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TASK-4967 - ArrayOutOfBounds using cellbase client #664

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merged 1 commit into from
Sep 11, 2023
Merged

TASK-4967 - ArrayOutOfBounds using cellbase client #664

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47 changes: 38 additions & 9 deletions cellbase-client/src/main/java/org/opencb/cellbase/client/rest/ParentRestClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,8 @@ public class ParentRestClient<T> {
protected static final String META = "meta";
protected static final String WEBSERVICES = "webservices";
protected static final String REST = "rest";

private String apiKeyParam;
private String serverVersion;

@Deprecated
ParentRestClient(ClientConfiguration configuration) {
Expand Down Expand Up @@ -234,6 +235,8 @@ protected <U> CellBaseDataResponse<U> execute(List<String> idList, String resour
return new CellBaseDataResponse<>();
}

lazyInit();

// If the list contain less than REST_CALL_BATCH_SIZE variants then we can make a normal REST call.
if (idList.size() <= REST_CALL_BATCH_SIZE) {
return fetchData(idList, resource, options, clazz, post);
Expand Down Expand Up @@ -445,13 +448,6 @@ private <U> CellBaseDataResponse<U> restCall(List<String> hosts, String version,
// Add the last URL part, the 'action' or 'resource'
callUrl = callUrl.path(resource);

// Attention: parameter 'token' was renamed to 'apiKey' in CelBase v5.7
String apiKeyParam = null;
if (VersionUtils.isMinVersion("v5.7", configuration.getVersion())) {
apiKeyParam = API_KEY_PARAM;
} else if (VersionUtils.isMinVersion("v5.4", configuration.getVersion())) {
apiKeyParam = TOKEN_PARAM;
}

if (queryOptions != null) {
for (String s : queryOptions.keySet()) {
Expand All @@ -463,7 +459,7 @@ private <U> CellBaseDataResponse<U> restCall(List<String> hosts, String version,
if (dataRelease != null && StringUtils.isEmpty(queryOptions.getString(DATA_RELEASE_PARAM))) {
callUrl = callUrl.queryParam(DATA_RELEASE_PARAM, dataRelease);
}
if (apiKeyParam != null && apiKey != null && StringUtils.isEmpty(queryOptions.getString(API_KEY_PARAM))) {
if (apiKeyParam != null && apiKey != null && StringUtils.isEmpty(queryOptions.getString(apiKeyParam))) {
callUrl = callUrl.queryParam(apiKeyParam, apiKey);
}
} else {
Expand All @@ -490,6 +486,39 @@ private <U> CellBaseDataResponse<U> restCall(List<String> hosts, String version,
return parseResult(jsonString, clazz);
}

private void lazyInit() throws IOException {
// Lazy init other variables.
if (apiKey != null) {
String serverVersion = getServerVersion();

// Attention: parameter 'token' was renamed to 'apiKey' in CelBase v5.7
if (VersionUtils.isMinVersion("5.7.0", serverVersion)) {
apiKeyParam = API_KEY_PARAM;
} else if (VersionUtils.isMinVersion("5.4.0", serverVersion)) {
apiKeyParam = TOKEN_PARAM;
} // else { throw exception, api key not supported } ???
}
}

/**
* Get CellBase server version.
* @return CellBase full version
* @throws IOException on IOException
*/
public String getServerVersion() throws IOException {
if (serverVersion == null) {
initServerVersion();
}
return serverVersion;
}

private synchronized void initServerVersion() throws IOException {
if (serverVersion == null) {
ObjectMap about = new MetaClient(species, assembly, dataRelease, null, configuration).about().firstResult();
serverVersion = about.getString("Version");
}
}

protected WebTarget getBaseUrl(List<String> hosts, String version) {
return client
.target(URI.create(hosts.get(0)))
Expand Down
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