public List<BpTreeNode> getTree(String id, String ontology, String apiKey) throws IOException {
String url = BP_API_BASE + BP_ONTOLOGIES + ontology + "/" + BP_CLASSES + id + "/tree";
HttpResponse response =
HttpUtil.makeHttpRequest(
Request.Get(url)
.addHeader("Authorization", Util.getBioPortalAuthHeader(apiKey))
.connectTimeout(connectTimeout)
.socketTimeout(socketTimeout));
int statusCode = response.getStatusLine().getStatusCode();
// The tree was successfully retrieved
if (statusCode == 200) {
ObjectMapper mapper = new ObjectMapper();
JsonNode bpResult =
mapper.readTree(new String(EntityUtils.toByteArray(response.getEntity())));
List<BpTreeNode> nodes = new ArrayList<>();
for (JsonNode n : bpResult) {
nodes.add(mapper.convertValue(n, BpTreeNode.class));
}
return nodes;
} else {
throw new HTTPException(statusCode);
}
}
public BpPagedResults<BpClass> findAllClassesInOntology(
String ontology, int page, int pageSize, String apiKey) throws HTTPException, IOException {
String url =
BP_API_BASE
+ BP_ONTOLOGIES
+ ontology
+ "/"
+ BP_CLASSES
+ "?include=prefLabel,hasChildren,created,synonym,definition"
+ "&page="
+ page
+ "&pagesize="
+ pageSize;
HttpResponse response =
HttpUtil.makeHttpRequest(
Request.Get(url)
.addHeader("Authorization", Util.getBioPortalAuthHeader(apiKey))
.connectTimeout(connectTimeout)
.socketTimeout(socketTimeout));
int statusCode = response.getStatusLine().getStatusCode();
// The classes were successfully retrieved
if (statusCode == 200) {
ObjectMapper mapper = new ObjectMapper();
JsonNode bpResult =
mapper.readTree(new String(EntityUtils.toByteArray(response.getEntity())));
return mapper.readValue(
mapper.treeAsTokens(bpResult), new TypeReference<BpPagedResults<BpClass>>() {});
} else {
throw new HTTPException(statusCode);
}
}
public BpPagedResults<BpClass> findValueSetsByValueSetCollection(
String vsCollection, int page, int pageSize, String apiKey) throws IOException {
String url =
BP_API_BASE
+ BP_SEARCH
+ "?also_search_provisional=true&valueset_roots_only=true&ontology_types=VALUE_SET_COLLECTION&ontologies="
+ vsCollection
+ "&page="
+ page
+ "&pagesize="
+ pageSize;
HttpResponse response =
HttpUtil.makeHttpRequest(
Request.Get(url)
.addHeader("Authorization", Util.getBioPortalAuthHeader(apiKey))
.connectTimeout(connectTimeout)
.socketTimeout(socketTimeout));
int statusCode = response.getStatusLine().getStatusCode();
// Success
if (statusCode == 200) {
ObjectMapper mapper = new ObjectMapper();
JsonNode bpResult =
mapper.readTree(new String(EntityUtils.toByteArray(response.getEntity())));
return mapper.readValue(
mapper.treeAsTokens(bpResult), new TypeReference<BpPagedResults<BpClass>>() {});
} else {
throw new HTTPException(statusCode);
}
}
public BpClass find(String id, String ontology, String apiKey) throws HTTPException, IOException {
String url =
BP_API_BASE
+ BP_ONTOLOGIES
+ ontology
+ "/"
+ BP_CLASSES
+ id
+ "?include=prefLabel,hasChildren,created,synonym,definition";
HttpResponse response =
HttpUtil.makeHttpRequest(
Request.Get(url)
.addHeader("Authorization", Util.getBioPortalAuthHeader(apiKey))
.connectTimeout(connectTimeout)
.socketTimeout(socketTimeout));
int statusCode = response.getStatusLine().getStatusCode();
// The class was successfully retrieved
if (statusCode == 200) {
ObjectMapper mapper = new ObjectMapper();
JsonNode bpResult =
mapper.readTree(new String(EntityUtils.toByteArray(response.getEntity())));
return mapper.convertValue(bpResult, BpClass.class);
} else {
throw new HTTPException(statusCode);
}
}
public List<BpClass> getParents(String id, String ontology, String apiKey) throws IOException {
String url =
BP_API_BASE
+ BP_ONTOLOGIES
+ ontology
+ "/"
+ BP_CLASSES
+ id
+ "/parents"
+ "?include=prefLabel,hasChildren,created,synonym,definition";
HttpResponse response =
HttpUtil.makeHttpRequest(
Request.Get(url)
.addHeader("Authorization", Util.getBioPortalAuthHeader(apiKey))
.connectTimeout(connectTimeout)
.socketTimeout(socketTimeout));
int statusCode = response.getStatusLine().getStatusCode();
// Success
if (statusCode == 200) {
ObjectMapper mapper = new ObjectMapper();
JsonNode bpResult =
mapper.readTree(new String(EntityUtils.toByteArray(response.getEntity())));
List<BpClass> children = new ArrayList<>();
for (JsonNode n : bpResult) {
children.add(mapper.convertValue(n, BpClass.class));
}
return children;
} else {
throw new HTTPException(statusCode);
}
}