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Commit 61ceb1a5 authored by Karoly Erdos's avatar Karoly Erdos
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Merge elixir validator's library code to this repo

parent 2efc47fb
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Showing with 1250 additions and 73 deletions
examples/objects/graphRestriction_fail.json 0 → 100644
View file @ 61ceb1a5
{
"text": "cDNA",
"ontology": "EFO:0008481"
}
\ No newline at end of file
examples/objects/graphRestriction_normal.json 0 → 100644
View file @ 61ceb1a5
{
"text": "normal",
"ontology": "PATO:0000461"
}
\ No newline at end of file
examples/objects/graphRestriction_pass.json 0 → 100644
View file @ 61ceb1a5
{
"text": "glioblastoma",
"ontology": "MONDO:0018177"
}
\ No newline at end of file
examples/schemas/graphRestriction-schema.json 0 → 100644
View file @ 61ceb1a5
{
"$id": "http://subs/graphRestriction-schema.json",
"$schema": "http://json-schema.org/draft-07/schema#",
"description": "A term that may be associated with a disease-related ontology term",
"$async": true,
"additionalProperties": false,
"required": [
"text"
],
"title": "disease_ontology",
"properties": {
"describedBy": {
"pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/ontology/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/disease_ontology",
"type": "string"
},
"schema_version": {
"description": "Version number in major.minor.patch format.",
"type": "string",
"pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
"example": "4.6.1"
},
"text": {
"description": "The text for the term as the user provides it.",
"type": "string"
},
"ontology": {
"description": "An optional ontology reference in format where prefix_ indicates which ontology",
"type": "string",
"graph_restriction": {
"ontologies" : ["obo:mondo", "obo:efo"],
"classes": ["MONDO:0000001","PATO:0000461"],
"relations": ["rdfs:subClassOf"],
"direct": false,
"include_self": true
}
},
"ontology_label": {
"description": "The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field",
"type": "string"
}
},
"type": "object"
}
\ No newline at end of file
package-lock.json
View file @ 61ceb1a5
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"emoji-regex": "^8.0.0",
"is-fullwidth-code-point": "^3.0.0",
"strip-ansi": "^6.0.0"
}
},
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"resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-9.0.2.tgz",
"integrity": "sha1-nM9qQ0YP5O1Aqbto9I1DuKaMwHc=",
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"resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.0.tgz",
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"requires": {
"camelcase": "^4.1.0"
"ansi-regex": "^5.0.0"
}
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"version": "20.2.7",
"resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.7.tgz",
"integrity": "sha512-FiNkvbeHzB/syOjIUxFDCnhSfzAL8R5vs40MgLFBorXACCOAEaWu0gRZl14vG8MR9AOJIZbmkjhusqBYZ3HTHw=="
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"yn": {
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......
package.json
View file @ 61ceb1a5
......@@ -22,12 +22,14 @@
"author": "EMBL-EBI-SUBS, fpenim, ke4, haseeb-gh",
"license": "Apache-2.0",
"dependencies": {
"elixir-jsonschema-validator": "^2.0.0",
"ajv": "^6.10.2",
"express": "^4.17.1",
"npid": "^0.4.0",
"request": "^2.88.2",
"request-promise": "^4.2.4",
"winston": "^3.2.1",
"winston-daily-rotate-file": "^3.10.0"
"winston-daily-rotate-file": "^3.10.0",
"yargs": "^16.2.0"
},
"devDependencies": {
"bufferutil": "^4.0.2",
......
src/bio-validator.js 0 → 100644
View file @ 61ceb1a5
/**
* Created by rolando on 08/08/2018.
*/
const Promise = require('bluebird');
const path = require("path");
const fs = require('fs');
const ajv = require("ajv");
const request = require("request-promise");
const AppError = require("./model/application-error");
/**
*
* Wraps the generic validator, outputs errors in custom format.
*
*/
class BioValidator {
constructor(customKeywordValidators, baseSchemaPath){
this.validatorCache = {};
this.cachedSchemas = {};
this.ajvInstance = this.constructAjv(customKeywordValidators);
this.baseSchemaPath = baseSchemaPath;
this.customKeywordValidators = customKeywordValidators;
}
validate(inputSchema, inputObject) {
inputSchema["$async"] = true;
return new Promise((resolve, reject) => {
const compiledSchemaPromise = this.getValidationFunction(inputSchema);
compiledSchemaPromise.then((validate) => {
Promise.resolve(validate(inputObject))
.then((data) => {
if (validate.errors) {
resolve(validate.errors);
} else {
resolve([]);
}
}
).catch((err) => {
if (!(err instanceof ajv.ValidationError)) {
console.error("An error occurred while running the validation.");
reject(new AppError("An error occurred while running the validation."));
} else {
console.debug("debug", this.ajvInstance.errorsText(err.errors, {dataVar: inputObject.alias}));
resolve(err.errors);
}
});
}).catch((err) => {
console.error("async schema compiled encountered and error");
console.error(err.stack);
reject(err);
});
});
}
validateWithRemoteSchema(schemaUri, document) {
return this.getSchema(schemaUri)
.then(schema => {return this.validateSingleSchema(document, schema)})
}
getSchema(schemaUri) {
if(! this.cachedSchemas[schemaUri]) {
return new Promise((resolve, reject) => {
BioValidator.fetchSchema(schemaUri)
.then(schema => {
this.cachedSchemas[schemaUri] = schema;
resolve(schema);
})
.catch(err => {
reject(err);
})
});
} else {
return Promise.resolve(this.cachedSchemas[schemaUri]);
}
}
static fetchSchema(schemaUrl) {
return request({
method: "GET",
url: schemaUrl,
json: true,
});
}
getValidationFunction(inputSchema) {
const schemaId = inputSchema['$id'];
if(this.validatorCache[schemaId]) {
return Promise.resolve(this.validatorCache[schemaId]);
} else {
const compiledSchemaPromise = this.ajvInstance.compileAsync(inputSchema);
if(schemaId) {
this.validatorCache[schemaId] = compiledSchemaPromise;
}
return Promise.resolve(compiledSchemaPromise);
}
}
constructAjv(customKeywordValidators) {
const ajvInstance = new ajv({allErrors: true, schemaId: 'id', loadSchema: this.generateLoadSchemaRefFn()});
ajvInstance.addMetaSchema(require('ajv/lib/refs/json-schema-draft-04.json'));
BioValidator._addCustomKeywordValidators(ajvInstance, customKeywordValidators);
return ajvInstance