mxcubecore 1.369.0__tar.gz → 1.371.0__tar.gz

{mxcubecore-1.369.0 → mxcubecore-1.371.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mxcubecore
-Version: 1.369.0
+Version: 1.371.0
 Summary: Core libraries for the MXCuBE application
 License: LGPL-3.0-or-later
 Keywords: mxcube,mxcube3,mxcubecore

mxcubecore-1.371.0/mxcubecore/HardwareObjects/MAXIV/session.py

@@ -0,0 +1,158 @@
+"""MAXIV Session hardware object."""
+
+import time
+from pathlib import Path
+
+from sdm import storage
+
+import mxcubecore.HardwareObjects.Session
+from mxcubecore.model.queue_model_objects import PathTemplate
+
+
+class Session(mxcubecore.HardwareObjects.Session.Session):
+    def init(self):
+        super().init()
+        self.is_commissioning = False
+
+        # We initialize with an empty archive_folder,
+        # to be set once proposal is selected.
+        PathTemplate.set_archive_path(self.base_archive_directory, "")
+
+    def set_in_commissioning(self, proposal_info):
+        self.proposal_code = proposal_info["Proposal"]["code"]
+        self.proposal_number = proposal_info["Proposal"]["number"]
+        self.is_commissioning = True
+
+    def get_proposal(self) -> str:
+        """
+        Returns:
+            The proposal, 'local-user' if no proposal is available
+        """
+        proposal = "local-user"
+
+        if self.proposal_code and self.proposal_number:
+            if self.proposal_code == "ifx":
+                self.proposal_code = "fx"
+
+            proposal = str(self.proposal_number)
+
+        return proposal
+
+    def get_base_data_directory(self) -> str:
+        """Get base data directory.
+
+        Figure out the base data directory taking the 'contextual'
+        information into account, such as if the current user
+        is in-house.
+
+        Returns:
+            The base data path.
+        """
+        # /data/(user-type)/(beamline)/(proposal)/(visit)/raw
+        if self.session_start_date:
+            start_time = self.session_start_date.split(" ")[0].replace("-", "")
+        else:
+            start_time = time.strftime("%Y%m%d")
+        _proposal = self.get_proposal()
+
+        if not self.is_commissioning:
+            if self.is_proprietary():
+                directory = Path(
+                    self.base_directory,
+                    "proprietary",
+                    self.beamline_name.lower(),
+                    _proposal,
+                    start_time,
+                )
+            else:
+                directory = Path(
+                    self.base_directory,
+                    "visitors",
+                    self.beamline_name.lower(),
+                    _proposal,
+                    start_time,
+                )
+        else:
+            # /data/staff/biomax/commissioning/date
+            directory = Path(
+                self.base_directory,
+                "staff",
+                self.beamline_name.lower(),
+                "commissioning",
+                time.strftime("%Y%m%d"),
+            )
+
+        self.log.info(
+            "Data directory for proposal %s: %s",
+            self.get_proposal(),
+            directory,
+        )
+
+        return str(directory)
+
+    def prepare_directories(self, session):
+        self.log.info("Preparing Data directory for session: %s", session)
+        start_date = session.start_datetime.date().isoformat().replace("-", "")
+        self.set_session_start_date(start_date)
+
+        self.log.info("Preparing Data directory for proposal %s", self.get_proposal())
+        if self.is_commissioning:
+            category = "staff"
+        elif self.is_proprietary():
+            category = "proprietary"
+        else:
+            category = "visitors"
+
+        try:
+            self.storage = storage.Storage(
+                user_type=category, beamline=self.endstation_name
+            )
+        except Exception:
+            self.log.exception("error setting up SDM")
+
+        # This creates the path for the data and ensures proper permissions
+        # e.g. /data/visitors/biomax/<proposal>/<visit>/{raw, process}
+        if self.is_commissioning:
+            group = self.beamline_name.lower()
+        else:
+            group = self.storage.get_proposal_group(session.number)
+        try:
+            _raw_path = self.storage.create_path(
+                session.number, group, self.get_session_start_date()
+            )
+
+            self.log.info("SDM Data directory created: %s", _raw_path)
+        except Exception as exc:  # noqa: BLE001
+            self.log.warning("SDM Data directory creation failed. %s", exc)
+            self.log.info("SDM Data directory trying to create again after failure")
+            time.sleep(0.1)
+            try:
+                _raw_path = self.storage.create_path(
+                    session.number, group, self.get_session_start_date()
+                )
+
+                self.log.info("SDM Data directory created: %s", _raw_path)
+            except Exception:
+                self.log.exception("SDM Data directory creation failed.")
+                raise
+
+        if self.base_archive_directory:
+            archive_folder = "{}/{}".format(category, self.beamline_name.lower())
+            PathTemplate.set_archive_path(self.base_archive_directory, archive_folder)
+            _archive_path = Path(self.base_archive_directory, archive_folder)
+            self.log.info("Archive directory configured: %s", _archive_path)
+
+    def is_proprietary(self) -> bool:
+        """Determines if current proposal is considered to be proprietary.
+
+        Returns:
+            True if the proposal is proprietary, otherwise False.
+        """
+        return self.proposal_code == "IN"
+
+    def clear_session(self):
+        self.session_id = None
+        self.proposal_code = None
+        self.proposal_number = None
+        self.proposal_id = None
+        self.is_commissioning = False

{mxcubecore-1.369.0 → mxcubecore-1.371.0}/mxcubecore/queue_entry/base_queue_entry.py

@@ -764,6 +764,16 @@ class SampleQueueEntry(BaseQueueEntry):
         BaseQueueEntry.post_execute(self)
         params = []
 
+        # We want to make the sample entry enabled if it contains
+        # any skipped collections, so that the user can restart them
+        has_executable_child = False
+        for child_queue_entry in self._queue_entry_list:
+            if child_queue_entry.is_enabled():
+                has_executable_child = True
+                break
+        self.set_enabled(has_executable_child)
+        self.get_data_model().set_enabled(has_executable_child)
+
         # Start grouped processing, get information from each collection
         # and call autoproc with grouped processing option
         for child in self.get_data_model().get_children():

{mxcubecore-1.369.0 → mxcubecore-1.371.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mxcubecore"
-version = "1.369.0"
+version = "1.371.0"
 license = "LGPL-3.0-or-later"
 description = "Core libraries for the MXCuBE application"
 authors = [

mxcubecore-1.369.0/mxcubecore/HardwareObjects/MAXIV/MaxIVSession.py

@@ -1,231 +0,0 @@
-"""
-MAXIV Session hardware object.
-
-Adapting from original Session.py to adapt the names of data directories
-"""
-
-import logging
-import os
-import socket
-import time
-
-try:
-    from sdm import (
-        storage,
-    )
-except Exception:
-    raise Exception("Cannot import SDM library.")
-
-from mxcubecore.HardwareObjects.Session import Session
-from mxcubecore.model import queue_model_objects
-
-
-class MaxIVSession(Session):
-    def __init__(self, name):
-        Session.__init__(self, name)
-
-    # Framework-2 method, inherited from HardwareObject and called
-    # by the framework after the object has been initialized.
-    def init(self):
-        self.default_precision = 4
-        self.login = ""
-        self.is_commissioning = False
-        self.synchrotron_name = self.get_property("synchrotron_name")
-        self.endstation_name = self.get_property("endstation_name").lower()
-        self.suffix = self["file_info"].get_property("file_suffix")
-        self.base_directory = self["file_info"].get_property("base_directory")
-        self.base_process_directory = self["file_info"].get_property(
-            "processed_data_base_directory"
-        )
-
-        self.raw_data_folder_name = self["file_info"].get_property(
-            "raw_data_folder_name"
-        )
-
-        self.processed_data_folder_name = self["file_info"].get_property(
-            "processed_data_folder_name"
-        )
-
-        try:
-            self.in_house_users = self.get_property("inhouse_users").split(",")
-        except Exception:
-            self.in_house_users = []
-
-        try:
-            domain = socket.getfqdn().split(".")
-            self.email_extension = ".".join((domain[-2], domain[-1]))
-        except (TypeError, IndexError):
-            pass
-
-        archive_base_directory = self["file_info"].get_property(
-            "archive_base_directory"
-        )
-        if archive_base_directory:
-            queue_model_objects.PathTemplate.set_archive_path(
-                archive_base_directory, self["file_info"].get_property("archive_folder")
-            )
-
-        queue_model_objects.PathTemplate.set_path_template_style(self.synchrotron_name)
-        queue_model_objects.PathTemplate.set_data_base_path(self.base_directory)
-
-        self.commissioning_fake_proposal = {
-            "Laboratory": {
-                "address": None,
-                "city": "Lund",
-                "laboratoryId": 312171,
-                "name": "Lund University",
-            },
-            "Person": {
-                "familyName": "commissioning",
-                "givenName": "",
-                "laboratoryId": 312171,
-                "login": "",
-                "personId": 0,
-            },
-            "Proposal": {
-                "code": "MX",
-                "number": time.strftime("%Y"),
-                "proposalId": "0",
-                "timeStamp": time.strftime("%Y%m%d"),
-                "title": "Commissioning Proposal",
-                "type": "MX",
-            },
-            "Session": [
-                {
-                    "is_inhouse": True,
-                    "beamlineName": "BioMAX",
-                    "comments": "Fake session for commissioning",
-                    "endDate": "2027-12-31 23:59:59",
-                    "nbShifts": 100,
-                    "proposalId": "0",
-                    "scheduled": 0,
-                    "sessionId": 0,
-                    "startDate": "2016-01-01 00:00:00",
-                }
-            ],
-        }
-
-    def set_in_commissioning(self, proposal_info):
-        self.proposal_code = proposal_info["Proposal"]["code"]
-        self.proposal_number = proposal_info["Proposal"]["number"]
-        self.is_commissioning = True
-
-    def get_proposal(self):
-        """
-        :returns: The proposal, 'local-user' if no proposal is
-                  available
-        :rtype: str
-        """
-        proposal = "local-user"
-
-        if self.proposal_code and self.proposal_number:
-            if self.proposal_code == "ifx":
-                self.proposal_code = "fx"
-
-            proposal = str(self.proposal_number)
-
-        return proposal
-
-    def get_base_data_directory(self):
-        """
-        Returns the base data directory taking the 'contextual'
-        information into account, such as if the current user
-        is inhouse.
-
-        :returns: The base data path.
-        :rtype: str
-        """
-        if self.session_start_date:
-            start_time = self.session_start_date.split(" ")[0].replace("-", "")
-        else:
-            start_time = time.strftime("%Y%m%d")
-
-        if not self.is_commissioning:
-            # /data/visitors/biomax/prop/visit/
-            # /data/(user-type)/(beamline)/(proposal)/(visit)/raw
-            directory = os.path.join(
-                self.base_directory,
-                "visitors",  # self.get_user_category(self.login),
-                self.beamline_name.lower(),
-                self.get_proposal(),
-                start_time,
-            )
-        else:
-            # /data/staff/biomax/commissioning/date
-            directory = os.path.join(
-                self.base_directory,
-                "staff",
-                self.beamline_name.lower(),
-                "commissioning",
-                time.strftime("%Y%m%d"),
-            )
-
-        logging.getLogger("HWR").info(
-            "[MAX IV Session] Data directory for proposal %s: %s"
-            % (self.get_proposal(), directory)
-        )
-        return directory
-
-    def prepare_directories(self, proposal_info):
-        self.login = proposal_info["Person"]["login"]
-        start_time = proposal_info.get("Session")[0].get("startDate")
-
-        logging.getLogger("HWR").info(
-            "[MAX IV Session] Preparing Data directory for proposal %s" % proposal_info
-        )
-        if start_time:
-            start_date = start_time.split(" ")[0].replace("-", "")
-        else:
-            start_date = time.strftime("%Y%m%d")
-
-        self.set_session_start_date(start_date)
-
-        try:
-            self.storage = storage.Storage(
-                self.get_user_category(self.login), self.endstation_name
-            )
-        except Exception as ex:
-            print(ex)
-            # this creates the path for the data and ensures proper permissions.
-            # e.g. /data/visitors/biomax/<proposal>/<visit>/{raw, process}
-        if self.is_commissioning:
-            group = self.beamline_name.lower()
-        else:
-            group = self.storage.get_proposal_group(self.proposal_number)
-        try:
-            self.storage.create_path(
-                self.proposal_number, group, self.get_session_start_date()
-            )
-
-            proposal_path = "{0}/{1}".format(
-                self.storage.beamline_path, self.proposal_number
-            )
-            logging.getLogger("HWR").info(
-                "[MAX IV Session] SDM Data directory created: %s" % proposal_path
-            )
-        except Exception as ex:
-            msg = "[MAX IV Session] SDM Data directory creation failed. %s" % ex
-            logging.getLogger("HWR").error(msg)
-            raise Exception(msg)
-
-    def is_inhouse(self, user, code=None):
-        """
-        Determines if a given user is considered to be inhouse.
-        :param login: username
-        :type login: str
-        :returns: True if the user is inhouse, otherwise False.
-        :rtype: bool
-        """
-        if user in self.in_house_users:
-            return True
-        else:
-            return False
-
-    def get_user_category(self, user):
-        # 'staff','visitors', 'proprietary'
-        # missing industrial users
-        if self.is_inhouse(user):
-            user_category = "staff"
-        else:
-            user_category = "visitors"
-        return user_category