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Merged
Ezequiel-Valencia merged 3 commits into from
Jun 9, 2025
Merged

Remove Dead Functions #1530

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45643e8
Remove Dead Functions
Ezequiel-Valencia Jun 6, 2025
29153c2
Remove Dead Registration Function
Ezequiel-Valencia Jun 9, 2025
1d0c596
Remove RpcDb Methods Not Used
Ezequiel-Valencia Jun 9, 2025
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273 changes: 0 additions & 273 deletions vcell-apiclient/src/main/java/org/vcell/api/client/VCellApiClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -198,27 +198,6 @@ public void close() throws IOException {
httpclient.close();
}
}


public SimulationTaskRepresentation[] getSimTasks(SimTasksQuerySpec simTasksQuerySpec) throws IOException {

HttpGet httpget = new HttpGet(getApiUrlPrefix() + "/simtask?" + simTasksQuerySpec.getQueryString());
httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));

if (lg.isInfoEnabled()) {
lg.info("Executing request to retrieve simulation tasks " + httpget.getRequestLine());
}

String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getSimTasks()", httpget), httpClientContext);
String simTasksJson = responseBody;
if (lg.isInfoEnabled()) {
lg.info("returned: "+toStringTruncated(simTasksJson));
}

Gson gson = new Gson();
SimulationTaskRepresentation[] simTaskReps = gson.fromJson(simTasksJson,SimulationTaskRepresentation[].class);
return simTaskReps;
}

private String getApiUrlPrefix() {
final String scheme = httpHost.getSchemeName();
Expand All @@ -228,26 +207,6 @@ private String getApiUrlPrefix() {
return scheme+"://"+httpHost.getHostName()+this.pathPrefix_v0;
}
}

public BiomodelRepresentation[] getBioModels(BioModelsQuerySpec bioModelsQuerySpec) throws IOException {

HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/biomodel?"+bioModelsQuerySpec.getQueryString());
httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));

if (lg.isInfoEnabled()) {
lg.info("Executing request to retrieve biomodels " + httpget.getRequestLine());
}

String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getBioModels()", httpget), httpClientContext);
String bimodelsJson = responseBody;
if (lg.isInfoEnabled()) {
lg.info("returned: "+toStringTruncated(bimodelsJson));
}

Gson gson = new Gson();
BiomodelRepresentation[] biomodelReps = gson.fromJson(bimodelsJson,BiomodelRepresentation[].class);
return biomodelReps;
}

public EventWrapper[] getEvents(long beginTimestamp) throws IOException {

Expand All @@ -269,46 +228,6 @@ public EventWrapper[] getEvents(long beginTimestamp) throws IOException {
return eventWrappers;
}

public BiomodelRepresentation getBioModel(String bmId) throws IOException {

HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/biomodel/"+bmId);
httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));

if (lg.isInfoEnabled()) {
lg.info("Executing request to retrieve biomodel " + httpget.getRequestLine());
}

String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getBioModel()", httpget), httpClientContext);
String bimodelsJson = responseBody;
if (lg.isInfoEnabled()) {
lg.info("returned: "+toStringTruncated(bimodelsJson));
}

Gson gson = new Gson();
BiomodelRepresentation biomodelRep = gson.fromJson(bimodelsJson,BiomodelRepresentation.class);
return biomodelRep;
}

public SimulationRepresentation getSimulation(String bmId, String simKey) throws IOException {

HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/biomodel/"+bmId+"/simulation/"+simKey);
httpget.addHeader("Authorization","Bearer "+httpClientContext.getUserToken(String.class));

if (lg.isInfoEnabled()) {
lg.info("Executing request to retrieve simulation " + httpget.getRequestLine());
}

String responseBody = httpclient.execute(httpget, new VCellStringResponseHandler("getSimulation()", httpget), httpClientContext);
String simulationJson = responseBody;
if (lg.isInfoEnabled()) {
lg.info("returned: "+toStringTruncated(simulationJson));
}

Gson gson = new Gson();
SimulationRepresentation simulationRepresentation = gson.fromJson(simulationJson,SimulationRepresentation.class);
return simulationRepresentation;
}

public String getOptRunJson(String optimizationId,boolean bStop) throws IOException {

HttpGet httpget = new HttpGet(getApiUrlPrefix()+"/optimization/"+optimizationId+"?bStop="+bStop);
Expand Down Expand Up @@ -370,74 +289,6 @@ public String handleResponse(final HttpResponse response) throws ClientProtocolE
return responseUri;
}

/**
* from org.apache.http.impl.client.DefaultRedirectStrategy
*
* @param location
* @return
* @throws ProtocolException
*/
private URI createLocationURI(final String location) throws ClientProtocolException {
try {
final URIBuilder b = new URIBuilder(new URI(location).normalize());
final String host = b.getHost();
if (host != null) {
b.setHost(host.toLowerCase(Locale.US));
}
final String path = b.getPath();
if (TextUtils.isEmpty(path)) {
b.setPath("/");
}
return b.build();
} catch (final URISyntaxException ex) {
throw new ClientProtocolException("Invalid redirect URI: " + location, ex);
}
}

public SimulationTaskRepresentation[] startSimulation(String bmId, String simKey) throws IOException {

HttpPost httppost = new HttpPost(getApiUrlPrefix()+"/biomodel/"+bmId+"/simulation/"+simKey+"/startSimulation");
httppost.addHeader("Authorization", "Bearer "+httpClientContext.getUserToken(String.class));

if (lg.isInfoEnabled()) {
lg.info("Executing request to retrieve simulation " + httppost.getRequestLine());
}

String responseBody = httpclient.execute(httppost, new VCellStringResponseHandler("startSimulation()", httppost), httpClientContext);
String simTaskReps = responseBody;
if (lg.isInfoEnabled()) {
lg.info("returned: "+toStringTruncated(simTaskReps));
}

if (responseBody.equals("simulation start failed")){
throw new RuntimeException("simulation start failed for SimID="+simKey+" within BioModelKey="+bmId);
}else{
Gson gson = new Gson();
SimulationTaskRepresentation[] simulationTaskRepresentations = gson.fromJson(simTaskReps,SimulationTaskRepresentation[].class);
return simulationTaskRepresentations;
}
}

public SimulationTaskRepresentation[] stopSimulation(String bmId, String simKey) throws IOException {

HttpPost httppost = new HttpPost(getApiUrlPrefix()+"/biomodel/"+bmId+"/simulation/"+simKey+"/stopSimulation");
httppost.addHeader("Authorization", "Bearer "+httpClientContext.getUserToken(String.class));

if (lg.isInfoEnabled()) {
lg.info("Executing request to retrieve simulation " + httppost.getRequestLine());
}

String responseBody = httpclient.execute(httppost, new VCellStringResponseHandler("stopSimulation()", httppost), httpClientContext);
String simTaskReps = responseBody;
if (lg.isInfoEnabled()) {
lg.info("returned: "+toStringTruncated(simTaskReps));
}

Gson gson = new Gson();
SimulationTaskRepresentation[] simulationTaskRepresentations = gson.fromJson(simTaskReps,SimulationTaskRepresentation[].class);
return simulationTaskRepresentations;
}

public void createDefaultQuarkusClient(boolean bIgnoreCertProblems){
apiClient = new ApiClient(){{
if (bIgnoreCertProblems){setHttpClientBuilder(CustomApiClientCode.createInsecureHttpClientBuilder());};
Expand Down Expand Up @@ -541,130 +392,6 @@ public AccesTokenRepresentationRecord getGuestLegacyToken() throws ApiException
return accesTokenRepresentationRecord;
}

public void clearAuthentication() throws KeyManagementException, NoSuchAlgorithmException, KeyStoreException{
initClient();
httpClientContext = HttpClientContext.create();
}


private String createdDigestPassword(String clearTextPassword) {
if (clearTextPassword == null || clearTextPassword.length() == 0) {
throw new RuntimeException("Empty password not allowed");
}
java.security.MessageDigest messageDigest = null;
try {
messageDigest = java.security.MessageDigest.getInstance("SHA-1");
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("Error processing password, Couldn't get instance of MessageDigest " + e.getMessage());
}
messageDigest.reset();
messageDigest.update(clearTextPassword.getBytes());
byte[] digestedPasswordBytes = messageDigest.digest();
StringBuffer sb = new StringBuffer(digestedPasswordBytes.length * 2);
for (int i = 0; i < digestedPasswordBytes.length; i++) {
int v = digestedPasswordBytes[i] & 0xff;
if (v < 16) {
sb.append('0');
}
sb.append(Integer.toHexString(v));
}
return sb.toString().toUpperCase();
}

public UserInfo insertUserInfo(UserInfo newUserInfo) throws ClientProtocolException, IOException,IllegalArgumentException {

HttpPost httppost = new HttpPost(getApiUrlPrefix()+"/newuser");
Gson gson = new Gson();
String newUserInfoJSON = gson.toJson(newUserInfo);
StringEntity input = new StringEntity(newUserInfoJSON);
input.setContentType(ContentType.APPLICATION_JSON.getMimeType());
httppost.setEntity(input);

if (lg.isInfoEnabled()) {
lg.info("Executing request to submit new user " + httppost.getRequestLine());
}

ResponseHandler<UserInfo> handler = new ResponseHandler<UserInfo>() {

public UserInfo handleResponse(final HttpResponse response) throws ClientProtocolException, IOException {
int status = response.getStatusLine().getStatusCode();
if (status == HttpStatus.SC_CREATED) {
HttpEntity entity = response.getEntity();
try (BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent()));){
String json = reader.lines().collect(Collectors.joining());
UserInfo userInfo = gson.fromJson(json, UserInfo.class);
return userInfo;
}
} else if(status == HttpStatus.SC_FORBIDDEN){
HttpEntity entity = response.getEntity();
String message = null;
try (BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent()));){
message = reader.lines().collect(Collectors.joining());
}
final URI uri = httppost.getURI();
lg.error("insertUserInfo() ("+uri+") failed: response status: " + status + "\nreason: " + message);
throw new IllegalArgumentException("insertUserInfo() failed: response status: " + status + "\nreason: " + message);
} else {
HttpEntity entity = response.getEntity();
String message = null;
try (BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent()));){
message = reader.lines().collect(Collectors.joining());
}
final URI uri = httppost.getURI();
lg.error("insertUserInfo() ("+uri+") failed: response status: " + status + "\nreason: " + message);
throw new ClientProtocolException("insertUserInfo() failed: response status: " + status + "\nreason: " + message);
}
}

};
UserInfo insertedUserInfo = httpclient.execute(httppost,handler,httpClientContext);
if (lg.isInfoEnabled()) {
lg.info("returned userinfo: "+insertedUserInfo);
}

return insertedUserInfo;
}

public void sendLostPassword(String userid) throws ClientProtocolException, IOException {
HttpPost httppost = new HttpPost(getApiUrlPrefix()+"/lostpassword");
StringEntity input = new StringEntity(userid);
input.setContentType(ContentType.TEXT_PLAIN.getMimeType());
httppost.setEntity(input);

if (lg.isInfoEnabled()) {
lg.info("Executing request to send lost password " + httppost.getRequestLine());
}

ResponseHandler<String> handler = new ResponseHandler<String>() {

public String handleResponse(final HttpResponse response) throws ClientProtocolException, IOException {
int status = response.getStatusLine().getStatusCode();
if (status == HttpStatus.SC_ACCEPTED) {
HttpEntity entity = response.getEntity();
try (BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent()));){
String message = reader.lines().collect(Collectors.joining());
return message;
}
} else {
HttpEntity entity = response.getEntity();
String message = null;
try (BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent()));){
message = reader.lines().collect(Collectors.joining());
}
final URI uri = httppost.getURI();
lg.error("sendLostPassword() ("+uri+") failed: response status: " + status + "\nreason: " + message);
throw new ClientProtocolException("Failed to request lost password, response status: " + status + "\nreason: " + message);
}
}

};
String message = httpclient.execute(httppost,handler,httpClientContext);
if (lg.isInfoEnabled()) {
lg.info("requested lost password for user "+userid+", server returned "+message);
}
}



public Serializable sendRpcMessage(VCellApiRpcBody.RpcDestination rpcDestination, VCellApiRpcRequest rpcRequest, boolean returnRequired, int timeoutMS, String[] specialProperties, Object[] specialValues) throws ClientProtocolException, IOException {
Expand Down
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