Example usage for org.apache.commons.lang3 StringUtils substringAfter

List of usage examples for org.apache.commons.lang3 StringUtils substringAfter

  1. HOME
  2. Java
  3. org.apache.commons
  4. org.apache.commons.lang3.*
  5. StringUtils
  6. substringAfter

Introduction

In this page you can find the example usage for org.apache.commons.lang3 StringUtils substringAfter.

Prototype

public static String substringAfter(final String str, final String separator)

Source Link

Document

Gets the substring after the first occurrence of a separator.

Usage

From source file:org.pepstock.jem.springbatch.tasks.ChunkDataSourcesManager.java

/**
 * Replaces inside of property value system variables or properties loaded by Spring
 * @param value property value to change
 * @return value changed//from  ww w .  j  a v a 2 s  . co m
 */
private static String replaceProperties(String value) {
    String changed = null;
    // if property starts with jem.data
    // I need to ask to DataPaths Container in which data path I can put the file
    if (value.startsWith("${" + ConfigKeys.JEM_DATA_PATH_NAME + "}")) {
        // takes the rest of file name
        String fileName = StringUtils.substringAfter(value, "${" + ConfigKeys.JEM_DATA_PATH_NAME + "}");
        // checks all paths
        try {
            // gets datapaths
            PathsContainer paths = DataPathsContainer.getInstance().getPaths(fileName);
            // is relative!
            // creates a file with dataPath as parent, plus file name  
            File file = new File(paths.getCurrent().getContent(), fileName);
            // the absolute name of the file is property value
            changed = file.getAbsolutePath();
        } catch (InvalidDatasetNameException e) {
            throw new BuildException(e);
        }
    } else {
        // uses SB utilities to changed all properties
        changed = JobsProperties.getInstance().replacePlaceHolders(value);
    }
    return changed;
}

From source file:org.pepstock.jem.springbatch.tasks.DataSetManager.java

/**
 * /*from  w  w w .jav a2 s  . c  o m*/
 * @param ddImpl
 * @param ds
 * @return
 * @throws BuildException
 */
private static FileWrapper getFile(DataSet ds, String disposition) throws SpringBatchException {
    // gets the data path and checks
    // if dataset name starts
    String dataPath = DataPathsContainer.getInstance().getAbsoluteDataPath(ds.getName());

    //checks if the Dsname is a absolute file name
    // if absolute path is equals return the file 
    // otherwise checks datapath
    File file = null;
    String fileName = null;

    //checks if the Dsname is a absolute file name
    // if absolute path is equals return the file 
    // otherwise checks datapath
    if (dataPath != null) {
        // if name is absolute
        // creates a new FILE object with full pathname 
        file = new File(ds.getName());
        // normalizes using UNIX rules
        fileName = FilenameUtils.normalize(file.getAbsolutePath(), true);
        // extract the short name, taking the string after dataPath
        fileName = StringUtils.substringAfter(fileName, dataPath);
        // removes the first / of the filename
        fileName = fileName.substring(1);

        // we must check if full is correct in disposition NEW (only for new allocation)
        if (Disposition.NEW.equalsIgnoreCase(disposition)) {
            try {
                // checks all paths
                PathsContainer paths = DataPathsContainer.getInstance().getPaths(fileName);
                // creates a file with dataPath as parent, plus file name  
                file = new File(paths.getCurrent().getContent(), fileName);
            } catch (InvalidDatasetNameException e) {
                throw new SpringBatchException(e.getMessageInterface(), e, e.getObjects());
            }
        }
    } else {
        // should be relative
        file = new File(ds.getName());
        // normalizes the full path and checks again with the name
        // if equals means that is absolute because the previuos checks only if it's using the 
        // data paths
        if (FilenameUtils.normalize(file.getAbsolutePath(), true).equalsIgnoreCase(ds.getName())) {
            // normalizes using UNIX rules
            fileName = FilenameUtils.normalize(file.getAbsolutePath(), true);
        } else {
            try {
                // checks all paths
                PathsContainer paths = DataPathsContainer.getInstance().getPaths(ds.getName());
                // is relative!
                // creates a file with dataPath as parent, plus file name  
                file = new File(paths.getCurrent().getContent(), ds.getName());
                // if disposition is not in new allocation and the file with current path doesn't exists,
                // try to use the old path is exist
                if (!Disposition.NEW.equalsIgnoreCase(disposition) && !file.exists()
                        && paths.getOld() != null) {
                    file = new File(paths.getOld().getContent(), ds.getName());
                }
                // normalizes using UNIX rules
                fileName = FilenameUtils.normalize(ds.getName(), true);
            } catch (InvalidDatasetNameException e) {
                throw new SpringBatchException(e.getMessageInterface(), e, e.getObjects());
            }
        }
    }
    return new FileWrapper(file, fileName);
}

From source file:org.pepstock.jem.springbatch.tasks.DataSource.java

/**
 * Replaces inside of property value system variables or properties loaded by Spring
 * @param value property value to change
 * @return value changed/*w w w.ja v a 2  s . c  o m*/
 */
private String replaceProperties(String value) {
    String changed = null;
    // if property starts with jem.data
    // I need to ask to DataPaths Container in which data path I can put the file
    if (value.startsWith("${" + ConfigKeys.JEM_DATA_PATH_NAME + "}")) {
        // takes the rest of file name
        String fileName = StringUtils.substringAfter(value, "${" + ConfigKeys.JEM_DATA_PATH_NAME + "}");
        // checks all paths
        try {
            // gets datapaths
            PathsContainer paths = DataPathsContainer.getInstance().getPaths(fileName);
            // is relative!
            // creates a file with dataPath as parent, plus file name  
            File file = new File(paths.getCurrent().getContent(), fileName);
            // the absolute name of the file is property value
            changed = file.getAbsolutePath();
        } catch (InvalidDatasetNameException e) {
            throw new BuildException(e);
        }
    } else {
        // uses SB utilities to changed all properties
        changed = JobsProperties.getInstance().replacePlaceHolders(value);
    }
    return changed;
}

From source file:org.pepstock.jem.springbatch.tasks.SpringBatchSecurityManager.java

@Override
public void checkPermission(Permission perm) {
    // checks if someone add a security manager
    if (perm instanceof RuntimePermission && "setSecurityManager".equalsIgnoreCase(perm.getName())) {
        LogAppl.getInstance().emit(NodeMessage.JEMC274E);
        throw new SecurityException(NodeMessage.JEMC274E.toMessage().getMessage());
    }/*from   w  w  w  .  j  a v  a2 s .c o m*/
    // this check is necessary to avoid that someone
    // set jem properties, accessing outside of GFS
    if (perm instanceof PropertyPermission && "write".equalsIgnoreCase(perm.getActions())
            && perm.getName().startsWith("jem")) {
        LogAppl.getInstance().emit(NodeMessage.JEMC127E);
        throw new SecurityException(NodeMessage.JEMC127E.toMessage().getMessage());
    }
    // checks is administrator. if true return.
    if (isAdministrator() || isInternalAction()) {
        return;
    }
    // checks the file access
    // calling the right method, in according
    // with the action of permission
    if (perm instanceof FilePermission) {
        if ("read".equalsIgnoreCase(perm.getActions())) {
            checkRead(perm.getName());
        } else if ("write".equalsIgnoreCase(perm.getActions())) {
            checkWrite(perm.getName());
        } else if ("delete".equalsIgnoreCase(perm.getActions())) {
            checkDelete(perm.getName());
        } else {
            checkRead(perm.getName());
        }
    } else if (perm instanceof SocketPermission) {
        // checks the RMI access.
        // checks to RMI is not allowed if you're not a admin
        SocketPermission sperm = (SocketPermission) perm;
        int port = Parser.parseInt(StringUtils.substringAfter(sperm.getName(), ":"), Integer.MAX_VALUE);
        int portRmi = Parser.parseInt(System.getProperty(RmiKeys.JEM_RMI_PORT), Integer.MIN_VALUE);
        // if is going to RMI port and
        // is not executing JEM code and is not grantor
        if (port == portRmi && !isInternalAction() && !isGrantor()) {
            // extracts host name
            String hostname = StringUtils.substringBefore(sperm.getName(), ":");
            try {
                // gets hostname and localhost 
                String resolved = InetAddress.getByName(hostname).getHostAddress();
                String localhost = InetAddress.getLocalHost().getHostAddress();
                // if they are equals and the user
                // desn't have the internal service permission
                // EXCEPTION!!
                if (resolved.equalsIgnoreCase(localhost)
                        && !checkBatchPermission(Permissions.INTERNAL_SERVICES)) {
                    LogAppl.getInstance().emit(NodeMessage.JEMC128E);
                    throw new SecurityException(NodeMessage.JEMC128E.toMessage().getMessage());
                }
            } catch (UnknownHostException e) {
                // if there is an error on resolving the hostname
                LogAppl.getInstance().emit(NodeMessage.JEMC128E);
                throw new SecurityException(NodeMessage.JEMC128E.toMessage().getMessage(), e);
            }
        }
    }
}

From source file:org.phenotips.integration.lims247.internal.LimsSynchronizationEventListener.java

/**
 * Prepare a JSON payload to send to the registered LIMS servers to notify of the change. The JSON looks like:
 *
 * <pre>// w  ww  . ja va2s.  co m
 * {
 *   "eid": "ExternalId123",
 *   "event": "update", // or "create" or "delete"
 *   "pn": "wiki name",
 *   "username": "uname",
 *   "auth_token": "strtoken"
 * }
 * </pre>
 *
 * The username and authentication token is taken either from the cached LIMS authentication, or from the XWiki user
 * logged in.
 *
 * @param event the original event that notified of the change
 * @param doc the modified document, a patient sheet document
 * @param context the current request context
 * @return a JSON object
 */
private JSONObject getPayload(Event event, XWikiDocument doc, XWikiContext context) {
    JSONObject result = new JSONObject();

    String eid = doc.getXObject(PATIENT_CLASS).getStringValue(EXTERNAL_ID_PROPERTY_NAME);
    result.put(IDENTIFIER_KEY, eid);
    if (event instanceof DocumentCreatedEvent) {
        result.put(EVENT_KEY, "create");
    } else if (event instanceof DocumentUpdatedEvent) {
        result.put(EVENT_KEY, "update");
    } else if (event instanceof DocumentDeletedEvent) {
        result.put(EVENT_KEY, "delete");
    }
    LimsAuthentication auth = (LimsAuthentication) context.getRequest().getSession()
            .getAttribute(Lims247AuthServiceImpl.SESSION_KEY);
    if (auth != null) {
        // FIXME Reuse this authentication only if the authentication server is the same as the target server
        result.put(LimsServer.INSTANCE_IDENTIFIER_KEY, context.getDatabase());
        result.put(LimsServer.USERNAME_KEY, StringUtils.substringAfter(auth.getUser().getUser(), "."));
        result.put(LimsServer.TOKEN_KEY, auth.getToken());
    } else if (context.getUserReference() != null) {
        result.put(LimsServer.INSTANCE_IDENTIFIER_KEY, context.getUserReference().getWikiReference().getName());
        result.put(LimsServer.USERNAME_KEY, context.getUserReference().getName());
        result.put(LimsServer.TOKEN_KEY, this.token.getToken());
    } else {
        result.put(LimsServer.INSTANCE_IDENTIFIER_KEY, context.getDatabase());
        result.put(LimsServer.USERNAME_KEY, "");
        result.put(LimsServer.TOKEN_KEY, "");
    }
    return result;
}

From source file:org.phenotips.integration.lims247.script.PhenoTipsTokenAuthenticatorScriptService.java

/**
 * Check if the specified token is valid for the specified user.
 *
 * @param username the username whose authentication to check
 * @param token the token to check/*from www.j  a  v  a  2 s  . c o m*/
 * @return {@code true} if the token is valid for the user, {@code false} otherwise
 */
public boolean isTokenValid(String username, String token) {
    XWikiContext context = (XWikiContext) this.execution.getContext()
            .getProperty(XWikiContext.EXECUTIONCONTEXT_KEY);

    // First check if the token is valid on LIMS
    LimsAuthentication limsAuth = (LimsAuthentication) context.getRequest().getSession()
            .getAttribute(Lims247AuthServiceImpl.SESSION_KEY);
    if (limsAuth != null && StringUtils.equals(limsAuth.getToken(), token)
            && StringUtils.equals(StringUtils.substringAfter(limsAuth.getUser().getUser(), "."), username)) {
        return true;
    }
    DocumentReference previousUserReference = context.getUserReference();

    // Check if the token is valid in PhenoTips
    boolean result = false;
    try {
        DocumentReference ref = new DocumentReference(context.getDatabase(), "XWiki", username);
        context.setUserReference(ref);
        result = this.token.isTokenValid(token);
        if (!result) {
            ref = ref.replaceParent(ref.getWikiReference(), new WikiReference("xwiki"));
            context.setUserReference(ref);
            result = this.token.isTokenValid(token);
        }
    } finally {
        context.setUserReference(previousUserReference);
    }
    return result;
}

From source file:org.phenotips.ontology.internal.solr.MendelianInheritanceInMan.java

@Override
public OntologyTerm getTerm(String id) {
    OntologyTerm result = super.getTerm(id);
    if (result == null) {
        String optionalPrefix = STANDARD_NAME + ":";
        if (StringUtils.startsWith(id, optionalPrefix)) {
            result = getTerm(StringUtils.substringAfter(id, optionalPrefix));
        }//from w ww  .jav  a  2 s.c o m
    }
    return result;
}

From source file:org.phenotips.oo.OmimSourceParser.java

private void loadField(String name, String value) {
    if (StringUtils.isAnyBlank(name, value)) {
        return;//from w  w w  .  j av a2 s  .c o  m
    }
    switch (name) {
    case FIELD_MIM_NUMBER:
        this.crtTerm.addField(ID_FIELD, value);
        break;
    case FIELD_TITLE:
        String title = StringUtils.substringBefore(value, TITLE_SEPARATOR).trim();
        String[] synonyms = StringUtils.split(StringUtils.substringAfter(value, TITLE_SEPARATOR),
                TITLE_SEPARATOR);
        this.crtTerm.addField(NAME_FIELD, title);
        for (String synonym : synonyms) {
            this.crtTerm.addField(SYNONYM_FIELD, synonym.trim());
        }
        break;
    case FIELD_TEXT:
        this.crtTerm.addField("def", value);
        break;
    default:
        return;
    }
}

From source file:org.phenotips.vocabulary.internal.GeneNomenclature.java

@Override
public VocabularyTerm getTerm(String symbol) {
    if (StringUtils.isBlank(symbol)) {
        return null;
    }//w  ww  .  j a  v  a 2 s. c om

    String escapedSymbol = ClientUtils.escapeQueryChars(
            StringUtils.contains(symbol, ":") ? StringUtils.substringAfter(symbol, ":") : symbol);

    VocabularyTerm result = getTermById(escapedSymbol);
    if (result != null) {
        return result;
    }
    result = getTermBySymbolOrAlias(escapedSymbol);
    if (result != null) {
        return result;
    }
    result = getTermByAlternativeId(escapedSymbol);
    return result;
}

From source file:org.phenotips.vocabulary.internal.solr.AbstractOWLSolrVocabulary.java

/**
 * If the {@code id} stats with the optional prefix, removes the prefix and performs the search again.
 *
 * @param id the ID of the term of interest
 * @return the {@link VocabularyTerm} corresponding with the given ID, null if no such {@link VocabularyTerm} exists
 *///  ww w  .j  ava 2s  .  co  m
private VocabularyTerm searchTermWithoutPrefix(@Nonnull final String id) {
    final String optPrefix = this.getTermPrefix() + SEPARATOR;
    return StringUtils.startsWith(id.toUpperCase(), optPrefix.toUpperCase())
            ? getTerm(StringUtils.substringAfter(id, SEPARATOR))
            : null;
}