def add_records(self, records):
""" Recursively add records to database """
roots = []
nodes = defaultdict(list)
seen = set()
for record in records:
parents = record.pop("parents")
record = utils.tidy_nans(record)
node = self.table(**record)
seen.add(node.name)
if len(parents) == 0:
roots.append(node)
else:
for parent in parents:
nodes[parent].append(node)
for n in nodes.keys():
assert (n in seen), f"{n} not in nodes"
def recurse(node, memo):
for child in memo[node.name]:
node.children.append(recurse(child, memo))
return node
trees = [recurse(p, nodes) for p in roots]
with self.get_session() as session:
session.add_all(trees)
return
def add_records(self, records):
""" Recursively add records to database """
logger.info("Processing taxon file.")
root = None
nodes = defaultdict(list)
for record in records:
record = utils.tidy_nans(record)
node = self.table(**record)
if node.taxid == 1:
root = node
else:
nodes[node.parent_taxid].append(node)
logger.info("Constructing tree.")
def recurse(node, memo):
for child in memo[node.taxid]:
node.children.append(recurse(child, memo))
return node
tree = recurse(root, nodes)
logger.info("Adding to database.")
with self.get_session() as session:
session.add(tree)
return
def add_records(self, records):
""" Recursively add records to database """
logger.info("Processing taxon file.")
roots = []
nodes = defaultdict(list)
for record in records:
parents = record.pop("parents")
record = utils.tidy_nans(record)
node = self.table(**record)
if pd.isna(parents) or len(parents) == 0:
roots.append(node)
else:
for parent in parents:
nodes[parent].append(node)
def recurse(node, memo):
for child in memo[node.id]:
node.children.append(recurse(child, memo))
return node
tree = [recurse(root, nodes) for root in roots]
with self.get_session() as session:
session.add_all(tree)
return
def add_table(self, table):
records = []
for i, loc in table.iterrows():
this_loc = self._from_series(loc)
this_loc = utils.tidy_nans(this_loc)
records.append(this_loc)
self.add_records(records)
return
def add_records(self, records):
""" Recursively add records to database """
with self.get_session() as session:
for record in records:
record = utils.tidy_nans(record)
sample_id = record.pop("sample_id")
contributor_name = record.pop("contributor_name")
sample = session.query(
db.Sample).filter(db.Sample.id == sample_id).one()
contributor = session.query(db.Contributor).filter(
db.Contributor.name == contributor_name).one()
record["contributor"] = contributor
record["sample"] = sample
record = self.table(**record)
session.add(record)
return
def add_records(self, records):
""" Recursively add records to database """
with self.get_session() as session:
for record in records:
taxid = record.pop("taxid")
sample_id = record.pop("sample_id")
record = utils.tidy_nans(record)
sample = session.query(
db.Sample).filter(db.Sample.id == sample_id).one()
taxon = session.query(
db.Taxon).filter(db.Taxon.taxid == taxid).one()
record["taxon"] = taxon
record["sample"] = sample
record = self.table(**record)
session.add(record)
return
def add_records(self, records):
""" Recursively add records to database """
with self.get_session() as session:
for record in records:
record = utils.tidy_nans(record)
pesticide_name = record.pop("pesticide_name")
sample_id = record.pop("sample_id")
print(pesticide_name, sample_id)
sample = session.query(db.Sample).filter(
db.Sample.id == sample_id).one()
pesticide = session.query(db.Pesticide).filter(
db.Pesticide.name == pesticide_name).one()
record["pesticide"] = pesticide
record["sample"] = sample
record = self.table(**record)
session.add(record)
return