class AlphaDiversityDatum(mdb.EmbeddedDocument):
"""AlphaDiv datum type."""
metrics = mdb.ListField(mdb.StringField())
category_value = mdb.StringField(required=True)
# metric -> distribution
by_metric = mdb.MapField(field=mdb.ListField(mdb.FloatField()))
class AlphaDiversityResult(mdb.EmbeddedDocument):
"""Embedded results for alpha diversity."""
# Categories dict has form: {<category_name>: [<category_value>, ...]}
categories = mdb.MapField(field=mdb.ListField(mdb.StringField()),
required=True)
tool_names = mdb.ListField(mdb.StringField())
by_tool = mdb.MapField(field=EmDoc(AlphaDiversityTool), required=True)
class HMPResult(mdb.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""HMP document type."""
categories = mdb.MapField(field=StringList, required=True)
sites = mdb.ListField(mdb.StringField(), required=True)
data = mdb.MapField(field=EmDocList(HMPDatum), required=True)
def clean(self):
"""Ensure integrity of result content."""
for category, values in self.categories.items():
if category not in self.data:
msg = f'Category \'{category}\' is not present in \'data\'!'
raise ValidationError(msg)
values_present = [datum.name for datum in self.data[category]]
for value in values:
if value not in values_present:
msg = f'Value \'{value}\' is not present in \'data\'!'
raise ValidationError(msg)
for category_name, category_data in self.data.items():
if len(category_data) != len(self.categories[category_name]):
msg = (f'Category data for {category_name} does not match size of '
f'category values ({len(self.categories[category_name])})!')
raise ValidationError(msg)
for datum in category_data:
if len(datum.data) != len(self.sites):
msg = (f'Datum <{datum.name}> of size {len(datum.data)} '
f'does not match size of sites ({len(self.sites)})!')
raise ValidationError(msg)
class XYZPoint(mdb.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""Represent a 3d point."""
xval = mdb.FloatField(required=True)
yval = mdb.FloatField(required=True)
zval = mdb.FloatField(default=1)
name = mdb.StringField()
class AnalysisResultWrapper(mongoDB.Document): # pylint: disable=too-few-public-methods
"""Base mongo result class."""
status = mongoDB.StringField(required=True,
max_length=1,
choices=ANALYSIS_RESULT_STATUS,
default='P')
data = mongoDB.GenericEmbeddedDocumentField()
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
# pylint: disable=too-few-public-methods
"""Average Genome Size display models."""
from app.extensions import mongoDB as mdb
from app.display_modules.shared_models import DistributionResult
# Define aliases
EmbeddedDoc = mdb.EmbeddedDocumentField # pylint: disable=invalid-name
StringList = mdb.ListField(mdb.StringField()) # pylint: disable=invalid-name
class AGSResult(mdb.EmbeddedDocument):
"""AGS document type."""
# Categories dict has form: {<category_name>: [<category_value>, ...]}
categories = mdb.MapField(field=StringList, required=True)
# Distribution dict has form: {<category_name>: {<category_value>: <dist>}}
distributions = mdb.MapField(
field=mdb.MapField(field=EmbeddedDoc(DistributionResult)),
required=True)
class HMPDatum(mdb.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""HMP datum type."""
name = mdb.StringField(required=True)
data = mdb.ListField(mdb.ListField(mdb.FloatField()), required=True)
class ToolDocument(mdb.EmbeddedDocument): # pylint: disable=too-few-public-methods
"""Tool document type."""
x_label = mdb.StringField(required=True)
y_label = mdb.StringField(required=True)
class AlphaDiversityTool(mdb.EmbeddedDocument):
"""Store a map of rank -> AlphaDiversityRank."""
taxa_ranks = mdb.ListField(mdb.StringField())
by_taxa_rank = mdb.MapField(field=EmDoc(AlphaDiversityRank))