Marekhorst 1434 reimplement context importer module by replacing is lookup with RESTful endpoint

iis-wf/iis-wf-import/src/main/java/eu/dnetlib/iis/wf/importer/concept/RestfulEndpointBasedConceptImporter.java

@@ -0,0 +1,178 @@
+package eu.dnetlib.iis.wf.importer.concept;
+
+import static eu.dnetlib.iis.common.WorkflowRuntimeParameters.OOZIE_ACTION_OUTPUT_FILENAME;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import org.apache.avro.file.DataFileWriter;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.log4j.Logger;
+
+import com.google.common.base.Preconditions;
+import com.google.gson.Gson;
+
+import eu.dnetlib.iis.common.counter.NamedCounters;
+import eu.dnetlib.iis.common.counter.NamedCountersFileWriter;
+import eu.dnetlib.iis.common.java.PortBindings;
+import eu.dnetlib.iis.common.java.Process;
+import eu.dnetlib.iis.common.java.io.DataStore;
+import eu.dnetlib.iis.common.java.io.FileSystemPath;
+import eu.dnetlib.iis.common.java.porttype.AvroPortType;
+import eu.dnetlib.iis.common.java.porttype.PortType;
+import eu.dnetlib.iis.importer.schemas.Concept;
+import eu.dnetlib.iis.wf.importer.concept.model.Context;
+import eu.dnetlib.iis.wf.importer.concept.model.Param;
+import eu.dnetlib.iis.wf.importer.facade.ContextNotFoundException;
+import eu.dnetlib.iis.wf.importer.facade.ContextStreamingFacade;
+import eu.dnetlib.iis.wf.importer.facade.ServiceFacadeUtils;
+
+/**
+ * RESTful endpoint based importer reading contexts provided as JSON records.  
+ * @author mhorst
+ *
+ */
+public class RestfulEndpointBasedConceptImporter implements Process {
+
+	public static final String PARAM_IMPORT_CONTEXT_IDS_CSV = "import.context.ids.csv";
+
+	protected static final String CONCEPT_COUNTER_NAME = "CONCEPT_COUNTER";
+
+	private static final Logger log = Logger.getLogger(RestfulEndpointBasedConceptImporter.class);
+
+	private final NamedCountersFileWriter countersWriter = new NamedCountersFileWriter();
+
+
+	protected static final String PORT_OUT_CONCEPTS = "concepts";
+
+	private final Map<String, PortType> outputPorts = new HashMap<String, PortType>();
+
+
+	//------------------------ CONSTRUCTORS -------------------
+
+	public RestfulEndpointBasedConceptImporter() {
+	    outputPorts.put(PORT_OUT_CONCEPTS, new AvroPortType(Concept.SCHEMA$));
+	}
+
+    //------------------------ LOGIC --------------------------
+
+	@Override
+	public Map<String, PortType> getInputPorts() {
+		return Collections.emptyMap();
+	}
+
+	@Override
+	public Map<String, PortType> getOutputPorts() {
+		return outputPorts;
+	}
+
+	@Override
+	public void run(PortBindings portBindings, Configuration conf,
+			Map<String, String> parameters) throws Exception {
+
+		Preconditions.checkArgument(parameters.containsKey(PARAM_IMPORT_CONTEXT_IDS_CSV), 
+                "unknown context identifier, required parameter '%s' is missing!", PARAM_IMPORT_CONTEXT_IDS_CSV);
+		String contextIdsCSV = parameters.get(PARAM_IMPORT_CONTEXT_IDS_CSV);
+
+		try (DataFileWriter<Concept> conceptWriter = getWriter(FileSystem.get(conf), portBindings)) {
+
+            NamedCounters counters = new NamedCounters(new String[] { CONCEPT_COUNTER_NAME });
+
+			ContextStreamingFacade streamingFacade = ServiceFacadeUtils.instantiate(parameters);
+
+			String[] contextIds = StringUtils.split(contextIdsCSV, ',');
+
+            for (String contextId : contextIds) {
+
+                if (StringUtils.isNotEmpty(contextId)) {
+
+                    try {
+                        try (InputStream is = streamingFacade.getStream(contextId)) {
+
+                            Concept[] concepts = buildConcepts(IOUtils.toString(is, StandardCharsets.UTF_8.name()));
+
+                            for (Concept concept : concepts) {
+                                conceptWriter.append(concept);
+                            }
+
+                            counters.increment(CONCEPT_COUNTER_NAME, (long) concepts.length);
+                        }
+                    } catch (ContextNotFoundException e) {
+                        log.warn("context not found: " + contextId, e);
+                    }
+                }
+            }
+
+			countersWriter.writeCounters(counters, System.getProperty(OOZIE_ACTION_OUTPUT_FILENAME));
+		}
+	}
+
+	/**
+	 * Provides {@link Concept} writer consuming records.
+	 */
+	protected DataFileWriter<Concept> getWriter(FileSystem fs, PortBindings portBindings) throws IOException {
+	    return DataStore.create(
+                new FileSystemPath(fs, portBindings.getOutput().get(PORT_OUT_CONCEPTS)), Concept.SCHEMA$);
+	}
+
+	//------------------------ PRIVATE --------------------------
+
+	/**
+	 * Builds an array of concepts based on the JSON representation returned by the context endpoint.
+	 * @param contextsJson contexts encoded in JSON format
+	 * @return array of {@link Concept} avro records.
+	 */
+	private static Concept[] buildConcepts(String contextsJson) {
+
+	    return translate(new Gson().fromJson(contextsJson, Context[].class));
+	}
+
+	/**
+	 * Translates an array of {@link IISConfigurationEntry} from the JSON model into the array of {@link Concept} objects from avro model.
+	 */
+	private static Concept[] translate(Context[] source) {
+	    Concept[] results = new Concept[source.length];
+	    for (int i=0; i < source.length; i++) {
+	        results[i] = translate(source[i]);
+	    }
+	    return results;
+	}
+
+	/**
+	 * Translates {@link IISConfigurationEntry} from the JSON model into the {@link Concept} object from avro model.
+	 */
+	private static Concept translate(Context source) {
+	    Concept.Builder conceptBuilder = Concept.newBuilder();
+	    conceptBuilder.setId(source.getId());
+	    conceptBuilder.setLabel(source.getLabel());
+	    conceptBuilder.setParams(translate(source.getParams()));
+	    return conceptBuilder.build();
+	}
+
+	/**
+	 * Translates the list of {@link Param} from the JSON model into the list of {@link eu.dnetlib.iis.importer.schemas.Param} objects from avro model.
+	 */
+	private static List<eu.dnetlib.iis.importer.schemas.Param> translate(List<Param> source) {
+        return source.stream().map(x -> translate(x)).collect(Collectors.toList());
+    }
+
+	/**
+	 * Translates {@link Param} from the JSON model into the {@link eu.dnetlib.iis.importer.schemas.Param} object from avro model.
+	 */
+	private static eu.dnetlib.iis.importer.schemas.Param translate(Param source) {
+	    eu.dnetlib.iis.importer.schemas.Param.Builder paramBuilder = eu.dnetlib.iis.importer.schemas.Param.newBuilder();
+	    paramBuilder.setName(source.getName());
+	    paramBuilder.setValue(source.getValue());
+	    return paramBuilder.build();
+    }
+
+}

iis-wf/iis-wf-import/src/main/java/eu/dnetlib/iis/wf/importer/concept/model/Context.java

@@ -0,0 +1,42 @@
+package eu.dnetlib.iis.wf.importer.concept.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Class representing context record.
+ * 
+ * @author mhorst
+ * 
+ */
+public class Context {
+
+    private String id;
+    private String label;
+    private List<Param> params = new ArrayList<>();
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(final String id) {
+        this.id = id;
+    }
+
+    public String getLabel() {
+        return label;
+    }
+
+    public void setLabel(final String label) {
+        this.label = label;
+    }
+
+    public List<Param> getParams() {
+        return params;
+    }
+
+    public void setParams(final List<Param> params) {
+        this.params = params;
+    }
+
+}

iis-wf/iis-wf-import/src/main/java/eu/dnetlib/iis/wf/importer/concept/model/Param.java

@@ -0,0 +1,32 @@
+package eu.dnetlib.iis.wf.importer.concept.model;
+
+/**
+ * Class representing context parameter.
+ * 
+ * @author mhorst
+ */
+public class Param {
+
+    private String name;
+
+    private String value;
+
+    public String getName() {
+        return name;
+    }
+
+    public String getValue() {
+        return value;
+    }
+
+    public Param setName(final String name) {
+        this.name = name;
+        return this;
+    }
+
+    public Param setValue(final String value) {
+        this.value = value;
+        return this;
+    }
+
+}

iis-wf/iis-wf-import/src/main/java/eu/dnetlib/iis/wf/importer/facade/ContextNotFoundException.java

@@ -0,0 +1,17 @@
+package eu.dnetlib.iis.wf.importer.facade;
+
+/**
+ * An exception indicating given context was not found.
+ * @author mhorst 
+ */
+public class ContextNotFoundException extends ContextStreamingException {
+
+
+    private static final long serialVersionUID = -1546075729881700992L;
+
+    public ContextNotFoundException(String contextId) {
+        super(contextId);
+    }
+
+
+}

iis-wf/iis-wf-import/src/main/java/eu/dnetlib/iis/wf/importer/facade/ContextStreamingException.java

@@ -0,0 +1,31 @@
+package eu.dnetlib.iis.wf.importer.facade;
+
+/**
+ * An exception indicating fatal error when streaming context content.
+ * @author mhorst 
+ */
+public class ContextStreamingException extends Exception {
+
+    private static final long serialVersionUID = -711409479484772617L;
+
+    /**
+     * Context identifier.
+     */
+    private final String contextId;
+
+
+    public ContextStreamingException(String contextId) {
+        super("Problem occured while streaming context: " + contextId);
+        this.contextId = contextId;
+    }
+
+    public ContextStreamingException(String contextId, Exception e) {
+        super("Problem occured while streaming context: " + contextId, e);
+        this.contextId = contextId;
+    }
+
+    public String getContextId() {
+        return contextId;
+    }
+
+}

iis-wf/iis-wf-import/src/main/java/eu/dnetlib/iis/wf/importer/facade/ContextStreamingFacade.java

@@ -0,0 +1,18 @@
+package eu.dnetlib.iis.wf.importer.facade;
+
+import java.io.InputStream;
+
+/**
+ * Context API streaming facade.
+ * @author mhorst
+ *
+ */
+public interface ContextStreamingFacade {
+
+    /**
+     * Returns stream for a given context identifier. 
+     * @return underlying stream
+     */
+    InputStream getStream(String contextId) throws ContextNotFoundException, ContextStreamingException;
+
+}

iis-wf/iis-wf-import/src/main/java/eu/dnetlib/iis/wf/importer/facade/ContextUrlStreamingFacade.java

@@ -0,0 +1,69 @@
+package eu.dnetlib.iis.wf.importer.facade;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Context straming facade reading data from URL.
+ * @author mhorst
+ *
+ */
+public class ContextUrlStreamingFacade implements ContextStreamingFacade {
+
+    private static final Logger log = Logger.getLogger(ContextUrlStreamingFacade.class);
+
+    private final String endpointLocation;
+
+    private final int readTimeout;
+
+    private final int connectionTimeout;
+
+
+    //------------------------ CONSTRUCTOR --------------------------
+
+    /**
+     * @param endpointLocation stream endpoint URL location
+     * @param readTimeout url read timeout
+     * @param connectionTimeout url connection timeout
+     * @throws MalformedURLException
+     */
+    public ContextUrlStreamingFacade(String endpointLocation, 
+            int readTimeout, int connectionTimeout) throws MalformedURLException {
+        this.endpointLocation = endpointLocation;
+        this.readTimeout = readTimeout;
+        this.connectionTimeout = connectionTimeout;
+    }
+
+    //------------------------ LOGIC --------------------------
+
+    @Override
+    public InputStream getStream(String contextId) throws ContextNotFoundException, ContextStreamingException {
+        try {
+            log.info(String.format("setting timeouts for streaming service: read timeout (%s) and connect timeout (%s)", 
+                    this.readTimeout, this.connectionTimeout));
+            URL url = new URL(buildUrl(endpointLocation, contextId));
+            HttpURLConnection con = (HttpURLConnection) url.openConnection();
+            con.setReadTimeout(this.readTimeout);
+            con.setConnectTimeout(this.connectionTimeout);
+            if (HttpURLConnection.HTTP_NOT_FOUND == con.getResponseCode()) {
+                throw new ContextNotFoundException(contextId);
+            } else {
+                return con.getInputStream();    
+            }    
+        } catch (IOException e) {
+            throw new ContextStreamingException(contextId, e);
+        }
+
+    }
+
+    //------------------------ PRIVATE --------------------------
+
+    private static String buildUrl(String endpointLocation, String contextId) {
+        return endpointLocation + "/" + contextId;
+    }
+}