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changeset 0:7e01c6a6dbed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath commit e0575333e6f08ef02fc66c2764b43ebd15c6b04b
author iuc
date Fri, 10 Jun 2016 15:08:32 -0400
parents
children 1ba5c66e39c9
files macros.xml test-data/1.xml test-data/2.xml test-data/3.xml test-data/test.xml tool_dependencies.xml xpath xpath.xml
diffstat 8 files changed, 361 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="1.13">package_perl_xml_xpath</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@WRAPPER_VERSION@">1.0</token>
+  <xml name="stdio">
+    <stdio>
+      <exit_code range="1:"/>
+      <exit_code range=":-1"/>
+      <regex match="Error:"/>
+      <regex match="Exception:"/>
+    </stdio>
+  </xml>
+  <token name="@ATTRIBUTION@"><![CDATA[
+**Attribution**
+
+This Galaxy tool relies on the ``xpath`` tool provided in `libxml-xpath-perl`
+by the Debian Maintainers.
+  ]]>
+  </token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.xml	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,1 @@
+<b attr="value">1</b>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.xml	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,2 @@
+<b attr="value">1</b>
+<b attr="none">2</b>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.xml	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,3 @@
+1
+2
+3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.xml	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,12 @@
+<root>
+    <a>
+        <b attr="value">1</b>
+        <b attr="none">2</b>
+        <b>3</b>
+    </a>
+    <c>
+        <d>4</d>
+        <d>5</d>
+    </c>
+</root>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="package_perl_xml_xpath" version="1.13">
+    <repository changeset_revision="b0e8fcff8c27" name="package_perl_xml_xpath_1_13" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xpath	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,201 @@
+#!/usr/bin/perl -w
+eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
+    if 0; # not running under some shell
+use strict;
+
+$| = 1;
+
+use XML::XPath;
+
+my @paths;
+my $pipeline;
+my $SUFFIX = "\n";
+my $PREFIX = "";
+my $quiet = 0;
+
+
+PARSE: while ((@ARGV >= 1) && ($ARGV[0] =~ /^-./ )) {
+	OPTIONS: {
+		if ($ARGV[0] eq "-e") {
+			shift;
+			push @paths, shift;
+			last OPTIONS;
+		}
+		if ($ARGV[0] eq "-p") {
+			shift;
+			$PREFIX = shift;
+			last OPTIONS;
+		}
+		if ($ARGV[0] eq "-s") {
+			shift;
+			$SUFFIX = shift;
+			last OPTIONS;
+		}
+		if ($ARGV[0] eq "-q") {
+			$quiet = 1;
+			shift;
+			last OPTIONS;
+		}
+		print STDERR "Unknown option ignore: ", shift;
+	}
+}
+
+unless (@paths >= 1) {
+	print STDERR qq(Usage:
+$0 [options] -e query [-e query...] [filename...]
+
+	If no filenams are given, supply XML on STDIN.
+	You must provide at least one query. Each supplementary
+	query is done in order, the previous query giving the
+	context of the next one.
+
+	Options:
+
+	-q		quiet. Only output the resulting PATH
+	-s suffix	use suffix instead of linefeed.
+	-p postfix	use prefix instead of nothing.
+);
+	exit;
+}
+
+do
+{
+	my $xpath;
+	my @curpaths = @paths;
+	my $filename;
+	if (@ARGV >= 1) {
+		$filename = shift @ARGV;
+		$xpath = XML::XPath->new(filename => $filename);
+	}
+	else {
+		$filename = 'stdin';
+		$xpath = XML::XPath->new(ioref => \*STDIN);
+	}
+
+	my $nodes = $xpath->find(shift @curpaths);
+
+	if ($nodes->isa('XML::XPath::NodeSet')) {
+		while (@curpaths >= 1) {
+			$nodes = find_more($xpath, shift @curpaths, $nodes);
+			last unless $nodes->isa('XML::XPath::NodeSet');
+		}
+	}
+
+	if ($nodes->isa('XML::XPath::NodeSet')) {
+		if ($nodes->size) {
+			print STDERR "Found ", $nodes->size, " nodes in $filename:\n" unless $quiet;
+			foreach my $node ($nodes->get_nodelist) {
+				print STDERR "-- NODE --\n" unless $quiet;
+				print $PREFIX, $node->toString, $SUFFIX;
+			}
+		}
+		else {
+			print STDERR "No nodes found in $filename\n" unless $quiet;
+		}
+	}
+	else {
+		print STDERR "Query didn't return a nodeset. Value: ";
+		print $nodes->value, "\n";
+	}
+
+} until (@ARGV < 1);
+
+exit;
+
+sub find_more {
+	my $xpath = shift;
+	my $find = shift;
+	my ($nodes) = @_;
+
+	my $newnodes = XML::XPath::NodeSet->new;
+
+	foreach my $node ($nodes->get_nodelist) {
+		my $new = $xpath->find($find, $node);
+		if ($new->isa('XML::XPath::NodeSet')) {
+			$newnodes->append($new);
+		}
+		else {
+			warn "Not a nodeset: ", $new->value, "\n";
+		}
+	}
+
+	return $newnodes;
+}
+
+__END__
+
+=head1 NAME
+
+xpath - a script to query XPath statements in XML documents.
+
+=head1 SYNOPSIS
+
+B<xpath [-s suffix] [-p prefix] [-q] -e query [-e query] ... [file] ...>
+
+=head1 DESCRIPTION
+
+B<xpath> uses the L<XML::XPath|XML::XPath> perl module to make XPath queries
+to any XML document. The L<XML::XPath|XML::XPath> module aims to comply exactly
+to the XPath specification at C<http://www.w3.org/TR/xpath> and yet
+allows extensions to be added in the form of functions.
+
+The script takes any number of XPath pointers and tries to apply them
+to each XML document given on the command line. If no file arguments
+are given, the query is done using C<STDIN> as an XML document.
+
+When multiple queries exist, the result of the last query is used as
+context for the next query and only the result of the last one is output.
+The context of the first query is always the root of the current document.
+
+=head1 OPTIONS
+
+=head2 B<-q>
+
+Be quiet. Output only errors (and no separator) on stderr.
+
+=head2 B<-s suffix>
+
+Place C<suffix> at the end of each entry. Default is a linefeed.
+
+=head2 B<-p prefix>
+
+Place C<prefix> preceding each entry. Default is nothing.
+
+=head1 BUGS
+
+The author of this man page is not very fluant in english. Please,
+send him (L<fabien@tzone.org>) any corrections concerning this text.
+
+See also L<XML::XPath(3pm)>.
+
+=head1 SEE ALSO
+
+L<XML::XPath(3pm)>.
+
+=head1 HISTORY
+
+This module is copyright 2000 Fastnet Software Ltd. This is free
+software, and as such comes with NO WARRANTY. No dates are used in this
+module. You may distribute this module under the terms of either the
+Gnu GPL,  or under specific licencing from Fastnet Software Ltd.
+Special free licencing consideration will be given to similarly free
+software. Please don't flame me for this licence - I've put a lot of
+hours into this code, and if someone uses my software in their product
+I expect them to have the courtesy to contact me first.
+
+Full support for this module is available from Fastnet Software Ltd on
+a pay per incident basis. Alternatively subscribe to the Perl-XML
+mailing list by mailing lyris@activestate.com with the text:
+
+	SUBSCRIBE Perl-XML
+
+in the body of the message. There are lots of friendly people on the
+list, including myself, and we'll be glad to get you started.
+
+Matt Sergeant, matt@sergeant.org
+
+This man page was added as well as some serious modifications to the script
+by Fabien Ninoles <fabien@debian.org> for the Debian Project.
+
+=cut
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xpath.xml	Fri Jun 10 15:08:32 2016 -0400
@@ -0,0 +1,111 @@
+<?xml version="1.0"?>
+<tool id="xpath" name="XPath" version="@WRAPPER_VERSION@.0">
+  <description>compute xpath expressions on XML data</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command interpreter="bash"><![CDATA[xpath
+      -q
+      -e '$expression' $input > $output
+      ]]></command>
+  <inputs>
+    <param name="input" type="data" format="xml" label="Input XML data"/>
+    <param name="expression" type="text" label="XPath Query">
+      <sanitizer>
+        <valid>
+          <add value="&quot;"/>
+          <add value="["/>
+          <add value="]"/>
+          <add value="@"/>
+        </valid>
+      </sanitizer>
+    </param>
+  </inputs>
+  <outputs>
+      <!-- TODO: sometimes there's text output (e.g. text() queries) -->
+    <data format="xml" name="output" label="XPath expression on $input.name"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="test.xml"/>
+      <param name="expression" value="//b[@attr=&quot;value&quot;]" />
+      <output name="output" file="1.xml"/>
+    </test>
+    <test>
+      <param name="input" value="test.xml"/>
+      <param name="expression" value="//b[@attr]" />
+      <output name="output" file="2.xml"/>
+    </test>
+    <test>
+      <param name="input" value="test.xml"/>
+      <param name="expression" value="//b/text()" />
+      <output name="output" file="3.xml"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Query XML files with XPath expressions.
+
+For an example input file::
+
+    <root>
+        <IdList>
+            <Id>1234</Id>
+            <Id>1235</Id>
+            <Id>1236</Id>
+            <Id>1237</Id>
+        </IdList>
+    </root>
+
+One could query out the IDs specifically with a query like::
+
+    //Id/text()
+
+**XPath Expressions**
+
+There are many helpful tutorials on the internet for XPath expressions.
+`Wikipedia <https://en.wikipedia.org/wiki/XPath>`__ has a number of good
+examples.
+
+**Some More Examples**
+
+For an XML document like the following::
+
+    <root>
+        <a>
+            <b attr="value">1</b>
+            <b attr="none">2</b>
+            <b>3</b>
+        </a>
+        <c>
+            <d>4</d>
+            <e>5</e>
+        </c>
+    </root>
+
+Here are some example queries and their outputs:
+
++====================+===================================================+
+| Query              | Result                                            |
++--------------------+---------------------------------------------------+
+| //b[@attr="value"] | <b attr="value">1</b>                             |
++--------------------+---------------------------------------------------+
+| //b[@attr]         | <b attr="value">1</b><b attr="none">2</b>         |
++--------------------+---------------------------------------------------+
+| //b                | <b attr="value">1</b><b attr="none">2</b><b>3</b> |
++--------------------+---------------------------------------------------+
+| //b/text()         | 1\n2\n3                                           |
++--------------------+---------------------------------------------------+
+| /root/*/*/text()   | 1\n2\n3\n4\n5                                     |
++--------------------+---------------------------------------------------+
+
+
+
+@ATTRIBUTION@
+]]></help>
+  <citations>
+  </citations>
+</tool>