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This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.webapps.galaxy.api.tools
import logging
import os
from datetime import (
datetime,
timezone,
)
from json import loads
from typing import (
Any,
cast,
Optional,
)
from fastapi import (
Body,
Depends,
Query,
Request,
Response,
UploadFile,
)
from fastapi.responses import FileResponse
from pydantic import UUID4
from starlette.datastructures import UploadFile as StarletteUploadFile
from starlette.responses import StreamingResponse
from galaxy import (
exceptions,
util,
web,
)
from galaxy.datatypes.data import get_params_and_input_name
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.context import (
ProvidesHistoryContext,
ProvidesUserContext,
)
from galaxy.managers.hdas import HDAManager
from galaxy.managers.histories import HistoryManager
from galaxy.managers.landing import LandingRequestManager
from galaxy.model.dataset_collections.workbook_util import workbook_to_bytes
from galaxy.schema.fetch_data import (
CreateDataLandingPayload,
CreateFileLandingPayload,
FetchDataFormPayload,
FetchDataPayload,
)
from galaxy.schema.schema import (
ClaimLandingPayload,
CreateToolLandingRequestPayload,
ToolLandingRequest,
)
from galaxy.tool_util.verify import ToolTestDescriptionDict
from galaxy.tool_util_models import UserToolSource
from galaxy.tools.evaluation import global_tool_errors
from galaxy.tools.fetch.workbooks import (
FetchWorkbookCollectionType,
FetchWorkbookType,
generate,
GenerateFetchWorkbookRequest,
parse,
ParsedFetchWorkbook,
ParseFetchWorkbook,
)
from galaxy.util.hash_util import (
HashFunctionNameEnum,
memory_bound_hexdigest,
)
from galaxy.util.zipstream import ZipstreamWrapper
from galaxy.web import (
expose_api,
expose_api_anonymous,
expose_api_anonymous_and_sessionless,
expose_api_raw_anonymous_and_sessionless,
)
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.tools import ToolsService
from . import (
APIContentTypeRoute,
as_form,
BaseGalaxyAPIController,
depends,
DependsOnTrans,
LandingUuidPathParam,
Router,
)
log = logging.getLogger(__name__)
# Do not allow these tools to be called directly - they (it) enforces extra security and
# provides access via a different API endpoint.
PROTECTED_TOOLS = ["__DATA_FETCH__"]
# Tool search bypasses the fulltext for the following list of terms
SEARCH_RESERVED_TERMS_FAVORITES = ["#favs", "#favorites", "#favourites"]
ICON_CACHE_MAX_AGE = 2592000 # 30 days
FetchWorkbookTypeQueryParam: FetchWorkbookType = Query(
default="datasets",
title="Workbook Type",
description="Generate a workbook for simple datasets or a collection.",
)
FetchWorkbookCollectionTypeQueryParam: FetchWorkbookCollectionType = Query(
default="list",
title="Collection Type",
description="Generate workbook for specified collection type (not all collection types are supported)",
)
FetchWorkbookFilenameQueryParam: Optional[str] = Query(
None,
description="Filename of the workbook download to generate",
)
router = Router(tags=["tools"])
FetchDataForm = as_form(FetchDataFormPayload)
[docs]
async def get_files(request: Request, files: Optional[list[UploadFile]] = None):
# FastAPI's UploadFile is a very light wrapper around starlette's UploadFile
files2: list[StarletteUploadFile] = cast(list[StarletteUploadFile], files or [])
if not files2:
data = await request.form()
for value in data.values():
if isinstance(value, StarletteUploadFile):
files2.append(value)
return files2
[docs]
@router.cbv
class FetchTools:
service: ToolsService = depends(ToolsService)
landing_manager: LandingRequestManager = depends(LandingRequestManager)
[docs]
@router.post("/api/tools/fetch", summary="Upload files to Galaxy", route_class_override=JsonApiRoute)
def fetch_json(self, payload: FetchDataPayload = Body(...), trans: ProvidesHistoryContext = DependsOnTrans):
return self.service.create_fetch(trans, payload)
[docs]
@router.post(
"/api/tools/fetch",
summary="Upload files to Galaxy",
route_class_override=FormDataApiRoute,
)
def fetch_form(
self,
payload: FetchDataFormPayload = Depends(FetchDataForm.as_form),
trans: ProvidesHistoryContext = DependsOnTrans,
files: list[StarletteUploadFile] = Depends(get_files),
):
return self.service.create_fetch(trans, payload, files)
[docs]
@router.get(
"/api/tools/fetch/workbook",
summary="Generate a template workbook to use with the activity builder UI",
response_class=StreamingResponse,
operation_id="tools__fetch_workbook_download",
)
def fetch_workbook(
self,
trans: ProvidesHistoryContext = DependsOnTrans,
type: FetchWorkbookType = FetchWorkbookTypeQueryParam,
collection_type: FetchWorkbookCollectionType = FetchWorkbookCollectionTypeQueryParam,
filename: Optional[str] = FetchWorkbookFilenameQueryParam,
):
generate_request = GenerateFetchWorkbookRequest(
type=type,
collection_type=collection_type,
)
workbook = generate(generate_request)
contents = workbook_to_bytes(workbook)
return serve_workbook(contents, filename)
[docs]
@router.post(
"/api/tools/fetch/workbook/parse",
summary="Generate a template workbook to use with the activity builder UI",
operation_id="tools__fetch_workbook_parse",
)
def parse_workbook(
self,
trans: ProvidesHistoryContext = DependsOnTrans,
payload: ParseFetchWorkbook = Body(...),
) -> ParsedFetchWorkbook:
return parse(payload)
[docs]
@router.get(
"/api/tools/{tool_id:path}/icon",
summary="Get the icon image associated with a tool",
response_class=PNGIconResponse,
responses={
200: {
"content": {"image/png": {}},
"description": "Tool icon image in PNG format",
},
304: {
"description": "Tool icon image has not been modified since the last request",
},
404: {
"description": "Tool icon file not found or not provided by the tool",
},
},
)
def get_icon(self, request: Request, tool_id: str, trans: ProvidesHistoryContext = DependsOnTrans):
"""Returns the icon image associated with a tool.
The icon image is served with caching headers to allow for efficient
client-side caching. The icon image is expected to be in PNG format.
"""
tool_icon_path = self.service.get_tool_icon_path(trans=trans, tool_id=tool_id)
if tool_icon_path is None:
raise exceptions.ObjectNotFound(f"Tool icon file not found or not provided by the tool: {tool_id}")
# Get file modification time
file_stat = os.stat(tool_icon_path)
last_modified = datetime.fromtimestamp(file_stat.st_mtime, tz=timezone.utc).strftime(
"%a, %d %b %Y %H:%M:%S GMT"
)
# Check If-Modified-Since
if_modified_since = request.headers.get("If-Modified-Since")
if if_modified_since == last_modified:
return Response(status_code=304)
# Generate ETag based on file content
file_hash = memory_bound_hexdigest(hash_func_name=HashFunctionNameEnum.md5, path=tool_icon_path)
etag = f'"{file_hash}"'
# Check If-None-Match (ETag)
if_none_match = request.headers.get("If-None-Match", "").split(",")
if any(etag.strip() == e.strip(' W/"') for e in if_none_match): # Handle weak ETags
return Response(status_code=304)
# Serve the file with caching headers
response = PNGIconResponse(tool_icon_path)
response.headers["Cache-Control"] = f"public, max-age={ICON_CACHE_MAX_AGE}, immutable"
response.headers["ETag"] = etag
response.headers["Last-Modified"] = last_modified
return response
[docs]
@router.post("/api/file_landings", public=True, allow_cors=True)
def create_file_landing(
self,
trans: ProvidesUserContext = DependsOnTrans,
file_landing_request: CreateFileLandingPayload = Body(...),
) -> ToolLandingRequest:
tool_landing_request = self.service.file_landing_to_tool_landing(trans, file_landing_request)
return self.landing_manager.create_tool_landing_request(tool_landing_request)
[docs]
@router.post("/api/data_landings", public=True, allow_cors=True)
def create_data_landing(
self,
trans: ProvidesUserContext = DependsOnTrans,
data_landing_request: CreateDataLandingPayload = Body(...),
) -> ToolLandingRequest:
tool_landing_request = self.service.data_landing_to_tool_landing(trans, data_landing_request)
return self.landing_manager.create_tool_landing_request(tool_landing_request)
[docs]
@router.post("/api/tool_landings", public=True, allow_cors=True)
def create_landing(
self,
trans: ProvidesUserContext = DependsOnTrans,
tool_landing_request: CreateToolLandingRequestPayload = Body(...),
) -> ToolLandingRequest:
tool_id = tool_landing_request.tool_id
if tool_id in PROTECTED_TOOLS:
raise exceptions.RequestParameterInvalidException(
f"Cannot execute tool [{tool_id}] directly, must use alternative endpoint."
)
return self.landing_manager.create_tool_landing_request(tool_landing_request)
[docs]
@router.post("/api/tool_landings/{uuid}/claim")
def claim_landing(
self,
trans: ProvidesUserContext = DependsOnTrans,
uuid: UUID4 = LandingUuidPathParam,
payload: Optional[ClaimLandingPayload] = Body(...),
) -> ToolLandingRequest:
return self.landing_manager.claim_tool_landing_request(trans, uuid, payload)
[docs]
@router.get("/api/tool_landings/{uuid}")
def get_landing(
self,
trans: ProvidesUserContext = DependsOnTrans,
uuid: UUID4 = LandingUuidPathParam,
) -> ToolLandingRequest:
return self.landing_manager.get_tool_landing_request(trans, uuid)
[docs]
class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
"""
RESTful controller for interactions with tools.
"""
history_manager: HistoryManager = depends(HistoryManager)
hda_manager: HDAManager = depends(HDAManager)
hdca_manager: DatasetCollectionManager = depends(DatasetCollectionManager)
service: ToolsService = depends(ToolsService)
[docs]
@expose_api_anonymous_and_sessionless
def index(self, trans: GalaxyWebTransaction, **kwds):
"""
GET /api/tools
returns a list of tools defined by parameters
:param in_panel: if true, tools are returned in panel structure,
including sections and labels
:param view: ToolBox view to apply (default is 'default')
:param q: if present search on the given query will be performed
:param tool_id: if present the given tool_id will be searched for
all installed versions
"""
# Read params.
in_panel = util.string_as_bool(kwds.get("in_panel", "True"))
q = kwds.get("q", "")
tool_id = kwds.get("tool_id", "")
tool_help = util.string_as_bool(kwds.get("tool_help", "False"))
view = kwds.get("view", None)
# Find whether to search.
if q:
if trans.user and q in SEARCH_RESERVED_TERMS_FAVORITES:
if "favorites" in trans.user.preferences:
favorites = loads(trans.user.preferences["favorites"])
hits = favorites["tools"]
else:
hits = None
else:
hits = self.service._search(q, view)
results = []
if hits:
for hit in hits:
try:
tool = self.service._get_tool(trans, hit, user=trans.user)
if tool:
results.append(tool.id)
except exceptions.AuthenticationFailed:
pass
except exceptions.ObjectNotFound:
pass
return results
# Find whether to detect.
if tool_id:
detected_versions = self.service._detect(trans, tool_id)
return detected_versions
# Return everything.
try:
return self.app.toolbox.to_dict(trans, in_panel=in_panel, tool_help=tool_help, view=view)
except exceptions.MessageException:
raise
except Exception:
msg = "Error: Could not convert toolbox to dictionary"
log.exception(msg)
raise exceptions.InternalServerError(msg)
[docs]
@expose_api_anonymous_and_sessionless
def panel_views(self, trans: GalaxyWebTransaction, **kwds):
"""
GET /api/tool_panels
returns a dictionary of available tool panel views and default view
"""
rval = {}
rval["default_panel_view"] = self.app.toolbox._default_panel_view(trans)
rval["views"] = self.app.toolbox.panel_view_dicts()
return rval
[docs]
@expose_api_anonymous_and_sessionless
def panel_view(self, trans: GalaxyWebTransaction, view, **kwds):
"""
GET /api/tool_panels/{view}
returns a dictionary of tools and tool sections for the given view
"""
# Return panel view.
try:
return self.app.toolbox.to_panel_view(trans, view=view)
except exceptions.MessageException:
raise
except Exception:
raise exceptions.InternalServerError("Error: Could not convert toolbox to dictionary")
[docs]
@expose_api_anonymous_and_sessionless
def show(self, trans: GalaxyWebTransaction, id, **kwd):
"""
GET /api/tools/{tool_id}
Returns tool information
parameters:
io_details - if true, parameters and inputs are returned
link_details - if true, hyperlink to the tool is returned
tool_version - if provided return this tool version
"""
io_details = util.string_as_bool(kwd.get("io_details", False))
link_details = util.string_as_bool(kwd.get("link_details", False))
tool_version = kwd.get("tool_version")
tool = self.service._get_tool(trans, id, user=trans.user, tool_version=tool_version, tool_uuid=id)
return tool.to_dict(trans, io_details=io_details, link_details=link_details)
[docs]
@expose_api_anonymous
def build(self, trans: GalaxyWebTransaction, id, **kwd):
"""
GET /api/tools/{tool_id}/build
Returns a tool model including dynamic parameters and updated values, repeats block etc.
"""
kwd = _kwd_or_payload(kwd)
tool_version = kwd.get("tool_version")
tool_uuid = kwd.get("tool_uuid")
history = None
if history_id := kwd.pop("history_id", None):
history = self.history_manager.get_owned(
self.decode_id(history_id), trans.user, current_history=trans.history
)
tool = self.service._get_tool(trans, id, tool_version=tool_version, user=trans.user, tool_uuid=tool_uuid)
return tool.to_json(trans, kwd.get("inputs", kwd), history=history)
[docs]
@web.require_admin
@expose_api
def test_data_path(self, trans: GalaxyWebTransaction, id, **kwd):
"""
GET /api/tools/{tool_id}/test_data_path?tool_version={tool_version}
"""
kwd = _kwd_or_payload(kwd)
tool_version = kwd.get("tool_version", None)
tool = self.service._get_tool(trans, id, tool_version=tool_version, user=trans.user)
try:
path = tool.test_data_path(kwd.get("filename"))
except ValueError as e:
raise exceptions.MessageException(str(e))
if path:
return path
else:
raise exceptions.ObjectNotFound("Specified test data path not found.")
[docs]
@expose_api_raw_anonymous_and_sessionless
def test_data_download(self, trans: GalaxyWebTransaction, id, **kwd):
"""
GET /api/tools/{tool_id}/test_data_download?tool_version={tool_version}&filename={filename}
"""
tool_version = kwd.get("tool_version", None)
tool = self.service._get_tool(trans, id, tool_version=tool_version, user=trans.user)
filename = kwd.get("filename")
if filename is None:
raise exceptions.ObjectNotFound("Test data filename not specified.")
if path := tool.test_data_path(filename):
if os.path.isfile(path):
trans.response.headers["Content-Disposition"] = f'attachment; filename="{filename}"'
return open(path, mode="rb")
elif os.path.isdir(path):
# Set upstream_mod_zip to false, otherwise tool data must be among allowed internal routes
archive = ZipstreamWrapper(
upstream_mod_zip=False,
upstream_gzip=self.app.config.upstream_gzip,
archive_name=filename,
)
archive.write(path)
trans.response.headers.update(archive.get_headers())
return archive.response()
raise exceptions.ObjectNotFound("Specified test data path not found.")
[docs]
@expose_api_anonymous_and_sessionless
def tests_summary(self, trans: GalaxyWebTransaction, **kwd):
"""
GET /api/tools/tests_summary
Fetch summary information for each tool and version combination with tool tests
defined. This summary information currently includes tool name and a count of
the tests.
Fetch complete test data for each tool with /api/tools/{tool_id}/test_data?tool_version=<tool_version>
"""
test_counts_by_tool: dict[str, dict] = {}
for _id, tool in self.app.toolbox.tools():
if not tool.is_datatype_converter:
tests = tool.tests
if tests:
if tool.id not in test_counts_by_tool:
test_counts_by_tool[tool.id] = {}
available_versions = test_counts_by_tool[tool.id]
available_versions[tool.version] = {
"tool_name": tool.name,
"count": len(tests),
}
return test_counts_by_tool
[docs]
@expose_api_anonymous_and_sessionless
def test_data(self, trans: GalaxyWebTransaction, id, **kwd) -> list[ToolTestDescriptionDict]:
"""
GET /api/tools/{tool_id}/test_data?tool_version={tool_version}
This API endpoint is unstable and experimental. In particular the format of the
response has not been entirely nailed down (it exposes too many Galaxy
internals/Pythonisms in a rough way). If this endpoint is being used from outside
of scripts shipped with Galaxy let us know and please be prepared for the response
from this API to change its format in some ways.
If tool version is not passed, it is assumed to be latest. Tool version can be
set as '*' to get tests for all configured versions.
"""
kwd = _kwd_or_payload(kwd)
tool_version = kwd.get("tool_version", None)
if tool_version == "*":
tools = self.app.toolbox.get_tool(id, get_all_versions=True)
for tool in tools:
if not tool.allow_user_access(trans.user):
raise exceptions.AuthenticationFailed(f"Access denied, please login for tool with id '{id}'.")
else:
tools = [self.service._get_tool(trans, id, tool_version=tool_version, user=trans.user)]
test_defs = []
for tool in tools:
test_defs.extend([t.to_dict() for t in tool.tests])
return test_defs
[docs]
@web.require_admin
@expose_api
def reload(self, trans: GalaxyWebTransaction, id, **kwd):
"""
GET /api/tools/{tool_id}/reload
Reload specified tool.
"""
trans.app.queue_worker.send_control_task("reload_tool", noop_self=True, kwargs={"tool_id": id})
message, status = trans.app.toolbox.reload_tool_by_id(id)
if status == "error":
raise exceptions.MessageException(message)
return {"message": message}
[docs]
@web.require_admin
@expose_api
def all_requirements(self, trans: GalaxyWebTransaction, **kwds):
"""
GET /api/tools/all_requirements
Return list of unique requirements for all tools.
"""
return trans.app.toolbox.all_requirements
[docs]
@web.require_admin
@expose_api
def requirements(self, trans: GalaxyWebTransaction, id, **kwds):
"""
GET /api/tools/{tool_id}/requirements
Return the resolver status for a specific tool id.
[{"status": "installed", "name": "hisat2", "versionless": false, "resolver_type": "conda", "version": "2.0.3", "type": "package"}]
"""
tool = self.service._get_tool(trans, id, user=trans.user)
return tool.tool_requirements_status
[docs]
@web.require_admin
@expose_api
def install_dependencies(self, trans: GalaxyWebTransaction, id, **kwds):
"""
POST /api/tools/{tool_id}/dependencies
This endpoint is also available through POST /api/tools/{tool_id}/install_dependencies,
but will be deprecated in the future.
Attempts to install requirements via the dependency resolver
parameters:
index:
index of dependency resolver to use when installing dependency.
Defaults to using the highest ranking resolver
resolver_type: Use the dependency resolver of this resolver_type to install dependency.
build_dependency_cache: If true, attempts to cache dependencies for this tool
force_rebuild: If true and cache dir exists, attempts to delete cache dir
"""
tool = self.service._get_tool(trans, id, user=trans.user)
tool._view.install_dependencies(tool.requirements, **kwds)
if kwds.get("build_dependency_cache"):
tool.build_dependency_cache(**kwds)
# TODO: rework resolver install system to log and report what has been done.
# _view.install_dependencies should return a dict with stdout, stderr and success status
return tool.tool_requirements_status
[docs]
@web.require_admin
@expose_api
def uninstall_dependencies(self, trans: GalaxyWebTransaction, id, **kwds):
"""
DELETE /api/tools/{tool_id}/dependencies
Attempts to uninstall requirements via the dependency resolver
parameters:
index:
index of dependency resolver to use when installing dependency.
Defaults to using the highest ranking resolver
resolver_type: Use the dependency resolver of this resolver_type to install dependency
"""
tool = self.service._get_tool(trans, id, user=trans.user)
tool._view.uninstall_dependencies(requirements=tool.requirements, **kwds)
# TODO: rework resolver install system to log and report what has been done.
return tool.tool_requirements_status
[docs]
@web.require_admin
@expose_api
def build_dependency_cache(self, trans: GalaxyWebTransaction, id, **kwds):
"""
POST /api/tools/{tool_id}/build_dependency_cache
Attempts to cache installed dependencies.
parameters:
force_rebuild: If true and chache dir exists, attempts to delete cache dir
"""
tool = self.service._get_tool(trans, id)
tool.build_dependency_cache(**kwds)
# TODO: Should also have a more meaningful return.
return tool.tool_requirements_status
[docs]
@web.require_admin
@expose_api
def diagnostics(self, trans: GalaxyWebTransaction, id, **kwd):
"""
GET /api/tools/{tool_id}/diagnostics
Return diagnostic information to help debug panel
and dependency related problems.
"""
# TODO: Move this into tool.
def to_dict(x):
return x.to_dict()
tool = self.service._get_tool(trans, id, user=trans.user)
if hasattr(tool, "lineage"):
lineage_dict = tool.lineage.to_dict()
else:
lineage_dict = None
tool_shed_dependencies_dict: Optional[list] = None
if tool_shed_dependencies := tool.installed_tool_dependencies:
tool_shed_dependencies_dict = list(map(to_dict, tool_shed_dependencies))
return {
"tool_id": tool.id,
"tool_version": tool.version,
"dependency_shell_commands": tool.build_dependency_shell_commands(),
"lineage": lineage_dict,
"requirements": list(map(to_dict, tool.requirements)),
"installed_tool_shed_dependencies": tool_shed_dependencies_dict,
"tool_dir": tool.tool_dir,
"tool_shed": tool.tool_shed,
"repository_name": tool.repository_name,
"repository_owner": tool.repository_owner,
"installed_changeset_revision": None,
"guid": tool.guid,
}
[docs]
@expose_api_anonymous_and_sessionless
def citations(self, trans: GalaxyWebTransaction, id, **kwds):
tool = self.service._get_tool(trans, id, user=trans.user)
rval = []
for citation in tool.citations:
rval.append(citation.to_dict("bibtex"))
return rval
[docs]
@expose_api
def conversion(self, trans: GalaxyWebTransaction, tool_id, payload, **kwd):
converter = self.service._get_tool(trans, tool_id, user=trans.user)
target_type = payload.get("target_type")
source_type = payload.get("source_type")
input_src = payload.get("src")
input_id = payload.get("id")
# List of string of dependencies
try:
deps = trans.app.datatypes_registry.converter_deps[source_type][target_type]
except KeyError:
deps = {}
# Generate parameter dictionary
params, input_name = get_params_and_input_name(converter, deps)
params = {}
# determine input parameter name and add to params
params[input_name] = {
"values": [
{
"id": input_id,
"src": input_src,
}
],
"batch": input_src == "hdca",
}
if history_id := payload.get("history_id"):
decoded_id = self.decode_id(history_id)
target_history = self.history_manager.get_owned(decoded_id, trans.user, current_history=trans.history)
else:
if input_src == "hdca":
hdca = self.hdca_manager.get_dataset_collection_instance(trans, instance_type="history", id=input_id)
assert hdca.history
target_history = hdca.history
elif input_src == "hda":
decoded_id = trans.app.security.decode_id(input_id)
hda = self.hda_manager.get_accessible(decoded_id, trans.user)
assert hda.history
target_history = hda.history
self.history_manager.error_unless_owner(target_history, trans.user, current_history=trans.history)
else:
raise exceptions.RequestParameterInvalidException("Must run conversion on either hdca or hda.")
self.history_manager.error_unless_mutable(target_history)
# Make the target datatype available to the converter
params["__target_datatype__"] = target_type
vars = converter.handle_input(trans, params, history=target_history)
return self.service._handle_inputs_output_to_api_response(trans, converter, target_history, vars)
[docs]
@expose_api_anonymous_and_sessionless
def xrefs(self, trans: GalaxyWebTransaction, id, **kwds):
tool = self.service._get_tool(trans, id, user=trans.user)
return tool.xrefs
[docs]
@web.require_admin
@web.legacy_expose_api_raw
def download(self, trans: GalaxyWebTransaction, id, **kwds):
tool_tarball = trans.app.toolbox.package_tool(trans, id)
trans.response.set_content_type("application/x-gzip")
download_file = open(tool_tarball, "rb")
trans.response.headers["Content-Disposition"] = f'attachment; filename="{id}.tgz"'
return download_file
[docs]
@expose_api_raw_anonymous_and_sessionless
def raw_tool_source(self, trans: GalaxyWebTransaction, id, **kwds):
"""Returns tool source. ``language`` is included in the response header."""
if not trans.app.config.enable_tool_source_display and not trans.user_is_admin:
raise exceptions.InsufficientPermissionsException(
"Only administrators may display tool sources on this Galaxy server."
)
tool = self.service._get_tool(trans, id, user=trans.user, tool_version=kwds.get("tool_version"), tool_uuid=id)
trans.response.headers["language"] = tool.tool_source.language
if dynamic_tool := getattr(tool, "dynamic_tool", None):
if dynamic_tool.value.get("class") == "GalaxyUserTool":
return UserToolSource(**dynamic_tool.value).model_dump_json(
by_alias=True,
exclude_defaults=True,
exclude_unset=True,
)
return tool.tool_source.to_string()
[docs]
@web.require_admin
@expose_api
def error_stack(self, trans: GalaxyWebTransaction, **kwd):
"""
GET /api/tools/error_stack
Returns global tool error stack
"""
return global_tool_errors.error_stack
[docs]
@expose_api_anonymous
def create(self, trans: GalaxyWebTransaction, payload, **kwd):
"""
POST /api/tools
Execute tool with a given parameter payload
:param input_format: input format for the payload. Possible values are
the default 'legacy' (where inputs nested inside conditionals or
repeats are identified with e.g. '<conditional_name>|<input_name>') or
'21.01' (where inputs inside conditionals or repeats are nested
elements).
:type input_format: str
:param __tags: optional list of strings
Global tags to apply to all tool outputs (datasets and dataset
collections) in the target history. Example: "__tags": ["#tag1", "#tag2"].
:type __tags: list[str]
"""
tool_id = payload.get("tool_id")
tool_uuid = payload.get("tool_uuid")
if tool_id in PROTECTED_TOOLS:
raise exceptions.RequestParameterInvalidException(
f"Cannot execute tool [{tool_id}] directly, must use alternative endpoint."
)
if tool_id is None and tool_uuid is None:
raise exceptions.RequestParameterInvalidException("Must specify a valid tool_id to use this endpoint.")
__tags = payload.get("__tags", [])
if not isinstance(__tags, list) or not all(isinstance(tag, str) for tag in __tags):
raise exceptions.RequestParameterInvalidException("__tags must be a list of strings.")
return self.service._create(trans, payload, **kwd)
def _kwd_or_payload(kwd: dict[str, Any]) -> dict[str, Any]:
if "payload" in kwd:
kwd = cast(dict[str, Any], kwd.get("payload"))
return kwd