basedb-users — General BASE mailing list

[base] BASE 3.3.1 hase been released

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

Hello all,

We have released BASE 3.3.1 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+3.3.1&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] BASE3 paper?

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

Hi Bob,

We have been thinking about a NextGen BASE paper for some time now where 
we describe an RNAseq use case and highlight new features in BASE 3.x. 
We do not have a deadline for when the paper will be submitted but we do 
expect to submit the article during this fall.

Cheers,

Jari


On 2014-09-09 14:22, Bob MacCallum wrote:
> Hi Nicklas et al,
> Will there be a "Third generation" BASE paper we can cite any time soon?
> Happy to continue to cite the 2009 paper but I was just wondering!
> cheers,
> Bob
>
>
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[base] BASE3 paper?

[Bob M. <r.m...@im...>]

Hi Nicklas et al,
Will there be a "Third generation" BASE paper we can cite any time soon?
Happy to continue to cite the 2009 paper but I was just wondering!
cheers,
Bob

Re: [base] BASE Schema

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

On 2014-09-03 19:45, Rachad El-Badrawi wrote:
> Hi All,
>
> We are considering BASE as the molecular diagnostics backend system for
> a project, and I was trying to figure out some of the backend workings
> of the schema. I would appreciate some feedback on the following:
>
> 1) Is there a document that explains the PG schema that BASE uses, as
> far as the role of each table, and how it fits in the global model for BASE?

The best documentation related to this can be found at 
http://base.thep.lu.se/chrome/site/latest/html/developer/api/data_api.html

It's not really a database schema, but a mix of java classes and how 
they map to the database. It should be fairly up to date but may lack 
some information about the latest new features. There are lots of 
details and you probably also want to read 
http://base.thep.lu.se/chrome/site/latest/html/developer/documentation/magicdraw.html


> 2) Is there an instance of BASE which includes a comprehensive project
> that shows the meaningful use for the database?

There is a BASE demo server at http://base2.thep.lu.se/demo/ but it has 
not been maintained for some time so I think what you can see there may 
not be very helpful.

There is also a document describing a manual test procedure that is 
performed before any new major release at: 
http://base.thep.lu.se/chrome/site/latest/test/roles/index.html

This test go through most major features in BASE, but in a real scenario 
one would probably want to automate some of the steps since it requires 
a lot of clicking...

Also, the test data set we use is not publicly available so it may 
require several changes to work with other kind of data.

>
> At a more detailed level:
>
> 3) Patients/Subjects are entered as Biosources (from the web front end),
> and are saved in the BioMaterials table. Samples from these subjects are
> added as Samples (from the web front end) and are saved in the same
> BioMaterials table, too. Same for extracts. To relate these entries
> together, one can make use of the parent_id column and the discriminator
> level (i.e. 1, 2, 3). Is this explanation accurate?

Kind of, but it is not the full picture...

The parent_id column is a shortcut that is used only for items that has 
a single parent. If you, for example, pool several extracts into a 
single one, the parent_id column can't be used. The actual parent/child 
relationship is always stored in the BioMaterialEvents and 
BioMaterialEventSources2 tables, and is only duplicated in the parent_id 
column if possible.


> 4) Is there a way of entering/saving that a specific sample has been
> analyzed/complete?

You could use annotations for that. That is more or less what we do 
currently, combined with other annotations for flagging if something 
needs to re-done.

>
> 5) The number in the column event_type in the BioMaterialEvents table,
> what does it reference?

It is the type of the event. Every biomaterial has a single CREATION (1) 
event, then they can have any number of OTHER (3) events and BIOASSAY 
(2) creation events.

>
> 6) Where is the sample type saved in the database?

In the ItemSubtypes table.

Hope this helpful, you are always welcome with more questions.

/Nicklas

[base] BASE Schema

[Rachad El-B. <rel...@oc...>]

Hi All,

We are considering BASE as the molecular diagnostics backend system for a project, and I was trying to figure out some of the backend workings of the schema. I would appreciate some feedback on the following:

1) Is there a document that explains the PG schema that BASE uses, as far as the role of each table, and how it fits in the global model for BASE?

2) Is there an instance of BASE which includes a comprehensive project that shows the meaningful use for the database?

At a more detailed level:

3) Patients/Subjects are entered as Biosources (from the web front end), and are saved in the BioMaterials table. Samples from these subjects are added as Samples (from the web front end) and are saved in the same BioMaterials table, too. Same for extracts. To relate these entries together, one can make use of the parent_id column and the discriminator level (i.e. 1, 2, 3). Is this explanation accurate?

4) Is there a way of entering/saving that a specific sample has been analyzed/complete?

5) The number in the column event_type in the BioMaterialEvents table, what does it reference?

6) Where is the sample type saved in the database?

Thanks for your feedback.

Rachad Badrawi
Data Integration Manager,
Ontario Cancer Biomarker Network (OCBN).
Adjunct Lecturer,
Department of Pathology and Molecular Medicine,
Queen's University.

[base] BASE 3.3 has been released

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

Hello all,

We have released BASE 3.3! It is a new major release that includes 
several new features and enhancements. It may require some changes to 
the BASE server and/or and upgrade of the browser used to access BASE:

     * We now require Java 7 and Tomcat 7 on the server. If you
       are still using older versions, they should be upgraded
       before upgrading BASE.

     * The web interface has been reworked behind the scenes. Some
       (very old) browser may no longer work. It should be safe with
       IE 10 or a recent Firefox version.

     * The security in the web interface has been tightened in order
       to prevent cross-site scripting attacks. This can affect
       extensions. See the documentation for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3&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] Files with FTP locations only

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

>     So, I am currently working on an extension that add support for
>     accessing external files via FTP, FTPS and SFTP (see
>     http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles). I might be
>     able to release a first version later this week if you want to try it.

I have now "Xfiles 1.0". You'll need the BASE 3.3 beta 2 release to make 
it work. Download and documentation is available on:

http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles

/Nicklas

[base] BASE 3.3-beta-2 has been released

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

A new beta-version of BASE 3.3 is now available for download. This fixes 
some minor issues since the last release. I don't expect any major 
issues to popup, but due to summer vacations a final BASE 3.3 release 
should not be expected until August or September.

/Nicklas


-------- Original Message --------
Subject: [basedb-devel] BASE 3.3-beta-1 has been released
Date: Wed, 4 Jun 2014 09:52:30 +0200
From: Nicklas Nordborg <nic...@me...>
Reply-To: BASE dev <bas...@li...>
To: BASE ML <bas...@li...>, BASE dev 
<bas...@li...>, 
<bas...@li...>

Hello all,

We have released BASE 3.3-beta-1 today! It is a new major
release that includes several new features and enhancements.

     * We now require Java 7 and Tomcat 7 on the server. If you
       are still using older versions, they should be upgraded
       before upgrading BASE.

     * The web interface has been reworked behind the scenes. Some
       (very old) browser may no longer work. It should be safe with
       IE 10 or a recent Firefox version.

     * The security in the web interface has been tightened in order
       to prevent cross-site scripting attacks. This can affect
       extensions. See the documentation for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/3.3-beta/html/admin/installation.html

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

/Nicklas

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Re: [base] Files with FTP locations only

[Bob M. <r.m...@im...>]

Thanks Nicklas,
Sorry I hadn't seen the existing functionality - we will check it all out
and get back to you soon!



On Tue, Jun 24, 2014 at 12:42 PM, Nicklas Nordborg <
nic...@me...> wrote:

> On 2014-06-24 11:55, Bob MacCallum wrote:
> > Hi Nicklas et al,
> >
> > Getting up to speed with BASE3 and NGS - so far all seems good - even
> > upgrading our own API code has gone smoother than I expected.  Thanks!
>
> Great to hear that it is going well.
>
> >
> > A possible feature request for general discussion:
> >
> > Would it be possible to have "placeholder" files in the BASE file system
> > which weren't on disk but had an FTP location stored in the DB?   It
> > would be a bit like the current "offline" option but for our use case
> > (fastq and BAM files stored elsewhere and never processed by BASE3 or
> > plugins) we would never even upload the files in the first place (I
> > can't find a way to create a file that is offline from the start).
> >
> > The debate for other users/devs would be: should BASE automatically
> > retrieve the files when needed?  I say no need for that - treat them
> > like offline files are currently (if I understand correctly how offline
> > files work).
>
> There is already the *external files* feature. It can accessed with "New
> URL" in the BASE file manager. It's not the same as an *offline* file
> since by default BASE will try to check if it exists and download some
> metadata (such as size and modification date). And BASE will also
> retrieve the file if is requested by a plug-in or a user tries to
> download or view it.
>
> The external files feature is "pluggable" and the BASE core only provide
> support for files that can be accessed with http or https. In theory it
> is possible to register unsupported URLs (eg. ftp://...) but I guess
> error messages will popup here and there.
>
> As it happens, we discussed a similar problem last week. Up until now,
> our approach has been to simply store the file path as an annotation on
> bioassay items. In the future we'll need to provide access for external
> researchers to our data, but we really don't want to have them on our
> internal file servers so the idea is to let BASE act as a proxy.
>
> So, I am currently working on an extension that add support for
> accessing external files via FTP, FTPS and SFTP (see
> http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles). I might be
> able to release a first version later this week if you want to try it.
>
> If you prefer the *offline* files feature there is unfortunately no
> support in the GUI for creating offline files without first uploading
> them. A possible solution would be to modify the "New URL" dialog to
> make the "URL" field optional, and use this to decide between
> offline/external file.
>
> If you have any other ideas please let me know...
>
> /Nicklas
>
>
>
> ------------------------------------------------------------------------------
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Re: [base] Files with FTP locations only

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

On 2014-06-24 11:55, Bob MacCallum wrote:
> Hi Nicklas et al,
>
> Getting up to speed with BASE3 and NGS - so far all seems good - even
> upgrading our own API code has gone smoother than I expected.  Thanks!

Great to hear that it is going well.

>
> A possible feature request for general discussion:
>
> Would it be possible to have "placeholder" files in the BASE file system
> which weren't on disk but had an FTP location stored in the DB?   It
> would be a bit like the current "offline" option but for our use case
> (fastq and BAM files stored elsewhere and never processed by BASE3 or
> plugins) we would never even upload the files in the first place (I
> can't find a way to create a file that is offline from the start).
>
> The debate for other users/devs would be: should BASE automatically
> retrieve the files when needed?  I say no need for that - treat them
> like offline files are currently (if I understand correctly how offline
> files work).

There is already the *external files* feature. It can accessed with "New 
URL" in the BASE file manager. It's not the same as an *offline* file 
since by default BASE will try to check if it exists and download some 
metadata (such as size and modification date). And BASE will also 
retrieve the file if is requested by a plug-in or a user tries to 
download or view it.

The external files feature is "pluggable" and the BASE core only provide 
support for files that can be accessed with http or https. In theory it 
is possible to register unsupported URLs (eg. ftp://...) but I guess 
error messages will popup here and there.

As it happens, we discussed a similar problem last week. Up until now, 
our approach has been to simply store the file path as an annotation on 
bioassay items. In the future we'll need to provide access for external 
researchers to our data, but we really don't want to have them on our 
internal file servers so the idea is to let BASE act as a proxy.

So, I am currently working on an extension that add support for 
accessing external files via FTP, FTPS and SFTP (see 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles). I might be 
able to release a first version later this week if you want to try it.

If you prefer the *offline* files feature there is unfortunately no 
support in the GUI for creating offline files without first uploading 
them. A possible solution would be to modify the "New URL" dialog to 
make the "URL" field optional, and use this to decide between 
offline/external file.

If you have any other ideas please let me know...

/Nicklas

[base] Files with FTP locations only

[Bob M. <r.m...@im...>]

Hi Nicklas et al,

Getting up to speed with BASE3 and NGS - so far all seems good - even
upgrading our own API code has gone smoother than I expected.  Thanks!

A possible feature request for general discussion:

Would it be possible to have "placeholder" files in the BASE file system
which weren't on disk but had an FTP location stored in the DB?   It would
be a bit like the current "offline" option but for our use case (fastq and
BAM files stored elsewhere and never processed by BASE3 or plugins) we
would never even upload the files in the first place (I can't find a way to
create a file that is offline from the start).

The debate for other users/devs would be: should BASE automatically
retrieve the files when needed?  I say no need for that - treat them like
offline files are currently (if I understand correctly how offline files
work).

cheers,
Bob.

[base] BASE 3.3-beta-1 has been released

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

Hello all,

We have released BASE 3.3-beta-1 today! It is a new major
release that includes several new features and enhancements.

    * We now require Java 7 and Tomcat 7 on the server. If you
      are still using older versions, they should be upgraded
      before upgrading BASE.

    * The web interface has been reworked behind the scenes. Some
      (very old) browser may no longer work. It should be safe with
      IE 10 or a recent Firefox version.

    * The security in the web interface has been tightened in order
      to prevent cross-site scripting attacks. This can affect
      extensions. See the documentation for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/3.3-beta/html/admin/installation.html

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

/Nicklas

Re: [base] array design GTF import - not 9 columns

[Bob M. <r.m...@im...>]

Thanks for the quick reply Nicklas,
We'll strip out the comments for now and keep on testing.
cheers,
Bob


On Mon, May 26, 2014 at 7:37 AM, Nicklas Nordborg <
nic...@me...> wrote:

> Thanks for testing this. It feels like it was a long time ago this was
> implemented and we have not really started to use it yet. Anyway, you
> are correct that the problem is something deeper than the usual importer.
>
> To make GTF files parsable by the regular importers, there is a
> pre-parsing step that add headers and rewrites the "attributes" column
> (column 9) so that each attribute value is tab-separated instead of
> semicolon-separated.
>
> It is the pre-parser that complains if a line doesn't have at least 9
> columns. I checked the code and found a "TODO" comment about
> implementing support for comments, but for some reason it has been
> overlooked. It should be easy enough to implement this, and I can
> probably fix this for the next (BASE 3.3) release.
>
> But for now, the importer will choke on anything that is not a "Field"
> line as described by http://www.ensembl.org/info/website/upload/gff.html
>
> /Nicklas
>
>
> On 2014-05-23 18:17, Bob MacCallum wrote:
> > Hi all,
> >
> > [mods please delete the mail I sent from my gmail account, or add me
> > with that account but with no delivery, thank]
> >
> > Just upgraded from 2->3 and now trying out the NGS feaures.  Quick
> > question about GTF import for array designs...
> >
> > When doing array design->import the importer is complaining:
> >
> > "Error: A line must have at least 9 columns, at line: 1"
> > stack trace below
> > (using GTF reporter map importer (version 3.2.5-dev))
> >
> > The same error came up when we first created the array design (because I
> > checked the "validate files" box.
> >
> > I know the first line has fewer columns because it has some # commented
> > lines
> >
> > so in the importer configuration I configured the "Ignore" field like
> > this:  ^#.*
> >
> > But still the same error...
> >
> > Even if I set Default error handling = skip it's the same.  Seems to be
> > something deeper than the usual tab delimited importer parser settings.
> >
> > I guess we should make a new GTF file with no comments but I just wanted
> > to check if this was the intended behaviour?
> >
> > cheers,
> > Bob
> >
> >
> >
> ------------------------------------------------------------------------------
> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> > Instantly run your Selenium tests across 300+ browser/OS combos.
> > Get unparalleled scalability from the best Selenium testing platform
> available
> > Simple to use. Nothing to install. Get started now for free."
> > http://p.sf.net/sfu/SauceLabs
> >
> >
> >
> > _______________________________________________
> > The BASE general discussion mailing list
> > bas...@li...
> > unsubscribe: send a mail with subject "unsubscribe" to
> > bas...@li...
> >
>
>
>
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Re: [base] array design GTF import - not 9 columns

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

Thanks for testing this. It feels like it was a long time ago this was 
implemented and we have not really started to use it yet. Anyway, you 
are correct that the problem is something deeper than the usual importer.

To make GTF files parsable by the regular importers, there is a 
pre-parsing step that add headers and rewrites the "attributes" column 
(column 9) so that each attribute value is tab-separated instead of 
semicolon-separated.

It is the pre-parser that complains if a line doesn't have at least 9 
columns. I checked the code and found a "TODO" comment about 
implementing support for comments, but for some reason it has been 
overlooked. It should be easy enough to implement this, and I can 
probably fix this for the next (BASE 3.3) release.

But for now, the importer will choke on anything that is not a "Field" 
line as described by http://www.ensembl.org/info/website/upload/gff.html

/Nicklas


On 2014-05-23 18:17, Bob MacCallum wrote:
> Hi all,
>
> [mods please delete the mail I sent from my gmail account, or add me
> with that account but with no delivery, thank]
>
> Just upgraded from 2->3 and now trying out the NGS feaures.  Quick
> question about GTF import for array designs...
>
> When doing array design->import the importer is complaining:
>
> "Error: A line must have at least 9 columns, at line: 1"
> stack trace below
> (using GTF reporter map importer (version 3.2.5-dev))
>
> The same error came up when we first created the array design (because I
> checked the "validate files" box.
>
> I know the first line has fewer columns because it has some # commented
> lines
>
> so in the importer configuration I configured the "Ignore" field like
> this:  ^#.*
>
> But still the same error...
>
> Even if I set Default error handling = skip it's the same.  Seems to be
> something deeper than the usual tab delimited importer parser settings.
>
> I guess we should make a new GTF file with no comments but I just wanted
> to check if this was the intended behaviour?
>
> cheers,
> Bob
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform available
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
>
>
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...
>

Re: [base] array design GTF import - not 9 columns

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

On 2014-05-23 18:17, Bob MacCallum wrote:
> [mods please delete the mail I sent from my gmail account, or add me
> with that account but with no delivery, thank]

Added to the list.

For the issue with the GTF I'll let Nicklas respond.


Cheers,

Jari

[base] array design GTF import - not 9 columns

[Bob M. <r.m...@im...>]

Hi all,

[mods please delete the mail I sent from my gmail account, or add me with
that account but with no delivery, thank]

Just upgraded from 2->3 and now trying out the NGS feaures.  Quick question
about GTF import for array designs...

When doing array design->import the importer is complaining:

"Error: A line must have at least 9 columns, at line: 1"
stack trace below
(using GTF reporter map importer (version 3.2.5-dev))

The same error came up when we first created the array design (because I
checked the "validate files" box.

I know the first line has fewer columns because it has some # commented
lines

so in the importer configuration I configured the "Ignore" field like
this:  ^#.*

But still the same error...

Even if I set Default error handling = skip it's the same.  Seems to be
something deeper than the usual tab delimited importer parser settings.

I guess we should make a new GTF file with no comments but I just wanted to
check if this was the intended behaviour?

cheers,
Bob

Re: [base] reseting root password

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

On 2014-02-17 02:39, Ross Chapman wrote:
> Hi all
>
> I have inherited the management of a BASE 2 solution for managing
> microarray data.
>
> I do not have access to the Root password, but I do have administrator
> rights.
>
> Am I able to reset the root password, will this have any impact on how
> BASE operates?

As an administrator you should be able to change the password of the 
root account. This should not cause any problems.

/Nicklas

[base] reseting root password

[Ross C. <ros...@mo...>]

Hi all

I have inherited the management of a BASE 2 solution for managing
microarray data.

I do not have access to the Root password, but I do have administrator
rights.

Am I able to reset the root password, will this have any impact on how BASE
operates?

Thanks for your help.

Regards

Ross

[base] BASE 3.2.4 has been released

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

Hello all,

We have released BASE 3.2.4 today. This is a bugfix release that
fixes a few minor problems and a critical issue how average intensity 
values are calculated when working with data in log-space.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.4&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 installation issue

[François V. <fra...@an...>]

That was just a directory name with accents in the path.

Thank you !

Le 25/09/2013 11:19, Nicklas Nordborg a écrit :
> Hello,
>
> It could be an issue with the OpenJDK java version you are using. To
> confirm if this seems to be the case you can try to turn on info-level
> logging. Find the log4j.properties file inside the
> <base-install-dir>/www/WEB-INF/classes. A couple of lines down in that
> file is an entry for 'log4j.logger.net.sf.basedb.core=warn'. Change
> 'warn' to 'info' and try the installation again. This will print a lot
> of information, but just before it crashes there should a line
> containing something like:
>
> '... INFO core:268 - Loading mappings files from jar: ....'
>
> Check that path given in the log statement actually corresponds to the
> real path to the 'base-core-3.2.3.jar' file.
>
> If the path seems not be correct, try downloading and installing a Java
> version from Oracle instead.
>
> Hope this helps.
>
> /Nicklas
>
> On 2013-09-25 09:24, François Vallée wrote:
>> Hello,
>>
>> I am trying to install BASE-3.2.3 from pre-compiled release following
>> the instructions on this page :
>> http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html
>> and i am stuck at the database initialization step.
>>
>> When I use the command :
>>
>> ./initdb.sh [baseadmin] baseadmpwd
>>
>> I have the error:
>>
>> [0%]    --System information-----------------------------
>> BASE     : 3.2.3(build 6317)
>> Database : jdbc:postgresql:base2
>> Dialect  : org.hibernate.dialect.PostgreSQLDialect
>> JDBC     : org.postgresql.Driver; version 9.1
>> Java     : OpenJDK Runtime Environment; 1.6.0_27-b27; Sun Microsystems Inc.
>> OS       : Linux; amd64; 3.2.0-53-generic
>> -------------------------------------------------
>> ERROR core:308 - Exception while loading mapping files
>> java.util.zip.ZipException: error in opening zip file
>>        at java.util.zip.ZipFile.open(Native Method)
>>        at java.util.zip.ZipFile.<init>(ZipFile.java:132)
>>        at java.util.jar.JarFile.<init>(JarFile.java:151)
>>        at java.util.jar.JarFile.<init>(JarFile.java:88)
>>        at
>> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
>>        at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
>>        at net.sf.basedb.core.Application.start(Application.java:493)
>>        at net.sf.basedb.core.Install.createTables(Install.java:131)
>>        at net.sf.basedb.install.InitDB.main(InitDB.java:75)
>> 08:58:29,934 ERROR Application:655 - Exception when starting...
>> net.sf.basedb.core.BaseException: error in opening zip file
>>        at
>> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:309)
>>        at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
>>        at net.sf.basedb.core.Application.start(Application.java:493)
>>        at net.sf.basedb.core.Install.createTables(Install.java:131)
>>        at net.sf.basedb.install.InitDB.main(InitDB.java:75)
>> Caused by: java.util.zip.ZipException: error in opening zip file
>>        at java.util.zip.ZipFile.open(Native Method)
>>        at java.util.zip.ZipFile.<init>(ZipFile.java:132)
>>        at java.util.jar.JarFile.<init>(JarFile.java:151)
>>        at java.util.jar.JarFile.<init>(JarFile.java:88)
>>        at
>> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
>>        ... 4 more
>>
>> [30%]    Building database failed: error in opening zip file
>>
>> net.sf.basedb.core.BaseException: error in opening zip file
>>        at net.sf.basedb.core.Application.start(Application.java:658)
>>        at net.sf.basedb.core.Install.createTables(Install.java:131)
>>        at net.sf.basedb.install.InitDB.main(InitDB.java:75)
>> Caused by: net.sf.basedb.core.BaseException: error in opening zip file
>>        at
>> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:309)
>>        at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
>>        at net.sf.basedb.core.Application.start(Application.java:493)
>>        ... 2 more
>> Caused by: java.util.zip.ZipException: error in opening zip file
>>        at java.util.zip.ZipFile.open(Native Method)
>>        at java.util.zip.ZipFile.<init>(ZipFile.java:132)
>>        at java.util.jar.JarFile.<init>(JarFile.java:151)
>>        at java.util.jar.JarFile.<init>(JarFile.java:88)
>>        at
>> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
>>        ... 4 more
>>
>> Maybe my installation of hibernate fails somewhere but I can't figure
>> out what to do to check it.
>>
>> Cheers,
>> François
>>
>
> ------------------------------------------------------------------------------
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> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] BASE installation issue

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

Hello,

It could be an issue with the OpenJDK java version you are using. To 
confirm if this seems to be the case you can try to turn on info-level 
logging. Find the log4j.properties file inside the 
<base-install-dir>/www/WEB-INF/classes. A couple of lines down in that 
file is an entry for 'log4j.logger.net.sf.basedb.core=warn'. Change 
'warn' to 'info' and try the installation again. This will print a lot 
of information, but just before it crashes there should a line 
containing something like:

'... INFO core:268 - Loading mappings files from jar: ....'

Check that path given in the log statement actually corresponds to the 
real path to the 'base-core-3.2.3.jar' file.

If the path seems not be correct, try downloading and installing a Java 
version from Oracle instead.

Hope this helps.

/Nicklas

On 2013-09-25 09:24, François Vallée wrote:
> Hello,
>
> I am trying to install BASE-3.2.3 from pre-compiled release following
> the instructions on this page :
> http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html
> and i am stuck at the database initialization step.
>
> When I use the command :
>
> ./initdb.sh [baseadmin] baseadmpwd
>
> I have the error:
>
> [0%]    --System information-----------------------------
> BASE     : 3.2.3(build 6317)
> Database : jdbc:postgresql:base2
> Dialect  : org.hibernate.dialect.PostgreSQLDialect
> JDBC     : org.postgresql.Driver; version 9.1
> Java     : OpenJDK Runtime Environment; 1.6.0_27-b27; Sun Microsystems Inc.
> OS       : Linux; amd64; 3.2.0-53-generic
> -------------------------------------------------
> ERROR core:308 - Exception while loading mapping files
> java.util.zip.ZipException: error in opening zip file
>       at java.util.zip.ZipFile.open(Native Method)
>       at java.util.zip.ZipFile.<init>(ZipFile.java:132)
>       at java.util.jar.JarFile.<init>(JarFile.java:151)
>       at java.util.jar.JarFile.<init>(JarFile.java:88)
>       at
> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
>       at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
>       at net.sf.basedb.core.Application.start(Application.java:493)
>       at net.sf.basedb.core.Install.createTables(Install.java:131)
>       at net.sf.basedb.install.InitDB.main(InitDB.java:75)
> 08:58:29,934 ERROR Application:655 - Exception when starting...
> net.sf.basedb.core.BaseException: error in opening zip file
>       at
> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:309)
>       at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
>       at net.sf.basedb.core.Application.start(Application.java:493)
>       at net.sf.basedb.core.Install.createTables(Install.java:131)
>       at net.sf.basedb.install.InitDB.main(InitDB.java:75)
> Caused by: java.util.zip.ZipException: error in opening zip file
>       at java.util.zip.ZipFile.open(Native Method)
>       at java.util.zip.ZipFile.<init>(ZipFile.java:132)
>       at java.util.jar.JarFile.<init>(JarFile.java:151)
>       at java.util.jar.JarFile.<init>(JarFile.java:88)
>       at
> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
>       ... 4 more
>
> [30%]    Building database failed: error in opening zip file
>
> net.sf.basedb.core.BaseException: error in opening zip file
>       at net.sf.basedb.core.Application.start(Application.java:658)
>       at net.sf.basedb.core.Install.createTables(Install.java:131)
>       at net.sf.basedb.install.InitDB.main(InitDB.java:75)
> Caused by: net.sf.basedb.core.BaseException: error in opening zip file
>       at
> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:309)
>       at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
>       at net.sf.basedb.core.Application.start(Application.java:493)
>       ... 2 more
> Caused by: java.util.zip.ZipException: error in opening zip file
>       at java.util.zip.ZipFile.open(Native Method)
>       at java.util.zip.ZipFile.<init>(ZipFile.java:132)
>       at java.util.jar.JarFile.<init>(JarFile.java:151)
>       at java.util.jar.JarFile.<init>(JarFile.java:88)
>       at
> net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
>       ... 4 more
>
> Maybe my installation of hibernate fails somewhere but I can't figure
> out what to do to check it.
>
> Cheers,
> François
>

[base] BASE installation issue

[François V. <fra...@an...>]

Hello,

I am trying to install BASE-3.2.3 from pre-compiled release following 
the instructions on this page : 
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html 
and i am stuck at the database initialization step.

When I use the command :

./initdb.sh [baseadmin] baseadmpwd

I have the error:

[0%]    --System information-----------------------------
BASE     : 3.2.3(build 6317)
Database : jdbc:postgresql:base2
Dialect  : org.hibernate.dialect.PostgreSQLDialect
JDBC     : org.postgresql.Driver; version 9.1
Java     : OpenJDK Runtime Environment; 1.6.0_27-b27; Sun Microsystems Inc.
OS       : Linux; amd64; 3.2.0-53-generic
-------------------------------------------------
ERROR core:308 - Exception while loading mapping files
java.util.zip.ZipException: error in opening zip file
     at java.util.zip.ZipFile.open(Native Method)
     at java.util.zip.ZipFile.<init>(ZipFile.java:132)
     at java.util.jar.JarFile.<init>(JarFile.java:151)
     at java.util.jar.JarFile.<init>(JarFile.java:88)
     at 
net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
     at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
     at net.sf.basedb.core.Application.start(Application.java:493)
     at net.sf.basedb.core.Install.createTables(Install.java:131)
     at net.sf.basedb.install.InitDB.main(InitDB.java:75)
08:58:29,934 ERROR Application:655 - Exception when starting...
net.sf.basedb.core.BaseException: error in opening zip file
     at 
net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:309)
     at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
     at net.sf.basedb.core.Application.start(Application.java:493)
     at net.sf.basedb.core.Install.createTables(Install.java:131)
     at net.sf.basedb.install.InitDB.main(InitDB.java:75)
Caused by: java.util.zip.ZipException: error in opening zip file
     at java.util.zip.ZipFile.open(Native Method)
     at java.util.zip.ZipFile.<init>(ZipFile.java:132)
     at java.util.jar.JarFile.<init>(JarFile.java:151)
     at java.util.jar.JarFile.<init>(JarFile.java:88)
     at 
net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
     ... 4 more

[30%]    Building database failed: error in opening zip file

net.sf.basedb.core.BaseException: error in opening zip file
     at net.sf.basedb.core.Application.start(Application.java:658)
     at net.sf.basedb.core.Install.createTables(Install.java:131)
     at net.sf.basedb.install.InitDB.main(InitDB.java:75)
Caused by: net.sf.basedb.core.BaseException: error in opening zip file
     at 
net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:309)
     at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:207)
     at net.sf.basedb.core.Application.start(Application.java:493)
     ... 2 more
Caused by: java.util.zip.ZipException: error in opening zip file
     at java.util.zip.ZipFile.open(Native Method)
     at java.util.zip.ZipFile.<init>(ZipFile.java:132)
     at java.util.jar.JarFile.<init>(JarFile.java:151)
     at java.util.jar.JarFile.<init>(JarFile.java:88)
     at 
net.sf.basedb.core.HibernateUtil.addStaticMappings(HibernateUtil.java:269)
     ... 4 more

Maybe my installation of hibernate fails somewhere but I can't figure 
out what to do to check it.

Cheers,
François

-- 
François Vallée
INRA - Centre Angers-Nantes
42 rue Georges Morel - BP 60057
49071 Beaucouzé cedex - France
Tel. : +33 (0)2 41 22 57 40

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

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

On 2013-09-16 19:08, Laurent Troxler wrote:
> Dear all, I have a great news: IT WORKS !!

Great to hear!

Seems like Tomcat was a bit of PITA to get working on Mac. Hope you'll 
enjoy your BASE installation now. Don't hesitate to ask if you have more 
questions.

/Nicklas

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

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

Dear all,
I have a great news: IT WORKS !!
the localhost log file from Tomcat is now OK. It now can find the java files expected in /Library/Tomcat/work/Catalina/localhost/base2/org/apache/jsp/
Since then the tomcat-launchd.sdtout do not output any error message with the "Existing PID file found during start. Existing PID file found during start"
Catalina log file looks now also fine 

using "ps -e | grep Tomcat"
I can check that Catalina process is running with the right options:
-Xmx1G -Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false -Dcom.sun.media.jai.disableMediaLib=true -Djava.awt.headless=true

No more windowed application named org.apache.catalina.startup.Bootstrap that remain

On the Activity monitor, the java and sh processes owned by _appserver  keeps the same PID number (which was not the case before
/Library/Tomcat/catalina_pid.txt contains the java PID number

How did I get up to that stage. 
First I changed the owner of the /Library/Tomcat/work/Catalina directory: sudo chown -R _appserver /Library/Tomcat/work/Catalina
and removed its contained directories rm -f /Library/Tomcat/work/Catalina/*

Since I did not have any /Library/Tomcat/logs/tomcat.pid file I created a link to the catalina one: ln -s  /Library/Tomcat/catalina_pid.txt /Library/Tomcat/logs/tomcat.pid
I then follow up Jari's idea from his script:
Using the Activity Moniteur  I killed the java process from _appserver (it restarted a second after) and then the one from the shell also owned by _appserver.
This one took almost a minute to restart.
I could then check that the /Library/Tomcat/work/Catalina/localhost/base2/org/apache/jsp/ was built up.

And now from the browser, I can login from the webpage localhost:8080/base2
I can do it both on the server or from an other computer

It looks like now I can go on, creating the user accounts, etc…
Hope this summery will be helpful if some one else meets similar problems 

Thank you very much  to Jari and Nicklas for their patient help and deep analyses.
I just hope not to have any other questions from now…

Cheers,
Laurent


Le 13 sept. 2013 à 16:42, Jari Häkkinen <jar...@me...> a écrit :

> On 2013-09-13 13:08, Laurent Troxler wrote:
>> 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 ?
> 
> It is important that the headless option is set. One test is to print the variable at different points in the catalina.sh script to examine where it changes.
> 
> 
>> 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.
> 
> I think this is the krux of your issue. When this is resolved you should be good to go. Assuming that you did all steps in the BASE installation already there is no restart once you resolved the tomcat issues. Just log in to BASE and get started ;-)
> 
> The Apache/tomcat connector mentioned in the installation documents is not critical and is really useful for servers with heavy load.
> 
> 
>> 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…
> 
> Your observations above are exactly what I have seen on my system. There
> are two environment variables affecting the behaviour of the startup and
> shutdown of tomcat. I have attached my tomcat startup script to this
> mail. Since I am only testing BASE on my machine I created script to
> start and stop tomcat manually. The script is run like
>   tomcat.sh action
> where action is start, stop, status, restart.
> 
> Examine the environment variables in the script. I have three variables;
> JAVA_OPTS, CATALINA_OPTS, and CATALINA_PID. The two OPTS can probably be
> merged into JAVA_OPTS only but I haven't bothered to do that.
> 
> The important thing is that the shutdown script provided by
> tomcat/macports does not use CATALINA_OPTS at all but uses JAVA_OPTS.
> Therefore I place the headless option in JAVA_OPTS. The startup script
> provided by tomcat/macports uses both JAVA_OPTS and CATALINA_OPTS.
> 
> The use of PID within the different scripts provided by tomcat/macports
> on my system is not consistent. I notes that script tomcatctl provided
> by tomcat/macports expects to be the PID-file i defined in variable
> CATALINA_PID. That is why I set the CATALINA_PID and pass it on to the
> startup and shutdown scripts. The different scripts will now rely on the
> same PID-file and work consistently.
> 
> I created my script since I want to avoid changing system scripts since
> the system script may be replaced during upgrades. Of course, my script
> may fail later on but I have one script to fix in that case.
> 
> Use the ideas from my script and you should soon be accessing your BASE
> server.
> 
> 
>> Other informations:
>> 
>> Both /Library/Tomcat/work/Catalina/localhost/base2 and
>> /Library/Tomcat/work/Catalina/localhost/_/ directories are empty
> 
> Once you stop the tomcat server it is safe to remove the files and directories from /Library/Tomcat/work/Catalina and down, i.e.,
>  rm -f /Library/Tomcat/work/Catalina
> and then restart. This forces tomcat to recompile the webapps. Startup takes some additional time but you get a fresh compile. Once everything works there is no need to clean up the work directory.
> 
> 
>> 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.
> 
> I don't know why you have this and have not seen this behaviour. Maybe it is related to https://discussions.apple.com/thread/5270047?start=0&tstart=0 or hopefully it goes away once the above issue is resolved :-)
> 
> Cheers,
> 
> Jari
> <tomcat.sh>------------------------------------------------------------------------------
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> 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
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> 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 2013-09-13 13:08, Laurent Troxler wrote:
> 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 ?

It is important that the headless option is set. One test is to print 
the variable at different points in the catalina.sh script to examine 
where it changes.


> 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.

I think this is the krux of your issue. When this is resolved you should 
be good to go. Assuming that you did all steps in the BASE installation 
already there is no restart once you resolved the tomcat issues. Just 
log in to BASE and get started ;-)

The Apache/tomcat connector mentioned in the installation documents is 
not critical and is really useful for servers with heavy load.


> 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…

Your observations above are exactly what I have seen on my system. There
are two environment variables affecting the behaviour of the startup and
shutdown of tomcat. I have attached my tomcat startup script to this
mail. Since I am only testing BASE on my machine I created script to
start and stop tomcat manually. The script is run like
    tomcat.sh action
where action is start, stop, status, restart.

Examine the environment variables in the script. I have three variables;
JAVA_OPTS, CATALINA_OPTS, and CATALINA_PID. The two OPTS can probably be
merged into JAVA_OPTS only but I haven't bothered to do that.

The important thing is that the shutdown script provided by
tomcat/macports does not use CATALINA_OPTS at all but uses JAVA_OPTS.
Therefore I place the headless option in JAVA_OPTS. The startup script
provided by tomcat/macports uses both JAVA_OPTS and CATALINA_OPTS.

The use of PID within the different scripts provided by tomcat/macports
on my system is not consistent. I notes that script tomcatctl provided
by tomcat/macports expects to be the PID-file i defined in variable
CATALINA_PID. That is why I set the CATALINA_PID and pass it on to the
startup and shutdown scripts. The different scripts will now rely on the
same PID-file and work consistently.

I created my script since I want to avoid changing system scripts since
the system script may be replaced during upgrades. Of course, my script
may fail later on but I have one script to fix in that case.

Use the ideas from my script and you should soon be accessing your BASE
server.


> Other informations:
>
> Both /Library/Tomcat/work/Catalina/localhost/base2 and
> /Library/Tomcat/work/Catalina/localhost/_/ directories are empty

Once you stop the tomcat server it is safe to remove the files and 
directories from /Library/Tomcat/work/Catalina and down, i.e.,
   rm -f /Library/Tomcat/work/Catalina
and then restart. This forces tomcat to recompile the webapps. Startup 
takes some additional time but you get a fresh compile. Once everything 
works there is no need to clean up the work directory.


> 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.

I don't know why you have this and have not seen this behaviour. Maybe 
it is related to 
https://discussions.apple.com/thread/5270047?start=0&tstart=0 or 
hopefully it goes away once the above issue is resolved :-)

Cheers,

Jari