<?php
/**
* @file
* The Tripal Pub API
*
* @defgroup tripal_pub_api Publication Module API
* @ingroup tripal_api
*/
/*
* Retrieves a list of publications as an associated array where
* keys correspond directly with Tripal Pub CV terms.
*
* @param remote_db
* The name of the remote publication database to query. These names should
* match the name of the databases in the Chado 'db' table. Currently
* supported databass include
* 'PMID': PubMed
*
* @param search_array
* An associate array containing the search criteria. The following key
* are expected
* 'remote_db': Specifies the name of the remote publication database
* 'num_criteria': Specifies the number of criteria present in the search array
* 'days': The number of days to include in the search starting from today
* 'criteria': An associate array containing the search critiera. There should
* be no less than 'num_criteria' elements in this array.
*
* The following keys are expected in the 'criteria' array
* 'search_terms': A list of terms to search on, separated by spaces.
* 'scope': The fields to search in the remote database. Valid values
* include: 'title', 'abstract', 'author' and 'any'
* 'operation': The logical operation to use for this criteria. Valid
* values include: 'AND', 'OR' and 'NOT'.
* @param $num_to_retrieve
* The number of records to retrieve. In cases with large numbers of
* records to retrieve, the remote database may limit the size of each
* retrieval.
* @param $pager_id
* Optional. This function uses the 'tripal_pager_callback' function
* to page a set of results. This is helpful when generating results to
* be view online. The pager works identical to the pager_query function
* of drupal. Simply provide a unique integer value for this argument. Each
* form on a single page should have a unique $pager_id.
* @param $page
* Optional. If this function is called where the
* page for the pager cannot be set using the $_GET variable, use this
* argument to specify the page to retrieve.
*
* @return
* Returns an array of pubs where each element is
* an associative array where the keys are Tripal Pub CV terms.
*
* @ingroup tripal_pub_api
*/
function tripal_pub_get_remote_search_results($remote_db, $search_array,
$num_to_retrieve, $pager_id = 0, $page = 0) {
// manually set the $_GET['page'] parameter to trick the pager
// into giving us the requested page
if (is_int($page) and $page > 0) {
$_GET['page'] = $page;
}
// now call the callback function to get the results
$callback = "tripal_pub_remote_search_$remote_db";
$pubs = array();
if (function_exists($callback)) {
$pubs = call_user_func($callback, $search_array, $num_to_retrieve, $pager_id);
}
return $pubs;
}
/*
* @ingroup tripal_pub_api
*/
function tripal_pub_get_raw_data($dbxref) {
if(preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) {
$remote_db = $matches[1];
$accession = $matches[2];
// check that the database is supported
$supported_dbs = variable_get('tripal_pub_supported_dbs', array());
if(!in_array($remote_db, $supported_dbs)) {
return "Unsupported database: $dbxref";
}
$search = array(
'num_criteria' => 1,
'remote_db' => $remote_db,
'criteria' => array(
'1' => array(
'search_terms' => "$remote_db:$accession",
'scope' => 'id',
'operation' => '',
'is_phrase' => 0,
),
),
);
$pubs = tripal_pub_get_remote_search_results($remote_db, $search, 1, 0);
return '<textarea cols=80 rows=20>' . $pubs[0]['raw'] . '</textarea>';
}
return 'Invalid DB xref';
}
/*
* @ingroup tripal_pub_api
*/
function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db = NULL) {
// get a persistent connection
$connection = tripal_db_persistent_chado();
if (!$connection) {
print "A persistant connection was not obtained. Loading will be slow\n";
}
// if we cannot get a connection then let the user know the loading will be slow
tripal_db_start_transaction();
if ($connection) {
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";
}
// 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 = '%s' and DB.name = '%s' ";
$args[] = $accession;
$args[] = $dbname;
}
elseif ($db) {
$sql .= " WHERE DB.name = '%s' ";
$args[] = $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 = db_fetch_object($results)) {
$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,
),
),
);
$pubs = tripal_pub_get_remote_search_results($remote_db, $search, 1, 0);
tripal_pub_add_publications($pubs, $do_contact, TRUE);
$i++;
}
// transaction is complete
tripal_db_commit_transaction();
print "Transaction Complete\n";
// sync the newly added publications with Drupal
print "Syncing publications with Drupal...\n";
tripal_pub_sync_pubs();
// if the caller wants to create contacts then we should sync them
if ($do_contact) {
print "Syncing contacts with Drupal...\n";
tripal_contact_sync_contacts();
}
print "Done.\n";
}
/*
* @ingroup tripal_pub_api
*/
function tripal_pub_import_publications($report_email = FALSE, $do_update = FALSE) {
$num_to_retrieve = 100;
$pager_id = 0;
$page = 0;
$num_pubs = 0;
// get a persistent connection
$connection = tripal_db_persistent_chado();
if (!$connection) {
print "A persistant connection was not obtained. Loading will be slow\n";
}
// if we cannot get a connection then let the user know the loading will be slow
tripal_db_start_transaction();
if ($connection) {
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";
}
// get all of the loaders
$args = array();
$sql = "SELECT * FROM {tripal_pub_import} WHERE disabled = 0 ";
$results = db_query($sql, $args);
$do_contact = FALSE;
$reports = array();
while ($import = db_fetch_object($results)) {
print "Importing: " . $import->name . "\n";
// keep track if any of the importers want to create contacts from authors
if ($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 10 at a time
$pubs = tripal_pub_get_remote_search_results($remote_db, $criteria, $num_to_retrieve, $pager_id, $page);
$reports[$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);
}
// transaction is complete
tripal_db_commit_transaction();
print "Transaction Complete\n";
// 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
print "Syncing publications with Drupal...\n";
tripal_pub_sync_pubs();
// 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 = $pub['Title'];
if ($pub['pub_id']) {
$item = l($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, $site_email, TRUE);
}
// if any of the importers wanted to create contacts from the authors then sync them
if($do_contact) {
print "Syncing contacts with Drupal...\n";
tripal_contact_sync_contacts();
}
print "Done.\n";
}
/*
* @ingroup tripal_pub_api
*/
function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update) {
$num_to_retrieve = 1;
$pager_id = 0;
$page = 0;
$num_pubs = 0;
// get a persistent connection
$connection = tripal_db_persistent_chado();
if (!$connection) {
print "A persistant connection was not obtained. Loading will be slow\n";
}
// if we cannot get a connection then let the user know the loading will be slow
tripal_db_start_transaction();
if ($connection) {
print "\nNOTE: Loading of the publication is performed using a database transaction. \n" .
"If the load fails or is terminated prematurely then the entire set of \n" .
"insertions/updates is rolled back and will not be found in the database\n\n";
}
if(preg_match('/^(.*?):(.*?)$/', $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'];
$pubs = tripal_pub_get_remote_search_results($remote_db, $criteria, $num_to_retrieve, $pager_id, $page);
$pub_id = tripal_pub_add_publications($pubs, $do_contact, $do_update);
}
// transaction is complete
tripal_db_commit_transaction();
print "Transaction Complete\n";
// sync the newly added publications with Drupal
print "Syncing publications with Drupal...\n";
tripal_pub_sync_pubs();
// if any of the importers wanted to create contacts from the authors then sync them
if($do_contact) {
print "Syncing contacts with Drupal...\n";
tripal_contact_sync_contacts();
}
print "Done.\n";
}
/*
*
*/
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 $report;
}
/*
*
*/
function tripal_pub_add_pub_dbxref($pub_id, $pub_dbxref) {
// break apart the dbxref
$dbname = '';
$accession = '';
if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) {
$dbname = $matches[1];
$accession = $matches[2];
}
else {
return FALSE;
}
// check to see if the pub_dbxref record already exist
$values = array(
'dbxref_id' => array(
'accession' => $accession,
'db_id' => array(
'name' => $dbname,
),
),
'pub_id' => $pub_id,
);
$options = array('statement_name' => 'sel_pubdbxref_dbpu');
$results = tripal_core_chado_select('pub_dbxref', array('*'), $values, $options);
// if the pub_dbxref record exist then we don't need to re-add it.
if(count($results) > 0) {
return $results[0];
}
// make sure our database already exists
$db = tripal_db_add_db($dbname);
// get the database cross-reference
$dbxvalues = array(
'accession' => $accession,
'db_id' => $db->db_id,
);
$dbxoptions = array('statement_name' => 'sel_dbxref_acdb');
$results = tripal_core_chado_select('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions);
// if the accession doesn't exist then add it
if(count($results) == 0){
$dbxref = tripal_db_add_dbxref($db->db_id, $accession);
}
else {
$dbxref = $results[0];
}
// now add the record
$options = array('statement_name' => 'ins_pubdbxref_dbpu');
$results = tripal_core_chado_insert('pub_dbxref', $values, $options);
if (!$results) {
watchdog('tripal_pub', "Cannot add publication dbxref: %db:%accession.",
array('%db' => $dbname, '%accession' => $accession). WATCHDOG_ERROR);
return FALSE;
}
return $results;
}
/**
* 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 = tripal_core_chado_select('pub_dbxref', array('pub_id'), $values, $options);
foreach ($results as $index => $pub) {
$return[] = $pub->pub_id;
}
}
return $return;
}
/**
* Returns the list of publications that match a given title, type and year
*
* @param title
* The title of the publication to look for
* @param type
* Optional. The publication type. The value of this field should come from
* the Tripal Pub vocabulary. This should be the type name (e.g. cvterm.name)
* @param year
* Optional. The year the publication was published.
* @param series_name
* Optional. The name of the series (e.g. Journal name)
*
* @return
* Returns an array of all the publications that have the provided
* cross reference. If no publications match, then an empty array
* is returned.
*
* @ingroup tripal_pub_api
*
*/
function tripal_pub_get_pubs_by_title_type_pyear_series($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 = tripal_core_chado_select('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 = tripal_core_chado_select('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
* $action variable is set to 'error'
*
*/
function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE, $update_if_exists = FALSE) {
$pub_id = 0;
// first try to find the publication using the accession number. It will have
// one if the pub has already been loaded for the publication database
if ($pub_details['Publication Dbxref']) {
$results = tripal_pub_get_pubs_by_dbxref($pub_details['Publication Dbxref']);
if(count($results) == 1) {
$pub_id = $results[0];
}
elseif (count($results) > 1) {
watchdog('tripal_pub', "There are two publications with this accession: %db:%accession. Cannot determine which to update.",
array('%db' => $dbname, '%accession' => $accession), WATCHDOG_ERROR);
$action = 'error';
return FALSE;
}
}
// if we couldn't find a publication by the accession (which means it doesn't
// yet exist or it has been added using a different publication database) then
// try to find it using the title and publication year.
if (!$pub_id and $pub_details['Title']) {
$results = tripal_pub_get_pubs_by_title_type_pyear($pub_details['Title'], NULL, $pub_details['Year']);
if (count($results) == 1) {
$pub_id = $results[0];
}
elseif (count($results) > 1) {
watchdog('tripal_pub', "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']), WATCHDOG_ERROR);
$action = 'error';
return FALSE;
}
}
print "PUB ID: $pub_id\n";
// if there is a pub id and we've been told not to update then return
if ($pub_id and !$update_if_exists) {
$action = 'skipped';
return $pub_id;
}
// get the publication type (use the first publication type, any others will get stored as properties)
if (is_array($pub_details['Publication Type'])) {
$pub_type = tripal_cv_get_cvterm_by_name($pub_details['Publication Type'][0], NULL, 'tripal_pub');
}
elseif ($pub_details['Publication Type']) {
$pub_type = tripal_cv_get_cvterm_by_name($pub_details['Publication Type'], NULL, 'tripal_pub');
}
else {
watchdog('tripal_pub', "The Publication Type is a required property but is missing", array(), WATCHDOG_ERROR);
$action = 'error';
return FALSE;
}
if (!$pub_type) {
watchdog('tripal_pub', "Cannot find publication type: '%type'",
array('%type' => $pub_details['Publication Type'][0]), WATCHDOG_ERROR);
$action = 'error';
return FALSE;
}
// build the values array for inserting or updating
$values = array(
'title' => $pub_details['Title'],
'volume' => $pub_details['Volume'],
'series_name' => $pub_details['Journal Name'],
'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 = tripal_core_chado_insert('pub', $values, $options);
if (!$pub) {
watchdog('tripal_pub', "Cannot insert the publication with title: %title",
array('%title' => $pub_details['Title']), WATCHDOG_ERROR);
$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 = tripal_core_chado_update('pub', $match, $values, $options);
if (!$success) {
watchdog('tripal_pub', "Cannot update the publication with title: %title",
array('%title' => $pub_details['Title']), WATCHDOG_ERROR);
$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) {
$sql = "
DELETE FROM {pubprop}
WHERE
pub_id = %d AND
NOT type_id in (
SELECT cvterm_id
FROM {cvterm}
WHERE name = 'Publication Dbxref'
)
";
chado_query($sql, $pub_id);
}
// iterate through the properties and add them
foreach ($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) {
watchdog('tripal_pub', "Cannot find term: '%prop'. Skipping.", array('%prop' => $key), WATCHDOG_ERROR);
continue;
}
// skip details that won't be stored as properties
if ($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 = tripal_core_insert_property('pub', $pub_id, $key, 'tripal_pub', $subvalue, FALSE);
}
else {
$success = tripal_core_insert_property('pub', $pub_id, $subkey, 'tripal_pub', $subvalue, FALSE);
}
}
}
else {
$success = tripal_core_insert_property('pub', $pub_id, $key, 'tripal_pub', $value, TRUE);
}
if (!$success) {
watchdog('tripal_pub', "Cannot add property '%prop' to publication. Skipping.",
array('%prop' => $key), WATCHDOG_ERROR);
continue;
}
}
return $pub_id;
}
/*
*
*/
function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
$rank = 0;
// first remove any of the existing pubauthor entires
$sql = "DELETE FROM {pubauthor} WHERE pub_id = %d";
chado_query($sql, $pub_id);
// iterate through the authors and add them to the pubauthors and contact
// tables of chado, then link them through the custom pubauthors_contact table
foreach ($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'] ? $author['Surname'] : $author['Collective'],
'givennames' => $author['Given Name'],
'suffix' => $author['Suffix'],
);
$options = array('statement_name' => 'ins_pubauthor_idrasugisu');
$pubauthor = tripal_core_chado_insert('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 = tripal_core_chado_insert('pubauthor_contact', $values, $options);
if (!$pubauthor_contact) {
watchdog('tripal_pub', "Cannot link pub authro and contact.", array(), WATCHDOG_ERROR);
}
}
}
$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 tripal_core_get_property('pub', $pub_id, $property, 'tripal');
}
/**
* 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 tripal_core_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 tripal_core_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 tripal_core_delete_property('pub', $pub_id, $property, 'tripal');
}
/*
*
*/
function tripal_pub_create_citation($pub) {
$citation = $pub['Authors'] . '. ' . $pub['Title'] . '. ';
if ($pub['Journal Name']) {
$citation .= $pub['Journal Name'] . '. ';
}
elseif ($pub['Journal Abbreviation']) {
$citation .= $pub['Journal Abbreviation'] . '. ';
}
$citation .= $pub['Publication Date'];
if ($pub['Volume'] or $pub['Issue'] or $pub['Pages']) {
$citation .= '; ';
}
if ($pub['Volume']) {
$citation .= $pub['Volume'];
}
if ($pub['Issue']) {
$citation .= '(' . $pub['Issue'] . ')';
}
if ($pub['Pages']) {
if($pub['Volume']) {
$citation .= ':';
}
$citation .= $pub['Pages'];
}
$citation .= '.';
return $citation;
}