Fix long type for big numbers (#201)

* fix(long): change int to float

Author: thanh-nguyen-dang

peregrine/resources/submission/graphql/node.py

@@ -525,7 +525,7 @@ def lookup_graphql_type(T):
     return {
         bool: graphene.Boolean,
         float: graphene.Float,
-        int: graphene.Int,
+        int: graphene.Float,
         list: graphene.List(graphene.String),
     }.get(T, graphene.String)
 
@@ -580,7 +580,7 @@ def get_node_interface_args():
             of_type=graphene.List(graphene.String),
             project_id=graphene.String(),
             category=graphene.String(),
-        )
+        ),
     )
 
 
@@ -990,7 +990,7 @@ def get_withpathto_type():
                     for cls in psqlgraph.Node.get_subclasses()
                 ]
                 for k, v in cls_attrs.items()
-            }
+            },
         ),
     )
 

tests/graphql/data/bulk1.json

@@ -30,12 +30,12 @@
     "doc_format": "JSON"
   }, 
   {
-    "doc": "{\"file_name\": \"C500.CGCI-file1.bam\", \"md5sum\": \"35b39360cc41a7b635980159aef265ba\", \"submitter_id\": \"CGCI-file-1\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}", 
+    "doc": "{\"file_name\": \"C500.CGCI-file1.bam\", \"md5sum\": \"35b39360cc41a7b635980159aef265ba\", \"submitter_id\": \"CGCI-file-1\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}",
     "name": "CGCI-file-1.json", 
     "doc_format": "JSON"
   }, 
   {
-    "doc": "{\"file_name\": \"C500.CGCI-file2.bam\", \"md5sum\": \"35980159aef265ba35b39360cc41a7b6\", \"submitter_id\": \"CGCI-file-2\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}", 
+    "doc": "{\"file_name\": \"C500.CGCI-file2.bam\", \"md5sum\": \"35980159aef265ba35b39360cc41a7b6\", \"submitter_id\": \"CGCI-file-2\", \"aliquots\": {\"submitter_id\": \"BLGSP-71-06-00005-99A-01D\"}, \"file_size\": 5962718282, \"type\": \"file\"}",
     "name": "CGCI-file-2.json", 
     "doc_format": "JSON"
   }, 

tests/graphql/data/read_group.json

@@ -10,6 +10,6 @@
     "library_strategy": "WXS",
     "library_name": "library1",
     "is_paired_end": false,
-    "read_length": 12345,
+    "read_length": 59627182820,
     "read_group_name": "readgroup-1"
 }

tests/graphql/data/submitted_unaligned_reads.json

@@ -5,7 +5,7 @@
     },
     "submitter_id": "CGCI-file-2",
     "data_format": "BAM",
-    "file_size": 5962718282,
+    "file_size": 59627182820,
     "file_name": "C500.CGCI-file1.bam",
     "md5sum": "35b39360cc41a7b635980159aef265ba",
     "experimental_strategy": "WGS",

tests/graphql/test_graphql.py

@@ -1270,6 +1270,35 @@ def test_without_path_order(client, submitter, pg_driver_clean, cgci_blgsp):
     }, r.data
 
 
+def test_long_as_float_type(client, submitter, pg_driver_clean, cgci_blgsp):
+    """Assert the long type is working as float"""
+    post_example_entities_together(client, pg_driver_clean, submitter)
+
+    r = client.post(
+        path,
+        headers=submitter,
+        data=json.dumps(
+            {
+                "query": """
+                query Test {
+                    read_group (
+                      order_by_desc: "read_length",
+                    )
+                    { submitter_id, read_length }
+                }
+            """
+            }
+        ),
+    )
+    assert r.json == {
+        "data": {
+            "read_group": [
+                {"submitter_id": "test-readgroup-1", "read_length": 59627182820.0},
+            ]
+        }
+    }, r.data
+
+
 def test_read_group_with_path_to_case(client, submitter, pg_driver_clean, cgci_blgsp):
     """Regression for incorrect counts"""
     put_example_entities_together(client, pg_driver_clean, submitter)

tests/graphql/utils.py

@@ -25,6 +25,7 @@
     "diagnosis.json",
     "exposure.json",
     "treatment.json",
+    "read_group.json",
 ]
 
 PATH = "/v0/submission/graphql"