<?php
/**
* @file
* Provides an application programming interface (API) to manage chado publications
*/
/**
* @defgroup tripal_pub_api Publication Module API
* @ingroup tripal_api
* @{
* Provides an application programming interface (API) to manage chado publications
*
* @stephen add documentation here for how to add a new importer.
*
* @}
*/
/**
* Retrieves a chado publication array
*
* @param $identifier
* An array used to uniquely identify a publication. This array has the same
* format as that used by the chado_generate_var(). The following keys can be
* useful for uniquely identifying a publication as they should be unique:
* - pub_id: the chado pub.pub_id primary key
* - nid: the drupal nid of the publication
* - uniquename: A value to matach with the pub.uniquename field
* There are also some specially handled keys. They are:
* - property: An array describing the property to select records for. It
* should at least have either a 'type_name' key (if unique across cvs) or
* 'type_id' key. Other supported keys include: 'cv_id', 'cv_name' (of the type),
* 'value' and 'rank'
* - 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)
* - dbxref_id: The dbxref.dbxref_id of the publication.
* @param $options
* An array of options. Supported keys include:
* - Any keys supported by chado_generate_var(). See that function definition for
* additional details.
*
* NOTE: the $identifier parameter can really be any array similar to $values passed into
* chado_select_record(). It should fully specify the pub record to be returned.
*
* @return
* If a singe publication is retreived using the identifiers, then a publication
* array will be returned. The array is of the same format returned by the
* chado_generate_var() function. Otherwise, FALSE will be returned.
*
* @ingroup tripal_pub_api
*/
function tripal_get_publication($identifiers, $options = array()) {
// Error Checking of parameters
if (!is_array($identifiers)) {
tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
"chado_get_publication: The identifier passed in is expected to be an array with the key
matching a column name in the pub table (ie: pub_id or name). You passed in %identifier.",
array('%identifier'=> print_r($identifiers, TRUE))
);
}
elseif (empty($identifiers)) {
tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
"chado_get_publication: You did not pass in anything to identify the publication you want. The identifier
is expected to be an array with the key matching a column name in the pub table
(ie: pub_id or name). You passed in %identifier.",
array('%identifier'=> print_r($identifiers, TRUE))
);
}
// If one of the identifiers is property then use chado_get_record_with_property()
if (array_key_exists('property', $identifiers)) {
$property = $identifiers['property'];
unset($identifiers['property']);
$pub = chado_get_record_with_property(
array('table' => 'pub', 'base_records' => $identifiers),
array('type_name' => $property),
$options
);
}
elseif (array_key_exists('dbxref', $identifiers)) {
if(preg_match('/^(.*?):(.*?)$/', $identifiers['dbxref'], $matches)) {
$dbname = $matches[1];
$accession = $matches[2];
// First make sure the dbxref is present.
$values = array(
'accession' => $accession,
'db_id' => array(
'name' => $dbname
),
);
$dbxref = chado_select_record('dbxref', array('dbxref_id'), $values);
if (count($dbxref) == 0) {
return FALSE;
}
$pub_dbxref = chado_select_record('pub_dbxref', array('pub_id'), array('dbxref_id' => $dbxref[0]->dbxref_id));
if (count($pub_dbxref) == 0) {
return FALSE;
}
$pub = chado_generate_var('pub', array('pub_id' => $pub_dbxref[0]->pub_id), $options);
}
else {
tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
"chado_get_publication: The dbxref identifier is not correctly formatted.",
array('%identifier'=> print_r($identifiers, TRUE))
);
}
}
elseif (array_key_exists('dbxref_id', $identifiers)) {
// first get the pub_dbxref record
$values = array('dbxref_id' => $identifiers['dbxref_id']);
$pub_dbxref = chado_select_record('pub_dbxref', array('pub_id'), $values);
// now get the pub
if (count($pub_dbxref) > 0) {
$pub = chado_generate_var('pub', array('pub_id' => $pub_dbxref[0]->pub_id), $options);
}
else {
return FALSE;
}
}
// Else we have a simple case and we can just use chado_generate_var to get the pub
else {
// Try to get the pub
$pub = chado_generate_var('pub', $identifiers, $options);
}
// Ensure the pub is singular. If it's an array then it is not singular
if (is_array($pub)) {
tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
"chado_get_publication: The identifiers did not find a single unique record. Identifiers passed: %identifier.",
array('%identifier'=> print_r($identifiers, TRUE))
);
}
// Report an error if $pub is FALSE since then chado_generate_var has failed
elseif ($pub === FALSE) {
tripal_report_error('tripal_pub_api', TRIPAL_ERROR,
"chado_get_publication: Could not find a publication using the identifiers
provided. Check that the identifiers are correct. Identifiers passed: %identifier.",
array('%identifier'=> print_r($identifiers, TRUE))
);
}
// Else, as far we know, everything is fine so give them their pub :)
else {
return $pub;
}
}
/**
* The publication table of Chado only has a unique constraint for the
* uniquename of the publiation, but in reality a publication can be considered
* unique by a combination of the title, publication type, published year and
* series name (e.g. journal name or conference name). The site administrator
* can configure how publications are determined to be unique. This function
* uses the configuration specified by the administrator to look for publications
* that match the details specified by the $pub_details argument
* and indicates if one ore more publications match the criteria.
*
* @param $pub_details
* An associative array with details about the publications. The expected keys
* are:
* 'Title': The title of the publication
* 'Year': The published year of the publication
* 'Publication Type': An array of publication types. A publication can have more than one type.
* 'Series Name': The series name of the publication
* 'Journal Name': An alternative to 'Series Name'
* 'Conference Name': An alternative to 'Series Name'
* 'Citation': The publication citation (this is the value saved in the pub.uniquename field and must be unique)
* If this key is present it will also be checked
* 'Publication Dbxref': A database cross reference of the form DB:ACCESSION where DB is the name
* of the database and ACCESSION is the unique identifier (e.g PMID:3483139)
*
* @return
* An array containing the pub_id's of matching publications. Returns an
* empty array if no pubs match
*
* @ingroup tripal_pub_api
*/
function tripal_publication_exists($pub_details) {
// first try to find the publication using the accession number if that key exists in the details array
if (array_key_exists('Publication Dbxref', $pub_details)) {
$pub = tripal_get_publication(array('dbxref' => $pub_details['Publication Dbxref']));
if($pub) {
return array($pub->pub_id);
}
}
// make sure the citation is unique
if (array_key_exists('Citation', $pub_details)) {
$pub = tripal_get_publication(array('uniquename' => $pub_details['Citation']));
if($pub) {
return array($pub->pub_id);
}
}
// get the publication type (use the first publication type)
if (array_key_exists('Publication Type', $pub_details)) {
$type_name = '';
if(is_array($pub_details['Publication Type'])) {
$type_name = $pub_details['Publication Type'][0];
}
else {
$type_name = $pub_details['Publication Type'];
}
$identifiers = array(
'name' => $type_name,
'cv_id' => array(
'name' => 'tripal_pub',
),
);
$pub_type = tripal_get_cvterm($identifiers);
}
else {
tripal_report_error('tripal_pub', TRIPAL_ERROR,
"tripal_publication_exists(): The Publication Type is a " .
"required property but is missing", array());
return array();
}
if (!$pub_type) {
tripal_report_error('tripal_pub', TRIPAL_ERROR,
"tripal_publication_exists(): Cannot find publication type: '%type'",
array('%type' => $pub_details['Publication Type'][0]));
return array();
}
// get the series name. The pub.series_name field is only 255 chars so we must truncate to be safe
$series_name = '';
if (array_key_exists('Series Name', $pub_details)) {
$series_name = substr($pub_details['Series Name'], 0, 255);
}
if (array_key_exists('Journal Name', $pub_details)) {
$series_name = substr($pub_details['Journal Name'], 0, 255);
}
if (array_key_exists('Conference Name', $pub_details)) {
$series_name = substr($pub_details['Conference Name'], 0, 255);
}
// make sure the publication is unique using the prefereed import duplication check
$import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media');
$pubs = array();
switch ($import_dups_check) {
case 'title_year':
$identifiers = array(
'title' => $pub_details['Title'],
'pyear' => $pub_details['Year']
);
$pubs = chado_select_record('pub', array('pub_id'), $identifiers);
break;
case 'title_year_type':
$identifiers = array(
'title' => $pub_details['Title'],
'pyear' => $pub_details['Year'],
'type_id' => $pub_type->cvterm_id,
);
$pubs = chado_select_record('pub', array('pub_id'), $identifiers);
break;
case 'title_year_media':
$identifiers = array(
'title' => $pub_details['Title'],
'pyear' => $pub_details['Year'],
'series_name' => $series_name,
);
$pubs = chado_select_record('pub', array('pub_id'), $identifiers);
break;
}
$return = array();
foreach ($pubs as $pub) {
$return[] = $pub->pub_id;
}
return $return;
}
/**
* Used for autocomplete in forms for identifying for publications.
*
* @param $field
* The field in the publication to search on.
* @param $string
* The string to search for
*
* @return
* A json array of terms that begin with the provided string
*
* @ingroup tripal_chado_api
*/
function tripal_autocomplete_pub($string = '') {
$items = array();
$sql = "
SELECT pub_id, title, uniquename
FROM {pub}
WHERE lower(title) like lower(:str)
ORDER by title
LIMIT 25 OFFSET 0
";
$pubs = chado_query($sql, array(':str' => $string . '%'));
while ($pub = $pubs->fetchObject()) {
$items[$pub->uniquename] = $pub->uniquename;
}
drupal_json_output($items);
}
/**
* Imports a singe publication specified by a remote database cross reference.
*
* @param $pub_dbxref
* The unique database ID for the record to update. This value must
* be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
* database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
* for the record in the database.
* @param $do_contact
* Set to TRUE if authors should automatically have a contact record added
* to Chado.
* @param $do_update
* If set to TRUE then the publication will be updated if it already exists
* in the database.
*
* @ingroup tripal_pub
*/
function tripal_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update) {
$num_to_retrieve = 1;
$pager_id = 0;
$page = 0;
$num_pubs = 0;
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";
$transaction = db_transaction();
try {
if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) {
$dbname = $matches[1];
$accession = $matches[2];
$criteria = array(
'num_criteria' => 1,
'remote_db' => $dbname,
'criteria' => array(
'1' => array(
'search_terms' => "$dbname:$accession",
'scope' => 'id',
'operation' => '',
'is_phrase' => 0,
),
),
);
$remote_db = $criteria['remote_db'];
$results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
$pubs = $results['pubs'];
$search_str = $results['search_str'];
$total_records = $results['total_records'];
$pub_id = tripal_pub_add_publications($pubs, $do_contact, $do_update);
}
// For backwards compatibility check to see if the legacy pub module
// is enabled. If so, then sync the nodes.
if (module_exists('tripal_pub')) {
// sync the newly added publications with Drupal
print "Syncing publications with Drupal...\n";
chado_node_sync_records('pub');
// if any of the importers wanted to create contacts from the authors then sync them
if($do_contact) {
print "Syncing contacts with Drupal...\n";
chado_node_sync_records('contact');
}
}
}
catch (Exception $e) {
$transaction->rollback();
print "\n"; // make sure we start errors on new line
watchdog_exception('T_pub_import', $e);
print "FAILED: Rolling back database changes...\n";
return;
}
print "Done.\n";
}
/**
* Imports all publications for all active import setups.
*
* @param $report_email
* A list of email address, separated by commas, that should be notified
* once importing has completed
* @param $do_update
* If set to TRUE then publications that already exist in the Chado database
* will be updated, whereas if FALSE only new publications will be added
*
* @ingroup tripal_pub
*/
function tripal_execute_active_pub_importers($report_email = FALSE, $do_update = FALSE) {
$num_to_retrieve = 100;
$page = 0;
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";
// start the transaction
$transaction = db_transaction();
try {
// get all of the loaders
$args = array();
$sql = "SELECT * FROM {tripal_pub_import} WHERE disabled = 0 ";
$results = db_query($sql, $args);
$do_contact = FALSE;
$reports = array();
foreach ($results as $import) {
$page = 0;
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;
}
$criteria = unserialize($import->criteria);
$remote_db = $criteria['remote_db'];
do {
// retrieve the pubs for this page. We'll retreive 100 at a time
$results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
$pubs = $results['pubs'];
$reports[$import->name] = tripal_pub_add_publications($pubs, $import->do_contact, $do_update);
$page++;
}
// continue looping until we have a $pubs array that does not have
// our requested numer of records. This means we've hit the end
while (count($pubs) == $num_to_retrieve);
}
// sync the newly added publications with Drupal. If the user
// requested a report then we don't want to print any syncing information
// so pass 'FALSE' to the sync call
// For backwards compatibility check to see if the legacy pub module
// is enabled. If so, then sync the nodes.
if (module_exists('tripal_pub')) {
print "Syncing publications with Drupal...\n";
chado_node_sync_records('pub');
}
// iterate through each of the reports and generate a final report with HTML links
$HTML_report = '';
if ($report_email) {
$HTML_report .= "<html>";
global $base_url;
foreach ($reports as $importer => $report) {
$total = count($report['inserted']);
$HTML_report .= "<b>$total new publications from importer: $importer</b><br><ol>\n";
foreach ($report['inserted'] as $pub) {
$item = $pub['Title'];
if (array_key_exists('pub_id', $pub)) {
$item = l($pub['Title'], "$base_url/pub/" . $pub['pub_id']);
}
$HTML_report .= "<li>$item</li>\n";
}
$HTML_report .= "</ol>\n";
}
$HTML_report .= "</html>";
$site_email = variable_get('site_mail', '');
$params = array(
'message' => $HTML_report
);
drupal_mail('tripal_pub', 'import_report', $report_email, language_default(), $params, $site_email, TRUE);
}
// For backwards compatibility check to see if the legacy pub module
// is enabled. If so, then sync the nodes.
if (module_exists('tripal_pub')) {
// if any of the importers wanted to create contacts from the authors then sync them
if($do_contact) {
print "Syncing contacts with Drupal...\n";
chado_node_sync_records('contact');
}
}
}
catch (Exception $e) {
$transaction->rollback();
print "\n"; // make sure we start errors on new line
watchdog_exception('T_pub_import', $e);
print "FAILED: Rolling back database changes...\n";
return;
}
print "Done.\n";
}
/**
* Updates publication records.
*
* Updates publication records that currently exist in the Chado pub table
* with the most recent data in the remote database.
*
* @param $do_contact
* Set to TRUE if authors should automatically have a contact record added
* to Chado. Contacts are added using the name provided by the remote
* database.
* @param $dbxref
* The unique database ID for the record to update. This value must
* be of the format DB_NAME:ACCESSION where DB_NAME is the name of the
* database (e.g. PMID or AGL) and the ACCESSION is the unique identifier
* for the record in the database.
* @param $db
* The name of the remote database to update. If this value is provided and
* no dbxref then all of the publications currently in the Chado database
* for this remote database will be updated.
*
* @ingroup tripal_pub
*/
function tripal_reimport_publications($do_contact = FALSE, $dbxref = NULL, $db = 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";
$transaction = db_transaction();
try {
// get a list of all publications by their Dbxrefs that have supported databases
$sql = "
SELECT DB.name as db_name, DBX.accession
FROM pub P
INNER JOIN pub_dbxref PDBX ON P.pub_id = PDBX.pub_id
INNER JOIN dbxref DBX ON DBX.dbxref_id = PDBX.dbxref_id
INNER JOIN db DB ON DB.db_id = DBX.db_id
";
$args = array();
if ($dbxref and preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) {
$dbname = $matches[1];
$accession = $matches[2];
$sql .= "WHERE DBX.accession = :accession and DB.name = :dbname ";
$args[':accession'] = $accession;
$args[':dbname'] = $dbname;
}
elseif ($db) {
$sql .= " WHERE DB.name = :dbname ";
$args[':dbname'] = $db;
}
$sql .= "ORDER BY DB.name, P.pub_id";
$results = chado_query($sql, $args);
$num_to_retrieve = 100;
$i = 0; // count the number of IDs. When we hit $num_to_retrieve we'll do the query
$curr_db = ''; // keeps track of the current current database
$ids = array(); // the list of IDs for the database
$search = array(); // the search array passed to the search function
// iterate through the pub IDs
while ($pub = $results->fetchObject()) {
$accession = $pub->accession;
$remote_db = $pub->db_name;
// here we need to only update publications for databases we support
$supported_dbs = variable_get('tripal_pub_supported_dbs', array());
if(!in_array($remote_db, $supported_dbs)) {
continue;
}
$search = array(
'num_criteria' => 1,
'remote_db' => $remote_db,
'criteria' => array(
'1' => array(
'search_terms' => "$remote_db:$accession",
'scope' => 'id',
'operation' => '',
'is_phrase' => 0,
),
),
);
$pubs = tripal_get_remote_pubs($remote_db, $search, 1, 0);
tripal_pub_add_publications($pubs, $do_contact, TRUE);
$i++;
}
// For backwards compatibility check to see if the legacy pub module
// is enabled. If so, then sync the nodes.
if (module_exists('tripal_pub')) {
// sync the newly added publications with Drupal
print "Syncing publications with Drupal...\n";
chado_node_sync_records('pub');
// if the caller wants to create contacts then we should sync them
if ($do_contact) {
print "Syncing contacts with Drupal...\n";
chado_node_sync_records('contact');
}
}
}
catch (Exception $e) {
$transaction->rollback();
print "\n"; // make sure we start errors on new line
watchdog_exception('T_pub_import', $e);
print "FAILED: Rolling back database changes...\n";
return;
}
print "Done.\n";
}
/**
* Launch the Tripal job to generate citations.
*
* This function will recreate citations for all publications currently
* loaded into Tripal. This is useful to create a consistent format for
* all citations.
*
* @param $options
* Options pertaining to what publications to generate citations for.
* One of the following must be present:
* - all: Create and replace citation for all pubs
* - new: Create citation for pubs that don't already have one
*
* @ingroup tripal_pub
*/
function tripal_pub_create_citations($options) {
$skip_existing = TRUE;
$sql = "
SELECT cvterm_id
FROM {cvterm}
WHERE
name = 'Citation' AND
cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal_pub')
";
$citation_type_id = chado_query($sql)->fetchField();
// Create and replace citation for all pubs
if ($options == 'all') {
$sql = "SELECT pub_id FROM {pub} P WHERE pub_id <> 1";
$skip_existing = FALSE;
}
// Create citation for pubs that don't already have one
else if ($options == 'new') {
$sql = "
SELECT pub_id
FROM {pub} P
WHERE
(SELECT value
FROM {pubprop} PB
WHERE type_id = :type_id AND P.pub_id = PB.pub_id AND rank = 0) IS NULL
AND pub_id <> 1
";
$skip_existing = TRUE;
}
$result = chado_query($sql, array(':type_id' => $citation_type_id));
$counter_updated = 0;
$counter_generated = 0;
while ($pub = $result->fetchObject()) {
$pub_arr = tripal_pub_get_publication_array($pub->pub_id, $skip_existing);
if ($pub_arr) {
$citation = tripal_pub_create_citation($pub_arr);
print $citation . "\n\n";
// Replace if citation exists. This condition is never TRUE if $skip_existing is TRUE
if ($pub_arr['Citation']) {
$sql = "
UPDATE {pubprop} SET value = :value
WHERE pub_id = :pub_id AND type_id = :type_id AND rank = :rank
";
chado_query($sql, array(':value' => $citation, ':pub_id' => $pub->pub_id,
':type_id' => $citation_type_id, ':rank' => 0));
$counter_updated ++;
// Generate a new citation
} else {
$sql = "
INSERT INTO {pubprop} (pub_id, type_id, value, rank)
VALUES (:pub_id, :type_id, :value, :rank)
";
chado_query($sql, array(':pub_id' => $pub->pub_id, ':type_id' => $citation_type_id,
':value' => $citation, ':rank' => 0));
$counter_generated ++;
}
}
}
print "$counter_generated citations generated. $counter_updated citations updated.\n";
}
/**
* 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 $pub
* An array structure containing publication details where the keys
* are the publication ontology term names and values are the
* corresponding details. The pub array can contain the following
* keys with corresponding values:
* - Publication Type: an array of publication types. a publication can have more than one type
* - Authors: a string containing all of the authors of a publication
* - Journal Name: a string containing the journal name
* - Journal Abbreviation: a string containing the journal name abbreviation
* - Series Name: a string containing the series (e.g. conference proceedings) name
* - Series Abbreviation: a string containing the series name abbreviation
* - Volume: the serives volume number
* - Issue: the series issue number
* - Pages: the page numbers for the publication
* - Publication Date: A date in the format "Year Month Day"
*
* @return
* A text string containing the citation
*
* @ingroup tripal_pub
*/
function tripal_pub_create_citation($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 == 'Review') {
$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 = $ptype;
// we don't break because if the article is also a Journal Article
// we prefer that type
}
}
// If we don't have a recognized publication type, then just use the
// first one in the list.
if (!$pub_type) {
$pub_type = $pub['Publication Type'][0];
}
}
else {
$pub_type = $pub['Publication Type'];
}
//----------------------
// Journal Article
//----------------------
if ($pub_type == 'Journal Article') {
if (array_key_exists('Authors', $pub)) {
$citation = $pub['Authors'] . '. ';
}
$citation .= $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'];
}
$citation .= '.';
}
//----------------------
// Review
//----------------------
if ($pub_type == 'Review') {
if (array_key_exists('Authors', $pub)) {
$citation = $pub['Authors'] . '. ';
}
$citation .= $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") {
if (array_key_exists('Authors', $pub)) {
$citation = $pub['Authors'] . '. ';
}
$citation .= $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') {
if (array_key_exists('Authors', $pub)) {
$citation = $pub['Authors'] . '. ';
}
$citation .= $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'];
}
$citation .= '.';
}
//-----------------------
// Conference Proceedings
//-----------------------
elseif ($pub_type == 'Conference Proceedings') {
if (array_key_exists('Authors', $pub)) {
$citation = $pub['Authors'] . '. ';
}
$citation .= $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 .= '.';
}
//-----------------------
// Default
//-----------------------
else {
if (array_key_exists('Authors', $pub)) {
$citation = $pub['Authors'] . '. ';
}
$citation .= $pub['Title'] . '. ';
if (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;
}
/**
* Retrieves the minimal information to uniquely describe any publication.
*
* @param $pub
* A publication object as created by chado_generate_var()
*
* @return
* An array with the following keys: 'Citation', 'Abstract', 'Authors',
* 'URL'. All keys are term names in the Tripal Publication Ontology :TPUB.
*/
function tripal_get_minimal_pub_info($pub) {
// Chado has a null pub as default. We don't return anything for this.
if ($pub->uniquename == 'null') {
return array();
}
// expand the title
$pub = chado_expand_var($pub, 'field', 'pub.title');
$pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
// get the citation
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'Citation',
),
);
$options = array(
'include_fk' => array(
),
);
$citation = chado_generate_var('pubprop', $values, $options);
$citation = chado_expand_var($citation, 'field', 'pubprop.value');
$citation = $citation->value;
// get the abstract
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'Abstract',
),
);
$options = array(
'include_fk' => array(
),
);
$abstract = chado_generate_var('pubprop', $values, $options);
$abstract = chado_expand_var($abstract, 'field', 'pubprop.value');
$abstract_text = '';
if ($abstract) {
$abstract_text = htmlspecialchars($abstract->value);
}
// get the author list
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'Authors',
),
);
$options = array(
'include_fk' => array(
),
);
$authors = chado_generate_var('pubprop', $values, $options);
$authors = chado_expand_var($authors, 'field', 'pubprop.value');
$authors_list = 'N/A';
if ($authors) {
$authors_list = $authors->value;
}
// get the first database cross-reference with a url
$options = array('return_array' => 1);
$pub = chado_expand_var($pub, 'table', 'pub_dbxref', $options);
$dbxref = NULL;
if ($pub->pub_dbxref) {
foreach ($pub->pub_dbxref as $index => $pub_dbxref) {
if ($pub_dbxref->dbxref_id->db_id->urlprefix) {
$dbxref = $pub_dbxref->dbxref_id;
}
}
}
// get the URL
// get the author list
$values = array(
'pub_id' => $pub->pub_id,
'type_id' => array(
'name' => 'URL',
),
);
$options = array(
'return_array' => 1,
'include_fk' => array(),
);
$urls = chado_generate_var('pubprop', $values, $options);
$urls = chado_expand_var($urls, 'field', 'pubprop.value');
$url = '';
if (count($urls) > 0) {
$url = $urls[0]->value;
}
return array(
'Title' => $pub->title,
'Citation' => $citation,
'Abstract' => $abstract_text,
'Authors' => $authors_list,
'URL' => $url,
);
}