API: Added tripal_set_message and used it in chado node properties/dbxrefs/relationships api

tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc

@@ -140,6 +140,19 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
     }
   }
 
+  // Tell tripal administrators how to add terms to the property types drop down.
+  $importance = (empty($db_options)) ? TRIPAL_WARNING : TRIPAL_INFO;
+  $tripal_message = tripal_set_message(
+    t('To add databases to the drop down list, you need to <a href="@dblink">add
+      an external database reference</a>.',
+      array(
+        '@dblink' => url('admin/tripal/chado/tripal_db/add')
+      )
+    ),
+    $importance,
+    array('return_html' => TRUE)
+  );
+
   // the fieldset of the dbxref elements
   $form['addtl_dbxrefs'] = array(
     '#type' => 'fieldset',
@@ -153,6 +166,11 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
     '#weight'      => 9
   );
 
+  $form['addtl_dbxrefs']['admin_message'] = array(
+    '#type' => 'markup',
+    '#markup' => $tripal_message
+  );
+
   // this form element is a tree, so that we don't puke all of the values into then node variable
   // it is set as a tree, and keeps them in the $form_state['values']['dbxref_table'] heading.
   $form['addtl_dbxrefs']['dbxref_table'] = array(

tripal_core/api/tripal_core.chado_nodes.properties.api.inc

@@ -136,7 +136,7 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
       $property_options = array();
       $property_options[] = 'Select a Property';
       $sql = "
-        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
+        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition, CV.cv_id as cv_id
         FROM  {cvterm} CVT
           INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
         WHERE
@@ -147,12 +147,17 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
       $prop_types = chado_query($sql, array(':cv_name' => $details['cv_name']));
       while ($prop = $prop_types->fetchObject()) {
         $property_options[$prop->cvterm_id] = $prop->name;
+        $details['cv_id'] = $prop->cv_id;
+      }
+      if (!isset($details['cv_id'])) {
+        $result = chado_select_record('cv',array('cv_id'),array('name' => $details['cv_name']));
+        $details['cv_id'] = $result[0]->cv_id;
       }
     } elseif (isset($details['cv_id'])) {
       $property_options = array();
       $property_options[] = 'Select a Property';
       $sql = "
-        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
+        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition, CV.name as cv_name
         FROM  {cvterm} CVT
           INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
         WHERE
@@ -163,23 +168,62 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
       $prop_types = chado_query($sql, array(':cv_id' => $details['cv_id']));
       while ($prop = $prop_types->fetchObject()) {
         $property_options[$prop->cvterm_id] = $prop->name;
+        $details['cv_name'] = $prop->cv_name;
+      }
+      if (!isset($details['cv_name'])) {
+        $result = chado_select_record('cv',array('name'),array('cv_id' => $details['cv_id']));
+        $details['cv_name'] = $result[0]->name;
       }
     }
   }
 
+  // Tell tripal administrators how to add terms to the property types drop down.
+  if (empty($property_options)) {
+    $tripal_message = tripal_set_message(
+      t('There are currently no proeprty types! To add additional properties to the drop
+        down list, you need to <a href="@cvtermlink">add a controlled vocabulary term</a>
+        to the %cv_name controlled vocabulary.',
+        array(
+          '%cv_name' => $details['cv_name'],
+          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/'.$details['cv_id'].'/cvterm/add')
+        )
+      ),
+      TRIPAL_WARNING,
+      array('return_html' => TRUE)
+    );
+  }
+  else {
+    $tripal_message = tripal_set_message(
+      t('To add additional properties to the drop down list, you need to <a href="@cvtermlink">add
+        a controlled vocabulary term</a> to the %cv_name controlled vocabulary.',
+        array(
+          '%cv_name' => $details['cv_name'],
+          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/'.$details['cv_id'].'/cvterm/add')
+        )
+      ),
+      TRIPAL_INFO,
+      array('return_html' => TRUE)
+    );
+  }
+
   // the fieldset of the property elements
   $form['properties'] = array(
     '#type' => 'fieldset',
     '#title' => t($details['fieldset_title']),
     '#description' => t('You may add additional properties by selecting a property type
       from the dropdown and adding text. You may add as many properties as desired by
-      clicking the add button on the right. To remove a property, click the remove button.
-      To add additional properties to the drop down. ' . $details['additional_instructions']),
+      clicking the add button on the right. To remove a property, click the remove button.'
+      . $details['additional_instructions']),
     '#prefix' => "<div id='properties-fieldset'>",
     '#suffix' => '</div>',
     '#weight'      => 8
   );
 
+  $form['properties']['admin_message'] = array(
+    '#type' => 'markup',
+    '#markup' => $tripal_message
+  );
+
   // this form element is a tree, so that we don't puke all of the values into then node variable
   // it is set as a tree, and keeps them in the $form_state['values']['property_table'] heading.
   $form['properties']['property_table'] = array(

tripal_core/api/tripal_core.chado_nodes.relationships.api.inc

@@ -150,7 +150,7 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
       $type_options = array();
       $type_options[] = 'Select a Property';
       $sql = "
-        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
+        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition, CV.cv_id as cv_id
         FROM  {cvterm} CVT
           INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
         WHERE
@@ -161,12 +161,17 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
       $prop_types = chado_query($sql, array(':cv_name' => $details['cv_name']));
       while ($prop = $prop_types->fetchObject()) {
         $type_options[$prop->cvterm_id] = $prop->name;
+        $details['cv_id'] = $prop->cv_id;
+      }
+      if (!isset($details['cv_id'])) {
+        $result = chado_select_record('cv',array('cv_id'),array('name' => $details['cv_name']));
+        $details['cv_id'] = $result[0]->cv_id;
       }
     } elseif (isset($details['cv_id'])) {
       $type_options = array();
       $type_options[] = 'Select a Property';
       $sql = "
-        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
+        SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition, CV.name AS cv_name
         FROM  {cvterm} CVT
           INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
         WHERE
@@ -177,10 +182,44 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
       $prop_types = chado_query($sql, array(':cv_id' => $details['cv_id']));
       while ($prop = $prop_types->fetchObject()) {
         $type_options[$prop->cvterm_id] = $prop->name;
+        $details['cv_name'] = $prop->cv_name;
+      }
+      if (!isset($details['cv_name'])) {
+        $result = chado_select_record('cv',array('name'),array('cv_id' => $details['cv_id']));
+        $details['cv_name'] = $result[0]->name;
       }
     }
   }
 
+  // Tell tripal administrators how to add terms to the property types drop down.
+  if (empty($type_options)) {
+    $tripal_message = tripal_set_message(
+      t('There are currently no proeprty types! To add additional properties to the drop
+        down list, you need to <a href="@cvtermlink">add a controlled vocabulary term</a>
+        to the %cv_name controlled vocabulary.',
+        array(
+          '%cv_name' => $details['cv_name'],
+          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/'.$details['cv_id'].'/cvterm/add')
+        )
+      ),
+      TRIPAL_WARNING,
+      array('return_html' => TRUE)
+    );
+  }
+  else {
+    $tripal_message = tripal_set_message(
+      t('To add additional properties to the drop down list, you need to <a href="@cvtermlink">add
+        a controlled vocabulary term</a> to the %cv_name controlled vocabulary.',
+        array(
+          '%cv_name' => $details['cv_name'],
+          '@cvtermlink' => url('admin/tripal/chado/tripal_cv/cv/'.$details['cv_id'].'/cvterm/add')
+        )
+      ),
+      TRIPAL_INFO,
+      array('return_html' => TRUE)
+    );
+  }
+
   $form['relationships'] = array(
     '#type' => 'fieldset',
     '#title' => t($details['fieldset_title']),
@@ -194,6 +233,11 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
     '#weight'      => 10
   );
 
+  $form['relationships']['admin_message'] = array(
+    '#type' => 'markup',
+    '#markup' => $tripal_message
+  );
+
   // this form element is a tree, so that we don't puke all of the values into then node variable
   // it is set as a tree, and keeps them in the $form_state['values']['relationship_table'] heading.
   $form['relationships']['relationship_table'] = array(

tripal_core/api/tripal_core.tripal.api.inc

@@ -106,6 +106,73 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
   }
 }
 
+/**
+ * Display messages to tripal administrators. This can be used instead of
+ * drupal_set_message when you want to target tripal administrators.
+ *
+ * @param $message
+ *   The message to be displayed to the tripal administrators
+ * @param $importance
+ *   The level of importance for this message. In the future this will be used to allow
+ *   administrators to filter some of these messages. It can be one of the following:
+ *     - TRIPAL_CRITICAL: Critical conditions.
+ *     - TRIPAL_ERROR: Error conditions.
+ *     - TRIPAL_WARNING: Warning conditions.
+ *     - TRIPAL_NOTICE: Normal but significant conditions.
+ *     - TRIPAL_INFO: (default) Informational messages.
+ *     - TRIPAL_DEBUG: Debug-level messages.
+ * @param $options
+ *   Any options to apply to the current message. Supported options include:
+ *     - return_html: return HTML instead of setting a drupal message. This can be
+ *         used to place a tripal message in a particular place in the page.
+ *         The default is FALSE.
+ */
+function tripal_set_message($message, $importance = TRIPAL_INFO, $options = array()) {
+
+  // set defaults
+  $options['return_html'] = (isset($options['return_html'])) ? $options['return_html'] : FALSE;
+
+  // Get human-readable severity string
+  $importance_string = '';
+  switch ($importance) {
+    case TRIPAL_CRITICAL:
+      $importance_string = 'CRITICAL';
+      break;
+    case TRIPAL_ERROR:
+      $importance_string = 'ERROR';
+      break;
+    case TRIPAL_WARNING:
+      $importance_string = 'WARNING';
+      break;
+    case TRIPAL_NOTICE:
+      $importance_string = 'NOTICE';
+      break;
+    case TRIPAL_INFO:
+      $importance_string = 'INFO';
+      break;
+    case TRIPAL_DEBUG:
+      $importance_string = 'DEBUG';
+      break;
+  }
+
+  // Mark-up the Message
+  $full_message =
+     '<div class="tripal-site-admin-message">'
+       . '<span class="tripal-serverity-string ' . strtolower($importance_string) . '">' . $importance_string . ': </span>'
+       . $message
+   . '</div>';
+
+  // Handle whether to return the HTML & let the caller deal with it
+  // or to use drupal_set_message to put it near the top of the page  & let the theme deal with it
+  if ($options['return_html']) {
+    return '<div class="messages tripal-site-admin-only">' . $full_message . '</div>';
+  }
+  else {
+    drupal_set_message($full_message, 'tripal-site-admin-only');
+  }
+
+}
+
 /**
  * Use this function to encapsulate text intended to be
  * visible only by the site administrator. A small tripal logo

tripal_core/theme/css/tripal.css

@@ -1,8 +1,8 @@
 /**
  * The Tripal generic node template (node--chado-generc.tpl.php)
- * has an outer div box with class 'tripal-contents' and with an inner 
+ * has an outer div box with class 'tripal-contents' and with an inner
  * table with an id of 'tripal-contents-table'.  The table has a single
- * row with two columns.  The smaller left column houses the table of 
+ * row with two columns.  The smaller left column houses the table of
  * contents (TOC) for the node data.  The larger right column houses the data:
  *
  * |-----------------------------------------------|
@@ -42,9 +42,9 @@
  * the table is meant for organizing the sidebar and contents so they don't
  * slip and slide around as would happen with div boxes that were floated.
  * Therefore, we use !important to keep the default theme from overrideing
- * the table settings. 
+ * the table settings.
  */
- 
+
 .tripal-contents-table tbody {
   padding: 0px !important;
   margin:  0px !important;
@@ -57,7 +57,7 @@
   border:  none !important;
   background-color: transparent !important;
 }
-.tripal-contents-table-td-toc { 
+.tripal-contents-table-td-toc {
   border-right: 1px solid #CCCCCC !important;
   margin:  0px !important;
   padding: 0px !important;
@@ -65,7 +65,7 @@
   text-align: left !important;
   vertical-align: top !important;
 }
-.tripal-contents-table-td-data { 
+.tripal-contents-table-td-data {
   border: none !important;
   margin:  0px !important;
   padding: 0px 0px 0px 20px !important;
@@ -76,7 +76,7 @@
 
 /**
  * The table of contents is an unordered list. The following can are used
- * to style the list 
+ * to style the list
  */
 .tripal_toc_list {
 
@@ -93,11 +93,11 @@
  * Column. Initially, the JavaScript hids all "blocks" except for the "Details"
  * block.  There will be as many blocks as there are TOC links.
  *
- * By default, all blocks have the following layout that consists of a 
+ * By default, all blocks have the following layout that consists of a
  * container div box with the class 'tripal-info-box', a div box to house the
  * block title with the class 'tripal-info-box-title', and a div box to
- * house a brief description about the block with the class 
- * 'tripal-info-box-desc' 
+ * house a brief description about the block with the class
+ * 'tripal-info-box-desc'
  *
  * |-----------------------------------------------|
  * |  .tripal-data-block                           |
@@ -129,7 +129,7 @@
 }
 
 /**
- * Within the block data 
+ * Within the block data
  */
  .tripal-data-table {
    margin-top: 0px;
@@ -139,7 +139,7 @@
 /******************************************************************************
  * The teaser appears anywhere that a small snippet of the content is required.
  * When any node in Drupal is published to the home page a teaser is used.
- * Teasers can also be used in views to provide lists of content. The 
+ * Teasers can also be used in views to provide lists of content. The
  * teaser template is similar to the block but with the following sections and
  * classes
  *
@@ -168,35 +168,47 @@
 
 /**
  * some nodes such as the organism node may have images. This class
- * is used to format any image that appears in the teaser 
+ * is used to format any image that appears in the teaser
  */
 .tripal-teaser-img {
-  width: 100px; 
-  float: left; 
-  padding-right: 10px; 
+  width: 100px;
+  float: left;
+  padding-right: 10px;
   padding-bottom: 5px;
 }
 
 /******************************************************************************
  * Administrative CSS classes
  *****************************************************************************/
- 
+
  /**
-  * This class is used when providing hints or other instructions to the 
+  * This class is used when providing hints or other instructions to the
   * site administrator
-  */ 
- 
-.tripal-site-admin-only {
+  */
+
+div.messages.tripal-site-admin-only{
   background-image: url("../images/TripalLogo-sm.png");
   background-repeat: no-repeat;
   background-color: #cce3ff;
   margin-top: 10px;
   margin-bottom: 10px;
-  border: 1px solid #888888;
+  border: 1px solid #7DA1D4;
   min-height: 50px;
   clear: both;
 }
 
+.tripal-serverity-string {
+  font-weight: bold;
+}
+
+.tripal-serverity-string.critical, .tripal-serverity-string.error {
+  color: #FF0000;
+}
+
+.tripal-serverity-string.warning {
+  color: #FF8000;
+}
+
 .tripal-site-admin-message {
    padding: 10px 10px 10px 55px;
    font-style: italic;
@@ -204,6 +216,6 @@
 
 .tripal-site-admin-only-table-row {
   background-color: #cce3ff;
-  border: 1px solid #888888;
+  border: 1px solid #7DA1D4;
   color: black;
 }