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changeset 1:5972a5799e8f draft

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author saml
date Wed, 21 Nov 2012 12:20:28 -0500
parents bd5caa8e2290
children 62cfd14e2520
files semweb_tools/README.md semweb_tools/sparql_import.py semweb_tools/sparql_import.xml
diffstat 3 files changed, 0 insertions(+), 163 deletions(-) [+]
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--- a/semweb_tools/README.md	Wed Nov 21 12:19:18 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-# Semantic Web Tools for Galaxy #
-
-## SPARQL Import tool ##
-This [Galaxy (bioinformatics web portal)](http://galaxyproject.org/) toolkit currently just contains a tool that enables to specify an URL to a SPARQL endpoint, and a SPARQL query, and to save the returned data in tabular format, for further processing in Galaxy's tools.
-
-## Installation ##
-
-1. Create a folder "semweb_tools" under [galaxy_root]/tools/ and add these files.
-2. Add the following section right under the starting <toolbox> tag in [galaxy_root]/tool_conf.xml:
-
-````
-    <section name="Semantic Web Tools" id="semweb_tools">
-        <tool file="semweb_tools/sparql_import.xml" />
-    </section>
-````
-
-## Change log ##
-
-* 2012-11-16: Now works properly (at least for my simple test case)!
-* 2012-11-16: Created today, still under heavy development!
--- a/semweb_tools/sparql_import.py	Wed Nov 21 12:19:18 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-#!/usr/bin/python
-# --------------------------------------------------------
-# A Galaxy plugin for querying external SPARQL Endpoints
-# Samuel Lampa, samuel.lampa@gmail.com
-# Created: 2012-11-16
-# --------------------------------------------------------
-
-from xml.etree import ElementTree as et
-from optparse import OptionParser
-import urllib, sys, re
-
-# -----------------------
-# Option parsing
-# -----------------------
-
-parser = OptionParser()
-parser.add_option("-u", "--url",
-	help = "The URL to the SPARQL endpoint")
-parser.add_option("-q", "--sparql_query",
-	help = "A SPARQL query to send to a SPARQL endpoint")
-parser.add_option("-o", "--output_file",
-	help = "An output file for storing the results")
-(options, args) = parser.parse_args()
-
-if not options.url:
-	sys.exit("You have to specify an URL! Use the -h flag to view command line options!")
-if not options.sparql_query:
-	sys.exit("You have to specify a SPARQL query! Use the -h flag to view command line options!")
-if not options.output_file:
-	sys.exit("You have to specify an output file! Use the -h flag to view command line options!")
-
-if len(options.sparql_query) < 9: 
-	sys.exit("Your SPARQL query is too short (printed below)!\n" + options.sparql_query)
-
-if not re.match("^http", options.url):
-	sys.exit("The URL has to start with 'http://'! Please try again!")
-
-# -----------------------
-# The main code
-# -----------------------
-
-def main():
-	# Extract command line options
-	sparql_query = options.sparql_query
-	sparql_query = sparql_query.replace("__oc__","{")
-	sparql_query = sparql_query.replace("__ob__","[")
-	sparql_query = sparql_query.replace("__cc__","}")
-	sparql_query = sparql_query.replace("__cb__","]")
-	sparql_query = sparql_query.replace("__cr__"," ")
-	sparql_query = sparql_query.replace("__cn__"," ")
-	sparql_query = urllib.quote_plus(sparql_query)
-	url = options.url
-
-	output_file = options.output_file
-
-	# Create SPARQL query URL
-	sparql_query_url = url + "?query=" + sparql_query
-
-	# Read from SPARQL Endpoint
-	sparql_endpoint = urllib.urlopen(sparql_query_url)
-	results = sparql_endpoint.read()
-	sparql_endpoint.close()
-
-        # Convert to tabular format
-        if "<sparql" in results:
-                xmldata = extract_xml( results )
-                tabular = xml_to_tabular( xmldata )
-        else:
-                sys.exit("No SPARQL content found in returned data!\nReturned data:\n" + "-"*80 + "\n" + results)
-
-	# Print to file
-	of = open(output_file, "w")
-	of.write(tabular)
-	of.close()
-
-# -----------------------
-# Helper methods
-# -----------------------
-
-def extract_xml( content ):
-	'''Extract the part of the document starting with <?xml ...'''
-	xmlcontent = re.search("<sparql.*", content, re.DOTALL).group(0)
-	return xmlcontent
-
-def xml_to_tabular( xmldata ):
-	'''Convert SPARQL result set XML format to tabular text'''
-	root = et.fromstring(xmldata)
-	tree = et.ElementTree(root)
-	tabular = ""
-
-	results = root.getchildren()[1]
-	for result in results:
-		line_bits = [binding.getchildren()[0].text for binding in result.getchildren()]
-		line = "\t".join(line_bits)
-		tabular += line + "\n"	
-	return tabular
-
-if __name__ == '__main__':
-	main()
--- a/semweb_tools/sparql_import.xml	Wed Nov 21 12:19:18 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-<tool id="sparql_import" name="SPARQL Import" version="1.0.0">
-	<description>Import data from a SPARQL Endpoint</description>
-	<command interpreter="python">sparql_import.py -u $url -q "$sparqlquery" -o $outfile</command>
-	<inputs>
-		<param name="url" type="text" format="text" size="80" label="SPARQL Endpoint URL"/>
-		<param name="sparqlquery" type="text" format="text" area="True" size="5x80" label="SPARQL Query"/>
-	</inputs>
-	<outputs>
-		<data name="outfile" format="tabular"/>
-	</outputs>
-	<help>
-**What it does**
-
-The SPARQL import executes a SPARQL query against a SPARQL endpoint and returns the results in tabular format, with one column per variable in the SPARQL query.
-
--------
-
-**Example**
-
-You could for example use this SPARQL Endpoint URL:
-
-http://sparql.wikipathways.org/
-
-and the following SPARQL query, which will select 25 sets of "subject", "predicate" and "object" out of the database, with no filtering at all::
-
-    SELECT ?s ?p ?o
-    WHERE { ?s ?p ?o } 
-    LIMIT 10
-
-This will generate a 3-column tabular output like this::
-
-    http://identifiers.org/pubmed/12860264  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/15782111  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/11017945  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/10997684  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/19635799  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/16480962  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/15976321  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/17218259  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/17215298  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-    http://identifiers.org/pubmed/11177571  http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference
-
-</help>
-</tool>