Startup
This commit is contained in:
gac-S_Changer
4
script/data/get_samples_info.py
Normal file
4
script/data/get_samples_info.py
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@@ -0,0 +1,4 @@
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set_return(get_samples_info(as_json=False))
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51
script/data/pucks.py
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51
script/data/pucks.py
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@@ -0,0 +1,51 @@
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def get_puck_names():
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return [str(a)+str(b) for a in BLOCKS for b in range(1,6)]
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def get_puck_info():
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ret = []
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#for puck in get_puck_names():
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for puck in BasePlate.pucks:
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ret.append({"address" : str(puck.name), "status": str(puck.status), "barcode" : str(puck.id)})
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return ret
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def get_puck_obj(address):
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return BasePlate.getChild(address)
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def get_puck_obj_by_id(puck_id):
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for puck in BasePlate.pucks:
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if puck.id == puck_id:
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return puck
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return None
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def set_puck_info(puck_info):
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#print puck_info
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for i in puck_info:
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p=get_puck_obj(i["address"])
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if p is not None:
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if (p.status == 'Present') and ( i["status"] =='Present'):
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if i['barcode'] and (i['barcode'] != str(None)):
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#print "Setting ", p, " to ", i['barcode']
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p.id = i['barcode']
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def clear_puck_info():
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save_puck_info([])
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def save_puck_info():
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data = get_puck_info()
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output_file = open( get_context().setup.expandPath("{context}/pucks_info.json") , "w")
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output_file.write(json.dumps(data))
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output_file.close()
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def restore_puck_info():
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try:
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inputfile = open(get_context().setup.expandPath("{context}/pucks_info.json"), "r")
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info = json.loads(inputfile.read())
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except:
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print >> sys.stderr, "Error reading pucks info file: " + str(sys.exc_info()[1])
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info = []
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set_puck_info(info)
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39
script/data/reports.py
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39
script/data/reports.py
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@@ -0,0 +1,39 @@
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from statsutils import *
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def report(start, end):
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"""
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Data format for start and end: "dd/mm/yy" or "dd/mm/yy hh:mm:ss.mmm"
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"""
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cmds = ["mount%", "unmount%", "dry%", "recover%", "trash%", "robot_recover%", "scan%", "homing%"]
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conn = get_stats_connection()
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try:
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print_stats(cmds, start, end)
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for cmd in cmds:
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print_cmd_stats (cmd, start, end)
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finally:
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conn.close()
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def print_recs(cmd,start, end, result=("%%")):
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"""
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Data format for start and end: "dd/mm/yy" or "dd/mm/yy hh:mm:ss.mmm"
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Result: "error", "abort, "success". Defaulr for all
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"""
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conn = get_stats_connection()
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try:
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print_cmd_records(cmd,start, end, result)
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finally:
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conn.close()
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#Print all records:
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#
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#report("01/03/19","01/04/19")
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350
script/data/samples.py
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350
script/data/samples.py
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@@ -0,0 +1,350 @@
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import json
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import re
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import org.python.core.PyDictionary as PyDictionary
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SAMPLE_INFO_KEYS = ["userName", "dewarName", "puckName", "puckBarcode", "puckType", "puckAddress",
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"sampleName", "samplePosition", "sampleBarcode", "sampleStatus", "sampleMountCount"]
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samples_info = []
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def set_samples_info(info):
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global samples_info
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if (is_string(info)):
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info = json.loads(info)
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if not is_list(info):
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raise Exception("Sample info must be a list (given object type is " + str(type(info)) + ")")
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#Sanitize list
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remove = []
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for sample in info:
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try:
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if set(sample.keys()) != set(SAMPLE_INFO_KEYS):
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raise Exception()
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except:
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remove.append(sample)
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for el in remove:
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info.remove(el)
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print "Invalid samples info element: " + str(el)
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samples_info = info
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save_samples_info()
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#Trust beamline on assignments, so update puck info
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update_puck_table()
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def clear_samples_info():
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set_samples_info([])
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def save_samples_info():
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data = get_samples_info(True)
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output_file = open( get_context().setup.expandPath("{context}/samples_info.json") , "w")
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output_file.write(data)
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output_file.close()
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get_context().sendEvent("samples_updated", True)
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save_puck_info()
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def restore_samples_info():
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restore_puck_info()
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try:
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inputfile = open(get_context().setup.expandPath("{context}/samples_info.json"), "r")
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info = inputfile.read()
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except:
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print >> sys.stderr, "Error reading sample info file: " + str(sys.exc_info()[1])
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info = []
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set_samples_info(info)
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def get_samples_info(as_json=True):
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global samples_info
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return json.dumps(to_list(samples_info)) if as_json else samples_info
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def has_puck_datamatrix(datamatrix):
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if samples_info is not None:
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for si in samples_info:
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if si["puckBarcode"] == datamatrix:
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return True
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return False
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def add_puck_datamatrix(barcode, address = "", dewar = "Unknown", user = "Unknown", puck = "Unknown", type = "unipuck", sample_prefix = "Sample"):
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if has_puck_datamatrix(barcode):
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raise Exception("Datamatrix already defined: " + str(barcode))
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for s in range(1,17):
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info = \
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{ "userName": user, \
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"dewarName": dewar, \
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"puckName": puck, \
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"puckBarcode": address if barcode is None else barcode, \
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"puckType": type, \
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"puckAddress": address,\
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"sampleName": sample_prefix + " " + str(s), \
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"samplePosition": str(s),\
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"sampleStatus": "Unknown", \
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"sampleMountCount": "0",
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}
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samples_info.append(info)
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save_samples_info()
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def remove_puck_datamatrix(barcode):
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remove = []
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for si in samples_info:
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if si["puckBarcode"] == barcode:
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remove.append(si)
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for el in remove: samples_info.remove(el)
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save_samples_info()
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barcode_clean_re = re.compile("[^a-zA-Z0-9]")
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def is_same_datamatrix(table, reading):
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if table == reading:
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return True
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table2 = barcode_clean_re.sub("", table.upper())
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reading2 = barcode_clean_re.sub("", reading.upper())
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if table2 == reading2:
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log("Assigning aproximative datamatrix " + reading )
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return True
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return False
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def set_puck_datamatrix(puck, datamatrix):
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if puck is None:
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puck = ""
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if datamatrix is None:
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datamatrix = ""
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if samples_info is not None:
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for si in samples_info:
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#if si["puckBarcode"] == datamatrix:
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if is_same_datamatrix(si["puckBarcode"],datamatrix):
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si["puckAddress"] = puck
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elif si["puckAddress"] == puck:
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si["puckAddress"] = ""
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save_samples_info()
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def reset_puck_datamatrix(puck = None):
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if samples_info is not None:
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for si in samples_info:
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if (si["puckAddress"] == puck) or (puck is None):
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si["puckAddress"] = ""
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save_samples_info()
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for p in BasePlate.getChildren():
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if (p.name == puck) or (puck is None):
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p.id = None
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def get_puck_datamatrix():
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ret = {}
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for si in samples_info:
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if si["puckBarcode"] is not None and si["puckBarcode"]!="":
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ret[si["puckBarcode"]] = si["puckAddress"]
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return ret
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def get_puck_address(barcode):
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try:
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return get_puck_datamatrix()[barcode]
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except:
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return None
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def update_puck_table():
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dms = get_puck_datamatrix()
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for barcode in dms.keys():
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address = dms[barcode]
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puck = get_puck_obj(address)
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if puck is not None:
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puck.id = barcode
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#Sample mount/unmount
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def same_address(puck_add_1, sample_pos_1, puck_add_2, sample_pos_2):
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if str(puck_add_1) != str(puck_add_2):
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return False
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try:
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sample_pos_1 = int(sample_pos_1)
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except:
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return False
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try:
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sample_pos_2 = int(sample_pos_2)
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except:
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return False
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return sample_pos_1 == sample_pos_2
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def update_samples_info_sample_mount(puck_address, sample_position, sample_detected, sample_id):
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try:
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if (samples_info is not None) and (puck_address is not None):
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for si in samples_info:
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if same_address( si["puckAddress"], si["samplePosition"], puck_address, sample_position):
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if sample_detected:
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if si["sampleStatus"] != "Mounted":
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si["sampleStatus"] = "Mounted"
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try:
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mount_count = int(si["sampleMountCount"])
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except:
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mount_count = 0
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si["sampleMountCount"] = mount_count + 1
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else:
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si["sampleStatus"] = "Unknown"
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if sample_id is not None:
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si["sampleBarcode"] = sample_id
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else:
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if si["sampleStatus"] == "Mounted":
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si["sampleStatus"] = "HasBeenMounted"
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save_samples_info()
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except:
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pass
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def update_samples_info_sample_unmount(puck_address, sample_position):
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try:
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if (samples_info is not None) and (puck_address is not None):
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for si in samples_info:
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if same_address( si["puckAddress"], si["samplePosition"], puck_address, sample_position):
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si["sampleStatus"] = "HasBeenMounted"
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save_samples_info()
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return
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except:
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pass
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def update_samples_info_sample_scan(puck_address, sample_position, sample_detected, sample_id):
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try:
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if (samples_info is not None) and (puck_address is not None):
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for si in samples_info:
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if same_address( si["puckAddress"], si["samplePosition"], puck_address, sample_position):
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if sample_detected:
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if si["sampleStatus"] == "Unknown":
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si["sampleStatus"] = "Present"
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else:
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if si["sampleStatus"] == "Present":
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si["sampleStatus"] = "Unknown"
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if sample_id is not None:
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si["sampleBarcode"] = sample_id
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save_samples_info()
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return
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except:
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pass
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test_sample_data = [ \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0001", \
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"puckType": "unipuck", \
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"puckAddress": "A1",\
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"sampleName": "MySample 1", \
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"samplePosition": 1,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0001", \
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"puckType": "unipuck", \
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"puckAddress": "A1",\
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"sampleName": "MySample 2", \
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"samplePosition": 2,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0001", \
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"puckType": "unipuck", \
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"puckAddress": "A1",\
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"sampleName": "MySample 3", \
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"samplePosition": 3,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0001", \
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"puckType": "unipuck", \
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"puckAddress": "A1",\
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"sampleName": "MySample 4", \
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"samplePosition": 4,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0001", \
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"puckType": "unipuck", \
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"puckAddress": "A1",\
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"sampleName": "MySample 5", \
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"sampleBarcode": "", \
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"samplePosition": 5,\
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0002", \
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"puckType": "unipuck", \
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"puckAddress": "C2",\
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"sampleName": "MySample 1", \
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"samplePosition": 1,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0002", \
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"puckType": "unipuck", \
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"puckAddress": "C2",\
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"sampleName": "MySample 2", \
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"samplePosition": 2,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0002", \
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"puckType": "unipuck", \
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"puckAddress": "C2",\
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"sampleName": "MySample 3", \
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"samplePosition": 3,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0002", \
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"puckType": "unipuck", \
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"puckAddress": "C2",\
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"sampleName": "MySample 4", \
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"samplePosition": 4,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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{ "userName": "Alexandre", \
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"dewarName": "TEST", \
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"puckName": "My puck", \
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"puckBarcode": "AAA0002", \
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"puckType": "unipuck", \
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"puckAddress": "C2",\
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"sampleName": "MySample 5", \
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"samplePosition": 5,\
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"sampleBarcode": "", \
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"sampleStatus": "Present", \
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"sampleMountCount": 0,
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} , \
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]
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4
script/data/set_samples_info.py
Normal file
4
script/data/set_samples_info.py
Normal file
@@ -0,0 +1,4 @@
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set_samples_info(args[0])
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Reference in New Issue
Block a user