From 0546b979c05c0bf0d758ba2af712e237ddb7ee8c Mon Sep 17 00:00:00 2001
From: "Gerardo E. Cruz-Ortiz" <59618057+astrogeco@users.noreply.github.com>
Date: Fri, 21 Jan 2022 09:33:08 -0500
Subject: [PATCH] Fix #412, Git error in CodeQL Analyze Action

- Replace Checkout Action for bundle with git clone
- Use symlink to map calling repo workspace to expected cFS Bundle
directory location
- Replace bundle checkout action with git clone
- Adds component-path input parameter
- Adds "code snippets" to CodeQL Analyze action
---
 .github/workflows/codeql-build.yml | 131 ++++++++++++++++++-----------
 osal                               |   2 +-
 2 files changed, 83 insertions(+), 50 deletions(-)

diff --git a/.github/workflows/codeql-build.yml b/.github/workflows/codeql-build.yml
index 773b7ca2b..ff68b7e31 100644
--- a/.github/workflows/codeql-build.yml
+++ b/.github/workflows/codeql-build.yml
@@ -7,18 +7,26 @@ on:
         description: 'Build Prep'
         type: string
         default: 'cp ./cfe/cmake/Makefile.sample Makefile && cp -r ./cfe/cmake/sample_defs sample_defs'
+        required: false
       make-prep:
         description: 'Make Prep'
         type: string
-        default: ''
+        default: 'make prep'
+        required: false
       make:
-        description: 'Make Copy'
+        description: 'Build Command'
         type: string
-        default: 'make'      
+        default: '' #Typically `make` or `make install`. Default is blank for workflows that don't need to build source
+        required: false
       tests: 
-        description: 'Tests'
+        description: 'Tests Command'
         type: string
-        default: ''  
+        default: '' #Typically `make test` requires environment variable `ENABLE_UNIT_TEST=true` at `make prep` stage
+        required: false
+      component-path:
+        description: 'Path to repo being tested in a cFS bundle setup'
+        type: string
+        required: true
 
 env:
   SIMULATION: native
@@ -40,7 +48,7 @@ jobs:
           concurrent_skipping: 'same_content'
           skip_after_successful_duplicate: 'true'
           do_not_skip: '["pull_request", "workflow_dispatch", "schedule"]'
-          
+
   CodeQL-Security-Build:
     #Continue if check-for-duplicates found no duplicates. Always runs for pull-requests.
     needs: check-for-duplicates
@@ -48,40 +56,56 @@ jobs:
     runs-on: ubuntu-18.04
     timeout-minutes: 15
 
+    permissions:
+      security-events: write
+
     steps:
-      # Checks out a copy of your repository
-      - name: Checkout code
+      # Checks out a copy of calling repository
+      - name: Checkout Main Repo
         uses: actions/checkout@v2
-        with:
-          repository: nasa/cFS
-          submodules: true
 
-      - name: Check versions
+      - name: Clone cFS bundle
         run: |
-           git log -1 --pretty=oneline
-           git submodule
-           
+          cd ..
+          git clone https://github.com/nasa/cFS.git --recurse-submodules
+          cd cFS
+          git log -1 --pretty=oneline
+          git submodule
+          rm -r .git
+
+      - name: Create symlink to current repo
+        run: |
+          cd ../cFS
+          rm -r ${{ inputs.component-path }} 
+          ln -s ${{github.workspace}} ${{ inputs.component-path }} 
+
+        # Setup the build system
+      - name: cFS Build Setup
+        run: ${{ inputs.setup }}
+        working-directory: ../cFS
+
+      - name: Prep Build
+        run: ${{ inputs.make-prep }}
+        working-directory: ../cFS
+
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v1
         with:
           languages: c
           config-file: nasa/cFS/.github/codeql/codeql-security.yml@main
-          
-      - name: Copy sample_defs
-        run: ${{ inputs.setup }}
 
-      - name: Make prep
-        run: ${{ inputs.make-prep }}
-      
-      - name: Make Install
+      - name: Build
         run: ${{ inputs.make }}
+        working-directory: ../cFS 
 
-      - name: Run tests
-        run: ${{ inputs.tests }}
+      # - name: Run tests
+      #   run: ${{ inputs.tests }}
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v1
-        
+        with:
+          add-snippets: true 
+
   CodeQL-Coding-Standard-Build:
     #Continue if check-for-duplicates found no duplicates. Always runs for pull-requests.
     needs: check-for-duplicates
@@ -89,24 +113,36 @@ jobs:
     runs-on: ubuntu-18.04
     timeout-minutes: 15
 
+    permissions:
+      security-events: write
     steps:
-      # Checks out a copy of your repository
-      - name: Checkout code
+      # Checks out a copy of calling repository
+      - name: Checkout Main Repo
         uses: actions/checkout@v2
-        with:
-          repository: nasa/cFS
-          submodules: true
 
-      - name: Check versions
+      - name: Clone cFS bundle
         run: |
-           git log -1 --pretty=oneline
-           git submodule
-      - name: Checkout codeql code      
-        uses: actions/checkout@v2
-        with:
-          repository: github/codeql 
-          submodules: true 
-          path: codeql
+          cd ..
+          git clone https://github.com/nasa/cFS.git --recurse-submodules
+          cd cFS
+          git log -1 --pretty=oneline
+          git submodule
+          rm -r .git
+
+      - name: Create symlink to current repo
+        run: |
+          cd ../cFS
+          rm -r ${{ inputs.component-path }} 
+          ln -s ${{github.workspace}} ${{ inputs.component-path }} 
+
+        # Setup the build system
+      - name: cFS Build Setup
+        run: ${{ inputs.setup }}
+        working-directory: ../cFS
+
+      - name: Prep Build
+        run: ${{ inputs.make-prep }}
+        working-directory: ../cFS
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v1
@@ -114,17 +150,14 @@ jobs:
           languages: c
           config-file: nasa/cFS/.github/codeql/codeql-coding-standard.yml@main
 
-      - name: Copy sample_defs
-        run: ${{ inputs.setup }}
-
-      - name: Make prep
-        run: ${{ inputs.make-prep }}
-
-      - name: Make Install
+      - name: Build
         run: ${{ inputs.make }}
+        working-directory: ../cFS 
 
-      - name: Run tests
-        run: ${{ inputs.tests }}
+      # - name: Run tests
+      #   run: ${{ inputs.tests }}
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v1
\ No newline at end of file
+        uses: github/codeql-action/analyze@v1
+        with:
+          add-snippets: true 
diff --git a/osal b/osal
index 4cc6dbb50..e3d2f4c1c 160000
--- a/osal
+++ b/osal
@@ -1 +1 @@
-Subproject commit 4cc6dbb5019d0589d5ce52e3755a0b7a012ade3c
+Subproject commit e3d2f4c1c1e455dc7b5b42a7776451d3a1853c1a