Sync5

backend/src/main/java/uk/ac/ebi/spot/ols/config/CrossOriginResourceSharingFilter.java

@@ -32,18 +32,18 @@ public void doFilter(ServletRequest request, ServletResponse response, FilterCha
         HttpServletRequest httpRequest = (HttpServletRequest) request;
         HttpServletResponse httpResponse = (HttpServletResponse) response;
 
+        // Alwasy add CORS headers. add CORS "pre-flight" request headers
+        httpResponse.addHeader("Access-Control-Allow-Origin", "*");
+        httpResponse.addHeader("Access-Control-Allow-Headers", "*");
+        httpResponse.addHeader("Access-Control-Allow-Methods", "GET");
+        httpResponse.addHeader("Access-Control-Max-Age", "3600");
 
         // is this a CORS request?
         if (httpRequest.getHeader("Origin") != null) {
             String origin = httpRequest.getHeader("Origin");
             String requestURI = httpRequest.getRequestURI();
             getLog().trace("Possible cross-origin request received from '" + origin + "' to IRI: " +
                                    "'" + requestURI + "'.  Enabling CORS.");
-
-            // add CORS "pre-flight" request headers
-            httpResponse.addHeader("Access-Control-Allow-Origin", "*");
-            httpResponse.addHeader("Access-Control-Allow-Headers", "*");
-            httpResponse.addHeader("Access-Control-Allow-Methods", "GET");
         }
 
         chain.doFilter(request, response);

backend/src/main/java/uk/ac/ebi/spot/ols/config/SwaggerConfig.java

@@ -23,7 +23,7 @@ public OpenAPI customOpenApi(ServletContext context) {
                 .addServersItem(new Server().url(serverUrl))
                 .info(new Info()
                         .title("OLS Service")
-                        .description("REST API for OLS")
+                        .description("REST API for OLS. Please see <a href='"+OLS4_SERVER_URL+"/defined-response-fields' target='_blank'> this page</a> for defined response field in OLS.")
                         .version("3.0")
                         .termsOfService("https://www.ebi.ac.uk/about/terms-of-use/")
                         .license(new License()

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1IndividualController.java

@@ -55,7 +55,7 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividuals(
             @PathVariable("iri")
             @Parameter(name = "iri",
                     description = "The IRI of the individual, this value must be double URL encoded",
-                    example = "http%3A%252F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000124") String termId,
+                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGAZ_00043159") String termId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {
@@ -69,16 +69,16 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividuals(
     HttpEntity<PagedModel<V1Individual>> getAllIndividuals(
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the individual, this value must be double URL encoded",
-                    example = "http%3A%252F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000124") String iri,
+                    description = "The IRI of the individual.",
+                    example = "http://purl.obolibrary.org/obo/GAZ_00043159") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the individual.",
-                    example = "IAO_0000124") String shortForm,
+                    example = "GAZ_00043159") String shortForm,
             @RequestParam(value = "obo_id", required = false)
             @Parameter(name = "obo_id",
                     description = "This refers to the OBO ID of the individual.",
-                    example = "IAO:0000124") String oboId,
+                    example = "GAZ:00043159") String oboId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {
@@ -103,7 +103,7 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
             @PathVariable("iri")
             @Parameter(name = "iri",
                     description = "The IRI of the individual, this value must be double URL encoded",
-                    example = "http%3A%252F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000124") String termId,
+                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOHD_0000363") String termId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {
@@ -121,15 +121,15 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
                     description = "The IRI of the individual, this value must be double URL encoded",
-                    example = "http%3A%252F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000124") String iri,
+                    example = "http://purl.obolibrary.org/obo/OHD_0000363") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the individual.",
-                    example = "IAO_0000124") String shortForm,
+                    example = "OHD_0000363") String shortForm,
             @RequestParam(value = "obo_id", required = false)
             @Parameter(name = "obo_id",
                     description = "This refers to the OBO ID of the individual.",
-                    example = "IAO:0000124") String oboId,
+                    example = "OHD:0000363") String oboId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyIndividualController.java

@@ -65,16 +65,16 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividualsByOntology(
                     example = "iao") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the individual, this IRI should exist in the specified ontology by {onto} param. This value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000103") String iri,
+                    description = "The IRI of the individual, this IRI should exist in the specified ontology by {onto} param.",
+                    example = "http://purl.obolibrary.org/obo/IAO_0000002") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the individual, it should exist in the specified ontology by {onto} param.",
-                    example = "IAO_0000124") String shortForm,
+                    example = "IAO_0000002") String shortForm,
             @RequestParam(value = "obo_id", required = false)
             @Parameter(name = "obo_id",
                     description = "This refers to the OBO ID of the individual, it should exist in the specified ontology by {onto} param.",
-                    example = "IAO:0000124") String oboId,
+                    example = "IAO:0000002") String oboId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyPropertyController.java

@@ -55,8 +55,8 @@ HttpEntity<PagedModel<V1Property>> getAllPropertiesByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the property, this IRI should exist in the specified ontology by {onto} param. This value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000041") String iri,
+                    description = "The IRI of the property, this IRI should exist in the specified ontology by {onto} param.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000041") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the property, it should exist in the specified ontology by {onto} param.",
@@ -146,7 +146,7 @@ HttpEntity<PagedModel<V1Property>> getParents(
             @PathVariable("iri")
             @Parameter(name = "iri",
                     description = "The IRI of the property, this IRI should exist in the specified ontology by {onto} param. This value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000041") String termId,
+                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000179") String termId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {
@@ -161,12 +161,12 @@ HttpEntity<PagedModel<V1Property>> getParents(
     HttpEntity<PagedModel<V1Property>> children(
             @PathVariable("onto")
             @Parameter(name = "onto",
-                    description = "The ID of the ontology. For example for Data Use Ontology, the ID is duo.",
-                    example = "duo") String ontologyId,
+                    description = "The ID of the ontology.",
+                    example = "mondo") String ontologyId,
             @PathVariable("iri")
             @Parameter(name = "iri",
                     description = "The IRI of the property, this IRI should exist in the specified ontology by {onto} param. This value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000041") String termId,
+                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051") String termId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {
@@ -181,12 +181,12 @@ HttpEntity<PagedModel<V1Property>> children(
     HttpEntity<PagedModel<V1Property>> descendants(
             @PathVariable("onto")
             @Parameter(name = "onto",
-                    description = "The ID of the ontology. For example for Data Use Ontology, the ID is duo.",
-                    example = "duo") String ontologyId,
+                    description = "The ID of the ontology.",
+                    example = "mondo") String ontologyId,
             @PathVariable("iri")
             @Parameter(name = "iri",
                     description = "The IRI of the property, this IRI should exist in the specified ontology by {onto} param. This value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000041") String termId,
+                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051") String termId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {
@@ -201,12 +201,12 @@ HttpEntity<PagedModel<V1Property>> descendants(
     HttpEntity<PagedModel<V1Property>> ancestors(
             @PathVariable("onto")
             @Parameter(name = "onto",
-                    description = "The ID of the ontology. For example for Data Use Ontology, the ID is duo.",
-                    example = "duo") String ontologyId,
+                    description = "The ID of the ontology.",
+                    example = "mondo") String ontologyId,
             @PathVariable("iri")
             @Parameter(name = "iri",
                     description = "The IRI of the property, this IRI should exist in the specified ontology by {onto} param. This value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000041") String termId,
+                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051") String termId,
             @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
             @Parameter(hidden = true) Pageable pageable,
             @Parameter(hidden = true) PagedResourcesAssembler assembler) {

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyTermController.java

@@ -73,8 +73,8 @@ private HttpEntity<PagedModel<V1Term>> termsByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",
@@ -444,7 +444,7 @@ HttpEntity<String> graphJsTreeChildren(
             @PathVariable("iri")
             @Parameter(name = "iri",
                     description = "The IRI of the property, this IRI should exist in the specified ontology by {onto} param. This value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051") String termId,
+                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String termId,
             @PathVariable("nodeid")
             @Parameter(name = "nodeid",
                     description = "This is the id of the node in the jstree of ontology specified by {onto} parameter",
@@ -524,8 +524,8 @@ HttpEntity<PagedModel<V1Term>> termChildrenByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",
@@ -562,8 +562,8 @@ HttpEntity<PagedModel<V1Term>> termDescendantsByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",
@@ -600,8 +600,8 @@ HttpEntity<PagedModel<V1Term>> termHierarchicalChildrenByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",
@@ -638,8 +638,8 @@ HttpEntity<PagedModel<V1Term>> termHierarchicalDescendantsByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",
@@ -676,8 +676,8 @@ HttpEntity<PagedModel<V1Term>> termParentsByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",
@@ -714,8 +714,8 @@ HttpEntity<PagedModel<V1Term>> termAncestorsByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",
@@ -752,8 +752,8 @@ HttpEntity<PagedModel<V1Term>> termHierarchicalAncestorsByOntology(
                     example = "duo") String ontologyId,
             @RequestParam(value = "iri", required = false)
             @Parameter(name = "iri",
-                    description = "The IRI of the term, this value must be double URL encoded",
-                    example = "http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDUO_0000017") String iri,
+                    description = "The IRI of the term.",
+                    example = "http://purl.obolibrary.org/obo/DUO_0000017") String iri,
             @RequestParam(value = "short_form", required = false)
             @Parameter(name = "short_form",
                     description = "This refers to the short form of the term.",