Creating Prepare Chado Step

tripal_chado/includes/tripal_chado.chado_install.inc

@@ -1,413 +0,0 @@
-<?php
-/**
- * @file
- * Functions to install chado schema through Drupal
- */
-
-/**
- * Load Chado Schema Form
- *
- * @ingroup tripal_chado
- */
-function tripal_chado_chado_load_form() {
-
-  // we want to force the version of Chado to be set properly
-  $real_version = chado_get_version(TRUE);
-
-  // get the effective version.  Pass true as second argument
-  // to warn the user if the current version is not compatible
-  $version = chado_get_version(FALSE, TRUE);
-
-  $form['current_version'] = array(
-    '#type' => 'item',
-    '#title' => t("Current installed version of Chado:"),
-    '#description' => $real_version,
-  );
-
-  $form['action_to_do'] = array(
-     '#type' => 'radios',
-     '#title' => 'Installation/Upgrade Action',
-     '#options' => array(
-        'Install Chado v1.2' => t('New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)'),
-        'Upgrade Chado v1.11 to v1.2' => t('Upgrade existing Chado v1.11 to v1.2 (no data is lost)'),
-        'Install Chado v1.11' => t('New Install of Chado v1.11 (erases all existing Chado data if Chado already exists)')
-     ),
-     '#description' => t('Select an action to perform. If you want to install Chado all other Tripal modules must not be installed.'),
-     '#required' => TRUE,
-  );
-
-  $form['warning'] = array(
-    '#markup' => "<div><font color=\"red\">WARNING:</font>" . t('A new install of
-      Chado will remove and recreate the Chado database if it already exists.') . '</div>',
-  );
-
-  $form['button'] = array(
-    '#type' => 'submit',
-    '#value' => t('Install/Upgrade Chado'),
-  );
-
-  return $form;
-}
-
-function tripal_chado_chado_load_form_validate($form, &$form_state) {
-  // We do not want to allow re-installation of Chado if other
-  // Tripal modules are installed.  This is because the install files
-  // of those modules may add content to Chado and reinstalling Chado
-  // removes that content which may break the modules.
-
-  if ($form_state['values']['action_to_do'] == "Install Chado v1.2" or
-      $form_state['values']['action_to_do'] == "Install Chado v1.11") {
-
-    $modules = system_get_info('module');
-    $list = array();
-    foreach ($modules as $mname => $module) {
-      if (array_key_exists('dependencies', $module) and in_array('tripal_chado', $module['dependencies'])) {
-        $list[] = $module['name'] . " ($mname)";
-      }
-    }
-    if (count($list) > 0) {
-      form_set_error("action_to_do", "Chado cannot be installed while other Tripal modules
-          are enabled.  You must fully uninstall the following modules if you
-          would like to install or re-install chado.<br>" .
-          implode("<br>", $list));
-    }
-  }
-  if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.11 to v1.2") {
-    // Make sure we are already not at v1.2
-    $real_version = chado_get_version(TRUE);
-    if ($real_version == "1.2") {
-      form_set_error("action_to_do", "You are already at v1.2.  There is no need to upgrade.");
-    }
-  }
-}
-/**
- * Submit Load Chado Schema Form
- *
- * @ingroup tripal_chado
- */
-function tripal_chado_chado_load_form_submit($form, &$form_state) {
-  global $user;
-  $action_to_do = trim($form_state['values']['action_to_do']);
-  $args = array($action_to_do);
-  tripal_add_job($action_to_do, 'tripal_chado', 'tripal_chado_install_chado', $args, $user->uid);
-}
-
-/**
- * Install Chado Schema
- *
- * @ingroup tripal_chado
- */
-function tripal_chado_install_chado($action) {
-
-  $vsql = "
-    INSERT INTO {chadoprop} (type_id, value)
-      VALUES (
-       (SELECT cvterm_id
-        FROM {cvterm} CVT
-          INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
-         WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
-       :version)
-  ";
-
-  if ($action == 'Install Chado v1.2') {
-    $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.2.sql';
-    $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/initialize-1.2.sql';
-    if (tripal_chado_reset_chado_schema()) {
-      $success = tripal_chado_install_sql($schema_file);
-      if ($success) {
-        print "Install of Chado v1.2 (Step 1 of 2) Successful!\n";
-      }
-      else {
-        print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";
-        exit;
-      }
-      $success = tripal_chado_install_sql($init_file);
-      if ($success) {
-        print "Install of Chado v1.2 (Step 2 of 2) Successful.\nInstallation Complete\n";
-      }
-      else {
-        print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";
-        exit;
-      }
-      chado_query($vsql, array(':version' => '1.2')); # set the version
-    }
-    else {
-      print "ERROR: cannot install chado.  Please check database permissions\n";
-      exit;
-    }
-  }
-  elseif ($action == 'Upgrade Chado v1.11 to v1.2') {
-    $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11-1.2-diff.sql';
-    $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/upgrade-1.11-1.2.sql';
-    $success = tripal_chado_install_sql($schema_file);
-    if ($success) {
-      print "Upgrade from v1.11 to v1.2 (Step 1 of 2) Successful!\n";
-    }
-    else {
-      print "Upgrade (Step 1 of 2) problems!  Please check output above for errors.\n";
-      exit;
-    }
-    $success = tripal_chado_install_sql($init_file);
-    if ($success) {
-      print "Upgrade from v1.11 to v1.2 (Step 2 of 2) Successful.\nUpgrade Complete!\n";
-    }
-    else {
-      print "Upgrade (Step 2 of 2) problems!  Please check output above for errors.\n";
-      exit;
-    }
-    chado_query($vsql, array(':version' => '1.2')); # set the version
-  }
-  elseif ($action == 'Install Chado v1.11') {
-    $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11.sql';
-    $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/initialize-1.11.sql';
-    if (tripal_chado_reset_chado_schema()) {
-      $success = tripal_chado_install_sql($schema_file);
-      if ($success) {
-        print "Install of Chado v1.11 (Step 1 of 2) Successful!\n";
-      }
-      else {
-        print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";
-        exit;
-      }
-      $success = tripal_chado_install_sql($init_file);
-      if ($success) {
-        print "Install of Chado v1.11 (Step 2 of 2) Successful.\nInstallation Complete!\n";
-      }
-      else {
-        print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";
-        exit;
-      }
-    }
-    else {
-      print "ERROR: cannot install chado.  Please check database permissions\n";
-      exit;
-    }
-  }
-}
-
-/**
- * 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");
-}

tripal_chado/includes/tripal_chado.setup.inc

@@ -0,0 +1,2056 @@
+<?php
+/**
+ * @file
+ * Functions to install chado schema through Drupal
+ */
+
+/**
+ * Prepares Chado for Tripal use
+ */
+function tripal_chado_prepare_form($form, $form_state) {
+  $form = array();
+
+  // we want to force the version of Chado to be set properly
+  $real_version = chado_get_version(TRUE);
+
+  $form['current_version'] = array(
+    '#type' => 'item',
+    '#title' => t("Current installed version of Chado:"),
+    '#description' => $real_version,
+  );
+  $form['instructions'] = array(
+    '#type' => 'item',
+    '#description' => t("Click the button below to prepare a Chado installation for
+        use by Tripal.  If you used Tripal to install Chado then this step
+        is not necessary.  If Chado was installed outside of Tripal then
+        it should be prepared. Preparing Chado involves adding of
+        specific controlled vocabularies, custom tables and materialized views."),
+  );
+
+  $form['button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Prepare Chado'),
+    '#name' => 'prepare-chado',
+  );
+  return $form;
+}
+
+/**
+ * Submit function for the tripal_chado_prepare_form().
+ *
+ * @param $form
+ * @param $form_state
+ */
+function tripal_chado_prepare_form_submit($form, $form_state) {
+   if ($form_state['clicked_button']['#name'] == "prepare-chado") {
+     global $user;
+     $args = array();
+     tripal_add_job('Prepare Chado', 'tripal_chado', 'tripal_chado_prepare_chado', $args, $user->uid);
+   }
+}
+/**
+ * Load Chado Schema Form
+ *
+ * @ingroup tripal_chado
+ */
+function tripal_chado_load_form($form, $form_state) {
+
+  // we want to force the version of Chado to be set properly
+  $real_version = chado_get_version(TRUE);
+
+  // get the effective version.  Pass true as second argument
+  // to warn the user if the current version is not compatible
+  $version = chado_get_version(FALSE, TRUE);
+
+  $form['current_version'] = array(
+    '#type' => 'item',
+    '#title' => t("Current installed version of Chado:"),
+    '#description' => $real_version,
+  );
+
+  $form['action_to_do'] = array(
+     '#type' => 'radios',
+     '#title' => 'Installation/Upgrade Action',
+     '#options' => array(
+        'Install Chado v1.2' => t('New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)'),
+        'Upgrade Chado v1.11 to v1.2' => t('Upgrade existing Chado v1.11 to v1.2 (no data is lost)'),
+        'Install Chado v1.11' => t('New Install of Chado v1.11 (erases all existing Chado data if Chado already exists)')
+     ),
+     '#description' => t('Select an action to perform. If you want to install Chado all other Tripal modules must not be installed.'),
+     '#required' => TRUE,
+  );
+
+  $form['warning'] = array(
+    '#markup' => "<div><font color=\"red\">WARNING:</font>" . t('A new install of
+      Chado will remove and recreate the Chado database if it already exists.') . '</div>',
+  );
+
+  $form['button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Install/Upgrade Chado'),
+  );
+
+  return $form;
+}
+
+function tripal_chado_chado_load_form_validate($form, &$form_state) {
+  // We do not want to allow re-installation of Chado if other
+  // Tripal modules are installed.  This is because the install files
+  // of those modules may add content to Chado and reinstalling Chado
+  // removes that content which may break the modules.
+
+  if ($form_state['values']['action_to_do'] == "Install Chado v1.2" or
+      $form_state['values']['action_to_do'] == "Install Chado v1.11") {
+
+    $modules = system_get_info('module');
+    $list = array();
+    foreach ($modules as $mname => $module) {
+      if (array_key_exists('dependencies', $module) and in_array('tripal_chado', $module['dependencies'])) {
+        $list[] = $module['name'] . " ($mname)";
+      }
+    }
+    if (count($list) > 0) {
+      form_set_error("action_to_do", "Chado cannot be installed while other Tripal modules
+          are enabled.  You must fully uninstall the following modules if you
+          would like to install or re-install chado.<br>" .
+          implode("<br>", $list));
+    }
+  }
+  if ($form_state['values']['action_to_do'] == "Upgrade Chado v1.11 to v1.2") {
+    // Make sure we are already not at v1.2
+    $real_version = chado_get_version(TRUE);
+    if ($real_version == "1.2") {
+      form_set_error("action_to_do", "You are already at v1.2.  There is no need to upgrade.");
+    }
+  }
+}
+/**
+ * Submit Load Chado Schema Form
+ *
+ * @ingroup tripal_chado
+ */
+function tripal_chado_chado_load_form_submit($form, &$form_state) {
+  global $user;
+  $action_to_do = trim($form_state['values']['action_to_do']);
+  $args = array($action_to_do);
+  tripal_add_job($action_to_do, 'tripal_chado', 'tripal_chado_install_chado', $args, $user->uid);
+}
+
+/**
+ * Install Chado Schema
+ *
+ * @ingroup tripal_chado
+ */
+function tripal_chado_install_chado($action) {
+
+  $vsql = "
+    INSERT INTO {chadoprop} (type_id, value)
+      VALUES (
+       (SELECT cvterm_id
+        FROM {cvterm} CVT
+          INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
+         WHERE CV.name = 'chado_properties' AND CVT.name = 'version'),
+       :version)
+  ";
+
+  if ($action == 'Install Chado v1.2') {
+    $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.2.sql';
+    $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/initialize-1.2.sql';
+    if (tripal_chado_reset_chado_schema()) {
+      $success = tripal_chado_install_sql($schema_file);
+      if ($success) {
+        print "Install of Chado v1.2 (Step 1 of 2) Successful!\n";
+      }
+      else {
+        print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";
+        exit;
+      }
+      $success = tripal_chado_install_sql($init_file);
+      if ($success) {
+        print "Install of Chado v1.2 (Step 2 of 2) Successful.\nInstallation Complete\n";
+      }
+      else {
+        print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";
+        exit;
+      }
+      chado_query($vsql, array(':version' => '1.2')); # set the version
+    }
+    else {
+      print "ERROR: cannot install chado.  Please check database permissions\n";
+      exit;
+    }
+  }
+  elseif ($action == 'Upgrade Chado v1.11 to v1.2') {
+    $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11-1.2-diff.sql';
+    $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/upgrade-1.11-1.2.sql';
+    $success = tripal_chado_install_sql($schema_file);
+    if ($success) {
+      print "Upgrade from v1.11 to v1.2 (Step 1 of 2) Successful!\n";
+    }
+    else {
+      print "Upgrade (Step 1 of 2) problems!  Please check output above for errors.\n";
+      exit;
+    }
+    $success = tripal_chado_install_sql($init_file);
+    if ($success) {
+      print "Upgrade from v1.11 to v1.2 (Step 2 of 2) Successful.\nUpgrade Complete!\n";
+    }
+    else {
+      print "Upgrade (Step 2 of 2) problems!  Please check output above for errors.\n";
+      exit;
+    }
+    chado_query($vsql, array(':version' => '1.2')); # set the version
+  }
+  elseif ($action == 'Install Chado v1.11') {
+    $schema_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/default_schema-1.11.sql';
+    $init_file = drupal_get_path('module', 'tripal_chado') . '/chado_schema/initialize-1.11.sql';
+    if (tripal_chado_reset_chado_schema()) {
+      $success = tripal_chado_install_sql($schema_file);
+      if ($success) {
+        print "Install of Chado v1.11 (Step 1 of 2) Successful!\n";
+      }
+      else {
+        print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";
+        exit;
+      }
+      $success = tripal_chado_install_sql($init_file);
+      if ($success) {
+        print "Install of Chado v1.11 (Step 2 of 2) Successful.\nInstallation Complete!\n";
+      }
+      else {
+        print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";
+        exit;
+      }
+    }
+    else {
+      print "ERROR: cannot install chado.  Please check database permissions\n";
+      exit;
+    }
+  }
+}
+
+/**
+ * Prepares Chado for use by Tripal.
+ */
+function tripal_chado_prepare_chado() {
+  // we want to force the version of Chado to be set properly
+  $real_version = chado_get_version(TRUE);
+
+  // get the effective version.  Pass true as second argument
+  // to warn the user if the current version is not compatible
+  $version = chado_get_version(FALSE, FALSE);
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                          Chado CV Module
+  /////////////////////////////////////////////////////////////////////////////
+  // Add the cv_root_mview.
+  tripal_cv_add_cv_root_mview();
+
+  // Add defaults to the tables that correlate OBO files/references with
+  // a chado CV.
+  tripal_cv_add_obo_defaults();
+
+  // Add the Chado ontology CV.
+  $obo_path = '{tripal_chado}/files/cv_property.obo';
+  $obo_id = tripal_insert_obo('Chado CV Properties', $obo_path);
+  tripal_submit_obo_job(array('obo_id' => $obo_id));
+
+  // Create the temp table we will use for loading OBO files.
+  tripal_cv_create_tripal_obo_temp();
+
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                          Chado Organism Module
+  /////////////////////////////////////////////////////////////////////////////
+  tripal_insert_cv(
+  'organism_property',
+  'Contains properties for organisms'
+      );
+
+  // set the default vocabularies
+  tripal_set_default_cv('organismprop', 'type_id', 'organism_property');
+
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                        Chado CompAnalysis Module
+  /////////////////////////////////////////////////////////////////////////////
+  // we may need the analysisfeatureprop table if it doesn't already exist
+  tripal_analysis_create_analysisfeatureprop();
+
+  // add cvterms
+  tripal_analysis_add_cvterms();
+
+  // add materialized views
+  tripal_analysis_add_mview_analysis_organism();
+
+  // set the default vocabularies
+  tripal_set_default_cv('analysisprop', 'type_id', 'analysis_property');
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                        Chado Contact Module
+  /////////////////////////////////////////////////////////////////////////////
+  // Add the contactprop table to Chado.
+  tripal_contact_add_custom_tables();
+
+  // Add loading of the the tripal contact ontology to the job queue.
+  $obo_path = '{tripal_chado}/files/tcontact.obo';
+  $obo_id = tripal_insert_obo('Tripal Contacts', $obo_path);
+  tripal_submit_obo_job(array('obo_id' => $obo_id));
+
+    // Add cvterms for relationship types.
+  tripal_contact_add_cvs();
+
+  // Set the default vocabularies.
+  tripal_set_default_cv('contact', 'type_id', 'tripal_contact');
+  tripal_set_default_cv('contactprop', 'type_id', 'tripal_contact');
+      tripal_set_default_cv('contact_relationship', 'type_id', 'contact_relationship');
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                        Chado Feature Module
+  /////////////////////////////////////////////////////////////////////////////
+  // Note: the feature_property OBO that came with Chado v1.2 should not
+  // be automatically installed.  Some of the terms are duplicates of
+  // others in better maintained vocabularies.  New Tripal sites should
+  // use those.
+  // $obo_path = '{tripal_feature}/files/feature_property.obo';
+  // $obo_id = tripal_insert_obo('Chado Feature Properties', $obo_path);
+  // tripal_submit_obo_job(array('obo_id' => $obo_id));
+
+  // Add the materialized view.
+  tripal_feature_add_organism_count_mview();
+
+  // Add the custom tables.
+  tripal_feature_add_tripal_gff_temp_table();
+  tripal_feature_add_tripal_gffcds_temp_table();
+  tripal_feature_add_tripal_gffprotein_temp_table();
+
+  // Add the vocabularies used by the feature module.
+  tripal_feature_add_cvs();
+
+  // Set the default vocabularies.
+  tripal_set_default_cv('feature', 'type_id', 'sequence');
+  tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
+  tripal_set_default_cv('feature_relationship', 'type_id', 'feature_relationship');
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                            Chado Map Module
+  /////////////////////////////////////////////////////////////////////////////
+  // add the featuremapprop table to Chado
+  tripal_featuremap_add_custom_tables();
+
+  // Add cvterms
+  tripal_featuremap_add_cvs();
+  tripal_featuremap_add_cvterms();
+
+  // set the default vocabularies
+  tripal_set_default_cv('featuremapprop', 'type_id', 'featuremap_property');
+  tripal_set_default_cv('featureposprop', 'type_id', 'featurepos_property');
+  tripal_set_default_cv('featuremap', 'unittype_id', 'featuremap_units');
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                          Chado Library Module
+  /////////////////////////////////////////////////////////////////////////////
+  // add the materialized view
+  tripal_library_add_mview_library_feature_count();
+
+  // add cvterms
+  tripal_library_add_cvs();
+  tripal_library_add_cvterms();
+
+  // set the default vocabularies
+  tripal_set_default_cv('libraryprop', 'type_id', 'library_property');
+  tripal_set_default_cv('library', 'type_id', 'library_type');
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                          Chado NatDiv Module
+  /////////////////////////////////////////////////////////////////////////////
+  // add cvterms
+  tripal_natural_diversity_add_cvterms();
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                          Chado Project Module
+  /////////////////////////////////////////////////////////////////////////////
+  tripal_project_add_cvs();
+  tripal_project_add_cvterms();
+
+  // set the default vocabularies
+  tripal_set_default_cv('projectprop', 'type_id', 'project_property');
+  tripal_set_default_cv('project_relationship', 'type_id', 'project_relationship');
+
+  /////////////////////////////////////////////////////////////////////////////
+  //                          Chado Pub Module
+  /////////////////////////////////////////////////////////////////////////////
+  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);
+  }
+}

tripal_chado/tripal_chado.module

@@ -105,15 +105,32 @@ function tripal_chado_menu() {
     'weight' => -100,
     'access arguments' => array('administer tripal'),
   );
+
   $items['admin/tripal/storage/chado/chado_install'] = array(
-    'title' => 'Install Chado Schema',
+    'title' => 'Install Chado',
     'description' => t('Installs the Chado database tables, views, etc., inside the current Drupal database'),
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_chado_load_form'),
-    'access arguments' => array('install chado'),
     'type' => MENU_NORMAL_ITEM,
+    'access arguments' => array('install chado'),
+    'file' => 'includes/tripal_chado.setup.inc',
+    'file path' => drupal_get_path('module', 'tripal_chado'),
     'weight' => -100
   );
+  $items['admin/tripal/storage/chado/chado_prepare'] = array(
+    'title' => 'Prepare Chado',
+    'description' => t('After installation of Chado some preparation is required for Tripal. This includes adding
+        some Tripal required ontologies, materialized views and custom tables. This step
+        is only required if Chado was installed outside of Tripal. If you installed Tripal
+        using the "Install Chado" step above then Chado is prepared.'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_chado_prepare_form'),
+    'type' => MENU_NORMAL_ITEM,
+    'access arguments' => array('install chado'),
+    'file' => 'includes/tripal_chado.setup.inc',
+    'file path' => drupal_get_path('module', 'tripal_chado'),
+    'weight' => -99
+  );
 
   //////////////////////////////////////////////////////////////////////////////
   //                       Materialized Views