Fix 2530

qiita_db/test/test_commands.py

@@ -354,7 +354,8 @@ def tearDown(self):
         new_files = set(new_uploaded_files).difference(self.uploaded_files)
         path_builder = partial(
             join, qdb.util.get_mountpoint("uploads")[0][1], '1')
-        self._clean_up_files.extend([path_builder(fp) for _, fp in new_files])
+        self._clean_up_files.extend(
+            [path_builder(fp) for _, fp, _ in new_files])
         for f in self._clean_up_files:
             if exists(f):
                 remove(f)

qiita_db/test/test_util.py

@@ -584,9 +584,9 @@ def test_get_mountpoint_path_by_id(self):
     def test_get_files_from_uploads_folders(self):
         # something has been uploaded and ignoring hidden files/folders
         # and folders
-        exp = [(7, 'uploaded_file.txt')]
+        exp = (7, 'uploaded_file.txt', '0 Bytes')
         obs = qdb.util.get_files_from_uploads_folders("1")
-        self.assertEqual(obs, exp)
+        self.assertIn(exp, obs)
 
         # nothing has been uploaded
         exp = []
@@ -604,23 +604,22 @@ def test_move_upload_files_to_trash(self):
 
         self.files_to_remove.append(test_fp)
 
-        exp = [(fid, 'this_is_a_test_file.txt'), (fid, 'uploaded_file.txt')]
+        exp = (fid, 'this_is_a_test_file.txt', '4 Bytes')
         obs = qdb.util.get_files_from_uploads_folders("1")
-        self.assertItemsEqual(obs, exp)
+        self.assertIn(exp, obs)
 
         # move file
         qdb.util.move_upload_files_to_trash(1, [(fid, test_filename)])
-        exp = [(fid, 'uploaded_file.txt')]
         obs = qdb.util.get_files_from_uploads_folders("1")
-        self.assertItemsEqual(obs, exp)
+        self.assertNotIn(obs, exp)
 
         # if the file doesn't exist, don't raise any errors
         qdb.util.move_upload_files_to_trash(1, [(fid, test_filename)])
 
         # testing errors
         # - study doesn't exist
         with self.assertRaises(qdb.exceptions.QiitaDBError):
-            qdb.util.move_upload_files_to_trash(2, [(fid, test_filename)])
+            qdb.util.move_upload_files_to_trash(100, [(fid, test_filename)])
         # - fid doen't exist
         with self.assertRaises(qdb.exceptions.QiitaDBError):
             qdb.util.move_upload_files_to_trash(1, [(10, test_filename)])

qiita_db/util.py

@@ -57,6 +57,8 @@
 from contextlib import contextmanager
 from future.builtins import bytes, str
 import h5py
+from humanize import naturalsize
+from os.path import getsize
 import re
 
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
@@ -456,9 +458,10 @@ def get_files_from_uploads_folders(study_id):
     for pid, p in get_mountpoint("uploads", retrieve_all=True):
         t = join(p, study_id)
         if exists(t):
-            fp.extend([(pid, f)
-                       for f in listdir(t)
-                       if not f.startswith('.') and not isdir(join(t, f))])
+            for f in listdir(t):
+                d = join(t, f)
+                if not f.startswith('.') and not isdir(d):
+                    fp.append((pid, f, naturalsize(getsize(d))))
 
     return fp
 

qiita_pet/handlers/api_proxy/prep_template.py

@@ -63,7 +63,7 @@ def new_prep_template_get_req(study_id):
         The list of available data types
         The investigation type ontology information
     """
-    prep_files = [f for _, f in get_files_from_uploads_folders(study_id)
+    prep_files = [f for _, f, _ in get_files_from_uploads_folders(study_id)
                   if f.endswith(('.txt', '.tsv'))]
     data_types = sorted(Study.all_data_types())
 
@@ -131,7 +131,7 @@ def prep_template_ajax_get_req(user_id, prep_id):
 
     artifact_attached = pt.artifact is not None
     study_id = pt.study_id
-    files = [f for _, f in get_files_from_uploads_folders(study_id)
+    files = [f for _, f, _ in get_files_from_uploads_folders(study_id)
              if f.endswith(('.txt', '.tsv'))]
 
     # The call to list is needed because keys is an iterator

qiita_pet/handlers/api_proxy/studies.py

@@ -294,13 +294,13 @@ def study_files_get_req(user_id, study_id, prep_template_id, artifact_type):
         sfiles = defaultdict(list)
         for p in prep_prefixes:
             to_remove = []
-            for fid, f in uploaded:
+            for fid, f, _ in uploaded:
                 if f.startswith(p):
                     sfiles[p].append(f)
                     to_remove.append((fid, f))
             uploaded = [x for x in uploaded if x not in to_remove]
         inuse = [y for x in sfiles.values() for y in x]
-        remaining.extend([f for _, f in uploaded if f not in inuse])
+        remaining.extend([f for _, f, _ in uploaded if f not in inuse])
         supp_file_types_len = len(supp_file_types)
 
         for k, v in viewitems(sfiles):
@@ -316,7 +316,7 @@ def study_files_get_req(user_id, study_id, prep_template_id, artifact_type):
                 selected.append(v)
     else:
         num_prefixes = 0
-        remaining = [f for _, f in uploaded]
+        remaining = [f for _, f, _ in uploaded]
 
     # get file_types, format: filetype, required, list of files
     file_types = [(t, req, [x[i] for x in selected if i+1 <= len(x)])

qiita_pet/handlers/study_handlers/prep_template.py

@@ -90,7 +90,7 @@ def get(self):
                         not_selected.append(filename)
         else:
             per_prefix = False
-            not_selected = [f for _, f in uploaded]
+            not_selected = [f for _, f, _ in uploaded]
 
         # Write out if this prep template supports per-prefix files, and the
         # as well as pre-selected and remaining files

qiita_pet/handlers/study_handlers/sample_template.py

@@ -309,7 +309,7 @@ def sample_template_overview_handler_get_request(study_id, user):
     # The following information should always be provided:
     # The files that have been uploaded to the system and can be a
     # sample template file
-    files = [f for _, f in get_files_from_uploads_folders(study_id)
+    files = [f for _, f, _ in get_files_from_uploads_folders(study_id)
              if f.endswith(('txt', 'tsv'))]
     # If there is a job associated with the sample information, the job id
     job = None

qiita_pet/static/vendor/js/resumable-uploader.js

@@ -141,7 +141,8 @@
        var alphaNumFileName = fileName.replace(/[^0-9a-z]/gi, '');
        var iconClass = resumableFile.uploaded !== undefined ? 'glyphicon-ok' : 'blinking-message glyphicon-circle-arrow-up';
        var html = '<div class="row" class="checkbox">' +
-                    '<label>' + fileName + '&nbsp; <input type="checkbox" value="' + dirId + '-' + fileName  + '" name="files_to_erase">&nbsp;</label>' +
+                    '<label>' + fileName + '&nbsp;(' +  resumableFile.size + ')&nbsp; <input type="checkbox" value="' + dirId +
+                    '-' + fileName  + '" name="files_to_erase">&nbsp;</label>' +
                     '<i id="file-icon-' + alphaNumFileName + '" class="glyphicon ' + iconClass + '"></i>';
 
        if (is_admin) {

qiita_pet/templates/upload.html

@@ -93,8 +93,8 @@ <h3><u>Files</u></h3>
                                     '{% raw qiita_config.portal_dir %}/download_upload/{{study_id}}/'));
     })(jQuery);
 
-  {% for dirid, filename in files %}
-    uploader.addFile({ "dirid": "{{dirid}}", "fileName": "{{filename}}", "uploaded": "True" });
+  {% for dirid, filename, size in files %}
+    uploader.addFile({ "dirid": "{{dirid}}", "fileName": "{{filename}}", "size": "{{size}}", "uploaded": "True" });
   {% end  %}
 </script>
 

setup.py

@@ -105,7 +105,7 @@
                         'bcrypt', 'pandas >= 0.17', 'numpy >= 1.7',
                         'tornado==3.1.1', 'toredis', 'redis', 'six',
                         'pyparsing', 'h5py >= 2.3.1', 'biom-format',
-                        'natsort', 'networkx < 2.0',
+                        'natsort', 'networkx < 2.0', 'humanize',
                         'scikit-bio == 0.4.2', 'wtforms == 2.0.1',
                         'sphinx-bootstrap-theme', 'Sphinx >= 1.2.2',
                         'gitpython', 'qiita-files', 'redbiom==0.1.0-dev',