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Example1.xar.xml

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Example1.xar.xml ken_sin.lo  2006-01-13 12:59
Status: Closed
 
I have installed CPAS 1.1 on Fedora Core 4. Using MS Internet Explorer, I am trying to load Example1.xar.xml on my project by clicking "Upload Experiment" under the Experiment tab. I have an error when doing that, so I click on the link "upload.xar.log" only to see this:

13 Jan 2006 15:56:29,211 INFO : Experiment Import for Uploaded file: 1/13/2006 15:56:29
13 Jan 2006 15:56:29,211 INFO : =======================================
13 Jan 2006 15:56:29,347 INFO : Finished loading Experiment with LSID 'urn:lsid:localhost:Experiment.Folder-13:Tutorial'
13 Jan 2006 15:56:29,352 INFO : Finished loading Protocol with LSID 'urn:lsid:localhost:Protocol:MinimalRunProtocol.FixedLSID'
13 Jan 2006 15:56:29,356 INFO : Finished loading Protocol with LSID 'urn:lsid:localhost:Protocol:SamplePrep'
13 Jan 2006 15:56:29,361 INFO : Finished loading Protocol with LSID 'urn:lsid:localhost:Protocol:Analyze'
13 Jan 2006 15:56:29,365 INFO : Finished loading Protocol with LSID 'urn:lsid:localhost:Protocol:MarkRunOutput'
13 Jan 2006 15:56:29,385 INFO : Rolling back transaction in experiment loader.
13 Jan 2006 15:56:29,385 ERROR: Exception during load

java.lang.NullPointerException
    at org.fhcrc.cpas.data.Table.internalSelect(Table.java:922)
    at org.fhcrc.cpas.data.Table.select(Table.java:916)
    at org.fhcrc.cpas.exp.OntologyManager.getObjectPropertiesFromDb(OntologyManager.java:156)
    at org.fhcrc.cpas.exp.OntologyManager.getPropertyObjects(OntologyManager.java:142)
    at org.fhcrc.cpas.exp.OntologyManager.getProperties(OntologyManager.java:51)
    at org.fhcrc.cpas.exp.XarReader.loadPropertyCollection(XarReader.java:1873)
    at org.fhcrc.cpas.exp.XarReader.loadMaterial(XarReader.java:1504)
    at org.fhcrc.cpas.exp.XarReader.loadDoc(XarReader.java:275)
    at org.fhcrc.cpas.exp.XarReader.parseAndLoad(XarReader.java:163)
    at org.fhcrc.cpas.exp.XarReader.uploadRun(XarReader.java:128)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.loadExperiment(ExperimentPipelineJob.java:102)
    at org.fhcrc.cpas.exp.ExperimentPipelineJob.run(ExperimentPipelineJob.java:111)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    at java.util.concurrent.FutureTask.run(FutureTask.java:123)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    at java.lang.Thread.run(Thread.java:595)
13 Jan 2006 15:56:29,386 FATAL: Upload FAILED

I don't know why there is a NullPointerException? Thank you.


Ken Sin Lo
CHUL Research Center, Laval University
2705, Laurier boulevard
Ste-Foy (Quebec) Canada G1V 4G2
 
 
Peter responded:  2006-01-18 10:30
I suspect a problem with your install. Please post the tomcat/logs/cpas.log file and the cpas.xml file for further investigation. Cpas.xml contains passwords for the database and email that you may want to blank out before posting.
 
ken_sin.lo responded:  2006-01-20 06:54
Hi,

I have stopped Tomcat, and deleted the CPAS database with PGAdmin. I have then restarted Tomcat, and I got this error in the cpas.log:

java.sql.SQLException: ERROR: function information_schema._pg_keypositions() does not exist

So, I executed the following in PGAdmin:

CREATE FUNCTION information_schema._pg_keypositions() RETURNS SETOF integer    LANGUAGE sql    IMMUTABLE    AS 'select g.s        from generate_series(1,current_setting(''max_index_keys'')::int,1)        as g(s)';

I restarted Tomcat again after that, and I don't have the preceding error anymore.

Thus, I continued by opening my Internet browser at this location: http://localhost:7979/cpas

I entered my email and my password to register. And I signed in for the first time.

On the following page, I have pressed the "Express Install" button. I immediately got the following error:

The following error occurred while running SQL script(s) in module Core: prop-0.00-1.00.sql: ERROR: language "plpgsql" does not exist

So, I executed the following in a shell:

[root@hooloovoo ~?]# su - postgres -bash-3.00$ createlang plpgsql cpas -bash-3.00$ exit

And I run prop-0.00-1.00.sql again (from the browser), without having any problem.

I have then pressed the "Finish" button to let the Express Install continue.

Now, I get a new error never seen before:

exp-1.00-1.10.sql: ERROR: syntax error at or near "SELECT" Upgrading Experiment module from version 0.0 to version 1.1.

Here is my tomcat/logs/cpas.log file and the cpas.xml file. Thank you.

Ken Sin Lo CHUL Research Center, Laval University 2705, Laurier boulevard Ste-Foy (Quebec) Canada G1V 4G2
 
mbellew responded:  2006-01-20 10:16
Also, what version of postgres did you install? I'm assuming this was a manual setup (not using the Windows installer)?

PS: I think our logging is slightly cleaned up in the next version.
 
ken_sin.lo responded:  2006-01-23 08:07
It is a manual install, on Fedora Core 4. My version of Postgres is 8.1.2, the most recent one.
 
arauch responded:  2006-01-23 09:38
CPAS 1.1 will not work with PostgreSQL 8.1. Per the installation instructions, our officially supported versions of external components are:
  • Tomcat 5.5.9
  • PostgreSQL 8.0.3
These are the versions we've tested against and the versions we recommend you install. Other users have apparently used PostgreSQL 8.0.6 with success, but we haven't verified that. We know for a fact that PostgreSQL 8.1.x in incompatible with CPAS 1.1.
 
ken_sin.lo responded:  2006-01-23 13:23
I have now installed PostgreSQL 8.0.3.

I am now finally able to load the examples! .... but when I want to view the experiment, I've got an error:

Experiment Run Example 1 (using export format)

Standard Properties Name Example 1 (using export format) LSID urn:lsid:localhost:ExperimentRun:MinimalExperimentRun.FixedLSID Protocol Example 1 Protocol Created on 1/23/2006 13:51:34 Comments

error executing /_views/HomeTemplate.gm Unable to display graph view. (Cannot run dot.exe due to system configuration error)
 
jeckels responded:  2006-01-23 13:30
As noted in the installation instructions at https://cpas.fhcrc.org/Wiki/home/help/page.view?name=config%2Fmaninstall, there are a few related programs that need to be installed for certain CPAS features. The Windows installer takes care of these automatically, but when manually installing you'll need to handle them yourself.

In this case, you'll need to download Graphviz, which we use to generate some of our images. It's available pre-built for a number of platforms at http://www.graphviz.org/
 
ken_sin.lo responded:  2006-01-24 06:30
Thank you! It was my error! ....

It's now working fine!
 
adam responded:  2006-12-04 22:10