changeset 4:6501986529b0 draft

HTML or tabular option added

--- a/galaxy-dist/tools/sparql_galaxy/SPARQLGalaxy.xml	Fri Apr 25 15:42:31 2014 +0200
+++ b/galaxy-dist/tools/sparql_galaxy/SPARQLGalaxy.xml	Mon Apr 28 16:11:05 2014 +0200
@@ -1,18 +1,28 @@
 <tool id="SPARQLGalaxy" name="Execute an SPARQL query against an RDF file" version="1.0.1">
 	<description>It executes an SPARQL query against the input RDF file and generates an HTML file with the variables and bound entities</description>
 	<command interpreter="python">
-	  sparql.py $ontology "$pasted_query" > $output 2>/dev/null
+	  sparql.py $ontology "$pasted_query" $out_format > $output 2>/dev/null
 	</command>
 	<inputs>
 		<param name="ontology" type="data" format="rdf" label="Input RDF file"/>		   
 		<param name="pasted_query" type="text" area="True" size="10x50" label="SPARQL Query" value="SELECT * WHERE { ?s ?p ?o }">
 		  <sanitizer sanitize="False"/>
+		</param>	
+		<param name="out_format" type="select" label="Output format" help="">
+			<option value="html" selected="true">HTML</option>
+			<option value="tab">TABULAR</option>
 		</param>
+
 	</inputs>
 	<outputs>
-		<data format="html" name="output" />
+		<data format="html" name="output">
+		<change_format>
+			<when input="out_format" value="tab" format="tabular" />
+		 </change_format>
+		 </data>
 	</outputs>
 	<help>
+
 	  
 **Important note**
 

--- a/galaxy-dist/tools/sparql_galaxy/sparql.py	Fri Apr 25 15:42:31 2014 +0200
+++ b/galaxy-dist/tools/sparql_galaxy/sparql.py	Mon Apr 28 16:11:05 2014 +0200
@@ -1,13 +1,21 @@
-
 
 import sys
 import rdflib
+from operator import eq
 
 def main(argv):
 
     g = rdflib.Graph()
     g.parse(argv[1])
     results = g.query(argv[2])
+    render = argv[3]
+
+    if (render == "html"):
+        html_render(results)
+    else:
+        tab_render(results)
+    
+def html_render(results):
     print "<table>"
     print "<tr>"
     for key in results.bindings[1].keys():
@@ -23,5 +31,14 @@
         print "</tr>"
     print "</table>"
     
+def tab_render(results):
+    for key in results.bindings[1].keys():
+        print key + "\t",
+    print "\n"
+    for binding in results.bindings:
+        for value in binding.values():  
+            if isinstance(value, rdflib.term.URIRef):
+                print value + "\t",
+
 if __name__ == "__main__":
     main(sys.argv)
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