Added get_samples function to retrieve the acronym

mxcubecore/HardwareObjects/ICATLIMS.py

@@ -21,6 +21,7 @@
 from mxcubecore.model.lims_session import (
     Lims,
     LimsSessionManager,
+    SampleSheet,
     Session,
 )
 
@@ -127,7 +128,10 @@ def get_samples(self, lims_name):
                 self.session_manager.active_session.proposal_name,
                 lims_name,
             )
-            parcels = self.get_parcels_by_investigation_id()
+            parcels = self.get_parcels()
+
+            sample_sheets = self.get_samples_sheets()
+
             queue_samples = []
             for parcel in parcels:
                 pucks = parcel["content"]
@@ -150,7 +154,7 @@ def get_samples(self, lims_name):
                         )
                         for tracking_sample in tracking_samples:
                             queue_samples.append(
-                                self.__to_sample(tracking_sample, puck)
+                                self.__to_sample(tracking_sample, puck, sample_sheets)
                             )
 
         except Exception as e:
@@ -169,8 +173,32 @@ def find(self, arr, atribute_name):
                 return x["value"]
         return ""
 
-    def __to_sample(self, tracking_sample, puck):
+    def get_sample_sheet_by_id(
+        self, samples: List[SampleSheet], sample_id: int
+    ) -> Optional[SampleSheet]:
+        """
+        Retrieves a sample sheet by its unique ID.
+
+        Args:
+            samples (List[SampleSheet]): A list of Sample objects.
+            sample_id (int): The unique identifier of the sample sheet to retrieve.
+
+        Returns:
+            Optional[Sample]: The Sample object if found, otherwise None.
+        """
+        return next((sample for sample in samples if sample.id == sample_id), None)
+
+    def __to_sample(self, tracking_sample, puck, sample_sheets: List[SampleSheet]):
         """Converts the sample tracking into the expected sample data structure"""
+
+        sample_name = str(tracking_sample["name"])
+        protein_acronym = sample_name
+        sample_sheet = self.get_sample_sheet_by_id(
+            sample_sheets, tracking_sample["sampleId"]
+        )
+        if sample_sheet is not None:
+            protein_acronym = sample_sheet.name
+
         experiment_plan = tracking_sample["experimentPlan"]
         return {
             "cellA": self.find(experiment_plan, "unit_cell_a"),
@@ -201,10 +229,10 @@ def __to_sample(self, tracking_sample, puck):
                 "requiredResolution": self.find(experiment_plan, "requiredResolution"),
             },
             "experimentType": self.find(experiment_plan, "workflowType"),
-            "proteinAcronym": tracking_sample["name"],
+            "proteinAcronym": protein_acronym,
             "sampleId": tracking_sample["sampleId"],
             "sampleLocation": tracking_sample["sampleContainerPosition"],
-            "sampleName": str(tracking_sample["name"]),
+            "sampleName": sample_name,
             "smiles": None,
         }
 
@@ -481,7 +509,7 @@ def get_user_name(self):
     def to_sessions(self, investigations):
         return [self.__to_session(investigation) for investigation in investigations]
 
-    def get_parcels_by_investigation_id(self):
+    def get_parcels(self):
         """Returns the parcels associated to an investigation"""
         try:
             logging.getLogger("HWR").debug(
@@ -491,6 +519,7 @@ def get_parcels_by_investigation_id(self):
             parcels = self.icatClient.get_parcels_by(
                 self.session_manager.active_session.session_id
             )
+
             logging.getLogger("HWR").debug(
                 "[ICAT] Successfully retrieved %s parcels" % (len(parcels))
             )
@@ -501,6 +530,27 @@ def get_parcels_by_investigation_id(self):
             )
         return []
 
+    def get_samples_sheets(self) -> List[SampleSheet]:
+        """Returns the samples sheets associated to an investigation"""
+        try:
+            logging.getLogger("HWR").debug(
+                "[ICAT] Retrieving samples by investigation_id %s "
+                % (self.session_manager.active_session.session_id)
+            )
+            samples = self.icatClient.get_samples_by(
+                self.session_manager.active_session.session_id
+            )
+            logging.getLogger("HWR").debug(
+                "[ICAT] Successfully retrieved %s samples" % (len(samples))
+            )
+            # Convert to object
+            return [SampleSheet.parse_obj(sample) for sample in samples]
+        except Exception as e:
+            logging.getLogger("HWR").error(
+                "[ICAT] get_samples_by_investigation_id %s " % (str(e))
+            )
+        return []
+
     def echo(self):
         """Mockup for the echo method."""
         return True

mxcubecore/model/lims_session.py

@@ -3,6 +3,7 @@
     timedelta,
 )
 from typing import (
+    Any,
     Dict,
     List,
     Optional,
@@ -70,6 +71,43 @@ class Session(BaseModel):
     logbook_URL: Optional[str] = None
 
 
+class Instrument(BaseModel):
+    name: str
+    id: int
+    instrumentScientists: List[Any]
+
+
+class Investigation(BaseModel):
+    name: str
+    startDate: datetime
+    endDate: datetime
+    id: int
+    title: str
+    visitId: str
+    summary: str
+    parameters: Dict[str, Any]
+    instrument: Instrument
+    investigationUsers: List[Any]
+
+
+class Parameter(BaseModel):
+    name: str
+    value: str
+    id: int
+    units: str
+
+
+class MetaPage(BaseModel):
+    totalWithoutFilters: int
+    total: int
+    totalPages: int
+    currentPage: int
+
+
+class Meta(BaseModel):
+    page: MetaPage
+
+
 class LimsUser(BaseModel):
     user_name: str = ""
     sessions: Optional[List[Session]] = []
@@ -79,3 +117,13 @@ class LimsSessionManager(BaseModel):
     active_session: Optional[Session] = None
     sessions: Optional[List[Session]] = []
     users: Optional[Dict[str, LimsUser]] = {}
+
+
+class SampleSheet(BaseModel):
+    id: int
+    name: str
+    investigation: Investigation
+    modTime: datetime
+    parameters: List[Parameter]
+    datasets: List[Any]
+    meta: Meta

pyproject.toml

@@ -62,7 +62,7 @@ PyTango = "^9.3.6"
 python-ldap = "^3.4.0"
 requests = "^2.31.0"
 colorama = "^0.4.6"
-pyicat-plus = {version = "^0.5.1", optional = true}
+pyicat-plus = {version = "^0.6.0", optional = true}
 
 [tool.poetry.group.dev.dependencies]
 pre-commit = "^4.1.0"