PM cell down

[Vidhya Asuri]

Hi,

 I'm setting up i2b2 version 1.17.13 on Ubuntu 20.

When I login , I get a pop up saying "The PM Cell is down or the address in the properties file is incorrect."

Not sure if this is the correct forum, but I'm also setting up Shrine and trying to connect the Shrine instance to this i2b2 instance.

I have edited shrine.conf on the Shrine instance to match i2b2_config.js on the i2b2 instance.

I'd like some help on what configs to check, please.

thanks

Vidhya

[Jeff Klann]

You should look at the server.log in Wildfly to see what's happening on the backend. Frequently I've seen this when the Wildfly datasource is incorrect and Wildfly can't connect to the database.

Thanks,

Jeff Klann, PhD

[Xia, Yang]

I got the same PM cell down popup error while login, 

and wildfly server.log shows:

ERROR [org.apache.axis2.transport.http.AxisServlet] (default task-1) processAxisFault() found a null HTTP status from the MessageContext instance, setting HttpServletResponse status to: axis2.http.response.state

I've tried these <connection-url> in pm-ds.xml 
<connection-url>jdbc:sqlserver://localhost:1433</connection-url>

<connection-url>jdbc:sqlserver://localhost:1433;databaseName=i2b2pm</connection-url>

<connection-url>jdbc:sqlserver://localhost:1433;databaseName=i2b2pm.dbo</connection-url>

After each change, I've rebuild a war and copied into deployment folder and restarted wildfly.

But none of above works, all got same "null http status" error in log like above.

With wildfly running, http://localhost:8080/i2b2/services/listServices works fine, and I can see PM service is listed.

If I click into it, http://localhost:8080/i2b2/services/PMService?wsdl also shows correct xml content.

What else should we check?

Thank you very much!

[Xia, Yang]

I've also tried to copy pm-ds.xml into the deployment/ folder, but not much difference. The login popup with PM error still shows.

In http://localhost:8080/i2b2/services/PMService?wsdl xml page I can see several bindings:

...

<wsdl:service name="PMService">

<wsdl:port name="PMServiceHttpSoap11Endpoint" binding="ns:PMServiceSoap11Binding">

<soap:address location="http://<host_name>:8080/i2b2/services/PMService.PMServiceHttpSoap11Endpoint/"/>

</wsdl:port>

<wsdl:port name="PMServiceHttpSoap12Endpoint" binding="ns:PMServiceSoap12Binding">

<soap12:address location="http://<host_name>:8080/i2b2/services/PMService.PMServiceHttpSoap12Endpoint/"/>

</wsdl:port>

<wsdl:port name="PMServiceHttpEndpoint" binding="ns:PMServiceHttpBinding">

<http:address location="http://<host_name>:8080/i2b2/services/PMService.PMServiceHttpEndpoint/"/>

</wsdl:port>

</wsdl:service>

...

not sure if soap11 and soap12 coexistence would cause any issue in this case, but for http binding, it looks ok.

Also I've checked db i2b2pm, everything works fine. Tables are accessible through username and password specified in pm-ds.xml

table_name                                                                                                                                                                                                      row_count

----------------------------------------------------------------------------------------------------------------------------------------------------------------- -----------

[dbo].[PM_APPROVALS]                                                                                                                                                                                 0

[dbo].[PM_APPROVALS_PARAMS]                                                                                                                                                               0

[dbo].[PM_CELL_DATA]                                                                                                                                                                                  5

[dbo].[PM_CELL_PARAMS]                                                                                                                                                                            0

[dbo].[PM_GLOBAL_PARAMS]                                                                                                                                                                      0

[dbo].[PM_HIVE_DATA]                                                                                                                                                                                 1

[dbo].[PM_HIVE_PARAMS]                                                                                                                                                                           0

[dbo].[PM_PROJECT_DATA]                                                                                                                                                                          1

[dbo].[PM_PROJECT_PARAMS]                                                                                                                                                                    0

[dbo].[PM_PROJECT_REQUEST]                                                                                                                                                                   0

[dbo].[PM_PROJECT_USER_PARAMS]                                                                                                                                                        0

[dbo].[PM_PROJECT_USER_ROLES]                                                                                                                                                            21

[dbo].[PM_ROLE_REQUIREMENT]                                                                                                                                                              11

[dbo].[PM_USER_DATA]                                                                                                                                                                               5

[dbo].[PM_USER_LOGIN]                                                                                                                                                                             0

[dbo].[PM_USER_PARAMS]                                                                                                                                                                         0

[dbo].[PM_USER_SESSION]                                                                                                                                                                         0

(17 rows affected)

For <connection-url> in pm-ds.xml I've also tried upper case "DatabaseName" like this:

<connection-url>jdbc:sqlserver://localhost:1433;DatabaseName=i2b2pm</connection-url>

But the login is still not working, and the pm error popup still shows.

Thanks

[Jeff Klann]

It looks like i2b2 is having trouble connecting to the PM cell. Is your hive_cell_params table configured properly?

https://community.i2b2.org/wiki/display/getstarted/1.+Configure+cell+properties (see especially ontology.ws.pm.url)

Also, you could make sure your project is configured to point to the correct URLS...

https://community.i2b2.org/wiki/display/ServerSideDesign/Project+Setup

Thanks,
Jeff

[Xia, Yang]

In my hive_cell_params table:

       ontology.ws.pm.url /services/PMService/getServices
I've also tried adding a prefix to the value (so as to all other url values), restarted wildfly and apache2, but no difference in the popup error:

       ontology.ws.pm.url /i2b2/services/PMService/getServices

I've also changed /var/www/html/i2b2-webclient/i2b2_config_data.js and set urlCellPM into one of these values, restarted both wildfly and apache2 after each change:

       urlCellPM: "http://<host_name>:8080/i2b2/services/PMService/",                        // got same PM error popup.

       urlCellPM: "http://localhost:8080/i2b2/services/PMService/",                               // got same PM error popup.
       urlCellPM: "http://services.i2b2.org/i2b2/services/PMService/",                           // this works well, as it's using org's url.
       urlCellPM: "http://127.0.0.1:8080/i2b2/services/PMService/",                               // got same PM error popup.

For the Project+Setup doc, it seems it's under admin mode, and my admin login also shows the PM down error popup, therefore I'm not able to access to it.

The corresponding PM_PROJECT_DATA table has one row of default data, looks like it's matching with the first screenshot in the doc.

PM_PROJECT_PARAMS table is empty (I guess it's because it's a brand new setup, no input from admin yet, would that cause any issue?).

PM_PROJECT_USER_PARAMS table is empty (same as above empty table, it seems to be a brand new setup, no input from admin yet).

PM_PROJECT_USER_ROLES table has 21 records, all populated while installing, looks fine.
CRC_DB_LOOKUP has a record with C_PROJECT_PATH = /Demo/     // Tried to remove the first / to make it the same with others, and restarted servers, but no difference in the popup error.
IM_DB_LOOKUP has a record with C_PROJECT_PATH = Demo/
ONT_DB_LOOKUP has a record with C_PROJECT_PATH = Demo/
WORK_DB_LOOKUP has a record with C_PROJECT_PATH = Demo/

Not sure if anything else needs to be checked here...

Please guide, thank you very much!

[Pedro Rivera]

We get the "PM cell down' error everytime the JDK is updated on the server (currently Windows but we are migrating to Red Hat), then we have to update the JAVA_HOME environment to the location of the new version of the JDK and restart WildFly.