Reformat code style, clarify comments, fixed spacing and provided mor…

…e documentation detail

admin-guide.md

@@ -270,9 +270,14 @@ validator supported is `"script"`, which runs a calculate script on the output
 files and then runs a comparison script that checks that the calculate script's
 output matches the reference data.
 
-Users have an option to provide a directory filepath for the provisioned out file. If none is provided then 
-the provisioned out file will be symlinked into a temporary directory. The
-`"metrics_calculate"` script will be run in that directory receiving the path
+Users have an option to provide a filepath to a directory where they would like
+the provisioned out file. For example, adding the argument:
+`-o /scratch2/groups/gsi/development/` 
+will provision the output file to the gsi scratch2 development directory.  
+
+If none is provided then the provisioned out file will be symlinked into a 
+temporary directory. The `"metrics_calculate"` script will be run in that 
+directory receiving the path
 to that directory as the first argument. Anything it writes to standard output
 will be captured. Then `"metrics_calculate"` will be called with the
 `"output_metrics"` as the first argument and the file generated in the previous

changes/add_optional_output_directory_argument.md

@@ -1,4 +1,4 @@
-Add an optional output directory argument
+Add an optional output directory argument specifically for vidarr-cli 
 * Allows user to choose output directory for test outputs
 * This is an optional argument 
 * Default behaviour is to output to tmp directory 

vidarr-cli/src/main/java/ca/on/oicr/gsi/vidarr/cli/CommandTest.java

@@ -15,9 +15,12 @@
 import java.util.stream.Collectors;
 import picocli.CommandLine;
 
-/** Subcommand to running unit tests */
+/**
+ * Subcommand to running unit tests
+ */
 @CommandLine.Command(name = "test", description = "Run a test suite for a workflow")
 public class CommandTest implements Callable<Integer> {
+
   private static ObjectNode read(String argument) throws IOException {
     if (argument.startsWith("@")) {
       return MAPPER.readValue(new File(argument.substring(1)), ObjectNode.class);
@@ -112,7 +115,9 @@ public Integer call() throws Exception {
                 c -> {
                   // Will use output directory if provided, otherwise "null" is passed into createValidator
                   final var validator =
-                      Validator.all(c.getValidators().stream().map(TestValidator -> TestValidator.createValidator(outputDirectory, c.getId())));
+                      Validator.all(c.getValidators().stream().map(
+                          TestValidator -> TestValidator.createValidator(outputDirectory,
+                              c.getId())));
 
                   final var run =
                       runner.startAsync(

vidarr-cli/src/main/java/ca/on/oicr/gsi/vidarr/cli/TestValidatorScript.java

@@ -22,9 +22,12 @@ public final class TestValidatorScript extends TestValidator {
   public Validator createValidator(String outputDirectory, String id) {
     try {
       // If output directory provided, use that else we create temporary directory /tmp
-      final var finalDir = (outputDirectory != null) ? Path.of(outputDirectory) : Files.createTempDirectory("vidarr-test-script");
-      final var finalCalculateScript = (outputDirectory != null) ? Path.of(outputDirectory, id) : finalDir.resolve("calculate");
-      final var finalCalculateDir = (outputDirectory != null) ? Path.of(outputDirectory, "output") : finalDir.resolve("output");
+      final var finalDir = (outputDirectory != null) ? Path.of(outputDirectory)
+          : Files.createTempDirectory("vidarr-test-script");
+      final var finalCalculateScript =
+          (outputDirectory != null) ? Path.of(outputDirectory, id) : finalDir.resolve("calculate");
+      final var finalCalculateDir = (outputDirectory != null) ? Path.of(outputDirectory, "output")
+          : finalDir.resolve("output");
       final var finalOutputFile = (outputDirectory != null) ? id + ".output" : "calculate.output";
 
       // Directory creation
@@ -72,14 +75,16 @@ public boolean validate(String id) {
             System.err.printf("Location of output metrics %s \n", outputMetrics);
 
             // Directory where output file will be located
-            final var output = Path.of(String.valueOf(finalDir), finalOutputFile).toAbsolutePath().toFile();
+            final var output = Path.of(String.valueOf(finalDir), finalOutputFile).toAbsolutePath()
+                .toFile();
 
             System.err.printf("%s: [%s] Calculating output to %s...%n", id, Instant.now(), output);
             final var calculateProcess =
                 new ProcessBuilder()
                     .inheritIO()
                     .directory(finalCalculateDir.toFile())
-                    .command(finalCalculateScript.toAbsolutePath().toString(), finalCalculateDir.toString())
+                    .command(finalCalculateScript.toAbsolutePath().toString(),
+                        finalCalculateDir.toString())
                     .redirectOutput(output)
                     .start();
             calculateProcess.waitFor();
@@ -112,35 +117,29 @@ public boolean validate(String id) {
   }
 
   @JsonProperty("metrics_calculate")
-  public String getMetricsCalculate()
-  {
+  public String getMetricsCalculate() {
     return metricsCalculate;
   }
 
   @JsonProperty("metrics_compare")
-  public String getMetricsCompare()
-  {
+  public String getMetricsCompare() {
     return metricsCompare;
   }
 
   @JsonProperty("output_metrics")
-  public String getOutputMetrics()
-  {
+  public String getOutputMetrics() {
     return outputMetrics;
   }
 
-  public void setMetricsCalculate(String metricsCalculate)
-  {
+  public void setMetricsCalculate(String metricsCalculate) {
     this.metricsCalculate = metricsCalculate;
   }
 
-  public void setMetricsCompare(String metricsCompare)
-  {
+  public void setMetricsCompare(String metricsCompare) {
     this.metricsCompare = metricsCompare;
   }
 
-  public void setOutputMetrics(String outputMetrics)
-  {
+  public void setOutputMetrics(String outputMetrics) {
     this.outputMetrics = outputMetrics;
   }
 }