Clean up DAP4 code plus minor mods to other -- non-dap4 -- code

.github/workflows/deps.yml

@@ -1,4 +1,4 @@
-on: [pull_request]
+on: [push,pull_request]
 
 jobs:
   check-dependency-availability:

.github/workflows/style.yml

@@ -1,4 +1,4 @@
-on: [pull_request]
+on: [push,pull_request]
 
 jobs:
   check-style:

.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-on: [pull_request]
+on: [push,pull_request]
 
 jobs:
   netcdf-java-tests:

README.md

@@ -2,6 +2,7 @@
 <br>
 <br>
 
+
 # netCDF-Java/CDM
 
 The netCDF Java library provides an interface for scientific data access.

cdm-test-utils/src/main/java/ucar/unidata/util/test/UnitTestCommon.java

@@ -209,16 +209,6 @@ public String modify(String text) {
   //////////////////////////////////////////////////
   // Instance variables
 
-  // System properties
-  protected boolean prop_ascii = true;
-  protected boolean prop_diff = true;
-  protected boolean prop_baseline = false;
-  protected boolean prop_visual = false;
-  protected boolean prop_debug = DEBUG;
-  protected boolean prop_generate = true;
-  protected String prop_controls = null;
-  protected boolean prop_display = false;
-
   protected String title = "Testing";
   protected String name = "testcommon";
 
@@ -231,32 +221,6 @@ public UnitTestCommon() {
 
   public UnitTestCommon(String name) {
     this.title = name;
-    setSystemProperties();
-  }
-
-  /**
-   * Try to get the system properties
-   */
-  protected void setSystemProperties() {
-    if (System.getProperty("nodiff") != null)
-      prop_diff = false;
-    if (System.getProperty("baseline") != null)
-      prop_baseline = true;
-    if (System.getProperty("nogenerate") != null)
-      prop_generate = false;
-    if (System.getProperty("debug") != null)
-      prop_debug = true;
-    if (System.getProperty("visual") != null)
-      prop_visual = true;
-    if (System.getProperty("ascii") != null)
-      prop_ascii = true;
-    if (System.getProperty("utf8") != null)
-      prop_ascii = false;
-    if (System.getProperty("hasdisplay") != null)
-      prop_display = true;
-    if (prop_baseline && prop_diff)
-      prop_diff = false;
-    prop_controls = System.getProperty("controls", "");
   }
 
   //////////////////////////////////////////////////
@@ -379,12 +343,10 @@ protected void unbindstd() {
 
   // Copy result into the a specified dir
   public static void writefile(String path, String content) throws IOException {
-    File f = new File(path);
-    if (f.exists())
-      f.delete();
-    FileWriter out = new FileWriter(f);
-    out.write(content);
-    out.close();
+    // We need to set the Charset to UTF-8, but that is not possible
+    // until JDK level 11, so fake it.
+    byte utf8[] = content.getBytes("UTF-8");
+    writefile(path, utf8);
   }
 
   // Copy result into the a specified dir
@@ -616,75 +578,4 @@ protected static boolean check(int code, int[] ok) {
     return false;
   }
 
-  /*
-   * // Replacement for stderr & stdout
-   * static public class STDIO
-   * {
-   * public STDIO(String name)
-   * {
-   * }
-   * 
-   * public void
-   * printf(String format, Object... args)
-   * {
-   * System.err.println(String.format(format, args));
-   * }
-   * 
-   * public void
-   * println(String msg)
-   * {
-   * printf("%s%n", msg);
-   * }
-   * 
-   * public void
-   * print(String msg)
-   * {
-   * printf("%s", msg);
-   * }
-   * 
-   * public void
-   * flush()
-   * {
-   * }
-   * }
-   * 
-   * static public STDIO stderr = new STDIO("test");
-   * static public STDIO stdout = new STDIO("test");
-   * 
-   * static TemporaryFolder temporaryfolder = null;
-   * 
-   * static public File
-   * makeTemporaryDir(String name)
-   * throws IOException
-   * {
-   * if(temporaryfolder == null)
-   * temporaryfolder = new TemporaryFolder();
-   * return temporaryfolder.newFolder(name);
-   * }
-   * 
-   * static public File
-   * makeTemporaryFile(String name)
-   * throws IOException
-   * {
-   * if(temporaryfolder == null)
-   * temporaryfolder = new TemporaryFolder();
-   * return temporaryfolder.newFile(name);
-   * }
-   * static public void
-   * logify(String s)
-   * {
-   * StringReader rs = new StringReader(s);
-   * BufferedReader r = new BufferedReader(rs);
-   * String line = null;
-   * for(; ; ) {
-   * try {
-   * line = r.readLine();
-   * } catch (IOException ioe) {
-   * break;
-   * }
-   * if(line == null) break;
-   * System.err.println(line);
-   * }
-   * }
-   */
 }

cdm/core/src/main/java/ucar/ma2/Index.java

@@ -570,7 +570,7 @@ public Index set(int[] index) {
       throw new ArrayIndexOutOfBoundsException();
     if (rank == 0)
       return this;
-    int prefixrank = (hasvlen ? rank : rank - 1);
+    int prefixrank = (!hasvlen ? rank : rank - 1);
     System.arraycopy(index, 0, current, 0, prefixrank);
     if (hasvlen)
       current[prefixrank] = -1;

cdm/core/src/main/java/ucar/nc2/Attribute.java

@@ -32,15 +32,6 @@
  * @author caron
  */
 public class Attribute extends CDMNode {
-  /** @deprecated move to jni.Nc4Iosp */
-  @Deprecated
-  private static final String SPECIALPREFIX = "_";
-
-  /** @deprecated move to jni.Nc4Iosp */
-  @Deprecated
-  static public final String[] SPECIALS =
-      {CDM.NCPROPERTIES, CDM.ISNETCDF4, CDM.SUPERBLOCKVERSION, CDM.DAP4_LITTLE_ENDIAN, CDM.EDU_UCAR_PREFIX};
-
   /**
    * Turn a list into a map
    *
@@ -59,20 +50,6 @@ public static Map<String, Attribute> makeMap(List<Attribute> atts) {
     return result;
   }
 
-  /** @deprecated move to jni.Nc4Iosp */
-  @Deprecated
-  public static boolean isspecial(Attribute a) {
-    String nm = a.getShortName();
-    if (nm.startsWith(SPECIALPREFIX)) {
-      /* Check for selected special attributes */
-      for (String s : SPECIALS) {
-        if (nm.startsWith(s))
-          return true; /* is special */
-      }
-    }
-    return false; /* is not special */
-  }
-
   ///////////////////////////////////////////////////////////////////////////////////
 
   /**

cdm/core/src/main/java/ucar/nc2/Dimension.java

@@ -457,9 +457,6 @@ public void setLength(int n) {
     } else if (isUnlimited) {
       if (n < 0)
         throw new IllegalArgumentException("Unlimited Dimension length =" + n + " must >= 0");
-    } else {
-      if (n < 1)
-        throw new IllegalArgumentException("Dimension length =" + n + " must be > 0");
     }
     this.length = n;
   }

cdm/core/src/main/java/ucar/nc2/Group.java

@@ -20,6 +20,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import ucar.ma2.DataType;
+import ucar.nc2.constants.CDM;
 import ucar.nc2.util.EscapeStrings;
 import ucar.nc2.util.Indent;
 import java.util.ArrayList;
@@ -297,7 +298,7 @@ public Dimension findDimensionLocal(String shortName) {
 
   /** The attributes contained by this Group. */
   public AttributeContainer attributes() {
-    return AttributeContainer.filter(attributes, Attribute.SPECIALS);
+    return AttributeContainer.filter(attributes, CDM.SPECIALS);
   }
 
   /** Find the attribute by name, return null if not exist */
@@ -318,7 +319,7 @@ public String findAttributeString(String attName, String defaultValue) {
   /** @deprecated Use attributes() */
   @Deprecated
   public java.util.List<Attribute> getAttributes() {
-    return AttributeContainer.filter(attributes, Attribute.SPECIALS).getAttributes();
+    return attributes().getAttributes();
   }
 
   /** @deprecated Use attributes() */
@@ -526,7 +527,7 @@ void writeCDL(Formatter out, Indent indent, boolean strict) {
 
       for (Attribute att : attributes) {
         // String name = strict ? NetcdfFile.escapeNameCDL(getShortName()) : getShortName();
-        if (!Attribute.isspecial(att)) {
+        if (!CDM.isspecial(att)) {
           out.format("%s", indent);
           att.writeCDL(out, strict, null);
           out.format(";");

cdm/core/src/main/java/ucar/nc2/NetcdfFiles.java

@@ -70,7 +70,7 @@ public class NetcdfFiles {
       registerIOProvider("ucar.nc2.internal.iosp.hdf5.H5iospNew");
     } catch (Throwable e) {
       if (loadWarnings)
-        log.info("Cant load class H5iosp", e);
+        log.info("Cant load class H5iospNew", e);
     }
     try {
       registerIOProvider("ucar.nc2.stream.NcStreamIosp");

cdm/core/src/main/java/ucar/nc2/Structure.java

@@ -23,6 +23,7 @@
 import ucar.ma2.StructureData;
 import ucar.ma2.StructureDataIterator;
 import ucar.ma2.StructureMembers;
+import ucar.nc2.constants.CDM;
 import ucar.nc2.util.Indent;
 
 /**
@@ -635,7 +636,7 @@ protected void writeCDL(Formatter buf, Indent indent, boolean useFullName, boole
     buf.format(";%s%n", extraInfo());
 
     for (Attribute att : attributes()) {
-      if (Attribute.isspecial(att))
+      if (CDM.isspecial(att))
         continue;
       buf.format("%s", indent);
       att.writeCDL(buf, strict, getShortName());

cdm/core/src/main/java/ucar/nc2/Variable.java

@@ -1025,7 +1025,7 @@ else if (dataType.isEnum()) {
 
     indent.incr();
     for (Attribute att : attributes()) {
-      if (Attribute.isspecial(att))
+      if (CDM.isspecial(att))
         continue;
       buf.format("%s", indent);
       att.writeCDL(buf, strict, getShortName());

cdm/core/src/main/java/ucar/nc2/constants/CDM.java

@@ -5,6 +5,8 @@
 
 package ucar.nc2.constants;
 
+import ucar.nc2.Attribute;
+
 /**
  * CDM constants.
  *
@@ -55,12 +57,31 @@ public class CDM {
   public static final String TIME_OFFSET_HOUR = "hoursFrom0z";
   public static final String RUNTIME_COORDINATE = "runtimeCoordinate";
 
-  // Special Attribute Names used in jni.Nc4Iosp
+  // Special attributes
+
+  private static final String SPECIALPREFIX = "_";
+
+  // Define Special attributes that should be suppressed
   public static final String NCPROPERTIES = "_NCProperties";
   public static final String ISNETCDF4 = "_IsNetcdf4";
   public static final String SUPERBLOCKVERSION = "_SuperblockVersion";
-  public static final String DAP4_LITTLE_ENDIAN = "_DAP4_Little_Endian";
-  public static final String EDU_UCAR_PREFIX = "_edu.ucar";
+
+  static public final String[] SPECIALS = {NCPROPERTIES, ISNETCDF4, SUPERBLOCKVERSION};
+
+  // public static final String DAP4_LITTLE_ENDIAN = "_DAP4_Little_Endian";
+  // public static final String EDU_UCAR_PREFIX = "_edu.ucar";
+
+  public static boolean isspecial(Attribute a) {
+    String nm = a.getShortName();
+    if (nm.startsWith(SPECIALPREFIX)) {
+      /* Check for selected special attributes */
+      for (String s : SPECIALS) {
+        if (nm.startsWith(s))
+          return true; /* is special */
+      }
+    }
+    return false; /* is not special */
+  }
 
   // class not interface, per Bloch edition 2 item 19
   private CDM() {} // disable instantiation

cdm/core/src/main/java/ucar/nc2/dataset/DatasetUrl.java

@@ -287,7 +287,7 @@ private static ServiceType decodePathExtension(String path) {
     if (path.endsWith(".dds") || path.endsWith(".das") || path.endsWith(".dods"))
       return ServiceType.OPENDAP;
 
-    if (path.endsWith(".dmr") || path.endsWith(".dap") || path.endsWith(".dsr"))
+    if (path.matches("^.*[.](dmr|dap|dsr)([.](xml|html))?$"))
       return ServiceType.DAP4;
 
     if (path.endsWith(".xml") || path.endsWith(".ncml"))
@@ -365,7 +365,7 @@ private static ServiceType disambiguateHttp(String location) throws IOException
       checkDap2 = true;
     }
 
-    if (location.contains("dap4")) {
+    if (location.contains("dap4") || location.contains("d4ts")) {
       ServiceType result = checkIfDap4(location);
       if (result != null)
         return result;
@@ -445,27 +445,27 @@ private static ServiceType checkIfDods(String location) throws IOException {
 
   // check for dmr
   private static ServiceType checkIfDap4(String location) throws IOException {
-    // Strip off any trailing DAP4 prefix
-    if (location.endsWith(".dap"))
-      location = location.substring(0, location.length() - ".dap".length());
-    else if (location.endsWith(".dmr"))
-      location = location.substring(0, location.length() - ".dmr".length());
-    else if (location.endsWith(".dmr.xml"))
-      location = location.substring(0, location.length() - ".dmr.xml".length());
-    else if (location.endsWith(".dsr"))
-      location = location.substring(0, location.length() - ".dsr".length());
-    try (HTTPMethod method = HTTPFactory.Get(location + ".dmr.xml")) {
+    if (!location.matches("^.*[.](dmr|dap|dsr)([.](xml|html))?$"))
+      return null;
+    // Strip off any trailing DAP4 suffix
+    if (location.endsWith(".xml"))
+      location = location.substring(0, location.length() - ".xml".length());
+    else if (location.endsWith(".html"))
+      location = location.substring(0, location.length() - ".html".length());
+    // location must end with dap, dmr, or dsr
+    location = location.substring(0, location.length() - ".dxx".length());
+
+    try (HTTPMethod method = HTTPFactory.Get(location + ".dsr.xml")) {
       int status = method.execute();
       if (status == HTTP_OK) {
         Optional<String> value = method.getResponseHeaderValue("Content-Type");
         if (value.isPresent()) {
-          if (value.get().startsWith("application/vnd.opendap.org"))
+          if (value.get().contains("application/vnd.opendap.dap4"))
             return ServiceType.DAP4;
         }
       }
       if (status == HTTP_UNAUTHORIZED || status == HTTP_FORBIDDEN)
         throw new IOException("Unauthorized to open dataset " + location);
-
       // not dods
       return null;
     }