Import Catalog code

pom.xml

@@ -517,6 +517,11 @@
 			<artifactId>file-repository-ftpserver</artifactId>
 			<version>1.0-SNAPSHOT</version>
 		</dependency>
+		<dependency>
+			<groupId>org.freemarker</groupId>
+			<artifactId>freemarker</artifactId>
+			<version>2.3.23</version>
+		</dependency>
 		<dependency>
 			<groupId>org.mockito</groupId>
 			<artifactId>mockito-all</artifactId>
@@ -548,6 +553,16 @@
 			<artifactId>bsh</artifactId>
 			<version>2.0b6</version>
 		</dependency>
+		<dependency>
+			<groupId>com.vladsch.flexmark</groupId>
+			<artifactId>flexmark-all</artifactId>
+			<version>0.28.34</version>
+		</dependency>
+		<dependency>
+			<groupId>com.vdurmont</groupId>
+			<artifactId>semver4j</artifactId>
+			<version>2.2.0</version>
+		</dependency>
 	</dependencies>
 
 	<build>
@@ -566,6 +581,8 @@
 								<!-- List packages to be processed -->
 								<include>org.genesys2.server.model</include>
 								<include>org.genesys2.server.model.*</include>
+                                <include>org.genesys.catalog.server.model</include>
+                                <include>org.genesys.catalog.server.model.*</include>
 							</includes>
 							<outputDirectory>target/generated-sources/querydsl</outputDirectory>
 							<processor>com.querydsl.apt.jpa.JPAAnnotationProcessor</processor>

src/main/java/org/genesys/catalog/server/annotations/PublishValidation.java

+/*
+ * Copyright 2017 Global Crop Diversity Trust
+ *
+ * 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
+ *
+ *   http://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.
+ */
+package org.genesys.catalog.server.annotations;
+
+import org.genesys.catalog.server.service.PublishValidationInterface;
+
+import java.lang.annotation.Documented;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+import static java.lang.annotation.ElementType.FIELD;
+
+/**
+ * Fields with this annotation are required fields, they have to be filled
+ * during publication process. You should implement
+ * {@link PublishValidationInterface} for parent class. That give you use
+ * {@link PublishValidationInterface#validation()} for validate before publish.
+ * And if you want use {@link PublishValidation#innerCheck()} you should
+ * implement {@link PublishValidationInterface} for child class and override
+ * {@link PublishValidationInterface#validation()} method.
+ *
+ * @author Andrey Lugovskoy.
+ */
+@Documented
+@Target({ FIELD })
+@Retention(RetentionPolicy.RUNTIME)
+public @interface PublishValidation {
+
+	/**
+	 * If field is object and innerCheck=true than we have to check inner fields.
+	 *
+	 * @return boolean value
+	 */
+	boolean innerCheck() default false;
+
+	/**
+	 * You should set {@link Boolean#TRUE} for this field to avoid recursive invoke
+	 * {@link PublishValidationInterface#validation()} method if child class has
+	 * link to parent class.
+	 *
+	 * @return boolean value
+	 */
+	boolean ignoreValidation() default false;
+}

src/main/java/org/genesys/catalog/server/controller/DescriptorListExporter.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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
+ *
+ *   http://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.
+ */
+package org.genesys.catalog.server.controller;
+
+import com.vladsch.flexmark.ast.Node;
+import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension;
+import com.vladsch.flexmark.ext.tables.TablesExtension;
+import com.vladsch.flexmark.html.HtmlRenderer;
+import com.vladsch.flexmark.parser.Parser;
+import com.vladsch.flexmark.util.KeepType;
+import com.vladsch.flexmark.util.options.MutableDataHolder;
+import com.vladsch.flexmark.util.options.MutableDataSet;
+import org.apache.commons.lang3.StringUtils;
+import org.genesys.catalog.server.model.traits.DescriptorList;
+import org.genesys.catalog.server.service.FreemarkerTemplating;
+import org.genesys.catalog.server.service.FreemarkerTemplating.FreemarkerException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Export Descriptor list.
+ */
+@Component
+public class DescriptorListExporter {
+
+	@Autowired
+	private FreemarkerTemplating freemarker;
+
+	/** The Constant OPTIONS. */
+	/*@formatter:off*/
+	static final MutableDataHolder OPTIONS = new MutableDataSet()
+			.set(Parser.REFERENCES_KEEP, KeepType.LAST)
+			.set(Parser.HTML_BLOCK_PARSER, false)
+//			.set(Parser.HTML_BLOCK_DEEP_PARSER, true)
+//			.set(Parser.HTML_BLOCK_START_ONLY_ON_BLOCK_TAGS, true)
+			.set(HtmlRenderer.INDENT_SIZE, 2)
+			.set(HtmlRenderer.PERCENT_ENCODE_URLS, true)
+//			.set(HtmlRenderer.ESCAPE_HTML, false)
+
+			// for full GFM table compatibility add the following table extension options:
+			.set(TablesExtension.COLUMN_SPANS, false)
+			.set(TablesExtension.APPEND_MISSING_COLUMNS, true)
+			.set(TablesExtension.DISCARD_EXTRA_COLUMNS, true)
+			.set(TablesExtension.HEADER_SEPARATOR_COLUMN_MATCH, true)
+			.set(Parser.EXTENSIONS, Arrays.asList(
+				TablesExtension.create(),
+				StrikethroughExtension.create()
+			));
+	/*@formatter:on*/
+
+	/**
+	 * Markdown descriptor list.
+	 *
+	 * @param descriptorList the descriptor list
+	 * @return the string
+	 * @throws FreemarkerException the freemarker exception
+	 */
+	public String markdownDescriptorList(final DescriptorList descriptorList) throws FreemarkerException {
+		final Map<String, Object> root = new HashMap<>();
+		root.put("descriptorList", descriptorList);
+		return freemarker.processTemplateResource("descriptorlist/booklet.ftl", root);
+	}
+
+	/**
+	 * Html descriptor list.
+	 *
+	 * @param descriptorList the descriptor list
+	 * @return the string
+	 * @throws FreemarkerException the freemarker exception
+	 */
+	public String htmlDescriptorList(final DescriptorList descriptorList) throws FreemarkerException {
+		final Map<String, Object> root = new HashMap<>();
+		root.put("descriptorList", descriptorList);
+		final String markdown = freemarker.processTemplateResource("descriptorlist/booklet.ftl", root);
+		// System.err.println(markdown);
+
+		final Parser parser = Parser.builder(OPTIONS).build();
+		final Node document = parser.parse(markdown);
+		final HtmlRenderer renderer = HtmlRenderer.builder(OPTIONS).build();
+		final String html = renderer.render(document);
+		// System.err.println(html);
+
+		// HTML wrapper
+		root.clear();
+		root.put("title", descriptorList.getTitle());
+		root.put("author", StringUtils.defaultIfEmpty(descriptorList.getPublisher(), descriptorList.getOwner().getName()));
+		root.put("html", html);
+
+		return freemarker.processTemplateResource("html.ftl", root);
+	}
+
+}

src/main/java/org/genesys/catalog/server/controller/api/FilteredPage.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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
+ *
+ *   http://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.
+ */
+package org.genesys.catalog.server.controller.api;
+
+import com.fasterxml.jackson.annotation.JsonUnwrapped;
+import org.genesys.blocks.model.filters.BasicModelFilter;
+import org.springframework.data.domain.Page;
+
+import java.io.Serializable;
+
+/**
+ * The Class FilteredPage.
+ *
+ * @param <T> the generic type
+ */
+public class FilteredPage<T> implements Serializable {
+
+	private static final long serialVersionUID = 6965069448240229428L;
+
+	/** The data is serialized on the base JSON level. */
+	@JsonUnwrapped
+	public Page<T> page;
+
+	/** The filter. */
+	public BasicModelFilter filter;
+
+	/** The filter code. */
+	public String filterCode;
+
+	/**
+	 * Instantiates a new filtered page.
+	 *
+	 * @param filterCode the filter code
+	 * @param filter the filter
+	 * @param data the data
+	 */
+	public FilteredPage(final String filterCode, final BasicModelFilter filter, final Page<T> data) {
+		this.filterCode = filterCode;
+		this.filter = filter;
+		this.page = data;
+	}
+}

src/main/java/org/genesys/catalog/server/controller/api/v0/ApiError.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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
+ *
+ *   http://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.
+ */
+package org.genesys.catalog.server.controller.api.v0;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import org.genesys.blocks.model.JsonViews;
+
+/**
+ * The Class ApiError.
+ *
+ * @param <T> the generic type
+ */
+public class ApiError<T extends Throwable> {
+	@JsonView(JsonViews.Public.class)
+	private final String error;
+	@JsonView(JsonViews.Public.class)
+	private final String localizedError;
+
+	/**
+	 * Instantiates a new api error.
+	 *
+	 * @param ex the ex
+	 */
+	public ApiError(final T ex) {
+		this.error = ex.getMessage();
+		this.localizedError = ex.getLocalizedMessage();
+	}
+
+	/**
+	 * Gets the error.
+	 *
+	 * @return the error
+	 */
+	public String getError() {
+		return error;
+	}
+
+	/**
+	 * Gets the localized error.
+	 *
+	 * @return the localized error
+	 */
+	public String getLocalizedError() {
+		return localizedError;
+	}
+}

src/main/java/org/genesys/catalog/server/controller/api/v0/ApiExceptionHandler.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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
+ *
+ *   http://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.
+ */
+package org.genesys.catalog.server.controller.api.v0;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.genesys.catalog.server.exceptions.InvalidApiUsageException;
+import org.genesys.catalog.server.exceptions.NotFoundElement;
+import org.springframework.dao.ConcurrencyFailureException;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.converter.HttpMessageNotReadableException;
+import org.springframework.security.access.AccessDeniedException;
+import org.springframework.security.authentication.AuthenticationCredentialsNotFoundException;
+import org.springframework.web.bind.annotation.ControllerAdvice;
+import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.ResponseStatus;
+import org.springframework.web.context.request.WebRequest;
+
+/**
+ * API exception handler returns errors in {@link ApiError}.
+ *
+ * @author Matija Obreza
+ */
+@ControllerAdvice(basePackages = { "org.genesys.catalog.server.controller.api.v0" })
+public class ApiExceptionHandler {
+	
+	/** The log. */
+	protected final Log LOG = LogFactory.getLog(getClass());
+
+	// @ResponseStatus(code = HttpStatus.NOT_FOUND)
+	// @ExceptionHandler(NoSuchAccessionException.class)
+	// @ResponseBody
+	// public ApiError<Exception> handleMissingAccession(NoSuchAccessionException
+	// ex, WebRequest request) throws JsonProcessingException {
+	// LOG.warn("Returning BrAPI error: " + ex.getMessage());
+	// return new ApiError<>(ex);
+	// }
+
+	/**
+	 * Handle missing credentials.
+	 *
+	 * @param e the e
+	 * @param request the request
+	 * @return the api error
+	 */
+	@ResponseStatus(code = HttpStatus.FORBIDDEN)
+	@ExceptionHandler({ AuthenticationCredentialsNotFoundException.class })
+	@ResponseBody
+	public ApiError<Exception> handleMissingCredentials(final Exception e, final WebRequest request) {
+		LOG.warn("Authentication is required.", e);
+		return new ApiError<>(e);
+	}
+
+	/**
+	 * Handle access denied.
+	 *
+	 * @param e the e
+	 * @param request the request
+	 * @return the api error
+	 */
+	@ResponseStatus(code = HttpStatus.UNAUTHORIZED)
+	@ExceptionHandler({ AccessDeniedException.class })
+	@ResponseBody
+	public ApiError<Exception> handleAccessDenied(final Exception e, final WebRequest request) {
+		LOG.warn("Authentication is required.", e);
+		return new ApiError<>(e);
+	}
+
+	/**
+	 * Handle converter error.
+	 *
+	 * @param e the e
+	 * @param request the request
+	 * @return the api error
+	 */
+	@ResponseStatus(code = HttpStatus.BAD_REQUEST)
+	@ExceptionHandler(HttpMessageNotReadableException.class)
+	@ResponseBody
+	public ApiError<Exception> handleConverterError(final Exception e, final WebRequest request) {
+		LOG.warn("Invalid payload provided.", e);
+		return new ApiError<>(e);
+	}
+
+	/**
+	 * Handle invalid api usage.
+	 *
+	 * @param e the e
+	 * @param request the request
+	 * @return the api error
+	 */
+	@ResponseStatus(code = HttpStatus.BAD_REQUEST)
+	@ExceptionHandler({ InvalidApiUsageException.class, ConcurrencyFailureException.class })
+	@ResponseBody
+	public ApiError<Exception> handleInvalidApiUsage(final Exception e, final WebRequest request) {
+		LOG.warn("Invalid payload provided.", e);
+		return new ApiError<>(e);
+	}
+
+	/**
+	 * Handle not found.
+	 *
+	 * @param e the e
+	 * @param request the request
+	 * @return the api error
+	 */
+	@ResponseStatus(code = HttpStatus.NOT_FOUND)
+	@ExceptionHandler(NotFoundElement.class)
+	@ResponseBody
+	public ApiError<Exception> handleNotFound(final Exception e, final WebRequest request) {
+		LOG.warn("Element not found", e);
+		return new ApiError<>(e);
+	}
+
+	/**
+	 * Handle server error.
+	 *
+	 * @param e the e
+	 * @param request the request
+	 * @return the api error
+	 */
+	@ResponseStatus(code = HttpStatus.INTERNAL_SERVER_ERROR)
+	@ExceptionHandler(Throwable.class)
+	@ResponseBody
+	public ApiError<Exception> handleServerError(final Exception e, final WebRequest request) {
+		LOG.error("Wow! Such! Exception!", e);
+		return new ApiError<>(e);
+	}
+}

src/main/java/org/genesys/catalog/server/controller/api/v0/ApiInfoController.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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
+ *
+ *   http://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.
+ */
+package org.genesys.catalog.server.controller.api.v0;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.net.UnknownHostException;
+
+/**
+ * The Class ApiInfoController.
+ *
+ * @author Andrey Lugovskoy.
+ */
+@RestController
+@RequestMapping(ApiInfoController.API_BASE)
+@PreAuthorize("isAuthenticated()")
+public class ApiInfoController implements InitializingBean {
+
+	private static final Logger LOG = LoggerFactory.getLogger(ApiInfoController.class);
+
+	/** The Constant API_BASE. */
+	public static final String API_BASE = "/api/v0/info";
+
+	@Value("${build.version}")
+	private String version;
+
+	@Value("${build.artifactId}")
+	private String artifactId;
+
+	@Value("${build.revision}")
+	private String revision;
+
+	private ApiInfo apiInfo;
+
+	@Override
+	public void afterPropertiesSet() throws Exception {
+		String hN;
+		try {
+			hN = java.net.InetAddress.getLocalHost().getHostName();
+		} catch (final UnknownHostException e) {
+			LOG.error("Error getting Host Name");
+			hN = "";
+		}
+		apiInfo = new ApiInfo(artifactId, version, revision, hN);
+		LOG.info("API Info: art=" + artifactId + " ver=" + version + " rev=" + revision);
+	}
+
+	/**
+	 * Api info.
+	 *
+	 * @return the api info
+	 */
+	@RequestMapping(value = "/version", method = RequestMethod.GET)
+	public ApiInfo apiInfo() {
+		return apiInfo;
+	}
+
+	/**
+	 * The Class ApiInfo.
+	 */
+	public static class ApiInfo {
+
+		private final String artifactId;
+
+		private final String version;
+
+		private final String revision;
+
+		private final String hostName;
+
+		/**
+		 * Instantiates a new api info.
+		 *
+		 * @param artifactId the artifact id
+		 * @param version the version
+		 * @param revision the revision
+		 * @param hostName the host name
+		 */
+		public ApiInfo(final String artifactId, final String version, final String revision, final String hostName) {
+
+			this.artifactId = artifactId;
+
+			this.version = version;
+
+			this.revision = revision;
+
+			this.hostName = hostName;
+		}
+
+		/**
+		 * Gets the host name.
+		 *
+		 * @return the host name
+		 */
+		public String getHostName() {
+			return hostName;
+		}
+