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

Example 1 with Step

use of org.molgenis.emx2.tasks.Step 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 Step

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

the class SqlTable method insertBatch.

private static int insertBatch(SqlTable table, List<Row> rows, boolean updateOnConflict, Set<String> updateColumns) {
    boolean inherit = table.getMetadata().getInherit() != null;
    if (inherit) {
        SqlTable inheritedTable = table.getInheritedTable();
        inheritedTable.insertBatch(inheritedTable, rows, updateOnConflict, updateColumns);
    }
    // get metadata
    Set<Column> columns = table.getColumnsToBeUpdated(updateColumns);
    // check that columns exist for validation
    checkForMissingVariablesColumns(columns);
    List<Column> allColumns = table.getMetadata().getMutationColumns();
    List<Field> insertFields = columns.stream().map(c -> c.getJooqField()).collect(Collectors.toList());
    if (!inherit) {
        insertFields.add(field(name(MG_INSERTEDBY)));
        insertFields.add(field(name(MG_INSERTEDON)));
        insertFields.add(field(name(MG_UPDATEDBY)));
        insertFields.add(field(name(MG_UPDATEDON)));
    }
    // define the insert step
    InsertValuesStepN<org.jooq.Record> step = table.getJooq().insertInto(table.getJooqTable(), insertFields.toArray(new Field[0]));
    // add all the rows as steps
    String user = table.getSchema().getDatabase().getActiveUser();
    if (user == null) {
        user = ADMIN_USER;
    }
    LocalDateTime now = LocalDateTime.now();
    for (Row row : rows) {
        // get values
        Map values = SqlTypeUtils.getValuesAsMap(row, columns);
        if (!inherit) {
            values.put(MG_INSERTEDBY, user);
            values.put(MG_INSERTEDON, now);
            values.put(MG_UPDATEDBY, user);
            values.put(MG_UPDATEDON, now);
        }
        // when insert, we should include all columns, not only 'updateColumns'
        if (!row.isDraft()) {
            checkRequired(row, allColumns);
            checkValidation(values, columns);
        }
        step.values(values.values());
    }
    // optionally, add conflict clause
    if (updateOnConflict) {
        InsertOnDuplicateSetStep<org.jooq.Record> step2 = step.onConflict(table.getMetadata().getPrimaryKeyFields().toArray(new Field[0])).doUpdate();
        for (Column column : columns) {
            step2.set(column.getJooqField(), (Object) field(unquotedName("excluded.\"" + column.getName() + "\"")));
        }
        if (!inherit) {
            step2.set(field(name(MG_UPDATEDBY)), user);
            step2.set(field(name(MG_UPDATEDON)), now);
        }
    }
    return step.execute();
}

Example 3 with Step

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

the class GraphqlApi method executeQuery.

private static String executeQuery(GraphQL g, Request request) throws IOException {
    String query = getQueryFromRequest(request);
    Map<String, Object> variables = getVariablesFromRequest(request);
    long start = System.currentTimeMillis();
    // we don't log password calls
    if (logger.isInfoEnabled()) {
        if (query.contains("password")) {
            logger.info("query: obfuscated because contains parameter with name 'password'");
        } else {
            logger.info("query: {}", query.replaceAll("[\n|\r|\t]", "").replaceAll(" +", " "));
        }
    }
    // tests show overhead of this step is about 20ms (jooq takes the rest)
    ExecutionResult executionResult = null;
    if (variables != null) {
        executionResult = g.execute(ExecutionInput.newExecutionInput(query).variables(variables));
    } else {
        executionResult = g.execute(query);
    }
    String result = GraphqlApiFactory.convertExecutionResultToJson(executionResult);
    for (GraphQLError err : executionResult.getErrors()) {
        if (logger.isErrorEnabled()) {
            logger.error(err.getMessage());
        }
    }
    if (executionResult.getErrors().size() > 0) {
        throw new MolgenisException("Error", executionResult.getErrors().get(0).getMessage());
    }
    if (logger.isInfoEnabled())
        logger.info("graphql request completed in {}ms", +(System.currentTimeMillis() - start));
    return result;
}