Proto commits in semihsalihoglu/graft

These 15 commits are when the Protocol Buffers files have changed:

Commit:4f17753
Author:Semih Salihoglu

- Removes vv violations wrapper and removes it from proto. Now the server should infer this from traces that are prefixed by vv_intgrty_stp_. - Moves common code between the server and the instrumenter to DebugUtils.java.

The documentation is generated from this commit.

Commit:3975cb5
Author:Jaeho Shin

Turned backend/ into the root of the source tree

Commit:7dc4089
Author:Jaeho Shin
Committer:Jaeho Shin

Renamed package name in protobuf files and moved under backend/

Commit:3db5fc1
Author:Semih Salihoglu

- Adding master.compute()'s instrumentation. Adds AbstractInterceptingMasterCompute.java, BottomInterceptingMasterCompute.java, and UserMasterCompute.java, mimicking Jaeho's previous commit. - Extracts what's commong between AbstractInterceptingComputation.java and AbstractInterceptingMasterCompute.java into CommonVertexMasterInterceptionUtil.java. - Reorder's the protocol buffers IDs.

Commit:2a9f5e7
Author:Semih Salihoglu

- Huge refactorization in scenario.proto. Moves common information between master's context and vertex's context into a CommonVertexMasterContext. Adds a VertexScenarioClasses message to capture all the classes for each vertex. - Refactorization in the Wrapper classes. They all now extend BaseWrapper and have consistent names. - Fixes a bug in the sandwich instrumentations where the ImmutableGiraphClassesConfig was using the wrong class name for user's class.

Commit:1436fee
Author:Semih Salihoglu

- Forgot to add most of the classes related to commit fb61d27821dc9367077be6e7aa94f88f3e100cf3.

Commit:fb61d27
Author:Semih Salihoglu

- Adds capturing config, numTotalVertices, numTotalEdges, and aggregators: currently an aggregator is captured only if it is read by some vertex. Also we do not yet do anything for adding new aggregators. - Adds the necessary proto files for aggregators and their wrapper classes, AggregatorWrapper.java and AggregatedValueWrapper.java. - Refactors the wrapper classes to accomodate for the aggregator wrapper classes. - Fixes the exmaples for msg integrity and value integrity.

Commit:58b0dbe
Author:Semih Salihoglu

- Adding Exception catching - Adding message violation integrity check - Adding vertex value violation integrity check.

Commit:62c1392
Author:Semih Salihoglu

- Changing the scenario to include superstepNo and changing vertexValue to vertexValueBefore and vertexValueAfter. - Fixing TestCaseScnearioWriter and GiraphScenarioWrapper according to the .proto change. - Adding initial AbstractInterceptingComputation class and DebugConfig and an example SimpleShortestPathsDebugComputation. (currently does not save anything as a .proto though some code is initiated to do so.)

Commit:3755791
Author:Semih Salihoglu

- Renaming the Scenario proto message under scenario.proto to Context. - Changing the proto file to contain only one "context" (in Brian's checkin this was repeated). - Renaming ProtobufGiraphScenarioWrapper.java to GiraphScenarioWrapper.java for simplification. Similarly renaming ProtobufGiraphScenearioSaverLoader.java to GiraphScenearioSaverLoader.java. - Renaming all the java classes that we have wrapped with XXXWrapper, e.g. vertexId => vertexIdWrapper, Context => ContextWrapper. - Simplifying some the of the generics inside GiraphScenarioWrapper.java. They're now declared only once at the GiraphScenarioWrapper level. - Adding a toString method to GiraphScenarioWrapper (and all other wrapper classes) to make it easier to debug and print. - Changing the GiraphTestScenarioWriter.java to use GiraphScenearioSaverLoader.java. - A small pom.xml change to compile the debugger with giraph from trunk, that is assumed to be somewhere in the local disk.

Commit:0bf0a6f
Author:tbq

Protobuf

Commit:7cd6805
Author:tbq

Test Generator

Commit:9794343
Author:tbq

Test Generator

Commit:e2d577e
Author:Semih Salihoglu

- Adding vertex value to scenario.proto and changing GiraphTestScenarioWriter to write a dummy text as the vertex value.

Commit:6b0c70e
Author:Semih Salihoglu

- Reorganizing the directory structure. server, instrumentor, and editor are now all under src/main/java/stanford/infolab/debugger/ subdirectories of a top directory named backend. - Adding a pom.xml for the backend directory. (We're starting to use maven.) - Adding a protocol buffer for scenarios. For now contains a GiraphScenario message that contains an ID, a set of msgs, and a list of neighbors. - Adding a simple java file under utils that spits out a simple GiraphScenario.