<?php
/**
* Retrieves an entity that matches the given table and record id.
*
* @param $table
* The name of the Chado table.
* @param $record_id
* The record's primary key in the table specified by $table.
*
* @return
* A chado_entity object.
*/
function tripal_load_chado_entity($table, $record_id) {
$entity_id = db_select('chado_entity', 'ce')
->fields('ce', array('entity_id'))
->condition('ce.record_id', $record_id)
->condition('ce.data_table', $table)
->execute()
->fetchField();
if ($entity_id) {
$entity = entity_load('TripalEntity', array($entity_id));
return reset($entity);
}
return NULL;
}
/**
* Publishes content in Chado as a new TripalEntity entity.
*
* @param $values
* A key/value associative array that supports the following keys:
* - bundle_name: The name of the the TripalBundle (e.g. bio_data-12345).
* @param $job_id
* (Optional) The numeric job ID as provided by the Tripal jobs system. There
* is no need to specify this argument if this function is being called
* outside of the jobs systems.
*
* @return boolean
* TRUE if all of the records of the given bundle type were published, and
* FALSE if a failure occured.
*/
function tripal_chado_publish_records($values, $job_id = NULL) {
$bundle_name = $values['bundle_name'];
$sync_node = array_key_exists('sync_node', $values) ? $values['sync_node'] : '';
if (!array_key_exists('bundle_name', $values) or !$values['bundle_name']) {
tripal_report_error('tripal_chado', TRIPAL_ERROR, "Could not publish record: @error", array('@error' => 'The bundle name was not provided'));
return FALSE;
}
$bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
$bundle_id = $bundle->id;
$table = tripal_get_bundle_variable('chado_table', $bundle_id);
$column = tripal_get_bundle_variable('chado_column', $bundle_id);
$cvterm_id = tripal_get_bundle_variable('chado_cvterm_id', $bundle_id);
// Get the table information
$table_schema = chado_get_schema($table);
$pkey_field = $table_schema['primary key'][0];
$select = "SELECT $pkey_field as record_id ";
$from = "FROM {" . $table . "} T
LEFT JOIN public.chado_entity CE on CE.record_id = T.$pkey_field
AND CE.data_table = '$table'
";
if ($sync_node && db_table_exists('chado_' . $table)) {
$select = "SELECT T.$pkey_field as record_id, CT.nid ";
$from .= "INNER JOIN public.chado_$table CT ON CT.$pkey_field = T.$pkey_field";
}
$where = " WHERE CE.record_id IS NULL ";
if ($table != 'analysis' and $table != 'organism') {
$where .= "AND $column = $cvterm_id";
}
$sql = $select . $from . $where;
$records = chado_query($sql);
$num_published = 0;
$transaction = db_transaction();
try {
while($record = $records->fetchObject()) {
// First save the tripal_entity record.
$record_id = $record->record_id;
$ec = entity_get_controller('TripalEntity');
$entity = $ec->create(array(
'bundle' => $bundle_name,
'term_id' => $bundle->term_id,
));
if (!$entity->save()) {
throw new Exception('Could not create entity.');
}
// Next save the chado_entity record.
$entity_record = array(
'entity_id' => $entity->id,
'record_id' => $record_id,
'data_table' => $table,
'type_table' => $table,
'field' => $column,
);
// For the Tv2 to Tv3 migration we want to add the nid to the
// entity so we can associate the node with the entity.
if (property_exists($record, 'nid')) {
$entity_record['nid'] = $record->nid;
}
$success = drupal_write_record('chado_entity', $entity_record);
$entity = entity_load('TripalEntity', array($entity->id));
$entity = reset($entity);
$title_format = tripal_get_title_format($bundle);
$title = tripal_replace_entity_tokens($title_format, $entity, $bundle);
$ec->setTitle($entity, $title);
$num_published++;
}
}
catch (Exception $e) {
$transaction->rollback();
$error = $e->getMessage();
tripal_report_error('tripal_chado', TRIPAL_ERROR, "Could not publish record: @error", array('@error' => $error));
drupal_set_message('Failed publishing record. See recent logs for more details.', 'error');
return FALSE;
}
drupal_set_message("Succesfully published $num_published " . $bundle->label . " record(s).");
return TRUE;
}
/**
* Returns an array of tokens based on Tripal Entity Fields.
*
* @param $base_table
* The name of a base table in Chado.
* @return
* An array of tokens where the key is the machine_name of the token.
*/
function tripal_get_chado_tokens($base_table) {
$tokens = array();
$table_descrip = chado_get_schema($base_table);
foreach ($table_descrip['fields'] as $field_name => $field_details) {
$token = '[' . $base_table . '.' . $field_name . ']';
$location = implode(' > ',array($base_table, $field_name));
$tokens[$token] = array(
'name' => ucwords(str_replace('_',' ',$base_table)) . ': ' . ucwords(str_replace('_',' ',$field_name)),
'table' => $base_table,
'field' => $field_name,
'token' => $token,
'description' => array_key_exists('description', $field_details) ? $field_details['description'] : '',
'location' => $location
);
if (!array_key_exists('description', $field_details) or preg_match('/TODO/',$field_details['description'])) {
$tokens[$token]['description'] = 'The '.$field_name.' field of the '.$base_table.' table.';
}
}
// RECURSION:
// Follow the foreign key relationships recursively
if (array_key_exists('foreign keys', $table_descrip)) {
foreach ($table_descrip['foreign keys'] as $table => $details) {
foreach ($details['columns'] as $left_field => $right_field) {
$sub_token_prefix = $base_table . '.' . $left_field;
$sub_location_prefix = implode(' > ',array($base_table, $left_field));
$sub_tokens = tripal_get_chado_tokens($table);
if (is_array($sub_tokens)) {
$tokens = array_merge($tokens, $sub_tokens);
}
}
}
}
return $tokens;
}
/**
* Replace all Chado Tokens in a given string.
*
* NOTE: If there is no value for a token then the token is removed.
*
* @param string $string
* The string containing tokens.
* @param $record
* A Chado record as generated by chado_generate_var()
*
* @return
* The string will all tokens replaced with values.
*/
function tripal_replace_chado_tokens($string, $record) {
// Get the list of tokens
$tokens = tripal_get_chado_tokens($record->tablename);
// Determine which tokens were used in the format string
if (preg_match_all('/\[[^]]+\]/', $string, $used_tokens)) {
// Get the value for each token used
foreach ($used_tokens[0] as $token) {
$token_info = $tokens[$token];
if (!empty($token_info)) {
$table = $token_info['table'];
$var = $record;
$value = '';
// Iterate through each portion of the location string. An example string
// might be: stock > type_id > name.
$location = explode('>', $token_info['location']);
foreach ($location as $index) {
$index = trim($index);
// if $var is an object then it is the $node object or a table
// that has been expanded.
if (is_object($var)) {
// check to see if the index is a member of the object. If so,
// then reset the $var to this value.
if (property_exists($var, $index)) {
$value = $var->$index;
}
else {
tripal_report_error('tripal_chado', TRIPAL_WARNING,
'Tokens: Unable to determine the value of %token. Things went awry when trying ' .
'to access \'%index\' for the following: \'%var\'.',
array('%token' => $token, '%index' => $index, '%var' => print_r($var,TRUE))
);
}
}
// if the $var is an array then there are multiple instances of the same
// table in a FK relationship (e.g. relationship tables)
elseif (is_array($var)) {
$value = $var[$index];
}
else {
tripal_report_error('tripal_chado', TRIPAL_WARNING,
'Tokens: Unable to determine the value of %token. Things went awry when trying ' .
'to access \'%index\' for the following: \'%var\'.',
array('%token' => $token, '%index' => $index, '%var' => print_r($var,TRUE))
);
}
}
$string = str_replace($token, $value, $string);
}
}
}
return $string;
}