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code formatting

This commit is contained in:
Claudio Atzori 2023-12-15 10:37:02 +01:00
parent a59be5779e 1763d377ad
commit 1726f49790
34 changed files with 2905 additions and 1160 deletions
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53
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/InputStreamRequestBody.java
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@ -1,53 +0,0 @@
package eu.dnetlib.dhp.common.api;
import java.io.IOException;
import java.io.InputStream;
import okhttp3.MediaType;
import okhttp3.RequestBody;
import okhttp3.internal.Util;
import okio.BufferedSink;
import okio.Okio;
import okio.Source;
public class InputStreamRequestBody extends RequestBody {
private final InputStream inputStream;
private final MediaType mediaType;
private final long lenght;
public static RequestBody create(final MediaType mediaType, final InputStream inputStream, final long len) {
return new InputStreamRequestBody(inputStream, mediaType, len);
}
private InputStreamRequestBody(InputStream inputStream, MediaType mediaType, long len) {
this.inputStream = inputStream;
this.mediaType = mediaType;
this.lenght = len;
}
@Override
public MediaType contentType() {
return mediaType;
}
@Override
public long contentLength() {
return lenght;
}
@Override
public void writeTo(BufferedSink sink) throws IOException {
Source source = null;
try {
source = Okio.source(inputStream);
sink.writeAll(source);
} finally {
Util.closeQuietly(source);
}
}
}

8
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java
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package eu.dnetlib.dhp.common.api;
public class MissingConceptDoiException extends Throwable {
public MissingConceptDoiException(String message) {
super(message);
}
}

365
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java
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@ -1,365 +0,0 @@
package eu.dnetlib.dhp.common.api;
import java.io.*;
import java.io.IOException;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.concurrent.TimeUnit;
import org.apache.http.HttpHeaders;
import org.apache.http.entity.ContentType;
import org.jetbrains.annotations.NotNull;
import com.google.gson.Gson;
import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel;
import eu.dnetlib.dhp.common.api.zenodo.ZenodoModelList;
import okhttp3.*;
public class ZenodoAPIClient implements Serializable {
String urlString;
String bucket;
String deposition_id;
String access_token;
public static final MediaType MEDIA_TYPE_JSON = MediaType.parse("application/json; charset=utf-8");
private static final MediaType MEDIA_TYPE_ZIP = MediaType.parse("application/zip");
public String getUrlString() {
return urlString;
}
public void setUrlString(String urlString) {
this.urlString = urlString;
}
public String getBucket() {
return bucket;
}
public void setBucket(String bucket) {
this.bucket = bucket;
}
public void setDeposition_id(String deposition_id) {
this.deposition_id = deposition_id;
}
public ZenodoAPIClient(String urlString, String access_token) {
this.urlString = urlString;
this.access_token = access_token;
}
/**
* Brand new deposition in Zenodo. It sets the deposition_id and the bucket where to store the files to upload
*
* @return response code
* @throws IOException
*/
public int newDeposition() throws IOException {
String json = "{}";
URL url = new URL(urlString);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setRequestMethod("POST");
conn.setDoOutput(true);
try (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
}
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel newSubmission = new Gson().fromJson(body, ZenodoModel.class);
this.bucket = newSubmission.getLinks().getBucket();
this.deposition_id = newSubmission.getId();
return responseCode;
}
/**
* Upload files in Zenodo.
*
* @param is the inputStream for the file to upload
* @param file_name the name of the file as it will appear on Zenodo
* @return the response code
*/
public int uploadIS(InputStream is, String file_name) throws IOException {
URL url = new URL(bucket + "/" + file_name);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, "application/zip");
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("PUT");
byte[] buf = new byte[8192];
int length;
try (OutputStream os = conn.getOutputStream()) {
while ((length = is.read(buf)) != -1) {
os.write(buf, 0, length);
}
}
int responseCode = conn.getResponseCode();
if (!checkOKStatus(responseCode)) {
throw new IOException("Unexpected code " + responseCode + getBody(conn));
}
return responseCode;
}
@NotNull
private String getBody(HttpURLConnection conn) throws IOException {
String body = "{}";
try (BufferedReader br = new BufferedReader(
new InputStreamReader(conn.getInputStream(), "utf-8"))) {
StringBuilder response = new StringBuilder();
String responseLine = null;
while ((responseLine = br.readLine()) != null) {
response.append(responseLine.trim());
}
body = response.toString();
}
return body;
}
/**
* Associates metadata information to the current deposition
*
* @param metadata the metadata
* @return response code
* @throws IOException
*/
public int sendMretadata(String metadata) throws IOException {
URL url = new URL(urlString + "/" + deposition_id);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("PUT");
try (OutputStream os = conn.getOutputStream()) {
byte[] input = metadata.getBytes("utf-8");
os.write(input, 0, input.length);
}
final int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + getBody(conn));
return responseCode;
}
private boolean checkOKStatus(int responseCode) {
if (HttpURLConnection.HTTP_OK != responseCode ||
HttpURLConnection.HTTP_CREATED != responseCode)
return true;
return false;
}
/**
* To publish the current deposition. It works for both new deposition or new version of an old deposition
*
* @return response code
* @throws IOException
*/
@Deprecated
public int publish() throws IOException {
String json = "{}";
OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON);
Request request = new Request.Builder()
.url(urlString + "/" + deposition_id + "/actions/publish")
.addHeader("Authorization", "Bearer " + access_token)
.post(body)
.build();
try (Response response = httpClient.newCall(request).execute()) {
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
return response.code();
}
}
/**
* To create a new version of an already published deposition. It sets the deposition_id and the bucket to be used
* for the new version.
*
* @param concept_rec_id the concept record id of the deposition for which to create a new version. It is the last
* part of the url for the DOI Zenodo suggests to use to cite all versions: DOI: 10.xxx/zenodo.656930
* concept_rec_id = 656930
* @return response code
* @throws IOException
* @throws MissingConceptDoiException
*/
public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException {
setDepositionId(concept_rec_id, 1);
String json = "{}";
URL url = new URL(urlString + "/" + deposition_id + "/actions/newversion");
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("POST");
try (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
}
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
String latest_draft = zenodoModel.getLinks().getLatest_draft();
deposition_id = latest_draft.substring(latest_draft.lastIndexOf("/") + 1);
bucket = getBucket(latest_draft);
return responseCode;
}
/**
* To finish uploading a version or new deposition not published
* It sets the deposition_id and the bucket to be used
*
*
* @param deposition_id the deposition id of the not yet published upload
* concept_rec_id = 656930
* @return response code
* @throws IOException
* @throws MissingConceptDoiException
*/
public int uploadOpenDeposition(String deposition_id) throws IOException, MissingConceptDoiException {
this.deposition_id = deposition_id;
String json = "{}";
URL url = new URL(urlString + "/" + deposition_id);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setRequestMethod("POST");
conn.setDoOutput(true);
try (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
}
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
bucket = zenodoModel.getLinks().getBucket();
return responseCode;
}
private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException {
ZenodoModelList zenodoModelList = new Gson()
.fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class);
for (ZenodoModel zm : zenodoModelList) {
if (zm.getConceptrecid().equals(concept_rec_id)) {
deposition_id = zm.getId();
return;
}
}
if (zenodoModelList.size() == 0)
throw new MissingConceptDoiException(
"The concept record id specified was missing in the list of depositions");
setDepositionId(concept_rec_id, page + 1);
}
private String getPrevDepositions(String page) throws IOException {
HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder();
urlBuilder.addQueryParameter("page", page);
URL url = new URL(urlBuilder.build().toString());
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("GET");
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
return body;
}
private String getBucket(String inputUurl) throws IOException {
URL url = new URL(inputUurl);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("GET");
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
return zenodoModel.getLinks().getBucket();
}
}

14
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Community.java
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package eu.dnetlib.dhp.common.api.zenodo;
public class Community {
private String identifier;
public String getIdentifier() {
return identifier;
}
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
}

47
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java
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package eu.dnetlib.dhp.common.api.zenodo;
public class Creator {
private String affiliation;
private String name;
private String orcid;
public String getAffiliation() {
return affiliation;
}
public void setAffiliation(String affiliation) {
this.affiliation = affiliation;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getOrcid() {
return orcid;
}
public void setOrcid(String orcid) {
this.orcid = orcid;
}
public static Creator newInstance(String name, String affiliation, String orcid) {
Creator c = new Creator();
if (name != null) {
c.name = name;
}
if (affiliation != null) {
c.affiliation = affiliation;
}
if (orcid != null) {
c.orcid = orcid;
}
return c;
}
}

44
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java
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package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
public class File implements Serializable {
private String checksum;
private String filename;
private long filesize;
private String id;
public String getChecksum() {
return checksum;
}
public void setChecksum(String checksum) {
this.checksum = checksum;
}
public String getFilename() {
return filename;
}
public void setFilename(String filename) {
this.filename = filename;
}
public long getFilesize() {
return filesize;
}
public void setFilesize(long filesize) {
this.filesize = filesize;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
}

23
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Grant.java
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package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
public class Grant implements Serializable {
private String id;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public static Grant newInstance(String id) {
Grant g = new Grant();
g.id = id;
return g;
}
}

92
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Links.java
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package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
public class Links implements Serializable {
private String bucket;
private String discard;
private String edit;
private String files;
private String html;
private String latest_draft;
private String latest_draft_html;
private String publish;
private String self;
public String getBucket() {
return bucket;
}
public void setBucket(String bucket) {
this.bucket = bucket;
}
public String getDiscard() {
return discard;
}
public void setDiscard(String discard) {
this.discard = discard;
}
public String getEdit() {
return edit;
}
public void setEdit(String edit) {
this.edit = edit;
}
public String getFiles() {
return files;
}
public void setFiles(String files) {
this.files = files;
}
public String getHtml() {
return html;
}
public void setHtml(String html) {
this.html = html;
}
public String getLatest_draft() {
return latest_draft;
}
public void setLatest_draft(String latest_draft) {
this.latest_draft = latest_draft;
}
public String getLatest_draft_html() {
return latest_draft_html;
}
public void setLatest_draft_html(String latest_draft_html) {
this.latest_draft_html = latest_draft_html;
}
public String getPublish() {
return publish;
}
public void setPublish(String publish) {
this.publish = publish;
}
public String getSelf() {
return self;
}
public void setSelf(String self) {
this.self = self;
}
}

153
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Metadata.java
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package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
import java.util.List;
public class Metadata implements Serializable {
private String access_right;
private List<Community> communities;
private List<Creator> creators;
private String description;
private String doi;
private List<Grant> grants;
private List<String> keywords;
private String language;
private String license;
private PrereserveDoi prereserve_doi;
private String publication_date;
private List<String> references;
private List<RelatedIdentifier> related_identifiers;
private String title;
private String upload_type;
private String version;
public String getUpload_type() {
return upload_type;
}
public void setUpload_type(String upload_type) {
this.upload_type = upload_type;
}
public String getVersion() {
return version;
}
public void setVersion(String version) {
this.version = version;
}
public String getAccess_right() {
return access_right;
}
public void setAccess_right(String access_right) {
this.access_right = access_right;
}
public List<Community> getCommunities() {
return communities;
}
public void setCommunities(List<Community> communities) {
this.communities = communities;
}
public List<Creator> getCreators() {
return creators;
}
public void setCreators(List<Creator> creators) {
this.creators = creators;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public List<Grant> getGrants() {
return grants;
}
public void setGrants(List<Grant> grants) {
this.grants = grants;
}
public List<String> getKeywords() {
return keywords;
}
public void setKeywords(List<String> keywords) {
this.keywords = keywords;
}
public String getLanguage() {
return language;
}
public void setLanguage(String language) {
this.language = language;
}
public String getLicense() {
return license;
}
public void setLicense(String license) {
this.license = license;
}
public PrereserveDoi getPrereserve_doi() {
return prereserve_doi;
}
public void setPrereserve_doi(PrereserveDoi prereserve_doi) {
this.prereserve_doi = prereserve_doi;
}
public String getPublication_date() {
return publication_date;
}
public void setPublication_date(String publication_date) {
this.publication_date = publication_date;
}
public List<String> getReferences() {
return references;
}
public void setReferences(List<String> references) {
this.references = references;
}
public List<RelatedIdentifier> getRelated_identifiers() {
return related_identifiers;
}
public void setRelated_identifiers(List<RelatedIdentifier> related_identifiers) {
this.related_identifiers = related_identifiers;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
}

25
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/PrereserveDoi.java
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package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
public class PrereserveDoi implements Serializable {
private String doi;
private String recid;
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public String getRecid() {
return recid;
}
public void setRecid(String recid) {
this.recid = recid;
}
}

43
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/RelatedIdentifier.java
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package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
public class RelatedIdentifier implements Serializable {
private String identifier;
private String relation;
private String resource_type;
private String scheme;
public String getIdentifier() {
return identifier;
}
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
public String getRelation() {
return relation;
}
public void setRelation(String relation) {
this.relation = relation;
}
public String getResource_type() {
return resource_type;
}
public void setResource_type(String resource_type) {
this.resource_type = resource_type;
}
public String getScheme() {
return scheme;
}
public void setScheme(String scheme) {
this.scheme = scheme;
}
}

118
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModel.java
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@ -1,118 +0,0 @@
package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
import java.util.List;
public class ZenodoModel implements Serializable {
private String conceptrecid;
private String created;
private List<File> files;
private String id;
private Links links;
private Metadata metadata;
private String modified;
private String owner;
private String record_id;
private String state;
private boolean submitted;
private String title;
public String getConceptrecid() {
return conceptrecid;
}
public void setConceptrecid(String conceptrecid) {
this.conceptrecid = conceptrecid;
}
public String getCreated() {
return created;
}
public void setCreated(String created) {
this.created = created;
}
public List<File> getFiles() {
return files;
}
public void setFiles(List<File> files) {
this.files = files;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public Links getLinks() {
return links;
}
public void setLinks(Links links) {
this.links = links;
}
public Metadata getMetadata() {
return metadata;
}
public void setMetadata(Metadata metadata) {
this.metadata = metadata;
}
public String getModified() {
return modified;
}
public void setModified(String modified) {
this.modified = modified;
}
public String getOwner() {
return owner;
}
public void setOwner(String owner) {
this.owner = owner;
}
public String getRecord_id() {
return record_id;
}
public void setRecord_id(String record_id) {
this.record_id = record_id;
}
public String getState() {
return state;
}
public void setState(String state) {
this.state = state;
}
public boolean isSubmitted() {
return submitted;
}
public void setSubmitted(boolean submitted) {
this.submitted = submitted;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
}

7
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java
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@ -1,7 +0,0 @@
package eu.dnetlib.dhp.common.api.zenodo;
import java.util.ArrayList;
public class ZenodoModelList extends ArrayList<ZenodoModel> {
}

109
dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java
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@ -1,109 +0,0 @@
package eu.dnetlib.dhp.common.api;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
class ZenodoAPIClientTest {
private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions";
private final String ACCESS_TOKEN = "";
private final String CONCEPT_REC_ID = "657113";
private final String depositionId = "674915";
@Test
void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
Assertions.assertEquals(200, client.uploadOpenDeposition(depositionId));
File file = new File(getClass()
.getResource("/eu/dnetlib/dhp/common/api/COVID-19.json.gz")
.getPath());
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz"));
String metadata = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/common/api/metadata.json"));
Assertions.assertEquals(200, client.sendMretadata(metadata));
Assertions.assertEquals(202, client.publish());
}
@Test
void testNewDeposition() throws IOException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
Assertions.assertEquals(201, client.newDeposition());
File file = new File(getClass()
.getResource("/eu/dnetlib/dhp/common/api/COVID-19.json.gz")
.getPath());
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz"));
String metadata = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/common/api/metadata.json"));
Assertions.assertEquals(200, client.sendMretadata(metadata));
Assertions.assertEquals(202, client.publish());
}
@Test
void testNewVersionNewName() throws IOException, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
Assertions.assertEquals(201, client.newVersion(CONCEPT_REC_ID));
File file = new File(getClass()
.getResource("/eu/dnetlib/dhp/common/api/newVersion")
.getPath());
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition"));
Assertions.assertEquals(202, client.publish());
}
@Test
void testNewVersionOldName() throws IOException, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
Assertions.assertEquals(201, client.newVersion(CONCEPT_REC_ID));
File file = new File(getClass()
.getResource("/eu/dnetlib/dhp/common/api/newVersion2")
.getPath());
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition"));
Assertions.assertEquals(202, client.publish());
}
}

2
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
View File

@ -231,7 +231,7 @@ object BioDBToOAF {
def uniprotToOAF(input: String): List[Oaf] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val pid = (json \ "pid").extract[String]
val pid = (json \ "pid").extract[String].trim()
val d = new Dataset

59
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump
View File

@ -1,15 +1,44 @@
{"pdb": "1CW0", "title": "crystal structure analysis of very short patch repair (vsr) endonuclease in complex with a duplex dna", "authors": ["S.E.Tsutakawa", "H.Jingami", "K.Morikawa"], "doi": "10.1016/S0092-8674(00)81550-0", "pmid": "10612397"}
{"pdb": "2CWW", "title": "crystal structure of thermus thermophilus ttha1280, a putative sam- dependent rna methyltransferase, in complex with s-adenosyl-l- homocysteine", "authors": ["A.A.Pioszak", "K.Murayama", "N.Nakagawa", "A.Ebihara", "S.Kuramitsu", "M.Shirouzu", "S.Yokoyama", "Riken Structural Genomics/proteomics Initiative (Rsgi)"], "doi": "10.1107/S1744309105029842", "pmid": "16511182"}
{"pdb": "6CWE", "title": "structure of alpha-gsa[8,6p] bound by cd1d and in complex with the va14vb8.2 tcr", "authors": ["J.Wang", "D.Zajonc"], "doi": null, "pmid": null}
{"pdb": "5CWS", "title": "crystal structure of the intact chaetomium thermophilum nsp1-nup49- nup57 channel nucleoporin heterotrimer bound to its nic96 nuclear pore complex attachment site", "authors": ["C.J.Bley", "S.Petrovic", "M.Paduch", "V.Lu", "A.A.Kossiakoff", "A.Hoelz"], "doi": "10.1126/SCIENCE.AAC9176", "pmid": "26316600"}
{"pdb": "5CWE", "title": "structure of cyp107l2 from streptomyces avermitilis with lauric acid", "authors": ["T.-V.Pham", "S.-H.Han", "J.-H.Kim", "D.-H.Kim", "L.-W.Kang"], "doi": null, "pmid": null}
{"pdb": "7CW4", "title": "acetyl-coa acetyltransferase from bacillus cereus atcc 14579", "authors": ["J.Hong", "K.J.Kim"], "doi": "10.1016/J.BBRC.2020.09.048", "pmid": "32972748"}
{"pdb": "2CWP", "title": "crystal structure of metrs related protein from pyrococcus horikoshii", "authors": ["K.Murayama", "M.Kato-Murayama", "M.Shirouzu", "S.Yokoyama", "Riken StructuralGenomics/proteomics Initiative (Rsgi)"], "doi": null, "pmid": null}
{"pdb": "2CW7", "title": "crystal structure of intein homing endonuclease ii", "authors": ["H.Matsumura", "H.Takahashi", "T.Inoue", "H.Hashimoto", "M.Nishioka", "S.Fujiwara", "M.Takagi", "T.Imanaka", "Y.Kai"], "doi": "10.1002/PROT.20858", "pmid": "16493661"}
{"pdb": "1CWU", "title": "brassica napus enoyl acp reductase a138g mutant complexed with nad+ and thienodiazaborine", "authors": ["A.Roujeinikova", "J.B.Rafferty", "D.W.Rice"], "doi": "10.1074/JBC.274.43.30811", "pmid": "10521472"}
{"pdb": "3CWN", "title": "escherichia coli transaldolase b mutant f178y", "authors": ["T.Sandalova", "G.Schneider", "A.Samland"], "doi": "10.1074/JBC.M803184200", "pmid": "18687684"}
{"pdb": "1CWL", "title": "human cyclophilin a complexed with 4 4-hydroxy-meleu cyclosporin", "authors": ["V.Mikol", "J.Kallen", "P.Taylor", "M.D.Walkinshaw"], "doi": "10.1006/JMBI.1998.2108", "pmid": "9769216"}
{"pdb": "3CW2", "title": "crystal structure of the intact archaeal translation initiation factor 2 from sulfolobus solfataricus .", "authors": ["E.A.Stolboushkina", "S.V.Nikonov", "A.D.Nikulin", "U.Blaesi", "D.J.Manstein", "R.V.Fedorov", "M.B.Garber", "O.S.Nikonov"], "doi": "10.1016/J.JMB.2008.07.039", "pmid": "18675278"}
{"pdb": "3CW9", "title": "4-chlorobenzoyl-coa ligase/synthetase in the thioester-forming conformation, bound to 4-chlorophenacyl-coa", "authors": ["A.S.Reger", "J.Cao", "R.Wu", "D.Dunaway-Mariano", "A.M.Gulick"], "doi": "10.1021/BI800696Y", "pmid": "18620418"}
{"pdb": "3CWU", "title": "crystal structure of an alka host/guest complex 2'-fluoro-2'-deoxy-1, n6-ethenoadenine:thymine base pair", "authors": ["B.R.Bowman", "S.Lee", "S.Wang", "G.L.Verdine"], "doi": "10.1016/J.STR.2008.04.012", "pmid": "18682218"}
{"pdb": "5CWF", "title": "crystal structure of de novo designed helical repeat protein dhr8", "authors": ["G.Bhabha", "D.C.Ekiert"], "doi": "10.1038/NATURE16162", "pmid": "26675729"}
{"classification": "Signaling protein", "pdb": "5NM4", "deposition_date": "2017-04-05", "title": "A2a adenosine receptor room-temperature structure determined by serial Femtosecond crystallography", "Keywords": ["Oom-temperature", " serial crystallography", " signaling protein"], "authors": ["T.weinert", "R.cheng", "D.james", "D.gashi", "P.nogly", "K.jaeger", "M.hennig", "", "J.standfuss"], "pmid": "28912485", "doi": "10.1038/S41467-017-00630-4"}
{"classification": "Oxidoreductase/oxidoreductase inhibitor", "pdb": "4KN3", "deposition_date": "2013-05-08", "title": "Structure of the y34ns91g double mutant of dehaloperoxidase from Amphitrite ornata with 2,4,6-trichlorophenol", "Keywords": ["Lobin", " oxygen storage", " peroxidase", " oxidoreductase", " oxidoreductase-", "Oxidoreductase inhibitor complex"], "authors": ["C.wang", "L.lovelace", "L.lebioda"], "pmid": "23952341", "doi": "10.1021/BI400627W"}
{"classification": "Transport protein", "pdb": "8HKM", "deposition_date": "2022-11-27", "title": "Ion channel", "Keywords": ["On channel", " transport protein"], "authors": ["D.h.jiang", "J.t.zhang"], "pmid": "37494189", "doi": "10.1016/J.CELREP.2023.112858"}
{"classification": "Signaling protein", "pdb": "6JT1", "deposition_date": "2019-04-08", "title": "Structure of human soluble guanylate cyclase in the heme oxidised State", "Keywords": ["Oluble guanylate cyclase", " signaling protein"], "authors": ["L.chen", "Y.kang", "R.liu", "J.-x.wu"], "pmid": "31514202", "doi": "10.1038/S41586-019-1584-6"}
{"classification": "Immune system", "pdb": "7OW6", "deposition_date": "2021-06-16", "title": "Crystal structure of a tcr in complex with hla-a*11:01 bound to kras G12d peptide (vvvgadgvgk)", "Keywords": ["La", " kras", " tcr", " immune system"], "authors": ["V.karuppiah", "R.a.robinson"], "doi": "10.1038/S41467-022-32811-1"}
{"classification": "Biosynthetic protein", "pdb": "5EQ8", "deposition_date": "2015-11-12", "title": "Crystal structure of medicago truncatula histidinol-phosphate Phosphatase (mthpp) in complex with l-histidinol", "Keywords": ["Istidine biosynthesis", " metabolic pathways", " dimer", " plant", "", "Biosynthetic protein"], "authors": ["M.ruszkowski", "Z.dauter"], "pmid": "26994138", "doi": "10.1074/JBC.M115.708727"}
{"classification": "De novo protein", "pdb": "8CWA", "deposition_date": "2022-05-18", "title": "Solution nmr structure of 8-residue rosetta-designed cyclic peptide D8.21 in cdcl3 with cis/trans switching (tc conformation, 53%)", "Keywords": ["Yclic peptide", " non natural amino acids", " cis/trans", " switch peptides", "", "De novo design", "Membrane permeability", "De novo protein"], "authors": ["T.a.ramelot", "R.tejero", "G.t.montelione"], "pmid": "36041435", "doi": "10.1016/J.CELL.2022.07.019"}
{"classification": "Hydrolase", "pdb": "3R6M", "deposition_date": "2011-03-21", "title": "Crystal structure of vibrio parahaemolyticus yeaz", "Keywords": ["Ctin/hsp70 nucleotide-binding fold", " bacterial resuscitation", " viable", "But non-culturable state", "Resuscitation promoting factor", "Ygjd", "", "Yjee", "Vibrio parahaemolyticus", "Hydrolase"], "authors": ["A.roujeinikova", "I.aydin"], "pmid": "21858042", "doi": "10.1371/JOURNAL.PONE.0023245"}
{"classification": "Hydrolase", "pdb": "2W5J", "deposition_date": "2008-12-10", "title": "Structure of the c14-rotor ring of the proton translocating Chloroplast atp synthase", "Keywords": ["Ydrolase", " chloroplast", " atp synthase", " lipid-binding", " cf(0)", " membrane", "", "Transport", "Formylation", "Energy transduction", "Hydrogen ion transport", "", "Ion transport", "Transmembrane", "Membrane protein"], "authors": ["M.vollmar", "D.schlieper", "M.winn", "C.buechner", "G.groth"], "pmid": "19423706", "doi": "10.1074/JBC.M109.006916"}
{"classification": "De novo protein", "pdb": "4GLU", "deposition_date": "2012-08-14", "title": "Crystal structure of the mirror image form of vegf-a", "Keywords": ["-protein", " covalent dimer", " cysteine knot protein", " growth factor", " de", "Novo protein"], "authors": ["K.mandal", "M.uppalapati", "D.ault-riche", "J.kenney", "J.lowitz", "S.sidhu", "", "S.b.h.kent"], "pmid": "22927390", "doi": "10.1073/PNAS.1210483109"}
{"classification": "Hydrolase/hydrolase inhibitor", "pdb": "3WYL", "deposition_date": "2014-09-01", "title": "Crystal structure of the catalytic domain of pde10a complexed with 5- Methoxy-3-(1-phenyl-1h-pyrazol-5-yl)-1-(3-(trifluoromethyl)phenyl) Pyridazin-4(1h)-one", "Keywords": ["Ydrolase-hydrolase inhibitor complex"], "authors": ["H.oki", "Y.hayano"], "pmid": "25384088", "doi": "10.1021/JM5013648"}
{"classification": "Isomerase", "pdb": "5BOR", "deposition_date": "2015-05-27", "title": "Structure of acetobacter aceti pure-s57c, sulfonate form", "Keywords": ["Cidophile", " pure", " purine biosynthesis", " isomerase"], "authors": ["K.l.sullivan", "T.j.kappock"]}
{"classification": "Hydrolase", "pdb": "1X0C", "deposition_date": "2005-03-17", "title": "Improved crystal structure of isopullulanase from aspergillus niger Atcc 9642", "Keywords": ["Ullulan", " glycoside hydrolase family 49", " glycoprotein", " hydrolase"], "authors": ["M.mizuno", "T.tonozuka", "A.yamamura", "Y.miyasaka", "H.akeboshi", "S.kamitori", "", "A.nishikawa", "Y.sakano"], "pmid": "18155243", "doi": "10.1016/J.JMB.2007.11.098"}
{"classification": "Oxidoreductase", "pdb": "7CUP", "deposition_date": "2020-08-23", "title": "Structure of 2,5-dihydroxypridine dioxygenase from pseudomonas putida Kt2440", "Keywords": ["On-heme dioxygenase", " oxidoreductase"], "authors": ["G.q.liu", "H.z.tang"]}
{"classification": "Ligase", "pdb": "1VCN", "deposition_date": "2004-03-10", "title": "Crystal structure of t.th. hb8 ctp synthetase complex with sulfate Anion", "Keywords": ["Etramer", " riken structural genomics/proteomics initiative", " rsgi", "", "Structural genomics", "Ligase"], "authors": ["M.goto", "Riken structural genomics/proteomics initiative (rsgi)"], "pmid": "15296735", "doi": "10.1016/J.STR.2004.05.013"}
{"classification": "Transferase/transferase inhibitor", "pdb": "6C9V", "deposition_date": "2018-01-28", "title": "Mycobacterium tuberculosis adenosine kinase bound to (2r,3s,4r,5r)-2- (hydroxymethyl)-5-(6-(4-phenylpiperazin-1-yl)-9h-purin-9-yl) Tetrahydrofuran-3,4-diol", "Keywords": ["Ucleoside analog", " complex", " inhibitor", " structural genomics", " psi-2", "", "Protein structure initiative", "Tb structural genomics consortium", "", "Tbsgc", "Transferase-transferase inhibitor complex"], "authors": ["R.a.crespo", "Tb structural genomics consortium (tbsgc)"], "pmid": "31002508", "doi": "10.1021/ACS.JMEDCHEM.9B00020"}
{"classification": "De novo protein", "pdb": "4LPY", "deposition_date": "2013-07-16", "title": "Crystal structure of tencon variant g10", "Keywords": ["Ibronectin type iii fold", " alternate scaffold", " de novo protein"], "authors": ["A.teplyakov", "G.obmolova", "G.l.gilliland"], "pmid": "24375666", "doi": "10.1002/PROT.24502"}
{"classification": "Isomerase", "pdb": "2Y88", "deposition_date": "2011-02-03", "title": "Crystal structure of mycobacterium tuberculosis phosphoribosyl Isomerase (variant d11n) with bound prfar", "Keywords": ["Romatic amino acid biosynthesis", " isomerase", " tim-barrel", " histidine", "Biosynthesis", "Tryptophan biosynthesis"], "authors": ["J.kuper", "A.v.due", "A.geerlof", "M.wilmanns"], "pmid": "21321225", "doi": "10.1073/PNAS.1015996108"}
{"classification": "Unknown function", "pdb": "1SR0", "deposition_date": "2004-03-22", "title": "Crystal structure of signalling protein from sheep(sps-40) at 3.0a Resolution using crystal grown in the presence of polysaccharides", "Keywords": ["Ignalling protein", " involution", " unknown function"], "authors": ["D.b.srivastava", "A.s.ethayathulla", "N.singh", "J.kumar", "S.sharma", "T.p.singh"]}
{"classification": "Dna binding protein", "pdb": "3RH2", "deposition_date": "2011-04-11", "title": "Crystal structure of a tetr-like transcriptional regulator (sama_0099) From shewanella amazonensis sb2b at 2.42 a resolution", "Keywords": ["Na/rna-binding 3-helical bundle", " structural genomics", " joint center", "For structural genomics", "Jcsg", "Protein structure initiative", "Psi-", "Biology", "Dna binding protein"], "authors": ["Joint center for structural genomics (jcsg)"]}
{"classification": "Transferase", "pdb": "2WK5", "deposition_date": "2009-06-05", "title": "Structural features of native human thymidine phosphorylase And in complex with 5-iodouracil", "Keywords": ["Lycosyltransferase", " developmental protein", " angiogenesis", "", "5-iodouracil", "Growth factor", "Enzyme kinetics", "", "Differentiation", "Disease mutation", "Thymidine", "Phosphorylase", "Chemotaxis", "Transferase", "Mutagenesis", "", "Polymorphism"], "authors": ["E.mitsiki", "A.c.papageorgiou", "S.iyer", "N.thiyagarajan", "S.h.prior", "", "D.sleep", "C.finnis", "K.r.acharya"], "pmid": "19555658", "doi": "10.1016/J.BBRC.2009.06.104"}
{"classification": "Hydrolase", "pdb": "3P9Y", "deposition_date": "2010-10-18", "title": "Crystal structure of the drosophila melanogaster ssu72-pctd complex", "Keywords": ["Hosphatase", " cis proline", " lmw ptp-like fold", " rna polymerase ii ctd", "", "Hydrolase"], "authors": ["J.w.werner-allen", "P.zhou"], "pmid": "21159777", "doi": "10.1074/JBC.M110.197129"}
{"classification": "Recombination/dna", "pdb": "6OEO", "deposition_date": "2019-03-27", "title": "Cryo-em structure of mouse rag1/2 nfc complex (dna1)", "Keywords": ["(d)j recombination", " dna transposition", " rag", " scid", " recombination", "", "Recombination-dna complex"], "authors": ["X.chen", "Y.cui", "Z.h.zhou", "W.yang", "M.gellert"], "pmid": "32015552", "doi": "10.1038/S41594-019-0363-2"}
{"classification": "Hydrolase", "pdb": "4ECA", "deposition_date": "1997-02-21", "title": "Asparaginase from e. coli, mutant t89v with covalently bound aspartate", "Keywords": ["Ydrolase", " acyl-enzyme intermediate", " threonine amidohydrolase"], "authors": ["G.j.palm", "J.lubkowski", "A.wlodawer"], "pmid": "8706862", "doi": "10.1016/0014-5793(96)00660-6"}
{"classification": "Transcription/protein binding", "pdb": "3UVX", "deposition_date": "2011-11-30", "title": "Crystal structure of the first bromodomain of human brd4 in complex With a diacetylated histone 4 peptide (h4k12ack16ac)", "Keywords": ["Romodomain", " bromodomain containing protein 4", " cap", " hunk1", " mcap", "", "Mitotic chromosome associated protein", "Peptide complex", "Structural", "Genomics consortium", "Sgc", "Transcription-protein binding complex"], "authors": ["P.filippakopoulos", "S.picaud", "T.keates", "E.ugochukwu", "F.von delft", "", "C.h.arrowsmith", "A.m.edwards", "J.weigelt", "C.bountra", "S.knapp", "Structural", "Genomics consortium (sgc)"], "pmid": "22464331", "doi": "10.1016/J.CELL.2012.02.013"}
{"classification": "Membrane protein", "pdb": "1TLZ", "deposition_date": "2004-06-10", "title": "Tsx structure complexed with uridine", "Keywords": ["Ucleoside transporter", " beta barrel", " uridine", " membrane", "Protein"], "authors": ["J.ye", "B.van den berg"], "pmid": "15272310", "doi": "10.1038/SJ.EMBOJ.7600330"}
{"classification": "Dna binding protein", "pdb": "7AZD", "deposition_date": "2020-11-16", "title": "Dna polymerase sliding clamp from escherichia coli with peptide 20 Bound", "Keywords": ["Ntibacterial drug", " dna binding protein"], "authors": ["C.monsarrat", "G.compain", "C.andre", "I.martiel", "S.engilberge", "V.olieric", "", "P.wolff", "K.brillet", "M.landolfo", "C.silva da veiga", "J.wagner", "G.guichard", "", "D.y.burnouf"], "pmid": "34806883", "doi": "10.1021/ACS.JMEDCHEM.1C00918"}
{"classification": "Transferase", "pdb": "5N3K", "deposition_date": "2017-02-08", "title": "Camp-dependent protein kinase a from cricetulus griseus in complex With fragment like molecule o-guanidino-l-homoserine", "Keywords": ["Ragment", " complex", " transferase", " serine threonine kinase", " camp", "", "Kinase", "Pka"], "authors": ["C.siefker", "A.heine", "G.klebe"]}
{"classification": "Biosynthetic protein", "pdb": "8H52", "deposition_date": "2022-10-11", "title": "Crystal structure of helicobacter pylori carboxyspermidine Dehydrogenase in complex with nadp", "Keywords": ["Arboxyspermidine dehydrogenase", " biosynthetic protein"], "authors": ["K.y.ko", "S.c.park", "S.y.cho", "S.i.yoon"], "pmid": "36283333", "doi": "10.1016/J.BBRC.2022.10.049"}
{"classification": "Metal binding protein", "pdb": "6DYC", "deposition_date": "2018-07-01", "title": "Co(ii)-bound structure of the engineered cyt cb562 variant, ch3", "Keywords": ["Esigned protein", " 4-helix bundle", " electron transport", " metal binding", "Protein"], "authors": ["F.a.tezcan", "J.rittle"], "pmid": "30778140", "doi": "10.1038/S41557-019-0218-9"}
{"classification": "Protein fibril", "pdb": "6A6B", "deposition_date": "2018-06-27", "title": "Cryo-em structure of alpha-synuclein fiber", "Keywords": ["Lpha-syn fiber", " parkinson disease", " protein fibril"], "authors": ["Y.w.li", "C.y.zhao", "F.luo", "Z.liu", "X.gui", "Z.luo", "X.zhang", "D.li", "C.liu", "X.li"], "pmid": "30065316", "doi": "10.1038/S41422-018-0075-X"}
{"classification": "Dna", "pdb": "7D5E", "deposition_date": "2020-09-25", "title": "Left-handed g-quadruplex containing two bulges", "Keywords": ["-quadruplex", " bulge", " dna", " left-handed"], "authors": ["P.das", "A.maity", "K.h.ngo", "F.r.winnerdy", "B.bakalar", "Y.mechulam", "E.schmitt", "", "A.t.phan"], "pmid": "33503265", "doi": "10.1093/NAR/GKAA1259"}
{"classification": "Transferase", "pdb": "3RSY", "deposition_date": "2011-05-02", "title": "Cellobiose phosphorylase from cellulomonas uda in complex with sulfate And glycerol", "Keywords": ["H94", " alpha barrel", " cellobiose phosphorylase", " disaccharide", "Phosphorylase", "Transferase"], "authors": ["A.van hoorebeke", "J.stout", "W.soetaert", "J.van beeumen", "T.desmet", "S.savvides"]}
{"classification": "Oxidoreductase", "pdb": "7MCI", "deposition_date": "2021-04-02", "title": "Mofe protein from azotobacter vinelandii with a sulfur-replenished Cofactor", "Keywords": ["Zotobacter vinelandii", " mofe-protein", " nitrogenase", " oxidoreductase"], "authors": ["W.kang", "C.lee", "Y.hu", "M.w.ribbe"], "doi": "10.1038/S41929-022-00782-7"}
{"classification": "Dna", "pdb": "1XUW", "deposition_date": "2004-10-26", "title": "Structural rationalization of a large difference in rna affinity Despite a small difference in chemistry between two 2'-o-modified Nucleic acid analogs", "Keywords": ["Na mimetic methylcarbamate amide analog", " dna"], "authors": ["R.pattanayek", "L.sethaphong", "C.pan", "M.prhavc", "T.p.prakash", "M.manoharan", "", "M.egli"], "pmid": "15547979", "doi": "10.1021/JA044637K"}
{"classification": "Lyase", "pdb": "7C0D", "deposition_date": "2020-05-01", "title": "Crystal structure of azospirillum brasilense l-2-keto-3-deoxyarabonate Dehydratase (hydroxypyruvate-bound form)", "Keywords": ["-2-keto-3-deoxyarabonate dehydratase", " lyase"], "authors": ["Y.watanabe", "S.watanabe"], "pmid": "32697085", "doi": "10.1021/ACS.BIOCHEM.0C00515"}
{"classification": "Signaling protein", "pdb": "5LYK", "deposition_date": "2016-09-28", "title": "Crystal structure of intracellular b30.2 domain of btn3a1 bound to Citrate", "Keywords": ["30.2", " butyrophilin", " signaling protein"], "authors": ["F.mohammed", "A.t.baker", "M.salim", "B.e.willcox"], "pmid": "28862425", "doi": "10.1021/ACSCHEMBIO.7B00694"}
{"classification": "Toxin", "pdb": "4IZL", "deposition_date": "2013-01-30", "title": "Structure of the n248a mutant of the panton-valentine leucocidin s Component from staphylococcus aureus", "Keywords": ["I-component leucotoxin", " staphylococcus aureus", " s component", "Leucocidin", "Beta-barrel pore forming toxin", "Toxin"], "authors": ["L.maveyraud", "B.j.laventie", "G.prevost", "L.mourey"], "pmid": "24643034", "doi": "10.1371/JOURNAL.PONE.0092094"}
{"classification": "Dna", "pdb": "6F3C", "deposition_date": "2017-11-28", "title": "The cytotoxic [pt(h2bapbpy)] platinum complex interacting with the Cgtacg hexamer", "Keywords": ["Rug-dna complex", " four-way junction", " dna"], "authors": ["M.ferraroni", "C.bazzicalupi", "P.gratteri", "F.papi"], "pmid": "31046177", "doi": "10.1002/ANIE.201814532"}
{"classification": "Signaling protein/inhibitor", "pdb": "4L5M", "deposition_date": "2013-06-11", "title": "Complexe of arno sec7 domain with the protein-protein interaction Inhibitor n-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide at ph6.5", "Keywords": ["Ec-7domain", " signaling protein-inhibitor complex"], "authors": ["F.hoh", "J.rouhana"], "pmid": "24112024", "doi": "10.1021/JM4009357"}
{"classification": "Signaling protein", "pdb": "5I6J", "deposition_date": "2016-02-16", "title": "Crystal structure of srgap2 f-barx", "Keywords": ["Rgap2", " f-bar", " fx", " signaling protein"], "authors": ["M.sporny", "J.guez-haddad", "M.n.isupov", "Y.opatowsky"], "pmid": "28333212", "doi": "10.1093/MOLBEV/MSX094"}
{"classification": "Metal binding protein", "pdb": "1Q80", "deposition_date": "2003-08-20", "title": "Solution structure and dynamics of nereis sarcoplasmic calcium binding Protein", "Keywords": ["Ll-alpha", " metal binding protein"], "authors": ["G.rabah", "R.popescu", "J.a.cox", "Y.engelborghs", "C.t.craescu"], "pmid": "15819893", "doi": "10.1111/J.1742-4658.2005.04629.X"}
{"classification": "Transferase", "pdb": "1TW1", "deposition_date": "2004-06-30", "title": "Beta-1,4-galactosyltransferase mutant met344his (m344h-gal-t1) complex With udp-galactose and magnesium", "Keywords": ["Et344his mutation; closed conformation; mn binding", " transferase"], "authors": ["B.ramakrishnan", "E.boeggeman", "P.k.qasba"], "pmid": "15449940", "doi": "10.1021/BI049007+"}
{"classification": "Rna", "pdb": "2PN4", "deposition_date": "2007-04-23", "title": "Crystal structure of hepatitis c virus ires subdomain iia", "Keywords": ["Cv", " ires", " subdoamin iia", " rna", " strontium", " hepatitis"], "authors": ["Q.zhao", "Q.han", "C.r.kissinger", "P.a.thompson"], "pmid": "18391410", "doi": "10.1107/S0907444908002011"}

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{"pid": "Q6GZX4", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 41."}], "title": "Putative transcription factor 001R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": "Q6GZX3", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 42."}], "title": "Uncharacterized protein 002L;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": "Q197F8", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 27."}], "title": "Uncharacterized protein 002R;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]}
{"pid": "Q197F7", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 23."}], "title": "Uncharacterized protein 003L;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]}
{"pid": "Q6GZX2", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 36."}], "title": "Uncharacterized protein 3R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": "Q6GZX1", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 34."}], "title": "Uncharacterized protein 004R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZX4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 43"}], "title": "Putative transcription factor 001R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZX3", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 45"}], "title": "Uncharacterized protein 002L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197F8", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-02-23", "date_info": "entry version 29"}], "title": "Uncharacterized protein 002R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q197F7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2020-08-12", "date_info": "entry version 23"}], "title": "Uncharacterized protein 003L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q6GZX2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 3R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZX1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 38"}], "title": "Uncharacterized protein 004R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197F5", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-10-12", "date_info": "entry version 32"}], "title": "Uncharacterized protein 005L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q6GZX0", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 47"}], "title": "Uncharacterized protein 005R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q91G88", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2023-06-28", "date_info": "entry version 53"}], "title": "Putative KilA-N domain-containing protein 006L", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]}
{"pid": " Q6GZW9", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 34"}], "title": "Uncharacterized protein 006R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZW8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 32"}], "title": "Uncharacterized protein 007R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197F3", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 28"}], "title": "Uncharacterized protein 007R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q197F2", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-02-23", "date_info": "entry version 22"}], "title": "Uncharacterized protein 008L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q6GZW6", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 67"}], "title": "Putative helicase 009L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q91G85", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 38"}], "title": "Uncharacterized protein 009R", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]}
{"pid": " Q6GZW5", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 010R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197E9", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 28"}], "title": "Uncharacterized protein 011L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q6GZW4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 011R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZW3", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 012L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197E7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 37"}], "title": "Uncharacterized protein IIV3-013L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q6GZW2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 30"}], "title": "Uncharacterized protein 013R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZW1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 014R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZW0", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 50"}], "title": "Uncharacterized protein 015R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZV8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 017L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZV7", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 33"}], "title": "Uncharacterized protein 018L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZV6", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 87"}], "title": "Putative serine/threonine-protein kinase 019R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZV5", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 40"}], "title": "Uncharacterized protein 020R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZV4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 021L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197D8", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-12-14", "date_info": "entry version 35"}], "title": "Transmembrane protein 022L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q6GZV2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 33"}], "title": "Uncharacterized protein 023R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197D7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 25"}], "title": "Uncharacterized protein 023R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q6GZV1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 024R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q197D5", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-10-12", "date_info": "entry version 24"}], "title": "Uncharacterized protein 025R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
{"pid": " Q91G70", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2020-08-12", "date_info": "entry version 32"}], "title": "Uncharacterized protein 026R", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]}
{"pid": " Q6GZU9", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 49"}], "title": "Uncharacterized protein 027R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
{"pid": " Q6GZU8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 55"}], "title": "Uncharacterized protein 028R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}

30
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java
View File

@ -14,6 +14,7 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
@ -84,19 +85,26 @@ public class SparkCountryPropagationJob {
Dataset<R> res = readPath(spark, sourcePath, resultClazz);
log.info("Reading prepared info: {}", preparedInfoPath);
Dataset<ResultCountrySet> prepared = spark
final Dataset<Row> preparedInfoRaw = spark
.read()
.json(preparedInfoPath)
.as(Encoders.bean(ResultCountrySet.class));
res
.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
.map(getCountryMergeFn(), Encoders.bean(resultClazz))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
.json(preparedInfoPath);
if (!preparedInfoRaw.isEmpty()) {
final Dataset<ResultCountrySet> prepared = preparedInfoRaw.as(Encoders.bean(ResultCountrySet.class));
res
.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
.map(getCountryMergeFn(), Encoders.bean(resultClazz))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
} else {
res
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {

10
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/config-default.xml
View File

@ -45,10 +45,14 @@
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
<value>5G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
<name>memoryOverhead</name>
<value>3g</value>
</property>
<property>
<name>partitions</name>
<value>3284</value>
</property>
</configuration>

4
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml
View File

@ -260,6 +260,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--conf spark.sql.shuffle.partitions=10000
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
@ -289,6 +290,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--conf spark.sql.shuffle.partitions=5000
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
@ -318,6 +320,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--conf spark.sql.shuffle.partitions=2000
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
@ -347,6 +350,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--conf spark.sql.shuffle.partitions=1000
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/mergedCommunityAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>

1555
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/communityconfiguration/tagging_conf_remove.xml Normal file
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File diff suppressed because it is too large Load Diff

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/dataset → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/dataset/dataset
View File

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/otherresearchproduct → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/otherresearchproduct/otherresearchproduct
View File

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/publication → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/otherresearchproduct~HEAD
View File

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/software → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/publication/publication
View File

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/software/software Normal file
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2
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java
View File

@ -82,7 +82,7 @@ public class IndexRecordTransformerTest {
void testPeerReviewed() throws IOException, TransformerException {
final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
XmlConverterJob.schemaLocation);
XmlConverterJob.schemaLocation);
final Publication p = load("publication.json", Publication.class);

29
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java
View File

@ -1,6 +1,8 @@
package eu.dnetlib.dhp.oa.provision;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.io.StringReader;
import java.net.URI;
@ -32,8 +34,6 @@ import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ExtendWith(MockitoExtension.class)
public class XmlIndexingJobTest extends SolrTest {
@ -110,34 +110,33 @@ public class XmlIndexingJobTest extends SolrTest {
QueryResponse rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "*:*"));
assertEquals(
nRecord, rsp.getResults().getNumFound(),
"the number of indexed records should be equal to the number of input records");
nRecord, rsp.getResults().getNumFound(),
"the number of indexed records should be equal to the number of input records");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isgreen:true"));
assertEquals(
0, rsp.getResults().getNumFound(),
"the number of indexed records having isgreen = true");
0, rsp.getResults().getNumFound(),
"the number of indexed records having isgreen = true");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "openaccesscolor:bronze"));
assertEquals(
0, rsp.getResults().getNumFound(),
"the number of indexed records having openaccesscolor = bronze");
0, rsp.getResults().getNumFound(),
"the number of indexed records having openaccesscolor = bronze");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isindiamondjournal:true"));
assertEquals(
0, rsp.getResults().getNumFound(),
"the number of indexed records having isindiamondjournal = true");
0, rsp.getResults().getNumFound(),
"the number of indexed records having isindiamondjournal = true");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "publiclyfunded:true"));
assertEquals(
0, rsp.getResults().getNumFound(),
"the number of indexed records having publiclyfunded = true");
0, rsp.getResults().getNumFound(),
"the number of indexed records having publiclyfunded = true");
rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "peerreviewed:true"));
assertEquals(
0, rsp.getResults().getNumFound(),
"the number of indexed records having peerreviewed = true");
0, rsp.getResults().getNumFound(),
"the number of indexed records having peerreviewed = true");
}
@Test

586
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.1098-rsta.2020.0257.xml Normal file
View File

@ -0,0 +1,586 @@
<record>
<result xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<header>
<dri:objIdentifier>doi_dedup___::e225555a08a082ad8f53f179bc59c5d0</dri:objIdentifier>
<dri:dateOfCollection>2023-01-27T05:32:10Z</dri:dateOfCollection>
</header>
<metadata>
<oaf:entity xmlns:oaf="http://namespace.openaire.eu/oaf"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://namespace.openaire.eu/oaf http://namespace.openaire.eu/oaf http://www.openaire.eu/schema/0.2/oaf-0.2.xsd">
<oaf:result>
<collectedfrom name="Crossref" id="openaire____::081b82f96300b6a6e3d282bad31cb6e2"/>
<collectedfrom name="UnpayWall" id="openaire____::8ac8380272269217cb09a928c8caa993"/>
<collectedfrom name="ORCID" id="openaire____::806360c771262b4d6770e7cdf04b5c5a"/>
<collectedfrom name="Microsoft Academic Graph" id="openaire____::5f532a3fc4f1ea403f37070f59a7a53a"/>
<collectedfrom name="Oxford University Research Archive"
id="opendoar____::2290a7385ed77cc5592dc2153229f082"/>
<collectedfrom name="PubMed Central" id="opendoar____::eda80a3d5b344bc40f3bc04f65b7a357"/>
<collectedfrom name="Europe PubMed Central" id="opendoar____::8b6dd7db9af49e67306feb59a8bdc52c"/>
<originalId>10.1098/rsta.2020.0257</originalId>
<originalId>50|doiboost____::e225555a08a082ad8f53f179bc59c5d0</originalId>
<originalId>3211056089</originalId>
<originalId>50|od______1064::83eb0f76b60445d72bb7428a1b68ef1a</originalId>
<originalId>oai:ora.ox.ac.uk:uuid:9fc4563a-07e1-41d1-8b99-31ce2f8ac027</originalId>
<originalId>50|od_______267::6d978e42c57dfc79d61a84ab5be28cb8</originalId>
<originalId>oai:pubmedcentral.nih.gov:8543046</originalId>
<originalId>od_______267::6d978e42c57dfc79d61a84ab5be28cb8</originalId>
<originalId>34689630</originalId>
<originalId>PMC8543046</originalId>
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
schemename="dnet:pid_types">10.1098/rsta.2020.0257
</pid>
<pid classid="pmc" classname="PubMed Central ID" schemeid="dnet:pid_types"
schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:crosswalk:repository"
trust="0.9">PMC8543046
</pid>
<pid classid="pmid" classname="PubMed ID" schemeid="dnet:pid_types" schemename="dnet:pid_types"
inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">34689630
</pid>
<measure id="influence" score="5.534974E-9" class="C"/>
<measure id="popularity" score="2.0811036E-8" class="C"/>
<measure id="influence_alt" score="8" class="C"/>
<measure id="popularity_alt" score="2.736" class="C"/>
<measure id="impulse" score="8" class="C"/>
<measure id="downloads" count="1"/>
<measure id="views" count="4"/>
<title classid="alternative title" classname="alternative title" schemeid="dnet:dataCite_title"
schemename="dnet:dataCite_title">A completely automated pipeline for 3D reconstruction of
human heart from 2D cine magnetic resonance slices.
</title>
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title"
schemename="dnet:dataCite_title">A completely automated pipeline for 3D reconstruction of
human heart from 2D cine magnetic resonance slices
</title>
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
schemename="dnet:access_modes"/>
<creator rank="8" URL="https://academic.microsoft.com/#/detail/2103042895">Vicente Grau</creator>
<creator rank="1" orcid="0000-0001-8198-5128"
URL="https://academic.microsoft.com/#/detail/2693349397">Abhirup Banerjee
</creator>
<creator rank="3" URL="https://academic.microsoft.com/#/detail/1425738153">Ernesto Zacur</creator>
<creator rank="6" URL="https://academic.microsoft.com/#/detail/2043191934">Robin P. Choudhury
</creator>
<creator rank="7" URL="https://academic.microsoft.com/#/detail/2166186014">Blanca Rodriguez
</creator>
<creator rank="2" URL="https://academic.microsoft.com/#/detail/2889449215">Julia Camps</creator>
<creator rank="5" URL="https://academic.microsoft.com/#/detail/264390263">Yoram Rudy</creator>
<creator rank="4" URL="https://academic.microsoft.com/#/detail/2713879776">Christopher M. Andrews
</creator>
<country classid="GB" classname="United Kingdom" schemeid="dnet:countries"
schemename="dnet:countries"/>
<dateofacceptance>2021-10-01</dateofacceptance>
<description>Cardiac magnetic resonance (CMR) imaging is a valuable modality in the diagnosis and
characterization of cardiovascular diseases, since it can identify abnormalities in structure
and function of the myocardium non-invasively and without the need for ionizing radiation.
However, in clinical practice, it is commonly acquired as a collection of separated and
independent 2D image planes, which limits its accuracy in 3D analysis. This paper presents a
completely automated pipeline for generating patient-specific 3D biventricular heart models from
cine magnetic resonance (MR) slices. Our pipeline automatically selects the relevant cine MR
images, segments them using a deep learning-based method to extract the heart contours, and
aligns the contours in 3D space correcting possible misalignments due to breathing or subject
motion first using the intensity and contours information from the cine data and next with the
help of a statistical shape model. Finally, the sparse 3D representation of the contours is used
to generate a smooth 3D biventricular mesh. The computational pipeline is applied and evaluated
in a CMR dataset of 20 healthy subjects. Our results show an average reduction of misalignment
artefacts from 1.82 ± 1.60 mm to 0.72 ± 0.73 mm over 20 subjects, in terms of distance from the
final reconstructed mesh. The high-resolution 3D biventricular meshes obtained with our
computational pipeline are used for simulations of electrical activation patterns, showing
agreement with non-invasive electrocardiographic imaging. The automatic methodologies presented
here for patient-specific MR imaging-based 3D biventricular representations contribute to the
efficient realization of precision medicine, enabling the enhanced interpretability of clinical
data, the digital twin vision through patient-specific image-based modelling and simulation, and
augmented reality applications.
This article is part of the theme issue ‘Advanced computation in cardiovascular physiology: new
challenges and opportunities’.
</description>
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">General Physics and Astronomy
</subject>
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">General Engineering
</subject>
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">General Mathematics
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Pipeline (computing)
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Cine mri
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Structure and function
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Cardiac magnetic resonance
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
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<description>Background: The concept of digital twins has great potential for transforming the existing health care system by making it more personalized. As a convergence of health care, artificial intelligence, and information and communication technologies, personalized health care services that are developed under the concept of digital twins raise a myriad of ethical issues. Although some of the ethical issues are known to researchers working on digital health and personalized medicine, currently, there is no comprehensive review that maps the major ethical risks of digital twins for personalized health care services. Objective This study aims to fill the research gap by identifying the major ethical risks of digital twins for personalized health care services. We first propose a working definition for digital twins for personalized health care services to facilitate future discussions on the ethical issues related to these emerging digital health services. We then develop a process-oriented ethical map to identify the major ethical risks in each of the different data processing phases. MethodsWe resorted to the literature on eHealth, personalized medicine, precision medicine, and information engineering to identify potential issues and developed a process-oriented ethical map to structure the inquiry in a more systematic way. The ethical map allows us to see how each of the major ethical concerns emerges during the process of transforming raw data into valuable information. Developers of a digital twin for personalized health care service may use this map to identify ethical risks during the development stage in a more systematic way and can proactively address them. ResultsThis paper provides a working definition of digital twins for personalized health care services by identifying 3 features that distinguish the new application from other eHealth services. On the basis of the working definition, this paper further layouts 10 major operational problems and the corresponding ethical risks. ConclusionsIt is challenging to address all the major ethical risks that a digital twin for a personalized health care service might encounter proactively without a conceptual map at hand. The process-oriented ethical map we propose here can assist the developers of digital twins for personalized health care services in analyzing ethical risks in a more systematic manner. </description>
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<measure id="popularity" score="2.4479982E-8" class="C"/>
<measure id="influence_alt" score="10" class="C"/>
<measure id="popularity_alt" score="3.6" class="C"/>
<measure id="impulse" score="10" class="C"/>
<title classid="alternative title" classname="alternative title" schemeid="dnet:dataCite_title"
schemename="dnet:dataCite_title">Digital Twins for Continuous mRNA Production
</title>
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
schemename="dnet:access_modes"/>
<dateofacceptance>2021-11-04</dateofacceptance>
<description>The global coronavirus pandemic continues to restrict public life worldwide. An
effective means of limiting the pandemic is vaccination. Messenger ribonucleic acid (mRNA)
vaccines currently available on the market have proven to be a well-tolerated and effective
class of vaccine against coronavirus type 2 (CoV2). Accordingly, demand is presently
outstripping mRNA vaccine production. One way to increase productivity is to switch from the
currently performed batch to continuous in vitro transcription, which has proven to be a crucial
material-consuming step. In this article, a physico-chemical model of in vitro mRNA
transcription in a tubular reactor is presented and compared to classical batch and continuous
in vitro transcription in a stirred tank. The three models are validated based on a distinct and
quantitative validation workflow. Statistically significant parameters are identified as part of
the parameter determination concept. Monte Carlo simulations showed that the model is precise,
with a deviation of less than 1%. The advantages of continuous production are pointed out
compared to batchwise in vitro transcription by optimization of the space–time yield.
Improvements of a factor of 56 (0.011 µM/min) in the case of the continuously stirred tank
reactor (CSTR) and 68 (0.013 µM/min) in the case of the plug flow reactor (PFR) were found.
</description>
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schemename="dnet:subject_classification_typologies">Process Chemistry and Technology
</subject>
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Chemical Engineering (miscellaneous)
</subject>
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Bioengineering
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Coronavirus
</subject>
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schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="false"
provenanceaction="sysimport:actionset" trust="0.4019353">medicine.disease_cause
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schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="false"
provenanceaction="sysimport:actionset" trust="0.4019353">medicine
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Continuous production
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Messenger RNA
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Continuous stirred-tank reactor
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Plug flow reactor model
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Mathematics
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">In vitro transcription
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Biological system
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Yield (chemistry)
</subject>
<subject classid="MAG" classname="Microsoft Academic Graph classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies">Public life
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">03 medical and health sciences
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<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">0301 basic medicine
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">030104 Developmental Biology
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">0303 health sciences
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">030304 Developmental Biology
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">02 engineering and technology
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">0210 nano-technology
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">021001 Nanoscience &amp;
Nanotechnology
</subject>
<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">01 natural sciences
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<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">0104 chemical sciences
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<subject classid="FOS" classname="Fields of Science and Technology classification"
schemeid="dnet:subject_classification_typologies"
schemename="dnet:subject_classification_typologies" inferred="true"
inferenceprovenance="update" provenanceaction="subject:fos">010405 Organic Chemistry
</subject>
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schemename="dnet:languages"/>
<relevantdate classid="created" classname="created" schemeid="dnet:dataCite_date"
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</relevantdate>
<source>Crossref</source>
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<journal issn="2227-9717">Processes</journal>
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<context id="dth" label="Digital Twins in Health" type="community"/>
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138
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/sentinel.xml Normal file
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<description>These datasets are used for training purposes. See https://pangeo-data.github.io/foss4g-2022/intro.html</description>
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<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">vegetaion</subject>
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<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">pangeo</subject>
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29
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
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@ -1,10 +1,10 @@
{
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],
"measures": [
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"value": "VIRTA"
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}
],
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17
dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
View File

@ -48,16 +48,25 @@
<case to="get-file-names">${wf:conf('resume') eq "format-results"}</case>
<case to="map-openaire-to-doi">${wf:conf('resume') eq "map-ids"}</case>
<case to="map-scores-to-dois">${wf:conf('resume') eq "map-scores"}</case>
<case to="create-openaire-ranking-graph">${wf:conf('resume') eq "start"}</case>
<case to="clear-working-dir">${wf:conf('resume') eq "start"}</case>
<!-- Aggregation of impact scores on the project level -->
<case to="project-impact-indicators">${wf:conf('resume') eq "projects-impact"}</case>
<case to="create-actionset">${wf:conf('resume') eq "create-actionset"}</case>
<default to="create-openaire-ranking-graph" />
<default to="clear-working-dir" />
</switch>
</decision>
<action name="clear-working-dir">
<fs>
<delete path="${workingDir}"/>
<mkdir path="${workingDir}"/>
</fs>
<ok to="create-openaire-ranking-graph"/>
<error to="clear-working-dir-fail"/>
</action>
<!-- initial step: create citation network -->
<action name="create-openaire-ranking-graph">
<spark xmlns="uri:oozie:spark-action:0.2">
@ -606,6 +615,10 @@
<message>Calculating project impact indicators failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<kill name="clear-working-dir-fail">
<message>Re-create working dir failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<!-- Define ending node -->
<end name="end" />