Please find, for review, the debconf templates and packages descriptions for the biomaj source package. This review will last from Thursday, December 29, 2011 to Sunday, January 08, 2012. Please send reviews as unified diffs (diff -u) against the original files. Comments about your proposed changes will be appreciated. Your review should be sent as an answer to this mail. When appropriate, I will send intermediate requests for review, with "[RFRn]" (n>=2) as a subject tag. When we will reach a consensus, I send a "Last Chance For Comments" mail with "[LCFC]" as a subject tag. Finally, a summary will be sent to the review bug report, and a mail will be sent to this list with "[BTS]" as a subject tag. Rationale: --- biomaj.old/debian/templates 2011-12-27 22:20:05.845944392 +0100 +++ biomaj/debian/templates 2011-12-29 17:09:55.323508195 +0100 @@ -1,19 +1,32 @@ Template: biomaj/jdk_home Type: string -_Description: The JDK home directory: +_Description: JDK home directory: + Please enter the directory where the Java Development Kit, + which is used by BioMAJ, is installed. Give more details. I however wonder why this has to be configured. Shouldn't the package depends on a JDK and therefore "know" where it is installed? Template: biomaj/mysql Type: boolean -_Description: Want to configure MySQL connection now ? +_Description: Configure MySQL connection now? + Please choose whether you want to configure connection + parameters for the BioMAJ MySQL database. + . + Please note that the database has to be created and configured + before it can be used. Use "BioMAJ" as this seems to be the "official" way to write the software name? Template: biomaj/mysql_host Type: string -_Description: Enter MySQL server address: +_Description: MySQL server: + Please enter the hostname or IP address of the + MySQL server you want to use. Template: biomaj/mysql_login Type: string -_Description: User login for biomaj database: +_Description: MySQL login for BioMAJ database: + Please enter the login to use when connecting to the MySQL database + server to access the biomaj_log database. Template: biomaj/mysql_passwd Type: password -_Description: User password for biomaj database: +_Description: MySQL password for BioMAJ database: + Please enter the password to use when connecting to the MySQL database + server to access the biomaj_log database. "biomaj_log" comes from your own proposal for templates. --- biomaj.old/debian/control 2011-12-27 22:20:05.845944392 +0100 +++ biomaj/debian/control 2011-12-29 08:58:46.776705863 +0100 @@ -27,9 +27,9 @@ libcommons-httpclient-java, libcommons-logging-java,libjets3t-java, perl, mysql-server Suggests: ncbi-tools-bin, blast2 -Description: Biological banks updater - BioMAJ downloads remote data banks, check their status and apply transformation - workflows, with consistent state,to provide ready-to-use data to biologists and +Description: biological banks updater + BioMAJ downloads remote data banks, checks their status and applies transformation + workflows, with consistent state, to provide ready-to-use data to biologists and bioinformaticians. For example, it can transform original fasta files to blast indexes. It is very flexible and post-processes can be extended very easily. No leading uppercase in synopsis. Some grammar corrections. @@ -38,6 +38,6 @@ Depends: ${misc:Depends} Description: bank properties file examples This package contains a set of bank properties that can be used as - examples for biomaj. It contains many existing banks descriptions - with or without workflows to transform data. Some files may required - additional programs for post processes (blast..). + examples for BioMAJ. It contains many existing banks descriptions + with or without workflows to transform data. Some files may require + additional programs for post-processes such as blast. Proper spelling of BioMAJ. Spelling correction. --
Template: biomaj/jdk_home Type: string _Description: JDK home directory: Please enter the directory where the Java Development Kit, which is used by BioMAJ, is installed. Template: biomaj/mysql Type: boolean _Description: Configure MySQL connection now? Please choose whether you want to configure connection parameters for the BioMAJ MySQL database. . Please note that the database has to be created and configured before it can be used. Template: biomaj/mysql_host Type: string _Description: MySQL server: Please enter the hostname or IP address of the MySQL server you want to use. Template: biomaj/mysql_login Type: string _Description: MySQL login for BioMAJ database: Please enter the login to use when connecting to the MySQL database server to access the biomaj_log database. Template: biomaj/mysql_passwd Type: password _Description: MySQL password for BioMAJ database: Please enter the password to use when connecting to the MySQL database server to access the biomaj_log database.
--- biomaj.old/debian/templates 2011-12-27 22:20:05.845944392 +0100 +++ biomaj/debian/templates 2011-12-29 17:09:55.323508195 +0100 @@ -1,19 +1,32 @@ Template: biomaj/jdk_home Type: string -_Description: The JDK home directory: +_Description: JDK home directory: + Please enter the directory where the Java Development Kit, + which is used by BioMAJ, is installed. Template: biomaj/mysql Type: boolean -_Description: Want to configure MySQL connection now ? +_Description: Configure MySQL connection now? + Please choose whether you want to configure connection + parameters for the BioMAJ MySQL database. + . + Please note that the database has to be created and configured + before it can be used. Template: biomaj/mysql_host Type: string -_Description: Enter MySQL server address: +_Description: MySQL server: + Please enter the hostname or IP address of the + MySQL server you want to use. Template: biomaj/mysql_login Type: string -_Description: User login for biomaj database: +_Description: MySQL login for BioMAJ database: + Please enter the login to use when connecting to the MySQL database + server to access the biomaj_log database. Template: biomaj/mysql_passwd Type: password -_Description: User password for biomaj database: +_Description: MySQL password for BioMAJ database: + Please enter the password to use when connecting to the MySQL database + server to access the biomaj_log database. --- biomaj.old/debian/control 2011-12-27 22:20:05.845944392 +0100 +++ biomaj/debian/control 2011-12-29 08:58:46.776705863 +0100 @@ -27,9 +27,9 @@ libcommons-httpclient-java, libcommons-logging-java,libjets3t-java, perl, mysql-server Suggests: ncbi-tools-bin, blast2 -Description: Biological banks updater - BioMAJ downloads remote data banks, check their status and apply transformation - workflows, with consistent state,to provide ready-to-use data to biologists and +Description: biological banks updater + BioMAJ downloads remote data banks, checks their status and applies transformation + workflows, with consistent state, to provide ready-to-use data to biologists and bioinformaticians. For example, it can transform original fasta files to blast indexes. It is very flexible and post-processes can be extended very easily. @@ -38,6 +38,6 @@ Depends: ${misc:Depends} Description: bank properties file examples This package contains a set of bank properties that can be used as - examples for biomaj. It contains many existing banks descriptions - with or without workflows to transform data. Some files may required - additional programs for post processes (blast..). + examples for BioMAJ. It contains many existing banks descriptions + with or without workflows to transform data. Some files may require + additional programs for post-processes such as blast.
Source: biomaj Section: science Priority: optional Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Uploaders: Olivier Sallou <olivier.sallou@irisa.fr> DM-Upload-Allowed: yes Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/biomaj/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biomaj/trunk/?rev=0&sc=0 Homepage: http://biomaj.genouest.org Build-Depends: debhelper (>= 7.1) Build-Depends-Indep: debconf, po-debconf, openjdk-6-jdk|default-jdk|sun-java6-jdk, ant, libhsqldb-java, ant-contrib, liblog4j1.2-java, libcommons-net2-java, libcommons-dbcp-java, libgnumail-java, libcommons-pool-java, libgnujaf-java, libjgoodies-forms-java, liboro-java, libregexp-java, libjcommon-java, libjsch-java, libjdom1-java, junit4, libsaxonb-java, libjdepend-java, javahelper (>=0.25), libcommons-cli-java, libcommons-codec-java, libcommons-httpclient-java, libcommons-logging-java, libjets3t-java Standards-Version: 3.9.2 Package: biomaj Architecture: all Depends: ${misc:Depends}, ${java:Depends}, openjdk-6-jdk|default-jdk|sun-java6-jdk, ant, libmysql-java, debconf, libhsqldb-java,ant-contrib,liblog4j1.2-java,libcommons-net2-java (>= 2.2),libcommons-dbcp-java (>= 1.2), libgnumail-java, libcommons-pool-java (>= 1.5), libgnujaf-java, libjgoodies-forms-java (>= 1.2), liboro-java (>= 2.0),libregexp-java (>= 1.4),libjcommon-java (>= 1.0),libjsch-java (>= 0.1.42), libjdom1-java (>= 1.1),junit4,libsaxonb-java (>= 0.9), libcommons-cli-java, libcommons-codec-java, libcommons-httpclient-java, libcommons-logging-java,libjets3t-java, perl, mysql-server Suggests: ncbi-tools-bin, blast2 Description: biological banks updater BioMAJ downloads remote data banks, checks their status and applies transformation workflows, with consistent state, to provide ready-to-use data to biologists and bioinformaticians. For example, it can transform original fasta files to blast indexes. It is very flexible and post-processes can be extended very easily. Package: biomaj-properties Architecture: all Depends: ${misc:Depends} Description: bank properties file examples This package contains a set of bank properties that can be used as examples for BioMAJ. It contains many existing banks descriptions with or without workflows to transform data. Some files may require additional programs for post-processes such as blast.
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