Example usage for javax.xml.bind JAXBException printStackTrace

List of usage examples for javax.xml.bind JAXBException printStackTrace

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Introduction

In this page you can find the example usage for javax.xml.bind JAXBException printStackTrace.

Prototype

public void printStackTrace()

Source Link

Document

Prints this JAXBException and its stack trace (including the stack trace of the linkedException if it is non-null) to System.err .

Usage

From source file:org.energyos.espi.thirdparty.web.AuthorizationController.java

@RequestMapping(value = Routes.THIRD_PARTY_OAUTH_CODE_CALLBACK, method = RequestMethod.GET)
public String authorization(String code, String state, ModelMap model, Principal principal,
        @RequestParam(value = "error", required = false) String error,
        @RequestParam(value = "error_description", required = false) String error_description,
        @RequestParam(value = "error_uri", required = false) String error_uri) {

    try {//from  w  w  w  .j  a va  2 s .  c o m

        // Is /oauth/authorization response valid (i.e. is the "state"
        // element correct)?
        Authorization authorization = authorizationService.findByState(state);

        // Process valid /oauth/authorization response
        ApplicationInformation applicationInformation = authorization.getApplicationInformation();

        // Verify /oauth/authorization Endpoint process completed
        // successfully
        if (code != null) {
            try {

                // Update Authorization record with returned authorization
                // code for audit purposes
                authorization.setCode(code);
                authorization.setGrantType("authorization_code");
                authorization.setUpdated(new GregorianCalendar());
                authorizationService.merge(authorization);

                // Format /oauth/token Endpoint request
                String url = String.format("%s?redirect_uri=%s&code=%s&grant_type=authorization_code",
                        applicationInformation.getAuthorizationServerTokenEndpoint(),
                        applicationInformation.getRedirectUri(), code);

                // Build /oauth/token Endpoint request
                ClientRestTemplate restTemplate = templateFactory.newClientRestTemplate(
                        applicationInformation.getClientId(), applicationInformation.getClientSecret());

                // Issue /oauth/token Endpoint request
                AccessToken token = restTemplate.getForObject(url, AccessToken.class);

                // Process /oauth/token Endpoint response

                if (token.getAccessToken() != null) {
                    authorization.setAccessToken(token.getAccessToken());
                    authorization.setTokenType(token.getTokenType());
                    authorization.setExpiresIn(token.getExpiresIn());
                    authorization.setRefreshToken(token.getRefreshToken());
                    authorization.setScope(token.getScope());
                    authorization.setAuthorizationURI(token.getAuthorizationURI());
                    authorization.setResourceURI(token.getResourceURI());
                    authorization.setUpdated(new GregorianCalendar());
                    authorization.setStatus("1"); // Set authorization
                    // record status as
                    // "Active"
                    authorization.setState(null); // Clear State as a
                    // security measure

                    // Update authorization record with /oauth/token
                    // response data
                    authorizationService.merge(authorization);

                    // now do the initial import of the Authorized Resource,
                    // if it is
                    // not ready, then we will wait till we receive a Notify
                    // or the UX call for it.
                    // TODO: create a Subscription to work with if needed

                    RetailCustomer currentCustomer = currentCustomer(principal);

                    try {
                        usagePointRESTRepository.findAllByRetailCustomerId(currentCustomer.getId());

                    } catch (JAXBException e) {
                        // nothing there, so log the fact and move on. It
                        // will get imported later.
                        System.out.printf("\nThirdParty Import Exception: %s\n", e.toString());
                        e.printStackTrace();
                    }
                } else {

                    System.out.printf("\n/oauth/token Request did not return an access token\n");
                }

            } catch (HttpClientErrorException x) {

                // TODO: Extract error, error_description and error_uri from
                // JSON response. Currently recording null for all three
                // fields.

                // Update authorization record
                System.out.printf("\nHTTPClientException: %s\n", x.toString());

                authorization.setError(error);
                authorization.setErrorDescription(error_description);
                authorization.setErrorUri(error_uri);
                authorization.setUpdated(new GregorianCalendar());
                authorization.setStatus("2"); // Set authorization record
                // status as "Denied"
                authorization.setState(null); // Clear State as a security
                // measure
                authorizationService.merge(authorization);

                // TODO: Should the "message" differ based on the exception?
                throw new UserDeniedAuthorizationException("Unable to retrieve OAuth token", x);
            }
        } else {

            System.out.printf("\nOAuth2 authorization_request returned an error:\n");
            System.out.printf("Error:             " + error + "\n");
            System.out.printf("Error_description: " + error_description + "\n");
            System.out.printf("Error_uri:         " + error_uri + "\n");

            // Update authorization record with error response
            authorization.setError(error);
            authorization.setErrorDescription(error_description);
            authorization.setErrorUri(error_uri);
            authorization.setUpdated(new GregorianCalendar());
            authorization.setStatus("2"); // Set authorization record status
            // as "Denied"
            authorization.setState(null); // Clear State as a security
            // measure
            authorizationService.merge(authorization);

            throw new UserDeniedAuthorizationException("Error: " + error_description);

        }

    } catch (NoResultException | EmptyResultDataAccessException e) {

        // We received an invalid /oauth/authorization response
        // TODO: Log receipt of an invalid /oauth/authorization response
        return "/home";

    }

    return "redirect:/RetailCustomer/" + currentCustomer(principal).getId() + "/AuthorizationList";
}

From source file:com.vmware.vchs.publicapi.samples.GatewayRuleSample.java

/**
 * This method is to configure NAT and Firewall Rules to the EdgeGateway
 * //ww w  .  j  av a2  s. co  m
 * @param networkHref
 *            the href to the network on which nat rules to be applied
 * @param serviceConfHref
 *            the href to the service configure action of gateway
 * @return
 */
private void configureRules(String networkHref, String serviceConfHref) {
    // NAT Rules
    NatServiceType natService = new NatServiceType();

    // To Enable the service using this flag
    natService.setIsEnabled(Boolean.TRUE);

    // Configuring Destination nat
    NatRuleType dnatRule = new NatRuleType();

    // Setting Rule type Destination Nat DNAT
    dnatRule.setRuleType("DNAT");
    dnatRule.setIsEnabled(Boolean.TRUE);
    GatewayNatRuleType dgatewayNat = new GatewayNatRuleType();
    ReferenceType refd = new ReferenceType();
    refd.setHref(networkHref);

    // Network on which nat rules to be applied
    dgatewayNat.setInterface(refd);

    // Setting Original IP
    dgatewayNat.setOriginalIp(options.externalIp);
    dgatewayNat.setOriginalPort("any");

    dgatewayNat.setTranslatedIp(options.internalIp);

    // To allow all ports and all protocols
    // dgatewayNat.setTranslatedPort("any");
    // dgatewayNat.setProtocol("Any");

    // To allow only https use Port 443 and TCP protocol
    dgatewayNat.setTranslatedPort("any");
    dgatewayNat.setProtocol("TCP");

    // To allow only ssh use Port 22 and TCP protocol
    // dgatewayNat.setTranslatedPort("22");
    // dgatewayNat.setProtocol("TCP");
    // Setting Destination IP
    dnatRule.setGatewayNatRule(dgatewayNat);
    natService.getNatRule().add(dnatRule);

    // Configuring Source nat
    NatRuleType snatRule = new NatRuleType();

    // Setting Rule type Source Nat SNAT
    snatRule.setRuleType("SNAT");
    snatRule.setIsEnabled(Boolean.TRUE);
    GatewayNatRuleType sgatewayNat = new GatewayNatRuleType();
    //ReferenceType refd = new ReferenceType();
    //refd.setHref(networkHref);

    // Network on which nat rules to be applied
    sgatewayNat.setInterface(refd);

    // Setting Original IP
    sgatewayNat.setOriginalIp(options.internalIp);
    //sgatewayNat.setOriginalPort("any");

    sgatewayNat.setTranslatedIp(options.externalIp);

    // Setting Source IP
    snatRule.setGatewayNatRule(sgatewayNat);
    natService.getNatRule().add(snatRule);

    // Firewall Rules
    FirewallServiceType firewallService = new FirewallServiceType();

    // Enable or disable the service using this flag
    firewallService.setIsEnabled(Boolean.TRUE);

    // Default action of the firewall set to drop
    firewallService.setDefaultAction("drop");

    // Flag to enable logging for default action
    firewallService.setLogDefaultAction(Boolean.FALSE);

    // Firewall Rule settings
    FirewallRuleType firewallInRule = new FirewallRuleType();
    firewallInRule.setIsEnabled(Boolean.TRUE);
    firewallInRule.setMatchOnTranslate(Boolean.FALSE);
    firewallInRule.setDescription("Allow incoming https access");
    firewallInRule.setPolicy("allow");
    FirewallRuleProtocols firewallProtocol = new FirewallRuleProtocols();
    firewallProtocol.setAny(Boolean.TRUE);
    firewallInRule.setProtocols(firewallProtocol);
    firewallInRule.setDestinationPortRange("any");
    firewallInRule.setDestinationIp(options.externalIp);
    firewallInRule.setSourcePortRange("Any");
    firewallInRule.setSourceIp("external");
    firewallInRule.setEnableLogging(Boolean.FALSE);
    firewallService.getFirewallRule().add(firewallInRule);

    // To create the HttpPost request Body
    ObjectFactory objectFactory = new ObjectFactory();
    GatewayFeaturesType gatewayFeatures = new GatewayFeaturesType();
    JAXBElement<NetworkServiceType> serviceType = objectFactory.createNetworkService(natService);
    JAXBElement<NetworkServiceType> firewallserviceType = objectFactory.createNetworkService(firewallService);
    gatewayFeatures.getNetworkService().add(serviceType);
    gatewayFeatures.getNetworkService().add(firewallserviceType);
    JAXBContext jaxbContexts = null;

    try {
        jaxbContexts = JAXBContext.newInstance(GatewayFeaturesType.class);
    } catch (JAXBException ex) {
        ex.printStackTrace();
    }

    OutputStream os = null;
    JAXBElement<GatewayFeaturesType> gateway_Features = objectFactory
            .createEdgeGatewayServiceConfiguration(gatewayFeatures);

    try {
        javax.xml.bind.Marshaller marshaller = jaxbContexts.createMarshaller();
        marshaller.setProperty(javax.xml.bind.Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
        os = new ByteArrayOutputStream();

        // Marshal the JAXB class to XML
        marshaller.marshal(gateway_Features, os);
    } catch (JAXBException e) {
        e.printStackTrace();
    }

    HttpPost httpPost = vcd.post(serviceConfHref, options);
    ContentType contentType = ContentType.create(SampleConstants.CONTENT_TYPE_EDGE_GATEWAY, "ISO-8859-1");
    StringEntity rules = new StringEntity(os.toString(), contentType);
    httpPost.setEntity(rules);
    InputStream is = null;

    // Invoking api to add rules to gateway
    HttpResponse response = HttpUtils.httpInvoke(httpPost);

    // Make sure the response code is 202 ACCEPTED
    if (response.getStatusLine().getStatusCode() == HttpStatus.SC_ACCEPTED) {
        // System.out.println("ResponseCode : " + response.getStatusLine().getStatusCode());
        System.out.println("\nRequest To update Gateway initiated sucessfully");
        System.out.print("\nUpdating EdgeGateways to add NAT and Firewall Rules...");
        taskStatus(response);
    }
}

From source file:controllers.WorkflowViewController.java

private void mapExperimentalProperties(String id, List<String> fileNames) {
    Map<String, Object> params = new HashMap<String, Object>();
    List<String> codes = new ArrayList<String>();
    for (Sample s : datahandler.getOpenBisClient().getSamplesOfProjectBySearchService(id))
        codes.add(s.getCode());//from  ww w .  j a va 2 s.c  o  m
    params.put("codes", codes);
    QueryTableModel res = datahandler.getOpenBisClient().getAggregationService("get-property-tsv", params);

    Set<String> factorNames = new HashSet<String>();
    Map<String, String> fileProps = new HashMap<String, String>();

    // XML Parser
    XMLParser p = new XMLParser();

    Set<String> secondaryNames = new HashSet<String>();

    for (Serializable[] ss : res.getRows()) {

        String xml = (String) ss[3];
        String code = (String) ss[0];
        List<String> matches = getMatchingStrings(fileNames, code);
        if (!xml.isEmpty() && !matches.isEmpty()) {
            for (String match : matches) {
                StringBuilder row = new StringBuilder();
                String extID = (String) ss[1];// how to use this if it is preferred over secondary name?
                String secondaryName = (String) ss[2];
                while (secondaryNames.contains(secondaryName))
                    secondaryName += "1";
                secondaryNames.add(secondaryName);
                row.append(secondaryName);
                List<Property> properties = new ArrayList<Property>();
                try {
                    properties = p.getAllPropertiesFromXML(xml);
                } catch (JAXBException e) {
                    e.printStackTrace();
                }
                for (Property f : properties) {
                    factorNames.add(f.getLabel());
                    String val = f.getValue();
                    if (f.hasUnit())
                        val += f.getUnit();
                    row.append("\t" + val);
                }
                fileProps.put(match, row.toString());
            }
        }
    }
    this.expProps = fileProps;
    this.expFactors = factorNames;
}

From source file:gov.usgs.cida.coastalhazards.rest.data.util.MetadataUtilTest.java

/**
 * Test of getBoundingBoxFromFgdcMetadataCR method, of class MetadataUtil.
 *///from w  ww  .  ja v  a  2 s. com
@Test
public void testGetBoundingBoxFromFgdcMetadataCR() throws IOException {
    System.out.println("testGetBoundingBoxFromFgdcMetadataPAE");
    // This method tests the parsing that occurs in: Bbox result = MetadataUtil.getBoundingBoxFromFgdcMetadata(metadata); // file is ~40kb
    // spdom is the WGS84 bbox, format for the Bbox is "BOX(%f %f, %f %f)"

    //get the metadata from the test file as a string using this package to locate it ...
    String packageName = this.getClass().getCanonicalName();
    System.out.println("PackageName: " + packageName); //PackageName: gov.usgs.cida.coastalhazards.rest.data.util.MetadataUtilTest
    // this is where the test resource is located - gov.usgs.cida.coastalhazards.rest.data + /ne_AEmeta.xml
    String replaced = packageName.replaceAll("[.]", "/");
    String[] names = replaced.split("/util/MetadataUtilTest");
    String packageNameShort = names[0];
    String testFileFullName = packageNameShort + "/" + CRxml;

    String metadataXml = loadResourceAsString(testFileFullName);

    InputStream in = new ByteArrayInputStream(metadataXml.getBytes("UTF-8"));
    Metadata metadata = null;

    // JAXB will require jaxb-api.jar and jaxb-impl.jar part of java 1.6. Much safer way to interrogate xml and maintain than regex
    try {
        //File file = new File(xmlFile);  // FYI: can also be done via file rather than inputStream
        JAXBContext jaxbContext = JAXBContext.newInstance(Metadata.class);
        Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
        metadata = (Metadata) jaxbUnmarshaller.unmarshal(in);

    } catch (JAXBException e) {
        e.printStackTrace();
    }

    assertNotNull(metadata);
    Idinfo idinfo = metadata.getIdinfo();
    Spdom spdom = idinfo.getSpdom();
    Bounding bounding = spdom.getBounding();

    double minx = bounding.getWestbc();
    double miny = bounding.getSouthbc();
    double maxx = bounding.getEastbc();
    double maxy = bounding.getNorthbc();

    Bbox result = new Bbox();
    result.setBbox(minx, miny, maxx, maxy);

    System.out.println("Parsed Bbox is: " + result.getBbox());

    Bbox expResult = new Bbox();
    expResult.setBbox("BOX(-77.830618 35.344738, -66.813170 46.642941)");

    assertNotNull(result);
    assertTrue(expResult.getBbox().startsWith("BOX(-77.830618 35."));
    assertTrue(expResult.getBbox().equalsIgnoreCase(result.getBbox()));
}

From source file:gov.usgs.cida.coastalhazards.rest.data.util.MetadataUtilTest.java

/**
 * Test of getBoundingBoxFromFgdcMetadataAE method, of class MetadataUtil.
 *///from  w ww  .  ja  va 2s  . c  o  m
@Test

public void testGetBoundingBoxFromFgdcMetadataAE() throws IOException {
    System.out.println("testGetBoundingBoxFromFgdcMetadataAE");
    // This method tests the parsing that occurs in: Bbox result = MetadataUtil.getBoundingBoxFromFgdcMetadata(metadata); // file is ~40kb
    // spdom is the WGS84 bbox, format for the Bbox is "BOX(%f %f, %f %f)"

    //get the metadata from the test file as a string using this package to locate it ...
    String packageName = this.getClass().getCanonicalName();
    System.out.println("PackageName: " + packageName); //PackageName: gov.usgs.cida.coastalhazards.rest.data.util.MetadataUtilTest
    // this is where the test resource is located - gov.usgs.cida.coastalhazards.rest.data + /ne_AEmeta.xml
    String replaced = packageName.replaceAll("[.]", "/");
    String[] names = replaced.split("/util/MetadataUtilTest");
    String packageNameShort = names[0];
    String testFileFullName = packageNameShort + "/" + AExml;

    String metadataXml = loadResourceAsString(testFileFullName);

    InputStream in = new ByteArrayInputStream(metadataXml.getBytes("UTF-8"));
    Metadata metadata = null;

    // JAXB will require jaxb-api.jar and jaxb-impl.jar part of java 1.6. Much safer way to interrogate xml and maintain than regex
    try {
        //File file = new File(xmlFile);  // FYI: can also be done via file rather than inputStream
        JAXBContext jaxbContext = JAXBContext.newInstance(Metadata.class);
        Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
        metadata = (Metadata) jaxbUnmarshaller.unmarshal(in);

    } catch (JAXBException e) {
        e.printStackTrace();
    }

    assertNotNull(metadata);
    Idinfo idinfo = metadata.getIdinfo();
    Spdom spdom = idinfo.getSpdom();
    Bounding bounding = spdom.getBounding();

    double minx = bounding.getWestbc();
    double miny = bounding.getSouthbc();
    double maxx = bounding.getEastbc();
    double maxy = bounding.getNorthbc();

    Bbox result = new Bbox();
    result.setBbox(minx, miny, maxx, maxy);

    System.out.println("Parsed Bbox is: " + result.getBbox());

    Bbox expResult = new Bbox();
    expResult.setBbox("BOX(-77.830618 35.344738, -66.813170 46.642941)");

    assertNotNull(result);
    assertTrue(expResult.getBbox().startsWith("BOX(-77.830618 35."));
    assertTrue(expResult.getBbox().equalsIgnoreCase(result.getBbox()));
}

From source file:gov.usgs.cida.coastalhazards.rest.data.util.MetadataUtilTest.java

/**
 * Test of getCrsFromFgdcMetadata method, of class MetadataUtil.
 *///from   www. j a v a2s  .co  m
@Test
public void testGetCrsFromFgdcMetadata() throws IOException {
    System.out.println("getCrsFromFgdcMetadata");
    //spref is used to determine hte SRS

    System.out.println("testGetBoundingBoxFromFgdcMetadataAE");

    //get the metadata from the test file as a string using this package to locate it ...
    String packageName = this.getClass().getCanonicalName();
    System.out.println("PackageName: " + packageName); //PackageName: gov.usgs.cida.coastalhazards.rest.data.util.MetadataUtilTest
    // this is where the test resource is located - gov.usgs.cida.coastalhazards.rest.data + /ne_AEmeta.xml
    String replaced = packageName.replaceAll("[.]", "/");
    String[] names = replaced.split("/util/MetadataUtilTest");
    String packageNameShort = names[0];
    String testFileFullName = packageNameShort + "/" + CRxml;

    String metadataXml = loadResourceAsString(testFileFullName);

    InputStream in = new ByteArrayInputStream(metadataXml.getBytes("UTF-8"));
    Metadata metadata = null;

    // JAXB will require jaxb-api.jar and jaxb-impl.jar part of java 1.6. Much safer way to interrogate xml and maintain than regex
    try {
        //File file = new File(xmlFile);  // FYI: can also be done via file rather than inputStream
        JAXBContext jaxbContext = JAXBContext.newInstance(Metadata.class);
        Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
        metadata = (Metadata) jaxbUnmarshaller.unmarshal(in);

    } catch (JAXBException e) {
        e.printStackTrace();
    }

    assertNotNull(metadata);

    //Spref spref = metadata.getSpref();
    Horizsys horizsys = metadata.getSpref().getHorizsys();

    assertNotNull(horizsys);

    String expEllips = "GRS 1980";
    String expHorizdn = "North American Datum 1983";
    double expDenflat = 298.257222101;
    double expSemiaxis = 6378137.0;

    // part I
    String ellips = horizsys.getGeodetic().getEllips();
    String horizdn = horizsys.getGeodetic().getHorizdn();
    double denflat = horizsys.getGeodetic().getDenflat();
    double semiaxis = horizsys.getGeodetic().getSemiaxis();

    assertTrue(expEllips.equalsIgnoreCase(ellips));
    assertTrue(expHorizdn.equalsIgnoreCase(horizdn));
    assertEquals(expDenflat, denflat, expDenflat - denflat);
    assertEquals(expSemiaxis, semiaxis, expSemiaxis - semiaxis);
    // part II
    String mapprojn = horizsys.getPlanar().getMapproj().getMapprojn();
    double feast = horizsys.getPlanar().getMapproj().getMapprojp().getFeast();
    double fnorth = horizsys.getPlanar().getMapproj().getMapprojp().getFnorth();
    double latprjo = horizsys.getPlanar().getMapproj().getMapprojp().getLatprjo();
    double longcm = horizsys.getPlanar().getMapproj().getMapprojp().getLongcm();
    double stdparll = horizsys.getPlanar().getMapproj().getMapprojp().getStdparll();

    String expMapprojn = "Albers Conical Equal Area";
    double expFeast = 0.0;
    double expFnorth = 0.0;
    double expLatprjo = 23.0;
    double expLongcm = -96.0;
    double expStdparll = 45.5; // the second of the two children

    assertTrue(expMapprojn.equalsIgnoreCase(mapprojn));
    assertEquals(expFeast, feast, expFeast - feast);
    assertEquals(expFnorth, fnorth, expFnorth - fnorth);
    assertEquals(expLatprjo, latprjo, expLatprjo - latprjo);
    assertEquals(expLongcm, longcm, expLongcm - longcm);
    assertEquals(expStdparll, stdparll, expStdparll - stdparll);
    //CoordinateReferenceSystem expResult = null;
    //CoordinateReferenceSystem result = MetadataUtil.getCrsFromFgdcMetadata(metadata);
    //assertEquals(expResult, result);

}

From source file:it.cnr.icar.eric.client.ui.common.UIUtility.java

public Object convertToRimBinding(Object uiBindingObj) throws JAXRException {
    Object rimBindingObj = null;/*from   www  .ja  va  2  s  .  c o m*/
    StringWriter sw = new StringWriter();
    try {
        Marshaller marshaller = uiJaxbContext.createMarshaller();
        if (uiBindingObj instanceof it.cnr.icar.eric.client.ui.common.conf.bindings.InternationalStringType) {
            it.cnr.icar.eric.client.ui.common.conf.bindings.ObjectFactory oF = new it.cnr.icar.eric.client.ui.common.conf.bindings.ObjectFactory();
            marshaller.marshal(oF.createInternationalString((InternationalStringType) uiBindingObj), sw);

            Unmarshaller unmarshaller = BindingUtility.getInstance().getJAXBContext().createUnmarshaller();
            rimBindingObj = JAXBIntrospector
                    .getValue(unmarshaller.unmarshal(new StreamSource(new StringReader(sw.toString()))));
        } else {
            marshaller.marshal(uiBindingObj, sw);
            Unmarshaller unmarshaller = BindingUtility.getInstance().getJAXBContext().createUnmarshaller();
            //unmarshaller.setValidating(true);
            unmarshaller.setEventHandler(new ValidationEventHandler() {
                public boolean handleEvent(ValidationEvent event) {
                    boolean keepOn = false;

                    return keepOn;
                }
            });

            rimBindingObj = unmarshaller.unmarshal(new StreamSource(new StringReader(sw.toString())));
        }

    } catch (JAXBException e) {
        e.printStackTrace();
        throw new JAXRException(e);
    }
    return rimBindingObj;
}

From source file:controllers.WorkflowViewController.java

public String submitAndRegisterWf(String type, String id, Workflow workflow, List<DatasetBean> selectedDatasets)
        throws ConnectException, IllegalArgumentException, SubmitFailedException {

    SpaceAndProjectCodes spaceandproject = getSpaceAndProjects(type, id);

    String spaceCode = spaceandproject.space;
    String projectCode = spaceandproject.project;

    ParameterSet params = workflow.getParameters();
    List<Property> factors = new ArrayList<Property>();

    XMLParser xmlParser = new XMLParser();

    for (Map.Entry<String, Parameter> entry : workflow.getData().getData().entrySet()) {
        String key = entry.getKey();
        Parameter value = entry.getValue();

        if (key.contains("input")) {
            List<String> files = (List<String>) value.getValue();
            List<String> inputFiles = new ArrayList<String>();

            for (String f : files) {
                String[] splitted = f.split("/");
                String fileName = splitted[splitted.length - 1];
                inputFiles.add(fileName);
            }// ww  w . j  a  v a2  s.  c o  m

            System.out.println(inputFiles.toString());
            String concat = String.join("; ", inputFiles);
            System.out.println(concat);
            Property newProperty = new Property("input_files", concat, PropertyType.Property);
            factors.add(newProperty);
        }

        else {
            Property newProperty = new Property("database",
                    value.getValue().toString().replace("/lustre_cfc/qbic/reference_genomes/", ""),
                    PropertyType.Property);
            factors.add(newProperty);
        }
    }

    for (String p : params.getParamNames()) {
        Parameter par = params.getParam(p);
        String[] splitted = par.getTitle().split("\\.");
        String parName = splitted[splitted.length - 1].replace(" ", "_").toLowerCase();

        Property newProperty = new Property(parName, par.getValue().toString(), PropertyType.Property);
        factors.add(newProperty);
    }

    String qProperties = "";

    try {
        qProperties = xmlParser.toString(xmlParser.createXMLFromProperties(factors));
        System.out.println(qProperties);
    } catch (JAXBException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    String experimentCode = registerWFExperiment(spaceCode, projectCode, workflow.getExperimentType(),
            workflow.getID(), workflow.getVersion(), user, qProperties);

    List<String> parents = getConnectedSamples(selectedDatasets);
    String sampleType = workflow.getSampleType();

    String sampleCode = registerWFSample(spaceCode, projectCode, experimentCode, sampleType, parents,
            selectedDatasets);

    String openbisId = String.format("%s-%s-%s-%s", spaceCode, projectCode, experimentCode, sampleCode);

    LOGGER.info(
            "User: " + user + " is submitting workflow " + workflow.getID() + " openbis id is:" + openbisId);

    String submit_id = submitter.submit(workflow, openbisId, user);
    LOGGER.info("Workflow has guse id: " + submit_id);

    setWorkflowID(spaceCode, projectCode, experimentCode, submit_id);
    return openbisId;
}

From source file:eu.betaas.service.securitymanager.service.impl.AuthorizationService.java

/**
 * Check the condition specified in the token with the condition saved in the 
 * GW (concerning the specific thingService)
 * @param ct: extracted Condition from the token
 * @param req: RequestCtx (required by XACML API)
 * @return boolean true or false (true if the condition matches)
 *///  w  w  w.j a v a 2 s.co m
private boolean checkCondition(ConditionType ct, RequestCtx req) {
    boolean access = false;

    JAXBElement<ConditionType> jaxbCT = of.createCondition(ct);
    JAXBContext jc = null;
    try {
        jc = JAXBContext.newInstance(ConditionType.class);
        Marshaller mar = jc.createMarshaller();

        // create DOM Document
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder db = dbf.newDocumentBuilder();
        Document doc = db.newDocument();

        mar.marshal(jaxbCT, doc);

        // convert ConditionType to XML Node (org.w3c.dom.Node)
        DOMResult res = new DOMResult();
        res.setNode(doc.getDocumentElement());
        Node conditionNode = res.getNode();

        // prepare for the Condition
        PolicyMetaData metadata = new PolicyMetaData(2, 0);
        VariableManager vm = new VariableManager(new HashMap(), metadata);
        Condition condition = Condition.getInstance(conditionNode, metadata, vm);

        // evaluate condition -- first convert RequestCtx into EvaluationCtx
        EvaluationCtx context = new BasicEvaluationCtx(req);
        EvaluationResult result = condition.evaluate(context);
        BooleanAttribute bool = (BooleanAttribute) (result.getAttributeValue());
        // get the condition evaluation result in boolean
        access = bool.getValue();
    } catch (JAXBException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (ParserConfigurationException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (ParsingException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    log.info("Checking Condition in the Access Right return: " + access);

    return access;
}

From source file:edu.duke.cabig.c3pr.dao.StudyDao.java

public String generateHQL(List<AdvancedSearchCriteriaParameter> searchParameters) {
    InputStream inputStream = Thread.currentThread().getContextClassLoader()
            .getResourceAsStream("study-advanced-search.xml");
    Unmarshaller unmarshaller;//from  w ww . ja  v a  2s  . co  m
    QueryBuilder queryBuilder = new QueryBuilder();
    try {
        unmarshaller = JAXBContext.newInstance("com.semanticbits.querybuilder").createUnmarshaller();
        queryBuilder = (QueryBuilder) unmarshaller.unmarshal(inputStream);
    } catch (JAXBException e) {
        e.printStackTrace();
    }

    TargetObject targetObject = (TargetObject) queryBuilder.getTargetObject().get(0);
    try {
        return QueryGenerator.generateHQL(targetObject, searchParameters, true);
    } catch (Exception e) {
        e.printStackTrace();
    }
    return "";
}