Moved some functions to their proper location. Added shortcut for adding biological data

tripal_entities/includes/TripalEntityUIController.inc

@@ -26,6 +26,7 @@ class TripalEntityUIController extends EntityDefaultUIController {
       'type' => MENU_LOCAL_TASK,
     );
 
+
     $items['BioData/add'] = array(
       'title' => 'Add Biological Data',
       'page callback' => 'tripal_entities_add_page',
@@ -46,7 +47,7 @@ class TripalEntityUIController extends EntityDefaultUIController {
 
       // Set a custom page for adding new tripal data entities.
       $items['BioData/add/' . $dbxref_id] = array(
-        'title' => 'Add ' . ucfirst($cvterm->name),
+        'title' => ucfirst($cvterm->name),
         'description' => 'A ' . $cvterm->name . ' record.',
         'page callback'  => 'drupal_get_form',
         'page arguments' => array('tripal_entities_entity_form', 2),

tripal_entities/includes/tripal_entities.admin.inc

@@ -81,11 +81,12 @@ function tripal_entities_content_overview_form($form, &$form_state) {
   $headers = array('Title', 'Vocabulary', 'Term', 'Author', 'Status', 'Updated', 'Operations');
   $rows = array();
   while ($entity = $entities->fetchObject()) {
+    $cvterm = chado_generate_var('cvterm', array('cvterm_id' => $entity->cvterm_id));
     $author = user_load($entity->uid);
     $rows[] = array(
       l($entity->title, 'BioData/' . $entity->id),
-      $entity->type,
-      $entity->bundle,
+      $cvterm->cv_id->name . ' (' . $cvterm->dbxref_id->db_id->name . ')',
+      $cvterm->name,
       l($author->name, 'user/' . $entity->uid),
       $entity->status == 1 ? 'published' : 'unpublished',
       format_date($entity->changed, 'short'),
@@ -330,7 +331,242 @@ function tripal_entities_admin_add_type_form_submit($form, &$form_state) {
     }
   }
 }
+/**
+ * Implements hook_submit() for the tripal_entities_admin_publish_form.
+ *
+ */
+function tripal_entities_add_bundle($cvterm) {
+
+  // Create the bundle name and entity type name.  The bundle name is the
+  // dbxref ID.  This isn't very human readable, but the alternative is to
+  // use the accession which may not always be alpha-numeric.
+  $bundle_name = 'dbxref_' . $cvterm->dbxref_id->dbxref_id;
+
+  // Check to see if this bundle exists. If not then create it
+  $bundle = db_select('tripal_bundle', 't')
+  ->fields('t')
+  ->condition('type', 'BioData')
+  ->condition('bundle', $bundle_name)
+  ->execute()
+  ->fetchObject();
+
+  if (!$bundle) {
+    // The TripalBundle Entity manages the bundles we have available.
+    // Therefore, we need to add a new entity for each bundle "type".
+    $vals = array(
+      'label' => $cvterm->name,
+      'type' => 'BioData',
+      'bundle' => $bundle_name,
+      'data' => serialize(array()),
+      'module' => 'tripal_entities'
+    );
+    $tripal_bundle = new TripalBundle($vals, 'BioData_bundles');
+    $tripal_bundle->save();
+  }
+
+  // Allow modules to now add fields to the bundle
+  module_invoke_all('add_bundle_fields', 'BioData', $bundle_name, $cvterm);
+
+}
+/**
+ * Implements hook_add_bundle_fields().
+ *
+ * @param $entity_type_name
+ * @param $bundle_name
+ * @param $cvterm
+ */
+function tripal_entities_add_bundle_fields($entity_type_name, $bundle_name, $cvterm) {
+
+  // Adds the fields for the base table to the entity.
+  tripal_entities_add_bundle_base_fields($entity_type_name, $bundle_name, $cvterm);
+
+  // Check to see if there are any kv-property tables associated to this
+  // base table. If so, add the fields for that type of table.
+  tripal_entities_add_bundle_kvproperty_adder_field($entity_type_name, $bundle_name, 'featureprop');
+}
+
+/**
+ * Adds the fields for a kv-property table fields
+ *
+ * @param $entity_type_name
+ * @param $bundle_name
+ * @param $kv_table
+ */
+function tripal_entities_add_bundle_kvproperty_adder_field($entity_type_name, $bundle_name, $kv_table) {
+  // First add a generic property field so that users can add new proeprty types.
+  $field_name = $kv_table;
+
+  // Initialize the field array.
+  $field_info = array(
+    'field_type' => 'kvproperty_adder',
+    'widget_type' => 'tripal_fields_kvproperty_adder_widget',
+    'field_settings' => array(),
+    'widget_settings' => array('display_label' => 1),
+    'description' => '',
+    'label' => 'Additional Properties',
+    'is_required' => 0,
+  );
+  tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
+}
+
+/**
+ * Adds the fields for the base table to the entity.
+ */
+function tripal_entities_add_bundle_base_fields($entity_type_name, $bundle_name, $cvterm) {
+  // Get the list of tables where this cvterm is used.
+  $match = array('cvterm_id' => $cvterm->cvterm_id);
+  $term = chado_select_record('tripal_term', array('*'), $match);
+  $values = array('term_id' => $term[0]->term_id);
+  $tables = chado_select_record('tripal_term_usage', array('*'), $values);
+
+  // Iterate through the tables.
+  foreach ($tables as $table) {
+    $table_name = $table->data_table;
+    $type_table = $table->type_table;
+    $type_field = $table->field;
+
+    // We only want to look at base tables.
+    if ($table_name == 'cvterm_dbxref' || $table_name == 'cvterm_relationship' ||
+        $table_name == 'cvtermpath' || $table_name == 'cvtermprop' || $table_name == 'chadoprop' ||
+        $table_name == 'cvtermsynonym' || preg_match('/_relationship$/', $table_name) ||
+        preg_match('/_cvterm$/', $table_name)) {
+      continue;
+    }
+
+    // Iterate through the columns of the table and see if fields have been
+    // created for each one. If not, then create them.
+    $schema = chado_get_schema($table_name);
+    $columns = $schema['fields'];
+    foreach ($columns as $column_name => $details) {
+      $field_name = $table_name . '__' . $column_name;
+
+      // Skip the primary key field.
+      if ($column_name == $schema['primary key'][0]) {
+        continue;
+      }
+
+      // Skip the type field.
+      if ($table_name == $type_table and $column_name == $type_field) {
+        continue;
+      }
+
+      // Get the field defaults for this column.
+      $field_info = tripal_entities_get_table_column_field_default($table_name, $schema, $column_name);
+
+
+      // Determine if the field is required.
+      if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
+        $field_info['is_required'] = array_key_exists('default', $details) ? 0 : 1;
+      }
+
+      // If we don't have a field type then we don't need to create a field.
+      if (!$field_info['field_type']) {
+        // If we don't have a field type but it is required and doesn't have
+        // a default value then we are in trouble.
+        if ($field_info['is_required'] and !array_key_exists('default', $details)) {
+          throw new Exception(t('The %table.%field type, %type, is not yet supported for Entity fields, but it is required,',
+              array('%table' => $table_name, '%field' => $column_name, '%type' => $details['type'])));
+        }
+        continue;
+      }
+
+      // If this field is a foreign key field then we will have a special custom
+      // field provided by Tripal.
+      $is_fk = FALSE;
+      if (array_key_exists('foreign keys', $schema)) {
+        foreach ($schema['foreign keys'] as $remote_table => $fk_details) {
+          if (array_key_exists($column_name, $fk_details['columns'])) {
+            $is_fk = TRUE;
+          }
+        }
+      }
 
+      // Add the field to the bundle.
+      tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
+    }
+  }
+}
+
+/**
+ * Returns a $field_info array for a field based on a databaes column.
+ *
+ */
+function tripal_entities_get_table_column_field_default($table_name, $schema, $column_name) {
+  $details = $schema['fields'][$column_name];
+
+  // Create an array with information about this field.
+  $field_info = array(
+    'field_type' => '',
+    'widget_type' => '',
+    'field_settings' => array(
+      'chado_table' => $table_name,
+      'chado_column' => $column_name,
+    ),
+    'widget_settings' => array('display_label' => 1),
+    'description' => '',
+    'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
+    'is_required' => 0,
+  );
+
+  // Alter the field info array depending on the column details.
+  switch($details['type']) {
+    case 'char':
+      $field_info['field_type'] = 'text';
+      $field_info['widget_type'] = 'text_textfield';
+      $field_info['field_settings']['max_length'] = $details['length'];
+      break;
+    case 'varchar':
+      $field_info['field_type'] = 'text';
+      $field_info['widget_type'] = 'text_textfield';
+      $field_info['field_settings']['max_length'] = $details['length'];
+      break;
+    case 'text':
+      $field_info['field_type'] = 'text';
+      $field_info['widget_type'] = 'text_textarea';
+      $field_info['field_settings']['max_length'] = 17179869184;
+      break;
+    case 'blob':
+      // not sure how to support a blob field.
+      continue;
+      break;
+    case 'int':
+      $field_info['field_type'] = 'number_integer';
+      $field_info['widget_type'] = 'number';
+      break;
+    case 'float':
+      $field_info['field_type'] = 'number_float';
+      $field_info['widget_type'] = 'number';
+      $field_info['field_settings']['precision'] = 10;
+      $field_info['field_settings']['scale'] = 2;
+      $field_info['field_settings']['decimal_separator'] = '.';
+      break;
+    case 'numeric':
+      $field_info['field_type'] = 'number_decimal';
+      $field_info['widget_type'] = 'number';
+      break;
+    case 'serial':
+      // Serial fields are most likely not needed as a field.
+      break;
+    case 'boolean':
+      $field_info['field_type'] = 'list_boolean';
+      $field_info['widget_type'] = 'options_onoff';
+      $field_info['field_settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
+      break;
+    case 'datetime':
+      // Use the Drupal Date and Date API to create the field/widget
+      $field_info['field_type'] = 'datetime';
+      $field_info['widget_type'] = 'date_select';
+      $field_info['widget_settings']['increment'] = 1;
+      $field_info['widget_settings']['tz_handling'] = 'none';
+      $field_info['widget_settings']['collapsible'] = TRUE;
+
+      // TODO: Add settings so that the minutes increment by 1.
+      // And turn off the timezone, as the Chado field doesn't support it.
+      break;
+  }
+
+  return $field_info;
+}
 /**
  * Adds a vocabulary and term to the Tripal term usage tables.
  *

tripal_entities/includes/tripal_entities.entity_form.inc

@@ -179,239 +179,6 @@ function tripal_entities_entity_delete_form_submit($form, &$form_state) {
 }
 
 
-/**
- * Implements hook_submit() for the tripal_entities_admin_publish_form.
- *
- */
-function tripal_entities_add_bundle($cvterm) {
-
-  // Create the bundle name and entity type name.  The bundle name is the
-  // dbxref ID.  This isn't very human readable, but the alternative is to
-  // use the accession which may not always be alpha-numeric.
-  $bundle_name = 'dbxref_' . $cvterm->dbxref_id->dbxref_id;
-
-  // Check to see if this bundle exists. If not then create it
-  $bundle = db_select('tripal_bundle', 't')
-    ->fields('t')
-    ->condition('type', 'BioData')
-    ->condition('bundle', $bundle_name)
-    ->execute()
-    ->fetchObject();
-
-  if (!$bundle) {
-    // The TripalBundle Entity manages the bundles we have available.
-    // Therefore, we need to add a new entity for each bundle "type".
-    $vals = array(
-      'label' => $cvterm->name,
-      'type' => 'BioData',
-      'bundle' => $bundle_name,
-      'data' => serialize(array()),
-      'module' => 'tripal_entities'
-    );
-    $tripal_bundle = new TripalBundle($vals, 'BioData_bundles');
-    $tripal_bundle->save();
-  }
-
-  // Allow modules to now add fields to the bundle
-  module_invoke_all('add_bundle_fields', 'BioData', $bundle_name, $cvterm);
-
-}
-/**
- * Implements hook_add_bundle_fields().
- *
- * @param $entity_type_name
- * @param $bundle_name
- * @param $cvterm
- */
-function tripal_entities_add_bundle_fields($entity_type_name, $bundle_name, $cvterm) {
-
-  // Adds the fields for the base table to the entity.
-  tripal_entities_add_bundle_base_fields($entity_type_name, $bundle_name, $cvterm);
-
-  // Check to see if there are any kv-property tables associated to this
-  // base table. If so, add the fields for that type of table.
-  tripal_entities_add_bundle_kvproperty_adder_field($entity_type_name, $bundle_name, 'featureprop');
-}
-
-/**
- * Adds the fields for a kv-property table fields
- *
- * @param $entity_type_name
- * @param $bundle_name
- * @param $kv_table
- */
-function tripal_entities_add_bundle_kvproperty_adder_field($entity_type_name, $bundle_name, $kv_table) {
-  // First add a generic property field so that users can add new proeprty types.
-  $field_name = $kv_table;
-
-  // Initialize the field array.
-  $field_info = array(
-    'field_type' => 'kvproperty_adder',
-    'widget_type' => 'tripal_fields_kvproperty_adder_widget',
-    'field_settings' => array(),
-    'widget_settings' => array('display_label' => 1),
-    'description' => '',
-    'label' => 'Additional Properties',
-    'is_required' => 0,
-  );
-  tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
-}
 
-/**
- * Adds the fields for the base table to the entity.
- */
-function tripal_entities_add_bundle_base_fields($entity_type_name, $bundle_name, $cvterm) {
-  // Get the list of tables where this cvterm is used.
-  $match = array('cvterm_id' => $cvterm->cvterm_id);
-  $term = chado_select_record('tripal_term', array('*'), $match);
-  $values = array('term_id' => $term[0]->term_id);
-  $tables = chado_select_record('tripal_term_usage', array('*'), $values);
-
-  // Iterate through the tables.
-  foreach ($tables as $table) {
-    $table_name = $table->data_table;
-    $type_table = $table->type_table;
-    $type_field = $table->field;
-
-    // We only want to look at base tables.
-    if ($table_name == 'cvterm_dbxref' || $table_name == 'cvterm_relationship' ||
-        $table_name == 'cvtermpath' || $table_name == 'cvtermprop' || $table_name == 'chadoprop' ||
-        $table_name == 'cvtermsynonym' || preg_match('/_relationship$/', $table_name) ||
-      preg_match('/_cvterm$/', $table_name)) {
-      continue;
-    }
 
-    // Iterate through the columns of the table and see if fields have been
-    // created for each one. If not, then create them.
-    $schema = chado_get_schema($table_name);
-    $columns = $schema['fields'];
-    foreach ($columns as $column_name => $details) {
-      $field_name = $table_name . '__' . $column_name;
-
-      // Skip the primary key field.
-      if ($column_name == $schema['primary key'][0]) {
-        continue;
-      }
-
-      // Skip the type field.
-      if ($table_name == $type_table and $column_name == $type_field) {
-        continue;
-      }
-
-      // Get the field defaults for this column.
-      $field_info = tripal_entities_get_table_column_field_default($table_name, $schema, $column_name);
-
-
-      // Determine if the field is required.
-      if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
-        $field_info['is_required'] = array_key_exists('default', $details) ? 0 : 1;
-      }
-
-      // If we don't have a field type then we don't need to create a field.
-      if (!$field_info['field_type']) {
-        // If we don't have a field type but it is required and doesn't have
-        // a default value then we are in trouble.
-        if ($field_info['is_required'] and !array_key_exists('default', $details)) {
-          throw new Exception(t('The %table.%field type, %type, is not yet supported for Entity fields, but it is required,',
-              array('%table' => $table_name, '%field' => $column_name, '%type' => $details['type'])));
-        }
-        continue;
-      }
-
-      // If this field is a foreign key field then we will have a special custom
-      // field provided by Tripal.
-      $is_fk = FALSE;
-      if (array_key_exists('foreign keys', $schema)) {
-        foreach ($schema['foreign keys'] as $remote_table => $fk_details) {
-          if (array_key_exists($column_name, $fk_details['columns'])) {
-            $is_fk = TRUE;
-          }
-        }
-      }
-
-      // Add the field to the bundle.
-      tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
-    }
-  }
-}
 
-/**
- * Returns a $field_info array for a field based on a databaes column.
- *
- */
-function tripal_entities_get_table_column_field_default($table_name, $schema, $column_name) {
-  $details = $schema['fields'][$column_name];
-
-  // Create an array with information about this field.
-  $field_info = array(
-    'field_type' => '',
-    'widget_type' => '',
-    'field_settings' => array(
-      'chado_table' => $table_name,
-      'chado_column' => $column_name,
-    ),
-    'widget_settings' => array('display_label' => 1),
-    'description' => '',
-    'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
-    'is_required' => 0,
-  );
-
-  // Alter the field info array depending on the column details.
-  switch($details['type']) {
-    case 'char':
-      $field_info['field_type'] = 'text';
-      $field_info['widget_type'] = 'text_textfield';
-      $field_info['field_settings']['max_length'] = $details['length'];
-      break;
-    case 'varchar':
-      $field_info['field_type'] = 'text';
-      $field_info['widget_type'] = 'text_textfield';
-      $field_info['field_settings']['max_length'] = $details['length'];
-      break;
-    case 'text':
-      $field_info['field_type'] = 'text';
-      $field_info['widget_type'] = 'text_textarea';
-      $field_info['field_settings']['max_length'] = 17179869184;
-      break;
-    case 'blob':
-      // not sure how to support a blob field.
-      continue;
-      break;
-    case 'int':
-      $field_info['field_type'] = 'number_integer';
-      $field_info['widget_type'] = 'number';
-      break;
-    case 'float':
-      $field_info['field_type'] = 'number_float';
-      $field_info['widget_type'] = 'number';
-      $field_info['field_settings']['precision'] = 10;
-      $field_info['field_settings']['scale'] = 2;
-      $field_info['field_settings']['decimal_separator'] = '.';
-      break;
-    case 'numeric':
-      $field_info['field_type'] = 'number_decimal';
-      $field_info['widget_type'] = 'number';
-      break;
-    case 'serial':
-      // Serial fields are most likely not needed as a field.
-      break;
-    case 'boolean':
-      $field_info['field_type'] = 'list_boolean';
-      $field_info['widget_type'] = 'options_onoff';
-      $field_info['field_settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
-      break;
-    case 'datetime':
-      // Use the Drupal Date and Date API to create the field/widget
-      $field_info['field_type'] = 'datetime';
-      $field_info['widget_type'] = 'date_select';
-      $field_info['widget_settings']['increment'] = 1;
-      $field_info['widget_settings']['tz_handling'] = 'none';
-      $field_info['widget_settings']['collapsible'] = TRUE;
-
-      // TODO: Add settings so that the minutes increment by 1.
-      // And turn off the timezone, as the Chado field doesn't support it.
-      break;
-  }
-
-  return $field_info;
-}

tripal_entities/tripal_entities.install

@@ -13,6 +13,7 @@ function tripal_entities_install() {
 
 }
 
+
 /**
  *
  */

tripal_entities/tripal_entities.module

@@ -72,7 +72,62 @@ function tripal_entities_admin_paths() {
     return $paths;
   }
 }
+/**
+ * Implements hook_menu_local_tasks_alter().
+ */
+function tripal_entities_menu_local_tasks_alter(&$data, $router_item, $root_path) {
+  // Add action link to 'BioData/add' on 'admin/content/BioData' page.
+  if ($root_path == 'admin/content/BioData') {
+    $item = menu_get_item('BioData/add');
+    if ($item['access']) {
+      $data['actions']['output'][] = array(
+        '#theme' => 'menu_local_action',
+        '#link' => $item,
+      );
+    }
+  }
+}
 
+function tripal_entities_shortcut_default_set($account) {
+  $sets = shortcut_sets();
+  $found = FALSE;
+  foreach ($sets as $set) {
+    if ($set->title == 'TripalDefault') {
+      $found = TRUE;
+    }
+  }
+  if (!$found) {
+    $t = get_t();
+    // Create an initial default shortcut set.
+    $shortcut_set = new stdClass();
+    $shortcut_set->title = $t('TripalDefault');
+    $shortcut_set->links = array(
+      array(
+        'link_path' => 'BioData/add',
+        'link_title' => 'Add Biological Data',
+        'weight' => -20,
+      ),
+      array(
+        'link_path' => 'node/add',
+        'link_title' => $t('Add content'),
+        'weight' => -21,
+      ),
+      array(
+        'link_path' => 'admin/content',
+        'link_title' => $t('Find content'),
+        'weight' => -22,
+      ),
+    );
+    shortcut_set_save($shortcut_set);
+  }
+
+  $sets = shortcut_sets();
+  foreach ($sets as $set) {
+   if ($set->title == 'TripalDefault') {
+     return $set->set_name;
+   }
+  }
+}
 
 /**
  * Implements hook_permission().