mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
Nicola Soranzo
30f60493c3
with manual fixes to 3 files to make them compatible with black 22.12.0 . We need to keep black pinned at `<23` until we vendorise `packaging`, since the new version of black depends on `packaging >=22.0` which is the version where `LegacyVersion` (which we use for tool lineages) was removed.
74 lines
1.8 KiB
Python
74 lines
1.8 KiB
Python
import pytest
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from galaxy.model.unittest_utils import GalaxyDataTestApp
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from galaxy.tool_util.parser import get_tool_source
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from galaxy.tool_util.parser.cwl import CwlToolSource
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from galaxy.tools import create_tool_from_source
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XML_TOOL = """
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<tool id="tool_id" name="xml tool" version="1"/>
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"""
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CWL_TOOL = """
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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inputs:
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message:
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type: string
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inputBinding:
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position: 1
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outputs: []
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"""
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YAML_TOOL = """
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id: simple_constructs_y
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name: simple_constructs_y
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version: 1.0
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command:
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>
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echo "$booltest" >> $out_file1;
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inputs:
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- name: booltest
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type: boolean
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truevalue: booltrue
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falsevalue: boolfalse
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checked: false
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outputs:
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out_file1:
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format: txt
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"""
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class ToolApp(GalaxyDataTestApp):
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name = "galaxy"
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biotools_metadata_source = None
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job_search = None
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@pytest.fixture
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def tool_app():
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return ToolApp()
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def _deserialize(app, tool_source_class, raw_tool_source):
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tool_source = get_tool_source(tool_source_class=tool_source_class, raw_tool_source=raw_tool_source)
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assert type(tool_source).__name__ == tool_source_class
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return create_tool_from_source(app, tool_source=tool_source)
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def test_deserialize_xml_tool(tool_app):
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tool = _deserialize(tool_app, tool_source_class="XmlToolSource", raw_tool_source=XML_TOOL)
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assert tool.id == "tool_id"
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assert tool.name == "xml tool"
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def test_deserialize_yaml_tool(tool_app):
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tool = _deserialize(tool_app, tool_source_class="YamlToolSource", raw_tool_source=YAML_TOOL)
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assert tool.id == "simple_constructs_y"
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assert tool.name == "simple_constructs_y"
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def test_deserialize_cwl_tool(tool_app):
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# Can't verify much about cwl tools at this point
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tool_source = get_tool_source(tool_app, tool_source_class="CwlToolSource", raw_tool_source=CWL_TOOL)
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assert isinstance(tool_source, CwlToolSource)
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