[Clean] Clean run nondex

auto-run-nondex/README.md

@@ -1,50 +1,48 @@
-# `runNondex`
+# runNondex
 
-This script runs individual modules in the specified project with the `Nondex` tool and shows results automatically in the `markdown` format.
 
-Output file is located inside the project folder and called `report_md.md` The output would only contain tests that are detected by the nondex tool as flaky, and the result includes the seeds used for the test and the status of the test result.
+What repo we want to run Nondex on?
 
-All the log information would be stored inside the `.runNondex` folder inside the project. 
+1. This repo has not appeared in the latest `pr-data.csv`
+2. This repo contains pom.xml file.
 
-Inside the `.runNondex` folder: 
-- `./LOGSSS` contains nondex logs for all submodules.
-- `LOGresult` contains a list of file paths that contain test errors.
-- `htmlOutput` contains a list of file paths for the HTML files generated by the nondex tool.
+
+
+# Dependencies
 
 It is recommended to use a virtual python environment for the required modules:
 ```bash
 python3 -m venv <path_to_the_new_virtual_environment>
 source <path_to_the_new_virtual_environment>/bin/activate
 ```
-
 Make sure to first install packages in `requirements.txt`.
 
 ```bash
 # sudo apt install python3-pip
 cd auto-run-nondex
 pip install -r requirements.txt
 ```
+# runNondexAll
 
-# `runNondexUnderAuthor`
-
-This script runs all the valid repos under a given author using the `runNondex` script above. 
+This is simplified script for quick start
+Go to folder of .pom.xml files, and check all the result in result.log
 
-The valid repo is defined as:
+# runNondex module:
+```bash
+./runNondex.sh <project_folder_path> <optional-directory-name>
+```
 
-1. This repo has not appeared in the latest `pr-data.csv`
-2. This repo contains pom.xml file.
+With the second parameter in `./runNondex.sh`, you can only run Nondex on modules in a certain directory instead of the entire project.
 
 
+# runNondexUnderAuthor
 
 
-### Usage:
 ```bash
-./runNondex.sh <project_folder_path> <optional-directory-name>
 ./runNondexUnderAuthor.sh <author_repository_url> <path_where_you_want_to_clone_those repos>
 ```
 
-With the second parameter in `./runNondex.sh`, you can only run Nondex on modules in a certain directory instead of the entire project.
-
+How to find the Author?
 
 >  To find the author_repository_url, find the author that you want to run Nondex with, and get this author's repository overview url (e.g., https://github.com/orgs/spotify/repositories). Note that you don't need to provide the url with other parameters, as the script will automatically add the parameters needed.
 >
@@ -65,3 +63,10 @@ With the second parameter in `./runNondex.sh`, you can only run Nondex on module
 >  `find . -maxdepth 1 -type d \( ! -name . \) -exec bash -c "cd '{}' &&  git rev-parse HEAD && git config --get remote.origin.url | rev | cut -c5- | rev  && cat .runNondex/htmlOutput && cat report_md.md" \; &> progress_stats.md`
 
 
+# Folder structure
+
+All the log information would be stored inside the `.runNondex` folder inside the project.
+
+- `./modulelog` contains nondex logs for all submodules.
+- `result` contains a list of file paths that contain test errors.
+- `htmlOutput` contains a list of file paths for the HTML files generated by the nondex tool.

auto-run-nondex/runNondex.sh

@@ -1,25 +1,33 @@
 #!/bin/bash
 DIR="${PWD}"
-nondex_version="2.1.1"
+nondex_version="2.1.1" #LST version
+
 runNondex () {
+    #get the modules
     cd $1
     mvn install -DskipTests
     mvn -Dexec.executable='echo' -Dexec.args='${project.artifactId}' exec:exec -q -fn | tee modnames
     if grep -q "[ERROR]" modnames; then
-        echo !!!!!
+        echo "ERROR: There are errors in the project"
         exit 1
     else
-        echo OK
+        echo "No errors detected"
     fi
+
     mkdir .runNondex
-    mkdir ./.runNondex/LOGSSS
+    mkdir ./.runNondex/modulelog
+
+
+    # run nondex on each module
     input="modnames"
     while IFS= read -r line
     do
-        mvn edu.illinois:nondex-maven-plugin:$nondex_version:nondex -pl :$line -Dlicense.skip=true | tee ./.runNondex/LOGSSS/$line.log
+        mvn edu.illinois:nondex-maven-plugin:$nondex_version:nondex -pl :$line -Dlicense.skip -Drat.skip --fail-at-end | tee ./.runNondex/modulelog/$line.log
     done < "$input"
-    grep -rnil "There are test failures" ./.runNondex/LOGSSS/* | tee ./.runNondex/LOGresult
-    input=".runNondex/LOGresult"
+    grep -rnil "There are test failures" ./.runNondex/modulelog/* | tee ./.runNondex/result
+
+    # format the result
+    input=".runNondex/result"
     while IFS= read -r line
     do
         grep "test_results.html" $line | tee ./.runNondex/htmlOutput

auto-run-nondex/runNondexAll.sh

@@ -0,0 +1,5 @@
+# Assume this script is run from the folder of .pom.xml files
+
+mvn edu.illinois:nondex-maven-plugin:2.1.1:nondex -Dlicense.skip -Drat.skip --fail-at-end | tee ./nondex.log
+
+awk '/\[INFO\] Across all seeds:/{flag=1; next} /\[INFO\] Test results can be found at:/{flag=0} flag' "./nondex.log" > "./result"