From bb36f8068c714b5005450f16a229293fcdb0b30b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gregor=20Jer=C5=A1e?= <gregor.jerse@genialis.com>
Date: Mon, 18 Mar 2024 10:40:17 +0100
Subject: [PATCH] Add variants related models

---
 docs/CHANGELOG.rst              |   1 +
 src/resdk/resolwe.py            |   6 ++
 src/resdk/resources/__init__.py |   8 +++
 src/resdk/resources/variants.py | 101 ++++++++++++++++++++++++++++++++
 4 files changed, 116 insertions(+)
 create mode 100644 src/resdk/resources/variants.py

diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index 199ae462..ccedcb7c 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -16,6 +16,7 @@ Changed
 Added
 -----
 - Add ``restart`` method to the ``Data`` resource
+- Add variants related models
 
 Fixed
 -----
diff --git a/src/resdk/resolwe.py b/src/resdk/resolwe.py
index 63268dc1..02cbf016 100644
--- a/src/resdk/resolwe.py
+++ b/src/resdk/resolwe.py
@@ -47,6 +47,9 @@
     Relation,
     Sample,
     User,
+    Variant,
+    VariantCall,
+    VariantExperiment,
 )
 from .resources.base import BaseResource
 from .resources.kb import Feature, Mapping
@@ -114,6 +117,9 @@ class Resolwe:
     resource_query_mapping = {
         AnnotationField: "annotation_field",
         AnnotationValue: "annotation_value",
+        Variant: "variant",
+        VariantExperiment: "variant_experiment",
+        VariantCall: "variant_calls",
         Data: "data",
         Collection: "collection",
         Sample: "sample",
diff --git a/src/resdk/resources/__init__.py b/src/resdk/resources/__init__.py
index 061a7964..4a2ecc72 100644
--- a/src/resdk/resources/__init__.py
+++ b/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, VariantCall, VariantExperiment
 
 __all__ = (
     "AnnotationField",
@@ -117,4 +122,7 @@
     "Process",
     "Relation",
     "User",
+    "Variant",
+    "VariantCall",
+    "VariantExperiment",
 )
diff --git a/src/resdk/resources/variants.py b/src/resdk/resources/variants.py
new file mode 100644
index 00000000..a18c2edc
--- /dev/null
+++ b/src/resdk/resources/variants.py
@@ -0,0 +1,101 @@
+"""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 __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_annotation"
+
+    READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+        "variant",
+        "type",
+        "clinical_diagnosis",
+        "clinical_significance",
+        "dbsnp_id",
+        "clinvar_id",
+        "data",
+    )
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return f"VariantAnnotation <variant: {self.variant}>"
+
+
+class VariantAnnotationTranscript(BaseResource):
+    """VariantAnnotationTranscript resource."""
+
+    endpoint = "variant_annotation_transcript"
+
+    READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+        "variant_annotation",
+        "annotation",
+        "annotation_impact",
+        "gene",
+        "protein_impact",
+        "transcript_ids",
+        "cananical",
+    )
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return f"VariantAnnotationTrascript <variant annotation: {self.variant_annotation}>"
+
+
+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",
+        "unfiltered_allele_depth",
+        "depth",
+        "genotype",
+        "genotype_quality",
+        "filter",
+        "data",
+    )
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return f"VariantCall <pk: {self.id}>"