Added private file support to file transfer classes. Improvements to …

…auxiliary testing code. Added missing example and test scripts.

examples/wgs_raw_seq_set.py

@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+
+import json
+import logging
+from cutlass import WgsRawSeqSet
+from cutlass import iHMPSession
+from pprint import pprint
+import tempfile
+import sys
+
+username = "test"
+password = "test"
+
+def set_logging():
+    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)
+
+set_logging()
+
+session = iHMPSession(username, password)
+
+print("Required fields: ")
+print(WgsRawSeqSet.required_fields())
+
+seq_set = WgsRawSeqSet()
+
+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"
+seq_set.private_files = False
+
+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 = { "sequenced_from": [ "b9af32d3ab623bcfbdce2ea3a5016b61" ] }
+
+seq_set.tags = [ "wgs_raw_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 prep. ID: %s" % seq_set_id)
+
+        seq_set2 = WgsRawSeqSet.load(seq_set_id)
+
+        print(seq_set.to_json(indent=4))
+
+        deletion_success = seq_set.delete()
+
+        if deletion_success:
+            print("Deleted sequence set with ID %s" % seq_set_id)
+        else:
+            print("Deletion of sequence set %s failed." % seq_set_id)
+    else:
+        print("Save failed")
+else:
+    print("Invalid...")
+    validation_errors = seq_set.validate()
+    pprint(validation_errors)