Merge pull request #2334 from jplag/develop

Merge develop into Main

Author: tsaglam

.github/workflows/complete-e2e.yml

@@ -31,23 +31,23 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-  
+
       - name: Set up JDK
         uses: actions/setup-java@v4
         with:
           java-version: 21
           distribution: 'temurin'
-  
+
       - uses: actions/setup-node@v4
         with:
           node-version: "18"
-  
+
       - name: Build Assembly
         run: mvn -DskipTests clean package assembly:single
-      
+
       - name: Rename Jar
         run: mv cli/target/jplag-*-jar-with-dependencies.jar cli/target/jplag.jar
-  
+
       - name: Upload Assembly
         uses: actions/upload-artifact@v4
         with:
@@ -84,7 +84,7 @@ jobs:
         with:
           java-version: 21
           distribution: 'temurin'
-      
+
       - name: Get JAR
         uses: actions/download-artifact@v4
         with:
@@ -94,7 +94,7 @@ jobs:
         if: ${{ matrix.os == 'windows-latest' }}
         run: |
           Expand-Archive -LiteralPath .github/workflows/files/${{ matrix.dataset.zip }} -DestinationPath ./
-      
+
       - name: Copy and unzip dataset macos and ubuntu
         if: ${{ matrix.os == 'macos-latest' || matrix.os == 'ubuntu-latest'}}
         run: |
@@ -103,12 +103,12 @@ jobs:
       - name: Run JPlag
         run: |
           java -jar jplag.jar ${{ matrix.dataset.folder }} -l ${{ matrix.dataset.language }} -r ${{ matrix.dataset.name }}-report ${{ matrix.dataset.cliArgs }}
-      
+
       - name: Upload result
         uses: actions/upload-artifact@v4
         with:
           name: "${{ matrix.dataset.name }}-${{ matrix.os }}"
-          path: "${{ matrix.dataset.name }}-report.zip"
+          path: "${{ matrix.dataset.name }}-report.jplag"
           retention-days: 30
 
   e2e_test:
@@ -132,7 +132,7 @@ jobs:
         run: |
           npm install
           npm run build
-        
+
       - name: Install playwright
         working-directory: report-viewer
         run: npx playwright install --with-deps

.github/workflows/report-viewer-demo.yml

@@ -5,7 +5,7 @@ on:
   push:
     branches:
       - main
-      
+
 jobs:
   build-jar:
     runs-on: ubuntu-latest
@@ -19,10 +19,10 @@ jobs:
         with:
           java-version: 21
           distribution: 'temurin'
-        
+
       - name: Build Assembly
         run: mvn clean package assembly:single
-        
+
       - name: Upload Assembly
         uses: actions/upload-artifact@v4
         with:
@@ -43,39 +43,39 @@ jobs:
         with:
           java-version: 21
           distribution: 'temurin'
-      
+
       - name: Get JAR
         uses: actions/download-artifact@v4
         with:
           name: JPlag
-      
+
       - name: Copy and unzip submissions
         run: unzip ./.github/workflows/files/progpedia.zip
-        
+
       - name: Rename jar
         run: mv *.jar ./jplag.jar
-  
+
       - name: Run JPlag
         run: java -jar jplag.jar ACCEPTED -bc base -r example
-      
+
       - name: Upload Result
         uses: actions/upload-artifact@v4
         with:
           name: "Result"
-          path: "example.zip"
-            
+          path: "example.jplag"
+
 
   build-and-deploy:
     needs: run-example
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
         uses: actions/checkout@v4
-              
+
       - uses: actions/setup-node@v4
         with:
           node-version: "18"
-        
+
       - name: Set version of Report Viewer
         shell: bash
         run: |
@@ -88,7 +88,7 @@ jobs:
           echo "$json" >  report-viewer/src/version.json
           echo "Version of Report Viewer:"
           cat report-viewer/src/version.json
-      
+
       - name: Download Results
         uses: actions/download-artifact@v4
         with:
@@ -100,14 +100,14 @@ jobs:
         run: |
           npm install
           npm run build-demo
-        
+
       - name: Deploy 🚀
-        uses: JamesIves/[email protected].2
+        uses: JamesIves/[email protected].3
         with:
           branch: gh-pages
           folder: report-viewer/dist
           repository-name: JPlag/Demo
           token: ${{ secrets.SDQ_DEV_DEPLOY_TOKEN }}
           clean: true
           single-commit: true
-  
+

.github/workflows/report-viewer-dev-demo.yml

@@ -0,0 +1,100 @@
+name: Report Viewer Develop Demo Deployment
+
+on:
+  workflow_dispatch: # Use this to dispatch from the Actions Tab
+  push:
+    branches:
+      - develop
+      
+jobs:
+  build-jar:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21
+          distribution: 'temurin'
+        
+      - name: Build Assembly
+        run: mvn clean package assembly:single
+        
+      - name: Upload Assembly
+        uses: actions/upload-artifact@v4
+        with:
+          name: "JPlag"
+          path: "cli/target/jplag-*-jar-with-dependencies.jar"
+
+
+  run-example:
+    needs: build-jar
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21
+          distribution: 'temurin'
+      
+      - name: Get JAR
+        uses: actions/download-artifact@v4
+        with:
+          name: JPlag
+      
+      - name: Copy and unzip submissions
+        run: unzip ./.github/workflows/files/progpedia.zip
+        
+      - name: Rename jar
+        run: mv *.jar ./jplag.jar
+  
+      - name: Run JPlag
+        run: java -jar jplag.jar ACCEPTED -bc base -r example
+      
+      - name: Upload Result
+        uses: actions/upload-artifact@v4
+        with:
+          name: "Result"
+          path: "example.jplag"
+            
+
+  build-and-deploy:
+    needs: run-example
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+              
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "18"
+      
+      - name: Download Results
+        uses: actions/download-artifact@v4
+        with:
+          name: Result
+          path: report-viewer/public
+
+      - name: Install and Build 🔧
+        working-directory: report-viewer
+        run: |
+          npm install
+          npm run build-dev-demo
+        
+      - name: Deploy 🚀
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages
+          folder: report-viewer/dist
+          repository-name: JPlag/DevDemo
+          token: ${{ secrets.SDQ_DEV_DEPLOY_TOKEN }}
+          clean: true
+          single-commit: true
+  

.github/workflows/report-viewer-dev.yml

@@ -27,7 +27,7 @@ jobs:
           npm run build-dev
 
       - name: Deploy 🚀
-        uses: JamesIves/[email protected].2
+        uses: JamesIves/[email protected].3
         with:
           branch: gh-pages
           folder: report-viewer/dist

.github/workflows/scripts/checkHelpText.py

@@ -0,0 +1,115 @@
+'''
+This script extracts all help text parameter descriptions from the documentation and compares it to the help text generated by the jar file.
+Steps:
+1) Get content of files that should contain the help text (mentioned in variable filesToCheck).
+2) Extract all triple fenced code blocks from the file content. (```)
+3) Find the code block that starts with "Parameter descriptions:". This is the one that contains the CLI text.
+4) Remove empty lines at the end of the code block, as this can mess up the comparison.
+5) Get the help text from the jar file using the command "java -jar jplag.jar -h".
+6) Compare the CLI text from the jar with the one in the documentation. If they do not match, add an error to the list of errors.
+7) Print the errors found, if any. If no errors are found, print "No errors found." and exit with code 0.
+
+Important: This script relies on the help text being inside a tripple fe4nced code block (```) starting with "Parameter descriptions:". If this ever changes this script will fail.
+'''
+import subprocess
+
+# Extract all triple fenced blocks from the text and returns them without the ```
+# Each section is a list of lines, and the list of sections is a list of lists
+def getAllCodeSections(text):
+    codeSections = []
+    currentSection = None
+
+    for line in text:
+        if line.startswith("```"):
+            if currentSection is not None:
+                codeSections.append(currentSection)
+                currentSection = None
+            else:
+                currentSection = []
+        else:
+            if currentSection is not None:
+                currentSection.append(line)
+
+    if currentSection is not None:
+        codeSections.append(currentSection)
+
+    return codeSections
+
+# Reads a file as a list of lines
+def getFilesText(file):
+    f = open(file, 'r', encoding='utf-8')
+    return f.read().split('\n')
+
+# Filters the sections to find the one that starts with "Parameter descriptions:", which is the one indicating the CLI text
+def getCliTextCodeSection(sections):
+    for section in sections:
+        if section[0].startswith("Parameter descriptions:"):
+            return section
+    return None
+
+# Removes empty lines at the end of the list
+def removeEmptyLinesAtEndOfDocument(text):
+    while len(text) > 0 and text[-1].strip() == "":
+        text.pop()
+    return text
+
+# Stores the offset of the CLI text in the original file
+lineOffset = {}
+
+# Reads the file and extracts the CLI text from it
+def getCliTextFromFile(file):
+    text = getFilesText(file)
+    codeSections = getAllCodeSections(text)
+    cliTextSection = getCliTextCodeSection(codeSections)
+    if cliTextSection is None:
+        return None
+    removedEmptyLines = removeEmptyLinesAtEndOfDocument(cliTextSection)
+    lineOffset[file] = text.index(cliTextSection[0]) + 1 if cliTextSection else 0
+    return removedEmptyLines
+
+class Error:
+    def __init__(self, fileName, lineNumber, message):
+        self.fileName = fileName
+        self.lineNumber = lineNumber
+        self.message = message
+
+    def __str__(self):
+        offset = lineOffset[self.fileName] if self.fileName in lineOffset else 0
+        return f"{self.fileName.split('/')[-1]}:{self.lineNumber+offset}: {self.message}"
+
+errors = []
+
+# get help text from jar, the first 5 lines get removed as they are not part of the help text in our markdown documents
+helpTextLines = subprocess.run(["java", "-jar", "jplag.jar", "-h"], capture_output=True, text=True).stdout.split('\n')[5::]
+helpTextLines = removeEmptyLinesAtEndOfDocument(helpTextLines)
+
+# these are the files that contain the help text
+filesToCheck = ["../../../README.md", "../../../docs/1.-How-to-Use-JPlag.md"]
+
+# Verifies that the CLI text from the jar matches the one in the md file
+def checkCliTextAgainstHelpText(mdText, fileName):
+    minLines = min(len(mdText), len(helpTextLines))
+    if (len(mdText) != len(helpTextLines)):
+        errors.append(Error(fileName, minLines, f"The number of lines in the CLI text from the jar({len(helpTextLines)}) does not match the md text({len(mdText)})."))
+    for i in range(minLines):
+        if (mdText[i] != helpTextLines[i]):
+            helpSpace = helpTextLines[i].replace(" ", '\u23B5')
+            mdSpace = mdText[i].replace(" ", '\u23B5')
+            errors.append(Error(fileName, i, f"Does not match the CLI text from the jar. Expected: '{helpSpace}', Found: '{mdSpace}'."))
+
+for file in filesToCheck:
+    cliText = getCliTextFromFile(file)
+
+    if cliText is None:
+        errors.append(Error(file, 0, "No CLI text found in the file."))
+    else:
+        checkCliTextAgainstHelpText(cliText, file)
+
+if len(errors) > 0:
+    print("Errors found:")
+    for error in errors:
+        print(error)
+    exit(1)
+else:
+    print("No errors found.")
+    exit(0)