This commit is contained in:
gac-S_Changer
@@ -1,23 +1,279 @@
|
||||
import json
|
||||
import org.python.core.PyDictionary as PyDictionary
|
||||
|
||||
|
||||
SAMPLE_INFO_KEYS = ["userName", "dewarName", "puckName", "puckBarcode", "puckType", "puckAddress",
|
||||
"sampleName", "samplePosition", "sampleStatus", "sampleMountCount"]
|
||||
samples_info = []
|
||||
|
||||
|
||||
def set_samples_info(info):
|
||||
global samples_info
|
||||
if (is_string(info)):
|
||||
info = json.loads(info)
|
||||
if not is_list(info):
|
||||
raise Exception("Sample info must be a list (given object type is " + str(type(info)) + ")")
|
||||
#for sample in info:
|
||||
# if not (type(sample) is PyDictionary):
|
||||
# raise Exception("Sample info element must be a dictionary (given object type is " + str(type(sample)) + ")")
|
||||
#Sanitize list
|
||||
remove = []
|
||||
for sample in info:
|
||||
try:
|
||||
if set(sample.keys()) != set(SAMPLE_INFO_KEYS):
|
||||
raise Exception()
|
||||
except:
|
||||
remove.append(sample)
|
||||
for el in remove:
|
||||
info.remove(el)
|
||||
print "Invalid samples info element: " + str(el)
|
||||
samples_info = info
|
||||
return samples_info
|
||||
save_samples_info()
|
||||
#Trust beamline on assignments, so update puck info
|
||||
update_puck_table()
|
||||
|
||||
|
||||
def clear_samples_info():
|
||||
set_samples_info([])
|
||||
|
||||
def save_samples_info():
|
||||
data = get_samples_info(True)
|
||||
output_file = open( get_context().setup.expandPath("{context}/samples_info.json") , "w")
|
||||
output_file.write(data)
|
||||
output_file.close()
|
||||
|
||||
def restore_samples_info():
|
||||
try:
|
||||
inputfile = open(get_context().setup.expandPath("{context}/samples_info.json"), "r")
|
||||
info = inputfile.read()
|
||||
except:
|
||||
print >> sys.stderr, "Error reading sample info file: " + str(sys.exc_info()[1])
|
||||
info = []
|
||||
set_samples_info(info)
|
||||
|
||||
def get_samples_info(as_json=True):
|
||||
global sample_info
|
||||
return json.dumps(samples_info) if as_json else samples_info
|
||||
return json.dumps(samples_info) if as_json else samples_info
|
||||
|
||||
def has_puck_datamatrix(datamatrix):
|
||||
if samples_info is not None:
|
||||
for si in samples_info:
|
||||
if si["puckBarcode"] == datamatrix:
|
||||
return True
|
||||
return False
|
||||
|
||||
def add_puck_datamatrix(barcode, address = "", dewar = "Unknown", user = "Unknown", puck = "Unknown", type = "unipuck", sample_prefix = "Sample"):
|
||||
if has_puck_datamatrix(barcode):
|
||||
raise Exception("Datamatrix already defined: " + str(barcode))
|
||||
for s in range(1,17):
|
||||
info = \
|
||||
{ "userName": user, \
|
||||
"dewarName": dewar, \
|
||||
"puckName": puck, \
|
||||
"puckBarcode": address if barcode is None else barcode, \
|
||||
"puckType": type, \
|
||||
"puckAddress": address,\
|
||||
"sampleName": sample_prefix + " " + str(s), \
|
||||
"samplePosition": str(s),\
|
||||
"sampleStatus": "Unknown", \
|
||||
"sampleMountCount": "0",
|
||||
}
|
||||
samples_info.append(info)
|
||||
save_samples_info()
|
||||
|
||||
def remove_puck_datamatrix(barcode):
|
||||
remove = []
|
||||
for si in samples_info:
|
||||
if si["puckBarcode"] == barcode:
|
||||
remove.append(si)
|
||||
for el in remove: samples_info.remove(el)
|
||||
save_samples_info()
|
||||
|
||||
def set_puck_datamatrix(puck, datamatrix):
|
||||
if puck is None:
|
||||
puck = ""
|
||||
if datamatrix is None:
|
||||
datamatrix = ""
|
||||
if samples_info is not None:
|
||||
for si in samples_info:
|
||||
if si["puckBarcode"] == datamatrix:
|
||||
si["puckAddress"] = puck
|
||||
elif si["puckAddress"] == puck:
|
||||
si["puckAddress"] = ""
|
||||
save_samples_info()
|
||||
|
||||
def reset_puck_datamatrix(puck = None):
|
||||
if samples_info is not None:
|
||||
for si in samples_info:
|
||||
if (si["puckAddress"] == puck) or (puck is None):
|
||||
si["puckAddress"] = ""
|
||||
save_samples_info()
|
||||
|
||||
def get_puck_datamatrix():
|
||||
ret = {}
|
||||
for si in samples_info:
|
||||
if si["puckBarcode"] is not None and si["puckBarcode"]!="":
|
||||
ret[si["puckBarcode"]] = si["puckAddress"]
|
||||
return ret
|
||||
|
||||
def get_puck_address(barcode):
|
||||
try:
|
||||
return get_puck_datamatrix()[barcode]
|
||||
except:
|
||||
return None
|
||||
|
||||
|
||||
def update_puck_table():
|
||||
dms = get_puck_datamatrix()
|
||||
for barcode in dms.keys():
|
||||
address = dms[barcode]
|
||||
puck = get_puck_obj(address)
|
||||
if puck is not None:
|
||||
puck.id = barcode
|
||||
|
||||
|
||||
#Sample mount/unmount
|
||||
|
||||
def update_samples_info_sample_mount(puck_address, sample_position, sample_detected):
|
||||
try:
|
||||
if (samples_info is not None) and (puck_address is not None):
|
||||
for si in samples_info:
|
||||
if str(si["puckAddress"]) == str(puck_address) and str(si["samplePosition"]) == str(sample_position):
|
||||
if sample_detected:
|
||||
if si["sampleStatus"] != "Mounted":
|
||||
si["sampleStatus"] = "Mounted"
|
||||
try:
|
||||
mount_count = int(si["sampleMountCount"])
|
||||
except:
|
||||
mount_count = 0
|
||||
si["sampleMountCount"] = mount_count + 1
|
||||
else:
|
||||
si["sampleStatus"] = "Unknown"
|
||||
save_samples_info()
|
||||
return
|
||||
except:
|
||||
pass
|
||||
|
||||
def update_samples_info_sample_unmount(puck_address, sample_position):
|
||||
try:
|
||||
if (samples_info is not None) and (puck_address is not None):
|
||||
for si in samples_info:
|
||||
if str(si["puckAddress"]) == str(puck_address) and str(si["samplePosition"]) == str(sample_position):
|
||||
si["sampleStatus"] = "HasBeenMounted"
|
||||
save_samples_info()
|
||||
return
|
||||
except:
|
||||
pass
|
||||
|
||||
|
||||
|
||||
test_sample_data = [ \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0001", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "A1",\
|
||||
"sampleName": "MySample 1", \
|
||||
"samplePosition": 1,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0001", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "A1",\
|
||||
"sampleName": "MySample 2", \
|
||||
"samplePosition": 2,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0001", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "A1",\
|
||||
"sampleName": "MySample 3", \
|
||||
"samplePosition": 3,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0001", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "A1",\
|
||||
"sampleName": "MySample 4", \
|
||||
"samplePosition": 4,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0001", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "A1",\
|
||||
"sampleName": "MySample 5", \
|
||||
"samplePosition": 5,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0002", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "C2",\
|
||||
"sampleName": "MySample 1", \
|
||||
"samplePosition": 1,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0002", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "C2",\
|
||||
"sampleName": "MySample 2", \
|
||||
"samplePosition": 2,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0002", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "C2",\
|
||||
"sampleName": "MySample 3", \
|
||||
"samplePosition": 3,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0002", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "C2",\
|
||||
"sampleName": "MySample 4", \
|
||||
"samplePosition": 4,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
{ "userName": "Alexandre", \
|
||||
"dewarName": "TEST", \
|
||||
"puckName": "My puck", \
|
||||
"puckBarcode": "AAA0002", \
|
||||
"puckType": "unipuck", \
|
||||
"puckAddress": "C2",\
|
||||
"sampleName": "MySample 5", \
|
||||
"samplePosition": 5,\
|
||||
"sampleStatus": "Present", \
|
||||
"sampleMountCount": 0,
|
||||
} , \
|
||||
]
|
||||
|
||||
Reference in New Issue
Block a user