Examples with Document com.forgerock.openbanking.common.model.openbanking.obie.pain00200109.Document used on opensource projects

Example 66 with Document

use of com.forgerock.openbanking.common.model.openbanking.obie.pain00200109.Document in project goobi-workflow by intranda.

the class MetadataUtils method extractMetadataFromFile.

private static void extractMetadataFromFile(Path metsPath, RestProcess p, Map<String, Map<String, String>> labelMap, SearchRequest req) {
    if (!Files.exists(metsPath)) {
        return;
    }
    Document doc;
    try (InputStream in = Files.newInputStream(metsPath)) {
        doc = builder.build(in);
    } catch (JDOMException | IOException e) {
        log.error(e);
        return;
    }
    for (Element el : authorityMetaXpath.evaluate(doc)) {
        RestMetadata meta = new RestMetadata();
        String name = el.getAttributeValue("name");
        if (req.getWantedFields() != null && !req.getWantedFields().contains(name)) {
            continue;
        }
        String type = el.getAttributeValue("type");
        if ("person".equals(type)) {
            meta.setValue(el.getChildText("displayName", goobiNamespace));
        } else {
            meta.setValue(el.getText());
        }
        meta.setAuthorityID(el.getChildText("authorityID", goobiNamespace));
        meta.setAuthorityURI(el.getChildText("authorityURI", goobiNamespace));
        meta.setAuthorityValue(el.getChildText("authorityValue", goobiNamespace));
        meta.setLabels(labelMap.get(name));
        p.addMetadata(name, meta);
    }
}

Example 67 with Document

use of com.forgerock.openbanking.common.model.openbanking.obie.pain00200109.Document in project goobi-workflow by intranda.

the class SRUClient method getResponseObject.

/**
 * <p>
 * Parse an XML String response and populate a response Object.
 * </p>
 *
 * @param xmlData The XML String returned from the search
 * @return SRUResponse An instantiated response object
 */
public SRUResponse getResponseObject(String xmlData) {
    // Parsing
    Document xmlResponse = parseXml(xmlData);
    if (xmlResponse == null) {
        log.error("Can't get results after XML parsing failed.");
        return null;
    }
    // Processing
    SRUResponse response = null;
    try {
        response = new SRUResponse(xmlResponse);
    } catch (JDOMException ex) {
        log.error("Error processing XML response:", ex);
    }
    return response;
}

Example 68 with Document

use of com.forgerock.openbanking.common.model.openbanking.obie.pain00200109.Document in project webin-cli by enasequence.

the class ReadsXmlWriter method createRunXml.

String createRunXml(ReadsManifest manifest, String submissionTitle, String submissionAlias, String centerName, Path inputDir, Path uploadDir) {
    try {
        String title = submissionTitle;
        Element runSetE = new Element("RUN_SET");
        Element runE = new Element("RUN");
        runSetE.addContent(runE);
        Document doc = new Document(runSetE);
        runE.setAttribute("alias", submissionAlias);
        if (null != centerName && !centerName.isEmpty()) {
            runE.setAttribute("center_name", centerName);
        }
        runE.addContent(new Element("TITLE").setText(title));
        Element experimentRefE = new Element("EXPERIMENT_REF");
        runE.addContent(experimentRefE);
        experimentRefE.setAttribute("refname", submissionAlias);
        Element dataBlockE = new Element("DATA_BLOCK");
        runE.addContent(dataBlockE);
        Element filesE = new Element("FILES");
        dataBlockE.addContent(filesE);
        manifest.files(FileType.BAM).stream().map(file -> file.getFile().toPath()).forEach(file -> filesE.addContent(createFileElement(inputDir, uploadDir, file, "bam", null)));
        manifest.files(FileType.CRAM).stream().map(file -> file.getFile().toPath()).forEach(file -> filesE.addContent(createFileElement(inputDir, uploadDir, file, "cram", null)));
        manifest.files(FileType.FASTQ).stream().forEach(file -> filesE.addContent(createFileElement(inputDir, uploadDir, file.getFile().toPath(), "fastq", file.getAttributes())));
        Element runAttributesE = new Element("RUN_ATTRIBUTES");
        if (manifest.getSubmissionTool() != null && !manifest.getSubmissionTool().isEmpty()) {
            Element submissionToolRunAttributeTagE = new Element("TAG").setText("SUBMISSION_TOOL");
            Element submissionToolRunAttributeValueE = new Element("VALUE").setText(manifest.getSubmissionTool());
            Element submissionToolRunAttributeE = new Element("RUN_ATTRIBUTE");
            submissionToolRunAttributeE.addContent(submissionToolRunAttributeTagE);
            submissionToolRunAttributeE.addContent(submissionToolRunAttributeValueE);
            runAttributesE.addContent(submissionToolRunAttributeE);
        }
        if (manifest.getSubmissionToolVersion() != null && !manifest.getSubmissionToolVersion().isEmpty()) {
            Element submissionToolVersionRunAttributeTagE = new Element("TAG").setText("SUBMISSION_TOOL_VERSION");
            Element submissionToolVersionRunAttributeValueE = new Element("VALUE").setText(manifest.getSubmissionToolVersion());
            Element submissionToolVersionRunAttributeE = new Element("RUN_ATTRIBUTE");
            submissionToolVersionRunAttributeE.addContent(submissionToolVersionRunAttributeTagE);
            submissionToolVersionRunAttributeE.addContent(submissionToolVersionRunAttributeValueE);
            runAttributesE.addContent(submissionToolVersionRunAttributeE);
        }
        if (runAttributesE.getContentSize() > 0) {
            runE.addContent(runAttributesE);
        }
        XMLOutputter xmlOutput = new XMLOutputter();
        xmlOutput.setFormat(Format.getPrettyFormat());
        StringWriter stringWriter = new StringWriter();
        xmlOutput.output(doc, stringWriter);
        return stringWriter.toString();
    } catch (IOException ex) {
        throw WebinCliException.systemError(ex);
    }
}

Example 69 with Document

use of com.forgerock.openbanking.common.model.openbanking.obie.pain00200109.Document in project webin-cli by enasequence.

the class ReadsXmlWriter method createExperimentXml.

private String createExperimentXml(ReadsManifest manifest, ReadsValidationResponse response, String submissionTitle, String submissionAlias, String centerName) {
    String instrument = manifest.getInstrument();
    String description = StringUtils.isBlank(manifest.getDescription()) ? "unspecified" : manifest.getDescription();
    String libraryStrategy = manifest.getLibraryStrategy();
    String librarySource = manifest.getLibrarySource();
    String librarySelection = manifest.getLibrarySelection();
    String libraryName = manifest.getLibraryName();
    String platform = manifest.getPlatform();
    Integer insertSize = manifest.getInsertSize();
    try {
        String title = submissionTitle;
        Element experimentSetE = new Element("EXPERIMENT_SET");
        Element experimentE = new Element("EXPERIMENT");
        experimentSetE.addContent(experimentE);
        Document doc = new Document(experimentSetE);
        experimentE.setAttribute("alias", submissionAlias);
        if (null != centerName && !centerName.isEmpty()) {
            experimentE.setAttribute("center_name", centerName);
        }
        experimentE.addContent(new Element("TITLE").setText(title));
        Element studyRefE = new Element("STUDY_REF");
        experimentE.addContent(studyRefE);
        if (manifest.getStudy() != null) {
            studyRefE.setAttribute("accession", manifest.getStudy().getBioProjectId());
        }
        Element designE = new Element("DESIGN");
        experimentE.addContent(designE);
        Element designDescriptionE = new Element("DESIGN_DESCRIPTION");
        designDescriptionE.setText(description);
        designE.addContent(designDescriptionE);
        Element sampleDescriptorE = new Element("SAMPLE_DESCRIPTOR");
        if (manifest.getStudy() != null) {
            sampleDescriptorE.setAttribute("accession", manifest.getSample().getBioSampleId());
        }
        designE.addContent(sampleDescriptorE);
        Element libraryDescriptorE = new Element("LIBRARY_DESCRIPTOR");
        designE.addContent(libraryDescriptorE);
        if (null != libraryName) {
            Element libraryNameE = new Element("LIBRARY_NAME");
            libraryNameE.setText(libraryName);
            libraryDescriptorE.addContent(libraryNameE);
        }
        Element libraryStrategyE = new Element("LIBRARY_STRATEGY");
        libraryStrategyE.setText(libraryStrategy);
        libraryDescriptorE.addContent(libraryStrategyE);
        Element librarySourceE = new Element("LIBRARY_SOURCE");
        librarySourceE.setText(librarySource);
        libraryDescriptorE.addContent(librarySourceE);
        Element librarySelectionE = new Element("LIBRARY_SELECTION");
        librarySelectionE.setText(librarySelection);
        libraryDescriptorE.addContent(librarySelectionE);
        Element libraryLayoutE = new Element("LIBRARY_LAYOUT");
        if (!response.isPaired()) {
            libraryLayoutE.addContent(new Element("SINGLE"));
        } else {
            Element pairedE = new Element("PAIRED");
            libraryLayoutE.addContent(pairedE);
            if (null != insertSize) {
                pairedE.setAttribute("NOMINAL_LENGTH", String.valueOf(insertSize));
            }
        }
        libraryDescriptorE.addContent(libraryLayoutE);
        Element platformE = new Element("PLATFORM");
        experimentE.addContent(platformE);
        Element platformRefE = new Element(platform);
        platformE.addContent(platformRefE);
        Element instrumentModelE = new Element("INSTRUMENT_MODEL");
        instrumentModelE.setText(instrument);
        platformRefE.addContent(instrumentModelE);
        Element expAttributesE = new Element("EXPERIMENT_ATTRIBUTES");
        if (manifest.getSubmissionTool() != null && !manifest.getSubmissionTool().isEmpty()) {
            Element submissionToolExpAttributeTagE = new Element("TAG").setText("SUBMISSION_TOOL");
            Element submissionToolExpAttributeValueE = new Element("VALUE").setText(manifest.getSubmissionTool());
            Element submissionToolExpAttributeE = new Element("EXPERIMENT_ATTRIBUTE");
            submissionToolExpAttributeE.addContent(submissionToolExpAttributeTagE);
            submissionToolExpAttributeE.addContent(submissionToolExpAttributeValueE);
            expAttributesE.addContent(submissionToolExpAttributeE);
        }
        if (manifest.getSubmissionToolVersion() != null && !manifest.getSubmissionToolVersion().isEmpty()) {
            Element submissionToolVersionExpAttributeTagE = new Element("TAG").setText("SUBMISSION_TOOL_VERSION");
            Element submissionToolVersionExpAttributeValueE = new Element("VALUE").setText(manifest.getSubmissionToolVersion());
            Element submissionToolVersionExpAttributeE = new Element("EXPERIMENT_ATTRIBUTE");
            submissionToolVersionExpAttributeE.addContent(submissionToolVersionExpAttributeTagE);
            submissionToolVersionExpAttributeE.addContent(submissionToolVersionExpAttributeValueE);
            expAttributesE.addContent(submissionToolVersionExpAttributeE);
        }
        if (expAttributesE.getContentSize() > 0) {
            experimentE.addContent(expAttributesE);
        }
        XMLOutputter xmlOutput = new XMLOutputter();
        xmlOutput.setFormat(Format.getPrettyFormat());
        StringWriter stringWriter = new StringWriter();
        xmlOutput.output(doc, stringWriter);
        return stringWriter.toString();
    } catch (IOException ex) {
        throw WebinCliException.systemError(ex);
    }
}

Example 70 with Document

use of com.forgerock.openbanking.common.model.openbanking.obie.pain00200109.Document in project n2o-framework by i-novus-llc.

the class SelectiveUtil method readByPath.

@SuppressWarnings("unchecked")
public static <N> N readByPath(String uri, NamespaceReaderFactory readerFactory) {
    try (InputStream inputStream = FileSystemUtil.getContentAsStream(uri)) {
        SAXBuilder builder = new SAXBuilder();
        Document doc = builder.build(inputStream);
        Element root = doc.getRootElement();
        return (N) readerFactory.produce(root).read(root);
    } catch (JDOMException | IOException e) {
        throw new RuntimeException(e);
    }
}