swap echo_coordinate for confirmed_microns

Author: David Erb

src/echolocator_lib/composers/html.py

@@ -54,7 +54,7 @@ def compose_image_list(self, models: List[CrystalWellNeedingDroplocationModel]):
             {"text": "well centroid x,y", "class": "T_well_centroid_x_y"},
             {"text": "auto x,y", "class": "T_auto_target_x_y"},
             {"text": "confirmed x,y", "class": "T_confirmed_target_x_y"},
-            {"text": "echo coordinate x,y", "class": "T_echo_coordinate_x_y"},
+            {"text": "echo coordinate x,y", "class": "T_confirmed_microns_x_y"},
             {"text": "use", "class": "T_is_usable"},
             {"text": "error", "class": "T_error"},
         ]
@@ -146,11 +146,11 @@ def compose_image_list(self, models: List[CrystalWellNeedingDroplocationModel]):
                 t = f"{model.confirmed_target_x}, {model.confirmed_target_y}"
             html_lines.append("<td class='T_confirmed_target_x_y'>" + t + "</td>")
 
-            if model.echo_coordinate_x is None or model.echo_coordinate_y is None:
+            if model.confirmed_microns_x is None or model.confirmed_microns_y is None:
                 t = "-"
             else:
-                t = f"{model.echo_coordinate_x}, {model.echo_coordinate_y}"
-            html_lines.append("<td class='T_echo_coordinate_x_y'>" + t + "</td>")
+                t = f"{model.confirmed_microns_x}, {model.confirmed_microns_y}"
+            html_lines.append("<td class='T_confirmed_microns_x_y'>" + t + "</td>")
 
             t = model.is_usable
             if t is None:

src/echolocator_lib/guis/aiohttp.py

@@ -479,8 +479,8 @@ async def _export(self, opaque, request_dict):
             for m in crystal_well_models:
                 row = []
                 row.append(m.position)
-                row.append(m.echo_coordinate_x or "")
-                row.append(m.echo_coordinate_y or "")
+                row.append(m.confirmed_microns_x or "")
+                row.append(m.confirmed_microns_y or "")
                 writer.writerow(row)
 
         response = {
@@ -494,8 +494,8 @@ async def _export(self, opaque, request_dict):
                     LabVisit=visit,
                     CrystalPlate=crystal_plate_model.rockminer_collected_stem,
                     CrystalWell=m.position,
-                    EchoX=m.echo_coordinate_x,
-                    EchoY=m.echo_coordinate_y,
+                    EchoX=m.confirmed_microns_x,
+                    EchoY=m.confirmed_microns_y,
                 )
             )
 

tests/base.py

@@ -8,6 +8,11 @@
 
 # Configurator.
 from dls_multiconf_lib.multiconfs import Multiconfs, multiconfs_set_default
+
+# Types which the CrystalPlateObjects factory can use to build an instance.
+from xchembku_api.crystal_plate_objects.constants import (
+    ThingTypes as CrystalPlateObjectThingTypes,
+)
 from xchembku_api.models.crystal_plate_model import CrystalPlateModel
 from xchembku_api.models.crystal_well_autolocation_model import (
     CrystalWellAutolocationModel,
@@ -100,6 +105,7 @@ async def inject_plate(self, xchembku):
             barcode=self.barcode,
             rockminer_collected_stem=self.rockminer_collected_stem,
             visit=self.visit,
+            thing_type=CrystalPlateObjectThingTypes.SWISS3,
         )
 
         await xchembku.upsert_crystal_plates([crystal_plate_model])

tests/test_fetch_images.py

@@ -13,14 +13,6 @@
 # Things xchembku provides.
 from xchembku_api.datafaces.context import Context as XchembkuDatafaceClientContext
 from xchembku_api.datafaces.datafaces import xchembku_datafaces_get_default
-from xchembku_api.models.crystal_plate_model import CrystalPlateModel
-from xchembku_api.models.crystal_well_autolocation_model import (
-    CrystalWellAutolocationModel,
-)
-from xchembku_api.models.crystal_well_droplocation_model import (
-    CrystalWellDroplocationModel,
-)
-from xchembku_api.models.crystal_well_model import CrystalWellModel
 
 # Client context creator.
 from echolocator_api.guis.context import Context as GuiClientContext
@@ -108,26 +100,15 @@ async def __run_part1(self, constants, output_directory):
 
         await self.__request_initial()
 
-        # Make the plate on which the wells reside.
-        visit = "cm00001-1"
-        crystal_plate_model = CrystalPlateModel(
-            formulatrix__plate__id=10,
-            barcode="98ab",
-            visit=visit,
-        )
-
-        await xchembku.upsert_crystal_plates([crystal_plate_model])
-        self.__crystal_plate_uuid = crystal_plate_model.uuid
-
         crystal_wells = []
 
         # Inject some wells.
-        crystal_wells.append(await self.__inject(xchembku, False, False))
-        crystal_wells.append(await self.__inject(xchembku, True, True))
-        crystal_wells.append(await self.__inject(xchembku, True, False))
-        crystal_wells.append(await self.__inject(xchembku, True, True))
-        crystal_wells.append(await self.__inject(xchembku, True, True))
-        crystal_wells.append(await self.__inject(xchembku, True, False))
+        crystal_wells.append(await self.inject(xchembku, False, False))
+        crystal_wells.append(await self.inject(xchembku, True, True))
+        crystal_wells.append(await self.inject(xchembku, True, False))
+        crystal_wells.append(await self.inject(xchembku, True, True))
+        crystal_wells.append(await self.inject(xchembku, True, True))
+        crystal_wells.append(await self.inject(xchembku, True, False))
 
         await self.__request_all(crystal_wells)
 
@@ -200,46 +181,3 @@ async def __request_all(self, crystal_wells):
         columns = row.find_all(class_="T_filename")
         assert len(columns) == 1
         assert columns[0].get_text() == Path(crystal_wells[5].filename).stem
-
-    # ----------------------------------------------------------------------------------------
-
-    async def __inject(self, xchembku, autolocation: bool, droplocation: bool):
-        """ """
-        if not hasattr(self, "injected_count"):
-            self.injected_count = 0
-
-        filename = "/tmp/aaaa_%03d_1.jpg" % (self.injected_count)
-
-        # Write well record.
-        m = CrystalWellModel(
-            position="01A_1",
-            filename=filename,
-            crystal_plate_uuid=self.__crystal_plate_uuid,
-        )
-
-        await xchembku.upsert_crystal_wells([m])
-
-        if autolocation:
-            # Add a crystal well autolocation.
-            t = CrystalWellAutolocationModel(
-                crystal_well_uuid=m.uuid,
-                number_of_crystals=self.injected_count,
-                auto_target_x=self.injected_count * 10 + 1,
-                auto_target_y=self.injected_count * 10 + 2,
-            )
-
-            await xchembku.originate_crystal_well_autolocations([t])
-
-        if droplocation:
-            # Add a crystal well droplocation.
-            t = CrystalWellDroplocationModel(
-                crystal_well_uuid=m.uuid,
-                confirmed_target_x=self.injected_count * 10 + 3,
-                confirmed_target_y=self.injected_count * 10 + 4,
-            )
-
-            await xchembku.originate_crystal_well_droplocations([t])
-
-        self.injected_count += 1
-
-        return m