Examples with InvalidFormatException org.apache.poi.openxml4j.exceptions.InvalidFormatException used on opensource projects

Example 31 with InvalidFormatException

use of org.apache.poi.openxml4j.exceptions.InvalidFormatException in project goci by EBISPOT.

the class AssociationFileUploadService method processAndValidateAssociationFile.

/**
     * Process uploaded file and return a list of errors
     *
     * @param file XLSX file supplied by user
     */
public ValidationSummary processAndValidateAssociationFile(File file, String validationLevel) throws FileNotFoundException, SheetProcessingException {
    ValidationSummary validationSummary = new ValidationSummary();
    Collection<RowValidationSummary> rowValidationSummaries = new ArrayList<>();
    Collection<AssociationSummary> associationSummaries = new ArrayList<>();
    Collection<AssociationUploadRow> fileRows = new ArrayList<>();
    if (file.exists()) {
        // Create sheet
        XSSFSheet sheet = null;
        try {
            // Create a sheet for reading
            sheet = sheetCreationService.createSheet(file.getAbsolutePath());
            // Process file, depending on validation level, into a generic row object
            UploadSheetProcessor uploadSheetProcessor = uploadSheetProcessorBuilder.buildProcessor(validationLevel);
            fileRows = uploadSheetProcessor.readSheetRows(sheet);
        } catch (InvalidFormatException | InvalidOperationException | IOException e) {
            getLog().error("File: " + file.getName() + " cannot be processed", e);
            file.delete();
            throw new SheetProcessingException("File: " + file.getName() + " cannot be processed", e);
        }
    } else {
        getLog().error("File: " + file.getName() + " cannot be found");
        throw new FileNotFoundException("File does not exist");
    }
    String eRelease = ensemblRestTemplateService.getRelease();
    // Error check each row
    if (!fileRows.isEmpty()) {
        // Check for missing values and syntax errors that would prevent code creating an association
        for (AssociationUploadRow row : fileRows) {
            getLog().info("Syntax checking row: " + row.getRowNumber() + " of file, " + file.getAbsolutePath());
            RowValidationSummary rowValidationSummary = createRowValidationSummary(row, eRelease);
            // Only store summary if there is an error
            if (!rowValidationSummary.getErrors().isEmpty()) {
                rowValidationSummaries.add(rowValidationSummary);
            }
        }
        if (rowValidationSummaries.isEmpty()) {
            //Proceed to carry out full checks of values
            fileRows.forEach(row -> {
                associationSummaries.add(createAssociationSummary(row, validationLevel, eRelease));
            });
        }
    } else {
        getLog().error("Parsing file failed");
    }
    validationSummary.setAssociationSummaries(associationSummaries);
    validationSummary.setRowValidationSummaries(rowValidationSummaries);
    return validationSummary;
}

Example 32 with InvalidFormatException

use of org.apache.poi.openxml4j.exceptions.InvalidFormatException in project poi by apache.

the class XWPFDocument method initHyperlinks.

private void initHyperlinks() {
    // TODO: make me optional/separated in private function
    try {
        Iterator<PackageRelationship> relIter = getPackagePart().getRelationshipsByType(XWPFRelation.HYPERLINK.getRelation()).iterator();
        while (relIter.hasNext()) {
            PackageRelationship rel = relIter.next();
            hyperlinks.add(new XWPFHyperlink(rel.getId(), rel.getTargetURI().toString()));
        }
    } catch (InvalidFormatException e) {
        throw new POIXMLException(e);
    }
}

Example 33 with InvalidFormatException

use of org.apache.poi.openxml4j.exceptions.InvalidFormatException in project poi by apache.

the class SignatureInfo method writeDocument.

/**
     * Write XML signature into the OPC package
     *
     * @param document the xml signature document
     * @throws MarshalException
     */
protected void writeDocument(Document document) throws MarshalException {
    XmlOptions xo = new XmlOptions();
    Map<String, String> namespaceMap = new HashMap<String, String>();
    for (Map.Entry<String, String> entry : signatureConfig.getNamespacePrefixes().entrySet()) {
        namespaceMap.put(entry.getValue(), entry.getKey());
    }
    xo.setSaveSuggestedPrefixes(namespaceMap);
    xo.setUseDefaultNamespace();
    LOG.log(POILogger.DEBUG, "output signed Office OpenXML document");
    /*
         * Copy the original OOXML content to the signed OOXML package. During
         * copying some files need to changed.
         */
    OPCPackage pkg = signatureConfig.getOpcPackage();
    PackagePartName sigPartName, sigsPartName;
    try {
        // <Override PartName="/_xmlsignatures/sig1.xml" ContentType="application/vnd.openxmlformats-package.digital-signature-xmlsignature+xml"/>
        sigPartName = PackagingURIHelper.createPartName("/_xmlsignatures/sig1.xml");
        // <Default Extension="sigs" ContentType="application/vnd.openxmlformats-package.digital-signature-origin"/>
        sigsPartName = PackagingURIHelper.createPartName("/_xmlsignatures/origin.sigs");
    } catch (InvalidFormatException e) {
        throw new MarshalException(e);
    }
    PackagePart sigPart = pkg.getPart(sigPartName);
    if (sigPart == null) {
        sigPart = pkg.createPart(sigPartName, ContentTypes.DIGITAL_SIGNATURE_XML_SIGNATURE_PART);
    }
    try {
        OutputStream os = sigPart.getOutputStream();
        SignatureDocument sigDoc = SignatureDocument.Factory.parse(document, DEFAULT_XML_OPTIONS);
        sigDoc.save(os, xo);
        os.close();
    } catch (Exception e) {
        throw new MarshalException("Unable to write signature document", e);
    }
    PackagePart sigsPart = pkg.getPart(sigsPartName);
    if (sigsPart == null) {
        // touch empty marker file
        sigsPart = pkg.createPart(sigsPartName, ContentTypes.DIGITAL_SIGNATURE_ORIGIN_PART);
    }
    PackageRelationshipCollection relCol = pkg.getRelationshipsByType(PackageRelationshipTypes.DIGITAL_SIGNATURE_ORIGIN);
    for (PackageRelationship pr : relCol) {
        pkg.removeRelationship(pr.getId());
    }
    pkg.addRelationship(sigsPartName, TargetMode.INTERNAL, PackageRelationshipTypes.DIGITAL_SIGNATURE_ORIGIN);
    sigsPart.addRelationship(sigPartName, TargetMode.INTERNAL, PackageRelationshipTypes.DIGITAL_SIGNATURE);
}

Example 34 with InvalidFormatException

use of org.apache.poi.openxml4j.exceptions.InvalidFormatException in project poi by apache.

the class OOXMLSignatureFacet method addManifestReferences.

@SuppressWarnings("resource")
protected void addManifestReferences(List<Reference> manifestReferences) throws XMLSignatureException {
    OPCPackage ooxml = signatureConfig.getOpcPackage();
    List<PackagePart> relsEntryNames = ooxml.getPartsByContentType(ContentTypes.RELATIONSHIPS_PART);
    Set<String> digestedPartNames = new HashSet<String>();
    for (PackagePart pp : relsEntryNames) {
        String baseUri = pp.getPartName().getName().replaceFirst("(.*)/_rels/.*", "$1");
        PackageRelationshipCollection prc;
        try {
            prc = new PackageRelationshipCollection(ooxml);
            prc.parseRelationshipsPart(pp);
        } catch (InvalidFormatException e) {
            throw new XMLSignatureException("Invalid relationship descriptor: " + pp.getPartName().getName(), e);
        }
        RelationshipTransformParameterSpec parameterSpec = new RelationshipTransformParameterSpec();
        for (PackageRelationship relationship : prc) {
            String relationshipType = relationship.getRelationshipType();
            /*
                 * ECMA-376 Part 2 - 3rd edition
                 * 13.2.4.16 Manifest Element
                 * "The producer shall not create a Manifest element that references any data outside of the package."
                 */
            if (TargetMode.EXTERNAL == relationship.getTargetMode()) {
                continue;
            }
            if (!isSignedRelationship(relationshipType))
                continue;
            parameterSpec.addRelationshipReference(relationship.getId());
            // TODO: find a better way ...
            String partName = relationship.getTargetURI().toString();
            if (!partName.startsWith(baseUri)) {
                partName = baseUri + partName;
            }
            try {
                partName = new URI(partName).normalize().getPath().replace('\\', '/');
                LOG.log(POILogger.DEBUG, "part name: " + partName);
            } catch (URISyntaxException e) {
                throw new XMLSignatureException(e);
            }
            String contentType;
            try {
                PackagePartName relName = PackagingURIHelper.createPartName(partName);
                PackagePart pp2 = ooxml.getPart(relName);
                contentType = pp2.getContentType();
            } catch (InvalidFormatException e) {
                throw new XMLSignatureException(e);
            }
            if (relationshipType.endsWith("customXml") && !(contentType.equals("inkml+xml") || contentType.equals("text/xml"))) {
                LOG.log(POILogger.DEBUG, "skipping customXml with content type: " + contentType);
                continue;
            }
            if (!digestedPartNames.contains(partName)) {
                // We only digest a part once.
                String uri = partName + "?ContentType=" + contentType;
                Reference reference = newReference(uri, null, null, null, null);
                manifestReferences.add(reference);
                digestedPartNames.add(partName);
            }
        }
        if (parameterSpec.hasSourceIds()) {
            List<Transform> transforms = new ArrayList<Transform>();
            transforms.add(newTransform(RelationshipTransformService.TRANSFORM_URI, parameterSpec));
            transforms.add(newTransform(CanonicalizationMethod.INCLUSIVE));
            String uri = pp.getPartName().getName() + "?ContentType=application/vnd.openxmlformats-package.relationships+xml";
            Reference reference = newReference(uri, transforms, null, null, null);
            manifestReferences.add(reference);
        }
    }
}

Example 35 with InvalidFormatException

use of org.apache.poi.openxml4j.exceptions.InvalidFormatException in project poi by apache.

the class TestWorkbookFactory method testCreateGeneric.

/**
     * Creates the appropriate kind of Workbook, but
     *  checking the mime magic at the start of the
     *  InputStream, then creating what's required.
     */
@Test
public void testCreateGeneric() throws Exception {
    Workbook wb;
    // InputStream -> either
    wb = WorkbookFactory.create(HSSFTestDataSamples.openSampleFileStream(xls));
    assertNotNull(wb);
    assertTrue(wb instanceof HSSFWorkbook);
    assertCloseDoesNotModifyFile(xls, wb);
    wb = WorkbookFactory.create(HSSFTestDataSamples.openSampleFileStream(xlsx));
    assertNotNull(wb);
    assertTrue(wb instanceof XSSFWorkbook);
    assertCloseDoesNotModifyFile(xlsx, wb);
    // File -> either
    wb = WorkbookFactory.create(HSSFTestDataSamples.getSampleFile(xls));
    assertNotNull(wb);
    assertTrue(wb instanceof HSSFWorkbook);
    assertCloseDoesNotModifyFile(xls, wb);
    wb = WorkbookFactory.create(HSSFTestDataSamples.getSampleFile(xlsx));
    assertNotNull(wb);
    assertTrue(wb instanceof XSSFWorkbook);
    assertCloseDoesNotModifyFile(xlsx, wb);
    // Invalid type -> exception
    final byte[] before = HSSFTestDataSamples.getTestDataFileContent(txt);
    try {
        InputStream stream = HSSFTestDataSamples.openSampleFileStream(txt);
        try {
            wb = WorkbookFactory.create(stream);
        } finally {
            stream.close();
        }
        fail();
    } catch (InvalidFormatException e) {
    // Good
    }
    final byte[] after = HSSFTestDataSamples.getTestDataFileContent(txt);
    assertArrayEquals("Invalid type file was modified after trying to open the file as a spreadsheet", before, after);
}