v2.16

Author: Bob Simons

WEB-INF/ArchiveADataset.bat

@@ -2,4 +2,4 @@ rem This is the Windows batch file to run ArchiveADataset.
 rem See http://coastwatch.pfeg.noaa.gov/erddap/download/setupDatasetsXml.html#Tools
 
 rem You'll need to change java's path to make this work:
-C:\programs\jdk8u292-b10\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1500M -Xmx1500M  gov.noaa.pfel.erddap.ArchiveADataset %*
+C:\programs\jdk8u312-b07\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1500M -Xmx1500M  gov.noaa.pfel.erddap.ArchiveADataset %*

WEB-INF/DasDds.bat

@@ -2,4 +2,4 @@ rem This is the Windows batch file to run DasDds.
 rem See http://coastwatch.pfeg.noaa.gov/erddap/download/setupDatasetsXml.html#Tools
 
 # You'll need to change java's path to make this work:
-C:\programs\jdk8u292-b10\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/*  -Xms1000M -Xmx1000M  gov.noaa.pfel.erddap.DasDds %*
+C:\programs\jdk8u312-b07\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/*  -Xms1000M -Xmx1000M  gov.noaa.pfel.erddap.DasDds %*

WEB-INF/FindDuplicateTime.bat

@@ -5,4 +5,4 @@ rem Parameters: directory fileNameRegex timeVarName
 rem This is recursive.
 rem Written by Bob Simons  original 2021-01-20
 
-C:\programs\jdk8u292-b10\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1300M -Xmx1300M -verbose:gc gov.noaa.pfel.erddap.dataset.FindDuplicateTime %*
+C:\programs\jdk8u312-b07\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1300M -Xmx1300M -verbose:gc gov.noaa.pfel.erddap.dataset.FindDuplicateTime %*

WEB-INF/GenerateDatasetsXml.bat

@@ -2,4 +2,4 @@ rem This is the Windows batch file to run GenerateDatasetsXml.
 rem See http://coastwatch.pfeg.noaa.gov/erddap/download/setupDatasetsXml.html#Tools
 
 rem You'll need to change java's path to make this work:
-C:\programs\jdk8u292-b10\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1000M -Xmx1000M  gov.noaa.pfel.erddap.GenerateDatasetsXml %*
+C:\programs\jdk8u312-b07\bin\java.exe -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1000M -Xmx1000M  gov.noaa.pfel.erddap.GenerateDatasetsXml %*

WEB-INF/NetCheck.bat

@@ -4,4 +4,4 @@ rem Then run this from an MS-DOS Prompt (command line) window.
 # Use "NetCheck -testMode" to just send emails to the NetCheck administrator.
 
 set thisDir=%~dp0
-java -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1000M -Xmx1000M gov.noaa.pfel.coastwatch.netcheck.NetCheck NetCheck.xml %*
+java -cp classes;../../../lib/servlet-api.jar;lib/* -Xms1400M -Xmx1400M gov.noaa.pfel.coastwatch.netcheck.NetCheck NetCheck.xml %*

WEB-INF/NetCheck.sh

@@ -8,4 +8,4 @@
 commandLine=$0
 tDir=`echo $commandLine | dirname $0`
 
-java -cp classes:../../../lib/servlet-api.jar:lib/* -Xms1000M -Xmx1000M gov.noaa.pfel.coastwatch.netcheck.NetCheck NetCheck.xml "$@"
+java -cp classes:../../../lib/servlet-api.jar:lib/* -Xms1400M -Xmx1400M gov.noaa.pfel.coastwatch.netcheck.NetCheck NetCheck.xml "$@"

WEB-INF/classes/com/cohort/array/StringArray.java

@@ -294,12 +294,16 @@ public StringArray(Map map) {
     } */
 
     /**
-     * This reads the text contents of the specified file using this computer's default charset.
-     * 
+     * This reads the text contents of the specified file using File2.ISO_8859_1.
      */
-    public static StringArray fromFile(String fileName) throws Exception {
-   
-        return fromFile(fileName, null);
+    public static StringArray fromFile88591(String fileName) throws Exception {
+        return fromFile(fileName, File2.ISO_8859_1);
+    }
+    /**
+     * This reads the text contents of the specified file using File2.UTF_8.
+     */
+    public static StringArray fromFileUtf8(String fileName) throws Exception {
+        return fromFile(fileName, File2.UTF_8);
     }
 
 
@@ -2508,11 +2512,12 @@ public int[] getNMinMaxIndex() {
      *  
      * @param fileName1 a complete file name
      * @param fileName2 a complete file name
+     * @param charset e.g., File2.ISO_8859_1 or File2.UTF_8.
      * @throws Exception if files are different
      */
-    public static void diff(String fileName1, String fileName2) throws Exception {
-        StringArray sa1 = fromFile(fileName1);
-        StringArray sa2 = fromFile(fileName2);
+    public static void diff(String fileName1, String fileName2, String charset) throws Exception {
+        StringArray sa1 = fromFile(fileName1, charset);
+        StringArray sa2 = fromFile(fileName2, charset);
         sa1.diff(sa2);
     }
 
@@ -2523,15 +2528,16 @@ public static void diff(String fileName1, String fileName2) throws Exception {
      *  
      * @param fileName1 a complete file name
      * @param fileName2 a complete file name
+     * @param charset e.g., File2.ISO_8859_1 or File2.UTF_8.
      * @throws Exception if files are different
      */
-    public static void repeatedDiff(String fileName1, String fileName2) throws Exception {
+    public static void repeatedDiff(String fileName1, String fileName2, String charset) throws Exception {
         while (true) {
             try {
                 String2.log("\nComparing " + fileName1 + 
                             "\n      and " + fileName2);
-                StringArray sa1 = fromFile(fileName1);
-                StringArray sa2 = fromFile(fileName2);
+                StringArray sa1 = fromFile(fileName1, charset);
+                StringArray sa2 = fromFile(fileName2, charset);
                 sa1.diff(sa2);
                 String2.log("!!! The files are the same!!!");
                 break;

WEB-INF/classes/com/cohort/util/TestUtil.java

@@ -1887,10 +1887,10 @@ public static void testString2() throws Throwable {
         //for (int i = 0; i < 10000000; i++)
         //    sb.append("a");
         //String s9 = sb2.toString();
-        //File2.writeToFile(fileName, s9); //warm up
-        //File2.writeToFile(fileName, s9);
+        //File2.writeToFile88591(fileName, s9); //warm up
+        //File2.writeToFile88591(fileName, s9);
         //long tTime = System.currentTimeMillis();
-        //File2.writeToFile(fileName, s9);
+        //File2.writeToFile88591(fileName, s9);
         //String2.log("time=" + (System.currentTimeMillis() - tTime));
         //sb2 = null;
         //s9 = null;
@@ -2973,13 +2973,13 @@ public static void interactiveTestCalendar2() throws Exception {
                 "\nOracle Java versus AdoptOpenJDK may be slightly different for these."); 
         }
 
-        String2.log("getCurrentISODateTimeString = " + Calendar2.formatAsISODateTimeT(Calendar2.newGCalendarLocal()));
-        String2.log("    *** Check that HOUR accounts for daylight saving time!\n");
-        String2.log("current UTC time = " + Calendar2.formatAsISODateTimeT(Calendar2.newGCalendarZulu()));
-        String2.log("    *** Check that HOUR is local+7 in summer (DST), local+8 in winter (in California).");
-        String2.log("    See current UTC time at http://www.xav.com/time.cgi");
-        String2.pressEnterToContinue();
-
+        String2.pressEnterToContinue(
+            "getCurrentISODateTimeString = " + Calendar2.formatAsISODateTimeT(Calendar2.newGCalendarLocal()) +
+            "    *** Check that HOUR accounts for daylight saving time!\n\n" +
+            "current UTC time = " + Calendar2.formatAsISODateTimeT(Calendar2.newGCalendarZulu()) + "\n" +
+            "    *** Check that HOUR is local+7 in summer (DST), local+8 in winter (in California)\n" +
+            "                        or local+4 in summer (DST), local+5 in winter (on East Coast).\n" +
+            "    See current UTC time at http://www.xav.com/time.cgi");
     }
 
     /**

WEB-INF/classes/com/cohort/util/Units2.java

@@ -1796,7 +1796,7 @@ public static HashMap<String, String> getHashMapStringString(String fileName, St
      */
     public static void checkUdunits2File(String fileName) throws Exception {
         String2.log("\n*** Units2.checkUdUnits2File " + fileName);
-        StringArray sa = StringArray.fromFile(fileName);
+        StringArray sa = StringArray.fromFileUtf8(fileName);
         StringArray names = new StringArray();
         int n = sa.size();
         int nDef = 0, nPlural = 0, nSingular = 0, nSymbol = 0;
@@ -1952,7 +1952,7 @@ public static StringArray getTestUdunits() throws Exception {
                  f == 1? "datasetsFEDCW.xml" :
                          "uniqueCFUnits.txt");
 
-            ArrayList<String> lines = File2.readLinesFromFile(fileName, File2.ISO_8859_1, 1); //nAttempts
+            ArrayList<String> lines = File2.readLinesFromFile(fileName, File2.UTF_8, 1); //nAttempts
             int nLines = lines.size();
             for (int i = 0; i < nLines; i++) {
                 String s = String2.extractCaptureGroup(lines.get(i), pattern, 1); //captureGroupNumber
@@ -2207,7 +2207,7 @@ else if (Calendar2.isStringTimeUnits(oUnits))
      * This tests if the canonical units for each unique CF unit is unique.
      */
     public static void testIfCFCanonicalUnitsUnique() throws Throwable {
-        StringArray sa = StringArray.fromFile(cfUnique, File2.UTF_8);
+        StringArray sa = StringArray.fromFileUtf8(cfUnique);
         Attributes atts = new Attributes(); //use it as a hashmap: canon -> source
         for (int i = 0; i < sa.size(); i++) {
             String s = sa.get(i);

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

@@ -3317,11 +3317,11 @@ public static void testHdf4() throws Exception {
         String[] list = RegexFilenameFilter.recursiveFullNameList(
             "c:/programs/_tomcat/webapps/cwexperimental/WEB-INF/classes/ucar4", ".*\\.java", false);
         for (int i = 0; i < list.length; i++) {
-            String content[] = File2.readFromFile(list[i]);
+            String content[] = File2.readFromFileUtf8(list[i]);
             if (content[0].length() == 0) {
                 String2.log("processing " + list[i]);
                 content[1] = String2.replaceAll(content[1], "ucar.", "ucar4.");
-                File2.writeToFile(list[i], content[1]);
+                File2.writeToFileUtf8(list[i], content[1]);
             } else {
                 String2.log(content[0]);
             } 
@@ -6367,7 +6367,7 @@ public static void nodcPJJU(
         for (int f = 0; f < fileNames.length; f++) {
             try {
                 String2.log("\n#" + f + " " + fileNames[f]);
-                ArrayList<String> lines = File2.readLinesFromFile(inDir + fileNames[f], null, 2);
+                ArrayList<String> lines = File2.readLinesFromFile(inDir + fileNames[f], File2.ISO_8859_1, 2);
 
                 //BOTTLE,20030711WHPSIODMB
                 //#code : jjward hyd_to_exchange.pl 
@@ -6984,10 +6984,9 @@ public static String makeNetcheckErddapTests(String erddapUrl) throws Throwable
      */
     public static void fixKeywords(String fileName) throws Exception {
         String2.log("fixKeywords " + fileName);
-        String charset = File2.ISO_8859_1;
         String attKeywords = "<att name=\"keywords\">";
         int attKeywordsLength = attKeywords.length();
-        StringArray lines = StringArray.fromFile(fileName, charset);
+        StringArray lines = StringArray.fromFileUtf8(fileName);
         int linesSize = lines.size();
         for (int i = 0; i < linesSize; i++) {
             //start keywords?
@@ -7012,7 +7011,7 @@ public static void fixKeywords(String fileName) throws Exception {
                 }
             }
         }
-        lines.toFile(fileName);
+        lines.toFile(fileName, File2.UTF_8, null);
     }
 
     /**
@@ -7339,7 +7338,7 @@ public static void convertGlobecCsvToNc() throws Exception {
     public static void splitRockfish() throws Exception {
         String2.log("\n*** splitRockfish");
         String fileDir = "c:/data/globec/";
-        StringArray sa = StringArray.fromFile(fileDir + "rockfish_view.csv");
+        StringArray sa = StringArray.fromFile88591(fileDir + "rockfish_view.csv");
         int size = sa.size();
 
         //this file has \N for missing values.  change to ""
@@ -7352,7 +7351,7 @@ public static void splitRockfish() throws Exception {
         while (size > 1) { 
             int stop = Math.min(100000, size - 1);
             sa.subset(subset, 0, 1, stop); //stop is inclusive
-            subset.toFile(fileDir + "rockfish" + (chunk++) + ".csv");
+            subset.toFile(fileDir + "rockfish" + (chunk++) + ".csv", File2.ISO_8859_1, null);
             sa.removeRange(1, stop + 1); //end is exclusive
             size = sa.size();
         }
@@ -9504,7 +9503,7 @@ public static void makePH2Ncml(String sstdn)
 
         //String names[] = RegexFilenameFilter.list(dir, regex);
         ArrayList<String> names = File2.readLinesFromFile(
-            "/u00/satellite/PH2/" + sstdn + "/names.txt", null, 1);
+            "/u00/satellite/PH2/" + sstdn + "/names.txt", File2.ISO_8859_1, 1);
 
         //for each file
         int nNames = names.size();
@@ -9559,7 +9558,7 @@ public static void makePH53Ncml()
             for (int daynight = 0; daynight < 2; daynight++) {
 
                 ArrayList<String> names = File2.readLinesFromFile(
-                    ncmlDir + dayNight[daynight] + "names" + year + ".txt", null, 1);
+                    ncmlDir + dayNight[daynight] + "names" + year + ".txt", File2.ISO_8859_1, 1);
                 HashMap<String,String> hm = new HashMap();
                 //for each file
                 //19811101145206-NODC-L3C_GHRSST-SSTskin-AVHRR_Pathfinder-PFV5.2_NOAA07_G_1981305_day-v02.0-fv01.0.nc