miriam.baglioni
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dnet-hadoop
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Merge branch 'master' of https://github.com/dnet-team/dnet-hadoop

This commit is contained in:
Sandro La Bruzzo 2019-03-20 09:49:53 +01:00
parent 6156562893 46bc3e1f53
commit 859957d0fd
19 changed files with 785 additions and 1 deletions
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13
.gitignore vendored
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.idea
*.iml
*~
.classpath
/*/.classpath
/*/*/.classpath
.metadata
/*/.metadata
/*/*/.metadata
.project
.log
.settings
/*/*/target
/*/target
/target
/*/*/build
/*/build
/build
spark-warehouse
spark-warehouse

1
README.md
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# dnet-hadoop
...test

92
dhp-applications/dhp-mdstore-manager-app/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib</groupId>
<artifactId>dhp-mdstore-manager-app</artifactId>
<version>1.1.0-SNAPSHOT</version>
<!-- Inherit defaults from Spring Boot -->
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.1.3.RELEASE</version>
<relativePath></relativePath>
</parent>
<!-- <repositories> <repository> <id>dnet-deps</id> <name>dnet-dependencies</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet-deps</url>
<layout>default</layout> </repository> <repository> <id>dnet45-releases</id>
<name>D-Net 45 Releases</name> <url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases</url>
<layout>default</layout> <snapshots> <enabled>true</enabled> </snapshots>
</repository> <repository> <id>dnet45-snapshots</id> <name>D-Net 45 Snapshots</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots</url>
<layout>default</layout> <snapshots> <enabled>true</enabled> </snapshots>
</repository> </repositories> -->
<!-- Add typical dependencies for a web application -->
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</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>
<dependency>
<groupId>com.vladmihalcea</groupId>
<artifactId>hibernate-types-52</artifactId>
<version>2.3.5</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.6</version>
</dependency>
<!-- Swagger -->
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger2</artifactId>
<version>2.9.2</version>
</dependency>
<dependency>
<groupId>io.springfox</groupId>
<artifactId>springfox-swagger-ui</artifactId>
<version>2.9.2</version>
</dependency>
<!-- JUnit -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<executable>true</executable>
</configuration>
</plugin>
</plugins>
</build>
</project>

30
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/MDStoreManagerException.java Normal file
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package eu.dnetlib.data.mdstore.manager;
public class MDStoreManagerException extends Exception{
/**
*
*/
private static final long serialVersionUID = -7503316126409002675L;
public MDStoreManagerException() {
super();
}
public MDStoreManagerException(String message, Throwable cause, boolean enableSuppression,
boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public MDStoreManagerException(String message, Throwable cause) {
super(message, cause);
}
public MDStoreManagerException(String message) {
super(message);
}
public MDStoreManagerException(Throwable cause) {
super(cause);
}
}

49
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/MainApplication.java Normal file
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package eu.dnetlib.data.mdstore.manager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.cache.annotation.EnableCaching;
import org.springframework.context.annotation.Bean;
import springfox.documentation.builders.ApiInfoBuilder;
import springfox.documentation.builders.RequestHandlerSelectors;
import springfox.documentation.service.ApiInfo;
import springfox.documentation.spi.DocumentationType;
import springfox.documentation.spring.web.plugins.Docket;
import springfox.documentation.swagger2.annotations.EnableSwagger2;
@SpringBootApplication
@EnableSwagger2
@EnableCaching
public class MainApplication {
private static final Logger log = LoggerFactory.getLogger(MainApplication.class);
public static void main(final String[] args) {
SpringApplication.run(MainApplication.class, args);
}
@Bean
public static Docket newSwaggerDocket() {
log.info("Initializing SWAGGER...");
return new Docket(DocumentationType.SWAGGER_2)
.select()
.apis(RequestHandlerSelectors.any())
.paths(p -> p.startsWith("/api/"))
.build().apiInfo(new ApiInfoBuilder()
.title("MDStore Manager APIs")
.description("APIs documentation")
.version("1.1")
.contact(ApiInfo.DEFAULT_CONTACT)
.license("Apache 2.0")
.licenseUrl("http://www.apache.org/licenses/LICENSE-2.0")
.build());
}
}

14
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/SwaggerController.java Normal file
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package eu.dnetlib.data.mdstore.manager;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
@Controller
public class SwaggerController {
@RequestMapping(value = { "/", "/apidoc", "/api-doc", "/doc", "/swagger" }, method = RequestMethod.GET)
public String apiDoc() {
return "redirect:swagger-ui.html";
}
}

79
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/controller/MDStoreController.java Normal file
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package eu.dnetlib.data.mdstore.manager.controller;
import java.util.List;
import java.util.stream.Collectors;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import eu.dnetlib.data.mdstore.manager.MDStoreManagerException;
import eu.dnetlib.data.mdstore.manager.model.MDStore;
import eu.dnetlib.data.mdstore.manager.model.MDStoreWithInfo;
import eu.dnetlib.data.mdstore.manager.model.Transaction;
import eu.dnetlib.data.mdstore.manager.repository.MDStoreRepository;
import eu.dnetlib.data.mdstore.manager.repository.MDStoreWithInfoRepository;
import eu.dnetlib.data.mdstore.manager.repository.TransactionRepository;
@RestController
@RequestMapping("/api/mdstores")
public class MDStoreController {
@Autowired
private MDStoreRepository mdstoreRepository;
@Autowired
private TransactionRepository transactionRepository;
@Autowired
private MDStoreWithInfoRepository mdstoreWithInfoRepository;
@RequestMapping(value = "/", method = RequestMethod.GET)
public final Iterable<MDStoreWithInfo> find() {
return mdstoreWithInfoRepository.findAll();
}
@RequestMapping(value = "/identifiers", method = RequestMethod.GET)
public final List<String> findIdentifiers() {
return mdstoreRepository.findAll().stream().map(MDStore::getId).collect(Collectors.toList());
}
@RequestMapping(value = "/byId/{id}", method = RequestMethod.GET)
public final MDStoreWithInfo get(@PathVariable final String id) {
return mdstoreWithInfoRepository.findById(id).orElse(null);
}
@RequestMapping(value = "/count", method = RequestMethod.GET)
public final long count() {
return mdstoreRepository.count();
}
@RequestMapping(value = "/new/{format}/{layout}/{interpretation}", method = RequestMethod.PUT)
public MDStoreWithInfo createMDStore(
@PathVariable String format,
@PathVariable String layout,
@PathVariable String interpretation,
@RequestParam(required=false) String dsId,
@RequestParam(required=false) String apiId) throws MDStoreManagerException {
final MDStore md = MDStore.newInstance(dsId, apiId, format, layout, interpretation);
mdstoreRepository.save(md);
final Transaction t = Transaction.newInstance(md.getId());
t.setCurrent(true);
transactionRepository.save(t);
return mdstoreWithInfoRepository.findById(md.getId()).orElseThrow(() -> new MDStoreManagerException("MDStore not found"));
}
@RequestMapping(value = "/{id}", method = RequestMethod.DELETE)
public void delete(@PathVariable final String id) throws MDStoreManagerException {
if (transactionRepository.countByMdstoreAndActive(id, true) == 0) {
transactionRepository.deleteByMdstore(id);
mdstoreRepository.deleteById(id);
} else {
throw new MDStoreManagerException("Active transactions found on mdstore : " + id);
}
}
}

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dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/controller/TransactionController.java Normal file
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package eu.dnetlib.data.mdstore.manager.controller;
import java.util.List;
import java.util.stream.Collectors;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import eu.dnetlib.data.mdstore.manager.model.Transaction;
import eu.dnetlib.data.mdstore.manager.repository.TransactionRepository;
@RestController
@RequestMapping("/api/transactions")
public class TransactionController {
@Autowired
private TransactionRepository repo;
@RequestMapping(value = "/", method = RequestMethod.GET)
public final List<Transaction> find() {
return repo.findAll();
}
@RequestMapping(value = "/identifiers", method = RequestMethod.GET)
public final List<String> findIdentifiers() {
return repo.findAll().stream().map(Transaction::getId).collect(Collectors.toList());
}
@RequestMapping(value = "/{id}", method = RequestMethod.GET)
public final Transaction get(@PathVariable final String id) {
return repo.findById(id).orElse(null);
}
@RequestMapping(value = "/count", method = RequestMethod.GET)
public final long count() {
return repo.count();
}
}

108
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/model/MDStore.java Normal file
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package eu.dnetlib.data.mdstore.manager.model;
import java.io.Serializable;
import java.util.UUID;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
@Entity
@Table(name = "mdstores")
public class MDStore implements Serializable {
/**
*
*/
private static final long serialVersionUID = 3160530489149700055L;
@Id
@Column(name = "id")
private String id;
@Column(name = "format")
private String format;
@Column(name = "layout")
private String layout;
@Column(name = "interpretation")
private String interpretation;
@Column(name = "datasource_id")
private String datasourceId;
@Column(name = "api_id")
private String apiId ;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getFormat() {
return format;
}
public void setFormat(String format) {
this.format = format;
}
public String getLayout() {
return layout;
}
public void setLayout(String layout) {
this.layout = layout;
}
public String getInterpretation() {
return interpretation;
}
public void setInterpretation(String interpretation) {
this.interpretation = interpretation;
}
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public String getApiId() {
return apiId;
}
public void setApiId(String apiId) {
this.apiId = apiId;
}
public static MDStore newInstance(final String format, final String layout, final String interpretation) {
return newInstance(null, null, format, layout, interpretation);
}
public static MDStore newInstance(final String dsId, final String apiId, final String format, final String layout, final String interpretation) {
final MDStore md = new MDStore();
md.setId("md-" + UUID.randomUUID());
md.setDatasourceId(dsId);
md.setApiId(apiId);
md.setFormat(format);
md.setLayout(layout);
md.setInterpretation(interpretation);
return md;
}
}

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dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/model/MDStoreWithInfo.java Normal file
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package eu.dnetlib.data.mdstore.manager.model;
import java.io.Serializable;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
@Entity
@Table(name = "mdstores_with_info")
public class MDStoreWithInfo implements Serializable {
/**
*
*/
private static final long serialVersionUID = -8445784770687571492L;
@Id
@Column(name = "id")
private String id;
@Column(name = "format")
private String format;
@Column(name = "layout")
private String layout;
@Column(name = "interpretation")
private String interpretation;
@Column(name = "datasource_id")
private String datasourceId;
@Column(name = "api_id")
private String apiId ;
@Column(name = "current_version")
private String currentVersion;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
@Column(name = "size")
private int size;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getFormat() {
return format;
}
public void setFormat(String format) {
this.format = format;
}
public String getLayout() {
return layout;
}
public void setLayout(String layout) {
this.layout = layout;
}
public String getInterpretation() {
return interpretation;
}
public void setInterpretation(String interpretation) {
this.interpretation = interpretation;
}
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public String getApiId() {
return apiId;
}
public void setApiId(String apiId) {
this.apiId = apiId;
}
public String getCurrentVersion() {
return currentVersion;
}
public void setCurrentVersion(String currentVersion) {
this.currentVersion = currentVersion;
}
public Date getLastUpdate() {
return lastUpdate;
}
public void setLastUpdate(Date lastUpdate) {
this.lastUpdate = lastUpdate;
}
public int getSize() {
return size;
}
public void setSize(int size) {
this.size = size;
}
}

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dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/model/Transaction.java Normal file
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package eu.dnetlib.data.mdstore.manager.model;
import java.io.Serializable;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.Temporal;
import javax.persistence.TemporalType;
@Entity
@Table(name = "transactions")
public class Transaction implements Serializable{
/**
*
*/
private static final long serialVersionUID = -4763494442274298339L;
@Id
@Column(name = "id")
private String id;
@Column(name = "mdstore")
private String mdstore;
@Column(name = "current")
private boolean current;
@Column(name = "active")
private boolean active;
@Column(name = "readcount")
private int readCount;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
@Column(name = "size")
private int size;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getMdstore() {
return mdstore;
}
public void setMdstore(String mdstore) {
this.mdstore = mdstore;
}
public boolean isCurrent() {
return current;
}
public void setCurrent(boolean current) {
this.current = current;
}
public boolean isActive() {
return active;
}
public void setActive(boolean active) {
this.active = active;
}
public int getReadCount() {
return readCount;
}
public void setReadCount(int readCount) {
this.readCount = readCount;
}
public Date getLastUpdate() {
return lastUpdate;
}
public void setLastUpdate(Date lastUpdate) {
this.lastUpdate = lastUpdate;
}
public int getSize() {
return size;
}
public void setSize(int size) {
this.size = size;
}
public static Transaction newInstance(final String mdId) {
final Transaction t = new Transaction();
t.setId(mdId + "-" + new Date().getTime());
t.setMdstore(mdId);
t.setLastUpdate(null);
t.setActive(false);
t.setCurrent(false);
t.setReadCount(0);
t.setSize(0);
return t;
}
}

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dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/repository/MDStoreRepository.java Normal file
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package eu.dnetlib.data.mdstore.manager.repository;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository;
import eu.dnetlib.data.mdstore.manager.model.MDStore;
@Repository
public interface MDStoreRepository extends JpaRepository<MDStore, String> {
}

10
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/repository/MDStoreWithInfoRepository.java Normal file
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package eu.dnetlib.data.mdstore.manager.repository;
import org.springframework.stereotype.Repository;
import eu.dnetlib.data.mdstore.manager.model.MDStoreWithInfo;
@Repository
public interface MDStoreWithInfoRepository extends ReadOnlyRepository<MDStoreWithInfo, String> {
}

18
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/repository/ReadOnlyRepository.java Normal file
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package eu.dnetlib.data.mdstore.manager.repository;
import java.util.Optional;
import org.springframework.data.repository.NoRepositoryBean;
import org.springframework.data.repository.Repository;
@NoRepositoryBean
public interface ReadOnlyRepository<T, ID> extends Repository<T, ID> {
Optional<T> findById(ID id);
boolean existsById(ID id);
Iterable<T> findAll();
long count();
}

14
dhp-applications/dhp-mdstore-manager-app/src/main/java/eu/dnetlib/data/mdstore/manager/repository/TransactionRepository.java Normal file
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package eu.dnetlib.data.mdstore.manager.repository;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.stereotype.Repository;
import eu.dnetlib.data.mdstore.manager.model.Transaction;
@Repository
public interface TransactionRepository extends JpaRepository<Transaction, String> {
void deleteByMdstore(String id);
int countByMdstoreAndActive(String id, boolean active);
}

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dhp-applications/dhp-mdstore-manager-app/src/main/resources/application.properties Normal file
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spring.main.banner-mode = console
logging.level.root = INFO
spring.datasource.url=jdbc:postgresql://localhost:5432/mdstoremanager
spring.datasource.username=
spring.datasource.password=
spring.jpa.properties.hibernate.dialect = org.hibernate.dialect.PostgreSQLDialect
# Hibernate ddl auto (create, create-drop, validate, update)
spring.jpa.hibernate.ddl-auto = validate
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

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dhp-applications/dhp-mdstore-manager-app/src/main/resources/schema.sql Normal file
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DROP VIEW IF EXISTS mdstores_with_info;
DROP TABLE IF EXISTS transactions;
DROP TABLE IF EXISTS mdstores;
CREATE TABLE mdstores (
id text PRIMARY KEY,
format text,
layout text,
interpretation text,
datasource_id text,
api_id text
);
CREATE TABLE transactions (
id text PRIMARY KEY,
mdstore text REFERENCES mdstores(id),
current boolean,
active boolean,
readcount int,
lastupdate timestamp,
size int
);
CREATE VIEW mdstores_with_info AS SELECT
md.id AS id,
md.format AS format,
md.layout AS layout,
md.interpretation AS interpretation,
md.datasource_id AS datasource_id,
md.api_id AS api_id,
t.id AS current_version,
t.lastupdate AS lastupdate,
t.size AS size
FROM
mdstores md
LEFT OUTER JOIN transactions t ON (md.id = t.mdstore)
WHERE
t.current = TRUE;

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dhp-applications/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.0.0-SNAPSHOT</version>
</parent>
<artifactId>dhp-applications</artifactId>
<packaging>pom</packaging>
<modules>
<module>dhp-mdstore-manager-app</module>
</modules>
</project>

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pom.xml
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<!--<module>dhp-build</module>-->
<module>dhp-common</module>
<module>dhp-workflows</module>
<module>dhp-applications</module>
</modules>
<issueManagement>