The PM Cell is down

[Pat B]

I went through chapters 1 through 9 in the https://community.i2b2.org/wiki/display/getstarted/i2b2+Installation+Guide
and consulted this forum multiple times. I've spent many hours trying to solve this problem. I have a related post up there but the error message is different.

My guess is that IIS and JBoss are not communicating in Windows 8. The Javascript does not seem to be able to access the web services even though JBoss lists them fine in http://localhost:9090/i2b2/services/listServices

When I use the WebClient or the Workbench and try to log in there is nothing logged in the JBoss server.log file and it both cases I get the same error "The PM cell is down or the PM address in the properties file is incorrect".

Again, any help will be very much appreciated. At least some hint of where to look!

My i2b2_config_data.js in webclient is very similar to the admin one without the HarvardDemo

{
    urlProxy: "index.php",
    urlFramework: "js-i2b2/",
    //-------------------------------------------------------------------------------------------
    // THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
    lstDomains: [
        { domain: "i2b2demo",
          name: "HarvardDemo",
          urlCellPM: "http://webservices.i2b2.org/i2b2/services/PMService/",
          allowAnalysis: true,
          debug: false
        },
        { domain: "i2b2demo",
          name: "i2b2demo (1.7)",
          urlCellPM: "http://localhost:9090/i2b2/services/PMService/",
          allowAnalysis: true,
          debug: true
        }
    ]
    //-------------------------------------------------------------------------------------------
}

[Peter Beninato]

Hi,

 

A couple of things

1)      There is a PHP framework curl, that may be commented out in , I think it is php.ini.

2)      There was a thread about doing some updates and inserts ( I think I was on that thread) to overcome in particular the error about needing to be Admin.

 

And some other stuff, you are using a domain i2b2demo in your section.

 

In the table in the i2b2pm schema in the table: pm_hive_data

Do the values in the Domain and domain name match the domain and name in your i2b2_config_data.js?

 

Anyways some things to look at consider. Hope it might help.

-Peter

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[Pat B]

Thank you Peter, that is very nice of you to provide some hints. I went to work on these hints with great enthusiasm, unfortunately with no luck. And nothing gets logged in the  JBoss server.log.

Re (1) I had already looked into the curl issue as I saw it mentioned in many forum threads.
I created a version.php file that calls
 <?php
phpinfo();
?>
And it says  under CURL
"cURL support:    enabled"

That same page lists "Configuration File (php.ini) Path:    C:\WINDOWS" but there is nothing in C:\WIndows
it also lists "Loaded Configuration File:    C:\Program Files (x86)\PHP\v5.3\php.ini", and there is a "extension=php_curl.dll" in the Extension List section. I guess that means it is enabled. Nothing is commented out.

BTW, I am learning a lot about PHP, Javacript, JBOSS, servers, etc with this little excercise!

Re (2) I ran "SELECT *  FROM [i2b2pm].[dbo].[PM_HIVE_DATA]"
and get:
DOMAIN_ID    HELPURL    DOMAIN_NAME    ENVIRONMENT_CD    ACTIVE    CHANGE_DATE    ENTRY_DATE    CHANGEBY_CHAR    STATUS_CD
i2b2    http://www.i2b2.org    i2b2demo    DEVELOPMENT    1    NULL    NULL    NULL    A

Based on that I changed the i2b2_config_data.js to this:

{
    urlProxy: "index.php",
    urlFramework: "js-i2b2/",
    //-------------------------------------------------------------------------------------------
    // THESE ARE ALL THE DOMAINS A USER CAN LOGIN TO
    lstDomains: [

        { domain: "i2b2",
          name: "i2b2demo",

          urlCellPM: "http://localhost:9090/i2b2/services/PMService/",
          allowAnalysis: true,

          debug: false
        }
    ]
    //-------------------------------------------------------------------------------------------
}


I get the same error: "The PM cell is down or the address in the properties file is incorrect"

[Peter Beninato]

Ok…

 

Well then let’s step back from i2b2, There must be some happy jboss home page, which presumably could/should write to the jboss log.

 

Also, are you sure JBOSS is on 9090?

 

And forgive my dusty, old windows IE knowledge, but do you need it? I have installed locally in the past on Windows 7 (not  a server), and don’t recall needing IIS.

 

-Peter

[Pat B]

You keep my hopes up! I may figure it out! But oh well, not yet.

http://localhost:9090/i2b2/services/listServices works fine, it lists what I installed

Version

OntologyService

PMService

so, my take is that JBoss is on 9090!
As for IE, I am using Firefox and Chrome, not IE. The installation says I need IIS. And I am using the IIS C:\inetpub\wwwroot directory to drop the i2b2 directories "admin" and "webclient". But the workbench.exe does not work either! I get the exact same error!

I thought the connection string may be wrong but I created a lil Java program that uses the jdbc:microsoft:sqlserver driver to connect to the SQL Server i2b2 sever with username i2b2pm and password demouser and reads all schema names. That works.
The problem is, as it seems, that the php, javascript code is not communicating with the JBoss server. But why not... I am clueless.

Thanks for your help!

[Peter Beninato]

There is a whole thing with SQL Server about the owner and dbo, and since I don’t use that DBMS I kinda of ignore it, but it might be worth exploring.

 

So, getting the thick client to work is probably a good first step.

[Pat B]

Yes. Since I get the same error with the Workbench I know there is a problem calling JBoss and connecting to the SQL Server.

I know JBoss is working fine because
http://localhost:9090/i2b2/services/PMService/

brings up the same msg as the Harvard service page
http://services.i2b2.org/i2b2/services/PMService/

I tested the com.microsoft.sqlserver.jdbc.SQLServerDriver from some Java code I wrote using the settings from pm-ds.xml and it connects to the SQL Server fine. Got that idea from reading another thread.

The next step for me is to look at the i2b2 source code and find that call to JBoss and run it in my Java code using the settings from pm-ds.xml, but that will take me some time (that I don't have). Can you pinpoint where that code snippet is located?
Just in case I have attached the pm-ds.xml file.

I appreciate your help Peter! Thanks!

[Phillips, Lori C.]

Pat,

 

Did you check that you are connecting to the correct PM?  i.e. that the jboss URL in the properties file is correct?

 

Lori

 

From: i2b2-ins...@googlegroups.com [mailto:i2b2-ins...@googlegroups.com] On Behalf Of Pat B
Sent: Thursday, October 30, 2014 11:37 AM
To: i2b2-ins...@googlegroups.com
Cc: 4pa...@gmail.com; beni...@ohsu.edu
Subject: Re: The PM Cell is down

 

Yes. Since I get the same error with the Workbench I know there is a problem calling JBoss and connecting to the SQL Server.

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[Pat B]

Thanks for chiming in Lori!
That is the problem, I cannot connect to the PM.
But how do I know if the URL is correct?

I get the exact same message (an error but that is to be expected) when calling either of the two URLs in the "i2b2workbench.properties" file. These are the contents of the file :
writeTimelineFile=yes
applicationName=i2b2
messageversion=1.1
demoUser=no
I2b2.1=i2b2demo,REST,http://services.i2b2.org/i2b2/services/PMService/
I2b2.2=i2b2demo,REST,http://localhost:9090/i2b2/services/PMService/

I do NOT get the "PM Cell is down" error when connecting to services.i2b2.org!

What I just tested is connecting to the i2b2pm SQL Server database from JBoss using this and this guidelines and the link http://localhost:9090/jdbcclient/client.jsp. And it works!
So JBoss can connect to the i2b2pm database. We can rule out that problem.

[Billy Shuman]

Can you try installing something to inspect what is going on at the network layer?  Wireshark or something equivalent.  With a tool like that you can see if a request is being made from either the webclient or the workbench.

Billy

[Phillips, Lori C.]

When you tell the client to connect to //localhost:9090… you are literally saying jboss is running on the computer you are running the client on.  Is that the case?

 

From: i2b2-ins...@googlegroups.com [mailto:i2b2-ins...@googlegroups.com] On Behalf Of Pat B
Sent: Thursday, October 30, 2014 1:36 PM
To: i2b2-ins...@googlegroups.com
Subject: Re: The PM Cell is down

 

Thanks for chiming in Lori!

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[Pat B]

Yes Lori, both IIS, SQL Server and JBoss are running on the same computer. They are all using different ports.

I need to clarify that when I enter the URL //localhost:9090  in a browser I get the JBoss page. I also see the list of i2b2 services in the browser with the URL http://localhost:9090/i2b2/services/listServices
When using the workbench.exe or the webclient, I seem not to be able to access JBoss at //localhost:9090 as there is nothing in the server.log and I get the "PM Cell is down" error.

[Pat B]

Hi Billy, Will try wireshark but not sure I can do it today. Thanks for the tip!

[shariqtariq]

Make sure you disable SeLinux and turn iptables off in CentOS - that will give you that error repeatedly!

[Pat B]

Thanks shariqtariq. I did read that advice in other threads but it does not apply to me as I am installing client and server on the same Windows machine!

I had to move on to a new project but it is bugging me that I cannot get i2b2 to work being that everything else I tested works, just not the communication between webclient or workbench with JBoss. When I get some time I will look into this again and will post here if I find a solution. In the meanwhile I am happy for anyone who can provide some clue on how to solve this puzzle!

[Pat B]

Billy: I installed Wireshark with RawCap but no packets are captured when using either the webclient or the workbench. When accessing http://localhost:9090/i2b2/services/PMService/getVersion through the browser the traffic is captured.

Can more i2b2 logging be enabled? The workbench i2b2.log file reads:

2014-11-10 16:35:50,487 INFO main edu.harvard.i2b2.eclipse.login.LoginDialog - workbench message version=1.1
2014-11-10 16:35:51,237 INFO main edu.harvard.i2b2.eclipse.login.LoginDialog - http://localhost:9090/i2b2/services/PMService/getVersion
2014-11-10 16:35:51,237 INFO main edu.harvard.i2b2.eclipse.login.LoginDialog - version response: <soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/"><soapenv:Header xmlns:wsa="http://www.w3.org/2005/08/addressing"><wsa:Action>http://www.w3.org/2005/08/addressing/soap/fault</wsa:Action></soapenv:Header><soapenv:Body><soapenv:Fault><faultcode>soapenv:</faultcode><faultstring>First Element must contain the local name, Envelope , but found request</faultstring><detail /></soapenv:Fault></soapenv:Body></soapenv:Envelope>
2014-11-10 16:35:51,253 ERROR main edu.harvard.i2b2.eclipse.login.LoginDialog - Error marshalling get version request message

[Pat B]

There was one thing I changed early on in the build.properties file in the edu.harvard.i2b2.server-common directory: I added double backslashes to the jboss path as it was not working with single ones. Now I wonder if ant can read the "bin.includes" paths in Windows?? Maybe the whole problem is related to that? My build.properties file contents are below:

#Ant build property file

## JBOSS HOME

jboss.home=C:\\Tools\\jboss-as-7.1.1.Final

axis2.war.name=i2b2.war

bin.includes = lib/jdom/jdom.jar

bin.includes = lib/jdom/jdom-contrib.jar

[Richard Santee]

I'm getting this same error. Did you find a fix?

[Brian Mallow]

I was getting a similar error on my installation on WIndows Server 12.  I ended up having to reinstall PHP 5.3 using Windows Web Platform installer located here: http://www.microsoft.com/web/downloads/platform.aspx

When accessing the webclient i was getting the PM Cell is down and on the admin it was saying something about admin role.  In the application error logs from windows I was getting this:

Faulting application name: php-cgi.exe, version: 7.0.3.0, time stamp: 0x56b1382c

Faulting module name: VCRUNTIME140.dll, version: 6.3.9600.18202, time stamp: 0x569e7d02

Exception code: 0xc0000135

Fault offset: 0x00000000000ecdd0

Faulting process id: 0x1988

Faulting application start time: 0x01d16f6a93c42a23

Faulting application path: c:\tools\php\php-cgi.exe

Faulting module path: VCRUNTIME140.dll

Report Id: d1730e46-db5d-11e5-80bd-000c29469079

Faulting package full name: 

Faulting package-relative application ID: 

May help someone else... 

[msingh...@gmail.com]

for PHP 7.0.4
uninstall all the VS C++ and install Visual C++ Redistributable for Visual Studio 2015  (32bit)

[John Nguyen]

This worked for me:

By default the webclient i2b2_config_domains.json has the urlProxy set to "urlProxy": "/~proxy"

You need to change it to 

 "urlProxy": "/proxy.php"