/**
* @see MetadataDataObjectAdapter::injectMetadataIntoDataObject()
* @param $metadataDescription MetadataDescription
* @param $dataObject Citation
* @param $replace boolean whether existing meta-data should be replaced
* @return DataObject
*/
function &injectMetadataIntoDataObject(&$metadataDescription, &$dataObject, $replace)
{
// Did we get an existing citation object or should we create a new one?
if (is_null($dataObject)) {
import('citation.Citation');
$dataObject = new Citation();
}
// Add new meta-data statements to the citation. Add the schema
// name space to each property name so that it becomes unique
// across schemas.
$metadataSchemaNamespace = $this->getMetadataNamespace();
$nullVar = null;
foreach ($metadataDescription->getPropertyNames() as $propertyName) {
$dataObjectKey = $metadataSchemaNamespace . ':' . $propertyName;
if ($metadataDescription->hasStatement($propertyName)) {
// Directly retrieve the internal data so that we don't
// have to care about cardinality and translation.
$value =& $metadataDescription->getData($propertyName);
if (in_array($propertyName, array('person-group[@person-group-type="author"]', 'person-group[@person-group-type="editor"]'))) {
// Convert MetadataDescription objects to simple key/value arrays.
assert(is_array($value));
foreach ($value as $key => $nameComposite) {
assert(is_a($nameComposite, 'MetadataDescription'));
$value[$key] =& $nameComposite->getAllData();
}
}
$dataObject->setData($dataObjectKey, $value);
unset($value);
} elseif ($replace && $dataObject->hasData($dataObjectKey)) {
// Delete existing property data
$dataObject->setData($dataObjectKey, $nullVar);
}
}
return $dataObject;
}
function indexAction()
{
$this->metas(array('DC.Title' => 'Citations'));
$this->view->citations = $table = new Citation();
$s = $table->select()->order('date DESC');
$this->view->model = new Strass_Pages_Model_Rowset($s, 10, $this->_getParam('page'));
$this->actions->append("Enregistrer un citation", array('action' => 'enregistrer'));
}
/**
* Inject the given meta-data into a new citation object.
* @param $metadataDescription MetadataDescription
* @return Citation
*/
protected function &getCitation($citationDescription)
{
// Instantiate the citation and inject the meta-data.
import('lib.pkp.classes.citation.Citation');
$citation = new Citation('raw citation');
$citation->setAssocType($this->assocType);
$citation->setAssocId($this->assocId);
$citation->injectMetadata($citationDescription);
return $citation;
}
/**
* @return Citation[]
*/
public function find()
{
$result = parent::find();
$citations = array();
foreach ($result as $row) {
$citation = new Citation($row);
$repo = new PublicationRepository($this->db);
$citation->setCitationPublication($repo->where('id', '=', $citation->getCitationId())->findSingle());
$citations[] = $citation;
}
return $citations;
}
function indexAction()
{
$this->metas(array('DC.Title' => 'Administration'));
$this->actions->append("Paramètres du site", array('action' => 'parametres'));
$this->view->indicateurs = $m = new Wtk_Table_Model('label', 'url', 'compteur', 'level');
$config = Zend_Registry::get('config');
$m->append('Version', null, Strass_Version::PROJET, array('version-produit', 'notice'));
$m->append('Version des données', null, Strass_Version::dataCurrent(), array('version-data', strass_admin_count_level(Strass_Version::DATA - Strass_Version::dataCurrent(), 1, 1)));
$m->append('Association', null, strtoupper($config->system->association), 'notice');
$t = new Inscriptions();
$count = $t->countRows();
$m->append("Inscriptions à valider", $this->_helper->Url('valider', 'membres'), $count, strass_admin_count_level($count, 1, 5));
$t = new Unites();
$count = $t->countRows();
$m->append("Unités", $this->_helper->Url('unites'), $count, strass_admin_count_level(0 - $count, 0, 0));
$t = new Individus();
$count = $t->countRows();
$m->append("Fiches d'individu", $this->_helper->Url('index', 'individus'), $count, 'notice');
$t = new Users();
$count = $t->countRows();
$m->append("Membres", $this->_helper->Url('index', 'individus', null, array('filtre' => 'membres')), $count, 'notice');
$t = new Citation();
$count = $t->countRows();
$m->append("Citations", $this->_helper->Url('index', 'citation'), $count, 'notice');
$this->view->log = $m = new Wtk_Table_Model('date', 'level', 'logger', 'label', 'url', 'prenom-nom', 'fiche', 'detail-url');
$t = new Logs();
$events = $t->fetchAll($t->select()->order('date DESC')->limit(20));
foreach ($events as $e) {
$url = $this->_helper->Url('event', null, null, array('id' => $e->id));
$u = $e->findParentUsers();
if ($u) {
$i = $u->findParentIndividus();
$pn = $i->getFullname();
$fiche = $this->_helper->Url('fiche', 'individus', null, array('individu' => $i->slug));
} else {
$pn = 'Visiteur';
$fiche = null;
}
$m->append($e->date, strtolower($e->level), $e->logger, $e->message, $e->url, $pn, $fiche, $url);
}
$this->view->connexions = $m = new Wtk_Table_Model('date', 'prenom-nom', 'fiche');
$t = new Users();
$users = $t->fetchAll($t->select()->where('last_login')->order('last_login DESC')->limit(8));
foreach ($users as $u) {
$i = $u->findParentIndividus();
$m->append($u->last_login, $i->getFullname(false, false), $this->_helper->Url('fiche', 'individus', null, array('individu' => $i->slug)));
}
}
/**
* Import citations from a raw citation list to the object
* described by the given association type and id.
* @param $request Request
* @param $assocType int
* @param $assocId int
* @param $rawCitationList string
* @return integer the number of spawned citation checking processes
*/
function importCitations(&$request, $assocType, $assocId, $rawCitationList)
{
assert(is_numeric($assocType) && is_numeric($assocId));
$assocType = (int) $assocType;
$assocId = (int) $assocId;
// Remove existing citations.
$this->deleteObjectsByAssocId($assocType, $assocId);
// Tokenize raw citations
import('lib.pkp.classes.citation.CitationListTokenizerFilter');
$citationTokenizer = new CitationListTokenizerFilter();
$citationStrings = $citationTokenizer->execute($rawCitationList);
// Instantiate and persist citations
$citations = array();
if (is_array($citationStrings)) {
foreach ($citationStrings as $seq => $citationString) {
$citation = new Citation($citationString);
// Initialize the citation with the raw
// citation string.
$citation->setRawCitation($citationString);
// Set the object association
$citation->setAssocType($assocType);
$citation->setAssocId($assocId);
// Set the counter
$citation->setSeq($seq + 1);
$this->insertObject($citation);
$citations[$citation->getId()] = $citation;
unset($citation);
}
}
// Check new citations in parallel.
$noOfProcesses = (int) Config::getVar('general', 'citation_checking_max_processes');
$processDao =& DAORegistry::getDAO('ProcessDAO');
return $processDao->spawnProcesses($request, 'api.citation.CitationApiHandler', 'checkAllCitations', PROCESS_TYPE_CITATION_CHECKING, $noOfProcesses);
}
public function testCitationCrud()
{
$nameSchema = new NlmNameSchema();
$nameDescription = new MetadataDescription($nameSchema, ASSOC_TYPE_AUTHOR);
$nameDescription->addStatement('given-names', $value = 'Peter');
$nameDescription->addStatement('given-names', $value = 'B');
$nameDescription->addStatement('surname', $value = 'Bork');
$nameDescription->addStatement('prefix', $value = 'Mr.');
$citationSchema = new NlmCitationSchema();
$citationDescription = new MetadataDescription($citationSchema, ASSOC_TYPE_CITATION);
$citationDescription->addStatement('person-group[@person-group-type="author"]', $nameDescription);
$citationDescription->addStatement('article-title', $value = 'PHPUnit in a nutshell', 'en_US');
$citationDescription->addStatement('article-title', $value = 'PHPUnit in Kürze', 'de_DE');
$citationDescription->addStatement('date', $value = '2009-08-17');
$citationDescription->addStatement('size', $value = 320);
$citationDescription->addStatement('uri', $value = 'http://phpunit.org/nutshell');
$citation = new Citation('raw citation');
$citation->setAssocType(ASSOC_TYPE_ARTICLE);
$citation->setAssocId(999999);
$citation->setEditedCitation('edited citation');
$citation->setParseScore(50);
$citation->injectMetadata($citationDescription);
// Create citation
$citationId = $this->citationDAO->insertCitation($citation);
self::assertTrue(is_numeric($citationId));
self::assertTrue($citationId > 0);
// Retrieve citation
$citationById = $this->citationDAO->getCitation($citationId);
$citationById->getMetadataFieldNames();
// Initializes internal state for comparison.
self::assertEquals($citation, $citationById);
$citationsByAssocIdDaoFactory = $this->citationDAO->getCitationsByAssocId(ASSOC_TYPE_ARTICLE, 999999);
$citationsByAssocId = $citationsByAssocIdDaoFactory->toArray();
self::assertEquals(1, count($citationsByAssocId));
$citationsByAssocId[0]->getMetadataFieldNames();
// Initializes internal state for comparison.
self::assertEquals($citation, $citationsByAssocId[0]);
// Update citation
$citationDescription->removeStatement('date');
$citationDescription->addStatement('article-title', $value = 'PHPUnit rápido', 'pt_BR');
$updatedCitation = new Citation('another raw citation');
$updatedCitation->setId($citationId);
$updatedCitation->setAssocType(ASSOC_TYPE_ARTICLE);
$updatedCitation->setAssocId(999998);
$updatedCitation->setEditedCitation('another edited citation');
$updatedCitation->setParseScore(50);
$updatedCitation->injectMetadata($citationDescription);
$this->citationDAO->updateCitation($updatedCitation);
$citationAfterUpdate = $this->citationDAO->getCitation($citationId);
$citationAfterUpdate->getMetadataFieldNames();
// Initializes internal state for comparison.
self::assertEquals($updatedCitation, $citationAfterUpdate);
// Delete citation
$this->citationDAO->deleteCitationsByAssocId(ASSOC_TYPE_ARTICLE, 999998);
self::assertNull($this->citationDAO->getCitation($citationId));
}
/**
* @see MetadataDataObjectAdapter::injectMetadataIntoDataObject()
* @param $metadataDescription MetadataDescription
* @param $dataObject Citation
* @param $replace boolean whether existing meta-data should be replaced
* @return DataObject
*/
function &injectMetadataIntoDataObject(&$metadataDescription, &$dataObject, $replace)
{
// Did we get an existing citation object or should we create a new one?
if (is_null($dataObject)) {
import('lib.pkp.classes.citation.Citation');
$dataObject = new Citation();
}
// Add new meta-data statements to the citation. Add the schema
// name space to each property name so that it becomes unique
// across schemas.
$metadataSchemaNamespace = $this->getMetadataNamespace();
$nullVar = null;
foreach ($metadataDescription->getPropertyNames() as $propertyName) {
$dataObjectKey = $metadataSchemaNamespace . ':' . $propertyName;
if ($metadataDescription->hasStatement($propertyName)) {
// Directly retrieve the internal data so that we don't
// have to care about cardinality and translation.
$value =& $metadataDescription->getData($propertyName);
if (in_array($propertyName, array('person-group[@person-group-type="author"]', 'person-group[@person-group-type="editor"]'))) {
assert(is_array($value));
// Dereference the value to make sure that we don't destroy
// the original MetadataDescription.
$tmpValue = $value;
unset($value);
$value =& $tmpValue;
// Convert MetadataDescription objects to simple key/value arrays.
foreach ($value as $key => $name) {
if (is_a($name, 'MetadataDescription')) {
// A name can either be a full name description...
$value[$key] =& $name->getAllData();
} else {
// ...or an 'et-al' string.
assert($name == PERSON_STRING_FILTER_ETAL);
// No need to change the value encoding.
}
}
}
$dataObject->setData($dataObjectKey, $value);
unset($value);
} elseif ($replace && $dataObject->hasData($dataObjectKey)) {
// Delete existing property data
$dataObject->setData($dataObjectKey, $nullVar);
}
}
return $dataObject;
}
public function testCitationCrud()
{
$nameSchema = new NlmNameSchema();
$nameDescription = new MetadataDescription($nameSchema, ASSOC_TYPE_AUTHOR);
$nameDescription->addStatement('given-names', $value = 'Peter');
$nameDescription->addStatement('given-names', $value = 'B');
$nameDescription->addStatement('surname', $value = 'Bork');
$nameDescription->addStatement('prefix', $value = 'Mr.');
$citationSchema = new NlmCitationSchema();
$citationDescription = new MetadataDescription($citationSchema, ASSOC_TYPE_CITATION);
$citationDescription->addStatement('person-group[@person-group-type="author"]', $nameDescription);
$citationDescription->addStatement('article-title', $value = 'PHPUnit in a nutshell', 'en_US');
$citationDescription->addStatement('article-title', $value = 'PHPUnit in Kürze', 'de_DE');
$citationDescription->addStatement('date', $value = '2009-08-17');
$citationDescription->addStatement('size', $value = 320);
$citationDescription->addStatement('uri', $value = 'http://phpunit.org/nutshell');
$citation = new Citation('raw citation');
$citation->setAssocType(ASSOC_TYPE_ARTICLE);
$citation->setAssocId(5);
$citation->setEditedCitation('edited citation');
$citation->setParseScore(50);
$citation->injectMetadata($citationDescription);
$citationId = $this->citationDAO->insertCitation($citation);
self::assertTrue(is_numeric($citationId));
self::assertTrue($citationId > 0);
}
/**
* @covers CitationParserService::parse
*/
public function testParse()
{
$citation = new Citation(METADATA_GENRE_JOURNALARTICLE, 'rawCitation');
// Set an "unclean" article title and add a comment
// to test whether parse() cleans this up.
$citation->setArticleTitle('Article Title with Punctuation.');
$citation->addComment('Comment with Punctuation.');
// Mock CitationParserService->parseInternal() which will usually
// be implemented by sub-classes.
$mockCPService =& $this->getMock('CitationParserService', array('parseInternal'));
// Set up the parseInternal() method
$mockCPService->expects($this->once())->method('parseInternal')->with($this->equalTo($mockCPService->getCitationString($citation)))->will($this->returnValue($citation));
// Call the SUT
$citation = $mockCPService->parse($citation);
// Test whether the citation has been cleaned up.
self::assertEquals('Article Title with Punctuation', $citation->getArticleTitle());
self::assertEquals(array('Comment with Punctuation'), $citation->getComments());
}
public static function nonPatentLiterature($text, $citedBy = null, $country = null, $citationDate = null)
{
$citation = new Citation(Citation::NON_PATENT_LITERATURE);
$citation->setText($text);
$citation->setCitedBy($citedBy);
$citation->setCitationDate($citationDate);
$citation->setCountry($country);
return $citation;
}
/**
* Custom implementation of Form::validate() that validates
* meta-data form data and injects it into the internal citation
* object.
*
* NB: The configuration of the internal citation object
* would normally be done in readInputData(). Validation and
* injection can easily be done in one step. It therefore avoids
* code duplication and improves performance to do both here.
*/
function validate()
{
// Make sure that this method is not called twice which
// would corrupt internal state.
assert(empty($this->_metadataDescriptions));
parent::validate();
// Validate form data and inject it into
// the associated citation object.
$citation =& $this->getCitation();
$citation->setRawCitation($this->getData('rawCitation'));
if ($this->getData('citationApproved') == 'citationApproved') {
// Editor's shortcut to the approved state, e.g. for manually edited citations.
$citation->setCitationState(CITATION_APPROVED);
} elseif (in_array($this->getData('citationState'), Citation::_getSupportedCitationStates())) {
// Reset citation state if necessary
if ($this->getData('citationState') == CITATION_APPROVED) {
$this->setData('citationState', CITATION_LOOKED_UP);
}
$citation->setCitationState($this->getData('citationState'));
}
// Extract data from citation form fields and inject it into the citation
import('lib.pkp.classes.metadata.MetadataDescription');
$metadataSchemas = $citation->getSupportedMetadataSchemas();
foreach ($metadataSchemas as $metadataSchema) {
/* @var $metadataSchema MetadataSchema */
// Instantiate a meta-data description for the given schema
$metadataDescription = new MetadataDescription($metadataSchema->getClassName(), ASSOC_TYPE_CITATION);
// Set the meta-data statements
foreach ($metadataSchema->getProperties() as $propertyName => $property) {
$fieldName = $metadataSchema->getNamespacedPropertyId($propertyName);
$fieldValue = trim($this->getData($fieldName));
if (empty($fieldValue)) {
// Delete empty statements so that previously set
// statements (if any) will be deleted.
$metadataDescription->removeStatement($propertyName);
if ($property->getMandatory()) {
// A mandatory field is missing - add a validation error.
$this->addError($fieldName, __($property->getValidationMessage()));
$this->addErrorField($fieldName);
}
} else {
// Try to convert the field value to (a) strongly
// typed object(s) if applicable. Start with the most
// specific allowed type so that we always get the
// most strongly typed result possible.
$allowedTypes = $property->getAllowedTypes();
switch (true) {
case isset($allowedTypes[METADATA_PROPERTY_TYPE_VOCABULARY]) && is_numeric($fieldValue):
case isset($allowedTypes[METADATA_PROPERTY_TYPE_INTEGER]) && is_numeric($fieldValue):
$typedFieldValues = array((int) $fieldValue);
break;
case isset($allowedTypes[METADATA_PROPERTY_TYPE_DATE]):
import('lib.pkp.classes.metadata.DateStringNormalizerFilter');
$dateStringFilter = new DateStringNormalizerFilter();
assert($dateStringFilter->supportsAsInput($fieldValue));
$typedFieldValues = array($dateStringFilter->execute($fieldValue));
break;
case isset($allowedTypes[METADATA_PROPERTY_TYPE_COMPOSITE]):
// We currently only support name composites
$allowedAssocIds = $allowedTypes[METADATA_PROPERTY_TYPE_COMPOSITE];
if (in_array(ASSOC_TYPE_AUTHOR, $allowedAssocIds)) {
$assocType = ASSOC_TYPE_AUTHOR;
} elseif (in_array(ASSOC_TYPE_EDITOR, $allowedAssocIds)) {
$assocType = ASSOC_TYPE_EDITOR;
} else {
assert(false);
}
// Try to transform the field to a name composite.
import('lib.pkp.plugins.metadata.nlm30.filter.PersonStringNlm30NameSchemaFilter');
$personStringFilter = new PersonStringNlm30NameSchemaFilter($assocType, PERSON_STRING_FILTER_MULTIPLE);
assert($personStringFilter->supportsAsInput($fieldValue));
$typedFieldValues =& $personStringFilter->execute($fieldValue);
break;
default:
$typedFieldValues = array($fieldValue);
}
// Inject data into the meta-data description and thereby
// implicitly validate the field value.
foreach ($typedFieldValues as $typedFieldValue) {
if (!$metadataDescription->addStatement($propertyName, $typedFieldValue)) {
// Add form field error
$this->addError($fieldName, __($property->getValidationMessage()));
$this->addErrorField($fieldName);
}
unset($typedFieldValue);
}
unset($typedFieldValues);
}
}
// Inject the meta-data into the citation.
$citation->injectMetadata($metadataDescription);
// Save the meta-data description for later usage.
$this->_metadataDescriptions[] =& $metadataDescription;
unset($metadataDescription);
}
return $this->isValid();
}
/**
* @covers CitationDAO
*/
public function testCitationCrud()
{
$citationDao = DAORegistry::getDAO('CitationDAO');
/* @var $citationDao CitationDAO */
$nameSchemaName = 'lib.pkp.plugins.metadata.nlm30.schema.Nlm30NameSchema';
$nameDescription = new MetadataDescription($nameSchemaName, ASSOC_TYPE_AUTHOR);
$nameDescription->addStatement('given-names', $value = 'Peter');
$nameDescription->addStatement('given-names', $value = 'B');
$nameDescription->addStatement('surname', $value = 'Bork');
$nameDescription->addStatement('prefix', $value = 'Mr.');
$citationSchemaName = 'lib.pkp.plugins.metadata.nlm30.schema.Nlm30CitationSchema';
$citationDescription = new MetadataDescription($citationSchemaName, ASSOC_TYPE_CITATION);
$citationDescription->addStatement('person-group[@person-group-type="author"]', $nameDescription);
$citationDescription->addStatement('article-title', $value = 'PHPUnit in a nutshell', 'en_US');
$citationDescription->addStatement('article-title', $value = 'PHPUnit in Kürze', 'de_DE');
$citationDescription->addStatement('date', $value = '2009-08-17');
$citationDescription->addStatement('size', $value = 320);
$citationDescription->addStatement('uri', $value = 'http://phpunit.org/nutshell');
// Add a simple source description.
$sourceDescription = new MetadataDescription($citationSchemaName, ASSOC_TYPE_CITATION);
$sourceDescription->setDisplayName('test');
$sourceDescription->addStatement('article-title', $value = 'a simple source description', 'en_US');
$sourceDescription->setSeq(0);
$citation = new Citation('raw citation');
$citation->setAssocType(ASSOC_TYPE_ARTICLE);
$citation->setAssocId(999999);
$citation->setSeq(50);
$citation->addSourceDescription($sourceDescription);
$citation->injectMetadata($citationDescription);
// Create citation.
$citationId = $citationDao->insertObject($citation);
self::assertTrue(is_numeric($citationId));
self::assertTrue($citationId > 0);
// Retrieve citation.
$citationById = $citationDao->getObjectById($citationId);
// Fix state differences for comparison.
$citation->removeSupportedMetadataAdapter($citationSchemaName);
$citationById->removeSupportedMetadataAdapter($citationSchemaName);
$citationById->_extractionAdaptersLoaded = true;
$citationById->_injectionAdaptersLoaded = true;
$sourceDescription->setAssocId($citationId);
$sourceDescription->removeSupportedMetadataAdapter($citationSchemaName);
$sourceDescriptions = $citationById->getSourceDescriptions();
$sourceDescriptions['test']->getMetadataSchema();
// this will instantiate the meta-data schema internally.
self::assertEquals($citation, $citationById);
$citationsByAssocIdDaoFactory = $citationDao->getObjectsByAssocId(ASSOC_TYPE_ARTICLE, 999999);
$citationsByAssocId = $citationsByAssocIdDaoFactory->toArray();
self::assertEquals(1, count($citationsByAssocId));
// Fix state differences for comparison.
$citationsByAssocId[0]->_extractionAdaptersLoaded = true;
$citationsByAssocId[0]->_injectionAdaptersLoaded = true;
$citationsByAssocId[0]->removeSupportedMetadataAdapter($citationSchemaName);
$sourceDescriptionsByAssocId = $citationsByAssocId[0]->getSourceDescriptions();
$sourceDescriptionsByAssocId['test']->getMetadataSchema();
// this will instantiate the meta-data schema internally.
self::assertEquals($citation, $citationsByAssocId[0]);
// Update citation.
$citationDescription->removeStatement('date');
$citationDescription->addStatement('article-title', $value = 'PHPUnit rápido', 'pt_BR');
// Update source descriptions.
$sourceDescription->addStatement('article-title', $value = 'edited source description', 'en_US', true);
$updatedCitation = new Citation('another raw citation');
$updatedCitation->setId($citationId);
$updatedCitation->setAssocType(ASSOC_TYPE_ARTICLE);
$updatedCitation->setAssocId(999998);
$updatedCitation->setSeq(50);
$updatedCitation->addSourceDescription($sourceDescription);
$updatedCitation->injectMetadata($citationDescription);
$citationDao->updateObject($updatedCitation);
$citationAfterUpdate = $citationDao->getObjectById($citationId);
// Fix state differences for comparison.
$updatedCitation->removeSupportedMetadataAdapter($citationSchemaName);
$citationAfterUpdate->removeSupportedMetadataAdapter($citationSchemaName);
$citationAfterUpdate->_extractionAdaptersLoaded = true;
$citationAfterUpdate->_injectionAdaptersLoaded = true;
$sourceDescriptionsAfterUpdate = $citationAfterUpdate->getSourceDescriptions();
$sourceDescriptionsAfterUpdate['test']->getMetadataSchema();
// this will instantiate the meta-data schema internally.
$sourceDescription->removeSupportedMetadataAdapter($citationSchemaName);
self::assertEquals($updatedCitation, $citationAfterUpdate);
// Delete citation
$citationDao->deleteObjectsByAssocId(ASSOC_TYPE_ARTICLE, 999998);
self::assertNull($citationDao->getObjectById($citationId));
}
/**
* Our construct function.
*/
public function __construct( $parser, $frame, $args ) {
parent::__construct($parser, $frame, $args);
}
function initView($view)
{
$view->document->addStyleComponents('citation');
$t = new Citation();
$view->citation = $t->findRandom();
}
/**
* Take an array of citation parse/lookup results and derive a citation
* with one "best" set of values.
*
* We determine the best values within the citations that have a score above
* the given threshold. Citations with a score below the threshold will be
* ignored.
*
* For these citations we count the frequency of values per meta-data property.
* The most frequent value will be chosen as "best" value.
*
* If two values have the same frequency then decide based on the score. If
* this is still ambivalent then return the first of the remaining values.
*
* @param $scoredCitations
* @param $scoreThreshold integer a number between 0 (=no threshold) and 100
* @return Citation one citation with the "best" values set
*/
function &_guessValues(&$scoredCitations, $scoreThreshold)
{
assert($scoreThreshold >= 0 && $scoreThreshold <= 100);
// Create the target citation description.
$targetDescription = new MetadataDescription('lib.pkp.plugins.metadata.nlm30.schema.Nlm30CitationSchema', ASSOC_TYPE_CITATION);
// Step 1: List all values and max scores that have been identified for a given element
// but only include values from results above a given scoring threshold
// Initialize variables for the first step.
$valuesByPropertyName = array();
$maxScoresByPropertyNameAndValue = array();
// Sort the scored citations by score with the highest score first.
krsort($scoredCitations);
foreach ($scoredCitations as $currentScore => $citationsForCurrentScore) {
// Check whether the current score is below the threshold, if so
// stop the loop. We've sorted our citations by score so the remaining
// citations all have scores below the threshold and we can forget
// about them.
if ($currentScore < $scoreThreshold) {
break;
}
foreach ($citationsForCurrentScore as $citationForCurrentScore) {
$statements = $citationForCurrentScore->getStatements();
// Add the property values and scores of this citation
// to the overall property lists
foreach ($statements as $propertyName => $value) {
// Initialize sub-arrays if necessary
if (!isset($valuesByPropertyName[$propertyName])) {
$valuesByPropertyName[$propertyName] = array();
}
if (!isset($maxScoresByPropertyNameAndValue[$propertyName])) {
$maxScoresByPropertyNameAndValue[$propertyName] = array();
}
// Add the value for the given property, as we want to count
// value frequencies later, we explicitly allow duplicates.
$serializedValue = serialize($value);
$valuesByPropertyName[$propertyName][] = $serializedValue;
// As we have ordered our citations descending by score, the
// first score found for a value is also the maximum score.
if (!isset($maxScoresByPropertyNameAndValue[$propertyName][$serializedValue])) {
$maxScoresByPropertyNameAndValue[$propertyName][$serializedValue] = $currentScore;
}
}
}
}
// Step 2: Find out the values that occur most frequently for each element
// and order these by score.
foreach ($valuesByPropertyName as $propertyName => $values) {
// Count the occurrences of each value within the given element
$valueFrequencies = array_count_values($values);
// Order the most frequent values to the beginning of the array
arsort($valueFrequencies);
// Get the most frequent values (may be several if there are more than one
// with the same frequency).
$scoresOfMostFrequentValues = array();
$previousValueFrequency = 0;
foreach ($valueFrequencies as $value => $valueFrequency) {
// Only extract the most frequent values, jump out of the
// loop when less frequent values start.
if ($previousValueFrequency > $valueFrequency) {
break;
}
$previousValueFrequency = $valueFrequency;
$scoresOfMostFrequentValues[$value] = $maxScoresByPropertyNameAndValue[$propertyName][$value];
}
// Now we can order the most frequent values by score, starting
// with the highest score.
arsort($scoresOfMostFrequentValues);
// Now get the first key which represents the value with the
// highest frequency and the highest score.
reset($scoresOfMostFrequentValues);
$bestValue = unserialize(key($scoresOfMostFrequentValues));
// Set the found "best" element value in the result citation.
$statements = array($propertyName => $bestValue);
$success = $targetDescription->setStatements($statements);
assert($success);
}
// Instantiate the target citation
$targetCitation = new Citation();
$targetCitation->injectMetadata($targetDescription);
return $targetCitation;
}
/**
* Set the citationState
* @param $citationState integer
*/
function setCitationState($citationState)
{
assert(in_array($citationState, Citation::_getSupportedCitationStates()));
$this->_citationState = $citationState;
}
/**
* Save citation
*/
function execute()
{
$citation =& $this->getCitation();
$citation->setEditedCitation($this->getData('editedCitation'));
if (in_array($this->getData('citationState'), Citation::_getSupportedCitationStates())) {
$citation->setCitationState($this->getData('citationState'));
}
// Extract data from citation form fields and inject it into the citation
$metadataAdapters = $citation->getSupportedMetadataAdapters();
foreach ($metadataAdapters as $metadataAdapter) {
// Instantiate a meta-data description for the given schema
$metadataSchema =& $metadataAdapter->getMetadataSchema();
import('metadata.MetadataDescription');
$metadataDescription = new MetadataDescription($metadataSchema, ASSOC_TYPE_CITATION);
// Set the meta-data statements
$metadataSchemaNamespace = $metadataSchema->getNamespace();
foreach ($metadataSchema->getProperties() as $propertyName => $property) {
$fieldName = $metadataSchema->getNamespacedPropertyId($propertyName);
$fieldValue = trim($this->getData($fieldName));
if (empty($fieldValue)) {
$metadataDescription->removeStatement($propertyName);
} else {
$foundValidType = false;
foreach ($property->getTypes() as $type) {
// Some property types need to be converted first
switch ($type) {
// We currently only support name composites
case array(METADATA_PROPERTY_TYPE_COMPOSITE => ASSOC_TYPE_AUTHOR):
case array(METADATA_PROPERTY_TYPE_COMPOSITE => ASSOC_TYPE_EDITOR):
import('metadata.nlm.PersonStringNlmNameSchemaFilter');
$personStringFilter = new PersonStringNlmNameSchemaFilter($type[METADATA_PROPERTY_TYPE_COMPOSITE], PERSON_STRING_FILTER_MULTIPLE);
assert($personStringFilter->supportsAsInput($fieldValue));
$fieldValue =& $personStringFilter->execute($fieldValue);
$foundValidType = true;
break;
case METADATA_PROPERTY_TYPE_INTEGER:
$fieldValue = array((int) $fieldValue);
$foundValidType = true;
break;
case METADATA_PROPERTY_TYPE_DATE:
import('metadata.DateStringNormalizerFilter');
$dateStringFilter = new DateStringNormalizerFilter();
assert($dateStringFilter->supportsAsInput($fieldValue));
$fieldValue = array($dateStringFilter->execute($fieldValue));
$foundValidType = true;
break;
default:
if ($property->isValid($fieldValue)) {
$fieldValue = array($fieldValue);
$foundValidType = true;
break;
}
}
// Break the outer loop once we found a valid
// interpretation for our form field.
if ($foundValidType) {
break;
}
}
foreach ($fieldValue as $fieldValueStatement) {
$metadataDescription->addStatement($propertyName, $fieldValueStatement);
unset($fieldValueStatement);
}
}
}
// Inject the meta-data into the citation
$citation->injectMetadata($metadataDescription, true);
}
// Persist citation
$citationDAO =& DAORegistry::getDAO('CitationDAO');
if (is_numeric($citation->getId())) {
$citationDAO->updateCitation($citation);
} else {
$citationDAO->insertCitation($citation);
}
return true;
}
/**
* This will retrieve a citation object from the
* grids data source based on the request arguments.
* If no citation can be found then this will raise
* a fatal error.
* @param $args array
* @param $createIfMissing boolean If this is set to true
* then a citation object will be instantiated if no
* citation id is in the request.
* @return Citation
*/
function &getCitationFromArgs($request, &$args, $createIfMissing = false)
{
// Identify the citation id and retrieve the
// corresponding element from the grid's data source.
if (isset($args['citationId'])) {
$citation =& $this->getRowDataElement($request, $args['citationId']);
if (is_null($citation)) {
fatalError('Invalid citation id!');
}
} else {
if ($createIfMissing) {
// It seems that a new citation is being edited/updated
import('lib.pkp.classes.citation.Citation');
$citation = new Citation();
$citation->setAssocType($this->getAssocType());
$citation->setAssocId($this->getAssocId());
} else {
fatalError('Missing citation id!');
}
}
return $citation;
}
/**
* This will retrieve a citation object from the
* grids data source based on the request arguments.
* If no citation can be found then this will raise
* a fatal error.
* @param $args array
* @param $createIfMissing boolean If this is set to true
* then a citation object will be instantiated if no
* citation id is in the request.
* @return Citation
*/
function &_getCitationFromArgs(&$args, $createIfMissing = false)
{
// Identify the citation id and retrieve the
// corresponding element from the grid's data source.
if (!isset($args['citationId'])) {
if ($createIfMissing) {
// It seems that a new citation is being edited/updated
import('citation.Citation');
$citation = new Citation();
$citation->setAssocType(ASSOC_TYPE_ARTICLE);
$article =& $this->getArticle();
$citation->setAssocId($article->getId());
} else {
fatalError('Missing citation id!');
}
} else {
$citation =& $this->getRowDataElement($args['citationId']);
if (is_null($citation)) {
fatalError('Invalid citation id!');
}
}
return $citation;
}