fixed javadocs

java/cli/src/main/java/org/brapi/schematools/cli/BrAPICommand.java

@@ -2,6 +2,9 @@
 
 import picocli.CommandLine;
 
+/**
+ * Main class for the BrAPI application
+ */
 @CommandLine.Command(
     name = "brapi",
     description = "Command line tools for the BrAPI JSON schema, see the sub-commands for details",
@@ -14,6 +17,11 @@
     mixinStandardHelpOptions = true
 )
 public class BrAPICommand {
+
+    /**
+     * Main method for application
+     * @param args arguments for application
+     */
     public static void main(String[] args) {
         new CommandLine(new BrAPICommand()).execute(args);
     }

java/cli/src/main/java/org/brapi/schematools/cli/OutputFormat.java

@@ -1,8 +1,24 @@
 package org.brapi.schematools.cli;
 
+/**
+ * Enumeration that provides the possible outputs for generator
+ */
 public enum OutputFormat {
+
+    /**
+     * Use this format to generate an OpenAPI specification
+     */
     OPEN_API,
+    /**
+     * Use this format to generate an GraphQL schema
+     */
     GRAPHQL,
+    /**
+     * Use this format to generate OWL specification in turtle format
+     */
     OWL,
+    /**
+     * Use this format to generate Markdown for type and their field descriptions
+     */
     MARKDOWN
 }

java/cli/src/main/java/org/brapi/schematools/cli/ValidateSubCommand.java

@@ -8,6 +8,9 @@
 import java.nio.file.Path;
 import java.util.List;
 
+/**
+ * The Validate Sub-command
+ */
 @CommandLine.Command(
     name = "validate", mixinStandardHelpOptions = true,
     description = "Validates the BrAPI JSON schema"

java/core/src/main/java/org/brapi/schematools/core/markdown/MarkdownGenerator.java

@@ -1,7 +1,9 @@
 package org.brapi.schematools.core.markdown;
 
+import graphql.schema.GraphQLSchema;
 import lombok.AllArgsConstructor;
 import org.brapi.schematools.core.brapischema.BrAPISchemaReader;
+import org.brapi.schematools.core.graphql.options.GraphQLGeneratorOptions;
 import org.brapi.schematools.core.model.BrAPIClass;
 import org.brapi.schematools.core.model.BrAPIEnumType;
 import org.brapi.schematools.core.model.BrAPIObjectProperty;
@@ -21,18 +23,31 @@
 
 import static org.brapi.schematools.core.response.Response.fail;
 import static org.brapi.schematools.core.response.Response.success;
-
+/**
+ * Generates a Markdown files for type and their field descriptions from a BrAPI Json Schema.
+ */
 @AllArgsConstructor
 public class MarkdownGenerator {
     private final BrAPISchemaReader schemaReader = new BrAPISchemaReader() ;
 
     private Path outputPath ;
     private boolean overwrite ;
+
+    /**
+     * Generates Markdown files for type and their field descriptions
+     * from the complete BrAPI Specification in
+     * a directory contains a subdirectories for each module that contain
+     * the BrAPI Json schema and the additional subdirectories called 'Requests'
+     * that contains the request schemas and BrAPI-Common that contains common schemas
+     * for use across modules.
+     * @param schemaDirectory the path to the complete BrAPI Specification
+     * @return the paths of the Markdown files generated from the complete BrAPI Specification
+     */
     public Response<List<Path>> generate(Path schemaDirectory) {
         return schemaReader.readDirectories(schemaDirectory).mapResultToResponse(brAPISchemas -> new MarkdownGenerator.Generator(brAPISchemas).generate()) ;
     }
 
-    public class Generator {
+    private class Generator {
 
         private final List<BrAPIClass> brAPISchemas ;
         private final Path descriptionsPath ;

java/core/src/main/java/org/brapi/schematools/core/openapi/options/PropertiesOptions.java

@@ -34,7 +34,14 @@ public Validation validate() {
             .assertNotNull(id, "'id' option on %s is null", this.getClass().getSimpleName()) ;
     }
 
-
+    /**
+     * Gets the list of link properties that are used to generate links to the
+     * provided object type.
+     *
+     * This is usually the object dbId, but can also be the name and/or PUI.
+     * @param brAPIObjectType the object type from which the properties will be obtained
+     * @return list of link properties that are used to generate links to the object
+     */
     public List<BrAPIObjectProperty> getLinkPropertiesFor(BrAPIObjectType brAPIObjectType) {
         List<BrAPIObjectProperty> linkProperties = new ArrayList<>() ;
 

java/core/src/main/java/org/brapi/schematools/core/openapi/options/PropertyOptions.java

@@ -39,7 +39,8 @@ public Validation validate() {
 
     /**
      * Gets the property name for a specific primary model. For example the id property (or field)
-     * name of Study, would be 'studyDbiId' by default. Use {@link #setIDParameterFor} to override this value.
+     * name of Study, would be 'studyDbiId' by default. Use {@link #setPropertyNameFor(String, String)}
+     * to override this value.
      * @param name the name of the primary model
      * @return property name for a specific primary model
      */
@@ -50,7 +51,8 @@ public String getPropertyNameFor(String name) {
 
     /**
      * Gets the property name for a specific primary model. For example the id property (or field)
-     * name of Study, would be 'studyDbiId' by default. Use {@link #setIDParameterFor} to override this value.
+     * name of Study, would be 'studyDbiId' by default. Use {@link #setPropertyNameFor(String, String)}
+     * to override this value.
      * @param type the primary model
      * @return property name for a specific primary model
      */
@@ -86,7 +88,8 @@ public PropertyOptions setPropertyNameFor(BrAPIType type, String parameterName)
 
     /**
      * Gets the plural property name for a specific primary model. For example the id property (or field)
-     * name of Study, would be 'studyDbiId' by default. Use {@link #setIDParameterFor} to override this value.
+     * name of Study, would be 'studyDbiId' by default. Use {@link #setPluralPropertyNameFor} to
+     * override this value.
      * @param name the name of the primary model
      * @return property name for a specific primary model
      */
@@ -97,7 +100,8 @@ public String getPluralPropertyNameFor(String name) {
 
     /**
      * Gets the plural property name for a specific primary model. For example the id property (or field)
-     * name of Study, would be 'studyDbiId' by default. Use {@link #setIDParameterFor} to override this value.
+     * name of Study, would be 'studyDbiId' by default. Use {@link #setPluralPropertyNameFor}
+     * to override this value.
      * @param type the primary model
      * @return property name for a specific primary model
      */

java/core/src/main/java/org/brapi/schematools/core/valdiation/Validatable.java

@@ -1,5 +1,8 @@
 package org.brapi.schematools.core.valdiation;
 
+/**
+ * Interface that markers a class that can be validated.
+ */
 public interface Validatable {
     /**
      * Checks if the Validatable object is valid, return a list of errors if it is not valid