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deploying 3.0 within the Spring framework ...

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Comments

  • smithsmith Posts: 120
    Hi Paul,
    I looked at eventWsdl and I see I need to provide subject, study, eventDefinitionOID, startDate and something called 'location'.
    I think 'subject' corresponds to study_subject_id in study_subject, 'study' corresponds to unique_identifier in study
    and 'eventDefinitionOID' corresponds to oc_oid in study_event_definition. But what does 'location' refer to?
    So it seems these wsdl files are generated on-the-fly ... that's news to me. I've got alot to learn.
    Thanks
    -----Original Message-----
    Sent: Thu 6/25/2009 10:51 AM
    To: [email protected]
    Subject: RE: [Developers] deploying 3.0 within the Spring framework ...

    Hi Colton,
    There is an event.wsdl similar to the subject.wsdl. It can be found by adding ws/event/v1/eventWsdl.wsdl to the OpenClinica instance URL you are using.
    With 3.0 we will have the data import scheduler, so you can drop files off at a particular location to then be imported into event CRFs. You will need to make sure the file is ODM 1.2 or 1.3 compliant and contains the correct OIDs, but I think this should help you.
    If you go to Jobs under the Administration section, you can see where you can schedule data import jobs. I would be interested in your feedback if you have a chance to test the feature out.
    Thanks,
    Paul
    -----------------------------------------------------------------------
    Paul J. Galvin
    Project Manager
    Akaza Research
    617-621-8585 x25
    www.akazaresearch.com
    www.openclinica.org
    ~ OpenClinica Enterprise ~ Ask me about professional training, support, and services for OpenClinica
    -----Original Message-----
    Sent: Wednesday, June 24, 2009 12:43 PM
    To: [email protected]
    Subject: RE: [Developers] deploying 3.0 within the Spring framework ...
    Hi,
    For event scheduling, is there an event.wsdl file somewhere? A file
    analogous to subject.wsdl?
    At Geneuity, we are very, very interested in these web services. Ultimately, we'd like
    to see a web service that could handle inserts into item_data. We have a very specific
    scenario in mind that we hope the developers at OpenClinica will consider.
    We use OpenClinica from the POV of a clinical laboratory. In our case, every 'event' is
    characterized by the arrival of a specimen from a particular patient drawn at a particular
    time during the trial. Every specimen comes with an accession number. Before testing,
    each specimen is 'accessioned' into OpenClinica by filling in the 'accessioning section' of
    the appropriate CRF. This section includes fields for accession number, receipt date,
    shipping deviations, freezer location and the like. After accessioning, the specimen
    is tested, sometimes singly but often in batches on an automated clinical platform. When the latter is done,
    the platform outputs (usually) a file that contains the results tagged with the accession
    numbers of the specimens. Right now, we configure a Mirth channel to take
    parse this file, look up the corresponding event_crf_id for each accession and insert
    the results into item_data directly, subverting OpenClinica's interfaces. Of course, as pointed
    out numerous times by Paul, this isn't ideal. A web service would be.
    But, as you can discern, we need a web service that is smart enough to associate
    an item value with a particular scheduled event by virtue of a 'key' that both the platform
    and OpenClinica (item_data) are already aware of.
    I don't think this need is unique to us. Most every clinical trial nowadays has a laboratory
    component and consequently a need for specimen tracking and automated data uploads.
    Thanks!
    -----Original Message-----
    Sent: Wed 6/24/2009 11:21 AM
    To: [email protected]
    Subject: Re: [Developers] deploying 3.0 within the Spring framework ...

    Great,
    I will add that to the source code. I still don¹t get why the order is being
    switched specifically on your machine.
    I¹ll look into it some more.
    Thank you again
    Krikor
    On 6/24/09 11:11 AM, "Colton Smith" wrote:
    > > Hi Krikor,
    > >
    > > Indeed, that edit works ...
    > >
    > > FYI: I tested 3.0alpha2's web services feature (subject enrollment) and it
    > > works for me as well. I had
    > > been testing against 3.0alpha1.
    > >
    > > Thanks
    > >
    > >
    > > -----Original Message-----
    > > From: Krikor Krumlian [mailto:[email protected]]
    > > Sent: Wed 6/24/2009 8:40 AM
    > > To: [email protected]; Colton Smith
    > > Subject: Re: [Developers] deploying 3.0 within the Spring framework ...
    > >
    > > Hey Colton ,
    > >
    > > Yes that¹s definitly one option. Can you also try the following.
    > > Edit the
    > > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-scheduler.xml
    > > file and add the text in red to the bean definition
    > >
    > > > class="org.springframework.scheduling.quartz.SchedulerFactoryBean"
    > > depends-on="liquibase"> ...
    > >
    > > If you could let me know the outcome that would be great
    > >
    > > Thank you
    > > Krikor
    > >
    > > On 6/23/09 1:26 PM, "Colton Smith" wrote:
    > >
    >>> >> > Hi,
    >>> >> >
    >>> >> > When I edit web.xml thusly:
    >>> >> > ************************************************************************
    >>> >> >
    >>> >> > contextConfigLocation
    >>> >> >
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-db.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-email.xml
    >>> >> >
    >>> >> >
    >> >> /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-hibernate.xml
    >>> >> >
    >>> >> >
    >> >> /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-scheduler.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-service.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-spring.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-timer.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-security.xml
    >>> >> >
    >>> >> >
    >>> >> >
    >> >>
    ******************************************************************************
    >>> >> > *
    >>> >> > I'm able to deploy, no problems! 3.0 looks great! I love it.
    >>> >> >
    >>> >> > Thanks
    >>> >> >
    >>> >> >
    >>> >> > -----Original Message-----
    >>> >> >
    >>> >> > Sent: Tue 6/23/2009 12:08 PM
    >>> >> > To: [email protected]
    >>> >> > Subject: RE: [Developers] deploying 3.0 within the Spring framework ...
    >>> >> >
    >>> >> > Hi,
    >>> >> >
    >>> >> > Correction (or amendment): on my system, Tomcat is configured to use SUN
    >>> >> > java-1.5.0 ...
    >>> >> >
    >>> >> > Thanks
    >>> >> >
    >>> >> >
    >>> >> > -----Original Message-----
    >>> >> >
    >>> >> > Sent: Tue 6/23/2009 11:37 AM
    >>> >> > To: [email protected]
    >>> >> > Subject: RE: [Developers] deploying 3.0 within the Spring framework ...
    >>> >> >
    >>> >> > Hi,
    >>> >> >
    >>> >> > Indeed, here's what my openclinica.log file looks like when spring
    >> >> initiates:
    >>> >> > **************************************************
    >>> >> > 06/23 11:20:25 INFO o.s.w.c.s.XmlWebApplicationContext:411 - Refreshing
    >>> >> > o[email protected]4dd014:
    >>> >> > display name [Root WebApplicationContext]; startup date [Tue Jun 23
    >> >> 11:20:25
    >>> >> > EDT 2009]; root of context hierarchy
    >>> >> >
    >>> >> > 06/23 11:20:25 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-security.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 DEBUG o.s.s.i.w.DefaultFilterInvocationDefinitionSource:120
    -
    >>> >> > Added URL pattern: /**; attributes: [ROLE_USER]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-hibernate.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-scheduler.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-spring.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-email.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-service.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-timer.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-db.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.w.c.s.XmlWebApplicationContext:426 - Bean factory
    >>> >> > for application context
    >>> >> > [o[email protected]4dd014]:
    >>> >> >
    >> >> org.s[email protected]1ad5d46
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.c.PropertiesFactoryBean:178 - Loading
    >> >> properties
    >>> >> > file from class path resource [datainfo.properties]
    >>> >> >
    >>> >> > ************************************************
    >>> >> > -core-db.xml is LAST on my list!
    >>> >> >
    >>> >> > I'm using Ubuntu 8.04 LTS, Sun Java 1.6.0 and Tomcat5.5.
    >>> >> >
    >>> >> > Maybe a system call is done to retrieve applicationContext*.xml. But when
    I
    >>> >> > do so, I get:
    >>> >> > *****************************************************
    >>> >> > UNIX>ls applicationContext*.xml
    >>> >> > applicationContext-core-db.xml applicationContext-core-hibernate.xml
    >>> >> > applicationContext-core-service.xml applicationContext-core-timer.xml
    >>> >> >
    >>> >> > applicationContext-core-email.xml applicationContext-core-scheduler.xml
    >>> >> > applicationContext-core-spring.xml applicationContext-security.xml
    >>> >> >
    >>> >> > *********************************************************
    >>> >> > ... which looks OK (-core-db.xml is first in this listing).
    >>> >> >
    >>> >> > Is there a way in Spring to force an order?
    >>> >> >
    >>> >> > Thanks!
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> > -----Original Message-----
    >>> >> >
    >>> >> > Sent: Tue 6/23/2009 10:25 AM
    >>> >> > To: [email protected]
    >>> >> > Subject: Re: [Developers] deploying 3.0 within the Spring framework ...
    >>> >> >
    >>> >> > Hello Colton,
    >>> >> >
    >>> >> > What you are describing below makes perfect sense. I Just loaded my app and
    >>> >> > here¹s the order of xmls
    >>> >> >
    >>> >> > WebApplicationContext]; startup date [Tue Jun 23 10:21:05 EDT 2009]; root
    >> >> of
    >>> >> > context hierarchy
    >>> >> > 06/23 10:21:05 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-db.xml]
    >>> >> > 06/23 10:21:07 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-email.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-hibernate.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-scheduler.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-service.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-spring.xml]
    >>> >> > 06/23 10:21:09 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-timer.xml]
    >>> >> > 06/23 10:21:09 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-security.xml]
    >>> >> >
    >>> >> > As you may notice applicationContext-core.db.xml loads first. I wonder why
    >>> >> > it doesn¹t on your system. I will also check to see if I
    >>> >> > Can force core-db.xml to load first.
    >>> >> >
    >>> >> > Developers internally are using XP & MAC Oses with Java 5 what is your
    >>> >> > configuration ?
    >>> >> >
    >>> >> > Thank you
    >>> >> > Krikor
    >>> >> >
    >>> >> >
    >>> >> > On 6/23/09 9:10 AM, "Colton Smith" wrote:
    >>> >> >
    >>>>>>> >>>> >> > Hi,
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > I'm trying to understand what Spring does when OpenClinica.war is
    >>>> >>>> first
    >>>>>>> >>>> >> > deployed by Tomcat.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > Here's what I've gleaned so far ... Tomcat looks at web.xml, spots
    the
    >>>>>>> >>>> >> > listener tags and knows
    >>>>>>> >>>> >> > to start the springframework for web applications. It does so. Spring
    >>>>>>> >>>> >> > functions as a broker
    >>>>>>> >>>> >> > between beans and services, and springs into action by first looking
    for
    >>>>>>> >>>> >> > instructions on how to function as such
    >>>>>>> >>>> >> > by inspecting the applicationContext files located in
    >>>>>>> >>>> >> > classes/org/akaza/openclinica. There are seven
    >>>>>>> >>>> >> > of these and Spring digests them one by one, wiring itself and
    >>>> >>>> performing
    >>>>> >>> >> any
    >>>>>>> >>>> >> > initializations specified
    >>>>>>> >>>> >> > therein.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > On my system, Spring seems to deal with
    >>>> >>>> applicationContext-security.xml
    >>>>>>> >>>> >> > first, then -hibernate.xml
    >>>>>>> >>>> >> > and then -core-schedular.xml. But it bombs out on the latter,
    >>>> >>>> complaining
    >>>>>>> >>>> >> > that the table oc_qrtz_locks
    >>>>>>> >>>> >> > does not exist. But how can it exist? Spring has not yet processed
    the
    >>>>>>> >>>> >> > directives found in -core-db.xml
    >>>>>>> >>>> >> > which commands Liquibase to create OpenClinica's tables.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > Am I way off in my understanding? Probably so. Any clarifications
    >>>> >>>> will be
    >>>>>>> >>>> >> > greatly appreciated.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > Thanks!
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> >
  • Paul GalvinPaul Galvin Posts: 886
    Hi Colton,
    Location is a required field when you schedule an event for a study subject in the application. It is a free form text field so it could say Boston, My House, The Office etc.
    Thanks,
    Paul
    -----------------------------------------------------------------------
    Paul J. Galvin
    Project Manager
    Akaza Research
    617-621-8585 x25
    www.akazaresearch.com
    www.openclinica.org
    ~ OpenClinica Enterprise ~ Ask me about professional training, support, and services for OpenClinica
    -----Original Message-----
    Sent: Thursday, June 25, 2009 12:24 PM
    To: [email protected]
    Subject: RE: [Developers] deploying 3.0 within the Spring framework ...
    Hi Paul,
    I looked at eventWsdl and I see I need to provide subject, study, eventDefinitionOID, startDate and something called 'location'.
    I think 'subject' corresponds to study_subject_id in study_subject, 'study' corresponds to unique_identifier in study
    and 'eventDefinitionOID' corresponds to oc_oid in study_event_definition. But what does 'location' refer to?
    So it seems these wsdl files are generated on-the-fly ... that's news to me. I've got alot to learn.
    Thanks
    -----Original Message-----
    Sent: Thu 6/25/2009 10:51 AM
    To: [email protected]
    Subject: RE: [Developers] deploying 3.0 within the Spring framework ...

    Hi Colton,
    There is an event.wsdl similar to the subject.wsdl. It can be found by adding ws/event/v1/eventWsdl.wsdl to the OpenClinica instance URL you are using.
    With 3.0 we will have the data import scheduler, so you can drop files off at a particular location to then be imported into event CRFs. You will need to make sure the file is ODM 1.2 or 1.3 compliant and contains the correct OIDs, but I think this should help you.
    If you go to Jobs under the Administration section, you can see where you can schedule data import jobs. I would be interested in your feedback if you have a chance to test the feature out.
    Thanks,
    Paul
    -----------------------------------------------------------------------
    Paul J. Galvin
    Project Manager
    Akaza Research
    617-621-8585 x25
    www.akazaresearch.com
    www.openclinica.org
    ~ OpenClinica Enterprise ~ Ask me about professional training, support, and services for OpenClinica
    -----Original Message-----
    Sent: Wednesday, June 24, 2009 12:43 PM
    To: [email protected]
    Subject: RE: [Developers] deploying 3.0 within the Spring framework ...
    Hi,
    For event scheduling, is there an event.wsdl file somewhere? A file
    analogous to subject.wsdl?
    At Geneuity, we are very, very interested in these web services. Ultimately, we'd like
    to see a web service that could handle inserts into item_data. We have a very specific
    scenario in mind that we hope the developers at OpenClinica will consider.
    We use OpenClinica from the POV of a clinical laboratory. In our case, every 'event' is
    characterized by the arrival of a specimen from a particular patient drawn at a particular
    time during the trial. Every specimen comes with an accession number. Before testing,
    each specimen is 'accessioned' into OpenClinica by filling in the 'accessioning section' of
    the appropriate CRF. This section includes fields for accession number, receipt date,
    shipping deviations, freezer location and the like. After accessioning, the specimen
    is tested, sometimes singly but often in batches on an automated clinical platform. When the latter is done,
    the platform outputs (usually) a file that contains the results tagged with the accession
    numbers of the specimens. Right now, we configure a Mirth channel to take
    parse this file, look up the corresponding event_crf_id for each accession and insert
    the results into item_data directly, subverting OpenClinica's interfaces. Of course, as pointed
    out numerous times by Paul, this isn't ideal. A web service would be.
    But, as you can discern, we need a web service that is smart enough to associate
    an item value with a particular scheduled event by virtue of a 'key' that both the platform
    and OpenClinica (item_data) are already aware of.
    I don't think this need is unique to us. Most every clinical trial nowadays has a laboratory
    component and consequently a need for specimen tracking and automated data uploads.
    Thanks!
    -----Original Message-----
    Sent: Wed 6/24/2009 11:21 AM
    To: [email protected]
    Subject: Re: [Developers] deploying 3.0 within the Spring framework ...

    Great,
    I will add that to the source code. I still don¹t get why the order is being
    switched specifically on your machine.
    I¹ll look into it some more.
    Thank you again
    Krikor
    On 6/24/09 11:11 AM, "Colton Smith" wrote:
    > > Hi Krikor,
    > >
    > > Indeed, that edit works ...
    > >
    > > FYI: I tested 3.0alpha2's web services feature (subject enrollment) and it
    > > works for me as well. I had
    > > been testing against 3.0alpha1.
    > >
    > > Thanks
    > >
    > >
    > > -----Original Message-----
    > > From: Krikor Krumlian [mailto:[email protected]]
    > > Sent: Wed 6/24/2009 8:40 AM
    > > To: [email protected]; Colton Smith
    > > Subject: Re: [Developers] deploying 3.0 within the Spring framework ...
    > >
    > > Hey Colton ,
    > >
    > > Yes that¹s definitly one option. Can you also try the following.
    > > Edit the
    > > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-scheduler.xml
    > > file and add the text in red to the bean definition
    > >
    > > > class="org.springframework.scheduling.quartz.SchedulerFactoryBean"
    > > depends-on="liquibase"> ...
    > >
    > > If you could let me know the outcome that would be great
    > >
    > > Thank you
    > > Krikor
    > >
    > > On 6/23/09 1:26 PM, "Colton Smith" wrote:
    > >
    >>> >> > Hi,
    >>> >> >
    >>> >> > When I edit web.xml thusly:
    >>> >> > ************************************************************************
    >>> >> >
    >>> >> > contextConfigLocation
    >>> >> >
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-db.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-email.xml
    >>> >> >
    >>> >> >
    >> >> /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-hibernate.xml
    >>> >> >
    >>> >> >
    >> >> /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-scheduler.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-service.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-spring.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-timer.xml
    >>> >> >
    >>> >> > /WEB-INF/classes/org/akaza/openclinica/applicationContext-security.xml
    >>> >> >
    >>> >> >
    >>> >> >
    >> >>
    ******************************************************************************
    >>> >> > *
    >>> >> > I'm able to deploy, no problems! 3.0 looks great! I love it.
    >>> >> >
    >>> >> > Thanks
    >>> >> >
    >>> >> >
    >>> >> > -----Original Message-----
    >>> >> >
    >>> >> > Sent: Tue 6/23/2009 12:08 PM
    >>> >> > To: [email protected]
    >>> >> > Subject: RE: [Developers] deploying 3.0 within the Spring framework ...
    >>> >> >
    >>> >> > Hi,
    >>> >> >
    >>> >> > Correction (or amendment): on my system, Tomcat is configured to use SUN
    >>> >> > java-1.5.0 ...
    >>> >> >
    >>> >> > Thanks
    >>> >> >
    >>> >> >
    >>> >> > -----Original Message-----
    >>> >> >
    >>> >> > Sent: Tue 6/23/2009 11:37 AM
    >>> >> > To: [email protected]
    >>> >> > Subject: RE: [Developers] deploying 3.0 within the Spring framework ...
    >>> >> >
    >>> >> > Hi,
    >>> >> >
    >>> >> > Indeed, here's what my openclinica.log file looks like when spring
    >> >> initiates:
    >>> >> > **************************************************
    >>> >> > 06/23 11:20:25 INFO o.s.w.c.s.XmlWebApplicationContext:411 - Refreshing
    >>> >> > o[email protected]4dd014:
    >>> >> > display name [Root WebApplicationContext]; startup date [Tue Jun 23
    >> >> 11:20:25
    >>> >> > EDT 2009]; root of context hierarchy
    >>> >> >
    >>> >> > 06/23 11:20:25 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-security.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 DEBUG o.s.s.i.w.DefaultFilterInvocationDefinitionSource:120
    -
    >>> >> > Added URL pattern: /**; attributes: [ROLE_USER]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-hibernate.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-scheduler.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-spring.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-email.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-service.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-timer.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >> >> bean
    >>> >> > definitions from file
    >>> >> >
    >> >>
    [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/app
    >>> >> > licationContext-core-db.xml]
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.w.c.s.XmlWebApplicationContext:426 - Bean factory
    >>> >> > for application context
    >>> >> > [o[email protected]4dd014]:
    >>> >> >
    >> >> org.s[email protected]1ad5d46
    >>> >> >
    >>> >> > 06/23 11:20:26 INFO o.s.b.f.c.PropertiesFactoryBean:178 - Loading
    >> >> properties
    >>> >> > file from class path resource [datainfo.properties]
    >>> >> >
    >>> >> > ************************************************
    >>> >> > -core-db.xml is LAST on my list!
    >>> >> >
    >>> >> > I'm using Ubuntu 8.04 LTS, Sun Java 1.6.0 and Tomcat5.5.
    >>> >> >
    >>> >> > Maybe a system call is done to retrieve applicationContext*.xml. But when
    I
    >>> >> > do so, I get:
    >>> >> > *****************************************************
    >>> >> > UNIX>ls applicationContext*.xml
    >>> >> > applicationContext-core-db.xml applicationContext-core-hibernate.xml
    >>> >> > applicationContext-core-service.xml applicationContext-core-timer.xml
    >>> >> >
    >>> >> > applicationContext-core-email.xml applicationContext-core-scheduler.xml
    >>> >> > applicationContext-core-spring.xml applicationContext-security.xml
    >>> >> >
    >>> >> > *********************************************************
    >>> >> > ... which looks OK (-core-db.xml is first in this listing).
    >>> >> >
    >>> >> > Is there a way in Spring to force an order?
    >>> >> >
    >>> >> > Thanks!
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> >
    >>> >> > -----Original Message-----
    >>> >> >
    >>> >> > Sent: Tue 6/23/2009 10:25 AM
    >>> >> > To: [email protected]
    >>> >> > Subject: Re: [Developers] deploying 3.0 within the Spring framework ...
    >>> >> >
    >>> >> > Hello Colton,
    >>> >> >
    >>> >> > What you are describing below makes perfect sense. I Just loaded my app and
    >>> >> > here¹s the order of xmls
    >>> >> >
    >>> >> > WebApplicationContext]; startup date [Tue Jun 23 10:21:05 EDT 2009]; root
    >> >> of
    >>> >> > context hierarchy
    >>> >> > 06/23 10:21:05 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-db.xml]
    >>> >> > 06/23 10:21:07 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-email.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-hibernate.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-scheduler.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-service.xml]
    >>> >> > 06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-spring.xml]
    >>> >> > 06/23 10:21:09 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-core-timer.xml]
    >>> >> > 06/23 10:21:09 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    >>> >> > bean definitions from file
    >>> >> >
    >> >> [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    >>> >> > s/org/akaza/openclinica/applicationContext-security.xml]
    >>> >> >
    >>> >> > As you may notice applicationContext-core.db.xml loads first. I wonder why
    >>> >> > it doesn¹t on your system. I will also check to see if I
    >>> >> > Can force core-db.xml to load first.
    >>> >> >
    >>> >> > Developers internally are using XP & MAC Oses with Java 5 what is your
    >>> >> > configuration ?
    >>> >> >
    >>> >> > Thank you
    >>> >> > Krikor
    >>> >> >
    >>> >> >
    >>> >> > On 6/23/09 9:10 AM, "Colton Smith" wrote:
    >>> >> >
    >>>>>>> >>>> >> > Hi,
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > I'm trying to understand what Spring does when OpenClinica.war is
    >>>> >>>> first
    >>>>>>> >>>> >> > deployed by Tomcat.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > Here's what I've gleaned so far ... Tomcat looks at web.xml, spots
    the
    >>>>>>> >>>> >> > listener tags and knows
    >>>>>>> >>>> >> > to start the springframework for web applications. It does so. Spring
    >>>>>>> >>>> >> > functions as a broker
    >>>>>>> >>>> >> > between beans and services, and springs into action by first looking
    for
    >>>>>>> >>>> >> > instructions on how to function as such
    >>>>>>> >>>> >> > by inspecting the applicationContext files located in
    >>>>>>> >>>> >> > classes/org/akaza/openclinica. There are seven
    >>>>>>> >>>> >> > of these and Spring digests them one by one, wiring itself and
    >>>> >>>> performing
    >>>>> >>> >> any
    >>>>>>> >>>> >> > initializations specified
    >>>>>>> >>>> >> > therein.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > On my system, Spring seems to deal with
    >>>> >>>> applicationContext-security.xml
    >>>>>>> >>>> >> > first, then -hibernate.xml
    >>>>>>> >>>> >> > and then -core-schedular.xml. But it bombs out on the latter,
    >>>> >>>> complaining
    >>>>>>> >>>> >> > that the table oc_qrtz_locks
    >>>>>>> >>>> >> > does not exist. But how can it exist? Spring has not yet processed
    the
    >>>>>>> >>>> >> > directives found in -core-db.xml
    >>>>>>> >>>> >> > which commands Liquibase to create OpenClinica's tables.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > Am I way off in my understanding? Probably so. Any clarifications
    >>>> >>>> will be
    >>>>>>> >>>> >> > greatly appreciated.
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> > Thanks!
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> >
    >>>>>>> >>>> >> >
  • susportsusport Posts: 6
    ----- Mensaje original -----
    De: "Colton Smith"
    Para: [email protected]
    Enviados: Martes, 23 de Junio 2009 13:26:07 (GMT-0500) Auto-Detected
    Asunto: RE: [Developers] deploying 3.0 within the Spring framework ...
    Hi,
    When I edit web.xml thusly:
    ************************************************************************

    contextConfigLocation

    /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-db.xml
    /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-email.xml
    /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-hibernate.xml
    /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-scheduler.xml
    /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-service.xml
    /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-spring.xml
    /WEB-INF/classes/org/akaza/openclinica/applicationContext-core-timer.xml
    /WEB-INF/classes/org/akaza/openclinica/applicationContext-security.xml


    *******************************************************************************
    I'm able to deploy, no problems! 3.0 looks great! I love it.
    Thanks
    -----Original Message-----
    Sent: Tue 6/23/2009 12:08 PM
    To: [email protected]
    Subject: RE: [Developers] deploying 3.0 within the Spring framework ...

    Hi,
    Correction (or amendment): on my system, Tomcat is configured to use SUN java-1.5.0 ...
    Thanks
    -----Original Message-----
    Sent: Tue 6/23/2009 11:37 AM
    To: [email protected]
    Subject: RE: [Developers] deploying 3.0 within the Spring framework ...

    Hi,
    Indeed, here's what my openclinica.log file looks like when spring initiates:
    **************************************************
    06/23 11:20:25 INFO o.s.w.c.s.XmlWebApplicationContext:411 - Refreshing o[email protected]4dd014: display name [Root WebApplicationContext]; startup date [Tue Jun 23 11:20:25 EDT 2009]; root of context hierarchy
    06/23 11:20:25 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-security.xml]
    06/23 11:20:26 DEBUG o.s.s.i.w.DefaultFilterInvocationDefinitionSource:120 - Added URL pattern: /**; attributes: [ROLE_USER]
    06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-core-hibernate.xml]
    06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-core-scheduler.xml]
    06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-core-spring.xml]
    06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-core-email.xml]
    06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-core-service.xml]
    06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-core-timer.xml]
    06/23 11:20:26 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML bean definitions from file [/usr/local/tomcat5.5/webapps/alpha2/WEB-INF/classes/org/akaza/openclinica/applicationContext-core-db.xml]
    06/23 11:20:26 INFO o.s.w.c.s.XmlWebApplicationContext:426 - Bean factory for application context [o[email protected]4dd014]: org.s[email protected]1ad5d46
    06/23 11:20:26 INFO o.s.b.f.c.PropertiesFactoryBean:178 - Loading properties file from class path resource [datainfo.properties]
    ************************************************
    -core-db.xml is LAST on my list!
    I'm using Ubuntu 8.04 LTS, Sun Java 1.6.0 and Tomcat5.5.
    Maybe a system call is done to retrieve applicationContext*.xml. But when I do so, I get:
    *****************************************************
    UNIX>ls applicationContext*.xml
    applicationContext-core-db.xml applicationContext-core-hibernate.xml applicationContext-core-service.xml applicationContext-core-timer.xml
    applicationContext-core-email.xml applicationContext-core-scheduler.xml applicationContext-core-spring.xml applicationContext-security.xml
    *********************************************************
    ... which looks OK (-core-db.xml is first in this listing).
    Is there a way in Spring to force an order?
    Thanks!
    -----Original Message-----
    Sent: Tue 6/23/2009 10:25 AM
    To: [email protected]
    Subject: Re: [Developers] deploying 3.0 within the Spring framework ...

    Hello Colton,
    What you are describing below makes perfect sense. I Just loaded my app and
    here¹s the order of xmls
    WebApplicationContext]; startup date [Tue Jun 23 10:21:05 EDT 2009]; root of
    context hierarchy
    06/23 10:21:05 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-core-db.xml]
    06/23 10:21:07 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-core-email.xml]
    06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-core-hibernate.xml]
    06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-core-scheduler.xml]
    06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-core-service.xml]
    06/23 10:21:08 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-core-spring.xml]
    06/23 10:21:09 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-core-timer.xml]
    06/23 10:21:09 INFO o.s.b.f.x.XmlBeanDefinitionReader:323 - Loading XML
    bean definitions from file
    [/usr/local/apache-tomcat-6.0.18/webapps/OpenClinica-SNAPSHOT/WEB-INF/classe
    s/org/akaza/openclinica/applicationContext-security.xml]
    As you may notice applicationContext-core.db.xml loads first. I wonder why
    it doesn¹t on your system. I will also check to see if I
    Can force core-db.xml to load first.
    Developers internally are using XP & MAC Oses with Java 5 what is your
    configuration ?
    Thank you
    Krikor
    On 6/23/09 9:10 AM, "Colton Smith" wrote:
    > > Hi,
    > >
    > > I'm trying to understand what Spring does when OpenClinica.war is first
    > > deployed by Tomcat.
    > >
    > > Here's what I've gleaned so far ... Tomcat looks at web.xml, spots the
    > > listener tags and knows
    > > to start the springframework for web applications. It does so. Spring
    > > functions as a broker
    > > between beans and services, and springs into action by first looking for
    > > instructions on how to function as such
    > > by inspecting the applicationContext files located in
    > > classes/org/akaza/openclinica. There are seven
    > > of these and Spring digests them one by one, wiring itself and performing any
    > > initializations specified
    > > therein.
    > >
    > > On my system, Spring seems to deal with applicationContext-security.xml
    > > first, then -hibernate.xml
    > > and then -core-schedular.xml. But it bombs out on the latter, complaining
    > > that the table oc_qrtz_locks
    > > does not exist. But how can it exist? Spring has not yet processed the
    > > directives found in -core-db.xml
    > > which commands Liquibase to create OpenClinica's tables.
    > >
    > > Am I way off in my understanding? Probably so. Any clarifications will be
    > > greatly appreciated.
    > >
    > > Thanks!
    > >
    > >
    > >
This discussion has been closed.