Empty project page after upgrade to 1.8.2

Sven De Vilder

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Jun 2, 2021, 12:15:10 PM6/2/21

to xnat_discussion

Hello,

I've been trying to upgrade our test environment from 1.7.5.6 build 1651 to 1.8.3 build 3, but everytime I go from a 1.7.x to 1.8.x everything seems fine until I open certain projects to show the subjects (not all projects though, most are fine). Then it doesn't show any patients, not even the table for the patients. The data can still be accessed through other ways (searching/direct link to the exam). This is for all users. I also tried to create a new user to no avail.

Screenshot of the page:

In the logfiles there are several entries :

turbine.log :

ERROR org.apache.turbine.services.velocity.TurbineVelocityService - Class org.nrg.xdat.om.XnatProjectdata.getBundles threw Exception java.lang.NullPointerException: null

tasks.log :

2021-06-02 15:42:12,559 [taskScheduler-2] WARN org.nrg.xnat.initialization.tasks.FixMismatchedMappingElements - Found and fixed 13 misconfigured data-type permission mappings

2021-06-02 15:42:12,577 [taskScheduler-2] WARN org.nrg.xnat.initialization.tasks.FixMismatchedMappingElements - Found project groups with irregular permission mappings:

I'm not going to try to fix these issues automatically. You can request that these be fixed by making a POST request to the URL:

http://x.x.x.x/xapi/access/permissions/irregular/fix

xdat.log:

2021-06-02 15:42:10,150 [main] ERROR org.nrg.xdat.servlet.XDATServlet - Preparing create SQL and got 18 optional SQL statements. Please review this optional SQL and consider executing it if required:

Optional SQL:

--Database column xnat_addfield.addfield is now required.

--ALTER TABLE xnat_addfield ALTER COLUMN addfield SET NOT NULL;

--Database column xnat_imagescandata.note type mis-match ('TEXT'!='varchar').

----Unable to resolve type mis-match for the following reason(s).

----Please review these factors before uncommenting this code.

----2 row(s) contain values.

----Fix xnat_imagescandata_history table.

--ALTER TABLE xnat_imagescandata_history ADD COLUMN note_cp varchar;

--UPDATE xnat_imagescandata_history SET note_cp=note;

--ALTER TABLE xnat_imagescandata_history DROP COLUMN note;

--ALTER TABLE xnat_imagescandata_history ADD COLUMN note TEXT;

--UPDATE xnat_imagescandata_history SET note=CAST(note_cp AS TEXT);

--CREATE OR REPLACE FUNCTION after_update_xnat_imagescandata() RETURNS TRIGGER AS ' begin RETURN NULL; end; ' LANGUAGE 'plpgsql' VOLATILE;

----Fix xnat_imagescandata table.

--ALTER TABLE xnat_imagescandata ADD COLUMN note_cp varchar;

--UPDATE xnat_imagescandata SET note_cp=note;

--ALTER TABLE xnat_imagescandata DROP COLUMN note;

--ALTER TABLE xnat_imagescandata ADD COLUMN note TEXT;

--UPDATE xnat_imagescandata SET note=CAST(note_cp AS TEXT);

2021-06-02 15:42:13,096 [main] ERROR org.nrg.xft.db.DBAction - Preparing to convert table 'xhbm_event_service_payload_entity' to use sequence for default value.

2021-06-02 15:42:13,096 [main] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:

2021-06-02 15:42:13,096 [main] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_event_service_payload_entity_id_seq

2021-06-02 15:42:13,096 [main] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_event_service_payload_entity ALTER COLUMN id SET DEFAULT nextval('xhbm_event_service_payload_entity_id_seq')

2021-06-02 15:42:13,096 [main] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_event_service_payload_entity ALTER COLUMN id SET NOT NULL

2021-06-02 15:42:13,096 [main] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_event_service_payload_entity_id_seq OWNED BY xhbm_event_service_payload_entity.id

2021-06-02 15:42:13,108 [main] ERROR org.nrg.xft.db.DBAction - Ran the query 'SELECT (MAX(id) + 1) AS value FROM xhbm_event_service_payload_entity' and got the value 1. Now preparing to run the query: SELECT setval('xhbm_event_service_payload_entity_id_seq', 1) AS value

2021-06-02 15:42:13,120 [main] ERROR org.nrg.xft.db.DBAction - Preparing to convert table 'xhbm_file_store_info_aud' to use sequence for default value.

2021-06-02 15:42:13,120 [main] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:

2021-06-02 15:42:13,120 [main] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_file_store_info_aud_id_seq

2021-06-02 15:42:13,120 [main] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_file_store_info_aud ALTER COLUMN id SET DEFAULT nextval('xhbm_file_store_info_aud_id_seq')

2021-06-02 15:42:13,120 [main] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_file_store_info_aud ALTER COLUMN id SET NOT NULL

2021-06-02 15:42:13,120 [main] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_file_store_info_aud_id_seq OWNED BY xhbm_file_store_info_aud.id

2021-06-02 15:42:13,132 [main] ERROR org.nrg.xft.db.DBAction - Ran the query 'SELECT (MAX(id) + 1) AS value FROM xhbm_file_store_info_aud' and got the value 1. Now preparing to run the query: SELECT setval('xhbm_file_store_info_aud_id_seq', 1) AS value

I've executed the api call from tasks.log to fix the mappings, but that didn't change anything (also not after a restart of tomcat).

I've also executed the SQL from xdat.log and that also didn't change anything (neither after restart of tomcat).

I've tried everything multiple times by going back to an earlier snapshot, but the result was always the same. I also tried to first upgrade to 1.7.6 and that went fine. Everything was still visible. Then I tried to upgrade to 1.8.0.1 and then the problem was present, so it seems to be there a while.

I also tried both Postgresql 12 and 10 because for the first upgrade I used 12 and wanted to see if that might have caused the problem.

I've also removed all plugins to if that might be the problem.

Can anyone advise on how to proceed ?

Kind regards,

Sven De Vilder

UMC Utrecht

Herrick, Rick

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Jun 2, 2021, 12:22:02 PM6/2/21

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I think this is the critical error:

turbine.log :

ERROR org.apache.turbine.services.velocity.TurbineVelocityService - Class org.nrg.xdat.om.XnatProjectdata.getBundles threw Exception java.lang.NullPointerException: null

Is there any other info along with that error? A stack trace would be hugely useful.

You may also look in the Tomcat log files to see if there’s any other info logged.

--

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Sven De Vilder <s.dev...@gmail.com>
Date: Wednesday, June 2, 2021 at 11:15 AM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] Empty project page after upgrade to 1.8.2

* External Email - Caution *

Hello,

I've been trying to upgrade our test environment from 1.7.5.6 build 1651 to 1.8.3 build 3, but everytime I go from a 1.7.x to 1.8.x everything seems fine until I open certain projects to show the subjects (not all projects though, most are fine). Then it doesn't show any patients, not even the table for the patients. The data can still be accessed through other ways (searching/direct link to the exam). This is for all users. I also tried to create a new user to no avail.

Screenshot of the page:

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Moore, Charlie

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Jun 2, 2021, 12:28:22 PM6/2/21

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Hi Sven,

Are any of your plugins providing data types? XNAT does not respond well if you remove data type plugins. With XNAT 1.8.2, you'll also need tomcat9 unless you modify the war. What breaks if you try 1.8.2 with tomcat7 is picking up plugins, so a missing data type plugin could explain this behavior, I think.

Thanks,

Charlie

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Herrick, Rick <jrhe...@wustl.edu>
Sent: Wednesday, June 2, 2021 11:21 AM
To: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] Empty project page after upgrade to 1.8.2

To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/SN6PR02MB51185CBCA81E4D9FC3E88D56BD3D9%40SN6PR02MB5118.namprd02.prod.outlook.com.

Sven De Vilder

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Jun 2, 2021, 12:35:53 PM6/2/21

to xnat_discussion

Hi Rick,

No problem. It's a big one :

2021-06-02 16:27:36,778 [http-nio-8080-exec-6] ERROR org.apache.turbine.services.velocity.TurbineVelocityService - Class org.nrg.xdat.om.XnatProjectdata.getBundles threw Exception

java.lang.NullPointerException: null

at java.util.Hashtable.put(Hashtable.java:465)

at org.nrg.xdat.om.base.BaseXnatProjectdata.getScanCountByXSIType(BaseXnatProjectdata.java:182)

at org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.java:520)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.doInvoke(UberspectImpl.java:395)

at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:384)

at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:173)

at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:280)

at org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:567)

at org.apache.velocity.runtime.parser.node.ASTExpression.value(ASTExpression.java:71)

at org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:142)

at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:342)

at org.apache.velocity.runtime.directive.Parse.render(Parse.java:260)

at org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:207)

at org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:72)

at org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:87)

at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:342)

at org.apache.velocity.Template.merge(Template.java:356)

at org.apache.velocity.Template.merge(Template.java:260)

at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:339)

at org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:412)

at org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:284)

at org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:74)

at org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:122)

at org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:104)

at org.apache.turbine.modules.Screen.build(Screen.java:60)

at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:110)

at org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:95)

at org.apache.turbine.modules.Layout.build(Layout.java:56)

at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:104)

at org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:149)

at org.apache.turbine.modules.Page.build(Page.java:56)

at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:104)

at org.apache.turbine.Turbine.doGet(Turbine.java:796)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:634)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:741)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:239)

at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:215)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)

at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:317)

at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)

at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)