Examples with AuthenticationException org.vcell.util.AuthenticationException used on opensource projects

Example 1 with AuthenticationException

use of org.vcell.util.AuthenticationException in project vcell by virtualcell.

the class ClientServerManager method connectToServer.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 4:48:13 PM)
 */
private VCellConnection connectToServer(InteractiveContext requester) {
    VCellThreadChecker.checkRemoteInvocation();
    VCellConnection newVCellConnection = null;
    VCellConnectionFactory vcConnFactory = null;
    String badConnStr = "";
    try {
        switch(getClientServerInfo().getServerType()) {
            case SERVER_REMOTE:
                {
                    String apihost = getClientServerInfo().getApihost();
                    Integer apiport = getClientServerInfo().getApiport();
                    try {
                        badConnStr += apihost + ":" + apiport;
                        vcConnFactory = new RemoteProxyVCellConnectionFactory(apihost, apiport, getClientServerInfo().getUserLoginInfo());
                        setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), apihost, apiport, ConnectionStatus.INITIALIZING));
                        newVCellConnection = vcConnFactory.createVCellConnection();
                    } catch (AuthenticationException ex) {
                        throw ex;
                    }
                    break;
                }
            case SERVER_LOCAL:
                {
                    new PropertyLoader();
                    LocalVCellConnectionService localVCellConnectionService = VCellServiceHelper.getInstance().loadService(LocalVCellConnectionService.class);
                    vcConnFactory = localVCellConnectionService.getLocalVCellConnectionFactory(getClientServerInfo().getUserLoginInfo());
                    setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), null, null, ConnectionStatus.INITIALIZING));
                    newVCellConnection = vcConnFactory.createVCellConnection();
                    break;
                }
        }
        requester.clearConnectWarning();
        reconnectStat = ReconnectStatus.NOT;
    } catch (AuthenticationException aexc) {
        aexc.printStackTrace(System.out);
        requester.showErrorDialog(aexc.getMessage());
    } catch (ConnectionException cexc) {
        String msg = badConnectMessage(badConnStr) + "\n" + cexc.getMessage();
        cexc.printStackTrace(System.out);
        ErrorUtils.sendRemoteLogMessage(getClientServerInfo().getUserLoginInfo(), msg);
        if (reconnectStat != ReconnectStatus.SUBSEQUENT) {
            requester.showConnectWarning(msg);
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        String msg = badConnectMessage(badConnStr) + "\nException:\n" + exc.getMessage();
        ErrorUtils.sendRemoteLogMessage(getClientServerInfo().getUserLoginInfo(), msg);
        requester.showErrorDialog(msg);
    }
    return newVCellConnection;
}

Example 2 with AuthenticationException

use of org.vcell.util.AuthenticationException in project vcell by virtualcell.

the class AmplistorUtilsTest method test.

@Test
public void test() throws Exception {
    // 
    // Create amplistor full access credential
    // 
    AmplistorCredential amplistorCredential = getAmplistorCredential();
    // must set this property in eclipse debug configuration
    if (amplistorCredential.userName == null || amplistorCredential.password == null) {
        throw new Exception("Amplistor full access credential required for test");
    }
    // 
    // Define Amplistor test dir
    // 
    final String AMPLI_REST_TEST_DIR = "Ampli_REST_Test_Dir";
    String dirNameURL = AmplistorUtils.DEFAULT_AMPLI_SERVICE_VCELL_URL + AMPLI_REST_TEST_DIR;
    // 
    // Define Local test dir and file
    // 
    Random rand = new Random();
    byte[] rndBytes = new byte[10000];
    rand.nextBytes(rndBytes);
    File tmpDir = Files.createTempDirectory("rnd_").toFile();
    File[] tmpFiles = new File[NUMFILES];
    final String SIMID_PREFIX = "SimID_";
    for (int i = 0; i < NUMFILES; i++) {
        tmpFiles[i] = File.createTempFile(SIMID_PREFIX + i + "_0_", ".rndbin", tmpDir);
        FileOutputStream fos = new FileOutputStream(tmpFiles[i]);
        BufferedOutputStream bos = new BufferedOutputStream(fos);
        bos.write(rndBytes);
        bos.close();
    }
    // 
    try {
        deleteDirAndAllFiles(dirNameURL, amplistorCredential);
    } catch (FileNotFoundException e) {
    // this is OK, ignore
    }
    // 
    // Create test dir on amplistor
    // 
    AmplistorUtils.createDir(dirNameURL, amplistorCredential);
    // 
    // Upload rnd file
    // 
    Hashtable<File, Exception> failures = AmplistorUtils.uploadFilesOperation(tmpDir, new URL(dirNameURL), amplistorCredential);
    if (failures != null) {
        throw new Exception("Upload failed " + failures.values().iterator().next().getMessage());
    }
    // 
    // List amplistor test dir we created and populated
    // 
    ArrayList<String> fileNames = AmplistorUtils.listDir(dirNameURL, null, amplistorCredential);
    if (fileNames.size() != NUMFILES) {
        throw new Exception("Expected " + NUMFILES + " files but got " + fileNames.size());
    }
    for (String fileName : fileNames) {
        System.out.println("listing:" + fileName);
    }
    String file0url = dirNameURL + "/" + fileNames.get(0);
    // 
    if (!AmplistorUtils.bFileExists(new URL(file0url), amplistorCredential)) {
        throw new Exception("Expected " + file0url + " 'bFileExist' to be true");
    }
    // 
    // check filter returns correct results
    // 
    AmplistorUtils.AmplistorFileNameMatcher onlyTheseMatchingFiles = new AmplistorUtils.AmplistorFileNameMatcher() {

        @Override
        public boolean accept(String fileName) {
            return fileName.equals(tmpFiles[0].getName());
        }
    };
    ArrayList<String> filteredNames = AmplistorUtils.listDir(dirNameURL, onlyTheseMatchingFiles, amplistorCredential);
    if (filteredNames.size() != 1 || !filteredNames.get(0).equals(tmpFiles[0].getName())) {
        throw new Exception("Filter test failed, expecting 1==" + filteredNames.size() + " and " + tmpFiles[0].getName() + "==" + (filteredNames.size() == 0 ? "null" : filteredNames.get(0)));
    }
    // 
    // set metadata on first file (this is done during upload using lastmodified of file but do it again to demonstrate)
    // 
    Calendar calendar = Calendar.getInstance();
    calendar.set(2010, 2, 3, 5, 15, 30);
    calendar.set(Calendar.MILLISECOND, 0);
    System.out.println("Set Custom Modification time----- " + calendar.getTime());
    // AmplistorUtils.setFileMetaData(dirNameURL+"/"+tmpFiles[0].getName(), amplistorCredential, SimulationData.AmplistorHelper.CUSTOM_FILE_MODIFICATION_DATE, tmpFiles[0].lastModified()/1000+".0");
    AmplistorUtils.setFileMetaData(file0url, amplistorCredential, AmplistorUtils.CUSTOM_FILE_MODIFICATION_DATE, calendar.getTime().getTime() / 1000 + ".0");
    // 
    // Print the http header info for one of the uploaded files
    // 
    AmplistorUtils.AmpliCustomHeaderHelper ampliCustomHeaderHelper = AmplistorUtils.printHeaderFields(file0url, amplistorCredential);
    if (ampliCustomHeaderHelper.customModification == null || !ampliCustomHeaderHelper.customModification.equals(calendar.getTime())) {
        throw new Exception("Queried custom modification date " + ampliCustomHeaderHelper.customModification + " does not match set custom modification date " + calendar.getTime());
    }
    // 
    // Download 1 of the files
    // 
    byte[] downloadBytes = AmplistorUtils.getObjectData(file0url, amplistorCredential);
    // 
    if (downloadBytes.length != tmpFiles[0].length() || rndBytes.length != downloadBytes.length) {
        throw new Exception("round trip file sizes are different local = " + tmpFiles[0].length() + " remote = " + downloadBytes.length + " memory = " + rndBytes.length);
    }
    FileInputStream fis = new FileInputStream(tmpFiles[0]);
    BufferedInputStream bis = new BufferedInputStream(fis);
    DataInputStream dis = new DataInputStream(bis);
    byte[] localBytes = new byte[rndBytes.length];
    dis.readFully(localBytes);
    dis.close();
    if (!Arrays.equals(localBytes, downloadBytes) || !Arrays.equals(rndBytes, downloadBytes)) {
        throw new Exception("download bytes not match local bytes after round trip");
    }
    // 
    // Check special SimID parsing for delete
    // 
    HashSet<KeyValue> doNotDeleteTheseSimKeys = new HashSet<KeyValue>();
    doNotDeleteTheseSimKeys.add(new KeyValue("0"));
    doNotDeleteTheseSimKeys.add(new KeyValue("1"));
    long numDeleted = AmplistorUtils.deleteSimFilesNotInHash(dirNameURL, doNotDeleteTheseSimKeys, false, amplistorCredential).size();
    if (numDeleted != (NUMFILES - doNotDeleteTheseSimKeys.size())) {
        throw new Exception("Expected to delete " + (NUMFILES - doNotDeleteTheseSimKeys.size()) + " but deleted " + numDeleted);
    }
    // 
    // remove one of the remaining files on amplistor
    // 
    AmplistorUtils.deleteFilesOperation(new String[] { tmpFiles[0].getName() }, dirNameURL, amplistorCredential);
    // 
    if (AmplistorUtils.bFileExists(new URL(dirNameURL + "/" + tmpFiles[0].getName()), amplistorCredential)) {
        throw new Exception("Expected " + dirNameURL + "/" + tmpFiles[0].getName() + " 'bFileExist' to be false");
    }
    // 
    try {
        AmplistorUtils.deleteFilesOperation(new String[] { "blahblah" }, dirNameURL, amplistorCredential);
        throw new Exception("We shouldn't have gotten here, Expecting FileNotFoundException");
    } catch (FileNotFoundException e) {
    // ignore, this should happen
    }
    // 
    // there should be 1 file left
    // 
    int numleft = AmplistorUtils.listDir(dirNameURL, null, amplistorCredential).size();
    if (numleft != 1) {
        throw new Exception("Expecting 1 file in list but got " + numleft);
    }
    // 
    // Remove test from amplistor
    // 
    // do not ignore FileNotFound
    deleteDirAndAllFiles(dirNameURL, amplistorCredential);
    // 
    // vcell_logs Amplistor test
    // 
    // 
    // try to upload to vcell_logs without credentials
    // 
    AmplistorUtils.uploadFile(new URL(AmplistorUtils.DEFAULT_AMPLI_VCELL_LOGS_URL), tmpFiles[0], null);
    // 
    try {
        AmplistorUtils.listDir(AmplistorUtils.DEFAULT_AMPLI_VCELL_LOGS_URL, null, null);
        throw new Exception("Souldn't have gotten here, Expecting failure to get vcell_logs with no authentication");
    } catch (AuthenticationException e) {
    // ignore, this should happen
    }
    // 
    // try to get dir list from vcell_logs with credentials (should succeed)
    // 
    ArrayList<String> vcell_logs_dirlist = AmplistorUtils.listDir(AmplistorUtils.DEFAULT_AMPLI_VCELL_LOGS_URL, null, amplistorCredential);
    System.out.println("Found " + vcell_logs_dirlist.size() + " files in vcell_logs directory");
    // 
    try {
        AmplistorUtils.deleteFilesOperation(new String[] { tmpFiles[0].getName() }, AmplistorUtils.DEFAULT_AMPLI_VCELL_LOGS_URL, null);
        throw new Exception("Souldn't have gotten here, Expecting failure to get vcell_logs with no authentication");
    } catch (AuthenticationException e) {
    // ignore, this should happen
    }
    // 
    // try to delete file from vcell_logs with credentials (should succeed)
    // 
    AmplistorUtils.deleteFilesOperation(new String[] { tmpFiles[0].getName() }, AmplistorUtils.DEFAULT_AMPLI_VCELL_LOGS_URL, amplistorCredential);
    // 
    try {
        for (int i = 0; i < NUMFILES; i++) {
            tmpFiles[i].delete();
        }
        tmpDir.delete();
    } catch (Exception e) {
    // ignore, not part of test
    }
}

Example 3 with AuthenticationException

use of org.vcell.util.AuthenticationException in project vcell by virtualcell.

the class ClientServerManager method connectToServer.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 4:48:13 PM)
 */
private VCellConnection connectToServer(InteractiveContext requester, boolean bShowErrors) {
    BeanUtils.updateDynamicClientProperties();
    VCellThreadChecker.checkRemoteInvocation();
    VCellConnection newVCellConnection = null;
    VCellConnectionFactory vcConnFactory = null;
    String badConnStr = "";
    try {
        try {
            switch(getClientServerInfo().getServerType()) {
                case SERVER_REMOTE:
                    {
                        String apihost = getClientServerInfo().getApihost();
                        Integer apiport = getClientServerInfo().getApiport();
                        try {
                            badConnStr += apihost + ":" + apiport;
                            vcConnFactory = new RemoteProxyVCellConnectionFactory(apihost, apiport, getClientServerInfo().getUserLoginInfo());
                            setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), apihost, apiport, ConnectionStatus.INITIALIZING));
                            newVCellConnection = vcConnFactory.createVCellConnection();
                        } catch (AuthenticationException ex) {
                            throw ex;
                        }
                        break;
                    }
                case SERVER_LOCAL:
                    {
                        new PropertyLoader();
                        LocalVCellConnectionService localVCellConnectionService = VCellServiceHelper.getInstance().loadService(LocalVCellConnectionService.class);
                        vcConnFactory = localVCellConnectionService.getLocalVCellConnectionFactory(getClientServerInfo().getUserLoginInfo());
                        setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), null, null, ConnectionStatus.INITIALIZING));
                        newVCellConnection = vcConnFactory.createVCellConnection();
                        break;
                    }
            }
            requester.clearConnectWarning();
            reconnectStat = ReconnectStatus.NOT;
        } catch (Exception e) {
            e.printStackTrace();
            if (bShowErrors) {
                throw e;
            }
        }
    } catch (AuthenticationException aexc) {
        aexc.printStackTrace(System.out);
        requester.showErrorDialog(aexc.getMessage());
    } catch (ConnectionException cexc) {
        String msg = badConnectMessage(badConnStr) + "\n" + cexc.getMessage();
        cexc.printStackTrace(System.out);
        ErrorUtils.sendRemoteLogMessage(getClientServerInfo().getUserLoginInfo(), msg);
        if (reconnectStat != ReconnectStatus.SUBSEQUENT) {
            requester.showConnectWarning(msg);
        }
    } catch (HttpResponseException httpexc) {
        httpexc.printStackTrace(System.out);
        if (httpexc.getStatusCode() == HttpStatus.SC_UNAUTHORIZED) {
            requester.showErrorDialog("Invalid Userid or Password\n\n" + httpexc.getMessage());
        } else {
            String msg = "Exception: " + httpexc.getMessage() + "\n\n" + badConnectMessage(badConnStr);
            ErrorUtils.sendRemoteLogMessage(getClientServerInfo().getUserLoginInfo(), msg);
            requester.showErrorDialog(msg);
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        String msg = "Exception: " + exc.getMessage() + "\n\n" + badConnectMessage(badConnStr);
        ErrorUtils.sendRemoteLogMessage(getClientServerInfo().getUserLoginInfo(), msg);
        requester.showErrorDialog(msg);
    }
    return newVCellConnection;
}

Example 4 with AuthenticationException

use of org.vcell.util.AuthenticationException in project vcell by virtualcell.

the class AmplistorUtils method ampliCheckOP.

private static CheckOPHelper ampliCheckOP(URL httpURL, AmplistorCredential amplistorCredential, AMPLI_OP_METHOD ampliOpMethod, String authorizationResponse, AMPLI_OP_KIND ampliOpKind, HashMap<String, String> metaData) throws Exception {
    HttpURLConnection httpURLConnection = null;
    CheckOPHelper checkOPHelper = null;
    try {
        httpURLConnection = ampliOperationConnection(httpURL, ampliOpMethod, authorizationResponse, ampliOpKind, metaData);
        int responseCode = httpURLConnection.getResponseCode();
        // System.out.println("Status code: " + responseCode);
        if (responseCode == HttpURLConnection.HTTP_UNAUTHORIZED && amplistorCredential == null) {
            throw new AuthenticationException("Authentication required but no credentials available");
        } else if (responseCode == HttpURLConnection.HTTP_UNAUTHORIZED && authorizationResponse == null) {
            // System.out.println("Responding to Amplistor server authentication request...");
            String authorizationRequestNew = respondToChallenge(httpURLConnection, amplistorCredential, ampliOpMethod);
            httpURLConnection.disconnect();
            return ampliCheckOP(httpURL, amplistorCredential, ampliOpMethod, authorizationRequestNew, ampliOpKind, metaData);
        } else if (responseCode == HttpURLConnection.HTTP_UNAUTHORIZED && authorizationResponse != null) {
            throw new AuthenticationException("User " + amplistorCredential.userName + " authentication failed for URL=" + httpURL);
        } else if (responseCode == HttpURLConnection.HTTP_NOT_FOUND && (ampliOpMethod == AMPLI_OP_METHOD.GET || ampliOpMethod == AMPLI_OP_METHOD.DELETE)) {
            throw new FileNotFoundException("File not found " + httpURL);
        } else if (responseCode == HttpURLConnection.HTTP_OK && ampliOpMethod == AMPLI_OP_METHOD.GET && ampliOpKind == AMPLI_OP_KIND.DIR) {
            checkOPHelper = new CheckOPHelper(getResponseXML(httpURLConnection), httpURLConnection);
        } else if (responseCode == HttpURLConnection.HTTP_OK && ampliOpMethod == AMPLI_OP_METHOD.GET && ampliOpKind == AMPLI_OP_KIND.FILE) {
            checkOPHelper = new CheckOPHelper(null, httpURLConnection);
        } else if ((ampliOpMethod == AMPLI_OP_METHOD.PUT && responseCode != HttpURLConnection.HTTP_OK && responseCode != HttpURLConnection.HTTP_CREATED) || (ampliOpMethod == AMPLI_OP_METHOD.DELETE && responseCode != HttpURLConnection.HTTP_NO_CONTENT) || (ampliOpMethod == AMPLI_OP_METHOD.GET && responseCode != HttpURLConnection.HTTP_OK)) {
            throw new Exception("Unexpected response code=" + responseCode + " from amplistor for URL=" + httpURL);
        }
        return checkOPHelper;
    } finally {
        if (httpURLConnection != null && checkOPHelper == null) {
            httpURLConnection.disconnect();
        }
    }
}

Example 5 with AuthenticationException

use of org.vcell.util.AuthenticationException in project vcell by virtualcell.

the class LocalVCellConnectionFactory method createVCellConnection.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.server.VCellConnection
 */
public VCellConnection createVCellConnection() throws AuthenticationException, ConnectionException {
    try {
        if (connectionFactory == null) {
            connectionFactory = DatabaseService.getInstance().createConnectionFactory();
        }
        KeyFactory keyFactory = connectionFactory.getKeyFactory();
        LocalVCellConnection.setDatabaseResources(connectionFactory, keyFactory);
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(connectionFactory);
        boolean bEnableRetry = false;
        boolean isLocal = true;
        User user = adminDbTopLevel.getUser(userLoginInfo.getUserName(), userLoginInfo.getDigestedPassword(), bEnableRetry, isLocal);
        if (user != null) {
            userLoginInfo.setUser(user);
        } else {
            throw new AuthenticationException("failed to authenticate as user " + userLoginInfo.getUserName());
        }
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(connectionFactory, keyFactory);
        boolean bCache = false;
        Cachetable cacheTable = null;
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getRequiredProperty(PropertyLoader.secondarySimDataDirInternalProperty)));
        SimulationDatabaseDirect simulationDatabase = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, bCache);
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        LocalVCellConnection vcConn = new LocalVCellConnection(userLoginInfo, simulationDatabase, dataSetControllerImpl, exportServiceImpl);
        linkHDFLib();
        return vcConn;
    } catch (Throwable exc) {
        lg.error(exc.getMessage(), exc);
        throw new ConnectionException(exc.getMessage());
    }
}