Skip to content

Commit

Permalink
OutputTest code cleanup
Browse files Browse the repository at this point in the history
  • Loading branch information
@lszeremeta
lszeremeta committed Oct 19, 2020
1 parent 2cdf678 commit cf0e8f8
Showing 1 changed file with 2 additions and 48 deletions.
50 changes: 2 additions & 48 deletions src/test/java/pl/edu/uwb/ii/sdfeater/OutputTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,11 @@
* Output data tests
*/
class OutputTest {
//private final PrintStream standardOut = System.out;
private final ByteArrayOutputStream outputStreamCaptor = new ByteArrayOutputStream();
private final String[] testMoleculeDataFields = {"alternateName", "description", "identifier", "inChI", "inChIKey", "iupacName", "molecularFormula", "molecularWeight", "smiles"};
private final String[] testMoleculeData = {"(+)-2-fenchanone", "A fenchone that has", "4695-62-9", "InChI=1S/C10H16O/c1-9(2)7-4-5-10(3,6-7)8(9)11/h7H,4-6H2,1-3H3/t7-,10+/m1/s1", "LHXDLQBQYFFVNW-XCBNKYQSSA-N", "(1S,4R)-fenchan-2-one", "C10H16O", "152.23340", "CC1(C)[C@@H]2CC[C@@](C)(C2)C1=O", "(-)-Epicatechin", "A catechin with", "490-46-0", "InChI=1S/C15H14O6/c16-8-4-11(18)9-6-13(20)15(21-14(9)5-8)7-1-2-10(17)12(19)3-7/h1-5,13,15-20H,6H2/t13-,15-/m1/s1", "PFTAWBLQPZVEMU-UKRRQHHQSA-N", "(2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol", "C15H14O6", "290.26810", "[H][C@@]1(Oc2cc(O)cc(O)c2C[C@H]1O)c1ccc(O)c(O)c1"};
private final File file = new File(Paths.get("src", "test", "resources", "chebi_test.sdf").toFile().getAbsolutePath());
private Molecule molecule;
private File file;

/**
* Check if String contains all values from String array
Expand All @@ -41,20 +40,11 @@ private static boolean stringContainsAllValues(String str, String[] values) {
}

@BeforeEach
void redirectSystemOutStream() {
void setUp() {
System.setOut(new PrintStream(outputStreamCaptor));
}

@BeforeEach
void initializeObjects() {
molecule = new Molecule();
file = new File(Paths.get("src", "test", "resources", "chebi_test.sdf").toFile().getAbsolutePath());
}

// @AfterEach
// void restoreSystemOutStream() {
// System.setOut(standardOut);
// }

// CYPHER (raw)

Expand All @@ -64,10 +54,8 @@ void initializeObjects() {
@Test
void cypherRawContainsRequiredStrings() {
file.parse(molecule, 'c', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"CREATE (", "{", "}", ",", ")", ":", "[", "]", "'", ":", "->", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -89,10 +77,8 @@ void cypherRawContainsAllMoleculeData() {
@Test
void cypherURLContainsRequiredStrings() {
file.parse(molecule, 'c', true, false);

String out = outputStreamCaptor.toString();
String[] required = {"CREATE (", "{", "}", ",", ")", ":", "'", ":", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:", "http", "//", "/"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -115,10 +101,8 @@ void cypherURLContainsAllMoleculeData() {
void cypherPeriodicContainsRequiredStrings() {
loadPeriodicTableData();
file.parse(molecule, 'c', false, true);

String out = outputStreamCaptor.toString();
String[] required = {"CREATE (", "{", "}", ",", ")", ":", "'", ":", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:", "atomicNumber:", "name:", "Carbon", "atomicMass:", "bondingType:"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -142,10 +126,8 @@ void cypherPeriodicContainsAllMoleculeData() {
void cypherAllContainsRequiredStrings() {
loadPeriodicTableData();
file.parse(molecule, 'c', true, true);

String out = outputStreamCaptor.toString();
String[] required = {"CREATE (", "{", "}", ",", ")", ":", "'", ":", ")-[:", "]->(", "symbol:", "C", "x:", "y:", "z:", "http", "//", "/", "atomicNumber:", "name:", "Carbon", "atomicMass:", "bondingType:"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -168,10 +150,8 @@ void cypherAllContainsAllMoleculeData() {
@Test
void cvmeContainsRequiredStrings() {
file.parse(molecule, 'r', true, false);

String out = outputStreamCaptor.toString();
String[] required = {"skos:altLabel", "skos:definition", "skos:notation", "skos:prefLabel", "rdfs:seeAlso", "dbo:inchi", "dbp:inchikey", "dbo:casNumber", "skos:hiddenLabel", "skos:example", "urn:uuid:", "^^", "@", "chemskos:SMILES", ".", "<", ">", "http", ":", "//", "\"\"\"", "END", "C"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -193,10 +173,8 @@ void cvmeContainsAllMoleculeData() {
@Test
void smilesContainsSMILES() {
file.parse(molecule, 's', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"[H][C@@]1(Oc2cc(O)cc(O)c2C[C@H]1O)c1ccc(O)c(O)c1", "CC1(C)[C@@H]2CC[C@@](C)(C2)C1=O"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -208,10 +186,8 @@ void smilesContainsSMILES() {
@Test
void inchiContainsInChI() {
file.parse(molecule, 'i', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"InChI=1S/C15H14O6/c16-8-4-11(18)9-6-13(20)15(21-14(9)5-8)7-1-2-10(17)12(19)3-7/h1-5,13,15-20H,6H2/t13-,15-/m1/s1", "InChI=1S/C10H16O/c1-9(2)7-4-5-10(3,6-7)8(9)11/h7H,4-6H2,1-3H3/t7-,10+/m1/s1"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -224,10 +200,8 @@ void inchiContainsInChI() {
void turtleContainsRequiredStrings() {
initializeJenaModel();
file.parse(molecule, 't', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"@prefix", "schema.org", "rdf", "MolecularEntity", "[", ";", "]", ".", "<", ">", "http", "//", ":", "\""};

assertTrue(stringContainsAllValues(out, required));
}

Expand Down Expand Up @@ -262,10 +236,8 @@ void turtleContainsAllMoleculeData() {
void nTriplesContainsRequiredStrings() {
initializeJenaModel();
file.parse(molecule, 'n', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"schema.org", "rdf", "MolecularEntity", ".", "<", ">", "http", "//", ":", "\""};

assertTrue(stringContainsAllValues(out, required));
}

Expand Down Expand Up @@ -300,10 +272,8 @@ void nTriplesContainsAllMoleculeData() {
void rdfXMLContainsRequiredStrings() {
initializeJenaModel();
file.parse(molecule, 'x', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"<", ">", "rdf:RDF", "xmlns:", "<rdf:Description>", "type", "MolecularEntity", "schema", "</", "&lt;", "&gt;"};

assertTrue(stringContainsAllValues(out, required));
}

Expand Down Expand Up @@ -338,10 +308,8 @@ void rdfXMLContainsAllMoleculeData() {
void rdfthriftContainsRequiredStrings() {
initializeJenaModel();
file.parse(molecule, 'h', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"schema", "rdf"};

assertTrue(stringContainsAllValues(out, required));
}

Expand Down Expand Up @@ -376,10 +344,8 @@ void rdfthriftContainsAllMoleculeData() {
void jsonldHtmlContainsRequiredStrings() {
initializeJenaModel();
file.parse(molecule, 'd', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"<", ">", "</", "script>", "@id", "{", "}", ",", "MolecularEntity"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -401,9 +367,7 @@ void jsonldHtmlContainsAllMoleculeDataFields() {
void jsonldHtmlContainsAllMoleculeData() {
initializeJenaModel();
file.parse(molecule, 'd', false, false);

String out = outputStreamCaptor.toString();

assertTrue(stringContainsAllValues(out, testMoleculeData));
}

Expand All @@ -416,10 +380,8 @@ void jsonldHtmlContainsAllMoleculeData() {
void jsonldContainsRequiredStrings() {
initializeJenaModel();
file.parse(molecule, 'j', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"@id", "{", "}", ",", "MolecularEntity"};

assertTrue(stringContainsAllValues(out, required));
}

Expand Down Expand Up @@ -453,10 +415,8 @@ void jsonldContainsAllMoleculeData() {
@Test
void rdfaContainsRequiredStrings() {
file.parse(molecule, 'a', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"<", ">", "</", "typeof", "property", "MolecularEntity", "&lt;", "&gt;"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -476,9 +436,7 @@ void rdfaContainsAllMoleculeDataFields() {
@Test
void rdfaContainsAllMoleculeData() {
file.parse(molecule, 'a', false, false);

String out = outputStreamCaptor.toString();

assertTrue(stringContainsAllValues(out, testMoleculeData));
}

Expand All @@ -490,10 +448,8 @@ void rdfaContainsAllMoleculeData() {
@Test
void microdataContainsRequiredStrings() {
file.parse(molecule, 'm', false, false);

String out = outputStreamCaptor.toString();
String[] required = {"<", ">", "</", "itemscope", "itemtype", "itemprop", "MolecularEntity", "&lt;", "&gt;"};

assertTrue(stringContainsAllValues(out, required));
}

Expand All @@ -513,9 +469,7 @@ void microdataContainsAllMoleculeDataFields() {
@Test
void microdataContainsAllMoleculeData() {
file.parse(molecule, 'm', false, false);

String out = outputStreamCaptor.toString();

assertTrue(stringContainsAllValues(out, testMoleculeData));
}

Expand Down

0 comments on commit cf0e8f8

Please sign in to comment.