{"action":"created","comment":{"url":"https://api.github.com/repos/OpenSILEX/phis-ws/pulls/comments/198133116","pull_request_review_id":132001683,"id":198133116,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5ODEzMzExNg==","diff_hunk":"@@ -0,0 +1,416 @@\n+//******************************************************************************\n+//                                       AnnotationDAOSesame.java\n+//\n+// Author(s): Arnaud Charleroy <arnaud.charleroy@inra.fr>\n+// PHIS-SILEX version 1.0\n+// Copyright © - INRA - 2018\n+// Creation date: 14 juin 2018\n+// Contact: arnaud.charleroy@inra.fr, anne.tireau@inra.fr, pascal.neveu@inra.fr\n+// Last modification date:  21 juin 2018\n+// Subject: This class manages operation on annotation in database\n+//******************************************************************************\n+package phis2ws.service.dao.sesame;\n+\n+import java.util.ArrayList;\n+import java.util.List;\n+import java.util.Map;\n+import org.eclipse.rdf4j.query.BindingSet;\n+import org.eclipse.rdf4j.query.MalformedQueryException;\n+import org.eclipse.rdf4j.query.QueryEvaluationException;\n+import org.eclipse.rdf4j.query.QueryLanguage;\n+import org.eclipse.rdf4j.query.TupleQuery;\n+import org.eclipse.rdf4j.query.TupleQueryResult;\n+import org.eclipse.rdf4j.query.Update;\n+import org.eclipse.rdf4j.repository.RepositoryException;\n+import org.joda.time.DateTime;\n+import org.joda.time.format.DateTimeFormat;\n+import org.joda.time.format.DateTimeFormatter;\n+import org.slf4j.Logger;\n+import org.slf4j.LoggerFactory;\n+import phis2ws.service.configuration.DateFormats;\n+import phis2ws.service.configuration.URINamespaces;\n+import phis2ws.service.dao.manager.DAOSesame;\n+import phis2ws.service.dao.phis.UserDaoPhisBrapi;\n+import phis2ws.service.documentation.StatusCodeMsg;\n+import phis2ws.service.utils.sparql.SPARQLQueryBuilder;\n+import phis2ws.service.resources.dto.AnnotationDTO;\n+import phis2ws.service.resources.dto.manager.AbstractVerifiedClass;\n+import phis2ws.service.utils.POSTResultsReturn;\n+import phis2ws.service.utils.UriGenerator;\n+import phis2ws.service.utils.dates.Dates;\n+import phis2ws.service.utils.sparql.SPARQLUpdateBuilder;\n+import phis2ws.service.view.brapi.Status;\n+import phis2ws.service.view.model.phis.Annotation;\n+\n+/**\n+ *\n+ * @author Arnaud Charleroy <arnaud.charleroy@inra.fr>\n+ */\n+public class AnnotationDAOSesame extends DAOSesame<Annotation> {\n+\n+    final static Logger LOGGER = LoggerFactory.getLogger(AnnotationDAOSesame.class);\n+\n+    private final static URINamespaces NAMESPACES = new URINamespaces();\n+\n+    final static String TRIPLESTORE_CONTEXT_ANNOTATION = NAMESPACES.getContextsProperty(\"annotations\");\n+\n+    final static String TRIPLESTORE_RELATION_TYPE = NAMESPACES.getRelationsProperty(\"type\");\n+    final static String TRIPLESTORE_RELATION_BODYVALUE = NAMESPACES.getRelationsProperty(\"rOaBodyValue\");\n+    final static String TRIPLESTORE_RELATION_CREATOR = NAMESPACES.getRelationsProperty(\"rDCCreator\");\n+    final static String TRIPLESTORE_RELATION_CREATED = NAMESPACES.getRelationsProperty(\"rDCCreated\");\n+    final static String TRIPLESTORE_RELATION_TARGET = NAMESPACES.getRelationsProperty(\"rOaTarget\");\n+    final static String TRIPLESTORE_RELATION_MOTIVATEDBY = NAMESPACES.getRelationsProperty(\"rOaMotivatedBy\");\n+\n+    // Search parameters\n+    public String uri;\n+    public static final String URI = \"uri\";\n+    public String created;\n+    public static final String CREATED = \"created\";\n+    public String bodyValue;\n+    public static final String BODYVALUE = \"bodyValue\";\n+    public String creator;\n+    public static final String CREATOR = \"creator\";\n+    public ArrayList<String> targets = new ArrayList<>();\n+    public static final String TARGET = \"target\";\n+    public String motivatedBy;\n+    public static final String MOTIVATEDBY = \"motivatedBy\";\n+\n+    /**\n+     * \n+     * @inheritdoc \n+     */\n+    @Override\n+    protected SPARQLQueryBuilder prepareSearchQuery() {\n+        SPARQLQueryBuilder query = new SPARQLQueryBuilder();\n+        query.appendDistinct(Boolean.TRUE);\n+\n+        String annotationUri;\n+        if (uri != null) {\n+            annotationUri = \"<\" + uri + \">\";\n+        } else {\n+            annotationUri = \"?\" + URI;\n+            query.appendSelect(annotationUri);\n+        }\n+\n+        DateTime stringToDateTime = null;\n+        if (created != null) {\n+            stringToDateTime = Dates.stringToDateTime(created);\n+            if (stringToDateTime != null) {\n+                query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_CREATED, created, null);\n+            }\n+        }\n+        if (created == null && stringToDateTime == null) {\n+            query.appendSelect(\"?\" + CREATED);\n+            query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_CREATED, \"?\" + CREATED, null);\n+        }\n+\n+        if (creator != null) {\n+            query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_CREATOR, creator, null);\n+        } else {\n+            query.appendSelect(\" ?\" + CREATOR);\n+            query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_CREATOR, \"?\" + CREATOR, null);\n+        }\n+\n+        if (motivatedBy != null) {\n+            query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_MOTIVATEDBY, motivatedBy, null);\n+        } else {\n+            query.appendSelect(\" ?\" + MOTIVATEDBY);\n+            query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_MOTIVATEDBY, \"?\" + MOTIVATEDBY, null);\n+        }\n+\n+        if (targets != null && !targets.isEmpty()) {\n+            UriDaoSesame uriDao = new UriDaoSesame();\n+            for (String target : targets) {\n+                if (uriDao.existObject(target)) {\n+                    query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_TARGET, target, null);\n+                }\n+\n+            }\n+        } else {\n+            query.appendSelect(\"?\" + TARGET);\n+            query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_TARGET, \"?\" + TARGET, null);\n+        }\n+\n+        query.appendSelect(\"?\" + BODYVALUE);\n+        query.appendTriplet(annotationUri, TRIPLESTORE_RELATION_BODYVALUE, \"?\" + BODYVALUE, null);\n+        if (bodyValue != null) {\n+            query.appendFilter(\"regex(STR(?\" + BODYVALUE + \"), '\" + bodyValue + \"', 'i')\");\n+        }\n+\n+        query.appendLimit(this.getPageSize());\n+        query.appendOffset(this.getPage() * this.getPageSize());\n+        LOGGER.debug(SPARQL_SELECT_QUERY + query.toString());\n+        return query;\n+\n+    }\n+\n+    /**\n+     * \n+     * @inheritdoc \n+     */\n+    @Override\n+    public Integer count() throws RepositoryException, MalformedQueryException, QueryEvaluationException {\n+        SPARQLQueryBuilder prepareCount = prepareCount();\n+        TupleQuery tupleQuery = getConnection().prepareTupleQuery(QueryLanguage.SPARQL, prepareCount.toString());\n+        Integer count = 0;\n+        try (TupleQueryResult result = tupleQuery.evaluate()) {\n+            if (result.hasNext()) {\n+                BindingSet bindingSet = result.next();\n+                count = Integer.parseInt(bindingSet.getValue(COUNT_ELEMENT_QUERY).stringValue());\n+            }\n+        }\n+\n+        return count;\n+    }\n+\n+    private SPARQLQueryBuilder prepareCount() 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Don't forget to add an example of generated query","created_at":"2018-06-26T13:01:09Z","updated_at":"2018-06-26T13:21:42Z","html_url":"https://github.com/OpenSILEX/phis-ws/pull/77#discussion_r198133116","pull_request_url":"https://api.github.com/repos/OpenSILEX/phis-ws/pulls/77","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/OpenSILEX/phis-ws/pulls/comments/198133116"},"html":{"href":"https://github.com/OpenSILEX/phis-ws/pull/77#discussion_r198133116"},"pull_request":{"href":"https://api.github.com/repos/OpenSILEX/phis-ws/pulls/77"}}},"pull_request":{"url":"https://api.github.com/repos/OpenSILEX/phis-ws/pulls/77","id":197136026,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk3MTM2MDI2","html_url":"https://github.com/OpenSILEX/phis-ws/pull/77","diff_url":"https://github.com/OpenSILEX/phis-ws/pull/77.diff","patch_url":"https://github.com/OpenSILEX/phis-ws/pull/77.patch","issue_url":"https://api.github.com/repos/OpenSILEX/phis-ws/issues/77","number":77,"state":"open","locked":false,"title":"Add annotation service","user":{"login":"niio972","id":17789831,"node_id":"MDQ6VXNlcjE3Nzg5ODMx","avatar_url":"https://avatars3.githubusercontent.com/u/17789831?v=4","gravatar_id":"","url":"https://api.github.com/users/niio972","html_url":"https://github.com/niio972","followers_url":"https://api.github.com/users/niio972/followers","following_url":"https://api.github.com/users/niio972/following{/other_user}","gists_url":"https://api.github.com/users/niio972/gists{/gist_id}","starred_url":"https://api.github.com/users/niio972/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/niio972/subscriptions","organizations_url":"https://api.github.com/users/niio972/orgs","repos_url":"https://api.github.com/users/niio972/repos","events_url":"https://api.github.com/users/niio972/events{/privacy}","received_events_url":"https://api.github.com/users/niio972/received_events","type":"User","site_admin":false},"body":"References #76 \r\nFixes  #64 \r\n\r\n- Add annotation service with GET method 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