Updated README.md

Docker/README.md

+# Docker
+
+This directory contains the docker containers for easy setup of the project.
+
+## Structure
+
+Every container has its own directory along with a `Dockerfile` if necessary and a `data/` directory which is mounted to the container. It persists the data even if the container is removed.
+
+The directory contains the following containers (folders):
+
+### `mongo/`
+
+This container is used to run the MongoDB database. It is used to store the CVE-Search database.
+
+### `mysql/`
+
+This container is used to run the MySQL database. It is used to store the mapping database.
+
+### `python/`
+
+This container is used along the MongoDB container. It is used to run the CVE-Search tool to populate the MongoDB database.
+
+### `redis/`
+
+The redis container is used along the MongoDB container. It is used as a cache for the CVE-Search tool.
+
+### `commit-analysis/`
+
+This is the main container. It includes an `init_scripts` folder which is run when the container is started.
+
+#### The init_scripts
+
+The init_scripts are run when the container is started.
+
+It includes the following scripts:
+
+- `clone_repos.sh`: This script clones the repositories from GitHub which are used in the project.
+- `get_linux_full.sh`: Usually, the GitHub repository is used to get the Linux kernel. However, the repository does not
+  include the full history. This script clones the full history of the Linux kernel.
+- `get_mappings_all.sh`: Runs all mapping scripts to populate the MySQL database.
+- `run_heuristic_all_parallel.sh`: Runs the heuristic on all the entries in the MySQL database. It runs the script in
+  parallel to speed up the process.
+- `run_all.sh`: This script runs all the other scripts in the correct order.
+- `repo_urls.txt`: This file contains the URLs to the repositories which are used in the project. It is used by the
+  `clone_repos.sh` script.
+
+> **_NOTE:_** Make sure to look into the `run_all.sh` script if you do not want to run all scripts.
+> You can comment out the scripts you do not want to run.
\ No newline at end of file

README.md

-# Commit-based static analysis for Vulnerability Detection
+# Studying the Effect of Data in Commit-Based Static Analysis
 
 ## Introduction
 
@@ -21,7 +21,7 @@ developing more effective methods for identifying and addressing vulnerabilities
 
 ## Contents
 
-- `Data/`: contains the vulnerable code commit dataset used in the thesis and the methods for generating the dataset.
+- `Data/`: contains the datasets used in the project and the scripts to process them.
 - `Docker/`: contains the docker containers for easy setup of the project.
 - `README.md`: this file provides an overview of the repository.
 
@@ -32,7 +32,28 @@ developing more effective methods for identifying and addressing vulnerabilities
 
 ## Usage
 
-TODO
+Make sure to install the dependencies before running the project.
+
+### Setup with Docker
+
+1. Run `docker compose up -d mongo redis mysql` in the root directory of the project to start the databases.
+2. Run `docker compose up -d mongo_python` to start populating the CVE-Search database.
+3. Run `docker compose up -d --build commit_analysis` to start the main container.
+
+> _NOTE_: Check the README.md in the `Docker/` directory for more information!
+
+### Rebuilding the commit_analysis container
+
+The current code is copied to the `commit_analysis` container.
+If any changes are made in the init_scripts, the container needs to be rebuilt.
+This can be done by running `docker compose up -d --build commit_analysis`.
+
+### Use of the pre-populated database
+
+The databases expose their ports to the host machine.
+To get the ports, check the `docker-compose.yml` file.
+You can use those ports to connect to the databases and pre-populate them with the data provided.
+Then you do not need to run all mappings.
 
 ## License