Re: [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available

To: Roland Schweitzer <Roland.Schweitzer@xxxxxxxx>
Subject: Re: [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available
From: John Relph <John.Relph@xxxxxxxx>
Date: Wed, 22 Dec 2010 08:11:27 -0500
Cc: las_users <oar.pmel.las_users@xxxxxxxx>
In-reply-to: <4D1122B6.9020209@xxxxxxxx>
References: <4D0B946D.3060708@xxxxxxxx> <4D10D532.4020001@xxxxxxxx> <4D10E4BA.8080108@xxxxxxxx> <4D10FD9F.5080201@xxxxxxxx> <4D1122B6.9020209@xxxxxxxx>
Sender: owner-las_users@xxxxxxxx
User-agent: Thunderbird 2.0.0.24 (X11/20101201)
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.jnl
>
>    1. 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.

        -- John

> If 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 seconds
>>
>>
>>     
>>> Roland
>>>
>>> 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".
>>>>
>>>>          -- John
>>>>
>>>>         
>>>>> Roland
>>>>>
>>>>>
>>>>>    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.
>>>>>
>>>>>           
>>>       
>>     
>


-- 
John Relph <John.Relph@xxxxxxxx>
ISSO, NOAA/NESDIS/National Oceanographic Data Center
Follow-Ups:
- Re: [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available
  - From: Roland Schweitzer
References:
- [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available
  - From: Roland Schweitzer
- Re: [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available
  - From: John Relph
- Re: [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available
  - From: Roland Schweitzer
- Re: [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available
  - From: John Relph
- Re: [las_users] ANNOUNCEMENT: LAS v7.2 with vectors and multiple variable selection is now available
  - From: Roland Schweitzer
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