Updating actions to create a build/test matrix. Report version when s…

…tarting kb-sdk. Add release notes. Fix KBase report class name error in Java version.

.github/workflows/kb_sdk-actions.yml

@@ -5,8 +5,16 @@ on:
 
 jobs:
 
-  kb_sdk_build:
-    runs-on: ubuntu-latest
+  test_kb-sdk_builds:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-16.04, ubuntu-18.04, ubuntu-20.04]
+        language: [perl, python, java]
+        test_type: [base, example]
+
     steps:
       - name: Checkout
         uses: actions/checkout@v2
@@ -16,43 +24,113 @@ jobs:
         with:
           java-version: 1.8
 
+      - name: Build with Ant
+        run: |
+          make
+
       - name: Add bin to $PATH
         run: |
           echo "::add-path::$GITHUB_WORKSPACE/bin"
 
+      - name: checking kb-sdk functions
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          env
+          kb-sdk help
+          kb-sdk version
+
+      - name: init base repo
+        if: matrix.test_type == 'base'
+        env:
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          kb-sdk init -l $LANGUAGE_TOKEN -u user SampleApp
+
+      - name: init example repo
+        if: matrix.test_type == 'example'
+        env:
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          kb-sdk init -l $LANGUAGE_TOKEN -u user --example SampleApp
+
+      - name: test ${{ matrix.test_type }} repo
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          cd SampleApp
+          kb-sdk test || true
+          sed -i "s/test_token=/test_token=$KBASE_TEST_TOKEN/" test_local/test.cfg
+          kb-sdk test
+
+      - name: make resulting app available as artefact in case of failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: kbaseapp-${{ matrix.language }}-${{ matrix.test_type }}-${{ matrix.os }}
+          path: SampleApp
+
+
+  test_existing_repos:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-16.04, ubuntu-18.04, ubuntu-20.04]
+        app: [WsLargeDataIO, KBaseReport]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v1
+        with:
+          java-version: 1.8
+
       - name: Build with Ant
         run: |
           make
+
+      - name: Add bin to $PATH
+        run: |
+          echo "::add-path::$GITHUB_WORKSPACE/bin"
+
+      - name: checking basic kb-sdk functions
+        run: |
           env
+          kb-sdk help
+          kb-sdk version
 
-      - name: Upload kb-sdk build
-        uses: actions/upload-artifact@v2
+      - name: Checkout existing kbase module ${{ matrix.app }}
+        uses: actions/checkout@v2
         with:
-          name: kb-sdk_build
-          path: bin/kb-sdk
+          repository: kbaseapps/${{ matrix.app }}
+          path: kbase_app
 
-      - name: checking kb-sdk functions
+      - name: prep for repo tests
+        run: |
+          cd kbase_app
+          kb-sdk test || true
+
+      - name: edit test.cfg
         env:
           KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
         run: |
-          kb-sdk help
-          kb-sdk version
-          kb-sdk init -l perl -u user PerlBase
-          cd PerlBase
-          kb-sdk test
-          cd ..
-          rm -rf PerlBase
-          kb-sdk init -l perl -u user --example PerlExample
-          cd PerlExample
-          kb-sdk test
-          cd ..
-          rm -rf PerlExample
-          kb-sdk init -l python -u user --example PythonExample
-          cd PythonExample
-          make
-          kb-sdk test
-          cd ..
-          rm -rf PythonExample
-          kb-sdk init -l java -u user --example JavaExample
-          cd JavaExample
+          cd kbase_app
+          sed -i "s/test_token=/test_token=$KBASE_TEST_TOKEN/" test_local/test.cfg
+
+      - name: run test
+        run: |
+          cd kbase_app
           kb-sdk test
+
+      - name: make resulting app available as artefact in case of failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: kbaseapp-${{ matrix.app }}-${{ matrix.os }}
+          path: kbase_app

RELEASE_NOTES.txt

@@ -1,11 +1,21 @@
 OVERVIEW
 -----------------------------------------
-The KBase SDK is a set of tools for developing new modules 
-that can be dynamically registered and run on the KBase 
-platform.  Modules include all code, specification files, and 
-documentation needed to define and run a set of methods 
+The KBase SDK is a set of tools for developing new modules
+that can be dynamically registered and run on the KBase
+platform.  Modules include all code, specification files, and
+documentation needed to define and run a set of methods
 in the KBase Narrative interface.
 
+VERSION: 1.2.2 (Released 06/xx/2020)
+------------------------------------
+NEW FEATURES:
+- kb-sdk version reports the build time and date of the instance
+- kb-sdk can use the environment variable KBASE_TEST_TOKEN if a test token is not present in the test.cfg file
+- GitHub Actions now used to run basic tests on initialising and testing new base and sample repos.
+
+BUG FIXES:
+- Java client uses the correct name for KBase report
+
 VERSION: 1.2.0 (Released 11/14/2018)
 ------------------------------------
 NEW FEATURES:
@@ -74,7 +84,7 @@ VERSION: 1.0.0 (Released 11/19/2015)
 ------------------------------------------
 NEW FEATURES:
 - R language is now supported for generation of clients and server stubs.
-- Test sub-command is fully implemented for all 4 languages (perl, 
+- Test sub-command is fully implemented for all 4 languages (perl,
    python, java and R).
 - Version sub-command was added
 

src/java/us/kbase/mobu/ModuleBuilder.java

@@ -49,7 +49,7 @@ public class ModuleBuilder {
     public static final String GLOBAL_SDK_HOME_ENV_VAR = "KB_SDK_HOME";
     public static final String DEFAULT_METHOD_STORE_URL = "https://appdev.kbase.us/services/narrative_method_store/rpc";
 
-    public static final String VERSION = "1.2.0";
+    public static final String VERSION = "1.2.2";
 
     public static void main(String[] args) throws Exception {
 
@@ -58,7 +58,6 @@ public static void main(String[] args) throws Exception {
         JCommander jc = new JCommander(gArgs);
         jc.setProgramName(MODULE_BUILDER_SH_NAME);
 
-
         // add the 'init' command
         InitCommandArgs initArgs = new InitCommandArgs();
         jc.addCommand(INIT_COMMAND, initArgs);
@@ -95,6 +94,9 @@ public static void main(String[] args) throws Exception {
         RunCommandArgs runArgs = new RunCommandArgs();
         jc.addCommand(RUN_COMMAND, runArgs);
 
+        // print name and version
+        printVersion();
+
         // parse the arguments and gracefully catch any errors
         try {
             jc.parse(args);
@@ -383,7 +385,7 @@ public static String getGitProp(String propertyToGet) {
 
 
     private static int runVersionCommand(VersionCommandArgs testArgs, JCommander jc) {
-        printVersion();
+        // version was printed at start up, so just exit
         return 0;
     }
 

src/java/us/kbase/templates/module_java_impl.vm.properties

@@ -22,7 +22,7 @@ import assemblyutil.GetAssemblyParams;
 import assemblyutil.SaveAssemblyParams;
 import kbasereport.CreateParams;
 import kbasereport.KBaseReportClient;
-import kbasereport.Report;
+import kbasereport.SimpleReport;
 import kbasereport.ReportInfo;
 import kbasereport.WorkspaceObject;
 import net.sf.jfasta.FASTAElement;
@@ -73,11 +73,11 @@ public class ${java_module_name}Server extends JsonServerServlet {
     public FilterContigsResults filterContigs(FilterContigsParams params, AuthToken authPart, RpcContext jsonRpcContext) throws Exception {
         FilterContigsResults returnVal = null;
         //BEGIN run_${module_name}
-        
+
         // Print statements to stdout/stderr are captured and available as the App log
         System.out.println("Starting filter contigs. Parameters:");
         System.out.println(params);
-        
+
         /* Step 1 - Parse/examine the parameters and catch any errors
          * It is important to check that parameters exist and are defined, and that nice error
          * messages are returned to users.  Parameter values go through basic validation when
@@ -103,7 +103,7 @@ public class ${java_module_name}Server extends JsonServerServlet {
             throw new IllegalArgumentException("min_length parameter cannot be negative (" +
                     minLength + ")");
         }
-        
+
         /* Step 2 - Download the input data as a Fasta file
          * We can use the AssemblyUtils module to download a FASTA file from our Assembly data
          * object. The return object gives us the path to the file that was created.
@@ -142,26 +142,26 @@ public class ${java_module_name}Server extends JsonServerServlet {
         final String resultText = String.format("Filtered assembly to %s contigs out of %s",
                 remaining, total);
         System.out.println(resultText);
-        
+
         // Step 4 - Save the new Assembly back to the system
-        
+
         final String newAssyRef = assyUtil.saveAssemblyFromFasta(new SaveAssemblyParams()
                 .withAssemblyName(fileobj.getAssemblyName())
                 .withWorkspaceName(workspaceName)
                 .withFile(new FastaAssemblyFile().withPath(out.toString())));
-        
+
         // Step 5 - Build a Report and return
-        
+
         final KBaseReportClient kbr = new KBaseReportClient(callbackURL, authPart);
         // see note above about bad practice
         kbr.setIsInsecureHttpConnectionAllowed(true);
         final ReportInfo report = kbr.create(new CreateParams().withWorkspaceName(workspaceName)
-                .withReport(new Report().withTextMessage(resultText)
+                .withReport(new SimpleReport().withTextMessage(resultText)
                         .withObjectsCreated(Arrays.asList(new WorkspaceObject()
                                 .withDescription("Filtered contigs")
                                 .withRef(newAssyRef)))));
         // Step 6: contruct the output to send back
-        
+
         returnVal = new ReportResults()
                 .withReportName(report.getName())
                 .withReportRef(report.getRef());
@@ -195,7 +195,7 @@ import java.net.MalformedURLException;
 
 import kbasereport.CreateParams;
 import kbasereport.KBaseReportClient;
-import kbasereport.Report;
+import kbasereport.SimpleReport;
 import kbasereport.ReportInfo;
 import kbasereport.WorkspaceObject;
 import ${java_package}.ReportResults;
@@ -221,7 +221,7 @@ import ${java_package}.ReportResults;
         final String parameter_1 = params.get("parameter_1").asInstance();
         final ReportInfo report = kbr.create(new CreateParams()
                                         .withWorkspaceName(ws_name)
-                                        .withReport(new Report()
+                                        .withReport(new SimpleReport()
                                                 .withTextMessage(parameter_1)
                                                 .withObjectsCreated(new java.util.ArrayList<WorkspaceObject>())));
 
@@ -230,4 +230,4 @@ import ${java_package}.ReportResults;
                         .withReportRef(report.getRef());
 
 //END run_${module_name}
-#end
+#end