Add variants related models

docs/CHANGELOG.rst

@@ -16,6 +16,7 @@ Changed
 Added
 -----
 - Add ``restart`` method to the ``Data`` resource
+- Add variants related models
 
 Fixed
 -----

src/resdk/query.py

@@ -175,7 +175,9 @@ def _add_filter(self, filter_):
         """Add filtering parameters."""
         for key, value in filter_.items():
             # 'sample' is called 'entity' in the backend.
-            key = key.replace("sample", "entity")
+            if not key.startswith("variant_calls__"):
+                key = key.replace("sample", "entity")
+            print("Adding filter", key, value)
             value = self._dehydrate_resources(value)
             if self._non_string_iterable(value):
                 value = ",".join(map(str, value))

src/resdk/resolwe.py

@@ -47,6 +47,10 @@
     Relation,
     Sample,
     User,
+    Variant,
+    VariantAnnotation,
+    VariantCall,
+    VariantExperiment,
 )
 from .resources.base import BaseResource
 from .resources.kb import Feature, Mapping
@@ -114,6 +118,10 @@ class Resolwe:
     resource_query_mapping = {
         AnnotationField: "annotation_field",
         AnnotationValue: "annotation_value",
+        Variant: "variant",
+        VariantAnnotation: "variant_annotation",
+        VariantExperiment: "variant_experiment",
+        VariantCall: "variant_calls",
         Data: "data",
         Collection: "collection",
         Sample: "sample",
@@ -126,6 +134,7 @@ class Resolwe:
         Mapping: "mapping",
         Geneset: "geneset",
         Metadata: "metadata",
+        Variant: "variant",
     }
     # Map ResolweQuery name to it's slug_field
     slug_field_mapping = {

src/resdk/resources/__init__.py

@@ -54,6 +54,10 @@
    :members:
    :inherited-members:
 
+.. autoclass:: resdk.resources.Variants
+   :members:
+   :inherited-members:
+
 .. autoclass:: resdk.resources.User
    :members:
    :inherited-members:
@@ -102,6 +106,7 @@
 from .relation import Relation
 from .sample import Sample
 from .user import Group, User
+from .variants import Variant, VariantAnnotation, VariantCall, VariantExperiment
 
 __all__ = (
     "AnnotationField",
@@ -117,4 +122,8 @@
     "Process",
     "Relation",
     "User",
+    "Variant",
+    "VariantAnnotation",
+    "VariantCall",
+    "VariantExperiment",
 )

src/resdk/resources/sample.py

@@ -1,14 +1,15 @@
 """Sample resource."""
 
 import logging
-from typing import TYPE_CHECKING, Any, Dict, Optional
+from typing import TYPE_CHECKING, Any, Dict, List, Optional
 
 from resdk.exceptions import ResolweServerError
 from resdk.shortcuts.sample import SampleUtilsMixin
 
 from ..utils.decorators import assert_object_exists
 from .background_task import BackgroundTask
 from .collection import BaseCollection, Collection
+from .variants import Variant
 
 if TYPE_CHECKING:
     from .annotations import AnnotationValue
@@ -39,6 +40,8 @@ def __init__(self, resolwe, **model_data):
         self._background = None
         #: is this sample background to any other sample?
         self._is_background = None
+        #: list of ``Variant`` objects attached to the sample
+        self._variants = None
 
         super().__init__(resolwe, **model_data)
 
@@ -60,6 +63,13 @@ def data(self):
 
         return self._data
 
+    @property
+    def variants(self):
+        """Get variants."""
+        if self._variants is None:
+            self._variants = self.resolwe.variant.filter(variant_calls__sample=self.id)
+        return self._variants
+
     @property
     def collection(self):
         """Get collection."""

src/resdk/resources/variants.py

@@ -0,0 +1,94 @@
+"""Variant resources."""
+
+from .base import BaseResource
+
+
+class Variant(BaseResource):
+    """ResolweBio Variant resource."""
+
+    endpoint = "variant"
+
+    READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+        "species",
+        "genome_assembly",
+        "chromosome",
+        "position",
+        "reference",
+        "alternative",
+    )
+
+    def __init__(self, resolwe, **model_data):
+        """Initialize object."""
+        super().__init__(resolwe, **model_data)
+        self._annotations = None
+
+    @property
+    def annotations(self):
+        """Get the annotations for this variant."""
+        if self._annotations is None:
+            self._annotations = self.resolwe.variant_annotation.filter(id=self.id)
+        return self._annotations
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return (
+            f"Variant <chr: {self.chromosome}, pos: {self.position}, "
+            f"ref: {self.reference}, alt: {self.alternative}>"
+        )
+
+
+class VariantAnnotation(BaseResource):
+    """VariantAnnotation resource."""
+
+    endpoint = "variant_annotations"
+
+    READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+        "variant_id",
+        "type",
+        "clinical_diagnosis",
+        "clinical_significance",
+        "dbsnp_id",
+        "clinvar_id",
+        "data",
+        "transcripts",
+    )
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return f"VariantAnnotation <variant: {self.variant_id}>"
+
+
+class VariantExperiment(BaseResource):
+    """Variant experiment resource."""
+
+    endpoint = "variant_experiment"
+
+    READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+        "variant_data_source",
+        "timestamp",
+        "contributor",
+    )
+
+
+class VariantCall(BaseResource):
+    """VariantCall resource."""
+
+    endpoint = "variant_calls"
+
+    READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+        "sample",
+        "variant",
+        "experiment",
+        "quality",
+        "depth_norm_quality",
+        "alternative_allele_depth",
+        "depth",
+        "genotype",
+        "genotype_quality",
+        "filter",
+        "data",
+    )
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return f"VariantCall <pk: {self.id}>"