merge from CTDS

requirements.txt

@@ -11,11 +11,11 @@ fuzzywuzzy==0.6.1
 gen3authz==0.2.1
 graphene==2.0.1
 jsonschema==3.2
-lxml==4.4.2
+lxml==4.6.3
 pbr==2.0.0
 psycopg2==2.8.4
 python-keystoneclient==1.8.1
-PyYAML==5.1
+PyYAML==5.4
 requests==2.22.0
 setuptools==40.3.0
 six==1.12.0
@@ -33,6 +33,6 @@ cdiserrors==0.1.2
 cdislogging==1.0.0
 git+https://git@github.com/NCI-GDC/cdisutils.git@f54e393c89939b2200dfae45c6235cbe2bae1206#egg=cdisutils
 gen3dictionary==2.0.1
-gen3datamodel==3.0.2
+gen3datamodel==3.0.3
 git+https://git@github.com/uc-cdis/indexclient.git@2.0.0#egg=indexclient
 git+https://git@github.com/uc-cdis/storage-client.git@1.0.0#egg=storageclient

sheepdog/utils/transforms/__init__.py

@@ -33,11 +33,18 @@ def parse_bool_from_string(value):
 def parse_list_from_string(value):
     """
     Handle array fields by converting them to a list.
+    Try to cast to float to handle arrays of numbers.
 
     Example:
-        1,2,3 -> ['1','2','3']
+        a,b,c -> ['a','b','c']
+        1,2,3 -> [1,2,3]
     """
-    return [x.strip() for x in value.split(",")]
+    items = [x.strip() for x in value.split(",")]
+    try:
+        items = [float(x) for x in items]
+    except ValueError:
+        pass  # not an array of numbers
+    return items
 
 
 def set_row_type(row):

sheepdog/utils/transforms/graph_to_doc.py

@@ -153,13 +153,13 @@ def list_to_comma_string(val, file_format):
     """
 
     if val is None:
-        """ If a field is empty we must replace it with an empty string for tsv/csv exports and leave it as None for json exports """
+        """If a field is empty we must replace it with an empty string for tsv/csv exports and leave it as None for json exports"""
         if file_format == "json":
             return val
         return ""
 
     if isinstance(val, list):
-        val = ",".join(val)
+        val = ",".join((str(x) for x in val))
     return val