Fix Mykrobe

hAMRonization/MykrobeIO.py

@@ -75,6 +75,8 @@ def parse(self, handle):
         data = json.load(handle)
 
         sample_names = list(data.keys())
+        if len(sample_names) == 0:
+            return  # take an empty JSON object as a success but with no results
         assert len(sample_names) == 1, "can only parse output with a single "
         "sample currently, found {}".format(len(sample_names))
         sample_name = sample_names[0]

hAMRonization/__init__.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "1.1.8"
+__version__ = "1.1.9"
 
 from hAMRonization import AbricateIO
 from hAMRonization import AmrFinderPlusIO

test/data/dummy/mykrobe/empty.json

@@ -0,0 +1 @@
+{}

test/test_parsing_validity.py

@@ -823,6 +823,15 @@ def test_tbprofiler():
         assert result.reference_gene_stop is None
 
 
+def test_mykrobe_empty():
+    metadata = {}
+    parsed_report = hAMRonization.parse(
+        "data/dummy/mykrobe/empty.json", metadata, "mykrobe"
+    )
+    for result in parsed_report:
+        assert False # there should be none
+
+
 def test_mykrobe():
     metadata = {}
     parsed_report = hAMRonization.parse(