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Source code for galaxy.webapps.galaxy.api.tools
import logging
import os
from json import dumps, loads
from typing import Any, cast, Dict, Optional
from galaxy import exceptions, util, web
from galaxy.managers.collections_util import dictify_dataset_collection_instance
from galaxy.managers.hdas import HDAManager
from galaxy.managers.histories import HistoryManager
from galaxy.model import PostJobAction
from galaxy.tools import global_tool_errors
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 . import BaseGalaxyAPIController, depends
from ._fetch_util import validate_and_normalize_targets
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']
[docs]class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
"""
RESTful controller for interactions with tools.
"""
history_manager: HistoryManager = depends(HistoryManager)
hda_manager: HDAManager = depends(HDAManager)
[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 trackster: if true, only tools that are compatible with
Trackster are returned
: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'))
trackster = util.string_as_bool(kwds.get('trackster', 'False'))
q = kwds.get('q', '')
tool_id = kwds.get('tool_id', '')
tool_help = util.string_as_bool(kwds.get('tool_help', 'False'))
# 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._search(q)
results = []
if hits:
for hit in hits:
try:
tool = self._get_tool(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._detect(trans, tool_id)
return detected_versions
# Return everything.
try:
return self.app.toolbox.to_dict(trans, in_panel=in_panel, trackster=trackster, tool_help=tool_help)
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._get_tool(id, user=trans.user, tool_version=tool_version)
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')
history_id = kwd.pop('history_id', None)
history = None
if history_id:
history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
tool = self._get_tool(id, tool_version=tool_version, user=trans.user)
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._get_tool(id, tool_version=tool_version, user=trans.user)
path = tool.test_data_path(kwd.get("filename"))
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._get_tool(id, tool_version=tool_version, user=trans.user)
filename = kwd.get("filename")
if filename is None:
raise exceptions.ObjectNotFound("Test data filename not specified.")
path = tool.test_data_path(filename)
if path:
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):
"""
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("Access denied, please login for tool with id '%s'." % id)
else:
tools = [self._get_tool(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._get_tool(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._get_tool(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._get_tool(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._get_tool(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._get_tool(id, user=trans.user)
if hasattr(tool, 'lineage'):
lineage_dict = tool.lineage.to_dict()
else:
lineage_dict = None
tool_shed_dependencies = tool.installed_tool_dependencies
tool_shed_dependencies_dict: Optional[list] = None
if tool_shed_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,
}
def _detect(self, trans: GalaxyWebTransaction, tool_id):
"""
Detect whether the tool with the given id is installed.
:param tool_id: exact id of the tool
:type tool_id: str
:return: list with available versions
"return type: list
"""
tools = self.app.toolbox.get_tool(tool_id, get_all_versions=True)
detected_versions = []
if tools:
for tool in tools:
if tool and tool.allow_user_access(trans.user):
detected_versions.append(tool.version)
return detected_versions
def _search(self, q):
"""
Perform the search on the given query.
Boosts and numer of results are configurable in galaxy.ini file.
:param q: the query to search with
:type q: str
:return: Dictionary containing the tools' ids of the best hits.
:return type: dict
"""
tool_name_boost = self.app.config.get('tool_name_boost', 9)
tool_id_boost = self.app.config.get('tool_id_boost', 9)
tool_section_boost = self.app.config.get('tool_section_boost', 3)
tool_description_boost = self.app.config.get('tool_description_boost', 2)
tool_label_boost = self.app.config.get('tool_label_boost', 1)
tool_stub_boost = self.app.config.get('tool_stub_boost', 5)
tool_help_boost = self.app.config.get('tool_help_boost', 0.5)
tool_search_limit = self.app.config.get('tool_search_limit', 20)
tool_enable_ngram_search = self.app.config.get('tool_enable_ngram_search', False)
tool_ngram_minsize = self.app.config.get('tool_ngram_minsize', 3)
tool_ngram_maxsize = self.app.config.get('tool_ngram_maxsize', 4)
results = self.app.toolbox_search.search(q=q,
tool_name_boost=tool_name_boost,
tool_id_boost=tool_id_boost,
tool_section_boost=tool_section_boost,
tool_description_boost=tool_description_boost,
tool_label_boost=tool_label_boost,
tool_stub_boost=tool_stub_boost,
tool_help_boost=tool_help_boost,
tool_search_limit=tool_search_limit,
tool_enable_ngram_search=tool_enable_ngram_search,
tool_ngram_minsize=tool_ngram_minsize,
tool_ngram_maxsize=tool_ngram_maxsize)
return results
[docs] @expose_api_anonymous_and_sessionless
def citations(self, trans: GalaxyWebTransaction, id, **kwds):
tool = self._get_tool(id, user=trans.user)
rval = []
for citation in tool.citations:
rval.append(citation.to_dict('bibtex'))
return rval
[docs] @expose_api_anonymous_and_sessionless
def xrefs(self, trans: GalaxyWebTransaction, id, **kwds):
tool = self._get_tool(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"] = 'attachment; filename="%s.tgz"' % (id)
return download_file
[docs] @expose_api_anonymous
def fetch(self, trans: GalaxyWebTransaction, payload, **kwd):
"""Adapt clean API to tool-constrained API.
"""
request_version = '1'
if "history_id" not in payload:
raise exceptions.RequestParameterMissingException("history_id must be specified")
history_id = payload.pop("history_id")
clean_payload = {}
files_payload = {}
for key, value in payload.items():
if key == "key":
continue
if key.startswith('files_') or key.startswith('__files_'):
files_payload[key] = value
continue
clean_payload[key] = value
validate_and_normalize_targets(trans, clean_payload)
clean_payload["check_content"] = trans.app.config.check_upload_content
request = dumps(clean_payload)
create_payload = {
'tool_id': "__DATA_FETCH__",
'history_id': history_id,
'inputs': {
'request_version': request_version,
'request_json': request,
'file_count': str(len(files_payload))
},
}
create_payload.update(files_payload)
return self._create(trans, create_payload, **kwd)
[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
"""
tool_id = payload.get("tool_id")
tool_uuid = payload.get("tool_uuid")
if tool_id in PROTECTED_TOOLS:
raise exceptions.RequestParameterInvalidException("Cannot execute tool [%s] directly, must use alternative endpoint." % tool_id)
if tool_id is None and tool_uuid is None:
raise exceptions.RequestParameterInvalidException("Must specify a valid tool_id to use this endpoint.")
return self._create(trans, payload, **kwd)
def _create(self, trans: GalaxyWebTransaction, payload, **kwd):
if trans.user_is_bootstrap_admin:
raise exceptions.RealUserRequiredException("Only real users can execute tools or run jobs.")
action = payload.get('action')
if action == 'rerun':
raise Exception("'rerun' action has been deprecated")
# Get tool.
tool_version = payload.get('tool_version')
tool_id = payload.get('tool_id')
tool_uuid = payload.get('tool_uuid')
get_kwds = dict(
tool_id=tool_id,
tool_uuid=tool_uuid,
tool_version=tool_version,
)
if tool_id is None and tool_uuid is None:
raise exceptions.RequestParameterMissingException("Must specify either a tool_id or a tool_uuid.")
tool = trans.app.toolbox.get_tool(**get_kwds)
if not tool:
log.debug(f"Not found tool with kwds [{get_kwds}]")
raise exceptions.ToolMissingException('Tool not found.')
if not tool.allow_user_access(trans.user):
raise exceptions.ItemAccessibilityException('Tool not accessible.')
if trans.app.config.user_activation_on:
if not trans.user:
log.warning("Anonymous user attempts to execute tool, but account activation is turned on.")
elif not trans.user.active:
log.warning("User \"%s\" attempts to execute tool, but account activation is turned on and user account is not active." % trans.user.email)
# Set running history from payload parameters.
# History not set correctly as part of this API call for
# dataset upload.
history_id = payload.get('history_id')
if 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:
target_history = None
# Set up inputs.
inputs = payload.get('inputs', {})
if not isinstance(inputs, dict):
raise exceptions.RequestParameterInvalidException("inputs invalid %s" % inputs)
# Find files coming in as multipart file data and add to inputs.
for k, v in payload.items():
if k.startswith('files_') or k.startswith('__files_'):
inputs[k] = v
# for inputs that are coming from the Library, copy them into the history
self._patch_library_inputs(trans, inputs, target_history)
# TODO: encode data ids and decode ids.
# TODO: handle dbkeys
params = util.Params(inputs, sanitize=False)
incoming = params.__dict__
# use_cached_job can be passed in via the top-level payload or among the tool inputs.
# I think it should be a top-level parameter, but because the selector is implemented
# as a regular tool parameter we accept both.
use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false'))
input_format = str(payload.get('input_format', 'legacy'))
vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format)
# TODO: check for errors and ensure that output dataset(s) are available.
output_datasets = vars.get('out_data', [])
rval: Dict[str, Any] = {'outputs': [], 'output_collections': [], 'jobs': [], 'implicit_collections': []}
rval['produces_entry_points'] = tool.produces_entry_points
job_errors = vars.get('job_errors', [])
if job_errors:
# If we are here - some jobs were successfully executed but some failed.
rval['errors'] = job_errors
outputs = rval['outputs']
# TODO:?? poss. only return ids?
for output_name, output in output_datasets:
output_dict = output.to_dict()
# add the output name back into the output data structure
# so it's possible to figure out which newly created elements
# correspond with which tool file outputs
output_dict['output_name'] = output_name
outputs.append(trans.security.encode_dict_ids(output_dict, skip_startswith="metadata_"))
new_pja_flush = False
for job in vars.get('jobs', []):
rval['jobs'].append(self.encode_all_ids(trans, job.to_dict(view='collection'), recursive=True))
if inputs.get('send_email_notification', False):
# Unless an anonymous user is invoking this via the API it
# should never be an option, but check and enforce that here
if trans.user is None:
raise exceptions.ToolExecutionError("Anonymously run jobs cannot send an email notification.")
else:
job_email_action = PostJobAction('EmailAction')
job.add_post_job_action(job_email_action)
new_pja_flush = True
if new_pja_flush:
trans.sa_session.flush()
for output_name, collection_instance in vars.get('output_collections', []):
history = target_history or trans.history
output_dict = dictify_dataset_collection_instance(collection_instance, security=trans.security, parent=history)
output_dict['output_name'] = output_name
rval['output_collections'].append(output_dict)
for output_name, collection_instance in vars.get('implicit_collections', {}).items():
history = target_history or trans.history
output_dict = dictify_dataset_collection_instance(collection_instance, security=trans.security, parent=history)
output_dict['output_name'] = output_name
rval['implicit_collections'].append(output_dict)
return rval
def _patch_library_inputs(self, trans: GalaxyWebTransaction, inputs, target_history):
"""
Transform inputs from the data libaray to history items.
"""
for k, v in inputs.items():
new_value = self._patch_library_dataset(trans, v, target_history)
if new_value:
v = new_value
elif isinstance(v, dict) and 'values' in v:
for index, value in enumerate(v['values']):
patched = self._patch_library_dataset(trans, value, target_history)
if patched:
v['values'][index] = patched
inputs[k] = v
def _patch_library_dataset(self, trans: GalaxyWebTransaction, v, target_history):
if isinstance(v, dict) and 'id' in v and v.get('src') == 'ldda':
ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v['id']))
if trans.user_is_admin or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset):
return ldda.to_history_dataset_association(target_history, add_to_history=True)
#
# -- Helper methods --
#
def _get_tool(self, id, tool_version=None, user=None):
tool = self.app.toolbox.get_tool(id, tool_version)
if not tool:
raise exceptions.ObjectNotFound("Could not find tool with id '%s'." % id)
if not tool.allow_user_access(user):
raise exceptions.AuthenticationFailed("Access denied, please login for tool with id '%s'." % id)
return tool
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