Examples of Cv


Examples of inspector.jqcml.model.Cv

    QcML qcml = new QcML();
    qcml.setFileName("Invalid_version.qcML");
    String version = "My.version.number";
    qcml.setVersion(version);

    Cv cv = new Cv("name", "uri", "cv");
    qcml.addCv(cv);

    QualityAssessment run = new QualityAssessment("run");
    QualityParameter param = new QualityParameter("name", cv, "param");
    param.setAccession("accession");
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Examples of inspector.jqcml.model.Cv

        writer.writeCv(null);
    }

    @Test(expected = UnsupportedOperationException.class)
    public void writeCv_valid() {
        writer.writeCv(new Cv("name", "uri", "id"));
    }
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Examples of inspector.jqcml.model.Cv

    @Test(expected = IllegalStateException.class)
    public void writeQcML_duplicateID() {
        QcML qcml = new QcML();
        qcml.setFileName("Invalid.qcML");

        Cv cv = new Cv("name", "uri", "id");
        qcml.addCv(cv);

        QualityAssessment run = new QualityAssessment("id");
        QualityParameter param = new QualityParameter("name", cv, "id");
        param.setAccession("accession");
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Examples of inspector.jqcml.model.Cv

    public void writeQcML_missingContent() {
        QcML qcml = new QcML();
        qcml.setFileName("Invalid.qcML");

        QualityAssessment run = new QualityAssessment("run");
        QualityParameter param = new QualityParameter("name", new Cv("name", "uri", "cv"), "param");
        param.setAccession("accession");
        run.addQualityParameter(param);
        qcml.addRunQuality(run);

        writer.writeQcML(qcml);
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Examples of inspector.jqcml.model.Cv

                // replace duplicate Cv's
                TypedQuery<IdKeyPair> cvQuery = entityManager.createQuery("SELECT NEW inspector.jqcml.io.db.IdKeyPair(cv.id, cv.primaryKey) FROM Cv cv", IdKeyPair.class);
                Map<String, Integer> cvIds = getIdMap(cvQuery);
                // check the id's and apply the primary keys in case of a duplication
                for(Iterator<Cv> it = qcml.getCvIterator(); it.hasNext(); ) {
                    Cv cv = it.next();
                    Integer key = cvIds.get(cv.getId());
                    if(key != null) {
                        logger.info("Duplicate CV <id={}>: assign primary key <{}>", cv.getId(), key);
                        cv.setPrimaryKey(key);
                    }
                }

                // store the new qcML
                entityManager.getTransaction().begin();
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Examples of inspector.jqcml.model.Cv

    // constructed qcML
    SecureRandom random = new SecureRandom();
    qcmlExpected = new QcML();
    // add Cv's
    for(int i = 0; i < 5; i++) {
      Cv cv = new Cv();
      cv.setFullName("cv item " + i);
      cv.setUri("/path/to/cv/" + i);
      cv.setId("cv_" + i);
      qcmlExpected.addCv(cv);
    }
    // add RunQuality's
    for(int i = 0; i < 5; i++) {
      QualityAssessment runQuality = new QualityAssessment("run_" + i);
      // add MetaDataParameters
      for(int j = 0; j < (i+1) * 2; j++) {
        MetaDataParameter param = new MetaDataParameter();
        param.setName("metadata parameter " + i + "-" + j);
        param.setId("mp_run" + i + "_param" + j);
        param.setCvRef(qcmlExpected.getCv("cv_" + (i+j) % qcmlExpected.getNumberOfCvs()));
        param.setAccession("QC:00000" + j);
        param.setValue(Integer.toString((int)(Math.random()*1000)));
        runQuality.addMetaDataParameter(param);
      }
      // add QualityParameters
      for(int j = 0; j < (i+1) * 3; j++) {
        QualityParameter param = new QualityParameter();
        param.setName("quality parameter " + i + "-" + j);
        param.setId("qp_run" + i + "_param" + j);
        param.setCvRef(qcmlExpected.getCv("cv_" + (i+j) % qcmlExpected.getNumberOfCvs()));
        param.setAccession("QC:00000" + j);
        param.setValue(Integer.toString((int)(Math.random()*1000)));
        runQuality.addQualityParameter(param);
      }
      // add AttachmentParameters
      for(int j = 0; j < (i+1) * 2; j++) {
        AttachmentParameter param = new AttachmentParameter();
        param.setName("attachment parameter " + i + "-" + j);
        param.setId("ap_run" + i + "_param" + j);
        param.setCvRef(qcmlExpected.getCv("cv_" + (i+j) % qcmlExpected.getNumberOfCvs()));
        param.setAccession("QC:00000" + j);
        param.setQualityParameterRef(runQuality.getQualityParameter("qp_run" + i + "_param" + j));
        param.setBinary(DatatypeConverter.printBase64Binary(new BigInteger(1024, random).toByteArray()));
        runQuality.addAttachmentParameter(param);
      }
      qcmlExpected.addRunQuality(runQuality);
    }
    // add SetQuality's
    for(int i = 0; i < 2; i++) {
      QualityAssessment setQuality = new QualityAssessment("set_" + i);
      // add MetaDataParameters
      for(int j = 0; j < (i+1) * 2; j++) {
        MetaDataParameter param = new MetaDataParameter();
        param.setName("metadata parameter " + i + "-" + j);
        param.setId("mp_set" + i + "_param" + j);
        param.setCvRef(qcmlExpected.getCv("cv_" + (i+j) % qcmlExpected.getNumberOfCvs()));
        param.setAccession("QC:00000" + j);
        param.setValue(Integer.toString((int)(Math.random()*1000)));
        setQuality.addMetaDataParameter(param);
      }
      // add QualityParameters
      for(int j = 0; j < (i+1) * 5; j++) {
        QualityParameter param = new QualityParameter();
        param.setName("quality parameter " + i + "-" + j);
        param.setId("qp_set" + i + "_param" + j);
        param.setCvRef(qcmlExpected.getCv("cv_" + (i+j) % qcmlExpected.getNumberOfCvs()));
        param.setAccession("QC:00000" + j);
        param.setValue(Integer.toString((int)(Math.random()*1000)));
        setQuality.addQualityParameter(param);
      }
      // add AttachmentParameters
      for(int j = 0; j < (i+1) * 3; j++) {
        AttachmentParameter param = new AttachmentParameter();
        param.setName("attachment parameter " + i + "-" + j);
        param.setId("ap_set" + i + "_param" + j);
        param.setCvRef(qcmlExpected.getCv("cv_" + (i+j) % qcmlExpected.getNumberOfCvs()));
        param.setAccession("QC:00000" + j);
        param.setQualityParameterRef(setQuality.getQualityParameter("qp_set" + i + "_param" + j));
        param.setBinary(DatatypeConverter.printBase64Binary(new BigInteger(1024, random).toByteArray()));
        setQuality.addAttachmentParameter(param);
      }
      qcmlExpected.addSetQuality(setQuality);
    }
    qcmlExpected.addCv(new Cv("cv item 5", "/path/to/cv/5", "cv_5"));
    qcmlExpected.addCv(new Cv("cv item 6", "/path/to/cv/6", "cv_6"));
    qcmlExpected.addCv(new Cv("cv item 7", "/path/to/cv/7", "cv_7"));
    qcmlExpected.addCv(new Cv("cv item 8", "/path/to/cv/8", "cv_8"));
    qcmlExpected.addCv(new Cv("cv item 9", "/path/to/cv/9", "cv_9"));
    qcmlExpected.addCv(new Cv("cv item 10", "/path/to/cv/10", "cv_10"));
    qcmlExpected.addCv(new Cv("cv item 11", "/path/to/cv/11", "cv_11"));
    qcmlExpected.addCv(new Cv("cv item 12", "/path/to/cv/12", "cv_12"));
   
    // read qcML
    qcml = new QcMLFileReader().getQcML(getClass().getResource("/QcMLTest.qcML").getFile());
  }
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Examples of inspector.jqcml.model.Cv

  public void addCv_new() {
    int count = qcml.getNumberOfCvs();
    // new Cv is absent
    assertNull(qcml.getCv("new cv"));
    // add new Cv
    qcml.addCv(new Cv("new Cv name", "/path/to/cv/", "new cv"));
    // new Cv is present
    assertEquals(qcml.getNumberOfCvs(), count+1);
    assertNotNull(qcml.getCv("new cv"));
  }
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Examples of inspector.jqcml.model.Cv

  @Test
  public void addCv_duplicate() {
    int count = qcml.getNumberOfCvs();
    // new Cv is present
    assertNotNull(qcml.getCv("cv_3"));
    Cv old = qcml.getCv("cv_3");
    // add new Cv
    qcml.addCv(new Cv("new Cv name", "/path/to/cv/", "cv_3"));
    // new Cv is present
    assertEquals(qcml.getNumberOfCvs(), count);
    assertNotNull(qcml.getCv("cv_3"));
    assertNotSame(old, qcml.getSetQuality("cv_3"));
  }
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