def run(self, data, config=None, pipeline=None):
"""Write file."""
with Stream(self.output, "w") as out:
for key1, value1 in data.items():
out.write(key1 + ":" + str(type(value1)) + "\n")
# If it is a list then
if isinstance(value1, list):
value1 = value1[0]
if isinstance(value1, dict):
for key2, value2 in value1.items():
out.write("\t" + key2 + ":" + str(type(value2)) + "\n")
return data
def run(self, data, config=None, pipeline=None):
"""Write CSV file."""
jmespath_opts = jmespath.Options(custom_functions=JMESExtensions(data))
results = jmespath.search(self.select_expr, data, jmespath_opts)
with Stream(self.output, "w") as csv_out:
if not results:
print("# No results", file=csv_out)
else:
writer = csv.DictWriter(csv_out,
sorted(results[0].keys()),
restval=self.null_placeholder)
if self.header:
writer.writeheader()
for record in results:
self._fill_placeholders(record)
writer.writerow(record)
return data
def run(self, data, config=None, pipeline=None):
"""Load pipeline state from pickle."""
with Stream(self.input_source, "rb") as in_fh:
loaded = pickle.load(in_fh)
data.update(loaded)
return data
def run(self, data, config=None, pipeline=None):
with Stream(self.input_source, "r") as in_fh:
loaded = yaml.load(in_fh, SafeLoader)
data.update(loaded)
return data
def run(self, data, config=None, pipeline=None):
"""Dump pipeline state."""
with Stream(self.input_source, "r") as in_fh:
loaded = json.load(in_fh)
data.update(loaded)
return data
def run(self, data, config=None, pipeline=None):
with Stream(self.output, "wb") as out_fh:
pickle.dump(self._filter(data), out_fh)
return data
def run(self, data, config=None, pipeline=None):
with Stream(self.output, "w") as out_fh:
yaml.dump(self._filter(data), out_fh, Dumper=YamlStateDumper)
return data
def run(self, data, config=None, pipeline=None):
"""Dump pipeline state."""
with Stream(self.output, "w") as out_fh:
json.dump(self._filter(data), out_fh, cls=JsonStateEncoder)
return data
def __init__(self, file, query_name):
"""Parse a tabulated file produced by an hhsuite tool."""
self.hits = []
self.query_name = query_name
with Stream(file, "r") as fh:
self._parse_file(fh)