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merged with maaster

This commit is contained in:
Sandro La Bruzzo 2020-04-29 13:20:57 +02:00
parent 920c0f19c3 e0d14fe4f8
commit a6b1a59d0a
344 changed files with 24732 additions and 24626 deletions
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92
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java
View File

@ -17,57 +17,55 @@ import org.apache.maven.plugin.MojoFailureException;
*/ */
public class GenerateOoziePropertiesMojo extends AbstractMojo { public class GenerateOoziePropertiesMojo extends AbstractMojo {
public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir"; 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_SANDBOX_NAME = "sandboxName";
private final String[] limiters = {"dhp", "dnetlib", "eu"}; private final String[] limiters = {"dhp", "dnetlib", "eu"};
@Override @Override
public void execute() throws MojoExecutionException, MojoFailureException { public void execute() throws MojoExecutionException, MojoFailureException {
if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR) if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
&& !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) { && !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
String generatedSandboxName = String generatedSandboxName =
generateSandboxName( generateSandboxName(System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR)); if (generatedSandboxName != null) {
if (generatedSandboxName != null) { System.getProperties().setProperty(PROPERTY_NAME_SANDBOX_NAME, generatedSandboxName);
System.getProperties() } else {
.setProperty(PROPERTY_NAME_SANDBOX_NAME, generatedSandboxName); System.out.println(
} else { "unable to generate sandbox name from path: "
System.out.println( + System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
"unable to generate sandbox name from path: " }
+ System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
}
}
} }
}
/** /**
* Generates sandbox name from workflow source directory. * Generates sandbox name from workflow source directory.
* *
* @param wfSourceDir * @param wfSourceDir
* @return generated sandbox name * @return generated sandbox name
*/ */
private String generateSandboxName(String wfSourceDir) { private String generateSandboxName(String wfSourceDir) {
// utilize all dir names until finding one of the limiters // utilize all dir names until finding one of the limiters
List<String> sandboxNameParts = new ArrayList<String>(); List<String> sandboxNameParts = new ArrayList<String>();
String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar); String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar);
ArrayUtils.reverse(tokens); ArrayUtils.reverse(tokens);
if (tokens.length > 0) { if (tokens.length > 0) {
for (String token : tokens) { for (String token : tokens) {
for (String limiter : limiters) { for (String limiter : limiters) {
if (limiter.equals(token)) { if (limiter.equals(token)) {
return sandboxNameParts.size() > 0 return sandboxNameParts.size() > 0
? StringUtils.join(sandboxNameParts.toArray()) ? StringUtils.join(sandboxNameParts.toArray())
: null; : null;
} }
}
if (sandboxNameParts.size() > 0) {
sandboxNameParts.add(0, File.separator);
}
sandboxNameParts.add(0, token);
}
return StringUtils.join(sandboxNameParts.toArray());
} else {
return null;
} }
if (sandboxNameParts.size() > 0) {
sandboxNameParts.add(0, File.separator);
}
sandboxNameParts.add(0, token);
}
return StringUtils.join(sandboxNameParts.toArray());
} else {
return null;
} }
}
} }

700
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java
View File

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

130
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java
View File

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

648
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java
View File

@ -20,343 +20,337 @@ import org.mockito.junit.jupiter.MockitoExtension;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class WritePredefinedProjectPropertiesTest { public class WritePredefinedProjectPropertiesTest {
@Mock private MavenProject mavenProject; @Mock private MavenProject mavenProject;
private WritePredefinedProjectProperties mojo; private WritePredefinedProjectProperties mojo;
@BeforeEach @BeforeEach
public void init(@TempDir File testFolder) { public void init(@TempDir File testFolder) {
MockitoAnnotations.initMocks(this); MockitoAnnotations.initMocks(this);
mojo = new WritePredefinedProjectProperties(); mojo = new WritePredefinedProjectProperties();
mojo.outputFile = getPropertiesFileLocation(testFolder); mojo.outputFile = getPropertiesFileLocation(testFolder);
mojo.project = mavenProject; mojo.project = mavenProject;
lenient().doReturn(new Properties()).when(mavenProject).getProperties(); lenient().doReturn(new Properties()).when(mavenProject).getProperties();
}
// ----------------------------------- TESTS ---------------------------------------------
@Test
public void testExecuteEmpty() throws Exception {
// execute
mojo.execute();
// 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();
// 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));
}
@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());
}
@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();
// 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);
// 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));
}
@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);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()});
// 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));
}
@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"});
// 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));
}
@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[] {""});
// 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();
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()});
// 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));
}
@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);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()});
// 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"});
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(0, storedProperties.size());
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() {
// given
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
// given
mojo.setIncludeEnvironmentVariables(true);
// 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));
} }
}
// ----------------------------------- TESTS --------------------------------------------- @Test
public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
// given
String key = "systemPropertyKey";
String value = "systemPropertyValue";
System.setProperty(key, value);
mojo.setIncludeSystemProperties(true);
@Test // execute
public void testExecuteEmpty() throws Exception { mojo.execute();
// execute
mojo.execute();
// assert // assert
assertTrue(mojo.outputFile.exists()); assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile()); Properties storedProperties = getStoredProperties(testFolder);
assertEquals(0, storedProperties.size()); assertTrue(storedProperties.size() > 0);
} assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test @Test
public void testExecuteWithProjectProperties() throws Exception { public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
// given throws Exception {
String key = "projectPropertyKey"; // given
String value = "projectPropertyValue"; String key = "systemPropertyKey ";
Properties projectProperties = new Properties(); String value = "systemPropertyValue";
projectProperties.setProperty(key, value); System.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties(); mojo.setIncludeSystemProperties(true);
String escapeChars = "cr,lf,tab,|";
mojo.setEscapeChars(escapeChars);
// execute // execute
mojo.execute(); mojo.execute();
// assert // assert
assertTrue(mojo.outputFile.exists()); assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile()); Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size()); assertTrue(storedProperties.size() > 0);
assertTrue(storedProperties.containsKey(key)); assertFalse(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key)); assertTrue(storedProperties.containsKey(key.trim()));
} assertEquals(value, storedProperties.getProperty(key.trim()));
}
@Test() // ----------------------------------- PRIVATE -------------------------------------------
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 private File getPropertiesFileLocation(File testFolder) {
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); return new File(testFolder, "test.properties");
} }
@Test private Properties getStoredProperties(File testFolder)
public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws FileNotFoundException, IOException {
throws Exception { Properties properties = new Properties();
// given properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
String key = "projectPropertyKey"; return properties;
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();
// 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);
// 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));
}
@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);
mojo.setIncludePropertyKeysFromFiles(
new String[] {includedPropertiesFile.getAbsolutePath()});
// 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));
}
@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"});
// 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));
}
@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[] {""});
// 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();
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()});
// 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));
}
@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);
mojo.setIncludePropertyKeysFromFiles(
new String[] {includedPropertiesFile.getAbsolutePath()});
// 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"});
// execute
mojo.execute();
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(0, storedProperties.size());
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() {
// given
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"});
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
// given
mojo.setIncludeEnvironmentVariables(true);
// 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));
}
}
@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();
// 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);
// 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()));
}
// ----------------------------------- PRIVATE -------------------------------------------
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;
}
} }

18
dhp-build/dhp-code-style/pom.xml Normal file
View File

@ -0,0 +1,18 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-code-style</artifactId>
<version>1.1.7-SNAPSHOT</version>
<packaging>jar</packaging>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
</project>

252
dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_aosp.xml Normal file
View File

@ -0,0 +1,252 @@
<?xml version="1.0" encoding="UTF-8"?>
<profiles version="10">
<profile kind="CodeFormatterProfile" name="Android" version="10">
<setting id="org.eclipse.jdt.core.formatter.align_type_members_on_columns" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_assignment" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_compact_if" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression" value="80"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_multiple_fields" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_package" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_field" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_imports" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_member_type" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_method" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_package" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_array_initializer" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block_in_case" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_constant" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_method_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_switch" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.comment.clear_blank_lines" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_comments" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_header" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_html" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_source_code" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.indent_parameter_description" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.indent_root_tags" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.line_length" value="120"/>
<setting id="org.eclipse.jdt.core.formatter.compact_else_if" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.continuation_indentation" value="2"/>
<setting id="org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer" value="2"/>
<setting id="org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_empty_lines" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_block" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_body" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.indentation.size" value="4"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_opening_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation_type_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_binary_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_case" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_labeled_statement" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_explicitconstructorcall_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_throws" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_superinterfaces" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_bracket_in_array_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_catch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_if" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_question_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_question_in_wildcard" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_unary_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_assignment_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_binary_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_cast" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_if" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_switch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_ellipsis" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_constant" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_enum_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_switch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_if" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_return" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_prefix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_unary_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_brackets_in_array_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_brackets_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.lineSplit" value="100"/>
<setting id="org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.tabulation.char" value="tab"/>
<setting id="org.eclipse.jdt.core.formatter.tabulation.size" value="4"/>
<setting id="org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.join_wrapped_lines" value="false"/>
</profile>
</profiles>

727
dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml Normal file
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@ -0,0 +1,727 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<profiles version="18">
<profile kind="CodeFormatterProfile" name="Android_custom" version="18">
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment" value="common_lines"/>
<setting id="org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_logical_operator" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation" value="common_lines"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement" value="common_lines"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.join_lines_in_comments" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.indent_parameter_description" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_code_block" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.tabulation.char" value="tab"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch" value="insert"/>
</profile>
</profiles>

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dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_google.xml Normal file
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@ -0,0 +1,337 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<profiles version="13">
<profile kind="CodeFormatterProfile" name="GoogleStyle" version="13">
<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags" value="insert"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters" value="do not insert"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_field" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.use_on_off_tags" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement" value="do not insert"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_parameter" value="1040"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_type.count_dependent" value="1585|-1|1585"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression" value="80"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for" value="insert"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard" value="do not insert"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_package" value="1"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration.count_dependent" value="16|4|49"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation" value="16"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces" value="do not insert"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_cascading_method_invocation_with_arguments" value="16"/>
<setting id="org.eclipse.jdt.core.compiler.source" value="1.7"/>
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<setting id="org.eclipse.jdt.core.formatter.comment.format_line_comments" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.join_wrapped_lines" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.lineSplit" value="100"/>
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<setting id="org.eclipse.jdt.core.formatter.enabling_tag" value="@formatter:on"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_local_variable.count_dependent" value="1585|-1|1585"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference" value="do not insert"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while" value="do not insert"/>
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<setting id="org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode" value="enabled"/>
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<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_imports" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_field" value="1585"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_html" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer.count_dependent" value="16|5|80"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_source_code" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.compiler.codegen.targetPlatform" value="1.7"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_resources_in_try" value="80"/>
<setting id="org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation" value="16"/>
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<setting id="org.eclipse.jdt.core.formatter.comment.format_block_comments" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration.count_dependent" value="16|4|48"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_method.count_dependent" value="1585|-1|1585"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration" value="end_of_line"/>
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<setting id="org.eclipse.jdt.core.formatter.wrap_non_simple_member_annotation" value="true"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call.count_dependent" value="16|5|80"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_generic_type_arguments.count_dependent" value="16|-1|16"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_for_statement" value="16"/>
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<setting id="org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line" value="false"/>
</profile>
</profiles>

1
dhp-build/pom.xml
View File

@ -9,6 +9,7 @@
<artifactId>dhp-build</artifactId> <artifactId>dhp-build</artifactId>
<packaging>pom</packaging> <packaging>pom</packaging>
<modules> <modules>
<module>dhp-code-style</module>
<module>dhp-build-assembly-resources</module> <module>dhp-build-assembly-resources</module>
<module>dhp-build-properties-maven-plugin</module> <module>dhp-build-properties-maven-plugin</module>
</modules> </modules>

56
dhp-common/src/main/java/eu/dnetlib/collector/worker/model/ApiDescriptor.java
View File

@ -5,43 +5,43 @@ import java.util.Map;
public class ApiDescriptor { 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() { public String getBaseUrl() {
return baseUrl; return baseUrl;
} }
public void setBaseUrl(final String baseUrl) { public void setBaseUrl(final String baseUrl) {
this.baseUrl = baseUrl; this.baseUrl = baseUrl;
} }
public String getId() { public String getId() {
return id; return id;
} }
public void setId(final String id) { public void setId(final String id) {
this.id = id; this.id = id;
} }
public Map<String, String> getParams() { public Map<String, String> getParams() {
return params; return params;
} }
public void setParams(final HashMap<String, String> params) { public void setParams(final HashMap<String, String> params) {
this.params = params; this.params = params;
} }
public String getProtocol() { public String getProtocol() {
return protocol; return protocol;
} }
public void setProtocol(final String protocol) { public void setProtocol(final String protocol) {
this.protocol = protocol; this.protocol = protocol;
} }
} }

160
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStore.java
View File

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

56
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreCurrentVersion.java
View File

@ -10,40 +10,40 @@ import javax.persistence.Table;
@Table(name = "mdstore_current_versions") @Table(name = "mdstore_current_versions")
public class MDStoreCurrentVersion implements Serializable { public class MDStoreCurrentVersion implements Serializable {
/** */ /** */
private static final long serialVersionUID = -4757725888593745773L; private static final long serialVersionUID = -4757725888593745773L;
@Id @Id
@Column(name = "mdstore") @Column(name = "mdstore")
private String mdstore; private String mdstore;
@Column(name = "current_version") @Column(name = "current_version")
private String currentVersion; private String currentVersion;
public String getMdstore() { public String getMdstore() {
return mdstore; return mdstore;
} }
public void setMdstore(final String mdstore) { public void setMdstore(final String mdstore) {
this.mdstore = mdstore; this.mdstore = mdstore;
} }
public String getCurrentVersion() { public String getCurrentVersion() {
return currentVersion; return currentVersion;
} }
public void setCurrentVersion(final String currentVersion) { public void setCurrentVersion(final String currentVersion) {
this.currentVersion = currentVersion; this.currentVersion = currentVersion;
} }
public static MDStoreCurrentVersion newInstance(final String mdId, final String versionId) { public static MDStoreCurrentVersion newInstance(final String mdId, final String versionId) {
final MDStoreCurrentVersion cv = new MDStoreCurrentVersion(); final MDStoreCurrentVersion cv = new MDStoreCurrentVersion();
cv.setMdstore(mdId); cv.setMdstore(mdId);
cv.setCurrentVersion(versionId); cv.setCurrentVersion(versionId);
return cv; return cv;
} }
public static MDStoreCurrentVersion newInstance(final MDStoreVersion v) { public static MDStoreCurrentVersion newInstance(final MDStoreVersion v) {
return newInstance(v.getMdstore(), v.getId()); return newInstance(v.getMdstore(), v.getId());
} }
} }

124
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreVersion.java
View File

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

184
dhp-common/src/main/java/eu/dnetlib/data/mdstore/manager/common/model/MDStoreWithInfo.java
View File

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

142
dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java
View File

@ -14,83 +14,81 @@ import org.apache.commons.io.IOUtils;
public class ArgumentApplicationParser implements Serializable { public class ArgumentApplicationParser implements Serializable {
private final Options options = new Options(); private final Options options = new Options();
private final Map<String, String> objectMap = new HashMap<>(); 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 { public ArgumentApplicationParser(final String json_configuration) throws Exception {
final ObjectMapper mapper = new ObjectMapper(); final ObjectMapper mapper = new ObjectMapper();
final OptionsParameter[] configuration = final OptionsParameter[] configuration =
mapper.readValue(json_configuration, OptionsParameter[].class); mapper.readValue(json_configuration, OptionsParameter[].class);
createOptionMap(configuration); createOptionMap(configuration);
}
public ArgumentApplicationParser(final OptionsParameter[] configuration) {
createOptionMap(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);
// 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 ArgumentApplicationParser(final OptionsParameter[] configuration) { public static String compressArgument(final String value) throws Exception {
createOptionMap(configuration); ByteArrayOutputStream out = new ByteArrayOutputStream();
} GZIPOutputStream gzip = new GZIPOutputStream(out);
gzip.write(value.getBytes());
gzip.close();
return java.util.Base64.getEncoder().encodeToString(out.toByteArray());
}
private void createOptionMap(final OptionsParameter[] configuration) { 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()));
}
Arrays.stream(configuration) public String get(final String key) {
.map( return objectMap.get(key);
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(); public Map<String, String> getObjectMap() {
// formatter.printHelp("myapp", null, options, null, true); return objectMap;
}
}
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 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 Map<String, String> getObjectMap() {
return objectMap;
}
} }

48
dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java
View File

@ -2,35 +2,35 @@ package eu.dnetlib.dhp.application;
public class OptionsParameter { public class OptionsParameter {
private String paramName; private String paramName;
private String paramLongName; private String paramLongName;
private String paramDescription; private String paramDescription;
private boolean paramRequired; private boolean paramRequired;
private boolean compressed; private boolean compressed;
public OptionsParameter() {} public OptionsParameter() {}
public String getParamName() { public String getParamName() {
return paramName; return paramName;
} }
public String getParamLongName() { public String getParamLongName() {
return paramLongName; return paramLongName;
} }
public String getParamDescription() { public String getParamDescription() {
return paramDescription; return paramDescription;
} }
public boolean isParamRequired() { public boolean isParamRequired() {
return paramRequired; return paramRequired;
} }
public boolean isCompressed() { public boolean isCompressed() {
return compressed; return compressed;
} }
public void setCompressed(boolean compressed) { public void setCompressed(boolean compressed) {
this.compressed = compressed; this.compressed = compressed;
} }
} }

76
dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java
View File

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

100
dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java
View File

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

123
dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java
View File

@ -9,73 +9,66 @@ import org.apache.spark.sql.SparkSession;
/** SparkSession utility methods. */ /** SparkSession utility methods. */
public class SparkSessionSupport { public class SparkSessionSupport {
private SparkSessionSupport() {} private SparkSessionSupport() {}
/** /**
* Runs a given function using SparkSession created using default builder and supplied * Runs a given function using SparkSession created using default builder and supplied SparkConf.
* SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession * Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created
* created externally. * externally.
* *
* @param conf SparkConf instance * @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession * @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession * @param fn Consumer to be applied to constructed SparkSession
*/ */
public static void runWithSparkSession( public static void runWithSparkSession(
SparkConf conf, SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
Boolean isSparkSessionManaged, runWithSparkSession(
ThrowingConsumer<SparkSession, Exception> fn) { c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, 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 * 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 * and supplied SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse
* SparkSession created externally. * SparkSession created externally.
* *
* @param conf SparkConf instance * @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession * @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession * @param fn Consumer to be applied to constructed SparkSession
*/ */
public static void runWithSparkHiveSession( public static void runWithSparkHiveSession(
SparkConf conf, SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
Boolean isSparkSessionManaged, runWithSparkSession(
ThrowingConsumer<SparkSession, Exception> fn) { c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(),
runWithSparkSession( conf,
c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(), isSparkSessionManaged,
conf, fn);
isSparkSessionManaged, }
fn);
}
/** /**
* Runs a given function using SparkSession created using supplied builder and supplied * Runs a given function using SparkSession created using supplied builder and supplied SparkConf.
* SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession * Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created
* created externally. * externally.
* *
* @param sparkSessionBuilder Builder of SparkSession * @param sparkSessionBuilder Builder of SparkSession
* @param conf SparkConf instance * @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession * @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession * @param fn Consumer to be applied to constructed SparkSession
*/ */
public static void runWithSparkSession( public static void runWithSparkSession(
Function<SparkConf, SparkSession> sparkSessionBuilder, Function<SparkConf, SparkSession> sparkSessionBuilder,
SparkConf conf, SparkConf conf,
Boolean isSparkSessionManaged, Boolean isSparkSessionManaged,
ThrowingConsumer<SparkSession, Exception> fn) { ThrowingConsumer<SparkSession, Exception> fn) {
SparkSession spark = null; SparkSession spark = null;
try { try {
spark = sparkSessionBuilder.apply(conf); spark = sparkSessionBuilder.apply(conf);
fn.accept(spark); fn.accept(spark);
} catch (Exception e) { } catch (Exception e) {
throw new RuntimeException(e); throw new RuntimeException(e);
} finally { } finally {
if (Objects.nonNull(spark) && isSparkSessionManaged) { if (Objects.nonNull(spark) && isSparkSessionManaged) {
spark.stop(); spark.stop();
} }
}
} }
}
} }

114
dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java
View File

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

204
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/MetadataRecord.java
View File

@ -6,115 +6,115 @@ import java.io.Serializable;
/** This class models a record inside the new Metadata store collection on HDFS * */ /** This class models a record inside the new Metadata store collection on HDFS * */
public class MetadataRecord implements Serializable { public class MetadataRecord implements Serializable {
/** The D-Net Identifier associated to the record */ /** The D-Net Identifier associated to the record */
private String id; private String id;
/** The original Identifier of the record */ /** The original Identifier of the record */
private String originalId; private String originalId;
/** The encoding of the record, should be JSON or XML */ /** The encoding of the record, should be JSON or XML */
private String encoding; private String encoding;
/** /**
* The information about the provenance of the record see @{@link Provenance} for the model of * The information about the provenance of the record see @{@link Provenance} for the model of
* this information * this information
*/ */
private Provenance provenance; private Provenance provenance;
/** The content of the metadata */ /** The content of the metadata */
private String body; private String body;
/** the date when the record has been stored */ /** the date when the record has been stored */
private long dateOfCollection; private long dateOfCollection;
/** the date when the record has been stored */ /** the date when the record has been stored */
private long dateOfTransformation; private long dateOfTransformation;
public MetadataRecord() { public MetadataRecord() {
this.dateOfCollection = System.currentTimeMillis(); this.dateOfCollection = System.currentTimeMillis();
}
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());
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getOriginalId() {
return originalId;
}
public void setOriginalId(String originalId) {
this.originalId = originalId;
}
public String getEncoding() {
return encoding;
}
public void setEncoding(String encoding) {
this.encoding = encoding;
}
public Provenance getProvenance() {
return provenance;
}
public void setProvenance(Provenance provenance) {
this.provenance = provenance;
}
public String getBody() {
return body;
}
public void setBody(String body) {
this.body = body;
}
public long getDateOfCollection() {
return dateOfCollection;
}
public void setDateOfCollection(long dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
public long getDateOfTransformation() {
return 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);
}
public MetadataRecord( @Override
String originalId, public int hashCode() {
String encoding, return id.hashCode();
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());
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getOriginalId() {
return originalId;
}
public void setOriginalId(String originalId) {
this.originalId = originalId;
}
public String getEncoding() {
return encoding;
}
public void setEncoding(String encoding) {
this.encoding = encoding;
}
public Provenance getProvenance() {
return provenance;
}
public void setProvenance(Provenance provenance) {
this.provenance = provenance;
}
public String getBody() {
return body;
}
public void setBody(String body) {
this.body = body;
}
public long getDateOfCollection() {
return dateOfCollection;
}
public void setDateOfCollection(long dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
public long getDateOfTransformation() {
return 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 int hashCode() {
return id.hashCode();
}
} }

54
dhp-common/src/main/java/eu/dnetlib/dhp/model/mdstore/Provenance.java
View File

@ -9,41 +9,41 @@ import java.io.Serializable;
*/ */
public class Provenance implements Serializable { 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) { public Provenance(String datasourceId, String datasourceName, String nsPrefix) {
this.datasourceId = datasourceId; this.datasourceId = datasourceId;
this.datasourceName = datasourceName; this.datasourceName = datasourceName;
this.nsPrefix = nsPrefix; this.nsPrefix = nsPrefix;
} }
public String getDatasourceId() { public String getDatasourceId() {
return datasourceId; return datasourceId;
} }
public void setDatasourceId(String datasourceId) { public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId; this.datasourceId = datasourceId;
} }
public String getDatasourceName() { public String getDatasourceName() {
return datasourceName; return datasourceName;
} }
public void setDatasourceName(String datasourceName) { public void setDatasourceName(String datasourceName) {
this.datasourceName = datasourceName; this.datasourceName = datasourceName;
} }
public String getNsPrefix() { public String getNsPrefix() {
return nsPrefix; return nsPrefix;
} }
public void setNsPrefix(String nsPrefix) { public void setNsPrefix(String nsPrefix) {
this.nsPrefix = nsPrefix; this.nsPrefix = nsPrefix;
} }
} }

12
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdException.java
View File

@ -2,11 +2,11 @@ package eu.dnetlib.dhp.parser.utility;
public class VtdException extends Exception { public class VtdException extends Exception {
public VtdException(final Exception e) { public VtdException(final Exception e) {
super(e); super(e);
} }
public VtdException(final Throwable e) { public VtdException(final Throwable e) {
super(e); super(e);
} }
} }

167
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java
View File

@ -10,97 +10,96 @@ import java.util.Map;
/** Created by sandro on 9/29/16. */ /** Created by sandro on 9/29/16. */
public class VtdUtilityParser { public class VtdUtilityParser {
public static List<Node> getTextValuesWithAttributes( public static List<Node> getTextValuesWithAttributes(
final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes) final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes)
throws VtdException { throws VtdException {
final List<Node> results = new ArrayList<>(); final List<Node> results = new ArrayList<>();
try { try {
ap.selectXPath(xpath); ap.selectXPath(xpath);
while (ap.evalXPath() != -1) { while (ap.evalXPath() != -1) {
final Node currentNode = new Node(); final Node currentNode = new Node();
int t = vn.getText(); int t = vn.getText();
if (t >= 0) { if (t >= 0) {
currentNode.setTextValue(vn.toNormalizedString(t)); currentNode.setTextValue(vn.toNormalizedString(t));
} }
currentNode.setAttributes(getAttributes(vn, attributes)); currentNode.setAttributes(getAttributes(vn, attributes));
results.add(currentNode); 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) {
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 results; });
} catch (Exception e) { }
throw new VtdException(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 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 {
private String textValue;
private Map<String, String> attributes;
public String getTextValue() {
return textValue;
} }
private static Map<String, String> getAttributes( public void setTextValue(final String textValue) {
final VTDNav vn, final List<String> attributes) { this.textValue = textValue;
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;
} }
public static List<String> getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath) public Map<String, String> getAttributes() {
throws VtdException { return attributes;
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) public void setAttributes(final Map<String, String> attributes) {
throws VtdException { this.attributes = attributes;
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 {
private String textValue;
private Map<String, String> attributes;
public String getTextValue() {
return textValue;
}
public void setTextValue(final String textValue) {
this.textValue = textValue;
}
public Map<String, String> getAttributes() {
return attributes;
}
public void setAttributes(final Map<String, String> attributes) {
this.attributes = attributes;
}
} }
}
} }

90
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
View File

@ -14,57 +14,57 @@ import org.apache.commons.codec.binary.Hex;
public class DHPUtils { public class DHPUtils {
public static String md5(final String s) { public static String md5(final String s) {
try { try {
final MessageDigest md = MessageDigest.getInstance("MD5"); final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8")); md.update(s.getBytes("UTF-8"));
return new String(Hex.encodeHex(md.digest())); return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) { } catch (final Exception e) {
System.err.println("Error creating id"); System.err.println("Error creating id");
return null; return null;
}
} }
}
public static String generateIdentifier(final String originalId, final String nsPrefix) { public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId)); return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
} }
public static String compressString(final String input) { public static String compressString(final String input) {
try (ByteArrayOutputStream out = new ByteArrayOutputStream(); try (ByteArrayOutputStream out = new ByteArrayOutputStream();
Base64OutputStream b64os = new Base64OutputStream(out)) { Base64OutputStream b64os = new Base64OutputStream(out)) {
GZIPOutputStream gzip = new GZIPOutputStream(b64os); GZIPOutputStream gzip = new GZIPOutputStream(b64os);
gzip.write(input.getBytes(StandardCharsets.UTF_8)); gzip.write(input.getBytes(StandardCharsets.UTF_8));
gzip.close(); gzip.close();
return out.toString(); return out.toString();
} catch (Throwable e) { } catch (Throwable e) {
return null; return null;
}
} }
}
public static String decompressString(final String input) { public static String decompressString(final String input) {
byte[] byteArray = Base64.decodeBase64(input.getBytes()); byte[] byteArray = Base64.decodeBase64(input.getBytes());
int len; int len;
try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray))); try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray)));
ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) { ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) {
byte[] buffer = new byte[1024]; byte[] buffer = new byte[1024];
while ((len = gis.read(buffer)) != -1) { while ((len = gis.read(buffer)) != -1) {
bos.write(buffer, 0, len); bos.write(buffer, 0, len);
} }
return bos.toString(); return bos.toString();
} catch (Exception e) { } catch (Exception e) {
return null; return null;
}
} }
}
public static String getJPathString(final String jsonPath, final String json) { public static String getJPathString(final String jsonPath, final String json) {
try { try {
Object o = JsonPath.read(json, jsonPath); Object o = JsonPath.read(json, jsonPath);
if (o instanceof String) return (String) o; if (o instanceof String) return (String) o;
if (o instanceof JSONArray && ((JSONArray) o).size() > 0) if (o instanceof JSONArray && ((JSONArray) o).size() > 0)
return (String) ((JSONArray) o).get(0); return (String) ((JSONArray) o).get(0);
return o.toString(); return o.toString();
} catch (Exception e) { } catch (Exception e) {
return ""; return "";
}
} }
}
} }

24
dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java
View File

@ -7,18 +7,18 @@ import org.apache.cxf.jaxws.JaxWsProxyFactoryBean;
public class ISLookupClientFactory { 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) { public static ISLookUpService getLookUpService(final String isLookupUrl) {
return getServiceStub(ISLookUpService.class, isLookupUrl); return getServiceStub(ISLookUpService.class, isLookupUrl);
} }
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
private static <T> T getServiceStub(final Class<T> clazz, final String endpoint) { private static <T> T getServiceStub(final Class<T> clazz, final String endpoint) {
log.info(String.format("creating %s stub from %s", clazz.getName(), endpoint)); log.info(String.format("creating %s stub from %s", clazz.getName(), endpoint));
final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean(); final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean();
jaxWsProxyFactory.setServiceClass(clazz); jaxWsProxyFactory.setServiceClass(clazz);
jaxWsProxyFactory.setAddress(endpoint); jaxWsProxyFactory.setAddress(endpoint);
return (T) jaxWsProxyFactory.create(); return (T) jaxWsProxyFactory.create();
} }
} }

35
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java
View File

@ -9,26 +9,25 @@ import net.sf.saxon.trans.XPathException;
public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition { public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition {
public static String DEFAULT_SAXON_EXT_NS_URI = public static String DEFAULT_SAXON_EXT_NS_URI =
"http://www.d-net.research-infrastructures.eu/saxon-extension"; "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) public abstract Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException;
throws XPathException;
@Override @Override
public StructuredQName getFunctionQName() { public StructuredQName getFunctionQName() {
return new StructuredQName("dnet", DEFAULT_SAXON_EXT_NS_URI, getName()); return new StructuredQName("dnet", DEFAULT_SAXON_EXT_NS_URI, getName());
} }
@Override @Override
public ExtensionFunctionCall makeCallExpression() { public ExtensionFunctionCall makeCallExpression() {
return new ExtensionFunctionCall() { return new ExtensionFunctionCall() {
@Override @Override
public Sequence call(XPathContext context, Sequence[] arguments) throws XPathException { public Sequence call(XPathContext context, Sequence[] arguments) throws XPathException {
return doCall(context, arguments); return doCall(context, arguments);
} }
}; };
} }
} }

84
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java
View File

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

96
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java
View File

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

75
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java
View File

@ -10,51 +10,50 @@ import org.apache.commons.lang3.StringUtils;
public class PickFirst extends AbstractExtensionFunction { public class PickFirst extends AbstractExtensionFunction {
@Override @Override
public String getName() { public String getName() {
return "pickFirst"; return "pickFirst";
}
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
return new StringValue("");
} }
@Override final String s1 = getValue(arguments[0]);
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException { final String s2 = getValue(arguments[1]);
if (arguments == null | arguments.length == 0) {
return new StringValue("");
}
final String s1 = getValue(arguments[0]); return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : "");
final String s2 = getValue(arguments[1]); }
return new StringValue( private String getValue(final Sequence arg) throws XPathException {
StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : ""); if (arg != null) {
final Item item = arg.head();
if (item != null) {
return item.getStringValue();
}
} }
return "";
}
private String getValue(final Sequence arg) throws XPathException { @Override
if (arg != null) { public int getMinimumNumberOfArguments() {
final Item item = arg.head(); return 0;
if (item != null) { }
return item.getStringValue();
}
}
return "";
}
@Override @Override
public int getMinimumNumberOfArguments() { public int getMaximumNumberOfArguments() {
return 0; return 2;
} }
@Override @Override
public int getMaximumNumberOfArguments() { public SequenceType[] getArgumentTypes() {
return 2; return new SequenceType[] {SequenceType.OPTIONAL_ITEM};
} }
@Override @Override
public SequenceType[] getArgumentTypes() { public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return new SequenceType[] {SequenceType.OPTIONAL_ITEM}; return SequenceType.SINGLE_STRING;
} }
@Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING;
}
} }

30
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java
View File

@ -9,21 +9,21 @@ import net.sf.saxon.TransformerFactoryImpl;
public class SaxonTransformerFactory { public class SaxonTransformerFactory {
/** /**
* Creates the index record transformer from the given XSLT * Creates the index record transformer from the given XSLT
* *
* @param xslt * @param xslt
* @return * @return
* @throws TransformerException * @throws TransformerException
*/ */
public static Transformer newInstance(final String xslt) throws TransformerException { public static Transformer newInstance(final String xslt) throws TransformerException {
final TransformerFactoryImpl factory = new TransformerFactoryImpl(); final TransformerFactoryImpl factory = new TransformerFactoryImpl();
final Configuration conf = factory.getConfiguration(); final Configuration conf = factory.getConfiguration();
conf.registerExtensionFunction(new ExtractYear()); conf.registerExtensionFunction(new ExtractYear());
conf.registerExtensionFunction(new NormalizeDate()); conf.registerExtensionFunction(new NormalizeDate());
conf.registerExtensionFunction(new PickFirst()); conf.registerExtensionFunction(new PickFirst());
return factory.newTransformer(new StreamSource(new StringReader(xslt))); return factory.newTransformer(new StreamSource(new StringReader(xslt)));
} }
} }

116
dhp-common/src/main/java/eu/dnetlib/message/Message.java
View File

@ -7,67 +7,67 @@ import java.util.Map;
public class Message { 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 { public static Message fromJson(final String json) throws IOException {
final ObjectMapper jsonMapper = new ObjectMapper(); final ObjectMapper jsonMapper = new ObjectMapper();
return jsonMapper.readValue(json, Message.class); return jsonMapper.readValue(json, Message.class);
} }
public Message() {} public Message() {}
public Message(String workflowId, String jobName, MessageType type, Map<String, String> body) { public Message(String workflowId, String jobName, MessageType type, Map<String, String> body) {
this.workflowId = workflowId; this.workflowId = workflowId;
this.jobName = jobName; this.jobName = jobName;
this.type = type; this.type = type;
this.body = body; this.body = body;
} }
public String getWorkflowId() { public String getWorkflowId() {
return workflowId; return workflowId;
} }
public void setWorkflowId(String workflowId) { public void setWorkflowId(String workflowId) {
this.workflowId = workflowId; this.workflowId = workflowId;
} }
public String getJobName() { public String getJobName() {
return jobName; return jobName;
} }
public void setJobName(String jobName) { public void setJobName(String jobName) {
this.jobName = jobName; this.jobName = jobName;
} }
public MessageType getType() { public MessageType getType() {
return type; return type;
} }
public void setType(MessageType type) { public void setType(MessageType type) {
this.type = type; this.type = type;
} }
public Map<String, String> getBody() { public Map<String, String> getBody() {
return body; return body;
} }
public void setBody(Map<String, String> body) { public void setBody(Map<String, String> body) {
this.body = body; this.body = body;
} }
@Override @Override
public String toString() { public String toString() {
final ObjectMapper jsonMapper = new ObjectMapper(); final ObjectMapper jsonMapper = new ObjectMapper();
try { try {
return jsonMapper.writeValueAsString(this); return jsonMapper.writeValueAsString(this);
} catch (JsonProcessingException e) { } catch (JsonProcessingException e) {
return null; return null;
}
} }
}
} }

58
dhp-common/src/main/java/eu/dnetlib/message/MessageConsumer.java
View File

@ -10,36 +10,36 @@ import java.util.concurrent.LinkedBlockingQueue;
public class MessageConsumer extends DefaultConsumer { 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. * Constructs a new instance and records its association to the passed-in channel.
* *
* @param channel the channel to which this consumer is attached * @param channel the channel to which this consumer is attached
* @param queueMessages * @param queueMessages
*/ */
public MessageConsumer(Channel channel, LinkedBlockingQueue<Message> queueMessages) { public MessageConsumer(Channel channel, LinkedBlockingQueue<Message> queueMessages) {
super(channel); super(channel);
this.queueMessages = queueMessages; this.queueMessages = queueMessages;
} }
@Override @Override
public void handleDelivery( public void handleDelivery(
String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body) String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body)
throws IOException { throws IOException {
final String json = new String(body, StandardCharsets.UTF_8); final String json = new String(body, StandardCharsets.UTF_8);
Message message = Message.fromJson(json); Message message = Message.fromJson(json);
try { try {
this.queueMessages.put(message); this.queueMessages.put(message);
System.out.println("Receiving Message " + message); System.out.println("Receiving Message " + message);
} catch (InterruptedException e) { } catch (InterruptedException e) {
if (message.getType() == MessageType.REPORT) if (message.getType() == MessageType.REPORT)
throw new RuntimeException("Error on sending message"); throw new RuntimeException("Error on sending message");
else { else {
// TODO LOGGING EXCEPTION // TODO LOGGING EXCEPTION
} }
} finally { } finally {
getChannel().basicAck(envelope.getDeliveryTag(), false); getChannel().basicAck(envelope.getDeliveryTag(), false);
}
} }
}
} }

206
dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java
View File

@ -11,124 +11,124 @@ import java.util.concurrent.TimeoutException;
public class MessageManager { 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( public MessageManager(
String messageHost, String messageHost,
String username, String username,
String password, String password,
final LinkedBlockingQueue<Message> queueMessages) { final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages; this.queueMessages = queueMessages;
this.messageHost = messageHost; this.messageHost = messageHost;
this.username = username; this.username = username;
this.password = password; 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;
}
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 getOrCreateChannel(final String queueName, boolean durable, boolean autodelete)
throws Exception {
if (channels.containsKey(queueName)) {
return channels.get(queueName);
} }
public MessageManager( if (this.connection == null) {
String messageHost, this.connection = createConnection();
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;
} }
channels.put(queueName, createChannel(this.connection, queueName, durable, autodelete));
return channels.get(queueName);
}
private Connection createConnection() throws IOException, TimeoutException { public void close() throws IOException {
ConnectionFactory factory = new ConnectionFactory(); channels
factory.setHost(this.messageHost); .values()
factory.setUsername(this.username); .forEach(
factory.setPassword(this.password); ch -> {
return factory.newConnection(); try {
ch.close();
} catch (Exception e) {
// TODO LOG
}
});
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);
} }
}
private Channel createChannel( public boolean sendMessage(
final Connection connection, final Message message, String queueName, boolean durable_var, boolean autodelete_var)
final String queueName, throws Exception {
final boolean durable, try {
final boolean autodelete) Channel channel = getOrCreateChannel(queueName, durable_var, autodelete_var);
throws Exception { channel.basicPublish("", queueName, null, message.toString().getBytes());
Map<String, Object> args = new HashMap<>(); return true;
args.put("x-message-ttl", 10000); } catch (Throwable e) {
Channel channel = connection.createChannel(); throw new RuntimeException(e);
channel.queueDeclare(queueName, durable, false, this.autodelete, args);
return channel;
} }
}
private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete) public void startConsumingMessage(
throws Exception { final String queueName, final boolean durable, final boolean autodelete) throws Exception {
if (channels.containsKey(queueName)) {
return channels.get(queueName);
}
if (this.connection == null) { Channel channel = createChannel(createConnection(), queueName, durable, autodelete);
this.connection = createConnection(); channel.basicConsume(queueName, false, new MessageConsumer(channel, queueMessages));
} }
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
}
});
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, 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 {
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; package eu.dnetlib.message;
public enum MessageType { public enum MessageType {
ONGOING, ONGOING,
REPORT REPORT
} }

28
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java
View File

@ -3,22 +3,22 @@ package eu.dnetlib.scholexplorer.relation;
import java.io.Serializable; import java.io.Serializable;
public class RelInfo implements Serializable { public class RelInfo implements Serializable {
private String original; private String original;
private String inverse; private String inverse;
public String getOriginal() { public String getOriginal() {
return original; return original;
} }
public void setOriginal(String original) { public void setOriginal(String original) {
this.original = original; this.original = original;
} }
public String getInverse() { public String getInverse() {
return inverse; return inverse;
} }
public void setInverse(String inverse) { public void setInverse(String inverse) {
this.inverse = inverse; this.inverse = inverse;
} }
} }

12
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java
View File

@ -7,12 +7,12 @@ import org.apache.commons.io.IOUtils;
public class RelationMapper extends HashMap<String, RelInfo> implements Serializable { public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
public static RelationMapper load() throws Exception { public static RelationMapper load() throws Exception {
final String json = final String json =
IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json")); IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json"));
ObjectMapper mapper = new ObjectMapper(); ObjectMapper mapper = new ObjectMapper();
return mapper.readValue(json, RelationMapper.class); return mapper.readValue(json, RelationMapper.class);
} }
} }

109
dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java
View File

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

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

@ -15,65 +15,63 @@ import org.junit.jupiter.api.io.TempDir;
public class HdfsSupportTest { public class HdfsSupportTest {
@Nested @Nested
class Remove { class Remove {
@Test @Test
public void shouldThrowARuntimeExceptionOnError() { public void shouldThrowARuntimeExceptionOnError() {
// when // when
assertThrows( assertThrows(RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
}
@Test
public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
// when
HdfsSupport.remove(tempDir.toString(), new Configuration());
// then
assertFalse(Files.exists(tempDir));
}
@Test
public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
// given
Path file = Files.createTempFile(tempDir, "p", "s");
// when
HdfsSupport.remove(file.toString(), new Configuration());
// then
assertFalse(Files.exists(file));
}
} }
@Nested @Test
class ListFiles { public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
// when
HdfsSupport.remove(tempDir.toString(), new Configuration());
@Test // then
public void shouldThrowARuntimeExceptionOnError() { assertFalse(Files.exists(tempDir));
// 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");
// 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)));
}
} }
@Test
public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
// given
Path file = Files.createTempFile(tempDir, "p", "s");
// when
HdfsSupport.remove(file.toString(), new Configuration());
// then
assertFalse(Files.exists(file));
}
}
@Nested
class ListFiles {
@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");
// 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)));
}
}
} }

74
dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java
View File

@ -11,45 +11,45 @@ import org.junit.jupiter.api.Test;
public class SparkSessionSupportTest { public class SparkSessionSupportTest {
@Nested @Nested
class RunWithSparkSession { class RunWithSparkSession {
@Test @Test
public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged() public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
throws Exception { throws Exception {
// given // given
SparkSession spark = mock(SparkSession.class); SparkSession spark = mock(SparkSession.class);
SparkConf conf = mock(SparkConf.class); SparkConf conf = mock(SparkConf.class);
Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class); Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class);
when(sparkSessionBuilder.apply(conf)).thenReturn(spark); when(sparkSessionBuilder.apply(conf)).thenReturn(spark);
ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class); ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class);
// when // when
SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, false, fn); SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, false, fn);
// then // then
verify(sparkSessionBuilder).apply(conf); verify(sparkSessionBuilder).apply(conf);
verify(fn).accept(spark); verify(fn).accept(spark);
verify(spark, never()).stop(); 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);
// when
SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, true, fn);
// then
verify(sparkSessionBuilder).apply(conf);
verify(fn).accept(spark);
verify(spark, times(1)).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);
// when
SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, true, fn);
// then
verify(sparkSessionBuilder).apply(conf);
verify(fn).accept(spark);
verify(spark, times(1)).stop();
}
}
} }

10
dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java
View File

@ -6,10 +6,10 @@ import org.junit.jupiter.api.Test;
public class MetadataRecordTest { public class MetadataRecordTest {
@Test @Test
public void getTimestamp() { public void getTimestamp() {
MetadataRecord r = new MetadataRecord(); MetadataRecord r = new MetadataRecord();
assertTrue(r.getDateOfCollection() > 0); assertTrue(r.getDateOfCollection() > 0);
} }
} }

68
dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java
View File

@ -9,44 +9,42 @@ import org.junit.jupiter.api.Test;
public class MessageTest { public class MessageTest {
@Test @Test
public void fromJsonTest() throws IOException { public void fromJsonTest() throws IOException {
Message m = new Message(); Message m = new Message();
m.setWorkflowId("wId"); m.setWorkflowId("wId");
m.setType(MessageType.ONGOING); m.setType(MessageType.ONGOING);
m.setJobName("Collection"); m.setJobName("Collection");
Map<String, String> body = new HashMap<>(); Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300"); body.put("parsedItem", "300");
body.put("ExecutionTime", "30s"); body.put("ExecutionTime", "30s");
m.setBody(body); m.setBody(body);
System.out.println("m = " + m); System.out.println("m = " + m);
Message m1 = Message.fromJson(m.toString()); Message m1 = Message.fromJson(m.toString());
assertEquals(m1.getWorkflowId(), m.getWorkflowId()); assertEquals(m1.getWorkflowId(), m.getWorkflowId());
assertEquals(m1.getType(), m.getType()); assertEquals(m1.getType(), m.getType());
assertEquals(m1.getJobName(), m.getJobName()); assertEquals(m1.getJobName(), m.getJobName());
assertNotNull(m1.getBody()); assertNotNull(m1.getBody());
m1.getBody() m1.getBody().keySet().forEach(it -> assertEquals(m1.getBody().get(it), m.getBody().get(it)));
.keySet() assertEquals(m1.getJobName(), m.getJobName());
.forEach(it -> assertEquals(m1.getBody().get(it), m.getBody().get(it))); }
assertEquals(m1.getJobName(), m.getJobName());
}
@Test @Test
public void toStringTest() { public void toStringTest() {
final String expectedJson = final String expectedJson =
"{\"workflowId\":\"wId\",\"jobName\":\"Collection\",\"type\":\"ONGOING\",\"body\":{\"ExecutionTime\":\"30s\",\"parsedItem\":\"300\"}}"; "{\"workflowId\":\"wId\",\"jobName\":\"Collection\",\"type\":\"ONGOING\",\"body\":{\"ExecutionTime\":\"30s\",\"parsedItem\":\"300\"}}";
Message m = new Message(); Message m = new Message();
m.setWorkflowId("wId"); m.setWorkflowId("wId");
m.setType(MessageType.ONGOING); m.setType(MessageType.ONGOING);
m.setJobName("Collection"); m.setJobName("Collection");
Map<String, String> body = new HashMap<>(); Map<String, String> body = new HashMap<>();
body.put("parsedItem", "300"); body.put("parsedItem", "300");
body.put("ExecutionTime", "30s"); body.put("ExecutionTime", "30s");
m.setBody(body); m.setBody(body);
assertEquals(expectedJson, m.toString()); assertEquals(expectedJson, m.toString());
} }
} }

10
dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java
View File

@ -4,10 +4,10 @@ import org.junit.jupiter.api.Test;
public class RelationMapperTest { public class RelationMapperTest {
@Test @Test
public void testLoadRels() throws Exception { public void testLoadRels() throws Exception {
RelationMapper relationMapper = RelationMapper.load(); RelationMapper relationMapper = RelationMapper.load();
relationMapper.keySet().forEach(System.out::println); relationMapper.keySet().forEach(System.out::println);
} }
} }

38
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicAction.java
View File

@ -7,30 +7,30 @@ import java.io.Serializable;
@JsonDeserialize(using = AtomicActionDeserializer.class) @JsonDeserialize(using = AtomicActionDeserializer.class)
public class AtomicAction<T extends Oaf> implements Serializable { 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) { public AtomicAction(Class<T> clazz, T payload) {
this.clazz = clazz; this.clazz = clazz;
this.payload = payload; this.payload = payload;
} }
public Class<T> getClazz() { public Class<T> getClazz() {
return clazz; return clazz;
} }
public void setClazz(Class<T> clazz) { public void setClazz(Class<T> clazz) {
this.clazz = clazz; this.clazz = clazz;
} }
public T getPayload() { public T getPayload() {
return payload; return payload;
} }
public void setPayload(T payload) { public void setPayload(T payload) {
this.payload = payload; this.payload = payload;
} }
} }

26
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java
View File

@ -11,19 +11,19 @@ import java.io.IOException;
public class AtomicActionDeserializer extends JsonDeserializer { public class AtomicActionDeserializer extends JsonDeserializer {
@Override @Override
public Object deserialize(JsonParser jp, DeserializationContext ctxt) public Object deserialize(JsonParser jp, DeserializationContext ctxt)
throws IOException, JsonProcessingException { throws IOException, JsonProcessingException {
JsonNode node = jp.getCodec().readTree(jp); JsonNode node = jp.getCodec().readTree(jp);
String classTag = node.get("clazz").asText(); String classTag = node.get("clazz").asText();
JsonNode payload = node.get("payload"); JsonNode payload = node.get("payload");
ObjectMapper mapper = new ObjectMapper(); ObjectMapper mapper = new ObjectMapper();
try { try {
final Class<?> clazz = Class.forName(classTag); final Class<?> clazz = Class.forName(classTag);
return new AtomicAction(clazz, (Oaf) mapper.readValue(payload.toString(), clazz)); return new AtomicAction(clazz, (Oaf) mapper.readValue(payload.toString(), clazz));
} catch (ClassNotFoundException e) { } catch (ClassNotFoundException e) {
throw new IOException(e); throw new IOException(e);
}
} }
}
} }

34
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java
View File

@ -4,23 +4,23 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity;
/** Actual entity types in the Graph */ /** Actual entity types in the Graph */
public enum EntityType { public enum EntityType {
publication, publication,
dataset, dataset,
otherresearchproduct, otherresearchproduct,
software, software,
datasource, datasource,
organization, organization,
project; project;
/** /**
* Resolves the EntityType, given the relative class name * Resolves the EntityType, given the relative class name
* *
* @param clazz the given class name * @param clazz the given class name
* @param <T> actual OafEntity subclass * @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class * @return the EntityType associated to the given class
*/ */
public static <T extends OafEntity> EntityType fromClass(Class<T> clazz) { public static <T extends OafEntity> EntityType fromClass(Class<T> clazz) {
return EntityType.valueOf(clazz.getSimpleName().toLowerCase()); return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
} }
} }

8
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java
View File

@ -2,8 +2,8 @@ package eu.dnetlib.dhp.schema.common;
/** Main entity types in the Graph */ /** Main entity types in the Graph */
public enum MainEntityType { public enum MainEntityType {
result, result,
datasource, datasource,
organization, organization,
project project
} }

40
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java Normal file
View File

@ -0,0 +1,40 @@
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 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();
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);
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);
}
}

299
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
View File

@ -3,147 +3,196 @@ package eu.dnetlib.dhp.schema.common;
import com.google.common.collect.Maps; import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import java.util.Map; import java.util.Map;
import java.util.Optional;
import java.util.function.Function;
/** Oaf model utility methods. */ /** Oaf model utility methods. */
public class ModelSupport { public class ModelSupport {
/** Defines the mapping between the actual entity type and the main entity type */ /** Defines the mapping between the actual entity type and the main entity type */
private static Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap(); private static Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
static { static {
entityMapping.put(EntityType.publication, MainEntityType.result); entityMapping.put(EntityType.publication, MainEntityType.result);
entityMapping.put(EntityType.dataset, MainEntityType.result); entityMapping.put(EntityType.dataset, MainEntityType.result);
entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result); entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result);
entityMapping.put(EntityType.software, MainEntityType.result); entityMapping.put(EntityType.software, MainEntityType.result);
entityMapping.put(EntityType.datasource, MainEntityType.datasource); entityMapping.put(EntityType.datasource, MainEntityType.datasource);
entityMapping.put(EntityType.organization, MainEntityType.organization); entityMapping.put(EntityType.organization, MainEntityType.organization);
entityMapping.put(EntityType.project, MainEntityType.project); entityMapping.put(EntityType.project, MainEntityType.project);
} }
/** /**
* Defines the mapping between the actual entity types and the relative classes implementing * Defines the mapping between the actual entity types and the relative classes implementing them
* them */
*/ public static final Map<EntityType, Class> entityTypes = Maps.newHashMap();
public static final Map<EntityType, Class> entityTypes = Maps.newHashMap();
static { static {
entityTypes.put(EntityType.datasource, Datasource.class); entityTypes.put(EntityType.datasource, Datasource.class);
entityTypes.put(EntityType.organization, Organization.class); entityTypes.put(EntityType.organization, Organization.class);
entityTypes.put(EntityType.project, Project.class); entityTypes.put(EntityType.project, Project.class);
entityTypes.put(EntityType.dataset, Dataset.class); entityTypes.put(EntityType.dataset, Dataset.class);
entityTypes.put(EntityType.otherresearchproduct, OtherResearchProduct.class); entityTypes.put(EntityType.otherresearchproduct, OtherResearchProduct.class);
entityTypes.put(EntityType.software, Software.class); entityTypes.put(EntityType.software, Software.class);
entityTypes.put(EntityType.publication, Publication.class); entityTypes.put(EntityType.publication, Publication.class);
} }
public static final Map<String, Class> oafTypes = Maps.newHashMap(); public static final Map<String, Class> oafTypes = Maps.newHashMap();
static { static {
oafTypes.put("datasource", Datasource.class); oafTypes.put("datasource", Datasource.class);
oafTypes.put("organization", Organization.class); oafTypes.put("organization", Organization.class);
oafTypes.put("project", Project.class); oafTypes.put("project", Project.class);
oafTypes.put("dataset", Dataset.class); oafTypes.put("dataset", Dataset.class);
oafTypes.put("otherresearchproduct", OtherResearchProduct.class); oafTypes.put("otherresearchproduct", OtherResearchProduct.class);
oafTypes.put("software", Software.class); oafTypes.put("software", Software.class);
oafTypes.put("publication", Publication.class); oafTypes.put("publication", Publication.class);
oafTypes.put("relation", Relation.class); oafTypes.put("relation", Relation.class);
} }
private static final String schemeTemplate = "dnet:%s_%s_relations"; private static final String schemeTemplate = "dnet:%s_%s_relations";
private ModelSupport() {} private ModelSupport() {}
/** /**
* Checks subclass-superclass relationship. * Checks subclass-superclass relationship.
* *
* @param subClazzObject Subclass object instance * @param subClazzObject Subclass object instance
* @param superClazzObject Superclass object instance * @param superClazzObject Superclass object instance
* @param <X> Subclass type * @param <X> Subclass type
* @param <Y> Superclass type * @param <Y> Superclass type
* @return True if X is a subclass of Y * @return True if X is a subclass of Y
*/ */
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass( public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Y superClazzObject) { X subClazzObject, Y superClazzObject) {
return isSubClass(subClazzObject.getClass(), superClazzObject.getClass()); return isSubClass(subClazzObject.getClass(), superClazzObject.getClass());
} }
/** /**
* Checks subclass-superclass relationship. * Checks subclass-superclass relationship.
* *
* @param subClazzObject Subclass object instance * @param subClazzObject Subclass object instance
* @param superClazz Superclass class * @param superClazz Superclass class
* @param <X> Subclass type * @param <X> Subclass type
* @param <Y> Superclass type * @param <Y> Superclass type
* @return True if X is a subclass of Y * @return True if X is a subclass of Y
*/ */
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass( public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Class<Y> superClazz) { X subClazzObject, Class<Y> superClazz) {
return isSubClass(subClazzObject.getClass(), superClazz); return isSubClass(subClazzObject.getClass(), superClazz);
} }
/** /**
* Checks subclass-superclass relationship. * Checks subclass-superclass relationship.
* *
* @param subClazz Subclass class * @param subClazz Subclass class
* @param superClazz Superclass class * @param superClazz Superclass class
* @param <X> Subclass type * @param <X> Subclass type
* @param <Y> Superclass type * @param <Y> Superclass type
* @return True if X is a subclass of Y * @return True if X is a subclass of Y
*/ */
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass( public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
Class<X> subClazz, Class<Y> superClazz) { Class<X> subClazz, Class<Y> superClazz) {
return superClazz.isAssignableFrom(subClazz); return superClazz.isAssignableFrom(subClazz);
} }
/** /**
* Lists all the OAF model classes * Lists all the OAF model classes
* *
* @param <T> * @param <T>
* @return * @return
*/ */
public static <T extends Oaf> Class<T>[] getOafModelClasses() { public static <T extends Oaf> Class<T>[] getOafModelClasses() {
return new Class[] { return new Class[] {
Author.class, Author.class,
Context.class, Context.class,
Country.class, Country.class,
DataInfo.class, DataInfo.class,
Dataset.class, Dataset.class,
Datasource.class, Datasource.class,
ExternalReference.class, ExternalReference.class,
ExtraInfo.class, ExtraInfo.class,
Field.class, Field.class,
GeoLocation.class, GeoLocation.class,
Instance.class, Instance.class,
Journal.class, Journal.class,
KeyValue.class, KeyValue.class,
Oaf.class, Oaf.class,
OafEntity.class, OafEntity.class,
OAIProvenance.class, OAIProvenance.class,
Organization.class, Organization.class,
OriginDescription.class, OriginDescription.class,
OtherResearchProduct.class, OtherResearchProduct.class,
Project.class, Project.class,
Publication.class, Publication.class,
Qualifier.class, Qualifier.class,
Relation.class, Relation.class,
Result.class, Result.class,
Software.class, Software.class,
StructuredProperty.class StructuredProperty.class
}; };
} }
public static String getMainType(final EntityType type) { public static String getMainType(final EntityType type) {
return entityMapping.get(type).name(); return entityMapping.get(type).name();
} }
public static boolean isResult(EntityType type) { public static boolean isResult(EntityType type) {
return MainEntityType.result.name().equals(getMainType(type)); return MainEntityType.result.name().equals(getMainType(type));
} }
public static String getScheme(final String sourceType, final String targetType) { public static String getScheme(final String sourceType, final String targetType) {
return String.format( return String.format(
schemeTemplate, schemeTemplate,
entityMapping.get(EntityType.valueOf(sourceType)).name(), entityMapping.get(EntityType.valueOf(sourceType)).name(),
entityMapping.get(EntityType.valueOf(targetType)).name()); entityMapping.get(EntityType.valueOf(targetType)).name());
} }
public static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional.ofNullable(r.getSource())
.map(
source ->
Optional.ofNullable(r.getTarget())
.map(
target ->
Optional.ofNullable(r.getRelType())
.map(
relType ->
Optional.ofNullable(r.getSubRelType())
.map(
subRelType ->
Optional.ofNullable(r.getRelClass())
.map(
relClass ->
String.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String.join(
source,
target,
relType,
subRelType)))
.orElse(String.join(source, target, relType)))
.orElse(String.join(source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
} }

116
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java
View File

@ -6,81 +6,81 @@ import java.util.Objects;
public class Author implements Serializable { 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() { public String getFullname() {
return fullname; return fullname;
} }
public void setFullname(String fullname) { public void setFullname(String fullname) {
this.fullname = fullname; this.fullname = fullname;
} }
public String getName() { public String getName() {
return name; return name;
} }
public void setName(String name) { public void setName(String name) {
this.name = name; this.name = name;
} }
public String getSurname() { public String getSurname() {
return surname; return surname;
} }
public void setSurname(String surname) { public void setSurname(String surname) {
this.surname = surname; this.surname = surname;
} }
public Integer getRank() { public Integer getRank() {
return rank; return rank;
} }
public void setRank(Integer rank) { public void setRank(Integer rank) {
this.rank = rank; this.rank = rank;
} }
public List<StructuredProperty> getPid() { public List<StructuredProperty> getPid() {
return pid; return pid;
} }
public void setPid(List<StructuredProperty> pid) { public void setPid(List<StructuredProperty> pid) {
this.pid = pid; this.pid = pid;
} }
public List<Field<String>> getAffiliation() { public List<Field<String>> getAffiliation() {
return affiliation; return affiliation;
} }
public void setAffiliation(List<Field<String>> affiliation) { public void setAffiliation(List<Field<String>> affiliation) {
this.affiliation = affiliation; this.affiliation = affiliation;
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
Author author = (Author) o; Author author = (Author) o;
return Objects.equals(fullname, author.fullname) return Objects.equals(fullname, author.fullname)
&& Objects.equals(name, author.name) && Objects.equals(name, author.name)
&& Objects.equals(surname, author.surname) && Objects.equals(surname, author.surname)
&& Objects.equals(rank, author.rank) && Objects.equals(rank, author.rank)
&& Objects.equals(pid, author.pid) && Objects.equals(pid, author.pid)
&& Objects.equals(affiliation, author.affiliation); && Objects.equals(affiliation, author.affiliation);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(fullname, name, surname, rank, pid, affiliation); return Objects.hash(fullname, name, surname, rank, pid, affiliation);
} }
} }

52
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Context.java
View File

@ -4,39 +4,39 @@ import java.io.Serializable;
import java.util.List; import java.util.List;
public class Context implements Serializable { public class Context implements Serializable {
private String id; private String id;
private List<DataInfo> dataInfo; private List<DataInfo> dataInfo;
public String getId() { public String getId() {
return id; return id;
} }
public void setId(String id) { public void setId(String id) {
this.id = id; this.id = id;
} }
public List<DataInfo> getDataInfo() { public List<DataInfo> getDataInfo() {
return dataInfo; return dataInfo;
} }
public void setDataInfo(List<DataInfo> dataInfo) { public void setDataInfo(List<DataInfo> dataInfo) {
this.dataInfo = dataInfo; this.dataInfo = dataInfo;
} }
@Override @Override
public int hashCode() { public int hashCode() {
return id == null ? 0 : id.hashCode(); return id == null ? 0 : id.hashCode();
} }
@Override @Override
public boolean equals(Object obj) { public boolean equals(Object obj) {
if (this == obj) return true; if (this == obj) return true;
if (obj == null) return false; if (obj == null) return false;
if (getClass() != obj.getClass()) 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());
} }
} }

38
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java
View File

@ -4,27 +4,27 @@ import java.util.Objects;
public class Country extends Qualifier { public class Country extends Qualifier {
private DataInfo dataInfo; private DataInfo dataInfo;
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; return dataInfo;
} }
public void setDataInfo(DataInfo dataInfo) { public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo; this.dataInfo = dataInfo;
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false; if (!super.equals(o)) return false;
Country country = (Country) o; Country country = (Country) o;
return Objects.equals(dataInfo, country.dataInfo); return Objects.equals(dataInfo, country.dataInfo);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(super.hashCode(), dataInfo); return Objects.hash(super.hashCode(), dataInfo);
} }
} }

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

@ -5,82 +5,77 @@ import java.util.Objects;
public class DataInfo implements Serializable { public class DataInfo implements Serializable {
private Boolean invisible = false; private Boolean invisible = false;
private Boolean inferred; private Boolean inferred;
private Boolean deletedbyinference; private Boolean deletedbyinference;
private String trust; private String trust;
private String inferenceprovenance; private String inferenceprovenance;
private Qualifier provenanceaction; private Qualifier provenanceaction;
public Boolean getInvisible() { public Boolean getInvisible() {
return invisible; return invisible;
} }
public void setInvisible(Boolean invisible) { public void setInvisible(Boolean invisible) {
this.invisible = invisible; this.invisible = invisible;
} }
public Boolean getInferred() { public Boolean getInferred() {
return inferred; return inferred;
} }
public void setInferred(Boolean inferred) { public void setInferred(Boolean inferred) {
this.inferred = inferred; this.inferred = inferred;
} }
public Boolean getDeletedbyinference() { public Boolean getDeletedbyinference() {
return deletedbyinference; return deletedbyinference;
} }
public void setDeletedbyinference(Boolean deletedbyinference) { public void setDeletedbyinference(Boolean deletedbyinference) {
this.deletedbyinference = deletedbyinference; this.deletedbyinference = deletedbyinference;
} }
public String getTrust() { public String getTrust() {
return trust; return trust;
} }
public void setTrust(String trust) { public void setTrust(String trust) {
this.trust = trust; this.trust = trust;
} }
public String getInferenceprovenance() { public String getInferenceprovenance() {
return inferenceprovenance; return inferenceprovenance;
} }
public void setInferenceprovenance(String inferenceprovenance) { public void setInferenceprovenance(String inferenceprovenance) {
this.inferenceprovenance = inferenceprovenance; this.inferenceprovenance = inferenceprovenance;
} }
public Qualifier getProvenanceaction() { public Qualifier getProvenanceaction() {
return provenanceaction; return provenanceaction;
} }
public void setProvenanceaction(Qualifier provenanceaction) { public void setProvenanceaction(Qualifier provenanceaction) {
this.provenanceaction = provenanceaction; this.provenanceaction = provenanceaction;
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
DataInfo dataInfo = (DataInfo) o; DataInfo dataInfo = (DataInfo) o;
return Objects.equals(invisible, dataInfo.invisible) return Objects.equals(invisible, dataInfo.invisible)
&& Objects.equals(inferred, dataInfo.inferred) && Objects.equals(inferred, dataInfo.inferred)
&& Objects.equals(deletedbyinference, dataInfo.deletedbyinference) && Objects.equals(deletedbyinference, dataInfo.deletedbyinference)
&& Objects.equals(trust, dataInfo.trust) && Objects.equals(trust, dataInfo.trust)
&& Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance) && Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance)
&& Objects.equals(provenanceaction, dataInfo.provenanceaction); && Objects.equals(provenanceaction, dataInfo.provenanceaction);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash( return Objects.hash(
invisible, invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction);
inferred, }
deletedbyinference,
trust,
inferenceprovenance,
provenanceaction);
}
} }

208
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java
View File

@ -1,142 +1,116 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Dataset extends Result implements Serializable { 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 Field<String> getStoragedate() { public Dataset() {
return storagedate; setResulttype(ModelConstants.DATASET_DEFAULT_RESULTTYPE);
}
public Field<String> getStoragedate() {
return storagedate;
}
public void setStoragedate(Field<String> storagedate) {
this.storagedate = storagedate;
}
public Field<String> getDevice() {
return device;
}
public void setDevice(Field<String> device) {
this.device = device;
}
public Field<String> getSize() {
return size;
}
public void setSize(Field<String> size) {
this.size = size;
}
public Field<String> getVersion() {
return version;
}
public void setVersion(Field<String> version) {
this.version = version;
}
public Field<String> getLastmetadataupdate() {
return lastmetadataupdate;
}
public void setLastmetadataupdate(Field<String> lastmetadataupdate) {
this.lastmetadataupdate = lastmetadataupdate;
}
public Field<String> getMetadataversionnumber() {
return metadataversionnumber;
}
public void setMetadataversionnumber(Field<String> metadataversionnumber) {
this.metadataversionnumber = metadataversionnumber;
}
public List<GeoLocation> getGeolocation() {
return geolocation;
}
public void setGeolocation(List<GeoLocation> geolocation) {
this.geolocation = geolocation;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Dataset.class.isAssignableFrom(e.getClass())) {
return;
} }
public void setStoragedate(Field<String> storagedate) { final Dataset d = (Dataset) e;
this.storagedate = storagedate;
}
public Field<String> getDevice() { storagedate =
return device; d.getStoragedate() != null && compareTrust(this, e) < 0 ? d.getStoragedate() : storagedate;
}
public void setDevice(Field<String> device) { device = d.getDevice() != null && compareTrust(this, e) < 0 ? d.getDevice() : device;
this.device = device;
}
public Field<String> getSize() { size = d.getSize() != null && compareTrust(this, e) < 0 ? d.getSize() : size;
return size;
}
public void setSize(Field<String> size) { version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version;
this.size = size;
}
public Field<String> getVersion() { lastmetadataupdate =
return version; d.getLastmetadataupdate() != null && compareTrust(this, e) < 0
} ? d.getLastmetadataupdate()
: lastmetadataupdate;
public void setVersion(Field<String> version) { metadataversionnumber =
this.version = version; d.getMetadataversionnumber() != null && compareTrust(this, e) < 0
} ? d.getMetadataversionnumber()
: metadataversionnumber;
public Field<String> getLastmetadataupdate() { geolocation = mergeLists(geolocation, d.getGeolocation());
return lastmetadataupdate;
}
public void setLastmetadataupdate(Field<String> lastmetadataupdate) { mergeOAFDataInfo(d);
this.lastmetadataupdate = lastmetadataupdate; }
}
public Field<String> getMetadataversionnumber() {
return metadataversionnumber;
}
public void setMetadataversionnumber(Field<String> metadataversionnumber) {
this.metadataversionnumber = metadataversionnumber;
}
public List<GeoLocation> getGeolocation() {
return geolocation;
}
public void setGeolocation(List<GeoLocation> geolocation) {
this.geolocation = geolocation;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Dataset.class.isAssignableFrom(e.getClass())) {
return;
}
final Dataset d = (Dataset) e;
storagedate =
d.getStoragedate() != null && compareTrust(this, e) < 0
? d.getStoragedate()
: storagedate;
device = d.getDevice() != null && compareTrust(this, e) < 0 ? d.getDevice() : device;
size = d.getSize() != null && compareTrust(this, e) < 0 ? d.getSize() : size;
version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version;
lastmetadataupdate =
d.getLastmetadataupdate() != null && compareTrust(this, e) < 0
? d.getLastmetadataupdate()
: lastmetadataupdate;
metadataversionnumber =
d.getMetadataversionnumber() != null && compareTrust(this, e) < 0
? d.getMetadataversionnumber()
: metadataversionnumber;
geolocation = mergeLists(geolocation, d.getGeolocation());
mergeOAFDataInfo(d);
}
@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;
Dataset dataset = (Dataset) o;
return Objects.equals(storagedate, dataset.storagedate)
&& Objects.equals(device, dataset.device)
&& Objects.equals(size, dataset.size)
&& Objects.equals(version, dataset.version)
&& Objects.equals(lastmetadataupdate, dataset.lastmetadataupdate)
&& Objects.equals(metadataversionnumber, dataset.metadataversionnumber)
&& Objects.equals(geolocation, dataset.geolocation);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
storagedate,
device,
size,
version,
lastmetadataupdate,
metadataversionnumber,
geolocation);
}
} }

1033
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java
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166
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java
View File

@ -4,112 +4,112 @@ import java.io.Serializable;
import java.util.Objects; import java.util.Objects;
public class ExternalReference implements Serializable { public class ExternalReference implements Serializable {
// source // source
private String sitename; private String sitename;
// title // title
private String label; private String label;
// text() // text()
private String url; private String url;
// ?? not mapped yet ?? // ?? not mapped yet ??
private String description; private String description;
// type // type
private Qualifier qualifier; private Qualifier qualifier;
// site internal identifier // site internal identifier
private String refidentifier; private String refidentifier;
// maps the oaf:reference/@query attribute // maps the oaf:reference/@query attribute
private String query; private String query;
// ExternalReferences might be also inferred // ExternalReferences might be also inferred
private DataInfo dataInfo; private DataInfo dataInfo;
public String getSitename() { public String getSitename() {
return sitename; return sitename;
} }
public void setSitename(String sitename) { public void setSitename(String sitename) {
this.sitename = sitename; this.sitename = sitename;
} }
public String getLabel() { public String getLabel() {
return label; return label;
} }
public void setLabel(String label) { public void setLabel(String label) {
this.label = label; this.label = label;
} }
public String getUrl() { public String getUrl() {
return url; return url;
} }
public void setUrl(String url) { public void setUrl(String url) {
this.url = url; this.url = url;
} }
public String getDescription() { public String getDescription() {
return description; return description;
} }
public void setDescription(String description) { public void setDescription(String description) {
this.description = description; this.description = description;
} }
public Qualifier getQualifier() { public Qualifier getQualifier() {
return qualifier; return qualifier;
} }
public void setQualifier(Qualifier qualifier) { public void setQualifier(Qualifier qualifier) {
this.qualifier = qualifier; this.qualifier = qualifier;
} }
public String getRefidentifier() { public String getRefidentifier() {
return refidentifier; return refidentifier;
} }
public void setRefidentifier(String refidentifier) { public void setRefidentifier(String refidentifier) {
this.refidentifier = refidentifier; this.refidentifier = refidentifier;
} }
public String getQuery() { public String getQuery() {
return query; return query;
} }
public void setQuery(String query) { public void setQuery(String query) {
this.query = query; this.query = query;
} }
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; return dataInfo;
} }
public void setDataInfo(DataInfo dataInfo) { public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo; this.dataInfo = dataInfo;
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
ExternalReference that = (ExternalReference) o; ExternalReference that = (ExternalReference) o;
return Objects.equals(sitename, that.sitename) return Objects.equals(sitename, that.sitename)
&& Objects.equals(label, that.label) && Objects.equals(label, that.label)
&& Objects.equals(url, that.url) && Objects.equals(url, that.url)
&& Objects.equals(description, that.description) && Objects.equals(description, that.description)
&& Objects.equals(qualifier, that.qualifier) && Objects.equals(qualifier, that.qualifier)
&& Objects.equals(refidentifier, that.refidentifier) && Objects.equals(refidentifier, that.refidentifier)
&& Objects.equals(query, that.query) && Objects.equals(query, that.query)
&& Objects.equals(dataInfo, that.dataInfo); && Objects.equals(dataInfo, that.dataInfo);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash( return Objects.hash(
sitename, label, url, description, qualifier, refidentifier, query, dataInfo); sitename, label, url, description, qualifier, refidentifier, query, dataInfo);
} }
} }

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

@ -4,71 +4,71 @@ import java.io.Serializable;
import java.util.Objects; import java.util.Objects;
public class ExtraInfo implements Serializable { 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 // json containing a Citation or Statistics
private String value; private String value;
public String getName() { public String getName() {
return name; return name;
} }
public void setName(String name) { public void setName(String name) {
this.name = name; this.name = name;
} }
public String getTypology() { public String getTypology() {
return typology; return typology;
} }
public void setTypology(String typology) { public void setTypology(String typology) {
this.typology = typology; this.typology = typology;
} }
public String getProvenance() { public String getProvenance() {
return provenance; return provenance;
} }
public void setProvenance(String provenance) { public void setProvenance(String provenance) {
this.provenance = provenance; this.provenance = provenance;
} }
public String getTrust() { public String getTrust() {
return trust; return trust;
} }
public void setTrust(String trust) { public void setTrust(String trust) {
this.trust = trust; this.trust = trust;
} }
public String getValue() { public String getValue() {
return value; return value;
} }
public void setValue(String value) { public void setValue(String value) {
this.value = value; this.value = value;
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
ExtraInfo extraInfo = (ExtraInfo) o; ExtraInfo extraInfo = (ExtraInfo) o;
return Objects.equals(name, extraInfo.name) return Objects.equals(name, extraInfo.name)
&& Objects.equals(typology, extraInfo.typology) && Objects.equals(typology, extraInfo.typology)
&& Objects.equals(provenance, extraInfo.provenance) && Objects.equals(provenance, extraInfo.provenance)
&& Objects.equals(trust, extraInfo.trust) && Objects.equals(trust, extraInfo.trust)
&& Objects.equals(value, extraInfo.value); && Objects.equals(value, extraInfo.value);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(name, typology, provenance, trust, value); return Objects.hash(name, typology, provenance, trust, value);
} }
} }

52
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Field.java
View File

@ -4,37 +4,37 @@ import java.io.Serializable;
public class Field<T> implements Serializable { public class Field<T> implements Serializable {
private T value; private T value;
private DataInfo dataInfo; private DataInfo dataInfo;
public T getValue() { public T getValue() {
return value; return value;
} }
public void setValue(T value) { public void setValue(T value) {
this.value = value; this.value = value;
} }
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; return dataInfo;
} }
public void setDataInfo(DataInfo dataInfo) { public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo; this.dataInfo = dataInfo;
} }
@Override @Override
public int hashCode() { public int hashCode() {
return getValue() == null ? 0 : getValue().hashCode(); return getValue() == null ? 0 : getValue().hashCode();
} }
@Override @Override
public boolean equals(Object obj) { public boolean equals(Object obj) {
if (this == obj) return true; if (this == obj) return true;
if (obj == null) return false; if (obj == null) return false;
if (getClass() != obj.getClass()) return false; if (getClass() != obj.getClass()) return false;
Field<T> other = (Field<T>) obj; Field<T> other = (Field<T>) obj;
return getValue().equals(other.getValue()); return getValue().equals(other.getValue());
} }
} }

92
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/GeoLocation.java
View File

@ -6,64 +6,64 @@ import org.apache.commons.lang3.StringUtils;
public class GeoLocation implements Serializable { 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() { public String getPoint() {
return point; return point;
} }
public void setPoint(String point) { public void setPoint(String point) {
this.point = point; this.point = point;
} }
public String getBox() { public String getBox() {
return box; return box;
} }
public void setBox(String box) { public void setBox(String box) {
this.box = box; this.box = box;
} }
public String getPlace() { public String getPlace() {
return place; return place;
} }
public void setPlace(String place) { public void setPlace(String place) {
this.place = place; this.place = place;
} }
@JsonIgnore @JsonIgnore
public boolean isBlank() { public boolean isBlank() {
return StringUtils.isBlank(point) && StringUtils.isBlank(box) && StringUtils.isBlank(place); return StringUtils.isBlank(point) && StringUtils.isBlank(box) && StringUtils.isBlank(place);
} }
public String toComparableString() { public String toComparableString() {
return isBlank() return isBlank()
? "" ? ""
: String.format( : String.format(
"%s::%s%s", "%s::%s%s",
point != null ? point.toLowerCase() : "", point != null ? point.toLowerCase() : "",
box != null ? box.toLowerCase() : "", box != null ? box.toLowerCase() : "",
place != null ? place.toLowerCase() : ""); place != null ? place.toLowerCase() : "");
} }
@Override @Override
public int hashCode() { public int hashCode() {
return toComparableString().hashCode(); return toComparableString().hashCode();
} }
@Override @Override
public boolean equals(Object obj) { public boolean equals(Object obj) {
if (this == obj) return true; if (this == obj) return true;
if (obj == null) return false; if (obj == null) return false;
if (getClass() != obj.getClass()) 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());
} }
} }

210
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
View File

@ -5,149 +5,143 @@ import java.util.List;
public class Instance implements Serializable { 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 // other research products specifc
private String distributionlocation; 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 // ( article | book ) processing charges. Defined here to cope with possible wrongly typed
// results // results
private Field<String> processingchargeamount; private Field<String> processingchargeamount;
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
// typed results // typed results
private Field<String> processingchargecurrency; private Field<String> processingchargecurrency;
private Field<String> refereed; // peer-review status private Field<String> refereed; // peer-review status
public Field<String> getLicense() { public Field<String> getLicense() {
return license; return license;
} }
public void setLicense(Field<String> license) { public void setLicense(Field<String> license) {
this.license = license; this.license = license;
} }
public Qualifier getAccessright() { public Qualifier getAccessright() {
return accessright; return accessright;
} }
public void setAccessright(Qualifier accessright) { public void setAccessright(Qualifier accessright) {
this.accessright = accessright; this.accessright = accessright;
} }
public Qualifier getInstancetype() { public Qualifier getInstancetype() {
return instancetype; return instancetype;
} }
public void setInstancetype(Qualifier instancetype) { public void setInstancetype(Qualifier instancetype) {
this.instancetype = instancetype; this.instancetype = instancetype;
} }
public KeyValue getHostedby() { public KeyValue getHostedby() {
return hostedby; return hostedby;
} }
public void setHostedby(KeyValue hostedby) { public void setHostedby(KeyValue hostedby) {
this.hostedby = hostedby; this.hostedby = hostedby;
} }
public List<String> getUrl() { public List<String> getUrl() {
return url; return url;
} }
public void setUrl(List<String> url) { public void setUrl(List<String> url) {
this.url = url; this.url = url;
} }
public String getDistributionlocation() { public String getDistributionlocation() {
return distributionlocation; return distributionlocation;
} }
public void setDistributionlocation(String distributionlocation) { public void setDistributionlocation(String distributionlocation) {
this.distributionlocation = distributionlocation; this.distributionlocation = distributionlocation;
} }
public KeyValue getCollectedfrom() { public KeyValue getCollectedfrom() {
return collectedfrom; return collectedfrom;
} }
public void setCollectedfrom(KeyValue collectedfrom) { public void setCollectedfrom(KeyValue collectedfrom) {
this.collectedfrom = collectedfrom; this.collectedfrom = collectedfrom;
} }
public Field<String> getDateofacceptance() { public Field<String> getDateofacceptance() {
return dateofacceptance; return dateofacceptance;
} }
public void setDateofacceptance(Field<String> dateofacceptance) { public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance; this.dateofacceptance = dateofacceptance;
} }
public Field<String> getProcessingchargeamount() { public Field<String> getProcessingchargeamount() {
return processingchargeamount; return processingchargeamount;
} }
public void setProcessingchargeamount(Field<String> processingchargeamount) { public void setProcessingchargeamount(Field<String> processingchargeamount) {
this.processingchargeamount = processingchargeamount; this.processingchargeamount = processingchargeamount;
} }
public Field<String> getProcessingchargecurrency() { public Field<String> getProcessingchargecurrency() {
return processingchargecurrency; return processingchargecurrency;
} }
public void setProcessingchargecurrency(Field<String> processingchargecurrency) { public void setProcessingchargecurrency(Field<String> processingchargecurrency) {
this.processingchargecurrency = processingchargecurrency; this.processingchargecurrency = processingchargecurrency;
} }
public Field<String> getRefereed() { public Field<String> getRefereed() {
return refereed; return refereed;
} }
public void setRefereed(Field<String> refereed) { public void setRefereed(Field<String> refereed) {
this.refereed = refereed; this.refereed = refereed;
} }
public String toComparableString() { public String toComparableString() {
return String.format( return String.format(
"%s::%s::%s::%s", "%s::%s::%s::%s",
hostedby != null && hostedby.getKey() != null hostedby != null && hostedby.getKey() != null ? hostedby.getKey().toLowerCase() : "",
? hostedby.getKey().toLowerCase() accessright != null && accessright.getClassid() != null ? accessright.getClassid() : "",
: "", instancetype != null && instancetype.getClassid() != null ? instancetype.getClassid() : "",
accessright != null && accessright.getClassid() != null url != null ? url : "");
? accessright.getClassid() }
: "",
instancetype != null && instancetype.getClassid() != null
? instancetype.getClassid()
: "",
url != null ? url : "");
}
@Override @Override
public int hashCode() { public int hashCode() {
return toComparableString().hashCode(); return toComparableString().hashCode();
} }
@Override @Override
public boolean equals(Object obj) { public boolean equals(Object obj) {
if (this == obj) return true; if (this == obj) return true;
if (obj == null) return false; if (obj == null) return false;
if (getClass() != obj.getClass()) 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());
} }
} }

236
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java
View File

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

89
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/KeyValue.java
View File

@ -6,63 +6,62 @@ import org.apache.commons.lang3.StringUtils;
public class KeyValue implements Serializable { 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() { public String getKey() {
return key; return key;
} }
public void setKey(String key) { public void setKey(String key) {
this.key = key; this.key = key;
} }
public String getValue() { public String getValue() {
return value; return value;
} }
public void setValue(String value) { public void setValue(String value) {
this.value = value; this.value = value;
} }
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; return dataInfo;
} }
public void setDataInfo(DataInfo dataInfo) { public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo; this.dataInfo = dataInfo;
} }
public String toComparableString() { public String toComparableString() {
return isBlank() return isBlank()
? "" ? ""
: String.format( : String.format(
"%s::%s", "%s::%s",
key != null ? key.toLowerCase() : "", key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : "");
value != null ? value.toLowerCase() : ""); }
}
@JsonIgnore @JsonIgnore
public boolean isBlank() { public boolean isBlank() {
return StringUtils.isBlank(key) && StringUtils.isBlank(value); return StringUtils.isBlank(key) && StringUtils.isBlank(value);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return toComparableString().hashCode(); return toComparableString().hashCode();
} }
@Override @Override
public boolean equals(Object obj) { public boolean equals(Object obj) {
if (this == obj) return true; if (this == obj) return true;
if (obj == null) return false; if (obj == null) return false;
if (getClass() != obj.getClass()) 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());
} }
} }

36
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java
View File

@ -5,26 +5,26 @@ import java.util.Objects;
public class OAIProvenance implements Serializable { public class OAIProvenance implements Serializable {
private OriginDescription originDescription; private OriginDescription originDescription;
public OriginDescription getOriginDescription() { public OriginDescription getOriginDescription() {
return originDescription; return originDescription;
} }
public void setOriginDescription(OriginDescription originDescription) { public void setOriginDescription(OriginDescription originDescription) {
this.originDescription = originDescription; this.originDescription = originDescription;
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
OAIProvenance that = (OAIProvenance) o; OAIProvenance that = (OAIProvenance) o;
return Objects.equals(originDescription, that.originDescription); return Objects.equals(originDescription, that.originDescription);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(originDescription); return Objects.hash(originDescription);
} }
} }

87
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
View File

@ -6,61 +6,60 @@ import java.util.Objects;
public abstract class Oaf implements Serializable { 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() { public List<KeyValue> getCollectedfrom() {
return collectedfrom; return collectedfrom;
} }
public void setCollectedfrom(List<KeyValue> collectedfrom) { public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom; this.collectedfrom = collectedfrom;
} }
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; return dataInfo;
} }
public void setDataInfo(DataInfo dataInfo) { public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo; this.dataInfo = dataInfo;
} }
public Long getLastupdatetimestamp() { public Long getLastupdatetimestamp() {
return lastupdatetimestamp; return lastupdatetimestamp;
} }
public void setLastupdatetimestamp(Long lastupdatetimestamp) { public void setLastupdatetimestamp(Long lastupdatetimestamp) {
this.lastupdatetimestamp = lastupdatetimestamp; this.lastupdatetimestamp = lastupdatetimestamp;
} }
public void mergeOAFDataInfo(Oaf e) { public void mergeOAFDataInfo(Oaf e) {
if (e.getDataInfo() != null && compareTrust(this, e) < 0) dataInfo = e.getDataInfo(); if (e.getDataInfo() != null && compareTrust(this, e) < 0) dataInfo = e.getDataInfo();
} }
protected String extractTrust(Oaf e) { protected String extractTrust(Oaf e) {
if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null) if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null) return "0.0";
return "0.0"; return e.getDataInfo().getTrust();
return e.getDataInfo().getTrust(); }
}
protected int compareTrust(Oaf a, Oaf b) { protected int compareTrust(Oaf a, Oaf b) {
return extractTrust(a).compareTo(extractTrust(b)); return extractTrust(a).compareTo(extractTrust(b));
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
Oaf oaf = (Oaf) o; Oaf oaf = (Oaf) o;
return Objects.equals(dataInfo, oaf.dataInfo) return Objects.equals(dataInfo, oaf.dataInfo)
&& Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); && Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(dataInfo, lastupdatetimestamp); return Objects.hash(dataInfo, lastupdatetimestamp);
} }
} }

178
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java
View File

@ -6,134 +6,118 @@ import java.util.stream.Collectors;
public abstract class OafEntity extends Oaf implements Serializable { 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() { public String getId() {
return id; return id;
} }
public void setId(String id) { public void setId(String id) {
this.id = id; this.id = id;
} }
public List<String> getOriginalId() { public List<String> getOriginalId() {
return originalId; return originalId;
} }
public void setOriginalId(List<String> originalId) { public void setOriginalId(List<String> originalId) {
this.originalId = originalId; this.originalId = originalId;
} }
public List<StructuredProperty> getPid() { public List<StructuredProperty> getPid() {
return pid; return pid;
} }
public void setPid(List<StructuredProperty> pid) { public void setPid(List<StructuredProperty> pid) {
this.pid = pid; this.pid = pid;
} }
public String getDateofcollection() { public String getDateofcollection() {
return dateofcollection; return dateofcollection;
} }
public void setDateofcollection(String dateofcollection) { public void setDateofcollection(String dateofcollection) {
this.dateofcollection = dateofcollection; this.dateofcollection = dateofcollection;
} }
public String getDateoftransformation() { public String getDateoftransformation() {
return dateoftransformation; return dateoftransformation;
} }
public void setDateoftransformation(String dateoftransformation) { public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation; this.dateoftransformation = dateoftransformation;
} }
public List<ExtraInfo> getExtraInfo() { public List<ExtraInfo> getExtraInfo() {
return extraInfo; return extraInfo;
} }
public void setExtraInfo(List<ExtraInfo> extraInfo) { public void setExtraInfo(List<ExtraInfo> extraInfo) {
this.extraInfo = extraInfo; this.extraInfo = extraInfo;
} }
public OAIProvenance getOaiprovenance() { public OAIProvenance getOaiprovenance() {
return oaiprovenance; return oaiprovenance;
} }
public void setOaiprovenance(OAIProvenance oaiprovenance) { public void setOaiprovenance(OAIProvenance oaiprovenance) {
this.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) if (e.getDateofcollection() != null && compareTrust(this, e) < 0)
dateofcollection = e.getDateofcollection(); dateofcollection = e.getDateofcollection();
if (e.getDateoftransformation() != null && compareTrust(this, e) < 0) if (e.getDateoftransformation() != null && compareTrust(this, e) < 0)
dateoftransformation = e.getDateoftransformation(); dateoftransformation = e.getDateoftransformation();
extraInfo = mergeLists(extraInfo, e.getExtraInfo()); extraInfo = mergeLists(extraInfo, e.getExtraInfo());
if (e.getOaiprovenance() != null && compareTrust(this, e) < 0) if (e.getOaiprovenance() != null && compareTrust(this, e) < 0)
oaiprovenance = e.getOaiprovenance(); 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) return Arrays.stream(lists)
.filter(Objects::nonNull) .filter(Objects::nonNull)
.flatMap(List::stream) .flatMap(List::stream)
.distinct() .distinct()
.collect(Collectors.toList()); .collect(Collectors.toList());
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false; if (!super.equals(o)) return false;
OafEntity oafEntity = (OafEntity) o; OafEntity oafEntity = (OafEntity) o;
return Objects.equals(id, oafEntity.id) return Objects.equals(id, oafEntity.id);
&& Objects.equals(originalId, oafEntity.originalId) }
&& Objects.equals(collectedfrom, oafEntity.collectedfrom)
&& Objects.equals(pid, oafEntity.pid)
&& Objects.equals(dateofcollection, oafEntity.dateofcollection)
&& Objects.equals(dateoftransformation, oafEntity.dateoftransformation)
&& Objects.equals(extraInfo, oafEntity.extraInfo)
&& Objects.equals(oaiprovenance, oafEntity.oaiprovenance);
}
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash( return Objects.hash(super.hashCode(), id);
super.hashCode(), }
id,
originalId,
collectedfrom,
pid,
dateofcollection,
dateoftransformation,
extraInfo,
oaiprovenance);
}
} }

457
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java
View File

@ -2,283 +2,224 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Organization extends OafEntity implements Serializable { 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() { public Field<String> getLegalshortname() {
return legalshortname; return legalshortname;
}
public void setLegalshortname(Field<String> legalshortname) {
this.legalshortname = legalshortname;
}
public Field<String> getLegalname() {
return legalname;
}
public void setLegalname(Field<String> legalname) {
this.legalname = legalname;
}
public List<Field<String>> getAlternativeNames() {
return alternativeNames;
}
public void setAlternativeNames(List<Field<String>> alternativeNames) {
this.alternativeNames = alternativeNames;
}
public Field<String> getWebsiteurl() {
return websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public Field<String> getLogourl() {
return logourl;
}
public void setLogourl(Field<String> logourl) {
this.logourl = logourl;
}
public Field<String> getEclegalbody() {
return eclegalbody;
}
public void setEclegalbody(Field<String> eclegalbody) {
this.eclegalbody = eclegalbody;
}
public Field<String> getEclegalperson() {
return eclegalperson;
}
public void setEclegalperson(Field<String> eclegalperson) {
this.eclegalperson = eclegalperson;
}
public Field<String> getEcnonprofit() {
return ecnonprofit;
}
public void setEcnonprofit(Field<String> ecnonprofit) {
this.ecnonprofit = ecnonprofit;
}
public Field<String> getEcresearchorganization() {
return ecresearchorganization;
}
public void setEcresearchorganization(Field<String> ecresearchorganization) {
this.ecresearchorganization = ecresearchorganization;
}
public Field<String> getEchighereducation() {
return echighereducation;
}
public void setEchighereducation(Field<String> echighereducation) {
this.echighereducation = echighereducation;
}
public Field<String> getEcinternationalorganizationeurinterests() {
return ecinternationalorganizationeurinterests;
}
public void setEcinternationalorganizationeurinterests(
Field<String> ecinternationalorganizationeurinterests) {
this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests;
}
public Field<String> getEcinternationalorganization() {
return ecinternationalorganization;
}
public void setEcinternationalorganization(Field<String> ecinternationalorganization) {
this.ecinternationalorganization = ecinternationalorganization;
}
public Field<String> getEcenterprise() {
return ecenterprise;
}
public void setEcenterprise(Field<String> ecenterprise) {
this.ecenterprise = ecenterprise;
}
public Field<String> getEcsmevalidated() {
return ecsmevalidated;
}
public void setEcsmevalidated(Field<String> ecsmevalidated) {
this.ecsmevalidated = ecsmevalidated;
}
public Field<String> getEcnutscode() {
return ecnutscode;
}
public void setEcnutscode(Field<String> ecnutscode) {
this.ecnutscode = ecnutscode;
}
public Qualifier getCountry() {
return country;
}
public void setCountry(Qualifier country) {
this.country = country;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Organization.class.isAssignableFrom(e.getClass())) {
return;
} }
public void setLegalshortname(Field<String> legalshortname) { final Organization o = (Organization) e;
this.legalshortname = legalshortname; legalshortname =
} o.getLegalshortname() != null && compareTrust(this, e) < 0
? o.getLegalshortname()
public Field<String> getLegalname() { : legalshortname;
return legalname; legalname =
} o.getLegalname() != null && compareTrust(this, e) < 0 ? o.getLegalname() : legalname;
alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames);
public void setLegalname(Field<String> legalname) { websiteurl =
this.legalname = legalname; o.getWebsiteurl() != null && compareTrust(this, e) < 0 ? o.getWebsiteurl() : websiteurl;
} logourl = o.getLogourl() != null && compareTrust(this, e) < 0 ? o.getLogourl() : logourl;
eclegalbody =
public List<Field<String>> getAlternativeNames() { o.getEclegalbody() != null && compareTrust(this, e) < 0 ? o.getEclegalbody() : eclegalbody;
return alternativeNames; eclegalperson =
} o.getEclegalperson() != null && compareTrust(this, e) < 0
? o.getEclegalperson()
public void setAlternativeNames(List<Field<String>> alternativeNames) { : eclegalperson;
this.alternativeNames = alternativeNames; ecnonprofit =
} o.getEcnonprofit() != null && compareTrust(this, e) < 0 ? o.getEcnonprofit() : ecnonprofit;
ecresearchorganization =
public Field<String> getWebsiteurl() { o.getEcresearchorganization() != null && compareTrust(this, e) < 0
return websiteurl; ? o.getEcresearchorganization()
} : ecresearchorganization;
echighereducation =
public void setWebsiteurl(Field<String> websiteurl) { o.getEchighereducation() != null && compareTrust(this, e) < 0
this.websiteurl = websiteurl; ? o.getEchighereducation()
} : echighereducation;
ecinternationalorganizationeurinterests =
public Field<String> getLogourl() { o.getEcinternationalorganizationeurinterests() != null && compareTrust(this, e) < 0
return logourl; ? o.getEcinternationalorganizationeurinterests()
} : ecinternationalorganizationeurinterests;
ecinternationalorganization =
public void setLogourl(Field<String> logourl) { o.getEcinternationalorganization() != null && compareTrust(this, e) < 0
this.logourl = logourl; ? o.getEcinternationalorganization()
} : ecinternationalorganization;
ecenterprise =
public Field<String> getEclegalbody() { o.getEcenterprise() != null && compareTrust(this, e) < 0
return eclegalbody; ? o.getEcenterprise()
} : ecenterprise;
ecsmevalidated =
public void setEclegalbody(Field<String> eclegalbody) { o.getEcsmevalidated() != null && compareTrust(this, e) < 0
this.eclegalbody = eclegalbody; ? o.getEcsmevalidated()
} : ecsmevalidated;
ecnutscode =
public Field<String> getEclegalperson() { o.getEcnutscode() != null && compareTrust(this, e) < 0 ? o.getEcnutscode() : ecnutscode;
return eclegalperson; country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country;
} mergeOAFDataInfo(o);
}
public void setEclegalperson(Field<String> eclegalperson) {
this.eclegalperson = eclegalperson;
}
public Field<String> getEcnonprofit() {
return ecnonprofit;
}
public void setEcnonprofit(Field<String> ecnonprofit) {
this.ecnonprofit = ecnonprofit;
}
public Field<String> getEcresearchorganization() {
return ecresearchorganization;
}
public void setEcresearchorganization(Field<String> ecresearchorganization) {
this.ecresearchorganization = ecresearchorganization;
}
public Field<String> getEchighereducation() {
return echighereducation;
}
public void setEchighereducation(Field<String> echighereducation) {
this.echighereducation = echighereducation;
}
public Field<String> getEcinternationalorganizationeurinterests() {
return ecinternationalorganizationeurinterests;
}
public void setEcinternationalorganizationeurinterests(
Field<String> ecinternationalorganizationeurinterests) {
this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests;
}
public Field<String> getEcinternationalorganization() {
return ecinternationalorganization;
}
public void setEcinternationalorganization(Field<String> ecinternationalorganization) {
this.ecinternationalorganization = ecinternationalorganization;
}
public Field<String> getEcenterprise() {
return ecenterprise;
}
public void setEcenterprise(Field<String> ecenterprise) {
this.ecenterprise = ecenterprise;
}
public Field<String> getEcsmevalidated() {
return ecsmevalidated;
}
public void setEcsmevalidated(Field<String> ecsmevalidated) {
this.ecsmevalidated = ecsmevalidated;
}
public Field<String> getEcnutscode() {
return ecnutscode;
}
public void setEcnutscode(Field<String> ecnutscode) {
this.ecnutscode = ecnutscode;
}
public Qualifier getCountry() {
return country;
}
public void setCountry(Qualifier country) {
this.country = country;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
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);
}
@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;
Organization that = (Organization) o;
return Objects.equals(legalshortname, that.legalshortname)
&& Objects.equals(legalname, that.legalname)
&& Objects.equals(alternativeNames, that.alternativeNames)
&& Objects.equals(websiteurl, that.websiteurl)
&& Objects.equals(logourl, that.logourl)
&& Objects.equals(eclegalbody, that.eclegalbody)
&& Objects.equals(eclegalperson, that.eclegalperson)
&& Objects.equals(ecnonprofit, that.ecnonprofit)
&& Objects.equals(ecresearchorganization, that.ecresearchorganization)
&& Objects.equals(echighereducation, that.echighereducation)
&& Objects.equals(
ecinternationalorganizationeurinterests,
that.ecinternationalorganizationeurinterests)
&& Objects.equals(ecinternationalorganization, that.ecinternationalorganization)
&& Objects.equals(ecenterprise, that.ecenterprise)
&& Objects.equals(ecsmevalidated, that.ecsmevalidated)
&& Objects.equals(ecnutscode, that.ecnutscode)
&& Objects.equals(country, that.country);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
legalshortname,
legalname,
alternativeNames,
websiteurl,
logourl,
eclegalbody,
eclegalperson,
ecnonprofit,
ecresearchorganization,
echighereducation,
ecinternationalorganizationeurinterests,
ecinternationalorganization,
ecenterprise,
ecsmevalidated,
ecnutscode,
country);
}
} }

117
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java
View File

@ -5,82 +5,81 @@ import java.util.Objects;
public class OriginDescription implements Serializable { 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() { public String getHarvestDate() {
return harvestDate; return harvestDate;
} }
public void setHarvestDate(String harvestDate) { public void setHarvestDate(String harvestDate) {
this.harvestDate = harvestDate; this.harvestDate = harvestDate;
} }
public Boolean getAltered() { public Boolean getAltered() {
return altered; return altered;
} }
public void setAltered(Boolean altered) { public void setAltered(Boolean altered) {
this.altered = altered; this.altered = altered;
} }
public String getBaseURL() { public String getBaseURL() {
return baseURL; return baseURL;
} }
public void setBaseURL(String baseURL) { public void setBaseURL(String baseURL) {
this.baseURL = baseURL; this.baseURL = baseURL;
} }
public String getIdentifier() { public String getIdentifier() {
return identifier; return identifier;
} }
public void setIdentifier(String identifier) { public void setIdentifier(String identifier) {
this.identifier = identifier; this.identifier = identifier;
} }
public String getDatestamp() { public String getDatestamp() {
return datestamp; return datestamp;
} }
public void setDatestamp(String datestamp) { public void setDatestamp(String datestamp) {
this.datestamp = datestamp; this.datestamp = datestamp;
} }
public String getMetadataNamespace() { public String getMetadataNamespace() {
return metadataNamespace; return metadataNamespace;
} }
public void setMetadataNamespace(String metadataNamespace) { public void setMetadataNamespace(String metadataNamespace) {
this.metadataNamespace = metadataNamespace; this.metadataNamespace = metadataNamespace;
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false; if (o == null || getClass() != o.getClass()) return false;
OriginDescription that = (OriginDescription) o; OriginDescription that = (OriginDescription) o;
return Objects.equals(harvestDate, that.harvestDate) return Objects.equals(harvestDate, that.harvestDate)
&& Objects.equals(altered, that.altered) && Objects.equals(altered, that.altered)
&& Objects.equals(baseURL, that.baseURL) && Objects.equals(baseURL, that.baseURL)
&& Objects.equals(identifier, that.identifier) && Objects.equals(identifier, that.identifier)
&& Objects.equals(datestamp, that.datestamp) && Objects.equals(datestamp, that.datestamp)
&& Objects.equals(metadataNamespace, that.metadataNamespace); && Objects.equals(metadataNamespace, that.metadataNamespace);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash( return Objects.hash(harvestDate, altered, baseURL, identifier, datestamp, metadataNamespace);
harvestDate, altered, baseURL, identifier, datestamp, metadataNamespace); }
}
} }

100
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java
View File

@ -1,70 +1,58 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class OtherResearchProduct extends Result implements Serializable { 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 List<Field<String>> getContactperson() { public OtherResearchProduct() {
return contactperson; setResulttype(ModelConstants.ORP_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getContactperson() {
return contactperson;
}
public void setContactperson(List<Field<String>> contactperson) {
this.contactperson = contactperson;
}
public List<Field<String>> getContactgroup() {
return contactgroup;
}
public void setContactgroup(List<Field<String>> contactgroup) {
this.contactgroup = contactgroup;
}
public List<Field<String>> getTool() {
return tool;
}
public void setTool(List<Field<String>> tool) {
this.tool = tool;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())) {
return;
} }
public void setContactperson(List<Field<String>> contactperson) { OtherResearchProduct o = (OtherResearchProduct) e;
this.contactperson = contactperson;
}
public List<Field<String>> getContactgroup() { contactperson = mergeLists(contactperson, o.getContactperson());
return contactgroup; contactgroup = mergeLists(contactgroup, o.getContactgroup());
} tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e);
public void setContactgroup(List<Field<String>> contactgroup) { }
this.contactgroup = contactgroup;
}
public List<Field<String>> getTool() {
return tool;
}
public void setTool(List<Field<String>> tool) {
this.tool = tool;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())) {
return;
}
OtherResearchProduct o = (OtherResearchProduct) e;
contactperson = mergeLists(contactperson, o.getContactperson());
contactgroup = mergeLists(contactgroup, o.getContactgroup());
tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e);
}
@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;
OtherResearchProduct that = (OtherResearchProduct) o;
return Objects.equals(contactperson, that.contactperson)
&& Objects.equals(contactgroup, that.contactgroup)
&& Objects.equals(tool, that.tool);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), contactperson, contactgroup, tool);
}
} }

686
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java
View File

@ -2,420 +2,338 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Project extends OafEntity implements Serializable { 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() { public Field<String> getWebsiteurl() {
return websiteurl; return websiteurl;
}
public void setWebsiteurl(Field<String> websiteurl) {
this.websiteurl = websiteurl;
}
public Field<String> getCode() {
return code;
}
public void setCode(Field<String> code) {
this.code = code;
}
public Field<String> getAcronym() {
return acronym;
}
public void setAcronym(Field<String> acronym) {
this.acronym = acronym;
}
public Field<String> getTitle() {
return title;
}
public void setTitle(Field<String> title) {
this.title = title;
}
public Field<String> getStartdate() {
return startdate;
}
public void setStartdate(Field<String> startdate) {
this.startdate = startdate;
}
public Field<String> getEnddate() {
return enddate;
}
public void setEnddate(Field<String> enddate) {
this.enddate = enddate;
}
public Field<String> getCallidentifier() {
return callidentifier;
}
public void setCallidentifier(Field<String> callidentifier) {
this.callidentifier = callidentifier;
}
public Field<String> getKeywords() {
return keywords;
}
public void setKeywords(Field<String> keywords) {
this.keywords = keywords;
}
public Field<String> getDuration() {
return duration;
}
public void setDuration(Field<String> duration) {
this.duration = duration;
}
public Field<String> getEcsc39() {
return ecsc39;
}
public void setEcsc39(Field<String> ecsc39) {
this.ecsc39 = ecsc39;
}
public Field<String> getOamandatepublications() {
return oamandatepublications;
}
public void setOamandatepublications(Field<String> oamandatepublications) {
this.oamandatepublications = oamandatepublications;
}
public Field<String> getEcarticle29_3() {
return ecarticle29_3;
}
public void setEcarticle29_3(Field<String> ecarticle29_3) {
this.ecarticle29_3 = ecarticle29_3;
}
public List<StructuredProperty> getSubjects() {
return subjects;
}
public void setSubjects(List<StructuredProperty> subjects) {
this.subjects = subjects;
}
public List<Field<String>> getFundingtree() {
return fundingtree;
}
public void setFundingtree(List<Field<String>> fundingtree) {
this.fundingtree = fundingtree;
}
public Qualifier getContracttype() {
return contracttype;
}
public void setContracttype(Qualifier contracttype) {
this.contracttype = contracttype;
}
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;
} }
public void setWebsiteurl(Field<String> websiteurl) { Project p = (Project) e;
this.websiteurl = websiteurl;
}
public Field<String> getCode() { websiteurl =
return code; 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;
public void setCode(Field<String> code) { title = p.getTitle() != null && compareTrust(this, e) < 0 ? p.getTitle() : title;
this.code = code; startdate =
} p.getStartdate() != null && compareTrust(this, e) < 0 ? p.getStartdate() : startdate;
enddate = p.getEnddate() != null && compareTrust(this, e) < 0 ? p.getEnddate() : enddate;
public Field<String> getAcronym() { callidentifier =
return acronym; p.getCallidentifier() != null && compareTrust(this, e) < 0
} ? p.getCallidentifier()
: callidentifier;
public void setAcronym(Field<String> acronym) { keywords = p.getKeywords() != null && compareTrust(this, e) < 0 ? p.getKeywords() : keywords;
this.acronym = acronym; duration = p.getDuration() != null && compareTrust(this, e) < 0 ? p.getDuration() : duration;
} ecsc39 = p.getEcsc39() != null && compareTrust(this, e) < 0 ? p.getEcsc39() : ecsc39;
oamandatepublications =
public Field<String> getTitle() { p.getOamandatepublications() != null && compareTrust(this, e) < 0
return title; ? p.getOamandatepublications()
} : oamandatepublications;
ecarticle29_3 =
public void setTitle(Field<String> title) { p.getEcarticle29_3() != null && compareTrust(this, e) < 0
this.title = title; ? p.getEcarticle29_3()
} : ecarticle29_3;
subjects = mergeLists(subjects, p.getSubjects());
public Field<String> getStartdate() { fundingtree = mergeLists(fundingtree, p.getFundingtree());
return startdate; contracttype =
} p.getContracttype() != null && compareTrust(this, e) < 0
? p.getContracttype()
public void setStartdate(Field<String> startdate) { : contracttype;
this.startdate = startdate; optional1 =
} p.getOptional1() != null && compareTrust(this, e) < 0 ? p.getOptional1() : optional1;
optional2 =
public Field<String> getEnddate() { p.getOptional2() != null && compareTrust(this, e) < 0 ? p.getOptional2() : optional2;
return enddate; jsonextrainfo =
} p.getJsonextrainfo() != null && compareTrust(this, e) < 0
? p.getJsonextrainfo()
public void setEnddate(Field<String> enddate) { : jsonextrainfo;
this.enddate = enddate; contactfullname =
} p.getContactfullname() != null && compareTrust(this, e) < 0
? p.getContactfullname()
public Field<String> getCallidentifier() { : contactfullname;
return callidentifier; contactfax =
} p.getContactfax() != null && compareTrust(this, e) < 0 ? p.getContactfax() : contactfax;
contactphone =
public void setCallidentifier(Field<String> callidentifier) { p.getContactphone() != null && compareTrust(this, e) < 0
this.callidentifier = callidentifier; ? p.getContactphone()
} : contactphone;
contactemail =
public Field<String> getKeywords() { p.getContactemail() != null && compareTrust(this, e) < 0
return keywords; ? p.getContactemail()
} : contactemail;
summary = p.getSummary() != null && compareTrust(this, e) < 0 ? p.getSummary() : summary;
public void setKeywords(Field<String> keywords) { currency = p.getCurrency() != null && compareTrust(this, e) < 0 ? p.getCurrency() : currency;
this.keywords = keywords; totalcost =
} p.getTotalcost() != null && compareTrust(this, e) < 0 ? p.getTotalcost() : totalcost;
fundedamount =
public Field<String> getDuration() { p.getFundedamount() != null && compareTrust(this, e) < 0
return duration; ? p.getFundedamount()
} : fundedamount;
mergeOAFDataInfo(e);
public void setDuration(Field<String> duration) { }
this.duration = duration;
}
public Field<String> getEcsc39() {
return ecsc39;
}
public void setEcsc39(Field<String> ecsc39) {
this.ecsc39 = ecsc39;
}
public Field<String> getOamandatepublications() {
return oamandatepublications;
}
public void setOamandatepublications(Field<String> oamandatepublications) {
this.oamandatepublications = oamandatepublications;
}
public Field<String> getEcarticle29_3() {
return ecarticle29_3;
}
public void setEcarticle29_3(Field<String> ecarticle29_3) {
this.ecarticle29_3 = ecarticle29_3;
}
public List<StructuredProperty> getSubjects() {
return subjects;
}
public void setSubjects(List<StructuredProperty> subjects) {
this.subjects = subjects;
}
public List<Field<String>> getFundingtree() {
return fundingtree;
}
public void setFundingtree(List<Field<String>> fundingtree) {
this.fundingtree = fundingtree;
}
public Qualifier getContracttype() {
return contracttype;
}
public void setContracttype(Qualifier contracttype) {
this.contracttype = contracttype;
}
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);
}
@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;
Project project = (Project) o;
return Objects.equals(websiteurl, project.websiteurl)
&& Objects.equals(code, project.code)
&& Objects.equals(acronym, project.acronym)
&& Objects.equals(title, project.title)
&& Objects.equals(startdate, project.startdate)
&& Objects.equals(enddate, project.enddate)
&& Objects.equals(callidentifier, project.callidentifier)
&& Objects.equals(keywords, project.keywords)
&& Objects.equals(duration, project.duration)
&& Objects.equals(ecsc39, project.ecsc39)
&& Objects.equals(oamandatepublications, project.oamandatepublications)
&& Objects.equals(ecarticle29_3, project.ecarticle29_3)
&& Objects.equals(subjects, project.subjects)
&& Objects.equals(fundingtree, project.fundingtree)
&& Objects.equals(contracttype, project.contracttype)
&& Objects.equals(optional1, project.optional1)
&& Objects.equals(optional2, project.optional2)
&& Objects.equals(jsonextrainfo, project.jsonextrainfo)
&& Objects.equals(contactfullname, project.contactfullname)
&& Objects.equals(contactfax, project.contactfax)
&& Objects.equals(contactphone, project.contactphone)
&& Objects.equals(contactemail, project.contactemail)
&& Objects.equals(summary, project.summary)
&& Objects.equals(currency, project.currency)
&& Objects.equals(totalcost, project.totalcost)
&& Objects.equals(fundedamount, project.fundedamount);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
websiteurl,
code,
acronym,
title,
startdate,
enddate,
callidentifier,
keywords,
duration,
ecsc39,
oamandatepublications,
ecarticle29_3,
subjects,
fundingtree,
contracttype,
optional1,
optional2,
jsonextrainfo,
contactfullname,
contactfax,
contactphone,
contactemail,
summary,
currency,
totalcost,
fundedamount);
}
} }

60
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java
View File

@ -1,46 +1,36 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.Objects;
public class Publication extends Result implements Serializable { public class Publication extends Result implements Serializable {
// publication specific // publication specific
private Journal journal; private Journal journal;
public Journal getJournal() { public Publication() {
return journal; setResulttype(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE);
}
public Journal getJournal() {
return journal;
}
public void setJournal(Journal journal) {
this.journal = journal;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Publication.class.isAssignableFrom(e.getClass())) {
return;
} }
public void setJournal(Journal journal) { Publication p = (Publication) e;
this.journal = journal;
}
@Override if (p.getJournal() != null && compareTrust(this, e) < 0) journal = p.getJournal();
public void mergeFrom(OafEntity e) { mergeOAFDataInfo(e);
super.mergeFrom(e); }
if (!Publication.class.isAssignableFrom(e.getClass())) {
return;
}
Publication p = (Publication) e;
if (p.getJournal() != null && compareTrust(this, e) < 0) journal = p.getJournal();
mergeOAFDataInfo(e);
}
@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;
Publication that = (Publication) o;
return Objects.equals(journal, that.journal);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), journal);
}
} }

114
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Qualifier.java
View File

@ -6,75 +6,75 @@ import org.apache.commons.lang3.StringUtils;
public class Qualifier implements Serializable { public class Qualifier implements Serializable {
private String classid; private String classid;
private String classname; private String classname;
private String schemeid; private String schemeid;
private String schemename; private String schemename;
public String getClassid() { public String getClassid() {
return classid; return classid;
} }
public void setClassid(String classid) { public void setClassid(String classid) {
this.classid = classid; this.classid = classid;
} }
public String getClassname() { public String getClassname() {
return classname; return classname;
} }
public void setClassname(String classname) { public void setClassname(String classname) {
this.classname = classname; this.classname = classname;
} }
public String getSchemeid() { public String getSchemeid() {
return schemeid; return schemeid;
} }
public void setSchemeid(String schemeid) { public void setSchemeid(String schemeid) {
this.schemeid = schemeid; this.schemeid = schemeid;
} }
public String getSchemename() { public String getSchemename() {
return schemename; return schemename;
} }
public void setSchemename(String schemename) { public void setSchemename(String schemename) {
this.schemename = schemename; this.schemename = schemename;
} }
public String toComparableString() { public String toComparableString() {
return isBlank() return isBlank()
? "" ? ""
: String.format( : String.format(
"%s::%s::%s::%s", "%s::%s::%s::%s",
classid != null ? classid : "", classid != null ? classid : "",
classname != null ? classname : "", classname != null ? classname : "",
schemeid != null ? schemeid : "", schemeid != null ? schemeid : "",
schemename != null ? schemename : ""); schemename != null ? schemename : "");
} }
@JsonIgnore @JsonIgnore
public boolean isBlank() { public boolean isBlank() {
return StringUtils.isBlank(classid) return StringUtils.isBlank(classid)
&& StringUtils.isBlank(classname) && StringUtils.isBlank(classname)
&& StringUtils.isBlank(schemeid) && StringUtils.isBlank(schemeid)
&& StringUtils.isBlank(schemename); && StringUtils.isBlank(schemename);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return toComparableString().hashCode(); return toComparableString().hashCode();
} }
@Override @Override
public boolean equals(Object obj) { public boolean equals(Object obj) {
if (this == obj) return true; if (this == obj) return true;
if (obj == null) return false; if (obj == null) return false;
if (getClass() != obj.getClass()) 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());
} }
} }

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

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

570
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -3,343 +3,289 @@ package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.Comparator; import java.util.Comparator;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Result extends OafEntity implements Serializable { public class Result extends OafEntity implements Serializable {
private List<Author> author; private List<Author> author;
// resulttype allows subclassing results into publications | datasets | software // resulttype allows subclassing results into publications | datasets | software
private Qualifier resulttype; private Qualifier resulttype;
// common fields // common fields
private Qualifier language; 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() { public List<Author> getAuthor() {
return author; return author;
}
public void setAuthor(List<Author> author) {
this.author = author;
}
public Qualifier getResulttype() {
return resulttype;
}
public void setResulttype(Qualifier resulttype) {
this.resulttype = resulttype;
}
public Qualifier getLanguage() {
return language;
}
public void setLanguage(Qualifier language) {
this.language = language;
}
public List<Country> getCountry() {
return country;
}
public void setCountry(List<Country> country) {
this.country = country;
}
public List<StructuredProperty> getSubject() {
return subject;
}
public void setSubject(List<StructuredProperty> subject) {
this.subject = subject;
}
public List<StructuredProperty> getTitle() {
return title;
}
public void setTitle(List<StructuredProperty> title) {
this.title = title;
}
public List<StructuredProperty> getRelevantdate() {
return relevantdate;
}
public void setRelevantdate(List<StructuredProperty> relevantdate) {
this.relevantdate = relevantdate;
}
public List<Field<String>> getDescription() {
return description;
}
public void setDescription(List<Field<String>> description) {
this.description = description;
}
public Field<String> getDateofacceptance() {
return dateofacceptance;
}
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public Field<String> getPublisher() {
return publisher;
}
public void setPublisher(Field<String> publisher) {
this.publisher = publisher;
}
public Field<String> getEmbargoenddate() {
return embargoenddate;
}
public void setEmbargoenddate(Field<String> embargoenddate) {
this.embargoenddate = embargoenddate;
}
public List<Field<String>> getSource() {
return source;
}
public void setSource(List<Field<String>> source) {
this.source = source;
}
public List<Field<String>> getFulltext() {
return fulltext;
}
public void setFulltext(List<Field<String>> fulltext) {
this.fulltext = fulltext;
}
public List<Field<String>> getFormat() {
return format;
}
public void setFormat(List<Field<String>> format) {
this.format = format;
}
public List<Field<String>> getContributor() {
return contributor;
}
public void setContributor(List<Field<String>> contributor) {
this.contributor = contributor;
}
public Qualifier getResourcetype() {
return resourcetype;
}
public void setResourcetype(Qualifier resourcetype) {
this.resourcetype = resourcetype;
}
public List<Field<String>> getCoverage() {
return coverage;
}
public void setCoverage(List<Field<String>> coverage) {
this.coverage = coverage;
}
public Qualifier getBestaccessright() {
return bestaccessright;
}
public void setBestaccessright(Qualifier bestaccessright) {
this.bestaccessright = bestaccessright;
}
public List<Context> getContext() {
return context;
}
public void setContext(List<Context> context) {
this.context = context;
}
public List<ExternalReference> getExternalReference() {
return externalReference;
}
public void setExternalReference(List<ExternalReference> externalReference) {
this.externalReference = externalReference;
}
public List<Instance> getInstance() {
return instance;
}
public void setInstance(List<Instance> instance) {
this.instance = instance;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Result.class.isAssignableFrom(e.getClass())) {
return;
} }
public void setAuthor(List<Author> author) { Result r = (Result) e;
this.author = author;
} instance = mergeLists(instance, r.getInstance());
public Qualifier getResulttype() { if (r.getBestaccessright() != null && compareTrust(this, r) < 0)
return resulttype; bestaccessright = r.getBestaccessright();
}
if (r.getResulttype() != null && compareTrust(this, r) < 0) resulttype = r.getResulttype();
public void setResulttype(Qualifier resulttype) {
this.resulttype = resulttype; if (r.getLanguage() != null && compareTrust(this, r) < 0) language = r.getLanguage();
}
country = mergeLists(country, r.getCountry());
public Qualifier getLanguage() {
return language; subject = mergeLists(subject, r.getSubject());
}
title = mergeLists(title, r.getTitle());
public void setLanguage(Qualifier language) {
this.language = language; relevantdate = mergeLists(relevantdate, r.getRelevantdate());
}
description = longestLists(description, r.getDescription());
public List<Country> getCountry() {
return country; if (r.getPublisher() != null && compareTrust(this, r) < 0) publisher = r.getPublisher();
}
if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0)
public void setCountry(List<Country> country) { embargoenddate = r.getEmbargoenddate();
this.country = country;
} source = mergeLists(source, r.getSource());
public List<StructuredProperty> getSubject() { fulltext = mergeLists(fulltext, r.getFulltext());
return subject;
} format = mergeLists(format, r.getFormat());
public void setSubject(List<StructuredProperty> subject) { contributor = mergeLists(contributor, r.getContributor());
this.subject = subject;
} if (r.getResourcetype() != null) resourcetype = r.getResourcetype();
public List<StructuredProperty> getTitle() { coverage = mergeLists(coverage, r.getCoverage());
return title;
} context = mergeLists(context, r.getContext());
public void setTitle(List<StructuredProperty> title) { externalReference = mergeLists(externalReference, r.getExternalReference());
this.title = title; }
}
private List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
public List<StructuredProperty> getRelevantdate() { if (a == null || b == null) return a == null ? b : a;
return relevantdate; if (a.size() == b.size()) {
} int msa =
a.stream()
public void setRelevantdate(List<StructuredProperty> relevantdate) { .filter(i -> i.getValue() != null)
this.relevantdate = relevantdate; .map(i -> i.getValue().length())
} .max(Comparator.naturalOrder())
.orElse(0);
public List<Field<String>> getDescription() { int msb =
return description; b.stream()
} .filter(i -> i.getValue() != null)
.map(i -> i.getValue().length())
public void setDescription(List<Field<String>> description) { .max(Comparator.naturalOrder())
this.description = description; .orElse(0);
} return msa > msb ? a : b;
public Field<String> getDateofacceptance() {
return dateofacceptance;
}
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public Field<String> getPublisher() {
return publisher;
}
public void setPublisher(Field<String> publisher) {
this.publisher = publisher;
}
public Field<String> getEmbargoenddate() {
return embargoenddate;
}
public void setEmbargoenddate(Field<String> embargoenddate) {
this.embargoenddate = embargoenddate;
}
public List<Field<String>> getSource() {
return source;
}
public void setSource(List<Field<String>> source) {
this.source = source;
}
public List<Field<String>> getFulltext() {
return fulltext;
}
public void setFulltext(List<Field<String>> fulltext) {
this.fulltext = fulltext;
}
public List<Field<String>> getFormat() {
return format;
}
public void setFormat(List<Field<String>> format) {
this.format = format;
}
public List<Field<String>> getContributor() {
return contributor;
}
public void setContributor(List<Field<String>> contributor) {
this.contributor = contributor;
}
public Qualifier getResourcetype() {
return resourcetype;
}
public void setResourcetype(Qualifier resourcetype) {
this.resourcetype = resourcetype;
}
public List<Field<String>> getCoverage() {
return coverage;
}
public void setCoverage(List<Field<String>> coverage) {
this.coverage = coverage;
}
public Qualifier getBestaccessright() {
return bestaccessright;
}
public void setBestaccessright(Qualifier bestaccessright) {
this.bestaccessright = bestaccessright;
}
public List<Context> getContext() {
return context;
}
public void setContext(List<Context> context) {
this.context = context;
}
public List<ExternalReference> getExternalReference() {
return externalReference;
}
public void setExternalReference(List<ExternalReference> externalReference) {
this.externalReference = externalReference;
}
public List<Instance> getInstance() {
return instance;
}
public void setInstance(List<Instance> instance) {
this.instance = instance;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Result.class.isAssignableFrom(e.getClass())) {
return;
}
Result r = (Result) e;
instance = mergeLists(instance, r.getInstance());
if (r.getResulttype() != null && compareTrust(this, r) < 0) resulttype = r.getResulttype();
if (r.getLanguage() != null && compareTrust(this, r) < 0) language = r.getLanguage();
country = mergeLists(country, r.getCountry());
subject = mergeLists(subject, r.getSubject());
title = mergeLists(title, r.getTitle());
relevantdate = mergeLists(relevantdate, r.getRelevantdate());
description = longestLists(description, r.getDescription());
if (r.getPublisher() != null && compareTrust(this, r) < 0) publisher = r.getPublisher();
if (r.getEmbargoenddate() != null && compareTrust(this, r) < 0)
embargoenddate = r.getEmbargoenddate();
source = mergeLists(source, r.getSource());
fulltext = mergeLists(fulltext, r.getFulltext());
format = mergeLists(format, r.getFormat());
contributor = mergeLists(contributor, r.getContributor());
if (r.getResourcetype() != null) resourcetype = r.getResourcetype();
coverage = mergeLists(coverage, r.getCoverage());
context = mergeLists(context, r.getContext());
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;
}
@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;
Result result = (Result) o;
return Objects.equals(author, result.author)
&& Objects.equals(resulttype, result.resulttype)
&& Objects.equals(language, result.language)
&& Objects.equals(country, result.country)
&& Objects.equals(subject, result.subject)
&& Objects.equals(title, result.title)
&& Objects.equals(relevantdate, result.relevantdate)
&& Objects.equals(description, result.description)
&& Objects.equals(dateofacceptance, result.dateofacceptance)
&& Objects.equals(publisher, result.publisher)
&& Objects.equals(embargoenddate, result.embargoenddate)
&& Objects.equals(source, result.source)
&& Objects.equals(fulltext, result.fulltext)
&& Objects.equals(format, result.format)
&& Objects.equals(contributor, result.contributor)
&& Objects.equals(resourcetype, result.resourcetype)
&& Objects.equals(coverage, result.coverage)
&& Objects.equals(bestaccessright, result.bestaccessright)
&& Objects.equals(context, result.context)
&& Objects.equals(externalReference, result.externalReference)
&& Objects.equals(instance, result.instance);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
author,
resulttype,
language,
country,
subject,
title,
relevantdate,
description,
dateofacceptance,
publisher,
embargoenddate,
source,
fulltext,
format,
contributor,
resourcetype,
coverage,
bestaccessright,
context,
externalReference,
instance);
} }
return a.size() > b.size() ? a : b;
}
} }

138
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -1,96 +1,78 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Software extends Result implements Serializable { 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 List<Field<String>> getDocumentationUrl() { public Software() {
return documentationUrl; setResulttype(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getDocumentationUrl() {
return documentationUrl;
}
public void setDocumentationUrl(List<Field<String>> documentationUrl) {
this.documentationUrl = documentationUrl;
}
public List<StructuredProperty> getLicense() {
return license;
}
public void setLicense(List<StructuredProperty> license) {
this.license = license;
}
public Field<String> getCodeRepositoryUrl() {
return codeRepositoryUrl;
}
public void setCodeRepositoryUrl(Field<String> codeRepositoryUrl) {
this.codeRepositoryUrl = codeRepositoryUrl;
}
public Qualifier getProgrammingLanguage() {
return programmingLanguage;
}
public void setProgrammingLanguage(Qualifier programmingLanguage) {
this.programmingLanguage = programmingLanguage;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Software.class.isAssignableFrom(e.getClass())) {
return;
} }
public void setDocumentationUrl(List<Field<String>> documentationUrl) { final Software s = (Software) e;
this.documentationUrl = documentationUrl; documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl());
}
public List<StructuredProperty> getLicense() { license = mergeLists(license, s.getLicense());
return license;
}
public void setLicense(List<StructuredProperty> license) { codeRepositoryUrl =
this.license = license; s.getCodeRepositoryUrl() != null && compareTrust(this, s) < 0
} ? s.getCodeRepositoryUrl()
: codeRepositoryUrl;
public Field<String> getCodeRepositoryUrl() { programmingLanguage =
return codeRepositoryUrl; s.getProgrammingLanguage() != null && compareTrust(this, s) < 0
} ? s.getProgrammingLanguage()
: programmingLanguage;
public void setCodeRepositoryUrl(Field<String> codeRepositoryUrl) { mergeOAFDataInfo(e);
this.codeRepositoryUrl = codeRepositoryUrl; }
}
public Qualifier getProgrammingLanguage() {
return programmingLanguage;
}
public void setProgrammingLanguage(Qualifier programmingLanguage) {
this.programmingLanguage = programmingLanguage;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
if (!Software.class.isAssignableFrom(e.getClass())) {
return;
}
final Software s = (Software) e;
documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl());
license = mergeLists(license, s.getLicense());
codeRepositoryUrl =
s.getCodeRepositoryUrl() != null && compareTrust(this, s) < 0
? s.getCodeRepositoryUrl()
: codeRepositoryUrl;
programmingLanguage =
s.getProgrammingLanguage() != null && compareTrust(this, s) < 0
? s.getProgrammingLanguage()
: programmingLanguage;
mergeOAFDataInfo(e);
}
@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;
Software software = (Software) o;
return Objects.equals(documentationUrl, software.documentationUrl)
&& Objects.equals(license, software.license)
&& Objects.equals(codeRepositoryUrl, software.codeRepositoryUrl)
&& Objects.equals(programmingLanguage, software.programmingLanguage);
}
@Override
public int hashCode() {
return Objects.hash(
super.hashCode(),
documentationUrl,
license,
codeRepositoryUrl,
programmingLanguage);
}
} }

72
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java
View File

@ -4,53 +4,53 @@ import java.io.Serializable;
public class StructuredProperty implements 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() { public String getValue() {
return value; return value;
} }
public void setValue(String value) { public void setValue(String value) {
this.value = value; this.value = value;
} }
public Qualifier getQualifier() { public Qualifier getQualifier() {
return qualifier; return qualifier;
} }
public void setQualifier(Qualifier qualifier) { public void setQualifier(Qualifier qualifier) {
this.qualifier = qualifier; this.qualifier = qualifier;
} }
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; return dataInfo;
} }
public void setDataInfo(DataInfo dataInfo) { public void setDataInfo(DataInfo dataInfo) {
this.dataInfo = dataInfo; this.dataInfo = dataInfo;
} }
public String toComparableString() { public String toComparableString() {
return value != null ? value.toLowerCase() : ""; return value != null ? value.toLowerCase() : "";
} }
@Override @Override
public int hashCode() { public int hashCode() {
return toComparableString().hashCode(); return toComparableString().hashCode();
} }
@Override @Override
public boolean equals(Object obj) { public boolean equals(Object obj) {
if (this == obj) return true; if (this == obj) return true;
if (obj == null) return false; if (obj == null) return false;
if (getClass() != obj.getClass()) 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());
} }
} }

122
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java
View File

@ -10,82 +10,74 @@ import org.apache.commons.lang3.StringUtils;
public class DLIDataset extends Dataset { 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() { public String getCompletionStatus() {
return completionStatus; return completionStatus;
} }
public void setCompletionStatus(String completionStatus) { public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus; this.completionStatus = completionStatus;
} }
public List<ProvenaceInfo> getDlicollectedfrom() { public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom; return dlicollectedfrom;
} }
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) { public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom; this.dlicollectedfrom = dlicollectedfrom;
} }
public String getOriginalObjIdentifier() { public String getOriginalObjIdentifier() {
return originalObjIdentifier; return originalObjIdentifier;
} }
public void setOriginalObjIdentifier(String originalObjIdentifier) { public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier; this.originalObjIdentifier = originalObjIdentifier;
} }
@Override @Override
public void mergeFrom(OafEntity e) { public void mergeFrom(OafEntity e) {
super.mergeFrom(e); super.mergeFrom(e);
DLIDataset p = (DLIDataset) e; DLIDataset p = (DLIDataset) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus)) if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus; completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete"; if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
} }
private List<ProvenaceInfo> mergeProvenance( private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) { final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>(); Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null) if (a != null)
a.forEach( a.forEach(
p -> { p -> {
if (p != null if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
&& StringUtils.isNotBlank(p.getId()) if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& result.containsKey(p.getId())) { && StringUtils.isNotBlank(p.getCompletionStatus())) {
if ("incomplete" result.put(p.getId(), p);
.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())) } else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
if (b != null) if (b != null)
b.forEach( b.forEach(
p -> { p -> {
if (p != null if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
&& StringUtils.isNotBlank(p.getId()) if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& result.containsKey(p.getId())) { && StringUtils.isNotBlank(p.getCompletionStatus())) {
if ("incomplete" result.put(p.getId(), p);
.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())) } else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
return new ArrayList<>(result.values()); return new ArrayList<>(result.values());
} }
} }

122
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java
View File

@ -8,82 +8,74 @@ import org.apache.commons.lang3.StringUtils;
public class DLIPublication extends Publication implements Serializable { 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() { public String getCompletionStatus() {
return completionStatus; return completionStatus;
} }
public void setCompletionStatus(String completionStatus) { public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus; this.completionStatus = completionStatus;
} }
public List<ProvenaceInfo> getDlicollectedfrom() { public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom; return dlicollectedfrom;
} }
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) { public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom; this.dlicollectedfrom = dlicollectedfrom;
} }
public String getOriginalObjIdentifier() { public String getOriginalObjIdentifier() {
return originalObjIdentifier; return originalObjIdentifier;
} }
public void setOriginalObjIdentifier(String originalObjIdentifier) { public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier; this.originalObjIdentifier = originalObjIdentifier;
} }
@Override @Override
public void mergeFrom(OafEntity e) { public void mergeFrom(OafEntity e) {
super.mergeFrom(e); super.mergeFrom(e);
DLIPublication p = (DLIPublication) e; DLIPublication p = (DLIPublication) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus)) if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus; completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete"; if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
} }
private List<ProvenaceInfo> mergeProvenance( private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) { final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>(); Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null) if (a != null)
a.forEach( a.forEach(
p -> { p -> {
if (p != null if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
&& StringUtils.isNotBlank(p.getId()) if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& result.containsKey(p.getId())) { && StringUtils.isNotBlank(p.getCompletionStatus())) {
if ("incomplete" result.put(p.getId(), p);
.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())) } else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
if (b != null) if (b != null)
b.forEach( b.forEach(
p -> { p -> {
if (p != null if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
&& StringUtils.isNotBlank(p.getId()) if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& result.containsKey(p.getId())) { && StringUtils.isNotBlank(p.getCompletionStatus())) {
if ("incomplete" result.put(p.getId(), p);
.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())) } else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
return new ArrayList<>(result.values()); return new ArrayList<>(result.values());
} }
} }

14
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java
View File

@ -3,13 +3,13 @@ package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
public class DLIRelation extends Relation { public class DLIRelation extends Relation {
private String dateOfCollection; private String dateOfCollection;
public String getDateOfCollection() { public String getDateOfCollection() {
return dateOfCollection; return dateOfCollection;
} }
public void setDateOfCollection(String dateOfCollection) { public void setDateOfCollection(String dateOfCollection) {
this.dateOfCollection = dateOfCollection; this.dateOfCollection = dateOfCollection;
} }
} }

154
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java
View File

@ -11,107 +11,99 @@ import org.apache.commons.lang3.StringUtils;
public class DLIUnknown extends Oaf implements Serializable { 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() { public String getCompletionStatus() {
return completionStatus; return completionStatus;
} }
public void setCompletionStatus(String completionStatus) { public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus; this.completionStatus = completionStatus;
} }
public List<ProvenaceInfo> getDlicollectedfrom() { public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom; return dlicollectedfrom;
} }
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) { public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom; this.dlicollectedfrom = dlicollectedfrom;
} }
public String getId() { public String getId() {
return id; return id;
} }
public void setId(String id) { public void setId(String id) {
this.id = id; this.id = id;
} }
public List<StructuredProperty> getPid() { public List<StructuredProperty> getPid() {
return pid; return pid;
} }
public void setPid(List<StructuredProperty> pid) { public void setPid(List<StructuredProperty> pid) {
this.pid = pid; this.pid = pid;
} }
public String getDateofcollection() { public String getDateofcollection() {
return dateofcollection; return dateofcollection;
} }
public void setDateofcollection(String dateofcollection) { public void setDateofcollection(String dateofcollection) {
this.dateofcollection = dateofcollection; this.dateofcollection = dateofcollection;
} }
public String getDateoftransformation() { public String getDateoftransformation() {
return dateoftransformation; return dateoftransformation;
} }
public void setDateoftransformation(String dateoftransformation) { public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation; this.dateoftransformation = dateoftransformation;
} }
public void mergeFrom(DLIUnknown p) { public void mergeFrom(DLIUnknown p) {
if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete"; if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
} }
private List<ProvenaceInfo> mergeProvenance( private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) { final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>(); Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null) if (a != null)
a.forEach( a.forEach(
p -> { p -> {
if (p != null if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
&& StringUtils.isNotBlank(p.getId()) if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& result.containsKey(p.getId())) { && StringUtils.isNotBlank(p.getCompletionStatus())) {
if ("incomplete" result.put(p.getId(), p);
.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())) } else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
if (b != null) if (b != null)
b.forEach( b.forEach(
p -> { p -> {
if (p != null if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
&& StringUtils.isNotBlank(p.getId()) if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& result.containsKey(p.getId())) { && StringUtils.isNotBlank(p.getCompletionStatus())) {
if ("incomplete" result.put(p.getId(), p);
.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())) } else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
return new ArrayList<>(result.values()); return new ArrayList<>(result.values());
} }
} }

56
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/ProvenaceInfo.java
View File

@ -4,43 +4,43 @@ import java.io.Serializable;
public class ProvenaceInfo implements 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() { public String getId() {
return id; return id;
} }
public void setId(String id) { public void setId(String id) {
this.id = id; this.id = id;
} }
public String getName() { public String getName() {
return name; return name;
} }
public void setName(String name) { public void setName(String name) {
this.name = name; this.name = name;
} }
public String getCompletionStatus() { public String getCompletionStatus() {
return completionStatus; return completionStatus;
} }
public void setCompletionStatus(String completionStatus) { public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus; this.completionStatus = completionStatus;
} }
public String getCollectionMode() { public String getCollectionMode() {
return collectionMode; return collectionMode;
} }
public void setCollectionMode(String collectionMode) { public void setCollectionMode(String collectionMode) {
this.collectionMode = collectionMode; this.collectionMode = collectionMode;
} }
} }

32
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java
View File

@ -11,26 +11,26 @@ import org.junit.jupiter.api.Test;
/** @author claudio.atzori */ /** @author claudio.atzori */
public class AtomicActionTest { public class AtomicActionTest {
@Test @Test
public void serializationTest() throws IOException { public void serializationTest() throws IOException {
Relation rel = new Relation(); Relation rel = new Relation();
rel.setSource("1"); rel.setSource("1");
rel.setTarget("2"); rel.setTarget("2");
rel.setRelType("resultResult"); rel.setRelType("resultResult");
rel.setSubRelType("dedup"); rel.setSubRelType("dedup");
rel.setRelClass("merges"); rel.setRelClass("merges");
AtomicAction aa1 = new AtomicAction(Relation.class, rel); AtomicAction aa1 = new AtomicAction(Relation.class, rel);
final ObjectMapper mapper = new ObjectMapper(); final ObjectMapper mapper = new ObjectMapper();
String json = mapper.writeValueAsString(aa1); 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.getClazz(), aa2.getClazz());
assertEquals(aa1.getPayload(), aa2.getPayload()); assertEquals(aa1.getPayload(), aa2.getPayload());
} }
} }

36
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java
View File

@ -11,25 +11,25 @@ import org.junit.jupiter.api.Test;
public class ModelSupportTest { public class ModelSupportTest {
@Nested @Nested
class IsSubClass { class IsSubClass {
@Test @Test
public void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() { public void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() {
// when // when
Boolean result = ModelSupport.isSubClass(Relation.class, OafEntity.class); Boolean result = ModelSupport.isSubClass(Relation.class, OafEntity.class);
// then // then
assertFalse(result); assertFalse(result);
}
@Test
public void shouldReturnTrueWhenSubClassExtendsSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Result.class, OafEntity.class);
// then
assertTrue(result);
}
} }
@Test
public void shouldReturnTrueWhenSubClassExtendsSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Result.class, OafEntity.class);
// then
assertTrue(result);
}
}
} }

106
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java
View File

@ -9,78 +9,78 @@ import org.junit.jupiter.api.Test;
public class MergeTest { public class MergeTest {
OafEntity oaf; OafEntity oaf;
@BeforeEach @BeforeEach
public void setUp() { public void setUp() {
oaf = new Publication(); oaf = new Publication();
} }
@Test @Test
public void mergeListsTest() { public void mergeListsTest() {
// string list merge test // string list merge test
List<String> a = Arrays.asList("a", "b", "c", "e"); List<String> a = Arrays.asList("a", "b", "c", "e");
List<String> b = Arrays.asList("a", "b", "c", "d"); List<String> b = Arrays.asList("a", "b", "c", "d");
List<String> c = null; 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 @Test
public void mergePublicationCollectedFromTest() { public void mergePublicationCollectedFromTest() {
Publication a = new Publication(); Publication a = new Publication();
Publication b = new Publication(); Publication b = new Publication();
a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed"))); a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed")));
b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open"))); b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open")));
a.mergeFrom(b); a.mergeFrom(b);
assertNotNull(a.getCollectedfrom()); assertNotNull(a.getCollectedfrom());
assertEquals(3, a.getCollectedfrom().size()); assertEquals(3, a.getCollectedfrom().size());
} }
@Test @Test
public void mergePublicationSubjectTest() { public void mergePublicationSubjectTest() {
Publication a = new Publication(); Publication a = new Publication();
Publication b = new Publication(); Publication b = new Publication();
a.setSubject(Arrays.asList(setSP("a", "open", "classe"), setSP("b", "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"))); b.setSubject(Arrays.asList(setSP("A", "open", "classe"), setSP("c", "open", "classe")));
a.mergeFrom(b); a.mergeFrom(b);
assertNotNull(a.getSubject()); assertNotNull(a.getSubject());
assertEquals(3, a.getSubject().size()); 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.setKey(key);
k.setValue(value); k.setValue(value);
return k; return k;
} }
private StructuredProperty setSP( private StructuredProperty setSP(
final String value, final String schema, final String classname) { final String value, final String schema, final String classname) {
StructuredProperty s = new StructuredProperty(); StructuredProperty s = new StructuredProperty();
s.setValue(value); s.setValue(value);
Qualifier q = new Qualifier(); Qualifier q = new Qualifier();
q.setClassname(classname); q.setClassname(classname);
q.setClassid(classname); q.setClassid(classname);
q.setSchemename(schema); q.setSchemename(schema);
q.setSchemeid(schema); q.setSchemeid(schema);
s.setQualifier(q); s.setQualifier(q);
return s; return s;
} }
} }

104
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java
View File

@ -13,64 +13,64 @@ import org.junit.jupiter.api.Test;
public class DLItest { public class DLItest {
@Test @Test
public void testMergePublication() throws JsonProcessingException { public void testMergePublication() throws JsonProcessingException {
DLIPublication a1 = new DLIPublication(); DLIPublication a1 = new DLIPublication();
a1.setPid(Arrays.asList(createSP("123456", "pdb", "dnet:pid_types"))); a1.setPid(Arrays.asList(createSP("123456", "pdb", "dnet:pid_types")));
a1.setTitle(Collections.singletonList(createSP("Un Titolo", "title", "dnetTitle"))); a1.setTitle(Collections.singletonList(createSP("Un Titolo", "title", "dnetTitle")));
a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd", "Zenodo", "complete"))); a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd", "Zenodo", "complete")));
a1.setCompletionStatus("complete"); a1.setCompletionStatus("complete");
DLIPublication a = new DLIPublication(); DLIPublication a = new DLIPublication();
a.setPid( a.setPid(
Arrays.asList( Arrays.asList(
createSP("10.11", "doi", "dnet:pid_types"), createSP("10.11", "doi", "dnet:pid_types"),
createSP("123456", "pdb", "dnet:pid_types"))); createSP("123456", "pdb", "dnet:pid_types")));
a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle"))); a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle")));
a.setDlicollectedfrom( a.setDlicollectedfrom(
Arrays.asList( Arrays.asList(
createCollectedFrom("dct", "datacite", "complete"), createCollectedFrom("dct", "datacite", "complete"),
createCollectedFrom("dct", "datacite", "incomplete"))); createCollectedFrom("dct", "datacite", "incomplete")));
a.setCompletionStatus("incomplete"); a.setCompletionStatus("incomplete");
a.mergeFrom(a1); a.mergeFrom(a1);
ObjectMapper mapper = new ObjectMapper(); ObjectMapper mapper = new ObjectMapper();
System.out.println(mapper.writeValueAsString(a)); System.out.println(mapper.writeValueAsString(a));
} }
@Test @Test
public void testDeserialization() throws IOException { public void testDeserialization() throws IOException {
final String json = 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\"}"; "{\"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(); ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
DLIDataset dliDataset = mapper.readValue(json, DLIDataset.class); DLIDataset dliDataset = mapper.readValue(json, DLIDataset.class);
mapper.enable(SerializationFeature.INDENT_OUTPUT); mapper.enable(SerializationFeature.INDENT_OUTPUT);
System.out.println(mapper.writeValueAsString(dliDataset)); System.out.println(mapper.writeValueAsString(dliDataset));
} }
private ProvenaceInfo createCollectedFrom( private ProvenaceInfo createCollectedFrom(
final String id, final String name, final String completionStatus) { final String id, final String name, final String completionStatus) {
ProvenaceInfo p = new ProvenaceInfo(); ProvenaceInfo p = new ProvenaceInfo();
p.setId(id); p.setId(id);
p.setName(name); p.setName(name);
p.setCompletionStatus(completionStatus); p.setCompletionStatus(completionStatus);
return p; return p;
} }
private StructuredProperty createSP( private StructuredProperty createSP(
final String value, final String className, final String schemeName) { final String value, final String className, final String schemeName) {
StructuredProperty p = new StructuredProperty(); StructuredProperty p = new StructuredProperty();
p.setValue(value); p.setValue(value);
Qualifier schema = new Qualifier(); Qualifier schema = new Qualifier();
schema.setClassname(className); schema.setClassname(className);
schema.setClassid(className); schema.setClassid(className);
schema.setSchemename(schemeName); schema.setSchemename(schemeName);
schema.setSchemeid(schemeName); schema.setSchemeid(schemeName);
p.setQualifier(schema); p.setQualifier(schema);
return p; return p;
} }
} }

200
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
View File

@ -24,116 +24,116 @@ import org.slf4j.LoggerFactory;
public class ISClient implements Serializable { public class ISClient implements Serializable {
private static final Logger log = private static final Logger log =
LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); 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) { public ISClient(String isLookupUrl) {
isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
}
public List<String> getLatestRawsetPaths(String 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));
}
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";
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);
} }
}
public List<String> getLatestRawsetPaths(String setIds) { private ActionManagerSet getActionManagerSet(final String basePath, final String profile)
throws ActionManagerException {
final SAXReader reader = new SAXReader();
final ActionManagerSet set = new ActionManagerSet();
List<String> ids = try {
Lists.newArrayList( final Document doc = reader.read(new StringReader(profile));
Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR)
.omitEmptyStrings()
.trimResults()
.split(setIds));
return ids.stream() set.setId(doc.valueOf("//SET/@id").trim());
.map(id -> getSet(isLookup, id)) set.setName(doc.valueOf("//SET").trim());
.map(as -> as.getPathToLatest()) set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim()));
.collect(Collectors.toCollection(ArrayList::new)); set.setLatest(
} doc.valueOf("//RAW_SETS/LATEST/@id"),
doc.valueOf("//RAW_SETS/LATEST/@creationDate"),
private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) { doc.valueOf("//RAW_SETS/LATEST/@lastUpdate"));
set.setDirectory(doc.valueOf("//SET/@directory"));
final String q = final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED");
"for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') " if (expiredNodes != null) {
+ "where $x//SET/@id = '" for (int i = 0; i < expiredNodes.size(); i++) {
+ setId Element ex = (Element) expiredNodes.get(i);
+ "' return $x"; set.addExpired(
ex.attributeValue("id"),
try { ex.attributeValue("creationDate"),
final String basePath = getBasePathHDFS(isLookup); ex.attributeValue("lastUpdate"));
final String setProfile = isLookup.getResourceProfileByQuery(q);
return getActionManagerSet(basePath, setProfile);
} catch (ISLookUpException | ActionManagerException e) {
throw new RuntimeException("Error accessing Sets, using query: " + q);
} }
}
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);
} }
}
private ActionManagerSet getActionManagerSet(final String basePath, final String profile) private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
throws ActionManagerException { return queryServiceProperty(isLookup, "basePath");
final SAXReader reader = new SAXReader(); }
final ActionManagerSet set = new ActionManagerSet();
try { private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
final Document doc = reader.read(new StringReader(profile)); throws ActionManagerException {
final String q =
set.setId(doc.valueOf("//SET/@id").trim()); "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
set.setName(doc.valueOf("//SET").trim()); + propertyName
set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim())); + "']/@value/string()";
set.setLatest( log.debug("quering for service property: " + q);
doc.valueOf("//RAW_SETS/LATEST/@id"), try {
doc.valueOf("//RAW_SETS/LATEST/@creationDate"), final List<String> value = isLookup.quickSearchProfile(q);
doc.valueOf("//RAW_SETS/LATEST/@lastUpdate")); return Iterables.getOnlyElement(value);
set.setDirectory(doc.valueOf("//SET/@directory")); } catch (ISLookUpException e) {
final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED"); String msg = "Error accessing service profile, using query: " + q;
if (expiredNodes != null) { log.error(msg, e);
for (int i = 0; i < expiredNodes.size(); i++) { throw new ActionManagerException(msg, e);
Element ex = (Element) expiredNodes.get(i); } catch (NoSuchElementException e) {
set.addExpired( String msg = "missing service property: " + propertyName;
ex.attributeValue("id"), log.error(msg, e);
ex.attributeValue("creationDate"), throw new ActionManagerException(msg, e);
ex.attributeValue("lastUpdate")); } catch (IllegalArgumentException e) {
} String msg = "found more than one service property: " + propertyName;
} log.error(msg, e);
throw new ActionManagerException(msg, e);
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);
}
}
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);
}
} }
}
} }

54
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/LicenseComparator.java
View File

@ -5,43 +5,43 @@ import java.util.Comparator;
public class LicenseComparator implements Comparator<Qualifier> { public class LicenseComparator implements Comparator<Qualifier> {
@Override @Override
public int compare(Qualifier left, Qualifier right) { public int compare(Qualifier left, Qualifier right) {
if (left == null && right == null) return 0; if (left == null && right == null) return 0;
if (left == null) return 1; if (left == null) return 1;
if (right == null) return -1; if (right == null) return -1;
String lClass = left.getClassid(); String lClass = left.getClassid();
String rClass = right.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 (lClass.equals("OPEN SOURCE")) return -1;
if (rClass.equals("OPEN SOURCE")) return 1; if (rClass.equals("OPEN SOURCE")) return 1;
if (lClass.equals("OPEN")) return -1; if (lClass.equals("OPEN")) return -1;
if (rClass.equals("OPEN")) return 1; if (rClass.equals("OPEN")) return 1;
if (lClass.equals("6MONTHS")) return -1; if (lClass.equals("6MONTHS")) return -1;
if (rClass.equals("6MONTHS")) return 1; if (rClass.equals("6MONTHS")) return 1;
if (lClass.equals("12MONTHS")) return -1; if (lClass.equals("12MONTHS")) return -1;
if (rClass.equals("12MONTHS")) return 1; if (rClass.equals("12MONTHS")) return 1;
if (lClass.equals("EMBARGO")) return -1; if (lClass.equals("EMBARGO")) return -1;
if (rClass.equals("EMBARGO")) return 1; if (rClass.equals("EMBARGO")) return 1;
if (lClass.equals("RESTRICTED")) return -1; if (lClass.equals("RESTRICTED")) return -1;
if (rClass.equals("RESTRICTED")) return 1; if (rClass.equals("RESTRICTED")) return 1;
if (lClass.equals("CLOSED")) return -1; if (lClass.equals("CLOSED")) return -1;
if (rClass.equals("CLOSED")) return 1; if (rClass.equals("CLOSED")) return 1;
if (lClass.equals("UNKNOWN")) return -1; if (lClass.equals("UNKNOWN")) return -1;
if (rClass.equals("UNKNOWN")) return 1; if (rClass.equals("UNKNOWN")) return 1;
// Else (but unlikely), lexicographical ordering will do. // Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass); return lClass.compareTo(rClass);
} }
} }

261
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/MigrateActionSet.java
View File

@ -27,175 +27,162 @@ import org.slf4j.LoggerFactory;
public class MigrateActionSet { 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 SEPARATOR = "/";
private static final String TARGET_PATHS = "target_paths"; private static final String TARGET_PATHS = "target_paths";
private static final String RAWSET_PREFIX = "rawset_"; private static final String RAWSET_PREFIX = "rawset_";
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = final ArgumentApplicationParser parser =
new ArgumentApplicationParser( new ArgumentApplicationParser(
IOUtils.toString( IOUtils.toString(
MigrateActionSet.class.getResourceAsStream( MigrateActionSet.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json"))); "/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
parser.parseArgument(args); 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 isLookupUrl = parser.get("isLookupUrl");
final String sourceNN = parser.get("sourceNameNode"); final String sourceNN = parser.get("sourceNameNode");
final String targetNN = parser.get("targetNameNode"); final String targetNN = parser.get("targetNameNode");
final String workDir = parser.get("workingDirectory"); final String workDir = parser.get("workingDirectory");
final Integer distcp_num_maps = Integer.parseInt(parser.get("distcp_num_maps")); 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_memory_mb = parser.get("distcp_memory_mb");
final String distcp_task_timeout = parser.get("distcp_task_timeout"); 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 = Configuration conf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps); FileSystem targetFS = FileSystem.get(conf);
FileSystem targetFS = FileSystem.get(conf);
Configuration sourceConf = Configuration sourceConf =
getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps); getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
sourceConf.set(FileSystem.FS_DEFAULT_NAME_KEY, sourceNN); sourceConf.set(FileSystem.FS_DEFAULT_NAME_KEY, sourceNN);
FileSystem sourceFS = FileSystem.get(sourceConf); 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); final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
log.info( log.info(
"paths to process:\n{}", "paths to process:\n{}",
sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n"))); sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
for (Path source : sourcePaths) { for (Path source : sourcePaths) {
if (!sourceFS.exists(source)) { if (!sourceFS.exists(source)) {
log.warn("skipping unexisting path: {}", source); log.warn("skipping unexisting path: {}", source);
} else { } else {
LinkedList<String> pathQ = LinkedList<String> pathQ =
Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath())); Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
final String rawSet = pathQ.pollLast(); final String rawSet = pathQ.pollLast();
log.info("got RAWSET: {}", rawSet); 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 = final Path targetPath =
new Path( new Path(targetNN + workDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawSet);
targetNN
+ workDir
+ SEPARATOR
+ actionSetDirectory
+ SEPARATOR
+ rawSet);
log.info("using TARGET PATH: {}", targetPath); log.info("using TARGET PATH: {}", targetPath);
if (!transformOnly) { if (!transformOnly) {
if (targetFS.exists(targetPath)) { if (targetFS.exists(targetPath)) {
targetFS.delete(targetPath, true); targetFS.delete(targetPath, true);
}
runDistcp(
distcp_num_maps,
distcp_memory_mb,
distcp_task_timeout,
conf,
source,
targetPath);
}
targetPaths.add(targetPath);
}
} }
runDistcp(
distcp_num_maps, distcp_memory_mb, distcp_task_timeout, conf, source, 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"));
try (OutputStream os = new FileOutputStream(file)) {
props.store(os, "");
}
System.out.println(file.getAbsolutePath());
} }
private void runDistcp( props.setProperty(
Integer distcp_num_maps, TARGET_PATHS, targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(",")));
String distcp_memory_mb, File file = new File(System.getProperty("oozie.action.output.properties"));
String distcp_task_timeout,
Configuration conf,
Path source,
Path targetPath)
throws Exception {
final DistCpOptions op = new DistCpOptions(source, targetPath); try (OutputStream os = new FileOutputStream(file)) {
op.setMaxMaps(distcp_num_maps); props.store(os, "");
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()
});
if (res != 0) {
throw new RuntimeException(String.format("distcp exited with code %s", res));
}
} }
System.out.println(file.getAbsolutePath());
}
private Configuration getConfiguration( private void runDistcp(
String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) { Integer distcp_num_maps,
final Configuration conf = new Configuration(); String distcp_memory_mb,
conf.set("dfs.webhdfs.socket.connect-timeout", distcp_task_timeout); String distcp_task_timeout,
conf.set("dfs.webhdfs.socket.read-timeout", distcp_task_timeout); Configuration conf,
conf.set("dfs.http.client.retry.policy.enabled", "true"); Path source,
conf.set("mapred.task.timeout", distcp_task_timeout); Path targetPath)
conf.set("mapreduce.map.memory.mb", distcp_memory_mb); throws Exception {
conf.set("mapred.map.tasks", String.valueOf(distcp_num_maps));
return conf; 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()
});
if (res != 0) {
throw new RuntimeException(String.format("distcp exited with code %s", res));
} }
}
private List<Path> getSourcePaths(String sourceNN, ISLookUpService isLookUp) private Configuration getConfiguration(
throws ISLookUpException { String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) {
String XQUERY = final Configuration conf = new Configuration();
"distinct-values(\n" conf.set("dfs.webhdfs.socket.connect-timeout", distcp_task_timeout);
+ "let $basePath := collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()\n" conf.set("dfs.webhdfs.socket.read-timeout", distcp_task_timeout);
+ "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') \n" conf.set("dfs.http.client.retry.policy.enabled", "true");
+ "let $setDir := $x//SET/@directory/string()\n" conf.set("mapred.task.timeout", distcp_task_timeout);
+ "let $rawSet := $x//RAW_SETS/LATEST/@id/string()\n" conf.set("mapreduce.map.memory.mb", distcp_memory_mb);
+ "return concat($basePath, '/', $setDir, '/', $rawSet))"; conf.set("mapred.map.tasks", String.valueOf(distcp_num_maps));
return conf;
}
log.info(String.format("running xquery:\n%s", XQUERY)); private List<Path> getSourcePaths(String sourceNN, ISLookUpService isLookUp)
return isLookUp.quickSearchProfile(XQUERY).stream() throws ISLookUpException {
.map(p -> sourceNN + p) String XQUERY =
.map(Path::new) "distinct-values(\n"
.collect(Collectors.toList()); + "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());
}
} }

1068
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

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235
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/TransformActions.java
View File

@ -33,147 +33,132 @@ import scala.Tuple2;
public class TransformActions implements Serializable { 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 { public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = final ArgumentApplicationParser parser =
new ArgumentApplicationParser( new ArgumentApplicationParser(
IOUtils.toString( IOUtils.toString(
MigrateActionSet.class.getResourceAsStream( MigrateActionSet.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json"))); "/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Boolean isSparkSessionManaged =
Optional.ofNullable(parser.get("isSparkSessionManaged")) Optional.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String isLookupUrl = parser.get("isLookupUrl"); final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl); log.info("isLookupUrl: {}", isLookupUrl);
final String inputPaths = parser.get("inputPaths"); final String inputPaths = parser.get("inputPaths");
if (StringUtils.isBlank(inputPaths)) { if (StringUtils.isBlank(inputPaths)) {
throw new RuntimeException("empty inputPaths"); throw new RuntimeException("empty inputPaths");
}
log.info("inputPaths: {}", inputPaths);
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> transformActions(inputPaths, targetBaseDir, spark));
} }
log.info("inputPaths: {}", inputPaths);
private static void transformActions( final String targetBaseDir = getTargetBaseDir(isLookupUrl);
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))) { SparkConf conf = new SparkConf();
LinkedList<String> pathQ = runWithSparkSession(
Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath)); conf, isSparkSessionManaged, spark -> transformActions(inputPaths, targetBaseDir, spark));
}
final String rawset = pathQ.pollLast(); private static void transformActions(String inputPaths, String targetBaseDir, SparkSession spark)
final String actionSetDirectory = pathQ.pollLast(); throws IOException {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
final Path targetDirectory = for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
if (fs.exists(targetDirectory)) { LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
log.info("found target directory '{}", targetDirectory);
fs.delete(targetDirectory, true); final String rawset = pathQ.pollLast();
log.info("deleted target directory '{}", targetDirectory); final String actionSetDirectory = pathQ.pollLast();
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);
}
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());
}
}
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:
log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory); throw new IllegalArgumentException(
"invalid entity type: " + proto_oaf.getEntity().getType());
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());
} }
case relation:
return new AtomicAction<>(Relation.class, (Relation) oaf);
default:
throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
} }
}
private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa) private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
throws InvalidProtocolBufferException { ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
String XQUERY =
// dedup similarity relations had empty target value, don't migrate them "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
if (aa.getTargetValue().length == 0) { return isLookUp.getResourceProfileByQuery(XQUERY);
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);
}
} }

178
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java
View File

@ -23,120 +23,114 @@ import org.slf4j.LoggerFactory;
/** Partitions given set of action sets by payload type. */ /** Partitions given set of action sets by payload type. */
public class PartitionActionSetsByPayloadTypeJob { public class PartitionActionSetsByPayloadTypeJob {
private static final Logger logger = private static final Logger logger =
LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final StructType KV_SCHEMA = private static final StructType KV_SCHEMA =
StructType$.MODULE$.apply( StructType$.MODULE$.apply(
Arrays.asList( Arrays.asList(
StructField$.MODULE$.apply( StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
"key", DataTypes.StringType, false, Metadata.empty()), StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())));
StructField$.MODULE$.apply(
"value", DataTypes.StringType, false, Metadata.empty())));
private static final StructType ATOMIC_ACTION_SCHEMA = private static final StructType ATOMIC_ACTION_SCHEMA =
StructType$.MODULE$.apply( StructType$.MODULE$.apply(
Arrays.asList( Arrays.asList(
StructField$.MODULE$.apply( StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
"clazz", DataTypes.StringType, false, Metadata.empty()), StructField$.MODULE$.apply(
StructField$.MODULE$.apply( "payload", DataTypes.StringType, false, Metadata.empty())));
"payload", DataTypes.StringType, false, Metadata.empty())));
private ISClient isClient; private ISClient isClient;
public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) { public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) {
this.isClient = new ISClient(isLookupUrl); this.isClient = new ISClient(isLookupUrl);
} }
public PartitionActionSetsByPayloadTypeJob() {} public PartitionActionSetsByPayloadTypeJob() {}
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = String jsonConfiguration =
IOUtils.toString( IOUtils.toString(
PromoteActionPayloadForGraphTableJob.class.getResourceAsStream( PromoteActionPayloadForGraphTableJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json")); "/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Boolean isSparkSessionManaged =
Optional.ofNullable(parser.get("isSparkSessionManaged")) Optional.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputActionSetIds = parser.get("inputActionSetIds"); String inputActionSetIds = parser.get("inputActionSetIds");
logger.info("inputActionSetIds: {}", inputActionSetIds); logger.info("inputActionSetIds: {}", inputActionSetIds);
String outputPath = parser.get("outputPath"); String outputPath = parser.get("outputPath");
logger.info("outputPath: {}", outputPath); logger.info("outputPath: {}", outputPath);
String isLookupUrl = parser.get("isLookupUrl"); String isLookupUrl = parser.get("isLookupUrl");
logger.info("isLookupUrl: {}", isLookupUrl); logger.info("isLookupUrl: {}", isLookupUrl);
new PartitionActionSetsByPayloadTypeJob(isLookupUrl) new PartitionActionSetsByPayloadTypeJob(isLookupUrl)
.run(isSparkSessionManaged, inputActionSetIds, outputPath); .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); List<String> inputActionSetPaths = getIsClient().getLatestRawsetPaths(inputActionSetIds);
logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths)); logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths));
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, outputPath); removeOutputDir(spark, outputPath);
readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath); readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath);
}); });
} }
private static void removeOutputDir(SparkSession spark, String path) { private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
} }
private static void readAndWriteActionSetsFromPaths( private static void readAndWriteActionSetsFromPaths(
SparkSession spark, List<String> inputActionSetPaths, String outputPath) { SparkSession spark, List<String> inputActionSetPaths, String outputPath) {
inputActionSetPaths.stream() inputActionSetPaths.stream()
.filter( .filter(path -> HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration()))
path -> .forEach(
HdfsSupport.exists( inputActionSetPath -> {
path, spark.sparkContext().hadoopConfiguration())) Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath);
.forEach( saveActions(actionDS, outputPath);
inputActionSetPath -> { });
Dataset<Row> actionDS = }
readActionSetFromPath(spark, inputActionSetPath);
saveActions(actionDS, outputPath);
});
}
private static Dataset<Row> readActionSetFromPath(SparkSession spark, String path) { private static Dataset<Row> readActionSetFromPath(SparkSession spark, String path) {
logger.info("Reading actions from path: {}", path); logger.info("Reading actions from path: {}", path);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Row> rdd = JavaRDD<Row> rdd =
sc.sequenceFile(path, Text.class, Text.class) sc.sequenceFile(path, Text.class, Text.class)
.map(x -> RowFactory.create(x._1().toString(), x._2().toString())); .map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
return spark.createDataFrame(rdd, KV_SCHEMA) return spark
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) .createDataFrame(rdd, KV_SCHEMA)
.select(expr("atomic_action.*")); .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
} .select(expr("atomic_action.*"));
}
private static void saveActions(Dataset<Row> actionDS, String path) { private static void saveActions(Dataset<Row> actionDS, String path) {
logger.info("Saving actions to path: {}", path); logger.info("Saving actions to path: {}", path);
actionDS.write().partitionBy("clazz").mode(SaveMode.Append).parquet(path); actionDS.write().partitionBy("clazz").mode(SaveMode.Append).parquet(path);
} }
public ISClient getIsClient() { public ISClient getIsClient() {
return isClient; return isClient;
} }
public void setIsClient(ISClient isClient) { public void setIsClient(ISClient isClient) {
this.isClient = isClient; this.isClient = isClient;
} }
} }

122
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java
View File

@ -11,72 +11,72 @@ import java.util.function.BiFunction;
/** OAF model merging support. */ /** OAF model merging support. */
public class MergeAndGet { public class MergeAndGet {
private MergeAndGet() {} private MergeAndGet() {}
/** /**
* Strategy for merging OAF model objects. * Strategy for merging OAF model objects.
* *
* <p>MERGE_FROM_AND_GET: use OAF 'mergeFrom' method SELECT_NEWER_AND_GET: use last update * <p>MERGE_FROM_AND_GET: use OAF 'mergeFrom' method SELECT_NEWER_AND_GET: use last update
* timestamp to return newer instance * timestamp to return newer instance
*/ */
public enum Strategy { public enum Strategy {
MERGE_FROM_AND_GET, MERGE_FROM_AND_GET,
SELECT_NEWER_AND_GET SELECT_NEWER_AND_GET
} }
/** /**
* Returns a function for merging OAF model objects. * Returns a function for merging OAF model objects.
* *
* @param strategy Strategy to be used to merge objects * @param strategy Strategy to be used to merge objects
* @param <G> Graph table type * @param <G> Graph table type
* @param <A> Action payload type * @param <A> Action payload type
* @return BiFunction to be used to merge OAF objects * @return BiFunction to be used to merge OAF objects
*/ */
public static <G extends Oaf, A extends Oaf> public static <G extends Oaf, A extends Oaf>
SerializableSupplier<BiFunction<G, A, G>> functionFor(Strategy strategy) { SerializableSupplier<BiFunction<G, A, G>> functionFor(Strategy strategy) {
switch (strategy) { switch (strategy) {
case MERGE_FROM_AND_GET: case MERGE_FROM_AND_GET:
return () -> MergeAndGet::mergeFromAndGet; return () -> MergeAndGet::mergeFromAndGet;
case SELECT_NEWER_AND_GET: case SELECT_NEWER_AND_GET:
return () -> MergeAndGet::selectNewerAndGet; return () -> MergeAndGet::selectNewerAndGet;
}
throw new RuntimeException();
} }
throw new RuntimeException();
}
private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) { private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) {
if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) { if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) {
((Relation) x).mergeFrom((Relation) y); ((Relation) x).mergeFrom((Relation) y);
return x; return x;
} else if (isSubClass(x, OafEntity.class) } else if (isSubClass(x, OafEntity.class)
&& isSubClass(y, OafEntity.class) && isSubClass(y, OafEntity.class)
&& isSubClass(x, y)) { && isSubClass(x, y)) {
((OafEntity) x).mergeFrom((OafEntity) y); ((OafEntity) x).mergeFrom((OafEntity) y);
return x; return x;
}
throw new RuntimeException(
String.format(
"MERGE_FROM_AND_GET incompatible types: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
} }
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) { private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) {
if (x.getClass().equals(y.getClass()) if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x; return x;
} else if (x.getClass().equals(y.getClass()) } else if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
return (G) y; return (G) y;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { } else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x; return x;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { } else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
throw new RuntimeException( throw new RuntimeException(
String.format( String.format(
"SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s", "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())); 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()));
} }
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()));
}
} }

427
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
View File

@ -25,269 +25,202 @@ import org.slf4j.LoggerFactory;
/** Applies a given action payload file to graph table of compatible type. */ /** Applies a given action payload file to graph table of compatible type. */
public class PromoteActionPayloadForGraphTableJob { public class PromoteActionPayloadForGraphTableJob {
private static final Logger logger = private static final Logger logger =
LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class); 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 { public static void main(String[] args) throws Exception {
String jsonConfiguration = String jsonConfiguration =
IOUtils.toString( IOUtils.toString(
PromoteActionPayloadForGraphTableJob.class.getResourceAsStream( PromoteActionPayloadForGraphTableJob.class.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json")); "/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
Boolean isSparkSessionManaged = Boolean isSparkSessionManaged =
Optional.ofNullable(parser.get("isSparkSessionManaged")) Optional.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf) .map(Boolean::valueOf)
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputGraphTablePath = parser.get("inputGraphTablePath"); String inputGraphTablePath = parser.get("inputGraphTablePath");
logger.info("inputGraphTablePath: {}", inputGraphTablePath); logger.info("inputGraphTablePath: {}", inputGraphTablePath);
String graphTableClassName = parser.get("graphTableClassName"); String graphTableClassName = parser.get("graphTableClassName");
logger.info("graphTableClassName: {}", graphTableClassName); logger.info("graphTableClassName: {}", graphTableClassName);
String inputActionPayloadPath = parser.get("inputActionPayloadPath"); String inputActionPayloadPath = parser.get("inputActionPayloadPath");
logger.info("inputActionPayloadPath: {}", inputActionPayloadPath); logger.info("inputActionPayloadPath: {}", inputActionPayloadPath);
String actionPayloadClassName = parser.get("actionPayloadClassName"); String actionPayloadClassName = parser.get("actionPayloadClassName");
logger.info("actionPayloadClassName: {}", actionPayloadClassName); logger.info("actionPayloadClassName: {}", actionPayloadClassName);
String outputGraphTablePath = parser.get("outputGraphTablePath"); String outputGraphTablePath = parser.get("outputGraphTablePath");
logger.info("outputGraphTablePath: {}", outputGraphTablePath); logger.info("outputGraphTablePath: {}", outputGraphTablePath);
MergeAndGet.Strategy strategy = MergeAndGet.Strategy strategy =
MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase()); MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
logger.info("strategy: {}", strategy); logger.info("strategy: {}", strategy);
Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName); Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
Class<? extends Oaf> actionPayloadClazz = Class<? extends Oaf> actionPayloadClazz =
(Class<? extends Oaf>) Class.forName(actionPayloadClassName); (Class<? extends Oaf>) Class.forName(actionPayloadClassName);
throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz); throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses()); conf.registerKryoClasses(ModelSupport.getOafModelClasses());
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, outputGraphTablePath); removeOutputDir(spark, outputGraphTablePath);
promoteActionPayloadForGraphTable( promoteActionPayloadForGraphTable(
spark, spark,
inputGraphTablePath, inputGraphTablePath,
inputActionPayloadPath, inputActionPayloadPath,
outputGraphTablePath, outputGraphTablePath,
strategy, strategy,
rowClazz, rowClazz,
actionPayloadClazz); 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( private static void removeOutputDir(SparkSession spark, String path) {
Class<? extends Oaf> rowClazz, Class<? extends Oaf> actionPayloadClazz) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
if (!isSubClass(rowClazz, actionPayloadClazz)) { }
String msg =
String.format( private static <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable(
"graph table class is not a subclass of action payload class: graph=%s, action=%s", SparkSession spark,
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); String inputGraphTablePath,
throw new RuntimeException(msg); 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));
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);
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));
*/
}
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());
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);
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 void removeOutputDir(SparkSession spark, String path) { private static <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSource() {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); return t -> {
} if (isSubClass(t, Relation.class)) {
return Objects.nonNull(((Relation) t).getSource());
}
return Objects.nonNull(((OafEntity) t).getId());
};
}
private static <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable( private static <G extends Oaf> void saveGraphTable(Dataset<G> result, String path) {
SparkSession spark, logger.info("Saving graph table to path: {}", path);
String inputGraphTablePath, result.toJSON().write().option("compression", "gzip").text(path);
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));
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);
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));
*/
}
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());
SerializableSupplier<Function<G, String>> rowIdFn =
PromoteActionPayloadForGraphTableJob::idFn;
SerializableSupplier<Function<A, String>> actionPayloadIdFn =
PromoteActionPayloadForGraphTableJob::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);
return PromoteActionPayloadFunctions.groupGraphTableByIdAndMerge(
joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
}
private static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional.ofNullable(r.getSource())
.map(
source ->
Optional.ofNullable(r.getTarget())
.map(
target ->
Optional.ofNullable(r.getRelType())
.map(
relType ->
Optional.ofNullable(
r
.getSubRelType())
.map(
subRelType ->
Optional
.ofNullable(
r
.getRelClass())
.map(
relClass ->
String
.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String
.join(
source,
target,
relType,
subRelType)))
.orElse(
String
.join(
source,
target,
relType)))
.orElse(
String.join(
source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
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 <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);
}
} }

319
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java
View File

@ -20,177 +20,166 @@ import scala.Tuple2;
/** Promote action payload functions. */ /** Promote action payload functions. */
public class PromoteActionPayloadFunctions { public class PromoteActionPayloadFunctions {
private PromoteActionPayloadFunctions() {} private PromoteActionPayloadFunctions() {}
/** /**
* Joins dataset representing graph table with dataset representing action payload using * Joins dataset representing graph table with dataset representing action payload using supplied
* supplied functions. * functions.
* *
* @param rowDS Dataset representing graph table * @param rowDS Dataset representing graph table
* @param actionPayloadDS Dataset representing action payload * @param actionPayloadDS Dataset representing action payload
* @param rowIdFn Function used to get the id of graph table row * @param rowIdFn Function used to get the id of graph table row
* @param actionPayloadIdFn Function used to get id of action payload instance * @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 mergeAndGetFn Function used to merge graph table row and action payload instance
* @param rowClazz Class of graph table * @param rowClazz Class of graph table
* @param actionPayloadClazz Class of action payload * @param actionPayloadClazz Class of action payload
* @param <G> Type of graph table row * @param <G> Type of graph table row
* @param <A> Type of action payload instance * @param <A> Type of action payload instance
* @return Dataset of merged graph table rows and action payload instances * @return Dataset of merged graph table rows and action payload instances
*/ */
public static <G extends Oaf, A extends Oaf> Dataset<G> joinGraphTableWithActionPayloadAndMerge( public static <G extends Oaf, A extends Oaf> Dataset<G> joinGraphTableWithActionPayloadAndMerge(
Dataset<G> rowDS, Dataset<G> rowDS,
Dataset<A> actionPayloadDS, Dataset<A> actionPayloadDS,
SerializableSupplier<Function<G, String>> rowIdFn, SerializableSupplier<Function<G, String>> rowIdFn,
SerializableSupplier<Function<A, String>> actionPayloadIdFn, SerializableSupplier<Function<A, String>> actionPayloadIdFn,
SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn, SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn,
Class<G> rowClazz, Class<G> rowClazz,
Class<A> actionPayloadClazz) { Class<A> actionPayloadClazz) {
if (!isSubClass(rowClazz, actionPayloadClazz)) { if (!isSubClass(rowClazz, actionPayloadClazz)) {
throw new RuntimeException( throw new RuntimeException(
"action payload type must be the same or be a super type of table row type"); "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);
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<Tuple2<String, G>> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz);
Dataset<T> ds, SerializableSupplier<Function<T, String>> idFn, Class<T> clazz) { Dataset<Tuple2<String, A>> actionPayloadWithIdDS =
return ds.map( mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz);
(MapFunction<T, Tuple2<String, T>>)
value -> new Tuple2<>(idFn.get().apply(value), value), return rowWithIdDS
Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); .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)));
}
/**
* 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;
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
* Groups graph table by id and aggregates using supplied functions. public G zero() {
* return zeroFn.get();
* @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));
} }
/** @Override
* Aggregator to be used for aggregating graph table rows during grouping. public G reduce(G b, G a) {
* return zeroSafeMergeAndGet(b, a);
* @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;
}
@Override
public G zero() {
return zeroFn.get();
}
@Override
public G reduce(G b, G a) {
return zeroSafeMergeAndGet(b, a);
}
@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");
}
@Override
public G finish(G reduction) {
return reduction;
}
@Override
public Encoder<G> bufferEncoder() {
return Encoders.kryo(rowClazz);
}
@Override
public Encoder<G> outputEncoder() {
return Encoders.kryo(rowClazz);
}
} }
@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");
}
@Override
public G finish(G reduction) {
return reduction;
}
@Override
public Encoder<G> bufferEncoder() {
return Encoders.kryo(rowClazz);
}
@Override
public Encoder<G> outputEncoder() {
return Encoders.kryo(rowClazz);
}
}
} }

349
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java
View File

@ -37,209 +37,192 @@ import scala.collection.mutable.Seq;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class PartitionActionSetsByPayloadTypeJobTest { public class PartitionActionSetsByPayloadTypeJobTest {
private static final ClassLoader cl = private static final ClassLoader cl =
PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader(); PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader();
private static Configuration configuration; private static Configuration configuration;
private static SparkSession spark; 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 = private static final StructType ATOMIC_ACTION_SCHEMA =
StructType$.MODULE$.apply( StructType$.MODULE$.apply(
Arrays.asList( Arrays.asList(
StructField$.MODULE$.apply( StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
"clazz", DataTypes.StringType, false, Metadata.empty()), StructField$.MODULE$.apply(
StructField$.MODULE$.apply( "payload", DataTypes.StringType, false, Metadata.empty())));
"payload", DataTypes.StringType, false, Metadata.empty())));
@BeforeAll @BeforeAll
public static void beforeAll() throws IOException { public static void beforeAll() throws IOException {
configuration = Job.getInstance().getConfiguration(); configuration = Job.getInstance().getConfiguration();
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
conf.setMaster("local"); conf.setMaster("local");
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
spark = SparkSession.builder().config(conf).getOrCreate(); spark = SparkSession.builder().config(conf).getOrCreate();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@DisplayName("Job")
@Nested
class Main {
@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");
Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsBaseDir);
List<String> inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir);
// 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());
// 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);
} }
}
@AfterAll private List<String> resolveInputActionSetPaths(Path inputActionSetsBaseDir) throws IOException {
public static void afterAll() { Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
spark.stop(); return Files.list(inputActionSetJsonDumpsDir)
} .map(
path -> {
String inputActionSetId = path.getFileName().toString();
return inputActionSetsBaseDir.resolve(inputActionSetId).toString();
})
.collect(Collectors.toCollection(ArrayList::new));
}
@DisplayName("Job") private static Map<String, List<String>> createActionSets(Path inputActionSetsDir)
@Nested throws IOException {
class Main { Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
@Mock private ISClient isClient; Map<String, List<String>> oafsByType = new HashMap<>();
Files.list(inputActionSetJsonDumpsDir)
.forEach(
inputActionSetJsonDumpFile -> {
String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString();
Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId);
@Test Dataset<String> actionDS =
public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()).cache();
throws Exception {
// given
Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets");
Path outputDir = workingDir.resolve("output");
Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsBaseDir); writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString());
List<String> inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir); 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));
// when actionSetOafsByType
Mockito.when(isClient.getLatestRawsetPaths(Mockito.anyString())) .keySet()
.thenReturn(inputActionSetsPaths); .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));
}
});
});
PartitionActionSetsByPayloadTypeJob job = new PartitionActionSetsByPayloadTypeJob(); return oafsByType;
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 private static Path getInputActionSetJsonDumpsDir() {
Files.exists(outputDir); return Paths.get(
Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
.getFile());
}
assertForOafType(outputDir, oafsByClassName, eu.dnetlib.dhp.schema.oaf.Dataset.class); private static Dataset<String> readActionsFromJsonDump(String path) {
assertForOafType(outputDir, oafsByClassName, Datasource.class); return spark.read().textFile(path);
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) private static void writeActionsAsJobInput(
throws IOException { Dataset<String> actionDS, String inputActionSetId, String path) {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir(); actionDS
return Files.list(inputActionSetJsonDumpsDir) .javaRDD()
.map( .mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json)))
path -> { .saveAsNewAPIHadoopFile(
String inputActionSetId = path.getFileName().toString(); path, Text.class, Text.class, SequenceFileOutputFormat.class, configuration);
return inputActionSetsBaseDir.resolve(inputActionSetId).toString(); }
})
.collect(Collectors.toCollection(ArrayList::new));
}
private static Map<String, List<String>> createActionSets(Path inputActionSetsDir) private static <T extends Oaf> void assertForOafType(
throws IOException { Path outputDir, Map<String, List<String>> oafsByClassName, Class<T> clazz) {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir(); Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName()));
Files.exists(outputDatasetDir);
Map<String, List<String>> oafsByType = new HashMap<>(); List<T> actuals =
Files.list(inputActionSetJsonDumpsDir) readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList();
.forEach( actuals.sort(Comparator.comparingInt(Object::hashCode));
inputActionSetJsonDumpFile -> {
String inputActionSetId =
inputActionSetJsonDumpFile.getFileName().toString();
Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId);
Dataset<String> actionDS = List<T> expecteds =
readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()) oafsByClassName.get(clazz.getCanonicalName()).stream()
.cache(); .map(json -> mapToOaf(json, clazz))
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
writeActionsAsJobInput( assertIterableEquals(expecteds, actuals);
actionDS, inputActionSetId, inputActionSetDir.toString()); }
Map<String, List<String>> actionSetOafsByType = private static <T extends Oaf> Dataset<T> readActionPayloadFromJobOutput(
actionDS String path, Class<T> clazz) {
.withColumn( return spark
"atomic_action", .read()
from_json(col("value"), ATOMIC_ACTION_SCHEMA)) .parquet(path)
.select(expr("atomic_action.*")).groupBy(col("clazz")) .map(
.agg(collect_list(col("payload")).as("payload_list")) (MapFunction<Row, T>)
.collectAsList().stream() value -> OBJECT_MAPPER.readValue(value.<String>getAs("payload"), clazz),
.map( Encoders.bean(clazz));
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 private static <T extends Oaf> T mapToOaf(String json, Class<T> clazz) {
.keySet() return rethrowAsRuntimeException(
.forEach( () -> OBJECT_MAPPER.readValue(json, clazz),
x -> { String.format(
if (oafsByType.containsKey(x)) { "failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName()));
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;
}
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 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);
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());
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> 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()));
}
} }

478
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java
View File

@ -13,256 +13,246 @@ import org.junit.jupiter.api.Test;
public class MergeAndGetTest { public class MergeAndGetTest {
@Nested @Nested
class MergeFromAndGetStrategy { class MergeFromAndGetStrategy {
@Test @Test
public void shouldThrowForOafAndOaf() { public void shouldThrowForOafAndOaf() {
// given // given
Oaf a = mock(Oaf.class); Oaf a = mock(Oaf.class);
Oaf b = mock(Oaf.class); Oaf b = mock(Oaf.class);
// when // when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
functionFor(Strategy.MERGE_FROM_AND_GET);
// then // then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b)); assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// 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);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
// given
class OafEntitySub1 extends OafEntity {}
class OafEntitySub2 extends OafEntity {}
OafEntitySub1 a = mock(OafEntitySub1.class);
OafEntitySub2 b = mock(OafEntitySub2.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
assertEquals(a, x);
}
} }
@Nested @Test
class SelectNewerAndGetStrategy { public void shouldThrowForOafAndRelation() {
// given
Oaf a = mock(Oaf.class);
Relation b = mock(Relation.class);
@Test // when
public void shouldThrowForOafEntityAndRelation() { SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// given
OafEntity a = mock(OafEntity.class);
Relation b = mock(Relation.class);
// when // then
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// 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);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// 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);
// 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);
}
@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);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
assertEquals(a, x);
}
} }
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// 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);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@Test
public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
// given
class OafEntitySub1 extends OafEntity {}
class OafEntitySub2 extends OafEntity {}
OafEntitySub1 a = mock(OafEntitySub1.class);
OafEntitySub2 b = mock(OafEntitySub2.class);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn = functionFor(Strategy.MERGE_FROM_AND_GET);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
assertEquals(a, x);
}
}
@Nested
class SelectNewerAndGetStrategy {
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// then
assertThrows(RuntimeException.class, () -> fn.get().apply(a, b));
}
@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);
// 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);
// when
SerializableSupplier<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// 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);
// 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);
}
@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);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
assertEquals(a, x);
}
}
} }

467
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java
View File

@ -27,261 +27,252 @@ import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource; import org.junit.jupiter.params.provider.MethodSource;
public class PromoteActionPayloadForGraphTableJobTest { public class PromoteActionPayloadForGraphTableJobTest {
private static final ClassLoader cl = private static final ClassLoader cl =
PromoteActionPayloadForGraphTableJobTest.class.getClassLoader(); PromoteActionPayloadForGraphTableJobTest.class.getClassLoader();
private static SparkSession spark; private static SparkSession spark;
private Path workingDir; private Path workingDir;
private Path inputDir; private Path inputDir;
private Path inputGraphRootDir; private Path inputGraphRootDir;
private Path inputActionPayloadRootDir; private Path inputActionPayloadRootDir;
private Path outputDir; private Path outputDir;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@BeforeAll @BeforeAll
public static void beforeAll() { public static void beforeAll() {
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName());
conf.setMaster("local"); conf.setMaster("local");
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses()); conf.registerKryoClasses(ModelSupport.getOafModelClasses());
spark = SparkSession.builder().config(conf).getOrCreate(); 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");
}
@AfterEach
public void afterEach() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@DisplayName("Job")
@Nested
class Main {
@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()
}));
// 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));
} }
@BeforeEach @ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}")
public void beforeEach() throws IOException { @MethodSource(
workingDir = "eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams")
Files.createTempDirectory( public void shouldPromoteActionPayloadForGraphTable(
PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); MergeAndGet.Strategy strategy,
inputDir = workingDir.resolve("input"); Class<? extends Oaf> rowClazz,
inputGraphRootDir = inputDir.resolve("graph"); Class<? extends Oaf> actionPayloadClazz)
inputActionPayloadRootDir = inputDir.resolve("action_payload"); throws Exception {
outputDir = workingDir.resolve("output"); // 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()
});
// 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);
} }
}
@AfterEach public static Stream<Arguments> promoteJobTestParams() {
public void afterEach() throws IOException { return Stream.of(
FileUtils.deleteDirectory(workingDir.toFile()); 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));
}
@AfterAll private static <G extends Oaf> Path createGraphTable(Path inputGraphRootDir, Class<G> rowClazz) {
public static void afterAll() { String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz);
spark.stop(); 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;
}
@DisplayName("Job") private static String inputGraphTableJsonDumpLocation(Class<? extends Oaf> rowClazz) {
@Nested return String.format(
class Main { "%s/%s.json",
"eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase());
}
@Test private static <G extends Oaf> Dataset<G> readGraphTableFromJsonDump(
public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() { String path, Class<G> rowClazz) {
// given return spark
Class<Relation> rowClazz = Relation.class; .read()
Class<OafEntity> actionPayloadClazz = OafEntity.class; .textFile(path)
.map(
(MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz),
Encoders.bean(rowClazz));
}
// when private static <G extends Oaf> void writeGraphTableAaJobInput(Dataset<G> rowDS, String path) {
RuntimeException exception = rowDS.write().option("compression", "gzip").json(path);
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 private static <G extends Oaf, A extends Oaf> Path createActionPayload(
String msg = Path inputActionPayloadRootDir, Class<G> rowClazz, Class<A> actionPayloadClazz) {
String.format( String inputActionPayloadJsonDumpPath =
"graph table class is not a subclass of action payload class: graph=%s, action=%s", inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz);
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); Path inputActionPayloadJsonDumpFile =
assertTrue(exception.getMessage().contains(msg)); 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;
}
@ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}") private static String inputActionPayloadJsonDumpLocation(
@MethodSource( Class<? extends Oaf> rowClazz, Class<? extends Oaf> actionPayloadClazz) {
"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 return String.format(
PromoteActionPayloadForGraphTableJob.main( "eu/dnetlib/dhp/actionmanager/promote/input/action_payload/%s_table/%s.json",
new String[] { rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase());
"-isSparkSessionManaged", Boolean.FALSE.toString(), }
"-inputGraphTablePath", inputGraphTableDir.toString(),
"-graphTableClassName", rowClazz.getCanonicalName(),
"-inputActionPayloadPath", inputActionPayloadDir.toString(),
"-actionPayloadClassName", actionPayloadClazz.getCanonicalName(),
"-outputGraphTablePath", outputGraphTableDir.toString(),
"-mergeAndGetStrategy", strategy.name()
});
// then private static Dataset<String> readActionPayloadFromJsonDump(String path) {
assertTrue(Files.exists(outputGraphTableDir)); return spark.read().textFile(path);
}
List<? extends Oaf> actualOutputRows = private static void writeActionPayloadAsJobInput(Dataset<String> actionPayloadDS, String path) {
readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) actionPayloadDS.withColumnRenamed("value", "payload").write().parquet(path);
.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() { private static <G extends Oaf> Dataset<G> readGraphTableFromJobOutput(
return Stream.of( String path, Class<G> rowClazz) {
arguments( return spark
MergeAndGet.Strategy.MERGE_FROM_AND_GET, .read()
eu.dnetlib.dhp.schema.oaf.Dataset.class, .textFile(path)
eu.dnetlib.dhp.schema.oaf.Dataset.class), .map(
arguments( (MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz),
MergeAndGet.Strategy.MERGE_FROM_AND_GET, Encoders.bean(rowClazz));
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( private static String resultFileLocation(
Path inputGraphRootDir, Class<G> rowClazz) { MergeAndGet.Strategy strategy,
String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz); Class<? extends Oaf> rowClazz,
Path inputGraphTableJsonDumpFile = Class<? extends Oaf> actionPayloadClazz) {
Paths.get( return String.format(
Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)) "eu/dnetlib/dhp/actionmanager/promote/output/graph/%s/%s/%s_action_payload/result.json",
.getFile()); strategy.name().toLowerCase(),
Dataset<G> rowDS = rowClazz.getSimpleName().toLowerCase(),
readGraphTableFromJsonDump(inputGraphTableJsonDumpFile.toString(), rowClazz); actionPayloadClazz.getSimpleName().toLowerCase());
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 <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, 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) {
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 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 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());
}
} }

569
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java
View File

@ -21,329 +21,312 @@ import org.junit.jupiter.api.Test;
public class PromoteActionPayloadFunctionsTest { public class PromoteActionPayloadFunctionsTest {
private static SparkSession spark; private static SparkSession spark;
@BeforeAll @BeforeAll
public static void beforeAll() { public static void beforeAll() {
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.setMaster("local"); conf.setMaster("local");
conf.setAppName(PromoteActionPayloadFunctionsTest.class.getSimpleName()); conf.setAppName(PromoteActionPayloadFunctionsTest.class.getSimpleName());
conf.set("spark.driver.host", "localhost"); conf.set("spark.driver.host", "localhost");
spark = SparkSession.builder().config(conf).getOrCreate(); spark = SparkSession.builder().config(conf).getOrCreate();
}
@AfterAll
public static void afterAll() {
spark.stop();
}
@Nested
class JoinTableWithActionPayloadAndMerge {
@Test
public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
// given
class OafImpl extends Oaf {}
// when
assertThrows(
RuntimeException.class,
() ->
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge(
null, null, null, null, null, OafImplSubSub.class, OafImpl.class));
} }
@AfterAll @Test
public static void afterAll() { public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
spark.stop(); // 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));
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();
// 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();
}
});
} }
@Nested @Test
class JoinTableWithActionPayloadAndMerge { 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 List<OafImplSub> actionPayloadData =
public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() { Arrays.asList(
// given createOafImplSub(id1),
class OafImpl extends Oaf {} 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));
// when SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
assertThrows( SerializableSupplier<Function<OafImplSub, String>> actionPayloadIdFn =
RuntimeException.class, () -> OafImplRoot::getId;
() -> SerializableSupplier<BiFunction<OafImplSubSub, OafImplSub, OafImplSubSub>> mergeAndGetFn =
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge( () ->
null, (x, y) -> {
null, x.merge(y);
null, return x;
null, };
null,
OafImplSubSub.class,
OafImpl.class));
}
@Test // when
public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() { List<OafImplSubSub> results =
// given PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge(
String id0 = "id0"; rowDS,
String id1 = "id1"; actionPayloadDS,
String id2 = "id2"; rowIdFn,
String id3 = "id3"; actionPayloadIdFn,
String id4 = "id4"; mergeAndGetFn,
List<OafImplSubSub> rowData = OafImplSubSub.class,
Arrays.asList( OafImplSub.class)
createOafImplSubSub(id0), .collectAsList();
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id3));
Dataset<OafImplSubSub> rowDS =
spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
List<OafImplSubSub> actionPayloadData = // then
Arrays.asList( assertEquals(7, results.size());
createOafImplSubSub(id1), assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count());
createOafImplSubSub(id2), assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
createOafImplSubSub(id2), assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count());
createOafImplSubSub(id3), assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count());
createOafImplSubSub(id3), assertEquals(0, results.stream().filter(x -> x.getId().equals(id4)).count());
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 = results.forEach(
() -> OafImplRoot::getId; result -> {
SerializableSupplier<Function<OafImplSubSub, String>> actionPayloadIdFn = switch (result.getId()) {
() -> OafImplRoot::getId; case "id0":
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> assertEquals(1, result.getMerged());
mergeAndGetFn = break;
() -> case "id1":
(x, y) -> { case "id2":
x.merge(y); case "id3":
return x; assertEquals(2, result.getMerged());
}; break;
default:
throw new RuntimeException();
}
});
}
}
// when @Nested
List<OafImplSubSub> results = class GroupTableByIdAndMerge {
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeAndGetFn,
OafImplSubSub.class,
OafImplSubSub.class)
.collectAsList();
// then @Test
assertEquals(11, results.size()); public void shouldRunProperly() {
assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count()); // given
assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count()); String id1 = "id1";
assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count()); String id2 = "id2";
assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count()); String id3 = "id3";
assertEquals(4, results.stream().filter(x -> x.getId().equals(id4)).count()); 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));
results.forEach( SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
result -> { SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn =
switch (result.getId()) { () ->
case "id0": (x, y) -> {
assertEquals(1, result.getMerged()); x.merge(y);
break; return x;
case "id1": };
case "id2": SerializableSupplier<OafImplSubSub> zeroFn = OafImplSubSub::new;
case "id3": SerializableSupplier<Function<OafImplSubSub, Boolean>> isNotZeroFn =
assertEquals(2, result.getMerged()); () -> x -> Objects.nonNull(x.getId());
break;
case "id4":
assertEquals(1, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
@Test // when
public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() { List<OafImplSubSub> results =
// given PromoteActionPayloadFunctions.groupGraphTableByIdAndMerge(
String id0 = "id0"; rowDS, rowIdFn, mergeAndGetFn, zeroFn, isNotZeroFn, OafImplSubSub.class)
String id1 = "id1"; .collectAsList();
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 = // then
Arrays.asList( assertEquals(3, results.size());
createOafImplSub(id1), assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count());
createOafImplSub(id2), assertEquals(1, results.stream().filter(x -> x.getId().equals(id2)).count());
createOafImplSub(id2), assertEquals(1, results.stream().filter(x -> x.getId().equals(id3)).count());
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 = results.forEach(
() -> OafImplRoot::getId; result -> {
SerializableSupplier<Function<OafImplSub, String>> actionPayloadIdFn = switch (result.getId()) {
() -> OafImplRoot::getId; case "id1":
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSub, OafImplSubSub>> assertEquals(1, result.getMerged());
mergeAndGetFn = break;
() -> case "id2":
(x, y) -> { assertEquals(2, result.getMerged());
x.merge(y); break;
return x; case "id3":
}; assertEquals(3, result.getMerged());
break;
default:
throw new RuntimeException();
}
});
}
}
// when public static class OafImplRoot extends Oaf {
List<OafImplSubSub> results = private String id;
PromoteActionPayloadFunctions.joinGraphTableWithActionPayloadAndMerge( private int merged = 1;
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeAndGetFn,
OafImplSubSub.class,
OafImplSub.class)
.collectAsList();
// then public void merge(OafImplRoot e) {
assertEquals(7, results.size()); merged += e.merged;
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();
}
});
}
} }
@Nested public String getId() {
class GroupTableByIdAndMerge { return id;
@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());
// 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());
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 { public void setId(String id) {
private String id; this.id = id;
private int merged = 1;
public void merge(OafImplRoot e) {
merged += e.merged;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public int getMerged() {
return merged;
}
public void setMerged(int merged) {
this.merged = merged;
}
} }
public static class OafImplSub extends OafImplRoot { public int getMerged() {
return merged;
@Override
public void merge(OafImplRoot e) {
super.merge(e);
}
} }
private static OafImplSub createOafImplSub(String id) { public void setMerged(int merged) {
OafImplSub x = new OafImplSub(); this.merged = merged;
x.setId(id);
return x;
} }
}
public static class OafImplSubSub extends OafImplSub { public static class OafImplSub extends OafImplRoot {
@Override @Override
public void merge(OafImplRoot e) { public void merge(OafImplRoot e) {
super.merge(e); super.merge(e);
}
} }
}
private static OafImplSubSub createOafImplSubSub(String id) { private static OafImplSub createOafImplSub(String id) {
OafImplSubSub x = new OafImplSubSub(); OafImplSub x = new OafImplSub();
x.setId(id); x.setId(id);
return x; return x;
}
public static class OafImplSubSub extends OafImplSub {
@Override
public void merge(OafImplRoot e) {
super.merge(e);
} }
}
private static OafImplSubSub createOafImplSubSub(String id) {
OafImplSubSub x = new OafImplSubSub();
x.setId(id);
return x;
}
} }

242
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -31,133 +31,125 @@ import org.dom4j.io.SAXReader;
public class GenerateNativeStoreSparkJob { public class GenerateNativeStoreSparkJob {
public static MetadataRecord parseRecord( public static MetadataRecord parseRecord(
final String input, final String input,
final String xpath, final String xpath,
final String encoding, final String encoding,
final Provenance provenance, final Provenance provenance,
final Long dateOfCollection, final Long dateOfCollection,
final LongAccumulator totalItems, final LongAccumulator totalItems,
final LongAccumulator invalidRecords) { final LongAccumulator invalidRecords) {
if (totalItems != null) totalItems.add(1); if (totalItems != null) totalItems.add(1);
try { try {
SAXReader reader = new SAXReader(); SAXReader reader = new SAXReader();
Document document = Document document =
reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8))); reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
Node node = document.selectSingleNode(xpath); Node node = document.selectSingleNode(xpath);
final String originalIdentifier = node.getText(); final String originalIdentifier = node.getText();
if (StringUtils.isBlank(originalIdentifier)) { if (StringUtils.isBlank(originalIdentifier)) {
if (invalidRecords != null) invalidRecords.add(1); if (invalidRecords != null) invalidRecords.add(1);
return null; return null;
} }
return new MetadataRecord( return new MetadataRecord(originalIdentifier, encoding, provenance, input, dateOfCollection);
originalIdentifier, encoding, provenance, input, dateOfCollection); } catch (Throwable e) {
} catch (Throwable e) { if (invalidRecords != null) invalidRecords.add(1);
if (invalidRecords != null) invalidRecords.add(1); e.printStackTrace();
e.printStackTrace(); return null;
return null; }
} }
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 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 boolean test =
parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final JavaPairRDD<IntWritable, Text> inputRDD =
sc.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
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 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);
} }
public static void main(String[] args) throws Exception { final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
final Dataset<MetadataRecord> mdstore = spark.createDataset(mappeRDD.rdd(), encoder);
final ArgumentApplicationParser parser = final LongAccumulator mdStoreRecords = sc.sc().longAccumulator("MDStoreRecords");
new ArgumentApplicationParser( mdStoreRecords.add(mdstore.count());
IOUtils.toString( ongoingMap.put("ongoing", "" + totalItems.value());
GenerateNativeStoreSparkJob.class.getResourceAsStream( if (!test) {
"/eu/dnetlib/dhp/collection/collection_input_parameters.json"))); manager.sendMessage(
parser.parseArgument(args); new Message(
final ObjectMapper jsonMapper = new ObjectMapper(); parser.get("workflowId"), "DataFrameCreation", MessageType.ONGOING, ongoingMap),
final Provenance provenance = parser.get("rabbitOngoingQueue"),
jsonMapper.readValue(parser.get("provenance"), Provenance.class); true,
final long dateOfCollection = new Long(parser.get("dateOfCollection")); false);
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 boolean test =
parser.get("isTest") == null ? false : Boolean.valueOf(parser.get("isTest"));
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final JavaPairRDD<IntWritable, Text> inputRDD =
sc.sequenceFile(parser.get("input"), IntWritable.class, Text.class);
final LongAccumulator totalItems = sc.sc().longAccumulator("TotalItems");
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 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);
}
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();
}
} }
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();
}
}
} }

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
View File

@ -6,5 +6,5 @@ import java.util.stream.Stream;
public interface CollectorPlugin { public interface CollectorPlugin {
Stream<String> collect(ApiDescriptor api) throws DnetCollectorException; Stream<String> collect(ApiDescriptor api) throws DnetCollectorException;
} }

110
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java
View File

@ -16,67 +16,63 @@ import java.util.stream.StreamSupport;
public class OaiCollectorPlugin implements CollectorPlugin { public class OaiCollectorPlugin implements CollectorPlugin {
private static final String FORMAT_PARAM = "format"; private static final String FORMAT_PARAM = "format";
private static final String OAI_SET_PARAM = "set"; private static final String OAI_SET_PARAM = "set";
private static final Object OAI_FROM_DATE_PARAM = "fromDate"; private static final Object OAI_FROM_DATE_PARAM = "fromDate";
private static final Object OAI_UNTIL_DATE_PARAM = "untilDate"; private static final Object OAI_UNTIL_DATE_PARAM = "untilDate";
private OaiIteratorFactory oaiIteratorFactory; private OaiIteratorFactory oaiIteratorFactory;
@Override @Override
public Stream<String> collect(final ApiDescriptor api) throws DnetCollectorException { public Stream<String> collect(final ApiDescriptor api) throws DnetCollectorException {
final String baseUrl = api.getBaseUrl(); final String baseUrl = api.getBaseUrl();
final String mdFormat = api.getParams().get(FORMAT_PARAM); final String mdFormat = api.getParams().get(FORMAT_PARAM);
final String setParam = api.getParams().get(OAI_SET_PARAM); final String setParam = api.getParams().get(OAI_SET_PARAM);
final String fromDate = api.getParams().get(OAI_FROM_DATE_PARAM); final String fromDate = api.getParams().get(OAI_FROM_DATE_PARAM);
final String untilDate = api.getParams().get(OAI_UNTIL_DATE_PARAM); final String untilDate = api.getParams().get(OAI_UNTIL_DATE_PARAM);
final List<String> sets = new ArrayList<>(); final List<String> sets = new ArrayList<>();
if (setParam != null) { if (setParam != null) {
sets.addAll( sets.addAll(
Lists.newArrayList( Lists.newArrayList(Splitter.on(",").omitEmptyStrings().trimResults().split(setParam)));
Splitter.on(",").omitEmptyStrings().trimResults().split(setParam))); }
} if (sets.isEmpty()) {
if (sets.isEmpty()) { // If no set is defined, ALL the sets must be harvested
// If no set is defined, ALL the sets must be harvested sets.add("");
sets.add("");
}
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 (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);
}
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);
} }
public OaiIteratorFactory getOaiIteratorFactory() { if (baseUrl == null || baseUrl.isEmpty()) {
if (oaiIteratorFactory == null) { throw new DnetCollectorException("Param 'baseurl' is null or empty");
oaiIteratorFactory = new OaiIteratorFactory();
}
return oaiIteratorFactory;
} }
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 (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();
return StreamSupport.stream(
Spliterators.spliteratorUnknownSize(Iterators.concat(iters), Spliterator.ORDERED), false);
}
public OaiIteratorFactory getOaiIteratorFactory() {
if (oaiIteratorFactory == null) {
oaiIteratorFactory = new OaiIteratorFactory();
}
return oaiIteratorFactory;
}
} }

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