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- <?php
- /**
- * @file
- * Provides an application programming interface (API) to manage data withing
- * the Chado database.
- */
- /**
- * @defgroup tripal_chado_prop_api Chado Properties
- * @ingroup tripal_api
- * @{
- * The Chado Properties API provides a set of functions for interacting
- * with the any chado prop table.
- * @}
- */
- /**
- * Retrieve a property for a given base table record.
- *
- * @param $record
- * An array used to identify the record to which the property is associated.
- * The following keys must be used:
- * -table: The base table for which the property should be updated.
- * Thus to update a property for a feature the base_table=feature.
- * -id: The primary key value of the base table. The property will be
- * associated with the record that matches this id.
- * -prop_id: The primary key in the [table]prop table. If this value
- * is supplied then the 'id' key is not needed.
- * @param $property
- * An associative array used to specify the property to be selected. It can
- * contain the following keys. The keys must be specified to uniquely identify
- * the term to be applied. If the options identify more than one CV term
- * then an error will occur.
- * -type_name: The cvterm name to be selected.
- * -type_id: The cvterm_id of the term to be selected.
- * -cv_id: The cv_id of the CV that contains the term.
- * -cv_name: The name of the CV that contains the term.
- * -value: The specific value for the property.
- * -rank: The specific rank for the property.
- *
- * @return
- * An array in the same format as that generated by the function
- * chado_generate_var(). If only one record is returned it
- * is a single object. If more than one record is returned then it is an
- * array of objects
- *
- * @ingroup tripal_chado_prop_api
- */
- function chado_get_property($record, $property) {
- $base_table = array_key_exists('table', $record) ? $record['table'] : '';
- $base_id = array_key_exists('id', $record) ? $record['id'] : '';
- $prop_id = array_key_exists('prop_id', $record) ? $record['prop_id'] : '';
- $type_name = array_key_exists('type_name', $property) ? $property['type_name'] : '';
- $type_id = array_key_exists('type_id', $property) ? $property['type_id'] : '';
- $cv_name = array_key_exists('cv_name', $property) ? $property['cv_name'] : '';
- $cv_id = array_key_exists('cv_id', $property) ? $property['cv_id'] : '';
- $value = array_key_exists('value', $property) ? $property['value'] : '';
- $rank = array_key_exists('rank', $property) ? $property['rank'] : 0;
- // Build the values array for checking if the CVterm exists and for
- // retrieving the term as a property.
- $type = [];
- if ($cv_id) {
- $type['cv_id'] = $cv_id;
- }
- if ($cv_name) {
- $type['cv_id'] = [
- 'name' => $cv_name,
- ];
- }
- if ($type_name) {
- $type['name'] = $type_name;
- }
- if ($type_id) {
- $type['cvterm_id'] = $type_id;
- }
- // Make sure the CV term exists.
- $options = [];
- $term = chado_select_record('cvterm', ['cvterm_id'], $type, $options);
- if (!$term or count($term) == 0) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_get_property: " .
- "Cannot find the term described by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- if (count($term) > 1) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_get_property: " .
- "Multiple terms found. Cannot add the property. Property was described " .
- "by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- // Get the foreign key for this property table.
- $table_desc = chado_get_schema($base_table . 'prop');
- $fkcol = key($table_desc['foreign keys'][$base_table]['columns']);
- // Construct the array of values to be selected.
- $values = [
- 'type_id' => $type,
- ];
- //Can supply either base_id or prop_id.
- if ($base_id) {
- $values[$fkcol] = $base_id;
- }
- // If we have the unique property_id make sure to add that to the values.
- if ($prop_id) {
- $property_pkey = $table_desc['primary key'][0];
- $values[$property_pkey] = $prop_id;
- }
- $results = chado_generate_var($base_table . 'prop', $values);
- if ($results) {
- $results = chado_expand_var($results, 'field', $base_table . 'prop.value');
- }
- return $results;
- }
- /**
- * Insert a property for a given base table.
- *
- * By default if the property already exists a new property is added with the
- * next available rank. If the option 'update_if_present' is specified then
- * the record will be updated if it exists rather than adding a new property.
- *
- * @param $record
- * An associative array used to identify the record to which the property
- * should be assigned. The following keys must be used:
- * -table: The base table for which the property should be inserted.
- * Thus to insert a property for a feature the base_table=feature and
- * property is inserted into featureprop.
- * -id: The primary key value of the base table. The property will be
- * associated with the record that matches this id.
- * @param $property
- * An associative array used to specify the property to be added. It can
- * contain the following keys. The keys must be specified to uniquely identify
- * the term to be applied. If the options identify more than one CV term
- * then an error will occur.
- * -type_name: The cvterm name to be selected.
- * -type_id: The cvterm_id of the term to be selected.
- * -cv_id: The cv_id of the CV that contains the term.
- * -cv_name: The name of the CV that contains the term.
- * -value: The specific value for the property.
- * -rank: The specific rank for the property.
- * @param $options
- * An associative array containing the following keys:
- * -update_if_present: A boolean indicating whether an existing record
- * should be updated. If the property already exists and this value is
- * not specified or is zero then a new property will be added with the
- * next largest rank.
- * -force_rank: If the specified rank is already used by another property
- * recrod for the same base_id, then set force_rank to TRUE to require
- * that only the specified rank can be used. Otherwise, the next
- * available rank will be used. If 'update_if_present' is FALSE and
- * 'force_rank' is set then an error will occur.
- *
- * @return
- * Return TRUE if successful and FALSE otherwise.
- *
- * @ingroup tripal_chado_prop_api
- */
- function chado_insert_property($record, $property, $options = []) {
- $base_table = array_key_exists('table', $record) ? $record['table'] : '';
- $base_id = array_key_exists('id', $record) ? $record['id'] : '';
- $type_name = array_key_exists('type_name', $property) ? $property['type_name'] : '';
- $type_id = array_key_exists('type_id', $property) ? $property['type_id'] : '';
- $cv_name = array_key_exists('cv_name', $property) ? $property['cv_name'] : '';
- $cv_id = array_key_exists('cv_id', $property) ? $property['cv_id'] : '';
- $value = array_key_exists('value', $property) ? $property['value'] : '';
- $rank = array_key_exists('rank', $property) ? $property['rank'] : 0;
- $cvalue_id = array_key_exists('cvalue_id', $property) ? $property['cvalue_id'] : '';
- $update_if_present = array_key_exists('update_if_present', $options) ? $options['update_if_present'] : FALSE;
- $force_rank = array_key_exists('force_rank', $options) ? $options['force_rank'] : FALSE;
- // First see if the property is already assigned to the record. I
- $props = chado_get_property($record, $property);
- if (!is_array($props)) {
- if ($props) {
- $props = [$props];
- }
- else {
- $props = [];
- }
- }
- if (count($props) > 0) {
- // The property is already assigned, so, see if we should update it.
- if ($update_if_present) {
- return chado_update_property($record, $property);
- }
- else {
- if (!$force_rank) {
- // Iterate through the properties returned and check to see if the
- // property with this value already exists if not, get the largest rank
- // and insert the same property but with this new value.
- foreach ($props as $prop) {
- if ($prop->rank > $rank) {
- $rank = $prop->rank;
- }
- if (strcmp($prop->value, $value) == 0) {
- return TRUE;
- }
- }
- // Now add 1 to the rank.
- $rank++;
- }
- else {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_insert_property: " .
- "The property is already assigned to the record with the following " .
- "rank. And, because the 'force_rank' option is used, the property " .
- "cannot be added: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- }
- }
- // Build the values array for checking if the CVterm exists and for
- // inserting the term as a property.
- $values = [];
- if ($cv_id) {
- $values['cv_id'] = $cv_id;
- }
- if ($cv_name) {
- $values['cv_id'] = [
- 'name' => $cv_name,
- ];
- }
- if ($type_name) {
- $values['name'] = $type_name;
- }
- if ($type_id) {
- $values['cvterm_id'] = $type_id;
- }
- // Make sure the CV term exists.
- $options = [];
- $term = chado_select_record('cvterm', ['cvterm_id'], $values, $options);
- if (!$term or count($term) == 0) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_insert_property: " .
- "Cannot find the term described by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- if (count($term) > 1) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_insert_property: " .
- "Multiple terms found. Cannot add the property. Property was described " .
- "by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- // Check that the cvalue property exists.
- if ($cvalue_id) {
- $term = chado_select_record('cvterm', ['cvterm_id'], ['cvterm_id' => $cvalue_id], $options);
- if (!$term or count($term) == 0) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_insert_property: " .
- "Cannot find the term for the property value described by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- $values['cvalue'] = $cvalue_id;
- }
- // Get the foreign key for this property table.
- $table_desc = chado_get_schema($base_table . 'prop');
- $fkcol = key($table_desc['foreign keys'][$base_table]['columns']);
- // Add the property to the record.
- $values = [
- $fkcol => $base_id,
- 'type_id' => $values,
- 'value' => $value,
- 'rank' => $rank,
- ];
- $result = chado_insert_record($base_table . 'prop', $values);
- return $result;
- }
- /**
- * Update a property for a given base table record and property name.
- *
- * @param $record
- * An associative array used to identify the record to which the property
- * should be updated. The following keys must be used:
- * -table: The base table for which the property should be updated.
- * Thus to update a property for a feature the base_table=feature.
- * -id: The primary key value of the base table. The property will be
- * associated with the record that matches this id.
- * -prop_id: The primary key in the [table]prop table. If this value
- * is supplied then the 'table' and 'id' keys are not needed.
- * @param $property
- * An associative array used to specify the property to be updated. It can
- * contain the following keys. The keys must be specified to uniquely identify
- * the term to be applied. If the options identify more than one CV term
- * then an error will occur.
- * -type_name: The cvterm name to be selected.
- * -type_id: The cvterm_id of the term to be selected.
- * -cv_id: The cv_id of the CV that contains the term.
- * -cv_name: The name of the CV that contains the term.
- * -value: The specific value for the property.
- * -rank: The specific rank for the property.
- * -cvalue_id: The cvterm_id of the value for the property.
- * **note** cvalue_id is an anticipated column in the the next Chado
- * release (1.4). It is included here for early adopters.
- *
- * @param $options
- * An associative array containing the following keys:
- * -insert_if_missing: A boolean indicating whether a record should be
- * inserted if one doesn't exist to update.
- *
- *
- * @return
- * Return TRUE on Update/Insert and FALSE otherwise.
- *
- * @ingroup tripal_chado_prop_api
- */
- function chado_update_property($record, $property, $options = []) {
- $base_table = array_key_exists('table', $record) ? $record['table'] : '';
- $base_id = array_key_exists('id', $record) ? $record['id'] : '';
- $prop_id = array_key_exists('prop_id', $record) ? $record['prop_id'] : '';
- $type_name = array_key_exists('type_name', $property) ? $property['type_name'] : '';
- $type_id = array_key_exists('type_id', $property) ? $property['type_id'] : '';
- $cv_name = array_key_exists('cv_name', $property) ? $property['cv_name'] : '';
- $cv_id = array_key_exists('cv_id', $property) ? $property['cv_id'] : '';
- $value = array_key_exists('value', $property) ? $property['value'] : '';
- $rank = array_key_exists('rank', $property) ? $property['rank'] : 0;
- $cvalue_id = array_key_exists('cvalue_id', $property) ? $property['cvalue_id'] : '';
- $insert_if_missing = array_key_exists('insert_if_missing', $options) ? $options['insert_if_missing'] : FALSE;
- // First see if the property is missing (we can't update a missing property.
- $prop = chado_get_property($record, $property);
- if (empty($prop)) {
- if ($insert_if_missing) {
- return chado_insert_property($record, $property);
- }
- else {
- return FALSE;
- }
- }
- // Build the values array for checking if the CVterm exists.
- $type = [];
- if ($cv_id) {
- $type['cv_id'] = $cv_id;
- }
- if ($cv_name) {
- $type['cv_id'] = [
- 'name' => $cv_name,
- ];
- }
- if ($type_name) {
- $type['name'] = $type_name;
- }
- if ($type_id) {
- $type['cvterm_id'] = $type_id;
- }
- // Make sure the CV term exists.
- $options = [];
- $term = chado_select_record('cvterm', ['cvterm_id'], $type, $options);
- if (!$term or count($term) == 0) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_update_property: " .
- "Cannot find the term described by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- if (count($term) > 1) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_update_property: " .
- "Multiple terms found. Cannot add the property. Property was described " .
- "by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- // Get the foreign key for this property table.
- $table_desc = chado_get_schema($base_table . 'prop');
- $fkcol = key($table_desc['foreign keys'][$base_table]['columns']);
- // Construct the array that will match the exact record to update.
- $match = [
- $fkcol => $base_id,
- 'type_id' => $type,
- ];
- // If we have the unique property_id, make sure to use it in the match to
- // ensure we get the exact record. Doesn't rely on there only being one
- // property of that type.
- if ($prop_id) {
- $property_pkey = $table_desc['primary key'][0];
- $match = [
- $property_pkey => $prop_id,
- ];
- }
- // Construct the array of values to be updated.
- $values = [];
- $values['value'] = $value;
- if ($rank) {
- $values['rank'] = $rank;
- }
- // If a cvalue_id is supplied, check that it is a valid cvterm.
- if ($cvalue_id) {
- $term = chado_select_record('cvterm', ['cvterm_id'], ['cvterm_id' => $cvalue_id], $options);
- if (!$term or count($term) == 0) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_insert_property: " .
- "Cannot find the term for the property value described by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- $values['cvalue_id'] = $cvalue_id;
- }
- // If we have the unique property_id then we can also update the type
- // thus add it to the values to be updated.
- if ($prop_id) {
- $values['type_id'] = $type;
- }
- return chado_update_record($base_table . 'prop', $match, $values);
- }
- /**
- * Deletes a property for a given base table record using the property name.
- *
- * @param $record
- * An associative array used to identify the record to which the property
- * should be deleted. The following keys must be used:
- * -table: The base table for which the property should be deleted.
- * Thus to update a property for a feature the base_table=feature.
- * -id: The primary key value of the base table. The property will be
- * deleted from the record that matches this id.
- * -prop_id: The primary key in the [table]prop table to be deleted. If
- * this value is supplied then the 'id' key is not needed.
- * @param $property
- * An associative array used to specify the property to be updated. It can
- * contain the following keys. The keys must be specified to uniquely identify
- * the term to be applied. If the options identify more than one CV term
- * then an error will occur.
- * -type_name: The cvterm name to be selected.
- * -type_id: The cvterm_id of the term to be selected.
- * -cv_id: The cv_id of the CV that contains the term.
- * -cv_name: The name of the CV that contains the term.
- * -value: The specific value for the property.
- * -rank: The specific rank for the property.
- *
- * @return
- * Return TRUE on successful deletion and FALSE otherwise.
- *
- * @ingroup tripal_chado_prop_api
- */
- function chado_delete_property($record, $property) {
- $base_table = array_key_exists('table', $record) ? $record['table'] : '';
- $base_id = array_key_exists('id', $record) ? $record['id'] : '';
- $prop_id = array_key_exists('prop_id', $record) ? $record['prop_id'] : '';
- $type_name = array_key_exists('type_name', $property) ? $property['type_name'] : '';
- $type_id = array_key_exists('type_id', $property) ? $property['type_id'] : '';
- $cv_name = array_key_exists('cv_name', $property) ? $property['cv_name'] : '';
- $cv_id = array_key_exists('cv_id', $property) ? $property['cv_id'] : '';
- $value = array_key_exists('value', $property) ? $property['value'] : '';
- $rank = array_key_exists('rank', $property) ? $property['rank'] : 0;
- // Build the values array for checking if the CVterm exists.
- $type = [];
- if ($cv_id) {
- $type['cv_id'] = $cv_id;
- }
- if ($cv_name) {
- $type['cv_id'] = [
- 'name' => $cv_name,
- ];
- }
- if ($type_name) {
- $type['name'] = $type_name;
- }
- if ($type_id) {
- $type['cvterm_id'] = $type_id;
- }
- // Make sure the CV term exists.
- $options = [];
- $term = chado_select_record('cvterm', ['cvterm_id'], $type, $options);
- if (!$term or count($term) == 0) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_delete_property: " .
- "Cannot find the term described by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- if (count($term) > 1) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_delete_property: " .
- "Multiple terms found. Cannot add the property. Property was described " .
- "by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- // Get the foreign key for this property table.
- $table_desc = chado_get_schema($base_table . 'prop');
- $fkcol = key($table_desc['foreign keys'][$base_table]['columns']);
- // If we have the unique property_id, make sure to use it in the match to
- // ensure we get the exact record. Doesn't rely on there only being one
- // property of that type.
- if ($prop_id) {
- $property_pkey = $table_desc['primary key'][0];
- $match = [
- $property_pkey => $prop_id,
- ];
- }
- // Construct the array that will match the exact record to update.
- else {
- $match = [
- $fkcol => $base_id,
- 'type_id' => $type,
- ];
- }
- return chado_delete_record($base_table . 'prop', $match);
- }
- /**
- * Get all records in the base table assigned one or more properties.
- *
- * The property or properties of interest are specified using the $property
- * argument.
- *
- * @param $record
- * An associative array used to identify the table and subset of records to
- * to be searched:
- * -table: The base table for which the property should be updated.
- * Thus to update a property for a feature the base_table=feature.
- * -base_records: An array in the format accepted by the chado_select_record
- * for specifying a subset of records in the base table.
- * @param $property
- * An associative array used to specify the property to be selected for. It
- * can contain the following keys. The keys must be specified to uniquely
- * identify the term to be searched. If the options identify more than one
- * CV term then an error will occur.
- * -type_name: The cvterm name to be selected.
- * -type_id: The cvterm_id of the term to be selected.
- * -cv_id: The cv_id of the CV that contains the term.
- * -cv_name: The name of the CV that contains the term.
- * -value: The specific value for the property.
- * -rank: The specific rank for the property.
- * -cvalue_id: The cvterm_id of the value for the property.
- * **note** cvalue_id is an anticipated column in the the next Chado
- * release (1.4). It is included here for early adopters.
- *
- * @param $options
- * An array of options supported by chado_generate_var(). These keys
- * are used for generating the cvterm objects returned by this function.
- *
- * @return
- * An array of chado variables with the given property.
- *
- * @ingroup tripal_chado_prop_api
- */
- function chado_get_record_with_property($record, $property, $options = []) {
- $base_table = array_key_exists('table', $record) ? $record['table'] : '';
- $base_records = array_key_exists('base_records', $record) ? $record['base_records'] : [];
- $type_name = array_key_exists('type_name', $property) ? $property['type_name'] : '';
- $type_id = array_key_exists('type_id', $property) ? $property['type_id'] : '';
- $cv_name = array_key_exists('cv_name', $property) ? $property['cv_name'] : '';
- $cv_id = array_key_exists('cv_id', $property) ? $property['cv_id'] : '';
- $value = array_key_exists('value', $property) ? $property['value'] : '';
- $rank = array_key_exists('rank', $property) ? $property['rank'] : '';
- $property_table = $base_table . 'prop';
- $foreignkey_name = $base_table . '_id';
- // Build the values array for checking if the CVterm exists and for
- // inserting the term as a property.
- $type = [];
- if ($cv_id) {
- $type['cv_id'] = $cv_id;
- }
- if ($cv_name) {
- $type['cv_id'] = [
- 'name' => $cv_name,
- ];
- }
- if ($type_name) {
- $type['name'] = $type_name;
- }
- if ($type_id) {
- $type['cvterm_id'] = $type_id;
- }
- // Make sure the CV term exists;
- $term = chado_select_record('cvterm', ['cvterm_id'], $type);
- if (!$term or count($term) == 0) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_update_property: " .
- "Cannot find the term described by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- if (count($term) > 1) {
- tripal_report_error('tripal_chado', TRIPAL_ERROR, "chado_update_property: " .
- "Multiple terms found. Cannot add the property. Property was described " .
- "by: %property.",
- ['%property' => print_r($property, TRUE)]);
- return FALSE;
- }
- // Build the array for identifying the property.
- $values = [];
- $values['type_id'] = $type;
- if ($rank) {
- $values['rank'] = $rank;
- }
- if ($value) {
- $values['value'] = $value;
- }
- // Add the base records details to the values array.
- if (!empty($base_records)) {
- $values[$foreignkey_name] = $base_records;
- }
- // Now select the ids of the base table that have the properties we want that
- // match.
- $select = chado_select_record($property_table, [$foreignkey_name], $values);
- // For each of these ids, pull out the full base records.
- $records = [];
- foreach ($select as $s) {
- $id = $s->{$foreignkey_name};
- $values = [$foreignkey_name => $id];
- $records[$id] = chado_generate_var($base_table, $values, $options);
- }
- return $records;
- }
- /**
- * Retrieves all of the property types currently availalbe in a prop table.
- *
- * @param $prop_table
- * The name of the property table.
- *
- * @throws Exception
- *
- * @return
- * An array of cvterm objects as created by chado_generate_var().
- *
- * @ingroup tripal_chado_prop_api
- */
- function chado_get_table_property_types($prop_table) {
- // Make sure this is a prop table.
- if (!preg_match('/prop$/', $prop_table)) {
- throw new Exception('Please provide a valid Chado property table');
- }
- $sql = 'SELECT DISTINCT type_id FROM {' . $prop_table . '}';
- $results = chado_query($sql);
- $types = [];
- foreach ($results as $result) {
- $types[] = chado_generate_var('cvterm', ['cvterm_id' => $result->type_id]);
- }
- return $types;
- }
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