Merge branch 'master' into optimized-autoraster

config_params.py

@@ -38,6 +38,8 @@
 BEAM_CHECK = "beamCheck"
 UNMOUNT_COLD_CHECK = "unmountColdCheck"
 ON_MOUNT_OPTION = "onMountOption"
+SET_ENERGY_CHECK = "setEnergyCheck"
+
 
 # raster request status updates
 class RasterStatus(Enum):
@@ -85,14 +87,13 @@ class OnMountAvailOptions(Enum):
 DETECTOR_OBJECT_TYPE_OPHYD = "ophyd"  # instantiated in start_bs, using Bluesky scans
 DETECTOR_OBJECT_TYPE = "detectorObjectType"
 
-DETECTOR_SAFE_DISTANCE = 200.0
-
+DETECTOR_SAFE_DISTANCE = {"fmx": 200.0, "amx": 180.0, "nyx": 200.0}
 GOVERNOR_TIMEOUT = 120  # seconds for a governor move
 
 DEWAR_SECTORS = {"amx": 8, "fmx": 8, "nyx": 5}
 PUCKS_PER_DEWAR_SECTOR = {"amx": 3, "fmx": 3, "nyx": 3}
 
-cryostreamTempPV = {"amx": "AMX:cs700:gasT-I", "fmx": "FMX:cs700:gasT-I"}
+cryostreamTempPV = {"amx": "XF:17IDB-ES:AMX{CS:1}SAMPLE_TEMP_RBV", "fmx": "FMX:cs700:gasT-I"}
 
 VALID_EXP_TIMES = {
     "amx": {"min": 0.005, "max": 1, "digits": 3},
@@ -117,9 +118,16 @@ class OnMountAvailOptions(Enum):
     "nyx": {"min": 0.001, "max": 0.999, "digits": 3},
 }
 
+MINIMUM_RASTER_SIZE = {"amx": 6, "fmx": 6, "nyx": 2}
+
 LSDC_SERVICE_USERS = ("lsdc-amx", "lsdc-fmx", "lsdc-nyx")
 IS_STAFF = (
     True
-    if os.environ["STAFF_GROUP"] in [grp.getgrgid(g).gr_name for g in os.getgroups()]
+    if os.environ.get("STAFF_GROUP") is not None and os.environ["STAFF_GROUP"] in [grp.getgrgid(g).gr_name for g in os.getgroups()]
     else False
 )
+
+EMBL_SERVER_PV_BASE = {
+    "amx": "XF:17IDB-ES:AMX{EMBL}",
+    "fmx": "XF:17IDC-ES:FMX{EMBL}"
+}

daq_lib.py

@@ -21,7 +21,7 @@
 from bluesky.preprocessors import finalize_wrapper
 import bluesky.plan_stubs as bps
 import logging
-import albulaUtils
+from utils import validation
 logger = logging.getLogger(__name__)
 
 try:
@@ -631,7 +631,7 @@ def collectData(currentRequest):
       filename = f"{data_directory_name}/{file_prefix}_{seqNum}_master.h5"
       logger.info(f"Checking integrity of {filename}")
       timeout_index = 0
-      while not albulaUtils.validate_master_HDF5_file(filename):
+      while not validation.validate_master_HDF5_file(filename):
         timeout_index += 1
         time.sleep(3)
         if timeout_index > 15:

daq_macros.py

@@ -42,6 +42,9 @@
 from config_params import ON_MOUNT_OPTION, OnMountAvailOptions
 from mxbluesky.plans import detect_loop, topview_optimized
 
+from setenergy_lsdc import setELsdc
+
+
 try:
   import ispybLib
 except Exception as e:
@@ -90,6 +93,22 @@ def abortBS():
       RE.abort()
     except super_state_machine.errors.TransitionError:
       logger.error("caught BS")
+
+def set_energy(energy):
+  try:
+    daq_lib.set_field("program_state","Setting Energy")
+    RE(setELsdc(energy))
+  except Exception as e:
+    logger.error(f"Exception while running set_energy: {e}")
+    daq_lib.set_field("program_state","Program Ready")
+
+def move_omega(omega, relative=True):
+  """Moves omega by a certain amount"""
+  if gov_robot.state.get() == "SA":
+    if relative:
+      RE(bps.mvr(samplexyz.omega, omega))
+    else:
+      RE(bps.mv(samplexyz.omega, omega))
 
 def changeImageCenterLowMag(x,y,czoom):
   zoom = int(czoom)
@@ -4078,10 +4097,6 @@ def vertRasterOff():
   """vertRasterOff() : only raster vertically for single-column (line) rasters"""
   setBlConfig("vertRasterOn",0)
 
-def newVisit():
-  """newVisit() : Trick LSDC into creating a new visit on the next request creation"""
-  setBlConfig("proposal",987654) #a kludge to cause the next collection to generate a new visit
-
 
 def logMe():
   """logMe() : Edwin asked for this"""
@@ -4106,18 +4121,6 @@ def emptyQueue():
   reqList = list(db_lib.getQueue(daq_utils.beamline))
   for i in range (0,len(reqList)):
     db_lib.deleteRequest(reqList[i]["uid"])
-
-def addPersonToProposal(personLogin,propNum):
-  """addPersonToProposal(personLogin,propNum) : add person to ISPyB proposal - personLogin must be quoted, proposal number is a number (not quoted)"""    
-  ispybLib.addPersonToProposal(personLogin,propNum)
-
-def createPerson(firstName,lastName,loginName):
-  """createPerson(firstName,lastName,loginName) : create person for ISPyB - be sure to quote all arguments"""  
-  ispybLib.createPerson(firstName,lastName,loginName)
-
-def createProposal(propNum,PI_login="boaty"):
-  """createProposal(propNum,PI_login) : create proposal for ISPyB - be sure to quote the login name, Proposal number is a number (not quoted)"""    
-  ispybLib.createProposal(propNum,PI_login)
 
 
 def topViewCheckOn():
@@ -4193,12 +4196,8 @@ def lsdcHelp():
   print(enableMount.__doc__)
   print(vertRasterOn.__doc__)
   print(vertRasterOff.__doc__)
-  print(newVisit.__doc__)
   print(emptyQueue.__doc__)
   print(logMe.__doc__)
-  print(addPersonToProposal.__doc__)
-  print(createPerson.__doc__)
-  print(createProposal.__doc__)
   print(setAttenBCU.__doc__)
   print(setAttenRI.__doc__)
   print(unlockGUI.__doc__)

daq_main_common.py

@@ -75,7 +75,19 @@ def setGovState(state):
   setSlit1X,
   setSlit1Y,
   testRobot,
-  setGovState]
+  setGovState,
+  move_omega,
+  lockGUI,
+  unlockGUI,
+  DewarAutoFillOff,
+  DewarAutoFillOn,
+  logMe,
+  unlatchGov,
+  backoffDetector,
+  enableMount,
+  robotOn,
+  set_energy
+  ]
 
 whitelisted_functions: "Dict[str, Callable]" = {
     func.__name__: func for func in functions

daq_utils.py

@@ -131,7 +131,7 @@ def init_environment():
   if varname in os.environ:
     detectorOffline = int(os.environ[varname])
   setBlConfig(BEAM_CHECK,1)
-  setBlConfig(UNMOUNT_COLD_CHECK,0)
+  setBlConfig(UNMOUNT_COLD_CHECK,1)
 
 def calc_reso(det_radius,detDistance,wave,theta):
 

db_lib.py

@@ -485,7 +485,7 @@ def getContainerByID(container_id):
     c = getContainers(filters={'uid': container_id})[0]
     return c
 
-def get_dewar_tree_data(dewar_name, beamline):
+def get_dewar_tree_data(dewar_name, beamline, get_latest_pucks=False):
     """
     returns all data required to show dewar tree data with minimum number of database accesses
     """
@@ -496,6 +496,16 @@ def get_dewar_tree_data(dewar_name, beamline):
     ]  # removes blank ids
     pucks = getContainers(filters={"uid": {"$in": puck_ids}})
 
+    if get_latest_pucks:
+        # If get_latest_pucks is true, get the puck most recently updated in the database
+        # This is for cases when the excel sheet has been uploaded after puck_to_dewar
+        # Or when staff manually refreshes the dewar tree
+        new_pucks = []
+        for puck in pucks:
+            all_pucks = getContainers(filters={"name":puck["name"]})
+            latest_puck = max(all_pucks, key=lambda x: x.get("modified_time", 0.0))
+            new_pucks.append(latest_puck)
+        pucks = new_pucks  
     # Create a mega list of sample ids from puck information
     sample_ids = [
         sample_id

docs/source/developer_notes/release_notes.rst

@@ -2,6 +2,31 @@
  Release History
 =================
 
+2.0.3 (2024-01-22, a.k.a. 2024-1)
+=================================
+
+Fixes and other changes
+-----------------------
+
+* GUI
+
+  * For users, do not show pucks that do not belong to their proposal
+  * Speed up dewar tree refresh
+  * Refresh dewar tree button
+  * Albula now running in a separate instance
+  * No more automatic pre-fill of parameters upon request click - user option to do the pre-fill
+  * Moved unmount cold to the button panel. Added "End Visit" button, only unmounts warm currently
+
+* Server
+
+  * Datapath fix
+  * Fix ISPyB processing population and crystal snapshot creation problems
+  * Remove population of ISPyB database while infrastructure to update user proposal membership for SynchWeb is being developed
+
+* Server and GUI security improvements
+
+  * White-listing functions that can be called on the server to prevent execution of arbitrary code
+
 2.0.2 (2023-09-12, a.k.a. 2023-3)
 =================================