def loaded_sample_changed(sample):
if not isinstance(sample, Pin):
return
if sample is not None:
address = sample.getAddress()
barcode = sample.getID()
else:
address = ''
barcode = ''
logging.getLogger("HWR").info('loaded sample changed now is: ' + address)
try:
# recreate the dict with the sample info
q = queue_to_dict()
sampleID = sample.getAddress()
sample_data = q.get(sampleID, {})
scutils.set_current_sample(sample_data)
msg = {'signal': 'loadReady', 'location': address}
socketio.emit('sc', msg, namespace='/hwr')
socketio.emit("loaded_sample_changed", {'address': address, 'barcode': barcode}, namespace="/hwr")
except Exception, msg:
logging.getLogger("HWR").error('error setting loaded sample: %s' + str(msg))
def get_method(sample_id, method_id):
"""
Get the information of the given task, beloging to the given sample
:parameter sampleid: sample identifier, integer
:parameter methodid: task identifier, integer
:response Content-Type: application/json, object containing the
parameter(s) of the task. Example without parameters
{"QueueId": 52, "Type": 'Centring'...}
:statuscode: 200: no error
:statuscode: 409: task could not be added to the sample
"""
sample = qutils.queue_to_dict().get(int(id), None)
if not sample:
msg = "[QUEUE] sample info could not be retrieved"
logging.getLogger('HWR').error(msg)
return Response(status=409)
else:
# Find task with queue id method_id
for task in sample.tasks:
if task['queueID'] == int(method_id):
resp = jsonify(task)
resp.status_code = 200
return resp
msg = "[QUEUE] method info could not be retrieved, it does not exits for"
msg += " the given sample"
logging.getLogger('HWR').exception(msg)
return Response(status=409)
def get_method(sample_id, method_id):
"""
Get the information of the given task, beloging to the given sample
:parameter sampleid: sample identifier, integer
:parameter methodid: task identifier, integer
:response Content-Type: application/json, object containing the
parameter(s) of the task. Example without parameters
{"QueueId": 52, "Type": 'Centring'...}
:statuscode: 200: no error
:statuscode: 409: task could not be added to the sample
"""
sample = qutils.queue_to_dict().get(int(id), None)
if not sample:
msg = "[QUEUE] sample info could not be retrieved"
logging.getLogger('HWR').error(msg)
return Response(status=409)
else:
# Find task with queue id method_id
for task in sample.tasks:
if task['queueID'] == int(method_id):
resp = jsonify(task)
resp.status_code = 200
return resp
msg = "[QUEUE] method info could not be retrieved, it does not exits for"
msg += " the given sample"
logging.getLogger('HWR').exception(msg)
return Response(status=409)
def queue_start():
"""
Start execution of the queue.
:returns: Respons object, status code set to:
200: On success
409: Queue could not be started
"""
logging.getLogger('HWR').info('[QUEUE] Queue going to start')
try:
queue = qutils.queue_to_dict()
sample_id = queue["sample_order"][0]
# If auto mount sample is false, just run the first one
if not qutils.get_auto_mount_sample():
sid = scutils.get_current_sample() or sample_id
qutils.execute_entry_with_id(sid)
else:
mxcube.queue.queue_hwobj.set_pause(False)
mxcube.queue.queue_hwobj.execute()
except Exception as ex:
signals.queue_execution_failed(ex)
logging.getLogger('HWR').info('[QUEUE] Queue started')
return Response(status=200)
def loaded_sample_changed(sample):
# If sample is a "No sample loaded value" None or ''
if sample in [None, '']:
msg = {'signal': 'loadReady', 'location': ''}
socketio.emit('sc', msg, namespace='/hwr')
socketio.emit("loaded_sample_changed", {'address': '', 'barcode': ''}, namespace="/hwr")
# If sample is not Pin, Sample pin just return
if not (isinstance(sample, Pin) or isinstance(sample, Sample)):
return
if sample is not None:
address = sample.getAddress()
barcode = sample.getID()
else:
address = ''
barcode = ''
logging.getLogger("HWR").info('loaded sample changed now is: ' + address)
try:
# recreate the dict with the sample info
q = queue_to_dict()
sampleID = sample.getAddress()
sample_data = q.get(sampleID, {})
scutils.set_current_sample(sample_data)
msg = {'signal': 'loadReady', 'location': address}
socketio.emit('sc', msg, namespace='/hwr')
socketio.emit("loaded_sample_changed", {'address': address, 'barcode': barcode}, namespace="/hwr")
except Exception, msg:
logging.getLogger("HWR").error('error setting loaded sample: %s' + str(msg))
def get_current_sample():
current_queue = qutils.queue_to_dict()
if mxcube.CURRENTLY_MOUNTED_SAMPLE and \
mxcube.CURRENTLY_MOUNTED_SAMPLE["sampleID"] in current_queue:
return mxcube.CURRENTLY_MOUNTED_SAMPLE
else:
return {}
def get_current_sample():
current_queue = qutils.queue_to_dict()
if mxcube.CURRENTLY_MOUNTED_SAMPLE and \
mxcube.CURRENTLY_MOUNTED_SAMPLE["sampleID"] in current_queue:
return mxcube.CURRENTLY_MOUNTED_SAMPLE
else:
return {}
def queue_update_item(sid, tindex):
data = request.get_json()
current_queue = qutils.queue_to_dict()
if tindex in ['undefined']:
node_id = current_queue[sid]["queueID"]
else:
node_id = current_queue[sid]["tasks"][int(tindex)]["queueID"]
model, entry = qutils.get_entry(node_id)
if data["type"] == "DataCollection":
qutils.set_dc_params(model, entry, data)
elif data["type"] == "Characterisation":
qutils.set_char_params(model, entry, data)
logging.getLogger('HWR').info('[QUEUE] is:\n%s ' % qutils.queue_to_json())
return Response(status=200)
def get_sample(id):
"""
Get the information of the given sample.
:parameter id: sample identifier, integer
:response Content-Type: application/json, object containing the
parameter(s) of the sample. Example without parameters
{"QueueId": 22, "SampleId": "3:02", "methods": []}
:statuscode: 200: no error
:statuscode: 409: sample could not be retrieved
"""
sample = qutils.queue_to_dict().get(int(id), None)
if not sample:
logging.getLogger('HWR').error('[QUEUE] sample info could not be retrieved')
return Response(status=409)
else:
resp = jsonify(sample)
resp.status_code = 200
return resp
def synch_sample_list_with_queue(current_queue=None):
if not current_queue:
current_queue = qutils.queue_to_dict(include_lims_data=True)
sample_order = current_queue.get("sample_order", [])
for loc, data in mxcube.SAMPLE_LIST["sampleList"].iteritems():
if loc in current_queue:
sample = current_queue[loc]
# Don't synchronize, lims attributes from queue sample, if
# they are already set by sc or lims
if data.get("sampleName", ""):
sample.pop("sampleName")
if data.get("proteinAcronym", ""):
sample.pop("proteinAcronym")
sample_list_update_sample(loc, sample)
def get_sample(id):
"""
Get the information of the given sample.
:parameter id: sample identifier, integer
:response Content-Type: application/json, object containing the
parameter(s) of the sample. Example without parameters
{"QueueId": 22, "SampleId": "3:02", "methods": []}
:statuscode: 200: no error
:statuscode: 409: sample could not be retrieved
"""
sample = qutils.queue_to_dict().get(int(id), None)
if not sample:
logging.getLogger('HWR').error('[QUEUE] sample info could not be retrieved')
return Response(status=409)
else:
resp = jsonify(sample)
resp.status_code = 200
return resp
def synch_sample_list_with_queue(current_queue=None):
if not current_queue:
current_queue = qutils.queue_to_dict()
sample_order = current_queue.get("sample_order", [])
for loc, data in mxcube.SAMPLE_LIST["sampleList"].iteritems():
if loc in current_queue:
sample = current_queue[loc]
# Don't synchronize, lims attributes from queue sample, if
# they are already set by sc or lims
if data.get("sampleName", ""):
sample.pop("sampleName")
if data.get("proteinAcronym", ""):
sample.pop("proteinAcronym")
sample_list_update_sample(loc, sample)
def queue_delete_item():
item_pos_list = request.get_json()
current_queue = qutils.queue_to_dict()
for (sid, tindex) in item_pos_list:
if tindex in ['undefined', None]:
node_id = current_queue[sid]["queueID"]
model, entry = qutils.get_entry(node_id)
else:
node_id = current_queue[sid]["tasks"][int(tindex)]["queueID"]
model, entry = qutils.get_entry(node_id)
# Get the TaskGroup of the item, there is currently only one
# task per TaskGroup so we have to remove the entire TaskGroup
# with its task.
entry = entry.get_container()
qutils.delete_entry(entry)
logging.getLogger('HWR').info('[QUEUE] is:\n%s ' % qutils.queue_to_json())
return Response(status=200)
def toggle_node(node_id):
'''
Toggle a sample or a method checked status
:parameter id: node identifier, integer
:statuscode: 200: no error
:statuscode: 409: node could not be toggled
'''
node_id = int(node_id) # params['QueueId']
node = mxcube.queue.get_node(node_id)
entry = mxcube.queue.queue_hwobj.get_entry_with_model(node)
queue = qutils.queue_to_dict()
if isinstance(entry, qe.SampleQueueEntry):
# this is a sample entry, thus, go through its checked children and toggle those
if entry.is_enabled():
entry.set_enabled(False)
node.set_enabled(False)
else:
entry.set_enabled(True)
node.set_enabled(True)
new_state = entry.is_enabled()
for elem in queue[node_id]:
child_node = mxcube.queue.get_node(elem['queueID'])
child_entry = mxcube.queue.queue_hwobj.get_entry_with_model(child_node)
if new_state:
child_entry.set_enabled(True)
child_node.set_enabled(True)
else:
child_entry.set_enabled(False)
child_node.set_enabled(False)
else:
# not a sample so find the parent and toggle directly
logging.getLogger('HWR').info('[QUEUE] toggling entry with id: %s' % node_id)
parent_node = node.get_parent() # this is a TaskGroup, so it is not in the parsed queue
# go a level up,
parent_node = parent_node.get_parent() # this is a TaskGroup for a Char, a sampleQueueEntry if DataCol
if isinstance(parent_node, qmo.TaskGroup):
parent_node = parent_node.get_parent()
parent = parent_node._node_id
parent_entry = mxcube.queue.queue_hwobj.get_entry_with_model(parent_node)
# now that we know the sample parent no matter what is the entry (char, dc)
# check if the brother&sisters are enabled (and enable the parent)
checked = 0
for i in queue[parent]:
if i['queueID'] != node_id and i['checked'] == 1: # at least one brother is enabled, no need to change parent
checked = 1
break
if entry.is_enabled():
entry.set_enabled(False)
node.set_enabled(False)
else:
entry.set_enabled(True)
node.set_enabled(True)
new_state = entry.is_enabled()
for met in queue[parent]:
if int(met.get('queueID')) == node_id:
if new_state == 0 and checked == 0:
parent_entry.set_enabled(False)
parent_node.set_enabled(False)
elif new_state == 1 and checked == 0:
parent_entry.set_enabled(True)
parent_node.set_enabled(True)
return Response(status=200)
def toggle_node(node_id):
'''
Toggle a sample or a method checked status
:parameter id: node identifier, integer
:statuscode: 200: no error
:statuscode: 409: node could not be toggled
'''
node_id = int(node_id) # params['QueueId']
node = mxcube.queue.get_node(node_id)
entry = mxcube.queue.queue_hwobj.get_entry_with_model(node)
queue = qutils.queue_to_dict()
if isinstance(entry, qe.SampleQueueEntry):
# this is a sample entry, thus, go through its checked children and toggle those
if entry.is_enabled():
entry.set_enabled(False)
node.set_enabled(False)
else:
entry.set_enabled(True)
node.set_enabled(True)
new_state = entry.is_enabled()
for elem in queue[node_id]:
child_node = mxcube.queue.get_node(elem['queueID'])
child_entry = mxcube.queue.queue_hwobj.get_entry_with_model(child_node)
if new_state:
child_entry.set_enabled(True)
child_node.set_enabled(True)
else:
child_entry.set_enabled(False)
child_node.set_enabled(False)
else:
# not a sample so find the parent and toggle directly
logging.getLogger('HWR').info('[QUEUE] toggling entry with id: %s' % node_id)
parent_node = node.get_parent() # this is a TaskGroup, so it is not in the parsed queue
# go a level up,
parent_node = parent_node.get_parent() # this is a TaskGroup for a Char, a sampleQueueEntry if DataCol
if isinstance(parent_node, qmo.TaskGroup):
parent_node = parent_node.get_parent()
parent = parent_node._node_id
parent_entry = mxcube.queue.queue_hwobj.get_entry_with_model(parent_node)
# now that we know the sample parent no matter what is the entry (char, dc)
# check if the brother&sisters are enabled (and enable the parent)
checked = 0
for i in queue[parent]:
if i['queueID'] != node_id and i['checked'] == 1: # at least one brother is enabled, no need to change parent
checked = 1
break
if entry.is_enabled():
entry.set_enabled(False)
node.set_enabled(False)
else:
entry.set_enabled(True)
node.set_enabled(True)
new_state = entry.is_enabled()
for met in queue[parent]:
if int(met.get('queueID')) == node_id:
if new_state == 0 and checked == 0:
parent_entry.set_enabled(False)
parent_node.set_enabled(False)
elif new_state == 1 and checked == 0:
parent_entry.set_enabled(True)
parent_node.set_enabled(True)
return Response(status=200)