Merge pull request #62 from elixir-europe/dev

Release v2.1.0

README.md

@@ -14,6 +14,7 @@ The biovalidator currently supports JSON Schema draft-06/07/2019-09.
 - Changes to arguments accepted at the startup
  - `--json` renamed to `--data`
  - Added `--ref`, `--port`, `--baseUrl`, `pidPath` 
+- Support for new keyword `isValidIdentifier`. Validate accessions/IDs using identifiers.org API. 
 
 ## Contents
 - [Getting Started](#getting-started)
@@ -27,6 +28,7 @@ The biovalidator currently supports JSON Schema draft-06/07/2019-09.
  - [isChildTermOf](#ischildtermof)
  - [isValidTerm](#isvalidterm)
  - [isValidTaxonomy](#isvalidtaxonomy)
+ - [isValidIdentifier](#isvalididentifier)
 - [Running in Docker](#running-in-docker)
 - [License](#license)
 
@@ -232,6 +234,8 @@ The biovalidator supports four extended keywords for ontology and taxonomy valid
 This custom keyword *evaluates if an ontology term is child of another*. This keyword is applied to a string (CURIE) and **passes validation if the term is a child of the term defined in the schema**.
 The keyword requires one or more **parent terms** *(classes)* and **ontology ids** *(ontologies)*, both of which should exist in [OLS - Ontology Lookup Service](https://www.ebi.ac.uk/ols).
 
+* **ontologies** should be present in EBI OLS and are case-sensitive (most of the OLS ontologies are in lower case)
+
 This keyword works by doing an asynchronous call to the [OLS API](https://www.ebi.ac.uk/ols/api/) that will respond with the required information to know if a given term is child of another.
 Being an async validation step, whenever used in a schema, the schema must have the flag: `"$async": true` in its object root.
 
@@ -351,6 +355,64 @@ Data:
 }
 ```
 
+### isValidIdentifier
+Evaluates if a given *identifier* has a correct format using identifiers.org resolution API. The keyword is applicable to the `string` data type. 
+
+The keyword will do an asynchronous call to the [identifier.org API](https://resolver.api.identifiers.org/) to resolve the URL for the given CURIE. 
+Being an async validation step, whenever used in a schema, the schema must have the flag: `"$async": true` in its object root.
+
+The keyword has two properties: `prefixes` and `prefix`. Only one of them is allowed in a block and `prefix` will take the priority in case both are provided. 
+- `prefix` define one namespace/prefix for the expected identifier/accession. In the data, field should only contain the ID/accession without the namespace. 
+- `prefixes` define a set of allowed namespaces/prefixes. In the data, field should contain a valid CURIE (namespace:id format)
+
+:warning: At the moment only the format of the identifier/accession is checked against the identifier.org. Therefore, this does not guarantee the existence of the data record.
+
+#### isValidIdentifier example 1
+Schema:
+```json
+{
+ "$schema": "http://json-schema.org/draft-07/schema#",
+ "$async": true,
+ "properties": {
+ "SampleId": {
+ "type": "string",
+ "isValidIdentifier": {
+ "prefix": "biosample"
+ }
+ }
+ }
+}
+```
+Data:
+```json
+{
+ "SampleId": "SAMEA2397676"
+}
+```
+
+#### isValidIdentifier example 2
+Schema:
+```json
+{
+ "$schema": "http://json-schema.org/draft-07/schema#",
+ "$async": true,
+ "properties": {
+ "resourceId": {
+ "type": "string",
+ "isValidIdentifier": {
+ "prefixes": ["biosample", "arrayexpress"]
+ }
+ }
+ }
+}
+```
+Data:
+```json
+{
+ "resourceId": "biosample:SAMEA2397676"
+}
+```
+
 ## Running in Docker
 A Dockerized version of biovalidator is available on [quay.io](https://quay.io/repository/ebi-ait/biovalidator). 
 This image can be used to run the validator without cloning this repository. 

examples/objects/isValidIdentifier-single-prefix_pass.json

@@ -0,0 +1,4 @@
+{
+ "sampleName": "test sample",
+ "SampleId": "SAMEA2397676"
+}

examples/objects/isValidIdentifier_fail.json

@@ -0,0 +1,4 @@
+{
+ "sampleName": "test sample",
+ "SampleId": "biosample:INVALID_ID"
+}

examples/objects/isValidIdentifier_fail_namespace.json

@@ -0,0 +1,4 @@
+{
+ "sampleName": "test sample",
+ "SampleId": "arrayexpress:E-MEXP-1712"
+}

examples/objects/isValidIdentifier_pass.json

@@ -0,0 +1,4 @@
+{
+ "sampleName": "test sample",
+ "SampleId": "biosample:SAMEA2397676"
+}

examples/schemas/biosamples-schema.json

@@ -1,5 +1,6 @@
 {
  "$schema": "http://json-schema.org/draft-07/schema#",
+ "$id": "test/biosamples/schema",
  "title": "Sample",
  "description": "A BioSamples sample.",
 

examples/schemas/isValidIdentifier-schema.json

@@ -0,0 +1,27 @@
+{
+ "$id": "http://subs/isValidIdentifier-schema.json",
+ "$schema": "http://json-schema.org/draft-07/schema#",
+ "description": "Test schema for BioSample accession",
+ "$async": true,
+ "additionalProperties": false,
+ "required": [
+ "SampleId"
+ ],
+ "title": "disease_ontology",
+ "properties": {
+ "sampleName": {
+ "description": "The text for the term as the user provides it.",
+ "type": "string"
+ },
+ "SampleId": {
+ "description": "An optional ontology reference in format where prefix_ indicates which ontology",
+ "type": "string",
+ "isValidIdentifier": {
+ "prefixes": [
+ "biosample"
+ ]
+ }
+ }
+ },
+ "type": "object"
+}

examples/schemas/isValidIdentifier-single-prefix-schema.json

@@ -0,0 +1,25 @@
+{
+ "$id": "http://subs/isValidIdentifier-schema.json",
+ "$schema": "http://json-schema.org/draft-07/schema#",
+ "description": "Test schema for BioSample accession",
+ "$async": true,
+ "additionalProperties": false,
+ "required": [
+ "SampleId"
+ ],
+ "title": "disease_ontology",
+ "properties": {
+ "sampleName": {
+ "description": "The text for the term as the user provides it.",
+ "type": "string"
+ },
+ "SampleId": {
+ "description": "An optional ontology reference in format where prefix_ indicates which ontology",
+ "type": "string",
+ "isValidIdentifier": {
+ "prefix": "biosample"
+ }
+ }
+ },
+ "type": "object"
+}