Merge branch 'master' into update_molwitches

.github/workflows/codeql.yml

@@ -0,0 +1,93 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  schedule:
+    - cron: '41 6 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: java-kotlin
+          build-mode: none # This mode only analyzes Java. Set this to 'autobuild' or 'manual' to analyze Kotlin too.
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

pom.xml

@@ -25,7 +25,6 @@
     <groupId>gov.nih.ncats</groupId>
     <artifactId>molwitch-renderer</artifactId>
     <version>1.0.18</version>
-
     <name>Molwitch Renderer</name>
 
     <url>https://github.com/ncats/molwitch-renderer</url>

src/main/java/gov/nih/ncats/molwitch/renderer/NchemicalRenderer.java

@@ -936,6 +936,10 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
 				}
 			}
 
+			//MM experiment 30 May 2024
+			if(ca.getBonds().size()==0) {
+				forceDraw = true;
+			}
 			if (!attatch.equals("")) {
 				attachments.add(attatch);
 				if (ca.getBondCount() == 0) {

src/test/java/gov/nih/ncats/molwitch/renderer/TestRendering.java

@@ -372,5 +372,27 @@ public void testBoundCalc() throws Exception{
         });
     }
 
+    @Test
+    public void renderSingleAtom0Valence() throws Exception{
+        String folder ="images\\";
+        ChemicalRenderer renderer = new ChemicalRenderer();
+        String name = "4XYU5U00C4";
+        Chemical c = Chemical.parseMol(new File(getClass().getResource( "/" + name + ".mol").getFile()));
+        File renderedImageFile = new File(folder + "/" + MolWitch.getModuleName() +"_" + name + ".png");
+        ImageIO.write(renderer.createImage(c, 600), "PNG", renderedImageFile);
+        Assert.assertTrue(renderedImageFile.length()> 4000);
+    }
+
+    @Test
+    public void renderSingleAtomNoValence() throws Exception{
+        String folder ="images\\";
+        ChemicalRenderer renderer = new ChemicalRenderer();
+        String name = "4XYU5U00C4_no_valence";
+        Chemical c = Chemical.parseMol(new File(getClass().getResource(  "/" + name + ".mol").getFile()));
+        File renderedImageFile =new File(folder + MolWitch.getModuleName() +"_" + name + ".png");
+        ImageIO.write(renderer.createImage(c, 600), "PNG", renderedImageFile);
+        Assert.assertTrue(renderedImageFile.length()> 4000);
+    }
+
 }
 

src/test/resources/4XYU5U00C4.mol

@@ -0,0 +1,6 @@
+
+  Marvin  01132105152D          
+
+  1  0  0  0  0  0            999 V2000
+    1.7167   -1.6208    0.0000 C   0  0  0  0  0 15  0  0  0  0  0  0
+M  END

src/test/resources/4XYU5U00C4_no_valence.mol

@@ -0,0 +1,6 @@
+
+
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    7.9279   -7.5332    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+M  END