mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
c35d8f2a06
Also: - Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected by pytest only because they were `unittest.TestCase` derived, but normally pytest collects only test classes whose name starts with `Test`, see https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
112 lines
4.1 KiB
Python
112 lines
4.1 KiB
Python
import os
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import tempfile
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from unittest.mock import patch
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from galaxy.exceptions import (
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ObjectNotFound,
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ReferenceDataError,
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)
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from galaxy_test.driver import integration_util
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BUILDS_DATA = (
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"?\tunspecified (?)",
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"hg_test\tdescription of hg_test",
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"hg_test_nolen\tdescription of hg_test_nolen",
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)
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LEN_DATA = (
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"chr1\t248956422",
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"chr2\t242193529",
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"chr3\t198295559",
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)
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def get_key(has_len_file=True):
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pos = 1 if has_len_file else 2
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return BUILDS_DATA[pos].split("\t")[0]
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class TestGenomes(integration_util.IntegrationTestCase):
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@classmethod
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def handle_galaxy_config_kwds(cls, config):
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super().handle_galaxy_config_kwds(config)
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genomes_dir = cls.temp_config_dir("test_genomes")
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os.makedirs(genomes_dir)
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cls._setup_builds_file(config, genomes_dir)
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cls._setup_len_file(config, genomes_dir)
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@classmethod
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def _setup_builds_file(cls, config, genomes_dir):
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"""Create builds file + set config option."""
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builds_file_path = os.path.join(genomes_dir, "builds.txt")
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config["builds_file_path"] = builds_file_path
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with open(builds_file_path, "w") as f:
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f.write("\n".join(BUILDS_DATA))
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@classmethod
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def _setup_len_file(cls, config, genomes_dir):
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"""Create len file + set config option."""
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config["len_file_path"] = genomes_dir # the config option is a dir
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key = get_key()
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len_file_path = os.path.join(genomes_dir, f"{key}.len")
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with open(len_file_path, "w") as f:
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f.write("\n".join(LEN_DATA))
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def test_index(self):
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response = self._get("genomes")
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self._assert_status_code_is(response, 200)
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rval = response.json()
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expected_data = [item.split("\t")[::-1] for item in BUILDS_DATA]
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assert rval == expected_data
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def test_show_valid(self):
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key = get_key()
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response = self._get(f"genomes/{key}")
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self._assert_status_code_is(response, 200)
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rval = response.json()
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assert rval["id"] == key
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assert len(rval["chrom_info"]) == len(LEN_DATA)
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def test_show_valid_no_refdata(self):
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key = get_key(has_len_file=False)
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response = self._get(f"genomes/{key}")
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self._assert_status_code_is(response, 500)
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assert response.json()["err_code"] == ReferenceDataError.err_code.code
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def test_show_invalid(self):
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response = self._get("genomes/invalid")
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self._assert_status_code_is(response, 404)
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assert response.json()["err_code"] == ObjectNotFound.err_code.code
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def test_sequences(self):
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class RefDataMock:
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sequence = "test-value"
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key = get_key()
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with patch.object(self._app.genomes, "has_reference_data", return_value=True), patch.object(
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self._app.genomes, "_get_reference_data", return_value=RefDataMock()
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):
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response = self._get(f"genomes/{key}/sequences")
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self._assert_status_code_is(response, 200)
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assert response.content == bytes(RefDataMock.sequence, "utf-8")
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def test_sequences_no_data(self):
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key = get_key()
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with patch.object(self._app.genomes, "has_reference_data", return_value=False):
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response = self._get(f"genomes/{key}/sequences")
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self._assert_status_code_is(response, 500)
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assert response.json()["err_code"] == ReferenceDataError.err_code.code
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def test_indexes(self):
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mock_key, mock_content, index_type, suffix = "mykey", "mydata", "fasta_indexes", ".fai"
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# write some data to a tempfile
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with tempfile.NamedTemporaryFile(dir=self._tempdir, suffix=suffix, mode="w", delete=False) as tf:
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tf.write(mock_content)
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# make a mock containing the path to the tempfile
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tmpfile_path = tf.name[: -len(suffix)] # chop off the extention
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mock_data = [[mock_key, tmpfile_path]]
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with patch.object(self._app.tool_data_tables.data_tables[index_type], "data", new=mock_data):
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response = self._get(f"genomes/{mock_key}/indexes?type={index_type}")
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self._assert_status_code_is(response, 200)
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assert response.content == bytes(mock_content, "utf-8")
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