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Fix 2338 uniquenamesearch (#2339)
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* fixed a small bug

* looking up all by ID

* formatted row limit

* search lookups look good

* cleaned out and fixed some formatting

* show all box makes sense now

* some small cleanup
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@nathandunn
nathandunn committed Dec 18, 2019
1 parent 3c0b6e2 commit a91557a
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Showing 13 changed files with 641 additions and 247 deletions.
5 changes: 3 additions & 2 deletions client/apollo/js/View/Track/AnnotTrack.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2367,12 +2367,12 @@ define([
var selectedFeatureDetails = selectedFeature.afeature;
while(selectedFeature ){
if(topTypes.indexOf(selectedFeatureDetails.type.name)>=0){
this.getApollo().viewInAnnotationPanel(selectedFeatureDetails.name);
this.getApollo().viewInAnnotationPanel(selectedFeatureDetails.uniquename);
return ;
}
else
if(topTypes.indexOf(selectedFeatureDetails.parent_type.name)>=0){
this.getApollo().viewInAnnotationPanel(selectedFeatureDetails.parent_name);
this.getApollo().viewInAnnotationPanel(selectedFeatureDetails.parent_id);
return ;
}
selectedFeature = selectedFeature._parent ;
Expand Down Expand Up @@ -7763,6 +7763,7 @@ define([
*/
updateRemoveVariantEffect: function(){
var menuItem = this.getMenuItem("remove_variant_effect");
if(!menuItem) return ;
var selected = this.selectionManager.getSelection();
menuItem.set("disabled", true);
if (selected.length === 0) {
Expand Down
10 changes: 8 additions & 2 deletions grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -296,9 +296,10 @@ class AnnotatorController {
* @param max
* @param sortorder
* @param sort
* @param searchUniqueName
* @return
*/
def findAnnotationsForSequence(String sequenceName, String request, String annotationName, String type, String user, Integer offset, Integer max, String sortorder, String sort, String clientToken,Boolean showOnlyGoAnnotations) {
def findAnnotationsForSequence(String sequenceName, String request, String annotationName, String type, String user, Integer offset, Integer max, String sortorder, String sort, String clientToken,Boolean showOnlyGoAnnotations,Boolean searchUniqueName) {
try {
JSONObject returnObject = jsonWebUtilityService.createJSONFeatureContainer()
returnObject.clientToken = clientToken
Expand Down Expand Up @@ -369,7 +370,12 @@ class AnnotatorController {
order('lastUpdated', sortorder)
}
if (annotationName) {
ilike('name', '%' + annotationName + '%')
if(searchUniqueName){
ilike('uniqueName', '%' + annotationName + '%')
}
else{
ilike('name', '%' + annotationName + '%')
}
}
if (user) {
owners {
Expand Down
182 changes: 61 additions & 121 deletions src/gwt/org/bbop/apollo/gwt/client/AnnotatorPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,9 +29,8 @@
import com.google.gwt.uibinder.client.UiBinder;
import com.google.gwt.uibinder.client.UiField;
import com.google.gwt.uibinder.client.UiHandler;
import com.google.gwt.user.cellview.client.*;
import com.google.gwt.user.cellview.client.Column;
import com.google.gwt.user.client.Window;
import com.google.gwt.user.cellview.client.*;
import com.google.gwt.user.client.ui.*;
import com.google.gwt.view.client.*;
import org.bbop.apollo.gwt.client.dto.AnnotationInfo;
Expand All @@ -44,19 +43,18 @@
import org.bbop.apollo.gwt.client.event.UserChangeEventHandler;
import org.bbop.apollo.gwt.client.oracles.ReferenceSequenceOracle;
import org.bbop.apollo.gwt.client.resources.TableResources;
import org.bbop.apollo.gwt.client.rest.AnnotationRestService;
import org.bbop.apollo.gwt.client.rest.UserRestService;
import org.bbop.apollo.gwt.shared.FeatureStringEnum;
import org.bbop.apollo.gwt.shared.PermissionEnum;
import org.gwtbootstrap3.client.ui.Button;
import org.gwtbootstrap3.client.ui.*;
import org.gwtbootstrap3.client.ui.CheckBox;
import org.gwtbootstrap3.client.ui.Label;
import org.gwtbootstrap3.client.ui.ListBox;
import org.gwtbootstrap3.client.ui.TextBox;
import org.gwtbootstrap3.client.ui.*;
import org.gwtbootstrap3.client.ui.constants.ButtonType;
import org.gwtbootstrap3.client.ui.constants.IconType;
import org.gwtbootstrap3.extras.bootbox.client.Bootbox;
import org.gwtbootstrap3.extras.bootbox.client.callback.ConfirmCallback;

import java.util.Date;
import java.util.HashSet;
Expand Down Expand Up @@ -127,12 +125,8 @@ interface AnnotatorPanelUiBinder extends UiBinder<com.google.gwt.user.client.ui.
DockLayoutPanel splitPanel;
@UiField
Container northPanelContainer;
@UiField
static Button gotoAnnotation;
@UiField
static Button deleteAnnotation;
@UiField
Button toggleAnnotation;
// @UiField
// Button toggleAnnotation;
@UiField
com.google.gwt.user.client.ui.ListBox pageSizeSelector;
@UiField
Expand All @@ -145,10 +139,14 @@ interface AnnotatorPanelUiBinder extends UiBinder<com.google.gwt.user.client.ui.
static CommentPanel commentPanel;
@UiField
static AttributePanel attributePanel;
@UiField
CheckBox uniqueNameCheckBox;
@UiField
Button showAllSequences;


// manage UI-state
private Boolean showDetails = true ;
private Boolean showDetails = true;

static AnnotationInfo selectedAnnotationInfo;
private MultiWordSuggestOracle sequenceOracle = new ReferenceSequenceOracle();
Expand All @@ -169,14 +167,15 @@ public enum TAB_INDEX {
ATTRIBUTES(8),
;

public int index ;
TAB_INDEX(int index){
public int index;

TAB_INDEX(int index) {
this.index = index;
}

public static TAB_INDEX getTabEnumForIndex(int selectedSubTabIndex) {
for(TAB_INDEX value: values()){
if(value.index==selectedSubTabIndex){
for (TAB_INDEX value : values()) {
if (value.index == selectedSubTabIndex) {
return value;
}
}
Expand Down Expand Up @@ -236,10 +235,12 @@ protected void onRangeChanged(HasData<AnnotationInfo> display) {
String url = Annotator.getRootUrl() + "annotator/findAnnotationsForSequence/?sequenceName=" + sequenceName;
url += "&request=" + requestIndex;
url += "&offset=" + start + "&max=" + length;
url += "&annotationName=" + nameSearchBox.getText() + "&type=" + typeList.getSelectedValue();
url += "&annotationName=" + nameSearchBox.getText();
url += "&type=" + typeList.getSelectedValue();
url += "&user=" + userField.getSelectedValue();
url += "&clientToken=" + Annotator.getClientToken();
url += "&showOnlyGoAnnotations=" + goOnlyCheckBox.getValue();
url += "&searchUniqueName=" + uniqueNameCheckBox.getValue();


ColumnSortList.ColumnSortInfo nameSortInfo = sortList.get(0);
Expand Down Expand Up @@ -469,9 +470,9 @@ public void execute() {

}

void selectGoPanel(){
goPanel.redraw();
tabPanel.selectTab(5);
void selectGoPanel() {
goPanel.redraw();
tabPanel.selectTab(5);
}


Expand Down Expand Up @@ -781,24 +782,20 @@ public void onDoubleClick(DoubleClickEvent event) {
@Override
public void onSelectionChange(SelectionChangeEvent event) {
selectedAnnotationInfo = singleSelectionModel.getSelectedObject();
tabPanel.setVisible(showDetails && selectedAnnotationInfo!=null);
GWT.log("select info"+selectedAnnotationInfo);
tabPanel.setVisible(showDetails && selectedAnnotationInfo != null);
GWT.log("select info" + selectedAnnotationInfo);
if (selectedAnnotationInfo != null) {
exonDetailPanel.updateData(selectedAnnotationInfo);
goPanel.updateData(selectedAnnotationInfo);
dbXrefPanel.updateData(selectedAnnotationInfo);
commentPanel.updateData(selectedAnnotationInfo);
attributePanel.updateData(selectedAnnotationInfo);
gotoAnnotation.setEnabled(true);
deleteAnnotation.setEnabled(true);
} else {
exonDetailPanel.updateData();
goPanel.updateData();
dbXrefPanel.updateData();
commentPanel.updateData();
attributePanel.updateData();
gotoAnnotation.setEnabled(false);
deleteAnnotation.setEnabled(false);
}
}
});
Expand All @@ -825,6 +822,8 @@ private String getType(JSONObject internalData) {
}

public void reload(Boolean forceReload) {
showAllSequences.setEnabled(isSearchDirty());
showAllSequences.setType(isSearchDirty() ? ButtonType.INFO : ButtonType.DEFAULT);
if (MainPanel.annotatorPanel.isVisible() || forceReload) {
hideDetailPanels();
pager.setPageStart(0);
Expand All @@ -836,14 +835,26 @@ public void reload() {
reload(false);
}

private Boolean isSearchDirty() {
if(typeList.getSelectedIndex()>0) return true;
if(userField.getSelectedIndex()>0) return true;
if(goOnlyCheckBox.getValue()) return true;
if(uniqueNameCheckBox.getValue()) return true;
if(uniqueNameCheckBox.getValue()) return true;
if(nameSearchBox.getText().trim().length()>0) return true;
if(sequenceList.getValue().trim().length()>0) return true;

return false ;
}

@UiHandler(value = {"pageSizeSelector"})
public void changePageSize(ChangeEvent changeEvent) {
pageSize = Integer.parseInt(pageSizeSelector.getSelectedValue());
dataGrid.setPageSize(pageSize);
reload();
}

@UiHandler(value = {"typeList", "userField","goOnlyCheckBox"})
@UiHandler(value = {"typeList", "userField", "goOnlyCheckBox","uniqueNameCheckBox"})
public void searchType(ChangeEvent changeEvent) {
reload();
}
Expand All @@ -857,102 +868,33 @@ public void searchName(KeyUpEvent keyUpEvent) {
public void setShowAllSequences(ClickEvent clickEvent) {
nameSearchBox.setText("");
sequenceList.setText("");
userField.setSelectedIndex(0);
typeList.setSelectedIndex(0);
uniqueNameCheckBox.setValue(false);
goOnlyCheckBox.setValue(false);
reload();
}

@UiHandler("gotoAnnotation")
void gotoAnnotation(ClickEvent clickEvent) {
Integer min = selectedAnnotationInfo.getMin() - 50;
Integer max = selectedAnnotationInfo.getMax() + 50;
min = min < 0 ? 0 : min;
MainPanel.updateGenomicViewerForLocation(selectedAnnotationInfo.getSequence(), min, max, false, false);
}


private void handleDetails(){
if(showDetails) {
toggleAnnotation.setText("Hide Details");
toggleAnnotation.setIcon(IconType.EYE_SLASH);
} else{
toggleAnnotation.setText("Show Details");
toggleAnnotation.setIcon(IconType.INFO_CIRCLE);
}

tabPanel.setVisible(showDetails && singleSelectionModel.getSelectedObject()!=null);
}

@UiHandler("toggleAnnotation")
void toggleAnnotation(ClickEvent clickEvent) {
showDetails = !showDetails;
handleDetails();
}

@UiHandler("deleteAnnotation")
void deleteAnnotation(ClickEvent clickEvent) {
final Set<AnnotationInfo> deletableChildren = getDeletableChildren(selectedAnnotationInfo);
String confirmString = "";
if (deletableChildren.size() > 0) {
confirmString = "Delete the " + deletableChildren.size() + " annotation" + (deletableChildren.size() > 1 ? "s" : "") + " belonging to the " + selectedAnnotationInfo.getType() + " " + selectedAnnotationInfo.getName() + "?";
} else {
confirmString = "Delete the " + selectedAnnotationInfo.getType() + " " + selectedAnnotationInfo.getName() + "?";
}


final RequestCallback requestCallback = new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
if (response.getStatusCode() == 200) {
// parse to make sure we return the complete amount
try {
JSONValue returnValue = JSONParser.parseStrict(response.getText());
GWT.log("Return: "+returnValue.toString());
Bootbox.confirm("Success. Reload page to reflect results?", new ConfirmCallback() {
@Override
public void callback(boolean result) {
if(result){
Window.Location.reload();
}
}
});
} catch (Exception e) {
Bootbox.alert(e.getMessage());
}
} else {
Bootbox.alert("Problem with deletion: " + response.getText());
}
}

@Override
public void onError(Request request, Throwable exception) {
Bootbox.alert("Problem with deletion: " + exception.getMessage());
}
};
private void handleDetails() {
// if (showDetails) {
// toggleAnnotation.setText("Hide Details");
// toggleAnnotation.setIcon(IconType.EYE_SLASH);
// } else {
// toggleAnnotation.setText("Show Details");
// toggleAnnotation.setIcon(IconType.INFO_CIRCLE);
// }

Bootbox.confirm(confirmString, new ConfirmCallback() {
@Override
public void callback(boolean result) {
if (result) {
if (deletableChildren.size() == 0) {
Set<AnnotationInfo> annotationInfoSet = new HashSet<>();
annotationInfoSet.add(selectedAnnotationInfo);
AnnotationRestService.deleteAnnotations(requestCallback, annotationInfoSet);
} else {
JSONObject jsonObject = AnnotationRestService.deleteAnnotations(requestCallback, deletableChildren);
}
}
}
});
tabPanel.setVisible(showDetails && singleSelectionModel.getSelectedObject() != null);
}
//
// @UiHandler("toggleAnnotation")
// void toggleAnnotation(ClickEvent clickEvent) {
// showDetails = !showDetails;
// handleDetails();
// }


private Set<AnnotationInfo> getDeletableChildren(AnnotationInfo selectedAnnotationInfo) {
String type = selectedAnnotationInfo.getType();
if (type.equalsIgnoreCase(FeatureStringEnum.GENE.getValue()) || type.equalsIgnoreCase(FeatureStringEnum.PSEUDOGENE.getValue())) {
return selectedAnnotationInfo.getChildAnnotations();
}
return new HashSet<>();
}

private static AnnotationInfo getChildAnnotation(AnnotationInfo annotationInfo, String uniqueName) {
for (AnnotationInfo childAnnotation : annotationInfo.getChildAnnotations()) {
if (childAnnotation.getUniqueName().equalsIgnoreCase(uniqueName)) {
Expand All @@ -969,16 +911,14 @@ public void enableGoto(int geneIndex, String uniqueName) {
selectedAnnotationInfo = getChildAnnotation(annotationInfo, uniqueName);
exonDetailPanel.updateData(selectedAnnotationInfo);
updateAnnotationInfo(selectedAnnotationInfo);
gotoAnnotation.setEnabled(true);
deleteAnnotation.setEnabled(true);
selectedChildUniqueName = selectedAnnotationInfo.getUniqueName();
}

// used by javascript function
public void displayTranscript(int geneIndex, String uniqueName) {

// for some reason doesn't like call enableGoto
enableGoto(geneIndex,uniqueName);
enableGoto(geneIndex, uniqueName);

// for some reason doesn't like call gotoAnnotation
Integer min = selectedAnnotationInfo.getMin() - 50;
Expand All @@ -991,13 +931,13 @@ public void displayTranscript(int geneIndex, String uniqueName) {
public void displayFeature(int featureIndex) {
AnnotationInfo annotationInfo = dataGrid.getVisibleItem(Math.abs(dataGrid.getVisibleRange().getStart() - featureIndex));
String type = annotationInfo.getType();
if (type.equals("transposable_element") || type.equals("repeat_region") || type.equals("terminator") ) {
if (type.equals("transposable_element") || type.equals("repeat_region") || type.equals("terminator")) {
// do nothing
} else {
exonDetailPanel.updateData(annotationInfo);
}
gotoAnnotation.setEnabled(true);
deleteAnnotation.setEnabled(true);
// gotoAnnotation.setEnabled(true);
// deleteAnnotation.setEnabled(true);
Integer min = selectedAnnotationInfo.getMin() - 50;
Integer max = selectedAnnotationInfo.getMax() + 50;
min = min < 0 ? 0 : min;
Expand Down
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