Wrapper around standard FileChannel with additional safety net for closing if user does not close
+ and ability to run custom function during cleanup/closing.
This represents an object_component to read from or write to (or raise issues with) An
+ object_component without a name is the 'whole_object' component.
+
+
+
+
diff --git a/api/build.gradle b/api/build.gradle
deleted file mode 100644
index 70f9295..0000000
--- a/api/build.gradle
+++ /dev/null
@@ -1,140 +0,0 @@
-plugins {
- id 'java'
- id "com.diffplug.gradle.spotless" version "4.4.0"
- id "maven-publish"
- id "signing"
- id "jacoco"
-}
-
-group 'org.fairdatapipeline'
-version '1.0.0-rc3'
-
-repositories {
- mavenCentral()
-}
-
-java {
- sourceCompatibility = JavaVersion.VERSION_11
- targetCompatibility = JavaVersion.VERSION_11
- withJavadocJar()
- withSourcesJar()
-}
-
-javadoc {
- options.overview = "src/main/java/org/fairdatapipeline/overview.html"
-}
-
-
-dependencies {
- implementation project(':dataregistry')
- annotationProcessor 'org.immutables:value:2.9.0'
- implementation 'commons-codec:commons-codec:1.15'
- implementation 'com.google.guava:guava:31.1-jre'
- implementation 'com.moandjiezana.toml:toml4j:0.7.2'
- implementation 'commons-io:commons-io:2.11.0'
- implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.0.0'
- implementation 'org.apache.commons:commons-math3:3.6.1'
- implementation 'org.apache.maven:maven-artifact:3.8.4'
- implementation 'org.glassfish.jersey.core:jersey-client:3.0.4'
- implementation 'org.glassfish.jersey.inject:jersey-hk2:3.0.4'
- implementation 'org.glassfish.jersey:jersey-bom:3.0.4'
- implementation 'org.immutables:value-annotations:2.9.0'
- implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.15.2'
- implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.15.2'
- implementation 'com.fasterxml.jackson.datatype:jackson-datatype-guava:2.15.2'
- implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.15.2'
- implementation 'com.fasterxml.jackson.core:jackson-annotations:2.15.2'
- implementation 'com.fasterxml.jackson.module:jackson-module-parameter-names:2.15.2'
- implementation 'org.slf4j:slf4j-api:1.7.36'
- implementation 'org.slf4j:slf4j-simple:1.7.36'
- testAnnotationProcessor 'org.immutables:value:2.9.0'
- testImplementation(platform('org.junit:junit-bom:5.8.1'))
- testImplementation('org.junit.jupiter:junit-jupiter:5.8.2')
- testImplementation 'org.skyscreamer:jsonassert:1.5.0'
- testImplementation 'org.mockito:mockito-core:4.3.1'
- testImplementation 'org.assertj:assertj-core:3.22.0'
- testImplementation 'org.javatuples:javatuples:1.2'
-}
-
-test {
- useJUnitPlatform()
- testLogging {
- events "passed", "skipped", "failed"
- }
- finalizedBy jacocoTestReport
-}
-
-jacocoTestReport {
- dependsOn test
- reports {
- xml.enabled true
- html.enabled false
- }
-}
-
-spotless {
- java {
- googleJavaFormat()
- }
-}
-
-publishing {
- publications {
- mavenJava(MavenPublication) {
- artifactId = 'api'
- from components.java
- versionMapping {
- usage('java-api') {
- fromResolutionOf('runtimeClasspath')
- }
- usage('java-runtime') {
- fromResolutionResult()
- }
- }
- pom {
- name = 'javaDataPipeline API'
- description = 'javaDataPipeline API'
- url = 'http://www.fairdatapipeline.org/'
- licenses {
- license {
- name = 'GNU LESSER GENERAL PUBLIC LICENSE, Version 3.0'
- url = 'https://www.gnu.org/licenses/lgpl-3.0.html'
- }
- }
- organization {
- name = 'THE SCOTTISH COVID-19 RESPONSE CONSORTIUM'
- url = 'https://www.gla.ac.uk/research/az/scrc/'
- }
- developers {
- developer {
- id = 'bram'
- name = 'Bram Boskamp'
- email = 'bram@boska.mp'
- organization = 'Biomathematics and Statistics Scotland'
- organizationUrl = 'https://www.bioss.ac.uk/'
- }
- }
- scm {
- connection = 'scm:git:https://github.com/FAIRDataPipeline/javaDataPipeline.git'
- developerConnection = 'scm:git:https://github.com/FAIRDataPipeline/javaDataPipeline.git'
- url = 'https://github.com/FAIRDataPipeline/javaDataPipeline'
- }
- }
- }
- }
- repositories {
- maven {
- url = 'https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/'
- credentials {
- username findProperty('ossrhUsername')
- password findProperty('ossrhPassword')
- }
- }
- }
-}
-
-signing {
- if (project.hasProperty('signing.keyId') && project.hasProperty('signing.secretKeyRingFile')) {
- sign publishing.publications.mavenJava
- }
-}
diff --git a/api/gradle.properties b/api/gradle.properties
deleted file mode 100644
index e69de29..0000000
diff --git a/api/src/main/java/org/fairdatapipeline/api/Author.java b/api/src/main/java/org/fairdatapipeline/api/Author.java
deleted file mode 100644
index 1dc9de2..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Author.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.util.Collections;
-import org.fairdatapipeline.dataregistry.content.RegistryAuthor;
-import org.fairdatapipeline.dataregistry.content.RegistryUser_author;
-import org.fairdatapipeline.dataregistry.content.RegistryUsers;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-import org.fairdatapipeline.dataregistry.restclient.RestClient;
-
-/** Retrieve the Author from the local registry. */
-class Author {
- RegistryAuthor registryAuthor;
-
- /**
- * 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.
- */
- Author(RestClient restClient) {
- RegistryUsers u =
- (RegistryUsers)
- restClient.getFirst(RegistryUsers.class, Collections.singletonMap("username", "admin"));
- if (u == null) {
- 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) {
- throw (new RegistryObjectNotfoundException(
- "Couldn't find a User_author in the local registry!"));
- }
- this.registryAuthor = (RegistryAuthor) restClient.get(RegistryAuthor.class, ua.getAuthor());
- }
-
- APIURL getUrl() {
- return this.registryAuthor.getUrl();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/CodeRepo.java b/api/src/main/java/org/fairdatapipeline/api/CodeRepo.java
deleted file mode 100644
index fea5e0a..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/CodeRepo.java
+++ /dev/null
@@ -1,38 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.net.URL;
-import java.util.List;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * Create a CodeRepo registryStorage_location storing the repo URL and latest_commit hash (if not
- * 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)
- */
-class CodeRepo {
- final Storage_location storage_location;
- final FileObject fileObject;
-
- CodeRepo(
- String latest_commit,
- URL repo_url,
- String description,
- List authors,
- Coderun coderun) {
- this.storage_location = new Storage_location(repo_url, latest_commit, coderun);
- this.fileObject = new FileObject(this.storage_location, description, authors, coderun);
- }
-
- /**
- * Retrieve the FileObject for this CodeRepo. (probably to raise an issue with it)
- *
- * @return The FileObject for this CodeRepo. (probably to raise an issue with it)
- */
- public FileObject getFileObject() {
- return this.fileObject;
- }
-
- APIURL getUrl() {
- return this.fileObject.getUrl();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Coderun.java b/api/src/main/java/org/fairdatapipeline/api/Coderun.java
deleted file mode 100644
index 0128de3..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Coderun.java
+++ /dev/null
@@ -1,438 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URI;
-import java.net.URL;
-import java.nio.file.*;
-import java.time.LocalDateTime;
-import java.util.*;
-import org.apache.commons.math3.random.RandomDataGenerator;
-import org.apache.commons.math3.random.RandomGenerator;
-import org.checkerframework.checker.nullness.qual.Nullable;
-import org.fairdatapipeline.config.Config;
-import org.fairdatapipeline.config.ConfigException;
-import org.fairdatapipeline.config.ConfigFactory;
-import org.fairdatapipeline.dataregistry.content.RegistryCode_run;
-import org.fairdatapipeline.dataregistry.content.RegistryStorage_root;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-import org.fairdatapipeline.dataregistry.restclient.RestClient;
-import org.fairdatapipeline.file.FileReader;
-import org.fairdatapipeline.hash.Hasher;
-import org.fairdatapipeline.parameters.ParameterDataReader;
-import org.fairdatapipeline.parameters.ParameterDataReaderImpl;
-import org.fairdatapipeline.parameters.ParameterDataWriter;
-import org.fairdatapipeline.parameters.ParameterDataWriterImpl;
-import org.fairdatapipeline.toml.TOMLMapper;
-import org.fairdatapipeline.toml.TomlReader;
-import org.fairdatapipeline.toml.TomlWriter;
-import org.fairdatapipeline.yaml.YamlFactory;
-import org.fairdatapipeline.yaml.YamlReader;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Java implementation of the FAIR Data Pipeline API
- *
- *
Users should initialise this library using a try-with-resources block or ensure that .close()
- * is explicitly closed when the required file handles have been accessed.
- *
- *
- */
-public class Coderun implements AutoCloseable {
- private static final Logger logger = LoggerFactory.getLogger(Coderun.class);
- final Config config;
- final RestClient restClient;
- private final Map
- dp_info_map; // TODO: if we can have one and the same DP open for read & write we need 2 maps
- RegistryCode_run registryCode_run;
- final Hasher hasher = new Hasher();
- Storage_location script_storage_location;
- Storage_location config_storage_location;
- private final Storage_root write_data_store_root;
- final ParameterDataReader parameterDataReader;
- final ParameterDataWriter parameterDataWriter;
- RandomGenerator rng;
- List issues;
- Path coderuns_txt;
- FileObject script_object;
- FileObject config_object;
- CodeRepo codeRepo;
- List authors;
-
- /**
- * Constructor using only configFilePath - scriptPath is read from the config.
- *
- * @param configFilePath the Path to the config file, which must be located in the local data
- * store CodeRun folder with timestamp name.
- */
- public Coderun(Path configFilePath) {
- this(configFilePath, null);
- }
-
- /**
- * Constructor using both configFilePath and ScriptPath
- *
- * @param configFilePath the Path to the {@link Config config.yaml} file
- * @param scriptPath the Path to the script file - this may be null if the script path is given in
- * the config file.
- *
both startup files are usually provided by fair run in the
- * local data registry jobs/{timestamp} folder.
- */
- public Coderun(Path configFilePath, @Nullable Path scriptPath) {
- this(configFilePath, scriptPath, null);
- }
-
- /**
- * Constructor specifying configPath, scriptPath, and registryToken.
- *
- * @param configFilePath the Path to the {@link Config config.yaml} file
- * @param scriptPath the Path to the script file - this may be null if the script path is given in
- * the config file.
- *
both startup files are usually provided by fair run in the
- * local data registry jobs/{timestamp} folder.
- * @param registryToken the authentication token of the local registry (or null if the token is to
- * be read from the config or from ~/.fair/registry/token)
- */
- public Coderun(Path configFilePath, @Nullable Path scriptPath, @Nullable String registryToken) {
- YamlReader yamlReader = new YamlFactory().yamlReader();
- if (!new File(configFilePath.toString()).isFile()) {
- throw (new IllegalArgumentException(
- "Coderun -- configFilePath argument must be a Path to a config file."));
- }
- if (scriptPath != null && !new File(scriptPath.toString()).isFile()) {
- throw (new IllegalArgumentException(
- "Coderun -- scriptPath argument must be a Path to a script file."));
- }
-
- this.coderuns_txt = configFilePath.getParent().resolve("coderuns.txt");
- this.rng = new RandomDataGenerator().getRandomGenerator();
- this.parameterDataReader = new ParameterDataReaderImpl(new TomlReader(new TOMLMapper(rng)));
- this.parameterDataWriter = new ParameterDataWriterImpl(new TomlWriter(new TOMLMapper(rng)));
-
- this.config = new ConfigFactory().config(yamlReader, configFilePath);
- if (registryToken == null) {
- if (config.run_metadata().token().isPresent())
- registryToken = config.run_metadata().token().get();
- else {
- String filename = "~/.fair/registry/token";
- if (Files.isReadable(Path.of(filename))) {
- registryToken = new FileReader().read(filename);
- } else {
- throw (new IllegalActionException(
- "No registry token given. Giving up. (Token can be given in the config or in the Coderun constructor)"));
- }
- }
- }
- restClient =
- new RestClient(
- this.config
- .run_metadata()
- .local_data_registry_url()
- .orElse("http://localhost:8000/api/"),
- registryToken);
-
- URI storageRootURI;
- if (config.run_metadata().write_data_store().isPresent()) {
- try {
- storageRootURI = URI.create(config.run_metadata().write_data_store().get());
- if (storageRootURI.getScheme() == null) {
- storageRootURI = Path.of(storageRootURI.toString()).toUri();
- logger.trace(
- "added file:/// scheme to write_data_store from config: {}",
- config.run_metadata().write_data_store().get());
- }
- } catch (Exception e) {
- Path wdsPath = Path.of(config.run_metadata().write_data_store().get());
- storageRootURI = wdsPath.toUri();
- logger.trace("tried to create write_data_store URI after Exception: {}", storageRootURI);
- }
- } else {
- storageRootURI = configFilePath.getParent().getParent().getParent().toUri();
- logger.trace(
- "Using configFilePath.parent.parent.parent as storageRootURI: {}", storageRootURI);
- }
- this.write_data_store_root = new Storage_root(storageRootURI, restClient);
-
- if (scriptPath == null) {
- if (config.run_metadata().script_path().isPresent())
- scriptPath = Path.of(config.run_metadata().script_path().get());
- else {
- throw (new ConfigException(
- "Coderun() -- Script path must be given either in constructor args or in config."));
- }
- }
- this.config_storage_location =
- new Storage_location(configFilePath, write_data_store_root, this, false);
- this.script_storage_location =
- new Storage_location(scriptPath, write_data_store_root, this, false);
- prepare_code_run();
- dp_info_map = new HashMap<>();
- this.issues = new ArrayList<>();
- }
-
- RegistryStorage_root getWriteStorage_root() {
- return this.write_data_store_root.registryStorage_root;
- }
-
- private void prepare_code_run() {
- Author a = new Author(this.restClient);
- this.authors = List.of(a.getUrl());
- this.config_object =
- new FileObject(
- new File_type("yaml", restClient),
- this.config_storage_location,
- "Working config.yaml file location in local datastore",
- this.authors,
- this);
- this.registryCode_run = new RegistryCode_run();
- this.registryCode_run.setModel_config(this.config_object.getUrl());
-
- this.script_object =
- new FileObject(
- new File_type("sh", restClient),
- this.script_storage_location,
- "Submission script location in local datastore",
- this.authors,
- this);
- this.registryCode_run.setSubmission_script(this.script_object.getUrl());
- String latest_commit = this.config.run_metadata().latest_commit().orElse("");
- String remote_repo = this.config.run_metadata().remote_repo().orElse("");
- URL remote_repo_url;
- try {
- remote_repo_url = new URL(remote_repo);
- } catch (MalformedURLException e) {
- throw (new ConfigException(
- "Remote repo must be a valid URL; (" + remote_repo + " isn't)", e));
- }
-
- this.codeRepo =
- new CodeRepo(
- latest_commit,
- remote_repo_url,
- "Analysis / processing script location",
- this.authors,
- this);
-
- this.registryCode_run.setCode_repo(this.codeRepo.getUrl());
- this.registryCode_run.setModel_config(this.config_object.getUrl());
- this.registryCode_run.setRun_date(
- LocalDateTime.now()); // or should this be config.openTimestamp??
- this.registryCode_run.setDescription(this.config.run_metadata().description().orElse(""));
- }
-
- /**
- * Access the Submission_script; in order to raise a Submission_script issue.
- *
- * @return the FileObject representing the Submission_script.
- *
Usage:
- *
- * coderun.getScript.raise_issue("this is a very bad script", 10);
- *
- * OR
- *
- * Issue i = coderun.raise_issue("Seriously bad stuff", 10);
- * i.add_fileObjects(coderun.getScript(), coderun.getConfig());
- *
- */
- public FileObject getScript() {
- return this.script_object;
- }
-
- /**
- * Access the configuration file (config.yaml); in order to raise a Config issue.
- *
- * @return the FileObject representing the config file.
- *
Usage:
- *
- * coderun.getConfig.raise_issue("this is a very bad config file", 10);
- *
- * OR
- *
- * Issue i = coderun.raise_issue("Seriously bad stuff", 10);
- * i.add_fileObjects(coderun.getScript(), coderun.getConfig());
- *
- */
- public FileObject getConfig() {
- return this.config_object;
- }
-
- /**
- * Access the code repository in order to raise a code repository issue.
- *
- * @return the FileObject representing the code repository (which is given in the config file)
- *
Usage:
- *
- * coderun.getCode_repo.raise_issue("this contains very bad code", 10);
- *
- * OR
- *
- * Issue i = coderun.raise_issue("Seriously bad stuff", 10);
- * i.add_fileObjects(coderun.getCode_repo(), coderun.getConfig());
- *
- */
- public FileObject getCode_repo() {
- return this.codeRepo.getFileObject();
- }
-
- /**
- * Obtain a data product for reading.
- *
- * @param dataProduct_name the name of the dataProduct to obtain.
- * @return the data product.
- */
- 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) {
- 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);
- }
- Data_product_read dp = new Data_product_read(dataProduct_name, this);
- dp_info_map.put(dataProduct_name, dp);
- return dp;
- }
-
- /**
- * Obtain a data product for writing.
- *
- * @param dataProduct_name the name of the dataProduct to obtain.
- * @param extension the file extension representing the file type we will write, e.g. csv or toml
- * @return the data product
- */
- public Data_product_write get_dp_for_write(String dataProduct_name, String extension) {
- 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) {
- 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)) {
- 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);
- }
- Data_product_write dp = new Data_product_write(dataProduct_name, this, extension);
- dp_info_map.put(dataProduct_name, dp);
- return dp;
- }
-
- /**
- * Obtain a data product for writing. (gets the extension from config)
- *
- * @param dataProduct_name the name of the dataProduct to obtain.
- * @return the data product
- */
- 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) {
- 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);
- }
- Data_product_write dp = new Data_product_write(dataProduct_name, this);
- // if dp.extension != dp_info_map.get(dataProduct_name).extension) -> FAIL
- dp_info_map.put(dataProduct_name, dp);
- return dp;
- }
-
- /**
- * create an Issue that can be linked to a number of {@link Object_component object components}
- * and/or {@link FileObject fileObjects}.
- *
- * @param description text description of the issue
- * @param severity integer representing the severity of the issue, larger integer means more
- * severe
- * @return the Issue
- */
- public Issue raise_issue(String description, Integer severity) {
- Issue i = new Issue(description, severity);
- this.issues.add(i);
- return i;
- }
-
- private void register_issues() {
- this.issues.stream()
- .filter(
- issue ->
- !(issue.components.isEmpty()
- && issue.registryIssue.getComponent_issues().isEmpty()))
- .forEach(issue -> restClient.post(issue.getRegistryIssue()));
- }
-
- void addInput(APIURL input) {
- this.registryCode_run.addInput(input);
- }
-
- void addOutput(APIURL output) {
- this.registryCode_run.addOutput(output);
- }
-
- void append_code_run_uuid(String uuid) {
- try (FileWriter fw = new FileWriter(this.coderuns_txt.toString(), true)) {
- fw.write(uuid + "\n");
- } catch (IOException e) {
- logger.error("IOException: append_code_run_uuid() failed.", e);
- }
- }
-
- /**
- * Finalize and register the coderun. (this gets called automatically when using Coderun in a
- * try-with-resources block)
- */
- @Override
- public void close() {
- dp_info_map.forEach((key, value) -> value.close());
- RegistryCode_run coderun = (RegistryCode_run) restClient.post(this.registryCode_run);
- if (coderun == null) {
- throw (new RegistryException(
- "Failed to create Code_run in registry: " + this.registryCode_run));
- }
- this.register_issues();
- this.append_code_run_uuid(coderun.getUuid());
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Data_product.java b/api/src/main/java/org/fairdatapipeline/api/Data_product.java
deleted file mode 100644
index 271e7da..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Data_product.java
+++ /dev/null
@@ -1,144 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import org.fairdatapipeline.config.ImmutableConfigItem;
-import org.fairdatapipeline.dataregistry.content.*;
-import org.fairdatapipeline.file.CleanableFileChannel;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Data product is created: {@link Coderun#get_dp_for_write(String, String)} or {@link
- * Coderun#get_dp_for_read(String)}
- *
- *
Upon {@link Coderun#close()} it will try to register itself and its components in the
- * registry, and then register itself in the coderun.
- */
-public abstract class Data_product implements AutoCloseable {
- private static final Logger logger = LoggerFactory.getLogger(Data_product.class);
- final Coderun coderun;
- final RegistryNamespace registryNamespace;
- String namespace_name;
- String extension;
- final String version;
- final String description;
- RegistryData_product registryData_product;
- RegistryObject registryObject;
- RegistryStorage_location registryStorage_location;
- RegistryStorage_root registryStorage_root;
- Path filePath;
- CleanableFileChannel filechannel;
- Object_component whole_obj_oc;
- /** the name given by the user (asked for in the FileApi.get_dp_for_xxx() call) */
- final String givenDataProduct_name;
- /**
- * usually the same as the given name, unless the config use section has given an alternative data
- * product name to open.
- */
- String actualDataProduct_name;
-
- final Map componentMap = new HashMap<>();
- final List configItems;
- boolean been_used = false;
-
- Data_product(String dataProduct_name, Coderun coderun) {
- this(dataProduct_name, coderun, null);
- }
-
- Data_product(String dataProduct_name, Coderun coderun, String extension) {
- this.extension = extension;
- this.coderun = coderun;
- this.givenDataProduct_name = dataProduct_name;
- this.actualDataProduct_name = dataProduct_name;
- this.configItems = this.getConfigItems();
- this.namespace_name = this.getDefaultNamespace_name();
- ImmutableConfigItem configItem = this.getConfigItem(dataProduct_name);
- if (configItem.use().namespace().isPresent())
- namespace_name = configItem.use().namespace().get();
- if (configItem.use().data_product().isPresent())
- this.actualDataProduct_name = configItem.use().data_product().get();
- if (configItem.file_type().isPresent()) {
- if (extension != null && !configItem.file_type().get().equals(extension))
- logger.warn(
- "file type conflict: code says {}, config says {}",
- extension,
- configItem.file_type().get());
- this.extension = configItem.file_type().get();
- }
- this.description = configItem.description().orElse("");
- this.version = configItem.use().version();
- this.registryNamespace = this.getRegistryNamespace(this.namespace_name);
- this.populate_data_product();
- }
-
- /*
- * this should populate the main data fields: data_product, storage_location and fdpObject
- * for READ: by reading these from the registry
- * for WRITE: by preparing empty ones that can later by posted to registry
- */
- abstract void populate_data_product();
-
- abstract List getConfigItems();
-
- abstract String getDefaultNamespace_name();
-
- RegistryNamespace getRegistryNamespace(String namespace_name) {
- return (RegistryNamespace)
- coderun.restClient.getFirst(
- RegistryNamespace.class, Collections.singletonMap("name", namespace_name));
- }
-
- RegistryData_product getRegistryData_product() {
- Map dp_map =
- Map.of(
- "name",
- this.actualDataProduct_name,
- "namespace",
- this.registryNamespace.get_id().toString(),
- "version",
- version);
- return (RegistryData_product) coderun.restClient.getFirst(RegistryData_product.class, dp_map);
- }
-
- ImmutableConfigItem getConfigItem(String dataProduct_name) {
-
- return this.getConfigItems().stream()
- .filter(ci -> ci.data_product().equals(dataProduct_name))
- .findFirst()
- .orElse(null);
- }
-
- /*
- *
- */
- abstract Path getFilePath();
-
- /** please make sure the implementation set been_used = true; */
- abstract CleanableFileChannel getFilechannel() throws IOException;
-
- void closeFileChannel() {
- if (this.filechannel != null) {
- this.filechannel.close();
- this.filechannel = null;
- }
- }
-
- abstract void objects_to_registry();
-
- void InputsOutputsToCoderun() {
- if (this.whole_obj_oc != null) this.whole_obj_oc.register_me_in_code_run();
- this.componentMap.forEach((key, value) -> value.register_me_in_code_run());
- }
-
- @Override
- public void close() {
- this.closeFileChannel();
- this.objects_to_registry();
- this.InputsOutputsToCoderun();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Data_product_read.java b/api/src/main/java/org/fairdatapipeline/api/Data_product_read.java
deleted file mode 100644
index 1799d16..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Data_product_read.java
+++ /dev/null
@@ -1,173 +0,0 @@
-package org.fairdatapipeline.api;
-
-import static java.nio.file.StandardOpenOption.*;
-
-import java.io.IOException;
-import java.nio.channels.FileChannel;
-import java.nio.file.Path;
-import java.util.List;
-import org.fairdatapipeline.config.ConfigException;
-import org.fairdatapipeline.config.ImmutableConfigItem;
-import org.fairdatapipeline.dataregistry.content.RegistryNamespace;
-import org.fairdatapipeline.dataregistry.content.RegistryObject;
-import org.fairdatapipeline.dataregistry.content.RegistryStorage_location;
-import org.fairdatapipeline.dataregistry.content.RegistryStorage_root;
-import org.fairdatapipeline.file.CleanableFileChannel;
-
-/**
- * Data_product_read is created by Coderun: {@link Coderun#get_dp_for_read(String)}
- *
- *
Upon {@link Coderun#close()} it will register its components in the coderun.
- */
-public class Data_product_read extends Data_product {
- private boolean hash_checked = false;
-
- Data_product_read(String dataProduct_name, Coderun coderun) {
- super(dataProduct_name, coderun);
- }
-
- void populate_data_product() {
- // called from the constructor
- this.registryData_product = this.getRegistryData_product();
- if (this.registryData_product == null) {
- throw (new RegistryObjectNotfoundException(
- "Trying to read from non-existing data_product "
- + this.actualDataProduct_name
- + "; NS "
- + this.registryNamespace.getName()
- + "; version "
- + version));
- }
- this.registryObject =
- (RegistryObject)
- coderun.restClient.get(RegistryObject.class, this.registryData_product.getObject());
- if (this.registryObject == null) {
- throw (new RegistryObjectNotfoundException(
- "couldn't retrieve the fdpObject for this READ dp "
- + this.givenDataProduct_name
- + " ("
- + this.actualDataProduct_name
- + ")"));
- }
- this.registryStorage_location =
- (RegistryStorage_location)
- coderun.restClient.get(
- RegistryStorage_location.class, this.registryObject.getStorage_location());
- if (this.registryStorage_location == null) {
- throw (new RegistryObjectNotfoundException(
- "Couldn't retrieve the StorageLocation for this READ dp "
- + this.givenDataProduct_name
- + " ("
- + this.actualDataProduct_name
- + ")"));
- }
- this.registryStorage_root =
- (RegistryStorage_root)
- coderun.restClient.get(
- RegistryStorage_root.class, this.registryStorage_location.getStorage_root());
- if (this.registryStorage_root == null) {
- throw (new RegistryObjectNotfoundException(
- "Couldn't retrieve the StorageRoot for this READ dp "
- + this.givenDataProduct_name
- + " ("
- + this.actualDataProduct_name
- + ")"));
- }
- this.filePath =
- this.registryStorage_root
- .getPath()
- .resolve(Path.of(this.registryStorage_location.getPath()));
- }
-
- List getConfigItems() {
- return coderun.config.readItems();
- }
-
- String getDefaultNamespace_name() {
- return this.coderun.config.run_metadata().default_input_namespace().orElse("");
- }
-
- @Override
- RegistryNamespace getRegistryNamespace(String namespace_name) {
- // for a READ dp we must have the namespace from the config or we will have to give up
- RegistryNamespace ns = super.getRegistryNamespace(namespace_name);
- if (ns == null) {
- throw (new RegistryObjectNotfoundException("Can't find the namespace " + namespace_name));
- }
- return ns;
- }
-
- @Override
- ImmutableConfigItem getConfigItem(String dataProduct_name) {
- ImmutableConfigItem configItem = super.getConfigItem(dataProduct_name);
- if (configItem == null) {
- throw (new ConfigException("dataProduct " + dataProduct_name + " not found in config"));
- }
- return configItem;
- }
-
- private void check_hash() {
- // Do nothing for now. Unsure if we will implement hash checking.
- }
-
- private void executeOnCloseFileHandleDP() {
- // don't need to Hash READ objects
- }
-
- protected Path getFilePath() {
- this.been_used = true;
- if (!hash_checked) this.check_hash();
- return this.filePath;
- }
-
- CleanableFileChannel getFilechannel() throws IOException {
- this.been_used = true;
- Runnable onClose = this::executeOnCloseFileHandleDP;
- if (!hash_checked) this.check_hash();
- if (this.filechannel == null) {
- this.filechannel = new CleanableFileChannel(FileChannel.open(this.filePath, READ), onClose);
- } else {
- if (!this.filechannel.isOpen()) {
- this.filechannel = new CleanableFileChannel(FileChannel.open(this.filePath, READ), onClose);
- }
- }
- return this.filechannel;
- }
-
- /**
- * Obtain an Object_component for reading.
- *
- * @param component_name the name of the object component to read.
- * @return the Object_component class
- */
- public Object_component_read getComponent(String component_name) {
- if (componentMap.containsKey(component_name))
- return (Object_component_read) componentMap.get(component_name);
- Object_component_read dc = new Object_component_read(this, component_name);
- componentMap.put(component_name, dc);
- return dc;
- }
-
- /**
- * Obtain an Object_component (whole_object) for reading.
- *
- * @return the Object_component class
- */
- public Object_component_read getComponent() {
- if (this.whole_obj_oc == null) this.whole_obj_oc = new Object_component_read(this);
- return (Object_component_read) this.whole_obj_oc;
- }
-
- void components_to_registry() {
- // this is just to make sure the components can register their issues
- this.componentMap.entrySet().stream()
- .filter(c -> c.getValue().been_used)
- .forEach(component -> component.getValue().register_me_in_registry());
- }
-
- void objects_to_registry() {
- // this is called upon close; but since this is a READ dp, it won't have a DP, Stolo, fdpObj, or
- // any new components to register
- this.components_to_registry();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Data_product_write.java b/api/src/main/java/org/fairdatapipeline/api/Data_product_write.java
deleted file mode 100644
index 2766c21..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Data_product_write.java
+++ /dev/null
@@ -1,259 +0,0 @@
-package org.fairdatapipeline.api;
-
-import static java.nio.file.StandardOpenOption.*;
-
-import java.io.IOException;
-import java.nio.channels.FileChannel;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
-import org.fairdatapipeline.config.ConfigException;
-import org.fairdatapipeline.config.ImmutableConfigItem;
-import org.fairdatapipeline.dataregistry.content.*;
-import org.fairdatapipeline.file.CleanableFileChannel;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * Data_product_write is created by Coderun: {@link Coderun#get_dp_for_write(String, String)}
- *
- *
Upon {@link Coderun#close()} it will register itself and its components in the registry, and
- * then register its components in the coderun.
- */
-public class Data_product_write extends Data_product {
- private static final Logger logger = LoggerFactory.getLogger(Data_product_write.class);
- private boolean is_hashed;
-
- Data_product_write(String dataProduct_name, Coderun coderun) {
- super(dataProduct_name, coderun);
- }
-
- Data_product_write(String dataProduct_name, Coderun coderun, String extension) {
- super(dataProduct_name, coderun, extension);
- }
-
- void populate_data_product() {
- // called from the constructor
- if (this.getRegistryData_product() != null) {
- throw (new IllegalActionException(
- "You can't write to a Data Product that already exists: "
- + this.actualDataProduct_name
- + ", version "
- + this.version
- + ", namespace: "
- + this.namespace_name));
- }
- File_type file_type = new File_type(this.extension, coderun.restClient);
-
- this.registryStorage_root = this.coderun.getWriteStorage_root();
- this.registryStorage_location = new RegistryStorage_location();
- this.registryStorage_location.setStorage_root(this.registryStorage_root.getUrl());
- String filename = this.version + "." + this.extension;
- Path my_stolo_path =
- Paths.get(this.namespace_name).resolve(this.actualDataProduct_name).resolve(filename);
- this.filePath = this.registryStorage_root.getPath().resolve(my_stolo_path);
- this.registryStorage_location.setPath(my_stolo_path.toString());
- this.registryObject = new RegistryObject();
- this.registryObject.setDescription(this.description);
- this.registryObject.setAuthors(this.coderun.authors);
- this.registryObject.setFile_type(file_type.getUrl());
- this.registryData_product = new RegistryData_product();
- this.registryData_product.setName(this.actualDataProduct_name);
- this.registryData_product.setNamespace(this.registryNamespace.getUrl());
- this.registryData_product.setVersion(this.version);
- }
-
- List getConfigItems() {
- return coderun.config.writeItems();
- }
-
- String getDefaultNamespace_name() {
- return this.coderun.config.run_metadata().default_output_namespace().orElse("");
- }
-
- @Override
- RegistryNamespace getRegistryNamespace(String namespace_name) {
- RegistryNamespace ns = super.getRegistryNamespace(namespace_name);
- if (ns == null) {
- ns = (RegistryNamespace) coderun.restClient.post(new RegistryNamespace(namespace_name));
- if (ns == null) {
- throw (new RegistryException(
- "Failed to create in registry: namespace '" + namespace_name + "'"));
- }
- }
- return ns;
- }
-
- private boolean globMatch(String pattern, String dataProduct_name) {
- if (pattern.endsWith("/*")) {
- return dataProduct_name.startsWith(pattern.substring(0, pattern.length() - 1));
- }
- return pattern.equals(dataProduct_name);
- }
-
- @Override
- ImmutableConfigItem getConfigItem(String dataProduct_name) {
- ImmutableConfigItem configItem = super.getConfigItem(dataProduct_name);
- if (configItem == null) {
- // for WRITING dp's; we allow /* globbing if there is no exact match we look for a /* match
- configItem =
- this.getConfigItems().stream()
- .filter(ci -> globMatch(ci.data_product(), dataProduct_name))
- .findFirst()
- .orElse(null);
- }
- if (configItem == null) {
- throw (new ConfigException("DataProduct " + dataProduct_name + " not found in config"));
- }
- return configItem;
- }
-
- private void executeOnCloseFileHandleDP() {
- this.do_hash();
- }
-
- private void do_hash() {
- if (this.is_hashed) return;
- String hash = coderun.hasher.fileHash(this.filePath.toString());
- this.registryStorage_location.setHash(hash);
- this.is_hashed = true;
- }
-
- Path getFilePath() {
- this.been_used = true;
- this.is_hashed = false;
- if (!this.filePath.getParent().toFile().exists()) {
- try {
- Files.createDirectories(this.filePath.getParent());
- } catch (IOException e) {
- logger.error("failed to create directory {}", this.filePath.getParent());
- // throw, or continue?
- return null;
- }
- }
- return this.filePath;
- }
-
- CleanableFileChannel getFilechannel() throws IOException {
- this.been_used = true;
- Runnable onClose = this::executeOnCloseFileHandleDP;
- if (this.filechannel == null) {
- if (!this.filePath.getParent().toFile().exists()) {
- Files.createDirectories(this.filePath.getParent());
- }
- this.filechannel =
- new CleanableFileChannel(FileChannel.open(this.filePath, CREATE_NEW, WRITE), onClose);
- } else {
- if (!this.filechannel.isOpen()) {
- this.filechannel =
- new CleanableFileChannel(FileChannel.open(this.filePath, APPEND, WRITE), onClose);
- }
- }
- this.is_hashed = false;
- return this.filechannel;
- }
-
- @Override
- void closeFileChannel() {
- if (this.filechannel != null) {
- this.filechannel.close();
- this.filechannel = null;
- }
- }
-
- /**
- * Obtain an Object_component for writing.
- *
- * @param component_name the name of the object component.
- * @return the Object_component_write object.
- */
- public Object_component_write getComponent(String component_name) {
- if (componentMap.containsKey(component_name))
- return (Object_component_write) componentMap.get(component_name);
- Object_component_write dc;
- dc =
- new Object_component_write(
- this, Objects.requireNonNullElse(component_name, "whole_object"));
- componentMap.put(component_name, dc);
- return dc;
- }
-
- /**
- * Obtain an Object_component (whole_object) for writing.
- *
- * @return the Object_component class
- */
- public Object_component_write getComponent() {
- if (this.whole_obj_oc == null) this.whole_obj_oc = new Object_component_write(this);
- return (Object_component_write) this.whole_obj_oc;
- }
-
- void stolo_obj_and_dp_to_registry() {
- if (this.registryStorage_location.getUrl() == null) {
- Map find_identical =
- Map.of(
- "storage_root",
- Registry_RootObject.get_id(this.registryStorage_location.getStorage_root())
- .toString(),
- "hash",
- this.registryStorage_location.getHash(),
- "public",
- this.registryStorage_location.isIs_public() ? "true" : "false");
- RegistryStorage_location identical_sl =
- (RegistryStorage_location)
- this.coderun.restClient.getFirst(RegistryStorage_location.class, find_identical);
- if (identical_sl != null) {
- // we've found an existing stolo with matching hash. delete this one.
- try {
- Files.delete(this.filePath);
- } catch (IOException e) {
- logger.warn(
- "Failed to delete current data file which is identical to a file already in the local registry.",
- e);
- }
- this.registryStorage_location = identical_sl;
- // my FilePath is now wrong!
- } else {
- // we've not found an existing stolo with matching hash. store this one.
- RegistryStorage_location sl =
- (RegistryStorage_location) this.coderun.restClient.post(this.registryStorage_location);
- if (sl == null) {
- throw (new RegistryException(
- "Failed to create in registry: new storage location "
- + this.registryStorage_location.getPath()));
- } else {
- this.registryStorage_location = sl;
- }
- }
- }
- this.registryObject.setStorage_location(this.registryStorage_location.getUrl());
- final RegistryObject o = (RegistryObject) this.coderun.restClient.post(this.registryObject);
- if (o == null) {
- throw (new RegistryException(
- "Failed to create in registry: Object " + this.registryObject.getDescription()));
- }
- this.registryObject = o;
- this.registryData_product.setObject(o.getUrl());
- RegistryData_product dp =
- (RegistryData_product) this.coderun.restClient.post(this.registryData_product);
- if (dp == null) {
- throw (new RegistryException(
- "Failed to create in registry: Data_product " + this.registryData_product.getName()));
- }
- this.registryData_product = dp;
- }
-
- void components_to_registry() {
- if (this.whole_obj_oc != null) this.whole_obj_oc.register_me_in_registry();
- this.componentMap.forEach((key, value) -> value.register_me_in_registry());
- }
-
- void objects_to_registry() {
- this.do_hash();
- this.stolo_obj_and_dp_to_registry();
- this.components_to_registry();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/FileObject.java b/api/src/main/java/org/fairdatapipeline/api/FileObject.java
deleted file mode 100644
index 50ead15..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/FileObject.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.util.List;
-import org.fairdatapipeline.dataregistry.content.RegistryObject;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * 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 {
- final Coderun coderun;
- RegistryObject o;
-
- /**
- * This constructor is used to store actual files, such as the config and script files the coderun
- * needs to store.
- *
- * @param file_type The File_type (extension) for this file. (the file type must have already been
- * registered in the registry)
- * @param storage_location The Storage_location given must be already registered in the registry.
- * @param description name/description for this object.
- * @param authors a list of Author API URLS.
- * @param coderun link back to the coderun; to access its restClient.
- */
- FileObject(
- File_type file_type,
- Storage_location storage_location,
- String description,
- List authors,
- Coderun coderun) {
- this.coderun = coderun;
- this.o = new RegistryObject();
- this.o.setStorage_location(storage_location.getUrl());
- this.o.setDescription(description);
- if (file_type != null) this.o.setFile_type(file_type.getUrl());
- this.o.setAuthors(authors);
- this.o = (RegistryObject) coderun.restClient.post(this.o);
- if (this.o == null) {
- throw (new RegistryException(
- "Failed to create Object in registry: " + storage_location.getUrl()));
- }
- }
-
- /**
- * this constructor is used to store an Object without a file_type, such as the Object for a
- * code_repo
- *
- * @param storage_location The storage location must be already registered in the registry.
- * @param description name/description for this Object.
- * @param authors list of Author API urls.
- * @param coderun link back to the coderun; to access its restClient.
- */
- FileObject(
- Storage_location storage_location,
- String description,
- List authors,
- Coderun coderun) {
- this(null, storage_location, description, authors, coderun);
- }
-
- /**
- * raise an issue with this component
- *
- * @param description the text description of this issue
- * @param severity Integer - higher means more severe
- */
- public void raise_issue(String description, Integer severity) {
- if (o.getComponents().isEmpty()) {
- throw (new IllegalActionException("Object component not found."));
- }
- Issue i = this.coderun.raise_issue(description, severity);
- i.add_registryObject_component(getWholeObjectComponentUrl());
- }
-
- APIURL getWholeObjectComponentUrl() {
- return this.o.getComponents().get(0);
- }
-
- APIURL getUrl() {
- return this.o.getUrl();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/File_type.java b/api/src/main/java/org/fairdatapipeline/api/File_type.java
deleted file mode 100644
index b9be400..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/File_type.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.util.Collections;
-import org.fairdatapipeline.dataregistry.content.RegistryFile_type;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-import org.fairdatapipeline.dataregistry.restclient.RestClient;
-
-/** Encapsulates the registryFile_type object */
-class File_type {
- RegistryFile_type registryFile_type;
-
- /**
- * Given the @param extension, retrieve (or create if not exists) the corresponding
- * registryFile_type from the registry
- *
- * @param extension the filetype extension we're looking for (txt, yaml, toml, cvs)
- * @param restClient the restClient to access the registry.
- */
- File_type(String extension, RestClient restClient) {
- this.registryFile_type =
- (RegistryFile_type)
- restClient.getFirst(
- RegistryFile_type.class, Collections.singletonMap("extension", extension));
- if (this.registryFile_type == null) {
- this.registryFile_type =
- (RegistryFile_type) restClient.post(new RegistryFile_type(extension, extension));
- if (this.registryFile_type == null) {
- throw (new RegistryException("Failed to create File_type in Registry: " + extension));
- }
- }
- }
-
- APIURL getUrl() {
- return this.registryFile_type.getUrl();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/IllegalActionException.java b/api/src/main/java/org/fairdatapipeline/api/IllegalActionException.java
deleted file mode 100644
index 3aa3331..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/IllegalActionException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.fairdatapipeline.api;
-
-/** The consumer is probably trying to do something they aren't supposed to be doing. */
-public class IllegalActionException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public IllegalActionException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public IllegalActionException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Issue.java b/api/src/main/java/org/fairdatapipeline/api/Issue.java
deleted file mode 100644
index 162eae7..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Issue.java
+++ /dev/null
@@ -1,109 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import org.fairdatapipeline.dataregistry.content.RegistryIssue;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * An issue that can be raised with objects or their components.
- *
- *
Issues can be created using {@link Coderun#raise_issue(String, Integer)} or with {@link
- * Object_component#raise_issue(String, Integer)}.
- *
- *
Usage example
- *
- *
- *
- *
- * Object_component_write oc1 = dp.getComponent(component1);
- * oc1.raise_issue("something is terribly wrong with this component", 10);
- *
- *
- *
- *
- * or
- *
- *
- *
- *
- * Issue i = coderun.raise_issue("moderately bad data", 7);
- * i.add_components(oc1, oc2, oc3);
- *
- */
-public class Issue {
- final RegistryIssue registryIssue;
- final String description;
- final Integer severity;
- final List components;
-
- /**
- * Constructor is not public, for issues should be created by coderun.
- *
- * @param description the text (description) for this issue
- * @param severity an integer indicating the severity of the issue - high is more severe
- */
- Issue(String description, Integer severity) {
- this.description = description;
- this.severity = severity;
- this.registryIssue = new RegistryIssue(description, severity);
- this.components = new ArrayList<>();
- }
-
- /**
- * at the end of coderun the obj_components have been registered, and the registryIssue can
- * receive the obj_component URLs to put in its component_issues List.
- *
- * @return the registryIssue with its Component_issues filled in
- */
- RegistryIssue getRegistryIssue() {
- this.components.forEach(
- component ->
- this.registryIssue.addComponent_issue(component.registryObject_component.getUrl()));
- return registryIssue;
- }
-
- /**
- * When we have created an issue using coderun.raise_issue() we still need to attach this issue to
- * one or more object components. Note: attach the issue to the 'whole_object' component to
- * indicate that it is linked to the object rather than a specific component.
- *
- * @param components - any number of components can be listed as arguments
- */
- public void add_components(Object_component... components) {
- this.components.addAll(Arrays.asList(components));
- }
-
- /**
- * When we have created an issue using coderun.raise_issue() we can also attach FileObjects to
- * this issue. This can be used to raise issues with Code_repo, Submission Script, and/or Config
- * File.
- *
- * @param objects any number of FileObjects, e.g. coderun.getScript(), coderun.getConfig(),
- * coderun.getCode_repo()
- */
- public void add_fileObjects(FileObject... objects) {
- Arrays.asList(objects)
- .forEach(
- object -> this.registryIssue.addComponent_issue(object.getWholeObjectComponentUrl()));
- }
-
- void add_registryObject_component(APIURL objectComponentUrl) {
- this.registryIssue.addComponent_issue(objectComponentUrl);
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Object_component.java b/api/src/main/java/org/fairdatapipeline/api/Object_component.java
deleted file mode 100644
index ab62eaf..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Object_component.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-import org.fairdatapipeline.dataregistry.content.RegistryObject_component;
-import org.fairdatapipeline.file.CleanableFileChannel;
-
-/**
- * This represents an object_component to read from or write to (or raise issues with) An
- * object_component without a name is the 'whole_object' component.
- */
-public abstract class Object_component {
- final String component_name;
- final boolean whole_object;
- final Data_product dp;
- RegistryObject_component registryObject_component;
- boolean been_used = false;
-
- Object_component(Data_product dp, String component_name) {
- this(dp, component_name, false);
- }
-
- Object_component(Data_product dp) {
- this(dp, "whole_object", true);
- }
-
- Object_component(Data_product dp, String component_name, boolean whole_object) {
- this.dp = dp;
- this.whole_object = whole_object;
- this.component_name = component_name;
- this.populate_component();
- }
-
- /**
- * raise an issue with this component
- *
- * @param description the text description of this issue
- * @param severity Integer - higher means more severe
- */
- public void raise_issue(String description, Integer severity) {
- Issue i = this.dp.coderun.raise_issue(description, severity);
- i.add_components(this);
- }
-
- CleanableFileChannel getFileChannel() throws IOException {
- this.been_used = true;
- return this.dp.getFilechannel();
- }
-
- abstract void populate_component();
-
- RegistryObject_component retrieveObject_component() {
- Map objcompmap = new HashMap<>();
- objcompmap.put("object", dp.registryObject.get_id().toString());
- if (this.whole_object) objcompmap.put("whole_object", "true");
- else objcompmap.put("name", component_name);
- return (RegistryObject_component)
- dp.coderun.restClient.getFirst(RegistryObject_component.class, objcompmap);
- }
-
- /** POST this registryObject_component to the registry, unless it's not been used */
- abstract void register_me_in_registry();
-
- /** Add this registryObject_component to the Coderun inputs/outputs. */
- abstract void register_me_in_code_run();
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Object_component_read.java b/api/src/main/java/org/fairdatapipeline/api/Object_component_read.java
deleted file mode 100644
index 9df0b69..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Object_component_read.java
+++ /dev/null
@@ -1,121 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.List;
-import org.fairdatapipeline.distribution.Distribution;
-import org.fairdatapipeline.file.CleanableFileChannel;
-import org.fairdatapipeline.parameters.ReadComponent;
-
-/**
- * This represents an object_component to read from (or raise issues with) An object_component
- * without a name is the 'whole_object' component. Ideally the user should only read from named
- * components on toml and h5 files, and only read from the 'whole_object' on any other files. This
- * is not enforced at the moment.
- */
-public class Object_component_read extends Object_component {
-
- Object_component_read(Data_product_read dp, String component_name) {
- super(dp, component_name);
- }
-
- Object_component_read(Data_product_read dp) {
- super(dp);
- }
-
- protected void populate_component() {
- this.registryObject_component = this.retrieveObject_component();
- if (this.registryObject_component == null) {
- throw (new RegistryObjectNotfoundException(
- "Object Component '"
- + this.component_name
- + "' for Object "
- + this.dp.registryObject.get_id().toString()
- + " not found in registry."));
- }
- }
-
- /**
- * get the filePath to read from; only for whole_object component
- *
- * @return Path the Path of the data object.
- */
- public Path readLink() {
- if (!this.whole_object) {
- throw (new IllegalActionException(
- "You shouldn't try to read directly from a Data Product with named components."));
- }
- this.been_used = true;
- return this.dp.getFilePath();
- }
-
- /**
- * get the CleanableFileChannel to read directly from the file. only for whole_object component.
- *
- * @return CleanableFileChannel the filechannel to read from.
- * @throws IOException if the file can't be opened.
- */
- public CleanableFileChannel readFileChannel() throws IOException {
- if (!this.whole_object) {
- throw (new IllegalActionException(
- "You shouldn't try to read directly from a Data Product with named components."));
- }
- this.been_used = true;
- return this.getFileChannel();
- }
-
- /**
- * read the Estimate that was stored as this component in a TOML file.
- *
- * @return the estimate as Number
- */
- public Number readEstimate() {
- ReadComponent data;
- try (CleanableFileChannel fileChannel = this.getFileChannel()) {
- data =
- dp.coderun.parameterDataReader.read(fileChannel, this.registryObject_component.getName());
- } catch (IOException e) {
- throw (new RuntimeException("readEstimate() -- IOException trying to read from file", e));
- }
- return data.getEstimate();
- }
-
- /**
- * read the Distribution that was stored as this component in a TOML file.
- *
- * @return the Distribution
- */
- public Distribution readDistribution() {
- ReadComponent data;
- try (CleanableFileChannel fileChannel = this.getFileChannel()) {
- data = this.dp.coderun.parameterDataReader.read(fileChannel, this.component_name);
- } catch (IOException e) {
- throw (new RuntimeException(
- "readDistribution() -- IOException trying to read from file.", e));
- }
- return data.getDistribution();
- }
-
- /**
- * read the Samples that were stored as this component in a TOML file.
- *
- * @return the Samples object
- */
- public List readSamples() {
- ReadComponent data;
- try (CleanableFileChannel fileChannel = this.getFileChannel()) {
- data = this.dp.coderun.parameterDataReader.read(fileChannel, this.component_name);
- } catch (IOException e) {
- throw (new RuntimeException("readSamples() -- IOException trying to read from file.", e));
- }
- return data.getSamples();
- }
-
- void register_me_in_registry() {
- // I am a read component, so I am already registered.
- }
-
- void register_me_in_code_run() {
- if (this.been_used) this.dp.coderun.addInput(this.registryObject_component.getUrl());
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Object_component_write.java b/api/src/main/java/org/fairdatapipeline/api/Object_component_write.java
deleted file mode 100644
index 5204143..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Object_component_write.java
+++ /dev/null
@@ -1,142 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.Map;
-import org.fairdatapipeline.dataregistry.content.RegistryObject_component;
-import org.fairdatapipeline.distribution.Distribution;
-import org.fairdatapipeline.estimate.ImmutableEstimate;
-import org.fairdatapipeline.file.CleanableFileChannel;
-import org.fairdatapipeline.samples.Samples;
-
-/**
- * This represents an object_component to write to (or raise issues with) An object_component
- * without a name is the 'whole_object' component. Ideally the user should only write to named
- * components on toml and h5 files, and only write to the 'whole_object' on any other files. This is
- * not enforced at the moment. You should only ever either write to the whole_object, OR to the
- * named components, not both. This also is not enforced at the moment.
- */
-public class Object_component_write extends Object_component {
- Object_component_write(Data_product dp, String component_name) {
- super(dp, component_name);
- }
-
- Object_component_write(Data_product dp) {
- super(dp, "whole_object", true);
- }
-
- protected void populate_component() {
- this.registryObject_component = new RegistryObject_component(component_name);
- }
-
- /**
- * get the filePath to write; only for whole_object component
- *
- * @return Path the Path of the data object.
- */
- public Path writeLink() {
- if (!this.whole_object) {
- throw (new IllegalActionException(
- "You shouldn't try to write directly to a Data Product with named components."));
- }
- this.been_used = true;
- return this.dp.getFilePath();
- }
-
- /**
- * get the CleanableFileChannel to write directly to the file. only for whole_object component.
- *
- * @return CleanableFileChannel the filechannel to write to.
- * @throws IOException if the file can't be opened.
- */
- public CleanableFileChannel writeFileChannel() throws IOException {
- if (!this.whole_object) {
- throw (new IllegalActionException(
- "You shouldn't try to write directly to a Data Product with named components."));
- }
- this.been_used = true;
- return this.getFileChannel();
- }
-
- /**
- * write a Number as an Estimate, as this named component in the data product.
- *
- * @param estimateNumber the number to write.
- */
- public void writeEstimate(Number estimateNumber) {
- var estimate =
- ImmutableEstimate.builder().internalValue(estimateNumber).rng(this.dp.coderun.rng).build();
-
- try (CleanableFileChannel fileChannel = this.getFileChannel()) {
- dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, estimate);
- } catch (IOException e) {
- throw (new RuntimeException("writeEstimate() -- IOException trying to write to file.", e));
- }
- }
-
- /**
- * write a Distribution, as this named component in the data product.
- *
- * @param distribution the Distribution to write
- */
- public void writeDistribution(Distribution distribution) {
- try (CleanableFileChannel fileChannel = this.getFileChannel()) {
- this.dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, distribution);
- } catch (IOException e) {
- throw (new RuntimeException(
- "writeDistribution() -- IOException trying to write to file.", e));
- }
- }
-
- /**
- * write Samples, as this named component in the data product.
- *
- * @param samples a Samples object containing the samples
- */
- public void writeSamples(Samples samples) {
- try (CleanableFileChannel fileChannel = this.getFileChannel()) {
- this.dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, samples);
- } catch (IOException e) {
- throw (new RuntimeException("writeSamples() -- IOException trying to write to file.", e));
- }
- }
-
- void register_me_in_code_run() {
- if (this.been_used) this.dp.coderun.addOutput(this.registryObject_component.getUrl());
- }
-
- void register_me_in_registry() {
- if (!been_used) return; // don't register a component unless it has been written to
- if (this.whole_object) {
- Map find_whole_object =
- Map.of("object", dp.registryObject.get_id().toString(), "whole_object", "true");
- RegistryObject_component objComponent =
- (RegistryObject_component)
- dp.coderun.restClient.getFirst(RegistryObject_component.class, find_whole_object);
- if (objComponent == null) {
- throw (new RegistryObjectNotfoundException(
- "Can't find the 'whole_object' component for obj " + dp.registryObject.get_id()));
- }
- this.registryObject_component = objComponent;
- // we store the found 'whole obj' component as the object_component of
- // the referenced Object_component_write so that this can later be stored as a
- // code_run output.
- } else {
- // component != whole_object
- this.registryObject_component.setObject(dp.registryObject.getUrl());
- RegistryObject_component objComponent =
- (RegistryObject_component) dp.coderun.restClient.post(this.registryObject_component);
- if (objComponent == null) {
- throw (new RegistryException(
- "Failed to create in registry: object component "
- + this.component_name
- + " ("
- + dp.registryObject.get_id()
- + ")"));
- }
- this.registryObject_component = objComponent;
- // store the created object component so that this can later be stored as a code_run
- // output
- }
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/RegistryException.java b/api/src/main/java/org/fairdatapipeline/api/RegistryException.java
deleted file mode 100644
index 83fcfb9..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/RegistryException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.fairdatapipeline.api;
-
-/** Failure to create an Object in the registry. */
-public class RegistryException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public RegistryException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public RegistryException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/RegistryObjectNotfoundException.java b/api/src/main/java/org/fairdatapipeline/api/RegistryObjectNotfoundException.java
deleted file mode 100644
index 4a66045..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/RegistryObjectNotfoundException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.fairdatapipeline.api;
-
-/** Failure to retrieve an expected object from the registry. */
-public class RegistryObjectNotfoundException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public RegistryObjectNotfoundException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public RegistryObjectNotfoundException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Storage_location.java b/api/src/main/java/org/fairdatapipeline/api/Storage_location.java
deleted file mode 100644
index cf6022c..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Storage_location.java
+++ /dev/null
@@ -1,107 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.io.IOException;
-import java.net.URI;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.Map;
-import org.fairdatapipeline.dataregistry.content.RegistryStorage_location;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/** This is used to store a file or a remote repo to the registry as a RegistryStorage_location. */
-class Storage_location {
- private static final Logger logger = LoggerFactory.getLogger(Storage_location.class);
- RegistryStorage_location registryStorage_location;
-
- /**
- * Constructor used for storing remote_repo
- *
- * @param remote_repo the URL of the repository to store. (the protocol://server.com/ part is
- * stored as storage_root)
- * @param latest_commit the unique hash of the repository. if the repo/hash combo already exists,
- * we will use the existing one instead of storing this one.
- * @param coderun link back to the Coderun that created us.
- */
- Storage_location(URL remote_repo, String latest_commit, Coderun coderun) {
- String[] split_repo = Storage_root.url_to_root(remote_repo);
- Storage_root storage_root = new Storage_root(URI.create(split_repo[0]), coderun.restClient);
- create_storagelocation(latest_commit, storage_root, coderun, split_repo[1], null);
- }
-
- /**
- * Constructor used for storing an existing file.
- *
- * @param filePath the filePath of the file to store.
- * @param storage_root the storage root.
- * @param coderun link back to Coderun that created us.
- * @param delete_if_hash_exists we'll only create the RegistryStorage_location if the root/hash
- * combo is unique, but if delete_if_hash_exists we will also delete the file if the root/hash
- * combo already exists.
- */
- Storage_location(
- Path filePath, Storage_root storage_root, Coderun coderun, boolean delete_if_hash_exists) {
- String hash = coderun.hasher.fileHash(filePath.toString());
-
- Path storageRootPath = storage_root.getPath();
- Path relativePath = storageRootPath.relativize(filePath);
- Path filePath_to_delete = null;
- if (delete_if_hash_exists) filePath_to_delete = filePath;
- create_storagelocation(
- hash, storage_root, coderun, relativePath.toString(), filePath_to_delete);
- }
-
- void create_storagelocation(
- String hash,
- Storage_root storage_root,
- Coderun coderun,
- String path,
- Path filePath_to_delete_if_hash_exists) {
- Map find_stolo_from_hash =
- Map.of(
- "hash",
- hash,
- "public",
- "true",
- "storage_root",
- storage_root.registryStorage_root.get_id().toString());
- this.registryStorage_location =
- (RegistryStorage_location)
- coderun.restClient.getFirst(RegistryStorage_location.class, find_stolo_from_hash);
- if (this.registryStorage_location != null) {
- // there is an already existing StorageLocation for this hash; we may need to delete the file
- if (filePath_to_delete_if_hash_exists == null) {
- logger.trace(
- "Not deleting file after finding existing storage location with identical hash.");
- } else {
- try {
- Files.delete(filePath_to_delete_if_hash_exists);
- logger.trace(
- "Deleting file after finding existing storage location with identical hash.");
- } catch (IOException e) {
- logger.error(
- "Failed to delete file after finding existing storage location with identical hash: {}",
- filePath_to_delete_if_hash_exists);
- }
- }
- } else {
- // create the registryStorage_location
- this.registryStorage_location = new RegistryStorage_location();
- this.registryStorage_location.setHash(hash);
- this.registryStorage_location.setStorage_root(storage_root.getUrl());
- this.registryStorage_location.setIs_public(true);
- this.registryStorage_location.setPath(path);
- this.registryStorage_location =
- (RegistryStorage_location) coderun.restClient.post(this.registryStorage_location);
- if (this.registryStorage_location == null) {
- throw (new RegistryException("Failed to create in registry: StorageLocation for " + path));
- }
- }
- }
-
- APIURL getUrl() {
- return this.registryStorage_location.getUrl();
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/Storage_root.java b/api/src/main/java/org/fairdatapipeline/api/Storage_root.java
deleted file mode 100644
index 76229eb..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/Storage_root.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package org.fairdatapipeline.api;
-
-import java.net.URI;
-import java.net.URL;
-import java.nio.file.Path;
-import java.util.Collections;
-import org.fairdatapipeline.dataregistry.content.RegistryStorage_root;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-import org.fairdatapipeline.dataregistry.restclient.RestClient;
-
-/** Retrieve or create the RegistryStorage_root with a given 'root'. */
-class Storage_root {
- RegistryStorage_root registryStorage_root;
-
- /**
- * Retrieve or create the RegistryStorage_root with the given storageRootURI.
- *
- * @param storageRootURI the path/root for this Storage_root
- * @param restClient link to the restClient to access the registry.
- */
- Storage_root(URI storageRootURI, RestClient restClient) {
- this.registryStorage_root =
- (RegistryStorage_root)
- restClient.getFirst(
- RegistryStorage_root.class,
- Collections.singletonMap("root", storageRootURI.toString()));
- if (this.registryStorage_root == null) {
- this.registryStorage_root =
- (RegistryStorage_root) restClient.post(new RegistryStorage_root(storageRootURI));
- if (this.registryStorage_root == null) {
- throw (new RegistryException(
- "Failed to create in registry: Storage_root " + storageRootURI));
- }
- }
- }
-
- APIURL getUrl() {
- return this.registryStorage_root.getUrl();
- }
-
- URI getRoot() {
- return this.registryStorage_root.getRoot();
- }
-
- Path getPath() {
- return this.registryStorage_root.getPath();
- }
-
- /**
- * split the repository URL into a storage root (proto://authority/ part) and path (/xxx/xxx) part
- *
- * @param url the URL to split up into scheme/authority and path.
- * @return string array of length 2.
- */
- static String[] url_to_root(URL url) {
- String path = url.getPath().substring(1);
- String scheme_and_authority_part =
- url.toString().substring(0, url.toString().length() - path.length());
- return new String[] {scheme_and_authority_part, path};
- }
-}
diff --git a/api/src/main/java/org/fairdatapipeline/api/package-info.java b/api/src/main/java/org/fairdatapipeline/api/package-info.java
deleted file mode 100644
index 21c855c..0000000
--- a/api/src/main/java/org/fairdatapipeline/api/package-info.java
+++ /dev/null
@@ -1,27 +0,0 @@
-/**
- * Java implementation of the FAIR Data Pipeline API
- *
- *
The main class for the FAIR Data Pipeline JAVA API is {@link org.fairdatapipeline.api.Coderun}
- *
- *
Users should initialise this library using a try-with-resources block or ensure that .close()
- * is explicitly closed when the required file handles have been accessed.
- *
- *
+
+
+
+
diff --git a/dataregistry/build.gradle b/dataregistry/build.gradle
deleted file mode 100644
index d15123a..0000000
--- a/dataregistry/build.gradle
+++ /dev/null
@@ -1,127 +0,0 @@
-plugins {
- id 'java'
- id "com.diffplug.gradle.spotless" version "4.4.0"
- id "maven-publish"
- id "signing"
- id "jacoco"
-}
-
-group 'org.fairdatapipeline'
-version '1.0.0-rc3'
-
-java {
- sourceCompatibility = JavaVersion.VERSION_11
- targetCompatibility = JavaVersion.VERSION_11
- withJavadocJar()
- withSourcesJar()
-}
-
-javadoc {
- options.overview = "src/main/java/org/fairdatapipeline/dataregistry/overview.html"
-}
-
-repositories {
- mavenCentral()
-}
-
-dependencies {
- testImplementation(platform('org.junit:junit-bom:5.8.1'))
- testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
- testImplementation 'org.hamcrest:hamcrest:2.2'
- testImplementation 'org.mockito:mockito-core:4.3.1'
- implementation 'org.glassfish.jersey.core:jersey-client:3.0.4'
- implementation 'org.glassfish.jersey.inject:jersey-hk2:3.0.4'
- implementation 'org.glassfish.jersey:jersey-bom:3.0.4'
- implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.0.0'
- implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.15.2'
- implementation 'com.fasterxml.jackson.core:jackson-databind:2.15.2'
- implementation 'com.fasterxml.jackson.core:jackson-annotations:2.15.2'
- implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.15.2'
- implementation 'commons-io:commons-io:2.11.0'
- implementation 'org.apache.commons:commons-lang3:3.12.0'
- implementation 'jakarta.activation:jakarta.activation-api:2.1.0'
- implementation 'org.slf4j:slf4j-api:1.7.36'
- implementation 'org.slf4j:slf4j-simple:1.7.36'
-}
-
-spotless {
- java {
- googleJavaFormat()
- }
-}
-
-test {
- useJUnitPlatform()
- testLogging {
- events "passed", "skipped", "failed"
- }
- finalizedBy jacocoTestReport
-}
-jacocoTestReport {
- dependsOn test
- reports {
- xml.enabled true
- html.enabled false
- }
-}
-
-publishing {
- publications {
- mavenJava(MavenPublication) {
- artifactId = 'dataregistry'
- from components.java
- versionMapping {
- usage('java-api') {
- fromResolutionOf('runtimeClasspath')
- }
- usage('java-runtime') {
- fromResolutionResult()
- }
- }
- pom {
- name = 'javaDataPipeline Dataregistry'
- description = 'The library used by javaDataPipeline API to access the FAIR DataPipeline Registry'
- url = 'http://www.fairdatapipeline.org/'
- licenses {
- license {
- name = 'GNU LESSER GENERAL PUBLIC LICENSE, Version 3.0'
- url = 'https://www.gnu.org/licenses/lgpl-3.0.html'
- }
- }
- organization {
- name = 'THE SCOTTISH COVID-19 RESPONSE CONSORTIUM'
- url = 'https://www.gla.ac.uk/research/az/scrc/'
- }
- developers {
- developer {
- id = 'bram'
- name = 'Bram Boskamp'
- email = 'bram@boska.mp'
- organization = 'Biomathematics and Statistics Scotland'
- organizationUrl = 'https://www.bioss.ac.uk/'
- }
- }
- scm {
- connection = 'scm:git:https://github.com/FAIRDataPipeline/javaDataPipeline.git'
- developerConnection = 'scm:git:https://github.com/FAIRDataPipeline/javaDataPipeline.git'
- url = 'https://github.com/FAIRDataPipeline/javaDataPipeline'
- }
- }
- }
- }
- repositories {
- maven {
- url = 'https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/'
- credentials {
- username findProperty('ossrhUsername')
- password findProperty('ossrhPassword')
- }
- }
- }
-}
-
-signing {
- if (project.hasProperty('signing.keyId') && project.hasProperty('signing.secretKeyRingFile')) {
- sign publishing.publications.mavenJava
- }
-}
diff --git a/dataregistry/gradle.properties b/dataregistry/gradle.properties
deleted file mode 100644
index e69de29..0000000
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryAuthor.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryAuthor.java
deleted file mode 100644
index bc78e9e..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryAuthor.java
+++ /dev/null
@@ -1,66 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-/**
- * Authors that can be associated with an Object usually for use with ExternalObjects to record
- * paper authors, etc.
- */
-@XmlRootElement
-public class RegistryAuthor extends Registry_Updateable {
- @XmlElement private String name;
-
- @XmlElement private String identifier;
-
- @XmlElement private String uuid;
-
- /**
- * (optional): Full name or organisation name of the Author. Note that at least one of name or
- * identifier must be specified.
- *
- * @return Full name or organisation name of the Author.
- */
- public String getName() {
- return this.name;
- }
-
- /**
- * (optional): Full URL of identifier (e.g. ORCiD or ROR ID) of the Author.
- *
- * @return Full URL of identifier (e.g. ORCiD or ROR ID) of the Author.
- */
- public String getIdentifier() {
- return this.identifier;
- }
-
- /**
- * (optional): UUID of the Author. If not specified a UUID is generated automatically by Registry
- *
- * @return UUID of the Author.
- */
- public String getUuid() {
- return this.uuid;
- }
-
- /**
- * @param name (optional): Full name or organisation name of the Author. Note that at least one of
- * name or identifier must be specified.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /** @param identifier (optional): Full URL of identifier (e.g. ORCiD or ROR ID) of the Author. */
- public void setIdentifier(String identifier) {
- this.identifier = identifier;
- }
-
- /**
- * @param uuid (optional): UUID of the Author. If not specified a UUID is generated automatically
- * by Registry
- */
- public void setUuid(String uuid) {
- this.uuid = uuid;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_repo_release.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_repo_release.java
deleted file mode 100644
index 94c7041..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_repo_release.java
+++ /dev/null
@@ -1,80 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.net.URL;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** Information marking that an Object is an official release of a model code. */
-@XmlRootElement
-public class RegistryCode_repo_release extends Registry_Updateable {
- @XmlElement private String name;
-
- @XmlElement private String version;
-
- @XmlElement private URL website;
-
- @XmlElement private APIURL object;
-
- /**
- * Name of the CodeRepoRelease, unique in the context of the CodeRepoRelease.version
- *
- * @return Name of the CodeRepoRelease, unique in the context of the CodeRepoRelease.version
- */
- public String getName() {
- return this.name;
- }
-
- /**
- * Version identifier of the CodeRepoRelease, must conform to semantic versioning syntax, unique
- * in the context of the CodeRepoRelease.name.
- *
- * @return Version identifier of the CodeRepoRelease.
- */
- public String getVersion() {
- return this.version;
- }
-
- /**
- * (optional): URL of the website for this code release, if applicable.
- *
- * @return URL of the website for this code release.
- */
- public URL getWebsite() {
- return this.website;
- }
-
- /**
- * APIURL of the associated Object.
- *
- * @return APIURL of the associated Object.
- */
- public APIURL getObject() {
- return this.object;
- }
-
- /**
- * @param name Name of the CodeRepoRelease, unique in the context of the CodeRepoRelease.version
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @param version Version identifier of the CodeRepoRelease, must conform to semantic versioning
- * syntax, unique in the context of the CodeRepoRelease.name.
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /** @param website (optional): URL of the website for this code release, if applicable. */
- public void setWebsite(URL website) {
- this.website = website;
- }
-
- /** @param object APIURL of the associated Object. */
- public void setObject(APIURL object) {
- this.object = object;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_run.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_run.java
deleted file mode 100644
index f90bd59..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryCode_run.java
+++ /dev/null
@@ -1,210 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.time.LocalDateTime;
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** A code run along with its associated, code repo, configuration, input and outputs. */
-@XmlRootElement
-public class RegistryCode_run extends Registry_Updateable {
-
- @XmlElement private LocalDateTime run_date;
-
- @XmlElement private String description;
-
- @XmlElement private APIURL code_repo;
-
- @XmlElement private APIURL model_config;
-
- @XmlElement private APIURL submission_script;
-
- @XmlElement private List inputs;
-
- @XmlElement private List outputs;
-
- @XmlElement private String uuid;
-
- @XmlElement private APIURL prov_report;
-
- @XmlElement private APIURL ro_crate;
-
- /** Empty Constructor. */
- public RegistryCode_run() {
- methods_allowed = List.of("GET", "PUT", "PATCH", "DELETE", "HEAD", "OPTIONS");
- }
-
- /**
- * Datetime of the CodeRun.
- *
- * @return Datetime of the CodeRun.
- */
- public LocalDateTime getRun_date() {
- return this.run_date;
- }
-
- /**
- * (optional): Free text description of the CodeRun.
- *
- * @return Free text description of the CodeRun.
- */
- public String getDescription() {
- return this.description;
- }
-
- /**
- * (optional): Reference to the RegistryObject associated with the StorageLocation where the code
- * repository is stored.
- *
- * @return Reference to the RegistryObject associated with the StorageLocation where the code
- * repository is stored.
- */
- public APIURL getCode_repo() {
- return this.code_repo;
- }
-
- /**
- * Reference to the RegistryObject for the YAML configuration used for the CodeRun.
- *
- * @return Reference to the RegistryObject for the YAML configuration used for the CodeRun.
- */
- public APIURL getModel_config() {
- return this.model_config;
- }
-
- /**
- * Reference to the RegistryObject for the submission script used for the CodeRun.
- *
- * @return Reference to the RegistryObject for the submission script used for the CodeRun.
- */
- public APIURL getSubmission_script() {
- return this.submission_script;
- }
-
- /**
- * List of RegistryObject_component that the CodeRun used as inputs.
- *
- * @return List of RegistryObject_component that the CodeRun used as inputs.
- */
- public List getInputs() {
- // used to return empty arraylist when inputs==null, but we are more likely to be able to use
- // the PATCH method if unset items are null.
- return (this.inputs == null) ? null : new ArrayList<>(this.inputs);
- }
-
- /**
- * List of RegistryObject_component that the CodeRun produced as outputs.
- *
- * @return List of RegistryObject_component that the CodeRun produced as outputs.
- */
- public List getOutputs() {
- // used to return empty arraylist when outputs==null, but we are more likely to be able to use
- // the PATCH method if unset items are null.
- return (this.outputs == null) ? null : new ArrayList<>(this.outputs);
- }
-
- /**
- * (optional): UUID of the CodeRun. If not specified a UUID is generated automatically.
- *
- * @return UUID of the CodeRun.
- */
- public String getUuid() {
- return this.uuid;
- }
-
- /**
- * (read only): Reference to the PROV report for this Coderun.
- *
- * @return Reference to the PROV report for this Coderun.
- */
- public APIURL getProv_report() {
- return this.prov_report;
- }
-
- /**
- * APIURL reference to the ro_crate for this Data product
- *
- * @return APIURL reference to the ro_crate report for this Data product
- */
- public APIURL getRo_crate() {
- return this.ro_crate;
- }
-
- /** @param run_date Datetime of the CodeRun. */
- public void setRun_date(LocalDateTime run_date) {
- this.run_date = run_date;
- }
-
- /** @param description (optional): Free text description of the CodeRun. */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @param code_repo (optional): Reference to the RegistryObject associated with the
- * StorageLocation where the code repository is stored.
- */
- public void setCode_repo(APIURL code_repo) {
- this.code_repo = code_repo;
- }
-
- /**
- * @param model_config Reference to the RegistryObject for the YAML configuration used for the
- * CodeRun.
- */
- public void setModel_config(APIURL model_config) {
- this.model_config = model_config;
- }
-
- /**
- * @param submission_script Reference to the RegistryObject for the submission script used for the
- * CodeRun.
- */
- public void setSubmission_script(APIURL submission_script) {
- this.submission_script = submission_script;
- }
-
- /** @param inputs List of RegistryObject_component that the CodeRun used as inputs. */
- public void setInputs(List inputs) {
- this.inputs = (inputs == null) ? null : new ArrayList<>(inputs);
- }
-
- /** @param outputs List of RegistryObject_component that the CodeRun produced as outputs. */
- public void setOutputs(List outputs) {
- this.outputs = (outputs == null) ? null : new ArrayList<>(outputs);
- }
-
- /**
- * Add an output
- *
- * @param output Reference to a RegistryObject_component to add as an output of this Code_run
- */
- public void addOutput(APIURL output) {
- if (this.outputs == null) {
- this.outputs = new ArrayList<>();
- }
- this.outputs.add(output);
- }
-
- /**
- * Add an input
- *
- * @param input Reference to a RegistryObject_component to add as an input of this Code_run
- */
- public void addInput(APIURL input) {
- if (this.inputs == null) {
- this.inputs = new ArrayList<>();
- }
- this.inputs.add(input);
- }
-
- /**
- * @param uuid (optional): UUID of the CodeRun. If not specified a UUID is generated
- * automatically.
- */
- public void setUuid(String uuid) {
- this.uuid = uuid;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryData_product.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryData_product.java
deleted file mode 100644
index 4665761..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryData_product.java
+++ /dev/null
@@ -1,134 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import com.fasterxml.jackson.annotation.JsonFormat;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** A data product that is used by or generated by a model. */
-@XmlRootElement
-public class RegistryData_product extends Registry_Updateable {
-
- @XmlElement private String name;
-
- @XmlElement private String version;
-
- @XmlElement private APIURL object;
-
- @XmlElement private APIURL namespace;
-
- @XmlElement private APIURL external_object;
-
- @JsonFormat(shape = JsonFormat.Shape.NUMBER)
- @XmlElement
- private boolean internal_format;
-
- @XmlElement private APIURL prov_report;
-
- @XmlElement private APIURL ro_crate;
-
- /** Empty constructor. */
- public RegistryData_product() {
- this.methods_allowed = List.of("GET", "PUT", "PATCH", "HEAD", "OPTIONS");
- }
-
- /**
- * Name of the DataProduct, unique in the context of the triple (name, version, namespace)
- *
- * @return Name of the DataProduct.
- */
- public String getName() {
- return name;
- }
-
- /**
- * Version identifier of the DataProduct, must conform to semantic versioning syntax.
- *
- * @return Version identifier of the DataProduct, must conform to semantic versioning syntax.
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * APIURL of the associated Object.
- *
- * @return APIURL of the associated Object.
- */
- public APIURL getObject() {
- return object;
- }
-
- /**
- * API URL of the Namespace of the DataProduct.
- *
- * @return API URL of the Namespace of the DataProduct.
- */
- public APIURL getNamespace() {
- return namespace;
- }
-
- /**
- * read-only: ExternalObject API URL associated with this DataProduct.
- *
- * @return ExternalObject API URL associated with this DataProduct.
- */
- public APIURL getExternal_object() {
- return external_object;
- }
-
- /**
- * Whether this data product is in TOML/H5 format managed/specified by the data pipeline, I think.
- *
- * @return Whether this data product is in TOML/H5 format managed/specified by the data pipeline,
- * I think.
- */
- public boolean isInternal_format() {
- return this.internal_format;
- }
-
- /**
- * APIURL reference to the PROV report for this Data product
- *
- * @return APIURL reference to the PROV report for this Data product
- */
- public APIURL getProv_report() {
- return this.prov_report;
- }
-
- /**
- * APIURL reference to the ro_crate for this Data product
- *
- * @return APIURL reference to the ro_crate report for this Data product
- */
- public APIURL getRo_crate() {
- return this.ro_crate;
- }
-
- /**
- * @param name Name of the DataProduct, unique in the context of the triple (name, version,
- * namespace)
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @param version Version identifier of the DataProduct, must conform to semantic versioning
- * syntax.
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /** @param object APIURL of the associated Object. */
- public void setObject(APIURL object) {
- this.object = object;
- }
-
- /** @param namespace API URL of the Namespace of the DataProduct. */
- public void setNamespace(APIURL namespace) {
- this.namespace = namespace;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryExternal_object.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryExternal_object.java
deleted file mode 100644
index 99a2f0b..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryExternal_object.java
+++ /dev/null
@@ -1,197 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import com.fasterxml.jackson.annotation.JsonFormat;
-import java.net.URL;
-import java.time.LocalDateTime;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * An external data object, one that has come from somewhere other than being generated as part of
- * the modelling pipeline.
- */
-@XmlRootElement
-public class RegistryExternal_object extends Registry_Updateable {
- @XmlElement private URL identifier;
-
- @XmlElement private String alternate_identifier;
-
- @XmlElement private String alternate_identifier_type;
-
- @JsonFormat(shape = JsonFormat.Shape.NUMBER)
- @XmlElement
- private boolean primary_not_supplement;
-
- @XmlElement private LocalDateTime release_date;
-
- @XmlElement private String title;
-
- @XmlElement private String description;
-
- @XmlElement private APIURL data_product;
-
- @XmlElement private APIURL original_store;
-
- @XmlElement private String version;
-
- /**
- * Full URL of identifier (e.g. DataCite DOI) of the ExternalObject, unique in the context of the
- * triple (identifier, title, version). At least one of identifier and alternate_identifier must
- * be defined.
- *
- * @return Full URL of identifier (e.g. DataCite DOI) of the ExternalObject.
- */
- public URL getIdentifier() {
- return identifier;
- }
-
- /**
- * Name of the ExternalObject, unique in the context of the quadruple (alternate_identifier,
- * alternate_identifier_type, title, version). Unlike identifier, this is free text, not a url.
- * For instance, it can be a locally unique name for a data resource within the domain of issue.
- * It is associated with a alternate_identifier_type which describes its origin.
- *
- * @return Name of the ExternalObject. Unlike identifier, this is free text, not a url.
- */
- public String getAlternate_identifier() {
- return alternate_identifier;
- }
-
- /**
- * Type of alternate_identifier, required if alternate_identifier is defined.
- *
- * @return Type of alternate_identifier.
- */
- public String getAlternate_identifier_type() {
- return alternate_identifier_type;
- }
-
- /**
- * (optional): Boolean flag to indicate that the ExternalObject is a primary source.
- *
- * @return Boolean flag to indicate that the ExternalObject is a primary source.
- */
- public boolean isPrimary_not_supplement() {
- return primary_not_supplement;
- }
-
- /**
- * Date-time the ExternalObject was released.
- *
- * @return Date-time the ExternalObject was released.
- */
- public LocalDateTime getRelease_date() {
- return release_date;
- }
-
- /**
- * Title of the ExternalObject.
- *
- * @return Title of the ExternalObject.
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * (optional): Free text description of the ExternalObject.
- *
- * @return Free text description of the ExternalObject.
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * API URL of the associated DataProduct.
- *
- * @return API URL of the associated DataProduct.
- */
- public APIURL getData_product() {
- return data_product;
- }
-
- /**
- * (optional): StorageLocation that references the original location of this ExternalObject. For
- * example, if the original data location could be transient and so the data has been copied to a
- * more robust location, this would be the reference to the original data location.
- *
- * @return API URL of the StorageLocation that references the original location of this
- * ExternalObject.
- */
- public APIURL getOriginal_store() {
- return original_store;
- }
-
- /**
- * (read-only) Version identifier of the DataProduct associated with this ExternalObject.
- *
- * @return Version identifier of the DataProduct associated with this ExternalObject.
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param identifier Full URL of identifier (e.g. DataCite DOI) of the ExternalObject, unique in
- * the context of the triple (identifier, title, version). At least one of identifier and
- * alternate_identifier must be defined.
- */
- public void setIdentifier(URL identifier) {
- this.identifier = identifier;
- }
-
- /**
- * @param alternate_identifier Name of the ExternalObject, unique in the context of the quadruple
- * (alternate_identifier, alternate_identifier_type, title, version). Unlike identifier, this
- * is free text, not a url.
- */
- public void setAlternate_identifier(String alternate_identifier) {
- this.alternate_identifier = alternate_identifier;
- }
-
- /**
- * @param alternate_identifier_type Type of alternate_identifier, required if alternate_identifier
- * is defined.
- */
- public void setAlternate_identifier_type(String alternate_identifier_type) {
- this.alternate_identifier_type = alternate_identifier_type;
- }
-
- /**
- * @param primary_not_supplement (optional): Boolean flag to indicate that the ExternalObject is a
- * primary source.
- */
- public void setPrimary_not_supplement(boolean primary_not_supplement) {
- this.primary_not_supplement = primary_not_supplement;
- }
-
- /** @param release_date Date-time the ExternalObject was released. */
- public void setRelease_date(LocalDateTime release_date) {
- this.release_date = release_date;
- }
-
- /** @param title Title of the ExternalObject. */
- public void setTitle(String title) {
- this.title = title;
- }
-
- /** @param description (optional): Free text description of the ExternalObject. */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /** @param data_product API URL of the associated DataProduct. */
- public void setData_product(APIURL data_product) {
- this.data_product = data_product;
- }
-
- /**
- * @param original_store (optional): StorageLocation that references the original location of this
- * ExternalObject.
- */
- public void setOriginal_store(APIURL original_store) {
- this.original_store = original_store;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryFile_type.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryFile_type.java
deleted file mode 100644
index d6690bd..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryFile_type.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-/** The file type of an object. */
-@XmlRootElement
-public class RegistryFile_type extends Registry_Updateable {
- @XmlElement private String name;
-
- @XmlElement private String extension;
-
- /** Empty constructor */
- public RegistryFile_type() {}
-
- /**
- * Constructor
- *
- * @param name Name of the file type. (text description like 'Microsoft Excel Open XML
- * Spreadsheet')
- * @param extension Filename extension. (like csv)
- */
- public RegistryFile_type(String name, String extension) {
- this.name = name;
- this.extension = extension;
- }
-
- /**
- * Name of the file type. Examples:
- *
- *
- *
Hierarchical Data Format version 5
- *
Comma-separated values file
- *
Microsoft Excel Open XML Spreadsheet
- *
- *
- * @return Name of the file type.
- */
- public String getName() {
- return name;
- }
-
- /**
- * Filename extension. Examples:
- *
- *
- *
h5
- *
csv
- *
xlsx
- *
- *
- * @return The filename extension.
- */
- public String getExtension() {
- return extension;
- }
-
- /**
- * @param name Name of the file type. (text description like 'Microsoft Excel Open XML
- * Spreadsheet')
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /** @param extension Filename extension. (like csv) */
- public void setExtension(String extension) {
- this.extension = extension;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryIssue.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryIssue.java
deleted file mode 100644
index b6e0c9c..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryIssue.java
+++ /dev/null
@@ -1,121 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** A quality issue that can be attached to any Object or ObjectComponent. */
-@XmlRootElement
-public class RegistryIssue extends Registry_Updateable {
-
- @XmlElement private Integer severity;
-
- @XmlElement private String description;
-
- @XmlElement private List component_issues;
-
- @XmlElement private String uuid;
-
- /** Empty constructor */
- public RegistryIssue() {
- this.methods_allowed = List.of("GET", "PUT", "PATCH", "HEAD", "OPTIONS");
- }
-
- /**
- * Constructor
- *
- * @param description Free text description of the Issue.
- * @param severity Severity of this Issue as an integer, the larger the value the more severe the
- * Issue.
- */
- public RegistryIssue(String description, Integer severity) {
- this();
- this.description = description;
- this.severity = severity;
- }
-
- /**
- * Severity of this Issue as an integer, the larger the value the more severe the Issue.
- *
- * @return Severity of this Issue as an integer, the larger the value the more severe the Issue.
- */
- public Integer getSeverity() {
- return this.severity;
- }
-
- /**
- * Free text description of the Issue.
- *
- * @return Free text description of the Issue.
- */
- public String getDescription() {
- return this.description;
- }
-
- /**
- * List of ObjectComponent {@link APIURL APIURLs} which the Issue is associated with.
- *
- * @return List of ObjectComponent {@link APIURL APIURLs} which the Issue is associated with.
- */
- public List getComponent_issues() {
- return (this.component_issues == null)
- ? new ArrayList<>() {}
- : new ArrayList<>(this.component_issues);
- }
-
- /**
- * (optional): UUID of the Issue. If not specified a UUID is generated automatically.
- *
- * @return UUID of the Issue.
- */
- public String getUuid() {
- return this.uuid;
- }
-
- /**
- * Severity of this Issue as an integer, the larger the value the more severe the Issue.
- *
- * @param severity Severity of this Issue as an integer, the larger the value the more severe the
- * Issue.
- */
- public void setSeverity(Integer severity) {
- this.severity = severity;
- }
-
- /**
- * Free text description of the Issue.
- *
- * @param description Free text description of the Issue.
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * Set the list of Object_components associated with this Issue.
- *
- * @param component_issues The list of Object_components associated with this Issue.
- */
- public void setComponent_issues(List component_issues) {
- this.component_issues = new ArrayList<>(component_issues);
- }
-
- /**
- * Associate a Object_component with this Issue.
- *
- * @param object_component_url The RegistryObject_component APIURL to add to this Issue
- */
- public void addComponent_issue(APIURL object_component_url) {
- if (this.component_issues == null) this.component_issues = new ArrayList<>();
- if (object_component_url != null && !this.component_issues.contains(object_component_url)) {
- this.component_issues.add(object_component_url);
- }
- }
-
- /** @param uuid UUID of the Issue. If not specified a UUID is generated automatically. */
- public void setUuid(String uuid) {
- this.uuid = uuid;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryKey_value.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryKey_value.java
deleted file mode 100644
index 2f1c191..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryKey_value.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** Free meta-data key-values associated with an Object. */
-@XmlRootElement
-public class RegistryKey_value extends Registry_Updateable {
- @XmlElement private String key;
-
- @XmlElement private String value;
-
- @XmlElement private APIURL object;
-
- /**
- * Meta-data name
- *
- * @return Meta-data name
- */
- public String getKey() {
- return this.key;
- }
-
- /**
- * Meta-data value
- *
- * @return Meta-data value
- */
- public String getValue() {
- return this.value;
- }
-
- /**
- * APIURL of the associated Object.
- *
- * @return APIURL of the associated Object.
- */
- public APIURL getObject() {
- return this.object;
- }
-
- /** @param key Meta-data name */
- public void setKey(String key) {
- this.key = key;
- }
-
- /** @param value Meta-data value */
- public void setValue(String value) {
- this.value = value;
- }
-
- /** @param object APIURL of the associated Object. */
- public void setObject(APIURL object) {
- this.object = object;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryKeyword.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryKeyword.java
deleted file mode 100644
index 413e61c..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryKeyword.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.net.URL;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * Keywords that can be associated with an Object usually for use with ExternalObjects to record
- * paper keywords, etc.
- */
-@XmlRootElement
-public class RegistryKeyword extends Registry_Updateable {
- @XmlElement private APIURL object;
-
- @XmlElement private String keyphrase;
-
- @XmlElement private URL identifier;
-
- /**
- * {@link APIURL} of the associated Object.
- *
- * @return {@link APIURL} of the associated Object.
- */
- public APIURL getObject() {
- return this.object;
- }
-
- /**
- * Free text field for the key phrase to associate with the Object.
- *
- * @return Free text field for the key phrase to associate with the Object.
- */
- public String getKeyphrase() {
- return this.keyphrase;
- }
-
- /**
- * (optional): URL of ontology annotation to associate with this Keyword.
- *
- * @return URL of ontology annotation to associate with this Keyword.
- */
- public URL getIdentifier() {
- return this.identifier;
- }
-
- /** @param object {@link APIURL} of the associated Object. */
- public void setObject(APIURL object) {
- this.object = object;
- }
-
- /** @param keyphrase Free text field for the key phrase to associate with the Object. */
- public void setKeyphrase(String keyphrase) {
- this.keyphrase = keyphrase;
- }
-
- /** @param identifier (optional): URL of ontology annotation to associate with this Keyword. */
- public void setIdentifier(URL identifier) {
- this.identifier = identifier;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryNamespace.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryNamespace.java
deleted file mode 100644
index f4be74f..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryNamespace.java
+++ /dev/null
@@ -1,69 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.net.URL;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-/** A namespace that can be used to group DataProducts. */
-@XmlRootElement
-public class RegistryNamespace extends Registry_Updateable {
- @XmlElement private String name;
-
- @XmlElement private String full_name;
-
- @XmlElement private URL website;
-
- /** Empty constructor. */
- public RegistryNamespace() {}
-
- /**
- * Constructor.
- *
- * @param name The Namespace name.
- */
- public RegistryNamespace(String name) {
- this.name = name;
- }
-
- /**
- * The Namespace name.
- *
- * @return The Namespace name.
- */
- public String getName() {
- return this.name;
- }
-
- /**
- * (optional): The full name of the Namespace.
- *
- * @return The full name of the Namespace.
- */
- public String getFull_name() {
- return this.full_name;
- }
-
- /**
- * (optional): Website URL associated with the Namespace.
- *
- * @return Website URL associated with the Namespace.
- */
- public URL getWebsite() {
- return this.website;
- }
-
- /** @param name The Namespace name */
- public void setName(String name) {
- this.name = name;
- }
-
- /** @param full_name (optional): The full name of the Namespace. */
- public void setFull_name(String full_name) {
- this.full_name = full_name;
- }
-
- /** @param website (optional): Website URL associated with the Namespace. */
- public void setWebsite(URL website) {
- this.website = website;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryObject.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryObject.java
deleted file mode 100644
index e9b94de..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryObject.java
+++ /dev/null
@@ -1,174 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * Core traceability object used to represent any data object such DataProduct, CodeRepoRelease,
- * etc.
- */
-@XmlRootElement
-public class RegistryObject extends Registry_Updateable {
- @XmlElement private String description;
-
- @XmlElement private APIURL storage_location;
-
- @XmlElement private List authors;
-
- @XmlElement private String uuid;
-
- @XmlElement private APIURL file_type;
-
- @XmlElement private List components;
-
- @XmlElement private List data_products;
-
- @XmlElement private APIURL code_repo_release;
-
- @XmlElement private APIURL quality_control;
-
- @XmlElement private List licences;
-
- @XmlElement private List keywords;
-
- /**
- * (optional): Free text description of the Object.
- *
- * @return Free text description of the Object.
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * (optional): The APIURL of the StorageLocation which is the location of the physical data of
- * this object, if applicable.
- *
- * @return The APIURL of the StorageLocation which is the location of the physical data of this
- * object, if applicable.
- */
- public APIURL getStorage_location() {
- return storage_location;
- }
-
- /**
- * (optional): List of Author APIURLs associated with this Object.
- *
- * @return List of Author APIURLs associated with this Object.
- */
- public List getAuthors() {
- return (this.authors == null) ? new ArrayList<>() {} : new ArrayList<>(authors);
- }
-
- /**
- * (optional): UUID of the Object. If not specified a UUID is generated automatically.
- *
- * @return UUID of the Object.
- */
- public String getUuid() {
- return this.uuid;
- }
-
- /**
- * (optional): FileType of this Object.
- *
- * @return FileType of this Object.
- */
- public APIURL getFile_type() {
- return this.file_type;
- }
-
- /**
- * List of ObjectComponents APIURLs associated with this Object.
- *
- * @return List of ObjectComponents APIURLs associated with this Object.
- */
- public List getComponents() {
- return (this.components == null) ? new ArrayList<>() {} : new ArrayList<>(components);
- }
-
- /**
- * List of DataProduct APIURLs if one or more is associated with this Object.
- *
- * @return List of DataProduct APIURLs if one or more is associated with this Object.
- */
- public List getData_products() {
- return (this.data_products == null) ? new ArrayList<>() {} : new ArrayList<>(data_products);
- }
-
- /**
- * The CodeRepoRelease APIURL if one is associated with this Object.
- *
- * @return The CodeRepoRelease APIURL if one is associated with this Object.
- */
- public APIURL getCode_repo_release() {
- return code_repo_release;
- }
-
- /**
- * The QualityControl APIURL if one is associated with this Object.
- *
- * @return The QualityControl APIURL if one is associated with this Object
- */
- public APIURL getQuality_control() {
- return quality_control;
- }
-
- /**
- * List of Licence APIURLs associated with this Object.
- *
- * @return List of Licence APIURLs associated with this Object.
- */
- public List getLicences() {
- return (this.licences == null) ? new ArrayList<>() {} : new ArrayList<>(licences);
- }
-
- /**
- * List of Keyword APIURLs associated with this Object.
- *
- * @return List of Keyword APIURLs associated with this Object.
- */
- public List getKeywords() {
- return (this.keywords == null) ? new ArrayList<>() {} : new ArrayList<>(keywords);
- }
-
- /** @param description (optional): Free text description of the Object. */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @param storage_location (optional): The APIURL of the StorageLocation which is the location of
- * the physical data of this object, if applicable.
- */
- public void setStorage_location(APIURL storage_location) {
- this.storage_location = storage_location;
- }
-
- /** @param authors (optional): List of Author APIURLs associated with this Object. */
- public void setAuthors(List authors) {
- this.authors = new ArrayList<>(authors);
- }
-
- /**
- * @param uuid (optional): UUID of the Object. If not specified a UUID is generated automatically.
- */
- public void setUuid(String uuid) {
- this.uuid = uuid;
- }
-
- /** @param file_type (optional): FileType of this Object. */
- public void setFile_type(APIURL file_type) {
- this.file_type = file_type;
- }
-
- @Override
- @JsonIgnore
- public String get_django_path() {
- return "object/";
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryObject_component.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryObject_component.java
deleted file mode 100644
index f689ee7..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryObject_component.java
+++ /dev/null
@@ -1,129 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * A component of a Object being used as the input to a CodeRun or produced as an output from a
- * CodeRun.
- */
-@XmlRootElement
-public class RegistryObject_component extends Registry_Updateable {
- @XmlElement private APIURL object;
-
- @XmlElement private String name;
-
- @XmlElement private String description;
-
- @XmlElement private boolean whole_object;
-
- @XmlElement private List issues;
-
- @XmlElement private List inputs_of;
-
- @XmlElement private List outputs_of;
-
- /** Empty constructor */
- public RegistryObject_component() {}
-
- /**
- * Constructor
- *
- * @param name Name of the ObjectComponent, unique in the context of ObjectComponent and its
- * Object reference.
- */
- public RegistryObject_component(String name) {
- this.name = name;
- }
-
- /**
- * The APIURL of the Object to associate this ObjectComponent with.
- *
- * @return The APIURL of the Object associated with this ObjectComponent.
- */
- public APIURL getObject() {
- return this.object;
- }
-
- /**
- * Name of the ObjectComponent, unique in the context of ObjectComponent and its Object reference.
- *
- * @return Name of the ObjectComponent, unique in the context of ObjectComponent and its Object
- * reference.
- */
- public String getName() {
- return this.name;
- }
-
- /**
- * (optional): Free text description of the ObjectComponent.
- *
- * @return Free text description of the ObjectComponent.
- */
- public String getDescription() {
- return this.description;
- }
-
- /**
- * (optional): Specifies if this ObjectComponent refers to the whole object or not (by default
- * this is False)
- *
- * @return If this ObjectComponent refers to the whole object or not.
- */
- public boolean isWhole_object() {
- return this.whole_object;
- }
-
- /**
- * (optional): List of Issues APIURLs to associate with this ObjectComponent.
- *
- * @return List of Issues APIURLs to associate with this ObjectComponent.
- */
- public List getIssues() {
- return (this.issues == null) ? new ArrayList<>() {} : new ArrayList<>(this.issues);
- }
-
- /**
- * List of CodeRun APIURLs that the ObjectComponent is being used as an input to.
- *
- * @return List of CodeRun APIURLs that the ObjectComponent is being used as an input to.
- */
- public List getInputs_of() {
- return (inputs_of == null) ? new ArrayList<>() {} : new ArrayList<>(this.inputs_of);
- }
-
- /**
- * List of CodeRun APIURLs that the ObjectComponent was created as an output of.
- *
- * @return List of CodeRun APIURLs that the ObjectComponent was created as an output of.
- */
- public List getOutputs_of() {
- return (outputs_of == null) ? new ArrayList<>() {} : new ArrayList<>(this.outputs_of);
- }
-
- /** @param object The APIURL of the Object to associate this ObjectComponent with. */
- public void setObject(APIURL object) {
- this.object = object;
- }
-
- /**
- * @param name Name of the ObjectComponent, unique in the context of ObjectComponent and its
- * Object reference.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /** @param description (optional): Free text description of the ObjectComponent. */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /** @param whole_object If this ObjectComponent refers to the whole object or not. */
- public void setWhole_object(boolean whole_object) {
- this.whole_object = whole_object;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryStorage_location.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryStorage_location.java
deleted file mode 100644
index 3cf4965..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryStorage_location.java
+++ /dev/null
@@ -1,86 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import com.fasterxml.jackson.annotation.JsonFormat;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** The location of an item relative to a StorageRoot. */
-@XmlRootElement
-public class RegistryStorage_location extends Registry_Updateable {
- @XmlElement private String path;
-
- @XmlElement private String hash;
-
- @JsonFormat(shape = JsonFormat.Shape.NUMBER)
- @JsonProperty("public")
- private boolean is_public = true;
-
- @XmlElement private APIURL storage_root;
-
- /**
- * Path from a StorageRoot uri to the item location, when appended to a StorageRoot uri produces a
- * complete URI.
- *
- * @return Path from a StorageRoot uri to the item location, when appended to a StorageRoot uri
- * produces a complete URI.
- */
- public String getPath() {
- return path;
- }
-
- /**
- * If StorageLocation references a file, this is the calculated SHA1 hash of the file. For GIT
- * repositories this is the git hash.
- *
- * @return The calculated SHA1 hash of the file, or git hash of the repo.
- */
- public String getHash() {
- return hash;
- }
-
- /**
- * (optional): Boolean indicating whether the StorageLocation is public or not (default is True)
- *
- * @return Boolean indicating whether the StorageLocation is public or not (default is True)
- */
- public boolean isIs_public() {
- return this.is_public;
- }
-
- /**
- * Reference to the StorageRoot to append the path to.
- *
- * @return Reference to the StorageRoot to append the path to.
- */
- public APIURL getStorage_root() {
- return storage_root;
- }
-
- /**
- * @param path Path from a StorageRoot uri to the item location, when appended to a StorageRoot
- * uri produces a complete URI.
- */
- public void setPath(String path) {
- this.path = path;
- }
-
- /** @param hash The calculated SHA1 hash of the file, or git hash of the repo. */
- public void setHash(String hash) {
- this.hash = hash;
- }
-
- /**
- * @param is_public (optional): Boolean indicating whether the StorageLocation is public or not
- * (default is True)
- */
- public void setIs_public(boolean is_public) {
- this.is_public = is_public;
- }
-
- /** @param storage_root Reference to the StorageRoot to append the path to. */
- public void setStorage_root(APIURL storage_root) {
- this.storage_root = storage_root;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryStorage_root.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryStorage_root.java
deleted file mode 100644
index 2439259..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryStorage_root.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import com.fasterxml.jackson.annotation.JsonFormat;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import java.io.File;
-import java.net.URI;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** The root location of a storage cache where model files are stored. */
-@XmlRootElement
-public class RegistryStorage_root extends Registry_Updateable {
- @XmlElement private URI root;
-
- @XmlElement
- @JsonFormat(shape = JsonFormat.Shape.NUMBER)
- private boolean local;
-
- @XmlElement private List locations;
-
- /** Empty constructor */
- public RegistryStorage_root() {}
-
- /**
- * Constructor
- *
- * @param root URI (including protocol) to the root of a StorageLocation.
- */
- public RegistryStorage_root(URI root) {
- this.root = root;
- }
-
- /**
- * URI (including protocol) to the root of a StorageLocation, which when prepended to a
- * StorageLocation path produces a complete URI to a file. Examples:
- *
- *
- *
- * @return URI (including protocol) to the root of a StorageLocation.
- */
- public URI getRoot() {
- return this.root;
- }
-
- /**
- * Get the Path of the Root (if scheme is 'file')
- *
- * @return the Path of the Root (if scheme is 'file'), otherwise null.
- */
- @JsonIgnore
- public Path getPath() {
- if (this.root.getScheme().equals("file")) return Path.of(new File(getRoot()).getAbsolutePath());
- return null;
- }
-
- /**
- * (optional): Boolean indicating whether the StorageRoot is local or not (by default this is
- * False)
- *
- * @return Boolean indicating whether the StorageRoot is local or not (by default this is False)
- */
- public boolean isLocal() {
- return this.local;
- }
-
- /**
- * List of APIURL references of the StorageLocations stored under this Root.
- *
- * @return List of APIURL references of the StorageLocations stored under this Root.
- */
- public List getLocations() {
- return (this.locations == null) ? new ArrayList<>() {} : new ArrayList<>(this.locations);
- }
-
- /** @param root URI (including protocol) to the root of a StorageLocation. */
- public void setRoot(URI root) {
- this.root = root;
- }
-
- /**
- * @param local (optional): Boolean indicating whether the StorageRoot is local or not (by default
- * this is False)
- */
- public void setLocal(boolean local) {
- this.local = local;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryUser_author.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryUser_author.java
deleted file mode 100644
index b2fa15b..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryUser_author.java
+++ /dev/null
@@ -1,42 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** A combination of an Author associated with a particular user. */
-@XmlRootElement
-public class RegistryUser_author extends Registry_Updateable {
-
- @XmlElement private APIURL user;
-
- @XmlElement private APIURL author;
-
- /**
- * The API URL of the User to associate with this UserAuthor.
- *
- * @return The API URL of the User to associate with this UserAuthor.
- */
- public APIURL getUser() {
- return user;
- }
-
- /**
- * The API URL of the Author to associate with this UserAuthor.
- *
- * @return The API URL of the Author to associate with this UserAuthor.
- */
- public APIURL getAuthor() {
- return author;
- }
-
- /** @param user The API URL of the User to associate with this UserAuthor. */
- public void setUser(APIURL user) {
- this.user = user;
- }
-
- /** @param author The API URL of the Author to associate with this UserAuthor. */
- public void setAuthor(APIURL author) {
- this.author = author;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryUsers.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryUsers.java
deleted file mode 100644
index 92e0137..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/RegistryUsers.java
+++ /dev/null
@@ -1,55 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-/** A registry User. */
-@XmlRootElement
-public class RegistryUsers extends Registry_RootObject {
-
- @XmlElement private String username;
-
- @XmlElement private String full_name;
-
- @XmlElement private String email;
-
- @XmlElement private List orgs;
-
- /**
- * login/username
- *
- * @return login/username
- */
- public String getUsername() {
- return username;
- }
-
- /**
- * The users full name
- *
- * @return the users full name
- */
- public String getFull_name() {
- return full_name;
- }
-
- /**
- * the users email address
- *
- * @return the users email address
- */
- public String getEmail() {
- return email;
- }
-
- /**
- * List of Orgs.
- *
- * @return List of Orgs.
- */
- public List getOrgs() {
- return (orgs == null) ? new ArrayList<>() {} : new ArrayList<>(orgs);
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_ObjectList.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_ObjectList.java
deleted file mode 100644
index 7276ab4..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_ObjectList.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/**
- * List to contain result of search queries in the Registry.
- *
- * @param We can only search for 1 type of Registry resource; the List will only contain
- * registry objects of Class T (extends Registry_RootObject)
- */
-@XmlRootElement
-public class Registry_ObjectList {
- @XmlElement private Integer count;
-
- @XmlElement private APIURL next;
-
- @XmlElement private APIURL previous;
-
- @XmlElement private List results;
-
- /**
- * Number of items in this list.
- *
- * @return Number of items in this list.
- */
- public Integer getCount() {
- return count;
- }
-
- /**
- * Reference to the next page in this result set.
- *
- * @return Reference to the next page in this result set.
- */
- public APIURL getNext() {
- return next;
- }
-
- /**
- * Reference to the previous page in this result set.
- *
- * @return Reference to the previous page in this result set.
- */
- public APIURL getPrevious() {
- return previous;
- }
-
- /**
- * List of actual {link Registry_RootObject Registry_RootObjects} found.
- *
- * @return List of actual {link Registry_RootObject Registry_RootObjects} found.
- */
- public List getResults() {
- return (this.results == null) ? new ArrayList<>() {} : new ArrayList<>(results);
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_RootObject.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_RootObject.java
deleted file mode 100644
index 9cd0860..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_RootObject.java
+++ /dev/null
@@ -1,100 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.Locale;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.apache.commons.lang3.NotImplementedException;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** Abstract class that all registry resources inherit from. */
-@XmlRootElement
-public abstract class Registry_RootObject {
- @JsonIgnore List methods_allowed = List.of("GET", "HEAD", "OPTIONS");
-
- @XmlElement private APIURL url;
-
- /**
- * (read-only) The {@link APIURL} of this object; read-only: this is set by the registry upon
- * POSTing the object.
- *
- * @return The {@link APIURL} of this object.
- */
- public APIURL getUrl() {
- return url;
- }
-
- /**
- * The resource name on the django server, which is used to create the WebTarget URL.
- *
- * @return The resource name on the django server, which is used to create the WebTarget URL.
- */
- @JsonIgnore
- public String get_django_path() {
- return Registry_RootObject.get_django_path(this.getClass().getSimpleName());
- }
-
- /**
- * If the {@link APIURL} of this object is set, return the ID part of the APIURL (as an Integer)
- *
- * @return The ID part (Integer) of the APIURL of this object, or null if URL is not set.
- */
- @JsonIgnore
- public Integer get_id() {
- if (this.url == null) {
- return null;
- }
- return Registry_RootObject.get_id(this.url);
- }
-
- /**
- * Extract ID from {@link APIURL}
- *
- * @param url the {@link APIURL} we want to get the ID from
- * @return the ID part of the given {@link APIURL}
- */
- @JsonIgnore
- public static Integer get_id(APIURL url) {
- String id_part;
- id_part = Paths.get(url.getPath()).getFileName().toString();
- return Integer.parseInt(id_part);
- }
-
- /**
- * Create resource path from Class.simpleName
- *
- * @param simpleName SimpleName of a class inherited from Registry_RootObject
- * @return the resource name on the django FAIR DataRegistry for the class referred to by
- * simpleName.
- */
- @JsonIgnore
- public static String get_django_path(String simpleName) {
- if (simpleName.startsWith("Registry_")) {
- throw (new NotImplementedException("this abstract class doesn't have a django path"));
- }
- return simpleName.substring(8).toLowerCase(Locale.ROOT) + "/";
- }
-
- /**
- * Check if a given HTTP method is allowed for this resource
- *
- * @param method a HTTP method: GET, POST, PUT, DELETE or PATCH
- * @return Is this HTTP method allowed on this resource?
- */
- @JsonIgnore
- public boolean allow_method(String method) {
- return this.methods_allowed.stream().anyMatch(s -> s.equals(method));
- }
-
- /**
- * URL is supposed to be read-only so this shouldn't really be here. But it makes life so much
- * easier being able to set everything.
- *
- * @param url The {@link APIURL} to set.
- */
- public void setUrl(APIURL url) {
- this.url = url;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_Updateable.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_Updateable.java
deleted file mode 100644
index 6914271..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/Registry_Updateable.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import java.time.LocalDateTime;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-
-/** All updateable registry objects inherit from this one. (only Users aren't updateable) */
-@XmlRootElement
-public abstract class Registry_Updateable extends Registry_RootObject {
-
- @XmlElement private LocalDateTime last_updated;
-
- @XmlElement private APIURL updated_by;
-
- /**
- * (read-only) Datetime that this record was last updated.
- *
- * @return Datetime that this record was last updated.
- */
- public LocalDateTime getLast_updated() {
- return last_updated;
- }
-
- /**
- * (read-only) Reference to the user that updated this record.
- *
- * @return Reference to the user that updated this record.
- */
- public APIURL getUpdated_by() {
- return updated_by;
- }
-
- /**
- * Last_updated should be read-only, so setter shouldn't really exist.
- *
- * @param last_updated DateTime that this record was last updated.
- */
- public void setLast_updated(LocalDateTime last_updated) {
- this.last_updated = last_updated;
- }
-
- /**
- * Updated_by should be read-only, so setter shouldn't really exist.
- *
- * @param updated_by Reference to the user that updated this record.
- */
- public void setUpdated_by(APIURL updated_by) {
- this.updated_by = updated_by;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/package-info.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/package-info.java
deleted file mode 100644
index 5a5a4ee..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/content/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * The specification of the REST resources managed by the FAIR Data Pipeline Data Registry.
- */
-package org.fairdatapipeline.dataregistry.content;
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/OAuth2ClientTokenFeature.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/OAuth2ClientTokenFeature.java
deleted file mode 100644
index 319d68e..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/OAuth2ClientTokenFeature.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package org.fairdatapipeline.dataregistry.oauth2token;
-
-import jakarta.ws.rs.core.Feature;
-import jakarta.ws.rs.core.FeatureContext;
-
-/**
- * to register the tokenfilter as a feature. (after example by Miroslav Fuksa on
- * org.glassfish.jersey.client.oauth2)
- */
-public class OAuth2ClientTokenFeature implements Feature {
-
- private final OAuth2ClientTokenFilter filter;
-
- /**
- * Initialize an OAuth2ClientTokenFilter with given accessToken.
- *
- * @param accessToken the OAuth2 token to use. (it will be used with a 'Token' prefix)
- */
- public OAuth2ClientTokenFeature(String accessToken) {
- this.filter = new OAuth2ClientTokenFilter(accessToken);
- }
-
- @Override
- public boolean configure(FeatureContext context) {
- context.register(filter);
- return true;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/OAuth2ClientTokenFilter.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/OAuth2ClientTokenFilter.java
deleted file mode 100644
index 245dd3c..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/OAuth2ClientTokenFilter.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package org.fairdatapipeline.dataregistry.oauth2token;
-
-import jakarta.annotation.Priority;
-import jakarta.ws.rs.Priorities;
-import jakarta.ws.rs.client.ClientRequestContext;
-import jakarta.ws.rs.client.ClientRequestFilter;
-import jakarta.ws.rs.core.HttpHeaders;
-
-/** OAuth2 filter using 'Token' instead of 'Bearer' in the auth header. */
-@Priority(Priorities.AUTHENTICATION)
-class OAuth2ClientTokenFilter implements ClientRequestFilter {
-
- private final String accessToken;
-
- /**
- * Create a new filter with predefined access token.
- *
- * @param accessToken Access token.
- */
- public OAuth2ClientTokenFilter(String accessToken) {
- this.accessToken = accessToken;
- }
-
- @Override
- public void filter(ClientRequestContext request) {
- String authentication = "Token " + this.accessToken;
-
- if (!request.getHeaders().containsKey(HttpHeaders.AUTHORIZATION)) {
- request.getHeaders().add(HttpHeaders.AUTHORIZATION, authentication);
- }
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/package-info.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/package-info.java
deleted file mode 100644
index 5a17bd4..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * OAuth2 Filter/Feature that uses Token instead of Bearer in the token authentication. (as DJANGO
- * wants it) From the example by Miroslav Fuksa in org.glassfish.jersey.oauth2.
- */
-package org.fairdatapipeline.dataregistry.oauth2token;
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/overview.html b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/overview.html
deleted file mode 100644
index db608a7..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/overview.html
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-
-The Dataregistry module is used by org.fairdatapipeline.api to interact with the FAIR Data Pipeline Data Registry.
-
-
\ No newline at end of file
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/APIURL.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/APIURL.java
deleted file mode 100644
index ded131b..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/APIURL.java
+++ /dev/null
@@ -1,58 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import com.fasterxml.jackson.annotation.JsonValue;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.net.URL;
-
-/** API URL contains the URL references to API resources. */
-public class APIURL {
- private final URI uri;
-
- APIURL(String spec) throws URISyntaxException {
- this.uri = new URI(spec);
- }
-
- APIURL(URI uri) {
- this.uri = uri;
- }
-
- APIURL(URL url) throws URISyntaxException {
- this.uri = url.toURI();
- }
-
- @Override
- @JsonValue
- public String toString() {
- return uri.toString();
- }
-
- @Override
- public boolean equals(Object o) {
- if (o instanceof APIURL) return this.getUri().equals(((APIURL) o).getUri());
- return false;
- }
-
- @Override
- public int hashCode() {
- return this.uri.hashCode();
- }
-
- /**
- * The URL for the API resource of this APIURL.
- *
- * @return The URL for the API resource of this APIURL.
- */
- public URI getUri() {
- return uri;
- }
-
- /**
- * The Path part of the URL for the API resource of this APIURL.
- *
- * @return The Path part of the URL for the API resource of this APIURL.
- */
- public String getPath() {
- return uri.getPath();
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/ConnectException.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/ConnectException.java
deleted file mode 100644
index cf45d42..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/ConnectException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-/** Failing to connect to the Registry. */
-public class ConnectException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public ConnectException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public ConnectException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/ForbiddenException.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/ForbiddenException.java
deleted file mode 100644
index 52901e9..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/ForbiddenException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-/** Exception for HTTP 403 - the token might be wrong? */
-public class ForbiddenException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public ForbiddenException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public ForbiddenException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RegistryJSONException.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RegistryJSONException.java
deleted file mode 100644
index 869ce34..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RegistryJSONException.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-/**
- * Exception for JSON problems -- might suggest incompatibility between java library and the data
- * registry.
- */
-public class RegistryJSONException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public RegistryJSONException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public RegistryJSONException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RegistryVersionException.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RegistryVersionException.java
deleted file mode 100644
index 0ca0687..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RegistryVersionException.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-/**
- * HTTP 406 Not Acceptable: registry rejects our Accept: version header. Make sure the FAIR Data
- * Registry version matches the org.fairdatapipeline.dataregistry library version.
- */
-public class RegistryVersionException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public RegistryVersionException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public RegistryVersionException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_ObjectListReader.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_ObjectListReader.java
deleted file mode 100644
index 22a122c..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_ObjectListReader.java
+++ /dev/null
@@ -1,50 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import com.fasterxml.jackson.databind.JavaType;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import jakarta.ws.rs.ProcessingException;
-import jakarta.ws.rs.WebApplicationException;
-import jakarta.ws.rs.core.MediaType;
-import jakarta.ws.rs.core.MultivaluedMap;
-import jakarta.ws.rs.ext.MessageBodyReader;
-import java.io.InputStream;
-import java.lang.annotation.Annotation;
-import java.lang.reflect.ParameterizedType;
-import java.lang.reflect.Type;
-import org.fairdatapipeline.dataregistry.content.Registry_ObjectList;
-import org.fairdatapipeline.dataregistry.content.Registry_RootObject;
-
-/** Jakarta WS MessageBodyReader for Registry_ObjectList using Jackson ObjectMapper */
-class Registry_ObjectListReader
- implements MessageBodyReader> {
-
- @Override
- public boolean isReadable(
- Class type, Type genericType, Annotation[] annotations, MediaType mediaType) {
- return type == Registry_ObjectList.class;
- }
-
- @Override
- public Registry_ObjectList readFrom(
- Class> type,
- Type genericType,
- Annotation[] annotations,
- MediaType mediaType,
- MultivaluedMap httpHeaders,
- InputStream entityStream)
- throws WebApplicationException {
-
- try {
- ObjectMapper om = new ObjectMapper();
- om.registerModule(new JavaTimeModule());
- Type MyTypeParameter = ((ParameterizedType) genericType).getActualTypeArguments()[0];
- JavaType ptype =
- om.getTypeFactory()
- .constructParametricType(Registry_ObjectList.class, (Class) MyTypeParameter);
- return om.readValue(entityStream, ptype);
- } catch (Exception e) {
- throw new ProcessingException("Error deserializing Registry_ObjectList", e);
- }
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_RootObjectReader.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_RootObjectReader.java
deleted file mode 100644
index 1985eab..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_RootObjectReader.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import jakarta.ws.rs.ProcessingException;
-import jakarta.ws.rs.WebApplicationException;
-import jakarta.ws.rs.core.MediaType;
-import jakarta.ws.rs.core.MultivaluedMap;
-import jakarta.ws.rs.ext.MessageBodyReader;
-import java.io.InputStream;
-import java.lang.annotation.Annotation;
-import java.lang.reflect.Type;
-import org.fairdatapipeline.dataregistry.content.Registry_RootObject;
-
-/**
- * Jakarta WS MessageBodyReader for all classes inheriting from Registry_RootObject using Jackson
- * ObjectMapper
- */
-class Registry_RootObjectReader implements MessageBodyReader {
-
- @Override
- public boolean isReadable(
- Class type, Type genericType, Annotation[] annotations, MediaType mediaType) {
- return Registry_RootObject.class.isAssignableFrom(type);
- }
-
- @Override
- public Registry_RootObject readFrom(
- Class type,
- Type genericType,
- Annotation[] annotations,
- MediaType mediaType,
- MultivaluedMap httpHeaders,
- InputStream entityStream)
- throws WebApplicationException {
- try {
- ObjectMapper om = new ObjectMapper();
- om.registerModule(new JavaTimeModule());
- return om.readValue(entityStream, type);
- } catch (Exception e) {
- throw new ProcessingException("Error deserializing ", e);
- }
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_RootObjectWriter.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_RootObjectWriter.java
deleted file mode 100644
index 327c45a..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/Registry_RootObjectWriter.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import com.fasterxml.jackson.datatype.jsr310.ser.LocalDateTimeSerializer;
-import jakarta.ws.rs.ProcessingException;
-import jakarta.ws.rs.WebApplicationException;
-import jakarta.ws.rs.core.MediaType;
-import jakarta.ws.rs.core.MultivaluedMap;
-import jakarta.ws.rs.ext.MessageBodyWriter;
-import java.io.OutputStream;
-import java.io.PrintWriter;
-import java.io.Writer;
-import java.lang.annotation.Annotation;
-import java.lang.reflect.Type;
-import java.time.LocalDateTime;
-import java.time.format.DateTimeFormatter;
-import org.fairdatapipeline.dataregistry.content.Registry_RootObject;
-
-/**
- * Jakarta WS MessageBodyWriter for all classes inheriting from Registry_RootObject using Jackson
- * ObjectMapper
- */
-class Registry_RootObjectWriter implements MessageBodyWriter {
-
- @Override
- public boolean isWriteable(
- Class type, Type genericType, Annotation[] annotations, MediaType mediaType) {
- return Registry_RootObject.class.isAssignableFrom(type);
- }
-
- @Override
- public void writeTo(
- Registry_RootObject o,
- Class type,
- Type genericType,
- Annotation[] annotations,
- MediaType mediaType,
- MultivaluedMap httpHeaders,
- OutputStream outStream)
- throws WebApplicationException {
-
- try {
- ObjectMapper om = new ObjectMapper();
- JavaTimeModule jtm = new JavaTimeModule();
- jtm.addSerializer(
- LocalDateTime.class, new LocalDateTimeSerializer(DateTimeFormatter.ISO_DATE_TIME));
- om.registerModule(jtm);
- om.setSerializationInclusion(JsonInclude.Include.NON_NULL);
- Writer w = new PrintWriter(outStream);
- String s = om.writeValueAsString(o);
- w.write(s);
- w.flush();
- w.close();
- } catch (Exception e) {
- throw new ProcessingException("Error serializing " + type.getSimpleName(), e);
- }
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RestClient.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RestClient.java
deleted file mode 100644
index ac3d407..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RestClient.java
+++ /dev/null
@@ -1,396 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import com.fasterxml.jackson.databind.deser.impl.JavaUtilCollectionsDeserializers;
-import jakarta.ws.rs.NotFoundException;
-import jakarta.ws.rs.ProcessingException;
-import jakarta.ws.rs.client.*;
-import jakarta.ws.rs.core.GenericType;
-import jakarta.ws.rs.core.MediaType;
-import jakarta.ws.rs.core.Response;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.ParameterizedType;
-import java.net.URISyntaxException;
-import java.nio.charset.StandardCharsets;
-import java.util.Collections;
-import java.util.Map;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.reflect.TypeUtils;
-import org.fairdatapipeline.dataregistry.content.RegistryUsers;
-import org.fairdatapipeline.dataregistry.content.Registry_ObjectList;
-import org.fairdatapipeline.dataregistry.content.Registry_RootObject;
-import org.fairdatapipeline.dataregistry.content.Registry_Updateable;
-import org.fairdatapipeline.dataregistry.oauth2token.OAuth2ClientTokenFeature;
-import org.glassfish.jersey.client.HttpUrlConnectorProvider;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/** Jakarta WS client implementation for interacting with the FAIR Data Registry */
-public class RestClient {
- private static final Logger logger = LoggerFactory.getLogger(RestClient.class);
- private WebTarget wt;
- private Client client;
- private final MediaType jsonWithVersion =
- new MediaType("application", "json", Collections.singletonMap("version", "1.0.0"));
-
- private void init(String registry_url, String token) {
- client =
- ClientBuilder.newBuilder()
- .register(Registry_RootObjectReader.class)
- .register(Registry_RootObjectWriter.class)
- .register(Registry_ObjectListReader.class)
- .register(JavaUtilCollectionsDeserializers.class)
- .register(new OAuth2ClientTokenFeature(token))
- .property(HttpUrlConnectorProvider.SET_METHOD_WORKAROUND, true)
- .build();
- wt = client.target(registry_url);
- }
-
- /**
- * Constructor
- *
- * @param registry_url The URL of the FAIR Data Registry (usually http://127.0.0.1:8000/api/)
- * @param token The authentication token to use to access the FAIR Data Registry.
- */
- public RestClient(String registry_url, String token) {
- init(registry_url, token);
- }
-
- /**
- * retrieve only the first FDP registry entry found when searching for entries of Class c matching
- * all constraints in Map m
- *
- * @param c The Class of the FDP Object we're trying to retrieve
- * @param m The key-value constraint pairs
- * @return The first item found, or null if none are found.
- */
- public Registry_RootObject getFirst(Class c, Map m)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- // c = the class contained within the objectlist
- // return the first item found.
- WebTarget wt2 = wt.path(Registry_RootObject.get_django_path(c.getSimpleName()));
-
- for (Map.Entry e : m.entrySet()) {
- wt2 = wt2.queryParam(e.getKey(), e.getValue());
- }
- if (c != RegistryUsers.class) {
- /* and not RegistryGroup if we ever implement it */
- wt2 = wt2.queryParam("page_size", 1);
- }
- ParameterizedType p = TypeUtils.parameterize(Registry_ObjectList.class, c);
-
- try {
- Registry_ObjectList o = wt2.request(this.getJsonMediaType()).get(new GenericType<>(p));
- if (o.getCount() == 0) {
- logger.trace("getFirst({}, {}) returned 0 items", c.getSimpleName(), m);
- return null;
- }
- return o.getResults().get(0);
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- }
- return null;
- }
-
- void deal_with_jakarta_http_exceptions(Exception e)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- if (e.getClass() == ProcessingException.class
- || e.getClass() == ResponseProcessingException.class) {
- if (e.getCause().getClass() == java.net.ConnectException.class) {
- throw (new ConnectException(
- "Can't connect to registry at " + wt + "\nIs the local registry running?", e));
- } else if (e.getCause()
- .getClass()
- .getCanonicalName()
- .startsWith("com.fasterxml.jackson.databind.exc.")) {
- throw (new RegistryJSONException("Error processing JSON response from registry."));
- } else {
- throw (new RestClientException(
- "RestClient encountered unexpected Jakarta Processing exception", e));
- }
- } else if (e.getClass() == jakarta.ws.rs.ForbiddenException.class) {
- throw (new ForbiddenException("HTTP 403 Forbidden -- is the token wrong?", e));
- } else if (e.getClass() == jakarta.ws.rs.NotAcceptableException.class) {
- throw (new RegistryVersionException(
- "HTTP 406 Not Acceptable -- incompatible version of registry"));
- }
- }
-
- /**
- * retrieve a list of all FDP registry entries of Class c matching all the constraints in Map m
- *
- * @param c The Class of the FDP Object we're trying to retrieve
- * @param m The key-value constraint pairs
- * @return the Registry_ObjectList containing all items matching the constraints in the Map m
- */
- public Registry_ObjectList getList(
- Class c, Map m)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- // c is the class contained within the ObjectList
- WebTarget wt2 = wt.path(Registry_RootObject.get_django_path(c.getSimpleName()));
- for (Map.Entry e : m.entrySet()) {
- wt2 = wt2.queryParam(e.getKey(), e.getValue());
- }
- ParameterizedType p = TypeUtils.parameterize(Registry_ObjectList.class, c);
- GenericType> gt = new GenericType<>(p);
- try {
- return wt2.request(this.getJsonMediaType()).get(gt);
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- }
- return null;
- }
-
- /**
- * retrieve the FDP registry entry of Class c with ID i
- *
- * @param c The Class of the FDP Object we're trying to retrieve
- * @param i The ID of the FDP Object we're trying to retrieve
- * @return the FDP Object (or null if not found)
- */
- public Registry_RootObject get(Class c, int i)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- WebTarget wt2 =
- wt.path(Registry_RootObject.get_django_path(c.getSimpleName())).path(Integer.toString(i));
- try {
- return wt2.request(this.getJsonMediaType()).get(c);
- } catch (NotFoundException e) {
- logger.warn("get(Class, Int)", e);
- return null;
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- }
- return null;
- }
-
- /**
- * retrieve the FDP registry entry with given APIURL
- *
- * @param c The Class of the FDP Object we're trying to retrieve
- * @param apiurl The APIURL of the Object we are trying to retrieve
- * @return The Object, or null if not found.
- */
- public Registry_RootObject get(Class c, APIURL apiurl)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- WebTarget wt2 = client.target(apiurl.toString());
- try {
- return wt2.request(this.getJsonMediaType()).get(c);
- } catch (NotFoundException e) {
- logger.warn("get(Class, APIURL)", e);
- return null;
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- }
- return null;
- }
-
- /**
- * submit the new FDP registry object o; return the created object (with the APIURL, updated_by,
- * last_updated fields filled in by the registry)
- *
- * @param o The FDP Object we are submitting (should have no URL yet)
- * @return the FDP Object we get back from the registry, with its URL set, or null upon error.
- */
- public Registry_Updateable post(Registry_Updateable o)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- WebTarget wt2 = wt.path(o.get_django_path());
- if (o.getUrl() != null) {
- throw (new RestClientException(
- "post(Registry_Updateable) -- trying to post an already existing object "
- + o.get_django_path()
- + " (object already has an URL entry)"));
- }
- Response r;
- try {
- r = wt2.request(this.getJsonMediaType()).post(Entity.entity(o, this.getJsonMediaType()));
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- return null;
- }
- if (r.getStatus() != 201) {
- // in case we failed to create the object, log the error message
-
- InputStream i = (InputStream) r.getEntity();
- try {
- String text = IOUtils.toString(i, StandardCharsets.UTF_8.name());
- logger.error("post(Registry_Updateable) -- error: {}", text);
- } catch (IOException e) {
- logger.error("post(Registry_Updateable) -- IOException trying to read response entity.", e);
- }
- return null;
- } else {
- try {
- return r.readEntity(o.getClass());
- } catch (ProcessingException e) {
- throw (new RegistryJSONException("post() fails to read response JSON", e));
- }
- }
- }
-
- /**
- * patch Object o; this means change the fields set on O, leave the rest untouched. It seems to me
- * (from the tests I did) that patch and put do the same thing, and both appear to behave the way
- * I expect PATCH should behave: NULL fields don't get overwritten.
- *
- * @param o the Object to PATCH; its URL must be set.
- * @return the Object returned from the registry, or null upon error.
- */
- public Registry_Updateable patch(Registry_Updateable o)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- if (!o.allow_method("PATCH")) {
- throw (new IllegalArgumentException(
- "patch(Registry_Updateable) -- trying to use PATCH method on an object that can't be patched."
- + o));
- }
- if (o.getUrl() == null) {
- throw (new RestClientException(
- "patch(Registry_Updateable) -- can't patch an obj without URL"));
- }
-
- Response r;
- try {
- r =
- client
- .target(o.getUrl().toString())
- .request(this.getJsonMediaType())
- .build("PATCH", Entity.entity(o, this.getJsonMediaType()))
- .invoke();
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- return null;
- }
- if (r.getStatus() >= 200 && r.getStatus() < 300) {
- try {
- return r.readEntity(o.getClass());
- } catch (ProcessingException e) {
- throw (new RegistryJSONException("patch() fails to read response JSON", e));
- }
- }
- InputStream i = (InputStream) r.getEntity();
- try {
- String text = IOUtils.toString(i, StandardCharsets.UTF_8.name());
- logger.error("patch(Registry_Updateable) -- error: {}", text);
- } catch (IOException e) {
- logger.error("patch(Registry_Updateable) -- IOException trying to read response entity.", e);
- }
- return null;
- }
-
- /**
- * put Object o; this will replace the object at the set URL.
- *
- * @param o the Object to PUT; its URL must be set.
- * @return the Object returned from the registry, or null upon error.
- */
- public Registry_Updateable put(Registry_Updateable o)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- if (!o.allow_method("PUT")) {
- throw (new IllegalArgumentException(
- "put(Registry_Updateable) -- trying to use PUT method on an object that doesn't support PUT."
- + o));
- }
- if (o.getUrl() == null) {
- throw (new RestClientException(
- "put(Registry_Updateable) -- can't PUT an object without URL"));
- }
- Response r;
- try {
- r =
- client
- .target(o.getUrl().toString())
- .request(this.getJsonMediaType())
- .put(Entity.entity(o, this.getJsonMediaType()));
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- return null;
- }
- if (r.getStatus() >= 200 && r.getStatus() < 300) {
- try {
- return r.readEntity(o.getClass());
- } catch (ProcessingException e) {
- throw (new RegistryJSONException("put() fails to read response JSON", e));
- }
- }
- InputStream i = (InputStream) r.getEntity();
- try {
- String text = IOUtils.toString(i, StandardCharsets.UTF_8.name());
- logger.error("put(Registry_Updateable) -- error: {}", text);
- } catch (IOException e) {
- logger.error("put(Registry_Updateable) -- IOException trying to read response entity.", e);
- }
- return null;
- }
-
- /**
- * delete an Object by its ID number
- *
- * @param c The Class of the FDP Object we're trying to delete
- * @param i the ID of the FDP Object we're trying to delete
- */
- public void delete(Class c, int i)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- Registry_Updateable o = (Registry_Updateable) get(c, i);
- delete(o);
- }
-
- /**
- * delete an Object
- *
- * @param o the Object we are trying to delete
- */
- public void delete(Registry_Updateable o)
- throws ConnectException, RegistryVersionException, RegistryJSONException, ForbiddenException,
- RestClientException {
- if (!o.allow_method("DELETE")) {
- throw (new IllegalArgumentException(
- "delete(Registry_Updateable) -- trying to use DELETE on an object that doesn't support DELETE."
- + o));
- }
- if (o.getUrl() == null) {
- throw (new RestClientException(
- "delete(Registry_Updateable) -- can't DELETE an object without a set URL."));
- }
- Response r;
- try {
- r = client.target(o.getUrl().toString()).request(this.getJsonMediaType()).delete();
- } catch (Exception e) {
- deal_with_jakarta_http_exceptions(e);
- return;
- }
- if (r.getStatus() != 204) {
- throw (new RestClientException(
- "delete(Registry_Updateable) -- failed to delete " + o.getUrl()));
- }
- }
-
- /**
- * Create an APIURL (only for testing, I think)
- *
- * @param c The RegistryXXX class for the resource we are trying to access.
- * @param i the ID of the resource we are creating an APIURL for.
- * @return the APIURL to access the Registry resource.
- */
- public APIURL makeAPIURL(Class c, int i) {
- WebTarget wt2 =
- wt.path(Registry_RootObject.get_django_path(c.getSimpleName())).path(Integer.toString(i));
- try {
- return new APIURL(wt2.getUri() + "/");
- } catch (URISyntaxException e) {
- logger.error(e.toString());
- return null;
- }
- }
-
- MediaType getJsonMediaType() {
- return this.jsonWithVersion;
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RestClientException.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RestClientException.java
deleted file mode 100644
index 8126f6b..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/RestClientException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-/** General propagated ProcessingException from jakarta. */
-public class RestClientException extends RuntimeException {
- /**
- * Constructor
- *
- * @param message The error message.
- */
- public RestClientException(String message) {
- super(message);
- }
-
- /**
- * Constructor
- *
- * @param message The error message.
- * @param e The Exception that caused it.
- */
- public RestClientException(String message, Exception e) {
- super(message, e);
- }
-}
diff --git a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/package-info.java b/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/package-info.java
deleted file mode 100644
index e70c6ef..0000000
--- a/dataregistry/src/main/java/org/fairdatapipeline/dataregistry/restclient/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * The actual interface for interacting with the FAIR Data Pipeline Data Registry.
- */
-package org.fairdatapipeline.dataregistry.restclient;
diff --git a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/content/file_typeTest.java b/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/content/file_typeTest.java
deleted file mode 100644
index bd8e5ed..0000000
--- a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/content/file_typeTest.java
+++ /dev/null
@@ -1,80 +0,0 @@
-package org.fairdatapipeline.dataregistry.content;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.*;
-import static org.mockito.Mockito.mock;
-import static org.mockito.Mockito.when;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import com.fasterxml.jackson.datatype.jsr310.ser.LocalDateTimeSerializer;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.time.LocalDateTime;
-import java.time.format.DateTimeFormatter;
-import org.fairdatapipeline.dataregistry.restclient.APIURL;
-import org.junit.jupiter.api.*;
-
-@TestInstance(TestInstance.Lifecycle.PER_CLASS)
-class file_typeTest {
- String json_url = "https://data.scrc.uk/api/file_type/5/?format=json";
- String json_lastupdated = "2021-03-04T14:43:57.160401Z";
- String json_name = "YAML Ain't Markup Language";
- String json_updated_by = "https://data.scrc.uk/api/users/13/?format=json";
- String json_extension = "yaml";
- String JSONString =
- "{\"url\":\""
- + json_url
- + "\",\"last_updated\":\""
- + json_lastupdated
- + "\",\"name\":\""
- + json_name
- + "\",\"extension\":\""
- + json_extension
- + "\",\"updated_by\":\""
- + json_updated_by
- + "\"}";
- APIURL url;
- APIURL updated_by;
- LocalDateTime d = LocalDateTime.of(2021, 3, 4, 14, 43, 57, 160401000);
- RegistryFile_type expected;
-
- @BeforeAll
- public void setUp() throws URISyntaxException {
- url = mock(APIURL.class);
- when(url.getUri()).thenReturn(new URI(json_url));
- when(url.toString()).thenReturn(json_url);
- when(url.getPath()).thenReturn(new URI(json_url).getPath());
- updated_by = mock(APIURL.class);
- when(updated_by.getUri()).thenReturn(new URI(json_updated_by));
- when(updated_by.getPath()).thenReturn(new URI(json_updated_by).getPath());
- when(updated_by.toString()).thenReturn(json_updated_by);
- expected = new RegistryFile_type();
- expected.setUrl(url);
- expected.setLast_updated(d);
- expected.setUpdated_by(updated_by);
- expected.setName(json_name);
- expected.setExtension(json_extension);
- }
-
- @Test
- void testFile_typeReader() throws Exception {
- RegistryFile_type from_json;
- ObjectMapper om = new ObjectMapper();
- om.registerModule(new JavaTimeModule());
- from_json = om.readValue(JSONString, RegistryFile_type.class);
- assertThat(from_json, samePropertyValuesAs(expected));
- }
-
- @Test
- void testFile_typeTwoWayTest() throws Exception {
- ObjectMapper om = new ObjectMapper();
- JavaTimeModule jtm = new JavaTimeModule();
- jtm.addSerializer(
- LocalDateTime.class, new LocalDateTimeSerializer(DateTimeFormatter.ISO_DATE_TIME));
- om.registerModule(jtm);
- String s = om.writeValueAsString(expected);
- RegistryFile_type returned = om.readValue(s, RegistryFile_type.class);
- assertThat(returned, samePropertyValuesAs(expected));
- }
-}
diff --git a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/restClientTest.java b/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/restClientTest.java
deleted file mode 100644
index c323666..0000000
--- a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/restClientTest.java
+++ /dev/null
@@ -1,322 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.samePropertyValuesAs;
-
-import jakarta.ws.rs.core.MediaType;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.nio.file.Path;
-import java.time.LocalDateTime;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.Stream;
-import org.fairdatapipeline.dataregistry.content.*;
-import org.junit.jupiter.api.*;
-import org.junit.jupiter.api.condition.DisabledIf;
-import org.junit.jupiter.api.condition.EnabledIfEnvironmentVariable;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.MethodSource;
-import org.junit.jupiter.params.provider.ValueSource;
-
-@EnabledIfEnvironmentVariable(named = "LOCALREG", matches = "FRESHASADAISY")
-@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
-@TestInstance(TestInstance.Lifecycle.PER_CLASS)
-class restClientTest {
- String localReg = "http://localhost:8000/api/";
- String badReg = "http://localhost:1234/nothere/";
- RestClient lc;
- Map m;
-
- @BeforeAll
- public void setUp() {
- Assertions.assertNotNull(System.getenv("REGTOKEN"));
- lc = new RestClient(localReg, System.getenv("REGTOKEN"));
- create_author();
- this.m = Collections.emptyMap();
- }
-
- @Order(1)
- @ParameterizedTest
- @MethodSource("objectsToBeCreated")
- @DisabledIf("keyvalueExists")
- void createObjects(Registry_Updateable o) {
- Registry_Updateable r = lc.post(o);
- Assertions.assertNotNull(r);
- switch (o.getClass().getSimpleName()) {
- case ("RegistryCode_run"):
- assertThat(
- r,
- samePropertyValuesAs(
- o,
- "uuid",
- "url",
- "updated_by",
- "last_updated",
- "_id",
- "inputs",
- "outputs",
- "prov_report",
- "ro_crate",
- "run_date"));
- break;
- case ("RegistryIssue"):
- assertThat(
- r,
- samePropertyValuesAs(
- o, "uuid", "url", "updated_by", "last_updated", "_id", "component_issues"));
- break;
- case ("RegistryObject"):
- assertThat(
- r,
- samePropertyValuesAs(
- o,
- "uuid",
- "url",
- "updated_by",
- "last_updated",
- "_id",
- "authors",
- "components",
- "data_products",
- "licenses",
- "keywords"));
- break;
- case ("RegistryObject_component"):
- assertThat(
- r,
- samePropertyValuesAs(
- o,
- "uuid",
- "url",
- "updated_by",
- "last_updated",
- "_id",
- "issues",
- "inputs_of",
- "outputs_of"));
- break;
- case ("RegistryStorage_root"):
- assertThat(
- r,
- samePropertyValuesAs(
- o, "uuid", "url", "updated_by", "last_updated", "_id", "locations"));
- break;
- case ("RegistryUsers"):
- assertThat(
- r, samePropertyValuesAs(o, "uuid", "url", "updated_by", "last_updated", "_id", "orgs"));
- break;
- case ("RegistryExternal_object"):
- assertThat(
- r,
- samePropertyValuesAs(
- o, "uuid", "url", "updated_by", "last_updated", "_id", "release_date", "version"));
- break;
- case ("RegistryData_product"):
- assertThat(
- r,
- samePropertyValuesAs(
- o, "uuid", "url", "updated_by", "last_updated", "_id", "prov_report", "ro_crate"));
- break;
- default:
- assertThat(r, samePropertyValuesAs(o, "uuid", "url", "updated_by", "last_updated", "_id"));
- break;
- }
- }
-
- @Order(2)
- @ParameterizedTest
- @ValueSource(
- classes = {
- RegistryAuthor.class,
- RegistryCode_repo_release.class,
- RegistryCode_run.class,
- RegistryData_product.class,
- RegistryExternal_object.class,
- RegistryFile_type.class,
- RegistryObject.class,
- RegistryFile_type.class,
- RegistryIssue.class,
- RegistryKey_value.class,
- RegistryKeyword.class,
- RegistryNamespace.class,
- RegistryObject.class,
- RegistryObject_component.class,
- RegistryStorage_location.class,
- RegistryStorage_root.class,
- RegistryUsers.class
- })
- void get_object(Class c) {
- Registry_RootObject n = lc.getFirst(c, m);
- Assertions.assertNotNull(n.getUrl());
- }
-
- private Stream objectsToBeCreated() throws MalformedURLException {
- ArrayList al = new ArrayList<>();
- al.add(new RegistryNamespace("test namespace"));
- al.add(new RegistryFile_type("Test filetype", ".tst"));
- RegistryIssue i = new RegistryIssue();
- i.setDescription("the big issue");
- i.setSeverity(1);
- al.add(i);
- RegistryStorage_root sr = new RegistryStorage_root();
- sr.setRoot(Path.of("D:\\Datastore").toUri());
- sr.setLocal(true);
- al.add(sr);
- RegistryStorage_location sl = new RegistryStorage_location();
- sl.setPath("StorageLocation");
- sl.setStorage_root(lc.makeAPIURL(RegistryStorage_root.class, 1));
- sl.setHash("myHash");
- al.add(sl);
- RegistryObject o = new RegistryObject();
- o.setDescription("my new object description");
- o.setStorage_location(lc.makeAPIURL(RegistryStorage_location.class, 1));
- al.add(o);
- RegistryData_product dp = new RegistryData_product();
- dp.setName("Initial Data_product");
- dp.setObject(lc.makeAPIURL(RegistryObject.class, 1));
- dp.setVersion("1.0.0");
- dp.setNamespace(lc.makeAPIURL(RegistryNamespace.class, 1));
- al.add(dp);
- RegistryExternal_object eo = new RegistryExternal_object();
- eo.setDescription("My test external object");
- eo.setIdentifier(new URL("http://www.bbc.co.uk/"));
- eo.setRelease_date(LocalDateTime.of(2021, 4, 4, 4, 4, 4, 4));
- eo.setTitle("Initial External Object");
- eo.setData_product(lc.makeAPIURL(RegistryData_product.class, 1));
- eo.setPrimary_not_supplement(true);
- al.add(eo);
- RegistryObject_component oc = new RegistryObject_component();
- oc.setName("Initial object component");
- oc.setObject(lc.makeAPIURL(RegistryObject.class, 1));
- oc.setDescription("My test object component");
- al.add(oc);
- RegistryCode_run cr = new RegistryCode_run();
- cr.setDescription("My test codeRun");
- cr.setRun_date(LocalDateTime.of(2021, 3, 3, 3, 3, 3, 3));
- cr.setCode_repo(lc.makeAPIURL(RegistryObject.class, 1));
- cr.setSubmission_script(lc.makeAPIURL(RegistryObject.class, 1));
- al.add(cr);
- RegistryAuthor a = new RegistryAuthor();
- a.setName("Bram Boskamp");
- al.add(a);
- RegistryKeyword k = new RegistryKeyword();
- k.setObject(lc.makeAPIURL(RegistryObject.class, 1));
- k.setKeyphrase("huh");
- al.add(k);
- RegistryCode_repo_release crr = new RegistryCode_repo_release();
- crr.setName("Initial code repo release");
- crr.setObject(lc.makeAPIURL(RegistryObject.class, 1));
- crr.setVersion("1.0.0");
- crr.setWebsite(new URL("http://github.com/blabla"));
- al.add(crr);
- RegistryKey_value kv = new RegistryKey_value();
- kv.setObject(lc.makeAPIURL(RegistryObject.class, 1));
- kv.setKey("the key");
- kv.setValue("the value");
- al.add(kv);
-
- return al.stream();
- }
-
- private boolean keyvalueExists() {
- Registry_ObjectList sr = lc.getList(RegistryKey_value.class, new HashMap<>());
- return sr.getCount() != 0;
- }
-
- void create_author() {
- if (lc.getFirst(RegistryAuthor.class, Collections.emptyMap()) == null) {
- RegistryAuthor author = new RegistryAuthor();
- author.setName("An Anonymous Author");
- lc.post(author);
- }
- }
-
- @Order(3)
- @Test
- void wrongVersion() {
- class RestClient_wv extends RestClient {
- private final MediaType jsonWithVersion =
- new MediaType("application", "json", Collections.singletonMap("version", "0.0.0"));
-
- public RestClient_wv(String registry_url, String token) {
- super(registry_url, token);
- }
-
- @Override
- MediaType getJsonMediaType() {
- return this.jsonWithVersion;
- }
- }
- RestClient_wv restClient_wv = new RestClient_wv(localReg, System.getenv("REGTOKEN"));
- Map em = Collections.emptyMap();
- Assertions.assertThrows(
- RegistryVersionException.class, () -> restClient_wv.getFirst(RegistryUsers.class, em));
- }
-
- @Order(4)
- @Test
- void wrongToken() {
- RestClient lc2 = new RestClient(localReg, "bad token");
- Assertions.assertThrows(
- org.fairdatapipeline.dataregistry.restclient.ForbiddenException.class,
- () -> lc2.getFirst(RegistryUsers.class, Collections.emptyMap()));
- }
-
- @Order(5)
- @Test
- void wrongRegistry() {
- // I'm faking a JSON error by interpreting a user as a code_run.
- APIURL au = lc.makeAPIURL(RegistryUsers.class, 1);
- Assertions.assertThrows(RegistryJSONException.class, () -> lc.get(RegistryCode_run.class, au));
- }
-
- @Order(6)
- @Test
- void wrongReg() {
- RestClient lc2 = new RestClient(badReg, "any token");
- Assertions.assertThrows(
- org.fairdatapipeline.dataregistry.restclient.ConnectException.class,
- () -> lc2.getFirst(RegistryUsers.class, Collections.emptyMap()));
- }
-
- @Order(7)
- @Test
- void wisnaeThereAtAw_get_by_id() {
- RegistryNamespace n = (RegistryNamespace) lc.get(RegistryNamespace.class, 98765);
- Assertions.assertNull(n); // i'm expecting NULL cause namespace 98765 doesn't exist.
- }
-
- @Order(8)
- @Test
- void wisnaeThereAtAw_getList() {
- Registry_ObjectList ol =
- lc.getList(
- RegistryFile_type.class,
- Collections.singletonMap("extension", "AVeryUnlikelyExtension"));
- Assertions.assertEquals(0, ol.getCount());
- }
-
- @Order(9)
- @Test
- void wisnaeThereAtAw_getFirst() {
- RegistryFile_type f =
- (RegistryFile_type)
- lc.getFirst(
- RegistryFile_type.class,
- Collections.singletonMap("extension", "AVeryUnlikelyExtension"));
- Assertions.assertNull(f);
- }
-
- @Order(10)
- @Test
- void breakUniqueConstraint() {
- String name = "test namespace";
- if (lc.getFirst(RegistryNamespace.class, Collections.singletonMap("name", name)) == null) {
- lc.post(new RegistryNamespace(name));
- }
- Assertions.assertNull(lc.post(new RegistryNamespace(name)));
- }
-}
diff --git a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/testPatchAndDelete.java b/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/testPatchAndDelete.java
deleted file mode 100644
index b9c2f3e..0000000
--- a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/testPatchAndDelete.java
+++ /dev/null
@@ -1,207 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.*;
-
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.time.LocalDateTime;
-import java.util.Collections;
-import java.util.List;
-import org.fairdatapipeline.dataregistry.content.*;
-import org.junit.jupiter.api.*;
-import org.junit.jupiter.api.condition.EnabledIfEnvironmentVariable;
-
-@EnabledIfEnvironmentVariable(named = "LOCALREG", matches = "FRESHASADAISY")
-@TestInstance(TestInstance.Lifecycle.PER_CLASS)
-@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
-class testPatchAndDelete {
- String localReg = "http://localhost:8000/api/";
- RestClient lc;
- RegistryCode_run cr;
-
- @BeforeAll
- public void setUp() {
- Assertions.assertNotNull(System.getenv("REGTOKEN"));
- lc = new RestClient(localReg, System.getenv("REGTOKEN"));
- }
-
- private void fresh_cr() {
- this.cr = new RegistryCode_run();
- this.cr.setDescription("test code_run for put patch delete");
- this.cr.setRun_date(LocalDateTime.now());
- this.cr.setInputs(List.of(getObject_component().getUrl()));
- this.cr.setOutputs(List.of(getObject_component().getUrl()));
- RegistryObject o = getObject();
- this.cr.setCode_repo(o.getUrl());
- this.cr.setSubmission_script(o.getUrl());
- this.cr = (RegistryCode_run) lc.post(this.cr);
- if (this.cr == null)
- throw (new IllegalArgumentException("failed to post a fresh RegistryCode_run"));
- }
-
- @Test
- @Order(1)
- void putCode_run() {
- fresh_cr();
- RegistryCode_run cr2 = new RegistryCode_run();
- cr2.setUrl(cr.getUrl());
- cr2.setRun_date(LocalDateTime.now());
- cr2.setSubmission_script(getObject().getUrl());
- cr2.setDescription("changed desc for put");
- cr2.setInputs(getObject_components_2());
- RegistryCode_run cr3 = (RegistryCode_run) lc.put(cr2);
- assertThat(
- cr3,
- samePropertyValuesAs(
- cr2,
- "last_updated",
- "inputs",
- "outputs",
- "code_repo",
- "prov_report",
- "ro_crate",
- "run_date",
- "updated_by",
- "uuid"));
- Assertions.assertEquals(
- cr3.getCode_repo(), cr.getCode_repo()); // this indicates PATCH behaviour.
- Assertions.assertEquals(
- cr3.getInputs().size(), cr2.getInputs().size()); // inputs have been over-written
- Assertions.assertEquals(
- cr3.getOutputs().size(),
- cr.getOutputs().size()); // outputs have not. this indicates PATCH behaviour.
- //
- }
-
- @Test
- @Order(2)
- void patchCode_run() {
- fresh_cr();
- RegistryCode_run cr2 = new RegistryCode_run();
- cr2.setUrl(cr.getUrl());
- cr2.setRun_date(LocalDateTime.now());
- cr2.setSubmission_script(getObject().getUrl());
- cr2.setDescription("changed desc for patch");
- cr2.setInputs(getObject_components_2());
- RegistryCode_run cr3 = (RegistryCode_run) lc.patch(cr2);
- assertThat(
- cr3,
- samePropertyValuesAs(
- cr2,
- "last_updated",
- "inputs",
- "outputs",
- "code_repo",
- "prov_report",
- "ro_crate",
- "run_date",
- "updated_by",
- "uuid"));
- Assertions.assertEquals(
- cr3.getCode_repo(), cr.getCode_repo()); // this indicates PATCH behaviour.
- Assertions.assertEquals(
- cr3.getInputs().size(), cr2.getInputs().size()); // inputs have been over-written
- Assertions.assertEquals(
- cr3.getOutputs().size(),
- cr.getOutputs().size()); // outputs have not. this indicates PATCH behaviour.
- }
-
- @Test
- @Order(3)
- void delete_object() {
- fresh_cr();
- APIURL url = cr.getUrl();
- lc.delete(cr);
- Assertions.assertNull(lc.get(RegistryCode_run.class, url));
- }
-
- @Test
- @Order(4)
- void delete_by_id() {
- fresh_cr();
- APIURL url = cr.getUrl();
- lc.delete(RegistryCode_run.class, cr.get_id());
- Assertions.assertNull(lc.get(RegistryCode_run.class, url));
- }
-
- RegistryObject_component getObject_component() {
- RegistryObject_component oc =
- (RegistryObject_component)
- lc.getFirst(RegistryObject_component.class, Collections.emptyMap());
- if (oc == null) {
- getObject(); // this should create an object as well as an object component!
- oc =
- (RegistryObject_component)
- lc.getFirst(RegistryObject_component.class, Collections.emptyMap());
- if (oc == null)
- throw (new IllegalArgumentException(
- "failed to find object_component, even after creating an object"));
- }
- return oc;
- }
-
- List getObject_components_2() {
- RegistryObject o = getObject();
- RegistryObject_component wo =
- (RegistryObject_component)
- lc.getFirst(
- RegistryObject_component.class, Collections.singletonMap("whole_object", "true"));
- RegistryObject_component nowo =
- (RegistryObject_component)
- lc.getFirst(
- RegistryObject_component.class, Collections.singletonMap("whole_object", "false"));
- if (nowo == null) {
- RegistryObject_component oc = new RegistryObject_component();
- oc.setObject(o.getUrl());
- oc.setDescription("an extra oc");
- oc.setName("some measurement");
- nowo = (RegistryObject_component) lc.post(oc);
- }
- return List.of(wo.getUrl(), nowo.getUrl());
- }
-
- RegistryObject getObject() {
- RegistryObject o = (RegistryObject) lc.getFirst(RegistryObject.class, Collections.emptyMap());
- if (o == null) {
- o = new RegistryObject();
- o.setDescription("one random object");
- o.setStorage_location(getStorage_location().getUrl());
- o = (RegistryObject) lc.post(o);
- if (o == null) throw (new IllegalArgumentException("couldn't post Object"));
- }
- return o;
- }
-
- RegistryStorage_location getStorage_location() {
- RegistryStorage_location sl =
- (RegistryStorage_location)
- lc.getFirst(RegistryStorage_location.class, Collections.emptyMap());
- if (sl == null) {
- sl = new RegistryStorage_location();
- sl.setHash("70af0e7749896a9aadf7c999ca26b59c7bcf69af");
- sl.setPath("this/is/where/we/keep/the/bikes.txt");
- sl.setStorage_root(getStorage_root().getUrl());
- sl = (RegistryStorage_location) lc.post(sl);
- if (sl == null) throw (new IllegalArgumentException("couldn't post Storage_location"));
- }
- return sl;
- }
-
- RegistryStorage_root getStorage_root() {
- RegistryStorage_root sr =
- (RegistryStorage_root) lc.getFirst(RegistryStorage_root.class, Collections.emptyMap());
- if (sr == null) {
- sr = new RegistryStorage_root();
- try {
- sr.setRoot(new URI("http://bikehub.com"));
- } catch (URISyntaxException e) {
- Assertions.fail("URISyntaxException in test code");
- }
- sr.setLocal(true);
- sr = (RegistryStorage_root) lc.post(sr);
- if (sr == null) throw (new IllegalArgumentException("couldn't post storageRoot"));
- }
- return sr;
- }
-}
diff --git a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/test_Registry_RootObjectWriter.java b/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/test_Registry_RootObjectWriter.java
deleted file mode 100644
index e18a179..0000000
--- a/dataregistry/src/test/java/org/fairdatapipeline/dataregistry/restclient/test_Registry_RootObjectWriter.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package org.fairdatapipeline.dataregistry.restclient;
-
-import java.io.ByteArrayOutputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
-import org.fairdatapipeline.dataregistry.content.*;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.Test;
-
-class test_Registry_RootObjectWriter {
-
- public String write_json(Registry_RootObject o, Class type) {
- ByteArrayOutputStream ba = new ByteArrayOutputStream();
- new Registry_RootObjectWriter().writeTo(o, type, null, null, null, null, ba);
- return ba.toString();
- }
-
- @Test
- void test_File_type() {
- RegistryFile_type ft = new RegistryFile_type("bla", "blow");
- Assertions.assertEquals(
- "{\"name\":\"bla\",\"extension\":\"blow\"}", write_json(ft, ft.getClass()));
- }
-
- @Test
- void test_Namespace() throws MalformedURLException {
- RegistryNamespace ns = new RegistryNamespace();
- ns.setName("name");
- ns.setFull_name("Name Potter");
- ns.setWebsite(new URL("http://www.nos.nl/"));
- Assertions.assertEquals(
- "{\"name\":\"name\",\"full_name\":\"Name Potter\",\"website\":\"http://www.nos.nl/\"}",
- write_json(ns, ns.getClass()));
- }
-
- @Test
- void test_Storage_location() {
- RegistryStorage_location sl = new RegistryStorage_location();
- sl.setPath("/bla/blow");
- sl.setHash("ciouchsduichs");
- sl.setIs_public(true);
- RestClient rc = new RestClient("https://127.0.0.1:8000/api/", "dummy token");
- sl.setStorage_root(rc.makeAPIURL(RegistryStorage_root.class, 1));
- Assertions.assertEquals(
- "{\"path\":\"/bla/blow\",\"hash\":\"ciouchsduichs\",\"storage_root\":\"https://127.0.0.1:8000/api/storage_root/1/\",\"public\":1}",
- write_json(sl, sl.getClass()));
- }
-}
diff --git a/deprecated-list.html b/deprecated-list.html
new file mode 100644
index 0000000..0ee0e1e
--- /dev/null
+++ b/deprecated-list.html
@@ -0,0 +1,146 @@
+
+
+
+
+
+Deprecated List (api 1.0.0-rc3 API)
+
+
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+
+
Deprecated API
+
Contents
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+
+
+
+
diff --git a/element-list b/element-list
new file mode 100644
index 0000000..b33561c
--- /dev/null
+++ b/element-list
@@ -0,0 +1,12 @@
+org.fairdatapipeline.api
+org.fairdatapipeline.config
+org.fairdatapipeline.distribution
+org.fairdatapipeline.estimate
+org.fairdatapipeline.file
+org.fairdatapipeline.hash
+org.fairdatapipeline.mapper
+org.fairdatapipeline.objects
+org.fairdatapipeline.parameters
+org.fairdatapipeline.samples
+org.fairdatapipeline.toml
+org.fairdatapipeline.yaml
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
deleted file mode 100644
index 62d4c05..0000000
Binary files a/gradle/wrapper/gradle-wrapper.jar and /dev/null differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
deleted file mode 100644
index 5ceefc8..0000000
--- a/gradle/wrapper/gradle-wrapper.properties
+++ /dev/null
@@ -1,6 +0,0 @@
-#Fri Jul 10 10:20:32 BST 2020
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.5.1-all.zip
-distributionBase=GRADLE_USER_HOME
-distributionPath=wrapper/dists
-zipStorePath=wrapper/dists
-zipStoreBase=GRADLE_USER_HOME
diff --git a/gradlew b/gradlew
deleted file mode 100644
index fbd7c51..0000000
--- a/gradlew
+++ /dev/null
@@ -1,185 +0,0 @@
-#!/usr/bin/env sh
-
-#
-# Copyright 2015 the original author or authors.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# https://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-##############################################################################
-##
-## Gradle start up script for UN*X
-##
-##############################################################################
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
-
-# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
-
-warn () {
- echo "$*"
-}
-
-die () {
- echo
- echo "$*"
- echo
- exit 1
-}
-
-# OS specific support (must be 'true' or 'false').
-cygwin=false
-msys=false
-darwin=false
-nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
-esac
-
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
-
-
-# Determine the Java command to use to start the JVM.
-if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
- else
- JAVACMD="$JAVA_HOME/bin/java"
- fi
- if [ ! -x "$JAVACMD" ] ; then
- die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
- fi
-else
- JAVACMD="java"
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-fi
-
-# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
-fi
-
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
- # Now convert the arguments - kludge to limit ourselves to /bin/sh
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
- fi
- i=`expr $i + 1`
- done
- case $i in
- 0) set -- ;;
- 1) set -- "$args0" ;;
- 2) set -- "$args0" "$args1" ;;
- 3) set -- "$args0" "$args1" "$args2" ;;
- 4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
-fi
-
-# Escape application args
-save () {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=`save "$@"`
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
-
-exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
deleted file mode 100644
index 5093609..0000000
--- a/gradlew.bat
+++ /dev/null
@@ -1,104 +0,0 @@
-@rem
-@rem Copyright 2015 the original author or authors.
-@rem
-@rem Licensed under the Apache License, Version 2.0 (the "License");
-@rem you may not use this file except in compliance with the License.
-@rem You may obtain a copy of the License at
-@rem
-@rem https://www.apache.org/licenses/LICENSE-2.0
-@rem
-@rem Unless required by applicable law or agreed to in writing, software
-@rem distributed under the License is distributed on an "AS IS" BASIS,
-@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@rem See the License for the specific language governing permissions and
-@rem limitations under the License.
-@rem
-
-@if "%DEBUG%" == "" @echo off
-@rem ##########################################################################
-@rem
-@rem Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Resolve any "." and ".." in APP_HOME to make it shorter.
-for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto init
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
-
-:end
-@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
diff --git a/help-doc.html b/help-doc.html
new file mode 100644
index 0000000..9b145f1
--- /dev/null
+++ b/help-doc.html
@@ -0,0 +1,272 @@
+
+
+
+
+
+API Help (api 1.0.0-rc3 API)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
How This API Document Is Organized
+
This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.
+
+
+
+
+
+
Overview
+
The Overview page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.
+
+
+
+
+
Package
+
Each package has a page that contains a list of its classes and interfaces, with a summary for each. These pages may contain six categories:
+
+
Interfaces
+
Classes
+
Enums
+
Exceptions
+
Errors
+
Annotation Types
+
+
+
+
+
+
Class or Interface
+
Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:
+
+
Class Inheritance Diagram
+
Direct Subclasses
+
All Known Subinterfaces
+
All Known Implementing Classes
+
Class or Interface Declaration
+
Class or Interface Description
+
+
+
+
Nested Class Summary
+
Field Summary
+
Property Summary
+
Constructor Summary
+
Method Summary
+
+
+
+
Field Detail
+
Property Detail
+
Constructor Detail
+
Method Detail
+
+
Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.
+
+
+
+
+
Annotation Type
+
Each annotation type has its own separate page with the following sections:
+
+
Annotation Type Declaration
+
Annotation Type Description
+
Required Element Summary
+
Optional Element Summary
+
Element Detail
+
+
+
+
+
+
Enum
+
Each enum has its own separate page with the following sections:
+
+
Enum Declaration
+
Enum Description
+
Enum Constant Summary
+
Enum Constant Detail
+
+
+
+
+
+
Tree (Class Hierarchy)
+
There is a Class Hierarchy page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. Classes are organized by inheritance structure starting with java.lang.Object. Interfaces do not inherit from java.lang.Object.
+
+
When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.
+
When viewing a particular package, class or interface page, clicking on "Tree" displays the hierarchy for only that package.
+
+
+
+
+
+
Deprecated API
+
The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.
+
+
+
+
+
Index
+
The Index contains an alphabetic index of all classes, interfaces, constructors, methods, and fields, as well as lists of all packages and all classes.
+
+
+
+
+
All Classes
+
The All Classes link shows all classes and interfaces except non-static nested types.
+
+
+
+
+
Serialized Form
+
Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.
You can search for definitions of modules, packages, types, fields, methods and other terms defined in the API, using some or all of the name. "Camel-case" abbreviations are supported: for example, "InpStr" will find "InputStream" and "InputStreamReader".
+
+
+
+
+This help file applies to API documentation generated by the standard doclet.
Wrapper around standard FileChannel with additional safety net for closing if user does not close
+ and ability to run custom function during cleanup/closing.
This represents an object_component to read from or write to (or raise issues with) An
+ object_component without a name is the 'whole_object' component.
+
+
+
+
diff --git a/jitpack.yml b/jitpack.yml
deleted file mode 100644
index adb3fe1..0000000
--- a/jitpack.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-jdk:
- - openjdk11
diff --git a/jquery-ui.overrides.css b/jquery-ui.overrides.css
new file mode 100644
index 0000000..facf852
--- /dev/null
+++ b/jquery-ui.overrides.css
@@ -0,0 +1,35 @@
+/*
+ * Copyright (c) 2020, 2022, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+
+.ui-state-active,
+.ui-widget-content .ui-state-active,
+.ui-widget-header .ui-state-active,
+a.ui-button:active,
+.ui-button:active,
+.ui-button.ui-state-active:hover {
+ /* Overrides the color of selection used in jQuery UI */
+ background: #F8981D;
+ border: 1px solid #F8981D;
+}
diff --git a/jquery/external/jquery/jquery.js b/jquery/external/jquery/jquery.js
new file mode 100644
index 0000000..5093733
--- /dev/null
+++ b/jquery/external/jquery/jquery.js
@@ -0,0 +1,10872 @@
+/*!
+ * jQuery JavaScript Library v3.5.1
+ * https://jquery.com/
+ *
+ * Includes Sizzle.js
+ * https://sizzlejs.com/
+ *
+ * Copyright JS Foundation and other contributors
+ * Released under the MIT license
+ * https://jquery.org/license
+ *
+ * Date: 2020-05-04T22:49Z
+ */
+( function( global, factory ) {
+
+ "use strict";
+
+ if ( typeof module === "object" && typeof module.exports === "object" ) {
+
+ // For CommonJS and CommonJS-like environments where a proper `window`
+ // is present, execute the factory and get jQuery.
+ // For environments that do not have a `window` with a `document`
+ // (such as Node.js), expose a factory as module.exports.
+ // This accentuates the need for the creation of a real `window`.
+ // e.g. var jQuery = require("jquery")(window);
+ // See ticket #14549 for more info.
+ module.exports = global.document ?
+ factory( global, true ) :
+ function( w ) {
+ if ( !w.document ) {
+ throw new Error( "jQuery requires a window with a document" );
+ }
+ return factory( w );
+ };
+ } else {
+ factory( global );
+ }
+
+// Pass this if window is not defined yet
+} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
+
+// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
+// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
+// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
+// enough that all such attempts are guarded in a try block.
+"use strict";
+
+var arr = [];
+
+var getProto = Object.getPrototypeOf;
+
+var slice = arr.slice;
+
+var flat = arr.flat ? function( array ) {
+ return arr.flat.call( array );
+} : function( array ) {
+ return arr.concat.apply( [], array );
+};
+
+
+var push = arr.push;
+
+var indexOf = arr.indexOf;
+
+var class2type = {};
+
+var toString = class2type.toString;
+
+var hasOwn = class2type.hasOwnProperty;
+
+var fnToString = hasOwn.toString;
+
+var ObjectFunctionString = fnToString.call( Object );
+
+var support = {};
+
+var isFunction = function isFunction( obj ) {
+
+ // Support: Chrome <=57, Firefox <=52
+ // In some browsers, typeof returns "function" for HTML