Example usage for org.apache.commons.lang StringUtils containsIgnoreCase

List of usage examples for org.apache.commons.lang StringUtils containsIgnoreCase

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Introduction

In this page you can find the example usage for org.apache.commons.lang StringUtils containsIgnoreCase.

Prototype

public static boolean containsIgnoreCase(String str, String searchStr)

Source Link

Document

Checks if String contains a search String irrespective of case, handling null.

Usage

From source file:org.isatools.isatab.export.sra.SraExportSampleComponent.java

/**
 * Builds a single SRA sample, working only on the sample description and attributes. This is used by
 * {@link #buildSingleExportedSample(MaterialNode)}.
 *
 * @param sampleNode the ISATAB node about the input material. All the ISATAB material types are considered SRA samples
 *                   (there is a tag "Material Role" that have values like bio-source,sample, extract, etc.)
 * @return an instance of the SRA SAMPLE element.
 *///from w  ww  .  j  av a  2  s . com
private SampleType buildSingleExportedSample(MaterialNode sampleNode) {
    Material sample = sampleNode.getMaterial();

    SampleType xsample = SampleType.Factory.newInstance();
    SAMPLENAME xsampleName = SAMPLENAME.Factory.newInstance();

    xsample.setCenterName(centerName);
    xsample.setBrokerName(brokerName);

    String xsampleDescription = StringUtils.trimToEmpty(sample.getSingleAnnotationValue("description"));

    SAMPLEATTRIBUTES sampleAttrs = SAMPLEATTRIBUTES.Factory.newInstance();

    MaterialRole sampleType = sample.getType();

    if (StringUtils.containsIgnoreCase(sampleType.getAcc(), "sample")) {
        xsample.setAlias(sample.getAcc());

        String sampleName = StringUtils.trimToNull(sample.getName());
        if (sampleName != null) {
            // TODO: Common name is a GeneBank identifier and not supported for the moment
            // xsampleName.setCOMMONNAME ( sampleName );
            xsample.setTITLE(sampleName);

        }
    }

    extractNCBITaxonomyInformation(sample, sampleAttrs, xsampleName);

    // Lookup the sample this sample derives from and and collect all their characteristics. We think it makes sense to
    // do that cause we're not sure the sample members (in a pool) will be taken into account
    // by SRA software recipients. Moreover, we merge together biomaterials that are not samples (extracts,
    // labeled extracts).
    //
    Collection<MaterialNode> backwardNodes = ProcessingUtils.findBackwardMaterialNodes(sampleNode, "", false);
    for (MaterialNode backwardNode : backwardNodes) {
        Material backwardMaterial = backwardNode.getMaterial();

        sampleType = backwardMaterial.getType();
        if (StringUtils.trimToNull(xsample.getAlias()) == null
                && StringUtils.containsIgnoreCase(sampleType.getAcc(), "sample")) {
            xsample.setAlias(backwardMaterial.getAcc());

            String sampleName = StringUtils.trimToNull(backwardMaterial.getName());
            if (sampleName != null) {
                // TODO: Common name is a GeneBank identifier and not supported for the moment
                // xsampleName.setCOMMONNAME ( sampleName );
                //               sampleAttrs.addNewSAMPLEATTRIBUTE ();
                //               sampleAttrs.setSAMPLEATTRIBUTEArray ( sampleAttrs.sizeOfSAMPLEATTRIBUTEArray () - 1, 
                //                  buildSampleAttribute ( "Material Name", sampleName, null )
                //               );
                xsample.setTITLE(sampleName);
            }
        }

        extractNCBITaxonomyInformation(backwardMaterial, sampleAttrs, xsampleName);
    }

    // TODO: should we check that xsample.getAlias () is not null?
    //
    xsample.setSAMPLENAME(xsampleName);

    if (sampleAttrs.sizeOfSAMPLEATTRIBUTEArray() > 0) {
        xsample.setSAMPLEATTRIBUTES(sampleAttrs);
    }

    if (xsampleDescription.length() != 0) {
        xsample.setDESCRIPTION(xsampleDescription);
    }

    return xsample;
}

From source file:org.isatools.isatab.export.sra.SraExportSampleComponent.java

private void extractNCBITaxonomyInformation(Material material, SAMPLEATTRIBUTES sampleAttrs,
        SAMPLENAME xsampleName) {/* w ww  . j a  v  a2  s  .c o m*/
    for (CharacteristicValue cvalue : material.getCharacteristicValues()) {
        AttributeType xattr = characteristicValue2SampleAttr(cvalue);

        boolean isOrganismTag = checkCharacteristicValue(cvalue, "(?i)tax|(?i)organism");

        if (xattr != null) {
            if (!isOrganismTag) {
                sampleAttrs.addNewSAMPLEATTRIBUTE();
                sampleAttrs.setSAMPLEATTRIBUTEArray(sampleAttrs.sizeOfSAMPLEATTRIBUTEArray() - 1, xattr);
            }
        }

        // Set the NCBI term if found. TODO: factorize
        for (OntologyTerm oe : cvalue.getOntologyTerms()) {
            ReferenceSource src = oe.getSource();
            if (src == null) {
                break;
            }
            if ((!StringUtils.containsIgnoreCase(src.getDescription(), "NCBI"))
                    || (!StringUtils.containsIgnoreCase(src.getDescription(), "Taxonomy"))) {
                break;
            }
            String taxon = oe.getAcc();
            if (taxon == null) {
                break;
            }
            try {

                log.info("cvalue.getType().getValue()) = " + cvalue.getType().getValue());

                if (isOrganismTag) {
                    xsampleName.setTAXONID(Integer.parseInt(taxon));
                    xsampleName.setSCIENTIFICNAME(oe.getName());
                }

            } catch (NumberFormatException ex) {
                nonRepeatedMessages.add("Invalid NCBI ID '" + taxon + "', ignoring it");
            }
            break; // Only the first one
        }

    } // for ( cvalue )
}

From source file:org.isatools.isatab.export.sra.SraExportSampleComponent.java

/**
 * Attempts to build an SRA pool, starting from the BII owner's node. It assumes that the owner is a
 * sample and tries to see if left nodes are sample too. If not, or if there is more than one level of
 * pooling (not permitted in SRA), files an error message and returns null.
 * <p/>//from   w w w  .  j  a v a 2s. c o m
 * assay is used just to report user messages.
 */
private Set<SampleType> buildExportedPool(MaterialNode poolOwnerNode, Assay assay) {
    Set<SampleType> result = new HashSet<SampleType>();

    String firstLeftType = null;

    for (MaterialNode leftNode : ProcessingUtils.findBackwardMaterialNodes(poolOwnerNode, "", true)) {
        Material leftMat = leftNode.getMaterial();
        MaterialRole leftTypeTerm = leftMat.getType();
        String leftType = leftTypeTerm.getAcc();
        if (StringUtils.containsIgnoreCase(leftType, "sample")) {
            leftType = "sample";
        } else if (StringUtils.containsIgnoreCase(leftType, "source")) {
            leftType = "source";
        } else {
            String msg = MessageFormat.format(
                    "The assay file of type {0} / {1} for study {2} has biomaterials of type {3}"
                            + " before some sample, this is not valid for the SRA format. Please review the ISATAB/SRA formatting"
                            + " guidelines",
                    assay.getMeasurement().getName(), assay.getTechnologyName(), assay.getStudy().getAcc(),
                    leftTypeTerm.getName());
            nonRepeatedMessages.add(msg);
            log.trace(msg + ". Assay is: " + assay.getAcc());
            return null;
        }
        if (firstLeftType == null) {
            firstLeftType = leftType;
        }

        if ("sample".equals(firstLeftType)) {
            if (!"sample".equals(leftType)) {
                // Should never happen, cause we don't allow gaps, but anyway...
                String msg = MessageFormat.format(
                        "The assay file of type {0} / {1} for study {2} has an experimental graph structure that is not "
                                + "compatible with the SRA format (irregular pooling structure). "
                                + "Please review the ISATAB/SRA formatting guidelines",
                        assay.getMeasurement().getName(), assay.getTechnologyName(), assay.getStudy().getAcc());
                nonRepeatedMessages.add(msg);
                log.trace(msg + ". Assay is: " + assay.getAcc());
                return null;
            }

            Collection<MaterialNode> leftLeftNodes = ProcessingUtils.findBackwardMaterialNodes(leftNode, "",
                    true);
            if (leftLeftNodes.size() == 0) {
                // OK, doesn't have sources, strange, but let's say the left node is a pool member
                result.add(buildSingleExportedSample(leftNode));
                continue;
            }

            MaterialNode leftLeftNode = leftLeftNodes.iterator().next();
            Material leftLeftMaterial = leftLeftNode.getMaterial();
            MaterialRole leftLeftRole = leftLeftMaterial.getType();
            if (!StringUtils.containsIgnoreCase(leftLeftRole.getAcc(), "source")) {
                String msg = MessageFormat.format(
                        "The assay file of type {0} / {1} for study {2} has nested pooled samples, this is not supported by "
                                + "the SRA format. Please review the ISATAB/SRA formatting guidelines",
                        assay.getMeasurement().getName(), assay.getTechnologyName(), assay.getStudy().getAcc());
                nonRepeatedMessages.add(msg);
                log.trace(msg + ". Assay is: " + assay.getAcc());
                return null;
            }

            if (leftLeftNode.getDownstreamProcessings().size() != 0) {
                String msg = MessageFormat.format(
                        "The assay file of type {0} / {1} for study {2} has an experimental graph structure that is not "
                                + "compatible with the SRA format (sources with derived nodes). Please review the ISATAB/SRA "
                                + "formatting guidelines",
                        assay.getMeasurement().getName(), assay.getTechnologyName(), assay.getStudy().getAcc());
                nonRepeatedMessages.add(msg);
                log.trace(msg + ". Assay is: " + assay.getAcc());
                return null;
            }

            // OK, the structure is fine, let's add a new sample
            result.add(buildSingleExportedSample(leftNode));
        } else {
            // It's a source: check we have all sources on the left and that they are the first nodes.
            //
            if (!"source".equals(leftType)) {
                // Should never happen, cause we don't allow gaps, but anyway...
                String msg = MessageFormat.format(
                        "The assay file of type {0} / {1} for study {2} has an experimental graph structure that is not "
                                + "compatible with the SRA format (irregular pooling structure). "
                                + "Please review the ISATAB/SRA formatting guidelines",
                        assay.getMeasurement().getName(), assay.getTechnologyName(), assay.getStudy().getAcc());
                nonRepeatedMessages.add(msg);
                log.trace(msg + ". Assay is: " + assay.getAcc());
                return null;
            }

            if (leftNode.getDownstreamProcessings().size() != 0) {
                String msg = MessageFormat.format(
                        "The assay file of type {0} / {1} for study {2} has an experimental graph structure that is not "
                                + "compatible with the SRA format (sources with derived nodes). "
                                + "Please review the ISATAB/SRA formatting guidelines",
                        assay.getMeasurement().getName(), assay.getTechnologyName(), assay.getStudy().getAcc());
                nonRepeatedMessages.add(msg);
                log.trace(msg + ". Assay is: " + assay.getAcc());
                return null;
            }
        } // if on type cases
    } // for leftNode

    return result;
}

From source file:org.isatools.isatab.mapping.AssayTypeEntries.java

/**
 * @param measurmentTypeLabel/*from  ww  w.  ja va 2s . c o m*/
 * @param technologyTypeLabel
 * @return
 */
public static String getDispatchTargetIdFromLabels(String measurmentTypeLabel, String technologyTypeLabel) {
    measurmentTypeLabel = convertMeasurmentTypeLabel(measurmentTypeLabel);
    technologyTypeLabel = convertTechnologyLabel(technologyTypeLabel);

    // First try with the stuff in the ISA Configuration's Configurator
    //
    IsaTabConfigurationType cfg = isaConfiguratorCfg.getConfig(measurmentTypeLabel, technologyTypeLabel);
    if (cfg != null) {
        String conversionTarget = StringUtils.trimToNull(cfg.getIsatabConversionTarget());
        if (conversionTarget != null) {
            return conversionTarget;
        }
    }

    // TODO: we want to eventually remove the CSV file
    //

    for (String[] entry : getEntries()) {
        if (StringUtils.trimToEmpty(entry[COL_MEASURMENT_LABEL]).equalsIgnoreCase(measurmentTypeLabel)
                && StringUtils.trimToEmpty(entry[COL_TECHNOLOGY_LABEL]).equalsIgnoreCase(technologyTypeLabel)) {
            String dispatchTarget = StringUtils.trimToNull(entry[COL_DISPATCH_ID]);
            if (StringUtils.containsIgnoreCase(dispatchTarget, "New European Nucleotide Archive database")) {
                dispatchTarget = "sra";
            } else if (StringUtils.containsIgnoreCase(dispatchTarget, "ArrayExpress")) {
                dispatchTarget = "magetab";
            } else if (StringUtils.containsIgnoreCase(dispatchTarget, "Pride")) {
                dispatchTarget = "prideml";
            } else if (StringUtils.containsIgnoreCase(dispatchTarget, "BII metabolomic")) {
                dispatchTarget = "meda";
            } else if (StringUtils.containsIgnoreCase(dispatchTarget, "BII conventional assay")) {
                dispatchTarget = "generic";
            }

            return dispatchTarget;
        }
    }
    return null;
}

From source file:org.isatools.isatab.mapping.AssayTypeEntries.java

public static Measurement getMeasurementTypeFromLabel(String label) {
    label = convertMeasurmentTypeLabel(label);

    // First try with what you have in the ISA Configurator Information
    ///*from  w w w  .  j  ava2s .c o m*/
    OntologyEntryType ctype = isaConfiguratorCfg.getMeasurementFromLabel(label);

    if (ctype != null) {
        label = ctype.getTermLabel();
        String acc = StringUtils.trimToNull(ctype.getTermAccession());
        if (acc == null) {
            acc = "NULL-ACCESSION";
        }

        ReferenceSource osrc;
        String sourceAcc = StringUtils.trimToNull(ctype.getSourceAbbreviation());

        if (sourceAcc == null || "obi".equalsIgnoreCase(sourceAcc)) {
            osrc = getOBISource();
        } else {
            osrc = new ReferenceSource(sourceAcc, sourceAcc);
            osrc.setDescription(ctype.getSourceTitle());
            osrc.setUrl(ctype.getSourceTitle());
        }
        return new Measurement(acc, label, osrc);
    }

    for (String[] entry : getEntries()) {
        String epLabel = StringUtils.trimToEmpty(entry[COL_MEASURMENT_LABEL]);
        if (!label.equalsIgnoreCase(epLabel)) {
            continue;
        }

        String acc = StringUtils.trimToEmpty(entry[COL_MEASURMENT_ACC]);
        if (acc.length() == 0 || StringUtils.containsIgnoreCase(acc, "submitted to OBI")
                || StringUtils.containsIgnoreCase(acc, "old terms"))
        // There isn't much else I can do...
        {
            acc = "NULL-ACCESSION";
        }

        return new Measurement(acc, label, getOBISource());
    }
    return null;
}

From source file:org.isatools.isatab.mapping.AssayTypeEntries.java

public static AssayTechnology getAssayTechnologyFromLabel(String label) {
    label = convertTechnologyLabel(label);

    // First try with what you have in the ISA Configurator Information
    ////from   w w  w.j  a  v  a  2  s  .  co  m
    OntologyEntryType ctype = isaConfiguratorCfg.getTechnologyFromLabel(label);

    if (ctype != null) {
        label = ctype.getTermLabel();
        String acc = StringUtils.trimToNull(ctype.getTermAccession());
        if (acc == null) {
            acc = "NULL-ACCESSION";
        }

        ReferenceSource osrc;
        String sourceAcc = StringUtils.trimToNull(ctype.getSourceAbbreviation());

        if (sourceAcc == null || "obi".equalsIgnoreCase(sourceAcc)) {
            osrc = getOBISource();
        } else {
            osrc = new ReferenceSource(sourceAcc, sourceAcc);
            osrc.setDescription(ctype.getSourceTitle());
            osrc.setUrl(ctype.getSourceTitle());
        }
        return new AssayTechnology(acc, label, osrc);
    }

    for (String[] entry : getEntries()) {
        String techLabel = StringUtils.trimToEmpty(entry[COL_TECHNOLOGY_LABEL]);
        if (!label.equalsIgnoreCase(techLabel)) {
            continue;
        }

        String acc = StringUtils.trimToEmpty(entry[COL_TECHNOLOGY_ACC]);
        if (acc.length() == 0 || StringUtils.containsIgnoreCase(acc, "submitted to OBI")
                || StringUtils.containsIgnoreCase(acc, "old terms"))
        // There isn't much else I can do...
        {
            acc = "NULL-ACCESSION";
        }

        return new AssayTechnology(acc, label, getOBISource());
    }

    return null;
}

From source file:org.jahia.test.services.render.JSessionIDTest.java

private void findJSessionId(boolean removeJsessionId) throws IOException {
    SettingsBean.getInstance().setDisableJsessionIdParameter(removeJsessionId);
    SettingsBean.getInstance().setJsessionIdParameterName(jsessionid);

    GetMethod displayLoginMethod = new GetMethod(getBaseServerURL() + Jahia.getContextPath() + "/start");
    try {/*from   ww  w.  j a  v  a  2 s  . c  o  m*/
        int statusCode = httpClient.executeMethod(displayLoginMethod);

        assertEquals("Method failed: " + displayLoginMethod.getStatusLine(), HttpStatus.SC_UNAUTHORIZED,
                statusCode);

        String responseBodyAsString = displayLoginMethod.getResponseBodyAsString();

        Pattern p = Pattern.compile("action=\"([^\"]*)\"");
        Matcher m = p.matcher(responseBodyAsString);
        assertTrue(m.find());

        String url = m.group(1);
        if (!removeJsessionId) {
            logger.info("Unencoded URL: " + getBaseServerURL() + Jahia.getContextPath() + "/start");
            logger.info("Encoded redirect URL: "
                    + getResponse().encodeRedirectURL(getBaseServerURL() + Jahia.getContextPath() + "/start"));
            logger.info("Encoded URL: "
                    + getResponse().encodeURL(getBaseServerURL() + Jahia.getContextPath() + "/start"));
        }

        assertEquals(
                "jsession ID is not " + (removeJsessionId ? "removed" : "present")
                        + " in administration login url:" + url,
                removeJsessionId, !StringUtils.containsIgnoreCase(url, jsessionid));
    } finally {
        displayLoginMethod.releaseConnection();
    }
}

From source file:org.jajuk.util.filters.TestAudioFilter.java

/**
 * Test method for {@link org.jajuk.util.filters.AudioFilter#getDescription()}
 * ./*ww w .  j a v a 2  s.c om*/
 */
public void testGetDescription() {
    StartupCollectionService.registerTypes();
    assertTrue(AudioFilter.getInstance().getDescription(),
            StringUtils.containsIgnoreCase(AudioFilter.getInstance().getDescription(), "mp3"));
    assertTrue(AudioFilter.getInstance().getDescription(),
            StringUtils.containsIgnoreCase(AudioFilter.getInstance().getDescription(), "ogg"));
    // try removing all types
    TypeManager.getInstance().clear();
    assertEquals("", AudioFilter.getInstance().getDescription());
}

From source file:org.jdto.tools.verifiercases.NestedIncorrectVerifierCase.java

@Override
public void test(List<Diagnostic<? extends JavaFileObject>> diagnostics, String stdoutS, Boolean result) {

    //in this case we should have a compilation error saying that annotation has no effect on setters.

    for (Diagnostic<? extends JavaFileObject> diagnostic : diagnostics) {
        if (diagnostic.getKind() == Kind.MANDATORY_WARNING) {

            if (!StringUtils.containsIgnoreCase(diagnostic.getMessage(null), "not found on type")) {
                continue;
            } else {
                //test should succeed.
                return;
            }//from  www. j  a v  a2s  . co  m

        }
    }

    fail("No relevant compilation warning found.");
}

From source file:org.jdto.tools.verifiercases.SetterAnnotatedVerifierCase.java

@Override
public void test(List<Diagnostic<? extends JavaFileObject>> diagnostics, String stdoutS, Boolean result) {

    //in this case we should have a compilation error saying that annotation has no effect on setters.

    for (Diagnostic<? extends JavaFileObject> diagnostic : diagnostics) {
        if (diagnostic.getKind() == Kind.MANDATORY_WARNING) {

            if (!StringUtils.containsIgnoreCase(diagnostic.getMessage(null), "Setter")) {
                continue;
            } else {
                //test should succeed.
                return;
            }//w w w  .  jav  a2  s .  com

        }
    }

    fail("A warning saying that setters mustn't be annotated should have been printed.");
}