Filter datapoints in plot for ratio13/18/21

statina/API/v2/endpoints/batches.py

@@ -167,8 +167,16 @@ def ratio_plot(
                 tris_thresholds=get_trisomy_metadata(dataset=dataset),
                 chromosomes=[ncv],
                 ncv_chrom_data={ncv: get_tris_samples(adapter=adapter, chr=ncv, batch_id=batch_id)},
-                normal_data={ncv: get_tris_control_normal(adapter, ncv)},
-                abnormal_data={ncv: get_tris_control_abnormal(adapter, ncv, 0)},
+                normal_data={
+                    ncv: get_tris_control_normal(
+                        adapter=adapter, chr=ncv, dataset_name=dataset.name
+                    )
+                },
+                abnormal_data={
+                    ncv: get_tris_control_abnormal(
+                        adapter=adapter, chr=ncv, dataset_name=dataset.name, x_axis=0
+                    )
+                },
             ),
             by_alias=False,
         ),

statina/API/v2/endpoints/sample.py

@@ -100,10 +100,14 @@ def sample_tris(
     """Sample view with trisomi plot."""
 
     database_sample: DataBaseSample = find_samples.sample(sample_id=sample_id, adapter=adapter)
+    dataset = get_dataset(adapter=adapter, batch_id=database_sample.batch_id)
     abnormal_data: Dict[str, RatioSamples] = ratio_plot_data.get_abn_for_samp_tris_plot(
-        adapter=adapter
+        adapter=adapter, dataset_name=dataset.name
+    )
+
+    normal_data: Ratio131821 = ratio_plot_data.get_normal_for_samp_tris_plot(
+        adapter=adapter, dataset_name=dataset.name
     )
-    normal_data: Ratio131821 = ratio_plot_data.get_normal_for_samp_tris_plot(adapter=adapter)
     sample_data: RatioSamples = ratio_plot_data.get_sample_for_samp_tris_plot(database_sample)
 
     return JSONResponse(

statina/crud/find/batches.py

@@ -1,15 +1,16 @@
-from typing import Iterable, List, Optional, Literal
+from typing import Iterable, List, Optional, Literal, Any
 
 from pydantic import parse_obj_as
 
 from statina.adapter import StatinaAdapter
 from statina.constants import sort_table
 from statina.crud.utils import paginate
 from statina.models.database import DatabaseBatch
+from typing import List
 
 
 def get_batches_text_query(query_string: str) -> dict:
-    """Text search with regex, case insensitive"""
+    """Text search with regex, case-insensitive"""
     return {
         "$or": [
             {"batch_id": {"$regex": query_string, "$options": "i"}},
@@ -66,3 +67,11 @@ def count_query_batches(adapter: StatinaAdapter, query_string: Optional[str] = "
     return adapter.batch_collection.count_documents(
         filter=get_batches_text_query(query_string=query_string)
     )
+
+
+def get_batch_ids_by_dataset(adapter: StatinaAdapter, dataset_name: str) -> List[Any]:
+    batch_ids = [
+        doc["batch_id"]
+        for doc in adapter.batch_collection.find({"dataset": dataset_name}, {"batch_id": 1})
+    ]
+    return batch_ids

statina/crud/find/plots/ratio_plot_data.py

@@ -3,20 +3,26 @@
 
 import statina
 from statina.adapter import StatinaAdapter
+from statina.crud.find.batches import get_batch_ids_by_dataset
 from statina.models.database import DataBaseSample
 from statina.models.server.plots.ncv import Ratio131821, RatioSamples
 
 
-def get_tris_control_abnormal(adapter: StatinaAdapter, chr, x_axis) -> Dict[str, RatioSamples]:
+def get_tris_control_abnormal(
+    adapter: StatinaAdapter, chr, dataset_name: str, x_axis
+) -> Dict[str, RatioSamples]:
     """Abnormal Control Samples for trisomi plots"""
 
     plot_data = {}
 
+    batch_ids = get_batch_ids_by_dataset(adapter=adapter, dataset_name=dataset_name)
+
     pipe = [
         {
             "$match": {
-                f"status_{chr}": {"$ne": "Normal", "$exists": "True"},
+                f"status_{chr}": {"$ne": "Normal", "$exists": True},
                 "include": {"$eq": True},
+                "batch_id": {"$in": batch_ids},
             }
         },
         {
@@ -41,14 +47,16 @@ def get_tris_control_abnormal(adapter: StatinaAdapter, chr, x_axis) -> Dict[str,
     return plot_data
 
 
-def get_abn_for_samp_tris_plot(adapter: StatinaAdapter) -> Dict[str, RatioSamples]:
+def get_abn_for_samp_tris_plot(
+    adapter: StatinaAdapter, dataset_name: str
+) -> Dict[str, RatioSamples]:
     """Format abnormal Control Samples for Sample trisomi plot"""
 
     plot_data = {}
 
     for x_axis, abn in enumerate(["13", "18", "21"], start=1):
         tris_control_abnormal: Dict[str, RatioSamples] = get_tris_control_abnormal(
-            adapter, abn, x_axis
+            adapter=adapter, chr=abn, dataset_name=dataset_name, x_axis=x_axis
         )
         for status, data in tris_control_abnormal.items():
             if status not in plot_data:
@@ -64,12 +72,20 @@ def get_abn_for_samp_tris_plot(adapter: StatinaAdapter) -> Dict[str, RatioSample
 
 
 def get_tris_control_normal(
-    adapter: StatinaAdapter, chr: str, x_axis: Optional[int] = None
+    adapter: StatinaAdapter, chr: str, dataset_name: str, x_axis: Optional[int] = None
 ) -> RatioSamples:
     """Normal Control Samples for trisomi plots"""
 
+    batch_ids = get_batch_ids_by_dataset(adapter=adapter, dataset_name=dataset_name)
+
     pipe = [
-        {"$match": {f"status_{chr}": {"$eq": "Normal"}, "include": {"$eq": True}}},
+        {
+            "$match": {
+                f"status_{chr}": {"$eq": "Normal"},
+                "include": {"$eq": True},
+                "batch_id": {"$in": batch_ids},
+            }
+        },
         {
             "$group": {
                 "_id": {f"status_{chr}": f"$status_{chr}"},
@@ -88,26 +104,22 @@ def get_tris_control_normal(
     return RatioSamples(**data)
 
 
-def get_normal_for_samp_tris_plot(adapter: StatinaAdapter) -> Ratio131821:
+def get_normal_for_samp_tris_plot(adapter: StatinaAdapter, dataset_name: str) -> Ratio131821:
     """Format normal Control Samples for Sample trisomi plot"""
 
     return Ratio131821(
-        chr_13=get_tris_control_normal(adapter=adapter, chr="13", x_axis=1),
-        chr_18=get_tris_control_normal(adapter=adapter, chr="18", x_axis=2),
-        chr_21=get_tris_control_normal(adapter=adapter, chr="21", x_axis=3),
+        chr_13=get_tris_control_normal(
+            adapter=adapter, chr="13", dataset_name=dataset_name, x_axis=1
+        ),
+        chr_18=get_tris_control_normal(
+            adapter=adapter, chr="18", dataset_name=dataset_name, x_axis=2
+        ),
+        chr_21=get_tris_control_normal(
+            adapter=adapter, chr="21", dataset_name=dataset_name, x_axis=3
+        ),
     )
 
 
-def get_abnormal_for_samp_tris_plot(adapter: StatinaAdapter) -> dict:
-    """Format normal Control Samples for Sample trisomi plot"""
-
-    return {
-        "13": get_tris_control_abnormal(adapter=adapter, chr="13", x_axis=0),
-        "18": get_tris_control_abnormal(adapter=adapter, chr="18", x_axis=0),
-        "21": get_tris_control_abnormal(adapter=adapter, chr="21", x_axis=0),
-    }
-
-
 def get_samples_for_samp_tris_plot(adapter: StatinaAdapter, batch_id: str) -> Ratio131821:
     return Ratio131821(
         chr_13=get_tris_samples(adapter=adapter, chr="13", batch_id=batch_id),

tests/crud/find/test_batches.py

@@ -0,0 +1,21 @@
+from mongomock import MongoClient
+from statina.adapter.plugin import StatinaAdapter
+from statina.crud.find.batches import get_batch_ids_by_dataset
+
+
+def test_get_batch_ids_by_dataset(database):
+    # GIVEN a database with two batches belonging to "dataset_1" and one to "dataset_2"
+    adapter = StatinaAdapter(database.client, db_name="testdb")
+    adapter.batch_collection.insert_many(
+        [
+            {"batch_id": "batch_1", "dataset": "dataset_1"},
+            {"batch_id": "batch_2", "dataset": "dataset_1"},
+            {"batch_id": "batch_3", "dataset": "dataset_2"},
+        ]
+    )
+
+    # WHEN fetching batch_ids for "dataset_1"
+    batch_ids = get_batch_ids_by_dataset(adapter=adapter, dataset_name="dataset_1")
+
+    # THEN only the two batch_ids belonging to "dataset_1" should be returned
+    assert batch_ids == ["batch_1", "batch_2"]