[med-svn] [python-biomaj3] 01/03: use biomaj3-commons package for common directory structure and config
Olivier Sallou
osallou at debian.org
Sun Jan 15 07:55:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository python-biomaj3.
commit 2f023773d5db2cf4bdf764db807a704bd1db087d
Author: Olivier Sallou <osallou at debian.org>
Date: Sun Jan 15 07:45:37 2017 +0000
use biomaj3-commons package for common directory structure and config
---
debian/README.Debian | 3 +
debian/README.source | 2 -
debian/biomaj3-commons.dirs | 6 ++
...n-biomaj3.examples => biomaj3-commons.examples} | 0
...ython-biomaj3.postrm => biomaj3-commons.postrm} | 12 +--
debian/biomaj3-doc.dirs | 1 -
debian/biomaj3-doc.doc-base | 10 --
debian/control | 20 +++-
debian/{global.properties-py => global.properties} | 12 +--
debian/global.properties-py3 | 115 ---------------------
debian/python3-biomaj3.dirs | 6 --
debian/python3-biomaj3.examples | 1 -
debian/python3-biomaj3.postrm | 32 ------
debian/rules | 11 +-
14 files changed, 42 insertions(+), 189 deletions(-)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..14c423c
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,3 @@
+# Binary renaming
+
+biomaj-cli.py from upstream has been renamed to python-biomaj-cli and python3-biomaj-cli
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 0849e68..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,2 +0,0 @@
-TODO add global.properties in /etc
- add alu.properties in examples
diff --git a/debian/biomaj3-commons.dirs b/debian/biomaj3-commons.dirs
new file mode 100644
index 0000000..6187a0d
--- /dev/null
+++ b/debian/biomaj3-commons.dirs
@@ -0,0 +1,6 @@
+var/lib/biomaj3/banks
+var/log/biomaj3
+etc/biomaj3/process
+etc/biomaj3/properties
+var/cache/biomaj3
+var/lib/biomaj3/lock
diff --git a/debian/python-biomaj3.examples b/debian/biomaj3-commons.examples
similarity index 100%
rename from debian/python-biomaj3.examples
rename to debian/biomaj3-commons.examples
diff --git a/debian/python-biomaj3.postrm b/debian/biomaj3-commons.postrm
similarity index 64%
rename from debian/python-biomaj3.postrm
rename to debian/biomaj3-commons.postrm
index a4e2e6e..a6c554e 100644
--- a/debian/python-biomaj3.postrm
+++ b/debian/biomaj3-commons.postrm
@@ -8,14 +8,14 @@ set -e
case "$1" in
purge)
# Remove generated data and migration info
- if [ -e /var/lib/python-biomaj3 ]; then
- rm -rf /var/lib/python-biomaj3
+ if [ -e /var/lib/biomaj3 ]; then
+ rm -rf /var/lib/biomaj3
fi
- if [ -e /var/log/python-biomaj3 ]; then
- rm -rf /var/log/python-biomaj3
+ if [ -e /var/log/biomaj3 ]; then
+ rm -rf /var/log/biomaj3
fi
- if [ -e /var/cache/python-biomaj3 ]; then
- rm -rf /var/cache/python-biomaj3
+ if [ -e /var/cache/biomaj3 ]; then
+ rm -rf /var/cache/biomaj3
fi
;;
remove|upgrade|failed-upgrade|abort-install|disappear)
diff --git a/debian/biomaj3-doc.dirs b/debian/biomaj3-doc.dirs
deleted file mode 100644
index 69ace7b..0000000
--- a/debian/biomaj3-doc.dirs
+++ /dev/null
@@ -1 +0,0 @@
-usr/share/doc/biomaj3-doc
diff --git a/debian/biomaj3-doc.doc-base b/debian/biomaj3-doc.doc-base
deleted file mode 100644
index f9ebf5e..0000000
--- a/debian/biomaj3-doc.doc-base
+++ /dev/null
@@ -1,10 +0,0 @@
-Document: biomaj3
-Title: BioMAJ3 Manual
-Author: Olivier Sallou
-Abstract: This manual describes the API of biomaj3
- and how it can be used.
-Section: Science/Biology
-
-Format: HTML
-Index: /usr/share/doc/biomaj3-doc/html/index.html
-Files: /usr/share/doc/biomaj3-doc/html/*.html
diff --git a/debian/control b/debian/control
index b022db7..4b0f684 100644
--- a/debian/control
+++ b/debian/control
@@ -41,7 +41,8 @@ Package: python-biomaj3
Architecture: all
Depends: ${misc:Depends},
${python:Depends},
- ${shlibs:Depends}
+ ${shlibs:Depends},
+ biomaj3-commons
Suggests: mongodb-server, biomaj3-doc
Description: biological data-bank updater (Python 2)
BioMAJ downloads remote data banks, checks their status and applies
@@ -58,7 +59,8 @@ Package: python3-biomaj3
Architecture: all
Depends: ${misc:Depends},
${python3:Depends},
- ${shlibs:Depends}
+ ${shlibs:Depends},
+ biomaj3-commons
Suggests: mongodb-server, biomaj3-doc
Description: biological data-bank updater (Python 3)
BioMAJ downloads remote data banks, checks their status and applies
@@ -70,3 +72,17 @@ Description: biological data-bank updater (Python 3)
BioMAJ is a rewrite of BioMAJ, using Mongodb as backend. See wiki for migration.
.
This package contains the Python 3 module.
+
+Package: biomaj3-commons
+Architecture: all
+Depends: ${misc:Depends}
+ 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.
+ .
+ BioMAJ is a rewrite of BioMAJ, using Mongodb as backend. See wiki for migration.
+ .
+ This package contains the configuration files and directory structure (logs, ..)
+ to run BioMAJ.
diff --git a/debian/global.properties-py b/debian/global.properties
similarity index 91%
rename from debian/global.properties-py
rename to debian/global.properties
index 2f1c309..8e0b702 100644
--- a/debian/global.properties-py
+++ b/debian/global.properties
@@ -2,13 +2,13 @@
#The root directory where all databases are stored.
#If your data is not stored under one directory hirearchy
#you can override this value in the database properties file.
-data.dir=/var/lib/python-biomaj3/banks
+data.dir=/var/lib/biomaj3/banks
-conf.dir=/etc/python-biomaj3/properties
-log.dir=/var/log/python-biomaj3
-process.dir=/etc/python-biomaj3/process
-cache.dir=/var/cache/python-biomaj3
-lock.dir= /var/lib/python-biomaj3/lock
+conf.dir=/etc/biomaj3/properties
+log.dir=/var/log/biomaj3
+process.dir=/etc/biomaj3/process
+cache.dir=/var/cache/biomaj3
+lock.dir= /var/lib/biomaj3/lock
db.url=mongodb://localhost:27017
db.name=biomaj
diff --git a/debian/global.properties-py3 b/debian/global.properties-py3
deleted file mode 100644
index 437b0ea..0000000
--- a/debian/global.properties-py3
+++ /dev/null
@@ -1,115 +0,0 @@
-[GENERAL]
-#The root directory where all databases are stored.
-#If your data is not stored under one directory hirearchy
-#you can override this value in the database properties file.
-data.dir=/var/lib/python3-biomaj3/banks
-
-conf.dir=/etc/python3-biomaj3/properties
-log.dir=/var/log/python3-biomaj3
-process.dir=/etc/python3-biomaj3/process
-cache.dir=/var/cache/python3-biomaj3
-lock.dir= /var/lib/python3-biomaj3/lock
-
-db.url=mongodb://localhost:27017
-db.name=biomaj
-
-use_ldap=0
-ldap.host=localhost
-ldap.port=389
-ldap.dn=nodomain
-
-use_elastic=
-#Comma separated list of elasticsearch nodes host1,host2:port2
-elastic_nodes=
-elastic_index=biomaj
-
-# Calculate data.dir size stats
-data.stats=1
-
-# Auto publish on updates (do not need publish flag, can be ovveriden in bank property file)
-auto_publish=0
-
-celery.queue=
-celery.broker=
-########################
-# Global properties file
-
-
-#To override these settings for a specific database go to its
-#properties file and uncomment or add the specific line you want
-#to override.
-
-#----------------
-# Mail Configuration
-#---------------
-#Uncomment thes lines if you want receive mail when the workflow is finished
-
-mail.smtp.host=localhost
-mail.admin=
-mail.from=biomaj at localhost
-mail.user=
-mail.password=
-mail.tls=
-
-
-#Number of thread during the download
-bank.num.threads=4
-
-#Number of threads to use for downloading and processing
-files.num.threads=4
-
-#to keep more than one release increase this value
-keep.old.version=0
-
-#The historic log file is generated in log/
-#define level information for output : DEBUG,INFO,WARN,ERR
-historic.logfile.level=DEBUG
-
-http.parse.dir.line=<a[\\s]+href=\"([\\S]+)/\".*alt=\"\\[DIR\\]\">.*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})
-http.parse.file.line=<a[\\s]+href=\"([\\S]+)\".*([\\d]{2}-[\\w\\d]{2,5}-[\\d]{4}\\s[\\d]{2}:[\\d]{2})[\\s]+([\\d\\.]+[MKG]{0,1})
-
-http.group.dir.name=1
-http.group.dir.date=2
-http.group.file.name=1
-http.group.file.date=2
-http.group.file.size=3
-
-
-# Bank default access
-visibility.default=public
-
-# Proxy, optional proxy (see format at
-# http://curl.haxx.se/libcurl/c/CURLOPT_PROXY.html)
-# biomaj >= 3.0.7
-#proxy=myproxyhost:1080
-#proxy=myproxyhost
-# Set proxy authentication if any, else keep commented
-#proxy_auth=user:password
-
-[loggers]
-keys = root, biomaj
-
-[handlers]
-keys = console
-
-[formatters]
-keys = generic
-
-[logger_root]
-level =INFO
-handlers = console
-
-[logger_biomaj]
-level = INFO
-handlers = console
-qualname = biomaj
-propagate=0
-
-[handler_console]
-class = StreamHandler
-args = (sys.stderr,)
-level = INFO
-formatter = generic
-
-[formatter_generic]
-format = %(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s
diff --git a/debian/python3-biomaj3.dirs b/debian/python3-biomaj3.dirs
deleted file mode 100644
index 0e14a6b..0000000
--- a/debian/python3-biomaj3.dirs
+++ /dev/null
@@ -1,6 +0,0 @@
-var/lib/python3-biomaj3/banks
-var/log/python3-biomaj3
-etc/python3-biomaj3/process
-etc/python3-biomaj3/properties
-var/cache/python3-biomaj3
-var/lib/python3-biomaj3/lock
diff --git a/debian/python3-biomaj3.examples b/debian/python3-biomaj3.examples
deleted file mode 100644
index 13fe74c..0000000
--- a/debian/python3-biomaj3.examples
+++ /dev/null
@@ -1 +0,0 @@
-debian/alu.properties
diff --git a/debian/python3-biomaj3.postrm b/debian/python3-biomaj3.postrm
deleted file mode 100644
index e0f369f..0000000
--- a/debian/python3-biomaj3.postrm
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/bin/sh
-
-set -e
-
-# Source debconf library.
-. /usr/share/debconf/confmodule
-
-case "$1" in
- purge)
- # Remove generated data and migration info
- if [ -e /var/lib/python3-biomaj3 ]; then
- rm -rf /var/lib/python3-biomaj3
- fi
- if [ -e /var/log/python3-biomaj3 ]; then
- rm -rf /var/log/python3-biomaj3
- fi
- if [ -e /var/cache/python3-biomaj3 ]; then
- rm -rf /var/cache/python3-biomaj3
- fi
- ;;
- remove|upgrade|failed-upgrade|abort-install|disappear)
- echo "Warning, BioMAJ database in Mongodb is not deleted by process removal." ;;
- abort-upgrade)
- ;;
- *)
- echo "postrm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-
-
diff --git a/debian/rules b/debian/rules
index abaa27f..35dfdcd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -30,17 +30,12 @@ override_dh_auto_test:
override_dh_install:
dh_install
- cp debian/global.properties-py debian/python-biomaj3/etc/python-biomaj3/global.properties
- cp debian/global.properties-py3 debian/python3-biomaj3/etc/python3-biomaj3/global.properties
- mv debian/python3-biomaj3/usr/bin/biomaj-cli.py debian/python3-biomaj3/usr/bin/biomaj-cli3
- mv debian/python-biomaj3/usr/bin/biomaj-cli.py debian/python-biomaj3/usr/bin/biomaj-cli
+ cp debian/global.properties debian/biomaj3-commons/etc/biomaj3/global.properties
+ mv debian/python3-biomaj3/usr/bin/biomaj-cli.py debian/python3-biomaj3/usr/bin/python3-biomaj-cli
+ mv debian/python-biomaj3/usr/bin/biomaj-cli.py debian/python-biomaj3/usr/bin/python-biomaj-cli
# help2man fails because python needs to be interpreted
#override_dh_installman:
# help2man --no-discard-stderr --version-string="$(DEB_VERSION_UPSTREAM)" -o biomaj-cli3.1 bin/biomaj-cli.py
# help2man --no-discard-stderr --version-string="$(DEB_VERSION_UPSTREAM)" -o biomaj-cli.1 bin/biomaj-cli.py
# dh_installman
-
-#override_dh_python3:
-# # skip autoguessa as python3-drmaa is not available but we don't care, code manage case where drmaa is not available
-# dh_python3 -- --no-guessing-deps
--
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