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 SampleSimilarityResult(mdb.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""Sample Similarity document type."""
# Categories dict is of the form: {<category_name>: [<category_value>, ...]}
categories = mdb.MapField(field=StringList, required=True)
# Tools dict is of the form: {<tool_name>: <ToolDocument>}
tools = mdb.MapField(field=EmbeddedDoc(ToolDocument), required=True)
data_records = mdb.ListField(mdb.DictField(), required=True)
def clean(self):
"""Ensure that `data_records` contain valid records."""
category_names = self.categories.keys()
tool_names = self.tools.keys()
for record in self.data_records:
for category_name in category_names:
if category_name not in record:
msg = 'Record must have all categories.'
raise ValidationError(msg)
for tool_name in tool_names:
xname = '{}_x'.format(tool_name)
yname = '{}_y'.format(tool_name)
if (xname not in record) or (yname not in record):
msg = 'Record must x and y for all tools.'
raise ValidationError(msg)
class BetaDiversityToolResult(GroupToolResult): # pylint: disable=too-few-public-methods
"""Beta Diversity result type."""
# Accept any JSON
# Data: {<genus>: {<metric>: {<tool>: {<sample_name>: {<sample_name>: <value>}}}}}
data = mongoDB.DictField(required=True)
def clean(self):
"""Ensure data blob meets minimum requirements."""
ranks = self.data
for metric in ranks.values():
for tool in metric.values():
for entry in tool.values():
validate_entry(entry)
class BaseSample(Document):
"""Sample model."""
uuid = mongoDB.UUIDField(required=True,
primary_key=True,
binary=False,
default=uuid4)
name = mongoDB.StringField(unique=True)
metadata = mongoDB.DictField(default={})
analysis_result = mongoDB.LazyReferenceField(AnalysisResultMeta)
theme = mongoDB.StringField(default='')
created_at = mongoDB.DateTimeField(default=datetime.datetime.utcnow)
meta = {'allow_inheritance': True}
@property
def tool_result_names(self):
"""Return a list of all tool results present for this Sample."""
all_fields = [mod.name() for mod in all_tool_results]
return [
field for field in all_fields
if getattr(self, field, None) is not None
]
def fetch_safe(self, tools=None):
"""Return the sample with all tool result documents fetched and jsonified."""
if not tools:
tools = self.tool_result_names
safe_sample = {
tool: jsonify(getattr(self, tool).fetch())
for tool in tools
}
safe_sample['name'] = self.name
safe_sample['metadata'] = self.metadata
safe_sample['theme'] = self.theme
if self.analysis_result:
safe_sample['analysis_result'] = str(self.analysis_result.pk)
return safe_sample
class BetaDiversityResult(mdb.EmbeddedDocument):
"""Set of beta diversity results."""
data = mdb.DictField(required=True)
class MicrobeDirectoryResult(mdb.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""Set of microbe directory results."""
samples = mdb.DictField(required=True)