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fixed a bit of the note and flex tables
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@nathandunn
nathandunn committed May 23, 2019
1 parent 39baf40 commit 73450c7
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Showing 3 changed files with 48 additions and 31 deletions.
71 changes: 44 additions & 27 deletions src/gwt/org/bbop/apollo/gwt/client/GoPanel.java
View file
Expand Up @@ -28,6 +28,7 @@
import org.bbop.apollo.gwt.client.resources.TableResources;
import org.bbop.apollo.gwt.client.rest.GoRestService;
import org.bbop.apollo.gwt.shared.go.GoAnnotation;
import org.bbop.apollo.gwt.shared.go.Reference;
import org.bbop.apollo.gwt.shared.go.WithOrFrom;
import org.gwtbootstrap3.client.ui.Button;
import org.gwtbootstrap3.client.ui.Modal;
Expand All @@ -46,10 +47,11 @@ public class GoPanel extends Composite {

private final String GO_BASE = "http://amigo.geneontology.org/amigo/term/";
private final String ECO_BASE = "http://www.evidenceontology.org/term/";
// private final String RO_BASE = "http://purl.obolibrary.org/obo/";
// private final String RO_BASE = "http://purl.obolibrary.org/obo/";
private final String RO_BASE = "http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/";

interface GoPanelUiBinder extends UiBinder<Widget, GoPanel> { }
interface GoPanelUiBinder extends UiBinder<Widget, GoPanel> {
}

private static GoPanelUiBinder ourUiBinder = GWT.create(GoPanelUiBinder.class);

Expand Down Expand Up @@ -107,7 +109,7 @@ interface GoPanelUiBinder extends UiBinder<Widget, GoPanel> { }
@UiField
TextBox referenceFieldId;
@UiField
Button validateButton;
Button referenceValidateButton;
private static ListDataProvider<GoAnnotation> dataProvider = new ListDataProvider<>();
private static List<GoAnnotation> annotationInfoList = dataProvider.getList();
private SingleSelectionModel<GoAnnotation> selectionModel = new SingleSelectionModel<>();
Expand Down Expand Up @@ -264,11 +266,16 @@ private int findEntryRow(String entry) {


}
private void addWithSelection(WithOrFrom withOrFrom) {
withEntriesFlexTable.insertRow(0);
withEntriesFlexTable.setHTML(0, 0, withOrFrom.getDisplay());
withEntriesFlexTable.setWidget(0, 1, new RemoveTableEntryButton(withOrFrom.getDisplay(), withEntriesFlexTable));
}

private void addWithSelection(String with) {
private void addWithSelection(String prefixWith, String idWith) {
withEntriesFlexTable.insertRow(0);
withEntriesFlexTable.setHTML(0, 0, with);
withEntriesFlexTable.setWidget(0, 1, new RemoveTableEntryButton(with, withEntriesFlexTable));
withEntriesFlexTable.setHTML(0, 0, prefixWith + ":" + idWith);
withEntriesFlexTable.setWidget(0, 1, new RemoveTableEntryButton(prefixWith + ":" + idWith, withEntriesFlexTable));
}

private void addReferenceSelection(String referenceString) {
Expand Down Expand Up @@ -297,27 +304,27 @@ private void handleSelection() {
} else {
GoAnnotation selectedGoAnnotation = selectionModel.getSelectedObject();
goTermField.setText(selectedGoAnnotation.getGoTerm());
goTermLink.setHref(GO_BASE+selectedGoAnnotation.getGoTerm());
goTermLink.setHref(GO_BASE + selectedGoAnnotation.getGoTerm());
goTermLink.setHTML(selectedGoAnnotation.getGoTerm());
geneProductRelationshipField.setText(selectedGoAnnotation.getGeneRelationship());
geneProductRelationshipLink.setHref(RO_BASE+selectedGoAnnotation.getGeneRelationship().replaceAll(":","_"));
geneProductRelationshipLink.setHref(RO_BASE + selectedGoAnnotation.getGeneRelationship().replaceAll(":", "_"));
geneProductRelationshipLink.setHTML(selectedGoAnnotation.getGeneRelationship());
goTermLink.setHTML(selectedGoAnnotation.getGoTerm());
withEntriesFlexTable.removeAllRows();
for (WithOrFrom withOrFrom : selectedGoAnnotation.getWithOrFromList()) {
addWithSelection(withOrFrom.getDisplay());
addWithSelection(withOrFrom);
}

evidenceCodeField.setText(selectedGoAnnotation.getEvidenceCode());
evidenceCodeLink.setHref(ECO_BASE+selectedGoAnnotation.getEvidenceCode());
evidenceCodeLink.setHref(ECO_BASE + selectedGoAnnotation.getEvidenceCode());
evidenceCodeLink.setHTML(selectedGoAnnotation.getEvidenceCode());

notQualifierCheckBox.setValue(selectedGoAnnotation.isNegate());

withFieldPrefix.setText("");

notesFlexTable.removeAllRows();
for (String noteString: selectedGoAnnotation.getNoteList()) {
for (String noteString : selectedGoAnnotation.getNoteList()) {
addReferenceSelection(noteString);
}
noteField.setText("");
Expand Down Expand Up @@ -345,23 +352,25 @@ public void editGoAnnotation(ClickEvent e) {

@UiHandler("addWithButton")
public void addWith(ClickEvent e) {
String withFieldString = withFieldPrefix.getText();
if (!withFieldString.contains(":") || withFieldString.length() < 2) {
Bootbox.alert("Invalid with/from value '" + withFieldString + "'");
return;
}
addWithSelection(withFieldPrefix.getText());
// String withFieldString = withFieldPrefix.getText();
addWithSelection(withFieldPrefix.getText(), withFieldId.getText());
withFieldPrefix.clear();
withFieldId.clear();
}

@UiHandler("addNoteButton")
public void addReference(ClickEvent e) {
String referenceFieldString = noteField.getText();
if (!referenceFieldString.contains(":") || referenceFieldString.length() < 2) {
Bootbox.alert("Invalid reference value '" + referenceFieldString + "'");
return;
}
addReferenceSelection(referenceFieldString);
public void addNote(ClickEvent e) {
// String referenceFieldString = noteField.getText();
// if (!referenceFieldString.contains(":") || referenceFieldString.length() < 2) {
// Bootbox.alert("Invalid reference value '" + referenceFieldString + "'");
// return;
// }
// addReferenceSelection(referenceFieldString);
// addNote(noteField)
String noteText = noteField.getText();
notesFlexTable.insertRow(0);
notesFlexTable.setHTML(0, 0, noteText);
notesFlexTable.setWidget(0, 1, new RemoveTableEntryButton(noteText, notesFlexTable));
noteField.clear();
}

Expand Down Expand Up @@ -468,6 +477,8 @@ private GoAnnotation getEditedGoAnnotation() {
goAnnotation.setEvidenceCode(evidenceCodeField.getText());
goAnnotation.setNegate(notQualifierCheckBox.getValue());
goAnnotation.setWithOrFromList(getWithList());
Reference reference = new Reference(referenceFieldPrefix.getText(), referenceFieldId.getText());
goAnnotation.setReference(reference);
goAnnotation.setNoteList(getNoteList());
return goAnnotation;
}
Expand All @@ -477,10 +488,11 @@ private List<WithOrFrom> getWithList() {
for (int i = 0; i < withEntriesFlexTable.getRowCount(); i++) {
withOrFromList.add(new WithOrFrom(withEntriesFlexTable.getHTML(i, 0)));
}
String withString = withFieldPrefix.getText();
if (withString.length() > 0) {
String withPrefixText = withFieldPrefix.getText();
String withIdText = withFieldId.getText();
if (withPrefixText.length() > 0 && withIdText.length() > 0) {
withFieldPrefix.clear();
withOrFromList.add(new WithOrFrom(withString));
withOrFromList.add(new WithOrFrom(withPrefixText, withIdText));
}

return withOrFromList;
Expand All @@ -499,6 +511,11 @@ private List<String> getNoteList() {
return noteList;
}

@UiHandler("referenceValidateButton")
public void validateReference(ClickEvent clickEvent) {
GWT.log("not sure what to do here ");
}

@UiHandler("cancelNewGoAnnotation")
public void cancelNewGoAnnotationButton(ClickEvent e) {
editGoModal.hide();
Expand Down
2 changes: 1 addition & 1 deletion src/gwt/org/bbop/apollo/gwt/client/GoPanel.ui.xml
View file
Expand Up @@ -110,7 +110,7 @@
<b:TextBox ui:field="referenceFieldId" placeholder="ID"/>
</b:Column>
<b:Column size="MD_1">
<b:Button icon="PLUS" ui:field="validateButton">Validate</b:Button>
<b:Button icon="PLUS" ui:field="referenceValidateButton">Validate</b:Button>
</b:Column>
</b:Row>
<b:Row addStyleNames="{style.row}">
Expand Down
6 changes: 3 additions & 3 deletions src/gwt/org/bbop/apollo/gwt/shared/go/Reference.java
View file
Expand Up @@ -6,9 +6,9 @@ public class Reference {
private String lookupId;


public Reference(String lookup) {
this.prefix = lookup.split(":")[0];
this.lookupId = lookup.split(":")[1];
public Reference(String prefix,String id) {
this.prefix = prefix ;
this.lookupId = id ;
}

public String getPrefix() {
Expand Down

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