Add details of the the LabArchives server you want to use to a file named key.json.

{
    "akid": "utech_sydney",
    "password": "----SECRET-----",
    "baseurl": "https://au-mynotebook.labarchives.com",
    "api": "/api"
  }

Run

NOTE: Lab archives uses two kinds of ID. You can use a temporary "Password Token for External applications" to get access or there is a permanent User ID which gives you API access. The recommended way to use the API is to fetch the User ID using the temporary token then store it.

• For usage information use: node export.js --help

Response:

Usage: export [options]

Exports RO-Crate data packages from LabArchives - uses the 

Options:
  -V, --version                             output the version number
  -l,  --list-notebooks                     List notebooks
  -m --metadata [ro-crate-metadata.jsonld]  RO-Crate metadata file to use as a template for the root dataset and contextual entities (eg people)
  -u --username                             Email address used for LabArchives login
  -i --user-id  [file]                      Path to a file containing a LabArchives user ID secret
  -t --password-token [token]               Lab Arvhives 'Password Token for External applications' via the menu that shows your name at top right of the webiste under 'LA App Authentication
  -n,  --notebook-id [nbid]                 ID of the notebook to export. Get a list via -l
  -c --cratescript [crate]                  URL to the RO-Crate rendering script
  -h, --help                                output usage information

Get a user-id and write it to a file

• To get a secret ID, use: node export.js -u [email protected] -t TOKEN -i ~/.lauid

Get a list of notebooks

• To get a list of notebooks to which you have access use this command: node export.js -l -i ~/.lauid

Response:

NDYyMjIuOHwzNTU1Ni8zNTU1Ni9Ob3RlYm9vay8zMzc3ODg5ODY0fDExNzMzNC43OTk5OTk5OTk5OQ== Backup - Shared UTS procedures
NDYyMjQuMXwzNTU1Ny8zNTU1Ny9Ob3RlYm9vay80OTA2Nzk4NDF8MTE3MzM4LjA5OTk5OTk5OTk5 Backup - Template Supervise HDRS - copy
...
NDI0NDEuMXwzMjY0Ny8zMjY0Ny9Ob3RlYm9vay8zMjk5NTc3NzkxfDEwNzczNS4wOTk5OTk5OTk5OQ== UTS Rollout materials - use this to collaborate!

Export a notebook

To export a notebook into the crates directory given use one of the IDs:

node export.js -t test -i ~/.lauid -n NDI0NDEuMXwzMjY0Ny8zMjY0Ny9Ob3RlYm9vay8zMjk5NTc3NzkxfDEwNzczNS4wOTk5OTk5OTk5OQ==  -m samples/tse/ro-crate-metadata.jsonld crates

To export Edwin Tse's giant, current, exemplary notebook on Open Malaria drug research with addition top-level metadata from an existing RO-Crate (in samples/tse) using the -m option (WARNING: This is a BIG notebook):

node export.js -t test -i ~/.lauid -n MTYzLjh8MTUwOS8xMjYvVHJlZU5vZGUvMjUxNDEwNDEwOHw0MTUuOA==  -m samples/tse/ro-crate-metadata.jsonld crates

Library API

Usage:

Create laToRoCrate

key: json object
outDir: baseFile for exporting notebooks
metadataFileName: "ro-crate-metdatata.json"
log: boolean: display basic logs for debugging

const {LaToRoCrate} = require('labarchives-to-ro-crate');
const laToRoCrate = new LaToRoCrate(key, outDir, metadataFileName, log);

Export Notebook Sync

uid: user id
nbid: notebook id
rootDatasetName: name of the root dataset of the ro-crate
outputDirectoryName: directory name of the exported notebook
cratescript: <optional> crate script
metadataTemplate: <optional> metadata template from an existing ro-crate
pageMetaDescription: <optional> entry description to be written into ro-crate

await laToRoCrate.exportNotebookSync(uid, nbid, rootDatasetName, outputDirectoryName, cratescript, metadataTemplate, pageMetaDescription);