CSC553 Lab 1: SimpleDB

DEADLINES

Part 1 due: Sunday, April 3 12:00PM
Due: Thursday, April 14 12:00 PM

IMPORTANT: * You must use Git and commit all your changes. * Part 1 should take about 1 hour (if all goes well) and it's mostly just there to make sure you get set up with the lab early. * Part 2 requires a significant amount of time... really significant! It requires reading the code that we provide, figuring out how everything should work together, and then writing quite a bit of code yourself.

Version History:

• March 1st: First revision.

In the lab assignments in CSC553 you will write a basic database management system called SimpleDB. For this lab, you will focus on implementing the core modules required to access stored data on disk; in future labs, you will add support for various query processing operators, as well as transactions, locking, and concurrent queries.

SimpleDB is written in Java. We have provided you with a set of mostly unimplemented classes and interfaces. You will need to write the code for these classes. We will grade your code by running a set of system tests written using JUnit. We have also provided a number of unit tests, which we will not use for grading but that you may find useful in verifying that your code works.

The remainder of this document describes the basic architecture of SimpleDB, gives some suggestions about how to start coding, and discusses how to hand in your lab.

We strongly recommend that you start as early as possible on this lab. It requires you to write a fair amount of code!

1. Getting started

These instructions are written for a Unix-based platform (e.g., Linux, MacOS, etc.) Because the code is written in Java, it should work under Windows as well, though the directions in this document may not apply.

Download the code from http://dice.cs.depaul.edu/courses/553/labs/lab1/CSC553-lab1.tar.gz and untar it. For example:

$ wget http://dice.cs.depaul.edu/courses/553/labs/lab1/CSC553-lab1.tar.gz
$ tar xvzf CSC553-lab1.tar.gz
$ cd CSC553-lab1

SimpleDB uses the Ant build tool to compile the code and run tests. Ant is similar to make, but the build file is written in XML and is somewhat better suited to Java code. Most modern Linux distributions include Ant.

Download Ant from http://dice.cs.depaul.edu/courses/553/labs/lab1/apache-ant-1.10.12-bin.tar.gz and untar it.

To help you during development, we have provided a set of unit tests in addition to the end-to-end tests that we use for grading. These are by no means comprehensive, and you should not rely on them exclusively to verify the correctness of your project.

To run the unit tests use the test build target:

$ cd CSC553-lab1
$ # run all unit tests
$ ant test
$ # run a specific unit test
$ ant runtest -Dtest=TupleTest

# build output...

test:
    [junit] Running simpledb.CatalogTest
    [junit] Testsuite: simpledb.CatalogTest
    [junit] Tests run: 2, Failures: 0, Errors: 2, Time elapsed: 0.037 sec
    [junit] Tests run: 2, Failures: 0, Errors: 2, Time elapsed: 0.037 sec

# ... stack traces and error reports ...

The output above indicates that two errors occurred during compilation; this is because the code we have given you doesn't yet work. As you complete parts of the lab, you will work towards passing additional unit tests. If you wish to write new unit tests as you code, they should be added to the test/simpledb directory.

For more details about how to use Ant, see the manual. The Running Ant section provides details about using the ant command. However, the quick reference table below should be sufficient for working on the labs.

1.1. Running end-to-end tests

We have also provided a set of end-to-end tests that will eventually be used for grading. These tests are structured as JUnit tests that live in the test/simpledb/systemtest directory. To run all the system tests, use the systemtest build target:

$ ant systemtest

# ... build output ...

    [junit] Testcase: testSmall took 0.017 sec
    [junit] 	Caused an ERROR
    [junit] expected to find the following tuples:
    [junit] 	19128
    [junit]
    [junit] java.lang.AssertionError: expected to find the following tuples:
    [junit] 	19128
    [junit]
    [junit] 	at simpledb.systemtest.SystemTestUtil.matchTuples(SystemTestUtil.java:122)
    [junit] 	at simpledb.systemtest.SystemTestUtil.matchTuples(SystemTestUtil.java:83)
    [junit] 	at simpledb.systemtest.SystemTestUtil.matchTuples(SystemTestUtil.java:75)
    [junit] 	at simpledb.systemtest.ScanTest.validateScan(ScanTest.java:30)
    [junit] 	at simpledb.systemtest.ScanTest.testSmall(ScanTest.java:40)

# ... more error messages ...

This indicates that this test failed, showing the stack trace where the error was detected. To debug, start by reading the source code where the error occurred. Look at both your source code and the source code of the unit test. When the tests pass, you will see something like the following:

$ ant systemtest

# ... build output ...

    [junit] Testsuite: simpledb.systemtest.ScanTest
    [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 7.278 sec
    [junit] Tests run: 3, Failures: 0, Errors: 0, Time elapsed: 7.278 sec
    [junit]
    [junit] Testcase: testSmall took 0.937 sec
    [junit] Testcase: testLarge took 5.276 sec
    [junit] Testcase: testRandom took 1.049 sec

BUILD SUCCESSFUL
Total time: 52 seconds

1.1.1 Creating dummy tables

$ java -jar dist/simpledb.jar convert file.txt N

int1,int2,...,intN
int1,int2,...,intN
int1,int2,...,intN
int1,int2,...,intN

...where each intN is a non-negative integer.

To view the contents of a table, use the print command:

$ java -jar dist/simpledb.jar print file.dat N

where file.dat is the name of a table created with the convert command, and N is the number of columns in the file.

1.2. Working in Eclipse

Eclipse is a graphical software development environment that you might be more comfortable with working in. The instructions we provide were generated by using Eclipse 3.5.2 (Galileo) for Java Developers (not the enterprise edition) with Java 1.6.0_20 on Ubuntu 10.04 LTS. They should also work under Windows or on MacOS.

Setting the Lab Up in Eclipse

• Once Eclipse is installed, start it, and note that the first screen asks you to select a location for your workspace (we will refer to this directory as $W).
• On the file system, copy CSC553-lab1.tar.gz to $W/CSC553-lab1.tar.gz. Un-GZip and un-tar it, which will create a directory $W/CSC553-lab1 (to do this, you can type tar -pzxvf CSC553-lab1.tar.gz).
• Under terminal, cd $W/CSC553-lab1.
• Run ant eclipse. The eclipse ant target will generate the eclipse meta files .project and .classpath under $W/CSC553-lab1.
• Import the generated project to Eclipse using the steps here

Note: that this class assumes that you are using the official Sun release of Java. This is the default on MacOS X, and for most Windows Eclipse installs; but many Linux distributions default to alternate Java runtimes (like OpenJDK). There should be no problems using these alternatives. But if you meet any problems , these instructions for Ubuntu Linux may be of help in switching Java versions.

Running Individual Unit and System Tests

To run a unit test or system test (both are JUnit tests, and can be initialized the same way), go to the Package Explorer tab on the left side of your screen. Under the "CSC553-lab1" project, open the "test" directory. Unit tests are found in the "simpledb" package, and system tests are found in the "simpledb.systemtests" package. To run one of these tests, select the test (they are all called *Test.java - don't select TestUtil.java or SystemTestUtil.java), right click on it, select "Run As," and select "JUnit Test." This will bring up a JUnit tab, which will tell you the status of the individual tests within the JUnit test suite, and will show you exceptions and other errors that will help you debug problems.

Running Ant Build Targets

If you want to run commands such as "ant test" or "ant systemtest," right click on build.xml in the Package Explorer. Select "Run As," and then "Ant Build..." (note: select the option with the ellipsis (...), otherwise you won't be presented with a set of build targets to run). Then, in the "Targets" tab of the next screen, check off the targets you want to run (probably "dist" and one of "test" or "systemtest"). This should run the build targets and show you the results in Eclipse's console window.

1.3. Implementation hints

Before beginning to write code, we strongly encourage you to read through this entire document to get a feel for the high-level design of SimpleDB.

You will need to fill in any piece of code that is not implemented. It will be obvious where we think you should write code. You may need to add private methods and/or helper classes. You may change APIs, but make sure our grading tests still run and make sure to mention, explain, and defend your decisions in your writeup.

In addition to the methods that you need to fill out for this lab, the class interfaces contain numerous methods that you need not implement until subsequent labs. These will either be indicated per class:

// Not necessary for lab1.
public class Insert implements DbIterator {

public boolean deleteTuple(Tuple t) throws DbException {
    // some code goes here
    // not necessary for lab1
    return false;
}

We suggest exercises along this document to guide your implementation, but you may find that a different order makes more sense for you. Here's a rough outline of one way you might proceed with your SimpleDB implementation:

• Implement the classes to manage tuples, namely Tuple, TupleDesc. We have already implemented Field, IntField, StringField, and Type for you. Since you only need to support integer and (fixed length) string fields and fixed length tuples, these are straightforward.
• Implement the Catalog (this should be very simple).
• Implement the BufferPool constructor and the getPage() method.
• Implement the access methods, HeapPage and HeapFile and associated ID classes. A good portion of these files has already been written for you.
• Implement the operator SeqScan.
• At this point, you should be able to pass the ScanTest system test, which is the goal for this lab.

  Section 2 below walks you through these implementation steps and the unit tests corresponding to each one in more detail.

1.4. Transactions, locking, and recovery

2. SimpleDB Architecture and Implementation Guide

• Classes that represent fields, tuples, and tuple schemas;
• Classes that apply predicates and conditions to tuples;
• One or more access methods (e.g., heap files) that store relations on disk and provide a way to iterate through tuples of those relations;
• A collection of operator classes (e.g., select, join, insert, delete, etc.) that process tuples;
• A buffer pool that caches active tuples and pages in memory and handles concurrency control and transactions (neither of which you need to worry about for this lab); and,
• A catalog that stores information about available tables and their schemas.

SimpleDB does not include many things that you may think of as being a part of a "database." In particular, SimpleDB does not have:

• (In this lab), a SQL front end or parser that allows you to type queries directly into SimpleDB. Instead, queries are built up by chaining a set of operators together into a hand-built query plan (see Section 2.7). We will provide a simple parser for use in later labs.
• Views.
• Data types except integers and fixed length strings.
• (In this lab) Query optimizer.
• Indices.

In the rest of this Section, we describe each of the main components of SimpleDB that you will need to implement in this lab. You should use the exercises in this discussion to guide your implementation. This document is by no means a complete specification for SimpleDB; you will need to make decisions about how to design and implement various parts of the system. Note that for Lab 1 you do not need to implement any operators (e.g., select, join, project) except sequential scan. You will add support for additional operators in future labs.

2.1. The Database Class

2.2. Fields and Tuples

Tuples in SimpleDB are quite basic. They consist of a collection of Field objects, one per field in the Tuple. Field is an interface that different data types (e.g., integer, string) implement. Tuple objects are created by the underlying access methods (e.g., heap files, or B-trees), as described in the next section. Tuples also have a type (or schema), called a tuple descriptor, represented by a TupleDesc object. This object consists of a collection of Type objects, one per field in the tuple, each of which describes the type of the corresponding field.

End of Part 1. For this part of the lab, please submit your implementation of TupleDesc.java and Tuple.java (see the end of the assignment instructions for dropbox link). Submitting the first part of lab 1 on time is worth 10% of your final grade for lab 1 and will be graded all-or-nothing.

2.3. Catalog

The global catalog is a single instance of Catalog that is allocated for the entire SimpleDB process. The global catalog can be retrieved via the method Database.getCatalog(), and the same goes for the global buffer pool (using Database.getBufferPool()).

2.4. BufferPool

The buffer pool (class BufferPool in SimpleDB) is responsible for caching pages in memory that have been recently read from disk. All operators read and write pages from various files on disk through the buffer pool. It consists of a fixed number of pages, defined by the numPages parameter to the BufferPool constructor. In later labs, you will implement an eviction policy. For this lab, you only need to implement the constructor and the BufferPool.getPage() method used by the SeqScan operator. The BufferPool should store up to numPages pages. For this lab, if more than numPages requests are made for different pages, then instead of implementing an eviction policy, you may throw a DbException. In future labs you will be required to implement an eviction policy.

The Database class provides a static method, Database.getBufferPool(), that returns a reference to the single BufferPool instance for the entire SimpleDB process.

2.5. HeapFile access method

A HeapFile object is arranged into a set of pages, each of which consists of a fixed number of bytes for storing tuples, (defined by the constant BufferPool.PAGE_SIZE), including a header. In SimpleDB, there is one HeapFile object for each table in the database. Each page in a HeapFile is arranged as a set of slots, each of which can hold one tuple (tuples for a given table in SimpleDB are all of the same size). In addition to these slots, each page has a header that consists of a bitmap with one bit per tuple slot. If the bit corresponding to a particular tuple is 1, it indicates that the tuple is valid; if it is 0, the tuple is invalid (e.g., has been deleted or was never initialized.) Pages of HeapFile objects are of type HeapPage which implements the Page interface. Pages are stored in the buffer pool but are read and written by the HeapFile class.

SimpleDB stores heap files on disk in more or less the same format they are stored in memory. Each file consists of page data arranged consecutively on disk. Each page consists of one or more bytes representing the header, followed by the BufferPool.PAGE_SIZE - # header bytes bytes of actual page content. Each tuple requires tuple size * 8 bits for its content and 1 bit for the header. Thus, the number of tuples that can fit in a single page is:

tupsPerPage = floor((BufferPool.PAGE_SIZE * 8) / (tuple size * 8 + 1))

Where tuple size is the size of a tuple in the page in bytes. The idea here is that each tuple requires one additional bit of storage in the header. We compute the number of bits in a page (by mulitplying PAGE_SIZE by 8), and divide this quantity by the number of bits in a tuple (including this extra header bit) to get the number of tuples per page. The floor operation rounds down to the nearest integer number of tuples (we don't want to store partial tuples on a page!)

Once we know the number of tuples per page, the number of bytes required to store the header is simply:

headerBytes = ceiling(tupsPerPage/8)

The ceiling operation rounds up to the nearest integer number of bytes (we never store less than a full byte of header information.)

The low (least significant) bits of each byte represents the status of the slots that are earlier in the file. Hence, the lowest bit of the first byte represents whether or not the first slot in the page is in use. Also, note that the high-order bits of the last byte may not correspond to a slot that is actually in the file, since the number of slots may not be a multiple of 8. Also note that all Java virtual machines are big-endian.

After you have implemented HeapPage, you will write methods for HeapFile in this lab to calculate the number of pages in a file and to read a page from the file. You will then be able to fetch tuples from a file stored on disk.

2.6. Operators

Operators are connected together into a plan by passing lower-level operators into the constructors of higher-level operators, i.e., by 'chaining them together.' Special access method operators at the leaves of the plan are responsible for reading data from the disk (and hence do not have any operators below them).

At the top of the plan, the program interacting with SimpleDB simply calls getNext on the root operator; this operator then calls getNext on its children, and so on, until these leaf operators are called. They fetch tuples from disk and pass them up the tree (as return arguments to getNext); tuples propagate up the plan in this way until they are output at the root or combined or rejected by another operator in the plan.

For this lab, you will only need to implement one SimpleDB operator.

You will fill in other operators in subsequent labs.

2.7. A simple query

The purpose of this section is to illustrate how these various components are connected together to process a simple query. Suppose you have a data file, "some_data_file.txt", with the following contents:

1,1,1
2,2,2
3,4,4

You can convert this into a binary file that SimpleDB can query as follows:

java -jar dist/simpledb.jar convert some_data_file.txt 3

Here, the argument "3" tells conver that the input has 3 columns.

The following code implements a simple selection query over this file. This code is equivalent to the SQL statement SELECT * FROM some_data_file.

package simpledb;
import java.io.*;

public class test {

    public static void main(String[] argv) {

        // construct a 3-column table schema
        Type types[] = new Type[]{ Type.INT_TYPE, Type.INT_TYPE, Type.INT_TYPE };
        String names[] = new String[]{ "field0", "field1", "field2" };
        TupleDesc descriptor = new TupleDesc(types, names);

        // create the table, associate it with some_data_file.dat
        // and tell the catalog about the schema of this table.
        HeapFile table1 = new HeapFile(new File("some_data_file.dat"), descriptor);
        Database.getCatalog().addTable(table1, "test");

        // construct the query: we use a simple SeqScan, which spoonfeeds
        // tuples via its iterator.
        TransactionId tid = new TransactionId();
        SeqScan f = new SeqScan(tid, table1.getId());

        try {
            // and run it
            f.open();
            while (f.hasNext()) {
                Tuple tup = f.next();
                System.out.println(tup);
            }
            f.close();
            Database.getBufferPool().transactionComplete(tid);
        } catch (Exception e) {
            System.out.println ("Exception : " + e);
        }
    }

}

The table we create has three integer fields. To express this, we create a TupleDesc object and pass it an array of Type objects, and optionally an array of String field names. Once we have created this TupleDesc, we initialize a HeapFile object representing the table stored in some_data_file.dat. Once we have created the table, we add it to the catalog. If this were a database server that was already running, we would have this catalog information loaded. We need to load it explicitly to make this code self-contained.

Once we have finished initializing the database system, we create a query plan. Our plan consists only of the SeqScan operator that scans the tuples from disk. In general, these operators are instantiated with references to the appropriate table (in the case of SeqScan) or child operator (in the case of e.g. Filter). The test program then repeatedly calls hasNext and next on the SeqScan operator. As tuples are output from the SeqScan, they are printed out on the command line.

ant
java -classpath dist/simpledb.jar simpledb.test

3. Logistics

• Describe any design decisions you made. These may be minimal for Lab 1.
• Discuss and justify any changes you made to the API.
• Describe any missing or incomplete elements of your code.
• Describe how long you spent on the lab, and whether there was anything you found particularly difficult or confusing.

3.1. Collaboration

3.2. Submitting your assignment

To submit your code, please create a CSC553-lab1.tar.gz tarball (such that, untarred, it creates a CSC553-lab1/src/java/simpledb directory with your code) and submit it through the D2L. You can use the ant handin target to generate the tarball. Place the write-up in a file called answers.txt or answers.pdf in the top level of your CSC553-lab1 directory.

3.3. Submitting a bug

• A description of the bug.
• A .java file we can drop in the test/simpledb directory, compile, and run.
• A .txt file with the data that reproduces the bug. We should be able to convert it to a .dat file using HeapFileEncoder.

3.4 Grading

10% of your grade is for completing Part 1 of this lab in time.

75% of your grade will be based on two things (a) if you submitted the Git commit history and (b) whether or not your code passes the system test suite we will run over it. These tests will be a superset of the tests we have provided. Before handing in your code, you should make sure it produces no errors (passes all of the tests) from both ant test and ant systemtest.

Important: before testing, we will replace your build.xml and the entire contents of the test directory with our version of these files. This means you cannot change the format of .dat files! You should also be careful changing our APIs. You should test that your code compiles the unmodified tests. In other words, we will untar your tarball, replace the files mentioned above, compile it, and then grade it. It will look roughly like this:

$ tar xvzf CSC553-lab1.tar.gz
$ cd ./CSC553-lab1
[replace build.xml and test]
$ ant test
$ ant systemtest
[additional tests]

If any of these commands fail, we'll be unhappy, and, therefore, so will your grade.

An additional 15% of your grade will be based on the quality of your writeup and our subjective evaluation of your code.