On 12/22/2010 07:11 AM, John Relph wrote:
Roland Schweitzer wrote:John, The error you're getting now is actually the information you're seeking. It's telling us that your F-TDS is not configured correctly. The things to check: 1. Are the iosp classes installed in $TOMCAT_HOME/webapps/thredds/WEB-INF/classes (gov and resources/iosp)?/var/lib/tomcat5/webapps/thredds/WEB-INF/classes/gov/noaa/pmel/tmap/iosp contains FerretCommands.class FerretTool.class RuntimeEnvironment.class FerretConfig.class IOSPDocument.class Task.class FerretDataSource.class IOSPException.class Tool.class FerretIOServiceProvider.class JDOMUtils.class FerretNetcdfFile.class MyResolver.class /var/lib/tomcat5/webapps/thredds/WEB-INF/classes/resources/iosp contains FerretConfig.xml scripts/ ./scripts: data.jnl get_coord.jnl get_datavar.jnl header.jnl open_and_rename.jnl1. Are the IOSP and DataSource classes plugged-in in threddsConfig.xml?/var/lib/tomcat5/content/thredds/threddsConfig.xml contains <!-- LAS / Ferret configs --> <datasetSource>gov.noaa.pmel.tmap.iosp.FerretDataSource</datasetSource> <nj22Config> <ioServiceProvider class="gov.noaa.pmel.tmap.iosp.FerretIOServiceProvider"/> </nj22Config>1. Was the tomcat restarted after all these new classes were plugged-in?Definitely.1. Do you have the /las THREDDS path configured in the TDS catalog? Is it pointing to the correct directory?/var/lib/tomcat5/content/thredds/catalog.xml contains <!-- Live Access Server configuration --> <datasetScan name="Data From LAS" path="las" location="/var/lib/tomcat5/content/las/conf/server/data" serviceName="allServices"> <filter> <include wildcard="*.nc"/> <include wildcard="*.fds"/> <include wildcard="*.jnl"/> </filter> </datasetScan> But is that the correct directory? How would I know? The choice of directory has been taken away from me in LAS 7.2, so I had to guess.1. Did the /id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl and other such files get written when LAS started?Get written to which directory? Where do I look in the LAS configuration to figure out in which directory they should be created? Again, the choice of directory seems to have been taken away from me.
They get written to the "/var/lib/tomcat5/content/las/conf/server/data" directory which is marked in the LAS configuration in the <invoker> element of the FerretBackendConfig.xml. Though the documentation is out-of-date with regard to the choice of the directory in the configuration, the location of these data files and the fact they are created is all explained here: http://ferret.pmel.noaa.gov/LAS/documentation/the-ferret-thredds-data-server-f-tds/debugging-your-f-tds-and-las-integration
The choice of the directory location was removed from the configuration process in hopes of addressing your concerns about making the *.war relocatable from tomcat container to tomcat container. Though we haven't gotten there yet, having the directories accessed by the servlets under the tomcat directory structure somewhere seemed like a necessary first step.
Roland
-- JohnIf the answer is "yes" for all of these, we'll dig through the logs. Roland On 12/21/2010 01:18 PM, John Relph wrote:Roland Schweitzer wrote:Hi, John has uncovered a bug in the release. The testing code does indeed point to the old conf/server location. We'll bundle up a new tar with the fix, but in the meantime you'll have to edit in the correct location and recompile. Find $LAS_HOME/test/LASTest/src/LASTest.java and edit in the correct location in on line 186. Then "ant compile" should get the thing built and usable.Alright, I did that. But I still get an error: /free/las.v7.2/test/LASTest# ant lastest -Df=1 Buildfile: build.xml init: compileTest: lastest: [java] ==== LAS test: Are the FTDS URLs working? ================= [java] ---- Check dataset: http://abalone.nodc.noaa.gov:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl [java] DConnect FileNotFound; retry open (1) http://abalone.nodc.noaa.gov:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl.dds [java] DConnect FileNotFound; retry open (2) http://abalone.nodc.noaa.gov:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl.dds [java] DConnect FileNotFound; retry open (3) http://abalone.nodc.noaa.gov:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl.dds [java] An error was returned by the remote server. [java] Connection cannot be opened [java] java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 [java] at java.util.ArrayList.rangeCheck(ArrayList.java:571) [java] at java.util.ArrayList.get(ArrayList.java:349) [java] at LASDatasetTester.testFTDS(Unknown Source) [java] at LASTest.testFTDS(Unknown Source) [java] at LASTest.runTest(Unknown Source) [java] at LASTest.main(Unknown Source) [java] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [java] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) [java] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [java] at java.lang.reflect.Method.invoke(Method.java:616) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.run(ExecuteJava.java:202) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.execute(ExecuteJava.java:134) [java] at org.apache.tools.ant.taskdefs.Java.run(Java.java:710) [java] at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:178) [java] at org.apache.tools.ant.taskdefs.Java.execute(Java.java:84) [java] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [java] at org.apache.tools.ant.Task.perform(Task.java:364) [java] at org.apache.tools.ant.Target.execute(Target.java:341) [java] at org.apache.tools.ant.Target.performTasks(Target.java:369) [java] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [java] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [java] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [java] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [java] at org.apache.tools.ant.Main.runBuild(Main.java:668) [java] at org.apache.tools.ant.Main.startAnt(Main.java:187) [java] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [java] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) BUILD SUCCESSFUL Total time: 3 secondsRoland On 12/21/2010 10:26 AM, John Relph wrote:Roland Schweitzer wrote:Hi Folks, We are pleased to announce the release of LAS 7.2 (ftp://ftp.pmel.noaa.gov/pub/las/las.v7.2.tar.gz). This version includes new features for vector variables and new products and capabilities for multiple variables. The release notes (http://ferret.pmel.noaa.gov/LAS/documentation/las-release-notes-7-2/) have several example plots showing off the new features. Please upgrade to this release and send your feedback to the list.Roland, I have attempted to upgrade to LAS v7.2 but when I attempt to test the F-TDS installation I see an error: /free/las.v7.2# cd test/LASTest/ /free/las.v7.2/test/LASTest# !ant ant lastest -Df=1 Buildfile: build.xml init: [mkdir] Created dir: /stage/free-root/x86_64-redhat-el5/las.v7.2/test/LASTest/build [mkdir] Created dir: /stage/free-root/x86_64-redhat-el5/las.v7.2/test/LASTest/las [jar] Building jar: /stage/free-root/x86_64-redhat-el5/las.v7.2/test/LASTest/las/las.jar compileTest: [javac] Compiling 6 source files to /stage/free-root/x86_64-redhat-el5/las.v7.2/test/LASTest/build lastest: [java] java.io.FileNotFoundException: /stage/free-root/x86_64-redhat-el5/las.v7.2/test/LASTest/../../conf/server/operationsV7.xml (No such file or directory) [java] at java.io.FileInputStream.open(Native Method) [java] at java.io.FileInputStream.<init>(FileInputStream.java:137) [java] at java.io.FileInputStream.<init>(FileInputStream.java:96) [java] at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:87) [java] at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:178) [java] at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source) [java] at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source) [java] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [java] at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) [java] at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) [java] at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) [java] at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) [java] at org.jdom.input.SAXBuilder.build(SAXBuilder.java:453) [java] at org.jdom.input.SAXBuilder.build(SAXBuilder.java:810) [java] at org.jdom.input.SAXBuilder.build(SAXBuilder.java:789) [java] at gov.noaa.pmel.tmap.las.jdom.JDOMUtils.XML2JDOM(JDOMUtils.java:80) [java] at LASTest.<init>(Unknown Source) [java] at LASTest.main(Unknown Source) [java] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [java] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) [java] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [java] at java.lang.reflect.Method.invoke(Method.java:616) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.run(ExecuteJava.java:202) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.execute(ExecuteJava.java:134) [java] at org.apache.tools.ant.taskdefs.Java.run(Java.java:710) [java] at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:178) [java] at org.apache.tools.ant.taskdefs.Java.execute(Java.java:84) [java] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [java] at org.apache.tools.ant.Task.perform(Task.java:364) [java] at org.apache.tools.ant.Target.execute(Target.java:341) [java] at org.apache.tools.ant.Target.performTasks(Target.java:369) [java] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [java] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [java] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [java] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [java] at org.apache.tools.ant.Main.runBuild(Main.java:668) [java] at org.apache.tools.ant.Main.startAnt(Main.java:187) [java] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [java] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [java] ==== LAS test: Are the FTDS URLs working? ================= [java] ---- Check dataset: http://localhost:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl [java] DConnect FileNotFound; retry open (1) http://localhost:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl.dds [java] DConnect FileNotFound; retry open (2) http://localhost:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl.dds [java] DConnect FileNotFound; retry open (3) http://localhost:8080/thredds/dodsC/las/id-60b17e7fa9/data_data.nodc.noaa.gov_thredds_dodsC_woa_WOA09_NetCDFdata_temperature_seasonal_5deg.nc.jnl.dds [java] An error was returned by the remote server. [java] Connection cannot be opened [java] java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 [java] at java.util.ArrayList.rangeCheck(ArrayList.java:571) [java] at java.util.ArrayList.get(ArrayList.java:349) [java] at LASDatasetTester.testFTDS(Unknown Source) [java] at LASTest.testFTDS(Unknown Source) [java] at LASTest.runTest(Unknown Source) [java] at LASTest.main(Unknown Source) [java] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [java] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) [java] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [java] at java.lang.reflect.Method.invoke(Method.java:616) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.run(ExecuteJava.java:202) [java] at org.apache.tools.ant.taskdefs.ExecuteJava.execute(ExecuteJava.java:134) [java] at org.apache.tools.ant.taskdefs.Java.run(Java.java:710) [java] at org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:178) [java] at org.apache.tools.ant.taskdefs.Java.execute(Java.java:84) [java] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [java] at org.apache.tools.ant.Task.perform(Task.java:364) [java] at org.apache.tools.ant.Target.execute(Target.java:341) [java] at org.apache.tools.ant.Target.performTasks(Target.java:369) [java] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [java] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [java] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [java] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [java] at org.apache.tools.ant.Main.runBuild(Main.java:668) [java] at org.apache.tools.ant.Main.startAnt(Main.java:187) [java] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [java] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) BUILD SUCCESSFUL Total time: 7 seconds The script seems to be looking in the wrong place for "operationsV7.xml". -- JohnRoland LAS Release Notes (7.2) by roland — last modified 2010-12-16 19:38 The current release is LAS 7.2 (December 2010) This version of LAS requires Ferret 6.65. * * Important Housekeeping Detail *The server configuration directory will now be installed under $TOMCAT_HOME/content/las/ instead of the the directory where you unpack your LAS and run configure. You'll need to locate this directory and apply your changes to the configuration there after the install.* Major New Features Multiple Variable Selection LAS now supports selection of more than one variable from the same data set on the main interface. When more than one variable is selected you can make new visualizations appropriate for the number of variables you have chosen. 1. Time series line plots will include all of the variables selected with multiple axis scales and line colors. 2. You can make property-property scatter plots of two different variables. 3. You can also color the symbols in a property-property plot by the value of a third variable. Vector Variables 1. Vector variables and vector plots are now supported (in XY, XT and YT dimensions). 2. Vectors can be plotted in the vizGal comparison tool and the difference between to vector variable can be plotted in XY using vizGal. 3. vizGal itself has new layout and some new features that allow comparisons along any axis. For example, you can make time series plots with a different point in XY selected in each of the panels. 4. The addXML utility automatically detects and configures many vector variable when scanning a THREDDS catalog or other netCDF data source with containing multiple variables.