def create(labbook_id, ids):
# verify
if not plbCore.validID(args.labbook):
print("'" + labbook_id + "' contains invalid characters")
sys.exit()
# does module exist already?
modfile = labbook_id + ".py"
modffn = os.path.join(plbLabbookRoot, modfile)
if os.path.isfile(modffn):
printwarn("A module already exists for " + labbook_id + ".")
print("You can delete this labbook by using the delete command.")
sys.exit()
if args.dbfile != "":
if not os.path.isfile(args.dbfile):
print("Can't find database file " + args.dbfile + "...")
sys.exit()
try:
labbook = pyLabbook(
id=labbook_id,
root=plbRoot,
repositoryPath=os.path.join(plbRepositoryRoot_REL, labbook_id),
sheetFormat=args.sheetformat,
databasePath=plbDatabaseRoot_REL,
databaseFile=labbook_id + ".sqlite3",
databaseFormat=args.dbformat,
)
except Exception as e:
print("Error initializing: " + str(e))
sys.exit()
serialized = labbook.exportSerialized()
with open(modffn, 'w') as fh:
fh.write(labbook.exportSerialized())
# now try to import and create structure
try:
labbook = plbCore.import_initialize_labbook(labbook_id, plbRoot)
except Exception as e:
print("error importing: " + str(e))
sys.exit()
try:
labbook.createFileStructure()
except Exception as e:
print("error creating repository: " + str(e))
sys.exit()
if args.dbfile != "":
try:
dstfile = os.path.join(plbRoot, labbook.databasePath,
labbook.databaseFile)
plbCore.copyfile(args.dbfile, dstfile)
except Exception as e:
print("error copying " + args.dbfile + ": " + str(e))
print("Labbook will be created with empty database.")
print("You can copy " + args.dbfile + " manually to: \n" + dstfile)
print("Created " + ansi.magenta + modffn + ansi.clear)
print("Done.")
def remove(labbook_id, ids):
if len(ids) < 1:
print("No protocol ids specified... Nothing to do.")
sys.exit()
# validate ids
if not plbCore.validID(args.labbook):
print("'" + labbook_id + "' contains invalid characters")
sys.exit()
for pid in ids:
if not plbCore.validID(pid):
print("'" + pid + "' contains invalid characters")
sys.exit()
# warn user
printwarn("About to remove repository paths for:")
print("\n".join([
ansi.magenta + labbook_id + ansi.cyan + '@' + ansi.magenta + pid +
ansi.clear for pid in ids
]))
print("This will delete ALL associated files and subfolders including +"
"raw data files.")
try:
if prompt("is this what you want", ['y', 'n'], default='n') == 'n':
print("Okay, exiting.")
sys.exit()
except Exception as e:
print("Sorry, I didn't understand that.")
sys.exit()
# confirm
try:
if prompt("Are your really really sure", ['y', 'n'],
default='n') == 'n':
print("Okay, exiting.")
sys.exit()
except Exception as e:
print("Sorry, I didn't understand that.")
sys.exit()
# initialize labbook and import protocols
try:
labbook = plbCore.import_initialize_labbook(labbook_id, plbRoot)
except Exception as e:
print("Error importing " + labbook_id + ": " + str(e))
sys.exit()
print("Removing protocol paths:")
for pid in ids:
try:
protocol = plbCore.import_initialize_protocol(pid, labbook)
except Exception as e:
print(ansi.red + "ERROR" + ansi.clear)
print("couldn't initialize: " + str(e))
continue
print("Deleting path " + ansi.green + protocol.protocolroot() +
ansi.clear + ": ",
end='',
flush=True)
try:
plbCore.rmpath(protocol.protocolroot(), require_empty=False)
except Exception as e:
print(ansi.red + "ERROR" + ansi.clear)
print("Couldn't delete: " + str(e))
continue
print(ansi.green + "OK" + ansi.clear)
print("Done.")
def drop(labbook_id, ids):
if len(ids) < 1:
print("No protocol ids specified... Nothing to do.")
sys.exit()
# validate ids
if not plbCore.validID(args.labbook):
print("'" + labbook_id + "' contains invalid characters")
sys.exit()
for pid in ids:
if not plbCore.validID(pid):
print("'" + pid + "' contains invalid characters")
sys.exit()
# warn user
printwarn("About to drop the following protocol set/sample tables:")
print("\n".join([
ansi.magenta + labbook_id + ansi.cyan + '@' + ansi.magenta + pid +
ansi.clear for pid in ids
]))
print("This will delete all associated database records.")
try:
if prompt("is this what you want", ['y', 'n'], default='n') == 'n':
print("Okay, exiting.")
sys.exit()
except Exception as e:
print("Sorry, I didn't understand that.")
sys.exit()
# confirm
try:
if prompt("Are your really really sure", ['y', 'n'],
default='n') == 'n':
print("Okay, exiting.")
sys.exit()
except Exception as e:
print("Sorry, I didn't understand that.")
sys.exit()
# initialize labbook and import protocols
try:
labbook = plbCore.import_initialize_labbook(labbook_id, plbRoot)
except Exception as e:
print("Error importing " + labbook_id + ": " + str(e))
sys.exit()
print("Dropping protocol tables:")
for pid in ids:
print(ansi.magenta + labbook.id + ansi.cyan + '@' + ansi.magenta +
pid + ansi.clear + ": ",
end='',
flush=True)
try:
protocol = plbCore.import_initialize_protocol(pid, labbook)
except Exception as e:
print(ansi.red + "ERROR" + ansi.clear)
print("couldn't initialize: " + str(e))
continue
protocol.connect()
try:
protocol.dropSetSampleTables()
except Exception as e:
print(ansi.red + "ERROR" + ansi.clear)
print("Couldn't drop tables: " + str(e))
continue
protocol.disconnect()
print(ansi.green + "OK" + ansi.clear)
print("Done.")
def delete(labbook_id, ids):
# verify
if not plbCore.validID(args.labbook):
print("'" + labbook_id + "' contains invalid characters")
sys.exit()
# does module exist?
modfile = labbook_id + ".py"
modffn = os.path.join(plbLabbookRoot, modfile)
if not os.path.isfile(modffn):
print("No module found for " + labbook_id + "... Nothing to do.")
sys.exit()
# warn user
printwarn(ansi.red + "This action will delete all repository files and " +
"databases belonging to " + labbook_id + "." + ansi.clear)
try:
if prompt("Are you really really sure", ['y', 'n'],
default='n') == 'n':
print("Phew! That would have been awful...")
sys.exit()
except Exception as e:
print("Sorry, I don't understand that... Exiting.")
sys.exit()
# confirm
try:
if prompt("Are you sure you're sure", ['y', 'n'], default='n') == 'n':
print("Phew! That would have been awful...")
sys.exit()
except Exception as e:
print("Sorry, I don't understand that... Exiting.")
sys.exit()
# import and initialize and delete...
try:
labbook = plbCore.import_initialize_labbook(labbook_id, plbRoot)
except Exception as e:
print("can't import " + labbook_id + ": " + str(e))
sys.exit()
print("Deleting " + ansi.magenta + labbook.id + ansi.clear +
" repository: ",
end='',
flush=True)
try:
labbook.deleteFileStructure(require_empty=False)
except Exception as e:
print(ansi.red + "ERROR" + ansi.clear)
print(str(e))
sys.exit()
print(ansi.green + "OK" + ansi.clear)
print("Deleting " + ansi.magenta + modffn + ansi.clear + ": ",
end='',
flush=True)
try:
os.remove(modffn)
except Exception as e:
print(ansi.red + "ERROR" + ansi.clear)
print(str(e))
sys.exit()
print(ansi.green + "OK" + ansi.clear)
print("Done.")
"Note that each sample should represent a plasmid component with a "+
"concentration and molar mass.\n"+
"If the recipe calculation for a set generates an error, the sample "+
"file records for that set will remain UNALTERED, so you can preserve "+
"manual calculations if you like."
),
);
parser.add_argument( 'labbook',
help=("id of the labbook containing Transfection experiments"),
type=str,
);
parser.add_argument( 'experiment_ids',
nargs='+',
default=[],
help=("space separated list of experiment id's to calculate recipes for"),
);
args = parser.parse_args();
################################################################################
labbook = plbCore.import_initialize_labbook("testbook", plbRoot);
protocol = plbCore.import_initialize_protocol("Transfection", labbook);
################################################################################
try:
sets = protocol.loadSetFile(args.experiment_ids);
sams = protocol.loadSamFile(args.experiment_ids)
except Exception as e:
print("Error loading set/sample files: "+str(e));
sys.exit();
################################################################################
sets, sams = protocol.calculate_recipes(sets, sams);
protocol.writeSams(sams);
printok()
except Exception as e:
printerr(str(e))
try:
lb_modfile = os.path.join(plbLabbookRoot, 'testLabbook.py')
printtest("Serializing")
with open(lb_modfile, 'w') as fh:
fh.write(lb.exportSerialized())
printok()
except Exception as e:
printerr(str(e))
try:
printtest("Importing")
lb = core.import_initialize_labbook('testLabbook', plbRoot)
print(ansi.green + lb.id + ansi.clear)
except Exception as e:
printerr(str(e))
try:
printtest("Repository")
lb.createFileStructure()
if not os.path.isdir(os.path.join(lb.root, lb.repositoryPath)):
raise Exception("Not found")
printok()
except Exception as e:
printerr(str(e))
try:
printtest("Creating sample protocol")
if not plbCore.validID(labbook_id):
print("labbook '" + labbook_id + "' has invalid characters.")
sys.exit()
if not plbCore.validID(protocol_id):
print("labbook '" + protocol_id + "' has invalid characters.")
sys.exit()
# check for source labbook and protocol modules
protocol_module = protocol_id + '.py'
labbook_module = labbook_id + '.py'
if not os.path.isfile(os.path.join(plbLabbookRoot, labbook_module)):
print("Can't find labbook module file " + labbook_module + ".")
sys.exit()
if not os.path.isfile(os.path.join(plbProtocolRoot, protocol_module)):
print("Can't find protocol module file " + protocol_module + ".")
sys.exit()
# import and initialize source
try:
labbook = plbCore.import_initialize_labbook(labbook_id, plbRoot)
except Exception as e:
print("Error initializing " + labbook_id + ": " + str(e))
sys.exit()
try:
protocol = plbCore.import_initialize_protocol(protocol_id, labbook)
except Exception as e:
print("Error initializing " + protocol_id + ": " + str(e))
sys.exit()
# call command
command_map[args.command](labbook, protocol, args.arguments)
#
sys.exit()
try:
plbCore.import_protocol(pid)
except Exception as e:
print(str(e))
sys.exit()
# verify labbooks and initialize labbook@protocol combos
lp_objects = []
for lid in items['labbook_id'].unique():
file = os.path.join(plbLabbookRoot, lid + ".py")
if not os.path.isfile(file):
print("Can't find " + file + ".")
sys.exit()
try:
labbooks[id] = plbCore.import_initialize_labbook(lid, plbRoot)
except Exception as e:
print("Can't import module " + file + ".")
sys.exit()
# subset and do protocols
ss_lb = items[items['labbook_id'] == lid]
for pid in ss_lb['protocol_id'].unique():
# initialize and store into row
try:
protocol = plbCore.initialize_protocol(pid, labbooks[id])
except Exception as e:
print(str(e))
sys.exit()
row = pd.Series({
'labbook_id': lid,
'protocol_id': pid,
