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@@ -55,7 +55,7 @@
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*
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* @ingroup tripal_pub_api
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*/
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-function pub_search_remote($remote_db, $search_array, $num_to_retrieve, $page = 0) {
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+function tripal_get_remote_pubs($remote_db, $search_array, $num_to_retrieve, $page = 0) {
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// now call the callback function to get the results
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$callback = "tripal_pub_remote_search_$remote_db";
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@@ -70,6 +70,55 @@ function pub_search_remote($remote_db, $search_array, $num_to_retrieve, $page =
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return $pubs;
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}
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+/**
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+ * This function is used to perfom a query using one of the supported databases
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+ * and return the raw query results. This may be XML or some other format
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+ * as provided by the database.
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+ *
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+ * @param $dbxref
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+ * The unique database ID for the record to retrieve. This value must
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+ * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
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+ * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
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+ * for the record in the database.
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+ *
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+ * @return
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+ * Returns the raw output wrapped in an HTML textarea element or an
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+ * error message indicating if the database type is unsupported or the
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+ * dbxref is invalid
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+ *
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+ * @ingroup tripal_pub_api
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+ */
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+function tripal_get_remote_pub($dbxref) {
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+
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+ if(preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) {
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+ $remote_db = $matches[1];
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+ $accession = $matches[2];
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+
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+ // check that the database is supported
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+ $supported_dbs = variable_get('tripal_pub_supported_dbs', array());
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+ if(!in_array($remote_db, $supported_dbs)) {
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+ return "Unsupported database: $dbxref";
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+ }
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+
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+ $search = array(
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+ 'num_criteria' => 1,
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+ 'remote_db' => $remote_db,
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+ 'criteria' => array(
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+ '1' => array(
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+ 'search_terms' => "$remote_db:$accession",
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+ 'scope' => 'id',
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+ 'operation' => '',
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+ 'is_phrase' => 0,
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+ ),
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+ ),
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+ );
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+ $pubs = tripal_get_remote_pubs($remote_db, $search, 1, 0);
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+
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+ return $pubs[0]['raw'];
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+ }
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+ return 'Invalid DB xref';
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+}
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+
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/**
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* Builds the SQL statement need to search Chado for the publications
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* that match the user supplied criteria. Tpyically, this function is
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@@ -219,57 +268,257 @@ function pub_search($search_array, $offset, $limit, &$total_records) {
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}
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/**
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- * This function is used to perfom a query using one of the supported databases
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- * and return the raw query results. This may be XML or some other format
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- * as provided by the database.
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+ * Retrieves a chado publication array
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+ *
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+ * @param $identifier
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+ * An array used to uniquely identify a publication. This array has the same
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+ * format as that used by the chado_generate_var(). The following keys can be
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+ * useful for uniquely identifying a publication as they should be unique:
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+ * - pub_id: the chado pub.pub_id primary key
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+ * - nid: the drupal nid of the publication
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+ * - uniquename: A value to matach with the pub.uniquename field
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+ * There are also some specially handled keys. They are:
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+ * - property: An array describing the property to select records for. It
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+ * should at least have either a 'type_name' key (if unique across cvs) or
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+ * 'type_id' key. Other supported keys include: 'cv_id', 'cv_name' (of the type),
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+ * 'value' and 'rank'
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+ * - dbxref: The database cross reference accession. It should be in the form
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+ * DB:ACCESSION, where DB is the database name and ACCESSION is the
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+ * unique publication identifier (e.g. PMID:4382934)
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+ * - dbxref_id: The dbxref.dbxref_id of the publication.
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+ * @param $options
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+ * An array of options. Supported keys include:
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+ * - Any keys supported by chado_generate_var(). See that function definition for
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+ * additional details.
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+ *
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+ * NOTE: the $identifier parameter can really be any array similar to $values passed into
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+ * chado_select_record(). It should fully specify the pub record to be returned.
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*
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- * @param $dbxref
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- * The unique database ID for the record to retrieve. This value must
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- * be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
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- * database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
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- * for the record in the database.
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- *
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* @return
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- * Returns the raw output wrapped in an HTML textarea element or an
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- * error message indicating if the database type is unsupported or the
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- * dbxref is invalid
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+ * If a singe publication is retreived using the identifiers, then a publication
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+ * array will be returned. The array is of the same format returned by the
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+ * chado_generate_var() function. Otherwise, FALSE will be returned.
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*
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* @ingroup tripal_pub_api
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*/
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-function tripal_get_remote_pub_record($dbxref) {
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-
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- if(preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) {
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- $remote_db = $matches[1];
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- $accession = $matches[2];
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+function chado_get_publication($identifiers, $options = array()) {
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+
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+ // Error Checking of parameters
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+ if (!is_array($identifiers)) {
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+ tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
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+ "chado_get_publication: The identifier passed in is expected to be an array with the key
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+ matching a column name in the pub table (ie: pub_id or name). You passed in %identifier.",
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+ array('%identifier'=> print_r($identifiers, TRUE))
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+ );
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+ }
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+ elseif (empty($identifiers)) {
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+ tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
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+ "chado_get_publication: You did not pass in anything to identify the publication you want. The identifier
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+ is expected to be an array with the key matching a column name in the pub table
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+ (ie: pub_id or name). You passed in %identifier.",
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+ array('%identifier'=> print_r($identifiers, TRUE))
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+ );
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+ }
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+
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+ // If one of the identifiers is property then use chado_get_record_with_property()
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+ if (array_key_exists('property', $identifiers)) {
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+ $property = $identifiers['property'];
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+ unset($identifiers['property']);
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+ $pub = chado_get_record_with_property('pub', $property, $identifiers, $options);
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+ }
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+ elseif (array_key_exists('dbxref', $identifiers)) {
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+ if(preg_match('/^(.*?):(.*?)$/', $identifiers['dbxref'], $matches)) {
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+ $dbname = $matches[1];
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+ $accession = $matches[2];
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+
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+ $values = array(
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+ 'dbxref_id' => array (
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+ 'accession' => $accession,
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+ 'db_id' => array(
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+ 'name' => $dbname
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+ ),
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+ ),
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+ );
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+ $pub_dbxref = chado_select_record('pub_dbxref', array('pub_id'), $values);
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+ if (count($pub_dbxref) > 0) {
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+ $pub = chado_generate_var('pub', array('pub_id' => $pub_dbxref[0]->pub_id), $options);
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+ }
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+ else {
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+ return FALSE;
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+ }
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+ }
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+ else {
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+ tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
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+ "chado_get_publication: The dbxref identifier is not correctly formatted.",
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+ array('%identifier'=> print_r($identifiers, TRUE))
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+ );
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+ }
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+ }
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+ elseif (array_key_exists('dbxref_id', $identifiers)) {
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+ // first get the pub_dbxref record
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+ $values = array('dbxref_id' => $identifiers['dbxref_id']);
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+ $pub_dbxref = chado_select_record('pub_dbxref', array('pub_id'), $values);
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+
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+ // now get the pub
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+ if (count($pub_dbxref) > 0) {
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+ $pub = chado_generate_var('pub', array('pub_id' => $pub_dbxref[0]->pub_id), $options);
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+ }
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+ else {
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+ return FALSE;
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+ }
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+
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+ }
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+ // Else we have a simple case and we can just use chado_generate_var to get the pub
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+ else {
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+ // Try to get the pub
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+ $pub = chado_generate_var('pub', $identifiers, $options);
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+ }
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+
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+ // Ensure the pub is singular. If it's an array then it is not singular
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+ if (is_array($pub)) {
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+ tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
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+ "chado_get_publication: The identifiers did not find a single unique record. Identifiers passed: %identifier.",
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+ array('%identifier'=> print_r($identifiers, TRUE))
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+ );
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+ }
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+
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+ // Report an error if $pub is FALSE since then chado_generate_var has failed
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+ elseif ($pub === FALSE) {
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+ tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
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+ "chado_get_publication: Could not find a publication using the identifiers
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+ provided. Check that the identifiers are correct. Identifiers passed: %identifier.",
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+ array('%identifier'=> print_r($identifiers, TRUE))
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+ );
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+ }
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+
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+ // Else, as far we know, everything is fine so give them their pub :)
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+ else {
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+ return $pub;
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+ }
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+}
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+/**
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+ * The publication table of Chado only has a unique constraint for the
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+ * uniquename of the publiation, but in reality a publication can be considered
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+ * unique by a combination of the title, publication type, published year and
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+ * series name (e.g. journal name or conference name). The site administrator
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+ * can configure how publications are determined to be unique. This function
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+ * uses the configuration specified by the administrator to look for publications
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+ * that match the details specified by the $pub_details argument
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+ * and indicates if one ore more publications match the criteria.
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+ *
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+ * @param $pub_details
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+ * An associative array with details about the publications. The expected keys
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+ * are:
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+ * 'Title': The title of the publication
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+ * 'Year': The published year of the publication
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+ * 'Publication Type': An array of publication types. A publication can have more than one type.
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+ * 'Series Name': The series name of the publication
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+ * 'Journal Name': An alternative to 'Series Name' is 'Journal Name'
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+ * 'Citation': The publication citation (this is the value saved in the pub.uniquename field and must be unique)
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+ * If this key is present it will also be checked
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+ * 'Publication Dbxref': A database cross reference of the form DB:ACCESSION where DB is the name
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+ * of the database and ACCESSION is the unique identifier (e.g PMID:3483139)
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+ *
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+ * @return
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+ * An array containing the pub_id's of matching publications.
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+ */
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+function chado_does_pub_exist($pub_details) {
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+
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- // check that the database is supported
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- $supported_dbs = variable_get('tripal_pub_supported_dbs', array());
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- if(!in_array($remote_db, $supported_dbs)) {
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- return "Unsupported database: $dbxref";
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+ // first try to find the publication using the accession number if that key exists in the details array
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+ if (array_key_exists('Publication Dbxref', $pub_details)) {
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+ $pub = chado_get_publication(array('dbxref' => $pub_details['Publication Dbxref']));
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+ if($pub) {
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+ return array($pub->pub_id);
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+ }
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+ }
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+
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+ // make sure the citation is unique
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+ if (array_key_exists('Citation', $pub_details)) {
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+ $pub = chado_get_publication(array('uniquename' => $pub_details['Citation']));
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+ if($pub) {
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+ return array($pub->pub_id);
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}
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+ }
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- $search = array(
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- 'num_criteria' => 1,
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- 'remote_db' => $remote_db,
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- 'criteria' => array(
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- '1' => array(
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- 'search_terms' => "$remote_db:$accession",
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- 'scope' => 'id',
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- 'operation' => '',
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- 'is_phrase' => 0,
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- ),
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+ // get the publication type (use the first publication type)
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+ if (array_key_exists('Publication Type', $pub_details)) {
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+ $type_name = '';
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+ if(is_array($pub_details['Publication Type'])) {
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+ $type_name = $pub_details['Publication Type'][0];
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+ }
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+ else {
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+ $type_name = $pub_details['Publication Type'];
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+ }
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+ $identifiers = array(
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+ 'name' => $type_name,
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+ 'cv_id' => array(
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+ 'name' => 'tripal_pub',
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),
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);
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- $pubs = pub_search_remote($remote_db, $search, 1, 0);
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+ $pub_type = chado_get_cvterm($identifiers);
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+ }
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+ else {
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+ tripal_report_error('tripal_pub', TRIPAL_ERROR, "chado_does_pub_exist(): The Publication Type is a " .
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+ "required property but is missing", array());
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+ return FALSE;
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+ }
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+ if (!$pub_type) {
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+ tripal_report_error('tripal_pub', TRIPAL_ERROR, "chado_does_pub_exist(): Cannot find publication type: '%type'",
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+ array('%type' => $pub_details['Publication Type'][0]));
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+ return FALSE;
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+ }
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- return $pubs[0]['raw'];
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+ // get the series name. The pub.series_name field is only 255 chars so we must truncate to be safe
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+ $series_name = '';
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+ if (array_key_exists('Series_Name', $pub_details)) {
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+ $series_name = substr($pub_details['Series Name'], 0, 255);
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}
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- return 'Invalid DB xref';
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+ if (array_key_exists('Journal Name', $pub_details)) {
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+ $series_name = substr($pub_details['Journal Name'], 0, 255);
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+ }
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+
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+
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+ // make sure the publication is unique using the prefereed import duplication check
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+ $import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media');
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+ $pubs = array();
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+ switch ($import_dups_check) {
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+ case 'title_year':
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+ $identifiers = array(
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+ 'title' => $pub_details['Title'],
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+ 'pyear' => $pub_details['Year']
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+ );
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+ $pubs = chado_select_record('pub', array('pub_id'), $identifiers);
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+ break;
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+ case 'title_year_type':
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+ $identifiers = array(
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+ 'title' => $pub_details['Title'],
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+ 'pyear' => $pub_details['Year'],
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+ 'type_id' => $pub_type->cvterm_id,
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+ );
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+ $pubs = chado_select_record('pub', array('pub_id'), $identifiers);
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+ break;
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+ case 'title_year_media':
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+ $identifiers = array(
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+ 'title' => $pub_details['Title'],
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+ 'pyear' => $pub_details['Year'],
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+ 'series_name' => $series_name,
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+ );
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+ $pubs = chado_select_record('pub', array('pub_id'), $identifiers);
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+ break;
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+ }
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+
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+ $return = array();
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+ foreach ($pubs as $pub) {
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+ $return[] = $pub->pub_id;
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+ }
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+
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+ return $return;
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}
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/**
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- * Updates publication records with the most recent data in the remote
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- * database.
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+ * Updates publication records that currently exist in the Chado pub table
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+ * with the most recent data in the remote database.
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*
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* @param $do_contact
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* Set to TRUE if authors should automatically have a contact record added
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@@ -287,7 +536,7 @@ function tripal_get_remote_pub_record($dbxref) {
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*
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* @ingroup tripal_pub_api
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*/
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-function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db = NULL) {
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+function chado_reimport_publications($do_contact = FALSE, $dbxref = NULL, $db = NULL) {
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print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
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"If the load fails or is terminated prematurely then the entire set of \n" .
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@@ -346,7 +595,7 @@ function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db
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),
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),
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);
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- $pubs = pub_search_remote($remote_db, $search, 1, 0);
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+ $pubs = tripal_get_remote_pubs($remote_db, $search, 1, 0);
|
|
|
tripal_pub_add_publications($pubs, $do_contact, TRUE);
|
|
|
|
|
|
$i++;
|
|
|
@@ -354,12 +603,12 @@ function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db
|
|
|
|
|
|
// sync the newly added publications with Drupal
|
|
|
print "Syncing publications with Drupal...\n";
|
|
|
- tripal_pub_sync_pubs();
|
|
|
+ chado_node_sync_records('pub');
|
|
|
|
|
|
// if the caller wants to create contacts then we should sync them
|
|
|
if ($do_contact) {
|
|
|
print "Syncing contacts with Drupal...\n";
|
|
|
- tripal_contact_sync_contacts();
|
|
|
+ chado_node_sync_records('contact');
|
|
|
}
|
|
|
}
|
|
|
catch (Exception $e) {
|
|
|
@@ -382,7 +631,7 @@ function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db
|
|
|
*
|
|
|
* @ingroup tripal_pub_api
|
|
|
*/
|
|
|
-function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL) {
|
|
|
+function tripal_execute_pub_importer($import_id, $job_id = NULL) {
|
|
|
print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
|
|
|
"If the load fails or is terminated prematurely then the entire set of \n" .
|
|
|
"insertions/updates is rolled back and will not be found in the database\n\n";
|
|
|
@@ -400,14 +649,14 @@ function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL)
|
|
|
$sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id ";
|
|
|
$import = db_query($sql, $args)->fetchObject();
|
|
|
|
|
|
- print "Importing: " . $import->name . "\n";
|
|
|
+ print "Executing Importer: '" . $import->name . "'\n";
|
|
|
|
|
|
$criteria = unserialize($import->criteria);
|
|
|
$remote_db = $criteria['remote_db'];
|
|
|
$total_pubs = 0;
|
|
|
do {
|
|
|
// retrieve the pubs for this page. We'll retreive 100 at a time
|
|
|
- $results = pub_search_remote($remote_db, $criteria, $num_to_retrieve, $page);
|
|
|
+ $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
|
|
|
$pubs = $results['pubs'];
|
|
|
$num_pubs = $rseults['total_records'];
|
|
|
$total_pubs += $num_pubs;
|
|
|
@@ -422,12 +671,12 @@ function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL)
|
|
|
// requested a report then we don't want to print any syncing information
|
|
|
// so pass 'FALSE' to the sync call
|
|
|
print "Syncing publications with Drupal...\n";
|
|
|
- tripal_pub_sync_pubs();
|
|
|
+ chado_node_sync_records('pub');
|
|
|
|
|
|
// if any of the importers wanted to create contacts from the authors then sync them
|
|
|
if($import->do_contact) {
|
|
|
print "Syncing contacts with Drupal...\n";
|
|
|
- tripal_contact_sync_contacts();
|
|
|
+ chado_node_sync_records('contact');
|
|
|
}
|
|
|
tripal_set_job_progress($job_id, '100');
|
|
|
}
|
|
|
@@ -453,7 +702,7 @@ function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL)
|
|
|
*
|
|
|
* @ingroup tripal_pub_api
|
|
|
*/
|
|
|
-function tripal_pub_import_publications($report_email = FALSE, $do_update = FALSE) {
|
|
|
+function tripal_execute_active_pub_importers($report_email = FALSE, $do_update = FALSE) {
|
|
|
$num_to_retrieve = 100;
|
|
|
$page = 0;
|
|
|
|
|
|
@@ -473,7 +722,7 @@ function tripal_pub_import_publications($report_email = FALSE, $do_update = FALS
|
|
|
$reports = array();
|
|
|
foreach ($results as $import) {
|
|
|
$page = 0;
|
|
|
- print "Importing: " . $import->name . "\n";
|
|
|
+ print "Executing importer: '" . $import->name . "'\n";
|
|
|
// keep track if any of the importers want to create contacts from authors
|
|
|
if ($import->do_contact == 1) {
|
|
|
$do_contact = TRUE;
|
|
|
@@ -482,7 +731,7 @@ function tripal_pub_import_publications($report_email = FALSE, $do_update = FALS
|
|
|
$remote_db = $criteria['remote_db'];
|
|
|
do {
|
|
|
// retrieve the pubs for this page. We'll retreive 100 at a time
|
|
|
- $results = pub_search_remote($remote_db, $criteria, $num_to_retrieve, $page);
|
|
|
+ $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
|
|
|
$pubs = $results['pubs'];
|
|
|
$reports[$import->name] = tripal_pub_add_publications($pubs, $import->do_contact, $do_update);
|
|
|
$page++;
|
|
|
@@ -496,7 +745,7 @@ function tripal_pub_import_publications($report_email = FALSE, $do_update = FALS
|
|
|
// requested a report then we don't want to print any syncing information
|
|
|
// so pass 'FALSE' to the sync call
|
|
|
print "Syncing publications with Drupal...\n";
|
|
|
- tripal_pub_sync_pubs();
|
|
|
+ chado_node_sync_records('pub');
|
|
|
|
|
|
// iterate through each of the reports and generate a final report with HTML links
|
|
|
$HTML_report = '';
|
|
|
@@ -526,7 +775,7 @@ function tripal_pub_import_publications($report_email = FALSE, $do_update = FALS
|
|
|
// if any of the importers wanted to create contacts from the authors then sync them
|
|
|
if($do_contact) {
|
|
|
print "Syncing contacts with Drupal...\n";
|
|
|
- tripal_contact_sync_contacts();
|
|
|
+ chado_node_sync_records('contact');
|
|
|
}
|
|
|
}
|
|
|
catch (Exception $e) {
|
|
|
@@ -556,7 +805,7 @@ function tripal_pub_import_publications($report_email = FALSE, $do_update = FALS
|
|
|
*
|
|
|
* @ingroup tripal_pub_api
|
|
|
*/
|
|
|
-function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update) {
|
|
|
+function tripal_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update) {
|
|
|
$num_to_retrieve = 1;
|
|
|
$pager_id = 0;
|
|
|
$page = 0;
|
|
|
@@ -585,7 +834,7 @@ function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_updat
|
|
|
),
|
|
|
);
|
|
|
$remote_db = $criteria['remote_db'];
|
|
|
- $results = pub_search_remote($remote_db, $criteria, $num_to_retrieve, $page);
|
|
|
+ $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
|
|
|
$pubs = $results['pubs'];
|
|
|
$search_str = $results['search_str'];
|
|
|
$total_records = $results['total_records'];
|
|
|
@@ -594,12 +843,12 @@ function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_updat
|
|
|
|
|
|
// sync the newly added publications with Drupal
|
|
|
print "Syncing publications with Drupal...\n";
|
|
|
- tripal_pub_sync_pubs();
|
|
|
+ chado_node_sync_records('pub');
|
|
|
|
|
|
// if any of the importers wanted to create contacts from the authors then sync them
|
|
|
if($do_contact) {
|
|
|
print "Syncing contacts with Drupal...\n";
|
|
|
- tripal_contact_sync_contacts();
|
|
|
+ chado_node_sync_records('contact');
|
|
|
}
|
|
|
}
|
|
|
catch (Exception $e) {
|
|
|
@@ -611,1001 +860,4 @@ function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_updat
|
|
|
}
|
|
|
|
|
|
print "Done.\n";
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Adds publications that have been retrieved from a remote database and
|
|
|
- * consolidated into an array of details.
|
|
|
- *
|
|
|
- * @param $pubs
|
|
|
- * An array containing a list of publications to add to Chado. The
|
|
|
- * array contains a set of details for the publication.
|
|
|
- * @param $do_contact
|
|
|
- * Set to TRUE if authors should automatically have a contact record added
|
|
|
- * to Chado.
|
|
|
- * @param $update
|
|
|
- * If set to TRUE then publications that already exist in the Chado database
|
|
|
- * will be updated, whereas if FALSE only new publications will be added
|
|
|
- *
|
|
|
- * @return
|
|
|
- * Returns an array containing the number of publications that were
|
|
|
- * inserted, updated, skipped and which had an error during import.
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_add_publications($pubs, $do_contact, $update = FALSE) {
|
|
|
- $report = array();
|
|
|
- $report['error'] = 0;
|
|
|
- $report['inserted'] = array();
|
|
|
- $report['skipped'] = array();
|
|
|
- $total_pubs = count($pubs);
|
|
|
-
|
|
|
- // iterate through the publications and add each one
|
|
|
- $i = 1;
|
|
|
- foreach ($pubs as $pub) {
|
|
|
- $memory = number_format(memory_get_usage()) . " bytes";
|
|
|
- print "Processing $i of $total_pubs. Memory usage: $memory.\r";
|
|
|
-
|
|
|
- // add the publication to Chado
|
|
|
- $action = '';
|
|
|
- $pub_id = tripal_pub_add_publication($pub, $action, $do_contact, $update);
|
|
|
- if ($pub_id){
|
|
|
- // add the publication cross reference (e.g. to PubMed)
|
|
|
- if ($pub_id and $pub['Publication Dbxref']) {
|
|
|
- $pub_dbxref = tripal_pub_add_pub_dbxref($pub_id, $pub['Publication Dbxref']);
|
|
|
- }
|
|
|
- $pub['pub_id'] = $pub_id;
|
|
|
- }
|
|
|
-
|
|
|
- switch ($action) {
|
|
|
- case 'error':
|
|
|
- $report['error']++;
|
|
|
- break;
|
|
|
- case 'inserted':
|
|
|
- $report['inserted'][] = $pub;
|
|
|
- break;
|
|
|
- case 'updated':
|
|
|
- $report['updated'][] = $pub;
|
|
|
- break;
|
|
|
- case 'skipped':
|
|
|
- $report['skipped'][] = $pub;
|
|
|
- break;
|
|
|
- }
|
|
|
- $i++;
|
|
|
- }
|
|
|
- print "\n";
|
|
|
- return $report;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Returns the list of publications that are assigned the database
|
|
|
- * cross-reference provided
|
|
|
- *
|
|
|
- * @param $pub_dbxref
|
|
|
- * The database cross reference accession. It should be in the form
|
|
|
- * DB:ACCESSION, where DB is the database name and ACCESSION is the
|
|
|
- * unique publication identifier (e.g. PMID:4382934)
|
|
|
- *
|
|
|
- * @return
|
|
|
- * Returns an array of all the publications that have the provided
|
|
|
- * cross reference. If no publications match, then an empty array
|
|
|
- * is returned.
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_get_pubs_by_dbxref($pub_dbxref) {
|
|
|
-
|
|
|
- $return = array();
|
|
|
-
|
|
|
- if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) {
|
|
|
- $dbname = $matches[1];
|
|
|
- $accession = $matches[2];
|
|
|
-
|
|
|
- $values = array(
|
|
|
- 'dbxref_id' => array (
|
|
|
- 'accession' => $accession,
|
|
|
- 'db_id' => array(
|
|
|
- 'name' => $dbname
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- $options = array('statement_name' => 'sel_pubdbxref_db');
|
|
|
- $results = chado_select_record('pub_dbxref', array('pub_id'), $values, $options);
|
|
|
- foreach ($results as $index => $pub) {
|
|
|
- $return[] = $pub->pub_id;
|
|
|
- }
|
|
|
- }
|
|
|
- return $return;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Returns the list of publications that match a given title, type and year
|
|
|
- *
|
|
|
- * @param title
|
|
|
- * The title of the publication to look for
|
|
|
- * @param type
|
|
|
- * Optional. The publication type. The value of this field should come from
|
|
|
- * the Tripal Pub vocabulary. This should be the type name (e.g. cvterm.name)
|
|
|
- * @param pyear
|
|
|
- * Optional. The year the publication was published.
|
|
|
- * @param series_name
|
|
|
- * Optional. The name of the series (e.g. Journal name)
|
|
|
- *
|
|
|
- * @return
|
|
|
- * Returns an array of all the publications that have the provided
|
|
|
- * cross reference. If no publications match, then an empty array
|
|
|
- * is returned.
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_get_pubs_by_title_type_pyear_series($title, $type = NULL, $pyear = NULL, $series_name = NULL) {
|
|
|
-
|
|
|
- $return = array();
|
|
|
-
|
|
|
- // build the values array for the query.
|
|
|
- $values = array(
|
|
|
- 'title' => $title,
|
|
|
- );
|
|
|
- $stmnt_suffix = 'ti';
|
|
|
- if ($type) {
|
|
|
- $values['type_id'] = array(
|
|
|
- 'name' => $type,
|
|
|
- 'cv_id' => array(
|
|
|
- 'name' => 'tripal_pub'
|
|
|
- )
|
|
|
- );
|
|
|
- $stmnt_suffix .= 'ty';
|
|
|
- }
|
|
|
- if ($pyear) {
|
|
|
- $values['pyear'] = $pyear;
|
|
|
- $stmnt_suffix .= 'py';
|
|
|
- }
|
|
|
- if ($series_name) {
|
|
|
- $values['series_name'] = strtolower($series_name);
|
|
|
- $stmnt_suffix .= 'se';
|
|
|
- }
|
|
|
- $options = array(
|
|
|
- 'statement_name' => 'sel_pub_' . $stmnt_suffix,
|
|
|
- 'case_insensitive_columns' => array('title', 'series_name'),
|
|
|
- );
|
|
|
- $results = chado_select_record('pub', array('pub_id'), $values, $options);
|
|
|
-
|
|
|
- // iterate through any matches and pull out the pub_id
|
|
|
- foreach ($results as $index => $pub) {
|
|
|
- $return[] = $pub->pub_id;
|
|
|
- }
|
|
|
- return $return;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Returns the list of publications that match a given title, type and year
|
|
|
- *
|
|
|
- * @param title
|
|
|
- * The title of the publication to look for
|
|
|
- * @param type
|
|
|
- * Optional. The publication type. The value of this field should come from
|
|
|
- * the Tripal Pub vocabulary. This should be the type name (e.g. cvterm.name)
|
|
|
- * @param year
|
|
|
- * Optional. The year the publication was published.
|
|
|
- * @param series_name
|
|
|
- * Optional. The name of the series (e.g. Journal name)
|
|
|
- *
|
|
|
- * @return
|
|
|
- * Returns an array of all the publications that have the provided
|
|
|
- * cross reference. If no publications match, then an empty array
|
|
|
- * is returned.
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_get_pub_by_uniquename($name) {
|
|
|
-
|
|
|
- $return = array();
|
|
|
-
|
|
|
- // build the values array for the query.
|
|
|
- $values = array(
|
|
|
- 'uniquename' => $name,
|
|
|
- );
|
|
|
- $options = array(
|
|
|
- 'statement_name' => 'sel_pub_un',
|
|
|
- 'case_insensitive_columns' => array('uniquename'),
|
|
|
- );
|
|
|
- $results = chado_select_record('pub', array('pub_id'), $values, $options);
|
|
|
-
|
|
|
- // iterate through any matches and pull out the pub_id
|
|
|
- foreach ($results as $index => $pub) {
|
|
|
- $return[] = $pub->pub_id;
|
|
|
- }
|
|
|
- return $return;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Adds a new publication to the Chado, along with all properties and
|
|
|
- * database cross-references. If the publication does not already exist
|
|
|
- * in Chado then it is added. If it does exist nothing is done. If
|
|
|
- * the $update parameter is TRUE then the publication is updated if it exists.
|
|
|
- *
|
|
|
- * @param $pub_details
|
|
|
- * An associative array containing all of the details about the publication.
|
|
|
- * @param $action
|
|
|
- * This variable will get set to a text value indicating the action that was
|
|
|
- * performed. The values include 'skipped', 'inserted', 'updated' or 'error'.
|
|
|
- * @param $do_contact
|
|
|
- * Optional. Set to TRUE if a contact entry should be added to the Chado contact table
|
|
|
- * for authors of the publication.
|
|
|
- * @param $update_if_exists
|
|
|
- * Optional. If the publication already exists then this function will return
|
|
|
- * without adding a new publication. However, set this value to TRUE to force
|
|
|
- * the function to pudate the publication using the $pub_details that are provided.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * If the publication already exists, is inserted or updated then the publication
|
|
|
- * ID is returned, otherwise FALSE is returned. If the publication already exists
|
|
|
- * and $update_if_exists is not TRUE then the $action variable is set to 'skipped'.
|
|
|
- * If the publication already exists and $update_if_exists is TRUE and if the update
|
|
|
- * was successful then $action is set to 'updated'. Otherwise on successful insert
|
|
|
- * the $action variable is set to 'inserted'. If the function failes then the
|
|
|
- * $action variable is set to 'error'
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE, $update_if_exists = FALSE) {
|
|
|
- $pub_id = 0;
|
|
|
-
|
|
|
- if (!is_array($pub_details)) {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // first try to find the publication using the accession number. It will have
|
|
|
- // one if the pub has already been loaded for the publication database
|
|
|
- if (array_key_exists('Publication Dbxref', $pub_details)) {
|
|
|
- $results = tripal_pub_get_pubs_by_dbxref($pub_details['Publication Dbxref']);
|
|
|
- if(count($results) == 1) {
|
|
|
- $pub_id = $results[0];
|
|
|
- if ($pub_id and !$update_if_exists) {
|
|
|
- //tripal_core_report_error('tripal_pub', TRIPAL_WARNING, "A publication with this Dbxref already exists... Skipping: %dbxref",
|
|
|
- //array('%dbxref' => $pub_details['Publication Dbxref']));
|
|
|
- $action = 'skipped';
|
|
|
- return $pub_id;
|
|
|
- }
|
|
|
- }
|
|
|
- elseif (count($results) > 1) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "There are two publications with this accession: %db:%accession. Cannot determine which to update.",
|
|
|
- array('%db' => $dbname, '%accession' => $accession));
|
|
|
- $action = 'error';
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // if we couldn't find a publication by the accession (which means it doesn't
|
|
|
- // yet exist or it has been added using a different publication database) then
|
|
|
- // try to find it using the title and publication year.
|
|
|
- if (!$pub_id and array_key_exists('Title', $pub_details)) {
|
|
|
-
|
|
|
- $results = tripal_pub_get_pubs_by_title_type_pyear_series($pub_details['Title'], NULL, $pub_details['Year']);
|
|
|
- if (count($results) == 1) {
|
|
|
- $pub_id = $results[0];
|
|
|
- if ($pub_id and !$update_if_exists) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_WARNING, "The publication with the same title, type and year already exists. Skipping. ".
|
|
|
- " Title: '%title'. Type: '%type'. Year: '%year'",
|
|
|
- array('%title' => $pub_details['Title'], '%type' => $pub_details['Publication Type'], '%year' => $pub_details['Year']));
|
|
|
- $action = 'skipped';
|
|
|
- return $pub_id;
|
|
|
- }
|
|
|
- }
|
|
|
- elseif (count($results) > 1) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "The publication with the same title, type and year is present multiple times. Cannot ".
|
|
|
- "determine which to use. Title: '%title'. Type: '%type'. Year: '%year'",
|
|
|
- array('%title' => $pub_details['Title'], '%type' => $pub_details['Publication Type'], '%year' => $pub_details['Year']));
|
|
|
- $action = 'error';
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
- // get the publication type (use the first publication type, any others will get stored as properties)
|
|
|
- if (array_key_exists('Publication Type', $pub_details)) {
|
|
|
- if(is_array($pub_details['Publication Type'])) {
|
|
|
- $pub_type = tripal_cv_get_cvterm_by_name($pub_details['Publication Type'][0], NULL, 'tripal_pub');
|
|
|
- }
|
|
|
- else {
|
|
|
- $pub_type = tripal_cv_get_cvterm_by_name($pub_details['Publication Type'], NULL, 'tripal_pub');
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "The Publication Type is a required property but is missing", array());
|
|
|
- $action = 'error';
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if (!$pub_type) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot find publication type: '%type'",
|
|
|
- array('%type' => $pub_details['Publication Type'][0]));
|
|
|
- $action = 'error';
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // build the values array for inserting or updating
|
|
|
- $values = array(
|
|
|
- 'title' => $pub_details['Title'],
|
|
|
- 'volume' => $pub_details['Volume'],
|
|
|
- 'series_name' => substr($pub_details['Journal Name'], 0, 255),
|
|
|
- 'issue' => $pub_details['Issue'],
|
|
|
- 'pyear' => $pub_details['Year'],
|
|
|
- 'pages' => $pub_details['Pages'],
|
|
|
- 'uniquename' => $pub_details['Citation'],
|
|
|
- 'type_id' => $pub_type->cvterm_id,
|
|
|
- );
|
|
|
-
|
|
|
- // if there is no pub_id then we need to do an insert.
|
|
|
- if (!$pub_id) {
|
|
|
- $options = array('statement_name' => 'ins_pub_tivoseispypaunty');
|
|
|
- $pub = chado_insert_record('pub', $values, $options);
|
|
|
- if (!$pub) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot insert the publication with title: %title",
|
|
|
- array('%title' => $pub_details['Title']));
|
|
|
- $action = 'error';
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- $pub_id = $pub['pub_id'];
|
|
|
- $action = 'inserted';
|
|
|
- }
|
|
|
-
|
|
|
- // if there is a pub_id and we've been told to update, then do the update
|
|
|
- if ($pub_id and $update_if_exists) {
|
|
|
- $match = array('pub_id' => $pub_id);
|
|
|
- $options = array('statement_name' => 'up_pub_tivoseispypaunty');
|
|
|
- $success = chado_update_record('pub', $match, $values, $options);
|
|
|
- if (!$success) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot update the publication with title: %title",
|
|
|
- array('%title' => $pub_details['Title']));
|
|
|
- $action = 'error';
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- $action = 'updated';
|
|
|
- }
|
|
|
-
|
|
|
- // before we add any new properties we need to remove those that are there if this
|
|
|
- // is an update. The only thing we don't want to remove are the 'Publication Dbxref'
|
|
|
- if ($update_if_exists) {
|
|
|
- $sql = "
|
|
|
- DELETE FROM {pubprop}
|
|
|
- WHERE
|
|
|
- pub_id = :pub_id AND
|
|
|
- NOT type_id in (
|
|
|
- SELECT cvterm_id
|
|
|
- FROM {cvterm}
|
|
|
- WHERE name = 'Publication Dbxref'
|
|
|
- )
|
|
|
- ";
|
|
|
- chado_query($sql, array(':pub_id' => $pub_id));
|
|
|
- }
|
|
|
-
|
|
|
- // iterate through the properties and add them
|
|
|
- foreach ($pub_details as $key => $value) {
|
|
|
- // the pub_details may have the raw search data (e.g. in XML from PubMed. We'll irgnore this for now
|
|
|
- if($key == 'raw') {
|
|
|
- continue;
|
|
|
- }
|
|
|
- // get the cvterm by name or synonym
|
|
|
- $cvterm = tripal_cv_get_cvterm_by_name($key, NULL, 'tripal_pub');
|
|
|
- if (!$cvterm) {
|
|
|
- $cvterm = tripal_cv_get_cvterm_by_synonym($key, NULL, 'tripal_pub');
|
|
|
- }
|
|
|
- if (!$cvterm) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot find term: '%prop'. Skipping.", array('%prop' => $key));
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // skip details that won't be stored as properties
|
|
|
- if ($key == 'Author List') {
|
|
|
- tripal_pub_add_authors($pub_id, $value, $do_contact);
|
|
|
- continue;
|
|
|
- }
|
|
|
- if ($key == 'Title' or $key == 'Volume' or $key == 'Journal Name' or $key == 'Issue' or
|
|
|
- $key == 'Year' or $key == 'Pages') {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- $success = 0;
|
|
|
- if (is_array($value)) {
|
|
|
- foreach ($value as $subkey => $subvalue) {
|
|
|
- // if the key is an integer then this array is a simple list and
|
|
|
- // we will insert using the primary key. Otheriwse, use the new key
|
|
|
- if(is_int($subkey)) {
|
|
|
- $success = chado_insert_property('pub', $pub_id, $key, 'tripal_pub', $subvalue, FALSE);
|
|
|
- }
|
|
|
- else {
|
|
|
- $success = chado_insert_property('pub', $pub_id, $subkey, 'tripal_pub', $subvalue, FALSE);
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $success = chado_insert_property('pub', $pub_id, $key, 'tripal_pub', $value, TRUE);
|
|
|
- }
|
|
|
- if (!$success) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot add property '%prop' to publication. Skipping.",
|
|
|
- array('%prop' => $key));
|
|
|
- continue;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- return $pub_id;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Add one or more authors to a publication
|
|
|
- *
|
|
|
- * @param $pub_id
|
|
|
- * The publication ID of the pub in Chado.
|
|
|
- * @param $authors
|
|
|
- * An array of authors. Each author should have a set of keys/value pairs
|
|
|
- * describing the author.
|
|
|
- * @param $do_contact
|
|
|
- * Optional. Set to TRUE if a contact entry should be added to the Chado contact table
|
|
|
- * for authors of the publication.
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
|
|
|
- $rank = 0;
|
|
|
-
|
|
|
- // first remove any of the existing pubauthor entires
|
|
|
- $sql = "DELETE FROM {pubauthor} WHERE pub_id = :pub_id";
|
|
|
- chado_query($sql, array(':pub_id' => $pub_id));
|
|
|
-
|
|
|
- // iterate through the authors and add them to the pubauthors and contact
|
|
|
- // tables of chado, then link them through the custom pubauthors_contact table
|
|
|
- foreach ($authors as $author) {
|
|
|
- // skip invalid author entires
|
|
|
- if ($author['valid'] == 'N') {
|
|
|
- continue;
|
|
|
- }
|
|
|
- // remove the 'valid' property as we don't have a CV term for it
|
|
|
- unset($author['valid']);
|
|
|
-
|
|
|
- // construct the contact.name field using the author information
|
|
|
- $name = '';
|
|
|
- $type = 'Person';
|
|
|
- if ($author['Given Name']) {
|
|
|
- $name .= $author['Given Name'];
|
|
|
- }
|
|
|
- if ($author['Surname']) {
|
|
|
- $name .= ' ' . $author['Surname'];
|
|
|
- }
|
|
|
- if ($author['Suffix']) {
|
|
|
- $name .= ' ' . $author['Suffix'];
|
|
|
- }
|
|
|
- if ($author['Collective']) {
|
|
|
- $name = $author['Collective'];
|
|
|
- $type = 'Collective';
|
|
|
- }
|
|
|
- $name = trim($name);
|
|
|
-
|
|
|
- // add an entry to the pubauthors table
|
|
|
- $values = array(
|
|
|
- 'pub_id' => $pub_id,
|
|
|
- 'rank' => $rank,
|
|
|
- 'surname' => $author['Surname'] ? substr($author['Surname'], 0, 100) : substr($author['Collective'], 0, 100),
|
|
|
- 'givennames' => $author['Given Name'],
|
|
|
- 'suffix' => $author['Suffix'],
|
|
|
- );
|
|
|
- $options = array('statement_name' => 'ins_pubauthor_idrasugisu');
|
|
|
- $pubauthor = chado_insert_record('pubauthor', $values, $options);
|
|
|
-
|
|
|
- // if the user wants us to create a contact for each author then do it.
|
|
|
- if ($do_contact) {
|
|
|
- // Add the contact
|
|
|
- $contact = tripal_contact_add_contact($name, '', $type, $author);
|
|
|
-
|
|
|
- // if we have succesfully added the contact and the pubauthor entries then we want to
|
|
|
- // link them together
|
|
|
- if ($contact and $pubauthor) {
|
|
|
-
|
|
|
- // link the pubauthor entry to the contact
|
|
|
- $values = array(
|
|
|
- 'pubauthor_id' => $pubauthor['pubauthor_id'],
|
|
|
- 'contact_id' => $contact['contact_id'],
|
|
|
- );
|
|
|
- $options = array('statement_name' => 'ins_pubauthorcontact_puco');
|
|
|
- $pubauthor_contact = chado_insert_record('pubauthor_contact', $values, $options);
|
|
|
- if (!$pubauthor_contact) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot link pub authro and contact.", array());
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- $rank++;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Retrieve properties of a given type for a given pub
|
|
|
- *
|
|
|
- * @param $pub_id
|
|
|
- * The pub_id of the properties you would like to retrieve
|
|
|
- * @param $property
|
|
|
- * The cvterm name of the properties to retrieve
|
|
|
- *
|
|
|
- * @return
|
|
|
- * An pub chado variable with the specified properties expanded
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_get_property($pub_id, $property) {
|
|
|
- return chado_get_property('pub', $pub_id, $property, 'tripal_pub');
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Insert a given property
|
|
|
- *
|
|
|
- * @param $pub_id
|
|
|
- * The pub_id of the property to insert
|
|
|
- * @param $property
|
|
|
- * The cvterm name of the property to insert
|
|
|
- * @param $value
|
|
|
- * The value of the property to insert
|
|
|
- * @param $update_if_present
|
|
|
- * A boolean indicated whether to update the record if it's already present
|
|
|
- *
|
|
|
- * @return
|
|
|
- * True of success, False otherwise
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_insert_property($pub_id, $property, $value, $update_if_present = 0) {
|
|
|
- return chado_insert_property('pub', $pub_id, $property, 'tripal_pub', $value, $update_if_present);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Update a given property
|
|
|
- *
|
|
|
- * @param $pub_id
|
|
|
- * The pub_id of the property to update
|
|
|
- * @param $property
|
|
|
- * The cvterm name of the property to update
|
|
|
- * @param $value
|
|
|
- * The value of the property to update
|
|
|
- * @param $insert_if_missing
|
|
|
- * A boolean indicated whether to insert the record if it's absent
|
|
|
- *
|
|
|
- * Note: The property will be identified using the unique combination of the $pub_id and $property
|
|
|
- * and then it will be updated with the supplied value
|
|
|
- *
|
|
|
- * @return
|
|
|
- * True of success, False otherwise
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_update_property($pub_id, $property, $value, $insert_if_missing = 0) {
|
|
|
- return chado_update_property('pub', $pub_id, $property, 'tripal_pub', $value, $insert_if_missing);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Delete a given property
|
|
|
- *
|
|
|
- * @param $pub_id
|
|
|
- * The pub_id of the property to delete
|
|
|
- * @param $property
|
|
|
- * The cvterm name of the property to delete
|
|
|
- *
|
|
|
- * Note: The property will be identified using the unique combination of the $pub_id and $property
|
|
|
- * and then it will be deleted
|
|
|
- *
|
|
|
- * @return
|
|
|
- * True of success, False otherwise
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_delete_property($pub_id, $property) {
|
|
|
- return chado_delete_property('pub', $pub_id, $property, 'tripal_pub');
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * This function generates an array suitable for use with the
|
|
|
- * tripal_pub_create_citation function for any publication
|
|
|
- * already stored in the Chado tables.
|
|
|
- *
|
|
|
- * @param $pub_id
|
|
|
- * The publication ID
|
|
|
- * @param $skip_existing
|
|
|
- * Set to TRUE to skip publications that already have a citation
|
|
|
- * in the pubprop table. Set to FALSE to generate a citation
|
|
|
- * regardless if the citation already exists.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * An array suitable for the trpial_pub_create_citation function. On
|
|
|
- * failure returns FALSE.
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
|
|
|
-
|
|
|
- $options = array('return_array' => 1);
|
|
|
-
|
|
|
- // ---------------------------------
|
|
|
- // get the publication
|
|
|
- // ---------------------------------
|
|
|
- $values = array('pub_id' => $pub_id);
|
|
|
- $pub = chado_generate_var('pub', $values);
|
|
|
-
|
|
|
- // expand the title
|
|
|
- $pub = chado_expand_var($pub, 'field', 'pub.title');
|
|
|
- $pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
|
|
|
- $pub = chado_expand_var($pub, 'field', 'pub.uniquename');
|
|
|
- $pub_array = array();
|
|
|
- if (trim($pub->title)) {
|
|
|
- $pub_array['Title'] = $pub->title;
|
|
|
- }
|
|
|
- if (trim($pub->volumetitle)) {
|
|
|
- $pub_array['Volume Title'] = $pub->volumetitle;
|
|
|
- }
|
|
|
- if (trim($pub->volume)) {
|
|
|
- $pub_array['Volume'] = $pub->volume;
|
|
|
- }
|
|
|
- if (trim($pub->series_name)) {
|
|
|
- $pub_array['Series Name'] = $pub->series_name;
|
|
|
- }
|
|
|
- if (trim($pub->issue)) {
|
|
|
- $pub_array['Issue'] = $pub->issue;
|
|
|
- }
|
|
|
- if (trim($pub->pyear)) {
|
|
|
- $pub_array['Year'] = $pub->pyear;
|
|
|
- }
|
|
|
- if (trim($pub->pages)) {
|
|
|
- $pub_array['Pages'] = $pub->pages;
|
|
|
- }
|
|
|
- if (trim($pub->miniref)) {
|
|
|
- $pub_array['Mini Ref'] = $pub->miniref;
|
|
|
- }
|
|
|
- if (trim($pub->uniquename)) {
|
|
|
- $pub_array['Uniquename'] = $pub->uniquename;
|
|
|
- }
|
|
|
- $pub_array['Publication Type'][] = $pub->type_id->name;
|
|
|
-
|
|
|
- // ---------------------------------
|
|
|
- // get the citation
|
|
|
- // ---------------------------------
|
|
|
- $values = array(
|
|
|
- 'pub_id' => $pub->pub_id,
|
|
|
- 'type_id' => array(
|
|
|
- 'name' => 'Citation',
|
|
|
- ),
|
|
|
- );
|
|
|
- $citation = chado_generate_var('pubprop', $values);
|
|
|
- if ($citation) {
|
|
|
- $citation = chado_expand_var($citation, 'field', 'pubprop.value', $options);
|
|
|
- if (count($citation) > 1) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Publication has multiple citations already: %pub_id",
|
|
|
- array('%pub_id' => $pubid));
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- elseif (count($citation) == 1 and $skip_existing == TRUE) {
|
|
|
- // skip this publication, it already has a citation
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // ---------------------------------
|
|
|
- // get the publication types
|
|
|
- // ---------------------------------
|
|
|
- $values = array(
|
|
|
- 'pub_id' => $pub->pub_id,
|
|
|
- 'type_id' => array(
|
|
|
- 'name' => 'Publication Type',
|
|
|
- ),
|
|
|
- );
|
|
|
- $ptypes = chado_generate_var('pubprop', $values, $options);
|
|
|
- if ($ptypes) {
|
|
|
- $ptypes = chado_expand_var($ptypes, 'field', 'pubprop.value', $options);
|
|
|
- foreach ($ptypes as $ptype) {
|
|
|
- $pub_array['Publication Type'][] = $ptype->value;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // ---------------------------------
|
|
|
- // get the authors list
|
|
|
- // ---------------------------------
|
|
|
- $values = array(
|
|
|
- 'pub_id' => $pub->pub_id,
|
|
|
- 'type_id' => array(
|
|
|
- 'name' => 'Authors',
|
|
|
- ),
|
|
|
- );
|
|
|
- $authors = chado_generate_var('pubprop', $values);
|
|
|
- $authors = chado_expand_var($authors, 'field', 'pubprop.value', $options);
|
|
|
- if (count($authors) > 1) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Publication has multiple author lists. It should have only one list: %pub_id",
|
|
|
- array('%pub_id' => $pubid));
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- else if (trim($authors->value)) {
|
|
|
- $pub_array['Authors'] = $authors->value;
|
|
|
- }
|
|
|
- // if there is no 'Author's property then try to retreive authors from the pubauthor table
|
|
|
- else {
|
|
|
- $sql = "
|
|
|
- SELECT string_agg(surname || ' ' || givennames, ', ')
|
|
|
- FROM {pubauthor}
|
|
|
- WHERE pub_id = :pub_id
|
|
|
- GROUP BY pub_id
|
|
|
- ";
|
|
|
- $au = chado_query($sql, array(':pub_id' => $pub_id))->fetchField();
|
|
|
- if ($au) {
|
|
|
- $pub_array['Authors'] = $au;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- //Get other props
|
|
|
- $props = array(
|
|
|
- 'Journal Abbreviation',
|
|
|
- 'Elocation',
|
|
|
- 'Media Code',
|
|
|
- 'Conference Name',
|
|
|
- 'Keywords',
|
|
|
- 'Series Name',
|
|
|
- 'pISSN',
|
|
|
- 'Publication Date',
|
|
|
- 'Journal Code',
|
|
|
- 'Journal Alias',
|
|
|
- 'Journal Country',
|
|
|
- 'Published Location',
|
|
|
- 'Publication Model',
|
|
|
- 'Language Abbr',
|
|
|
- 'Alias',
|
|
|
- 'Publication Dbxref',
|
|
|
- 'Copyright',
|
|
|
- 'Abstract',
|
|
|
- 'Notes',
|
|
|
- 'Citation',
|
|
|
- 'Language',
|
|
|
- 'URL',
|
|
|
- 'eISSN',
|
|
|
- 'DOI',
|
|
|
- 'ISSN',
|
|
|
- 'Publication Code',
|
|
|
- 'Comments',
|
|
|
- 'Publisher',
|
|
|
- 'Media Alias',
|
|
|
- 'Original Title');
|
|
|
- foreach ($props AS $prop) {
|
|
|
- $sql =
|
|
|
- "SELECT value FROM {pubprop}
|
|
|
- WHERE type_id =
|
|
|
- (SELECT cvterm_id
|
|
|
- FROM {cvterm}
|
|
|
- WHERE name = :cvtname AND cv_id =
|
|
|
- (SELECT cv_id
|
|
|
- FROM {cv}
|
|
|
- WHERE name = 'tripal_pub'
|
|
|
- )
|
|
|
- )
|
|
|
- AND pub_id = :pub_id
|
|
|
- ";
|
|
|
- $val = trim(chado_query($sql, array(':cvtname' => $prop, ':pub_id' => $pub->pub_id))->fetchField());
|
|
|
- if ($val) {
|
|
|
- $pub_array[$prop] =$val;
|
|
|
- }
|
|
|
- }
|
|
|
- return $pub_array;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * This function generates citations for publications. It requires
|
|
|
- * an array structure with keys being the terms in the Tripal
|
|
|
- * publication ontology. This function is intended to be used
|
|
|
- * for any function that needs to generate a citation.
|
|
|
- *
|
|
|
- * @param $pub
|
|
|
- * An array structure containing publication details where the keys
|
|
|
- * are the publication ontology term names and values are the
|
|
|
- * corresponding details. The pub array can contain the following
|
|
|
- * keys with corresponding values:
|
|
|
- * - Publication Type: an array of publication types. a publication can have more than one type
|
|
|
- * - Authors: a string containing all of the authors of a publication
|
|
|
- * - Journal Name: a string containing the journal name
|
|
|
- * - Journal Abbreviation: a string containing the journal name abbreviation
|
|
|
- * - Series Name: a string containing the series (e.g. conference proceedings) name
|
|
|
- * - Series Abbreviation: a string containing the series name abbreviation
|
|
|
- * - Volume: the serives volume number
|
|
|
- * - Issue: the series issue number
|
|
|
- * - Pages: the page numbers for the publication
|
|
|
- * - Publication Date: A date in the format "Year Month Day"
|
|
|
- *
|
|
|
- * @return
|
|
|
- * A text string containing the citation
|
|
|
- *
|
|
|
- * @ingroup tripal_pub_api
|
|
|
- */
|
|
|
-function tripal_pub_create_citation($pub) {
|
|
|
- $citation = '';
|
|
|
- $pub_type = '';
|
|
|
-
|
|
|
- // An article may have more than one publication type. For example,
|
|
|
- // a publication type can be 'Journal Article' but also a 'Clinical Trial'.
|
|
|
- // Therefore, we need to select the type that makes most sense for
|
|
|
- // construction of the citation. Here we'll iterate through them all
|
|
|
- // and select the one that matches best.
|
|
|
- if(is_array($pub['Publication Type'])) {
|
|
|
- foreach ($pub['Publication Type'] as $ptype) {
|
|
|
- if ($ptype == 'Journal Article' ) {
|
|
|
- $pub_type = $ptype;
|
|
|
- break;
|
|
|
- }
|
|
|
- else if ($ptype == 'Conference Proceedings'){
|
|
|
- $pub_type = $ptype;
|
|
|
- break;
|
|
|
- }
|
|
|
- else if ($ptype == 'Book') {
|
|
|
- $pub_type = $ptype;
|
|
|
- break;
|
|
|
- }
|
|
|
- else if ($ptype == 'Letter') {
|
|
|
- $pub_type = $ptype;
|
|
|
- break;
|
|
|
- }
|
|
|
- else if ($ptype == 'Book Chapter') {
|
|
|
- $pub_type = $ptype;
|
|
|
- break;
|
|
|
- }
|
|
|
- else if ($ptype == "Research Support, Non-U.S. Gov't") {
|
|
|
- $pub_type = $ptype;
|
|
|
- // we don't break because if the article is also a Journal Article
|
|
|
- // we prefer that type
|
|
|
- }
|
|
|
- }
|
|
|
- if (!$pub_type) {
|
|
|
- tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot generate citation for publication type: %types",
|
|
|
- array('%types' => print_r($pub['Publication Type'], TRUE)));
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $pub_type = $pub['Publication Type'];
|
|
|
- }
|
|
|
- //----------------------
|
|
|
- // Journal Article
|
|
|
- //----------------------
|
|
|
- if ($pub_type == 'Journal Article') {
|
|
|
- $citation = $pub['Authors'] . '. ' . $pub['Title'] . '. ';
|
|
|
-
|
|
|
- if (array_key_exists('Journal Name', $pub)) {
|
|
|
- $citation .= $pub['Journal Name'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Journal Abbreviation', $pub)) {
|
|
|
- $citation .= $pub['Journal Abbreviation'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Series Name', $pub)) {
|
|
|
- $citation .= $pub['Series Name'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
- $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
- }
|
|
|
- if (array_key_exists('Publication Date', $pub)) {
|
|
|
- $citation .= $pub['Publication Date'];
|
|
|
- }
|
|
|
- elseif (array_key_exists('Year', $pub)) {
|
|
|
- $citation .= $pub['Year'];
|
|
|
- }
|
|
|
- if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
- $citation .= '; ';
|
|
|
- }
|
|
|
- if (array_key_exists('Volume', $pub)) {
|
|
|
- $citation .= $pub['Volume'];
|
|
|
- }
|
|
|
- if (array_key_exists('Issue', $pub)) {
|
|
|
- $citation .= '(' . $pub['Issue'] . ')';
|
|
|
- }
|
|
|
- if (array_key_exists('Pages', $pub)) {
|
|
|
- if (array_key_exists('Volume', $pub)) {
|
|
|
- $citation .= ':';
|
|
|
- }
|
|
|
- $citation .= $pub['Pages'];
|
|
|
- }
|
|
|
- $citation .= '.';
|
|
|
- }
|
|
|
- //----------------------
|
|
|
- // Research Support, Non-U.S. Gov't
|
|
|
- //----------------------
|
|
|
- elseif ($pub_type == "Research Support, Non-U.S. Gov't") {
|
|
|
- $citation = $pub['Authors'] . '. ' . $pub['Title'] . '. ';
|
|
|
-
|
|
|
- if (array_key_exists('Journal Name', $pub)) {
|
|
|
- $citation .= $pub['Journal Name'] . '. ';
|
|
|
- }
|
|
|
- if (array_key_exists('Publication Date', $pub)) {
|
|
|
- $citation .= $pub['Publication Date'];
|
|
|
- }
|
|
|
- elseif (array_key_exists('Year', $pub)) {
|
|
|
- $citation .= $pub['Year'];
|
|
|
- }
|
|
|
- $citation .= '.';
|
|
|
- }
|
|
|
- //----------------------
|
|
|
- // Letter
|
|
|
- //----------------------
|
|
|
- elseif ($pub_type == 'Letter') {
|
|
|
- $citation = $pub['Authors'] . '. ' . $pub['Title'] . '. ';
|
|
|
-
|
|
|
- if (array_key_exists('Journal Name', $pub)) {
|
|
|
- $citation .= $pub['Journal Name'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Journal Abbreviation', $pub)) {
|
|
|
- $citation .= $pub['Journal Abbreviation'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Series Name', $pub)) {
|
|
|
- $citation .= $pub['Series Name'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
- $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
- }
|
|
|
- if (array_key_exists('Publication Date', $pub)) {
|
|
|
- $citation .= $pub['Publication Date'];
|
|
|
- }
|
|
|
- elseif (array_key_exists('Year', $pub)) {
|
|
|
- $citation .= $pub['Year'];
|
|
|
- }
|
|
|
- if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
- $citation .= '; ';
|
|
|
- }
|
|
|
- if (array_key_exists('Volume', $pub)) {
|
|
|
- $citation .= $pub['Volume'];
|
|
|
- }
|
|
|
- if (array_key_exists('Issue', $pub)) {
|
|
|
- $citation .= '(' . $pub['Issue'] . ')';
|
|
|
- }
|
|
|
- if (array_key_exists('Pages', $pub)) {
|
|
|
- if (array_key_exists('Volume', $pub)) {
|
|
|
- $citation .= ':';
|
|
|
- }
|
|
|
- $citation .= $pub['Pages'];
|
|
|
- }
|
|
|
- $citation .= '.';
|
|
|
- }
|
|
|
- //----------------------
|
|
|
- // Book
|
|
|
- //----------------------
|
|
|
- elseif ($pub_type == 'Book') {
|
|
|
-
|
|
|
- }
|
|
|
- //----------------------
|
|
|
- // Book Chapter
|
|
|
- //----------------------
|
|
|
- elseif ($pub_type == 'Book Chapter') {
|
|
|
-
|
|
|
- }
|
|
|
- //----------------------
|
|
|
- // Conference Proceedings
|
|
|
- //----------------------
|
|
|
- elseif ($pub_type == 'Conference Proceedings') {
|
|
|
- $citation = $pub['Authors'] . '. ' . $pub['Title'] . '. ';
|
|
|
-
|
|
|
- if (array_key_exists('Conference Name', $pub)) {
|
|
|
- $citation .= $pub['Conference Name'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Series Name', $pub)) {
|
|
|
- $citation .= $pub['Series Name'] . '. ';
|
|
|
- }
|
|
|
- elseif (array_key_exists('Series Abbreviation', $pub)) {
|
|
|
- $citation .= $pub['Series Abbreviation'] . '. ';
|
|
|
- }
|
|
|
- if (array_key_exists('Publication Date', $pub)) {
|
|
|
- $citation .= $pub['Publication Date'];
|
|
|
- }
|
|
|
- elseif (array_key_exists('Year', $pub)) {
|
|
|
- $citation .= $pub['Year'];
|
|
|
- }
|
|
|
- if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {
|
|
|
- $citation .= '; ';
|
|
|
- }
|
|
|
- if (array_key_exists('Volume', $pub)) {
|
|
|
- $citation .= $pub['Volume'];
|
|
|
- }
|
|
|
- if (array_key_exists('Issue', $pub)) {
|
|
|
- $citation .= '(' . $pub['Issue'] . ')';
|
|
|
- }
|
|
|
- if (array_key_exists('Pages', $pub)) {
|
|
|
- if (array_key_exists('Volume', $pub)) {
|
|
|
- $citation .= ':';
|
|
|
- }
|
|
|
- $citation .= $pub['Pages'];
|
|
|
- }
|
|
|
- $citation .= '.';
|
|
|
- }
|
|
|
-
|
|
|
- return $citation;
|
|
|
-}
|
|
|
+}
|
Stephen Ficklin