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This commit is contained in:
Michele Artini 2022-06-15 14:39:36 +02:00
parent a17a7dc3a0
commit 0d722526c0
12 changed files with 390 additions and 28 deletions
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23
apps/dnet-is-application/pom.xml
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@ -24,29 +24,10 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-json</artifactId>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<!-- JAXB API, java.xml.bind module -->
<dependency>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
</dependency>
<!-- JAXB Runtime, com.sun.xml.bind module -->
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
</dependency>
<!-- hot swapping, disable cache for template, enable live reload -->

4
apps/dnet-is-application/src/main/java/eu/dnetlib/is/MainApplication.java
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@ -1,4 +1,4 @@
package eu.dnetlib.organizations;
package eu.dnetlib.is;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
@ -28,7 +28,7 @@ public class MainApplication extends AbstractDnetApp {
protected void configSwagger(final Docket docket) {
docket.select()
.apis(RequestHandlerSelectors.any())
.paths(p -> p.contains("/is/"))
.paths(p -> p.contains("/api/"))
.build()
.apiInfo(new ApiInfoBuilder()
.title("D-Net Information Service APIs")

16
apps/dnet-is-application/src/main/java/eu/dnetlib/is/SwaggerController.java Normal file
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@ -0,0 +1,16 @@
package eu.dnetlib.is;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.GetMapping;
@Controller
public class SwaggerController {
@GetMapping({
"/doc", "/swagger"
})
public String apiDoc() {
return "redirect:swagger-ui/";
}
}

107
apps/dnet-is-application/src/main/java/eu/dnetlib/is/vocabulary/VocabularyRestController.java Normal file
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@ -0,0 +1,107 @@
package eu.dnetlib.is.vocabulary;
import java.io.IOException;
import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.stream.Collectors;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.DeleteMapping;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController;
import eu.dnetlib.common.controller.AbstractDnetController;
import eu.dnetlib.is.vocabulary.model.Vocabulary;
import eu.dnetlib.is.vocabulary.model.VocabularyTerm;
import eu.dnetlib.is.vocabulary.repository.VocabularyRepository;
import eu.dnetlib.is.vocabulary.repository.VocabularyTermRepository;
import io.swagger.v3.oas.annotations.parameters.RequestBody;
@RestController
@RequestMapping("/api/vocs")
public class VocabularyRestController extends AbstractDnetController {
@Autowired
private VocabularyRepository vocabularyRepository;
@Autowired
private VocabularyTermRepository vocabularyTermRepository;
@GetMapping("/")
public List<Vocabulary> listVocs() {
return vocabularyRepository.findAll()
.stream()
.sorted((v1, v2) -> StringUtils.compare(v1.getName(), v2.getName()))
.collect(Collectors.toList());
}
@GetMapping("/{vocabulary}")
public Iterable<VocabularyTerm> listVocs(@PathVariable final String vocabulary) {
return vocabularyTermRepository.findByVocabularyOrderByCode(vocabulary);
}
@DeleteMapping("/{vocabulary}")
public List<Vocabulary> deleteVocs(@PathVariable final String vocabulary) {
vocabularyRepository.deleteById(vocabulary);
return listVocs();
}
@PostMapping("/")
public List<Vocabulary> saveVoc(@RequestBody final Vocabulary voc) {
vocabularyRepository.save(voc);
return listVocs();
}
@PostMapping(value = "/load", consumes = "text/plain")
public Vocabulary loadFromOldProfile(final HttpServletRequest request) throws DocumentException, IOException {
final String xml = IOUtils.toString(request.getInputStream(), StandardCharsets.UTF_8);
System.out.println(xml);
final SAXReader reader = new SAXReader();
final Document doc = reader.read(new StringReader(xml));
final Vocabulary voc = new Vocabulary();
final String vocId = doc.valueOf("//VOCABULARY_NAME/@code");
final String vocName = doc.valueOf("//VOCABULARY_NAME");
final String vocDesc = doc.valueOf("//VOCABULARY_DESCRIPTION");
voc.setId(vocId);
voc.setName(vocName);
voc.setDescription(vocDesc);
vocabularyRepository.save(voc);
for (final Node n : doc.selectNodes("//TERM")) {
final VocabularyTerm term = new VocabularyTerm();
term.setVocabulary(vocId);
term.setCode(n.valueOf("@code"));
term.setEnglishName(n.valueOf("@english_name"));
term.setNativeName(n.valueOf("@native_name"));
term.setSynonyms(n.selectNodes(".//SYNONYM")
.stream()
.map(ns -> ns.valueOf("@term"))
.sorted()
.distinct()
.toArray(String[]::new));
vocabularyTermRepository.save(term);
}
return voc;
}
}

29
apps/dnet-is-application/src/main/resources/application.properties Normal file
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@ -0,0 +1,29 @@
server.port=8280
spring.profiles.active=dev
maven.pom.path = /META-INF/maven/eu.dnetlib.dhp/dnet-is-application/effective-pom.xml
spring.main.banner-mode = off
logging.level.root = INFO
#logging.level.org.springframework = DEBUG
management.endpoints.web.exposure.include = prometheus,health
management.endpoints.web.base-path = /
management.endpoints.web.path-mapping.prometheus = metrics
management.endpoints.web.path-mapping.health = health
spring.datasource.url=jdbc:postgresql://localhost:5432/new_is
spring.datasource.username=
spring.datasource.password=
# Hibernate ddl auto (create, create-drop, validate, update)
spring.jpa.hibernate.ddl-auto = validate
spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.PostgreSQLDialect
spring.jpa.properties.hibernate.hbm2dll.extra_physical_table_types = MATERIALIZED VIEW
spring.jpa.properties.hibernate.jdbc.lob.non_contextual_creation=true
spring.jpa.open-in-view=true
spring.jpa.properties.hibernate.show_sql=false
spring.jpa.properties.hibernate.use_sql_comments=false
spring.jpa.properties.hibernate.format_sql=false

19
libs/dnet-is-common/pom.xml
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@ -12,12 +12,21 @@
<packaging>jar</packaging>
<dependencies>
<!-- Gson -->
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<scope>provided</scope>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-json</artifactId>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<dependency>
<groupId>com.vladmihalcea</groupId>
<artifactId>hibernate-types-52</artifactId>
</dependency>
<!-- Tests -->

50
libs/dnet-is-common/src/main/java/eu/dnetlib/is/vocabulary/model/Vocabulary.java Normal file
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@ -0,0 +1,50 @@
package eu.dnetlib.is.vocabulary.model;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
@Entity
@Table(name = "vocabularies")
public class Vocabulary implements Serializable {
private static final long serialVersionUID = 3769069980972518780L;
@Id
@Column(name = "id")
private String id;
@Column(name = "name")
private String name;
@Column(name = "description")
private String description;
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(final String name) {
this.name = name;
}
public String getDescription() {
return description;
}
public void setDescription(final String description) {
this.description = description;
}
}

85
libs/dnet-is-common/src/main/java/eu/dnetlib/is/vocabulary/model/VocabularyTerm.java Normal file
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@ -0,0 +1,85 @@
package eu.dnetlib.is.vocabulary.model;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.IdClass;
import javax.persistence.Table;
import org.hibernate.annotations.Type;
import org.hibernate.annotations.TypeDef;
import org.hibernate.annotations.TypeDefs;
import com.vladmihalcea.hibernate.type.array.StringArrayType;
@Entity
@Table(name = "vocabulary_terms")
@IdClass(VocabularyTermPK.class)
@TypeDefs({
@TypeDef(name = "string-array", typeClass = StringArrayType.class)
})
public class VocabularyTerm implements Serializable {
private static final long serialVersionUID = -3995855638130512114L;
@Id
@Column(name = "code")
private String code;
@Id
@Column(name = "vocabulary")
private String vocabulary;
@Column(name = "english_name")
private String englishName;
@Column(name = "native_name")
private String nativeName;
@Type(type = "string-array")
@Column(name = "synonyms", columnDefinition = "text[]")
private String[] synonyms;
public String getCode() {
return code;
}
public void setCode(final String code) {
this.code = code;
}
public String getVocabulary() {
return vocabulary;
}
public void setVocabulary(final String vocabulary) {
this.vocabulary = vocabulary;
}
public String getEnglishName() {
return englishName;
}
public void setEnglishName(final String englishName) {
this.englishName = englishName;
}
public String getNativeName() {
return nativeName;
}
public void setNativeName(final String nativeName) {
this.nativeName = nativeName;
}
public String[] getSynonyms() {
return synonyms;
}
public void setSynonyms(final String[] synonyms) {
this.synonyms = synonyms;
}
}

48
libs/dnet-is-common/src/main/java/eu/dnetlib/is/vocabulary/model/VocabularyTermPK.java Normal file
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@ -0,0 +1,48 @@
package eu.dnetlib.is.vocabulary.model;
import java.io.Serializable;
import java.util.Objects;
public class VocabularyTermPK implements Serializable {
private static final long serialVersionUID = -7726004241883017275L;
private String code;
private String vocabulary;
public String getCode() {
return code;
}
public void setCode(final String code) {
this.code = code;
}
public String getVocabulary() {
return vocabulary;
}
public void setVocabulary(final String vocabulary) {
this.vocabulary = vocabulary;
}
@Override
public int hashCode() {
return Objects.hash(code, vocabulary);
}
@Override
public boolean equals(final Object obj) {
if (this == obj) { return true; }
if (!(obj instanceof VocabularyTermPK)) { return false; }
final VocabularyTermPK other = (VocabularyTermPK) obj;
return Objects.equals(code, other.code) && Objects.equals(vocabulary, other.vocabulary);
}
@Override
public String toString() {
return String.format("VocabularyTermPK [code=%s, vocabulary=%s]", code, vocabulary);
}
}

9
libs/dnet-is-common/src/main/java/eu/dnetlib/is/vocabulary/repository/VocabularyRepository.java Normal file
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@ -0,0 +1,9 @@
package eu.dnetlib.is.vocabulary.repository;
import org.springframework.data.jpa.repository.JpaRepository;
import eu.dnetlib.is.vocabulary.model.Vocabulary;
public interface VocabularyRepository extends JpaRepository<Vocabulary, String> {
}

12
libs/dnet-is-common/src/main/java/eu/dnetlib/is/vocabulary/repository/VocabularyTermRepository.java Normal file
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@ -0,0 +1,12 @@
package eu.dnetlib.is.vocabulary.repository;
import org.springframework.data.jpa.repository.JpaRepository;
import eu.dnetlib.is.vocabulary.model.VocabularyTerm;
import eu.dnetlib.is.vocabulary.model.VocabularyTermPK;
public interface VocabularyTermRepository extends JpaRepository<VocabularyTerm, VocabularyTermPK> {
Iterable<VocabularyTerm> findByVocabularyOrderByCode(String vocabulary);
}

16
libs/dnet-is-common/src/main/resources/sql/schema.sql Normal file
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@ -0,0 +1,16 @@
CREATE TABLE vocabularies (
id text PRIMARY KEY,
name text NOT NULL,
description text
);
CREATE TABLE vocabulary_terms (
code text NOT NULL,
vocabulary text NOT NULL REFERENCES vocabularies(id),
english_name text NOT NULL,
native_name text NOT NULL,
synonyms text[],
PRIMARY KEY (code, vocabulary)
);
CREATE INDEX ON vocabulary_terms (vocabulary);