Fix a typo where the file given to the add track command was wrong

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt.api.inc

@@ -1,5 +1,9 @@
 <?php
 
+/**
+ * @file
+ */
+
 /**
  * Get saved settings.
  *
@@ -82,19 +86,20 @@ function tripal_jbrowse_mgmt_get_instances($conditions = NULL) {
  * @param $data
  *
  * @return \DatabaseStatementInterface|int
+ *
  * @throws \Exception
  */
 function tripal_jbrowse_mgmt_create_instance($data) {
   global $user;
 
   $instance_id = db_insert('tripal_jbrowse_mgmt_instances')->fields([
-      'uid' => $user->uid,
-      'organism_id' => $data['organism_id'],
-      'title' => $data['title'],
-      'description' => isset($data['description']) ? $data['description'] : '',
-      'created_at' => $data['created_at'],
-      'file' => $data['file'],
-    ])->execute();
+    'uid' => $user->uid,
+    'organism_id' => $data['organism_id'],
+    'title' => $data['title'],
+    'description' => isset($data['description']) ? $data['description'] : '',
+    'created_at' => $data['created_at'],
+    'file' => $data['file'],
+  ])->execute();
 
   if (!$instance_id) {
     return FALSE;
@@ -159,21 +164,22 @@ function tripal_jbrowse_mgmt_delete_instance($instance) {
  * @param $data
  *
  * @return bool|int Track ID or FALSE if an error occurs.
+ *
  * @throws \Exception
  */
 function tripal_jbrowse_mgmt_create_track($instance, $data) {
   global $user;
 
   $track_id = db_insert('tripal_jbrowse_mgmt_tracks')->fields([
-      'uid' => $user->uid,
-      'instance_id' => $instance->id,
-      'organism_id' => $instance->organism_id,
-      'label' => $data['label'],
-      'track_type' => $data['track_type'],
-      'file_type' => $data['file_type'],
-      'created_at' => $data['created_at'],
-      'file' => $data['file'],
-    ])->execute();
+    'uid' => $user->uid,
+    'instance_id' => $instance->id,
+    'organism_id' => $instance->organism_id,
+    'label' => $data['label'],
+    'track_type' => $data['track_type'],
+    'file_type' => $data['file_type'],
+    'created_at' => $data['created_at'],
+    'file' => $data['file'],
+  ])->execute();
 
   if (!$track_id) {
     return FALSE;
@@ -271,6 +277,15 @@ function tripal_jbrowse_mgmt_get_organisms_list() {
     ->fetchAll();
 }
 
+/**
+ * Format the name of the organism to `Genus species (Common Name)`.
+ *
+ * @param object $organism
+ *   The organism object as retrieved by
+ *   db_query()->fetchObject().
+ *
+ * @return string
+ */
 function tripal_jbrowse_mgmt_construct_organism_name($organism) {
   $name = $organism->genus;
   $name .= " $organism->species";
@@ -282,6 +297,15 @@ function tripal_jbrowse_mgmt_construct_organism_name($organism) {
   return $name;
 }
 
+/**
+ * Sanitize the string for the URL.
+ *
+ * @param string $string
+ *   The string to sanitize.
+ *
+ * @return string
+ *   The sanitized string.
+ */
 function tripal_jbrowse_mgmt_make_slug($string) {
   $slug = str_replace(' ', '_', $string);
   $slug = str_replace('(', '_', $slug);
@@ -298,27 +322,34 @@ function tripal_jbrowse_mgmt_make_slug($string) {
   return strtolower(trim($slug, '_'));
 }
 
+/**
+ * @param $field
+ *
+ * @return bool|\stdClass
+ */
 function tripal_jbrowse_mgmt_upload_file($field) {
   $file = file_save_upload($field, [
-      'file_validate_extensions' => ['fasta faa fna fastq txt gff vcf wig gz tbi bw'],
-      'file_validate_size' => [1024 * 1024 * 1024 * 20] // Make it 20 GB max
-    ]);
+    'file_validate_extensions' => ['fasta faa fna fastq txt gff vcf wig gz tbi bw'],
+    // Make it 20 GB max.
+    'file_validate_size' => [1024 * 1024 * 1024 * 20],
+  ]);
 
-  return !$file ? FALSE : $file; // drupal_realpath($file->uri);
+  // drupal_realpath($file->uri);.
+  return !$file ? FALSE : $file;
 }
 
 /**
  * Moves a file to an intermediate directory, then to the destination, if given.
  *
  * @param $file
- *  The file object.
+ *   The file object.
  *
  * @param $path
- *  The path to the directory of the new object.
- *  If the directory provided does not exist, it will be created.
+ *   The path to the directory of the new object.
+ *   If the directory provided does not exist, it will be created.
  *
  * @return
- *  The path to the moved file, or NULL on fail.
+ *   The path to the moved file, or NULL on fail.
  */
 function tripal_jbrowse_mgmt_move_file($file, $path = NULL) {
   $directory = 'public://tripal/tripal_jbrowse_mgmt';
@@ -342,9 +373,9 @@ function tripal_jbrowse_mgmt_move_file($file, $path = NULL) {
  * If the directory provided does not exist, it will be created.
  *
  * @param $source
- *  File path of the source file.
+ *   File path of the source file.
  * @param $destination
- *  File path to the destination directory.
+ *   File path to the destination directory.
  *
  * @return bool
  */
@@ -366,8 +397,8 @@ function tripal_jbrowse_mgmt_build_http_query($instance) {
   $tracks_path = '';
   if (!empty($tracks)) {
     $tracks_path = implode(',', array_map(function ($track) {
-        return tripal_jbrowse_mgmt_make_slug($track->label);
-      }, $tracks));
+      return tripal_jbrowse_mgmt_make_slug($track->label);
+    }, $tracks));
   }
 
   return [
@@ -396,6 +427,9 @@ function tripal_jbrowse_mgmt_get_json($instance) {
   return json_decode($contents, TRUE);
 }
 
+/**
+ *
+ */
 function tripal_jbrowse_mgmt_get_track_json($track) {
   if (!$track->instance) {
     $track->instance = tripal_jbrowse_mgmt_get_instance($track->instance_id);
@@ -415,8 +449,10 @@ function tripal_jbrowse_mgmt_get_track_json($track) {
 }
 
 /**
- * @param object $track Track object
- * @param array $track_json Edited track array.
+ * @param object $track
+ *   Track object.
+ * @param array $track_json
+ *   Edited track array.
  *
  * @throws \Exception
  */

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_commands.inc

@@ -110,7 +110,7 @@ function tripal_jbrowse_mgmt_cmd_add_track($track) {
       [
         $bin . '/flatfile-to-json.pl',
         '--' . $track->file_type,
-        $instance->file,
+        $track->file,
         '--trackLabel',
         tripal_jbrowse_mgmt_make_slug($track->label),
         '--key',

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_tracks.form.inc

@@ -1,17 +1,26 @@
 <?php
 
+/**
+ * @file tripal_jbrowse_mgmt_tracks.form.inc
+ */
+
 /**
  * Add a track to an instance form.
  *
- * @param $form
- * @param $form_state
- * @param $instance_id
+ * @param array $form
+ *   The drupal form.
+ * @param array $form_state
+ *   The form state array.
+ * @param int $instance_id
+ *   The parent instance ID to add the new track to.
  *
  * @return array
+ *   The modified form array.
  */
 function tripal_jbrowse_mgmt_add_track_form($form, &$form_state, $instance_id) {
   if (empty(tripal_jbrowse_mgmt_get_instance($instance_id))) {
     drupal_not_found();
+
     return [];
   }
 
@@ -96,8 +105,13 @@ function tripal_jbrowse_mgmt_add_track_form($form, &$form_state, $instance_id) {
 /**
  * Validate the add track form.
  *
+ * This function also takes care of the uploading of files.
+ * TODO: If the file is invalid, delete it!
+ *
  * @param array $form
+ *   The Drupal form.
  * @param array $form_state
+ *   The form state.
  */
 function tripal_jbrowse_mgmt_add_track_form_validate($form, &$form_state) {
   $values = $form_state['values'];
@@ -108,13 +122,13 @@ function tripal_jbrowse_mgmt_add_track_form_validate($form, &$form_state) {
   $file_type = $values['file_type'];
   $path = NULL;
 
-  switch ($file_type) {
-    case 'vcf':
-      $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title) . '/data/vcf';
-      break;
-    case 'bw':
-      $path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title) . '/data/wig';
-      break;
+  $base_path = $data . '/' . tripal_jbrowse_mgmt_make_slug($instance->title) . '/data';
+
+  if ($file_type === 'vcf') {
+    $path = $base_path . '/vcf';
+  }
+  elseif ($file === 'bw') {
+    $path = $base_path . '/wig';
   }
 
   switch ($file_type) {
@@ -148,7 +162,8 @@ function tripal_jbrowse_mgmt_add_track_form_validate($form, &$form_state) {
                 form_set_error('Failed to copy file' . $file_gz[0] . ' to ' . $path);
               }
               else {
-                if (!tripal_jbrowse_mgmt_copy_file($file_tbi[0], $path)) {
+                if (!tripal_jbrowse_mgmt_copy_file($file_tbi[0],
+                  $path)) {
                   form_set_error('Failed to copy file' . $file_gz[0] . ' to ' . $path);
                 }
               }
@@ -184,8 +199,7 @@ function tripal_jbrowse_mgmt_add_track_form_validate($form, &$form_state) {
         else {
           $tbi_uploaded = tripal_jbrowse_mgmt_move_file($tbi_uploaded, $path);
           if (!isset($tbi_uploaded)) {
-            form_set_error('file2',
-              'Failed to move tbi file to ' . $path . '.');
+            form_set_error('file2', 'Failed to move tbi file to ' . $path . '.');
           }
           else {
             $form_state['values']['uploaded_tbi'] = $tbi_uploaded;
@@ -265,9 +279,8 @@ function tripal_jbrowse_mgmt_add_track_form_submit($form, &$form_state) {
     'created_at' => time(),
   ]);
 
-  tripal_add_job('Add JBrowse track to ' . $instance->title,
-    'tripal_jbrowse_mgmt', 'tripal_jbrowse_mgmt_add_track_to_instance', [$track_id],
-    $user->uid);
+  tripal_add_job('Add JBrowse track to ' . $instance->title, 'tripal_jbrowse_mgmt',
+    'tripal_jbrowse_mgmt_add_track_to_instance', [$track_id], $user->uid);
 
   drupal_goto('admin/tripal/extension/tripal_jbrowse/management/instances/' . $instance->id);
 }
@@ -290,6 +303,7 @@ function tripal_jbrowse_mgmt_delete_track_form($form, &$form_state, $track_id) {
       '#type' => 'item',
       '#markup' => '<p style="color: red">Unable to find track.</p>',
     ];
+
     return $form;
   }