Fixes to SixteenSTrimmedSeqSet that was dropping the urls field data. New example file and improved test script.

Author: victor73

CHANGES

@@ -1,11 +1,18 @@
+cutlass 0.27
+
+  * Bug fix to SixteenSTrimmedSeqSet save() functionality which
+    was losing the urls property.
+  * Improved test for SixteenSTrimmedSeqSet class.
+  * Added missing example script for SixteenSTrimmedSeqSet data.
+
+ - Victor <victor73@github.com>  Tue, 17 Jan 2017 15:00:00 -0400
+
 cutlass 0.26
 
   * Added missing SubjectAttribute node, example and test.
   * Modified Subject node to add attributes() method for retrieval
     of SubjectAttribute information.
   * Modified Annotation class to require file size.
-  * Bug fix to SixteenSTrimmedSeqSet save() functionality which
-    was losing the urls property.
   * Removed WgsRawSeqSetPrivate class, test and example in favor
     of more generic solution.
   * Improved flexibility of test scripts by using a configuration

cutlass/SixteenSTrimmedSeqSet.py

@@ -618,6 +618,8 @@ def save(self):
             self.logger.error("Experienced an error uploading the sequence " + \
                               "set. Aborting save.")
             return success
+        else:
+            self._urls = [ "fasp://" + aspera_server + remote_path ]
 
         self.logger.info("Uploaded the %s to the iHMP Aspera server (%s) successfully." %
                     (self._local_file, aspera_server))
@@ -638,11 +640,9 @@ def save(self):
                 self.logger.info("Setting ID for " + __name__ + " %s." % node_id)
                 self._set_id(node_id)
                 self._version = 1
-                self._urls = [ "fasp://" + aspera_server + remote_path ]
 
                 success = True
             except Exception as e:
-                self.logger.exception(e)
                 self.logger.error("An error occurred while saving " + __name__ + ". " + \
                                   "Reason: %s" % e)
         else:

examples/16s_trimmed_seq_set.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+import json
+import logging
+from cutlass import SixteenSTrimmedSeqSet
+from cutlass import iHMPSession
+from pprint import pprint
+import tempfile
+import sys
+
+root = logging.getLogger()
+root.setLevel(logging.DEBUG)
+ch = logging.StreamHandler(sys.stdout)
+ch.setLevel(logging.DEBUG)
+formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+ch.setFormatter(formatter)
+root.addHandler(ch)
+
+username = "test"
+password = "test"
+
+session = iHMPSession(username, password)
+
+print("Required fields: ")
+print(SixteenSTrimmedSeqSet.required_fields())
+
+seq_set = SixteenSTrimmedSeqSet()
+
+seq_set.checksums = { "md5": "72bdc024d83226ccc90fbd2177e78d56" }
+seq_set.comment = "test comment. Hello world!"
+seq_set.exp_length = 2000
+seq_set.format = "fasta"
+seq_set.format_doc = "url"
+seq_set.seq_model = "a machine"
+seq_set.sequence_type = "nucleotide"
+seq_set.size = 3000
+seq_set.study = "prediabetes"
+
+print("Creating a temp file for example/testing purposes.")
+temp_file = tempfile.NamedTemporaryFile(delete=False).name
+print("Local file: %s" % temp_file)
+
+seq_set.local_file = temp_file
+
+seq_set.links = { "computed_from": [ "610a4911a5ca67de12cdc1e4b4014cd0" ] }
+
+seq_set.tags = [ "16s_trimmed_seq_set", "ihmp" ]
+seq_set.add_tag("another")
+seq_set.add_tag("and_another")
+
+print(seq_set.to_json(indent=2))
+
+if seq_set.is_valid():
+    print("Valid!")
+
+    success = seq_set.save()
+
+    if success:
+        seq_set_id = seq_set.id
+        print("Successfully saved sequence set with ID: %s" % seq_set_id)
+
+        seq_set2 = SixteenSTrimmedSeqSet.load(seq_set_id)
+
+        print(seq_set.to_json(indent=4))
+
+        deletion_success = seq_set.delete()
+
+        if deletion_success:
+            print("Deleted 16s_trimmed_seq_set with ID %s" % seq_set_id)
+        else:
+            print("Deletion of 16s_trimmed_seq_set %s failed." % seq_set_id)
+    else:
+        print("Save failed")
+else:
+    print("Invalid...")
+    validation_errors = seq_set.validate()
+    pprint(validation_errors)

tests/test_16s_trimmed_seq_set.py

@@ -5,6 +5,7 @@
 import random
 import string
 import sys
+import tempfile
 
 from cutlass import iHMPSession
 from cutlass import SixteenSTrimmedSeqSet
@@ -324,6 +325,8 @@ def testRequiredFields(self):
                         "required_field() did not return empty value.")
 
     def testLoadSaveDeleteSixteenSTrimmedSeqSet(self):
+        temp_file = tempfile.NamedTemporaryFile(delete=False).name
+
         # Attempt to save the sixteenSTrimmedSeqSet at all points before and
         # after adding the required fields
 
@@ -334,7 +337,6 @@ def testLoadSaveDeleteSixteenSTrimmedSeqSet(self):
         exp_length = 100
         test_format = "fasta"
         test_format_doc = "http://example.com"
-        local_fasta_file = "test.fasta"
         seq_model = "center for sequencing"
         size = 132
         study = "ibd"
@@ -366,7 +368,7 @@ def testLoadSaveDeleteSixteenSTrimmedSeqSet(self):
         sixteenSTrimmedSeqSet.format_doc = test_format_doc
         sixteenSTrimmedSeqSet.format = test_format
         sixteenSTrimmedSeqSet.seq_model = seq_model
-        sixteenSTrimmedSeqSet.local_file = local_fasta_file
+        sixteenSTrimmedSeqSet.local_file = temp_file
         sixteenSTrimmedSeqSet.size = size
         sixteenSTrimmedSeqSet.study = study