Add patch to make main look like Ziggy-0.3.0-20230214

Rebasing the Ziggy-0.3.0 release onto main didn't go smoothly this time.

buildSrc/src/main/java/gov/nasa/ziggy/buildutil/ZiggyCpp.java

@@ -7,7 +7,6 @@
 import org.gradle.api.Project;
 import org.gradle.api.tasks.InputFiles;
 import org.gradle.api.tasks.OutputFile;
-import org.gradle.api.tasks.Input;
 import org.gradle.api.tasks.TaskAction;
 import org.gradle.api.tasks.Input;
 
@@ -30,163 +29,6 @@
  *
  */
 public class ZiggyCpp extends DefaultTask {
-
-	/** 
-	 * Data and methods used to perform the C++ compile and link. 
-	 */
-	private ZiggyCppPojo ziggyCppPojo = new ZiggyCppPojo();
-
-	/**
-	 * Default constructor. Provides the ZiggyCppPojo object with directories for the
-	 * project and default options, if set
-	 */
-	public ZiggyCpp() {
-		Project project = getProject();
-		ziggyCppPojo.setBuildDir(project.getBuildDir());
-		ziggyCppPojo.setRootDir(pipelineRootDir(project));
-		if (project.hasProperty(ZiggyCppPojo.DEFAULT_COMPILE_OPTIONS_GRADLE_PROPERTY)) {
-			ziggyCppPojo.setCompileOptions(ZiggyCppPojo.gradlePropertyToList(
-					project.property(ZiggyCppPojo.DEFAULT_COMPILE_OPTIONS_GRADLE_PROPERTY)));
-		}
-		if (project.hasProperty(ZiggyCppPojo.DEFAULT_LINK_OPTIONS_GRADLE_PROPERTY)) {
-			ziggyCppPojo.setLinkOptions(ZiggyCppPojo.gradlePropertyToList(
-					project.property(ZiggyCppPojo.DEFAULT_LINK_OPTIONS_GRADLE_PROPERTY)));
-		}
-		if (project.hasProperty(ZiggyCppPojo.DEFAULT_RELEASE_OPTS_GRADLE_PROPERTY)) {
-			ziggyCppPojo.setReleaseOptimizations(ZiggyCppPojo.gradlePropertyToList(
-					project.findProperty(ZiggyCppPojo.DEFAULT_RELEASE_OPTS_GRADLE_PROPERTY)));
-		}
-		if (project.hasProperty(ZiggyCppPojo.DEFAULT_DEBUG_OPTS_GRADLE_PROPERTY)) {
-			ziggyCppPojo.setDebugOptimizations(ZiggyCppPojo.gradlePropertyToList(
-					project.findProperty(ZiggyCppPojo.DEFAULT_DEBUG_OPTS_GRADLE_PROPERTY)));
-		}
-	}
-
-	/**
-	 * Returns the root directory of the pipeline
-	 * @param project Current project
-	 * @return rootDir if the pipelineRootDir project property is not set; if that 
-	 * property is set, the contents of the pipelineRootDir property are returned as a File
-	 */
-	public static File pipelineRootDir(Project project) {
-		File pipelineRootDir = null;
-		if (project.hasProperty(ZiggyCppPojo.PIPELINE_ROOT_DIR_PROP_NAME)) {
-			pipelineRootDir = new File(project.property(
-					ZiggyCppPojo.PIPELINE_ROOT_DIR_PROP_NAME).toString());
-		} else {
-			pipelineRootDir = project.getRootDir();
-		}
-		return pipelineRootDir;
-	}
-
-	/** Provides access to the ZiggyCppPojo action() method for Gradle. */
-	@TaskAction
-	public void action() {
-		ziggyCppPojo.action();
-	}
-
-	/** 
-	 * Provides access to the ZiggyCppPojo list of C++ files for Gradle, and
-	 * specifies for gradle that those files are the inputs for this task.
-	 * @return List of C++ files found in the C++ source file directory.
-	 */
-	@InputFiles
-	public List<File> getCppFiles() {
-		return ziggyCppPojo.getCppFiles();
-	}
-
-	/**
-	 * Provides Gradle with access to the ZiggyCppPojo File that will be the final product
-	 * of the build. Also specifies that this file is the output for this task. 
-	 * @return File containing the target product for a task. 
-	 */
-	@OutputFile
-	public File getBuiltFile() {
-		return ziggyCppPojo.getBuiltFile();
-	}
-
-	//	Below are setters and getters for the ZiggyCppPojo members that must be mutated
-	//	by ZiggyCpp tasks in gradle. In principle only setters are needed, but in the
-	//	interest of sanity getters are also provided. Note that not all ZiggyCppPojo
-	//	members need to be set by ZiggyCpp, there are a number that are used internally
-	//	and are not set as part of a task. 
-	//
-	//	Note that the setters take Object and List<Object> rather than String and List<String>.
-	//	This is because Gradle allows its text string objects to be either Java String class or
-	//	Groovy GString class. Consequently, we pass everything to ZiggyCppPojo as Objects, and
-	//	ZiggyCppPojo uses the toString() methods to convert everything to Java Strings. 
-
-	//	Path to the C++ source files
-	public void setCppFilePaths(List<Object> cppFilePaths) {
-		ziggyCppPojo.setCppFilePaths(cppFilePaths);
-	}
-	@Input
-	public List<String> getCppFilePaths() {
-		return ziggyCppPojo.getCppFilePaths();
-	}
-
-	//	Paths for include files
-	public void setIncludeFilePaths(List<? extends Object> includeFilePaths) {
-		ziggyCppPojo.setIncludeFilePaths(includeFilePaths);
-	}
-	@Input
-	public List<String> getIncludeFilePaths() {
-		return ziggyCppPojo.getIncludeFilePaths();
-	}
-
-	//	paths for libraries that must be linked in 
-	public void setLibraryPaths(List<? extends Object> libraryPaths) {
-		ziggyCppPojo.setLibraryPaths(libraryPaths);
-	}
-	@Input
-	public List<String> getLibraryPaths() {
-		return ziggyCppPojo.getLibraryPaths();
-	}
-
-	//	Libraries that must be linked in
-	public void setLibraries(List<? extends Object> libraries) {
-		ziggyCppPojo.setLibraries(libraries);
-	}
-	@Input
-	public List<String> getLibraries() {
-		return ziggyCppPojo.getLibraries();
-	}
-
-	//	compiler options
-	public void setCompileOptions(List<? extends Object> compileOptions) {
-		ziggyCppPojo.setCompileOptions(compileOptions);;
-	}
-	@Input
-	public List<String> getCompileOptions() {
-		return ziggyCppPojo.getCompileOptions();
-	}
-
-	//	linker options
-	public void setLinkOptions(List<? extends Object> linkOptions) {
-		ziggyCppPojo.setLinkOptions(linkOptions);
-	}
-	@Input
-	public List<String> getLinkOptions() {
-		return ziggyCppPojo.getLinkOptions();
-	}
-
-	//	output type (executable, shared library, static library)
-	public void setOutputType(Object outputType) {
-		ziggyCppPojo.setOutputType(outputType);
-	}
-	@Input
-	public BuildType getOutputType() {
-		return ziggyCppPojo.getOutputType();
-	}
-
-	//	Name of file to be produced
-	public void setOutputName(Object name) {
-		ziggyCppPojo.setOutputName(name);
-	}
-	@Input
-	public String getOutputName() {
-		return ziggyCppPojo.getOutputName();
-	}
 
     /**
      * Data and methods used to perform the C++ compile and link.

doc/user-manual/data-receipt.md

@@ -18,4 +18,4 @@ Let's fix that now.
 
 [[Previous]](delete-tasks.md)
 [[Up]](user-manual.md)
-[[Next]](data-receipt-execution.md)
+[[Next]](data-receipt-execution.md)

doc/user-manual/delete-tasks.md

@@ -32,4 +32,4 @@ This is the same idea, except it's the pop-up menu for the instance table, and y
 
 [[Previous]](rerun-task.md)
 [[Up]](ziggy-gui-troubleshooting.md)
-[[Next]](select-hpc.md)data-receipt.md)
+[[Next]](select-hpc.md)

doc/user-manual/downloading-and-building-ziggy.md

@@ -1,4 +1,4 @@
-<a href="pipeline-architecture.md">[Previous]</a> <a href="user-manual.md">[Up]</a> <a href="configuring-pipeline.md">[Next]</a>
+<!-- -*-visual-line-*- -->
 
 [[Previous]](pipeline-architecture.md)
 [[Up]](user-manual.md)

doc/user-manual/event-handler-examples.md

@@ -4,7 +4,7 @@
 [[Up]](event-handler.md)
 [[Next]](event-handler-labels.md)
 
-## Event Handler: Examples
+## Event Handler Examples
 
 Now that we've looked at the general concept of event handlers, and we've talked about how to define an event handler, let's work through some examples using the sample pipeline. 
 
@@ -185,4 +185,3 @@ The first column is the event ID -- this is a simple, monotonically-increasing i
 [[Previous]](event-handler-definition.md)
 [[Up]](event-handler.md)
 [[Next]](event-handler-labels.md)
-

doc/user-manual/event-handler-intro.md

@@ -4,7 +4,7 @@
 [[Up]](event-handler.md)
 [[Next]](event-handler-definition.md)
 
-## Event Handler: Introduction
+## Introduction to Event Handlers
 
 Ziggy's predecessors in the pipeline infrastructure field (the Kepler SOC's PI module and TESS SPOC's Spiffy)  were designed to require a lot of in-person handling by pipeline users. In particular, they had no capacity to take actions without somebody, somewhere, issuing a command or pressing a button on the console. 
 
@@ -160,5 +160,4 @@ As soon as the pipeline starts, Ziggy deletes the ready files for reeves-gabrels
 
 [[Previous]](event-handler.md)
 [[Up]](event-handler.md)
-[[Next]](event-handler-definition.md)event-handler-definition.md)
-
+[[Next]](event-handler-definition.md))

doc/user-manual/event-handler-labels.md

@@ -4,7 +4,7 @@
 [[Up]](event-handler.md)
 [[Next]](dusty-corners.md)
 
-## Event Handler: Algorithms
+## Sending Event Information to Algorithms
 
 The event handler, and all of the information associated with it, is mainly intended for use by Ziggy: Ziggy uses the information to select a pipeline to start, to figure out which data receipt directories it can import, etc. That said, it's possible that event information can be useful to the algorithms as well. In the case when an algorithm runs in a pipeline that got kicked off by an event, there can be some value in giving the algorithm information about the handler and the event. 
 

doc/user-manual/remote-dialog.md

@@ -80,4 +80,4 @@ Alternately, you may want to discard all your changes and start over tuning the
 
 [[Previous]](select-hpc.md)
 [[Up]](select-hpc.md)
-[[Next]](hpc-cost.md)hpc-cost.md)
+[[Next]](hpc-cost.md)

src/main/java/gov/nasa/ziggy/data/management/Acknowledgement.java

@@ -149,8 +149,7 @@ public static boolean validAcknowledgementExists(Path workingDir, Manifest manif
             xmlManager = new ValidatingXmlManager<>(Acknowledgement.class);
             Acknowledgement ack = xmlManager.unmarshal(acknowledgementPath.toFile());
             return ack.transferStatus.equals(DataReceiptStatus.VALID);
-		} catch (InstantiationException | IllegalAccessException | SAXException | JAXBException
-				| IllegalArgumentException | InvocationTargetException | NoSuchMethodException | SecurityException e) {
+        } catch (InstantiationException | IllegalAccessException | SAXException | JAXBException e) {
             throw new PipelineException(
                 "Unable to read acknowledgement " + acknowledgementPath.toString(), e);
         }
@@ -417,11 +416,11 @@ public int hashCode() {
         @Override
         public boolean equals(Object obj) {
             if (this == obj) {
-				return true;
-			}
+                return true;
+            }
             if (obj == null || getClass() != obj.getClass()) {
-				return false;
-			}
+                return false;
+            }
             AcknowledgementEntry other = (AcknowledgementEntry) obj;
             return Objects.equals(name, other.name) && Objects.equals(checksum, other.checksum)
                 && size == other.size && transferStatus == other.transferStatus

src/main/java/gov/nasa/ziggy/data/management/Manifest.java

@@ -412,11 +412,11 @@ public int hashCode() {
         @Override
         public boolean equals(Object obj) {
             if (this == obj) {
-				return true;
-			}
+                return true;
+            }
             if (obj == null || getClass() != obj.getClass()) {
-				return false;
-			}
+                return false;
+            }
             ManifestEntry other = (ManifestEntry) obj;
             return Objects.equals(checksum, other.checksum) && Objects.equals(name, other.name)
                 && size == other.size;

src/main/java/gov/nasa/ziggy/module/PipelineInputs.java

@@ -255,17 +255,11 @@ public void writeSubTaskInputs(int seqNum) {
         String moduleName = moduleName();
         String filename = ModuleInterfaceUtils.inputsFileName(moduleName, seqNum);
         log.info("Writing file " + filename + " to sub-task directory");
-
-		// Note: you might think that we shouldn't need this getProperty call when
-		// constructing the File for use as the inputs file. And you'd be right! The
-		// problem is that starting in Java 11, changing the user.dir property doesn't
-		// change the working directory, but does change the value of the system
-		// property. Thus we need to include its value here so that unit tests work
-		// correctly.
-		File f = new File(System.getProperty("user.dir"), ModuleInterfaceUtils.inputsFileName(moduleName, seqNum));
-        hdf5ModuleInterface.writeFile(
-				f, this,
-				true);
+        hdf5ModuleInterface.writeFile(DirectoryProperties.workingDir()
+            .resolve(ModuleInterfaceUtils.inputsFileName(moduleName, seqNum))
+            .toFile(), this, true);
+//        hdf5ModuleInterface.writeFile(
+//            new File(ModuleInterfaceUtils.inputsFileName(moduleName, seqNum)), this, true);
         ModuleInterfaceUtils.writeCompanionXmlFile(this, moduleName, seqNum);
     }
 

src/main/java/gov/nasa/ziggy/util/io/FileUtil.java

@@ -272,7 +272,7 @@ public static Set<PosixFilePermission> modeToPosixFilePermissions(int mode) {
      */
     public static void cleanDirectoryTree(Path directory, boolean force) throws IOException {
         if (force) {
-            setPosixPermissionsRecursively(directory, "rw-r--r--", "rwxr-xr-x");
+            prepareDirectoryTreeForOverwrites(directory);
         }
         try (DirectoryStream<Path> stream = Files.newDirectoryStream(directory)) {
             for (Path file : stream) {

src/test/java/gov/nasa/ziggy/ZiggyDirectoryRule.java

@@ -54,7 +54,7 @@ public Statement apply(Statement statement, Description description) {
             Files.createDirectories(directory);
 
             // Clean the new directory prior to use.
-            FileUtil.cleanDirectoryTree(directory);
+            FileUtil.cleanDirectoryTree(directory, true);
 
             return new Statement() {
                 @Override

src/test/java/gov/nasa/ziggy/data/management/DataFileManagerTest.java

@@ -24,7 +24,6 @@
 import java.util.TreeSet;
 import java.util.stream.Collectors;
 
-import org.junit.After;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -34,8 +33,8 @@
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
-//import com.google.common.io.Files;
 
+import gov.nasa.ziggy.ZiggyDirectoryRule;
 import gov.nasa.ziggy.ZiggyPropertyRule;
 import gov.nasa.ziggy.data.management.DataFileTestUtils.DataFileInfoSample1;
 import gov.nasa.ziggy.data.management.DataFileTestUtils.DataFileInfoSample2;
@@ -46,7 +45,6 @@
 import gov.nasa.ziggy.pipeline.definition.PipelineDefinitionNode;
 import gov.nasa.ziggy.pipeline.definition.PipelineTask;
 import gov.nasa.ziggy.pipeline.definition.crud.PipelineTaskCrud;
-import gov.nasa.ziggy.services.config.PropertyNames;
 import gov.nasa.ziggy.uow.TaskConfigurationParameters;
 
 /**
@@ -56,7 +54,7 @@
  */
 public class DataFileManagerTest {
 
-    private String datastoreRoot = new File(Filenames.BUILD_TEST, "datastore").getAbsolutePath();
+    private String datastoreRoot;
     private String taskDirRoot;
     private String taskDir;
     private String subtaskDir;
@@ -76,7 +74,7 @@ public class DataFileManagerTest {
     public ZiggyDirectoryRule directoryRule = new ZiggyDirectoryRule();
 
     public ZiggyPropertyRule datastoreRootDirPropertyRule = new ZiggyPropertyRule(
-        DATASTORE_ROOT_DIR_PROP_NAME, datastoreRoot);
+        DATASTORE_ROOT_DIR_PROP_NAME, directoryRule, "datastore");
 
     @Rule
     public ZiggyPropertyRule useSymlinksPropertyRule = new ZiggyPropertyRule(USE_SYMLINKS_PROP_NAME,
@@ -101,7 +99,7 @@ public void setup() throws IOException {
         this.taskDirRoot = taskDirRoot.toString();
         makeTaskDir("pa-5-10");
 
-        Path externalTemp = dirRule.testDirPath().resolve("tmp");
+        Path externalTemp = directoryRule.directory().resolve("tmp");
         Files.createDirectories(externalTemp);
         externalTempDir = externalTemp.toAbsolutePath().toString();
 
@@ -131,17 +129,6 @@ public void setup() throws IOException {
         DataFileTestUtils.initializeDataFileTypeSamples();
     }
 
-    @After
-    public void teardown() throws InterruptedException, IOException {
-        // NB: execution is so fast that some deleteDirectory commands fail because
-        // (apparently) write-locks have not yet had time to release! Address this by
-        // adding a short nap.
-        Thread.sleep(10);
-        FileUtils.deleteDirectory(new File(taskDirRoot));
-        FileUtil.setPosixPermissionsRecursively(new File(datastoreRoot).toPath(), "rwxrwxrwx");
-        FileUtils.forceDelete(new File(Filenames.BUILD_TEST));
-    }
-
     private void makeTaskDir(String taskDirName) {
         File taskDir = new File(taskDirRoot, taskDirName);
         taskDir.mkdirs();