mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
John Chilton
f91012244b
The galaxy-tool-shed-schema package is basically pydantic models for the whole tool shed API. It is used by both the backend code for the new tool shed and the testing code that runs on both the old and new tool shed. The creation of galaxy-tool-util-models package is something I've wanted to do for a while - it should solve some TODOs I've left in the base. I think beyond enabling galaxy-tool-shed-schema package - the other nice thing is that galaxy-schema code can now rely on various tool stuff without requiring dependency on any of the parser or runtime code. This should also fix things for the new record types in #19377. I've introduced a type that can be used tools and is included schema for collection creation. The galaxy-tool-util-models packages can now be dependended on by galaxy-schema and galaxy-tool-util and these two packages do not need to depend on each other - either direction of that dependency would make me uncomfortable. xref https://github.com/galaxyproject/galaxy/actions/runs/13704893929/job/38327692654?pr=19377
247 lines
12 KiB
Python
247 lines
12 KiB
Python
import sys
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from string import Template
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import lxml.etree as ET
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import pytest
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from pydantic import ValidationError
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from galaxy.tool_util.verify.codegen import galaxy_xsd_path
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from galaxy.tool_util.verify.parse import assertion_xml_els_to_models
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from galaxy.tool_util_models.assertions import assertion_list
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from galaxy.util.commands import shell
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from galaxy.util.unittest_utils import skip_unless_executable
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valid_assertions = [
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{"that": "has_size", "size": "5G"},
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{"that": "has_size", "size": 1},
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{"that": "has_size", "size": "5Mi"},
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{"that": "has_text", "text": "JBrowseDefaultMainPage"},
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{"that": "has_line", "line": "'>Wildtype Staphylococcus aureus strain WT.'"},
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{"that": "has_n_columns", "n": 2},
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{"that": "is_valid_xml"},
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{"that": "has_element_with_path", "path": "//el"},
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{"that": "has_n_elements_with_path", "path": "//el", "n": 4},
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{"that": "element_text_matches", "expression": "foob[a]r", "path": "//el"},
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{"that": "element_text_is", "text": "foobar", "path": "//el"},
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{
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"that": "xml_element",
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"path": "./elem/more[2]",
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"children": [{"that": "has_text_matching", "expression": "foo$"}],
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},
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{"that": "xml_element", "path": "./elem/more[2]"},
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{"that": "element_text", "path": "./elem/more[2]", "children": [{"that": "has_text", "text": "foo"}]},
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{"that": "has_json_property_with_value", "property": "foobar", "value": "'6'"},
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{"that": "has_json_property_with_text", "property": "foobar", "text": "cowdog"},
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{"that": "has_archive_member", "path": ".*/my-file.txt"},
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{"that": "has_archive_member", "path": ".*/my-file.txt", "children": [{"that": "has_text", "text": "1235abc"}]},
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{"that": "has_image_width", "width": 560},
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{"that": "has_image_width", "width": 560, "delta": 490},
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{"that": "has_image_height", "height": 560, "delta": 490},
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{"that": "has_image_height", "min": 45, "max": 90},
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{"that": "has_image_channels", "channels": 3},
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{"that": "has_image_channels", "channels": 3, "delta": 1},
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{"that": "has_image_channels", "min": 1, "max": 4},
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{"that": "has_image_channels", "min": 1, "max": 4, "negate": True},
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{"that": "has_image_mean_intensity", "mean_intensity": 3.4},
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{"that": "has_image_mean_intensity", "mean_intensity": 3.4, "eps": 0.2},
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{"that": "has_image_mean_intensity", "mean_intensity": 3.4, "eps": 0.2, "channel": 1},
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{"that": "has_image_mean_intensity", "min": 0.4, "max": 0.6, "channel": 1},
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{"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34"},
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{"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34", "channel": 1},
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{"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34", "channel": 1, "eps": 0.2},
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{"that": "has_image_n_labels", "n": 85},
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{"that": "has_image_n_labels", "labels": [1, 3, 4]},
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{"that": "has_image_n_labels", "n": 9, "exclude_labels": [1, 3, 4]},
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{"that": "has_image_n_labels", "n": 9, "exclude_labels": [1, 3, 4], "negate": True},
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{"that": "has_image_mean_object_size", "mean_object_size": 9, "exclude_labels": [1, 3, 4]},
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{"that": "has_image_mean_object_size", "mean_object_size": 9, "labels": [1, 3, 4]},
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{"that": "has_image_mean_object_size", "mean_object_size": 9, "channel": 1, "eps": 0.2},
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{"that": "has_json_property_with_value", "property": "skipped_columns", "value": "[1, 3, 5]"},
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{"that": "has_json_property_with_text", "property": "color", "text": "red"},
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{"that": "has_n_columns", "n": 30},
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{"that": "has_n_columns", "n": 30, "delta": 4},
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{"that": "has_n_columns", "n": 30, "delta": 4, "sep": " ", "comment": "####"},
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]
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valid_xml_assertions = [
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"""<has_size value="5G" />""",
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"""<has_size size="5G" />""",
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"""<has_size size="5G" />""",
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"""<has_text text="JBrowseDefaultMainPage" />""",
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"""<has_line line="'>Wildtype Staphylococcus aureus strain WT.'" />""",
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"""<xml_element path="./elem/more[2]" attribute="name"><has_text_matching expression="foo$"/></xml_element>""",
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"""<xml_element path="./elem/more[2]" attribute="name"></xml_element>""",
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"""<element_text path="./elem/more[2]"><has_text text="foo" /></element_text>""",
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"""<has_element_with_path path="BlastOutput_param/Parameters/Parameters_matrix" />""",
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r"""<element_text_matches path="BlastOutput_version" expression="BLASTP\s+2\.2.*"/>""",
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"""<element_text_is path="BlastOutput_program" text="blastp" />""",
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r"""<attribute_matches path="outerElement/innerElement2" attribute="foo2" expression="bar\d+" />""",
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"""<element_text path="BlastOutput_iterations/Iteration/Iteration_hits/Hit/Hit_def"><not_has_text text="EDK72998.1" /></element_text>""",
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"""<has_archive_member path=".*/my-file.txt"><not_has_text text="EDK72998.1"/></has_archive_member>""",
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"""<has_archive_member path=".*/my-file.txt"></has_archive_member>""",
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"""<has_image_n_labels n="85" />""",
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"""<has_image_center_of_mass center_of_mass="511.07, 223.34" />""",
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"""<has_image_center_of_mass center_of_mass="511.07, 223.34" eps=".2" />""",
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"""<has_image_mean_intensity mean_intensity="0.83" />""",
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"""<has_image_height height="512" delta="2" />""",
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"""<has_image_width width="512" delta="2" />""",
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"""<has_image_channels channels="3" />""",
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"""<has_image_channels channels="3" delta="1" />""",
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"""<has_image_channels min="3" max="5" />""",
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"""<has_image_channels min="3" max="5" negate="true" />""",
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"""<has_json_property_with_value property="skipped_columns" value="[1, 3, 5]" />""",
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"""<has_json_property_with_text property="color" text="red" />""",
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"""<has_n_columns n="30" />""",
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"""<has_n_columns n="30" delta="4" />""",
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"""<has_n_columns n="30" delta="4" sep=" " comment="###" />""",
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"""<has_image_width min="500" />""",
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"""<has_image_height min="500" />""",
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]
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invalid_assertions = [
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{"that": "has_size", "size": "5Gigabytes"},
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# negative sizes not allowed
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{"that": "has_size", "size": -1},
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{"that": "has_n_columns", "n": [2]},
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{"that": "has_n_columns", "n": -2},
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{"that": "is_valid_xml_foo"},
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{"that": "has_element_with_path", "path": 45},
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{"that": "has_n_elements_with_path", "n": 4},
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{"that": "has_n_elements_with_path", "n": -4},
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{"that": "element_text_matches", "expression": 12, "path": "//el"},
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# unclosed regex group
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{"that": "element_text_matches", "expression": "[12", "path": "//el"},
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{"that": "xml_element", "path": "./elem/more[2]", "children": [{"that": "foobar"}]},
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{
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"that": "xml_element",
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"path": "./elem/more[2]",
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"children": [{"that": "has_text_matching", "line": "invalidprop"}],
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},
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# must specify children for element_text
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{"that": "element_text", "path": "./elem/more[2]"},
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{"that": "has_json_property_with_value", "property": 42, "value": "cowdog"},
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{"that": "has_json_property_with_text", "property": "foobar", "text": 6},
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{"that": "has_archive_member", "path": ".*/my-file.txt", "extra": "param"},
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{"that": "has_archive_member", "path": ".*/my-file.txt", "children": [{"that": "invalid"}]},
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{"that": "has_image_width", "width": "560"},
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{"that": "has_image_width", "width": -560},
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{"that": "has_image_width", "width": 560, "delta": "wrong"},
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{"that": "has_image_height", "height": -560},
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{"that": "has_image_center_of_mass", "center_of_mass": "511.07, 223.34, foobar"},
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{"that": "has_image_center_of_mass", "center_of_mass": "511.07"},
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{"that": "has_image_center_of_mass", "center_of_mass": "511.07, cow"},
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# negative mean object sizes are not allowed
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{"that": "has_image_n_labels", "n": -85},
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{"that": "has_image_n_labels", "n": 85, "delta": -3},
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# negative mean object sizes are not allowed
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{"that": "has_image_mean_object_size", "mean_object_size": -9, "exclude_labels": [1, 3, 4]},
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{"that": "has_image_mean_object_size", "mean_object_size": -9.0, "exclude_labels": [1, 3, 4]},
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{"that": "has_image_mean_object_size", "mean_object_size": 9, "exclude_labels": [1, 3, 4], "eps": -0.2},
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# looks a little odd in JSON but value is JSON loaded so must be a string
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{"that": "has_json_property_with_value", "property": "skipped_columns", "value": [1, 3, 5]},
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# missing property
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{"that": "has_json_property_with_value", "property": "skipped_columns"},
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{"that": "has_json_property_with_text", "property": "color"},
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{"that": "has_n_columns", "n": 30, "delta": "wrongtype"},
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{"that": "has_n_columns", "n": 30, "delta": -2},
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{"that": "has_n_columns", "n": 30, "delta": 4, "sep": " ", "comment": "####", "extra": "param"},
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invalid_xml_assertions = [
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"""<has_n_columns n="cow" />""",
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"""<has_text line="JBrowseDefaultMainPage" />""",
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"""<has_line text="JBrowseDefaultMainPage" />""",
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# at least one child assertion is required here...
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"""<element_text path="./elem/more[2]"></element_text>""",
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"""<has_archive_member path=".*/my-file.txt"><not_has_text line="EDK72998.1"/></has_archive_member>""",
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"""<has_archive_member path=".*/my-file.txt"><foobar /></has_archive_member>""",
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"""<has_image_center_of_mass center_of_mass="511.07, 223.34" extra="param" />""",
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"""<has_image_center_of_mass center_of_mass="511.07, 223.34" eps="foobar" />""",
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# negative numbers not allowed
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"""<has_image_n_labels n="-85" />""",
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"""<has_image_n_labels n="85" delta="-3" />""",
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"""<has_image_mean_intensity mean_intensity="not_a_number" />""",
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"""<has_image_mean_intensity mean_intensity=".83" extra="param" />""",
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"""<has_image_height height="512" delta="notanumber" />""",
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"""<has_image_width width="512" delta="2" extra="param" />""",
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"""<has_image_height height="512" delta="-2" />""",
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"""<has_image_width width="512" delta="-2" />""",
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"""<has_image_height height="-512" />""",
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"""<has_image_width width="-512" />""",
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"""<has_image_channels channels="3" exclude="wrong" />""",
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"""<has_image_channels channels="3" delta="not_a_number" />""",
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"""<has_image_channels min="3" max="5" foo="bar" />""",
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"""<has_image_channels min="3" max="5" negate="NOTABOOLEAN" />""",
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# missing required arguments...
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"""<has_json_property_with_value property="skipped_columns" />""",
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"""<has_json_property_with_text property="color" />""",
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"""<has_n_columns n="30" delta="wrong_type" />""",
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"""<has_n_columns n="30" delta="4" sep=" " comment="###" extra="param"/>""",
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TOOL_TEMPLATE = Template(
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"""
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<tool id="gx_test" name="gx_test" version="1.0.0">
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<command><![CDATA[
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echo '$parameter' >> '$output'
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]]></command>
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<inputs>
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<param name="parameter" value="1" type="integer" />
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</inputs>
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<outputs>
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<data name="output" format="txt" />
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</outputs>
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<tests>
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<test>
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<param name="parameter" value_json="12456" />
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<output name="output">
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<assert_contents>
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$assertion_xml
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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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</tool>
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"""
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)
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if sys.version_info < (3, 8): # noqa: UP036
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pytest.skip(reason="Pydantic assertion models require python3.8 or higher", allow_module_level=True)
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def test_valid_json_models_validate():
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assertion_list.model_validate(valid_assertions)
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def test_invalid_json_models_do_not_validate():
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for invalid_assertion in invalid_assertions:
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with pytest.raises(ValidationError):
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assertion_list.model_validate([invalid_assertion])
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@skip_unless_executable("xmllint")
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def test_valid_xsd(tmp_path):
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for assertion_xml in valid_xml_assertions:
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tool_xml = TOOL_TEMPLATE.safe_substitute(assertion_xml=assertion_xml)
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tool_path = tmp_path / "tool.xml"
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tool_path.write_text(tool_xml)
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ret = shell(["xmllint", "--nowarning", "--noout", "--schema", galaxy_xsd_path, str(tool_path)])
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assert ret == 0, f"{assertion_xml} failed to validate"
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@skip_unless_executable("xmllint")
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def test_invalid_xsd(tmp_path):
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for assertion_xml in invalid_xml_assertions:
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tool_xml = TOOL_TEMPLATE.safe_substitute(assertion_xml=assertion_xml)
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tool_path = tmp_path / "tool.xml"
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tool_path.write_text(tool_xml)
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ret = shell(["xmllint", "--nowarning", "--noout", "--schema", galaxy_xsd_path, str(tool_path)])
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assert ret != 0, f"{assertion_xml} validated when error expected"
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def test_valid_xml_models_validate_after_json_transform():
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for assertion_xml in valid_xml_assertions:
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assertion_xml_els_to_models([ET.fromstring(assertion_xml)])
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