Hello,
I have downloaded the code from https://github.com/krishagni/openspecimen/archive/os_v10.zip
It is working fine.The db consists of 198 tables.
I just want to confirm, Whether I have downloaded the correct code or not.
Can you please confirm so that I can proceed and start testing the version.
Awaiting for your response.
Regards,
Madhavi Latha
Hi @MADHAVI_LATHA,
Os-v1.0 is the older version. After this there are many changes happened in OpenSpecimen. So we will suggest you to download the latest build OS-v1.1. The build is available at release directory.
For deployment details please refer deployment guide.
~Nitesh
Hi Nitesh_Marwaha,
Thank you very much for your immediate response.
I will start working on it.
Regards,
Madhavi Latha
Hello Nitesh,
I have downloaded open specimen version 1.1 from release directory.
When I try to execute deploy_all based on deployment guide, After 2-4min.,
I am getting java.lang.OutOfMemoryError: PermGen space.
I have already set Java opts to JAVA_OPTS=-Xms128M -Xmx2048M -XX:MaxPermSize=1024M in jboss(run.bat),windows and command prompt too.
I am pasteing the error for your reference.
========================================================================================
upgrade_db_plusv4.0:
[echo] Upgrading DataBase with URL jdbc:oracle:thin:@localhost:1521:ora11g
[propertyfile] Updating property file: C:\madhavi\OpenSpecimen1.0_kit\modules\ca
Tissue\conf\allTokens.properties
[echo] Setting Global DRIVER and URL Property
upgrade_de_db:
[delete] Deleting directory C:\madhavi\OpenSpecimen1.0_kit\temp\detemp
[mkdir] Created dir: C:\madhavi\OpenSpecimen1.0_kit\temp\detemp
[unzip] Expanding: C:\madhavi\OpenSpecimen1.0_kit\modules\dynamic_extensions
\lib\dynamicextensions.zip into C:\madhavi\OpenSpecimen1.0_kit\temp\detemp
BUILD FAILED
C:\madhavi\OpenSpecimen1.0_kit\build.xml:987: The following error occurred while
executing this line:
C:\madhavi\OpenSpecimen1.0_kit\build.xml:1641: The following error occurred whil
e executing this line:
C:\madhavi\OpenSpecimen1.0_kit\build.xml:5548: The following error occurred whil
e executing this line:
C:\madhavi\OpenSpecimen1.0_kit\build.xml:5582: java.lang.OutOfMemoryError: PermG
en space
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:14
1)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at oracle.jdbc.driver.T4CConnection.logon(T4CConnection.java:278)
at oracle.jdbc.driver.PhysicalConnection.(PhysicalConnection.java:
441)
at oracle.jdbc.driver.T4CConnection.(T4CConnection.java:165)
at oracle.jdbc.driver.T4CDriverExtension.getConnection(T4CDriverExtensio
n.java:35)
at oracle.jdbc.driver.OracleDriver.connect(OracleDriver.java:801)
at liquibase.integration.ant.BaseLiquibaseTask.createDatabaseObject(Base
LiquibaseTask.java:238)
at liquibase.integration.ant.BaseLiquibaseTask.createLiquibase(BaseLiqui
baseTask.java:175)
at liquibase.integration.ant.DatabaseUpdateTask.execute(DatabaseUpdateTa
sk.java:33)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.GeneratedMethodAccessor51.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.jav
a:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:390)
at org.apache.tools.ant.Target.performTasks(Target.java:411)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(Single
CheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
at org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
Any help in this aspect can be appreciated.
Thanks & Regards,
Madhavi Latha
Hello @MADHAVI_LATHA
JAVA_OPTS environment variable is for JBoss/Tomcat. It has no impact on Java programs started by Ant.
Can you please retry deploy_all on fresh database with following options set?
set ANT_OPTS="-Xms128M -Xmx1024M -XX:MaxPermSize=512M -XX:+CMSClassUnloadingEnabled -XX:+UseConcMarkSweepGC"
Sorry for inconvenience caused to you.
In mean time, we’ll update deployment guide as well.
Thanks.
Hello vpawar,
I have set the ANT_OPTS as you mentioned:
C:\madhavi\OpenSpecimen1.0_kit>set ANT_OPTS="-Xms128M -Xmx1024M -XX:MaxPermSize=
512M -XX:+CMSClassUnloadingEnabled -XX:+UseConcMarkSweepGC"
and I am getting the following error:
C:\madhavi\OpenSpecimen1.0_kit>ant deploy_all -Dusername=admin@admin.com
Invalid initial heap size: -Xms128M -Xmx1024M -XX:MaxPermSize=512M -XX:+CMSClass
UnloadingEnabled -XX:+UseConcMarkSweepGC
Could not create the Java virtual machine.
Am I doing any thing wrong?
Please help me further.
Thanks & Regards,
Madhavi Latha
Hi @MADHAVI_LATHA,
You need not to enclose the ANT_OPTS in double quotes(""). Set the ANT_OPTS like below:
[quote]set ANT_OPTS=-Xms128M -Xmx1024M -XX:MaxPermSize=512M -XX:+CMSClassUnloadingEnabled -XX:+UseConcMarkSweepGC
[/quote]
This will resolve the issue.
~Nitesh
Hello Nitesh,
Thank you very much. It resolved the issue.
Now I could deploy it successfully and able to view it from browser.
But If I want to make any changes to java, or jsp files where should I modify and how to deploy it again.
I saw catissuecore.war in OpenSpecimen_v1.1_Installable_RC1- modules-catissue-lib and catissuecore in temp folder.
Can you please help me in this aspect too.
Thanks & Regards,
Madhavi Latha
Hi @MADHAVI_LATHA,
For making any changes in java and jsp files, you need the source code. Source code for the OS_v11 is available on GIT on branch named “OS_v11”. You can download the code and make changes. For deployment instructions you can refer how to build from source code?
It will be great if you will let us know what changes you are doing in the code.
There might be chances that same change is being done by us in next version or
we can guide you to do it in a generic way to be merged to main code. If you do
local changes, you will be stuck with custom version.
~Nitesh
Hello @nitesh_marwaha,
While testing openspecimen11, I faced some issues like,
When creating the aliquots, if you select the checkbox ‘Do you want to dispose the parent specimen’ then Error is coming(on the server it is showing java.lang.NullPointerException).
If you uncheck the ‘Do you want to dispose the parent specimen’ , then it is creating the Aliquots.
May I know what might be the reason.
On the specimen page we have Specimen Events tab and View Annotaions tab.Both are showing empty pages in fresh installation. Earlier in catissueplus, We used to have several events on the Specimen Events tab. Is there any way to get the events back.
Please help me in this aspects.
Regards,
Madhavi Patnala
Hello @MADHAVI_LATHA
We confirmed the same error on OS v1.1 instance and created the following JIRA: https://catissueplus.atlassian.net/i#browse/OPSMN-1723
By default, we do have (null) Specimen Events forms, and we do not have null Specimen Annotations forms. I recall from caTissue Plus v3.0 that specimen pathology forms were present in the Annotations tab by default, though frankly we did not have a need for those forms. Perhaps those forms are recoverable somehow and could be loaded into OS v1.1?
@bob_lange for reference
@MADHAVI_LATHA attached is a screenshot of the Specimen Events that are present by default in OS v1.1 - is this what you are referencing?
In v1.1, specimen events are based on DE forms. By default, these specimen event forms get created and deployed at time of upgrade to v1.1.
The reasons for missing event forms could be:
Please run below command to deploy specimen events…
If app deployed from source directory:
ant -f deploy.xml migrate_specimen_events -Dusername=admin@admin.com
If app deployed from OS release tarball:
ant migrate_specimen_events -Dusername=admin@admin.com
Replace admin@admin.com with active admin username for your instance.
Thanks.
Hello @Matthew_Marcetich,
Thank you very much for your immediate response.
I am talking about the events, we used to have in catissueplus3.1 as shown below.
In openspecimen 11, the events page is looking like this.
I have also executed the below command from openspecimen_home as mentioned by @vpawar.
ant -f deploy.xml migrate_specimen_events -Dusername=admin@admin.com
The build was successful but still not able to see the events.
One more thing I tried is creating custom forms, Administration Menu->Manage Forms and created the forms, but after saving it also it is not showing the list of forms created. It is always showing the empty page. In the database, DYEXTN_CONTAINERS, I saw all the form names I have created.
I tried by redeploying and restarting the server.
Can anyone help me in this aspect.
Regards,
Madhavi Patnala
Hello,
When I do upgrade from catissueplus, I am able to see the events as @Matthew_Marcetich screen-shot, and also I can create custom forms and able to see the forms I have created.
But in fresh installation, If I am creating any custom forms, it is getting created but it is not showing the forms I have created, as I mentioned in the earlier mail(screen-shot).
Any help is appreciated.
Thanks & Regards,
Madhavi Latha Patnala
Hello @MADHAVI_LATHA,
Do you have the deployment log for the fresh install? If not, please reinstall with below command to redirect to an output file so that we know what went wrong in the deployment.
For Linux: nohup ant deploy_all -Dusername=replace_with_login_name (this will redirect the log to nohup.out)
For Windows: ant deploy_all -Dusername=replace_with_login_name > nohup.out 2 > &1
Please note you will lose data when you do fresh install again.
Thanks,
Poornima
