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APPENDIX: Implementation notes

Table of contents

  1. Programming with JSON-LD
  2. Combining with other packaging schemes
    1. Adding RO-Crate to Bagit
      1. Base URI in BagIt
      2. Referencing external files
      3. Snapshots of external files
    2. Example of wrapping a BagIt bag in an RO-Crate
  3. Repository-specific identifiers

Programming with JSON-LD

When implementing tools to work with RO-Crate it is not necessary to use JSON-LD software libraries, however, programmers should keep in mind the following:

  • RO-Crate JSON-lD has a flat structure; every entity is a JSON object directly within the @graph array in the RO-Crate Metadata File. A useful strategy when processing a crate is to build a look-up table and/or function so that entities can be found via their ID, for example provide a method such as getEntity(id) which returns an entity by its id or a null value if it’s not there.

  • Code defensively. Code should not assume that values will always be a String; values for properties may be single scalar values such as strings or integers ("2" or 2), or references to other entities such as {"@id", "_:1"} (where the referenced entity may or may not be described in the crate, see the point above about having a getEntity() method).

  • Read the whole specification. The RO-Crate specification addresses common use cases individually, introducing aspects of the specification as in a progressive manner. Some key points, such as entities may have more than one value for @type, may not be apparent from a quick reading.

Combining with other packaging schemes

RO-Crates may co-exist with other packaging schemes, such as BagIt using two general approaches; either (a) adding RO-Crate into a package as part of the payload or (b) wrapping another kind of package. Examples using BagIt follow.

BagIt is described in RFC 8493:

[BagIt is] … a set of hierarchical file layout conventions for storage and transfer of arbitrary digital content. A “bag” has just enough structure to enclose descriptive metadata “tags” and a file “payload” but does not require knowledge of the payload’s internal semantics. This BagIt format is suitable for reliable storage and transfer.

BagIt and RO-Crate have largely separate concerns - RO-Crate is focussed on rich metadata, the semantics of data, while BagIt is about reliable transfer.

Adding RO-Crate to Bagit

RO-Crate can be combined with BagIt simply by placing the RO-Crate files within the BagIt payload (data/) directory.

<BagIt base directory>/
  |   bagit.txt                 # As per BagIt specification
  |   bag-info.txt              # As per BagIt specification
  |   manifest-<algorithm>.txt  # As per BagIt specification
  |   fetch.txt                 # Optional, per BagIt Specification
  |   data/                     # Payload: RO-Crate root directory
      |   ro-crate-metadata.json           # RO-Crate Metadata File MUST be present
      |   ro-crate-preview.html            # RO-Crate Website homepage MAY be present
      |   ro-crate-preview_files/          # MAY be present
      |   [payload files and directories]  # 1 or more SHOULD be present

The Bag declaration bagit.txt MUST be present, the main role of this file is to mark the folder as a bag according to RFC8493. The file SHOULD have this fixed content in UTF-8:

BagIt-version: 1.0
Tag-File-Character-Encoding: UTF-8

The BagIt base directory containing bagit.txt can have any name, and can be archived/transferred in any way, e.g. within a ZIP archive, SFTP or even be exposed on the web.

The manifest file contains file checksums; the BagIt specifications recommends SHA-512 as default algorithm, that is manifest-sha512.txt SHOULD be present.

The BagIt manifest file MUST list the checksum of all payload files in data/ and its subdirectories. Where data/ is also the RO-Crate Root the manifest therefore MUST include ro-crate-metadata.json:

41846747…ee71  data/ro-crate-metadata.json
e1105ed0…5e13  data/chipseq_20200910.json
37fd3a02…bb95  data/results/pipeline_info/design_reads.csv

The SHA-512 checksums have been shortened in the above example.

Creating the manifest file without using BagIt tools/libraries can be done using the equivalent of:

$ find data -type f -print0 | xargs -0 sha512sum > manifest-sha512.txt

Similarly checking the payload directory:

$ sha512sum --quiet -c manifest-sha512.txt
data/chipseq_20200910.json: FAILED
data/ro-crate-metadata.json: FAILED
sha512sum: WARNING: 2 computed checksums did NOT match

The BagIt manifest complements the RO-Crate structure as it provide a complete listing of all payload files with cryptographically strong checksums, ensuring the crate has been fully archived/transferred, which the weak CRC-32 checksum (TCP/IP, ZIP, gzip) is insufficient to guarantee, particularly for large crates.

To ensure the manifest file itself is complete, it is RECOMMENDED to include its checksum in tagmanifest-sha512.txt:

b0556450…8802  bag-info.txt
000b27e3…c52e  manifest-sha512.txt

The BagIt manifest is intended to detect “bit rot” and accidental damage, it does not provide proof the RO-Crate has not been deliberately tampered with, as a malicious actor can also update the checksums.

Guarding against such scenarious would require additional cryptographic measures, e.g.
gpg --detach-sign --armor --output tagmanifest-sha512.txt.asc tagmanifest-sha512.txt in combination with a secure PGP key exchange or equivalent trust network.

Base URI in BagIt

The arcp specification suggests how BagIt UUID identifiers can be used to calculate the base URI of a bag, see section Establishing a base URI inside a ZIP file. For this purpose it is RECOMMENDED that bag-info.txt includes a fresh UUID like:

External-Identifier: urn:uuid:24e51ca2-5067-4598-935a-dac4e327d05a

Referencing external files

The BagIt fetch file MAY be used to reference files to be downloaded into particular data/ paths to complete the bag. These files may be large, require authentication or otherwise inconvenient to transfer within the BagIt folder.

Example fetch.txt using Git LFS:

https://media.githubusercontent.com/…/SPT5_INPUT_R1.bigWig 963489 data/results/SPT5_INPUT_R1.bigWig

BagIt tools can help complete the bag and verify the checksum of the downloaded files according to the manifest.

The RO-Crate contained in data/ MAY describe the bag with data entities as if the bag was complete, even if the large file is not (yet) present:

  {
    "@id": "results/SPT5_INPUT_R1.bigWig",
    "@type": "File",
    "name": "Normalized SPT5_INPUT_R1 bigWig for genome browsers",
    "encodingFormat": {"@id": "http://edamontology.org/format_3006"},
    "url": "https://media.githubusercontent.com/media/biocompute-objects/bco-ro-example-chipseq/main/data/results/bwa/mergedLibrary/bigwig/SPT5_INPUT_R1.bigWig"}
  }

It is RECOMMENDED that the url is provided in the data entity and consistent with the line in fetch.txt in case the RO-Crate is transferred outside its BagIt container.

The fetch.txt approach can also be useful where other files in the RO-Crate reference a downloadable file by relative paths within data/, even if this file is not itself described in the RO-Crate metadata.

Snapshots of external files

As an alternative to the above, web-based data entities can be used in the RO-Crate:

  {
    "@id": "https://media.githubusercontent.com/media/biocompute-objects/bco-ro-example-chipseq/main/data/results/bwa/mergedLibrary/bigwig/SPT5_INPUT_R1.bigWig",
    "@type": "File",
    "name": "Normalized SPT5_INPUT_R1 bigWig for genome browsers",
    "encodingFormat": {"@id": "http://edamontology.org/format_3006"}
  }

The above data entity MAY be combined with fetch.txt in the BagIt base directory:

https://media.githubusercontent.com/…/SPT5_INPUT_R1.bigWig 963489 data/snapshots/SPT5_INPUT_R1.bigWig

In this case the file data/snapshots/SPT5_INPUT_R1.bigWig may be present, but unknown by RO-Crate; BagIt contains a checksummed snapshot of the web resource. Compared with the first approach, the RO-Crate is here primarily pointing at a web resource which is allowed to change without causing a BagIt checksum error.

Example of wrapping a BagIt bag in an RO-Crate

Alternatively, an RO-Crate can wrap a BagIt bag, so that the RO-Crate metadata is outside of the bag directory and can be changed without changing the payload’s checksums.

<RO-Crate root directory>/
  |   ro-crate-metadata.json    # RO-Crate Metadata File MUST be present
  |   ro-crate-preview.html     # RO-Crate Website homepage MAY be present
  |   ro-crate-preview_files/   # MAY be present
  |   bag1/                     # "Wrapped" bag - could have any name
  |      bagit.txt                 # As per BagIt specification
  |      bag-info.txt              # As per BagIt specification
  |      manifest-<algorithm>.txt  # As per BagIt specification
  |      fetch.txt                 # Optional, per BagIt Specification
  |      data/
  |         [payload files and directories]  # 1 or more SHOULD be present
  |         example.txt 

A Data Entity describing example.txt in this scenario would have an @id of bag1/data/example.txt:

{
  "@id": "bag1/data/example.txt",
  "name": "Example file"
}

Repository-specific identifiers

Root Data Entities MAY include repository-specific identifiers, described using Contextual Entities using a PropertyValue, with a name that identifies the repository and the identifier as a value. The same identifier MAY be used in multiple different repositories and effectively namespaced using the name of the ProperyValue.

{
  "@id": "./",
  "@type": "Dataset",
  "identifier": ["https://doi.org/10.4225/59/59672c09f4a4b", {"@id": "_:localid:my-repo:my-id"}, {"@id": "_:localid:other-repo:https://doi.org/10.4225/59/59672c09f4a4b"}]
}

 {
   "@id": "_:localid:my-repo:my-id",
   "@type": "PropertyValue",
   "name": "my-repo",
   "value": "my-id"
 }

  {
   "@id": "_:localid:other-repo:https://doi.org/10.4225/59/59672c09f4a4b",
   "@type": "PropertyValue",
   "name": "other-repo",
   "value": "https://doi.org/10.4225/59/59672c09f4a4b"
 }