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

Introduction

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

Prototype

public static String removeEnd(final String str, final String remove) 

Source Link

Document

Removes a substring only if it is at the end of a source string, otherwise returns the source string.

A null source string will return null .

Usage

From source file:org.yamj.core.service.metadata.online.SearchEngineToolsTest.java

@Test
public void roundTripIMDB() {
    LOG.info("roundTripIMDB");
    SearchEngineTools search = new SearchEngineTools(httpClient);

    // movie/*from   ww w. j a v a2  s  .c  o m*/
    for (int i = 0; i < search.countSearchSites(); i++) {
        String engine = search.getCurrentSearchEngine();
        LOG.info("Testing " + engine);
        String url = search.searchURL("Avatar", 2009, "www.imdb.com/title", false);
        url = StringUtils.removeEnd(url, "/");
        assertEquals("Search engine '" + engine + "' failed", "http://www.imdb.com/title/tt0499549", url);
    }

    // TV show, must leave out the year and search for TV series
    for (int i = 0; i < search.countSearchSites(); i++) {
        String engine = search.getCurrentSearchEngine();
        LOG.info("Testing " + engine);
        String url = search.searchURL("Two and a Half Men", -1, "www.imdb.com/title", "TV series", false);
        url = StringUtils.removeEnd(url, "/");
        assertEquals("Search engine '" + engine + "' failed", "http://www.imdb.com/title/tt0369179", url);
    }
}

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From source file:org.zanata.util.GlossaryUtil.java

/**
 * Generate qualifiedName from namespace and name.
 * e.g project/zanata, global/default//from  www .j a v a2s  .  c o m
 *
 * {@link QUALIFIED_NAME_SEPARATOR} at the end of namespace will be removed.
 */
public static String generateQualifiedName(String namespace, String name) {
    String processedNamespace = StringUtils.removeEnd(namespace, QUALIFIED_NAME_SEPARATOR);
    return processedNamespace + QUALIFIED_NAME_SEPARATOR + name;
}

---

From source file:pcgen.system.PluginClassLoader.java

private void loadClasses(final File pluginJar) throws IOException {
    try (JarClassLoader loader = new JarClassLoader(pluginJar.toURI().toURL());
            ZipFile file = new ZipFile(pluginJar)) {
        final Collection<String> classList = new LinkedList<>();
        Enumeration<? extends ZipEntry> entries = file.entries();
        while (entries.hasMoreElements()) {
            ZipEntry entry = entries.nextElement();
            String name = entry.getName();
            if (!name.endsWith(".class")) {
                continue;
            }/*w  w  w.j a v a  2  s. c o  m*/
            name = StringUtils.removeEnd(name, ".class").replace('/', '.');
            int size = (int) entry.getSize();
            byte[] buffer = new byte[size];

            InputStream in = file.getInputStream(entry);
            int rb = 0;
            int chunk;
            while ((size - rb) > 0) {
                chunk = in.read(buffer, rb, size - rb);
                if (chunk == -1) {
                    break;
                }
                rb += chunk;
            }
            in.close();
            loader.storeClassDef(name, buffer);
            classList.add(name);
        }
        file.close();
        /*
         * Loading files and loading classes can both be lengthy processes. This splits the tasks
         * so that class loading occurs in another thread thus allowing both processes to
         * operate at the same time.
         */
        dispatcher.execute(new Runnable() {

            @Override
            public void run() {
                boolean pluginFound = false;
                for (final String string : classList) {
                    try {
                        pluginFound |= processClass(Class.forName(string, true, loader));
                    } catch (ClassNotFoundException | NoClassDefFoundError ex) {
                        Logging.errorPrint("Error occurred while loading plugin: " + pluginJar.getName(), ex);
                    }
                }
                if (!pluginFound) {
                    Logging.log(Logging.WARNING, "Plugin not found in " + pluginJar.getName());
                }
                progress++;
                setProgress(progress);
            }

        });
    }
}

---

From source file:se.trixon.jota.client.ui.editor.module.task.TaskSourceDestPanel.java

private void noAdditionalDirUpdate(boolean selected) {
    String path = sourcePanel.getPath();

    while (path.endsWith("/")) {
        path = StringUtils.removeEnd(path, "/");
    }//from  w  w  w  .  j a v  a 2s .com

    if (selected) {
        path = StringUtils.appendIfMissing(path, "/");
    }

    sourcePanel.setPath(path);
}

---

From source file:tectonicus.blockTypes.BlockRegistry.java

public void deserializeBlockstates() {
    List<BlockVariant> blockVariants = new ArrayList<>();

    Enumeration<? extends ZipEntry> entries = zips.getBaseEntries();
    while (entries.hasMoreElements()) {
        ZipEntry entry = entries.nextElement();
        String entryName = entry.getName();
        if (entryName.contains("blockstates")) {
            ZipStackEntry zse = zips.getEntry(entryName);
            try {
                JSONObject obj = new JSONObject(FileUtils.loadJSON(zse.getInputStream()));
                JSONObject variants = obj.getJSONObject("variants");

                Iterator<?> keys = variants.keys();
                while (keys.hasNext()) {
                    String key = (String) keys.next();
                    Object variant = variants.get(key);

                    blockVariants.add(BlockVariant.deserializeVariant(key, variant));
                }/*from w w  w. j  a  v  a 2 s .c o m*/
            } catch (Exception e) {
                e.printStackTrace();
            }

            String name = "minecraft:"
                    + StringUtils.removeEnd(entryName.substring(entryName.lastIndexOf("/") + 1), ".json");
            blockStates.put(name, blockVariants);
        }
    }
}

---

From source file:ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl.java

@Override
public ExperimentalFactorValueObject configExperimentalFactorValueObject(ExperimentalFactor ef) {
    ExperimentalFactorValueObject efvo = new ExperimentalFactorValueObject(ef.getId());
    efvo.setName(ef.getName());/*from   ww w. j  av  a2 s .co  m*/
    efvo.setDescription(ef.getDescription());
    Characteristic category = ef.getCategory();
    if (category != null) {
        efvo.setCategory(category.getCategory());
        efvo.setCategoryUri(category.getCategoryUri());
    }
    Collection<FactorValue> fvs = ef.getFactorValues();
    StringBuilder factorValuesAsString = new StringBuilder(StringUtils.EMPTY);

    for (FactorValue fv : fvs) {
        String fvName = fv.toString();
        if (StringUtils.isNotBlank(fvName)) {
            factorValuesAsString.append(fvName).append(GeneDifferentialExpressionServiceImpl.FV_SEP);
        }
    }

    /* clean up the start and end of the string */
    factorValuesAsString = new StringBuilder(
            StringUtils.remove(factorValuesAsString.toString(), ef.getName() + ":"));
    factorValuesAsString = new StringBuilder(StringUtils.removeEnd(factorValuesAsString.toString(),
            GeneDifferentialExpressionServiceImpl.FV_SEP));

    /*
     * Preformat the factor name; due to Ext PropertyGrid limitations we can't do this on the client.
     */
    efvo.setName(ef.getName() + " (" + StringUtils.abbreviate(factorValuesAsString.toString(), 50) + ")");

    efvo.setFactorValues(factorValuesAsString.toString());
    return efvo;
}

---

From source file:ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl.java

private void generateDatasetView(Integer limit, Collection<ExpressionExperiment> experiments)
        throws IOException {

    DatabaseViewGeneratorImpl.log.info("Generating dataset summary view");

    /*/*from   w  w  w  .j  a va 2  s.  c  om*/
     * Get handle to output file
     */
    File file = this.getViewFile(DatabaseViewGeneratorImpl.DATASET_SUMMARY_VIEW_BASENAME);
    DatabaseViewGeneratorImpl.log.info("Writing to " + file);
    try (Writer writer = new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file)))) {

        writer.write("GemmaDsId\tSource\tSourceAccession\tShortName\tName\tDescription\ttaxon\tManufacturer\n");

        /*
         * Print out their names etc.
         */
        int i = 0;
        for (ExpressionExperiment ee : experiments) {
            ee = expressionExperimentService.thawLite(ee);
            DatabaseViewGeneratorImpl.log.info("Processing: " + ee.getShortName());

            String acc = "";
            String source = "";

            if (ee.getAccession() != null && ee.getAccession().getAccession() != null) {
                acc = ee.getAccession().getAccession();
                source = ee.getAccession().getExternalDatabase().getName();
            }

            Long gemmaId = ee.getId();
            String shortName = ee.getShortName();
            String name = ee.getName();
            String description = ee.getDescription();
            description = StringUtils.replaceChars(description, '\t', ' ');
            description = StringUtils.replaceChars(description, '\n', ' ');
            description = StringUtils.replaceChars(description, '\r', ' ');

            Taxon taxon = expressionExperimentService.getTaxon(ee);

            if (taxon == null)
                continue;

            Collection<ArrayDesign> ads = expressionExperimentService.getArrayDesignsUsed(ee);
            StringBuilder manufacturers = new StringBuilder();

            // TODO could cache the arrayDesigns to make faster, thawing ad is time consuming
            for (ArrayDesign ad : ads) {
                ad = arrayDesignService.thawLite(ad);
                if (ad.getDesignProvider() == null) {
                    DatabaseViewGeneratorImpl.log.debug("Array Design: " + ad.getShortName()
                            + " has no design provoider assoicated with it. Skipping");
                    continue;
                }
                manufacturers.append(ad.getDesignProvider().getName()).append(",");
            }

            writer.write(String.format("%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", gemmaId, source, acc, shortName,
                    name, description, taxon.getCommonName(),
                    StringUtils.removeEnd(manufacturers.toString(), ",")));

            if (limit != null && (limit > 0 && ++i > limit))
                break;

        }

    }
}

---

From source file:ubic.gemma.core.analysis.report.DatabaseViewGeneratorImpl.java

private void generateDifferentialExpressionView(Integer limit, Collection<ExpressionExperiment> experiments)
        throws IOException {
    DatabaseViewGeneratorImpl.log.info("Generating dataset diffex view");

    /*// w  w  w.  j  ava 2 s.  c  om
     * Get handle to output file
     */
    File file = this.getViewFile(DatabaseViewGeneratorImpl.DATASET_DIFFEX_VIEW_BASENAME);
    DatabaseViewGeneratorImpl.log.info("Writing to " + file);
    try (Writer writer = new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file)))) {

        /*
         * For each gene that is differentially expressed, print out a line per contrast
         */
        writer.write(
                "GemmaDsId\tEEShortName\tGeneNCBIId\tGemmaGeneId\tFactor\tFactorURI\tBaseline\tContrasting\tDirection\n");
        int i = 0;
        for (ExpressionExperiment ee : experiments) {
            ee = expressionExperimentService.thawLite(ee);

            Collection<DifferentialExpressionAnalysis> results = differentialExpressionAnalysisService
                    .getAnalyses(ee);
            if (results == null || results.isEmpty()) {
                DatabaseViewGeneratorImpl.log.warn("No differential expression results found for " + ee);
                continue;
            }

            //noinspection StatementWithEmptyBody // FIXME. Should probably skip for this purpose.
            if (results.size() > 1) {
            }

            DatabaseViewGeneratorImpl.log.info("Processing: " + ee.getShortName());

            for (DifferentialExpressionAnalysis analysis : results) {

                analysis = this.differentialExpressionAnalysisService.thawFully(analysis);

                for (ExpressionAnalysisResultSet ears : analysis.getResultSets()) {

                    // ears = differentialExpressionResultService.thawRawAndProcessed( ears );

                    FactorValue baselineGroup = ears.getBaselineGroup();

                    if (baselineGroup == null) {
                        // log.warn( "No baseline defined for " + ee ); // interaction
                        continue;
                    }

                    if (ExperimentalDesignUtils.isBatch(baselineGroup.getExperimentalFactor())) {
                        continue;
                    }

                    String baselineDescription = ExperimentalDesignUtils.prettyString(baselineGroup);

                    // Get the factor category name
                    StringBuilder factorName = new StringBuilder();
                    StringBuilder factorURI = new StringBuilder();

                    for (ExperimentalFactor ef : ears.getExperimentalFactors()) {
                        factorName.append(ef.getName()).append(",");
                        if (StringUtils.isNotBlank(ef.getCategory().getCategoryUri())) {
                            factorURI.append(ef.getCategory().getCategoryUri()).append(",");
                        }
                    }
                    factorName = new StringBuilder(StringUtils.removeEnd(factorName.toString(), ","));
                    factorURI = new StringBuilder(StringUtils.removeEnd(factorURI.toString(), ","));

                    if (ears.getResults() == null || ears.getResults().isEmpty()) {
                        DatabaseViewGeneratorImpl.log
                                .warn("No  differential expression analysis results found for " + ee);
                        continue;
                    }

                    // Generate probe details
                    for (DifferentialExpressionAnalysisResult dear : ears.getResults()) {

                        if (dear == null) {
                            DatabaseViewGeneratorImpl.log
                                    .warn("Missing results for " + ee + " skipping to next. ");
                            continue;
                        }

                        if (dear.getCorrectedPvalue() == null
                                || dear.getCorrectedPvalue() > DatabaseViewGeneratorImpl.THRESH_HOLD)
                            continue;

                        String formatted = this.formatDiffExResult(ee, dear, factorName.toString(),
                                factorURI.toString(), baselineDescription);

                        if (StringUtils.isNotBlank(formatted))
                            writer.write(formatted);

                    } // dear loop
                } // ears loop
            } // analysis loop

            if (limit != null && (limit > 0 && ++i > limit))
                break;

        } // EE loop
    }
}

---

From source file:ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl.java

@Override
public List<DifferentialExpressionAnalysisResult> analysisResultSetToString(ExpressionAnalysisResultSet ears,
        Map<Long, String[]> geneAnnotations, StringBuilder buf, Map<Long, StringBuilder> probe2String,
        List<DifferentialExpressionAnalysisResult> sortedFirstColumnOfResults) {

    if (sortedFirstColumnOfResults == null) { // Sort P values in ears (because 1st column)
        sortedFirstColumnOfResults = new ArrayList<>(ears.getResults());
        Collections.sort(sortedFirstColumnOfResults,
                DifferentialExpressionAnalysisResultComparator.Factory.newInstance());
    }// www .  jav  a2s .co  m

    // Generate a description of the factors involved "factor1_factor2", trying to be R-friendly
    StringBuilder factorColumnName = new StringBuilder();
    for (ExperimentalFactor ef : ears.getExperimentalFactors()) {
        factorColumnName.append(ef.getName().replaceAll("\\s+", "_")).append("_");
    }
    factorColumnName = new StringBuilder(
            StringUtil.makeValidForR(StringUtils.removeEnd(factorColumnName.toString(), "_")));

    // Generate headers
    buf.append("\tQValue_").append(factorColumnName);
    buf.append("\tPValue_").append(factorColumnName);

    // Generate probe details
    for (DifferentialExpressionAnalysisResult dear : ears.getResults()) {
        StringBuilder probeBuffer = new StringBuilder();

        CompositeSequence cs = dear.getProbe();

        // Make a hashMap so we can organize the data by probe with factors as columns
        // Need to cache the information until we have it organized in the correct format to write
        Long csid = cs.getId();
        if (probe2String.containsKey(csid)) {
            probeBuffer = probe2String.get(csid);
        } else {// no entry for probe yet
            probeBuffer.append(cs.getName());
            if (geneAnnotations.containsKey(csid)) {
                String[] annotationStrings = geneAnnotations.get(csid);
                /*
                 * Fields:
                 *
                 * 1: gene symbols
                 * 2: gene name
                 * 4: ncbi ID
                 */
                probeBuffer.append("\t").append(annotationStrings[1]).append("\t").append(annotationStrings[2])
                        .append("\t").append(annotationStrings[4]);
            } else {
                probeBuffer.append("\t\t\t");
            }

            probe2String.put(csid, probeBuffer);
        }

        Double correctedPvalue = dear.getCorrectedPvalue();
        Double pvalue = dear.getPvalue();

        String formattedCP = correctedPvalue == null ? ""
                : String.format(ExpressionDataFileServiceImpl.DECIMAL_FORMAT, correctedPvalue);
        String formattedP = pvalue == null ? ""
                : String.format(ExpressionDataFileServiceImpl.DECIMAL_FORMAT, pvalue);
        probeBuffer.append("\t").append(formattedCP).append("\t").append(formattedP);

    }
    return sortedFirstColumnOfResults;

}

---

From source file:ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl.java

private String getFactorValueString(FactorValue fv) {
    String result;/*from  w  ww . j ava  2s.  co  m*/
    if (fv == null)
        return "null";

    if (fv.getCharacteristics() != null && fv.getCharacteristics().size() > 0) {
        StringBuilder fvString = new StringBuilder();
        for (Characteristic c : fv.getCharacteristics()) {
            fvString.append(c.getValue()).append("_");
        }
        result = StringUtils.removeEnd(fvString.toString(), "_");
    } else if (fv.getMeasurement() != null) {
        result = fv.getMeasurement().getValue();
    } else if (fv.getValue() != null && !fv.getValue().isEmpty()) {
        result = fv.getValue();
    } else
        return "no_data";

    // R-friendly, but no need to add "X" to the beginning since this is a suffix.
    return result.replaceAll("[\\W]+", ".");
}

---

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