From 54734a8934a2858b8b1bea258d6d4c90167a8441 Mon Sep 17 00:00:00 2001
From: gaellafond <g.lafond@aims.gov.au>
Date: Thu, 3 Nov 2022 16:24:11 +0800
Subject: [PATCH] Version 0.7.0 NcAnimate: - Fixed bug with arrowVariable
 overwrites not applied properly. - Added extraAmountOutOfRangeLow and
 extraAmountOutOfRangeHigh properties to NcAnimateLegendBean. - Added
 ColourSchemeType.ARROW_THRESHOLDS - Added arrowColour and arrowThresholds
 properties to NcAnimateNetCDFVariableBean.

---
 pom.xml                                       |   2 +-
 .../bean/ncanimate/NcAnimateLegendBean.java   |  18 ++++
 .../NcAnimateNetCDFVariableBean.java          |  90 +++++++++++++---
 .../ereefs/helper/NcAnimateConfigHelper.java  | 102 +++++++++---------
 4 files changed, 150 insertions(+), 62 deletions(-)

diff --git a/pom.xml b/pom.xml
index 6f29336..f71b945 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>au.gov.aims</groupId>
     <artifactId>ereefs-database</artifactId>
-    <version>0.6.26</version>
+    <version>0.7.0</version>
 
     <!--
         *** IMPORTANT ***
diff --git a/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateLegendBean.java b/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateLegendBean.java
index 5529d7c..a31448d 100644
--- a/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateLegendBean.java
+++ b/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateLegendBean.java
@@ -68,6 +68,10 @@ public class NcAnimateLegendBean extends AbstractNcAnimateBean {
     private Integer colourBandHeight;
     private Integer colourBandColourCount; // Number of colours used to render the layer and the legend
 
+    // Add extra space at the top and bottom of the colour band
+    private Float extraAmountOutOfRangeLow;
+    private Float extraAmountOutOfRangeHigh;
+
     private Integer majorTickMarkLength;
     private Integer minorTickMarkLength;
 
@@ -143,6 +147,9 @@ protected void parse(JSONWrapperObject jsonLegend) throws Exception {
             this.colourBandHeight = jsonLegend.get(Integer.class, "colourBandHeight");
             this.colourBandColourCount = jsonLegend.get(Integer.class, "colourBandColourCount");
 
+            this.extraAmountOutOfRangeLow = jsonLegend.get(Float.class, "extraAmountOutOfRangeLow");
+            this.extraAmountOutOfRangeHigh = jsonLegend.get(Float.class, "extraAmountOutOfRangeHigh");
+
             this.majorTickMarkLength = jsonLegend.get(Integer.class, "majorTickMarkLength");
             this.minorTickMarkLength = jsonLegend.get(Integer.class, "minorTickMarkLength");
         }
@@ -297,6 +304,14 @@ public Integer getColourBandColourCount() {
         return this.colourBandColourCount;
     }
 
+    public Float getExtraAmountOutOfRangeLow() {
+        return this.extraAmountOutOfRangeLow;
+    }
+
+    public Float getExtraAmountOutOfRangeHigh() {
+        return this.extraAmountOutOfRangeHigh;
+    }
+
     /**
      * Returns the length of the major tick marks in the legend, in pixels.
      * @return the length of the major tick marks in the legend, in pixels.
@@ -347,6 +362,9 @@ public JSONObject toJSON() {
         json.put("colourBandHeight", this.colourBandHeight);
         json.put("colourBandColourCount", this.colourBandColourCount);
 
+        json.put("extraAmountOutOfRangeLow", this.extraAmountOutOfRangeLow);
+        json.put("extraAmountOutOfRangeHigh", this.extraAmountOutOfRangeHigh);
+
         json.put("majorTickMarkLength", this.majorTickMarkLength);
         json.put("minorTickMarkLength", this.minorTickMarkLength);
 
diff --git a/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateNetCDFVariableBean.java b/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateNetCDFVariableBean.java
index 449ba22..45a1186 100644
--- a/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateNetCDFVariableBean.java
+++ b/src/main/java/au/gov/aims/ereefs/bean/ncanimate/NcAnimateNetCDFVariableBean.java
@@ -10,7 +10,9 @@
 import org.json.JSONArray;
 import org.json.JSONObject;
 
+import java.io.InvalidClassException;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * NcAnimate {@code NetCDF} variable bean part.
@@ -43,21 +45,22 @@
  * }</pre>
  */
 public class NcAnimateNetCDFVariableBean extends AbstractNcAnimateBean {
-    
+
     public enum ColourSchemeType {
-        SCALE(),
-        THRESHOLDS()
+        SCALE,
+        THRESHOLDS,
+        ARROW_THRESHOLDS,
     }
-    
+
     private String variableId;
     private String colourPaletteName;
     private Boolean logarithmic;
-    
+
     private ColourSchemeType colourSchemeType;
 
     private Float scaleMin;
     private Float scaleMax;
-    
+
     private ArrayList<Float> thresholds;
 
     // Used with direction variable
@@ -73,7 +76,7 @@ public enum ColourSchemeType {
     // For radian:
     //     directionTurns = 6.2831853 // 2*PI
     // See: https://en.wikipedia.org/wiki/Angular_unit
-    // NOTE: For counter clockwise angle, use a negative directionTurns
+    // NOTE: For counter-clockwise angle, use a negative directionTurns
     //     directionTurns = 360:
     //         North: 0
     //         East: 90
@@ -90,6 +93,15 @@ public enum ColourSchemeType {
     // Legend
     private NcAnimateLegendBean legend;
 
+    private String arrowColour;
+
+    // Arrow thresholds.
+    // Each value is formatted this way:
+    //   Threshold value:Hex colour
+    // Example:
+    //   "8.1:#009900"
+    private List<String> arrowThresholds;
+
     /**
      * Create a NcAnimate NetCDF layer variable bean part from a {@code JSONWrapperObject}.
      *
@@ -151,20 +163,31 @@ protected void parse(JSONWrapperObject jsonVariable) throws Exception {
         if (jsonVariable != null) {
             this.variableId = jsonVariable.get(String.class, "variableId");
             this.colourPaletteName = jsonVariable.get(String.class, "colourPaletteName");
-            
+
             this.setColourSchemeType(jsonVariable.get(String.class, "colourSchemeType"));
-            
+
             this.scaleMax = jsonVariable.get(Float.class, "scaleMax");
             this.scaleMin = jsonVariable.get(Float.class, "scaleMin");
 
             this.setThresholds(jsonVariable.get(JSONWrapperArray.class, "thresholds"));
-            
+
             this.northAngle = jsonVariable.get(Float.class, "northAngle");
             this.directionTurns = jsonVariable.get(Float.class, "directionTurns");
 
             this.logarithmic = jsonVariable.get(Boolean.class, "logarithmic");
 
             this.setLegend(jsonVariable.get(JSONWrapperObject.class, "legend"));
+
+            this.arrowColour = jsonVariable.get(String.class, "arrowColour");
+
+            this.arrowThresholds = null;
+            Class arrowThresholdsClass = jsonVariable.getClass("arrowThresholds");
+            if (arrowThresholdsClass != null) {
+                if (JSONWrapperArray.class.equals(arrowThresholdsClass)) {
+                    this.setArrowThresholds(
+                        jsonVariable.get(JSONWrapperArray.class, "arrowThresholds"));
+                }
+            }
         }
     }
 
@@ -176,6 +199,17 @@ private void setLegend(JSONWrapperObject jsonLegend) throws Exception {
         }
     }
 
+    private void setArrowThresholds(JSONWrapperArray jsonArrowThresholds) throws InvalidClassException {
+        this.arrowThresholds = null;
+
+        if (jsonArrowThresholds != null) {
+            this.arrowThresholds = new ArrayList<String>();
+            for (int i=0; i<jsonArrowThresholds.length(); i++) {
+                this.arrowThresholds.add(jsonArrowThresholds.get(String.class, i));
+            }
+        }
+    }
+
     /**
      * Returns the variable ID, as defined in the NetCDF file.
      * @return the variable ID.
@@ -190,11 +224,14 @@ public String getVariableId() {
      */
     public void setColourSchemeType(String typeString) {
         this.colourSchemeType = null;
-        
+
         if (typeString != null) {
             if (typeString.equalsIgnoreCase(ColourSchemeType.THRESHOLDS.toString())) {
                 this.colourSchemeType = ColourSchemeType.THRESHOLDS;
             }
+            else if (typeString.equalsIgnoreCase(ColourSchemeType.ARROW_THRESHOLDS.toString())) {
+                this.colourSchemeType = ColourSchemeType.ARROW_THRESHOLDS;
+            }
             else if (typeString.equalsIgnoreCase(ColourSchemeType.SCALE.toString())) {
                 this.colourSchemeType = ColourSchemeType.SCALE;
             }
@@ -242,7 +279,7 @@ public void setThresholds(JSONWrapperArray thresholdsWrapperArray) throws Except
         this.thresholds = null;
 
         if (thresholdsWrapperArray != null && thresholdsWrapperArray.length() > 0) {
-            this.thresholds = new ArrayList<>();
+            this.thresholds = new ArrayList<Float>();
 
             for (int i = 0; i < thresholdsWrapperArray.length(); i++) {
                 this.thresholds.add(thresholdsWrapperArray.get(Float.class, i));
@@ -304,6 +341,23 @@ public void setLegend(NcAnimateLegendBean legend) {
         this.legend = legend;
     }
 
+    /**
+     * Returns the colour of the arrows, in hexadecimal format.
+     * @return the colour of the arrows.
+     */
+    public String getArrowColour() {
+        return this.arrowColour;
+    }
+
+    /**
+     * Returns the list of arrow threshold colours.
+     * Used with {@link NcAnimateLayerBean.LayerType#NETCDF} and {@link NcAnimateLayerBean.LayerType#GRIB2}.
+     * @return the list of arrow threshold colours.
+     */
+    public List<String> getArrowThresholds() {
+        return arrowThresholds;
+    }
+
     // NOTE: equals and hashcode are defined in AbstractNcAnimateBean
 
     /**
@@ -318,7 +372,7 @@ public JSONObject toJSON() {
         json.put("colourPaletteName", this.colourPaletteName);
 
         json.put("colourSchemeType", this.colourSchemeType);
-        
+
         json.put("scaleMax", this.scaleMax);
         json.put("scaleMin", this.scaleMin);
 
@@ -335,6 +389,16 @@ public JSONObject toJSON() {
             json.put("legend", this.legend.toJSON());
         }
 
+        json.put("arrowColour", this.arrowColour);
+
+        if (this.arrowThresholds != null) {
+            JSONArray jsonArrowThresholds = new JSONArray();
+            for (String arrowThreshold : this.arrowThresholds) {
+                jsonArrowThresholds.put(arrowThreshold);
+            }
+            json.put("arrowThresholds", jsonArrowThresholds);
+        }
+
         return json.isEmpty() ? null : json;
     }
 }
diff --git a/src/main/java/au/gov/aims/ereefs/helper/NcAnimateConfigHelper.java b/src/main/java/au/gov/aims/ereefs/helper/NcAnimateConfigHelper.java
index 3e297b3..6240eaa 100644
--- a/src/main/java/au/gov/aims/ereefs/helper/NcAnimateConfigHelper.java
+++ b/src/main/java/au/gov/aims/ereefs/helper/NcAnimateConfigHelper.java
@@ -383,6 +383,9 @@ private NcAnimateConfigBean combineParts(NcAnimateConfigBean config) throws Exce
     }
 
     private void combineLegendParts(NcAnimateConfigBean config, NcAnimateLegendBean legend) throws Exception {
+        // If "defaults.legend" refer to a legend ID, find that legend from the DB
+        // and put that object in "defaults.legend".
+        // The legend overwrite in layers appends in "combinePanelParts".
         if (legend != null) {
             // Legend part
             NcAnimateIdBean legendId = legend.getId();
@@ -501,60 +504,63 @@ private void combineLayerParts(NcAnimateConfigBean config, NcAnimateLayerBean la
 
                 // Variable
                 NcAnimateNetCDFVariableBean variableOverwrites = layer.getVariable();
-                if (variableOverwrites != null) {
-                    NcAnimateIdBean variableId = variableOverwrites.getId();
-                    if (variableId != null) {
-                        String variableIdStr = variableId.getValue();
-                        if (variableIdStr != null && !variableIdStr.isEmpty()) {
-                            JSONObject jsonVariable = this.configPartManager.select(ConfigPartManager.Datatype.VARIABLE, variableIdStr);
-                            if (jsonVariable != null) {
-                                NcAnimateNetCDFVariableBean variable = new NcAnimateNetCDFVariableBean(new JSONWrapperObject(jsonVariable));
-                                variableOverwrites.overwrite(variable, variableOverwrites);
-
-                                layer.addAllNeverVisited("variable["+variableIdStr+"]", variable.getNeverVisited());
-                                config.addLastModifiedConfigPart(variable);
-                            } else {
-                                LOGGER.error(String.format("Layer variable ID \"%s\" could not be found in the database. Using variable config found in NcAnimate config:%n%s",
-                                    variableIdStr, variableOverwrites));
-                            }
-                        }
-                    }
+                this.applyVariableOverwrites(config, layer, variableOverwrites, "variable", defaultLegend);
 
-                    if (defaultLegend != null) {
-                        NcAnimateLegendBean legendConfOverwrite = variableOverwrites.getLegend();
-                        if (legendConfOverwrite == null) {
-                            legendConfOverwrite = defaultLegend;
-                            this.combineLegendParts(config, legendConfOverwrite);
-                            variableOverwrites.setLegend(legendConfOverwrite);
-                        } else {
-                            this.combineLegendParts(config, legendConfOverwrite);
-                            legendConfOverwrite.overwrite(defaultLegend, legendConfOverwrite);
-                        }
+                // Arrow variable
+                NcAnimateNetCDFVariableBean arrowVariableOverwrites = layer.getArrowVariable();
+                this.applyVariableOverwrites(config, layer, arrowVariableOverwrites, "arrowVariable", defaultLegend);
+            }
+        }
+    }
 
-                        variableOverwrites.addAllNeverVisited("legend", legendConfOverwrite.getNeverVisited());
+    /**
+     * Private method used to apply variable overwrites
+     * and legend default values (found in "defaults.legend").
+     * @param config the {@link NcAnimateConfigBean} configuration document.
+     * @param layer the {@link NcAnimateLayerBean} layer containing the variable to overwrite.
+     * @param variableOverwrites the {@link NcAnimateNetCDFVariableBean} variable to overwrite.
+     * @param variableType "variable" or "arrowVariable", used with error messages.
+     * @param defaultLegend the {@link NcAnimateLegendBean} default values found in "defaults.legend".
+     * @throws Exception if the database is unreachable.
+     */
+    private void applyVariableOverwrites(
+            NcAnimateConfigBean config,
+            NcAnimateLayerBean layer,
+            NcAnimateNetCDFVariableBean variableOverwrites,
+            String variableType, // "variable" or "arrowVariable"
+            NcAnimateLegendBean defaultLegend
+    ) throws Exception {
+        if (variableOverwrites != null) {
+            NcAnimateIdBean variableId = variableOverwrites.getId();
+            if (variableId != null) {
+                String variableIdStr = variableId.getValue();
+                if (variableIdStr != null && !variableIdStr.isEmpty()) {
+                    JSONObject jsonVariable = this.configPartManager.select(ConfigPartManager.Datatype.VARIABLE, variableIdStr);
+                    if (jsonVariable != null) {
+                        NcAnimateNetCDFVariableBean variable = new NcAnimateNetCDFVariableBean(new JSONWrapperObject(jsonVariable));
+                        variableOverwrites.overwrite(variable, variableOverwrites);
+
+                        layer.addAllNeverVisited(variableType+"["+variableIdStr+"]", variable.getNeverVisited());
+                        config.addLastModifiedConfigPart(variable);
+                    } else {
+                        LOGGER.error(String.format("Layer %s ID \"%s\" could not be found in the database. Using variable config found in NcAnimate config:%n%s",
+                            variableType, variableIdStr, variableOverwrites));
                     }
                 }
+            }
 
-                // Arrow variable
-                NcAnimateNetCDFVariableBean arrowVariableOverwrites = layer.getArrowVariable();
-                if (arrowVariableOverwrites != null) {
-                    NcAnimateIdBean arrowVariableId = arrowVariableOverwrites.getId();
-                    if (arrowVariableId != null) {
-                        String arrowVariableIdStr = arrowVariableId.getValue();
-                        if (arrowVariableIdStr != null && !arrowVariableIdStr.isEmpty()) {
-                            JSONObject jsonArrowVariable = this.configPartManager.select(ConfigPartManager.Datatype.VARIABLE, arrowVariableIdStr);
-                            if (jsonArrowVariable != null) {
-                                NcAnimateNetCDFVariableBean arrowVariable = new NcAnimateNetCDFVariableBean(new JSONWrapperObject(jsonArrowVariable));
-                                arrowVariableOverwrites.overwrite(arrowVariable, arrowVariableOverwrites);
-                                layer.addAllNeverVisited("arrowVariable["+arrowVariableIdStr+"]", arrowVariable.getNeverVisited());
-                                config.addLastModifiedConfigPart(arrowVariable);
-                            } else {
-                                LOGGER.error(String.format("Layer arrowVariable ID \"%s\" could not be found in the database. Using variable config found in NcAnimate config:%n%s",
-                                    arrowVariableIdStr, arrowVariableOverwrites));
-                            }
-                        }
-                    }
+            if (defaultLegend != null) {
+                NcAnimateLegendBean legendConfOverwrite = variableOverwrites.getLegend();
+                if (legendConfOverwrite == null) {
+                    legendConfOverwrite = defaultLegend;
+                    this.combineLegendParts(config, legendConfOverwrite);
+                    variableOverwrites.setLegend(legendConfOverwrite);
+                } else {
+                    this.combineLegendParts(config, legendConfOverwrite);
+                    legendConfOverwrite.overwrite(defaultLegend, legendConfOverwrite);
                 }
+
+                variableOverwrites.addAllNeverVisited("legend", legendConfOverwrite.getNeverVisited());
             }
         }
     }