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- <?php
- // This Tripal_cv.owl_loader.php and OWLStanza.inc(CLASS) file is being developed to read and parse through any scientific
- // ontology XML Owl file to have the vocabularies be inserted into the Chado database for the open source project
- // Tripal.info to be used.
- /**
- * @file
- * @add file from header
- */
- require_once('OWLStanza.inc');
- /**
- * Parses an OWL XML file and imports the CV terms into Chado
- *
- * @param $filename The
- * full path to the OWL XML file.
- *
- * @return No return value.
- *
- * @throws Exception
- */
- function tripal_cv_parse_owl($filename) {
- // TODO: need to pass in the $db_name as the cv name into the function when you see the
- // oboInOwl:default-namespace that is not the same as $db_name.
- //
- // TODO: this all should occur inside of a transaction.
- // Opening the OWL file for parsing.
- $owl = new XMLReader();
- // This command will open and read the any Owl file.
- if (!$owl->open($filename)) {
- print "ERROR opening OWL file: '$filename'\n";
- exit();
- }
- // Get the RDF stanza. We pass FALSE as the second parameter to prevent
- // the object from reading the entire file into memory.
- $rdf = new OWLStanza($owl, FALSE);
- // Get the ontology stanza. It will contain the values for the database
- // name for this ontology.
- $ontology = new OWLStanza($owl);
- // Look for the db name in using the 'oboInOwl:default-namespace term. If it's
- // not present then we'll use the 'about' element to get the namespace.
- $namespace = $ontology->getChild('oboInOwl:default-namespace');
- if ($namespace) {
- $db_name = $namespace->getValue();
- }
- else {
- // Insert the database record into Chado using the owl:Ontology stanza of the owl file.
- $about = $ontology->getAttribute('rdf:about');
- // We wrote the regular expression on the rdf.about line to get the database name for any particular Owl file.
- if (preg_match('/^.*\/(.*?)\..*$/', $about, $matches)) {
- $db_name = strtoupper($matches[1]);
- }
- }
- //
- // Step 1: Make sure that all dependencies (database names) are met for each Owl ontology file.
- //
- // loop through each stanza, one at a time, and handle each one
- // based on the tag name.
- $stanza = new OWLStanza($owl);
- // Set an empty array for the dependencies to go in.
- $deps = [
- 'db' => [],
- 'dbxref' => [],
- ];
- // Start looping and parsing through the owl:Class stanza section of the Owl file.
- while (!$stanza->isFinished()) {
- // Use the tag name from OWLStanza.inc to identify which function should be called.
- switch ($stanza->getTagName()) {
- case 'owl:Class':
- tripal_owl_check_class_depedencies($stanza, $vocab_db_name, $deps);
- break;
- }
- // Get to the next stanza in the OWL file.
- $stanza = new OWLStanza($owl);
- }
- if (count(array_keys($deps['db'])) > 0 or count(array_keys($deps['dbxref'])) > 0) {
- // We have unmet dependencies. Print those out and return.
- // The deps array will have DB’s, then terms' . "\n");
- if (count($deps['db']) > 0) {
- drupal_set_message('Cannot import ontology, "' . $db_name . '", as the following ' . 'dependent vocabularies must first be imported: ' . print_r(array_keys($deps['db']), TRUE) . '\n', 'error');
- }
- if (count($deps['dbxref']) > 0) {
- drupal_set_message('Cannot import ontology, "' . $db_name . '", as the following ' . 'dependent terms must first be imported: ' . print_r(array_keys($deps['dbxref']), TRUE) . '\n', 'error');
- }
- return;
- }
- //
- // Step 2: If we pass the dependency check in step 1 then we can insert
- // the terms.
- //
- // Holds an array of CV and DB records that have already been
- // inserted (reduces number of queires).
- $vocabs = [
- 'db' => [],
- 'cv' => [],
- 'this' => [],
- ];
- // Reload the ontology to reposition at the beginning of the OWl file for inserting the
- // new terms into Chado.
- $owl = new XMLReader();
- if (!$owl->open($filename)) {
- print "ERROR opening OWL file: '$filename'\n";
- exit();
- }
- $rdf = new OWLStanza($owl, FALSE);
- $ontology = new OWLStanza($owl);
- // Insert the database record into Chado using the
- // owl:Ontology stanza.
- $url = '';
- $homepage = $ontology->getChild('foaf:homepage');
- if ($homepage) {
- $url = $homepage->getValue();
- }
- $db = [
- 'url' => $url,
- 'name' => $db_name,
- ];
- // Using the Tripal API function to insert the term into the Chado database.
- $db = chado_insert_db($db);
- // Get the description for this vocabulary. This should be in the
- // dc:description element. If that element is missing then the
- // description should default to the empty string.
- $cv_description = '';
- $description = $ontology->getChild('dc:description');
- if ($description) {
- $cv_description = $description->getValue();
- }
- // Get the name for the CV. This should be in the 'dc:title' element. If the
- // title is not present then the cv name should default to the database name.
- $cv_name == $namespace = $ontology->getChild('oboInOwl:default-namespace');
- if ($namespace) {
- $cv_name = $namespace->getValue();
- }
- $title = $ontology->getChild('dc:title');
- if ($title) {
- $cv_name = preg_replace("/[^\w]/", "_", strtolower($title->getValue()));
- }
- // Insert the CV record into Chado.
- $cv = chado_insert_cv($cv_name, $cv_description);
- // Add this CV and DB to our vocabs array so we can reuse it later.
- $vocabs[$db_name]['cv'] = $namespace_cv;
- $vocabs[$db_name]['db'] = $db;
- $vocabs['this'] = $db_name;
- // loop through each stanza of the owl file, one at a time, and handle each one
- // based on the tag name from the OWLStanza.inc file.
- $stanza = new OWLStanza($owl);
- while (!$stanza->isFinished()) {
- // Use the tag name to identify which function should be called.
- switch ($stanza->getTagName()) {
- case 'owl:AnnotationProperty':
- // tripal_owl_handle_annotation_property($stanza, $vocabs);
- break;
- case 'rdf:Description':
- // tripal_owl_handle_description($stanza, $vocabs);
- break;
- case 'owl:ObjectProperty':
- // tripal_owl_handle_object_property($stanza, $vocabs);
- break;
- case 'owl:Class':
- tripal_owl_handle_class($stanza, $vocabs);
- break;
- case 'owl:Axiom':
- break;
- case 'owl:Restriction':
- break;
- default:
- throw new Exception("Unhandled stanza: " . $stanza->getTagName());
- exit();
- break;
- }
- // Get the next stanza in the OWL file.
- $stanza = new OWLStanza($owl);
- }
- // Close the XMLReader $owl object.
- $owl->close();
- }
- /**
- * Checks for required vocabularies that are not loaded into Chado.
- *
- * Some vocabularies use terms from other ontologies. If this is happens
- * we need to ensure that the dependent vocabularies are present in the
- * database prior to loading this one. This function adds to the $deps
- * array all of the database names and term accessions that are missing in
- * Chado.
- *
- * @param $stanza The
- * OWLStanza object for the current stanza from the OWL file.
- * @param $vocab_db_name The
- * name of the database for the vocabulary being loded.
- * @param $deps The
- * dependencies array. The missing databases are provided in array
- * using a 'db' key, and missing terms are in a second array using a
- * 'dbxref' key.
- */
- function tripal_owl_check_class_depedencies(OWLStanza $stanza, $vocab_db_name, &$deps) {
- // Initialize the variables.
- $db_name = '';
- $accession = '';
- $db = NULL;
- // Get the DB name and accession from the "rdf:about" attribute.
- $about = $stanza->getAttribute('rdf:about');
- if (!$about) {
- // TODO: some owl:Class stanzas do not have an about. What are these?
- // how should we handle them.
- return;
- }
- // We wrote the regular expression on the rdf.about line to get the database
- // name and accession term for any particular Owl file.
- if (preg_match('/.*\/(.+)_(.+)/', $about, $matches)) {
- $db_name = strtoupper($matches[1]);
- $accession = $matches[2];
- }
- else {
- throw new Exception("owl:Class stanza 'rdf:about' attribute is not formated as expected: '$about'. " . "This is necessary to determine the term's accession: \n\n" . $stanza->getXML());
- }
- // If the database name for this term is the same as the vocabulary
- // we are trying to load, then don't include it in the $deps array.
- if ($db_name !== $vocab_db_name) {
- return;
- }
- // Check if the db_name does not exist in the chado.db table. If it
- // does not exist then add it to our $deps array. If the query fails then
- // throw an exception.
- $db = chado_select_record('db', [
- 'db_id',
- ], [
- 'name' => $db_name,
- ]);
- if ($db === FALSE) {
- throw new Exception("Failed to execute query to find vocabulary in chado.db table\n\n" . $stanza->getXML());
- }
- else {
- if (count($db) == 0) {
- $deps['db'][$db_name] = TRUE;
- // Does this stanza provide the URL for the OWL file of this missing
- // dependency. If so then add it to our deps array.
- $imported_from = $stanza->getChild('obo:IAO_0000412');
- if ($imported_from == NULL) {
- return;
- }
- $url = $imported_from->getAttribute('rdf:resource');
- if ($url) {
- $deps['db'][$db_name] = $url;
- }
- return;
- }
- }
- // If the db_name exists, then check if the accession exists in
- // the chado.dbxref table. If it doesn't exist then add an entry to the
- // $deps array. If the query fails then throw an exception.
- $values = [
- 'db_id' => $db[0]->db_id,
- 'accession' => $accession,
- ];
- $dbxref = chado_select_record('dbxref', [
- 'dbxref_id',
- 'db_id',
- ], $values);
- if ($dbxref === FALSE) {
- throw new Exception("Failed to execute query to find vocabulary term in chado.dbxref table\n\n" . $stanza->getXML());
- }
- elseif (count($accession) == 0) {
- $deps['dbxref'][$db_name . ':' . $accesson] = TRUE;
- }
- return;
- }
- /**
- *
- * @param
- * $stanza
- * @param
- * $vocabs
- *
- * @throws Exception
- */
- function tripal_owl_handle_object_property($stanza, $vocabs) {
- }
- /**
- *
- * @param
- * $stanza
- * @param
- * $vocabs
- *
- * @throws Exception
- */
- function tripal_owl_handle_annotation_property($stanza, $vocabs) {
- // $matches = array();
- // $db_name = '';
- // $accession = '';
- // $about = $stanza->getAttribute('rdf:about');
- // // Get the DB name and accession from the about attribute using the preg match function.
- // if (preg_match('/.*\/(.+)_(.+)/', $about, $matches)) {
- // $db_name = ($matches[1]);
- // $accession = $matches[2];
- // }
- // else {
- // throw new Exception("owl:Class stanza 'rdf:about' attribute is not formated as expected: '$about'. " . "This is necessary to determine the term's accession: \n\n" . $stanza->getXML());
- // }
- // // Insert a DB Record
- // if (array_key_exists($db_name, $vocabs)) {
- // $db = $vocabs[$db_name]['db'];
- // $default_namespace_cv = $vocabs[$db_name]['cv'];
- // }
- // else {
- // // Unfortunately, all we have is the name. The OWL format
- // // doesn't provides us the URL, description, etc.
- // $values = array(
- // 'name' => $db_name
- // );
- // $db = chado_insert_db($values);
- // // Insert a dbxref record.
- // $values = array(
- // 'db_id' => $db->db_id,
- // 'accession' => $accession
- // );
- // $dbxref = chado_insert_dbxref($values);
- // $imported_from = $stanza->getChild('obo:IAO_0000114');
- // if ($imported_from == NULL) {
- // return;
- // }
- // $url = $imported_from->getAttribute('rdf:resource');
- // if ($url) {
- // $vocabs['db'][$db_name] = $url;
- // }
- // return;
- // }
- // // Insert a new cvterm record.
- // $cvterm_name = '';
- // $definition = '';
- // $cvterm_name = $stanza->getChild('rdfs:label');
- // if ($cvterm_name) {
- // $cvterm_name = $stanza->getValue();
- // }
- // $definition = $stanza->getChild('obo:IAO_0000115');
- // if ($definition) {
- // $definition = $stanza->getValue();
- // }
- // $term = array(
- // 'id' => $db->name .':'. $dbxref->accession,
- // 'name' => $cvterm_name,
- // 'cv_name' => $cv->name,
- // 'definition' => $definition,
- // );
- // $option =array();
- // if ($vocabs['this'] != $db->name){
- // $option['update_existing'] = FALSE;
- // }
- // $cvterm = chado_insert_cvterm($term, $option);
- // }
- }
- /**
- *
- * @param
- * $stanza
- * @param
- * $vocabs
- *
- * @throws Exception
- */
- function tripal_owl_handle_description($stanza, $vocabs) {
- }
- /**
- *
- * The function goes through owl:Class stanza to insert new vocabularies.
- *
- * @param $stanza The
- * OWLStanza object for the current stanza from the OWL file.
- * @param
- * $vocabs
- *
- * @throws Exception
- */
- function tripal_owl_handle_class(OWLStanza $stanza, $vocabs) {
- // Initialize the database and cv variables.
- $db_name = $vocabs['this'];
- $accession = '';
- $is_a = '';
- $namespace_cv = $vocabs[$db_name]['cv'];
- $db = $vocabs[$db_name]['db'];
- // Insert the dbxref record into Chado using the owl:Class stanza of the owl file.
- // Any oboInOwl:id supercedes what we find in the rdf:about in the owl file.
- $obo_id = $stanza->getChild('oboInOwl:id');
- if ($obo_id) {
- if (preg_match('/.*>(.+):(.+)<.*/', $about, $matches)) {
- $db_name = strtoupper($matches[1]);
- $accession = $matches[2];
- }
- else {
- $about = $stanza->getAttribute('rdf:about');
- // We wrote the regular expression on the rdf.about line to get the
- // db_name and accession for any particular Owl file.
- if (preg_match('/.*\/(.+)_(.+)/', $about, $matches)) {
- $db_name = strtoupper($matches[1]);
- $accession = $matches[2];
- }
- else {
- throw new Exception("owl:Class stanza 'rdf:about' attribute is not formated as expected: '$about'. " . "This is necessary to determine the term's accession: \n\n" . $stanza->getXML());
- }
- }
- }
- // If the database name for this term is the same as the vocabulary
- // we are trying to load, then do include it in the $vocabs array.
- if ($db_name == $vocabs['this']) {
- return;
- }
- // insert dbxref
- $values = [
- 'db_id' => $db->db_id,
- 'accession' => $accession,
- ];
- $dbxref = chado_insert_dbxref($values);
- $cvterm_name = $stanza->getChild('rdfs:label');
- if ($cvterm_name) {
- $cvterm_name = $stanza->getValue();
- }
- $definition = $stanza->getChild('obo:IAO_0000115');
- if ($definition) {
- $definition = $stanza->getValue();
- }
- $term = [
- 'id' => $db->name . ':' . $dbxref->accession,
- 'name' => $db->name,
- 'cv_name' => $stanza->getValue(),
- 'definition' => $stanza->getValue(),
- ];
- $options = [];
- if ($vocabs['this'] != $db->name) {
- $options['update_existing'] = FALSE;
- }
- $cvterm = chado_insert_cvterm($term, $options);
- // // Add a record to the chado relationship table if an ‘rdfs:subClassOf’ child exists.
- // $cvterm_name = $stanza->getChild('rdfs:subClassOf');
- // Insert a new cvterm record.
- // $cvterm_name = '';
- // $definition = '';
- // $cvterm_name = $stanza->getChild('rdfs:label');
- // if ($cvterm_name) {
- // $cvterm_name = $stanza->getValue();
- //}
- // $definition = $stanza->getChild('obo:IAO_0000115');
- // if ($definition) {
- //$definition = $stanza->getValue();
- //}
- // $term = array (
- // 'id' => $db->name . ':' . $dbxref->accession,
- // 'name' => $cvterm_name,
- // 'cv_name' => $cv->name,
- // 'definition' => $definition
- // );
- // $option = array ();
- // if ($vocabs['this'] != $db->name) {
- // $option['update_existing'] = FALSE;
- // }
- // $cvterm = chado_insert_cvterm($term, $option);
- }
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