Esempio n. 1
0
  @SuppressWarnings("deprecation")
  private Form getRemoveForm(final String admin) {

    removeExperimentForm = new Form();
    removeExperimentForm.setCaption("Remove Existing Experiment");
    removeExperimentForm.setWidth("50%");
    expList = eh.getExperiments(null);
    List<String> strExpList = new ArrayList<String>();
    for (ExperimentBean exp : expList.values()) {

      if (user.getEmail().equalsIgnoreCase("*****@*****.**")
          || exp.getEmail().equalsIgnoreCase(user.getEmail())) {
        String str = exp.getExpId() + "	" + exp.getName() + "	( " + exp.getUploadedByName() + " )";

        strExpList.add(str);
      }
    }

    final Select selectExp = new Select("Experiment ID", strExpList);

    selectExp.setWidth("100%");

    removeExperimentForm.addField(Integer.valueOf(1), selectExp);
    Button removeExpButton = new Button("Remove Experiment");
    removeExpButton.setStyle(Reindeer.BUTTON_SMALL);
    removeExperimentForm.addField(Integer.valueOf(2), removeExpButton);
    removeExpButton.addListener(
        new ClickListener() {
          /** */
          private static final long serialVersionUID = 1L;

          @Override
          public void buttonClick(ClickEvent event) {
            String str = selectExp.getValue().toString();
            String[] strArr = str.split("\t");
            Integer expId = (Integer.valueOf(strArr[0]));
            if (expId != null) {
              boolean test = auth.removeExp(expId);
              if (test) {
                updateComponents(user);
              } else {

                getWindow().showNotification("Failed to Remove The Experiment! ");
              }
            } else {
            }
          }
        });

    return removeExperimentForm;
  }
Esempio n. 2
0
  @SuppressWarnings({"deprecation", "serial"})
  private void updateComponents(final User user) {
    if (container != null) {
      container.removeAllComponents();
    }
    container = new Panel();
    root = new Panel();
    root.setStyle(Reindeer.PANEL_LIGHT);
    container.setHeight("100%");
    container.setStyle(Reindeer.PANEL_LIGHT);
    setCompositionRoot(container);

    // Create the Form
    newExpForm = new Form();
    newExpForm.setCaption("New Experiment");
    newExpForm.setWriteThrough(false); // we want explicit 'apply'
    newExpForm.setInvalidCommitted(false); // no invalid values in data model
    // Determines which properties are shown, and in which order:
    expNameField = new TextField("Experiment Name:");
    expNameField.setStyle(Reindeer.TEXTFIELD_SMALL);
    expNameField.setRequired(true);
    expNameField.setRequiredError("EXPERIMENT NAME CAN NOT BE EMPTY!");
    expNameField.setWidth("350px");
    expNameField.setMaxLength(70);

    speciesField = new TextField("Species:");
    speciesField.setStyle(Reindeer.TEXTFIELD_SMALL);
    speciesField.setRequired(true);
    speciesField.setRequiredError("EXPERIMENT SPECIES CAN NOT BE EMPTY!");
    speciesField.setWidth("350px");
    speciesField.setMaxLength(70);

    sampleTypeField = new TextField("Sample Type:");
    sampleTypeField.setStyle(Reindeer.TEXTFIELD_SMALL);
    sampleTypeField.setRequired(true);
    sampleTypeField.setRequiredError("EXPERIMENT SAMPLE TYPE CAN NOT BE EMPTY!");
    sampleTypeField.setWidth("350px");
    sampleTypeField.setMaxLength(70);

    sampleProcessingField = new TextField("Sample Processing:");
    sampleProcessingField.setStyle(Reindeer.TEXTFIELD_SMALL);
    sampleProcessingField.setRequired(true);
    sampleProcessingField.setRequiredError("EXPERIMENT SAMPLE PROCESSING CAN NOT BE EMPTY!");
    sampleProcessingField.setWidth("350px");
    sampleProcessingField.setMaxLength(70);

    instrumentTypeField = new TextField("Instrument Type:");
    instrumentTypeField.setStyle(Reindeer.TEXTFIELD_SMALL);
    instrumentTypeField.setRequired(true);
    instrumentTypeField.setRequiredError("EXPERIMENT INSTURMENT TYPE CAN NOT BE EMPTY!");
    instrumentTypeField.setWidth("350px");
    instrumentTypeField.setMaxLength(70);

    fragModeField = new TextField("Frag Mode:");
    fragModeField.setStyle(Reindeer.TEXTFIELD_SMALL);
    fragModeField.setRequired(true);
    fragModeField.setRequiredError("EXPERIMENT FRAG MODE CAN NOT BE EMPTY!");
    fragModeField.setWidth("350px");
    fragModeField.setMaxLength(70);

    UploadedByNameField = new TextField("Uploaded By:");
    UploadedByNameField.setStyle(Reindeer.TEXTFIELD_SMALL);
    UploadedByNameField.setRequired(true);
    UploadedByNameField.setRequiredError("EXPERIMENT UPLOADED BY CAN NOT BE EMPTY!");
    UploadedByNameField.setValue(user.getUsername());
    UploadedByNameField.setEnabled(false);
    UploadedByNameField.setWidth("350px");
    UploadedByNameField.setMaxLength(70);

    emailField = new TextField("Email:");
    emailField.setStyle(Reindeer.TEXTFIELD_SMALL);
    emailField.setRequired(true);
    emailField.setValue(user.getEmail());
    emailField.setEnabled(false);
    emailField.setRequiredError("EXPERIMENT EMAIL CAN NOT BE EMPTY!");
    emailField.setWidth("350px");
    emailField.setMaxLength(70);

    descriptionField = new TextArea("Description:");
    descriptionField.setStyle(Reindeer.TEXTFIELD_SMALL);
    descriptionField.setRequired(true);
    descriptionField.setRequiredError("EXPERIMENT Description CAN NOT BE EMPTY!");
    descriptionField.setWidth("350px");
    descriptionField.setMaxLength(950);

    publicationLinkField = new TextField("Publication Link:");
    publicationLinkField.setStyle(Reindeer.TEXTFIELD_SMALL);
    publicationLinkField.setWidth("350px");
    publicationLinkField.setMaxLength(300);

    newExpForm.addField(Integer.valueOf(1), expNameField);
    newExpForm.addField(Integer.valueOf(2), descriptionField);

    newExpForm.addField(Integer.valueOf(3), speciesField);
    newExpForm.addField(Integer.valueOf(4), sampleTypeField);
    newExpForm.addField(Integer.valueOf(5), sampleProcessingField);
    newExpForm.addField(Integer.valueOf(6), instrumentTypeField);
    newExpForm.addField(Integer.valueOf(7), fragModeField);
    newExpForm.addField(Integer.valueOf(8), UploadedByNameField);
    newExpForm.addField(Integer.valueOf(9), emailField);
    newExpForm.addField(Integer.valueOf(10), publicationLinkField);

    // Add form to layout
    container.addComponent(newExpForm);

    Panel p = new Panel();
    Label l =
        new Label(
            "<h4 style='color:blue'>Or Update Existing Experiments !</h4><h4 style='color:blue'>For New Experiment Please Leave Experiment ID Blank!</h4><h4 style='color:blue'><strong style='color:red'>* </strong> For New Experiment Please Remember to Upload Protein file first!</h4>");
    l.setContentMode(Label.CONTENT_XHTML);
    p.addComponent(l);
    container.addComponent(p);

    // Create the Form
    Form existExpForm = new Form();
    existExpForm.setCaption("Exist Experiments");
    expList = eh.getExperiments(null);
    List<String> strExpList = new ArrayList<String>();
    for (ExperimentBean exp : expList.values()) {
      if (user.getEmail().equalsIgnoreCase("*****@*****.**")
          || exp.getEmail().equalsIgnoreCase(user.getEmail())) {
        String str = exp.getExpId() + "	" + exp.getName() + "	( " + exp.getUploadedByName() + " )";
        strExpList.add(str);
      }
    }
    select = new Select("Experiment ID", strExpList);
    select.setImmediate(true);
    select.addListener(
        new Property.ValueChangeListener() {
          @Override
          public void valueChange(ValueChangeEvent event) {
            Object o = select.getValue();
            if (o != null) {
              String str = select.getValue().toString();
              String[] strArr = str.split("\t");
              int id = (Integer.valueOf(strArr[0]));
              ExperimentBean expDet = expList.get(id);
              if (expDetails != null) {
                expDetails.removeAllComponents();

                if (expDet.getProteinsNumber() == 0) {
                  Label l = new Label("<h4 style='color:red'>1) Protein File is Missing</h4>");
                  l.setContentMode(Label.CONTENT_XHTML);
                  expDetails.addComponent(l);
                } else {
                  Label l = new Label("<h4 style='color:blue'>1) Protein File is Uploaded</h4>");
                  l.setContentMode(Label.CONTENT_XHTML);
                  expDetails.addComponent(l);
                }
                if (expDet.getFractionsNumber() == 0) {
                  Label l = new Label("<h4 style='color:red'>2) Fraction File is Missing</h4>");
                  l.setContentMode(Label.CONTENT_XHTML);
                  expDetails.addComponent(l);
                } else {
                  Label l = new Label("<h4 style='color:blue'>2) Fraction File Uploaded</h4>");
                  l.setContentMode(Label.CONTENT_XHTML);
                  expDetails.addComponent(l);
                }
                //                        if (expDet.getFractionRange() == 0) {
                //                            Label l = new Label("<h4 style='color:red'>3) Fraction
                // Range File is Missing</h4>");
                //                            l.setContentMode(Label.CONTENT_XHTML);
                //                            expDetails.addComponent(l);
                //                        } else {
                //                            Label l = new Label("<h4 style='color:blue'>3)
                // Fraction Range File Uploaded</h4>");
                //                            l.setContentMode(Label.CONTENT_XHTML);
                //                            expDetails.addComponent(l);
                //                        }
                if (expDet.getPeptidesNumber() == 0) {
                  Label l = new Label("<h4 style='color:red'>3) Peptides File is Missing</h4>");
                  l.setContentMode(Label.CONTENT_XHTML);
                  expDetails.addComponent(l);
                } else {
                  Label l = new Label("<h4 style='color:blue'>3) Peptides File Uploaded</h4>");
                  l.setContentMode(Label.CONTENT_XHTML);
                  expDetails.addComponent(l);
                }
              }
            } else {
              expDetails.removeAllComponents();
              Label labelDetails =
                  new Label(
                      "<h4 style='color:red;'>Please Select Experiment To Show the Details.</h4>");
              labelDetails.setContentMode(Label.CONTENT_XHTML);
              expDetails.addComponent(labelDetails);
            }
          }
        });
    select.setWidth("60%");
    existExpForm.addField(Integer.valueOf(1), select);

    // Add form to layout
    VerticalLayout vlo = new VerticalLayout();

    if (hslo != null) {
      vlo.removeComponent(hslo);
    }
    hslo = new HorizontalLayout();
    hslo.setSizeFull();
    hslo.addComponent(existExpForm);
    vlo.addComponent(hslo);
    if (removeExperimentLayout != null) {
      hslo.removeComponent(removeExperimentLayout);
    }
    removeExperimentLayout = this.getRemoveForm(user.getEmail());
    hslo.addComponent(removeExperimentLayout);
    hslo.setComponentAlignment(removeExperimentForm, Alignment.MIDDLE_CENTER);
    vlo.addComponent(hslo);
    container.addComponent(vlo);

    // Create the Upload component.

    upload = new Upload(null, this);
    upload.setStyleName("small");
    upload.setVisible(true);
    upload.setHeight("30px");
    upload.setButtonCaption("ADD / EDIT EXPERIMENT !");

    // *****************************************************
    upload.addListener(
        new Upload.StartedListener() {
          @SuppressWarnings("static-access")
          @Override
          public void uploadStarted(StartedEvent event) {
            try {

              Thread.currentThread().sleep(1000);
              Thread t =
                  new Thread(
                      new Runnable() {
                        @Override
                        public void run() {
                          pi.setVisible(true);
                        }
                      });
              t.start();
              t.join();
            } catch (InterruptedException e) {
            }

            mainTabs.setReadOnly(true);
            subTabs.setReadOnly(true);
          }
        });

    upload.addListener(
        new Upload.FinishedListener() {
          @Override
          public void uploadFinished(FinishedEvent event) {
            pi.setVisible(false);
            mainTabs.setReadOnly(false);
            subTabs.setReadOnly(false);
            file = new File(event.getFilename());
          }
        });

    // ***********************************

    upload.addListener((Upload.SucceededListener) this);
    upload.addListener((Upload.FailedListener) this);
    if (helpNote != null) {
      vlo.removeComponent(helpNote);
    }
    Label label =
        new Label(
            "<h4 style='color:red;'>Please upload proteins file first</h4><h4 style='color:red;'>Please upload proteins files in (.txt) format.</h4><h4 style='color:red;'>Upload fraction range file after upload protein fraction file.</h4><h4 style='color:red;'>Upload fraction range file in (.xlsx) format.</h4>");
    label.setContentMode(Label.CONTENT_XHTML);
    helpNote = help.getHelpNote(label);
    helpNote.setMargin(false, true, true, true);

    vlo.addComponent(upload);
    vlo.addComponent(pi);
    vlo.addComponent(helpNote);
    vlo.setComponentAlignment(helpNote, Alignment.MIDDLE_RIGHT);

    expDetails = new Panel("Experiment Details");
    Label labelDetails =
        new Label("<h4 style='color:red;'>Please Select Experiment To Show the Details.</h4>");
    labelDetails.setContentMode(Label.CONTENT_XHTML);
    expDetails.addComponent(labelDetails);

    vlo.addComponent(expDetails);
    root.addComponent(vlo);
    container.addComponent(root);
  }