forked from enviPath/enviPy
85 lines
3.4 KiB
Python
85 lines
3.4 KiB
Python
from collections import defaultdict
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from datetime import datetime
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from tempfile import TemporaryDirectory
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from django.test import TestCase, tag
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from epdb.logic import PackageManager
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from epdb.models import User, EnviFormer, Package, Setting
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from epdb.tasks import predict_simple, predict
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def measure_predict(mod, pathway_pk=None):
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# Measure and return the prediction time
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start = datetime.now()
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if pathway_pk:
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s = Setting()
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s.model = mod
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s.model_threshold = 0.2
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s.max_depth = 4
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s.max_nodes = 20
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s.save()
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pred_result = predict.delay(pathway_pk, s.pk, limit=s.max_depth)
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else:
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pred_result = predict_simple.delay(mod.pk, "C1=CC=C(CSCC2=CC=CC=C2)C=C1")
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_ = pred_result.get()
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return round((datetime.now() - start).total_seconds(), 2)
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@tag("slow")
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class EnviFormerTest(TestCase):
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fixtures = ["test_fixtures.jsonl.gz"]
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@classmethod
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def setUpClass(cls):
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super(EnviFormerTest, cls).setUpClass()
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cls.user = User.objects.get(username="anonymous")
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cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
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cls.BBD_SUBSET = Package.objects.get(name="Fixtures")
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def test_model_flow(self):
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"""Test the full flow of EnviFormer, dataset build -> model finetune -> model evaluate -> model inference"""
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with TemporaryDirectory() as tmpdir:
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with self.settings(MODEL_DIR=tmpdir):
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threshold = float(0.5)
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data_package_objs = [self.BBD_SUBSET]
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eval_packages_objs = [self.BBD_SUBSET]
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mod = EnviFormer.create(
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self.package, data_package_objs, eval_packages_objs, threshold=threshold
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)
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mod.build_dataset()
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mod.build_model()
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mod.evaluate_model(True, eval_packages_objs, n_splits=2)
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mod.predict("CCN(CC)C(=O)C1=CC(=CC=C1)C")
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def test_predict_runtime(self):
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with TemporaryDirectory() as tmpdir:
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with self.settings(MODEL_DIR=tmpdir):
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threshold = float(0.5)
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data_package_objs = [self.BBD_SUBSET]
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eval_packages_objs = [self.BBD_SUBSET]
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mods = []
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for _ in range(4):
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mod = EnviFormer.create(
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self.package, data_package_objs, eval_packages_objs, threshold=threshold
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)
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mod.build_dataset()
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mod.build_model()
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mods.append(mod)
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# Test prediction time drops after first prediction
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times = [measure_predict(mods[0]) for _ in range(5)]
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print(f"First prediction took {times[0]} seconds, subsequent ones took {times[1:]}")
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# Test pathway prediction
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times = [measure_predict(mods[1], self.BBD_SUBSET.pathways[0].pk) for _ in range(5)]
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print(f"First pathway prediction took {times[0]} seconds, subsequent ones took {times[1:]}")
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# Test eviction by performing three prediction with every model, twice.
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times = defaultdict(list)
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for _ in range(2): # Eviction should cause the second iteration here to have to reload the models
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for mod in mods:
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for _ in range(3):
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times[mod.pk].append(measure_predict(mod))
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print(times)
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