forked from D-Net/dnet-hadoop
Merge pull request 'Improve OAF Generation from Baseline PubMed Collection' (#504) from pubmed_fix into beta
Reviewed-on: D-Net/dnet-hadoop#504
This commit is contained in:
commit
a48d080e08
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@ -26,16 +26,16 @@
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<dependencies>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-actionmanager</artifactId>
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<version>${project.version}</version>
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</dependency>
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-aggregation</artifactId>-->
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<!-- <artifactId>dhp-actionmanager</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-aggregation</artifactId>
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<version>${project.version}</version>
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</dependency>
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-blacklist</artifactId>-->
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@ -56,61 +56,61 @@
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<!-- <artifactId>dhp-enrichment</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-graph-mapper</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-graph-provision</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-impact-indicators</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-stats-actionsets</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-stats-hist-snaps</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-stats-monitor-irish</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-stats-promote</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-stats-update</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-swh</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-usage-raw-data-update</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-usage-stats-build</artifactId>
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<version>${project.version}</version>
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</dependency>
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-graph-mapper</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-graph-provision</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-impact-indicators</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-stats-actionsets</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-stats-hist-snaps</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-stats-monitor-irish</artifactId>-->
|
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-stats-promote</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-stats-update</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-swh</artifactId>-->
|
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-usage-raw-data-update</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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<!-- <dependency>-->
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<!-- <groupId>eu.dnetlib.dhp</groupId>-->
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<!-- <artifactId>dhp-usage-stats-build</artifactId>-->
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<!-- <version>${project.version}</version>-->
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<!-- </dependency>-->
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</dependencies>
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@ -15,7 +15,7 @@ import java.util.stream.Collectors;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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@ -30,7 +30,6 @@ import org.apache.spark.sql.Dataset;
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import org.jetbrains.annotations.NotNull;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.spark_project.jetty.util.StringUtil;
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import com.fasterxml.jackson.databind.ObjectMapper;
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@ -207,7 +206,7 @@ public class ExtractPerson implements Serializable {
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null);
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relation.setValidated(true);
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if (StringUtil.isNotBlank(role)) {
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if (StringUtils.isNotBlank(role)) {
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KeyValue kv = new KeyValue();
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kv.setKey("role");
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kv.setValue(role);
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@ -347,15 +346,19 @@ public class ExtractPerson implements Serializable {
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.structuredProperty(
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op.getOrcid(), ModelConstants.ORCID, ModelConstants.ORCID_CLASSNAME,
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ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,
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OafMapperUtils.dataInfo(false,
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null,
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false,
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false,
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OafMapperUtils.qualifier(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
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ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES),
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"0.91")));
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OafMapperUtils
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.dataInfo(
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false,
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null,
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false,
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false,
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OafMapperUtils
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.qualifier(
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ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
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ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES),
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"0.91")));
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person.setDateofcollection(op.getLastModifiedDate());
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person.setOriginalId(Arrays.asList(op.getOrcid()));
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person.setDataInfo(ORCIDDATAINFO);
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@ -449,13 +452,13 @@ public class ExtractPerson implements Serializable {
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null);
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relation.setValidated(true);
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if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) {
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if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtils.isNotBlank(row.getStartDate())) {
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KeyValue kv = new KeyValue();
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kv.setKey("startDate");
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kv.setValue(row.getStartDate());
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properties.add(kv);
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}
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if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
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if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtils.isNotBlank(row.getEndDate())) {
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KeyValue kv = new KeyValue();
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kv.setKey("endDate");
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kv.setValue(row.getEndDate());
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@ -1,6 +1,9 @@
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package eu.dnetlib.dhp.collection.plugin.gtr2;
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import java.nio.charset.StandardCharsets;
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import java.time.LocalDate;
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import java.time.format.DateTimeFormatter;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Iterator;
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@ -16,9 +19,6 @@ import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.joda.time.DateTime;
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import org.joda.time.format.DateTimeFormat;
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import org.joda.time.format.DateTimeFormatter;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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|
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@ -33,7 +33,7 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
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private static final Logger log = LoggerFactory.getLogger(Gtr2PublicationsIterator.class);
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private final HttpConnector2 connector;
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private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormat.forPattern("yyyy-MM-dd");
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private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormatter.ofPattern("yyyy-MM-dd");
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private static final int MAX_ATTEMPTS = 10;
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@ -41,7 +41,7 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
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private int currPage;
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private int endPage;
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private boolean incremental = false;
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private DateTime fromDate;
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private LocalDate fromDate;
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|
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private final Map<String, String> cache = new HashMap<>();
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|
||||
|
|
@ -188,28 +188,28 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
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|||
|
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private Document loadURL(final String cleanUrl, final int attempt) {
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try {
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log.debug(" * Downloading Url: " + cleanUrl);
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final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes("UTF-8");
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log.debug(" * Downloading Url: {}", cleanUrl);
|
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final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes(StandardCharsets.UTF_8);
|
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return DocumentHelper.parseText(new String(bytes));
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} catch (final Throwable e) {
|
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log.error("Error dowloading url: " + cleanUrl + ", attempt = " + attempt, e);
|
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log.error("Error dowloading url: {}, attempt = {}", cleanUrl, attempt, e);
|
||||
if (attempt >= MAX_ATTEMPTS) {
|
||||
throw new RuntimeException("Error dowloading url: " + cleanUrl, e);
|
||||
throw new RuntimeException("Error downloading url: " + cleanUrl, e);
|
||||
}
|
||||
try {
|
||||
Thread.sleep(60000); // I wait for a minute
|
||||
} catch (final InterruptedException e1) {
|
||||
throw new RuntimeException("Error dowloading url: " + cleanUrl, e);
|
||||
throw new RuntimeException("Error downloading url: " + cleanUrl, e);
|
||||
}
|
||||
return loadURL(cleanUrl, attempt + 1);
|
||||
}
|
||||
}
|
||||
|
||||
private DateTime parseDate(final String s) {
|
||||
return DateTime.parse(s.contains("T") ? s.substring(0, s.indexOf("T")) : s, simpleDateTimeFormatter);
|
||||
private LocalDate parseDate(final String s) {
|
||||
return LocalDate.parse(s.contains("T") ? s.substring(0, s.indexOf("T")) : s, simpleDateTimeFormatter);
|
||||
}
|
||||
|
||||
private boolean isAfter(final String d, final DateTime fromDate) {
|
||||
private boolean isAfter(final String d, final LocalDate fromDate) {
|
||||
return StringUtils.isNotBlank(d) && parseDate(d).isAfter(fromDate);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,39 @@
|
|||
package eu.dnetlib.dhp.sx.bio.pubmed;
|
||||
|
||||
/**
|
||||
* The type Pubmed Affiliation.
|
||||
*
|
||||
* @author Sandro La Bruzzo
|
||||
*/
|
||||
public class PMAffiliation {
|
||||
|
||||
private String name;
|
||||
|
||||
private PMIdentifier identifier;
|
||||
|
||||
public PMAffiliation() {
|
||||
|
||||
}
|
||||
public PMAffiliation(String name, PMIdentifier identifier) {
|
||||
this.name = name;
|
||||
this.identifier = identifier;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public PMAffiliation setName(String name) {
|
||||
this.name = name;
|
||||
return this;
|
||||
}
|
||||
|
||||
public PMIdentifier getIdentifier() {
|
||||
return identifier;
|
||||
}
|
||||
|
||||
public PMAffiliation setIdentifier(PMIdentifier identifier) {
|
||||
this.identifier = identifier;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
@ -8,259 +8,115 @@ import java.util.List;
|
|||
/**
|
||||
* This class represent an instance of Pubmed Article extracted from the native XML
|
||||
*
|
||||
* @author Sandro La Bruzzo
|
||||
*/
|
||||
|
||||
public class PMArticle implements Serializable {
|
||||
|
||||
/**
|
||||
* the Pubmed Identifier
|
||||
*/
|
||||
private String pmid;
|
||||
|
||||
private String pmcId;
|
||||
|
||||
/**
|
||||
* the DOI
|
||||
*/
|
||||
private String doi;
|
||||
/**
|
||||
* the Pubmed Date extracted from <PubmedPubDate> Specifies a date significant to either the article's history or the citation's processing.
|
||||
* All <History> dates will have a <Year>, <Month>, and <Day> elements. Some may have an <Hour>, <Minute>, and <Second> element(s).
|
||||
*/
|
||||
private String date;
|
||||
/**
|
||||
* This is an 'envelop' element that contains various elements describing the journal cited; i.e., ISSN, Volume, Issue, and PubDate and author name(s), however, it does not contain data itself.
|
||||
*/
|
||||
private PMJournal journal;
|
||||
/**
|
||||
* The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. The NLM journal title abbreviation is exported in the <MedlineTA> element.
|
||||
*/
|
||||
private String title;
|
||||
/**
|
||||
* English-language abstracts are taken directly from the published article.
|
||||
* If the article does not have a published abstract, the National Library of Medicine does not create one,
|
||||
* thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
|
||||
* labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
|
||||
*/
|
||||
private String description;
|
||||
/**
|
||||
* the language in which an article was published is recorded in <Language>.
|
||||
* All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single
|
||||
* record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value.
|
||||
* Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined.
|
||||
*/
|
||||
private String language;
|
||||
|
||||
/**
|
||||
* NLM controlled vocabulary, Medical Subject Headings (MeSH®), is used to characterize the content of the articles represented by MEDLINE citations. *
|
||||
*/
|
||||
private final List<PMSubject> subjects = new ArrayList<>();
|
||||
/**
|
||||
* This element is used to identify the type of article indexed for MEDLINE;
|
||||
* it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
|
||||
* research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
|
||||
*/
|
||||
private final List<PMSubject> publicationTypes = new ArrayList<>();
|
||||
/**
|
||||
* Personal and collective (corporate) author names published with the article are found in <AuthorList>.
|
||||
*/
|
||||
private List<PMSubject> subjects;
|
||||
private List<PMSubject> publicationTypes = new ArrayList<>();
|
||||
private List<PMAuthor> authors = new ArrayList<>();
|
||||
private List<PMGrant> grants = new ArrayList<>();
|
||||
|
||||
/**
|
||||
* <GrantID> contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service
|
||||
* or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations.
|
||||
*/
|
||||
private final List<PMGrant> grants = new ArrayList<>();
|
||||
|
||||
/**
|
||||
* get the DOI
|
||||
* @return a DOI
|
||||
*/
|
||||
public String getDoi() {
|
||||
return doi;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the DOI
|
||||
* @param doi a DOI
|
||||
*/
|
||||
public void setDoi(String doi) {
|
||||
this.doi = doi;
|
||||
}
|
||||
|
||||
/**
|
||||
* get the Pubmed Identifier
|
||||
* @return the PMID
|
||||
*/
|
||||
public String getPmid() {
|
||||
return pmid;
|
||||
}
|
||||
|
||||
/**
|
||||
* set the Pubmed Identifier
|
||||
* @param pmid the Pubmed Identifier
|
||||
*/
|
||||
public void setPmid(String pmid) {
|
||||
this.pmid = pmid;
|
||||
}
|
||||
|
||||
/**
|
||||
* the Pubmed Date extracted from <PubmedPubDate> Specifies a date significant to either the article's history or the citation's processing.
|
||||
* All <History> dates will have a <Year>, <Month>, and <Day> elements. Some may have an <Hour>, <Minute>, and <Second> element(s).
|
||||
*
|
||||
* @return the Pubmed Date
|
||||
*/
|
||||
public String getDate() {
|
||||
return date;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the pubmed Date
|
||||
* @param date
|
||||
*/
|
||||
public void setDate(String date) {
|
||||
this.date = date;
|
||||
}
|
||||
|
||||
/**
|
||||
* The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element.
|
||||
* Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles.
|
||||
* The NLM journal title abbreviation is exported in the <MedlineTA> element.
|
||||
*
|
||||
* @return the pubmed Journal Extracted
|
||||
*/
|
||||
public PMJournal getJournal() {
|
||||
return journal;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the mapped pubmed Journal
|
||||
* @param journal
|
||||
*/
|
||||
public void setJournal(PMJournal journal) {
|
||||
this.journal = journal;
|
||||
}
|
||||
|
||||
/**
|
||||
* <ArticleTitle> contains the entire title of the journal article. <ArticleTitle> is always in English;
|
||||
* those titles originally published in a non-English language and translated for <ArticleTitle> are enclosed in square brackets.
|
||||
* All titles end with a period unless another punctuation mark such as a question mark or bracket is present.
|
||||
* Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl).
|
||||
* Corporate/collective authors may appear at the end of <ArticleTitle> for citations up to about the year 2000.
|
||||
*
|
||||
* @return the extracted pubmed Title
|
||||
*/
|
||||
public String getTitle() {
|
||||
return title;
|
||||
}
|
||||
|
||||
/**
|
||||
* set the pubmed title
|
||||
* @param title
|
||||
*/
|
||||
public void setTitle(String title) {
|
||||
this.title = title;
|
||||
}
|
||||
|
||||
/**
|
||||
* English-language abstracts are taken directly from the published article.
|
||||
* If the article does not have a published abstract, the National Library of Medicine does not create one,
|
||||
* thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
|
||||
* labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
|
||||
*
|
||||
* @return the Mapped Pubmed Article Abstracts
|
||||
*/
|
||||
public String getDescription() {
|
||||
return description;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the Mapped Pubmed Article Abstracts
|
||||
* @param description
|
||||
*/
|
||||
public void setDescription(String description) {
|
||||
this.description = description;
|
||||
}
|
||||
|
||||
/**
|
||||
* Personal and collective (corporate) author names published with the article are found in <AuthorList>.
|
||||
*
|
||||
* @return get the Mapped Authors lists
|
||||
*/
|
||||
public List<PMAuthor> getAuthors() {
|
||||
return authors;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the Mapped Authors lists
|
||||
* @param authors
|
||||
*/
|
||||
public void setAuthors(List<PMAuthor> authors) {
|
||||
this.authors = authors;
|
||||
}
|
||||
|
||||
/**
|
||||
* This element is used to identify the type of article indexed for MEDLINE;
|
||||
* it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
|
||||
* research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
|
||||
*
|
||||
* @return the mapped Subjects
|
||||
*/
|
||||
public List<PMSubject> getSubjects() {
|
||||
return subjects;
|
||||
}
|
||||
|
||||
/**
|
||||
*
|
||||
* the language in which an article was published is recorded in <Language>.
|
||||
* All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single
|
||||
* record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value.
|
||||
* Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined.
|
||||
*
|
||||
* @return The mapped Language
|
||||
*/
|
||||
public String getLanguage() {
|
||||
return language;
|
||||
}
|
||||
|
||||
/**
|
||||
*
|
||||
* Set The mapped Language
|
||||
*
|
||||
* @param language the mapped Language
|
||||
*/
|
||||
public void setLanguage(String language) {
|
||||
this.language = language;
|
||||
}
|
||||
|
||||
/**
|
||||
* This element is used to identify the type of article indexed for MEDLINE;
|
||||
* it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
|
||||
* research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
|
||||
*
|
||||
* @return the mapped Publication Type
|
||||
*/
|
||||
public List<PMSubject> getPublicationTypes() {
|
||||
return publicationTypes;
|
||||
}
|
||||
|
||||
/**
|
||||
* <GrantID> contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service
|
||||
* or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations.
|
||||
* @return the mapped grants
|
||||
*/
|
||||
|
||||
public List<PMGrant> getGrants() {
|
||||
return grants;
|
||||
}
|
||||
|
||||
public String getPmcId() {
|
||||
return pmcId;
|
||||
}
|
||||
|
||||
public PMArticle setPmcId(String pmcId) {
|
||||
public void setPmcId(String pmcId) {
|
||||
this.pmcId = pmcId;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getDoi() {
|
||||
return doi;
|
||||
}
|
||||
|
||||
public void setDoi(String doi) {
|
||||
this.doi = doi;
|
||||
}
|
||||
|
||||
public String getDate() {
|
||||
return date;
|
||||
}
|
||||
|
||||
public void setDate(String date) {
|
||||
this.date = date;
|
||||
}
|
||||
|
||||
public PMJournal getJournal() {
|
||||
return journal;
|
||||
}
|
||||
|
||||
public void setJournal(PMJournal journal) {
|
||||
this.journal = journal;
|
||||
}
|
||||
|
||||
public String getTitle() {
|
||||
return title;
|
||||
}
|
||||
|
||||
public void setTitle(String title) {
|
||||
this.title = title;
|
||||
}
|
||||
|
||||
public String getDescription() {
|
||||
return description;
|
||||
}
|
||||
|
||||
public void setDescription(String description) {
|
||||
this.description = description;
|
||||
}
|
||||
|
||||
public String getLanguage() {
|
||||
return language;
|
||||
}
|
||||
|
||||
public void setLanguage(String language) {
|
||||
this.language = language;
|
||||
}
|
||||
|
||||
public List<PMSubject> getSubjects() {
|
||||
return subjects;
|
||||
}
|
||||
|
||||
public void setSubjects(List<PMSubject> subjects) {
|
||||
this.subjects = subjects;
|
||||
}
|
||||
|
||||
public List<PMSubject> getPublicationTypes() {
|
||||
return publicationTypes;
|
||||
}
|
||||
|
||||
public void setPublicationTypes(List<PMSubject> publicationTypes) {
|
||||
this.publicationTypes = publicationTypes;
|
||||
}
|
||||
|
||||
public List<PMAuthor> getAuthors() {
|
||||
return authors;
|
||||
}
|
||||
|
||||
public void setAuthors(List<PMAuthor> authors) {
|
||||
this.authors = authors;
|
||||
}
|
||||
|
||||
public List<PMGrant> getGrants() {
|
||||
return grants;
|
||||
}
|
||||
|
||||
public void setGrants(List<PMGrant> grants) {
|
||||
this.grants = grants;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,6 +12,8 @@ public class PMAuthor implements Serializable {
|
|||
|
||||
private String lastName;
|
||||
private String foreName;
|
||||
private PMIdentifier identifier;
|
||||
private PMAffiliation affiliation;
|
||||
|
||||
/**
|
||||
* Gets last name.
|
||||
|
|
@ -59,4 +61,41 @@ public class PMAuthor implements Serializable {
|
|||
.format("%s, %s", this.foreName != null ? this.foreName : "", this.lastName != null ? this.lastName : "");
|
||||
}
|
||||
|
||||
/**
|
||||
* Gets identifier.
|
||||
*
|
||||
* @return the identifier
|
||||
*/
|
||||
public PMIdentifier getIdentifier() {
|
||||
return identifier;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets identifier.
|
||||
*
|
||||
* @param identifier the identifier
|
||||
*/
|
||||
public void setIdentifier(PMIdentifier identifier) {
|
||||
this.identifier = identifier;
|
||||
}
|
||||
|
||||
/**
|
||||
* Gets affiliation.
|
||||
*
|
||||
* @return the affiliation
|
||||
*/
|
||||
public PMAffiliation getAffiliation() {
|
||||
return affiliation;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets affiliation.
|
||||
*
|
||||
* @param affiliation the affiliation
|
||||
*/
|
||||
public void setAffiliation(PMAffiliation affiliation) {
|
||||
this.affiliation = affiliation;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,53 @@
|
|||
package eu.dnetlib.dhp.sx.bio.pubmed;
|
||||
|
||||
public class PMIdentifier {
|
||||
|
||||
private String pid;
|
||||
private String type;
|
||||
|
||||
|
||||
public PMIdentifier(String pid, String type) {
|
||||
this.pid = cleanPid(pid);
|
||||
this.type = type;
|
||||
}
|
||||
|
||||
public PMIdentifier() {
|
||||
|
||||
}
|
||||
|
||||
private String cleanPid(String pid) {
|
||||
|
||||
if (pid == null) {
|
||||
return null;
|
||||
}
|
||||
|
||||
// clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
|
||||
if (pid.matches("[0-9]{15}[0-9X]")) {
|
||||
return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
|
||||
}
|
||||
|
||||
// clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
|
||||
if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
|
||||
return pid.replaceAll("http://orcid.org/", "");
|
||||
}
|
||||
return pid;
|
||||
}
|
||||
|
||||
public String getPid() {
|
||||
return pid;
|
||||
}
|
||||
|
||||
public PMIdentifier setPid(String pid) {
|
||||
this.pid = cleanPid(pid);
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
||||
public PMIdentifier setType(String type) {
|
||||
this.type = type;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,8 +1,7 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"mo", "paramLongName":"mdstoreOutputVersion", "paramDescription": "the oaf path ", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"skipUpdate", "paramDescription": "skip update ", "paramRequired": false},
|
||||
{"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true}
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the baseline path", "paramRequired": true},
|
||||
{"paramName":"mo", "paramLongName":"mdstoreOutputVersion", "paramDescription": "the mdstore path to save", "paramRequired": true}
|
||||
|
||||
]
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
<workflow-app name="Download_Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>baselineWorkingPath</name>
|
||||
|
|
@ -16,11 +16,6 @@
|
|||
<name>mdStoreManagerURI</name>
|
||||
<description>the path of the cleaned mdstore</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>skipUpdate</name>
|
||||
<value>false</value>
|
||||
<description>The request block size</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="StartTransaction"/>
|
||||
|
|
@ -44,16 +39,16 @@
|
|||
<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
|
||||
<capture-output/>
|
||||
</java>
|
||||
<ok to="ConvertDataset"/>
|
||||
<ok to="TransformPubMed"/>
|
||||
<error to="RollBack"/>
|
||||
</action>
|
||||
|
||||
<action name="ConvertDataset">
|
||||
<action name="TransformPubMed">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Baseline to OAF Dataset</name>
|
||||
<class>eu.dnetlib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame</class>
|
||||
<name>Convert Baseline Pubmed to OAF Dataset</name>
|
||||
<class>eu.dnetlib.dhp.sx.bio.ebi.SparkCreatePubmedDump</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
|
|
@ -65,12 +60,10 @@
|
|||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--workingPath</arg><arg>${baselineWorkingPath}</arg>
|
||||
<arg>--sourcePath</arg><arg>${baselineWorkingPath}</arg>
|
||||
<arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--skipUpdate</arg><arg>${skipUpdate}</arg>
|
||||
</spark>
|
||||
<ok to="CommitVersion"/>
|
||||
<error to="RollBack"/>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,97 @@
|
|||
package eu.dnetlib.dhp.sx.bio.ebi
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.AbstractScalaApplication
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser2, PubMedToOaf}
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
class SparkCreatePubmedDump(propertyPath: String, args: Array[String], log: Logger)
|
||||
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
|
||||
|
||||
/** Here all the spark applications runs this method
|
||||
* where the whole logic of the spark node is defined
|
||||
*/
|
||||
override def run(): Unit = {
|
||||
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||
log.info("isLookupUrl: {}", isLookupUrl)
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"SourcePath is '$sourcePath'")
|
||||
val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
|
||||
log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")
|
||||
val mapper = new ObjectMapper()
|
||||
val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
|
||||
val outputBasePath = cleanedMdStoreVersion.getHdfsPath
|
||||
log.info(s"outputBasePath is '$outputBasePath'")
|
||||
|
||||
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
||||
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||
|
||||
createPubmedDump(spark, sourcePath, outputBasePath, vocabularies)
|
||||
|
||||
}
|
||||
|
||||
/** This method creates a dump of the pubmed articles
|
||||
* @param spark the spark session
|
||||
* @param sourcePath the path of the source file
|
||||
* @param targetPath the path of the target file
|
||||
* @param vocabularies the vocabularies
|
||||
*/
|
||||
def createPubmedDump(
|
||||
spark: SparkSession,
|
||||
sourcePath: String,
|
||||
targetPath: String,
|
||||
vocabularies: VocabularyGroup
|
||||
): Unit = {
|
||||
require(spark != null)
|
||||
|
||||
implicit val PMEncoder: Encoder[PMArticle] = Encoders.bean(classOf[PMArticle])
|
||||
|
||||
import spark.implicits._
|
||||
val df = spark.read.option("lineSep", "</PubmedArticle>").text(sourcePath)
|
||||
val mapper = new ObjectMapper()
|
||||
df.as[String]
|
||||
.map(s => {
|
||||
val id = s.indexOf("<PubmedArticle>")
|
||||
if (id >= 0) s"${s.substring(id)}</PubmedArticle>" else null
|
||||
})
|
||||
.filter(s => s != null)
|
||||
.map { i =>
|
||||
//remove try catch
|
||||
try {
|
||||
new PMParser2().parse(i)
|
||||
} catch {
|
||||
case _: Exception => {
|
||||
throw new RuntimeException(s"Error parsing article: $i")
|
||||
}
|
||||
}
|
||||
}
|
||||
.dropDuplicates("pmid")
|
||||
.map { a =>
|
||||
val oaf = PubMedToOaf.convert(a, vocabularies)
|
||||
if (oaf != null)
|
||||
mapper.writeValueAsString(oaf)
|
||||
else
|
||||
null
|
||||
}
|
||||
.as[String]
|
||||
.filter(s => s != null)
|
||||
.write
|
||||
.option("compression", "gzip")
|
||||
.mode("overwrite")
|
||||
.text(targetPath)
|
||||
}
|
||||
}
|
||||
|
||||
object SparkCreatePubmedDump {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
||||
new SparkCreatePubmedDump("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json", args, log).initialize().run()
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,276 @@
|
|||
package eu.dnetlib.dhp.sx.bio.pubmed
|
||||
|
||||
import org.apache.commons.lang3.StringUtils
|
||||
|
||||
import javax.xml.stream.XMLEventReader
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.xml.{MetaData, NodeSeq}
|
||||
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText}
|
||||
|
||||
class PMParser2 {
|
||||
|
||||
/** Extracts the value of an attribute from a MetaData object.
|
||||
* @param attrs the MetaData object
|
||||
* @param key the key of the attribute
|
||||
* @return the value of the attribute or null if the attribute is not found
|
||||
*/
|
||||
private def extractAttributes(attrs: MetaData, key: String): String = {
|
||||
|
||||
val res = attrs.get(key)
|
||||
if (res.isDefined) {
|
||||
val s = res.get
|
||||
if (s != null && s.nonEmpty)
|
||||
s.head.text
|
||||
else
|
||||
null
|
||||
} else null
|
||||
}
|
||||
|
||||
/** Validates and formats a date given the year, month, and day as strings.
|
||||
*
|
||||
* @param year the year as a string
|
||||
* @param month the month as a string
|
||||
* @param day the day as a string
|
||||
* @return the formatted date as "YYYY-MM-DD" or null if the date is invalid
|
||||
*/
|
||||
private def validate_Date(year: String, month: String, day: String): String = {
|
||||
try {
|
||||
f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d"
|
||||
|
||||
} catch {
|
||||
case _: Throwable => null
|
||||
}
|
||||
}
|
||||
|
||||
/** Extracts the grant information from a NodeSeq object.
|
||||
*
|
||||
* @param gNode the NodeSeq object
|
||||
* @return the grant information or an empty list if the grant information is not found
|
||||
*/
|
||||
private def extractGrant(gNode: NodeSeq): List[PMGrant] = {
|
||||
gNode
|
||||
.map(node => {
|
||||
val grantId = (node \ "GrantID").text
|
||||
val agency = (node \ "Agency").text
|
||||
val country = (node \ "Country").text
|
||||
new PMGrant(grantId, agency, country)
|
||||
})
|
||||
.toList
|
||||
}
|
||||
|
||||
/** Extracts the journal information from a NodeSeq object.
|
||||
*
|
||||
* @param jNode the NodeSeq object
|
||||
* @return the journal information or null if the journal information is not found
|
||||
*/
|
||||
private def extractJournal(jNode: NodeSeq): PMJournal = {
|
||||
val journal = new PMJournal
|
||||
journal.setTitle((jNode \ "Title").text)
|
||||
journal.setIssn((jNode \ "ISSN").text)
|
||||
journal.setVolume((jNode \ "JournalIssue" \ "Volume").text)
|
||||
journal.setIssue((jNode \ "JournalIssue" \ "Issue").text)
|
||||
if (journal.getTitle != null && StringUtils.isNotEmpty(journal.getTitle))
|
||||
journal
|
||||
else
|
||||
null
|
||||
}
|
||||
|
||||
private def extractAuthors(aNode: NodeSeq): List[PMAuthor] = {
|
||||
aNode
|
||||
.map(author => {
|
||||
val a = new PMAuthor
|
||||
a.setLastName((author \ "LastName").text)
|
||||
a.setForeName((author \ "ForeName").text)
|
||||
val id = (author \ "Identifier").text
|
||||
val idType =(author \ "Identifier" \ "@Source").text
|
||||
|
||||
if(id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
|
||||
a.setIdentifier(new PMIdentifier(id, idType))
|
||||
}
|
||||
|
||||
|
||||
val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text
|
||||
val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text
|
||||
val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text
|
||||
|
||||
if(affiliation != null && affiliation.nonEmpty) {
|
||||
val aff = new PMAffiliation()
|
||||
aff.setName(affiliation)
|
||||
if(affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty) {
|
||||
aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType))
|
||||
}
|
||||
a.setAffiliation(aff)
|
||||
}
|
||||
a
|
||||
})
|
||||
.toList
|
||||
}
|
||||
|
||||
def parse(input: String): PMArticle = {
|
||||
val xml = scala.xml.XML.loadString(input)
|
||||
val article = new PMArticle
|
||||
|
||||
val grantNodes = xml \ "MedlineCitation" \\ "Grant"
|
||||
article.setGrants(extractGrant(grantNodes).asJava)
|
||||
|
||||
val journal = xml \ "MedlineCitation" \ "Article" \ "Journal"
|
||||
article.setJournal(extractJournal(journal))
|
||||
|
||||
val authors = xml \ "MedlineCitation" \ "Article" \ "AuthorList" \ "Author"
|
||||
|
||||
article.setAuthors(
|
||||
extractAuthors(authors).asJava
|
||||
)
|
||||
|
||||
val pmId = xml \ "MedlineCitation" \ "PMID"
|
||||
|
||||
val articleIds = xml \ "PubmedData" \ "ArticleIdList" \ "ArticleId"
|
||||
articleIds.foreach(articleId => {
|
||||
val idType = (articleId \ "@IdType").text
|
||||
val id = articleId.text
|
||||
if ("doi".equalsIgnoreCase(idType)) article.setDoi(id)
|
||||
if ("pmc".equalsIgnoreCase(idType)) article.setPmcId(id)
|
||||
})
|
||||
article.setPmid(pmId.text)
|
||||
|
||||
val pubMedPubDate = xml \ "MedlineCitation" \ "DateCompleted"
|
||||
val currentDate =
|
||||
validate_Date((pubMedPubDate \ "Year").text, (pubMedPubDate \ "Month").text, (pubMedPubDate \ "Day").text)
|
||||
if (currentDate != null) article.setDate(currentDate)
|
||||
|
||||
val articleTitle = xml \ "MedlineCitation" \ "Article" \ "ArticleTitle"
|
||||
article.setTitle(articleTitle.text)
|
||||
|
||||
val abstractText = xml \ "MedlineCitation" \ "Article" \ "Abstract" \ "AbstractText"
|
||||
if (abstractText != null && abstractText.text != null && abstractText.text.nonEmpty)
|
||||
article.setDescription(abstractText.text.split("\n").map(s => s.trim).mkString(" ").trim)
|
||||
|
||||
val language = xml \ "MedlineCitation" \ "Article" \ "Language"
|
||||
article.setLanguage(language.text)
|
||||
|
||||
val subjects = xml \ "MedlineCitation" \ "MeshHeadingList" \ "MeshHeading"
|
||||
article.setSubjects(
|
||||
subjects
|
||||
.take(20)
|
||||
.map(subject => {
|
||||
val descriptorName = (subject \ "DescriptorName").text
|
||||
val ui = (subject \ "DescriptorName" \ "@UI").text
|
||||
val s = new PMSubject
|
||||
s.setValue(descriptorName)
|
||||
s.setMeshId(ui)
|
||||
s
|
||||
})
|
||||
.toList
|
||||
.asJava
|
||||
)
|
||||
val publicationTypes = xml \ "MedlineCitation" \ "Article" \ "PublicationTypeList" \ "PublicationType"
|
||||
article.setPublicationTypes(
|
||||
publicationTypes
|
||||
.map(pt => {
|
||||
val s = new PMSubject
|
||||
s.setValue(pt.text)
|
||||
s
|
||||
})
|
||||
.toList
|
||||
.asJava
|
||||
)
|
||||
|
||||
article
|
||||
}
|
||||
|
||||
def parse2(xml: XMLEventReader): PMArticle = {
|
||||
var currentArticle: PMArticle = null
|
||||
var currentSubject: PMSubject = null
|
||||
var currentAuthor: PMAuthor = null
|
||||
var currentJournal: PMJournal = null
|
||||
var currentGrant: PMGrant = null
|
||||
var currNode: String = null
|
||||
var currentYear = "0"
|
||||
var currentMonth = "01"
|
||||
var currentDay = "01"
|
||||
var currentArticleType: String = null
|
||||
|
||||
while (xml.hasNext) {
|
||||
val ne = xml.next
|
||||
ne match {
|
||||
case EvElemStart(_, label, attrs, _) =>
|
||||
currNode = label
|
||||
|
||||
label match {
|
||||
case "PubmedArticle" => currentArticle = new PMArticle
|
||||
case "Author" => currentAuthor = new PMAuthor
|
||||
case "Journal" => currentJournal = new PMJournal
|
||||
case "Grant" => currentGrant = new PMGrant
|
||||
case "PublicationType" | "DescriptorName" =>
|
||||
currentSubject = new PMSubject
|
||||
currentSubject.setMeshId(extractAttributes(attrs, "UI"))
|
||||
case "ArticleId" => currentArticleType = extractAttributes(attrs, "IdType")
|
||||
case _ =>
|
||||
}
|
||||
case EvElemEnd(_, label) =>
|
||||
label match {
|
||||
case "PubmedArticle" => return currentArticle
|
||||
case "Author" => currentArticle.getAuthors.add(currentAuthor)
|
||||
case "Journal" => currentArticle.setJournal(currentJournal)
|
||||
case "Grant" => currentArticle.getGrants.add(currentGrant)
|
||||
case "PubMedPubDate" =>
|
||||
if (currentArticle.getDate == null)
|
||||
currentArticle.setDate(validate_Date(currentYear, currentMonth, currentDay))
|
||||
case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay")
|
||||
case "DescriptorName" => currentArticle.getSubjects.add(currentSubject)
|
||||
case "PublicationType" => currentArticle.getPublicationTypes.add(currentSubject)
|
||||
case _ =>
|
||||
}
|
||||
case EvText(text) =>
|
||||
if (currNode != null && text.trim.nonEmpty)
|
||||
currNode match {
|
||||
case "ArticleTitle" => {
|
||||
if (currentArticle.getTitle == null)
|
||||
currentArticle.setTitle(text.trim)
|
||||
else
|
||||
currentArticle.setTitle(currentArticle.getTitle + text.trim)
|
||||
}
|
||||
case "AbstractText" => {
|
||||
if (currentArticle.getDescription == null)
|
||||
currentArticle.setDescription(text.trim)
|
||||
else
|
||||
currentArticle.setDescription(currentArticle.getDescription + text.trim)
|
||||
}
|
||||
case "PMID" => currentArticle.setPmid(text.trim)
|
||||
case "ArticleId" =>
|
||||
if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
|
||||
if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim)
|
||||
case "Language" => currentArticle.setLanguage(text.trim)
|
||||
case "ISSN" => currentJournal.setIssn(text.trim)
|
||||
case "GrantID" => currentGrant.setGrantID(text.trim)
|
||||
case "Agency" => currentGrant.setAgency(text.trim)
|
||||
case "Country" => if (currentGrant != null) currentGrant.setCountry(text.trim)
|
||||
case "Year" => currentYear = text.trim
|
||||
case "Month" => currentMonth = text.trim
|
||||
case "Day" => currentDay = text.trim
|
||||
case "Volume" => currentJournal.setVolume(text.trim)
|
||||
case "Issue" => currentJournal.setIssue(text.trim)
|
||||
case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim)
|
||||
case "LastName" => {
|
||||
if (currentAuthor != null)
|
||||
currentAuthor.setLastName(text.trim)
|
||||
}
|
||||
case "ForeName" =>
|
||||
if (currentAuthor != null)
|
||||
currentAuthor.setForeName(text.trim)
|
||||
case "Title" =>
|
||||
if (currentJournal.getTitle == null)
|
||||
currentJournal.setTitle(text.trim)
|
||||
else
|
||||
currentJournal.setTitle(currentJournal.getTitle + text.trim)
|
||||
case _ =>
|
||||
|
||||
}
|
||||
case _ =>
|
||||
}
|
||||
|
||||
}
|
||||
null
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -294,6 +294,12 @@ object PubMedToOaf {
|
|||
author.setName(a.getForeName)
|
||||
author.setSurname(a.getLastName)
|
||||
author.setFullname(a.getFullName)
|
||||
if(a.getIdentifier != null) {
|
||||
author.setPid(List(OafMapperUtils.structuredProperty(a.getIdentifier.getPid,
|
||||
OafMapperUtils.qualifier(a.getIdentifier.getType,a.getIdentifier.getType,ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES), dataInfo)).asJava)
|
||||
}
|
||||
if (a.getAffiliation!= null)
|
||||
author.setRawAffiliationString(List(a.getAffiliation.getName).asJava)
|
||||
author.setRank(index + 1)
|
||||
author
|
||||
}(collection.breakOut)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,157 @@
|
|||
<PubmedArticle>
|
||||
<MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM">
|
||||
<PMID Version="1">37318999</PMID>
|
||||
<DateCompleted>
|
||||
<Year>2024</Year>
|
||||
<Month>02</Month>
|
||||
<Day>09</Day>
|
||||
</DateCompleted>
|
||||
<DateRevised>
|
||||
<Year>2024</Year>
|
||||
<Month>02</Month>
|
||||
<Day>09</Day>
|
||||
</DateRevised>
|
||||
<Article PubModel="Print-Electronic">
|
||||
<Journal>
|
||||
<ISSN IssnType="Electronic">1522-1229</ISSN>
|
||||
<JournalIssue CitedMedium="Internet">
|
||||
<Volume>47</Volume>
|
||||
<Issue>3</Issue>
|
||||
<PubDate>
|
||||
<Year>2023</Year>
|
||||
<Month>Sep</Month>
|
||||
<Day>01</Day>
|
||||
</PubDate>
|
||||
</JournalIssue>
|
||||
<Title>Advances in physiology education</Title>
|
||||
<ISOAbbreviation>Adv Physiol Educ</ISOAbbreviation>
|
||||
</Journal>
|
||||
<ArticleTitle>Providing the choice of in-person or videoconference attendance in a clinical physiology course may harm learning outcomes for the entire cohort.</ArticleTitle>
|
||||
<Pagination>
|
||||
<MedlinePgn>548-556</MedlinePgn>
|
||||
</Pagination>
|
||||
<ELocationID EIdType="doi" ValidYN="Y">10.1152/advan.00160.2022</ELocationID>
|
||||
<Abstract>
|
||||
<AbstractText>Clinical Physiology 1 and 2 are flipped classes in which students watch prerecorded videos before class. During the 3-h class, students take practice assessments, work in groups on critical thinking exercises, work through case studies, and engage in drawing exercises. Due to the COVID pandemic, these courses were transitioned from in-person classes to online classes. Despite the university's return-to-class policy, some students were reluctant to return to in-person classes; therefore during the 2021-2022 academic year, Clinical Physiology 1 and 2 were offered as flipped, hybrid courses. In a hybrid format, students either attended the synchronous class in person or online. Here we evaluate the learning outcomes and the perceptions of the learning experience for students who attended Clinical Physiology 1 and 2 either online (2020-2021) or in a hybrid format (2021-2022). In addition to exam scores, in-class surveys and end of course evaluations were compiled to describe the student experience in the flipped hybrid setting. Retrospective linear mixed-model regression analysis of exam scores revealed that a hybrid modality (2021-2022) was associated with lower exam scores when controlling for sex, graduate/undergraduate status, delivery method, and the order in which the courses were taken (<i>F</i> test: <i>F</i> = 8.65, df1 = 2, df2 = 179.28, <i>P</i> = 0.0003). In addition, being a Black Indigenous Person of Color (BIPOC) student is associated with a lower exam score, controlling for the same previous factors (<i>F</i> test: <i>F</i> = 4.23, df1 = 1, df2 = 130.28, <i>P</i> = 0.04), albeit with lower confidence; the BIPOC representation in this sample is small (BIPOC: <i>n</i> = 144; total: <i>n</i> = 504). There is no significant interaction between the hybrid modality and race, meaning that BIPOC and White students are both negatively affected in a hybrid flipped course. Instructors should consider carefully about offering hybrid courses and build in extra student support.<b>NEW & NOTEWORTHY</b> The transition from online to in-person teaching has been as challenging as the original transition to remote teaching with the onset of the pandemic. Since not all students were ready to return to the classroom, students could choose to take this course in person or online. This arrangement provided flexibility and opportunities for innovative class activities for students but introduced tradeoffs in lower test scores from the hybrid modality than fully online or fully in-person modalities.</AbstractText>
|
||||
</Abstract>
|
||||
<AuthorList CompleteYN="Y">
|
||||
<Author ValidYN="Y">
|
||||
<LastName>Anderson</LastName>
|
||||
<ForeName>Lisa Carney</ForeName>
|
||||
<Initials>LC</Initials>
|
||||
<Identifier Source="ORCID">0000-0003-2261-1921</Identifier>
|
||||
<AffiliationInfo>
|
||||
<Affiliation>Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota, United States.</Affiliation>
|
||||
<Identifier Source="ROR">https://ror.org/017zqws13</Identifier>
|
||||
</AffiliationInfo>
|
||||
</Author>
|
||||
<Author ValidYN="Y">
|
||||
<LastName>Jacobson</LastName>
|
||||
<ForeName>Tate</ForeName>
|
||||
<Initials>T</Initials>
|
||||
<AffiliationInfo>
|
||||
<Affiliation>Department of Statistics, University of Minnesota, Minneapolis, Minnesota, United States.</Affiliation>
|
||||
</AffiliationInfo>
|
||||
</Author>
|
||||
</AuthorList>
|
||||
<Language>eng</Language>
|
||||
<PublicationTypeList>
|
||||
<PublicationType UI="D016428">Journal Article</PublicationType>
|
||||
</PublicationTypeList>
|
||||
<ArticleDate DateType="Electronic">
|
||||
<Year>2023</Year>
|
||||
<Month>06</Month>
|
||||
<Day>15</Day>
|
||||
</ArticleDate>
|
||||
</Article>
|
||||
<MedlineJournalInfo>
|
||||
<Country>United States</Country>
|
||||
<MedlineTA>Adv Physiol Educ</MedlineTA>
|
||||
<NlmUniqueID>100913944</NlmUniqueID>
|
||||
<ISSNLinking>1043-4046</ISSNLinking>
|
||||
</MedlineJournalInfo>
|
||||
<CitationSubset>IM</CitationSubset>
|
||||
<MeshHeadingList>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D010827" MajorTopicYN="Y">Physiology</DescriptorName>
|
||||
<QualifierName UI="Q000193" MajorTopicYN="N">education</QualifierName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D012189" MajorTopicYN="N">Retrospective Studies</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D007858" MajorTopicYN="N">Learning</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D000086382" MajorTopicYN="N">COVID-19</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D012044" MajorTopicYN="N">Regression Analysis</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D013334" MajorTopicYN="N">Students</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D044465" MajorTopicYN="N">White People</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D044383" MajorTopicYN="N">Black People</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D020375" MajorTopicYN="N">Education, Distance</DescriptorName>
|
||||
</MeshHeading>
|
||||
<MeshHeading>
|
||||
<DescriptorName UI="D003479" MajorTopicYN="N">Curriculum</DescriptorName>
|
||||
</MeshHeading>
|
||||
</MeshHeadingList>
|
||||
<KeywordList Owner="NOTNLM">
|
||||
<Keyword MajorTopicYN="N">flipped teaching</Keyword>
|
||||
<Keyword MajorTopicYN="N">hybrid teaching</Keyword>
|
||||
<Keyword MajorTopicYN="N">inequity</Keyword>
|
||||
<Keyword MajorTopicYN="N">learning outcomes</Keyword>
|
||||
<Keyword MajorTopicYN="N">responsive teaching</Keyword>
|
||||
</KeywordList>
|
||||
</MedlineCitation>
|
||||
<PubmedData>
|
||||
<History>
|
||||
<PubMedPubDate PubStatus="medline">
|
||||
<Year>2023</Year>
|
||||
<Month>7</Month>
|
||||
<Day>21</Day>
|
||||
<Hour>6</Hour>
|
||||
<Minute>44</Minute>
|
||||
</PubMedPubDate>
|
||||
<PubMedPubDate PubStatus="pubmed">
|
||||
<Year>2023</Year>
|
||||
<Month>6</Month>
|
||||
<Day>15</Day>
|
||||
<Hour>19</Hour>
|
||||
<Minute>14</Minute>
|
||||
</PubMedPubDate>
|
||||
<PubMedPubDate PubStatus="entrez">
|
||||
<Year>2023</Year>
|
||||
<Month>6</Month>
|
||||
<Day>15</Day>
|
||||
<Hour>12</Hour>
|
||||
<Minute>53</Minute>
|
||||
</PubMedPubDate>
|
||||
</History>
|
||||
<PublicationStatus>ppublish</PublicationStatus>
|
||||
<ArticleIdList>
|
||||
<ArticleId IdType="pubmed">37318999</ArticleId>
|
||||
<ArticleId IdType="doi">10.1152/advan.00160.2022</ArticleId>
|
||||
</ArticleIdList>
|
||||
</PubmedData>
|
||||
</PubmedArticle>
|
||||
|
|
@ -5,7 +5,10 @@ import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
|||
import eu.dnetlib.dhp.schema.oaf.utils.PidType
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result}
|
||||
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf}
|
||||
import eu.dnetlib.dhp.sx.bio.ebi.SparkCreatePubmedDump
|
||||
import eu.dnetlib.dhp.sx.bio.pubmed._
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.sql.SparkSession
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
|
@ -13,14 +16,16 @@ import org.junit.jupiter.api.Assertions._
|
|||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.api.{BeforeEach, Test}
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
import org.slf4j.LoggerFactory
|
||||
|
||||
import java.io.{BufferedReader, InputStream, InputStreamReader}
|
||||
import java.util.regex.Pattern
|
||||
import java.util.zip.GZIPInputStream
|
||||
import javax.xml.stream.XMLInputFactory
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.collection.mutable
|
||||
import scala.collection.mutable.ListBuffer
|
||||
import scala.io.Source
|
||||
import scala.xml.pull.XMLEventReader
|
||||
|
||||
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||
class BioScholixTest extends AbstractVocabularyTest {
|
||||
|
|
@ -48,6 +53,77 @@ class BioScholixTest extends AbstractVocabularyTest {
|
|||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
def testPid(): Unit = {
|
||||
val pids = List(
|
||||
"0000000163025705",
|
||||
"000000018494732X",
|
||||
"0000000308873343",
|
||||
"0000000335964515",
|
||||
"0000000333457333",
|
||||
"0000000335964515",
|
||||
"0000000302921949",
|
||||
|
||||
"http://orcid.org/0000-0001-8567-3543",
|
||||
"http://orcid.org/0000-0001-7868-8528",
|
||||
"0000-0001-9189-1440",
|
||||
"0000-0003-3727-9247",
|
||||
"0000-0001-7246-1058",
|
||||
"000000033962389X",
|
||||
"0000000330371470",
|
||||
"0000000171236123",
|
||||
"0000000272569752",
|
||||
"0000000293231371",
|
||||
"http://orcid.org/0000-0003-3345-7333",
|
||||
"0000000340145688",
|
||||
"http://orcid.org/0000-0003-4894-1689"
|
||||
)
|
||||
|
||||
pids.foreach(pid => {
|
||||
val pidCleaned = new PMIdentifier(pid, "ORCID").getPid
|
||||
// assert pid is in the format of ORCID
|
||||
println(pidCleaned)
|
||||
assertTrue(pidCleaned.matches("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]"))
|
||||
})
|
||||
}
|
||||
|
||||
def extractAffiliation(s: String): List[String] = {
|
||||
val regex: String = "<Affiliation>(.*)<\\/Affiliation>"
|
||||
val pattern = Pattern.compile(regex, Pattern.MULTILINE)
|
||||
val matcher = pattern.matcher(s)
|
||||
val l: mutable.ListBuffer[String] = mutable.ListBuffer()
|
||||
while (matcher.find()) {
|
||||
l += matcher.group(1)
|
||||
}
|
||||
l.toList
|
||||
}
|
||||
|
||||
case class AuthorPID(pidType: String, pid: String) {}
|
||||
|
||||
def extractAuthorIdentifier(s: String): List[AuthorPID] = {
|
||||
val regex: String = "<Identifier Source=\"(.*)\">(.*)<\\/Identifier>"
|
||||
val pattern = Pattern.compile(regex, Pattern.MULTILINE)
|
||||
val matcher = pattern.matcher(s)
|
||||
val l: mutable.ListBuffer[AuthorPID] = mutable.ListBuffer()
|
||||
while (matcher.find()) {
|
||||
l += AuthorPID(pidType = matcher.group(1), pid = matcher.group(2))
|
||||
}
|
||||
l.toList
|
||||
}
|
||||
|
||||
@Test
|
||||
def testParsingPubmed2(): Unit = {
|
||||
val mapper = new ObjectMapper()
|
||||
val xml = IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml"))
|
||||
val parser = new PMParser2()
|
||||
val article = parser.parse(xml)
|
||||
|
||||
// println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(article))
|
||||
|
||||
println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(PubMedToOaf.convert(article, vocabularies)))
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
def testEBIData() = {
|
||||
val inputFactory = XMLInputFactory.newInstance
|
||||
|
|
@ -124,6 +200,14 @@ class BioScholixTest extends AbstractVocabularyTest {
|
|||
}
|
||||
}
|
||||
|
||||
def testPubmedSplitting(): Unit = {
|
||||
|
||||
val spark: SparkSession = SparkSession.builder().appName("test").master("local").getOrCreate()
|
||||
new SparkCreatePubmedDump("", Array.empty, LoggerFactory.getLogger(getClass))
|
||||
.createPubmedDump(spark, "/home/sandro/Downloads/pubmed", "/home/sandro/Downloads/pubmed_mapped", vocabularies)
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
def testPubmedOriginalID(): Unit = {
|
||||
val article: PMArticle = new PMArticle
|
||||
|
|
|
|||
Loading…
Reference in New Issue