Add parent git commit nodes and connect them

.github/pull_request_template.md

@@ -0,0 +1,15 @@
+### 🚀 Feature
+
+- 
+
+### ⚙️ Optimization
+
+- 
+
+### 🛠 Fix
+
+- 
+
+### 📖 Documentation
+
+- 

COMMANDS.md

@@ -234,6 +234,7 @@ It uses `git log` to extract commits, their authors and the names of the files c
 
 ```Cypher
 (Git:Log:Author)-[:AUTHORED]->(Git:Log:Commit)->[:CONTAINS]->(Git:Log:File)
+(Git:Log:Commit)->[:HAS_PARENT]-(Git:Log:Commit)
 ```
 
 👉**Note:** Commit messages containing `[bot]` are filtered out to ignore changes made by bots.

README.md

@@ -125,6 +125,7 @@ The [Code Structure Analysis Pipeline](./.github/workflows/java-code-analysis.ym
   - [openTSNE](https://github.com/pavlin-policar/openTSNE)
   - [wordcloud](https://github.com/amueller/word_cloud)
 - [Graph Visualization](./graph-visualization/README.md) uses [node.js](https://nodejs.org/de) and the dependencies listed in [package.json](./graph-visualization/package.json).
+- [Check links in markdown documentation (GitHub workflow)](./.github/workflows/check-links-in-documentation.yml) uses [markdown-link-check](https://github.com/tcort/markdown-link-check).
 
 **Big shout-out** 📣 to all the creators and contributors of these great libraries 👍. Projects like this wouldn't be possible without them. Feel free to [create an issue](https://github.com/JohT/code-graph-analysis-pipeline/issues/new/choose) if something is missing or wrong in the list.
 

cypher/GitLog/Add_HAS_PARENT_relationships_to_commits.cypher

@@ -0,0 +1,6 @@
+// Creates a HAS_PARENT relationship between Git Commit nodes and their parent.
+
+MATCH (git_commit:Git:Commit)
+MATCH (parent_commit:Git:Commit{hash: git_commit.parent})
+MERGE (git_commit)-[:HAS_PARENT]->(parent_commit)
+RETURN count(DISTINCT git_commit.hash)  AS numberOfCommitsWithParent

cypher/GitLog/Import_git_log_csv_data.cypher

@@ -5,6 +5,7 @@ CALL { WITH row
     MERGE (git_author:Git:Log:Author {name: row.author, email: row.email})
     MERGE (git_commit:Git:Log:Commit {
         hash:           row.hash, 
+        parent:         coalesce(row.parent, ''), 
         message:        row.message,
         timestamp:      datetime(row.timestamp),
         timestamp_unix: toInteger(row.timestamp_unix)

cypher/GitLog/Index_commit_parent.cypher

@@ -0,0 +1,3 @@
+// Create index for parent commit hash (git data)
+
+CREATE INDEX INDEX_COMMIT_PARENT IF NOT EXISTS FOR (n:Commit) ON (n.parent)

markdown-lint-check-config.json

@@ -4,5 +4,9 @@
             "pattern": "^http://localhost"
         }
     ],
+    "timeout": "30s",
+    "retryOn429": true,
+    "retryCount": 3,
+    "fallbackRetryDelay": "60s",  
     "aliveStatusCodes": [200, 202, 206]
 }

scripts/importGitLog.sh

@@ -78,17 +78,18 @@ echo "importGitLog: Creating ${OUTPUT_CSV_FILENAME} from git log..."
   cd "${repository}" || exit
 
   # Prints the header line of the CSV file with the names of the columns.
-  echo "hash,author,email,timestamp,timestamp_unix,message,filename" > "${OUTPUT_CSV_FILENAME}"
+  echo "hash,parent,author,email,timestamp,timestamp_unix,message,filename" > "${OUTPUT_CSV_FILENAME}"
 
   # Prints the git log in CSV format including the changed files.
   # Includes quoted strings, double quote escaping and supports commas in strings.
-  git log --no-merges --pretty=format:' %h,,,%an,,,%ae,,,%aI,,,%ct,,,%s' --name-only | \
-  awk 'BEGIN { COMMA=",";QUOTE="\"" } /^ / { split($0, a, ",,,"); gsub(/^ /, "", a[1]); gsub(/"/, "\"\"", a[2]); gsub(/"/, "\"\"", a[3]); gsub(/"/, "\"\"", a[6]); gsub(/\\/, " ", a[6]); commit=a[1] COMMA QUOTE a[2] QUOTE COMMA QUOTE a[3] QUOTE COMMA a[4] COMMA a[5] COMMA QUOTE a[6] QUOTE } NF && !/^\ / { print commit ",\""$0"\"" }' | \
+  git log --no-merges --pretty=format:' %h,,,%p,,,%an,,,%ae,,,%aI,,,%ct,,,%s' --name-only | \
+  awk 'BEGIN { COMMA=",";QUOTE="\"" } /^ / { split($0, a, ",,,"); gsub(/^ /, "", a[1]); gsub(/"/, "\"\"", a[3]); gsub(/"/, "\"\"", a[4]); gsub(/"/, "\"\"", a[7]); gsub(/\\/, " ", a[7]); commit=a[1] COMMA a[2] COMMA QUOTE a[3] QUOTE COMMA QUOTE a[4] QUOTE COMMA a[5] COMMA a[6] COMMA QUOTE a[7] QUOTE } NF && !/^\ / { print commit ",\""$0"\"" }' | \
   grep -v -F '[bot]' >> "${OUTPUT_CSV_FILENAME}"
   # Explanation:
   #
   # - --no-merges: Excludes merge commits from the log.
   # - %h: Abbreviated commit hash
+  # - %p: Abbreviated parent commit hash
   # - %an: Author name
   # - %ae: Author email
   # - %aI: Author date, ISO 8601 format
@@ -125,6 +126,7 @@ GIT_LOG_CYPHER_DIR="${CYPHER_DIR}/GitLog"
 echo "importGitLog: Prepare import by creating indexes..."
 execute_cypher "${GIT_LOG_CYPHER_DIR}/Index_author_name.cypher"
 execute_cypher "${GIT_LOG_CYPHER_DIR}/Index_commit_hash.cypher"
+execute_cypher "${GIT_LOG_CYPHER_DIR}/Index_commit_parent.cypher"
 execute_cypher "${GIT_LOG_CYPHER_DIR}/Index_file_name.cypher"
 
 echo "importGitLog: Deleting all existing git data in the Graph..."
@@ -133,7 +135,10 @@ execute_cypher "${GIT_LOG_CYPHER_DIR}/Delete_git_log_data.cypher"
 echo "importGitLog: Importing git log data into the Graph..."
 time execute_cypher "${GIT_LOG_CYPHER_DIR}/Import_git_log_csv_data.cypher"
 
-echo "importGitLog: Creating connections to nodes with matching file names..."
+echo "importGitLog: Creating relationships for parent commits..."
+execute_cypher "${GIT_LOG_CYPHER_DIR}/Add_HAS_PARENT_relationships_to_commits.cypher"
+
+echo "importGitLog: Creating relationships to nodes with matching file names..."
 execute_cypher "${GIT_LOG_CYPHER_DIR}/Add_RESOLVES_TO_relationships_to_git_files_for_Java.cypher"
 execute_cypher "${GIT_LOG_CYPHER_DIR}/Add_RESOLVES_TO_relationships_to_git_files_for_Typescript.cypher"
 execute_cypher "${GIT_LOG_CYPHER_DIR}/Set_number_of_git_commits.cypher"