def __init__(self,
cache_dirname=None,
collection_str='taxon_tree',
verbose=False,
max_entries=float('inf'),
username=None,
MongoDB=None,
password=None,
db='datanator-test',
authSource='admin',
readPreference='nearest',
replicaSet=None):
self.collection_str = collection_str
super().__init__(cache_dirname=cache_dirname,
MongoDB=MongoDB,
db=db,
verbose=verbose,
max_entries=max_entries,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference,
replicaSet=replicaSet)
self.pipeline_manager = pipelines.Pipeline()
self.chem_manager = chem_util.ChemUtil()
self.file_manager = file_util.FileUtil()
self.collection = self.db_obj[self.collection_str]
self.collation = Collation(locale='en',
strength=CollationStrength.SECONDARY)
def get(parameter):
if parameter == 'k_is':
docs = r_manager.db_obj['sabio_rk_old'].aggregate([{
"$project": {
"parameter": 1
}
}, {
"$match": {
"parameter.observed_name": "Ki"
}
}, {
"$unwind":
"$parameter"
}, {
"$group": {
"_id": "$parameter.observed_name",
"count": {
"$sum": 1
}
}
}])
count = 0
for doc in docs:
count += 1
return count
else:
pipeline = pipelines.Pipeline().aggregate_total_array_length(
parameter)
for doc in r_manager.db_obj['ec'].aggregate(pipeline):
return doc['total']
def __init__(self,
MongoDB=None,
db=None,
username=None,
password=None,
authSource=None,
readPreference=None,
max_entries=float('inf'),
verbose=True):
super().__init__(MongoDB=MongoDB,
db=db,
username=username,
password=password,
authSource=authSource,
readPreference=readPreference,
max_entries=max_entries,
verbose=verbose)
self.verbose = verbose
self.max_entries = max_entries
self.uniprot_col = self.db_obj['uniprot']
self.pipeline_manager = pipelines.Pipeline()
def get():
pipeline = pipelines.Pipeline().aggregate_total_array_length(
"observation")
for doc in p_manager.db_obj['pax'].aggregate(pipeline):
return doc['total']
def setUpClass(cls):
cls.src = pipelines.Pipeline()
def get():
pipeline = pipelines.Pipeline().aggregate_total_array_length(
"halflives")
for doc in rna_manager.collection.aggregate(pipeline):
return doc['total']
def get():
pipeline = pipelines.Pipeline().aggregate_total_array_length(
"modifications")
for doc in rna_manager.db_obj['rna_modification'].aggregate(
pipeline):
return doc['total']