Merge pull request #3229 from antgonza/add-filesize-ArtifactHandler

add filesize ArtifactHandler

Author: charles-cowart

qiita_db/artifact.py

@@ -658,13 +658,15 @@ def delete(cls, artifact_id):
             qdb.sql_connection.TRN.add(sql, [all_ids])
 
     @classmethod
-    def archive(cls, artifact_id):
+    def archive(cls, artifact_id, clean_ancestors=True):
         """Archive artifact with artifact_id
 
         Parameters
         ----------
         artifact_id : int
             The artifact to be archived
+        clean_ancestors : bool
+            If other childless artifacts should be deleted
 
         Raises
         ------
@@ -689,15 +691,18 @@ def archive(cls, artifact_id):
             raise qdb.exceptions.QiitaDBOperationNotPermittedError(
                 'Only non raw artifacts can be archived')
 
-        # let's find all ancestors that can be deleted (it has parents and no
-        # ancestors (that have no descendants), and delete them
-        to_delete = [x for x in artifact.ancestors.nodes()
-                     if x.id != artifact_id and x.parents and
-                     not [y for y in x.descendants.nodes()
-                     if y.id not in (artifact_id, x.id)]]
-        # ignore artifacts that can and has been submitted to EBI
-        to_delete = [x for x in to_delete if not x.can_be_submitted_to_ebi or
-                     x.is_submitted_to_vamps]
+        to_delete = []
+        if clean_ancestors:
+            # let's find all ancestors that can be deleted (it has parents and
+            # no ancestors (that have no descendants), and delete them
+            to_delete = [x for x in artifact.ancestors.nodes()
+                         if x.id != artifact_id and x.parents and
+                         not [y for y in x.descendants.nodes()
+                         if y.id not in (artifact_id, x.id)]]
+            # ignore artifacts that can and has been submitted to EBI
+            to_delete = [x for x in to_delete if not x.can_be_submitted_to_ebi
+                         and not x.is_submitted_to_ebi
+                         and not x.is_submitted_to_vamps]
 
         # get the log file so we can delete
         fids = [x['fp_id'] for x in artifact.filepaths

qiita_db/handlers/artifact.py

@@ -109,7 +109,8 @@ def get(self, artifact_id):
             # dictionary keyed by filepath type
             response['files'] = defaultdict(list)
             for x in artifact.filepaths:
-                response['files'][x['fp_type']].append(x['fp'])
+                response['files'][x['fp_type']].append(
+                    {'filepath': x['fp'], 'size': x['fp_size']})
 
         self.write(response)
 

qiita_db/handlers/tests/test_artifact.py

@@ -66,9 +66,13 @@ def test_get_artifact(self):
         path_builder = partial(join, db_test_raw_dir)
         exp_fps = {
             "raw_forward_seqs":
-                [path_builder('1_s_G1_L001_sequences.fastq.gz')],
+                [{'filepath': path_builder('1_s_G1_L001_sequences.fastq.gz'),
+                  'size': 58}],
             "raw_barcodes":
-                [path_builder('1_s_G1_L001_sequences_barcodes.fastq.gz')]}
+                [{'filepath': path_builder(
+                  '1_s_G1_L001_sequences_barcodes.fastq.gz'),
+                  'size': 58}]
+        }
         exp = {
             'name': 'Raw data 1',
             'timestamp': '2012-10-01 09:30:27',
@@ -90,7 +94,9 @@ def test_get_artifact(self):
         self.assertEqual(obs.code, 200)
         db_test_raw_dir = qdb.util.get_mountpoint('analysis')[0][1]
         path_builder = partial(join, db_test_raw_dir)
-        exp_fps = {"biom": [path_builder('1_analysis_18S.biom')]}
+        exp_fps = {
+            "biom": [{'filepath': path_builder('1_analysis_18S.biom'),
+                      'size': 1093210}]}
         exp = {
             'name': 'noname',
             'visibility': 'sandbox',