class ReadStatsSample(mdb.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""A set of consistent fields for read stats."""
num_reads = mdb.IntField()
gc_content = mdb.FloatField()
codons = mdb.MapField(field=mdb.IntField(), required=True)
tetramers = mdb.MapField(field=mdb.IntField(), required=True)
class ReadStatsToolResult(ToolResult): # pylint: disable=too-few-public-methods
"""A set of consistent fields for read stats."""
num_reads = mongoDB.IntField()
gc_content = mongoDB.FloatField()
codons = mongoDB.MapField(field=mongoDB.IntField(), required=True)
tetramers = mongoDB.MapField(field=mongoDB.IntField(), required=True)
@staticmethod
def stat_fields():
"""Return a list of the stats collected."""
return ['num_reads', 'gc_content', 'codons', 'tetramers']
class FoodPetResult(ToolResult): # pylint: disable=too-few-public-methods
"""Food/Pet tool's result type."""
# DictFields are of the form: {<sample_id>: <sample_value>}
vegetables = mongoDB.DictField(default={})
fruits = mongoDB.DictField(default={})
pets = mongoDB.DictField(default={})
meats = mongoDB.DictField(default={})
total_reads = mongoDB.IntField()
class MicrobeCensusResult(ToolResult): # pylint: disable=too-few-public-methods
"""Mic Census tool's result type."""
average_genome_size = mongoDB.FloatField(required=True)
total_bases = mongoDB.IntField(required=True)
genome_equivalents = mongoDB.FloatField(required=True)
def clean(self):
"""Check all values are non-negative, if not raise an error."""
def validate(*vals):
"""Check vals are non-negative, return a bool."""
for val in vals:
if val is not None and val < 0:
return False
return True
if not validate(self.average_genome_size,
self.total_bases,
self.genome_equivalents):
msg = 'MicrobeCensusResult values must be non-negative'
raise ValidationError(msg)
class MacrobialRow(mongoDB.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""Row for a gene in Macrobial."""
total_reads = mongoDB.IntField()
rpkm = mongoDB.FloatField()
class KrakenResult(ToolResult): # pylint: disable=too-few-public-methods
"""Kraken tool's result type."""
# Taxa is of the form: {<taxon_name>: <abundance_value>}
taxa = mongoDB.MapField(mongoDB.IntField(), required=True)
class KrakenHLLResult(ToolResult):
"""Kraken tool's result type."""
# Taxa is of the form: {<taxon_name>: <abundance_value>}
taxa = mongoDB.MapField(mongoDB.IntField(), required=True)