Examples with MolgenisException org.molgenis.emx2.MolgenisException used on opensource projects

Example 11 with MolgenisException

use of org.molgenis.emx2.MolgenisException in project molgenis-emx2 by molgenis.

the class ExcelApi method getExcelTable.

static String getExcelTable(Request request, Response response) throws IOException {
    Table table = getTable(request);
    if (table == null)
        throw new MolgenisException("Table " + request.params(TABLE) + " unknown");
    Path tempDir = Files.createTempDirectory(MolgenisWebservice.TEMPFILES_DELETE_ON_EXIT);
    tempDir.toFile().deleteOnExit();
    try (OutputStream outputStream = response.raw().getOutputStream()) {
        Path excelFile = tempDir.resolve("download.xlsx");
        MolgenisIO.toExcelFile(excelFile, table);
        response.type("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
        response.header("Content-Disposition", "attachment; filename=" + table.getSchema().getMetadata().getName() + "_" + table.getName() + System.currentTimeMillis() + ".xlsx");
        outputStream.write(Files.readAllBytes(excelFile));
        return "Export success";
    }
}

Example 12 with MolgenisException

use of org.molgenis.emx2.MolgenisException in project molgenis-emx2 by molgenis.

the class FileApi method getFile.

public static String getFile(Request request, Response response) throws IOException {
    String tableName = request.params("table");
    String columnName = request.params("column");
    String id = request.params("id");
    Schema schema = getSchema(request);
    Table t = schema.getTable(tableName);
    if (t == null) {
        throw new MolgenisException("Download failed: Table '" + tableName + "' not found in schema " + schema.getName());
    }
    Column c = t.getMetadata().getColumn(columnName);
    if (c == null) {
        throw new MolgenisException("Download failed: Column '" + columnName + "' not found in table " + schema.getName() + "." + tableName);
    }
    List<Row> result = t.query().select(t.getMetadata().getPrimaryKeyFields().stream().map(f -> s(f.getName())).toArray(SelectColumn[]::new)).select(s(columnName, s("contents"), s("mimetype"), s("extension"))).where(f(columnName, f("id", EQUALS, id))).retrieveRows();
    if (result.size() != 1) {
        throw new MolgenisException("Download failed: file id '" + id + "' not found in table " + tableName);
    }
    String ext = result.get(0).getString(columnName + "_extension");
    String mimetype = result.get(0).getString(columnName + "_mimetype");
    byte[] contents = result.get(0).getBinary(columnName + "_contents");
    response.raw().setHeader("Content-Disposition", "attachment; filename=" + c.getName() + "." + ext);
    response.raw().setContentType(mimetype);
    try (OutputStream out = response.raw().getOutputStream()) {
        // autoclosing
        out.write(contents);
        out.flush();
    }
    return "";
}

Example 13 with MolgenisException

use of org.molgenis.emx2.MolgenisException in project molgenis-emx2 by molgenis.

the class GraphqlApi method getVariablesFromRequest.

private static Map<String, Object> getVariablesFromRequest(Request request) {
    if ("POST".equals(request.requestMethod())) {
        try {
            if (request.headers("Content-Type").startsWith("multipart/form-data")) {
                Map<String, Object> variables = new ObjectMapper().readValue(request.queryParams(VARIABLES), Map.class);
                // now replace each part id with the part
                putPartsIntoMap(variables, request.raw().getParts().stream().filter(p -> !p.getName().equals(VARIABLES) && !p.getName().equals(QUERY)).collect(Collectors.toList()));
                // 
                return variables;
            } else {
                Map<String, Object> node = new ObjectMapper().readValue(request.body(), Map.class);
                return (Map<String, Object>) node.get(VARIABLES);
            }
        } catch (Exception e) {
            throw new MolgenisException("Parsing of graphql variables failed. Should be an object with each graphql variable a key. " + e.getMessage(), e);
        }
    }
    return null;
}

Example 14 with MolgenisException

use of org.molgenis.emx2.MolgenisException in project molgenis-emx2 by molgenis.

the class TestReadWriteStores method executeTest.

public static void executeTest(TableStore store) throws IOException, MolgenisException {
    List<Row> rows = new ArrayList<>();
    int count = 10;
    for (int i = 1; i <= count; i++) {
        rows.add(new Row().setString("stringCol", "test" + i).setInt("intCol", i).setDecimal("decimalCol", Double.valueOf(i / 2)).setUuid("uuidCol", UUID.randomUUID()).setDate("dateCol", LocalDate.of(2019, 12, 12)).setDateTime("datetimeCol", LocalDateTime.now()).setBool("boolCol", true).setStringArray("stringarrayCol", new String[] { "a", "b,including comma," }).setIntArray("intarrayCol", new Integer[] { 1, 2 }).setDecimalArray("doubleArrayCol", new Double[] { 1.0, 2.0 }).setDecimalArray("doubleArrayCol", new Double[] { 1.0, 2.0 }).setDateArray("dateArray", new LocalDate[] { LocalDate.of(2019, 12, 12), LocalDate.of(2019, 12, 12) }).setDateTimeArray("datetimeArrayCol", new LocalDateTime[] { LocalDateTime.now(), LocalDateTime.now() }).setBoolArray("booleanArrayCol", new Boolean[] { true, false }));
    }
    StopWatch.start("created some rows");
    // write them
    store.writeTable("test", List.of(), rows);
    store.writeTable("test2", List.of(), rows);
    StopWatch.print("wrote them to " + store.getClass().getSimpleName(), count);
    List<Row> rows2 = StreamSupport.stream(store.readTable("test2").spliterator(), false).collect(Collectors.toList());
    // for (Row r : rows2) System.out.println(r);
    StopWatch.print("fromReader them back from " + store.getClass().getSimpleName(), count);
    // compare
    CompareTools.assertEquals(rows, rows2);
    // write another one
    store.writeTable("test3", List.of(), rows);
    StopWatch.print("wrote them to " + store.getClass().getSimpleName(), count);
    rows2 = StreamSupport.stream(store.readTable("test3").spliterator(), false).collect(Collectors.toList());
    // for (Row r : rows2) System.out.println(r);
    StopWatch.print("fromReader them back from " + store.getClass().getSimpleName(), count);
    // compare
    CompareTools.assertEquals(rows, rows2);
    StopWatch.print("compared succesfully");
    // write empty
    store.writeTable("test4", List.of("empty"), new ArrayList<>());
    // test that reading store that doesn't exist errors properly
    try {
        store.readTable("fake");
        fail("should have failed");
    } catch (MolgenisException me) {
        System.out.println("errored correctly:" + me);
    }
}

Example 15 with MolgenisException

use of org.molgenis.emx2.MolgenisException in project molgenis-emx2 by molgenis.

the class TestReadWriteStores method testExcelStore.

@Test
public void testExcelStore() throws IOException {
    Path tmp = Files.createTempDirectory(null);
    try {
        Path excelFile = tmp.resolve("test.xlsx");
        System.out.println("defined excel file " + excelFile);
        TableStoreForXlsxFile store = new TableStoreForXlsxFile(excelFile);
        executeTest(store);
    } catch (MolgenisException e) {
        e.printStackTrace();
    } finally {
        Files.walk(tmp).sorted(Comparator.reverseOrder()).map(Path::toFile).forEach(File::delete);
    }
    if (Files.exists(tmp))
        throw new RuntimeException("TMP directory " + tmp + " not deleted. This should never happen.");
}