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added test for composite key reference/refback
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@svandenhoek
svandenhoek committed Dec 12, 2024
1 parent 01a3e4c commit 719beff
Showing 1 changed file with 77 additions and 10 deletions.
87 changes: 77 additions & 10 deletions backend/molgenis-emx2-rdf/src/test/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapperTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,8 @@ class ColumnTypeRdfMapperTest {
static final String TEST_TABLE = "TestTable";
static final String REF_TABLE = "TestRefTable";
static final String REFBACK_TABLE = "TestRefBackTable";
static final String COMPOSITE_REF_TABLE = "TestCompositeRefTable";
static final String COMPOSITE_REFBACK_TABLE = "TestCompositeRefbackTable";
static final String ONT_TABLE = "TestOntology";

static final String BASE_URL = "http://localhost:8080/";
Expand All @@ -38,6 +40,10 @@ class ColumnTypeRdfMapperTest {
static final File TEST_FILE =
new File(classLoader.getResource("testfiles/molgenis.png").getFile());

static final String COLUMN_COMPOSITE_REF = "composite_ref";
static final String COLUMN_COMPOSITE_REF_ARRAY = "composite_ref_array";
static final String COLUMN_COMPOSITE_REFBACK = "composite_refback";

static Database database;
static Schema allColumnTypes;
static Row firstRow;
Expand All @@ -50,33 +56,49 @@ public static void setup() {

// Generates a column for each ColumnType.
// Filters out REFBACK so that it can be added as last step when all REFs are generated.
Column[] columns =
List<Column> columnList =
Arrays.stream(ColumnType.values())
.map((value) -> column(value.name(), value))
.filter((column -> !column.getColumnType().equals(ColumnType.REFBACK)))
.toArray(Column[]::new);
.collect(Collectors.toList());

// Defines column-specific settings.
for (Column column : columns) {
for (Column column : columnList) {
switch (column.getColumnType()) {
case STRING -> column.setPkey();
case REF, REF_ARRAY -> column.setRefTable(REF_TABLE);
case ONTOLOGY, ONTOLOGY_ARRAY -> column.setRefTable(ONT_TABLE);
}
}

// Add extra custom columns for additional tests.
columnList.add(column(COLUMN_COMPOSITE_REF, ColumnType.REF).setRefTable(COMPOSITE_REF_TABLE));
columnList.add(
column(COLUMN_COMPOSITE_REF_ARRAY, ColumnType.REF).setRefTable(COMPOSITE_REF_TABLE));

// Creates tables.
allColumnTypes.create(
// Ontology table
table(ONT_TABLE).setTableType(TableType.ONTOLOGIES),
// Table to ref towards
table(REF_TABLE, column("id", ColumnType.STRING).setPkey()),
// Table to test on
table(TEST_TABLE, columns),
table(TEST_TABLE, columnList.toArray(Column[]::new)),
// Table to get refbacks from
table(
REFBACK_TABLE,
column("id", ColumnType.STRING).setPkey(),
column("ref", ColumnType.REF).setRefTable(TEST_TABLE)),
// Table containing composite primary key to ref towards
table(
COMPOSITE_REF_TABLE,
column("ids", ColumnType.STRING).setPkey(),
column("idi", ColumnType.INT).setPkey()),
// Table containing composite primary key to get refback from
table(
COMPOSITE_REFBACK_TABLE,
column("id1", ColumnType.STRING).setPkey(),

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@BrendaHijmans

BrendaHijmans Dec 12, 2024 •
edited
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Contributor

There are also refbacks and refs and ref_arrays to tables with composite keys with 2+ columns as composite key. Should we also include tests to cover those? or is this covered?

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@svandenhoek

svandenhoek Dec 16, 2024

Author Contributor

I think the main issue is that composite & non-composite have different behaviour, the number of composite keys should not matter (though creating a test shouldn't hurt either).
column("id2", ColumnType.STRING).setPkey(),
column("ref", ColumnType.REF).setRefTable(TEST_TABLE)));

// Adds REFBACK.
Expand All @@ -86,6 +108,9 @@ public static void setup() {
.add(
column(ColumnType.REFBACK.name(), ColumnType.REFBACK)
.setRefTable(REFBACK_TABLE)
.setRefBack("ref"),
column(COLUMN_COMPOSITE_REFBACK, ColumnType.REFBACK)
.setRefTable(COMPOSITE_REFBACK_TABLE)
.setRefBack("ref"));

// Inserts table data
Expand All @@ -98,6 +123,11 @@ public static void setup() {

allColumnTypes.getTable(REF_TABLE).insert(row("id", "1"), row("id", "2"), row("id", "3"));

allColumnTypes
.getTable(COMPOSITE_REF_TABLE)
.insert(
row("ids", "a", "idi", "1"), row("ids", "b", "idi", "2"), row("ids", "c", "idi", "3"));

allColumnTypes
.getTable(TEST_TABLE)
.insert(
Expand Down Expand Up @@ -171,9 +201,25 @@ public static void setup() {
ColumnType.HYPERLINK.name(),
"https://molgenis.org",
ColumnType.HYPERLINK_ARRAY.name(),
"https://molgenis.org, https://github.com/molgenis"));
"https://molgenis.org, https://github.com/molgenis",
// Extra columns for composite key testing
// -- no manual entry: COLUMN_COMPOSITE_REFBACK
COLUMN_COMPOSITE_REF + ".ids",
"a",
COLUMN_COMPOSITE_REF + ".idi",
"1",
COLUMN_COMPOSITE_REF_ARRAY + ".id1",
"b,c",
COLUMN_COMPOSITE_REF_ARRAY + ".id2",
"2,3"),
row(ColumnType.STRING.name(), "secondRowKey"));

allColumnTypes.getTable(REFBACK_TABLE).insert(row("id", "1", "ref", "lonelyString"));
allColumnTypes
.getTable(COMPOSITE_REFBACK_TABLE)
.insert(
row("id1", "a", "id2", "b", "ref", "lonelyString"),
row("id1", "c", "id2", "d", "ref", "secondRowKey"));

// Use query to explicitly retrieve all rows as the following would exclude REFBACK values:
// allColumnTypes.getTable(TEST_TABLE).retrieveRows()
Expand Down Expand Up @@ -251,7 +297,11 @@ void validateValueTypes() {
() -> Assertions.assertTrue(retrieveFirstValue(ColumnType.AUTO_ID.name()).isLiteral()),
() -> Assertions.assertTrue(retrieveFirstValue(ColumnType.ONTOLOGY.name()).isIRI()),
() -> Assertions.assertTrue(retrieveFirstValue(ColumnType.EMAIL.name()).isIRI()),
() -> Assertions.assertTrue(retrieveFirstValue(ColumnType.HYPERLINK.name()).isIRI()));
() -> Assertions.assertTrue(retrieveFirstValue(ColumnType.HYPERLINK.name()).isIRI()),

// Composite keys
() -> Assertions.assertTrue(retrieveFirstValue(COMPOSITE_REF_TABLE).isIRI()),
() -> Assertions.assertTrue(retrieveFirstValue(COMPOSITE_REFBACK_TABLE).isIRI()));
}

@Test
Expand Down Expand Up @@ -395,13 +445,13 @@ void validateValuesRetrieval() {
.matches("[0-9a-zA-Z]+")),
() ->
Assertions.assertEquals(
Set.of(Values.iri(rdfApiUrlPrefix + ONT_TABLE + "?name=aa")),
Set.of(Values.iri(RDF_API_URL_PREFIX + ONT_TABLE + "?name=aa")),
retrieveValues(ColumnType.ONTOLOGY.name())),
() ->
Assertions.assertEquals(
Set.of(
Values.iri(rdfApiUrlPrefix + ONT_TABLE + "?name=bb"),
Values.iri(rdfApiUrlPrefix + ONT_TABLE + "?name=cc")),
Values.iri(RDF_API_URL_PREFIX + ONT_TABLE + "?name=bb"),
Values.iri(RDF_API_URL_PREFIX + ONT_TABLE + "?name=cc")),
retrieveValues(ColumnType.ONTOLOGY_ARRAY.name())),
() ->
Assertions.assertEquals(
Expand All @@ -420,6 +470,23 @@ void validateValuesRetrieval() {
Assertions.assertEquals(
Set.of(
Values.iri("https://molgenis.org"), Values.iri("https://github.com/molgenis")),
retrieveValues(ColumnType.HYPERLINK_ARRAY.name())));
retrieveValues(ColumnType.HYPERLINK_ARRAY.name())),
// Composite reference / refback
() ->
Assertions.assertEquals(
Set.of(Values.iri(RDF_API_URL_PREFIX + COMPOSITE_REF_TABLE + "?ids=a&idi=1")),
retrieveValues(COLUMN_COMPOSITE_REF)),
() ->
Assertions.assertEquals(
Set.of(
Values.iri(RDF_API_URL_PREFIX + COMPOSITE_REF_TABLE + "?ids=b&idi=2"),
Values.iri(RDF_API_URL_PREFIX + COMPOSITE_REF_TABLE + "?ids=c&idi=3")),
retrieveValues(COLUMN_COMPOSITE_REF_ARRAY)),
() ->
Assertions.assertEquals(
Set.of(
Values.iri(RDF_API_URL_PREFIX + COMPOSITE_REFBACK_TABLE + "?id1=a&id2=b"),
Values.iri(RDF_API_URL_PREFIX + COMPOSITE_REFBACK_TABLE + "?id1=c&id2=d")),
retrieveValues(COLUMN_COMPOSITE_REFBACK)));
}
}

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