Tuesday, August 28, 2007

GNUmed - user first reports bugs then success

GNUmed is free as in freedom but many users think it comes at a price. The price tag shows the resources you put in to make it run on your systems.

A long time ago I decided to make the installation process easier. This involved producing an installer for MS Windows. Few users have reported on their experience but it seems GNUmed benefits from its packaged versions. This holds true for Debian , Ubuntu and MS Windows.

Just a few days ago a German doctor reported a problem with GNUmed One E-Mail and a fix later he has been successful in bootstrapping a GNUmed database and running the client against it. Congrats. Way to go. While we don't know about his computer skills he is a doctor by profession and not a fulltime IT-guy.

He asked about the scanner connectivity and framegrabber options and has since reported success.

But what's worth even more is the bug he triggered and reported which makes us release version in a few days which holds a number of fixes.

He even supplied us with valuable information on how to connect the German legacy app 'DocConcept' to GNUmed through our great XML-RPC interface. As of now we have four (4) legacy apps in our Wiki which can interact with GNUmed without a single code change.

Well thanks to our testers. For him updating to future versions will be a piece of cake.

Dank eines Kollegen wissen wir nun von einer weiteren erfolgreichen GNUmed Installation. Nach zwei E-Mails und einem Fehlerreport durch den Kollegen konnte auf seinem Windowssystem eine GNUmed-Datenbank erzeugt werden und auch ein Client damit verbinden.

Ich nenne das Erfolg. So schwer kann die Installation nicht sein. Obwohl ich vermute, dass der Kollegen überdurchschnittliche PC-Kenntnisse hat.

Nun nachdem durch ihn ein Fehler entdeckt und gemeldet wurde wird demnächst die Version als Zwischversion vor der 0.2.7 veröffentlicht.

Beigesteuert hat er auch seine Erfahrungen bei der Anbindung von 'DocConcept' an GNUmed. Wir haben jetzt also 4 Praxisprogramme , die über die Schnittstelle mit GNUmed interagieren können.

Und jetzt sind für den Kollegen Updates nur einen Mausklick entfernt denn den vermeintlich schwierigen Teil der Installation hat er ja bereits gemeistert.

Monday, August 20, 2007

GNUmed and OpenClinica

OpenClinca is a enterprise grade clinical study management solution. It runs on the Apache tomcat webserver version 5.5. OpenSuse 10.2 provides all packages once you add JAVA:addon/openSUSE_10.2 to the channel list for smart. Install tomcat5.5. Dependencies will be pulled automatically. In my setting a lot of symlinks were not created so follow the Openclinics install instructions for the basics. Once done make sure you have the following setup (took me hours)

ls -l /srv/www/tomcat55/base/common/lib/
insgesamt 396
lrwxrwxrwx 1 root root 24 16. Aug 16:41 bcel.jar -> /usr/share/java/bcel.jar
lrwxrwxrwx 1 root root 34 16. Aug 16:41 catalina-ant55.jar -> /usr/share/java/catalina-ant55.jar
lrwxrwxrwx 1 root root 45 16. Aug 15:58 jakarta-commons-beanutils.jar -> /usr/share/java/jakarta-commons-beanutils.jar
lrwxrwxrwx 1 root root 40 16. Aug 16:19 jakarta-commons-dbcp.jar -> /usr/share/java/jakarta-commons-dbcp.jar
lrwxrwxrwx 1 root root 44 16. Aug 15:58 jakarta-commons-digester.jar -> /usr/share/java/jakarta-commons-digester.jar
lrwxrwxrwx 1 root root 38 16. Aug 15:58 jakarta-commons-el.jar -> /usr/share/java/jakarta-commons-el.jar
lrwxrwxrwx 1 root root 43 16. Aug 15:58 jakarta-commons-modeler.jar -> /usr/share/java/jakarta-commons-modeler.jar
lrwxrwxrwx 1 root root 45 16. Aug 15:58 jakarta-commons-validator.jar -> /usr/share/java/jakarta-commons-validator.jar
lrwxrwxrwx 1 root root 40 19. Aug 17:47 jakarta-taglibs-core.jar -> /usr/share/java/jakarta-taglibs-core.jar
lrwxrwxrwx 1 root root 44 19. Aug 17:35 jakarta-taglibs-standard.jar -> /usr/share/java/jakarta-taglibs-standard.jar
lrwxrwxrwx 1 root root 37 19. Aug 17:24 jasper55-compiler.jar -> /usr/share/java/jasper55-compiler.jar
lrwxrwxrwx 1 root root 36 19. Aug 17:24 jasper55-runtime.jar -> /usr/share/java/jasper55-runtime.jar
lrwxrwxrwx 1 root root 37 19. Aug 17:44 jasper-compiler -> /usr/share/java/jasper55-compiler.jar
lrwxrwxrwx 1 root root 26 19. Aug 17:52 javacc.jar -> /usr/share/java/javacc.jar
lrwxrwxrwx 1 root root 27 19. Aug 17:55 jdtcore.jar -> /usr/share/java/jdtcore.jar
lrwxrwxrwx 1 root root 41 19. Aug 17:43 jsp-api.jar -> /usr/share/tomcat55/common/lib/jspapi.jar
lrwxrwxrwx 1 root root 26 16. Aug 15:58 jspapi.jar -> /usr/share/java/jspapi.jar
lrwxrwxrwx 1 root root 23 19. Aug 17:40 jsp.jar -> /usr/share/java/jsp.jar
lrwxrwxrwx 1 root root 43 19. Aug 14:58 naming-factory.jar -> /usr/share/java/tomcat55/naming-factory.jar
lrwxrwxrwx 1 root root 45 19. Aug 14:58 naming-resources.jar -> /usr/share/java/tomcat55/naming-resources.jar
-rw-r--r-- 1 tomcat tomcat 402505 3. Mär 00:13 postgresql-8.1-405.jdbc3.jar
lrwxrwxrwx 1 root root 45 16. Aug 15:58 postgresql-8.2-506.jdbc3.jar -> /usr/share/pgsql/postgresql-8.2-506.jdbc3.jar
lrwxrwxrwx 1 root root 26 16. Aug 15:58 regexp.jar -> /usr/share/java/regexp.jar
lrwxrwxrwx 1 root root 32 16. Aug 16:32 servletapi55.jar -> /usr/share/java/servletapi55.jar
lrwxrwxrwx 1 root root 31 16. Aug 15:58 servletapi5.jar -> /usr/share/java/servletapi5.jar
lrwxrwxrwx 1 root root 16 19. Aug 17:43 servlet-api.jar -> servletapi55.jar
lrwxrwxrwx 1 root root 26 16. Aug 15:58 struts.jar -> /usr/share/java/struts.jar

start with 'rctomcat55 start' and watch /var/log/tomcat55/catalina.out for messages.

go to http://localhost:8080 in a webbrowser and test the jsp and servlet examples. If that works fine go to http://localhost:8080/OpenClinica and you will be greeted by the login screen

With respect to GNUmed one can think of a feature to submit patients to studies in OpenClinica or import follow-up visits as encounters in GNUmed.

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GNUmed OpenOffice.org support

GNUmed 0.2.7 is about to be released and it brings an exciting new feature. Since OpenOffice.org comes with a python api that allows us to control it Karsten expanded the work of a kind person on the mailing list and developed a GNUmed letter writer. Based on OpenOffice templates that are stored in the GNUmed database documents like referral letters are filled with patient data like SOAP, lab results and more.

But there is more. Since a document in OpenOffice can have a background image we are thinking about using it for printing forms such as prescriptions here in Germany.

On document completion a copy of the final document is imported into the GNUmed archive.

One needs to have recent OpenOffice.org along with the pyuno extension installed. For Debian Linux it seems to work out of the box. On Opensuse Linux one needs to add the Openoffice directory to the $PYTHONPATH variable.

MS Windows and MacOSX deliver OpenOffice and pyuno as well so I don't forsee any problems.

GNUmed 0.2.7 steht vor der Fertigstellung und bringt einige aufregende Programmfunktionen mit. GNUmed hat eine OpenOffice-Schnittstelle bekommen. Die OpenOffice API für Python erlaubt es OO mittels Python zu steuern. GNUmed nutzt das für die Briefschreibung. Karteieinträge und z.B. Laborwerte können so in Briefe übergeben werden. Erzeugt werden die Briefe aus Vorlagen, die in der GNUmed-Datenbank gespeichert sind und so unabhängig von der OpenOffice Installation zur Verfügung stehen.

OO kann aber auch Hintergrundbilder im Dokument einbinden und so wird GNUmed für den Formulardruck eingesetzt werden. Rezepte kommen da in den Sinn.
Nach Fertigstellung des Dokuments wird eine Kopie ins GNUmed-Archiv importiert.

Bei Debian scheint alles ohne Konfiguration zu funktionieren. Bei Opensuse muss der Pfad zu OpenOffice der Variable $PYTHONPATH hinzugefügt werden. Damit können wir ausdrucken, pdf exportieren und sogar per email verschicken.

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