$items,
'title' => '',
'type' => 'ul',
'attributes' => [],
]);
drupal_set_message('Please note: the upgrade of Chado from v1.2 to v1.3 may
require several fixes to your database. Please review the following
list to ensure a safe upgrade. The Tripal upgrader is
not able to fix these problems automatically: ' . $list, 'warning');
}
if ($form_state['values']['action_to_do'] == "Install Chado v1.3" or
$form_state['values']['action_to_do'] == "Install Chado v1.2" or
$form_state['values']['action_to_do'] == "Install Chado v1.11") {
drupal_set_message('Please note: if Chado is already installed it will
be removed and recreated and all data will be lost. If this is
desired or if this is the first time Chado has been installed
you can ignore this issue.', 'warning');
}
}
$form['current_version'] = [
'#type' => 'item',
'#title' => t("Current installed version of Chado:"),
'#description' => $real_version,
];
$form['action_to_do'] = [
'#type' => 'select',
'#title' => 'Installation/Upgrade Action',
'#options' => [
'Install Chado v1.3' => t('New Install of Chado v1.3 (erases all existing Chado data if Chado already exists)'),
'Upgrade Chado v1.2 to v1.3' => t('Upgrade existing Chado v1.2 to v1.3 (no data is lost)'),
'Install Chado v1.2' => t('New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)'),
'Upgrade Chado v1.11 to v1.2' => t('Upgrade existing Chado v1.11 to v1.2 (no data is lost)'),
'Install Chado v1.11' => t('New Install of Chado v1.11 (erases all existing Chado data if Chado already exists)'),
],
'#description' => t('Select an action to perform.'),
'#required' => TRUE,
'#ajax' => [
'callback' => "tripal_chado_load_form_ajax_callback",
'wrapper' => 'tripal_chado_load_form',
'effect' => 'fade',
'method' => 'replace',
],
];
$form['button'] = [
'#type' => 'submit',
'#value' => t('Install/Upgrade Chado'),
];
$form['#prefix'] = '';
$form['#suffix'] = '
';
return $form;
}
/**
* Ajax callback function for the gensas_job_view_panel_form.
*
* @param $form
* @param $form_state
*/
function tripal_chado_load_form_ajax_callback($form, $form_state) {
return $form;
}
function tripal_chado_load_form_validate($form, &$form_state) {
// We do not want to allow re-installation of Chado if other
// Tripal modules are installed. This is because the install files
// of those modules may add content to Chado and reinstalling Chado
// removes that content which may break the modules.
if ($form_state['values']['action_to_do'] == "Install Chado v1.3" or
$form_state['values']['action_to_do'] == "Install Chado v1.2" or
$form_state['values']['action_to_do'] == "Install Chado v1.11") {
$modules = system_get_info('module');
// The tripal_chado_views module should not be included as it's a required
// dependency of tripal_chado
unset($modules['tripal_chado_views']);
$list = [];
foreach ($modules as $mname => $module) {
if (array_key_exists('dependencies', $module) and in_array('tripal_chado', $module['dependencies'])) {
$list[] = $module['name'] . " ($mname)";
}
}
if (count($list) > 0) {
form_set_error("action_to_do", "Chado cannot be installed while other Tripal modules
are enabled. You must fully uninstall the following modules if you
would like to install or re-install chado.
" .
implode("
", $list));
}
}
if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.11 to v1.2") {
// Make sure we are already not at v1.2
$real_version = chado_get_version(TRUE);
if ($real_version == "1.2") {
form_set_error("action_to_do", "You are already at v1.2. There is no need to upgrade.");
}
}
if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.2 to v1.3") {
// Make sure we are already not at v1.3
$real_version = chado_get_version(TRUE);
if ($real_version == "1.3") {
form_set_error("action_to_do", "You are already at v1.3. There is no need to upgrade.");
}
}
}
/**
* Submit Load Chado Schema Form
*
* @ingroup tripal_chado
*/
function tripal_chado_load_form_submit($form, &$form_state) {
global $user;
$action_to_do = trim($form_state['values']['action_to_do']);
$args = [$action_to_do];
$includes = [module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.install')];
tripal_add_job($action_to_do, 'tripal_chado',
'tripal_chado_install_chado', $args, $user->uid, 10, $includes);
}
/**
* Submit Load Chado Schema Form
*
* @ingroup tripal_chado
*/
function tripal_chado_load_drush_submit($version) {
$args = [$version];
$includes = [module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.install')];
tripal_add_job($version, 'tripal_chado',
'tripal_chado_install_chado', $args, 1, 10, $includes);
}
/**
* Install Chado Schema
*
* @ingroup tripal_chado
*/
function tripal_chado_install_chado($action, TripalJob $job = NULL) {
$vsql = "
INSERT INTO {chadoprop} (type_id, value)
VALUES (
(SELECT cvterm_id
FROM {cvterm} CVT
INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
:version)
";
$vusql = "
UPDATE {chadoprop}
SET value = :version
WHERE type_id = (SELECT cvterm_id
FROM {cvterm} CVT
INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
WHERE CV.name = 'chado_properties' AND CVT.name = 'version')
";
$transaction = db_transaction();
try {
if ($action == 'Install Chado v1.3') {
tripal_chado_install_chado_1_3();
chado_query($vsql, [':version' => '1.3']);
}
elseif ($action == 'Upgrade Chado v1.2 to v1.3') {
tripal_chado_upgrade_chado_1_2_to_1_3();
chado_query($vusql, [':version' => '1.3']);
}
elseif ($action == 'Install Chado v1.2') {
tripal_chado_install_chado_1_2();
chado_query($vsql, [':version' => '1.2']);
}
elseif ($action == 'Upgrade Chado v1.11 to v1.2') {
tripal_chado_upgrade_chado_1_11_to_1_2();
chado_query($vsql, [':version' => '1.2']);
}
elseif ($action == 'Install Chado v1.11') {
tripal_chado_install_chado_1_11();
}
} catch (Exception $e) {
$transaction->rollback();
tripal_chado_install_done();
tripal_report_error('tripal_chado', TRIPAL_ERROR, $e->getMessage(), ['print' => TRUE]);
return FALSE;
}
return TRUE;
}
/**
* Installs Chado v1.3.
*/
function tripal_chado_install_chado_1_3(TripalJob $job = NULL) {
// Get the path to the schema and init SQL files.
$schema_file = drupal_get_path('module', 'tripal_chado') .
'/chado_schema/default_schema-1.3.sql';
$init_file = drupal_get_path('module', 'tripal_chado') .
'/chado_schema/initialize-1.3.sql';
// Erase the Chado schema if it exists and perform the install.
if (tripal_chado_reset_chado_schema()) {
$success = tripal_chado_install_sql($schema_file);
if ($success) {
print "Install of Chado v1.3 (Step 1 of 2) Successful!\n";
}
else {
throw new Exception("Installation (Step 1 of 2) Problems! Please check output above for errors.");
}
$success = tripal_chado_install_sql($init_file);
if ($success) {
print "Install of Chado v1.3 (Step 2 of 2) Successful.\nInstallation Complete\n";
}
else {
throw new Exception("Installation (Step 2 of 2) Problems! Please check output above for errors.");
}
}
else {
throw new Exception("ERROR: cannot install chado. Please check database permissions");
}
}
/**
* Installs Chado v1.2.
*/
function tripal_chado_install_chado_1_2() {
// Get the path to the schema and init SQL files.
$schema_file = drupal_get_path('module', 'tripal_chado') .
'/chado_schema/default_schema-1.2.sql';
$init_file = drupal_get_path('module', 'tripal_chado') .
'/chado_schema/initialize-1.2.sql';
// Erase the Chado schema if it exists and perform the install.
if (tripal_chado_reset_chado_schema()) {
$success = tripal_chado_install_sql($schema_file);
if ($success) {
print "Install of Chado v1.2 (Step 1 of 2) Successful!\n";
}
else {
throw new Exception("Installation (Step 1 of 2) Problems! Please check output above for errors.");
}
$success = tripal_chado_install_sql($init_file);
if ($success) {
print "Install of Chado v1.2 (Step 2 of 2) Successful.\nInstallation Complete\n";
}
else {
throw new Exception("Installation (Step 2 of 2) Problems! Please check output above for errors.");
}
}
else {
throw new Exception("ERROR: cannot install chado. Please check database permissions");
}
}
/**
*
*/
function tripal_chado_install_chado_1_11() {
// Get the path to the schema and init SQL files.
$schema_file = drupal_get_path('module', 'tripal_chado') .
'/chado_schema/default_schema-1.11.sql';
$init_file = drupal_get_path('module', 'tripal_chado') .
'/chado_schema/initialize-1.11.sql';
// Erase the Chado schema if it exists and perform the install.
if (tripal_chado_reset_chado_schema()) {
$success = tripal_chado_install_sql($schema_file);
if ($success) {
print "Install of Chado v1.11 (Step 1 of 2) Successful!\n";
}
else {
throw new Exception("Installation (Step 1 of 2) Problems! Please check output above for errors.");
}
$success = tripal_chado_install_sql($init_file);
if ($success) {
print "Install of Chado v1.11 (Step 2 of 2) Successful.\nInstallation Complete!\n";
}
else {
throw new Exception("Installation (Step 2 of 2) Problems! Please check output above for errors.");
}
}
else {
throw new Exception("ERROR: cannot install chado. Please check database permissions");
}
}
/**
* Upgrades Chado from v1.2 to v1.3
*/
function tripal_chado_upgrade_chado_1_2_to_1_3() {
// Upgrade some of the custom tables that Tripal created that are now in
// Chado v1.3. We'll do this ahead of time because the upgrade script won't
// upgrade tables if they already exist.
print "Checking for existing v1.3 tables in v1.2 and fixing bigints...\n";
tripal_chado_upgrade_chado_1_2_to_1_3_pre_alter();
// Get the path to the diff schema and upgrade SQL files.
print "Incorporating additional changes...\n";
$diff_file = drupal_get_path('module', 'tripal_chado') .
'/chado_schema/default_schema-1.2-1.3-diff.sql';
$success = tripal_chado_install_sql($diff_file);
if ($success) {
print "Upgrade from v1.2 to v1.3 Successful!\n";
}
else {
throw new Exception("Upgrade problems! Please check output above for errors.");
}
}
/**
* Upgrade custom tables that may match the tables now in Chado v1.3.
*
* There were many new tables that were added to Chado v1.3 that were
* suggested by the Chado user community. Some of those were Tripal users.
* Therefore, to help these Tripal users upgrade more seemlessly this function
* checks if those custom tables already exists, and if so updates them as
* best it can to match. At a minimum it will create the table if it doesn't
* exist and if it does it will change the primary keys and foreign keys to
* be big ints.
*/
function tripal_chado_upgrade_chado_1_2_to_1_3_pre_alter() {
// Include the Chado v1.3 schema definitions.
module_load_include('inc', 'tripal_chado', '/api/tripal_chado.schema_v1.3.api');
// The list of new tables in Chado v1.3
$new_tables = [
'analysis_cvterm',
'analysis_dbxref',
'analysis_pub',
'analysis_relationship',
'contactprop',
'dbprop',
'feature_contact',
'featuremap_contact',
'featuremap_dbxref',
'featuremap_organism',
'featuremapprop',
'featureposprop',
'library_contact',
'library_expression',
'library_expressionprop',
'library_featureprop',
'library_relationship',
'library_relationship_pub',
'nd_experiment_analysis',
'organism_cvterm',
'organism_cvtermprop',
'organism_pub',
'organism_relationship',
'organismprop_pub',
'phenotypeprop',
'phylotreeprop',
'project_analysis',
'project_dbxref',
'project_feature',
'project_stock',
'pubauthor_contact',
'stock_feature',
'stock_featuremap',
'stock_library',
'stockcollection_db',
];
// Get the name of the chado schema.
$chado_schema = chado_get_schema_name('chado');
// Iterate through the new Chado tables and create them or if they already
// exist then update them.
foreach ($new_tables as $table) {
// Get the schema for this table.
$function = 'tripal_chado_chado_schema_v1_3_' . $table;
$schema = $function();
// If the table exists then fix the pkeys and fkeys.
if (chado_table_exists($table)) {
// Update the primary key fields to be bigints.
$fields = $schema['fields'];
foreach ($fields as $field_name => $field) {
if ($field['type'] == 'serial') {
if (chado_column_exists($table, $field_name)) {
$sql = 'ALTER TABLE {' . $table . '} ALTER COLUMN ' . $field_name . ' TYPE bigint';
chado_query($sql);
}
else {
throw new Exception('Could not alter primary key to bigint: ' . $table . '.' . $field_name);
}
}
}
// Update the foreign key fields to be bigints.
$fkeys = $schema['foreign keys'];
foreach ($fkeys as $fktable => $details) {
foreach ($details['columns'] as $leftkey => $rightkey) {
if (chado_column_exists($table, $leftkey)) {
$sql = 'ALTER TABLE {' . $table . '} ALTER COLUMN ' . $leftkey . ' TYPE bigint';
chado_query($sql);
}
else {
throw new Exception('Could not alter foreign key to bigint: ' . $table . '.' . $leftkey);
}
}
}
}
}
// Now create the sequences if they don't already exist.
$sequences = [
'analysis_cvterm_analysis_cvterm_id_seq',
'analysis_dbxref_analysis_dbxref_id_seq',
'analysis_pub_analysis_pub_id_seq',
'analysis_relationship_analysis_relationship_id_seq',
'contactprop_contactprop_id_seq',
'dbprop_dbprop_id_seq',
'feature_contact_feature_contact_id_seq',
'featuremap_contact_featuremap_contact_id_seq',
'featuremap_dbxref_featuremap_dbxref_id_seq',
'featuremap_organism_featuremap_organism_id_seq',
'featuremapprop_featuremapprop_id_seq',
'featureposprop_featureposprop_id_seq',
'library_contact_library_contact_id_seq',
'library_expression_library_expression_id_seq',
'library_expressionprop_library_expressionprop_id_seq',
'library_featureprop_library_featureprop_id_seq',
'library_relationship_library_relationship_id_seq',
'library_relationship_pub_library_relationship_pub_id_seq',
'nd_experiment_analysis_nd_experiment_analysis_id_seq',
'organism_cvterm_organism_cvterm_id_seq',
'organism_cvtermprop_organism_cvtermprop_id_seq',
'organism_pub_organism_pub_id_seq',
'organism_relationship_organism_relationship_id_seq',
'organismprop_pub_organismprop_pub_id_seq',
'phenotypeprop_phenotypeprop_id_seq',
'phylotreeprop_phylotreeprop_id_seq',
'project_analysis_project_analysis_id_seq',
'project_dbxref_project_dbxref_id_seq',
'project_feature_project_feature_id_seq',
'project_stock_project_stock_id_seq',
'pubauthor_contact_pubauthor_contact_id_seq',
'stock_feature_stock_feature_id_seq',
'stock_featuremap_stock_featuremap_id_seq',
'stock_library_stock_library_id_seq',
'stockcollection_db_stockcollection_db_id_seq',
];
foreach ($sequences as $sequence) {
// Now add in the sequences if they don't already exist. There is no
// PostgreSQL 'CREATE SEQUENCE IF NOT EXIST' so we're forced to do it here
// and these create statements were removed from the diff upgrade file.
if (!chado_sequence_exists($sequence)) {
$sql = "CREATE SEQUENCE {" . $sequence . "} START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1";
chado_query($sql);
}
}
}
/**
* Upgrades Chado from v1.11 to v1.2
*/
function tripal_chado_upgrade_chado_1_11_to_1_2() {
// Get the path to the schema diff and upgarde SQL files.
$schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11-1.2-diff.sql';
$init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/upgrade-1.11-1.2.sql';
$success = tripal_chado_install_sql($schema_file);
if ($success) {
print "Upgrade from v1.11 to v1.2 (Step 1 of 2) Successful!\n";
}
else {
throw new Exception("Upgrade (Step 1 of 2) problems! Please check output above for errors.");
}
$success = tripal_chado_install_sql($init_file);
if ($success) {
print "Upgrade from v1.11 to v1.2 (Step 2 of 2) Successful.\nUpgrade Complete!\n";
}
else {
throw new Exception("Upgrade (Step 2 of 2) problems! Please check output above for errors.");
}
}
/**
* Reset the Chado Schema
* This drops the current chado and chado-related schema and re-creates it
*
* @ingroup tripal_chado
*/
function tripal_chado_reset_chado_schema() {
// determine the schema name.
$chado_schema = chado_get_schema_name('chado');
$chado_dot = $chado_schema . '.';
// drop current chado and chado-related schema
if (chado_dbschema_exists('genetic_code')) {
print "Dropping existing 'genetic_code' schema\n";
db_query("drop schema genetic_code cascade");
}
if (chado_dbschema_exists('so')) {
print "Dropping existing 'so' schema\n";
db_query("drop schema so cascade");
}
if (chado_dbschema_exists('frange')) {
print "Dropping existing 'frange' schema\n";
db_query("drop schema frange cascade");
}
if (chado_dbschema_exists($chado_schema)) {
if ($chado_schema != 'chado') {
print "Dropping existing Chado ('$chado_schema') schema\n";
}
else {
print "Dropping existing 'chado' schema\n";
}
db_query("drop schema $chado_schema cascade");
}
// create the new chado schema
print "Creating 'chado' schema\n";
db_query("create schema $chado_schema");
if (chado_dbschema_exists('chado')) {
// before creating the plpgsql language let's check to make sure
// it doesn't already exists
$sql = "SELECT COUNT(*) FROM pg_language WHERE lanname = 'plpgsql'";
$results = db_query($sql);
$count = $results->fetchObject();
if (!$count or $count->count == 0) {
db_query("create language plpgsql");
}
return TRUE;
}
return FALSE;
}
/**
* Execute the provided SQL
*
* @param $sql_file
* Contains SQL statements to be executed
*
* @ingroup tripal_chado
*/
function tripal_chado_install_sql($sql_file) {
$chado_local = chado_dbschema_exists('chado');
// determine the schema name.
$chado_schema = chado_get_schema_name('chado');
$chado_dot = $chado_schema . '.';
if ($chado_local) {
db_query("set search_path to $chado_schema");
}
print "Loading $sql_file...\n";
$lines = file($sql_file, FILE_SKIP_EMPTY_LINES);
if (!$lines) {
return 'Cannot open $schema_file';
}
$stack = [];
$in_string = 0;
$in_function = FALSE;
$query = '';
$i = 0;
$success = 1;
foreach ($lines as $line_num => $line) {
$i++;
$type = '';
// find and remove comments except when inside of strings
if (preg_match('/--/', $line) and !$in_string and !preg_match("/'.*?--.*?'/", $line)) {
$line = preg_replace('/--.*$/', '', $line); // remove comments
}
if (preg_match('/\/\*.*?\*\//', $line)) {
$line = preg_replace('/\/\*.*?\*\//', '', $line); // remove comments
}
// skip empty lines
if (preg_match('/^\s*$/', $line) or strcmp($line, '') == 0) {
continue;
}
// Find SQL for new objects
if (preg_match('/^\s*CREATE\s+TABLE/i', $line) and !$in_string and !$in_function) {
$stack[] = 'table';
$line = preg_replace("/public\./", $chado_dot, $line);
}
if (preg_match('/^\s*ALTER\s+TABLE\s+/i', $line) and !$in_string and !$in_function) {
$stack[] = 'alter_table';
$line = preg_replace("/public\./", $chado_dot, $line);
}
if (preg_match('/^\s*SET/i', $line) and !$in_string and !$in_function) {
$stack[] = 'set';
}
if (preg_match('/^\s*CREATE\s+SCHEMA/i', $line) and !$in_string and !$in_function) {
$stack[] = 'schema';
}
if (preg_match('/^\s*CREATE\s+SEQUENCE/i', $line) and !$in_string and !$in_function) {
$stack[] = 'sequence';
$line = preg_replace("/public\./", $chado_dot, $line);
}
if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*VIEW/i', $line) and !$in_string and !$in_function) {
$stack[] = 'view';
$line = preg_replace("/public\./", $chado_dot, $line);
}
if (preg_match('/^\s*COMMENT/i', $line) and !$in_string and sizeof($stack) == 0 and !$in_function) {
$stack[] = 'comment';
$line = preg_replace("/public\./", $chado_dot, $line);
}
if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*FUNCTION/i', $line) and !$in_string and !$in_function) {
$in_function = TRUE;
$stack[] = 'function';
$line = preg_replace("/public\./", $chado_dot, $line);
}
if (preg_match('/^\s*CREATE\s+INDEX/i', $line) and !$in_string and !$in_function) {
$stack[] = 'index';
}
if (preg_match('/^\s*INSERT\s+INTO/i', $line) and !$in_string and !$in_function) {
$stack[] = 'insert';
$line = preg_replace("/public\./", $chado_dot, $line);
}
if (preg_match('/^\s*CREATE\s+TYPE/i', $line) and !$in_string and !$in_function) {
$stack[] = 'type';
}
if (preg_match('/^\s*GRANT/i', $line) and !$in_string and !$in_function) {
$stack[] = 'grant';
}
if (preg_match('/^\s*CREATE\s+AGGREGATE/i', $line) and !$in_string and !$in_function) {
$stack[] = 'aggregate';
}
if (preg_match('/^\s*DROP\s+FUNCTION/i', $line) and !$in_string and !$in_function) {
$stack[] = 'drop_function';
}
if (preg_match('/^\s*DROP\s+VIEW/i', $line) and !$in_string and !$in_function) {
$stack[] = 'drop_view';
}
if (preg_match('/^\s*DROP\s+INDEX/i', $line) and !$in_string and !$in_function) {
$stack[] = 'drop_index';
}
if (preg_match('/^\s*DROP\s+SEQUENCE/i', $line) and !$in_string and !$in_function) {
$stack[] = 'drop_seq';
}
if (preg_match('/^\s*ALTER\s+TYPE\s+/i', $line) and !$in_string and !$in_function) {
$stack[] = 'alter_type';
}
if (preg_match('/^\s*ALTER\s+SEQUENCE\s+/i', $line) and !$in_string and !$in_function) {
$stack[] = 'alter_seq';
}
// determine if we are in a string that spans a line
$matches = preg_match_all("/[']/i", $line, $temp);
$in_string = $in_string - ($matches % 2);
$in_string = abs($in_string);
// if we've reached the end of an object then pop the stack
if (strcmp($stack[sizeof($stack) - 1], 'table') == 0 and preg_match('/\);\s*$/', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'alter_table') == 0 and preg_match('/;\s*$/', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'set') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'schema') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'sequence') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'view') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'comment') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'function') == 0) {
if (preg_match('/LANGUAGE.*?;\s*$/i', $line)) {
$type = array_pop($stack);
$in_function = FALSE;
//print "FUNCTION DONE ($i): $line";
}
else {
if (preg_match('/\$_\$;\s*$/i', $line)) {
$type = array_pop($stack);
$in_function = FALSE;
//print "FUNCTION DONE ($i): $line";
}
else {
if (preg_match('/\$\$;\s*$/i', $line)) {
$type = array_pop($stack);
$in_function = FALSE;
// print "FUNCTION DONE ($i): $line";
}
else {
// print "FUNCTION ($i): $line";
}
}
}
}
elseif (strcmp($stack[sizeof($stack) - 1], 'index') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'insert') == 0 and preg_match('/\);\s*$/', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'type') == 0 and preg_match('/\);\s*$/', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'grant') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'aggregate') == 0 and preg_match('/\);\s*$/', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'drop_function') == 0 and preg_match('/;\s*$/i', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'drop_view') == 0 and preg_match('/;\s*$/i', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'drop_index') == 0 and preg_match("/;\s*$/i", $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'drop_seq') == 0 and preg_match("/;\s*$/i", $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'alter_type') == 0 and preg_match('/;\s*$/i', $line)) {
$type = array_pop($stack);
}
elseif (strcmp($stack[sizeof($stack) - 1], 'alter_seq') == 0 and preg_match('/;\s*$/i', $line)) {
$type = array_pop($stack);
}
// if we're in a recognized SQL statement then let's keep track of lines
if ($type or sizeof($stack) > 0) {
$query .= "$line";
}
else {
throw new Exception("UNHANDLED $i, $in_string: $line");
}
if (preg_match_all("/\n/", $query, $temp) > 1000) {
throw new Exception("SQL query is too long. Terminating:\n$query\n");
}
if ($type and sizeof($stack) == 0) {
//print "Adding $type: line $i\n";
// rewrite the set search_path to make 'public' be 'chado', but only if the
// chado schema exists
if (strcmp($type, 'set') == 0 and $chado_local) {
$query = preg_replace("/public/m", $chado_schema, $query);
}
// execute the statement
try {
$result = db_query($query);
} catch (Exception $e) {
$error = $e->getMessage();
throw new Exception("FAILED. Line $i, $in_string\n$error:\n$query\n\n");
}
if (!$result) {
$error = pg_last_error();
throw new Exception("FAILED. Line $i, $in_string\n$error:\n$query\n\n");
}
$query = '';
}
}
tripal_chado_install_done();
return $success;
}
/**
* Finish the Chado Schema Installation
*
* @ingroup tripal_chado
*/
function tripal_chado_install_done() {
$drupal_schema = chado_get_schema_name('drupal');
db_query("set search_path to $drupal_schema");
}