def create_document(row, test=False):
# Creates and returns a Genotype document from the values in the row
db_alias = TEST_DB_ALIAS if test else 'default'
build_dic = {}
for key in row:
if 'date' == key[-4:] or key == 'dtt':
# Assumes values ending in 'date' are for date fields
build_dic[key] = datetime.strptime(row[key],
"%Y-%m-%d %H:%M:%S.%f")
# Searches through the other collections for the reference field values
elif 'datasource' in key:
with switch_db(DataSource, db_alias) as TestDat:
datasource, created = fetch_or_save(TestDat,
db_alias=db_alias,
name=row[key])
build_dic['datasource'] = datasource
elif 'study' in key:
with switch_db(Experiment, db_alias) as TestEx:
study, created = fetch_or_save(TestEx,
db_alias=db_alias,
name=row[key])
build_dic['study'] = study
elif key == 'obs':
# Extracts the dictionary from the obs field
build_dic[key] = ast.literal_eval(row[key])
else:
build_dic[key] = row[key]
with switch_db(Genotype, db_alias) as TestGen:
gen, created = fetch_or_save(TestGen,
db_alias=db_alias,
**build_dic)
return gen
def create_document(row, test=False):
# Creates and returns a Genotype document from the values in the row
db_alias = TEST_DB_ALIAS if test else 'default'
build_dic = {}
for key in row:
if 'date' == key[-4:] or key == 'dtt':
# Assumes values ending in 'date' are for date fields
build_dic[key] = datetime.strptime(row[key], "%Y-%m-%d %H:%M:%S.%f")
# Searches through the other collections for the reference field values
elif 'datasource' in key:
with switch_db(DataSource, db_alias) as TestDat:
datasource, created = fetch_or_save(
TestDat, db_alias=db_alias, name=row[key]
)
build_dic['datasource'] = datasource
elif 'study' in key:
with switch_db(Experiment, db_alias) as TestEx:
study, created = fetch_or_save(
TestEx, db_alias=db_alias, name=row[key]
)
build_dic['study'] = study
elif key == 'obs':
# Extracts the dictionary from the obs field
build_dic[key] = ast.literal_eval(row[key])
else:
build_dic[key] = row[key]
with switch_db(Genotype, db_alias) as TestGen:
gen, created = fetch_or_save(TestGen, db_alias=db_alias, **build_dic)
return gen
def init(fn):
dt = datetime.datetime.now()
ds, created = fetch_or_save(
DataSource,
name='Import Kiwifruit Ach',
supplieddate=dt,
supplier='John McCallum',
typ="CSV",
source=fn,
)
st, created = fetch_or_save(Experiment, name='Kiwifruit Ach')
Import.study = st
Import.ds = ds
def init(fn):
dt = datetime.datetime.now()
ds, created = fetch_or_save(
DataSource,
name='Import Kiwifruit Ach',
supplieddate=dt,
supplier='John McCallum',
typ="CSV",
source=fn,
)
st, created = fetch_or_save(
Experiment,
name='Kiwifruit Ach'
)
Import.study = st
Import.ds = ds
def init(fn):
dt = datetime.datetime.now()
ds, created = fetch_or_save(
DataSource,
name='Import Kiwifruit East12',
supplieddate=dt,
supplier='John McCallum',
typ="CSV",
source=fn,
)
st, created = fetch_or_save(Experiment, name='Kiwifruit 12East')
Import.study = st
if ds is None:
raise ValueError("None Type: " + fn + " created a None datasource")
if not isinstance(ds, Document):
raise TypeError("Wrong type of datasouce: " + str(type(ds)))
Import.ds = ds
def init(fn, experi_name, supplier, fruit):
dt = datetime.datetime.now()
if fruit:
name_used = fruit + ' ' + experi_name
else:
name_used = experi_name
ds, created = fetch_or_save(
DataSource,
name='Import ' + name_used,
supplieddate=dt,
supplier=supplier,
typ="CSV",
source=fn,
)
st, created = fetch_or_save(Experiment, name=name_used)
Import.study = st
Import.ds = ds
def init_file(file_path, build_dic):
posix_path = file_path.as_posix()
build_dic['source'] = posix_path
with switch_db(DataSource, db_alias) as DatS:
ds, created = fetch_or_save(DatS, db_alias=db_alias, **make_field_dic(DatS, build_dic))
if created: # add to record of docs saved to db by this run through
created_doc_ids.append((DataSource, ds.id))
ds.supplier = build_dic["pi"]
ds.group = build_dic["Experiment Code"]
ds.save()
return ds
def init(fn):
dt = datetime.datetime.now()
ds, created = fetch_or_save(
DataSource,
name='Import Kiwifruit East12',
supplieddate=dt,
supplier='John McCallum',
typ="CSV",
source=fn,
)
st, created = fetch_or_save(
Experiment, name='Kiwifruit 12East'
)
Import.study = st
if ds is None:
raise ValueError("None Type: " + fn + " created a None datasource")
if not isinstance(ds, Document):
raise TypeError("Wrong type of datasouce: " + str(type(ds)))
Import.ds = ds
def create_document(row, test=False):
# Creates and returns an experiment document from the values in the row
name = row['name']
pi = row['pi']
creator = row['createdby']
when = string_to_datetime(row['createddate'])
descr = row['description']
db_alias = TEST_DB_ALIAS if test else 'default'
with switch_db(Experiment, db_alias) as TestEx:
experi, created = fetch_or_save(
TestEx, db_alias=db_alias, name=name, createddate=when,
pi=pi, createdby=creator, description=descr
)
return experi
def init_file(file_path, build_dic):
posix_path = file_path.as_posix()
build_dic['source'] = posix_path
with switch_db(DataSource, db_alias) as DatS:
ds, created = fetch_or_save(DatS,
db_alias=db_alias,
**make_field_dic(DatS, build_dic))
if created: # add to record of docs saved to db by this run through
created_doc_ids.append((DataSource, ds.id))
ds.supplier = build_dic["pi"]
ds.group = build_dic["Experiment Code"]
ds.save()
return ds
def create_document(row, test=False):
# Creates and returns a Datasource document from the values in the row
supplieddate = datetime.strptime(row['supplieddate'], "%Y-%m-%d").date()
name = row['name']
typ = row['typ']
source = row['source']
supplier = row['supplier']
comment = row['comment']
is_active = row['is_active'] == 'True'
db_alias = TEST_DB_ALIAS if test else 'default'
with switch_db(DataSource, db_alias) as TestDs:
ds, created = fetch_or_save(
TestDs, db_alias=db_alias, name=name, source=source,
supplieddate=supplieddate, typ=typ, supplier=supplier, comment=comment,
is_active=is_active
)
return ds
def create_document(row, test=False):
# Creates and returns an experiment document from the values in the row
name = row['name']
pi = row['pi']
creator = row['createdby']
when = string_to_datetime(row['createddate'])
descr = row['description']
db_alias = TEST_DB_ALIAS if test else 'default'
with switch_db(Experiment, db_alias) as TestEx:
experi, created = fetch_or_save(TestEx,
db_alias=db_alias,
name=name,
createddate=when,
pi=pi,
createdby=creator,
description=descr)
return experi
def init_for_all(path, config_dic):
# Gets the name for the experiment and data_source documents from the directory name
posix_path = path.as_posix()
dir_list = posix_path.split("/")
name = config_dic["Experiment Code"]
# creates the dictionary to use for keyword args to fetch or save documents with
build_dic = config_dic_to_build_dic(config_dic)
build_dic['name'] = name
build_dic['realm'] = build_dic['Realm']
with switch_db(Experiment, db_alias) as Exper:
ex, created = fetch_or_save(Exper, db_alias=db_alias, **make_field_dic(Exper, build_dic))
if created: # add to record of docs saved to db by this run through
created_doc_ids.append((Experiment, ex.id))
Logger.Error("Experiment: " + name + " loaded.")
return build_dic, ex
def init_for_all(path, config_dic):
# Gets the name for the experiment and data_source documents from the directory name
posix_path = path.as_posix()
dir_list = posix_path.split("/")
name = config_dic["Experiment Code"]
# creates the dictionary to use for keyword args to fetch or save documents with
build_dic = config_dic_to_build_dic(config_dic)
build_dic['name'] = name
build_dic['realm'] = build_dic['Realm']
with switch_db(Experiment, db_alias) as Exper:
ex, created = fetch_or_save(Exper,
db_alias=db_alias,
**make_field_dic(Exper, build_dic))
if created: # add to record of docs saved to db by this run through
created_doc_ids.append((Experiment, ex.id))
Logger.Error("Experiment: " + name + " loaded.")
return build_dic, ex
def create_document(row, test=False):
# Creates and returns a Datasource document from the values in the row
supplieddate = datetime.strptime(row['supplieddate'],
"%Y-%m-%d").date()
name = row['name']
typ = row['typ']
source = row['source']
supplier = row['supplier']
comment = row['comment']
is_active = row['is_active'] == 'True'
db_alias = TEST_DB_ALIAS if test else 'default'
with switch_db(DataSource, db_alias) as TestDs:
ds, created = fetch_or_save(TestDs,
db_alias=db_alias,
name=name,
source=source,
supplieddate=supplieddate,
typ=typ,
supplier=supplier,
comment=comment,
is_active=is_active)
return ds
