Unable to submit specimen containers after loading

kunleoyafajo · August 18, 2019, 11:04am

Hello Guys,

I will like to bring to your attention one of the challenges we are facing with the OpenSpecimen software. We have been unable to submit specimen containers after loading. This has been occurring for some time now, even on version 6.1 that we are currently running.

Has anyone face similar issue before?

Tushar_Tajane · August 19, 2019, 4:25am

Hi @kunleoyafajo,

Can you please provide us the screenshot of error message and the steps you followed to assign the container?

Thanks,
Tushar

Banke_Ipadeola · August 27, 2019, 11:29am

Screenshot%20(158)|690x358

These are the screenshots.
Thank you sincerely.

Tushar_Tajane · September 2, 2019, 12:00pm

Hi @kunleoyafajo,

In the screenshot you provided, we have not able to find any error message.
Can you please provide us screen-shot of the error message and os.log file.

Thanks,
Tushar

Banke_Ipadeola · September 2, 2019, 2:34pm

It is not bringing out any error message, but when clicked on submit button there is no response. There is no error message and there is no success message.

Thank you sincerely,
Olubanke Ipadeola

kunleoyafajo · September 4, 2019, 7:45am

Hello @Tushar_Tajane

Do you have any suggestion for us on this issue?

Tushar_Tajane · September 4, 2019, 10:47am

Hi @kunleoyafajo,

This happens when barcoding is enabled and the specimen labels are not auto-generated.

We are not clear from the screenshot whether your are inputting barcode or labels in the collection data entry form.

If this is not the case, can you please provide us the browser console error, if any, when you clicks on submit button?

Thanks,
Tushar

Banke_Ipadeola · September 10, 2019, 1:23pm

We have disabled the barcoding in the settings, but the issue is still the same: submit button still does nothing.
Here is the browser console error:

vendor.c291a963.js:5 TypeError: Cannot read property 'toLowerCase' of undefined
    at n (vendor.c291a963.js:28)
    at vendor.c291a963.js:23
    at Object.e [as invoke] (vendor.c291a963.js:4)
    at vendor.c291a963.js:4
    at f (vendor.c291a963.js:3)
    at Object.<anonymous> (vendor.c291a963.js:4)
    at Object.e [as invoke] (vendor.c291a963.js:4)
    at Object.$get (vendor.c291a963.js:4)
    at Object.e [as invoke] (vendor.c291a963.js:4)
    at vendor.c291a963.js:4
(anonymous) @ vendor.c291a963.js:5
vendor.c291a963.js:5 TypeError: Cannot read property 'toLowerCase' of undefined
    at n (vendor.c291a963.js:28)
    at vendor.c291a963.js:23
    at Object.e [as invoke] (vendor.c291a963.js:4)
    at vendor.c291a963.js:4
    at f (vendor.c291a963.js:3)
    at Object.<anonymous> (vendor.c291a963.js:4)
    at Object.e [as invoke] (vendor.c291a963.js:4)
    at Object.$get (vendor.c291a963.js:4)
    at Object.e [as invoke] (vendor.c291a963.js:4)
    at vendor.c291a963.js:4
(anonymous) @ vendor.c291a963.js:5
%7B%7Bglobal.siteAssets.siteLogo%7D%7D:1 Failed to load resource: the server responded with a status of 404 ()
14vendor.c291a963.js:5 TypeError: Cannot read property 'classList' of null
    at link (root/openspecimen/scripts/scripts.8e04461a.js:3:11055)
    at fa (root/openspecimen/scripts/vendor.c291a963.js:4:23108)
    at v (root/openspecimen/scripts/vendor.c291a963.js:4:17192)
    at h (root/openspecimen/scripts/vendor.c291a963.js:4:13013)
    at h (root/openspecimen/scripts/vendor.c291a963.js:4:13030)
    at root/openspecimen/scripts/vendor.c291a963.js:4:12509
    at e (root/openspecimen/scripts/vendor.c291a963.js:4:13504)
    at Object.k [as transclude] (root/openspecimen/scripts/vendor.c291a963.js:4:15685)
    at root/openspecimen/scripts/vendor.c291a963.js:7:16792
    at f (root/openspecimen/scripts/vendor.c291a963.js:3:20175) <div class="os-md-input">
(anonymous) @ vendor.c291a963.js:5
scripts.8e04461a.js:13 Uncaught TypeError: Cannot read property 'expanded' of undefined
    at scripts.8e04461a.js:13
    at Object.f [as forEach] (vendor.c291a963.js:3)
    at Z (scripts.8e04461a.js:13)
    at n.a.saveSpecimens (scripts.8e04461a.js:13)
    at vendor.c291a963.js:6
    at n.$eval (vendor.c291a963.js:5)
    at f (scripts.8e04461a.js:1)
    at HTMLDocument.<anonymous> (scripts.8e04461a.js:1)
    at HTMLDocument.dispatch (vendor.c291a963.js:2)
    at HTMLDocument.r.handle (vendor.c291a963.js:2)

Thank you.

Tushar_Tajane · September 13, 2019, 12:09pm

Hi @Banke_Ipadeola,

Can you please share a small video demonstrating the problem.
The demonstration will include - selecting specimens, navigating to collection tree, and doing submit.

Thanks,
Tushar

Oyediran_Tobiloba · October 2, 2019, 12:35pm

Here is a link to the video detailing the current configuration and the steps taken.

https://www.dropbox.com/s/v2k5h74z0gczpx7/Openspecimen-video.mp4?dl=0

Thank you.

Tushar_Tajane · October 8, 2019, 10:29am

Hi @Oyediran_Tobiloba,

This happens when barcoding is enabled and the specimen labels are not auto-generated.

In the video you shared- You showed the barcoding of specimens is enabled in the system settings. But doesn’t show the CP label setting - auto generated or manual. If it is manual, the UI crashes. This is the known issue that we will fix in v6.3.

Rule:
When barcoding is enabled, and barcodes are manually entered then it is expected the specimen labels are auto-generated. This condition is not satisfied is what I believe.

Thanks,
Tushar

Oyediran_Tobiloba · October 16, 2019, 1:52pm

Hi @Tushar_Tajane,

Thanks for the suggestion.
I have disabled specimen barcoding, now I am getting the error below when I try to submit.

Error: SQLIntegrityConstraintViolationException:Duplicate entry ‘0’ for key ‘PRIMARY’ (COMMON_SERVER_ERROR)

Can you help identify the cause of this?

kunleoyafajo · April 30, 2020, 10:30pm

Dear @Tushar_Tajane,

This is just to notify you that this issue still exist.

As part of what you suggested in your earlier post, we are now trying to update Openspecimen to version 6.3.

However, this upgrade process is throwing this error

liquibase.exception.DatabaseException: Cannot add foreign key constraint [Failed SQL: ALTER TABLE specimendb.OS_CP_GROUP_FORMS ADD CONSTRAINT FK_GRP_FORMS_FORM_ID FOREIGN KEY (FORM_ID) REFERENCES specimendb.DYEXTN_CONTAINERS (IDENTIFIER)]

See the full log below;

***************************************************
 OpenSpecimen, a Krishagni Product
 Build Version : v6.3.x
 Build Date    : Wed Feb 05 08:16:20 EST 2020
 Commit        : 526b00d
 Present Time  : Thu Apr 30 18:11:35 EDT 2020
 ***************************************************
30-Apr-2020 18:11:35.520 INFO [Catalina-utility-1] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
30-Apr-2020 18:11:43.018 SEVERE [Catalina-utility-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.springframework.web.context.ContextLoaderListener]
	org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'os-liquibase' defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/6.2/schema.xml::CP Group: FK on group form ID::vpawar:
     Reason: liquibase.exception.DatabaseException: Cannot add foreign key constraint [Failed SQL: ALTER TABLE specimendb.OS_CP_GROUP_FORMS ADD CONSTRAINT FK_GRP_FORMS_FORM_ID FOREIGN KEY (FORM_ID) REFERENCES specimendb.DYEXTN_CONTAINERS (IDENTIFIER)]
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
		at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
		at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
		at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
		at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
		at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
		at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
		at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
		at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
		at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
		at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
		at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4682)
		at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5143)
		at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
		at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
		at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
		at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:705)
		at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:978)
		at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1849)
		at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
		at java.util.concurrent.FutureTask.run(FutureTask.java:266)
		at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
		at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
		at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:773)
		at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:427)
		at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1620)
		at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:305)
		at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
		at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1151)
		at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1353)
		at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1357)
		at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1335)
		at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
		at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
		at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
		at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
		at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
		at java.lang.Thread.run(Thread.java:748)
	Caused by: liquibase.exception.MigrationFailedException: Migration failed for change set db/6.2/schema.xml::CP Group: FK on group form ID::vpawar:
     Reason: liquibase.exception.DatabaseException: Cannot add foreign key constraint [Failed SQL: ALTER TABLE specimendb.OS_CP_GROUP_FORMS ADD CONSTRAINT FK_GRP_FORMS_FORM_ID FOREIGN KEY (FORM_ID) REFERENCES specimendb.DYEXTN_CONTAINERS (IDENTIFIER)]
		at liquibase.changelog.ChangeSet.execute(ChangeSet.java:637)
		at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:53)
		at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:83)
		at liquibase.Liquibase.update(Liquibase.java:202)
		at liquibase.Liquibase.update(Liquibase.java:179)
		at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:353)
		at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:305)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
		at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
		... 41 more
	Caused by: liquibase.exception.DatabaseException: Cannot add foreign key constraint [Failed SQL: ALTER TABLE specimendb.OS_CP_GROUP_FORMS ADD CONSTRAINT FK_GRP_FORMS_FORM_ID FOREIGN KEY (FORM_ID) REFERENCES specimendb.DYEXTN_CONTAINERS (IDENTIFIER)]
		at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:356)
		at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:57)
		at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:125)
		at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1229)
		at liquibase.database.AbstractJdbcDatabase.executeStatements(AbstractJdbcDatabase.java:1211)
		at liquibase.changelog.ChangeSet.execute(ChangeSet.java:600)
		... 49 more
	Caused by: java.sql.SQLException: Cannot add foreign key constraint
		at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:129)
		at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:97)
		at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:122)
		at com.mysql.cj.jdbc.StatementImpl.executeInternal(StatementImpl.java:782)
		at com.mysql.cj.jdbc.StatementImpl.execute(StatementImpl.java:666)
		at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:175)
		at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:175)
		at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:352)
		... 54 more
30-Apr-2020 18:11:43.019 SEVERE [Catalina-utility-1] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
30-Apr-2020 18:11:43.020 SEVERE [Catalina-utility-1] org.apache.catalina.core.StandardContext.startInternal Context [/openspecimen] startup failed due to previous errors
30-Apr-2020 18:11:43.021 INFO [Catalina-utility-1] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
30-Apr-2020 18:11:43.029 WARNING [Catalina-utility-1] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [openspecimen] appears to have started a thread named [FileWatchdog] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java.lang.Thread.sleep(Native Method)
 org.apache.log4j.helpers.FileWatchdog.run(FileWatchdog.java:104)
30-Apr-2020 18:11:43.031 INFO [Catalina-utility-1] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/volume1/@appstore/Tomcat9/webapps/openspecimen.war] has finished in [11,900] ms

kunleoyafajo · May 3, 2020, 9:36pm

Hi,

I have gone pass the error above by adding index on DYEXTN_CONTAINERS. IDENTIFIER

Now I’m unto another error shown below***************************************************
Caused by: liquibase.exception.MigrationFailedException: Migration failed for change set db/6.2/migration.xml::PV: participant fields::vpawar:
Reason: liquibase.exception.DatabaseException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ‘d.vital_status_id = pv.identifier’ at line 1 [Failed SQL: call set_pv_ids(‘catissue_participant’, ‘vital_status’, ‘vital_status_id’, ‘vital_status’)]

Detail Tomcat log below;
OpenSpecimen, a Krishagni Product
Build Version : v6.3.x
Build Date : Wed Feb 05 08:16:20 EST 2020
Commit : 526b00d
Present Time : Sun May 03 16:58:21 EDT 2020
***************************************************
03-May-2020 16:58:21.490 INFO [Catalina-utility-2] org.apache.catalina.core.ApplicationContext.log Initializing Spring root WebApplicationContext
OpenJDK 64-Bit Server VM warning: CodeCache is full. Compiler has been disabled.
OpenJDK 64-Bit Server VM warning: Try increasing the code cache size using -XX:ReservedCodeCacheSize=
CodeCache: size=245760Kb used=243460Kb max_used=243485Kb free=2299Kb
bounds [0x00007f7c39000000, 0x00007f7c48000000, 0x00007f7c48000000]
total_blobs=74298 nmethods=73602 adapters=605
compilation: disabled (not enough contiguous free space left)
03-May-2020 16:58:31.652 SEVERE [Catalina-utility-2] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.springframework.web.context.ContextLoaderListener]
org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘os-liquibase’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of init method failed; nested exception is liquibase.exception.MigrationFailedException: Migration failed for change set db/6.2/migration.xml::PV: participant fields::vpawar:
Reason: liquibase.exception.DatabaseException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ‘d.vital_status_id = pv.identifier’ at line 1 [Failed SQL: call set_pv_ids(‘catissue_participant’, ‘vital_status’, ‘vital_status_id’, ‘vital_status’)]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1631)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4682)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5143)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:705)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:978)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1849)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:773)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:427)
at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1620)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:305)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1151)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1353)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1357)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1335)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: liquibase.exception.MigrationFailedException: Migration failed for change set db/6.2/migration.xml::PV: participant fields::vpawar:
Reason: liquibase.exception.DatabaseException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ‘d.vital_status_id = pv.identifier’ at line 1 [Failed SQL: call set_pv_ids(‘catissue_participant’, ‘vital_status’, ‘vital_status_id’, ‘vital_status’)]
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:637)
at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:53)
at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:83)
at liquibase.Liquibase.update(Liquibase.java:202)
at liquibase.Liquibase.update(Liquibase.java:179)
at liquibase.integration.spring.SpringLiquibase.performUpdate(SpringLiquibase.java:353)
at liquibase.integration.spring.SpringLiquibase.afterPropertiesSet(SpringLiquibase.java:305)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1689)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1627)
… 41 more
Caused by: liquibase.exception.DatabaseException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ‘d.vital_status_id = pv.identifier’ at line 1 [Failed SQL: call set_pv_ids(‘catissue_participant’, ‘vital_status’, ‘vital_status_id’, ‘vital_status’)]
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:356)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:57)
at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:125)
at liquibase.database.AbstractJdbcDatabase.execute(AbstractJdbcDatabase.java:1229)
at liquibase.database.AbstractJdbcDatabase.executeStatements(AbstractJdbcDatabase.java:1211)
at liquibase.changelog.ChangeSet.execute(ChangeSet.java:600)
… 49 more
Caused by: java.sql.SQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ‘d.vital_status_id = pv.identifier’ at line 1
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:120)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:97)
at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:122)
at com.mysql.cj.jdbc.StatementImpl.executeInternal(StatementImpl.java:782)
at com.mysql.cj.jdbc.StatementImpl.execute(StatementImpl.java:666)
at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:175)
at org.apache.tomcat.dbcp.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:175)
at liquibase.executor.jvm.JdbcExecutor$ExecuteStatementCallback.doInStatement(JdbcExecutor.java:352)
… 54 more
03-May-2020 16:58:31.657 SEVERE [Catalina-utility-2] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
03-May-2020 16:58:31.658 SEVERE [Catalina-utility-2] org.apache.catalina.core.StandardContext.startInternal Context [/openspecimen] startup failed due to previous errors
03-May-2020 16:58:31.661 INFO [Catalina-utility-2] org.apache.catalina.core.ApplicationContext.log Closing Spring root WebApplicationContext
03-May-2020 16:58:31.678 WARNING [Catalina-utility-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [openspecimen] appears to have started a thread named [FileWatchdog] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
java.lang.Thread.sleep(Native Method)
org.apache.log4j.helpers.FileWatchdog.run(FileWatchdog.java:104)
03-May-2020 16:58:31.685 INFO [Catalina-utility-2] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/volume1/@appstore/Tomcat9/webapps/openspecimen.war] has finished in [14,738] ms

Swapnil_Ingle · May 4, 2020, 3:15pm

Hi @kunleoyafajo,

It seems like manual SQL queries were fired in the DB to fix some issues which should not have occurred in the first place. (Ex: Adding an index on dyextn_containers.identifier - This index is already present and we don’t how it went missing)

This leads us to believe that the present database might be in an unstable state.

If this is not production data, we recommend to fresh-install OpenSpecimen on an empty database.

Thanks,
Swapnil I.

kunleoyafajo · May 11, 2020, 10:13am

Hi @Swapnil_Ingle,

Thank you for your feedback.

I have setup a fresh Openspecimen environment using the latest version (v7.0.RC1).

Is it advisable to try to move some data from the old database into the new one? If yes how would you advise us to approach this i.e. what are the essential data (table data) that can be moved?

Swapnil_Ingle · May 11, 2020, 1:26pm

Hi @kunleoyafajo,

You can use the “Export/Import” from the UI of the older instance of OpenSpecimen.

Export data/records from the older instance using the “Export” feature of OpenSpecimen. (wiki-page)
Import the CSVs into the new instance using the “Bulk Import” feature of OpenSpecimen. (wiki-page)

A direct database to database transfer is not guaranteed to work without the extensive guidance and monitoring from our team.

Thanks,
Swapnil I.