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@@ -1,2613 +0,0 @@
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-<?php
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-
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-require_once "tripal_core.schema_v1.2.api.inc";
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-require_once "tripal_core.schema_v1.11.api.inc";
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-
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-// Globals used by Tripals Error catching functions
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-// Should match those defined by watchdog
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-define('TRIPAL_CRITICAL',2);
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-define('TRIPAL_ERROR',3);
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-define('TRIPAL_WARNING',4);
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-define('TRIPAL_NOTICE',5);
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-define('TRIPAL_INFO',6);
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-define('TRIPAL_DEBUG',7);
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-
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-
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-/**
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- * This function is used to set the global Chado variables
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- */
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-function tripal_core_set_globals() {
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- // these global variables are meant to be accessed by all Tripal
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- // modules to find the chado version installed and if Chado is local.
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- // these variables are stored as globals rather than using the drupal_set_variable
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- // functions because the Drupal functions make databaes queries and for long
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- // running loaders we don't want those queries repeatedly.
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- $GLOBALS["chado_is_installed"] = tripal_core_is_chado_installed();
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- if ($GLOBALS["chado_is_installed"]) {
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- $GLOBALS["chado_is_local"] = tripal_core_is_chado_local();
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- $GLOBALS["chado_version"] = tripal_core_get_chado_version();
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- $GLOBALS["exact_chado_version"] = tripal_core_get_chado_version(TRUE);
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- }
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-}
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-/**
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- * Provide better error notice for Tripal
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- * @param $type
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- * The catagory to which this message belongs. Can be any string, but the general
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- * practice is to use the name of the module.
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- * @param $message
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- * The message to store in the log. Keep $message translatable by not concatenating
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- * dynamic values into it! Variables in the message should be added by using placeholder
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- * strings alongside the variables argument to declare the value of the placeholders.
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- * See t() for documentation on how $message and $variables interact.
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- * @param $variables
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- * Array of variables to replace in the message on display or NULL if message is
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- * already translated or not possible to translate.
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- * @param $severity
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- * The severity of the message; one of the following values:
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- * - TRIPAL_CRITICAL: Critical conditions.
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- * - TRIPAL_ERROR: Error conditions.
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- * - TRIPAL_WARNING: Warning conditions.
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- * - TRIPAL_NOTICE: (default) Normal but significant conditions.
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- * - TRIPAL_INFO: Informational messages.
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- * - TRIPAL_DEBUG: Debug-level messages.
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- * @param $options
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- * An array of options. Some available options include:
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- * - print: prints the error message to the screen. Useful when display is the command-line
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- */
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-function tripal_core_report_error($type, $severity, $message, $variables = array(), $options = array()) {
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-
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- // Get human-readable severity string
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- $severity_string = '';
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- switch ($severity) {
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- case TRIPAL_CRITICAL:
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- $severity_string = 'CRITICAL';
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- break;
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- case TRIPAL_ERROR:
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- $severity_string = 'ERROR';
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- break;
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- case TRIPAL_WARNING:
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- $severity_string = 'WARNING';
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- break;
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- case TRIPAL_NOTICE:
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- $severity_string = 'NOTICE';
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- break;
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- case TRIPAL_INFO:
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- $severity_string = 'INFO';
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- break;
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- case TRIPAL_DEBUG:
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- $severity_string = 'DEBUG';
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- break;
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- }
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-
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- // Send to watchdog
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- try {
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- watchdog($type, $message, $variables, $severity);
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- }
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- catch (Exception $e) {
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- print "CRITICAL (TRIPAL_CORE): Unable to register error message with watchdog";
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- $options['print'] = TRUE;
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- }
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-
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- // If print option supplied then print directly to the screen
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- if (isset($options['print'])) {
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- if (sizeof($variables) > 0) {
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- $message = str_replace(array_keys($variables), $variables, $message);
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- }
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- print $severity_string . ' (' . strtoupper($type) . '):' . $message . "\n";
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- }
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-}
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-
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-/**
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- * @file
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- * The Tripal Core API
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- *
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- * This file provides the API needed for all other Tripal and Tripal dependent
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- * modules.
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- *
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- *
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- * @defgroup tripal_chado_api Chado API
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- * @ingroup tripal_core_api
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- * @{
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- * Provides an application programming interface (API) to manage data withing the Chado database.
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- * This includes functions for selecting, inserting, updating and deleting records
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- * in Chado tables. The functions will ensure proper integrity contraints are met
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- * for inserts and updates.
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- *
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- * Also, a set of functions is provided for creating template variables. First,
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- * is the tripal_core_generate_chado_vars which is used to select one ore more
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- * records from a table and return an array with foreign key relationships fully
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- * populated. For example, if selecting a feature, the organism_id and type_id
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- * would be present in the returned array as a nested array with their respective
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- * foreign keys also nested. The only fields that are not included are text
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- * fields (which may be very large) or many-to-many foreign key relationships.
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- * However, these fields and relationships can be expanded using the
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- * tripal_core_expand_chado_vars.
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- *
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- * When a row from a chado table is selected using these two functions, it provides
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- * a way for users who want to cutomize Drupal template files to access all data
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- * associate with a specific record.
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- *
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- * Finally, the property tables in Chado generally follow the same format. Therefore
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- * there is a set of functions for inserting, updating and deleting properties for
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- * any table. This provides quick lookup of properties (provided the CV term is
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- * known).
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- *
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- * @}
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- *
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- */
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-
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- /**
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- * Provides a generic routine for inserting into any Chado table
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- *
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- * Use this function to insert a record into any Chado table. The first
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- * argument specifies the table for inserting and the second is an array
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- * of values to be inserted. The array is mutli-dimensional such that
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- * foreign key lookup values can be specified.
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- *
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- * @param $table
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- * The name of the chado table for inserting
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- * @param $values
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- * An associative array containing the values for inserting.
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- * @param $options
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- * An array of options such as:
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- * - skip_validation: TRUE or FALSE. If TRUE will skip all the validation steps and
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- * just try to insert as is. This is much faster but results in unhandled
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- * non user-friendly errors if the insert fails.
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- * - return_record: by default, the function will return the record but with
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- * the primary keys added after insertion. To simply return TRUE on success
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- * set this option to FALSE
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- *
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- * @return
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- * On success this function returns the inserted record with the new primary keys
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- * added to the returned array. On failure, it returns FALSE.
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- *
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- * Example usage:
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- * @code
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- * $values = array(
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- * 'organism_id' => array(
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- * 'genus' => 'Citrus',
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- * 'species' => 'sinensis',
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- * ),
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- * 'name' => 'orange1.1g000034m.g',
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- * 'uniquename' => 'orange1.1g000034m.g',
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- * 'type_id' => array (
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- * 'cv_id' => array (
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- * 'name' => 'sequence',
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- * ),
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- * 'name' => 'gene',
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- * 'is_obsolete' => 0
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- * ),
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- * );
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- * $result = tripal_core_chado_insert('feature',$values);
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- * @endcode
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- * The above code inserts a record into the feature table. The $values array is
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- * nested such that the organism is selected by way of the organism_id foreign
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- * key constraint by specifying the genus and species. The cvterm is also
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- * specified using its foreign key and the cv_id for the cvterm is nested as
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- * well.
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- *
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- * @ingroup tripal_chado_api
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- */
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-function tripal_core_chado_insert($table, $values, $options = array()) {
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-
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- $print_errors = (isset($options['print_errors'])) ? $options['print_errors'] : FALSE;
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-
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- if (!is_array($values)) {
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- tripal_core_report_error(
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- 'tripal_core',
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- TRIPAL_ERROR,
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- 'Cannot pass non array as values for inserting.',
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- array(),
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- array('print' => $print_errors)
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- );
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- return FALSE;
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- }
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- if (count($values)==0) {
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- tripal_core_report_error(
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- 'tripal_core',
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- TRIPAL_ERROR,
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- 'Cannot pass an empty array as values for inserting.',
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- array(),
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- array('print' => $print_errors)
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- );
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- return FALSE;
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- }
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-
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- // set defaults for options. If we don't set defaults then
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- // we get memory leaks when we try to access the elements
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- if (!is_array($options)) {
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- $options = array();
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- }
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-
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- if (!array_key_exists('skip_validation', $options)) {
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- $options['skip_validation'] = FALSE;
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- }
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- if (!array_key_exists('return_record', $options)) {
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- $options['return_record'] = TRUE;
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- }
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-
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- $insert_values = array();
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-
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- if (array_key_exists('skip_validation', $options)) {
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- $validate = !$options['skip_validation'];
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- }
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- else {
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- $validate = TRUE;
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- }
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-
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- // get the table description
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- $table_desc = tripal_core_get_chado_table_schema($table);
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- if (empty($table_desc)) {
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- tripal_core_report_error('tripal_core', TRIPAL_WARNING,
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- 'tripal_core_chado_insert; There is no table description for !table_name',
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- array('!table_name' => $table), array('print' => $print_errors)
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- );
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- }
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-
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- // iterate through the values array and create a new 'insert_values' array
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- // that has all the values needed for insert with all foreign relationsihps
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- // resolved.
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- foreach ($values as $field => $value) {
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- // make sure the field is in the table description. If not then return an error
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- // message
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- if (!array_key_exists($field, $table_desc['fields'])) {
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- tripal_core_report_error(
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- 'tripal_core',
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- TRIPAL_ERROR,
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- "tripal_core_chado_insert; The field '%field' does not exist " .
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- "for the table '%table'. Cannot perform insert. Values: %array",
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- array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)),
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- array('print' => $print_errors)
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- );
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- return FALSE;
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- }
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-
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- if (is_array($value)) {
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- // select the value from the foreign key relationship for this value
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- $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value);
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-
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- if (sizeof($results) > 1) {
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- tripal_core_report_error(
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- 'tripal_core',
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- TRIPAL_ERROR,
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- 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)',
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- array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
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- array('print' => $print_errors)
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- );
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- }
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- elseif (sizeof($results) < 1) {
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- tripal_core_report_error(
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- 'tripal_core',
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- TRIPAL_DEBUG,
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- 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)',
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- array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
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- array('print' => $print_errors)
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- );
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- }
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- else {
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- $insert_values[$field] = $results[0];
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- }
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- }
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- else {
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- $insert_values[$field] = $value;
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- }
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- }
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-
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- if ($validate) {
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-
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- // check for violation of any unique constraints
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- $ukeys = array();
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- if (array_key_exists('unique keys', $table_desc)) {
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- $ukeys = $table_desc['unique keys'];
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- }
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- $ukselect_cols = array();
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- $ukselect_vals = array();
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- if ($ukeys) {
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- foreach ($ukeys as $name => $fields) {
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- foreach ($fields as $index => $field) {
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- // build the arrays for performing a select that will check the contraint
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- $ukselect_cols[] = $field;
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- if (!array_key_exists($field, $insert_values)) {
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- if (array_key_exists('default', $table_desc['fields'][$field])) {
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- $ukselect_vals[$field] = $table_desc['fields'][$field]['default'];
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- }
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- }
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- else {
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- $ukselect_vals[$field] = $insert_values[$field];
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- }
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- }
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- // now check the constraint
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- if (tripal_core_chado_select($table, $ukselect_cols, $ukselect_vals)) {
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- tripal_core_report_error('tripal_core', TRIPAL_ERROR,
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- "tripal_core_chado_insert; Cannot insert duplicate record into $table table: !values",
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- array('!values' => print_r($values, TRUE)), array('print' => $print_errors)
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- );
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- return FALSE;
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- }
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- }
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- }
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-
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- // if trying to insert a field that is the primary key, make sure it also is unique
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- if (array_key_exists('primary key', $table_desc)) {
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- $pkey = $table_desc['primary key'][0];
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- if (array_key_exists($pkey, $insert_values)) {
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- $coptions = array();
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- if (tripal_core_chado_select($table, array($pkey), array($pkey => $insert_values[$pkey]), $coptions)) {
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- tripal_core_report_error('tripal_core', TRIPAL_ERROR,
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- 'tripal_core_chado_insert; Cannot insert duplicate primary key into !table table: !values',
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- array('!table' => $table, '!values' => print_r($values, TRUE)),
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- array('print' => $print_errors)
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- );
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- return FALSE;
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- }
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- }
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- }
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-
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- // make sure required fields have a value
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- if (!is_array($table_desc['fields'])) {
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- $table_desc['fields'] = array();
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- tripal_core_report_error(
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- 'tripal_core',
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- TRIPAL_WARNING,
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- "tripal_core_chado_insert; %table missing fields: \n %schema",
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- array('%table' => $table, '%schema' => print_r($table_desc, 1)),
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- array('print' => $print_errors)
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- );
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- }
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- foreach ($table_desc['fields'] as $field => $def) {
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- // a field is considered missing if it cannot be NULL and there is no default
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- // value for it or it is of type 'serial'
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- if (array_key_exists('NOT NULL', $def) and
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- !array_key_exists($field, $insert_values) and
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- !array_key_exists('default', $def) and
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- strcmp($def['type'], serial) != 0) {
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- tripal_core_report_error(
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- 'tripal_core',
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- TRIPAL_ERROR,
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- "tripal_core_chado_insert; Field %table.%field cannot be NULL: %values",
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- array('%table' => $table, '%field' => $field, '%values' => print_r($values, 1)),
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- array('print' => $print_errors)
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- );
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- return FALSE;
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- }
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- }
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- } //end of validation
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-
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- // Now build the insert SQL statement
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- $ifields = array(); // contains the names of the fields
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- $itypes = array(); // contains placeholders for the sql query
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- $ivalues = array(); // contains the values of the fields
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- $i = 1;
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- foreach ($insert_values as $field => $value) {
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- $ifields[] = $field;
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- $ivalues[":$field"] = $value;
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- $i++;
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- if (strcmp($value, '__NULL__')==0) {
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- $itypes[] = "NULL";
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- }
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- else {
|
|
|
- $itypes[] = ":$field";
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // create the SQL
|
|
|
- $sql = 'INSERT INTO {' . $table . '} (' . implode(", ", $ifields) . ") VALUES (" . implode(", ", $itypes) . ")";
|
|
|
- $result = chado_query($sql, $ivalues);
|
|
|
-
|
|
|
- // if we have a result then add primary keys to return array
|
|
|
- if ($options['return_record'] == TRUE and $result) {
|
|
|
- if (array_key_exists('primary key', $table_desc) and is_array($table_desc['primary key'])) {
|
|
|
- foreach ($table_desc['primary key'] as $field) {
|
|
|
- $sql = "SELECT CURRVAL('{" . $table . "_" . $field . "_seq}')";
|
|
|
- $results = chado_query($sql);
|
|
|
- $value = $results->fetchField();
|
|
|
- if (!$value) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- "tripal_core_chado_insert; not able to retrieve primary key after insert: %sql",
|
|
|
- array('%sql' => $sql),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- $values[$field] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
- return $values;
|
|
|
- }
|
|
|
- elseif ($options['return_record'] == FALSE and $result) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'tripal_core_chado_insert; Cannot insert record into "%table": %values',
|
|
|
- array('%table' => $table, '%values' => print_r($values, 1)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- return FALSE;
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Provides a generic routine for updating into any Chado table
|
|
|
- *
|
|
|
- * Use this function to update a record in any Chado table. The first
|
|
|
- * argument specifies the table for inserting, the second is an array
|
|
|
- * of values to matched for locating the record for updating, and the third
|
|
|
- * argument give the values to update. The arrays are mutli-dimensional such
|
|
|
- * that foreign key lookup values can be specified.
|
|
|
- *
|
|
|
- * @param $table
|
|
|
- * The name of the chado table for inserting
|
|
|
- * @param $match
|
|
|
- * An associative array containing the values for locating a record to update.
|
|
|
- * @param $values
|
|
|
- * An associative array containing the values for updating.
|
|
|
- * @param $options
|
|
|
- * An array of options such as:
|
|
|
- * - return_record: by default, the function will return the TRUE if the record
|
|
|
- * was succesfully updated. However, set this option to TRUE to return the
|
|
|
- * record that was updated. The returned record will have the fields provided
|
|
|
- * but the primary key (if available for the table) will be added to the record.
|
|
|
- * @return
|
|
|
- * On success this function returns TRUE. On failure, it returns FALSE.
|
|
|
- *
|
|
|
- * Example usage:
|
|
|
- * @code
|
|
|
- $umatch = array(
|
|
|
- 'organism_id' => array(
|
|
|
- 'genus' => 'Citrus',
|
|
|
- 'species' => 'sinensis',
|
|
|
- ),
|
|
|
- 'uniquename' => 'orange1.1g000034m.g7',
|
|
|
- 'type_id' => array (
|
|
|
- 'cv_id' => array (
|
|
|
- 'name' => 'sequence',
|
|
|
- ),
|
|
|
- 'name' => 'gene',
|
|
|
- 'is_obsolete' => 0
|
|
|
- ),
|
|
|
- );
|
|
|
- $uvalues = array(
|
|
|
- 'name' => 'orange1.1g000034m.g',
|
|
|
- 'type_id' => array (
|
|
|
- 'cv_id' => array (
|
|
|
- 'name' => 'sequence',
|
|
|
- ),
|
|
|
- 'name' => 'mRNA',
|
|
|
- 'is_obsolete' => 0
|
|
|
- ),
|
|
|
- );
|
|
|
- * $result = tripal_core_chado_update('feature',$umatch,$uvalues);
|
|
|
- * @endcode
|
|
|
- * The above code species that a feature with a given uniquename, organism_id,
|
|
|
- * and type_id (the unique constraint for the feature table) will be updated.
|
|
|
- * The organism_id is specified as a nested array that uses the organism_id
|
|
|
- * foreign key constraint to lookup the specified values to find the exact
|
|
|
- * organism_id. The same nested struture is also used for specifying the
|
|
|
- * values to update. The function will find the record that matches the
|
|
|
- * columns specified and update the record with the avlues in the $uvalues array.
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_chado_update($table, $match, $values, $options = NULL) {
|
|
|
-
|
|
|
- $print_errors = (isset($options['print_errors'])) ? $options['print_errors'] : FALSE;
|
|
|
-
|
|
|
- if (!is_array($values)) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'Cannot pass non array as values for updating.',
|
|
|
- array(),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if (count($values)==0) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'Cannot pass an empty array as values for updating.',
|
|
|
- array(),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- if (!is_array($match)) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'Cannot pass non array as values for matching.',
|
|
|
- array(),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if (count($match)==0) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'Cannot pass an empty array as values for matching.',
|
|
|
- array(),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // set defaults for options. If we don't set defaults then
|
|
|
- // we get memory leaks when we try to access the elements
|
|
|
- if (!is_array($options)) {
|
|
|
- $options = array();
|
|
|
- }
|
|
|
-
|
|
|
- if (!array_key_exists('return_record', $options)) {
|
|
|
- $options['return_record'] = FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- $update_values = array(); // contains the values to be updated
|
|
|
- $update_matches = array(); // contains the values for the where clause
|
|
|
-
|
|
|
-
|
|
|
- // get the table description
|
|
|
- $table_desc = tripal_core_get_chado_table_schema($table);
|
|
|
-
|
|
|
- // if the user wants us to return the record then we need to get the
|
|
|
- // unique primary key if one exists. That way we can add it to the
|
|
|
- // values that get returned at the end of the function
|
|
|
- $pkeys = array();
|
|
|
- if ($options['return_record'] == TRUE) {
|
|
|
- if (array_key_exists('primary key', $table_desc) and is_array($table_desc['primary key'])) {
|
|
|
- $columns = array();
|
|
|
- $stmt_suffix = '';
|
|
|
- foreach ($table_desc['primary key'] as $field) {
|
|
|
- $columns[] = $field;
|
|
|
- $stmt_suffix .= substr($field, 0, 2);
|
|
|
- }
|
|
|
- $options2 = array();
|
|
|
- $results = tripal_core_chado_select($table, $columns, $match, $options2);
|
|
|
- if (count($results) > 0) {
|
|
|
- foreach ($results as $index => $pkey) {
|
|
|
- $pkeys[] = $pkey;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // get the values needed for matching in the SQL statement
|
|
|
- foreach ($match as $field => $value) {
|
|
|
- if (is_array($value)) {
|
|
|
- $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value);
|
|
|
- if (sizeof($results) > 1) {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
- 'tripal_core_chado_update: When trying to find record to update, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)',
|
|
|
- array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- }
|
|
|
- elseif (sizeof($results) < 1) {
|
|
|
- tripal_core_report_error('tripal_core',TRIPAL_DEBUG,
|
|
|
- 'tripal_core_chado_update: When trying to find record to update, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)',
|
|
|
- array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- }
|
|
|
- else {
|
|
|
- $update_matches[$field] = $results[0];
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $update_matches[$field] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // get the values used for updating
|
|
|
- foreach ($values as $field => $value) {
|
|
|
- if (is_array($value)) {
|
|
|
- $foreign_options = array();
|
|
|
- // select the value from the foreign key relationship for this value
|
|
|
- $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
|
|
|
- if (sizeof($results) > 1) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'tripal_core_chado_update: When trying to find update values, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)',
|
|
|
- array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- }
|
|
|
- elseif (sizeof($results) < 1) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_DEBUG,
|
|
|
- 'tripal_core_chado_update: When trying to find update values, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)',
|
|
|
- array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- }
|
|
|
- else {
|
|
|
- $update_values[$field] = $results[0];
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $update_values[$field] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // now build the SQL statement
|
|
|
- $sql = 'UPDATE {' . $table . '} SET ';
|
|
|
- $args = array(); // arguments passed to chado_query
|
|
|
- foreach ($update_values as $field => $value) {
|
|
|
- if (strcmp($value, '__NULL__') == 0) {
|
|
|
- $sql .= " $field = NULL, ";
|
|
|
- }
|
|
|
- else {
|
|
|
- $sql .= " $field = :$field, ";
|
|
|
- $args[":$field"] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
- $sql = drupal_substr($sql, 0, -2); // get rid of the trailing comma & space
|
|
|
-
|
|
|
- $sql .= " WHERE ";
|
|
|
- foreach ($update_matches as $field => $value) {
|
|
|
- if (strcmp($value, '__NULL__')==0) {
|
|
|
- $sql .= " $field = NULL AND ";
|
|
|
- }
|
|
|
- else {
|
|
|
- $sql .= " $field = :$field AND ";
|
|
|
- $args[":$field"] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
- $sql = drupal_substr($sql, 0, -4); // get rid of the trailing 'AND'
|
|
|
-
|
|
|
- $result = chado_query($sql, $args);
|
|
|
-
|
|
|
- // if we have a result then add primary keys to return array
|
|
|
- if ($options['return_record'] == TRUE and $result) {
|
|
|
- // only if we have a single result do we want to add the primary keys to the values
|
|
|
- // array. If the update matched many records we can't add the pkeys
|
|
|
-
|
|
|
- if (count($pkeys) == 1) {
|
|
|
- foreach ($pkeys as $index => $pkey) {
|
|
|
- foreach ($pkey as $field => $fvalue) {
|
|
|
- $values[$field] = $fvalue;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- return $values;
|
|
|
- }
|
|
|
- elseif ($options['return_record'] == FALSE and $result) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- "tripal_core_chado_update: Cannot update record in %table table. \nMatch: %match \nValues: %values",
|
|
|
- array('%table' => table, '%match' => print_r($match,TRUE), '%values' => print_r($values, 1)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- return FALSE;
|
|
|
-}
|
|
|
-/**
|
|
|
- * Provides a generic function for deleting a record(s) from any chado table
|
|
|
- *
|
|
|
- * Use this function to delete a record(s) in any Chado table. The first
|
|
|
- * argument specifies the table to delete from and the second is an array
|
|
|
- * of values to match for locating the record(s) to be deleted. The arrays
|
|
|
- * are mutli-dimensional such that foreign key lookup values can be specified.
|
|
|
- *
|
|
|
- * @param $table
|
|
|
- * The name of the chado table for inserting
|
|
|
- * @param $match
|
|
|
- * An associative array containing the values for locating a record to update.
|
|
|
- * @param $options
|
|
|
- * Currently there are no options
|
|
|
- * @return
|
|
|
- * On success this function returns TRUE. On failure, it returns FALSE.
|
|
|
- *
|
|
|
- * Example usage:
|
|
|
- * @code
|
|
|
- $umatch = array(
|
|
|
- 'organism_id' => array(
|
|
|
- 'genus' => 'Citrus',
|
|
|
- 'species' => 'sinensis',
|
|
|
- ),
|
|
|
- 'uniquename' => 'orange1.1g000034m.g7',
|
|
|
- 'type_id' => array (
|
|
|
- 'cv_id' => array (
|
|
|
- 'name' => 'sequence',
|
|
|
- ),
|
|
|
- 'name' => 'gene',
|
|
|
- 'is_obsolete' => 0
|
|
|
- ),
|
|
|
- );
|
|
|
- $uvalues = array(
|
|
|
- 'name' => 'orange1.1g000034m.g',
|
|
|
- 'type_id' => array (
|
|
|
- 'cv_id' => array (
|
|
|
- 'name' => 'sequence',
|
|
|
- ),
|
|
|
- 'name' => 'mRNA',
|
|
|
- 'is_obsolete' => 0
|
|
|
- ),
|
|
|
- );
|
|
|
- * $result = tripal_core_chado_update('feature', $umatch, $uvalues);
|
|
|
- * @endcode
|
|
|
- * The above code species that a feature with a given uniquename, organism_id,
|
|
|
- * and type_id (the unique constraint for the feature table) will be deleted.
|
|
|
- * The organism_id is specified as a nested array that uses the organism_id
|
|
|
- * foreign key constraint to lookup the specified values to find the exact
|
|
|
- * organism_id. The same nested struture is also used for specifying the
|
|
|
- * values to update. The function will find all records that match the
|
|
|
- * columns specified and delete them.
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_chado_delete($table, $match, $options = NULL) {
|
|
|
-
|
|
|
- if (!is_array($match)) {
|
|
|
- watchdog('tripal_core', 'Cannot pass non array as values for matching.', array(),
|
|
|
- WATCHDOG_ERROR);
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if (count($match)==0) {
|
|
|
- watchdog('tripal_core', 'Cannot pass an empty array as values for matching.', array(),
|
|
|
- WATCHDOG_ERROR);
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // set defaults for options. If we don't set defaults then
|
|
|
- // we get memory leaks when we try to access the elements
|
|
|
- if (!is_array($options)) {
|
|
|
- $options = array();
|
|
|
- }
|
|
|
-
|
|
|
- $delete_matches = array(); // contains the values for the where clause
|
|
|
-
|
|
|
- // get the table description
|
|
|
- $table_desc = tripal_core_get_chado_table_schema($table);
|
|
|
- $fields = $table_desc['fields'];
|
|
|
-
|
|
|
- // get the values needed for matching in the SQL statement
|
|
|
- foreach ($match as $field => $value) {
|
|
|
- if (is_array($value)) {
|
|
|
- // if the user has specified an array of values to delete rather than
|
|
|
- // FK relationships the keep those in our match
|
|
|
- if (array_values($value) === $value) {
|
|
|
- $delete_matches[$field] = $value;
|
|
|
- }
|
|
|
- else {
|
|
|
- $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value);
|
|
|
- if (sizeof($results) > 1) {
|
|
|
- watchdog('tripal_core', 'tripal_core_chado_delete: When trying to find record to delete, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
|
|
|
- }
|
|
|
- elseif (sizeof($results) < 1) {
|
|
|
- //watchdog('tripal_core', 'tripal_core_chado_delete: When trying to find record to delete, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
|
|
|
- }
|
|
|
- else {
|
|
|
- $delete_matches[$field] = $results[0];
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- $delete_matches[$field] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // now build the SQL statement
|
|
|
- $sql = 'DELETE FROM {' . $table . '} WHERE ';
|
|
|
- $args = array();
|
|
|
- foreach ($delete_matches as $field => $value) {
|
|
|
- // if we have an array values then this is an "IN" clasue.
|
|
|
- // we cannot use prepared statements with these
|
|
|
-
|
|
|
- if (count($value) > 1) {
|
|
|
- $sql .= "$field IN (";
|
|
|
- $index = 0;
|
|
|
- foreach ($value as $v) {
|
|
|
- $sql .= ":$field" . $index . ", ";
|
|
|
- $args[":$field" . $index] = $v;
|
|
|
- $index++;
|
|
|
- }
|
|
|
- $sql = drupal_substr($sql, 0, -2); // get rid of trailing ', '
|
|
|
- $sql .= ") AND ";
|
|
|
- }
|
|
|
- else {
|
|
|
- if (strcmp($value, '__NULL__') == 0) {
|
|
|
- $sql .= " $field = NULL AND ";
|
|
|
- }
|
|
|
- else {
|
|
|
- $sql .= " $field = :$field AND ";
|
|
|
- $args[":$field"] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- $sql = drupal_substr($sql, 0, -4); // get rid of the trailing 'AND'
|
|
|
-
|
|
|
- // finally perform the delete. If successful, return the updated record
|
|
|
- $result = chado_query($sql, $args);
|
|
|
- if ($result) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- watchdog('tripal_core', "Cannot delete record in $table table. Match:" . print_r($match, 1) . ". Values: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- return FALSE;
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Provides a generic routine for selecting data from a Chado table
|
|
|
- *
|
|
|
- * Use this function to perform a simple select from any Chado table.
|
|
|
- *
|
|
|
- * @param $table
|
|
|
- * The name of the chado table for inserting
|
|
|
- * @param $columns
|
|
|
- * An array of column names
|
|
|
- * @param $values
|
|
|
- * An associative array containing the values for filtering the results. In the
|
|
|
- * case where multiple values for the same time are to be selected an additional
|
|
|
- * entry for the field should appear for each value
|
|
|
- * @param $options
|
|
|
- * An associative array of additional options where the key is the option
|
|
|
- * and the value is the value of that option.
|
|
|
- *
|
|
|
- * Additional Options Include:
|
|
|
- * - has_record
|
|
|
- * Set this argument to 'TRUE' to have this function return a numeric
|
|
|
- * value for the number of recrods rather than the array of records. this
|
|
|
- * can be useful in 'if' statements to check the presence of particula records.
|
|
|
- * - return_sql
|
|
|
- * Set this to 'TRUE' to have this function return an array where the first
|
|
|
- * element is the sql that would have been run and the second is an array of
|
|
|
- * arguments.
|
|
|
- * - case_insensitive_columns
|
|
|
- * An array of columns to do a case insensitive search on.
|
|
|
- * - regex_columns
|
|
|
- * An array of columns where the value passed in should be treated as a regular expression
|
|
|
- * - order_by
|
|
|
- * An associative array containing the column names of the table as keys
|
|
|
- * and the type of sort (i.e. ASC, DESC) as the values. The results in the
|
|
|
- * query will be sorted by the key values in the direction listed by the value
|
|
|
- * - is_duplicate: TRUE or FALSE. Checks the values submited to see if
|
|
|
- * they violate any of the unique constraints. If so, the record
|
|
|
- * is returned, if not, FALSE is returned.
|
|
|
- * - pager: Use this option if it is desired to return only a subset of results
|
|
|
- * so that they may be shown with in a Drupal-style pager. This should be
|
|
|
- * an array with two keys: 'limit' and 'element'. The value of 'limit'
|
|
|
- * should specify the number of records to return and 'element' is a
|
|
|
- * unique integer to differentiate between pagers when more than one
|
|
|
- * appear on a page. The 'element' should start with zero and increment by
|
|
|
- * one for each pager.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * An array of results, FALSE if the query was not executed
|
|
|
- * correctly, an empty array if no records were matched, or the number of records
|
|
|
- * in the dataset if $has_record is set.
|
|
|
- * If the option 'is_duplicate' is provided and the record is a duplicate it
|
|
|
- * will return the duplicated record. If the 'has_record' option is provided
|
|
|
- * a value of TRUE will be returned if a record exists and FALSE will bee
|
|
|
- * returned if there are not records.
|
|
|
- *
|
|
|
- * Example usage:
|
|
|
- * @code
|
|
|
- * $columns = array('feature_id', 'name');
|
|
|
- * $values = array(
|
|
|
- * 'organism_id' => array(
|
|
|
- * 'genus' => 'Citrus',
|
|
|
- * 'species' => array('sinensis', 'clementina'),
|
|
|
- * ),
|
|
|
- * 'uniquename' => 'orange1.1g000034m.g',
|
|
|
- * 'type_id' => array (
|
|
|
- * 'cv_id' => array (
|
|
|
- * 'name' => 'sequence',
|
|
|
- * ),
|
|
|
- * 'name' => 'gene',
|
|
|
- * 'is_obsolete' => 0
|
|
|
- * ),
|
|
|
- * );
|
|
|
- * $options = array(
|
|
|
- * 'order_by' => array(
|
|
|
- * 'name' => 'ASC'
|
|
|
- * ),
|
|
|
- * );
|
|
|
- * $result = tripal_core_chado_select('feature',$columns,$values,$options);
|
|
|
- * @endcode
|
|
|
- * The above code selects a record from the feature table using the three fields
|
|
|
- * that uniquely identify a feature. The $columns array simply lists the columns
|
|
|
- * to select. The $values array is nested such that the organism is identified by
|
|
|
- * way of the organism_id foreign key constraint by specifying the genus and
|
|
|
- * species. The cvterm is also specified using its foreign key and the cv_id
|
|
|
- * for the cvterm is nested as well. In the example above, two different species
|
|
|
- * are allowed to match
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
|
|
|
-
|
|
|
- $print_errors = (isset($options['print_errors'])) ? $options['print_errors'] : FALSE;
|
|
|
-
|
|
|
- if (!is_array($values)) {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR, 'Cannot pass non array as values for selecting.',
|
|
|
- array(), array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if (!is_array($columns)) {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR, 'Cannot pass non array as columns for selecting.',
|
|
|
- array(), array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if (count($columns)==0) {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR, 'Cannot pass an empty array as columns for selecting.',
|
|
|
- array(), array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // set defaults for options. If we don't set defaults then
|
|
|
- // we get memory leaks when we try to access the elements
|
|
|
- if (!is_array($options)) {
|
|
|
- $options = array();
|
|
|
- }
|
|
|
- if (!array_key_exists('case_insensitive_columns', $options)) {
|
|
|
- $options['case_insensitive_columns'] = array();
|
|
|
- }
|
|
|
- if (!array_key_exists('regex_columns', $options)) {
|
|
|
- $options['regex_columns'] = array();
|
|
|
- }
|
|
|
- if (!array_key_exists('order_by', $options)) {
|
|
|
- $options['order_by'] = array();
|
|
|
- }
|
|
|
- if (!array_key_exists('return_sql', $options)) {
|
|
|
- $options['return_sql'] = FALSE;
|
|
|
- }
|
|
|
- if (!array_key_exists('has_record', $options)) {
|
|
|
- $options['has_record'] = FALSE;
|
|
|
- }
|
|
|
- if (!array_key_exists('is_duplicate', $options)) {
|
|
|
- $options['is_duplicate'] = FALSE;
|
|
|
- }
|
|
|
- $pager = array();
|
|
|
- if (array_key_exists('pager', $options)) {
|
|
|
- $pager = $options['pager'];
|
|
|
- }
|
|
|
-
|
|
|
- // check that our columns and values arguments are proper arrays
|
|
|
- if (!is_array($columns)) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'tripal_core_chado_select; the $columns argument must be an array. Columns:%columns',
|
|
|
- array('%columns' => print_r($columns, TRUE)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- if (!is_array($values)) {
|
|
|
- tripal_core_report_error(
|
|
|
- 'tripal_core',
|
|
|
- TRIPAL_ERROR,
|
|
|
- 'tripal_core_chado_select; the $values argument must be an array. Values:%values',
|
|
|
- array('%values' => print_r($values, TRUE)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // get the table description
|
|
|
- $table_desc = tripal_core_get_chado_table_schema($table);
|
|
|
- $select = '';
|
|
|
- $from = '';
|
|
|
- $where = array();
|
|
|
- $args = array();
|
|
|
-
|
|
|
- // if the 'use_unique' option is turned on then we want
|
|
|
- // to remove all but unique keys
|
|
|
- if ($options['is_duplicate'] and array_key_exists('unique keys', $table_desc)) {
|
|
|
- $ukeys = $table_desc['unique keys'];
|
|
|
- $has_results = 0;
|
|
|
-
|
|
|
- // iterate through the unique constraints and reset the values and columns
|
|
|
- // arrays to only include these fields
|
|
|
- foreach ($ukeys as $cname => $fields) {
|
|
|
- if ($has_results) {
|
|
|
- continue;
|
|
|
- }
|
|
|
- $new_values = array();
|
|
|
- $new_columns = array();
|
|
|
- $new_options = array();
|
|
|
- $uq_sname = "uq_" . $table . "_";
|
|
|
- $has_pkey = 0;
|
|
|
-
|
|
|
-
|
|
|
- // include the primary key in the results returned
|
|
|
- if (array_key_exists('primary key', $table_desc)) {
|
|
|
- $has_pkey = 1;
|
|
|
- $pkeys = $table_desc['primary key'];
|
|
|
- foreach ($pkeys as $index => $key) {
|
|
|
- array_push($new_columns, $key);
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // recreate the $values and $columns arrays
|
|
|
- foreach ($fields as $field) {
|
|
|
- if (array_key_exists($field, $values)) {
|
|
|
- $new_values[$field] = $values[$field];
|
|
|
- $uq_sname .= substr($field, 0, 2);
|
|
|
- // if there is no primary key then use the unique contraint fields
|
|
|
- if (!$has_pkey) {
|
|
|
- array_push($new_columns, $field);
|
|
|
- }
|
|
|
- }
|
|
|
- // if the field doesn't exist in the values array then
|
|
|
- // substitute any default values
|
|
|
- elseif (array_key_exists('default', $table_desc['fields'][$field])) {
|
|
|
- $new_values[$field] = $table_desc['fields'][$field]['default'];
|
|
|
- $uq_sname .= substr($field, 0, 2);
|
|
|
- if (!$has_pkey) {
|
|
|
- array_push($new_columns, $field);
|
|
|
- }
|
|
|
- }
|
|
|
- // if there is no value (default or otherwise) check if this field is
|
|
|
- // allowed to be null
|
|
|
- elseif (!$table_desc['fields'][$field]['not null']) {
|
|
|
- $new_values[$field] = NULL;
|
|
|
- $uq_sname .= "n" . substr($field, 0, 2);
|
|
|
- if (!$has_pkey) {
|
|
|
- array_push($new_columns, $field);
|
|
|
- }
|
|
|
- }
|
|
|
- // if the array key doesn't exist in the values given by the caller
|
|
|
- // and there is no default value then we cannot check if the record
|
|
|
- // is a duplicate so return FALSE
|
|
|
- else {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
- 'tripal_core_chado_select: There is no value for %field thus we cannot check if this record is unique',
|
|
|
- array('%field' => $field), array('print' => $print_errors));
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- $results = tripal_core_chado_select($table, $new_columns, $new_values, $new_options);
|
|
|
- // if we have a duplicate record then return the results
|
|
|
- if (count($results) > 0) {
|
|
|
- $has_results = 1;
|
|
|
- }
|
|
|
- unset($new_columns);
|
|
|
- unset($new_values);
|
|
|
- unset($new_options);
|
|
|
- }
|
|
|
- if ($options['has_record'] and $has_results) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- return $results;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- foreach ($values as $field => $value) {
|
|
|
- // make sure the field is in the table description. If not then return an error
|
|
|
- // message
|
|
|
- if (!array_key_exists($field, $table_desc['fields'])) {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
- 'tripal_core_chado_select: The field "%field" does not exist for the table "%table". Cannot perform query. Values: %array',
|
|
|
- array('%field' => $field, '%table' => $table, '%array' => print_r($values, 1)),
|
|
|
- array('print' => $print_errors)
|
|
|
- );
|
|
|
- return array();
|
|
|
- }
|
|
|
-
|
|
|
- $select[] = $field;
|
|
|
- if (is_array($value)) {
|
|
|
- // if the user has specified multiple values for matching then this we
|
|
|
- // want to catch that and save them in our $where array, otherwise
|
|
|
- // we'll descend for a foreign key relationship
|
|
|
- if (array_values($value) === $value) {
|
|
|
- $where[$field] = $value;
|
|
|
- }
|
|
|
- else {
|
|
|
- // select the value from the foreign key relationship for this value
|
|
|
- $foreign_options = array(
|
|
|
- 'regex_columns' => $options['regex_columns'],
|
|
|
- );
|
|
|
-
|
|
|
- $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
|
|
|
- if (!$results or count($results)==0) {
|
|
|
- return array();
|
|
|
- }
|
|
|
- else {
|
|
|
- $where[$field] = $results;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- // need to catch a 0 and make int if integer field
|
|
|
- // but we don't want to catch a NULL
|
|
|
- if ($value === NULL) {
|
|
|
- $where[$field] = NULL;
|
|
|
- }
|
|
|
- elseif ($table_desc['fields'][$field]['type'] == 'int') {
|
|
|
- $where[$field][] = (int) $value;
|
|
|
- }
|
|
|
- else {
|
|
|
- $where[$field][] = $value;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
-
|
|
|
- // now build the SQL and prepared SQL statements. We may not use
|
|
|
- // the prepared statement if it wasn't requested in the options or if the
|
|
|
- // argument in a where statement has multiple values.
|
|
|
- if (empty($where)) {
|
|
|
- // sometimes want to select everything
|
|
|
- $sql = "SELECT " . implode(', ', $columns) . " ";
|
|
|
- $sql .= 'FROM {' . $table . '} ';
|
|
|
- // we don't prepare a statement if there is no where clause
|
|
|
- $prepared = FALSE;
|
|
|
- }
|
|
|
- else {
|
|
|
- $sql = "SELECT " . implode(', ', $columns) . " ";
|
|
|
- $sql .= 'FROM {' . $table . '} ';
|
|
|
-
|
|
|
- // if $values is empty then we want all results so no where clause
|
|
|
- if (!empty($values)) {
|
|
|
- $sql .= "WHERE ";
|
|
|
- }
|
|
|
- foreach ($where as $field => $value) {
|
|
|
-
|
|
|
- // if we have multiple values returned then we need an 'IN' statement
|
|
|
- // in our where statement
|
|
|
- if (count($value) > 1) {
|
|
|
- $sql .= "$field IN (";
|
|
|
- $index = 0;
|
|
|
- foreach ($value as $v) {
|
|
|
- $sql .= ":$field" . $index . ', ';
|
|
|
- $args[":$field" . $index] = $v;
|
|
|
- $index++;
|
|
|
- }
|
|
|
- $sql = drupal_substr($sql, 0, -2); // remove trailing ', '
|
|
|
- $sql .= ") AND ";
|
|
|
- }
|
|
|
- // if we have a null value then we need an IS NULL in our where statement
|
|
|
- elseif ($value === NULL) {
|
|
|
- $sql .= "$field IS NULL AND ";
|
|
|
- // Need to remove one from the argument count b/c nulls don't add an argument
|
|
|
- }
|
|
|
- // if we have a single value then we need an = in our where statement
|
|
|
- else {
|
|
|
- $operator = '=';
|
|
|
- if (in_array($field, $options['regex_columns'])) {
|
|
|
- $operator = '~*';
|
|
|
- }
|
|
|
- if (in_array($field, $options['case_insensitive_columns'])) {
|
|
|
- $sql .= "lower($field) $operator lower(:$field) AND ";
|
|
|
- $args[":$field"] = $value[0];
|
|
|
- }
|
|
|
- else {
|
|
|
- $sql .= "$field $operator :$field AND ";
|
|
|
- $args[":$field"] = $value[0];
|
|
|
- }
|
|
|
- }
|
|
|
- } // end foreach item in where clause
|
|
|
- $sql = drupal_substr($sql, 0, -4); // get rid of the trailing 'AND '
|
|
|
- } // end if (empty($where)){ } else {
|
|
|
-
|
|
|
- // finally add any ordering of the results to the SQL statement
|
|
|
- if (count($options['order_by']) > 0) {
|
|
|
- $sql .= " ORDER BY ";
|
|
|
- foreach ($options['order_by'] as $field => $dir) {
|
|
|
- $sql .= "$field $dir, ";
|
|
|
- }
|
|
|
- $sql = drupal_substr($sql, 0, -2); // get rid of the trailing ', '
|
|
|
- }
|
|
|
-
|
|
|
- // if the caller has requested the SQL rather than the results then do so
|
|
|
- if ($options['return_sql'] == TRUE) {
|
|
|
- return array('sql' => $sql, 'args' => $args);
|
|
|
- }
|
|
|
- if (array_key_exists('limit', $pager)) {
|
|
|
- $total_records = 0;
|
|
|
- $resource = chado_pager_query($sql, $args, $pager['limit'], $pager['element'], NULL, $total_records);
|
|
|
- }
|
|
|
- else {
|
|
|
- $resource = chado_query($sql, $args);
|
|
|
- }
|
|
|
-
|
|
|
- // format results into an array
|
|
|
- $results = array();
|
|
|
- foreach ($resource as $r) {
|
|
|
- $results[] = $r;
|
|
|
- }
|
|
|
- if ($options['has_record']) {
|
|
|
- return count($results);
|
|
|
- }
|
|
|
- return $results;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Gets the value of a foreign key relationship
|
|
|
- *
|
|
|
- * This function is used by tripal_core_chado_select, tripal_core_chado_insert,
|
|
|
- * and tripal_core_chado_update to iterate through the associate array of
|
|
|
- * values that gets passed to each of those routines. The values array
|
|
|
- * is nested where foreign key contraints are used to specify a value that. See
|
|
|
- * documentation for any of those functions for further information.
|
|
|
- *
|
|
|
- * @param $table_desc
|
|
|
- * A table description for the table with the foreign key relationship to be identified generated by
|
|
|
- * hook_chado_<table name>_schema()
|
|
|
- * @param $field
|
|
|
- * The field in the table that is the foreign key.
|
|
|
- * @param $values
|
|
|
- * An associative array containing the values
|
|
|
- * @param $options
|
|
|
- * An associative array of additional options where the key is the option
|
|
|
- * and the value is the value of that option. These options are passed on to tripal_core_chado_select.
|
|
|
- *
|
|
|
- * Additional Options Include:
|
|
|
- * - case_insensitive_columns
|
|
|
- * An array of columns to do a case insensitive search on.
|
|
|
- * - regex_columns
|
|
|
- * An array of columns where the value passed in should be treated as a regular expression
|
|
|
- *
|
|
|
- * @return
|
|
|
- * A string containg the results of the foreign key lookup, or FALSE if failed.
|
|
|
- *
|
|
|
- * Example usage:
|
|
|
- * @code
|
|
|
- *
|
|
|
- * $values = array(
|
|
|
- * 'genus' => 'Citrus',
|
|
|
- * 'species' => 'sinensis',
|
|
|
- * );
|
|
|
- * $value = tripal_core_chado_get_foreign_key('feature', 'organism_id',$values);
|
|
|
- *
|
|
|
- * @endcode
|
|
|
- * The above code selects a record from the feature table using the three fields
|
|
|
- * that uniquely identify a feature. The $columns array simply lists the columns
|
|
|
- * to select. The $values array is nested such that the organism is identified by
|
|
|
- * way of the organism_id foreign key constraint by specifying the genus and
|
|
|
- * species. The cvterm is also specified using its foreign key and the cv_id
|
|
|
- * for the cvterm is nested as well.
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_chado_get_foreign_key($table_desc, $field, $values, $options = NULL) {
|
|
|
-
|
|
|
- // set defaults for options. If we don't set defaults then
|
|
|
- // we get memory leaks when we try to access the elements
|
|
|
- if (!is_array($options)) {
|
|
|
- $options = array();
|
|
|
- }
|
|
|
- if (!array_key_exists('case_insensitive_columns', $options)) {
|
|
|
- $options['case_insensitive_columns'] = array();
|
|
|
- }
|
|
|
- if (!array_key_exists('regex_columns', $options)) {
|
|
|
- $options['regex_columns'] = array();
|
|
|
- }
|
|
|
-
|
|
|
- // get the list of foreign keys for this table description and
|
|
|
- // iterate through those until we find the one we're looking for
|
|
|
- $fkeys = '';
|
|
|
- if (array_key_exists('foreign keys', $table_desc)) {
|
|
|
- $fkeys = $table_desc['foreign keys'];
|
|
|
- }
|
|
|
- if ($fkeys) {
|
|
|
- foreach ($fkeys as $name => $def) {
|
|
|
- if (is_array($def['table'])) {
|
|
|
- //foreign key was described 2X
|
|
|
- $message = "The foreign key " . $name . " was defined twice. Please check modules "
|
|
|
- . "to determine if hook_chado_schema_<version>_" . $table_desc['table'] . "() was "
|
|
|
- . "implemented and defined this foreign key when it wasn't supposed to. Modules "
|
|
|
- . "this hook was implemented in: " . implode(', ',
|
|
|
- module_implements("chado_" . $table_desc['table'] . "_schema")) . ".";
|
|
|
- watchdog('tripal_core', $message);
|
|
|
- drupal_set_message(check_plain($message), 'error');
|
|
|
- continue;
|
|
|
- }
|
|
|
- $table = $def['table'];
|
|
|
- $columns = $def['columns'];
|
|
|
-
|
|
|
- // iterate through the columns of the foreign key relationship
|
|
|
- foreach ($columns as $left => $right) {
|
|
|
- // does the left column in the relationship match our field?
|
|
|
- if (strcmp($field, $left) == 0) {
|
|
|
- // the column name of the foreign key matches the field we want
|
|
|
- // so this is the right relationship. Now we want to select
|
|
|
- $select_cols = array($right);
|
|
|
- $result = tripal_core_chado_select($table, $select_cols, $values, $options);
|
|
|
- $fields = array();
|
|
|
- if ($result and count($result) > 0) {
|
|
|
- foreach ($result as $obj) {
|
|
|
- $fields[] = $obj->$right;
|
|
|
- }
|
|
|
- return $fields;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- // TODO: what do we do if we get to this point and we have a fk
|
|
|
- // relationship expected but we don't have any definition for one in the
|
|
|
- // table schema??
|
|
|
- $version = $GLOBALS["chado_version"];
|
|
|
- $message = t("There is no foreign key relationship defined for " . $field . " .
|
|
|
- To define a foreign key relationship, determine the table this foreign
|
|
|
- key referrs to (<foreign table>) and then implement
|
|
|
- hook_chado_chado_schema_v<version>_<foreign table>(). See
|
|
|
- tripal_feature_chado_v1_2_schema_feature for an example. Chado version: $version");
|
|
|
- watchdog('tripal_core', $message);
|
|
|
- drupal_set_message(check_plain($message), 'error');
|
|
|
- }
|
|
|
-
|
|
|
- return array();
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Generates an object containing the full details of a record(s) in chado.
|
|
|
- *
|
|
|
- * This differs from the objects returned by tripal_core_chado_select in so far as all foreign key
|
|
|
- * relationships have been followed meaning you have more complete details. Thus this function
|
|
|
- * should be used whenever you need a full variable and tripal_core_chado_select should be used if
|
|
|
- * you only case about a few columns.
|
|
|
- *
|
|
|
- * @param $table
|
|
|
- * The name of the base table to generate a variable for
|
|
|
- * @param $values
|
|
|
- * A select values array that selects the records you want from the base table
|
|
|
- * (this has the same form as tripal_core_chado_select)
|
|
|
- * @param $base_options
|
|
|
- * An array containing options for the base table. For example, an
|
|
|
- * option of 'order_by' may be used to sort results in the base table
|
|
|
- * if more than one are returned. The options must be compatible with
|
|
|
- * the options accepted by the tripal_core_chado_select() function.
|
|
|
- * Additionally, These options are available for this function:
|
|
|
- * -return_array:
|
|
|
- * can be provided to force the function to always return an array. Default
|
|
|
- * behavior is to return a single record if only one record exists or to return
|
|
|
- * an array if multiple records exist.
|
|
|
- * - include_fk:
|
|
|
- * an array of FK relationships to follow. By default, the
|
|
|
- * tripal_core_chado_select function will follow all FK relationships but this
|
|
|
- * may generate more queries then is desired slowing down this function call when
|
|
|
- * there are lots of FK relationships to follow. Provide an array specifying the
|
|
|
- * fields to include. For example, if expanding a property table (e.g. featureprop)
|
|
|
- * and you want the CV and accession but do not want the DB the following
|
|
|
- * array would work:
|
|
|
- *
|
|
|
- * $table_options = array(
|
|
|
- * 'include_fk' => array(
|
|
|
- * 'type_id' => array(
|
|
|
- * 'cv_id' => 1,
|
|
|
- * 'dbxref_id' => 1,
|
|
|
- * )
|
|
|
- * )
|
|
|
- * );
|
|
|
- *
|
|
|
- * The above array will expand the 'type_id' of the property table but only
|
|
|
- * further expand the cv_id and the dbxref_id and will go no further.
|
|
|
- * - pager:
|
|
|
- * Use this option if it is desired to return only a subset of results
|
|
|
- * so that they may be shown within a Drupal-style pager. This should be
|
|
|
- * an array with two keys: 'limit' and 'element'. The value of 'limit'
|
|
|
- * should specify the number of records to return and 'element' is a
|
|
|
- * unique integer to differentiate between pagers when more than one
|
|
|
- * appear on a page. The 'element' should start with zero and increment by
|
|
|
- * one for each pager. This only works when type is a 'table'.
|
|
|
- * @return
|
|
|
- * Either an object (if only one record was selected from the base table)
|
|
|
- * or an array of objects (if more than one record was selected from the base table).
|
|
|
- * If the option 'return_array' is provided the function always returns an array.
|
|
|
- *
|
|
|
- * Example Usage:
|
|
|
- * @code
|
|
|
- $values = array(
|
|
|
- 'name' => 'Medtr4g030710'
|
|
|
- );
|
|
|
- $features = tripal_core_generate_chado_var('feature', $values);
|
|
|
- * @endcode
|
|
|
- * This will return an object if there is only one feature with the name Medtr4g030710 or it will
|
|
|
- * return an array of feature objects if more than one feature has that name.
|
|
|
- *
|
|
|
- * Note to Module Designers: Fields can be excluded by default from these objects by implementing
|
|
|
- * one of the following hooks:
|
|
|
- * - hook_exclude_field_from_tablename_by_default (where tablename is the name of the table):
|
|
|
- * This hook allows you to add fields to be excluded on a per table basis. Simply implement
|
|
|
- * this hook to return an array of fields to be excluded. For example:
|
|
|
- * @code
|
|
|
- mymodule_exclude_field_from_feature_by_default() {
|
|
|
- return array('residues' => TRUE);
|
|
|
- }
|
|
|
- * @endcode
|
|
|
- * will ensure that feature.residues is ecluded from a feature object by default.
|
|
|
- * - hook_exclude_type_by_default:
|
|
|
- * This hook allows you to exclude fields from all tables that are of a given postgresql field
|
|
|
- * type. Simply implement this hook to return an array of postgresql types mapped to criteria.
|
|
|
- * Then all fields of that type where the criteria supplied returns TRUE will be excluded from
|
|
|
- * any table. Tokens available in criteria are >field_value< and >field_name< . For example:
|
|
|
- * @code
|
|
|
- mymodule_exclude_type_by_default() {
|
|
|
- return array('text' => 'length(>field_value< ) > 50');
|
|
|
- }
|
|
|
- * @endcode
|
|
|
- * will exclude all text fields with a length > 50. Thus if $feature.residues is longer than 50 * it will be excluded, otherwise it will be added.
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_generate_chado_var($table, $values, $base_options = array()) {
|
|
|
- $all = new stdClass();
|
|
|
-
|
|
|
- $return_array = 0;
|
|
|
- if (array_key_exists('return_array', $base_options)) {
|
|
|
- $return_array = 1;
|
|
|
- }
|
|
|
- $include_fk = 0;
|
|
|
- if (array_key_exists('include_fk', $base_options)) {
|
|
|
- $include_fk = $base_options['include_fk'];
|
|
|
- }
|
|
|
- $pager = array();
|
|
|
- if (array_key_exists('pager', $base_options)) {
|
|
|
- $pager = $base_options['pager'];
|
|
|
- }
|
|
|
- // get description for the current table----------------------------------------------------------
|
|
|
- $table_desc = tripal_core_get_chado_table_schema($table);
|
|
|
- if (!$table_desc or count($table_desc) == 0) {
|
|
|
- watchdog('tripal_core', "tripal_core_generate_chado_var: The table '%table' has not been defined. " .
|
|
|
- "and cannot be expanded. If this is a custom table, please add it using the Tripal " .
|
|
|
- "custom table interface.", array('%table' => $table), WATCHDOG_ERROR);
|
|
|
- if ($return_array) {
|
|
|
- return array();
|
|
|
- }
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- $table_primary_key = $table_desc['primary key'][0];
|
|
|
- $table_columns = array_keys($table_desc['fields']);
|
|
|
-
|
|
|
- // Expandable fields without value needed for criteria--------------------------------------------
|
|
|
- $all->expandable_fields = array();
|
|
|
- if (array_key_exists('referring_tables', $table_desc) and $table_desc['referring_tables']) {
|
|
|
- $all->expandable_tables = $table_desc['referring_tables'];
|
|
|
- }
|
|
|
- else {
|
|
|
- $all->expandable_tables = array();
|
|
|
- }
|
|
|
- $all->expandable_nodes = array();
|
|
|
-
|
|
|
- /*
|
|
|
- // Get fields to be removed by name.................................
|
|
|
- $fields_to_remove = module_invoke_all('exclude_field_from_' . $table . '_by_default');
|
|
|
- foreach ($fields_to_remove as $field_name => $criteria) {
|
|
|
- //replace >field_name< with the current field name &
|
|
|
- $criteria = preg_replace('/>field_name< /', addslashes($field_name), $criteria);
|
|
|
- // if field_value needed we can't deal with this field yet
|
|
|
- if (preg_match('/>field_value< /', $criteria)) {
|
|
|
- break;
|
|
|
- }
|
|
|
-
|
|
|
- //if criteria then remove from query
|
|
|
- // @coder-ignore: only module designers can populate $criteria -not security risk
|
|
|
- $success = php_eval('<?php return ' . $criteria . '; ?>');
|
|
|
- if ($success) {
|
|
|
- unset($table_columns[array_search($field_name, $table_columns)]);
|
|
|
- unset($fields_to_remove[$field_name]);
|
|
|
- $all->expandable_fields[] = $table . '.' . $field_name;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- //Get fields to be removed by type................................
|
|
|
- $types_to_remove = module_invoke_all('exclude_type_by_default');
|
|
|
- $field_types = array();
|
|
|
- foreach ($table_desc['fields'] as $field_name => $field_array) {
|
|
|
- $field_types[$field_array['type']][] = $field_name;
|
|
|
- }
|
|
|
- foreach ($types_to_remove as $field_type => $criteria) {
|
|
|
- // if there are fields of that type to remove
|
|
|
- if (is_array($field_types[$field_type])) {
|
|
|
- //replace >field_name< with the current field name &
|
|
|
- $criteria = preg_replace('/>field_name< /', addslashes($field_name), $criteria);
|
|
|
- foreach ($field_types[$field_type] as $field_name) {
|
|
|
- // if field_value needed we can't deal with this field yet
|
|
|
- if (preg_match('/>field_value< /', $criteria)) {
|
|
|
- $fields_to_remove[$field_name] = $criteria;
|
|
|
- continue;
|
|
|
- }
|
|
|
- // if field_value needed we can't deal with this field yet
|
|
|
- if (preg_match('/>field_value< /', $criteria)) {
|
|
|
- break;
|
|
|
- }
|
|
|
- //if criteria then remove from query
|
|
|
- // @coder-ignore: only module designers can populate $criteria -not security risk
|
|
|
- $success = php_eval('<?php return ' . $criteria . '; ?>');
|
|
|
- if ($success) {
|
|
|
- unset($table_columns[array_search($field_name, $table_columns)]);
|
|
|
- $all->expandable_fields[] = $table . '.' . $field_name;
|
|
|
- }
|
|
|
- } //end of foreach field of that type
|
|
|
- }
|
|
|
- } //end of foreach type to be removed
|
|
|
-*/
|
|
|
- // get the values for the record in the current table---------------------------------------------
|
|
|
- $results = tripal_core_chado_select($table, $table_columns, $values, $base_options);
|
|
|
-
|
|
|
- if ($results) {
|
|
|
- foreach ($results as $key => $object) {
|
|
|
- // Add empty expandable_x arrays
|
|
|
- $object->expandable_fields = $all->expandable_fields;
|
|
|
- $object->expandable_tables = $all->expandable_tables;
|
|
|
- $object->expandable_nodes = $all->expandable_nodes;
|
|
|
- // add curent table
|
|
|
- $object->tablename = $table;
|
|
|
-
|
|
|
- // check if the current table maps to a node type-----------------------------------------------
|
|
|
- // if this table is connected to a node there will be a chado_tablename table in drupal
|
|
|
- if (db_table_exists('chado_' . $table)) {
|
|
|
- // that has a foreign key to this one ($table_desc['primary key'][0]
|
|
|
- // and to the node table (nid)
|
|
|
- $sql = "
|
|
|
- SELECT $table_primary_key, nid
|
|
|
- FROM {chado_$table}
|
|
|
- WHERE $table_primary_key = :$table_primary_key
|
|
|
- ";
|
|
|
- $mapping = db_query($sql, array(":$table_primary_key" => $object->{$table_primary_key}))->fetchObject();
|
|
|
- if ($mapping and $mapping->$table_primary_key) {
|
|
|
- $object->nid = $mapping->nid;
|
|
|
- $object->expandable_nodes[] = $table;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // remove any fields where criteria needs to be evalulated---------------------------------------
|
|
|
-/* foreach ($fields_to_remove as $field_name => $criteria) {
|
|
|
- if (!isset($object->{$field_name})) {
|
|
|
- break;
|
|
|
- }
|
|
|
- $criteria = preg_replace('/>field_value< /', addslashes($object->{$field_name}), $criteria);
|
|
|
- $success = php_eval('<?php return ' . $criteria . '; ?>');
|
|
|
- if ($success) {
|
|
|
- unset($object->{$field_name});
|
|
|
- $object->expandable_fields[] = $table . '.' . $field_name;
|
|
|
- }
|
|
|
- }
|
|
|
-*/
|
|
|
- // recursively follow foreign key relationships nesting objects as we go------------------------
|
|
|
- if ($table_desc['foreign keys']) {
|
|
|
- foreach ($table_desc['foreign keys'] as $foreign_key_array) {
|
|
|
- $foreign_table = $foreign_key_array['table'];
|
|
|
- foreach ($foreign_key_array['columns'] as $foreign_key => $primary_key) {
|
|
|
- // Note: Foreign key is the field in the current table whereas primary_key is the field in
|
|
|
- // the table referenced by the foreign key
|
|
|
- //Dont do anything if the foreign key is empty
|
|
|
- if (empty($object->{$foreign_key})) {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- if ($include_fk) {
|
|
|
- // don't recurse if the callee has supplied an $fk_include list and this
|
|
|
- // FK table is not in the list.
|
|
|
- if (is_array($include_fk) and !array_key_exists($foreign_key, $include_fk)) {
|
|
|
- continue;
|
|
|
- }
|
|
|
- // if we have the option but it is not an array then we don't recurse any furutehr
|
|
|
- if (!is_array($include_fk)) {
|
|
|
- continue;
|
|
|
- }
|
|
|
- }
|
|
|
- // get the record from the foreign table
|
|
|
- $foreign_values = array($primary_key => $object->{$foreign_key});
|
|
|
- $options = array();
|
|
|
- if (is_array($include_fk)) {
|
|
|
- $options['include_fk'] = $include_fk[$foreign_key];
|
|
|
- }
|
|
|
-
|
|
|
- $foreign_object = tripal_core_generate_chado_var($foreign_table, $foreign_values, $options);
|
|
|
-
|
|
|
- // add the foreign record to the current object in a nested manner
|
|
|
- $object->{$foreign_key} = $foreign_object;
|
|
|
- // Flatten expandable_x arrays so only in the bottom object
|
|
|
- if (property_exists($object->{$foreign_key}, 'expandable_fields') and
|
|
|
- is_array($object->{$foreign_key}->expandable_fields)) {
|
|
|
- $object->expandable_fields = array_merge(
|
|
|
- $object->expandable_fields,
|
|
|
- $object->{$foreign_key}->expandable_fields
|
|
|
- );
|
|
|
- unset($object->{$foreign_key}->expandable_fields);
|
|
|
- }
|
|
|
- if (property_exists($object->{$foreign_key}, 'expandable_tables') and
|
|
|
- is_array($object->{$foreign_key}->expandable_tables)) {
|
|
|
- $object->expandable_tables = array_merge(
|
|
|
- $object->expandable_tables,
|
|
|
- $object->{$foreign_key}->expandable_tables
|
|
|
- );
|
|
|
- unset($object->{$foreign_key}->expandable_tables);
|
|
|
- }
|
|
|
- if (property_exists($object->{$foreign_key}, 'expandable_nodes') and
|
|
|
- is_array($object->{$foreign_key}->expandable_nodes)) {
|
|
|
- $object->expandable_nodes = array_merge(
|
|
|
- $object->expandable_nodes,
|
|
|
- $object->{$foreign_key}->expandable_nodes
|
|
|
- );
|
|
|
- unset($object->{$foreign_key}->expandable_nodes);
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- $results[$key] = $object;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // convert the results into an array
|
|
|
- $results_arr = array();
|
|
|
- foreach ($results as $record) {
|
|
|
- $results_arr[] = $record;
|
|
|
- }
|
|
|
- // check only one result returned
|
|
|
- if (!$return_array) {
|
|
|
- if (sizeof($results_arr) == 1) {
|
|
|
- // add results to object
|
|
|
- return $results_arr[0];
|
|
|
- }
|
|
|
- elseif (!empty($results_arr)) {
|
|
|
- return $results_arr;
|
|
|
- }
|
|
|
- else {
|
|
|
- // no results returned
|
|
|
- }
|
|
|
- }
|
|
|
- // the caller has requested results are always returned as
|
|
|
- // an array
|
|
|
- else {
|
|
|
- if (!$results_arr) {
|
|
|
- return array();
|
|
|
- }
|
|
|
- else {
|
|
|
- return $results_arr;
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Retrieves fields/tables/nodes that were excluded by default from a variable and adds them
|
|
|
- *
|
|
|
- * This function exists to allow tripal_core_generate_chado_var() to excldue some
|
|
|
- * fields/tables/nodes from the default form of a variable without making it extremely difficult for
|
|
|
- * the tripal admin to get at these variables if he/she wants them.
|
|
|
- *
|
|
|
- * @param $object
|
|
|
- * This must be an object generated using tripal_core_generate_chado_var()
|
|
|
- * @param $type
|
|
|
- * Must be one of 'field', 'table', 'node'. Indicates what is being expanded.
|
|
|
- * @param $to_expand
|
|
|
- * The name of the field/table/node to be expanded
|
|
|
- * @param $table_options
|
|
|
- * - order_by:
|
|
|
- * An array containing options for the base table. For example, an
|
|
|
- * option of 'order_by' may be used to sort results in the base table
|
|
|
- * if more than one are returned. The options must be compatible with
|
|
|
- * the options accepted by the tripal_core_chado_select() function.
|
|
|
- * - return_array:
|
|
|
- * Additionally, The option 'return_array' can be provided to force
|
|
|
- * the function to expand tables as an array. Default behavior is to expand
|
|
|
- * a table as single record if only one record exists or to expand as an array if
|
|
|
- * multiple records exist.
|
|
|
- * - include_fk:
|
|
|
- * an array of FK relationships to follow. By default, the
|
|
|
- * tripal_core_expand_chado_vars function will follow all FK relationships but this
|
|
|
- * may generate more queries then is desired slowing down this function call when
|
|
|
- * there are lots of FK relationships to follow. Provide an array specifying the
|
|
|
- * fields to include. For example, if expanding a property table (e.g. featureprop)
|
|
|
- * and you want the CV and accession but do not want the DB the following
|
|
|
- * array would work:
|
|
|
- * $table_options = array(
|
|
|
- * 'include_fk' => array(
|
|
|
- * 'type_id' => array(
|
|
|
- * 'cv_id' => 1,
|
|
|
- * 'dbxref_id' => 1,
|
|
|
- * )
|
|
|
- * )
|
|
|
- * );
|
|
|
- *
|
|
|
- * The above array will expand the 'type_id' of the property table but only
|
|
|
- * further expand the cv_id and the dbxref_id and will go no further.
|
|
|
- * - pager:
|
|
|
- * Use this option if it is desired to return only a subset of results
|
|
|
- * so that they may be shown within a Drupal-style pager. This should be
|
|
|
- * an array with two keys: 'limit' and 'element'. The value of 'limit'
|
|
|
- * should specify the number of records to return and 'element' is a
|
|
|
- * unique integer to differentiate between pagers when more than one
|
|
|
- * appear on a page. The 'element' should start with zero and increment by
|
|
|
- * one for each pager. This only works when type is a 'table'.
|
|
|
- * @return
|
|
|
- * A chado object supplemented with the field/table/node requested to be expanded.
|
|
|
- * If the type is a table and it has already been expanded no changes is made to the
|
|
|
- * returned object
|
|
|
- *
|
|
|
- * Example Usage:
|
|
|
- * @code
|
|
|
- // Get a chado object to be expanded
|
|
|
- $values = array(
|
|
|
- 'name' => 'Medtr4g030710'
|
|
|
- );
|
|
|
- $features = tripal_core_generate_chado_var('feature', $values);
|
|
|
- // Expand the organism node
|
|
|
- $feature = tripal_core_expand_chado_vars($feature, 'node', 'organism');
|
|
|
- // Expand the feature.residues field
|
|
|
- $feature = tripal_core_expand_chado_vars($feature, 'field', 'feature.residues');
|
|
|
- // Expand the feature properties (featureprop table)
|
|
|
- $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureprop');
|
|
|
- * @endcode
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_expand_chado_vars($object, $type, $to_expand, $table_options = array()) {
|
|
|
-
|
|
|
- // make sure we have a value
|
|
|
- if (!$object) {
|
|
|
- watchdog('tripal_core', 'Cannot pass non array as argument, $object, to tripal_core_expand_chado_vars function.', array(), WATCHDOG_ERROR);
|
|
|
- return $object;
|
|
|
- }
|
|
|
-
|
|
|
- // check to see if we are expanding an array of objects
|
|
|
- if (is_array($object)) {
|
|
|
- foreach ($object as $index => $o) {
|
|
|
- $object[$index] = tripal_core_expand_chado_vars($o, $type, $to_expand);
|
|
|
- }
|
|
|
- return $object;
|
|
|
- }
|
|
|
-
|
|
|
- // get the base table name
|
|
|
- $base_table = $object->tablename;
|
|
|
-
|
|
|
- switch ($type) {
|
|
|
- case "field": //--------------------------------------------------------------------------------
|
|
|
- if (preg_match('/(\w+)\.(\w+)/', $to_expand, $matches)) {
|
|
|
- $tablename = $matches[1];
|
|
|
- $fieldname = $matches[2];
|
|
|
- $table_desc = tripal_core_get_chado_table_schema($tablename);
|
|
|
- $values = array();
|
|
|
- foreach ($table_desc['primary key'] as $key) {
|
|
|
- if(property_exists($object, $key)) {
|
|
|
- $values[$key] = $object->{$key};
|
|
|
- }
|
|
|
- }
|
|
|
- if ($base_table == $tablename) {
|
|
|
- //get the field
|
|
|
- $results = tripal_core_chado_select($tablename, array($fieldname), $values);
|
|
|
- $object->{$fieldname} = $results[0]->{$fieldname};
|
|
|
- $object->expanded = $to_expand;
|
|
|
- }
|
|
|
- else {
|
|
|
- //We need to recurse -the field is in a nested object
|
|
|
- foreach ((array) $object as $field_name => $field_value) {
|
|
|
- if (is_object($field_value)) {
|
|
|
- $object->{$field_name} = tripal_core_expand_chado_vars(
|
|
|
- $field_value,
|
|
|
- 'field',
|
|
|
- $to_expand
|
|
|
- );
|
|
|
- }
|
|
|
- } //end of for each field in the current object
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- watchdog('tripal_core', 'tripal_core_expand_chado_vars: Field (%field) not in the right format. " .
|
|
|
- "It should be <tablename>.<fieldname>', WATCHDOG_ERROR);
|
|
|
- }
|
|
|
- break;
|
|
|
- case "table": //--------------------------------------------------------------------------------
|
|
|
- $foreign_table = $to_expand;
|
|
|
-
|
|
|
- // don't expand the table it already is expanded
|
|
|
- if (array_key_exists($foreign_table, $object)) {
|
|
|
- return $object;
|
|
|
- }
|
|
|
- $foreign_table_desc = tripal_core_get_chado_table_schema($foreign_table);
|
|
|
-
|
|
|
- // If it's connected to the base table via a FK constraint
|
|
|
- if (array_key_exists($base_table, $foreign_table_desc['foreign keys'])) {
|
|
|
- foreach ($foreign_table_desc['foreign keys'][$base_table]['columns'] as $left => $right) {
|
|
|
- // if the FK value in the base table is not there then we can't expand it, so just skip it.
|
|
|
- if (!$object->{$right}) {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // generate a new object for this table using the FK values in the base table.
|
|
|
- $new_options = $table_options;
|
|
|
- $foreign_object = tripal_core_generate_chado_var($foreign_table, array($left => $object->{$right}), $new_options);
|
|
|
-
|
|
|
- // if the generation of the object was successful, update the base object to include it.
|
|
|
- if ($foreign_object) {
|
|
|
- // in the case where the foreign key relationship exists more
|
|
|
- // than once with the same table we want to alter the array structure to
|
|
|
- // include the field name.
|
|
|
- if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
|
|
|
- if (!property_exists($object, $foreign_table)) {
|
|
|
- $object->{$foreign_table} = new stdClass();
|
|
|
- }
|
|
|
- $object->{$foreign_table}->{$left} = $foreign_object;
|
|
|
- $object->expanded = $to_expand;
|
|
|
-
|
|
|
- }
|
|
|
- else {
|
|
|
- if (!property_exists($object, $foreign_table)) {
|
|
|
- $object->{$foreign_table} = new stdClass();
|
|
|
- }
|
|
|
- $object->{$foreign_table} = $foreign_object;
|
|
|
- $object->expanded = $to_expand;
|
|
|
- }
|
|
|
- }
|
|
|
- // if the object returned is NULL then handle that
|
|
|
- else {
|
|
|
- // in the case where the foreign key relationship exists more
|
|
|
- // than once with the same table we want to alter the array structure to
|
|
|
- // include the field name.
|
|
|
- if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
|
|
|
- if (!property_exists($object, $foreign_table)) {
|
|
|
- $object->{$foreign_table} = new stdClass();
|
|
|
- }
|
|
|
- $object->{$foreign_table}->{$left} = NULL;
|
|
|
- }
|
|
|
- else {
|
|
|
- $object->{$foreign_table} = NULL;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- // if the foreign table is not connected to the base table through a FK constraint
|
|
|
- else {
|
|
|
- // We need to recurse -the table has a relationship to one of the nested objects
|
|
|
- $did_expansion = 0;
|
|
|
- foreach ((array) $object as $field_name => $field_value) {
|
|
|
- // if we have a nested object ->expand the table in it
|
|
|
- // check to see if the $field_name is a valid chado table, we don't need
|
|
|
- // to call tripal_core_expand_chado_vars on fields that aren't tables
|
|
|
- $check = tripal_core_get_chado_table_schema($field_name);
|
|
|
- if ($check) {
|
|
|
- $did_expansion = 1;
|
|
|
- $object->{$field_name} = tripal_core_expand_chado_vars($field_value, 'table', $foreign_table);
|
|
|
- }
|
|
|
- }
|
|
|
- // if we did not expand this table we should return a message that the foreign table
|
|
|
- // could not be expanded
|
|
|
- if (!$did_expansion) {
|
|
|
- watchdog('tripal_core', 'tripal_core_expand_chado_vars: Could not expand table, %table. It is ' .
|
|
|
- 'not in a foreign key relationship with the base object nor with any other expanded table. ' .
|
|
|
- 'Check the table definition to ensure that a proper foreign key relationship is present.',
|
|
|
- array('%table' => $foreign_table), WATCHDOG_ERROR);
|
|
|
- }
|
|
|
- }
|
|
|
- break;
|
|
|
- case "node": //---------------------------------------------------------------------------------
|
|
|
- //if the node to be expanded is for our base table, then just expand it
|
|
|
- if ($object->tablename == $to_expand) {
|
|
|
- $node = node_load($object->nid);
|
|
|
- if ($node) {
|
|
|
- $object->expanded = $to_expand;
|
|
|
- $node->expandable_fields = $object->expandable_fields;
|
|
|
- unset($object->expandable_fields);
|
|
|
- $node->expandable_tables = $object->expandable_tables;
|
|
|
- unset($object->expandable_tables);
|
|
|
- $node->expandable_nodes = $object->expandable_nodes;
|
|
|
- unset($object->expandable_nodes);
|
|
|
- $node->{$base_table} = $object;
|
|
|
- $object = $node;
|
|
|
- }
|
|
|
- else {
|
|
|
- watchdog('tripal_core', 'tripal_core_expand_chado_vars: No node matches the nid (%nid) supplied.',
|
|
|
- array('%nid' => $object->nid), WATCHDOG_ERROR);
|
|
|
- } //end of if node
|
|
|
- }
|
|
|
- else {
|
|
|
- //We need to recurse -the node to expand is one of the nested objects
|
|
|
- foreach ((array) $object as $field_name => $field_value) {
|
|
|
- if (is_object($field_value)) {
|
|
|
- $object->{$field_name} = tripal_core_expand_chado_vars(
|
|
|
- $field_value,
|
|
|
- 'node',
|
|
|
- $to_expand
|
|
|
- );
|
|
|
- }
|
|
|
- } //end of for each field in the current object
|
|
|
- }
|
|
|
- break;
|
|
|
- default:
|
|
|
- watchdog('tripal_core', 'tripal_core_expand_chado_vars: Unrecognized type (%type). Should be one of "field", "table", "node".',
|
|
|
- array('%type' => $type), WATCHDOG_ERROR);
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // move extended array downwards
|
|
|
- if (!property_exists($object, 'expanded')) {
|
|
|
- //if there's no extended field then go hunting for it
|
|
|
- foreach ( (array)$object as $field_name => $field_value) {
|
|
|
- if (is_object($field_value)) {
|
|
|
- if (isset($field_value->expanded)) {
|
|
|
- $object->expanded = $field_value->expanded;
|
|
|
- unset($field_value->expanded);
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- //try again becasue now we might have moved it down
|
|
|
- if (property_exists($object, 'expanded')) {
|
|
|
- $expandable_name = 'expandable_' . $type . 's';
|
|
|
- if (property_exists($object, $expandable_name) and $object->{$expandable_name}) {
|
|
|
- $key_to_remove = array_search($object->expanded, $object->{$expandable_name});
|
|
|
- unset($object->{$expandable_name}[$key_to_remove]);
|
|
|
- unset($object->expanded);
|
|
|
- }
|
|
|
- else {
|
|
|
- // if there is an expandable array then we've reached the base object
|
|
|
- // if we get here and don't have anything expanded then something went wrong
|
|
|
- // watchdog(
|
|
|
- // 'tripal_core',
|
|
|
- // 'tripal_core_expand_chado_vars: Unable to expand the %type %to_expand',
|
|
|
- // array('%type'=>$type, '%to_expand'=>$to_expand),
|
|
|
- // WATCHDOG_ERROR
|
|
|
- // );
|
|
|
- } //end of it we've reached the base object
|
|
|
- }
|
|
|
-
|
|
|
- return $object;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_exclude_type_by_default()
|
|
|
- *
|
|
|
- * This hooks allows fields of a specified type that match a specified criteria to be excluded by
|
|
|
- * default from any table when tripal_core_generate_chado_var() is called. Keep in mind that if
|
|
|
- * fields are excluded by default they can always be expanded at a later date using
|
|
|
- * tripal_core_expand_chado_vars().
|
|
|
- *
|
|
|
- * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
|
|
|
- * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
|
|
|
- * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
|
|
|
- * contain the following tokens:
|
|
|
- * - >field_name<
|
|
|
- * Replaced by the name of the field to be excluded
|
|
|
- * - >field_value<
|
|
|
- * Replaced by the value of the field in the current record
|
|
|
- * Also keep in mind that if your criteria doesn't contain the >field_value< token then it will be
|
|
|
- * evaluated before the query is executed and if the field is excluded it won't be included in the
|
|
|
- * query.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_exclude_type_by_default() {
|
|
|
- return array('text' => 'strlen(">field_value< ") > 100');
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_exclude_field_from_<tablename>_by_default()
|
|
|
- *
|
|
|
- * This hooks allows fields from a specified table that match a specified criteria to be excluded by
|
|
|
- * default from any table when tripal_core_generate_chado_var() is called. Keep in mind that if
|
|
|
- * fields are excluded by default they can always be expanded at a later date using
|
|
|
- * tripal_core_expand_chado_vars().
|
|
|
- *
|
|
|
- * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
|
|
|
- * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
|
|
|
- * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
|
|
|
- * contain the following tokens:
|
|
|
- * - >field_name<
|
|
|
- * Replaced by the name of the field to be excluded
|
|
|
- * - >field_value<
|
|
|
- * Replaced by the value of the field in the current record
|
|
|
- * Also keep in mind that if your criteria doesn't contain the >field_value< token then it will be
|
|
|
- * evaluated before the query is executed and if the field is excluded it won't be included in the
|
|
|
- * query.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_exclude_field_from_feature_by_default() {
|
|
|
- return array();
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Use this function instead of pager_query() when selecting a
|
|
|
- * subset of records from a Chado table.
|
|
|
- *
|
|
|
- * @param $query
|
|
|
- * The SQL statement to execute, this is followed by a variable number of args
|
|
|
- * used as substitution values in the SQL statement.
|
|
|
- * @param $args
|
|
|
- * The array of arguments for the query. They keys are the placeholders
|
|
|
- * @param $limit
|
|
|
- * The number of query results to display per page.
|
|
|
- * @param $element
|
|
|
- * An optional integer to distinguish between multiple pagers on one page.
|
|
|
- * @param $count_query
|
|
|
- * An SQL query used to count matching records.
|
|
|
- *
|
|
|
- * @returns
|
|
|
- * A database query result resource or FALSE if the query was not
|
|
|
- * executed correctly
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function chado_pager_query($query, $args, $limit, $element, $count_query = '') {
|
|
|
-
|
|
|
- // get the page and offset for the pager
|
|
|
- $page = isset($_GET['page']) ? $_GET['page'] : '0';
|
|
|
- $offset = $limit * $page;
|
|
|
-
|
|
|
- // Construct a count query if none was given.
|
|
|
- if (!isset($count_query)) {
|
|
|
- $count_query = preg_replace(array('/SELECT.*?FROM /As', '/ORDER BY .*/'),
|
|
|
- array('SELECT COUNT(*) FROM ', ''), $query);
|
|
|
- }
|
|
|
-
|
|
|
- // We calculate the total of pages as ceil(items / limit).
|
|
|
- $results = chado_query($count_query, $args);
|
|
|
- if (!$results) {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
- "chado_pager_query(): Query failed: %cq", array('%cq' => $count_query));
|
|
|
- return;
|
|
|
- }
|
|
|
- $total_records = $results->fetchField();
|
|
|
-
|
|
|
- // set a session variable for storing the total number of records
|
|
|
- $_SESSION['chado_pager'][$element]['total_records'] = $total_records;
|
|
|
-
|
|
|
- pager_default_initialize($total_records, $limit, $element);
|
|
|
-
|
|
|
- $query .= ' LIMIT ' . (int) $limit . ' OFFSET ' . (int) $offset;
|
|
|
- $results = chado_query($query, $args);
|
|
|
- return $results;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Use this function instead of db_query() to avoid switching databases
|
|
|
- * when making query to the chado database
|
|
|
- *
|
|
|
- * Will use a chado persistent connection if it already exists
|
|
|
- *
|
|
|
- * @param $sql
|
|
|
- * The sql statement to execute
|
|
|
- *
|
|
|
- * @param $args
|
|
|
- * The array of arguments, with the same structure as passed to
|
|
|
- * the db_query() function of Drupal.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * DatabaseStatementInterface A prepared statement object, already executed.
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function chado_query($sql, $args = array()) {
|
|
|
- $is_local = $GLOBALS["chado_is_local"];
|
|
|
-
|
|
|
- // Args should be an array
|
|
|
- if (!is_array($args)) {
|
|
|
- tripal_core_report_error('tripal_core', TRIPAL_ERROR,
|
|
|
- 'chado_query; Need to pass an array to chado_query, "%value" passed instead. Query: %query',
|
|
|
- array('%value' => $args, '%query' => $sql)
|
|
|
- );
|
|
|
- $args = array($args);
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // if Chado is local to the database then prefix the Chado table
|
|
|
- // names with 'chado'.
|
|
|
- if ($is_local) {
|
|
|
- $sql = preg_replace('/\n/', '', $sql); // remove carriage returns
|
|
|
- $sql = preg_replace('/\{(.*?)\}/', 'chado.$1', $sql);
|
|
|
-
|
|
|
- // the featureloc table has some indexes that use function that call other functions
|
|
|
- // and those calls do not reference a schema, therefore, any tables with featureloc
|
|
|
- // must automaticaly have the chado schema set as active to find
|
|
|
- if(preg_match('/chado.featureloc/i', $sql)) {
|
|
|
- $previous_db = tripal_db_set_active('chado') ;
|
|
|
- $results = db_query($sql, $args);
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
- }
|
|
|
- // for all other tables we should have everything in scope so just run the query
|
|
|
- else {
|
|
|
- $results = db_query($sql, $args);
|
|
|
- }
|
|
|
- }
|
|
|
- // if Chado is not local to the Drupal database then we have to
|
|
|
- // switch to another database
|
|
|
- else {
|
|
|
- $previous_db = tripal_db_set_active('chado') ;
|
|
|
- $results = db_query($sql, $args);
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
- }
|
|
|
-
|
|
|
- return $results;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Get chado id for a node. E.g, if you want to get 'analysis_id' from the
|
|
|
- * 'analysis' table for a synced 'chado_analysis' node, (the same for
|
|
|
- * organisms and features):
|
|
|
- * $analysis_id = chado_get_id_for_node ('analysis', $node->nid)
|
|
|
- * $organism_id = chado_get_id_for_node ('organism', $node->nid)
|
|
|
- * $feature_id = chado_get_id_for_node ('feature', $node->nid)
|
|
|
- *
|
|
|
- * @param $table
|
|
|
- * @param $nid
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function chado_get_id_for_node($table, $nid) {
|
|
|
- $sql = "SELECT " . $table . "_id as id FROM {chado_$table} WHERE nid = :nid";
|
|
|
- return db_query($sql, array(':nid' => $nid))->fetchField();
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Get node id for a chado feature/organism/analysis. E.g, if you want to
|
|
|
- * get the node id for an analysis, use:
|
|
|
- * $nid = chado_get_node_id ('analysis', $analysis_id)
|
|
|
- * Likewise,
|
|
|
- * $nid = chado_get_node_id ('organism', $organism_id)
|
|
|
- * $nid = chado_get_node_id ('feature', $feature_id)
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function chado_get_node_id($table, $id) {
|
|
|
- $sql = "SELECT nid FROM {chado_$table} WHERE " . $table . "_id = :" . $table . "_id";
|
|
|
- return db_query($sql, array(":" . $table . "_id" => $id))->fetchField();
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Retrieves the schema in an array for the specified custom table.
|
|
|
- *
|
|
|
- * @param $table
|
|
|
- * The name of the table to create.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * A Drupal-style Schema API array definition of the table. Returns
|
|
|
- * FALSE on failure.
|
|
|
- *
|
|
|
- * @ingroup tripal_core_api
|
|
|
- */
|
|
|
-function tripal_get_chado_custom_schema($table) {
|
|
|
-
|
|
|
- $sql = "SELECT schema FROM {tripal_custom_tables} WHERE table_name = :table_name";
|
|
|
- $results = db_query($sql, array(':table_name' => $table));
|
|
|
- $custom = $results->fetchObject();
|
|
|
- if (!$custom) {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- else {
|
|
|
- return unserialize($custom->schema);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Check that any given Chado table exists. This function
|
|
|
- * is necessary because Drupa's db_table_exists function
|
|
|
- * hardcodes the 'public'
|
|
|
- *
|
|
|
- * @return
|
|
|
- * TRUE/FALSE depending upon whether it exists
|
|
|
- */
|
|
|
-function chado_table_exists($table) {
|
|
|
- global $databases;
|
|
|
-
|
|
|
- $default_db = $databases['default']['default']['database'];
|
|
|
-
|
|
|
- $sql = "
|
|
|
- SELECT 1
|
|
|
- FROM information_schema.tables
|
|
|
- WHERE
|
|
|
- table_name = :table_name AND
|
|
|
- table_schema = 'chado' AND
|
|
|
- table_catalog = '$default_db'
|
|
|
- ";
|
|
|
- $results = db_query($sql, array(':table_name' => $table));
|
|
|
- $exists = $results->fetchObject();
|
|
|
- if (!$exists) {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- return TRUE;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Check that any given schema exists
|
|
|
- *
|
|
|
- * @param $schema
|
|
|
- * The name of the schema to check the existence of
|
|
|
- *
|
|
|
- * @return
|
|
|
- * TRUE/FALSE depending upon whether or not the schema exists
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_schema_exists($schema) {
|
|
|
-
|
|
|
- // check that the chado schema now exists
|
|
|
- $sql = "
|
|
|
- SELECT nspname
|
|
|
- FROM pg_namespace
|
|
|
- WHERE
|
|
|
- has_schema_privilege(nspname, 'USAGE') AND
|
|
|
- nspname = :nspname
|
|
|
- ORDER BY nspname
|
|
|
- ";
|
|
|
- $results = db_query($sql, array(':nspname' => $schema));
|
|
|
- $name = $results->fetchObject();
|
|
|
- if (strcmp($name->nspname, $schema) != 0) {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
- return TRUE;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Retrieves the list tables in the Chado schema. By default it only retursn
|
|
|
- * the default Chado tables, but may also return custom tables added to the
|
|
|
- * Chado schema as well.
|
|
|
- *
|
|
|
- * @param $include_custom
|
|
|
- * Optional. Set as TRUE to include any custom tables created in the
|
|
|
- * Chado schema. Custom tables are added to Chado using the
|
|
|
- * tripal_core_chado_create_table() function.
|
|
|
- *
|
|
|
- * @returns
|
|
|
- * An associative array where the key and value pairs are the Chado table names.
|
|
|
- *
|
|
|
- * @ingroup tripal_core_api
|
|
|
- */
|
|
|
-function tripal_core_get_chado_tables($include_custom = NULL) {
|
|
|
-
|
|
|
- // first get the chado version that is installed
|
|
|
- $v = $GLOBALS["chado_version"];
|
|
|
-
|
|
|
- $tables = array();
|
|
|
- if ($v == '1.2') {
|
|
|
- $tables_v1_2 = tripal_core_chado_get_v1_2_tables();
|
|
|
- foreach ($tables_v1_2 as $table) {
|
|
|
- $tables[$table] = $table;
|
|
|
- }
|
|
|
- }
|
|
|
- if ($v == '1.11' or $v == '1.11 or older') {
|
|
|
- $tables_v1_11 = tripal_core_chado_get_v1_11_tables();
|
|
|
- foreach ($tables_v1_11 as $table) {
|
|
|
- $tables[$table] = $table;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // now add in the custom tables too if requested
|
|
|
- if ($include_custom) {
|
|
|
- $sql = "SELECT table_name FROM {tripal_custom_tables}";
|
|
|
- $resource = db_query($sql);
|
|
|
-
|
|
|
- foreach ($resource as $r) {
|
|
|
- $tables[$r->table_name] = $r->table_name;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- asort($tables);
|
|
|
- return $tables;
|
|
|
-}
|
|
|
-/**
|
|
|
- * Returns the version number of the currently installed Chado instance.
|
|
|
- * It can return the real or effective version. Note, this function
|
|
|
- * is executed in the hook_init() of the tripal_core module which then
|
|
|
- * sets the $GLOBAL['exact_chado_version'] and $GLOBAL['chado_version']
|
|
|
- * variable. You can access these variables rather than calling this function.
|
|
|
- *
|
|
|
- * @param $exact
|
|
|
- * Set this argument to 1 to retrieve the exact version that is installed.
|
|
|
- * Otherwise, this function will set the version to the nearest 'tenth'.
|
|
|
- * Chado versioning numbers in the hundreds represent changes to the
|
|
|
- * software and not the schema. Changes in the tenth's represent changes
|
|
|
- * in the schema.
|
|
|
- *
|
|
|
- * @param $warn_if_unsupported
|
|
|
- * If the currently installed version of Chado is not supported by Tripal
|
|
|
- * this generates a Drupal warning.
|
|
|
- *
|
|
|
- * @returns
|
|
|
- * The version of Chado
|
|
|
- *
|
|
|
- * @ingroup tripal_core_api
|
|
|
- */
|
|
|
-function tripal_core_get_chado_version($exact = FALSE, $warn_if_unsupported = FALSE) {
|
|
|
-
|
|
|
- global $databases;
|
|
|
- $version = '';
|
|
|
- $is_local = 0;
|
|
|
-
|
|
|
- // check that Chado is installed if not return 'uninstalled as the version'
|
|
|
- $chado_exists = tripal_core_chado_schema_exists();
|
|
|
- if (!$chado_exists) {
|
|
|
- // if it's not in the drupal database check to see if it's specified in the $db_url
|
|
|
- // in the settings.php
|
|
|
- if (!array_key_exists('chado', $databases)) {
|
|
|
- // if it's not in the drupal database or specified in the $db_url then
|
|
|
- // return uninstalled as the version
|
|
|
- return 'not installed';
|
|
|
- }
|
|
|
- $is_local = 0;
|
|
|
- $previous_db = tripal_db_set_active('chado');
|
|
|
- $prop_exists = db_table_exists('chadoprop');
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
- }
|
|
|
- else {
|
|
|
- $is_local = 1;
|
|
|
- $prop_exists = db_table_exists('chado.chadoprop');
|
|
|
- }
|
|
|
-
|
|
|
- // if the table doesn't exist then we don't know what version but we know
|
|
|
- // it must be 1.11 or older.
|
|
|
- if (!$prop_exists) {
|
|
|
- $version = "1.11 or older";
|
|
|
- }
|
|
|
- else {
|
|
|
- $sql = "
|
|
|
- SELECT value
|
|
|
- FROM {chadoprop} CP
|
|
|
- INNER JOIN {cvterm} CVT on CVT.cvterm_id = CP.type_id
|
|
|
- INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
|
|
|
- WHERE CV.name = 'chado_properties' and CVT.name = 'version'
|
|
|
- ";
|
|
|
- if (!$is_local) {
|
|
|
- $previous_db = tripal_db_set_active('chado');
|
|
|
- $results = db_query($sql);
|
|
|
- tripal_db_set_active($previous_db);
|
|
|
- }
|
|
|
- else {
|
|
|
- $results = chado_query($sql);
|
|
|
- }
|
|
|
- $v = $results->fetchObject();
|
|
|
-
|
|
|
- // if we don't have a version in the chadoprop table then it must be
|
|
|
- // v1.11 or older
|
|
|
- if (!$v) {
|
|
|
- $version = "1.11 or older";
|
|
|
- }
|
|
|
- $version = $v->value;
|
|
|
- }
|
|
|
-
|
|
|
- // next get the exact Chado version that is installed
|
|
|
- $exact_version = $version;
|
|
|
-
|
|
|
- // Tripal only supports v1.11 or newer.. really this is the same as v1.1
|
|
|
- // but at the time the v1.11 schema API was written we didn't know that so
|
|
|
- // we'll return the version 1.11 so the schema API will work.
|
|
|
- if (strcmp($exact_version, '1.11 or older') == 0) {
|
|
|
- $exact_version = "1.11";
|
|
|
- if ($warn_if_unsupported) {
|
|
|
- drupal_set_message(t("WARNING: Tripal does not fully support Chado version less than v1.11. If you are certain this is v1.11
|
|
|
- or if Chado was installed using an earlier version of Tripal then all is well. If not please upgrade to v1.11 or later"),
|
|
|
- 'warning');
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // if not returing an exact version, return the version to the nearest 10th.
|
|
|
- // return 1.2 for all versions of 1.2x
|
|
|
- $effective_version = $exact_version;
|
|
|
- if (preg_match('/^1\.2\d+$/', $effective_version)) {
|
|
|
- $effective_version = "1.2";
|
|
|
- }
|
|
|
- if ($warn_if_unsupported and ($effective_version != 1.11 and $effective_version != 1.2 and $effective_version != 'not installed')) {
|
|
|
- drupal_set_message(t("WARNING: The currently installed version of Chado, v$exact_version, is not fully compatible with Tripal."), 'warning');
|
|
|
- }
|
|
|
- // if the callee has requested the exact version then return it
|
|
|
- if ($exact) {
|
|
|
- return $exact_version;
|
|
|
- }
|
|
|
-
|
|
|
- return $effective_version;
|
|
|
-}
|
|
|
-/**
|
|
|
- * Retrieves the chado tables Schema API array.
|
|
|
- *
|
|
|
- * @param $table
|
|
|
- * The name of the table to retrieve. The function will use the appopriate
|
|
|
- * Tripal chado schema API hooks (e.g. v1.11 or v1.2).
|
|
|
- *
|
|
|
- * @returns
|
|
|
- * A Drupal Schema API array defining the table.
|
|
|
- *
|
|
|
- * @ingroup tripal_core_api
|
|
|
- */
|
|
|
-function tripal_core_get_chado_table_schema($table) {
|
|
|
-
|
|
|
- // first get the chado version that is installed
|
|
|
- $v = $GLOBALS["chado_version"];
|
|
|
-
|
|
|
- // get the table array from the proper chado schema
|
|
|
- $v = preg_replace("/\./", "_", $v); // reformat version for hook name
|
|
|
- $table_arr = module_invoke_all("chado_schema_v" . $v . "_" . $table);
|
|
|
-
|
|
|
- // if the table_arr is empty then maybe this is a custom table
|
|
|
- if (!is_array($table_arr) or count($table_arr) == 0) {
|
|
|
- $table_arr = tripal_get_chado_custom_schema($table);
|
|
|
- }
|
|
|
-
|
|
|
- return $table_arr;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Check that the Chado schema exists within the local database
|
|
|
- *
|
|
|
- * @return
|
|
|
- * TRUE/FALSE depending upon whether it exists
|
|
|
- */
|
|
|
-function tripal_core_chado_schema_exists() {
|
|
|
-
|
|
|
- // This is postgresql-specific code to check the existence of the chado schema
|
|
|
- // @coder-ignore: acting on pg_catalog schema rather then drupal schema therefore, table prefixing does not apply
|
|
|
- $sql = "
|
|
|
- SELECT nspname
|
|
|
- FROM pg_namespace
|
|
|
- WHERE
|
|
|
- has_schema_privilege(nspname, 'USAGE') AND
|
|
|
- nspname = 'chado'
|
|
|
- ";
|
|
|
- $results = db_query($sql);
|
|
|
- $name = $results->fetchObject();
|
|
|
- if ($name) {
|
|
|
- variable_set('chado_schema_exists', FALSE);
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- variable_set('chado_schema_exists', TRUE);
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-}
|
|
|
-/**
|
|
|
- * Check whether chado is installed (either in the same or a different database)
|
|
|
- *
|
|
|
- * @return
|
|
|
- * TRUE/FALSE depending upon whether chado is installed.
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_is_chado_installed() {
|
|
|
- global $databases;
|
|
|
-
|
|
|
- // first check if chado is in the $databases variable of the settings.php file
|
|
|
- if (array_key_exists('chado', $databases)) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
-
|
|
|
- // check to make sure the chado schema exists
|
|
|
- return tripal_core_chado_schema_exists();
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Check whether chado is installed local to the Drupal database
|
|
|
- * in its own Chado schema.
|
|
|
- *
|
|
|
- * @return
|
|
|
- * TRUE/FALSE depending upon whether chado is local.
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_core_is_chado_local() {
|
|
|
- global $databases, $db_type;
|
|
|
-
|
|
|
- // first check if chado is in the $databases variable of the settings.php file
|
|
|
- if (array_key_exists('chado', $databases)) {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-
|
|
|
- // check to make sure the chado schema exists
|
|
|
- return tripal_core_chado_schema_exists();
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Determine whether a given chado table is directly linked to a node
|
|
|
- *
|
|
|
- * @param $chado_table
|
|
|
- * The name of a chado table to check (ie: feature)
|
|
|
- * @return
|
|
|
- * TRUE if it is linked to a node and FALSE otherwise
|
|
|
- */
|
|
|
-function tripal_core_is_tripal_node_type($chado_table) {
|
|
|
- $linking_table = 'chado_' . $chado_table;
|
|
|
- if (db_table_exists($linking_table)) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- return FALSE;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Set the Tripal Database
|
|
|
- *
|
|
|
- * The tripal_db_set_active function is used to prevent namespace collisions
|
|
|
- * when chado and drupal are installed in the same database but in different
|
|
|
- * schemas. It is also used for backwards compatibility with older versions
|
|
|
- * of tripal or in cases where chado is located outside of the Drupal database.
|
|
|
- * or when using Drupal functions such as db_table_exists()
|
|
|
- *
|
|
|
- * @ingroup tripal_chado_api
|
|
|
- */
|
|
|
-function tripal_db_set_active($dbname = 'default') {
|
|
|
- global $databases, $active_db;
|
|
|
-
|
|
|
- if ($dbname ) {
|
|
|
- if ($dbname == 'chado') {
|
|
|
- db_query('set search_path to chado,public');
|
|
|
- return 'default';
|
|
|
- }
|
|
|
- else {
|
|
|
- db_query('set search_path to public');
|
|
|
- return 'chado';
|
|
|
- }
|
|
|
- }
|
|
|
- // if the 'chado' database is in the $db_url variable then chado is
|
|
|
- // not in the same Drupal database, so we don't need to set any
|
|
|
- // search_path and can just change the database
|
|
|
- elseif (array_key_exists($dbname, $databases)) {
|
|
|
- return db_set_active($dbname);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Get max rank for a given set of criteria
|
|
|
- * This function was developed with the many property tables in chado in mind but will
|
|
|
- * work for any table with a rank
|
|
|
- *
|
|
|
- * @params tablename: the name of the chado table you want to select the max rank from
|
|
|
- * this table must contain a rank column of type integer
|
|
|
- * @params where_options: array(
|
|
|
- * <column_name> => array(
|
|
|
- * 'type' => <type of column: INT/STRING>,
|
|
|
- * 'value' => <the value you want to filter on>,
|
|
|
- * 'exact' => <if TRUE use =; if FALSE use ~>,
|
|
|
- * )
|
|
|
- * )
|
|
|
- * where options should include the id and type for that table to correctly
|
|
|
- * group a set of records together where the only difference are the value and rank
|
|
|
- * @return the maximum rank
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_core_get_max_chado_rank($tablename, $where_options) {
|
|
|
-
|
|
|
- $where_clauses = array();
|
|
|
- $where_args = array();
|
|
|
-
|
|
|
- //generate the where clause from supplied options
|
|
|
- // the key is the column name
|
|
|
- $i = 0;
|
|
|
- $sql = "
|
|
|
- SELECT max(rank) as max_rank, count(rank) as count
|
|
|
- FROM {".$tablename."}
|
|
|
- WHERE
|
|
|
- ";
|
|
|
- foreach ($where_options as $key => $value) {
|
|
|
- $where_clauses[] = "$key = :$key";
|
|
|
- $where_args[":$key"] = $value;
|
|
|
- }
|
|
|
- $sql .= implode($where_clauses, ' AND ');
|
|
|
-
|
|
|
- $result = chado_query($sql, $where_args)->fetchObject();
|
|
|
- if ($result->count > 0) {
|
|
|
- return $result->max_rank;
|
|
|
- }
|
|
|
- else {
|
|
|
- return -1;
|
|
|
- }
|
|
|
-
|
|
|
-}
|
Lacey Sanderson