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Merge pull request #23105 from jmchilton/tool_schema_apis

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Implement more tool validation APIs in Galaxy to mirror the Tool Shed.
This commit is contained in:
Marius van den Beek
2026-07-17 15:46:56 +02:00
committed by GitHub
parent 1d7d5d707a f2ecbfaa58
commit 1a688b60c4
7 changed files with 870 additions and 5 deletions
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client/packages/api-client/src/schema/schema.ts
+637 -4
View File
@@ -5644,6 +5644,23 @@ export interface paths {
patch?: never;
trace?: never;
};
"/api/tools/{tool_id}/interop": {
parameters: {
query?: never;
header?: never;
path?: never;
cookie?: never;
};
/** Return Galaxy's meta model description of the tool's metadata, inputs, and outputs. */
get: operations["tools__interop"];
put?: never;
post?: never;
delete?: never;
options?: never;
head?: never;
patch?: never;
trace?: never;
};
"/api/tools/{tool_id}/parameter_landing_request_schema": {
parameters: {
query?: never;
@@ -5698,6 +5715,74 @@ export interface paths {
patch?: never;
trace?: never;
};
"/api/tools/{tool_id}/versions/{tool_version}/interop": {
parameters: {
query?: never;
header?: never;
path?: never;
cookie?: never;
};
/** Return Galaxy's meta model description of the tool's metadata, inputs, and outputs. */
get: operations["tools__versioned_interop"];
put?: never;
post?: never;
delete?: never;
options?: never;
head?: never;
patch?: never;
trace?: never;
};
"/api/tools/{tool_id}/versions/{tool_version}/parameter_landing_request_schema": {
parameters: {
query?: never;
header?: never;
path?: never;
cookie?: never;
};
/** Return a JSON schema description of the tool's inputs for the tool landing request API. */
get: operations["tools__versioned_parameter_landing_request_schema"];
put?: never;
post?: never;
delete?: never;
options?: never;
head?: never;
patch?: never;
trace?: never;
};
"/api/tools/{tool_id}/versions/{tool_version}/parameter_request_schema": {
parameters: {
query?: never;
header?: never;
path?: never;
cookie?: never;
};
/** Return a JSON schema description of the tool's inputs for the tool request API. */
get: operations["tools__versioned_parameter_request_schema"];
put?: never;
post?: never;
delete?: never;
options?: never;
head?: never;
patch?: never;
trace?: never;
};
"/api/tools/{tool_id}/versions/{tool_version}/parameter_test_case_xml_schema": {
parameters: {
query?: never;
header?: never;
path?: never;
cookie?: never;
};
/** Return a JSON schema description of the tool's inputs for test case construction. */
get: operations["tools__versioned_parameter_test_case_xml_schema"];
put?: never;
post?: never;
delete?: never;
options?: never;
head?: never;
patch?: never;
trace?: never;
};
"/api/tours": {
parameters: {
query?: never;
@@ -20036,6 +20121,18 @@ export interface components {
*/
output_name: string | null;
};
/** PackageRequirement */
PackageRequirement: {
/** Name */
name: string;
/**
* Type
* @constant
*/
type: "package";
/** Version */
version?: string | null;
};
/**
* PageContentFormat
* @enum {string}
@@ -20479,6 +20576,79 @@ export interface components {
*/
workbook_type: "datasets" | "collection" | "collections";
};
/** ParsedTool */
ParsedTool: {
/** Citations */
citations: components["schemas"]["Citation"][];
/** Containers */
containers?: components["schemas"]["Container"][];
/** Description */
description: string | null;
/** Edam Operations */
edam_operations: string[];
/** Edam Topics */
edam_topics: string[];
help: components["schemas"]["HelpContent"] | null;
/** Id */
id: string;
/** Inputs */
inputs: (
| components["schemas"]["CwlIntegerParameterModel"]
| components["schemas"]["CwlFloatParameterModel"]
| components["schemas"]["CwlStringParameterModel"]
| components["schemas"]["CwlBooleanParameterModel"]
| components["schemas"]["CwlNullParameterModel"]
| components["schemas"]["CwlFileParameterModel"]
| components["schemas"]["CwlDirectoryParameterModel"]
| components["schemas"]["CwlUnionParameterModel"]
| components["schemas"]["TextParameterModel"]
| components["schemas"]["IntegerParameterModel"]
| components["schemas"]["FloatParameterModel"]
| components["schemas"]["BooleanParameterModel"]
| components["schemas"]["HiddenParameterModel"]
| components["schemas"]["SelectParameterModel"]
| components["schemas"]["DataParameterModel"]
| components["schemas"]["DataCollectionParameterModel"]
| components["schemas"]["DataColumnParameterModel"]
| components["schemas"]["DirectoryUriParameterModel"]
| components["schemas"]["RulesParameterModel"]
| components["schemas"]["DrillDownParameterModel"]
| components["schemas"]["GroupTagParameterModel"]
| components["schemas"]["BaseUrlParameterModel"]
| components["schemas"]["GenomeBuildParameterModel"]
| components["schemas"]["ColorParameterModel"]
| components["schemas"]["ConditionalParameterModel"]
| components["schemas"]["RepeatParameterModel"]
| components["schemas"]["SectionParameterModel"]
)[];
/** License */
license: string | null;
/** Name */
name: string;
/** Outputs */
outputs: (
| components["schemas"]["ToolOutputDataset"]
| components["schemas"]["ToolOutputCollection"]
| components["schemas"]["ToolOutputText"]
| components["schemas"]["ToolOutputInteger"]
| components["schemas"]["ToolOutputFloat"]
| components["schemas"]["ToolOutputBoolean"]
)[];
/** Profile */
profile: string | null;
/** Requirements */
requirements?: (
| components["schemas"]["PackageRequirement"]
| components["schemas"]["SetEnvironmentRequirement"]
| components["schemas"]["ResourceRequirement"]
| components["schemas"]["JavascriptRequirement"]
)[];
stdio?: components["schemas"]["Stdio"];
/** Version */
version: string | null;
/** Xrefs */
xrefs: components["schemas"]["XrefDict-Output"][];
};
/** ParsedWorkbook */
ParsedWorkbook: {
/** Extra Columns */
@@ -22476,6 +22646,16 @@ export interface components {
*/
version: string;
};
/** SetEnvironmentRequirement */
SetEnvironmentRequirement: {
/** Environment */
environment: string;
/**
* Type
* @constant
*/
type: "set_environment";
};
/** SetSlugPayload */
SetSlugPayload: {
/**
@@ -22934,6 +23114,37 @@ export interface components {
| "CANCELED"
| "CANCELING"
| "PREEMPTED";
/** Stdio */
Stdio: {
/** Exit Codes */
exit_codes?: components["schemas"]["StdioExitCode"][];
/** Regexes */
regexes?: components["schemas"]["StdioRegex"][];
};
/** StdioExitCode */
StdioExitCode: {
/** Desc */
desc?: string | null;
/** Error Level */
error_level: number;
/** Range End */
range_end: number | ("-inf" | "inf");
/** Range Start */
range_start: number | ("-inf" | "inf");
};
/** StdioRegex */
StdioRegex: {
/** Desc */
desc?: string | null;
/** Error Level */
error_level: number;
/** Match */
match: string;
/** Stderr Match */
stderr_match: boolean;
/** Stdout Match */
stdout_match: boolean;
};
/** StepReferenceByLabel */
StepReferenceByLabel: {
/**
@@ -24472,6 +24683,191 @@ export interface components {
*/
uuid: string;
};
/** ToolOutputBoolean */
ToolOutputBoolean: {
/**
* Hidden
* @description If true, the output will not be shown in the history.
*/
hidden: boolean;
/**
* Label
* @description Output label. Will be used as dataset name in history.
*/
label?: string | null;
/**
* Name
* @description Parameter name. Used when referencing parameter in workflows.
*/
name: string;
/**
* @description discriminator enum property added by openapi-typescript
* @enum {string}
*/
type: "boolean";
};
/** ToolOutputCollection */
ToolOutputCollection: {
/** Collection Type */
collection_type?: string | null;
/** Collection Type From Rules */
collection_type_from_rules?: string | null;
/** Collection Type Source */
collection_type_source?: string | null;
/** Discover Datasets */
discover_datasets?:
| (
| components["schemas"]["FilePatternDatasetCollectionDescription"]
| components["schemas"]["ToolProvidedMetadataDatasetCollection"]
)[]
| null;
/**
* Hidden
* @description If true, the output will not be shown in the history.
*/
hidden: boolean;
/**
* Label
* @description Output label. Will be used as dataset name in history.
*/
label?: string | null;
/**
* Name
* @description Parameter name. Used when referencing parameter in workflows.
*/
name: string;
/** Structured Like */
structured_like?: string | null;
/**
* @description discriminator enum property added by openapi-typescript
* @enum {string}
*/
type: "collection";
};
/** ToolOutputDataset */
ToolOutputDataset: {
/** Discover Datasets */
discover_datasets?:
| (
| components["schemas"]["FilePatternDatasetCollectionDescription"]
| components["schemas"]["ToolProvidedMetadataDatasetCollection"]
)[]
| null;
/**
* Format
* @description The short name for the output datatype.
*/
format: string;
/**
* Format Source
* @description This sets the data type of the output dataset(s) to be the same format as that of the specified tool input.
*/
format_source?: string | null;
/**
* from_work_dir
* @description Relative path to a file produced by the tool in its working directory. Output’s contents are set to this file’s contents.
*/
from_work_dir?: string | null;
/**
* Hidden
* @description If true, the output will not be shown in the history.
*/
hidden: boolean;
/**
* Label
* @description Output label. Will be used as dataset name in history.
*/
label?: string | null;
/**
* Metadata Source
* @description This copies the metadata information from the tool’s input dataset to serve as default for information that cannot be detected from the output. One prominent use case is interval data with a non-standard column order that cannot be deduced from a header line, but which is known to be identical in the input and output datasets.
*/
metadata_source?: string | null;
/**
* Name
* @description Parameter name. Used when referencing parameter in workflows.
*/
name: string;
/**
* Precreate Directory
* @default false
*/
precreate_directory: boolean | null;
/**
* @description discriminator enum property added by openapi-typescript
* @enum {string}
*/
type: "data";
};
/** ToolOutputFloat */
ToolOutputFloat: {
/**
* Hidden
* @description If true, the output will not be shown in the history.
*/
hidden: boolean;
/**
* Label
* @description Output label. Will be used as dataset name in history.
*/
label?: string | null;
/**
* Name
* @description Parameter name. Used when referencing parameter in workflows.
*/
name: string;
/**
* @description discriminator enum property added by openapi-typescript
* @enum {string}
*/
type: "float";
};
/** ToolOutputInteger */
ToolOutputInteger: {
/**
* Hidden
* @description If true, the output will not be shown in the history.
*/
hidden: boolean;
/**
* Label
* @description Output label. Will be used as dataset name in history.
*/
label?: string | null;
/**
* Name
* @description Parameter name. Used when referencing parameter in workflows.
*/
name: string;
/**
* @description discriminator enum property added by openapi-typescript
* @enum {string}
*/
type: "integer";
};
/** ToolOutputText */
ToolOutputText: {
/**
* Hidden
* @description If true, the output will not be shown in the history.
*/
hidden: boolean;
/**
* Label
* @description Output label. Will be used as dataset name in history.
*/
label?: string | null;
/**
* Name
* @description Parameter name. Used when referencing parameter in workflows.
*/
name: string;
/**
* @description discriminator enum property added by openapi-typescript
* @enum {string}
*/
type: "text";
};
/** ToolProvidedMetadataDatasetCollection */
ToolProvidedMetadataDatasetCollection: {
/**
@@ -26016,7 +26412,7 @@ export interface components {
*/
version: string;
/** xrefs */
xrefs?: components["schemas"]["XrefDict"][] | null;
xrefs?: components["schemas"]["XrefDict-Input"][] | null;
};
/**
* UserToolSource
@@ -26123,7 +26519,7 @@ export interface components {
*/
version: string;
/** xrefs */
xrefs?: components["schemas"]["XrefDict"][] | null;
xrefs?: components["schemas"]["XrefDict-Output"][] | null;
};
/** UserUpdatePayload */
UserUpdatePayload: {
@@ -27299,12 +27695,19 @@ export interface components {
target_uri: string;
};
/** XrefDict */
XrefDict: {
"XrefDict-Input": {
/** type */
type: string;
/** value */
value: string;
};
/** XrefDict */
"XrefDict-Output": {
/** Type */
type: string;
/** Value */
value: string;
};
/** XrefItem */
XrefItem: {
/**
@@ -27927,7 +28330,7 @@ export interface components {
*/
version?: string | null;
/** xrefs */
xrefs?: components["schemas"]["XrefDict"][] | null;
xrefs?: components["schemas"]["XrefDict-Input"][] | null;
};
/**
* YamlToolTest
@@ -48920,6 +49323,52 @@ export interface operations {
};
};
};
tools__interop: {
parameters: {
query?: {
tool_version?: string | null;
};
header?: {
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
"run-as"?: string | null;
};
path: {
/** @description The tool ID for the lineage stored in Galaxy's toolbox. */
tool_id: string;
};
cookie?: never;
};
requestBody?: never;
responses: {
/** @description Successful Response */
200: {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["ParsedTool"];
};
};
/** @description Request Error */
"4XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
/** @description Server Error */
"5XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
};
};
tools__parameter_landing_request_schema: {
parameters: {
query?: {
@@ -49058,6 +49507,190 @@ export interface operations {
};
};
};
tools__versioned_interop: {
parameters: {
query?: never;
header?: {
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
"run-as"?: string | null;
};
path: {
/** @description The tool ID for the lineage stored in Galaxy's toolbox. */
tool_id: string;
/** @description The full version string defined on the Galaxy tool wrapper. */
tool_version: string;
};
cookie?: never;
};
requestBody?: never;
responses: {
/** @description Successful Response */
200: {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["ParsedTool"];
};
};
/** @description Request Error */
"4XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
/** @description Server Error */
"5XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
};
};
tools__versioned_parameter_landing_request_schema: {
parameters: {
query?: never;
header?: {
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
"run-as"?: string | null;
};
path: {
/** @description The tool ID for the lineage stored in Galaxy's toolbox. */
tool_id: string;
/** @description The full version string defined on the Galaxy tool wrapper. */
tool_version: string;
};
cookie?: never;
};
requestBody?: never;
responses: {
/** @description Successful Response */
200: {
headers: {
[name: string]: unknown;
};
content: {
"application/json": unknown;
};
};
/** @description Request Error */
"4XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
/** @description Server Error */
"5XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
};
};
tools__versioned_parameter_request_schema: {
parameters: {
query?: never;
header?: {
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
"run-as"?: string | null;
};
path: {
/** @description The tool ID for the lineage stored in Galaxy's toolbox. */
tool_id: string;
/** @description The full version string defined on the Galaxy tool wrapper. */
tool_version: string;
};
cookie?: never;
};
requestBody?: never;
responses: {
/** @description Successful Response */
200: {
headers: {
[name: string]: unknown;
};
content: {
"application/json": unknown;
};
};
/** @description Request Error */
"4XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
/** @description Server Error */
"5XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
};
};
tools__versioned_parameter_test_case_xml_schema: {
parameters: {
query?: never;
header?: {
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
"run-as"?: string | null;
};
path: {
/** @description The tool ID for the lineage stored in Galaxy's toolbox. */
tool_id: string;
/** @description The full version string defined on the Galaxy tool wrapper. */
tool_version: string;
};
cookie?: never;
};
requestBody?: never;
responses: {
/** @description Successful Response */
200: {
headers: {
[name: string]: unknown;
};
content: {
"application/json": unknown;
};
};
/** @description Request Error */
"4XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
/** @description Server Error */
"5XX": {
headers: {
[name: string]: unknown;
};
content: {
"application/json": components["schemas"]["MessageExceptionModel"];
};
};
};
};
index_api_tours_get: {
parameters: {
query?: never;
lib/galaxy/tools/__init__.py
+14
View File
@@ -82,6 +82,7 @@ from galaxy.tool_util.loader import (
template_macro_params,
)
from galaxy.tool_util.loader_directory import looks_like_a_tool
from galaxy.tool_util.model_factory import parse_tool
from galaxy.tool_util.ontologies.ontology_data import (
biotools_reference,
expand_ontology_data,
@@ -132,6 +133,7 @@ from galaxy.tool_util.version import (
parse_version,
)
from galaxy.tool_util.version_updates import WORKFLOW_SAFE_TOOL_VERSION_UPDATES
from galaxy.tool_util_models import ParsedTool
from galaxy.tool_util_models.parameters import (
MaybeToolParameterBundle,
ToolParameterBundleModel,
@@ -203,6 +205,7 @@ from galaxy.util import (
in_directory,
Params,
parse_xml_string,
parse_xml_string_to_etree,
rst_to_html,
string_as_bool,
unicodify,
@@ -1101,6 +1104,17 @@ class Tool(UsesDictVisibleKeys, MaybeToolParameterBundle):
def history_manager(self):
return self.app.history_manager
def parsed_tool(self) -> ParsedTool:
"""Return a ParsedTool model for this tool.
After tool loading, mem_optimize destroys the XML tree to save memory.
When that has happened, re-parse from the stored string representation.
"""
tool_source = self.tool_source
if getattr(tool_source, "root", None) is None:
tool_source = get_tool_source(xml_tree=parse_xml_string_to_etree(tool_source.to_string()))
return parse_tool(tool_source)
@property
def _view(self):
return self.app.dependency_resolvers_view
lib/galaxy/webapps/galaxy/api/tools.py
+91 -1
View File
@@ -64,6 +64,7 @@ from galaxy.tool_util.parameters import (
from galaxy.tool_util.verify import ToolTestDescriptionDict
from galaxy.tool_util_models import (
lift_user_tool_source,
ParsedTool,
UserToolSource,
)
from galaxy.tools.evaluation import global_tool_errors
@@ -92,7 +93,10 @@ from galaxy.webapps.base.controller import UsesVisualizationMixin
from galaxy.webapps.base.webapp import GalaxyWebTransaction
from galaxy.webapps.galaxy.api.common import serve_workbook
from galaxy.webapps.galaxy.services.base import tool_request_detailed_to_model
from galaxy.webapps.galaxy.services.tools import ToolsService
from galaxy.webapps.galaxy.services.tools import (
get_tool,
ToolsService,
)
from . import (
APIContentTypeRoute,
as_form,
@@ -152,6 +156,11 @@ ToolIDPathParam: str = Path(
title="Tool ID",
description="The tool ID for the lineage stored in Galaxy's toolbox.",
)
ToolVersionPathParam: str = Path(
...,
title="Tool Version",
description="The full version string defined on the Galaxy tool wrapper.",
)
ToolVersionQueryParam: str | None = Query(default=None, title="Tool Version", description="")
@@ -433,6 +442,87 @@ class FetchTools:
def tool_tags(self, trans: ProvidesHistoryContext = DependsOnTrans) -> dict[str, list[str]]:
return self.service.curated_tool_tags_by_id(trans)
@router.get(
"/api/tools/{tool_id}/interop",
operation_id="tools__interop",
summary="Return Galaxy's meta model description of the tool's metadata, inputs, and outputs.",
)
def parsed_tool(
self,
tool_id: str = ToolIDPathParam,
tool_version: str | None = ToolVersionQueryParam,
trans: ProvidesHistoryContext = DependsOnTrans,
) -> ParsedTool:
return self._parsed_tool(trans, tool_id, tool_version)
@router.get(
"/api/tools/{tool_id}/versions/{tool_version}/interop",
operation_id="tools__versioned_interop",
summary="Return Galaxy's meta model description of the tool's metadata, inputs, and outputs.",
)
def parsed_tool_versioned(
self,
tool_id: str = ToolIDPathParam,
tool_version: str = ToolVersionPathParam,
trans: ProvidesHistoryContext = DependsOnTrans,
) -> ParsedTool:
return self._parsed_tool(trans, tool_id, tool_version)
@router.get(
"/api/tools/{tool_id}/versions/{tool_version}/parameter_request_schema",
operation_id="tools__versioned_parameter_request_schema",
summary="Return a JSON schema description of the tool's inputs for the tool request API.",
)
def tool_state_request_versioned(
self,
tool_id: str = ToolIDPathParam,
tool_version: str = ToolVersionPathParam,
trans: ProvidesHistoryContext = DependsOnTrans,
) -> Response:
tool_run_ref = ToolRunReference(tool_id=tool_id, tool_version=tool_version, tool_uuid=None)
inputs = self.service.inputs(trans, tool_run_ref)
return json_schema_response_for_tool_state_model(RequestToolState, inputs)
@router.get(
"/api/tools/{tool_id}/versions/{tool_version}/parameter_landing_request_schema",
operation_id="tools__versioned_parameter_landing_request_schema",
summary="Return a JSON schema description of the tool's inputs for the tool landing request API.",
)
def tool_state_landing_request_versioned(
self,
tool_id: str = ToolIDPathParam,
tool_version: str = ToolVersionPathParam,
trans: ProvidesHistoryContext = DependsOnTrans,
) -> Response:
tool_run_ref = ToolRunReference(tool_id=tool_id, tool_version=tool_version, tool_uuid=None)
inputs = self.service.inputs(trans, tool_run_ref)
return json_schema_response_for_tool_state_model(LandingRequestToolState, inputs)
@router.get(
"/api/tools/{tool_id}/versions/{tool_version}/parameter_test_case_xml_schema",
operation_id="tools__versioned_parameter_test_case_xml_schema",
summary="Return a JSON schema description of the tool's inputs for test case construction.",
)
def tool_state_test_case_xml_versioned(
self,
tool_id: str = ToolIDPathParam,
tool_version: str = ToolVersionPathParam,
trans: ProvidesHistoryContext = DependsOnTrans,
) -> Response:
tool_run_ref = ToolRunReference(tool_id=tool_id, tool_version=tool_version, tool_uuid=None)
inputs = self.service.inputs(trans, tool_run_ref)
return json_schema_response_for_tool_state_model(TestCaseToolState, inputs)
def _parsed_tool(
self,
trans: ProvidesHistoryContext,
tool_id: str,
tool_version: str | None,
) -> ParsedTool:
tool_run_ref = ToolRunReference(tool_id=tool_id, tool_version=tool_version, tool_uuid=None)
tool = get_tool(trans, tool_run_ref)
return tool.parsed_tool()
class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
"""
lib/galaxy_test/api/test_tools.py
+41
View File
@@ -768,6 +768,47 @@ class TestToolsApi(ApiTestCase, TestsTools):
assert "--ex1" in option_values
assert "ex2" in option_values
@skip_without_tool("gx_int")
def test_tool_interop(self):
"""GET /api/tools/{tool_id}/interop returns ParsedTool JSON."""
response = self._get("tools/gx_int/interop")
self._assert_status_code_is(response, 200)
interop = response.json()
assert interop["id"] == "gx_int"
assert "inputs" in interop
assert "outputs" in interop
assert len(interop["inputs"]) > 0
@skip_without_tool("gx_int")
def test_tool_interop_versioned(self):
"""GET /api/tools/{tool_id}/versions/{version}/interop returns same result."""
# Get version from the unversioned endpoint first
response = self._get("tools/gx_int/interop")
self._assert_status_code_is(response, 200)
interop = response.json()
version = interop["version"]
versioned_response = self._get(f"tools/gx_int/versions/{version}/interop")
self._assert_status_code_is(versioned_response, 200)
versioned_interop = versioned_response.json()
assert versioned_interop["id"] == interop["id"]
assert versioned_interop["version"] == version
assert len(versioned_interop["inputs"]) == len(interop["inputs"])
@skip_without_tool("gx_int")
def test_versioned_schema_endpoints(self):
"""Versioned /versions/{v}/parameter_*_schema endpoints mirror unversioned ones."""
response = self._get("tools/gx_int/interop")
version = response.json()["version"]
for schema_type in ["request", "landing_request", "test_case_xml"]:
unversioned = self._get(f"tools/gx_int/parameter_{schema_type}_schema")
self._assert_status_code_is(unversioned, 200)
versioned = self._get(f"tools/gx_int/versions/{version}/parameter_{schema_type}_schema")
self._assert_status_code_is(versioned, 200)
assert unversioned.json() == versioned.json()
@skip_without_tool("test_data_source")
def test_data_source_ok_request(self, mock_http_server):
with self.dataset_populator.test_history() as history_id:
lib/tool_shed/test/functional/test_shed_tools.py
+14
View File
@@ -70,6 +70,20 @@ class TestShedToolsApi(ShedApiTestCase):
tool_response = self.api_interactor.get(url)
tool_response.raise_for_status()
def test_tool_interop(self):
populator = self.populator
repository = populator.setup_column_maker_repo(prefix="toolinterop")
tool_id = populator.tool_guid(self, repository, "Add_a_column1")
tool_shed_base, encoded_tool_id = encode_identifier(tool_id)
url = f"tools/{encoded_tool_id}/versions/1.1.0/interop"
tool_response = self.api_interactor.get(url)
tool_response.raise_for_status()
parsed = tool_response.json()
assert parsed["id"] == "Add_a_column1"
assert parsed["version"] == "1.1.0"
assert "inputs" in parsed
assert "outputs" in parsed
def test_tool_source(self):
populator = self.populator
repository = populator.setup_column_maker_repo(prefix="toolsource")
lib/tool_shed/webapp/api2/tools.py
+13
View File
@@ -157,6 +157,19 @@ class FastAPITools:
) -> ShedParsedTool:
return parsed_tool_model_cached_for(trans, tool_id, tool_version)
@router.get(
"/api/tools/{tool_id}/versions/{tool_version}/interop",
operation_id="tools__interop",
summary="Return Galaxy's meta model description of the tool's metadata, inputs, and outputs.",
)
def interop(
self,
trans: SessionRequestContext = DependsOnTrans,
tool_id: str = TOOL_ID_PATH_PARAM,
tool_version: str = TOOL_VERSION_PATH_PARAM,
) -> ShedParsedTool:
return parsed_tool_model_cached_for(trans, tool_id, tool_version)
@router.get(
"/api/tools/{tool_id}/versions/{tool_version}/parameter_request_schema",
operation_id="tools__parameter_request_schema",
lib/tool_shed/webapp/frontend/src/schema/schema.ts
+60
View File
@@ -587,6 +587,23 @@ export interface paths {
patch?: never
trace?: never
}
"/api/tools/{tool_id}/versions/{tool_version}/interop": {
parameters: {
query?: never
header?: never
path?: never
cookie?: never
}
/** Return Galaxy's meta model description of the tool's metadata, inputs, and outputs. */
get: operations["tools__interop"]
put?: never
post?: never
delete?: never
options?: never
head?: never
patch?: never
trace?: never
}
"/api/tools/{tool_id}/versions/{tool_version}/parameter_landing_request_schema": {
parameters: {
query?: never
@@ -5676,6 +5693,49 @@ export interface operations {
}
}
}
tools__interop: {
parameters: {
query?: never
header?: never
path: {
/** @description See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids */
tool_id: string
/** @description The full version string defined on the Galaxy tool wrapper. */
tool_version: string
}
cookie?: never
}
requestBody?: never
responses: {
/** @description Successful Response */
200: {
headers: {
[name: string]: unknown
}
content: {
"application/json": components["schemas"]["ShedParsedTool"]
}
}
/** @description Request Error */
"4XX": {
headers: {
[name: string]: unknown
}
content: {
"application/json": components["schemas"]["MessageExceptionModel"]
}
}
/** @description Server Error */
"5XX": {
headers: {
[name: string]: unknown
}
content: {
"application/json": components["schemas"]["MessageExceptionModel"]
}
}
}
}
tools__parameter_landing_request_schema: {
parameters: {
query?: never