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Merge pull request #980 from WildMeOrg/920_annotation_create_post
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Annotation create POST api
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@erinz2020
erinz2020 authored Jan 22, 2025
2 parents fbac158 + f6cad3b commit 00f0af7
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Showing 3 changed files with 303 additions and 10 deletions.
266 changes: 266 additions & 0 deletions src/main/java/org/ecocean/Annotation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.core.JsonProcessingException;
import java.awt.Rectangle;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
Expand All @@ -16,11 +17,14 @@
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.ecocean.api.ApiException;
import org.ecocean.ia.IA;
import org.ecocean.ia.Task;
import org.ecocean.identity.IBEISIA;
import org.ecocean.media.Feature;
import org.ecocean.media.FeatureType;
import org.ecocean.media.MediaAsset;
import org.ecocean.media.MediaAssetFactory;
import org.json.JSONArray;
import org.json.JSONObject;

Expand Down Expand Up @@ -327,6 +331,8 @@ public boolean isTrivial() {
for (Feature ft : getFeatures()) {
if (ft.isUnity()) return true;
}
// prevents zero-values from return true on final test
if ((getWidth() == 0) || (getHeight() == 0)) return false;
return (!needsTransform() && (getWidth() == (int)ma.getWidth()) &&
(getHeight() == (int)ma.getHeight()));
}
Expand Down Expand Up @@ -1184,6 +1190,266 @@ public Annotation shallowCopy() {
return ann;
}

public static Base createFromApi(JSONObject payload, List<File> files, Shepherd myShepherd)
throws ApiException {
if (payload == null) throw new ApiException("empty payload");
User user = (User)payload.opt("_currentUser");
int maId = (Integer)validateFieldValue("mediaAssetId", payload);
int x = (Integer)validateFieldValue("x", payload);
int y = (Integer)validateFieldValue("y", payload);
int width = (Integer)validateFieldValue("width", payload);
int height = (Integer)validateFieldValue("height", payload);
double theta = (Double)validateFieldValue("theta", payload);
String iaClass = (String)validateFieldValue("iaClass", payload);
String viewpoint = (String)validateFieldValue("viewpoint", payload);
// dont need to validate encId, as it is optional and we load encounter below which effectively validates if set
// UPDATE: switching gears on this -- now requiring encounter; but leaving this code as-is in case we switch back
// (see comments below as well)
String encId = payload.optString("encounterId", null);
JSONObject error = new JSONObject();
MediaAsset ma = MediaAssetFactory.load(maId, myShepherd);
if (ma == null) {
error.put("code", ApiException.ERROR_RETURN_CODE_INVALID);
error.put("fieldName", "mediaAssetId");
error.put("value", maId);
throw new ApiException("invalid MediaAsset id=" + maId, error);
}
Encounter enc = null;
if (encId != null) {
enc = myShepherd.getEncounter(encId);
if (enc == null) {
error.put("code", ApiException.ERROR_RETURN_CODE_INVALID);
error.put("fieldName", "encounterId");
error.put("value", encId);
throw new ApiException("invalid Encounter id=" + maId, error);
}
// TODO manualAnnotation.jsp did *not* restrict who can edit which encounter, as long as they had researcher role
// should this be locked down tighter as to who can add an annotation to an encounter?
}
// as noted above, last-minute decision to make an encounter required:
if (enc == null) {
error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED);
error.put("fieldName", "encounterId");
throw new ApiException("Encounter required", error);
}
// validate iaClass; this is a little janky
IAJsonProperties iaConf = IAJsonProperties.iaConfig();
if (enc != null) {
Taxonomy tx = enc.getTaxonomy(myShepherd);
if (!iaConf.isValidIAClass(tx, iaClass)) {
error.put("code", ApiException.ERROR_RETURN_CODE_INVALID);
error.put("fieldName", "iaClass");
error.put("value", iaClass);
throw new ApiException("iaClass=" + iaClass + " invalid for taxonomy " + tx +
" on " + enc, error);
}
}
// must have all we need now
String context = myShepherd.getContext();
List<Annotation> annots = ma.getAnnotations(); // get before we add ours
FeatureType.initAll(myShepherd);
JSONObject fparams = new JSONObject();
fparams.put("x", x);
fparams.put("y", y);
fparams.put("width", width);
fparams.put("height", height);
fparams.put("theta", theta);
fparams.put("viewpoint", viewpoint); // not sure when/how this is used, but seems here historically
fparams.put("_manualAnnotationViaApiV3", System.currentTimeMillis());
Feature ft = new Feature("org.ecocean.boundingBox", fparams);
Annotation ann = new Annotation(null, ft, iaClass);
ann.setViewpoint(viewpoint);
ma.addFeature(ft);
ma.setDetectionStatus("complete");
myShepherd.getPM().makePersistent(ft);
myShepherd.getPM().makePersistent(ann);
/*
believe this is overly complicated, but saving it from manualAnnotation.jsp logic
if (enc != null) {
if (IBEISIA.validForIdentification(ann, context) && iaConf.isValidIAClass(enc.getTaxonomy(myShepherd), iaClass)) {
ann.setMatchAgainst(true);
}
}
*/
// NOTE: manualAnnotation.jsp once allowed featureId to be passed; that functionality is not handled here
//
// we replace trivial if applicable; otherwise this logic determines if we should
// clone the encounter (based off historic logic in manualAnnotation.jsp)
if (enc != null) {
ann.setMatchAgainst(true);
boolean cloneEncounter = false;
// we would expect at least a trivial annotation, so if annots>=2, we know we need to clone
if ((annots.size() > 1) && (iaClass != null)) {
System.out.println("DEBUG Annotation.createFromApi(): cloneEncounter [0]");
cloneEncounter = true;

// also don't clone if this is a part
// if the one annot isn't trivial, then we have to clone the encounter as well
} else if ((annots.size() == 1) && !annots.get(0).isTrivial() && (iaClass != null) &&
(iaClass.indexOf("+") == -1)) {
System.out.println("DEBUG Annotation.createFromApi(): cloneEncounter [1]");
cloneEncounter = true;
// exception case - if there is only one annotation and it is a part
Annotation annot1 = annots.get(0);
if ((annot1.getIAClass() != null) && (annot1.getIAClass().indexOf("+") != -1)) {
System.out.println("DEBUG Annotation.createFromApi(): cloneEncounter [2]");
cloneEncounter = false;
}
// exception case - if there is only one annotation and it is a part
} else if ((annots.size() == 1) && !annots.get(0).isTrivial() && (iaClass != null) &&
(iaClass.indexOf("+") > -1)) {
System.out.println("DEBUG Annotation.createFromApi(): cloneEncounter [3]");
Annotation annot1 = annots.get(0);
if ((annot1.getIAClass() != null) && (annot1.getIAClass().indexOf("+") != -1)) {
System.out.println("DEBUG Annotation.createFromApi(): cloneEncounter [4]");
cloneEncounter = true;
}
}
if (cloneEncounter) {
try {
Encounter clone = enc.cloneWithoutAnnotations(myShepherd);
clone.addAnnotation(ann);
clone.addComments("<p data-annot-id=\"" + ann.getId() +
"\">Encounter cloned and <i>new Annotation</i> manually added by " +
user.getDisplayName() + "</p>");
myShepherd.getPM().makePersistent(clone);
Occurrence occ = myShepherd.getOccurrence(enc);
if (occ != null) {
occ.addEncounterAndUpdateIt(clone);
occ.setDWCDateLastModified();
} else {
// let's create an occurrence to link these two Encounters
occ = new Occurrence(Util.generateUUID(), clone);
occ.addEncounter(enc);
myShepherd.getPM().makePersistent(occ);
}
System.out.println("Annotation.createFromApi(): " + ann + " added to clone " +
clone + " in " + occ);
myShepherd.updateDBTransaction();
} catch (Exception ex) {
throw new ApiException("cloning encounter " + enc.getId() + " failed: " +
ex.toString());
}
} else { // not cloned
enc.addAnnotation(ann);
enc.addComments("<p data-annot-id=\"" + ann.getId() +
"\"><i>new Annotation</i> manually added by " + user.getDisplayName() + "</p>");
System.out.println("Annotation.createFromApi(): " + ann + " added to " + enc);
}
}
// NOTE: manualAnnotation.jsp allowed 'removeTrivial' (boolean) to be set via url, but was default true
Annotation foundTrivial = null; // note this will only remove (at most) ONE (but "should never" have > 1 anyway)
for (Annotation a : ma.getAnnotations()) {
if (a.isTrivial()) foundTrivial = a;
}
if (foundTrivial == null) {
System.out.println(
"Annotation.createFromApi(): no trivial annotation found to remove from " + ma);
} else {
foundTrivial.detachFromMediaAsset();
if (enc == null) {
System.out.println("Annotation.createFromApi(): removeTrivial detached " +
foundTrivial + " (and Feature) from " + ma);
} else {
enc.removeAnnotation(foundTrivial);
System.out.println("Annotation.createFromApi(): removeTrivial detached " +
foundTrivial + " (and Feature) from " + ma + " and " + enc);
}
}
// send to IA as needed
try {
if (ma.getAcmId() == null) {
ArrayList<MediaAsset> mas = new ArrayList<MediaAsset>();
mas.add(ma);
IBEISIA.sendMediaAssetsNew(mas, context);
}
ArrayList<Annotation> anns = new ArrayList<Annotation>();
anns.add(ann);
IBEISIA.sendAnnotationsNew(anns, context, myShepherd);
} catch (Exception ex) {} // silently fail; they will be synced up later
return ann;
}

public static Object validateFieldValue(String fieldName, JSONObject data)
throws ApiException {
if (data == null) throw new ApiException("empty payload");
org.json.JSONObject error = new org.json.JSONObject();
error.put("fieldName", fieldName);
String exMessage = "invalid value for " + fieldName;
Object returnValue = null;
switch (fieldName) {
case "mediaAssetId":
returnValue = data.optInt(fieldName, 0);
if ((int)returnValue < 1) {
error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED);
throw new ApiException(exMessage, error);
}
break;

case "width":
case "height":
// value must be > 0 (also will catch unset)
returnValue = data.optInt(fieldName, -1);
if ((int)returnValue < 1) {
error.put("code", ApiException.ERROR_RETURN_CODE_INVALID);
error.put("value", returnValue);
throw new ApiException(exMessage, error);
}
break;

case "x":
case "y":
// x/y can be negative or zero, but they are required
// little hacky as prevents this actual x/y value, but um...
returnValue = data.optInt(fieldName, -999999);
if ((int)returnValue == -999999) {
error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED);
throw new ApiException(exMessage, error);
}
break;

case "theta":
returnValue = data.optDouble(fieldName, 9999.9);
double dval = (double)returnValue;
if (dval == 9999.9) {
returnValue = 0.0d; // theta (passed-in) is optional, but results in 0.0
} else if ((dval < -6.2832) || (dval > 6.2832)) {
error.put("code", ApiException.ERROR_RETURN_CODE_INVALID);
error.put("value", dval);
throw new ApiException("invalid theta value in radians", error);
}
break;

case "viewpoint":
returnValue = data.optString(fieldName, null);
if (returnValue == null) {
error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED);
throw new ApiException(exMessage, error);
}
if (!isValidViewpoint((String)returnValue)) {
error.put("code", ApiException.ERROR_RETURN_CODE_INVALID);
error.put("value", returnValue);
throw new ApiException(exMessage, error);
}
break;

case "iaClass":
// TODO is iaClass required???
returnValue = data.optString(fieldName, null);
if (returnValue == null) {
error.put("code", ApiException.ERROR_RETURN_CODE_REQUIRED);
throw new ApiException(exMessage, error);
}
// validity is checked in main createFromApi
break;

default:
System.out.println("Encounter.validateFieldValue(): WARNING unsupported fieldName=" +
fieldName);
}
return returnValue;
}

public List<Task> getRootIATasks(Shepherd myShepherd) { // convenience
return Task.getRootTasksFor(this, myShepherd);
}
Expand Down
43 changes: 33 additions & 10 deletions src/main/java/org/ecocean/api/BaseObject.java
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Original file line number Diff line number Diff line change
Expand Up @@ -152,20 +152,41 @@ protected JSONObject processPost(HttpServletRequest request, String[] args, JSON
// these are needed for display in results
rtn.put("locationId", enc.getLocationID());
rtn.put("submissionDate", enc.getDWCDateAdded());
rtn.put("statusCode", 200);
break;
case "occurrences":
obj = Occurrence.createFromApi(payload, files, myShepherd);
if (currentUser == null) {
rtn.put("statusCode", 401);
rtn.put("error", "access denied");
} else {
obj = Occurrence.createFromApi(payload, files, myShepherd);
}
break;
case "individuals":
obj = MarkedIndividual.createFromApi(payload, files, myShepherd);
if (currentUser == null) {
rtn.put("statusCode", 401);
rtn.put("error", "access denied");
} else {
obj = MarkedIndividual.createFromApi(payload, files, myShepherd);
}
break;
case "annotations":
if (currentUser == null) {
rtn.put("statusCode", 401);
rtn.put("error", "access denied");
} else {
obj = Annotation.createFromApi(payload, files, myShepherd);
}
break;
default:
throw new ApiException("bad class");
}
rtn.put("id", obj.getId());
rtn.put("class", cls);
rtn.put("success", true);
// add for any flavor of Base
if (obj != null) {
rtn.put("id", obj.getId());
rtn.put("class", cls);
rtn.put("statusCode", 200);
rtn.put("success", true);
}
} catch (ApiException apiEx) {
System.out.println("BaseObject.processPost() returning 400 due to " + apiEx +
" [errors=" + apiEx.getErrors() + "] on payload " + payload);
Expand All @@ -176,12 +197,14 @@ protected JSONObject processPost(HttpServletRequest request, String[] args, JSON
if ((obj != null) && (rtn.optInt("statusCode", 0) == 200)) {
System.out.println("BaseObject.processPost() success (200) creating " + obj +
" from payload " + payload);
OpenSearch.setPermissionsNeeded(myShepherd, true);
myShepherd.commitDBTransaction();
MediaAsset.updateStandardChildrenBackground(context, maIds);
if (encounterForIA != null) {
if (encounterForIA != null) { // encounter-specific needs
OpenSearch.setPermissionsNeeded(myShepherd, true);
myShepherd.commitDBTransaction();
MediaAsset.updateStandardChildrenBackground(context, maIds);
encounterForIA.sendToIA(myShepherd);
encounterForIA.sendCreationEmails(myShepherd, langCode);
} else {
myShepherd.commitDBTransaction();
}
// not sure what this is for, but servlet/EncounterForm did it so guessing its important
org.ecocean.ShepherdPMF.getPMF(context).getDataStoreCache().evictAll();
Expand Down
4 changes: 4 additions & 0 deletions src/main/webapp/WEB-INF/web.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -572,6 +572,10 @@
<servlet-name>ApiBaseObject</servlet-name>
<url-pattern>/api/v3/occurrences/*</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>ApiBaseObject</servlet-name>
<url-pattern>/api/v3/annotations/*</url-pattern>
</servlet-mapping>


<servlet>
Expand Down

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