cutout: modifies SodaImpl to use vlkb-cutout instead on two calls to vlkb-overlap + vlkb-imcopy

data-access/engine/src/vlkb/src/imcopy.cpp

@@ -32,13 +32,12 @@ int stream_cutout(string pathname, int extnum, string region)
 		string pixfilter{ to_cfitsio_format(bnds) };
 
 		imcopy(pathname, extnum, pixfilter);
-      return EXIT_SUCCESS;
-
+      // pixfilter must be within NAXIS[] otherwise cfitsio-error
+      return 0; // EXIT_SUCCESS
 	}
 	else if((ov_code == 1) || (ov_code == 6))
 	{
-      // no overlap
-      return EXIT_SUCCESS;
+		return 1; // no overlap EXIT_SUCCESS
 	}
    else
    {
@@ -47,7 +46,6 @@ int stream_cutout(string pathname, int extnum, string region)
 }
 
 
-
 // ----------------------------------------------------------------------------------
 
 int fits_copy_image_section2(

data-access/engine/src/vlkb/src/main.cpp

@@ -259,10 +259,16 @@ int cmd_cutout(int argc, char * argv[])
    if (argc != 4)
    {
       std::cerr
-         << "Usage:  cutout <filename.fits> <extnum> <region>\n"
-         << "\n"
-         << "Calculate overlap between HDU in file and region.\n\nregion in JSON form of VO-SODA params. For example 'POS=CIRCLE 21.4458 -1.373 0.1' :\n"
-         " \'{\"pos\":{\"circle\":{\"lat\":-1.373,\"lon\":21.4458,\"radius\":0.1},\"system\":\"ICRS\"},\"service\":\"SUBIMG\"}\'\n";
+         << "Usage:  cutout <filename.fits> <extnum> <region>"
+			<< endl
+         << endl
+         << "Calculate overlap between HDU in file and region. Returns 0 (ok), 1 (no overlap) or EXIT_FAILURE"
+			<< endl
+         << endl
+         << "region in JSON form of VO-SODA params. For example 'POS=CIRCLE 21.4458 -1.373 0.1' :"
+			<< endl
+         << " \'{\"pos\":{\"circle\":{\"lat\":-1.373,\"lon\":21.4458,\"radius\":0.1},\"system\":\"ICRS\"},\"service\":\"SUBIMG\"}\'"
+         << endl;
       return EXIT_FAILURE;
    }
    else
@@ -272,8 +278,8 @@ int cmd_cutout(int argc, char * argv[])
       string region{argv[3]};
 
       int rc = stream_cutout(pathname, extnum, region);
-      if(!rc)
-         return EXIT_SUCCESS;
+      if( (rc == 0) || (rc == 1))
+				return rc; // OK or no overlap
    }
    return EXIT_FAILURE;
 }

data-access/servlet/src/main/java/cutout/Soda.java

@@ -14,7 +14,7 @@ import vo.parameter.*;
 public interface Soda
 {
 
-   public void doStream(String relPathname, int hdunum,
+   public int doStream(String relPathname, int hdunum,
          Pos pos, Band band, Time time, Pol pol, String pixels,
          OutputStream outputStream) throws IOException, InterruptedException;
 

data-access/servlet/src/main/java/cutout/SodaImpl.java

@@ -43,32 +43,28 @@ class SodaImpl implements Soda
    }
 
 
-   public void doStream(String relPathname, int hdunum,
+   public int doStream(String relPathname, int hdunum,
          Pos pos, Band band, Time time, Pol pol, String pixels,
          OutputStream outputStream)  throws IOException, InterruptedException
    {
-      LOGGER.fine("trace");
-
       Instant start = Instant.now();
+      LOGGER.fine("trace");
 
-      boolean has_overlap  = false;
-      boolean pixels_valid = (pixels != null);
-
-      String boundsString = "";
+		if(outputStream == null)
+			LOGGER.finest("supplied outputStream for cut-file is null");
+			// FIXME throw excpetion here
 
-      final boolean isDavCall = relPathname.startsWith("http://") || relPathname.startsWith("https://");
-      final boolean isAbsPath = relPathname.startsWith("/"); // Resolver removes schema from file://
+      //boolean pixels_valid = (pixels != null);
+      //final boolean isDavCall = relPathname.startsWith("http://") 
+																			// || relPathname.startsWith("https://");
+      //final boolean isAbsPath = relPathname.startsWith("/"); // Resolver removes schema from file://
                                                            //  file:///some_abs_path -> /soma_abs_path
                                                            //  file://some_rel_path -> some_rel_path
+      //String absPathname = (isDavCall || isAbsPath) ? relPathname 
+																		// : (fitsPaths.surveys() +"/"+ relPathname);
 
-      String absPathname = (isDavCall || isAbsPath) ? relPathname : (fitsPaths.surveys() +"/"+ relPathname);
-
-      if( !pixels_valid )
-      {
-         ByteArrayOutputStream bos = new ByteArrayOutputStream();
-         if(bos == null)
-            throw new AssertionError("byte output stream for bounds was not created, is null");
-
+      boolean has_overlap  = false;
+      String boundsString = "";
 		JsonEncoder jReq = new JsonEncoder();
 		jReq.add(pos);
 		jReq.add(band);
@@ -77,203 +73,37 @@ class SodaImpl implements Soda
 		String coordString = jReq.toString();
 		LOGGER.finest("coordString: " + coordString);
 
-         /* calc bounds */
-
-         String[] cmdBounds = new String[4];
-         cmdBounds[0] = "/usr/local/bin/vlkb";
-         cmdBounds[1] = "overlap";
-         cmdBounds[2] = absPathname;
-         cmdBounds[3] = coordString;
-
-         LOGGER.finest(String.join(" ", cmdBounds));
+		String[] cmd = new String[5];
+		cmd[0] = "/usr/local/bin/vlkb";
+		cmd[1] = "cutout";
+		cmd[2] = fitsPaths.surveys() + "/" + relPathname;
+		cmd[3] = String.valueOf(hdunum);
+		cmd[4] = coordString;
+		LOGGER.finest(String.join(" ", cmd));
 
-         ExecCmd execBounds = new ExecCmd();
-         execBounds.doRun(bos, cmdBounds);
-         LOGGER.finest("execBounds exitValue: " + execBounds.exitValue);
-
-         boolean has_result = (execBounds.exitValue == 0);
-
-         if(has_result)
-         {
-            boundsString = new String(bos.toByteArray());
+		StringBuilder errorStrBuilder = new StringBuilder();
 
-            /* FIXME disable GRID not supported
-            boundsString = replaceWithGrid(boundsString, pos, band, time, pol);
-            LOGGER.finest("boundsString(with GRID): " + boundsString);
-            */
-            LOGGER.warning("GRID support was disabled");
-            has_overlap = !((boundsString != null) && boundsString.trim().isEmpty());
+		ExecCmd exec = new ExecCmd();
+		exec.doRun(outputStream, cmd, errorStrBuilder);
+		int rc = exec.exitValue;
+		LOGGER.finest("exec cutout exitValue: " + rc);
+		LOGGER.finer("EXECTIME    cutoutDone: " + Duration.between(start, Instant.now()));
 
-            if( !has_overlap )
+		if(rc == 0)
 		{
-               throw new IllegalArgumentException(
-                     "region in file does not overlap with region defined by SODA parameters");
-            }
+          return rc; // OK
 		}
-         bos.close();
-
-         Instant boundsDone = Instant.now();
-         LOGGER.finer("EXECTIME boundsDone: " + Duration.between(start, boundsDone));
-      }
-
-      if(has_overlap || pixels_valid)
+		else if(rc == 1)
 		{
-         /* cutout -> outputStream */
-
-         String pixFilterString = pixels_valid ? pixels : boundsString;
-
-         String[] cmdCut = new String[5];
-         cmdCut[0] = "/usr/local/bin/vlkb";
-         cmdCut[1] = isDavCall ? "imcopydav" : "imcopy";
-         cmdCut[2] = absPathname;
-         cmdCut[3] = String.valueOf(hdunum-1);
-         cmdCut[4] = pixFilterString;
-
-         LOGGER.finest(String.join(" ", cmdCut));
-
-         if(outputStream == null)
-            LOGGER.finest("supplied outputStream for cut-file is null");
-
-         ExecCmd execCut = new ExecCmd();
-         execCut.doRun(outputStream, cmdCut);
-
-         LOGGER.finest("execCut exitValue: " + execCut.exitValue);
-
-         boolean cut_successful = (execCut.exitValue == 0);
-
-         if(!cut_successful)
-         {
-            throw new IllegalArgumentException("cut by pixels not completed for pixels : " + pixFilterString);
-         }
-
-         Instant cutDone = Instant.now();
-         LOGGER.finer("EXECTIME    cutDone: " + Duration.between(start, cutDone));
+          return rc; // OK, but no overlap
 		}
 		else
 		{
 			throw new IllegalArgumentException(
-               "overlap computation could not be completed with the given arguments");
+					"overlap computation could not be completed with the given arguments. "
+                + errorStrBuilder.toString());
 		}
 	}
 
-
-   private String genRegionForVlkbOverlapCmd(Pos pos, Band band)
-   {
-      LOGGER.fine("trace");
-
-      String region = "";
-
-      if(pos != null)
-      {
-         String skySystem = pos.system.name();
-
-         if(pos.shape.equals("CIRCLE"))
-         {
-            double l = pos.circle.lon;
-            double b = pos.circle.lat;
-            double r = pos.circle.radius;
-            region = region + "skysystem=" + skySystem + "&l=" + String.valueOf(l) + "&b=" + String.valueOf(b)
-               + "&r=" + String.valueOf(r);
-         }
-         else if(pos.shape.equals("RANGE"))
-         {
-            double l =  (pos.range.lon1 + pos.range.lon2)/2.0;
-            double b =  (pos.range.lat1 + pos.range.lat2)/2.0;
-            double dl = (pos.range.lon2 - pos.range.lon1);
-            double db = (pos.range.lat2 - pos.range.lat1);
-            region = region + "skysystem=" + skySystem + "&l=" + String.valueOf(l) + "&b=" + String.valueOf(b)
-               + "&dl=" + String.valueOf(dl) + "&db=" + String.valueOf(db);
-         }
-         else 
-         {
-            LOGGER.finest("FIXME here Exception: POLYGON not supported or pos.shape invalid: " + pos.shape);
-         }
-
-      }
-
-      if(band != null)
-      {
-         String specSystem = band.system.name();
-         double vl = band.min;
-         double vu = band.max;
-
-         region =region + "specsystem=" + specSystem + "&vl=" + String.valueOf(vl) + "&vu=" + String.valueOf(vu);
-      }
-
-      return region;
-   }
-
-/*
-   private String replaceWithGrid(String wcsBounds, Pos pos, Band band, Time time, Pol pol)
-   {
-      // remove end-of-line (was added by vlkb_ast.cpp: cout << ... << endl)
-      String lineSeparator = System.lineSeparator();
-      wcsBounds = wcsBounds.replace(lineSeparator, "");
-      LOGGER.finest("BOUNDS: " + wcsBounds);
-
-      // replace in wcsBounds those bounds where pos,band,time or pol has system=GRID
-
-      String[] substr = wcsBounds.split("(?=AXES)", 2);
-      for(String ss : substr) LOGGER.finest("boundsResult: " + ss);
-
-      String boundsString = substr[0];
-      boolean noOverlap = ((boundsString != null) && boundsString.trim().isEmpty());
-      if(noOverlap)
-      {
-         boundsString = ""; // no overlap
-      }
-      else
-      {
-         String axesTypes = "";
-         if(substr.length > 1)
-         {
-            axesTypes = substr[1].replace("AXES"," ").trim();
-            LOGGER.finest("AXES TYPES: " + axesTypes);
-
-            String[] bnds  = normalize(boundsString);
-            String[] types = normalize(axesTypes);
-            // assert: bnds.length == types.length
-            LOGGER.finest("boundsCount: " + bnds.length  + " typesCount: " + types.length);
-
-            if(bnds.length == types.length)
-               boundsString = replaceBounds(bnds, types, pos, band);
-         }
-      }
-      return boundsString;
-   }
-
-   private String replaceBounds(String[] bnds, String[] types, Pos pos, Band band)
-   {
-      int ix;
-      for(ix=0; ix<bnds.length; ix++)
-      {
-         if( types[ix].equals("LON") && ((pos != null) && (pos.system == Pos.System.GRID)) )
-         {
-            bnds[ix] = pos.lonBoundsString();
-         }
-         else if(types[ix].equals("LAT") && ((pos != null) && (pos.system == Pos.System.GRID)))
-         {
-            bnds[ix] = pos.latBoundsString();
-         }
-         else if(types[ix].equals("BAND") && ((band != null) && (band.system == Band.System.GRID)))
-         {
-            bnds[ix] = band.boundsString();
-         }
-      }
-
-      LOGGER.finest("replaced: " + String.join(" ", bnds)) ;
-
-      return "[" + String.join(" ", bnds)  + "]";
-   }
-
-   // MAKE SURE vlkb overlap returns space delimited bounds: [ a:b c:d ]
-   // normalize: strip [,] if any, and split into array by space
-   private String[] normalize(String spaceStr)
-   {
-      String other = spaceStr.replace("[","").replace("]","");
-      LOGGER.finest("normalize: " + other);
-      return other.split("\\s+");
-   }
-*/
 }
 

data-access/servlet/src/main/java/cutout/engine/cli/ExecCmd.java

@@ -11,10 +11,14 @@ class StreamGobbler extends Thread
    InputStream is;
    String type;
    OutputStream os;
+   StringBuilder sb;
 
-   StreamGobbler(InputStream is, String type)
+   StreamGobbler(InputStream is, String type, StringBuilder sb)
    {
-      this(is, type, null);
+      this.is = is;
+      this.type = type;
+		this.os = null;
+		this.sb = sb;
    }
 
    StreamGobbler(InputStream is, String type, OutputStream redirect)
@@ -48,7 +52,9 @@ class StreamGobbler extends Thread
             }
             else
             {
-               LOGGER.finest(type + ">" + new String(buffer, 0, nread, "utf-8"));
+               String str = new String(buffer, 0, nread, "utf-8");
+               LOGGER.finest(type + ">" + str);//new String(buffer, 0, nread, "utf-8"));
+               sb.append(str);
             }
          }
 
@@ -69,7 +75,7 @@ class ExecCmd
 
    public int exitValue;
 
-   public void doRun(OutputStream outputStream, String[] cmd)
+   public void doRun(OutputStream outputStream, String[] cmd, StringBuilder error)
       throws IOException, InterruptedException
    {
       LOGGER.fine("trace CMD: " + Arrays.toString(cmd));
@@ -82,7 +88,7 @@ class ExecCmd
       Process proc = rt.exec(cmd);
 
       // any error message?
-      StreamGobbler errorGobbler = new StreamGobbler(proc.getErrorStream(), "ERROR");
+      StreamGobbler errorGobbler = new StreamGobbler(proc.getErrorStream(), "ERROR", error);
 
       // any output?
       StreamGobbler outputGobbler = new StreamGobbler(proc.getInputStream(), "OUTPUT", outputStream);

data-access/servlet/src/main/java/cutout/webapi/ServletCutout.java

@@ -115,7 +115,7 @@ public class ServletCutout extends HttpServlet
    }
 
 
-   protected void doCutoutStream(String id, Pos pos, Band band, Time time, Pol pol, String pixels,
+   protected int doCutoutStream(String id, Pos pos, Band band, Time time, Pol pol, String pixels,
          OutputStream respOutputStream) throws IOException, InterruptedException
    {
       LOGGER.fine("trace " + pos);
@@ -128,7 +128,7 @@ public class ServletCutout extends HttpServlet
 
       resolver.resolve(id);
 
-      soda.doStream(resolver.relPathname(), resolver.hdunum(), pos, band, time, pol, pixels, respOutputStream);
+      return soda.doStream(resolver.relPathname(), resolver.hdunum(), pos, band, time, pol, pixels, respOutputStream);
    }
 
 
@@ -270,7 +270,8 @@ public class ServletCutout extends HttpServlet
             if(respFormat.startsWith("application/fits"))
             {
                response.setContentType(respFormat);
-               doCutoutStream(id, pos, band, time, pol, pixels, respOutputStream);
+               int rc = doCutoutStream(id, pos, band, time, pol, pixels, respOutputStream);
+               if(rc == 1) response.setStatus(HttpServletResponse.SC_NO_CONTENT);
             }
             else if(respFormat.startsWith("application/x-vlkb+xml"))
             {

data-access/servlet/src/main/java/mcutout/VlkbCli.java

@@ -347,8 +347,9 @@ class VlkbCli implements Vlkb
 			cmdBounds[1] = "nullvals";
 			cmdBounds[2] = absPathname;
 
+			StringBuilder errorStrBuilder = new StringBuilder();
 			ExecCmd exec = new ExecCmd();
-			exec.doRun(bos, cmdBounds);
+			exec.doRun(bos, cmdBounds, errorStrBuilder);
 			LOGGER.finest("exec NullVals exitValue: " + exec.exitValue);
 
 			bos.close();
@@ -378,7 +379,8 @@ class VlkbCli implements Vlkb
 			}
 			else
 			{
-				throw new AssertionError("'vlkb nullvals' exited without results for: " + absPathname);
+				throw new AssertionError("'vlkb nullvals' exited with error: "
+                      + errorStrBuilder.toString() + " for: " + absPathname);
 			}
 		}