diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java index dc6f46771..ca1c10611 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java @@ -17,8 +17,8 @@ import org.apache.hadoop.fs.Path; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; /** * Applies the parsing of a csv file and writes the Serialization of it in hdfs diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java index e665bc704..585a408f3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java @@ -4,7 +4,6 @@ package eu.dnetlib.dhp.actionmanager.project.utils; import java.io.*; import java.nio.charset.StandardCharsets; -import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; import org.apache.commons.io.IOUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -15,8 +14,8 @@ import org.apache.hadoop.fs.Path; import com.fasterxml.jackson.databind.ObjectMapper; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; /** * Applies the parsing of an excel file and writes the Serialization of it in hdfs diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregationCounter.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregationCounter.java new file mode 100644 index 000000000..bf2fd22cb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregationCounter.java @@ -0,0 +1,45 @@ + +package eu.dnetlib.dhp.aggregation.common; + +import java.io.Serializable; + +import org.apache.spark.util.LongAccumulator; + +public class AggregationCounter implements Serializable { + private LongAccumulator totalItems; + private LongAccumulator errorItems; + private LongAccumulator processedItems; + + public AggregationCounter() { + } + + public AggregationCounter(LongAccumulator totalItems, LongAccumulator errorItems, LongAccumulator processedItems) { + this.totalItems = totalItems; + this.errorItems = errorItems; + this.processedItems = processedItems; + } + + public LongAccumulator getTotalItems() { + return totalItems; + } + + public void setTotalItems(LongAccumulator totalItems) { + this.totalItems = totalItems; + } + + public LongAccumulator getErrorItems() { + return errorItems; + } + + public void setErrorItems(LongAccumulator errorItems) { + this.errorItems = errorItems; + } + + public LongAccumulator getProcessedItems() { + return processedItems; + } + + public void setProcessedItems(LongAccumulator processedItems) { + this.processedItems = processedItems; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java index c0bd4c940..c9c29b4ea 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java @@ -5,12 +5,9 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.ByteArrayInputStream; import java.nio.charset.StandardCharsets; -import java.util.HashMap; -import java.util.Map; import java.util.Objects; import java.util.Optional; -import org.apache.commons.cli.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.IntWritable; @@ -22,7 +19,6 @@ import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; import org.dom4j.Node; @@ -35,9 +31,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; import eu.dnetlib.dhp.model.mdstore.Provenance; -import eu.dnetlib.message.Message; import eu.dnetlib.message.MessageManager; -import eu.dnetlib.message.MessageType; public class GenerateNativeStoreSparkJob { @@ -46,100 +40,62 @@ public class GenerateNativeStoreSparkJob { public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - GenerateNativeStoreSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/collection/collection_input_parameters.json"))); + IOUtils + .toString( + GenerateNativeStoreSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/collection_input_parameters.json"))); parser.parseArgument(args); final ObjectMapper jsonMapper = new ObjectMapper(); - final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class); - final long dateOfCollection = new Long(parser.get("dateOfCollection")); + final String provenanceArgument = parser.get("provenance"); + log.info("Provenance is {}", provenanceArgument); + final Provenance provenance = jsonMapper.readValue(provenanceArgument, Provenance.class); + final String dateOfCollectionArgs = parser.get("dateOfCollection"); + log.info("dateOfCollection is {}", dateOfCollectionArgs); + final long dateOfCollection = new Long(dateOfCollectionArgs); + final String sequenceFileInputPath = parser.get("input"); + log.info("sequenceFileInputPath is {}", dateOfCollectionArgs); Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final Map ongoingMap = new HashMap<>(); - final Map reportMap = new HashMap<>(); - - final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest")); - SparkConf conf = new SparkConf(); runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + conf, + isSparkSessionManaged, + spark -> { + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - final JavaPairRDD inputRDD = sc - .sequenceFile(parser.get("input"), IntWritable.class, Text.class); + final JavaPairRDD inputRDD = sc + .sequenceFile(sequenceFileInputPath, IntWritable.class, Text.class); - final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems"); - final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords"); + final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems"); + final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords"); - final MessageManager manager = new MessageManager( - parser.get("rabbitHost"), - parser.get("rabbitUser"), - parser.get("rabbitPassword"), - false, - false, - null); + final JavaRDD nativeStore = inputRDD + .map( + item -> parseRecord( + item._2().toString(), + parser.get("xpath"), + parser.get("encoding"), + provenance, + dateOfCollection, + totalItems, + invalidRecords)) + .filter(Objects::nonNull) + .distinct(); - final JavaRDD mappeRDD = inputRDD - .map( - item -> parseRecord( - item._2().toString(), - parser.get("xpath"), - parser.get("encoding"), - provenance, - dateOfCollection, - totalItems, - invalidRecords)) - .filter(Objects::nonNull) - .distinct(); + final Encoder encoder = Encoders.bean(MetadataRecord.class); + final Dataset mdstore = spark.createDataset(nativeStore.rdd(), encoder); + final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords"); + mdStoreRecords.add(mdstore.count()); - ongoingMap.put("ongoing", "0"); - if (!test) { - manager - .sendMessage( - new Message( - parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap), - parser.get("rabbitOngoingQueue"), - true, - false); - } + mdstore.write().format("parquet").save(parser.get("output")); - final Encoder encoder = Encoders.bean(MetadataRecord.class); - final Dataset mdstore = spark.createDataset(mappeRDD.rdd(), encoder); - final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords"); - mdStoreRecords.add(mdstore.count()); - ongoingMap.put("ongoing", "" + totalItems.value()); - if (!test) { - manager - .sendMessage( - new Message( - parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap), - parser.get("rabbitOngoingQueue"), - true, - false); - } - mdstore.write().format("parquet").save(parser.get("output")); - reportMap.put("inputItem", "" + totalItems.value()); - reportMap.put("invalidRecords", "" + invalidRecords.value()); - reportMap.put("mdStoreSize", "" + mdStoreRecords.value()); - if (!test) { - manager - .sendMessage( - new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap), - parser.get("rabbitReportQueue"), - true, - false); - manager.close(); - } - }); + }); } @@ -166,12 +122,9 @@ public class GenerateNativeStoreSparkJob { } return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection); } catch (Throwable e) { - if (invalidRecords != null) - invalidRecords.add(1); - e.printStackTrace(); + invalidRecords.add(1); return null; } } - } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 4a0c70c45..7146e610e 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -4,9 +4,9 @@ package eu.dnetlib.dhp.collection.plugin; import java.util.stream.Stream; import eu.dnetlib.collector.worker.model.ApiDescriptor; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; +import eu.dnetlib.dhp.collection.worker.CollectorException; public interface CollectorPlugin { - Stream collect(ApiDescriptor api) throws DnetCollectorException; + Stream collect(ApiDescriptor api) throws CollectorException; } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java index 7f71f401d..c4c52271a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java @@ -15,7 +15,7 @@ import com.google.common.collect.Lists; import eu.dnetlib.collector.worker.model.ApiDescriptor; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; +import eu.dnetlib.dhp.collection.worker.CollectorException; public class OaiCollectorPlugin implements CollectorPlugin { @@ -27,7 +27,7 @@ public class OaiCollectorPlugin implements CollectorPlugin { private OaiIteratorFactory oaiIteratorFactory; @Override - public Stream collect(final ApiDescriptor api) throws DnetCollectorException { + public Stream collect(final ApiDescriptor api) throws CollectorException { final String baseUrl = api.getBaseUrl(); final String mdFormat = api.getParams().get(FORMAT_PARAM); final String setParam = api.getParams().get(OAI_SET_PARAM); @@ -46,19 +46,19 @@ public class OaiCollectorPlugin implements CollectorPlugin { } if (baseUrl == null || baseUrl.isEmpty()) { - throw new DnetCollectorException("Param 'baseurl' is null or empty"); + throw new CollectorException("Param 'baseurl' is null or empty"); } if (mdFormat == null || mdFormat.isEmpty()) { - throw new DnetCollectorException("Param 'mdFormat' is null or empty"); + throw new CollectorException("Param 'mdFormat' is null or empty"); } if (fromDate != null && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { - throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + fromDate); + throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate); } if (untilDate != null && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) { - throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + untilDate); + throw new CollectorException("Invalid date (YYYY-MM-DD): " + untilDate); } final Iterator> iters = sets diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java index d61f13fb5..e54bae67d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java @@ -16,7 +16,7 @@ import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; +import eu.dnetlib.dhp.collection.worker.CollectorException; import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner; @@ -58,7 +58,7 @@ public class OaiIterator implements Iterator { this.started = true; try { this.token = firstPage(); - } catch (final DnetCollectorException e) { + } catch (final CollectorException e) { throw new RuntimeException(e); } } @@ -80,7 +80,7 @@ public class OaiIterator implements Iterator { while (queue.isEmpty() && token != null && !token.isEmpty()) { try { token = otherPages(token); - } catch (final DnetCollectorException e) { + } catch (final CollectorException e) { throw new RuntimeException(e); } } @@ -92,7 +92,7 @@ public class OaiIterator implements Iterator { public void remove() { } - private String firstPage() throws DnetCollectorException { + private String firstPage() throws CollectorException { try { String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8"); if (set != null && !set.isEmpty()) { @@ -108,7 +108,7 @@ public class OaiIterator implements Iterator { return downloadPage(url); } catch (final UnsupportedEncodingException e) { - throw new DnetCollectorException(e); + throw new CollectorException(e); } } @@ -126,18 +126,18 @@ public class OaiIterator implements Iterator { return result.trim(); } - private String otherPages(final String resumptionToken) throws DnetCollectorException { + private String otherPages(final String resumptionToken) throws CollectorException { try { return downloadPage( baseUrl + "?verb=ListRecords&resumptionToken=" + URLEncoder.encode(resumptionToken, "UTF-8")); } catch (final UnsupportedEncodingException e) { - throw new DnetCollectorException(e); + throw new CollectorException(e); } } - private String downloadPage(final String url) throws DnetCollectorException { + private String downloadPage(final String url) throws CollectorException { final String xml = httpConnector.getInputSource(url); Document doc; @@ -151,7 +151,7 @@ public class OaiIterator implements Iterator { } catch (final DocumentException e1) { final String resumptionToken = extractResumptionToken(xml); if (resumptionToken == null) { - throw new DnetCollectorException("Error parsing cleaned document:" + cleaned, e1); + throw new CollectorException("Error parsing cleaned document:" + cleaned, e1); } return resumptionToken; } @@ -164,7 +164,7 @@ public class OaiIterator implements Iterator { log.warn("noRecordsMatch for oai call: " + url); return null; } else { - throw new DnetCollectorException(code + " - " + errorNode.getText()); + throw new CollectorException(code + " - " + errorNode.getText()); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorException.java similarity index 56% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorException.java index f40962c21..71d225f13 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorException.java @@ -1,16 +1,16 @@ package eu.dnetlib.dhp.collection.worker; -public class DnetCollectorException extends Exception { +public class CollectorException extends Exception { /** */ private static final long serialVersionUID = -290723075076039757L; - public DnetCollectorException() { + public CollectorException() { super(); } - public DnetCollectorException( + public CollectorException( final String message, final Throwable cause, final boolean enableSuppression, @@ -18,15 +18,15 @@ public class DnetCollectorException extends Exception { super(message, cause, enableSuppression, writableStackTrace); } - public DnetCollectorException(final String message, final Throwable cause) { + public CollectorException(final String message, final Throwable cause) { super(message, cause); } - public DnetCollectorException(final String message) { + public CollectorException(final String message) { super(message); } - public DnetCollectorException(final Throwable cause) { + public CollectorException(final Throwable cause) { super(cause); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorker.java new file mode 100644 index 000000000..380db641a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorker.java @@ -0,0 +1,93 @@ + +package eu.dnetlib.dhp.collection.worker; + +import java.io.IOException; +import java.net.URI; +import java.util.concurrent.atomic.AtomicInteger; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IntWritable; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.collector.worker.model.ApiDescriptor; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; + +public class CollectorWorker { + + private static final Logger log = LoggerFactory.getLogger(CollectorWorker.class); + + private final CollectorPluginFactory collectorPluginFactory; + + private final ApiDescriptor api; + + private final String hdfsuri; + + private final String hdfsPath; + + public CollectorWorker( + final CollectorPluginFactory collectorPluginFactory, + final ApiDescriptor api, + final String hdfsuri, + final String hdfsPath) { + this.collectorPluginFactory = collectorPluginFactory; + this.api = api; + this.hdfsuri = hdfsuri; + this.hdfsPath = hdfsPath; + + } + + public void collect() throws CollectorException { + try { + final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol()); + + // ====== Init HDFS File System Object + Configuration conf = new Configuration(); + // Set FileSystem URI + conf.set("fs.defaultFS", hdfsuri); + // Because of Maven + conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); + conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); + + System.setProperty("hadoop.home.dir", "/"); + // Get the filesystem - HDFS + FileSystem.get(URI.create(hdfsuri), conf); + Path hdfswritepath = new Path(hdfsPath); + + log.info("Created path " + hdfswritepath.toString()); + + final AtomicInteger counter = new AtomicInteger(0); + try (SequenceFile.Writer writer = SequenceFile + .createWriter( + conf, + SequenceFile.Writer.file(hdfswritepath), + SequenceFile.Writer.keyClass(IntWritable.class), + SequenceFile.Writer.valueClass(Text.class))) { + final IntWritable key = new IntWritable(counter.get()); + final Text value = new Text(); + plugin + .collect(api) + .forEach( + content -> { + key.set(counter.getAndIncrement()); + value.set(content); + try { + writer.append(key, value); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + } + } catch (Throwable e) { + throw new CollectorException("Error on collecting ", e); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorkerApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorkerApplication.java new file mode 100644 index 000000000..5e8d0f9c2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorkerApplication.java @@ -0,0 +1,55 @@ + +package eu.dnetlib.dhp.collection.worker; + +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.collector.worker.model.ApiDescriptor; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; + +/** + * DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into HDFS. This module + * will be executed on the hadoop cluster and taking in input some parameters that tells it which is the right collector + * plugin to use and where store the data into HDFS path + * + * @author Sandro La Bruzzo + */ +public class CollectorWorkerApplication { + + private static final Logger log = LoggerFactory.getLogger(CollectorWorkerApplication.class); + + private static final CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory(); + + /** + * @param args + */ + public static void main(final String[] args) throws Exception { + + final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser( + IOUtils + .toString( + CollectorWorker.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/collector_parameter.json"))); + argumentParser.parseArgument(args); + + final String hdfsuri = argumentParser.get("namenode"); + + log.info("hdfsURI is {}", hdfsuri); + final String hdfsPath = argumentParser.get("hdfsPath"); + log.info("hdfsPath is {}" + hdfsPath); + final String apiDescriptor = argumentParser.get("apidescriptor"); + log.info("apiDescriptor is {}" + apiDescriptor); + + final ObjectMapper jsonMapper = new ObjectMapper(); + + final ApiDescriptor api = jsonMapper.readValue(apiDescriptor, ApiDescriptor.class); + + final CollectorWorker worker = new CollectorWorker(collectorPluginFactory, api, hdfsuri, hdfsPath); + worker.collect(); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java deleted file mode 100644 index e686ad518..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java +++ /dev/null @@ -1,139 +0,0 @@ - -package eu.dnetlib.dhp.collection.worker; - -import java.io.IOException; -import java.net.URI; -import java.util.HashMap; -import java.util.Map; -import java.util.concurrent.atomic.AtomicInteger; - -import org.apache.hadoop.conf.Configuration; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.hadoop.io.IntWritable; -import org.apache.hadoop.io.SequenceFile; -import org.apache.hadoop.io.Text; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.collector.worker.model.ApiDescriptor; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; -import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; -import eu.dnetlib.message.Message; -import eu.dnetlib.message.MessageManager; -import eu.dnetlib.message.MessageType; - -public class DnetCollectorWorker { - - private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class); - - private final CollectorPluginFactory collectorPluginFactory; - - private final ArgumentApplicationParser argumentParser; - - private final MessageManager manager; - - public DnetCollectorWorker( - final CollectorPluginFactory collectorPluginFactory, - final ArgumentApplicationParser argumentParser, - final MessageManager manager) - throws DnetCollectorException { - this.collectorPluginFactory = collectorPluginFactory; - this.argumentParser = argumentParser; - this.manager = manager; - } - - public void collect() throws DnetCollectorException { - try { - final ObjectMapper jsonMapper = new ObjectMapper(); - final ApiDescriptor api = jsonMapper.readValue(argumentParser.get("apidescriptor"), ApiDescriptor.class); - - final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol()); - - final String hdfsuri = argumentParser.get("namenode"); - - // ====== Init HDFS File System Object - Configuration conf = new Configuration(); - // Set FileSystem URI - conf.set("fs.defaultFS", hdfsuri); - // Because of Maven - conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); - conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); - - System.setProperty("HADOOP_USER_NAME", argumentParser.get("userHDFS")); - System.setProperty("hadoop.home.dir", "/"); - // Get the filesystem - HDFS - FileSystem.get(URI.create(hdfsuri), conf); - Path hdfswritepath = new Path(argumentParser.get("hdfsPath")); - - log.info("Created path " + hdfswritepath.toString()); - - final Map ongoingMap = new HashMap<>(); - final Map reportMap = new HashMap<>(); - final AtomicInteger counter = new AtomicInteger(0); - try (SequenceFile.Writer writer = SequenceFile - .createWriter( - conf, - SequenceFile.Writer.file(hdfswritepath), - SequenceFile.Writer.keyClass(IntWritable.class), - SequenceFile.Writer.valueClass(Text.class))) { - final IntWritable key = new IntWritable(counter.get()); - final Text value = new Text(); - plugin - .collect(api) - .forEach( - content -> { - key.set(counter.getAndIncrement()); - value.set(content); - if (counter.get() % 10 == 0) { - try { - ongoingMap.put("ongoing", "" + counter.get()); - log - .debug( - "Sending message: " - + manager - .sendMessage( - new Message( - argumentParser.get("workflowId"), - "Collection", - MessageType.ONGOING, - ongoingMap), - argumentParser.get("rabbitOngoingQueue"), - true, - false)); - } catch (Exception e) { - log.error("Error on sending message ", e); - } - } - try { - writer.append(key, value); - } catch (IOException e) { - throw new RuntimeException(e); - } - }); - } - ongoingMap.put("ongoing", "" + counter.get()); - manager - .sendMessage( - new Message( - argumentParser.get("workflowId"), "Collection", MessageType.ONGOING, ongoingMap), - argumentParser.get("rabbitOngoingQueue"), - true, - false); - reportMap.put("collected", "" + counter.get()); - manager - .sendMessage( - new Message( - argumentParser.get("workflowId"), "Collection", MessageType.REPORT, reportMap), - argumentParser.get("rabbitOngoingQueue"), - true, - false); - manager.close(); - } catch (Throwable e) { - throw new DnetCollectorException("Error on collecting ", e); - } - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java deleted file mode 100644 index da30e8793..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java +++ /dev/null @@ -1,49 +0,0 @@ - -package eu.dnetlib.dhp.collection.worker; - -import org.apache.commons.io.IOUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; -import eu.dnetlib.message.MessageManager; - -/** - * DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into HDFS. This module - * will be executed on the hadoop cluster and taking in input some parameters that tells it which is the right collector - * plugin to use and where store the data into HDFS path - * - * @author Sandro La Bruzzo - */ -public class DnetCollectorWorkerApplication { - - private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class); - - private static final CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory(); - - private static ArgumentApplicationParser argumentParser; - - /** @param args */ - public static void main(final String[] args) throws Exception { - - argumentParser = new ArgumentApplicationParser( - IOUtils - .toString( - DnetCollectorWorker.class - .getResourceAsStream( - "/eu/dnetlib/collector/worker/collector_parameter.json"))); - argumentParser.parseArgument(args); - log.info("hdfsPath =" + argumentParser.get("hdfsPath")); - log.info("json = " + argumentParser.get("apidescriptor")); - final MessageManager manager = new MessageManager( - argumentParser.get("rabbitHost"), - argumentParser.get("rabbitUser"), - argumentParser.get("rabbitPassword"), - false, - false, - null); - final DnetCollectorWorker worker = new DnetCollectorWorker(collectorPluginFactory, argumentParser, manager); - worker.collect(); - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java index 7a0028e79..6b070b191 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginFactory.java @@ -3,18 +3,18 @@ package eu.dnetlib.dhp.collection.worker.utils; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; +import eu.dnetlib.dhp.collection.worker.CollectorException; public class CollectorPluginFactory { - public CollectorPlugin getPluginByProtocol(final String protocol) throws DnetCollectorException { + public CollectorPlugin getPluginByProtocol(final String protocol) throws CollectorException { if (protocol == null) - throw new DnetCollectorException("protocol cannot be null"); + throw new CollectorException("protocol cannot be null"); switch (protocol.toLowerCase().trim()) { case "oai": return new OaiCollectorPlugin(); default: - throw new DnetCollectorException("UNknown protocol"); + throw new CollectorException("UNknown protocol"); } } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java index 5d6108fad..ff3c18aba 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/HttpConnector.java @@ -19,7 +19,7 @@ import org.apache.commons.lang.math.NumberUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; +import eu.dnetlib.dhp.collection.worker.CollectorException; public class HttpConnector { @@ -42,9 +42,9 @@ public class HttpConnector { * * @param requestUrl the URL * @return the content of the downloaded resource - * @throws DnetCollectorException when retrying more than maxNumberOfRetry times + * @throws CollectorException when retrying more than maxNumberOfRetry times */ - public String getInputSource(final String requestUrl) throws DnetCollectorException { + public String getInputSource(final String requestUrl) throws CollectorException { return attemptDownlaodAsString(requestUrl, 1, new CollectorPluginErrorLogList()); } @@ -53,15 +53,15 @@ public class HttpConnector { * * @param requestUrl the URL * @return the content of the downloaded resource as InputStream - * @throws DnetCollectorException when retrying more than maxNumberOfRetry times + * @throws CollectorException when retrying more than maxNumberOfRetry times */ - public InputStream getInputSourceAsStream(final String requestUrl) throws DnetCollectorException { + public InputStream getInputSourceAsStream(final String requestUrl) throws CollectorException { return attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); } private String attemptDownlaodAsString( final String requestUrl, final int retryNumber, final CollectorPluginErrorLogList errorList) - throws DnetCollectorException { + throws CollectorException { try { final InputStream s = attemptDownload(requestUrl, 1, new CollectorPluginErrorLogList()); try { @@ -75,16 +75,16 @@ public class HttpConnector { IOUtils.closeQuietly(s); } } catch (final InterruptedException e) { - throw new DnetCollectorException(e); + throw new CollectorException(e); } } private InputStream attemptDownload( final String requestUrl, final int retryNumber, final CollectorPluginErrorLogList errorList) - throws DnetCollectorException { + throws CollectorException { if (retryNumber > maxNumberOfRetry) { - throw new DnetCollectorException("Max number of retries exceeded. Cause: \n " + errorList); + throw new CollectorException("Max number of retries exceeded. Cause: \n " + errorList); } log.debug("Downloading " + requestUrl + " - try: " + retryNumber); @@ -144,7 +144,7 @@ public class HttpConnector { return attemptDownload(requestUrl, retryNumber + 1, errorList); } } catch (final InterruptedException e) { - throw new DnetCollectorException(e); + throw new CollectorException(e); } } @@ -173,13 +173,13 @@ public class HttpConnector { } private String obtainNewLocation(final Map> headerMap) - throws DnetCollectorException { + throws CollectorException { for (final String key : headerMap.keySet()) { if (key != null && key.toLowerCase().equals("location") && headerMap.get(key).size() > 0) { return headerMap.get(key).get(0); } } - throw new DnetCollectorException( + throw new CollectorException( "The requested url has been MOVED, but 'location' param is MISSING"); } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/DnetTransformationException.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/DnetTransformationException.java new file mode 100644 index 000000000..45bd844e2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/DnetTransformationException.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.transformation; + +public class DnetTransformationException extends Exception { + + public DnetTransformationException() { + super(); + } + + public DnetTransformationException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public DnetTransformationException(final String message, final Throwable cause) { + super(message, cause); + } + + public DnetTransformationException(final String message) { + super(message); + } + + public DnetTransformationException(final Throwable cause) { + super(cause); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java index 8737d36ef..c6ed5a1e3 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformSparkJobNode.java @@ -9,9 +9,10 @@ import java.util.Map; import java.util.Objects; import java.util.Optional; -import org.apache.commons.cli.*; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; @@ -24,12 +25,15 @@ import org.dom4j.io.SAXReader; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import eu.dnetlib.dhp.aggregation.common.AggregationCounter; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; -import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper; +import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction; import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.message.Message; import eu.dnetlib.message.MessageManager; import eu.dnetlib.message.MessageType; @@ -55,67 +59,38 @@ public class TransformSparkJobNode { .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("input"); - final String outputPath = parser.get("output"); - final String workflowId = parser.get("workflowId"); - final String trasformationRule = extractXSLTFromTR( - Objects.requireNonNull(DHPUtils.decompressString(parser.get("transformationRule")))); + final String inputPath = parser.get("mdstoreInputPath"); + final String outputPath = parser.get("mdstoreOutputPath"); + // TODO this variable will be used after implementing Messaging with DNet Aggregator - final String rabbitUser = parser.get("rabbitUser"); - final String rabbitPassword = parser.get("rabbitPassword"); - final String rabbitHost = parser.get("rabbitHost"); - final String rabbitReportQueue = parser.get("rabbitReportQueue"); - final long dateOfCollection = new Long(parser.get("dateOfCollection")); - final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest")); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info(String.format("isLookupUrl: %s", isLookupUrl)); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, - spark -> { - final Encoder encoder = Encoders.bean(MetadataRecord.class); - final Dataset mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder); - final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems"); - final LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems"); - final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems"); - final Map vocabularies = new HashMap<>(); - vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages")); - final TransformFunction transformFunction = new TransformFunction( - totalItems, - errorItems, - transformedItems, - trasformationRule, - dateOfCollection, - vocabularies); - mdstoreInput.map(transformFunction, encoder).write().format("parquet").save(outputPath); - if (rabbitHost != null) { - System.out.println("SEND FINAL REPORT"); - final Map reportMap = new HashMap<>(); - reportMap.put("inputItem", "" + totalItems.value()); - reportMap.put("invalidRecords", "" + errorItems.value()); - reportMap.put("mdStoreSize", "" + transformedItems.value()); - System.out.println(new Message(workflowId, "Transform", MessageType.REPORT, reportMap)); - if (!test) { - final MessageManager manager = new MessageManager(rabbitHost, rabbitUser, rabbitPassword, false, - false, - null); - manager - .sendMessage( - new Message(workflowId, "Transform", MessageType.REPORT, reportMap), - rabbitReportQueue, - true, - false); - manager.close(); - } - } - }); - + spark -> transformRecords(parser.getObjectMap(), isLookupService, spark, inputPath, outputPath)); } - private static String extractXSLTFromTR(final String tr) throws DocumentException { - SAXReader reader = new SAXReader(); - Document document = reader.read(new ByteArrayInputStream(tr.getBytes())); - Node node = document.selectSingleNode("//CODE/*[local-name()='stylesheet']"); - return node.asXML(); + public static void transformRecords(final Map args, final ISLookUpService isLookUpService, + final SparkSession spark, final String inputPath, final String outputPath) throws DnetTransformationException { + + final LongAccumulator totalItems = spark.sparkContext().longAccumulator("TotalItems"); + final LongAccumulator errorItems = spark.sparkContext().longAccumulator("errorItems"); + final LongAccumulator transformedItems = spark.sparkContext().longAccumulator("transformedItems"); + final AggregationCounter ct = new AggregationCounter(totalItems, errorItems, transformedItems); + final Encoder encoder = Encoders.bean(MetadataRecord.class); + final Dataset mdstoreInput = spark.read().format("parquet").load(inputPath).as(encoder); + final MapFunction XSLTTransformationFunction = TransformationFactory + .getTransformationPlugin(args, ct, isLookUpService); + mdstoreInput.map(XSLTTransformationFunction, encoder).write().save(outputPath); + + log.info("Transformed item " + ct.getProcessedItems().count()); + log.info("Total item " + ct.getTotalItems().count()); + log.info("Transformation Error item " + ct.getErrorItems().count()); } + } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformationFactory.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformationFactory.java new file mode 100644 index 000000000..58292139a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformationFactory.java @@ -0,0 +1,69 @@ + +package eu.dnetlib.dhp.transformation; + +import java.util.List; +import java.util.Map; + +import org.apache.commons.lang3.StringUtils; +import org.apache.spark.api.java.function.MapFunction; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.aggregation.common.AggregationCounter; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.model.mdstore.MetadataRecord; +import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class TransformationFactory { + + private static final Logger log = LoggerFactory.getLogger(TransformationFactory.class); + public static final String TRULE_XQUERY = "for $x in collection('/db/DRIVER/TransformationRuleDSResources/TransformationRuleDSResourceType') where $x//TITLE = \"%s\" return $x//CODE/text()"; + + public static MapFunction getTransformationPlugin( + final Map jobArgument, final AggregationCounter counters, final ISLookUpService isLookupService) + throws DnetTransformationException { + + try { + final String transformationPlugin = jobArgument.get("transformationPlugin"); + + log.info("Transformation plugin required " + transformationPlugin); + switch (transformationPlugin) { + case "XSLT_TRANSFORM": { + final String transformationRuleName = jobArgument.get("transformationRuleTitle"); + if (StringUtils.isBlank(transformationRuleName)) + throw new DnetTransformationException("Missing Parameter transformationRule"); + final VocabularyGroup vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService); + + final String transformationRule = queryTransformationRuleFromIS( + transformationRuleName, isLookupService); + + final long dateOfTransformation = new Long(jobArgument.get("dateOfTransformation")); + return new XSLTTransformationFunction(counters, transformationRule, dateOfTransformation, + vocabularies); + + } + default: + throw new DnetTransformationException( + "transformation plugin does not exists for " + transformationPlugin); + + } + + } catch (Throwable e) { + throw new DnetTransformationException(e); + } + } + + private static String queryTransformationRuleFromIS(final String transformationRuleName, + final ISLookUpService isLookUpService) throws Exception { + final String query = String.format(TRULE_XQUERY, transformationRuleName); + log.info("asking query to IS: " + query); + List result = isLookUpService.quickSearchProfile(query); + + if (result == null || result.isEmpty()) + throw new DnetTransformationException( + "Unable to find transformation rule with name: " + transformationRuleName); + return result.get(0); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java similarity index 61% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java index 7f9b6646c..7b0fdd484 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/functions/Cleaner.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/Cleaner.java @@ -1,19 +1,16 @@ -package eu.dnetlib.dhp.transformation.functions; +package eu.dnetlib.dhp.transformation.xslt; -import java.util.Map; -import java.util.Optional; - -import eu.dnetlib.dhp.transformation.vocabulary.Term; -import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Qualifier; import net.sf.saxon.s9api.*; import scala.Serializable; public class Cleaner implements ExtensionFunction, Serializable { - private final Map vocabularies; + private final VocabularyGroup vocabularies; - public Cleaner(Map vocabularies) { + public Cleaner(final VocabularyGroup vocabularies) { this.vocabularies = vocabularies; } @@ -39,14 +36,9 @@ public class Cleaner implements ExtensionFunction, Serializable { public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException { final String currentValue = xdmValues[0].itemAt(0).getStringValue(); final String vocabularyName = xdmValues[1].itemAt(0).getStringValue(); - Optional cleanedValue = vocabularies - .get(vocabularyName) - .getTerms() - .stream() - .filter(it -> it.getNativeName().equalsIgnoreCase(currentValue)) - .findAny(); + Qualifier cleanedValue = vocabularies.getSynonymAsQualifier(vocabularyName, currentValue); return new XdmAtomicValue( - cleanedValue.isPresent() ? cleanedValue.get().getCode() : currentValue); + cleanedValue != null ? cleanedValue.getClassid() : currentValue); } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java similarity index 67% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java index f4bf78e18..d8707cd76 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/TransformFunction.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java @@ -1,41 +1,35 @@ -package eu.dnetlib.dhp.transformation; +package eu.dnetlib.dhp.transformation.xslt; import java.io.ByteArrayInputStream; import java.io.StringWriter; -import java.util.Map; import javax.xml.transform.stream.StreamSource; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.util.LongAccumulator; +import eu.dnetlib.dhp.aggregation.common.AggregationCounter; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; -import eu.dnetlib.dhp.transformation.functions.Cleaner; -import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; import net.sf.saxon.s9api.*; -public class TransformFunction implements MapFunction { +public class XSLTTransformationFunction implements MapFunction { + + private final AggregationCounter aggregationCounter; - private final LongAccumulator totalItems; - private final LongAccumulator errorItems; - private final LongAccumulator transformedItems; private final String transformationRule; + private final Cleaner cleanFunction; private final long dateOfTransformation; - public TransformFunction( - LongAccumulator totalItems, - LongAccumulator errorItems, - LongAccumulator transformedItems, + public XSLTTransformationFunction( + final AggregationCounter aggregationCounter, final String transformationRule, long dateOfTransformation, - final Map vocabularies) + final VocabularyGroup vocabularies) throws Exception { - this.totalItems = totalItems; - this.errorItems = errorItems; - this.transformedItems = transformedItems; + this.aggregationCounter = aggregationCounter; this.transformationRule = transformationRule; this.dateOfTransformation = dateOfTransformation; cleanFunction = new Cleaner(vocabularies); @@ -43,7 +37,7 @@ public class TransformFunction implements MapFunction + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml index 3e7f68401..38cd83da7 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml @@ -1,10 +1,5 @@ - - sequenceFilePath - the path to store the sequence file of the native metadata collected - - mdStorePath the path of the native mdstore @@ -39,72 +34,52 @@ The identifier of the workflow + + ${jobTracker} + ${nameNode} + - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - + - ${jobTracker} - ${nameNode} - eu.dnetlib.dhp.collection.worker.DnetCollectorWorker - -p${sequenceFilePath} - -a${apiDescription} - -n${nameNode} - -rh${rmq_host} - -ru${rmq_user} - -rp${rmq_pwd} - -rr${rmq_report} - -ro${rmq_ongoing} - -usandro.labruzzo - -w${workflowId} + eu.dnetlib.dhp.collection.worker.CollectorWorkerApplication + --hdfsPath${workingDir}/sequenceFile_${mdstoreVersion} + --apidescriptor${apiDescription} + --namenode${nameNode} + - ${jobTracker} - ${nameNode} yarn cluster - GenerateNativeStoreSparkJob + Generate Native MetadataStore eu.dnetlib.dhp.collection.GenerateNativeStoreSparkJob - dhp-aggregations-1.0.0-SNAPSHOT.jar - --num-executors 50 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" - --encoding ${metadataEncoding} - --dateOfCollection ${timestamp} - --provenance ${dataSourceInfo} + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --encoding${metadataEncoding} + --dateOfCollection${timestamp} + --provenance${dataSourceInfo} --xpath${identifierPath} - --input${sequenceFilePath} + --input${workingDir}/sequenceFile --output${mdStorePath} - -rh${rmq_host} - -ru${rmq_user} - -rp${rmq_pwd} - -rr${rmq_report} - -ro${rmq_ongoing} -w${workflowId} - - - - - - - - diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collector/worker/collector_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collector/worker/collector_parameter.json deleted file mode 100644 index c247d15e4..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collector/worker/collector_parameter.json +++ /dev/null @@ -1,12 +0,0 @@ -[ - {"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true}, - {"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true}, - {"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true}, - {"paramName":"u", "paramLongName":"userHDFS", "paramDescription": "the user wich create the hdfs seq file", "paramRequired": true}, - {"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rp", "paramLongName":"rabbitPassword", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true}, - {"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true}, - {"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true}, - {"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true} -] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/config-default.xml new file mode 100644 index 000000000..2e0ed9aee --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/config-default.xml @@ -0,0 +1,18 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/workflow.xml index 4b1e3d84b..b36bc3766 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/oozie_app/workflow.xml @@ -2,7 +2,7 @@ mdstoreInputPath - the path of the input MDStore + the path of the native MDStore @@ -11,66 +11,57 @@ - transformationRule + transformationRuleTitle The transformation Rule to apply - timestamp - The timestamp of the collection date + transformationPlugin + The transformation Plugin - workflowId - The identifier of the workflow + dateOfTransformation + The timestamp of the transformation date + + - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - + - ${jobTracker} - ${nameNode} yarn cluster - MDBuilder + Transform MetadataStore eu.dnetlib.dhp.transformation.TransformSparkJobNode - dhp-aggregations-1.0.0-SNAPSHOT.jar - --num-executors 50 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" - --dateOfCollection ${timestamp} - -mt yarn - --input${mdstoreInputPath} - --output${mdstoreOutputPath} - -w${workflowId} - -tr${transformationRule} - -ru${rmq_user} - -rp${rmq_pwd} - -rh${rmq_host} - -ro${rmq_ongoing} - -rr${rmq_report} + dhp-aggregations-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --mdstoreInputPath${mdstoreInputPath} + --mdstoreOutputPath${mdstoreOutputPath} + --dateOfTransformation${dateOfTransformation} + --transformationPlugin${transformationPlugin} + --transformationRuleTitle${transformationRuleTitle} + + - - - - - - - - + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json index 4bb5fd56a..cbd2f25ab 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/transformation/transformation_input_parameters.json @@ -7,68 +7,42 @@ }, { "paramName": "d", - "paramLongName": "dateOfCollection", + "paramLongName": "dateOfTransformation", "paramDescription": "the date when the record has been stored", "paramRequired": true }, { "paramName": "i", - "paramLongName": "input", + "paramLongName": "mdstoreInputPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true }, { "paramName": "o", - "paramLongName": "output", + "paramLongName": "mdstoreOutputPath", "paramDescription": "the path of the result DataFrame on HDFS", "paramRequired": true }, - { - "paramName": "w", - "paramLongName": "workflowId", - "paramDescription": "the identifier of the dnet Workflow", - "paramRequired": true - }, { "paramName": "tr", - "paramLongName": "transformationRule", + "paramLongName": "transformationRuleTitle", "paramDescription": "the transformation Rule to apply to the input MDStore", "paramRequired": true }, + { - "paramName": "ru", - "paramLongName": "rabbitUser", - "paramDescription": "the user to connect with RabbitMq for messaging", + "paramName": "i", + "paramLongName": "isLookupUrl", + "paramDescription": "the Information System Service LookUp URL", "paramRequired": true }, + + + { - "paramName": "rp", - "paramLongName": "rabbitPassword", - "paramDescription": "the password to connect with RabbitMq for messaging", + "paramName": "tp", + "paramLongName": "transformationPlugin", + "paramDescription": "the transformation plugin to apply", "paramRequired": true - }, - { - "paramName": "rh", - "paramLongName": "rabbitHost", - "paramDescription": "the host of the RabbitMq server", - "paramRequired": true - }, - { - "paramName": "ro", - "paramLongName": "rabbitOngoingQueue", - "paramDescription": "the name of the ongoing queue", - "paramRequired": true - }, - { - "paramName": "rr", - "paramLongName": "rabbitReportQueue", - "paramDescription": "the name of the report queue", - "paramRequired": true - }, - { - "paramName": "t", - "paramLongName": "isTest", - "paramDescription": "the name of the report queue", - "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java index c1142ad9c..5c37e9ec3 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java @@ -6,16 +6,15 @@ import java.nio.file.Files; import java.nio.file.Path; import java.util.List; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; -import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; import org.apache.poi.openxml4j.exceptions.InvalidFormatException; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; - import eu.dnetlib.dhp.actionmanager.project.utils.EXCELParser; +import eu.dnetlib.dhp.collection.worker.CollectorException; +import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; @Disabled public class EXCELParserTest { @@ -31,7 +30,7 @@ public class EXCELParserTest { } @Test - public void test1() throws DnetCollectorException, IOException, InvalidFormatException, ClassNotFoundException, + public void test1() throws CollectorException, IOException, InvalidFormatException, ClassNotFoundException, IllegalAccessException, InstantiationException { EXCELParser excelParser = new EXCELParser(); diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java index 3b9d1c3ab..f5ef280a0 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java @@ -1,8 +1,6 @@ package eu.dnetlib.dhp.actionmanager.project.httpconnector; -import eu.dnetlib.dhp.collection.worker.DnetCollectorException; -import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.http.conn.ssl.SSLConnectionSocketFactory; @@ -11,6 +9,9 @@ import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +import eu.dnetlib.dhp.collection.worker.CollectorException; +import eu.dnetlib.dhp.collection.worker.utils.HttpConnector; + @Disabled public class HttpConnectorTest { @@ -31,12 +32,12 @@ public class HttpConnectorTest { @Test - public void testGetInputSource() throws DnetCollectorException { + public void testGetInputSource() throws CollectorException { System.out.println(connector.getInputSource(URL)); } @Test - public void testGoodServers() throws DnetCollectorException { + public void testGoodServers() throws CollectorException { System.out.println(connector.getInputSource(URL_GOODSNI_SERVER)); } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java index c745219fe..fc19f2064 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java @@ -5,17 +5,19 @@ import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.mockito.Mockito.*; import java.io.File; +import java.nio.file.Path; import org.junit.jupiter.api.AfterEach; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.collector.worker.model.ApiDescriptor; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.collection.worker.DnetCollectorWorker; +import eu.dnetlib.dhp.collection.worker.CollectorWorker; import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory; import eu.dnetlib.message.Message; import eu.dnetlib.message.MessageManager; @@ -23,43 +25,6 @@ import eu.dnetlib.message.MessageManager; @Disabled public class DnetCollectorWorkerApplicationTests { - private final ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class); - private final MessageManager messageManager = mock(MessageManager.class); - - private DnetCollectorWorker worker; - - @BeforeEach - public void setup() throws Exception { - ObjectMapper mapper = new ObjectMapper(); - final String apiJson = mapper.writeValueAsString(getApi()); - when(argumentParser.get("apidescriptor")).thenReturn(apiJson); - when(argumentParser.get("namenode")).thenReturn("file://tmp/test.seq"); - when(argumentParser.get("hdfsPath")).thenReturn("/tmp/file.seq"); - when(argumentParser.get("userHDFS")).thenReturn("sandro"); - when(argumentParser.get("workflowId")).thenReturn("sandro"); - when(argumentParser.get("rabbitOngoingQueue")).thenReturn("sandro"); - - when(messageManager.sendMessage(any(Message.class), anyString(), anyBoolean(), anyBoolean())) - .thenAnswer( - a -> { - System.out.println("sent message: " + a.getArguments()[0]); - return true; - }); - when(messageManager.sendMessage(any(Message.class), anyString())) - .thenAnswer( - a -> { - System.out.println("Called"); - return true; - }); - worker = new DnetCollectorWorker(new CollectorPluginFactory(), argumentParser, messageManager); - } - - @AfterEach - public void dropDown() { - File f = new File("/tmp/file.seq"); - f.delete(); - } - @Test public void testFindPlugin() throws Exception { final CollectorPluginFactory collectorPluginEnumerator = new CollectorPluginFactory(); @@ -79,8 +44,14 @@ public class DnetCollectorWorkerApplicationTests { } @Test - public void testFeeding() throws Exception { + public void testFeeding(@TempDir Path testDir) throws Exception { + + System.out.println(testDir.toString()); + CollectorWorker worker = new CollectorWorker(new CollectorPluginFactory(), getApi(), + "file://" + testDir.toString() + "/file.seq", testDir.toString() + "/file.seq"); worker.collect(); + + // TODO create ASSERT HERE } private ApiDescriptor getApi() { diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index 98c8cf66c..6a80e01e2 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -1,45 +1,66 @@ package eu.dnetlib.dhp.transformation; +import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.mockito.Mockito.lenient; +import java.io.IOException; import java.io.StringWriter; import java.nio.file.Files; import java.nio.file.Path; -import java.util.HashMap; -import java.util.Map; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; import javax.xml.transform.stream.StreamSource; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; -import org.junit.jupiter.api.AfterAll; -import org.junit.jupiter.api.BeforeAll; -import org.junit.jupiter.api.DisplayName; -import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.*; import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.io.TempDir; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import eu.dnetlib.dhp.aggregation.common.AggregationCounter; import eu.dnetlib.dhp.collection.CollectionJobTest; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.model.mdstore.MetadataRecord; -import eu.dnetlib.dhp.transformation.functions.Cleaner; -import eu.dnetlib.dhp.transformation.vocabulary.Vocabulary; -import eu.dnetlib.dhp.transformation.vocabulary.VocabularyHelper; -import eu.dnetlib.dhp.utils.DHPUtils; -import net.sf.saxon.s9api.*; +import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) public class TransformationJobTest { private static SparkSession spark; + @Mock + private ISLookUpService isLookUpService; + + private VocabularyGroup vocabularies; + + @BeforeEach + public void setUp() throws ISLookUpException, IOException { + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService); + } + @BeforeAll public static void beforeAll() { SparkConf conf = new SparkConf(); @@ -53,66 +74,68 @@ public class TransformationJobTest { spark.stop(); } - @Mock - private LongAccumulator accumulator; - @Test + @DisplayName("Test Transform Single XML using XSLTTransformator") public void testTransformSaxonHE() throws Exception { - Map vocabularies = new HashMap<>(); - vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages")); - Cleaner cleanFunction = new Cleaner(vocabularies); - Processor proc = new Processor(false); - proc.registerExtensionFunction(cleanFunction); - final XsltCompiler comp = proc.newXsltCompiler(); - XsltExecutable exp = comp - .compile( - new StreamSource( - this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/ext_simple.xsl"))); - XdmNode source = proc - .newDocumentBuilder() - .build( - new StreamSource( - this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input.xml"))); - XsltTransformer trans = exp.load(); - trans.setInitialContextNode(source); - final StringWriter output = new StringWriter(); - Serializer out = proc.newSerializer(output); - out.setOutputProperty(Serializer.Property.METHOD, "xml"); - out.setOutputProperty(Serializer.Property.INDENT, "yes"); - trans.setDestination(out); - trans.transform(); - System.out.println(output.toString()); + // We Set the input Record getting the XML from the classpath + final MetadataRecord mr = new MetadataRecord(); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input.xml"))); + + // We Load the XSLT transformation Rule from the classpath + XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/ext_simple.xsl"); + + // Print the record + System.out.println(tr.call(mr).getBody()); + // TODO Create significant Assert + } @DisplayName("Test TransformSparkJobNode.main") @Test public void transformTest(@TempDir Path testDir) throws Exception { + final String mdstore_input = this.getClass().getResource("/eu/dnetlib/dhp/transform/mdstorenative").getFile(); final String mdstore_output = testDir.toString() + "/version"; - final String xslt = DHPUtils - .compressString( - IOUtils - .toString( - this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml"))); - TransformSparkJobNode - .main( - new String[] { - "-issm", "true", - "-i", mdstore_input, - "-o", mdstore_output, - "-d", "1", - "-w", "1", - "-tr", xslt, - "-t", "true", - "-ru", "", - "-rp", "", - "-rh", "", - "-ro", "", - "-rr", "" - }); + + mockupTrasformationRule("simpleTRule", "/eu/dnetlib/dhp/transform/ext_simple.xsl"); + +// final String arguments = "-issm true -i %s -o %s -d 1 -w 1 -tp XSLT_TRANSFORM -tr simpleTRule"; + + final Map parameters = Stream.of(new String[][] { + { + "dateOfTransformation", "1234" + }, + { + "transformationPlugin", "XSLT_TRANSFORM" + }, + { + "transformationRuleTitle", "simpleTRule" + }, + + }).collect(Collectors.toMap(data -> data[0], data -> data[1])); + + TransformSparkJobNode.transformRecords(parameters, isLookUpService, spark, mdstore_input, mdstore_output); // TODO introduce useful assertions + + final Encoder encoder = Encoders.bean(MetadataRecord.class); + final Dataset mOutput = spark.read().format("parquet").load(mdstore_output).as(encoder); + + final Long total = mOutput.count(); + + final long recordTs = mOutput + .filter((FilterFunction) p -> p.getDateOfTransformation() == 1234) + .count(); + + final long recordNotEmpty = mOutput + .filter((FilterFunction) p -> !StringUtils.isBlank(p.getBody())) + .count(); + + assertEquals(total, recordTs); + + assertEquals(total, recordNotEmpty); + } @Test @@ -127,39 +150,27 @@ public class TransformationJobTest { Files.deleteIfExists(tempDirWithPrefix); } - @Test - public void testTransformFunction() throws Exception { - SAXReader reader = new SAXReader(); - Document document = reader.read(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); - Node node = document.selectSingleNode("//CODE/*[local-name()='stylesheet']"); - final String xslt = node.asXML(); - Map vocabularies = new HashMap<>(); - vocabularies.put("dnet:languages", VocabularyHelper.getVocabularyFromAPI("dnet:languages")); + private void mockupTrasformationRule(final String trule, final String path) throws Exception { + final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); - TransformFunction tf = new TransformFunction(accumulator, accumulator, accumulator, xslt, 1, vocabularies); - - MetadataRecord record = new MetadataRecord(); - record - .setBody( - IOUtils - .toString( - this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input.xml"))); - - final MetadataRecord result = tf.call(record); - assertNotNull(result.getBody()); - - System.out.println(result.getBody()); + lenient() + .when(isLookUpService.quickSearchProfile(String.format(TransformationFactory.TRULE_XQUERY, trule))) + .thenReturn(Collections.singletonList(trValue)); } - @Test - public void extractTr() throws Exception { + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { + final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); + final LongAccumulator la = new LongAccumulator(); + return new XSLTTransformationFunction(new AggregationCounter(la, la, la), trValue, 0, vocabularies); + } - final String xmlTr = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); + private List vocs() throws IOException { + return IOUtils + .readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/terms.txt")); + } - SAXReader reader = new SAXReader(); - Document document = reader.read(this.getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/tr.xml")); - Node node = document.selectSingleNode("//CODE/*[local-name()='stylesheet']"); - - System.out.println(node.asXML()); + private List synonyms() throws IOException { + return IOUtils + .readLines(TransformationJobTest.class.getResourceAsStream("/eu/dnetlib/dhp/transform/synonyms.txt")); } } diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl index f22db961b..9e5f84c11 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl @@ -1,15 +1,16 @@ + exclude-result-prefixes="xsl vocabulary"> - - + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml index 8760d3117..8efb3c487 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input.xml @@ -1,37 +1,68 @@ - -
- oai:research.chalmers.se:243692 - 2018-01-25T18:04:43Z - openaire -
- - - Incipient Berezinskii-Kosterlitz-Thouless transition in two-dimensional coplanar Josephson junctions - https://research.chalmers.se/en/publication/243692 - 2016 - Massarotti, D. - Jouault, B. - Rouco, V. - Charpentier, Sophie - Bauch, Thilo - Michon, A. - De Candia, A. - Lucignano, P. - Lombardi, Floriana - Tafuri, F. - Tagliacozzo, A. - Acoli - Abkhazian - Condensed Matter Physics - Superconducting hybrid junctions are revealing a variety of effects. Some of them are due to the special layout of these devices, which often use a coplanar configuration with relatively large barrier channels and the possibility of hosting Pearl vortices. A Josephson junction with a quasi-ideal two-dimensional barrier has been realized by growing graphene on SiC with Al electrodes. Chemical vapor deposition offers centimeter size monolayer areas where it is possible to realize a comparative analysis of different devices with nominally the same barrier. In samples with a graphene gap below 400 nm, we have found evidence of Josephson coherence in the presence of an incipient Berezinskii-Kosterlitz-Thouless transition. When the magnetic field is cycled, a remarkable hysteretic collapse and revival of the Josephson supercurrent occurs. Similar hysteresis are found in granular systems and are usually justified within the Bean critical state model (CSM). We show that the CSM, with appropriate account for the low-dimensional geometry, can partly explain the odd features measured in these junctions. - info:eu-repo/grantAgreement/EC/FP7/604391//Graphene-Based Revolutions in ICT And Beyond (Graphene Flagship)/ - info:eu-repo/semantics/altIdentifier/doi/10.1103/PhysRevB.94.054525 - info:eu-repo/semantics/article - Physical Review B vol.94(2016) - info:eu-repo/semantics/openAccess + + + + od______2294::00029b7f0a2a7e090e55b625a9079d83 + oai:pub.uni-bielefeld.de:2578942 + 2018-11-23T15:15:33.974+01:00 + od______2294 + oai:pub.uni-bielefeld.de:2578942 + 2018-07-24T13:01:16Z + conference + ddc:000 + conferenceFtxt + driver + open_access + + + + Mobile recommendation agents making online use of visual attention information at the point of sale + Pfeiffer, Thies + Pfeiffer, Jella + Meißner, Martin + Davis, Fred + Riedl, René + Jan, vom Brocke + Léger, Pierre-Majorique + Randolph, Adriane + Mobile Cognitive Assistance Systems + Information Systems + ddc:000 + We aim to utilize online information about visual attention for developing mobile recommendation agents (RAs) for use at the point of sale. Up to now, most RAs are focussed exclusively at personalization in an e-commerce setting. Very little is known, however, about mobile RAs that offer information and assistance at the point of sale based on individual-level feature based preference models (Murray and Häubl 2009). Current attempts provide information about products at the point of sale by manually scanning barcodes or using RFID (Kowatsch et al. 2011, Heijden 2005), e.g. using specific apps for smartphones. We argue that an online access to the current visual attention of the user offers a much larger potential. Integrating mobile eye tracking into ordinary glasses would yield a direct benefit of applying neuroscience methods in the user’s everyday life. First, learning from consumers’ attentional processes over time and adapting recommendations based on this learning allows us to provide very accurate and relevant recommendations, potentially increasing the perceived usefulness. Second, our proposed system needs little explicit user input (no scanning or navigation on screen) making it easy to use. Thus, instead of learning from click behaviour and past customer ratings, as it is the case in the e-commerce setting, the mobile RA learns from eye movements by participating online in every day decision processes. We argue that mobile RAs should be built based on current research in human judgment and decision making (Murray et al. 2010). In our project, we therefore follow a two-step approach: In the empirical basic research stream, we aim to understand the user’s interaction with the product shelf: the actions and patterns of user’s behaviour (eye movements, gestures, approaching a product closer) and their correspondence to the user’s informational needs. In the empirical system development stream, we create prototypes of mobile RAs and test experimentally the factors that influence the user’s adoption. For example, we suggest that a user’s involvement in the process, such as a need for exact nutritional information or for assistance (e.g., reading support for elderly) will influence the user’s intention to use such as system. The experiments are conducted both in our immersive virtual reality supermarket presented in a CAVE, where we can also easily display information to the user and track the eye movement in great accuracy, as well as in real-world supermarkets (see Figure 1), so that the findings can be better generalized to natural decision situations (Gidlöf et al. 2013). In a first pilot study with five randomly chosen participants in a supermarket, we evaluated which sort of mobile RAs consumers favour in order to get a first impression of the user’s acceptance of the technology. Figure 1 shows an excerpt of one consumer’s eye movements during a decision process. First results show long eye cascades and short fixations on many products in situations where users are uncertain and in need for support. Furthermore, we find a surprising acceptance of the technology itself throughout all ages (23 – 61 years). At the same time, consumers express serious fear of being manipulated by such a technology. For that reason, they strongly prefer the information to be provided by trusted third party or shared with family members and friends (see also Murray and Häubl 2009). Our pilot will be followed by a larger field experiment in March in order to learn more about factors that influence the user’s acceptance as well as the eye movement patterns that reflect typical phases of decision processes and indicate the need for support by a RA. + 2013 + info:eu-repo/semantics/conferenceObject + doc-type:conferenceObject + text + https://pub.uni-bielefeld.de/record/2578942 + https://pub.uni-bielefeld.de/download/2578942/2602478 + Pfeiffer T, Pfeiffer J, Meißner M. Mobile recommendation agents making online use of visual attention information at the point of sale. In: Davis F, Riedl R, Jan vom B, Léger P-M, Randolph A, eds. Proceedings of the Gmunden Retreat on NeuroIS 2013. 2013: 3-3. eng - Researchers - application/pdf + info:eu-repo/semantics/openAccess - + + + + http://pub.uni-bielefeld.de/oai + oai:pub.uni-bielefeld.de:2578942 + 2018-07-24T13:01:16Z + http://www.openarchives.org/OAI/2.0/oai_dc/ + + + + false + false + 0.9 + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt new file mode 100644 index 000000000..729296522 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt @@ -0,0 +1,1234 @@ +dnet:access_modes @=@ CLOSED @=@ http://purl.org/coar/access_right/c_14cb +dnet:access_modes @=@ CLOSED @=@ info:eu-repo/semantics/closedAccess +dnet:access_modes @=@ EMBARGO @=@ http://purl.org/coar/access_right/c_f1cf +dnet:access_modes @=@ EMBARGO @=@ info:eu-repo/semantics/embargoedAccess +dnet:access_modes @=@ 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A publication that supplements your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SOFTWARE @=@ A software referred by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/OPENACCESS_VERSION @=@ Another Open Access version of a publication +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/PID @=@ Another persistent identifier associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/MESHEUROPMC @=@ A classification term from the Medical Subject Headings (MeSH) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/ABSTRACT @=@ An abstract describing among your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PUBLICATION_DATE @=@ A date of publication missing in your content +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PID @=@ A persistent identifier associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/ACM @=@ Another ACM classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/ARXIV @=@ Another ARXIV classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/DDC @=@ Another Dewey Decimal classification term (DDC) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/JEL @=@ Another Journal of Economic Literature (JEL) classification term that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MORE/SUBJECT/MESHEUROPMC @=@ Another classification term from the Medical Subject Headings (MeSH) that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/PROJECT @=@ A project reference that can be associated to your publications +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY @=@ A dataset that is supplemented by your records +dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications +dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown +dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed +dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index db1a2ef57..7ff06e428 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -55,9 +55,9 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; import eu.dnetlib.dhp.oa.graph.raw.common.VerifyNsPrefixPredicate; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Dataset; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java index 8293faac4..83303ae8e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -15,8 +15,8 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 35a829c71..dbfa6290d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -21,8 +21,8 @@ import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Dataset;