Removed non-used tripal_search module

tripal_bulk_loader/tripal_bulk_loader.module

@@ -489,7 +489,7 @@ function tripal_bulk_loader_preprocess_tripal_bulk_loader_template(&$variables)
  *     num_records = the number of records successfully inserted
  */
 function tripal_bulk_loader_progess_file_get_progress($job_id, $update_progress = TRUE) {
-  $filename = '/tmp/tripal_bulk_loader_progress-'.$job_id.'.out';
+  $filename = '/tmp/tripal_bulk_loader_progress-' . $job_id . '.out';
   if (!file_exists($filename)) {
     return (object) array();
   }
@@ -507,7 +507,7 @@ function tripal_bulk_loader_progess_file_get_progress($job_id, $update_progress
                                 ) c ON c.nid=b.nid
                               WHERE j.job_id=%d", $job_id));
   if ($job->num_constant_sets) {
-    $num_constant_sets_loaded = round($job->progress / (100 / $job->num_constant_sets),4);
+    $num_constant_sets_loaded = round($job->progress / (100 / $job->num_constant_sets), 4);
 
     // If the next constant set has started loading
     if ($job->num_constant_sets != $num_constant_sets_loaded) {
@@ -576,4 +576,4 @@ function tripal_bulk_loader_coder_ignore() {
     'path' => drupal_get_path('module', 'tripal_bulk_loader'),
     'line prefix' => drupal_get_path('module', 'tripal_bulk_loader'),
   );
-}
+}

tripal_search/tripal_search.coder_ignores.txt

@@ -1,8 +0,0 @@
-; The file should be formatted this way :
-; file:line:warning-type
-; where warning-type is one of security, style, sql, i18n, comment, etc.
-
-; Can't use db placeholders in this case since the variable contains the SQL describing
-; a join and this would be sanitized if that was added through a placeholder
-tripal_search.module:126:sql
-tripal_search.module:136:sql

tripal_search/tripal_search.info

@@ -1,10 +0,0 @@
-
-name = Tripal Search
-description = A module that adds advanced search functions to Drupal, including feature fasta file export from the search result.
-core = 6.x
-project = tripal_search
-package = Tripal
-version = 6.x-0.3.1b
-dependencies[] = search
-dependencies[] = tripal_core
-dependencies[] = tripal_feature

tripal_search/tripal_search.module

@@ -1,159 +0,0 @@
-<?php
-/**
- * @file
- * @todo Add file header description
- */
-
-//
-// Copyright 2009 Clemson University
-//
-/**
- * Tripal Search initiation
- */
-function tripal_search_init() {
-  // Add javascript
-  drupal_add_js(drupal_get_path('theme', 'tripal') .
-                                  '/js/tripal_search.js');
-}
-/**
- *  Tripal Search adds advanced search functions to Drupal's Search module
- */
-function tripal_search_menu() {
-  $items = array();
-  foreach (module_list() as $name) {
-    if (module_hook($name, 'search') && $title = module_invoke($name, 'search', 'name')) {
-      $items['tripal_search/'. $name] = array(
-        'title' => $title,
-        'page callback' => 'tripal_search_view',
-        'access arguments' => array('search content'),
-        'type' => MENU_LOCAL_TASK
-      );
-    }
-  }
-  return $items;
-}
-
-/**
- * Implementation of hook_form_alter().
- */
-function tripal_search_form_alter(&$form, $form_state, $form_id) {
-  if ($form_id == 'search_form' && arg(2)) {
-    // for pagination etc.
-    $get = drupal_query_string_encode($_GET, array('q'));
-    if (preg_match("/node/", arg(1))) {
-      $form['basic']['inline']['fasta'] = array('#type' => 'markup',
-          '#value' => "<br /><br /><a id=\"tripal_search_link\" href=\"".
-                      url('tripal_search/'. arg(1) .'/'. urlencode(search_get_keys()),
-                      array('query' => trim($get)?$get:NULL)) .
-                      "\">Download features (multi-FASTA format)</a><br /><br />");
-
-    }
-  }
-}
-
-/*******************************************************************************
- * Menu callback; presents an tripal_search results page.
- */
-function tripal_search_view() {
-  $type = arg(1);
-  $keys = search_get_keys();
-
-  // Only perform search if there is non-whitespace search term:
-  if (!module_hook($type, 'search')) {
-    return drupal_not_found();
-  }
-
-  if (trim($keys)) {
-    $results = tripal_do_search($keys, $type);    //var_dump($pager_total['0']);
-    return tripal_search_file($type, $keys, $results);
-  }
-}
-
-/*******************************************************************************
- * Return an open search results file.
- */
-function tripal_search_file($type, $keys, $results) {
-
-  drupal_set_header('Content-Type: text');
-  drupal_set_header('Content-Disposition: attachment; filename="searchresults.fasta"');
-
-  foreach ($results as $result) {
-    // Get feature id from drupal database
-    $sqld = "SELECT * FROM {chado_feature} CF INNER JOIN {node} N on N.nid = CF.nid WHERE CF.nid = %d";
-    if ($f_objd = db_fetch_object(db_query($sqld, $result->sid))) {
-
-      // Get sequence from chado database
-      $previous_db = tripal_db_set_active('chado');  // use chado database
-      $sqlc = "SELECT * FROM {feature} WHERE feature_id = '%s'";
-      $f_objc = db_fetch_object(db_query($sqlc, $f_objd->feature_id));
-      tripal_db_set_active($previous_db);  // now use drupal database
-      print tripal_feature_return_fasta($f_objc, $desc);
-    }
-  }
-}
-
-/*******************************************************************************
- *  This code is a duplicate of the do_search function but with the paging
- *  call replaced by a simle db_query call.
- */
-function tripal_do_search($keywords, $type, $join1 = '', $where1 = '1 = 1', $arguments1 = array(), $columns2 = 'i.relevance AS score', $join2 = '', $arguments2 = array(), $sort_parameters = 'ORDER BY score DESC') {
-  $query = search_parse_query($keywords);
-
-  if ($query[2] == '') {
-    form_set_error('keys', t('You must include at least one positive keyword with @count characters or more.', array('@count' => variable_get('minimum_word_size', 3))));
-  }
-  if ($query[6]) {
-    if ($query[6] == 'or') {
-      drupal_set_message(t('Search for either of the two terms with uppercase <strong>OR</strong>. For example, <strong>cats OR dogs</strong>.'));
-    }
-  }
-  if ($query === NULL || $query[0] == '' || $query[2] == '') {
-    return array();
-  }
-
-  // Build query for keyword normalization.
-  $conditions = "$where1 AND ($query[2]) AND i.type = '%s'";
-  $arguments1 = array_merge($arguments1, $query[3], array($type));
-  $join = "INNER JOIN {search_total} t ON i.word = t.word $join1";
-  if (!$query[5]) {
-    $conditions .= " AND ($query[0])";
-    $arguments1 = array_merge($arguments1, $query[1]);
-    $join .= " INNER JOIN {search_dataset} d ON i.sid = d.sid AND i.type = d.type";
-  }
-
-  // Calculate maximum keyword relevance, to normalize it.
-  // @coder-ignore: can't use placeholders since variable defines a join
-  $select = "SELECT SUM(i.score * t.count) AS score FROM {search_index} i " . $join . " WHERE $conditions GROUP BY i.type, i.sid HAVING COUNT(*) >= %d ORDER BY score DESC";
-  $arguments = array_merge($arguments1, array($query[4]));
-  $normalize = db_result(db_query_range($select, $arguments, 0, 1));
-  if (!$normalize) {
-    return array();
-  }
-  $columns2 = str_replace('i.relevance', '('. (1.0 / $normalize) .' * SUM(i.score * t.count))', $columns2);
-
-  // Build query to retrieve results.
-  // @coder-ignore: can't use placeholders since variable defines a join
-  $select = "SELECT i.type, i.sid, $columns2 FROM {search_index} i " . $join . " " . $join2 . " WHERE $conditions GROUP BY i.type, i.sid HAVING COUNT(*) >= %d";
-  $count_select =  "SELECT COUNT(*) FROM ($select) n1";
-  $arguments = array_merge($arguments2, $arguments1, array($query[4]));
-
-  // Do actual search query
-//  $result = pager_query("$select $sort_parameters", 10, 0, $count_select, $arguments);
-  $result = db_query("$select $sort_parameters", $arguments);
-  $results = array();
-  while ($item = db_fetch_object($result)) {
-    $results[] = $item;
-  }
-  return $results;
-}
-
-/**
- * Implements hook_coder_ignore().
- * Defines the path to the file (tripal_search.coder_ignores.txt) where ignore rules for coder are stored
- */
-function tripal_search_coder_ignore() {
-  return array(
-    'path' => drupal_get_path('module', 'tripal_search'),
-    'line prefix' => drupal_get_path('module', 'tripal_search'),
-  );
-}