move to @Service

apps/dnet-is-application/src/main/java/eu/dnetlib/is/context/ContextRestController.java

@@ -1,120 +1,52 @@
 package eu.dnetlib.is.context;
 
 import java.util.List;
-import java.util.stream.Collectors;
 
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
+import eu.dnetlib.common.controller.AbstractDnetController;
 import eu.dnetlib.is.context.model.Category;
-import eu.dnetlib.is.context.model.ConceptLevel0;
-import eu.dnetlib.is.context.model.ConceptLevel1;
-import eu.dnetlib.is.context.model.ConceptLevel2;
 import eu.dnetlib.is.context.model.Context;
 import eu.dnetlib.is.context.model.CtxChildInfo;
-import eu.dnetlib.is.context.model.repository.CategoryRepository;
+import eu.dnetlib.is.util.InformationServiceException;
-import eu.dnetlib.is.context.model.repository.ConceptLevel0Repository;
-import eu.dnetlib.is.context.model.repository.ConceptLevel1Repository;
-import eu.dnetlib.is.context.model.repository.ConceptLevel2Repository;
-import eu.dnetlib.is.context.model.repository.ContextRepository;
 
 @RestController
 @RequestMapping("/api/contexts")
-public class ContextRestController {
+public class ContextRestController extends AbstractDnetController {
 
 	@Autowired
-	private ContextRepository contextRepository;
+	private ContextService contextService;
-	@Autowired
-	private CategoryRepository categoryRepository;
-	@Autowired
-	private ConceptLevel0Repository conceptLevel0Repository;
-	@Autowired
-	private ConceptLevel1Repository conceptLevel1Repository;
-	@Autowired
-	private ConceptLevel2Repository conceptLevel2Repository;
-
-	private static final Log log = LogFactory.getLog(ContextRestController.class);
 
 	@GetMapping("/")
 	public List<Context> listContexts() {
-		return contextRepository.findAll()
+		return contextService.listContexts();
-			.stream()
-			.sorted((v1, v2) -> StringUtils.compareIgnoreCase(v1.getId(), v2.getId()))
-			.collect(Collectors.toList());
 	}
 
 	@GetMapping("/{ctxId}")
-	public Context getContext(@PathVariable final String ctxId) {
+	public Context getContext(@PathVariable final String ctxId) throws InformationServiceException {
-		return contextRepository.findById(ctxId).get();
+		return contextService.getContext(ctxId);
 	}
 
 	@GetMapping("/{ctxId}/full")
-	public ObjectNode getContextFull(@PathVariable final String ctxId) {
+	public ObjectNode getContextFull(@PathVariable final String ctxId) throws InformationServiceException {
-
+		return contextService.getContextFull(ctxId);
-		final ObjectMapper mapper = new ObjectMapper();
-		final Context ctx = contextRepository.findById(ctxId).get();
-
-		final ObjectNode ctxNode = mapper.convertValue(ctx, ObjectNode.class);
-
-		final ArrayNode catArray = mapper.createArrayNode();
-
-		for (final Category cat : categoryRepository.findByParentOrderById(ctxId)) {
-			final ObjectNode catNode = mapper.convertValue(cat, ObjectNode.class);
-			catArray.add(catNode);
-
-			final ArrayNode c0Array = mapper.createArrayNode();
-			for (final ConceptLevel0 c0 : conceptLevel0Repository.findByParentOrderById(cat.getId())) {
-				final ObjectNode c0Node = mapper.convertValue(c0, ObjectNode.class);
-				c0Array.add(c0Node);
-
-				final ArrayNode c1Array = mapper.createArrayNode();
-				for (final ConceptLevel1 c1 : conceptLevel1Repository.findByParentOrderById(c0.getId())) {
-					final ObjectNode c1Node = mapper.convertValue(c1, ObjectNode.class);
-					c1Array.add(c1Node);
-
-					final ArrayNode c2Array = mapper.createArrayNode();
-					for (final ConceptLevel2 c2 : conceptLevel2Repository.findByParentOrderById(c1.getId())) {
-						final ObjectNode c2Node = mapper.convertValue(c2, ObjectNode.class);
-						c2Array.add(c2Node);
-					}
-					c1Node.set("concepts", c2Array);
-				}
-				c0Node.set("concepts", c1Array);
-			}
-			catNode.set("concepts", c0Array);
-		}
-		ctxNode.set("categories", catArray);
-
-		return ctxNode;
 	}
 
 	@GetMapping("/{parent}/categories")
 	public Iterable<Category> listCategories(@PathVariable final String parent) {
-		return categoryRepository.findByParentOrderById(parent);
+		return contextService.listCategories(parent);
 	}
 
 	@GetMapping("/{level}/{parent}/concepts")
-	public Iterable<? extends CtxChildInfo> listCategories(@PathVariable final int level, @PathVariable final String parent) {
+	public Iterable<? extends CtxChildInfo> listCategories(@PathVariable final int level, @PathVariable final String parent)
-		switch (level) {
+		throws InformationServiceException {
-		case 0:
+		return contextService.listCategories(level, parent);
-			return conceptLevel0Repository.findByParentOrderById(parent);
-		case 1:
-			return conceptLevel1Repository.findByParentOrderById(parent);
-		case 2:
-			return conceptLevel2Repository.findByParentOrderById(parent);
-		default:
-			throw new RuntimeException("Invalid concept level - valid levels are 0, 1, 2");
-		}
 	}
 
 }

apps/dnet-is-application/src/main/java/eu/dnetlib/is/context/ContextService.java

@@ -0,0 +1,112 @@
+package eu.dnetlib.is.context;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import eu.dnetlib.is.context.model.Category;
+import eu.dnetlib.is.context.model.ConceptLevel0;
+import eu.dnetlib.is.context.model.ConceptLevel1;
+import eu.dnetlib.is.context.model.ConceptLevel2;
+import eu.dnetlib.is.context.model.Context;
+import eu.dnetlib.is.context.model.CtxChildInfo;
+import eu.dnetlib.is.context.model.repository.CategoryRepository;
+import eu.dnetlib.is.context.model.repository.ConceptLevel0Repository;
+import eu.dnetlib.is.context.model.repository.ConceptLevel1Repository;
+import eu.dnetlib.is.context.model.repository.ConceptLevel2Repository;
+import eu.dnetlib.is.context.model.repository.ContextRepository;
+import eu.dnetlib.is.util.InformationServiceException;
+
+@Service
+public class ContextService {
+
+	@Autowired
+	private ContextRepository contextRepository;
+	@Autowired
+	private CategoryRepository categoryRepository;
+	@Autowired
+	private ConceptLevel0Repository conceptLevel0Repository;
+	@Autowired
+	private ConceptLevel1Repository conceptLevel1Repository;
+	@Autowired
+	private ConceptLevel2Repository conceptLevel2Repository;
+
+	private static final Log log = LogFactory.getLog(ContextService.class);
+
+	public List<Context> listContexts() {
+		return contextRepository.findAll()
+			.stream()
+			.sorted((v1, v2) -> StringUtils.compareIgnoreCase(v1.getId(), v2.getId()))
+			.collect(Collectors.toList());
+	}
+
+	public Context getContext(final String ctxId) throws InformationServiceException {
+		return contextRepository.findById(ctxId).orElseThrow(() -> new InformationServiceException("Context Not found"));
+	}
+
+	public ObjectNode getContextFull(final String ctxId) throws InformationServiceException {
+
+		final ObjectMapper mapper = new ObjectMapper();
+		final Context ctx = getContext(ctxId);
+
+		final ObjectNode ctxNode = mapper.convertValue(ctx, ObjectNode.class);
+
+		final ArrayNode catArray = mapper.createArrayNode();
+
+		for (final Category cat : categoryRepository.findByParentOrderById(ctxId)) {
+			final ObjectNode catNode = mapper.convertValue(cat, ObjectNode.class);
+			catArray.add(catNode);
+
+			final ArrayNode c0Array = mapper.createArrayNode();
+			for (final ConceptLevel0 c0 : conceptLevel0Repository.findByParentOrderById(cat.getId())) {
+				final ObjectNode c0Node = mapper.convertValue(c0, ObjectNode.class);
+				c0Array.add(c0Node);
+
+				final ArrayNode c1Array = mapper.createArrayNode();
+				for (final ConceptLevel1 c1 : conceptLevel1Repository.findByParentOrderById(c0.getId())) {
+					final ObjectNode c1Node = mapper.convertValue(c1, ObjectNode.class);
+					c1Array.add(c1Node);
+
+					final ArrayNode c2Array = mapper.createArrayNode();
+					for (final ConceptLevel2 c2 : conceptLevel2Repository.findByParentOrderById(c1.getId())) {
+						final ObjectNode c2Node = mapper.convertValue(c2, ObjectNode.class);
+						c2Array.add(c2Node);
+					}
+					c1Node.set("concepts", c2Array);
+				}
+				c0Node.set("concepts", c1Array);
+			}
+			catNode.set("concepts", c0Array);
+		}
+		ctxNode.set("categories", catArray);
+
+		return ctxNode;
+	}
+
+	public Iterable<Category> listCategories(final String parent) {
+		return categoryRepository.findByParentOrderById(parent);
+	}
+
+	public Iterable<? extends CtxChildInfo> listCategories(final int level, final String parent) throws InformationServiceException {
+		switch (level) {
+		case 0:
+			return conceptLevel0Repository.findByParentOrderById(parent);
+		case 1:
+			return conceptLevel1Repository.findByParentOrderById(parent);
+		case 2:
+			return conceptLevel2Repository.findByParentOrderById(parent);
+		default:
+			throw new InformationServiceException("Invalid concept level - valid levels are 0, 1, 2");
+		}
+	}
+
+}

apps/dnet-is-application/src/main/java/eu/dnetlib/is/importer/ContextImporter.java

@@ -11,7 +11,7 @@ import org.dom4j.DocumentException;
 import org.dom4j.Node;
 import org.dom4j.io.SAXReader;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
+import org.springframework.stereotype.Service;
 
 import eu.dnetlib.is.context.model.Category;
 import eu.dnetlib.is.context.model.ConceptLevel0;
@@ -27,7 +27,7 @@ import eu.dnetlib.is.context.model.repository.ConceptLevel1Repository;
 import eu.dnetlib.is.context.model.repository.ConceptLevel2Repository;
 import eu.dnetlib.is.context.model.repository.ContextRepository;
 
-@Component
+@Service
 public class ContextImporter {
 
 	@Autowired

apps/dnet-is-application/src/main/java/eu/dnetlib/is/importer/ImporterController.java

@@ -17,12 +17,13 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 
+import eu.dnetlib.common.controller.AbstractDnetController;
 import eu.dnetlib.is.resource.model.SimpleResource;
 import eu.dnetlib.is.vocabulary.model.Vocabulary;
 
 @RestController
 @RequestMapping("/api/import")
-public class ImporterController {
+public class ImporterController extends AbstractDnetController {
 
 	@Autowired
 	private ContextImporter contextImporter;

apps/dnet-is-application/src/main/java/eu/dnetlib/is/importer/OldProfilesImporter.java

@@ -11,7 +11,7 @@ import org.dom4j.DocumentException;
 import org.dom4j.Node;
 import org.dom4j.io.SAXReader;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
+import org.springframework.stereotype.Service;
 
 import eu.dnetlib.is.resource.model.SimpleResource;
 import eu.dnetlib.is.resource.repository.SimpleResourceRepository;
@@ -22,7 +22,7 @@ import eu.dnetlib.is.vocabulary.model.VocabularyTerm;
 import eu.dnetlib.is.vocabulary.repository.VocabularyRepository;
 import eu.dnetlib.is.vocabulary.repository.VocabularyTermRepository;
 
-@Component
+@Service
 public class OldProfilesImporter {
 
 	@Autowired

apps/dnet-is-application/src/main/java/eu/dnetlib/is/importer/WfHistoryImporter.java

@@ -12,7 +12,7 @@ import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Component;
+import org.springframework.stereotype.Service;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -20,7 +20,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.is.wf.model.WfProcessExecution;
 import eu.dnetlib.is.wf.repository.WfProcessExecutionRepository;
 
-@Component
+@Service
 public class WfHistoryImporter {
 
 	private static final Log log = LogFactory.getLog(WfHistoryImporter.class);

apps/dnet-is-application/src/main/java/eu/dnetlib/is/resources/ResourcesRestController.java

@@ -19,12 +19,13 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 
+import eu.dnetlib.common.controller.AbstractDnetController;
 import eu.dnetlib.is.resource.model.SimpleResource;
 import eu.dnetlib.is.util.InformationServiceException;
 
 @RestController
 @RequestMapping("/api/resources")
-public class ResourcesRestController {
+public class ResourcesRestController extends AbstractDnetController {
 
 	@Autowired
 	private SimpleResourceService service;

apps/dnet-is-application/src/main/java/eu/dnetlib/is/vocabulary/VocabularyRestController.java

@@ -1,11 +1,7 @@
 package eu.dnetlib.is.vocabulary;
 
 import java.util.List;
-import java.util.stream.Collectors;
 
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.web.bind.annotation.DeleteMapping;
 import org.springframework.web.bind.annotation.GetMapping;
@@ -16,74 +12,54 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 
 import eu.dnetlib.common.controller.AbstractDnetController;
-import eu.dnetlib.is.importer.OldProfilesImporter;
+import eu.dnetlib.is.util.InformationServiceException;
 import eu.dnetlib.is.vocabulary.model.Vocabulary;
 import eu.dnetlib.is.vocabulary.model.VocabularyTerm;
-import eu.dnetlib.is.vocabulary.model.VocabularyTermPK;
-import eu.dnetlib.is.vocabulary.repository.VocabularyRepository;
-import eu.dnetlib.is.vocabulary.repository.VocabularyTermRepository;
 
 @RestController
 @RequestMapping("/api/vocs")
 public class VocabularyRestController extends AbstractDnetController {
 
 	@Autowired
-	private VocabularyRepository vocabularyRepository;
+	private VocabularyService vocabularyService;
-
-	@Autowired
-	private VocabularyTermRepository vocabularyTermRepository;
-
-	@Autowired
-	private OldProfilesImporter oldProfilesImporter;
-
-	private static final Log log = LogFactory.getLog(VocabularyRestController.class);
 
 	@GetMapping("/")
 	public List<Vocabulary> listVocs() {
-		return vocabularyRepository.findAll()
+		return vocabularyService.listVocs();
-			.stream()
-			.sorted((v1, v2) -> StringUtils.compareIgnoreCase(v1.getId(), v2.getId()))
-			.collect(Collectors.toList());
 	}
 
 	@GetMapping("/{vocabulary}")
-	public Vocabulary getVoc(@PathVariable final String vocabulary) {
+	public Vocabulary getVoc(@PathVariable final String vocabulary) throws InformationServiceException {
-		return vocabularyRepository.getById(vocabulary);
+		return vocabularyService.getVoc(vocabulary);
 	}
 
 	@DeleteMapping("/{vocabulary}")
 	public List<Vocabulary> deleteVocs(@PathVariable final String vocabulary) {
-		log.info("Deleting vocabulary: " + vocabulary);
+		vocabularyService.deleteVocs(vocabulary);
-		vocabularyRepository.deleteById(vocabulary);
+		return vocabularyService.listVocs();
-		return listVocs();
 	}
 
 	@PostMapping("/")
 	public List<Vocabulary> saveVoc(@RequestBody final Vocabulary voc) {
-		log.info("Saving vocabulary: " + voc);
+		vocabularyService.saveVoc(voc);
-		vocabularyRepository.save(voc);
+		return vocabularyService.listVocs();
-		return listVocs();
 	}
 
 	@GetMapping("/{vocabulary}/terms")
 	public Iterable<VocabularyTerm> listTerms(@PathVariable final String vocabulary) {
-		return vocabularyTermRepository.findByVocabularyOrderByCode(vocabulary);
+		return vocabularyService.listTerms(vocabulary);
 	}
 
 	@PostMapping("/{vocabulary}/terms")
 	public Iterable<VocabularyTerm> saveTerm(@PathVariable final String vocabulary, @RequestBody final VocabularyTerm term) {
-		term.setVocabulary(vocabulary);
+		vocabularyService.saveTerms(vocabulary, term);
-		vocabularyTermRepository.save(term);
+		return vocabularyService.listTerms(vocabulary);
-		return vocabularyTermRepository.findByVocabularyOrderByCode(vocabulary);
 	}
 
 	@DeleteMapping("/{vocabulary}/terms/{term}")
-	public Iterable<VocabularyTerm> listTerms(@PathVariable final String vocabulary, @PathVariable final String term) {
+	public Iterable<VocabularyTerm> deleteTerms(@PathVariable final String vocabulary, @PathVariable final String term) {
-		final VocabularyTermPK pk = new VocabularyTermPK();
+		vocabularyService.deleteTerms(vocabulary, term);
-		pk.setCode(term);
+		return vocabularyService.listTerms(vocabulary);
-		pk.setVocabulary(vocabulary);
-		vocabularyTermRepository.deleteById(pk);
-		return vocabularyTermRepository.findByVocabularyOrderByCode(vocabulary);
 	}
 
 }

apps/dnet-is-application/src/main/java/eu/dnetlib/is/vocabulary/VocabularyService.java

@@ -0,0 +1,77 @@
+package eu.dnetlib.is.vocabulary;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import javax.transaction.Transactional;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import eu.dnetlib.is.util.InformationServiceException;
+import eu.dnetlib.is.vocabulary.model.Vocabulary;
+import eu.dnetlib.is.vocabulary.model.VocabularyTerm;
+import eu.dnetlib.is.vocabulary.model.VocabularyTermPK;
+import eu.dnetlib.is.vocabulary.repository.VocabularyRepository;
+import eu.dnetlib.is.vocabulary.repository.VocabularyTermRepository;
+
+@Service
+public class VocabularyService {
+
+	@Autowired
+	private VocabularyRepository vocabularyRepository;
+
+	@Autowired
+	private VocabularyTermRepository vocabularyTermRepository;
+
+	private static final Log log = LogFactory.getLog(VocabularyService.class);
+
+	public List<Vocabulary> listVocs() {
+		return vocabularyRepository.findAll()
+			.stream()
+			.sorted((v1, v2) -> StringUtils.compareIgnoreCase(v1.getId(), v2.getId()))
+			.collect(Collectors.toList());
+	}
+
+	public Vocabulary getVoc(final String vocabulary) throws InformationServiceException {
+		return vocabularyRepository.findById(vocabulary).orElseThrow(() -> new InformationServiceException("Vocabulary not found"));
+	}
+
+	@Transactional
+	public void deleteVocs(final String... ids) {
+		for (final String id : ids) {
+			vocabularyRepository.deleteById(id);
+		}
+	}
+
+	public void saveVoc(final Vocabulary voc) {
+		log.info("Saving vocabulary: " + voc);
+		vocabularyRepository.save(voc);
+	}
+
+	public Iterable<VocabularyTerm> listTerms(final String vocabulary) {
+		return vocabularyTermRepository.findByVocabularyOrderByCode(vocabulary);
+	}
+
+	@Transactional
+	public void saveTerms(final String vocabulary, final VocabularyTerm... terms) {
+		for (final VocabularyTerm t : terms) {
+			t.setVocabulary(vocabulary);
+			vocabularyTermRepository.save(t);
+		}
+	}
+
+	@Transactional
+	public void deleteTerms(final String vocabulary, final String... terms) {
+		for (final String t : terms) {
+			final VocabularyTermPK pk = new VocabularyTermPK();
+			pk.setCode(t);
+			pk.setVocabulary(vocabulary);
+			vocabularyTermRepository.deleteById(pk);
+		}
+	}
+
+}

apps/dnet-is-application/src/main/resources/templates/contextEditor.html

@@ -24,7 +24,7 @@
 						<b>Parameters: </b><a href="javascript:void(0)" data-toggle="modal" data-target="#showParametersModal" ng-click="loadContextParameters()">[show]</a>
 					</p>
 					<p>
-						<a class="btn btn-sm btn-primary" href="/contexts">Return to contexts list</a>					
+						<a class="btn btn-sm btn-primary" href="./resources?type=context">Return to contexts list</a>					
 					</p>
 				
 					<ul>

apps/dnet-is-application/src/main/resources/templates/vocabularyEditor.html

@@ -23,7 +23,7 @@
 						<b>Description: </b><span th:text="${vocDesc}"></span>
 					</p>
 					<p>
-						<a class="btn btn-sm btn-primary" href="/vocabularies">Return to vocabulary list</a>					
+						<a class="btn btn-sm btn-primary" href="./resources?type=vocabulary">Return to vocabulary list</a>					
 					</p>
 					<p>
 						<button class="btn btn-sm btn-primary" data-toggle="modal" data-target="#editVocabularyTermModal" ng-click="prepareNewTerm()">create a new term</button>