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Merged
josemduarte merged 7 commits into from
Sep 20, 2021
Merged

Multiple OBO altids fix for #964 #960

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82c3a3f
Merge branch 'master' of https://github.com/biojava/biojava
otter606 Aug 17, 2021
0791542
Merge branch 'master' of https://github.com/biojava/biojava
Aug 18, 2021
4358236
Merge branch 'master' of https://github.com/richarda23/biojava
otter606 Aug 25, 2021
2cc46f8
Merge branch 'master' of https://github.com/biojava/biojava
otter606 Aug 28, 2021
c44cdc5
use list as an annotation value for Alt_id
otter606 Aug 28, 2021
a32f209
add test for multiple altids
otter606 Aug 28, 2021
016ff70
minor refactor
otter606 Aug 28, 2021
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35 changes: 16 additions & 19 deletions biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileEventListener.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,40 +33,37 @@
*/
public interface OboFileEventListener {

/** starting to parse a new OBO file
*
*
/**
* starting to parse a new OBO file
*/
public void documentStart();
void documentStart();

/** end of parsing a new OBO file
*
*
/**
* end of parsing a new OBO file
*/
public void documentEnd();
void documentEnd();

/** parsed a new OBO file header
*
*
/**
* parsed a new OBO file header
*/
public void newOboFileHeader();
void newOboFileHeader();

/** parsed a new stanza in the file
*
/**
* parsed a new stanza in the file
* @param stanza
*/
public void newStanza(String stanza);
void newStanza(String stanza);

/**found a new key in the file
*
/**
* found a new key in the file
* @param key
* @param value
*/
public void newKey(String key, String value );
void newKey(String key, String value );

/** a new synonym has been found
*
* @param synonym
*/
public void newSynonym(Synonym synonym);
void newSynonym(Synonym synonym);
}
14 changes: 10 additions & 4 deletions biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,6 @@ public OboFileHandler(Ontology ontology){

//Term isa = onto.importTerm(OntoTools.IS_A, null);
//Term partof = onto.importTerm(OntoTools.PART_OF, null);;

}

@Override
Expand Down Expand Up @@ -108,7 +107,6 @@ public void newStanza(String stanza) {
} else {
isTerm = false;
}

}

@Override
Expand Down Expand Up @@ -155,7 +153,7 @@ else if (key.equals(NAME)){
// ignore obsolete Terms...
//logger.info("obsolete: {}", currentTerm);
Annotation anno = currentTerm.getAnnotation();
anno.setProperty(IS_OBSOLETE, new Boolean(true));
anno.setProperty(IS_OBSOLETE, Boolean.TRUE);

} else if (key.equals(IS_A) ||
key.equals(RELATIONSHIP) ||
Expand All @@ -174,8 +172,16 @@ else if (key.equals(NAME)){
Annotation anno = currentTerm.getAnnotation();
anno.setProperty(COMMENT, value);
} else if (key.equals(ALT_ID)){
// #964
Annotation anno = currentTerm.getAnnotation();
anno.setProperty(ALT_ID, value);
if (anno.containsProperty(ALT_ID)) {
List<String> alts = (List<String>) anno.getProperty(ALT_ID);
alts.add(value);
} else {
List<String> alts = new ArrayList<>();
alts.add(value);
anno.setProperty(ALT_ID, alts);
}
}
else if (key.equals(REPLACED_BY)) {
Annotation anno = currentTerm.getAnnotation();
Expand Down
72 changes: 48 additions & 24 deletions biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,44 +23,68 @@
package org.biojava.nbio.ontology;

import org.biojava.nbio.ontology.io.OboParser;
import org.junit.Assert;
import org.biojava.nbio.ontology.utils.Annotation;
import org.junit.Test;

import java.io.*;
import java.text.ParseException;
import java.util.List;
import java.util.Set;

import static org.biojava.nbio.ontology.obo.OboFileHandler.NAMESPACE;
import static org.biojava.nbio.ontology.obo.OboFileHandler.ALT_ID;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;

public class TestParseOBO {

@Test
public void testNamespace() throws IOException, ParseException {

String testTermEntry = "\n[Term]\n" +
"id: SO:0000691\n" +
"name: cleaved_initiator_methionine \n" +
"namespace: sequence\n" +
"alt_id: BS:00067\n" +
"def: \"The initiator methionine that has been cleaved from a mature polypeptide sequence.\" [EBIBS:GAR]\n" +
"subset: biosapiens\n" +
"synonym: \"cleaved initiator methionine\" EXACT []\n" +
"synonym: \"init_met\" RELATED [uniprot:feature_type]\n" +
"synonym: \"initiator methionine\" RELATED []\n" +
"is_a: SO:0100011 ! cleaved_peptide_region\n\n";
private OboParser parser;

OboParser parser = new OboParser();
InputStream inStream = new ByteArrayInputStream(testTermEntry.getBytes());
final String testTermEntry = "\n[Term]\n"
+ "id: SO:0000691\n"
+ "name: cleaved_initiator_methionine \n"
+ "namespace: sequence\n"
+ "alt_id: BS:00067\n"
+ "def: \"The initiator methionine that has been cleaved from a mature polypeptide sequence.\" [EBIBS:GAR]\n"
+ "subset: biosapiens\n"
+ "synonym: \"cleaved initiator methionine\" EXACT []\n"
+ "synonym: \"init_met\" RELATED [uniprot:feature_type]\n"
+ "synonym: \"initiator methionine\" RELATED []\n" + "is_a: SO:0100011 ! cleaved_peptide_region\n\n";

Assert.assertNotNull(inStream);
public Ontology readObo(String input) throws ParseException, IOException {
parser = new OboParser();
InputStream inStream = new ByteArrayInputStream(input.getBytes());
assertNotNull(inStream);
BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream));
return parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
"snippet from biosapiens protein feature ontology");
}

BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );
Ontology ontology = parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
"snippet from biosapiens protein feature ontology");
@Test
public void testNamespace() throws IOException, ParseException {
Ontology ontology = readObo(testTermEntry);
Set<Term> keys = ontology.getTerms();
assertTrue(keys.size() > 1);
assertTrue(getAnnotationForTerm(ontology).containsProperty(NAMESPACE));
assertEquals("sequence", getAnnotationForTerm(ontology).getProperty(NAMESPACE));
//#964
assertTrue(getAnnotationForTerm(ontology).getProperty(ALT_ID) instanceof List);
}

@Test
public void testMultipleAltIds() throws IOException, ParseException {

String oboWith2AltIds = testTermEntry.replace("BS:00067", "BS:00067\nalt_id: BS:00068");
Ontology ontology = readObo(oboWith2AltIds);
List<String> altIds = (List<String>) getAnnotationForTerm(ontology).getProperty(ALT_ID);
assertEquals(2, altIds.size());
assertEquals("BS:00067", altIds.get(0));
assertEquals("BS:00068", altIds.get(1));
}

private Annotation getAnnotationForTerm(Ontology ontology) {
return ontology.getTerm("SO:0000691").getAnnotation();

Assert.assertTrue(keys.size() > 1);
Assert.assertTrue(ontology.getTerm("SO:0000691").getAnnotation().containsProperty(NAMESPACE));
Assert.assertEquals("sequence", ontology.getTerm("SO:0000691").getAnnotation().getProperty(NAMESPACE));
}
}