def test_run_taxa_tree_sample(self): # pylint: disable=invalid-name
"""Ensure TaxaTree run_sample produces correct results."""
kwargs = {
KrakenResultModule.name(): create_kraken(),
KrakenHLLResultModule.name(): create_krakenhll(),
Metaphlan2ResultModule.name(): create_metaphlan2(),
}
self.generic_run_sample_test(kwargs, TaxaTreeDisplayModule)
def tool_name_to_param(tool_name):
"""Convert tool short names to param names."""
for param_name in [
KrakenResultModule.name(),
Metaphlan2ResultModule.name()
]:
if tool_name in param_name:
return param_name
return tool_name
def create_sample(i):
"""Create unique sample for index i."""
args = {
'name': f'Sample{i}',
'metadata': {'foobar': f'baz{i}'},
CARDAMRResultModule.name(): create_card_amr(),
KrakenResultModule.name(): create_kraken(),
Metaphlan2ResultModule.name(): create_metaphlan2(),
}
return Sample(**args).save()
def create_sample(i):
"""Create unique sample for index i."""
return Sample(
**{
'name': f'Sample{i}',
'metadata': {
'foobar': f'baz{i}'
},
KrakenResultModule.name(): create_kraken(),
KrakenHLLResultModule.name(): create_krakenhll(),
Metaphlan2ResultModule.name(): create_metaphlan2(),
}).save()
def trees_from_sample(sample):
"""Build taxa trees for a given sample."""
metaphlan2 = sample[Metaphlan2ResultModule.name()]
metaphlan2 = reduce_taxa_list(metaphlan2['taxa'])
kraken = sample[KrakenResultModule.name()]
kraken = reduce_taxa_list(kraken['taxa'])
krakenhll = sample[KrakenHLLResultModule.name()]
krakenhll = reduce_taxa_list(krakenhll['taxa'])
return {
'kraken': kraken,
'metaphlan2': metaphlan2,
'krakenhll': krakenhll,
}
def run_sample_group(cls, sample_group, samples):
"""Gather samples and process."""
reducer = sample_similarity_reducer.s(samples)
persist_task = persist_result.s(sample_group.analysis_result_uuid)
categories_task = categories_from_metadata.s(samples)
kraken_task = taxa_tool_tsne.s(samples, KrakenResultModule.name())
krakenhll_task = taxa_tool_tsne.s(samples,
KrakenHLLResultModule.name())
metaphlan2_task = taxa_tool_tsne.s(samples,
Metaphlan2ResultModule.name())
middle_tasks = [
categories_task, kraken_task, krakenhll_task, metaphlan2_task
]
return chord(middle_tasks)(reducer | persist_task)
def make_all_flows(samples):
"""Determine flows by tool."""
flow_tbl = {}
tool_names = [
Metaphlan2ResultModule.name(),
KrakenResultModule.name(),
KrakenHLLResultModule.name(),
]
for tool_name in tool_names:
taxa_tbl = make_taxa_table(samples, tool_name)
save_tool_name = 'kraken'
if 'metaphlan2' in tool_name:
save_tool_name = 'metaphlan2'
elif 'krakenhll' in tool_name:
save_tool_name = 'krakenhll'
flow_tbl[save_tool_name] = make_flow(taxa_tbl)
return {'by_tool': flow_tbl}
def sample_similarity_reducer(args, samples):
"""Combine Sample Similarity components."""
categories = args[0]
kraken_tool, kraken_labeled = args[1]
krakenhll_tool, krakenhll_labeled = args[2]
metaphlan_tool, metaphlan_labeled = args[3]
data_records = update_data_records(samples, categories, kraken_labeled,
krakenhll_labeled, metaphlan_labeled)
tools = {
KrakenResultModule.name(): kraken_tool,
KrakenHLLResultModule.name(): krakenhll_tool,
Metaphlan2ResultModule.name(): metaphlan_tool,
}
result_data = {
'categories': categories,
'tools': tools,
'data_records': data_records,
}
return result_data
def make_volcanos(categories, samples):
"""Return the JSON for a VolcanoResult."""
dataframe_keys = {
KrakenResultModule.name(): 'taxa',
Metaphlan2ResultModule.name(): 'taxa',
}
out = {'categories': categories, 'tools': {}}
for tool_name, dataframe_key in dataframe_keys.items():
out['tools'][tool_name] = {'tool_categories': {}}
tool_tbl = out['tools'][tool_name]['tool_categories']
for category_name, category_values in categories.items():
tool_tbl[category_name] = {}
for category_value in category_values:
category_value = scrub_category_val(category_value)
scatter_plot = handle_one_tool_category(
category_name,
category_value,
samples,
tool_name,
dataframe_key,
)
if scatter_plot is not None:
tool_tbl[category_name][category_value] = scatter_plot
return out
from app import db
from app.display_modules.sample_similarity import SampleSimilarityDisplayModule
from app.display_modules.sample_similarity.wrangler import SampleSimilarityWrangler
from app.samples.sample_models import Sample
from app.tool_results.kraken import KrakenResultModule
from app.tool_results.kraken.tests.factory import create_kraken
from app.tool_results.krakenhll import KrakenHLLResultModule
from app.tool_results.krakenhll.tests.factory import create_krakenhll
from app.tool_results.metaphlan2 import Metaphlan2ResultModule
from app.tool_results.metaphlan2.tests.factory import create_metaphlan2
from tests.base import BaseTestCase
from tests.utils import add_sample_group
KRAKEN_NAME = KrakenResultModule.name()
KRAKENHLL_NAME = KrakenHLLResultModule.name()
METAPHLAN2_NAME = Metaphlan2ResultModule.name()
class TestSampleSimilarityWrangler(BaseTestCase):
"""Test suite for Sample Similarity Wrangler."""
def test_run_sample_group(self):
"""Ensure run_sample_group produces correct results."""
def create_sample(i):
"""Create unique sample for index i."""
metadata = {'foobar': f'baz{i}'}
sample_data = {
'name': f'Sample{i}',
'metadata': metadata,
KRAKEN_NAME: create_kraken(),