AW: [Bio-linux-devel] phoenix clinical trial management system integration
Hi, thx4re, here just a short update, still on the road to moving everything to debian default packages...
>. It has currently tomcat 8.5.30 and OpenJDK 9.0.4.
Transition to debian's default tomcat8 is done.
https://github.com/phoenixctms/install-debian/commit/84e47398ec971aa5ae2aaa283819b329652dff84
https://github.com/phoenixctms/install-debian/commit/a93f0fe984ce74d45c4fb86f0efaa3f98bd0cd70
For now it is ensured tomcat runs with the "ctsms" user instead of "tomcat8" user, the reason is to avoid any potential issues with permissions of tempfiles created by hibernate's query region caching, which were observed once iirc. So both the tomcat webapp and the "dbtool" cli program should therefore run with "ctsms" user.
Also debian's default "maven" is used now and works. Still can't believe that.
so far also dont see objections for the phoenix webapp with moving to java9, will check that in detail at some other weekend.
> The perl-based ETL framework
> This seems to be a pretty nice target to learn packaging.
Hm, yes; but a pain. :-)
> Another optional one would be the public subject signup portal, which is a perl dancer webapp.
> libdancer2-perl - lightweight yet powerful web application framework is packaged so you can base upon this.
libdancer-perl is used atm, can consider migrating to dancer2.
However, the recruitement portal is not yet covered by install.sh. Also the code is not yet in any public github repo, as the branding/appearance parts (see http://probanden.medunigraz.at for instance) are not yet configurable. Better to delay the latter, as it will be more efford.
regards,rene
-----Ursprüngliche Nachricht-----
Von: Andreas Tille [mailto:andreas@an3as.eu]
Gesendet: Dienstag, 22. Mai 2018 10:00
An: Rene Krenn <rkrenn@phoenixctms.org>; Debian Med Project List <debian-med@lists.debian.org>
Cc: 'Kojzar, Harald' <harald.kojzar@medunigraz.at>; 'Trajanoski, Slave' <slave.trajanoski@medunigraz.at>
Betreff: Re: [Bio-linux-devel] phoenix clinical trial management system integration
[Removing bio-linux-devel@bioinformatics.org from CC since I understood Tony that it is not relevant for this list.]
Hi Rene,
On Tue, May 22, 2018 at 09:13:45AM +0200, Rene Krenn wrote:
>
> ok regarding packaging, jfyi this is the script to get (and build) it on a minimal debian 9.4 (or ubuntu 16.04):
> https://github.com/phoenixctms/install-debian/blob/master/install.sh
Its good to have this kind of script to have a plan what to do.
However, I see lots of wget calls there. We need to make sure that every needed component is available as Debian package - in other words:
We need to replace wget by apt-get.
> To get rid of outdated dependencies, we already moved on to OpenJDK8 successfully last week.
> The next task will be to ensure it works with more recent versions of tomcat.
Please note new packages are targeting at Debian unstable. It has currently tomcat 8.5.30 and OpenJDK 9.0.4. I'm not a Java expert at all and thus don't now what a OpenJDK8 to OpenJDK9 move might mean in practice but some of the Debian Med Java packages needed adaptations to OpenJDK9.
> The perl-based ETL framework
> (https://github.com/phoenixctms/bulk-processor ) should most likely become a separate package.
This seems to be a pretty nice target to learn packaging.
> So i suggest there should be one package for the main tomcat webapp, and one for the bulk-processor.
This sound sensible.
> Another optional one would be the public subject signup portal, which is a perl dancer webapp.
I admit I have never heard about perl dancer but
libdancer2-perl - lightweight yet powerful web application framework is packaged so you can base upon this.
Kind regards
Andreas.
> -----Ursprüngliche Nachricht-----
> Von: Andreas Tille [mailto:andreas@an3as.eu]
> Gesendet: Dienstag, 22. Mai 2018 08:02
> An: Tony Travis <tony.travis@abdn.ac.uk>
> Cc: bio-linux-devel@bioinformatics.org; Debian Med Project List
> <debian-med@lists.debian.org>; rkrenn@phoenixctms.org
> Betreff: Re: [Bio-linux-devel] phoenix clinical trial management
> system integration
>
> Hi,
>
> @Tony: Thanks a lot for forwarding this. :-)
>
> On Sat, May 19, 2018 at 02:56:18PM +0100, Tony Travis wrote:
> > On 18/05/18 23:19, Rene Krenn wrote:
> > > hello,
> > >
> > >
> > >
> > > would like to probe if there is an interest to include
> > > https://github.com/phoenixctms ?
> > >
> > > it’s the most powerful EDC system we know.
> > >
> > >
> > >
> > > pls let me know if it makes sense and someone can/wants to help
> > > with packaging.
>
> For sure we would love to help you in packaging. We have quite some
> record in teaching upstream how to package. We have formalised this
> process in so called "Mentoring of the Month" (MoM)[1]. You are more
> than welcome to add yourself to the list of students (or simply
> confirm here on this list[2] if you are scared by just another random
> Wiki login in the web. However, you should subscribe in any case this
> list since the mentoring is done in public.)
>
> > Hi, Rene.
> >
> > Bio-Linux is a platform for bioinformatics, rather than collecting
> > and analysing clinical trials data.
>
> It looks like a good target for the task "Research"[3] which has no existing package yet which is a real shame - but may be you consider other of our tasks[4] fitting better / in addition.
>
> > However, many packages from Debian-Med are included in Bio-Linux and
> > the two projects work together to avoid duplication of effort
> > packaging the same bioinformatics software.
> >
> > The Debian-Med project is much broader than Bio-Linux and
> > specifically includes biomedical applications like your clinical
> > trials management software. I've CC'ed your message to the
> > Debian-Med mailing list so we can discuss the possibility of packaging your software there.
> >
> > Please post a message to the Debian-Med list explaining clearly what
> > the licence is for your software and what, exactly, you want to package.
>
> Nothing to add to Tony's kid explanation.
>
> Kind regards
>
> Andreas.
>
> [1] https://wiki.debian.org/DebianMed/MoM
> [2] https://lists.debian.org/debian-med
> [3] https://blends.debian.org/med/tasks/research
> [4] https://blends.debian.org/med/tasks
>
> --
> http://fam-tille.de
>
>
--
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