lsmyrnaios
/
dnet-hadoop
forked from D-Net/dnet-hadoop
1
0
Fork 0
Code Pull Requests Activity

-

This commit is contained in:
Miriam Baglioni 2020-04-30 11:05:17 +02:00
parent 3cffee74b9
commit 638a3c465b
281 changed files with 26243 additions and 24828 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

101
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java
View File

@ -1,8 +1,10 @@
package eu.dnetlib.maven.plugin.properties;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.maven.plugin.AbstractMojo;
@ -17,55 +19,58 @@ import org.apache.maven.plugin.MojoFailureException;
*/
public class GenerateOoziePropertiesMojo extends AbstractMojo {
public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir";
public static final String PROPERTY_NAME_SANDBOX_NAME = "sandboxName";
public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir";
public static final String PROPERTY_NAME_SANDBOX_NAME = "sandboxName";
private final String[] limiters = {"dhp", "dnetlib", "eu"};
private final String[] limiters = {
"dhp", "dnetlib", "eu"
};
@Override
public void execute() throws MojoExecutionException, MojoFailureException {
if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
&& !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
String generatedSandboxName =
generateSandboxName(System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
if (generatedSandboxName != null) {
System.getProperties().setProperty(PROPERTY_NAME_SANDBOX_NAME, generatedSandboxName);
} else {
System.out.println(
"unable to generate sandbox name from path: "
+ System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
}
}
}
@Override
public void execute() throws MojoExecutionException, MojoFailureException {
if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
&& !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
String generatedSandboxName = generateSandboxName(
System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
if (generatedSandboxName != null) {
System.getProperties().setProperty(PROPERTY_NAME_SANDBOX_NAME, generatedSandboxName);
} else {
System.out
.println(
"unable to generate sandbox name from path: "
+ System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
}
}
}
/**
* Generates sandbox name from workflow source directory.
*
* @param wfSourceDir
* @return generated sandbox name
*/
private String generateSandboxName(String wfSourceDir) {
// utilize all dir names until finding one of the limiters
List<String> sandboxNameParts = new ArrayList<String>();
String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar);
ArrayUtils.reverse(tokens);
if (tokens.length > 0) {
for (String token : tokens) {
for (String limiter : limiters) {
if (limiter.equals(token)) {
return sandboxNameParts.size() > 0
? StringUtils.join(sandboxNameParts.toArray())
: null;
}
}
if (sandboxNameParts.size() > 0) {
sandboxNameParts.add(0, File.separator);
}
sandboxNameParts.add(0, token);
}
return StringUtils.join(sandboxNameParts.toArray());
} else {
return null;
}
}
/**
* Generates sandbox name from workflow source directory.
*
* @param wfSourceDir
* @return generated sandbox name
*/
private String generateSandboxName(String wfSourceDir) {
// utilize all dir names until finding one of the limiters
List<String> sandboxNameParts = new ArrayList<String>();
String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar);
ArrayUtils.reverse(tokens);
if (tokens.length > 0) {
for (String token : tokens) {
for (String limiter : limiters) {
if (limiter.equals(token)) {
return sandboxNameParts.size() > 0
? StringUtils.join(sandboxNameParts.toArray())
: null;
}
}
if (sandboxNameParts.size() > 0) {
sandboxNameParts.add(0, File.separator);
}
sandboxNameParts.add(0, token);
}
return StringUtils.join(sandboxNameParts.toArray());
} else {
return null;
}
}
}

731
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java
View File

@ -9,9 +9,9 @@
* express or implied. See the License for the specific language governing permissions and
* limitations under the License.
*/
package eu.dnetlib.maven.plugin.properties;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
@ -24,6 +24,7 @@ import java.util.List;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
@ -35,6 +36,8 @@ import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import org.springframework.core.io.ResourceLoader;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
/**
* Writes project properties for the keys listed in specified properties files. Based on:
* http://site.kuali.org/maven/plugins/properties-maven-plugin/1.3.2/write-project-properties-mojo.html
@ -44,401 +47,401 @@ import org.springframework.core.io.ResourceLoader;
*/
public class WritePredefinedProjectProperties extends AbstractMojo {
private static final String CR = "\r";
private static final String LF = "\n";
private static final String TAB = "\t";
protected static final String PROPERTY_PREFIX_ENV = "env.";
private static final String ENCODING_UTF8 = "utf8";
private static final String CR = "\r";
private static final String LF = "\n";
private static final String TAB = "\t";
protected static final String PROPERTY_PREFIX_ENV = "env.";
private static final String ENCODING_UTF8 = "utf8";
/** @parameter property="properties.includePropertyKeysFromFiles" */
private String[] includePropertyKeysFromFiles;
/** @parameter property="properties.includePropertyKeysFromFiles" */
private String[] includePropertyKeysFromFiles;
/**
* @parameter default-value="${project}"
* @required
* @readonly
*/
protected MavenProject project;
/**
* @parameter default-value="${project}"
* @required
* @readonly
*/
protected MavenProject project;
/**
* The file that properties will be written to
*
* @parameter property="properties.outputFile"
* default-value="${project.build.directory}/properties/project.properties";
* @required
*/
protected File outputFile;
/**
* The file that properties will be written to
*
* @parameter property="properties.outputFile"
* default-value="${project.build.directory}/properties/project.properties";
* @required
*/
protected File outputFile;
/**
* If true, the plugin will silently ignore any non-existent properties files, and the build will
* continue
*
* @parameter property="properties.quiet" default-value="true"
*/
private boolean quiet;
/**
* If true, the plugin will silently ignore any non-existent properties files, and the build will continue
*
* @parameter property="properties.quiet" default-value="true"
*/
private boolean quiet;
/**
* Comma separated list of characters to escape when writing property values. cr=carriage return,
* lf=linefeed, tab=tab. Any other values are taken literally.
*
* @parameter default-value="cr,lf,tab" property="properties.escapeChars"
*/
private String escapeChars;
/**
* Comma separated list of characters to escape when writing property values. cr=carriage return, lf=linefeed,
* tab=tab. Any other values are taken literally.
*
* @parameter default-value="cr,lf,tab" property="properties.escapeChars"
*/
private String escapeChars;
/**
* If true, the plugin will include system properties when writing the properties file. System
* properties override both environment variables and project properties.
*
* @parameter default-value="false" property="properties.includeSystemProperties"
*/
private boolean includeSystemProperties;
/**
* If true, the plugin will include system properties when writing the properties file. System properties override
* both environment variables and project properties.
*
* @parameter default-value="false" property="properties.includeSystemProperties"
*/
private boolean includeSystemProperties;
/**
* If true, the plugin will include environment variables when writing the properties file.
* Environment variables are prefixed with "env". Environment variables override project
* properties.
*
* @parameter default-value="false" property="properties.includeEnvironmentVariables"
*/
private boolean includeEnvironmentVariables;
/**
* If true, the plugin will include environment variables when writing the properties file. Environment variables
* are prefixed with "env". Environment variables override project properties.
*
* @parameter default-value="false" property="properties.includeEnvironmentVariables"
*/
private boolean includeEnvironmentVariables;
/**
* Comma separated set of properties to exclude when writing the properties file
*
* @parameter property="properties.exclude"
*/
private String exclude;
/**
* Comma separated set of properties to exclude when writing the properties file
*
* @parameter property="properties.exclude"
*/
private String exclude;
/**
* Comma separated set of properties to write to the properties file. If provided, only the
* properties matching those supplied here will be written to the properties file.
*
* @parameter property="properties.include"
*/
private String include;
/**
* Comma separated set of properties to write to the properties file. If provided, only the properties matching
* those supplied here will be written to the properties file.
*
* @parameter property="properties.include"
*/
private String include;
/*
* (non-Javadoc)
* @see org.apache.maven.plugin.AbstractMojo#execute()
*/
@Override
@SuppressFBWarnings({"NP_UNWRITTEN_FIELD", "UWF_UNWRITTEN_FIELD"})
public void execute() throws MojoExecutionException, MojoFailureException {
Properties properties = new Properties();
// Add project properties
properties.putAll(project.getProperties());
if (includeEnvironmentVariables) {
// Add environment variables, overriding any existing properties with the same key
properties.putAll(getEnvironmentVariables());
}
if (includeSystemProperties) {
// Add system properties, overriding any existing properties with the same key
properties.putAll(System.getProperties());
}
/*
* (non-Javadoc)
* @see org.apache.maven.plugin.AbstractMojo#execute()
*/
@Override
@SuppressFBWarnings({
"NP_UNWRITTEN_FIELD", "UWF_UNWRITTEN_FIELD"
})
public void execute() throws MojoExecutionException, MojoFailureException {
Properties properties = new Properties();
// Add project properties
properties.putAll(project.getProperties());
if (includeEnvironmentVariables) {
// Add environment variables, overriding any existing properties with the same key
properties.putAll(getEnvironmentVariables());
}
if (includeSystemProperties) {
// Add system properties, overriding any existing properties with the same key
properties.putAll(System.getProperties());
}
// Remove properties as appropriate
trim(properties, exclude, include);
// Remove properties as appropriate
trim(properties, exclude, include);
String comment = "# " + new Date() + "\n";
List<String> escapeTokens = getEscapeChars(escapeChars);
String comment = "# " + new Date() + "\n";
List<String> escapeTokens = getEscapeChars(escapeChars);
getLog().info("Creating " + outputFile);
writeProperties(outputFile, comment, properties, escapeTokens);
}
getLog().info("Creating " + outputFile);
writeProperties(outputFile, comment, properties, escapeTokens);
}
/**
* Provides environment variables.
*
* @return environment variables
*/
protected static Properties getEnvironmentVariables() {
Properties props = new Properties();
for (Entry<String, String> entry : System.getenv().entrySet()) {
props.setProperty(PROPERTY_PREFIX_ENV + entry.getKey(), entry.getValue());
}
return props;
}
/**
* Provides environment variables.
*
* @return environment variables
*/
protected static Properties getEnvironmentVariables() {
Properties props = new Properties();
for (Entry<String, String> entry : System.getenv().entrySet()) {
props.setProperty(PROPERTY_PREFIX_ENV + entry.getKey(), entry.getValue());
}
return props;
}
/**
* Removes properties which should not be written.
*
* @param properties
* @param omitCSV
* @param includeCSV
* @throws MojoExecutionException
*/
protected void trim(Properties properties, String omitCSV, String includeCSV)
throws MojoExecutionException {
List<String> omitKeys = getListFromCSV(omitCSV);
for (String key : omitKeys) {
properties.remove(key);
}
/**
* Removes properties which should not be written.
*
* @param properties
* @param omitCSV
* @param includeCSV
* @throws MojoExecutionException
*/
protected void trim(Properties properties, String omitCSV, String includeCSV)
throws MojoExecutionException {
List<String> omitKeys = getListFromCSV(omitCSV);
for (String key : omitKeys) {
properties.remove(key);
}
List<String> includeKeys = getListFromCSV(includeCSV);
// mh: including keys from predefined properties
if (includePropertyKeysFromFiles != null && includePropertyKeysFromFiles.length > 0) {
for (String currentIncludeLoc : includePropertyKeysFromFiles) {
if (validate(currentIncludeLoc)) {
Properties p = getProperties(currentIncludeLoc);
for (String key : p.stringPropertyNames()) {
includeKeys.add(key);
}
}
}
}
if (includeKeys != null && !includeKeys.isEmpty()) {
// removing only when include keys provided
Set<String> keys = properties.stringPropertyNames();
for (String key : keys) {
if (!includeKeys.contains(key)) {
properties.remove(key);
}
}
}
}
List<String> includeKeys = getListFromCSV(includeCSV);
// mh: including keys from predefined properties
if (includePropertyKeysFromFiles != null && includePropertyKeysFromFiles.length > 0) {
for (String currentIncludeLoc : includePropertyKeysFromFiles) {
if (validate(currentIncludeLoc)) {
Properties p = getProperties(currentIncludeLoc);
for (String key : p.stringPropertyNames()) {
includeKeys.add(key);
}
}
}
}
if (includeKeys != null && !includeKeys.isEmpty()) {
// removing only when include keys provided
Set<String> keys = properties.stringPropertyNames();
for (String key : keys) {
if (!includeKeys.contains(key)) {
properties.remove(key);
}
}
}
}
/**
* Checks whether file exists.
*
* @param location
* @return true when exists, false otherwise.
*/
protected boolean exists(String location) {
if (StringUtils.isBlank(location)) {
return false;
}
File file = new File(location);
if (file.exists()) {
return true;
}
ResourceLoader loader = new DefaultResourceLoader();
Resource resource = loader.getResource(location);
return resource.exists();
}
/**
* Checks whether file exists.
*
* @param location
* @return true when exists, false otherwise.
*/
protected boolean exists(String location) {
if (StringUtils.isBlank(location)) {
return false;
}
File file = new File(location);
if (file.exists()) {
return true;
}
ResourceLoader loader = new DefaultResourceLoader();
Resource resource = loader.getResource(location);
return resource.exists();
}
/**
* Validates resource location.
*
* @param location
* @return true when valid, false otherwise
* @throws MojoExecutionException
*/
protected boolean validate(String location) throws MojoExecutionException {
boolean exists = exists(location);
if (exists) {
return true;
}
if (quiet) {
getLog().info("Ignoring non-existent properties file '" + location + "'");
return false;
} else {
throw new MojoExecutionException("Non-existent properties file '" + location + "'");
}
}
/**
* Validates resource location.
*
* @param location
* @return true when valid, false otherwise
* @throws MojoExecutionException
*/
protected boolean validate(String location) throws MojoExecutionException {
boolean exists = exists(location);
if (exists) {
return true;
}
if (quiet) {
getLog().info("Ignoring non-existent properties file '" + location + "'");
return false;
} else {
throw new MojoExecutionException("Non-existent properties file '" + location + "'");
}
}
/**
* Provides input stream.
*
* @param location
* @return input stream
* @throws IOException
*/
protected InputStream getInputStream(String location) throws IOException {
File file = new File(location);
if (file.exists()) {
return new FileInputStream(location);
}
ResourceLoader loader = new DefaultResourceLoader();
Resource resource = loader.getResource(location);
return resource.getInputStream();
}
/**
* Provides input stream.
*
* @param location
* @return input stream
* @throws IOException
*/
protected InputStream getInputStream(String location) throws IOException {
File file = new File(location);
if (file.exists()) {
return new FileInputStream(location);
}
ResourceLoader loader = new DefaultResourceLoader();
Resource resource = loader.getResource(location);
return resource.getInputStream();
}
/**
* Creates properties for given location.
*
* @param location
* @return properties for given location
* @throws MojoExecutionException
*/
protected Properties getProperties(String location) throws MojoExecutionException {
InputStream in = null;
try {
Properties properties = new Properties();
in = getInputStream(location);
if (location.toLowerCase().endsWith(".xml")) {
properties.loadFromXML(in);
} else {
properties.load(in);
}
return properties;
} catch (IOException e) {
throw new MojoExecutionException("Error reading properties file " + location, e);
} finally {
IOUtils.closeQuietly(in);
}
}
/**
* Creates properties for given location.
*
* @param location
* @return properties for given location
* @throws MojoExecutionException
*/
protected Properties getProperties(String location) throws MojoExecutionException {
InputStream in = null;
try {
Properties properties = new Properties();
in = getInputStream(location);
if (location.toLowerCase().endsWith(".xml")) {
properties.loadFromXML(in);
} else {
properties.load(in);
}
return properties;
} catch (IOException e) {
throw new MojoExecutionException("Error reading properties file " + location, e);
} finally {
IOUtils.closeQuietly(in);
}
}
/**
* Provides escape characters.
*
* @param escapeChars
* @return escape characters
*/
protected List<String> getEscapeChars(String escapeChars) {
List<String> tokens = getListFromCSV(escapeChars);
List<String> realTokens = new ArrayList<String>();
for (String token : tokens) {
String realToken = getRealToken(token);
realTokens.add(realToken);
}
return realTokens;
}
/**
* Provides escape characters.
*
* @param escapeChars
* @return escape characters
*/
protected List<String> getEscapeChars(String escapeChars) {
List<String> tokens = getListFromCSV(escapeChars);
List<String> realTokens = new ArrayList<String>();
for (String token : tokens) {
String realToken = getRealToken(token);
realTokens.add(realToken);
}
return realTokens;
}
/**
* Provides real token.
*
* @param token
* @return real token
*/
protected String getRealToken(String token) {
if (token.equalsIgnoreCase("CR")) {
return CR;
} else if (token.equalsIgnoreCase("LF")) {
return LF;
} else if (token.equalsIgnoreCase("TAB")) {
return TAB;
} else {
return token;
}
}
/**
* Provides real token.
*
* @param token
* @return real token
*/
protected String getRealToken(String token) {
if (token.equalsIgnoreCase("CR")) {
return CR;
} else if (token.equalsIgnoreCase("LF")) {
return LF;
} else if (token.equalsIgnoreCase("TAB")) {
return TAB;
} else {
return token;
}
}
/**
* Returns content.
*
* @param comment
* @param properties
* @param escapeTokens
* @return content
*/
protected String getContent(String comment, Properties properties, List<String> escapeTokens) {
List<String> names = new ArrayList<String>(properties.stringPropertyNames());
Collections.sort(names);
StringBuilder sb = new StringBuilder();
if (!StringUtils.isBlank(comment)) {
sb.append(comment);
}
for (String name : names) {
String value = properties.getProperty(name);
String escapedValue = escape(value, escapeTokens);
sb.append(name + "=" + escapedValue + "\n");
}
return sb.toString();
}
/**
* Returns content.
*
* @param comment
* @param properties
* @param escapeTokens
* @return content
*/
protected String getContent(String comment, Properties properties, List<String> escapeTokens) {
List<String> names = new ArrayList<String>(properties.stringPropertyNames());
Collections.sort(names);
StringBuilder sb = new StringBuilder();
if (!StringUtils.isBlank(comment)) {
sb.append(comment);
}
for (String name : names) {
String value = properties.getProperty(name);
String escapedValue = escape(value, escapeTokens);
sb.append(name + "=" + escapedValue + "\n");
}
return sb.toString();
}
/**
* Writes properties to given file.
*
* @param file
* @param comment
* @param properties
* @param escapeTokens
* @throws MojoExecutionException
*/
protected void writeProperties(
File file, String comment, Properties properties, List<String> escapeTokens)
throws MojoExecutionException {
try {
String content = getContent(comment, properties, escapeTokens);
FileUtils.writeStringToFile(file, content, ENCODING_UTF8);
} catch (IOException e) {
throw new MojoExecutionException("Error creating properties file", e);
}
}
/**
* Writes properties to given file.
*
* @param file
* @param comment
* @param properties
* @param escapeTokens
* @throws MojoExecutionException
*/
protected void writeProperties(
File file, String comment, Properties properties, List<String> escapeTokens)
throws MojoExecutionException {
try {
String content = getContent(comment, properties, escapeTokens);
FileUtils.writeStringToFile(file, content, ENCODING_UTF8);
} catch (IOException e) {
throw new MojoExecutionException("Error creating properties file", e);
}
}
/**
* Escapes characters.
*
* @param s
* @param escapeChars
* @return
*/
protected String escape(String s, List<String> escapeChars) {
String result = s;
for (String escapeChar : escapeChars) {
result = result.replace(escapeChar, getReplacementToken(escapeChar));
}
return result;
}
/**
* Escapes characters.
*
* @param s
* @param escapeChars
* @return
*/
protected String escape(String s, List<String> escapeChars) {
String result = s;
for (String escapeChar : escapeChars) {
result = result.replace(escapeChar, getReplacementToken(escapeChar));
}
return result;
}
/**
* Provides replacement token.
*
* @param escapeChar
* @return replacement token
*/
protected String getReplacementToken(String escapeChar) {
if (escapeChar.equals(CR)) {
return "\\r";
} else if (escapeChar.equals(LF)) {
return "\\n";
} else if (escapeChar.equals(TAB)) {
return "\\t";
} else {
return "\\" + escapeChar;
}
}
/**
* Provides replacement token.
*
* @param escapeChar
* @return replacement token
*/
protected String getReplacementToken(String escapeChar) {
if (escapeChar.equals(CR)) {
return "\\r";
} else if (escapeChar.equals(LF)) {
return "\\n";
} else if (escapeChar.equals(TAB)) {
return "\\t";
} else {
return "\\" + escapeChar;
}
}
/**
* Returns list from csv.
*
* @param csv
* @return list of values generated from CSV
*/
protected static final List<String> getListFromCSV(String csv) {
if (StringUtils.isBlank(csv)) {
return new ArrayList<String>();
}
List<String> list = new ArrayList<String>();
String[] tokens = StringUtils.split(csv, ",");
for (String token : tokens) {
list.add(token.trim());
}
return list;
}
/**
* Returns list from csv.
*
* @param csv
* @return list of values generated from CSV
*/
protected static final List<String> getListFromCSV(String csv) {
if (StringUtils.isBlank(csv)) {
return new ArrayList<String>();
}
List<String> list = new ArrayList<String>();
String[] tokens = StringUtils.split(csv, ",");
for (String token : tokens) {
list.add(token.trim());
}
return list;
}
public void setIncludeSystemProperties(boolean includeSystemProperties) {
this.includeSystemProperties = includeSystemProperties;
}
public void setIncludeSystemProperties(boolean includeSystemProperties) {
this.includeSystemProperties = includeSystemProperties;
}
public void setEscapeChars(String escapeChars) {
this.escapeChars = escapeChars;
}
public void setEscapeChars(String escapeChars) {
this.escapeChars = escapeChars;
}
public void setIncludeEnvironmentVariables(boolean includeEnvironmentVariables) {
this.includeEnvironmentVariables = includeEnvironmentVariables;
}
public void setIncludeEnvironmentVariables(boolean includeEnvironmentVariables) {
this.includeEnvironmentVariables = includeEnvironmentVariables;
}
public void setExclude(String exclude) {
this.exclude = exclude;
}
public void setExclude(String exclude) {
this.exclude = exclude;
}
public void setInclude(String include) {
this.include = include;
}
public void setInclude(String include) {
this.include = include;
}
public void setQuiet(boolean quiet) {
this.quiet = quiet;
}
public void setQuiet(boolean quiet) {
this.quiet = quiet;
}
/**
* Sets property files for which keys properties should be included.
*
* @param includePropertyKeysFromFiles
*/
public void setIncludePropertyKeysFromFiles(String[] includePropertyKeysFromFiles) {
if (includePropertyKeysFromFiles != null) {
this.includePropertyKeysFromFiles =
Arrays.copyOf(includePropertyKeysFromFiles, includePropertyKeysFromFiles.length);
}
}
/**
* Sets property files for which keys properties should be included.
*
* @param includePropertyKeysFromFiles
*/
public void setIncludePropertyKeysFromFiles(String[] includePropertyKeysFromFiles) {
if (includePropertyKeysFromFiles != null) {
this.includePropertyKeysFromFiles = Arrays
.copyOf(includePropertyKeysFromFiles, includePropertyKeysFromFiles.length);
}
}
}

131
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.maven.plugin.properties;
import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_SANDBOX_NAME;
@ -10,87 +11,87 @@ import org.junit.jupiter.api.Test;
/** @author mhorst, claudio.atzori */
public class GenerateOoziePropertiesMojoTest {
private GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
private GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
@BeforeEach
public void clearSystemProperties() {
System.clearProperty(PROPERTY_NAME_SANDBOX_NAME);
System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR);
}
@BeforeEach
public void clearSystemProperties() {
System.clearProperty(PROPERTY_NAME_SANDBOX_NAME);
System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR);
}
@Test
public void testExecuteEmpty() throws Exception {
// execute
mojo.execute();
@Test
public void testExecuteEmpty() throws Exception {
// execute
mojo.execute();
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecuteSandboxNameAlreadySet() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
String sandboxName = "originalSandboxName";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
System.setProperty(PROPERTY_NAME_SANDBOX_NAME, sandboxName);
@Test
public void testExecuteSandboxNameAlreadySet() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
String sandboxName = "originalSandboxName";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
System.setProperty(PROPERTY_NAME_SANDBOX_NAME, sandboxName);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertEquals(sandboxName, System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
// assert
assertEquals(sandboxName, System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecuteEmptyWorkflowSourceDir() throws Exception {
// given
String workflowSourceDir = "";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@Test
public void testExecuteEmptyWorkflowSourceDir() throws Exception {
// given
String workflowSourceDir = "";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecuteNullSandboxNameGenerated() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@Test
public void testExecuteNullSandboxNameGenerated() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
// assert
assertNull(System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecute() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@Test
public void testExecute() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
// assert
assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
@Test
public void testExecuteWithoutRoot() throws Exception {
// given
String workflowSourceDir = "wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@Test
public void testExecuteWithoutRoot() throws Exception {
// given
String workflowSourceDir = "wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
// assert
assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
}
}

576
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.maven.plugin.properties;
import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV;
@ -7,6 +8,7 @@ import static org.mockito.Mockito.lenient;
import java.io.*;
import java.util.Properties;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.project.MavenProject;
import org.junit.jupiter.api.*;
@ -20,337 +22,353 @@ import org.mockito.junit.jupiter.MockitoExtension;
@ExtendWith(MockitoExtension.class)
public class WritePredefinedProjectPropertiesTest {
@Mock private MavenProject mavenProject;
@Mock
private MavenProject mavenProject;
private WritePredefinedProjectProperties mojo;
private WritePredefinedProjectProperties mojo;
@BeforeEach
public void init(@TempDir File testFolder) {
MockitoAnnotations.initMocks(this);
mojo = new WritePredefinedProjectProperties();
mojo.outputFile = getPropertiesFileLocation(testFolder);
mojo.project = mavenProject;
lenient().doReturn(new Properties()).when(mavenProject).getProperties();
}
@BeforeEach
public void init(@TempDir File testFolder) {
MockitoAnnotations.initMocks(this);
mojo = new WritePredefinedProjectProperties();
mojo.outputFile = getPropertiesFileLocation(testFolder);
mojo.project = mavenProject;
lenient().doReturn(new Properties()).when(mavenProject).getProperties();
}
// ----------------------------------- TESTS ---------------------------------------------
// ----------------------------------- TESTS ---------------------------------------------
@Test
public void testExecuteEmpty() throws Exception {
// execute
mojo.execute();
@Test
public void testExecuteEmpty() throws Exception {
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(0, storedProperties.size());
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(0, storedProperties.size());
}
@Test
public void testExecuteWithProjectProperties() throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties();
@Test
public void testExecuteWithProjectProperties() throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties();
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test()
public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.outputFile = testFolder;
@Test()
public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.outputFile = testFolder;
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String excludedKey = "excludedPropertyKey";
String excludedValue = "excludedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(excludedKey, excludedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setExclude(excludedKey);
@Test
public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String excludedKey = "excludedPropertyKey";
String excludedValue = "excludedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(excludedKey, excludedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setExclude(excludedKey);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test
public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setInclude(includedKey);
@Test
public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setInclude(includedKey);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
@Test
public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder, "included.properties");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileWriter(includedPropertiesFile), null);
File includedPropertiesFile = new File(testFolder, "included.properties");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileWriter(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()});
mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
@Test
public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setIncludePropertyKeysFromFiles(
new String[] {"/eu/dnetlib/maven/plugin/properties/included.properties"});
mojo
.setIncludePropertyKeysFromFiles(
new String[] {
"/eu/dnetlib/maven/plugin/properties/included.properties"
});
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromBlankLocation() {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
@Test
public void testExecuteIncludingPropertyKeysFromBlankLocation() {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setIncludePropertyKeysFromFiles(new String[] {""});
mojo.setIncludePropertyKeysFromFiles(new String[] {
""
});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
@Test
public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.storeToXML(new FileOutputStream(includedPropertiesFile), null);
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.storeToXML(new FileOutputStream(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()});
mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
@Test
public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
String includedKey = "includedPropertyKey";
String includedValue = "includedPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileOutputStream(includedPropertiesFile), null);
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileOutputStream(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()});
mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
// given
mojo.setQuiet(true);
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"});
@Test
public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
// given
mojo.setQuiet(true);
mojo.setIncludePropertyKeysFromFiles(new String[] {
"invalid location"
});
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(0, storedProperties.size());
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(0, storedProperties.size());
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() {
// given
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"});
@Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() {
// given
mojo.setIncludePropertyKeysFromFiles(new String[] {
"invalid location"
});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
// given
mojo.setIncludeEnvironmentVariables(true);
@Test
public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
// given
mojo.setIncludeEnvironmentVariables(true);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
for (Object currentKey : storedProperties.keySet()) {
assertTrue(((String) currentKey).startsWith(PROPERTY_PREFIX_ENV));
}
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
for (Object currentKey : storedProperties.keySet()) {
assertTrue(((String) currentKey).startsWith(PROPERTY_PREFIX_ENV));
}
}
@Test
public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
// given
String key = "systemPropertyKey";
String value = "systemPropertyValue";
System.setProperty(key, value);
mojo.setIncludeSystemProperties(true);
@Test
public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
// given
String key = "systemPropertyKey";
String value = "systemPropertyValue";
System.setProperty(key, value);
mojo.setIncludeSystemProperties(true);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test
public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
throws Exception {
// given
String key = "systemPropertyKey ";
String value = "systemPropertyValue";
System.setProperty(key, value);
mojo.setIncludeSystemProperties(true);
String escapeChars = "cr,lf,tab,|";
mojo.setEscapeChars(escapeChars);
@Test
public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
throws Exception {
// given
String key = "systemPropertyKey ";
String value = "systemPropertyValue";
System.setProperty(key, value);
mojo.setIncludeSystemProperties(true);
String escapeChars = "cr,lf,tab,|";
mojo.setEscapeChars(escapeChars);
// execute
mojo.execute();
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertFalse(storedProperties.containsKey(key));
assertTrue(storedProperties.containsKey(key.trim()));
assertEquals(value, storedProperties.getProperty(key.trim()));
}
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertFalse(storedProperties.containsKey(key));
assertTrue(storedProperties.containsKey(key.trim()));
assertEquals(value, storedProperties.getProperty(key.trim()));
}
// ----------------------------------- PRIVATE -------------------------------------------
// ----------------------------------- PRIVATE -------------------------------------------
private File getPropertiesFileLocation(File testFolder) {
return new File(testFolder, "test.properties");
}
private File getPropertiesFileLocation(File testFolder) {
return new File(testFolder, "test.properties");
}
private Properties getStoredProperties(File testFolder)
throws FileNotFoundException, IOException {
Properties properties = new Properties();
properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
return properties;
}
private Properties getStoredProperties(File testFolder)
throws FileNotFoundException, IOException {
Properties properties = new Properties();
properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
return properties;
}
}

57
dhp-common/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.collector.worker.model;
import java.util.HashMap;
@ -5,43 +6,43 @@ import java.util.Map;
public class ApiDescriptor {
private String id;
private String id;
private String baseUrl;
private String baseUrl;
private String protocol;
private String protocol;
private Map<String, String> params = new HashMap<>();
private Map<String, String> params = new HashMap<>();
public String getBaseUrl() {
return baseUrl;
}
public String getBaseUrl() {
return baseUrl;
}
public void setBaseUrl(final String baseUrl) {
this.baseUrl = baseUrl;
}
public void setBaseUrl(final String baseUrl) {
this.baseUrl = baseUrl;
}
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public void setId(final String id) {
this.id = id;
}
public Map<String, String> getParams() {
return params;
}
public Map<String, String> getParams() {
return params;
}
public void setParams(final HashMap<String, String> params) {
this.params = params;
}
public void setParams(final HashMap<String, String> params) {
this.params = params;
}
public String getProtocol() {
return protocol;
}
public String getProtocol() {
return protocol;
}
public void setProtocol(final String protocol) {
this.protocol = protocol;
}
public void setProtocol(final String protocol) {
this.protocol = protocol;
}
}

162
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java
View File

@ -1,7 +1,9 @@
package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.UUID;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
@ -11,107 +13,107 @@ import javax.persistence.Table;
@Table(name = "mdstores")
public class MDStore implements Serializable {
/** */
private static final long serialVersionUID = 3160530489149700055L;
/** */
private static final long serialVersionUID = 3160530489149700055L;
@Id
@Column(name = "id")
private String id;
@Id
@Column(name = "id")
private String id;
@Column(name = "format")
private String format;
@Column(name = "format")
private String format;
@Column(name = "layout")
private String layout;
@Column(name = "layout")
private String layout;
@Column(name = "interpretation")
private String interpretation;
@Column(name = "interpretation")
private String interpretation;
@Column(name = "datasource_name")
private String datasourceName;
@Column(name = "datasource_name")
private String datasourceName;
@Column(name = "datasource_id")
private String datasourceId;
@Column(name = "datasource_id")
private String datasourceId;
@Column(name = "api_id")
private String apiId;
@Column(name = "api_id")
private String apiId;
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public void setId(final String id) {
this.id = id;
}
public String getFormat() {
return format;
}
public String getFormat() {
return format;
}
public void setFormat(final String format) {
this.format = format;
}
public void setFormat(final String format) {
this.format = format;
}
public String getLayout() {
return layout;
}
public String getLayout() {
return layout;
}
public void setLayout(final String layout) {
this.layout = layout;
}
public void setLayout(final String layout) {
this.layout = layout;
}
public String getInterpretation() {
return interpretation;
}
public String getInterpretation() {
return interpretation;
}
public void setInterpretation(final String interpretation) {
this.interpretation = interpretation;
}
public void setInterpretation(final String interpretation) {
this.interpretation = interpretation;
}
public String getDatasourceName() {
return datasourceName;
}
public String getDatasourceName() {
return datasourceName;
}
public void setDatasourceName(final String datasourceName) {
this.datasourceName = datasourceName;
}
public void setDatasourceName(final String datasourceName) {
this.datasourceName = datasourceName;
}
public String getDatasourceId() {
return datasourceId;
}
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(final String datasourceId) {
this.datasourceId = datasourceId;
}
public void setDatasourceId(final String datasourceId) {
this.datasourceId = datasourceId;
}
public String getApiId() {
return apiId;
}
public String getApiId() {
return apiId;
}
public void setApiId(final String apiId) {
this.apiId = apiId;
}
public void setApiId(final String apiId) {
this.apiId = apiId;
}
public static MDStore newInstance(
final String format, final String layout, final String interpretation) {
return newInstance(format, layout, interpretation, null, null, null);
}
public static MDStore newInstance(
final String format, final String layout, final String interpretation) {
return newInstance(format, layout, interpretation, null, null, null);
}
public static MDStore newInstance(
final String format,
final String layout,
final String interpretation,
final String dsName,
final String dsId,
final String apiId) {
final MDStore md = new MDStore();
md.setId("md-" + UUID.randomUUID());
md.setFormat(format);
md.setLayout(layout);
md.setInterpretation(interpretation);
md.setDatasourceName(dsName);
md.setDatasourceId(dsId);
md.setApiId(apiId);
return md;
}
public static MDStore newInstance(
final String format,
final String layout,
final String interpretation,
final String dsName,
final String dsId,
final String apiId) {
final MDStore md = new MDStore();
md.setId("md-" + UUID.randomUUID());
md.setFormat(format);
md.setLayout(layout);
md.setInterpretation(interpretation);
md.setDatasourceName(dsName);
md.setDatasourceId(dsId);
md.setApiId(apiId);
return md;
}
}

58
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java
View File

@ -1,6 +1,8 @@
package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
@ -10,40 +12,40 @@ import javax.persistence.Table;
@Table(name = "mdstore_current_versions")
public class MDStoreCurrentVersion implements Serializable {
/** */
private static final long serialVersionUID = -4757725888593745773L;
/** */
private static final long serialVersionUID = -4757725888593745773L;
@Id
@Column(name = "mdstore")
private String mdstore;
@Id
@Column(name = "mdstore")
private String mdstore;
@Column(name = "current_version")
private String currentVersion;
@Column(name = "current_version")
private String currentVersion;
public String getMdstore() {
return mdstore;
}
public String getMdstore() {
return mdstore;
}
public void setMdstore(final String mdstore) {
this.mdstore = mdstore;
}
public void setMdstore(final String mdstore) {
this.mdstore = mdstore;
}
public String getCurrentVersion() {
return currentVersion;
}
public String getCurrentVersion() {
return currentVersion;
}
public void setCurrentVersion(final String currentVersion) {
this.currentVersion = currentVersion;
}
public void setCurrentVersion(final String currentVersion) {
this.currentVersion = currentVersion;
}
public static MDStoreCurrentVersion newInstance(final String mdId, final String versionId) {
final MDStoreCurrentVersion cv = new MDStoreCurrentVersion();
cv.setMdstore(mdId);
cv.setCurrentVersion(versionId);
return cv;
}
public static MDStoreCurrentVersion newInstance(final String mdId, final String versionId) {
final MDStoreCurrentVersion cv = new MDStoreCurrentVersion();
cv.setMdstore(mdId);
cv.setCurrentVersion(versionId);
return cv;
}
public static MDStoreCurrentVersion newInstance(final MDStoreVersion v) {
return newInstance(v.getMdstore(), v.getId());
}
public static MDStoreCurrentVersion newInstance(final MDStoreVersion v) {
return newInstance(v.getMdstore(), v.getId());
}
}

126
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java
View File

@ -1,7 +1,9 @@
package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
@ -13,85 +15,85 @@ import javax.persistence.TemporalType;
@Table(name = "mdstore_versions")
public class MDStoreVersion implements Serializable {
/** */
private static final long serialVersionUID = -4763494442274298339L;
/** */
private static final long serialVersionUID = -4763494442274298339L;
@Id
@Column(name = "id")
private String id;
@Id
@Column(name = "id")
private String id;
@Column(name = "mdstore")
private String mdstore;
@Column(name = "mdstore")
private String mdstore;
@Column(name = "writing")
private boolean writing;
@Column(name = "writing")
private boolean writing;
@Column(name = "readcount")
private int readCount = 0;
@Column(name = "readcount")
private int readCount = 0;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
@Column(name = "size")
private long size = 0;
@Column(name = "size")
private long size = 0;
public static MDStoreVersion newInstance(final String mdId, final boolean writing) {
final MDStoreVersion t = new MDStoreVersion();
t.setId(mdId + "-" + new Date().getTime());
t.setMdstore(mdId);
t.setLastUpdate(null);
t.setWriting(writing);
t.setReadCount(0);
t.setSize(0);
return t;
}
public static MDStoreVersion newInstance(final String mdId, final boolean writing) {
final MDStoreVersion t = new MDStoreVersion();
t.setId(mdId + "-" + new Date().getTime());
t.setMdstore(mdId);
t.setLastUpdate(null);
t.setWriting(writing);
t.setReadCount(0);
t.setSize(0);
return t;
}
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public void setId(final String id) {
this.id = id;
}
public String getMdstore() {
return mdstore;
}
public String getMdstore() {
return mdstore;
}
public void setMdstore(final String mdstore) {
this.mdstore = mdstore;
}
public void setMdstore(final String mdstore) {
this.mdstore = mdstore;
}
public boolean isWriting() {
return writing;
}
public boolean isWriting() {
return writing;
}
public void setWriting(final boolean writing) {
this.writing = writing;
}
public void setWriting(final boolean writing) {
this.writing = writing;
}
public int getReadCount() {
return readCount;
}
public int getReadCount() {
return readCount;
}
public void setReadCount(final int readCount) {
this.readCount = readCount;
}
public void setReadCount(final int readCount) {
this.readCount = readCount;
}
public Date getLastUpdate() {
return lastUpdate;
}
public Date getLastUpdate() {
return lastUpdate;
}
public void setLastUpdate(final Date lastUpdate) {
this.lastUpdate = lastUpdate;
}
public void setLastUpdate(final Date lastUpdate) {
this.lastUpdate = lastUpdate;
}
public long getSize() {
return size;
}
public long getSize() {
return size;
}
public void setSize(final long size) {
this.size = size;
}
public void setSize(final long size) {
this.size = size;
}
}

186
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java
View File

@ -1,7 +1,9 @@
package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable;
import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
@ -13,129 +15,129 @@ import javax.persistence.TemporalType;
@Table(name = "mdstores_with_info")
public class MDStoreWithInfo implements Serializable {
/** */
private static final long serialVersionUID = -8445784770687571492L;
/** */
private static final long serialVersionUID = -8445784770687571492L;
@Id
@Column(name = "id")
private String id;
@Id
@Column(name = "id")
private String id;
@Column(name = "format")
private String format;
@Column(name = "format")
private String format;
@Column(name = "layout")
private String layout;
@Column(name = "layout")
private String layout;
@Column(name = "interpretation")
private String interpretation;
@Column(name = "interpretation")
private String interpretation;
@Column(name = "datasource_name")
private String datasourceName;
@Column(name = "datasource_name")
private String datasourceName;
@Column(name = "datasource_id")
private String datasourceId;
@Column(name = "datasource_id")
private String datasourceId;
@Column(name = "api_id")
private String apiId;
@Column(name = "api_id")
private String apiId;
@Column(name = "current_version")
private String currentVersion;
@Column(name = "current_version")
private String currentVersion;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
@Column(name = "lastupdate")
@Temporal(TemporalType.TIMESTAMP)
private Date lastUpdate;
@Column(name = "size")
private long size = 0;
@Column(name = "size")
private long size = 0;
@Column(name = "n_versions")
private long numberOfVersions = 0;
@Column(name = "n_versions")
private long numberOfVersions = 0;
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(final String id) {
this.id = id;
}
public void setId(final String id) {
this.id = id;
}
public String getFormat() {
return format;
}
public String getFormat() {
return format;
}
public void setFormat(final String format) {
this.format = format;
}
public void setFormat(final String format) {
this.format = format;
}
public String getLayout() {
return layout;
}
public String getLayout() {
return layout;
}
public void setLayout(final String layout) {
this.layout = layout;
}
public void setLayout(final String layout) {
this.layout = layout;
}
public String getInterpretation() {
return interpretation;
}
public String getInterpretation() {
return interpretation;
}
public void setInterpretation(final String interpretation) {
this.interpretation = interpretation;
}
public void setInterpretation(final String interpretation) {
this.interpretation = interpretation;
}
public String getDatasourceName() {
return datasourceName;
}
public String getDatasourceName() {
return datasourceName;
}
public void setDatasourceName(final String datasourceName) {
this.datasourceName = datasourceName;
}
public void setDatasourceName(final String datasourceName) {
this.datasourceName = datasourceName;
}
public String getDatasourceId() {
return datasourceId;
}
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(final String datasourceId) {
this.datasourceId = datasourceId;
}
public void setDatasourceId(final String datasourceId) {
this.datasourceId = datasourceId;
}
public String getApiId() {
return apiId;
}
public String getApiId() {
return apiId;
}
public void setApiId(final String apiId) {
this.apiId = apiId;
}
public void setApiId(final String apiId) {
this.apiId = apiId;
}
public String getCurrentVersion() {
return currentVersion;
}
public String getCurrentVersion() {
return currentVersion;
}
public void setCurrentVersion(final String currentVersion) {
this.currentVersion = currentVersion;
}
public void setCurrentVersion(final String currentVersion) {
this.currentVersion = currentVersion;
}
public Date getLastUpdate() {
return lastUpdate;
}
public Date getLastUpdate() {
return lastUpdate;
}
public void setLastUpdate(final Date lastUpdate) {
this.lastUpdate = lastUpdate;
}
public void setLastUpdate(final Date lastUpdate) {
this.lastUpdate = lastUpdate;
}
public long getSize() {
return size;
}
public long getSize() {
return size;
}
public void setSize(final long size) {
this.size = size;
}
public void setSize(final long size) {
this.size = size;
}
public long getNumberOfVersions() {
return numberOfVersions;
}
public long getNumberOfVersions() {
return numberOfVersions;
}
public void setNumberOfVersions(final long numberOfVersions) {
this.numberOfVersions = numberOfVersions;
}
public void setNumberOfVersions(final long numberOfVersions) {
this.numberOfVersions = numberOfVersions;
}
}

136
dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dhp.application;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.Serializable;
@ -8,87 +8,91 @@ import java.io.StringWriter;
import java.util.*;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import org.apache.commons.cli.*;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class ArgumentApplicationParser implements Serializable {
private final Options options = new Options();
private final Map<String, String> objectMap = new HashMap<>();
private final Options options = new Options();
private final Map<String, String> objectMap = new HashMap<>();
private final List<String> compressedValues = new ArrayList<>();
private final List<String> compressedValues = new ArrayList<>();
public ArgumentApplicationParser(final String json_configuration) throws Exception {
final ObjectMapper mapper = new ObjectMapper();
final OptionsParameter[] configuration =
mapper.readValue(json_configuration, OptionsParameter[].class);
createOptionMap(configuration);
}
public ArgumentApplicationParser(final String json_configuration) throws Exception {
final ObjectMapper mapper = new ObjectMapper();
final OptionsParameter[] configuration = mapper.readValue(json_configuration, OptionsParameter[].class);
createOptionMap(configuration);
}
public ArgumentApplicationParser(final OptionsParameter[] configuration) {
createOptionMap(configuration);
}
public ArgumentApplicationParser(final OptionsParameter[] configuration) {
createOptionMap(configuration);
}
private void createOptionMap(final OptionsParameter[] configuration) {
private void createOptionMap(final OptionsParameter[] configuration) {
Arrays.stream(configuration)
.map(
conf -> {
final Option o = new Option(conf.getParamName(), true, conf.getParamDescription());
o.setLongOpt(conf.getParamLongName());
o.setRequired(conf.isParamRequired());
if (conf.isCompressed()) {
compressedValues.add(conf.getParamLongName());
}
return o;
})
.forEach(options::addOption);
Arrays
.stream(configuration)
.map(
conf -> {
final Option o = new Option(conf.getParamName(), true, conf.getParamDescription());
o.setLongOpt(conf.getParamLongName());
o.setRequired(conf.isParamRequired());
if (conf.isCompressed()) {
compressedValues.add(conf.getParamLongName());
}
return o;
})
.forEach(options::addOption);
// HelpFormatter formatter = new HelpFormatter();
// formatter.printHelp("myapp", null, options, null, true);
// HelpFormatter formatter = new HelpFormatter();
// formatter.printHelp("myapp", null, options, null, true);
}
}
public static String decompressValue(final String abstractCompressed) {
try {
byte[] byteArray = Base64.decodeBase64(abstractCompressed.getBytes());
GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(byteArray));
final StringWriter stringWriter = new StringWriter();
IOUtils.copy(gis, stringWriter);
return stringWriter.toString();
} catch (Throwable e) {
System.out.println("Wrong value to decompress:" + abstractCompressed);
throw new RuntimeException(e);
}
}
public static String decompressValue(final String abstractCompressed) {
try {
byte[] byteArray = Base64.decodeBase64(abstractCompressed.getBytes());
GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(byteArray));
final StringWriter stringWriter = new StringWriter();
IOUtils.copy(gis, stringWriter);
return stringWriter.toString();
} catch (Throwable e) {
System.out.println("Wrong value to decompress:" + abstractCompressed);
throw new RuntimeException(e);
}
}
public static String compressArgument(final String value) throws Exception {
ByteArrayOutputStream out = new ByteArrayOutputStream();
GZIPOutputStream gzip = new GZIPOutputStream(out);
gzip.write(value.getBytes());
gzip.close();
return java.util.Base64.getEncoder().encodeToString(out.toByteArray());
}
public static String compressArgument(final String value) throws Exception {
ByteArrayOutputStream out = new ByteArrayOutputStream();
GZIPOutputStream gzip = new GZIPOutputStream(out);
gzip.write(value.getBytes());
gzip.close();
return java.util.Base64.getEncoder().encodeToString(out.toByteArray());
}
public void parseArgument(final String[] args) throws Exception {
CommandLineParser parser = new BasicParser();
CommandLine cmd = parser.parse(options, args);
Arrays.stream(cmd.getOptions())
.forEach(
it ->
objectMap.put(
it.getLongOpt(),
compressedValues.contains(it.getLongOpt())
? decompressValue(it.getValue())
: it.getValue()));
}
public void parseArgument(final String[] args) throws Exception {
CommandLineParser parser = new BasicParser();
CommandLine cmd = parser.parse(options, args);
Arrays
.stream(cmd.getOptions())
.forEach(
it -> objectMap
.put(
it.getLongOpt(),
compressedValues.contains(it.getLongOpt())
? decompressValue(it.getValue())
: it.getValue()));
}
public String get(final String key) {
return objectMap.get(key);
}
public String get(final String key) {
return objectMap.get(key);
}
public Map<String, String> getObjectMap() {
return objectMap;
}
public Map<String, String> getObjectMap() {
return objectMap;
}
}

50
dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java
View File

@ -1,36 +1,38 @@
package eu.dnetlib.dhp.application;
public class OptionsParameter {
private String paramName;
private String paramLongName;
private String paramDescription;
private boolean paramRequired;
private boolean compressed;
private String paramName;
private String paramLongName;
private String paramDescription;
private boolean paramRequired;
private boolean compressed;
public OptionsParameter() {}
public OptionsParameter() {
}
public String getParamName() {
return paramName;
}
public String getParamName() {
return paramName;
}
public String getParamLongName() {
return paramLongName;
}
public String getParamLongName() {
return paramLongName;
}
public String getParamDescription() {
return paramDescription;
}
public String getParamDescription() {
return paramDescription;
}
public boolean isParamRequired() {
return paramRequired;
}
public boolean isParamRequired() {
return paramRequired;
}
public boolean isCompressed() {
return compressed;
}
public boolean isCompressed() {
return compressed;
}
public void setCompressed(boolean compressed) {
this.compressed = compressed;
}
public void setCompressed(boolean compressed) {
this.compressed = compressed;
}
}

79
dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.common;
import java.io.Serializable;
@ -6,46 +7,48 @@ import java.util.function.Supplier;
/** Provides serializable and throwing extensions to standard functional interfaces. */
public class FunctionalInterfaceSupport {
private FunctionalInterfaceSupport() {}
private FunctionalInterfaceSupport() {
}
/**
* Serializable supplier of any kind of objects. To be used withing spark processing pipelines
* when supplying functions externally.
*
* @param <T>
*/
@FunctionalInterface
public interface SerializableSupplier<T> extends Supplier<T>, Serializable {}
/**
* Serializable supplier of any kind of objects. To be used withing spark processing pipelines when supplying
* functions externally.
*
* @param <T>
*/
@FunctionalInterface
public interface SerializableSupplier<T> extends Supplier<T>, Serializable {
}
/**
* Extension of consumer accepting functions throwing an exception.
*
* @param <T>
* @param <E>
*/
@FunctionalInterface
public interface ThrowingConsumer<T, E extends Exception> {
void accept(T t) throws E;
}
/**
* Extension of consumer accepting functions throwing an exception.
*
* @param <T>
* @param <E>
*/
@FunctionalInterface
public interface ThrowingConsumer<T, E extends Exception> {
void accept(T t) throws E;
}
/**
* Extension of supplier accepting functions throwing an exception.
*
* @param <T>
* @param <E>
*/
@FunctionalInterface
public interface ThrowingSupplier<T, E extends Exception> {
T get() throws E;
}
/**
* Extension of supplier accepting functions throwing an exception.
*
* @param <T>
* @param <E>
*/
@FunctionalInterface
public interface ThrowingSupplier<T, E extends Exception> {
T get() throws E;
}
/**
* Extension of runnable accepting functions throwing an exception.
*
* @param <E>
*/
@FunctionalInterface
public interface ThrowingRunnable<E extends Exception> {
void run() throws E;
}
/**
* Extension of runnable accepting functions throwing an exception.
*
* @param <E>
*/
@FunctionalInterface
public interface ThrowingRunnable<E extends Exception> {
void run() throws E;
}
}

103
dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.common;
import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
@ -5,6 +6,7 @@ import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
@ -14,58 +16,59 @@ import org.slf4j.LoggerFactory;
/** HDFS utility methods. */
public class HdfsSupport {
private static final Logger logger = LoggerFactory.getLogger(HdfsSupport.class);
private static final Logger logger = LoggerFactory.getLogger(HdfsSupport.class);
private HdfsSupport() {}
private HdfsSupport() {
}
/**
* Checks a path (file or dir) exists on HDFS.
*
* @param path Path to be checked
* @param configuration Configuration of hadoop env
*/
public static boolean exists(String path, Configuration configuration) {
logger.info("Removing path: {}", path);
return rethrowAsRuntimeException(
() -> {
Path f = new Path(path);
FileSystem fileSystem = FileSystem.get(configuration);
return fileSystem.exists(f);
});
}
/**
* Checks a path (file or dir) exists on HDFS.
*
* @param path Path to be checked
* @param configuration Configuration of hadoop env
*/
public static boolean exists(String path, Configuration configuration) {
logger.info("Removing path: {}", path);
return rethrowAsRuntimeException(
() -> {
Path f = new Path(path);
FileSystem fileSystem = FileSystem.get(configuration);
return fileSystem.exists(f);
});
}
/**
* Removes a path (file or dir) from HDFS.
*
* @param path Path to be removed
* @param configuration Configuration of hadoop env
*/
public static void remove(String path, Configuration configuration) {
logger.info("Removing path: {}", path);
rethrowAsRuntimeException(
() -> {
Path f = new Path(path);
FileSystem fileSystem = FileSystem.get(configuration);
if (fileSystem.exists(f)) {
fileSystem.delete(f, true);
}
});
}
/**
* Removes a path (file or dir) from HDFS.
*
* @param path Path to be removed
* @param configuration Configuration of hadoop env
*/
public static void remove(String path, Configuration configuration) {
logger.info("Removing path: {}", path);
rethrowAsRuntimeException(
() -> {
Path f = new Path(path);
FileSystem fileSystem = FileSystem.get(configuration);
if (fileSystem.exists(f)) {
fileSystem.delete(f, true);
}
});
}
/**
* Lists hadoop files located below path or alternatively lists subdirs under path.
*
* @param path Path to be listed for hadoop files
* @param configuration Configuration of hadoop env
* @return List with string locations of hadoop files
*/
public static List<String> listFiles(String path, Configuration configuration) {
logger.info("Listing files in path: {}", path);
return rethrowAsRuntimeException(
() ->
Arrays.stream(FileSystem.get(configuration).listStatus(new Path(path)))
.filter(FileStatus::isDirectory)
.map(x -> x.getPath().toString())
.collect(Collectors.toList()));
}
/**
* Lists hadoop files located below path or alternatively lists subdirs under path.
*
* @param path Path to be listed for hadoop files
* @param configuration Configuration of hadoop env
* @return List with string locations of hadoop files
*/
public static List<String> listFiles(String path, Configuration configuration) {
logger.info("Listing files in path: {}", path);
return rethrowAsRuntimeException(
() -> Arrays
.stream(FileSystem.get(configuration).listStatus(new Path(path)))
.filter(FileStatus::isDirectory)
.map(x -> x.getPath().toString())
.collect(Collectors.toList()));
}
}

121
dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java
View File

@ -1,74 +1,75 @@
package eu.dnetlib.dhp.common;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
import java.util.Objects;
import java.util.function.Function;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
/** SparkSession utility methods. */
public class SparkSessionSupport {
private SparkSessionSupport() {}
private SparkSessionSupport() {
}
/**
* Runs a given function using SparkSession created using default builder and supplied SparkConf.
* Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created
* externally.
*
* @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession
*/
public static void runWithSparkSession(
SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
runWithSparkSession(
c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn);
}
/**
* Runs a given function using SparkSession created using default builder and supplied SparkConf. Stops SparkSession
* when SparkSession is managed. Allows to reuse SparkSession created externally.
*
* @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession
*/
public static void runWithSparkSession(
SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
runWithSparkSession(
c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn);
}
/**
* Runs a given function using SparkSession created with hive support and using default builder
* and supplied SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse
* SparkSession created externally.
*
* @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession
*/
public static void runWithSparkHiveSession(
SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
runWithSparkSession(
c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(),
conf,
isSparkSessionManaged,
fn);
}
/**
* Runs a given function using SparkSession created with hive support and using default builder and supplied
* SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created externally.
*
* @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession
*/
public static void runWithSparkHiveSession(
SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
runWithSparkSession(
c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(),
conf,
isSparkSessionManaged,
fn);
}
/**
* Runs a given function using SparkSession created using supplied builder and supplied SparkConf.
* Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created
* externally.
*
* @param sparkSessionBuilder Builder of SparkSession
* @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession
*/
public static void runWithSparkSession(
Function<SparkConf, SparkSession> sparkSessionBuilder,
SparkConf conf,
Boolean isSparkSessionManaged,
ThrowingConsumer<SparkSession, Exception> fn) {
SparkSession spark = null;
try {
spark = sparkSessionBuilder.apply(conf);
fn.accept(spark);
} catch (Exception e) {
throw new RuntimeException(e);
} finally {
if (Objects.nonNull(spark) && isSparkSessionManaged) {
spark.stop();
}
}
}
/**
* Runs a given function using SparkSession created using supplied builder and supplied SparkConf. Stops
* SparkSession when SparkSession is managed. Allows to reuse SparkSession created externally.
*
* @param sparkSessionBuilder Builder of SparkSession
* @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession
*/
public static void runWithSparkSession(
Function<SparkConf, SparkSession> sparkSessionBuilder,
SparkConf conf,
Boolean isSparkSessionManaged,
ThrowingConsumer<SparkSession, Exception> fn) {
SparkSession spark = null;
try {
spark = sparkSessionBuilder.apply(conf);
fn.accept(spark);
} catch (Exception e) {
throw new RuntimeException(e);
} finally {
if (Objects.nonNull(spark) && isSparkSessionManaged) {
spark.stop();
}
}
}
}

124
dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.common;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingRunnable;
@ -6,69 +7,70 @@ import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingSupplier;
/** Exception handling utility methods. */
public class ThrowingSupport {
private ThrowingSupport() {}
private ThrowingSupport() {
}
/**
* Executes given runnable and rethrows any exceptions as RuntimeException.
*
* @param fn Runnable to be executed
* @param <E> Type of exception thrown
*/
public static <E extends Exception> void rethrowAsRuntimeException(ThrowingRunnable<E> fn) {
try {
fn.run();
} catch (Exception e) {
throw new RuntimeException(e);
}
}
/**
* Executes given runnable and rethrows any exceptions as RuntimeException.
*
* @param fn Runnable to be executed
* @param <E> Type of exception thrown
*/
public static <E extends Exception> void rethrowAsRuntimeException(ThrowingRunnable<E> fn) {
try {
fn.run();
} catch (Exception e) {
throw new RuntimeException(e);
}
}
/**
* Executes given runnable and rethrows any exceptions as RuntimeException with custom message.
*
* @param fn Runnable to be executed
* @param msg Message to be set for rethrown exception
* @param <E> Type of exception thrown
*/
public static <E extends Exception> void rethrowAsRuntimeException(
ThrowingRunnable<E> fn, String msg) {
try {
fn.run();
} catch (Exception e) {
throw new RuntimeException(msg, e);
}
}
/**
* Executes given runnable and rethrows any exceptions as RuntimeException with custom message.
*
* @param fn Runnable to be executed
* @param msg Message to be set for rethrown exception
* @param <E> Type of exception thrown
*/
public static <E extends Exception> void rethrowAsRuntimeException(
ThrowingRunnable<E> fn, String msg) {
try {
fn.run();
} catch (Exception e) {
throw new RuntimeException(msg, e);
}
}
/**
* Executes given supplier and rethrows any exceptions as RuntimeException.
*
* @param fn Supplier to be executed
* @param <T> Type of returned value
* @param <E> Type of exception thrown
* @return Result of supplier execution
*/
public static <T, E extends Exception> T rethrowAsRuntimeException(ThrowingSupplier<T, E> fn) {
try {
return fn.get();
} catch (Exception e) {
throw new RuntimeException(e);
}
}
/**
* Executes given supplier and rethrows any exceptions as RuntimeException.
*
* @param fn Supplier to be executed
* @param <T> Type of returned value
* @param <E> Type of exception thrown
* @return Result of supplier execution
*/
public static <T, E extends Exception> T rethrowAsRuntimeException(ThrowingSupplier<T, E> fn) {
try {
return fn.get();
} catch (Exception e) {
throw new RuntimeException(e);
}
}
/**
* Executes given supplier and rethrows any exceptions as RuntimeException with custom message.
*
* @param fn Supplier to be executed
* @param msg Message to be set for rethrown exception
* @param <T> Type of returned value
* @param <E> Type of exception thrown
* @return Result of supplier execution
*/
public static <T, E extends Exception> T rethrowAsRuntimeException(
ThrowingSupplier<T, E> fn, String msg) {
try {
return fn.get();
} catch (Exception e) {
throw new RuntimeException(msg, e);
}
}
/**
* Executes given supplier and rethrows any exceptions as RuntimeException with custom message.
*
* @param fn Supplier to be executed
* @param msg Message to be set for rethrown exception
* @param <T> Type of returned value
* @param <E> Type of exception thrown
* @return Result of supplier execution
*/
public static <T, E extends Exception> T rethrowAsRuntimeException(
ThrowingSupplier<T, E> fn, String msg) {
try {
return fn.get();
} catch (Exception e) {
throw new RuntimeException(msg, e);
}
}
}

175
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java
View File

@ -1,120 +1,121 @@
package eu.dnetlib.dhp.model.mdstore;
import eu.dnetlib.dhp.utils.DHPUtils;
import java.io.Serializable;
import eu.dnetlib.dhp.utils.DHPUtils;
/** This class models a record inside the new Metadata store collection on HDFS * */
public class MetadataRecord implements Serializable {
/** The D-Net Identifier associated to the record */
private String id;
/** The D-Net Identifier associated to the record */
private String id;
/** The original Identifier of the record */
private String originalId;
/** The original Identifier of the record */
private String originalId;
/** The encoding of the record, should be JSON or XML */
private String encoding;
/** The encoding of the record, should be JSON or XML */
private String encoding;
/**
* The information about the provenance of the record see @{@link Provenance} for the model of
* this information
*/
private Provenance provenance;
/**
* The information about the provenance of the record see @{@link Provenance} for the model of this information
*/
private Provenance provenance;
/** The content of the metadata */
private String body;
/** The content of the metadata */
private String body;
/** the date when the record has been stored */
private long dateOfCollection;
/** the date when the record has been stored */
private long dateOfCollection;
/** the date when the record has been stored */
private long dateOfTransformation;
/** the date when the record has been stored */
private long dateOfTransformation;
public MetadataRecord() {
this.dateOfCollection = System.currentTimeMillis();
}
public MetadataRecord() {
this.dateOfCollection = System.currentTimeMillis();
}
public MetadataRecord(
String originalId,
String encoding,
Provenance provenance,
String body,
long dateOfCollection) {
public MetadataRecord(
String originalId,
String encoding,
Provenance provenance,
String body,
long dateOfCollection) {
this.originalId = originalId;
this.encoding = encoding;
this.provenance = provenance;
this.body = body;
this.dateOfCollection = dateOfCollection;
this.id = DHPUtils.generateIdentifier(originalId, this.provenance.getNsPrefix());
}
this.originalId = originalId;
this.encoding = encoding;
this.provenance = provenance;
this.body = body;
this.dateOfCollection = dateOfCollection;
this.id = DHPUtils.generateIdentifier(originalId, this.provenance.getNsPrefix());
}
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public void setId(String id) {
this.id = id;
}
public String getOriginalId() {
return originalId;
}
public String getOriginalId() {
return originalId;
}
public void setOriginalId(String originalId) {
this.originalId = originalId;
}
public void setOriginalId(String originalId) {
this.originalId = originalId;
}
public String getEncoding() {
return encoding;
}
public String getEncoding() {
return encoding;
}
public void setEncoding(String encoding) {
this.encoding = encoding;
}
public void setEncoding(String encoding) {
this.encoding = encoding;
}
public Provenance getProvenance() {
return provenance;
}
public Provenance getProvenance() {
return provenance;
}
public void setProvenance(Provenance provenance) {
this.provenance = provenance;
}
public void setProvenance(Provenance provenance) {
this.provenance = provenance;
}
public String getBody() {
return body;
}
public String getBody() {
return body;
}
public void setBody(String body) {
this.body = body;
}
public void setBody(String body) {
this.body = body;
}
public long getDateOfCollection() {
return dateOfCollection;
}
public long getDateOfCollection() {
return dateOfCollection;
}
public void setDateOfCollection(long dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
public void setDateOfCollection(long dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
public long getDateOfTransformation() {
return dateOfTransformation;
}
public long getDateOfTransformation() {
return dateOfTransformation;
}
public void setDateOfTransformation(long dateOfTransformation) {
this.dateOfTransformation = dateOfTransformation;
}
public void setDateOfTransformation(long dateOfTransformation) {
this.dateOfTransformation = dateOfTransformation;
}
@Override
public boolean equals(Object o) {
if (!(o instanceof MetadataRecord)) {
return false;
}
return ((MetadataRecord) o).getId().equalsIgnoreCase(id);
}
@Override
public boolean equals(Object o) {
if (!(o instanceof MetadataRecord)) {
return false;
}
return ((MetadataRecord) o).getId().equalsIgnoreCase(id);
}
@Override
public int hashCode() {
return id.hashCode();
}
@Override
public int hashCode() {
return id.hashCode();
}
}

61
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java
View File

@ -1,49 +1,52 @@
package eu.dnetlib.dhp.model.mdstore;
import java.io.Serializable;
/**
* @author Sandro La Bruzzo
* <p>Provenace class models the provenance of the record in the metadataStore It contains the
* identifier and the name of the datasource that gives the record
* <p>
* Provenace class models the provenance of the record in the metadataStore It contains the identifier and the
* name of the datasource that gives the record
*/
public class Provenance implements Serializable {
private String datasourceId;
private String datasourceId;
private String datasourceName;
private String datasourceName;
private String nsPrefix;
private String nsPrefix;
public Provenance() {}
public Provenance() {
}
public Provenance(String datasourceId, String datasourceName, String nsPrefix) {
this.datasourceId = datasourceId;
this.datasourceName = datasourceName;
this.nsPrefix = nsPrefix;
}
public Provenance(String datasourceId, String datasourceName, String nsPrefix) {
this.datasourceId = datasourceId;
this.datasourceName = datasourceName;
this.nsPrefix = nsPrefix;
}
public String getDatasourceId() {
return datasourceId;
}
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public String getDatasourceName() {
return datasourceName;
}
public String getDatasourceName() {
return datasourceName;
}
public void setDatasourceName(String datasourceName) {
this.datasourceName = datasourceName;
}
public void setDatasourceName(String datasourceName) {
this.datasourceName = datasourceName;
}
public String getNsPrefix() {
return nsPrefix;
}
public String getNsPrefix() {
return nsPrefix;
}
public void setNsPrefix(String nsPrefix) {
this.nsPrefix = nsPrefix;
}
public void setNsPrefix(String nsPrefix) {
this.nsPrefix = nsPrefix;
}
}

13
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdException.java
View File

@ -1,12 +1,13 @@
package eu.dnetlib.dhp.parser.utility;
public class VtdException extends Exception {
public VtdException(final Exception e) {
super(e);
}
public VtdException(final Exception e) {
super(e);
}
public VtdException(final Throwable e) {
super(e);
}
public VtdException(final Throwable e) {
super(e);
}
}

169
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java
View File

@ -1,105 +1,110 @@
package eu.dnetlib.dhp.parser.utility;
import com.ximpleware.AutoPilot;
import com.ximpleware.VTDNav;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import com.ximpleware.AutoPilot;
import com.ximpleware.VTDNav;
/** Created by sandro on 9/29/16. */
public class VtdUtilityParser {
public static List<Node> getTextValuesWithAttributes(
final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes)
throws VtdException {
final List<Node> results = new ArrayList<>();
try {
ap.selectXPath(xpath);
public static List<Node> getTextValuesWithAttributes(
final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes)
throws VtdException {
final List<Node> results = new ArrayList<>();
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
final Node currentNode = new Node();
int t = vn.getText();
if (t >= 0) {
currentNode.setTextValue(vn.toNormalizedString(t));
}
currentNode.setAttributes(getAttributes(vn, attributes));
results.add(currentNode);
}
return results;
} catch (Exception e) {
throw new VtdException(e);
}
}
while (ap.evalXPath() != -1) {
final Node currentNode = new Node();
int t = vn.getText();
if (t >= 0) {
currentNode.setTextValue(vn.toNormalizedString(t));
}
currentNode.setAttributes(getAttributes(vn, attributes));
results.add(currentNode);
}
return results;
} catch (Exception e) {
throw new VtdException(e);
}
}
private static Map<String, String> getAttributes(final VTDNav vn, final List<String> attributes) {
final Map<String, String> currentAttributes = new HashMap<>();
if (attributes != null) {
private static Map<String, String> getAttributes(final VTDNav vn, final List<String> attributes) {
final Map<String, String> currentAttributes = new HashMap<>();
if (attributes != null) {
attributes.forEach(
attributeKey -> {
try {
int attr = vn.getAttrVal(attributeKey);
if (attr > -1) {
currentAttributes.put(attributeKey, vn.toNormalizedString(attr));
}
} catch (Throwable e) {
throw new RuntimeException(e);
}
});
}
return currentAttributes;
}
attributes
.forEach(
attributeKey -> {
try {
int attr = vn.getAttrVal(attributeKey);
if (attr > -1) {
currentAttributes.put(attributeKey, vn.toNormalizedString(attr));
}
} catch (Throwable e) {
throw new RuntimeException(e);
}
});
}
return currentAttributes;
}
public static List<String> getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath)
throws VtdException {
List<String> results = new ArrayList<>();
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t > -1) results.add(vn.toNormalizedString(t));
}
return results;
} catch (Exception e) {
throw new VtdException(e);
}
}
public static List<String> getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath)
throws VtdException {
List<String> results = new ArrayList<>();
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t > -1)
results.add(vn.toNormalizedString(t));
}
return results;
} catch (Exception e) {
throw new VtdException(e);
}
}
public static String getSingleValue(final AutoPilot ap, final VTDNav nav, final String xpath)
throws VtdException {
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
int it = nav.getText();
if (it > -1) return nav.toNormalizedString(it);
}
return null;
} catch (Exception e) {
throw new VtdException(e);
}
}
public static String getSingleValue(final AutoPilot ap, final VTDNav nav, final String xpath)
throws VtdException {
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
int it = nav.getText();
if (it > -1)
return nav.toNormalizedString(it);
}
return null;
} catch (Exception e) {
throw new VtdException(e);
}
}
public static class Node {
public static class Node {
private String textValue;
private String textValue;
private Map<String, String> attributes;
private Map<String, String> attributes;
public String getTextValue() {
return textValue;
}
public String getTextValue() {
return textValue;
}
public void setTextValue(final String textValue) {
this.textValue = textValue;
}
public void setTextValue(final String textValue) {
this.textValue = textValue;
}
public Map<String, String> getAttributes() {
return attributes;
}
public Map<String, String> getAttributes() {
return attributes;
}
public void setAttributes(final Map<String, String> attributes) {
this.attributes = attributes;
}
}
public void setAttributes(final Map<String, String> attributes) {
this.attributes = attributes;
}
}
}

107
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
View File

@ -1,70 +1,75 @@
package eu.dnetlib.dhp.utils;
import com.jayway.jsonpath.JsonPath;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import net.minidev.json.JSONArray;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.codec.binary.Base64OutputStream;
import org.apache.commons.codec.binary.Hex;
import com.jayway.jsonpath.JsonPath;
import net.minidev.json.JSONArray;
public class DHPUtils {
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8"));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");
return null;
}
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8"));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");
return null;
}
}
public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
}
public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
}
public static String compressString(final String input) {
try (ByteArrayOutputStream out = new ByteArrayOutputStream();
Base64OutputStream b64os = new Base64OutputStream(out)) {
GZIPOutputStream gzip = new GZIPOutputStream(b64os);
gzip.write(input.getBytes(StandardCharsets.UTF_8));
gzip.close();
return out.toString();
} catch (Throwable e) {
return null;
}
}
public static String compressString(final String input) {
try (ByteArrayOutputStream out = new ByteArrayOutputStream();
Base64OutputStream b64os = new Base64OutputStream(out)) {
GZIPOutputStream gzip = new GZIPOutputStream(b64os);
gzip.write(input.getBytes(StandardCharsets.UTF_8));
gzip.close();
return out.toString();
} catch (Throwable e) {
return null;
}
}
public static String decompressString(final String input) {
byte[] byteArray = Base64.decodeBase64(input.getBytes());
int len;
try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray)));
ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) {
byte[] buffer = new byte[1024];
while ((len = gis.read(buffer)) != -1) {
bos.write(buffer, 0, len);
}
return bos.toString();
} catch (Exception e) {
return null;
}
}
public static String decompressString(final String input) {
byte[] byteArray = Base64.decodeBase64(input.getBytes());
int len;
try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray)));
ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) {
byte[] buffer = new byte[1024];
while ((len = gis.read(buffer)) != -1) {
bos.write(buffer, 0, len);
}
return bos.toString();
} catch (Exception e) {
return null;
}
}
public static String getJPathString(final String jsonPath, final String json) {
try {
Object o = JsonPath.read(json, jsonPath);
if (o instanceof String) return (String) o;
if (o instanceof JSONArray && ((JSONArray) o).size() > 0)
return (String) ((JSONArray) o).get(0);
return o.toString();
} catch (Exception e) {
return "";
}
}
public static String getJPathString(final String jsonPath, final String json) {
try {
Object o = JsonPath.read(json, jsonPath);
if (o instanceof String)
return (String) o;
if (o instanceof JSONArray && ((JSONArray) o).size() > 0)
return (String) ((JSONArray) o).get(0);
return o.toString();
} catch (Exception e) {
return "";
}
}
}

28
dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java
View File

@ -1,24 +1,26 @@
package eu.dnetlib.dhp.utils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.cxf.jaxws.JaxWsProxyFactoryBean;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class ISLookupClientFactory {
private static final Log log = LogFactory.getLog(ISLookupClientFactory.class);
private static final Log log = LogFactory.getLog(ISLookupClientFactory.class);
public static ISLookUpService getLookUpService(final String isLookupUrl) {
return getServiceStub(ISLookUpService.class, isLookupUrl);
}
public static ISLookUpService getLookUpService(final String isLookupUrl) {
return getServiceStub(ISLookUpService.class, isLookupUrl);
}
@SuppressWarnings("unchecked")
private static <T> T getServiceStub(final Class<T> clazz, final String endpoint) {
log.info(String.format("creating %s stub from %s", clazz.getName(), endpoint));
final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean();
jaxWsProxyFactory.setServiceClass(clazz);
jaxWsProxyFactory.setAddress(endpoint);
return (T) jaxWsProxyFactory.create();
}
@SuppressWarnings("unchecked")
private static <T> T getServiceStub(final Class<T> clazz, final String endpoint) {
log.info(String.format("creating %s stub from %s", clazz.getName(), endpoint));
final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean();
jaxWsProxyFactory.setServiceClass(clazz);
jaxWsProxyFactory.setAddress(endpoint);
return (T) jaxWsProxyFactory.create();
}
}

34
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.utils.saxon;
import net.sf.saxon.expr.XPathContext;
@ -9,25 +10,24 @@ import net.sf.saxon.trans.XPathException;
public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition {
public static String DEFAULT_SAXON_EXT_NS_URI =
"http://www.d-net.research-infrastructures.eu/saxon-extension";
public static String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension";
public abstract String getName();
public abstract String getName();
public abstract Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException;
public abstract Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException;
@Override
public StructuredQName getFunctionQName() {
return new StructuredQName("dnet", DEFAULT_SAXON_EXT_NS_URI, getName());
}
@Override
public StructuredQName getFunctionQName() {
return new StructuredQName("dnet", DEFAULT_SAXON_EXT_NS_URI, getName());
}
@Override
public ExtensionFunctionCall makeCallExpression() {
return new ExtensionFunctionCall() {
@Override
public Sequence call(XPathContext context, Sequence[] arguments) throws XPathException {
return doCall(context, arguments);
}
};
}
@Override
public ExtensionFunctionCall makeCallExpression() {
return new ExtensionFunctionCall() {
@Override
public Sequence call(XPathContext context, Sequence[] arguments) throws XPathException {
return doCall(context, arguments);
}
};
}
}

94
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java
View File

@ -1,9 +1,11 @@
package eu.dnetlib.dhp.utils.saxon;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.GregorianCalendar;
import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Item;
import net.sf.saxon.om.Sequence;
@ -13,55 +15,59 @@ import net.sf.saxon.value.StringValue;
public class ExtractYear extends AbstractExtensionFunction {
private static final String[] dateFormats = {"yyyy-MM-dd", "yyyy/MM/dd"};
private static final String[] dateFormats = {
"yyyy-MM-dd", "yyyy/MM/dd"
};
@Override
public String getName() {
return "extractYear";
}
@Override
public String getName() {
return "extractYear";
}
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
return new StringValue("");
}
final Item item = arguments[0].head();
if (item == null) {
return new StringValue("");
}
return new StringValue(_year(item.getStringValue()));
}
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
return new StringValue("");
}
final Item item = arguments[0].head();
if (item == null) {
return new StringValue("");
}
return new StringValue(_year(item.getStringValue()));
}
@Override
public int getMinimumNumberOfArguments() {
return 0;
}
@Override
public int getMinimumNumberOfArguments() {
return 0;
}
@Override
public int getMaximumNumberOfArguments() {
return 1;
}
@Override
public int getMaximumNumberOfArguments() {
return 1;
}
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {SequenceType.OPTIONAL_ITEM};
}
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {
SequenceType.OPTIONAL_ITEM
};
}
@Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING;
}
@Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING;
}
private String _year(String s) {
Calendar c = new GregorianCalendar();
for (String format : dateFormats) {
try {
c.setTime(new SimpleDateFormat(format).parse(s));
String year = String.valueOf(c.get(Calendar.YEAR));
return year;
} catch (ParseException e) {
}
}
return "";
}
private String _year(String s) {
Calendar c = new GregorianCalendar();
for (String format : dateFormats) {
try {
c.setTime(new SimpleDateFormat(format).parse(s));
String year = String.valueOf(c.get(Calendar.YEAR));
return year;
} catch (ParseException e) {
}
}
return "";
}
}

92
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java
View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.utils.saxon;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Sequence;
import net.sf.saxon.trans.XPathException;
@ -11,57 +13,59 @@ import net.sf.saxon.value.StringValue;
public class NormalizeDate extends AbstractExtensionFunction {
private static final String[] normalizeDateFormats = {
"yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy"
};
private static final String[] normalizeDateFormats = {
"yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy"
};
private static final String normalizeOutFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'");
private static final String normalizeOutFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'");
@Override
public String getName() {
return "normalizeDate";
}
@Override
public String getName() {
return "normalizeDate";
}
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
return new StringValue("");
}
String s = arguments[0].head().getStringValue();
return new StringValue(_year(s));
}
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
return new StringValue("");
}
String s = arguments[0].head().getStringValue();
return new StringValue(_year(s));
}
@Override
public int getMinimumNumberOfArguments() {
return 0;
}
@Override
public int getMinimumNumberOfArguments() {
return 0;
}
@Override
public int getMaximumNumberOfArguments() {
return 1;
}
@Override
public int getMaximumNumberOfArguments() {
return 1;
}
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {SequenceType.OPTIONAL_ITEM};
}
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {
SequenceType.OPTIONAL_ITEM
};
}
@Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING;
}
@Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING;
}
private String _year(String s) {
final String date = s != null ? s.trim() : "";
private String _year(String s) {
final String date = s != null ? s.trim() : "";
for (String format : normalizeDateFormats) {
try {
Date parse = new SimpleDateFormat(format).parse(date);
String res = new SimpleDateFormat(normalizeOutFormat).format(parse);
return res;
} catch (ParseException e) {
}
}
return "";
}
for (String format : normalizeDateFormats) {
try {
Date parse = new SimpleDateFormat(format).parse(date);
String res = new SimpleDateFormat(normalizeOutFormat).format(parse);
return res;
} catch (ParseException e) {
}
}
return "";
}
}

82
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java
View File

@ -1,59 +1,63 @@
package eu.dnetlib.dhp.utils.saxon;
import org.apache.commons.lang3.StringUtils;
import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Item;
import net.sf.saxon.om.Sequence;
import net.sf.saxon.trans.XPathException;
import net.sf.saxon.value.SequenceType;
import net.sf.saxon.value.StringValue;
import org.apache.commons.lang3.StringUtils;
public class PickFirst extends AbstractExtensionFunction {
@Override
public String getName() {
return "pickFirst";
}
@Override
public String getName() {
return "pickFirst";
}
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
return new StringValue("");
}
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
return new StringValue("");
}
final String s1 = getValue(arguments[0]);
final String s2 = getValue(arguments[1]);
final String s1 = getValue(arguments[0]);
final String s2 = getValue(arguments[1]);
return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : "");
}
return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : "");
}
private String getValue(final Sequence arg) throws XPathException {
if (arg != null) {
final Item item = arg.head();
if (item != null) {
return item.getStringValue();
}
}
return "";
}
private String getValue(final Sequence arg) throws XPathException {
if (arg != null) {
final Item item = arg.head();
if (item != null) {
return item.getStringValue();
}
}
return "";
}
@Override
public int getMinimumNumberOfArguments() {
return 0;
}
@Override
public int getMinimumNumberOfArguments() {
return 0;
}
@Override
public int getMaximumNumberOfArguments() {
return 2;
}
@Override
public int getMaximumNumberOfArguments() {
return 2;
}
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {SequenceType.OPTIONAL_ITEM};
}
@Override
public SequenceType[] getArgumentTypes() {
return new SequenceType[] {
SequenceType.OPTIONAL_ITEM
};
}
@Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING;
}
@Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING;
}
}

33
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java
View File

@ -1,29 +1,32 @@
package eu.dnetlib.dhp.utils.saxon;
import java.io.StringReader;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.stream.StreamSource;
import net.sf.saxon.Configuration;
import net.sf.saxon.TransformerFactoryImpl;
public class SaxonTransformerFactory {
/**
* Creates the index record transformer from the given XSLT
*
* @param xslt
* @return
* @throws TransformerException
*/
public static Transformer newInstance(final String xslt) throws TransformerException {
/**
* Creates the index record transformer from the given XSLT
*
* @param xslt
* @return
* @throws TransformerException
*/
public static Transformer newInstance(final String xslt) throws TransformerException {
final TransformerFactoryImpl factory = new TransformerFactoryImpl();
final Configuration conf = factory.getConfiguration();
conf.registerExtensionFunction(new ExtractYear());
conf.registerExtensionFunction(new NormalizeDate());
conf.registerExtensionFunction(new PickFirst());
final TransformerFactoryImpl factory = new TransformerFactoryImpl();
final Configuration conf = factory.getConfiguration();
conf.registerExtensionFunction(new ExtractYear());
conf.registerExtensionFunction(new NormalizeDate());
conf.registerExtensionFunction(new PickFirst());
return factory.newTransformer(new StreamSource(new StringReader(xslt)));
}
return factory.newTransformer(new StreamSource(new StringReader(xslt)));
}
}

103
dhp-common/src/main/java/eu/dnetlib/message/Message.java
View File

@ -1,73 +1,76 @@
package eu.dnetlib.message;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.IOException;
import java.util.Map;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class Message {
private String workflowId;
private String workflowId;
private String jobName;
private String jobName;
private MessageType type;
private MessageType type;
private Map<String, String> body;
private Map<String, String> body;
public static Message fromJson(final String json) throws IOException {
final ObjectMapper jsonMapper = new ObjectMapper();
return jsonMapper.readValue(json, Message.class);
}
public static Message fromJson(final String json) throws IOException {
final ObjectMapper jsonMapper = new ObjectMapper();
return jsonMapper.readValue(json, Message.class);
}
public Message() {}
public Message() {
}
public Message(String workflowId, String jobName, MessageType type, Map<String, String> body) {
this.workflowId = workflowId;
this.jobName = jobName;
this.type = type;
this.body = body;
}
public Message(String workflowId, String jobName, MessageType type, Map<String, String> body) {
this.workflowId = workflowId;
this.jobName = jobName;
this.type = type;
this.body = body;
}
public String getWorkflowId() {
return workflowId;
}
public String getWorkflowId() {
return workflowId;
}
public void setWorkflowId(String workflowId) {
this.workflowId = workflowId;
}
public void setWorkflowId(String workflowId) {
this.workflowId = workflowId;
}
public String getJobName() {
return jobName;
}
public String getJobName() {
return jobName;
}
public void setJobName(String jobName) {
this.jobName = jobName;
}
public void setJobName(String jobName) {
this.jobName = jobName;
}
public MessageType getType() {
return type;
}
public MessageType getType() {
return type;
}
public void setType(MessageType type) {
this.type = type;
}
public void setType(MessageType type) {
this.type = type;
}
public Map<String, String> getBody() {
return body;
}
public Map<String, String> getBody() {
return body;
}
public void setBody(Map<String, String> body) {
this.body = body;
}
public void setBody(Map<String, String> body) {
this.body = body;
}
@Override
public String toString() {
final ObjectMapper jsonMapper = new ObjectMapper();
try {
return jsonMapper.writeValueAsString(this);
} catch (JsonProcessingException e) {
return null;
}
}
@Override
public String toString() {
final ObjectMapper jsonMapper = new ObjectMapper();
try {
return jsonMapper.writeValueAsString(this);
} catch (JsonProcessingException e) {
return null;
}
}
}

68
dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java
View File

@ -1,45 +1,47 @@
package eu.dnetlib.message;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.LinkedBlockingQueue;
import com.rabbitmq.client.AMQP;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.DefaultConsumer;
import com.rabbitmq.client.Envelope;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.LinkedBlockingQueue;
public class MessageConsumer extends DefaultConsumer {
final LinkedBlockingQueue<Message> queueMessages;
final LinkedBlockingQueue<Message> queueMessages;
/**
* Constructs a new instance and records its association to the passed-in channel.
*
* @param channel the channel to which this consumer is attached
* @param queueMessages
*/
public MessageConsumer(Channel channel, LinkedBlockingQueue<Message> queueMessages) {
super(channel);
this.queueMessages = queueMessages;
}
/**
* Constructs a new instance and records its association to the passed-in channel.
*
* @param channel the channel to which this consumer is attached
* @param queueMessages
*/
public MessageConsumer(Channel channel, LinkedBlockingQueue<Message> queueMessages) {
super(channel);
this.queueMessages = queueMessages;
}
@Override
public void handleDelivery(
String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body)
throws IOException {
final String json = new String(body, StandardCharsets.UTF_8);
Message message = Message.fromJson(json);
try {
this.queueMessages.put(message);
System.out.println("Receiving Message " + message);
} catch (InterruptedException e) {
if (message.getType() == MessageType.REPORT)
throw new RuntimeException("Error on sending message");
else {
// TODO LOGGING EXCEPTION
}
} finally {
getChannel().basicAck(envelope.getDeliveryTag(), false);
}
}
@Override
public void handleDelivery(
String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body)
throws IOException {
final String json = new String(body, StandardCharsets.UTF_8);
Message message = Message.fromJson(json);
try {
this.queueMessages.put(message);
System.out.println("Receiving Message " + message);
} catch (InterruptedException e) {
if (message.getType() == MessageType.REPORT)
throw new RuntimeException("Error on sending message");
else {
// TODO LOGGING EXCEPTION
}
} finally {
getChannel().basicAck(envelope.getDeliveryTag(), false);
}
}
}

208
dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java
View File

@ -1,134 +1,136 @@
package eu.dnetlib.message;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.Connection;
import com.rabbitmq.client.ConnectionFactory;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.TimeoutException;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.Connection;
import com.rabbitmq.client.ConnectionFactory;
public class MessageManager {
private final String messageHost;
private final String messageHost;
private final String username;
private final String username;
private final String password;
private final String password;
private Connection connection;
private Connection connection;
private Map<String, Channel> channels = new HashMap<>();
private Map<String, Channel> channels = new HashMap<>();
private boolean durable;
private boolean durable;
private boolean autodelete;
private boolean autodelete;
private final LinkedBlockingQueue<Message> queueMessages;
private final LinkedBlockingQueue<Message> queueMessages;
public MessageManager(
String messageHost,
String username,
String password,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages;
this.messageHost = messageHost;
this.username = username;
this.password = password;
}
public MessageManager(
String messageHost,
String username,
String password,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages;
this.messageHost = messageHost;
this.username = username;
this.password = password;
}
public MessageManager(
String messageHost,
String username,
String password,
boolean durable,
boolean autodelete,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages;
this.messageHost = messageHost;
this.username = username;
this.password = password;
public MessageManager(
String messageHost,
String username,
String password,
boolean durable,
boolean autodelete,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages;
this.messageHost = messageHost;
this.username = username;
this.password = password;
this.durable = durable;
this.autodelete = autodelete;
}
this.durable = durable;
this.autodelete = autodelete;
}
private Connection createConnection() throws IOException, TimeoutException {
ConnectionFactory factory = new ConnectionFactory();
factory.setHost(this.messageHost);
factory.setUsername(this.username);
factory.setPassword(this.password);
return factory.newConnection();
}
private Connection createConnection() throws IOException, TimeoutException {
ConnectionFactory factory = new ConnectionFactory();
factory.setHost(this.messageHost);
factory.setUsername(this.username);
factory.setPassword(this.password);
return factory.newConnection();
}
private Channel createChannel(
final Connection connection,
final String queueName,
final boolean durable,
final boolean autodelete)
throws Exception {
Map<String, Object> args = new HashMap<>();
args.put("x-message-ttl", 10000);
Channel channel = connection.createChannel();
channel.queueDeclare(queueName, durable, false, this.autodelete, args);
return channel;
}
private Channel createChannel(
final Connection connection,
final String queueName,
final boolean durable,
final boolean autodelete)
throws Exception {
Map<String, Object> args = new HashMap<>();
args.put("x-message-ttl", 10000);
Channel channel = connection.createChannel();
channel.queueDeclare(queueName, durable, false, this.autodelete, args);
return channel;
}
private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete)
throws Exception {
if (channels.containsKey(queueName)) {
return channels.get(queueName);
}
private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete)
throws Exception {
if (channels.containsKey(queueName)) {
return channels.get(queueName);
}
if (this.connection == null) {
this.connection = createConnection();
}
channels.put(queueName, createChannel(this.connection, queueName, durable, autodelete));
return channels.get(queueName);
}
if (this.connection == null) {
this.connection = createConnection();
}
channels.put(queueName, createChannel(this.connection, queueName, durable, autodelete));
return channels.get(queueName);
}
public void close() throws IOException {
channels
.values()
.forEach(
ch -> {
try {
ch.close();
} catch (Exception e) {
// TODO LOG
}
});
public void close() throws IOException {
channels
.values()
.forEach(
ch -> {
try {
ch.close();
} catch (Exception e) {
// TODO LOG
}
});
this.connection.close();
}
this.connection.close();
}
public boolean sendMessage(final Message message, String queueName) throws Exception {
try {
Channel channel = getOrCreateChannel(queueName, this.durable, this.autodelete);
channel.basicPublish("", queueName, null, message.toString().getBytes());
return true;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
public boolean sendMessage(final Message message, String queueName) throws Exception {
try {
Channel channel = getOrCreateChannel(queueName, this.durable, this.autodelete);
channel.basicPublish("", queueName, null, message.toString().getBytes());
return true;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
public boolean sendMessage(
final Message message, String queueName, boolean durable_var, boolean autodelete_var)
throws Exception {
try {
Channel channel = getOrCreateChannel(queueName, durable_var, autodelete_var);
channel.basicPublish("", queueName, null, message.toString().getBytes());
return true;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
public boolean sendMessage(
final Message message, String queueName, boolean durable_var, boolean autodelete_var)
throws Exception {
try {
Channel channel = getOrCreateChannel(queueName, durable_var, autodelete_var);
channel.basicPublish("", queueName, null, message.toString().getBytes());
return true;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
public void startConsumingMessage(
final String queueName, final boolean durable, final boolean autodelete) throws Exception {
public void startConsumingMessage(
final String queueName, final boolean durable, final boolean autodelete) throws Exception {
Channel channel = createChannel(createConnection(), queueName, durable, autodelete);
channel.basicConsume(queueName, false, new MessageConsumer(channel, queueMessages));
}
Channel channel = createChannel(createConnection(), queueName, durable, autodelete);
channel.basicConsume(queueName, false, new MessageConsumer(channel, queueMessages));
}
}

4
dhp-common/src/main/java/eu/dnetlib/message/MessageType.java
View File

@ -1,6 +1,6 @@
package eu.dnetlib.message;
public enum MessageType {
ONGOING,
REPORT
ONGOING, REPORT
}

29
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java
View File

@ -1,24 +1,25 @@
package eu.dnetlib.scholexplorer.relation;
import java.io.Serializable;
public class RelInfo implements Serializable {
private String original;
private String inverse;
private String original;
private String inverse;
public String getOriginal() {
return original;
}
public String getOriginal() {
return original;
}
public void setOriginal(String original) {
this.original = original;
}
public void setOriginal(String original) {
this.original = original;
}
public String getInverse() {
return inverse;
}
public String getInverse() {
return inverse;
}
public void setInverse(String inverse) {
this.inverse = inverse;
}
public void setInverse(String inverse) {
this.inverse = inverse;
}
}

16
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java
View File

@ -1,18 +1,20 @@
package eu.dnetlib.scholexplorer.relation;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.Serializable;
import java.util.HashMap;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
public static RelationMapper load() throws Exception {
public static RelationMapper load() throws Exception {
final String json =
IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json"));
final String json = IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json"));
ObjectMapper mapper = new ObjectMapper();
return mapper.readValue(json, RelationMapper.class);
}
ObjectMapper mapper = new ObjectMapper();
return mapper.readValue(json, RelationMapper.class);
}
}

110
dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.application;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -8,58 +9,59 @@ import org.junit.jupiter.api.Test;
public class ArgumentApplicationParserTest {
@Test
public void testParseParameter() throws Exception {
final String jsonConfiguration =
IOUtils.toString(
this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json"));
assertNotNull(jsonConfiguration);
ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(
new String[] {
"-p",
"value0",
"-a",
"value1",
"-n",
"value2",
"-u",
"value3",
"-ru",
"value4",
"-rp",
"value5",
"-rh",
"value6",
"-ro",
"value7",
"-rr",
"value8",
"-w",
"value9",
"-cc",
ArgumentApplicationParser.compressArgument(jsonConfiguration)
});
assertNotNull(parser.get("hdfsPath"));
assertNotNull(parser.get("apidescriptor"));
assertNotNull(parser.get("namenode"));
assertNotNull(parser.get("userHDFS"));
assertNotNull(parser.get("rabbitUser"));
assertNotNull(parser.get("rabbitPassWord"));
assertNotNull(parser.get("rabbitHost"));
assertNotNull(parser.get("rabbitOngoingQueue"));
assertNotNull(parser.get("rabbitReportQueue"));
assertNotNull(parser.get("workflowId"));
assertEquals("value0", parser.get("hdfsPath"));
assertEquals("value1", parser.get("apidescriptor"));
assertEquals("value2", parser.get("namenode"));
assertEquals("value3", parser.get("userHDFS"));
assertEquals("value4", parser.get("rabbitUser"));
assertEquals("value5", parser.get("rabbitPassWord"));
assertEquals("value6", parser.get("rabbitHost"));
assertEquals("value7", parser.get("rabbitOngoingQueue"));
assertEquals("value8", parser.get("rabbitReportQueue"));
assertEquals("value9", parser.get("workflowId"));
assertEquals(jsonConfiguration, parser.get("ccCoco"));
}
@Test
public void testParseParameter() throws Exception {
final String jsonConfiguration = IOUtils
.toString(
this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json"));
assertNotNull(jsonConfiguration);
ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser
.parseArgument(
new String[] {
"-p",
"value0",
"-a",
"value1",
"-n",
"value2",
"-u",
"value3",
"-ru",
"value4",
"-rp",
"value5",
"-rh",
"value6",
"-ro",
"value7",
"-rr",
"value8",
"-w",
"value9",
"-cc",
ArgumentApplicationParser.compressArgument(jsonConfiguration)
});
assertNotNull(parser.get("hdfsPath"));
assertNotNull(parser.get("apidescriptor"));
assertNotNull(parser.get("namenode"));
assertNotNull(parser.get("userHDFS"));
assertNotNull(parser.get("rabbitUser"));
assertNotNull(parser.get("rabbitPassWord"));
assertNotNull(parser.get("rabbitHost"));
assertNotNull(parser.get("rabbitOngoingQueue"));
assertNotNull(parser.get("rabbitReportQueue"));
assertNotNull(parser.get("workflowId"));
assertEquals("value0", parser.get("hdfsPath"));
assertEquals("value1", parser.get("apidescriptor"));
assertEquals("value2", parser.get("namenode"));
assertEquals("value3", parser.get("userHDFS"));
assertEquals("value4", parser.get("rabbitUser"));
assertEquals("value5", parser.get("rabbitPassWord"));
assertEquals("value6", parser.get("rabbitHost"));
assertEquals("value7", parser.get("rabbitOngoingQueue"));
assertEquals("value8", parser.get("rabbitReportQueue"));
assertEquals("value9", parser.get("workflowId"));
assertEquals(jsonConfiguration, parser.get("ccCoco"));
}
}

99
dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.common;
import static org.junit.jupiter.api.Assertions.*;
@ -8,6 +9,7 @@ import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.hadoop.conf.Configuration;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
@ -15,63 +17,64 @@ import org.junit.jupiter.api.io.TempDir;
public class HdfsSupportTest {
@Nested
class Remove {
@Nested
class Remove {
@Test
public void shouldThrowARuntimeExceptionOnError() {
// when
assertThrows(RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
}
@Test
public void shouldThrowARuntimeExceptionOnError() {
// when
assertThrows(RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
}
@Test
public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
// when
HdfsSupport.remove(tempDir.toString(), new Configuration());
@Test
public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
// when
HdfsSupport.remove(tempDir.toString(), new Configuration());
// then
assertFalse(Files.exists(tempDir));
}
// then
assertFalse(Files.exists(tempDir));
}
@Test
public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
// given
Path file = Files.createTempFile(tempDir, "p", "s");
@Test
public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
// given
Path file = Files.createTempFile(tempDir, "p", "s");
// when
HdfsSupport.remove(file.toString(), new Configuration());
// when
HdfsSupport.remove(file.toString(), new Configuration());
// then
assertFalse(Files.exists(file));
}
}
// then
assertFalse(Files.exists(file));
}
}
@Nested
class ListFiles {
@Nested
class ListFiles {
@Test
public void shouldThrowARuntimeExceptionOnError() {
// when
assertThrows(RuntimeException.class, () -> HdfsSupport.listFiles(null, new Configuration()));
}
@Test
public void shouldThrowARuntimeExceptionOnError() {
// when
assertThrows(RuntimeException.class, () -> HdfsSupport.listFiles(null, new Configuration()));
}
@Test
public void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
Path subDir1 = Files.createTempDirectory(tempDir, "list_me");
Path subDir2 = Files.createTempDirectory(tempDir, "list_me");
@Test
public void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
Path subDir1 = Files.createTempDirectory(tempDir, "list_me");
Path subDir2 = Files.createTempDirectory(tempDir, "list_me");
// when
List<String> paths = HdfsSupport.listFiles(tempDir.toString(), new Configuration());
// when
List<String> paths = HdfsSupport.listFiles(tempDir.toString(), new Configuration());
// then
assertEquals(2, paths.size());
List<String> expecteds =
Arrays.stream(new String[] {subDir1.toString(), subDir2.toString()})
.sorted()
.collect(Collectors.toList());
List<String> actuals = paths.stream().sorted().collect(Collectors.toList());
assertTrue(actuals.get(0).contains(expecteds.get(0)));
assertTrue(actuals.get(1).contains(expecteds.get(1)));
}
}
// then
assertEquals(2, paths.size());
List<String> expecteds = Arrays.stream(new String[] {
subDir1.toString(), subDir2.toString()
})
.sorted()
.collect(Collectors.toList());
List<String> actuals = paths.stream().sorted().collect(Collectors.toList());
assertTrue(actuals.get(0).contains(expecteds.get(0)));
assertTrue(actuals.get(1).contains(expecteds.get(1)));
}
}
}

75
dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java
View File

@ -1,55 +1,58 @@
package eu.dnetlib.dhp.common;
import static org.mockito.Mockito.*;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
import java.util.function.Function;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
public class SparkSessionSupportTest {
@Nested
class RunWithSparkSession {
@Nested
class RunWithSparkSession {
@Test
public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
throws Exception {
// given
SparkSession spark = mock(SparkSession.class);
SparkConf conf = mock(SparkConf.class);
Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class);
when(sparkSessionBuilder.apply(conf)).thenReturn(spark);
ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class);
@Test
public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
throws Exception {
// given
SparkSession spark = mock(SparkSession.class);
SparkConf conf = mock(SparkConf.class);
Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class);
when(sparkSessionBuilder.apply(conf)).thenReturn(spark);
ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class);
// when
SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, false, fn);
// when
SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, false, fn);
// then
verify(sparkSessionBuilder).apply(conf);
verify(fn).accept(spark);
verify(spark, never()).stop();
}
// then
verify(sparkSessionBuilder).apply(conf);
verify(fn).accept(spark);
verify(spark, never()).stop();
}
@Test
public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
throws Exception {
// given
SparkSession spark = mock(SparkSession.class);
SparkConf conf = mock(SparkConf.class);
Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class);
when(sparkSessionBuilder.apply(conf)).thenReturn(spark);
ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class);
@Test
public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
throws Exception {
// given
SparkSession spark = mock(SparkSession.class);
SparkConf conf = mock(SparkConf.class);
Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class);
when(sparkSessionBuilder.apply(conf)).thenReturn(spark);
ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class);
// when
SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, true, fn);
// when
SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, true, fn);
// then
verify(sparkSessionBuilder).apply(conf);
verify(fn).accept(spark);
verify(spark, times(1)).stop();
}
}
// then
verify(sparkSessionBuilder).apply(conf);
verify(fn).accept(spark);
verify(spark, times(1)).stop();
}
}
}

11
dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.model.mdstore;
import static org.junit.jupiter.api.Assertions.assertTrue;
@ -6,10 +7,10 @@ import org.junit.jupiter.api.Test;
public class MetadataRecordTest {
@Test
public void getTimestamp() {
@Test
public void getTimestamp() {
MetadataRecord r = new MetadataRecord();
assertTrue(r.getDateOfCollection() > 0);
}
MetadataRecord r = new MetadataRecord();
assertTrue(r.getDateOfCollection() > 0);
}
}

67
dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.message;
import static org.junit.jupiter.api.Assertions.*;
@ -5,46 +6,46 @@ import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import org.junit.jupiter.api.Test;
public class MessageTest {
@Test
public void fromJsonTest() throws IOException {
Message m = new Message();
m.setWorkflowId("wId");
m.setType(MessageType.ONGOING);
m.setJobName("Collection");
Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300");
body.put("ExecutionTime", "30s");
@Test
public void fromJsonTest() throws IOException {
Message m = new Message();
m.setWorkflowId("wId");
m.setType(MessageType.ONGOING);
m.setJobName("Collection");
Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300");
body.put("ExecutionTime", "30s");
m.setBody(body);
System.out.println("m = " + m);
Message m1 = Message.fromJson(m.toString());
assertEquals(m1.getWorkflowId(), m.getWorkflowId());
assertEquals(m1.getType(), m.getType());
assertEquals(m1.getJobName(), m.getJobName());
m.setBody(body);
System.out.println("m = " + m);
Message m1 = Message.fromJson(m.toString());
assertEquals(m1.getWorkflowId(), m.getWorkflowId());
assertEquals(m1.getType(), m.getType());
assertEquals(m1.getJobName(), m.getJobName());
assertNotNull(m1.getBody());
m1.getBody().keySet().forEach(it -> assertEquals(m1.getBody().get(it), m.getBody().get(it)));
assertEquals(m1.getJobName(), m.getJobName());
}
assertNotNull(m1.getBody());
m1.getBody().keySet().forEach(it -> assertEquals(m1.getBody().get(it), m.getBody().get(it)));
assertEquals(m1.getJobName(), m.getJobName());
}
@Test
public void toStringTest() {
final String expectedJson =
"{\"workflowId\":\"wId\",\"jobName\":\"Collection\",\"type\":\"ONGOING\",\"body\":{\"ExecutionTime\":\"30s\",\"parsedItem\":\"300\"}}";
Message m = new Message();
m.setWorkflowId("wId");
m.setType(MessageType.ONGOING);
m.setJobName("Collection");
Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300");
body.put("ExecutionTime", "30s");
@Test
public void toStringTest() {
final String expectedJson = "{\"workflowId\":\"wId\",\"jobName\":\"Collection\",\"type\":\"ONGOING\",\"body\":{\"ExecutionTime\":\"30s\",\"parsedItem\":\"300\"}}";
Message m = new Message();
m.setWorkflowId("wId");
m.setType(MessageType.ONGOING);
m.setJobName("Collection");
Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300");
body.put("ExecutionTime", "30s");
m.setBody(body);
m.setBody(body);
assertEquals(expectedJson, m.toString());
}
assertEquals(expectedJson, m.toString());
}
}

11
dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java
View File

@ -1,13 +1,14 @@
package eu.dnetlib.scholexplorer.relation;
import org.junit.jupiter.api.Test;
public class RelationMapperTest {
@Test
public void testLoadRels() throws Exception {
@Test
public void testLoadRels() throws Exception {
RelationMapper relationMapper = RelationMapper.load();
relationMapper.keySet().forEach(System.out::println);
}
RelationMapper relationMapper = RelationMapper.load();
relationMapper.keySet().forEach(System.out::println);
}
}

46
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicAction.java
View File

@ -1,36 +1,40 @@
package eu.dnetlib.dhp.schema.action;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.io.Serializable;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import eu.dnetlib.dhp.schema.oaf.Oaf;
@JsonDeserialize(using = AtomicActionDeserializer.class)
public class AtomicAction<T extends Oaf> implements Serializable {
private Class<T> clazz;
private Class<T> clazz;
private T payload;
private T payload;
public AtomicAction() {}
public AtomicAction() {
}
public AtomicAction(Class<T> clazz, T payload) {
this.clazz = clazz;
this.payload = payload;
}
public AtomicAction(Class<T> clazz, T payload) {
this.clazz = clazz;
this.payload = payload;
}
public Class<T> getClazz() {
return clazz;
}
public Class<T> getClazz() {
return clazz;
}
public void setClazz(Class<T> clazz) {
this.clazz = clazz;
}
public void setClazz(Class<T> clazz) {
this.clazz = clazz;
}
public T getPayload() {
return payload;
}
public T getPayload() {
return payload;
}
public void setPayload(T payload) {
this.payload = payload;
}
public void setPayload(T payload) {
this.payload = payload;
}
}

33
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java
View File

@ -1,29 +1,32 @@
package eu.dnetlib.dhp.schema.action;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.io.IOException;
public class AtomicActionDeserializer extends JsonDeserializer {
@Override
public Object deserialize(JsonParser jp, DeserializationContext ctxt)
throws IOException, JsonProcessingException {
JsonNode node = jp.getCodec().readTree(jp);
String classTag = node.get("clazz").asText();
JsonNode payload = node.get("payload");
ObjectMapper mapper = new ObjectMapper();
@Override
public Object deserialize(JsonParser jp, DeserializationContext ctxt)
throws IOException, JsonProcessingException {
JsonNode node = jp.getCodec().readTree(jp);
String classTag = node.get("clazz").asText();
JsonNode payload = node.get("payload");
ObjectMapper mapper = new ObjectMapper();
try {
final Class<?> clazz = Class.forName(classTag);
return new AtomicAction(clazz, (Oaf) mapper.readValue(payload.toString(), clazz));
} catch (ClassNotFoundException e) {
throw new IOException(e);
}
}
try {
final Class<?> clazz = Class.forName(classTag);
return new AtomicAction(clazz, (Oaf) mapper.readValue(payload.toString(), clazz));
} catch (ClassNotFoundException e) {
throw new IOException(e);
}
}
}

29
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java
View File

@ -1,26 +1,21 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
/** Actual entity types in the Graph */
public enum EntityType {
publication,
dataset,
otherresearchproduct,
software,
datasource,
organization,
project;
publication, dataset, otherresearchproduct, software, datasource, organization, project;
/**
* Resolves the EntityType, given the relative class name
*
* @param clazz the given class name
* @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class
*/
public static <T extends OafEntity> EntityType fromClass(Class<T> clazz) {
/**
* Resolves the EntityType, given the relative class name
*
* @param clazz the given class name
* @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class
*/
public static <T extends OafEntity> EntityType fromClass(Class<T> clazz) {
return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
}
return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
}
}

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java
View File

@ -1,9 +1,7 @@
package eu.dnetlib.dhp.schema.common;
/** Main entity types in the Graph */
public enum MainEntityType {
result,
datasource,
organization,
project
result, datasource, organization, project
}

55
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
View File

@ -1,40 +1,41 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class ModelConstants {
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DATASET_RESULTTYPE_CLASSID = "dataset";
public static final String PUBLICATION_RESULTTYPE_CLASSID = "publication";
public static final String SOFTWARE_RESULTTYPE_CLASSID = "software";
public static final String ORP_RESULTTYPE_CLASSID = "other";
public static final String DATASET_RESULTTYPE_CLASSID = "dataset";
public static final String PUBLICATION_RESULTTYPE_CLASSID = "publication";
public static final String SOFTWARE_RESULTTYPE_CLASSID = "software";
public static final String ORP_RESULTTYPE_CLASSID = "other";
public static Qualifier PUBLICATION_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier DATASET_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier SOFTWARE_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier ORP_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier PUBLICATION_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier DATASET_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier SOFTWARE_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier ORP_DEFAULT_RESULTTYPE = new Qualifier();
static {
PUBLICATION_DEFAULT_RESULTTYPE.setClassid(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setClassname(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
static {
PUBLICATION_DEFAULT_RESULTTYPE.setClassid(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setClassname(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setClassid(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setClassname(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setClassid(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setClassname(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setClassid(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setClassname(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setClassid(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setClassname(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
ORP_DEFAULT_RESULTTYPE.setClassid(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setClassname(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
ORP_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
}
ORP_DEFAULT_RESULTTYPE.setClassid(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setClassname(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
ORP_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
}
}

136
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,92 +6,95 @@ import java.util.*;
public class Author implements Serializable {
private String fullname;
private String fullname;
private String name;
private String name;
private String surname;
private String surname;
private Integer rank;
private Integer rank;
private List<StructuredProperty> pid;
private List<StructuredProperty> pid;
private List<Field<String>> affiliation;
private List<Field<String>> affiliation;
public String getFullname() {
return fullname;
}
public String getFullname() {
return fullname;
}
public void setFullname(String fullname) {
this.fullname = fullname;
}
public void setFullname(String fullname) {
this.fullname = fullname;
}
public String getName() {
return name;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public void setName(String name) {
this.name = name;
}
public String getSurname() {
return surname;
}
public String getSurname() {
return surname;
}
public void setSurname(String surname) {
this.surname = surname;
}
public void setSurname(String surname) {
this.surname = surname;
}
public Integer getRank() {
return rank;
}
public Integer getRank() {
return rank;
}
public void setRank(Integer rank) {
this.rank = rank;
}
public void setRank(Integer rank) {
this.rank = rank;
}
public List<StructuredProperty> getPid() {
return pid;
}
public List<StructuredProperty> getPid() {
return pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public List<Field<String>> getAffiliation() {
return affiliation;
}
public List<Field<String>> getAffiliation() {
return affiliation;
}
public void setAffiliation(List<Field<String>> affiliation) {
this.affiliation = affiliation;
}
public void setAffiliation(List<Field<String>> affiliation) {
this.affiliation = affiliation;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
Author author = (Author) o;
return Objects.equals(fullname, author.fullname)
&& Objects.equals(name, author.name)
&& Objects.equals(surname, author.surname)
&& Objects.equals(rank, author.rank)
&& Objects.equals(pid, author.pid)
&& Objects.equals(affiliation, author.affiliation);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
Author author = (Author) o;
return Objects.equals(fullname, author.fullname)
&& Objects.equals(name, author.name)
&& Objects.equals(surname, author.surname)
&& Objects.equals(rank, author.rank)
&& Objects.equals(pid, author.pid)
&& Objects.equals(affiliation, author.affiliation);
}
@Override
public int hashCode() {
return Objects.hash(fullname, name, surname, rank, pid, affiliation);
}
@Override
public int hashCode() {
return Objects.hash(fullname, name, surname, rank, pid, affiliation);
}
public void addPid(StructuredProperty pid) {
public void addPid(StructuredProperty pid) {
if (pid == null) return;
if (pid == null)
return;
if (this.pid == null) {
this.pid = Arrays.asList(pid);
} else {
this.pid.add(pid);
}
}
if (this.pid == null) {
this.pid = Arrays.asList(pid);
} else {
this.pid.add(pid);
}
}
}

56
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java
View File

@ -1,42 +1,46 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.List;
public class Context implements Serializable {
private String id;
private String id;
private List<DataInfo> dataInfo;
private List<DataInfo> dataInfo;
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public void setId(String id) {
this.id = id;
}
public List<DataInfo> getDataInfo() {
return dataInfo;
}
public List<DataInfo> getDataInfo() {
return dataInfo;
}
public void setDataInfo(List<DataInfo> dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(List<DataInfo> dataInfo) {
this.dataInfo = dataInfo;
}
@Override
public int hashCode() {
return id == null ? 0 : id.hashCode();
}
@Override
public int hashCode() {
return id == null ? 0 : id.hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Context other = (Context) obj;
Context other = (Context) obj;
return id.equals(other.getId());
}
return id.equals(other.getId());
}
}

42
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java
View File

@ -1,30 +1,34 @@
package eu.dnetlib.dhp.schema.oaf;
import java.util.Objects;
public class Country extends Qualifier {
private DataInfo dataInfo;
private DataInfo dataInfo;
public DataInfo getDataInfo() {
return dataInfo;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Country country = (Country) o;
return Objects.equals(dataInfo, country.dataInfo);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
if (!super.equals(o))
return false;
Country country = (Country) o;
return Objects.equals(dataInfo, country.dataInfo);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), dataInfo);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), dataInfo);
}
}

122
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,77 +6,80 @@ import java.util.Objects;
public class DataInfo implements Serializable {
private Boolean invisible = false;
private Boolean inferred;
private Boolean deletedbyinference;
private String trust;
private String inferenceprovenance;
private Qualifier provenanceaction;
private Boolean invisible = false;
private Boolean inferred;
private Boolean deletedbyinference;
private String trust;
private String inferenceprovenance;
private Qualifier provenanceaction;
public Boolean getInvisible() {
return invisible;
}
public Boolean getInvisible() {
return invisible;
}
public void setInvisible(Boolean invisible) {
this.invisible = invisible;
}
public void setInvisible(Boolean invisible) {
this.invisible = invisible;
}
public Boolean getInferred() {
return inferred;
}
public Boolean getInferred() {
return inferred;
}
public void setInferred(Boolean inferred) {
this.inferred = inferred;
}
public void setInferred(Boolean inferred) {
this.inferred = inferred;
}
public Boolean getDeletedbyinference() {
return deletedbyinference;
}
public Boolean getDeletedbyinference() {
return deletedbyinference;
}
public void setDeletedbyinference(Boolean deletedbyinference) {
this.deletedbyinference = deletedbyinference;
}
public void setDeletedbyinference(Boolean deletedbyinference) {
this.deletedbyinference = deletedbyinference;
}
public String getTrust() {
return trust;
}
public String getTrust() {
return trust;
}
public void setTrust(String trust) {
this.trust = trust;
}
public void setTrust(String trust) {
this.trust = trust;
}
public String getInferenceprovenance() {
return inferenceprovenance;
}
public String getInferenceprovenance() {
return inferenceprovenance;
}
public void setInferenceprovenance(String inferenceprovenance) {
this.inferenceprovenance = inferenceprovenance;
}
public void setInferenceprovenance(String inferenceprovenance) {
this.inferenceprovenance = inferenceprovenance;
}
public Qualifier getProvenanceaction() {
return provenanceaction;
}
public Qualifier getProvenanceaction() {
return provenanceaction;
}
public void setProvenanceaction(Qualifier provenanceaction) {
this.provenanceaction = provenanceaction;
}
public void setProvenanceaction(Qualifier provenanceaction) {
this.provenanceaction = provenanceaction;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
DataInfo dataInfo = (DataInfo) o;
return Objects.equals(invisible, dataInfo.invisible)
&& Objects.equals(inferred, dataInfo.inferred)
&& Objects.equals(deletedbyinference, dataInfo.deletedbyinference)
&& Objects.equals(trust, dataInfo.trust)
&& Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance)
&& Objects.equals(provenanceaction, dataInfo.provenanceaction);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
DataInfo dataInfo = (DataInfo) o;
return Objects.equals(invisible, dataInfo.invisible)
&& Objects.equals(inferred, dataInfo.inferred)
&& Objects.equals(deletedbyinference, dataInfo.deletedbyinference)
&& Objects.equals(trust, dataInfo.trust)
&& Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance)
&& Objects.equals(provenanceaction, dataInfo.provenanceaction);
}
@Override
public int hashCode() {
return Objects.hash(
invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction);
}
@Override
public int hashCode() {
return Objects
.hash(
invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction);
}
}

151
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java
View File

@ -1,116 +1,115 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Dataset extends Result implements Serializable {
private Field<String> storagedate;
private Field<String> storagedate;
private Field<String> device;
private Field<String> device;
private Field<String> size;
private Field<String> size;
private Field<String> version;
private Field<String> version;
private Field<String> lastmetadataupdate;
private Field<String> lastmetadataupdate;
private Field<String> metadataversionnumber;
private Field<String> metadataversionnumber;
private List<GeoLocation> geolocation;
private List<GeoLocation> geolocation;
public Dataset() {
setResulttype(ModelConstants.DATASET_DEFAULT_RESULTTYPE);
}
public Dataset() {
setResulttype(ModelConstants.DATASET_DEFAULT_RESULTTYPE);
}
public Field<String> getStoragedate() {
return storagedate;
}
public Field<String> getStoragedate() {
return storagedate;
}
public void setStoragedate(Field<String> storagedate) {
this.storagedate = storagedate;
}
public void setStoragedate(Field<String> storagedate) {
this.storagedate = storagedate;
}
public Field<String> getDevice() {
return device;
}
public Field<String> getDevice() {
return device;
}
public void setDevice(Field<String> device) {
this.device = device;
}
public void setDevice(Field<String> device) {
this.device = device;
}
public Field<String> getSize() {
return size;
}
public Field<String> getSize() {
return size;
}
public void setSize(Field<String> size) {
this.size = size;
}
public void setSize(Field<String> size) {
this.size = size;
}
public Field<String> getVersion() {
return version;
}
public Field<String> getVersion() {
return version;
}
public void setVersion(Field<String> version) {
this.version = version;
}
public void setVersion(Field<String> version) {
this.version = version;
}
public Field<String> getLastmetadataupdate() {
return lastmetadataupdate;
}
public Field<String> getLastmetadataupdate() {
return lastmetadataupdate;
}
public void setLastmetadataupdate(Field<String> lastmetadataupdate) {
this.lastmetadataupdate = lastmetadataupdate;
}
public void setLastmetadataupdate(Field<String> lastmetadataupdate) {
this.lastmetadataupdate = lastmetadataupdate;
}
public Field<String> getMetadataversionnumber() {
return metadataversionnumber;
}
public Field<String> getMetadataversionnumber() {
return metadataversionnumber;
}
public void setMetadataversionnumber(Field<String> metadataversionnumber) {
this.metadataversionnumber = metadataversionnumber;
}
public void setMetadataversionnumber(Field<String> metadataversionnumber) {
this.metadataversionnumber = metadataversionnumber;
}
public List<GeoLocation> getGeolocation() {
return geolocation;
}
public List<GeoLocation> getGeolocation() {
return geolocation;
}
public void setGeolocation(List<GeoLocation> geolocation) {
this.geolocation = geolocation;
}
public void setGeolocation(List<GeoLocation> geolocation) {
this.geolocation = geolocation;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Dataset.class.isAssignableFrom(e.getClass())) {
return;
}
if (!Dataset.class.isAssignableFrom(e.getClass())) {
return;
}
final Dataset d = (Dataset) e;
final Dataset d = (Dataset) e;
storagedate =
d.getStoragedate() != null && compareTrust(this, e) < 0 ? d.getStoragedate() : storagedate;
storagedate = d.getStoragedate() != null && compareTrust(this, e) < 0 ? d.getStoragedate() : storagedate;
device = d.getDevice() != null && compareTrust(this, e) < 0 ? d.getDevice() : device;
device = d.getDevice() != null && compareTrust(this, e) < 0 ? d.getDevice() : device;
size = d.getSize() != null && compareTrust(this, e) < 0 ? d.getSize() : size;
size = d.getSize() != null && compareTrust(this, e) < 0 ? d.getSize() : size;
version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version;
version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version;
lastmetadataupdate =
d.getLastmetadataupdate() != null && compareTrust(this, e) < 0
? d.getLastmetadataupdate()
: lastmetadataupdate;
lastmetadataupdate = d.getLastmetadataupdate() != null && compareTrust(this, e) < 0
? d.getLastmetadataupdate()
: lastmetadataupdate;
metadataversionnumber =
d.getMetadataversionnumber() != null && compareTrust(this, e) < 0
? d.getMetadataversionnumber()
: metadataversionnumber;
metadataversionnumber = d.getMetadataversionnumber() != null && compareTrust(this, e) < 0
? d.getMetadataversionnumber()
: metadataversionnumber;
geolocation = mergeLists(geolocation, d.getGeolocation());
geolocation = mergeLists(geolocation, d.getGeolocation());
mergeOAFDataInfo(d);
}
mergeOAFDataInfo(d);
}
}

786
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,494 +6,467 @@ import java.util.List;
public class Datasource extends OafEntity implements Serializable {
private Qualifier datasourcetype;
private Qualifier datasourcetype;
private Qualifier openairecompatibility;
private Qualifier openairecompatibility;
private Field<String> officialname;
private Field<String> officialname;
private Field<String> englishname;
private Field<String> englishname;
private Field<String> websiteurl;
private Field<String> websiteurl;
private Field<String> logourl;
private Field<String> logourl;
private Field<String> contactemail;
private Field<String> contactemail;
private Field<String> namespaceprefix;
private Field<String> namespaceprefix;
private Field<String> latitude;
private Field<String> latitude;
private Field<String> longitude;
private Field<String> longitude;
private Field<String> dateofvalidation;
private Field<String> dateofvalidation;
private Field<String> description;
private Field<String> description;
private List<StructuredProperty> subjects;
private List<StructuredProperty> subjects;
// opendoar specific fields (od*)
private Field<String> odnumberofitems;
// opendoar specific fields (od*)
private Field<String> odnumberofitems;
private Field<String> odnumberofitemsdate;
private Field<String> odnumberofitemsdate;
private Field<String> odpolicies;
private Field<String> odpolicies;
private List<Field<String>> odlanguages;
private List<Field<String>> odlanguages;
private List<Field<String>> odcontenttypes;
private List<Field<String>> odcontenttypes;
private List<Field<String>> accessinfopackage;
private List<Field<String>> accessinfopackage;
// re3data fields
private Field<String> releasestartdate;
// re3data fields
private Field<String> releasestartdate;
private Field<String> releaseenddate;
private Field<String> releaseenddate;
private Field<String> missionstatementurl;
private Field<String> missionstatementurl;
private Field<Boolean> dataprovider;
private Field<Boolean> dataprovider;
private Field<Boolean> serviceprovider;
private Field<Boolean> serviceprovider;
// {open, restricted or closed}
private Field<String> databaseaccesstype;
// {open, restricted or closed}
private Field<String> databaseaccesstype;
// {open, restricted or closed}
private Field<String> datauploadtype;
// {open, restricted or closed}
private Field<String> datauploadtype;
// {feeRequired, registration, other}
private Field<String> databaseaccessrestriction;
// {feeRequired, registration, other}
private Field<String> databaseaccessrestriction;
// {feeRequired, registration, other}
private Field<String> datauploadrestriction;
// {feeRequired, registration, other}
private Field<String> datauploadrestriction;
private Field<Boolean> versioning;
private Field<Boolean> versioning;
private Field<String> citationguidelineurl;
private Field<String> citationguidelineurl;
// {yes, no, uknown}
private Field<String> qualitymanagementkind;
// {yes, no, uknown}
private Field<String> qualitymanagementkind;
private Field<String> pidsystems;
private Field<String> pidsystems;
private Field<String> certificates;
private Field<String> certificates;
private List<KeyValue> policies;
private List<KeyValue> policies;
private Journal journal;
private Journal journal;
public Qualifier getDatasourcetype() {
return datasourcetype;
}
public Qualifier getDatasourcetype() {
return datasourcetype;
}
public void setDatasourcetype(Qualifier datasourcetype) {
this.datasourcetype = datasourcetype;
}
public void setDatasourcetype(Qualifier datasourcetype) {
this.datasourcetype = datasourcetype;
}
public Qualifier getOpenairecompatibility() {
return openairecompatibility;
}
public Qualifier getOpenairecompatibility() {
return openairecompatibility;
}
public void setOpenairecompatibility(Qualifier openairecompatibility) {
this.openairecompatibility = openairecompatibility;
}
public void setOpenairecompatibility(Qualifier openairecompatibility) {
this.openairecompatibility = openairecompatibility;
}
public Field<String> getOfficialname() {
return officialname;
}
public Field<String> getOfficialname() {
return officialname;
}
public void setOfficialname(Field<String> officialname) {
this.officialname = officialname;
}
public void setOfficialname(Field<String> officialname) {
this.officialname = officialname;
}
public Field<String> getEnglishname() {
return englishname;
}
public Field<String> getEnglishname() {
return englishname;
}
public void setEnglishname(Field<String> englishname) {
this.englishname = englishname;
}
public void setEnglishname(Field<String> englishname) {
this.englishname = englishname;
}
public Field<String> getWebsiteurl() {
return websiteurl;
}
public Field<String> getWebsiteurl() {
return websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public Field<String> getLogourl() {
return logourl;
}
public Field<String> getLogourl() {
return logourl;
}
public void setLogourl(Field<String> logourl) {
this.logourl = logourl;
}
public void setLogourl(Field<String> logourl) {
this.logourl = logourl;
}
public Field<String> getContactemail() {
return contactemail;
}
public Field<String> getContactemail() {
return contactemail;
}
public void setContactemail(Field<String> contactemail) {
this.contactemail = contactemail;
}
public void setContactemail(Field<String> contactemail) {
this.contactemail = contactemail;
}
public Field<String> getNamespaceprefix() {
return namespaceprefix;
}
public Field<String> getNamespaceprefix() {
return namespaceprefix;
}
public void setNamespaceprefix(Field<String> namespaceprefix) {
this.namespaceprefix = namespaceprefix;
}
public void setNamespaceprefix(Field<String> namespaceprefix) {
this.namespaceprefix = namespaceprefix;
}
public Field<String> getLatitude() {
return latitude;
}
public Field<String> getLatitude() {
return latitude;
}
public void setLatitude(Field<String> latitude) {
this.latitude = latitude;
}
public void setLatitude(Field<String> latitude) {
this.latitude = latitude;
}
public Field<String> getLongitude() {
return longitude;
}
public Field<String> getLongitude() {
return longitude;
}
public void setLongitude(Field<String> longitude) {
this.longitude = longitude;
}
public void setLongitude(Field<String> longitude) {
this.longitude = longitude;
}
public Field<String> getDateofvalidation() {
return dateofvalidation;
}
public Field<String> getDateofvalidation() {
return dateofvalidation;
}
public void setDateofvalidation(Field<String> dateofvalidation) {
this.dateofvalidation = dateofvalidation;
}
public void setDateofvalidation(Field<String> dateofvalidation) {
this.dateofvalidation = dateofvalidation;
}
public Field<String> getDescription() {
return description;
}
public Field<String> getDescription() {
return description;
}
public void setDescription(Field<String> description) {
this.description = description;
}
public void setDescription(Field<String> description) {
this.description = description;
}
public List<StructuredProperty> getSubjects() {
return subjects;
}
public List<StructuredProperty> getSubjects() {
return subjects;
}
public void setSubjects(List<StructuredProperty> subjects) {
this.subjects = subjects;
}
public void setSubjects(List<StructuredProperty> subjects) {
this.subjects = subjects;
}
public Field<String> getOdnumberofitems() {
return odnumberofitems;
}
public Field<String> getOdnumberofitems() {
return odnumberofitems;
}
public void setOdnumberofitems(Field<String> odnumberofitems) {
this.odnumberofitems = odnumberofitems;
}
public void setOdnumberofitems(Field<String> odnumberofitems) {
this.odnumberofitems = odnumberofitems;
}
public Field<String> getOdnumberofitemsdate() {
return odnumberofitemsdate;
}
public Field<String> getOdnumberofitemsdate() {
return odnumberofitemsdate;
}
public void setOdnumberofitemsdate(Field<String> odnumberofitemsdate) {
this.odnumberofitemsdate = odnumberofitemsdate;
}
public void setOdnumberofitemsdate(Field<String> odnumberofitemsdate) {
this.odnumberofitemsdate = odnumberofitemsdate;
}
public Field<String> getOdpolicies() {
return odpolicies;
}
public Field<String> getOdpolicies() {
return odpolicies;
}
public void setOdpolicies(Field<String> odpolicies) {
this.odpolicies = odpolicies;
}
public void setOdpolicies(Field<String> odpolicies) {
this.odpolicies = odpolicies;
}
public List<Field<String>> getOdlanguages() {
return odlanguages;
}
public List<Field<String>> getOdlanguages() {
return odlanguages;
}
public void setOdlanguages(List<Field<String>> odlanguages) {
this.odlanguages = odlanguages;
}
public void setOdlanguages(List<Field<String>> odlanguages) {
this.odlanguages = odlanguages;
}
public List<Field<String>> getOdcontenttypes() {
return odcontenttypes;
}
public List<Field<String>> getOdcontenttypes() {
return odcontenttypes;
}
public void setOdcontenttypes(List<Field<String>> odcontenttypes) {
this.odcontenttypes = odcontenttypes;
}
public void setOdcontenttypes(List<Field<String>> odcontenttypes) {
this.odcontenttypes = odcontenttypes;
}
public List<Field<String>> getAccessinfopackage() {
return accessinfopackage;
}
public List<Field<String>> getAccessinfopackage() {
return accessinfopackage;
}
public void setAccessinfopackage(List<Field<String>> accessinfopackage) {
this.accessinfopackage = accessinfopackage;
}
public void setAccessinfopackage(List<Field<String>> accessinfopackage) {
this.accessinfopackage = accessinfopackage;
}
public Field<String> getReleasestartdate() {
return releasestartdate;
}
public Field<String> getReleasestartdate() {
return releasestartdate;
}
public void setReleasestartdate(Field<String> releasestartdate) {
this.releasestartdate = releasestartdate;
}
public void setReleasestartdate(Field<String> releasestartdate) {
this.releasestartdate = releasestartdate;
}
public Field<String> getReleaseenddate() {
return releaseenddate;
}
public Field<String> getReleaseenddate() {
return releaseenddate;
}
public void setReleaseenddate(Field<String> releaseenddate) {
this.releaseenddate = releaseenddate;
}
public void setReleaseenddate(Field<String> releaseenddate) {
this.releaseenddate = releaseenddate;
}
public Field<String> getMissionstatementurl() {
return missionstatementurl;
}
public Field<String> getMissionstatementurl() {
return missionstatementurl;
}
public void setMissionstatementurl(Field<String> missionstatementurl) {
this.missionstatementurl = missionstatementurl;
}
public void setMissionstatementurl(Field<String> missionstatementurl) {
this.missionstatementurl = missionstatementurl;
}
public Field<Boolean> getDataprovider() {
return dataprovider;
}
public Field<Boolean> getDataprovider() {
return dataprovider;
}
public void setDataprovider(Field<Boolean> dataprovider) {
this.dataprovider = dataprovider;
}
public void setDataprovider(Field<Boolean> dataprovider) {
this.dataprovider = dataprovider;
}
public Field<Boolean> getServiceprovider() {
return serviceprovider;
}
public Field<Boolean> getServiceprovider() {
return serviceprovider;
}
public void setServiceprovider(Field<Boolean> serviceprovider) {
this.serviceprovider = serviceprovider;
}
public void setServiceprovider(Field<Boolean> serviceprovider) {
this.serviceprovider = serviceprovider;
}
public Field<String> getDatabaseaccesstype() {
return databaseaccesstype;
}
public Field<String> getDatabaseaccesstype() {
return databaseaccesstype;
}
public void setDatabaseaccesstype(Field<String> databaseaccesstype) {
this.databaseaccesstype = databaseaccesstype;
}
public Field<String> getDatauploadtype() {
return datauploadtype;
}
public void setDatauploadtype(Field<String> datauploadtype) {
this.datauploadtype = datauploadtype;
}
public Field<String> getDatabaseaccessrestriction() {
return databaseaccessrestriction;
}
public void setDatabaseaccessrestriction(Field<String> databaseaccessrestriction) {
this.databaseaccessrestriction = databaseaccessrestriction;
}
public Field<String> getDatauploadrestriction() {
return datauploadrestriction;
}
public void setDatauploadrestriction(Field<String> datauploadrestriction) {
this.datauploadrestriction = datauploadrestriction;
}
public Field<Boolean> getVersioning() {
return versioning;
}
public void setVersioning(Field<Boolean> versioning) {
this.versioning = versioning;
}
public Field<String> getCitationguidelineurl() {
return citationguidelineurl;
}
public void setCitationguidelineurl(Field<String> citationguidelineurl) {
this.citationguidelineurl = citationguidelineurl;
}
public Field<String> getQualitymanagementkind() {
return qualitymanagementkind;
}
public void setQualitymanagementkind(Field<String> qualitymanagementkind) {
this.qualitymanagementkind = qualitymanagementkind;
}
public Field<String> getPidsystems() {
return pidsystems;
}
public void setPidsystems(Field<String> pidsystems) {
this.pidsystems = pidsystems;
}
public Field<String> getCertificates() {
return certificates;
}
public void setCertificates(Field<String> certificates) {
this.certificates = certificates;
}
public List<KeyValue> getPolicies() {
return policies;
}
public void setPolicies(List<KeyValue> policies) {
this.policies = policies;
}
public Journal getJournal() {
return journal;
}
public void setJournal(Journal journal) {
this.journal = journal;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Datasource.class.isAssignableFrom(e.getClass())) {
return;
}
Datasource d = (Datasource) e;
datasourcetype =
d.getDatasourcetype() != null && compareTrust(this, e) < 0
? d.getDatasourcetype()
: datasourcetype;
openairecompatibility =
d.getOpenairecompatibility() != null && compareTrust(this, e) < 0
? d.getOpenairecompatibility()
: openairecompatibility;
officialname =
d.getOfficialname() != null && compareTrust(this, e) < 0
? d.getOfficialname()
: officialname;
englishname =
d.getEnglishname() != null && compareTrust(this, e) < 0 ? d.getEnglishname() : officialname;
websiteurl =
d.getWebsiteurl() != null && compareTrust(this, e) < 0 ? d.getWebsiteurl() : websiteurl;
logourl = d.getLogourl() != null && compareTrust(this, e) < 0 ? d.getLogourl() : getLogourl();
contactemail =
d.getContactemail() != null && compareTrust(this, e) < 0
? d.getContactemail()
: contactemail;
namespaceprefix =
d.getNamespaceprefix() != null && compareTrust(this, e) < 0
? d.getNamespaceprefix()
: namespaceprefix;
latitude = d.getLatitude() != null && compareTrust(this, e) < 0 ? d.getLatitude() : latitude;
longitude =
d.getLongitude() != null && compareTrust(this, e) < 0 ? d.getLongitude() : longitude;
dateofvalidation =
d.getDateofvalidation() != null && compareTrust(this, e) < 0
? d.getDateofvalidation()
: dateofvalidation;
description =
d.getDescription() != null && compareTrust(this, e) < 0 ? d.getDescription() : description;
subjects = mergeLists(subjects, d.getSubjects());
// opendoar specific fields (od*)
odnumberofitems =
d.getOdnumberofitems() != null && compareTrust(this, e) < 0
? d.getOdnumberofitems()
: odnumberofitems;
odnumberofitemsdate =
d.getOdnumberofitemsdate() != null && compareTrust(this, e) < 0
? d.getOdnumberofitemsdate()
: odnumberofitemsdate;
odpolicies =
d.getOdpolicies() != null && compareTrust(this, e) < 0 ? d.getOdpolicies() : odpolicies;
odlanguages = mergeLists(odlanguages, d.getOdlanguages());
odcontenttypes = mergeLists(odcontenttypes, d.getOdcontenttypes());
accessinfopackage = mergeLists(accessinfopackage, d.getAccessinfopackage());
// re3data fields
releasestartdate =
d.getReleasestartdate() != null && compareTrust(this, e) < 0
? d.getReleasestartdate()
: releasestartdate;
releaseenddate =
d.getReleaseenddate() != null && compareTrust(this, e) < 0
? d.getReleaseenddate()
: releaseenddate;
missionstatementurl =
d.getMissionstatementurl() != null && compareTrust(this, e) < 0
? d.getMissionstatementurl()
: missionstatementurl;
dataprovider =
d.getDataprovider() != null && compareTrust(this, e) < 0
? d.getDataprovider()
: dataprovider;
serviceprovider =
d.getServiceprovider() != null && compareTrust(this, e) < 0
? d.getServiceprovider()
: serviceprovider;
// {open, restricted or closed}
databaseaccesstype =
d.getDatabaseaccesstype() != null && compareTrust(this, e) < 0
? d.getDatabaseaccesstype()
: databaseaccesstype;
// {open, restricted or closed}
datauploadtype =
d.getDatauploadtype() != null && compareTrust(this, e) < 0
? d.getDatauploadtype()
: datauploadtype;
// {feeRequired, registration, other}
databaseaccessrestriction =
d.getDatabaseaccessrestriction() != null && compareTrust(this, e) < 0
? d.getDatabaseaccessrestriction()
: databaseaccessrestriction;
// {feeRequired, registration, other}
datauploadrestriction =
d.getDatauploadrestriction() != null && compareTrust(this, e) < 0
? d.getDatauploadrestriction()
: datauploadrestriction;
versioning =
d.getVersioning() != null && compareTrust(this, e) < 0 ? d.getVersioning() : versioning;
citationguidelineurl =
d.getCitationguidelineurl() != null && compareTrust(this, e) < 0
? d.getCitationguidelineurl()
: citationguidelineurl;
// {yes, no, unknown}
qualitymanagementkind =
d.getQualitymanagementkind() != null && compareTrust(this, e) < 0
? d.getQualitymanagementkind()
: qualitymanagementkind;
pidsystems =
d.getPidsystems() != null && compareTrust(this, e) < 0 ? d.getPidsystems() : pidsystems;
certificates =
d.getCertificates() != null && compareTrust(this, e) < 0
? d.getCertificates()
: certificates;
policies = mergeLists(policies, d.getPolicies());
journal = d.getJournal() != null && compareTrust(this, e) < 0 ? d.getJournal() : journal;
mergeOAFDataInfo(e);
}
public void setDatabaseaccesstype(Field<String> databaseaccesstype) {
this.databaseaccesstype = databaseaccesstype;
}
public Field<String> getDatauploadtype() {
return datauploadtype;
}
public void setDatauploadtype(Field<String> datauploadtype) {
this.datauploadtype = datauploadtype;
}
public Field<String> getDatabaseaccessrestriction() {
return databaseaccessrestriction;
}
public void setDatabaseaccessrestriction(Field<String> databaseaccessrestriction) {
this.databaseaccessrestriction = databaseaccessrestriction;
}
public Field<String> getDatauploadrestriction() {
return datauploadrestriction;
}
public void setDatauploadrestriction(Field<String> datauploadrestriction) {
this.datauploadrestriction = datauploadrestriction;
}
public Field<Boolean> getVersioning() {
return versioning;
}
public void setVersioning(Field<Boolean> versioning) {
this.versioning = versioning;
}
public Field<String> getCitationguidelineurl() {
return citationguidelineurl;
}
public void setCitationguidelineurl(Field<String> citationguidelineurl) {
this.citationguidelineurl = citationguidelineurl;
}
public Field<String> getQualitymanagementkind() {
return qualitymanagementkind;
}
public void setQualitymanagementkind(Field<String> qualitymanagementkind) {
this.qualitymanagementkind = qualitymanagementkind;
}
public Field<String> getPidsystems() {
return pidsystems;
}
public void setPidsystems(Field<String> pidsystems) {
this.pidsystems = pidsystems;
}
public Field<String> getCertificates() {
return certificates;
}
public void setCertificates(Field<String> certificates) {
this.certificates = certificates;
}
public List<KeyValue> getPolicies() {
return policies;
}
public void setPolicies(List<KeyValue> policies) {
this.policies = policies;
}
public Journal getJournal() {
return journal;
}
public void setJournal(Journal journal) {
this.journal = journal;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Datasource.class.isAssignableFrom(e.getClass())) {
return;
}
Datasource d = (Datasource) e;
datasourcetype = d.getDatasourcetype() != null && compareTrust(this, e) < 0
? d.getDatasourcetype()
: datasourcetype;
openairecompatibility = d.getOpenairecompatibility() != null && compareTrust(this, e) < 0
? d.getOpenairecompatibility()
: openairecompatibility;
officialname = d.getOfficialname() != null && compareTrust(this, e) < 0
? d.getOfficialname()
: officialname;
englishname = d.getEnglishname() != null && compareTrust(this, e) < 0 ? d.getEnglishname() : officialname;
websiteurl = d.getWebsiteurl() != null && compareTrust(this, e) < 0 ? d.getWebsiteurl() : websiteurl;
logourl = d.getLogourl() != null && compareTrust(this, e) < 0 ? d.getLogourl() : getLogourl();
contactemail = d.getContactemail() != null && compareTrust(this, e) < 0
? d.getContactemail()
: contactemail;
namespaceprefix = d.getNamespaceprefix() != null && compareTrust(this, e) < 0
? d.getNamespaceprefix()
: namespaceprefix;
latitude = d.getLatitude() != null && compareTrust(this, e) < 0 ? d.getLatitude() : latitude;
longitude = d.getLongitude() != null && compareTrust(this, e) < 0 ? d.getLongitude() : longitude;
dateofvalidation = d.getDateofvalidation() != null && compareTrust(this, e) < 0
? d.getDateofvalidation()
: dateofvalidation;
description = d.getDescription() != null && compareTrust(this, e) < 0 ? d.getDescription() : description;
subjects = mergeLists(subjects, d.getSubjects());
// opendoar specific fields (od*)
odnumberofitems = d.getOdnumberofitems() != null && compareTrust(this, e) < 0
? d.getOdnumberofitems()
: odnumberofitems;
odnumberofitemsdate = d.getOdnumberofitemsdate() != null && compareTrust(this, e) < 0
? d.getOdnumberofitemsdate()
: odnumberofitemsdate;
odpolicies = d.getOdpolicies() != null && compareTrust(this, e) < 0 ? d.getOdpolicies() : odpolicies;
odlanguages = mergeLists(odlanguages, d.getOdlanguages());
odcontenttypes = mergeLists(odcontenttypes, d.getOdcontenttypes());
accessinfopackage = mergeLists(accessinfopackage, d.getAccessinfopackage());
// re3data fields
releasestartdate = d.getReleasestartdate() != null && compareTrust(this, e) < 0
? d.getReleasestartdate()
: releasestartdate;
releaseenddate = d.getReleaseenddate() != null && compareTrust(this, e) < 0
? d.getReleaseenddate()
: releaseenddate;
missionstatementurl = d.getMissionstatementurl() != null && compareTrust(this, e) < 0
? d.getMissionstatementurl()
: missionstatementurl;
dataprovider = d.getDataprovider() != null && compareTrust(this, e) < 0
? d.getDataprovider()
: dataprovider;
serviceprovider = d.getServiceprovider() != null && compareTrust(this, e) < 0
? d.getServiceprovider()
: serviceprovider;
// {open, restricted or closed}
databaseaccesstype = d.getDatabaseaccesstype() != null && compareTrust(this, e) < 0
? d.getDatabaseaccesstype()
: databaseaccesstype;
// {open, restricted or closed}
datauploadtype = d.getDatauploadtype() != null && compareTrust(this, e) < 0
? d.getDatauploadtype()
: datauploadtype;
// {feeRequired, registration, other}
databaseaccessrestriction = d.getDatabaseaccessrestriction() != null && compareTrust(this, e) < 0
? d.getDatabaseaccessrestriction()
: databaseaccessrestriction;
// {feeRequired, registration, other}
datauploadrestriction = d.getDatauploadrestriction() != null && compareTrust(this, e) < 0
? d.getDatauploadrestriction()
: datauploadrestriction;
versioning = d.getVersioning() != null && compareTrust(this, e) < 0 ? d.getVersioning() : versioning;
citationguidelineurl = d.getCitationguidelineurl() != null && compareTrust(this, e) < 0
? d.getCitationguidelineurl()
: citationguidelineurl;
// {yes, no, unknown}
qualitymanagementkind = d.getQualitymanagementkind() != null && compareTrust(this, e) < 0
? d.getQualitymanagementkind()
: qualitymanagementkind;
pidsystems = d.getPidsystems() != null && compareTrust(this, e) < 0 ? d.getPidsystems() : pidsystems;
certificates = d.getCertificates() != null && compareTrust(this, e) < 0
? d.getCertificates()
: certificates;
policies = mergeLists(policies, d.getPolicies());
journal = d.getJournal() != null && compareTrust(this, e) < 0 ? d.getJournal() : journal;
mergeOAFDataInfo(e);
}
}

170
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java
View File

@ -1,115 +1,119 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.Objects;
public class ExternalReference implements Serializable {
// source
private String sitename;
// source
private String sitename;
// title
private String label;
// title
private String label;
// text()
private String url;
// text()
private String url;
// ?? not mapped yet ??
private String description;
// ?? not mapped yet ??
private String description;
// type
private Qualifier qualifier;
// type
private Qualifier qualifier;
// site internal identifier
private String refidentifier;
// site internal identifier
private String refidentifier;
// maps the oaf:reference/@query attribute
private String query;
// maps the oaf:reference/@query attribute
private String query;
// ExternalReferences might be also inferred
private DataInfo dataInfo;
// ExternalReferences might be also inferred
private DataInfo dataInfo;
public String getSitename() {
return sitename;
}
public String getSitename() {
return sitename;
}
public void setSitename(String sitename) {
this.sitename = sitename;
}
public void setSitename(String sitename) {
this.sitename = sitename;
}
public String getLabel() {
return label;
}
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
public void setLabel(String label) {
this.label = label;
}
public String getUrl() {
return url;
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public void setUrl(String url) {
this.url = url;
}
public String getDescription() {
return description;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public void setDescription(String description) {
this.description = description;
}
public Qualifier getQualifier() {
return qualifier;
}
public Qualifier getQualifier() {
return qualifier;
}
public void setQualifier(Qualifier qualifier) {
this.qualifier = qualifier;
}
public void setQualifier(Qualifier qualifier) {
this.qualifier = qualifier;
}
public String getRefidentifier() {
return refidentifier;
}
public String getRefidentifier() {
return refidentifier;
}
public void setRefidentifier(String refidentifier) {
this.refidentifier = refidentifier;
}
public void setRefidentifier(String refidentifier) {
this.refidentifier = refidentifier;
}
public String getQuery() {
return query;
}
public String getQuery() {
return query;
}
public void setQuery(String query) {
this.query = query;
}
public void setQuery(String query) {
this.query = query;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
ExternalReference that = (ExternalReference) o;
return Objects.equals(sitename, that.sitename)
&& Objects.equals(label, that.label)
&& Objects.equals(url, that.url)
&& Objects.equals(description, that.description)
&& Objects.equals(qualifier, that.qualifier)
&& Objects.equals(refidentifier, that.refidentifier)
&& Objects.equals(query, that.query)
&& Objects.equals(dataInfo, that.dataInfo);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
ExternalReference that = (ExternalReference) o;
return Objects.equals(sitename, that.sitename)
&& Objects.equals(label, that.label)
&& Objects.equals(url, that.url)
&& Objects.equals(description, that.description)
&& Objects.equals(qualifier, that.qualifier)
&& Objects.equals(refidentifier, that.refidentifier)
&& Objects.equals(query, that.query)
&& Objects.equals(dataInfo, that.dataInfo);
}
@Override
public int hashCode() {
return Objects.hash(
sitename, label, url, description, qualifier, refidentifier, query, dataInfo);
}
@Override
public int hashCode() {
return Objects
.hash(
sitename, label, url, description, qualifier, refidentifier, query, dataInfo);
}
}

105
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java
View File

@ -1,74 +1,77 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.Objects;
public class ExtraInfo implements Serializable {
private String name;
private String name;
private String typology;
private String typology;
private String provenance;
private String provenance;
private String trust;
private String trust;
// json containing a Citation or Statistics
private String value;
// json containing a Citation or Statistics
private String value;
public String getName() {
return name;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public void setName(String name) {
this.name = name;
}
public String getTypology() {
return typology;
}
public String getTypology() {
return typology;
}
public void setTypology(String typology) {
this.typology = typology;
}
public void setTypology(String typology) {
this.typology = typology;
}
public String getProvenance() {
return provenance;
}
public String getProvenance() {
return provenance;
}
public void setProvenance(String provenance) {
this.provenance = provenance;
}
public void setProvenance(String provenance) {
this.provenance = provenance;
}
public String getTrust() {
return trust;
}
public String getTrust() {
return trust;
}
public void setTrust(String trust) {
this.trust = trust;
}
public void setTrust(String trust) {
this.trust = trust;
}
public String getValue() {
return value;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
public void setValue(String value) {
this.value = value;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
ExtraInfo extraInfo = (ExtraInfo) o;
return Objects.equals(name, extraInfo.name)
&& Objects.equals(typology, extraInfo.typology)
&& Objects.equals(provenance, extraInfo.provenance)
&& Objects.equals(trust, extraInfo.trust)
&& Objects.equals(value, extraInfo.value);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
ExtraInfo extraInfo = (ExtraInfo) o;
return Objects.equals(name, extraInfo.name)
&& Objects.equals(typology, extraInfo.typology)
&& Objects.equals(provenance, extraInfo.provenance)
&& Objects.equals(trust, extraInfo.trust)
&& Objects.equals(value, extraInfo.value);
}
@Override
public int hashCode() {
return Objects.hash(name, typology, provenance, trust, value);
}
@Override
public int hashCode() {
return Objects.hash(name, typology, provenance, trust, value);
}
}

56
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java
View File

@ -1,40 +1,44 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
public class Field<T> implements Serializable {
private T value;
private T value;
private DataInfo dataInfo;
private DataInfo dataInfo;
public T getValue() {
return value;
}
public T getValue() {
return value;
}
public void setValue(T value) {
this.value = value;
}
public void setValue(T value) {
this.value = value;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
@Override
public int hashCode() {
return getValue() == null ? 0 : getValue().hashCode();
}
@Override
public int hashCode() {
return getValue() == null ? 0 : getValue().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
Field<T> other = (Field<T>) obj;
return getValue().equals(other.getValue());
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Field<T> other = (Field<T>) obj;
return getValue().equals(other.getValue());
}
}

101
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java
View File

@ -1,69 +1,76 @@
package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore;
import java.io.Serializable;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class GeoLocation implements Serializable {
private String point;
private String point;
private String box;
private String box;
private String place;
private String place;
public String getPoint() {
return point;
}
public String getPoint() {
return point;
}
public void setPoint(String point) {
this.point = point;
}
public void setPoint(String point) {
this.point = point;
}
public String getBox() {
return box;
}
public String getBox() {
return box;
}
public void setBox(String box) {
this.box = box;
}
public void setBox(String box) {
this.box = box;
}
public String getPlace() {
return place;
}
public String getPlace() {
return place;
}
public void setPlace(String place) {
this.place = place;
}
public void setPlace(String place) {
this.place = place;
}
@JsonIgnore
public boolean isBlank() {
return StringUtils.isBlank(point) && StringUtils.isBlank(box) && StringUtils.isBlank(place);
}
@JsonIgnore
public boolean isBlank() {
return StringUtils.isBlank(point) && StringUtils.isBlank(box) && StringUtils.isBlank(place);
}
public String toComparableString() {
return isBlank()
? ""
: String.format(
"%s::%s%s",
point != null ? point.toLowerCase() : "",
box != null ? box.toLowerCase() : "",
place != null ? place.toLowerCase() : "");
}
public String toComparableString() {
return isBlank()
? ""
: String
.format(
"%s::%s%s",
point != null ? point.toLowerCase() : "",
box != null ? box.toLowerCase() : "",
place != null ? place.toLowerCase() : "");
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
GeoLocation other = (GeoLocation) obj;
GeoLocation other = (GeoLocation) obj;
return toComparableString().equals(other.toComparableString());
}
return toComparableString().equals(other.toComparableString());
}
}

209
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,143 +6,147 @@ import java.util.List;
public class Instance implements Serializable {
private Field<String> license;
private Field<String> license;
private Qualifier accessright;
private Qualifier accessright;
private Qualifier instancetype;
private Qualifier instancetype;
private KeyValue hostedby;
private KeyValue hostedby;
private List<String> url;
private List<String> url;
// other research products specifc
private String distributionlocation;
// other research products specifc
private String distributionlocation;
private KeyValue collectedfrom;
private KeyValue collectedfrom;
private Field<String> dateofacceptance;
private Field<String> dateofacceptance;
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed
// results
private Field<String> processingchargeamount;
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed
// results
private Field<String> processingchargeamount;
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
// typed results
private Field<String> processingchargecurrency;
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
// typed results
private Field<String> processingchargecurrency;
private Field<String> refereed; // peer-review status
private Field<String> refereed; // peer-review status
public Field<String> getLicense() {
return license;
}
public Field<String> getLicense() {
return license;
}
public void setLicense(Field<String> license) {
this.license = license;
}
public void setLicense(Field<String> license) {
this.license = license;
}
public Qualifier getAccessright() {
return accessright;
}
public Qualifier getAccessright() {
return accessright;
}
public void setAccessright(Qualifier accessright) {
this.accessright = accessright;
}
public void setAccessright(Qualifier accessright) {
this.accessright = accessright;
}
public Qualifier getInstancetype() {
return instancetype;
}
public Qualifier getInstancetype() {
return instancetype;
}
public void setInstancetype(Qualifier instancetype) {
this.instancetype = instancetype;
}
public void setInstancetype(Qualifier instancetype) {
this.instancetype = instancetype;
}
public KeyValue getHostedby() {
return hostedby;
}
public KeyValue getHostedby() {
return hostedby;
}
public void setHostedby(KeyValue hostedby) {
this.hostedby = hostedby;
}
public void setHostedby(KeyValue hostedby) {
this.hostedby = hostedby;
}
public List<String> getUrl() {
return url;
}
public List<String> getUrl() {
return url;
}
public void setUrl(List<String> url) {
this.url = url;
}
public void setUrl(List<String> url) {
this.url = url;
}
public String getDistributionlocation() {
return distributionlocation;
}
public String getDistributionlocation() {
return distributionlocation;
}
public void setDistributionlocation(String distributionlocation) {
this.distributionlocation = distributionlocation;
}
public void setDistributionlocation(String distributionlocation) {
this.distributionlocation = distributionlocation;
}
public KeyValue getCollectedfrom() {
return collectedfrom;
}
public KeyValue getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(KeyValue collectedfrom) {
this.collectedfrom = collectedfrom;
}
public void setCollectedfrom(KeyValue collectedfrom) {
this.collectedfrom = collectedfrom;
}
public Field<String> getDateofacceptance() {
return dateofacceptance;
}
public Field<String> getDateofacceptance() {
return dateofacceptance;
}
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public Field<String> getProcessingchargeamount() {
return processingchargeamount;
}
public Field<String> getProcessingchargeamount() {
return processingchargeamount;
}
public void setProcessingchargeamount(Field<String> processingchargeamount) {
this.processingchargeamount = processingchargeamount;
}
public void setProcessingchargeamount(Field<String> processingchargeamount) {
this.processingchargeamount = processingchargeamount;
}
public Field<String> getProcessingchargecurrency() {
return processingchargecurrency;
}
public Field<String> getProcessingchargecurrency() {
return processingchargecurrency;
}
public void setProcessingchargecurrency(Field<String> processingchargecurrency) {
this.processingchargecurrency = processingchargecurrency;
}
public void setProcessingchargecurrency(Field<String> processingchargecurrency) {
this.processingchargecurrency = processingchargecurrency;
}
public Field<String> getRefereed() {
return refereed;
}
public Field<String> getRefereed() {
return refereed;
}
public void setRefereed(Field<String> refereed) {
this.refereed = refereed;
}
public void setRefereed(Field<String> refereed) {
this.refereed = refereed;
}
public String toComparableString() {
return String.format(
"%s::%s::%s::%s",
hostedby != null && hostedby.getKey() != null ? hostedby.getKey().toLowerCase() : "",
accessright != null && accessright.getClassid() != null ? accessright.getClassid() : "",
instancetype != null && instancetype.getClassid() != null ? instancetype.getClassid() : "",
url != null ? url : "");
}
public String toComparableString() {
return String
.format(
"%s::%s::%s::%s",
hostedby != null && hostedby.getKey() != null ? hostedby.getKey().toLowerCase() : "",
accessright != null && accessright.getClassid() != null ? accessright.getClassid() : "",
instancetype != null && instancetype.getClassid() != null ? instancetype.getClassid() : "",
url != null ? url : "");
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Instance other = (Instance) obj;
Instance other = (Instance) obj;
return toComparableString().equals(other.toComparableString());
}
return toComparableString().equals(other.toComparableString());
}
}

240
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,159 +6,162 @@ import java.util.Objects;
public class Journal implements Serializable {
private String name;
private String name;
private String issnPrinted;
private String issnPrinted;
private String issnOnline;
private String issnOnline;
private String issnLinking;
private String issnLinking;
private String ep;
private String ep;
private String iss;
private String iss;
private String sp;
private String sp;
private String vol;
private String vol;
private String edition;
private String edition;
private String conferenceplace;
private String conferenceplace;
private String conferencedate;
private String conferencedate;
private DataInfo dataInfo;
private DataInfo dataInfo;
public String getName() {
return name;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public void setName(String name) {
this.name = name;
}
public String getIssnPrinted() {
return issnPrinted;
}
public String getIssnPrinted() {
return issnPrinted;
}
public void setIssnPrinted(String issnPrinted) {
this.issnPrinted = issnPrinted;
}
public void setIssnPrinted(String issnPrinted) {
this.issnPrinted = issnPrinted;
}
public String getIssnOnline() {
return issnOnline;
}
public String getIssnOnline() {
return issnOnline;
}
public void setIssnOnline(String issnOnline) {
this.issnOnline = issnOnline;
}
public void setIssnOnline(String issnOnline) {
this.issnOnline = issnOnline;
}
public String getIssnLinking() {
return issnLinking;
}
public String getIssnLinking() {
return issnLinking;
}
public void setIssnLinking(String issnLinking) {
this.issnLinking = issnLinking;
}
public void setIssnLinking(String issnLinking) {
this.issnLinking = issnLinking;
}
public String getEp() {
return ep;
}
public String getEp() {
return ep;
}
public void setEp(String ep) {
this.ep = ep;
}
public void setEp(String ep) {
this.ep = ep;
}
public String getIss() {
return iss;
}
public String getIss() {
return iss;
}
public void setIss(String iss) {
this.iss = iss;
}
public void setIss(String iss) {
this.iss = iss;
}
public String getSp() {
return sp;
}
public String getSp() {
return sp;
}
public void setSp(String sp) {
this.sp = sp;
}
public void setSp(String sp) {
this.sp = sp;
}
public String getVol() {
return vol;
}
public String getVol() {
return vol;
}
public void setVol(String vol) {
this.vol = vol;
}
public void setVol(String vol) {
this.vol = vol;
}
public String getEdition() {
return edition;
}
public String getEdition() {
return edition;
}
public void setEdition(String edition) {
this.edition = edition;
}
public void setEdition(String edition) {
this.edition = edition;
}
public String getConferenceplace() {
return conferenceplace;
}
public String getConferenceplace() {
return conferenceplace;
}
public void setConferenceplace(String conferenceplace) {
this.conferenceplace = conferenceplace;
}
public void setConferenceplace(String conferenceplace) {
this.conferenceplace = conferenceplace;
}
public String getConferencedate() {
return conferencedate;
}
public String getConferencedate() {
return conferencedate;
}
public void setConferencedate(String conferencedate) {
this.conferencedate = conferencedate;
}
public void setConferencedate(String conferencedate) {
this.conferencedate = conferencedate;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
Journal journal = (Journal) o;
return Objects.equals(name, journal.name)
&& Objects.equals(issnPrinted, journal.issnPrinted)
&& Objects.equals(issnOnline, journal.issnOnline)
&& Objects.equals(issnLinking, journal.issnLinking)
&& Objects.equals(ep, journal.ep)
&& Objects.equals(iss, journal.iss)
&& Objects.equals(sp, journal.sp)
&& Objects.equals(vol, journal.vol)
&& Objects.equals(edition, journal.edition)
&& Objects.equals(conferenceplace, journal.conferenceplace)
&& Objects.equals(conferencedate, journal.conferencedate)
&& Objects.equals(dataInfo, journal.dataInfo);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
Journal journal = (Journal) o;
return Objects.equals(name, journal.name)
&& Objects.equals(issnPrinted, journal.issnPrinted)
&& Objects.equals(issnOnline, journal.issnOnline)
&& Objects.equals(issnLinking, journal.issnLinking)
&& Objects.equals(ep, journal.ep)
&& Objects.equals(iss, journal.iss)
&& Objects.equals(sp, journal.sp)
&& Objects.equals(vol, journal.vol)
&& Objects.equals(edition, journal.edition)
&& Objects.equals(conferenceplace, journal.conferenceplace)
&& Objects.equals(conferencedate, journal.conferencedate)
&& Objects.equals(dataInfo, journal.dataInfo);
}
@Override
public int hashCode() {
return Objects.hash(
name,
issnPrinted,
issnOnline,
issnLinking,
ep,
iss,
sp,
vol,
edition,
conferenceplace,
conferencedate,
dataInfo);
}
@Override
public int hashCode() {
return Objects
.hash(
name,
issnPrinted,
issnOnline,
issnLinking,
ep,
iss,
sp,
vol,
edition,
conferenceplace,
conferencedate,
dataInfo);
}
}

97
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java
View File

@ -1,67 +1,74 @@
package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore;
import java.io.Serializable;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class KeyValue implements Serializable {
private String key;
private String key;
private String value;
private String value;
private DataInfo dataInfo;
private DataInfo dataInfo;
public String getKey() {
return key;
}
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public void setKey(String key) {
this.key = key;
}
public String getValue() {
return value;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
public void setValue(String value) {
this.value = value;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public String toComparableString() {
return isBlank()
? ""
: String.format(
"%s::%s",
key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : "");
}
public String toComparableString() {
return isBlank()
? ""
: String
.format(
"%s::%s",
key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : "");
}
@JsonIgnore
public boolean isBlank() {
return StringUtils.isBlank(key) && StringUtils.isBlank(value);
}
@JsonIgnore
public boolean isBlank() {
return StringUtils.isBlank(key) && StringUtils.isBlank(value);
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
KeyValue other = (KeyValue) obj;
KeyValue other = (KeyValue) obj;
return toComparableString().equals(other.toComparableString());
}
return toComparableString().equals(other.toComparableString());
}
}

39
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,26 +6,28 @@ import java.util.Objects;
public class OAIProvenance implements Serializable {
private OriginDescription originDescription;
private OriginDescription originDescription;
public OriginDescription getOriginDescription() {
return originDescription;
}
public OriginDescription getOriginDescription() {
return originDescription;
}
public void setOriginDescription(OriginDescription originDescription) {
this.originDescription = originDescription;
}
public void setOriginDescription(OriginDescription originDescription) {
this.originDescription = originDescription;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
OAIProvenance that = (OAIProvenance) o;
return Objects.equals(originDescription, that.originDescription);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
OAIProvenance that = (OAIProvenance) o;
return Objects.equals(originDescription, that.originDescription);
}
@Override
public int hashCode() {
return Objects.hash(originDescription);
}
@Override
public int hashCode() {
return Objects.hash(originDescription);
}
}

91
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -6,60 +7,64 @@ import java.util.Objects;
public abstract class Oaf implements Serializable {
protected List<KeyValue> collectedfrom;
protected List<KeyValue> collectedfrom;
private DataInfo dataInfo;
private DataInfo dataInfo;
private Long lastupdatetimestamp;
private Long lastupdatetimestamp;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public Long getLastupdatetimestamp() {
return lastupdatetimestamp;
}
public Long getLastupdatetimestamp() {
return lastupdatetimestamp;
}
public void setLastupdatetimestamp(Long lastupdatetimestamp) {
this.lastupdatetimestamp = lastupdatetimestamp;
}
public void setLastupdatetimestamp(Long lastupdatetimestamp) {
this.lastupdatetimestamp = lastupdatetimestamp;
}
public void mergeOAFDataInfo(Oaf e) {
if (e.getDataInfo() != null && compareTrust(this, e) < 0) dataInfo = e.getDataInfo();
}
public void mergeOAFDataInfo(Oaf e) {
if (e.getDataInfo() != null && compareTrust(this, e) < 0)
dataInfo = e.getDataInfo();
}
protected String extractTrust(Oaf e) {
if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null) return "0.0";
return e.getDataInfo().getTrust();
}
protected String extractTrust(Oaf e) {
if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null)
return "0.0";
return e.getDataInfo().getTrust();
}
protected int compareTrust(Oaf a, Oaf b) {
return extractTrust(a).compareTo(extractTrust(b));
}
protected int compareTrust(Oaf a, Oaf b) {
return extractTrust(a).compareTo(extractTrust(b));
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
Oaf oaf = (Oaf) o;
return Objects.equals(dataInfo, oaf.dataInfo)
&& Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
Oaf oaf = (Oaf) o;
return Objects.equals(dataInfo, oaf.dataInfo)
&& Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp);
}
@Override
public int hashCode() {
return Objects.hash(dataInfo, lastupdatetimestamp);
}
@Override
public int hashCode() {
return Objects.hash(dataInfo, lastupdatetimestamp);
}
}

168
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -6,118 +7,123 @@ import java.util.stream.Collectors;
public abstract class OafEntity extends Oaf implements Serializable {
private String id;
private String id;
private List<String> originalId;
private List<String> originalId;
private List<StructuredProperty> pid;
private List<StructuredProperty> pid;
private String dateofcollection;
private String dateofcollection;
private String dateoftransformation;
private String dateoftransformation;
private List<ExtraInfo> extraInfo;
private List<ExtraInfo> extraInfo;
private OAIProvenance oaiprovenance;
private OAIProvenance oaiprovenance;
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public void setId(String id) {
this.id = id;
}
public List<String> getOriginalId() {
return originalId;
}
public List<String> getOriginalId() {
return originalId;
}
public void setOriginalId(List<String> originalId) {
this.originalId = originalId;
}
public void setOriginalId(List<String> originalId) {
this.originalId = originalId;
}
public List<StructuredProperty> getPid() {
return pid;
}
public List<StructuredProperty> getPid() {
return pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public String getDateofcollection() {
return dateofcollection;
}
public String getDateofcollection() {
return dateofcollection;
}
public void setDateofcollection(String dateofcollection) {
this.dateofcollection = dateofcollection;
}
public void setDateofcollection(String dateofcollection) {
this.dateofcollection = dateofcollection;
}
public String getDateoftransformation() {
return dateoftransformation;
}
public String getDateoftransformation() {
return dateoftransformation;
}
public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation;
}
public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation;
}
public List<ExtraInfo> getExtraInfo() {
return extraInfo;
}
public List<ExtraInfo> getExtraInfo() {
return extraInfo;
}
public void setExtraInfo(List<ExtraInfo> extraInfo) {
this.extraInfo = extraInfo;
}
public void setExtraInfo(List<ExtraInfo> extraInfo) {
this.extraInfo = extraInfo;
}
public OAIProvenance getOaiprovenance() {
return oaiprovenance;
}
public OAIProvenance getOaiprovenance() {
return oaiprovenance;
}
public void setOaiprovenance(OAIProvenance oaiprovenance) {
this.oaiprovenance = oaiprovenance;
}
public void setOaiprovenance(OAIProvenance oaiprovenance) {
this.oaiprovenance = oaiprovenance;
}
public void mergeFrom(OafEntity e) {
public void mergeFrom(OafEntity e) {
if (e == null) return;
if (e == null)
return;
originalId = mergeLists(originalId, e.getOriginalId());
originalId = mergeLists(originalId, e.getOriginalId());
collectedfrom = mergeLists(collectedfrom, e.getCollectedfrom());
collectedfrom = mergeLists(collectedfrom, e.getCollectedfrom());
pid = mergeLists(pid, e.getPid());
pid = mergeLists(pid, e.getPid());
if (e.getDateofcollection() != null && compareTrust(this, e) < 0)
dateofcollection = e.getDateofcollection();
if (e.getDateofcollection() != null && compareTrust(this, e) < 0)
dateofcollection = e.getDateofcollection();
if (e.getDateoftransformation() != null && compareTrust(this, e) < 0)
dateoftransformation = e.getDateoftransformation();
if (e.getDateoftransformation() != null && compareTrust(this, e) < 0)
dateoftransformation = e.getDateoftransformation();
extraInfo = mergeLists(extraInfo, e.getExtraInfo());
extraInfo = mergeLists(extraInfo, e.getExtraInfo());
if (e.getOaiprovenance() != null && compareTrust(this, e) < 0)
oaiprovenance = e.getOaiprovenance();
}
if (e.getOaiprovenance() != null && compareTrust(this, e) < 0)
oaiprovenance = e.getOaiprovenance();
}
protected <T> List<T> mergeLists(final List<T>... lists) {
protected <T> List<T> mergeLists(final List<T>... lists) {
return Arrays.stream(lists)
.filter(Objects::nonNull)
.flatMap(List::stream)
.distinct()
.collect(Collectors.toList());
}
return Arrays
.stream(lists)
.filter(Objects::nonNull)
.flatMap(List::stream)
.distinct()
.collect(Collectors.toList());
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
OafEntity oafEntity = (OafEntity) o;
return Objects.equals(id, oafEntity.id);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
if (!super.equals(o))
return false;
OafEntity oafEntity = (OafEntity) o;
return Objects.equals(id, oafEntity.id);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), id);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), id);
}
}

323
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,221 +6,209 @@ import java.util.List;
public class Organization extends OafEntity implements Serializable {
private Field<String> legalshortname;
private Field<String> legalshortname;
private Field<String> legalname;
private Field<String> legalname;
private List<Field<String>> alternativeNames;
private List<Field<String>> alternativeNames;
private Field<String> websiteurl;
private Field<String> websiteurl;
private Field<String> logourl;
private Field<String> logourl;
private Field<String> eclegalbody;
private Field<String> eclegalbody;
private Field<String> eclegalperson;
private Field<String> eclegalperson;
private Field<String> ecnonprofit;
private Field<String> ecnonprofit;
private Field<String> ecresearchorganization;
private Field<String> ecresearchorganization;
private Field<String> echighereducation;
private Field<String> echighereducation;
private Field<String> ecinternationalorganizationeurinterests;
private Field<String> ecinternationalorganizationeurinterests;
private Field<String> ecinternationalorganization;
private Field<String> ecinternationalorganization;
private Field<String> ecenterprise;
private Field<String> ecenterprise;
private Field<String> ecsmevalidated;
private Field<String> ecsmevalidated;
private Field<String> ecnutscode;
private Field<String> ecnutscode;
private Qualifier country;
private Qualifier country;
public Field<String> getLegalshortname() {
return legalshortname;
}
public Field<String> getLegalshortname() {
return legalshortname;
}
public void setLegalshortname(Field<String> legalshortname) {
this.legalshortname = legalshortname;
}
public void setLegalshortname(Field<String> legalshortname) {
this.legalshortname = legalshortname;
}
public Field<String> getLegalname() {
return legalname;
}
public Field<String> getLegalname() {
return legalname;
}
public void setLegalname(Field<String> legalname) {
this.legalname = legalname;
}
public void setLegalname(Field<String> legalname) {
this.legalname = legalname;
}
public List<Field<String>> getAlternativeNames() {
return alternativeNames;
}
public List<Field<String>> getAlternativeNames() {
return alternativeNames;
}
public void setAlternativeNames(List<Field<String>> alternativeNames) {
this.alternativeNames = alternativeNames;
}
public void setAlternativeNames(List<Field<String>> alternativeNames) {
this.alternativeNames = alternativeNames;
}
public Field<String> getWebsiteurl() {
return websiteurl;
}
public Field<String> getWebsiteurl() {
return websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public Field<String> getLogourl() {
return logourl;
}
public Field<String> getLogourl() {
return logourl;
}
public void setLogourl(Field<String> logourl) {
this.logourl = logourl;
}
public void setLogourl(Field<String> logourl) {
this.logourl = logourl;
}
public Field<String> getEclegalbody() {
return eclegalbody;
}
public Field<String> getEclegalbody() {
return eclegalbody;
}
public void setEclegalbody(Field<String> eclegalbody) {
this.eclegalbody = eclegalbody;
}
public void setEclegalbody(Field<String> eclegalbody) {
this.eclegalbody = eclegalbody;
}
public Field<String> getEclegalperson() {
return eclegalperson;
}
public Field<String> getEclegalperson() {
return eclegalperson;
}
public void setEclegalperson(Field<String> eclegalperson) {
this.eclegalperson = eclegalperson;
}
public void setEclegalperson(Field<String> eclegalperson) {
this.eclegalperson = eclegalperson;
}
public Field<String> getEcnonprofit() {
return ecnonprofit;
}
public Field<String> getEcnonprofit() {
return ecnonprofit;
}
public void setEcnonprofit(Field<String> ecnonprofit) {
this.ecnonprofit = ecnonprofit;
}
public void setEcnonprofit(Field<String> ecnonprofit) {
this.ecnonprofit = ecnonprofit;
}
public Field<String> getEcresearchorganization() {
return ecresearchorganization;
}
public Field<String> getEcresearchorganization() {
return ecresearchorganization;
}
public void setEcresearchorganization(Field<String> ecresearchorganization) {
this.ecresearchorganization = ecresearchorganization;
}
public void setEcresearchorganization(Field<String> ecresearchorganization) {
this.ecresearchorganization = ecresearchorganization;
}
public Field<String> getEchighereducation() {
return echighereducation;
}
public Field<String> getEchighereducation() {
return echighereducation;
}
public void setEchighereducation(Field<String> echighereducation) {
this.echighereducation = echighereducation;
}
public void setEchighereducation(Field<String> echighereducation) {
this.echighereducation = echighereducation;
}
public Field<String> getEcinternationalorganizationeurinterests() {
return ecinternationalorganizationeurinterests;
}
public Field<String> getEcinternationalorganizationeurinterests() {
return ecinternationalorganizationeurinterests;
}
public void setEcinternationalorganizationeurinterests(
Field<String> ecinternationalorganizationeurinterests) {
this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests;
}
public void setEcinternationalorganizationeurinterests(
Field<String> ecinternationalorganizationeurinterests) {
this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests;
}
public Field<String> getEcinternationalorganization() {
return ecinternationalorganization;
}
public Field<String> getEcinternationalorganization() {
return ecinternationalorganization;
}
public void setEcinternationalorganization(Field<String> ecinternationalorganization) {
this.ecinternationalorganization = ecinternationalorganization;
}
public void setEcinternationalorganization(Field<String> ecinternationalorganization) {
this.ecinternationalorganization = ecinternationalorganization;
}
public Field<String> getEcenterprise() {
return ecenterprise;
}
public Field<String> getEcenterprise() {
return ecenterprise;
}
public void setEcenterprise(Field<String> ecenterprise) {
this.ecenterprise = ecenterprise;
}
public void setEcenterprise(Field<String> ecenterprise) {
this.ecenterprise = ecenterprise;
}
public Field<String> getEcsmevalidated() {
return ecsmevalidated;
}
public Field<String> getEcsmevalidated() {
return ecsmevalidated;
}
public void setEcsmevalidated(Field<String> ecsmevalidated) {
this.ecsmevalidated = ecsmevalidated;
}
public void setEcsmevalidated(Field<String> ecsmevalidated) {
this.ecsmevalidated = ecsmevalidated;
}
public Field<String> getEcnutscode() {
return ecnutscode;
}
public Field<String> getEcnutscode() {
return ecnutscode;
}
public void setEcnutscode(Field<String> ecnutscode) {
this.ecnutscode = ecnutscode;
}
public void setEcnutscode(Field<String> ecnutscode) {
this.ecnutscode = ecnutscode;
}
public Qualifier getCountry() {
return country;
}
public Qualifier getCountry() {
return country;
}
public void setCountry(Qualifier country) {
this.country = country;
}
public void setCountry(Qualifier country) {
this.country = country;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Organization.class.isAssignableFrom(e.getClass())) {
return;
}
if (!Organization.class.isAssignableFrom(e.getClass())) {
return;
}
final Organization o = (Organization) e;
legalshortname =
o.getLegalshortname() != null && compareTrust(this, e) < 0
? o.getLegalshortname()
: legalshortname;
legalname =
o.getLegalname() != null && compareTrust(this, e) < 0 ? o.getLegalname() : legalname;
alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames);
websiteurl =
o.getWebsiteurl() != null && compareTrust(this, e) < 0 ? o.getWebsiteurl() : websiteurl;
logourl = o.getLogourl() != null && compareTrust(this, e) < 0 ? o.getLogourl() : logourl;
eclegalbody =
o.getEclegalbody() != null && compareTrust(this, e) < 0 ? o.getEclegalbody() : eclegalbody;
eclegalperson =
o.getEclegalperson() != null && compareTrust(this, e) < 0
? o.getEclegalperson()
: eclegalperson;
ecnonprofit =
o.getEcnonprofit() != null && compareTrust(this, e) < 0 ? o.getEcnonprofit() : ecnonprofit;
ecresearchorganization =
o.getEcresearchorganization() != null && compareTrust(this, e) < 0
? o.getEcresearchorganization()
: ecresearchorganization;
echighereducation =
o.getEchighereducation() != null && compareTrust(this, e) < 0
? o.getEchighereducation()
: echighereducation;
ecinternationalorganizationeurinterests =
o.getEcinternationalorganizationeurinterests() != null && compareTrust(this, e) < 0
? o.getEcinternationalorganizationeurinterests()
: ecinternationalorganizationeurinterests;
ecinternationalorganization =
o.getEcinternationalorganization() != null && compareTrust(this, e) < 0
? o.getEcinternationalorganization()
: ecinternationalorganization;
ecenterprise =
o.getEcenterprise() != null && compareTrust(this, e) < 0
? o.getEcenterprise()
: ecenterprise;
ecsmevalidated =
o.getEcsmevalidated() != null && compareTrust(this, e) < 0
? o.getEcsmevalidated()
: ecsmevalidated;
ecnutscode =
o.getEcnutscode() != null && compareTrust(this, e) < 0 ? o.getEcnutscode() : ecnutscode;
country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country;
mergeOAFDataInfo(o);
}
final Organization o = (Organization) e;
legalshortname = o.getLegalshortname() != null && compareTrust(this, e) < 0
? o.getLegalshortname()
: legalshortname;
legalname = o.getLegalname() != null && compareTrust(this, e) < 0 ? o.getLegalname() : legalname;
alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames);
websiteurl = o.getWebsiteurl() != null && compareTrust(this, e) < 0 ? o.getWebsiteurl() : websiteurl;
logourl = o.getLogourl() != null && compareTrust(this, e) < 0 ? o.getLogourl() : logourl;
eclegalbody = o.getEclegalbody() != null && compareTrust(this, e) < 0 ? o.getEclegalbody() : eclegalbody;
eclegalperson = o.getEclegalperson() != null && compareTrust(this, e) < 0
? o.getEclegalperson()
: eclegalperson;
ecnonprofit = o.getEcnonprofit() != null && compareTrust(this, e) < 0 ? o.getEcnonprofit() : ecnonprofit;
ecresearchorganization = o.getEcresearchorganization() != null && compareTrust(this, e) < 0
? o.getEcresearchorganization()
: ecresearchorganization;
echighereducation = o.getEchighereducation() != null && compareTrust(this, e) < 0
? o.getEchighereducation()
: echighereducation;
ecinternationalorganizationeurinterests = o.getEcinternationalorganizationeurinterests() != null
&& compareTrust(this, e) < 0
? o.getEcinternationalorganizationeurinterests()
: ecinternationalorganizationeurinterests;
ecinternationalorganization = o.getEcinternationalorganization() != null && compareTrust(this, e) < 0
? o.getEcinternationalorganization()
: ecinternationalorganization;
ecenterprise = o.getEcenterprise() != null && compareTrust(this, e) < 0
? o.getEcenterprise()
: ecenterprise;
ecsmevalidated = o.getEcsmevalidated() != null && compareTrust(this, e) < 0
? o.getEcsmevalidated()
: ecsmevalidated;
ecnutscode = o.getEcnutscode() != null && compareTrust(this, e) < 0 ? o.getEcnutscode() : ecnutscode;
country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country;
mergeOAFDataInfo(o);
}
}

119
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,81 +6,83 @@ import java.util.Objects;
public class OriginDescription implements Serializable {
private String harvestDate;
private String harvestDate;
private Boolean altered = true;
private Boolean altered = true;
private String baseURL;
private String baseURL;
private String identifier;
private String identifier;
private String datestamp;
private String datestamp;
private String metadataNamespace;
private String metadataNamespace;
public String getHarvestDate() {
return harvestDate;
}
public String getHarvestDate() {
return harvestDate;
}
public void setHarvestDate(String harvestDate) {
this.harvestDate = harvestDate;
}
public void setHarvestDate(String harvestDate) {
this.harvestDate = harvestDate;
}
public Boolean getAltered() {
return altered;
}
public Boolean getAltered() {
return altered;
}
public void setAltered(Boolean altered) {
this.altered = altered;
}
public void setAltered(Boolean altered) {
this.altered = altered;
}
public String getBaseURL() {
return baseURL;
}
public String getBaseURL() {
return baseURL;
}
public void setBaseURL(String baseURL) {
this.baseURL = baseURL;
}
public void setBaseURL(String baseURL) {
this.baseURL = baseURL;
}
public String getIdentifier() {
return identifier;
}
public String getIdentifier() {
return identifier;
}
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
public String getDatestamp() {
return datestamp;
}
public String getDatestamp() {
return datestamp;
}
public void setDatestamp(String datestamp) {
this.datestamp = datestamp;
}
public void setDatestamp(String datestamp) {
this.datestamp = datestamp;
}
public String getMetadataNamespace() {
return metadataNamespace;
}
public String getMetadataNamespace() {
return metadataNamespace;
}
public void setMetadataNamespace(String metadataNamespace) {
this.metadataNamespace = metadataNamespace;
}
public void setMetadataNamespace(String metadataNamespace) {
this.metadataNamespace = metadataNamespace;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
OriginDescription that = (OriginDescription) o;
return Objects.equals(harvestDate, that.harvestDate)
&& Objects.equals(altered, that.altered)
&& Objects.equals(baseURL, that.baseURL)
&& Objects.equals(identifier, that.identifier)
&& Objects.equals(datestamp, that.datestamp)
&& Objects.equals(metadataNamespace, that.metadataNamespace);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
OriginDescription that = (OriginDescription) o;
return Objects.equals(harvestDate, that.harvestDate)
&& Objects.equals(altered, that.altered)
&& Objects.equals(baseURL, that.baseURL)
&& Objects.equals(identifier, that.identifier)
&& Objects.equals(datestamp, that.datestamp)
&& Objects.equals(metadataNamespace, that.metadataNamespace);
}
@Override
public int hashCode() {
return Objects.hash(harvestDate, altered, baseURL, identifier, datestamp, metadataNamespace);
}
@Override
public int hashCode() {
return Objects.hash(harvestDate, altered, baseURL, identifier, datestamp, metadataNamespace);
}
}

76
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java
View File

@ -1,58 +1,60 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class OtherResearchProduct extends Result implements Serializable {
private List<Field<String>> contactperson;
private List<Field<String>> contactperson;
private List<Field<String>> contactgroup;
private List<Field<String>> contactgroup;
private List<Field<String>> tool;
private List<Field<String>> tool;
public OtherResearchProduct() {
setResulttype(ModelConstants.ORP_DEFAULT_RESULTTYPE);
}
public OtherResearchProduct() {
setResulttype(ModelConstants.ORP_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getContactperson() {
return contactperson;
}
public List<Field<String>> getContactperson() {
return contactperson;
}
public void setContactperson(List<Field<String>> contactperson) {
this.contactperson = contactperson;
}
public void setContactperson(List<Field<String>> contactperson) {
this.contactperson = contactperson;
}
public List<Field<String>> getContactgroup() {
return contactgroup;
}
public List<Field<String>> getContactgroup() {
return contactgroup;
}
public void setContactgroup(List<Field<String>> contactgroup) {
this.contactgroup = contactgroup;
}
public void setContactgroup(List<Field<String>> contactgroup) {
this.contactgroup = contactgroup;
}
public List<Field<String>> getTool() {
return tool;
}
public List<Field<String>> getTool() {
return tool;
}
public void setTool(List<Field<String>> tool) {
this.tool = tool;
}
public void setTool(List<Field<String>> tool) {
this.tool = tool;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())) {
return;
}
if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())) {
return;
}
OtherResearchProduct o = (OtherResearchProduct) e;
OtherResearchProduct o = (OtherResearchProduct) e;
contactperson = mergeLists(contactperson, o.getContactperson());
contactgroup = mergeLists(contactgroup, o.getContactgroup());
tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e);
}
contactperson = mergeLists(contactperson, o.getContactperson());
contactgroup = mergeLists(contactgroup, o.getContactgroup());
tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e);
}
}

534
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -5,335 +6,320 @@ import java.util.List;
public class Project extends OafEntity implements Serializable {
private Field<String> websiteurl;
private Field<String> websiteurl;
private Field<String> code;
private Field<String> code;
private Field<String> acronym;
private Field<String> acronym;
private Field<String> title;
private Field<String> title;
private Field<String> startdate;
private Field<String> startdate;
private Field<String> enddate;
private Field<String> enddate;
private Field<String> callidentifier;
private Field<String> callidentifier;
private Field<String> keywords;
private Field<String> keywords;
private Field<String> duration;
private Field<String> duration;
private Field<String> ecsc39;
private Field<String> ecsc39;
private Field<String> oamandatepublications;
private Field<String> oamandatepublications;
private Field<String> ecarticle29_3;
private Field<String> ecarticle29_3;
private List<StructuredProperty> subjects;
private List<StructuredProperty> subjects;
private List<Field<String>> fundingtree;
private List<Field<String>> fundingtree;
private Qualifier contracttype;
private Qualifier contracttype;
private Field<String> optional1;
private Field<String> optional1;
private Field<String> optional2;
private Field<String> optional2;
private Field<String> jsonextrainfo;
private Field<String> jsonextrainfo;
private Field<String> contactfullname;
private Field<String> contactfullname;
private Field<String> contactfax;
private Field<String> contactfax;
private Field<String> contactphone;
private Field<String> contactphone;
private Field<String> contactemail;
private Field<String> contactemail;
private Field<String> summary;
private Field<String> summary;
private Field<String> currency;
private Field<String> currency;
private Float totalcost;
private Float totalcost;
private Float fundedamount;
private Float fundedamount;
public Field<String> getWebsiteurl() {
return websiteurl;
}
public Field<String> getWebsiteurl() {
return websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public Field<String> getCode() {
return code;
}
public Field<String> getCode() {
return code;
}
public void setCode(Field<String> code) {
this.code = code;
}
public void setCode(Field<String> code) {
this.code = code;
}
public Field<String> getAcronym() {
return acronym;
}
public Field<String> getAcronym() {
return acronym;
}
public void setAcronym(Field<String> acronym) {
this.acronym = acronym;
}
public void setAcronym(Field<String> acronym) {
this.acronym = acronym;
}
public Field<String> getTitle() {
return title;
}
public Field<String> getTitle() {
return title;
}
public void setTitle(Field<String> title) {
this.title = title;
}
public void setTitle(Field<String> title) {
this.title = title;
}
public Field<String> getStartdate() {
return startdate;
}
public Field<String> getStartdate() {
return startdate;
}
public void setStartdate(Field<String> startdate) {
this.startdate = startdate;
}
public void setStartdate(Field<String> startdate) {
this.startdate = startdate;
}
public Field<String> getEnddate() {
return enddate;
}
public Field<String> getEnddate() {
return enddate;
}
public void setEnddate(Field<String> enddate) {
this.enddate = enddate;
}
public void setEnddate(Field<String> enddate) {
this.enddate = enddate;
}
public Field<String> getCallidentifier() {
return callidentifier;
}
public Field<String> getCallidentifier() {
return callidentifier;
}
public void setCallidentifier(Field<String> callidentifier) {
this.callidentifier = callidentifier;
}
public void setCallidentifier(Field<String> callidentifier) {
this.callidentifier = callidentifier;
}
public Field<String> getKeywords() {
return keywords;
}
public Field<String> getKeywords() {
return keywords;
}
public void setKeywords(Field<String> keywords) {
this.keywords = keywords;
}
public void setKeywords(Field<String> keywords) {
this.keywords = keywords;
}
public Field<String> getDuration() {
return duration;
}
public Field<String> getDuration() {
return duration;
}
public void setDuration(Field<String> duration) {
this.duration = duration;
}
public void setDuration(Field<String> duration) {
this.duration = duration;
}
public Field<String> getEcsc39() {
return ecsc39;
}
public Field<String> getEcsc39() {
return ecsc39;
}
public void setEcsc39(Field<String> ecsc39) {
this.ecsc39 = ecsc39;
}
public void setEcsc39(Field<String> ecsc39) {
this.ecsc39 = ecsc39;
}
public Field<String> getOamandatepublications() {
return oamandatepublications;
}
public Field<String> getOamandatepublications() {
return oamandatepublications;
}
public void setOamandatepublications(Field<String> oamandatepublications) {
this.oamandatepublications = oamandatepublications;
}
public void setOamandatepublications(Field<String> oamandatepublications) {
this.oamandatepublications = oamandatepublications;
}
public Field<String> getEcarticle29_3() {
return ecarticle29_3;
}
public Field<String> getEcarticle29_3() {
return ecarticle29_3;
}
public void setEcarticle29_3(Field<String> ecarticle29_3) {
this.ecarticle29_3 = ecarticle29_3;
}
public void setEcarticle29_3(Field<String> ecarticle29_3) {
this.ecarticle29_3 = ecarticle29_3;
}
public List<StructuredProperty> getSubjects() {
return subjects;
}
public List<StructuredProperty> getSubjects() {
return subjects;
}
public void setSubjects(List<StructuredProperty> subjects) {
this.subjects = subjects;
}
public void setSubjects(List<StructuredProperty> subjects) {
this.subjects = subjects;
}
public List<Field<String>> getFundingtree() {
return fundingtree;
}
public List<Field<String>> getFundingtree() {
return fundingtree;
}
public void setFundingtree(List<Field<String>> fundingtree) {
this.fundingtree = fundingtree;
}
public void setFundingtree(List<Field<String>> fundingtree) {
this.fundingtree = fundingtree;
}
public Qualifier getContracttype() {
return contracttype;
}
public Qualifier getContracttype() {
return contracttype;
}
public void setContracttype(Qualifier contracttype) {
this.contracttype = contracttype;
}
public void setContracttype(Qualifier contracttype) {
this.contracttype = contracttype;
}
public Field<String> getOptional1() {
return optional1;
}
public Field<String> getOptional1() {
return optional1;
}
public void setOptional1(Field<String> optional1) {
this.optional1 = optional1;
}
public Field<String> getOptional2() {
return optional2;
}
public void setOptional2(Field<String> optional2) {
this.optional2 = optional2;
}
public Field<String> getJsonextrainfo() {
return jsonextrainfo;
}
public void setJsonextrainfo(Field<String> jsonextrainfo) {
this.jsonextrainfo = jsonextrainfo;
}
public Field<String> getContactfullname() {
return contactfullname;
}
public void setContactfullname(Field<String> contactfullname) {
this.contactfullname = contactfullname;
}
public Field<String> getContactfax() {
return contactfax;
}
public void setContactfax(Field<String> contactfax) {
this.contactfax = contactfax;
}
public Field<String> getContactphone() {
return contactphone;
}
public void setContactphone(Field<String> contactphone) {
this.contactphone = contactphone;
}
public Field<String> getContactemail() {
return contactemail;
}
public void setContactemail(Field<String> contactemail) {
this.contactemail = contactemail;
}
public Field<String> getSummary() {
return summary;
}
public void setSummary(Field<String> summary) {
this.summary = summary;
}
public Field<String> getCurrency() {
return currency;
}
public void setCurrency(Field<String> currency) {
this.currency = currency;
}
public Float getTotalcost() {
return totalcost;
}
public void setTotalcost(Float totalcost) {
this.totalcost = totalcost;
}
public Float getFundedamount() {
return fundedamount;
}
public void setFundedamount(Float fundedamount) {
this.fundedamount = fundedamount;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Project.class.isAssignableFrom(e.getClass())) {
return;
}
Project p = (Project) e;
websiteurl =
p.getWebsiteurl() != null && compareTrust(this, e) < 0 ? p.getWebsiteurl() : websiteurl;
code = p.getCode() != null && compareTrust(this, e) < 0 ? p.getCode() : code;
acronym = p.getAcronym() != null && compareTrust(this, e) < 0 ? p.getAcronym() : acronym;
title = p.getTitle() != null && compareTrust(this, e) < 0 ? p.getTitle() : title;
startdate =
p.getStartdate() != null && compareTrust(this, e) < 0 ? p.getStartdate() : startdate;
enddate = p.getEnddate() != null && compareTrust(this, e) < 0 ? p.getEnddate() : enddate;
callidentifier =
p.getCallidentifier() != null && compareTrust(this, e) < 0
? p.getCallidentifier()
: callidentifier;
keywords = p.getKeywords() != null && compareTrust(this, e) < 0 ? p.getKeywords() : keywords;
duration = p.getDuration() != null && compareTrust(this, e) < 0 ? p.getDuration() : duration;
ecsc39 = p.getEcsc39() != null && compareTrust(this, e) < 0 ? p.getEcsc39() : ecsc39;
oamandatepublications =
p.getOamandatepublications() != null && compareTrust(this, e) < 0
? p.getOamandatepublications()
: oamandatepublications;
ecarticle29_3 =
p.getEcarticle29_3() != null && compareTrust(this, e) < 0
? p.getEcarticle29_3()
: ecarticle29_3;
subjects = mergeLists(subjects, p.getSubjects());
fundingtree = mergeLists(fundingtree, p.getFundingtree());
contracttype =
p.getContracttype() != null && compareTrust(this, e) < 0
? p.getContracttype()
: contracttype;
optional1 =
p.getOptional1() != null && compareTrust(this, e) < 0 ? p.getOptional1() : optional1;
optional2 =
p.getOptional2() != null && compareTrust(this, e) < 0 ? p.getOptional2() : optional2;
jsonextrainfo =
p.getJsonextrainfo() != null && compareTrust(this, e) < 0
? p.getJsonextrainfo()
: jsonextrainfo;
contactfullname =
p.getContactfullname() != null && compareTrust(this, e) < 0
? p.getContactfullname()
: contactfullname;
contactfax =
p.getContactfax() != null && compareTrust(this, e) < 0 ? p.getContactfax() : contactfax;
contactphone =
p.getContactphone() != null && compareTrust(this, e) < 0
? p.getContactphone()
: contactphone;
contactemail =
p.getContactemail() != null && compareTrust(this, e) < 0
? p.getContactemail()
: contactemail;
summary = p.getSummary() != null && compareTrust(this, e) < 0 ? p.getSummary() : summary;
currency = p.getCurrency() != null && compareTrust(this, e) < 0 ? p.getCurrency() : currency;
totalcost =
p.getTotalcost() != null && compareTrust(this, e) < 0 ? p.getTotalcost() : totalcost;
fundedamount =
p.getFundedamount() != null && compareTrust(this, e) < 0
? p.getFundedamount()
: fundedamount;
mergeOAFDataInfo(e);
}
public void setOptional1(Field<String> optional1) {
this.optional1 = optional1;
}
public Field<String> getOptional2() {
return optional2;
}
public void setOptional2(Field<String> optional2) {
this.optional2 = optional2;
}
public Field<String> getJsonextrainfo() {
return jsonextrainfo;
}
public void setJsonextrainfo(Field<String> jsonextrainfo) {
this.jsonextrainfo = jsonextrainfo;
}
public Field<String> getContactfullname() {
return contactfullname;
}
public void setContactfullname(Field<String> contactfullname) {
this.contactfullname = contactfullname;
}
public Field<String> getContactfax() {
return contactfax;
}
public void setContactfax(Field<String> contactfax) {
this.contactfax = contactfax;
}
public Field<String> getContactphone() {
return contactphone;
}
public void setContactphone(Field<String> contactphone) {
this.contactphone = contactphone;
}
public Field<String> getContactemail() {
return contactemail;
}
public void setContactemail(Field<String> contactemail) {
this.contactemail = contactemail;
}
public Field<String> getSummary() {
return summary;
}
public void setSummary(Field<String> summary) {
this.summary = summary;
}
public Field<String> getCurrency() {
return currency;
}
public void setCurrency(Field<String> currency) {
this.currency = currency;
}
public Float getTotalcost() {
return totalcost;
}
public void setTotalcost(Float totalcost) {
this.totalcost = totalcost;
}
public Float getFundedamount() {
return fundedamount;
}
public void setFundedamount(Float fundedamount) {
this.fundedamount = fundedamount;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Project.class.isAssignableFrom(e.getClass())) {
return;
}
Project p = (Project) e;
websiteurl = p.getWebsiteurl() != null && compareTrust(this, e) < 0 ? p.getWebsiteurl() : websiteurl;
code = p.getCode() != null && compareTrust(this, e) < 0 ? p.getCode() : code;
acronym = p.getAcronym() != null && compareTrust(this, e) < 0 ? p.getAcronym() : acronym;
title = p.getTitle() != null && compareTrust(this, e) < 0 ? p.getTitle() : title;
startdate = p.getStartdate() != null && compareTrust(this, e) < 0 ? p.getStartdate() : startdate;
enddate = p.getEnddate() != null && compareTrust(this, e) < 0 ? p.getEnddate() : enddate;
callidentifier = p.getCallidentifier() != null && compareTrust(this, e) < 0
? p.getCallidentifier()
: callidentifier;
keywords = p.getKeywords() != null && compareTrust(this, e) < 0 ? p.getKeywords() : keywords;
duration = p.getDuration() != null && compareTrust(this, e) < 0 ? p.getDuration() : duration;
ecsc39 = p.getEcsc39() != null && compareTrust(this, e) < 0 ? p.getEcsc39() : ecsc39;
oamandatepublications = p.getOamandatepublications() != null && compareTrust(this, e) < 0
? p.getOamandatepublications()
: oamandatepublications;
ecarticle29_3 = p.getEcarticle29_3() != null && compareTrust(this, e) < 0
? p.getEcarticle29_3()
: ecarticle29_3;
subjects = mergeLists(subjects, p.getSubjects());
fundingtree = mergeLists(fundingtree, p.getFundingtree());
contracttype = p.getContracttype() != null && compareTrust(this, e) < 0
? p.getContracttype()
: contracttype;
optional1 = p.getOptional1() != null && compareTrust(this, e) < 0 ? p.getOptional1() : optional1;
optional2 = p.getOptional2() != null && compareTrust(this, e) < 0 ? p.getOptional2() : optional2;
jsonextrainfo = p.getJsonextrainfo() != null && compareTrust(this, e) < 0
? p.getJsonextrainfo()
: jsonextrainfo;
contactfullname = p.getContactfullname() != null && compareTrust(this, e) < 0
? p.getContactfullname()
: contactfullname;
contactfax = p.getContactfax() != null && compareTrust(this, e) < 0 ? p.getContactfax() : contactfax;
contactphone = p.getContactphone() != null && compareTrust(this, e) < 0
? p.getContactphone()
: contactphone;
contactemail = p.getContactemail() != null && compareTrust(this, e) < 0
? p.getContactemail()
: contactemail;
summary = p.getSummary() != null && compareTrust(this, e) < 0 ? p.getSummary() : summary;
currency = p.getCurrency() != null && compareTrust(this, e) < 0 ? p.getCurrency() : currency;
totalcost = p.getTotalcost() != null && compareTrust(this, e) < 0 ? p.getTotalcost() : totalcost;
fundedamount = p.getFundedamount() != null && compareTrust(this, e) < 0
? p.getFundedamount()
: fundedamount;
mergeOAFDataInfo(e);
}
}

47
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java
View File

@ -1,36 +1,39 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Publication extends Result implements Serializable {
// publication specific
private Journal journal;
// publication specific
private Journal journal;
public Publication() {
setResulttype(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE);
}
public Publication() {
setResulttype(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE);
}
public Journal getJournal() {
return journal;
}
public Journal getJournal() {
return journal;
}
public void setJournal(Journal journal) {
this.journal = journal;
}
public void setJournal(Journal journal) {
this.journal = journal;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Publication.class.isAssignableFrom(e.getClass())) {
return;
}
if (!Publication.class.isAssignableFrom(e.getClass())) {
return;
}
Publication p = (Publication) e;
Publication p = (Publication) e;
if (p.getJournal() != null && compareTrust(this, e) < 0) journal = p.getJournal();
mergeOAFDataInfo(e);
}
if (p.getJournal() != null && compareTrust(this, e) < 0)
journal = p.getJournal();
mergeOAFDataInfo(e);
}
}

123
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java
View File

@ -1,80 +1,87 @@
package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore;
import java.io.Serializable;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore;
public class Qualifier implements Serializable {
private String classid;
private String classname;
private String schemeid;
private String schemename;
private String classid;
private String classname;
private String schemeid;
private String schemename;
public String getClassid() {
return classid;
}
public String getClassid() {
return classid;
}
public void setClassid(String classid) {
this.classid = classid;
}
public void setClassid(String classid) {
this.classid = classid;
}
public String getClassname() {
return classname;
}
public String getClassname() {
return classname;
}
public void setClassname(String classname) {
this.classname = classname;
}
public void setClassname(String classname) {
this.classname = classname;
}
public String getSchemeid() {
return schemeid;
}
public String getSchemeid() {
return schemeid;
}
public void setSchemeid(String schemeid) {
this.schemeid = schemeid;
}
public void setSchemeid(String schemeid) {
this.schemeid = schemeid;
}
public String getSchemename() {
return schemename;
}
public String getSchemename() {
return schemename;
}
public void setSchemename(String schemename) {
this.schemename = schemename;
}
public void setSchemename(String schemename) {
this.schemename = schemename;
}
public String toComparableString() {
return isBlank()
? ""
: String.format(
"%s::%s::%s::%s",
classid != null ? classid : "",
classname != null ? classname : "",
schemeid != null ? schemeid : "",
schemename != null ? schemename : "");
}
public String toComparableString() {
return isBlank()
? ""
: String
.format(
"%s::%s::%s::%s",
classid != null ? classid : "",
classname != null ? classname : "",
schemeid != null ? schemeid : "",
schemename != null ? schemename : "");
}
@JsonIgnore
public boolean isBlank() {
return StringUtils.isBlank(classid)
&& StringUtils.isBlank(classname)
&& StringUtils.isBlank(schemeid)
&& StringUtils.isBlank(schemename);
}
@JsonIgnore
public boolean isBlank() {
return StringUtils.isBlank(classid)
&& StringUtils.isBlank(classname)
&& StringUtils.isBlank(schemeid)
&& StringUtils.isBlank(schemename);
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Qualifier other = (Qualifier) obj;
Qualifier other = (Qualifier) obj;
return toComparableString().equals(other.toComparableString());
}
return toComparableString().equals(other.toComparableString());
}
}

142
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import static com.google.common.base.Preconditions.checkArgument;
@ -8,91 +9,96 @@ import java.util.stream.Stream;
public class Relation extends Oaf {
private String relType;
private String relType;
private String subRelType;
private String subRelType;
private String relClass;
private String relClass;
private String source;
private String source;
private String target;
private String target;
public String getRelType() {
return relType;
}
public String getRelType() {
return relType;
}
public void setRelType(final String relType) {
this.relType = relType;
}
public void setRelType(final String relType) {
this.relType = relType;
}
public String getSubRelType() {
return subRelType;
}
public String getSubRelType() {
return subRelType;
}
public void setSubRelType(final String subRelType) {
this.subRelType = subRelType;
}
public void setSubRelType(final String subRelType) {
this.subRelType = subRelType;
}
public String getRelClass() {
return relClass;
}
public String getRelClass() {
return relClass;
}
public void setRelClass(final String relClass) {
this.relClass = relClass;
}
public void setRelClass(final String relClass) {
this.relClass = relClass;
}
public String getSource() {
return source;
}
public String getSource() {
return source;
}
public void setSource(final String source) {
this.source = source;
}
public void setSource(final String source) {
this.source = source;
}
public String getTarget() {
return target;
}
public String getTarget() {
return target;
}
public void setTarget(final String target) {
this.target = target;
}
public void setTarget(final String target) {
this.target = target;
}
public void mergeFrom(final Relation r) {
public void mergeFrom(final Relation r) {
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal");
checkArgument(Objects.equals(getTarget(), r.getTarget()), "target ids must be equal");
checkArgument(Objects.equals(getRelType(), r.getRelType()), "relType(s) must be equal");
checkArgument(
Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal");
checkArgument(Objects.equals(getTarget(), r.getTarget()), "target ids must be equal");
checkArgument(Objects.equals(getRelType(), r.getRelType()), "relType(s) must be equal");
checkArgument(
Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
setCollectedfrom(
Stream.concat(
Optional.ofNullable(getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional.ofNullable(r.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
}
setCollectedfrom(
Stream
.concat(
Optional
.ofNullable(getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional
.ofNullable(r.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
Relation relation = (Relation) o;
return relType.equals(relation.relType)
&& subRelType.equals(relation.subRelType)
&& relClass.equals(relation.relClass)
&& source.equals(relation.source)
&& target.equals(relation.target);
}
@Override
public boolean equals(Object o) {
if (this == o)
return true;
if (o == null || getClass() != o.getClass())
return false;
Relation relation = (Relation) o;
return relType.equals(relation.relType)
&& subRelType.equals(relation.subRelType)
&& relClass.equals(relation.relClass)
&& source.equals(relation.source)
&& target.equals(relation.target);
}
@Override
public int hashCode() {
return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom);
}
@Override
public int hashCode() {
return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom);
}
}

400
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
@ -6,286 +7,291 @@ import java.util.List;
public class Result extends OafEntity implements Serializable {
private List<Author> author;
private List<Author> author;
// resulttype allows subclassing results into publications | datasets | software
private Qualifier resulttype;
// resulttype allows subclassing results into publications | datasets | software
private Qualifier resulttype;
// common fields
private Qualifier language;
// common fields
private Qualifier language;
private List<Country> country;
private List<Country> country;
private List<StructuredProperty> subject;
private List<StructuredProperty> subject;
private List<StructuredProperty> title;
private List<StructuredProperty> title;
private List<StructuredProperty> relevantdate;
private List<StructuredProperty> relevantdate;
private List<Field<String>> description;
private List<Field<String>> description;
private Field<String> dateofacceptance;
private Field<String> dateofacceptance;
private Field<String> publisher;
private Field<String> publisher;
private Field<String> embargoenddate;
private Field<String> embargoenddate;
private List<Field<String>> source;
private List<Field<String>> source;
private List<Field<String>> fulltext; // remove candidate
private List<Field<String>> fulltext; // remove candidate
private List<Field<String>> format;
private List<Field<String>> format;
private List<Field<String>> contributor;
private List<Field<String>> contributor;
private Qualifier resourcetype;
private Qualifier resourcetype;
private List<Field<String>> coverage;
private List<Field<String>> coverage;
private Qualifier bestaccessright;
private Qualifier bestaccessright;
private List<Context> context;
private List<Context> context;
private List<ExternalReference> externalReference;
private List<ExternalReference> externalReference;
private List<Instance> instance;
private List<Instance> instance;
public List<Author> getAuthor() {
return author;
}
public List<Author> getAuthor() {
return author;
}
public void setAuthor(List<Author> author) {
this.author = author;
}
public void setAuthor(List<Author> author) {
this.author = author;
}
public Qualifier getResulttype() {
return resulttype;
}
public Qualifier getResulttype() {
return resulttype;
}
public void setResulttype(Qualifier resulttype) {
this.resulttype = resulttype;
}
public void setResulttype(Qualifier resulttype) {
this.resulttype = resulttype;
}
public Qualifier getLanguage() {
return language;
}
public Qualifier getLanguage() {
return language;
}
public void setLanguage(Qualifier language) {
this.language = language;
}
public void setLanguage(Qualifier language) {
this.language = language;
}
public List<Country> getCountry() {
return country;
}
public List<Country> getCountry() {
return country;
}
public void setCountry(List<Country> country) {
this.country = country;
}
public void setCountry(List<Country> country) {
this.country = country;
}
public List<StructuredProperty> getSubject() {
return subject;
}
public List<StructuredProperty> getSubject() {
return subject;
}
public void setSubject(List<StructuredProperty> subject) {
this.subject = subject;
}
public void setSubject(List<StructuredProperty> subject) {
this.subject = subject;
}
public List<StructuredProperty> getTitle() {
return title;
}
public List<StructuredProperty> getTitle() {
return title;
}
public void setTitle(List<StructuredProperty> title) {
this.title = title;
}
public void setTitle(List<StructuredProperty> title) {
this.title = title;
}
public List<StructuredProperty> getRelevantdate() {
return relevantdate;
}
public List<StructuredProperty> getRelevantdate() {
return relevantdate;
}
public void setRelevantdate(List<StructuredProperty> relevantdate) {
this.relevantdate = relevantdate;
}
public void setRelevantdate(List<StructuredProperty> relevantdate) {
this.relevantdate = relevantdate;
}
public List<Field<String>> getDescription() {
return description;
}
public List<Field<String>> getDescription() {
return description;
}
public void setDescription(List<Field<String>> description) {
this.description = description;
}
public void setDescription(List<Field<String>> description) {
this.description = description;
}
public Field<String> getDateofacceptance() {
return dateofacceptance;
}
public Field<String> getDateofacceptance() {
return dateofacceptance;
}
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public Field<String> getPublisher() {
return publisher;
}
public Field<String> getPublisher() {
return publisher;
}
public void setPublisher(Field<String> publisher) {
this.publisher = publisher;
}
public void setPublisher(Field<String> publisher) {
this.publisher = publisher;
}
public Field<String> getEmbargoenddate() {
return embargoenddate;
}
public Field<String> getEmbargoenddate() {
return embargoenddate;
}
public void setEmbargoenddate(Field<String> embargoenddate) {
this.embargoenddate = embargoenddate;
}
public void setEmbargoenddate(Field<String> embargoenddate) {
this.embargoenddate = embargoenddate;
}
public List<Field<String>> getSource() {
return source;
}
public List<Field<String>> getSource() {
return source;
}
public void setSource(List<Field<String>> source) {
this.source = source;
}
public void setSource(List<Field<String>> source) {
this.source = source;
}
public List<Field<String>> getFulltext() {
return fulltext;
}
public List<Field<String>> getFulltext() {
return fulltext;
}
public void setFulltext(List<Field<String>> fulltext) {
this.fulltext = fulltext;
}
public void setFulltext(List<Field<String>> fulltext) {
this.fulltext = fulltext;
}
public List<Field<String>> getFormat() {
return format;
}
public List<Field<String>> getFormat() {
return format;
}
public void setFormat(List<Field<String>> format) {
this.format = format;
}
public void setFormat(List<Field<String>> format) {
this.format = format;
}
public List<Field<String>> getContributor() {
return contributor;
}
public List<Field<String>> getContributor() {
return contributor;
}
public void setContributor(List<Field<String>> contributor) {
this.contributor = contributor;
}
public void setContributor(List<Field<String>> contributor) {
this.contributor = contributor;
}
public Qualifier getResourcetype() {
return resourcetype;
}
public Qualifier getResourcetype() {
return resourcetype;
}
public void setResourcetype(Qualifier resourcetype) {
this.resourcetype = resourcetype;
}
public void setResourcetype(Qualifier resourcetype) {
this.resourcetype = resourcetype;
}
public List<Field<String>> getCoverage() {
return coverage;
}
public List<Field<String>> getCoverage() {
return coverage;
}
public void setCoverage(List<Field<String>> coverage) {
this.coverage = coverage;
}
public void setCoverage(List<Field<String>> coverage) {
this.coverage = coverage;
}
public Qualifier getBestaccessright() {
return bestaccessright;
}
public Qualifier getBestaccessright() {
return bestaccessright;
}
public void setBestaccessright(Qualifier bestaccessright) {
this.bestaccessright = bestaccessright;
}
public void setBestaccessright(Qualifier bestaccessright) {
this.bestaccessright = bestaccessright;
}
public List<Context> getContext() {
return context;
}
public List<Context> getContext() {
return context;
}
public void setContext(List<Context> context) {
this.context = context;
}
public void setContext(List<Context> context) {
this.context = context;
}
public List<ExternalReference> getExternalReference() {
return externalReference;
}
public List<ExternalReference> getExternalReference() {
return externalReference;
}
public void setExternalReference(List<ExternalReference> externalReference) {
this.externalReference = externalReference;
}
public void setExternalReference(List<ExternalReference> externalReference) {
this.externalReference = externalReference;
}
public List<Instance> getInstance() {
return instance;
}
public List<Instance> getInstance() {
return instance;
}
public void setInstance(List<Instance> instance) {
this.instance = instance;
}
public void setInstance(List<Instance> instance) {
this.instance = instance;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Result.class.isAssignableFrom(e.getClass())) {
return;
}
if (!Result.class.isAssignableFrom(e.getClass())) {
return;
}
Result r = (Result) e;
Result r = (Result) e;
instance = mergeLists(instance, r.getInstance());
instance = mergeLists(instance, r.getInstance());
if (r.getBestaccessright() != null && compareTrust(this, r) < 0)
bestaccessright = r.getBestaccessright();
if (r.getBestaccessright() != null && compareTrust(this, r) < 0)
bestaccessright = r.getBestaccessright();
if (r.getResulttype() != null && compareTrust(this, r) < 0) resulttype = r.getResulttype();
if (r.getResulttype() != null && compareTrust(this, r) < 0)
resulttype = r.getResulttype();
if (r.getLanguage() != null && compareTrust(this, r) < 0) language = r.getLanguage();
if (r.getLanguage() != null && compareTrust(this, r) < 0)
language = r.getLanguage();
country = mergeLists(country, r.getCountry());
country = mergeLists(country, r.getCountry());
subject = mergeLists(subject, r.getSubject());
subject = mergeLists(subject, r.getSubject());
title = mergeLists(title, r.getTitle());
title = mergeLists(title, r.getTitle());
relevantdate = mergeLists(relevantdate, r.getRelevantdate());
relevantdate = mergeLists(relevantdate, r.getRelevantdate());
description = longestLists(description, r.getDescription());
description = longestLists(description, r.getDescription());
if (r.getPublisher() != null && compareTrust(this, r) < 0) publisher = r.getPublisher();
if (r.getPublisher() != null && compareTrust(this, r) < 0)
publisher = r.getPublisher();
if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0)
embargoenddate = r.getEmbargoenddate();
if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0)
embargoenddate = r.getEmbargoenddate();
source = mergeLists(source, r.getSource());
source = mergeLists(source, r.getSource());
fulltext = mergeLists(fulltext, r.getFulltext());
fulltext = mergeLists(fulltext, r.getFulltext());
format = mergeLists(format, r.getFormat());
format = mergeLists(format, r.getFormat());
contributor = mergeLists(contributor, r.getContributor());
contributor = mergeLists(contributor, r.getContributor());
if (r.getResourcetype() != null) resourcetype = r.getResourcetype();
if (r.getResourcetype() != null)
resourcetype = r.getResourcetype();
coverage = mergeLists(coverage, r.getCoverage());
coverage = mergeLists(coverage, r.getCoverage());
context = mergeLists(context, r.getContext());
context = mergeLists(context, r.getContext());
externalReference = mergeLists(externalReference, r.getExternalReference());
}
externalReference = mergeLists(externalReference, r.getExternalReference());
}
private List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
if (a == null || b == null) return a == null ? b : a;
if (a.size() == b.size()) {
int msa =
a.stream()
.filter(i -> i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb =
b.stream()
.filter(i -> i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
return msa > msb ? a : b;
}
return a.size() > b.size() ? a : b;
}
private List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
if (a == null || b == null)
return a == null ? b : a;
if (a.size() == b.size()) {
int msa = a
.stream()
.filter(i -> i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb = b
.stream()
.filter(i -> i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
return msa > msb ? a : b;
}
return a.size() > b.size() ? a : b;
}
}

102
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -1,78 +1,78 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable;
import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Software extends Result implements Serializable {
private List<Field<String>> documentationUrl;
private List<Field<String>> documentationUrl;
private List<StructuredProperty> license;
private List<StructuredProperty> license;
private Field<String> codeRepositoryUrl;
private Field<String> codeRepositoryUrl;
private Qualifier programmingLanguage;
private Qualifier programmingLanguage;
public Software() {
setResulttype(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE);
}
public Software() {
setResulttype(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getDocumentationUrl() {
return documentationUrl;
}
public List<Field<String>> getDocumentationUrl() {
return documentationUrl;
}
public void setDocumentationUrl(List<Field<String>> documentationUrl) {
this.documentationUrl = documentationUrl;
}
public void setDocumentationUrl(List<Field<String>> documentationUrl) {
this.documentationUrl = documentationUrl;
}
public List<StructuredProperty> getLicense() {
return license;
}
public List<StructuredProperty> getLicense() {
return license;
}
public void setLicense(List<StructuredProperty> license) {
this.license = license;
}
public void setLicense(List<StructuredProperty> license) {
this.license = license;
}
public Field<String> getCodeRepositoryUrl() {
return codeRepositoryUrl;
}
public Field<String> getCodeRepositoryUrl() {
return codeRepositoryUrl;
}
public void setCodeRepositoryUrl(Field<String> codeRepositoryUrl) {
this.codeRepositoryUrl = codeRepositoryUrl;
}
public void setCodeRepositoryUrl(Field<String> codeRepositoryUrl) {
this.codeRepositoryUrl = codeRepositoryUrl;
}
public Qualifier getProgrammingLanguage() {
return programmingLanguage;
}
public Qualifier getProgrammingLanguage() {
return programmingLanguage;
}
public void setProgrammingLanguage(Qualifier programmingLanguage) {
this.programmingLanguage = programmingLanguage;
}
public void setProgrammingLanguage(Qualifier programmingLanguage) {
this.programmingLanguage = programmingLanguage;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Software.class.isAssignableFrom(e.getClass())) {
return;
}
if (!Software.class.isAssignableFrom(e.getClass())) {
return;
}
final Software s = (Software) e;
documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl());
final Software s = (Software) e;
documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl());
license = mergeLists(license, s.getLicense());
license = mergeLists(license, s.getLicense());
codeRepositoryUrl =
s.getCodeRepositoryUrl() != null && compareTrust(this, s) < 0
? s.getCodeRepositoryUrl()
: codeRepositoryUrl;
codeRepositoryUrl = s.getCodeRepositoryUrl() != null && compareTrust(this, s) < 0
? s.getCodeRepositoryUrl()
: codeRepositoryUrl;
programmingLanguage =
s.getProgrammingLanguage() != null && compareTrust(this, s) < 0
? s.getProgrammingLanguage()
: programmingLanguage;
programmingLanguage = s.getProgrammingLanguage() != null && compareTrust(this, s) < 0
? s.getProgrammingLanguage()
: programmingLanguage;
mergeOAFDataInfo(e);
}
mergeOAFDataInfo(e);
}
}

76
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java
View File

@ -1,56 +1,60 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
public class StructuredProperty implements Serializable {
private String value;
private String value;
private Qualifier qualifier;
private Qualifier qualifier;
private DataInfo dataInfo;
private DataInfo dataInfo;
public String getValue() {
return value;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
public void setValue(String value) {
this.value = value;
}
public Qualifier getQualifier() {
return qualifier;
}
public Qualifier getQualifier() {
return qualifier;
}
public void setQualifier(Qualifier qualifier) {
this.qualifier = qualifier;
}
public void setQualifier(Qualifier qualifier) {
this.qualifier = qualifier;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public DataInfo getDataInfo() {
return dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo;
}
public String toComparableString() {
return value != null ? value.toLowerCase() : "";
}
public String toComparableString() {
return value != null ? value.toLowerCase() : "";
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
StructuredProperty other = (StructuredProperty) obj;
StructuredProperty other = (StructuredProperty) obj;
return toComparableString().equals(other.toComparableString());
}
return toComparableString().equals(other.toComparableString());
}
}

124
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java
View File

@ -1,83 +1,89 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
public class DLIDataset extends Dataset {
private String originalObjIdentifier;
private String originalObjIdentifier;
private List<ProvenaceInfo> dlicollectedfrom;
private List<ProvenaceInfo> dlicollectedfrom;
private String completionStatus;
private String completionStatus;
public String getCompletionStatus() {
return completionStatus;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public String getOriginalObjIdentifier() {
return originalObjIdentifier;
}
public String getOriginalObjIdentifier() {
return originalObjIdentifier;
}
public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier;
}
public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
DLIDataset p = (DLIDataset) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
DLIDataset p = (DLIDataset) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus))
completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
return new ArrayList<>(result.values());
}
return new ArrayList<>(result.values());
}
}

126
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java
View File

@ -1,81 +1,87 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Publication;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
public class DLIPublication extends Publication implements Serializable {
private String originalObjIdentifier;
private String originalObjIdentifier;
private List<ProvenaceInfo> dlicollectedfrom;
private List<ProvenaceInfo> dlicollectedfrom;
private String completionStatus;
private String completionStatus;
public String getCompletionStatus() {
return completionStatus;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public String getOriginalObjIdentifier() {
return originalObjIdentifier;
}
public String getOriginalObjIdentifier() {
return originalObjIdentifier;
}
public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier;
}
public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
DLIPublication p = (DLIPublication) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
DLIPublication p = (DLIPublication) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus))
completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
return new ArrayList<>(result.values());
}
return new ArrayList<>(result.values());
}
}

15
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java
View File

@ -1,15 +1,16 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class DLIRelation extends Relation {
private String dateOfCollection;
private String dateOfCollection;
public String getDateOfCollection() {
return dateOfCollection;
}
public String getDateOfCollection() {
return dateOfCollection;
}
public void setDateOfCollection(String dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
public void setDateOfCollection(String dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
}

156
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java
View File

@ -1,109 +1,115 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class DLIUnknown extends Oaf implements Serializable {
private String id;
private String id;
private List<StructuredProperty> pid;
private List<StructuredProperty> pid;
private String dateofcollection;
private String dateofcollection;
private String dateoftransformation;
private String dateoftransformation;
private List<ProvenaceInfo> dlicollectedfrom;
private List<ProvenaceInfo> dlicollectedfrom;
private String completionStatus = "incomplete";
private String completionStatus = "incomplete";
public String getCompletionStatus() {
return completionStatus;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public void setId(String id) {
this.id = id;
}
public List<StructuredProperty> getPid() {
return pid;
}
public List<StructuredProperty> getPid() {
return pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public String getDateofcollection() {
return dateofcollection;
}
public String getDateofcollection() {
return dateofcollection;
}
public void setDateofcollection(String dateofcollection) {
this.dateofcollection = dateofcollection;
}
public void setDateofcollection(String dateofcollection) {
this.dateofcollection = dateofcollection;
}
public String getDateoftransformation() {
return dateoftransformation;
}
public String getDateoftransformation() {
return dateoftransformation;
}
public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation;
}
public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation;
}
public void mergeFrom(DLIUnknown p) {
if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
public void mergeFrom(DLIUnknown p) {
if ("complete".equalsIgnoreCase(p.completionStatus))
completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
return new ArrayList<>(result.values());
}
return new ArrayList<>(result.values());
}
}

57
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/ProvenaceInfo.java
View File

@ -1,46 +1,47 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import java.io.Serializable;
public class ProvenaceInfo implements Serializable {
private String id;
private String id;
private String name;
private String name;
private String completionStatus;
private String completionStatus;
private String collectionMode = "collected";
private String collectionMode = "collected";
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public void setName(String name) {
this.name = name;
}
public String getCompletionStatus() {
return completionStatus;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public String getCollectionMode() {
return collectionMode;
}
public String getCollectionMode() {
return collectionMode;
}
public void setCollectionMode(String collectionMode) {
this.collectionMode = collectionMode;
}
public void setCollectionMode(String collectionMode) {
this.collectionMode = collectionMode;
}
}

40
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java
View File

@ -1,36 +1,40 @@
package eu.dnetlib.dhp.schema.action;
import static org.junit.jupiter.api.Assertions.*;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.IOException;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
/** @author claudio.atzori */
public class AtomicActionTest {
@Test
public void serializationTest() throws IOException {
@Test
public void serializationTest() throws IOException {
Relation rel = new Relation();
rel.setSource("1");
rel.setTarget("2");
rel.setRelType("resultResult");
rel.setSubRelType("dedup");
rel.setRelClass("merges");
Relation rel = new Relation();
rel.setSource("1");
rel.setTarget("2");
rel.setRelType("resultResult");
rel.setSubRelType("dedup");
rel.setRelClass("merges");
AtomicAction aa1 = new AtomicAction(Relation.class, rel);
AtomicAction aa1 = new AtomicAction(Relation.class, rel);
final ObjectMapper mapper = new ObjectMapper();
String json = mapper.writeValueAsString(aa1);
final ObjectMapper mapper = new ObjectMapper();
String json = mapper.writeValueAsString(aa1);
assertTrue(StringUtils.isNotBlank(json));
assertTrue(StringUtils.isNotBlank(json));
AtomicAction aa2 = mapper.readValue(json, AtomicAction.class);
AtomicAction aa2 = mapper.readValue(json, AtomicAction.class);
assertEquals(aa1.getClazz(), aa2.getClazz());
assertEquals(aa1.getPayload(), aa2.getPayload());
}
assertEquals(aa1.getClazz(), aa2.getClazz());
assertEquals(aa1.getPayload(), aa2.getPayload());
}
}

42
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java
View File

@ -1,35 +1,37 @@
package eu.dnetlib.dhp.schema.common;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ModelSupportTest {
@Nested
class IsSubClass {
@Nested
class IsSubClass {
@Test
public void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Relation.class, OafEntity.class);
@Test
public void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Relation.class, OafEntity.class);
// then
assertFalse(result);
}
// then
assertFalse(result);
}
@Test
public void shouldReturnTrueWhenSubClassExtendsSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Result.class, OafEntity.class);
@Test
public void shouldReturnTrueWhenSubClassExtendsSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Result.class, OafEntity.class);
// then
assertTrue(result);
}
}
// then
assertTrue(result);
}
}
}

108
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java
View File

@ -1,86 +1,88 @@
package eu.dnetlib.dhp.schema.oaf;
import static org.junit.jupiter.api.Assertions.*;
import java.util.Arrays;
import java.util.List;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
public class MergeTest {
OafEntity oaf;
OafEntity oaf;
@BeforeEach
public void setUp() {
oaf = new Publication();
}
@BeforeEach
public void setUp() {
oaf = new Publication();
}
@Test
public void mergeListsTest() {
@Test
public void mergeListsTest() {
// string list merge test
List<String> a = Arrays.asList("a", "b", "c", "e");
List<String> b = Arrays.asList("a", "b", "c", "d");
List<String> c = null;
// string list merge test
List<String> a = Arrays.asList("a", "b", "c", "e");
List<String> b = Arrays.asList("a", "b", "c", "d");
List<String> c = null;
System.out.println("merge result 1 = " + oaf.mergeLists(a, b));
System.out.println("merge result 1 = " + oaf.mergeLists(a, b));
System.out.println("merge result 2 = " + oaf.mergeLists(a, c));
System.out.println("merge result 2 = " + oaf.mergeLists(a, c));
System.out.println("merge result 3 = " + oaf.mergeLists(c, c));
}
System.out.println("merge result 3 = " + oaf.mergeLists(c, c));
}
@Test
public void mergePublicationCollectedFromTest() {
@Test
public void mergePublicationCollectedFromTest() {
Publication a = new Publication();
Publication b = new Publication();
Publication a = new Publication();
Publication b = new Publication();
a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed")));
b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open")));
a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed")));
b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open")));
a.mergeFrom(b);
a.mergeFrom(b);
assertNotNull(a.getCollectedfrom());
assertEquals(3, a.getCollectedfrom().size());
}
assertNotNull(a.getCollectedfrom());
assertEquals(3, a.getCollectedfrom().size());
}
@Test
public void mergePublicationSubjectTest() {
@Test
public void mergePublicationSubjectTest() {
Publication a = new Publication();
Publication b = new Publication();
Publication a = new Publication();
Publication b = new Publication();
a.setSubject(Arrays.asList(setSP("a", "open", "classe"), setSP("b", "open", "classe")));
b.setSubject(Arrays.asList(setSP("A", "open", "classe"), setSP("c", "open", "classe")));
a.setSubject(Arrays.asList(setSP("a", "open", "classe"), setSP("b", "open", "classe")));
b.setSubject(Arrays.asList(setSP("A", "open", "classe"), setSP("c", "open", "classe")));
a.mergeFrom(b);
a.mergeFrom(b);
assertNotNull(a.getSubject());
assertEquals(3, a.getSubject().size());
}
assertNotNull(a.getSubject());
assertEquals(3, a.getSubject().size());
}
private KeyValue setKV(final String key, final String value) {
private KeyValue setKV(final String key, final String value) {
KeyValue k = new KeyValue();
KeyValue k = new KeyValue();
k.setKey(key);
k.setValue(value);
k.setKey(key);
k.setValue(value);
return k;
}
return k;
}
private StructuredProperty setSP(
final String value, final String schema, final String classname) {
StructuredProperty s = new StructuredProperty();
s.setValue(value);
Qualifier q = new Qualifier();
q.setClassname(classname);
q.setClassid(classname);
q.setSchemename(schema);
q.setSchemeid(schema);
s.setQualifier(q);
return s;
}
private StructuredProperty setSP(
final String value, final String schema, final String classname) {
StructuredProperty s = new StructuredProperty();
s.setValue(value);
Qualifier q = new Qualifier();
q.setClassname(classname);
q.setClassid(classname);
q.setSchemename(schema);
q.setSchemeid(schema);
s.setQualifier(q);
return s;
}
}

119
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java
View File

@ -1,76 +1,83 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import org.junit.jupiter.api.Test;
public class DLItest {
@Test
public void testMergePublication() throws JsonProcessingException {
DLIPublication a1 = new DLIPublication();
a1.setPid(Arrays.asList(createSP("123456", "pdb", "dnet:pid_types")));
a1.setTitle(Collections.singletonList(createSP("Un Titolo", "title", "dnetTitle")));
a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd", "Zenodo", "complete")));
a1.setCompletionStatus("complete");
@Test
public void testMergePublication() throws JsonProcessingException {
DLIPublication a1 = new DLIPublication();
a1.setPid(Arrays.asList(createSP("123456", "pdb", "dnet:pid_types")));
a1.setTitle(Collections.singletonList(createSP("Un Titolo", "title", "dnetTitle")));
a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd", "Zenodo", "complete")));
a1.setCompletionStatus("complete");
DLIPublication a = new DLIPublication();
a.setPid(
Arrays.asList(
createSP("10.11", "doi", "dnet:pid_types"),
createSP("123456", "pdb", "dnet:pid_types")));
a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle")));
a.setDlicollectedfrom(
Arrays.asList(
createCollectedFrom("dct", "datacite", "complete"),
createCollectedFrom("dct", "datacite", "incomplete")));
a.setCompletionStatus("incomplete");
DLIPublication a = new DLIPublication();
a
.setPid(
Arrays
.asList(
createSP("10.11", "doi", "dnet:pid_types"),
createSP("123456", "pdb", "dnet:pid_types")));
a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle")));
a
.setDlicollectedfrom(
Arrays
.asList(
createCollectedFrom("dct", "datacite", "complete"),
createCollectedFrom("dct", "datacite", "incomplete")));
a.setCompletionStatus("incomplete");
a.mergeFrom(a1);
a.mergeFrom(a1);
ObjectMapper mapper = new ObjectMapper();
System.out.println(mapper.writeValueAsString(a));
}
ObjectMapper mapper = new ObjectMapper();
System.out.println(mapper.writeValueAsString(a));
}
@Test
public void testDeserialization() throws IOException {
@Test
public void testDeserialization() throws IOException {
final String json =
"{\"dataInfo\":{\"invisible\":false,\"inferred\":null,\"deletedbyinference\":false,\"trust\":\"0.9\",\"inferenceprovenance\":null,\"provenanceaction\":null},\"lastupdatetimestamp\":null,\"id\":\"60|bd9352547098929a394655ad1a44a479\",\"originalId\":[\"bd9352547098929a394655ad1a44a479\"],\"collectedfrom\":[{\"key\":\"dli_________::datacite\",\"value\":\"Datasets in Datacite\",\"dataInfo\":null,\"blank\":false}],\"pid\":[{\"value\":\"10.7925/DRS1.DUCHAS_5078760\",\"qualifier\":{\"classid\":\"doi\",\"classname\":\"doi\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\",\"blank\":false},\"dataInfo\":null}],\"dateofcollection\":\"2020-01-09T08:29:31.885Z\",\"dateoftransformation\":null,\"extraInfo\":null,\"oaiprovenance\":null,\"author\":[{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Ireland. Department of Arts, Culture, and the Gaeltacht\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"University College Dublin\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"National Folklore Foundation\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null}],\"resulttype\":null,\"language\":null,\"country\":null,\"subject\":[{\"value\":\"Recreation\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Entertainments and recreational activities\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Siamsaíocht agus caitheamh aimsire\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null}],\"title\":[{\"value\":\"Games We Play\",\"qualifier\":null,\"dataInfo\":null}],\"relevantdate\":[{\"value\":\"1938-09-28\",\"qualifier\":{\"classid\":\"date\",\"classname\":\"date\",\"schemeid\":\"dnet::date\",\"schemename\":\"dnet::date\",\"blank\":false},\"dataInfo\":null}],\"description\":[{\"value\":\"Story collected by Breda Mc Donnell, a student at Tenure school (Tinure, Co. Louth) (no informant identified).\",\"dataInfo\":null}],\"dateofacceptance\":null,\"publisher\":{\"value\":\"University College Dublin\",\"dataInfo\":null},\"embargoenddate\":null,\"source\":null,\"fulltext\":null,\"format\":null,\"contributor\":null,\"resourcetype\":null,\"coverage\":null,\"refereed\":null,\"context\":null,\"processingchargeamount\":null,\"processingchargecurrency\":null,\"externalReference\":null,\"instance\":[],\"storagedate\":null,\"device\":null,\"size\":null,\"version\":null,\"lastmetadataupdate\":null,\"metadataversionnumber\":null,\"geolocation\":null,\"dlicollectedfrom\":[{\"id\":\"dli_________::datacite\",\"name\":\"Datasets in Datacite\",\"completionStatus\":\"complete\",\"collectionMode\":\"resolved\"}],\"completionStatus\":\"complete\"}";
final String json = "{\"dataInfo\":{\"invisible\":false,\"inferred\":null,\"deletedbyinference\":false,\"trust\":\"0.9\",\"inferenceprovenance\":null,\"provenanceaction\":null},\"lastupdatetimestamp\":null,\"id\":\"60|bd9352547098929a394655ad1a44a479\",\"originalId\":[\"bd9352547098929a394655ad1a44a479\"],\"collectedfrom\":[{\"key\":\"dli_________::datacite\",\"value\":\"Datasets in Datacite\",\"dataInfo\":null,\"blank\":false}],\"pid\":[{\"value\":\"10.7925/DRS1.DUCHAS_5078760\",\"qualifier\":{\"classid\":\"doi\",\"classname\":\"doi\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\",\"blank\":false},\"dataInfo\":null}],\"dateofcollection\":\"2020-01-09T08:29:31.885Z\",\"dateoftransformation\":null,\"extraInfo\":null,\"oaiprovenance\":null,\"author\":[{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Ireland. Department of Arts, Culture, and the Gaeltacht\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"University College Dublin\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"National Folklore Foundation\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null}],\"resulttype\":null,\"language\":null,\"country\":null,\"subject\":[{\"value\":\"Recreation\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Entertainments and recreational activities\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Siamsaíocht agus caitheamh aimsire\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null}],\"title\":[{\"value\":\"Games We Play\",\"qualifier\":null,\"dataInfo\":null}],\"relevantdate\":[{\"value\":\"1938-09-28\",\"qualifier\":{\"classid\":\"date\",\"classname\":\"date\",\"schemeid\":\"dnet::date\",\"schemename\":\"dnet::date\",\"blank\":false},\"dataInfo\":null}],\"description\":[{\"value\":\"Story collected by Breda Mc Donnell, a student at Tenure school (Tinure, Co. Louth) (no informant identified).\",\"dataInfo\":null}],\"dateofacceptance\":null,\"publisher\":{\"value\":\"University College Dublin\",\"dataInfo\":null},\"embargoenddate\":null,\"source\":null,\"fulltext\":null,\"format\":null,\"contributor\":null,\"resourcetype\":null,\"coverage\":null,\"refereed\":null,\"context\":null,\"processingchargeamount\":null,\"processingchargecurrency\":null,\"externalReference\":null,\"instance\":[],\"storagedate\":null,\"device\":null,\"size\":null,\"version\":null,\"lastmetadataupdate\":null,\"metadataversionnumber\":null,\"geolocation\":null,\"dlicollectedfrom\":[{\"id\":\"dli_________::datacite\",\"name\":\"Datasets in Datacite\",\"completionStatus\":\"complete\",\"collectionMode\":\"resolved\"}],\"completionStatus\":\"complete\"}";
ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
DLIDataset dliDataset = mapper.readValue(json, DLIDataset.class);
mapper.enable(SerializationFeature.INDENT_OUTPUT);
System.out.println(mapper.writeValueAsString(dliDataset));
}
ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
DLIDataset dliDataset = mapper.readValue(json, DLIDataset.class);
mapper.enable(SerializationFeature.INDENT_OUTPUT);
System.out.println(mapper.writeValueAsString(dliDataset));
}
private ProvenaceInfo createCollectedFrom(
final String id, final String name, final String completionStatus) {
ProvenaceInfo p = new ProvenaceInfo();
p.setId(id);
p.setName(name);
p.setCompletionStatus(completionStatus);
return p;
}
private ProvenaceInfo createCollectedFrom(
final String id, final String name, final String completionStatus) {
ProvenaceInfo p = new ProvenaceInfo();
p.setId(id);
p.setName(name);
p.setCompletionStatus(completionStatus);
return p;
}
private StructuredProperty createSP(
final String value, final String className, final String schemeName) {
StructuredProperty p = new StructuredProperty();
p.setValue(value);
Qualifier schema = new Qualifier();
schema.setClassname(className);
schema.setClassid(className);
schema.setSchemename(schemeName);
schema.setSchemeid(schemeName);
p.setQualifier(schema);
return p;
}
private StructuredProperty createSP(
final String value, final String className, final String schemeName) {
StructuredProperty p = new StructuredProperty();
p.setValue(value);
Qualifier schema = new Qualifier();
schema.setClassname(className);
schema.setClassid(className);
schema.setSchemename(schemeName);
schema.setSchemeid(schemeName);
p.setQualifier(schema);
return p;
}
}

219
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
View File

@ -1,8 +1,23 @@
package eu.dnetlib.dhp.actionmanager;
import java.io.Serializable;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.stream.Collectors;
import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
import eu.dnetlib.actionmanager.rmi.ActionManagerException;
import eu.dnetlib.actionmanager.set.ActionManagerSet;
import eu.dnetlib.actionmanager.set.ActionManagerSet.ImpactTypes;
@ -10,130 +25,120 @@ import eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJo
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import java.io.Serializable;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.stream.Collectors;
import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class ISClient implements Serializable {
private static final Logger log =
LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final Logger log = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
private ISLookUpService isLookup;
private ISLookUpService isLookup;
public ISClient(String isLookupUrl) {
isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
}
public ISClient(String isLookupUrl) {
isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
}
public List<String> getLatestRawsetPaths(String setIds) {
public List<String> getLatestRawsetPaths(String setIds) {
List<String> ids =
Lists.newArrayList(
Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR)
.omitEmptyStrings()
.trimResults()
.split(setIds));
List<String> ids = Lists
.newArrayList(
Splitter
.on(INPUT_ACTION_SET_ID_SEPARATOR)
.omitEmptyStrings()
.trimResults()
.split(setIds));
return ids.stream()
.map(id -> getSet(isLookup, id))
.map(as -> as.getPathToLatest())
.collect(Collectors.toCollection(ArrayList::new));
}
return ids
.stream()
.map(id -> getSet(isLookup, id))
.map(as -> as.getPathToLatest())
.collect(Collectors.toCollection(ArrayList::new));
}
private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) {
private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) {
final String q =
"for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') "
+ "where $x//SET/@id = '"
+ setId
+ "' return $x";
final String q = "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') "
+ "where $x//SET/@id = '"
+ setId
+ "' return $x";
try {
final String basePath = getBasePathHDFS(isLookup);
final String setProfile = isLookup.getResourceProfileByQuery(q);
return getActionManagerSet(basePath, setProfile);
} catch (ISLookUpException | ActionManagerException e) {
throw new RuntimeException("Error accessing Sets, using query: " + q);
}
}
try {
final String basePath = getBasePathHDFS(isLookup);
final String setProfile = isLookup.getResourceProfileByQuery(q);
return getActionManagerSet(basePath, setProfile);
} catch (ISLookUpException | ActionManagerException e) {
throw new RuntimeException("Error accessing Sets, using query: " + q);
}
}
private ActionManagerSet getActionManagerSet(final String basePath, final String profile)
throws ActionManagerException {
final SAXReader reader = new SAXReader();
final ActionManagerSet set = new ActionManagerSet();
private ActionManagerSet getActionManagerSet(final String basePath, final String profile)
throws ActionManagerException {
final SAXReader reader = new SAXReader();
final ActionManagerSet set = new ActionManagerSet();
try {
final Document doc = reader.read(new StringReader(profile));
try {
final Document doc = reader.read(new StringReader(profile));
set.setId(doc.valueOf("//SET/@id").trim());
set.setName(doc.valueOf("//SET").trim());
set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim()));
set.setLatest(
doc.valueOf("//RAW_SETS/LATEST/@id"),
doc.valueOf("//RAW_SETS/LATEST/@creationDate"),
doc.valueOf("//RAW_SETS/LATEST/@lastUpdate"));
set.setDirectory(doc.valueOf("//SET/@directory"));
final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED");
if (expiredNodes != null) {
for (int i = 0; i < expiredNodes.size(); i++) {
Element ex = (Element) expiredNodes.get(i);
set.addExpired(
ex.attributeValue("id"),
ex.attributeValue("creationDate"),
ex.attributeValue("lastUpdate"));
}
}
set.setId(doc.valueOf("//SET/@id").trim());
set.setName(doc.valueOf("//SET").trim());
set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim()));
set
.setLatest(
doc.valueOf("//RAW_SETS/LATEST/@id"),
doc.valueOf("//RAW_SETS/LATEST/@creationDate"),
doc.valueOf("//RAW_SETS/LATEST/@lastUpdate"));
set.setDirectory(doc.valueOf("//SET/@directory"));
final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED");
if (expiredNodes != null) {
for (int i = 0; i < expiredNodes.size(); i++) {
Element ex = (Element) expiredNodes.get(i);
set
.addExpired(
ex.attributeValue("id"),
ex.attributeValue("creationDate"),
ex.attributeValue("lastUpdate"));
}
}
final StringBuilder sb = new StringBuilder();
sb.append(basePath);
sb.append("/");
sb.append(doc.valueOf("//SET/@directory"));
sb.append("/");
sb.append(doc.valueOf("//RAW_SETS/LATEST/@id"));
set.setPathToLatest(sb.toString());
final StringBuilder sb = new StringBuilder();
sb.append(basePath);
sb.append("/");
sb.append(doc.valueOf("//SET/@directory"));
sb.append("/");
sb.append(doc.valueOf("//RAW_SETS/LATEST/@id"));
set.setPathToLatest(sb.toString());
return set;
} catch (Exception e) {
throw new ActionManagerException("Error creating set from profile: " + profile, e);
}
}
return set;
} catch (Exception e) {
throw new ActionManagerException("Error creating set from profile: " + profile, e);
}
}
private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
return queryServiceProperty(isLookup, "basePath");
}
private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
return queryServiceProperty(isLookup, "basePath");
}
private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
throws ActionManagerException {
final String q =
"for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
+ propertyName
+ "']/@value/string()";
log.debug("quering for service property: " + q);
try {
final List<String> value = isLookup.quickSearchProfile(q);
return Iterables.getOnlyElement(value);
} catch (ISLookUpException e) {
String msg = "Error accessing service profile, using query: " + q;
log.error(msg, e);
throw new ActionManagerException(msg, e);
} catch (NoSuchElementException e) {
String msg = "missing service property: " + propertyName;
log.error(msg, e);
throw new ActionManagerException(msg, e);
} catch (IllegalArgumentException e) {
String msg = "found more than one service property: " + propertyName;
log.error(msg, e);
throw new ActionManagerException(msg, e);
}
}
private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
throws ActionManagerException {
final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
+ propertyName
+ "']/@value/string()";
log.debug("quering for service property: " + q);
try {
final List<String> value = isLookup.quickSearchProfile(q);
return Iterables.getOnlyElement(value);
} catch (ISLookUpException e) {
String msg = "Error accessing service profile, using query: " + q;
log.error(msg, e);
throw new ActionManagerException(msg, e);
} catch (NoSuchElementException e) {
String msg = "missing service property: " + propertyName;
log.error(msg, e);
throw new ActionManagerException(msg, e);
} catch (IllegalArgumentException e) {
String msg = "found more than one service property: " + propertyName;
log.error(msg, e);
throw new ActionManagerException(msg, e);
}
}
}

78
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java
View File

@ -1,47 +1,69 @@
package eu.dnetlib.dhp.actionmanager.migration;
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
import java.util.Comparator;
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
public class LicenseComparator implements Comparator<Qualifier> {
@Override
public int compare(Qualifier left, Qualifier right) {
@Override
public int compare(Qualifier left, Qualifier right) {
if (left == null && right == null) return 0;
if (left == null) return 1;
if (right == null) return -1;
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
String lClass = left.getClassid();
String rClass = right.getClassid();
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass)) return 0;
if (lClass.equals(rClass))
return 0;
if (lClass.equals("OPEN SOURCE")) return -1;
if (rClass.equals("OPEN SOURCE")) return 1;
if (lClass.equals("OPEN SOURCE"))
return -1;
if (rClass.equals("OPEN SOURCE"))
return 1;
if (lClass.equals("OPEN")) return -1;
if (rClass.equals("OPEN")) return 1;
if (lClass.equals("OPEN"))
return -1;
if (rClass.equals("OPEN"))
return 1;
if (lClass.equals("6MONTHS")) return -1;
if (rClass.equals("6MONTHS")) return 1;
if (lClass.equals("6MONTHS"))
return -1;
if (rClass.equals("6MONTHS"))
return 1;
if (lClass.equals("12MONTHS")) return -1;
if (rClass.equals("12MONTHS")) return 1;
if (lClass.equals("12MONTHS"))
return -1;
if (rClass.equals("12MONTHS"))
return 1;
if (lClass.equals("EMBARGO")) return -1;
if (rClass.equals("EMBARGO")) return 1;
if (lClass.equals("EMBARGO"))
return -1;
if (rClass.equals("EMBARGO"))
return 1;
if (lClass.equals("RESTRICTED")) return -1;
if (rClass.equals("RESTRICTED")) return 1;
if (lClass.equals("RESTRICTED"))
return -1;
if (rClass.equals("RESTRICTED"))
return 1;
if (lClass.equals("CLOSED")) return -1;
if (rClass.equals("CLOSED")) return 1;
if (lClass.equals("CLOSED"))
return -1;
if (rClass.equals("CLOSED"))
return 1;
if (lClass.equals("UNKNOWN")) return -1;
if (rClass.equals("UNKNOWN")) return 1;
if (lClass.equals("UNKNOWN"))
return -1;
if (rClass.equals("UNKNOWN"))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
}

266
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java
View File

@ -1,11 +1,6 @@
package eu.dnetlib.dhp.actionmanager.migration;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStream;
@ -14,6 +9,7 @@ import java.util.LinkedList;
import java.util.List;
import java.util.Properties;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
@ -25,164 +21,174 @@ import org.apache.hadoop.util.ToolRunner;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class MigrateActionSet {
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
private static final String SEPARATOR = "/";
private static final String TARGET_PATHS = "target_paths";
private static final String RAWSET_PREFIX = "rawset_";
private static final String SEPARATOR = "/";
private static final String TARGET_PATHS = "target_paths";
private static final String RAWSET_PREFIX = "rawset_";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
MigrateActionSet.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
parser.parseArgument(args);
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
MigrateActionSet.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
parser.parseArgument(args);
new MigrateActionSet().run(parser);
}
new MigrateActionSet().run(parser);
}
private void run(ArgumentApplicationParser parser) throws Exception {
private void run(ArgumentApplicationParser parser) throws Exception {
final String isLookupUrl = parser.get("isLookupUrl");
final String sourceNN = parser.get("sourceNameNode");
final String targetNN = parser.get("targetNameNode");
final String workDir = parser.get("workingDirectory");
final Integer distcp_num_maps = Integer.parseInt(parser.get("distcp_num_maps"));
final String isLookupUrl = parser.get("isLookupUrl");
final String sourceNN = parser.get("sourceNameNode");
final String targetNN = parser.get("targetNameNode");
final String workDir = parser.get("workingDirectory");
final Integer distcp_num_maps = Integer.parseInt(parser.get("distcp_num_maps"));
final String distcp_memory_mb = parser.get("distcp_memory_mb");
final String distcp_task_timeout = parser.get("distcp_task_timeout");
final String distcp_memory_mb = parser.get("distcp_memory_mb");
final String distcp_task_timeout = parser.get("distcp_task_timeout");
final String transform_only_s = parser.get("transform_only");
final String transform_only_s = parser.get("transform_only");
log.info("transform only param: {}", transform_only_s);
log.info("transform only param: {}", transform_only_s);
final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
log.info("transform only: {}", transformOnly);
log.info("transform only: {}", transformOnly);
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
Configuration conf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
FileSystem targetFS = FileSystem.get(conf);
Configuration conf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
FileSystem targetFS = FileSystem.get(conf);
Configuration sourceConf =
getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
sourceConf.set(FileSystem.FS_DEFAULT_NAME_KEY, sourceNN);
FileSystem sourceFS = FileSystem.get(sourceConf);
Configuration sourceConf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
sourceConf.set(FileSystem.FS_DEFAULT_NAME_KEY, sourceNN);
FileSystem sourceFS = FileSystem.get(sourceConf);
Properties props = new Properties();
Properties props = new Properties();
List<Path> targetPaths = new ArrayList<>();
List<Path> targetPaths = new ArrayList<>();
final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
log.info(
"paths to process:\n{}",
sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
for (Path source : sourcePaths) {
final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
log
.info(
"paths to process:\n{}",
sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
for (Path source : sourcePaths) {
if (!sourceFS.exists(source)) {
log.warn("skipping unexisting path: {}", source);
} else {
if (!sourceFS.exists(source)) {
log.warn("skipping unexisting path: {}", source);
} else {
LinkedList<String> pathQ =
Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
final String rawSet = pathQ.pollLast();
log.info("got RAWSET: {}", rawSet);
final String rawSet = pathQ.pollLast();
log.info("got RAWSET: {}", rawSet);
if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
final String actionSetDirectory = pathQ.pollLast();
final String actionSetDirectory = pathQ.pollLast();
final Path targetPath =
new Path(targetNN + workDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawSet);
final Path targetPath = new Path(
targetNN + workDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawSet);
log.info("using TARGET PATH: {}", targetPath);
log.info("using TARGET PATH: {}", targetPath);
if (!transformOnly) {
if (targetFS.exists(targetPath)) {
targetFS.delete(targetPath, true);
}
runDistcp(
distcp_num_maps, distcp_memory_mb, distcp_task_timeout, conf, source, targetPath);
}
if (!transformOnly) {
if (targetFS.exists(targetPath)) {
targetFS.delete(targetPath, true);
}
runDistcp(
distcp_num_maps, distcp_memory_mb, distcp_task_timeout, conf, source, targetPath);
}
targetPaths.add(targetPath);
}
}
}
targetPaths.add(targetPath);
}
}
}
props.setProperty(
TARGET_PATHS, targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(",")));
File file = new File(System.getProperty("oozie.action.output.properties"));
props
.setProperty(
TARGET_PATHS, targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(",")));
File file = new File(System.getProperty("oozie.action.output.properties"));
try (OutputStream os = new FileOutputStream(file)) {
props.store(os, "");
}
System.out.println(file.getAbsolutePath());
}
try (OutputStream os = new FileOutputStream(file)) {
props.store(os, "");
}
System.out.println(file.getAbsolutePath());
}
private void runDistcp(
Integer distcp_num_maps,
String distcp_memory_mb,
String distcp_task_timeout,
Configuration conf,
Path source,
Path targetPath)
throws Exception {
private void runDistcp(
Integer distcp_num_maps,
String distcp_memory_mb,
String distcp_task_timeout,
Configuration conf,
Path source,
Path targetPath)
throws Exception {
final DistCpOptions op = new DistCpOptions(source, targetPath);
op.setMaxMaps(distcp_num_maps);
op.preserve(DistCpOptions.FileAttribute.BLOCKSIZE);
op.preserve(DistCpOptions.FileAttribute.REPLICATION);
op.preserve(DistCpOptions.FileAttribute.CHECKSUMTYPE);
final DistCpOptions op = new DistCpOptions(source, targetPath);
op.setMaxMaps(distcp_num_maps);
op.preserve(DistCpOptions.FileAttribute.BLOCKSIZE);
op.preserve(DistCpOptions.FileAttribute.REPLICATION);
op.preserve(DistCpOptions.FileAttribute.CHECKSUMTYPE);
int res =
ToolRunner.run(
new DistCp(conf, op),
new String[] {
"-Dmapred.task.timeout=" + distcp_task_timeout,
"-Dmapreduce.map.memory.mb=" + distcp_memory_mb,
"-pb",
"-m " + distcp_num_maps,
source.toString(),
targetPath.toString()
});
int res = ToolRunner
.run(
new DistCp(conf, op),
new String[] {
"-Dmapred.task.timeout=" + distcp_task_timeout,
"-Dmapreduce.map.memory.mb=" + distcp_memory_mb,
"-pb",
"-m " + distcp_num_maps,
source.toString(),
targetPath.toString()
});
if (res != 0) {
throw new RuntimeException(String.format("distcp exited with code %s", res));
}
}
if (res != 0) {
throw new RuntimeException(String.format("distcp exited with code %s", res));
}
}
private Configuration getConfiguration(
String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) {
final Configuration conf = new Configuration();
conf.set("dfs.webhdfs.socket.connect-timeout", distcp_task_timeout);
conf.set("dfs.webhdfs.socket.read-timeout", distcp_task_timeout);
conf.set("dfs.http.client.retry.policy.enabled", "true");
conf.set("mapred.task.timeout", distcp_task_timeout);
conf.set("mapreduce.map.memory.mb", distcp_memory_mb);
conf.set("mapred.map.tasks", String.valueOf(distcp_num_maps));
return conf;
}
private Configuration getConfiguration(
String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) {
final Configuration conf = new Configuration();
conf.set("dfs.webhdfs.socket.connect-timeout", distcp_task_timeout);
conf.set("dfs.webhdfs.socket.read-timeout", distcp_task_timeout);
conf.set("dfs.http.client.retry.policy.enabled", "true");
conf.set("mapred.task.timeout", distcp_task_timeout);
conf.set("mapreduce.map.memory.mb", distcp_memory_mb);
conf.set("mapred.map.tasks", String.valueOf(distcp_num_maps));
return conf;
}
private List<Path> getSourcePaths(String sourceNN, ISLookUpService isLookUp)
throws ISLookUpException {
String XQUERY =
"distinct-values(\n"
+ "let $basePath := collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()\n"
+ "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') \n"
+ "let $setDir := $x//SET/@directory/string()\n"
+ "let $rawSet := $x//RAW_SETS/LATEST/@id/string()\n"
+ "return concat($basePath, '/', $setDir, '/', $rawSet))";
private List<Path> getSourcePaths(String sourceNN, ISLookUpService isLookUp)
throws ISLookUpException {
String XQUERY = "distinct-values(\n"
+ "let $basePath := collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()\n"
+ "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') \n"
+ "let $setDir := $x//SET/@directory/string()\n"
+ "let $rawSet := $x//RAW_SETS/LATEST/@id/string()\n"
+ "return concat($basePath, '/', $setDir, '/', $rawSet))";
log.info(String.format("running xquery:\n%s", XQUERY));
return isLookUp.quickSearchProfile(XQUERY).stream()
.map(p -> sourceNN + p)
.map(Path::new)
.collect(Collectors.toList());
}
log.info(String.format("running xquery:\n%s", XQUERY));
return isLookUp
.quickSearchProfile(XQUERY)
.stream()
.map(p -> sourceNN + p)
.map(Path::new)
.collect(Collectors.toList());
}
}

1113
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

File diff suppressed because it is too large Load Diff

244
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java
View File

@ -1,23 +1,14 @@
package eu.dnetlib.dhp.actionmanager.migration;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import com.google.protobuf.InvalidProtocolBufferException;
import eu.dnetlib.data.proto.OafProtos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import java.io.IOException;
import java.io.Serializable;
import java.util.LinkedList;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.fs.FileSystem;
@ -29,136 +20,153 @@ import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import com.google.protobuf.InvalidProtocolBufferException;
import eu.dnetlib.data.proto.OafProtos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2;
public class TransformActions implements Serializable {
private static final Logger log = LoggerFactory.getLogger(TransformActions.class);
private static final Logger log = LoggerFactory.getLogger(TransformActions.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String SEPARATOR = "/";
private static final String SEPARATOR = "/";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
MigrateActionSet.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json")));
parser.parseArgument(args);
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
MigrateActionSet.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged =
Optional.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final String inputPaths = parser.get("inputPaths");
final String inputPaths = parser.get("inputPaths");
if (StringUtils.isBlank(inputPaths)) {
throw new RuntimeException("empty inputPaths");
}
log.info("inputPaths: {}", inputPaths);
if (StringUtils.isBlank(inputPaths)) {
throw new RuntimeException("empty inputPaths");
}
log.info("inputPaths: {}", inputPaths);
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
SparkConf conf = new SparkConf();
SparkConf conf = new SparkConf();
runWithSparkSession(
conf, isSparkSessionManaged, spark -> transformActions(inputPaths, targetBaseDir, spark));
}
runWithSparkSession(
conf, isSparkSessionManaged, spark -> transformActions(inputPaths, targetBaseDir, spark));
}
private static void transformActions(String inputPaths, String targetBaseDir, SparkSession spark)
throws IOException {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
private static void transformActions(String inputPaths, String targetBaseDir, SparkSession spark)
throws IOException {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
final String rawset = pathQ.pollLast();
final String actionSetDirectory = pathQ.pollLast();
final String rawset = pathQ.pollLast();
final String actionSetDirectory = pathQ.pollLast();
final Path targetDirectory =
new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
final Path targetDirectory = new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
if (fs.exists(targetDirectory)) {
log.info("found target directory '{}", targetDirectory);
fs.delete(targetDirectory, true);
log.info("deleted target directory '{}", targetDirectory);
}
if (fs.exists(targetDirectory)) {
log.info("found target directory '{}", targetDirectory);
fs.delete(targetDirectory, true);
log.info("deleted target directory '{}", targetDirectory);
}
log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory);
log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory);
sc.sequenceFile(sourcePath, Text.class, Text.class)
.map(a -> eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(a._2().toString()))
.map(TransformActions::doTransform)
.filter(Objects::nonNull)
.mapToPair(
a -> new Tuple2<>(a.getClazz().toString(), OBJECT_MAPPER.writeValueAsString(a)))
.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
.saveAsNewAPIHadoopFile(
targetDirectory.toString(),
Text.class,
Text.class,
SequenceFileOutputFormat.class,
sc.hadoopConfiguration());
}
}
sc
.sequenceFile(sourcePath, Text.class, Text.class)
.map(a -> eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(a._2().toString()))
.map(TransformActions::doTransform)
.filter(Objects::nonNull)
.mapToPair(
a -> new Tuple2<>(a.getClazz().toString(), OBJECT_MAPPER.writeValueAsString(a)))
.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
.saveAsNewAPIHadoopFile(
targetDirectory.toString(),
Text.class,
Text.class,
SequenceFileOutputFormat.class,
sc.hadoopConfiguration());
}
}
private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
throws InvalidProtocolBufferException {
private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
throws InvalidProtocolBufferException {
// dedup similarity relations had empty target value, don't migrate them
if (aa.getTargetValue().length == 0) {
return null;
}
final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
final Oaf oaf = ProtoConverter.convert(proto_oaf);
switch (proto_oaf.getKind()) {
case entity:
switch (proto_oaf.getEntity().getType()) {
case datasource:
return new AtomicAction<>(Datasource.class, (Datasource) oaf);
case organization:
return new AtomicAction<>(Organization.class, (Organization) oaf);
case project:
return new AtomicAction<>(Project.class, (Project) oaf);
case result:
final String resulttypeid =
proto_oaf.getEntity().getResult().getMetadata().getResulttype().getClassid();
switch (resulttypeid) {
case "publication":
return new AtomicAction<>(Publication.class, (Publication) oaf);
case "software":
return new AtomicAction<>(Software.class, (Software) oaf);
case "other":
return new AtomicAction<>(OtherResearchProduct.class, (OtherResearchProduct) oaf);
case "dataset":
return new AtomicAction<>(Dataset.class, (Dataset) oaf);
default:
// can be an update, where the resulttype is not specified
return new AtomicAction<>(Result.class, (Result) oaf);
}
default:
throw new IllegalArgumentException(
"invalid entity type: " + proto_oaf.getEntity().getType());
}
case relation:
return new AtomicAction<>(Relation.class, (Relation) oaf);
default:
throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
}
}
// dedup similarity relations had empty target value, don't migrate them
if (aa.getTargetValue().length == 0) {
return null;
}
final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
final Oaf oaf = ProtoConverter.convert(proto_oaf);
switch (proto_oaf.getKind()) {
case entity:
switch (proto_oaf.getEntity().getType()) {
case datasource:
return new AtomicAction<>(Datasource.class, (Datasource) oaf);
case organization:
return new AtomicAction<>(Organization.class, (Organization) oaf);
case project:
return new AtomicAction<>(Project.class, (Project) oaf);
case result:
final String resulttypeid = proto_oaf
.getEntity()
.getResult()
.getMetadata()
.getResulttype()
.getClassid();
switch (resulttypeid) {
case "publication":
return new AtomicAction<>(Publication.class, (Publication) oaf);
case "software":
return new AtomicAction<>(Software.class, (Software) oaf);
case "other":
return new AtomicAction<>(OtherResearchProduct.class, (OtherResearchProduct) oaf);
case "dataset":
return new AtomicAction<>(Dataset.class, (Dataset) oaf);
default:
// can be an update, where the resulttype is not specified
return new AtomicAction<>(Result.class, (Result) oaf);
}
default:
throw new IllegalArgumentException(
"invalid entity type: " + proto_oaf.getEntity().getType());
}
case relation:
return new AtomicAction<>(Relation.class, (Relation) oaf);
default:
throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
}
}
private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
String XQUERY =
"collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
return isLookUp.getResourceProfileByQuery(XQUERY);
}
private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
String XQUERY = "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
return isLookUp.getResourceProfileByQuery(XQUERY);
}
}

188
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java
View File

@ -1,15 +1,13 @@
package eu.dnetlib.dhp.actionmanager.partition;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static org.apache.spark.sql.functions.*;
import eu.dnetlib.dhp.actionmanager.ISClient;
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
@ -20,117 +18,127 @@ import org.apache.spark.sql.types.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.ISClient;
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
/** Partitions given set of action sets by payload type. */
public class PartitionActionSetsByPayloadTypeJob {
private static final Logger logger =
LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final Logger logger = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final StructType KV_SCHEMA =
StructType$.MODULE$.apply(
Arrays.asList(
StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())));
private static final StructType KV_SCHEMA = StructType$.MODULE$
.apply(
Arrays
.asList(
StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())));
private static final StructType ATOMIC_ACTION_SCHEMA =
StructType$.MODULE$.apply(
Arrays.asList(
StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply(
"payload", DataTypes.StringType, false, Metadata.empty())));
private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$
.apply(
Arrays
.asList(
StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$
.apply(
"payload", DataTypes.StringType, false, Metadata.empty())));
private ISClient isClient;
private ISClient isClient;
public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) {
this.isClient = new ISClient(isLookupUrl);
}
public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) {
this.isClient = new ISClient(isLookupUrl);
}
public PartitionActionSetsByPayloadTypeJob() {}
public PartitionActionSetsByPayloadTypeJob() {
}
public static void main(String[] args) throws Exception {
String jsonConfiguration =
IOUtils.toString(
PromoteActionPayloadForGraphTableJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PromoteActionPayloadForGraphTableJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged =
Optional.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputActionSetIds = parser.get("inputActionSetIds");
logger.info("inputActionSetIds: {}", inputActionSetIds);
String inputActionSetIds = parser.get("inputActionSetIds");
logger.info("inputActionSetIds: {}", inputActionSetIds);
String outputPath = parser.get("outputPath");
logger.info("outputPath: {}", outputPath);
String outputPath = parser.get("outputPath");
logger.info("outputPath: {}", outputPath);
String isLookupUrl = parser.get("isLookupUrl");
logger.info("isLookupUrl: {}", isLookupUrl);
String isLookupUrl = parser.get("isLookupUrl");
logger.info("isLookupUrl: {}", isLookupUrl);
new PartitionActionSetsByPayloadTypeJob(isLookupUrl)
.run(isSparkSessionManaged, inputActionSetIds, outputPath);
}
new PartitionActionSetsByPayloadTypeJob(isLookupUrl)
.run(isSparkSessionManaged, inputActionSetIds, outputPath);
}
protected void run(Boolean isSparkSessionManaged, String inputActionSetIds, String outputPath) {
protected void run(Boolean isSparkSessionManaged, String inputActionSetIds, String outputPath) {
List<String> inputActionSetPaths = getIsClient().getLatestRawsetPaths(inputActionSetIds);
logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths));
List<String> inputActionSetPaths = getIsClient().getLatestRawsetPaths(inputActionSetIds);
logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths));
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath);
});
}
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath);
});
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
private static void readAndWriteActionSetsFromPaths(
SparkSession spark, List<String> inputActionSetPaths, String outputPath) {
inputActionSetPaths.stream()
.filter(path -> HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration()))
.forEach(
inputActionSetPath -> {
Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath);
saveActions(actionDS, outputPath);
});
}
private static void readAndWriteActionSetsFromPaths(
SparkSession spark, List<String> inputActionSetPaths, String outputPath) {
inputActionSetPaths
.stream()
.filter(path -> HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration()))
.forEach(
inputActionSetPath -> {
Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath);
saveActions(actionDS, outputPath);
});
}
private static Dataset<Row> readActionSetFromPath(SparkSession spark, String path) {
logger.info("Reading actions from path: {}", path);
private static Dataset<Row> readActionSetFromPath(SparkSession spark, String path) {
logger.info("Reading actions from path: {}", path);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Row> rdd =
sc.sequenceFile(path, Text.class, Text.class)
.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
JavaRDD<Row> rdd = sc
.sequenceFile(path, Text.class, Text.class)
.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
return spark
.createDataFrame(rdd, KV_SCHEMA)
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
.select(expr("atomic_action.*"));
}
return spark
.createDataFrame(rdd, KV_SCHEMA)
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
.select(expr("atomic_action.*"));
}
private static void saveActions(Dataset<Row> actionDS, String path) {
logger.info("Saving actions to path: {}", path);
actionDS.write().partitionBy("clazz").mode(SaveMode.Append).parquet(path);
}
private static void saveActions(Dataset<Row> actionDS, String path) {
logger.info("Saving actions to path: {}", path);
actionDS.write().partitionBy("clazz").mode(SaveMode.Append).parquet(path);
}
public ISClient getIsClient() {
return isClient;
}
public ISClient getIsClient() {
return isClient;
}
public void setIsClient(ISClient isClient) {
this.isClient = isClient;
}
public void setIsClient(ISClient isClient) {
this.isClient = isClient;
}
}

135
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java
View File

@ -1,82 +1,87 @@
package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import java.util.function.BiFunction;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.util.function.BiFunction;
/** OAF model merging support. */
public class MergeAndGet {
private MergeAndGet() {}
private MergeAndGet() {
}
/**
* Strategy for merging OAF model objects.
*
* <p>MERGE_FROM_AND_GET: use OAF 'mergeFrom' method SELECT_NEWER_AND_GET: use last update
* timestamp to return newer instance
*/
public enum Strategy {
MERGE_FROM_AND_GET,
SELECT_NEWER_AND_GET
}
/**
* Strategy for merging OAF model objects.
* <p>
* MERGE_FROM_AND_GET: use OAF 'mergeFrom' method SELECT_NEWER_AND_GET: use last update timestamp to return newer
* instance
*/
public enum Strategy {
MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET
}
/**
* Returns a function for merging OAF model objects.
*
* @param strategy Strategy to be used to merge objects
* @param <G> Graph table type
* @param <A> Action payload type
* @return BiFunction to be used to merge OAF objects
*/
public static <G extends Oaf, A extends Oaf>
SerializableSupplier<BiFunction<G, A, G>> functionFor(Strategy strategy) {
switch (strategy) {
case MERGE_FROM_AND_GET:
return () -> MergeAndGet::mergeFromAndGet;
case SELECT_NEWER_AND_GET:
return () -> MergeAndGet::selectNewerAndGet;
}
throw new RuntimeException();
}
/**
* Returns a function for merging OAF model objects.
*
* @param strategy Strategy to be used to merge objects
* @param <G> Graph table type
* @param <A> Action payload type
* @return BiFunction to be used to merge OAF objects
*/
public static <G extends Oaf, A extends Oaf> SerializableSupplier<BiFunction<G, A, G>> functionFor(
Strategy strategy) {
switch (strategy) {
case MERGE_FROM_AND_GET:
return () -> MergeAndGet::mergeFromAndGet;
case SELECT_NEWER_AND_GET:
return () -> MergeAndGet::selectNewerAndGet;
}
throw new RuntimeException();
}
private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) {
if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) {
((Relation) x).mergeFrom((Relation) y);
return x;
} else if (isSubClass(x, OafEntity.class)
&& isSubClass(y, OafEntity.class)
&& isSubClass(x, y)) {
((OafEntity) x).mergeFrom((OafEntity) y);
return x;
}
throw new RuntimeException(
String.format(
"MERGE_FROM_AND_GET incompatible types: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
}
private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) {
if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) {
((Relation) x).mergeFrom((Relation) y);
return x;
} else if (isSubClass(x, OafEntity.class)
&& isSubClass(y, OafEntity.class)
&& isSubClass(x, y)) {
((OafEntity) x).mergeFrom((OafEntity) y);
return x;
}
throw new RuntimeException(
String
.format(
"MERGE_FROM_AND_GET incompatible types: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
}
private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) {
if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x;
} else if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
return (G) y;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
throw new RuntimeException(
String.format(
"SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
}
throw new RuntimeException(
String.format(
"SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
}
private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) {
if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x;
} else if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
return (G) y;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
throw new RuntimeException(
String
.format(
"SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
}
throw new RuntimeException(
String
.format(
"SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
}
}

349
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
View File

@ -1,18 +1,14 @@
package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import java.util.Objects;
import java.util.Optional;
import java.util.function.BiFunction;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -23,204 +19,207 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
/** Applies a given action payload file to graph table of compatible type. */
public class PromoteActionPayloadForGraphTableJob {
private static final Logger logger =
LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class);
private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration =
IOUtils.toString(
PromoteActionPayloadForGraphTableJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PromoteActionPayloadForGraphTableJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged =
Optional.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputGraphTablePath = parser.get("inputGraphTablePath");
logger.info("inputGraphTablePath: {}", inputGraphTablePath);
String inputGraphTablePath = parser.get("inputGraphTablePath");
logger.info("inputGraphTablePath: {}", inputGraphTablePath);
String graphTableClassName = parser.get("graphTableClassName");
logger.info("graphTableClassName: {}", graphTableClassName);
String graphTableClassName = parser.get("graphTableClassName");
logger.info("graphTableClassName: {}", graphTableClassName);
String inputActionPayloadPath = parser.get("inputActionPayloadPath");
logger.info("inputActionPayloadPath: {}", inputActionPayloadPath);
String inputActionPayloadPath = parser.get("inputActionPayloadPath");
logger.info("inputActionPayloadPath: {}", inputActionPayloadPath);
String actionPayloadClassName = parser.get("actionPayloadClassName");
logger.info("actionPayloadClassName: {}", actionPayloadClassName);
String actionPayloadClassName = parser.get("actionPayloadClassName");
logger.info("actionPayloadClassName: {}", actionPayloadClassName);
String outputGraphTablePath = parser.get("outputGraphTablePath");
logger.info("outputGraphTablePath: {}", outputGraphTablePath);
String outputGraphTablePath = parser.get("outputGraphTablePath");
logger.info("outputGraphTablePath: {}", outputGraphTablePath);
MergeAndGet.Strategy strategy =
MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
logger.info("strategy: {}", strategy);
MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
logger.info("strategy: {}", strategy);
Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
Class<? extends Oaf> actionPayloadClazz =
(Class<? extends Oaf>) Class.forName(actionPayloadClassName);
Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
Class<? extends Oaf> actionPayloadClazz = (Class<? extends Oaf>) Class.forName(actionPayloadClassName);
throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz);
throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz);
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputGraphTablePath);
promoteActionPayloadForGraphTable(
spark,
inputGraphTablePath,
inputActionPayloadPath,
outputGraphTablePath,
strategy,
rowClazz,
actionPayloadClazz);
});
}
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputGraphTablePath);
promoteActionPayloadForGraphTable(
spark,
inputGraphTablePath,
inputActionPayloadPath,
outputGraphTablePath,
strategy,
rowClazz,
actionPayloadClazz);
});
}
private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(
Class<? extends Oaf> rowClazz, Class<? extends Oaf> actionPayloadClazz) {
if (!isSubClass(rowClazz, actionPayloadClazz)) {
String msg =
String.format(
"graph table class is not a subclass of action payload class: graph=%s, action=%s",
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName());
throw new RuntimeException(msg);
}
}
private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(
Class<? extends Oaf> rowClazz, Class<? extends Oaf> actionPayloadClazz) {
if (!isSubClass(rowClazz, actionPayloadClazz)) {
String msg = String
.format(
"graph table class is not a subclass of action payload class: graph=%s, action=%s",
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName());
throw new RuntimeException(msg);
}
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
private static <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable(
SparkSession spark,
String inputGraphTablePath,
String inputActionPayloadPath,
String outputGraphTablePath,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
Dataset<A> actionPayloadDS =
readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
private static <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable(
SparkSession spark,
String inputGraphTablePath,
String inputActionPayloadPath,
String outputGraphTablePath,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
Dataset<G> result =
promoteActionPayloadForGraphTable(
rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz)
.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
Dataset<G> result = promoteActionPayloadForGraphTable(
rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz)
.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
saveGraphTable(result, outputGraphTablePath);
}
saveGraphTable(result, outputGraphTablePath);
}
private static <G extends Oaf> Dataset<G> readGraphTable(
SparkSession spark, String path, Class<G> rowClazz) {
logger.info("Reading graph table from path: {}", path);
private static <G extends Oaf> Dataset<G> readGraphTable(
SparkSession spark, String path, Class<G> rowClazz) {
logger.info("Reading graph table from path: {}", path);
return spark
.read()
.textFile(path)
.map(
(MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz),
Encoders.bean(rowClazz));
return spark
.read()
.textFile(path)
.map(
(MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz),
Encoders.bean(rowClazz));
/*
* return spark .read() .parquet(path) .as(Encoders.bean(rowClazz));
*/
}
/*
* return spark .read() .parquet(path) .as(Encoders.bean(rowClazz));
*/
}
private static <A extends Oaf> Dataset<A> readActionPayload(
SparkSession spark, String path, Class<A> actionPayloadClazz) {
logger.info("Reading action payload from path: {}", path);
return spark
.read()
.parquet(path)
.map(
(MapFunction<Row, A>)
value ->
OBJECT_MAPPER.readValue(value.<String>getAs("payload"), actionPayloadClazz),
Encoders.bean(actionPayloadClazz));
}
private static <A extends Oaf> Dataset<A> readActionPayload(
SparkSession spark, String path, Class<A> actionPayloadClazz) {
logger.info("Reading action payload from path: {}", path);
return spark
.read()
.parquet(path)
.map(
(MapFunction<Row, A>) value -> OBJECT_MAPPER
.readValue(value.<String> getAs("payload"), actionPayloadClazz),
Encoders.bean(actionPayloadClazz));
}
private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(
Dataset<G> rowDS,
Dataset<A> actionPayloadDS,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
logger.info(
"Promoting action payload for graph table: payload={}, table={}",
actionPayloadClazz.getSimpleName(),
rowClazz.getSimpleName());
private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(
Dataset<G> rowDS,
Dataset<A> actionPayloadDS,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
logger
.info(
"Promoting action payload for graph table: payload={}, table={}",
actionPayloadClazz.getSimpleName(),
rowClazz.getSimpleName());
SerializableSupplier<Function<G, String>> rowIdFn = ModelSupport::idFn;
SerializableSupplier<Function<A, String>> actionPayloadIdFn = ModelSupport::idFn;
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn =
MergeAndGet.functionFor(strategy);
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy);
SerializableSupplier<G> zeroFn = zeroFn(rowClazz);
SerializableSupplier<Function<G, Boolean>> isNotZeroFn =
PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource;
SerializableSupplier<Function<G, String>> rowIdFn = ModelSupport::idFn;
SerializableSupplier<Function<A, String>> actionPayloadIdFn = ModelSupport::idFn;
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy);
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy);
SerializableSupplier<G> zeroFn = zeroFn(rowClazz);
SerializableSupplier<Function<G, Boolean>> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource;
Dataset<G> joinedAndMerged =
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeRowWithActionPayloadAndGetFn,
rowClazz,
actionPayloadClazz);
Dataset<G> joinedAndMerged = PromoteActionPayloadFunctions
.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeRowWithActionPayloadAndGetFn,
rowClazz,
actionPayloadClazz);
return PromoteActionPayloadFunctions.groupGraphTableByIdAndMerge(
joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
}
return PromoteActionPayloadFunctions
.groupGraphTableByIdAndMerge(
joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
}
private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) {
switch (clazz.getCanonicalName()) {
case "eu.dnetlib.dhp.schema.oaf.Dataset":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Dataset());
case "eu.dnetlib.dhp.schema.oaf.Datasource":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Datasource());
case "eu.dnetlib.dhp.schema.oaf.Organization":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Organization());
case "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.OtherResearchProduct());
case "eu.dnetlib.dhp.schema.oaf.Project":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Project());
case "eu.dnetlib.dhp.schema.oaf.Publication":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Publication());
case "eu.dnetlib.dhp.schema.oaf.Relation":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Relation());
case "eu.dnetlib.dhp.schema.oaf.Software":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Software());
default:
throw new RuntimeException("unknown class: " + clazz.getCanonicalName());
}
}
private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) {
switch (clazz.getCanonicalName()) {
case "eu.dnetlib.dhp.schema.oaf.Dataset":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Dataset());
case "eu.dnetlib.dhp.schema.oaf.Datasource":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Datasource());
case "eu.dnetlib.dhp.schema.oaf.Organization":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Organization());
case "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.OtherResearchProduct());
case "eu.dnetlib.dhp.schema.oaf.Project":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Project());
case "eu.dnetlib.dhp.schema.oaf.Publication":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Publication());
case "eu.dnetlib.dhp.schema.oaf.Relation":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Relation());
case "eu.dnetlib.dhp.schema.oaf.Software":
return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Software());
default:
throw new RuntimeException("unknown class: " + clazz.getCanonicalName());
}
}
private static <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSource() {
return t -> {
if (isSubClass(t, Relation.class)) {
return Objects.nonNull(((Relation) t).getSource());
}
return Objects.nonNull(((OafEntity) t).getId());
};
}
private static <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSource() {
return t -> {
if (isSubClass(t, Relation.class)) {
return Objects.nonNull(((Relation) t).getSource());
}
return Objects.nonNull(((OafEntity) t).getId());
};
}
private static <G extends Oaf> void saveGraphTable(Dataset<G> result, String path) {
logger.info("Saving graph table to path: {}", path);
result.toJSON().write().option("compression", "gzip").text(path);
}
private static <G extends Oaf> void saveGraphTable(Dataset<G> result, String path) {
logger.info("Saving graph table to path: {}", path);
result.toJSON().write().option("compression", "gzip").text(path);
}
}

299
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java
View File

@ -1,13 +1,13 @@
package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.util.Objects;
import java.util.Optional;
import java.util.function.BiFunction;
import java.util.function.Function;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
@ -15,171 +15,170 @@ import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.TypedColumn;
import org.apache.spark.sql.expressions.Aggregator;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import scala.Tuple2;
/** Promote action payload functions. */
public class PromoteActionPayloadFunctions {
private PromoteActionPayloadFunctions() {}
private PromoteActionPayloadFunctions() {
}
/**
* Joins dataset representing graph table with dataset representing action payload using supplied
* functions.
*
* @param rowDS Dataset representing graph table
* @param actionPayloadDS Dataset representing action payload
* @param rowIdFn Function used to get the id of graph table row
* @param actionPayloadIdFn Function used to get id of action payload instance
* @param mergeAndGetFn Function used to merge graph table row and action payload instance
* @param rowClazz Class of graph table
* @param actionPayloadClazz Class of action payload
* @param <G> Type of graph table row
* @param <A> Type of action payload instance
* @return Dataset of merged graph table rows and action payload instances
*/
public static <G extends Oaf, A extends Oaf> Dataset<G> joinGraphTableWithActionPayloadAndMerge(
Dataset<G> rowDS,
Dataset<A> actionPayloadDS,
SerializableSupplier<Function<G, String>> rowIdFn,
SerializableSupplier<Function<A, String>> actionPayloadIdFn,
SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
if (!isSubClass(rowClazz, actionPayloadClazz)) {
throw new RuntimeException(
"action payload type must be the same or be a super type of table row type");
}
/**
* Joins dataset representing graph table with dataset representing action payload using supplied functions.
*
* @param rowDS Dataset representing graph table
* @param actionPayloadDS Dataset representing action payload
* @param rowIdFn Function used to get the id of graph table row
* @param actionPayloadIdFn Function used to get id of action payload instance
* @param mergeAndGetFn Function used to merge graph table row and action payload instance
* @param rowClazz Class of graph table
* @param actionPayloadClazz Class of action payload
* @param <G> Type of graph table row
* @param <A> Type of action payload instance
* @return Dataset of merged graph table rows and action payload instances
*/
public static <G extends Oaf, A extends Oaf> Dataset<G> joinGraphTableWithActionPayloadAndMerge(
Dataset<G> rowDS,
Dataset<A> actionPayloadDS,
SerializableSupplier<Function<G, String>> rowIdFn,
SerializableSupplier<Function<A, String>> actionPayloadIdFn,
SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
if (!isSubClass(rowClazz, actionPayloadClazz)) {
throw new RuntimeException(
"action payload type must be the same or be a super type of table row type");
}
Dataset<Tuple2<String, G>> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz);
Dataset<Tuple2<String, A>> actionPayloadWithIdDS =
mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz);
Dataset<Tuple2<String, G>> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz);
Dataset<Tuple2<String, A>> actionPayloadWithIdDS = mapToTupleWithId(
actionPayloadDS, actionPayloadIdFn, actionPayloadClazz);
return rowWithIdDS
.joinWith(
actionPayloadWithIdDS,
rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")),
"full_outer")
.map(
(MapFunction<Tuple2<Tuple2<String, G>, Tuple2<String, A>>, G>)
value -> {
Optional<G> rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2);
Optional<A> actionPayloadOpt = Optional.ofNullable(value._2()).map(Tuple2::_2);
return rowOpt
.map(
row ->
actionPayloadOpt
.map(
actionPayload ->
mergeAndGetFn.get().apply(row, actionPayload))
.orElse(row))
.orElseGet(
() ->
actionPayloadOpt
.filter(
actionPayload -> actionPayload.getClass().equals(rowClazz))
.map(rowClazz::cast)
.orElse(null));
},
Encoders.kryo(rowClazz))
.filter((FilterFunction<G>) Objects::nonNull);
}
return rowWithIdDS
.joinWith(
actionPayloadWithIdDS,
rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")),
"full_outer")
.map(
(MapFunction<Tuple2<Tuple2<String, G>, Tuple2<String, A>>, G>) value -> {
Optional<G> rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2);
Optional<A> actionPayloadOpt = Optional.ofNullable(value._2()).map(Tuple2::_2);
return rowOpt
.map(
row -> actionPayloadOpt
.map(
actionPayload -> mergeAndGetFn.get().apply(row, actionPayload))
.orElse(row))
.orElseGet(
() -> actionPayloadOpt
.filter(
actionPayload -> actionPayload.getClass().equals(rowClazz))
.map(rowClazz::cast)
.orElse(null));
},
Encoders.kryo(rowClazz))
.filter((FilterFunction<G>) Objects::nonNull);
}
private static <T extends Oaf> Dataset<Tuple2<String, T>> mapToTupleWithId(
Dataset<T> ds, SerializableSupplier<Function<T, String>> idFn, Class<T> clazz) {
return ds.map(
(MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(idFn.get().apply(value), value),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
}
private static <T extends Oaf> Dataset<Tuple2<String, T>> mapToTupleWithId(
Dataset<T> ds, SerializableSupplier<Function<T, String>> idFn, Class<T> clazz) {
return ds
.map(
(MapFunction<T, Tuple2<String, T>>) value -> new Tuple2<>(idFn.get().apply(value), value),
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz)));
}
/**
* Groups graph table by id and aggregates using supplied functions.
*
* @param rowDS Dataset representing graph table
* @param rowIdFn Function used to get the id of graph table row
* @param mergeAndGetFn Function used to merge graph table rows
* @param zeroFn Function to create a zero/empty instance of graph table row
* @param isNotZeroFn Function to check if graph table row is not zero/empty
* @param rowClazz Class of graph table
* @param <G> Type of graph table row
* @return Dataset of aggregated graph table rows
*/
public static <G extends Oaf> Dataset<G> groupGraphTableByIdAndMerge(
Dataset<G> rowDS,
SerializableSupplier<Function<G, String>> rowIdFn,
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
SerializableSupplier<G> zeroFn,
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
Class<G> rowClazz) {
TypedColumn<G, G> aggregator =
new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn();
return rowDS
.groupByKey((MapFunction<G, String>) x -> rowIdFn.get().apply(x), Encoders.STRING())
.agg(aggregator)
.map((MapFunction<Tuple2<String, G>, G>) Tuple2::_2, Encoders.kryo(rowClazz));
}
/**
* Groups graph table by id and aggregates using supplied functions.
*
* @param rowDS Dataset representing graph table
* @param rowIdFn Function used to get the id of graph table row
* @param mergeAndGetFn Function used to merge graph table rows
* @param zeroFn Function to create a zero/empty instance of graph table row
* @param isNotZeroFn Function to check if graph table row is not zero/empty
* @param rowClazz Class of graph table
* @param <G> Type of graph table row
* @return Dataset of aggregated graph table rows
*/
public static <G extends Oaf> Dataset<G> groupGraphTableByIdAndMerge(
Dataset<G> rowDS,
SerializableSupplier<Function<G, String>> rowIdFn,
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
SerializableSupplier<G> zeroFn,
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
Class<G> rowClazz) {
TypedColumn<G, G> aggregator = new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn();
return rowDS
.groupByKey((MapFunction<G, String>) x -> rowIdFn.get().apply(x), Encoders.STRING())
.agg(aggregator)
.map((MapFunction<Tuple2<String, G>, G>) Tuple2::_2, Encoders.kryo(rowClazz));
}
/**
* Aggregator to be used for aggregating graph table rows during grouping.
*
* @param <G> Type of graph table row
*/
public static class TableAggregator<G extends Oaf> extends Aggregator<G, G, G> {
private SerializableSupplier<G> zeroFn;
private SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
private SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
private Class<G> rowClazz;
/**
* Aggregator to be used for aggregating graph table rows during grouping.
*
* @param <G> Type of graph table row
*/
public static class TableAggregator<G extends Oaf> extends Aggregator<G, G, G> {
private SerializableSupplier<G> zeroFn;
private SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
private SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
private Class<G> rowClazz;
public TableAggregator(
SerializableSupplier<G> zeroFn,
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
Class<G> rowClazz) {
this.zeroFn = zeroFn;
this.mergeAndGetFn = mergeAndGetFn;
this.isNotZeroFn = isNotZeroFn;
this.rowClazz = rowClazz;
}
public TableAggregator(
SerializableSupplier<G> zeroFn,
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
Class<G> rowClazz) {
this.zeroFn = zeroFn;
this.mergeAndGetFn = mergeAndGetFn;
this.isNotZeroFn = isNotZeroFn;
this.rowClazz = rowClazz;
}
@Override
public G zero() {
return zeroFn.get();
}
@Override
public G zero() {
return zeroFn.get();
}
@Override
public G reduce(G b, G a) {
return zeroSafeMergeAndGet(b, a);
}
@Override
public G reduce(G b, G a) {
return zeroSafeMergeAndGet(b, a);
}
@Override
public G merge(G b1, G b2) {
return zeroSafeMergeAndGet(b1, b2);
}
@Override
public G merge(G b1, G b2) {
return zeroSafeMergeAndGet(b1, b2);
}
private G zeroSafeMergeAndGet(G left, G right) {
Function<G, Boolean> isNotZero = isNotZeroFn.get();
if (isNotZero.apply(left) && isNotZero.apply(right)) {
return mergeAndGetFn.get().apply(left, right);
} else if (isNotZero.apply(left) && !isNotZero.apply(right)) {
return left;
} else if (!isNotZero.apply(left) && isNotZero.apply(right)) {
return right;
}
throw new RuntimeException("internal aggregation error: left and right objects are zero");
}
private G zeroSafeMergeAndGet(G left, G right) {
Function<G, Boolean> isNotZero = isNotZeroFn.get();
if (isNotZero.apply(left) && isNotZero.apply(right)) {
return mergeAndGetFn.get().apply(left, right);
} else if (isNotZero.apply(left) && !isNotZero.apply(right)) {
return left;
} else if (!isNotZero.apply(left) && isNotZero.apply(right)) {
return right;
}
throw new RuntimeException("internal aggregation error: left and right objects are zero");
}
@Override
public G finish(G reduction) {
return reduction;
}
@Override
public G finish(G reduction) {
return reduction;
}
@Override
public Encoder<G> bufferEncoder() {
return Encoders.kryo(rowClazz);
}
@Override
public Encoder<G> bufferEncoder() {
return Encoders.kryo(rowClazz);
}
@Override
public Encoder<G> outputEncoder() {
return Encoders.kryo(rowClazz);
}
}
@Override
public Encoder<G> outputEncoder() {
return Encoders.kryo(rowClazz);
}
}
}

335
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.actionmanager.partition;
import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
@ -5,16 +6,13 @@ import static org.apache.spark.sql.functions.*;
import static org.junit.jupiter.api.Assertions.assertIterableEquals;
import static scala.collection.JavaConversions.mutableSeqAsJavaList;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.ISClient;
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest;
import eu.dnetlib.dhp.schema.oaf.*;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
@ -32,197 +30,212 @@ import org.junit.jupiter.api.io.TempDir;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.ISClient;
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
import scala.collection.mutable.Seq;
@ExtendWith(MockitoExtension.class)
public class PartitionActionSetsByPayloadTypeJobTest {
private static final ClassLoader cl =
PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader();
private static final ClassLoader cl = PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader();
private static Configuration configuration;
private static SparkSession spark;
private static Configuration configuration;
private static SparkSession spark;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final StructType ATOMIC_ACTION_SCHEMA =
StructType$.MODULE$.apply(
Arrays.asList(
StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply(
"payload", DataTypes.StringType, false, Metadata.empty())));
private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$
.apply(
Arrays
.asList(
StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$
.apply(
"payload", DataTypes.StringType, false, Metadata.empty())));
@BeforeAll
public static void beforeAll() throws IOException {
configuration = Job.getInstance().getConfiguration();
SparkConf conf = new SparkConf();
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
conf.setMaster("local");
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
spark = SparkSession.builder().config(conf).getOrCreate();
}
@BeforeAll
public static void beforeAll() throws IOException {
configuration = Job.getInstance().getConfiguration();
SparkConf conf = new SparkConf();
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
conf.setMaster("local");
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
spark = SparkSession.builder().config(conf).getOrCreate();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@DisplayName("Job")
@Nested
class Main {
@DisplayName("Job")
@Nested
class Main {
@Mock private ISClient isClient;
@Mock
private ISClient isClient;
@Test
public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
// given
Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets");
Path outputDir = workingDir.resolve("output");
@Test
public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
// given
Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets");
Path outputDir = workingDir.resolve("output");
Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsBaseDir);
Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsBaseDir);
List<String> inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir);
List<String> inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir);
// when
Mockito.when(isClient.getLatestRawsetPaths(Mockito.anyString()))
.thenReturn(inputActionSetsPaths);
// when
Mockito
.when(isClient.getLatestRawsetPaths(Mockito.anyString()))
.thenReturn(inputActionSetsPaths);
PartitionActionSetsByPayloadTypeJob job = new PartitionActionSetsByPayloadTypeJob();
job.setIsClient(isClient);
job.run(
Boolean.FALSE,
"", // it can be empty we're mocking the response from isClient
// to
// resolve the
// paths
outputDir.toString());
PartitionActionSetsByPayloadTypeJob job = new PartitionActionSetsByPayloadTypeJob();
job.setIsClient(isClient);
job
.run(
Boolean.FALSE,
"", // it can be empty we're mocking the response from isClient
// to
// resolve the
// paths
outputDir.toString());
// then
Files.exists(outputDir);
// then
Files.exists(outputDir);
assertForOafType(outputDir, oafsByClassName, eu.dnetlib.dhp.schema.oaf.Dataset.class);
assertForOafType(outputDir, oafsByClassName, Datasource.class);
assertForOafType(outputDir, oafsByClassName, Organization.class);
assertForOafType(outputDir, oafsByClassName, OtherResearchProduct.class);
assertForOafType(outputDir, oafsByClassName, Project.class);
assertForOafType(outputDir, oafsByClassName, Publication.class);
assertForOafType(outputDir, oafsByClassName, Result.class);
assertForOafType(outputDir, oafsByClassName, Relation.class);
assertForOafType(outputDir, oafsByClassName, Software.class);
}
}
assertForOafType(outputDir, oafsByClassName, eu.dnetlib.dhp.schema.oaf.Dataset.class);
assertForOafType(outputDir, oafsByClassName, Datasource.class);
assertForOafType(outputDir, oafsByClassName, Organization.class);
assertForOafType(outputDir, oafsByClassName, OtherResearchProduct.class);
assertForOafType(outputDir, oafsByClassName, Project.class);
assertForOafType(outputDir, oafsByClassName, Publication.class);
assertForOafType(outputDir, oafsByClassName, Result.class);
assertForOafType(outputDir, oafsByClassName, Relation.class);
assertForOafType(outputDir, oafsByClassName, Software.class);
}
}
private List<String> resolveInputActionSetPaths(Path inputActionSetsBaseDir) throws IOException {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
return Files.list(inputActionSetJsonDumpsDir)
.map(
path -> {
String inputActionSetId = path.getFileName().toString();
return inputActionSetsBaseDir.resolve(inputActionSetId).toString();
})
.collect(Collectors.toCollection(ArrayList::new));
}
private List<String> resolveInputActionSetPaths(Path inputActionSetsBaseDir) throws IOException {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
return Files
.list(inputActionSetJsonDumpsDir)
.map(
path -> {
String inputActionSetId = path.getFileName().toString();
return inputActionSetsBaseDir.resolve(inputActionSetId).toString();
})
.collect(Collectors.toCollection(ArrayList::new));
}
private static Map<String, List<String>> createActionSets(Path inputActionSetsDir)
throws IOException {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
private static Map<String, List<String>> createActionSets(Path inputActionSetsDir)
throws IOException {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
Map<String, List<String>> oafsByType = new HashMap<>();
Files.list(inputActionSetJsonDumpsDir)
.forEach(
inputActionSetJsonDumpFile -> {
String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString();
Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId);
Map<String, List<String>> oafsByType = new HashMap<>();
Files
.list(inputActionSetJsonDumpsDir)
.forEach(
inputActionSetJsonDumpFile -> {
String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString();
Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId);
Dataset<String> actionDS =
readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()).cache();
Dataset<String> actionDS = readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()).cache();
writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString());
writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString());
Map<String, List<String>> actionSetOafsByType =
actionDS
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
.select(expr("atomic_action.*")).groupBy(col("clazz"))
.agg(collect_list(col("payload")).as("payload_list")).collectAsList().stream()
.map(
row ->
new AbstractMap.SimpleEntry<>(
row.<String>getAs("clazz"),
mutableSeqAsJavaList(row.<Seq<String>>getAs("payload_list"))))
.collect(
Collectors.toMap(
AbstractMap.SimpleEntry::getKey, AbstractMap.SimpleEntry::getValue));
Map<String, List<String>> actionSetOafsByType = actionDS
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
.select(expr("atomic_action.*"))
.groupBy(col("clazz"))
.agg(collect_list(col("payload")).as("payload_list"))
.collectAsList()
.stream()
.map(
row -> new AbstractMap.SimpleEntry<>(
row.<String> getAs("clazz"),
mutableSeqAsJavaList(row.<Seq<String>> getAs("payload_list"))))
.collect(
Collectors
.toMap(
AbstractMap.SimpleEntry::getKey, AbstractMap.SimpleEntry::getValue));
actionSetOafsByType
.keySet()
.forEach(
x -> {
if (oafsByType.containsKey(x)) {
List<String> collected = new ArrayList<>();
collected.addAll(oafsByType.get(x));
collected.addAll(actionSetOafsByType.get(x));
oafsByType.put(x, collected);
} else {
oafsByType.put(x, actionSetOafsByType.get(x));
}
});
});
actionSetOafsByType
.keySet()
.forEach(
x -> {
if (oafsByType.containsKey(x)) {
List<String> collected = new ArrayList<>();
collected.addAll(oafsByType.get(x));
collected.addAll(actionSetOafsByType.get(x));
oafsByType.put(x, collected);
} else {
oafsByType.put(x, actionSetOafsByType.get(x));
}
});
});
return oafsByType;
}
return oafsByType;
}
private static Path getInputActionSetJsonDumpsDir() {
return Paths.get(
Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
.getFile());
}
private static Path getInputActionSetJsonDumpsDir() {
return Paths
.get(
Objects
.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
.getFile());
}
private static Dataset<String> readActionsFromJsonDump(String path) {
return spark.read().textFile(path);
}
private static Dataset<String> readActionsFromJsonDump(String path) {
return spark.read().textFile(path);
}
private static void writeActionsAsJobInput(
Dataset<String> actionDS, String inputActionSetId, String path) {
actionDS
.javaRDD()
.mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json)))
.saveAsNewAPIHadoopFile(
path, Text.class, Text.class, SequenceFileOutputFormat.class, configuration);
}
private static void writeActionsAsJobInput(
Dataset<String> actionDS, String inputActionSetId, String path) {
actionDS
.javaRDD()
.mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json)))
.saveAsNewAPIHadoopFile(
path, Text.class, Text.class, SequenceFileOutputFormat.class, configuration);
}
private static <T extends Oaf> void assertForOafType(
Path outputDir, Map<String, List<String>> oafsByClassName, Class<T> clazz) {
Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName()));
Files.exists(outputDatasetDir);
private static <T extends Oaf> void assertForOafType(
Path outputDir, Map<String, List<String>> oafsByClassName, Class<T> clazz) {
Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName()));
Files.exists(outputDatasetDir);
List<T> actuals =
readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList();
actuals.sort(Comparator.comparingInt(Object::hashCode));
List<T> actuals = readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList();
actuals.sort(Comparator.comparingInt(Object::hashCode));
List<T> expecteds =
oafsByClassName.get(clazz.getCanonicalName()).stream()
.map(json -> mapToOaf(json, clazz))
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
List<T> expecteds = oafsByClassName
.get(clazz.getCanonicalName())
.stream()
.map(json -> mapToOaf(json, clazz))
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
assertIterableEquals(expecteds, actuals);
}
assertIterableEquals(expecteds, actuals);
}
private static <T extends Oaf> Dataset<T> readActionPayloadFromJobOutput(
String path, Class<T> clazz) {
return spark
.read()
.parquet(path)
.map(
(MapFunction<Row, T>)
value -> OBJECT_MAPPER.readValue(value.<String>getAs("payload"), clazz),
Encoders.bean(clazz));
}
private static <T extends Oaf> Dataset<T> readActionPayloadFromJobOutput(
String path, Class<T> clazz) {
return spark
.read()
.parquet(path)
.map(
(MapFunction<Row, T>) value -> OBJECT_MAPPER.readValue(value.<String> getAs("payload"), clazz),
Encoders.bean(clazz));
}
private static <T extends Oaf> T mapToOaf(String json, Class<T> clazz) {
return rethrowAsRuntimeException(
() -> OBJECT_MAPPER.readValue(json, clazz),
String.format(
"failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName()));
}
private static <T extends Oaf> T mapToOaf(String json, Class<T> clazz) {
return rethrowAsRuntimeException(
() -> OBJECT_MAPPER.readValue(json, clazz),
String
.format(
"failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName()));
}
}

387
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.Strategy;
@ -5,254 +6,252 @@ import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.functionFor;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.*;
import java.util.function.BiFunction;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.*;
public class MergeAndGetTest {
@Nested
class MergeFromAndGetStrategy {
@Nested
class MergeFromAndGetStrategy {
@Test
public void shouldThrowForOafAndOaf() {
// given
Oaf a = mock(Oaf.class);
Oaf b = mock(Oaf.class);
@Test
public void shouldThrowForOafAndOaf() {
// given
Oaf a = mock(Oaf.class);
Oaf b = mock(Oaf.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForOafAndRelation() {
// given
Oaf a = mock(Oaf.class);
Relation b = mock(Relation.class);
@Test
public void shouldThrowForOafAndRelation() {
// given
Oaf a = mock(Oaf.class);
Relation b = mock(Relation.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForOafAndOafEntity() {
// given
Oaf a = mock(Oaf.class);
OafEntity b = mock(OafEntity.class);
@Test
public void shouldThrowForOafAndOafEntity() {
// given
Oaf a = mock(Oaf.class);
OafEntity b = mock(OafEntity.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForRelationAndOaf() {
// given
Relation a = mock(Relation.class);
Oaf b = mock(Oaf.class);
@Test
public void shouldThrowForRelationAndOaf() {
// given
Relation a = mock(Relation.class);
Oaf b = mock(Oaf.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForRelationAndOafEntity() {
// given
Relation a = mock(Relation.class);
OafEntity b = mock(OafEntity.class);
@Test
public void shouldThrowForRelationAndOafEntity() {
// given
Relation a = mock(Relation.class);
OafEntity b = mock(OafEntity.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldBehaveProperlyForRelationAndRelation() {
// given
Relation a = mock(Relation.class);
Relation b = mock(Relation.class);
@Test
public void shouldBehaveProperlyForRelationAndRelation() {
// given
Relation a = mock(Relation.class);
Relation b = mock(Relation.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(Relation.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
assertEquals(a, x);
}
// then
Oaf x = fn.get().apply(a, b);
assertTrue(Relation.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
assertEquals(a, x);
}
@Test
public void shouldThrowForOafEntityAndOaf() {
// given
OafEntity a = mock(OafEntity.class);
Oaf b = mock(Oaf.class);
@Test
public void shouldThrowForOafEntityAndOaf() {
// given
OafEntity a = mock(OafEntity.class);
Oaf b = mock(Oaf.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForOafEntityAndRelation() {
// given
OafEntity a = mock(OafEntity.class);
Relation b = mock(Relation.class);
@Test
public void shouldThrowForOafEntityAndRelation() {
// given
OafEntity a = mock(OafEntity.class);
Relation b = mock(Relation.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
// given
class OafEntitySub1 extends OafEntity {}
class OafEntitySub2 extends OafEntity {}
@Test
public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
// given
class OafEntitySub1 extends OafEntity {
}
class OafEntitySub2 extends OafEntity {
}
OafEntitySub1 a = mock(OafEntitySub1.class);
OafEntitySub2 b = mock(OafEntitySub2.class);
OafEntitySub1 a = mock(OafEntitySub1.class);
OafEntitySub2 b = mock(OafEntitySub2.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldBehaveProperlyForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
OafEntity b = mock(OafEntity.class);
@Test
public void shouldBehaveProperlyForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
OafEntity b = mock(OafEntity.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
assertEquals(a, x);
}
}
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
assertEquals(a, x);
}
}
@Nested
class SelectNewerAndGetStrategy {
@Nested
class SelectNewerAndGetStrategy {
@Test
public void shouldThrowForOafEntityAndRelation() {
// given
OafEntity a = mock(OafEntity.class);
Relation b = mock(Relation.class);
@Test
public void shouldThrowForOafEntityAndRelation() {
// given
OafEntity a = mock(OafEntity.class);
Relation b = mock(Relation.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForRelationAndOafEntity() {
// given
Relation a = mock(Relation.class);
OafEntity b = mock(OafEntity.class);
@Test
public void shouldThrowForRelationAndOafEntity() {
// given
Relation a = mock(Relation.class);
OafEntity b = mock(OafEntity.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForOafEntityAndResult() {
// given
OafEntity a = mock(OafEntity.class);
Result b = mock(Result.class);
@Test
public void shouldThrowForOafEntityAndResult() {
// given
OafEntity a = mock(OafEntity.class);
Result b = mock(Result.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
// given
// real types must be used because subclass-superclass resolution does not work for
// mocks
Dataset a = new Dataset();
a.setLastupdatetimestamp(1L);
Result b = new Result();
b.setLastupdatetimestamp(2L);
@Test
public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
// given
// real types must be used because subclass-superclass resolution does not work for
// mocks
Dataset a = new Dataset();
a.setLastupdatetimestamp(1L);
Result b = new Result();
b.setLastupdatetimestamp(2L);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldShouldReturnLeftForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
when(a.getLastupdatetimestamp()).thenReturn(1L);
OafEntity b = mock(OafEntity.class);
when(b.getLastupdatetimestamp()).thenReturn(2L);
@Test
public void shouldShouldReturnLeftForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
when(a.getLastupdatetimestamp()).thenReturn(1L);
OafEntity b = mock(OafEntity.class);
when(b.getLastupdatetimestamp()).thenReturn(2L);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
assertEquals(b, x);
}
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
assertEquals(b, x);
}
@Test
public void shouldShouldReturnRightForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
when(a.getLastupdatetimestamp()).thenReturn(2L);
OafEntity b = mock(OafEntity.class);
when(b.getLastupdatetimestamp()).thenReturn(1L);
@Test
public void shouldShouldReturnRightForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
when(a.getLastupdatetimestamp()).thenReturn(2L);
OafEntity b = mock(OafEntity.class);
when(b.getLastupdatetimestamp()).thenReturn(1L);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
assertEquals(a, x);
}
}
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
assertEquals(a, x);
}
}
}

450
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java
View File

@ -1,11 +1,9 @@
package eu.dnetlib.dhp.actionmanager.promote;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.params.provider.Arguments.arguments;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
@ -15,6 +13,7 @@ import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -26,253 +25,256 @@ import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
public class PromoteActionPayloadForGraphTableJobTest {
private static final ClassLoader cl =
PromoteActionPayloadForGraphTableJobTest.class.getClassLoader();
private static final ClassLoader cl = PromoteActionPayloadForGraphTableJobTest.class.getClassLoader();
private static SparkSession spark;
private static SparkSession spark;
private Path workingDir;
private Path inputDir;
private Path inputGraphRootDir;
private Path inputActionPayloadRootDir;
private Path outputDir;
private Path workingDir;
private Path inputDir;
private Path inputGraphRootDir;
private Path inputActionPayloadRootDir;
private Path outputDir;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@BeforeAll
public static void beforeAll() {
SparkConf conf = new SparkConf();
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
conf.setMaster("local");
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
spark = SparkSession.builder().config(conf).getOrCreate();
}
@BeforeAll
public static void beforeAll() {
SparkConf conf = new SparkConf();
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
conf.setMaster("local");
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
spark = SparkSession.builder().config(conf).getOrCreate();
}
@BeforeEach
public void beforeEach() throws IOException {
workingDir =
Files.createTempDirectory(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
inputDir = workingDir.resolve("input");
inputGraphRootDir = inputDir.resolve("graph");
inputActionPayloadRootDir = inputDir.resolve("action_payload");
outputDir = workingDir.resolve("output");
}
@BeforeEach
public void beforeEach() throws IOException {
workingDir = Files.createTempDirectory(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
inputDir = workingDir.resolve("input");
inputGraphRootDir = inputDir.resolve("graph");
inputActionPayloadRootDir = inputDir.resolve("action_payload");
outputDir = workingDir.resolve("output");
}
@AfterEach
public void afterEach() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
}
@AfterEach
public void afterEach() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@DisplayName("Job")
@Nested
class Main {
@DisplayName("Job")
@Nested
class Main {
@Test
public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
// given
Class<Relation> rowClazz = Relation.class;
Class<OafEntity> actionPayloadClazz = OafEntity.class;
@Test
public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
// given
Class<Relation> rowClazz = Relation.class;
Class<OafEntity> actionPayloadClazz = OafEntity.class;
// when
RuntimeException exception =
assertThrows(
RuntimeException.class,
() ->
PromoteActionPayloadForGraphTableJob.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputGraphTablePath",
"",
"-graphTableClassName",
rowClazz.getCanonicalName(),
"-inputActionPayloadPath",
"",
"-actionPayloadClassName",
actionPayloadClazz.getCanonicalName(),
"-outputGraphTablePath",
"",
"-mergeAndGetStrategy",
MergeAndGet.Strategy.SELECT_NEWER_AND_GET.name()
}));
// when
RuntimeException exception = assertThrows(
RuntimeException.class,
() -> PromoteActionPayloadForGraphTableJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputGraphTablePath",
"",
"-graphTableClassName",
rowClazz.getCanonicalName(),
"-inputActionPayloadPath",
"",
"-actionPayloadClassName",
actionPayloadClazz.getCanonicalName(),
"-outputGraphTablePath",
"",
"-mergeAndGetStrategy",
MergeAndGet.Strategy.SELECT_NEWER_AND_GET.name()
}));
// then
String msg =
String.format(
"graph table class is not a subclass of action payload class: graph=%s, action=%s",
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName());
assertTrue(exception.getMessage().contains(msg));
}
// then
String msg = String
.format(
"graph table class is not a subclass of action payload class: graph=%s, action=%s",
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName());
assertTrue(exception.getMessage().contains(msg));
}
@ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}")
@MethodSource(
"eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams")
public void shouldPromoteActionPayloadForGraphTable(
MergeAndGet.Strategy strategy,
Class<? extends Oaf> rowClazz,
Class<? extends Oaf> actionPayloadClazz)
throws Exception {
// given
Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz);
Path inputActionPayloadDir =
createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz);
Path outputGraphTableDir =
outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase());
@ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}")
@MethodSource("eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams")
public void shouldPromoteActionPayloadForGraphTable(
MergeAndGet.Strategy strategy,
Class<? extends Oaf> rowClazz,
Class<? extends Oaf> actionPayloadClazz)
throws Exception {
// given
Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz);
Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz);
Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase());
// when
PromoteActionPayloadForGraphTableJob.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputGraphTablePath",
inputGraphTableDir.toString(),
"-graphTableClassName",
rowClazz.getCanonicalName(),
"-inputActionPayloadPath",
inputActionPayloadDir.toString(),
"-actionPayloadClassName",
actionPayloadClazz.getCanonicalName(),
"-outputGraphTablePath",
outputGraphTableDir.toString(),
"-mergeAndGetStrategy",
strategy.name()
});
// when
PromoteActionPayloadForGraphTableJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputGraphTablePath",
inputGraphTableDir.toString(),
"-graphTableClassName",
rowClazz.getCanonicalName(),
"-inputActionPayloadPath",
inputActionPayloadDir.toString(),
"-actionPayloadClassName",
actionPayloadClazz.getCanonicalName(),
"-outputGraphTablePath",
outputGraphTableDir.toString(),
"-mergeAndGetStrategy",
strategy.name()
});
// then
assertTrue(Files.exists(outputGraphTableDir));
// then
assertTrue(Files.exists(outputGraphTableDir));
List<? extends Oaf> actualOutputRows =
readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz).collectAsList()
.stream()
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
String expectedOutputGraphTableJsonDumpPath =
resultFileLocation(strategy, rowClazz, actionPayloadClazz);
Path expectedOutputGraphTableJsonDumpFile =
Paths.get(
Objects.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath))
.getFile());
List<? extends Oaf> expectedOutputRows =
readGraphTableFromJsonDump(expectedOutputGraphTableJsonDumpFile.toString(), rowClazz)
.collectAsList().stream()
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
assertIterableEquals(expectedOutputRows, actualOutputRows);
}
}
List<? extends Oaf> actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz)
.collectAsList()
.stream()
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
String expectedOutputGraphTableJsonDumpPath = resultFileLocation(strategy, rowClazz, actionPayloadClazz);
Path expectedOutputGraphTableJsonDumpFile = Paths
.get(
Objects
.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath))
.getFile());
List<? extends Oaf> expectedOutputRows = readGraphTableFromJsonDump(
expectedOutputGraphTableJsonDumpFile.toString(), rowClazz)
.collectAsList()
.stream()
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
assertIterableEquals(expectedOutputRows, actualOutputRows);
}
}
public static Stream<Arguments> promoteJobTestParams() {
return Stream.of(
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET,
eu.dnetlib.dhp.schema.oaf.Dataset.class,
eu.dnetlib.dhp.schema.oaf.Dataset.class),
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET,
eu.dnetlib.dhp.schema.oaf.Dataset.class,
eu.dnetlib.dhp.schema.oaf.Result.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Datasource.class, Datasource.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Organization.class, Organization.class),
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET,
OtherResearchProduct.class,
OtherResearchProduct.class),
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, Result.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Project.class, Project.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Publication.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Result.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Relation.class, Relation.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Software.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Result.class));
}
public static Stream<Arguments> promoteJobTestParams() {
return Stream
.of(
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET,
eu.dnetlib.dhp.schema.oaf.Dataset.class,
eu.dnetlib.dhp.schema.oaf.Dataset.class),
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET,
eu.dnetlib.dhp.schema.oaf.Dataset.class,
eu.dnetlib.dhp.schema.oaf.Result.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Datasource.class, Datasource.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Organization.class, Organization.class),
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET,
OtherResearchProduct.class,
OtherResearchProduct.class),
arguments(
MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, Result.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Project.class, Project.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Publication.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Result.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Relation.class, Relation.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Software.class),
arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Result.class));
}
private static <G extends Oaf> Path createGraphTable(Path inputGraphRootDir, Class<G> rowClazz) {
String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz);
Path inputGraphTableJsonDumpFile =
Paths.get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile());
Dataset<G> rowDS = readGraphTableFromJsonDump(inputGraphTableJsonDumpFile.toString(), rowClazz);
String inputGraphTableName = rowClazz.getSimpleName().toLowerCase();
Path inputGraphTableDir = inputGraphRootDir.resolve(inputGraphTableName);
writeGraphTableAaJobInput(rowDS, inputGraphTableDir.toString());
return inputGraphTableDir;
}
private static <G extends Oaf> Path createGraphTable(Path inputGraphRootDir, Class<G> rowClazz) {
String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz);
Path inputGraphTableJsonDumpFile = Paths
.get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile());
Dataset<G> rowDS = readGraphTableFromJsonDump(inputGraphTableJsonDumpFile.toString(), rowClazz);
String inputGraphTableName = rowClazz.getSimpleName().toLowerCase();
Path inputGraphTableDir = inputGraphRootDir.resolve(inputGraphTableName);
writeGraphTableAaJobInput(rowDS, inputGraphTableDir.toString());
return inputGraphTableDir;
}
private static String inputGraphTableJsonDumpLocation(Class<? extends Oaf> rowClazz) {
return String.format(
"%s/%s.json",
"eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase());
}
private static String inputGraphTableJsonDumpLocation(Class<? extends Oaf> rowClazz) {
return String
.format(
"%s/%s.json",
"eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase());
}
private static <G extends Oaf> Dataset<G> readGraphTableFromJsonDump(
String path, Class<G> rowClazz) {
return spark
.read()
.textFile(path)
.map(
(MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz),
Encoders.bean(rowClazz));
}
private static <G extends Oaf> Dataset<G> readGraphTableFromJsonDump(
String path, Class<G> rowClazz) {
return spark
.read()
.textFile(path)
.map(
(MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz),
Encoders.bean(rowClazz));
}
private static <G extends Oaf> void writeGraphTableAaJobInput(Dataset<G> rowDS, String path) {
rowDS.write().option("compression", "gzip").json(path);
}
private static <G extends Oaf> void writeGraphTableAaJobInput(Dataset<G> rowDS, String path) {
rowDS.write().option("compression", "gzip").json(path);
}
private static <G extends Oaf, A extends Oaf> Path createActionPayload(
Path inputActionPayloadRootDir, Class<G> rowClazz, Class<A> actionPayloadClazz) {
String inputActionPayloadJsonDumpPath =
inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz);
Path inputActionPayloadJsonDumpFile =
Paths.get(Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)).getFile());
Dataset<String> actionPayloadDS =
readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString());
Path inputActionPayloadDir =
inputActionPayloadRootDir.resolve(actionPayloadClazz.getSimpleName().toLowerCase());
writeActionPayloadAsJobInput(actionPayloadDS, inputActionPayloadDir.toString());
return inputActionPayloadDir;
}
private static <G extends Oaf, A extends Oaf> Path createActionPayload(
Path inputActionPayloadRootDir, Class<G> rowClazz, Class<A> actionPayloadClazz) {
String inputActionPayloadJsonDumpPath = inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz);
Path inputActionPayloadJsonDumpFile = Paths
.get(Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)).getFile());
Dataset<String> actionPayloadDS = readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString());
Path inputActionPayloadDir = inputActionPayloadRootDir
.resolve(actionPayloadClazz.getSimpleName().toLowerCase());
writeActionPayloadAsJobInput(actionPayloadDS, inputActionPayloadDir.toString());
return inputActionPayloadDir;
}
private static String inputActionPayloadJsonDumpLocation(
Class<? extends Oaf> rowClazz, Class<? extends Oaf> actionPayloadClazz) {
private static String inputActionPayloadJsonDumpLocation(
Class<? extends Oaf> rowClazz, Class<? extends Oaf> actionPayloadClazz) {
return String.format(
"eu/dnetlib/dhp/actionmanager/promote/input/action_payload/%s_table/%s.json",
rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase());
}
return String
.format(
"eu/dnetlib/dhp/actionmanager/promote/input/action_payload/%s_table/%s.json",
rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase());
}
private static Dataset<String> readActionPayloadFromJsonDump(String path) {
return spark.read().textFile(path);
}
private static Dataset<String> readActionPayloadFromJsonDump(String path) {
return spark.read().textFile(path);
}
private static void writeActionPayloadAsJobInput(Dataset<String> actionPayloadDS, String path) {
actionPayloadDS.withColumnRenamed("value", "payload").write().parquet(path);
}
private static void writeActionPayloadAsJobInput(Dataset<String> actionPayloadDS, String path) {
actionPayloadDS.withColumnRenamed("value", "payload").write().parquet(path);
}
private static <G extends Oaf> Dataset<G> readGraphTableFromJobOutput(
String path, Class<G> rowClazz) {
return spark
.read()
.textFile(path)
.map(
(MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz),
Encoders.bean(rowClazz));
}
private static <G extends Oaf> Dataset<G> readGraphTableFromJobOutput(
String path, Class<G> rowClazz) {
return spark
.read()
.textFile(path)
.map(
(MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz),
Encoders.bean(rowClazz));
}
private static String resultFileLocation(
MergeAndGet.Strategy strategy,
Class<? extends Oaf> rowClazz,
Class<? extends Oaf> actionPayloadClazz) {
return String.format(
"eu/dnetlib/dhp/actionmanager/promote/output/graph/%s/%s/%s_action_payload/result.json",
strategy.name().toLowerCase(),
rowClazz.getSimpleName().toLowerCase(),
actionPayloadClazz.getSimpleName().toLowerCase());
}
private static String resultFileLocation(
MergeAndGet.Strategy strategy,
Class<? extends Oaf> rowClazz,
Class<? extends Oaf> actionPayloadClazz) {
return String
.format(
"eu/dnetlib/dhp/actionmanager/promote/output/graph/%s/%s/%s_action_payload/result.json",
strategy.name().toLowerCase(),
rowClazz.getSimpleName().toLowerCase(),
actionPayloadClazz.getSimpleName().toLowerCase());
}
}

547
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java
View File

@ -1,15 +1,15 @@
package eu.dnetlib.dhp.actionmanager.promote;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.function.BiFunction;
import java.util.function.Function;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
@ -19,314 +19,311 @@ import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
public class PromoteActionPayloadFunctionsTest {
private static SparkSession spark;
private static SparkSession spark;
@BeforeAll
public static void beforeAll() {
SparkConf conf = new SparkConf();
conf.setMaster("local");
conf.setAppName(PromoteActionPayloadFunctionsTest.class.getSimpleName());
conf.set("spark.driver.host", "localhost");
spark = SparkSession.builder().config(conf).getOrCreate();
}
@BeforeAll
public static void beforeAll() {
SparkConf conf = new SparkConf();
conf.setMaster("local");
conf.setAppName(PromoteActionPayloadFunctionsTest.class.getSimpleName());
conf.set("spark.driver.host", "localhost");
spark = SparkSession.builder().config(conf).getOrCreate();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@Nested
class JoinTableWithActionPayloadAndMerge {
@Nested
class JoinTableWithActionPayloadAndMerge {
@Test
public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
// given
class OafImpl extends Oaf {}
@Test
public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
// given
class OafImpl extends Oaf {
}
// when
assertThrows(
RuntimeException.class,
() ->
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge(
null, null, null, null, null, OafImplSubSub.class, OafImpl.class));
}
// when
assertThrows(
RuntimeException.class,
() -> PromoteActionPayloadFunctions
.joinGraphTableWithActionPayloadAndMerge(
null, null, null, null, null, OafImplSubSub.class, OafImpl.class));
}
@Test
public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
// given
String id0 = "id0";
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
String id4 = "id4";
List<OafImplSubSub> rowData =
Arrays.asList(
createOafImplSubSub(id0),
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id3));
Dataset<OafImplSubSub> rowDS =
spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
@Test
public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
// given
String id0 = "id0";
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
String id4 = "id4";
List<OafImplSubSub> rowData = Arrays
.asList(
createOafImplSubSub(id0),
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id3));
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
List<OafImplSubSub> actionPayloadData =
Arrays.asList(
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id2),
createOafImplSubSub(id3),
createOafImplSubSub(id3),
createOafImplSubSub(id3),
createOafImplSubSub(id4),
createOafImplSubSub(id4),
createOafImplSubSub(id4),
createOafImplSubSub(id4));
Dataset<OafImplSubSub> actionPayloadDS =
spark.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class));
List<OafImplSubSub> actionPayloadData = Arrays
.asList(
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id2),
createOafImplSubSub(id3),
createOafImplSubSub(id3),
createOafImplSubSub(id3),
createOafImplSubSub(id4),
createOafImplSubSub(id4),
createOafImplSubSub(id4),
createOafImplSubSub(id4));
Dataset<OafImplSubSub> actionPayloadDS = spark
.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class));
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<Function<OafImplSubSub, String>> actionPayloadIdFn =
() -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn =
() ->
(x, y) -> {
x.merge(y);
return x;
};
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<Function<OafImplSubSub, String>> actionPayloadIdFn = () -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn = () -> (x,
y) -> {
x.merge(y);
return x;
};
// when
List<OafImplSubSub> results =
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeAndGetFn,
OafImplSubSub.class,
OafImplSubSub.class)
.collectAsList();
// when
List<OafImplSubSub> results = PromoteActionPayloadFunctions
.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeAndGetFn,
OafImplSubSub.class,
OafImplSubSub.class)
.collectAsList();
// then
assertEquals(11, results.size());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count());
assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count());
assertEquals(4, results.stream().filter(x -> x.getId().equals(id4)).count());
// then
assertEquals(11, results.size());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count());
assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count());
assertEquals(4, results.stream().filter(x -> x.getId().equals(id4)).count());
results.forEach(
result -> {
switch (result.getId()) {
case "id0":
assertEquals(1, result.getMerged());
break;
case "id1":
case "id2":
case "id3":
assertEquals(2, result.getMerged());
break;
case "id4":
assertEquals(1, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
results
.forEach(
result -> {
switch (result.getId()) {
case "id0":
assertEquals(1, result.getMerged());
break;
case "id1":
case "id2":
case "id3":
assertEquals(2, result.getMerged());
break;
case "id4":
assertEquals(1, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
@Test
public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
// given
String id0 = "id0";
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
String id4 = "id4";
List<OafImplSubSub> rowData =
Arrays.asList(
createOafImplSubSub(id0),
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id3));
Dataset<OafImplSubSub> rowDS =
spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
@Test
public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
// given
String id0 = "id0";
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
String id4 = "id4";
List<OafImplSubSub> rowData = Arrays
.asList(
createOafImplSubSub(id0),
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id3));
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
List<OafImplSub> actionPayloadData =
Arrays.asList(
createOafImplSub(id1),
createOafImplSub(id2),
createOafImplSub(id2),
createOafImplSub(id3),
createOafImplSub(id3),
createOafImplSub(id3),
createOafImplSub(id4),
createOafImplSub(id4),
createOafImplSub(id4),
createOafImplSub(id4));
Dataset<OafImplSub> actionPayloadDS =
spark.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class));
List<OafImplSub> actionPayloadData = Arrays
.asList(
createOafImplSub(id1),
createOafImplSub(id2),
createOafImplSub(id2),
createOafImplSub(id3),
createOafImplSub(id3),
createOafImplSub(id3),
createOafImplSub(id4),
createOafImplSub(id4),
createOafImplSub(id4),
createOafImplSub(id4));
Dataset<OafImplSub> actionPayloadDS = spark
.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class));
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<Function<OafImplSub, String>> actionPayloadIdFn =
() -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSub, OafImplSubSub>> mergeAndGetFn =
() ->
(x, y) -> {
x.merge(y);
return x;
};
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<Function<OafImplSub, String>> actionPayloadIdFn = () -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSub, OafImplSubSub>> mergeAndGetFn = () -> (x, y) -> {
x.merge(y);
return x;
};
// when
List<OafImplSubSub> results =
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeAndGetFn,
OafImplSubSub.class,
OafImplSub.class)
.collectAsList();
// when
List<OafImplSubSub> results = PromoteActionPayloadFunctions
.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeAndGetFn,
OafImplSubSub.class,
OafImplSub.class)
.collectAsList();
// then
assertEquals(7, results.size());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count());
assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count());
assertEquals(0, results.stream().filter(x -> x.getId().equals(id4)).count());
// then
assertEquals(7, results.size());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count());
assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count());
assertEquals(0, results.stream().filter(x -> x.getId().equals(id4)).count());
results.forEach(
result -> {
switch (result.getId()) {
case "id0":
assertEquals(1, result.getMerged());
break;
case "id1":
case "id2":
case "id3":
assertEquals(2, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
}
results
.forEach(
result -> {
switch (result.getId()) {
case "id0":
assertEquals(1, result.getMerged());
break;
case "id1":
case "id2":
case "id3":
assertEquals(2, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
}
@Nested
class GroupTableByIdAndMerge {
@Nested
class GroupTableByIdAndMerge {
@Test
public void shouldRunProperly() {
// given
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
List<OafImplSubSub> rowData =
Arrays.asList(
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id2),
createOafImplSubSub(id3),
createOafImplSubSub(id3),
createOafImplSubSub(id3));
Dataset<OafImplSubSub> rowDS =
spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
@Test
public void shouldRunProperly() {
// given
String id1 = "id1";
String id2 = "id2";
String id3 = "id3";
List<OafImplSubSub> rowData = Arrays
.asList(
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id2),
createOafImplSubSub(id3),
createOafImplSubSub(id3),
createOafImplSubSub(id3));
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn =
() ->
(x, y) -> {
x.merge(y);
return x;
};
SerializableSupplier<OafImplSubSub> zeroFn = OafImplSubSub::new;
SerializableSupplier<Function<OafImplSubSub, Boolean>> isNotZeroFn =
() -> x -> Objects.nonNull(x.getId());
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn = () -> (x,
y) -> {
x.merge(y);
return x;
};
SerializableSupplier<OafImplSubSub> zeroFn = OafImplSubSub::new;
SerializableSupplier<Function<OafImplSubSub, Boolean>> isNotZeroFn = () -> x -> Objects.nonNull(x.getId());
// when
List<OafImplSubSub> results =
PromoteActionPayloadFunctions.groupGraphTableByIdAndMerge(
rowDS, rowIdFn, mergeAndGetFn, zeroFn, isNotZeroFn, OafImplSubSub.class)
.collectAsList();
// when
List<OafImplSubSub> results = PromoteActionPayloadFunctions
.groupGraphTableByIdAndMerge(
rowDS, rowIdFn, mergeAndGetFn, zeroFn, isNotZeroFn, OafImplSubSub.class)
.collectAsList();
// then
assertEquals(3, results.size());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id2)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id3)).count());
// then
assertEquals(3, results.size());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id2)).count());
assertEquals(1, results.stream().filter(x -> x.getId().equals(id3)).count());
results.forEach(
result -> {
switch (result.getId()) {
case "id1":
assertEquals(1, result.getMerged());
break;
case "id2":
assertEquals(2, result.getMerged());
break;
case "id3":
assertEquals(3, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
}
results
.forEach(
result -> {
switch (result.getId()) {
case "id1":
assertEquals(1, result.getMerged());
break;
case "id2":
assertEquals(2, result.getMerged());
break;
case "id3":
assertEquals(3, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
}
public static class OafImplRoot extends Oaf {
private String id;
private int merged = 1;
public static class OafImplRoot extends Oaf {
private String id;
private int merged = 1;
public void merge(OafImplRoot e) {
merged += e.merged;
}
public void merge(OafImplRoot e) {
merged += e.merged;
}
public String getId() {
return id;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public void setId(String id) {
this.id = id;
}
public int getMerged() {
return merged;
}
public int getMerged() {
return merged;
}
public void setMerged(int merged) {
this.merged = merged;
}
}
public void setMerged(int merged) {
this.merged = merged;
}
}
public static class OafImplSub extends OafImplRoot {
public static class OafImplSub extends OafImplRoot {
@Override
public void merge(OafImplRoot e) {
super.merge(e);
}
}
@Override
public void merge(OafImplRoot e) {
super.merge(e);
}
}
private static OafImplSub createOafImplSub(String id) {
OafImplSub x = new OafImplSub();
x.setId(id);
return x;
}
private static OafImplSub createOafImplSub(String id) {
OafImplSub x = new OafImplSub();
x.setId(id);
return x;
}
public static class OafImplSubSub extends OafImplSub {
public static class OafImplSubSub extends OafImplSub {
@Override
public void merge(OafImplRoot e) {
super.merge(e);
}
}
@Override
public void merge(OafImplRoot e) {
super.merge(e);
}
}
private static OafImplSubSub createOafImplSubSub(String id) {
OafImplSubSub x = new OafImplSubSub();
x.setId(id);
return x;
}
private static OafImplSubSub createOafImplSubSub(String id) {
OafImplSubSub x = new OafImplSubSub();
x.setId(id);
return x;
}
}

234
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -1,17 +1,12 @@
package eu.dnetlib.dhp.collection;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;
import java.io.ByteArrayInputStream;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import org.apache.commons.cli.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -29,127 +24,138 @@ import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;
public class GenerateNativeStoreSparkJob {
public static MetadataRecord parseRecord(
final String input,
final String xpath,
final String encoding,
final Provenance provenance,
final Long dateOfCollection,
final LongAccumulator totalItems,
final LongAccumulator invalidRecords) {
public static MetadataRecord parseRecord(
final String input,
final String xpath,
final String encoding,
final Provenance provenance,
final Long dateOfCollection,
final LongAccumulator totalItems,
final LongAccumulator invalidRecords) {
if (totalItems != null) totalItems.add(1);
try {
SAXReader reader = new SAXReader();
Document document =
reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
Node node = document.selectSingleNode(xpath);
final String originalIdentifier = node.getText();
if (StringUtils.isBlank(originalIdentifier)) {
if (invalidRecords != null) invalidRecords.add(1);
return null;
}
return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection);
} catch (Throwable e) {
if (invalidRecords != null) invalidRecords.add(1);
e.printStackTrace();
return null;
}
}
if (totalItems != null)
totalItems.add(1);
try {
SAXReader reader = new SAXReader();
Document document = reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
Node node = document.selectSingleNode(xpath);
final String originalIdentifier = node.getText();
if (StringUtils.isBlank(originalIdentifier)) {
if (invalidRecords != null)
invalidRecords.add(1);
return null;
}
return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection);
} catch (Throwable e) {
if (invalidRecords != null)
invalidRecords.add(1);
e.printStackTrace();
return null;
}
}
public static void main(String[] args) throws Exception {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
GenerateNativeStoreSparkJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/collection/collection_input_parameters.json")));
parser.parseArgument(args);
final ObjectMapper jsonMapper = new ObjectMapper();
final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class);
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
GenerateNativeStoreSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/collection/collection_input_parameters.json")));
parser.parseArgument(args);
final ObjectMapper jsonMapper = new ObjectMapper();
final Provenance provenance = jsonMapper.readValue(parser.get("provenance"), Provenance.class);
final long dateOfCollection = new Long(parser.get("dateOfCollection"));
final SparkSession spark =
SparkSession.builder()
.appName("GenerateNativeStoreSparkJob")
.master(parser.get("master"))
.getOrCreate();
final SparkSession spark = SparkSession
.builder()
.appName("GenerateNativeStoreSparkJob")
.master(parser.get("master"))
.getOrCreate();
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final boolean test =
parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
final boolean test = parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final JavaPairRDD<IntWritable, Text> inputRDD =
sc.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final JavaPairRDD<IntWritable, Text> inputRDD = sc
.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
final LongAccumulator invalidRecords = sc.sc().longAccumulator("InvalidRecords");
final MessageManager manager =
new MessageManager(
parser.get("rabbitHost"),
parser.get("rabbitUser"),
parser.get("rabbitPassword"),
false,
false,
null);
final MessageManager manager = new MessageManager(
parser.get("rabbitHost"),
parser.get("rabbitUser"),
parser.get("rabbitPassword"),
false,
false,
null);
final JavaRDD<MetadataRecord> mappeRDD =
inputRDD
.map(
item ->
parseRecord(
item._2().toString(),
parser.get("xpath"),
parser.get("encoding"),
provenance,
dateOfCollection,
totalItems,
invalidRecords))
.filter(Objects::nonNull)
.distinct();
final JavaRDD<MetadataRecord> mappeRDD = inputRDD
.map(
item -> parseRecord(
item._2().toString(),
parser.get("xpath"),
parser.get("encoding"),
provenance,
dateOfCollection,
totalItems,
invalidRecords))
.filter(Objects::nonNull)
.distinct();
ongoingMap.put("ongoing", "0");
if (!test) {
manager.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
ongoingMap.put("ongoing", "0");
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
mdStoreRecords.add(mdstore.count());
ongoingMap.put("ongoing", "" + totalItems.value());
if (!test) {
manager.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
mdstore.write().format("parquet").save(parser.get("output"));
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + invalidRecords.value());
reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
if (!test) {
manager.sendMessage(
new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
parser.get("rabbitReportQueue"),
true,
false);
manager.close();
}
}
final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
mdStoreRecords.add(mdstore.count());
ongoingMap.put("ongoing", "" + totalItems.value());
if (!test) {
manager
.sendMessage(
new Message(
parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
parser.get("rabbitOngoingQueue"),
true,
false);
}
mdstore.write().format("parquet").save(parser.get("output"));
reportMap.put("inputItem", "" + totalItems.value());
reportMap.put("invalidRecords", "" + invalidRecords.value());
reportMap.put("mdStoreSize", "" + mdStoreRecords.value());
if (!test) {
manager
.sendMessage(
new Message(parser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
parser.get("rabbitReportQueue"),
true,
false);
manager.close();
}
}
}

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
View File

@ -1,10 +1,12 @@
package eu.dnetlib.dhp.collection.plugin;
import java.util.stream.Stream;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import java.util.stream.Stream;
public interface CollectorPlugin {
Stream<String> collect(ApiDescriptor api) throws DnetCollectorException;
Stream<String> collect(ApiDescriptor api) throws DnetCollectorException;
}

114
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java
View File

@ -1,11 +1,6 @@
package eu.dnetlib.dhp.collection.plugin.oai;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterators;
import com.google.common.collect.Lists;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
@ -14,65 +9,74 @@ import java.util.Spliterators;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterators;
import com.google.common.collect.Lists;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
public class OaiCollectorPlugin implements CollectorPlugin {
private static final String FORMAT_PARAM = "format";
private static final String OAI_SET_PARAM = "set";
private static final Object OAI_FROM_DATE_PARAM = "fromDate";
private static final Object OAI_UNTIL_DATE_PARAM = "untilDate";
private static final String FORMAT_PARAM = "format";
private static final String OAI_SET_PARAM = "set";
private static final Object OAI_FROM_DATE_PARAM = "fromDate";
private static final Object OAI_UNTIL_DATE_PARAM = "untilDate";
private OaiIteratorFactory oaiIteratorFactory;
private OaiIteratorFactory oaiIteratorFactory;
@Override
public Stream<String> collect(final ApiDescriptor api) throws DnetCollectorException {
final String baseUrl = api.getBaseUrl();
final String mdFormat = api.getParams().get(FORMAT_PARAM);
final String setParam = api.getParams().get(OAI_SET_PARAM);
final String fromDate = api.getParams().get(OAI_FROM_DATE_PARAM);
final String untilDate = api.getParams().get(OAI_UNTIL_DATE_PARAM);
@Override
public Stream<String> collect(final ApiDescriptor api) throws DnetCollectorException {
final String baseUrl = api.getBaseUrl();
final String mdFormat = api.getParams().get(FORMAT_PARAM);
final String setParam = api.getParams().get(OAI_SET_PARAM);
final String fromDate = api.getParams().get(OAI_FROM_DATE_PARAM);
final String untilDate = api.getParams().get(OAI_UNTIL_DATE_PARAM);
final List<String> sets = new ArrayList<>();
if (setParam != null) {
sets.addAll(
Lists.newArrayList(Splitter.on(",").omitEmptyStrings().trimResults().split(setParam)));
}
if (sets.isEmpty()) {
// If no set is defined, ALL the sets must be harvested
sets.add("");
}
final List<String> sets = new ArrayList<>();
if (setParam != null) {
sets
.addAll(
Lists.newArrayList(Splitter.on(",").omitEmptyStrings().trimResults().split(setParam)));
}
if (sets.isEmpty()) {
// If no set is defined, ALL the sets must be harvested
sets.add("");
}
if (baseUrl == null || baseUrl.isEmpty()) {
throw new DnetCollectorException("Param 'baseurl' is null or empty");
}
if (baseUrl == null || baseUrl.isEmpty()) {
throw new DnetCollectorException("Param 'baseurl' is null or empty");
}
if (mdFormat == null || mdFormat.isEmpty()) {
throw new DnetCollectorException("Param 'mdFormat' is null or empty");
}
if (mdFormat == null || mdFormat.isEmpty()) {
throw new DnetCollectorException("Param 'mdFormat' is null or empty");
}
if (fromDate != null && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + fromDate);
}
if (fromDate != null && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + fromDate);
}
if (untilDate != null && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + untilDate);
}
if (untilDate != null && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
throw new DnetCollectorException("Invalid date (YYYY-MM-DD): " + untilDate);
}
final Iterator<Iterator<String>> iters =
sets.stream()
.map(
set ->
getOaiIteratorFactory()
.newIterator(baseUrl, mdFormat, set, fromDate, untilDate))
.iterator();
final Iterator<Iterator<String>> iters = sets
.stream()
.map(
set -> getOaiIteratorFactory()
.newIterator(baseUrl, mdFormat, set, fromDate, untilDate))
.iterator();
return StreamSupport.stream(
Spliterators.spliteratorUnknownSize(Iterators.concat(iters), Spliterator.ORDERED), false);
}
return StreamSupport
.stream(
Spliterators.spliteratorUnknownSize(Iterators.concat(iters), Spliterator.ORDERED), false);
}
public OaiIteratorFactory getOaiIteratorFactory() {
if (oaiIteratorFactory == null) {
oaiIteratorFactory = new OaiIteratorFactory();
}
return oaiIteratorFactory;
}
public OaiIteratorFactory getOaiIteratorFactory() {
if (oaiIteratorFactory == null) {
oaiIteratorFactory = new OaiIteratorFactory();
}
return oaiIteratorFactory;
}
}

279
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java
View File

@ -1,14 +1,13 @@
package eu.dnetlib.dhp.collection.plugin.oai;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner;
import java.io.StringReader;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.Iterator;
import java.util.Queue;
import java.util.concurrent.PriorityBlockingQueue;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -17,160 +16,162 @@ import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import eu.dnetlib.dhp.collection.worker.DnetCollectorException;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import eu.dnetlib.dhp.collection.worker.utils.XmlCleaner;
public class OaiIterator implements Iterator<String> {
private static final Log log = LogFactory.getLog(OaiIterator.class); // NOPMD by marko on
// 11/24/08 5:02 PM
private static final Log log = LogFactory.getLog(OaiIterator.class); // NOPMD by marko on
// 11/24/08 5:02 PM
private final Queue<String> queue = new PriorityBlockingQueue<>();
private final SAXReader reader = new SAXReader();
private final Queue<String> queue = new PriorityBlockingQueue<>();
private final SAXReader reader = new SAXReader();
private final String baseUrl;
private final String set;
private final String mdFormat;
private final String fromDate;
private final String untilDate;
private String token;
private boolean started;
private final HttpConnector httpConnector;
private final String baseUrl;
private final String set;
private final String mdFormat;
private final String fromDate;
private final String untilDate;
private String token;
private boolean started;
private final HttpConnector httpConnector;
public OaiIterator(
final String baseUrl,
final String mdFormat,
final String set,
final String fromDate,
final String untilDate,
final HttpConnector httpConnector) {
this.baseUrl = baseUrl;
this.mdFormat = mdFormat;
this.set = set;
this.fromDate = fromDate;
this.untilDate = untilDate;
this.started = false;
this.httpConnector = httpConnector;
}
public OaiIterator(
final String baseUrl,
final String mdFormat,
final String set,
final String fromDate,
final String untilDate,
final HttpConnector httpConnector) {
this.baseUrl = baseUrl;
this.mdFormat = mdFormat;
this.set = set;
this.fromDate = fromDate;
this.untilDate = untilDate;
this.started = false;
this.httpConnector = httpConnector;
}
private void verifyStarted() {
if (!this.started) {
this.started = true;
try {
this.token = firstPage();
} catch (final DnetCollectorException e) {
throw new RuntimeException(e);
}
}
}
private void verifyStarted() {
if (!this.started) {
this.started = true;
try {
this.token = firstPage();
} catch (final DnetCollectorException e) {
throw new RuntimeException(e);
}
}
}
@Override
public boolean hasNext() {
synchronized (queue) {
verifyStarted();
return !queue.isEmpty();
}
}
@Override
public boolean hasNext() {
synchronized (queue) {
verifyStarted();
return !queue.isEmpty();
}
}
@Override
public String next() {
synchronized (queue) {
verifyStarted();
final String res = queue.poll();
while (queue.isEmpty() && token != null && !token.isEmpty()) {
try {
token = otherPages(token);
} catch (final DnetCollectorException e) {
throw new RuntimeException(e);
}
}
return res;
}
}
@Override
public String next() {
synchronized (queue) {
verifyStarted();
final String res = queue.poll();
while (queue.isEmpty() && token != null && !token.isEmpty()) {
try {
token = otherPages(token);
} catch (final DnetCollectorException e) {
throw new RuntimeException(e);
}
}
return res;
}
}
@Override
public void remove() {}
@Override
public void remove() {
}
private String firstPage() throws DnetCollectorException {
try {
String url =
baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8");
if (set != null && !set.isEmpty()) {
url += "&set=" + URLEncoder.encode(set, "UTF-8");
}
if (fromDate != null && fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
url += "&from=" + URLEncoder.encode(fromDate, "UTF-8");
}
if (untilDate != null && untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
url += "&until=" + URLEncoder.encode(untilDate, "UTF-8");
}
log.info("Start harvesting using url: " + url);
private String firstPage() throws DnetCollectorException {
try {
String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8");
if (set != null && !set.isEmpty()) {
url += "&set=" + URLEncoder.encode(set, "UTF-8");
}
if (fromDate != null && fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
url += "&from=" + URLEncoder.encode(fromDate, "UTF-8");
}
if (untilDate != null && untilDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
url += "&until=" + URLEncoder.encode(untilDate, "UTF-8");
}
log.info("Start harvesting using url: " + url);
return downloadPage(url);
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
}
}
return downloadPage(url);
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
}
}
private String extractResumptionToken(final String xml) {
private String extractResumptionToken(final String xml) {
final String s = StringUtils.substringAfter(xml, "<resumptionToken");
if (s == null) {
return null;
}
final String s = StringUtils.substringAfter(xml, "<resumptionToken");
if (s == null) {
return null;
}
final String result = StringUtils.substringBetween(s, ">", "</");
if (result == null) {
return null;
}
return result.trim();
}
final String result = StringUtils.substringBetween(s, ">", "</");
if (result == null) {
return null;
}
return result.trim();
}
private String otherPages(final String resumptionToken) throws DnetCollectorException {
try {
return downloadPage(
baseUrl
+ "?verb=ListRecords&resumptionToken="
+ URLEncoder.encode(resumptionToken, "UTF-8"));
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
}
}
private String otherPages(final String resumptionToken) throws DnetCollectorException {
try {
return downloadPage(
baseUrl
+ "?verb=ListRecords&resumptionToken="
+ URLEncoder.encode(resumptionToken, "UTF-8"));
} catch (final UnsupportedEncodingException e) {
throw new DnetCollectorException(e);
}
}
private String downloadPage(final String url) throws DnetCollectorException {
private String downloadPage(final String url) throws DnetCollectorException {
final String xml = httpConnector.getInputSource(url);
Document doc;
try {
doc = reader.read(new StringReader(xml));
} catch (final DocumentException e) {
log.warn("Error parsing xml, I try to clean it: " + xml, e);
final String cleaned = XmlCleaner.cleanAllEntities(xml);
try {
doc = reader.read(new StringReader(cleaned));
} catch (final DocumentException e1) {
final String resumptionToken = extractResumptionToken(xml);
if (resumptionToken == null) {
throw new DnetCollectorException("Error parsing cleaned document:" + cleaned, e1);
}
return resumptionToken;
}
}
final String xml = httpConnector.getInputSource(url);
Document doc;
try {
doc = reader.read(new StringReader(xml));
} catch (final DocumentException e) {
log.warn("Error parsing xml, I try to clean it: " + xml, e);
final String cleaned = XmlCleaner.cleanAllEntities(xml);
try {
doc = reader.read(new StringReader(cleaned));
} catch (final DocumentException e1) {
final String resumptionToken = extractResumptionToken(xml);
if (resumptionToken == null) {
throw new DnetCollectorException("Error parsing cleaned document:" + cleaned, e1);
}
return resumptionToken;
}
}
final Node errorNode =
doc.selectSingleNode("/*[local-name()='OAI-PMH']/*[local-name()='error']");
if (errorNode != null) {
final String code = errorNode.valueOf("@code");
if ("noRecordsMatch".equalsIgnoreCase(code.trim())) {
log.warn("noRecordsMatch for oai call: " + url);
return null;
} else {
throw new DnetCollectorException(code + " - " + errorNode.getText());
}
}
final Node errorNode = doc.selectSingleNode("/*[local-name()='OAI-PMH']/*[local-name()='error']");
if (errorNode != null) {
final String code = errorNode.valueOf("@code");
if ("noRecordsMatch".equalsIgnoreCase(code.trim())) {
log.warn("noRecordsMatch for oai call: " + url);
return null;
} else {
throw new DnetCollectorException(code + " - " + errorNode.getText());
}
}
for (final Object o :
doc.selectNodes("//*[local-name()='ListRecords']/*[local-name()='record']")) {
queue.add(((Node) o).asXML());
}
for (final Object o : doc.selectNodes("//*[local-name()='ListRecords']/*[local-name()='record']")) {
queue.add(((Node) o).asXML());
}
return doc.valueOf("//*[local-name()='resumptionToken']");
}
return doc.valueOf("//*[local-name()='resumptionToken']");
}
}

31
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIteratorFactory.java
View File

@ -1,23 +1,26 @@
package eu.dnetlib.dhp.collection.plugin.oai;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
import java.util.Iterator;
import eu.dnetlib.dhp.collection.worker.utils.HttpConnector;
public class OaiIteratorFactory {
private HttpConnector httpConnector;
private HttpConnector httpConnector;
public Iterator<String> newIterator(
final String baseUrl,
final String mdFormat,
final String set,
final String fromDate,
final String untilDate) {
return new OaiIterator(baseUrl, mdFormat, set, fromDate, untilDate, getHttpConnector());
}
public Iterator<String> newIterator(
final String baseUrl,
final String mdFormat,
final String set,
final String fromDate,
final String untilDate) {
return new OaiIterator(baseUrl, mdFormat, set, fromDate, untilDate, getHttpConnector());
}
private HttpConnector getHttpConnector() {
if (httpConnector == null) httpConnector = new HttpConnector();
return httpConnector;
}
private HttpConnector getHttpConnector() {
if (httpConnector == null)
httpConnector = new HttpConnector();
return httpConnector;
}
}

43
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorException.java
View File

@ -1,31 +1,32 @@
package eu.dnetlib.dhp.collection.worker;
public class DnetCollectorException extends Exception {
/** */
private static final long serialVersionUID = -290723075076039757L;
/** */
private static final long serialVersionUID = -290723075076039757L;
public DnetCollectorException() {
super();
}
public DnetCollectorException() {
super();
}
public DnetCollectorException(
final String message,
final Throwable cause,
final boolean enableSuppression,
final boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public DnetCollectorException(
final String message,
final Throwable cause,
final boolean enableSuppression,
final boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public DnetCollectorException(final String message, final Throwable cause) {
super(message, cause);
}
public DnetCollectorException(final String message, final Throwable cause) {
super(message, cause);
}
public DnetCollectorException(final String message) {
super(message);
}
public DnetCollectorException(final String message) {
super(message);
}
public DnetCollectorException(final Throwable cause) {
super(cause);
}
public DnetCollectorException(final Throwable cause) {
super(cause);
}
}

211
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorker.java
View File

@ -1,18 +1,12 @@
package eu.dnetlib.dhp.collection.worker;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;
import java.io.IOException;
import java.net.URI;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.atomic.AtomicInteger;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
@ -22,111 +16,124 @@ import org.apache.hadoop.io.Text;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.collector.worker.model.ApiDescriptor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.Message;
import eu.dnetlib.message.MessageManager;
import eu.dnetlib.message.MessageType;
public class DnetCollectorWorker {
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class);
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorker.class);
private final CollectorPluginFactory collectorPluginFactory;
private final CollectorPluginFactory collectorPluginFactory;
private final ArgumentApplicationParser argumentParser;
private final ArgumentApplicationParser argumentParser;
private final MessageManager manager;
private final MessageManager manager;
public DnetCollectorWorker(
final CollectorPluginFactory collectorPluginFactory,
final ArgumentApplicationParser argumentParser,
final MessageManager manager)
throws DnetCollectorException {
this.collectorPluginFactory = collectorPluginFactory;
this.argumentParser = argumentParser;
this.manager = manager;
}
public DnetCollectorWorker(
final CollectorPluginFactory collectorPluginFactory,
final ArgumentApplicationParser argumentParser,
final MessageManager manager)
throws DnetCollectorException {
this.collectorPluginFactory = collectorPluginFactory;
this.argumentParser = argumentParser;
this.manager = manager;
}
public void collect() throws DnetCollectorException {
try {
final ObjectMapper jsonMapper = new ObjectMapper();
final ApiDescriptor api =
jsonMapper.readValue(argumentParser.get("apidescriptor"), ApiDescriptor.class);
public void collect() throws DnetCollectorException {
try {
final ObjectMapper jsonMapper = new ObjectMapper();
final ApiDescriptor api = jsonMapper.readValue(argumentParser.get("apidescriptor"), ApiDescriptor.class);
final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol());
final CollectorPlugin plugin = collectorPluginFactory.getPluginByProtocol(api.getProtocol());
final String hdfsuri = argumentParser.get("namenode");
final String hdfsuri = argumentParser.get("namenode");
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri);
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri);
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
System.setProperty("HADOOP_USER_NAME", argumentParser.get("userHDFS"));
System.setProperty("hadoop.home.dir", "/");
// Get the filesystem - HDFS
FileSystem.get(URI.create(hdfsuri), conf);
Path hdfswritepath = new Path(argumentParser.get("hdfsPath"));
System.setProperty("HADOOP_USER_NAME", argumentParser.get("userHDFS"));
System.setProperty("hadoop.home.dir", "/");
// Get the filesystem - HDFS
FileSystem.get(URI.create(hdfsuri), conf);
Path hdfswritepath = new Path(argumentParser.get("hdfsPath"));
log.info("Created path " + hdfswritepath.toString());
log.info("Created path " + hdfswritepath.toString());
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final AtomicInteger counter = new AtomicInteger(0);
try (SequenceFile.Writer writer =
SequenceFile.createWriter(
conf,
SequenceFile.Writer.file(hdfswritepath),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
final IntWritable key = new IntWritable(counter.get());
final Text value = new Text();
plugin
.collect(api)
.forEach(
content -> {
key.set(counter.getAndIncrement());
value.set(content);
if (counter.get() % 10 == 0) {
try {
ongoingMap.put("ongoing", "" + counter.get());
log.debug(
"Sending message: "
+ manager.sendMessage(
new Message(
argumentParser.get("workflowId"),
"Collection",
MessageType.ONGOING,
ongoingMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false));
} catch (Exception e) {
log.error("Error on sending message ", e);
}
}
try {
writer.append(key, value);
} catch (IOException e) {
throw new RuntimeException(e);
}
});
}
ongoingMap.put("ongoing", "" + counter.get());
manager.sendMessage(
new Message(
argumentParser.get("workflowId"), "Collection", MessageType.ONGOING, ongoingMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false);
reportMap.put("collected", "" + counter.get());
manager.sendMessage(
new Message(
argumentParser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false);
manager.close();
} catch (Throwable e) {
throw new DnetCollectorException("Error on collecting ", e);
}
}
final Map<String, String> ongoingMap = new HashMap<>();
final Map<String, String> reportMap = new HashMap<>();
final AtomicInteger counter = new AtomicInteger(0);
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(hdfswritepath),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
final IntWritable key = new IntWritable(counter.get());
final Text value = new Text();
plugin
.collect(api)
.forEach(
content -> {
key.set(counter.getAndIncrement());
value.set(content);
if (counter.get() % 10 == 0) {
try {
ongoingMap.put("ongoing", "" + counter.get());
log
.debug(
"Sending message: "
+ manager
.sendMessage(
new Message(
argumentParser.get("workflowId"),
"Collection",
MessageType.ONGOING,
ongoingMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false));
} catch (Exception e) {
log.error("Error on sending message ", e);
}
}
try {
writer.append(key, value);
} catch (IOException e) {
throw new RuntimeException(e);
}
});
}
ongoingMap.put("ongoing", "" + counter.get());
manager
.sendMessage(
new Message(
argumentParser.get("workflowId"), "Collection", MessageType.ONGOING, ongoingMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false);
reportMap.put("collected", "" + counter.get());
manager
.sendMessage(
new Message(
argumentParser.get("workflowId"), "Collection", MessageType.REPORT, reportMap),
argumentParser.get("rabbitOngoingQueue"),
true,
false);
manager.close();
} catch (Throwable e) {
throw new DnetCollectorException("Error on collecting ", e);
}
}
}

63
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java
View File

@ -1,48 +1,49 @@
package eu.dnetlib.dhp.collection.worker;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.MessageManager;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.worker.utils.CollectorPluginFactory;
import eu.dnetlib.message.MessageManager;
/**
* DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into
* HDFS. This module will be executed on the hadoop cluster and taking in input some parameters that
* tells it which is the right collector plugin to use and where store the data into HDFS path
* DnetCollectortWorkerApplication is the main class responsible to start the Dnet Collection into HDFS. This module
* will be executed on the hadoop cluster and taking in input some parameters that tells it which is the right collector
* plugin to use and where store the data into HDFS path
*
* @author Sandro La Bruzzo
*/
public class DnetCollectorWorkerApplication {
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class);
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class);
private static CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
private static CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
private static ArgumentApplicationParser argumentParser;
private static ArgumentApplicationParser argumentParser;
/** @param args */
public static void main(final String[] args) throws Exception {
/** @param args */
public static void main(final String[] args) throws Exception {
argumentParser =
new ArgumentApplicationParser(
IOUtils.toString(
DnetCollectorWorker.class.getResourceAsStream(
"/eu/dnetlib/collector/worker/collector_parameter.json")));
argumentParser.parseArgument(args);
log.info("hdfsPath =" + argumentParser.get("hdfsPath"));
log.info("json = " + argumentParser.get("apidescriptor"));
final MessageManager manager =
new MessageManager(
argumentParser.get("rabbitHost"),
argumentParser.get("rabbitUser"),
argumentParser.get("rabbitPassword"),
false,
false,
null);
final DnetCollectorWorker worker =
new DnetCollectorWorker(collectorPluginFactory, argumentParser, manager);
worker.collect();
}
argumentParser = new ArgumentApplicationParser(
IOUtils
.toString(
DnetCollectorWorker.class
.getResourceAsStream(
"/eu/dnetlib/collector/worker/collector_parameter.json")));
argumentParser.parseArgument(args);
log.info("hdfsPath =" + argumentParser.get("hdfsPath"));
log.info("json = " + argumentParser.get("apidescriptor"));
final MessageManager manager = new MessageManager(
argumentParser.get("rabbitHost"),
argumentParser.get("rabbitUser"),
argumentParser.get("rabbitPassword"),
false,
false,
null);
final DnetCollectorWorker worker = new DnetCollectorWorker(collectorPluginFactory, argumentParser, manager);
worker.collect();
}
}

21
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java
View File

@ -1,18 +1,19 @@
package eu.dnetlib.dhp.collection.worker.utils;
import java.util.LinkedList;
public class CollectorPluginErrorLogList extends LinkedList<String> {
private static final long serialVersionUID = -6925786561303289704L;
private static final long serialVersionUID = -6925786561303289704L;
@Override
public String toString() {
String log = new String();
int index = 0;
for (final String errorMessage : this) {
log += String.format("Retry #%s: %s / ", index++, errorMessage);
}
return log;
}
@Override
public String toString() {
String log = new String();
int index = 0;
for (final String errorMessage : this) {
log += String.format("Retry #%s: %s / ", index++, errorMessage);
}
return log;
}
}

Some files were not shown because too many files have changed in this diff Show More