Examples with Sequence com.google.showcase.v1beta1.Sequence used on opensource projects

Example 36 with Sequence

use of com.google.showcase.v1beta1.Sequence in project OpenAM by OpenRock.

the class SecureLogHelperJSSImpl method readFromSecretStore.

/**
     * Returns matched secret data from from the secret Storage. 
     * At a time there are only 3 things in logger's secure store file 
     *    - initialkey, currentkey and current signature
     * In the verifier secure store file there is just the initial key of the
     * logger and the currentKey
     * @param filename file for secret storage
     * @param dataType The kind of data to be read, whether it is a
     *                 signature or a key
     * @param password password for the file
     * @return secure data that is matched with dataType
     * @throws Exception if it fails to read secret data from secret store
     */
byte[] readFromSecretStore(String filename, String dataType, AMPassword password) throws Exception {
    // open input file for reading
    FileInputStream infile = null;
    infile = new FileInputStream(filename);
    // Decode the P12 file
    PFX.Template pfxt = new PFX.Template();
    PFX pfx = (PFX) pfxt.decode(new BufferedInputStream(infile, 2048));
    // Verify the MAC on the PFX.  This is important to be sure
    // it hasn't been tampered with.
    StringBuffer reason = new StringBuffer();
    MessageDigest md = MessageDigest.getInstance("SHA");
    Password jssPasswd = new Password(new String(md.digest(password.getByteCopy()), "UTF-8").toCharArray());
    md.reset();
    if (!pfx.verifyAuthSafes(jssPasswd, reason)) {
        throw new Exception("AuthSafes failed to verify because: " + reason.toString());
    }
    AuthenticatedSafes authSafes = pfx.getAuthSafes();
    SEQUENCE safeContentsSequence = authSafes.getSequence();
    byte[] cryptoData = null;
    // Loop over contents of the authenticated safes
    for (int i = 0; i < safeContentsSequence.size(); i++) {
        // The safeContents may or may not be encrypted.  We always send
        // the password in.  It will get used if it is needed.  If the
        // decryption of the safeContents fails for some reason (like
        // a bad password), then this method will throw an exception
        SEQUENCE safeContents = authSafes.getSafeContentsAt(jssPasswd, i);
        SafeBag safeBag = null;
        ASN1Value val = null;
        // Go through all the bags in this SafeContents
        for (int j = 0; j < safeContents.size(); j++) {
            safeBag = (SafeBag) safeContents.elementAt(j);
            // look for bag attributes and then choose the key
            SET attribs = safeBag.getBagAttributes();
            if (attribs == null) {
                Debug.error("Bag has no attributes");
            } else {
                for (int b = 0; b < attribs.size(); b++) {
                    Attribute a = (Attribute) attribs.elementAt(b);
                    if (a.getType().equals(SafeBag.FRIENDLY_NAME)) {
                        // the friendly name attribute is a nickname
                        BMPString bs = (BMPString) ((ANY) a.getValues().elementAt(0)).decodeWith(BMPString.getTemplate());
                        if (dataType.equals(bs.toString())) {
                            // look at the contents of the bag
                            val = safeBag.getInterpretedBagContent();
                            break;
                        }
                    }
                }
            }
        }
        if (val instanceof ANY)
            cryptoData = ((ANY) val).getContents();
    }
    // Close the file
    infile.close();
    return cryptoData;
}

Example 37 with Sequence

use of com.google.showcase.v1beta1.Sequence in project OpenAM by OpenRock.

the class SecureLogHelperJSSImpl method writeToSecretStore.

/**
     * Writes to the secret Storage. If the data to be written is a key, then
     * writes the older signature also. If it is a signature then writes the
     * older key also
     * @param cryptoMaterial The data to be written to the secret storage
     * @param filename The file for secret storage
     * @param password The password for the file
     * @param dataType The kind of cryptoMaterial, whether it is a signature
     * or a key
     * @throws Exception if it fails to write secret data from secret store
     */
void writeToSecretStore(byte[] cryptoMaterial, String filename, AMPassword password, String dataType) throws Exception {
    byte[] oldDataFromSecretStorage = null;
    String oldDataType = null;
    MessageDigest md = MessageDigest.getInstance("SHA");
    Password jssPasswd = new Password(new String(md.digest(password.getByteCopy()), "UTF-8").toCharArray());
    md.reset();
    // Do this only when the logger's file is being used
    if (filename.equals(logFileName) && loggerInitialized) {
        // current signature in the PKCS12 file
        if (dataType.equals(currentSignature)) {
            oldDataFromSecretStorage = readFromSecretStore(logFileName, currentKey, password);
            oldDataType = currentKey;
        } else if (dataType.equals(currentKey)) {
            // need to read the currentSignature 
            // for the same reason as above
            oldDataFromSecretStorage = readFromSecretStore(logFileName, currentSignature, password);
            oldDataType = currentSignature;
        }
    }
    // Start building the new contents by adding the older content first
    AuthenticatedSafes newAuthSafes = new AuthenticatedSafes();
    if (oldDataFromSecretStorage != null) {
        SEQUENCE oldSafeContents = AddToSecretStore(oldDataFromSecretStorage, oldDataType);
        // Add the old contents to the existing safe
        newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, oldSafeContents);
    }
    // not being added for the first time
    if ((filename.equals(logFileName)) && !dataType.equals(initialKey) && loggerInitialized) {
        byte[] key = readFromSecretStore(filename, initialKey, password);
        if (key != null) {
            SEQUENCE initialKeySafeContents = AddToSecretStore(key, initialKey);
            newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, initialKeySafeContents);
        }
    }
    if ((filename.equals(verifierFileName)) && !dataType.equals(initialKey) && verifierInitialized) {
        byte[] key = readFromSecretStore(filename, initialKey, password);
        if (key != null) {
            SEQUENCE initialKeySafeContents = AddToSecretStore(key, initialKey);
            newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, initialKeySafeContents);
        }
    }
    // Add the new contents
    SEQUENCE encSafeContents = AddToSecretStore(cryptoMaterial, dataType);
    // Add the new contents to the existing safe
    newAuthSafes.addEncryptedSafeContents(PBEAlgorithm.PBE_SHA1_DES3_CBC, jssPasswd, null, AuthenticatedSafes.DEFAULT_ITERATIONS, encSafeContents);
    PFX newpfx = new PFX(newAuthSafes);
    newpfx.computeMacData(jssPasswd, null, 5);
    // write the new PFX out to the logger
    FileOutputStream fos = new FileOutputStream(filename);
    newpfx.encode(fos);
    fos.close();
}

Example 38 with Sequence

use of com.google.showcase.v1beta1.Sequence in project jasn1 by openmuc.

the class ModulesTest method encodingDecoding.

@Test
public void encodingDecoding() throws IOException {
    ReverseByteArrayOutputStream berOS = new ReverseByteArrayOutputStream(1000);
    MyDate1 dateOfHire = new MyDate1();
    // MyDate1 dateOfHire = new MyDate1("19710917");
    dateOfHire.value = new String("19710917").getBytes();
    dateOfHire.encode(berOS, true);
    MyInt2 myInt2Encode = new MyInt2(2);
    berOS.reset();
    myInt2Encode.encode(berOS, true);
    MyInt2 myInt2Decode = new MyInt2();
    byte[] code = HexConverter.fromShortHexString("a303020102");
    InputStream is = new ByteArrayInputStream(code);
    myInt2Decode.decode(is, true);
    Assert.assertEquals(myInt2Decode.value.intValue(), 2);
    PersonnelRecord pr = new PersonnelRecord();
    Name name = new Name();
    name.setGivenName(new BerVisibleString("givenName".getBytes()));
    name.setFamilyName(new BerVisibleString("familyName".getBytes()));
    name.setInitial(new BerVisibleString("initial".getBytes()));
    pr.setName(name);
    pr.setTitle(new BerVisibleString("title".getBytes()));
    pr.setNumber(new EmployeeNumberZ(1));
    pr.setDateOfHire(new Date("23121981".getBytes()));
    pr.setNameOfSpouse(name);
    ChildInformation child = new ChildInformation();
    child.setName(new Name("child name".getBytes()));
    child.setDateOfBirth(new Date("12121912".getBytes()));
    PersonnelRecord.Children children = new PersonnelRecord.Children();
    List<ChildInformation> childInformation = children.getChildInformation();
    childInformation.add(child);
    childInformation.add(child);
    pr.setTestBitString(new MyBitString(new byte[] { (byte) 0x80, (byte) 0xff }, 10));
    pr.setTest(new MyInt(3));
    TestChoice testChoice = new TestChoice();
    testChoice.setChoiceElement1(child);
    pr.setTest2(testChoice);
    pr.setTest3(testChoice);
    pr.setTest4(testChoice);
    pr.setTest5(testChoice);
    pr.setTest6(testChoice);
    TestSequenceOf testSequenceOf = new TestSequenceOf();
    List<BerInteger> berIntegers = testSequenceOf.getBerInteger();
    for (int i = 0; i < 10; i++) {
        berIntegers.add(new BerInteger(i));
    }
    pr.setTestSequenceOf(testSequenceOf);
    TestSequenceOf2 testSequenceOf2 = new TestSequenceOf2();
    List<SEQUENCE> sequences = testSequenceOf2.getSEQUENCE();
    for (int i = 0; i < 10; i++) {
        SEQUENCE sequence = new SEQUENCE();
        sequence.setTest1(new BerInteger(i++));
        sequence.setTest2(new BerInteger(i));
        sequences.add(sequence);
    }
    pr.setTestSequenceOf2(testSequenceOf2);
    BerEmbeddedPdv berEmbeddedPdv = new BerEmbeddedPdv();
    pr.setEmbeddedPdv(berEmbeddedPdv);
    System.out.println("PersonnelRecord.toString():\n" + pr);
}

Example 39 with Sequence

use of com.google.showcase.v1beta1.Sequence in project libSBOLj by SynBioDex.

the class CutExample method main.

public static void main(String[] args) throws Exception {
    String prURI = "http://partsregistry.org/";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.addRole(URI.create("http://identifiers.org/so/SO:0000613"));
    promoter.setName("J23119 promoter");
    promoter.setDescription("Constitutive promoter");
    promoter.addWasDerivedFrom(URI.create("http://partsregistry.org/Part:BBa_J23119"));
    document.setDefaultURIprefix(prURI);
    Sequence seq = document.createSequence("BBa_J23119", "", "ttgacagctagctcagtcctaggtataatgctagc", URI.create("http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"));
    seq.addWasDerivedFrom(URI.create("http://parts.igem.org/Part:BBa_J23119:Design"));
    promoter.addSequence(seq.getIdentity());
    promoter.createSequenceAnnotation("cutat10", "cut1", 10, OrientationType.INLINE);
    promoter.createSequenceAnnotation("cutat12", "cut2", 12, OrientationType.INLINE);
    SBOLWriter.write(document, (System.out));
}

Example 40 with Sequence

use of com.google.showcase.v1beta1.Sequence in project libSBOLj by SynBioDex.

the class ModuleDefinitionOutput method getSequenceLength.

private static int getSequenceLength(SBOLDocument document, ComponentDefinition componentDef) throws Exception {
    if (componentDef.getSequences() != null && componentDef.getSequences().size() > 0) {
        Sequence sequence = componentDef.getSequences().iterator().next();
        return sequence.getElements().length();
    } else {
        int total = 0;
        for (SequenceAnnotation annotation : componentDef.getSequenceAnnotations()) {
            if (annotation.getComponent() != null) {
                Component component = annotation.getComponent();
                ComponentDefinition subComponentDef = component.getDefinition();
                total = total + getSequenceLength(document, subComponentDef);
            } else {
                throw new Exception("Can't get sequence length for an incomplete design");
            }
        }
        return total;
    }
}