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81 lines
3.8 KiB
Python
81 lines
3.8 KiB
Python
import os
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import shutil
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import tarfile
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import tempfile
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from contextlib import contextmanager
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from galaxy.tools.repositories import ValidationContext
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from galaxy.util import galaxy_directory
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from tool_shed.tools.tool_validator import ToolValidator
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from ..unittest_utils.galaxy_mock import MockApp
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BISMARK_TAR = os.path.join(galaxy_directory(), 'lib/tool_shed/test/test_data/bismark/bismark.tar')
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BOWTIE2_INDICES = os.path.join(galaxy_directory(), 'lib/tool_shed/test/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample')
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def test_validate_valid_tool():
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with get_tool_validator() as tv, setup_bismark() as repo_dir:
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full_path = os.path.join(repo_dir, 'bismark_methylation_extractor.xml')
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tool, valid, message = tv.load_tool_from_config(repository_id=None,
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full_path=full_path)
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assert tool.name == 'Bismark'
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assert not tool.params_with_missing_data_table_entry
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assert not tool.params_with_missing_index_file
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assert valid is True
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assert message is None
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def test_tool_validation_denies_allow_codefile():
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with get_tool_validator() as tv, setup_bismark() as repo_dir:
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full_path = os.path.join(repo_dir, 'bismark_methylation_extractor.xml')
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tool, valid, message = tv.load_tool_from_config(repository_id=None,
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full_path=full_path)
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assert tool._allow_code_files is False
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def test_validate_tool_without_index():
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with get_tool_validator() as tv, setup_bismark() as repo_dir:
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full_path = os.path.join(repo_dir, 'bismark_bowtie2_wrapper.xml')
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tool, valid, message = tv.load_tool_from_config(repository_id=None,
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full_path=full_path)
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assert valid is True
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# tool is missing a data table
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assert tool.params_with_missing_data_table_entry
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# check input parameters, which will set up the missing data table (if present in repo_dir)
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invalid_files_and_errors_tups = tv.check_tool_input_params(repo_dir=os.path.dirname(full_path),
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tool_config_name=full_path,
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tool=tool,
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sample_files=[])
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# tool is invalid because loc file is not present, but data table is present now
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assert len(invalid_files_and_errors_tups) == 1
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assert invalid_files_and_errors_tups[0][1].startswith('This file refers to a file named')
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assert not tool.params_with_missing_data_table_entry
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assert tool.params_with_missing_index_file
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# copy a loc file
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shutil.copy(BOWTIE2_INDICES, repo_dir)
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tool, valid, message, sample_files = tv.handle_sample_files_and_load_tool_from_disk(repo_dir, None, full_path, repo_dir)
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invalid_files_and_errors_tups = tv.check_tool_input_params(repo_dir=repo_dir,
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tool_config_name=full_path,
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tool=tool,
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sample_files=sample_files)
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# no parameters should be missing
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assert len(invalid_files_and_errors_tups) == 0
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assert not tool.params_with_missing_data_table_entry
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assert not tool.params_with_missing_index_file
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@contextmanager
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def setup_bismark():
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repo_dir = tempfile.mkdtemp()
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with tarfile.open(BISMARK_TAR) as archive:
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archive.extractall(repo_dir)
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yield repo_dir
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shutil.rmtree(repo_dir, ignore_errors=True)
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@contextmanager
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def get_tool_validator():
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app = MockApp()
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with ValidationContext.from_app(app) as validation_context:
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yield ToolValidator(validation_context)
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