package owltools.cli;

import static junit.framework.Assert.*;

import java.io.File;

import org.junit.Test;

import owltools.OWLToolsTestBasics;

/**
 * Tests for {@link CommandRunner}.
 * 
 * these are somewhat ad-hoc at the moment - output is written to stdout;
 * no attempt made to check results
 * 
 */
public class CommandRunnerSpeciesMergeTest extends AbstractCommandRunnerTest {
	
	@Test
	public void testMMergeSpecies() throws Exception {
		init();
		//String obo = "http://purl.obolibrary.org/obo";
		load("forebrain.obo");
		//run("--list-class-axioms NCBITaxon:7954");
		
		run("--reasoner elk --merge-species-ontology -s Danio -t NCBITaxon:7954");
		run("-o -f obo target/forebrain-merged.obo");
		run("--assert-inferred-subclass-axioms --removeRedundant");
		run("-o -f obo target/forebrain-merged-trimmed.obo");
		run("--descendants telencephalon");
		//run("-a tentacle");

		//run("--make-subset-by-properties part_of // -o -f obo /tmp/foo.obo");
		
		//run("-o -f obo /tmp/foo.obo");
		
	}
	


	
	
}

@@ -761,20 +761,41 @@
 edundant
+ --allowEquivalencies
 %22);%0A
-
 %09%09run(%22-
@@ -834,32 +834,32 @@
 -trimmed.obo%22);%0A
+
 %09%09run(%22--descend
@@ -884,145 +884,8 @@
 %22);%0A
-%09%09//run(%22-a tentacle%22);%0A%0A%09%09//run(%22--make-subset-by-properties part_of // -o -f obo /tmp/foo.obo%22);%0A%09%09%0A%09%09//run(%22-o -f obo /tmp/foo.obo%22);%0A
 %09%09%0A%09

allow equivalencies