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This commit is contained in:
Miriam Baglioni 2020-07-08 10:29:37 +02:00
parent 375ef07d7b
commit 7fe00cb4fb
5 changed files with 11 additions and 23 deletions
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5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java
View File

@ -20,15 +20,14 @@ public class QueryInformationSystem {
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+ +
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') "
+
" return " + " return " +
"<community> " + "<community> " +
"{$x//CONFIGURATION/context/@id}" + "{$x//CONFIGURATION/context/@id}" +
"{$x//CONFIGURATION/context/@label}" + "{$x//CONFIGURATION/context/@label}" +
"</community>"; "</community>";
public CommunityMap getCommunityMap() public CommunityMap getCommunityMap()
throws ISLookUpException { throws ISLookUpException {
return getMap(isLookUp.quickSearchProfile(XQUERY)); return getMap(isLookUp.quickSearchProfile(XQUERY));

15
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SparkSplitForCommunity.java
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@ -99,14 +99,15 @@ public class SparkSplitForCommunity implements Serializable {
private static void printResult(String c, Dataset<Result> result, String outputPath) { private static void printResult(String c, Dataset<Result> result, String outputPath) {
Dataset<Result> community_products = result Dataset<Result> community_products = result
.filter(r -> containsCommunity(r, c)); .filter(r -> containsCommunity(r, c));
if(community_products.count() > 0){ if (community_products.count() > 0) {
community_products.repartition(1) community_products
.write() .repartition(1)
.option("compression", "gzip") .write()
.mode(SaveMode.Overwrite) .option("compression", "gzip")
.json(outputPath + "/" + c); .mode(SaveMode.Overwrite)
.json(outputPath + "/" + c);
} }
} }

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/workflow.xml
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@ -362,7 +362,7 @@
<arg>--outputPath</arg><arg>${outputPath}</arg> <arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg> <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark> </spark>
<ok to="End"/> <ok to="send_zenodo"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>

8
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java
View File

@ -63,8 +63,6 @@ public class DumpJobTest {
} }
List<String> communityMap = Arrays List<String> communityMap = Arrays
.asList( .asList(
"<community id=\"egi\" label=\"EGI Federation\"/>", "<community id=\"egi\" label=\"EGI Federation\"/>",
@ -122,8 +120,6 @@ public class DumpJobTest {
.getOrCreate(); .getOrCreate();
} }
@AfterAll @AfterAll
public static void afterAll() throws IOException { public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile()); FileUtils.deleteDirectory(workingDir.toFile());
@ -146,7 +142,6 @@ public class DumpJobTest {
"-communityMap", new Gson().toJson(map) "-communityMap", new Gson().toJson(map)
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.Result> tmp = sc JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.Result> tmp = sc
@ -186,7 +181,6 @@ public class DumpJobTest {
Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90);
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) //TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
} }
@ -275,7 +269,6 @@ public class DumpJobTest {
"-communityMap", new Gson().toJson(map) "-communityMap", new Gson().toJson(map)
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.Result> tmp = sc JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.Result> tmp = sc
@ -294,7 +287,6 @@ public class DumpJobTest {
} }
@Test @Test
public void testRecord() throws Exception { public void testRecord() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()

4
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java
View File

@ -37,7 +37,6 @@ public class ZenodoUploadTest {
.toString(); .toString();
} }
@Test @Test
public void HDFSConnection() throws IOException { public void HDFSConnection() throws IOException {
CommunityMap communityMap = new CommunityMap(); CommunityMap communityMap = new CommunityMap();
@ -58,7 +57,6 @@ public class ZenodoUploadTest {
.getPath()), .getPath()),
new Path(workingDir + "/zenodo/dh-ch/dh-ch")); new Path(workingDir + "/zenodo/dh-ch/dh-ch"));
APIClient client = new APIClient(URL_STRING, APIClient client = new APIClient(URL_STRING,
ACCESS_TOKEN); ACCESS_TOKEN);
client.connect(); client.connect();
@ -88,7 +86,6 @@ public class ZenodoUploadTest {
} }
String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}"; String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}";
System.out.println(client.sendMretadata(metadata)); System.out.println(client.sendMretadata(metadata));
@ -97,5 +94,4 @@ public class ZenodoUploadTest {
} }
} }