Examples with Schema com.google.cloud.datacatalog.v1beta1.Schema used on opensource projects

Example 46 with Schema

use of com.google.cloud.datacatalog.v1beta1.Schema in project molgenis-emx2 by molgenis.

the class CatalogueSiteMapTest method buildSiteMap.

@Test
public void buildSiteMap() {
    Schema schema = mock(Schema.class);
    Table table = mock(Table.class);
    Query query = mock(Query.class);
    List<Row> row = Collections.singletonList(new Row("pid", "my-cohort-pid"));
    when(schema.getTable("Cohorts")).thenReturn(table);
    when(table.select(any())).thenReturn(query);
    when(query.retrieveRows()).thenReturn(row);
    CatalogueSiteMap catalogueSiteMap = new CatalogueSiteMap(schema, "https://my/base/url");
    String expected = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<urlset xmlns=\"http://www.sitemaps.org/schemas/sitemap/0.9\" >\n" + "  <url>\n" + "    <loc>https://my/base/url/ssr-catalogue/Cohorts/my-cohort-pid</loc>\n" + "  </url>\n" + "</urlset>";
    assertEquals(expected, catalogueSiteMap.buildSiteMap());
}

Example 47 with Schema

use of com.google.cloud.datacatalog.v1beta1.Schema in project molgenis-emx2 by molgenis.

the class MolgenisSession method getGraphqlForSchema.

public GraphQL getGraphqlForSchema(String schemaName) {
    logger.info("getting graphql schema '{}' for user '{}'", schemaName, getSessionUser());
    if (graphqlPerSchema.get(schemaName) == null) {
        Schema schema = database.getSchema(schemaName);
        if (schema == null)
            throw new MolgenisException("Schema not found: Schema with name '" + schemaName + "' does not exist or permission denied");
        graphqlPerSchema.put(schemaName, new GraphqlApiFactory().createGraphqlForSchema(schema, TaskApi.taskService));
        logger.info("created graphql schema '{}' for user '{}'", schemaName, getSessionUser());
    }
    logger.info("return graphql schema '{}' for user '{}'", schemaName, getSessionUser());
    return graphqlPerSchema.get(schemaName);
}

Example 48 with Schema

use of com.google.cloud.datacatalog.v1beta1.Schema in project molgenis-emx2 by molgenis.

the class Benchmark method testCopyInAndOut.

public void testCopyInAndOut() {
    Database database = TestDatabaseFactory.getTestDatabase();
    Schema schema = database.dropCreateSchema(Benchmark.class.getSimpleName());
    int aSize = 50;
    int bSize = 100000;
    Table a = schema.create(table("TableA").add(column("ID").setPkey()));
    List<String> values = new ArrayList<>();
    Table b = schema.create(table("TableB").add(column("ID").setPkey()).add(column("ref").setType(REF_ARRAY).setRefTable("TableA")));
    // Table c =
    // schema.create(
    // table("TableC")
    // .add(column("ID").setPkey())
    // .add(column("ref").setType(MREF).setRefTable("TableA")));
    StopWatch.start("benchmark started");
    List<Row> aRows = new ArrayList<>();
    for (int i = 0; i < aSize; i++) {
        aRows.add(new Row().set("ID", "row" + i));
        values.add("row" + i);
    }
    StopWatch.start("benchmark1");
    a.insert(aRows);
    StopWatch.print("inserted primary", aSize);
    aRows.clear();
    List<Row> bRows = new ArrayList<>();
    for (int i = 0; i < bSize; i++) {
        bRows.add(new Row().set("ID", "row" + i).set("ref", values));
    }
    StopWatch.start("benchmark2 started");
    b.insert(bRows);
    StopWatch.print("inserted ref_array", bSize);
    bRows.clear();
// List<Row> cRows = new ArrayList<>();
// for (int i = 0; i < bSize; i++) {
// cRows.add(new Row().set("ID", "row" + i).set("ref", values));
// }
// StopWatch.start("benchmark3 started");
// c.insert(cRows);
// StopWatch.print("inserted mref", bSize);
// cRows.clear();
// StopWatch.print("inserted mref", bSize);
// ref_array
}

Example 49 with Schema

use of com.google.cloud.datacatalog.v1beta1.Schema in project molgenis-emx2 by molgenis.

the class TestCompositeForeignKeys method testCompositeRef.

@Test
public void testCompositeRef() {
    Schema schema = database.dropCreateSchema(TestCompositeForeignKeys.class.getSimpleName() + "Ref");
    schema.create(table("Person", column("firstName").setPkey(), column("lastName").setPkey(), column("uncle", REF).setRefTable("Person")));
    Table p = schema.getTable("Person");
    p.insert(new Row().setString("firstName", "Donald").setString("lastName", "Duck"));
    try {
        p.insert(new Row().setString("firstName", "Kwik").setString("lastName", "Duck").setString("uncle.firstName", "Donald").setString("uncle.lastName", "MISSING"));
        fail("should have failed on missing foreign key");
    } catch (Exception e) {
        System.out.println("errored correctly: " + e);
    }
    p.insert(new Row().setString("firstName", "Kwik").setString("lastName", "Duck").setString("uncle.firstName", "Donald").setString("uncle.lastName", "Duck"));
    p.insert(new Row().setString("firstName", "Kwek").setString("lastName", "Duck").setString("uncle.firstName", "Donald").setString("uncle.lastName", "Duck"));
    p.insert(new Row().setString("firstName", "Kwak").setString("lastName", "Duck").setString("uncle.firstName", "Donald").setString("uncle.lastName", "Duck"));
    try {
        p.delete(new Row().setString("firstName", "Donald").setString("lastName", "Duck"));
        fail("should have failed on foreign key (Donald is used in foreign key)");
    } catch (Exception e) {
        System.out.println("errored correctly: " + e);
    }
    schema.create(table("Student").setInherit("Person"));
    Table s = schema.getTable("Student");
    s.insert(new Row().setString("firstName", "Mickey").setString("lastName", "Mouse").setString("uncle.firstName", "Kwik").setString("uncle.lastName", "Duck"));
    String result = schema.query("Student", s("firstName"), s("lastName"), s("uncle", s("firstName"), s("lastName")), s("uncle", s("firstName"), s("lastName"))).retrieveJSON();
    System.out.println(result);
    result = schema.query("Student").select(s("firstName"), s("lastName")).where(or(and(f("firstName", EQUALS, "Donald"), f("lastName", EQUALS, "Duck")), and(f("firstName", EQUALS, "Mickey"), f("lastName", EQUALS, "Mouse")))).retrieveJSON();
    System.out.println(result);
    assertTrue(result.contains("Mouse"));
    assertFalse(result.contains("Duck"));
    result = schema.query("Person").select(s("firstName"), s("lastName")).where(or(and(f("firstName", EQUALS, "Donald"), f("lastName", EQUALS, "Duck")), and(f("firstName", EQUALS, "Mickey"), f("lastName", EQUALS, "Mouse")))).retrieveJSON();
    System.out.println(result);
    assertTrue(result.contains("Mouse"));
    assertTrue(result.contains("Duck"));
    // composite key filter
    result = schema.query("Person").select(s("firstName"), s("lastName")).where(f("uncle", or(and(f("firstName", EQUALS, "Donald"), f("lastName", EQUALS, "Duck")), and(f("firstName", EQUALS, "Mickey"), f("lastName", EQUALS, "Mouse"))))).retrieveJSON();
    System.out.println(result);
    assertTrue(result.contains("Kwik"));
    assertFalse(result.contains("Mouse"));
    // refback
    schema.getTable("Person").getMetadata().add(column("nephew").setType(REFBACK).setRefTable("Person").setRefBack("uncle"));
    s.insert(new Row().setString("firstName", "Katrien").setString("lastName", "Duck").setString("nephew.firstName", "Kwik").setString("nephew.lastName", // I know, not true
    "Duck"));
    assertTrue(List.of(s.query().select(s("firstName"), s("lastName"), s("nephew", s("firstName"), s("lastName")), s("uncle", s("firstName"), s("lastName"))).where(f("firstName", EQUALS, "Katrien")).retrieveRows().get(0).getStringArray("nephew-firstName")).contains("Kwik"));
    assertTrue(List.of(p.query().select(s("firstName"), s("lastName"), s("nephew", s("firstName"), s("lastName")), s("uncle", s("firstName"), s("lastName"))).where(f("firstName", EQUALS, "Kwik")).retrieveRows().get(0).getStringArray("uncle-firstName")).contains("Katrien"));
    // test order by for refback
    p.query().select(s("firstName"), s("lastName"), s("nephew", s("firstName"), s("lastName")), s("uncle", s("firstName"), s("lastName"))).orderBy("nephew").retrieveJSON();
}

Example 50 with Schema

use of com.google.cloud.datacatalog.v1beta1.Schema in project molgenis-emx2 by molgenis.

the class TestRowLevelSecurity method testRls.

@Test
public void testRls() {
    try {
        // create schema
        Schema s = database.dropCreateSchema(TEST_RLS);
        // create two users
        database.addUser(TEST_RLS_HAS_NO_PERMISSION);
        assertEquals(true, database.hasUser(TEST_RLS_HAS_NO_PERMISSION));
        database.addUser(TESTRLS_HAS_RLS_VIEW);
        // grant both owner on TestRLS schema so can add row level security
        s.addMember("testrls1", Privileges.OWNER.toString());
        s.addMember("testrls2", Privileges.OWNER.toString());
        s.addMember(TESTRLS_HAS_RLS_VIEW, // can view table but only rows with right RLS
        Privileges.VIEWER.toString());
        // let one user create the table
        database.setActiveUser("testrls1");
        database.tx(db -> {
            db.getSchema(TEST_RLS).create(table(TEST_RLS).add(column("col1").setPkey()));
        });
        // let the other user add RLS
        database.setActiveUser("testrls2");
        database.tx(db -> {
            db.getSchema(TEST_RLS).getTable(TEST_RLS).getMetadata().enableRowLevelSecurity();
        });
        // let the first add a row (checks if admin permissions are setup correctly)
        database.setActiveUser("testrls1");
        database.tx(db -> {
            db.getSchema(TEST_RLS).getTable(TEST_RLS).insert(new Row().setString("col1", "Hello World").set(MG_EDIT_ROLE, TESTRLS_HAS_RLS_VIEW), new Row().setString("col1", "Hello World2").set(MG_EDIT_ROLE, TEST_RLS_HAS_NO_PERMISSION));
        });
        // let the second admin see it
        database.setActiveUser("testrls2");
        database.tx(db -> {
            assertEquals(2, db.getSchema(TEST_RLS).getTable(TEST_RLS).retrieveRows().size());
        });
        // have RLS user query and see one row
        database.setActiveUser(TESTRLS_HAS_RLS_VIEW);
        database.tx(db -> {
            assertEquals(1, db.getSchema(TEST_RLS).getTable(TEST_RLS).retrieveRows().size());
        });
        database.becomeAdmin();
        database.removeUser(TESTRLS_HAS_RLS_VIEW);
        assertEquals(false, database.hasUser(TESTRLS_HAS_RLS_VIEW));
    } finally {
        database.becomeAdmin();
    }
}