chado_install.inc

Functions to install chado schema through Drupal

File

tripal_core/includes/chado_install.inc
View source
  1. <?php

  2. 

  3. /**

  4.  * @file

  5.  * Functions to install chado schema through Drupal

  6.  */

  7. 

  8. /**

  9.  * Load Chado Schema Form

  10.  *

  11.  * @ingroup tripal_core

  12.  */

  13. function tripal_core_chado_load_form() {

  14. 

  15.   // we want to force the version of Chado to be set properly

  16.   $real_version = tripal_core_set_chado_version();

  17. 

  18.   // get the effective version.  Pass true as second argument

  19.   // to warn the user if the current version is not compatible

  20.   $version = tripal_core_get_chado_version(FALSE, TRUE);

  21. 

  22.   $form['current_version'] = array(

  23.     '#type' => 'item',

  24.     '#title' => t("Current installed version of Chado"),

  25.     '#value' => $real_version,

  26.   );

  27. 

  28.   $form['action_to_do'] = array(

  29.      '#type' => 'radios',

  30.      '#title' => 'Installation/Upgrade Action',

  31.      '#options' => array(

  32.         'Install Chado v1.2' => t('New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)'),

  33.         'Upgrade Chado v1.11 to v1.2' => t('Upgrade existing Chado v1.11 to v1.2 (no data is lost)'),

  34.         'Install Chado v1.11' => t('New Install of Chado v1.11 (erases all existing Chado data if Chado already exists)')

  35.      ),

  36.      '#description' => t('Select an action to perform'),

  37.      '#required' => TRUE

  38.   );

  39. 

  40.   $form['description'] = array(

  41.     '#type' => 'item',

  42.     '#value' => t("<font color=\"red\">WARNING:</font> A new install of Chado v1.2 or v1.11 "

  43.       ."will install Chado within the Drupal database in a \"chado\" schema. If the \"chado\" schema already exists it will "

  44.       ."be overwritten and all data will be lost.  You may choose to update an existing Chado v1.11 if it was installed with a previous "

  45.       ."version of Tripal (e.g. v0.3b or v0.3.1). The update will not erase any data. "

  46.       ."If you are using chado in a database external to the "

  47.       ."Drupal database with a 'chado' entry in the 'settings.php' \$db_url argument "

  48.       ."then Chado will be installed but will not be used .  The external "

  49.       ."database specified in the settings.php file takes precedence."),

  50.   );

  51. 

  52.   $form['button'] = array(

  53.     '#type' => 'submit',

  54.     '#value' => t('Install/Upgrade Chado'),

  55.     '#weight' => 2,

  56.   );

  57. 

  58.   return $form;

  59. }

  60. 

  61. /**

  62.  * Submit Load Chado Schema 1.11 Form

  63.  *

  64.  * @ingroup tripal_core

  65.  */

  66. function tripal_core_chado_load_form_submit($form, &$form_state) {

  67.   global $user;

  68.   $action_to_do   = trim($form_state['values']['action_to_do']);

  69. 

  70.   $args = array($action_to_do);

  71.   tripal_add_job($action_to_do, 'tripal_core',

  72.     'tripal_core_install_chado', $args, $user->uid);

  73. }

  74. 

  75. /**

  76.  * Install Chado Schema

  77.  *

  78.  * @ingroup tripal_core

  79.  */

  80. function tripal_core_install_chado($action) {

  81. 

  82.   $vsql = "INSERT INTO {chadoprop} (type_id, value) VALUES  " .

  83.           "((SELECT cvterm_id " .

  84.           "FROM {cvterm} CVT " .

  85.           " INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id " .

  86.           "WHERE CV.name = 'chado_properties' AND CVT.name = 'version'), " .

  87.           "'%s') ";

  88. 

  89.   if($action == 'Install Chado v1.2'){

  90.     $schema_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/default_schema-1.2.sql';

  91.     $init_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/initialize-1.2.sql';

  92.     if (tripal_core_reset_chado_schema()) {

  93.       $success = tripal_core_install_sql($schema_file);

  94.       if ($success) {

  95.         print "Install of Chado v1.2 (Step 1 of 2) Successful!\n";

  96.       }

  97.       else {

  98.         print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";

  99.         exit;

  100.       }

  101.       $success = tripal_core_install_sql($init_file);

  102.       if ($success) {

  103.         print "Install of Chado v1.2 (Step 2 of 2) Successful.\nInstallation Complete\n";

  104.       }

  105.       else {

  106.         print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";

  107.         exit;

  108.       }

  109.       chado_query($vsql,'1.2'); # set the version

  110.     }

  111.     else {

  112.       print "ERROR: cannot install chado.  Please check database permissions\n";

  113.       exit;

  114.     }

  115.   }

  116.   elseif($action == 'Upgrade Chado v1.11 to v1.2') {

  117.     $schema_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/default_schema-1.11-1.2-diff.sql';

  118.     $init_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/upgrade-1.11-1.2.sql';

  119.     $success = tripal_core_install_sql($schema_file);

  120.     if ($success) {

  121.       print "Upgrade from v1.11 to v1.2 (Step 1 of 2) Successful!\n";

  122.     }

  123.     else {

  124.       print "Upgrade (Step 1 of 2) problems!  Please check output above for errors.\n";

  125.       exit;

  126.     }

  127.     $success = tripal_core_install_sql($init_file);

  128.     if ($success) {

  129.       print "Upgrade from v1.11 to v1.2 (Step 2 of 2) Successful.\nUpgrade Complete!\n";

  130.     }

  131.     else {

  132.       print "Upgrade (Step 2 of 2) problems!  Please check output above for errors.\n";

  133.       exit;

  134.     }

  135.     chado_query($vsql,'1.2'); # set the version

  136.   }

  137.   elseif($action == 'Install Chado v1.11'){

  138.     $schema_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/default_schema-1.11.sql';

  139.     $init_file = drupal_get_path('module', 'tripal_core') . '/chado_schema/initialize-1.11.sql';

  140.     if (tripal_core_reset_chado_schema()) {

  141.       $success = tripal_core_install_sql($schema_file);

  142.       if ($success) {

  143.         print "Install of Chado v1.11 (Step 1 of 2) Successful!\n";

  144.       }

  145.       else {

  146.         print "Installation (Step 1 of 2) Problems!  Please check output above for errors.\n";

  147.         exit;

  148.       }

  149.       $success = tripal_core_install_sql($init_file);

  150.       if ($success) {

  151.         print "Install of Chado v1.11 (Step 2 of 2) Successful.\nInstallation Complete!\n";

  152.       }

  153.       else {

  154.         print "Installation (Step 2 of 2) Problems!  Please check output above for errors.\n";

  155.         exit;

  156.       }

  157.     }

  158.     else {

  159.       print "ERROR: cannot install chado.  Please check database permissions\n";

  160.       exit;

  161.     }

  162.   }

  163. }

  164. 

  165. /**

  166.  * Reset the Chado Schema

  167.  * This drops the current chado and chado-related schema and re-creates it

  168.  *

  169.  * @ingroup tripal_core

  170.  */

  171. function tripal_core_reset_chado_schema() {

  172.   global $active_db;

  173. 

  174.   // drop current chado and chado-related schema

  175.   if (tripal_core_schema_exists('chado')) {

  176.     print "Dropping existing 'chado' schema\n";

  177.     db_query("drop schema chado cascade");

  178.   }

  179.   if (tripal_core_schema_exists('genetic_code')) {

  180.     print "Dropping existing 'genetic_code' schema\n";

  181.     db_query("drop schema genetic_code cascade");

  182.   }

  183.   if (tripal_core_schema_exists('so')) {

  184.     print "Dropping existing 'so' schema\n";

  185.     db_query("drop schema so cascade");

  186.   }

  187.   if (tripal_core_schema_exists('frange')) {

  188.     print "Dropping existing 'frange' schema\n";

  189.     db_query("drop schema frange cascade");

  190.   }

  191. 

  192.   // create the new chado schema

  193.   print "Creating 'chado' schema\n";

  194.   db_query("create schema chado");

  195.   if (tripal_core_schema_exists('chado')) {

  196.     // before creating the plpgsql language let's check to make sure

  197.     // it doesn't already exists

  198.     $sql = "SELECT COUNT(*) FROM pg_language WHERE lanname = 'plpgsql'";

  199.     $count = db_fetch_object(db_query($sql));

  200.     if (!$count or $count->count == 0) {

  201.       db_query("create language plpgsql");

  202.     }

  203.     return TRUE;

  204.   }

  205. 

  206.   return FALSE;

  207. }

  208. 

  209. /**

  210.  * Execute the provided SQL

  211.  *

  212.  * @param $sql_file

  213.  *   Contains SQL statements to be executed

  214.  *

  215.  * @ingroup tripal_core

  216.  */

  217. function tripal_core_install_sql($sql_file) {

  218.   

  219.   $chado_local = tripal_core_schema_exists('chado');

  220. 

  221.   if($chado_local) {

  222.     db_query("set search_path to chado");

  223.   }

  224.   print "Loading $sql_file...\n";

  225.   $lines = file($sql_file, FILE_SKIP_EMPTY_LINES);

  226. 

  227.   if (!$lines) {

  228.     return 'Cannot open $schema_file';

  229.   }

  230. 

  231.   $stack = array();

  232.   $in_string = 0;

  233.   $query = '';

  234.   $i = 0;

  235.   $success = 1;

  236.   foreach ($lines as $line_num => $line) {

  237.     $i++;

  238.     $type = '';

  239.     // find and remove comments except when inside of strings

  240.     if (preg_match('/--/', $line) and !$in_string and !preg_match("/'.*?--.*?'/", $line)) {

  241.       $line = preg_replace('/--.*$/', '', $line);  // remove comments

  242.     }

  243.     if (preg_match('/\/\*.*?\*\//', $line)) {

  244.       $line = preg_replace('/\/\*.*?\*\//', '', $line);  // remove comments

  245.     }

  246.     // skip empty lines

  247.     if (preg_match('/^\s*$/', $line) or strcmp($line, '')==0) {

  248.       continue;

  249.     }

  250.     // Find SQL for new objects

  251.     if (preg_match('/^\s*CREATE\s+TABLE/i', $line) and !$in_string) {

  252.       $stack[] = 'table';

  253.       $line = preg_replace("/public./", "chado.", $line);

  254.     }

  255.     if (preg_match('/^\s*ALTER\s+TABLE/i', $line) and !$in_string) {

  256.       $stack[] = 'alter table';

  257.       $line = preg_replace("/public./", "chado.", $line);

  258.     }

  259.     if (preg_match('/^\s*SET/i', $line) and !$in_string) {

  260.       $stack[] = 'set';

  261.     }

  262.     if (preg_match('/^\s*CREATE\s+SCHEMA/i', $line) and !$in_string) {

  263.       $stack[] = 'schema';

  264.     }

  265.     if (preg_match('/^\s*CREATE\s+SEQUENCE/i', $line) and !$in_string) {

  266.       $stack[] = 'sequence';

  267.       $line = preg_replace("/public./", "chado.", $line);

  268.     }

  269.     if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*VIEW/i', $line) and !$in_string) {

  270.       $stack[] = 'view';

  271.       $line = preg_replace("/public./", "chado.", $line);

  272.     }

  273.     if (preg_match('/^\s*COMMENT/i', $line) and !$in_string and sizeof($stack)==0) {

  274.       $stack[] = 'comment';

  275.       $line = preg_replace("/public./", "chado.", $line);

  276.     }

  277.     if (preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*FUNCTION/i', $line) and !$in_string) {

  278.       $stack[] = 'function';

  279.       $line = preg_replace("/public./", "chado.", $line);

  280.     }

  281.     if (preg_match('/^\s*CREATE\s+INDEX/i', $line) and !$in_string) {

  282.       $stack[] = 'index';

  283.     }

  284.     if (preg_match('/^\s*INSERT\s+INTO/i', $line) and !$in_string) {

  285.       $stack[] = 'insert';

  286.       $line = preg_replace("/public./", "chado.", $line);

  287.     }

  288.     if (preg_match('/^\s*CREATE\s+TYPE/i', $line) and !$in_string) {

  289.       $stack[] = 'type';

  290.     }

  291.     if (preg_match('/^\s*GRANT/i', $line) and !$in_string) {

  292.       $stack[] = 'grant';

  293.     }

  294.     if (preg_match('/^\s*CREATE\s+AGGREGATE/i', $line) and !$in_string) {

  295.       $stack[] = 'aggregate';

  296.     }

  297. 

  298.     // determine if we are in a string that spans a line

  299.     $matches = preg_match_all("/[']/i", $line, $temp);

  300.     $in_string = $in_string - ($matches % 2);

  301.     $in_string = abs($in_string);

  302. 

  303.     // if we've reached the end of an object the pop the stack

  304.     if (strcmp($stack[sizeof($stack)-1], 'table') == 0 and preg_match('/\);\s*$/', $line)) {

  305.       $type = array_pop($stack);

  306.     }

  307.     if (strcmp($stack[sizeof($stack)-1], 'alter table') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  308.       $type = array_pop($stack);

  309.     }

  310.     if (strcmp($stack[sizeof($stack)-1], 'set') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  311.       $type = array_pop($stack);

  312.     }

  313.     if (strcmp($stack[sizeof($stack)-1], 'schema') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  314.       $type = array_pop($stack);

  315.     }

  316.     if (strcmp($stack[sizeof($stack)-1], 'sequence') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  317.       $type = array_pop($stack);

  318.     }

  319.     if (strcmp($stack[sizeof($stack)-1], 'view') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  320.       $type = array_pop($stack);

  321.     }

  322.     if (strcmp($stack[sizeof($stack)-1], 'comment') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  323.       $type = array_pop($stack);

  324.     }

  325.     if (strcmp($stack[sizeof($stack)-1], 'function') == 0 and preg_match("/LANGUAGE.*?;\s+$/i", $line)) {

  326.       $type = array_pop($stack);

  327.     }

  328.     if (strcmp($stack[sizeof($stack)-1], 'index') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  329.       $type = array_pop($stack);

  330.     }

  331.     if (strcmp($stack[sizeof($stack)-1], 'insert') == 0 and preg_match('/\);\s*$/', $line)) {

  332.       $type = array_pop($stack);

  333.     }

  334.     if (strcmp($stack[sizeof($stack)-1], 'type') == 0 and preg_match('/\);\s*$/', $line)) {

  335.       $type = array_pop($stack);

  336.     }

  337.     if (strcmp($stack[sizeof($stack)-1], 'grant') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {

  338.       $type = array_pop($stack);

  339.     }

  340.     if (strcmp($stack[sizeof($stack)-1], 'aggregate') == 0 and preg_match('/\);\s*$/', $line)) {

  341.       $type = array_pop($stack);

  342.     }

  343.     // if we're in a recognized SQL statement then let's keep track of lines

  344.     if ($type or sizeof($stack) > 0) {

  345.       $query .= "$line";

  346.     }

  347.     else {

  348.       print "UNHANDLED $i, $in_string: $line";

  349.       tripal_core_chado_install_done();

  350.       return FALSE;

  351.     }

  352.     if (preg_match_all("/\n/", $query, $temp) > 100) {

  353.       print "SQL query is too long.  Terminating:\n$query\n";

  354.       tripal_core_chado_install_done();

  355.       return FALSE;

  356.     }

  357.     if ($type and sizeof($stack) == 0) {

  358.       //print "Adding $type: line $i\n";

  359.       // rewrite the set search_path to make 'public' be 'chado', but only if the

  360.       // chado schema exists

  361.       if (strcmp($type, 'set')==0 and $chado_local){

  362.         $query = preg_replace("/public/m", "chado", $query);

  363.       }

  364.       

  365.       if (!$chado_local) {

  366.         $previous = tripal_db_set_active('chado');

  367.       }

  368.       $result = db_query($query);

  369.       if (!$chado_local) {

  370.         tripal_db_set_active($previous);

  371.       }

  372.       if (!$result) {

  373.         $error  = pg_last_error();

  374.         print "FAILED. Line  $i, $in_string\n$error:\n$query\n\n";        

  375.         tripal_core_chado_install_done();

  376.         $success = 0;

  377.         return $success;

  378.       }

  379.       $query = '';

  380.     }

  381.   }

  382.   tripal_core_chado_install_done();

  383.   return $success;

  384. }

  385. 

  386. /**

  387.  * Finish the Chado Schema Installation

  388.  *

  389.  * @ingroup tripal_core

  390.  */

  391. function tripal_core_chado_install_done() {

  392. 

  393.   // return the search path to normal

  394.   db_query("set search_path to public");

  395. }