408 lines
13 KiB
Java
408 lines
13 KiB
Java
package org.gcube.gcat.persistence.grsf;
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import java.io.BufferedWriter;
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import java.io.File;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.io.StringWriter;
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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 java.util.SortedSet;
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import java.util.TreeSet;
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import javax.ws.rs.core.MultivaluedHashMap;
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import javax.ws.rs.core.MultivaluedMap;
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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.authorization.client.exceptions.ObjectNotFound;
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import org.gcube.common.authorization.utils.manager.SecretManagerProvider;
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import org.gcube.common.scope.impl.ScopeBean;
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import org.gcube.gcat.ContextTest;
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import org.gcube.gcat.api.GCatConstants;
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import org.gcube.gcat.persistence.ckan.CKANGroup;
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import org.gcube.gcat.persistence.ckan.CKANGroupTest;
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import org.gcube.gcat.persistence.ckan.CKANOrganization;
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import org.gcube.gcat.persistence.ckan.CKANOrganizationTest;
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import org.gcube.gcat.persistence.ckan.CKANPackage;
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import org.gcube.gcat.persistence.ckan.CKANPackageTest;
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import org.gcube.gcat.persistence.ckan.CKANUser;
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import org.gcube.gcat.persistence.ckan.CKANUtility;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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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 GRSFUtilities extends ContextTest {
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private static Logger logger = LoggerFactory.getLogger(GRSFUtilities.class);
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public static final String PRODUCTION_GRSF = "/d4science.research-infrastructures.eu/FARM/GRSF";
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public static final String PRODUCTION_GRSF_ADMIN = "/d4science.research-infrastructures.eu/FARM/GRSF_Admin";
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public static final String PRODUCTION_GRSF_PRE = "/d4science.research-infrastructures.eu/FARM/GRSF_Pre";
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public static final String PREPROD_GRSF_PRE = "/pred4s/preprod/GRSF_Pre";
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@Before
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public void before() throws Exception {
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// ContextTest.setContextByName(PREPROD_GRSF_PRE);
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// ContextTest.setContextByName(PRODUCTION_GRSF);
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// ContextTest.setContextByName(PRODUCTION_GRSF_ADMIN);
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// ContextTest.setContextByName(PRODUCTION_GRSF_PRE);
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// logger.debug(SecretManagerProvider.instance.get().getUser().getUsername());
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// logger.debug(SecretManagerProvider.instance.get().getContext());
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}
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private void create(Set<String> createdGroup, Map<String, String> groups, String name) throws JsonProcessingException, IOException {
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if(createdGroup.contains(name)) {
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return;
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}
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String sysAdminAPI = ""; // CKANUtility.getSysAdminAPI();
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CKANGroup ckanGroupToCreate = new CKANGroup();
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ckanGroupToCreate.setApiKey(sysAdminAPI);
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ckanGroupToCreate.setName(name);
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// ckanGroupToCreate.purge();
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ObjectMapper objectMapper = new ObjectMapper();
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JsonNode jsonNode = objectMapper.readTree(groups.get(name));
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ArrayNode array = (ArrayNode) jsonNode.get("groups");
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for(JsonNode node : array) {
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String parentName = node.get("name").asText();
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if(!createdGroup.contains(parentName)) {
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create(createdGroup, groups, parentName);
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}
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}
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ckanGroupToCreate.create(groups.get(name));
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createdGroup.add(name);
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}
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// @Test
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public void createGRSFGroups() throws ObjectNotFound, Exception {
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String key = CKANUtility.getSysAdminAPI();
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List<String> groupNames = CKANGroupTest.listGroup();
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Map<String, String> groups = new HashMap<>();
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for(String name : groupNames) {
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CKANGroup ckanGroup = new CKANGroup();
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ckanGroup.setApiKey(key);
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ckanGroup.setName(name);
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String read = ckanGroup.read();
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groups.put(name, read);
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}
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Set<String> createdGroup = new HashSet<>();
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for(String name : groupNames) {
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create(createdGroup, groups, name);
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}
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}
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public static String getGroupNameOnCkan(String origName){
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if(origName == null) {
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throw new IllegalArgumentException("origName cannot be null");
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}
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String modified = origName.replaceAll("\\(", "");
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modified = modified.replaceAll("\\)", "");
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modified = modified.trim().toLowerCase().replaceAll("[^A-Za-z0-9-]", "-");
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if(modified.startsWith("-")) {
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modified = modified.substring(1);
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}
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if(modified.endsWith("-")) {
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modified = modified.substring(0, modified.length() -1);
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}
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return modified;
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}
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public static final String GROUP_SUFFIX = "-group";
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public static String getGroupId(String name) {
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StringBuffer stringBuffer = new StringBuffer();
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stringBuffer.append(getGroupNameOnCkan(name));
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if(!name.endsWith(GROUP_SUFFIX)) {
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stringBuffer.append(GROUP_SUFFIX);
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}
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return stringBuffer.toString();
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}
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@Test
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public void testGroupName() {
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String[] groupNames = new String[] {
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"GRSF", "Legacy", "Fishery", "Stock", "FIRMS", "FishSource", "RAM",
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"Catch", "Landing", "Assessment Method",
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"Abundance Level", "Abundance Level (FIRMS Standard)", "Biomass",
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"Fishing Pressure", "Fishing Pressure (FIRMS Standard)", "State and Trend",
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"FAO Stock Status Category", "Scientific Advice",
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"GRSF SDG Flag", "GRSF Traceability Flag"
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};
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for(String name : groupNames) {
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String ckanGroupName = getGroupId(name);
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String groupName = CKANGroup.fromGroupTitleToName(name) + GROUP_SUFFIX;
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logger.info("{} -> {}", name, ckanGroupName, groupName);
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Assert.assertTrue(ckanGroupName.compareTo(groupName)==0);
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}
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}
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@Test
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public void createNewGRSFGroups() throws ObjectNotFound, Exception {
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String sysAdminAPI = CKANUtility.getSysAdminAPI();
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String[] groupNames = new String[] {
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"GRSF", "Legacy", "Fishery", "Stock", "FIRMS", "FishSource", "RAM",
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"Catch", "Landing", "Assessment Method",
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"Abundance Level", "Abundance Level (FIRMS Standard)", "Biomass",
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"Fishing Pressure", "Fishing Pressure (FIRMS Standard)", "State and Trend",
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"FAO Stock Status Category", "Scientific Advice",
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"GRSF SDG Flag", "GRSF Traceability Flag"
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};
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groupNames = new String[] {"Assessment Method"};
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ObjectMapper objectMapper = new ObjectMapper();
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for(String name : groupNames) {
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CKANGroup ckanGroupToCreate = new CKANGroup();
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ckanGroupToCreate.setApiKey(sysAdminAPI);
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ckanGroupToCreate.setName(name);
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ObjectNode node = objectMapper.createObjectNode();
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node.put("display_name", name);
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node.put("title", name);
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node.put("name", getGroupId(name));
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String json = objectMapper.writeValueAsString(node);
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logger.info(json);
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ckanGroupToCreate.create(json);
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}
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}
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// @Test
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public void deleteNewGRSFGroups() throws ObjectNotFound, Exception {
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String sysAdminAPI = CKANUtility.getSysAdminAPI();
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// String[] groupNames = new String[] {
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// "GRSF", "Legacy", "Fishery", "Stock", "FIRMS", "FishSource", "RAM",
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// "Catch", "Landing",
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// "Abundance Level", "Abundance Level (FIRMS Standard)", "Biomass",
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// "Fishing Pressure", "Fishing Pressure (FIRMS Standard)", "State and Trend",
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// "FAO Stock Status Category", "Scientific Advice",
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// "GRSF SDG Flag", "GRSF Traceability Flag"
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// };
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//
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List<String> groupNames = CKANGroupTest.listGroup();
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logger.debug(SecretManagerProvider.instance.get().getUser().getUsername());
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logger.debug(SecretManagerProvider.instance.get().getContext());
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for(String name : groupNames) {
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CKANGroup ckanGroupToCreate = new CKANGroup();
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ckanGroupToCreate.setApiKey(sysAdminAPI);
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// ckanGroupToCreate.setName(getGroupId(name));
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ckanGroupToCreate.setName(name);
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try {
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// ckanGroupToCreate.purge();
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}catch (Exception e) {
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}
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}
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}
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// @Test
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public void associateUserToAllCKANGroupsAndOrganization() throws ObjectNotFound, Exception {
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String[] usernames = new String[] { "grsf_publisher", "luca_frosini", "francesco_mangiacrapa"};
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String sysAdminAPI = CKANUtility.getSysAdminAPI();
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List<String> groupNames = CKANGroupTest.listGroup();
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for(String groupName : groupNames) {
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CKANUser ckanUser = new CKANUser();
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ckanUser.setApiKey(sysAdminAPI);
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for(String username : usernames) {
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ckanUser.setName(username);
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ckanUser.addToGroup(groupName);
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}
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}
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List<String> orgs = CKANOrganizationTest.listOrg();
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for(String org : orgs) {
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CKANUser ckanUser = new CKANUser();
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ckanUser.setApiKey(sysAdminAPI);
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for(String username : usernames) {
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ckanUser.addUserToOrganization(org, username, "admin");
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}
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}
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}
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// @Test
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public void manageOrganizations() throws JsonProcessingException {
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String sysAdminAPI = CKANUtility.getSysAdminAPI();
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String[] organizations = new String[] {
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"GRSF_Pre", "FIRMS", "FishSource", "RAM"
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};
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ObjectMapper objectMapper = new ObjectMapper();
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for(String org : organizations) {
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CKANOrganization ckanOrganization = new CKANOrganization();
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ckanOrganization.setApiKey(sysAdminAPI);
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ckanOrganization.setName(org.toLowerCase());
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ObjectNode node = objectMapper.createObjectNode();
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node.put("display_name", org);
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node.put("title", org);
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node.put("name", org.toLowerCase());
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String json = objectMapper.writeValueAsString(node);
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try {
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// ckanOrganization.create(json);
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// ckanOrganization.purge();
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}catch (Exception e) {
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}
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}
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}
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protected void printLine(File file, String line) throws Exception {
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try (FileWriter fw = new FileWriter(file, true);
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BufferedWriter bw = new BufferedWriter(fw);
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PrintWriter out = new PrintWriter(bw)) {
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out.println(line);
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out.flush();
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} catch (IOException e) {
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throw e;
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}
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}
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public Map<String,String> getListParameter(int limit, int offset, String type, String org) {
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Map<String,String> parameters = new HashMap<>();
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if(limit <= 0) {
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// According to CKAN documentation
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// the number of matching rows to return. There is a hard limit of 1000 datasets per query.
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// see https://docs.ckan.org/en/2.6/api/index.html#ckan.logic.action.get.package_search
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limit = 1000;
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}
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parameters.put(CKANPackage.ROWS_KEY, String.valueOf(limit));
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if(offset < 0) {
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offset = 0;
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}
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parameters.put(CKANPackage.START_KEY, String.valueOf(offset));
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String q = null;
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if(type!=null) {
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// This filter by type
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StringWriter qStringWriter = new StringWriter();
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qStringWriter.append("extras_systemtype:");
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qStringWriter.append(type);
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q = qStringWriter.toString();
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}
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if(org!=null) {
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StringWriter qStringWriter = new StringWriter();
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qStringWriter.append("organization:");
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qStringWriter.append(org);
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if(q!=null) {
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q = q + " AND " + qStringWriter.toString();
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}
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}
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if(q!=null) {
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q = q + " AND (StatusoftheRecord:Approved OR StatusoftheRecord:Archived)";
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// q = q + " AND (groups:stock-group)";
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}
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if(q!=null) {
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parameters.put(GCatConstants.Q_KEY, q);
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}
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return parameters;
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}
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// @Test
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public void list() throws Exception {
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ObjectMapper mapper = new ObjectMapper();
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int limit = 100;
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// String[] contexts = new String[] {PRODUCTION_GRSF, PRODUCTION_GRSF_ADMIN};
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String[] contexts = new String[] {PRODUCTION_GRSF};
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for(String context : contexts) {
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ContextTest.setContextByName(context);
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logger.debug(SecretManagerProvider.instance.get().getUser().getUsername());
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logger.debug(SecretManagerProvider.instance.get().getContext());
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CKANPackage ckanPackage = new CKANPackage();
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SortedSet<String> sortedSet = new TreeSet<>();
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String[] types = new String[] {"Marine Resource", "Assessment Unit"};
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for(String type : types) {
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int offset = 0;
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boolean go = true;
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ScopeBean scopeBean = new ScopeBean(context);
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while(go) {
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Map<String,String> parameters = getListParameter(limit, offset==0 ? 0 : (offset*limit), type, scopeBean.name().toLowerCase());
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String ret = ckanPackage.list(parameters);
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JsonNode gotList = mapper.readTree(ret);
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Assert.assertTrue(gotList instanceof ArrayNode);
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ArrayNode itemsArray = (ArrayNode) gotList;
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if(itemsArray.size()>0) {
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for(JsonNode jsonNode : itemsArray) {
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String name = jsonNode.asText();
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sortedSet.add(name);
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}
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offset++;
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}else {
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go=false;
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}
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}
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File file = new File(scopeBean.name() + "-" + type.replace(" ", "_")+".txt");
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if(file.exists()) {
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file.delete();
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}
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for(String name : sortedSet) {
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printLine(file, name);
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}
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}
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}
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}
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private void purgeGRSFRecords(int limit, int offset) throws Exception {
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logger.debug("Going to purge {} records, starting from {}", limit, limit*offset);
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CKANPackage ckanPackage = new CKANPackage();
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MultivaluedMap<String, String> mvm = new MultivaluedHashMap<String,String>();
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UriInfo uriInfo = CKANPackageTest.getUriInfo(mvm);
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ckanPackage.setUriInfo(uriInfo);
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ObjectMapper mapper = new ObjectMapper();
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boolean go = true;
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while(go) {
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Map<String,String> parameters = getListParameter(limit, offset, null, null);
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String ret = ckanPackage.list(parameters);
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JsonNode gotList = mapper.readTree(ret);
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Assert.assertTrue(gotList instanceof ArrayNode);
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ArrayNode itemsArray = (ArrayNode) gotList;
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if(itemsArray.size()>0) {
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for(JsonNode jsonNode : itemsArray) {
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String name = jsonNode.asText();
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logger.debug("Going to purge record with name {}", name);
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ckanPackage.setName(name);
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try {
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ckanPackage.purgeNoCheckNoDeleteFiles();
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}catch (Exception e) {
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logger.error("Unable to purge record with name {}", name, e);
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}
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}
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Thread.sleep(500);
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}else {
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go=false;
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}
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}
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}
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// @Test
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public void purgeAllGRSFRecords() throws Exception {
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purgeGRSFRecords(100, 0);
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}
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}
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