Added publication search tool (non Drupal Views)

tripal_core/api/tripal_core_chado.api.inc

@@ -2339,6 +2339,8 @@ function tripal_core_exclude_field_from_feature_by_default() {
  *   The number of query results to display per page.
  * @param $element
  *   An optional integer to distinguish between multiple pagers on one page.
+ * @param $count_query
+ *   An SQL query used to count matching records.
  *
  * @returns
  *   A database query result resource or FALSE if the query was not
@@ -2346,7 +2348,7 @@ function tripal_core_exclude_field_from_feature_by_default() {
  *
  * @ingroup tripal_chado_api
  */
-function chado_pager_query($query, $limit, $element, $count) {
+function chado_pager_query($query, $limit, $element, $count_query) {
 
   // The following code is almost an exact duplicate of the
   // Drupal pager_query function. However, substitions have
@@ -2465,6 +2467,7 @@ function chado_query($sql) {
     }
     // if we're local we can just run the query
     if ($is_local) {
+      //dpm($query);
       $last_result = pg_query($persistent_chado, $query);
     }
     else {

tripal_pub/includes/pub_search.inc

@@ -0,0 +1,353 @@
+<?php
+/*
+ * 
+ */
+function tripal_pub_search_page() {
+  global $pager_total, $pager_total_items;
+  
+  $pager_id = 0;
+  $limit = 10;
+  
+  // generate the search form 
+  $form = drupal_get_form('tripal_pub_search_form');  
+  $output .= $form;
+
+  // retrieve any results       
+  if ($_SESSION['tripal_pub_search_form']['perform_search']) {
+    $num_criteria = $_SESSION['tripal_pub_search_form']['num_criteria'];
+     
+    $search_array = array();
+    $search_array['num_criteria'] = $num_criteria;
+    for ($i = 0; $i <= $num_criteria; $i++) {
+      $search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_search_form']['criteria'][$i]['search_terms'];
+      $search_array['criteria'][$i]['scope']        = $_SESSION['tripal_pub_search_form']['criteria'][$i]['scope'];  
+      $search_array['criteria'][$i]['mode']         = $_SESSION['tripal_pub_search_form']['criteria'][$i]['mode'];
+      $search_array['criteria'][$i]['operation']    = $_SESSION['tripal_pub_search_form']['criteria'][$i]['operation'];
+    }
+  
+    // get the list of publications from the remote database using the search criteria.  
+    $pubs = tripal_pub_get_search_results($search_array, $limit, $pager_id);
+  
+    // generate the pager
+    $total_pages = $pager_total[$pager_id];
+    $total_items = $pager_total_items[$pager_id];
+    $page = isset($_GET['page']) ? $_GET['page'] : '0';
+    $pager = theme('pager');
+    
+    // iterate through the results and construct the table displaying the publications
+    $rows = array();
+    $i = $page * $limit + 1;
+    while($pub = db_fetch_object($pubs)) {
+      $title =  $pub->title;
+      if ($pub->nid) {
+        $title = l($pub->title,'node/' . $pub->nid, array('attributes' => array('target' => '_blank')));
+      }
+      $rows[] = array(number_format($i), $pub->pyear, $title);
+      $i++;
+    }
+
+    $headers = array('', 'Year', 'Title');
+    $table = theme('table', $headers, $rows);   
+  
+    // join all to form the results
+    $output .= "<br><p><b>Found " . number_format($total_items) .  
+      ". Page " . ($page + 1) . " of $total_pages. " .
+      " Results</b></br>" . $table . '</p>' . $pager;    
+  }
+  return $output;
+}
+/**
+ * Purpose: Provides the form to search pubmed
+ *
+  * @ingroup tripal_pub
+ */
+function tripal_pub_search_form(&$form_state = NULL) {
+  tripal_core_ahah_init_form();
+ 
+  // Set the default values. If the pub_import_id isn't already defined by the form values 
+  // and one is provided then look it up in the database
+  $criteria = NULL;
+
+  // if the session has variables then use those.  This should only happen when
+  // the 'Test Criteria' button is clicked.
+  $num_criteria = $_SESSION['tripal_pub_search_form']['num_criteria'] ? $_SESSION['tripal_pub_search_form']['num_criteria'] : $num_criteria;    
+ 
+  
+  // If the form_state has variables then use those.  This happens when an error occurs on the form or the 
+  // form is resbumitted using AJAX
+  $num_criteria = $form_state['values']['num_criteria'] ? $form_state['values']['num_criteria'] : $num_criteria;    
+  
+   
+  // change the number of criteria based on form_state post data.
+  if (!$num_criteria) {
+    $num_criteria = 0;
+  }
+  if($form_state['post']["add-$num_criteria"]) {    
+    $num_criteria++;
+  }
+  if($form_state['post']["remove-$num_criteria"]) {    
+    $num_criteria--;
+  }
+  
+  $form['num_criteria']= array(
+    '#type'          => 'hidden',
+    '#default_value' => $num_criteria,
+  );
+  
+  // get publication properties list 
+  $properties = array();
+  $properties[] = 'Any Field';
+  $sql = "
+    SELECT CVTS.cvterm_id, CVTS.name, CVTS.definition
+    FROM {cvtermpath} CVTP
+      INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
+      INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
+      INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
+    WHERE CV.name = 'tripal_pub' and CVTO.name = 'Publication Details' and 
+      NOT CVTS.is_obsolete = 1
+    ORDER BY CVTS.name ASC 
+  ";
+  $prop_types = chado_query($sql); 
+  while ($prop = db_fetch_object($prop_types)) {
+    $properties[$prop->cvterm_id] = $prop->name;
+  }
+  
+  for($i = 0; $i <= $num_criteria; $i++) {
+    // if we have criteria supplied from the database then use that, othrewise look from the form_state or the session
+    if ($criteria) {
+      $search_terms = $criteria['criteria'][$i]['search_terms'];
+      $scope = $criteria['criteria'][$i]['scope'];
+      $operation = $criteria['criteria'][$i]['operation'];
+    }
+    // first populate defaults using any values in the SESSION variable
+    $search_terms = $_SESSION['tripal_pub_search_form']['criteria'][$i]['search_terms'] ? $_SESSION['tripal_pub_search_form']['criteria'][$i]['search_terms'] : $search_terms;
+    $scope        = $_SESSION['tripal_pub_search_form']['criteria'][$i]['scope']        ? $_SESSION['tripal_pub_search_form']['criteria'][$i]['scope']        : $scope;
+    $operation    = $_SESSION['tripal_pub_search_form']['criteria'][$i]['operation']    ? $_SESSION['tripal_pub_search_form']['criteria'][$i]['operation']    : $operation;
+    
+    // next populate defaults using any form values
+    $search_terms = $form_state['values']["search_terms-$i"] ? $form_state['values']["search_terms-$i"] : $search_terms;
+    $scope        = $form_state['values']["scope-$i"]        ? $form_state['values']["scope-$i"]        : $scope;
+    $operation    = $form_state['values']["operation-$i"]    ? $form_state['values']["operation-$i"]    : $operation;
+    
+    // default to searching the title and abstract
+    if (!$scope) {
+      $scope = 'abstract';
+    }
+  
+    $form['criteria'][$i]["search_terms-$i"] = array(
+      '#type'          => 'textfield',
+      '#description'   => t('Please provide a list of words for searching"'),
+      '#default_value' => $search_terms,
+      '#required'      => TRUE,
+    );
+    $form['criteria'][$i]["scope-$i"] = array(
+      '#type'          => 'select',
+      '#description'   => t('Please select the fields to search for this term.'),
+      '#options'       => $properties,
+      '#default_value' => $scope,
+    );  
+    $form['criteria'][$i]["mode-$i"] = array(
+      '#type'          => 'select',
+      '#options'       => array(
+        'Contains'    => 'Contains',
+        'Starts With' => 'Starts With',
+        'Ends With'   => 'Ends With',
+        'Exactly'     => 'Exactly'),
+      '#default_value' => $mode,
+    );   
+    
+    if ($i > 0) {
+      $form['criteria'][$i]["operation-$i"] = array(
+        '#type'          => 'select',
+        '#options'       => array(
+          'AND' => 'AND',
+          'OR'  => 'OR',
+          'NOT' => 'NOT'),
+        '#default_value' => $operation,
+      );
+    }
+    if ($i == $num_criteria) {    
+      if($i > 0) {
+        $form['criteria'][$i]["remove-$i"] = array(
+          '#type'         => 'image_button',
+          '#value'        => t('Remove'),
+          '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
+          '#ahah' => array(
+            'path'    => "find/publications/criteria/minus/$i",
+            'wrapper' => 'tripal-pub-search-form',
+            'event'   => 'click',
+            'method'  => 'replace',
+          ), 
+          '#attributes' => array('onClick' => 'return false;'),
+        );
+      }
+      $form['criteria'][$i]["add-$i"] = array(
+        '#type'         => 'image_button',      
+        '#value'        => t('Add'),
+        '#src'          => drupal_get_path('theme', 'tripal') . '/images/add.png',
+        '#ahah' => array(
+          'path'    => "find/publications/criteria/add/$i",
+          'wrapper' => 'tripal-pub-search-form',
+          'event'   => 'click',
+          'method'  => 'replace',          
+        ),   
+        '#attributes' => array('onClick' => 'return false;'),
+      );
+    }
+  }
+  
+  $form['search'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Search'),
+  );
+
+  return $form;
+}
+/*
+ * 
+ */
+function theme_tripal_pub_search_form($form) {
+  $rows = array();
+  foreach ($form['criteria'] as $i => $element) {
+    if(is_numeric($i)) {
+      $rows[] = array(  
+        array('data' => drupal_render($element["operation-$i"]), 'width' => '10%'),    
+        array('data' => drupal_render($element["scope-$i"]), 'width' => '10%'),
+        drupal_render($element["mode-$i"]) . drupal_render($element["search_terms-$i"]),
+        array('data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]), 'width' => '5%'),
+      );
+    }
+  } 
+  $headers = array('Operation','Scope', 'Search Terms', '');  
+  $markup = theme('table', $headers, $rows, array('id' => 'tripal-pub-search-table'));
+  
+  $form['criteria'] = array(
+    '#type' => 'markup',
+    '#value' =>  $markup,
+    '#weight' => -10,
+  );
+  return drupal_render($form);
+}
+/**
+ *
+ */
+function tripal_pub_search_form_submit($form, &$form_state) {
+   
+  $num_criteria = $form_state['values']['num_criteria'];
+
+  // set the session variables
+  $_SESSION['tripal_pub_search_form']['num_criteria'] = $num_criteria;  
+  unset($_SESSION['tripal_pub_search_form']['criteria']);
+  for ($i = 0; $i <= $num_criteria; $i++) {
+    $search_terms =  trim($form_state['values']["search_terms-$i"]);
+    $scope =  $form_state['values']["scope-$i"];
+    $mode =  $form_state['values']["mode-$i"];
+    $operation =  $form_state['values']["operation-$i"];
+    
+    $_SESSION['tripal_pub_search_form']['criteria'][$i] = array(
+      'search_terms' => $search_terms,
+      'scope' => $scope,
+      'mode' => $mode,
+      'operation' => $operation
+    );
+  }
+  
+  $_SESSION['tripal_pub_search_form']['perform_search'] = 1;
+}
+
+/*
+ * AHAH callback
+ */
+function tripal_pub_search_page_update_criteria($action, $i) {
+  $status = TRUE;
+
+  // prepare and render the form
+  $form = tripal_core_ahah_prepare_form();   
+  $data = theme('tripal_pub_search_form', $form);  
+
+  // bind javascript events to the new objects that will be returned 
+  // so that AHAH enabled elements will work.
+  $settings = tripal_core_ahah_bind_events();
+
+  // return the updated JSON
+  drupal_json(
+    array(
+      'status'   => $status, 
+      'data'     => $data,
+      'settings' => $settings,
+    )  
+  );
+}
+/*
+ * 
+ */
+function tripal_pub_get_search_results($search_array, $limit, $pager_id) {
+
+  // build the SQL based on the criteria provided by the user
+  $select = "SELECT P.*, CP.nid ";
+  $from   = "FROM {pub} P
+               LEFT JOIN public.chado_pub CP on P.pub_id = CP.pub_id 
+            ";
+  $where  = "WHERE ";
+  $order  = "ORDER BY P.pyear DESC, P.title ASC";
+  $args = array();
+  $join = 0;
+  
+  $num_criteria = $search_array['num_criteria'];
+  for ($i = 0; $i <= $num_criteria; $i++) {
+    $value = $search_array['criteria'][$i]['search_terms'];
+    $type_id = $search_array['criteria'][$i]['scope'];
+    $mode = $search_array['criteria'][$i]['mode'];
+    $op = $search_array['criteria'][$i]['operation'];
+    
+    // to prevent SQL injection make sure our operator is
+    // what we expect    
+    if ($op and $op != "AND" and $op != "OR" and $op != 'NOT') {
+      $op = 'AND';
+    }
+    
+    $action = "= lower('%s')";
+    if($mode == 'Contains') {
+      $action = "LIKE lower('%%%s%%')";
+    }
+    if($mode == 'Starts With') {
+      $action = "= lower('%%%s')";  
+    }
+    if($mode == 'Ends With') {
+      $action = "= lower('%s%%')";  
+    }
+   
+    // get the scope type
+    $values = array('cvterm_id' => $type_id);
+    $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
+    $type_name = $cvterm[0]->name;
+    if ($type_name == 'Title') {
+      $where .= " $op (lower(P.title)  $action) ";
+      $args[] = $value;
+    }
+    elseif ($type_name == 'Year') {
+      $where .= " $op (lower(P.pyear)  $action) ";
+      $args[] = $value;
+    }
+    elseif ($type_name == 'Volume') {
+      $where .= " $op (lower(P.volume)  $action) ";
+      $args[] = $value;
+    }
+    elseif ($type_name == 'Issue') {
+      $where .= " $op (lower(P.issue)  $action)";
+      $args[] = $value;
+    }
+    else {
+      $join = 1;
+      $where .= " $op (lower(PP.value) $action AND PP.type_id = %d) ";
+      $args[] = $value;
+      $args[] = $type_id;
+    }
+  }  
+  if ($join) {
+    $from .= " INNER JOIN {pubprop} PP ON PP.pub_id = P.pub_id ";    
+  }
+  $sql = "$select $from $where $order";
+  //dpm(array($mode, $sql, $args));
+  return chado_pager_query($sql, $limit, $pager_id, NULL, $args);
+}

tripal_pub/tripal_pub.module

@@ -7,6 +7,7 @@ require_once "includes/pub_form.inc";
 require_once "includes/pub_importers.inc";
 require_once "includes/pubmed.inc";
 require_once "includes/agricola.inc";
+require_once "includes/pub_search.inc";
 /**
  * @file
  *
@@ -65,7 +66,23 @@ function tripal_pub_node_info() {
 function tripal_pub_menu() {
   $items = array();
   
-  $items['admin/tripal/tripal_pub' ]= array(
+  
+  $items['find/publications' ]= array(
+    'title' => 'Publication Search',
+    'description' => ('Search for publications'),
+    'page callback' => 'tripal_pub_search_page',
+    'access arguments' => array('access chado_pub content'),
+    'type' => MENU_NORMAL_ITEM
+  );
+  
+  $items['find/publications/criteria/%/%'] = array(
+    'page callback' => 'tripal_pub_search_page_update_criteria',
+    'page arguments' => array(5, 6),
+    'access arguments' => array('administer tripal pubs'),    
+    'type ' => MENU_CALLBACK,
+  );
+  
+  $items['admin/tripal/tripal_pub']= array(
     'title' => 'Publications',
     'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
     'page callback' => 'theme',
@@ -164,6 +181,7 @@ function tripal_pub_menu() {
 function tripal_pub_theme() {
 
   return array(
+    // node templates
     'tripal_pub_base' => array(
       'arguments' => array('node' => NULL),
     ),
@@ -179,16 +197,23 @@ function tripal_pub_theme() {
     'tripal_pub_relationships' => array(
       'arguments' => array('node' => NULL)
     ),
+    
+    // instructions page for the pub module
+    'tripal_pub_admin' => array(
+      'template' => 'tripal_pub_admin',  
+      'arguments' =>  array(NULL),  
+      'path' => drupal_get_path('module', 'tripal_pub') . '/theme' 
+    ),
+    
+    // themed forms
     'tripal_pub_importer_setup_form' => array(
        'arguments' => array('form'),
     ),
-    'chado_pub_node_form' => array(
+    'tripal_pub_search_form' => array(
        'arguments' => array('form'),
     ),
-    'tripal_pub_admin' => array(
-      'template' => 'tripal_pub_admin',  
-      'arguments' =>  array(NULL),  
-      'path' => drupal_get_path('module', 'tripal_pub') . '/theme' 
+    'chado_pub_node_form' => array(
+       'arguments' => array('form'),
     ),
   );
 }
@@ -685,6 +710,9 @@ function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
       $form['#action'] = url("admin/tripal/tripal_pub/import/new");
     }
   }
+  if ($form_id == "tripal_pub_search_form") {    
+    $form['#action'] = url("find/publications");
+  }
   if ($form_id == "chado_pub_node_form") {
   }
 }