added code to dump the relations between organizaiton and projects in the subset of entities relevant for EOSC
This commit is contained in:
parent
da19f117d8
commit
a821371af2
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@ -1,28 +1,27 @@
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package eu.dnetlib.dhp.eosc.model;
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/**
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* @author miriam.baglioni
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* @Date 25/10/23
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*/
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import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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/**
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* To store information about the funder funding the project related to the result. It extends
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* eu.dnetlib.dhp.schema.dump.oaf.Funder with the following parameter: - - private
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* eu.dnetdlib.dhp.schema.dump.oaf.graph.Fundings funding_stream to store the fundingstream
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*/
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public class Funder extends FunderShort {
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public class Funder extends FunderShort {
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@JsonSchema(description = "Description of the funding stream")
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private Fundings funding_stream;
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@JsonSchema(description = "Description of the funding stream")
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private Fundings funding_stream;
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public Fundings getFunding_stream() {
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return funding_stream;
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}
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public Fundings getFunding_stream() {
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return funding_stream;
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}
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public void setFunding_stream(Fundings funding_stream) {
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this.funding_stream = funding_stream;
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}
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}
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public void setFunding_stream(Fundings funding_stream) {
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this.funding_stream = funding_stream;
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}
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}
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@ -1,12 +1,10 @@
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package eu.dnetlib.dhp.eosc.model;
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/**
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* @author miriam.baglioni
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* @Date 25/10/23
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*/
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import java.io.Serializable;
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import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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@ -22,23 +20,23 @@ import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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*/
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public class Fundings implements Serializable {
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@JsonSchema(description = "Id of the funding stream")
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private String id;
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private String description;
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@JsonSchema(description = "Id of the funding stream")
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private String id;
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private String description;
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public String getId() {
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return id;
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}
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public String getDescription() {
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return description;
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}
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public String getDescription() {
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return description;
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}
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public void setDescription(String description) {
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this.description = description;
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}
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public void setDescription(String description) {
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this.description = description;
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}
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}
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@ -1,11 +1,10 @@
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package eu.dnetlib.dhp.eosc.model;
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/**
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* @author miriam.baglioni
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* @Date 25/10/23
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*/
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import java.io.Serializable;
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import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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@ -16,51 +15,51 @@ import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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* funded amount by the funder
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*/
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public class Granted implements Serializable {
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@JsonSchema(description = "The currency of the granted amount (e.g. EUR)")
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private String currency;
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@JsonSchema(description = "The currency of the granted amount (e.g. EUR)")
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private String currency;
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@JsonSchema(description = "The total cost of the project")
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private float totalcost;
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@JsonSchema(description = "The total cost of the project")
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private float totalcost;
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@JsonSchema(description = "The funded amount")
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private float fundedamount;
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@JsonSchema(description = "The funded amount")
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private float fundedamount;
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public String getCurrency() {
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return currency;
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}
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public String getCurrency() {
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return currency;
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}
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public void setCurrency(String currency) {
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this.currency = currency;
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}
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public void setCurrency(String currency) {
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this.currency = currency;
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}
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public float getTotalcost() {
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return totalcost;
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}
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public float getTotalcost() {
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return totalcost;
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}
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public void setTotalcost(float totalcost) {
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this.totalcost = totalcost;
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}
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public void setTotalcost(float totalcost) {
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this.totalcost = totalcost;
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}
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public float getFundedamount() {
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return fundedamount;
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}
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public float getFundedamount() {
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return fundedamount;
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}
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public void setFundedamount(float fundedamount) {
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this.fundedamount = fundedamount;
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}
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public void setFundedamount(float fundedamount) {
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this.fundedamount = fundedamount;
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}
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public static Granted newInstance(String currency, float totalcost, float fundedamount) {
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Granted granted = new Granted();
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granted.currency = currency;
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granted.totalcost = totalcost;
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granted.fundedamount = fundedamount;
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return granted;
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}
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public static Granted newInstance(String currency, float totalcost, float fundedamount) {
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Granted granted = new Granted();
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granted.currency = currency;
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granted.totalcost = totalcost;
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granted.fundedamount = fundedamount;
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return granted;
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}
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public static Granted newInstance(String currency, float fundedamount) {
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Granted granted = new Granted();
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granted.currency = currency;
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granted.fundedamount = fundedamount;
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return granted;
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}
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public static Granted newInstance(String currency, float fundedamount) {
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Granted granted = new Granted();
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granted.currency = currency;
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granted.fundedamount = fundedamount;
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return granted;
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}
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}
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@ -1,3 +1,4 @@
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package eu.dnetlib.dhp.eosc.model;
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import java.io.Serializable;
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@ -16,76 +17,76 @@ import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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* - private List<OrganizationPid> pid to store the list of pids for the organization
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*/
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public class Organization implements Serializable {
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private String legalshortname;
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private String legalname;
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private String websiteurl;
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private String legalshortname;
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private String legalname;
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private String websiteurl;
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@JsonSchema(description = "Alternative names that identify the organisation")
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private List<String> alternativenames;
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@JsonSchema(description = "Alternative names that identify the organisation")
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private List<String> alternativenames;
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@JsonSchema(description = "The organisation country")
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private Country country;
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@JsonSchema(description = "The organisation country")
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private Country country;
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@JsonSchema(description = "The OpenAIRE id for the organisation")
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private String id;
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@JsonSchema(description = "The OpenAIRE id for the organisation")
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private String id;
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@JsonSchema(description = "Persistent identifiers for the organisation i.e. isni 0000000090326370")
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private List<OrganizationPid> pid;
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@JsonSchema(description = "Persistent identifiers for the organisation i.e. isni 0000000090326370")
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private List<OrganizationPid> pid;
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public String getLegalshortname() {
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return legalshortname;
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}
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public String getLegalshortname() {
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return legalshortname;
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}
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public void setLegalshortname(String legalshortname) {
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this.legalshortname = legalshortname;
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}
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public void setLegalshortname(String legalshortname) {
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this.legalshortname = legalshortname;
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}
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public String getLegalname() {
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return legalname;
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}
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public String getLegalname() {
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return legalname;
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}
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public void setLegalname(String legalname) {
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this.legalname = legalname;
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}
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public void setLegalname(String legalname) {
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this.legalname = legalname;
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}
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public String getWebsiteurl() {
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return websiteurl;
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}
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public String getWebsiteurl() {
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return websiteurl;
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}
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public void setWebsiteurl(String websiteurl) {
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this.websiteurl = websiteurl;
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}
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public void setWebsiteurl(String websiteurl) {
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this.websiteurl = websiteurl;
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}
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public List<String> getAlternativenames() {
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return alternativenames;
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}
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public List<String> getAlternativenames() {
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return alternativenames;
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}
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public void setAlternativenames(List<String> alternativenames) {
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this.alternativenames = alternativenames;
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}
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public void setAlternativenames(List<String> alternativenames) {
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this.alternativenames = alternativenames;
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}
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public Country getCountry() {
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return country;
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}
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public Country getCountry() {
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return country;
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}
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public void setCountry(Country country) {
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this.country = country;
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}
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public void setCountry(Country country) {
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this.country = country;
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}
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public String getId() {
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return id;
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}
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public List<OrganizationPid> getPid() {
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return pid;
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}
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public List<OrganizationPid> getPid() {
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return pid;
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}
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public void setPid(List<OrganizationPid> pid) {
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this.pid = pid;
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}
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public void setPid(List<OrganizationPid> pid) {
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this.pid = pid;
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}
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}
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@ -33,7 +33,7 @@ public class OrganizationPid implements Serializable {
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this.value = value;
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}
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public static OrganizationPid newInstance(String type, String value){
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public static OrganizationPid newInstance(String type, String value) {
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OrganizationPid op = new OrganizationPid();
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op.type = type;
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op.value = value;
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package eu.dnetlib.dhp.eosc.model;
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/**
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* @author miriam.baglioni
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* @Date 25/10/23
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*/
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import java.io.Serializable;
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import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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* to store the code of the programme - private String description to store the description of the programme
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*/
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public class Programme implements Serializable {
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@JsonSchema(description = "The code of the programme")
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private String code;
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@JsonSchema(description = "The code of the programme")
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private String code;
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@JsonSchema(description = "The description of the programme")
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private String description;
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@JsonSchema(description = "The description of the programme")
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private String description;
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public String getCode() {
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return code;
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}
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public String getCode() {
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return code;
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}
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public void setCode(String code) {
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this.code = code;
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}
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public void setCode(String code) {
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this.code = code;
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}
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public String getDescription() {
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return description;
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}
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public String getDescription() {
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return description;
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}
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public void setDescription(String description) {
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this.description = description;
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}
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public void setDescription(String description) {
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this.description = description;
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}
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public static Programme newInstance(String code, String description) {
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Programme p = new Programme();
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p.code = code;
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p.description = description;
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return p;
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}
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public static Programme newInstance(String code, String description) {
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Programme p = new Programme();
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p.code = code;
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p.description = description;
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return p;
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}
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}
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@ -1,17 +1,15 @@
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package eu.dnetlib.dhp.eosc.model;
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/**
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* @author miriam.baglioni
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* @Date 25/10/23
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*/
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import java.io.Serializable;
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import java.util.List;
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import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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/**
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* This is the class representing the Project in the model used for the dumps of the whole graph. At the moment the dump
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* of the Projects differs from the other dumps because we do not create relations between Funders (Organization) and
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@ -43,164 +41,162 @@ import com.github.imifou.jsonschema.module.addon.annotation.JsonSchema;
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*/
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public class Project implements Serializable {
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private String id;
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private String id;
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private String websiteurl;
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private String code;
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private String acronym;
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private String title;
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private String websiteurl;
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private String code;
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private String acronym;
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private String title;
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private String startdate;
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private String startdate;
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private String enddate;
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private String enddate;
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private String callidentifier;
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private String callidentifier;
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private String keywords;
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private String keywords;
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private boolean openaccessmandateforpublications;
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private boolean openaccessmandateforpublications;
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private boolean openaccessmandatefordataset;
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private List<String> subject;
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private boolean openaccessmandatefordataset;
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private List<String> subject;
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@JsonSchema(description = "Funding information for the project")
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private List<Funder> funding;
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@JsonSchema(description = "Funding information for the project")
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private List<Funder> funding;
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private String summary;
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private String summary;
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@JsonSchema(description = "The money granted to the project")
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private Granted granted;
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@JsonSchema(description = "The money granted to the project")
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private Granted granted;
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@JsonSchema(description = "The h2020 programme funding the project")
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private List<Programme> h2020programme;
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@JsonSchema(description = "The h2020 programme funding the project")
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private List<Programme> h2020programme;
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public String getId() {
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return id;
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}
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public String getWebsiteurl() {
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return websiteurl;
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}
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public void setId(String id) {
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this.id = id;
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}
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public void setWebsiteurl(String websiteurl) {
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this.websiteurl = websiteurl;
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}
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public String getWebsiteurl() {
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return websiteurl;
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}
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public String getCode() {
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return code;
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}
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public void setWebsiteurl(String websiteurl) {
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this.websiteurl = websiteurl;
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}
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public void setCode(String code) {
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this.code = code;
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}
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public String getCode() {
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return code;
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}
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public String getAcronym() {
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return acronym;
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}
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public void setCode(String code) {
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this.code = code;
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}
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public void setAcronym(String acronym) {
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this.acronym = acronym;
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}
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public String getAcronym() {
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return acronym;
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}
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public String getTitle() {
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return title;
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}
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public void setAcronym(String acronym) {
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this.acronym = acronym;
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}
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public void setTitle(String title) {
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this.title = title;
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}
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public String getTitle() {
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return title;
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}
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public String getStartdate() {
|
||||
return startdate;
|
||||
}
|
||||
|
||||
public void setTitle(String title) {
|
||||
this.title = title;
|
||||
}
|
||||
public void setStartdate(String startdate) {
|
||||
this.startdate = startdate;
|
||||
}
|
||||
|
||||
public String getStartdate() {
|
||||
return startdate;
|
||||
}
|
||||
public String getEnddate() {
|
||||
return enddate;
|
||||
}
|
||||
|
||||
public void setStartdate(String startdate) {
|
||||
this.startdate = startdate;
|
||||
}
|
||||
public void setEnddate(String enddate) {
|
||||
this.enddate = enddate;
|
||||
}
|
||||
|
||||
public String getEnddate() {
|
||||
return enddate;
|
||||
}
|
||||
public String getCallidentifier() {
|
||||
return callidentifier;
|
||||
}
|
||||
|
||||
public void setEnddate(String enddate) {
|
||||
this.enddate = enddate;
|
||||
}
|
||||
public void setCallidentifier(String callidentifier) {
|
||||
this.callidentifier = callidentifier;
|
||||
}
|
||||
|
||||
public String getCallidentifier() {
|
||||
return callidentifier;
|
||||
}
|
||||
public String getKeywords() {
|
||||
return keywords;
|
||||
}
|
||||
|
||||
public void setCallidentifier(String callidentifier) {
|
||||
this.callidentifier = callidentifier;
|
||||
}
|
||||
public void setKeywords(String keywords) {
|
||||
this.keywords = keywords;
|
||||
}
|
||||
|
||||
public String getKeywords() {
|
||||
return keywords;
|
||||
}
|
||||
public boolean isOpenaccessmandateforpublications() {
|
||||
return openaccessmandateforpublications;
|
||||
}
|
||||
|
||||
public void setKeywords(String keywords) {
|
||||
this.keywords = keywords;
|
||||
}
|
||||
public void setOpenaccessmandateforpublications(boolean openaccessmandateforpublications) {
|
||||
this.openaccessmandateforpublications = openaccessmandateforpublications;
|
||||
}
|
||||
|
||||
public boolean isOpenaccessmandateforpublications() {
|
||||
return openaccessmandateforpublications;
|
||||
}
|
||||
public boolean isOpenaccessmandatefordataset() {
|
||||
return openaccessmandatefordataset;
|
||||
}
|
||||
|
||||
public void setOpenaccessmandateforpublications(boolean openaccessmandateforpublications) {
|
||||
this.openaccessmandateforpublications = openaccessmandateforpublications;
|
||||
}
|
||||
public void setOpenaccessmandatefordataset(boolean openaccessmandatefordataset) {
|
||||
this.openaccessmandatefordataset = openaccessmandatefordataset;
|
||||
}
|
||||
|
||||
public boolean isOpenaccessmandatefordataset() {
|
||||
return openaccessmandatefordataset;
|
||||
}
|
||||
public List<String> getSubject() {
|
||||
return subject;
|
||||
}
|
||||
|
||||
public void setOpenaccessmandatefordataset(boolean openaccessmandatefordataset) {
|
||||
this.openaccessmandatefordataset = openaccessmandatefordataset;
|
||||
}
|
||||
public void setSubject(List<String> subject) {
|
||||
this.subject = subject;
|
||||
}
|
||||
|
||||
public List<String> getSubject() {
|
||||
return subject;
|
||||
}
|
||||
public List<Funder> getFunding() {
|
||||
return funding;
|
||||
}
|
||||
|
||||
public void setSubject(List<String> subject) {
|
||||
this.subject = subject;
|
||||
}
|
||||
public void setFunding(List<Funder> funding) {
|
||||
this.funding = funding;
|
||||
}
|
||||
|
||||
public List<Funder> getFunding() {
|
||||
return funding;
|
||||
}
|
||||
public String getSummary() {
|
||||
return summary;
|
||||
}
|
||||
|
||||
public void setFunding(List<Funder> funding) {
|
||||
this.funding = funding;
|
||||
}
|
||||
public void setSummary(String summary) {
|
||||
this.summary = summary;
|
||||
}
|
||||
|
||||
public String getSummary() {
|
||||
return summary;
|
||||
}
|
||||
public Granted getGranted() {
|
||||
return granted;
|
||||
}
|
||||
|
||||
public void setSummary(String summary) {
|
||||
this.summary = summary;
|
||||
}
|
||||
public void setGranted(Granted granted) {
|
||||
this.granted = granted;
|
||||
}
|
||||
|
||||
public Granted getGranted() {
|
||||
return granted;
|
||||
}
|
||||
public List<Programme> getH2020programme() {
|
||||
return h2020programme;
|
||||
}
|
||||
|
||||
public void setGranted(Granted granted) {
|
||||
this.granted = granted;
|
||||
}
|
||||
|
||||
public List<Programme> getH2020programme() {
|
||||
return h2020programme;
|
||||
}
|
||||
|
||||
public void setH2020programme(List<Programme> h2020programme) {
|
||||
this.h2020programme = h2020programme;
|
||||
}
|
||||
public void setH2020programme(List<Programme> h2020programme) {
|
||||
this.h2020programme = h2020programme;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
|||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
|
||||
import eu.dnetlib.dhp.eosc.model.Affiliation;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
|
|
@ -20,6 +19,7 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.eosc.model.Affiliation;
|
||||
import eu.dnetlib.dhp.eosc.model.OrganizationPid;
|
||||
import eu.dnetlib.dhp.eosc.model.Result;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
|
|
|||
|
|
@ -7,8 +7,6 @@ import java.io.Serializable;
|
|||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.eosc.model.Affiliation;
|
||||
import eu.dnetlib.dhp.eosc.model.Country;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
|
|
@ -22,6 +20,8 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.eosc.model.Affiliation;
|
||||
import eu.dnetlib.dhp.eosc.model.Country;
|
||||
import eu.dnetlib.dhp.eosc.model.OrganizationPid;
|
||||
import eu.dnetlib.dhp.eosc.model.Result;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
|
@ -70,7 +70,7 @@ public class ExtendEoscResultWithOrganizationStep2 implements Serializable {
|
|||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Utils.removeOutputDir(spark, workingPath + "publicationextendedaffiliation");
|
||||
addOrganizations(spark, inputPath, workingPath , outputPath);
|
||||
addOrganizations(spark, inputPath, workingPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
|
|
@ -156,85 +156,89 @@ public class ExtendEoscResultWithOrganizationStep2 implements Serializable {
|
|||
.json(workingPath + "publicationextendedaffiliation");
|
||||
|
||||
relations
|
||||
.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
|
||||
.map((MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Organization>) t2 -> mapOrganization(t2._2()),Encoders.bean(eu.dnetlib.dhp.eosc.model.Organization.class))
|
||||
.filter(Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath + "organization");
|
||||
.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
|
||||
.map(
|
||||
(MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Organization>) t2 -> mapOrganization(
|
||||
t2._2()),
|
||||
Encoders.bean(eu.dnetlib.dhp.eosc.model.Organization.class))
|
||||
.filter(Objects::nonNull)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "organization");
|
||||
|
||||
relations
|
||||
.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
|
||||
.map((MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Relation>) t2 -> eu.dnetlib.dhp.eosc.model.Relation.newInstance(t2._1().getSource(), t2._1().getTarget()), Encoders.bean(eu.dnetlib.dhp.eosc.model.Relation.class) )
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath + "resultOrganization");
|
||||
.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
|
||||
.map(
|
||||
(MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Relation>) t2 -> eu.dnetlib.dhp.eosc.model.Relation
|
||||
.newInstance(t2._1().getSource(), t2._1().getTarget()),
|
||||
Encoders.bean(eu.dnetlib.dhp.eosc.model.Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "resultOrganization");
|
||||
|
||||
}
|
||||
|
||||
private static eu.dnetlib.dhp.eosc.model.Organization mapOrganization(Organization org){
|
||||
private static eu.dnetlib.dhp.eosc.model.Organization mapOrganization(Organization org) {
|
||||
|
||||
if (Boolean.TRUE.equals(org.getDataInfo().getDeletedbyinference()))
|
||||
return null;
|
||||
if (!Optional.ofNullable(org.getLegalname()).isPresent()
|
||||
&& !Optional.ofNullable(org.getLegalshortname()).isPresent())
|
||||
return null;
|
||||
if (Boolean.TRUE.equals(org.getDataInfo().getDeletedbyinference()))
|
||||
return null;
|
||||
if (!Optional.ofNullable(org.getLegalname()).isPresent()
|
||||
&& !Optional.ofNullable(org.getLegalshortname()).isPresent())
|
||||
return null;
|
||||
|
||||
eu.dnetlib.dhp.eosc.model.Organization organization = new eu.dnetlib.dhp.eosc.model.Organization();
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getLegalshortname())
|
||||
.ifPresent(value -> organization.setLegalshortname(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(org.getLegalshortname())
|
||||
.ifPresent(value -> organization.setLegalshortname(value.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getLegalname())
|
||||
.ifPresent(value -> organization.setLegalname(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(org.getLegalname())
|
||||
.ifPresent(value -> organization.setLegalname(value.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getWebsiteurl())
|
||||
.ifPresent(value -> organization.setWebsiteurl(value.getValue()));
|
||||
Optional
|
||||
.ofNullable(org.getWebsiteurl())
|
||||
.ifPresent(value -> organization.setWebsiteurl(value.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getAlternativeNames())
|
||||
.ifPresent(
|
||||
value -> organization
|
||||
.setAlternativenames(
|
||||
value
|
||||
.stream()
|
||||
.map(v -> v.getValue())
|
||||
.collect(Collectors.toList())));
|
||||
Optional
|
||||
.ofNullable(org.getAlternativeNames())
|
||||
.ifPresent(
|
||||
value -> organization
|
||||
.setAlternativenames(
|
||||
value
|
||||
.stream()
|
||||
.map(v -> v.getValue())
|
||||
.collect(Collectors.toList())));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getCountry())
|
||||
.ifPresent(
|
||||
value -> {
|
||||
if (!value.getClassid().equals(UNKNOWN)) {
|
||||
organization
|
||||
.setCountry(
|
||||
Country.newInstance(value.getClassid(), value.getClassname()));
|
||||
}
|
||||
Optional
|
||||
.ofNullable(org.getCountry())
|
||||
.ifPresent(
|
||||
value -> {
|
||||
if (!value.getClassid().equals(UNKNOWN)) {
|
||||
organization
|
||||
.setCountry(
|
||||
Country.newInstance(value.getClassid(), value.getClassname()));
|
||||
}
|
||||
|
||||
});
|
||||
});
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getId())
|
||||
.ifPresent(value -> organization.setId(value));
|
||||
Optional
|
||||
.ofNullable(org.getId())
|
||||
.ifPresent(value -> organization.setId(value));
|
||||
|
||||
Optional
|
||||
.ofNullable(org.getPid())
|
||||
.ifPresent(
|
||||
value -> organization
|
||||
.setPid(
|
||||
value
|
||||
.stream()
|
||||
.map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue()))
|
||||
.collect(Collectors.toList())));
|
||||
|
||||
return organization;
|
||||
}
|
||||
Optional
|
||||
.ofNullable(org.getPid())
|
||||
.ifPresent(
|
||||
value -> organization
|
||||
.setPid(
|
||||
value
|
||||
.stream()
|
||||
.map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue()))
|
||||
.collect(Collectors.toList())));
|
||||
|
||||
return organization;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,8 +6,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
|||
import java.io.Serializable;
|
||||
import java.util.Optional;
|
||||
|
||||
import eu.dnetlib.dhp.eosc.model.Organization;
|
||||
import eu.dnetlib.dhp.eosc.model.Project;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
|
|
@ -21,19 +25,20 @@ import eu.dnetlib.dhp.eosc.model.Provenance;
|
|||
import eu.dnetlib.dhp.eosc.model.RelType;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import scala.Tuple2;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 12/01/23
|
||||
*/
|
||||
public class SparkDumpRelation implements Serializable {
|
||||
public class SparkDumpOrganizationProject implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkDumpRelation.class);
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkDumpOrganizationProject.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
SparkDumpRelation.class
|
||||
SparkDumpOrganizationProject.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
|
||||
|
||||
|
|
@ -66,49 +71,21 @@ public class SparkDumpRelation implements Serializable {
|
|||
}
|
||||
|
||||
private static void dumpRelation(SparkSession spark, String inputPath, String outputPath) {
|
||||
Dataset<Relation> relations = Utils.readPath(spark, inputPath, Relation.class);
|
||||
relations
|
||||
Dataset<Organization> organization = Utils.readPath(spark, outputPath + "organization", Organization.class);
|
||||
Dataset<Project> project = Utils.readPath(spark, outputPath + "project", Project.class);
|
||||
|
||||
.map((MapFunction<Relation, eu.dnetlib.dhp.eosc.model.Relation>) relation -> {
|
||||
eu.dnetlib.dhp.eosc.model.Relation relNew = new eu.dnetlib.dhp.eosc.model.Relation();
|
||||
relNew
|
||||
.setSource(
|
||||
Dataset<Relation> relation = Utils.readPath(spark, inputPath + "/relation", Relation.class)
|
||||
.filter((FilterFunction<Relation>) r-> !r.getDataInfo().getDeletedbyinference() && r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PARTICIPANT));
|
||||
|
||||
relation.getSource());
|
||||
Dataset<Relation> eoscOrgs = relation.joinWith(organization, relation.col("source").equalTo(organization.col("id")))
|
||||
.map((MapFunction<Tuple2<Relation, Organization>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class));
|
||||
|
||||
relNew
|
||||
.setTarget(
|
||||
|
||||
relation.getTarget());
|
||||
|
||||
relNew
|
||||
.setReltype(
|
||||
RelType
|
||||
.newInstance(
|
||||
relation.getRelClass(),
|
||||
relation.getSubRelType()));
|
||||
|
||||
Optional<DataInfo> odInfo = Optional.ofNullable(relation.getDataInfo());
|
||||
if (odInfo.isPresent()) {
|
||||
DataInfo dInfo = odInfo.get();
|
||||
if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() &&
|
||||
Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) {
|
||||
relNew
|
||||
.setProvenance(
|
||||
Provenance
|
||||
.newInstance(
|
||||
dInfo.getProvenanceaction().getClassname(),
|
||||
dInfo.getTrust()));
|
||||
}
|
||||
}
|
||||
|
||||
return relNew;
|
||||
|
||||
}, Encoders.bean(eu.dnetlib.dhp.eosc.model.Relation.class))
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Append)
|
||||
.json(outputPath);
|
||||
eoscOrgs.joinWith(project, eoscOrgs.col("target").equalTo(project.col("id")))
|
||||
.map((MapFunction<Tuple2<Relation, Project>, eu.dnetlib.dhp.eosc.model.Relation>) t2-> eu.dnetlib.dhp.eosc.model.Relation.newInstance(t2._1().getSource(), t2._1().getTarget()), Encoders.bean(eu.dnetlib.dhp.eosc.model.Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath + "organizationProject");
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -10,9 +10,6 @@ import java.util.List;
|
|||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.eosc.model.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FlatMapFunction;
|
||||
|
|
@ -31,7 +28,10 @@ import org.slf4j.LoggerFactory;
|
|||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.eosc.model.*;
|
||||
import eu.dnetlib.dhp.oa.graph.dump.Constants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||
import scala.Array;
|
||||
import scala.Tuple2;
|
||||
|
||||
|
|
@ -110,68 +110,86 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
|
||||
Dataset<Project> project = Utils.readPath(spark, inputPath + "/project", Project.class);
|
||||
|
||||
Dataset<String> projectIds = result.joinWith(resultProject, result.col("id").equalTo(resultProject.col("resultId")))
|
||||
.flatMap((FlatMapFunction<Tuple2<Result, ResultProject>, String>) t2 -> t2._2().getProjectsList()
|
||||
.stream().map(p -> p.getId()).collect(Collectors.toList()).iterator(), Encoders.STRING())
|
||||
.distinct();
|
||||
Dataset<String> projectIds = result
|
||||
.joinWith(resultProject, result.col("id").equalTo(resultProject.col("resultId")))
|
||||
.flatMap(
|
||||
(FlatMapFunction<Tuple2<Result, ResultProject>, String>) t2 -> t2
|
||||
._2()
|
||||
.getProjectsList()
|
||||
.stream()
|
||||
.map(p -> p.getId())
|
||||
.collect(Collectors.toList())
|
||||
.iterator(),
|
||||
Encoders.STRING())
|
||||
.distinct();
|
||||
|
||||
projectIds.joinWith(project, projectIds.col("value").equalTo(project.col("id")))
|
||||
.map((MapFunction<Tuple2<String, Project>, eu.dnetlib.dhp.eosc.model.Project>)t2->mapProject(t2._2()), Encoders.bean(eu.dnetlib.dhp.eosc.model.Project.class) )
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath + "project");
|
||||
projectIds
|
||||
.joinWith(project, projectIds.col("value").equalTo(project.col("id")))
|
||||
.map(
|
||||
(MapFunction<Tuple2<String, Project>, eu.dnetlib.dhp.eosc.model.Project>) t2 -> mapProject(t2._2()),
|
||||
Encoders.bean(eu.dnetlib.dhp.eosc.model.Project.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "project");
|
||||
|
||||
resultProject.flatMap((FlatMapFunction<ResultProject, Relation>) rp ->
|
||||
rp.getProjectsList().stream().map(p -> Relation.newInstance(rp.getResultId(), p.getId()))
|
||||
.collect(Collectors.toList()).iterator(), Encoders.bean(Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(outputPath + "resultProject");
|
||||
resultProject
|
||||
.flatMap(
|
||||
(FlatMapFunction<ResultProject, Relation>) rp -> rp
|
||||
.getProjectsList()
|
||||
.stream()
|
||||
.map(p -> Relation.newInstance(rp.getResultId(), p.getId()))
|
||||
.collect(Collectors.toList())
|
||||
.iterator(),
|
||||
Encoders.bean(Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath + "resultProject");
|
||||
}
|
||||
|
||||
private static eu.dnetlib.dhp.eosc.model.Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) throws DocumentException {
|
||||
private static eu.dnetlib.dhp.eosc.model.Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p)
|
||||
throws DocumentException {
|
||||
if (Boolean.TRUE.equals(p.getDataInfo().getDeletedbyinference()))
|
||||
return null;
|
||||
|
||||
eu.dnetlib.dhp.eosc.model.Project project = new eu.dnetlib.dhp.eosc.model.Project();
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getId())
|
||||
.ifPresent(id -> project.setId(id));
|
||||
.ofNullable(p.getId())
|
||||
.ifPresent(id -> project.setId(id));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getWebsiteurl())
|
||||
.ifPresent(w -> project.setWebsiteurl(w.getValue()));
|
||||
.ofNullable(p.getWebsiteurl())
|
||||
.ifPresent(w -> project.setWebsiteurl(w.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getCode())
|
||||
.ifPresent(code -> project.setCode(code.getValue()));
|
||||
.ofNullable(p.getCode())
|
||||
.ifPresent(code -> project.setCode(code.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getAcronym())
|
||||
.ifPresent(acronynim -> project.setAcronym(acronynim.getValue()));
|
||||
.ofNullable(p.getAcronym())
|
||||
.ifPresent(acronynim -> project.setAcronym(acronynim.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getTitle())
|
||||
.ifPresent(title -> project.setTitle(title.getValue()));
|
||||
.ofNullable(p.getTitle())
|
||||
.ifPresent(title -> project.setTitle(title.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getStartdate())
|
||||
.ifPresent(sdate -> project.setStartdate(sdate.getValue()));
|
||||
.ofNullable(p.getStartdate())
|
||||
.ifPresent(sdate -> project.setStartdate(sdate.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getEnddate())
|
||||
.ifPresent(edate -> project.setEnddate(edate.getValue()));
|
||||
.ofNullable(p.getEnddate())
|
||||
.ifPresent(edate -> project.setEnddate(edate.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getCallidentifier())
|
||||
.ifPresent(cide -> project.setCallidentifier(cide.getValue()));
|
||||
.ofNullable(p.getCallidentifier())
|
||||
.ifPresent(cide -> project.setCallidentifier(cide.getValue()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getKeywords())
|
||||
.ifPresent(key -> project.setKeywords(key.getValue()));
|
||||
.ofNullable(p.getKeywords())
|
||||
.ifPresent(key -> project.setKeywords(key.getValue()));
|
||||
|
||||
Optional<Field<String>> omandate = Optional.ofNullable(p.getOamandatepublications());
|
||||
Optional<Field<String>> oecsc39 = Optional.ofNullable(p.getEcsc39());
|
||||
|
|
@ -191,19 +209,19 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
project.setOpenaccessmandatefordataset(false);
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getEcarticle29_3())
|
||||
.ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true")));
|
||||
.ofNullable(p.getEcarticle29_3())
|
||||
.ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true")));
|
||||
|
||||
project
|
||||
.setSubject(
|
||||
Optional
|
||||
.ofNullable(p.getSubjects())
|
||||
.map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
.setSubject(
|
||||
Optional
|
||||
.ofNullable(p.getSubjects())
|
||||
.map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
|
||||
Optional
|
||||
.ofNullable(p.getSummary())
|
||||
.ifPresent(summary -> project.setSummary(summary.getValue()));
|
||||
.ofNullable(p.getSummary())
|
||||
.ifPresent(summary -> project.setSummary(summary.getValue()));
|
||||
|
||||
Optional<Float> ofundedamount = Optional.ofNullable(p.getFundedamount());
|
||||
Optional<Field<String>> ocurrency = Optional.ofNullable(p.getCurrency());
|
||||
|
|
@ -213,8 +231,8 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
if (ofundedamount.isPresent()) {
|
||||
if (ototalcost.isPresent()) {
|
||||
project
|
||||
.setGranted(
|
||||
Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get()));
|
||||
.setGranted(
|
||||
Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get()));
|
||||
} else {
|
||||
project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get()));
|
||||
}
|
||||
|
|
@ -222,21 +240,21 @@ public class SparkUpdateProjectInfo implements Serializable {
|
|||
}
|
||||
|
||||
project
|
||||
.setH2020programme(
|
||||
Optional
|
||||
.ofNullable(p.getH2020classification())
|
||||
.map(
|
||||
classification -> classification
|
||||
.stream()
|
||||
.map(
|
||||
c -> Programme
|
||||
.newInstance(
|
||||
c.getH2020Programme().getCode(), c.getH2020Programme().getDescription()))
|
||||
.collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
.setH2020programme(
|
||||
Optional
|
||||
.ofNullable(p.getH2020classification())
|
||||
.map(
|
||||
classification -> classification
|
||||
.stream()
|
||||
.map(
|
||||
c -> Programme
|
||||
.newInstance(
|
||||
c.getH2020Programme().getCode(), c.getH2020Programme().getDescription()))
|
||||
.collect(Collectors.toList()))
|
||||
.orElse(new ArrayList<>()));
|
||||
|
||||
Optional<List<Field<String>>> ofundTree = Optional
|
||||
.ofNullable(p.getFundingtree());
|
||||
.ofNullable(p.getFundingtree());
|
||||
List<Funder> funList = new ArrayList<>();
|
||||
if (ofundTree.isPresent()) {
|
||||
for (Field<String> fundingtree : ofundTree.get()) {
|
||||
|
|
|
|||
|
|
@ -0,0 +1,26 @@
|
|||
|
||||
[
|
||||
|
||||
|
||||
{
|
||||
"paramName":"s",
|
||||
"paramLongName":"sourcePath",
|
||||
"paramDescription": "the name node",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "out",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the path used to store temporary output files",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "the path used to store temporary output files",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
||||
|
||||
|
||||
|
||||
|
|
@ -24,8 +24,8 @@ import org.slf4j.LoggerFactory;
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.eosc.model.Indicator;
|
||||
import eu.dnetlib.dhp.eosc.model.Affiliation;
|
||||
import eu.dnetlib.dhp.eosc.model.Indicator;
|
||||
import eu.dnetlib.dhp.eosc.model.Result;
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||
import scala.Tuple2;
|
||||
|
|
|
|||
Loading…
Reference in New Issue