v2.17

Author: Bob Simons

WEB-INF/classes/gov/noaa/pfel/coastwatch/TestAll.java

@@ -240,10 +240,10 @@ public static void main(String args[]) throws Throwable {
 //      1) run:
 //           EDD.verbose = true;
 //           EDDGridFromDap.testUAFSubThreddsCatalog(0); //0= entire official clean catalog  ~16hrs
-//      2) Results file is /data/_erddapBPD/logs/UAFdatasets[uafi]_[dateTime].xml          
-//         Log file is     /data/_erddapBPD/logs/UAFdatasets[uafi]_[dateTime].xml.log.txt
+//      2) Results file is /erddapBPD/logs/UAFdatasets[uafi]_[dateTime].xml          
+//         Log file is     /erddapBPD/logs/UAFdatasets[uafi]_[dateTime].xml.log.txt
 //      3) Look at problems, creator_, title, .... Make improvements.
-//         from /data/_erddapBPD/logs:
+//         from /erddapBPD/logs:
 //         grep "SimpleException: Error while getting DAS from" 
 //         grep "unable to get axis" 
 //         grep "unsorted axis" 
@@ -375,7 +375,7 @@ public static void main(String args[]) throws Throwable {
 
       /* 
       //This downloads AWS S3 directory into to a jsonlCSV file 
-      //The lower level copy (written to file as it is downloaded) is in _erddapBPD/datasets/_GenerateDatasetsXml
+      //The lower level copy (written to file as it is downloaded) is in erddapBPD/datasets/_GenerateDatasetsXml
       FileVisitorDNLS.verbose=true; 
       FileVisitorDNLS.reallyVerbose=true;
       FileVisitorDNLS.debugMode=true;
@@ -393,7 +393,7 @@ public static void main(String args[]) throws Throwable {
       String2.log(File2.directReadFrom88591File(outName));
       String2.log("The Results are in " + outName + "\n" +
           "The lower level (partial?) copy (written to file as it is downloaded)\n" +
-          "is in _erddapBPD/datasets/_GenerateDatasetsXml .");
+          "is in erddapBPD/datasets/_GenerateDatasetsXml .");
       /* */      
 
 //    Do this periodically to update the local cache of InPort xml files
@@ -1090,9 +1090,6 @@ public static void main(String args[]) throws Throwable {
         boolean interactive = false;
         boolean doSlowTestsToo = false;
 
-//TestSSR.testAwsTransferManager();
-//DasDds.main(new String[]{"nceiPH53sstn1day", "-verbose"});
-
 //EDDGridFromNcFiles.testNcml();
 
 /* for releases, this line should have open/close comment */

WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/NcHelper.java

@@ -147,7 +147,7 @@ public static String decodeNcDump(String s) {
         int sLength = s.length();
 
         //remove dir name from first line (since this is sometimes sent to ERDDAP users)    
-        //"netcdf /data/_erddapBPD/cache/_test/EDDGridFromDap_Axis.nc {\n" +
+        //"netcdf /erddapBPD/cache/_test/EDDGridFromDap_Axis.nc {\n" +
         int po = 0;
         int brPo = s.indexOf(" {"); 
         if (brPo >= 0) {

WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/OQNux10S1day_20050712_x-135_X-105_y22_Y50.nc

@@ -9810,7 +9810,7 @@ public static void testReadNDNc() throws Exception {
         Test.ensureEqual(results, expected, "results=\n" + results);
 
         //test String vars 
-        fiName = "c:/data/_erddapBPD/copy/cPostDet3/BARBARAx20BLOCK/LAMNAx20DITROPIS/Nx2fA/52038_A69-1303_1059305.nc";
+        fiName = "c:/erddapBPD/copy/cPostDet3/BARBARAx20BLOCK/LAMNAx20DITROPIS/Nx2fA/52038_A69-1303_1059305.nc";
         table.readNDNc(fiName, null, 0,  //standardizeWhat=0
             null, 0, 0);
         results = table.dataToString(4);

WEB-INF/classes/gov/noaa/pfel/coastwatch/pointdata/Table.java

@@ -2268,7 +2268,7 @@ public void doDataProviderForm1(int language, HttpServletRequest request,
                 //convert the info into pseudo datasets.xml
                 String content = 
                     "Data Provider Form - Part 1\n" + //important! Bob's erd.data gmail filter looks for 'Data Provider Form'
-                    "  from " + fromInfo + "\n" +
+                    "  from " + XML.encodeAsHTML(fromInfo) + "\n" +
                     "  ipAddress=" + ipAddress + "\n" +
                     "\n" +
                     "griddedOption=" + griddedOptions[griddedOption] + "\n" +
@@ -2318,7 +2318,7 @@ public void doDataProviderForm1(int language, HttpServletRequest request,
 
             //hidden fields
             writer.write(
-                widgets.hidden("timestamp", XML.encodeAsHTML(tTimestamp)) + 
+                widgets.hidden("timestamp", tTimestamp) + 
                 "\n");
 
 //begin text
@@ -2344,7 +2344,7 @@ public void doDataProviderForm1(int language, HttpServletRequest request,
         30, 50, tYourName, ""))
     .replace("&widgetEmailAddress;", widgets.textField("emailAddress", "", //tooltip
         30, 50, tEmailAddress, ""))
-    .replace("&tTimestamp;", tTimestamp);
+    .replace("&tTimestamp;", XML.encodeAsHTML(tTimestamp));
 writer.write(dataProviderContactInfo
 /*
 "<h2>Your Contact Information</h2>\n" +
@@ -2356,7 +2356,7 @@ public void doDataProviderForm1(int language, HttpServletRequest request,
 "  <br>What is your email address? " +
 widgets.textField("emailAddress", "", //tooltip
     30, 50, tEmailAddress, "") +
-"  <br>This dataset submission's timestamp is " + tTimestamp + ".\n" + 
+"  <br>This dataset submission's timestamp is " + XML.encodeAsHTML(tTimestamp) + ".\n" + 
 "\n"
 */);
 String dataProviderData = EDStatic.dataProviderDataAr[language]
@@ -2594,7 +2594,7 @@ public void doDataProviderForm2(int language, HttpServletRequest request,
                 tKeywords.sortIgnoreCase();
                 String content = 
 "Data Provider Form - Part 2\n" + //important! Bob's erd.data gmail filter looks for this
-"  from " + fromInfo + "\n" +
+"  from " + XML.encodeAsHTML(fromInfo) + "\n" +
 "  ipAddress=" + ipAddress + "\n" +
 "\n" +
 "    <addAttributes>\n" +
@@ -2671,9 +2671,9 @@ public void doDataProviderForm2(int language, HttpServletRequest request,
 
             //hidden fields
             writer.write(
-                widgets.hidden("yourName",     XML.encodeAsHTML(tYourName)) +
-                widgets.hidden("emailAddress", XML.encodeAsHTML(tEmailAddress)) +
-                widgets.hidden("timestamp",    XML.encodeAsHTML(tTimestamp)) + 
+                widgets.hidden("yourName",     tYourName) +
+                widgets.hidden("emailAddress", tEmailAddress) +
+                widgets.hidden("timestamp",    tTimestamp) + 
                 "\n");
 
 //begin text
@@ -3066,7 +3066,7 @@ public void doDataProviderForm3(int language, HttpServletRequest request,
                 StringBuilder content = new StringBuilder();
                 content.append(
                     "Data Provider Form - Part 3\n" + //important! Bob's erd.data gmail filter looks for this
-                    "  from " + fromInfo + "\n" +
+                    "  from " + XML.encodeAsHTML(fromInfo) + "\n" +
                     "  ipAddress=" + ipAddress + "\n" +
                     "\n" +
                     "groupOf10=" + groupOptions[tGroup] + "\n" +
@@ -3138,9 +3138,9 @@ public void doDataProviderForm3(int language, HttpServletRequest request,
 
             //hidden fields
             writer.write(
-                widgets.hidden("yourName",     XML.encodeAsHTML(tYourName)) +
-                widgets.hidden("emailAddress", XML.encodeAsHTML(tEmailAddress)) +
-                widgets.hidden("timestamp",    XML.encodeAsHTML(tTimestamp)) + 
+                widgets.hidden("yourName",     tYourName) +
+                widgets.hidden("emailAddress", tEmailAddress) +
+                widgets.hidden("timestamp",    tTimestamp) + 
                 "\n");
 
 //begin text
@@ -3383,7 +3383,7 @@ public void doDataProviderForm4(int language, HttpServletRequest request,
                 //convert the info into pseudo datasets.xml
                 String content = 
                     "Data Provider Form - Part 4\n" + //important! Bob's erd.data gmail filter looks for this
-                    "  from " + fromInfo + "\n" +
+                    "  from " + XML.encodeAsHTML(fromInfo) + "\n" +
                     "  ipAddress=" + ipAddress + "\n" +
                     "\n" +
                     "Other comments:\n" + 
@@ -3432,9 +3432,9 @@ public void doDataProviderForm4(int language, HttpServletRequest request,
 
             //hidden fields
             writer.write(
-                widgets.hidden("yourName",     XML.encodeAsHTML(tYourName)) +
-                widgets.hidden("emailAddress", XML.encodeAsHTML(tEmailAddress)) +
-                widgets.hidden("timestamp",    XML.encodeAsHTML(tTimestamp)) + 
+                widgets.hidden("yourName",     tYourName) +
+                widgets.hidden("emailAddress", tEmailAddress) +
+                widgets.hidden("timestamp",    tTimestamp) + 
                 "\n");
 
 //begin text
@@ -3532,10 +3532,10 @@ public void doDataProviderFormDone(int language, HttpServletRequest request,
 
 //begin text
 writer.write(EDStatic.dpf_congratulationAr[language]
-    .replace("&tTimestamp;", tTimestamp)
+    .replace("&tTimestamp;", XML.encodeAsHTML(tTimestamp))
     .replaceAll("&tErddapUrl;", tErddapUrl)
-    .replace("&tYourName;", SSR.minimalPercentEncode(tYourName))
-    .replace("&tEmailAddress;", SSR.minimalPercentEncode(tEmailAddress))
+    .replace("&tYourName;", XML.encodeAsHTML(tYourName))
+    .replace("&tEmailAddress;", XML.encodeAsHTML(tEmailAddress))
 
 // "<h2>You're done! Congratulations! Thank you!</h2>\n" +
 // "The ERDDAP administrator will email you soon to figure out the best way transfer\n" +

WEB-INF/classes/gov/noaa/pfel/erddap/Erddap.java

@@ -7081,12 +7081,12 @@ private double validateGreaterThanThrowOrRepair(int precision, double value,
      * 
      * @param language the index of the selected language
      * @param minX     the minimum X / longitude value to validate. minX should
-     *                 be < maxX
+     *                 be &lt; maxX
      * @param maxX     the maximum X / longitude value to check. minX should be
-     *                 < maxX
-     * @param minY     the minimum Y / latitude value to check. minY should be <
+     *                 &lt; maxX
+     * @param minY     the minimum Y / latitude value to check. minY should be &lt;
      *                 maxY
-     * @param maxY     the minimum Y / latitude value to check. minY should be <
+     * @param maxY     the minimum Y / latitude value to check. minY should be &lt;
      *                 maxY
      */
     public void validateLatLon(int language, double minX, double maxX,
@@ -7451,7 +7451,7 @@ public boolean saveAsKml(int language,
         //.transparentPng uses Sgt.makeCleanMap which projects data (even, e.g., Mercator)
         //so resulting .png will use a geographic projection.
 
-        //although the Google docs say lon must be +-180, lon > 180 is sortof ok!
+        //although the Google docs say lon must be +-180, lon > 180 is sort of ok!
         EDVLonGridAxis lonEdv = (EDVLonGridAxis)axisVariables[lonIndex];
         EDVLatGridAxis latEdv = (EDVLatGridAxis)axisVariables[latIndex];
 
@@ -14762,7 +14762,7 @@ public static void testSaveAsImage() throws Throwable {
 
         // Make fully valid image
         testSaveAsImageVsExpected(eddGrid, dir, requestUrl,
-                MessageFormat.format(userDapQueryTemplate, 30, 40, 210, 220),
+                MessageFormat.format(userDapQueryTemplate, 30, 40, 210, 220), //#'s are minY, maxY, minX, maxX
                 fileTypeName,
                 "46bbbefee2b781a7eed98f8e3b855527ba45711cf806a04cf2704a141e0a6c6f" /* expected */);
 

WEB-INF/classes/gov/noaa/pfel/erddap/dataset/EDDGrid.java

@@ -7803,7 +7803,7 @@ public static void testMatchAxisNDigits() throws Throwable {
         int language = 0; 
 
         //force reload files
-        File2.delete("/data/_erddapBPD/dataset/ay/erdATssta3day/fileTable.nc");
+        File2.delete("/erddapBPD/dataset/ay/erdATssta3day/fileTable.nc");
 
         //load dataset
         testVerboseOn();
@@ -15451,7 +15451,7 @@ public static void test(StringBuilder errorSB, boolean interactive,
                     if (test ==  0) testNc(deleteCachedDatasetInfo);
                     if (test ==  1) testCwHdf(deleteCachedDatasetInfo);
                     if (test ==  2) testHdf();
-                    if (test ==  3) testNcml();
+                    if (test ==  3) testNcml(); //!!!this is the only test which fails when I use separate netcdf-java Maven artifacts 
                     if (test ==  4) testNccsv();
                     if (test ==  5) testGrib_43(deleteCachedDatasetInfo);  //42 or 43 for netcdfAll 4.2- or 4.3+
                     if (test ==  6) testGrib2_43(deleteCachedDatasetInfo); //42 or 43 for netcdfAll 4.2- or 4.3+

WEB-INF/classes/gov/noaa/pfel/erddap/dataset/EDDGridFromNcFiles.java

@@ -148,18 +148,17 @@ public abstract class EDDTable extends EDD {
     public static String orderByOptions[] = { "",
         "orderBy", "orderByClosest", "orderByCount", "orderByLimit", 
         "orderByMax", "orderByMin", "orderByMinMax", "orderByMean", "orderBySum"};
-    public static String DEFAULT_ORDERBYCLOSEST = "1 hour";
     public static String DEFAULT_ORDERBYLIMIT   = "100";
     /** These are used on web pages when a user changes orderBy. 
      *  They parallel the orderByOptions. */    
     public static String orderByExtraDefaults[] = { "",
-        "", DEFAULT_ORDERBYCLOSEST,         "",      DEFAULT_ORDERBYLIMIT,          
-        "",                     "",         "",      ""};
+        "",    "",     "",      DEFAULT_ORDERBYLIMIT,          
+        "",    "",     "",      "",                    ""};
      /** This is the minimum number of orderBy variables that must be specified
        (not counting the orderByExtra item). */
     public static byte minOrderByVariables[] = { 0,
         1,        1,       0,      0,
-        1,        1,       1,      0};
+        1,        1,       1,      0,     0};
 
     /** This is used in many file types as the row identifier. */
     public final static String ROW_NAME = "row";  //see also Table.ROW_NAME
@@ -10160,16 +10159,20 @@ else if (tOp == REGEX_OP_INDEX ||
                 StringArray names = StringArray.fromCSV(
                     obPart.substring(start.length(), obPart.length() - 2));
                 StringArray goodNames = new StringArray();
-                boolean usesExtra = orderByExtraDefaults[i].length() > 0; //e.g., orderByLimit, orderByClosest
+                boolean usesExtra = orderByExtraDefaults[i].length() > 0; //e.g., orderByLimit
                 int nNames = names.size() - (usesExtra? 1 : 0); //if uses extra, don't check last item
                 if (nNames < minOrderByVariables[i]) 
                     continue;  //too few items in csv
                 for (int n = 0; n < nNames; n++) {
-                    if (String2.indexOf(dataVariableDestinationNames, names.get(n)) < 0)
+                    String tName = names.get(n);
+                    int divPo = tName.indexOf('/');
+                    if (divPo > 0)
+                        tName = tName.substring(0, divPo);
+                    if (String2.indexOf(dataVariableDestinationNames, tName) < 0)
                         continue;
                     goodNames.add(names.get(n));
-                    if (resultsVariables.indexOf(names.get(n)) < 0)
-                        resultsVariables.add(names.get(n));
+                    if (resultsVariables.indexOf(tName) < 0)
+                        resultsVariables.add(tName);
                 }
                 if (goodNames.size() >= minOrderByVariables[i]) {
                     //success

WEB-INF/classes/gov/noaa/pfel/erddap/dataset/EDDTable.java

@@ -1359,7 +1359,7 @@ public class EDDTableCopyPost extends EDDTableCopy {
 
         //find activation_time is after surgery_time
         TableWriterAll twa = new TableWriterAll(tedd, null, 
-            "c:/data/_erddapBPD/cache/cPostSurg3/", "findSurgeryBeforeActivation");
+            "c:/erddapBPD/cache/cPostSurg3/", "findSurgeryBeforeActivation");
         tedd.getDataForDapQuery(language, loggedInAs, "requestUrl", 
             "unique_tag_id,activation_time,surgery_time,PI", twa);
         Table table = twa.cumulativeTable();