Ubuntu-debian package bugs

system · April 30, 2014, 4:23am

bradymiller wrote on Wednesday, April 30, 2014:

ok,

Think we are close to a solution.

Here are proposed changes in the packages:

And here is the updated script that builds the packages:
https://gist.github.com/bradymiller/5786409
(note that the packages will include the openemr-apache.conf scripts in the correct place to be used by apache)

Proposed steps to do this:

Commit in the webroot fix (https://github.com/bradymiller/openemr/commit/99601fe1220fb6978edad3536e06812fd8ace325)
Test packages created by above mechanism to ensure they work
Release patch 6 for 4.1.2, which will include these changes
Release a new 4.1.2 ubuntu package off of patch 6.

-brady
OpenEMR

system · April 30, 2014, 5:07pm

sunsetsystems wrote on Wednesday, April 30, 2014:

Hi Brady, seems reasonable on skimming. I added a couple of review notes related to code commenting. Thanks!

Rod
http://www.sunsetsystems.com/

system · April 30, 2014, 11:30pm

iankarlwallace wrote on Wednesday, April 30, 2014:

Rod - In reading some of the Debian Policy stuff this is what they suggest
that you do (install your web application under /usr/share and symlink it
from /var/www)

Taken from (
11. Customized programs — Debian Policy Manual v4.7.0.1)

Web Document Root

Web Applications should try to avoid storing files in the Web Document
Root. Instead they should use the /usr/share/doc/package directory for
documents and register the Web Application via the doc-base package. If
access to the web document root is unavoidable then use

    /var/www

as the Document Root. This might be just a symbolic link to the

location where the system administrator has put the real document root.

With the long standing history of the debian package plunking stuff down in
/var/www this would probably be a longer term fix but it would be worth the
effort over the long haul.

We should definitely add a set of /etc/apache2/sites-available. Could
either run the a2ensite in the postinst script or the user could do such .

On Mon, Apr 28, 2014 at 7:01 AM, Rod Roark sunsetsystems@users.sf.netwrote:

Also look at what happens when you install phpmyadmin. Its web directory
is actually installed to /usr/share, and /etc/apache2/conf-available and
conf-enabled are added to access it via an Alias. Perhaps openemr should do
something similar.

Rod
http://www.sunsetsystems.com/

ubuntu-debian package bugshttps://sourceforge.net/p/openemr/discussion/202506/thread/e82523fd/?limit=25#2154

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system · May 1, 2014, 12:18am

sunsetsystems wrote on Thursday, May 01, 2014:

Thanks Ian. Looks like most everything in /etc and /usr/share is owned and writable only by root. I suspect the “right” thing to do includes putting the read-only web scripts into /usr/share/openemr and the “sites” directory stuff (files that might change) into /var/lib/openemr. This would be an interesting project.

Rod
http://www.sunsetsystems.com/

system · May 1, 2014, 2:54am

iankarlwallace wrote on Thursday, May 01, 2014:

Brady and Rod - Whatever fixes you guys come up with seems ok with myself.
I am going to go dark for a few weeks on this camping trip. I’ll pick back
up with PHPUnit and the Debian packages stuff when I re-surface on the
other side. We could definitely tighten things up in terms of Debian
compliance - our package produces lots of output from ‘lintian’ - which I
guess if your package is really up to snuff should produce nothing.

I guess going forward we should decide if OpenEMR is a ‘site’ or a ‘conf’
for apache (I vote site … since it makes sense in my mind). Otherwise I
will setup a VM that can host the 12.04 and 14.04 LTS versions for some
testing, I could also snag a Debian 7 version as well. I am just having
some problems with the networking not playing well with my wireless card on
a System 76 laptop. A little debugging and I think I can probably get
bridged mode working.

If we can polish the package to the point that lintian is quite, and we
move the code base to the recommended location (I’ll look at phpmyadmin for
pointers) we could actually think about submitting to the repos and adding
it in so that people can install with apt-get or synamptic or whatever
other flavor of package tool they like. We are a ways off from that …
but it would be a nice touch to the project.

cheers
ian

On Wed, Apr 30, 2014 at 4:30 PM, Ian Wallace iankarlwallace@gmail.comwrote:

Rod - In reading some of the Debian Policy stuff this is what they suggest
that you do (install your web application under /usr/share and symlink it
from /var/www)

Taken from (
11. Customized programs — Debian Policy Manual v4.7.0.1)

Web Document Root

Web Applications should try to avoid storing files in the Web Document
Root. Instead they should use the /usr/share/doc/package directory for
documents and register the Web Application via the doc-base package.
If access to the web document root is unavoidable then use
    /var/www

as the Document Root. This might be just a symbolic link to the
location where the system administrator has put the real document root.

With the long standing history of the debian package plunking stuff down
in /var/www this would probably be a longer term fix but it would be worth
the effort over the long haul.

We should definitely add a set of /etc/apache2/sites-available. Could
either run the a2ensite in the postinst script or the user could do such .

On Mon, Apr 28, 2014 at 7:01 AM, Rod Roark sunsetsystems@users.sf.netwrote:

Also look at what happens when you install phpmyadmin. Its web directory
is actually installed to /usr/share, and /etc/apache2/conf-available and
conf-enabled are added to access it via an Alias. Perhaps openemr should do
something similar.

Rod
http://www.sunsetsystems.com/

ubuntu-debian package bugshttps://sourceforge.net/p/openemr/discussion/202506/thread/e82523fd/?limit=25#2154

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–
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303.681.5732

system · May 1, 2014, 5:08am

sunsetsystems wrote on Thursday, May 01, 2014:

Ian, I like your thinking about this. Enjoy your camping adventure!

Rod
http://www.sunsetsystems.com/

system · May 1, 2014, 7:11am

bradymiller wrote on Thursday, May 01, 2014:

Hi Ian,

The current fixes are essentially “quick” fixes to get the packages working on Ubuntu 14.04, 13.10 and 12.10. Regarding using site or conf, the nice thing in the proposed package is they are files provided by the package (so it will be easy to adjust/fix/remove in the next offical openemr release package).

Agree that it would be nice to shoot for a official Debian package for the next official OpenEMR release. There’s actually a good mailing list to join to get guidance on doing this(I have been following it for several years, but just never had the time to pursue it):
https://lists.debian.org/debian-med/
Obviously, there are things that need to be done, but they are doable; just a matter of resources. The current php auto mods will likely need to go, but looking at the phpmyadmin package, it appears they do this via some php5 mod thingy within the apache conf scripts. One key thing will be to ensure the OpenEMR version upgrading works, which is actually where the package really shines (the maintainer scripts do all the upgrading steps without any manual intervention; it will even upgrade and convert a non-package OpenEMR version into a package version; note it also upgrades all of the “sites” when multisite module is used).

Happy Camping,
-brady
OpenEMR

system · May 2, 2014, 4:09am

iankarlwallace wrote on Friday, May 02, 2014:

Brady - I realize the need for a quick fix to get people back to installing and using openemr. Just seems like it might be time to finally put in some elbow grease to get us into the official repo. When I finish the camping trip I can start working on it.

Didn’t know about the mailing list for Debian-med bit probably should join so that I can get help once I need it.

The way to tackle this is probably fix the directories/file perms and get that portion of the package worked out and then run through some of the most likely scenarios for testing: fresh install, vanilla upgrade, upgrade from non pkg’d tar ball and see how things break.

The apache2 stuff bears looking at more to see how some other projects tackle this problem. Setting things up as a site would still include the files in the package they just live under a different directory.

I noticed as well that phpmyadmin uses a dir in /etc to store configuration files.

Ian

p.s. Oh and I am still fiddling with the php unit testing. Jenkins is a great tool and could be used to manage the demo farm but I haven’t gotten there yet. Your script seems to be working very well. One benefit for running at least one Jenkins project is all the stats it provides from the different tools (duplicate code, cyclometric complexity so we could clean up overly complicated code … Etc.

Ian Wallace 303-681-5732

On May 1, 2014, at 1:11 AM, “Brady Miller” bradymiller@users.sf.net wrote:

Hi Ian,

The current fixes are essentially “quick” fixes to get the packages working on Ubuntu 14.04, 13.10 and 12.10. Regarding using site or conf, the nice thing in the proposed package is they are files provided by the package (so it will be easy to adjust/fix/remove in the next offical openemr release package).

Agree that it would be nice to shoot for a official Debian package for the next official OpenEMR release. There’s actually a good mailing list to join to get guidance on doing this(I have been following it for several years, but just never had the time to pursue it):
Debian Mailing Lists -- Index for debian-med
Obviously, there are things that need to be done, but they are doable; just a matter of resources. The current php auto mods will likely need to go, but looking at the phpmyadmin package, it appears they do this via some php5 mod thingy within the apache conf scripts. One key thing will be to ensure the OpenEMR version upgrading works, which is actually where the package really shines (the maintainer scripts do all the upgrading steps without any manual intervention; it will even upgrade and convert a non-package OpenEMR version into a package version; note it also upgrades all of the “sites” when multisite module is used).

Happy Camping,
-brady
OpenEMR

ubuntu-debian package bugs

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system · May 2, 2014, 4:17am

iankarlwallace wrote on Friday, May 02, 2014:

Rod - See other response to Brady. Basically once I am done camping for 2+ weeks with the family I will jump back in.

I think it would be a huge win to be a package hosted in the Debian/ubuntu repos. Makes installing a breeze and gets us a bit more visibility.

Ian

Ian Wallace 303-681-5732

On Apr 30, 2014, at 6:18 PM, “Rod Roark” sunsetsystems@users.sf.net wrote:

Thanks Ian. Looks like most everything in /etc and /usr/share is owned and writable only by root. I suspect the “right” thing to do includes putting the read-only web scripts into /usr/share/openemr and the “sites” directory stuff (files that might change) into /var/lib/openemr. This would be an interesting project.

Rod
http://www.sunsetsystems.com/

ubuntu-debian package bugs

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system · May 2, 2014, 7:34am

bradymiller wrote on Friday, May 02, 2014:

Hi Ian,

Sounds like a plan. Suggest introducing yourself on the Debian-med list very early on in the process. The first thing they’ll likely recommend (our project package was discussed on the mailing list a couple years back) is building the package correctly(ie. the basics); I was told I made a very common error in building the package itself. There didn’t seem to be much issue with the paths used, although guessing it may come up at some point. Another thing to keep in mind is the current patch mechanism (probably want to avoid having the patch mechanism not work on ubuntu package installs). Definitely will take some elbow grease and looking forward to see what you come up with. (Note that the package does store a file in /etc/openemr/ in addition to a log in /var/log/openemr/ ).

Regarding Jenkins (sorry for thread hijack), what would be key is if there was a set of bash commands that could get it installed/configured (then with a simple toggle on the demo farm ip config script, we could turn on a auto Jenkins analysis on any demo).

-brady

system · May 6, 2014, 4:14am

bradymiller wrote on Tuesday, May 06, 2014:

Hi,

Am now middle of the way through step 2 in proposal above. Have fully tested and released a new “development” ubuntu-debian package that has been tested to work on Debian 7 and ubuntu 10.04,12.04 and 14.04:
http://www.open-emr.org/wiki/index.php/Ubuntu-Debian_OpenEMR_Development_Package_Installation
(note I used Ian’s advice above and made it a apache “site” and used a2ensite command to turn it on in postinst script: https://github.com/bradymiller/openemr/commit/1581b779a6f29b926b278f4825d4f287b0a1ca88)

The next item is to test the production package (and then will still need to release a patch 6 and then build the official production package off of this; so still a ways to go).

-brady
OpenEMR

system · May 21, 2014, 4:49am

iankarlwallace wrote on Wednesday, May 21, 2014:

Brady - Have re-surfaced from my camping trip but we are still in the
process of completing move to California. Added myself to the Debian-Med
list and will start process of asking for sponsor/requirements so that we
can add the OpenEMR Debian package to the repo’s. Would be a nice
enhancement to the project.

ian

On Mon, May 5, 2014 at 9:15 PM, Brady Miller bradymiller@users.sf.netwrote:

Hi,

Am now middle of the way through step 2 in proposal above. Have fully
tested and released a new “development” ubuntu-debian package that has been
tested to work on Debian 7 and ubuntu 10.04,12.04 and 14.04:

Ubuntu-Debian OpenEMR Development Package Installation - OpenEMR Project Wiki
(note I used Ian’s advice above and made it a apache “site” and used
a2ensite command to turn it on in postinst script:
Updates and fixes to ubuntu packages to work with modern ubuntu and d… · bradymiller/openemr@1581b77 · GitHub
)

The next item is to test the production package (and then will still need
to release a patch 6 and then build the official production package off of
this; so still a ways to go).

-brady
OpenEMR http://www.open-emr.org/

ubuntu-debian package bugshttps://sourceforge.net/p/openemr/discussion/202506/thread/e82523fd/?limit=25&page=1#5f7a

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system · May 21, 2014, 6:54am

bradymiller wrote on Wednesday, May 21, 2014:

Hi Ian,

Still cranking along on a fixed 4.1.2 package:

I think I’ve crushed all the bugs, but still doing testing on all the debian derivatives (At this point, I have virtual appliances going for ubuntu 10.04,12.04,13.10,14.04; debian 6,7; mint 16,17). The testing actually takes a large amount of time, because need to ensure it never hangs or errors out since this is a killer for typical users.

-brady
OpenEMR

system · May 24, 2014, 4:20am

iankarlwallace wrote on Saturday, May 24, 2014:

Nice. I would think that once you had tested on Ubuntu 10.04/12.04/14.04
and deb 6,7 you could probably stop but nice to add in the Mint 16/17 since
looks like lots of people use that on the list. I am still getting my feet
back under me since we won’t be into our apartment until end of June.

Once you are finished with the fixes we’ll have to discuss how to morph the
scripts such that they create correct debian pkgs (and source packages so
that others could build from source). I still need to down load the
phpMyAdmin stuff to look at that.

cheers
ian

On Tue, May 20, 2014 at 11:54 PM, Brady Miller bradymiller@users.sf.net
wrote:

Hi Ian,

Still cranking along on a fixed 4.1.2 package:
Commits · bradymiller/openemr · GitHub

I think I’ve crushed all the bugs, but still doing testing on all the
debian derivatives (At this point, I have virtual appliances going for
ubuntu 10.04,12.04, 10.04; debian 6,7; mint 16,17). The testing actually
takes a large amount of time, because need to ensure it never hangs or
errors out since this is a killer for typical users.

-brady
OpenEMR http://www.open-emr.org/

ubuntu-debian package bugs
https://sourceforge.net/p/openemr/discussion/202506/thread/e82523fd/?limit=25&page=1#5f7a/e3b0/331d

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system · May 25, 2014, 6:47am

bradymiller wrote on Sunday, May 25, 2014:

Noted an interesting aside. I also am testing on a debian “testing” appliance (this is their rolling version which is what the releases get forked from when released) and lo and behold debian also has made the move to change web from /var/www to /var/www/html (thus debian 8 will be using /var/www/html) so my blame towards ubuntu in my above post was unwarranted.
-brady
OpenEMR

system · May 27, 2014, 8:05am

bradymiller wrote on Tuesday, May 27, 2014:

Hi,

Almost done with step 2 (still need to complete testing on Ubuntu 12.04 and Mint 16 for the production package). Testing has been extensive and have been testing each item on each OS(Mint-16, Mint-17-rc DEBIAN 6, DEBIAN 7, DEBIAN TESTING, Ubuntu 10.04, Ubuntu 12.04, Ubuntu 13.10, Ubntu 14.04):
TEST INSTALL
TEST REMOVE
TEST SECURITY OF PATIENT DIRECTORIES
TEST TO ENSURE WORKS WITH THE GIT-OPENEMR PACKAGE
TEST WHEN THERE IS A NON-BLANK MYSQL ROOT USER

Since pretty much almost done and have exposed/fixed all bugs, I have committed the fixes to the packages to sourceforge. When testing’s complete, will then release patch 6 for 4.1.2 which will contain these fixes (and allow a new build of a ubuntu-debian package).

Here’s the commit that just went into the official codebase:

-brady
OpenEMR

system · May 28, 2014, 4:32am

iankarlwallace wrote on Wednesday, May 28, 2014:

Brady - Thanks for all the testing. Looked at the scripts briefly on
GitHub and look good. I will be starting a Mentor of the Mouth project
with Andreas from debian-med in June once he’s back from vacation. I am
sure the conversion over to a debian uploadable pkg will be aided by your
hard work in the testing and such.

cheers
ian

On Tue, May 27, 2014 at 1:05 AM, Brady Miller bradymiller@users.sf.net
wrote:

Hi,

Almost done with step 2 (still need to complete testing on Ubuntu 12.04
and Mint 16 for the production package). Testing has been extensive and
have been testing each item on each OS(Mint-16, Mint-17-rc DEBIAN 6, DEBIAN
7, DEBIAN TESTING, Ubuntu 10.04, Ubuntu 12.04, Ubuntu 13.10, Ubntu 14.04):
TEST INSTALL
TEST REMOVE
TEST SECURITY OF PATIENT DIRECTORIES
TEST TO ENSURE WORKS WITH THE GIT-OPENEMR PACKAGE
TEST WHEN THERE IS A NON-BLANK MYSQL ROOT USER

Since pretty much almost done and have exposed/fixed all bugs, I have
committing the fixes to the packages to sourceforge. When testing’s
complete, will then release patch 6 for 4.1.2 which will contain these
fixes (and allow a new build of a ubuntu-debian package).

Here’s the commit that just went into the official codebase:

Updates and fixes to ubuntu packages to work with modern ubuntu and d… · openemr/openemr@4b5930b · GitHub

-brady
OpenEMR http://www.open-emr.org/

ubuntu-debian package bugs
https://sourceforge.net/p/openemr/discussion/202506/thread/e82523fd/?limit=25&page=1#c26e

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system · June 2, 2014, 12:06am

bradymiller wrote on Monday, June 02, 2014:

Quick update,

Testing is done. Now onto step 3, which is release of next 4.1.2 patch. Note a windows bug still needs to be fixed for the patch(which is directly related to making the ubuntu package work):
https://github.com/openemr/openemr/commit/adf4751a4a281ea3d09ce2602bccfdbfabb472d7
(guessing the package will go out in a couple weeks or so)

-brady
OpenEMR

system · June 6, 2014, 7:37am

bradymiller wrote on Friday, June 06, 2014:

Another quick update,

Just committed a fix for windows to sourceforge (I finally broke down and purchased Windows 8.1, which is now running as a virtual machine on my Mint OS). Next step is release of patch #6 for 4.1.2, which will hopefully do this weekend.

-brady
OpenEMR

system · June 10, 2014, 5:48am

bradymiller wrote on Tuesday, June 10, 2014:

Update,

Patch has been released.

Now working on the new packages. On testing of new packages built from the new patch, released there will be an issue in upgrading OpenEMR versions with the new packages (database changes in sql_patch.php file are not happening). Likely needs a quick fix (won’t need another patch) and then another round of testing before release (ETA of 1-2 weeks or so).

-brady
OpenEMR

Ubuntu-debian package bugs

Rod
http://www.sunsetsystems.com/