Merge pull request #41 from Jiu9Shen/38-track_manage_edit_json

38 track manage edit json

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_tracks.form.inc

@@ -367,3 +367,140 @@ function tripal_jbrowse_mgmt_delete_track_form_submit($form, &$form_state) {
 
   drupal_goto('admin/tripal/extension/tripal_jbrowse/management/instances/' . $track->instance_id);
 }
+
+/**
+ * Track json editor advance form.
+ * allow user to make all configurations of a track
+ *
+ * @param array $form
+ * @param array $form_state
+ * @param int $track_id
+ *
+ * @return array
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_json_editor_advance_form($form, &$form_state, $track_id) {
+  $track = tripal_jbrowse_mgmt_get_track($track_id);
+
+  if (!$track->id) {
+    $form['error'] = [
+      '#type' => 'item',
+      '#markup' => '<p style="color: red">Unable to find track.</p>',
+    ];
+
+    return $form;
+  }
+
+  $instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
+  $json = tripal_jbrowse_mgmt_get_json($instance);
+  $form_state['track_json'] = $json;
+
+  $key = tripal_jbrowse_mgmt_make_slug($track->label);
+  $track_json = NULL;
+  $track_index = NULL;
+  foreach ($json['tracks'] as $index => $jtrack) {
+    if ($jtrack['label'] === $key) {
+      $track_json = $jtrack;
+      $track_index = $index;
+      break;
+    }
+  }
+
+  if (!$track_json) {
+    $form['error'] = [
+      '#type' => 'item',
+      '#markup' => '<p style="color: red">Unable to find track in json!</p>',
+    ];
+    return $form;
+  }
+
+  $form['track_index'] = [
+    '#type' => 'hidden',
+    '#value' => $track_index,
+  ];
+
+  $form['track_id'] = [
+    '#type' => 'hidden',
+    '#value' => $track->id,
+  ];
+
+  $instr_detail = '<p><strong>Only use this functionality if the configuration option you want is not included in the "Track Manage" form.</strong>. For more information on the JBrowse track configuration see the '.l('JBrowse Documentation', 'http://jbrowse.org/docs/canvas_features.html').'.</p>
+    <div class="messages warning">Please be extra cautious while editing track configuration, since it will make changes in file trackList.json directly. Also, do not change the "label" since it will disconnect this track from the JBrowse Management form.</div>';
+
+  $form['Instruction']=[
+    '#type' => 'markup',
+    '#markup' => $instr_detail,
+  ];
+
+  $form['track_all_config'] = [
+    '#type' => 'textarea',
+    '#title' => t('Track configuration in json'),
+    '#description' => t('The track info from trackList.json. Only '),
+    '#default_value' => json_encode($track_json, JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES),
+    '#rows' => '10',
+    '#required' => TRUE,
+  ];
+
+
+  $form['submit'] = [
+    '#type' => 'submit',
+    '#value' => 'Save Track Configuration',
+  ];
+
+  return $form;
+}
+
+/**
+ * Validate the form.
+ *
+ * @param $form
+ * @param $form_state
+ */
+function tripal_jbrowse_mgmt_json_editor_advance_form_validate($form, &$form_state) {
+  $values = $form_state['values'];
+  $track_all_config = $values['track_all_config'] ?? NULL;
+  $track_key = $values['track_index'];
+
+  if ($track_all_config && !empty($track_all_config)) {
+    if (!json_decode($track_all_config)) {
+      form_set_error(
+        'track_all_config',
+        'Invalid JSON. Please verify that the menu template contains only valid JSON.'
+      );
+    }
+  }
+  $json_before_edit = $form_state['track_json']['tracks'][$track_key];
+  $json_after_edit = json_decode($form_state['values']['track_all_config'], TRUE);
+  if (($json_before_edit['key'] !=  $json_after_edit['key']) OR ($json_before_edit['label'] != $json_after_edit['label'])){
+    form_set_error('track_all_config', 'Key or Label changed. Please don\'t change Key or Label here. The functionality is provided in "Track Manage" form.');
+  }
+
+
+}
+
+/**
+ * @param array $form
+ * @param array $form_state
+ *
+ * @throws \Exception
+ */
+function tripal_jbrowse_mgmt_json_editor_advance_form_submit($form, &$form_state) {
+  $values = $form_state['values'];
+  $track_index = $values['track_index'];
+  $track_all_config = $values['track_all_config'] ?? NULL;
+
+  $track = tripal_jbrowse_mgmt_get_track($values['track_id']);
+
+  $json = $form_state['track_json'];
+  $json['tracks'][$track_index] = json_decode($track_all_config, TRUE);
+  tripal_jbrowse_mgmt_update_track($track, ['label' => $json['tracks'][$track_index]['key']]);
+
+  if (tripal_jbrowse_mgmt_save_json($track->instance, $json) === FALSE) {
+    drupal_set_message(
+      'Unable to save JSON file. Please make sure it\'s editable.'
+    );
+    return;
+  }
+
+  drupal_set_message('Track updated successfully');
+}

tripal_jbrowse_mgmt/tripal_jbrowse_mgmt.module

@@ -125,6 +125,15 @@ function tripal_jbrowse_mgmt_menu() {
     'type' => MENU_LOCAL_ACTION,
   ];
 
+  $items['admin/tripal/extension/tripal_jbrowse/management/tracks/%/edit_json'] = [
+    'title' => 'Edit Json',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => ['tripal_jbrowse_mgmt_json_editor_advance_form', 6],
+    'access arguments' => ['administer tripal_jbrowse_mgmt'],
+    'file' => 'includes/tripal_jbrowse_mgmt_tracks.form.inc',
+    'type' => MENU_LOCAL_ACTION,
+  ];
+
   return $items;
 }