temporary files (for testing etc.)

11 files changed, 271 insertions, 0 deletions

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..bc4dc2e
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,17 @@
+# runs tests
+EXAMPLES = ./examples
+
+PY_DESC_TESTER = ./run_descreader.py
+PY_NOP = ./nop.py
+
+.PHONY: default test test-desc test-nop
+
+default: test
+
+test-desc: $(PY_DESC_TESER) $(EXAMPLES)/DESCRIPTION
+	$(PY_DESC_TESTER) $(EXAMPLES)/DESCRIPTION/*.desc
+
+test-nop: $(PY_NOP)
+	@$(PY_NOP)
+
+test: test-nop test-desc
diff --git a/examples/DESCRIPTION/NbClust.desc b/examples/DESCRIPTION/NbClust.desc
new file mode 100644
index 0000000..817adfd
--- /dev/null
+++ b/examples/DESCRIPTION/NbClust.desc
@@ -0,0 +1,21 @@
+Package: NbClust
+Type: Package
+Title: An examination of indices for determining the number of clusters
+        : NbClust Package
+Version: 1.0
+Date: 2012-05-01
+Author: Malika Charrad <malika.charrad.1@ulaval.ca> and Nadia Ghazzali
+        <nadia.ghazzali@mat.ulaval.ca> and Veronique Boiteau
+        <veronique.boiteau.1@ulaval.ca> and Azam Niknafs
+        <azam.niknafs.1@ulaval.ca>
+Maintainer: : Nadia Ghazzali <nadia.ghazzali@mat.ulaval.ca>
+Description: This package provides most of the popular indices for
+        cluster validation ready to use for the outputs produced by
+        functions coming from the same package. It also proposes to
+        user the best clustering scheme from the different results
+        obtained by varying all combinations of number of clusters,
+        distance measures, and clustering methods.
+License: GPL-2
+Packaged: 2012-05-23 14:26:58 UTC; CRSNG-INAL-3
+Repository: CRAN
+Date/Publication: 2012-05-23 16:21:05
diff --git a/examples/DESCRIPTION/SPARQL.desc b/examples/DESCRIPTION/SPARQL.desc
new file mode 100644
index 0000000..555866d
--- /dev/null
+++ b/examples/DESCRIPTION/SPARQL.desc
@@ -0,0 +1,19 @@
+Package: SPARQL
+Type: Package
+Title: SPARQL client
+Version: 1.9
+Date: 2012-05-22
+Author: Willem Robert van Hage <W.R.van.Hage@vu.nl> and Tomi Kauppinen
+        <tomi.kauppinen@uni-muenster.de>, with contributions from
+        Christopher Davis <C.B.Davis@tudelft.nl> and Jesper Hoeksema
+        <J.E.Hoeksema@vu.nl>
+Maintainer: Willem Robert van Hage <W.R.van.Hage@vu.nl> and Tomi
+        Kauppinen <tomi.kauppinen@uni-muenster.de>
+Description: Use SPARQL to pose SELECT or UPDATE queries to an
+        end-point.
+License: GPL-3
+Depends: XML, RCurl
+LazyLoad: yes
+Packaged: 2012-05-22 09:39:27 UTC; wrvhage
+Repository: CRAN
+Date/Publication: 2012-05-22 13:05:32
diff --git a/examples/DESCRIPTION/Taxonstand.desc b/examples/DESCRIPTION/Taxonstand.desc
new file mode 100644
index 0000000..94355f7
--- /dev/null
+++ b/examples/DESCRIPTION/Taxonstand.desc
@@ -0,0 +1,15 @@
+Package: Taxonstand
+Type: Package
+Title: Taxonomic standardization of plant species names
+Version: 1.0
+Date: 2012-03-21
+Author: Luis Cayuela
+Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
+Description: Automated standardization of taxonomic names and removal
+        of orthograhpic errors in plant species names using the The
+        Plant List (TPL) website (www.theplantlist.org)
+License: GPL (>= 2)
+LazyLoad: yes
+Packaged: 2012-05-21 08:14:50 UTC; luis
+Repository: CRAN
+Date/Publication: 2012-05-21 08:36:09
diff --git a/examples/packages/NbClust.desc b/examples/packages/NbClust.desc
new file mode 100644
index 0000000..817adfd
--- /dev/null
+++ b/examples/packages/NbClust.desc
@@ -0,0 +1,21 @@
+Package: NbClust
+Type: Package
+Title: An examination of indices for determining the number of clusters
+        : NbClust Package
+Version: 1.0
+Date: 2012-05-01
+Author: Malika Charrad <malika.charrad.1@ulaval.ca> and Nadia Ghazzali
+        <nadia.ghazzali@mat.ulaval.ca> and Veronique Boiteau
+        <veronique.boiteau.1@ulaval.ca> and Azam Niknafs
+        <azam.niknafs.1@ulaval.ca>
+Maintainer: : Nadia Ghazzali <nadia.ghazzali@mat.ulaval.ca>
+Description: This package provides most of the popular indices for
+        cluster validation ready to use for the outputs produced by
+        functions coming from the same package. It also proposes to
+        user the best clustering scheme from the different results
+        obtained by varying all combinations of number of clusters,
+        distance measures, and clustering methods.
+License: GPL-2
+Packaged: 2012-05-23 14:26:58 UTC; CRSNG-INAL-3
+Repository: CRAN
+Date/Publication: 2012-05-23 16:21:05
diff --git a/examples/packages/SPARQL.desc b/examples/packages/SPARQL.desc
new file mode 100644
index 0000000..555866d
--- /dev/null
+++ b/examples/packages/SPARQL.desc
@@ -0,0 +1,19 @@
+Package: SPARQL
+Type: Package
+Title: SPARQL client
+Version: 1.9
+Date: 2012-05-22
+Author: Willem Robert van Hage <W.R.van.Hage@vu.nl> and Tomi Kauppinen
+        <tomi.kauppinen@uni-muenster.de>, with contributions from
+        Christopher Davis <C.B.Davis@tudelft.nl> and Jesper Hoeksema
+        <J.E.Hoeksema@vu.nl>
+Maintainer: Willem Robert van Hage <W.R.van.Hage@vu.nl> and Tomi
+        Kauppinen <tomi.kauppinen@uni-muenster.de>
+Description: Use SPARQL to pose SELECT or UPDATE queries to an
+        end-point.
+License: GPL-3
+Depends: XML, RCurl
+LazyLoad: yes
+Packaged: 2012-05-22 09:39:27 UTC; wrvhage
+Repository: CRAN
+Date/Publication: 2012-05-22 13:05:32
diff --git a/examples/packages/Taxonstand.desc b/examples/packages/Taxonstand.desc
new file mode 100644
index 0000000..94355f7
--- /dev/null
+++ b/examples/packages/Taxonstand.desc
@@ -0,0 +1,15 @@
+Package: Taxonstand
+Type: Package
+Title: Taxonomic standardization of plant species names
+Version: 1.0
+Date: 2012-03-21
+Author: Luis Cayuela
+Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
+Description: Automated standardization of taxonomic names and removal
+        of orthograhpic errors in plant species names using the The
+        Plant List (TPL) website (www.theplantlist.org)
+License: GPL (>= 2)
+LazyLoad: yes
+Packaged: 2012-05-21 08:14:50 UTC; luis
+Repository: CRAN
+Date/Publication: 2012-05-21 08:36:09
diff --git a/examples/packages/get.sh b/examples/packages/get.sh
new file mode 100755
index 0000000..a274cda
--- /dev/null
+++ b/examples/packages/get.sh
@@ -0,0 +1,54 @@
+#!/bin/bash
+# temporary script
+#  extracts data (=files) out of a R src package
+#
+
+## this is a multicall script whose only functionality is get(file, *info) - don't rename
+
+readonly _ARGV="$*"
+_SELF="${0##*/}"
+_SELF="${_SELF%.*sh}"
+readonly _SELF
+set --
+set -u
+
+# get (file, *info)
+#  extracts *info out of file (or all gzip-tarballs in `pwd`)
+#
+get() {
+	local file="${1:-}" x fname name
+	shift ||:
+
+	[[ "$file" ]] || return ${undone:-101}
+
+	if [[ "$file" == "all" ]]; then
+		for x in *.tar.gz *.tgz; do
+			if [[ -r "$x" ]]; then
+				get "$x" $* || return $?
+			fi
+		done
+		return 0
+	fi
+
+	fname="${file##*/}"
+	fname="${fname%%.*}"
+	name="${fname%%_*}"
+	for x in $*; do
+		case "${x}" in
+			desc) tar xvzf "$file" "${name}/DESCRIPTION" && \
+						mv -f -v -- "${name}/DESCRIPTION" "${name}.desc" &&
+						rmdir "${name}" && chmod a=r "${name}.desc" || return $?
+					;;
+			*) return ${undef:-56} ;;
+		esac
+	done
+	return 0
+}
+
+__error__() {
+	local -i _ret=$?
+	1>&2 echo "error when calling method '${1:-$_SELF}'."
+	return $_ret
+}
+
+${_SELF} $_ARGV || __error__ "${_SELF}"
diff --git a/nop.py b/nop.py
new file mode 100755
index 0000000..8c963b5
--- /dev/null
+++ b/nop.py
@@ -0,0 +1,5 @@
+#!/usr/bin/env python3
+# Copyright 2006-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+import roverlay
diff --git a/roverlay/tmpconst.py b/roverlay/tmpconst.py
new file mode 100644
index 0000000..8a44d22
--- /dev/null
+++ b/roverlay/tmpconst.py
@@ -0,0 +1,71 @@
+# R overlay -- constants (temporary file)
+# Copyright 2006-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+DESCRIPTION_FIELD_SEPARATOR = ':'
+
+DESCRIPTION_COMMENT_CHAR = '#'
+
+DESCRIPTION_LIST_SPLIT_REGEX = '\s*[,;]{1}\s*'
+
+DESCRIPTION_VALID_OS_TYPES = [ "unix" ]
+
+
+# note for 2012-05-25: make this struct more organized, assign real values
+"""The map of used fields in the DESCRIPTION file
+
+	stores the real field name as well as field flags and aliases
+	that can be case-sensitive (withcase) or not (nocase)
+
+	access to these values is
+	* for aliases
+		DESCRIPTION_FIELD_MAP [<field name>] [case sensitive? withcase : nocase] [<index>]
+
+	* for flags
+		DESCRIPTION_FIELD_MAP [<field name>] [flags] [<index>]
+
+	notable flags:
+	* isList : indicates that this field has several values that are
+	           separated by commata/semicolons =:<DESCRIPTION_LIST_SPLIT_REGEX>
+	   this disables isWhitespaceList
+
+	* isWhitespaceList : indicates that this field has several values separated
+	                     by whitespace
+
+	* joinValues : indicates that the values of this field should be concatenated
+	               after reading them (with a ' ' as separator)
+	   (this implies that the read values are one string)
+
+	* mandatory : cannot proceed if a file does not contain this field (implies ignoring default values)
+
+"""
+
+DESCRIPTION_FIELD_MAP = {
+	'Description' : {
+		'flags' : [ 'joinValues' ],
+	},
+	'Title' : '',
+	'Package' : '',
+	'License' : '',
+	'Suggests' : {
+		'nocase' : [ 'Suggests', 'Suggest',
+							'%Suggests', 'Suggets', 'Recommends' ]
+	},
+	'Depends' : {
+		'nocase' : [ 'Depends', 'Dependencies', 'Dependes',
+							'%Depends', 'Depents', 'Require', 'Requires' ],
+		'flags' : [ 'isList', 'mandatory' ],
+	},
+	'Imports' : {
+		'nocase' : [ 'Imports', 'Import' ]
+	},
+	'LinkingTo' : {
+		'nocase' : [ 'LinkingTo', 'LinkingdTo' ]
+	},
+	'SystemRequirements' : {
+		'nocase' : [ 'SystemRequirements', 'SystemRequirement' ]
+	},
+	'OS_Type' : {
+		'nocase' : [ 'OS_TYPE' ]
+	}
+}
diff --git a/run_descreader.py b/run_descreader.py
new file mode 100755
index 0000000..b876f7b
--- /dev/null
+++ b/run_descreader.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+# Copyright 2006-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+import sys
+
+import roverlay.fileio
+
+reader = roverlay.fileio.DescriptionReader()
+
+for descfile in sys.argv[1:]:
+	reader.readfile ( descfile )
+
+