mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-13 00:44:55 +08:00
John Chilton
0fe2b601ce
If present, it can be one of
- "default", no-op fallback to stdio tags and erroring on standard error output.
- "exit_code", error if tool exit code is not 0. (The @jmchilton recommendation).
- "aggressive", error if tool exit code is not 0 or either Exception: or Error: appears in standard error/output. (The @bgruening recommendation).
Refactoring and unit/functional tests to support and demonstrate this.
Run functional test with:
./run_tests.sh -framework -id detect_errors_aggressive
Run relevant unit tests:
nosetests test/unit/tools/test_parsing.py
Updated from original version to reflect comments on pull request #117 - in particular the ``detect_errors`` tag was moved from ``tool`` to ``command``.
429 lines
14 KiB
Python
429 lines
14 KiB
Python
from math import isinf
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import os.path
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import tempfile
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import shutil
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from galaxy.tools.parser.factory import get_tool_source
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from galaxy.tools.imp_exp import EXPORT_HISTORY_TEXT
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import unittest
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TOOL_XML_1 = """
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<tool name="BWA Mapper" id="bwa" version="1.0.1" is_multi_byte="true" display_interface="true" require_login="true" hidden="true">
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<description>The BWA Mapper</description>
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<version_command interpreter="python">bwa.py --version</version_command>
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<parallelism method="multi" split_inputs="input1" split_mode="to_size" split_size="1" merge_outputs="out_file1" />
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<command interpreter="python">bwa.py --arg1=42</command>
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<requirements>
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<container type="docker">mycool/bwa</container>
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<requirement type="package" version="1.0">bwa</requirement>
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</requirements>
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<outputs>
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<data name="out1" format="bam" from_work_dir="out1.bam" />
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</outputs>
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<stdio>
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<exit_code range="1:" level="fatal" />
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</stdio>
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<help>This is HELP TEXT1!!!</help>
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<tests>
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<test>
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<param name="foo" value="5" />
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<output name="out1" file="moo.txt" />
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</test>
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<test>
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<param name="foo" value="5">
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</param>
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<output name="out1" lines_diff="4" compare="sim_size">
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<metadata name="dbkey" value="hg19" />
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</output>
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</test>
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</tests>
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</tool>
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"""
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TOOL_YAML_1 = """
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name: "Bowtie Mapper"
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id: bowtie
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version: 1.0.2
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description: "The Bowtie Mapper"
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command: "bowtie_wrapper.pl --map-the-stuff"
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interpreter: "perl"
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runtime_version:
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command: "bowtie --version"
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requirements:
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- type: package
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name: bwa
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version: 1.0.1
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containers:
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- type: docker
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identifier: "awesome/bowtie"
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outputs:
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out1:
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format: bam
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from_work_dir: out1.bam
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inputs:
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- name: input1
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type: integer
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min: 7
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max: 8
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- name: moo
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label: cow
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type: repeat
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blocks:
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- name: nestinput
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type: data
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- name: nestsample
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type: text
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help:
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This is HELP TEXT2!!!
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tests:
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- inputs:
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foo: 5
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outputs:
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out1: moo.txt
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- inputs:
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foo:
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value: 5
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outputs:
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out1:
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lines_diff: 4
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compare: sim_size
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"""
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class BaseLoaderTestCase(unittest.TestCase):
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def setUp(self):
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self.temp_directory = tempfile.mkdtemp()
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def tearDown(self):
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shutil.rmtree(self.temp_directory)
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@property
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def _tool_source(self):
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return self._get_tool_source()
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def _get_tool_source(self, source_file_name=None, source_contents=None):
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if source_file_name is None:
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source_file_name = self.source_file_name
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if source_contents is None:
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source_contents = self.source_contents
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path = os.path.join(self.temp_directory, source_file_name)
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open(path, "w").write(source_contents)
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tool_source = get_tool_source(path)
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return tool_source
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class XmlLoaderTestCase(BaseLoaderTestCase):
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source_file_name = "bwa.xml"
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source_contents = TOOL_XML_1
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def test_version(self):
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assert self._tool_source.parse_version() == "1.0.1"
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def test_id(self):
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assert self._tool_source.parse_id() == "bwa"
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def test_module_and_type(self):
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assert self._tool_source.parse_tool_module() is None
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assert self._tool_source.parse_tool_type() is None
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def test_name(self):
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assert self._tool_source.parse_name() == "BWA Mapper"
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def test_is_multi_byte(self):
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assert self._tool_source.parse_is_multi_byte()
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def test_display_interface(self):
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assert self._tool_source.parse_display_interface(False)
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def test_require_login(self):
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assert self._tool_source.parse_require_login(False)
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def test_parse_request_param_translation_elem(self):
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assert self._tool_source.parse_request_param_translation_elem() is None
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def test_command_parsing(self):
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assert self._tool_source.parse_command() == "bwa.py --arg1=42"
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assert self._tool_source.parse_interpreter() == "python"
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def test_descripting_parsing(self):
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assert self._tool_source.parse_description() == "The BWA Mapper"
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def test_version_command(self):
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assert self._tool_source.parse_version_command() == "bwa.py --version"
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assert self._tool_source.parse_version_command_interpreter() == "python"
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def test_parallelism(self):
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parallelism_info = self._tool_source.parse_parallelism()
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assert parallelism_info.method == "multi"
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assert parallelism_info.attributes["split_inputs"] == "input1"
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def test_hidden(self):
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assert self._tool_source.parse_hidden()
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def test_action(self):
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assert self._tool_source.parse_action_module() is None
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def test_requirements(self):
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requirements, containers = self._tool_source.parse_requirements_and_containers()
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assert requirements[0].type == "package"
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assert containers[0].identifier == "mycool/bwa"
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def test_outputs(self):
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outputs, output_collections = self._tool_source.parse_outputs(object())
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assert len(outputs) == 1
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assert len(output_collections) == 0
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def test_stdio(self):
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exit, regexes = self._tool_source.parse_stdio()
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assert len(exit) == 1
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assert len(regexes) == 0
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assert exit[0].range_start == 1
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assert isinf(exit[0].range_end)
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def test_help(self):
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help_text = self._tool_source.parse_help()
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assert help_text.strip() == "This is HELP TEXT1!!!"
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def test_tests(self):
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tests_dict = self._tool_source.parse_tests_to_dict()
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tests = tests_dict["tests"]
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assert len(tests) == 2
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test_dict = tests[0]
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inputs = test_dict["inputs"]
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assert len(inputs) == 1
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input1 = inputs[0]
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assert input1[0] == "foo"
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assert input1[1] == "5"
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outputs = test_dict["outputs"]
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assert len(outputs) == 1
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output1 = outputs[0]
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assert output1[0] == 'out1'
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assert output1[1] == 'moo.txt'
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attributes1 = output1[2]
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assert attributes1["compare"] == "diff"
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assert attributes1["lines_diff"] == 0
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test2 = tests[1]
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outputs = test2["outputs"]
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assert len(outputs) == 1
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output2 = outputs[0]
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assert output2[0] == 'out1'
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assert output2[1] is None
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attributes1 = output2[2]
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assert attributes1["compare"] == "sim_size"
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assert attributes1["lines_diff"] == 4
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def test_exit_code(self):
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tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
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<command detect_errors="exit_code">
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ls
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</command>
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</tool>
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""")
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exit, regexes = tool_source.parse_stdio()
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assert len(exit) == 2, exit
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assert len(regexes) == 0, regexes
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tool_source = self._get_tool_source(source_contents="""<tool id="bwa" name="bwa">
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<command detect_errors="aggressive">
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ls
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</command>
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</tool>
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""")
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exit, regexes = tool_source.parse_stdio()
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assert len(exit) == 2, exit
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assert len(regexes) == 2, regexes
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class YamlLoaderTestCase(BaseLoaderTestCase):
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source_file_name = "bwa.yml"
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source_contents = TOOL_YAML_1
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def test_version(self):
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assert self._tool_source.parse_version() == "1.0.2"
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def test_id(self):
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assert self._tool_source.parse_id() == "bowtie"
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def test_module_and_type(self):
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# These just rely on defaults
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assert self._tool_source.parse_tool_module() is None
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assert self._tool_source.parse_tool_type() is None
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def test_name(self):
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assert self._tool_source.parse_name() == "Bowtie Mapper"
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def test_is_multi_byte(self):
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assert not self._tool_source.parse_is_multi_byte()
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def test_display_interface(self):
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assert not self._tool_source.parse_display_interface(False)
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assert self._tool_source.parse_display_interface(True)
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def test_require_login(self):
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assert not self._tool_source.parse_require_login(False)
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def test_parse_request_param_translation_elem(self):
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assert self._tool_source.parse_request_param_translation_elem() is None
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def test_command_parsing(self):
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assert self._tool_source.parse_command() == "bowtie_wrapper.pl --map-the-stuff"
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assert self._tool_source.parse_interpreter() == "perl"
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def test_parse_redirect_url_params_elem(self):
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assert self._tool_source.parse_redirect_url_params_elem() is None
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def test_descripting_parsing(self):
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assert self._tool_source.parse_description() == "The Bowtie Mapper"
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def test_version_command(self):
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assert self._tool_source.parse_version_command() == "bowtie --version"
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assert self._tool_source.parse_version_command_interpreter() is None
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def test_parallelism(self):
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assert self._tool_source.parse_parallelism() is None
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def test_hidden(self):
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assert not self._tool_source.parse_hidden()
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def test_action(self):
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assert self._tool_source.parse_action_module() is None
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def test_requirements(self):
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requirements, containers = self._tool_source.parse_requirements_and_containers()
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assert requirements[0].type == "package"
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assert requirements[0].name == "bwa"
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assert containers[0].identifier == "awesome/bowtie"
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def test_outputs(self):
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outputs, output_collections = self._tool_source.parse_outputs(object())
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assert len(outputs) == 1
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assert len(output_collections) == 0
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def test_stdio(self):
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exit, regexes = self._tool_source.parse_stdio()
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assert len(exit) == 2
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assert isinf(exit[0].range_start)
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assert exit[0].range_start == float("-inf")
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assert exit[1].range_start == 1
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assert isinf(exit[1].range_end)
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def test_help(self):
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help_text = self._tool_source.parse_help()
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assert help_text.strip() == "This is HELP TEXT2!!!"
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def test_inputs(self):
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input_pages = self._tool_source.parse_input_pages()
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assert input_pages.inputs_defined
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page_sources = input_pages.page_sources
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assert len(page_sources) == 1
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page_source = page_sources[0]
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input_sources = page_source.parse_input_sources()
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assert len(input_sources) == 2
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def test_tests(self):
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tests_dict = self._tool_source.parse_tests_to_dict()
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tests = tests_dict["tests"]
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assert len(tests) == 2
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test_dict = tests[0]
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inputs = test_dict["inputs"]
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assert len(inputs) == 1
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input1 = inputs[0]
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assert input1[0] == "foo"
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assert input1[1] == 5
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outputs = test_dict["outputs"]
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assert len(outputs) == 1
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output1 = outputs[0]
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assert output1[0] == 'out1'
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assert output1[1] == 'moo.txt'
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attributes1 = output1[2]
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assert attributes1["compare"] == "diff"
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assert attributes1["lines_diff"] == 0
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test2 = tests[1]
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outputs = test2["outputs"]
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assert len(outputs) == 1
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output2 = outputs[0]
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assert output2[0] == 'out1'
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assert output2[1] is None
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attributes1 = output2[2]
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assert attributes1["compare"] == "sim_size"
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assert attributes1["lines_diff"] == 4
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class DataSourceLoaderTestCase(BaseLoaderTestCase):
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source_file_name = "ds.xml"
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source_contents = """<?xml version="1.0"?>
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<tool name="YeastMine" id="yeastmine" tool_type="data_source">
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<description>server</description>
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<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
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<inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get">
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<display>go to yeastMine server $GALAXY_URL</display>
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</inputs>
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<request_param_translation>
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<request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
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<value_translation>
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<value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
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</value_translation>
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</request_param>
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</request_param_translation>
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<!-- Following block doesn't really belong here - not sure what block is suppose to do actually cannot
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find actual usage. -->
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<redirect_url_params>cow</redirect_url_params>
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<uihints minwidth="800"/>
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<outputs>
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<data name="output" format="txt" />
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</outputs>
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<options sanitize="False" refresh="True"/>
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</tool>
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"""
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def test_tool_type(self):
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assert self._tool_source.parse_tool_type() == "data_source"
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def test_parse_request_param_translation_elem(self):
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assert self._tool_source.parse_request_param_translation_elem() is not None
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def test_redirect_url_params_elem(self):
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assert self._tool_source.parse_redirect_url_params_elem() is not None
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def test_parallelism(self):
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assert self._tool_source.parse_parallelism() is None
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def test_hidden(self):
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assert not self._tool_source.parse_hidden()
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class SpecialToolLoaderTestCase(BaseLoaderTestCase):
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source_file_name = "export.xml"
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source_contents = EXPORT_HISTORY_TEXT
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def test_tool_type(self):
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tool_module = self._tool_source.parse_tool_module()
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# Probably we don't parse_tool_module any more? -
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# tool_type seems sufficient.
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assert tool_module[0] == "galaxy.tools"
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assert tool_module[1] == "ExportHistoryTool"
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assert self._tool_source.parse_tool_type() == "export_history"
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def test_is_multi_byte(self):
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assert not self._tool_source.parse_is_multi_byte()
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def test_version_command(self):
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assert self._tool_source.parse_version_command() is None
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assert self._tool_source.parse_version_command_interpreter() is None
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def test_action(self):
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action = self._tool_source.parse_action_module()
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assert action[0] == "galaxy.tools.actions.history_imp_exp"
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assert action[1] == "ExportHistoryToolAction"
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