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 <[email protected]> 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@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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-biomaj3.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
