public ASearchComponent getAnnotationSearchComponent(IDomeo domeo, String annotationName) {
if (annotationSearchComponents.containsKey(annotationName)) {
return annotationSearchComponents.get(annotationName);
} else {
domeo.getLogger().exception(this, "No search component found for: " + annotationName);
domeo.getLogger().warn(this, "Default search component applied");
return new ASearchComponent(domeo);
}
}
public void createSocialBar(HorizontalPanel socialBar, final MAnnotation annotation) {
try {
socialBar.clear();
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_COMMENTING))
.getValue()) {
Resources resource = Domeo.resources;
Image commentIcon = new Image(resource.littleCommentIcon());
commentIcon.setTitle("Comment on Item");
commentIcon.setStyleName(ATileComponent.tileResources.css().button());
commentIcon.addClickHandler(
ActionCommentAnnotation.getClickHandler(_domeo, this, annotation));
commentIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
socialBar.add(commentIcon);
socialBar.add(new Label("(10)"));
Image usersIcon = new Image(resource.usersIcon());
usersIcon.setTitle("Involved users");
usersIcon.setStyleName(ATileComponent.tileResources.css().button());
usersIcon.addClickHandler(
ActionCommentAnnotation.getClickHandler(_domeo, this, annotation));
usersIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
socialBar.add(usersIcon);
socialBar.setCellWidth(usersIcon, "24px");
socialBar.setCellHorizontalAlignment(usersIcon, HasHorizontalAlignment.ALIGN_RIGHT);
socialBar.add(new Label("(2)"));
}
} catch (Exception e) {
_domeo.getLogger().exception(this, "create social bar" + e.getMessage());
}
}
public boolean selectConnector(IDomeo domeo) {
if (_connector != null) return true;
_domeo = domeo;
if (domeo.isStandaloneMode()) {
_connector = new StandaloneBioPortalConnector();
} else {
if (domeo.isHostedMode()) {
_connector = new GwtBioPortalServiceConnector();
} else {
// Real service
_connector = new JsonBioPortalConnector(domeo);
}
}
domeo
.getLogger()
.debug(this, "BioPortal Connector selected: " + _connector.getClass().getName());
return false;
}
public void initializeLens(MGenericResource resource, HashMap<String, String> parameters) {
Resources _resources = Domeo.resources;
try {
_resource = (MOpenTrialsDocument) resource;
_parameters = parameters;
if (parameters.containsKey(MOpenTrialsDocument.PARAM_URI_READONLY)) {
if (parameters.get(MOpenTrialsDocument.PARAM_URI_READONLY).equals("true")) {
uriField.setReadOnly(true);
}
}
if (_iconClickHandler != null) _iconClickHandler.removeHandler();
_iconClickHandler =
urlImage.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
Window.alert("Show extractor details not implemented yet");
}
});
refresh();
} catch (Exception e) {
_domeo
.getLogger()
.exception(this, "Exception while initialing resource info " + e.getMessage());
body.clear();
body.add(
new HTML(
"<img src='"
+ _resources.crossLittleIcon().getSafeUri().asString()
+ "'/> Exception while initialing OpenTrials resource info "
+ e.getMessage()));
}
}
public void injectButtons(String plugin, FlowPanel content, final MAnnotation annotation) {
try {
if (!((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_DISPLAY_PROVENANCE))
.getValue()
|| !(((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_DISPLAY_USER_PROVENANCE))
.getValue())) {
Resources resource = Domeo.resources;
Image commentIcon = null;
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_COMMENTING))
.getValue()) {
commentIcon = new Image(resource.littleCommentIcon());
commentIcon.setTitle("Comment on Item");
commentIcon.setStyleName(ATileComponent.tileResources.css().button());
commentIcon.addClickHandler(
ActionCommentAnnotation.getClickHandler(_domeo, this, annotation));
commentIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
}
Image editIcon = new Image(resource.editLittleIcon());
editIcon.setTitle("Edit Item");
if (_domeo.getProfileManager().getUserCurrentProfile().isPluginEnabled(plugin)) {
editIcon.setStyleName(ATileComponent.tileResources.css().button());
editIcon.addClickHandler(ActionEditAnnotation.getClickHandler(_domeo, this, annotation));
editIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
}
Image deleteIcon = new Image(resource.deleteLittleIcon());
deleteIcon.setTitle("Delete Item");
deleteIcon.setStyleName(ATileComponent.tileResources.css().button());
deleteIcon.addClickHandler(
ActionDeleteAnnotation.getClickHandler(_domeo, this, annotation));
deleteIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_COMMENTING))
.getValue()) {
content.add(commentIcon);
}
content.add(editIcon);
content.add(deleteIcon);
}
} catch (Exception e) {
_domeo.getLogger().exception(this, "injectButtons: " + e.getMessage());
}
}
public void createCurationBar(HorizontalPanel curationBar, final MAnnotation annotation) {
try {
curationBar.clear();
String myToken = CurationUtils.countCurationTokens(_domeo, annotation);
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_CURATION))
.getValue()) {
Resources resource = Domeo.resources;
HorizontalPanel curationPanel = new HorizontalPanel();
int maxCount = 0;
String maximum = "";
Map<String, Integer> counts = countCurationToken(annotation);
Set<String> keys = counts.keySet();
for (String key : keys) {
if (counts.containsKey(key)) {
if (counts.get(key) > maxCount) {
maximum = key;
maxCount = counts.get(key);
}
}
}
final CustomButton correctButton = new CustomButton();
final CustomButton broadButton = new CustomButton();
final CustomButton incorrectButton = new CustomButton();
if (counts.containsKey(MCurationToken.CORRECT)) {
correctButton.setText("Correct [" + counts.get(MCurationToken.CORRECT) + "]");
} else correctButton.setText("Correct");
if (maximum.equals(MCurationToken.CORRECT)) {
if (myToken.equals(MCurationToken.CORRECT))
correctButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonBoldGreen());
else correctButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonBold());
} else {
if (myToken.equals(MCurationToken.CORRECT))
correctButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonGreen());
else correctButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
}
correctButton.setResource(resource.acceptIcon());
correctButton.addClickHandler(
new ClickHandler() {
public void onClick(ClickEvent event) {
correctButton.setStyleName(
widgetUtilsResources.widgetCss().curationButtonBoldGreen());
broadButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
incorrectButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
if (_span != null) {
_span.setClassName(StylesManager.LIGHTGREEN_HIGHLIGHT);
_span.setAttribute("annotationdefcss", StylesManager.LIGHTGREEN_HIGHLIGHT);
}
modifyCurationToken(annotation, MCurationToken.CORRECT);
// MAnnotationSet set =
// _domeo.getAnnotationPersistenceManager().getSetByAnnotationId(annotation.getLocalId());
//
// MCurationToken ann = CurationFactory.createCurationToken(_domeo,
// _domeo.getAgentManager().getUserPerson(),
// _domeo.getAgentManager().getSoftware(),
// annotation, MCurationToken.CORRECT, "");
//
// _domeo.getAnnotationPersistenceManager().addAnnotationOfAnnotation(ann,
// annotation, _domeo.getAnnotationPersistenceManager().getCurrentSet());
// _domeo.refreshAnnotationComponents();
//
// if(!_annotator.getPreferencesManager().isDontOpenCurationPanelWhenConfirming() &&
// _annotator.getPreferencesManager().isAutomaticallyOpenCurationPanel()) {
// _this.hide();
// _annotator.showAnnotationItemHistory(info, CurationTokenDTO.CORRECT,
// currentItems, currentSpans);
// } else curateAnnotationItem(span, info, CurationTokenDTO.CORRECT);
}
});
curationPanel.add(correctButton);
if (counts.containsKey(MCurationToken.CORRECT_BROAD)) {
broadButton.setText("Broad [" + counts.get(MCurationToken.CORRECT_BROAD) + "]");
} else broadButton.setText("Broad");
if (maximum.equals(MCurationToken.CORRECT_BROAD)) {
if (myToken.equals(MCurationToken.CORRECT_BROAD))
broadButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonBoldGreen());
else broadButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonBold());
} else {
if (myToken.equals(MCurationToken.CORRECT_BROAD))
broadButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonGreen());
else broadButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
}
broadButton.setResource(resource.acceptBroadIcon());
broadButton.addClickHandler(
new ClickHandler() {
public void onClick(ClickEvent event) {
broadButton.setStyleName(
widgetUtilsResources.widgetCss().curationButtonBoldGreen());
correctButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
incorrectButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
if (_span != null) {
_span.setClassName(StylesManager.LIGHTGREEN_HIGHLIGHT);
_span.setAttribute("annotationdefcss", StylesManager.LIGHTGREEN_HIGHLIGHT);
}
modifyCurationToken(annotation, MCurationToken.CORRECT_BROAD);
// MAnnotationSet set =
// _domeo.getAnnotationPersistenceManager().getSetByAnnotationId(annotation.getLocalId());
//
// MCurationToken ann = CurationFactory.createCurationToken(_domeo,
// _domeo.getAgentManager().getUserPerson(),
// _domeo.getAgentManager().getSoftware(),
// annotation, MCurationToken.CORRECT_BROAD, "");
//
// _domeo.getAnnotationPersistenceManager().addAnnotationOfAnnotation(ann,
// annotation, _domeo.getAnnotationPersistenceManager().getCurrentSet());
// _domeo.refreshAnnotationComponents();
// if(_annotator.getPreferencesManager().isAutomaticallyOpenCurationPanel()) {
// _this.hide();
// _annotator.showAnnotationItemHistory(info, CurationTokenDTO.CORRECT_BROAD,
// currentItems, currentSpans);
// } else curateAnnotationItem(span, info, CurationTokenDTO.CORRECT_BROAD);
}
});
curationPanel.add(broadButton);
if (counts.containsKey(MCurationToken.INCORRECT)) {
incorrectButton.setText("Wrong [" + counts.get(MCurationToken.INCORRECT) + "]");
} else incorrectButton.setText("Wrong");
if (maximum.equals(MCurationToken.INCORRECT)) {
if (myToken.equals(MCurationToken.INCORRECT))
incorrectButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonBoldRed());
else incorrectButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonBold());
} else {
if (myToken.equals(MCurationToken.INCORRECT))
incorrectButton.setStyleName(widgetUtilsResources.widgetCss().curationButtonRed());
else incorrectButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
}
incorrectButton.setResource(resource.rejectIcon());
incorrectButton.addClickHandler(
new ClickHandler() {
public void onClick(ClickEvent event) {
incorrectButton.setStyleName(
widgetUtilsResources.widgetCss().curationButtonBoldRed());
correctButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
broadButton.setStyleName(widgetUtilsResources.widgetCss().curationButton());
if (_span != null) {
_span.setClassName(StylesManager.LIGHTRED_HIGHLIGHT);
_span.setAttribute("annotationdefcss", StylesManager.LIGHTRED_HIGHLIGHT);
}
modifyCurationToken(annotation, MCurationToken.INCORRECT);
// MAnnotationSet set =
// _domeo.getAnnotationPersistenceManager().getSetByAnnotationId(annotation.getLocalId());
// MCurationToken ann = CurationFactory.createCurationToken(_domeo,
// _domeo.getAgentManager().getUserPerson(),
// _domeo.getAgentManager().getSoftware(),
// annotation, MCurationToken.INCORRECT, "");
//
//
//
////
// if(((BooleanPreference)_domeo.getPreferences().getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_CURATION_MOTIVATION)).getValue()) {
//// _curationPopup.hide();
//// CurationViewer lwp = new CurationViewer(_domeo, annotation, null);
//// new EnhancedGlassPanel(_domeo, lwp, lwp.getTitle(), false,
// false, false);
//// } else {
// _domeo.getAnnotationPersistenceManager().addAnnotationOfAnnotation(ann,
// annotation, _domeo.getAnnotationPersistenceManager().getCurrentSet());
// _domeo.refreshAnnotationComponents();
// //}
// if(_annotator.getPreferencesManager().isAutomaticallyOpenCurationPanel()) {
// _this.hide();
// _annotator.showAnnotationItemHistory(info, CurationTokenDTO.INCORRECT,
// currentItems, currentSpans);
// } else curateAnnotationItem(span, info, CurationTokenDTO.INCORRECT);
}
});
curationPanel.add(incorrectButton);
curationBar.add(curationPanel);
// curationBar.add(new HTML("WIP: curation bar"));
}
} catch (Exception e) {
_domeo.getLogger().exception(this, "create curation bar" + e.getMessage());
}
}
public void createProvenanceBar(
String plugin, HorizontalPanel provenance, final MAnnotation annotation) {
try {
Resources resource = Domeo.resources;
Image commentIcon = null;
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_COMMENTING))
.getValue()) {
commentIcon = new Image(resource.littleCommentIcon());
commentIcon.setTitle("Comment on Item");
commentIcon.setStyleName(ATileComponent.tileResources.css().button());
commentIcon.addClickHandler(
ActionCommentAnnotation.getClickHandler(_domeo, this, annotation));
commentIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
}
Image editIcon = new Image(resource.editLittleIcon());
editIcon.setTitle("Edit Item");
if (_domeo.getProfileManager().getUserCurrentProfile().isPluginEnabled(plugin)) {
editIcon.setStyleName(ATileComponent.tileResources.css().button());
editIcon.addClickHandler(ActionEditAnnotation.getClickHandler(_domeo, this, annotation));
editIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
}
Image deleteIcon = new Image(resource.deleteLittleIcon());
deleteIcon.setTitle("Delete Item");
deleteIcon.setStyleName(ATileComponent.tileResources.css().button());
deleteIcon.addClickHandler(ActionDeleteAnnotation.getClickHandler(_domeo, this, annotation));
deleteIcon.addClickHandler(
new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
_curationPopup.hide();
}
});
// TODO move to an abstract tile class
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_DISPLAY_PROVENANCE))
.getValue()) {
if (annotation
.getCreator()
.getUri()
.equals(_domeo.getAgentManager().getUserPerson().getUri())) {
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_DISPLAY_USER_PROVENANCE))
.getValue()) {
provenance.clear();
// TODO Externalize the icon management to the plugins
if (SelectorUtils.isOnMultipleTargets(annotation.getSelectors())) {
Image ic = new Image(Domeo.resources.multipleLittleIcon());
ic.setTitle("Annotation on multiple targets");
provenance.add(ic);
provenance.setCellWidth(ic, "18px");
} else if (annotation.getSelector() != null
&& annotation.getSelector().getTarget() instanceof MOnlineImage) {
Image ic = new Image(Domeo.resources.littleImageIcon());
ic.setTitle("Annotation on image");
provenance.add(ic);
provenance.setCellWidth(ic, "18px");
} else {
Image ic = new Image(Domeo.resources.littleTextIcon());
ic.setTitle("Annotation on text");
provenance.add(ic);
provenance.setCellWidth(ic, "18px");
}
provenance.add(new Label("By Me on " + annotation.getFormattedCreationDate()));
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_COMMENTING))
.getValue()) {
provenance.add(commentIcon);
provenance.setCellWidth(commentIcon, "20px");
provenance.setCellHorizontalAlignment(
commentIcon, HasHorizontalAlignment.ALIGN_RIGHT);
}
provenance.add(editIcon);
provenance.setCellWidth(editIcon, "20px");
provenance.setCellHorizontalAlignment(editIcon, HasHorizontalAlignment.ALIGN_RIGHT);
provenance.add(deleteIcon);
provenance.setCellWidth(deleteIcon, "20px");
provenance.setCellHorizontalAlignment(deleteIcon, HasHorizontalAlignment.ALIGN_RIGHT);
} else {
provenance.setVisible(false);
}
} else {
provenance.clear();
// TODO Externalize the icon management to the plugins
if (SelectorUtils.isOnMultipleTargets(annotation.getSelectors())) {
Image ic = new Image(Domeo.resources.multipleLittleIcon());
ic.setTitle("Annotation on multiple targets");
provenance.add(ic);
provenance.setCellWidth(ic, "18px");
} else if (annotation.getSelector() != null
&& annotation.getSelector().getTarget() instanceof MOnlineImage) {
Image ic = new Image(Domeo.resources.littleImageIcon());
ic.setTitle("Annotation on image");
provenance.add(ic);
provenance.setCellWidth(ic, "18px");
} else {
Image ic = new Image(Domeo.resources.littleTextIcon());
ic.setTitle("Annotation on text");
provenance.add(ic);
provenance.setCellWidth(ic, "18px");
}
provenance.add(
new Label(
"By "
+ annotation.getCreator().getName()
+ " on "
+ annotation.getFormattedCreationDate()));
if (((BooleanPreference)
_domeo
.getPreferences()
.getPreferenceItem(Domeo.class.getName(), Domeo.PREF_ALLOW_COMMENTING))
.getValue()) {
provenance.add(commentIcon);
provenance.setCellWidth(commentIcon, "20px");
provenance.setCellHorizontalAlignment(commentIcon, HasHorizontalAlignment.ALIGN_RIGHT);
}
provenance.add(editIcon);
provenance.setCellWidth(editIcon, "20px");
provenance.setCellHorizontalAlignment(editIcon, HasHorizontalAlignment.ALIGN_RIGHT);
provenance.add(deleteIcon);
provenance.setCellWidth(deleteIcon, "20px");
provenance.setCellHorizontalAlignment(deleteIcon, HasHorizontalAlignment.ALIGN_RIGHT);
}
} else {
provenance.setVisible(false);
}
} catch (Exception e) {
_domeo.getLogger().exception(this, "createProvenanceBar2" + e.getMessage());
}
}
public void refresh() {
Resources _resources = Domeo.resources;
try {
init();
uriField.setValue(_resource.getUrl());
// sourceField.add(new HTML("<img src='" + Domeo.resources.externalLinkIcon().getURL() + "'/>
// <a href='" +
// _resource.getSource().getHomepage() + "' target='_blank'>"+_resource.getSource().getName()
// + "</a> "));
String synonyms = _resource.getIsAbout().getSynonyms();
aboutField.add(
new HTML(
_resource.getIsAbout().getLabel()
+ " "
+ (_resource.getIsAbout().getSynonyms() != null ? synonyms : "")));
if (_domeo.getExtractorsManager().isExtractorDefined()) {
urlImage.setResource(_resources.checkIcon());
urlImage.setTitle(
"Known resource, executed extractor '"
+ _domeo.getExtractorsManager().getExtractorLabel()
+ "'");
urlImage.setVisible(true);
} else {
urlImage.setVisible(false);
}
if (_resource != null) {
extractionProvenanceImage.setUrl(
Domeo.resources.pluginsGrayLittleIcon().getSafeUri().asString());
extractionProvenanceImage.setTitle(_resource.getCreator().getName());
extractorProvenanceDetails.setText("Extracted by " + _resource.getCreator().getName());
extractionSourceDetails.setHTML(
"Source <a href='"
+ _resource.getSource().getHomepage()
+ "' target='_blank'> <img src='"
+ Domeo.resources.externalLinkIcon().getSafeUri().asString()
+ "'/> "
+ _resource.getSource().getName()
+ "</a>");
extractionDateDetails.setText("On " + _resource.getFormattedCreationDate());
}
} catch (Exception e) {
_domeo
.getLogger()
.exception(this, "Exception while rendering OpenTrials resource info " + e.getMessage());
body.clear();
body.add(
new HTML(
"<img src='"
+ _resources.crossLittleIcon().getSafeUri().asString()
+ "'/> Exception while rendering OpenTrials resource info "
+ e.getMessage()));
}
// References
try {
CitationReferencesPanel p = new CitationReferencesPanel(_domeo, false);
referencesPanel.clear();
referencesPanel.add(p);
} catch (Exception e) {
_domeo
.getLogger()
.exception(this, "Exception while rendering resource info " + e.getMessage());
referencesPanel.clear();
referencesPanel.add(
new HTML(
"<img src='"
+ _resources.crossLittleIcon().getSafeUri().asString()
+ "'/> Exception while rendering PubMed resource info "
+ e.getMessage()));
}
// Generic Document Resource
try {
LDocumentResourceCardPanel d = new LDocumentResourceCardPanel(_domeo);
d.initializeLens(_resource, _parameters);
contentPanel.clear();
contentPanel.add(d);
} catch (Exception e) {
_domeo
.getLogger()
.exception(this, "Exception while rendering resource info " + e.getMessage());
body.clear();
body.add(
new HTML(
"<img src='"
+ _resources.crossLittleIcon().getSafeUri().asString()
+ "'/> Exception while rendering OpenTrials resource info "
+ e.getMessage()));
}
}