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jmchiltonjmchilton
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Make lint --conda_requirements check that an actual requirement is found.
Add test cases .
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+90
-4
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5 files changed

+90
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‎planemo/linters/conda_requirements.py‎

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@@ -10,6 +10,10 @@
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def lint_requirements_in_conda(tool_source, lint_ctx):
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"""Check requirements of tool source against best practice Conda channels."""
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conda_targets = tool_source_conda_targets(tool_source)
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if not conda_targets:
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lint_ctx.warn("No valid package requirement tags found to check against Conda.")
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return
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for conda_target in conda_targets:
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(best_hit, exact) = best_search_result(conda_target, channels_override=BEST_PRACTICE_CHANNELS)
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conda_target_str = conda_target.package

‎tests/data/tools/bwa_invalid_version.xml‎

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<tool id="bwa" name="BWA" version="0.1.0">
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<requirements>
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<requirement type="package" version="0.4.12">bwa</requirement>
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</requirements>
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<stdio>
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<exit_code range="2:" />
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</stdio>
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<command><![CDATA[
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bwa > $output_1 2>&1
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]]></command>
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<inputs>
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<param name="ignored" type="text" value="the default" />
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</inputs>
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<outputs>
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<data name="output_1" format="txt" />
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</outputs>
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<tests>
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<test>
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<output name="output_1">
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<assert_contents>
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<has_text text="Version: 0.7.10" />
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</assert_contents>
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</output>
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</test>
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</tests>
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<help><![CDATA[
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BWA is a mapper.
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]]></help>
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<citations>
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<citation type="doi">10.1093/bioinformatics/btp324</citation>
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<citation type="doi">10.1093/bioinformatics/btp698</citation>
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</citations>
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</tool>

‎tests/data/tools/bwa_without_requirements.xml‎

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<tool id="bwa" name="BWA" version="0.1.0">
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<stdio>
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<exit_code range="2:" />
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</stdio>
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<command><![CDATA[
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bwa > $output_1 2>&1
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]]></command>
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<inputs>
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<param name="ignored" type="text" value="the default" />
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</inputs>
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<outputs>
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<data name="output_1" format="txt" />
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</outputs>
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<tests>
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<test>
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<output name="output_1">
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<assert_contents>
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<has_text text="Version: 0.7.10" />
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</assert_contents>
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</output>
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</test>
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</tests>
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<help><![CDATA[
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BWA is a mapper.
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]]></help>
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<citations>
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<citation type="doi">10.1093/bioinformatics/btp324</citation>
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<citation type="doi">10.1093/bioinformatics/btp698</citation>
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</citations>
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</tool>

‎tests/data/tools/bwa_wrong_version.xml‎

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@@ -9,13 +9,11 @@
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bwa > $output_1 2>&1
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]]></command>
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<inputs>
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<param name="ignored" type="text" value="the default" />
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</inputs>
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<outputs>
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<data name="output_1" />
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<data name="output_1" format="txt" />
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</outputs>
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<help><![CDATA[
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TODO: Fill in help.
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]]></help>
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<tests>
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<test>
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<output name="output_1">
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</output>
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</test>
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</tests>
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<help><![CDATA[
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BWA is a mapper.
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]]></help>
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<citations>
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<citation type="doi">10.1093/bioinformatics/btp324</citation>
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<citation type="doi">10.1093/bioinformatics/btp698</citation>
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</citations>
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</tool>

‎tests/test_lint.py‎

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@@ -69,3 +69,17 @@ def test_lint_doi(self):
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fail_doi = os.path.join(TEST_TOOLS_DIR, "invalid_doi.xml")
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lint_cmd = ["lint", "--doi", fail_doi]
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self._check_exit_code(lint_cmd, exit_code=1)
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def test_lint_conda_requirements_empty(self):
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bwa_no_reqs = os.path.join(TEST_TOOLS_DIR, "bwa_without_requirements.xml")
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lint_cmd = ["lint", bwa_no_reqs]
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self._check_exit_code(lint_cmd)
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lint_cmd = ["lint", "--conda_requirements", bwa_no_reqs]
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self._check_exit_code(lint_cmd, exit_code=1)
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def test_lint_conda_requirements_wrong_version(self):
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bwa_wrong_version = os.path.join(TEST_TOOLS_DIR, "bwa_invalid_version.xml")
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lint_cmd = ["lint", bwa_wrong_version]
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self._check_exit_code(lint_cmd)
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lint_cmd = ["lint", "--conda_requirements", bwa_wrong_version]
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self._check_exit_code(lint_cmd, exit_code=1)

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