Implementing service
This commit is contained in:
parent
e659628dc7
commit
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20
pom.xml
20
pom.xml
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@ -83,16 +83,36 @@
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<groupId>org.glassfish.jersey.containers</groupId>
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<artifactId>jersey-container-servlet</artifactId>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.media</groupId>
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<artifactId>jersey-media-multipart</artifactId>
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</dependency>
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<dependency>
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<groupId>javax.ws.rs</groupId>
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<artifactId>javax.ws.rs-api</artifactId>
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</dependency>
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<dependency>
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<groupId>org.gcube.portlets.user</groupId>
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<artifactId>uri-resolver-manager</artifactId>
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<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
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</dependency>
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<dependency>
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<groupId>org.freemarker</groupId>
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<artifactId>freemarker</artifactId>
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<version>2.3.32</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.common</groupId>
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<artifactId>storagehub-model</artifactId>
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</dependency>
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<dependency>
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<groupId>org.gcube.data-publishing</groupId>
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<artifactId>storagehub-application-persistence</artifactId>
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<version>[3.0.0,4.0.0-SNAPSHOT)</version>
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</dependency>
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<!-- Added to support Java 11 JDK -->
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<dependency>
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@ -1,52 +1,69 @@
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package org.gcube.grsf.publisher.record;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.Writer;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import javax.ws.rs.InternalServerErrorException;
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import javax.ws.rs.WebApplicationException;
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import javax.ws.rs.core.UriInfo;
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import org.gcube.com.fasterxml.jackson.core.JsonProcessingException;
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import org.gcube.com.fasterxml.jackson.databind.JsonNode;
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import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
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import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
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import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
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import org.gcube.common.storagehub.client.dsl.FileContainer;
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import org.gcube.common.storagehub.model.Metadata;
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import org.gcube.common.storagehub.model.exceptions.StorageHubException;
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import org.gcube.gcat.persistence.ckan.CKANPackage;
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import org.gcube.gcat.persistence.ckan.CKANUserCache;
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import org.gcube.grsf.publisher.freemarker.FreeMarker;
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import org.gcube.storagehub.StorageHubManagement;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import freemarker.template.Template;
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import freemarker.template.TemplateException;
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/**
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* @author Luca Frosini (ISTI - CNR)
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*/
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public abstract class Record {
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public abstract class Record extends CKANPackage {
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private final Logger logger = LoggerFactory.getLogger(this.getClass());
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public static final String GRSF_UUID_PROPERTY = "grsf_uuid";
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public static final String RESOURCES_PROPERTY = "resources";
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public static final String RESOURCE_ELEMENT_NAME_PROPERTY = "name";
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public static final String RESOURCE_ELEMENT_URL_PROPERTY = "url";
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public static final String TIMESERIES_PROPERTY = "timeseries";
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public static final String TIMESERIES_ELEMENT_PROPERTY_PROPERTY = "property";
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public static final String TIMESERIES_ELEMENT_FILENAME_PROPERTY = "filename";
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protected UriInfo uriInfo;
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protected String id;
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protected String grsfUUID;
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protected ObjectMapper objectMapper;
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protected JsonNode jsonNode;
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protected Set<String> groups;
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protected Set<String> tags;
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protected Set<String> resources;
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protected Set<FileContainer> wsUploadedFiles;
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public Record() {
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this.objectMapper = new ObjectMapper();
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this.groups = new HashSet<>();
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this.tags = new HashSet<>();
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this.resources = new HashSet<>();
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}
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public abstract String getType();
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@ -59,26 +76,24 @@ public abstract class Record {
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this.tags.add(tag);
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}
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public void setId(String id) {
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this.id = id;
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public void setGRSFUUID(String grsfUUID) {
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this.grsfUUID = grsfUUID;
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}
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public String getId() {
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return this.id;
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public String getGRSFUUID() {
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return this.grsfUUID;
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}
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public void setUriInfo(UriInfo uriInfo) {
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this.uriInfo = uriInfo;
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}
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public void elaborate() throws Exception {
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public JsonNode elaborate(JsonNode node) throws Exception {
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FreeMarker freeMarker = new FreeMarker();
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Template tsTemplate = freeMarker.getTemplate("timeseries.ftl");
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Template template = freeMarker.getTemplate(getType() + ".ftl");
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Map<String, Object> map = getMapFromSourceJson();
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Map<String, Object> map = getMapFromSourceJson(node);
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grsfUUID = map.get(Record.GRSF_UUID_PROPERTY).toString();
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File transformedJson = getTransformedJsonFile(template,map);
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List<File> timeseriesFiles = elaborateTimeSeries(tsTemplate,map,transformedJson);
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// TODO save files on workspace using storagehub-application-persistence
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jsonNode = mapper.readTree(transformedJson);
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jsonNode = elaborateTimeSeries(tsTemplate,map);
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return jsonNode;
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}
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public String list(int limit, int offset) {
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@ -86,7 +101,24 @@ public abstract class Record {
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return null;
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}
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protected Map<String, Object> getMapFromSourceJson() throws JsonProcessingException {
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/**
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* Save the file in the workspace using storagehub-application-persistence
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* @param file the file to persist in the workspace
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* @return
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* @throws Exception
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*/
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protected FileContainer persistFile(File file) throws Exception{
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StorageHubManagement shm = new StorageHubManagement();
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FileInputStream fis = new FileInputStream(file);
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Map<String,Object> map = new HashMap<>();
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map.put(Record.GRSF_UUID_PROPERTY, grsfUUID);
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Metadata metadata = new Metadata(map);
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shm.persistFile(fis, file.getName(), "text/csv", metadata);
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FileContainer fileContainer = shm.getPersistedFile();
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return fileContainer;
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}
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protected Map<String, Object> getMapFromSourceJson(JsonNode jsonNode) throws JsonProcessingException {
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@SuppressWarnings("unchecked")
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Map<String, Object> map = objectMapper.treeToValue(jsonNode, Map.class);
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@ -99,7 +131,7 @@ public abstract class Record {
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}
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protected File getTransformedJsonFile(Template template, Map<String, Object> map) throws Exception {
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File out = new File(map.get("grsf_uuid").toString()+".json");
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File out = new File(grsfUUID+".json");
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out.delete();
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Writer writer = new FileWriter(out);
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@ -110,47 +142,115 @@ public abstract class Record {
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return out;
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}
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protected List<File> elaborateTimeSeries(Template tsTemplate,Map<String, Object> map, File transformedJson) throws IOException, TemplateException {
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protected JsonNode elaborateTimeSeries(Template tsTemplate, Map<String, Object> map) throws Exception {
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ArrayNode resources = (ArrayNode) jsonNode.get(Record.RESOURCES_PROPERTY);
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this.wsUploadedFiles = new HashSet<>();
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ArrayNode timeseries = (ArrayNode) jsonNode.get(Record.TIMESERIES_PROPERTY);
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List<File> timeseriesFiles = new ArrayList<>();
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JsonNode node = objectMapper.readTree(transformedJson);
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ArrayNode timeseries = (ArrayNode) node.get("timeseries");
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for(JsonNode n : timeseries) {
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String key = n.get("property").asText();
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String fileName = n.get("filename").asText();
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logger.trace("Elaborating {} timeseries {} from file {}", getType(), key, transformedJson.getName());
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map.put("timeseries", map.get(key));
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File tsOut = new File(transformedJson.getName().replace(".json","")+"-"+fileName+".csv");
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tsOut.delete();
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Writer tsWriter = new FileWriter(tsOut);
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tsTemplate.process(map, tsWriter);
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tsWriter.flush();
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tsWriter.close();
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timeseriesFiles.add(tsOut);
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map.remove("timeseries");
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}
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return timeseriesFiles;
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try {
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for(JsonNode n : timeseries) {
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String key = n.get(Record.TIMESERIES_ELEMENT_PROPERTY_PROPERTY).asText();
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try {
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String fileName = n.get(Record.TIMESERIES_ELEMENT_FILENAME_PROPERTY).asText();
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logger.trace("Elaborating {} timeseries from property {} of Record with GRSF UUID {}", getType(), key, grsfUUID);
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/*
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* Adding to map the name of the property containing the timeseries
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* It is used by the FreeMarker template to get json property to be used
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* to generate the timeseries
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*/
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map.put(Record.TIMESERIES_PROPERTY, map.get(key));
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File tsOut = new File(grsfUUID + ".json-"+fileName+".csv");
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tsOut.delete();
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Writer tsWriter = new FileWriter(tsOut);
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tsTemplate.process(map, tsWriter);
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tsWriter.flush();
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tsWriter.close();
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timeseriesFiles.add(tsOut);
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/*
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* Removing the property form the map keep clean the map
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* generated using the input json
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*/
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map.remove(Record.TIMESERIES_PROPERTY);
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FileContainer fc = persistFile(tsOut);
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this.wsUploadedFiles.add(fc);
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URL url = fc.getPublicLink();
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ObjectNode resourceNode = objectMapper.createObjectNode();
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resourceNode.put(RESOURCE_ELEMENT_NAME_PROPERTY, fileName);
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resourceNode.put(RESOURCE_ELEMENT_URL_PROPERTY, url.toString());
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resources.add(resourceNode);
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((ObjectNode)jsonNode).replace(RESOURCES_PROPERTY, resources);
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timeseriesFiles.remove(tsOut);
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tsOut.delete();
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}catch (Exception e) {
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logger.error("Something went wrong generating {} timeseries from property {} of Record with GRSF UUID {}", getType(), key, grsfUUID);
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throw e;
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}
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}
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((ObjectNode)jsonNode).remove(Record.TIMESERIES_PROPERTY);
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} finally {
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/*
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* Remove the local files of timeseries
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* if an error occurs to keep the environment clean
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*/
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for(File f : timeseriesFiles) {
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f.delete();
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}
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}
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return jsonNode;
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}
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@Override
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public String create(String json) {
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try {
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this.jsonNode = objectMapper.readTree(json);
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elaborate();
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// TODO
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} catch (Exception e) {
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JsonNode jsonNode = objectMapper.readTree(json);
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elaborate(jsonNode);
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sendPostRequest(CREATE, json);
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parseResult();
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String userFullName = CKANUserCache.getCurrrentCKANUser().getNameSurname();
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sendSocialPost(userFullName);
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return getAsCleanedString(result);
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} catch(WebApplicationException e) {
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deleteUploadedFiles();
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throw e;
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} catch(Exception e) {
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deleteUploadedFiles();
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throw new InternalServerErrorException(e);
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}
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return null;
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}
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private void deleteUploadedFiles() {
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for(FileContainer fileContainer : wsUploadedFiles) {
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try {
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fileContainer.delete();
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} catch (StorageHubException e) {
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logger.warn("Unable to delete from StorageHub the file with ID:{}", fileContainer.getId());
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}
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}
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}
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@Override
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public String update(String json) {
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try {
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this.jsonNode = objectMapper.readTree(json);
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elaborate();
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JsonNode jsonNode = objectMapper.readTree(json);
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elaborate(jsonNode);
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// TODO
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} catch (Exception e) {
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throw new InternalServerErrorException(e);
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@ -158,10 +258,11 @@ public abstract class Record {
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return null;
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}
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@Override
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public String patch(String json) {
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try {
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this.jsonNode = objectMapper.readTree(json);
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elaborate();
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JsonNode jsonNode = objectMapper.readTree(json);
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elaborate(jsonNode);
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// TODO
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} catch (Exception e) {
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throw new InternalServerErrorException(e);
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@ -173,11 +274,13 @@ public abstract class Record {
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// TODO
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}
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@Override
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public String read() {
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// TODO
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return null;
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}
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@Override
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public int count() {
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// TODO
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return 0;
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@ -115,28 +115,28 @@ public class BaseRESTAPIs<R extends Record> {
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String ret = record.create(json);
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ResponseBuilder responseBuilder = Response.status(Status.CREATED).entity(ret);
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responseBuilder = addLocation(responseBuilder, record.getId());
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responseBuilder = addLocation(responseBuilder, record.getGRSFUUID());
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return responseBuilder.type(GCatConstants.APPLICATION_JSON_CHARSET_UTF_8).build();
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}
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public String read(String id) {
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setCalledMethod("GET /" + COLLECTION_PARAMETER + "/{" + ID_PARAMETER + "}");
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Record record = getInstance();
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record.setId(id);
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record.setGRSFUUID(id);
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return record.read();
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}
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public String update(String id, String json) {
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setCalledMethod("PUT /" + COLLECTION_PARAMETER + "/{" + ID_PARAMETER + "}");
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Record record = getInstance();
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record.setId(id);
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record.setGRSFUUID(id);
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return record.update(json);
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}
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public String patch(String id, String json) {
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setCalledMethod("PATCH /" + COLLECTION_PARAMETER + "/{" + ID_PARAMETER + "}");
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Record record = getInstance();
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record.setId(id);
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record.setGRSFUUID(id);
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return record.patch(json);
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}
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@ -151,7 +151,7 @@ public class BaseRESTAPIs<R extends Record> {
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setCalledMethod("DELETE /" + COLLECTION_PARAMETER + "/{" + ID_PARAMETER + "}");
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}
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Record record = getInstance();
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record.setId(id);
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record.setGRSFUUID(id);
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record.delete(purge);
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return Response.status(Status.NO_CONTENT).build();
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}
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@ -0,0 +1,122 @@
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/**
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*
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*/
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package org.gcube.grsf.publisher;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.Properties;
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import org.gcube.common.authorization.utils.manager.SecretManager;
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import org.gcube.common.authorization.utils.manager.SecretManagerProvider;
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import org.gcube.common.authorization.utils.secret.JWTSecret;
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import org.gcube.common.authorization.utils.secret.Secret;
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import org.gcube.common.authorization.utils.secret.SecretUtility;
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import org.gcube.common.keycloak.KeycloakClientFactory;
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import org.gcube.common.keycloak.model.TokenResponse;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.junit.AfterClass;
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import org.junit.BeforeClass;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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/**
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* @author Luca Frosini (ISTI - CNR)
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*/
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public class ContextTest {
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private static final Logger logger = LoggerFactory.getLogger(ContextTest.class);
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protected static final String CONFIG_INI_FILENAME = "config.ini";
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public static final String PARENT_DEFAULT_TEST_SCOPE;
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public static final String DEFAULT_TEST_SCOPE;
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public static final String ALTERNATIVE_TEST_SCOPE;
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public static final String GCUBE;
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public static final String DEVNEXT;
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public static final String NEXTNEXT;
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public static final String DEVSEC;
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public static final String DEVVRE;
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protected static final Properties properties;
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protected static final String CLIENT_ID_PROPERTY_KEY = "client_id";
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protected static final String CLIENT_SECRET_PROPERTY_KEY = "client_secret";
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protected static final String clientID;
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protected static final String clientSecret;
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static {
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GCUBE = "/gcube";
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DEVNEXT = GCUBE + "/devNext";
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NEXTNEXT = DEVNEXT + "/NextNext";
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DEVSEC = GCUBE + "/devsec";
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DEVVRE = DEVSEC + "/devVRE";
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PARENT_DEFAULT_TEST_SCOPE = "/gcube";
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DEFAULT_TEST_SCOPE = DEVSEC;
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ALTERNATIVE_TEST_SCOPE = DEVVRE;
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properties = new Properties();
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InputStream input = ContextTest.class.getClassLoader().getResourceAsStream(CONFIG_INI_FILENAME);
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try {
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// load the properties file
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properties.load(input);
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clientID = properties.getProperty(CLIENT_ID_PROPERTY_KEY);
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clientSecret = properties.getProperty(CLIENT_SECRET_PROPERTY_KEY);
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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public static void set(Secret secret) throws Exception {
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SecretManagerProvider.instance.reset();
|
||||
SecretManager secretManager = new SecretManager();
|
||||
secretManager.addSecret(secret);
|
||||
SecretManagerProvider.instance.set(secretManager);
|
||||
SecretManagerProvider.instance.get().set();
|
||||
}
|
||||
|
||||
public static void setContextByName(String fullContextName) throws Exception {
|
||||
Secret secret = getSecretByContextName(fullContextName);
|
||||
set(secret);
|
||||
}
|
||||
|
||||
|
||||
private static TokenResponse getJWTAccessToken(String context) throws Exception {
|
||||
ScopeProvider.instance.set(context);
|
||||
TokenResponse tr = KeycloakClientFactory.newInstance().queryUMAToken(clientID, clientSecret, context, null);
|
||||
return tr;
|
||||
}
|
||||
|
||||
public static Secret getSecretByContextName(String context) throws Exception {
|
||||
TokenResponse tr = getJWTAccessToken(context);
|
||||
Secret secret = new JWTSecret(tr.getAccessToken());
|
||||
return secret;
|
||||
}
|
||||
|
||||
public static void setContext(String token) throws Exception {
|
||||
Secret secret = getSecret(token);
|
||||
set(secret);
|
||||
}
|
||||
|
||||
private static Secret getSecret(String token) throws Exception {
|
||||
Secret secret = SecretUtility.getSecretByTokenString(token);
|
||||
return secret;
|
||||
}
|
||||
|
||||
@BeforeClass
|
||||
public static void beforeClass() throws Exception {
|
||||
setContextByName(DEFAULT_TEST_SCOPE);
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClass() throws Exception {
|
||||
SecretManagerProvider.instance.reset();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -85,7 +85,7 @@ public class FreeMarkerTest {
|
|||
for(File jsonFile : jsonFiles) {
|
||||
ObjectMapper mapper = new ObjectMapper();
|
||||
|
||||
JsonNode test = mapper.readTree(jsonFile);
|
||||
mapper.readTree(jsonFile);
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
Map<String, Object> map = mapper.readValue(jsonFile, Map.class);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,110 @@
|
|||
package org.gcube.grsf.publisher.record;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FilenameFilter;
|
||||
import java.util.Calendar;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
|
||||
import org.gcube.grsf.publisher.ContextTest;
|
||||
import org.gcube.grsf.publisher.freemarker.FreeMarker;
|
||||
import org.junit.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
public class RecordTest extends ContextTest {
|
||||
|
||||
private static Logger logger = LoggerFactory.getLogger(RecordTest.class);
|
||||
|
||||
public File getExampleDirectory(String type) throws Exception {
|
||||
File resourcesDirectory = FreeMarker.getResourcesDirectory();
|
||||
return new File(resourcesDirectory, "examples/" + type);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testRecords() throws Exception {
|
||||
// String[] types = new String[] {"Stock", "Fishery", "TraceabilityUnit"};
|
||||
String[] types = new String[] { "Stock" };
|
||||
// String[] types = new String[] {"Fishery"};
|
||||
// String[] types = new String[] {"TraceabilityUnit"};
|
||||
|
||||
Calendar start = Calendar.getInstance();
|
||||
|
||||
int countRecord = 0;
|
||||
int countTimeSeries = 0;
|
||||
|
||||
File outputDir = new File(FreeMarker.getResourcesDirectory(), "output");
|
||||
outputDir.mkdir();
|
||||
|
||||
FilenameFilter dirnameFilter = new FilenameFilter() {
|
||||
@Override
|
||||
public boolean accept(File dir, String name) {
|
||||
File f = new File(dir, name);
|
||||
return f.isDirectory();
|
||||
}
|
||||
};
|
||||
|
||||
FilenameFilter filenameFilter = new FilenameFilter() {
|
||||
@Override
|
||||
public boolean accept(File dir, String name) {
|
||||
return name.toLowerCase().endsWith(".json");
|
||||
}
|
||||
};
|
||||
|
||||
for (String type : types) {
|
||||
File examplesDir = getExampleDirectory(type);
|
||||
|
||||
File outputTypeDir = new File(outputDir, type);
|
||||
outputTypeDir.mkdir();
|
||||
|
||||
// File[] sourceFiles = examplesDir.listFiles(dirnameFilter);
|
||||
File[] sourceFiles = new File[] { new File(examplesDir, "grsf") };
|
||||
|
||||
for (File source : sourceFiles) {
|
||||
|
||||
String sourceString = source.getName();
|
||||
|
||||
File outputSourceDir = new File(outputTypeDir, sourceString);
|
||||
outputSourceDir.mkdir();
|
||||
|
||||
// File[] jsonFiles = source.listFiles(filenameFilter);
|
||||
File[] jsonFiles = new File[] {new File(source,"88818c3f-7120-322b-9637-7c7d2e9fc1e5.json")};
|
||||
|
||||
for (File jsonFile : jsonFiles) {
|
||||
ObjectMapper mapper = new ObjectMapper();
|
||||
|
||||
ObjectNode input = (ObjectNode) mapper.readTree(jsonFile);
|
||||
input.put("source", sourceString);
|
||||
|
||||
Record record;
|
||||
switch (type) {
|
||||
case "Fishery":
|
||||
record = new Fishery();
|
||||
break;
|
||||
|
||||
case "Stock":
|
||||
record = new Stock();
|
||||
break;
|
||||
|
||||
case "TraceabilityUnit":
|
||||
record = new TraceabilityUnit();
|
||||
break;
|
||||
|
||||
default:
|
||||
return;
|
||||
}
|
||||
|
||||
record.create(mapper.writeValueAsString(input));
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Calendar end = Calendar.getInstance();
|
||||
long diff = end.getTimeInMillis() - start.getTimeInMillis();
|
||||
logger.info("Generated {} records and {} CSV files from TimeSeries in {} milliseconds (~{} seconds)",
|
||||
countRecord, countTimeSeries, diff, TimeUnit.MILLISECONDS.toSeconds(diff));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,3 +1,5 @@
|
|||
/FARM.gcubekey
|
||||
/token.properties
|
||||
/config.properties
|
||||
/*.gcubekey
|
||||
/config.ini
|
||||
|
|
|
|||
Loading…
Reference in New Issue