/**
* '$RCSfile: DataPackage.java,v $'
*
* '$Author: leinfelder $'
* '$Date: 2008-08-12 23:28:18 $'
* '$Revision: 1.6 $'
*
* For Details: http://kepler.ecoinformatics.org
*
* Copyright (c) 2003 The Regents of the University of California.
* All rights reserved.
*
* Permission is hereby granted, without written agreement and without
* license or royalty fees, to use, copy, modify, and distribute this
* software and its documentation for any purpose, provided that the
* above copyright notice and the following two paragraphs appear in
* all copies of this software.
*
* IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
* FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
* ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN
* IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY
* OF SUCH DAMAGE.
*
* THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
* INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
* MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
* PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY
* OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
* UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
*/
package org.ecoinformatics.datamanager.parser;
import java.io.File;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.StringTokenizer;
import java.util.TreeSet;
import java.util.Vector;
import java.util.regex.Pattern;
import javax.xml.transform.Result;
import javax.xml.transform.Source;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import org.ecoinformatics.datamanager.quality.EntityReport;
import org.ecoinformatics.datamanager.quality.QualityReport;
import org.ecoinformatics.datamanager.quality.QualityCheck;
import org.ecoinformatics.datamanager.quality.QualityCheck.Status;
import org.ecoinformatics.eml.EMLParser;
import org.ecoinformatics.eml.SAXValidate;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import edu.ucsb.nceas.utilities.XMLUtilities;
/**
* This class represents a metadata package information to describe entity
*
* @author tao
*/
public class DataPackage
{
/*
* Class fields
*/
private static final String IDENTIFIER_WITH_LEADING_ZERO_PATTERN = "^[A-Za-z_0-9\\-]+\\.0\\d+\\.\\d+$";
private static final String REVISION_WITH_LEADING_ZERO_PATTERN = "^[A-Za-z_0-9\\-]+\\.\\d+\\.0\\d+$";
//private static final String LTER_PACKAGE_ID_PATTERN = "^knb-lter-[a-z][a-z][a-z]\\.\\d+\\.\\d+$";
private static final String METACAT_PACKAGE_ID_PATTERN = "^[A-Za-z_0-9\\-]+\\.\\d+\\.\\d+$";
/* A comma-separated list of allowable scope values. This value should be set
* to non-null by applications that use the 'packageIdPattern' quality check.
*/
private static String scopeRegistry = null;
/*
* Used for the 'schemaValid' quality check
*/
private static final String schemaLocation =
"eml://ecoinformatics.org/eml-2.0.0 http://nis.lternet.edu/schemas/eml/eml-2.0.0/eml.xsd " +
"eml://ecoinformatics.org/eml-2.0.1 http://nis.lternet.edu/schemas/eml/eml-2.0.1/eml.xsd " +
"eml://ecoinformatics.org/eml-2.1.0 http://nis.lternet.edu/schemas/eml/eml-2.1.0/eml.xsd " +
"eml://ecoinformatics.org/literature-2.1.0 http://nis.lternet.edu/schemas/eml/eml-2.1.0/eml-literature.xsd " +
"eml://ecoinformatics.org/project-2.1.0 http://nis.lternet.edu/schemas/eml/eml-2.1.0/eml-project.xsd " +
"eml://ecoinformatics.org/eml-2.1.1 http://knb.ecoinformatics.org/emlparser/schema/eml-2.1.1/eml.xsd " +
"eml://ecoinformatics.org/literature-2.1.1 eml-literature.xsd " +
"eml://ecoinformatics.org/project-2.1.1 eml-project.xsd " +
"http://www.xml-cml.org/schema/stmml http://nis.lternet.edu/schemas/eml/eml-2.0.1/stmml.xsd " +
"http://www.xml-cml.org/schema/stmml-1.1 http://nis.lternet.edu/schemas/eml/eml-2.1.0/stmml.xsd";
/*
* Instance fields
*/
private String accessXML = null; // <access> element XML string
private String emlNamespace = null; // e.g. "eml://ecoinformatics.org/eml-2.1.0"
private Entity[] entityList = null;
private boolean parserValid = false;
private boolean schemaValid = false;
private int numberOfKeywordElements = 0;
private int numberOfMethodsElements = 0;
private int numberOfCoverageElements = 0;
private int numberOfGeographicCoverageElements = 0;
private int numberOfTaxonomicCoverageElements = 0;
private int numberOfTemporalCoverageElements = 0;
private String packageId = null;
private String pubDate;
private QualityReport qualityReport = null;
private String system = null;
private String title = null;
/*
* Constructors
*/
/**
* Constructs a DataPackage object.
*
* @param packageId Identifier of this DataPackage
*/
public DataPackage(String packageId)
{
this.packageId = packageId;
this.qualityReport = new QualityReport(this);
qualityCheckPackageId(packageId);
}
/*
* Class methods
*/
/**
* Applies the EML dereferencing stylesheet (whose path is set in the
* properties file and stored in the QualityReport class) to transform
* the original EML document to a fully dereferenced EML document.
*
* @param originalEmlString the original EML XML string
* @return emlString the result of the transformation from the
* original EML to the dereferenced EML
* @throws IllegalStateException
* if an error occurs during the transformation process
*/
public static String dereferenceEML(String originalEmlString)
throws IllegalStateException {
String dereferencedEmlString = "";
Result result;
StringWriter stringWriter = new StringWriter();
javax.xml.transform.Transformer transformer;
javax.xml.transform.TransformerFactory transformerFactory;
final String xslPath = QualityReport.getEmlDereferencerXSLTPath();
Source xmlSource;
File xsltFile = new File(xslPath);
Source xsltSource;
StringReader stringReader = new StringReader(originalEmlString);
xmlSource = new javax.xml.transform.stream.StreamSource(stringReader);
xsltSource = new javax.xml.transform.stream.StreamSource(xsltFile);
result = new javax.xml.transform.stream.StreamResult(stringWriter);
String transformerFactoryValue = System.getProperty("javax.xml.transform.TransformerFactory");
System.out.println("javax.xml.transform.TransformerFactory :" + transformerFactoryValue);
transformerFactory = javax.xml.transform.TransformerFactory.newInstance();
try {
transformer = transformerFactory.newTransformer(xsltSource);
transformer.transform(xmlSource, result);
dereferencedEmlString = stringWriter.toString();
}
catch (TransformerConfigurationException e) {
Throwable x = e;
if (e.getException() != null) {
x = e.getException();
}
x.printStackTrace();
throw new IllegalStateException(e);
}
catch (TransformerException e) {
Throwable x = e;
if (e.getException() != null) {
x = e.getException();
}
x.printStackTrace();
throw new IllegalStateException(e);
}
return dereferencedEmlString;
}
/**
* Sets the value of the scope registry, for use by the
* 'packageIdPattern' quality check.
*
* @param scopeRegistry A comma-separated list of allowable
* data package scope values, e.g. "scope1,scope2,scope3".
*/
public static void setScopeRegistry(String scopeRegistry) {
DataPackage.scopeRegistry = scopeRegistry;
}
/*
* Instance methods
*/
/**
* Adds a dataset-level quality check to the data packages's associated
* qualityReport object.
*
* @param qualityCheck the new quality check to add
*/
public void addDatasetQualityCheck(QualityCheck qualityCheck) {
if (qualityReport != null) {
qualityReport.addDatasetQualityCheck(qualityCheck);
}
}
/**
* Getter method for the accessXML field
*
* @return the value of the accessXML field
*/
public String getAccessXML() {
return accessXML;
}
/**
* Getter method for the emlNamespace field
* @return
*/
public String getEmlNamespace() {
return emlNamespace;
}
public Entity[] getEntities(String name)
{
Vector list = new Vector();
if (entityList != null) {
for (int i=0; i < entityList.length; i++) {
if (entityList[i].getName().equals(name)) {
list.add(entityList[i]);
}
}
}
return (Entity[]) list.toArray(new Entity[0]);
}
public Entity getEntity(String name) {
if (getEntities(name).length > 0) {
return getEntities(name)[0];
}
return null;
}
/**
* Determine whether the data package contains
* two entities with the same entityName value.
*
* @return The duplicate name, or null if no
* duplicate entity names were found
*/
public String findDuplicateEntityName() {
String duplicateName = null;
Entity[] entityArray = getEntityList();
if (entityArray != null) {
int len = entityArray.length;
TreeSet<String> treeSet = new TreeSet<String>();
for (int i = 0; i < len; i++) {
Entity entity = entityArray[i];
String entityName = entity.getName();
if (entityName != null) {
if (treeSet.contains(entityName)) {
duplicateName = entityName;
break;
}
else {
treeSet.add(entityName);
}
}
}
}
return duplicateName;
}
/**
* Adds an entity into the DataPackage
*
* @param entity The entity which will be added
*/
public void add(Entity entity)
{
addEntityIntoArray(entity);
}
/**
* Gets the entity array which is in this DataPackage.
*
* @return Entity array in the DataPackage
*/
public Entity[] getEntityList()
{
return entityList;
}
/**
* Gets the number of entities in this DataPackage.
*
* @return an int representing the number of entities
*/
public int getEntityNumber()
{
if (entityList == null) {
return 0;
}
else {
return entityList.length;
}
}
/**
* Gets the qualityReport object associated with this data package.
*
* @return the qualityReport instance variable
*/
public QualityReport getQualityReport()
{
return qualityReport;
}
/**
* Gets the value of the system attribute.
*
* @return a String, e.g. "knb"
*/
public String getSystem() {
return system;
}
/**
* Gets the package identifier for this DataPackage.
*
* @return a string representing the DataPackage identifier
*/
public String getPackageId()
{
return packageId;
}
/*
* Add an entity into the entityList array.
*
* @param entity the entity object to be added to the array
*/
private void addEntityIntoArray(Entity entity) {
if (entityList == null) {
entityList = new Entity[1];
entityList[0] = entity;
}
else {
int size = entityList.length;
Entity[] tmp = new Entity[size + 1];
for (int i = 0; i < size; i++) {
tmp[i] = entityList[i];
}
tmp[size] = entity;
entityList = tmp;
}
}
/**
* Removes ALL previously added Entity objects from the DataPackage
*/
public void clearEntityList() {
entityList = null;
}
/**
* Boolean to determine whether this data package has at
* least one dataset-level quality error. This can be called
* after parsing the metadata. If a data package is found to
* have a dataset-level quality error, an application may want
* to halt processing at that point instead of drilling down
* to the entity-level.
*
* @return true if one or more dataset-level quality errors are
* found, else false
*/
public boolean hasDatasetQualityError() {
boolean hasError = (qualityReport != null &&
qualityReport.hasDatasetQualityError());
return hasError;
}
/**
* Boolean to determine whether this data package has at
* least one entity-level quality error.
*
* @return true if one or more entity-level quality errors are
* found, else false
*/
public boolean hasEntityQualityError() {
boolean hasError = false;
Entity[] entityArray = getEntityList();
for (int i = 0; i < entityArray.length; i++) {
Entity entity = entityArray[i];
EntityReport entityReport = entity.getEntityReport();
if (entityReport != null) {
if (entityReport.hasEntityQualityError()) {
hasError = true;
}
}
}
return hasError;
}
/*
* Gets the value of the numberOfKeywordElements variable.
*
* @return the number of keyword elements detected in this
* data package
*/
public int getNumberOfKeywordElements() {
return numberOfKeywordElements;
}
/*
* Gets the value of the numberOfMethodsElements variable.
*
* @return the number of methods elements detected in this
* data package
*/
public int getNumberOfMethodsElements() {
return numberOfMethodsElements;
}
/**
* Boolean to determine whether this data package has at
* least one dataset-level or entity-level quality error.
*
* @return true if one or more quality errors are
* found, else false
*/
public boolean hasQualityError() {
return hasDatasetQualityError() || hasEntityQualityError();
}
/*
* Boolean to determine whether a given packageId has an
* identifier with a leading zero character. This usually causes problems
* with subsequent processing of the data package and should be
* flagged as an error. A zero by itself is acceptable, however.
*
* Examples:
*
* "datapackage.012.12" // returns true
* "datapackage.0.12" // returns false
* "datapackage.10.12" // returns false
*/
private boolean identifierHasLeadingZero(String packageId) {
boolean hasLeadingZero = false;
String regexPattern = IDENTIFIER_WITH_LEADING_ZERO_PATTERN;
hasLeadingZero = Pattern.matches(regexPattern, packageId);
return hasLeadingZero;
}
/*
* Boolean to determine whether a given packageId has a
* revision with a leading zero character. If true, this may cause problems
* with subsequent processing of the data package and should be
* flagged as an error. A zero by itself is acceptable, however.
*
* Examples:
*
* "datapackage.12.012" // returns true
* "datapackage.12.0" // returns false
* "datapackage.12.11" // returns false
*/
private boolean revisionHasLeadingZero(String packageId) {
boolean hasLeadingZero = false;
String regexPattern = REVISION_WITH_LEADING_ZERO_PATTERN;
hasLeadingZero = Pattern.matches(regexPattern, packageId);
return hasLeadingZero;
}
/**
* Gets the parserValid value
*
* @return the value of the parserValid variable
*/
public boolean isParserValid() {
return parserValid;
}
/**
* Gets the schemaValid value
*
* @return the value of the schemaValid variable
*/
public boolean isSchemaValid() {
return schemaValid;
}
/*
* Boolean to determine whether a given packageId conforms to
* the string pattern of a particular organization such as LTER.
* If the specified system value does not have a regular
* expression pattern declared for its packageId, then the
* packageId is assumed to be valid by default.
*/
private boolean isValidPackageIdForMetacat(String packageId) {
boolean isValid = true;
String regexPattern = METACAT_PACKAGE_ID_PATTERN;
isValid = Pattern.matches(regexPattern, packageId);
return isValid;
}
/*
* Boolean to determine whether a given packageId scope value conforms to
* the allowed set of scopes of a particular organization such as LTER.
*/
private boolean isValidScope(String packageId) {
boolean isValid = false;
if (packageId == null)
return false;
if (scopeRegistry == null)
return true;
StringTokenizer stringTokenizer = new StringTokenizer(scopeRegistry, ",");
final int tokenCount = stringTokenizer.countTokens();
for (int i = 0; i < tokenCount; i++) {
String token = stringTokenizer.nextToken();
if (packageId.startsWith(token + ".")) {
isValid = true;
break;
}
}
return isValid;
}
/**
* Setter method for accessXML field.
*
* @param xmlString the XML string to assign to the
* accessXML field. Should be a block
* of <access> XML.
*/
public void setAccessXML(String xmlString) {
this.accessXML = xmlString;
}
/*
* Executes the "EML packageId check" when applicable
*/
private void qualityCheckPackageId(String packageId) {
// Check the value of the 'packageId' attribute
String packageIdIdentifier = "packageIdPattern";
QualityCheck packageIdTemplate = QualityReport.getQualityCheckTemplate(packageIdIdentifier);
QualityCheck packageIdQualityCheck = new QualityCheck(packageIdIdentifier, packageIdTemplate);
String systemAttribute = packageIdQualityCheck.getSystem();
if (QualityCheck.shouldRunQualityCheck(this, packageIdQualityCheck)) {
if (scopeRegistry != null) {
packageIdQualityCheck.setExpected("'scope.n.m', where 'n' and 'm' are integers and 'scope' is one of an allowed set of values");
}
if (packageId != null) {
packageIdQualityCheck.setFound(packageId);
}
if (!isValidPackageIdForMetacat(packageId)) {
packageIdQualityCheck.setStatus(Status.error);
packageIdQualityCheck.setExplanation("The packageId value should match the pattern 'scope.identifier.revision'.");
}
else if (identifierHasLeadingZero(packageId)) {
packageIdQualityCheck.setStatus(Status.error);
packageIdQualityCheck.setExplanation("A leading zero was found in the identifier. The identifier value must be a whole number.");
packageIdQualityCheck.setSuggestion("Remove leading zeros from the identifier value.");
}
else if (revisionHasLeadingZero(packageId)) {
packageIdQualityCheck.setStatus(Status.error);
packageIdQualityCheck.setExplanation("A leading zero was found in the revision. The revision value must be a whole number.");
packageIdQualityCheck.setSuggestion("Remove leading zeros from the revision value.");
}
else if (isValidScope(packageId)) {
packageIdQualityCheck.setStatus(Status.valid);
packageIdQualityCheck.setSuggestion("");
}
else {
packageIdQualityCheck.setFailedStatus();
if (scopeRegistry != null) {
packageIdQualityCheck.setExplanation(String.format(
"A packageId should start with one of the following scope values: %s",
scopeRegistry));
if (systemAttribute != null && systemAttribute.equals("lter")) {
packageIdQualityCheck.setSuggestion(
"Use a scope value that you are authorized to use for your site or project, " +
"or you may request that a new scope value be added to the list of allowed " +
"values by contacting tech_support@LTERnet.edu.");
}
}
}
this.addDatasetQualityCheck(packageIdQualityCheck);
}
}
/**
* Setter method for emlNamespace field.
*
* @param emlNamespace the emlNamespace value to set,
* e.g. "eml://ecoinformatics.org/eml-2.1.0"
*/
public void setEmlNamespace(String emlNamespace) {
this.emlNamespace = emlNamespace;
// Check the value of the 'xmlns:eml' attribute
String emlVersionIdentifier = "emlVersion";
QualityCheck emlVersionTemplate = QualityReport.getQualityCheckTemplate(emlVersionIdentifier);
QualityCheck emlVersionQualityCheck = new QualityCheck(emlVersionIdentifier, emlVersionTemplate);
if (QualityCheck.shouldRunQualityCheck(this, emlVersionQualityCheck)) {
// Initialize the emlNamespaceQualityCheck
boolean isValidNamespace = false;
if (emlNamespace != null) {
emlVersionQualityCheck.setFound(emlNamespace);
if (emlNamespace.equals("eml://ecoinformatics.org/eml-2.1.0") ||
emlNamespace.equals("eml://ecoinformatics.org/eml-2.1.1")
) {
isValidNamespace = true;
}
}
if (isValidNamespace) {
emlVersionQualityCheck.setStatus(Status.valid);
emlVersionQualityCheck.setSuggestion("");
}
else {
emlVersionQualityCheck.setFailedStatus();
}
this.addDatasetQualityCheck(emlVersionQualityCheck);
}
}
/**
* Performs the 'schemaValid' quality check.
*
* @param doc the XML DOM document object
* @param namespaceInDoc the namespace value specified in the document
*/
public void checkSchemaValid(Document doc, String namespaceInDoc) {
String schemaValidIdentifier = "schemaValid";
QualityCheck schemaValidTemplate =
QualityReport.getQualityCheckTemplate(schemaValidIdentifier);
QualityCheck schemaValidQualityCheck =
new QualityCheck(schemaValidIdentifier, schemaValidTemplate);
if (QualityCheck.shouldRunQualityCheck(this, schemaValidQualityCheck)) {
// Initialize the schemaValidQualityCheck
boolean validateSchema = true;
String found = "";
final String parserName = "DEFAULT";
Node documentElement = doc.getDocumentElement();
String xmlString = XMLUtilities.getDOMTreeAsString(documentElement);
StringReader stringReader = new StringReader(xmlString);
SAXValidate saxValidate = new SAXValidate(validateSchema);
try {
saxValidate.runTest(stringReader, parserName, schemaLocation, namespaceInDoc);
found = "Document validated for namespace: '" + namespaceInDoc + "'";
schemaValidQualityCheck.setStatus(Status.valid);
schemaValidQualityCheck.setSuggestion("");
this.schemaValid = true;
}
catch (Exception e) {
found = "Failed to validate for namespace: '" + namespaceInDoc +
"'; " + e.getMessage();
schemaValidQualityCheck.setFailedStatus();
}
schemaValidQualityCheck.setFound(found);
this.addDatasetQualityCheck(schemaValidQualityCheck);
}
}
/**
* Performs the 'parserValid' quality check, using the 'EML IDs
* and References Parser' code in the org.ecoinformatics.eml.EMLParser
* class.
*
* @param doc the XML DOM document object
*/
public void checkParserValid(Document doc) {
String parserValidIdentifier = "parserValid";
QualityCheck parserValidTemplate =
QualityReport.getQualityCheckTemplate(parserValidIdentifier);
QualityCheck parserValidQualityCheck =
new QualityCheck(parserValidIdentifier, parserValidTemplate);
if (QualityCheck.shouldRunQualityCheck(this, parserValidQualityCheck)) {
// Initialize the parserValidQualityCheck
String found = "";
Node documentElement = doc.getDocumentElement();
String xmlString = XMLUtilities.getDOMTreeAsString(documentElement);
try {
EMLParser emlParser = new EMLParser(xmlString);
found = "EML IDs and references parser succeeded";
parserValidQualityCheck.setStatus(Status.valid);
parserValidQualityCheck.setSuggestion("");
this.parserValid = true;
}
catch (Exception e) {
found = "Failed to parse IDs and references: " + e.getMessage();
parserValidQualityCheck.setFailedStatus();
}
parserValidQualityCheck.setFound(found);
this.addDatasetQualityCheck(parserValidQualityCheck);
}
}
/**
* Performs the 'schemaValidDereferenced' quality check.
* Checks schema validity after the original document has
* been dereferenced (i.e. all references to "id" elements
* have been substituted with the actual elements.) An XSLT
* stylesheet is used for performing the dereferencing.
*
* @param doc the XML DOM document object
* @param namespaceInDoc the namespace value specified in the document
*/
public void checkSchemaValidDereferenced(Document doc, String namespaceInDoc) {
String identifier = "schemaValidDereferenced";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
// Initialize the schemaValidQualityCheck
boolean validateSchema = true;
String found = "";
final String parserName = "DEFAULT";
Node documentElement = doc.getDocumentElement();
String xmlString = XMLUtilities.getDOMTreeAsString(documentElement);
String deferencedXmlString = DataPackage.dereferenceEML(xmlString);
StringReader stringReader = new StringReader(deferencedXmlString);
SAXValidate saxValidate = new SAXValidate(validateSchema);
try {
saxValidate.runTest(stringReader, parserName, schemaLocation, namespaceInDoc);
found = "Dereferenced document validated for namespace: '" + namespaceInDoc + "'";
qualityCheck.setStatus(Status.valid);
qualityCheck.setSuggestion("");
this.schemaValid = true;
}
catch (Exception e) {
found = "Failed to validate dereferenced document for namespace: '" + namespaceInDoc +
"'; " + e.getMessage();
qualityCheck.setFailedStatus();
}
qualityCheck.setFound(found);
this.addDatasetQualityCheck(qualityCheck);
}
}
/**
* Set the value of the numberOfKeywordElements instance variable
* and run a quality check based on the value.
*
* @param n the number of keyword elements detected in
* this data package by the parser
*/
public void setNumberOfKeywordElements(int n) {
this.numberOfKeywordElements = n;
/*
* Do a quality check for the presence of at least
* one 'keyword' element
*/
String qualityCheckIdentifier = "keywordPresent";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(qualityCheckIdentifier);
QualityCheck qualityCheck =
new QualityCheck(qualityCheckIdentifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
String found = numberOfKeywordElements + " 'keyword' element(s) found";
qualityCheck.setFound(found);
if (numberOfKeywordElements > 0) {
qualityCheck.setStatus(Status.valid);
qualityCheck.setExplanation("");
qualityCheck.setSuggestion("");
}
else {
qualityCheck.setFailedStatus();
}
addDatasetQualityCheck(qualityCheck);
}
}
/**
* Set the value of the numberOfMethodsElements instance variable
* and run a quality check based on the value.
*
* @param n the number of methods elements detected in
* this data package by the parser
*/
public void setNumberOfMethodsElements(int n) {
this.numberOfMethodsElements = n;
/*
* Do a quality check for the presence of at least
* one 'methods' element
*/
String methodsElementIdentifier = "methodsElementPresent";
QualityCheck methodsElementTemplate =
QualityReport.getQualityCheckTemplate(methodsElementIdentifier);
QualityCheck methodsElementQualityCheck =
new QualityCheck(methodsElementIdentifier, methodsElementTemplate);
if (QualityCheck.shouldRunQualityCheck(this, methodsElementQualityCheck)) {
String found = numberOfMethodsElements + " 'methods' element(s) found";
methodsElementQualityCheck.setFound(found);
if (numberOfMethodsElements > 0) {
methodsElementQualityCheck.setStatus(Status.valid);
methodsElementQualityCheck.setExplanation("");
methodsElementQualityCheck.setSuggestion("");
}
else {
methodsElementQualityCheck.setFailedStatus();
}
addDatasetQualityCheck(methodsElementQualityCheck);
}
}
/**
* Set the value of the numberOfCoverageElements instance variable
* and run a quality check based on the value.
*
* @param n the number of coverage elements detected in
* this data package by the parser
*/
public void setNumberOfCoverageElements(int n) {
this.numberOfCoverageElements = n;
/*
* Do a quality check for the presence of at least
* one 'coverage' element
*/
String identifier = "coveragePresent";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
String found = numberOfCoverageElements + " 'coverage' element(s) found";
qualityCheck.setFound(found);
if (numberOfCoverageElements > 0) {
qualityCheck.setStatus(Status.valid);
qualityCheck.setExplanation("");
qualityCheck.setSuggestion("");
}
else {
qualityCheck.setFailedStatus();
}
addDatasetQualityCheck(qualityCheck);
}
}
/**
* Set the value of the numberOfGeographicCoverageElements instance
* variable and run a quality check based on the value.
*
* @param n the number of geographicCoverage elements detected in
* this data package by the parser
*/
public void setNumberOfGeographicCoverageElements(int n) {
this.numberOfGeographicCoverageElements = n;
/*
* Do a quality check to report the number of
* 'geographicCoverage' elements detected
*/
String identifier = "geographicCoveragePresent";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
String found = numberOfGeographicCoverageElements + " 'geographicCoverage' element(s) found";
qualityCheck.setFound(found);
addDatasetQualityCheck(qualityCheck);
}
}
/**
* Set the value of the numberOfTaxonomicCoverageElements instance
* variable and run a quality check based on the value.
*
* @param n the number of taxonomicCoverage elements detected in
* this data package by the parser
*/
public void setNumberOfTaxonomicCoverageElements(int n) {
this.numberOfTaxonomicCoverageElements = n;
/*
* Do a quality check to report the number of
* 'taxonomicCoverage' elements detected
*/
String identifier = "taxonomicCoveragePresent";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
String found = numberOfTaxonomicCoverageElements + " 'taxonomicCoverage' element(s) found";
qualityCheck.setFound(found);
addDatasetQualityCheck(qualityCheck);
}
}
/**
* Set the value of the numberOfTemporalCoverageElements instance
* variable and run a quality check based on the value.
*
* @param n the number of temporalCoverage elements detected in
* this data package by the parser
*/
public void setNumberOfTemporalCoverageElements(int n) {
this.numberOfTemporalCoverageElements = n;
/*
* Do a quality check to report the number of
* 'temporalCoverage' elements detected
*/
String identifier = "temporalCoveragePresent";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
String found = numberOfTemporalCoverageElements + " 'temporalCoverage' element(s) found";
qualityCheck.setFound(found);
addDatasetQualityCheck(qualityCheck);
}
}
/**
* Sets the value of the 'pubDate' to the specified String
* value.
*
* @param systemValue the 'pubDate' value to set
*/
public void setPubDate(String pubDate) {
this.pubDate = pubDate;
/*
* Do a quality check on pubDate presence
*/
String identifier = "pubDatePresent";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
boolean hasPubDate = ((pubDate != null) && (pubDate.length() >= 4));
String found = pubDate;
if (hasPubDate) {
qualityCheck.setStatus(Status.valid);
qualityCheck.setExplanation("");
qualityCheck.setSuggestion("");
}
else {
found = "pubDate not found";
qualityCheck.setFailedStatus();
}
qualityCheck.setFound(found);
addDatasetQualityCheck(qualityCheck);
}
}
/**
* Sets the value of the 'system' to the specified String
* value.
*
* @param systemValue the 'system' value to set
*/
public void setSystem(String systemValue) {
this.system = systemValue;
}
/**
* Sets the value of the 'title' to the specified String
* value.
*
* @param titleText the title value to set
*/
public void setTitle(String titleText) {
this.title = titleText;
/*
* Do a quality check on the number of words in the
* dataset title text
*/
String identifier = "titleLength";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
int wordCount = wordCount(titleText);
String found = wordCount + " words found.";
qualityCheck.setFound(found);
if (wordCount >= 5) {
qualityCheck.setStatus(Status.valid);
qualityCheck.setExplanation("");
qualityCheck.setSuggestion("");
}
else {
qualityCheck.setFailedStatus();
}
addDatasetQualityCheck(qualityCheck);
}
}
/**
* Returns the package title
* @return
*/
public String getTitle() {
return this.title;
}
/**
* Checks the number of words in the dataset abstract text.
*
* @param abstractText the abstract text to be analyzed
*/
public void checkDatasetAbstract(String abstractText) {
/*
* Do a quality check on the number of words in the
* dataset abstract text
*/
String identifier = "datasetAbstractLength";
QualityCheck qualityCheckTemplate =
QualityReport.getQualityCheckTemplate(identifier);
QualityCheck qualityCheck =
new QualityCheck(identifier, qualityCheckTemplate);
if (QualityCheck.shouldRunQualityCheck(this, qualityCheck)) {
int wordCount = wordCount(abstractText);
String found = wordCount + " words found.";
qualityCheck.setFound(found);
if (wordCount >= 20) {
qualityCheck.setStatus(Status.valid);
qualityCheck.setExplanation("");
qualityCheck.setSuggestion("");
}
else {
qualityCheck.setFailedStatus();
}
addDatasetQualityCheck(qualityCheck);
}
}
/*
* Count the words in a string of text. Useful for several different
* quality checks.
*/
private int wordCount(String text) {
int wordCount = 0;
if ((text != null) && (!text.equals(""))) {
String[] wordList = text.split("[\\s\\n]");
int listLength = wordList.length;
for (int i = 0; i < listLength; i++) {
String word = wordList[i];
if (word.length() >= 3) {
wordCount++;
}
}
}
return wordCount;
}
}