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nbproject/project.properties

@@ -34,7 +34,7 @@
 j2ee.copy.static.files.on.save=false
 j2ee.deploy.on.save=false
 j2ee.platform=1.6-web
-j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar:${j2ee.server.home}/lib/catalina-ant.jar:${j2ee.server.home}/lib/catalina-ha.jar:${j2ee.server.home}/lib/catalina-storeconfig.jar:${j2ee.server.home}/lib/catalina-tribes.jar:${j2ee.server.home}/lib/catalina.jar:${j2ee.server.home}/lib/ecj-4.4.2.jar:${j2ee.server.home}/lib/el-api.jar:${j2ee.server.home}/lib/jasper-el.jar:${j2ee.server.home}/lib/jasper.jar:${j2ee.server.home}/lib/jsp-api.jar:${j2ee.server.home}/lib/servlet-api.jar:${j2ee.server.home}/lib/tomcat-api.jar:${j2ee.server.home}/lib/tomcat-coyote.jar:${j2ee.server.home}/lib/tomcat-dbcp.jar:${j2ee.server.home}/lib/tomcat-i18n-es.jar:${j2ee.server.home}/lib/tomcat-i18n-fr.jar:${j2ee.server.home}/lib/tomcat-i18n-ja.jar:${j2ee.server.home}/lib/tomcat-jdbc.jar:${j2ee.server.home}/lib/tomcat-jni.jar:${j2ee.server.home}/lib/tomcat-util-scan.jar:${j2ee.server.home}/lib/tomcat-util.jar:${j2ee.server.home}/lib/tomcat-websocket.jar:${j2ee.server.home}/lib/websocket-api.jar
+j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar:${j2ee.server.home}/lib/catalina-ant.jar:${j2ee.server.home}/lib/catalina-ha.jar:${j2ee.server.home}/lib/catalina-ssi.jar:${j2ee.server.home}/lib/catalina-storeconfig.jar:${j2ee.server.home}/lib/catalina-tribes.jar:${j2ee.server.home}/lib/catalina.jar:${j2ee.server.home}/lib/ecj-4.20.jar:${j2ee.server.home}/lib/el-api.jar:${j2ee.server.home}/lib/jasper-el.jar:${j2ee.server.home}/lib/jasper.jar:${j2ee.server.home}/lib/jaspic-api.jar:${j2ee.server.home}/lib/jsp-api.jar:${j2ee.server.home}/lib/servlet-api.jar:${j2ee.server.home}/lib/tomcat-api.jar:${j2ee.server.home}/lib/tomcat-coyote.jar:${j2ee.server.home}/lib/tomcat-dbcp.jar:${j2ee.server.home}/lib/tomcat-i18n-cs.jar:${j2ee.server.home}/lib/tomcat-i18n-de.jar:${j2ee.server.home}/lib/tomcat-i18n-es.jar:${j2ee.server.home}/lib/tomcat-i18n-fr.jar:${j2ee.server.home}/lib/tomcat-i18n-ja.jar:${j2ee.server.home}/lib/tomcat-i18n-ko.jar:${j2ee.server.home}/lib/tomcat-i18n-pt-BR.jar:${j2ee.server.home}/lib/tomcat-i18n-ru.jar:${j2ee.server.home}/lib/tomcat-i18n-zh-CN.jar:${j2ee.server.home}/lib/tomcat-jdbc.jar:${j2ee.server.home}/lib/tomcat-jni.jar:${j2ee.server.home}/lib/tomcat-util-scan.jar:${j2ee.server.home}/lib/tomcat-util.jar:${j2ee.server.home}/lib/tomcat-websocket.jar:${j2ee.server.home}/lib/websocket-api.jar
 j2ee.server.type=Tomcat
 jar.compress=false
 javac.classpath=\

src/java/m/hydraulics/ApplicationConfig.java

@@ -6,7 +6,9 @@
 
 import csip.Config;
 import java.util.Set;
+import javax.servlet.ServletContext;
 import javax.ws.rs.core.Application;
+import javax.ws.rs.core.Context;
 import org.glassfish.jersey.media.multipart.MultiPartFeature;
 
 /**
@@ -15,13 +17,17 @@
  */
 @javax.ws.rs.ApplicationPath("")
 public class ApplicationConfig extends Application {
+    
+    @Context
+    private ServletContext context;
 
     @Override
     public Set<Class<?>> getClasses() {
         Set<Class<?>> resources = new java.util.HashSet<Class<?>>();
         resources.add(MultiPartFeature.class);
         addRestResourceClasses(resources);
-        Config.registry().register(resources);
+        
+        Config.register(resources, context);
         return resources;
     }
 

src/java/m/hydraulics/channelgeometry/V1_0.java

@@ -3,9 +3,9 @@
 import csip.annotations.Description;
 import csip.annotations.Name;
 import csip.annotations.VersionInfo;
+import csip.api.server.PayloadParameter;
+import csip.api.server.PayloadResults;
 import csip.ModelDataService;
-import csip.PayloadParameter;
-import csip.PayloadResults;
 import hydraulics.ChannelGeometry;
 import javax.ws.rs.Path;
 

src/java/m/hydraulics/effectivedischarge/EffectiveDischarge.java

@@ -32,7 +32,7 @@
 * @since Java version: 16-October-2012
 */
 public class EffectiveDischarge {
-    String mainFolder = "C:/Projects/TylerWible/CodeDirectories/NetBeans/data/Hydraulics";
+    String directory = "C:/Projects/TylerWible/CodeDirectories/NetBeans/data/Hydraulics";
     double[][] fdcData = {{1.0,550},    //a matrix of with the first column of flow duration curve exceedence(s) (1-0) and second column of their assosicated flows
                          {0.75,380},    //(set by 'setFlowDurationCurve')
                          {0.50,376},
@@ -78,32 +78,32 @@
     //Gets
     public File getEffectiveDischargeOutput(){
         //This output file is for use with JSHighCharts
-        return new File(mainFolder, "effective_discharge_graph.out");
+        return new File(directory, "effective_discharge_graph.out");
     }
     public File getCummulativeSedimentYieldOutput(){
         //This output file is for use with JSHighCharts
-        return new File(mainFolder, "sediment_yield_graph.out");
+        return new File(directory, "sediment_yield_graph.out");
     }
     public File getHistogramOutput(){
         //This output file is for use with JSHighCharts
-        return new File(mainFolder, "flow_histogram.outt");
+        return new File(directory, "flow_histogram.outt");
         //Note that this file has a different extension as a flag for eRAMS to parse the first column as strings not numbers
     }
     public File getRatingCurveOutput_sediment(){
         //This output file is for use with JSHighCharts
-        return new File(mainFolder, "ratingCurveGraph_sediment.out");
+        return new File(directory, "ratingCurveGraph_sediment.out");
     }
     public File getRatingCurveOutput_area(){
         //This output file is for use with JSHighCharts
-        return new File(mainFolder, "ratingCurveGraph_area.out");
+        return new File(directory, "ratingCurveGraph_area.out");
     }
     public File getRatingCurveOutput_depth(){
         //This output file is for use with JSHighCharts
-        return new File(mainFolder, "ratingCurveGraph_depth.out");
+        return new File(directory, "ratingCurveGraph_depth.out");
     }
     public File getRatingCurveOutput_hydRadius(){
         //This output file is for use with JSHighCharts
-        return new File(mainFolder, "ratingCurveGraph_hydRadius.out");
+        return new File(directory, "ratingCurveGraph_hydRadius.out");
     }
     public String getEffectiveDischargeGraph() {
         return "effective_discharge_graph.jpg";
@@ -137,8 +137,8 @@
     }
     
     //Sets
-    public void setMainFolder(String mainFolder) {
-        this.mainFolder = mainFolder;
+    public void setDirectory(String directory) {
+        this.directory = directory;
     }
     public void setFlowDurationCurve(String flowDurationCurve) throws IOException{
         //Break up formatted cross-section points and create a double array for easier use
@@ -374,7 +374,7 @@
             histogramData[j-1][1] = String.valueOf(count);
         }
         //Save histogram data for JHighCharts
-        general.writeXYseries(mainFolder, histogramData, getHistogramOutput().getName());
+        general.writeXYseries(directory, histogramData, getHistogramOutput().getName());
         
         //Define renderer properties for bar graph
         int seriesIndex = 0;
@@ -409,7 +409,7 @@
         
         //Save resulting graph for use later
         try{
-            String path = mainFolder + File.separator + getHistogram();
+            String path = directory + File.separator + getHistogram();
             ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
             System.out.println("JFreeChart created properly at: " + path);
         }catch(IOException e){
@@ -454,7 +454,7 @@
         }
         
         //Save results for graphing with JSHighcharts
-        general.writeXYseries(mainFolder, graphData, dataOutputName);
+        general.writeXYseries(directory, graphData, dataOutputName);
 
         //Graph the effective discharge curve
         XYPlot plot = new XYPlot();
@@ -501,7 +501,7 @@
         legendTitle.setItemFont(general.masterFont);
         
         try{
-            String path = mainFolder + File.separator + graphOutputName;
+            String path = directory + File.separator + graphOutputName;
             ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
             System.out.println("Graph located at:\t" + path);
         }catch(IOException e){
@@ -545,7 +545,7 @@
         }
         
         //Save results for graphing with JSHighcharts
-        general.writeXYseries(mainFolder, graphData, getCummulativeSedimentYieldOutput().getName());
+        general.writeXYseries(directory, graphData, getCummulativeSedimentYieldOutput().getName());
 
         //Graph the effective discharge curve
         XYPlot plot = new XYPlot();
@@ -593,7 +593,7 @@
         legendTitle.setItemFont(general.masterFont);
         
         try{
-            String path = mainFolder + File.separator + getSedimentYieldGraph();
+            String path = directory + File.separator + getSedimentYieldGraph();
             ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
             System.out.println("Graph located at:\t" + path);
         }catch(IOException e){
@@ -637,7 +637,7 @@
         //plot(q.e1, eff.e, type = "l")  (Joel)
         
         //Save results for graphing with JSHighcharts
-        general.writeXYseries(mainFolder, graphData, getEffectiveDischargeOutput().getName());
+        general.writeXYseries(directory, graphData, getEffectiveDischargeOutput().getName());
 
         //Graph the effective discharge curve
         XYPlot plot = new XYPlot();
@@ -685,7 +685,7 @@
         legendTitle.setItemFont(general.masterFont);
         
         try{
-            String path = mainFolder + File.separator + getEffectiveDischargeGraph();
+            String path = directory + File.separator + getEffectiveDischargeGraph();
             ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
             System.out.println("Graph located at:\t" + path);
         }catch(IOException e){

src/java/m/hydraulics/effectivedischarge/V1_0.java

@@ -3,9 +3,9 @@
 import csip.annotations.Description;
 import csip.annotations.Name;
 import csip.annotations.VersionInfo;
+import csip.api.server.PayloadParameter;
+import csip.api.server.PayloadResults;
 import csip.ModelDataService;
-import csip.PayloadParameter;
-import csip.PayloadResults;
 import java.io.File;
 import javax.ws.rs.Path;
 
@@ -19,7 +19,7 @@
     
     @Override
     protected void preProcess() throws Exception {
-        model.setMainFolder(getWorkspaceDir().toString());
+        model.setDirectory(workspace().getDir().toString());
         
         PayloadParameter inputPayload = parameter();
         model.setFlowDurationCurve(inputPayload.getString("flowDurationCurve"));
@@ -59,7 +59,7 @@
     protected void postProcess() throws Exception {
         PayloadResults resultPayload = results();
         // files
-        File wd = getWorkspaceDir();
+        File wd = workspace().getDir();
         resultPayload.put(new File(wd, model.getEffectiveDischargeGraph()),
                   new File(wd, model.getSedimentYieldGraph()),
                   new File(wd, model.getHistogram()),

src/java/m/hydraulics/sediment/V1_0.java

@@ -3,9 +3,9 @@
 import csip.annotations.Description;
 import csip.annotations.Name;
 import csip.annotations.VersionInfo;
+import csip.api.server.PayloadParameter;
+import csip.api.server.PayloadResults;
 import csip.ModelDataService;
-import csip.PayloadParameter;
-import csip.PayloadResults;
 import hydraulics.SedimentTransport;
 import javax.ws.rs.Path;
 

src/java/m/hydraulics/standardstep/StandardStepMethod.java

@@ -28,7 +28,7 @@
 */
 public class StandardStepMethod {
     //Inputs
-    String mainFolder = "U:/Java Projects/StandardStepMethod/RegularGeometryTest";
+    String directory = "U:/Java Projects/StandardStepMethod/RegularGeometryTest";
     boolean irregularGeometry = false;
     boolean downstreamCalculation = true;
     boolean useThalwegElevation = true;
@@ -76,8 +76,8 @@
     public void setNumberOfCrossSections(int numberOfCrossSections){
         this.numberOfCrossSections = numberOfCrossSections;
     }
-    public void setMainFolder(String mainFolder){
-        this.mainFolder = mainFolder;
+    public void setDirectory(String directory){
+        this.directory = directory;
     }
     public void setIrregularGeometry(boolean irregularGeometry){
         this.irregularGeometry = irregularGeometry;
@@ -118,11 +118,11 @@
     public File getElevationGraphOutput(){
         if (downstreamCalculation){
             String title = "_" + measuredDownstreamDepth + "m_StartDepth_DownstreamElevationProfile.out";
-            return new File(mainFolder, title);
+            return new File(directory, title);
         }
         else{
             String title = "_" + measuredDownstreamDepth + "m_StartDepth_UpstreamElevationProfile.out";
-            return new File(mainFolder, title);
+            return new File(directory, title);
         }
     }
     public String getSummaryTitle(){
@@ -175,7 +175,7 @@
         
         int numberOfReaches;
         if (irregularGeometry) {
-            numberOfReaches = readLines(mainFolder + File.separator + "reaches.txt");
+            numberOfReaches = readLines(directory + File.separator + "reaches.txt");
         }
         else{
             numberOfReaches = numberOfCrossSections-1;
@@ -590,8 +590,8 @@
      * @throws IOException
      */
     public int calcLargestCrossSection() throws IOException {
-        String[] sections = transferTXTFile(mainFolder + File.separator + "crossSections.txt");
-        int numberOfLines = readLines(mainFolder + File.separator + "crossSections.txt");
+        String[] sections = transferTXTFile(directory + File.separator + "crossSections.txt");
+        int numberOfLines = readLines(directory + File.separator + "crossSections.txt");
 
         int i;
         int n;
@@ -617,8 +617,8 @@
      * @throws IOException
      */
     public double[][][] setCrossSectionGeometries() throws IOException {
-        int numberOfSections = readLines(mainFolder + File.separator + "crossSections.txt");
-        String[] sections = transferTXTFile(mainFolder + File.separator + "crossSections.txt");
+        int numberOfSections = readLines(directory + File.separator + "crossSections.txt");
+        String[] sections = transferTXTFile(directory + File.separator + "crossSections.txt");
         int length = calcLargestCrossSection();
         String[][] xypointlist;
         int i;
@@ -649,8 +649,8 @@
      * @throws IOException
      */
     public double[][] setReachProperties() throws IOException {
-        int numberOfSections = readLines(mainFolder + File.separator + "reaches.txt");
-        String[] reaches = transferTXTFile(mainFolder + File.separator + "reaches.txt");
+        int numberOfSections = readLines(directory + File.separator + "reaches.txt");
+        String[] reaches = transferTXTFile(directory + File.separator + "reaches.txt");
         double[][] reachProperties = new double[numberOfSections][4];
         int i;
         for (i = 0; i < numberOfSections; i++) {
@@ -958,7 +958,7 @@
         legendTitle.setItemFont(general.masterFont);
 
         try {
-            String path = mainFolder + File.separator + graphOutputName;
+            String path = directory + File.separator + graphOutputName;
             ChartUtilities.saveChartAsJPEG(new File(path), chart, 1280, 800);
             System.out.println(path);
         } catch (IOException e) {
@@ -977,7 +977,7 @@
                                  double reachResultsArray[][]) throws IOException {
         //open the file writer and set path
         String summaryOutputName = getSummary();
-        String path = mainFolder + File.separator + summaryOutputName;
+        String path = directory + File.separator + summaryOutputName;
         FileWriter writer =  new FileWriter(path, false);
         PrintWriter print_line = new PrintWriter(writer);
         

src/java/m/hydraulics/standardstep/V1_0.java

@@ -3,9 +3,9 @@
 import csip.annotations.Description;
 import csip.annotations.Name;
 import csip.annotations.VersionInfo;
+import csip.api.server.PayloadParameter;
+import csip.api.server.PayloadResults;
 import csip.ModelDataService;
-import csip.PayloadParameter;
-import csip.PayloadResults;
 import java.io.File;
 import javax.ws.rs.Path;
 
@@ -20,7 +20,7 @@
     @Override
     protected void preProcess() throws Exception {
         //Also requires "reaches.txt" and "crossSections" input files
-        model.setMainFolder(getWorkspaceDir().toString());
+        model.setDirectory(workspace().getDir().toString());
         
         PayloadParameter inputPayload = parameter();
         model.setBottomWidth(inputPayload.getDouble("bottomWidth"));
@@ -47,7 +47,7 @@
     @Override
     protected void postProcess() throws Exception {
        PayloadResults resultPayload = results();
-       File wd = getWorkspaceDir();
+       File wd = workspace().getDir();
        resultPayload.put(new File(wd, model.getElevationGraph()),
                  new File(wd, model.getSummary()),
                  //Below are the result graph files for use by JHighCharts on eRAMS for duplicating the above graphs