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cleaned up and redid the rest doc for newer routes
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@nathandunn
nathandunn committed Dec 11, 2019
1 parent b0d4336 commit 8e8e091
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Showing 11 changed files with 1,228 additions and 1,252 deletions.
1 change: 0 additions & 1 deletion grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy
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Expand Up @@ -201,7 +201,6 @@ class AnnotatorController {
feature.name = data.name
feature.symbol = data.symbol
feature.description = data.description
println "status input ${data.status}"

if(data.status==null){
// delete old status if it existed
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1 change: 0 additions & 1 deletion grails-app/controllers/org/bbop/apollo/NcbiProxyServiceController.groovy
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Expand Up @@ -20,7 +20,6 @@ class NcbiProxyServiceController {
String db = params.db
String id = params.id
String operation = params.operation
println "params ${params}"
String urlString

switch (operation) {
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1 change: 0 additions & 1 deletion grails-app/services/org/bbop/apollo/FeaturePropertyService.groovy
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Expand Up @@ -52,7 +52,6 @@ class FeaturePropertyService {
@Transactional
boolean deleteComment(Feature feature, String commentString) {
Comment comment = Comment.findByFeatureAndValue(feature, commentString)
println "founda comment to dleete ${comment}"
if (comment) {
feature.removeFromFeatureProperties(comment)
Comment.deleteAll(comment)
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2 changes: 0 additions & 2 deletions grails-app/services/org/bbop/apollo/FeatureService.groovy
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Expand Up @@ -1603,9 +1603,7 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {
String cvString = jsonCVTerm.getJSONObject(FeatureStringEnum.CV.value).getString(FeatureStringEnum.NAME.value)
String cvTermString = jsonCVTerm.getString(FeatureStringEnum.NAME.value)

println "convertin from ${jsonCVTerm} ${cvString} ${cvTermString}"
if (cvString.equalsIgnoreCase(FeatureStringEnum.CV.value) || cvString.equalsIgnoreCase(FeatureStringEnum.SEQUENCE.value)) {
println "looking for ${cvTermString}"
switch (cvTermString.toUpperCase()) {
case MRNA.cvTerm.toUpperCase(): return MRNA.ontologyId
case MiRNA.cvTerm.toUpperCase(): return MiRNA.ontologyId
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1 change: 0 additions & 1 deletion grails-app/services/org/bbop/apollo/RequestHandlingService.groovy
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Expand Up @@ -397,7 +397,6 @@ class RequestHandlingService {
String uniqueName = jsonFeature.get(FeatureStringEnum.UNIQUENAME.value)
Feature feature = Feature.findByUniqueName(uniqueName)
JSONObject originalFeatureJsonObject = featureService.convertFeatureToJSON(feature)
println "deleting comments ${commentsArray} on feature $feature"

for (int commentIndex = 0; commentIndex < commentsArray.size(); commentIndex++) {
String commentString = commentsArray.getString(commentIndex);
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1 change: 0 additions & 1 deletion src/gwt/org/bbop/apollo/gwt/client/AnnotatorPanel.java
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Expand Up @@ -394,7 +394,6 @@ public void onKeyUp(KeyUpEvent event) {
@Override
public void onSelection(SelectionEvent<Integer> event) {
selectedSubTabIndex = event.getSelectedItem();
GWT.log("selected tab: "+ selectedSubTabIndex);
TAB_INDEX tab = TAB_INDEX.getTabEnumForIndex(selectedSubTabIndex);
switch (tab) {
case DETAILS:
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5 changes: 0 additions & 5 deletions src/gwt/org/bbop/apollo/gwt/client/AttributePanel.java
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Expand Up @@ -148,7 +148,6 @@ public void update(int i, AttributeInfo object, String s) {
dataGrid.redrawRow(i);
redrawTable();
} else if (!object.getTag().equals(s)) {
GWT.log("Tag Changed");
object.setTag(s);
selectAttributeData(object);
updateAttribute();
Expand All @@ -173,7 +172,6 @@ public void update(int i, AttributeInfo object, String s) {
dataGrid.redrawRow(i);
redrawTable();
} else if (!object.getValue().equals(s)) {
GWT.log("Value Changed");
object.setValue(s);
selectAttributeData(object);
updateAttribute();
Expand Down Expand Up @@ -210,15 +208,13 @@ public int compare(AttributeInfo o1, AttributeInfo o2) {
}

public void updateData(AnnotationInfo annotationInfo) {
GWT.log("updating annotation info: " + annotationInfo);
if (annotationInfo == null) {
return;
}
this.internalAnnotationInfo = annotationInfo;
attributeInfoList.clear();
attributeInfoList.addAll(annotationInfo.getAttributeList());
ColumnSortEvent.fire(dataGrid, dataGrid.getColumnSortList());
GWT.log("List size: " + attributeInfoList.size());
loadCannedKeys();
loadCannedValues();
redrawTable();
Expand Down Expand Up @@ -316,7 +312,6 @@ public void onError(Request request, Throwable exception) {
}

private void resetTags() {
GWT.log("reseting tag");
this.tag = this.oldTag;
this.value = this.oldValue;
updateData(this.internalAnnotationInfo);
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5 changes: 0 additions & 5 deletions src/gwt/org/bbop/apollo/gwt/client/CommentPanel.java
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Expand Up @@ -124,7 +124,6 @@ public void initializeTable() {
Column<CommentInfo, String> commentColumn = new Column<CommentInfo, String>(commentCell) {
@Override
public String getValue(CommentInfo commentInfo) {
GWT.log("getting comment info data: "+commentInfo.getComment());
return commentInfo.getComment();
}
};
Expand All @@ -137,7 +136,6 @@ public void update(int i, CommentInfo object, String s) {
dataGrid.redrawRow(i);
redrawTable();
} else if (!object.getComment().equals(s)) {
GWT.log("Value Changed");
object.setComment(s);
selectCommentData(object);
updateComment();
Expand Down Expand Up @@ -165,7 +163,6 @@ public int compare(CommentInfo o1, CommentInfo o2) {
}

public void updateData(AnnotationInfo annotationInfo) {
GWT.log("updating annotation info: " + annotationInfo);
if (annotationInfo == null) {
return;
}
Expand Down Expand Up @@ -193,9 +190,7 @@ public void selectCommentData(CommentInfo v) {
}

public void updateComment() {
GWT.log("updating comment "+this.comment);
if (this.comment!=null && !this.comment.isEmpty()) {
GWT.log("completely valid man"+this.comment);
final CommentInfo newCommentInfo = new CommentInfo(this.comment);
RequestCallback requestCallBack = new RequestCallback() {
@Override
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7 changes: 0 additions & 7 deletions src/gwt/org/bbop/apollo/gwt/client/DbXrefPanel.java
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Expand Up @@ -114,7 +114,6 @@ public void update(int i, DbXrefInfo object, String s) {
dataGrid.redrawRow(i);
redrawTable();
} else if (!object.getTag().equals(s)) {
GWT.log("Tag Changed");
object.setTag(s);
selectDbXrefData(object);
updateDbXref();
Expand All @@ -139,7 +138,6 @@ public void update(int i, DbXrefInfo object, String s) {
dataGrid.redrawRow(i);
redrawTable();
} else if (!object.getValue().equals(s)) {
GWT.log("Value Changed");
object.setValue(s);
selectDbXrefData(object);
updateDbXref();
Expand Down Expand Up @@ -176,15 +174,13 @@ public int compare(DbXrefInfo o1, DbXrefInfo o2) {
}

public void updateData(AnnotationInfo annotationInfo) {
GWT.log("updating annotation info: " + annotationInfo);
if (annotationInfo == null) {
return;
}
this.internalAnnotationInfo = annotationInfo;
dbXrefInfoList.clear();
dbXrefInfoList.addAll(annotationInfo.getDbXrefList());
ColumnSortEvent.fire(dataGrid, dataGrid.getColumnSortList());
GWT.log("List size: " + dbXrefInfoList.size());
redrawTable();
setVisible(true);
}
Expand Down Expand Up @@ -235,7 +231,6 @@ public void onError(Request request, Throwable exception) {
}

private void resetTags() {
GWT.log("reseting tag");
this.tag = this.oldTag;
this.value = this.oldValue;
updateData(this.internalAnnotationInfo);
Expand Down Expand Up @@ -320,8 +315,6 @@ public void onResponseReceived(Request request, Response response) {
try {
title = returnValue.isObject().get("PubmedArticleSet").isObject().get("PubmedArticle").isObject().get("MedlineCitation").isObject().get("Article").isObject().get("ArticleTitle").isString().stringValue();
} catch (Exception e) {
GWT.log("Could not find error: "+e.getMessage() );
GWT.log("Return object "+returnValue.toString() );
Bootbox.alert("No article found for " + pmidValue);
resetTags();
redrawTable();
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6 changes: 3 additions & 3 deletions src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -116,13 +116,13 @@ private void enableFields(boolean enabled) {

private void updateGene() {
final AnnotationInfo updatedInfo = this.internalAnnotationInfo;
// enableFields(false);
enableFields(false);

RequestCallback requestCallback = new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
// JSONValue returnValue = JSONParser.parseStrict(response.getText());
// enableFields(true);
JSONValue returnValue = JSONParser.parseStrict(response.getText());
enableFields(true);
// Annotator.eventBus.fireEvent(new AnnotationInfoChangeEvent(updatedInfo, AnnotationInfoChangeEvent.Action.UPDATE));
}

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