Commit 8b7c3383 authored by R.W.Majeed's avatar R.W.Majeed
Browse files

fixed using description for tooltip. Use readable path if no description is available.

parent 893dfbe6

histream-i2b2/src/main/java/de/sekmi/histream/i2b2/ont/Import.java

+47 −2
Original line number Diff line number Diff line
@@ -311,6 +311,49 @@ public class Import implements AutoCloseable{ 
		}

		return xmlbuf.toString();

	}

	/**

	 * Build a readable representation of a concept path.

	 * E.g. remove base path and namespace prefixes from path names

	 * @param path ontology path

	 * @return readable path

	 */

	public String readableConceptPath(String path){

		if( path.startsWith(metaBase) ){

			path = path.substring(metaBase.length());

		}

		StringBuilder b = new StringBuilder();

		int pos = 0;

		boolean done = false;

		char prefix_char;

		do{

			int sep = path.indexOf('\\', pos);

			if( sep == -1 ){

				done = true;

				sep = path.length();

			}else if( sep == path.length()-1 ){

				// empty backslash at end of path

				done = true;

			}

			// skip the http:// part of url prefixes

			if( path.substring(pos,pos+7).equals("http://") ){

				// prefixes will end in #

				prefix_char = '#';

				pos += 7;

			}else{

				// prefix will end in :

				prefix_char = ':';

			}

			// is there a prefix in the path segment?

			int pfx = path.indexOf(prefix_char, pos);

			if( pfx != -1 && pfx < sep ){

				// prefix found, ignore the prefix

				pos = pfx+1;

			}

			b.append('\\').append(path.substring(pos, sep));

			pos = sep+1;

		}while( !done );

		return b.toString();

	}

	private void insertMeta(int level, String path_prefix, Concept concept, boolean accessRoot) throws SQLException, OntologyException{

		insertMeta.setInt(1, level);

		String label = concept.getPrefLabel(locale);
@@ -399,8 +442,10 @@ public class Import implements AutoCloseable{ 
		// c_tooltip

		// try to use concept description

		String descr = concept.getDescription(locale);

		if( descr == null )descr = path; // use path if no description available

		insertMeta.setString(9, path);

		if( descr == null ){

			descr = readableConceptPath(path); // use path if no description available

		}

		insertMeta.setString(9, descr);

		

		// m_applied_path

		insertMeta.setString(10, "@");

histream-i2b2/src/test/java/de/sekmi/histream/i2b2/ont/TestOntologyImport.java

0 → 100644
+55 −0
Original line number Diff line number Diff line 
package de.sekmi.histream.i2b2.ont;



import java.sql.SQLException;

import java.util.HashMap;

import java.util.Map;



import org.junit.After;

import org.junit.Assert;

import org.junit.Before;

import org.junit.Test;



import de.sekmi.histream.i2b2.sql.VirtualConnection;



public class TestOntologyImport {

	VirtualConnection dbcData;

	VirtualConnection dbcMeta;

	Import imp;

	

	@Before

	public void prepareVirtualConnections() throws SQLException{

		dbcData = new VirtualConnection( a -> {} );

		dbcMeta = new VirtualConnection( a -> {} );

		Map<String, String> props = new HashMap<>();

		// set preferences

		props.put("meta.basepath", "\\i2b2\\");

		props.put("meta.sourcesystem_cd", "test");

		props.put("meta.table", "i2b2metadata.i2b2");

		props.put("meta.access", "i2b2metadata.table_access");

		props.put("data.concept.table", "i2b2crcdata.concepts");

		props.put("ont.language", "en");

		imp = new Import(dbcMeta, dbcData, props);

	}



	@After

	public void closeVirtualConnections() throws SQLException{

		imp.close();

//		dbcData.close();

//		dbcMeta.close();

	}

	@Test

	public void verifyReadablePath(){

		String path = "\\i2b2\\asdf:First\\k23kskd:Second\\";

		String readable = imp.readableConceptPath(path);

		// there should be no prefixes

		Assert.assertEquals(-1, readable.indexOf(':'));

		// print for debugging

		System.out.println(readable);



		// second test with url prefixes

		path = "\\i2b2\\http://lala/xyz#First\\asdf:Second";

		String readable2 = imp.readableConceptPath(path);

		System.out.println(readable);

		Assert.assertEquals(readable, readable2);

	}

}