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synced 2026-09-24 16:30:27 +08:00
make linter test xml more minimal
ie include only the tested features
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@@ -12,20 +12,13 @@ from galaxy.tool_util.linters import (
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from galaxy.tool_util.parser.xml import XmlToolSource
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from galaxy.util import etree
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# tests tool xml for general linter
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WHITESPACE_IN_VERSIONS_AND_NAMES = """
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<tool name=" BWA Mapper " id="bwa tool" version=" 1.0.1 " display_interface="true" require_login="true" hidden="true">
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<description>The BWA Mapper</description>
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<requirements>
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<requirement type="package" version=" 1.2.5 "> bwa </requirement>
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</requirements>
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<version_command interpreter="python">bwa.py --version</version_command>
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<inputs>
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<param name="select_fd_op" type="select">
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<options from_dataset="xyz"/>
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<options from_data_table="xyz"/>
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<option value="x">x</option>
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</param>
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</inputs>
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</tool>
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"""
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@@ -36,21 +29,12 @@ REQUIREMENT_WO_VERSION = """
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<requirement type="package">bwa</requirement>
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<requirement type="package" version="1.2.5"></requirement>
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</requirements>
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<version_command interpreter="python">bwa.py --version</version_command>
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<inputs>
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<param name="select_fd_op" type="select">
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<options from_dataset="xyz"/>
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<options from_data_table="xyz"/>
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<option value="x">x</option>
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</param>
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</inputs>
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</tool>
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"""
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NO_SECTIONS_XML = """
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<tool name="BWA Mapper" id="bwa" version="1.0.1" 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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# test tool xml for inputs linter
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NO_INPUTS_SECTION_XML = """
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<tool>
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</tool>
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"""
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@@ -63,9 +47,7 @@ INPUTS_REDUNDANT_NAME = """
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"""
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NO_WHEN_IN_CONDITIONAL_XML = """
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<tool name="BWA Mapper" id="bwa" version="1.0.1" 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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<tool>
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<inputs>
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<conditional name="labels">
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<param name="label_select" type="select" label="Points to label">
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@@ -119,9 +101,7 @@ SELECT_DUPLICATED_OPTIONS_WITH_DIFF_SELECTED = """
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"""
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SELECT_DEPRECATIONS = """
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<tool name="BWA Mapper" id="bwa" version="1.0.1" 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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<tool>
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<inputs>
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<param name="select_do" type="select" dynamic_options="blah()"/>
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<param name="select_ff" type="select">
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@@ -215,12 +195,12 @@ VALIDATOR_CORRECT = """
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</tool>
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"""
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# test tool xml for outputs linter
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# check that linter accepts format source for collection elements as means to specify format
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# and that the linter warns if format and format_source are used
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OUTPUTS_COLLECTION_FORMAT_SOURCE = """
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<tool name="BWA Mapper" id="bwa" version="1.0.1" 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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<tool>
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<outputs>
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<collection name="output_collection" type="paired">
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<data name="forward" format_source="input_readpair" />
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@@ -232,9 +212,7 @@ OUTPUTS_COLLECTION_FORMAT_SOURCE = """
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# check that linter does not complain about missing format if from_tool_provided_metadata is used
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OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA = """
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<tool name="BWA Mapper" id="bwa" version="1.0.1" 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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<tool>
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<outputs>
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<data name="output">
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<discover_datasets from_tool_provided_metadata="true"/>
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@@ -309,7 +287,7 @@ TESTS = [
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and len(x.warn_messages) == 1 and len(x.error_messages) == 1
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),
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(
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NO_SECTIONS_XML, inputs.lint_inputs,
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NO_INPUTS_SECTION_XML, inputs.lint_inputs,
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lambda x:
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'Found no input parameters.' in x.warn_messages
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and len(x.warn_messages) == 1 and len(x.error_messages) == 0
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