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project-schema.json
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project-schema.json
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{
"$schema": "http://json-schema.org/draft-06/schema#",
"definitions": {
"CommandSettings": {
"description": "\n Settings to be provided to a tool like ROBOT\n ",
"properties": {
"memory_gb": {
"type": "integer"
}
},
"type": "object"
},
"ComponentGroup": {
"allOf": [
{
"$ref": "#/definitions/ComponentProduct"
},
{
"properties": {
"directory": {
"default": "components",
"type": "string"
},
"products": {
"items": {
"$ref": "#/definitions/ComponentProduct"
},
"type": "array"
}
},
"type": "object"
}
],
"description": "\n A configuration section that consists of a list of `ComponentProduct` descriptions\n\n Controls extraction of import modules via robot extract into the \"components/\" directory\n "
},
"ComponentProduct": {
"description": "\n Represents an individual component\n Examples: a file external to the edit file that contains axioms that belong to this ontology\n Components are usually maintained manually.\n ",
"properties": {
"base_iris": {
"items": {
"type": "string"
},
"type": "array"
},
"filename": {
"type": "string"
},
"make_base": {
"default": false,
"type": "boolean"
},
"mappings": {
"items": {
"type": "string"
},
"type": "array"
},
"source": {
"type": "string"
},
"sssom_tool_options": {
"default": "",
"type": "string"
},
"template_options": {
"type": "string"
},
"templates": {
"items": {
"type": "string"
},
"type": "array"
},
"use_mappings": {
"default": false,
"type": "boolean"
},
"use_template": {
"default": false,
"type": "boolean"
}
},
"type": "object"
},
"DocumentationGroup": {
"description": "\n Setting for the repos documentation system\n ",
"properties": {
"documentation_system": {
"default": "mkdocs",
"type": "string"
}
},
"type": "object"
},
"ImportGroup": {
"allOf": [
{
"$ref": "#/definitions/ProductGroup"
},
{
"properties": {
"annotate_defined_by": {
"default": false,
"type": "boolean"
},
"annotation_properties": {
"default": [
"rdfs:label",
"IAO:0000115"
],
"items": {
"type": "string"
},
"type": "array"
},
"base_merge_drop_equivalent_class_axioms": {
"default": true,
"type": "boolean"
},
"directory": {
"default": "imports/",
"type": "string"
},
"exclude_iri_patterns": {
"items": {
"type": "string"
},
"type": "array"
},
"export_obo": {
"default": false,
"type": "boolean"
},
"mirror_max_time_download": {
"default": 200,
"type": "integer"
},
"mirror_retry_download": {
"default": 4,
"type": "integer"
},
"module_type": {
"default": "slme",
"type": "string"
},
"module_type_slme": {
"default": "BOT",
"type": "string"
},
"products": {
"items": {
"$ref": "#/definitions/ImportProduct"
},
"type": "array"
},
"release_imports": {
"default": false,
"type": "boolean"
},
"slme_individuals": {
"default": "include",
"type": "string"
},
"use_base_merging": {
"default": false,
"type": "boolean"
}
},
"type": "object"
}
],
"description": "\n A configuration section that consists of a list of `ImportProduct` descriptions\n\n Controls extraction of import modules via robot extract into the \"imports/\" directory\n "
},
"ImportProduct": {
"allOf": [
{
"$ref": "#/definitions/Product"
},
{
"properties": {
"annotation_properties": {
"default": [
"rdfs:label",
"IAO:0000115"
],
"items": {
"type": "string"
},
"type": "array"
},
"base_iris": {
"items": {
"type": "string"
},
"type": "array"
},
"is_large": {
"default": false,
"type": "boolean"
},
"make_base": {
"default": false,
"type": "boolean"
},
"mirror_from": {
"type": "string"
},
"mirror_type": {
"type": "string"
},
"module_type": {
"type": "string"
},
"module_type_slme": {
"default": "BOT",
"type": "string"
},
"slme_individuals": {
"default": "include",
"type": "string"
},
"use_base": {
"default": false,
"type": "boolean"
},
"use_gzipped": {
"default": false,
"type": "boolean"
}
},
"type": "object"
}
],
"description": "\n Represents an individual import\n Examples: 'uberon' (in go)\n Imports are typically built from an upstream source, but this can be configured\n "
},
"PatternPipelineGroup": {
"allOf": [
{
"$ref": "#/definitions/ProductGroup"
},
{
"properties": {
"directory": {
"default": "../patterns/",
"type": "string"
},
"matches": {
"items": {
"$ref": "#/definitions/PatternPipelineProduct"
},
"type": "array"
},
"products": {
"items": {
"$ref": "#/definitions/PatternPipelineProduct"
},
"type": "array"
}
},
"type": "object"
}
],
"description": "\n A configuration section that consists of a list of `PatternPipelineProduct` descriptions\n\n Controls the handling of patterns data in the \"src/patterns/data\" directory\n "
},
"PatternPipelineProduct": {
"allOf": [
{
"$ref": "#/definitions/Product"
},
{
"properties": {
"dosdp_tools_options": {
"default": "--obo-prefixes=true",
"type": "string"
},
"ontology": {
"default": "$(SRC)",
"type": "string"
}
},
"type": "object"
}
],
"description": "\n Represents an individual pattern pipeline\n Examples: manual curation pipeline, auto curation pipeline\n Each pipeline gets their own specific directory\n "
},
"Product": {
"description": "\n abstract base class for all products.\n\n Here, a product is something that is produced by an ontology workflow.\n A product can be manifested in different formats.\n \n For example, goslim_prok is a subset (aka slim) product from GO,\n this can be manifest as obo, owl, json\n ",
"properties": {
"description": {
"type": "string"
},
"id": {
"type": "string"
},
"maintenance": {
"default": "manual",
"type": "string"
},
"rebuild_if_source_changes": {
"default": true,
"type": "boolean"
},
"robot_settings": {
"$ref": "#/definitions/CommandSettings"
}
},
"required": [
"id"
],
"type": "object"
},
"ProductGroup": {
"description": "\n abstract base class for all product groups.\n\n A product group is a simple holder for a list of\n groups, with the ability to set configurations that\n hold by default for all within that group.\n\n Note: currently the configuration can specify\n EITHER a list of ontology ids (e.g. uberon, cl)\n OR a list of product objects\n OR some mixture\n\n For example, in specifying upstream imports I can\n be lazy and just list the ids, but if I need to\n configure each one individually then I need to specify\n the full product object.\n\n This buys some simplicity for the majority of projects\n that don't do anything fancy, but at the price of overall\n complexity\n ",
"properties": {
"disabled": {
"default": false,
"type": "boolean"
},
"ids": {
"items": {
"type": "string"
},
"type": "array"
},
"rebuild_if_source_changes": {
"default": true,
"type": "boolean"
}
},
"type": "object"
},
"SSSOMMappingSetGroup": {
"description": "\n A configuration section that consists of a list of `SSSOMMappingSetProduct` descriptions\n ",
"properties": {
"directory": {
"default": "../mappings",
"type": "string"
},
"products": {
"items": {
"$ref": "#/definitions/SSSOMMappingSetProduct"
},
"type": "array"
},
"release_mappings": {
"default": false,
"type": "boolean"
}
},
"type": "object"
},
"SSSOMMappingSetProduct": {
"allOf": [
{
"$ref": "#/definitions/Product"
},
{
"properties": {
"mirror_from": {
"type": "string"
},
"source_file": {
"type": "string"
},
"sssom_tool_options": {
"default": "",
"type": "string"
}
},
"type": "object"
}
],
"description": "\n Represents an SSSOM Mapping template template\n "
},
"SubsetGroup": {
"allOf": [
{
"$ref": "#/definitions/ProductGroup"
},
{
"properties": {
"directory": {
"default": "subsets/",
"type": "string"
},
"products": {
"items": {
"$ref": "#/definitions/SubsetProduct"
},
"type": "array"
}
},
"type": "object"
}
],
"description": "\n A configuration section that consists of a list of `SubsetProduct` descriptions\n\n Controls export of subsets/slims into the \"subsets/\" directory\n "
},
"SubsetProduct": {
"allOf": [
{
"$ref": "#/definitions/Product"
},
{
"properties": {
"creators": {
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
}
],
"description": "\n Represents an individual subset.\n Examples: goslim_prok (in go), eco_subset (in ro)\n "
}
},
"description": "\n A configuration for an ontology project/repository\n\n This is divided into project-wide settings, plus\n groups of products. Products are grouped into 4\n categories (more may be added)\n ",
"properties": {
"allow_equivalents": {
"default": "asserted-only",
"type": "string"
},
"catalog_file": {
"default": "catalog-v001.xml",
"type": "string"
},
"ci": {
"default": [
"github_actions"
],
"items": {
"type": "string"
},
"type": "array"
},
"components": {
"$ref": "#/definitions/ComponentGroup"
},
"contact": {
"type": "string"
},
"contributors": {
"items": {
"type": "string"
},
"type": "array"
},
"create_obo_metadata": {
"default": true,
"type": "boolean"
},
"creators": {
"items": {
"type": "string"
},
"type": "array"
},
"custom_makefile_header": {
"default": "\n# ----------------------------------------\n# More information: https://github.com/INCATools/ontology-development-kit/\n",
"type": "string"
},
"description": {
"default": "None",
"type": "string"
},
"documentation": {
"$ref": "#/definitions/DocumentationGroup"
},
"dosdp_tools_options": {
"default": "--obo-prefixes=true",
"type": "string"
},
"edit_format": {
"default": "owl",
"type": "string"
},
"ensure_valid_rdfxml": {
"default": true,
"type": "boolean"
},
"exclude_tautologies": {
"default": "structural",
"type": "string"
},
"export_formats": {
"default": [
"owl",
"obo"
],
"items": {
"type": "string"
},
"type": "array"
},
"export_project_yaml": {
"default": false,
"type": "boolean"
},
"extra_rdfxml_checks": {
"default": false,
"type": "boolean"
},
"git_main_branch": {
"default": "main",
"type": "string"
},
"git_user": {
"default": "",
"type": "string"
},
"github_org": {
"default": "",
"type": "string"
},
"gzip_main": {
"default": false,
"type": "boolean"
},
"id": {
"default": "",
"type": "string"
},
"import_component_format": {
"default": "ofn",
"type": "string"
},
"import_group": {
"$ref": "#/definitions/ImportGroup"
},
"import_pattern_ontology": {
"default": false,
"type": "boolean"
},
"license": {
"default": "https://creativecommons.org/licenses/unspecified",
"type": "string"
},
"namespaces": {
"items": {
"type": "string"
},
"type": "array"
},
"obo_format_options": {
"default": "",
"type": "string"
},
"owltools_memory": {
"default": "",
"type": "string"
},
"pattern_pipelines_group": {
"$ref": "#/definitions/PatternPipelineGroup"
},
"primary_release": {
"default": "full",
"type": "string"
},
"public_release": {
"default": "none",
"type": "string"
},
"public_release_assets": {
"items": {
"type": "string"
},
"type": "array"
},
"reasoner": {
"default": "ELK",
"type": "string"
},
"release_artefacts": {
"default": [
"full",
"base"
],
"items": {
"type": "string"
},
"type": "array"
},
"release_date": {
"default": false,
"type": "boolean"
},
"release_diff": {
"default": false,
"type": "boolean"
},
"release_materialize_object_properties": {
"items": {
"type": "string"
},
"type": "array"
},
"release_use_reasoner": {
"default": true,
"type": "boolean"
},
"remove_owl_nothing": {
"default": false,
"type": "boolean"
},
"repo": {
"default": "",
"type": "string"
},
"robot_java_args": {
"default": "",
"type": "string"
},
"robot_report": {
"default": {
"custom_profile": false,
"custom_sparql_checks": [
"owldef-self-reference",
"iri-range",
"label-with-iri",
"multiple-replaced_by",
"dc-properties"
],
"custom_sparql_exports": [
"basic-report",
"class-count-by-prefix",
"edges",
"xrefs",
"obsoletes",
"synonyms"
],
"ensure_owl2dl_profile": true,
"fail_on": null,
"release_reports": false,
"report_on": [
"edit"
],
"sparql_test_on": [
"edit"
],
"use_base_iris": true,
"use_labels": true
},
"type": "object"
},
"robot_settings": {
"$ref": "#/definitions/CommandSettings"
},
"robot_version": {
"type": "string"
},
"sssom_mappingset_group": {
"$ref": "#/definitions/SSSOMMappingSetGroup"
},
"subset_group": {
"$ref": "#/definitions/SubsetGroup"
},
"title": {
"default": "",
"type": "string"
},
"travis_emails": {
"items": {
"type": "string"
},
"type": "array"
},
"uribase": {
"default": "http://purl.obolibrary.org/obo",
"type": "string"
},
"uribase_suffix": {
"type": "string"
},
"use_context": {
"default": false,
"type": "boolean"
},
"use_custom_import_module": {
"default": false,
"type": "boolean"
},
"use_dosdps": {
"default": false,
"type": "boolean"
},
"use_edit_file_imports": {
"default": true,
"type": "boolean"
},
"use_env_file_docker": {
"default": false,
"type": "boolean"
},
"use_external_date": {
"default": false,
"type": "boolean"
},
"use_mappings": {
"default": false,
"type": "boolean"
},
"use_templates": {
"default": false,
"type": "boolean"
},
"workflows": {
"default": [
"docs"
],
"items": {
"type": "string"
},
"type": "array"
}
},
"type": "object"
}