ULIMS JSON schemas

A collection of whole or partial JSON schemas.

Available schemas

• checkdir - An example of JSON schemas that build from sets of JSON schemas, which validate data files. Provides repo self-testing with minimal depencencies.

Checking schemas and datafiles are okay

The check.py module provides a CLI to make it easier to confirm JSON schemas and sample datafile are valid. Use --help to see commands and options. It uses a local copy of the registry.py module from an unpublished package.

CLI Usage

• Create and activate virtenv. The following will prompt to install required packages: * ./install.sh or manually pip install jsonschema typer

• Confirm example schemas and datafile sample are still "good" using: ./check.py checkdir

Break schema(s) or data files

The CLI does minimal capture so requires users to interpret the output when it fails. Use the checkdir folder and command to see how change alters the error message.

*Make one change in checkdir folder and run: ./check.py checkdir

For example, editing checkdir/schemas/base.json and changing scan $ref (line 21) to a schema that does not exist will result in "Unresolvable: urn:ulims:scanschnoexist:1.0" error. Fix typo OR create as new schema file in schemas where the $id within MUST match $ref unresolved. In this case, the correct $ref is the $id in checkdir/schemas/scan.json

Checking a custom folder

All schemas should be kept in a custom folder with two subfolders like checkdir. Ideally, a large schema will be broken down into smaller schemas so fragments can be reused. A datafile sample should exist which is known to pass at commit time of any file in schemas folder.

Custom folders can be checked with: ./check.py confirm

The checkdir command above is calling this confirm command with these options. Use confirm --help to see short and long options mean.

./check.py confirm -d checkdir/datafiles/sample1.json -s checkdir/schemas -c 5 -r "urn:ulims:base:1.0"

Multiple roots in schema folder

The checkdir example has multiple schema roots which reuse smaller schemas. In this case, the sample file validates to both schemas because nothing was unique for instrument. Notice -r is now an instrument root. ./check.py confirm -d checkdir/datafiles/sample1.json -s checkdir/schemas -c 5 -r "urn:ulims:base:i07:1.0"

Adding CLI shortcut to custom folder.

Adding a CLI shortcut like checkdir is suggested if you use the confirm often and the schema is expected to be used for more than 6 months. Also, add to the list of available schemas at start of this document.

Single file schemas

The checkdir example breaks a large schema into smaller schemas, but requires use of a registry to cache all schema $id. The smaller schemas can be added as "definitions" in a single schema file. The effect will be to hard code so reuse more difficult, but some applications might require this.