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Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Laurent T. <l.t...@un...>]

I noticed what could be an interesting point.
In the /Library/Tomcat/bin/catalina.sh file is setted the following line as recommended:
CATALINA_OPTS="-Xmx1G -Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false -Dcom.sun.media.jai.disableMediaLib=true -Djava.awt.headless=true"

but when I type ps -e | grep Tomcat, it gives the following:
14952 ttys000    5:31.03 /Library/Java/Home/bin/java -Djava.util.logging.config.file=/Library/Tomcat/conf/logging.properties -Xms512m -Xmx1G -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1G -Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false -Dcom.sun.media.jai.disableMediaLib=true -Djava.endorsed.dirs=/Library/Tomcat/endorsed -classpath /Library/Tomcat/bin/bootstrap.jar -Dcatalina.base=/Library/Tomcat -Dcatalina.home=/Library/Tomcat -Djava.io.tmpdir=/Library/Tomcat/temp org.apache.catalina.startup.Bootstrap start
16845 ttys000    0:00.00 grep Tomcat

Thus the -Djava.awt.headless=true setting does not appear here.
Would it mean that the setting comes from somewhere else then the /Library/Tomcat/bin/catalina.sh file ?

If I do a modification on the /Library/Tomcat/bin/catalina.sh file, at what stage should I rester the installation procedure ? 
Just restart Tomcat (/Library/Tomcat/bin/shutdown.sh and then /Library/Tomcat/bin/startup.sh) ?
The other thing I noticed, confirming that the Djava.awt.headless option is not taken in account is that I get a windowed application named org.apache.catalina.startup.Bootstrap that remains as mentioned by Jari.

What surprises me is that when I type the command :
/Library/Tomcat/bin/shutdown.sh I get the following output:

Using CATALINA_BASE:   /Library/Tomcat
Using CATALINA_HOME:   /Library/Tomcat
Using CATALINA_TMPDIR: /Library/Tomcat/temp
Using JRE_HOME:        /Library/Java/Home
Using CLASSPATH:       /Library/Tomcat/bin/bootstrap.jar
Using CATALINA_PID:    /Library/Tomcat/catalina_pid.txt
PID file found but no matching process was found. Stop aborted.

And the Java process is still running…


Other informations:

Both /Library/Tomcat/work/Catalina/localhost/base2 and /Library/Tomcat/work/Catalina/localhost/_/ directories are empty

I have set the owner of /Library/Tomcat/work directory and inner files to _appserver user and _appserveradm group as defined for the tomcat process.
The other odd thing I am just discovering is that when typing the command line 'ps auxw | grep tomcat'
I only get one time out of three the shell process /Library/Tomcat/bin/tomcat-launchd.sh
And each time it has an other pid. Is it supposed to be so ?
That would explain why when I want to shutdown the Tomcat process it is aborted.

Thanks again for taking of your time.
Laurent

Le 12 sept. 2013 à 20:48, Nicklas Nordborg <nic...@me...> a écrit :

> On 2013-09-12 16:22, Jari Häkkinen wrote:
>> On 2013-09-11 10:57, Laurent Troxler wrote:
>>> going through the log files here is what I can get:
>>> system.log: repeating those two lines
>>> Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
>>> CGErrorBreakpoint() to catch errors as they are logged.
>>> Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
>>> Throttling respawn: Will start in 8 seconds
>>> 
>>> /Library/Tomcat/logs/catalina.2013-09-11.log :
>>> Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
>>> initClassLoaders
>>> SEVERE: Class loader creation threw exception
>>> java.lang.InternalError: Can't connect to window server - not enough
>>> permissions.
> 
> I think this could be that the Java runtime engine is starting up 
> various threads for handling GUI interactions. I have not seen this 
> preventing startup of Tomcat or BASE but it can lead to issues with 
> generating plots and other image handling (much) later.
> 
> The installation instructions mention that "headless mode" should be 
> enabled to prevent this. See 4:th bullet in the Tomcat section 
> (http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html). 
> 
> 
> In any case, I don't think this is related to BASE not working, but it 
> needs to be fixed sooner or later and better to rule it out as soon as 
> possible.
> 
> /Nicklas
> 
> 
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Nicklas N. <nic...@me...>]

On 2013-09-12 16:22, Jari Häkkinen wrote:
> On 2013-09-11 10:57, Laurent Troxler wrote:
>> going through the log files here is what I can get:
>> system.log: repeating those two lines
>> Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
>> CGErrorBreakpoint() to catch errors as they are logged.
>> Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
>> Throttling respawn: Will start in 8 seconds
>>
>> /Library/Tomcat/logs/catalina.2013-09-11.log :
>> Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
>> initClassLoaders
>> SEVERE: Class loader creation threw exception
>> java.lang.InternalError: Can't connect to window server - not enough
>> permissions.

I think this could be that the Java runtime engine is starting up 
various threads for handling GUI interactions. I have not seen this 
preventing startup of Tomcat or BASE but it can lead to issues with 
generating plots and other image handling (much) later.

The installation instructions mention that "headless mode" should be 
enabled to prevent this. See 4:th bullet in the Tomcat section 
(http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html). 


In any case, I don't think this is related to BASE not working, but it 
needs to be fixed sooner or later and better to rule it out as soon as 
possible.

/Nicklas

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Nicklas N. <nic...@me...>]

On 2013-09-12 16:47, Laurent TROXLER wrote:
> Yes, I can axes to Tomcat Home page and login as root. There I can see
> that base2 is uploaded.
> There isn't any obvious error on the web interface.
> To answer to Jari, I am working presently directly on the server to
> avoid any internet problem.
> What do you mean by "work directory hierarchy" ? Does it mean that each
> directory of the
> /Library/Tomcat/work/Catalina/localhost/base2 chain should be owned by
> www or it should be the case only for base2 ?

I think everything below /Library/Tomcat/work can be removed since 
Tomcat will re-created the structure as needed. I don't know if the 
owner matters as long as Tomcat is able to create files and directories 
in that folder.

Since Tomcat seems to be working, does this mean that 
/Library/Tomcat/work/Catalina/localhost/_/org/apache/jsp directory 
exists and contain a few *.java and *.class files?

A similar structure should be created in the 
/Library/Tomcat/work/Catalina/localhost/base2/ folder, but if it doesn't 
there must be something else that is preventing the files from being 
created, though at the moment I have no idea what that could be.

> At this time it is owned by root from the _appserveradm group (I guess
> setted by the system)
> I was also wondering if my base.config file was well setted. Should the
> db.username be setted to base2user or to root ?

The db.username and db.password settings in base.config is the 
username/password that BASE need to log in to the MySQL server. Since 
the initdb.sh script worked this should be ok as it is.

The username and password given as parameters to the initdb.sh script 
are for the root account to the BASE application and is needed when you 
login to the BASE web application at http://localhost:8080/base2. They 
are two different sets of username/password and doesn't have to be the same.

/Nicklas

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Jari H. <jar...@me...>]

On 2013-09-12 16:47, Laurent TROXLER wrote:
> Yes, I can axes to Tomcat Home page and login as root. There I can see
> that base2 is uploaded.
> There isn't any obvious error on the web interface.
> To answer to Jari, I am working presently directly on the server to
> avoid any internet problem.

Ok.


> What do you mean by "work directory hierarchy" ? Does it mean that each
> directory of the
> /Library/Tomcat/work/Catalina/localhost/base2 chain should be owned by
> www or it should be the case only for base2 ?
> At this time it is owned by root from the _appserveradm group (I guess
> setted by the system)

On my machine all files and directories in /Library/Tomcat/work are 
owned by the tomcat user. Normally the ownership should be correct if 
you have not tampered with them. To decide the tomcat user do 'ps auxw | 
grep tomcat' and you should see the userid in the leftmost column in the 
listing (assuming that the program is called tomcat on your system).

Another path is to look at the owner of the log files since these should 
be owned by the tomcat user on your system. Do 'ls -ls 
/Library/Tomcat/logs'. Change the ownership to match the owner of the 
log files with 'sudo chown -R userid:groupid /Library/Tomcat/work'

Anyhow, I do not think the above is the problem.


> I was also wondering if my base.config file was well setted. Should the
> db.username be setted to base2user or to root ?
> Thanks again for your help.

db.username should be set to the userid you used when you create the 
database in mysql, i.e., whatever you used as db_user in

GRANT ALL ON base2.* TO db_user@localhost IDENTIFIED BY 'db_password';

The root userid is used in the web interface once you get the server 
running. (Assuming that you did not set it to something else during 
installation which I do myself.)


 >>> going through the log files here is what I can get:
 >>> system.log: repeating those two lines
 >>> Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
 >>> CGErrorBreakpoint() to catch errors as they are logged.
 >>> Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
 >>> Throttling respawn: Will start in 8 seconds

There is a short discussion on this issue at 
https://discussions.apple.com/thread/5270047?start=0&tstart=0 maybe that 
can help you with the above issue?


>>> /Library/Tomcat/logs/catalina.2013-09-11.log :
>>> Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
>>> initClassLoaders
>>> SEVERE: Class loader creation threw exception
>>> java.lang.InternalError: Can't connect to window server - not enough
>>> permissions.
>>> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
>>> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827)
>>> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724)
>>> at java.lang.Runtime.loadLibrary0(Runtime.java:823)
>>> at java.lang.System.loadLibrary(System.java:1045)
>>> at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
>>> at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
>>> at sun.awt.AppContext$2.run(AppContext.java:240)
>>> at sun.awt.AppContext$2.run(AppContext.java:226)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at sun.awt.AppContext.initMainAppContext(AppContext.java:226)
>>> at sun.awt.AppContext.access$200(AppContext.java:112)
>>> at sun.awt.AppContext$3.run(AppContext.java:306)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at sun.awt.AppContext.getAppContext(AppContext.java:287)
>>> at com.sun.jmx.trace.Trace.out(Trace.java:180)
>>> at com.sun.jmx.trace.Trace.isSelected(Trace.java:88)

Have you set the following parameters for the tomcat server? (See 
section Tomcat at the top in 
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html

CATALINA_OPTS="-Xmx1G
-Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false
-Dcom.sun.media.jai.disableMediaLib=true
-Djava.awt.headless=true"

The last option is important, see 
http://stackoverflow.com/questions/11024555/elasticsearch-java-lang-internalerror-cant-connect-to-window-server 
since it will avoid the problem of connecting to the window server.

If I remove the last option myself, I get a windowed application named 
org.apache.catalina.startup.Bootstrap that remains until I shutdown 
tomcat (cf. attached png). If I kill the window application then tomcat 
dies. If the headless option is true then the windowed application does 
not appear and tomcat runs fine. However, I do not know how I have 
managed to allow java to connect to my window server though. I have been 
running BASE for years now so may be it was something I had to fix long 
time ago?


Cheers,

Jari

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Laurent T. <l.t...@un...>]

Yes, I can axes to Tomcat Home page and login as root. There I can see 
that base2 is uploaded.
There isn't any obvious error on the web interface.
To answer to Jari, I am working presently directly on the server to 
avoid any internet problem.
What do you mean by "work directory hierarchy" ? Does it mean that each 
directory of the
/Library/Tomcat/work/Catalina/localhost/base2 chain should be owned by 
www or it should be the case only for base2 ?
At this time it is owned by root from the _appserveradm group (I guess 
setted by the system)
I was also wondering if my base.config file was well setted. Should the 
db.username be setted to base2user or to root ?
Thanks again for your help.
Laurent

Le 11/09/2013 14:34, Nicklas Nordborg a écrit :
> Seems to me like there is some problem with the Tomcat installation.
> Unfortunately I am not very familiar with Mac so I am afraid I won't be
> of much help here.
>
> Have you checked if you can access the Tomcat welcome page?
>
> http://localhost:8080/
>
> /Nicklas
>
> On 2013-09-11 10:57, Laurent Troxler wrote:
>> Le 10 sept. 2013 à 20:26, Nicklas Nordborg <nic...@me...
>> <mailto:nic...@me...>> a écrit :
>>
>>> On 2013-09-10 16:35, Laurent Troxler wrote:
>>>> Thank you Nicolas for your answer.
>>>> It helped me to find out that I had missed the base.config file password
>>>> setting.
>>>> I thus could go through the all process.
>>> Great.
>>>
>>>> I am now facing an other problem linked to Tomcat.
>>>> After setting the symbolic link between Tomcat and Base, when I go on
>>>> the webpage http://hostname:8080/base2
>>>> I get alternatively  :
>>> The /Library/Tomcat/work directory and subdirectories are directories
>>> where Tomcat store temporary working files. Usually this is not
>>> something one has to worry about. I can think of two reasons why the
>>> directory referenced in the error message is empty:
>>>
>>>   1. The Tomcat process doesn't have write permission on the directory
>> I have given the full rights to every one on
>> /Library/Tomcat/work/Catalina/localhost/base2
>> drwxrwxrwx  8 root  _appserveradm  272 22 aoû 11:47
>> /Library/Tomcat/work/Catalina/localhost/base2
>> Should it also need to change the owner ? But I do not know which user
>> is Tomcat using
>>
>>>   2. The disk is full
>> there is over a hundred Go, It should be enough
>>> It might be possible that there is more information in one of Tomcat's
>>> log files (though I can't tell which one, the logging setup of Tomcat is
>>> still a bit of a mystery to me...). At least, it seems like Tomcat is up
>>> and running so it shouldn't be a Java issue.
>>>
>> going through the log files here is what I can get:
>> system.log: repeating those two lines
>> Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
>> CGErrorBreakpoint() to catch errors as they are logged.
>> Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
>> Throttling respawn: Will start in 8 seconds
>>
>> /Library/Tomcat/logs/catalina.2013-09-11.log :
>> Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
>> initClassLoaders
>> SEVERE: Class loader creation threw exception
>> java.lang.InternalError: Can't connect to window server - not enough
>> permissions.
>> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
>> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827)
>> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724)
>> at java.lang.Runtime.loadLibrary0(Runtime.java:823)
>> at java.lang.System.loadLibrary(System.java:1045)
>> at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
>> at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
>> at sun.awt.AppContext$2.run(AppContext.java:240)
>> at sun.awt.AppContext$2.run(AppContext.java:226)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at sun.awt.AppContext.initMainAppContext(AppContext.java:226)
>> at sun.awt.AppContext.access$200(AppContext.java:112)
>> at sun.awt.AppContext$3.run(AppContext.java:306)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at sun.awt.AppContext.getAppContext(AppContext.java:287)
>> at com.sun.jmx.trace.Trace.out(Trace.java:180)
>> at com.sun.jmx.trace.Trace.isSelected(Trace.java:88)
>> at
>> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.isTraceOn(DefaultMBeanServerInterceptor.java:1830)
>> at
>> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerDynamicMBean(DefaultMBeanServerInterceptor.java:929)
>> at
>> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerObject(DefaultMBeanServerInterceptor.java:916)
>> at
>> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerMBean(DefaultMBeanServerInterceptor.java:312)
>> at com.sun.jmx.mbeanserver.JmxMBeanServer$2.run(JmxMBeanServer.java:1195)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at
>> com.sun.jmx.mbeanserver.JmxMBeanServer.initialize(JmxMBeanServer.java:1193)
>> at com.sun.jmx.mbeanserver.JmxMBeanServer.<init>(JmxMBeanServer.java:225)
>> at com.sun.jmx.mbeanserver.JmxMBeanServer.<init>(JmxMBeanServer.java:170)
>> at
>> com.sun.jmx.mbeanserver.JmxMBeanServer.newMBeanServer(JmxMBeanServer.java:1401)
>> at
>> javax.management.MBeanServerBuilder.newMBeanServer(MBeanServerBuilder.java:93)
>> at
>> javax.management.MBeanServerFactory.newMBeanServer(MBeanServerFactory.java:311)
>> at
>> javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:214)
>> at
>> javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:175)
>> at
>> sun.management.ManagementFactory.createPlatformMBeanServer(ManagementFactory.java:302)
>> at
>> java.lang.management.ManagementFactory.getPlatformMBeanServer(ManagementFactory.java:504)
>> at
>> org.apache.catalina.startup.Bootstrap.createClassLoader(Bootstrap.java:183)
>> at org.apache.catalina.startup.Bootstrap.initClassLoaders(Bootstrap.java:92)
>> at org.apache.catalina.startup.Bootstrap.init(Bootstrap.java:207)
>> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:391)
>>
>> /Library/Tomcat/logs/tomcat-launchd.stdout :
>> Existing PID file found during start.
>> Removing/clearing stale PID file.
>> Existing PID file found during start.
>> Removing/clearing stale PID file.
>> Existing PID file found during start.
>> Removing/clearing stale PID file.
>> Existing PID file found during start.
>> Removing/clearing stale PID file.
>> Existing PID file found during start.
>> Removing/clearing stale PID file.
>>
>> Does it helps ?
>>
>>
>>> /Nicklas
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> How ServiceNow helps IT people transform IT departments:
>>> 1. Consolidate legacy IT systems to a single system of record for IT
>>> 2. Standardize and globalize service processes across IT
>>> 3. Implement zero-touch automation to replace manual, redundant tasks
>>> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> The BASE general discussion mailing list
>>> bas...@li...
>>> unsubscribe: send a mail with subject "unsubscribe" to
>>> bas...@li...
>
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...
>

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Jari H. <jar...@me...>]

On 2013-09-11 10:57, Laurent Troxler wrote:
> going through the log files here is what I can get:
> system.log: repeating those two lines
> Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
> CGErrorBreakpoint() to catch errors as they are logged.
> Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
> Throttling respawn: Will start in 8 seconds
>
> /Library/Tomcat/logs/catalina.2013-09-11.log :
> Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
> initClassLoaders
> SEVERE: Class loader creation threw exception
> java.lang.InternalError: Can't connect to window server - not enough
> permissions.


It seems like the tomcat process cannot connect to the window server. I 
have noticed that when I start (or stop) tomcat on my MacBook there is 
some interaction with the window server on my mac (i.e., the finder 
process). I have no idea why this happens but I think it is java that 
tries to connect to the window server.

Are you sitting directly in the machine you try to run tomcat on? If you 
ssh into the machine you may be unable to connect to the window server 
since you must own the window server process. Try to log in directly to 
the mac server and start the services from a terminal. You may see some 
windows flash by during the start up phase. This experiment would be 
interesting. On my machine I allow Remote login (under the Sharing pane 
in System preferences) ... maybe that option resolves something.

Can you connect to the tomcat server at all? As Nicklas points out, try 
connecting to http://hostname:8080 and you should see a Tomcat welcome 
page. Also, the tomcat server user should own the work directory 
hierarchy. On my machine this user is 'www'.

I have a running BASE 3.2.3 server with Tomcat 6.0.35 and PostgreSQL 
9.3.0. Non-Apple software I almost always install Macports packages 
(tomcat and Postgresql). I run on Mac OSX 10.7.5 non-server version.

I think your issues are symptoms of a tomcat/java/mac window server clash.


Cheers,

Jari

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Nicklas N. <nic...@me...>]

Seems to me like there is some problem with the Tomcat installation. 
Unfortunately I am not very familiar with Mac so I am afraid I won't be 
of much help here.

Have you checked if you can access the Tomcat welcome page?

http://localhost:8080/

/Nicklas

On 2013-09-11 10:57, Laurent Troxler wrote:
>
> Le 10 sept. 2013 à 20:26, Nicklas Nordborg <nic...@me...
> <mailto:nic...@me...>> a écrit :
>
>> On 2013-09-10 16:35, Laurent Troxler wrote:
>>> Thank you Nicolas for your answer.
>>> It helped me to find out that I had missed the base.config file password
>>> setting.
>>> I thus could go through the all process.
>>
>> Great.
>>
>>> I am now facing an other problem linked to Tomcat.
>>> After setting the symbolic link between Tomcat and Base, when I go on
>>> the webpage http://hostname:8080/base2
>>> I get alternatively  :
>>
>> The /Library/Tomcat/work directory and subdirectories are directories
>> where Tomcat store temporary working files. Usually this is not
>> something one has to worry about. I can think of two reasons why the
>> directory referenced in the error message is empty:
>>
>>  1. The Tomcat process doesn't have write permission on the directory
> I have given the full rights to every one on
> /Library/Tomcat/work/Catalina/localhost/base2
> drwxrwxrwx  8 root  _appserveradm  272 22 aoû 11:47
> /Library/Tomcat/work/Catalina/localhost/base2
> Should it also need to change the owner ? But I do not know which user
> is Tomcat using
>
>>  2. The disk is full
> there is over a hundred Go, It should be enough
>>
>> It might be possible that there is more information in one of Tomcat's
>> log files (though I can't tell which one, the logging setup of Tomcat is
>> still a bit of a mystery to me...). At least, it seems like Tomcat is up
>> and running so it shouldn't be a Java issue.
>>
> going through the log files here is what I can get:
> system.log: repeating those two lines
> Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
> CGErrorBreakpoint() to catch errors as they are logged.
> Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
> Throttling respawn: Will start in 8 seconds
>
> /Library/Tomcat/logs/catalina.2013-09-11.log :
> Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
> initClassLoaders
> SEVERE: Class loader creation threw exception
> java.lang.InternalError: Can't connect to window server - not enough
> permissions.
> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827)
> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724)
> at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> at java.lang.System.loadLibrary(System.java:1045)
> at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
> at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
> at sun.awt.AppContext$2.run(AppContext.java:240)
> at sun.awt.AppContext$2.run(AppContext.java:226)
> at java.security.AccessController.doPrivileged(Native Method)
> at sun.awt.AppContext.initMainAppContext(AppContext.java:226)
> at sun.awt.AppContext.access$200(AppContext.java:112)
> at sun.awt.AppContext$3.run(AppContext.java:306)
> at java.security.AccessController.doPrivileged(Native Method)
> at sun.awt.AppContext.getAppContext(AppContext.java:287)
> at com.sun.jmx.trace.Trace.out(Trace.java:180)
> at com.sun.jmx.trace.Trace.isSelected(Trace.java:88)
> at
> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.isTraceOn(DefaultMBeanServerInterceptor.java:1830)
> at
> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerDynamicMBean(DefaultMBeanServerInterceptor.java:929)
> at
> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerObject(DefaultMBeanServerInterceptor.java:916)
> at
> com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerMBean(DefaultMBeanServerInterceptor.java:312)
> at com.sun.jmx.mbeanserver.JmxMBeanServer$2.run(JmxMBeanServer.java:1195)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> com.sun.jmx.mbeanserver.JmxMBeanServer.initialize(JmxMBeanServer.java:1193)
> at com.sun.jmx.mbeanserver.JmxMBeanServer.<init>(JmxMBeanServer.java:225)
> at com.sun.jmx.mbeanserver.JmxMBeanServer.<init>(JmxMBeanServer.java:170)
> at
> com.sun.jmx.mbeanserver.JmxMBeanServer.newMBeanServer(JmxMBeanServer.java:1401)
> at
> javax.management.MBeanServerBuilder.newMBeanServer(MBeanServerBuilder.java:93)
> at
> javax.management.MBeanServerFactory.newMBeanServer(MBeanServerFactory.java:311)
> at
> javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:214)
> at
> javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:175)
> at
> sun.management.ManagementFactory.createPlatformMBeanServer(ManagementFactory.java:302)
> at
> java.lang.management.ManagementFactory.getPlatformMBeanServer(ManagementFactory.java:504)
> at
> org.apache.catalina.startup.Bootstrap.createClassLoader(Bootstrap.java:183)
> at org.apache.catalina.startup.Bootstrap.initClassLoaders(Bootstrap.java:92)
> at org.apache.catalina.startup.Bootstrap.init(Bootstrap.java:207)
> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:391)
>
> /Library/Tomcat/logs/tomcat-launchd.stdout :
> Existing PID file found during start.
> Removing/clearing stale PID file.
> Existing PID file found during start.
> Removing/clearing stale PID file.
> Existing PID file found during start.
> Removing/clearing stale PID file.
> Existing PID file found during start.
> Removing/clearing stale PID file.
> Existing PID file found during start.
> Removing/clearing stale PID file.
>
> Does it helps ?
>
>
>> /Nicklas
>>
>>
>> ------------------------------------------------------------------------------
>> How ServiceNow helps IT people transform IT departments:
>> 1. Consolidate legacy IT systems to a single system of record for IT
>> 2. Standardize and globalize service processes across IT
>> 3. Implement zero-touch automation to replace manual, redundant tasks
>> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
>> _______________________________________________
>> The BASE general discussion mailing list
>> bas...@li...
>> unsubscribe: send a mail with subject "unsubscribe" to
>> bas...@li...
>

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Laurent T. <l.t...@un...>]

Le 10 sept. 2013 à 20:26, Nicklas Nordborg <nic...@me...> a écrit :

> On 2013-09-10 16:35, Laurent Troxler wrote:
>> Thank you Nicolas for your answer.
>> It helped me to find out that I had missed the base.config file password
>> setting.
>> I thus could go through the all process.
> 
> Great.
> 
>> I am now facing an other problem linked to Tomcat.
>> After setting the symbolic link between Tomcat and Base, when I go on
>> the webpage http://hostname:8080/base2
>> I get alternatively  :
> 
> The /Library/Tomcat/work directory and subdirectories are directories 
> where Tomcat store temporary working files. Usually this is not 
> something one has to worry about. I can think of two reasons why the 
> directory referenced in the error message is empty:
> 
>  1. The Tomcat process doesn't have write permission on the directory
I have given the full rights to every one on /Library/Tomcat/work/Catalina/localhost/base2
drwxrwxrwx  8 root  _appserveradm  272 22 aoû 11:47  /Library/Tomcat/work/Catalina/localhost/base2
Should it also need to change the owner ? But I do not know which user is Tomcat using

>  2. The disk is full
there is over a hundred Go, It should be enough
> 
> It might be possible that there is more information in one of Tomcat's 
> log files (though I can't tell which one, the logging setup of Tomcat is 
> still a bit of a mystery to me...). At least, it seems like Tomcat is up 
> and running so it shouldn't be a Java issue.
> 
going through the log files here is what I can get:
system.log: repeating those two lines
Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.
Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat): Throttling respawn: Will start in 8 seconds

/Library/Tomcat/logs/catalina.2013-09-11.log :
Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap initClassLoaders
SEVERE: Class loader creation threw exception
java.lang.InternalError: Can't connect to window server - not enough permissions.
	at java.lang.ClassLoader$NativeLibrary.load(Native Method)
	at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827)
	at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724)
	at java.lang.Runtime.loadLibrary0(Runtime.java:823)
	at java.lang.System.loadLibrary(System.java:1045)
	at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
	at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
	at sun.awt.AppContext$2.run(AppContext.java:240)
	at sun.awt.AppContext$2.run(AppContext.java:226)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.awt.AppContext.initMainAppContext(AppContext.java:226)
	at sun.awt.AppContext.access$200(AppContext.java:112)
	at sun.awt.AppContext$3.run(AppContext.java:306)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.awt.AppContext.getAppContext(AppContext.java:287)
	at com.sun.jmx.trace.Trace.out(Trace.java:180)
	at com.sun.jmx.trace.Trace.isSelected(Trace.java:88)
	at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.isTraceOn(DefaultMBeanServerInterceptor.java:1830)
	at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerDynamicMBean(DefaultMBeanServerInterceptor.java:929)
	at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerObject(DefaultMBeanServerInterceptor.java:916)
	at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerMBean(DefaultMBeanServerInterceptor.java:312)
	at com.sun.jmx.mbeanserver.JmxMBeanServer$2.run(JmxMBeanServer.java:1195)
	at java.security.AccessController.doPrivileged(Native Method)
	at com.sun.jmx.mbeanserver.JmxMBeanServer.initialize(JmxMBeanServer.java:1193)
	at com.sun.jmx.mbeanserver.JmxMBeanServer.<init>(JmxMBeanServer.java:225)
	at com.sun.jmx.mbeanserver.JmxMBeanServer.<init>(JmxMBeanServer.java:170)
	at com.sun.jmx.mbeanserver.JmxMBeanServer.newMBeanServer(JmxMBeanServer.java:1401)
	at javax.management.MBeanServerBuilder.newMBeanServer(MBeanServerBuilder.java:93)
	at javax.management.MBeanServerFactory.newMBeanServer(MBeanServerFactory.java:311)
	at javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:214)
	at javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:175)
	at sun.management.ManagementFactory.createPlatformMBeanServer(ManagementFactory.java:302)
	at java.lang.management.ManagementFactory.getPlatformMBeanServer(ManagementFactory.java:504)
	at org.apache.catalina.startup.Bootstrap.createClassLoader(Bootstrap.java:183)
	at org.apache.catalina.startup.Bootstrap.initClassLoaders(Bootstrap.java:92)
	at org.apache.catalina.startup.Bootstrap.init(Bootstrap.java:207)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:391)

/Library/Tomcat/logs/tomcat-launchd.stdout :
Existing PID file found during start.
Removing/clearing stale PID file.
Existing PID file found during start.
Removing/clearing stale PID file.
Existing PID file found during start.
Removing/clearing stale PID file.
Existing PID file found during start.
Removing/clearing stale PID file.
Existing PID file found during start.
Removing/clearing stale PID file.

 
Does it helps ?


> /Nicklas
> 
> 
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Nicklas N. <nic...@me...>]

On 2013-09-10 16:35, Laurent Troxler wrote:
> Thank you Nicolas for your answer.
> It helped me to find out that I had missed the base.config file password
> setting.
> I thus could go through the all process.

Great.

> I am now facing an other problem linked to Tomcat.
> After setting the symbolic link between Tomcat and Base, when I go on
> the webpage http://hostname:8080/base2
> I get alternatively  :

The /Library/Tomcat/work directory and subdirectories are directories 
where Tomcat store temporary working files. Usually this is not 
something one has to worry about. I can think of two reasons why the 
directory referenced in the error message is empty:

  1. The Tomcat process doesn't have write permission on the directory
  2. The disk is full

It might be possible that there is more information in one of Tomcat's 
log files (though I can't tell which one, the logging setup of Tomcat is 
still a bit of a mystery to me...). At least, it seems like Tomcat is up 
and running so it shouldn't be a Java issue.

/Nicklas

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Laurent T. <l.t...@un...>]

Thank you Nicolas for your answer.
It helped me to find out that I had missed the base.config file password setting.
I thus could go through the all process.
I am now facing an other problem linked to Tomcat. 
After setting the symbolic link between Tomcat and Base, when I go on the webpage  http://hostname:8080/base2
I get alternatively  :

Etat HTTP 500 -

type Rapport d'exception

message

description Le serveur a rencontré une erreur interne () qui l'a empêché de satisfaire la requête.

exception

org.apache.jasper.JasperException: Impossible de charger la classe pour la JSP
	org.apache.jasper.JspCompilationContext.load(JspCompilationContext.java:630)
	org.apache.jasper.servlet.JspServletWrapper.getServlet(JspServletWrapper.java:149)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:340)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69)

cause mère

java.lang.ClassNotFoundException: org.apache.jsp.index_jsp
	java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	java.security.AccessController.doPrivileged(Native Method)
	java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:134)
	org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:66)
	org.apache.jasper.JspCompilationContext.load(JspCompilationContext.java:628)
	org.apache.jasper.servlet.JspServletWrapper.getServlet(JspServletWrapper.java:149)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:340)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69)


Or 

Etat HTTP 500 -

type Rapport d'exception

message

description Le serveur a rencontré une erreur interne () qui l'a empêché de satisfaire la requête.

exception

java.io.FileNotFoundException: /Library/Tomcat/work/Catalina/localhost/base2/org/apache/jsp/index_jsp.java (No such file or directory)
	java.io.FileOutputStream.open(Native Method)
	java.io.FileOutputStream.<init>(FileOutputStream.java:194)
	java.io.FileOutputStream.<init>(FileOutputStream.java:84)
	org.apache.jasper.compiler.Compiler.setupContextWriter(Compiler.java:298)
	org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:230)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:354)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:321)
	org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:592)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69)


I have looked in for the /Library/Tomcat/work/Catalina/localhost/base2/org/apache/jsp/index_jsp.java file but
the  /Library/Tomcat/work/Catalina/localhost/base2 directory is empty.
Another configuration problem ? I guess with Java this time. I am using Java 6

About Jari's suggestion for the firewall. Could it be also blocked when I am doing the test on the server it's self ?

Thanks for your help.

Le 10 sept. 2013 à 10:06, Jari Häkkinen <jar...@me...> a écrit :

> Make sure that the firewall isn't blocking the connection. I am not sure 
> how server internal connections to the database manager are treated by 
> the firewall.
> 
> Cheers,
> 
> Jari
> 
> On 2013-09-10 09:37, Nicklas Nordborg wrote:
>> On 2013-09-09 16:04, Laurent Troxler wrote:
>>> Hello  all, Ì am new at Base and trying to install it on a Mac OS
>>> 10.6 server. Looking in the mailing list archives did not bring me
>>> any helping information, Mac OS does not appear often. Therefore I
>>> submit you my problem. After downloading and unpacking Base, setting
>>> Apache, MySQL, TomCat, and configuring Base I reached the step of the
>>> database initialization with the instruction : ./initdb.sh
>>> [base_root_login] base_root_password Below is what I get in return on
>>> my terminal. I am using the Base root login and password defined in
>>> MySQL but it looks like it is not recognized. Is there anyone having
>>> faced such problem in similar configuration or having suggestion
>> 
>> It seems like the root problem is that MySQL is not letting the BASE
>> installation to connect to the database.
>> 
>> The first step is to verify/make sure that you can connect manually to
>> MySQL using the same username and password as you have specified in the
>> base.config file. Depending on how networking is set up it may help to
>> replace 'localhost' with '127.0.0.1' when granting access to MySQL and
>> in the 'base.config' file (db.url setting).
>> 
>> /Nicklas
>> 
>> 
>> ------------------------------------------------------------------------------
>> How ServiceNow helps IT people transform IT departments:
>> 1. Consolidate legacy IT systems to a single system of record for IT
>> 2. Standardize and globalize service processes across IT
>> 3. Implement zero-touch automation to replace manual, redundant tasks
>> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
>> _______________________________________________
>> The BASE general discussion mailing list
>> bas...@li...
>> unsubscribe: send a mail with subject "unsubscribe" to
>> bas...@li...
>> 
> 
> -- 
> "For a successful technology, reality must take precedence over public 
> relations, for nature cannot be fooled." - Richard P. Feynman, Rogers 
> Commission Report 1986
> 
> 
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Jari H. <jar...@me...>]

Make sure that the firewall isn't blocking the connection. I am not sure 
how server internal connections to the database manager are treated by 
the firewall.

Cheers,

Jari

On 2013-09-10 09:37, Nicklas Nordborg wrote:
> On 2013-09-09 16:04, Laurent Troxler wrote:
>> Hello  all, Ì am new at Base and trying to install it on a Mac OS
>> 10.6 server. Looking in the mailing list archives did not bring me
>> any helping information, Mac OS does not appear often. Therefore I
>> submit you my problem. After downloading and unpacking Base, setting
>> Apache, MySQL, TomCat, and configuring Base I reached the step of the
>> database initialization with the instruction : ./initdb.sh
>> [base_root_login] base_root_password Below is what I get in return on
>> my terminal. I am using the Base root login and password defined in
>> MySQL but it looks like it is not recognized. Is there anyone having
>> faced such problem in similar configuration or having suggestion
>
> It seems like the root problem is that MySQL is not letting the BASE
> installation to connect to the database.
>
> The first step is to verify/make sure that you can connect manually to
> MySQL using the same username and password as you have specified in the
> base.config file. Depending on how networking is set up it may help to
> replace 'localhost' with '127.0.0.1' when granting access to MySQL and
> in the 'base.config' file (db.url setting).
>
> /Nicklas
>
>
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...
>

-- 
"For a successful technology, reality must take precedence over public 
relations, for nature cannot be fooled." - Richard P. Feynman, Rogers 
Commission Report 1986

Re: [base] Base 3.2 installation on Mac OS 10.6 server

[Nicklas N. <nic...@me...>]

On 2013-09-09 16:04, Laurent Troxler wrote:
> Hello  all, Ì am new at Base and trying to install it on a Mac OS
> 10.6 server. Looking in the mailing list archives did not bring me
> any helping information, Mac OS does not appear often. Therefore I
> submit you my problem. After downloading and unpacking Base, setting
> Apache, MySQL, TomCat, and configuring Base I reached the step of the
> database initialization with the instruction : ./initdb.sh
> [base_root_login] base_root_password Below is what I get in return on
> my terminal. I am using the Base root login and password defined in
> MySQL but it looks like it is not recognized. Is there anyone having
> faced such problem in similar configuration or having suggestion

It seems like the root problem is that MySQL is not letting the BASE
installation to connect to the database.

The first step is to verify/make sure that you can connect manually to 
MySQL using the same username and password as you have specified in the 
base.config file. Depending on how networking is set up it may help to 
replace 'localhost' with '127.0.0.1' when granting access to MySQL and 
in the 'base.config' file (db.url setting).

/Nicklas

[base] Base 3.2 installation on Mac OS 10.6 server

[Laurent T. <l.t...@un...>]

Hello  all,
Ì am new at Base and trying to install it on a Mac OS 10.6 server.
Looking in the mailing list archives did not bring me any helping information, Mac OS does not appear often. 
Therefore I submit you my problem.
After downloading and unpacking Base, setting Apache, MySQL, TomCat, and configuring Base I reached the step of the database initialization with the instruction :
./initdb.sh [base_root_login] base_root_password
Below is what I get in return on my terminal. I am using the Base root login and password defined in MySQL but it looks like it is not recognized. 
Is there anyone having faced such problem in similar configuration or having suggestion
Thank in advance for your help
Laurent


[0%]	--System information-----------------------------
BASE     : 3.2.2(build 6266)
Database : jdbc:mysql://localhost/base2?characterEncoding=UTF-8&useCursorFetch=true&defaultFetchSize=100&useServerPrepStmts=true
Dialect  : org.hibernate.dialect.MySQL5InnoDBDialect
JDBC     : com.mysql.jdbc.Driver; version 5.1
Java     : Java(TM) SE Runtime Environment; 1.6.0_51-b11-457-10M4509; Apple Inc.
OS       : Mac OS X; x86_64; 10.6.8
-------------------------------------------------15:18:17,129  WARN ThreadPoolAsynchronousRunner:608 - com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector@7578a7d9 -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
15:18:17,134  WARN ThreadPoolAsynchronousRunner:624 - com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector@7578a7d9 -- APPARENT DEADLOCK!!! Complete Status: 
	Managed Threads: 3
	Active Threads: 3
	Active Tasks: 
		com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@6dabbec4 (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1)
		com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@26796e1c (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0)
		com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@6e2c03ff (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2)
	Pending Tasks: 
		com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@bba92db
Pool thread stack traces:
	Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1,5,main]
		java.lang.Thread.sleep(Native Method)
		com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1805)
		com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
	Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0,5,main]
		java.lang.Thread.sleep(Native Method)
		com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1805)
		com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
	Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2,5,main]
		java.lang.Thread.sleep(Native Method)
		com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1805)
		com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)


15:18:26,686  WARN BasicResourcePool:1841 - com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@6dabbec4 -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (30). Last acquisition attempt exception: 
java.sql.SQLException: Access denied for user 'base2user'@'localhost' (using password: YES)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1078)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4190)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4122)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:927)
	at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:4689)
	at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1304)
	at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2486)
	at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2519)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2304)
	at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
	at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
	at sun.reflect.GeneratedConstructorAccessor11.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
	at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
	at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:346)
	at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:135)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
	at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:137)
	at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1014)
	at com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
	at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1810)
	at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
15:18:26,687  WARN BasicResourcePool:1841 - com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@6e2c03ff -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (30). Last acquisition attempt exception: 
java.sql.SQLException: Access denied for user 'base2user'@'localhost' (using password: YES)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1078)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4190)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4122)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:927)
	at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:4689)
	at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1304)
	at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2486)
	at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2519)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2304)
	at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
	at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
	at sun.reflect.GeneratedConstructorAccessor11.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
	at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
	at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:346)
	at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:135)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
	at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:137)
	at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1014)
	at com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
	at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1810)
	at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
15:18:26,689  WARN BasicResourcePool:1841 - com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@26796e1c -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (30). Last acquisition attempt exception: 
java.sql.SQLException: Access denied for user 'base2user'@'localhost' (using password: YES)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1078)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4190)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4122)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:927)
	at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:4689)
	at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1304)
	at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2486)
	at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2519)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2304)
	at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
	at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
	at sun.reflect.GeneratedConstructorAccessor11.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
	at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
	at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:346)
	at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:135)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
	at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:137)
	at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1014)
	at com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
	at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1810)
	at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)

[0%]	Building database...15:18:46,242  WARN BasicResourcePool:1841 - com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask@bba92db -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (30). Last acquisition attempt exception: 
java.sql.SQLException: Access denied for user 'base2user'@'localhost' (using password: YES)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1078)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4190)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4122)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:927)
	at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:4689)
	at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1304)
	at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2486)
	at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2519)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2304)
	at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
	at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
	at sun.reflect.GeneratedConstructorAccessor11.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
	at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
	at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:346)
	at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:135)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
	at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
	at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:137)
	at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1014)
	at com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
	at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1810)
	at com.mchange.v2.async.ThreadPerTaskAsynchronousRunner$TaskThread.run(ThreadPerTaskAsynchronousRunner.java:255)

[30%]	Building database failed: Connections could not be acquired from the underlying database!


net.sf.basedb.core.BaseException: Connections could not be acquired from the underlying database!
	at net.sf.basedb.core.HibernateUtil.newSession(HibernateUtil.java:1053)
	at net.sf.basedb.core.HibernateUtil.newSession(HibernateUtil.java:995)
	at net.sf.basedb.core.HibernateUtil.isEmptyDatabase(HibernateUtil.java:666)
	at net.sf.basedb.core.HibernateUtil.createStaticTables(HibernateUtil.java:627)
	at net.sf.basedb.core.Install.createTables(Install.java:139)
	at net.sf.basedb.install.InitDB.main(InitDB.java:75)
Caused by: java.sql.SQLException: Connections could not be acquired from the underlying database!
	at com.mchange.v2.sql.SqlUtils.toSQLException(SqlUtils.java:106)
	at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C3P0PooledConnectionPool.java:529)
	at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getConnection(AbstractPoolBackedDataSource.java:128)
	at org.hibernate.connection.C3P0ConnectionProvider.getConnection(C3P0ConnectionProvider.java:78)
	at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446)
	at org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167)
	at org.hibernate.impl.SessionImpl.doWork(SessionImpl.java:1997)
	at net.sf.basedb.core.HibernateUtil.doJdbcWork(HibernateUtil.java:1146)
	at net.sf.basedb.core.HibernateUtil.newSession(HibernateUtil.java:1029)
	... 5 more
Caused by: com.mchange.v2.resourcepool.CannotAcquireResourceException: A ResourcePool could not acquire a resource from its primary factory or source.
	at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable(BasicResourcePool.java:1319)
	at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckoutResource(BasicResourcePool.java:557)
	at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResource(BasicResourcePool.java:477)
	at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C3P0PooledConnectionPool.java:525)
	... 12 more

[base] BASE 3.2.3 has been released

[Nicklas N. <nic...@me...>]

Hello all,

We have released BASE 3.2.3 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.3&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

Re: [base] BASE database

[Jari H. <jar...@me...>]

We have realized that migration from BASE 1.2 to BASE 2/3 is only 
supported from a BASE 1.2 server running MySQL.

We do think that adding support for other database engines is possible 
but we have not tested it and will not actively work on extending 
migration support beyond what can be found in BASE 2.15. I simply write 
this as information for interested users

The path forward to add support for BASE 1.2 migration from a non-MySQL 
installation is to create a version of

http://base.thep.lu.se/browser/tags/2.15/config/dist/mysql-migration-queries.sql

for the database engine in use. Then change parameter queryStatementFile 
in migrate.properties to point to your new sql definition file. Some 
change in the migration code may be needed as well.

We cannot estimate how much work is needed to be successful.


Jari

Re: [base] BASE database

[Jari H. <ja...@th...>]

Hi,

The procedure to upgrade from 1.2 to latest BASE is uncharted territory 
for us. We switched from 1.2 when BASE 2.6 was current. One path forward 
may be as outlined below. Each BASE 2 and newer distribution contains 
upgrade instructions. Please read them.

Please report if you succeed and use the mailing list for further 
assistance so we can share this experience with the community.

Good Luck,

Jari


0) Backup your precious data.

1) Upgrade to latest 1.2.x version, i.e., version 1.2.17b available from 
http://base2.thep.lu.se/base1.2/

There are some notes regarding upgrading I found in the waybackmachine, 
http://web.archive.org/web/20070210105058/http://base1.thep.lu.se/

Update from 1.2.17: Fixed compilation errors with gcc 4.0.
BASE 1.2.17: This release of BASE contains a number of minor fixes and 
some somewhat bigger changes. If you are upgrading from an older 
version, there are few things you need to do in addition to running the 
database migration script:
- If you are using PHP 4.4.x, you have to make some changes to the files 
in include/local (reporter_columns.inc.php and raw_columns.inc.php) to 
get rid of warnings about assign-by-reference. If you haven't modified 
these files, simply remove them from where you have installed BASE 
before doing the 'make install', and they will be replaced by the newest 
version. If you have modified them, you should instead replace all 
occurences of "=&" with a plain "=".
- The disk quota system has been extended to cover not only uploads but 
also experiments, raw data and other big things. For this to work the 
disk usage of existing users must be calculated and stored. Do this by 
running bin/refreshQuotaUsage.php before starting BASE after you've run 
dbmigrate_1.2_to_latest.php. There's more info in the new admin guide 
(in documentation/ and on the web site).
- When exporting data for plugins, files in the 'normal' BASEfile format 
are now created from the serial format by an external program to reduce 
the time it takes. The program requires a valid BASEfile, with a header 
called 'section', and this could cause problems with some plugins whose 
definitions do not have a hidden parameter called 'section'. Such 
plugins need to be corrected.
- It has been made easier to add new patterns for merging four 96-well 
plates into a 384-well plate. Changes to the PHP code are no longer 
necessary for this. The description of how to do it can be found in a 
couple of comments in plates.inc.php.

* PHP 5.0 has not yet been fully tested with BASE although it might 
actually work.


2) Following the advice in 
http://base.thep.lu.se/chrome/site/2.17/html/admindoc/installation_upgrade/installation_upgrade.migration.html 
Upgrade then to BASE version 2.15.0 available for download from 
http://base.thep.lu.se/wiki/DownloadOld

Read the migration program instructions carefully we haven't done that 
for several years ourselves. The migration may take long time.


3) Upgrade to latest BASE 2 version, 2.17.2 available from 
http://base.thep.lu.se/wiki/DownloadPage


4) Finally, upgrade to latest BASE 3 version 3.2.2 available at 
http://base.thep.lu.se/wiki/DownloadPage



On 2013-05-07 09:42, Franck Samson wrote:
> Hello Sir,
>
> I'm looking for help on the BASEprogram, here is our situation we have a
> very old version of BASE (1.2 I think, the php version) and we would
> like to make it evolve to the latest version available, however the
> update tool run with this old version, Is there a way to make an update
> of our database to the latest version of BASE interface?
>
> Thank you for your help,
> Sincerely,

[base] unsubscribe

[Huang, W. [AGRON] <we...@ia...>]

________________________________________
From: Nicklas Nordborg [nic...@me...]
Sent: Wednesday, April 10, 2013 4:42 AM
To: BASE ML; BASE dev; bas...@li...
Subject: [base] BASE 3.2.2 has been released

Hello all,

We have released BASE 3.2.2 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.2&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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apps and a phenomenal toolset for data science. Developers can use
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The BASE general discussion mailing list
bas...@li...
unsubscribe: send a mail with subject "unsubscribe" to
bas...@li...

[base] BASE 3.2.2 has been released

[Nicklas N. <nic...@me...>]

Hello all,

We have released BASE 3.2.2 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.2&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

[base] BASE 3.2.1 has been released

[Nicklas N. <ni...@th...>]

Hello all,

We have released BASE 3.2.1 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.1&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

Re: [base] Error on Biomaterials LIMS

[Paulo N. <nu...@ge...>]

It works fine now, thanks for the help. I guess I missed that spot on the second install I performed.

Thanks a lot

Paulo


On 2012-11-22, at 2:19 PM, Nicklas Nordborg <ni...@th...> wrote:

> On 2012-11-22 19:40, Paulo Nuin wrote:
>> Hi
>> 
>> We have a couple of instances of BASE installed in our systems. We are
>> getting a problem whenever we are accessing entities created in the
>> Biomaterial LIMS, either samples or biosources:
> 
> This is a Tomcat configuration problem and is described in the 
> installation documentation:
> 
> http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html
> 
> Check the section about STRICT_QUOTE_ESCAPING and make sure that this is 
> set to 'false'.
> 
> Hope this helps.
> 
> /Nicklas
> 
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] Error on Biomaterials LIMS

[Nicklas N. <ni...@th...>]

On 2012-11-22 19:40, Paulo Nuin wrote:
> Hi
>
> We have a couple of instances of BASE installed in our systems. We are
> getting a problem whenever we are accessing entities created in the
> Biomaterial LIMS, either samples or biosources:

This is a Tomcat configuration problem and is described in the 
installation documentation:

http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html

Check the section about STRICT_QUOTE_ESCAPING and make sure that this is 
set to 'false'.

Hope this helps.

/Nicklas

[base] Error on Biomaterials LIMS

[Paulo N. <nu...@ge...>]

Hi

We have a couple of instances of BASE installed in our systems. We are getting a problem whenever we are accessing entities created in the Biomaterial LIMS, either samples or biosources:

type Exception report

message

description The server encountered an internal error () that prevented it from fulfilling this request.

exception

org.apache.jasper.JasperException: /biomaterials/samples/view_sample.jsp(191,28) Attribute value "index.jsp?ID="+ID is quoted with " which must be escaped when used within the value
	org.apache.jasper.compiler.DefaultErrorHandler.jspError(DefaultErrorHandler.java:40)
	org.apache.jasper.compiler.ErrorDispatcher.dispatch(ErrorDispatcher.java:407)
	org.apache.jasper.compiler.ErrorDispatcher.jspError(ErrorDispatcher.java:88)
	org.apache.jasper.compiler.Parser.parseAttributeValue(Parser.java:256)
	org.apache.jasper.compiler.Parser.parseAttribute(Parser.java:205)
	org.apache.jasper.compiler.Parser.parseAttributes(Parser.java:148)
	org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1208)
	org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422)
	org.apache.jasper.compiler.Parser.parseBody(Parser.java:1634)
	org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:978)
	org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1246)
	org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422)
	org.apache.jasper.compiler.Parser.parseBody(Parser.java:1634)
	org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:978)
	org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1246)
	org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422)
	org.apache.jasper.compiler.Parser.parseBody(Parser.java:1634)
	org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:978)
	org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1246)
	org.apache.jasper.compiler.Parser.parseElements(Parser.java:1422)
	org.apache.jasper.compiler.Parser.parse(Parser.java:130)
	org.apache.jasper.compiler.ParserController.doParse(ParserController.java:255)
	org.apache.jasper.compiler.ParserController.parse(ParserController.java:103)
	org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:185)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:354)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:321)
	org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:592)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:709)
	org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:680)
	org.apache.jsp.biomaterials.samples.index_jsp._jspService(index_jsp.java:522)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:388)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69)

note The full stack trace of the root cause is available in the Apache Tomcat/6.0.33 logs.



Any help is appreciated.

Thanks
Paulo

Re: [base] loop designs and duplicate annotations

[Boer, T.E. d. <te....@vu...>]

Ah, thanks Nicklas!

I guess I should have picked this up from the manual,  I will give it a try

Tjalf

Re: [base] loop designs and duplicate annotations

[Nicklas N. <ni...@th...>]

On 2012-11-13 15:56, Boer, T.E. de wrote:
> Hello
>
> I have recently installed and started using BASE for our microarray
> data and I am at the moment importing already existing data into the
> database. We use custom two color Agilent microarrays and our
> experiments often use loop designs instead of reference designs.
> Using a loop design means that for most microarrays both labeled
> extracts are important for the analysis (since both contain exposure
> data instead of one being exposure data set against a reference
> sample). Because of this, raw bioassays have to inherit annotations
> from both extracts but when I design experiments I get errors and
> warnings about duplicate annotations. Is there a way that BASE can
> deal with dual color data where annotations have to be used for both
> color channels and if so how is this done?

When the "Overview" tab is visible, click on the "Validation options" 
button. In the popup dialog, expand the "Annotations" section and change 
the setting for "Inheriting multiple annotation of same type"
to "Ignore".

The documentation has some screen shots and more information: 
http://base.thep.lu.se/chrome/site/latest/html/user/webclient/itemoverview.html

Hope this helps.

/Nicklas

[base] loop designs and duplicate annotations

[Boer, T.E. d. <te....@vu...>]

Hello

I have recently installed and started using BASE for our microarray data and I am at the moment importing already existing data into the database. We use custom two color Agilent microarrays and our experiments often use loop designs instead of reference designs. Using a loop design means that for most microarrays both labeled extracts are important for the analysis (since both contain exposure data instead of one being exposure data set against a reference sample). Because of this, raw bioassays have to inherit annotations from both extracts but when I design experiments I get errors and warnings about duplicate annotations. Is there a way that BASE can deal with dual color data where annotations have to be used for both color channels and if so how is this done?


Thanks in advance and kind regards
Tjalf de Boer
VU University Amsterdam