Merge branch '7.x-3.x' of github.com:tripal/tripal into 7.x-3.x

tripal_chado/includes/tripal_chado.semweb.inc

@@ -288,7 +288,9 @@ function tripal_chado_semweb_form($form, &$form_state, $chado_table = NULL) {
 
   $chado_tables = chado_get_table_names(TRUE);
   $chado_tables = array_merge(array('Select a Chado Table'), $chado_tables);
-
+  // Make sure the table name exists. If not, reset it.
+  $chado_table = in_array($chado_table, $chado_tables) ? $chado_table: NULL;
+  
   $form['chado_table'] = array(
     '#type' => 'select',
     '#title' => 'Chado Table',
@@ -315,7 +317,7 @@ function tripal_chado_semweb_form($form, &$form_state, $chado_table = NULL) {
       ->execute()
       ->fetchField();
     $columns = $schema['fields'];
-    $headers = array('Field Name', 'Term', 'Description', 'Action');
+    $headers = array('Field Name', 'Vocabulary', 'Term Name', 'Term Description', 'Action');
     $rows = array();
     foreach ($columns AS $column => $detail) {
       // Do not show column if it's the primary key or default cv
@@ -327,20 +329,24 @@ function tripal_chado_semweb_form($form, &$form_state, $chado_table = NULL) {
           ->condition('chado_column', $column)
           ->execute()
           ->fetchField();
+        $sw_voc = '';
         $sw_term = '';
         $sw_desc = '';
         if($cvterm_id) {
           $term = tripal_get_cvterm(array(
             'cvterm_id' => $cvterm_id
           ));
+          $sw_voc = $term->cv_id->name;
           $sw_term = $term->name;
           $sw_desc = $term->definition;
         }
         $rows[] = array(
           $column,
+          $sw_voc,
           $sw_term,
           $sw_desc,
-          l('Edit', '/admin/tripal/storage/chado/semweb/edit/' . $chado_table . '/' . $column)
+          l('Edit', '/admin/tripal/storage/chado/semweb/edit/' . $chado_table . '/' . $column) . ' | ' .
+          l('Reset', '/admin/tripal/storage/chado/semweb/reset/' . $chado_table . '/' . $column)
         );
       }
     }
@@ -364,7 +370,14 @@ function tripal_chado_semweb_form($form, &$form_state, $chado_table = NULL) {
 }
 
 /**
- * Adds defaults to the chado_semweb table.
+ * Implements hook_form()
+ * Edit terms used by the semantic web
+ * 
+ * @param $form
+ * @param $form_state
+ * @param $table
+ * @param $column
+ * @return $form
  */
 function tripal_chado_semweb_edit_form($form, &$form_state, $table = NULL, $column = NULL) {
   
@@ -452,6 +465,13 @@ function tripal_chado_semweb_edit_form($form, &$form_state, $table = NULL, $colu
       '#name' => 'use_cvterm'
     );
   }
+  
+  $form['cancel_button'] = array(
+    '#type' => 'button',
+    '#value' => t('Cancel'),
+    '#name' => 'cancel_button',
+    '#limit_validation_errors' => array()
+  );
 
   $form['#prefix'] = '<div id = "tripal-chado-semweb-edit-form">';
   $form['#suffix'] = '</div>';
@@ -459,31 +479,54 @@ function tripal_chado_semweb_edit_form($form, &$form_state, $table = NULL, $colu
   return $form;
 }
 
+
+/**
+ * Implements hook_form_validate()
+ *
+ * Validate function for editing the semantic web term
+ *
+ * @param unknown $form
+ * @param unknown $form_state
+ */
 function tripal_chado_semweb_edit_form_validate($form, &$form_state) {
-  if (array_key_exists('clicked_button', $form_state) && $form_state['clicked_button']['#name'] =='use_cvterm') {
-    $cvterm_id = NULL;
-    // Make sure we have a cvterm selected
-    $num_selected = 0;
-    foreach ($form_state['values'] as $key => $value) {
-      $matches = array();
-      if (preg_match("/^term-(\d+)$/", $key, $matches) and
-          $form_state['values']['term-' . $matches[1]]) {
-        $cvterm_id = $matches[1];
-        $num_selected++;
+  if (array_key_exists('clicked_button', $form_state)) {
+    if ($form_state['clicked_button']['#name'] =='use_cvterm') {
+      $cvterm_id = NULL;
+      // Make sure we have a cvterm selected
+      $num_selected = 0;
+      foreach ($form_state['values'] as $key => $value) {
+        $matches = array();
+        if (preg_match("/^term-(\d+)$/", $key, $matches) and
+            $form_state['values']['term-' . $matches[1]]) {
+          $cvterm_id = $matches[1];
+          $num_selected++;
+        }
+      }
+      if ($num_selected == 0) {
+        form_set_error('', 'Please select at least one term.');
+      }
+      else if ($num_selected > 1) {
+        form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
+      }
+      else {
+        $form_state['values']['#selected_cvterm_id'] = $cvterm_id;
       }
     }
-    if ($num_selected == 0) {
-      form_set_error('', 'Please select at least one term.');
-    }
-    else if ($num_selected > 1) {
-      form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
-    }
-    else {
-      $form_state['values']['#selected_cvterm_id'] = $cvterm_id;
+    else if ($form_state['clicked_button']['#name'] =='cancel_button') {
+      $table_name = $form_state['values']['table_name'];
+      drupal_goto('/admin/tripal/storage/chado/semweb/' . $table_name);
     }
   }
 }
 
+/**
+ * Implements hook_form_submit()
+ *
+ * Submit function for editing the semantic web term
+ *
+ * @param unknown $form
+ * @param unknown $form_state
+ */
 function tripal_chado_semweb_edit_form_submit($form, &$form_state) {
   if (array_key_exists('clicked_button', $form_state) && $form_state['clicked_button']['#name'] =='use_cvterm') {
         $table_name = $form_state['values']['table_name'];
@@ -521,6 +564,124 @@ function tripal_chado_semweb_edit_form_submit($form, &$form_state) {
         drupal_goto('/admin/tripal/storage/chado/semweb/' . $table_name);
       }
 }
+
+
+/**
+ * Implements hook_form()
+ * Reset term used by semantic web
+ *
+ * @param $form
+ * @param $form_state
+ * @param $table
+ * @param $column
+ * @return $form
+ */
+function tripal_chado_semweb_reset_form($form, &$form_state, $table = NULL, $column = NULL) {
+
+  $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
+
+  $form['chado_table'] = array(
+    '#markup' => 'Are you sure you want to remove the use of this term? ',
+  );
+  $form['table_name'] = array(
+    '#type' => 'value',
+    '#value' => $table
+  );
+  $form['column'] = array(
+    '#type' => 'value',
+    '#value' => $column
+  );
+  
+  $form['submit_button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Reset'),
+    '#name' => 'reset_term'
+  );
+  
+  $form['cancel_button'] = array(
+    '#type' => 'button',
+    '#value' => t('Cancel'),
+    '#name' => 'cancel_button',
+    '#limit_validation_errors' => array()
+  );
+  
+  return $form;
+}
+
+/**
+ * Implements hook_form_validate()
+ * 
+ * Validate function for resetting the semantic web term
+ * 
+ * @param unknown $form
+ * @param unknown $form_state
+ */
+function tripal_chado_semweb_reset_form_validate($form, &$form_state) {
+  if (array_key_exists('clicked_button', $form_state)) {
+    if ($form_state['clicked_button']['#name'] =='use_cvterm') {
+      $cvterm_id = NULL;
+      // Make sure we have a cvterm selected
+      $num_selected = 0;
+      foreach ($form_state['values'] as $key => $value) {
+        $matches = array();
+        if (preg_match("/^term-(\d+)$/", $key, $matches) and
+            $form_state['values']['term-' . $matches[1]]) {
+              $cvterm_id = $matches[1];
+              $num_selected++;
+            }
+      }
+      if ($num_selected == 0) {
+        form_set_error('', 'Please select at least one term.');
+      }
+      else if ($num_selected > 1) {
+        form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
+      }
+      else {
+        $form_state['values']['#selected_cvterm_id'] = $cvterm_id;
+      }
+    }
+    else if ($form_state['clicked_button']['#name'] =='cancel_button') {
+      $table_name = $form_state['values']['table_name'];
+      drupal_goto('/admin/tripal/storage/chado/semweb/' . $table_name);
+    }
+  }
+}
+
+/**
+ * Implements hook_form_submit()
+ *
+ * Submit function for editing the semantic web term
+ *
+ * @param unknown $form
+ * @param unknown $form_state
+ */
+function tripal_chado_semweb_reset_form_submit($form, &$form_state) {
+  if (array_key_exists('clicked_button', $form_state) && $form_state['clicked_button']['#name'] =='reset_term') {
+    $table_name = $form_state['values']['table_name'];
+    $column = $form_state['values']['column'];
+    // Check if there is already a record
+    $record_id =
+    db_select('chado_semweb', 'cs')
+    ->fields('cs', array('chado_semweb_id'))
+    ->condition('chado_table', $table_name)
+    ->condition('chado_column', $column)
+    ->execute()
+    ->fetchField();
+
+    // If the record exists, reset it
+    if ($record_id) {
+      db_update('chado_semweb')
+      ->fields(array(
+        'cvterm_id' => NULL
+      ))
+      ->condition('chado_semweb_id', $record_id)
+      ->execute();
+    }
+    drupal_set_message('The term settings have been reset.');
+    drupal_goto('/admin/tripal/storage/chado/semweb/' . $table_name);
+  }
+}
+
 /**
  *
  */

tripal_chado/tripal_chado.module

@@ -492,7 +492,7 @@ function tripal_chado_menu() {
     'weight' => 10
   );
   $items['admin/tripal/storage/chado/semweb/edit/%/%'] = array(
-    'title' => 'Edit Web Services Term',
+    'title' => 'Edit Semantic Web Term',
     'description' => t('Edit terms used for the web services.'),
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_chado_semweb_edit_form', 6, 7),
@@ -501,6 +501,16 @@ function tripal_chado_menu() {
     'file' => 'includes/tripal_chado.semweb.inc',
     'file path' => drupal_get_path('module', 'tripal_chado'),
   );
+  $items['admin/tripal/storage/chado/semweb/reset/%/%'] = array(
+    'title' => 'Reset Semantic Web Term',
+    'description' => t('Edit terms used for the web services.'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_chado_semweb_reset_form', 6, 7),
+    'type' => MENU_CALLBACK,
+    'access arguments' => array('administer tripal'),
+    'file' => 'includes/tripal_chado.semweb.inc',
+    'file path' => drupal_get_path('module', 'tripal_chado'),
+  );
 
   //////////////////////////////////////////////////////////////////////////////
   //                           Auto Completes

tripal_ws/includes/tripal_ws.admin.inc

@@ -0,0 +1,20 @@
+<?php
+/**
+ * Provide form to store information of other Tripal sites
+ * 
+ * @param unknown $form
+ * @param unknown $form_state
+ */
+function tripal_ws_tripal_sites_form($form, &$form_state) {
+  $form = array();
+  $form['add_tripal_site'] = array(
+    '#markup' => l('Add Tripal site', '/admin/tripal/ws/tripal_sites/add') 
+  );
+  $sites = array('Select a Tripal site');
+  $form['edit_tripal_site'] = array(
+    '#type' => 'select',
+    '#description' => 'Make change to an existing Tripal site',
+    '#options' => $sites
+  );
+  return $form;
+}

tripal_ws/tripal_ws.install

@@ -0,0 +1,56 @@
+<?php
+
+/**
+ * Implementation of hook_schema().
+ *
+ * @ingroup tripal
+ */
+function tripal_ws_schema() {
+  $schema = array();
+  $schema['tripal_sites'] = tripal_ws_tripal_sites_schema();
+  return $schema;
+}
+
+/**
+ * The base table for TripalVocab schema.
+ *
+ * Table to store information about other Tripal sites.
+ */
+function tripal_ws_tripal_sites_schema() {
+  $schema = array(
+    'description' => 'The table for other Tripal sites.',
+    'fields' => array(
+      'id' => array(
+        'description' => 'The primary identifier for a record.',
+        'type' => 'serial',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+      ),
+      'name' => array(
+        'description' => 'Name of the Tripal site',
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+      ),
+      'url' => array(
+        'description' => 'The URL of the Tripal site.',
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+      ),
+      'description' => array(
+        'description' => 'The description of the Tripal site.',
+        'type' => 'varchar',
+        'length' => 255,
+      ),
+    ),
+    'indexes' => array(
+      'name' => array('name'),
+      'url' => array('url'),
+      'description' => array('description'),
+    ),
+    'unique keys' => array('name' => array('name')),
+    'primary key' => array('id'),
+  );
+  return $schema;
+}

tripal_ws/tripal_ws.module

@@ -37,6 +37,29 @@ function tripal_ws_menu() {
     'type' => MENU_CALLBACK,
   );
 
+  // Tripal Web Services setting groups
+  $items['admin/tripal/ws'] = array(
+    'title' => 'Web Services',
+    'description' => t("Exchange data between Tripal sites using the web services."),
+    'weight' => 20,
+    'page callback' => 'system_admin_menu_block_page',
+    'access arguments' => array('administer tripal'),
+    'file' => 'system.admin.inc',
+    'file path' => drupal_get_path('module', 'system'),
+  );
+  $items['admin/tripal/ws/tripal_sites'] = array(
+    'title' => 'Other Tripal Sites',
+    'description' => t('Provides information about other Tripal sites.
+        This allows data exchange and communication betwen Tripal
+        enabled sites through the web services.'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_ws_tripal_sites_form'),
+    'access arguments' => array('administer tripal'),
+    'type' => MENU_NORMAL_ITEM,
+    'weight' => 0,
+    'file' => 'includes/tripal_ws.admin.inc',
+    'file path' => drupal_get_path('module', 'tripal_ws'),
+  );
   return $items;
 }