Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
Robin Kämpe
I'm trying to upgrade our 1.6.5 to 1.7.4. I manage to get to the front page but neither my old 1.6.5 admin account with a custom password nor the admin admin account lets me in. When I try from a remote computer it redirects me to setup but does not display it after 2 tries. On localhost it just says it's the wrong password/credentials.
I think everything looks the same to our other server where I installed 1.7.4 from scratch for training and that server works. I used to deploy it to webapps/xnat but I changed the war file to ROOT.war. Here we go:
from /etc/tdefault7tomcat
# Use "-XX:+UseConcMarkSweepGC" to enable the CMS garbage collector (improved
# response time). If you use that option and you run Tomcat on a machine with
# exactly one CPU chip that contains one or two cores, you should also add
# the "-XX:+CMSIncrementalMode" option.
JAVA_OPTS="-Djava.awt.headless=true -Xms512m -Xmx2g -XX:+UseConcMarkSweepGC -XX:-OmitStackTraceInFastThrow"
JAVA_OPTS="${JAVA_OPTS} -XX:MaxPermSize=512m -XX:+CMSIncrementalMode -XX:+CMSClassUnloadingEnabled"
# To enable remote debugging uncomment the following line.
# You will then be able to use a java debugger on port 8000.
JAVA_OPTS="${JAVA_OPTS} -Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n"
JAVA_OPTS="${JAVA_OPTS} -Dxnat.home=/data/xnat/home"
/etc/tomcat7/server.xml:
......
..... (Changed appBase to webapps from "empty" and unpackWARs and autoDeploy to "true")
<Host name="localhost" appBase="webapps" unpackWARs="true" autoDeploy="true">
<Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
prefix="localhost_access_log." suffix=".txt"
pattern="%h %l %u %t "%r" %s %b" />
</Host>
</Engine>
</Service>
</Server>
xnat@xnatdev:/var/lib/tomcat7$
xnat@xnatdev:/var/lib/tomcat7$ cat /data/xnat/home/config/xnat-conf.properties
datasource.driver=org.postgresql.Driver
datasource.url=jdbc:postgresql://localhost/xnat
datasource.username=xnat
datasource.password=xnat
hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect
hibernate.hbm2ddl.auto=update
hibernate.show_sql=false
hibernate.cache.use_second_level_cache=true
hibernate.cache.use_query_cache=true
xnat@xnatdev:/var/lib/tomcat7$
/data/xnat/home/
├── config
│ └── xnat-conf.properties
├── logs
│ ├── access.log
│ ├── anon.log
│ ├── application.log
│ ├── automation.log
│ ├── avalon.log
│ ├── axis.log
│ ├── configuration.log
│ ├── dicom.log
│ ├── identifiers.log
│ ├── jms.log
│ ├── launch.log
│ ├── orm.log
│ ├── pipeline.log
│ ├── prearchive.log
│ ├── received.log
│ ├── remote.log
│ ├── restlet.log
│ ├── scheduler.log
│ ├── security.log
│ ├── spring.log
│ ├── sql.log
│ ├── tasks.log
│ ├── turbine.log
│ ├── velocity.log
│ ├── xapi.log
│ ├── xdat.log
│ └── xnatfs.log
├── plugins
└── work
├── cache
│ ├── %0044efault%0043atalog%0053ervice%0043ache.data
│ ├── nrg.data
│ ├── org%002ehibernate%002ecache%002einternal%002e%0053tandard%0051uery%0043ache.data
│ └── org%002ehibernate%002ecache%002espi%002e%0055pdate%0054imestamps%0043ache.data
└── xnat_38354699449677791573525152837919
6 directories, 32 files
xnat@xnatdev:/var/lib/tomcat7$
logs: (no error from tomcat7, as I see it)
xnat@xnatdev:/var/lib/tomcat7$ cat logs/catalina.out
Listening for transport dt_socket at address: 8000
Feb 26, 2018 8:25:48 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Feb 26, 2018 8:25:48 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 473 ms
Feb 26, 2018 8:25:48 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Feb 26, 2018 8:25:48 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
Feb 26, 2018 8:25:48 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/ROOT.war
Feb 26, 2018 8:26:31 PM org.apache.catalina.session.StandardManager startInternal
SEVERE: Exception loading sessions from persistent storage
java.lang.NullPointerException
at org.nrg.xft.ItemWrapper.getItem(ItemWrapper.java:212)
at org.nrg.xdat.base.BaseElement.readExternal(BaseElement.java:454)
at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1837)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1796)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
at org.apache.catalina.session.StandardSession.readObject(StandardSession.java:1595)
at org.apache.catalina.session.StandardSession.readObjectData(StandardSession.java:1060)
at org.apache.catalina.session.StandardManager.doLoad(StandardManager.java:282)
at org.apache.catalina.session.StandardManager.load(StandardManager.java:202)
at org.apache.catalina.session.StandardManager.startInternal(StandardManager.java:489)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5476)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1073)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
SOURCE: /var/lib/tomcat7/webapps/ROOT/
Database up to date.
Feb 26, 2018 8:26:44 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 26, 2018 8:26:44 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 56394 ms
From /data/xnat/home/logs: Just when tomcat 7 is booted.
xnat@xnatdev:/data/xnat/home/logs$ cat axis.log
12575 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
12741 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
xnat@xnatdev:/data/xnat/home/logs$
xnat@xnatdev:/data/xnat/home/logs$ cat tasks.log
2018-02-26 20:26:44,880 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - This service is the primary XNAT node, checking whether database updates are required.
2018-02-26 20:26:44,914 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - Initializing database views...
2018-02-26 20:26:48,445 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View initialization complete.
2018-02-26 20:26:48,810 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.AbstractInitializingTask - The system is not yet fully initialized. Delaying execution of the intializing task "System Path Verification" until initialization is completed.
2018-02-26 20:26:50,424 [taskScheduler-1] WARN org.nrg.xnat.initialization.tasks.UpdateConfigurationService - Processed configurations with project set to 12 metadata ID. Can't find a corresponding project.
xnat@xnatdev:/data/xnat/home/logs$
xnat@xnatdev:/data/xnat/home/logs$ cat xdat.log
2018-02-26 20:26:31,926 [localhost-startStop-1] ERROR org.nrg.xft.ItemWrapper -
org.nrg.xft.exception.ElementNotFoundException: Element not found: 'xdat:user'
at org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:189)
at org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:319)
at org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:145)
at org.nrg.xft.XFTItem.NewItem(XFTItem.java:202)
at org.nrg.xft.ItemWrapper.getItem(ItemWrapper.java:208)
at org.nrg.xdat.base.BaseElement.readExternal(BaseElement.java:454)
at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1837)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1796)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370)
at org.apache.catalina.session.StandardSession.readObject(StandardSession.java:1595)
at org.apache.catalina.session.StandardSession.readObjectData(StandardSession.java:1060)
at org.apache.catalina.session.StandardManager.doLoad(StandardManager.java:282)
at org.apache.catalina.session.StandardManager.load(StandardManager.java:202)
at org.apache.catalina.session.StandardManager.startInternal(StandardManager.java:489)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5476)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1073)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
xnat@xnatdev:/data/xnat/home/logs$
Changes that occur when I try to login using admin admin.
xnat@xnatdev:/data/xnat/home/logs$ cat access.log
2018-02-26 20:38:22,921 - admin 10.208.19.39 Authentication SUCCESS
2018-02-26 20:38:23,075 - admin 10.208.19.39 Authentication FAILED
xnat@xnatdev:/data/xnat/home/logs$
Then I try my old 1.6.5 account and:
xnat@xnatdev:/data/xnat/home/logs$ cat access.log
2018-02-26 20:38:22,921 - admin 10.208.19.39 Authentication SUCCESS
2018-02-26 20:38:23,075 - admin 10.208.19.39 Authentication FAILED
2018-02-26 20:39:58,922 - admin 10.208.19.39 Authentication SUCCESS
It seems like it suceeds? But I get
http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm
and
http://10.208.21.252/setup
With "The page isn’t redirecting properly" in the browser.
What could be wrong?
Robin Kämpe
xnat@xnatdev:~$ cat /etc/tomcat7/server.xml
<?xml version='1.0' encoding='utf-8'?>
<!--
Licensed to the Apache Software Foundation (ASF) under one or more
contributor license agreements. See the NOTICE file distributed with
this work for additional information regarding copyright ownership.
The ASF licenses this file to You under the Apache License, Version 2.0
(the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-->
<!-- Note: A "Server" is not itself a "Container", so you may not
define subcomponents such as "Valves" at this level.
Documentation at /docs/config/server.html
-->
<Server port="8005" shutdown="SHUTDOWN">
<!-- Security listener. Documentation at /docs/config/listeners.html
<Listener className="org.apache.catalina.security.SecurityListener" />
-->
<!--APR library loader. Documentation at /docs/apr.html -->
<!--
<Listener className="org.apache.catalina.core.AprLifecycleListener" SSLEngine="on" />
-->
<!--Initialize Jasper prior to webapps are loaded. Documentation at /docs/jasper-howto.html -->
<Listener className="org.apache.catalina.core.JasperListener" />
<!-- Prevent memory leaks due to use of particular java/javax APIs-->
<Listener className="org.apache.catalina.core.JreMemoryLeakPreventionListener" />
<Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener" />
<Listener className="org.apache.catalina.core.ThreadLocalLeakPreventionListener" />
<!-- Global JNDI resources
Documentation at /docs/jndi-resources-howto.html
-->
<GlobalNamingResources>
<!-- Editable user database that can also be used by
UserDatabaseRealm to authenticate users
-->
<Resource name="UserDatabase" auth="Container"
type="org.apache.catalina.UserDatabase"
description="User database that can be updated and saved"
factory="org.apache.catalina.users.MemoryUserDatabaseFactory"
pathname="conf/tomcat-users.xml" />
</GlobalNamingResources>
<!-- A "Service" is a collection of one or more "Connectors" that share
a single "Container" Note: A "Service" is not itself a "Container",
so you may not define subcomponents such as "Valves" at this level.
Documentation at /docs/config/service.html
-->
<Service name="Catalina">
<!--The connectors can use a shared executor, you can define one or more named thread pools-->
<!--
<Executor name="tomcatThreadPool" namePrefix="catalina-exec-"
maxThreads="150" minSpareThreads="4"/>
-->
<!-- A "Connector" represents an endpoint by which requests are received
and responses are returned. Documentation at :
Java HTTP Connector: /docs/config/http.html (blocking & non-blocking)
Java AJP Connector: /docs/config/ajp.html
APR (HTTP/AJP) Connector: /docs/apr.html
Define a non-SSL HTTP/1.1 Connector on port 8080
-->
<Connector port="8080" protocol="HTTP/1.1"
connectionTimeout="20000"
URIEncoding="UTF-8"
redirectPort="8443" />
<!-- A "Connector" using the shared thread pool-->
<!--
<Connector executor="tomcatThreadPool"
port="8080" protocol="HTTP/1.1"
connectionTimeout="20000"
redirectPort="8443" />
-->
<!-- Define a SSL HTTP/1.1 Connector on port 8443
This connector uses the JSSE configuration, when using APR, the
connector should be using the OpenSSL style configuration
described in the APR documentation -->
<!--
<Connector port="8443" protocol="HTTP/1.1" SSLEnabled="true"
maxThreads="150" scheme="https" secure="true"
clientAuth="false" sslProtocol="TLS" />
-->
<!-- Define an AJP 1.3 Connector on port 8009 -->
<!--
<Connector port="8009" protocol="AJP/1.3" redirectPort="8443" />
-->
<!-- An Engine represents the entry point (within Catalina) that processes
every request. The Engine implementation for Tomcat stand alone
analyzes the HTTP headers included with the request, and passes them
on to the appropriate Host (virtual host).
Documentation at /docs/config/engine.html -->
<!-- You should set jvmRoute to support load-balancing via AJP ie :
<Engine name="Catalina" defaultHost="localhost" jvmRoute="jvm1">
-->
<Engine name="Catalina" defaultHost="localhost">
<!--For clustering, please take a look at documentation at:
/docs/cluster-howto.html (simple how to)
/docs/config/cluster.html (reference documentation) -->
<!--
<Cluster className="org.apache.catalina.ha.tcp.SimpleTcpCluster"/>
-->
<!-- Use the LockOutRealm to prevent attempts to guess user passwords
via a brute-force attack -->
<Realm className="org.apache.catalina.realm.LockOutRealm">
<!-- This Realm uses the UserDatabase configured in the global JNDI
resources under the key "UserDatabase". Any edits
that are performed against this UserDatabase are immediately
available for use by the Realm. -->
<Realm className="org.apache.catalina.realm.UserDatabaseRealm"
resourceName="UserDatabase"/>
</Realm>
<Host name="localhost" appBase="webapps" unpackWARs="true" autoDeploy="true">
<Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
prefix="localhost_access_log." suffix=".txt"
pattern="%h %l %u %t "%r" %s %b" />
</Host>
</Engine>
</Service>
</Server>
Robin Kämpe
xnat@xnatdev:~$ sudo lsof -i TCP:8080
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
java 9434 xnat 43u IPv6 56470 0t0 TCP *:http-alt (LISTEN)
xnat@xnatdev:~$ sudo service tomcat7 status
* Tomcat servlet engine is running with pid 9434
xnat@xnatdev:~$
This is a little too little output right? My working server says this:
sudo service tomcat7 status
xnat@Vader:~$ sudo service tomcat7 status
Loaded: loaded (/etc/init.d/tomcat7; bad; vendor preset: enabled)
Docs: man:systemd-sysv-generator(8)
Process: 22707 ExecStop=/etc/init.d/tomcat7 stop (code=exited, status=0/SUCCESS)
Process: 1085 ExecStart=/etc/init.d/tomcat7 start (code=exited, status=0/SUCCESS)
CGroup: /system.slice/tomcat7.service
└─1142 /usr/lib/jvm/java-8-openjdk-
feb 05 11:17:14 Vader systemd[1]: Starting LSB: Start Tomcat....
feb 05 11:17:14 Vader tomcat7[1085]: * Starting Tomcat servlet engine tomcat7
feb 05 11:17:19 Vader tomcat7[1085]: ...done.
feb 05 11:17:19 Vader systemd[1]: Started LSB: Start Tomcat..
lines 1-13/13 (END)
McKay, Mike
Sorry, I just responded before I saw your earlier post, so I deleted that response. On the server where you tried to upgrade from XNAT 1.6.5 to 1.7.4, is the war currently named ROOT.war? If so, could you try shutting down Tomcat, renaming webapps/ROOT.war to webapps/xnat.war, deleting webapps/ROOT, and starting Tomcat? I wonder if trying to change the XNAT URL at the same time as upgrading is causing issues for you.
-Mike
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Robin Kämpe
Well, that is what I did the first time but that took me to the address:
http://my_ip/app/template/Login.vm
and just displays a white page with no text. That is why I changed it to root and then I got the login page but experienced the issues I listed above. Now the logs look like this:
xnat@xnatdev:/data/xnat/home/logs$ sudo lsof -i TCP:8080
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
xnat@xnatdev:/data/xnat/home/logs$
xnat@xnatdev:/data/xnat/home/logs$ sudo service tomcat7 status
* Tomcat servlet engine is running with pid 3375
xnat@xnatdev:/data/xnat/home/logs$
xnat@xnatdev:/data/xnat/home/logs$ ls -l /var/lib/tomcat7/webapps/
total 187536
drwxr-xr-x 18 xnat xnat 4096 Mar 1 15:00 xnat
-rwxr-xr-x 1 xnat xnat 192027012 Mar 1 14:59 xnat.war
xnat@xnatdev:/data/xnat/home/logs$
6 directories, 32 files
xnat@xnatdev:/var/lib/tomcat7/webapps$
Catalina.out
xnat@xnatdev:/var/lib/tomcat7/webapps$ cat ../logs/catalina.out
WARNING: Problem with directory [/usr/share/tomcat7/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Mar 01, 2018 2:59:51 PM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat7/shared], exists: [false], isDirectory: [false], canRead: [false]
Mar 01, 2018 2:59:51 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-bio-8080"]
Mar 01, 2018 2:59:51 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 506 ms
Mar 01, 2018 2:59:51 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Mar 01, 2018 2:59:51 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.52 (Ubuntu)
INFO: Deploying web application archive /var/lib/tomcat7/webapps/xnat.war
SOURCE: /var/lib/tomcat7/webapps/xnat/
===========================
Database out of date... updating
ALTER TABLE xnat_imageScanData_history ADD COLUMN scanner_softwareversion VARCHAR(255);
--Database column prov_processStep.cvs is no longer required.
ALTER TABLE prov_processStep ALTER COLUMN cvs DROP NOT NULL;
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_echospacing FLOAT;
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_pmc VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_inplanephaseencoding_polarityswap VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_diffusion_refocusflipangle VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_inplanephaseencoding_directionpositive VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_diffusion_bmax VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_phaseencodingdirection VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_acqtime VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_deltate FLOAT;
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_coilelements VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_subjectposition VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_inplanephaseencoding_direction VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_readoutsamplespacing VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN filenameuuid VARCHAR(255);
ALTER TABLE xnat_mrScanData_history ADD COLUMN parameters_inplanephaseencoding_rotation VARCHAR(255);
ALTER TABLE xnat_projectData_history ADD COLUMN type VARCHAR(255);
CREATE TABLE xnat_dicomCodedValue_meta_data (
xft_version VARCHAR(255)
, last_modified TIMESTAMP
, status VARCHAR(255)
, activation_date TIMESTAMP
, row_last_modified TIMESTAMP
, insert_date TIMESTAMP
, activation_user_xdat_user_id INTEGER
, insert_user_xdat_user_id INTEGER
, origin VARCHAR(255)
, modified INTEGER
, shareable INTEGER
, meta_data_id serial NOT NULL
, PRIMARY KEY (meta_data_id) ) WITH OIDS;
CREATE TABLE xnat_dicomCodedValue (
value VARCHAR(255)
, designator VARCHAR(255)
, version VARCHAR(255)
, meaning VARCHAR(255)
, dicomCodedValue_info INTEGER
, xnat_dicomcodedvalue_id serial NOT NULL
, PRIMARY KEY (xnat_dicomcodedvalue_id) ) WITH OIDS;
CREATE TABLE xnat_algorithm_history (
source VARCHAR(255)
, change_user INTEGER
, name VARCHAR(255)
, algorithm_info INTEGER
, previous_change_date TIMESTAMP
, namecode_xnat_dicomcodedvalue_id INTEGER
, version VARCHAR(255)
, history_id serial NOT NULL
, xnat_algorithm_id INTEGER
, family_xnat_dicomcodedvalue_id INTEGER
, parameters TEXT
, xft_version INTEGER
, change_date TIMESTAMP
, new_row_xnat_algorithm_id INTEGER
, PRIMARY KEY (history_id) ) WITH OIDS;
CREATE TABLE xnat_algorithm_meta_data (
xft_version VARCHAR(255)
, last_modified TIMESTAMP
, status VARCHAR(255)
, activation_date TIMESTAMP
, row_last_modified TIMESTAMP
, insert_date TIMESTAMP
, activation_user_xdat_user_id INTEGER
, insert_user_xdat_user_id INTEGER
, origin VARCHAR(255)
, modified INTEGER
, shareable INTEGER
, meta_data_id serial NOT NULL
, PRIMARY KEY (meta_data_id) ) WITH OIDS;
CREATE TABLE xnat_algorithm (
family_xnat_dicomcodedvalue_id INTEGER NOT NULL
, name VARCHAR(255)
, version VARCHAR(255)
, source VARCHAR(255)
, parameters TEXT
, namecode_xnat_dicomcodedvalue_id INTEGER
, algorithm_info INTEGER
, xnat_algorithm_id serial NOT NULL
, PRIMARY KEY (xnat_algorithm_id) ) WITH OIDS;
CREATE TABLE xnat_dicomCodedValue_history (
meaning VARCHAR(255)
, change_user INTEGER
, previous_change_date TIMESTAMP
, designator VARCHAR(255)
, xnat_dicomcodedvalue_id INTEGER
, dicomcodedvalue_info INTEGER
, version VARCHAR(255)
, history_id serial NOT NULL
, value VARCHAR(255)
, xft_version INTEGER
, change_date TIMESTAMP
, new_row_xnat_dicomcodedvalue_id INTEGER
, PRIMARY KEY (history_id) ) WITH OIDS;
ALTER TABLE xnat_ctScanData_history ADD COLUMN parameters_subjectposition VARCHAR(255);
ALTER TABLE xnat_imageScanData ADD COLUMN scanner_softwareversion VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN filenameuuid VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_subjectposition VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_deltate FLOAT;
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_readoutsamplespacing VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_coilelements VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_echospacing FLOAT;
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_phaseencodingdirection VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_acqtime VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_diffusion_bmax VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_diffusion_refocusflipangle VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_inplanephaseencoding_direction VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_inplanephaseencoding_rotation VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_inplanephaseencoding_polarityswap VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_inplanephaseencoding_directionpositive VARCHAR(255);
ALTER TABLE xnat_mrScanData ADD COLUMN parameters_pmc VARCHAR(255);
ALTER TABLE xnat_ctScanData ADD COLUMN parameters_subjectposition VARCHAR(255);
ALTER TABLE xnat_projectData ADD COLUMN type VARCHAR(255);
--Existing column has no values or constraints.
--Fix val_protocolData_condition_history table.
ALTER TABLE val_protocolData_condition_history DROP COLUMN verified;
ALTER TABLE val_protocolData_condition_history ADD COLUMN verified TEXT;
--Fix val_protocolData_condition table.
ALTER TABLE val_protocolData_condition DROP COLUMN verified;
ALTER TABLE val_protocolData_condition ADD COLUMN verified TEXT;
--Existing column has no values or constraints.
--Fix val_protocolData_scan_check_condition_history table.
ALTER TABLE val_protocolData_scan_check_condition_history DROP COLUMN verified;
ALTER TABLE val_protocolData_scan_check_condition_history ADD COLUMN verified TEXT;
--Fix val_protocolData_scan_check_condition table.
ALTER TABLE val_protocolData_scan_check_condition DROP COLUMN verified;
ALTER TABLE val_protocolData_scan_check_condition ADD COLUMN verified TEXT;
ALTER TABLE xnat_dicomCodedValue_meta_data
ADD FOREIGN KEY (activation_user_xdat_user_id) REFERENCES xdat_user(xdat_user_id) ON DELETE SET NULL ON UPDATE CASCADE;
ALTER TABLE xnat_dicomCodedValue_meta_data
ADD FOREIGN KEY (insert_user_xdat_user_id) REFERENCES xdat_user(xdat_user_id) ON DELETE SET NULL ON UPDATE CASCADE;
CREATE INDEX xnat_dicomcodedvalue_meta_data_insert_user_xdat_user_id1 ON xnat_dicomCodedValue_meta_data(insert_user_xdat_user_id);
CREATE INDEX xnat_dicomcodedvalue_meta_data_activation_user_xdat_user_1_hash ON xnat_dicomCodedValue_meta_data USING HASH (activation_user_xdat_user_id);
CREATE INDEX xnat_dicomcodedvalue_meta_data_activation_user_xdat_user_1 ON xnat_dicomCodedValue_meta_data(activation_user_xdat_user_id);
CREATE INDEX xnat_dicomcodedvalue_meta_data_insert_user_xdat_user_id1_hash ON xnat_dicomCodedValue_meta_data USING HASH (insert_user_xdat_user_id);
CREATE INDEX xnat_dicomcodedvalue_meta_data_meta_data_id1_hash ON xnat_dicomCodedValue_meta_data USING HASH (meta_data_id);
ALTER TABLE xnat_dicomCodedValue
ADD FOREIGN KEY (dicomCodedValue_info) REFERENCES xnat_dicomCodedValue_meta_data(meta_data_id) ON DELETE SET NULL ON UPDATE CASCADE;
CREATE INDEX xnat_dicomcodedvalue_xnat_dicomcodedvalue_id1_hash ON xnat_dicomCodedValue USING HASH (xnat_dicomcodedvalue_id);
CREATE INDEX xnat_dicomcodedvalue_dicomcodedvalue_info1_hash ON xnat_dicomCodedValue USING HASH (dicomCodedValue_info);
CREATE INDEX xnat_dicomcodedvalue_dicomcodedvalue_info1 ON xnat_dicomCodedValue(dicomCodedValue_info);
ALTER TABLE xnat_algorithm_meta_data
ADD FOREIGN KEY (activation_user_xdat_user_id) REFERENCES xdat_user(xdat_user_id) ON DELETE SET NULL ON UPDATE CASCADE;
ALTER TABLE xnat_algorithm_meta_data
ADD FOREIGN KEY (insert_user_xdat_user_id) REFERENCES xdat_user(xdat_user_id) ON DELETE SET NULL ON UPDATE CASCADE;
CREATE INDEX xnat_algorithm_meta_data_meta_data_id1_hash ON xnat_algorithm_meta_data USING HASH (meta_data_id);
CREATE INDEX xnat_algorithm_meta_data_activation_user_xdat_user_id1 ON xnat_algorithm_meta_data(activation_user_xdat_user_id);
CREATE INDEX xnat_algorithm_meta_data_insert_user_xdat_user_id1_hash ON xnat_algorithm_meta_data USING HASH (insert_user_xdat_user_id);
CREATE INDEX xnat_algorithm_meta_data_insert_user_xdat_user_id1 ON xnat_algorithm_meta_data(insert_user_xdat_user_id);
CREATE INDEX xnat_algorithm_meta_data_activation_user_xdat_user_id1_hash ON xnat_algorithm_meta_data USING HASH (activation_user_xdat_user_id);
ALTER TABLE xnat_algorithm
ADD FOREIGN KEY (family_xnat_dicomcodedvalue_id) REFERENCES xnat_dicomCodedValue(xnat_dicomcodedvalue_id) ON DELETE CASCADE ON UPDATE CASCADE;
ALTER TABLE xnat_algorithm
ADD FOREIGN KEY (namecode_xnat_dicomcodedvalue_id) REFERENCES xnat_dicomCodedValue(xnat_dicomcodedvalue_id) ON DELETE SET NULL ON UPDATE CASCADE;
ALTER TABLE xnat_algorithm
ADD FOREIGN KEY (algorithm_info) REFERENCES xnat_algorithm_meta_data(meta_data_id) ON DELETE SET NULL ON UPDATE CASCADE;
CREATE INDEX xnat_algorithm_xnat_algorithm_id1_hash ON xnat_algorithm USING HASH (xnat_algorithm_id);
CREATE INDEX xnat_algorithm_algorithm_info1 ON xnat_algorithm(algorithm_info);
CREATE INDEX xnat_algorithm_namecode_xnat_dicomcodedvalue_id1 ON xnat_algorithm(namecode_xnat_dicomcodedvalue_id);
CREATE INDEX xnat_algorithm_family_xnat_dicomcodedvalue_id1_hash ON xnat_algorithm USING HASH (family_xnat_dicomcodedvalue_id);
CREATE INDEX xnat_algorithm_family_xnat_dicomcodedvalue_id1 ON xnat_algorithm(family_xnat_dicomcodedvalue_id);
CREATE INDEX xnat_algorithm_algorithm_info1_hash ON xnat_algorithm USING HASH (algorithm_info);
CREATE INDEX xnat_algorithm_namecode_xnat_dicomcodedvalue_id1_hash ON xnat_algorithm USING HASH (namecode_xnat_dicomcodedvalue_id);
===========================
Mar 01, 2018 3:00:56 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Mar 01, 2018 3:00:57 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 65370 ms
xnat@xnatdev:/var/lib/tomcat7/webapps$
Xnat home directory logs
These were empty before I tried to reach the page. Post trying to reach the page:
xnat@xnatdev:/data/xnat/home/logs$ cat axis.log
2654 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
2831 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
xnat@xnatdev:/data/xnat/home/logs$
xnat@xnatdev:/data/xnat/home/logs$ cat tasks.log
2018-03-01 15:00:58,900 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - Drop views step complete. Begin rebuilding views.
2018-03-01 15:00:59,831 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View rebuild complete.
2018-03-01 15:01:00,103 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.AbstractInitializingTask - The system is not yet fully initialized. Delaying execution of the intializing task "System Path Verification" until initialization is completed.
2018-03-01 15:01:01,776 [taskScheduler-1] WARN org.nrg.xnat.initialization.tasks.UpdateConfigurationService - Processed configurations with project set to 12 metadata ID. Can't find a corresponding project.
xnat@xnatdev:/data/xnat/home/logs$
xnat@xnatdev:/data/xnat/home/logs$ cat xdat.log
2018-03-01 15:00:54,121 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-01 15:00:54,121 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_launch_request_event_id_seq
2018-03-01 15:00:54,121 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET DEFAULT nextval('xhbm_script_launch_request_event_id_seq')
2018-03-01 15:00:54,121 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET NOT NULL
2018-03-01 15:00:54,121 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_launch_request_event_id_seq OWNED BY xhbm_script_launch_request_event.id
2018-03-01 15:00:54,129 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_launch_request_event and got the value 1
2018-03-01 15:00:54,129 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_launch_request_event_id_seq', 1) AS value
2018-03-01 15:00:54,130 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_aud to use sequence for default value.
2018-03-01 15:00:54,130 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-01 15:00:54,130 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_aud_id_seq
2018-03-01 15:00:54,130 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET DEFAULT nextval('xhbm_script_aud_id_seq')
2018-03-01 15:00:54,130 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET NOT NULL
2018-03-01 15:00:54,130 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_aud_id_seq OWNED BY xhbm_script_aud.id
2018-03-01 15:00:54,135 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_aud and got the value 1
2018-03-01 15:00:54,135 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_aud_id_seq', 1) AS value
Perhaps I could try with a default server.xml file but don't know where to find one...
To check I also tried to rename it back to ROOT.war and I got the old problem...
I restored to my previous snapshot of the working 1.6.5 now, until I head back.
So strange... In the current machine it works with xnat.war (using the Ddeploy method). When I try to upgrade with the .war file it gives me a white page using xnat.war. using ROOT.war it gives me the xnat page but won't give me the setup page once I give it the corret login info:
using the admin admin login gives me a wrong credentials password. Using my custom admin admin-password seems to be correct but it's not able to present the setup page.
Really appreciate your help!
Robin Kämpe
Or is there anything I can try?
Thanks anyone! Really need to upgrade before I try to learn how to add new data types which is our next infrastructural step.
Michael McKay
Robin Kämpe
The thing is that the login seems to be OK since it takes me to the /setup page but it does not display it (using ROOT.war). Using xnat.war it just gives me a blank page. In the current xnat 1.6.5 build it is using xnat as the webapp name.
The only purpose of my upgrade is so that the database is upgraded so that I can export it to another server where an empty installation of xnat 1.7.4 is running right on the machine (I want to move away from using the WM where our current XNAT 1.6.5 is running). Even though I cannot log in, do you think the database upgrade is fine/complete? In that case I can just do pg_dump in the WM and pg_restore on the local server to "move" our xnat (database) to the new local install. Then I don't have to dig further into this. That is, if the upgrade is done updating the tables without a successful login. Hope that is the case?
Michael McKay
Robin Kämpe
I'm not very used to dealing with sql and databases, sorry. Can you tell me how I would do this?
Thanks for your patience!
Robin Kämpe
Michael McKay
Robin Kämpe
On my empty 1.7.5 clean install the command gives me:
xnat=> SELECT value FROM xhbm_preference WHERE name='initialized';
value
-------
true
(1 row)
On the upgraded WM it gives me:
xnat=> SELECT value FROM xhbm_preference WHERE name='initialized';
value
-------
false
(1 row)
I guess that means the upgrade was not complete...
What should work? The ROOT.war or the xnat.war? ROOT gets the correct login but takes me to a redirection error. Also true on localhost. Would xnat.war work if I kept the row in server.xml that says context path = /var/lib/tomcat7/webapps/xnat? Allthough I have heard xnat 1.7.5 should not need this.
Michael McKay
insert into xdat_r_xdat_role_type_assign_xdat_user (xdat_user_xdat_user_id,xdat_role_type_role_name) values ((select xdat_user_id from xdat_user where login = 'mike'),'Administrator');
update xdat_user set enabled=1, verified=1 where login = 'mike';
-Mikedelete from xs_item_cache where contents like '%mike%';
Robin Kämpe
Since I can't even get the login screen with xnat.war I will try it with ROOT.war. Would this work with the admin account as well?
So I would run:
psql
-->xnat....
insert into xdat_r_xdat_role_type_assign_xdat_user (xdat_user_xdat_user_id,xdat_role_type_role_name) values ((select xdat_user_id from xdat_user where login = 'admin'),'Administrator');update xdat_user set enabled=1, verified=1 where login = 'admin';
delete from xs_item_cache where contents like '%admin%';
Alltough, the login seems to work. It's the re-direct part that seems to fail (when using ROOT.war).
McKay, Mike
Yes, it would work with the admin account as you described. I would expect problems if you logged in and were redirected to the setup page as a user that was not an administrator. It probably won't fix your issue, but I want to be able to rule out that there's something that got messed up with your user accounts that is causing the setup page not to load.
-Mike
Sent: Wednesday, March 7, 2018 4:25:03 PM
To: xnat_discussion
Subject: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
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Robin Kämpe
xnat@xnatdev:/var/lib/tomcat7/logs$ psql
xnat=> insert into xdat_r_xdat_role_type_assign_xdat_user (xdat_user_xdat_user_id,xdat_role_type_role_name) values ((select xdat_user_id from xdat_user where login = 'admin'),'Administrator');
INSERT 0 1
xnat=> update xdat_user set enabled=1, verified=1 where login = 'admin';
UPDATE 1
xnat=> delete from xs_item_cache where contents like '%admin%';
DELETE 2
xnat=> \q
xnat@xnatdev:/var/lib/tomcat7/logs$ clear
Still gives me this in browser:
The page isn’t redirecting properly
This problem can sometimes be caused by disabling or refusing to accept cookies.
And this:
xnat=> SELECT value FROM xhbm_preference WHERE name='initialized';
value
-------
false
(1 row)
Tried to change to xnat.war also. Same problem. Did this bring you any usefull info?
I get a lot of these in the xnat log called security.log:
2018-03-08 09:40:45,384 [http-bio-8080-exec-7] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-08 09:40:45,559 [http-bio-8080-exec-9] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-08 09:40:45,708 [http-bio-8080-exec-2] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-08 09:40:45,828 [http-bio-8080-exec-4] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-08 09:40:45,959 [http-bio-8080-exec-10] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-08 09:40:46,067 [http-bio-8080-exec-8] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
And in the access log I get:
nat@xnatdev:/var/lib/tomcat7/webapps$ cat /data/xnat/home/logs/access.log
2018-03-08 09:40:45,029 - admin 10.208.19.39 Authentication SUCCESS
2018-03-08 09:50:46,763 - admin 10.208.19.39 Authentication SUCCESS
2018-03-08 09:50:54,635 - admin 127.0.0.1 Authentication SUCCESS
So the login seems to work, right? But it cannot re-direct me?!
:)
Michael McKay
Robin Kämpe
xnat=> SELECT value FROM xhbm_preference WHERE name='siteUrl';
ERROR: relation "xhbm_preference" does not exist
LINE 1: SELECT value FROM xhbm_preference WHERE name='siteUrl';
(I guess the old version of the db does not have the same variable names?)
Other Clean Install 1.7.4 (where we want to move the WM db after upgrade):
xnat@Vader:~$ psql
psql (10.1, server 9.3.20)
Type "help" for help.
xnat=> SELECT value FROM xhbm_preference WHERE name='siteUrl';
value
----------------------
http://10.208.21.31/
(1 row)
Post Upgrade WM 1.6.5 --- > 1.7.4 (using ROOT.war)
LINE 1: xnat@Vader:~$ psql
xnat=> value
xnat-> ----------------------
xnat-> http://10.208.21.31/
xnat-> (1 row)
xnat->
This is not the correct IP. This is the IP of the host machine (as you saw above). It should be the ip of the WM: 10.208.21.252. Although, you can reach the login-page via the correct IP (10.208.21.252). This seems like an important piece of the puzzle. What should I do? What can I do?
Btw, you get the same url 10.208.21.31 if you use xnat.war instead of ROOT.war.
McKay, Mike
I'd try shutting down Tomcat, fixing the value in the database ( UPDATE xhbm_preference SET value = 'http://10.208.21.252/' WHERE name='siteUrl'; ), restarting Tomcat and logging in.
The siteUrl shouldn't affect whether the login page shows up. But once a user is logged in, the siteUrl is used in figuring out what URLs to direct the user to. This could be the cause of your issues.
-Mike
To: xnat_discussion
Subject: Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
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Robin Kämpe
After the update of the url and re-start of tomcat I go get the correct IP:
xnat=> SELECT value FROM xhbm_preference WHERE name='siteUrl';
value
http://10.208.21.252/
(1 row)
But I still get the re-direction error when beeing re-directed to http://10.208.21.252/setup
Not that confuses me... I think the xnat-logs look similar... It felt like that url issue would be it?...
xnat@xnatdev:/data/xnat/home/logs$ cat access.log
2018-03-12 20:08:02,085 - admin 10.208.19.39 Authentication SUCCESS
2018-03-12 20:11:13,418 - admin 10.208.19.39 Authentication SUCCESS
2018-03-12 20:12:11,576 - admin 10.208.19.39 Authentication SUCCESS
xnat@xnatdev:/data/xnat/home/logs$ cat axis.log
3015 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
3289 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
12565 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
12729 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
xnat@xnatdev:/data/xnat/home/logs$ cat jms.log
2018-03-12 20:08:15,073 Encountered a JMSException - resetting the underlying JMS Connection
javax.jms.JMSException: Broker has been stopped: org.apache.activemq.broker.BrokerService$5@524bce9c
at org.apache.activemq.util.JMSExceptionSupport.create(JMSExceptionSupport.java:49)
at org.apache.activemq.ActiveMQConnection.onAsyncException(ActiveMQConnection.java:1949)
at org.apache.activemq.ActiveMQConnection$3$1.run(ActiveMQConnection.java:1869)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
at org.apache.activemq.broker.ErrorBroker.getBrokerService(ErrorBroker.java:252)
at org.apache.activemq.broker.MutableBrokerFilter.getBrokerService(MutableBrokerFilter.java:261)
at org.apache.activemq.broker.region.Queue.isSlave(Queue.java:1712)
at org.apache.activemq.broker.region.Queue.removeSubscription(Queue.java:583)
at org.apache.activemq.broker.region.AbstractRegion.removeConsumer(AbstractRegion.java:381)
at org.apache.activemq.broker.region.RegionBroker.removeConsumer(RegionBroker.java:445)
at org.apache.activemq.broker.BrokerFilter.removeConsumer(BrokerFilter.java:117)
at org.apache.activemq.advisory.AdvisoryBroker.removeConsumer(AdvisoryBroker.java:254)
at org.apache.activemq.broker.BrokerFilter.removeConsumer(BrokerFilter.java:117)
at org.apache.activemq.broker.BrokerFilter.removeConsumer(BrokerFilter.java:117)
at org.apache.activemq.broker.MutableBrokerFilter.removeConsumer(MutableBrokerFilter.java:123)
at org.apache.activemq.broker.TransportConnection.processRemoveConsumer(TransportConnection.java:593)
at org.apache.activemq.command.RemoveInfo.visit(RemoveInfo.java:76)
at org.apache.activemq.broker.TransportConnection.service(TransportConnection.java:294)
at org.apache.activemq.broker.TransportConnection$1.onCommand(TransportConnection.java:152)
at org.apache.activemq.transport.ResponseCorrelator.onCommand(ResponseCorrelator.java:116)
at org.apache.activemq.transport.MutexTransport.onCommand(MutexTransport.java:50)
at org.apache.activemq.transport.vm.VMTransport.iterate(VMTransport.java:241)
at org.apache.activemq.thread.PooledTaskRunner.runTask(PooledTaskRunner.java:129)
at org.apache.activemq.thread.PooledTaskRunner$1.run(PooledTaskRunner.java:47)
... 3 more
xnat@xnatdev:/data/xnat/home/logs$ cat security.log
2018-03-12 20:08:02,480 [http-bio-8080-exec-10] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:02,613 [http-bio-8080-exec-9] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:02,735 [http-bio-8080-exec-4] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:02,858 [http-bio-8080-exec-7] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:03,001 [http-bio-8080-exec-3] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:03,144 [http-bio-8080-exec-1] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:03,272 [http-bio-8080-exec-2] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:05,443 [http-bio-8080-exec-7] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:05,560 [http-bio-8080-exec-10] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:05,688 [http-bio-8080-exec-9] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:05,800 [http-bio-8080-exec-4] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:05,899 [http-bio-8080-exec-7] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:06,044 [http-bio-8080-exec-3] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:08:06,171 [http-bio-8080-exec-1] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:11:13,764 [http-bio-8080-exec-7] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:11:13,914 [http-bio-8080-exec-10] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:11:14,022 [http-bio-8080-exec-5] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:11:14,122 [http-bio-8080-exec-3] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:11:14,226 [http-bio-8080-exec-6] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:11:14,319 [http-bio-8080-exec-4] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:11:14,405 [http-bio-8080-exec-1] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:12:11,840 [http-bio-8080-exec-6] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:12:11,986 [http-bio-8080-exec-8] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:12:12,174 [http-bio-8080-exec-9] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:12:12,332 [http-bio-8080-exec-2] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:12:12,472 [http-bio-8080-exec-10] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:12:12,625 [http-bio-8080-exec-3] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:12:12,742 [http-bio-8080-exec-1] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:14:37,227 [http-bio-8080-exec-6] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:14:37,353 [http-bio-8080-exec-8] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:14:37,657 [http-bio-8080-exec-9] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:14:37,777 [http-bio-8080-exec-2] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:14:37,871 [http-bio-8080-exec-10] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:14:37,961 [http-bio-8080-exec-3] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
2018-03-12 20:14:38,088 [http-bio-8080-exec-1] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/setup
xnat@xnatdev:/data/xnat/home/logs$ cat tasks.log
2018-03-12 20:11:05,060 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - This service is the primary XNAT node, checking whether database updates are required.
2018-03-12 20:11:05,075 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - Initializing database views...
2018-03-12 20:11:09,699 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View initialization complete.
2018-03-12 20:11:09,848 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.AbstractInitializingTask - The system is not yet fully initialized. Delaying execution of the intializing task "System Path Verification" until initialization is completed.
2018-03-12 20:11:11,215 [taskScheduler-1] WARN org.nrg.xnat.initialization.tasks.UpdateConfigurationService - Processed configurations with project set to 12 metadata ID. Can't find a corresponding project.
xnat@xnatdev:/data/xnat/home/logs$
xnat@xnatdev:/data/xnat/home/logs$ cat xdat.log
2018-03-12 20:07:26,756 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-12 20:07:26,756 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_launch_request_event_id_seq
2018-03-12 20:07:26,756 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET DEFAULT nextval('xhbm_script_launch_request_event_id_seq')
2018-03-12 20:07:26,756 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET NOT NULL
2018-03-12 20:07:26,756 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_launch_request_event_id_seq OWNED BY xhbm_script_launch_request_event.id
2018-03-12 20:07:26,770 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_launch_request_event and got the value 1
2018-03-12 20:07:26,770 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_launch_request_event_id_seq', 1) AS value
2018-03-12 20:07:26,771 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_aud to use sequence for default value.
2018-03-12 20:07:26,771 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-12 20:07:26,771 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_aud_id_seq
2018-03-12 20:07:26,771 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET DEFAULT nextval('xhbm_script_aud_id_seq')
2018-03-12 20:07:26,771 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET NOT NULL
2018-03-12 20:07:26,771 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_aud_id_seq OWNED BY xhbm_script_aud.id
2018-03-12 20:07:26,775 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_aud and got the value 1
2018-03-12 20:07:26,775 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_aud_id_seq', 1) AS value
2018-03-12 20:10:51,628 [localhost-startStop-1] ERROR org.nrg.xft.ItemWrapper -
Robin Kämpe
They said that they "fixed" it by manually setting initialized to true in the database after upgrade. This did however cause other issues:
MarkC
Robin Kämpe
No more ideas after the info from the previous two posts with info?
Thanks...
McKay, Mike
You can try manually setting initialized to true, but as mentioned in that other thread, doing so can lead to other issues.
When you get the redirection error, what do you see in your Network tab in developer tools (F12 in Chrome or ctrl+shift+E in Firefox)?
-Mike
To: xnat_discussion
Subject: Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
No more ideas after the info from the previous two posts with info?
Thanks...
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Robin Kämpe
Tested this. So first, when I went to the ip in the adress-bar (10.208.21.252) as I normally do on the 1.6.5. version it took me to the white empty screen (same problem as before).
But when I tested to put in "10.208.21.252/xnat" (after I changed the url) I managed to come to the login screen! Just like when I use ROOT.war.
When I give it the correct password for the admin account I get en error. Before (ROOT.war) it said re-direction error. Now it just gives me the white screen (as when I used xnat.war and just used the ip trying to reach the login scrreen). It tries to take me here http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm. It has a double // where xnat should(?) be? If I manually add that: http://10.208.21.252/xnat/app/template/XDATScreen_UpdateUser.vm it updates and goes back to http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm.
The network manager (on my local firefox instance where I try to access the setup page says: See attached screen shots!
The "Params" tab shows me the correct username and password that I submitted. It also says 404 not found for the adress XDATscreen_Updateuser.vm. The prints contain the info of the header as well. The requested url is http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm
Logs from xnat/home/logs:
The xnat logs says:
xnat@xnatdev:/data/xnat/home/logs$ cat access.log
2018-03-21 11:14:31,277 - admin 10.208.19.39 Authentication SUCCESS
xnat@xnatdev:/data/xnat/home/logs$ cat security.log
2018-03-21 11:09:36,194 [http-bio-8080-exec-8] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/xnat/setup
2018-03-21 11:09:38,932 [http-bio-8080-exec-10] WARN org.nrg.xnat.security.XnatInitCheckFilter - Admin user admin has logged into the uninitialized server and is being redirected to http://10.208.21.252/xnat/setup
xnat@xnatdev:/data/xnat/home/logs$ cat tasks.log
2018-03-21 11:08:51,027 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - This service is the primary XNAT node, checking whether database updates are required.
2018-03-21 11:08:51,060 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - Initializing database views...
2018-03-21 11:08:54,697 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View initialization complete.
2018-03-21 11:08:54,975 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.AbstractInitializingTask - The system is not yet fully initialized. Delaying execution of the intializing task "System Path Verification" until initialization is completed.
2018-03-21 11:08:56,540 [taskScheduler-1] WARN org.nrg.xnat.initialization.tasks.UpdateConfigurationService - Processed configurations with project set to 12 metadata ID. Can't find a corresponding project.
xnat@xnatdev:/data/xnat/home/logs$ cat xdat.log
2018-03-21 11:06:52,697 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_launch_request_event to use sequence for default value.
2018-03-21 11:06:52,698 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-21 11:06:52,698 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_launch_request_event_id_seq
2018-03-21 11:06:52,698 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET DEFAULT nextval('xhbm_script_launch_request_event_id_seq')
2018-03-21 11:06:52,698 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET NOT NULL
2018-03-21 11:06:52,698 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_launch_request_event_id_seq OWNED BY xhbm_script_launch_request_event.id
2018-03-21 11:06:52,739 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_launch_request_event and got the value 1
2018-03-21 11:06:52,739 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_launch_request_event_id_seq', 1) AS value
2018-03-21 11:06:52,740 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_aud to use sequence for default value.
2018-03-21 11:06:52,740 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-21 11:06:52,740 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_aud_id_seq
2018-03-21 11:06:52,740 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET DEFAULT nextval('xhbm_script_aud_id_seq')
2018-03-21 11:06:52,740 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET NOT NULL
2018-03-21 11:06:52,740 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_aud_id_seq OWNED BY xhbm_script_aud.id
2018-03-21 11:06:52,743 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_aud and got the value 1
2018-03-21 11:06:52,743 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_aud_id_seq', 1) AS value
xnat@xnatdev:/data/xnat/home/logs$ cat jms.log
2018-03-21 11:07:06,540 Encountered a JMSException - resetting the underlying JMS Connection
javax.jms.JMSException: Broker has been stopped: org.apache.activemq.broker.BrokerService$5@41019991
at org.apache.activemq.util.JMSExceptionSupport.create(JMSExceptionSupport.java:49)
at org.apache.activemq.ActiveMQConnection.onAsyncException(ActiveMQConnection.java:1949)
at org.apache.activemq.ActiveMQConnection$3$1.run(ActiveMQConnection.java:1869)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Moore, Charlie
Is it possible the password is expired for your account? What happens when you run this in the database (replacing admin with your username)?
select password_updated from xhbm_xdat_user_auth where xdat_username='admin';
Thanks,
Charlie
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com]
On Behalf Of Robin Kämpe
Sent: Wednesday, March 21, 2018 5:38 AM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
Thanks for your reply!!
--
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Moore, Charlie
One more thing to try. Instead of modifying http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm to be http://10.208.21.252/xnat/app/template/XDATScreen_UpdateUser.vm, try deleting one of the two slashes instead.
Thanks,
Charlie
Robin Kämpe
Is it possible the password is expired for your account? What happens when you run this in the database (replacing admin with your username)?
select password_updated from xhbm_xdat_user_auth where xdat_username='admin';
One more thing to try. Instead of modifying http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm to be http://10.208.21.252/xnat/app/template/XDATScreen_UpdateUser.vm, try deleting one of the two slashes instead.
I'll get back to you soon. Thank you so much! Frustrating since this is in the way of our next step, to add new datatypes. I wanted to upgrade it first...
Robin Kämpe
1. Stop the WM - take a snapshot - start working
2. Stopping tomcat
3. fixing broken sym-links:
$ sudo ln -s /var/lib/tomcat7/common /usr/share/tomcat7/common
$ sudo ln -s /var/lib/tomcat7/server /usr/share/tomcat7/server
$ sudo ln -s /var/lib/tomcat7/shared /usr/share/tomcat7/shared
4.remove the xnat folder from tomcat7/webapps
5. Adding xnat.home to /etc/default/tomcat7
JAVA_OPTS="${JAVA_OPTS} -Dxnat.home=/data/xnat/home"
6. Going to /etc/tomcat7/server.xml and chaning this:
<Host name="localhost" appBase="empty" unpackWARs="false" autoDeploy="false">
<Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
prefix="localhost_access_log." suffix=".txt"
pattern="%h %l %u %t "%r" %s %b" />
<Context path="" docBase="/var/lib/tomcat7/webapps/xnat"/>
</Host>
To this:
<Host name="localhost" appBase="webapps" unpackWARs="true" autoDeploy="true">
<Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
prefix="localhost_access_log." suffix=".txt"
pattern="%h %l %u %t "%r" %s %b" />
(removed Context Path row)
</Host>
7. Copying the ROOT.war from my test 1.7.4 installation on the main server to the current WM and naming it xnat.war.
xnat@xnatdev:/var/lib/tomcat7/webapps$ scp xnat@vader:/var/lib/tomcat7/webapps/ROOT.war xnat.war
giving this:
xnat@xnatdev:/var/lib/tomcat7/webapps$ ls
xnat.war
8. Removing all old logs in tomcay7/logs/*
9. Starting tomcat. Waiting until the db has been updated.... Now I have xnat.war and xnat in the webapps directory.
10. Logs from xnat/home/logs:
cat xnat/home/logs/*
xnat@xnatdev:/var/lib/tomcat7/webapps$ cat /data/xnat/home/logs/*
2769 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
3038 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
2018-03-21 17:51:03,455 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View initialization threw exception (org.postgresql.util.PSQLException: ERROR: cannot change name of view column "invest_search" to "visit"). We'll drop views and rebuild them.
2018-03-21 17:51:03,604 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - Drop views step complete. Begin rebuilding views.
2018-03-21 17:51:04,536 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View rebuild complete.
2018-03-21 17:51:04,869 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.AbstractInitializingTask - The system is not yet fully initialized. Delaying execution of the intializing task "System Path Verification" until initialization is completed.
2018-03-21 17:51:06,610 [taskScheduler-1] WARN org.nrg.xnat.initialization.tasks.UpdateConfigurationService - Processed configurations with project set to 12 metadata ID. Can't find a corresponding project.
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_launch_request_event to use sequence for default value.
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_launch_request_event_id_seq
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET DEFAULT nextval('xhbm_script_launch_request_event_id_seq')
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET NOT NULL
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_launch_request_event_id_seq OWNED BY xhbm_script_launch_request_event.id
2018-03-21 17:50:59,584 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_launch_request_event and got the value 1
2018-03-21 17:50:59,584 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_launch_request_event_id_seq', 1) AS value
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_aud to use sequence for default value.
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_aud_id_seq
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET DEFAULT nextval('xhbm_script_aud_id_seq')
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET NOT NULL
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_aud_id_seq OWNED BY xhbm_script_aud.id
2018-03-21 17:50:59,590 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_aud and got the value 1
2018-03-21 17:50:59,590 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_aud_id_seq', 1) AS value
xnat@xnatdev:/var/lib/tomcat7/webapps$
11. Clearing cookies and testing is 10.208.21.252 is available via firefox. It is not. Just white screen
12. Checking if xnat is available at 10.208.21.252/xnat (without manually chaning the url of the database): it is. The network tool in firefox (when getting the login screen only shows green circles with status 200.
I get the login screen. Now the xnat logs look like this:
xnat@xnatdev:/var/lib/tomcat7/webapps$ cat /data/xnat/home/logs/*
2769 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
3038 [localhost-startStop-1] ERROR org.apache.axis.configuration.EngineConfigurationFactoryServlet - Unable to find config file. Creating new servlet engine config file: /WEB-INF/server-config.wsdd
2018-03-21 17:51:03,455 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View initialization threw exception (org.postgresql.util.PSQLException: ERROR: cannot change name of view column "invest_search" to "visit"). We'll drop views and rebuild them.
2018-03-21 17:51:03,604 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - Drop views step complete. Begin rebuilding views.
2018-03-21 17:51:04,536 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.CreateOrUpdateDatabaseViews - View rebuild complete.
2018-03-21 17:51:04,869 [taskScheduler-1] INFO org.nrg.xnat.initialization.tasks.AbstractInitializingTask - The system is not yet fully initialized. Delaying execution of the intializing task "System Path Verification" until initialization is completed.
2018-03-21 17:51:06,610 [taskScheduler-1] WARN org.nrg.xnat.initialization.tasks.UpdateConfigurationService - Processed configurations with project set to 12 metadata ID. Can't find a corresponding project.
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_launch_request_event to use sequence for default value.
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_launch_request_event_id_seq
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET DEFAULT nextval('xhbm_script_launch_request_event_id_seq')
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_launch_request_event ALTER COLUMN id SET NOT NULL
2018-03-21 17:50:59,571 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_launch_request_event_id_seq OWNED BY xhbm_script_launch_request_event.id
2018-03-21 17:50:59,584 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_launch_request_event and got the value 1
2018-03-21 17:50:59,584 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_launch_request_event_id_seq', 1) AS value
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Preparing to convert table xhbm_script_aud to use sequence for default value.
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Queries prepared for conversion:
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** CREATE SEQUENCE xhbm_script_aud_id_seq
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET DEFAULT nextval('xhbm_script_aud_id_seq')
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER TABLE xhbm_script_aud ALTER COLUMN id SET NOT NULL
2018-03-21 17:50:59,585 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - *** ALTER SEQUENCE xhbm_script_aud_id_seq OWNED BY xhbm_script_aud.id
2018-03-21 17:50:59,590 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Ran the query SELECT (MAX(id) + 1) AS value FROM xhbm_script_aud and got the value 1
2018-03-21 17:50:59,590 [localhost-startStop-1] ERROR org.nrg.xft.db.DBAction - Now preparing to run the query: SELECT setval('xhbm_script_aud_id_seq', 1) AS value
13. I now try to login with admin + my custom pw from the old xnat build. This directes me to http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm. Only a white webpage is visible. The network tool shows 4 entries:
orage triangle 302 Method: Post login Domain 10.208.21.252
green circle 200 Method get fontawesome-webfont.woff2?v=4.7.0 Domain 10.208.21.252
organge triangle 302 Method GET /xnat/ Domain 10.208.21.252
Purple Square 404 Method GET XDATScreen_UpdateUser.vm Domain 10.208.21.252
I then procede to try what has been said:
14. Removing the extra / gives the same white screen. Purple Square 404 GET XdatScreen_UpdateUser.vm Domain 10.208.21.252.
15. Now trying to update the admin pw and to update the url. Alltough it already seems to be correct:
xnat=> SELECT value FROM xhbm_preference WHERE name='siteUrl';
value
-----------------------
http://10.208.21.252/
(1 row)
xnat=>
UPDATE 1
xnat=> select password_updated from xhbm_xdat_user_auth where xdat_username='admin';
password_updated
------------------------
2015-11-12 16:20:55.46
(1 row)
15. Restarting tomcat. Clearing cookies. Trying to reach 10.208.21.252 = same story, white screen. Network tool:
Oragne 404 GET File: "/"
16. Instead trying 10.208.21.252/xnat = Reaching login screen with a lot of green circle 200 events in the network manager (as above).
17. Login in as admin: Same as above = White screen, adress = http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm
Network manager gives the same as above (the 4 events where the last (XDATScreen_UpdateUser.vm is 404).
18. Removing the extra / just gives me one event which is the 404 one (XDATScreen).
19. Trying to change the url to 10.208.21.252/xnat:
xnat=> UPDATE xhbm_preference SET value = 'http://10.208.21.252/xnat' WHERE name='siteUrl';
UPDATE 1
xnat=>
20. Restarting tomcat. clear cookies. Accesing 10.208.21.252 again is white screen. Just one 404 GET /
Trying 10.208.21.252/xnat. Again... Reach login screen. Use admin (which according to xnat/home/logs/access is sucessful:
xnat@xnatdev:/var/lib/tomcat7/webapps$ cat /data/xnat/home/logs/access.log
2018-03-21 17:56:45,581 - admin 10.208.19.39 Authentication SUCCESS
2018-03-21 18:07:43,281 - admin 10.208.19.39 Authentication SUCCESS
Not sure about that ip though... the old ldap setting messing arround? old xnat uses ldad. Alltough not for the admin account which is local.
Using 10.208.21.252/xnat. Again get the login screen...
I again get a lot of successful events in the network manager (e.g. loading_bar.gig, event.js, logo.png.. etc).
Try to login: using wrong pw on purpose = I get sent back to login screen since it fails.
Using correct login I get white screen for http://10.208.21.252//app/template/XDATScreen_UpdateUser.vm with the same 4 events (404 for the XDATScreen_UpdateUser.vm):
orange triangle 302 POST login
orange triangle 302 GET /xnat/
purple square 404 GET XDATScreen_UpdateUser.vm
Removing the extra slash just gives me one 404 GET XDATSsceen_UpdateUser.vm
The accesslog makes sense since I tried once with wrong pw:
xnat@xnatdev:/var/lib/tomcat7/webapps$ cat /data/xnat/home/logs/access.log
2018-03-21 17:56:45,581 - admin 10.208.19.39 Authentication SUCCESS
2018-03-21 18:07:43,281 - admin 10.208.19.39 Authentication SUCCESS
2018-03-21 18:15:57,820 - admin 10.208.19.39 Authentication SUCCESS
2018-03-21 18:15:58,015 - admin 10.208.19.39 Authentication FAILED
2018-03-21 18:16:27,720 - admin 10.208.19.39 Authentication SUCCESS
21. Proceed to lay down and cry :)
I seem to have tried the most of what you suggested? Should I try to dissable ldap on the 1.6.5 version before I upgrade?
Sorry for long post but it is good that you can see what I have done.
Thankful for comments
Moore, Charlie
Well, one thing to note is that the password for the admin account is very, very expired (at least with the default expiration time of 1 year). It’s possible that in 1.6, we whitelisted admin accounts from having their passwords expire, but I’m not sure about that. The only reason I can think of for you getting redirected to /app/template/XDATScreen_UpdateUser.vm is because your password is expired. You could try hacking it in the database to say it was updated yesterday:
UPDATE xhbm_xdat_user_auth SET password_updated = '2018-03-20 12:12:12.121' WHERE xdat_username = 'admin'
Restart tomcat after that, since it might cache some stuff for the account. Hopefully that will at least change the behavior? Unfortunately, I’m not really sure what else to add if that doesn’t work, since what you’re doing looks fairly reasonable to me.
Thanks,
Charlie
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com]
On Behalf Of Robin Kämpe
Sent: Wednesday, March 21, 2018 12:22 PM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
So this is what I'm doing:
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McKay, Mike
And after trying what Charlie suggested, if that doesn't work, could you post what is returned by:
SELECT * FROM xhbm_xdat_user_auth WHERE xdat_username = 'admin';
and what is returned by:
SELECT * FROM xdat_user WHERE login = 'admin';
(You should not include the values of the primary_password or salt fields when responding for security reasons, but I would like to know whether they have values.)
-Mike
Sent: Wednesday, March 21, 2018 12:47:15 PM
To: xnat_di...@googlegroups.com
Subject: RE: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
Robin Kämpe
First off, THANK YOU BOTH for your patience....
I don't want to take out anything in advance but it seems like that did the trick!!! I.e. I "hacked" the date of the latest password update like Charlie suggested. I did this using ROOT.war to get away from having to put in /xnat for the user. Now I get:
xnat=> SELECT value FROM xhbm_preference WHERE name='initialized';
value
-------
true
(1 row)
----+-------------------------+---------------------+---------+-------------------------+-------------+----------------+-----------+-----------------------+-------------------------+-------------------------+---------------+-------------------------+--------------
1 | 2014-11-11 11:03:51.583 | 1969-12-31 16:00:00 | t | 2018-03-23 15:12:38.173 | localdb | | admin | 0 | 2018-03-23 15:12:38.173 | 2018-03-20 12:12:12.121 | admin | 2018-03-23 15:12:38.173 |
(1 row)
and
-------+-----------+----------+---------------------+------------------------------------------------------------------+--------------------------+-----------------+---------+----------+------------------------------------------------------------------+-----------+--------------+-------------------------------------------
admin | Admin | Admin | ad...@yourplace.org | XXXXXXXXXXXXXXXXXXXX | | | 1 | 1 | AXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | 1 | 1 | 1
(1 row)
So now I have a question. I am able to login via the admin account that was (and is) a local account. The rest of the accounts cannot login - they fail. This is probably because they used to be authenticated via ldap (using the local domain). That makes sense since I have not setup (I did not manage to) ldap for xnat 1.7. And we plan on not doing ldap anymore to get away from issues with the domain. The users however are still in the list under Administer > users. E.g. me:
3 robka Kämpe, Robin my-email [two green circles] 3/21/2018, 6.24:46 PM
Is there a way to make these accounts local or should I create new users via the xnat web-interface (Create User)? Can I remove the old ones? I don’t see a delete user button. I guess there will be a conflict if I try to create me (robka) again since I'm already in the list?
THANK YOU guys so much :).
Although, the next step is to try to pd_dump this data base and use pd_restore on the other empty 1.7.4 install that I got to get away from using a WM. There might be new problems from that project ;)
McKay, Mike
I'm so glad you were able to get it working!
Regarding user account deletion, that is something we disallow as discussed here: https://groups.google.com/forum/#!topic/xnat_discussion/HRsUPijHmbc
The good news is that you should be able to allow existing users to log in by adding rows in the xhbm_xdat_user_auth table that have auth_user and xdat_username set to their username, and auth_method set to localdb. They should basically look like the xhbm_xdat_user_auth row for your admin user. Here is an query you can use as a template (replacing usernameOfExistingUser with the username of the existing user you want to be able to login via the local database):
INSERT INTO xhbm_xdat_user_auth (created, disabled,enabled,timestamp,auth_method,auth_user,failed_login_attempts,last_login_attempt,last_successful_login,password_updated,xdat_username)
VALUES ('2018-03-23 01:11:11.111','1969-12-31 18:00:00',true,'2018-03-23 01:11:11.111','localdb','usernameOfExistingUser',0,'2018-03-23 01:11:11.111','2018-03-23 01:11:11.111','2018-03-23 01:11:11.111','usernameOfExistingUser');
After you have added this row, you still have to set a temporary database password for that user (so they can log in and set their password to whatever they want). One way to do this is to log in as admin, go to Administer-> Users click on the user, change the password, and click Save. Another option is to do an SQL query to update their row in the xdat_user table, setting their salt to an empty string and their primary password to some 64 character string that they will need to enter as their password when they first log in. For example, you could do something like this:
UPDATE xdat_user SET salt='', primary_password='1234567890123456789012345678901234567890123456789012345678901234' WHERE login='usernameOfExistingUser';
You also should make sure these users are both enabled and verified (you can look either in the UI or in their row in xdat_user). I'd also recommend doing database operations on user accounts while Tomcat is shut down to be safe (so you don't have to worry that a task might be running to disable users if certain conditions are met when you're in the middle of getting things set up).
Good luck! And please let me know if there's anything else I can do to help you through the upgrade process!
-Mike
Sent: Friday, March 23, 2018 9:24:06 AM
To: xnat_discussion
Subject: Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
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Robin Kämpe
So I did as you said and it does seem to work :). All the users can low log in. Just to make sure. Is the command supposed to give this output?:
xnat=> INSERT INTO xhbm_xdat_user_auth (created, disabled,enabled,timestamp,auth_method,auth_user,failed_login_attempts,last_login_attempt,last_successful_login,password_updated,xdat_username) VALUES ('2018-03-23 01:11:11.111','1969-12-31 18:00:00',true,'2018-03-23 01:11:11.111','localdb','robka',0,'2018-03-23 01:11:11.111','2018-03-23 01:11:11.111','2018-03-23 01:11:11.111','robka');
INSERT 0 1
Thanks!
McKay, Mike
Yes, that is the output you should be getting. I'm glad your users are able to log in now!
-Mike
To: xnat_discussion
Subject: Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
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Herrick, Rick
Yes, that’s a good response. From the PostgreSQL documentation on this:
On successful completion, an INSERT command returns a command tag of the form
INSERT oid count
The count is the number of rows inserted or updated. If count is exactly one, and the target table has OIDs, then oid is the OID assigned to the inserted row. The single row must have been inserted rather than updated. Otherwise oid is zero.
That “INSERT 0 1” tells you that one row was inserted, and the resulting row doesn’t have an associated OID. None of the XNAT tables use OIDs,* so that value will almost always be zero.
* OIDs provide built-in identifiers within PostgreSQL that “uniquely” identify a particular row within the database instance. OID generation has been turned off by default in PostgreSQL since version 8.1 and is a deprecated feature. It turns out that putting bajillions of rows into a database (“bajillion” is a technical computer science term and is roughly equivalent to “oodles” or Carl Sagan’s go-to awe inspirer “billions and billions”) makes the OID counter reset, which results in duplicate OIDs within the instance, thus failing at its primary purpose.
--
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 Robin Kämpe <robin....@gmail.com>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Monday, March 26, 2018 at 8:38 AM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
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Robin Kämpe
I could just settle here and go on from the WM. We would prefer if we could move this xnat 1.7.4 WM to its host machine where an empty 1.7.4 is installed: i.e. move the database to the host server by replacing it.
I tried this:
on the WM:
sudo pg_dump -i -h localhost -p 5432 -U xnat -F c -b -v -f "test_pg_dump" xnat
This gives a lot of output and I can't see any errors.
On the host machine I tried:
sudo pg_restore -h localhost -p 5432 -U xnat -d xnat -v test_pg_dump
This also gives tones of output whith the last few lines beeing:
pg_restore: creating ACL "public"
pg_restore: WARNING: no privileges could be revoked for "public"
pg_restore: WARNING: no privileges could be revoked for "public"
pg_restore: WARNING: no privileges were granted for "public"
pg_restore: WARNING: no privileges were granted for "public"
pg_restore: creating ACL "xdat_search.xs_fav_entries"
pg_restore: creating ACL "xdat_search.xs_item_access"
pg_restore: creating ACL "public.xdat_searches"
pg_restore: creating ACL "xdat_search.xs_materialized_views"
WARNING: errors ignored on restore: 7112
When restarting tomcat on the host it did not seem to work. xnat is still initialized and the url is correct and I can log in with the old admin account (not the same pw as the WM one). But I have no users and no data (the data itself have been copied to the archive and pre-archive). So something is probably not correct. Should I instead try to just copy the postgres "main" folder and replace it? What could I do to see what went wrong?
Thanks!
McKay, Mike
This isn't something I personally have experience with, but you may find this helpful:
https://groups.google.com/forum/#!msg/xnat_discussion/y_VhyD-EW_Q/Y5NPHI0vKH4J
-Mike
To: xnat_discussion
Subject: [SPAM] Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
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Herrick, Rick
Yeah, my suggestion was going to be to use psql rather than pg_restore. It’s kind of counter-intuitive, but a standard database dump from pg_dump is meant to be run as a script, while other formats from pg_dump (like, I guess, directory or tar dumps) are what pg_restore handles. As the documentation for pg_restore says: “pg_restore is a utility for restoring a PostgreSQL database from an archive created by pg_dump in one of the non-plain-text formats.”
--
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 "McKay, Mike" <mfm...@wustl.edu>
Reply-To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Date: Tuesday, March 27, 2018 at 9:19 AM
To: "xnat_di...@googlegroups.com" <xnat_di...@googlegroups.com>
Subject: Re: [SPAM] Re: [SPAM] Re: [XNAT Discussion] Re: Can't log in for first the time after upgrade (1.6.5 ---> 1.7.4)
|
|
-Mike
Robin Kämpe
You may then think, well, given a clean server, I can just import the dump. Again, refer to reasonable yet erroneous. The default pg_dump output doesn't specify the target database nor will it create it, meaning a clean server install will fail."
Haha! I found this hillarious since that was my approach. Sorry...
Okay! Thanks! Again, since I'm not schooled in psql would either of you mind beeing a bit more explcit?
Step 1: Delete my "empty" db on the clean install: How do I do that?
Step 2: Create the xnat.sql file from the current (WM) xnat database. Is not via pg_dump, how do I do that?
Step 3: This seems pretty clear:
psql -f xnat.sql -U xnat_user -d xnat_db
"xnat.sql is your dump file, xnat_user is the xnat user, and xnat_db is your newly recreated database."
But why is the last part "-d xnat_db" and not "-d xnat". Isn't the database still going to be called xnat? So in my case:
psql -f xnat.sql -U xnat -d xnat
?
Thanks guys!
Robin Kämpe
1 On fresh install: xnat@Vader:~$ dropdb 'xnat'
2 On WM sudo pg_dump -i -h localhost -p 5432 -U xnat -b -v -f "test_pg_dump" xnat (removed the custom format to default, i.e. sql script format).
3 On fresh install: createdb -O xnat xnat (created the xnat db)
4 On fresh install: psql -f test_pg_dump -U xnat -d xnat
5 On fresh install: Change the IP to the correct IP (since the WM ip followed with the pg_dump).
It actually seems to work... Both user login and all the data. How could this be? Why would it go this smoothly? Something must be wrong? ;)
Although, the pipeline I had installed on the clean server does not work now. This must be because the path from the upgraded WM still points to /home/xnat/Development/pipeline-1.6.4. Is there a way to change the path via psql? Some UPDATE command I can run like I did with the URL?
Thanks!!
Robin Kämpe
xnat=> SELECT value FROM xhbm_preference WHERE name='pipelinePath';
value
----------------------------------------
/home/xnat/Development/pipeline-1.6.4/
(1 row)
xnat=> UPDATE xhbm_preference SET value ='/data/xnat/pipeline/' WHERE name='pipelinePath';
UPDATE 1
xnat=> SELECT value FROM xhbm_preference WHERE name='pipelinePath';
value
----------------------
/data/xnat/pipeline/
(1 row)
McKay, Mike
Yes, I think that'll work as long as you restart Tomcat. You can also set the pipeline path (and the other paths, except for archive path) in the UI by going to Administer -> Site Administration -> Advanced XNAT Settings -> File System. A listener is set up to respond to changes you make to paths there so you shouldn't need to restart Tomcat if you make edits that way. But if you change the database directly and restart Tomcat, your updated value should show up in the UI and everything should work find. But please let us know if anything seems wrong.
-Mike
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Robin Kämpe
So when I decide to actually move our WM XNAT the host server I'll just re-do this and rsync the archive/prearchive to the local disks and dismantle the WM. Wow, this was nice. Thank you so much!
Now that I have managed to install XNAT 1.7.4 from scratch and managed to upgrade 1.6.4 --- > 1.7.4 with your help (now documented in this thread) and managed to move a database I think my next step is to try to learn about pipelines, plugins and custom data types. I would like to have some automation done via pipelines and I need to add a few data types and would be cool to try to make a plug-in that changes the logo as a start project. I bet I will need help with that... I really hope there will be another XNAT workshop this year. Would be really awesome :).
Thanks again!!