package org.obolibrary.oboformat.writer;
import static org.junit.Assert.*;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.InputStreamReader;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import javax.annotation.Nonnull;
import org.junit.Test;
import org.obolibrary.obo2owl.OboFormatTestBasics;
import org.obolibrary.oboformat.model.Clause;
import org.obolibrary.oboformat.model.Frame;
import org.obolibrary.oboformat.model.OBODoc;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
/** Tests for {@link OBOFormatWriter}. */
@SuppressWarnings({ "javadoc", "null" })
public class OBOFormatWriterTest extends OboFormatTestBasics {
/**
* Test a special case of the specification. For intersections put the genus
* before the differentia, instead of the default case-insensitive
* alphabetical ordering.
*/
@Test
public void testSortTermClausesIntersectionOf() {
OBODoc oboDoc = parseOBOFile("equivtest.obo");
Frame frame = oboDoc.getTermFrame("X:1");
List<Clause> clauses = new ArrayList<>(
frame.getClauses(OboFormatTag.TAG_INTERSECTION_OF));
OBOFormatWriter.sortTermClauses(clauses);
assertEquals("Y:1", clauses.get(0).getValue());
assertEquals("R:1", clauses.get(1).getValue());
assertEquals("Z:1", clauses.get(1).getValue2());
}
/**
* Test for sorting clauses according to alphabetical case-insensitive
* order. Prefer upper-case over lower case for equal strings. Prefer
* shorter strings over longer strings.
*/
@Test
public void testSortTermClausesSynonyms() {
List<Clause> clauses = createSynonymClauses("cc", "ccc", "AAA", "aaa",
"bbbb");
OBOFormatWriter.sortTermClauses(clauses);
assertEquals("AAA", clauses.get(0).getValue());
assertEquals("aaa", clauses.get(1).getValue());
assertEquals("bbbb", clauses.get(2).getValue());
assertEquals("cc", clauses.get(3).getValue());
assertEquals("ccc", clauses.get(4).getValue());
}
@Nonnull
private static List<Clause> createSynonymClauses(@Nonnull String... labels) {
List<Clause> clauses = new ArrayList<>(labels.length);
for (String label : labels) {
Clause clause = new Clause(OboFormatTag.TAG_SYNONYM, label);
clauses.add(clause);
}
return clauses;
}
@Test
public void testWriteObsolete() throws Exception {
assertEquals("", writeObsolete(Boolean.FALSE));
assertEquals("", writeObsolete(Boolean.FALSE.toString()));
assertEquals("is_obsolete: true", writeObsolete(Boolean.TRUE));
assertEquals("is_obsolete: true",
writeObsolete(Boolean.TRUE.toString()));
}
@Nonnull
private static String writeObsolete(Object value) throws Exception {
Clause cl = new Clause(OboFormatTag.TAG_IS_OBSELETE);
cl.addValue(value);
StringWriter out = new StringWriter();
BufferedWriter bufferedWriter = new BufferedWriter(out);
OBOFormatWriter.write(cl, bufferedWriter, null);
bufferedWriter.close();
return out.toString().trim();
}
/**
* Test that the OBO format writer only writes one new-line at the end of
* the file.
*/
@Test
public void testWriteEndOfFile() throws Exception {
OBODoc oboDoc = parseOBOFile("caro.obo");
String oboString = renderOboToString(oboDoc);
int length = oboString.length();
assertTrue(length > 0);
int newLineCount = 0;
for (int i = length - 1; i >= 0; i--) {
char c = oboString.charAt(i);
if (Character.isWhitespace(c)) {
if (c == '\n') {
newLineCount++;
}
} else {
break;
}
}
assertEquals("GO always had an empty newline at the end.", 2,
newLineCount);
}
@Test
public void testWriteOpaqueIdsAsComments() throws Exception {
OBODoc oboDoc = parseOBOFile("opaque_ids_test.obo");
String oboString = renderOboToString(oboDoc);
String[] lines = oboString.split("\n");
boolean ok = false;
for (String line : lines) {
// System.out.println("LINE: "+line);
if (line.startsWith("relationship:")) {
if (line.contains("named relation y1")) {
ok = true;
}
}
}
assertTrue(ok);
}
@Test
public void testPropertyValueOrder() throws Exception {
BufferedReader reader = new BufferedReader(new InputStreamReader(
getInputStream("tag_order_test.obo")));
StringBuilder sb = new StringBuilder();
String line;
while ((line = reader.readLine()) != null) {
sb.append(line);
sb.append('\n');
}
reader.close();
String input = sb.toString();
OBODoc obodoc = parseOboToString(input);
String written = renderOboToString(obodoc);
assertEquals(input, written);
}
}