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from pipeline_utils.schemas import schema | ||
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yaml_reference_genome_schema = { | ||
## Schema ######################### | ||
schema.SCHEMA: 'https://json-schema.org/draft/2020-12/schema', | ||
schema.ID: '/schemas/YAMLReferenceGenome', | ||
schema.TITLE: 'YAMLReferenceGenome', | ||
schema.DESCRIPTION: 'Schema to validate a YAML description of a ReferenceGenome', | ||
schema.TYPE: schema.OBJECT, | ||
schema.PROPERTIES: { | ||
'name': { | ||
schema.DESCRIPTION: 'Name of the ReferenceGenome', | ||
schema.TYPE: schema.STRING | ||
}, | ||
'version': { | ||
schema.DESCRIPTION: 'Version of the ReferenceGenome', | ||
schema.TYPE: schema.STRING | ||
}, | ||
'code': { | ||
schema.DESCRIPTION: 'Code for the ReferenceGenome', | ||
schema.TYPE: schema.STRING | ||
}, | ||
'files': { | ||
schema.DESCRIPTION: 'Associated reference files', | ||
schema.TYPE: schema.ARRAY, | ||
schema.ITEMS: { | ||
schema.TYPE: schema.STRING | ||
} | ||
} | ||
}, | ||
schema.REQUIRED: ['name', 'version', 'code'] | ||
} |
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################################################################ | ||
# GRCh38 Genome Reference | ||
################################################################ | ||
name: GRCh38 | ||
version: GCA_000001405.15 | ||
files: | ||
- complete-reference-fasta-no-alt@GCA_000001405.15_GRCh38_no_decoy | ||
- complete-reference-bwt-no-alt@GCA_000001405.15_GRCh38_no_decoy | ||
# Required for displaying in the file name | ||
code: GRCh38 | ||
# This is required to sync with a previously generated object | ||
uuid: e89937e6-80d3-4605-8dea-4a74c7981a9f |
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################################################################# | ||
# Libraries | ||
################################################################# | ||
import sys, os | ||
import pytest | ||
from pipeline_utils.lib import yaml_parser | ||
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################################################################# | ||
# Tests | ||
################################################################# | ||
def test_software(): | ||
""" | ||
""" | ||
res = [ | ||
{"code": "GRCh38", | ||
"title": "GRCh38 [GCA_000001405.15]", | ||
"consortia": ["cgap-core"], | ||
"identifier": "grch38", | ||
"submission_centers": ["hms-dbmi"], | ||
"uuid": "e89937e6-80d3-4605-8dea-4a74c7981a9f", | ||
"files": [ | ||
"cgap-core:ReferenceFile-complete-reference-fasta-no-alt_GCA_000001405.15_GRCh38_no_decoy", | ||
"cgap-core:ReferenceFile-complete-reference-bwt-no-alt_GCA_000001405.15_GRCh38_no_decoy" | ||
], | ||
"aliases": ["cgap-core:ReferenceGenome-GRCh38_GCA_000001405.15"]} | ||
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] | ||
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for i, d in enumerate(yaml_parser.load_yaml('tests/repo_correct/portal_objects/reference_genome.yaml')): | ||
# creating JSON object | ||
d_ = yaml_parser.YAMLReferenceGenome(d).to_json( | ||
submission_centers=["hms-dbmi"], | ||
consortia=["cgap-core"] | ||
) | ||
# check | ||
assert d_ == res[i] |
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