r8811 - in /trunk/libdata-stag-perl: debian/ t/ t/data/
hanska-guest at users.alioth.debian.org
hanska-guest at users.alioth.debian.org
Sun Nov 4 00:05:08 UTC 2007
Author: hanska-guest
Date: Sun Nov 4 00:05:08 2007
New Revision: 8811
URL: http://svn.debian.org/wsvn/?sc=1&rev=8811
Log:
[svn-inject] Applying Debian modifications to trunk
Added:
trunk/libdata-stag-perl/debian/
trunk/libdata-stag-perl/debian/changelog
trunk/libdata-stag-perl/debian/compat
trunk/libdata-stag-perl/debian/control
trunk/libdata-stag-perl/debian/copyright
trunk/libdata-stag-perl/debian/fix_binaries
trunk/libdata-stag-perl/debian/lintian-overrides
trunk/libdata-stag-perl/debian/rules (with props)
trunk/libdata-stag-perl/debian/watch
trunk/libdata-stag-perl/t/data/attrs.xml.sxpr
trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml
trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext
trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext.xml
trunk/libdata-stag-perl/t/data/person-processed.el
trunk/libdata-stag-perl/t/data/test.sxpr
trunk/libdata-stag-perl/t/z.xml
Added: trunk/libdata-stag-perl/debian/changelog
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/changelog?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/changelog (added)
+++ trunk/libdata-stag-perl/debian/changelog Sun Nov 4 00:05:08 2007
@@ -1,0 +1,5 @@
+libdata-stag-perl (0.10-1) UNRELEASED; urgency=low
+
+ * Initial Release.
+
+ -- David Paleino <d.paleino at gmail.com> Sun, 04 Nov 2007 00:25:05 +0100
Added: trunk/libdata-stag-perl/debian/compat
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/compat?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/compat (added)
+++ trunk/libdata-stag-perl/debian/compat Sun Nov 4 00:05:08 2007
@@ -1,0 +1,1 @@
+5
Added: trunk/libdata-stag-perl/debian/control
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/control?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/control (added)
+++ trunk/libdata-stag-perl/debian/control Sun Nov 4 00:05:08 2007
@@ -1,0 +1,27 @@
+Source: libdata-stag-perl
+Section: perl
+Priority: optional
+Build-Depends: debhelper (>= 5.0.0), perl (>= 5.8.8-11.1)
+Maintainer: Debian Perl Group <pkg-perl-maintainers at lists.alioth.debian.org>
+Uploaders: David Paleino <d.paleino at gmail.com>
+Standards-Version: 3.7.2
+Homepage: http://search.cpan.org/dist/Data-Stag/
+Vcs-Svn: svn://svn.debian.org/pkg-perl/trunk/libdata-stag-perl/
+Vcs-Browser: http://svn.debian.org/wsvn/pkg-perl/trunk/libdata-stag-perl/
+
+Package: libdata-stag-perl
+Architecture: any
+Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}, libio-string-perl
+Description: Structured Tags datastructures
+ This module is for manipulating data as hierarchical tag/value
+ pairs (Structured TAGs or Simple Tree AGgreggates). These
+ datastructures can be represented as nested arrays, which have the
+ advantage of being native to perl. A simple example is shown below:
+ .
+ [ person=> [ [ family_name => $family_name ],
+ [ given_name => $given_name ],
+ [ phone_no => $phone_no ] ] ],
+ .
+ Data::Stag uses a subset of XML for import and export. This
+ means the module can also be used as a general XML parser/writer (with
+ certain caveats).
Added: trunk/libdata-stag-perl/debian/copyright
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/copyright?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/copyright (added)
+++ trunk/libdata-stag-perl/debian/copyright Sun Nov 4 00:05:08 2007
@@ -1,0 +1,21 @@
+This is the debian package for the Data-Stag module.
+It was created by David Paleino <d.paleino at gmail.com> using dh-make-perl.
+
+It was downloaded from http://search.cpan.org/dist/Data-Stag/
+
+The upstream author is:
+
+Chris Mungall <cjm AT fruitfly DOT org>.
+
+Copyright (c) 2004 Chris Mungall
+
+This module is free software.
+You may distribute this module under the same terms as Perl itself
+
+Perl is distributed under your choice of the GNU General Public License or
+the Artistic License. On Debian GNU/Linux systems, the complete text of the
+GNU General Public License can be found in `/usr/share/common-licenses/GPL'
+and the Artistic Licence in `/usr/share/common-licenses/Artistic'.
+
+The Debian packaging is (C) 2007, David Paleino <d.paleino at gmail.com> and
+is licensed under the same terms as the software itself (see above).
Added: trunk/libdata-stag-perl/debian/fix_binaries
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/fix_binaries?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/fix_binaries (added)
+++ trunk/libdata-stag-perl/debian/fix_binaries Sun Nov 4 00:05:08 2007
@@ -1,0 +1,8 @@
+#!/bin/bash
+
+CURDIR=$1
+
+for i in $(ls $CURDIR/debian/libdata-stag-perl/usr/bin/*.pl)
+do
+ mv $i $CURDIR/debian/libdata-stag-perl/usr/bin/$(basename $i .pl)
+done
Added: trunk/libdata-stag-perl/debian/lintian-overrides
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/lintian-overrides?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/lintian-overrides (added)
+++ trunk/libdata-stag-perl/debian/lintian-overrides Sun Nov 4 00:05:08 2007
@@ -1,0 +1,18 @@
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man1/stag-merge.pl.1p.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::Arr2HTML.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::ChainHandler.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::DTDWriter.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::GraphHandler.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::HashDB.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::ITextWriter.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::IndentWriter.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::PerlWriter.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::SAX2Stag.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::Simple.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::StagImpl.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::SxprWriter.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::Writer.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::XMLWriter.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::XSLHandler.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::XSLTHandler.3pm.gz
+libdata-stag-perl: manpage-has-bad-whatis-entry usr/share/man/man3/Data::Stag::null.3pm.gz
Added: trunk/libdata-stag-perl/debian/rules
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/rules?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/rules (added)
+++ trunk/libdata-stag-perl/debian/rules Sun Nov 4 00:05:08 2007
@@ -1,0 +1,88 @@
+#!/usr/bin/make -f
+# This debian/rules file is provided as a template for normal perl
+# packages. It was created by Marc Brockschmidt <marc at dch-faq.de> for
+# the Debian Perl Group (http://pkg-perl.alioth.debian.org/) but may
+# be used freely wherever it is useful.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# If set to a true value then MakeMaker's prompt function will
+# always return the default without waiting for user input.
+export PERL_MM_USE_DEFAULT=1
+
+PACKAGE=$(shell dh_listpackages)
+
+ifndef PERL
+PERL = /usr/bin/perl
+endif
+
+TMP =$(CURDIR)/debian/$(PACKAGE)
+
+# Allow disabling build optimation by setting noopt in
+# $DEB_BUILD_OPTIONS
+CFLAGS = -Wall -g
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+build: build-stamp
+build-stamp:
+ dh_testdir
+
+ $(PERL) Makefile.PL INSTALLDIRS=vendor \
+ INSTALLVENDORARCH=/usr/lib/perl5/ \
+ VENDORARCHEXP=/usr/lib/perl5/
+ $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH=""
+ $(MAKE) test
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+
+ dh_clean build-stamp install-stamp
+
+ [ ! -f Makefile ] || $(MAKE) realclean
+
+install: build install-stamp
+install-stamp:
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs /usr/share/lintian/overrides/
+
+ $(MAKE) install DESTDIR=$(TMP) PREFIX=/usr
+
+ chmod a+x $(CURDIR)/debian/fix_binaries
+ $(CURDIR)/debian/fix_binaries $(CURDIR)
+
+ install -m 644 $(CURDIR)/debian/lintian-overrides $(TMP)/usr/share/lintian/overrides/libdata-stag-perl
+
+ touch $@
+
+binary-indep: build install
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installexamples
+ dh_installdocs README c-ext/README.c-ext
+ dh_installchangelogs Changes
+ dh_shlibdeps
+ dh_strip
+ dh_perl
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+source diff:
+ @echo >&2 'source and diff are obsolete - use dpkg-source -b'; false
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary
Propchange: trunk/libdata-stag-perl/debian/rules
------------------------------------------------------------------------------
svn:executable = *
Added: trunk/libdata-stag-perl/debian/watch
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/debian/watch?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/debian/watch (added)
+++ trunk/libdata-stag-perl/debian/watch Sun Nov 4 00:05:08 2007
@@ -1,0 +1,3 @@
+# format version number, currently 3; this line is compulsory!
+version=3
+http://search.cpan.org/dist/Data-Stag/ .*/Data-Stag-([\.\d]+)\.(?:tar\.gz|tar|tgz)$
Added: trunk/libdata-stag-perl/t/data/attrs.xml.sxpr
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/t/data/attrs.xml.sxpr?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/t/data/attrs.xml.sxpr (added)
+++ trunk/libdata-stag-perl/t/data/attrs.xml.sxpr Sun Nov 4 00:05:08 2007
@@ -1,0 +1,194 @@
+'(html
+ (head
+ (title "Stag - Structured Tag Library"))
+ (body
+ (h1 "Stag - Structured Tag Library")
+ (table
+ (tr
+ (td
+ (@
+ (bgcolor "#000000")
+ (valign "top"))
+ (img
+ (@
+ (src "images/celtic-stag.gif"))))
+ (td
+ (.
+ "The Stag project currently consists of two perl modules,
+ both of which are available from"
+ )
+ (a
+ (@
+ (href "http://www.cpan.org"))
+ (. "CPAN"))
+ (. "or")
+ (a
+ (@
+ (href "http://sourceforge.net/projects/stag")
+ )
+ (. "sourceforge"))
+ (. ":")
+ (h3 "Data::Stag")
+ (.
+ "This module is for manipulating data as recursively
+ nested tag/value pairs \("
+ )
+ (b "S")
+ (. "tructured")
+ (b "tag")
+ (. "s or")
+ (b "S")
+ (. "imple")
+ (b "T")
+ (. "ree")
+ (b "ag")
+ (.
+ "greggates\). At this time there is only a perl
+ implementation,"
+ )
+ (a
+ (@
+ (href
+ "http://search.cpan.org/perldoc?Data::Stag"
+ ))
+ (. "Data::Stag"))
+ (.
+ ", but C and Lisp implementations
+ are planned."
+ )
+ (br)
+ (br)
+ (.
+ "Stags can easily be represented as XML or as lisp-style
+ S-expressions, or using the Stag native indented text
+ format. They can also be represented in perl using nested
+ arrays."
+ )
+ (h3 "DBIx::DBStag")
+ (.
+ "This module is for conversion between relational
+ representations and hierarchical \(Stag\)
+ representations. SQL query results are automatically
+ decomposed into the relations and a hierarchical structure
+ is inferred. This modules also allows you to create SQL
+ templates - a powerful way of reusing SQL statements
+ joining multiple tables."
+ )
+ (br)
+ (a
+ (@
+ (href
+ "http://search.cpan.org/perldoc?DBIx::DBStag"
+ ))
+ (. "DBIx::DBStag")))))
+ (hr)
+ (table
+ (tr
+ (td
+ (@
+ (bgcolor "#FF8888"))
+ (a
+ (@
+ (href
+ "http://www.godatabase.org/cgi-bin/ubiq/ubiq.cgi"
+ ))
+ (. "UBIQ Query Interface")))
+ (td
+ "A demo of DBStag for mapping query results to hierarchical
+ tag-value data. This interface provides WWW access to a
+ number of bioinformatics databases \(Gene Ontology, Ensembl, Chado,
+ BioSQL, GadFly\). Templates can be selected, or you can
+ feed in your own SQL."
+ ))
+ (tr
+ (td
+ (@
+ (bgcolor "#FF8888"))
+ (a
+ (@
+ (href "http://sourceforge.net/projects/stag")
+ )
+ (.
+ "Stag
+ project page on Sourceforge"
+ )))
+ (td
+ "Here you can find the Stag CVS repository, mail lists, etc"
+ ))
+ (tr
+ (td
+ (@
+ (bgcolor "#FF8888"))
+ (a
+ (@
+ (href
+ "http://www.fruitfly.org/~cjm/rel-talk/dbistag.html"
+ ))
+ (. "DBStag Tutorial")))
+ (td
+ "Brief tutorial on basic DBStag usage for biological
+ databases.
+ \(slightly out of date - some aspects of DBStag may have changed\)"
+ ))
+ (tr
+ (td
+ (@
+ (bgcolor "#FF8888"))
+ (a
+ (@
+ (href
+ "http://search.cpan.org/perldoc?DBIx::DBStag::Cookbook"
+ ))
+ (. "DBIx::DBStag::Cookbook")))
+ (td
+ "DBStag cookbook - shows how to generate a normalised
+ relational db from an XML source \(the CIA world factbook\),
+ create your own SQL templates and build a WWW query
+ interface"
+ ))
+ (tr
+ (td
+ (@
+ (bgcolor "#FF8888"))
+ (a
+ (@
+ (href
+ "http://search.cpan.org/perldoc?DBIx::DBStag::SQLTemplate"
+ ))
+ (. "DBIx::DBStag::SQLTemplate")))
+ (td
+ "The POD manpage describing SQL templates - a powerful way
+ of reusing complex SQL statements"
+ ))
+ (tr
+ (td
+ (@
+ (bgcolor "#FF8888"))
+ (a
+ (@
+ (href "stag-poster.html"))
+ (. "Stag Poster")))
+ (td
+ "DBStag poster from Genome Informatics 2003 at Cold Spring Harbor
+ Laboratory \(large image\)"
+ )))
+ (hr)
+ (a
+ (@
+ (href "http://sourceforge.net"))
+ (img
+ (@
+ (width "88")
+ (alt "SourceForge.net Logo")
+ (src
+ "http://sourceforge.net/sflogo.php?group_id=68482&type=1"
+ )
+ (height "31")
+ (border "0"))))
+ (hr)
+ (address
+ (a
+ (@
+ (href "mailto:cjm at fruitfly.org"))
+ (. "chris mungall")))
+ (. "Last modified: Mon Apr 12 11:33:36 PDT 2004")))
Added: trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml (added)
+++ trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml Sun Nov 4 00:05:08 2007
@@ -1,0 +1,109 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<html>
+ <head>
+ <title>Stag - Structured Tag Library</title>
+ </head>
+ <body>
+ <h1>Stag - Structured Tag Library</h1>
+ <table>
+ <tr>
+ <td bgcolor="#000000" valign="top">
+ <img src="images/celtic-stag.gif">
+ </img>
+ </td>
+ <td>The Stag project currently consists of two perl modules,
+ both of which are available from
+ <a href="http://www.cpan.org">CPAN</a>or
+ <a href="http://sourceforge.net/projects/stag">sourceforge</a>:
+ <h3>Data::Stag</h3>This module is for manipulating data as recursively
+ nested tag/value pairs (
+ <b>S</b>tructured
+ <b>tag</b>s or
+ <b>S</b>imple
+ <b>T</b>ree
+ <b>ag</b>greggates). At this time there is only a perl
+ implementation,
+ <a href="http://search.cpan.org/perldoc?Data::Stag">Data::Stag</a>, but C and Lisp implementations
+ are planned.
+ <br></br>
+ <br>
+ </br>Stags can easily be represented as XML or as lisp-style
+ S-expressions, or using the Stag native indented text
+ format. They can also be represented in perl using nested
+ arrays.
+ <h3>DBIx::DBStag</h3>This module is for conversion between relational
+ representations and hierarchical (Stag)
+ representations. SQL query results are automatically
+ decomposed into the relations and a hierarchical structure
+ is inferred. This modules also allows you to create SQL
+ templates - a powerful way of reusing SQL statements
+ joining multiple tables.
+ <br></br>
+ <a href="http://search.cpan.org/perldoc?DBIx::DBStag">DBIx::DBStag</a>
+ </td>
+ </tr>
+ </table>
+ <hr>
+ </hr>
+ <table>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://www.godatabase.org/cgi-bin/ubiq/ubiq.cgi">UBIQ Query Interface</a>
+ </td>
+ <td>A demo of DBStag for mapping query results to hierarchical
+ tag-value data. This interface provides WWW access to a
+ number of bioinformatics databases (Gene Ontology, Ensembl, Chado,
+ BioSQL, GadFly). Templates can be selected, or you can
+ feed in your own SQL.</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://sourceforge.net/projects/stag">Stag
+ project page on Sourceforge</a>
+ </td>
+ <td>Here you can find the Stag CVS repository, mail lists, etc</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://www.fruitfly.org/~cjm/rel-talk/dbistag.html">DBStag Tutorial</a>
+ </td>
+ <td>Brief tutorial on basic DBStag usage for biological
+ databases.
+ (slightly out of date - some aspects of DBStag may have changed)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://search.cpan.org/perldoc?DBIx::DBStag::Cookbook">DBIx::DBStag::Cookbook</a>
+ </td>
+ <td>DBStag cookbook - shows how to generate a normalised
+ relational db from an XML source (the CIA world factbook),
+ create your own SQL templates and build a WWW query
+ interface</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://search.cpan.org/perldoc?DBIx::DBStag::SQLTemplate">DBIx::DBStag::SQLTemplate</a>
+ </td>
+ <td>The POD manpage describing SQL templates - a powerful way
+ of reusing complex SQL statements</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="stag-poster.html">Stag Poster</a>
+ </td>
+ <td>DBStag poster from Genome Informatics 2003 at Cold Spring Harbor
+ Laboratory (large image)</td>
+ </tr>
+ </table>
+ <hr>
+ </hr>
+ <a href="http://sourceforge.net">
+ <img width="88" alt="SourceForge.net Logo" src="http://sourceforge.net/sflogo.php?group_id=68482&type=1" height="31" border="0">
+ </img>
+ </a>
+ <hr>
+ </hr>
+ <address>
+ <a href="mailto:cjm at fruitfly.org">chris mungall</a>
+ </address>Last modified: Mon Apr 12 11:33:36 PDT 2004</body>
+</html>
Added: trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext (added)
+++ trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext Sun Nov 4 00:05:08 2007
@@ -1,0 +1,153 @@
+
+html:
+ head:
+ title: Stag - Structured Tag Library
+ body:
+ h1: Stag - Structured Tag Library
+ table:
+ tr:
+ td:
+ @:
+ bgcolor: #000000
+ valign: top
+ img:
+ @:
+ src: images/celtic-stag.gif
+ td:
+ .: The Stag project currently consists of two perl modules,
+ both of which are available from
+ a:
+ @:
+ href: http\://www.cpan.org
+ .: CPAN
+ .: or
+ a:
+ @:
+ href: http\://sourceforge.net/projects/stag
+ .: sourceforge
+ .: \:
+ h3: Data\:\:Stag
+ .: This module is for manipulating data as recursively
+ nested tag/value pairs (
+ b: S
+ .: tructured
+ b: tag
+ .: s or
+ b: S
+ .: imple
+ b: T
+ .: ree
+ b: ag
+ .: greggates). At this time there is only a perl
+ implementation,
+ a:
+ @:
+ href: http\://search.cpan.org/perldoc?Data\:\:Stag
+ .: Data\:\:Stag
+ .: , but C and Lisp implementations
+ are planned.
+ br:
+ br:
+ .: Stags can easily be represented as XML or as lisp-style
+ S-expressions, or using the Stag native indented text
+ format. They can also be represented in perl using nested
+ arrays.
+ h3: DBIx\:\:DBStag
+ .: This module is for conversion between relational
+ representations and hierarchical (Stag)
+ representations. SQL query results are automatically
+ decomposed into the relations and a hierarchical structure
+ is inferred. This modules also allows you to create SQL
+ templates - a powerful way of reusing SQL statements
+ joining multiple tables.
+ br:
+ a:
+ @:
+ href: http\://search.cpan.org/perldoc?DBIx\:\:DBStag
+ .: DBIx\:\:DBStag
+ hr:
+ table:
+ tr:
+ td:
+ @:
+ bgcolor: #FF8888
+ a:
+ @:
+ href: http\://www.godatabase.org/cgi-bin/ubiq/ubiq.cgi
+ .: UBIQ Query Interface
+ td: A demo of DBStag for mapping query results to hierarchical
+ tag-value data. This interface provides WWW access to a
+ number of bioinformatics databases (Gene Ontology, Ensembl, Chado,
+ BioSQL, GadFly). Templates can be selected, or you can
+ feed in your own SQL.
+ tr:
+ td:
+ @:
+ bgcolor: #FF8888
+ a:
+ @:
+ href: http\://sourceforge.net/projects/stag
+ .: Stag
+ project page on Sourceforge
+ td: Here you can find the Stag CVS repository, mail lists, etc
+ tr:
+ td:
+ @:
+ bgcolor: #FF8888
+ a:
+ @:
+ href: http\://www.fruitfly.org/~cjm/rel-talk/dbistag.html
+ .: DBStag Tutorial
+ td: Brief tutorial on basic DBStag usage for biological
+ databases.
+ (slightly out of date - some aspects of DBStag may have changed)
+ tr:
+ td:
+ @:
+ bgcolor: #FF8888
+ a:
+ @:
+ href: http\://search.cpan.org/perldoc?DBIx\:\:DBStag\:\:Cookbook
+ .: DBIx\:\:DBStag\:\:Cookbook
+ td: DBStag cookbook - shows how to generate a normalised
+ relational db from an XML source (the CIA world factbook),
+ create your own SQL templates and build a WWW query
+ interface
+ tr:
+ td:
+ @:
+ bgcolor: #FF8888
+ a:
+ @:
+ href: http\://search.cpan.org/perldoc?DBIx\:\:DBStag\:\:SQLTemplate
+ .: DBIx\:\:DBStag\:\:SQLTemplate
+ td: The POD manpage describing SQL templates - a powerful way
+ of reusing complex SQL statements
+ tr:
+ td:
+ @:
+ bgcolor: #FF8888
+ a:
+ @:
+ href: stag-poster.html
+ .: Stag Poster
+ td: DBStag poster from Genome Informatics 2003 at Cold Spring Harbor
+ Laboratory (large image)
+ hr:
+ a:
+ @:
+ href: http\://sourceforge.net
+ img:
+ @:
+ width: 88
+ alt: SourceForge.net Logo
+ src: http\://sourceforge.net/sflogo.php?group_id=68482&type=1
+ height: 31
+ border: 0
+ hr:
+ address:
+ a:
+ @:
+ href: mailto\:cjm at fruitfly.org
+ .: chris mungall
+ .: Last modified\: Mon Apr 12 11\:33\:36 PDT 2004
Added: trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext.xml
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext.xml?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext.xml (added)
+++ trunk/libdata-stag-perl/t/data/attrs.xml.sxpr.xml.itext.xml Sun Nov 4 00:05:08 2007
@@ -1,0 +1,109 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<html>
+ <head>
+ <title>Stag - Structured Tag Library</title>
+ </head>
+ <body>
+ <h1>Stag - Structured Tag Library</h1>
+ <table>
+ <tr>
+ <td bgcolor="#000000" valign="top">
+ <img src="images/celtic-stag.gif">
+ </img>
+ </td>
+ <td>The Stag project currently consists of two perl modules,
+ both of which are available from
+ <a href="http://www.cpan.org">CPAN</a>or
+ <a href="http://sourceforge.net/projects/stag">sourceforge</a>:
+ <h3>Data::Stag</h3>This module is for manipulating data as recursively
+ nested tag/value pairs (
+ <b>S</b>tructured
+ <b>tag</b>s or
+ <b>S</b>imple
+ <b>T</b>ree
+ <b>ag</b>greggates). At this time there is only a perl
+ implementation,
+ <a href="http://search.cpan.org/perldoc?Data::Stag">Data::Stag</a>, but C and Lisp implementations
+ are planned.
+ <br></br>
+ <br>
+ </br>Stags can easily be represented as XML or as lisp-style
+ S-expressions, or using the Stag native indented text
+ format. They can also be represented in perl using nested
+ arrays.
+ <h3>DBIx::DBStag</h3>This module is for conversion between relational
+ representations and hierarchical (Stag)
+ representations. SQL query results are automatically
+ decomposed into the relations and a hierarchical structure
+ is inferred. This modules also allows you to create SQL
+ templates - a powerful way of reusing SQL statements
+ joining multiple tables.
+ <br></br>
+ <a href="http://search.cpan.org/perldoc?DBIx::DBStag">DBIx::DBStag</a>
+ </td>
+ </tr>
+ </table>
+ <hr>
+ </hr>
+ <table>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://www.godatabase.org/cgi-bin/ubiq/ubiq.cgi">UBIQ Query Interface</a>
+ </td>
+ <td>A demo of DBStag for mapping query results to hierarchical
+ tag-value data. This interface provides WWW access to a
+ number of bioinformatics databases (Gene Ontology, Ensembl, Chado,
+ BioSQL, GadFly). Templates can be selected, or you can
+ feed in your own SQL.</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://sourceforge.net/projects/stag">Stag
+ project page on Sourceforge</a>
+ </td>
+ <td>Here you can find the Stag CVS repository, mail lists, etc</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://www.fruitfly.org/~cjm/rel-talk/dbistag.html">DBStag Tutorial</a>
+ </td>
+ <td>Brief tutorial on basic DBStag usage for biological
+ databases.
+ (slightly out of date - some aspects of DBStag may have changed)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://search.cpan.org/perldoc?DBIx::DBStag::Cookbook">DBIx::DBStag::Cookbook</a>
+ </td>
+ <td>DBStag cookbook - shows how to generate a normalised
+ relational db from an XML source (the CIA world factbook),
+ create your own SQL templates and build a WWW query
+ interface</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="http://search.cpan.org/perldoc?DBIx::DBStag::SQLTemplate">DBIx::DBStag::SQLTemplate</a>
+ </td>
+ <td>The POD manpage describing SQL templates - a powerful way
+ of reusing complex SQL statements</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8888">
+ <a href="stag-poster.html">Stag Poster</a>
+ </td>
+ <td>DBStag poster from Genome Informatics 2003 at Cold Spring Harbor
+ Laboratory (large image)</td>
+ </tr>
+ </table>
+ <hr>
+ </hr>
+ <a href="http://sourceforge.net">
+ <img width="88" alt="SourceForge.net Logo" src="http://sourceforge.net/sflogo.php?group_id=68482&type=1" height="31" border="0">
+ </img>
+ </a>
+ <hr>
+ </hr>
+ <address>
+ <a href="mailto:cjm at fruitfly.org">chris mungall</a>
+ </address>Last modified: Mon Apr 12 11:33:36 PDT 2004</body>
+</html>
Added: trunk/libdata-stag-perl/t/data/person-processed.el
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/t/data/person-processed.el?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/t/data/person-processed.el (added)
+++ trunk/libdata-stag-perl/t/data/person-processed.el Sun Nov 4 00:05:08 2007
@@ -1,0 +1,9 @@
+'(data
+ (person
+ (firstname "joe")
+ (lastname "bloggs")
+ (fullname "joe bloggs"))
+ (person
+ (firstname "clark")
+ (lastname "kent")
+ (fullname "clark kent")))
Added: trunk/libdata-stag-perl/t/data/test.sxpr
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/t/data/test.sxpr?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/t/data/test.sxpr (added)
+++ trunk/libdata-stag-perl/t/data/test.sxpr Sun Nov 4 00:05:08 2007
@@ -1,0 +1,37 @@
+'(db
+ (species_set
+ (species
+ (common_name "house mouse")
+ (binomial "Mus musculus")
+ (tax_id "10090"))
+ (species
+ (common_name "fruitfly")
+ (binomial "Drosophila melanogaster")
+ (tax_id "7227"))
+ (species
+ (common_name "human")
+ (binomial "Homo sapiens")
+ (tax_id "9606")))
+ (gene_set
+ (gene
+ (symbol "HGNC")
+ (tax_id "9606")
+ (phenotype "Hemochromatosis")
+ (phenotype "Porphyria variegata")
+ (GO_term "iron homeostasis")
+ (map
+ (cytological
+ (chromosome "6")
+ (band "p21.3"))))
+ (gene
+ (symbol "Hfe")
+ (synonym "MR2")
+ (tax_id "10090")
+ (GO_term "integral membrane protein")))
+ (similarity_set
+ (pair
+ (symbol "HGNC")
+ (symbol "Hfe"))
+ (pair
+ (symbol "WNT3A")
+ (symbol "Wnt3a"))))
Added: trunk/libdata-stag-perl/t/z.xml
URL: http://svn.debian.org/wsvn/trunk/libdata-stag-perl/t/z.xml?rev=8811&op=file
==============================================================================
--- trunk/libdata-stag-perl/t/z.xml (added)
+++ trunk/libdata-stag-perl/t/z.xml Sun Nov 4 00:05:08 2007
@@ -1,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<top><personset><person><name>shuggy</name><job>bus driver</job><age>55</age></person><person><name>tam</name><job>forklift driver</job><favourite_food>chips</favourite_food></person></personset></top>
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