feat: digests take ordered property in arrays into consideration (#116)

src/ga4gh/core/_internal/identifiers.py

@@ -179,8 +179,19 @@ def dictify(vro, enref=True):
             return d
 
         if is_array(vro):
-            if is_curie_type(vro[0]):
-                return sorted(dictify(o) for o in vro.data)
+            if not vro.ordered:
+                # if ordered == False, then the array elements MUST be sorted during serialization
+                if is_curie_type(vro[0]):
+                    return sorted(dictify(o) for o in vro.data)
+
+                arr = list()
+                for o in vro.typed_elems:
+                    d = dictify(o)
+                    if isinstance(d, dict):
+                        d = sha512t24u(encode_canonical_json(d))
+                    arr.append(d)
+                return sorted(arr)
+
             return [dictify(o) for o in vro.typed_elems]
 
         raise ValueError(f"Don't know how to serialize {vro}")  # pragma: no cover

tests/test_vrs.py

@@ -1,27 +1,137 @@
+from copy import deepcopy
+
+import pytest
+
 from ga4gh.core import sha512t24u, ga4gh_digest, ga4gh_serialize, ga4gh_identify, is_pjs_instance
 from ga4gh.vrs import models, vrs_deref, vrs_enref
 
-allele_dict = {
-    'location': {
-        'interval': {
-            'end': {'value': 55181320, 'type': 'Number'},
-            'start': {'value': 55181319, 'type': 'Number'},
-            'type': 'SequenceInterval'
+@pytest.fixture(scope="module")
+def allele_dict():
+    return {
+        "type": "Allele",
+        "location": {
+            "type": "SequenceLocation",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "Number",
+                    "value": 55181319
+                },
+                "end": {
+                    "type": "Number",
+                    "value": 55181320
+                }
+            },
+            "sequence_id": "ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
+        },
+        "state": {
+            "type": "LiteralSequenceExpression",
+            "sequence": "T"
+        }
+    }
+
+@pytest.fixture(scope="module")
+def allele1():
+    a1 = {
+        "type": "Allele",
+        "location": {
+            "type": "SequenceLocation",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "Number",
+                    "value": 94842865
+                },
+                "end": {
+                    "type": "Number",
+                    "value": 94842866
+                }
+            },
+            "sequence_id": "ga4gh:SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB"
         },
-        'sequence_id': 'ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul',
-        'type': 'SequenceLocation'
-    },
-    'state': {
-        'sequence': 'T',
-        'type': 'LiteralSequenceExpression'
-    },
-    'type': 'Allele'
-}
+        "state": {
+            "type": "LiteralSequenceExpression",
+            "sequence": "G"
+        }
+    }
+    return models.Allele(**a1)
+
+
+@pytest.fixture(scope="module")
+def allele2():
+    a2 = {
+        "type": "Allele",
+        "location": {
+            "type": "SequenceLocation",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "Number",
+                    "value": 94761899
+                },
+                "end": {
+                    "type": "Number",
+                    "value": 94761900
+                }
+            },
+            "sequence_id": "ga4gh:SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB"
+        },
+        "state": {
+            "type": "LiteralSequenceExpression",
+            "sequence": "T"
+        }
+    }
+    return models.Allele(**a2)
 
-a = models.Allele(**allele_dict)
 
+@pytest.fixture(scope="module")
+def incomplete_allele_dict():
+    return {
+        "type": "Allele",
+        "location": {
+            "type": "SequenceLocation",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "Number",
+                    "value": 44908821
+                },
+                "end": {
+                    "type": "Number",
+                    "value": 44908822
+                }
+            },
+            "sequence_id": "ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl"
+        }
+    }
 
-def test_vr():
+
+@pytest.fixture(scope="module")
+def literal_seq_expr_dict():
+    return {
+        "type": "LiteralSequenceExpression",
+        "sequence": "C"
+    }
+
+
+@pytest.fixture(scope="module")
+def repeated_seq_expr_dict():
+    return {
+        "type": "RepeatedSequenceExpression",
+        "count": {
+            "type": "IndefiniteRange",
+            "value": 6,
+            "comparator": ">="
+        },
+        "seq_expr": {
+            "type": "LiteralSequenceExpression",
+            "sequence": "A"
+        }
+    }
+
+
+def test_vr(allele_dict):
+    a = models.Allele(**allele_dict)
 
     assert a.as_dict() == allele_dict
 
@@ -32,32 +142,17 @@ def test_vr():
     assert ga4gh_serialize(
         a.location
     ) == b'{"interval":{"end":{"type":"Number","value":55181320},"start":{"type":"Number","value":55181319},"type":"SequenceInterval"},"sequence_id":"F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul","type":"SequenceLocation"}'
-    assert sha512t24u(ga4gh_serialize(a.location)) == '1tI-5In290Gtp1DOlMxO6z-K3u0OzlXl'
-    assert ga4gh_digest(a.location) == '1tI-5In290Gtp1DOlMxO6z-K3u0OzlXl'
-    assert ga4gh_identify(a.location) == 'ga4gh:VSL.1tI-5In290Gtp1DOlMxO6z-K3u0OzlXl'
+    assert sha512t24u(ga4gh_serialize(a.location)) == "1tI-5In290Gtp1DOlMxO6z-K3u0OzlXl"
+    assert ga4gh_digest(a.location) == "1tI-5In290Gtp1DOlMxO6z-K3u0OzlXl"
+    assert ga4gh_identify(a.location) == "ga4gh:VSL.1tI-5In290Gtp1DOlMxO6z-K3u0OzlXl"
 
     assert ga4gh_serialize(
         a
     ) == b'{"location":"1tI-5In290Gtp1DOlMxO6z-K3u0OzlXl","state":{"sequence":"T","type":"LiteralSequenceExpression"},"type":"Allele"}'
-    assert ga4gh_digest(a) == '5Z7gWQGUuGAPe4Pw2_kJvnkhS2Q5jRhY'
-    assert ga4gh_identify(a) == 'ga4gh:VA.5Z7gWQGUuGAPe4Pw2_kJvnkhS2Q5jRhY'
-
-    assert a.as_dict() == {
-        'location': {
-            'interval': {
-                'end': {'value': 55181320, 'type': 'Number'},
-                'start': {'value': 55181319, 'type': 'Number'},
-                'type': 'SequenceInterval'
-            },
-            'sequence_id': 'ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul',
-            'type': 'SequenceLocation'
-        },
-        'state': {
-            'sequence': 'T',
-            'type': 'LiteralSequenceExpression'
-        },
-        'type': 'Allele'
-    }
+    assert ga4gh_digest(a) == "5Z7gWQGUuGAPe4Pw2_kJvnkhS2Q5jRhY"
+    assert ga4gh_identify(a) == "ga4gh:VA.5Z7gWQGUuGAPe4Pw2_kJvnkhS2Q5jRhY"
+
+    assert a.as_dict() == allele_dict
 
     vros = {}
     a2 = vrs_enref(a, vros)
@@ -68,3 +163,91 @@ def test_vr():
 
     a3 = vrs_deref(a2, vros)
     assert a == a3
+
+def test_ordered_false(allele1, allele2):
+    """Test that digests are generated correctly when ordered is False"""
+    assert ga4gh_serialize(
+        allele1.location
+    ) == b'{"interval":{"end":{"type":"Number","value":94842866},"start":{"type":"Number","value":94842865},"type":"SequenceInterval"},"sequence_id":"ss8r_wB0-b9r44TQTMmVTI92884QvBiB","type":"SequenceLocation"}'
+    assert sha512t24u(ga4gh_serialize(allele1.location)) == "yNuwN3VJz77KdF6mY0GN_S5bnw7ByV2L"
+    assert ga4gh_digest(allele1.location) == "yNuwN3VJz77KdF6mY0GN_S5bnw7ByV2L"
+    assert ga4gh_identify(allele1.location) == "ga4gh:VSL.yNuwN3VJz77KdF6mY0GN_S5bnw7ByV2L"
+
+    assert ga4gh_serialize(
+        allele1
+    ) == b'{"location":"yNuwN3VJz77KdF6mY0GN_S5bnw7ByV2L","state":{"sequence":"G","type":"LiteralSequenceExpression"},"type":"Allele"}'
+    assert ga4gh_digest(allele1) == "geQCxa1Enel8UBUAQQ2-rbphDjIR-cq0"
+    assert ga4gh_identify(allele1) == "ga4gh:VA.geQCxa1Enel8UBUAQQ2-rbphDjIR-cq0"
+
+    assert ga4gh_serialize(
+        allele2.location
+    ) == b'{"interval":{"end":{"type":"Number","value":94761900},"start":{"type":"Number","value":94761899},"type":"SequenceInterval"},"sequence_id":"ss8r_wB0-b9r44TQTMmVTI92884QvBiB","type":"SequenceLocation"}'
+    assert sha512t24u(ga4gh_serialize(allele2.location)) == "2b33Z0JsziOXLGOtKOu-jPwz0VL9Gfp-"
+    assert ga4gh_digest(allele2.location) == "2b33Z0JsziOXLGOtKOu-jPwz0VL9Gfp-"
+    assert ga4gh_identify(allele2.location) == "ga4gh:VSL.2b33Z0JsziOXLGOtKOu-jPwz0VL9Gfp-"
+
+    assert ga4gh_serialize(
+        allele2
+    ) == b'{"location":"2b33Z0JsziOXLGOtKOu-jPwz0VL9Gfp-","state":{"sequence":"T","type":"LiteralSequenceExpression"},"type":"Allele"}'
+    assert ga4gh_digest(allele2) == "jWqv036CdZJs4YjwEYptDIBcoT7Uxv5I"
+    assert ga4gh_identify(allele2) == "ga4gh:VA.jWqv036CdZJs4YjwEYptDIBcoT7Uxv5I"
+
+    expected_haplotype_serialization = b'{"members":["geQCxa1Enel8UBUAQQ2-rbphDjIR-cq0","jWqv036CdZJs4YjwEYptDIBcoT7Uxv5I"],"type":"Haplotype"}'
+    expected_haplotype_digest = "Ow_uE0YaVWHIno4pQfdmYpWmlGPNtXQr"
+    expected_haplotype_curie = f"ga4gh:VH.{expected_haplotype_digest}"
+
+    h1 = models.Haplotype(
+        type="Haplotype",
+        members=[allele1, allele2]
+    )
+    assert ga4gh_serialize(h1) == expected_haplotype_serialization
+    assert ga4gh_digest(h1) == expected_haplotype_digest
+    assert ga4gh_identify(h1) == expected_haplotype_curie
+
+    h2 = models.Haplotype(
+        type="Haplotype",
+        members=[allele2, allele1]
+    )
+    assert ga4gh_serialize(h2) == expected_haplotype_serialization
+    assert ga4gh_digest(h2) == expected_haplotype_digest
+    assert ga4gh_identify(h2) == expected_haplotype_curie
+
+    assert ga4gh_identify(h1) == ga4gh_identify(h2) == expected_haplotype_curie
+
+def test_ordered_true(incomplete_allele_dict, literal_seq_expr_dict, repeated_seq_expr_dict):
+    """Test that digests are generated correctly when ordered is True"""
+    a1 = deepcopy(incomplete_allele_dict)
+    a1["state"] = {
+        "type": "ComposedSequenceExpression",
+        "components": [literal_seq_expr_dict, repeated_seq_expr_dict]
+    }
+    a1 = models.Allele(**a1)
+    assert ga4gh_serialize(
+        a1.location
+    ) == b'{"interval":{"end":{"type":"Number","value":44908822},"start":{"type":"Number","value":44908821},"type":"SequenceInterval"},"sequence_id":"IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl","type":"SequenceLocation"}'
+    assert sha512t24u(ga4gh_serialize(a1.location)) == "QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg"
+    assert ga4gh_digest(a1.location) == "QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg"
+    assert ga4gh_identify(a1.location) == "ga4gh:VSL.QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg"
+
+    assert ga4gh_serialize(
+        a1
+    ) == b'{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"components":[{"sequence":"C","type":"LiteralSequenceExpression"},{"count":{"comparator":">=","type":"IndefiniteRange","value":6},"seq_expr":{"sequence":"A","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"}],"type":"ComposedSequenceExpression"},"type":"Allele"}'
+    assert ga4gh_digest(a1) == "HQeEhxKyJNirJAUlgyq-psa7UlE9l9X3"
+    assert ga4gh_identify(a1) == "ga4gh:VA.HQeEhxKyJNirJAUlgyq-psa7UlE9l9X3"
+
+
+    a2 = deepcopy(incomplete_allele_dict)
+    a2["state"] = {
+        "type": "ComposedSequenceExpression",
+        "components": [repeated_seq_expr_dict, literal_seq_expr_dict]
+    }
+    a2 = models.Allele(**a2)
+    assert ga4gh_identify(a2.location) == ga4gh_identify(a1.location)
+
+    assert ga4gh_serialize(
+        a2
+    ) == b'{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"components":[{"count":{"comparator":">=","type":"IndefiniteRange","value":6},"seq_expr":{"sequence":"A","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"},{"sequence":"C","type":"LiteralSequenceExpression"}],"type":"ComposedSequenceExpression"},"type":"Allele"}'
+    assert ga4gh_digest(a2) == "_rPRyTJwcgBmSrdtgrEcOmRY9qZLkc5N"
+    assert ga4gh_identify(a2) == "ga4gh:VA._rPRyTJwcgBmSrdtgrEcOmRY9qZLkc5N"
+
+    assert ga4gh_identify(a1) != ga4gh_identify(a2)