From 3b84b8e7112741aa25e8c6a87480bbd57556d4e2 Mon Sep 17 00:00:00 2001
From: daomcgill <77309217+daomcgill@users.noreply.github.com>
Date: Thu, 17 Oct 2024 16:26:48 -1000
Subject: [PATCH] i #313 Update Config File

- Remove unused settings
- Change ../ to ../../
- Update notebook to reflect changes

Signed-off-by: Dao McGill <dmcgill@hawaii.edu>
---
 conf/maven.yml                 | 26 ++++++--------------------
 vignettes/syntax_extractor.Rmd | 29 +++++++++++++++--------------
 2 files changed, 21 insertions(+), 34 deletions(-)

diff --git a/conf/maven.yml b/conf/maven.yml
index a74ea62a..6cdf8bf6 100644
--- a/conf/maven.yml
+++ b/conf/maven.yml
@@ -1,14 +1,7 @@
-# Project Configuration File for Maven Project #
+# Project Configuration File for Maven Project
 project:
   website: https://github.com/apache/maven
 
-version_control:
-  # Path to the .git directory of the Maven project
-  log: ../maven/maven-artifact/src/main/java/org/apache/maven/artifact/
-  # List of branches to analyze
-  branch:
-    - main
-
 filter:
   # File extensions to include in the analysis
   keep_filepaths_ending_with:
@@ -19,16 +12,9 @@ filter:
     - test
     - example
 
-tool:
-  # srcML binary path
+srcml:
+  # path to tool binary (change this location later)
   srcml_path: /usr/local/bin/srcml
-  # Path to output the XML annotation file generated by srcML
-  srcml_output_path: ../analysis/maven/srcml_output.xml
-
-# Analysis Configuration #
-analysis:
-  # A list of topics (keywords) for focused analysis
-  topics:
-    - class
-    - method
-    - documentation
+  # path to the folder to analyze
+  src_folder: ../../maven/maven-artifact/src/main/java/org/apache/maven/artifact/
+  srcml_filepath: ../../analysis/maven/srcml_output.xml
diff --git a/vignettes/syntax_extractor.Rmd b/vignettes/syntax_extractor.Rmd
index 7daa858f..1ad216e6 100644
--- a/vignettes/syntax_extractor.Rmd
+++ b/vignettes/syntax_extractor.Rmd
@@ -91,24 +91,25 @@ Here’s how you can set up the configuration:
 ``` {r eval=FALSE}
 # Load the project configuration
 tool <- yaml::read_yaml("tools.yml")
-conf <- yaml::read_yaml("conf/syntax.yml")
+conf <- yaml::read_yaml("conf/maven.yml")
 
 # Path to srcML binary
 srcml_path <- tool[["srcml"]]
 
-# Git repository and folder path (using Maven as an example)
-git_repo_path <- conf[["version_control"]][["log"]]
-folder_path <- stri_replace_last(git_repo_path, replacement="", regex=".git")
+# Paths from config
+srcml_path <- conf[["tool"]][["srcml_path"]]
+src_folder <- conf[["version_control"]][["log"]]
+srcml_output_path <- conf[["tool"]][["srcml_output_path"]]
+srcml_filepath <- conf[["tool"]][["srcml_output_path"]]
 
-# Tool Parameters 
-srcml_filepath <- conf[["tool"]][["srcml"]][["srcml_path"]]
 
-# Filters for file extensions and substrings in file paths
+# Filters
 file_extensions <- conf[["filter"]][["keep_filepaths_ending_with"]]
-substring_filepath <- conf[["filter"]][["remove_filepaths_containing"]]
+exclude_paths <- conf[["filter"]][["remove_filepaths_containing"]]
 
-# Analysis topics (optional)
+# Analysis topics
 topics <- conf[["analysis"]][["topics"]]
+
 ```
 
 # Running the Syntax Extractor
@@ -137,7 +138,7 @@ Here’s how you might use it:
 # Creating annotated XML from source code
 annotated_file <- annotate_src_text(
   srcml_path = srcml_path,
-  src_folder = folder_path,
+  src_folder = src_folder,
   srcml_filepath = srcml_filepath
 )
 ```
@@ -276,8 +277,8 @@ It calls query_src_text() with a specific query that looks for class names:
 ``` {r eval=FALSE}
 # Extracting class names from the XML
 class_names <- query_src_text_class_names(
-  srcml_path = "path/to/srcML",
-  srcml_filepath = "path/to/output.xml"
+  srcml_path = srcml_path,
+  srcml_filepath = srcml_filepath
 )
 
 # Display the result as a table
@@ -302,8 +303,8 @@ Here’s how you might use it:
 ``` {r eval=FALSE}
 # Extracting namespaces from the XML
 namespaces <- query_src_text_namespace(
-  srcml_path = "path/to/srcML",
-  srcml_filepath = "path/to/output.xml"
+  srcml_path = srcml_path,
+  srcml_filepath = srcml_filepath
 )
 
 # Display the namespaces