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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Go to the source code of this file.
Functions | |
| tripal_views_get_table_lightest_priority ($table_name) | |
| tripal_views_get_lightest_priority_setup ($table_name) | |
| tripal_views_is_integrated ($table_name, $priority=NULL) | |
| tripal_views_is_lightest_priority_setup ($setup_id, $table_name) | |
| tripal_views_integration_add_entry ($defn_array) | |
| tripal_views_integration_export_entry ($setup_id) | |
| tripal_views_integration_remove_entry_by_table_name ($table_name, $priority) | |
| tripal_views_integration_remove_entry_by_setup_id ($setup_id) | |
| tripal_views_integrate_all_chado_tables () | |
| tripal_views_get_integration_array_for_chado_table ($table_name, $base_table=TRUE, $priority=9) | |
| tripal_views_add_node_relationship_to_chado_table_integration ($defn_array) | |
API functions for Tripal Views Integration
Definition in file tripal_views.api.inc.
| tripal_views_add_node_relationship_to_chado_table_integration | ( | $ | defn_array | ) |
Adds the joins necessary to link a chado table to it's node counterpart
| &$defn_array | The current definition array for a given table |
Definition at line 574 of file tripal_views.api.inc.
{
$integrations[$defn_array['table']] = $defn_array;
$primary_key = $defn_array['table'] . '_id';
$chado_linking = 'chado_' . $defn_array['table'];
if (empty($defn_array['table'])) {
watchdog('tripal_views','Tried to add a node=>chado relationship for an empty table defn: %defn',
array('%defn' => print_r($defn_array,TRUE)),WATCHDOG_WARNING);
return FALSE;
}
// Add table.primary_key => chado_table.primary key join to $defn_array
$integrations[$defn_array['table']]['fields'][$primary_key]['joins'][$chado_linking] = array(
'table' => $chado_linking,
'field' => $primary_key,
);
// Create chado_table defn_array
$integrations[$chado_linking] = array(
'table' => $chado_linking,
'type' => 'drupal',
'name' => 'Chado ' . $defn_array['table'] . ' Node',
'description' => 'Links chado content to its drupal node counterpart',
'priority' => $defn_array['priority'],
'base_table' => FALSE,
'fields' => array(
$primary_key => array(
'name' => $primary_key,
'title' => ucwords(str_replace('_', ' ', $primary_key)),
'type' => 'int',
'description' => 'The primary key of the chado ' . $defn_array['table'] . ' table',
'handlers' => array(),
'joins' => array(
$defn_array['table'] => array(
'table' => $defn_array['table'],
'field' => $primary_key,
)
),
),
'nid' => array(
'name' => 'nid',
'title' => 'Node ID',
'type' => 'int',
'description' => 'Link ' . ucfirst($defn_array['table']) . ' to it\'s node',
'handlers' => array(
'relationship' => array(
'name' => 'chado_views_handler_relationship_to_node',
'title' => ucfirst($defn_array['table']) . ' to Node',
'label' => ucfirst($defn_array['table']) . ' to Node',
'base table' => $defn_array['table'],
'base field' => $primary_key
)
),
'joins' => array(
'node' => array(
'table' => 'node',
'field' => 'nid',
),
),
)
),
);
// Create node defn_array
$integrations['node'] = array(
'table' => 'node',
'name' => 'Node',
'description' => 'Primary Drupal Content',
'priority' => $defn_array['priority'],
'additional_content' => TRUE, // Allows multiple modules to add to the node setup
'fields' => array(
'nid' => array(
'name' => 'nid',
'title' => 'Node ID',
'type' => 'int',
'description' => 'the primary key of the drupal node table',
'handlers' => array(),
'joins' => array(
$defn_array['table'] => array(
'table' => $defn_array['table'],
'field' => 'nid',
),
$chado_linking => array(
'table' => $chado_linking,
'field' => 'nid',
),
),
),
),
);
return $integrations;
}
| tripal_views_get_integration_array_for_chado_table | ( | $ | table_name, |
| $ | base_table = TRUE, |
||
| $ | priority = 9 |
||
| ) |
Returns the array needed to integrate a given chado table with views
| $tablename | The table to generate the tripal views integration array for |
Definition at line 449 of file tripal_views.api.inc.
{
// Get the schema for this table (via the chado schema api)
$schema = tripal_core_get_chado_table_schema($table_name);
// Base definition array
$defn_array = array(
'table' => $table_name,
'type' => 'chado',
'name' => 'Chado ' . ucwords(str_replace('_', ' ', $table_name)),
'description' => (!empty($schema['description'])) ? $schema['description'] : ' ',
'priority' => $priority,
'base_table' => $base_table,
'fields' => array(),
);
// Add fields
if (!isset($schema['fields'])) {
watchdog('tripal_views', 'There are no fields defined for %table in the Chado Schema API.', array('%table' => $table_name), WATCHDOG_NOTICE);
return FALSE;
}
foreach ($schema['fields'] as $field_name => $field_schema) {
// Base field definition
if (!empty($field_name) && !empty($field_schema['type'])) {
$defn_array['fields'][$field_name] = array(
'name' => $field_name,
'title' => ucwords(str_replace('_', ' ', $field_name)),
'type' => $field_schema['type'],
'description' => ($field_schema['description']) ? $field_schema['description'] : ucwords(str_replace('_', ' ', $field_name)),
'handlers' => array(),
'joins' => array()
);
// Add handlers based on type
if (preg_match('/^int/', $field_schema['type'])) {
$defn_array['fields'][$field_name]['handlers'] = array(
'field' => array('name' => 'chado_views_handler_field_numeric'),
'filter' => array('name' => 'chado_views_handler_filter_numeric'),
'sort' => array('name' => 'chado_views_handler_sort'),
);
}
elseif (preg_match('/^serial/', $field_schema['type'])) {
$defn_array['fields'][$field_name]['handlers'] = array(
'field' => array('name' => 'chado_views_handler_field_numeric'),
'filter' => array('name' => 'chado_views_handler_filter_numeric'),
'sort' => array('name' => 'chado_views_handler_sort'),
);
$defn_array['fields'][$field_name]['type'] = 'int';
}
elseif (preg_match('/^varchar/', $field_schema['type'])) {
$defn_array['fields'][$field_name]['handlers'] = array(
'field' => array('name' => 'chado_views_handler_field'),
'filter' => array('name' => 'chado_views_handler_filter_string'),
'sort' => array('name' => 'chado_views_handler_sort'),
);
}
elseif (preg_match('/^text/', $field_schema['type'])) {
$defn_array['fields'][$field_name]['handlers'] = array(
'field' => array('name' => 'chado_views_handler_field'),
'filter' => array('name' => 'chado_views_handler_filter_string'),
'sort' => array('name' => 'chado_views_handler_sort'),
);
}
elseif (preg_match('/^boolean/', $field_schema['type'])) {
$defn_array['fields'][$field_name]['handlers'] = array(
'field' => array('name' => 'chado_views_handler_field_boolean'),
'filter' => array('name' => 'chado_views_handler_filter_boolean_operator'),
'sort' => array('name' => 'chado_views_handler_sort'),
);
}
elseif (preg_match('/^datetime/', $field_schema['type'])) {
$defn_array['fields'][$field_name]['handlers'] = array(
'field' => array('name' => 'chado_views_handler_field_date'),
'filter' => array('name' => 'chado_views_handler_filter_date'),
'sort' => array('name' => 'views_handler_sort_date'),
);
}
else {
$defn_array['fields'][$field_name]['handlers'] = array(
'field' => array('name' => 'chado_views_handler_field'),
'filter' => array('name' => 'chado_views_handler_filter_string'),
'sort' => array('name' => 'chado_views_handler_sort'),
);
}
// Specify specialty handlers
if ($field_name == 'type_id' OR $field_name == 'cvterm_id') {
$defn_array['fields'][$field_name]['handlers']['filter']['name'] = 'tripal_views_handler_filter_select_cvterm';
}
}
}
// Add Joins & Relationship Handlers to fields
if (!isset($schema['foreign keys'])) {
$schema['foreign keys'] = array();
watchdog('tripal_views', 'There are no foreign keys defined for %table in the Chado Schema API.', array('%table' => $table_name), WATCHDOG_WARNING);
}
foreach ($schema['foreign keys'] as $foreign_key_schema) {
foreach ($foreign_key_schema['columns'] as $left_field => $right_field) {
// Join
$defn_array['fields'][$left_field]['joins'][ $foreign_key_schema['table'] ] = array(
'table' => $foreign_key_schema['table'],
'field' => $right_field,
'handler' => 'views_handler_join_chado_aggregator'
);
// Relationship Handler
$defn_array['fields'][$left_field]['handlers']['relationship'] = array(
'name' => 'chado_views_handler_relationship',
'base' => $foreign_key_schema['table'],
'base field' => $right_field,
'label' => $table_name . ' ' . $left_field . ' to ' . $foreign_key_schema['table'] . ' ' . $right_field
);
}
}
return $defn_array;
}
| tripal_views_get_lightest_priority_setup | ( | $ | table_name | ) |
Retrieve the views integration setup with the lightest priority for a given table
NOTE: Uses lightest priority (drupal-style) where the range is from -10 to 10 and -10 is of highest priority.
| $table_name | The name of the table to retrieve the setup ID for. This can be either a materialized view or a chado table |
Definition at line 48 of file tripal_views.api.inc.
{
$sql = "SELECT setup_id FROM {tripal_views} WHERE table_name='%s' ORDER BY priority ASC";
$setup = db_fetch_object(db_query($sql, $table_name));
if ($setup) {
return $setup->setup_id;
}
else {
return FALSE;
}
}
| tripal_views_get_table_lightest_priority | ( | $ | table_name | ) |
Retrieve the priority of the lightest priority for a given table
NOTE: Uses lightest priority (drupal-style) where the range is from -10 to 10 and -10 is of highest priority.
| $table_name | The name of the table to retrieve the setup ID for. This can be either a materialized view or a chado table |
Definition at line 22 of file tripal_views.api.inc.
{
$sql = "SELECT priority FROM {tripal_views} WHERE table_name='%s' ORDER BY priority ASC";
$setup = db_fetch_object(db_query($sql, $table_name));
if ($setup) {
return $setup->priority;
}
else {
// default priority is 10
return 10;
}
}
| tripal_views_integrate_all_chado_tables | ( | ) |
Integrate all chado tables in the schema api. This integration only occurs once and sets all Chado tables to a priority of 10
Definition at line 425 of file tripal_views.api.inc.
{
$tables = tripal_core_get_chado_tables(TRUE);
foreach ($tables as $tablename) {
$priority = 10;
if (!tripal_views_is_integrated($tablename, $priority)) {
$table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename, TRUE, $priority);
if ($table_integration_array) {
tripal_views_integration_add_entry($table_integration_array);
}
}
}
}
| tripal_views_integration_add_entry | ( | $ | defn_array | ) |
Add views integration records into the tripal_views* tables
| $defn_array | An array describing the structure and fields of the table |
Example usage (in hook_install()):
$defn_array = array(
'table' => 'feature', //tablename or materialized view name
'name' => 'Sequence Features', // Human readable name
'type' => 'chado', //either chado or mview depending on tablename
'description' => 'Create a listing of features.', //description seen when creating a view of this type
'priority' => 10, //For Base tripal modules: 10; custom modules: 9 to 0;
'base_table' => TRUE //either TRUE or FALSE depending on whether the current table should show up in the add view list
'fields' => array(
'feature_id' => array(
'name' => 'feature_id', //field name in database
'title' => 'Feature ID', //human-readable name -seen in Views UI
'description' => 'This is the unique identifier for features', //help/description seen in Views UI
'type' => 'int', // the type of field
'handlers' => array( //possible keys are field, filter, sort, argument, relationship
'field' => array(
'name' => 'chado_views_handler_numeric' //name of handler
),
'filter' => array( ... ),
...
),
'join' => array( //describe a table that joins to this one via this field
'table' => 'featureprop', //table to join to
'field' => 'feature_id', //field in above table (featureprop)
'handler' => 'views_handler_join_chado_aggregator', //handler to use
),
)
),
);
tripal_views_integration_add_entry($defn_array);
Definition at line 155 of file tripal_views.api.inc.
{
$no_errors = TRUE;
if (empty($defn_array['table'])) {
watchdog('tripal_views','Recieved integration with no tablename: %defn', array('%defn' => print_r($defn_array,TRUE)), WATCHDOG_WARNING);
$no_errors = FALSE;
return $no_errors;
}
// First insert into tripal_views
$view_record = array(
'table_name' => $defn_array['table'],
'name' => $defn_array['name'],
'comment' => $defn_array['description'],
'priority' => $defn_array['priority'],
'base_table' => $defn_array['base_table'],
);
if ($defn_array['type'] == 'mview') {
$mview = db_fetch_object(db_query("SELECT mview_id FROM {tripal_mviews} WHERE mv_table='%s'", $defn_array['table']));
$view_record['mview_id'] = $mview->mview_id;
if (!$mview->mview_id) {
return FALSE;
}
}
if ($view_record['name']) { // && $view_record['comment']) { # SPF: commented out 9/24/2012 .. It's not required on the form
if ($defn_array['additional_content']) {
$setup = db_fetch_object(db_query("SELECT * FROM {tripal_views} WHERE table_name='%s' AND priority=%d", $view_record['table_name'], $view_record['priority']));
if (empty($setup->setup_id)) {
$status = drupal_write_record('tripal_views', $view_record);
}
else {
$view_record['setup_id'] = $setup->setup_id;
$status = drupal_write_record('tripal_views', $view_record, 'setup_id');
}
}
else {
$status = drupal_write_record('tripal_views', $view_record);
}
}
else {
$status = FALSE;
drupal_set_message(t('Unable to integrate "%table" table due to a missing name field.', array('%table' => $defn_array['table'])), 'error');
}
if ($status) {
// Need to update the tripal_views record so base_table can be false
// this is a fix because drupal_write_record() puts in defaults if !isset()
// and a variable is considered not set if it's null!
db_query(
"UPDATE {tripal_views} SET base_table=%d WHERE table_name='%s' AND priority=%d",
$defn_array['base_table'],
$defn_array['table'],
$defn_array['priority']
);
// Insert Field Definitions
foreach ($defn_array['fields'] as $field) {
$field_record = array(
'setup_id' => $view_record['setup_id'],
'column_name' => $field['name'],
'name' => $field['title'],
'description' => $field['description'],
'type' => $field['type'],
);
if ($view_record['setup_id'] && $field['name'] && $field['title'] && $field['description'] && $field['type']) {
if ($defn_array['additional_content']) {
$is = db_fetch_object(db_query("SELECT true as present FROM {tripal_views_field} WHERE column_name='%s' AND setup_id=%d", $field_record['column_name'], $field_record['setup_id']));
if (!$is->present) {
$status = drupal_write_record('tripal_views_field', $field_record);
}
else {
$status = drupal_write_record('tripal_views_field', $field_record, array('setup_id', 'column_name'));
}
}
else {
$status = drupal_write_record('tripal_views_field', $field_record);
}
}
else {
drupal_set_message(t('Unable to integrate %name field due to missing required fields.', array('%name' => $field['name'])), 'error');
$status = FALSE;
}
if ($status) {
// Insert Handler Definitions
foreach ($field['handlers'] as $handler_type => $handler) {
$handler_record = array(
'setup_id' => $view_record['setup_id'],
'column_name' => $field['name'],
'handler_type' => $handler_type,
'handler_name' => $handler['name'],
'arguments' => serialize($handler)
);
if ($view_record['setup_id'] && $field['name'] && $handler_type && $handler['name'] && $handler) {
$status = drupal_write_record('tripal_views_handlers', $handler_record);
}
else {
$status = FALSE;
}
if (!$status) {
drupal_set_message(t('Unable to integrate %handler_type handler: %handler_name', array('%handler_type' => $handler_type, '%handler_name' => $handler['name'])), 'error');
$no_errors = FALSE;
}
}
// Insert Joins
if (!is_array($field['joins'])) {
$field['joins'] = array();
}
foreach ($field['joins'] as $join) {
$join_record = array(
'setup_id' => $view_record['setup_id'],
'base_table' => $defn_array['table'],
'base_field' => $field['name'],
'left_table' => $join['table'],
'left_field' => $join['field'],
);
if (!empty($join['handler'])) {
$join_record['handler'] = $join['handler'];
}
else {
$join_record['handler'] = 'views_join';
}
if ($view_record['setup_id'] && $defn_array['table'] && $field['name'] && $join['table'] && $join['field']) {
$status = drupal_write_record('tripal_views_join', $join_record);
}
else {
$status = FALSE;
}
if (!$status) {
drupal_set_message(
t(
'Unable to join %left_table.%left_field with %table.%field',
array(
'%left_table' => $join['table'],
'%left_field' => $join['field'],
'%table' => $defn_array['table'],
'%field' => $field['name']
)
),
'error'
);
$no_errors = FALSE;
}
}
}
else {
drupal_set_message(t('Unable to integrate %field_name field', array('%field_name' => $field['name'])), 'error');
$no_errors = FALSE;
}
}
}
else {
drupal_set_message(t('Unable to set default tripal views integration'), 'error');
$no_errors = FALSE;
}
return $no_errors;
}
| tripal_views_integration_export_entry | ( | $ | setup_id | ) |
Export Views integration records
| $setup_id | The unique setup id of the tripal views integration |
Definition at line 330 of file tripal_views.api.inc.
{
// Main setup details
$r = db_fetch_object(db_query("SELECT * FROM {tripal_views} WHERE setup_id=%d", $setup_id));
$defn_array = array(
'table' => $r->table_name,
'name' => $r->name,
'type' => ($r->mview_id) ? 'mview' : 'chado',
'description' => $r->comment,
'priority' => $r->priority,
'base_table' => $r->base_table,
'fields' => array(),
);
// Add fields
$resource = db_query("SELECT * FROM {tripal_views_field} WHERE setup_id=%d", $setup_id);
while ($r = db_fetch_object($resource)) {
$defn_array['fields'][ $r->column_name ] = array(
'name' => $r->column_name,
'title' => $r->name,
'description' => $r->description,
'type' => $r->type,
'handlers' => array(),
'joins' => array()
);
}
// Add handlers
$resource = db_query("SELECT * FROM {tripal_views_handlers} WHERE setup_id=%d", $setup_id);
while ($r = db_fetch_object($resource)) {
$defn_array['fields'][ $r->column_name ]['handlers'][ $r->handler_type ] = array(
'name' => $r->handler_name
);
}
// Add joins
$resource = db_query("SELECT * FROM {tripal_views_join} WHERE setup_id=%d", $setup_id);
while ($r = db_fetch_object($resource)) {
$defn_array['fields'][ $r->base_field ]['joins'][ $r->left_table ] = array(
'table' => $r->left_table,
'field' => $r->left_field,
'handler' => $r->handler,
);
}
return $defn_array;
}
| tripal_views_integration_remove_entry_by_setup_id | ( | $ | setup_id | ) |
Removes a View Integration Entry
| $setup_id | The setup ID of the views integration entry to remove |
Definition at line 412 of file tripal_views.api.inc.
{
db_query('DELETE FROM {tripal_views} WHERE setup_id=%d', $setup_id);
db_query('DELETE FROM {tripal_views_field} WHERE setup_id=%d', $setup_id);
db_query('DELETE FROM {tripal_views_handlers} WHERE setup_id=%d', $setup_id);
db_query('DELETE FROM {tripal_views_join} WHERE setup_id=%d', $setup_id);
}
| tripal_views_integration_remove_entry_by_table_name | ( | $ | table_name, |
| $ | priority | ||
| ) |
Removes a View Integration Entry
| $table_name | The name of the table to remove a views integration entry for |
| $priority | The priority of the of views integration entry |
Definition at line 389 of file tripal_views.api.inc.
{
$views = db_fetch_object(db_query(
"SELECT * FROM {tripal_views} WHERE table_name='%s' AND priority=%d",
$table_name,
$priority
));
if ($views->setup_id) {
tripal_views_integration_remove_entry_by_setup_id($views->setup_id);
return TRUE;
}
else {
return FALSE;
}
}
| tripal_views_is_integrated | ( | $ | table_name, |
| $ | priority = NULL |
||
| ) |
Check to see if this table already has an integration record with the given priority
| $table_name | The name of the table to check for integration |
| $priority | (optional) The priority of record to check for |
Definition at line 73 of file tripal_views.api.inc.
{
if ($priority) {
$sql = "SELECT setup_id FROM {tripal_views} WHERE table_name='%s' AND priority=%d";
$setup = db_fetch_object(db_query($sql, $table_name, $priority));
}
else {
$sql = "SELECT setup_id FROM {tripal_views} WHERE table_name='%s' ORDER BY priority ASC";
$setup = db_fetch_object(db_query($sql, $table_name));
}
if ($setup) {
return $setup->setup_id;
}
else {
return FALSE;
}
}
| tripal_views_is_lightest_priority_setup | ( | $ | setup_id, |
| $ | table_name | ||
| ) |
Checks if you are dealing with the lightest priority setup for a given table
| $setup_id | The ID of the setup to check (is this setup the lightest one?) |
| $table_name | The name of the table associated with this setup |
Definition at line 101 of file tripal_views.api.inc.
{
$lightest_priority_setup_id = tripal_views_get_lightest_priority_setup($table_name);
if ($lightest_priority_setup_id == $setup_id) {
return TRUE;
}
else {
return FALSE;
}
}
1.7.4