mxcubecore 1.384.0__tar.gz → 1.386.0__tar.gz

{mxcubecore-1.384.0 → mxcubecore-1.386.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mxcubecore
-Version: 1.384.0
+Version: 1.386.0
 Summary: Core libraries for the MXCuBE application
 License: LGPL-3.0-or-later
 Keywords: mxcube,mxcube3,mxcubecore

{mxcubecore-1.384.0 → mxcubecore-1.386.0}/mxcubecore/HardwareObjects/ICATLIMS.py

@@ -326,9 +326,9 @@ class ICATLIMS(AbstractLims):
                 )
                 if sample_information is not None:
                     if len(HWR.beamline.session.get_full_path("", "")) > 0:
-                        destination_folder = HWR.beamline.session.get_full_path("", "")[
-                            0
-                        ]
+                        destination_folder = (
+                            HWR.beamline.session.get_base_process_directory()
+                        )
                         msg = "Download restource: "
                         msg += f"sample_sheet_id={sample_sheet_id} "
                         msg += f"destination_folder={destination_folder}"
@@ -820,21 +820,20 @@ class ICATLIMS(AbstractLims):
             msg = f"Sample {sample_id} not found"
             logging.getLogger("HWR").debug(msg)
 
-        start_time = datacollection_dict.get("startTime", "")
-        end_time = datacollection_dict.get("endTime", "")
+        start_time = datacollection_dict.get("collection_start_time", "")
+        end_time = datetime.now(ZoneInfo("Europe/Paris")).isoformat()
 
-        try:
-            dt_aware = datetime.strptime(start_time, "%Y-%m-%d %H:%M:%S").replace(
-                tzinfo=ZoneInfo("Europe/Paris")
-            )
-            dt_aware_end = datetime.strptime(end_time, "%Y-%m-%d %H:%M:%S").replace(
-                tzinfo=ZoneInfo("Europe/Paris")
-            )
+        if start_time:
+            try:
+                dt_aware = datetime.strptime(start_time, "%Y-%m-%d %H:%M:%S").replace(
+                    tzinfo=ZoneInfo("Europe/Paris")
+                )
+                start_time = dt_aware.isoformat(timespec="microseconds")
+            except (ValueError, TypeError):
+                logging.getLogger("HWR").exception("Cannot parse start time")
+        else:
+            start_time = datetime.now(ZoneInfo("Europe/Paris")).isoformat()
 
-            start_time = dt_aware.isoformat(timespec="microseconds")
-            end_time = dt_aware_end.isoformat(timespec="microseconds")
-        except TypeError:
-            logging.getLogger("HWR").exception("Cannot parse start and end time")
         bsx, bsy, shape, _ = HWR.beamline.beam.get_value()
         flux_end = datacollection_dict.get("flux_end") or HWR.beamline.flux.get_value()
 
@@ -887,6 +886,29 @@ class ICATLIMS(AbstractLims):
 
             directory = Path(energyscan_dict["scanFileFullPath"]).parent
 
+            start_time = energyscan_dict.get("startTime", "")
+            end_time = energyscan_dict.get("endTime", "")
+
+            if start_time:
+                try:
+                    dt_aware = datetime.strptime(
+                        start_time, "%Y-%m-%d %H:%M:%S"
+                    ).replace(tzinfo=ZoneInfo("Europe/Paris"))
+                    start_time = dt_aware.isoformat(timespec="microseconds")
+                    metadata.update({"startDate": start_time})
+                except (ValueError, TypeError):
+                    logging.getLogger("HWR").exception("Cannot parse start time")
+
+            if end_time:
+                try:
+                    dt_aware = datetime.strptime(end_time, "%Y-%m-%d %H:%M:%S").replace(
+                        tzinfo=ZoneInfo("Europe/Paris")
+                    )
+                    end_time = dt_aware.isoformat(timespec="microseconds")
+                    metadata.update({"endDate": end_time})
+                except (ValueError, TypeError):
+                    logging.getLogger("HWR").exception("Cannot parse start time")
+
             metadata.update(
                 {
                     "scanType": "energy_scan",
@@ -940,6 +962,29 @@ class ICATLIMS(AbstractLims):
 
             directory = Path(xfespectrum_dict["filename"]).parent
 
+            start_time = xfespectrum_dict.get("startTime", "")
+            end_time = xfespectrum_dict.get("endTime", "")
+
+            if start_time:
+                try:
+                    dt_aware = datetime.strptime(
+                        start_time, "%Y-%m-%d %H:%M:%S"
+                    ).replace(tzinfo=ZoneInfo("Europe/Paris"))
+                    start_time = dt_aware.isoformat(timespec="microseconds")
+                    metadata.update({"startDate": start_time})
+                except (ValueError, TypeError):
+                    logging.getLogger("HWR").exception("Cannot parse start time")
+
+            if end_time:
+                try:
+                    dt_aware = datetime.strptime(end_time, "%Y-%m-%d %H:%M:%S").replace(
+                        tzinfo=ZoneInfo("Europe/Paris")
+                    )
+                    end_time = dt_aware.isoformat(timespec="microseconds")
+                    metadata.update({"endDate": end_time})
+                except (ValueError, TypeError):
+                    logging.getLogger("HWR").exception("Cannot parse end time")
+
             metadata.update(
                 {
                     "scanType": "xrf",
@@ -1045,7 +1090,7 @@ class ICATLIMS(AbstractLims):
             try:
                 token = self.icat_session["sessionId"]
                 url = f"{self.url}/catalogue/{token}/files/download?sampleId={sample_id}&resourceId={resource.id}"
-                response = requests.get(url, stream=True, timeout=3)
+                response = requests.get(url, stream=True, timeout=30)
                 response.raise_for_status()
 
                 file_path = resource_folder / resource.filename
@@ -1110,15 +1155,6 @@ class ICATLIMS(AbstractLims):
             proposal = f"{HWR.beamline.session.proposal_code}"
             proposal += f"{HWR.beamline.session.proposal_number}"
 
-            try:
-                dt_aware = datetime.strptime(
-                    datacollection_dict.get("collection_start_time"),
-                    "%Y-%m-%d %H:%M:%S",
-                ).replace(tzinfo=ZoneInfo("Europe/Paris"))
-                start_time = dt_aware.isoformat(timespec="microseconds")
-            except RuntimeError:
-                logger.warning("Failed to parse start and end time")
-
             metadata.update(
                 {
                     "MX_dataCollectionId": datacollection_dict.get("collection_id"),
@@ -1149,7 +1185,6 @@ class ICATLIMS(AbstractLims):
                     ),
                     "MX_position_id": workflow_params.get("workflow_position_id"),
                     "group_by": workflow_params.get("workflow_group_by"),
-                    "startDate": start_time,
                 }
             )
 
@@ -1171,7 +1206,7 @@ class ICATLIMS(AbstractLims):
             )
 
             try:
-                metadata["lims"] = HWR.beamline.lims.get_active_lims()
+                metadata["lims"] = HWR.beamline.lims.get_active_lims().name
             except Exception:
                 logger.exception("Failed to read get_active_lims.")
 

{mxcubecore-1.384.0 → mxcubecore-1.386.0}/mxcubecore/HardwareObjects/abstract/AbstractSampleChanger.py

@@ -312,6 +312,98 @@ class SampleChanger(Container, HardwareObject):
         """
         return self.status
 
+    def get_contents_as_dict(self) -> dict:
+        """
+        Build and return the hierarchical structure of the sample changer contents.
+
+        Returns:
+            dict: A nested dictionary describing the sample changer contents.
+                {
+                    "name": <str>,  # root sample changer address
+                    "room_temperature_mode": <bool> (optional),
+                    "children": [
+                        {
+                            "name": <str>,       # element address
+                            "status": <str>,     # "Loaded", "Used", "Present", or ""
+                            "id": <str>,         # element ID
+                            "selected": <bool>,  # whether element is selected
+                            "children": [ ... ]  # nested elements, same structure
+                        },
+                        ...
+                    ]
+                }
+        """
+        contents = {"name": self.get_address()}
+
+        if hasattr(self, "get_room_temperature_mode"):
+            contents["room_temperature_mode"] = self.get_room_temperature_mode()
+
+        for element in self.get_components():
+            if element.is_present():
+                self._add_element(contents, element)
+
+        return contents
+
+    def _get_status(self, element) -> str:
+        """
+        Determine the status string for a sample changer element.
+
+        Args:
+            element: The element object to check.
+
+        Returns:
+            str: One of:
+                - "Loaded":  element is a leaf and currently loaded
+                - "Used":    element is a leaf and has been loaded before
+                - "Present": element is present in the changer
+                - "":        element is not present
+        """
+        if element.is_leaf():
+            if element.is_loaded():
+                return "Loaded"
+            if element.has_been_loaded():
+                return "Used"
+            return ""
+        return "Present" if element.is_present() else ""
+
+    def _get_id(self, element) -> str:
+        """
+        Get the unique identifier (ID or token) for a sample changer element.
+
+        Args:
+            element: The element to get the ID for.
+
+        Returns:
+            str: The token (if root sample changer and available),
+                 the element ID (if available), or an empty string.
+        """
+        if element == self:
+            token = element.get_token()
+            return token if token else ""
+
+        return element.get_id() or ""
+
+    def _add_element(self, parent, element) -> dict:
+        """
+        Recursively add an element and its children into the contents dictionary.
+
+        Args:
+            parent (dict): The parent dictionary to append the element to.
+            element: The element object to add.
+        """
+        new_element = {
+            "name": element.get_address(),
+            "status": self._get_status(element),
+            "id": self._get_id(element),
+            "selected": element.is_selected(),
+        }
+
+        parent.setdefault("children", []).append(new_element)
+
+        if not element.is_leaf():
+            for child in element.get_components():
+                self._add_element(new_element, child)
+
     @property
     def progress_message(self) -> str:
         """

{mxcubecore-1.384.0 → mxcubecore-1.386.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mxcubecore"
-version = "1.384.0"
+version = "1.386.0"
 license = "LGPL-3.0-or-later"
 description = "Core libraries for the MXCuBE application"
 authors = [