changes export sort order

Author: David Erb

src/echolocator_lib/guis/aiohttp.py

@@ -571,10 +571,16 @@ async def __export_to_soakdb3(self, opaque, request_dict):
             crystal_well_filter, why="[EXPFIL] get list to be epxorted"
         )
 
+        # Sort the list based on the (computed) row_first_position field.
+        sorted_models = sorted(
+            crystal_well_models,
+            key=lambda crystal_well_model: crystal_well_model.row_first_position(),
+        )
+
         logger.debug(f"[EXPFIL] found {len(crystal_well_models)} to be exported")
 
         # Export the crystal wells to the appropriate soakdb3 visit.
-        await self.__export_to_soakdb3_visit(visit_filter, crystal_well_models)
+        await self.__export_to_soakdb3_visit(visit_filter, sorted_models)
 
         # Make the list of droplocations to update with the exported flag.
         crystal_well_droplocation_models: List[CrystalWellDroplocationModel] = list()
@@ -692,9 +698,16 @@ async def __export_to_csv(self, opaque, request_dict):
             crystal_plate_uuid,
             plate_crystal_well_models,
         ) in plates_crystal_well_models.items():
+
+            # Sort the list based on the (computed) row_first_position field.
+            sorted_models = sorted(
+                plate_crystal_well_models,
+                key=lambda crystal_well_model: crystal_well_model.row_first_position(),
+            )
+
             # Export the crystal wells for this plate to the appropriate csv file named for the plate.
             filename = await self.__export_to_csv_plate(
-                visit_filter, crystal_plate_uuid, plate_crystal_well_models
+                visit_filter, crystal_plate_uuid, sorted_models
             )
 
             confirmations.append(

tests/base.py

@@ -35,7 +35,7 @@ def __init__(self):
         self.tasks_execution_outputs = {}
         self.residuals = ["stdout.txt", "stderr.txt", "main.log"]
 
-        self.injected_count = 0
+        self.__injected_count = 0
         self.visit = "cm00001-1"
         self.__barcode_template = "98a%d"
         self.crystal_plate_uuid = None
@@ -131,13 +131,33 @@ async def inject(self, xchembku, autolocation: bool, droplocation: bool):
         if self.crystal_plate_uuid is None:
             await self.inject_plate(xchembku)
 
-        self.injected_count += 1
-
-        filename = "/tmp/%03d.jpg" % (self.injected_count)
+        letter = "A"
+        if self.__injected_count > 3:
+            letter = "B"
+
+        self.__injected_count += 1
+        filename = "/tmp/%02d%s_1.jpg" % (self.__injected_count, letter)
+        position = "%s%02da" % (letter, self.__injected_count)
+
+        positions = [
+            "A01a",
+            "A02a",
+            "A03a",
+            "B01a",
+            "B02a",
+            "B02a",
+            "C01a",
+            "C02a",
+            "C03a",
+            "D01a",
+            "D02a",
+            "D03a",
+        ]
+        position = positions[self.__injected_count - 1]
 
         # Write well record.
         m = CrystalWellModel(
-            position="%02dA_1" % (self.injected_count),
+            position=position,
             filename=filename,
             crystal_plate_uuid=self.crystal_plate_uuid,
         )
@@ -148,11 +168,11 @@ async def inject(self, xchembku, autolocation: bool, droplocation: bool):
             # Add a crystal well autolocation.
             t = CrystalWellAutolocationModel(
                 crystal_well_uuid=m.uuid,
-                number_of_crystals=self.injected_count,
+                number_of_crystals=self.__injected_count,
                 well_centroid_x=400,
                 well_centroid_y=500,
-                auto_target_x=self.injected_count * 10 + 0,
-                auto_target_y=self.injected_count * 10 + 1,
+                auto_target_x=self.__injected_count * 10 + 0,
+                auto_target_y=self.__injected_count * 10 + 1,
             )
 
             await xchembku.originate_crystal_well_autolocations([t])
@@ -161,8 +181,8 @@ async def inject(self, xchembku, autolocation: bool, droplocation: bool):
             # Add a crystal well droplocation.
             t = CrystalWellDroplocationModel(
                 crystal_well_uuid=m.uuid,
-                confirmed_target_x=self.injected_count * 100 + 2,
-                confirmed_target_y=self.injected_count * 100 + 3,
+                confirmed_target_x=self.__injected_count * 100 + 2,
+                confirmed_target_y=self.__injected_count * 100 + 3,
                 is_usable=True,
             )
 

tests/test_export_to_csv.py

@@ -195,13 +195,16 @@ async def __export_wells(self, crystal_wells):
 
         # Check the well positions are those that are considered "confirmed".
         # The position constants are fromt the Swiss3 microns computation.
-        assert rows[0][0] == "02A_1"
-        assert int(rows[0][1]) == -561
-        assert int(rows[0][2]) == -842
-        assert rows[1][0] == "04A_1"
-        assert int(rows[1][1]) == 6
-        assert int(rows[1][2]) == -274
-        assert rows[2][0] == "05A_1"
+        # Note the order here: row_first_position gives get all letters in row 01 before any letters in row 02.
+        assert rows[0][0] == "B01a"
+        assert int(rows[0][1]) == 6
+        assert int(rows[0][2]) == -274
+
+        assert rows[1][0] == "A02a"
+        assert int(rows[1][1]) == -561
+        assert int(rows[1][2]) == -842
+
+        assert rows[2][0] == "B02a"
         assert int(rows[2][1]) == 289
         assert int(rows[2][2]) == 9
 

tests/test_export_to_soakdb3.py

@@ -211,13 +211,16 @@ async def __export_wells(self, crystal_wells):
         assert len(queried_models) == 3
 
         # The position constants are fromt the Swiss3 microns computation.
-        assert queried_models[0].CrystalWell == "02A_1"
-        assert int(queried_models[0].EchoX) == -561
-        assert int(queried_models[0].EchoY) == -842
-        assert queried_models[1].CrystalWell == "04A_1"
-        assert int(queried_models[1].EchoX) == 6
-        assert int(queried_models[1].EchoY) == -274
-        assert queried_models[2].CrystalWell == "05A_1"
+        # Note the order here: row_first_position gives get all letters in row 01 before any letters in row 02.
+        assert queried_models[0].CrystalWell == "B01a"
+        assert int(queried_models[0].EchoX) == 6
+        assert int(queried_models[0].EchoY) == -274
+
+        assert queried_models[1].CrystalWell == "A02a"
+        assert int(queried_models[1].EchoX) == -561
+        assert int(queried_models[1].EchoY) == -842
+
+        assert queried_models[2].CrystalWell == "B02a"
         assert int(queried_models[2].EchoX) == 289
         assert int(queried_models[2].EchoY) == 9
 

tests/test_fetch_image.py

@@ -205,7 +205,7 @@ async def __request_anchor(self, crystal_wells):
                 Cookies.IMAGE_LIST_UX,
             ],
             Keywords.COMMAND: Commands.FETCH_IMAGE,
-            Keywords.CRYSTAL_WELL_INDEX: 2,  # 04A_1
+            Keywords.CRYSTAL_WELL_INDEX: 2,  # B01a
         }
 
         response = await echolocator_guis_get_default().client_protocolj(
@@ -218,7 +218,7 @@ async def __request_anchor(self, crystal_wells):
 
         record = response["record"]
         assert record is not None
-        assert record["position"] == "04A_1"
+        assert record["position"] == "B01a"
 
         # -------------------------------------------------------------------------------------
         # Same query again, but rely on cookie for index.
@@ -230,4 +230,4 @@ async def __request_anchor(self, crystal_wells):
         )
 
         record = response["record"]
-        assert record["position"] == "04A_1"
+        assert record["position"] == "B01a"