removed long-commented out code, unneeded todos, updated with known T…

…ODO:

src/main/java/org/ecocean/Annotation.java

@@ -48,10 +48,10 @@ public Annotation() {}
     protected String acmId;
 
     // this is used to decide "should we match against this"  problem is: that is not very (IA-)algorithm agnostic
-    // TODO was this made obsolete by ACM and friends?
+    // TODO: was this made obsolete by ACM and friends?
     private boolean matchAgainst = false;
 
-    // TODO can these (thru mediaAsset) be removed now that there Features? 
+    // TODO: can these (thru mediaAsset) be removed now that there Features? 
     private int x;
     private int y;
     private int width;
@@ -369,7 +369,7 @@ JSONObject iaViewpointFromAnnotUUID(String uuid, String context) throws RuntimeE
        NoSuchAlgorithmException, InvalidKeyException {
  */
 
-// TODO Deprecate "all of this" now that deployed sites are migrated
+// TODO: Deprecate "all of this" now that deployed sites are migrated
     public MediaAsset __getMediaAsset() {
         return mediaAsset;
     }
@@ -882,7 +882,7 @@ private String getMatchingSetFilterFromParameters(JSONObject taskParams) {
                 if (opt.equals("me"))
                     f += " && user.uuid == '" + userId +
                         "' && (enc.submitters.contains(user) || enc.submitterID == user.username) ";
-                // TODO also handle user "collab"
+                // TODO: also handle user "collab"
             }
         }
         // add projectID to filter

src/main/java/org/ecocean/ApiAccess.java

@@ -70,7 +70,7 @@ public String checkRequest(Object obj, HttpServletRequest request, JSONObject js
 
     // returns map of (negative) permissions for this user (based on role) for this object class
     // note: no hash key for a property means all access, therefore a null value means user CANNOT write
-    // TODO this structure is subject to change for sure!
+    // TODO: this structure is subject to change for sure!
     public HashMap<String, String> permissions(Object o, HttpServletRequest request) {
         return permissions(o.getClass().getName(), request);
     }
@@ -120,7 +120,7 @@ public HashMap<String, String> permissions(String cname, HttpServletRequest requ
                                 Element pel = (Element)props.item(j);
                                 String propName = pel.getAttribute("name");
                                 if (propName != null) {
-                                    ///////////// TODO for now we assume we ONLY have a sub element for <write> perm here so we skip a step
+                                    // TODO: for now we assume we ONLY have a sub element for <write> perm here so we skip a step
                                     NodeList proles = pel.getElementsByTagName("role");
                                     boolean allowed = false;
                                     for (int k = 0; k < proles.getLength(); k++) {

src/main/java/org/ecocean/Cluster.java

@@ -1,3 +1,5 @@
+// TODO: #825 evaluate and remove as deprecated
+
 package org.ecocean;
 
 import org.joda.time.DateTime;
@@ -104,47 +106,6 @@ public static List<Occurrence> fromSmartXml(File smartXmlFile, List<MediaAsset>
                     System.out.println(" - valid observation found at waypoint id=" +
                         wel.getAttribute("id"));
 
-/* here is an example of stuff we have in an animal observation.  not sure if this is exhaustive??
-    a whole bunch of these were implemented for lewa in "previous ibeis branch" on the occurrence, such as:
-        occ.setNumBachMales(int);   see Occurrence.java for those... which will need to be ported... :/   TODO
-
-                <observations categoryKey="animals.liveanimals.">
-                    <attributes attributeKey="species">
-                        <itemKey>chordata_rl.mammalia_rl.perissodactyla_rl.equidae_rl.equus_rl.equusgrevyi_rl7950.</itemKey>
-                    </attributes>
-                    <attributes attributeKey="habitat">
-                        <itemKey>openwoodland</itemKey>
-                    </attributes>
-                    <attributes attributeKey="groupsize">
-                        <dValue>6.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="noofbm">
-                        <dValue>6.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="nooftm">
-                        <dValue>1.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="distancem">
-                        <dValue>51.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="noofnlf">
-                        <dValue>7.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="nooflf">
-                        <dValue>2.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="numberof612monthsfemales">
-                        <dValue>2.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="bearing">
-                        <dValue>30.0</dValue>
-                    </attributes>
-                    <attributes attributeKey="photonumber">
-                        <sValue>1</sValue>
-                    </attributes>
-                </observations>
-
- */
                     Occurrence occ = new Occurrence();
                     occ.setOccurrenceID(Util.generateUUID());
                     occ.setDecimalLatitude(decimalLatitude);
@@ -153,7 +114,6 @@ public static List<Occurrence> fromSmartXml(File smartXmlFile, List<MediaAsset>
 
                     Integer photoOffset = null;
                     NodeList alist = oel.getElementsByTagName("attributes");
-                    // TODO this is where we would build out the Occurrence
                     if (alist.getLength() > 0) {
                         for (int a = 0; a < alist.getLength(); a++) {
                             Node anode = alist.item(a);
@@ -172,37 +132,7 @@ public static List<Occurrence> fromSmartXml(File smartXmlFile, List<MediaAsset>
                                                 " > assets.size() " + assets.size());
                                 }
                                 break;
-                                /* legacy zebra stuff
-                                   case "habitat":
-                                    occ.setHabitat(getValueString(ael));
-                                    break;
-                                   case "bearing":
-                                    occ.setBearing(getValueDouble(ael));
-                                    break;
-                                   case "groupsize":
-                                    occ.setGroupSize(getValueDoubleAsInt(ael));
-                                    break;
-                                   case "noofbm":
-                                    occ.setNumBachMales(getValueDoubleAsInt(ael));
-                                    break;
-                                   case "nooftm":
-                                    occ.setNumTerMales(getValueDoubleAsInt(ael));
-                                    break;
-                                   case "distancem":
-                                    occ.setDistance(getValueDouble(ael));
-                                    break;
-                                   case "noofnlf":
-                                    occ.setNumNonLactFemales(getValueDoubleAsInt(ael));
-                                    break;
-                                   case "nooflf":
-                                    occ.setNumLactFemales(getValueDoubleAsInt(ael));
-                                    break;
-                                   case "numberof612monthsfemales":
-                                    //
-                                    break;
-                                 */
                             }
-                            // TODO ... do something with the value!
                         }
                     }
                     System.out.println(" - created Occurrence " + occ);

src/main/java/org/ecocean/Encounter.java

@@ -1752,7 +1752,7 @@ public void setSurveyID(String id) {
     public void setSurvey() {
     }
 
-    // TODO Get all this lat lon over to Locations
+    // TODO: Get all this lat lon over to Locations
 
     public void setDWCDecimalLatitude(double lat) {
         if (lat == -9999.0) {
@@ -2156,7 +2156,7 @@ public String getTaxonomyString() {
     }
 
     // hacky (as generates new Taxonomy -- with random uuid) but still should work for tax1.equals(tax2);
-    // TODO FIXME this should be superceded by the getter for Taxonomy property in the future....
+    // TODO: FIXME this should be superceded by the getter for Taxonomy property in the future....
     public Taxonomy getTaxonomy(Shepherd myShepherd) {
         String sciname = this.getTaxonomyString();
 
@@ -2624,7 +2624,7 @@ public Set<String> getAnnotationIAClasses() {
         for (Annotation ann : annotations) {
             if (ann.getIAClass() != null) classes.add(ann.getIAClass());
         }
-        // TODO we should find out how/where bunk iaClass values are getting set
+        // TODO: we should find out how/where bunk iaClass values are getting set
         // and stop the via isValidIAClass() or similar
         // also should be considered for any data integrity/repair tools
         classes.remove("____");
@@ -3302,7 +3302,7 @@ public boolean restAccess(HttpServletRequest request, org.json.JSONObject jsonob
         return true;
     }
 
-///////// these are bunk now - dont use Features  TODO fix these - perhaps by crawlng thru ma.getAnnotations() ?
+///////// these are bunk now - dont use Features  TODO: fix these - perhaps by crawlng thru ma.getAnnotations() ?
     public static Encounter findByMediaAsset(MediaAsset ma, Shepherd myShepherd) {
         String queryString =
             "SELECT FROM org.ecocean.Encounter WHERE annotations.contains(ann) && ann.mediaAsset.id =="
@@ -3487,7 +3487,7 @@ public ImportTask getImportTask(Shepherd myShepherd) {
     }
 
     // this is a special state only used now for match.jsp but basically means the data should be mostly hidden and soon deleted, roughly speaking???
-    // TODO figure out what this really means
+    // TODO: figure out what this really means
     public void setMatchingOnly() {
         this.setState(STATE_MATCHING_ONLY);
     }
@@ -3501,7 +3501,7 @@ public void detectedAnnotation(Shepherd myShepherd, Annotation ann) {
     /*
        note: these are baby steps into proper ownership of Encounters.  a similar (but cleaner) attempt is done in MediaAssets... however, really this
           probably should be upon some (mythical) BASE CLASS!!!! ... for now, this Encounter variation kinda fudges with existing "ownership" stuff,
-          namely, the submitterID - which maps (in theory!) to a User username. TODO much much much  ... incl call via constructor maybe ??  etc.
+          namely, the submitterID - which maps (in theory!) to a User username. TODO: much much much  ... incl call via constructor maybe ??  etc.
      */
     // NOTE: not going to currently persist the AccessControl object yet, but create on the fly...  clever? stupid?
     public AccessControl getAccessControl() {

src/main/java/org/ecocean/MarkedIndividual.java

@@ -84,7 +84,7 @@ public class MarkedIndividual extends Base implements java.io.Serializable {
     // first sighting
     private String dateFirstIdentified;
 
-    // points to thumbnail (usually of most recent encounter) - TODO evaluate and remove if has been superceded by MediaAsset
+    // points to thumbnail (usually of most recent encounter) - TODO: evaluate and remove if has been superceded by MediaAsset
     private String thumbnailUrl;
 
     // a Vector of Strings of email addresses to notify when this MarkedIndividual is modified
@@ -637,7 +637,7 @@ public boolean wasSightedInYearLeftTagsOnly(int year, String locCode) {
         return false;
     }
 
-    // TODO evaluate and remove if deprecated
+    // TODO: evaluate and remove if deprecated
     public double averageLengthInYear(int year) {
         int numLengths = 0;
         double total = 0;
@@ -657,7 +657,7 @@ public double averageLengthInYear(int year) {
         return avg;
     }
 
-    // TODO evaluate and remove if deprecated
+    // TODO: evaluate and remove if deprecated
     public double averageMeasuredLengthInYear(int year, boolean allowGuideGuess) {
         int numLengths = 0;
         double total = 0;
@@ -804,7 +804,7 @@ public String getName(Object keyHint) {
         return names.getValue(keyHint);
     }
 
-    // TODO evaluate and remove if deprecated:  ##DEPRECATED #509 - Base class getId() method
+    // TODO: evaluate and remove if deprecated:  ##DEPRECATED #509 - Base class getId() method
     public String getIndividualID() {
         return individualID;
     }
@@ -841,7 +841,7 @@ public String getLegacyIndividualID() {
         return legacyIndividualID;
     }
 
-    // TODO evaluate and remove if deprecated:  ##DEPRECATED #509 - Base class getId() method
+    // TODO: evaluate and remove if deprecated:  ##DEPRECATED #509 - Base class getId() method
     public void setIndividualID(String id) {
         individualID = id;
     }

src/main/java/org/ecocean/Occurrence.java

@@ -819,7 +819,7 @@ public boolean canUserAccess(HttpServletRequest request) {
         List<String> ids = new ArrayList<String>();
 
         for (User user : myShepherd.getAllUsers()) {
-/* TODO we do not have user-flavored Collaboration.canUserAccessOccurrence yet
+/* TODO: we do not have user-flavored Collaboration.canUserAccessOccurrence yet
             if ((user.getId() != null) && this.canUserAccess(user, myShepherd.getContext())) ids.add(user.getId());
  */
             if (user.getId() != null) ids.add(user.getId());
@@ -831,7 +831,7 @@ public boolean canUserAccess(HttpServletRequest request) {
         List<String> ids = new ArrayList<String>();
 
         for (User user : myShepherd.getAllUsers()) {
-/* TODO we do not have edit stuff for occurrence
+/* TODO: we do not have edit stuff for occurrence
             if ((user.getId() != null) && this.canUserEdit(user)) ids.add(user.getId());
  */
             if (user.getId() != null) ids.add(user.getId());

src/main/java/org/ecocean/OpenSearch.java

@@ -583,7 +583,7 @@ public static JSONObject querySanitize(JSONObject query, User user) {
         return newQuery;
     }
 
-    // TODO right now this respects index timestamp and only indexes objects with versions > timestamp.
+    // TODO: right now this respects index timestamp and only indexes objects with versions > timestamp.
     // want to make an option to index everything and ignore version/timestamp.
     public void indexAll(Shepherd myShepherd, Base obj)
     throws IOException {

src/main/java/org/ecocean/PatterningPassport.java

@@ -74,9 +74,9 @@ private Boolean makeNewPassportXml(String context) {
                 CommonConfiguration.getDataDirectoryName(context));
 
             // Universal passport fields for the XML
-            String encounterUrlString = "foo/" + this.encounterId; // TODO -- generate URL
-            String mediaSourceUrlString = "foo/" + this.mediaId; // TODO -- generate URL
-            String passportXmlUrlString = "foo"; // TODO -- generate URL
+            String encounterUrlString = "foo/" + this.encounterId; // TODO: -- generate URL
+            String mediaSourceUrlString = "foo/" + this.mediaId; // TODO: -- generate URL
+            String passportXmlUrlString = "foo"; // TODO: -- generate URL
             String encounterDir = this.webappsDir + "/shepherd_data_dir/encounters/" +
                 this.encounterId;
             String xmlFilePathString = encounterDir + "/" + mediaId + "_pp.xml";
@@ -182,7 +182,7 @@ public Boolean setPassportDataXml(String passportDataXml, String context) {
      * @return the encounterUrl
      */
     public String getEncounterUrl() {
-        // TODO read it from XML if needed
+        // TODO: read it from XML if needed
         return encounterUrl;
     }
 
@@ -198,7 +198,7 @@ public void setEncounterUrl(String encounterUrl) {
      * @return the mediaUrl
      */
     public String getMediaUrl() {
-        // TODO read it from XML if needed
+        // TODO: read it from XML if needed
         return mediaUrl;
     }
 
@@ -214,7 +214,7 @@ public void setMediaUrl(String mediaUrl) {
      * @return the patterningPassportXmlUrl
      */
     public String getPatterningPassportXmlUrl() {
-        // TODO read it from XML if needed
+        // TODO: read it from XML if needed
         return patterningPassportXmlUrl;
     }
 

src/main/java/org/ecocean/RestClient.java

@@ -239,7 +239,7 @@ public static void writeToFile(URL url, File file)
     }
 
     /***********************************************************************************************
-       TODO evaluate strategy, rewrite as needed and define future actions that need to be taken to truly update
+       TODO: evaluate strategy, rewrite as needed and define future actions that need to be taken to truly update
        some attempts to *truly* genericize these....
 
        rather than authUsername/authPassword, we might want to have our own credential class that allows us to set headers etc accordingly!

src/main/java/org/ecocean/Shepherd.java

@@ -3838,7 +3838,7 @@ public boolean isDBTransactionActive() {
     /**
      * Commits (makes permanent) any changes made to an open database
      */
-    // TODO Either (a) throw an exception itself or (b) return boolean of success (the latter was disabled, needs investigation)
+    // TODO: Either (a) throw an exception itself or (b) return boolean of success (the latter was disabled, needs investigation)
     public void commitDBTransaction() {
         try {
             // System.out.println("     shepherd:"+identifyMe+" is trying to commit a transaction");

src/main/java/org/ecocean/User.java

@@ -382,7 +382,7 @@ public void unsetSocial(String type) {
         social.remove(type);
     }
 
-    // TODO this needs to be dealt with better.  see: rant about saving usernames from forms
+    // TODO: this needs to be dealt with better.  see: rant about saving usernames from forms
     public static boolean isUsernameAnonymous(String uname) {
         return ((uname == null) || uname.trim().equals("") || uname.equals("N/A") ||
                    uname.equals("public"));

src/main/java/org/ecocean/api/SiteSettings.java

@@ -68,7 +68,7 @@ protected void doGet(HttpServletRequest request, HttpServletResponse response)
         settings.put("measurement",
             CommonConfiguration.getIndexedPropertyValues("measurement", context));
 
-        // TODO: there was some discussion in slack about this being derived differently
+        // TODO: evaluate deriving this differently
         // NOTE: historically this list was generated via CommonConfiguration using 
         //       List<String> states = CommonConfiguration.getIndexedPropertyValues("encounterState",context)
         settings.put("encounterState", VALUES_ENCOUNTER_STATES);

src/main/java/org/ecocean/cache/CachedQuery.java

@@ -242,7 +242,7 @@ public JSONObject convertToJson(Collection coll, ExecutionContext ec) {
         for (Object o : coll) {
             if (o instanceof Collection) {
                 jarr.put(convertToJson((Collection)o, ec));
-            } else { // TODO can it *only* be an JSONObject-worthy object at this point?
+            } else {
                 try {
                     jarr.put(Util.toggleJSONObject(RESTUtils.getJSONObjectFromPOJO(o, ec)));
                 } catch (Exception e) {