Re: OpenClinica in Debian-Med
Le 11/4/11 9:16 AM, Sebastian Hilbert a écrit :
> On Thursday, November 03, 2011 03:46:32 PM Olivier Sallou wrote:
>
> It looks like when building OC all of the jars mentioned below are compiled
> from source anyway.
I see in trunk it is a maven project [1]
It gets all dependencies from a maven repository.
Maven is quite an issue in Debian from my recent experience. While there
are some helpers to manage this, you need to get
all dependencies in Debian but also set for maven use.
For your package, you cannot use the maven repos.
One possibility, for libraries available in Debian is to patch the
pom.xml to use "system" scope, with path to the library. But for the
others not available in Debian, one still need to get them available....
[1]
https://svn.akazaresearch.com/openclinica/OpenClinica/trunk2/projects/pom.xml
Olivier
> They seem to be gotten from
> svn.akazaresearch.com/ocrepository/repository/
>
> So this looks like there is nothing to worry about ?
>
> The OC developers are interested in packaging this so if there are any specific
> questions we have someone to talk to upstream.
>
> the instructions for building OC from source are available at
> https://wiki.openclinica.com/doku.php?id=developerwiki:gettingstarted
>
> There they talk about trunk but I the path for OC 3.1 is
> https://svn.akazaresearch.com/openclinica/OpenClinica/branches/OpenClinica-3.1-
> SNAPSHOT/
>
> Please let me know if that makes it possible to package OC and what effort is
> involved ?
>
> Regards,
> Sebastian
>
>> Le 11/3/11 3:35 PM, Sebastian Hilbert a écrit :
>>> On Monday, October 31, 2011 01:59:44 PM Sebastian Hilbert wrote:
>>>
>>> I have done some more research on which jar files are needed by
>>> OpenClinica
>>>
>>> Here is a (maybe incomplete list)
>>>
>>> There are a few occurences where no package in Debian provides the jar.
>>> However for all jars sources exist and their is a license which should
>>> comply with Debian guidelines (see below)
>>>
>>> Please advise.
>> Regarding mail, there is gnumail I think that should match
>>
>>> activation-1.0.2.jar - libgnujaf-java in sid
>>> antlr-2.7.6.jar - antlr in sid
>>> aopalliance-1.0.jar - libaopalliance-java in sid
>>> aspectjrt-1.6.8.jar - libaspectj-java in sid
>>> aspectjweaver-1.6.8.jar - libaspectj-java in sid
>>> avalon-framework-api-4.3.1.jar - libavalon-framework-java in sid
>>> avalon-framework-impl-4.3.1.jar - libavalon-framework-java in sid
>>> batik-anim-1.7.jar - libbatik-java in sid
>>> batik-awt-util-1.7.jar - libbatik-java in sid
>>> batik-bridge-1.7.jar - libbatik-java in sid
>>> batik-css-1.7.jar - libbatik-java in sid
>>> batik-dom-1.7.jar - libbatik-java in sid
>>> batik-ext-1.7.jar - libbatik-java in sid
>>> batik-extension-1.7.jar - libbatik-java in sid
>>> batik-gvt-1.7.jar - libbatik-java in sid
>>> batik-parser-1.7.jar - libbatik-java in sid
>>> batik-script-1.7.jar - libbatik-java in sid
>>> batik-svg-dom-1.7.jar - libbatik-java in sid
>>> batik-svggen-1.7.jar - libbatik-java in sid
>>> batik-transcoder-1.7.jar - libbatik-java in sid
>>> batik-util-1.7.jar - libbatik-java in sid
>>> batik-xml-1.7.jar - libbatik-java in sid
>>> bcmail-jdk14-138.jar - libcmail-java in sid
>>> bcprov-jdk14-138.jar - libcprov-java in sid
>>> castor-1.2.jar - ?? not in debian - www.castor.org - Apache-2.0-style
>>> license castor-core-1.3.1.jar - libcastor-core-java in sid
>>> castor-xml-1.3.1.jar - libcastor-core-xml in sid
>>> cglib-nodep-2.1_3.jar - libcglib2.1-java in sid
>>> commons-beanutils-1.8.0.jar - libcommons-beantutils-java in sid
>>> commons-codec-1.3.jar - libcommons-codec-java in sid
>>> commons-collections-3.2.1.jar - libcommons-collections-java in sid
>>> commons-dbcp-1.2.2.jar - libcommons-dhcp-java in sid
>>> commons-digester-1.7.jar - libcommons-digester-java in sid
>>> commons-discovery-0.2.jar - libcommons-dicovery-java in sid
>>> commons-fileupload-1.2.1.jar - libcommons-fileupload-java in sid
>>> commons-httpclient-3.0.1.jar - libcommons-httpclient-java in sid
>>> commons-io-1.4.jar - libcommons-io-java in sid
>>> commons-lang-2.3.jar - libcommons-lang-java in sid
>>> commons-logging-1.0.4.jar - libcommons-logging-java in sid
>>> commons-logging-api-1.0.4.jar - libcommons-logging-java in sid
>>> commons-math-1.1.jar - libcommons-math-java in sid
>>> commons-pool-1.3.jar - libcommons-pool-java in sid
>>> commons-validator-1.3.1.jar - libcommons-validator-java in sid
>>> dom4j-1.6.1.jar - libdom4j-java in sid
>>> fop-1.0.jar - fop in sid
>>> hibernate-annotations-3.5.1-Final.jar - libhibernate-annotations-java
>>> (3.6) hibernate-commons-annotations-3.2.0.Final.jar -
>>> libhibernate-commons- annotations-java
>>> hibernate-core-3.5.1-Final.jar - libhibernate3-java (3.6)
>>> hibernate-jpa-2.0-api-1.0.0.Final.jar - not in Debian (LGPL)
>>> hibernate-validator-4.0.2.GA.jar - libhibernate-validator-java in sid
>>> itext-2.1.2.jar - libitext-java in sid
>>> jackson-core-asl-1.5.3.jar - libjackson-json-java in sid
>>> jackson-mapper-asl-1.5.3.jar - libjackson-json-java in sid
>>> janino-2.5.10.jar - janino in sid
>>> javassist-3.8.0.GA.jar - libjavassist-java (3.12 sid) (3.8 lenny)
>>> jaxb-api-2.1.jar - libjaxme-java in sid (jaxmeapi.jar) ? or included in
>>> openjdk ? license: CDDL / GPLv2
>>> jaxb-impl-2.1.3.jar - libjaxme-java in sid (jaxmeapi.jar) ? or included
>>> in openjdk ? license: CDDL / GPLv2
>>> jcl-over-slf4j-1.5.6.jar - libslj4j-java in sid
>>> jdom-1.1.jar - libjdom1-java in sid
>>> jmesa-2.4.2.jar - not in Debian - Apache 2 license
>>> joda-time-1.6.jar - libjoda-time-java
>>> jstl-1.1.2.jar - libjstl1.1-java
>>> jta-1.1.jar - not in Debian either from Oracle (GPL) or
>>> libgeronimo-jta-1-1- spec-java
>>> jul-to-slf4j-1.5.6.jar - libslj4j-java in sid
>>> jxl-2.6.6.jar - libjxcelapi-java in sid
>>> liquibase-core-1.9.5.jar - not in Debian (Apache 2.0)
>>> liquibase-plugin-1.9.5.0.jar - not in Debian (Apache 2.0)
>>> log4j-1.2.14.jar - liblog4j1.2-java in sid
>>> logback-access-0.9.20.jar - not in Debian (EPL v1.0 or LGPL 2.1)
>>> logback-classic-0.9.20.jar - liblogback-java in sid
>>> logback-core-0.9.20.jar - liblogback-java in sid
>>> mail-1.4.jar - not in Debian (CDDL license)
>>> ojdbc14-10g.jar - not in Debian - closed - some Oracle distribution
>>> license - can skipped when using PG
>>> OpenClinica-core-3.1.1-Community.jar - LPGL
>>> openclinica-odm-0.1.0.BUILD-SNAPSHOT.jar - LGPL
>>> oro-2.0.8.jar - liboro-java in sid
>>> persistence-api-1.0.jar - not in Debian (Oracle CDDL) - shipped by
>>> glassfish- javaee
>>> pjl-comp-filter-1.6.4.jar - not in Debian (Apache 2.0)
>>> poi-3.0.1-FINAL.jar - libapache-poi-java in sid
>>> postgresql-8.1-404.jdbc3.jar - libpg-java in sid
>>> quartz-1.8.0.jar - libquartz-java (1.7.3)
>>> quartz-oracle-1.8.0.jar - not in Debian (not needed for PG)
>>> rome-1.0.jar - librome-java in sid
>>> rome-fetcher-1.0.jar - not in Debian (Apache 2)
>>> saxon-8.7.jar - libsaxon-java in sid (6.5.5)
>>> saxon-dom-8.7.jar - not in Debian (Mozilla Public license)
>>> sitemesh-2.3.jar - libsitemesh-java in sid
>>> slf4j-api-1.5.6.jar - libslj4j-java in sid
>>> spring-aop-3.0.5.RELEASE.jar - libspring-aop-java in sid
>>> spring-asm-3.0.5.RELEASE.jar - not in Debian
>>> spring-aspects-3.0.5.RELEASE.jar - libspring-aspects-2.5-java !!
>>> spring-beans-3.0.5.RELEASE.jar - libspring-beans-java in sid
>>> spring-context-3.0.5.RELEASE.jar - libspring-context-java in sid
>>> spring-context-support-3.0.5.RELEASE.jar - libspring-context-support-java
>>> spring-core-3.0.5.RELEASE.jar - libspring-core-java in sid
>>> spring-expression-3.0.5.RELEASE.jar - libspring-expression-java
>>> spring-jdbc-3.0.5.RELEASE.jar - libspring-jdbc-java in sid
>>> spring-orm-3.0.5.RELEASE.jar - libspring-orm-java in sid
>>> spring-oxm-3.0.5.RELEASE.jar - libspring-oxm-java in sid
>>> spring-security-acl-3.0.5.RELEASE.jar - libspring-security-acl-2.0-java
>>> !! spring-security-config-3.0.5.RELEASE.jar - not in Debian (Apache 2.0
>>> license) spring-security-core-3.0.5.RELEASE.jar - not in Debian (Apache
>>> 2.0 license) spring-security-oauth-1.0.0.M2.jar - not in Debian (Apache
>>> 2.0 license) spring-security-taglibs-3.0.5.RELEASE.jar -
>>> libspring-security-taglibs-2.0- java !!
>>> spring-security-web-3.0.5.RELEASE.jar - not in Debian
>>> spring-test-3.0.5.RELEASE.jar - libstring-test-jav in sid
>>> spring-tx-3.0.5.RELEASE.jar - libspring-tx-2.5-java !!
>>> spring-web-3.0.5.RELEASE.jar - libspring-web-java in sid
>>> spring-webmvc-3.0.5.RELEASE.jar - libspring-webmvc-2.5-java
>>> standard-1.1.2.jar - not in Debian (license ?)
>>> stax-api-1.0-2.jar - libstax-java in sid
>>> transaction-api-1.1.jar - not in Debian (GPL) - shipped by
>>> glassfish-javaee validation-api-1.0.0.GA.jar - not in Debian (Apache 2)
>>> xalan-2.6.0.jar - libxalan2-java in sid
>>> xercesImpl-2.4.0.jar - libxerces2-java in sid
>>> xml-apis-1.0.b2.jar - libjaxp1.3-java in sid
>>> xml-apis-ext-1.3.04.jar - libxml-commons-external-java in sid
>>> xmlgraphics-commons-1.4.jar - libxmlgraphics-commons-java
>>>
>>> jars not availabe as Debian packages along with their licenses.
>>>
>>> castor-1.2.jar - ?? not in debian - www.castor.org - Apache-2.0-style
>>> license hibernate-jpa-2.0-api-1.0.0.Final.jar - not in Debian (LGPL)
>>> jaxb-api-2.1.jar - libjaxme-java in sid (jaxmeapi.jar) ? or included in
>>> openjdk ? license: CDDL / GPLv2
>>> jaxb-impl-2.1.3.jar - libjaxme-java in sid (jaxmeapi.jar) ? or included
>>> in openjdk ? license: CDDL / GPLv2
>>> jmesa-2.4.2.jar - not in Debian - Apache 2 license
>>> jta-1.1.jar - not in Debian either from Oracle (GPL) or
>>> libgeronimo-jta-1-1- spec-java
>>> liquibase-core-1.9.5.jar - not in Debian (Apache 2.0)
>>> logback-access-0.9.20.jar - not in Debian (EPL v1.0 or LGPL 2.1)
>>> mail-1.4.jar - not in Debian (CDDL license)
>>> ojdbc14-10g.jar - not in Debian - closed - some Oracle distribution
>>> license - can skipped when using PG
>>> OpenClinica-core-3.1.1-Community.jar - LPGL
>>> openclinica-odm-0.1.0.BUILD-SNAPSHOT.jar - LGPL
>>> persistence-api-1.0.jar - not in Debian (Oracle CDDL) - shipped by
>>> glassfish- javaee
>>> pjl-comp-filter-1.6.4.jar - not in Debian (Apache 2.0)
>>> pjl-comp-filter-1.6.4.jar - not in Debian (Apache 2.0)
>>> quartz-oracle-1.8.0.jar - not in Debian (not needed for PG)
>>> rome-fetcher-1.0.jar - not in Debian (Apache 2)
>>> saxon-dom-8.7.jar - not in Debian (Mozilla Public license)
>>> spring-asm-3.0.5.RELEASE.jar - not in Debian
>>> spring-security-config-3.0.5.RELEASE.jar - not in Debian (Apache 2.0
>>> license) spring-security-core-3.0.5.RELEASE.jar - not in Debian (Apache
>>> 2.0 license) spring-security-oauth-1.0.0.M2.jar - not in Debian (Apache
>>> 2.0 license) standard-1.1.2.jar - not in Debian (license ?)
>>> transaction-api-1.1.jar - not in Debian (GPL) - shipped by
>>> glassfish-javaee validation-api-1.0.0.GA.jar - not in Debian (Apache 2)
>>>
>>> Best regards,
>>> Sebastian Hilbert
>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (pgp.mit.edu)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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