Validate multiple YAML document structure using JSON Schema with jsonschema

[sujaypatil96]

Is there something wrong I'm doing when I try to validate the following multi YAML object file using its corresponding JSON Schema with the jsonschema validation tool?

File to be validated: instance.yaml

authors: GOA-UniProt curators
id: GO_REF:0000029
is_obsolete: true
year: 2007
layout: goref
title: OBSOLETE Gene Ontology annotation based on information extracted from curated
  UniProtKB entries
comments:
- Active 2001-2007.
- Method by which GO terms were manually assigned to UniProt KnowledgeBase accessions,
  using either a NAS or TAS evidence code, by applying information extracted from
  the corresponding publicly-available, manually curated UniProtKB entry. Such GO
  annotations were submitted by the GOA-UniProt group from 2001, but this annotation
  practice was discontinued in 2007.
---
authors: GO ontology editors
id: GO_REF:0000078
year: 2013
layout: goref
title: Representation for the transport or vesicle-mediated transport of a chemical
  from and/or to a cell component as biological process in the Gene Ontology
comments:
- 'We have created a standard template for classes describing the transport or vesicle-mediated
  transport of a chemical entity (ChEBI) from and/or to a cellular component as a
  biological process. The underlying equivalence axiom templates are "GO:0006810 and
  ''transports or maintains localization of'' some X [ and ''has_target_start_location''
  some F] [ and ''has_target_end_location'' some T]" (transport) and "GO:0016192 and
  ''transports or maintains localization of'' some X [ and ''has_target_start_location''
  some F] [ and ''has_target_end_location'' some T]" (vesicle-mediated transport),
  where F and T are cellular components and X is a chemical entity (CHEBI:24431).
  The approach to combine GO and ChEBI has been described in the following publication:
  PMID:23895341.'

JSON Schema validation file: project.schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://example.com/gorefs.schema.json",
    "title": "JSON Schema for validating gorefs.yaml",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "authors": {
                "type": "string",
                "description": ""
            },
            "id": {
                "type": "string",
                "pattern": "GO_REF:\\d{7}",
                "description": ""
            },
            "is_obsolete": {
                "type":"boolean",
                "description": ""
            },
            "year": {
                "type": "integer",
                "description": ""
            },
            "layout": {
                "type": "string",
                "description": ""
            },
            "title": {
                "type": "string",
                "description": ""
            },
            "comments": {
                "type": "array",
                "items": {
                    "type": "string"
                },
                "description": ""
            }
        }
    }
}

Here is my log:

> jsonschema -i instance.yaml project.schema.json
Failed to parse 'instance.yaml': Expecting value: line 1 column 1 (char 0)

[sujaypatil96]

Looks like the jsonschema library doesn't support validation of YAML files with JSON Schema through the CLI or the library methods.

Should this become a feature request?

[Julian]

Hi, have a look at check-jsonschema which will become the official CLI and supports additional things (I believe YAML). #910 and #582 have more details.

Or run the YAML through a simple converter like remarshal, i.e. jsonschema -i <(yaml2json foo.yaml) etc.