maint: test gene expressions

Note: Also, remove unused maptype kwarg from allen query. The official way to query with statistical maps is to get the regional mask with the desired threshold and query features with this volume.

e2e/features/molecular/test_genes.py

@@ -1,12 +1,20 @@
 import pytest
 import siibra
+from typing import Union, List
 
-test_params = [("hoc1 left", "MAOA")]
+test_params = [
+    ("julich 2.9", "hoc1 left", "MAOA"),
+    ("julich 3.0.3", "hoc1 left", "MAOA"),
+    ("julich 3.1", "hoc1 left", "MAOA"),
+    ("julich 3.1", "ifg 44 left", "MAOA"),
+    ("julich 3.1", "hoc1 left", ["GABRA1", "GABRA2", "GABRQ"]),
+    ("julich 3.1", "ifg 44 left", ["GABRA1", "GABRA2", "GABRQ"]),
+]
 
 
-@pytest.mark.parametrize("region_spec,gene", test_params)
-def test_genes(region_spec: str, gene: str):
-    parc = siibra.parcellations["2.9"]
+@pytest.mark.parametrize("parc_spec, region_spec, gene", test_params)
+def test_genes(parc_spec: str, region_spec: str, gene: Union[str, List[str]]):
+    parc = siibra.parcellations[parc_spec]
     region = parc.get_region(region_spec)
     features = siibra.features.get(region, "gene", gene=gene)
     assert len(features) > 0, "expecting at least 1 gene feature"
@@ -15,27 +23,18 @@ def test_genes(region_spec: str, gene: str):
     ), "expecting all features to be of type GeneExpression"
 
 
-def test_gene_exp():
-    kwargs = {"gene": "MAOA", "maptype": siibra.commons.MapType.STATISTICAL}
+def test_gene_exp_w_parent_structures():
+    kwargs = {"gene": "MAOA"}
     features_grandparent_struct = siibra.features.get(
-        *(siibra.parcellations["2.9"].get_region("frontal pole"), 'gene'), **kwargs
+        *(siibra.parcellations["2.9"].get_region("frontal pole"), "gene"), **kwargs
     )
     features_leaf_struct = siibra.features.get(
-        *(siibra.parcellations["2.9"].get_region("fp1 left"), 'gene'), **kwargs
+        *(siibra.parcellations["2.9"].get_region("fp1 left"), "gene"), **kwargs
     )
 
-    # should have received one gene expression feature each
+    # must find a gene expression for both
     assert len(features_grandparent_struct) == 1
     assert len(features_leaf_struct) == 1
 
-    # Using higher threshold should result in less gene expresssion measures
+    # grandparent area should contain more measurements
     assert len(features_grandparent_struct[0].data) > len(features_leaf_struct[0].data)
-
-
-def test_query_w_genelist():
-    genes = ["GABRA1", "GABRA2", "GABRQ"]
-    p = siibra.parcellations['julich 3']
-    regions = [p.get_region(spec) for spec in ["ifg 44 left", "hoc1 left"]]
-    for region in regions:
-        fts = siibra.features.get(region, "GeneExpressions", gene=genes)
-        assert len(fts) > 0

siibra/livequeries/allen.py

@@ -101,9 +101,6 @@ def __init__(self, **kwargs):
         """
         LiveQuery.__init__(self, **kwargs)
         gene = kwargs.get('gene')
-        self.maptype = kwargs.get("maptype", None)
-        if isinstance(self.maptype, str):
-            self.maptype = MapType[self.maptype.upper()]
 
         def parse_gene(spec):
             if isinstance(spec, str):