Merge pull request 'SWH_integration' (#343) from SWH_integration into beta
Reviewed-on: #343
This commit is contained in:
commit
6856ab28ab
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@ -51,6 +51,7 @@ public class Constants {
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public static final String RETRY_DELAY = "retryDelay";
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public static final String CONNECT_TIMEOUT = "connectTimeOut";
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public static final String READ_TIMEOUT = "readTimeOut";
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public static final String REQUEST_METHOD = "requestMethod";
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public static final String FROM_DATE_OVERRIDE = "fromDateOverride";
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public static final String UNTIL_DATE_OVERRIDE = "untilDateOverride";
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@ -1,6 +1,9 @@
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package eu.dnetlib.dhp.common.collection;
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import java.util.HashMap;
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import java.util.Map;
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/**
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* Bundles the http connection parameters driving the client behaviour.
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*/
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@ -13,6 +16,8 @@ public class HttpClientParams {
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public static int _connectTimeOut = 10; // seconds
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public static int _readTimeOut = 30; // seconds
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public static String _requestMethod = "GET";
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/**
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* Maximum number of allowed retires before failing
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*/
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@ -38,17 +43,30 @@ public class HttpClientParams {
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*/
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private int readTimeOut;
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/**
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* Custom http headers
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*/
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private Map<String, String> headers;
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/**
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* Request method (i.e., GET, POST etc)
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*/
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private String requestMethod;
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public HttpClientParams() {
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this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut);
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this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut, new HashMap<>(),
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_requestMethod);
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}
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public HttpClientParams(int maxNumberOfRetry, int requestDelay, int retryDelay, int connectTimeOut,
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int readTimeOut) {
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int readTimeOut, Map<String, String> headers, String requestMethod) {
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this.maxNumberOfRetry = maxNumberOfRetry;
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this.requestDelay = requestDelay;
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this.retryDelay = retryDelay;
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this.connectTimeOut = connectTimeOut;
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this.readTimeOut = readTimeOut;
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this.headers = headers;
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this.requestMethod = requestMethod;
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}
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public int getMaxNumberOfRetry() {
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@ -91,4 +109,19 @@ public class HttpClientParams {
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this.readTimeOut = readTimeOut;
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}
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public Map<String, String> getHeaders() {
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return headers;
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}
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public void setHeaders(Map<String, String> headers) {
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this.headers = headers;
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}
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public String getRequestMethod() {
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return requestMethod;
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}
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public void setRequestMethod(String requestMethod) {
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this.requestMethod = requestMethod;
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}
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}
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@ -107,7 +107,14 @@ public class HttpConnector2 {
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urlConn.setReadTimeout(getClientParams().getReadTimeOut() * 1000);
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urlConn.setConnectTimeout(getClientParams().getConnectTimeOut() * 1000);
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urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
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urlConn.setRequestMethod(getClientParams().getRequestMethod());
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// if provided, add custom headers
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if (!getClientParams().getHeaders().isEmpty()) {
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for (Map.Entry<String, String> headerEntry : getClientParams().getHeaders().entrySet()) {
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urlConn.addRequestProperty(headerEntry.getKey(), headerEntry.getValue());
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}
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}
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if (log.isDebugEnabled()) {
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logHeaderFields(urlConn);
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}
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@ -33,7 +33,7 @@ import scala.Tuple2;
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public class GroupEntitiesSparkJob {
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private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
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private static final Encoder<OafEntity> OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class);
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private static final Encoder<OafEntity> OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class);
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public static void main(String[] args) throws Exception {
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@ -114,7 +114,7 @@ public class GroupEntitiesSparkJob {
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Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC));
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// pivot on "_1" (classname of the entity)
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// created columns containing only entities of the same class
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// created columns containing only entities of the same class
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for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
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String entity = e.getKey().name();
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Class<? extends OafEntity> entityClass = e.getValue();
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@ -67,60 +67,60 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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log.info("graphOutputPath: '{}'", graphOutputPath);
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Dataset<Relation> mergeRels = spark
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.read()
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.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
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.as(REL_BEAN_ENC);
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.read()
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.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
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.as(REL_BEAN_ENC);
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// <mergedObjectID, dedupID>
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Dataset<Row> idsToMerge = mergeRels
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.where(col("relClass").equalTo(ModelConstants.MERGES))
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.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
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.distinct();
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.where(col("relClass").equalTo(ModelConstants.MERGES))
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.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
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.distinct();
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Dataset<Row> allRels = spark
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.read()
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.schema(REL_BEAN_ENC.schema())
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.json(graphBasePath + "/relation");
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.read()
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.schema(REL_BEAN_ENC.schema())
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.json(graphBasePath + "/relation");
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Dataset<Relation> dedupedRels = allRels
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.joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.select("_1._1", "_1._2.dedupID", "_2.dedupID")
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.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
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.map((MapFunction<Tuple3<Relation, String, String>, Relation>) t -> {
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Relation rel = t._1();
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String newSource = t._2();
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String newTarget = t._3();
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.joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.select("_1._1", "_1._2.dedupID", "_2.dedupID")
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.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
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.map((MapFunction<Tuple3<Relation, String, String>, Relation>) t -> {
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Relation rel = t._1();
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String newSource = t._2();
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String newTarget = t._3();
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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if (newSource != null || newTarget != null) {
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rel.getDataInfo().setDeletedbyinference(false);
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if (newSource != null || newTarget != null) {
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rel.getDataInfo().setDeletedbyinference(false);
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if (newSource != null)
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rel.setSource(newSource);
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if (newSource != null)
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rel.setSource(newSource);
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if (newTarget != null)
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rel.setTarget(newTarget);
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}
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if (newTarget != null)
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rel.setTarget(newTarget);
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}
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return rel;
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}, REL_BEAN_ENC);
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return rel;
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}, REL_BEAN_ENC);
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// ids of records that are both not deletedbyinference and not invisible
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Dataset<Row> ids = validIds(spark, graphBasePath);
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// filter relations that point to valid records, can force them to be visible
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Dataset<Relation> cleanedRels = dedupedRels
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.join(ids, col("source").equalTo(ids.col("id")), "leftsemi")
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.join(ids, col("target").equalTo(ids.col("id")), "leftsemi")
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.as(REL_BEAN_ENC)
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.map((MapFunction<Relation, Relation>) r -> {
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r.getDataInfo().setInvisible(false);
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return r;
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}, REL_KRYO_ENC);
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.join(ids, col("source").equalTo(ids.col("id")), "leftsemi")
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.join(ids, col("target").equalTo(ids.col("id")), "leftsemi")
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.as(REL_BEAN_ENC)
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.map((MapFunction<Relation, Relation>) r -> {
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r.getDataInfo().setInvisible(false);
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return r;
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}, REL_KRYO_ENC);
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Dataset<Relation> distinctRels = cleanedRels
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.groupByKey(
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@ -1,14 +1,14 @@
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package eu.dnetlib.dhp.oa.graph.group;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import java.io.IOException;
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import java.net.URISyntaxException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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@ -18,108 +18,108 @@ import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.*;
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import java.io.IOException;
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import java.net.URISyntaxException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.utils.DHPUtils;
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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public class GroupEntitiesSparkJobTest {
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private static SparkSession spark;
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private static SparkSession spark;
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private static ObjectMapper mapper = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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private static ObjectMapper mapper = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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private static Path workingDir;
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private Path dataInputPath;
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private static Path workingDir;
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private Path dataInputPath;
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private Path checkpointPath;
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private Path checkpointPath;
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private Path outputPath;
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private Path outputPath;
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
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SparkConf conf = new SparkConf();
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conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
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conf.setMaster("local");
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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spark = SparkSession.builder().config(conf).getOrCreate();
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}
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SparkConf conf = new SparkConf();
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conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
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conf.setMaster("local");
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ModelSupport.getOafModelClasses());
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spark = SparkSession.builder().config(conf).getOrCreate();
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}
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@BeforeEach
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public void beforeEach() throws IOException, URISyntaxException {
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dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
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checkpointPath = workingDir.resolve("grouped_entity");
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outputPath = workingDir.resolve("dispatched_entity");
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}
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@BeforeEach
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public void beforeEach() throws IOException, URISyntaxException {
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||||
dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
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checkpointPath = workingDir.resolve("grouped_entity");
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outputPath = workingDir.resolve("dispatched_entity");
|
||||
}
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|
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@AfterAll
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||||
public static void afterAll() throws IOException {
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spark.stop();
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||||
FileUtils.deleteDirectory(workingDir.toFile());
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||||
}
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||||
@AfterAll
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public static void afterAll() throws IOException {
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spark.stop();
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||||
FileUtils.deleteDirectory(workingDir.toFile());
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||||
}
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||||
|
||||
@Test
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@Order(1)
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||||
void testGroupEntities() throws Exception {
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||||
GroupEntitiesSparkJob.main(new String[]{
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
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||||
"-graphInputPath",
|
||||
dataInputPath.toString(),
|
||||
"-checkpointPath",
|
||||
checkpointPath.toString(),
|
||||
"-outputPath",
|
||||
outputPath.toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.FALSE.toString()
|
||||
});
|
||||
@Test
|
||||
@Order(1)
|
||||
void testGroupEntities() throws Exception {
|
||||
GroupEntitiesSparkJob.main(new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-graphInputPath",
|
||||
dataInputPath.toString(),
|
||||
"-checkpointPath",
|
||||
checkpointPath.toString(),
|
||||
"-outputPath",
|
||||
outputPath.toString(),
|
||||
"-filterInvisible",
|
||||
Boolean.FALSE.toString()
|
||||
});
|
||||
|
||||
Dataset<OafEntity> checkpointTable = spark
|
||||
.read()
|
||||
.load(checkpointPath.toString())
|
||||
.selectExpr("COALESCE(*)")
|
||||
.as(Encoders.kryo(OafEntity.class));
|
||||
Dataset<OafEntity> checkpointTable = spark
|
||||
.read()
|
||||
.load(checkpointPath.toString())
|
||||
.selectExpr("COALESCE(*)")
|
||||
.as(Encoders.kryo(OafEntity.class));
|
||||
|
||||
assertEquals(
|
||||
1,
|
||||
checkpointTable
|
||||
.filter(
|
||||
(FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
|
||||
.equals(r.getId()) &&
|
||||
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
||||
.count());
|
||||
|
||||
assertEquals(
|
||||
1,
|
||||
checkpointTable
|
||||
.filter(
|
||||
(FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
|
||||
.equals(r.getId()) &&
|
||||
r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
|
||||
.count());
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(
|
||||
DHPUtils
|
||||
.toSeq(
|
||||
HdfsSupport
|
||||
.listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
|
||||
|
||||
Dataset<Result> output = spark
|
||||
.read()
|
||||
.textFile(
|
||||
DHPUtils
|
||||
.toSeq(
|
||||
HdfsSupport
|
||||
.listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
|
||||
.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
|
||||
|
||||
assertEquals(3, output.count());
|
||||
assertEquals(
|
||||
2,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("publication"))
|
||||
.count());
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
}
|
||||
assertEquals(3, output.count());
|
||||
assertEquals(
|
||||
2,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("publication"))
|
||||
.count());
|
||||
assertEquals(
|
||||
1,
|
||||
output
|
||||
.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
|
||||
.filter((FilterFunction<String>) s -> s.equals("dataset"))
|
||||
.count());
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,110 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<parent>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<artifactId>dhp-workflows</artifactId>
|
||||
<version>1.2.5-SNAPSHOT</version>
|
||||
</parent>
|
||||
<artifactId>dhp-swh</artifactId>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-core_${scala.binary.version}</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.spark</groupId>
|
||||
<artifactId>spark-sql_${scala.binary.version}</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>eu.dnetlib.dhp</groupId>
|
||||
<artifactId>dhp-common</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>net.sf.saxon</groupId>
|
||||
<artifactId>Saxon-HE</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>dom4j</groupId>
|
||||
<artifactId>dom4j</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>xml-apis</groupId>
|
||||
<artifactId>xml-apis</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>jaxen</groupId>
|
||||
<artifactId>jaxen</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.hadoop</groupId>
|
||||
<artifactId>hadoop-distcp</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>eu.dnetlib</groupId>
|
||||
<artifactId>dnet-actionmanager-api</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>eu.dnetlib</groupId>
|
||||
<artifactId>dnet-actionmanager-common</artifactId>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>eu.dnetlib</groupId>
|
||||
<artifactId>dnet-openaireplus-mapping-utils</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>saxonica</groupId>
|
||||
<artifactId>saxon</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>saxonica</groupId>
|
||||
<artifactId>saxon-dom</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>jgrapht</groupId>
|
||||
<artifactId>jgrapht</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>net.sf.ehcache</groupId>
|
||||
<artifactId>ehcache</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>org.springframework</groupId>
|
||||
<artifactId>spring-test</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>org.apache.*</groupId>
|
||||
<artifactId>*</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>apache</groupId>
|
||||
<artifactId>*</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.httpcomponents</groupId>
|
||||
<artifactId>httpclient</artifactId>
|
||||
<version>4.5.13</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.datanucleus</groupId>
|
||||
<artifactId>datanucleus-core</artifactId>
|
||||
<version>3.2.10</version>
|
||||
<scope>compile</scope>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
</project>
|
||||
|
|
@ -0,0 +1,176 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh;
|
||||
|
||||
import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.URL;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Date;
|
||||
import java.util.Optional;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import org.apache.commons.cli.ParseException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
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.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.collection.CollectorException;
|
||||
import eu.dnetlib.dhp.common.collection.HttpClientParams;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
|
||||
import eu.dnetlib.dhp.swh.models.LastVisitData;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHConnection;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHConstants;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHUtils;
|
||||
|
||||
/**
|
||||
* Sends archive requests to the SWH API for those software repository URLs that are missing from them
|
||||
*
|
||||
* @author Serafeim Chatzopoulos
|
||||
*/
|
||||
public class ArchiveRepositoryURLs {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(ArchiveRepositoryURLs.class);
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SWHConnection swhConnection = null;
|
||||
|
||||
public static void main(final String[] args) throws IOException, ParseException {
|
||||
final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
CollectLastVisitRepositoryData.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/swh/input_archive_repository_urls.json")));
|
||||
argumentParser.parseArgument(args);
|
||||
|
||||
final String hdfsuri = argumentParser.get("namenode");
|
||||
log.info("hdfsURI: {}", hdfsuri);
|
||||
|
||||
final String inputPath = argumentParser.get("lastVisitsPath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = argumentParser.get("archiveRequestsPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final Integer archiveThresholdInDays = Integer.parseInt(argumentParser.get("archiveThresholdInDays"));
|
||||
log.info("archiveThresholdInDays: {}", archiveThresholdInDays);
|
||||
|
||||
final String apiAccessToken = argumentParser.get("apiAccessToken");
|
||||
log.info("apiAccessToken: {}", apiAccessToken);
|
||||
|
||||
final HttpClientParams clientParams = SWHUtils.getClientParams(argumentParser);
|
||||
|
||||
swhConnection = new SWHConnection(clientParams, apiAccessToken);
|
||||
|
||||
final FileSystem fs = FileSystem.get(getHadoopConfiguration(hdfsuri));
|
||||
|
||||
archive(fs, inputPath, outputPath, archiveThresholdInDays);
|
||||
|
||||
}
|
||||
|
||||
private static void archive(FileSystem fs, String inputPath, String outputPath, Integer archiveThresholdInDays)
|
||||
throws IOException {
|
||||
|
||||
SequenceFile.Reader fr = SWHUtils.getSequenceFileReader(fs, inputPath);
|
||||
SequenceFile.Writer fw = SWHUtils.getSequenceFileWriter(fs, outputPath);
|
||||
|
||||
// Create key and value objects to hold data
|
||||
Text repoUrl = new Text();
|
||||
Text lastVisitData = new Text();
|
||||
|
||||
// Read key-value pairs from the SequenceFile and handle appropriately
|
||||
while (fr.next(repoUrl, lastVisitData)) {
|
||||
|
||||
String response = null;
|
||||
try {
|
||||
response = handleRecord(repoUrl.toString(), lastVisitData.toString(), archiveThresholdInDays);
|
||||
} catch (java.text.ParseException e) {
|
||||
log.error("Could not handle record with repo Url: {}", repoUrl.toString());
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
|
||||
// response is equal to null when no need for request
|
||||
if (response != null) {
|
||||
SWHUtils.appendToSequenceFile(fw, repoUrl.toString(), response);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
// Close readers
|
||||
fw.close();
|
||||
fr.close();
|
||||
}
|
||||
|
||||
public static String handleRecord(String repoUrl, String lastVisitData, Integer archiveThresholdInDays)
|
||||
throws IOException, java.text.ParseException {
|
||||
|
||||
log.info("{ Key: {}, Value: {} }", repoUrl, lastVisitData);
|
||||
|
||||
LastVisitData lastVisit = OBJECT_MAPPER.readValue(lastVisitData, LastVisitData.class);
|
||||
|
||||
// a previous attempt for archival has been made, and repository URL was not found
|
||||
// avoid performing the same archive request again
|
||||
if (lastVisit.getStatus() != null &&
|
||||
lastVisit.getStatus().equals(SWHConstants.VISIT_STATUS_NOT_FOUND)) {
|
||||
|
||||
log.info("Avoid request -- previous archive request returned NOT_FOUND");
|
||||
return null;
|
||||
}
|
||||
|
||||
// if we have last visit data
|
||||
if (lastVisit.getSnapshot() != null) {
|
||||
|
||||
String cleanDate = GraphCleaningFunctions.cleanDate(lastVisit.getDate());
|
||||
|
||||
// and the last visit date can be parsed
|
||||
if (cleanDate != null) {
|
||||
|
||||
SimpleDateFormat formatter = new SimpleDateFormat(ModelSupport.DATE_FORMAT);
|
||||
Date lastVisitDate = formatter.parse(cleanDate);
|
||||
|
||||
// OR last visit time < (now() - archiveThresholdInDays)
|
||||
long diffInMillies = Math.abs((new Date()).getTime() - lastVisitDate.getTime());
|
||||
long diffInDays = TimeUnit.DAYS.convert(diffInMillies, TimeUnit.MILLISECONDS);
|
||||
log.info("Date diff from now (in days): {}", diffInDays);
|
||||
|
||||
// do not perform a request, if the last visit date is no older than $archiveThresholdInDays
|
||||
if (archiveThresholdInDays >= diffInDays) {
|
||||
log.info("Avoid request -- no older than {} days", archiveThresholdInDays);
|
||||
return null;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// ELSE perform an archive request
|
||||
log.info("Perform archive request for: {}", repoUrl);
|
||||
|
||||
// if last visit data are available, re-use version control type,
|
||||
// else use the default one (i.e., git)
|
||||
String visitType = Optional
|
||||
.ofNullable(lastVisit.getType())
|
||||
.orElse(SWHConstants.DEFAULT_VISIT_TYPE);
|
||||
|
||||
URL url = new URL(String.format(SWHConstants.SWH_ARCHIVE_URL, visitType, repoUrl.trim()));
|
||||
|
||||
log.info("Sending archive request: {}", url);
|
||||
|
||||
String response;
|
||||
try {
|
||||
response = swhConnection.call(url.toString());
|
||||
} catch (CollectorException e) {
|
||||
log.error("Error in request: {}", url);
|
||||
response = "{}";
|
||||
}
|
||||
|
||||
return response;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,119 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh;
|
||||
|
||||
import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.IOException;
|
||||
import java.net.URL;
|
||||
|
||||
import org.apache.commons.cli.ParseException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileStatus;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.SequenceFile;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.collection.CollectorException;
|
||||
import eu.dnetlib.dhp.common.collection.HttpClientParams;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHConnection;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHConstants;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHUtils;
|
||||
|
||||
/**
|
||||
* Given a file with software repository URLs, this class
|
||||
* collects last visit data from the Software Heritage API.
|
||||
*
|
||||
* @author Serafeim Chatzopoulos
|
||||
*/
|
||||
public class CollectLastVisitRepositoryData {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CollectLastVisitRepositoryData.class);
|
||||
private static SWHConnection swhConnection = null;
|
||||
|
||||
public static void main(final String[] args)
|
||||
throws IOException, ParseException {
|
||||
final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
CollectLastVisitRepositoryData.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/swh/input_collect_last_visit_repository_data.json")));
|
||||
argumentParser.parseArgument(args);
|
||||
|
||||
log.info("Java Xmx: {}m", Runtime.getRuntime().maxMemory() / (1024 * 1024));
|
||||
|
||||
final String hdfsuri = argumentParser.get("namenode");
|
||||
log.info("hdfsURI: {}", hdfsuri);
|
||||
|
||||
final String inputPath = argumentParser.get("softwareCodeRepositoryURLs");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String outputPath = argumentParser.get("lastVisitsPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
final String apiAccessToken = argumentParser.get("apiAccessToken");
|
||||
log.info("apiAccessToken: {}", apiAccessToken);
|
||||
|
||||
final HttpClientParams clientParams = SWHUtils.getClientParams(argumentParser);
|
||||
|
||||
swhConnection = new SWHConnection(clientParams, apiAccessToken);
|
||||
|
||||
final FileSystem fs = FileSystem.get(getHadoopConfiguration(hdfsuri));
|
||||
|
||||
collect(fs, inputPath, outputPath);
|
||||
|
||||
fs.close();
|
||||
}
|
||||
|
||||
private static void collect(FileSystem fs, String inputPath, String outputPath)
|
||||
throws IOException {
|
||||
|
||||
SequenceFile.Writer fw = SWHUtils.getSequenceFileWriter(fs, outputPath);
|
||||
|
||||
// Specify the HDFS directory path you want to read
|
||||
Path directoryPath = new Path(inputPath);
|
||||
|
||||
// List all files in the directory
|
||||
FileStatus[] partStatuses = fs.listStatus(directoryPath);
|
||||
|
||||
for (FileStatus partStatus : partStatuses) {
|
||||
|
||||
// Check if it's a file (not a directory)
|
||||
if (partStatus.isFile()) {
|
||||
handleFile(fs, partStatus.getPath(), fw);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
fw.close();
|
||||
}
|
||||
|
||||
private static void handleFile(FileSystem fs, Path partInputPath, SequenceFile.Writer fw)
|
||||
throws IOException {
|
||||
|
||||
BufferedReader br = SWHUtils.getFileReader(fs, partInputPath);
|
||||
|
||||
String repoUrl;
|
||||
while ((repoUrl = br.readLine()) != null) {
|
||||
|
||||
URL url = new URL(String.format(SWHConstants.SWH_LATEST_VISIT_URL, repoUrl.trim()));
|
||||
|
||||
String response;
|
||||
try {
|
||||
response = swhConnection.call(url.toString());
|
||||
} catch (CollectorException e) {
|
||||
log.error("Error in request: {}", url);
|
||||
response = "{}";
|
||||
}
|
||||
|
||||
SWHUtils.appendToSequenceFile(fw, repoUrl, response);
|
||||
}
|
||||
|
||||
br.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,93 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
/**
|
||||
* Collects unique software repository URLs in the Graph using Hive
|
||||
*
|
||||
* @author Serafeim Chatzopoulos
|
||||
*/
|
||||
public class CollectSoftwareRepositoryURLs {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CollectSoftwareRepositoryURLs.class);
|
||||
|
||||
public static <I extends Result> void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
CollectSoftwareRepositoryURLs.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/swh/input_collect_software_repository_urls.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
final Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String hiveDbName = parser.get("hiveDbName");
|
||||
log.info("hiveDbName: {}", hiveDbName);
|
||||
|
||||
final String outputPath = parser.get("softwareCodeRepositoryURLs");
|
||||
log.info("softwareCodeRepositoryURLs: {}", outputPath);
|
||||
|
||||
final String hiveMetastoreUris = parser.get("hiveMetastoreUris");
|
||||
log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
|
||||
|
||||
final Integer softwareLimit = Integer.parseInt(parser.get("softwareLimit"));
|
||||
log.info("softwareLimit: {}", softwareLimit);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", hiveMetastoreUris);
|
||||
|
||||
runWithSparkHiveSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
doRun(spark, hiveDbName, softwareLimit, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static <I extends Result> void doRun(SparkSession spark, String hiveDbName, Integer limit,
|
||||
String outputPath) {
|
||||
|
||||
String queryTemplate = "SELECT distinct coderepositoryurl.value " +
|
||||
"FROM %s.software " +
|
||||
"WHERE coderepositoryurl.value IS NOT NULL " +
|
||||
"AND datainfo.deletedbyinference = FALSE " +
|
||||
"AND datainfo.invisible = FALSE ";
|
||||
|
||||
if (limit != null) {
|
||||
queryTemplate += String.format("LIMIT %s", limit);
|
||||
}
|
||||
|
||||
String query = String.format(queryTemplate, hiveDbName);
|
||||
|
||||
log.info("Hive query to fetch software code URLs: {}", query);
|
||||
|
||||
Dataset<Row> df = spark.sql(query);
|
||||
|
||||
// write distinct repository URLs
|
||||
df
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.csv(outputPath);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,185 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.hadoop.io.compress.GzipCodec;
|
||||
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.types.DataTypes;
|
||||
import org.apache.spark.sql.types.StructField;
|
||||
import org.apache.spark.sql.types.StructType;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
||||
import eu.dnetlib.dhp.swh.models.LastVisitData;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHConstants;
|
||||
import scala.Tuple2;
|
||||
|
||||
/**
|
||||
* Creates action sets for Software Heritage data
|
||||
*
|
||||
* @author Serafeim Chatzopoulos
|
||||
*/
|
||||
public class PrepareSWHActionsets {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareSWHActionsets.class);
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static <I extends Result> void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
PrepareSWHActionsets.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/swh/input_prepare_swh_actionsets.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
final Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String inputPath = parser.get("lastVisitsPath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
final String softwareInputPath = parser.get("softwareInputPath");
|
||||
log.info("softwareInputPath: {}", softwareInputPath);
|
||||
|
||||
final String outputPath = parser.get("actionsetsPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
JavaPairRDD<Text, Text> softwareRDD = prepareActionsets(spark, inputPath, softwareInputPath);
|
||||
softwareRDD
|
||||
.saveAsHadoopFile(
|
||||
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
|
||||
});
|
||||
}
|
||||
|
||||
private static Dataset<Row> loadSWHData(SparkSession spark, String inputPath) {
|
||||
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
// read from file and transform to <origin, snapshotId> tuples
|
||||
// Note: snapshot id is the SWH id for us
|
||||
JavaRDD<Row> swhRDD = sc
|
||||
.sequenceFile(inputPath, Text.class, Text.class)
|
||||
.map(t -> t._2().toString())
|
||||
.map(t -> OBJECT_MAPPER.readValue(t, LastVisitData.class))
|
||||
.filter(t -> t.getOrigin() != null && t.getSnapshot() != null) // response from SWH API is empty if repo URL
|
||||
// was not found
|
||||
.map(item -> RowFactory.create(item.getOrigin(), item.getSnapshot()));
|
||||
|
||||
// convert RDD to 2-column DF
|
||||
List<StructField> fields = Arrays
|
||||
.asList(
|
||||
DataTypes.createStructField("repoUrl", DataTypes.StringType, true),
|
||||
DataTypes.createStructField("swhId", DataTypes.StringType, true));
|
||||
StructType schema = DataTypes.createStructType(fields);
|
||||
|
||||
return spark.createDataFrame(swhRDD, schema);
|
||||
}
|
||||
|
||||
private static Dataset<Row> loadGraphSoftwareData(SparkSession spark, String softwareInputPath) {
|
||||
return spark
|
||||
.read()
|
||||
.textFile(softwareInputPath)
|
||||
.map(
|
||||
(MapFunction<String, Software>) t -> OBJECT_MAPPER.readValue(t, Software.class),
|
||||
Encoders.bean(Software.class))
|
||||
.filter(t -> t.getCodeRepositoryUrl() != null)
|
||||
.select(col("id"), col("codeRepositoryUrl.value").as("repoUrl"));
|
||||
}
|
||||
|
||||
private static <I extends Software> JavaPairRDD<Text, Text> prepareActionsets(SparkSession spark, String inputPath,
|
||||
String softwareInputPath) {
|
||||
|
||||
Dataset<Row> swhDF = loadSWHData(spark, inputPath);
|
||||
// swhDF.show(false);
|
||||
|
||||
Dataset<Row> graphSoftwareDF = loadGraphSoftwareData(spark, softwareInputPath);
|
||||
// graphSoftwareDF.show(5);
|
||||
|
||||
Dataset<Row> joinedDF = graphSoftwareDF.join(swhDF, "repoUrl").select("id", "swhid");
|
||||
// joinedDF.show(false);
|
||||
|
||||
return joinedDF.map((MapFunction<Row, Software>) row -> {
|
||||
|
||||
Software s = new Software();
|
||||
|
||||
// set openaire id
|
||||
s.setId(row.getString(row.fieldIndex("id")));
|
||||
|
||||
// set swh id
|
||||
Qualifier qualifier = OafMapperUtils
|
||||
.qualifier(
|
||||
SWHConstants.SWHID,
|
||||
SWHConstants.SWHID_CLASSNAME,
|
||||
ModelConstants.DNET_PID_TYPES,
|
||||
ModelConstants.DNET_PID_TYPES);
|
||||
|
||||
DataInfo dataInfo = OafMapperUtils
|
||||
.dataInfo(
|
||||
false,
|
||||
null,
|
||||
false,
|
||||
false,
|
||||
ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER,
|
||||
"");
|
||||
|
||||
s
|
||||
.setPid(
|
||||
Arrays
|
||||
.asList(
|
||||
OafMapperUtils
|
||||
.structuredProperty(
|
||||
String.format("swh:1:snp:%s", row.getString(row.fieldIndex("swhid"))),
|
||||
qualifier,
|
||||
dataInfo)));
|
||||
|
||||
// add SWH in the `collectedFrom` field
|
||||
KeyValue kv = new KeyValue();
|
||||
kv.setKey(SWHConstants.SWH_ID);
|
||||
kv.setValue(SWHConstants.SWH_NAME);
|
||||
|
||||
s.setCollectedfrom(Arrays.asList(kv));
|
||||
|
||||
return s;
|
||||
}, Encoders.bean(Software.class))
|
||||
.toJavaRDD()
|
||||
.map(p -> new AtomicAction(Software.class, p))
|
||||
.mapToPair(
|
||||
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
|
||||
new Text(OBJECT_MAPPER.writeValueAsString(aa))));
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh.models;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
import com.cloudera.com.fasterxml.jackson.annotation.JsonProperty;
|
||||
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
|
||||
|
||||
@JsonIgnoreProperties(ignoreUnknown = true)
|
||||
public class LastVisitData implements Serializable {
|
||||
|
||||
private String origin;
|
||||
private String type;
|
||||
private String date;
|
||||
|
||||
@JsonProperty("snapshot")
|
||||
private String snapshotId;
|
||||
|
||||
private String status;
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
||||
public void setType(String type) {
|
||||
this.type = type;
|
||||
}
|
||||
|
||||
public String getDate() {
|
||||
return date;
|
||||
}
|
||||
|
||||
public void setDate(String date) {
|
||||
this.date = date;
|
||||
}
|
||||
|
||||
public String getSnapshot() {
|
||||
return snapshotId;
|
||||
}
|
||||
|
||||
public void setSnapshot(String snapshotId) {
|
||||
this.snapshotId = snapshotId;
|
||||
}
|
||||
|
||||
public String getStatus() {
|
||||
return status;
|
||||
}
|
||||
|
||||
public void setStatus(String status) {
|
||||
this.status = status;
|
||||
}
|
||||
|
||||
public String getOrigin() {
|
||||
return origin;
|
||||
}
|
||||
|
||||
public void setOrigin(String origin) {
|
||||
this.origin = origin;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return "LastVisitData{" +
|
||||
"origin='" + origin + '\'' +
|
||||
", type='" + type + '\'' +
|
||||
", date='" + date + '\'' +
|
||||
", snapshotId='" + snapshotId + '\'' +
|
||||
", status='" + status + '\'' +
|
||||
'}';
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh.utils;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.apache.http.HttpHeaders;
|
||||
|
||||
import eu.dnetlib.dhp.common.collection.CollectorException;
|
||||
import eu.dnetlib.dhp.common.collection.HttpClientParams;
|
||||
import eu.dnetlib.dhp.common.collection.HttpConnector2;
|
||||
|
||||
public class SWHConnection {
|
||||
|
||||
HttpConnector2 conn;
|
||||
|
||||
public SWHConnection(HttpClientParams clientParams, String accessToken) {
|
||||
|
||||
// set custom headers
|
||||
Map<String, String> headers = new HashMap<String, String>() {
|
||||
{
|
||||
put(HttpHeaders.ACCEPT, "application/json");
|
||||
if (accessToken != null) {
|
||||
put(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", accessToken));
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
clientParams.setHeaders(headers);
|
||||
|
||||
// create http connector
|
||||
conn = new HttpConnector2(clientParams);
|
||||
|
||||
}
|
||||
|
||||
public String call(String url) throws CollectorException {
|
||||
return conn.getInputSource(url);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh.utils;
|
||||
|
||||
public class SWHConstants {
|
||||
public static final String SWH_LATEST_VISIT_URL = "https://archive.softwareheritage.org/api/1/origin/%s/visit/latest/";
|
||||
|
||||
public static final String SWH_ARCHIVE_URL = "https://archive.softwareheritage.org/api/1/origin/save/%s/url/%s/";
|
||||
|
||||
public static final String DEFAULT_VISIT_TYPE = "git";
|
||||
|
||||
public static final String VISIT_STATUS_NOT_FOUND = "not_found";
|
||||
|
||||
public static final String SWHID = "swhid";
|
||||
|
||||
public static final String SWHID_CLASSNAME = "Software Heritage Identifier";
|
||||
|
||||
public static final String SWH_ID = "10|openaire____::dbfd07503aaa1ed31beed7dec942f3f4";
|
||||
|
||||
public static final String SWH_NAME = "Software Heritage";
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,95 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh.utils;
|
||||
|
||||
import static eu.dnetlib.dhp.common.Constants.*;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStreamReader;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.hadoop.fs.FSDataInputStream;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.SequenceFile;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.collection.HttpClientParams;
|
||||
|
||||
public class SWHUtils {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SWHUtils.class);
|
||||
|
||||
public static HttpClientParams getClientParams(ArgumentApplicationParser argumentParser) {
|
||||
|
||||
final HttpClientParams clientParams = new HttpClientParams();
|
||||
clientParams
|
||||
.setMaxNumberOfRetry(
|
||||
Optional
|
||||
.ofNullable(argumentParser.get(MAX_NUMBER_OF_RETRY))
|
||||
.map(Integer::parseInt)
|
||||
.orElse(HttpClientParams._maxNumberOfRetry));
|
||||
log.info("maxNumberOfRetry is {}", clientParams.getMaxNumberOfRetry());
|
||||
|
||||
clientParams
|
||||
.setRequestDelay(
|
||||
Optional
|
||||
.ofNullable(argumentParser.get(REQUEST_DELAY))
|
||||
.map(Integer::parseInt)
|
||||
.orElse(HttpClientParams._requestDelay));
|
||||
log.info("requestDelay is {}", clientParams.getRequestDelay());
|
||||
|
||||
clientParams
|
||||
.setRetryDelay(
|
||||
Optional
|
||||
.ofNullable(argumentParser.get(RETRY_DELAY))
|
||||
.map(Integer::parseInt)
|
||||
.orElse(HttpClientParams._retryDelay));
|
||||
log.info("retryDelay is {}", clientParams.getRetryDelay());
|
||||
|
||||
clientParams
|
||||
.setRequestMethod(
|
||||
Optional
|
||||
.ofNullable(argumentParser.get(REQUEST_METHOD))
|
||||
.orElse(HttpClientParams._requestMethod));
|
||||
log.info("requestMethod is {}", clientParams.getRequestMethod());
|
||||
|
||||
return clientParams;
|
||||
}
|
||||
|
||||
public static BufferedReader getFileReader(FileSystem fs, Path inputPath) throws IOException {
|
||||
FSDataInputStream inputStream = fs.open(inputPath);
|
||||
return new BufferedReader(
|
||||
new InputStreamReader(inputStream, StandardCharsets.UTF_8));
|
||||
}
|
||||
|
||||
public static SequenceFile.Writer getSequenceFileWriter(FileSystem fs, String outputPath) throws IOException {
|
||||
return SequenceFile
|
||||
.createWriter(
|
||||
fs.getConf(),
|
||||
SequenceFile.Writer.file(new Path(outputPath)),
|
||||
SequenceFile.Writer.keyClass(Text.class),
|
||||
SequenceFile.Writer.valueClass(Text.class));
|
||||
}
|
||||
|
||||
public static SequenceFile.Reader getSequenceFileReader(FileSystem fs, String inputPath) throws IOException {
|
||||
Path filePath = new Path(inputPath);
|
||||
SequenceFile.Reader.Option fileOption = SequenceFile.Reader.file(filePath);
|
||||
|
||||
return new SequenceFile.Reader(fs.getConf(), fileOption);
|
||||
}
|
||||
|
||||
public static void appendToSequenceFile(SequenceFile.Writer fw, String keyStr, String valueStr) throws IOException {
|
||||
Text key = new Text();
|
||||
key.set(keyStr);
|
||||
|
||||
Text value = new Text();
|
||||
value.set(valueStr);
|
||||
|
||||
fw.append(key, value);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
[
|
||||
{
|
||||
"paramName": "n",
|
||||
"paramLongName": "namenode",
|
||||
"paramDescription": "the Name Node URI",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "lv",
|
||||
"paramLongName": "lastVisitsPath",
|
||||
"paramDescription": "the URL where to store last visits data",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "arp",
|
||||
"paramLongName": "archiveRequestsPath",
|
||||
"paramDescription": "the URL where to store the responses of the archive requests",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "mnr",
|
||||
"paramLongName": "maxNumberOfRetry",
|
||||
"paramDescription": "the maximum number of admitted connection retries",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rqd",
|
||||
"paramLongName": "requestDelay",
|
||||
"paramDescription": "the delay (ms) between requests",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rtd",
|
||||
"paramLongName": "retryDelay",
|
||||
"paramDescription": "the delay (ms) between retries",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rm",
|
||||
"paramLongName": "requestMethod",
|
||||
"paramDescription": "the method of the requests to perform",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "atid",
|
||||
"paramLongName": "archiveThresholdInDays",
|
||||
"paramDescription": "the thershold (in days) required to issue an archive request",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "aat",
|
||||
"paramLongName": "apiAccessToken",
|
||||
"paramDescription": "the API access token of the SWH API",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
[
|
||||
{
|
||||
"paramName": "n",
|
||||
"paramLongName": "namenode",
|
||||
"paramDescription": "the Name Node URI",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "scr",
|
||||
"paramLongName": "softwareCodeRepositoryURLs",
|
||||
"paramDescription": "the URL from where to read software repository URLs",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "lv",
|
||||
"paramLongName": "lastVisitsPath",
|
||||
"paramDescription": "the URL where to store last visits data",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "mnr",
|
||||
"paramLongName": "maxNumberOfRetry",
|
||||
"paramDescription": "the maximum number of admitted connection retries",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rqd",
|
||||
"paramLongName": "requestDelay",
|
||||
"paramDescription": "the delay (ms) between requests",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rtd",
|
||||
"paramLongName": "retryDelay",
|
||||
"paramDescription": "the delay (ms) between retries",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "rm",
|
||||
"paramLongName": "requestMethod",
|
||||
"paramDescription": "the method of the requests to perform",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "aat",
|
||||
"paramLongName": "apiAccessToken",
|
||||
"paramDescription": "the API access token of the SWH API",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "scr",
|
||||
"paramLongName": "softwareCodeRepositoryURLs",
|
||||
"paramDescription": "the URL where to store software repository URLs",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "db",
|
||||
"paramLongName": "hiveDbName",
|
||||
"paramDescription": "the target hive database name",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "hmu",
|
||||
"paramLongName": "hiveMetastoreUris",
|
||||
"paramDescription": "the hive metastore uris",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "slim",
|
||||
"paramLongName": "softwareLimit",
|
||||
"paramDescription": "limit on the number of software repo URL to fetch",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "lv",
|
||||
"paramLongName": "lastVisitsPath",
|
||||
"paramDescription": "the URL where to store last visits data",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "ap",
|
||||
"paramLongName": "actionsetsPath",
|
||||
"paramDescription": "the URL path where to store actionsets",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "sip",
|
||||
"paramLongName": "softwareInputPath",
|
||||
"paramDescription": "the URL path of the software in the graph",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
# hive
|
||||
hiveDbName=openaire_prod_20230914
|
||||
|
||||
# input/output files
|
||||
softwareCodeRepositoryURLs=${workingDir}/1_code_repo_urls.csv
|
||||
lastVisitsPath=${workingDir}/2_last_visits.seq
|
||||
archiveRequestsPath=${workingDir}/3_archive_requests.seq
|
||||
actionsetsPath=${workingDir}/4_actionsets
|
||||
graphPath=/tmp/prod_provision/graph/18_graph_blacklisted
|
||||
|
||||
apiAccessToken=eyJhbGciOiJIUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJhMTMxYTQ1My1hM2IyLTQwMTUtODQ2Ny05MzAyZjk3MTFkOGEifQ.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.XHj1VIZu1dZ4Ej32-oU84mFmaox9cLNjXosNxwZM0Xs
|
||||
|
||||
maxNumberOfRetry=2
|
||||
retryDelay=1
|
||||
requestDelay=100
|
||||
|
||||
softwareLimit=500
|
||||
|
||||
resume=collect-software-repository-urls
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveMetastoreUris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/spark2ApplicationHistory</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozieActionShareLibForSpark2</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>resourceManager</name>
|
||||
<value>http://iis-cdh5-test-m2.ocean.icm.edu.pl:8088/cluster</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkSqlWarehouseDir</name>
|
||||
<value>/user/hive/warehouse</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,183 @@
|
|||
<workflow-app name="Software-Heritage-Integration-Workflow" xmlns="uri:oozie:workflow:0.5">
|
||||
|
||||
<!-- Custom parameters -->
|
||||
<parameters>
|
||||
<property>
|
||||
<name>hiveDbName</name>
|
||||
<description>The name of the Hive DB to be used</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>softwareCodeRepositoryURLs</name>
|
||||
<description>The path in the HDFS to save the software repository URLs</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>lastVisitsPath</name>
|
||||
<description>The path in the HDFS to save the responses of the last visit requests</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>archiveRequestsPath</name>
|
||||
<description>The path in the HDFS to save the responses of the archive requests</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>actionsetsPath</name>
|
||||
<description>The path in the HDFS to save the action sets</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>graphPath</name>
|
||||
<description>The path in the HDFS to the base folder of the graph</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>maxNumberOfRetry</name>
|
||||
<description>Max number of retries for failed API calls</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>retryDelay</name>
|
||||
<description>Retry delay for failed requests (in sec)</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>requestDelay</name>
|
||||
<description>Delay between API requests (in ms)</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>apiAccessToken</name>
|
||||
<description>The API Key of the SWH API</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>softwareLimit</name>
|
||||
<description>Limit on the number of repo URLs to use (Optional); for debug purposes</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>resumeFrom</name>
|
||||
<description>Variable that indicates the step to start from</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<!-- Global variables -->
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>actionsetsPath</name>
|
||||
<value>${actionsetsPath}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>apiAccessToken</name>
|
||||
<value>${apiAccessToken}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="startFrom"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<decision name="startFrom">
|
||||
<switch>
|
||||
<case to="collect-software-repository-urls">${wf:conf('resumeFrom') eq 'collect-software-repository-urls'}</case>
|
||||
<case to="create-swh-actionsets">${wf:conf('resumeFrom') eq 'create-swh-actionsets'}</case>
|
||||
<default to="collect-software-repository-urls"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<action name="collect-software-repository-urls">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Collect software repository URLs</name>
|
||||
<class>eu.dnetlib.dhp.swh.CollectSoftwareRepositoryURLs</class>
|
||||
<jar>dhp-swh-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
|
||||
<arg>--softwareCodeRepositoryURLs</arg><arg>${softwareCodeRepositoryURLs}</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
<arg>--softwareLimit</arg><arg>${softwareLimit}</arg>
|
||||
</spark>
|
||||
<ok to="collect-repository-last-visit-data"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="collect-repository-last-visit-data">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.swh.CollectLastVisitRepositoryData</main-class>
|
||||
|
||||
<arg>--namenode</arg><arg>${nameNode}</arg>
|
||||
<arg>--softwareCodeRepositoryURLs</arg><arg>${softwareCodeRepositoryURLs}</arg>
|
||||
<arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
|
||||
|
||||
<arg>--maxNumberOfRetry</arg><arg>${maxNumberOfRetry}</arg>
|
||||
<arg>--requestDelay</arg><arg>${requestDelay}</arg>
|
||||
<arg>--retryDelay</arg><arg>${retryDelay}</arg>
|
||||
<arg>--requestMethod</arg><arg>GET</arg>
|
||||
<arg>--apiAccessToken</arg><arg>${apiAccessToken}</arg>
|
||||
|
||||
</java>
|
||||
<ok to="archive-repository-urls"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="archive-repository-urls">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.swh.ArchiveRepositoryURLs</main-class>
|
||||
|
||||
<arg>--namenode</arg><arg>${nameNode}</arg>
|
||||
<arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
|
||||
<arg>--archiveRequestsPath</arg><arg>${archiveRequestsPath}</arg>
|
||||
<arg>--archiveThresholdInDays</arg><arg>365</arg>
|
||||
|
||||
<arg>--maxNumberOfRetry</arg><arg>${maxNumberOfRetry}</arg>
|
||||
<arg>--requestDelay</arg><arg>${requestDelay}</arg>
|
||||
<arg>--retryDelay</arg><arg>${retryDelay}</arg>
|
||||
<arg>--requestMethod</arg><arg>POST</arg>
|
||||
<arg>--apiAccessToken</arg><arg>${apiAccessToken}</arg>
|
||||
|
||||
</java>
|
||||
<ok to="create-swh-actionsets"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="create-swh-actionsets">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Create actionsets for SWH data</name>
|
||||
<class>eu.dnetlib.dhp.swh.PrepareSWHActionsets</class>
|
||||
<jar>dhp-swh-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
|
||||
<arg>--lastVisitsPath</arg><arg>${lastVisitsPath}</arg>
|
||||
<arg>--actionsetsPath</arg><arg>${actionsetsPath}</arg>
|
||||
<arg>--softwareInputPath</arg><arg>${graphPath}/software</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.File;
|
||||
import java.io.FileReader;
|
||||
import java.io.IOException;
|
||||
import java.text.ParseException;
|
||||
import java.util.Arrays;
|
||||
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import eu.dnetlib.dhp.swh.utils.SWHUtils;
|
||||
|
||||
public class ArchiveRepositoryURLsTest {
|
||||
|
||||
@Test
|
||||
void testArchive() throws IOException, ParseException {
|
||||
String inputPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/swh/lastVisitDataToArchive.csv")
|
||||
.getPath();
|
||||
|
||||
File file = new File(inputPath);
|
||||
FileReader fr = new FileReader(file);
|
||||
BufferedReader br = new BufferedReader(fr); // creates a buffering character input stream
|
||||
|
||||
String line;
|
||||
while ((line = br.readLine()) != null) {
|
||||
String[] tokens = line.split("\t");
|
||||
|
||||
String response = ArchiveRepositoryURLs.handleRecord(tokens[0], tokens[1], 365);
|
||||
System.out.println(tokens[0] + "\t" + response);
|
||||
System.out.println();
|
||||
}
|
||||
fr.close();
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,97 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeAll;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
|
||||
public class PrepareSWHActionsetsTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
|
||||
private static final Logger log = LoggerFactory
|
||||
.getLogger(PrepareSWHActionsetsTest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(PrepareSWHActionsetsTest.class.getSimpleName());
|
||||
|
||||
log.info("Using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(PrepareSWHActionsetsTest.class.getSimpleName());
|
||||
|
||||
conf.setMaster("local[*]");
|
||||
conf.set("spark.driver.host", "localhost");
|
||||
conf.set("hive.metastore.local", "true");
|
||||
conf.set("spark.ui.enabled", "false");
|
||||
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(PrepareSWHActionsetsTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRun() throws Exception {
|
||||
|
||||
String lastVisitsPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/swh/last_visits_data.seq")
|
||||
.getPath();
|
||||
|
||||
String outputPath = workingDir.toString() + "/actionSet";
|
||||
|
||||
String softwareInputPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/swh/software.json.gz")
|
||||
.getPath();
|
||||
|
||||
PrepareSWHActionsets
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-lastVisitsPath", lastVisitsPath,
|
||||
"-softwareInputPath", softwareInputPath,
|
||||
"-actionsetsPath", outputPath
|
||||
});
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,58 @@
|
|||
|
||||
package eu.dnetlib.dhp.swh;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.common.collection.CollectorException;
|
||||
import eu.dnetlib.dhp.common.collection.HttpClientParams;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHConnection;
|
||||
import eu.dnetlib.dhp.swh.utils.SWHConstants;
|
||||
|
||||
//import org.apache.hadoop.hdfs.MiniDFSCluster;
|
||||
|
||||
public class SWHConnectionTest {
|
||||
private static final Logger log = LoggerFactory.getLogger(SWHConnectionTest.class);
|
||||
|
||||
@Test
|
||||
void testGetCall() throws IOException {
|
||||
|
||||
HttpClientParams clientParams = new HttpClientParams();
|
||||
clientParams.setRequestMethod("GET");
|
||||
|
||||
SWHConnection swhConnection = new SWHConnection(clientParams, null);
|
||||
|
||||
String repoUrl = "https://github.com/stanford-futuredata/FAST";
|
||||
URL url = new URL(String.format(SWHConstants.SWH_LATEST_VISIT_URL, repoUrl));
|
||||
String response = null;
|
||||
try {
|
||||
response = swhConnection.call(url.toString());
|
||||
} catch (CollectorException e) {
|
||||
System.out.println("Error in request: " + url);
|
||||
}
|
||||
System.out.println(response);
|
||||
}
|
||||
|
||||
@Test
|
||||
void testPostCall() throws MalformedURLException {
|
||||
HttpClientParams clientParams = new HttpClientParams();
|
||||
clientParams.setRequestMethod("POST");
|
||||
|
||||
SWHConnection swhConnection = new SWHConnection(clientParams, null);
|
||||
|
||||
String repoUrl = "https://github.com/stanford-futuredata/FAST";
|
||||
URL url = new URL(String.format(SWHConstants.SWH_ARCHIVE_URL, SWHConstants.DEFAULT_VISIT_TYPE, repoUrl));
|
||||
String response = null;
|
||||
try {
|
||||
response = swhConnection.call(url.toString());
|
||||
} catch (CollectorException e) {
|
||||
System.out.println("Error in request: " + url);
|
||||
}
|
||||
System.out.println(response);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
https://bitbucket.org/samskillman/yt-stokes {"origin":"https://bitbucket.org/samskillman/yt-stokes","visit":43,"date":"2021-09-13T21:59:27.125171+00:00","status":"failed","snapshot":null,"type":"hg","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://bitbucket.org/samskillman/yt-stokes/get/","snapshot_url":null}
|
||||
https://github.com/bioinsilico/BIPSPI {"origin":"https://github.com/bioinsilico/BIPSPI","visit":1,"date":"2020-03-18T14:50:21.541822+00:00","status":"full","snapshot":"c6c69d2cd73ce89811448da5f031611df6f63bdb","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/bioinsilico/BIPSPI/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/c6c69d2cd73ce89811448da5f031611df6f63bdb/"}
|
||||
https://github.com/mloop/kdiff-type1-error-rate/blob/master/analysis/simulation.R {}
|
||||
https://github.com/schwanbeck/YSMR {"origin":"https://github.com/schwanbeck/YSMR","visit":6,"date":"2023-08-02T15:25:02.650676+00:00","status":"full","snapshot":"a9d1c5f0bca2def198b89f65bc9f7da3be8439ed","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/schwanbeck/YSMR/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/a9d1c5f0bca2def198b89f65bc9f7da3be8439ed/"}
|
||||
https://github.com/lvclark/TASSELGBS_combine {"origin":"https://github.com/lvclark/TASSELGBS_combine","visit":1,"date":"2020-04-12T20:44:09.405589+00:00","status":"full","snapshot":"ffa6fefd3f5becefbea9fe0e6d5d93859c95c071","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/lvclark/TASSELGBS_combine/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/ffa6fefd3f5becefbea9fe0e6d5d93859c95c071/"}
|
||||
https://github.com/PRIDE-Toolsuite/inspector-example-files {"origin":"https://github.com/PRIDE-Toolsuite/inspector-example-files","visit":12,"date":"2021-01-25T08:54:13.394674+00:00","status":"full","snapshot":"0b56eb0ad07cf778df6dabefc4b73636e0ae8b37","type":"git","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://github.com/PRIDE-Toolsuite/inspector-example-files/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/0b56eb0ad07cf778df6dabefc4b73636e0ae8b37/"}
|
||||
https://bitbucket.org/matwey/chelyabinsk {"origin":"https://bitbucket.org/matwey/chelyabinsk","visit":6,"date":"2021-09-24T19:32:43.322909+00:00","status":"full","snapshot":"215913858c3ee0e61e1aaea18241c5ee006da1b0","type":"hg","metadata":{},"origin_url":"https://archive.softwareheritage.org/api/1/origin/https://bitbucket.org/matwey/chelyabinsk/get/","snapshot_url":"https://archive.softwareheritage.org/api/1/snapshot/215913858c3ee0e61e1aaea18241c5ee006da1b0/"}
|
||||
|
Can't render this file because it contains an unexpected character in line 1 and column 46.
|
Binary file not shown.
Binary file not shown.
|
|
@ -39,6 +39,7 @@
|
|||
<module>dhp-broker-events</module>
|
||||
<module>dhp-doiboost</module>
|
||||
<module>dhp-impact-indicators</module>
|
||||
<module>dhp-swh</module>
|
||||
</modules>
|
||||
|
||||
<pluginRepositories>
|
||||
|
|
|
|||
Loading…
Reference in New Issue