updated Terminus/DerivativeMolecule changes from vrs 2.x and fixed te…

…sts.

src/ga4gh/vrs/models.py

@@ -144,8 +144,9 @@ class VrsType(str, Enum):
     ALLELE = "Allele"
     CIS_PHASED_BLOCK = "CisPhasedBlock"
     ADJACENCY = "Adjacency"
-    SEQ_TERMINUS = "SequenceTerminus"
-    DERIVATIVE_SEQ = "DerivativeSequence"
+    TERMINUS = "Terminus"
+    TRAVERSAL_BLOCK = "TraversalBlock"
+    DERIVATIVE_MOL = "DerivativeMolecule"
     CN_COUNT = "CopyNumberCount"
     CN_CHANGE = "CopyNumberChange"
 
@@ -163,14 +164,14 @@ class ResidueAlphabet(str, Enum):
 class CopyChange(str, Enum):
     """Define constraints for copy change"""
 
-    EFO_0030069 = 'efo:0030069'
-    EFO_0020073 = 'efo:0020073'
-    EFO_0030068 = 'efo:0030068'
-    EFO_0030067 = 'efo:0030067'
-    EFO_0030064 = 'efo:0030064'
-    EFO_0030070 = 'efo:0030070'
-    EFO_0030071 = 'efo:0030071'
-    EFO_0030072 = 'efo:0030072'
+    EFO_0030069 = 'EFO:0030069'
+    EFO_0020073 = 'EFO:0020073'
+    EFO_0030068 = 'EFO:0030068'
+    EFO_0030067 = 'EFO:0030067'
+    EFO_0030064 = 'EFO:0030064'
+    EFO_0030070 = 'EFO:0030070'
+    EFO_0030071 = 'EFO:0030071'
+    EFO_0030072 = 'EFO:0030072'
 
 
 def _recurse_ga4gh_serialize(obj):
@@ -419,7 +420,6 @@ class ga4gh(_ValueObject.ga4gh):
             'type'
         ]
 
-
 #########################################
 # vrs location
 #########################################
@@ -626,37 +626,60 @@ class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
         ]
 
 
-class SequenceTerminus(_VariationBase):
-    """The `SequenceTerminus` data class provides a structure for describing the end
+class Terminus(_VariationBase):
+    """The `Terminus` data class provides a structure for describing the end
     (terminus) of a sequence. Structurally similar to Adjacency but the linker sequence
     is not allowed and it removes the unnecessary array structure.
     """
 
-    type: Literal["SequenceTerminus"] = Field(VrsType.SEQ_TERMINUS.value, description=f'MUST be "{VrsType.SEQ_TERMINUS.value}"')
+    type: Literal["Terminus"] = Field(VrsType.TERMINUS.value, description=f'MUST be "{VrsType.TERMINUS.value}"')
     location: Union[IRI, SequenceLocation] = Field(..., description="The location of the terminus.")
 
     class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
-        prefix = "SQX"
+        prefix = "TM"
         keys = [
             "location",
             "type"
         ]
 
+class TraversalBlock(_ValueObject):
+    """A component used to describe the orientation of a molecular variation within
+    a DerivativeMolecule."""
+
+    type: Literal["TraversalBlock"] = Field(
+        VrsType.TRAVERSAL_BLOCK.value, description=f'MUST be "{VrsType.TRAVERSAL_BLOCK.value}"'
+    )
+    orientation: Literal["forward", "reverse_complement"] = Field(
+        ...,
+        description='The orientation of the traversal block, either forward or reverse_complement.'
+    )
+
+    component: Union[IRI, Adjacency, Allele, Terminus, CisPhasedBlock] = Field(
+        ...,
+        description="The component that make up the derivative molecule."
+    )
+
+    class ga4gh(_ValueObject.ga4gh):
+        keys = [
+            'component',
+            'orientation',
+            'type'
+        ]        
 
-class DerivativeSequence(_VariationBase):
-    """The "Derivative Sequence" data class is a structure for describing a derivate
-    sequence composed from multiple sequence adjacencies.
+class DerivativeMolecule(_VariationBase):
+    """The "Derivative Molecule" data class is a structure for describing a derivate
+    molecule composed from multiple sequence components.
     """
 
-    type: Literal["DerivativeSequence"] = Field(VrsType.DERIVATIVE_SEQ.value, description=f'MUST be "{VrsType.DERIVATIVE_SEQ.value}"')
-    components: List[Union[IRI, Adjacency, Allele, SequenceTerminus, CisPhasedBlock]] = Field(
+    type: Literal["DerivativeMolecule"] = Field(VrsType.DERIVATIVE_MOL.value, description=f'MUST be "{VrsType.DERIVATIVE_MOL.value}"')
+    components: List[TraversalBlock] = Field(
         ...,
-        description="The sequence components that make up the derivative sequence.",
+        description="The traversal block components that make up the derivative molecule.",
         min_length=2
     )
 
     class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
-        prefix = "DSQ"
+        prefix = "DM"
         keys = [
             "components",
             "type"
@@ -706,7 +729,7 @@ class CopyNumberChange(_CopyNumber):
     type: Literal["CopyNumberChange"] = Field(VrsType.CN_CHANGE.value, description=f'MUST be "{VrsType.CN_CHANGE.value}"')
     copyChange: CopyChange = Field(
         ...,
-        description='MUST be one of "efo:0030069" (complete genomic loss), "efo:0020073" (high-level loss), "efo:0030068" (low-level loss), "efo:0030067" (loss), "efo:0030064" (regional base ploidy), "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain).',
+        description='MUST be one of "EFO:0030069" (complete genomic loss), "EFO:0020073" (high-level loss), "EFO:0030068" (low-level loss), "EFO:0030067" (loss), "EFO:0030064" (regional base ploidy), "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072" (high-level gain).',
     )
 
     class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
@@ -726,7 +749,7 @@ class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
 class MolecularVariation(RootModel):
     """A `variation` on a contiguous molecule."""
 
-    root: Union[Allele, CisPhasedBlock, Adjacency, SequenceTerminus, DerivativeSequence] = Field(
+    root: Union[Allele, CisPhasedBlock, Adjacency, Terminus, DerivativeMolecule] = Field(
         ...,
         json_schema_extra={
             'description': 'A `variation` on a contiguous molecule.'
@@ -759,7 +782,7 @@ class Location(RootModel):
 class Variation(RootModel):
     """A representation of the state of one or more biomolecules."""
 
-    root: Union[Allele, CisPhasedBlock, Adjacency, SequenceTerminus, DerivativeSequence, CopyNumberChange, CopyNumberCount] = Field(
+    root: Union[Allele, CisPhasedBlock, Adjacency, Terminus, DerivativeMolecule, CopyNumberChange, CopyNumberCount] = Field(
         ...,
         json_schema_extra={
             'description': 'A representation of the state of one or more biomolecules.'

tests/extras/test_cnv_translator.py

@@ -17,8 +17,8 @@ def tlr(rest_dataproxy):
 from_hgvs_cx_tests = (
     ("NC_000013.11:g.26440969_26443305del", models.CopyChange.EFO_0030069,
      {'copyChange': 'EFO:0030069',
-      'digest': 'TvAhuGK6HYf53mXoUnon60cZ7DC_UgM3',
-      'id': 'ga4gh:CX.TvAhuGK6HYf53mXoUnon60cZ7DC_UgM3',
+      'digest': 'bY_40M893gdWmNhU598V-T_dYtPJs-pp',
+      'id': 'ga4gh:CX.bY_40M893gdWmNhU598V-T_dYtPJs-pp',
       'location': {'digest': '4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3',
                    'end': 26443305,
                    'id': 'ga4gh:SL.4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3',
@@ -29,8 +29,8 @@ def tlr(rest_dataproxy):
       'type': 'CopyNumberChange'}),
     ("NC_000013.11:g.32379315_32379819del", None,
      {'copyChange': 'EFO:0030067',
-      'digest': 'K1J2muiVvrDWqKnd5cMpFbTP0eJUfeuE',
-      'id': 'ga4gh:CX.K1J2muiVvrDWqKnd5cMpFbTP0eJUfeuE',
+      'digest': 'WKtHlbV6XCoKqvyeAJxdFj4ogw9ipDfQ',
+      'id': 'ga4gh:CX.WKtHlbV6XCoKqvyeAJxdFj4ogw9ipDfQ',
       'location': {'digest': '_TUGA9kX6JKdXzUklgN2zWkOvNu5pNmV',
                    'end': 32379819,
                    'id': 'ga4gh:SL._TUGA9kX6JKdXzUklgN2zWkOvNu5pNmV',
@@ -42,8 +42,8 @@ def tlr(rest_dataproxy):
      ),
     ("NC_000013.11:g.32332787_32333388dup", models.CopyChange.EFO_0030071,
      {'copyChange': 'EFO:0030071',
-      'digest': '5gODsVN83N1fe9Lc_Octy5rBlkYl8pGU',
-      'id': 'ga4gh:CX.5gODsVN83N1fe9Lc_Octy5rBlkYl8pGU',
+      'digest': 'EqI18-X9p8MUDr-Oz2J5GPQppEQKqWMU',
+      'id': 'ga4gh:CX.EqI18-X9p8MUDr-Oz2J5GPQppEQKqWMU',
       'location': {'digest': 'UOA3zJOPfQxxRord_7pBkoMBpt46xcQq',
                    'end': 32333388,
                    'id': 'ga4gh:SL.UOA3zJOPfQxxRord_7pBkoMBpt46xcQq',
@@ -55,8 +55,8 @@ def tlr(rest_dataproxy):
      ),
     ("NC_000013.11:g.32344743_32352093dup", None,
      {'copyChange': 'EFO:0030070',
-      'digest': '-sUe85R9UC_RxX7e_B1YsmsdyLsGvvmq',
-      'id': 'ga4gh:CX.-sUe85R9UC_RxX7e_B1YsmsdyLsGvvmq',
+      'digest': 'eZVvwCSineeWTGKG3vbJvqkSUMW2JTCH',
+      'id': 'ga4gh:CX.eZVvwCSineeWTGKG3vbJvqkSUMW2JTCH',
       'location': {'digest': '17-a6p7m6QznwxZyVz2QdA9oPf5jTCyT',
                    'end': 32352093,
                    'id': 'ga4gh:SL.17-a6p7m6QznwxZyVz2QdA9oPf5jTCyT',

tests/test_vrs.py

@@ -265,8 +265,8 @@ def test_class_refatt_map():
         'CopyNumberCount': ['location'],
         'CopyNumberChange': ['location'],
         'Adjacency': ['adjoinedSequences'],
-        'DerivativeSequence': ['components'],
-        'SequenceTerminus': ['location']
+        'TraversalBlock': ['component'],
+        'Terminus': ['location']
     }
     assert class_refatt_map_expected == models.class_refatt_map