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refactoring

This commit is contained in:
Miriam Baglioni 2020-04-16 10:48:41 +02:00
parent 3577219127
commit 79b978ec57
6 changed files with 96 additions and 101 deletions

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@ -1,34 +1,16 @@
package eu.dnetlib.dhp.projecttoresult; package eu.dnetlib.dhp.projecttoresult;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.countrypropagation.DatasourceCountry;
import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation; import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation;
import eu.dnetlib.dhp.countrypropagation.ResultCountrySet;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.arrow.flatbuf.Bool;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.FlatMapFunction2;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*; import org.apache.spark.sql.*;
import org.omg.CORBA.OBJ_ADAPTER;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.List; import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@ -50,9 +32,6 @@ public class SparkResultToProjectThroughSemRelJob3 {
Boolean isSparkSessionManaged = isSparkSessionManaged(parser); Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath); log.info("outputPath {}: ", outputPath);
@ -143,86 +122,6 @@ public class SparkResultToProjectThroughSemRelJob3 {
} }
private static void writeUpdates(JavaRDD<ProjectResultSet> potentialUpdates, String outputPath){
potentialUpdates.map(u -> OBJECT_MAPPER.writeValueAsString(u))
.saveAsTextFile(outputPath, GzipCodec.class);
}
//JavaPairRDD<String, TypedRow> result_result = getResultResultSemRel(allowedsemrel, relations);
// JavaPairRDD<String, TypedRow> result_project = relations
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
// .filter(r -> RELATION_RESULT_PROJECT_REL_CLASS.equals(r.getRelClass())
// && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
// .map(rel ->{
//
// TypedRow tr = new TypedRow();
// tr.setSourceId(rel.getSource());
// tr.setTargetId(rel.getTarget());
// return tr;
// })
// .mapToPair(toPair());
//
// //relationships from project to result. One pair for each relationship for results having allowed semantics relation with another result
// JavaPairRDD<String, TypedRow> project_result = result_project.join(result_result)
// .map(c -> {
// String projectId = c._2()._1().getTargetId();
// String resultId = c._2()._2().getTargetId();
// TypedRow tr = new TypedRow(); tr.setSourceId(projectId); tr.setTargetId(resultId);
// return tr;
// })
// .mapToPair(toPair());
//
// //relationships from project to result. One Pair for each project => project id list of results related to the project
// JavaPairRDD<String, TypedRow> project_results = relations
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
// .filter(r -> RELATION_PROJECT_RESULT_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()))
// .map(r -> {
// TypedRow tr = new TypedRow(); tr.setSourceId(r.getSource()); tr.setTargetId(r.getTarget());
// return tr;
// })
// .mapToPair(toPair())
// .reduceByKey((a, b) -> {
// if (a == null) {
// return b;
// }
// if (b == null) {
// return a;
// }
// a.addAll(b.getAccumulator());
// return a;
// });
//
//
//
// JavaRDD<Relation> newRels = project_result.join(project_results)
// .flatMap(c -> {
// String resId = c._2()._1().getTargetId();
//
// if (c._2()._2().getAccumulator().contains(resId)) {
// return null;
// }
// String progId = c._2()._1().getSourceId();
// List<Relation> rels = new ArrayList();
//
// rels.add(getRelation(progId, resId, RELATION_PROJECT_RESULT_REL_CLASS,
// RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
// PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
// rels.add(getRelation(resId, progId, RELATION_RESULT_PROJECT_REL_CLASS,
// RELATION_RESULTPROJECT_REL_TYPE, RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
// PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID, PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
// return rels.iterator();
// })
// .cache();
//
// newRels.map(p -> new ObjectMapper().writeValueAsString(p))
// .saveAsTextFile(outputPath + "/relation_new");
//
// newRels.union(relations).map(p -> new ObjectMapper().writeValueAsString(p))
// .saveAsTextFile(outputPath + "/relation");
//}
private static Dataset<ProjectResultSet> readAssocProjectResults(SparkSession spark, String potentialUpdatePath) { private static Dataset<ProjectResultSet> readAssocProjectResults(SparkSession spark, String potentialUpdatePath) {
return spark return spark
.read() .read()

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@ -0,0 +1,20 @@
{"resultId":"50|acm_________::3133635707788d2180bcef09e01a903c","organizationSet":["20|dedup_wf_001::5ab59ffa94c31a140d4a56c594ea5865"]}
{"resultId":"50|core________::0308a76f6f8bc4db75a817d53a7e76a4","organizationSet":["20|wt__________::a72760363ca885e6bef165804770e00c","20|nih_________::5c7f089c177ba49f92033f72e2aff724","20|dedup_wf_001::c88bf88e0a4dea271a3e2f832d952238"]}
{"resultId":"50|core________::04c8f896aef9e54867f2bf4236e9c810","organizationSet":["20|snsf________::1496b1b4fc4d5509b16f2c217be480dc","20|dedup_wf_001::06731b587a9ea654103a6b0ebcb234ff","20|nih_________::c5722b087a5e707a50aa8f9f2ebf785d","20|snsf________::71d0a944b61b1a94068595f840005a2f","20|nih_________::dd3428794aef214a3bc2cad6dd548ba6","20|rcuk________::45aac2108e54b6503d1e611aa5872c03","20|nih_________::e1d47fdb7bba9eaeed82a95c578d6e90","20|dedup_wf_001::e3b52200d2fd4ff883478f5bef312efe","20|snsf________::c5c565d3422a7eb22886f3a4c93c32ea","20|nih_________::91154321f75ba26021efa18f7eeaa541","20|wt__________::38013971ca0c021fd65abce2171b82eb","20|wt__________::a6114989a56a1dfae6cbb201d14823f0","20|snsf________::b7af2f99e1e06750a4664ae401802734","20|wt__________::757c54e33d4e925c8c17edf032cdfacc","20|wt__________::1d57a87af1bbc2b7e211305fc747c9ad","20|wt__________::7cbb8c06f702b8871948acd370df892f","20|dedup_wf_001::53a8606f32787c4b3c663fd90ee97b17","20|wt__________::8473a929b793e56d2299a1a5aa08f617","20|nih_________::5e0fc2ef31bc189207f250db818fea0e","20|nih_________::1cd08fd26ef03fd2f51e9aeb34ed9486","20|nih_________::1c270e0dd2552b4e3cf295cdb7db1cc9","20|wt__________::04abd842647bdbc751b1eebe2f142013","20|nsf_________::3eaa8be3f16b0f0d7563b9117cd1f660","20|dedup_wf_001::c1b81dadf1e4cbf23a61833ff9ae8a31","20|nih_________::3716e1c14ab7ca14161278c9bbb8bdbb","20|dedup_wf_001::b7b403a764ea4e3acb12d999675aa73c","20|nih_________::300049f12fa0f5bc37db3a5636869743","20|wt__________::ed1e2be693353d370066fddbf862f23a","20|nsf_________::72a3747a18c56f3701494a0c0eadc5c9","20|rcuk________::e8877abcab4bc187339a242aa5bc2e09","20|microsoft___::119a535bfd240d7560fe4efec416bcd2","20|wt__________::be4e939abf9617557a35862e255493da","20|dedup_wf_001::3f6f17996747467f6047dfe019c8e4c7","20|snsf________::1f4e34433767faf965f33849bb0f7fb1","20|dedup_wf_001::9f1647eae28911113d1dcbe49c42275b","20|opendoar____::6835febcf408fe892504bdfd2ebe669c","20|dedup_wf_001::528bd21573101493c6c7d120b17a67e9"]}
{"resultId":"50|core________::061dc912098a6a52e85a824161bd32a2","organizationSet":["20|dedup_wf_001::67f983a98e2c0cc0121e2db46d2bd00a","20|wt__________::59b5d99b2dde58df1655e0e5bb236c0a","20|wt__________::e84b06dbc1b26f413791c1304ca8d6a3","20|dedup_wf_001::7b118dab509f49b4fbd6dccfdbc479af","20|wt__________::53c2c2895613ff9b759f64c24b6cb17c","20|nih_________::43255cf9c16732bc4ec1d5f580f44928","20|gsrt________::455b984b47945e1fd04e92c9c0eeca04","20|dedup_wf_001::e712c08f721e8f167f93888f590314ea","20|rcuk________::8b0aee2a7026dc92d4c05683ae45c894","20|dedup_wf_001::3c19a02cea18f8eeb2034b6acc544b7e","20|wt__________::26a9d64d00b8e1005cb6bbad2b7364cf","20|rcuk________::e57ab9be7acd7b93ba34aafab1a5b96c","20|nih_________::ca09277064edbd89f71e1602d98b4dd8","20|gsrt________::7c309ee758e6c6e0dce43c67b9343e82","20|nsf_________::53c2c2895613ff9b759f64c24b6cb17c","20|nih_________::c57387345f51a40ad2284089b120be3f"]}
{"resultId":"50|core________::088190cf9dc9632e8d9ba5f5f1de1303","organizationSet":["20|dedup_wf_001::286621caef868bbdc52918699e3cdc79","20|dedup_wf_001::84707a912d45d666fef35c5cd77fc203","20|dedup_wf_001::30fd03f4977438b0471a1d4db6317e71","20|dedup_wf_001::83d9dc4a0eba8737819b87ce8e737a49","20|dedup_wf_001::aeb9e738d873acebdca52c9ccd9559bd","20|dedup_wf_001::427a8bfe68648f9e30cb47434144da68","20|nih_________::ffa0ea174845f1548e520a047cf53165"]}
{"resultId":"50|core________::117d295998199f498fa561e9c26e7ae3","organizationSet":["20|dedup_wf_001::d9f82e62c3114dc7f42b9da9b7f6fc64"]}
{"resultId":"50|core________::168a8f2e4ffe9b0e7c6bc100f34f2de5","organizationSet":["20|wt__________::63fe73f079c5ff4e925c6cfc1758a98b","20|dedup_wf_001::b3c2f5e700cee15ad9752ab961df5930"]}
{"resultId":"50|core________::16a3b520030d82ad16a30992b124e69d","organizationSet":["20|wt__________::a72760363ca885e6bef165804770e00c","20|nih_________::5c7f089c177ba49f92033f72e2aff724","20|dedup_wf_001::c88bf88e0a4dea271a3e2f832d952238"]}
{"resultId":"50|core________::172e3da668d18f41ea4ccdf7f2f39e53","organizationSet":["20|nih_________::126cbf4b13249e65098ddb4835f47456","20|aka_________::506e3d2f7507a66584b8b3430ade20cb","20|dedup_wf_001::4746df4ff8bbb7e991ad343ccff8bbc7","20|wt__________::aff5133ca9cf0b810cc331d498bac9b0","20|wt__________::0c3bf892603817e5eff6e4f08a530ea2"]}
{"resultId":"50|core________::19f2fc91fe1db2ad62db598aa9aa8ab3","organizationSet":["20|dedup_wf_001::dbbd988f8d57a9d11286caefdf35acaa"]}
{"resultId":"50|core________::1dceb5a29cd42728e410474fe0fda191","organizationSet":["20|wt__________::b1ef2f643c948a2ef49005f9145ed556","20|dedup_wf_001::866fa622e3c0ab6227cd462f40cdcac8","20|rcuk________::63ecf5736189d299fc3e043e14428b8d","20|nsf_________::fcf880eab7315e0a5f3937c5a16c04b0","20|dedup_wf_001::65862ec7d57f700a130dee916bea66de"]}
{"resultId":"50|core________::2580c0b59b7457f571acdc829d1765a3","organizationSet":["20|doajarticles::0f6e2c32a27c307b06edf7862c591973","20|opendoar____::4f10fb61c457cf124e5917391baaa3c2"]}
{"resultId":"50|core________::2624b8248a9febdad9bc456d358b30ed","organizationSet":["20|dedup_wf_001::fb4eba3cea53264bddd59a4ade9973b3","20|rcuk________::b00968d2100a4b62447841aef5bdff62"]}
{"resultId":"50|core________::26820a282ef54882f7a5be74767fc02b","organizationSet":["20|rcuk________::8ad6d06f3b4d09dc67142c158c7cf5b9","20|rcuk________::01ad471b66687b1213ceb08b5d7aa6c2"]}
{"resultId":"50|core________::2a8de3e0bbcab49066aa9de4bbb89bfa","organizationSet":["20|dedup_wf_001::2ea78875d19c8cea63f7e958e5204136","20|corda_______::6821a8e260b8b97f5fb5e80168329d5b","20|dedup_wf_001::9d0ba437d73b19f55b53c578ac970ea2"]}
{"resultId":"50|core________::2c7d139419d2895d3bf0112b50108f75","organizationSet":["20|dedup_wf_001::96ada508ea5d85a1e516bf9799413906","20|dedup_wf_001::d0ea749da6988bcdb2f30d77c64e2f1e","20|wt__________::f1ba5bd552edf15db494dc3020f27470","20|nih_________::ceeae4f78a5666daf4c45acdbbedde99","20|wt__________::84ef588eeeb4ef77e45ccfbbf3aef69c","20|wt__________::8eef7e1370ea81c2aa3dbc239b2bf5d8"]}
{"resultId":"50|core________::2cf1f6282498fa37aeaf678f8c6e5843","organizationSet":["20|snsf________::73999c828ca67fd2d006100a8369c1eb"]}
{"resultId":"50|core________::2dffff00500c2354b506814f6a1ec148","organizationSet":["20|wt__________::c6d89e908582fddf3e4c658a458807c3","20|wt__________::e7b2c9f3d3f3f1503092bf1ba2b163db","20|gsrt________::ab510bb43d6c654ed3d37b9c5ed5c971","20|dedup_wf_001::179d0313fa7d5fb2bef5f312ecdd16fe","20|gsrt________::cbffb510b01e81cc055fe61105c86154","20|opendoar____::5d462d78d512c1184dd384ef2dc35b7e","20|dedup_wf_001::646f14555ea42b260499239a7231b285","20|wt__________::5d462d78d512c1184dd384ef2dc35b7e","20|nih_________::a32a254b024265db2e24a66291c7c1e0","20|dedup_wf_001::5490ec18da9721e2c8d974fb73c62467","20|dedup_wf_001::3bc91ed90f44d0908258e132659bc754"]}
{"resultId":"50|core________::3031a50bf5c80865af4841ab42aaf57e","organizationSet":["20|nih_________::1b46e3665d8be2b524c285a27ca952b8","20|nsf_________::71450a4b98015592ee3f525a51584608","20|snsf________::fc921725875adb56f2275579b31f805c","20|aka_________::fa5b7357f86c71ea15734282054f1183","20|wt__________::18fdb5b42b22fdcc45e323eb4d20c91b","20|wt__________::71450a4b98015592ee3f525a51584608","20|dedup_wf_001::8aaf46d4e4919dc55b8a5cac7a15399f"]}
{"resultId":"50|core________::31116372ae189ee456fc06dfa0f6cf7a","organizationSet":["20|aka_________::c5b9aa0a905f89c51221f9f4fda22b20","20|aka_________::d9d3242062a7a3c483a7926fdba17bb6","20|nih_________::ede5c9e31cfb37a397d6cfe1940d045e","20|wt__________::8adcc12ffee195ae46679e8cf332a364","20|wt__________::5e954c57b0ac7aaf3fc16deeaf442389","20|snsf________::ddd964d550bfc6e1ce18f83655ba6901","20|rcuk________::a705d2ee7bf0bd225264b4a5794795ce","20|nih_________::8adcc12ffee195ae46679e8cf332a364","20|microsoft___::53732c6c7bb9daf5953fdb61fc0cd5bd"]}

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@ -0,0 +1,28 @@
{"datasourceId":"10|opendoar____::1068c6e4c8051cfd4e9ea8072e3189e2","organizationId":"20|opendoar____::4429502fa1936b0941f4647b69b844c8"}
{"datasourceId":"10|opendoar____::211ed78fe91938b90f84a51944b08d5a","organizationId":"20|opendoar____::124266ebc4ece2934eb80edfda3f2091"}
{"datasourceId":"10|opendoar____::21c5bba1dd6aed9ab48c2b34c1a0adde","organizationId":"20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2"}
{"datasourceId":"10|opendoar____::376c6b9ff3bedbbea56751a84fffc10c","organizationId":"20|opendoar____::c6ac1e6c39e6f3a36e274f8d3f9f7fce"}
{"datasourceId":"10|opendoar____::49c0fa7f96aa0a5fb95c62909d5190a6","organizationId":"20|dedup_wf_001::760a7568cbfdc750a5f92009a64bfc68"}
{"datasourceId":"10|opendoar____::4fa177df22864518b2d7818d4db5db2d","organizationId":"20|dedup_wf_001::b6b1fdfd98370bc44a5ecb215051fc61"}
{"datasourceId":"10|opendoar____::58521e4e2bd3d4b988cbd17d7365df3c","organizationId":"20|dedup_wf_001::09f3a5978add91bbfec7530e47c23fb6"}
{"datasourceId":"10|opendoar____::5dec707028b05bcbd3a1db5640f842c5","organizationId":"20|dedup_wf_001::7a34852b4b552a70789ccf070da2e558"}
{"datasourceId":"10|opendoar____::671d8d05d795091118b1344f715307c4","organizationId":"20|opendoar____::84e005eec7a780eafb0f5e54d438d56e"}
{"datasourceId":"10|opendoar____::79cc30c73507cfc25d20fe7f7bcfd91b","organizationId":"20|opendoar____::7230dc85992df9a4fa7026d44c9f5a24"}
{"datasourceId":"10|opendoar____::79e3eb7e992b7f766bdd77cc502ff082","organizationId":"20|dedup_wf_001::1e48cc6aee415348f0bdb3b7d3180091"}
{"datasourceId":"10|opendoar____::7af6266cc52234b5aa339b16695f7fc4","organizationId":"20|dedup_wf_001::cbfb7a433608c965dc59146c60e38dbf"}
{"datasourceId":"10|opendoar____::81e74d678581a3bb7a720b019f4f1a93","organizationId":"20|dedup_wf_001::3f6f17996747467f6047dfe019c8e4c7"}
{"datasourceId":"10|opendoar____::8744cf92c88433f8cb04a02e6db69a0d","organizationId":"20|opendoar____::f800da58d6ad6d35fc9cf57b982bbd1a"}
{"datasourceId":"10|opendoar____::8c01a75941549a705cf7275e41b21f0d","organizationId":"20|dedup_wf_001::ae993d8ee228ff161c2a8724f11c2403"}
{"datasourceId":"10|opendoar____::9cb67ffb59554ab1dabb65bcb370ddd9","organizationId":"20|opendoar____::2404720b8a764a4f576240a51a6cdd13"}
{"datasourceId":"10|opendoar____::9fc3d7152ba9336a670e36d0ed79bc43","organizationId":"20|dedup_wf_001::dc3a6f93b2cc529cd247a255b5127525"}
{"datasourceId":"10|opendoar____::a655fbe4b8d7439994aa37ddad80de56","organizationId":"20|opendoar____::bba529dfcc369815510999ccadff78d0"}
{"datasourceId":"10|opendoar____::aebf7782a3d445f43cf30ee2c0d84dee","organizationId":"20|opendoar____::931aa8950244dea6b3fe9f7798b916ea"}
{"datasourceId":"10|opendoar____::c4819d06b0ca810d38506453cfaae9d8","organizationId":"20|dedup_wf_001::bee19d6bbb94675a7a4aaf2b66f94ae3"}
{"datasourceId":"10|opendoar____::d88518acbcc3d08d1f18da62f9bb26ec","organizationId":"20|dedup_wf_001::f1914dbbcc2861e30d7e6b0e605013fd"}
{"datasourceId":"10|opendoar____::d8bf84be3800d12f74d8b05e9b89836f","organizationId":"20|dedup_wf_001::b19557d6f918479582295814b1dfb38b"}
{"datasourceId":"10|opendoar____::d8bf84be3800d12f74d8b05e9b89836f","organizationId":"20|opendoar____::c9c886345622486e072060cb814b9ebf"}
{"datasourceId":"10|opendoar____::e9fb2eda3d9c55a0d89c98d6c54b5b3e","organizationId":"20|opendoar____::64cf1b2094ff19786a573980568762b4"}
{"datasourceId":"10|opendoar____::f095cedd23b99f1696fc8caecbcf257e","organizationId":"20|dedup_wf_001::3f339760507dd23f9be59be2cff8204f"}
{"datasourceId":"10|opendoar____::f095cedd23b99f1696fc8caecbcf257e","organizationId":"20|dedup_wf_001::76548cf94fcd27f67759cc6148ee1e7f"}
{"datasourceId":"10|opendoar____::f35a2bc72dfdc2aae569a0c7370bd7f5","organizationId":"20|dedup_wf_001::2476836f27326ee53e586a82cbaedb1a"}
{"datasourceId":"10|opendoar____::f91e24dfe80012e2a7984afa4480a6d6","organizationId":"20|opendoar____::5d462d78d512c1184dd384ef2dc35b7e"}

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