diff options
| -rw-r--r-- | wqflask/base/species.py | 83 | ||||
| -rw-r--r-- | wqflask/tests/unit/base/test_species.py | 116 | ||||
| -rw-r--r-- | wqflask/wqflask/api/gen_menu.py | 10 |
3 files changed, 166 insertions, 43 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py index e3c29916..f303aabb 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -1,59 +1,66 @@ -import collections - -from flask import Flask, g - - -from utility.logger import getLogger -logger = getLogger(__name__) +from collections import OrderedDict +from dataclasses import dataclass +from dataclasses import InitVar +from typing import Optional, Dict +from flask import g +@dataclass class TheSpecies: - def __init__(self, dataset=None, species_name=None): - if species_name != None: - self.name = species_name + """Data related to species.""" + dataset: Optional[Dict] = None + species_name: Optional[str] = None + + def __post_init__(self): + if self.species_name is not None: + self.name = self.species_name self.chromosomes = Chromosomes(species=self.name) else: - self.dataset = dataset self.chromosomes = Chromosomes(dataset=self.dataset) +@dataclass class IndChromosome: - def __init__(self, name, length): - self.name = name - self.length = length + """Data related to IndChromosome""" + name: str + length: int @property def mb_length(self): - """Chromosome length in megabases""" + """Chromosome length in mega-bases""" return self.length / 1000000 +@dataclass class Chromosomes: - def __init__(self, dataset=None, species=None): - self.chromosomes = collections.OrderedDict() - if species != None: - query = """ - Select - Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species - where - Chr_Length.SpeciesId = Species.SpeciesId AND - Species.Name = '%s' - Order by OrderId - """ % species.capitalize() - else: + """Data related to a chromosome""" + dataset: InitVar[Dict] = None + species: Optional[str] = None + + def __post_init__(self, dataset): + if self.species is None: self.dataset = dataset - query = """ - Select - Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet - where - Chr_Length.SpeciesId = InbredSet.SpeciesId AND - InbredSet.Name = '%s' - Order by OrderId - """ % self.dataset.group.name - logger.sql(query) + @property + def chromosomes(self): + """Lazily fetch the chromosomes""" + chromosomes = OrderedDict() + if self.species is not None: + query = ( + "SELECT Chr_Length.Name, Chr_Length.OrderId, Length " + "FROM Chr_Length, Species WHERE " + "Chr_Length.SpeciesId = Species.SpeciesId AND " + "Species.Name = " + "'%s' ORDER BY OrderId" % self.species.capitalize()) + else: + query = ( + "SELECT Chr_Length.Name, Chr_Length.OrderId, " + "Length FROM Chr_Length, InbredSet WHERE " + "Chr_Length.SpeciesId = InbredSet.SpeciesId AND " + "InbredSet.Name = " + "'%s' ORDER BY OrderId" % self.dataset.group.name) results = g.db.execute(query).fetchall() - for item in results: - self.chromosomes[item.OrderId] = IndChromosome( + chromosomes[item.OrderId] = IndChromosome( item.Name, item.Length) + return chromosomes diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py new file mode 100644 index 00000000..9b5c023c --- /dev/null +++ b/wqflask/tests/unit/base/test_species.py @@ -0,0 +1,116 @@ +"""Tests wqflask/base/species.py""" + +import unittest +from unittest import mock +from base.species import TheSpecies +from base.species import IndChromosome +from base.species import Chromosomes +from collections import OrderedDict +from wqflask import app +from dataclasses import dataclass + + +@dataclass +class MockChromosome: + OrderId: int + Name: str + Length: int + + +@dataclass +class MockGroup: + name: str + + +@dataclass +class MockDataset: + group: MockGroup + + +class TestTheSpecies(unittest.TestCase): + """Tests for TheSpecies class""" + @mock.patch('base.species.Chromosomes') + def test_create_species_with_null_species_name(self, mock_chromosome): + """Test that TheSpecies is instantiated correctly when the +species_name is provided.""" + mock_chromosome.return_value = 1 + test_species = TheSpecies(dataset="random_dataset", species_name="a") + self.assertEqual(test_species.name, "a") + self.assertEqual(test_species.chromosomes, 1) + + @mock.patch('base.species.Chromosomes') + def test_create_species_with_species_name(self, mock_chromosome): + """Test that TheSpecies is instantiated correctly when the +species_name is not provided.""" + mock_chromosome.return_value = 1 + test_species = TheSpecies(dataset="random_dataset") + self.assertEqual(test_species.dataset, "random_dataset") + self.assertEqual(test_species.chromosomes, 1) + mock_chromosome.assert_called_once_with(dataset="random_dataset") + + +class TestIndChromosome(unittest.TestCase): + """Tests for IndChromosome class""" + + def test_create_ind_chromosome(self): + """Test that IndChromosome is instantiated correctly""" + test_ind_chromosome = IndChromosome(name="Test", length=10000000) + self.assertEqual(test_ind_chromosome.name, "Test") + self.assertEqual(test_ind_chromosome.length, 10000000) + self.assertEqual(test_ind_chromosome.mb_length, 10) + + +class TestChromosomes(unittest.TestCase): + """Tests for Chromosomes class""" + maxDiff = None + + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("base.species.g") + def test_create_chromosomes_with_no_species(self, mock_db): + """Test instantiating a chromosome without a species""" + mock_db.db.execute.return_value.fetchall.return_value = [ + MockChromosome(1, "X", 100), + MockChromosome(2, "Y", 1000), + MockChromosome(3, "Z", 10000), + ] + mock_dataset = MockDataset(MockGroup("Random")) + test_chromosomes = Chromosomes(dataset=mock_dataset) + self.assertEqual( + list(test_chromosomes.chromosomes.keys()), + [1, 2, 3] + ) + self.assertEqual(test_chromosomes.dataset, mock_dataset) + mock_db.db.execute.assert_called_with( + "SELECT Chr_Length.Name, Chr_Length.OrderId, Length " + "FROM Chr_Length, InbredSet WHERE " + "Chr_Length.SpeciesId = InbredSet.SpeciesId AND " + "InbredSet.Name = 'Random' ORDER BY OrderId" + ) + + @mock.patch("base.species.g") + def test_create_chromosomes_with_species(self, mock_db): + """Test instantiating a chromosome with a species""" + mock_db.db.execute.return_value.fetchall.return_value = [ + MockChromosome(1, "X", 100), + MockChromosome(2, "Y", 1000), + MockChromosome(3, "Z", 10000), + ] + mock_dataset = MockDataset(MockGroup("Random")) + test_chromosomes = Chromosomes(dataset=mock_dataset, + species="testSpecies") + self.assertEqual( + list(test_chromosomes.chromosomes.keys()), + [1, 2, 3] + ) + mock_db.db.execute.assert_called_with( + "SELECT Chr_Length.Name, Chr_Length.OrderId, Length " + "FROM Chr_Length, Species WHERE " + "Chr_Length.SpeciesId = Species.SpeciesId AND " + "Species.Name = 'Testspecies' ORDER BY OrderId" + ) diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index e65b36e4..7f4ec1bc 100644 --- a/wqflask/wqflask/api/gen_menu.py +++ b/wqflask/wqflask/api/gen_menu.py @@ -178,12 +178,12 @@ def build_datasets(species, group, type_name): elif type_name == "Genotypes": results = g.db.execute( - ("SELECT InfoFiles.GN_AccesionId " + + ("SELECT InfoFiles.GN_AccesionId " "FROM InfoFiles, GenoFreeze, InbredSet " - + "WHERE InbredSet.Name = '{}' AND " - + "GenoFreeze.InbredSetId = InbredSet.Id AND " - + "InfoFiles.InfoPageName = GenoFreeze.ShortName " - + "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone() + "WHERE InbredSet.Name = '{}' AND " + "GenoFreeze.InbredSetId = InbredSet.Id AND " + "InfoFiles.InfoPageName = GenoFreeze.ShortName " + "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone() dataset_id = "None" if bool(results): |