mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
2bf10821c0
Keep the refgenie stuff in Galaxy's app package because it brings in additional dependencies. This is a small part of a larger ongoing project to cleanup tool shed dependencies and allow tool shed repository installations with minimal dependencies.
164 lines
4.3 KiB
Python
164 lines
4.3 KiB
Python
import pytest
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from galaxy.tool_util.data import ToolDataTableManager
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LOC_ALPHA_CONTENTS = """
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data1 data1name ${__HERE__}/data1/entry.txt
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data2 data2name ${__HERE__}/data2/entry.txt
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"""
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LOC_ALPHA_CONTENTS_V2 = """
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data1 data1name ${__HERE__}/data1/entry.txt
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data2 data2name ${__HERE__}/data2/entry.txt
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data3 data3name ${__HERE__}/data3/entry.txt
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"""
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LOC_BETA_CONTENTS_1 = """
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beta1 beta1name ${__HERE__}/beta1/entry.txt
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"""
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LOC_BETA_CONTENTS_2 = """
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beta2 beta2name ${__HERE__}/beta2/entry.txt
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"""
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TOOL_DATA_TABLE_CONF_XML = """<tables>
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<table name="testalpha" comment_char="#">
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<columns>value, name, path</columns>
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<file path="${__HERE__}/testalpha.loc" />
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</table>
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</tables>
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"""
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MERGED_TOOL_DATA_TABLE_CONF_XML_1 = """<tables>
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<table name="testbeta" comment_char="#">
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<columns>value, name, path</columns>
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<file path="${__HERE__}/testbeta1.loc" />
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</table>
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</tables>
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"""
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MERGED_TOOL_DATA_TABLE_CONF_XML_2 = """<tables>
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<table name="testbeta" comment_char="#">
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<columns>value, name, path</columns>
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<file path="${__HERE__}/testbeta2.loc" />
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</table>
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</tables>
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"""
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@pytest.fixture
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def tdt_manager(tmp_path) -> ToolDataTableManager:
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_write_loc_files(tmp_path)
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conf = tmp_path / "tool_data_table_conf.xml"
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conf.write_text(TOOL_DATA_TABLE_CONF_XML)
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return ToolDataTableManager(tmp_path, conf)
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@pytest.fixture
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def merged_tdt_manager(tmp_path) -> ToolDataTableManager:
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_write_loc_files(tmp_path)
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conf1 = tmp_path / "tool_data_table_conf_1.xml"
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conf1.write_text(MERGED_TOOL_DATA_TABLE_CONF_XML_1)
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conf2 = tmp_path / "tool_data_table_conf_2.xml"
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conf2.write_text(MERGED_TOOL_DATA_TABLE_CONF_XML_2)
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return ToolDataTableManager(tmp_path, f"{conf1},{conf2}")
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def _write_loc_files(tmp_path):
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loc1 = tmp_path / "testalpha.loc"
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loc1.write_text(LOC_ALPHA_CONTENTS)
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loc2 = tmp_path / "testbeta1.loc"
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loc2.write_text(LOC_BETA_CONTENTS_1)
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loc3 = tmp_path / "testbeta2.loc"
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loc3.write_text(LOC_BETA_CONTENTS_2)
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data1 = tmp_path / "data1"
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data1.mkdir()
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data1_entry = data1 / "entry.txt"
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data1_entry.write_text("This is data 1.")
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data2 = tmp_path / "data2"
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data2.mkdir()
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data2_entry = data2 / "entry.txt"
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data2_entry.write_text("This is data 2.")
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data3 = tmp_path / "data3"
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data3.mkdir()
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data3_entry = data3 / "entry.txt"
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data3_entry.write_text("This is data 3.")
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beta1 = tmp_path / "beta1"
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beta1.mkdir()
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beta1_entry = beta1 / "entry.txt"
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beta1_entry.write_text("This is beta 1.")
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beta2 = tmp_path / "beta2"
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beta2.mkdir()
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beta2_entry = beta2 / "entry.txt"
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beta2_entry.write_text("This is beta 2.")
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def test_data_tables_as_dictionary(tdt_manager):
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assert "testalpha" in tdt_manager.data_tables
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assert "testdelta" not in tdt_manager.data_tables
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def test_to_dict(tdt_manager):
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as_dict = tdt_manager.to_dict()
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assert "testalpha" in as_dict
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assert "testdelta" not in as_dict
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testalpha_as_dict = as_dict["testalpha"]
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assert "columns" in testalpha_as_dict
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def test_index(tdt_manager):
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index = tdt_manager.index()
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assert len(index.__root__) >= 1
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entry = index.find_entry("testalpha")
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assert entry
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entry = index.find_entry("testomega")
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assert not entry
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def test_reload(tdt_manager, tmp_path):
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assert len(tdt_manager["testalpha"].data) == 2
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loc1 = tmp_path / "testalpha.loc"
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loc1.write_text(LOC_ALPHA_CONTENTS_V2)
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tdt_manager.reload_tables()
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assert len(tdt_manager["testalpha"].data) == 3
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def test_reload_by_path(tdt_manager, tmp_path):
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assert len(tdt_manager["testalpha"].data) == 2
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loc1 = tmp_path / "testalpha.loc"
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loc1.write_text(LOC_ALPHA_CONTENTS_V2)
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tdt_manager.reload_tables(path=str(loc1))
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assert len(tdt_manager["testalpha"].data) == 3
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def test_reload_by_name(tdt_manager, tmp_path):
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assert len(tdt_manager["testalpha"].data) == 2
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loc1 = tmp_path / "testalpha.loc"
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loc1.write_text(LOC_ALPHA_CONTENTS_V2)
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tdt_manager.reload_tables("testalpha")
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assert len(tdt_manager["testalpha"].data) == 3
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def test_merging_tables(merged_tdt_manager):
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assert len(merged_tdt_manager["testbeta"].data) == 2
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def test_to_json(merged_tdt_manager, tmp_path):
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json_path = tmp_path / "as_json.json"
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assert not json_path.exists()
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merged_tdt_manager.to_json(json_path)
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assert json_path.exists()
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