Index: src/org/biomart/processors/formatters/RDF.java =================================================================== --- src/org/biomart/processors/formatters/RDF.java (revision 9838) +++ src/org/biomart/processors/formatters/RDF.java (working copy) @@ -14,7 +14,7 @@ */ public class RDF extends TSVFormatter { - public enum FORMAT { N3 }; + public enum FORMAT { N3 , RDFXML}; private FORMAT format; @@ -26,6 +26,8 @@ protected String[] variableTypes; protected List columnValues = new LinkedList(); + private int variableNo; + public RDF(OutputStream out, String[] variableNames, String[] variableProperties, @@ -47,35 +49,32 @@ return; } - //out.write("\n".getBytes()); - - if (prelude != null && format != FORMAT.N3) - out.write(prelude.getBytes()); - this.variableNames = variableNames; this.variableProperties = variableProperties; this.variableTypes = variableTypes; this.visibleColumn = new boolean[variableNames.length]; - //out.write("\n\t\n".getBytes()); - - for (int i = 0, j = 0; i < variableNames.length; i++) { + for (int i = 0; i < variableNames.length; i++) { String variableName = variableNames[i]; if (!variableName.startsWith("?") && // Un-projected query variables !variableName.startsWith("!")) { // Virtual variables for filters - //out.write(("\t\t\n").getBytes()); visibleColumn[i] = true; - j = i; } } - //out.write("\t\n\t\n".getBytes()); switch(format) { case N3: for (String prefix : namespaces.keySet()) out.write(("@prefix " + prefix + " <" + namespaces.get(prefix) + ">\n").getBytes()); break; + case RDFXML: + out.write("\n".getBytes()); + out.write("\n".getBytes()); + break; default: break; } @@ -93,29 +92,76 @@ @Override public void writeStartOfLine() throws IOException { - //out.write(("\t\t\n").getBytes()); } @Override public void writeEndOfLine() throws IOException { - writeN3(); + switch(format) { + case N3: + writeN3(); + break; + default: + break; + } } @Override public void writeField(int column, String value) throws IOException { - columnValues.add(value); + switch(format) { + case N3: + columnValues.add(value); + break; + case RDFXML: // write out each property in its own element + if (visibleColumn[column]) + { + // write the opening tag + // TODO: seems like we only support blank nodes in results right now + out.write("<".getBytes()); + // write the predicate + // FIXME: unless this is always prefixed, will need to split it into base and localname and write ".getBytes()); + // write out the actual value as a literal + // FIXME: not clear how the N3 version is able to distinguish between URIs, plain literals, typed literals and language literals here + out.write(value.getBytes()); + // write out the end of the property element + out.write("".getBytes()); + // write out the end of the line + out.write("\n".getBytes()); + variableNo++; + } + break; + default: + break; + } } @Override public void close() throws IOException { if (exception) return; + + switch(format) { + case RDFXML: + out.write("".getBytes()); + break; + default: + break; + } - //out.write("\t\n\n".getBytes()); super.close(); } private void writeN3() throws IOException { - int variableNo = 0; + variableNo = 0; for (int column = 0; column < visibleColumn.length; column++) { if (!visibleColumn[column]) @@ -140,4 +186,5 @@ columnValues.clear(); } + } Index: src/org/biomart/processors/RDFXML.java =================================================================== --- src/org/biomart/processors/RDFXML.java (revision 0) +++ src/org/biomart/processors/RDFXML.java (revision 0) @@ -0,0 +1,78 @@ +/** + * + */ +package org.biomart.processors; + +import java.io.OutputStream; +import java.util.HashMap; +import java.util.Map; + +import org.biomart.processors.annotations.ContentType; +import org.jdom.Comment; + +import com.google.common.io.Closeables; + +/** + * + * @author Peter Ansell + * + */ +@ContentType("application/rdf+xml") +public class RDFXML extends ProcessorImpl +{ + @Override + public void setOutputStream(OutputStream out) { + String prelude = null; + Map namespaces = new HashMap(); + String[] variableNames = new String[0]; + String[] variableProperties = new String[0]; + String[] variableTypes = new String[0]; + Map variable2URIAttributes = new HashMap(); // TODO For now: only one URI attribute supported + String exception = null; + for (Object content : query.queryXMLobject.getContent()) { + if (content instanceof Comment) { + Comment comment = (Comment)content; + + // Variable names starting with a "?" are used only internally + // and their values are not returned. + + if (comment.getText().startsWith(" VARIABLES:")) { + variableNames = comment.getText().substring(11).trim().split(" "); + } else if (comment.getText().startsWith(" VARIABLEPROPERTIES:")) { + variableProperties = comment.getText().substring(20).trim().split(" "); + } else if (comment.getText().startsWith(" VARIABLETYPES:")) { + variableTypes = comment.getText().substring(15).trim().split(" "); + } else if (comment.getText().startsWith(" NAMESPACE:")) { + String[] prefix2URI = comment.getText().substring(11).trim().split(" "); + namespaces.put(prefix2URI[0], prefix2URI[1]); + } else if (comment.getText().startsWith(" NODEATTRIBUTES:")) { + String[] nodeAttributes = comment.getText().substring(16).trim().split(" "); + // TODO For now: only one URI attribute supported + for (String uri : nodeAttributes) { + String[] nameURIPair = uri.trim().split(":"); + variable2URIAttributes.put(nameURIPair[0], nameURIPair[1]); + } + } else if (comment.getText().startsWith(" BioMart XML-Query:")) { + prelude = "\n"; + } else if (comment.getText().startsWith(" SPARQL-Exception:")) { + exception = comment.getText().substring(18); + } + } + } + + this.out = new org.biomart.processors.formatters.RDF(out, + variableNames, + variableProperties, + variableTypes, + variable2URIAttributes, + namespaces, + prelude, + exception, + org.biomart.processors.formatters.RDF.FORMAT.RDFXML); + } + + @Override + public void done() { + Closeables.closeQuietly(out); + } +}