[Debian-med-packaging] Bug#653408: [RFR] templates://biomaj/{templates}

[Justin B Rye]

Christian PERRIER wrote:
>  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.

That's European-style relative clause punctuation.  You want:

    Please specify the directory where the Java Development Kit
    which is used by BioMAJ is installed.

Or, since the place where it's installed is the place where it is,
simplify to:

    Please specify the path to the Java Development Kit for BioMAJ.

> 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?

It does have a "Depends: openjdk-6-jdk|default-jdk|sun-java6-jdk", so
yes, this sounds like a job for policy and/or $JAVA_HOME.

>  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.
> 
> Use "BioMAJ" as this seems to be the "official" way to write the
> software name?

Upstream seem to think so.  I notice there's a bit more information in
the revised version, but it's still rather unclear to me exactly what
it is that needs to happen first or what this allows to happen second.

Candidates for both include:
a) the package mysql-server-x.y being fully installed
b) a "biomaj_log" database and dbadmin being created
c) the connection parameters being set up via debconf
d) BioMAJ being configured to populate the database automatically

I'm guessing that (a) is a prerequisite for (c) which gives you (d),
but is doing (b) also a prerequisite or is it automated?

Maybe:

    Once the MySQL database for BioMAJ has been created and configured, it
    can populate itself automatically instead of needing to be updated
    manually.
    .
    Please specify whether the database connection should be configured now.
  
>  Template: biomaj/mysql_host
[...]
>  Template: biomaj/mysql_login
[...]
>  Template: biomaj/mysql_passwd

These look good.

>  Package: biomaj
[...]
> +Description: biological banks updater

The top hits for "biological banks" are all talking about tissue
sample repositories.  What you mean is

   Description: biological data-bank 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.

Better, but: s/fasta/FASTA/, s/blast/BLAST/ (not to be confused with
the Debian package "blast"), and I'm not sure about "post-processes" -
maybe "its post-processing facilities"?

    BioMAJ downloads remote data banks, checks their status and applies
    transformation workflows, with consistent state, to provide ready-to-use
    data for biologists and bioinformaticians. For example, it can transform
    original FASTA files into BLAST indexes. It is very flexible and its
    post-processing facilities can be extended very easily.
  
>  Package: biomaj-properties
[...]
>  Description: bank properties file examples

Even worse - "bank properties" means land owned by financial
institutions...

   Description: biological data-bank updater - example properties files

>   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.

A couple of extra tweaks (for instance, they're existing data banks,
not existing descriptions):

    This package contains a set of data bank properties files that can be
    used as examples for BioMAJ. It contains descriptions for many existing
    data banks with or without workflows to transform data. Some files may
    require additional programs (such as BLAST) for post-processing.

-- 
JBR	with qualifications in linguistics, experience as a Debian
	sysadmin, and probably no clue about this particular package
-------------- next part --------------
diff -ru biomaj-1.2.0.pristine/debian/control biomaj-1.2.0/debian/control
--- biomaj-1.2.0.pristine/debian/control	2011-12-16 08:23:26.000000000 +0000
+++ biomaj-1.2.0/debian/control	2011-12-29 17:54:38.167362204 +0000
@@ -27,17 +27,18 @@
  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
- bioinformaticians. For example, it can transform original fasta files to blast 
- indexes. It is very flexible and post-processes can be extended very easily.
+Description: biological data-bank updater
+ BioMAJ downloads remote data banks, checks their status and applies
+ transformation workflows, with consistent state, to provide ready-to-use
+ data for biologists and bioinformaticians. For example, it can transform
+ original FASTA files into BLAST indexes. It is very flexible and its
+ post-processing facilities 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 required
- additional programs for post processes (blast..).
+Description: biological data-bank updater - example properties files
+ This package contains a set of data bank properties files that can be
+ used as examples for BioMAJ. It contains descriptions for many existing
+ data banks with or without workflows to transform data. Some files may
+ require additional programs (such as BLAST) for post-processing.
diff -ru biomaj-1.2.0.pristine/debian/templates biomaj-1.2.0/debian/templates
--- biomaj-1.2.0.pristine/debian/templates	2011-06-06 15:44:12.000000000 +0100
+++ biomaj-1.2.0/debian/templates	2011-12-29 17:53:17.983695397 +0000
@@ -1,19 +1,31 @@
 Template: biomaj/jdk_home
 Type: string
-_Description: The JDK home directory:
+_Description: JDK home directory:
+ Please specify the path to the Java Development Kit for BioMAJ.
 
 Template: biomaj/mysql
 Type: boolean
-_Description: Want to configure MySQL connection now ?
+_Description: Configure MySQL connection now?
+ Once the MySQL database for BioMAJ has been created and configured, it
+ can populate itself automatically instead of needing to be updated
+ manually.
+ .
+ Please specify whether the database connection should be configured now.
 
 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.
-------------- next part --------------
Template: biomaj/jdk_home
Type: string
_Description: JDK home directory:
 Please specify the path to the Java Development Kit for BioMAJ.

Template: biomaj/mysql
Type: boolean
_Description: Configure MySQL connection now?
 Once the MySQL database for BioMAJ has been created and configured, it
 can populate itself automatically instead of needing to be updated
 manually.
 .
 Please specify whether the database connection should be configured now.

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.
-------------- next part --------------
Source: biomaj
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Olivier Sallou <olivier.sallou at 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 data-bank updater
 BioMAJ downloads remote data banks, checks their status and applies
 transformation workflows, with consistent state, to provide ready-to-use
 data for biologists and bioinformaticians. For example, it can transform
 original FASTA files into BLAST indexes. It is very flexible and its
 post-processing facilities can be extended very easily.

Package: biomaj-properties
Architecture: all
Depends: ${misc:Depends}
Description: biological data-bank updater - example properties files
 This package contains a set of data bank properties files that can be
 used as examples for BioMAJ. It contains descriptions for many existing
 data banks with or without workflows to transform data. Some files may
 require additional programs (such as BLAST) for post-processing.