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dhp-graph-dump
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[dump] refactoring

This commit is contained in:
Miriam Baglioni 2023-07-19 09:40:48 +02:00
parent 2566b97138
commit a175ac2c7f
12 changed files with 56 additions and 49 deletions
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2
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java
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@ -53,7 +53,7 @@ public class Utils {
return String
.format(
"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
"%s::%s", Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5(id));
}

8
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/Constants.java
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.oa.graph.dump.csv;
import org.apache.commons.lang.StringUtils;
import java.io.Serializable;
import org.apache.commons.lang.StringUtils;
/**
* @author miriam.baglioni
* @Date 10/05/23
@ -13,8 +13,8 @@ public class Constants implements Serializable {
public final static String SEP = "\t";
public static final String addQuotes(String id) {
if(StringUtils.isNotEmpty(id))
return "\"" + id + "\"";
// if (StringUtils.isNotEmpty(id))
// return "\"" + id + "\"";
return id;
}
}

11
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/SparkDumpResults.java
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@ -347,12 +347,15 @@ public class SparkDumpResults implements Serializable {
}
private static String removeBreaks(String input) {
return input.replace("\n", " ")
if (StringUtils.isNotEmpty(input))
return input
.replace("\n", " ")
.replace("\t", " ")
.replace("\r", " ")
.replace("\\\"", " ")
.replace("\"", " ")
;
//.replace("\\", " ")
.replace("\"", " ");
return input;
}

4
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVAuthor.java
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.oa.graph.dump.csv.model;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
import java.io.Serializable;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
/**
* @author miriam.baglioni
* @Date 11/05/23

4
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVCitation.java
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.oa.graph.dump.csv.model;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
import java.io.Serializable;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
/**
* @author miriam.baglioni
* @Date 11/05/23

4
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVPid.java
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.oa.graph.dump.csv.model;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
import java.io.Serializable;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
/**
* @author miriam.baglioni
* @Date 11/05/23

4
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRELCommunityResult.java
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.oa.graph.dump.csv.model;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
import java.io.Serializable;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
/**
* @author miriam.baglioni
* @Date 11/05/23

4
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVRelResAut.java
View File

@ -1,10 +1,10 @@
package eu.dnetlib.dhp.oa.graph.dump.csv.model;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
import java.io.Serializable;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
/**
* @author miriam.baglioni
* @Date 11/05/23

9
dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/csv/model/CSVResult.java
View File

@ -3,13 +3,13 @@ package eu.dnetlib.dhp.oa.graph.dump.csv.model;
import java.io.Serializable;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
import org.apache.commons.lang.StringUtils;
import com.fasterxml.jackson.annotation.JsonGetter;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonSetter;
import eu.dnetlib.dhp.oa.graph.dump.csv.Constants;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import sun.swing.StringUIClientPropertyKey;
@ -38,7 +38,6 @@ public class CSVResult implements Serializable {
this.id = Constants.addQuotes(id);
}
public String getType() {
return type;
}
@ -52,8 +51,7 @@ public class CSVResult implements Serializable {
}
public void setTitle(String title) {
this.title =
Constants.addQuotes(title);
this.title = Constants.addQuotes(title);
}
public String getDescription() {
@ -61,8 +59,7 @@ public class CSVResult implements Serializable {
}
public void setDescription(String description) {
this.description =
Constants.addQuotes(description);
this.description = Constants.addQuotes(description);
}
public String getAccessright() {

34
dump/src/main/java/eu/dnetlib/dhp/oa/zenodoapi/ZenodoAPIClient.java
View File

@ -18,7 +18,7 @@ import org.apache.http.entity.ContentType;
import org.apache.http.entity.InputStreamEntity;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
//import org.apache.http.impl.client.HttpClients;
// import org.apache.http.impl.client.HttpClients;
import org.apache.http.util.EntityUtils;
import org.jetbrains.annotations.NotNull;
@ -108,11 +108,11 @@ public class ZenodoAPIClient implements Serializable {
RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON);
Request request = new Request.Builder()
.url(urlString)
.addHeader("Content-Type", "application/json") // add request headers
.addHeader("Authorization", "Bearer " + access_token)
.post(body)
.build();
.url(urlString)
.addHeader("Content-Type", "application/json") // add request headers
.addHeader("Authorization", "Bearer " + access_token)
.post(body)
.build();
try (Response response = httpClient.newCall(request).execute()) {
@ -122,7 +122,8 @@ public class ZenodoAPIClient implements Serializable {
// Get response body
json = response.body().string();
eu.dnetlib.dhp.common.api.zenodo.ZenodoModel newSubmission = new Gson().fromJson(json, eu.dnetlib.dhp.common.api.zenodo.ZenodoModel.class);
eu.dnetlib.dhp.common.api.zenodo.ZenodoModel newSubmission = new Gson()
.fromJson(json, eu.dnetlib.dhp.common.api.zenodo.ZenodoModel.class);
this.bucket = newSubmission.getLinks().getBucket();
this.deposition_id = newSubmission.getId();
@ -132,7 +133,6 @@ public class ZenodoAPIClient implements Serializable {
}
// public int uploadIS2(InputStream is, String fileName) throws IOException {
//
// final String crlf = "\r\n";
@ -340,10 +340,10 @@ public class ZenodoAPIClient implements Serializable {
RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON);
Request request = new Request.Builder()
.url(urlString + "/" + deposition_id + "/actions/newversion")
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.post(body)
.build();
.url(urlString + "/" + deposition_id + "/actions/newversion")
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.post(body)
.build();
try (Response response = httpClient.newCall(request).execute()) {
@ -445,11 +445,11 @@ public class ZenodoAPIClient implements Serializable {
String url = urlBuilder.build().toString();
Request request = new Request.Builder()
.url(url)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.get()
.build();
.url(url)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.get()
.build();
try (Response response = httpClient.newCall(request).execute()) {

13
dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java
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@ -7,8 +7,6 @@ import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import eu.dnetlib.dhp.oa.zenodoapi.ZenodoAPIClient;
import eu.dnetlib.dhp.oa.zenodoapi.MissingConceptDoiException;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import org.junit.jupiter.api.Assertions;
@ -19,7 +17,8 @@ import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.oa.zenodoapi.MissingConceptDoiException;
import eu.dnetlib.dhp.oa.zenodoapi.ZenodoAPIClient;
@Disabled
public class ZenodoUploadTest {
@ -86,8 +85,7 @@ public class ZenodoUploadTest {
System.out.println(client.sendMretadata(metadata));
//System.out.println(client.publish());
// System.out.println(client.publish());
}
@ -138,7 +136,7 @@ public class ZenodoUploadTest {
}
//System.out.println(client.publish());
// System.out.println(client.publish());
}
@ -146,7 +144,7 @@ public class ZenodoUploadTest {
void testNewVersion2() throws Exception, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
ACCESS_TOKEN);
client.newVersion("1210237");
@ -162,6 +160,7 @@ public class ZenodoUploadTest {
// Assertions.assertEquals(202, client.publish());
}
@Test
void readCommunityMap() throws IOException {
LocalFileSystem fs = FileSystem.getLocal(new Configuration());

8
dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/csv/DumpResultTest.java
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@ -347,4 +347,12 @@ public class DumpResultTest {
builder.append(((Node) (root.selectNodes("//description").get(0))).getText());
System.out.println(builder.toString());
}
@Test
public void provaReplacement(){
String st = "\"Person in the sand " + "\"";
System.out.println(st);
System.out.println(st.replace("\\\"", " "));
}
}