Merge branch 'master' into dependabot/maven/gsrs-module-substance-exa…

…mple/com.h2database-h2-2.2.220

.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: '38 1 * * 2'
+
+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}}"

gsrs-fda-substance-extension/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gsrs-module-substances</artifactId>
         <groupId>gov.nih.ncats</groupId>
-        <version>3.1-SNAPSHOT</version>
+        <version>3.1.1-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -139,7 +139,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>products-api</artifactId>
-            <version>3.1-SNAPSHOT</version>
+            <version>3.1.1-SNAPSHOT</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>
@@ -168,7 +168,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>clinical-trials-api</artifactId>
-            <version>3.1-SNAPSHOT</version>
+            <version>3.1.1-SNAPSHOT</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>
@@ -193,4 +193,39 @@
             </exclusions>
         </dependency>
     </dependencies>
+    <!-- Uncomment this for maven public release deployment
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-source-plugin</artifactId>
+                <version>2.2.1</version>
+                <executions>
+                    <execution>
+                        <id>attach-sources</id>
+                        <goals>
+                            <goal>jar-no-fork</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <configuration>
+                    <additionalparam>-Xdoclint:none</additionalparam>
+                    <additionalOptions>-Xdoclint:none</additionalOptions>
+                    <additionalJOption>-Xdoclint:none</additionalJOption>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>attach-javadocs</id>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build> -->
 </project>

gsrs-fda-substance-extension/src/main/java/fda/gsrs/substance/exporters/ExcelSubstanceRelatedProductsExporter.java

@@ -1,18 +1,14 @@
 package fda.gsrs.substance.exporters;
 
-import gsrs.api.AbstractLegacySearchGsrsEntityRestTemplate;
 import gsrs.api.AbstractLegacySearchGsrsEntityRestTemplate.SearchRequest;
 import gsrs.api.AbstractLegacySearchGsrsEntityRestTemplate.SearchResult;
-import ix.ginas.exporters.DefaultParameters;
 import ix.ginas.exporters.ExporterFactory;
 import ix.ginas.exporters.OutputFormat;
 import ix.ginas.exporters.Exporter;
 import ix.ginas.models.v1.Substance;
 
 import gov.hhs.gsrs.products.api.*;
 
-import org.springframework.beans.factory.annotation.Autowired;
-
 import java.io.IOException;
 import java.io.OutputStream;
 import java.util.List;
@@ -21,7 +17,7 @@
 public class ExcelSubstanceRelatedProductsExporter implements Exporter<Substance> {
 	private OutputStream os;
 	private ProductsApi productsApi;
-	private ProductAllDTOExporter prodExporter;
+	private ProductDTOExporter prodExporter;
 
 	public ExcelSubstanceRelatedProductsExporter(OutputStream os, ProductsApi productsApi){
 		this.os = os; //probably use a buffer instead
@@ -31,17 +27,17 @@ public ExcelSubstanceRelatedProductsExporter(OutputStream os, ProductsApi produc
 			//Export Application Factory
 			OutputFormat format = new OutputFormat("xlsx", "SRS Product Data");
 			ExporterFactory.Parameters params = new ExportParameters(format, true);
-			ProductAllDTOExporterFactory factory = new ProductAllDTOExporterFactory();
+			ProductDTOExporterFactory factory = new ProductDTOExporterFactory();
 			this.prodExporter = factory.createNewExporter(os, params);
 
 		} catch (Exception ex) {
 			ex.printStackTrace();
 		}
 	}
 
-	private void exportProduct(ProductMainAllDTO app){
+	private void exportProduct(ProductDTO prod){
 		try {
-			this.prodExporter.export(app);
+			this.prodExporter.export(prod);
 		}catch (Exception ex) {
 			ex.printStackTrace();
 		}
@@ -50,15 +46,15 @@ private void exportProduct(ProductMainAllDTO app){
 	@Override
 	public void export(Substance s) throws IOException{
 
-		SearchResult<ProductMainAllDTO> result = getAllProductsRelatedToSubstance(s);
-		List<ProductMainAllDTO> appList = result.getContent();
+		SearchResult<ProductDTO> result = getAllProductsRelatedToSubstance(s);
+		List<ProductDTO> prodList = result.getContent();
 
-		for (ProductMainAllDTO app: appList) {
+		for (ProductDTO app: prodList) {
 			exportProduct(app);
 		}
 	}
 
-	public SearchResult<ProductMainAllDTO> getAllProductsRelatedToSubstance(Substance s) {
+	public SearchResult<ProductDTO> getAllProductsRelatedToSubstance(Substance s) {
 		try {
 			SearchRequest searchRequest = SearchRequest.builder().q("entity_link_substances:\"" + s.uuid + "\"").top(1000000).simpleSearchOnly(true).build();
 			return productsApi.search(searchRequest);