Feature/rsmd-guidelines

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/AuthorDTO.java

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+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+public class AuthorDTO {
+
+    public String name;
+
+    public String type;
+
+    public String identifier;
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/FunderRequestDTO.java

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+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+public class FunderRequestDTO {
+
+    public String name;
+
+    public String type;
+
+    public String grantName;
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/FunderResponseDTO.java

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+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+public class FunderResponseDTO {
+
+    public String name;
+
+    public String type;
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/IndividualApiCommonCRUDUtility.java

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+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+import java.io.IOException;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Objects;
+import java.util.UUID;
+import java.util.function.BiConsumer;
+
+import javax.servlet.http.Cookie;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import edu.cornell.mannlib.vitro.webapp.application.ApplicationUtils;
+import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceDataset;
+import edu.cornell.mannlib.vitro.webapp.modules.searchIndexer.SearchIndexer;
+import org.apache.jena.query.Dataset;
+import org.apache.jena.query.ReadWrite;
+import org.apache.jena.update.GraphStore;
+import org.apache.jena.update.GraphStoreFactory;
+
+public class IndividualApiCommonCRUDUtility {
+
+    public static void executeWithTransaction(HttpServletRequest req, HttpServletResponse resp,
+                                              BiConsumer<GraphStore, String> action) throws IOException {
+        VitroRequest vreq = new VitroRequest(req);
+        SearchIndexer indexer = ApplicationUtils.instance().getSearchIndexer();
+        Dataset ds = new RDFServiceDataset(vreq.getUnfilteredRDFService());
+        GraphStore graphStore = GraphStoreFactory.create(ds);
+
+        String entityUri;
+        if (req.getMethod().equalsIgnoreCase("POST")) {
+            entityUri = IndividualApiSparqlUtility.buildIndividualUri(UUID.randomUUID().toString());
+        } else {
+            String pathInfo = req.getPathInfo();
+            if (Objects.isNull(pathInfo) || pathInfo.isEmpty()) {
+                IndividualApiNetworkUtility.do400BadRequest("You have to provide a record identifier.", resp);
+                return;
+            }
+
+            entityUri = IndividualApiSparqlUtility.buildIndividualUri(pathInfo.substring(1));
+        }
+
+        try {
+            pauseIndexer(indexer);
+            beginTransaction(ds);
+
+            action.accept(graphStore, entityUri);
+
+        } finally {
+            commitTransaction(ds);
+            unpauseIndexer(indexer);
+        }
+    }
+
+    private static void pauseIndexer(SearchIndexer indexer) {
+        if (indexer != null) {
+            indexer.pause();
+        }
+    }
+
+    private static void unpauseIndexer(SearchIndexer indexer) {
+        if (indexer != null) {
+            indexer.unpause();
+        }
+    }
+
+    private static void beginTransaction(Dataset ds) {
+        if (ds.supportsTransactions()) {
+            ds.begin(ReadWrite.WRITE);
+        }
+    }
+
+    private static void commitTransaction(Dataset ds) {
+        if (ds.supportsTransactions()) {
+            ds.commit();
+            ds.end();
+        }
+    }
+
+    public static void performDeleteOperation(HttpServletRequest req, HttpServletResponse resp)
+        throws IOException {
+        String pathInfo = req.getPathInfo();
+        if (Objects.isNull(pathInfo) || pathInfo.isEmpty()) {
+            IndividualApiNetworkUtility.do400BadRequest("You have to provide a record identifier.", resp);
+            return;
+        }
+
+        VitroRequest vreq = new VitroRequest(req);
+        ApplicationBean appBean = vreq.getAppBean();
+        String appName = appBean.getApplicationName().toLowerCase();
+        URL url = new URL("http://" + req.getServerName() + ":" + req.getServerPort() + "/" + appName +
+            "/deleteIndividualController?individualUri=" +
+            URLEncoder.encode(IndividualApiSparqlUtility.buildIndividualUri(pathInfo.substring(1))) +
+            "&redirectUrl=%2F");
+        HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+        connection.setRequestMethod("GET");
+        connection.setRequestProperty("Accept", "application/json");
+
+        addCookiesToRequest(req, connection);
+
+        connection.getResponseCode();
+
+        resp.setStatus(HttpServletResponse.SC_NO_CONTENT);
+
+        connection.disconnect();
+    }
+
+    private static void addCookiesToRequest(HttpServletRequest req, HttpURLConnection connection) {
+        Cookie[] cookies = req.getCookies();
+        if (cookies != null) {
+            StringBuilder cookieHeader = new StringBuilder();
+            for (Cookie cookie : cookies) {
+                cookieHeader.append(cookie.getName()).append("=").append(cookie.getValue()).append("; ");
+            }
+            // Remove the trailing "; " at the end of the cookie string
+            if (cookieHeader.length() > 0) {
+                cookieHeader.setLength(cookieHeader.length() - 2);
+            }
+            connection.setRequestProperty("Cookie", cookieHeader.toString());
+        }
+    }
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/IndividualApiNetworkUtility.java

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+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import edu.cornell.mannlib.vitro.webapp.controller.api.sparqlquery.InvalidQueryTypeException;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
+import org.apache.jena.query.QueryParseException;
+
+public class IndividualApiNetworkUtility {
+
+    public static void handleResponseContentType(HttpServletRequest req, HttpServletResponse resp) {
+        String acceptHeader = req.getHeader("Accept");
+        if (acceptHeader != null && !acceptHeader.isEmpty()) {
+            resp.setContentType(acceptHeader);
+        } else {
+            resp.setContentType("application/json");
+        }
+    }
+
+    public static String serializeToJSON(Object serializationObject) throws IOException {
+        ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.enable(SerializationFeature.INDENT_OUTPUT);
+        objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
+        objectMapper.setSerializationInclusion(JsonInclude.Include.NON_EMPTY);
+        return objectMapper.writeValueAsString(serializationObject);
+    }
+
+    public static boolean isJsonRequest(HttpServletRequest req) {
+        String acceptHeader = req.getHeader("Accept");
+        return acceptHeader != null && acceptHeader.equals("application/json");
+    }
+
+    public static <T> T parseRequestBody(HttpServletRequest req, Class<T> clazz) throws IOException {
+        ObjectMapper objectMapper = new ObjectMapper();
+        return objectMapper.readValue(req.getInputStream(), clazz);
+    }
+
+    public static void handleException(Exception e, String queryString, HttpServletResponse resp) throws IOException {
+        if (e instanceof InvalidQueryTypeException) {
+            do400BadRequest("Invalid query type: '" + queryString + "'", resp);
+        } else if (e instanceof QueryParseException) {
+            do400BadRequest("Failed to parse query: '" + queryString + "'", resp);
+        } else if (e instanceof RDFServiceException) {
+            do500InternalServerError("Problem executing the query.", e, resp);
+        }
+    }
+
+    public static void do400BadRequest(String message, HttpServletResponse resp)
+        throws IOException {
+        resp.setStatus(400);
+        resp.getWriter().println(message);
+    }
+
+    public static void do404NotFound(String message, HttpServletResponse resp)
+        throws IOException {
+        resp.setStatus(404);
+        resp.getWriter().println(message);
+    }
+
+    public static void do500InternalServerError(String message, Exception e,
+                                                HttpServletResponse resp) throws IOException {
+        resp.setStatus(500);
+        PrintWriter w = resp.getWriter();
+        w.println(message);
+        e.printStackTrace(w);
+    }
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/IndividualApiSparqlUtility.java

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+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
+import edu.cornell.mannlib.vitro.webapp.controller.api.sparqlquery.SparqlQueryApiExecutor;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.jena.update.GraphStore;
+import org.apache.jena.update.UpdateAction;
+import org.apache.jena.update.UpdateFactory;
+import org.apache.jena.update.UpdateRequest;
+
+public class IndividualApiSparqlUtility {
+
+    public static String getSparqlQueryResponse(SparqlQueryApiExecutor core) throws IOException, RDFServiceException {
+        ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+        core.executeAndFormat(outputStream);
+
+        String sparqlResponse = outputStream.toString("UTF-8");
+
+        outputStream.close();
+
+        return sparqlResponse;
+    }
+
+    public static List<Map<String, String>> parseBindings(String jsonResponse) throws IOException {
+        ObjectMapper objectMapper = new ObjectMapper();
+        JsonNode rootNode = objectMapper.readTree(jsonResponse);
+
+        JsonNode bindingsNode = rootNode.path("results").path("bindings");
+
+        List<Map<String, String>> recordsList = new ArrayList<>();
+
+        for (JsonNode bindingNode : bindingsNode) {
+            Map<String, String> recordMap = new HashMap<>();
+
+            Iterator<Map.Entry<String, JsonNode>> fieldsIterator = bindingNode.fields();
+            while (fieldsIterator.hasNext()) {
+                Map.Entry<String, JsonNode> field = fieldsIterator.next();
+
+                String fieldName = field.getKey();
+                String fieldValue = field.getValue().path("value").asText();
+
+                recordMap.put(fieldName, fieldValue);
+            }
+
+            recordsList.add(recordMap);
+        }
+
+        return recordsList;
+    }
+
+    public static void addPrefixClauses(StringBuilder queryBuilder) {
+        queryBuilder
+            .append("PREFIX rdf:      <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n")
+            .append("PREFIX rdfs:     <http://www.w3.org/2000/01/rdf-schema#>\n")
+            .append("PREFIX xsd:      <http://www.w3.org/2001/XMLSchema#>\n")
+            .append("PREFIX owl:      <http://www.w3.org/2002/07/owl#>\n")
+            .append("PREFIX swrl:     <http://www.w3.org/2003/11/swrl#>\n")
+            .append("PREFIX swrlb:    <http://www.w3.org/2003/11/swrlb#>\n")
+            .append("PREFIX vitro:    <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>\n")
+            .append("PREFIX bibo:     <http://purl.org/ontology/bibo/>\n")
+            .append("PREFIX c4o:      <http://purl.org/spar/c4o/>\n")
+            .append("PREFIX cito:     <http://purl.org/spar/cito/>\n")
+            .append("PREFIX dcterms:  <http://purl.org/dc/terms/>\n")
+            .append("PREFIX event:    <http://purl.org/NET/c4dm/event.owl#>\n")
+            .append("PREFIX fabio:    <http://purl.org/spar/fabio/>\n")
+            .append("PREFIX foaf:     <http://xmlns.com/foaf/0.1/>\n")
+            .append("PREFIX geo:      <http://aims.fao.org/aos/geopolitical.owl#>\n")
+            .append("PREFIX obo:      <http://purl.obolibrary.org/obo/>\n")
+            .append("PREFIX vivo:     <http://vivoweb.org/ontology/core#>\n")
+            .append("PREFIX vcard:    <http://www.w3.org/2006/vcard/ns#>\n");
+    }
+
+    public static void executeUpdate(GraphStore graphStore, String query) {
+        UpdateRequest updateRequest = UpdateFactory.create(query);
+        UpdateAction.execute(updateRequest, graphStore);
+    }
+
+    public static String buildIndividualUri(String entityId) {
+        String defaultNamespace =
+            Objects.requireNonNull(ConfigurationProperties.getInstance().getProperty("Vitro.defaultNamespace"));
+        return defaultNamespace + StringEscapeUtils.escapeJava(entityId);
+    }
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/InformationContentEntityResponseDTO.java

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+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class InformationContentEntityResponseDTO {
+
+    public String internalIdentifier;
+
+    public String name;
+
+    public String datePublished;
+
+    public List<AuthorDTO> authors = new ArrayList<>();
+
+    public List<String> fundings = new ArrayList<>();
+
+    public List<FunderResponseDTO> funders = new ArrayList<>();
+}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/software/InformationContentEntityResponseUtility.java

@@ -0,0 +1,50 @@
+package edu.cornell.mannlib.vitro.webapp.controller.software;
+
+import java.util.Map;
+import java.util.Objects;
+
+public class InformationContentEntityResponseUtility {
+
+    public static void addAuthorToICE(Map<String, String> binding, InformationContentEntityResponseDTO entity) {
+        if (!Objects.nonNull(binding.get("author"))) {
+            return;
+        }
+
+        if (entity.authors.stream().anyMatch(author -> author.name.equals(binding.get("author")))) {
+            return;
+        }
+
+        AuthorDTO author = new AuthorDTO();
+        author.name = binding.getOrDefault("author", null);
+        author.type = binding.getOrDefault("authorType", null);
+        author.identifier = binding.getOrDefault("authorIdentifier", null);
+        entity.authors.add(author);
+    }
+
+    public static void addFundingToICE(Map<String, String> binding, InformationContentEntityResponseDTO entity) {
+        if (!Objects.nonNull(binding.get("funding"))) {
+            return;
+        }
+
+        if (entity.fundings.stream().anyMatch(funding -> funding.equals(binding.get("funding")))) {
+            return;
+        }
+
+        entity.fundings.add(binding.get("funding"));
+    }
+
+    public static void addFundersToICE(Map<String, String> binding, InformationContentEntityResponseDTO entity) {
+        if (!Objects.nonNull(binding.get("funder"))) {
+            return;
+        }
+
+        if (entity.funders.stream().anyMatch(funder -> funder.name.equals(binding.get("funder")))) {
+            return;
+        }
+
+        FunderResponseDTO funder = new FunderResponseDTO();
+        funder.name = binding.get("funder");
+        funder.type = binding.getOrDefault("funderType", null);
+        entity.funders.add(funder);
+    }
+}