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@@ -0,0 +1,2056 @@
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+<?php
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+/**
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+ * @file
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+ * Functions to install chado schema through Drupal
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+ */
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+
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+/**
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+ * Prepares Chado for Tripal use
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+ */
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+function tripal_chado_prepare_form($form, $form_state) {
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+ $form = array();
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+
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+ // we want to force the version of Chado to be set properly
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+ $real_version = chado_get_version(TRUE);
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+
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+ $form['current_version'] = array(
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+ '#type' => 'item',
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+ '#title' => t("Current installed version of Chado:"),
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+ '#description' => $real_version,
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+ );
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+ $form['instructions'] = array(
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+ '#type' => 'item',
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+ '#description' => t("Click the button below to prepare a Chado installation for
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+ use by Tripal. If you used Tripal to install Chado then this step
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+ is not necessary. If Chado was installed outside of Tripal then
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+ it should be prepared. Preparing Chado involves adding of
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+ specific controlled vocabularies, custom tables and materialized views."),
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+ );
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+
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+ $form['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Prepare Chado'),
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+ '#name' => 'prepare-chado',
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+ );
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+ return $form;
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+}
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+
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+/**
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+ * Submit function for the tripal_chado_prepare_form().
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+ *
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+ * @param $form
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+ * @param $form_state
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+ */
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+function tripal_chado_prepare_form_submit($form, $form_state) {
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+ if ($form_state['clicked_button']['#name'] == "prepare-chado") {
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+ global $user;
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+ $args = array();
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+ tripal_add_job('Prepare Chado', 'tripal_chado', 'tripal_chado_prepare_chado', $args, $user->uid);
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+ }
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+}
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+/**
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+ * Load Chado Schema Form
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+ *
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+ * @ingroup tripal_chado
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+ */
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+function tripal_chado_load_form($form, $form_state) {
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+
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+ // we want to force the version of Chado to be set properly
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+ $real_version = chado_get_version(TRUE);
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+
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+ // get the effective version. Pass true as second argument
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+ // to warn the user if the current version is not compatible
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+ $version = chado_get_version(FALSE, TRUE);
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+
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+ $form['current_version'] = array(
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+ '#type' => 'item',
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+ '#title' => t("Current installed version of Chado:"),
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+ '#description' => $real_version,
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+ );
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+
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+ $form['action_to_do'] = array(
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+ '#type' => 'radios',
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+ '#title' => 'Installation/Upgrade Action',
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+ '#options' => array(
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+ 'Install Chado v1.2' => t('New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)'),
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+ 'Upgrade Chado v1.11 to v1.2' => t('Upgrade existing Chado v1.11 to v1.2 (no data is lost)'),
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+ 'Install Chado v1.11' => t('New Install of Chado v1.11 (erases all existing Chado data if Chado already exists)')
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+ ),
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+ '#description' => t('Select an action to perform. If you want to install Chado all other Tripal modules must not be installed.'),
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+ '#required' => TRUE,
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+ );
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+
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+ $form['warning'] = array(
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+ '#markup' => "<div><font color=\"red\">WARNING:</font>" . t('A new install of
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+ Chado will remove and recreate the Chado database if it already exists.') . '</div>',
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+ );
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+
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+ $form['button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Install/Upgrade Chado'),
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+ );
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+
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+ return $form;
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+}
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+
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+function tripal_chado_chado_load_form_validate($form, &$form_state) {
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+ // We do not want to allow re-installation of Chado if other
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+ // Tripal modules are installed. This is because the install files
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+ // of those modules may add content to Chado and reinstalling Chado
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+ // removes that content which may break the modules.
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+
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+ if ($form_state['values']['action_to_do'] == "Install Chado v1.2" or
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+ $form_state['values']['action_to_do'] == "Install Chado v1.11") {
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+
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+ $modules = system_get_info('module');
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+ $list = array();
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+ foreach ($modules as $mname => $module) {
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+ if (array_key_exists('dependencies', $module) and in_array('tripal_chado', $module['dependencies'])) {
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+ $list[] = $module['name'] . " ($mname)";
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+ }
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+ }
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+ if (count($list) > 0) {
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+ form_set_error("action_to_do", "Chado cannot be installed while other Tripal modules
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+ are enabled. You must fully uninstall the following modules if you
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+ would like to install or re-install chado.<br>" .
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+ implode("<br>", $list));
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+ }
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+ }
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+ if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.11 to v1.2") {
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+ // Make sure we are already not at v1.2
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+ $real_version = chado_get_version(TRUE);
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+ if ($real_version == "1.2") {
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+ form_set_error("action_to_do", "You are already at v1.2. There is no need to upgrade.");
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+ }
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+ }
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+}
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+/**
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+ * Submit Load Chado Schema Form
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+ *
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+ * @ingroup tripal_chado
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+ */
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+function tripal_chado_chado_load_form_submit($form, &$form_state) {
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+ global $user;
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+ $action_to_do = trim($form_state['values']['action_to_do']);
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+ $args = array($action_to_do);
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+ tripal_add_job($action_to_do, 'tripal_chado', 'tripal_chado_install_chado', $args, $user->uid);
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+}
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+
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+/**
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+ * Install Chado Schema
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+ *
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+ * @ingroup tripal_chado
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+ */
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+function tripal_chado_install_chado($action) {
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+
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+ $vsql = "
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+ INSERT INTO {chadoprop} (type_id, value)
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+ VALUES (
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+ (SELECT cvterm_id
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+ FROM {cvterm} CVT
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+ INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
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+ WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
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+ :version)
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+ ";
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+
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+ if ($action == 'Install Chado v1.2') {
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+ $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.2.sql';
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+ $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/initialize-1.2.sql';
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+ if (tripal_chado_reset_chado_schema()) {
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+ $success = tripal_chado_install_sql($schema_file);
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+ if ($success) {
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+ print "Install of Chado v1.2 (Step 1 of 2) Successful!\n";
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+ }
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+ else {
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+ print "Installation (Step 1 of 2) Problems! Please check output above for errors.\n";
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+ exit;
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+ }
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+ $success = tripal_chado_install_sql($init_file);
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+ if ($success) {
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+ print "Install of Chado v1.2 (Step 2 of 2) Successful.\nInstallation Complete\n";
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+ }
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+ else {
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+ print "Installation (Step 2 of 2) Problems! Please check output above for errors.\n";
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+ exit;
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+ }
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+ chado_query($vsql, array(':version' => '1.2')); # set the version
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+ }
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+ else {
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+ print "ERROR: cannot install chado. Please check database permissions\n";
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+ exit;
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+ }
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+ }
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+ elseif ($action == 'Upgrade Chado v1.11 to v1.2') {
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+ $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11-1.2-diff.sql';
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+ $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/upgrade-1.11-1.2.sql';
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+ $success = tripal_chado_install_sql($schema_file);
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+ if ($success) {
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+ print "Upgrade from v1.11 to v1.2 (Step 1 of 2) Successful!\n";
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+ }
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+ else {
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+ print "Upgrade (Step 1 of 2) problems! Please check output above for errors.\n";
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+ exit;
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+ }
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+ $success = tripal_chado_install_sql($init_file);
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+ if ($success) {
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+ print "Upgrade from v1.11 to v1.2 (Step 2 of 2) Successful.\nUpgrade Complete!\n";
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+ }
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+ else {
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+ print "Upgrade (Step 2 of 2) problems! Please check output above for errors.\n";
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+ exit;
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+ }
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+ chado_query($vsql, array(':version' => '1.2')); # set the version
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+ }
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+ elseif ($action == 'Install Chado v1.11') {
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+ $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11.sql';
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+ $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/initialize-1.11.sql';
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+ if (tripal_chado_reset_chado_schema()) {
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+ $success = tripal_chado_install_sql($schema_file);
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+ if ($success) {
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+ print "Install of Chado v1.11 (Step 1 of 2) Successful!\n";
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+ }
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+ else {
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+ print "Installation (Step 1 of 2) Problems! Please check output above for errors.\n";
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+ exit;
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+ }
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+ $success = tripal_chado_install_sql($init_file);
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+ if ($success) {
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+ print "Install of Chado v1.11 (Step 2 of 2) Successful.\nInstallation Complete!\n";
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+ }
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+ else {
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+ print "Installation (Step 2 of 2) Problems! Please check output above for errors.\n";
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+ exit;
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+ }
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+ }
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+ else {
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+ print "ERROR: cannot install chado. Please check database permissions\n";
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+ exit;
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+ }
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+ }
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+}
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+
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+/**
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+ * Prepares Chado for use by Tripal.
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+ */
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+function tripal_chado_prepare_chado() {
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+ // we want to force the version of Chado to be set properly
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+ $real_version = chado_get_version(TRUE);
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+
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+ // get the effective version. Pass true as second argument
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+ // to warn the user if the current version is not compatible
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+ $version = chado_get_version(FALSE, FALSE);
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado CV Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Add the cv_root_mview.
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+ tripal_cv_add_cv_root_mview();
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+
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+ // Add defaults to the tables that correlate OBO files/references with
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+ // a chado CV.
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+ tripal_cv_add_obo_defaults();
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+
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+ // Add the Chado ontology CV.
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+ $obo_path = '{tripal_chado}/files/cv_property.obo';
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+ $obo_id = tripal_insert_obo('Chado CV Properties', $obo_path);
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+ tripal_submit_obo_job(array('obo_id' => $obo_id));
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+
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+ // Create the temp table we will use for loading OBO files.
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+ tripal_cv_create_tripal_obo_temp();
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+
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado Organism Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ tripal_insert_cv(
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+ 'organism_property',
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+ 'Contains properties for organisms'
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+ );
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+
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+ // set the default vocabularies
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+ tripal_set_default_cv('organismprop', 'type_id', 'organism_property');
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+
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado CompAnalysis Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ // we may need the analysisfeatureprop table if it doesn't already exist
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+ tripal_analysis_create_analysisfeatureprop();
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+
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+ // add cvterms
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+ tripal_analysis_add_cvterms();
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+
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+ // add materialized views
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+ tripal_analysis_add_mview_analysis_organism();
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+
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+ // set the default vocabularies
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+ tripal_set_default_cv('analysisprop', 'type_id', 'analysis_property');
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado Contact Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Add the contactprop table to Chado.
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+ tripal_contact_add_custom_tables();
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+
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+ // Add loading of the the tripal contact ontology to the job queue.
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+ $obo_path = '{tripal_chado}/files/tcontact.obo';
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+ $obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
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+ tripal_submit_obo_job(array('obo_id' => $obo_id));
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+
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+ // Add cvterms for relationship types.
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+ tripal_contact_add_cvs();
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+
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+ // Set the default vocabularies.
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+ tripal_set_default_cv('contact', 'type_id', 'tripal_contact');
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+ tripal_set_default_cv('contactprop', 'type_id', 'tripal_contact');
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+ tripal_set_default_cv('contact_relationship', 'type_id', 'contact_relationship');
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado Feature Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Note: the feature_property OBO that came with Chado v1.2 should not
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+ // be automatically installed. Some of the terms are duplicates of
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+ // others in better maintained vocabularies. New Tripal sites should
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+ // use those.
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+ // $obo_path = '{tripal_feature}/files/feature_property.obo';
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+ // $obo_id = tripal_insert_obo('Chado Feature Properties', $obo_path);
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+ // tripal_submit_obo_job(array('obo_id' => $obo_id));
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+
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+ // Add the materialized view.
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+ tripal_feature_add_organism_count_mview();
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+
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+ // Add the custom tables.
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+ tripal_feature_add_tripal_gff_temp_table();
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+ tripal_feature_add_tripal_gffcds_temp_table();
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+ tripal_feature_add_tripal_gffprotein_temp_table();
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+
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+ // Add the vocabularies used by the feature module.
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+ tripal_feature_add_cvs();
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+
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+ // Set the default vocabularies.
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+ tripal_set_default_cv('feature', 'type_id', 'sequence');
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+ tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
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+ tripal_set_default_cv('feature_relationship', 'type_id', 'feature_relationship');
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado Map Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ // add the featuremapprop table to Chado
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+ tripal_featuremap_add_custom_tables();
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+
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+ // Add cvterms
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+ tripal_featuremap_add_cvs();
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+ tripal_featuremap_add_cvterms();
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+
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+ // set the default vocabularies
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+ tripal_set_default_cv('featuremapprop', 'type_id', 'featuremap_property');
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+ tripal_set_default_cv('featureposprop', 'type_id', 'featurepos_property');
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+ tripal_set_default_cv('featuremap', 'unittype_id', 'featuremap_units');
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado Library Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ // add the materialized view
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+ tripal_library_add_mview_library_feature_count();
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+
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+ // add cvterms
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+ tripal_library_add_cvs();
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+ tripal_library_add_cvterms();
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+
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+ // set the default vocabularies
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+ tripal_set_default_cv('libraryprop', 'type_id', 'library_property');
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+ tripal_set_default_cv('library', 'type_id', 'library_type');
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado NatDiv Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ // add cvterms
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+ tripal_natural_diversity_add_cvterms();
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado Project Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ tripal_project_add_cvs();
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+ tripal_project_add_cvterms();
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+
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+ // set the default vocabularies
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+ tripal_set_default_cv('projectprop', 'type_id', 'project_property');
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+ tripal_set_default_cv('project_relationship', 'type_id', 'project_relationship');
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+
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+ /////////////////////////////////////////////////////////////////////////////
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+ // Chado Pub Module
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+ /////////////////////////////////////////////////////////////////////////////
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+ global $base_path;
|
|
|
+
|
|
|
+ // add loading of the the tripal pub ontology to the job queue
|
|
|
+ $obo_path = '{tripal}/files/tpub.obo';
|
|
|
+ $obo_id = tripal_insert_obo('Tripal Publication', $obo_path);
|
|
|
+ tripal_submit_obo_job(array('obo_id' => $obo_id));
|
|
|
+
|
|
|
+ tripal_pub_add_cvs();
|
|
|
+
|
|
|
+ // add the custom tables
|
|
|
+ tripal_pub_add_custom_tables();
|
|
|
+
|
|
|
+ // set the default vocabularies
|
|
|
+ tripal_set_default_cv('pub', 'type_id', 'tripal_pub');
|
|
|
+ tripal_set_default_cv('pubprop', 'type_id', 'tripal_pub');
|
|
|
+ tripal_set_default_cv('pub_relationship', 'type_id', 'pub_relationship');
|
|
|
+
|
|
|
+ /////////////////////////////////////////////////////////////////////////////
|
|
|
+ // Chado Stock Module
|
|
|
+ /////////////////////////////////////////////////////////////////////////////
|
|
|
+ // add some controlled vocabularies
|
|
|
+ tripal_stock_add_cvs();
|
|
|
+
|
|
|
+ // set the default vocabularies
|
|
|
+ tripal_set_default_cv('stock', 'type_id', 'stock_type');
|
|
|
+ tripal_set_default_cv('stockprop', 'type_id', 'stock_property');
|
|
|
+ tripal_set_default_cv('stock_relationship', 'type_id', 'stock_relationship');
|
|
|
+
|
|
|
+ // add the materialized view
|
|
|
+ tripal_stock_add_organism_count_mview();
|
|
|
+
|
|
|
+ /////////////////////////////////////////////////////////////////////////////
|
|
|
+ // Entity Bundles
|
|
|
+ /////////////////////////////////////////////////////////////////////////////
|
|
|
+
|
|
|
+ // Unfortunately, some Chado base tables do not have a type_id, so we must
|
|
|
+ // take special action for those tables. These include: organism and
|
|
|
+ // analysis. Until we can find an appropriate controlled vocabulary
|
|
|
+ // that is well supported by the community with types for these tables we
|
|
|
+ // will have to use in-house terms.
|
|
|
+
|
|
|
+ // Add a term to be used for an inherent 'type_id' for the organism table.
|
|
|
+ tripal_insert_cvterm(array(
|
|
|
+ 'id' => 'local:organism',
|
|
|
+ 'name' => 'organism',
|
|
|
+ 'definition' => 'An individual form of life, such as a bacterium, protist, ' .
|
|
|
+ 'fungus, plant, or animal, composed of a single cell or a complex of cells ' .
|
|
|
+ 'in which organelles or organs work together to carry out the various ' .
|
|
|
+ 'processes of life. (American Heritage® Dictionary of the English ' .
|
|
|
+ 'Language, Fifth Edition. Copyright © 2011 by Houghton Mifflin ' .
|
|
|
+ 'Harcourt Publishing Company).',
|
|
|
+ 'cv_name' => 'local',
|
|
|
+ ));
|
|
|
+
|
|
|
+ // Add a term to be used for an inherent 'type_id' for the organism table.
|
|
|
+ tripal_insert_cvterm(array(
|
|
|
+ 'id' => 'local:analysis',
|
|
|
+ 'name' => 'analysis',
|
|
|
+ 'definition' => 'A process as a method of studying the nature of something ' .
|
|
|
+ 'or of determining its essential features and their relations. ' .
|
|
|
+ '(Random House Kernerman Webster\'s College Dictionary, © 2010 K ' .
|
|
|
+ 'Dictionaries Ltd).',
|
|
|
+ 'cv_name' => 'local',
|
|
|
+ ));
|
|
|
+
|
|
|
+ tripal_insert_cvterm(array(
|
|
|
+ 'id' => 'local:project',
|
|
|
+ 'name' => 'project',
|
|
|
+ 'definition' => 'A plan or proposal for accomplishing something. ' .
|
|
|
+ '(American Heritage® Dictionary of the English Language, Fifth Edition. ' .
|
|
|
+ 'Copyright © 2011 by Houghton Mifflin Harcourt Publishing Company).',
|
|
|
+ 'cv_name' => 'local',
|
|
|
+ ));
|
|
|
+
|
|
|
+ // For the TripalBundle entities we will want to associate the cvterm_id,
|
|
|
+ // and the chado table and field that it maps to. We will use a few
|
|
|
+ // variables to do this:
|
|
|
+ tripal_insert_variable('chado_cvterm_id', 'The cvterm_id that a TripalBundle maps to.');
|
|
|
+ tripal_insert_variable('chado_table', 'The name of the table to which a TripalBundle maps.');
|
|
|
+ tripal_insert_variable('chado_column', 'The name of the column within the table that a TripalBundle maps to.');
|
|
|
+
|
|
|
+ // We want to provide a set of commonly used entity types by default. This
|
|
|
+ // way when a user first installs Tripal there are some commonly used
|
|
|
+ // formats.
|
|
|
+ module_load_include('inc', 'tripal', 'api/tripal.api');
|
|
|
+ module_load_include('inc', 'tripal', 'includes/tripal.admin');
|
|
|
+
|
|
|
+ // Create the 'Organism' entity type. This uses the local:organism term.
|
|
|
+ $error = '';
|
|
|
+ $term = array('name' => 'organism', 'cv_id' => array('name' => 'local'));
|
|
|
+ $cvterm = chado_generate_var('cvterm', $term);
|
|
|
+ if (!tripal_create_bundle('local', 'organism', 'organism', $error)) {
|
|
|
+ throw new Exception($error);
|
|
|
+ }
|
|
|
+
|
|
|
+ // Create the 'Analysis' entity type. This uses the local:analysis term.
|
|
|
+ $error = '';
|
|
|
+ $term = array('name' => 'analysis', 'cv_id' => array('name' => 'local'));
|
|
|
+ $cvterm = chado_generate_var('cvterm', $term);
|
|
|
+ if (!tripal_create_bundle('local', 'analysis', 'analysis', $error)) {
|
|
|
+ throw new Exception($error);
|
|
|
+ }
|
|
|
+
|
|
|
+ // Create the 'Project' entity type. This uses the local:project term.
|
|
|
+ $error = '';
|
|
|
+ $term = array('name' => 'project', 'cv_id' => array('name' => 'local'));
|
|
|
+ $cvterm = chado_generate_var('cvterm', $term);
|
|
|
+ if (!tripal_create_bundle('local', 'project', 'project', $error)) {
|
|
|
+ throw new Exception($error);
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * 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() {
|
|
|
+
|
|
|
+ // 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')) {
|
|
|
+ print "Dropping existing 'chado' schema\n";
|
|
|
+ db_query("drop schema chado cascade");
|
|
|
+ }
|
|
|
+
|
|
|
+ // create the new chado schema
|
|
|
+ print "Creating 'chado' schema\n";
|
|
|
+ db_query("create schema chado");
|
|
|
+ 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) {
|
|
|
+
|
|
|
+ $chado_local = chado_dbschema_exists('chado');
|
|
|
+
|
|
|
+ if ($chado_local) {
|
|
|
+ db_query("set search_path to chado");
|
|
|
+ }
|
|
|
+ print "Loading $sql_file...\n";
|
|
|
+ $lines = file($sql_file, FILE_SKIP_EMPTY_LINES);
|
|
|
+
|
|
|
+ if (!$lines) {
|
|
|
+ return 'Cannot open $schema_file';
|
|
|
+ }
|
|
|
+
|
|
|
+ $stack = array();
|
|
|
+ $in_string = 0;
|
|
|
+ $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) {
|
|
|
+ $stack[] = 'table';
|
|
|
+ $line = preg_replace("/public\./", "chado.", $line);
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*ALTER\s+TABLE/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'alter table';
|
|
|
+ $line = preg_replace("/public\./", "chado.", $line);
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*SET/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'set';
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*CREATE\s+SCHEMA/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'schema';
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*CREATE\s+SEQUENCE/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'sequence';
|
|
|
+ $line = preg_replace("/public\./", "chado.", $line);
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*VIEW/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'view';
|
|
|
+ $line = preg_replace("/public\./", "chado.", $line);
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*COMMENT/i', $line) and !$in_string and sizeof($stack)==0) {
|
|
|
+ $stack[] = 'comment';
|
|
|
+ $line = preg_replace("/public\./", "chado.", $line);
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*FUNCTION/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'function';
|
|
|
+ $line = preg_replace("/public\./", "chado.", $line);
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*CREATE\s+INDEX/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'index';
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*INSERT\s+INTO/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'insert';
|
|
|
+ $line = preg_replace("/public\./", "chado.", $line);
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*CREATE\s+TYPE/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'type';
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*GRANT/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'grant';
|
|
|
+ }
|
|
|
+ if (preg_match('/^\s*CREATE\s+AGGREGATE/i', $line) and !$in_string) {
|
|
|
+ $stack[] = 'aggregate';
|
|
|
+ }
|
|
|
+
|
|
|
+ // 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 the pop the stack
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'table') == 0 and preg_match('/\);\s*$/', $line)) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'alter table') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'set') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'schema') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'sequence') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'view') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'comment') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'function') == 0 and preg_match("/LANGUAGE.*?;\s+$/i", $line)) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'index') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'insert') == 0 and preg_match('/\);\s*$/', $line)) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'type') == 0 and preg_match('/\);\s*$/', $line)) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'grant') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
|
|
|
+ $type = array_pop($stack);
|
|
|
+ }
|
|
|
+ if (strcmp($stack[sizeof($stack)-1], 'aggregate') == 0 and preg_match('/\);\s*$/', $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 {
|
|
|
+ print "UNHANDLED $i, $in_string: $line";
|
|
|
+ tripal_chado_chado_install_done();
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ if (preg_match_all("/\n/", $query, $temp) > 100) {
|
|
|
+ print "SQL query is too long. Terminating:\n$query\n";
|
|
|
+ tripal_chado_chado_install_done();
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ 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", $query);
|
|
|
+ }
|
|
|
+
|
|
|
+ // execute the statement
|
|
|
+ $result = db_query($query);
|
|
|
+
|
|
|
+ if (!$result) {
|
|
|
+ $error = pg_last_error();
|
|
|
+ print "FAILED. Line $i, $in_string\n$error:\n$query\n\n";
|
|
|
+ tripal_chado_chado_install_done();
|
|
|
+ $success = 0;
|
|
|
+ return $success;
|
|
|
+ }
|
|
|
+ $query = '';
|
|
|
+ }
|
|
|
+ }
|
|
|
+ tripal_chado_chado_install_done();
|
|
|
+ return $success;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Finish the Chado Schema Installation
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado
|
|
|
+ */
|
|
|
+function tripal_chado_chado_install_done() {
|
|
|
+
|
|
|
+ db_query("set search_path to default");
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Creates a materialized view that stores the type & number of stocks per organism
|
|
|
+ *
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_add_organism_count_mview() {
|
|
|
+ $view_name = 'organism_stock_count';
|
|
|
+ $comment = 'Stores the type and number of stocks per organism';
|
|
|
+
|
|
|
+ $schema = array(
|
|
|
+ 'description' => $comment,
|
|
|
+ 'table' => $view_name,
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genus' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'species' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'common_name' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_stocks' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_type' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_stock_count_idx1' => array('organism_id'),
|
|
|
+ 'organism_stock_count_idx2' => array('cvterm_id'),
|
|
|
+ 'organism_stock_count_idx3' => array('stock_type'),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT
|
|
|
+ O.organism_id, O.genus, O.species, O.common_name,
|
|
|
+ count(S.stock_id) as num_stocks,
|
|
|
+ CVT.cvterm_id, CVT.name as stock_type
|
|
|
+ FROM organism O
|
|
|
+ INNER JOIN stock S ON O.Organism_id = S.organism_id
|
|
|
+ INNER JOIN cvterm CVT ON S.type_id = CVT.cvterm_id
|
|
|
+ GROUP BY
|
|
|
+ O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
|
|
|
+ ";
|
|
|
+
|
|
|
+ tripal_add_mview($view_name, 'tripal_stock', $schema, $sql, $comment);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add cvs related to publications
|
|
|
+ *
|
|
|
+ * @ingroup tripal_pub
|
|
|
+ */
|
|
|
+function tripal_stock_add_cvs() {
|
|
|
+
|
|
|
+ // Add cv for relationship types
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'stock_relationship',
|
|
|
+ 'Contains types of relationships between stocks.'
|
|
|
+ );
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'stock_property',
|
|
|
+ 'Contains properties for stocks.'
|
|
|
+ );
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'stock_type',
|
|
|
+ 'Contains a list of types for stocks.'
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implementation of hook_schema().
|
|
|
+ *
|
|
|
+ * @ingroup tripal_pub
|
|
|
+ */
|
|
|
+function tripal_chado_tripal_pub_import_schema() {
|
|
|
+
|
|
|
+ return array(
|
|
|
+ 'fields' => array(
|
|
|
+ 'pub_import_id' => array(
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => 255,
|
|
|
+ 'not null' => TRUE
|
|
|
+ ),
|
|
|
+ 'criteria' => array(
|
|
|
+ 'type' => 'text',
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'description' => 'Contains a serialized PHP array containing the search criteria'
|
|
|
+ ),
|
|
|
+ 'disabled' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => TRUE,
|
|
|
+ 'not NULL' => TRUE,
|
|
|
+ 'default' => 0
|
|
|
+ ),
|
|
|
+ 'do_contact' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => TRUE,
|
|
|
+ 'not NULL' => TRUE,
|
|
|
+ 'default' => 0
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array('pub_import_id'),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'name' => array('name')
|
|
|
+ ),
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add custom table related to publications
|
|
|
+ * - pubauthor_contact
|
|
|
+ *
|
|
|
+ * @ingroup tripal_pub
|
|
|
+ */
|
|
|
+function tripal_pub_add_custom_tables() {
|
|
|
+ $schema = array (
|
|
|
+ 'table' => 'pubauthor_contact',
|
|
|
+ 'fields' => array (
|
|
|
+ 'pubauthor_contact_id' => array (
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'pubauthor_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array (
|
|
|
+ 0 => 'pubauthor_contact_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array (
|
|
|
+ 'pubauthor_contact_c1' => array (
|
|
|
+ 0 => 'contact_id',
|
|
|
+ 1 => 'pubauthor_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array (
|
|
|
+ 'contact' => array (
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array (
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pubauthor' => array (
|
|
|
+ 'table' => 'pubauthor',
|
|
|
+ 'columns' => array (
|
|
|
+ 'pubauthor_id' => 'pubauthor_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ chado_create_custom_table('pubauthor_contact', $schema, TRUE);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add cvs related to publications
|
|
|
+ *
|
|
|
+ * @ingroup tripal_pub
|
|
|
+ */
|
|
|
+function tripal_pub_add_cvs() {
|
|
|
+
|
|
|
+
|
|
|
+ // Add the cv for pub properties
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'tripal_pub',
|
|
|
+ 'A heirarchical set of terms for describing a publication. It is intended to be used as the default vocabularies in Tripal for publication types and contact properties.'
|
|
|
+ );
|
|
|
+
|
|
|
+ // Add the cv for pub types
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'pub_type',
|
|
|
+ 'Contains types of publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.'
|
|
|
+ );
|
|
|
+
|
|
|
+ // Add the cv for pub properties
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'pub_property',
|
|
|
+ 'Contains properties for publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.'
|
|
|
+ );
|
|
|
+
|
|
|
+ // Add cv for relationship types
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'pub_relationship',
|
|
|
+ 'Contains types of relationships between publications.'
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add cvs pertaining to projects
|
|
|
+ *
|
|
|
+ * @ingroup tripal_project
|
|
|
+ */
|
|
|
+function tripal_project_add_cvs() {
|
|
|
+ // Add the cv for project properties
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'project_property',
|
|
|
+ 'Contains properties for projects'
|
|
|
+ );
|
|
|
+
|
|
|
+ // Add cv for relationship types
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'project_relationship',
|
|
|
+ 'Contains Types of relationships between projects.'
|
|
|
+ );
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add cvterms pertaining to projects
|
|
|
+ *
|
|
|
+ * @ingroup tripal_project
|
|
|
+ */
|
|
|
+function tripal_project_add_cvterms() {
|
|
|
+
|
|
|
+ // Insert cvterm 'Project Description' into cvterm table of chado
|
|
|
+ // database. This CV term is used to keep track of the project
|
|
|
+ // description in the projectprop table.
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Project Description',
|
|
|
+ 'definition' => 'Description of a project',
|
|
|
+ 'cv_name' => 'project_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add cvterms related to natural diversity
|
|
|
+ *
|
|
|
+ * @ingroup tripal_natural_diversity
|
|
|
+ */
|
|
|
+function tripal_natural_diversity_add_cvterms(){
|
|
|
+
|
|
|
+ // add cvterms for the nd_experiment_types
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Genotyping',
|
|
|
+ 'definition' => 'An experiment where genotypes of individuals are identified.',
|
|
|
+ 'cv_name' => 'nd_experiment_types',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Phenotyping',
|
|
|
+ 'definition' => 'An experiment where phenotypes of individuals are identified.',
|
|
|
+ 'cv_name' => 'nd_experiment_types',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Location',
|
|
|
+ 'definition' => 'The name of the location.',
|
|
|
+ 'cv_name' => 'nd_geolocation_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Adds a materialized view keeping track of the type of features associated with each library
|
|
|
+ *
|
|
|
+ * @ingroup tripal_library
|
|
|
+ */
|
|
|
+function tripal_library_add_mview_library_feature_count(){
|
|
|
+ $view_name = 'library_feature_count';
|
|
|
+ $comment = 'Provides count of feature by type that are associated with all libraries';
|
|
|
+
|
|
|
+ $schema = array(
|
|
|
+ 'table' => $view_name,
|
|
|
+ 'description' => $comment,
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => 255,
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'num_features' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_type' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => 255,
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_feature_count_idx1' => array('library_id'),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT
|
|
|
+ L.library_id, L.name,
|
|
|
+ count(F.feature_id) as num_features,
|
|
|
+ CVT.name as feature_type
|
|
|
+ FROM library L
|
|
|
+ INNER JOIN library_feature LF ON LF.library_id = L.library_id
|
|
|
+ INNER JOIN feature F ON LF.feature_id = F.feature_id
|
|
|
+ INNER JOIN cvterm CVT ON F.type_id = CVT.cvterm_id
|
|
|
+ GROUP BY L.library_id, L.name, CVT.name
|
|
|
+ ";
|
|
|
+
|
|
|
+ tripal_add_mview($view_name, 'tripal_library', $schema, $sql, $comment);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Adds cvterms needed for the library module
|
|
|
+ *
|
|
|
+ * @ingroup tripal_library
|
|
|
+ */
|
|
|
+function tripal_library_add_cvterms() {
|
|
|
+
|
|
|
+ // Insert cvterm 'library_description' into cvterm table of chado
|
|
|
+ // database. This CV term is used to keep track of the library
|
|
|
+ // description in the libraryprop table.
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Library Description',
|
|
|
+ 'definition' => 'Description of a library',
|
|
|
+ 'cv_name' => 'library_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+ // add cvterms for the map unit types
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'cdna_library',
|
|
|
+ 'definition' => 'cDNA library',
|
|
|
+ 'cv_name' => 'library_type',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'bac_library',
|
|
|
+ 'definition' => 'Bacterial Artifical Chromsome (BAC) library',
|
|
|
+ 'cv_name' => 'library_type',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'fosmid_library',
|
|
|
+ 'definition' => 'Fosmid library',
|
|
|
+ 'cv_name' => 'library_type',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'cosmid_library',
|
|
|
+ 'definition' => 'Cosmid library',
|
|
|
+ 'cv_name' => 'library_type',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'yac_library',
|
|
|
+ 'definition' => 'Yeast Artificial Chromosome (YAC) library',
|
|
|
+ 'cv_name' => 'library_type',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'genomic_library',
|
|
|
+ 'definition' => 'Genomic Library',
|
|
|
+ 'cv_name' => 'library_type',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Adds new CV's used by this module
|
|
|
+ *
|
|
|
+ * @ingroup tripal_library
|
|
|
+ */
|
|
|
+function tripal_library_add_cvs(){
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'library_property',
|
|
|
+ 'Contains properties for libraries.'
|
|
|
+ );
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'library_type',
|
|
|
+ 'Contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).'
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add custom tables needed by the feature map module
|
|
|
+ * - featuremapprop
|
|
|
+ * - featuremap_dbxref
|
|
|
+ * - featureposprop
|
|
|
+ *
|
|
|
+ * @ingroup tripal_featuremap
|
|
|
+ */
|
|
|
+function tripal_featuremap_add_custom_tables(){
|
|
|
+ // add the featuremaprop table to Chado
|
|
|
+ $schema = array (
|
|
|
+ 'table' => 'featuremapprop',
|
|
|
+ 'fields' => array (
|
|
|
+ 'featuremapprop_id' => array (
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'type_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'value' => array (
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => false,
|
|
|
+ ),
|
|
|
+ 'rank' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array (
|
|
|
+ 0 => 'featuremapprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array (
|
|
|
+ 'featuremapprop_c1' => array (
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array (
|
|
|
+ 'featuremapprop_idx1' => array (
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featuremapprop_idx2' => array (
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array (
|
|
|
+ 'cvterm' => array (
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array (
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'featuremap' => array (
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array (
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ chado_create_custom_table('featuremapprop', $schema, TRUE);
|
|
|
+
|
|
|
+ // add the featuremap_dbxref table to Chado
|
|
|
+ $schema = array (
|
|
|
+ 'table' => 'featuremap_dbxref',
|
|
|
+ 'fields' => array (
|
|
|
+ 'featuremap_dbxref_id' => array (
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array (
|
|
|
+ 0 => 'featuremap_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array (
|
|
|
+ 'featuremap_dbxref_c1' => array (
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array (
|
|
|
+ 'featuremap_dbxref_idx1' => array (
|
|
|
+ 0 => 'featuremap_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'featuremap_dbxref_idx2' => array (
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array (
|
|
|
+ 'dbxref' => array (
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array (
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'featuremap' => array (
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array (
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => NULL,
|
|
|
+ );
|
|
|
+ chado_create_custom_table('featuremap_dbxref', $schema, TRUE);
|
|
|
+
|
|
|
+ $schema = array (
|
|
|
+ 'table' => 'featureposprop',
|
|
|
+ 'fields' => array (
|
|
|
+ 'featureposprop_id' => array (
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'featurepos_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'type_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'value' => array (
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => false,
|
|
|
+ ),
|
|
|
+ 'rank' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array (
|
|
|
+ 0 => 'featureposprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array (
|
|
|
+ 'featureposprop_id' => array (
|
|
|
+ 0 => 'featurepos_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array (
|
|
|
+ 'featureposprop_c1' => array (
|
|
|
+ 0 => 'featurepos_id',
|
|
|
+ ),
|
|
|
+ 'featureposprop_idx2' => array (
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array (
|
|
|
+ 'cvterm' => array (
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array (
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'featurepos' => array (
|
|
|
+ 'table' => 'featurepos',
|
|
|
+ 'columns' => array (
|
|
|
+ 'featurepos_id' => 'featurepos_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ chado_create_custom_table('featureposprop', $schema, TRUE);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add cv terms needed by the featuremap module
|
|
|
+ *
|
|
|
+ * @ingroup tripal_featuremap
|
|
|
+ */
|
|
|
+function tripal_featuremap_add_cvterms() {
|
|
|
+
|
|
|
+ // add cvterms for the map unit types
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'cM',
|
|
|
+ 'definition' => 'Centimorgan units',
|
|
|
+ 'cv_name' => 'featuremap_units',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'bp',
|
|
|
+ 'definition' => 'Base pairs units',
|
|
|
+ 'cv_name' => 'featuremap_units',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'bin_unit',
|
|
|
+ 'definition' => 'The bin unit',
|
|
|
+ 'cv_name' => 'featuremap_units',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'marker_order',
|
|
|
+ 'definition' => 'Units simply to define marker order.',
|
|
|
+ 'cv_name' => 'featuremap_units',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'undefined',
|
|
|
+ 'definition' => 'A catch-all for an undefined unit type',
|
|
|
+ 'cv_name' => 'featuremap_units',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+ // featurepos properties
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'start',
|
|
|
+ 'definition' => 'The start coordinate for a map feature.',
|
|
|
+ 'cv_name' => 'featurepos_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'stop',
|
|
|
+ 'definition' => 'The end coordinate for a map feature',
|
|
|
+ 'cv_name' => 'featurepos_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+ // add cvterms for map properties
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Map Dbxref',
|
|
|
+ 'definition' => 'A unique identifer for the map in a remote database. The '
|
|
|
+ . 'format is a database abbreviation and a unique accession separated '
|
|
|
+ . 'by a colon. (e.g. Gramene:tsh1996a)',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Map Type',
|
|
|
+ 'definition' => 'The type of Map (e.g. QTL, Physical, etc.)',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Genome Group',
|
|
|
+ 'definition' => '',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'URL',
|
|
|
+ 'definition' => 'A univeral resource locator (URL) reference where the '
|
|
|
+ . 'publication can be found. For maps found online, this would be '
|
|
|
+ . 'the web address for the map.',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Population Type',
|
|
|
+ 'definition' => 'A brief description of the population type used to generate '
|
|
|
+ . 'the map (e.g. RIL, F2, BC1, etc).',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Population Size',
|
|
|
+ 'definition' => 'The size of the population used to construct the map.',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Methods',
|
|
|
+ 'definition' => 'A brief description of the methods used to construct the map.',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Software',
|
|
|
+ 'definition' => 'The software used to construct the map.',
|
|
|
+ 'cv_name' => 'featuremap_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add cvs needed by the featuremap module
|
|
|
+ *
|
|
|
+ * @ingroup tripal_featuremap
|
|
|
+ */
|
|
|
+function tripal_featuremap_add_cvs() {
|
|
|
+
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'featuremap_units',
|
|
|
+ 'Contains map unit types for the unittype_id column of the featuremap table.'
|
|
|
+ );
|
|
|
+
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'featurepos_property',
|
|
|
+ 'Contains terms map properties.'
|
|
|
+ );
|
|
|
+
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'featuremap_property',
|
|
|
+ 'Contains positional types for the feature positions'
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add cvs related to features
|
|
|
+ *
|
|
|
+ * @ingroup tripal_pub
|
|
|
+ */
|
|
|
+function tripal_feature_add_cvs() {
|
|
|
+
|
|
|
+ // Add cv for relationship types
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'feature_relationship',
|
|
|
+ 'Contains types of relationships between features.'
|
|
|
+ );
|
|
|
+
|
|
|
+ // The feature_property CV may already exists. It comes with Chado, but
|
|
|
+ // we need to add it just in case it doesn't get added before the feature
|
|
|
+ // module is installed. But as of Tripal v3.0 the Chado version of this
|
|
|
+ // vocabulary is no longer loaded by default.
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'feature_property',
|
|
|
+ 'Stores properties about features'
|
|
|
+ );
|
|
|
+
|
|
|
+ // the feature type vocabulary should be the sequence ontology, and even though
|
|
|
+ // this ontology should get loaded we will create it here just so that we can
|
|
|
+ // set the default vocabulary for the feature.type_id field
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'sequence',
|
|
|
+ 'The Sequence Ontology'
|
|
|
+ );
|
|
|
+}
|
|
|
+function tripal_feature_add_tripal_gff_temp_table() {
|
|
|
+ $schema = array(
|
|
|
+ 'table' => 'tripal_gff_temp',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_name' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'tripal_gff_temp_idx0' => array('feature_id'),
|
|
|
+ 'tripal_gff_temp_idx0' => array('organism_id'),
|
|
|
+ 'tripal_gff_temp_idx1' => array('uniquename'),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'tripal_gff_temp_uq0' => array('feature_id'),
|
|
|
+ 'tripal_gff_temp_uq1' => array('uniquename', 'organism_id', 'type_name'),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ chado_create_custom_table('tripal_gff_temp', $schema, TRUE);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
|
|
|
+ $schema = array(
|
|
|
+ 'table' => 'tripal_gffcds_temp',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'parent_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phase' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'tripal_gff_temp_idx0' => array('feature_id'),
|
|
|
+ 'tripal_gff_temp_idx0' => array('parent_id'),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ chado_create_custom_table('tripal_gffcds_temp', $schema, $skip_recreate);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_feature_add_tripal_gffprotein_temp_table() {
|
|
|
+ $schema = array(
|
|
|
+ 'table' => 'tripal_gffprotein_temp',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'parent_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'tripal_gff_temp_idx0' => array('feature_id'),
|
|
|
+ 'tripal_gff_temp_idx0' => array('parent_id'),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'tripal_gff_temp_uq0' => array('feature_id'),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ chado_create_custom_table('tripal_gffprotein_temp', $schema, TRUE);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Creates a materialized view that stores the type & number of features per organism
|
|
|
+ *
|
|
|
+ * @ingroup tripal_feature
|
|
|
+ */
|
|
|
+function tripal_feature_add_organism_count_mview() {
|
|
|
+ $view_name = 'organism_feature_count';
|
|
|
+ $comment = 'Stores the type and number of features per organism';
|
|
|
+
|
|
|
+ $schema = array(
|
|
|
+ 'description' => $comment,
|
|
|
+ 'table' => $view_name,
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genus' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'species' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'common_name' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_features' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_type' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_feature_count_idx1' => array('organism_id'),
|
|
|
+ 'organism_feature_count_idx2' => array('cvterm_id'),
|
|
|
+ 'organism_feature_count_idx3' => array('feature_type'),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT
|
|
|
+ O.organism_id, O.genus, O.species, O.common_name,
|
|
|
+ count(F.feature_id) as num_features,
|
|
|
+ CVT.cvterm_id, CVT.name as feature_type
|
|
|
+ FROM organism O
|
|
|
+ INNER JOIN feature F ON O.Organism_id = F.organism_id
|
|
|
+ INNER JOIN cvterm CVT ON F.type_id = CVT.cvterm_id
|
|
|
+ GROUP BY
|
|
|
+ O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
|
|
|
+ ";
|
|
|
+
|
|
|
+ tripal_add_mview($view_name, 'tripal_feature', $schema, $sql, $comment);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Adds any cvs needed by this module.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_contact
|
|
|
+ */
|
|
|
+function tripal_contact_add_cvs() {
|
|
|
+
|
|
|
+ // Add the cv for contact properties. This is a default vocabulary in the event
|
|
|
+ // that a user does not want to use the tripal_contact vocabulary
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'contact_property',
|
|
|
+ 'Contains properties for contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
|
|
|
+ );
|
|
|
+
|
|
|
+ // add the cv for the contact type. This is a default vocabulary in the event
|
|
|
+ // that a user does not want to use the tripal_contact vocabulary
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'contact_type',
|
|
|
+ 'Contains types of contacts. This can be used if the tripal_contact vocabulary (which is default for contacts in Tripal) is not desired.'
|
|
|
+ );
|
|
|
+
|
|
|
+ // Add the cv for the tripal_contact vocabulary which is loaded via the OBO
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'tripal_contact',
|
|
|
+ 'A heirarchical set of terms for describing a contact. It is intended to be used as the default vocabularies in Tripal for contact types and contact properties.'
|
|
|
+ );
|
|
|
+
|
|
|
+ // add the cv for contact relationships
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'contact_relationship',
|
|
|
+ 'Contains types of relationships between contacts.'
|
|
|
+ );
|
|
|
+
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add any custom tables needed by this module.
|
|
|
+ * - Contactprop: keep track of properties of contact
|
|
|
+ *
|
|
|
+ * @ingroup tripal_contact
|
|
|
+ */
|
|
|
+function tripal_contact_add_custom_tables(){
|
|
|
+ $schema = array (
|
|
|
+ 'table' => 'contactprop',
|
|
|
+ 'fields' => array (
|
|
|
+ 'contactprop_id' => array (
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'type_id' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ ),
|
|
|
+ 'value' => array (
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => false,
|
|
|
+ ),
|
|
|
+ 'rank' => array (
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => true,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array (
|
|
|
+ 0 => 'contactprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array (
|
|
|
+ 'contactprop_c1' => array (
|
|
|
+ 0 => 'contact_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array (
|
|
|
+ 'contactprop_idx1' => array (
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ 'contactprop_idx2' => array (
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array (
|
|
|
+ 'cvterm' => array (
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array (
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array (
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array (
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ chado_create_custom_table('contactprop', $schema, TRUE);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Create a legacy custom chado table (analysisfeatureprop) to store properties of
|
|
|
+ * analysisfeature links.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_analysis
|
|
|
+ */
|
|
|
+function tripal_analysis_create_analysisfeatureprop() {
|
|
|
+
|
|
|
+ // Create analysisfeatureprop table in chado. This is needed for Chado
|
|
|
+ // version 1.11, the table exists in Chado 1.2.
|
|
|
+ if (!db_table_exists('chado.analysisfeatureprop')) {
|
|
|
+ $sql = "
|
|
|
+ CREATE TABLE {analysisfeatureprop} (
|
|
|
+ analysisfeatureprop_id SERIAL PRIMARY KEY,
|
|
|
+ analysisfeature_id INTEGER NOT NULL,
|
|
|
+ type_id INTEGER NOT NULL,
|
|
|
+ value TEXT,
|
|
|
+ rank INTEGER NOT NULL,
|
|
|
+ CONSTRAINT analysisfeature_id_type_id_rank UNIQUE (analysisfeature_id, type_id, rank),
|
|
|
+ CONSTRAINT analysisfeatureprop_analysisfeature_id_fkey FOREIGN KEY (analysisfeature_id) REFERENCES {analysisfeature}(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
|
|
|
+ CONSTRAINT analysisfeatureprop_type_id_fkey FOREIGN KEY (type_id) REFERENCES {cvterm}(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
|
|
|
+ )
|
|
|
+ ";
|
|
|
+ chado_query($sql);
|
|
|
+ }
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Creates a view showing the link between an organism & it's analysis through associated features.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_analysis
|
|
|
+ */
|
|
|
+function tripal_analysis_add_mview_analysis_organism() {
|
|
|
+ $view_name = 'analysis_organism';
|
|
|
+ $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
|
|
|
+
|
|
|
+ // this is the SQL used to identify the organism to which an analsysis
|
|
|
+ // has been used. This is obtained though the analysisfeature -> feature -> organism
|
|
|
+ // joins
|
|
|
+ $sql = "
|
|
|
+ SELECT DISTINCT A.analysis_id, O.organism_id
|
|
|
+ FROM analysis A
|
|
|
+ INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id
|
|
|
+ INNER JOIN feature F ON AF.feature_id = F.feature_id
|
|
|
+ INNER JOIN organism O ON O.organism_id = F.organism_id
|
|
|
+ ";
|
|
|
+
|
|
|
+ // the schema array for describing this view
|
|
|
+ $schema = array(
|
|
|
+ 'table' => $view_name,
|
|
|
+ 'description' => $comment,
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'networkmod_qtl_indx0' => array('analysis_id'),
|
|
|
+ 'networkmod_qtl_indx1' => array('organism_id'),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ // add the view
|
|
|
+ tripal_add_mview($view_name, 'tripal_analysis', $schema, $sql, $comment);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Adds controlled vocabulary terms needed by this module.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_analysis
|
|
|
+ */
|
|
|
+function tripal_analysis_add_cvterms() {
|
|
|
+
|
|
|
+ tripal_insert_cv(
|
|
|
+ 'tripal_analysis',
|
|
|
+ 'Terms used for managing analyses in Tripal'
|
|
|
+ );
|
|
|
+
|
|
|
+ // add analysis_date. This is no longer used (as far as we can tell) but we don't
|
|
|
+ // get rid of it in case it is used, so just keep it in the Tripal CV
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'analysis_date',
|
|
|
+ 'definition' => 'The date that an analysis was performed.',
|
|
|
+ 'cv_name' => 'tripal',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+ // add analysis_short_name. This is no longer used (as far as we can tell) but we don't
|
|
|
+ // get rid of it in case it is used, so just keep it in the Tripal CV
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'analysis_short_name',
|
|
|
+ 'definition' => 'A computer legible (no spaces or special characters) '
|
|
|
+ . 'abbreviation for the analysis.',
|
|
|
+ 'cv_name' => 'tripal',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+
|
|
|
+
|
|
|
+ // the 'analysis_property' vocabulary is for user definable properties wo we
|
|
|
+ // will add an 'Analysis Type' to this vocubulary
|
|
|
+ tripal_insert_cvterm(
|
|
|
+ array(
|
|
|
+ 'name' => 'Analysis Type',
|
|
|
+ 'definition' => 'The type of analysis that was performed.',
|
|
|
+ 'cv_name' => 'analysis_property',
|
|
|
+ 'is_relationship' => 0,
|
|
|
+ 'db_name' => 'tripal'
|
|
|
+ ),
|
|
|
+ array('update_existing' => TRUE)
|
|
|
+ );
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Add a materialized view of root terms for all chado cvs. This is needed for viewing cv trees
|
|
|
+ *
|
|
|
+ * @ingroup tripal_cv
|
|
|
+ */
|
|
|
+function tripal_cv_add_cv_root_mview() {
|
|
|
+ $mv_name = 'cv_root_mview';
|
|
|
+ $comment = 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';
|
|
|
+ $schema = array(
|
|
|
+ 'table' => $mv_name,
|
|
|
+ 'description' => $comment,
|
|
|
+ 'fields' => array(
|
|
|
+ 'name' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => 255,
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cv_name' => array(
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => 255,
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cv_root_mview_indx1' => array('cvterm_id'),
|
|
|
+ 'cv_root_mview_indx2' => array('cv_id'),
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name
|
|
|
+ FROM cvterm_relationship CVTR
|
|
|
+ INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
|
|
|
+ INNER JOIN cv CV on CV.cv_id = CVT.cv_id
|
|
|
+ WHERE CVTR.object_id not in
|
|
|
+ (SELECT subject_id FROM cvterm_relationship)
|
|
|
+ ";
|
|
|
+
|
|
|
+ // Create the MView
|
|
|
+ tripal_add_mview($mv_name, 'tripal_cv', $schema, $sql, $comment);
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Creates a temporary table to store obo details while loading an obo file
|
|
|
+ *
|
|
|
+ * @ingroup tripal_cv
|
|
|
+ */
|
|
|
+function tripal_cv_create_tripal_obo_temp() {
|
|
|
+ // the tripal_obo_temp table is used for temporary housing of records when loading OBO files
|
|
|
+ // we create it here using plain SQL because we want it to be in the chado schema but we
|
|
|
+ // do not want to use the Tripal Custom Table API because we don't want it to appear in the
|
|
|
+ // list of custom tables. It needs to be available for the Tripal Chado API so we create it
|
|
|
+ // here and then define it in the tripal_cv/api/tripal_cv.schema.api.inc
|
|
|
+ if (!db_table_exists('chado.tripal_obo_temp')) {
|
|
|
+ $sql = "
|
|
|
+ CREATE TABLE {tripal_obo_temp} (
|
|
|
+ id character varying(255) NOT NULL,
|
|
|
+ stanza text NOT NULL,
|
|
|
+ type character varying(50) NOT NULL,
|
|
|
+ CONSTRAINT tripal_obo_temp_uq0 UNIQUE (id)
|
|
|
+ );
|
|
|
+ ";
|
|
|
+ chado_query($sql);
|
|
|
+ $sql = "CREATE INDEX tripal_obo_temp_idx0 ON {tripal_obo_temp} USING btree (id)";
|
|
|
+ chado_query($sql);
|
|
|
+ $sql = "CREATE INDEX tripal_obo_temp_idx1 ON {tripal_obo_temp} USING btree (type)";
|
|
|
+ chado_query($sql);
|
|
|
+ }
|
|
|
+}
|
Stephen Ficklin