mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
John Chilton
ac18cbe978
Instead of writing out the tools on startup (a more expensive operation than reading), just read the existing files in. Add new abstraction to the tool panel to reduce some otherwise duplicated code. Testing: The following two API tests should cover the modified behavior, they verify that metadata is still detectable and that history import and export still works. ``` ./run_tests.sh -api test/api/test_histories.py:HistoriesApiTestCase.test_import_export ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_rdata_not_decompressed ```
432 lines
14 KiB
Python
432 lines
14 KiB
Python
from math import isinf
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import os
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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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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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if not os.path.isabs(source_file_name):
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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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else:
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path = source_file_name
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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 = os.path.join(os.getcwd(), "lib/galaxy/tools/imp_exp/exp_history_to_archive.xml")
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source_contents = None
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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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