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https://github.com/src-d/jgit-spark-connector

jgit-spark-connector is a library for running scalable data retrieval pipelines that process any number of Git repositories for source code analysis.
https://github.com/src-d/jgit-spark-connector

datasource git pyspark python scala spark

Last synced: 13 days ago
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jgit-spark-connector is a library for running scalable data retrieval pipelines that process any number of Git repositories for source code analysis.

Host: GitHub
URL: https://github.com/src-d/jgit-spark-connector
Owner: src-d
License: apache-2.0
Created: 2017-08-03T10:55:44.000Z (over 7 years ago)
Default Branch: master
Last Pushed: 2019-02-13T13:43:52.000Z (almost 6 years ago)
Last Synced: 2024-11-13T14:55:29.694Z (about 2 months ago)
Topics: datasource, git, pyspark, python, scala, spark
Language: Scala
Homepage:
Size: 8.55 MB
Stars: 71
Watchers: 11
Forks: 32
Open Issues: 11
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

# jgit-spark-connector [![Build Status](https://travis-ci.org/src-d/jgit-spark-connector.svg?branch=master)](https://travis-ci.org/src-d/jgit-spark-connector) [![codecov](https://codecov.io/gh/src-d/jgit-spark-connector/branch/master/graph/badge.svg)](https://codecov.io/gh/src-d/jgit-spark-connector) [![Maven Central](https://maven-badges.herokuapp.com/maven-central/tech.sourced/jgit-spark-connector/badge.svg)](https://maven-badges.herokuapp.com/maven-central/tech.sourced/jgit-spark-connector)

**jgit-spark-connector** is a library for running scalable data retrieval pipelines that process any number of Git repositories for source code analysis.

It is written in Scala and built on top of Apache Spark to enable rapid construction of custom analysis pipelines and processing large number of Git repositories stored in HDFS in [Siva file format](https://github.com/src-d/go-siva). It is accessible both via Scala and Python Spark APIs, and capable of running on large-scale distributed clusters.

Current implementation combines:
- [src-d/enry](https://github.com/src-d/enry) to detect programming language of every file
- [bblfsh/client-scala](https://github.com/bblfsh/client-scala) to parse every file to UAST
- [src-d/siva-java](https://github.com/src-d/siva-java) for reading Siva files in JVM
- [apache/spark](https://github.com/apache/spark) to extend DataFrame API
- [eclipse/jgit](https://github.com/eclipse/jgit) for working with Git .pack files

# Deprecated

jgit-spark-connector has been deprecated in favor of gitbase-spark-connector and there will be no further development of this tool.

# Quick-start

First, you need to download [Apache Spark](https://spark.apache.org/) somewhere on your machine:

```bash
$ cd /tmp && wget "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.2.1/spark-2.2.1-bin-hadoop2.7.tgz" -O spark-2.2.1-bin-hadoop2.7.tgz
```
The Apache Software Foundation suggests you the better mirror where you can download `Spark` from. If you wish to take a look and find the best option in your case, you can [do it here](https://www.apache.org/dyn/closer.lua/spark/spark-2.2.1/spark-2.2.1-bin-hadoop2.7.tgz).

Then you must extract `Spark` from the downloaded tar file:

```bash
$ tar -C ~/ -xvzf spark-2.2.1-bin-hadoop2.7.tgz
```

Binaries and scripts to run `Spark` are located in spark-2.2.1-bin-hadoop2.7/bin, so should set `PATH` and `SPARK_HOME` to point to this directory. It's advised to add this to your shell profile:

```bash
$ export SPARK_HOME=$HOME/spark-2.2.1-bin-hadoop2.7
$ export PATH=$PATH:$SPARK_HOME/bin
```

Look for the latest [**jgit-spark-connector** version](http://search.maven.org/#search%7Cga%7C1%7Ctech.sourced), and then replace in the command where `[version]` is showed:

```bash
$ spark-shell --packages "tech.sourced:jgit-spark-connector:[version]"

# or

$ pyspark --packages "tech.sourced:jgit-spark-connector:[version]"
```

Run [bblfsh daemon](https://github.com/bblfsh/bblfshd). You can start it easily in a container following its [quick start guide](https://github.com/bblfsh/bblfshd#quick-start).

If you run **jgit-spark-connector** in an UNIX like environment, you should set the `LANG` variable properly:

export LANG="en_US.UTF-8"

The rationale behind this is that UNIX file systems don't keep the encoding for each file name, they are just plain bytes,
so the `Java API for FS` looks for the `LANG` environment variable to apply certain encoding.

Either in case the `LANG` variable wouldn't be set to a UTF-8 encoding or it wouldn't be set at all (which results in handle encoding in C locale) you could get an exception during the ***jgit-spark-connector*** execution similar to `java.nio.file.InvalidPathException: Malformed input or input contains unmappable characters`.

# Pre-requisites

* Scala 2.11.x
* [Apache Spark Installation](http://spark.apache.org/docs/2.2.1/) 2.2.x or 2.3.x
* [bblfsh](https://github.com/bblfsh/bblfshd) >= 2.5.0: Used for UAST extraction

## Python pre-requisites:

* Python >= 3.4.x (jgit-spark-connector is tested with Python 3.4, 3.5 and 3.6 and these are the supported versions, even if it might still work with previous ones)
* `libxml2-dev` installed
* `python3-dev` installed
* `g++` installed

# Examples of jgit-spark-connector usage

**jgit-spark-connector** is available on [maven central](https://search.maven.org/#search%7Cga%7C1%7Ctech.sourced.jgit-spark-connector). To add it to your project as a dependency,

For projects managed by [maven](https://maven.apache.org/) add the following to your `pom.xml`:

```xml

tech.sourced
jgit-spark-connector
[version]

```

For [sbt](http://www.scala-sbt.org/) managed projects add the dependency:

libraryDependencies += "tech.sourced" % "jgit-spark-connector" % "[version]"

In both cases, replace `[version]` with the [latest jgit-spark-connector version](http://search.maven.org/#search%7Cga%7C1%7Ctech.sourced)

### Usage in applications as a dependency

The default jar published is a fatjar containing all the dependencies required by the jgit-spark-connector. It's meant to be used directly as a jar or through `--packages` for Spark usage.

If you want to use it in an application and built a fatjar with that you need to follow these steps to use what we call the "slim" jar:

With maven:

```xml

tech.sourced
jgit-spark-connector
[version]
slim

```

Or (for sbt):

```scala
libraryDependencies += "tech.sourced" % "jgit-spark-connector" % "[version]" % Compile classifier "slim"
```

If you run into problems with `io.netty.versions.properties` on sbt, you can add the following snippet to solve it:

In sbt:

```scala
assemblyMergeStrategy in assembly := {
case "META-INF/io.netty.versions.properties" => MergeStrategy.last
case x =>
val oldStrategy = (assemblyMergeStrategy in assembly).value
oldStrategy(x)
}
```

## pyspark

### Local mode

Install python-wrappers is necessary to use **jgit-spark-connector** from pyspark:

``` bash
$ pip install sourced-jgit-spark-connector
```

Then you should provide the **jgit-spark-connector's** maven coordinates to the pyspark's shell:
```bash
$ $SPARK_HOME/bin/pyspark --packages "tech.sourced:jgit-spark-connector:[version]"
```
Replace `[version]` with the [latest jgit-spark-connector version](http://search.maven.org/#search%7Cga%7C1%7Ctech.sourced)

### Cluster mode

Install **jgit-spark-connector** wrappers as in local mode:
```bash
$ pip install -e sourced-jgit-spark-connector
```

Then you should package and compress with `zip` the python wrappers to provide pyspark with it. It's required to distribute the code among the nodes of the cluster.

```bash
$ zip ./sourced-jgit-spark-connector.zip
$ $SPARK_HOME/bin/pyspark --py-files ./sourced-jgit-spark-connector.zip
```

### pyspark API usage

Run pyspark as explained before to start using the jgit-spark-connector, replacing `[version]` with the [latest jgit-spark-connector version](http://search.maven.org/#search%7Cga%7C1%7Ctech.sourced):

```bash
$ $SPARK_HOME/bin/pyspark --packages "tech.sourced:jgit-spark-connector:[version]"
Welcome to

spark version 2.2.1

Using Python version 3.6.2 (default, Jul 20 2017 03:52:27)
SparkSession available as 'spark'.
>>> from sourced.engine import Engine
>>> engine = Engine(spark, '/path/to/siva/files', 'siva')
>>> engine.repositories.filter('id = "github.com/mingrammer/funmath.git"').references.filter("name = 'refs/heads/HEAD'").show()
+--------------------+---------------+--------------------+
| repository_id| name| hash|
+--------------------+---------------+--------------------+
|github.com/mingra...|refs/heads/HEAD|290440b64a73f5c7e...|
+--------------------+---------------+--------------------+

```

## Scala API usage

You must provide **jgit-spark-connector** as a dependency in the following way, replacing `[version]` with the [latest jgit-spark-connector version](http://search.maven.org/#search%7Cga%7C1%7Ctech.sourced):

```bash
$ spark-shell --packages "tech.sourced:jgit-spark-connector:[version]"
```

To start using **jgit-spark-connector** from the shell you must import everything inside the `tech.sourced.engine` package (or, if you prefer, just import `Engine` and `EngineDataFrame` classes):

```bash
scala> import tech.sourced.engine._
import tech.sourced.engine._
```

Now, you need to create an instance of `Engine` and give it the spark session and the path of the directory containing the siva files:

```bash
scala> val engine = Engine(spark, "/path/to/siva-files", "siva")
```

Then, you will be able to perform queries over the repositories:

```bash
scala> engine.getRepositories.filter('id === "github.com/mawag/faq-xiyoulinux").
| getReferences.filter('name === "refs/heads/HEAD").
| getAllReferenceCommits.filter('message.contains("Initial")).
| select('repository_id, 'hash, 'message).
| show

```

## Supported repository formats

As you might have seen, you need to provide the repository format you will be reading when you create the `Engine` instance. Although the documentation always uses the `siva` format, there are more repository formats available.

These are all the supported formats at the moment:

- `siva`: rooted repositories packed in a single `.siva` file.
- `standard`: regular git repositories with a `.git` folder. Each in a folder of their own under the given repository path.
- `bare`: git bare repositories. Each in a folder of their own under the given repository path.

### Processing local repositories with the jgit-spark-connector

There are some design decisions that may surprise the user when processing local repositories, instead of siva files. This is the list of things you should take into account when doing so:

- All local branches will belong to a repository whose id is `file://$REPOSITORY_PATH`. So, if you clone `https://github.com/foo/bar.git` at `/home/foo/bar`, you will see two repositories `file:///home/foo/bar` and `github.com/foo/bar`, even if you only have one.
- Remote branches are transformed from `refs/remote/$REMOTE_NAME/$BRANCH_NAME` to `refs/heads/$BRANCH_NAME` as they will only belong to the repository id of their corresponding remote. So `refs/remote/origin/HEAD` becomes `refs/heads/HEAD`.

# Playing around with **jgit-spark-connector** on Jupyter

You can launch our docker container which contains some Notebooks examples just running:

docker run --name jgit-spark-connector-jupyter --rm -it -p 8080:8080 -v $(pwd)/path/to/siva-files:/repositories --link bblfshd:bblfshd srcd/jgit-spark-connector-jupyter

You must have some siva files in local to mount them on the container replacing the path `$(pwd)/path/to/siva-files`. You can get some siva-files from the project [here](https://github.com/src-d/jgit-spark-connector/tree/master/_examples/siva-files).

You should have a [bblfsh daemon](https://github.com/bblfsh/bblfshd) container running to link the jupyter container (see Pre-requisites).

When the `jgit-spark-connector-jupyter` container starts it will show you an URL that you can open in your browser.

# Using jgit-spark-connector directly from Python

If you are using the jgit-spark-connector directly from Python and are unable to modify the `PYTHON_SUBMIT_ARGS` you can copy the jgit-spark-connector jar to the pyspark jars to make it available there.

```
cp jgit-spark-connector.jar "$(python -c 'import pyspark; print(pyspark.__path__[0])')/jars"
```

This way, you can use it in the following way:

```python
import sys

pyspark_path = "/path/to/pyspark/python"
sys.path.append(pyspark_path)

from pyspark.sql import SparkSession
from sourced.engine import Engine

siva_folder = "/path/to/siva-files"
spark = SparkSession.builder.appName("test").master("local[*]").getOrCreate()
engine = Engine(spark, siva_folder, 'siva')
```

# Development

## Build fatjar

Build the fatjar is needed to build the docker image that contains the jupyter server, or test changes in spark-shell just passing the jar with `--jars` flag:

```bash
$ make build
```

It leaves the fatjar in `target/scala-2.11/jgit-spark-connector-uber.jar`

## Build and run docker to get a Jupyter server

To build an image with the last built of the project:

```bash
$ make docker-build
```

Notebooks under examples folder will be included on the image.

To run a container with the Jupyter server:

```bash
$ make docker-run
```

Before run the jupyter container you must run a [bblfsh daemon](https://github.com/bblfsh/bblfshd):

```bash
$ make docker-bblfsh
```

If it's the first time you run the [bblfsh daemon](https://github.com/bblfsh/bblfshd), you must install the drivers:

```bash
$ make docker-bblfsh-install-drivers
```

To see installed drivers:

```bash
$ make docker-bblfsh-list-drivers
```

To remove the development jupyter image generated:

```bash
$ make docker-clean
```

## Run tests

**jgit-spark-connector** uses [bblfsh](https://github.com/bblfsh) so you need an instance of a bblfsh server running:

```bash
$ make docker-bblfsh
```

To run tests:
```bash
$ make test
```

To run tests for python wrapper:

```bash
$ cd python
$ make test
```

### Windows support

There is no windows support in enry-java or bblfsh's client-scala right now, so all the language detection and UAST features are not available for the windows platform.

# Code of Conduct

See [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md)

# License

Apache License Version 2.0, see [LICENSE](LICENSE)