Fixed a misnamed element in the CV module, and continued development with pub module. Committing at end of day

tripal_cv/includes/tripal_cv_admin.inc

@@ -7,7 +7,7 @@
  */
 function tripal_cv_edit_page() {
   $output .= drupal_get_form('tripal_cv_select_form');
-  $output .= '<div id="db-edit-div">Please select a vocabulary above to view or edit</div>';
+  $output .= '<div id="cv-edit-div">Please select a vocabulary above to view or edit</div>';
 
   return $output;
 }
@@ -37,7 +37,7 @@ function tripal_cv_select_form() {
     '#options' => $cvs,
     '#ahah' => array(
       'path' => 'admin/tripal/tripal_cv/cv/edit/js',
-      'wrapper' => 'db-edit-div',
+      'wrapper' => 'cv-edit-div',
       'effect' => 'fade',
       'event' => 'change',
       'method' => 'replace',

tripal_pub/includes/pubmed.inc

@@ -14,16 +14,34 @@ function tripal_pub_remote_search_pubmed($search_array, $num_to_retrieve, $pager
   
   // convert the terms list provicded by the caller into a string with words
   // separated by a '+' symbol.
-  $terms = '';
-  if ($search_array['search_terms']) {
-    $terms = '(' . implode("+", preg_split('/\s+/', trim($search_array['search_terms']))) . '[Title/Abstract]) AND ';
-  }
-  if ($search_array['author']) {
-    $terms = "(" . $search_array . "[Author]) AND ";
-  }
-  $terms = substr($terms, 0, -4);
-  
+  $num_criteria = $search_array['num_criteria'];
+  $days = $search_array['num_criteria'];
+
+  $search_str = '';
+  for ($i = 0; $i <= $num_criteria; $i++) {
+    $search_terms = $search_array['criteria'][$i]['search_terms'];
+    $scope = $search_array['criteria'][$i]['scope'];
+    $op = $search_array['criteria'][$i]['operation'];
+    
+    if ($op) {
+      $search_str .= "$op";
+    }
+    
+    $search_str .= '(';
+    $search_str .= implode("+", preg_split('/\s+/', trim($search_terms)));
+    if($scope == 'title') {
+      $search_str .= '[Title]';
+    }    
+    elseif($scope == 'author') {
+      $search_str .= '[Author]';
+    }    
+    elseif($scope == 'abstract') {
+      $search_str .= '[Title/Abstract]';
+    }
+    $search_str .= ')'; 
+  }  
   $search_array['limit'] = $num_to_retrieve;
+  $search_array['search_terms'] = $search_str;
 
   // we want to get the list of pubs using the search terms but using a Drupal style pager
   $pubs = tripal_pager_callback('tripal_pub_remote_search_pubmed_range',  

tripal_pub/includes/remote_search.inc

@@ -1,16 +1,77 @@
 <?php
+
+/*
+ * 
+ */
+function tripal_pub_remote_search_page() {
+  global $pager_total, $pager_total_items;
+  
+  $pager_id = 0;
+  $limit = 10;
+  
+  // generate the search form 
+  $form = drupal_get_form('tripal_pub_remote_search_form');
+
+  // retrieve any results
+  $remote_db = $_SESSION['tripal_pub_search']['remote_db'];
+  $num_criteria = $_SESSION['tripal_pub_search']['num_criteria'];
+  $days = $_SESSION['tripal_pub_search']['days'];
+ 
+  $search_array = array();
+  $search_array['remote_db'] = $remote_db;
+  $search_array['num_criteria'] = $num_criteria;
+  $search_array['days'] = $days; 
+  for ($i = 0; $i <= $num_criteria; $i++) {
+    $search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'];
+    $search_array['criteria'][$i]['scope'] = $_SESSION['tripal_pub_search']['criteria'][$i]['scope'];  
+    $search_array['criteria'][$i]['operation'] = $_SESSION['tripal_pub_search']['criteria'][$i]['operation'];
+  }
+    
+  // get the list of publications from the remote database using the search criteria.
+  $pubs = tripal_pub_get_remote_search_results($remote_db, $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 * $limit + 1;
+  if (count($pubs) > 0) {
+    foreach ($pubs as $pub) {
+      $rows[] = array(number_format($i), $pub['citation']);
+      $i++;
+    }
+  }
+  $headers = array('', 'Citation');
+  $table = theme('table', $headers, $rows);
+  
+  
+  // join all to form the final page
+  $output =  $form . "<p><b>Found " . number_format($total_items) .  
+    ". Page " . ($page + 1) . " of $total_pages. " .
+    " Results</b></br>" . $table . '</p>' . $pager;    
+  
+  return $output;
+}
 /*
  * 
  */
 function theme_tripal_pub_remote_search_form($form) {
-  $rows = array(
-    array(            
-      drupal_render($form['scope']),
-      drupal_render($form['operation']),
-      drupal_render($form['search_terms']),
-    ),
-  );
-  $headers = array('Search Terms', 'Scope', 'Operation');
+  $rows = array();
+  foreach ($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["search_terms-$i"]),
+        array('data' => drupal_render($element["add-$i"]) . drupal_render($element["remove-$i"]), 'width' => '5%'),
+      );
+    }
+  }
+  $headers = array('Operation','Scope', 'Search Terms', '');
   $form['criteria'] = array(
     '#type' => 'markup',
     '#value' =>  theme('table', $headers, $rows),
@@ -24,12 +85,32 @@ function theme_tripal_pub_remote_search_form($form) {
   * @ingroup tripal_pub
  */
 function tripal_pub_remote_search_form(&$form_state = NULL) {
-  $remote_db = $_SESSION['tripal_pub_search_criteria']['remote_db'];
-  $search_terms = $_SESSION['tripal_pub_search_criteria']['search_terms'];
-  $days = $_SESSION['tripal_pub_search_criteria']['days'];
-  $scope = $_SESSION['tripal_pub_search_criteria']['scope'];
-  $operation = $_SESSION['tripal_pub_search_criteria']['operation'];
+  tripal_core_ahah_init_form();
+
+  // set default values.  First use what is in the form_state['values'] array. If nothing there then use the session variable.
+  $remote_db = $form_state['values']['remote_db'] ? $form_state['values']['remote_db'] : $_SESSION['tripal_pub_search']['remote_db'];
+  $days = $form_state['values']['days'] ? $form_state['values']['days'] : $_SESSION['tripal_pub_search']['days']; 
+  $num_criteria = $form_state['values']['num_criteria'] ? $form_state['values']['num_criteria'] : $_SESSION['tripal_pub_search']['num_criteria'];
+  $loader_name = $form_state['values']['loader_name'];
   
+  // 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['loader_name'] = array(
+    '#type'          => 'textfield',
+    '#title'         => t('Loader Name'),
+    '#description'   => t('Please provide a name for this loader setup..'),
+    '#default_value' => $loader_name,
+  );
+   
   $remote_dbs = array('Pubmed' => 'Pubmed');
   $form['remote_db'] = array(
     '#title' => t('Remote Publication Database'),
@@ -38,28 +119,79 @@ function tripal_pub_remote_search_form(&$form_state = NULL) {
     '#default_value' => $remote_db,
   );
 
-  $form['search_terms']= array(
-    '#type'          => 'textfield',
-    '#description'   => t('Please provide a list of words, separated by spaces for searching.'),
-    '#default_value' => $search_terms,
-  );
-  $form['scope']= array(
-    '#type'          => 'select',
-    '#description'   => t('Please select the fields to search for this term.'),
-    '#options'       => array('title'    => 'Title',
-                              'abstract' => 'Title/Abstract',
-                              'author'   => 'Author'),
-    '#default_value' => $scope,
-  );
-  $form['operation']= array(
-    '#type'          => 'select',
-    '#options'       => array('AND' => 'AND',
-                              'OR'  => 'OR',
-                              'NOT' => 'NOT'),
-    '#default_value' => $operation,
+  $form['num_criteria']= array(
+    '#type'          => 'hidden',
+    '#default_value' => $num_criteria,
   );
+  
+  for($i = 0; $i <= $num_criteria; $i++) {
+    $search_terms = $form_state['values']["search_terms-$i"] ? $form_state['values']["search_terms-$i"] : $_SESSION['tripal_pub_search']['criteria'][$i]['search_terms'];
+    $scope = $form_state['values']["scope-$i"] ? $form_state['values']["scope-$i"] : $_SESSION['tripal_pub_search']['criteria'][$i]['scope'];
+    $operation = $form_state['values']["operation-$i"] ? $form_state['values']["operation-$i"] : $_SESSION['tripal_pub_search']['criteria'][$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, separated by spaces for searching.'),
+      '#default_value' => $search_terms,
+    );
+    $form['criteria'][$i]["scope-$i"] = array(
+      '#type'          => 'select',
+      '#description'   => t('Please select the fields to search for this term.'),
+      '#options'       => array(
+        'any'      => 'Any Field',
+        'title'    => 'Title',
+        'abstract' => 'Title/Abstract',
+        'author'   => 'Author'),
+      '#default_value' => $scope,
+    );    
+    
+    if ($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-$i"] = array(
+          '#type'         => 'image_button',
+          '#value'        => t('Remove'),
+          '#src'          => drupal_get_path('theme', 'tripal') . '/images/minus.png',
+          '#ahah' => array(
+            'path'    => "admin/tripal/tripal_pub/import_setup/criteria/minus/$i",
+            'wrapper' => 'tripal-pub-remote-search-form',
+            'event'   => 'click',
+            'method'  => 'replace',
+          ), 
+          '#attributes' => array('onClick' => 'return false;'),
+        );
+      }
+      $form['criteria'][$i]["add-$i"] = array(
+        '#type'         => 'image_button',      
+        '#value'        => t('Add'),
+        '#src'          => drupal_get_path('theme', 'tripal') . '/images/add.png',
+        '#ahah' => array(
+          'path'    => "admin/tripal/tripal_pub/import_setup/criteria/add/$i",
+          'wrapper' => 'tripal-pub-remote-search-form',
+          'event'   => 'click',
+          'method'  => 'replace',          
+        ),   
+        '#attributes' => array('onClick' => 'return false;'),
+      );
+    }
+  }
 
-  $form['days']= array(
+  
+  $form['days'] = array(
     '#type'          => 'textfield',
     '#title'         => t('Number of Days'),
     '#description'   => t('Please provide the number of days to limit your search.  For example, to search only the last 60 days, enter the number 60 in the field.'),
@@ -68,8 +200,11 @@ function tripal_pub_remote_search_form(&$form_state = NULL) {
   
   $form['submit'] = array(
     '#type'         => 'submit',
-    '#value'        => t('Submit'),
-    '#executes_submit_callback' => TRUE,
+    '#value'        => t('Test Criteria'),
+  );
+  $form['submit'] = array(
+    '#type'         => 'submit',
+    '#value'        => t('Save Criteria'),
   );
 
   return $form;
@@ -79,14 +214,21 @@ function tripal_pub_remote_search_form(&$form_state = NULL) {
  *
  */
 function tripal_pub_remote_search_form_validate($form, &$form_state) {
-  $remote_db =  $form_state['values']['remote_db'];
-  $search_terms =  $form_state['values']['search_terms'];
-  $scope =  $form_state['values']['scope'];
-  $operation =  $form_state['values']['operation'];
-  $days =  $form_state['values']['days'];
-  
-  if ($days and !is_numeric($days) or preg_match('/\./', $days)) {
-    form_set_error('days', "Please enter a numeric, non decimal value, for the number of days.");
+  $num_criteria = $form_state['values']['num_criteria'];
+  $remote_db =  $form_state['values']["remote_db"];
+  $days =  trim($form_state['values']["days"]);
+
+  for ($i = 0; $i <= $num_criteria; $i++) {            
+    $search_terms =  trim($form_state['values']["search_terms-$i"]);
+    $scope =  $form_state['values']["scope-$i"];
+    $operation =  $form_state['values']["operation-$i"];
+    
+    if ($days and !is_numeric($days) or preg_match('/\./', $days)) {
+      form_set_error("days-$i", "Please enter a numeric, non decimal value, for the number of days.");
+    }
+    if (!$search_terms) {
+      form_set_error("search_terms-$i", "Please enter a value for searching.");
+    }
   }
 }
 
@@ -94,79 +236,25 @@ function tripal_pub_remote_search_form_validate($form, &$form_state) {
  *
  */
 function tripal_pub_remote_search_form_submit($form, &$form_state) {
-  
-  $remote_db =  $form_state['values']['remote_db'];
-  $search_terms =  $form_state['values']['search_terms'];
-  $scope =  $form_state['values']['scope'];
-  $operation =  $form_state['values']['operation'];
-  $days =  $form_state['values']['days'];
-  
-  // store the search settings in a session variable. Then when the page
-  // is refreshed these values will be available for the page to 
-  // generate results. 
-  if ($op == 'Reset') {   
-    unset($_SESSION['tripal_pub_search_criteria']); 
-    unset($form_state['values']);
-  }
-  else {
-    $_SESSION['tripal_pub_search_criteria'] = array(
-      'remote_db' => $remote_db,
+ 
+  $num_criteria = $form_state['values']['num_criteria'];
+  $remote_db =  $form_state['values']["remote_db"];
+  $days =  trim($form_state['values']["days"]);
+    
+  $_SESSION['tripal_pub_search']['remote_db'] = $remote_db;
+  $_SESSION['tripal_pub_search']['days'] = $days;
+  $_SESSION['tripal_pub_search']['num_criteria'] = $num_criteria;
+  for ($i = 0; $i <= $num_criteria; $i++) {
+    $search_terms =  trim($form_state['values']["search_terms-$i"]);
+    $scope =  $form_state['values']["scope-$i"];
+    $operation =  $form_state['values']["operation-$i"];
+    
+    $_SESSION['tripal_pub_search']['criteria'][$i] = array(
       'search_terms' => $search_terms,
       'scope' => $scope,
-      'operation' => $operation,
-      'days' => $days
+      'operation' => $operation
     );
-  }  
-}
-/*
- * 
- */
-function tripal_pub_remote_search_page() {
-  global $pager_total, $pager_total_items;
-  
-  $pager_id = 0;
-  $limit = 10;
-  
-  // generate the search form 
-  $form = drupal_get_form('tripal_pub_remote_search_form');
-
-  // retrieve any results
-  $remote_db = $_SESSION['tripal_pub_search_criteria']['remote_db'];
-  
-  $search_array['search_terms'] = $_SESSION['tripal_pub_search_criteria']['search_terms'];
-  $search_array['days'] = $_SESSION['tripal_pub_search_criteria']['days'];  
-  $search_array['scope'] = $_SESSION['tripal_pub_search_criteria']['scope'];  
-  $search_array['operation'] = $_SESSION['tripal_pub_search_criteria']['operation'];
-    
-  // get the list of publications from the remote database using the search criteria.
-  $pubs = tripal_pub_get_remote_search_results($remote_db, $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 * $limit + 1;
-  if (count($pubs) > 0) {
-    foreach ($pubs as $pub) {
-      $rows[] = array(number_format($i), $pub['citation']);
-      $i++;
-    }
-  }
-  $headers = array('', 'Citation');
-  $table = theme('table', $headers, $rows);
-  
-
-  
-  // join all to form the final page
-  $output = $form . "<p><b>Found " . number_format($total_items) .  
-    ". Page " . ($page + 1) . " of $total_pages. " .
-    " Results</b></br>" . $table . '</p>' . $pager;    
-  
-  return $output;
+  } 
 }
 /*
  * 
@@ -185,3 +273,26 @@ function tripal_pub_get_remote_search_results($remote_db, $search_array, $num_to
   return $pubs;  
 }
 
+/*
+ * AHAH callback
+ */
+function tripal_pub_remote_search_page_update_criteria($action, $i) {
+  $status = TRUE;
+
+  // prepare and render the form
+  $form = tripal_core_ahah_prepare_form();   
+  $data = theme('tripal_pub_remote_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,
+    )  
+  );
+}

tripal_pub/tripal_pub.module

@@ -15,6 +15,15 @@ require_once "includes/remote_search.inc";
  */
 
 
+/**
+ *
+ * @ingroup tripal_pub
+ */
+function tripal_pub_init() {
+  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_pub.js');
+}
+
+
 /**
  * Implementation of hook_tripal_pub_node_info().
  *
@@ -69,10 +78,17 @@ function tripal_pub_menu() {
   );
 
   $items['admin/tripal/tripal_pub/import_setup'] = array(
-    'title' => t('Publication Finder'),
+    'title' => t('Pub Loader Setup'),
     'description' => t('Finds publications using remote publication databases (e.g. PubMed).'),
     'page callback' => 'tripal_pub_remote_search_page',
-    'access arguments' => array('access content'),
+    'access arguments' => array('administer tripal pubs'),
+    'type ' => MENU_CALLBACK,
+  );
+  
+  $items['admin/tripal/tripal_pub/import_setup/criteria/%/%'] = array(
+    'page callback' => 'tripal_pub_remote_search_page_update_criteria',
+    'page arguments' => array(5, 6),
+    'access arguments' => array('administer tripal pubs'),    
     'type ' => MENU_CALLBACK,
   );
   
@@ -1246,5 +1262,15 @@ function publication_author_validate($element) {
   }
 }
 
+/*
+ * 
+ */
 
-
+function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
+  if ($form_id == "tripal_pub_remote_search_form") {    
+    // updating the form through the ahah callback sets the action of
+    // the form to the ahah callback URL. We need to set it back
+    // to the normal form URL
+    $form['#action'] = url("admin/tripal/tripal_pub/import_setup");
+  }
+}