adds crystal plate interface for making subwell positions

src/xchembku_api/crystal_plate_objects/interface.py

@@ -0,0 +1,38 @@
+from abc import ABC, abstractmethod
+from typing import Dict, Optional, Tuple
+
+
+class Interface(ABC):
+    """
+    This is the required API interface for an Authorizer object.
+    """
+
+    @abstractmethod
+    # ----------------------------------------------------------------------------------------
+    def get_well_count(self) -> int:
+        pass
+
+    # ----------------------------------------------------------------------------------------
+    @abstractmethod
+    def normalize_subwell_name(self, subwell_name: str) -> str:
+        """
+        Converts the name given to the subwell by Luigi into the "position" format shown in soakdb3.
+
+        Args:
+            subwell_name (str): stem part of the subwell's image filename
+
+        Raises:
+            ValueError: the value does not follow the convention
+
+        Returns:
+            str: the displayable subwell position
+        """
+        pass
+
+    # ----------------------------------------------------------------------------------------
+    @abstractmethod
+    def compute_drop_location_microns(
+        self,
+        crystal_well_record: Dict,
+    ) -> Tuple[Optional[int], Optional[int]]:
+        pass

src/xchembku_lib/crystal_plate_objects/crystal_plate_objects.py

@@ -8,6 +8,11 @@
 # Types which the CrystalPlateObjects factory can use to build an instance.
 from xchembku_api.crystal_plate_objects.constants import ThingTypes
 
+# Interface fulfilled by all CrystalPlateObject isntances.
+from xchembku_api.crystal_plate_objects.interface import (
+    Interface as CrystalPlateInterface,
+)
+
 # Exceptions.
 from xchembku_api.exceptions import NotFound
 
@@ -35,8 +40,10 @@ def get_treenode_names(self) -> List[str]:
         return list(self.__treenode_names_to_thing_type.keys())
 
     # ----------------------------------------------------------------------------------------
-    def build_object(self, specification):
-        """"""
+    def build_object(self, specification) -> CrystalPlateInterface:
+        """
+        TODO: CrystalPlateObjects build_object method should return an interface.
+        """
 
         object_class = self.lookup_class(specification["type"])
 

src/xchembku_lib/crystal_plate_objects/swiss3.py

@@ -9,12 +9,15 @@
 # Types.
 from xchembku_api.crystal_plate_objects.constants import ThingTypes
 
+# Interface.
+from xchembku_api.crystal_plate_objects.interface import Interface
+
 logger = logging.getLogger(__name__)
 
 thing_type = ThingTypes.SWISS3
 
 
-class Swiss3(Thing):
+class Swiss3(Thing, Interface):
     """ """
 
     __MICRONS_PER_PIXEL_X = 2.837
@@ -32,7 +35,7 @@ def get_well_count(self) -> int:
     # ----------------------------------------------------------------------------------------
     def normalize_subwell_name(self, subwell_name: str) -> str:
         """
-        Converts the name given to the subwell by Luigi into the format expected by the beamline.
+        Converts the name given to the subwell by Luigi into the "position" format shown in soakdb3.
 
         Args:
             subwell_name (str): stem part of the subwell's image filename

tests/test_crystal_plate.py

@@ -68,8 +68,6 @@ class CrystalPlateTester(Base):
 
     async def _main_coroutine(self, constants, output_directory):
         """ """
-        self.__injected_count = 0
-
         # Get the multiconf from the testing configuration yaml.
         multiconf = self.get_multiconf()
 

tests/test_swiss3.py

@@ -29,6 +29,10 @@ def test(
         assert position == "H12d"
 
         # Check invalid name formats.
+        with pytest.raises(ValueError) as excinfo:
+            swiss3.normalize_subwell_name("98ab_273A_1")
+        assert "expected format" in str(excinfo.value)
+
         with pytest.raises(ValueError) as excinfo:
             swiss3.normalize_subwell_name("98ju_01H_1.jpg")
         assert "expected format" in str(excinfo.value)