[med-svn] [openfreezer] 05/05: Metadata from tasks file
Andreas Tille
tille at debian.org
Fri Dec 30 17:01:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository openfreezer.
commit 09f768b011063ccf18fa5dfe18e95e4f8a008b40
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 30 17:57:29 2016 +0100
Metadata from tasks file
---
debian/control | 11 ++++++++--
debian/copyright | 29 +++++++++++++++++++++----
debian/doc-base | 20 ------------------
debian/get-orig-source | 55 ------------------------------------------------
debian/upstream/metadata | 21 +++++++++---------
debian/watch | 55 +++---------------------------------------------
6 files changed, 47 insertions(+), 144 deletions(-)
diff --git a/debian/control b/debian/control
index f2068b0..d2d295d 100644
--- a/debian/control
+++ b/debian/control
@@ -12,5 +12,12 @@ Homepage: http://www.openfreezer.org/
Package: openfreezer
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: <short_description>
- <long_description>
+Description: Laboratory analysis, research and investigation software application
+ OpenFreezer Laboratory Reagent Tracking and Workflow Management System is an
+ open-source information management system for biological laboratories. The
+ system tracks information on all reagents within the laboratory, including
+ specific properties of each reagent (i.e. sequences, external identifiers), and
+ on all the physical preparations of these reagents (storage locations, physical
+ characteristics). Complementing this repository are workflow tools, such as
+ primer design and automated feature mapping, making OpenFreezer a valuable tool
+ for the bench scientist.
diff --git a/debian/copyright b/debian/copyright
index 3416315..0109b6b 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,10 +1,31 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: <pkg>
-Source: <path_to_download>
+Upstream-Name: openfreezer
+Source: http://www.openfreezer.org/download.html
Files: *
-Copyright: © 20xx-20yy <upstream>
-License: <license>
+Copyright: 2010-2013 <upstream>
+License: GPL-3+
+ OpenFreezer is distributed under the GNU License, Version 3; you may not use this application except in compliance with the License. You may obtain a copy of the License at www.gnu.org/licenses.
+ .
+ Use of the Site
+ .
+ Please read and review these Terms and Conditions carefully before using this Site. By accessing or using this Site, you acknowledge that you have read, understood and agreed to these Terms and Conditions, without limitation or qualification. If you do not agree to the Terms and Conditions, do not use the Site or download or use materials from this Site.
+ .
+ Third Party Links
+ .
+ As a convenience to you, this Site may contain third-party owned content or information, and may also include links or references to other web sites maintained by third parties over whom Mount Sinai Hospital has no control. Mount Sinai Hospital does not endorse, sponsor, recommend, warrant, guarantee or otherwise accept any responsibility for such third party content, information or web sites. Access to any third-party owned content or information or web site is at your own risk, and Mo [...]
+ .
+ Disclaimer of Warranty; Limitation of Liability
+ .
+ MOUNT SINAI HOSPITAL DISCLAIMS ALL EXPRESS AND IMPLIED WARRANTIES WITH REGARD TO THIS SITE, THE INFORMATION, SERVICES AND MATERIALS DESCRIBED OR CONTAINED ON THIS SITE, INCLUDING WITHOUT LIMITATION ANY IMPLIED WARRANTIES OF MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT. YOUR ACCESS TO AND USE OF THIS SITE AND ITS CONTENTS ARE AT YOUR OWN RISK. ACCESS TO THIS SITE MAY BE INTERRUPTED AND INFORMATION, SERVICES AND MATERIALS CONTAINED HEREIN MAY NOT BE ERROR-FREE. MO [...]
+ .
+ Indemnification
+ .
+ You agree to indemnify, defend and hold harmless MOUNT SINAI HOSPITAL its officers, directors, employees, agents, consultants, suppliers and third party partners from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of these Terms and Conditions.
+ .
+ Applicable Laws
+ .
+ These Terms and Conditions and the resolution of any dispute related to these Terms and Conditions shall be construed in accordance with the laws of the province of Ontario, Canada, without regard to its conflicts of laws principles. Any legal action or proceeding related to this Site shall be brought exclusively by the federal and provincial courts of the province of Ontario, Canada.
Files: debian/*
Copyright: © 2016 maintainername <maintainer at e.mail>
diff --git a/debian/doc-base b/debian/doc-base
deleted file mode 100644
index 5e7e1d4..0000000
--- a/debian/doc-base
+++ /dev/null
@@ -1,20 +0,0 @@
-Document: <pkg>
-Title: <title for this doc>
-Author: <author of this doc>
-Abstract: <if you have no better clue the short and
- long description from debian/control might fit here as well>
-Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
-
-# pick one of the below options
-Format: Text
-Files: /usr/share/doc/<pkg>/<pkg>.txt.gz
-
-Format: html
-Index: /usr/share/doc/<pkg>/html/index.html
-Files: /usr/share/doc/<pkg>/html/*
-
-Format: pdf
-Files: /usr/share/doc/<pkg>/<pkg>.pdf.gz
-
-Format: postscript
-Files: /usr/share/doc/<pkg>/<pkg>.ps.gz
diff --git a/debian/get-orig-source b/debian/get-orig-source
deleted file mode 100755
index 2aa782f..0000000
--- a/debian/get-orig-source
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/sh
-# if you need to repack for whatever reason you can
-# use this script via uscan or directly
-#
-# FIXME: currently the code is not conform to Debian Policy
-# http://www.debian.org/doc/debian-policy/ch-source.html
-# "get-orig-source (optional)"
-# This target may be invoked in any directory, ...
-# --> currently it is assumed the script is called in the
-# source directory featuring the debian/ dir
-
-# Excluding files and repacking archives
-# --------------------------------------
-# See also mk-origtargz(1) and the --repack option to uscan(1), which
-# honor the Files-Excluded list in debian/copyright.
-# That may be all you need, especially since the repack option can be set
-# in debian/watch.
-
-# For an example how to fetch source from sourceforge SVN see
-# https://anonscm.debian.org/git/debian-med/kmer-tools.git
-
-COMPRESS=xz
-
-set -e
-NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-
-if ! echo $@ | grep -q upstream-version ; then
- VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
- uscan --force-download
-else
- VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
- if echo "$VERSION" | grep -q "upstream-version" ; then
- echo "Unable to parse version number"
- exit
- fi
-fi
-
-TARDIR=${NAME}-${VERSION}
-mkdir -p ../tarballs
-cd ../tarballs
-# need to clean up the tarballs dir first because upstream tarball might
-# contain a directory with unpredictable name
-rm -rf *
-tar -xaf ../${TARDIR}.tar.gz
-
-UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d`
-if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then
- mv "${UPSTREAMTARDIR}" "${TARDIR}"
-fi
-
-# Remove useless binaries
-# ... do something which needs to be done ...
-
-GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
-rm -rf ${TARDIR}
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index d8b5812..ac1dd7c 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,12 +1,11 @@
Reference:
- Author:
- Title:
- Journal:
- Year:
- Volume:
- Number:
- Pages:
- DOI:
- PMID:
- URL:
- eprint:
+ Author: "Marina Olhovsky and Kelly Williton and Anna Yue Dai and Adrian Pasculescu and John Paul Lee and Marilyn Goudreault and Clark D. Wells and Jin Gyoon Park and Anne-Claude Gingras and Rune Linding and Tony Pawson and Karen Colwill"
+ Title: "OpenFreezer: a reagent information management software system"
+ Journal: Nature Methods
+ Year: 2011
+ Volume: 8
+ Number: 8
+ Pages: 612–613
+ DOI: 10.1038/nmeth.1658
+ PMID: 21799493
+ URL: http://www.nature.com/nmeth/journal/v8/n8/full/nmeth.1658.html
diff --git a/debian/watch b/debian/watch
index 9e06566..da699d9 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,55 +1,6 @@
version=4
-# Uncomment to examine a Webpage
-# <Webpage URL> <string match>
-#http://www.example.com/downloads.php #PACKAGE#-(.*)\.tar\.gz
+# Upstream requires registration :-(
-# Uncomment to examine a Webserver directory
-#http://www.example.com/pub/#PACKAGE#-(.*)\.tar\.gz
-
-# Uncommment to examine a FTP server
-#ftp://ftp.example.com/pub/#PACKAGE#-(.*)\.tar\.gz debian uupdate
-
-# Uncomment to find new files on sourceforge
-# http://sf.net/#PACKAGE#/#PACKAGE#-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
-
-# Uncomment to find new files on Github
-# - when using releases:
-# https://github.com/#GITHUBUSER#/#PACKAGE#/releases .*/archive/#PREFIX#(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-# - when using tags
-# https://github.com/#GITHUBUSER#/#PACKAGE#/tags .*/#PREFIX#(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
-# Remark: frequently you can do s/#PREFIX#/v?/ since 'v' or nothing is quite common but there are other prefixes possible
-
-# PyPi repository of Python modules
-# see https://lists.debian.org/debian-python/2015/02/msg00027.html
-# http://pypi.debian.net/#module#/#module#-(.+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-
-# Bitbucket
-# https://bitbucket.org/<user>/<project>/downloads .*/(\d\S*)\.tar\.gz
-
-# Gitlab
-# opts=filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/<project>-$1\.tar\.gz/g \
-# https://gitlab.com/<user>/<project>/tags .*archive\.tar\.gz\?ref=v?(\d\S*)
-
-# if tweaking of source is needed
-# \
-# debian debian/get-orig-source
-
-# if you need to repack and choose +dfsg prefix
-# opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \
-
-# If there is no chance to create a sensible watch file please read here:
-#
-# https://people.debian.org/~eriberto/#fake-packages
-#
-#version=4
-#opts=dversionmangle=s/.*/0.No-Site/ \
-#https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz
-#
-#version=4
-#opts=dversionmangle=s/.*/0.No-Release/ \
-#https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz
-#
-#version=4
-#opts=dversionmangle=s/.*/0.No-Track/ \
-#https://people.debian.org/~eriberto/ FakeWatchNoUpstreamTrackingForThisPackage-(\d\S+)\.gz
+opts=dversionmangle=s/.*/0.No-Track/ \
+https://people.debian.org/~eriberto/ FakeWatchNoUpstreamTrackingForThisPackage-(\d\S+)\.gz
--
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