javadoc changes

Author: B0SKAMP

api/build.gradle

@@ -20,6 +20,11 @@ java {
     withSourcesJar()
 }
 
+javadoc {
+    options.overview = "src/main/java/org/fairdatapipeline/overview.html"
+}
+
+
 dependencies {
     implementation project(':dataregistry')
     annotationProcessor 'org.immutables:value:2.8.8'
@@ -130,9 +135,6 @@ publishing {
 
 signing {
     if (project.hasProperty('signing.keyId') && project.hasProperty('signing.secretKeyRingFile')) {
-        if(!project.hasProperty('signing.password')){
-            throw(new GradleException('Please give signing.password in gradle command line:\n\ngradle <task> -Psigning.password=<secret>\n'))
-        }
         sign publishing.publications.mavenJava
     }
 }

api/src/main/java/org/fairdatapipeline/api/Author.java

@@ -6,33 +6,14 @@
 import org.fairdatapipeline.dataregistry.content.RegistryUsers;
 import org.fairdatapipeline.dataregistry.restclient.APIURL;
 import org.fairdatapipeline.dataregistry.restclient.RestClient;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 /** Retrieve the Author from the local registry. */
-public class Author {
-  private static final Logger logger = LoggerFactory.getLogger(Author.class);
+class Author {
   RegistryAuthor registryAuthor;
 
   /**
-   * This implementation just retrieves the first Author it finds in the Registry.
-   *
-   * @param restClient link to the restClient to use.
-   */
-  void DummyAuthor(RestClient restClient) {
-    this.registryAuthor =
-        (RegistryAuthor) restClient.getFirst(RegistryAuthor.class, Collections.emptyMap());
-    if (this.registryAuthor == null) {
-      String msg = "Couldn't find an author in the local registry!";
-      logger.error(msg);
-      throw (new RegistryObjectNotfoundException(msg));
-    }
-  }
-
-  /**
-   * Not used. Sonia's version of the Author-retrieval code which finds the admin user, and then
-   * retrieves the Author it links to via the User_author table. (not using this as my user_author
-   * table is empty)
+   * Current implementation to find the author - find the admin user, then find the linked author
+   * via the User_author table.
    *
    * @param restClient link to the restClient to use.
    */
@@ -41,18 +22,15 @@ void DummyAuthor(RestClient restClient) {
         (RegistryUsers)
             restClient.getFirst(RegistryUsers.class, Collections.singletonMap("username", "admin"));
     if (u == null) {
-      String msg = "Couldn't find a User in the local registry!";
-      logger.error(msg);
-      throw (new RegistryObjectNotfoundException(msg));
+      throw (new RegistryObjectNotfoundException("Couldn't find a User in the local registry!"));
     }
     RegistryUser_author ua =
         (RegistryUser_author)
             restClient.getFirst(
                 RegistryUser_author.class, Collections.singletonMap("user", u.get_id().toString()));
     if (ua == null) {
-      String msg = "Couldn't find a User_author in the local registry!";
-      logger.error(msg);
-      throw (new RegistryObjectNotfoundException(msg));
+      throw (new RegistryObjectNotfoundException(
+          "Couldn't find a User_author in the local registry!"));
     }
     this.registryAuthor = (RegistryAuthor) restClient.get(RegistryAuthor.class, ua.getAuthor());
   }

api/src/main/java/org/fairdatapipeline/api/CodeRepo.java

@@ -9,7 +9,7 @@
  * exist yet). Also create a CodeRepo registryObject storing the storage_location, authors, and
  * description. (if an object pointing to the Storage_location does not exists yet)
  */
-public class CodeRepo {
+class CodeRepo {
   Storage_location storage_location;
   FileObject fileObject;
 

api/src/main/java/org/fairdatapipeline/api/Coderun.java

@@ -136,14 +136,12 @@ public Coderun(Path configFilePath, @Nullable Path scriptPath) {
   public Coderun(Path configFilePath, @Nullable Path scriptPath, @Nullable String registryToken) {
     YamlReader yamlReader = new YamlFactory().yamlReader();
     if (!new File(configFilePath.toString()).isFile()) {
-      String msg = "Coderun -- configFilePath argument must be a Path to a config file.";
-      logger.error(msg);
-      throw (new IllegalArgumentException(msg));
+      throw (new IllegalArgumentException(
+          "Coderun -- configFilePath argument must be a Path to a config file."));
     }
     if (scriptPath != null && !new File(scriptPath.toString()).isFile()) {
-      String msg = "Coderun -- scriptPath argument must be a Path to a script file.";
-      logger.error(msg);
-      throw (new IllegalArgumentException(msg));
+      throw (new IllegalArgumentException(
+          "Coderun -- scriptPath argument must be a Path to a script file."));
     }
 
     this.coderuns_txt = configFilePath.getParent().resolve("coderuns.txt");
@@ -160,9 +158,8 @@ public Coderun(Path configFilePath, @Nullable Path scriptPath, @Nullable String
         if (Files.isReadable(Path.of(filename))) {
           registryToken = new FileReader().read(filename);
         } else {
-          String msg = "No registry token given. Giving up.";
-          logger.error(msg);
-          throw (new IllegalActionException(msg));
+          throw (new IllegalActionException(
+              "No registry token given. Giving up. (Token can be given in the config or in the Coderun constructor)"));
         }
       }
     }
@@ -200,10 +197,8 @@ public Coderun(Path configFilePath, @Nullable Path scriptPath, @Nullable String
       if (config.run_metadata().script_path().isPresent()) {
         scriptPath = Path.of(config.run_metadata().script_path().get());
       } else {
-        String msg =
-            "Coderun() -- Script path must be given either in constructor args or in config.";
-        logger.error(msg);
-        throw (new ConfigException(msg));
+        throw (new ConfigException(
+            "Coderun() -- Script path must be given either in constructor args or in config."));
       }
     }
     this.config_storage_location =
@@ -246,9 +241,8 @@ private void prepare_code_run() {
     try {
       remote_repo_url = new URL(remote_repo);
     } catch (MalformedURLException e) {
-      String msg = "Remote repo must be a valid URL; (" + remote_repo + " isn't)";
-      logger.error(msg);
-      throw (new ConfigException(msg, e));
+      throw (new ConfigException(
+          "Remote repo must be a valid URL; (" + remote_repo + " isn't)", e));
     }
 
     this.codeRepo =
@@ -330,10 +324,8 @@ public Data_product_read get_dp_for_read(String dataProduct_name) {
     if (dp_info_map.containsKey(dataProduct_name)) {
       // I could of course refuse to serve up the same DP twice, but let's be friendly.
       if (dp_info_map.get(dataProduct_name).getClass() != Data_product_read.class) {
-        String msg =
-            "You are trying to open the same data product twice in the same coderun, first for write and then for read. Please don't.";
-        logger.error(msg);
-        throw (new IllegalActionException(msg));
+        throw (new IllegalActionException(
+            "You are trying to open the same data product twice in the same coderun, first for write and then for read. Please don't."));
       }
       return (Data_product_read) dp_info_map.get(dataProduct_name);
     }
@@ -353,16 +345,12 @@ public Data_product_write get_dp_for_write(String dataProduct_name, String exten
     if (dp_info_map.containsKey(dataProduct_name)) {
       // I could of course refuse to serve up the same DP twice, but let's be friendly.
       if (dp_info_map.get(dataProduct_name).getClass() != Data_product_write.class) {
-        String msg =
-            "You are trying to open the same data product twice in the same coderun, first for read and then for write. Please don't.";
-        logger.error(msg);
-        throw (new IllegalActionException(msg));
+        throw (new IllegalActionException(
+            "You are trying to open the same data product twice in the same coderun, first for read and then for write. Please don't."));
       }
       if (!dp_info_map.get(dataProduct_name).extension.equals(extension)) {
-        String msg =
-            "You are trying to open the same data product using two different file types. Please don't.";
-        logger.error(msg);
-        throw (new IllegalActionException(msg));
+        throw (new IllegalActionException(
+            "You are trying to open the same data product using two different file types. Please don't."));
       }
       return (Data_product_write) dp_info_map.get(dataProduct_name);
     }
@@ -381,10 +369,8 @@ public Data_product_write get_dp_for_write(String dataProduct_name) {
     if (dp_info_map.containsKey(dataProduct_name)) {
       // I could of course refuse to serve up the same DP twice, but let's be friendly.
       if (dp_info_map.get(dataProduct_name).getClass() != Data_product_write.class) {
-        String msg =
-            "You are trying to open the same data product twice in the same coderun, first for read and then for write. Please don't.";
-        logger.error(msg);
-        throw (new IllegalActionException(msg));
+        throw (new IllegalActionException(
+            "You are trying to open the same data product twice in the same coderun, first for read and then for write. Please don't."));
       }
       return (Data_product_write) dp_info_map.get(dataProduct_name);
     }
@@ -445,9 +431,8 @@ public void close() {
     dp_info_map.forEach((key, value) -> value.close());
     RegistryCode_run coderun = (RegistryCode_run) restClient.post(this.registryCode_run);
     if (coderun == null) {
-      String msg = "Failed to create Code_run in registry: " + this.registryCode_run;
-      logger.error(msg);
-      throw (new RegistryException(msg));
+      throw (new RegistryException(
+          "Failed to create Code_run in registry: " + this.registryCode_run));
     }
     this.register_issues();
     this.append_code_run_uuid(coderun.getUuid());

api/src/main/java/org/fairdatapipeline/api/FileObject.java

@@ -6,7 +6,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-/** create a new registryObject with given storage_location, description, authors, file_type. */
+/**
+ * A new registryObject with given storage_location, description, authors, file_type. Used for
+ * Submission Script, Code Repo, Config File, which can have issues raised on.
+ */
 public class FileObject {
   private static final Logger logger = LoggerFactory.getLogger(FileObject.class);
   Coderun coderun;

api/src/main/java/org/fairdatapipeline/api/IllegalActionException.java

@@ -1,6 +1,6 @@
 package org.fairdatapipeline.api;
 
-/** the consumer is probably trying to do something they aren't supposed to be doing. */
+/** The consumer is probably trying to do something they aren't supposed to be doing. */
 public class IllegalActionException extends RuntimeException {
   /**
    * Constructor

api/src/main/java/org/fairdatapipeline/api/RegistryException.java

@@ -1,6 +1,6 @@
 package org.fairdatapipeline.api;
 
-/** Failure to create an Object in the registry */
+/** Failure to create an Object in the registry. */
 public class RegistryException extends RuntimeException {
   /**
    * Constructor

api/src/main/java/org/fairdatapipeline/api/RegistryObjectNotfoundException.java

@@ -1,6 +1,6 @@
 package org.fairdatapipeline.api;
 
-/** Failure to retrieve an expected object from the registry */
+/** Failure to retrieve an expected object from the registry. */
 public class RegistryObjectNotfoundException extends RuntimeException {
   /**
    * Constructor

api/src/main/java/org/fairdatapipeline/api/Storage_location.java

@@ -13,7 +13,7 @@
 import org.slf4j.LoggerFactory;
 
 /** This is used to store a file or a remote repo to the registry as a RegistryStorage_location. */
-public class Storage_location {
+class Storage_location {
   private static final Logger logger = LoggerFactory.getLogger(Storage_location.class);
   RegistryStorage_location registryStorage_location;
 

api/src/main/java/org/fairdatapipeline/api/Storage_root.java

@@ -10,8 +10,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-/** retrieve or create the RegistryStorage_root with a given 'root'. */
-public class Storage_root {
+/** Retrieve or create the RegistryStorage_root with a given 'root'. */
+class Storage_root {
   private static final Logger logger = LoggerFactory.getLogger(Storage_root.class);
   RegistryStorage_root registryStorage_root;