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@@ -9,7 +9,7 @@
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*
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* @ingroup tripal_core
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*/
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-function tripal_core_chado_load_form() {
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+function tripal_core_chado_load_form($form, $form_state) {
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// we want to force the version of Chado to be set properly
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$real_version = chado_get_version(TRUE);
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@@ -17,23 +17,64 @@ function tripal_core_chado_load_form() {
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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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$version = chado_get_version(FALSE, TRUE);
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-
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- if ($real_version == '1.2') {
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- drupal_set_message('Please note: the upgrade of Chado from v1.2 to v1.3 may
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- require three fixes to your database. All of the primary keys
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- in Chado were changed from integers to big integers to support larger
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- tables. First, if your site has custom materialized views that will hold
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- data derived from fields changed to big integers then you may need to
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- alter the views to change the fields from integers to big integers
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- and repopulate those views. Second, if you have made
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- any custom PL/pgSQL functions that expect primary and foreign key fields
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- to be integers, then those functions will need to be altered to accept
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- big integers. Third, if you have PostgreSQL Views that use fields
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- that are converted to big integers then most likely this upgrade will
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- fail. You must first remove those views, perform the upgrade and then
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- recreate them with the appropriate fields change to big integers.
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- The Tripal upgrader is not able to fix these problems automatically',
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- 'warning');
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+ if (array_key_exists('values', $form_state)) {
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+ if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.2 to v1.3") {
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+ $tables_list = implode(', ', array('analysis_cvterm', 'analysis_dbxref', 'analysis_pub',
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+ 'analysis_relationship', 'contactprop', 'dbprop', 'feature_contact',
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+ 'featuremap_contact', 'featuremap_dbxref', 'featuremap_organism', 'featuremapprop',
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+ 'featureposprop', 'library_contact', 'library_expression', 'library_expressionprop',
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+ 'library_featureprop', 'library_relationship', 'library_relationship_pub', 'nd_experiment_analysis',
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+ 'organism_cvterm', 'organism_cvtermprop', 'organism_pub', 'organism_relationship',
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+ 'organismprop_pub', 'phenotypeprop', 'phylotreeprop', 'project_analysis',
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+ 'project_dbxref', 'project_feature', 'project_stock', 'pubauthor_contact',
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+ 'stock_feature', 'stock_featuremap', 'stock_library', 'stockcollection_db'));
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+ $items = array(
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+ 'PostgreSQL version 9.1 is required to perform this upgrade. If your Tripal
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+ site uses an older version please upgrade before proceeding.',
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+ 'A major change between Chado v1.2 and v1.3 is that primary and foreign
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+ keys were upgraded from integers to big integers. If your site has custom
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+ materialized views that will hold data derived from fields changed to
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+ big integers then you may need to alter the views to change the fields
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+ from integers to big integers and repopulate those views. If you have not
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+ added any materialized views you can ignore this issue.',
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+ 'Custom PL/pgSQL functions that expect primary and
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+ foreign key fields to be integers will not work after the upgrade.
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+ Those functions will need to be altered to accept big integers. If you
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+ do not have any custom PL/pgSQL functions you can ignore this issue.',
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+ 'PostgreSQL Views that use fields that are converted to big
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+ integers will cause this upgrade to fail. You must first remove
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+ those views, perform the upgrade and then recreate them with the
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+ appropriate fields change to big integers. If you do not have custom
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+ PostgreSQL Views you can ignore this issue.',
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+ 'Several new tables were added to Chado v1.3. However, some groups have
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+ added these tables to their Chado v1.2 installation. The Tripal upgrader
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+ will alter the primary and foreign keys of those tables to be "bigints"
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+ if they already exist but will otherwise leave them the same. You should
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+ verify that any tables with Chado v1.3 names correctly match the v1.3 schema.
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+ Otherwise you may have problems using Tripal. If you have not added any
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+ Chado v1.3 tables to your Chado v1.2 database you can ignore this issue.
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+ These are the newly added tables: ' .
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+ $tables_list . '.'
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+ );
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+ $list = theme_item_list(array(
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+ 'items' => $items,
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+ 'title' => '',
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+ 'type' => 'ul',
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+ 'attributes' => array(),
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+ ));
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+ drupal_set_message('Please note: the upgrade of Chado from v1.2 to v1.3 may
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+ require several fixes to your database. Please review the following
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+ list to ensure a safe upgrade. The Tripal upgrader is
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+ not able to fix these problems automatically: ' . $list, 'warning');
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+ }
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+ if ($form_state['values']['action_to_do'] == "Install Chado v1.3" or
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+ $form_state['values']['action_to_do'] == "Install Chado v1.2" or
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+ $form_state['values']['action_to_do'] == "Install Chado v1.11") {
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+ drupal_set_message('Please note: if Chado is already installed it will
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+ be removed and recreated and all data will be lost. If this is
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+ desired or if this is the first time Chado has been installed
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+ you can ignore this issue.', 'warning');
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+ }
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}
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$form['current_version'] = array(
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@@ -54,6 +95,12 @@ function tripal_core_chado_load_form() {
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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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+ '#ajax' => array(
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+ 'callback' => "tripal_core_chado_load_form_ajax_callback",
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+ 'wrapper' => 'tripal_core_chado_load_form',
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+ 'effect' => 'fade',
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+ 'method' => 'replace',
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+ ),
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);
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$form['warning'] = array(
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@@ -61,6 +108,9 @@ function tripal_core_chado_load_form() {
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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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+ $form['#prefix'] = '<div id="tripal_core_chado_load_form">';
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+ $form['#suffix'] = '</div>';
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+
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$form['button'] = array(
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'#type' => 'submit',
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'#value' => t('Install/Upgrade Chado'),
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@@ -69,6 +119,18 @@ function tripal_core_chado_load_form() {
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return $form;
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}
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+/**
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+ * Ajax callback function for the gensas_job_view_panel_form.
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+ *
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+ * @param $form
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+ * @param $form_state
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+ */
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+function tripal_core_chado_load_form_ajax_callback($form, $form_state) {
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+ // drupal_debug($form['tree_settings']['org_table']['num_orgs']);
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+
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+ return $form;
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+}
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+
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function tripal_core_chado_load_form_validate($form, &$form_state) {
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// We do not want to allow re-installation of Chado if other
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// Tripal modules are installed. This is because the install files
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@@ -281,7 +343,14 @@ function tripal_core_install_chado_1_11() {
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*/
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function tripal_core_upgrade_chado_1_2_to_1_3() {
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+ // Upgrade some of the custom tables that Tripal created that are now in
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+ // Chado v1.3. We'll do this ahead of time because the upgrade script won't
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+ // upgrade tables if they already exist.
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+ print "Checking for existing v1.3 tables in v1.2 and fixing bigints...\n";
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+ tripal_core_upgrade_chado_1_2_to_1_3_pre_alter();
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+
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// Get the path to the diff schema and upgrade SQL files.
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+ print "Incorporating additional changes...\n";
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$diff_file = drupal_get_path('module', 'tripal_core') .
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'/chado_schema/default_schema-1.2-1.3-diff.sql';
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@@ -293,6 +362,133 @@ function tripal_core_upgrade_chado_1_2_to_1_3() {
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throw new Exception("Upgrade problems! Please check output above for errors.");
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}
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}
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+
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+/**
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+ * Upgrade custom tables that may match the tables now in Chado v1.3.
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+ *
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+ * There were many new tables that were added to Chado v1.3 that were
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+ * suggested by the Chado user community. Some of those were Tripal users.
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+ * Therefore, to help these Tripal users upgrade more seemlessly this function
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+ * checks if those custom tables already exists, and if so updates them as
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+ * best it can to match. At a minimum it will create the table if it doesn't
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+ * exist and if it does it will change the primary keys and foreign keys to
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+ * be big ints.
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+ */
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+function tripal_core_upgrade_chado_1_2_to_1_3_pre_alter() {
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+
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+ // Include the Chado v1.3 schema definitions.
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+ module_load_include('inc', 'tripal_core', '/api/tripal_core.schema_v1.3.api');
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+
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+ // The list of new tables in Chado v1.3
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+ $new_tables = array('analysis_cvterm', 'analysis_dbxref', 'analysis_pub', 'analysis_relationship',
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+ 'contactprop', 'dbprop', 'feature_contact', 'featuremap_contact', 'featuremap_dbxref',
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+ 'featuremap_organism', 'featuremapprop', 'featureposprop', 'library_contact',
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+ 'library_expression', 'library_expressionprop', 'library_featureprop',
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+ 'library_relationship', 'library_relationship_pub', 'nd_experiment_analysis',
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+ 'organism_cvterm', 'organism_cvtermprop', 'organism_pub', 'organism_relationship',
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+ 'organismprop_pub', 'phenotypeprop', 'phylotreeprop', 'project_analysis',
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+ 'project_dbxref', 'project_feature', 'project_stock', 'pubauthor_contact',
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+ 'stock_feature', 'stock_featuremap', 'stock_library', 'stockcollection_db',
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+ );
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+
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+ // Get the name of the chado schema.
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+ $chado_schema = tripal_get_schema_name('chado');
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+
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+ // Iterate through the new Chado tables and create them or if they already
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+ // exist then update them.
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+ foreach ($new_tables as $table) {
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+
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+ // Get the schema for this table.
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+ $function = 'tripal_core_chado_schema_v1_3_' . $table;
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+ $schema = $function();
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+
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+ // If the table exists then fix the pkeys and fkeys.
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+ if (chado_table_exists($table)) {
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+
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+ // Update the primary key fields to be bigints.
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+ $fields = $schema['fields'];
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+ foreach ($fields as $field_name => $field) {
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+ if ($field['type'] == 'serial') {
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+ if (chado_column_exists($table, $field_name)) {
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+ $sql = 'ALTER TABLE {' . $table . '} ALTER COLUMN ' . $field_name . ' TYPE bigint';
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+ chado_query($sql);
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+ }
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+ else {
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+ throw new Exception('Could not alter primary key to bigint: ' . $table . '.' . $field_name);
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+ }
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+ }
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+ }
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+
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+ // Update the foreign key fields to be bigints.
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+ $fkeys = $schema['foreign keys'];
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+ foreach ($fkeys as $fktable => $details) {
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+ foreach ($details['columns'] as $leftkey => $rightkey) {
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+ if (chado_column_exists($table, $leftkey)) {
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+ $sql = 'ALTER TABLE {' . $table . '} ALTER COLUMN ' . $leftkey . ' TYPE bigint';
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+ chado_query($sql);
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+ }
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+ else {
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+ throw new Exception('Could not alter foreign key to bigint: ' . $table . '.' . $leftkey);
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+ }
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+ }
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+ }
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+
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+ }
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+ }
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+ // Now create the sequences if they don't already exist.
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+ $sequences = array(
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+ 'analysis_cvterm_analysis_cvterm_id_seq',
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+ 'analysis_dbxref_analysis_dbxref_id_seq',
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+ 'analysis_pub_analysis_pub_id_seq',
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+ 'analysis_relationship_analysis_relationship_id_seq',
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+ 'contactprop_contactprop_id_seq',
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+ 'dbprop_dbprop_id_seq',
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+ 'feature_contact_feature_contact_id_seq',
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+ 'featuremap_contact_featuremap_contact_id_seq',
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+ 'featuremap_dbxref_featuremap_dbxref_id_seq',
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+ 'featuremap_organism_featuremap_organism_id_seq',
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+ 'featuremapprop_featuremapprop_id_seq',
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+ 'featureposprop_featureposprop_id_seq',
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+ 'library_contact_library_contact_id_seq',
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+ 'library_expression_library_expression_id_seq',
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+ 'library_expressionprop_library_expressionprop_id_seq',
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+ 'library_featureprop_library_featureprop_id_seq',
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+ 'library_relationship_library_relationship_id_seq',
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+ 'library_relationship_pub_library_relationship_pub_id_seq',
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+ 'nd_experiment_analysis_nd_experiment_analysis_id_seq',
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+ 'organism_cvterm_organism_cvterm_id_seq',
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+ 'organism_cvtermprop_organism_cvtermprop_id_seq',
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+ 'organism_pub_organism_pub_id_seq',
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+ 'organism_relationship_organism_relationship_id_seq',
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+ 'organismprop_pub_organismprop_pub_id_seq',
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+ 'phenotypeprop_phenotypeprop_id_seq',
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+ 'phylotreeprop_phylotreeprop_id_seq',
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+ 'project_analysis_project_analysis_id_seq',
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+ 'project_dbxref_project_dbxref_id_seq',
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+ 'project_feature_project_feature_id_seq',
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+ 'project_stock_project_stock_id_seq',
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+ 'pubauthor_contact_pubauthor_contact_id_seq',
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+ 'stock_feature_stock_feature_id_seq',
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+ 'stock_featuremap_stock_featuremap_id_seq',
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+ 'stock_library_stock_library_id_seq',
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+ 'stockcollection_db_stockcollection_db_id_seq'
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+ );
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+ foreach ($sequences as $sequence) {
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+
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+ // Now add in the sequences if they don't already exist. There is no
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+ // PostgreSQL 'CREATE SEQUENCE IF NOT EXIST' so we're forced to do it here
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+ // and these create statements were removed from the diff upgrade file.
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+ if (!chado_sequence_exists($sequence)) {
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+ $sql = "CREATE SEQUENCE {" . $sequence . "} START WITH 1 INCREMENT BY 1 NO MINVALUE NO MAXVALUE CACHE 1";
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+ chado_query($sql);
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+ }
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+ }
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+}
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+
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+
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+
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+
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+
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/**
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* Upgrades Chado from v1.11 to v1.2
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*/
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Stephen Ficklin