Examples with Task org.molgenis.emx2.tasks.Task used on opensource projects

Example 1 with Task

use of org.molgenis.emx2.tasks.Task in project molgenis-emx2 by molgenis.

the class ImportSchemaTask method rollback.

private void rollback(Task task) {
    for (Step step : task.getSteps()) {
        if (step.getStatus().equals(COMPLETED)) {
            step.setStatus(SKIPPED);
            step.setDescription("Rolled back: " + step.getDescription());
        }
        if (step instanceof Task) {
            this.rollback((Task) step);
        }
    }
}

Example 2 with Task

use of org.molgenis.emx2.tasks.Task in project molgenis-emx2 by molgenis.

the class ImportDataTask method run.

@Override
public void run() {
    this.start();
    // create a task for each table
    boolean skipped = true;
    // create task for the import, including subtasks for each sheet
    for (Table table : schema.getTablesSorted()) {
        if (tableStore.containsTable(table.getName())) {
            ImportTableTask importTableTask = new ImportTableTask(tableStore, table, isStrict());
            this.addSubTask(importTableTask);
            importTableTask.run();
            skipped = false;
        }
    }
    // check what files we skipped
    Collection<String> tableNames = schema.getTableNames();
    try {
        for (String sheet : tableStore.tableNames()) {
            if (!sheet.startsWith("_files/") && !"molgenis".equals(sheet) && !"molgenis_settings".equals(sheet) && !"molgenis_members".equals(sheet) && !tableNames.contains(sheet)) {
                this.addSubTask("Sheet with name '" + sheet + "' was skipped: no table with that name found").setSkipped();
            }
        }
    } catch (UnsupportedOperationException e) {
    // ignore, not important
    }
    // execute the import tasks
    if (skipped) {
        this.addSubTask("Import data skipped: No data sheet included").setSkipped();
    }
    this.complete();
}

Example 3 with Task

use of org.molgenis.emx2.tasks.Task in project molgenis-emx2 by molgenis.

the class WebApiSmokeTests method testExcelApi.

@Test
public void testExcelApi() throws IOException, InterruptedException {
    // download json schema
    String schemaCSV = given().sessionId(SESSION_ID).accept(ACCEPT_CSV).when().get("/pet store/api/csv").asString();
    // create a new schema for excel
    db.dropCreateSchema("pet store excel");
    // download excel contents from schema
    byte[] excelContents = given().sessionId(SESSION_ID).accept(ACCEPT_EXCEL).when().get("/pet store/api/excel").asByteArray();
    File excelFile = createTempFile(excelContents, ".xlsx");
    // upload excel into new schema
    String message = given().sessionId(SESSION_ID).multiPart(excelFile).when().post("/pet store excel/api/excel?async=true").asString();
    Map<String, String> val = new ObjectMapper().readValue(message, Map.class);
    String url = val.get("url");
    String id = val.get("id");
    // poll task until complete
    Response poll = given().sessionId(SESSION_ID).when().get(url);
    int count = 0;
    // (previously we checked on 'complete' but then it also fired if subtask was complete)
    while (poll.body().asString().contains("UNKNOWN") || poll.body().asString().contains("RUNNING")) {
        if (count++ > 100) {
            throw new MolgenisException("failed: polling took too long");
        }
        poll = given().sessionId(SESSION_ID).when().get(url);
        Thread.sleep(500);
    }
    // check if id in tasks list
    assertTrue(given().sessionId(SESSION_ID).multiPart(excelFile).when().get("/pet store/api/tasks").asString().contains(id));
    // check if schema equal using json representation
    String schemaCSV2 = given().sessionId(SESSION_ID).accept(ACCEPT_CSV).when().get("/pet store excel/api/csv").asString();
    assertTrue(schemaCSV2.contains("Pet"));
    // delete a new schema for excel
    db.dropSchema("pet store excel");
}

Example 4 with Task

use of org.molgenis.emx2.tasks.Task in project molgenis-emx2 by molgenis.

the class DummyTask method run.

@Override
public void run() {
    start();
    System.out.println("started");
    for (Task t : this) {
        t.start();
        for (int item = 1; item <= noItems; item++) {
            try {
                Thread.sleep(5);
            } catch (InterruptedException e) {
                throw new MolgenisException("Error", e);
            }
            t.setProgress(item);
        }
        t.complete();
    }
    complete();
}

Example 5 with Task

use of org.molgenis.emx2.tasks.Task in project molgenis-emx2 by molgenis.

the class TestGraphqSchemaFields method testTasksApi.

@Test
public void testTasksApi() throws IOException {
    // fake something into taskservice
    Task task = new Task("test");
    task.addSubTask(new Task("subtest"));
    taskService.submit(task);
    // list all tasks
    assertTrue(execute("{_tasks{id,description,status}}").at("/_tasks/0/description").textValue().startsWith("test"));
    // load single task
    assertTrue(execute("{_tasks(id:\"" + task.getId() + "\"){id,description,status,subTasks{id,description,status,subTasks{id,description,status}}}}").at("/_tasks/0/description").textValue().startsWith("test"));
}