TRS models.

lib/galaxy/config/schemas/tool_shed_config_schema.yml

@@ -342,6 +342,58 @@ mapping:
         desc: |
           Address to join mailing list
 
+      ga4gh_service_id:
+        type: str
+        required: false
+        desc: |
+          Service ID for GA4GH services (exposed via the service-info endpoint for the Galaxy DRS API).
+          If unset, one will be generated using the URL the target API requests are made against.
+
+          For more information on GA4GH service definitions - check out
+          https://github.com/ga4gh-discovery/ga4gh-service-registry
+          and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
+
+          This value should likely reflect your service's URL. For instance for usegalaxy.org
+          this value should be org.usegalaxy. Particular Galaxy implementations will treat this
+          value as a prefix and append the service type to this ID. For instance for the DRS
+          service "id" (available via the DRS API) for the above configuration value would be
+          org.usegalaxy.drs.
+
+      ga4gh_service_organization_name:
+        type: str
+        required: false
+        desc: |
+          Service name for host organization (exposed via the service-info endpoint for the Galaxy DRS API).
+          If unset, one will be generated using ga4gh_service_id.
+
+          For more information on GA4GH service definitions - check out
+          https://github.com/ga4gh-discovery/ga4gh-service-registry
+          and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
+
+      ga4gh_service_organization_url:
+        type: str
+        required: False
+        desc: |
+          Organization URL for host organization (exposed via the service-info endpoint for the Galaxy DRS API).
+          If unset, one will be generated using the URL the target API requests are made against.
+
+          For more information on GA4GH service definitions - check out
+          https://github.com/ga4gh-discovery/ga4gh-service-registry
+          and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
+
+      ga4gh_service_environment:
+        type: str
+        required: False
+        desc: |
+          Service environment (exposed via the service-info endpoint for the Galaxy DRS API) for
+          implemented GA4GH services.
+
+          Suggested values are prod, test, dev, staging.
+
+          For more information on GA4GH service definitions - check out
+          https://github.com/ga4gh-discovery/ga4gh-service-registry
+          and https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
+
       use_heartbeat:
         type: bool
         default: true

lib/galaxy/webapps/base/api.py

@@ -159,7 +159,14 @@ def get_error_response_for_request(request: Request, exc: MessageException) -> J
     if "ga4gh" in path:
         # When serving GA4GH APIs use limited exceptions to conform their expected
         # error schema. Tailored to DRS currently.
-        content = {"status_code": status_code, "msg": error_dict["err_msg"]}
+        message = error_dict["err_msg"]
+        if "drs" in path:
+            content = {"status_code": status_code, "msg": message}
+        elif "trs" in path:
+            content = {"code": status_code, "message": message}
+        else:
+            # unknown schema - just yield the most useful error message
+            content = error_dict
     else:
         content = error_dict
 

lib/tool_shed/managers/trs.py

@@ -0,0 +1,153 @@
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+)
+
+from starlette.datastructures import URL
+
+from galaxy.exceptions import ObjectNotFound
+from galaxy.util.tool_shed.common_util import remove_protocol_and_user_from_clone_url
+from galaxy.version import VERSION
+from tool_shed.context import ProvidesRepositoriesContext
+from tool_shed.structured_app import ToolShedApp
+from tool_shed.util.metadata_util import get_current_repository_metadata_for_changeset_revision
+from tool_shed.webapp.model import (
+    Repository,
+    RepositoryMetadata,
+)
+from tool_shed_client.schema.trs import (
+    DescriptorType,
+    Tool,
+    ToolClass,
+    ToolVersion,
+)
+from tool_shed_client.schema.trs_service_info import (
+    Organization,
+    Service,
+    ServiceType,
+)
+from tool_shed_client.trs_util import decode_identifier
+from .repositories import guid_to_repository
+
+TRS_SERVICE_NAME = "Tool Shed TRS API"
+TRS_SERVICE_DESCRIPTION = "Serves tool shed repository tools according to the GA4GH TRS specification"
+
+
+def service_info(app: ToolShedApp, request_url: URL):
+    components = request_url.components
+    hostname = components.hostname
+    assert hostname
+    default_organization_id = ".".join(reversed(hostname.split(".")))
+    config = app.config
+    organization_id = cast(str, config.ga4gh_service_id or default_organization_id)
+    organization_name = cast(str, config.ga4gh_service_organization_name or organization_id)
+    organization_url = cast(str, config.ga4gh_service_organization_url or f"{components.scheme}://{components.netloc}")
+
+    organization = Organization(
+        url=organization_url,
+        name=organization_name,
+    )
+    service_type = ServiceType(
+        group="org.ga4gh",
+        artifact="trs",
+        version="2.1.0",
+    )
+    environment = config.ga4gh_service_environment
+    extra_kwds = {}
+    if environment:
+        extra_kwds["environment"] = environment
+    return Service(
+        id=organization_id + ".trs",
+        name=TRS_SERVICE_NAME,
+        description=TRS_SERVICE_DESCRIPTION,
+        organization=organization,
+        type=service_type,
+        version=VERSION,
+        **extra_kwds,
+    )
+
+
+def tool_classes() -> List[ToolClass]:
+    return [ToolClass(id="galaxy_tool", name="Galaxy Tool", description="Galaxy XML Tools")]
+
+
+def trs_tool_id_to_repository(trans: ProvidesRepositoriesContext, trs_tool_id: str) -> Repository:
+    guid = decode_identifier(trans.repositories_hostname, trs_tool_id)
+    guid = remove_protocol_and_user_from_clone_url(guid)
+    return guid_to_repository(trans.app, guid)
+
+
+def get_repository_metadata_by_tool_version(
+    app: ToolShedApp, repository: Repository, tool_id: str
+) -> Dict[str, RepositoryMetadata]:
+    versions = {}
+    for _, changeset in repository.installable_revisions(app):
+        metadata = get_current_repository_metadata_for_changeset_revision(app, repository, changeset)
+        tools: Optional[List[Dict[str, Any]]] = metadata.metadata.get("tools")
+        if not tools:
+            continue
+        for tool_metadata in tools:
+            if tool_metadata["id"] != tool_id:
+                continue
+            versions[tool_metadata["version"]] = metadata
+    return versions
+
+
+def get_tools_for(repository_metadata: RepositoryMetadata) -> List[Dict[str, Any]]:
+    tools: Optional[List[Dict[str, Any]]] = repository_metadata.metadata.get("tools")
+    assert tools
+    return tools
+
+
+def trs_tool_id_to_repository_metadata(
+    trans: ProvidesRepositoriesContext, trs_tool_id: str
+) -> Optional[Tuple[Repository, Dict[str, RepositoryMetadata]]]:
+    tool_guid = decode_identifier(trans.repositories_hostname, trs_tool_id)
+    tool_guid = remove_protocol_and_user_from_clone_url(tool_guid)
+    _, tool_id = tool_guid.rsplit("/", 1)
+    repository = guid_to_repository(trans.app, tool_guid)
+    app = trans.app
+    versions: Dict[str, RepositoryMetadata] = get_repository_metadata_by_tool_version(app, repository, tool_id)
+    if not versions:
+        return None
+
+    return repository, versions
+
+
+def get_tool(trans: ProvidesRepositoriesContext, trs_tool_id: str) -> Tool:
+    guid = decode_identifier(trans.repositories_hostname, trs_tool_id)
+    guid = remove_protocol_and_user_from_clone_url(guid)
+    repo_metadata = trs_tool_id_to_repository_metadata(trans, trs_tool_id)
+    if not repo_metadata:
+        raise ObjectNotFound()
+    repository, metadata_by_version = repo_metadata
+
+    repo_owner = repository.user.username
+    aliases: List[str] = [guid]
+    hostname = remove_protocol_and_user_from_clone_url(trans.repositories_hostname)
+    url = f"https://{hostname}/repos/{repo_owner}/{repository.name}"
+
+    versions: List[ToolVersion] = []
+    for tool_version_str, _ in metadata_by_version.items():
+        version_url = url  # TODO:
+        tool_version = ToolVersion(
+            author=[repo_owner],
+            containerfile=False,
+            descriptor_type=[DescriptorType.GALAXY],
+            id=tool_version_str,
+            url=version_url,
+            verified=False,
+        )
+        versions.append(tool_version)
+    return Tool(
+        aliases=aliases,
+        id=trs_tool_id,
+        url=url,
+        toolclass=tool_classes()[0],
+        organization=repo_owner,
+        versions=versions,
+    )

lib/tool_shed/test/functional/test_shed_tools.py

@@ -1,4 +1,12 @@
-from ..base.api import ShedApiTestCase
+from tool_shed_client.schema.trs import (
+    Tool,
+    ToolClass,
+)
+from tool_shed_client.trs_util import encode_identifier
+from ..base.api import (
+    ShedApiTestCase,
+    skip_if_api_v1,
+)
 
 
 class TestShedToolsApi(ShedApiTestCase):
@@ -32,3 +40,31 @@ def test_tool_search(self):
             # but if this tool has been installed a bunch by other tests - it might not be.
             tool_search_hit = response.find_search_hit(repository)
             assert tool_search_hit
+
+    @skip_if_api_v1
+    def test_trs_service_info(self):
+        service_info = self.api_interactor.get("ga4gh/trs/v2/service-info")
+        service_info.raise_for_status()
+
+    @skip_if_api_v1
+    def test_trs_tool_classes(self):
+        classes_response = self.api_interactor.get("ga4gh/trs/v2/toolClasses")
+        classes_response.raise_for_status()
+        classes = classes_response.json()
+        assert isinstance(classes, list)
+        assert len(classes) == 1
+        class0 = classes[0]
+        assert ToolClass(**class0)
+
+    @skip_if_api_v1
+    def test_trs_tool_list(self):
+        populator = self.populator
+        repository = populator.setup_column_maker_repo(prefix="toolstrsindex")
+        tool_id = populator.tool_guid(self, repository, "Add_a_column1")
+        tool_shed_base, encoded_tool_id = encode_identifier(tool_id)
+        print(encoded_tool_id)
+        url = f"ga4gh/trs/v2/tools/{encoded_tool_id}"
+        print(url)
+        tool_response = self.api_interactor.get(url)
+        tool_response.raise_for_status()
+        assert Tool(**tool_response.json())

lib/tool_shed/webapp/api2/tools.py

@@ -1,8 +1,27 @@
+import logging
+from typing import List
+
+from fastapi import (
+    Path,
+    Request,
+)
+
 from tool_shed.context import SessionRequestContext
 from tool_shed.managers.tools import search
+from tool_shed.managers.trs import (
+    get_tool,
+    service_info,
+    tool_classes,
+)
 from tool_shed.structured_app import ToolShedApp
 from tool_shed.util.shed_index import build_index
 from tool_shed_client.schema import BuildSearchIndexResponse
+from tool_shed_client.schema.trs import (
+    Tool,
+    ToolClass,
+    ToolVersion,
+)
+from tool_shed_client.schema.trs_service_info import Service
 from . import (
     depends,
     DependsOnTrans,
@@ -12,8 +31,16 @@
     ToolsIndexQueryParam,
 )
 
+log = logging.getLogger(__name__)
+
 router = Router(tags=["tools"])
 
+TOOL_ID_PATH_PARAM: str = Path(
+    ...,
+    title="GA4GH TRS Tool ID",
+    description="See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids",
+)
+
 
 @router.cbv
 class FastAPITools:
@@ -53,3 +80,44 @@ def build_search_index(self) -> BuildSearchIndexResponse:
             repositories_indexed=repos_indexed,
             tools_indexed=tools_indexed,
         )
+
+    @router.get("/api/ga4gh/trs/v2/service-info", operation_id="tools_trs_service_info")
+    def service_info(self, request: Request) -> Service:
+        return service_info(self.app, request.url)
+
+    @router.get("/api/ga4gh/trs/v2/toolClasses", operation_id="tools__trs_tool_classes")
+    def tool_classes(self) -> List[ToolClass]:
+        return tool_classes()
+
+    @router.get(
+        "/api/ga4gh/trs/v2/tools",
+        operation_id="tools__trs_index",
+    )
+    def trs_index(
+        self,
+    ):
+        # we probably want to be able to query the database at the
+        # tool level and such to do this right?
+        return []
+
+    @router.get(
+        "/api/ga4gh/trs/v2/tools/{tool_id}",
+        operation_id="tools__trs_get",
+    )
+    def trs_get(
+        self,
+        trans: SessionRequestContext = DependsOnTrans,
+        tool_id: str = TOOL_ID_PATH_PARAM,
+    ) -> Tool:
+        return get_tool(trans, tool_id)
+
+    @router.get(
+        "/api/ga4gh/trs/v2/tools/{tool_id}/versions",
+        operation_id="tools__trs_get_versions",
+    )
+    def trs_get_versions(
+        self,
+        trans: SessionRequestContext = DependsOnTrans,
+        tool_id: str = TOOL_ID_PATH_PARAM,
+    ) -> List[ToolVersion]:
+        return get_tool(trans, tool_id).versions

lib/tool_shed_client/schema/gen.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# must be run from a virtualenv with...
+# https://github.com/koxudaxi/datamodel-code-generator
+#for model in AccessMethod Checksum DrsObject Error AccessURL ContentsObject DrsService
+#do
+#    datamodel-codegen --url "https://raw.githubusercontent.com/ga4gh/tool-registry-service-schemas/develop/openapi/ga4gh-tool-discovery.yaml" --output "$model.py"
+#one
+
+#datamodel-codegen --url "https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/v1.0.0/service-info.yaml#/components/schemas/Service" --output Service.py
+
+datamodel-codegen --url "https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/v1.0.0/service-info.yaml#/paths/~1service-info" --output trs_service_info.py
+datamodel-codegen --url "https://raw.githubusercontent.com/ga4gh/tool-registry-service-schemas/develop/openapi/openapi.yaml" --output trs.py