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Source code for galaxy.tools.parameters.basic
"""
Basic tool parameters.
"""
import contextlib
import json
import logging
import os
import os.path
import re
import typing
import urllib.parse
from collections.abc import MutableMapping
from typing import (
Any,
Dict,
List,
Optional,
Tuple,
TYPE_CHECKING,
Union,
)
from packaging.version import Version
from webob.compat import cgi_FieldStorage
from galaxy import util
from galaxy.files import ProvidesFileSourcesUserContext
from galaxy.managers.dbkeys import read_dbnames
from galaxy.model import (
cached_id,
Dataset,
DatasetCollection,
DatasetCollectionElement,
DatasetHash,
DatasetInstance,
DatasetSource,
HistoryDatasetAssociation,
HistoryDatasetCollectionAssociation,
LibraryDatasetDatasetAssociation,
)
from galaxy.model.dataset_collections import builder
from galaxy.schema.fetch_data import FilesPayload
from galaxy.tool_util.parameters.factory import get_color_value
from galaxy.tool_util.parser import get_input_source as ensure_input_source
from galaxy.tool_util.parser.util import (
boolean_is_checked,
boolean_true_and_false_values,
ParameterParseException,
text_input_is_optional,
)
from galaxy.tools.parameters.workflow_utils import workflow_building_modes
from galaxy.util import (
sanitize_param,
string_as_bool,
string_as_bool_or_none,
unicodify,
)
from galaxy.util.dictifiable import UsesDictVisibleKeys
from galaxy.util.expressions import ExpressionContext
from galaxy.util.hash_util import HASH_NAMES
from galaxy.util.rules_dsl import RuleSet
from . import (
dynamic_options,
history_query,
validation,
)
from .dataset_matcher import get_dataset_matcher_factory
from .sanitize import ToolParameterSanitizer
from .workflow_utils import (
is_runtime_value,
runtime_to_json,
runtime_to_object,
RuntimeValue,
)
if TYPE_CHECKING:
from sqlalchemy.orm import Session
from galaxy.model import (
History,
HistoryItem,
)
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.structured_app import MinimalApp
log = logging.getLogger(__name__)
WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile(r"\$\{.+?\}")
[docs]def contains_workflow_parameter(value, search=False):
if not isinstance(value, str):
return False
if search and WORKFLOW_PARAMETER_REGULAR_EXPRESSION.search(value):
return True
if not search and WORKFLOW_PARAMETER_REGULAR_EXPRESSION.match(value):
return True
return False
[docs]def is_runtime_context(trans, other_values):
if trans.workflow_building_mode:
return True
for context_value in other_values.values():
if is_runtime_value(context_value):
return True
for v in util.listify(context_value):
if isinstance(v, HistoryDatasetAssociation) and (
(hasattr(v, "state") and v.state != Dataset.states.OK) or hasattr(v, "implicit_conversion")
):
return True
return False
[docs]def parse_dynamic_options(param, input_source):
dynamic_options_config = input_source.parse_dynamic_options()
if not dynamic_options_config:
return None
options_elem = dynamic_options_config.elem()
if options_elem is None:
return None
return dynamic_options.DynamicOptions(options_elem, param)
# Describe a parameter value error where there is no actual supplied
# parameter - e.g. just a specification issue.
NO_PARAMETER_VALUE = object()
[docs]@contextlib.contextmanager
def assert_throws_param_value_error(message):
exception_thrown = False
try:
yield
except ParameterValueError as e:
exception_thrown = True
assert str(e) == message
assert exception_thrown
[docs]class ParameterValueError(ValueError):
[docs] def __init__(self, message_suffix, parameter_name, parameter_value=NO_PARAMETER_VALUE, is_dynamic=None):
message = f"Parameter '{parameter_name}': {message_suffix}"
super().__init__(message)
self.message_suffix = message_suffix
self.parameter_name = parameter_name
self.parameter_value = parameter_value
self.is_dynamic = is_dynamic
[docs] def to_dict(self):
as_dict = {"message": unicodify(self)}
as_dict["message_suffix"] = self.message_suffix
as_dict["parameter_name"] = self.parameter_name
if self.parameter_value is not NO_PARAMETER_VALUE:
as_dict["parameter_value"] = self.parameter_value
if self.is_dynamic is not None:
as_dict["is_dynamic"] = self.is_dynamic
return as_dict
[docs]class ToolParameter(UsesDictVisibleKeys):
"""
Describes a parameter accepted by a tool. This is just a simple stub at the
moment but in the future should encapsulate more complex parameters (lists
of valid choices, validation logic, ...)
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None)
>>> p = ToolParameter(None, XML('<param argument="--parameter-name" type="text" value="default" />'))
>>> assert p.name == 'parameter_name'
>>> assert sorted(p.to_dict(trans).items()) == [('argument', '--parameter-name'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', None)]
"""
name: str
dict_collection_visible_keys = ["name", "argument", "type", "label", "help", "help_format", "refresh_on_change"]
[docs] def __init__(self, tool, input_source, context=None):
input_source = ensure_input_source(input_source)
self.tool = tool
self.argument = input_source.get("argument")
self.name = self.__class__.parse_name(input_source)
self.type = input_source.get("type")
self.hidden = input_source.get_bool("hidden", False)
self.refresh_on_change = input_source.get_bool("refresh_on_change", False)
self.optional = input_source.parse_optional()
self.is_dynamic = False
self.label = input_source.parse_label()
self.help = input_source.parse_help()
self.help_format = input_source.get("help_format") or "html"
if (sanitizer_elem := input_source.parse_sanitizer_elem()) is not None:
self.sanitizer = ToolParameterSanitizer.from_element(sanitizer_elem)
else:
self.sanitizer = None
self.validators = validation.to_validators(tool.app if tool else None, input_source.parse_validators())
@property
def visible(self) -> bool:
"""Return true if the parameter should be rendered on the form"""
return True
[docs] def get_label(self):
"""Return user friendly name for the parameter"""
return self.label if self.label else self.name
[docs] def from_json(self, value, trans, other_values=None):
"""
Convert a value from an HTML POST into the parameters preferred value
format.
"""
return value
[docs] def get_initial_value(self, trans, other_values):
"""
Return the starting value of the parameter
"""
return None
[docs] def get_required_enctype(self):
"""
If this parameter needs the form to have a specific encoding
return it, otherwise return None (indicating compatibility with
any encoding)
"""
return None
[docs] def get_dependencies(self):
"""
Return the names of any other parameters this parameter depends on
"""
return []
[docs] def to_json(self, value, app, use_security) -> str:
"""Convert a value to a string representation suitable for persisting"""
return unicodify(value)
[docs] def to_python(self, value, app):
"""Convert a value created with to_json back to an object representation"""
return value
[docs] def value_to_basic(self, value, app, use_security=False):
if is_runtime_value(value):
return runtime_to_json(value)
return self.to_json(value, app, use_security)
[docs] def value_from_basic(self, value, app, ignore_errors=False):
# Handle Runtime and Unvalidated values
if is_runtime_value(value):
if isinstance(self, HiddenToolParameter):
raise ParameterValueError(message_suffix="Runtime Parameter not valid", parameter_name=self.name)
return runtime_to_object(value)
elif isinstance(value, MutableMapping) and value.get("__class__") == "UnvalidatedValue":
return value["value"]
# Delegate to the 'to_python' method
if ignore_errors:
try:
return self.to_python(value, app)
except Exception:
return value
else:
return self.to_python(value, app)
[docs] def value_to_display_text(self, value) -> str:
if is_runtime_value(value):
return "Not available."
return self.to_text(value)
[docs] def to_text(self, value) -> str:
"""
Convert a value to a text representation suitable for displaying to
the user
>>> from galaxy.util import XML
>>> p = ToolParameter(None, XML('<param name="_name" />'))
>>> print(p.to_text(None))
Not available.
>>> print(p.to_text(''))
Empty.
>>> print(p.to_text('text'))
text
>>> print(p.to_text(True))
True
>>> print(p.to_text(False))
False
>>> print(p.to_text(0))
0
"""
if value is not None:
str_value = unicodify(value)
if not str_value:
return "Empty."
return str_value
return "Not available."
[docs] def to_param_dict_string(self, value, other_values=None) -> str:
"""Called via __str__ when used in the Cheetah template"""
if value is None:
value = ""
elif not isinstance(value, str):
value = str(value)
if self.tool is None or self.tool.options.sanitize:
if self.sanitizer:
value = self.sanitizer.sanitize_param(value)
else:
value = sanitize_param(value)
return value
[docs] def validate(self, value, trans=None) -> None:
if value in ["", None] and self.optional:
return
for validator in self.validators:
try:
validator.validate(value, trans)
except ValueError as e:
raise ParameterValueError(str(e), self.name, value) from None
[docs] def to_dict(self, trans, other_values=None):
"""to_dict tool parameter. This can be overridden by subclasses."""
other_values = other_values or {}
tool_dict = self._dictify_view_keys()
tool_dict["model_class"] = self.__class__.__name__
tool_dict["optional"] = self.optional
tool_dict["hidden"] = self.hidden
tool_dict["is_dynamic"] = self.is_dynamic
tool_dict["value"] = self.value_to_basic(
self.get_initial_value(trans, other_values), trans.app, use_security=True
)
return tool_dict
[docs] @classmethod
def build(cls, tool, input_source):
"""Factory method to create parameter of correct type"""
input_source = ensure_input_source(input_source)
param_name = cls.parse_name(input_source)
param_type = input_source.get("type")
if not param_type:
raise ValueError(f"parameter '{param_name}' requires a 'type'")
elif param_type not in parameter_types:
raise ValueError(f"parameter '{param_name}' uses an unknown type '{param_type}'")
else:
return parameter_types[param_type](tool, input_source)
[docs]class SimpleTextToolParameter(ToolParameter):
[docs] def __init__(self, tool, input_source):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
optional = input_source.get("optional", None)
if optional is not None:
optional = string_as_bool(optional)
else:
# Optionality not explicitly defined, default to False
optional = False
self.optional = optional
if self.optional:
self.value = None
else:
self.value = ""
[docs] def to_json(self, value, app, use_security):
"""Convert a value to a string representation suitable for persisting"""
return unicodify(value)
[docs]class TextToolParameter(SimpleTextToolParameter):
"""
Parameter that can take on any text value.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None)
>>> p = TextToolParameter(None, XML('<param name="_name" type="text" value="default" />'))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
"""
[docs] def __init__(self, tool, input_source):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
self.profile = tool.profile if tool else None
self.datalist = []
for title, value, _ in input_source.parse_static_options():
self.datalist.append({"label": title, "value": value})
# why does Integer and Float subclass this :_(
if self.type == "text":
self.optional, self.optionality_inferred = text_input_is_optional(input_source)
else:
self.optionality_inferred = False
self.value = input_source.get("value")
self.area = input_source.get_bool("area", False)
[docs] def validate(self, value, trans=None):
search = self.type == "text"
if not (
trans
and trans.workflow_building_mode is workflow_building_modes.ENABLED
and contains_workflow_parameter(value, search=search)
):
return super().validate(value, trans)
@property
def wrapper_default(self) -> Optional[str]:
"""Handle change in default handling pre and post 23.0 profiles."""
profile = self.profile
legacy_behavior = profile is None or Version(str(profile)) < Version("23.0")
default_value = None
if self.optional and self.optionality_inferred and legacy_behavior:
default_value = ""
return default_value
[docs] def to_dict(self, trans, other_values=None):
d = super().to_dict(trans)
other_values = other_values or {}
d["area"] = self.area
d["datalist"] = self.datalist
d["optional"] = self.optional
return d
[docs]class IntegerToolParameter(TextToolParameter):
"""
Parameter that takes an integer value.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=True)
>>> p = IntegerToolParameter(None, XML('<param name="_name" type="integer" value="10" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
>>> assert type(p.from_json("10", trans)) == int
>>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
... p.from_json("_string", trans)
"""
dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ["min", "max"]
[docs] def __init__(self, tool, input_source):
super().__init__(tool, input_source)
if self.value:
try:
int(self.value)
except ValueError:
raise ParameterValueError("the attribute 'value' must be an integer", self.name)
self.min = input_source.get("min")
self.max = input_source.get("max")
if self.min:
try:
self.min = int(self.min)
except ValueError:
raise ParameterValueError("attribute 'min' must be an integer", self.name, self.min)
if self.max:
try:
self.max = int(self.max)
except ValueError:
raise ParameterValueError("attribute 'max' must be an integer", self.name, self.max)
if self.min is not None or self.max is not None:
self.validators.append(validation.InRangeValidator.simple_range_validator(self.min, self.max))
[docs] def from_json(self, value, trans, other_values=None):
other_values = other_values or {}
try:
return int(value)
except (TypeError, ValueError):
if contains_workflow_parameter(value) and trans.workflow_building_mode is workflow_building_modes.ENABLED:
return value
if not value and self.optional:
return ""
if trans.workflow_building_mode is workflow_building_modes.ENABLED:
raise ParameterValueError("an integer or workflow parameter is required", self.name, value)
else:
raise ParameterValueError(
"the attribute 'value' must be set for non optional parameters", self.name, value
)
[docs] def to_python(self, value, app):
try:
return int(value)
except (TypeError, ValueError) as err:
if contains_workflow_parameter(value):
return value
if not value and self.optional:
return None
raise err
[docs] def get_initial_value(self, trans, other_values):
if self.value is not None and self.value != "":
return int(self.value)
else:
return None
[docs]class FloatToolParameter(TextToolParameter):
"""
Parameter that takes a real number value.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=True)
>>> p = FloatToolParameter(None, XML('<param name="_name" type="float" value="3.141592" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
>>> assert type(p.from_json("36.1", trans)) == float
>>> with assert_throws_param_value_error("Parameter '_name': an integer or workflow parameter is required"):
... p.from_json("_string", trans)
"""
dict_collection_visible_keys = ToolParameter.dict_collection_visible_keys + ["min", "max"]
[docs] def __init__(self, tool, input_source):
super().__init__(tool, input_source)
self.min = input_source.get("min")
self.max = input_source.get("max")
if self.value:
try:
float(self.value)
except ValueError:
raise ParameterValueError("the attribute 'value' must be a real number", self.name, self.value)
if self.min:
try:
self.min = float(self.min)
except ValueError:
raise ParameterValueError("attribute 'min' must be a real number", self.name, self.min)
if self.max:
try:
self.max = float(self.max)
except ValueError:
raise ParameterValueError("attribute 'max' must be a real number", self.name, self.max)
if self.min is not None or self.max is not None:
self.validators.append(validation.InRangeValidator.simple_range_validator(self.min, self.max))
[docs] def from_json(self, value, trans, other_values=None):
other_values = other_values or {}
try:
return float(value)
except (TypeError, ValueError):
if contains_workflow_parameter(value) and trans.workflow_building_mode is workflow_building_modes.ENABLED:
return value
if not value and self.optional:
return ""
if trans.workflow_building_mode is workflow_building_modes.ENABLED:
raise ParameterValueError("an integer or workflow parameter is required", self.name, value)
else:
raise ParameterValueError(
"the attribute 'value' must be set for non optional parameters", self.name, value
)
[docs] def to_python(self, value, app):
try:
return float(value)
except (TypeError, ValueError) as err:
if contains_workflow_parameter(value):
return value
if not value and self.optional:
return None
raise err
[docs] def get_initial_value(self, trans, other_values):
if self.value is None:
return None
try:
return float(self.value)
except Exception:
return None
[docs]class BooleanToolParameter(ToolParameter):
"""
Parameter that takes one of two values.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch())
>>> p = BooleanToolParameter(None, XML('<param name="_name" type="boolean" checked="yes" truevalue="_truevalue" falsevalue="_falsevalue" />'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', True)]
>>> print(p.from_json('true', trans))
True
>>> print(p.to_param_dict_string(True))
_truevalue
>>> print(p.from_json('false', trans))
False
>>> print(p.to_param_dict_string(False))
_falsevalue
>>> value = p.to_json('false', trans.app, use_security=False)
>>> assert isinstance(value, bool)
>>> assert value == False
>>> value = p.to_json(True, trans.app, use_security=False)
>>> assert isinstance(value, bool)
>>> assert value == True
"""
[docs] def __init__(self, tool, input_source):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
try:
truevalue, falsevalue = boolean_true_and_false_values(input_source, tool and tool.profile)
except ParameterParseException as ppe:
raise ParameterValueError(ppe.message, self.name)
self.truevalue = truevalue
self.falsevalue = falsevalue
self.optional = input_source.get_bool("optional", False)
self.checked = boolean_is_checked(input_source)
[docs] def to_python(self, value, app=None):
if not self.optional:
ret_val = string_as_bool(value)
else:
ret_val = string_as_bool_or_none(value)
return ret_val
[docs] def to_param_dict_string(self, value, other_values=None):
if self.to_python(value):
return self.truevalue
else:
return self.falsevalue
[docs] def to_dict(self, trans, other_values=None):
d = super().to_dict(trans)
d["truevalue"] = self.truevalue
d["falsevalue"] = self.falsevalue
d["optional"] = self.optional
return d
@property
def legal_values(self):
return [self.truevalue, self.falsevalue]
[docs]class FileToolParameter(ToolParameter):
"""
Parameter that takes an uploaded file as a value.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch())
>>> p = FileToolParameter(None, XML('<param name="_name" type="file"/>'))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FileToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'file'), ('value', None)]
"""
[docs] def from_json(self, value, trans, other_values=None):
# Middleware or proxies may encode files in special ways (TODO: this
# should be pluggable)
if isinstance(value, FilesPayload):
# multi-part upload handled and persisted in service layer
return value.model_dump()
elif isinstance(value, MutableMapping):
if "session_id" in value:
# handle api upload
session_id = value["session_id"]
upload_store = trans.app.config.tus_upload_store or trans.app.config.new_file_path
if re.match(r"^[\w-]+$", session_id) is None:
raise ValueError("Invalid session id format.")
local_filename = os.path.abspath(os.path.join(upload_store, session_id))
else:
# handle nginx upload
upload_store = trans.app.config.nginx_upload_store
assert (
upload_store
), "Request appears to have been processed by nginx_upload_module but Galaxy is not configured to recognize it."
local_filename = os.path.abspath(value["path"])
assert local_filename.startswith(
upload_store
), f"Filename provided by nginx ({local_filename}) is not in correct directory ({upload_store})."
value = dict(filename=value["name"], local_filename=local_filename)
return value
[docs] def get_required_enctype(self):
"""
File upload elements require the multipart/form-data encoding
"""
return "multipart/form-data"
[docs] def to_json(self, value, app, use_security):
if value in [None, ""]:
return None
elif isinstance(value, str):
return value
elif isinstance(value, MutableMapping):
# or should we jsonify?
try:
return value["local_filename"]
except KeyError:
return None
elif isinstance(value, cgi_FieldStorage):
return value.file.name
raise Exception("FileToolParameter cannot be persisted")
[docs] def to_python(self, value, app):
if value is None:
return None
elif isinstance(value, str):
return value
else:
raise Exception("FileToolParameter cannot be persisted")
[docs]class FTPFileToolParameter(ToolParameter):
"""
Parameter that takes a file uploaded via FTP as a value.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch(), user=None)
>>> p = FTPFileToolParameter(None, XML('<param name="_name" type="ftpfile"/>'))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'FTPFileToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('refresh_on_change', False), ('type', 'ftpfile'), ('value', None)]
"""
[docs] def __init__(self, tool, input_source):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
self.multiple = input_source.get_bool("multiple", True)
self.optional = input_source.parse_optional(True)
self.user_ftp_dir = ""
[docs] def get_initial_value(self, trans, other_values):
if trans is not None:
if trans.user is not None:
self.user_ftp_dir = f"{trans.user_ftp_dir}/"
return None
@property
def visible(self):
if self.tool.app.config.ftp_upload_dir is None or self.tool.app.config.ftp_upload_site is None:
return False
return True
[docs] def to_param_dict_string(self, value, other_values=None):
if value == "":
return "None"
lst = [f"{self.user_ftp_dir}{dataset}" for dataset in value]
if self.multiple:
return lst
else:
return lst[0]
[docs] def from_json(self, value, trans, other_values=None):
return self.to_python(value, trans.app, validate=True)
[docs] def to_python(self, value, app, validate=False):
if not isinstance(value, list):
value = [value]
lst: List[str] = []
for val in value:
if val in [None, ""]:
lst = []
break
if isinstance(val, MutableMapping):
lst.append(val["name"])
else:
lst.append(val)
if len(lst) == 0:
if not self.optional and validate:
raise ValueError("Please select a valid FTP file.")
return None
if validate and self.tool.app.config.ftp_upload_dir is None:
raise ValueError("The FTP directory is not configured.")
return lst
[docs] def to_dict(self, trans, other_values=None):
d = super().to_dict(trans)
d["multiple"] = self.multiple
return d
[docs]class HiddenToolParameter(ToolParameter):
"""
Parameter that takes one of two values.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch())
>>> p = HiddenToolParameter(None, XML('<param name="_name" type="hidden" value="_value"/>'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
"""
[docs] def __init__(self, tool, input_source):
super().__init__(tool, input_source)
self.value = input_source.get("value")
self.hidden = True
[docs]class ColorToolParameter(ToolParameter):
"""
Parameter that stores a color.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch())
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff"/>'))
>>> print(p.name)
_name
>>> print(p.to_param_dict_string("#ffffff"))
#ffffff
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color"/>'))
>>> print(p.get_initial_value(trans, {}))
#000000
>>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff" rgb="True"/>'))
>>> print(p.to_param_dict_string("#ffffff"))
(255, 255, 255)
>>> with assert_throws_param_value_error("Parameter '_name': Failed to convert 'None' to RGB."):
... p.to_param_dict_string(None)
"""
[docs] def __init__(self, tool, input_source):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
self.value = get_color_value(input_source)
self.rgb = input_source.get_bool("rgb", False)
[docs] def get_initial_value(self, trans, other_values):
if self.value is not None:
return self.value.lower()
[docs] def to_param_dict_string(self, value, other_values=None):
if self.rgb:
try:
return str(tuple(int(value.lstrip("#")[i : i + 2], 16) for i in (0, 2, 4)))
except Exception:
raise ParameterValueError(f"Failed to convert '{value}' to RGB.", self.name)
return str(value)
[docs]class BaseURLToolParameter(HiddenToolParameter):
"""
Returns a parameter that contains its value prepended by the
current server base url. Used in all redirects.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch())
>>> p = BaseURLToolParameter(None, XML('<param name="_name" type="base_url" value="_value"/>'))
>>> print(p.name)
_name
>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('help_format', 'html'), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
"""
[docs] def __init__(self, tool, input_source):
super().__init__(tool, input_source)
self.value = input_source.get("value", "")
def _get_value(self, trans):
try:
if not self.value.startswith("/"):
raise Exception("baseurl value must start with a /")
return trans.url_builder(self.value, qualified=True)
except Exception as e:
log.debug('Url creation failed for "%s": %s', self.name, unicodify(e))
return self.value
[docs]def iter_to_string(iterable: typing.Iterable[typing.Any]) -> typing.Generator[str, None, None]:
for item in iterable:
yield str(item)
[docs]class SelectToolParameter(ToolParameter):
"""
Parameter that takes on one (or many) or a specific set of values.
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch(), workflow_building_mode=False)
>>> p = SelectToolParameter(None, XML(
... '''
... <param name="_name" type="select">
... <option value="x">x_label</option>
... <option value="y" selected="true">y_label</option>
... <option value="z">z_label</option>
... </param>
... '''))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', False), ('name', '_name'), ('optional', False), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', False)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', 'y')]
>>> p = SelectToolParameter(None, XML(
... '''
... <param name="_name" type="select" multiple="true">
... <option value="x">x_label</option>
... <option value="y" selected="true">y_label</option>
... <option value="z" selected="true">z_label</option>
... </param>
... '''))
>>> print(p.name)
_name
>>> sorted(p.to_dict(trans).items())
[('argument', None), ('display', None), ('help', ''), ('help_format', 'html'), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'SelectToolParameter'), ('multiple', True), ('name', '_name'), ('optional', True), ('options', [('x_label', 'x', False), ('y_label', 'y', True), ('z_label', 'z', True)]), ('refresh_on_change', False), ('textable', False), ('type', 'select'), ('value', ['y', 'z'])]
>>> print(p.to_param_dict_string(["y", "z"]))
y,z
"""
value_label: str
[docs] def __init__(self, tool, input_source, context=None):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
self.multiple = input_source.get_bool("multiple", False)
# Multiple selects are optional by default, single selection is the inverse.
self.optional = input_source.parse_optional(self.multiple)
self.display = input_source.get("display", None)
self.separator = input_source.get("separator", ",")
self.legal_values = set()
self.dynamic_options = input_source.get("dynamic_options", None)
self.options = parse_dynamic_options(self, input_source)
if self.options is not None:
for validator in self.options.validators:
self.validators.append(validator)
if self.dynamic_options is None and self.options is None:
self.static_options = input_source.parse_static_options()
for _, value, _ in self.static_options:
self.legal_values.add(value)
self.is_dynamic = (self.dynamic_options is not None) or (self.options is not None)
def _get_dynamic_options_call_other_values(self, trans, other_values):
call_other_values = ExpressionContext({"__trans__": trans})
if other_values:
call_other_values.parent = other_values.parent
call_other_values.update(other_values.dict)
return call_other_values
[docs] def get_options(self, trans, other_values):
if self.options:
return self.options.get_options(trans, other_values)
elif self.dynamic_options:
call_other_values = self._get_dynamic_options_call_other_values(trans, other_values)
try:
return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
except Exception as e:
log.debug(
"Error determining dynamic options for parameter '%s' in tool '%s':",
self.name,
self.tool.id,
exc_info=e,
)
return []
else:
return self.static_options
[docs] def get_legal_values(self, trans, other_values, value):
"""
determine the set of values of legal options
"""
return {
history_item_dict_to_python(v, trans.app, self.name) or v
for _, v, _ in self.get_options(trans, other_values)
}
[docs] def get_legal_names(self, trans, other_values):
"""
determine a mapping from names to values for all legal options
"""
return {n: v for n, v, _ in self.get_options(trans, other_values)}
[docs] def from_json(self, value, trans, other_values=None):
return self._select_from_json(value, trans, other_values=other_values, require_legal_value=True)
def _select_from_json(self, value, trans, other_values=None, require_legal_value=True):
other_values = other_values or {}
try:
legal_values = self.get_legal_values(trans, other_values, value)
except ImplicitConversionRequired:
return value
# if the given value is not found in the set of values of the legal
# options we fall back to check if the value is in the set of names of
# the legal options. this is done with the fallback_values dict which
# allows to determine the corresponding legal values
fallback_values = self.get_legal_names(trans, other_values)
if (not legal_values or not require_legal_value) and is_runtime_context(trans, other_values):
if self.multiple:
# While it is generally allowed that a select value can be '',
# we do not allow this to be the case in a dynamically
# generated multiple select list being set in workflow building
# mode we instead treat '' as 'No option Selected' (None)
if value == "":
value = None
else:
if isinstance(value, str):
# Split on all whitespace. This not only provides flexibility
# in interpreting values but also is needed because many browsers
# use \r\n to separate lines.
value = value.split()
return value
elif value is None:
if self.optional:
return None
raise ParameterValueError(
"an invalid option (None) was selected, please verify", self.name, None, is_dynamic=self.is_dynamic
)
elif not legal_values:
if self.optional and Version(str(self.tool.profile)) < Version("18.09"):
# Covers optional parameters with default values that reference other optional parameters.
# These will have a value but no legal_values.
# See https://github.com/galaxyproject/tools-iuc/pull/1842#issuecomment-394083768 for context.
return None
raise ParameterValueError(
"requires a value, but no legal values defined", self.name, is_dynamic=self.is_dynamic
)
if isinstance(value, list):
if not self.multiple:
raise ParameterValueError(
"multiple values provided but parameter is not expecting multiple values",
self.name,
is_dynamic=self.is_dynamic,
)
if set(value).issubset(legal_values):
return value
elif set(value).issubset(set(fallback_values.keys())):
return [fallback_values[v] for v in value]
else:
invalid_options = iter_to_string(set(value) - set(legal_values))
raise ParameterValueError(
f"invalid options ({','.join(invalid_options)!r}) were selected (valid options: {','.join(iter_to_string(legal_values))})",
self.name,
is_dynamic=self.is_dynamic,
)
else:
value_is_none = value == "None" and "None" not in legal_values
if value_is_none or not value:
if self.multiple:
if self.optional:
return []
else:
raise ParameterValueError(
"no option was selected for non optional parameter", self.name, is_dynamic=self.is_dynamic
)
if is_runtime_value(value):
return None
if value in legal_values:
return value
elif value in fallback_values:
return fallback_values[value]
elif not require_legal_value:
return value
else:
raise ParameterValueError(
f"an invalid option ({value!r}) was selected (valid options: {','.join(iter_to_string(legal_values))})",
self.name,
value,
is_dynamic=self.is_dynamic,
)
[docs] def to_param_dict_string(self, value, other_values=None):
if value in (None, []):
return "None"
if isinstance(value, list):
if not self.multiple:
raise ParameterValueError(
"multiple values provided but parameter is not expecting multiple values",
self.name,
is_dynamic=self.is_dynamic,
)
value = list(map(str, value))
else:
value = str(value)
if self.tool is None or self.tool.options.sanitize:
if self.sanitizer:
value = self.sanitizer.sanitize_param(value)
else:
value = sanitize_param(value)
if isinstance(value, list):
value = self.separator.join(value)
return value
[docs] def to_json(self, value, app, use_security):
if isinstance(value, HistoryDatasetAssociation):
return history_item_to_json(value, app, use_security=use_security)
return value
[docs] def to_python(self, value, app):
return history_item_dict_to_python(value, app, self.name) or super().to_python(value, app)
[docs] def get_initial_value(self, trans, other_values):
try:
options = list(self.get_options(trans, other_values))
except ImplicitConversionRequired:
return None
if not options:
return None
value = [optval for _, optval, selected in options if selected]
if len(value) == 0:
if not self.optional and not self.multiple and options:
# Nothing selected, but not optional and not a multiple select, with some values,
# so we have to default to something (the HTML form will anyway)
value2 = options[0][1]
else:
value2 = None
elif len(value) == 1 or not self.multiple:
value2 = value[0]
else:
value2 = value
return value2
[docs] def to_text(self, value):
if not isinstance(value, list):
value = [value]
# FIXME: Currently only translating values back to labels if they
# are not dynamic
if self.is_dynamic:
rval = [str(_) for _ in value]
else:
options = list(self.static_options)
rval = []
for t, v, _ in options:
if v in value:
rval.append(t)
if rval:
return "\n".join(rval)
return "Nothing selected."
[docs] def get_dependencies(self):
"""
Get the *names* of the other params this param depends on.
"""
if self.options:
return self.options.get_dependency_names()
else:
return []
[docs] def to_dict(self, trans, other_values=None):
other_values = other_values or {}
d = super().to_dict(trans, other_values)
# Get options, value.
options = self.get_options(trans, other_values)
d["options"] = options
d["display"] = self.display
d["multiple"] = self.multiple
d["textable"] = is_runtime_context(trans, other_values)
return d
[docs] def validate(self, value, trans=None):
if not value:
super().validate(value, trans)
if self.multiple:
if not isinstance(value, list):
value = [value]
else:
value = [value]
for v in value:
super().validate(v, trans)
[docs]class GenomeBuildParameter(SelectToolParameter):
"""
Select list that sets the last used genome build for the current history as "selected".
>>> # Create a mock transaction with 'hg17' as the current build
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> trans = Bunch(app=None, history=Bunch(genome_build='hg17'), db_builds=read_dbnames(None))
>>> p = GenomeBuildParameter(None, XML('<param name="_name" type="genomebuild" value="hg17" />'))
>>> print(p.name)
_name
>>> d = p.to_dict(trans)
>>> o = d['options']
>>> [i for i in o if i[2] == True]
[('Human May 2004 (NCBI35/hg17) (hg17)', 'hg17', True)]
>>> [i for i in o if i[1] == 'hg18']
[('Human Mar. 2006 (NCBI36/hg18) (hg18)', 'hg18', False)]
>>> p.is_dynamic
True
"""
[docs] def __init__(self, *args, **kwds):
super().__init__(*args, **kwds)
if self.tool:
self.static_options = [(value, key, False) for key, value in self._get_dbkey_names()]
self.is_dynamic = True
[docs] def get_options(self, trans, other_values):
last_used_build = object()
if trans.history:
last_used_build = trans.history.genome_build
for dbkey, build_name in self._get_dbkey_names(trans=trans):
yield build_name, dbkey, (dbkey == last_used_build)
[docs] def get_legal_values(self, trans, other_values, value):
return {dbkey for dbkey, _ in self._get_dbkey_names(trans=trans)}
[docs] def to_dict(self, trans, other_values=None):
# skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
d = ToolParameter.to_dict(self, trans)
# Get options, value - options is a generator here, so compile to list
options = list(self.get_options(trans, {}))
value = options[0][1]
for option in options:
if option[2]:
# Found selected option.
value = option[1]
d.update(
{
"options": options,
"value": value,
"display": self.display,
"multiple": self.multiple,
}
)
return d
def _get_dbkey_names(self, trans=None):
if not self.tool:
# Hack for unit tests, since we have no tool
return read_dbnames(None)
return self.tool.app.genome_builds.get_genome_build_names(trans=trans)
[docs]class SelectTagParameter(SelectToolParameter):
"""
Select set that is composed of a set of tags available for an input.
"""
[docs] def __init__(self, tool, input_source):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
self.tool = tool
self.tag_key = input_source.get("group", False)
self.optional = input_source.get("optional", False)
self.multiple = input_source.get("multiple", False)
self.accept_default = input_source.get_bool("accept_default", False)
if self.accept_default:
self.optional = True
self.data_ref = input_source.get("data_ref", None)
self.ref_input = None
# Legacy style default value specification...
self.default_value = input_source.get("default_value", None)
if self.default_value is None:
# Newer style... more in line with other parameters.
self.default_value = input_source.get("value", None)
self.is_dynamic = True
[docs] def from_json(self, value, trans, other_values=None):
other_values = other_values or {}
if self.multiple:
tag_list = []
# split on newline and ,
if isinstance(value, list) or isinstance(value, str):
if not isinstance(value, list):
value = value.split("\n")
for tag_str in value:
for tag in str(tag_str).split(","):
tag = tag.strip()
if tag:
tag_list.append(tag)
if len(tag_list) == 0:
value = None
else:
value = tag_list
else:
if not value:
value = None
# We skip requiring legal values -- this is similar to optional, but allows only subset of datasets to be positive
# TODO: May not actually be required for (nested) collection input ?
return super()._select_from_json(value, trans, other_values, require_legal_value=False)
[docs] def get_tag_list(self, other_values):
"""
Generate a select list containing the tags of the associated dataset (if found).
"""
# Get the value of the associated data reference (a dataset)
history_items = other_values.get(self.data_ref, None)
# Check if a dataset is selected
if is_runtime_value(history_items):
return []
if not history_items:
return []
tags = set()
for history_item in util.listify(history_items):
if hasattr(history_item, "dataset_instances"):
for dataset in history_item.dataset_instances:
for tag in dataset.tags:
if tag.user_tname == "group":
tags.add(tag.user_value)
else:
for tag in history_item.tags:
if tag.user_tname == "group":
tags.add(tag.user_value)
return list(tags)
[docs] def get_options(self, trans, other_values):
"""
Show tags
"""
options = []
for tag in self.get_tag_list(other_values):
options.append((f"Tags: {tag}", tag, False))
return options
[docs] def get_initial_value(self, trans, other_values):
if self.default_value is not None:
return self.default_value
return super().get_initial_value(trans, other_values)
[docs] def get_legal_values(self, trans, other_values, value):
if self.data_ref not in other_values and not trans.workflow_building_mode:
raise ValueError("Value for associated data reference not found (data_ref).")
return set(self.get_tag_list(other_values))
[docs] def to_dict(self, trans, other_values=None):
other_values = other_values or {}
d = super().to_dict(trans, other_values=other_values)
d["data_ref"] = self.data_ref
return d
[docs]class ColumnListParameter(SelectToolParameter):
"""
Select list that consists of either the total number of columns or only
those columns that contain numerical values in the associated DataToolParameter.
# TODO: we need better testing here, but not sure how to associate a DatatoolParameter with a ColumnListParameter
# from a twill perspective...
>>> # Mock up a history (not connected to database)
>>> from galaxy.model import History, HistoryDatasetAssociation
>>> from galaxy.util.bunch import Bunch
>>> from galaxy.util import XML
>>> from galaxy.model.mapping import init
>>> sa_session = init("/tmp", "sqlite:///:memory:", create_tables=True).session
>>> hist = History()
>>> with sa_session.begin():
... sa_session.add(hist)
>>> hda = hist.add_dataset(HistoryDatasetAssociation(id=1, extension='interval', create_dataset=True, sa_session=sa_session))
>>> dtp = DataToolParameter(None, XML('<param name="blah" type="data" format="interval"/>'))
>>> print(dtp.name)
blah
>>> clp = ColumnListParameter(None, XML('<param name="numerical_column" type="data_column" data_ref="blah" numerical="true"/>'))
>>> print(clp.name)
numerical_column
"""
[docs] def __init__(self, tool, input_source):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
self.numerical = input_source.get_bool("numerical", False)
self.optional = input_source.parse_optional(False)
self.accept_default = input_source.get_bool("accept_default", False)
if self.accept_default:
self.optional = True
self.data_ref = input_source.get("data_ref", None)
profile = tool.profile if tool else None
assert (
profile is None or Version(str(profile)) < Version("24.2") or self.data_ref is not None
), f"data_column parameter {self.name} requires a valid data_ref attribute"
self.ref_input = None
# Legacy style default value specification...
self.default_value = input_source.get("default_value", None)
if self.default_value is None:
# Newer style... more in line with other parameters.
self.default_value = input_source.get("value", None)
if self.default_value is not None:
self.default_value = ColumnListParameter._strip_c(self.default_value)
self.is_dynamic = True
self.usecolnames = input_source.get_bool("use_header_names", False)
[docs] def to_json(self, value, app, use_security):
if isinstance(value, str):
return value.strip()
return value
[docs] def from_json(self, value, trans, other_values=None):
"""
Label convention prepends column number with a 'c', but tool uses the integer. This
removes the 'c' when entered into a workflow.
"""
other_values = other_values or {}
if self.multiple:
# split on newline and ,
if isinstance(value, list) or isinstance(value, str):
column_list = []
if not isinstance(value, list):
value = value.split("\n")
for column in value:
for column2 in str(column).split(","):
column2 = column2.strip()
if column2:
column_list.append(column2)
if len(column_list) == 0:
value = None
else:
value = list(map(ColumnListParameter._strip_c, column_list))
else:
value = None
else:
if value:
value = ColumnListParameter._strip_c(value)
else:
value = None
if not value and self.accept_default:
value = self.default_value or "1"
return [value] if self.multiple else value
return super().from_json(value, trans, other_values)
@staticmethod
def _strip_c(column):
column = str(column).strip()
if column.startswith("c") and len(column) > 1 and all(c.isdigit() for c in column[1:]):
column = column.lower()[1:]
return column
[docs] def get_column_list(self, trans, other_values):
"""
Generate a select list containing the columns of the associated
dataset (if found).
"""
# Get the value of the associated data reference (one or more datasets)
datasets = other_values.get(self.data_ref)
# Check if a dataset is selected
if not datasets:
return []
column_list = None
for dataset in util.listify(datasets):
# Use representative dataset if a dataset collection is parsed
if isinstance(dataset, HistoryDatasetCollectionAssociation):
dataset = dataset.to_hda_representative()
if isinstance(dataset, DatasetCollectionElement):
dataset = dataset.first_dataset_instance()
if isinstance(dataset, HistoryDatasetAssociation) and self.ref_input and self.ref_input.formats:
direct_match, target_ext, converted_dataset = dataset.find_conversion_destination(
self.ref_input.formats
)
if not direct_match and target_ext:
if not converted_dataset:
raise ImplicitConversionRequired
else:
dataset = converted_dataset
# Columns can only be identified if the dataset is ready and metadata is available
if (
not hasattr(dataset, "metadata")
or not hasattr(dataset.metadata, "columns")
or not dataset.metadata.columns
):
return []
# Build up possible columns for this dataset
this_column_list = []
if self.numerical:
# If numerical was requested, filter columns based on metadata
for i, col in enumerate(dataset.metadata.column_types):
if col == "int" or col == "float":
this_column_list.append(str(i + 1))
else:
this_column_list = [str(i) for i in range(1, dataset.metadata.columns + 1)]
# Take the intersection of these columns with the other columns.
if column_list is None:
column_list = this_column_list
else:
column_list = [c for c in column_list if c in this_column_list]
return column_list
[docs] def get_options(self, trans, other_values):
"""
Show column labels rather than c1..cn if use_header_names=True
"""
options: List[Tuple[str, Union[str, Tuple[str, str]], bool]] = []
column_list = self.get_column_list(trans, other_values)
if not column_list:
return options
# if available use column_names metadata for option names
# otherwise read first row - assume is a header with tab separated names
if self.usecolnames:
dataset = other_values.get(self.data_ref, None)
if (
hasattr(dataset, "metadata")
and hasattr(dataset.metadata, "column_names")
and dataset.metadata.element_is_set("column_names")
):
try:
options = [(f"c{c}: {dataset.metadata.column_names[int(c) - 1]}", c, False) for c in column_list]
except IndexError:
# ignore and rely on fallback
pass
else:
try:
with open(dataset.get_file_name()) as f:
head = f.readline()
cnames = head.rstrip("\n\r ").split("\t")
options = [(f"c{c}: {cnames[int(c) - 1]}", c, False) for c in column_list]
except Exception:
# ignore and rely on fallback
pass
if not options:
# fallback if no options list could be built so far
options = [(f"Column: {col}", col, False) for col in column_list]
return options
[docs] def get_initial_value(self, trans, other_values):
if self.default_value is not None:
return self.default_value
return super().get_initial_value(trans, other_values)
[docs] def get_legal_values(self, trans, other_values, value):
if self.data_ref not in other_values:
raise ValueError("Value for associated data reference not found (data_ref).")
legal_values = self.get_column_list(trans, other_values)
if value is not None:
# There are cases where 'value' is a string of comma separated values. This ensures
# that it is converted into a list, with extra whitespace around items removed.
value = util.listify(value, do_strip=True)
if not set(value).issubset(set(legal_values)) and self.is_file_empty(trans, other_values):
legal_values.extend(value)
return set(legal_values)
[docs] def is_file_empty(self, trans, other_values):
for dataset in util.listify(other_values.get(self.data_ref)):
# Use representative dataset if a dataset collection is parsed
if isinstance(dataset, HistoryDatasetCollectionAssociation):
if dataset.populated:
dataset = dataset.to_hda_representative()
else:
# That's fine, we'll check again on execution
return True
if isinstance(dataset, DatasetCollectionElement):
dataset = dataset.first_dataset_instance()
if isinstance(dataset, DatasetInstance):
return not dataset.has_data()
if is_runtime_value(dataset):
return True
else:
msg = f"Dataset '{dataset}' for data_ref attribute '{self.data_ref}' of parameter '{self.name}' is not a DatasetInstance"
log.debug(msg, exc_info=True)
raise ParameterValueError(msg, self.name)
return False
[docs] def to_dict(self, trans, other_values=None):
other_values = other_values or {}
d = super().to_dict(trans, other_values=other_values)
d["data_ref"] = self.data_ref
d["numerical"] = self.numerical
return d
[docs]class DrillDownSelectToolParameter(SelectToolParameter):
"""
Parameter that takes on one (or many) of a specific set of values.
Creating a hierarchical select menu, which allows users to 'drill down' a tree-like set of options.
>>> from galaxy.util import XML
>>> from galaxy.util.bunch import Bunch
>>> app = Bunch(config=Bunch(tool_data_path=None))
>>> tool = Bunch(app=app)
>>> trans = Bunch(app=app, history=Bunch(genome_build='hg17'), db_builds=read_dbnames(None))
>>> p = DrillDownSelectToolParameter(tool, XML(
... '''
... <param name="_name" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true">
... <options>
... <option name="Heading 1" value="heading1">
... <option name="Option 1" value="option1"/>
... <option name="Option 2" value="option2"/>
... <option name="Heading 2" value="heading2">
... <option name="Option 3" value="option3"/>
... <option name="Option 4" value="option4"/>
... </option>
... </option>
... <option name="Option 5" value="option5"/>
... </options>
... </param>
... '''))
>>> print(p.name)
_name
>>> d = p.to_dict(trans)
>>> assert d['multiple'] == True
>>> assert d['display'] == 'checkbox'
>>> assert d['options'][0]['name'] == 'Heading 1'
>>> assert d['options'][0]['value'] == 'heading1'
>>> assert d['options'][0]['options'][0]['name'] == 'Option 1'
>>> assert d['options'][0]['options'][0]['value'] == 'option1'
>>> assert d['options'][0]['options'][1]['name'] == 'Option 2'
>>> assert d['options'][0]['options'][1]['value'] == 'option2'
>>> assert d['options'][0]['options'][2]['name'] == 'Heading 2'
>>> assert d['options'][0]['options'][2]['value'] == 'heading2'
>>> assert d['options'][0]['options'][2]['options'][0]['name'] == 'Option 3'
>>> assert d['options'][0]['options'][2]['options'][0]['value'] == 'option3'
>>> assert d['options'][0]['options'][2]['options'][1]['name'] == 'Option 4'
>>> assert d['options'][0]['options'][2]['options'][1]['value'] == 'option4'
>>> assert d['options'][1]['name'] == 'Option 5'
>>> assert d['options'][1]['value'] == 'option5'
"""
[docs] def __init__(self, tool, input_source, context=None):
input_source = ensure_input_source(input_source)
ToolParameter.__init__(self, tool, input_source)
self.multiple = input_source.get_bool("multiple", False)
self.display = input_source.get("display", None)
self.hierarchy = input_source.get("hierarchy", "exact") # exact or recurse
self.separator = input_source.get("separator", ",")
tool_data_path = tool.app.config.tool_data_path
drill_down_dynamic_options = input_source.parse_drill_down_dynamic_options(tool_data_path)
if drill_down_dynamic_options is not None:
self.is_dynamic = True
self.dynamic_options = drill_down_dynamic_options.from_code_block()
self.options = []
else:
self.is_dynamic = False
self.dynamic_options = None
self.options = input_source.parse_drill_down_static_options(tool_data_path)
def _get_options_from_code(self, trans=None, other_values=None):
assert self.dynamic_options, Exception("dynamic_options was not specifed")
call_other_values = ExpressionContext({"__trans__": trans, "__value__": None})
if other_values:
call_other_values.parent = other_values.parent
call_other_values.update(other_values.dict)
try:
return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
except Exception:
return []
[docs] def get_options(self, trans=None, other_values=None):
other_values = other_values or {}
if self.is_dynamic:
if self.dynamic_options:
options = self._get_options_from_code(trans=trans, other_values=other_values)
else:
options = []
return options
return self.options
[docs] def get_legal_values(self, trans, other_values, value):
def recurse_options(legal_values, options):
for option in options:
legal_values.append(option["value"])
recurse_options(legal_values, option["options"])
legal_values: List[str] = []
recurse_options(legal_values, self.get_options(trans=trans, other_values=other_values))
return legal_values
[docs] def from_json(self, value, trans, other_values=None):
other_values = other_values or {}
legal_values = self.get_legal_values(trans, other_values, value)
if not legal_values and trans.workflow_building_mode:
if self.multiple:
if value == "": # No option selected
value = None
else:
value = value.split("\n")
return value
elif value is None:
if self.optional:
return None
raise ParameterValueError(f"an invalid option ({value!r}) was selected", self.name, value)
elif not legal_values:
raise ParameterValueError("requires a value, but no legal values defined", self.name)
if not isinstance(value, list):
value = [value]
if len(value) > 1 and not self.multiple:
raise ParameterValueError(
"multiple values provided but parameter is not expecting multiple values", self.name
)
rval = []
for val in value:
if val not in legal_values:
raise ParameterValueError(
f"an invalid option ({val!r}) was selected (valid options: {','.join(legal_values)})",
self.name,
val,
)
rval.append(val)
return rval
[docs] def to_param_dict_string(self, value, other_values=None):
other_values = other_values or {}
def get_options_list(value):
def get_base_option(value, options):
for option in options:
if value == option["value"]:
return option
rval = get_base_option(value, option["options"])
if rval:
return rval
return None # not found
def recurse_option(option_list, option):
if not option["options"]:
option_list.append(option["value"])
else:
for opt in option["options"]:
recurse_option(option_list, opt)
rval: List[str] = []
base_option = get_base_option(value, self.get_options(other_values=other_values))
recurse_option(rval, base_option)
return rval or [value]
if value is None:
return "None"
rval = []
if self.hierarchy == "exact":
rval = value
else:
for val in value:
options = get_options_list(val)
rval.extend(options)
rval = list(dict.fromkeys(rval))
if len(rval) > 1 and not self.multiple:
raise ParameterValueError(
"multiple values provided but parameter is not expecting multiple values", self.name
)
rval = self.separator.join(rval)
if self.tool is None or self.tool.options.sanitize:
if self.sanitizer:
rval = self.sanitizer.sanitize_param(rval)
else:
rval = sanitize_param(rval)
return rval
[docs] def get_initial_value(self, trans, other_values):
def recurse_options(initial_values, options):
for option in options:
if option["selected"]:
initial_values.append(option["value"])
recurse_options(initial_values, option["options"])
# More working around dynamic options for workflow
options = self.get_options(trans=trans, other_values=other_values)
if not options:
return None
initial_values: List[str] = []
recurse_options(initial_values, options)
if len(initial_values) == 0:
return None
return initial_values
[docs] def to_text(self, value):
def get_option_display(value, options):
for option in options:
if value == option["value"]:
return option["name"]
rval = get_option_display(value, option["options"])
if rval:
return rval
return None # not found
if not value:
value = []
elif not isinstance(value, list):
value = [value]
# FIXME: Currently only translating values back to labels if they
# are not dynamic
if self.is_dynamic:
if value:
if isinstance(value, list):
rval = value
else:
rval = [value]
else:
rval = []
else:
rval = []
for val in value:
rval.append(get_option_display(val, self.options) or val)
if rval:
return "\n".join(map(str, rval))
return "Nothing selected."
[docs] def to_dict(self, trans, other_values=None):
other_values = other_values or {}
# skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
d = ToolParameter.to_dict(self, trans)
d["options"] = self.get_options(trans=trans, other_values=other_values)
d["display"] = self.display
d["multiple"] = self.multiple
return d
[docs]class BaseDataToolParameter(ToolParameter):
multiple: bool
[docs] def __init__(self, tool, input_source, trans):
super().__init__(tool, input_source)
self.min = input_source.get("min")
self.max = input_source.get("max")
if self.min:
try:
self.min = int(self.min)
except ValueError:
raise ParameterValueError("attribute 'min' must be an integer", self.name)
if self.max:
try:
self.max = int(self.max)
except ValueError:
raise ParameterValueError("attribute 'max' must be an integer", self.name)
self.refresh_on_change = True
# Find datatypes_registry
if self.tool is None:
if trans:
# Must account for "Input Dataset" types, which while not a tool still need access to the real registry.
# A handle to the transaction (and thus app) will be given by the module.
self.datatypes_registry = trans.app.datatypes_registry
else:
# This occurs for things such as unit tests
import galaxy.datatypes.registry
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes()
else:
self.datatypes_registry = (
self.tool.app.datatypes_registry
) # can be None if self.tool.app is a ValidationContext
def _parse_formats(self, trans, input_source):
"""
Build list of classes for supported data formats
"""
self.extensions = [extension.strip().lower() for extension in input_source.get("format", "data").split(",")]
formats = []
if self.datatypes_registry: # This may be None when self.tool.app is a ValidationContext
for extension in self.extensions:
datatype = self.datatypes_registry.get_datatype_by_extension(extension)
if datatype is not None:
formats.append(datatype)
else:
log.warning(
f"Datatype class not found for extension '{extension}', which is used in the 'format' attribute of parameter '{self.name}'"
)
self.formats = formats
def _parse_options(self, input_source):
# TODO: Enhance dynamic options for DataToolParameters. Currently,
# only the special case key='build' of type='data_meta' is
# a valid filter
self.options_filter_attribute = None
self.options = parse_dynamic_options(self, input_source)
if self.options:
# TODO: Abstract away XML handling here.
options_elem = input_source.elem().find("options")
self.options_filter_attribute = options_elem.get("options_filter_attribute", None)
self.is_dynamic = self.options is not None
[docs] def get_initial_value(self, trans, other_values):
if trans.workflow_building_mode is workflow_building_modes.ENABLED or trans.app.name == "tool_shed":
return RuntimeValue()
if self.optional:
return None
if (history := trans.history) is not None:
dataset_matcher_factory = get_dataset_matcher_factory(trans)
dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
if isinstance(self, DataToolParameter):
for hda in reversed(history.active_visible_datasets_and_roles):
match = dataset_matcher.hda_match(hda)
if match:
return match.hda
else:
dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)
for hdca in reversed(history.active_visible_dataset_collections):
if dataset_collection_matcher.hdca_match(hdca):
return hdca
[docs] def to_json(self, value, app, use_security):
if value not in [None, "", "None"]:
if isinstance(value, list) and len(value) > 0:
values = [history_item_to_json(v, app, use_security) for v in value]
else:
values = [history_item_to_json(value, app, use_security)]
return {"values": values}
return None
[docs] def to_python(self, value, app):
if isinstance(value, MutableMapping) and "values" in value:
if hasattr(self, "multiple") and self.multiple is True:
return [history_item_dict_to_python(v, app, self.name) for v in value["values"]]
elif len(value["values"]) > 0:
return history_item_dict_to_python(value["values"][0], app, self.name)
# Handle legacy string values potentially stored in databases
none_values = [None, "", "None"]
if value in none_values:
return None
if isinstance(value, str) and value.find(",") > -1:
return [
app.model.context.get(HistoryDatasetAssociation, int(v))
for v in value.split(",")
if v not in none_values
]
elif str(value).startswith("__collection_reduce__|"):
decoded_id = str(value)[len("__collection_reduce__|") :]
if not decoded_id.isdigit():
decoded_id = app.security.decode_id(decoded_id)
return app.model.context.get(HistoryDatasetCollectionAssociation, int(decoded_id))
elif str(value).startswith("dce:"):
return app.model.context.get(DatasetCollectionElement, int(value[len("dce:") :]))
elif str(value).startswith("hdca:"):
return app.model.context.get(HistoryDatasetCollectionAssociation, int(value[len("hdca:") :]))
else:
return app.model.context.get(HistoryDatasetAssociation, int(value))
[docs] def validate(self, value, trans=None):
def do_validate(v):
for validator in self.validators:
if (
validator.requires_dataset_metadata
and v
and hasattr(v, "dataset")
and v.dataset.state != Dataset.states.OK
):
return
else:
try:
validator.validate(v, trans)
except ValueError as e:
raise ParameterValueError(str(e), self.name, v) from None
dataset_count = 0
if value:
if self.multiple:
if not isinstance(value, list):
value = [value]
else:
value = [value]
for v in value:
if isinstance(v, HistoryDatasetCollectionAssociation):
for dataset_instance in v.collection.dataset_instances:
dataset_count += 1
do_validate(dataset_instance)
elif isinstance(v, DatasetCollectionElement):
if v.hda:
dataset_count += 1
do_validate(v.hda)
else:
for dataset_instance in v.child_collection.dataset_instances:
dataset_count += 1
do_validate(dataset_instance)
else:
dataset_count += 1
do_validate(v)
if self.min is not None:
if self.min > dataset_count:
raise ValueError(f"At least {self.min} datasets are required for {self.name}")
if self.max is not None:
if self.max < dataset_count:
raise ValueError(f"At most {self.max} datasets are required for {self.name}")
[docs]def src_id_to_item(
sa_session: "Session", value: typing.MutableMapping[str, Any], security: "IdEncodingHelper"
) -> Union[
DatasetCollectionElement,
HistoryDatasetAssociation,
HistoryDatasetCollectionAssociation,
LibraryDatasetDatasetAssociation,
]:
src_to_class = {
"hda": HistoryDatasetAssociation,
"ldda": LibraryDatasetDatasetAssociation,
"dce": DatasetCollectionElement,
"hdca": HistoryDatasetCollectionAssociation,
}
id_value = value["id"]
decoded_id = id_value if isinstance(id_value, int) else security.decode_id(id_value)
try:
item = sa_session.get(src_to_class[value["src"]], decoded_id)
except KeyError:
raise ValueError(f"Unknown input source {value['src']} passed to job submission API.")
if not item:
raise ValueError("Invalid input id passed to job submission API.")
item.extra_params = {k: v for k, v in value.items() if k not in ("src", "id")}
return item
[docs]class DataToolParameter(BaseDataToolParameter):
# TODO, Nate: Make sure the following unit tests appropriately test the dataset security
# components. Add as many additional tests as necessary.
"""
Parameter that takes on one (or many) or a specific set of values.
TODO: There should be an alternate display that allows single selects to be
displayed as radio buttons and multiple selects as a set of checkboxes
TODO: The following must be fixed to test correctly for the new security_check tag in
the DataToolParameter (the last test below is broken) Nate's next pass at the dataset
security stuff will dramatically alter this anyway.
"""
[docs] def __init__(self, tool, input_source, trans=None):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source, trans)
self.load_contents = int(input_source.get("load_contents", 0))
# Add metadata validator
if not input_source.get_bool("no_validation", False):
self.validators.append(validation.MetadataValidator.default_metadata_validator())
self._parse_formats(trans, input_source)
tag = input_source.get("tag")
self.multiple = input_source.get_bool("multiple", False)
if not self.multiple and (self.min is not None):
raise ParameterValueError(
"cannot specify 'min' property on single data parameter. Set multiple=\"true\" to enable this option",
self.name,
)
if not self.multiple and (self.max is not None):
raise ParameterValueError(
"cannot specify 'max' property on single data parameter. Set multiple=\"true\" to enable this option",
self.name,
)
self.tag = tag
self.is_dynamic = True
self._parse_options(input_source)
self._parse_allow_uri_if_protocol(input_source)
# Load conversions required for the dataset input
self.conversions = []
self.default_object = input_source.parse_default()
if self.optional and self.default_object is not None:
raise ParameterValueError(
"Cannot specify a Galaxy tool data parameter to be both optional and have a default value.", self.name
)
for name, conv_extension in input_source.parse_conversion_tuples():
assert None not in [
name,
conv_extension,
], f"A name ({name}) and type ({conv_extension}) are required for explicit conversion"
if self.datatypes_registry:
conv_type = self.datatypes_registry.get_datatype_by_extension(conv_extension.lower())
if conv_type is None:
raise ParameterValueError(
f"datatype class not found for extension '{conv_type}', which is used as 'type' attribute in conversion of data parameter",
self.name,
)
self.conversions.append((name, conv_extension, [conv_type]))
def _parse_allow_uri_if_protocol(self, input_source):
# In case of deferred datasets, if the source URI is prefixed with one of the values in this list,
# the dataset will behave as an URI and will not be materialized into a file path.
allow_uri_if_protocol = input_source.get("allow_uri_if_protocol", None)
self.allow_uri_if_protocol = allow_uri_if_protocol.split(",") if allow_uri_if_protocol else []
[docs] def from_json(self, value, trans, other_values=None):
session = trans.sa_session
other_values = other_values or {}
if trans.workflow_building_mode is workflow_building_modes.ENABLED or is_runtime_value(value):
return None
if not value and not self.optional and not self.default_object:
raise ParameterValueError("specify a dataset of the required format / build for parameter", self.name)
if value in [None, "None", ""]:
if self.default_object:
return raw_to_galaxy(trans.app, trans.history, self.default_object)
return None
if isinstance(value, MutableMapping) and "values" in value:
value = self.to_python(value, trans.app)
if isinstance(value, str) and value.find(",") > 0:
value = [int(value_part) for value_part in value.split(",")]
rval: List[
Union[
DatasetCollectionElement,
HistoryDatasetAssociation,
HistoryDatasetCollectionAssociation,
LibraryDatasetDatasetAssociation,
]
] = []
if isinstance(value, list):
found_srcs = set()
for single_value in value:
if isinstance(single_value, MutableMapping) and "src" in single_value and "id" in single_value:
found_srcs.add(single_value["src"])
rval.append(
src_id_to_item(sa_session=trans.sa_session, value=single_value, security=trans.security)
)
elif isinstance(
single_value,
(
HistoryDatasetCollectionAssociation,
DatasetCollectionElement,
HistoryDatasetAssociation,
LibraryDatasetDatasetAssociation,
),
):
rval.append(single_value)
else:
if len(str(single_value)) == 16:
# Could never really have an ID this big anyway - postgres doesn't
# support that for integer column types.
log.warning("Encoded ID where unencoded ID expected.")
single_value = trans.security.decode_id(single_value)
rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(single_value))
if len(found_srcs) > 1 and "hdca" in found_srcs:
raise ParameterValueError(
"if collections are supplied to multiple data input parameter, only collections may be used",
self.name,
)
elif isinstance(value, (HistoryDatasetAssociation, LibraryDatasetDatasetAssociation)):
rval.append(value)
elif isinstance(value, MutableMapping) and "src" in value and "id" in value:
rval.append(src_id_to_item(sa_session=trans.sa_session, value=value, security=trans.security))
elif str(value).startswith("__collection_reduce__|"):
encoded_ids = [v[len("__collection_reduce__|") :] for v in str(value).split(",")]
decoded_ids = map(trans.security.decode_id, encoded_ids)
rval = []
for decoded_id in decoded_ids:
hdca = session.get(HistoryDatasetCollectionAssociation, decoded_id)
rval.append(hdca)
elif isinstance(value, HistoryDatasetCollectionAssociation) or isinstance(value, DatasetCollectionElement):
rval.append(value)
else:
rval.append(session.get(HistoryDatasetAssociation, int(value)))
dataset_matcher_factory = get_dataset_matcher_factory(trans)
dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
for v in rval:
if isinstance(v, DatasetCollectionElement):
if hda := v.hda:
v = hda
elif ldda := v.ldda:
v = ldda
elif collection := v.child_collection:
v = collection
elif not v.collection and v.collection.populated_optimized:
raise ParameterValueError("the selected collection has not been populated.", self.name)
else:
raise ParameterValueError("Collection element in unexpected state", self.name)
if isinstance(v, DatasetInstance):
if v.deleted:
raise ParameterValueError("the previously selected dataset has been deleted.", self.name)
elif v.dataset and v.dataset.state in [Dataset.states.ERROR, Dataset.states.DISCARDED]:
raise ParameterValueError(
"the previously selected dataset has entered an unusable state", self.name
)
match = dataset_matcher.hda_match(v)
if match and match.implicit_conversion:
v.implicit_conversion = True # type:ignore[union-attr]
elif isinstance(v, HistoryDatasetCollectionAssociation):
if v.deleted:
raise ParameterValueError("the previously selected dataset collection has been deleted.", self.name)
v = v.collection
if isinstance(v, DatasetCollection):
if v.elements_deleted:
raise ParameterValueError(
"the previously selected dataset collection has elements that are deleted.", self.name
)
if not self.multiple:
if len(rval) > 1:
raise ParameterValueError("more than one dataset supplied to single input dataset parameter", self.name)
if len(rval) > 0:
return rval[0]
else:
raise ParameterValueError("invalid dataset supplied to single input dataset parameter", self.name)
return rval
[docs] def to_param_dict_string(self, value, other_values=None):
if value is None:
return "None"
return value.get_file_name()
[docs] def to_text(self, value):
if value and not isinstance(value, list):
value = [value]
if value:
try:
return ", ".join(f"{item.hid}: {item.name}" for item in value)
except Exception:
pass
return "No dataset."
[docs] def get_dependencies(self):
"""
Get the *names* of the other params this param depends on.
"""
if self.options:
return self.options.get_dependency_names()
else:
return []
[docs] def converter_safe(self, other_values, trans):
if (
self.tool is None
or self.tool.has_multiple_pages
or not hasattr(trans, "workflow_building_mode")
or trans.workflow_building_mode
):
return False
if other_values is None:
return True # we don't know other values, so we can't check, assume ok
converter_safe = [True]
def visitor(prefix, input, value, parent=None):
if isinstance(input, SelectToolParameter) and self.name in input.get_dependencies():
if input.is_dynamic and (
input.dynamic_options
or (not input.dynamic_options and not input.options)
or not input.options.converter_safe
):
converter_safe[0] = (
False # This option does not allow for conversion, i.e. uses contents of dataset file to generate options
)
self.tool.visit_inputs(other_values, visitor)
return False not in converter_safe
[docs] def get_options_filter_attribute(self, value):
# HACK to get around current hardcoded limitation of when a set of dynamic options is defined for a DataToolParameter
# it always causes available datasets to be filtered by dbkey
# this behavior needs to be entirely reworked (in a backwards compatible manner)
options_filter_attribute = self.options_filter_attribute
if options_filter_attribute is None:
return value.get_dbkey()
if options_filter_attribute.endswith("()"):
call_attribute = True
options_filter_attribute = options_filter_attribute[:-2]
else:
call_attribute = False
ref = value
for attribute in options_filter_attribute.split("."):
ref = getattr(ref, attribute)
if call_attribute:
ref = ref()
return str(ref)
[docs] def to_dict(self, trans, other_values=None):
other_values = other_values or {}
# create dictionary and fill default parameters
d = super().to_dict(trans)
extensions = self.extensions
all_edam_formats = (
self.datatypes_registry.edam_formats if hasattr(self.datatypes_registry, "edam_formats") else {}
)
all_edam_data = self.datatypes_registry.edam_data if hasattr(self.datatypes_registry, "edam_formats") else {}
edam_formats = [all_edam_formats.get(ext, None) for ext in extensions]
edam_data = [all_edam_data.get(ext, None) for ext in extensions]
d["extensions"] = extensions
d["edam"] = {"edam_formats": edam_formats, "edam_data": edam_data}
d["multiple"] = self.multiple
if self.multiple:
# For consistency, should these just always be in the dict?
d["min"] = self.min
d["max"] = self.max
d["options"] = {"dce": [], "ldda": [], "hda": [], "hdca": []}
d["tag"] = self.tag
# return dictionary without options if context is unavailable
history = trans.history
if history is None or trans.workflow_building_mode is workflow_building_modes.ENABLED:
return d
# prepare dataset/collection matching
dataset_matcher_factory = get_dataset_matcher_factory(trans)
dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
multiple = self.multiple
# build and append a new select option
def append(list, hda, name, src, keep=False, subcollection_type=None):
value = {
"id": trans.security.encode_id(hda.id),
"hid": hda.hid if hda.hid is not None else -1,
"name": name,
"tags": [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hda.tags],
"src": src,
"keep": keep,
}
if subcollection_type:
value["map_over_type"] = subcollection_type
return list.append(value)
def append_dce(dce):
d["options"]["dce"].append(
{
"id": trans.security.encode_id(dce.id),
"name": dce.element_identifier,
"is_dataset": dce.hda is not None,
"src": "dce",
"tags": [],
"keep": True,
}
)
def append_ldda(ldda):
d["options"]["ldda"].append(
{
"id": trans.security.encode_id(ldda.id),
"name": ldda.name,
"src": "ldda",
"tags": [],
"keep": True,
}
)
# add datasets
hda_list = util.listify(other_values.get(self.name))
# Prefetch all at once, big list of visible, non-deleted datasets.
for hda in history.active_visible_datasets_and_roles:
match = dataset_matcher.hda_match(hda)
if match:
m = match.hda
hda_list = [h for h in hda_list if h != m and h != hda]
m_name = f"{match.original_hda.name} (as {match.target_ext})" if match.implicit_conversion else m.name
append(d["options"]["hda"], m, m_name, "hda")
for hda in hda_list:
if hasattr(hda, "hid"):
if hda.deleted:
hda_state = "deleted"
elif not hda.visible:
hda_state = "hidden"
else:
hda_state = "unavailable"
append(d["options"]["hda"], hda, f"({hda_state}) {hda.name}", "hda", True)
elif isinstance(hda, DatasetCollectionElement):
append_dce(hda)
elif isinstance(hda, LibraryDatasetDatasetAssociation):
append_ldda(hda)
# add dataset collections
dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)
for hdca in history.active_visible_dataset_collections:
match = dataset_collection_matcher.hdca_match(hdca)
if match:
subcollection_type = None
if multiple and hdca.collection.collection_type != "list":
collection_type_description = self._history_query(trans).can_map_over(hdca)
if collection_type_description:
subcollection_type = collection_type_description.collection_type
else:
continue
name = hdca.name
if match.implicit_conversion:
name = f"{name} (with implicit datatype conversion)"
append(d["options"]["hdca"], hdca, name, "hdca", subcollection_type=subcollection_type)
continue
# sort both lists
d["options"]["hda"] = sorted(d["options"]["hda"], key=lambda k: k.get("hid", -1), reverse=True)
d["options"]["hdca"] = sorted(d["options"]["hdca"], key=lambda k: k.get("hid", -1), reverse=True)
# return final dictionary
return d
def _history_query(self, trans):
assert self.multiple
dataset_collection_type_descriptions = trans.app.dataset_collection_manager.collection_type_descriptions
# If multiple data parameter, treat like a list parameter.
return history_query.HistoryQuery.from_collection_type("list", dataset_collection_type_descriptions)
[docs]class DataCollectionToolParameter(BaseDataToolParameter):
""" """
[docs] def __init__(self, tool, input_source, trans=None):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source, trans)
self._parse_formats(trans, input_source)
collection_types = input_source.get("collection_type", None)
tag = input_source.get("tag")
if collection_types:
collection_types = [t.strip() for t in collection_types.split(",")]
self._collection_types = collection_types
self.tag = tag
self.multiple = False # Accessed on DataToolParameter a lot, may want in future
self.is_dynamic = True
self._parse_options(input_source) # TODO: Review and test.
self.default_object = input_source.parse_default()
if self.optional and self.default_object is not None:
raise ParameterValueError(
"Cannot specify a Galaxy tool data parameter to be both optional and have a default value.", self.name
)
@property
def collection_types(self):
return self._collection_types
def _history_query(self, trans):
dataset_collection_type_descriptions = trans.app.dataset_collection_manager.collection_type_descriptions
return history_query.HistoryQuery.from_parameter(self, dataset_collection_type_descriptions)
[docs] def match_collections(self, trans, history, dataset_collection_matcher):
dataset_collections = trans.app.dataset_collection_manager.history_dataset_collections(
history, self._history_query(trans)
)
for dataset_collection_instance in dataset_collections:
match = dataset_collection_matcher.hdca_match(dataset_collection_instance)
if not match:
continue
yield dataset_collection_instance, match.implicit_conversion
[docs] def match_multirun_collections(self, trans, history, dataset_collection_matcher):
for history_dataset_collection in history.active_visible_dataset_collections:
if not self._history_query(trans).can_map_over(history_dataset_collection):
continue
match = dataset_collection_matcher.hdca_match(history_dataset_collection)
if match:
yield history_dataset_collection, match.implicit_conversion
[docs] def from_json(self, value, trans, other_values=None):
session = trans.sa_session
other_values = other_values or {}
rval: Optional[Union[DatasetCollectionElement, HistoryDatasetCollectionAssociation]] = None
if trans.workflow_building_mode is workflow_building_modes.ENABLED:
return None
if not value and not self.optional and not self.default_object:
raise ParameterValueError("specify a dataset collection of the correct type", self.name)
if value in [None, "None"]:
if self.default_object:
return raw_to_galaxy(trans.app, trans.history, self.default_object)
return None
if isinstance(value, MutableMapping) and "values" in value:
value = self.to_python(value, trans.app)
if isinstance(value, str) and value.find(",") > 0:
value = [int(value_part) for value_part in value.split(",")]
elif isinstance(value, HistoryDatasetCollectionAssociation):
rval = value
elif isinstance(value, DatasetCollectionElement):
# When mapping over nested collection - this parameter will receive
# a DatasetCollectionElement instead of a
# HistoryDatasetCollectionAssociation.
rval = value
elif isinstance(value, MutableMapping) and "src" in value and "id" in value:
if value["src"] == "hdca":
rval = session.get(HistoryDatasetCollectionAssociation, trans.security.decode_id(value["id"]))
elif isinstance(value, list):
if len(value) > 0:
value = value[0]
if isinstance(value, MutableMapping) and "src" in value and "id" in value:
if value["src"] == "hdca":
rval = session.get(HistoryDatasetCollectionAssociation, trans.security.decode_id(value["id"]))
elif value["src"] == "dce":
rval = session.get(DatasetCollectionElement, trans.security.decode_id(value["id"]))
elif isinstance(value, str):
if value.startswith("dce:"):
rval = session.get(DatasetCollectionElement, int(value[len("dce:") :]))
elif value.startswith("hdca:"):
rval = session.get(HistoryDatasetCollectionAssociation, int(value[len("hdca:") :]))
else:
rval = session.get(HistoryDatasetCollectionAssociation, int(value))
if rval:
if isinstance(rval, HistoryDatasetCollectionAssociation):
if rval.deleted:
raise ParameterValueError("the previously selected dataset collection has been deleted", self.name)
if rval.collection.elements_deleted:
raise ParameterValueError(
"the previously selected dataset collection has elements that are deleted.", self.name
)
if isinstance(rval, DatasetCollectionElement):
if (child_collection := rval.child_collection) and child_collection.elements_deleted:
raise ParameterValueError(
"the previously selected dataset collection has elements that are deleted.", self.name
)
return rval
[docs] def to_text(self, value):
try:
if isinstance(value, HistoryDatasetCollectionAssociation):
display_text = f"{value.hid}: {value.name}"
else:
display_text = f"Element {value.identifier_index}:{value.identifier_name}"
except AttributeError:
display_text = "No dataset collection."
return display_text
[docs] def to_dict(self, trans, other_values=None):
# create dictionary and fill default parameters
other_values = other_values or {}
d = super().to_dict(trans)
d["collection_types"] = self.collection_types
d["extensions"] = self.extensions
d["multiple"] = self.multiple
d["options"] = {"hda": [], "hdca": [], "dce": []}
d["tag"] = self.tag
# return dictionary without options if context is unavailable
history = trans.history
if history is None or trans.workflow_building_mode is workflow_building_modes.ENABLED:
return d
# prepare dataset/collection matching
dataset_matcher_factory = get_dataset_matcher_factory(trans)
dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
dataset_collection_matcher = dataset_matcher_factory.dataset_collection_matcher(dataset_matcher)
# append DCE
if isinstance(other_values.get(self.name), DatasetCollectionElement):
dce = other_values[self.name]
d["options"]["dce"].append(
{
"id": trans.security.encode_id(dce.id),
"hid": -1,
"name": dce.element_identifier,
"src": "dce",
"tags": [],
}
)
# append directly matched collections
for hdca, implicit_conversion in self.match_collections(trans, history, dataset_collection_matcher):
name = hdca.name
if implicit_conversion:
name = f"{name} (with implicit datatype conversion)"
d["options"]["hdca"].append(
{
"id": trans.security.encode_id(hdca.id),
"hid": hdca.hid,
"name": name,
"src": "hdca",
"tags": [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hdca.tags],
}
)
# append matching subcollections
for hdca, implicit_conversion in self.match_multirun_collections(trans, history, dataset_collection_matcher):
subcollection_type = self._history_query(trans).can_map_over(hdca).collection_type
name = hdca.name
if implicit_conversion:
name = f"{name} (with implicit datatype conversion)"
d["options"]["hdca"].append(
{
"id": trans.security.encode_id(hdca.id),
"hid": hdca.hid,
"map_over_type": subcollection_type,
"name": name,
"src": "hdca",
"tags": [t.user_tname if not t.value else f"{t.user_tname}:{t.value}" for t in hdca.tags],
}
)
# sort both lists
d["options"]["hdca"] = sorted(d["options"]["hdca"], key=lambda k: k.get("hid", -1), reverse=True)
# return final dictionary
return d
[docs]class HiddenDataToolParameter(HiddenToolParameter, DataToolParameter):
"""
Hidden parameter that behaves as a DataToolParameter. As with all hidden
parameters, this is a HACK.
"""
[docs] def __init__(self, tool, elem):
DataToolParameter.__init__(self, tool, elem)
self.value = "None"
self.type = "hidden_data"
self.hidden = True
[docs]class BaseJsonToolParameter(ToolParameter):
"""
Class of parameter that tries to keep values as close to JSON as possible.
In particular value_to_basic is overloaded to prevent params_to_strings from
double encoding JSON and to_python using loads to produce values.
"""
[docs] def value_to_basic(self, value, app, use_security=False):
if is_runtime_value(value):
return runtime_to_json(value)
return value
[docs] def to_json(self, value, app, use_security):
"""Convert a value to a string representation suitable for persisting"""
return json.dumps(value)
[docs] def to_python(self, value, app):
"""Convert a value created with to_json back to an object representation"""
return json.loads(value)
[docs]class DirectoryUriToolParameter(SimpleTextToolParameter):
"""galaxy.files URIs for directories."""
[docs] def __init__(self, tool, input_source, context=None):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
[docs] def validate(self, value, trans=None):
super().validate(value, trans=trans)
if not value:
return # value is not set yet, do not validate
file_source_path = trans.app.file_sources.get_file_source_path(value)
file_source = file_source_path.file_source
if file_source is None:
raise ParameterValueError(f"'{value}' is not a valid file source uri.", self.name)
user_context = ProvidesFileSourcesUserContext(trans)
user_has_access = file_source.user_has_access(user_context)
if not user_has_access:
raise ParameterValueError(f"The user cannot access {value}.", self.name)
[docs]class RulesListToolParameter(BaseJsonToolParameter):
"""
Parameter that allows for the creation of a list of rules using the Galaxy rules DSL.
"""
[docs] def __init__(self, tool, input_source, context=None):
input_source = ensure_input_source(input_source)
super().__init__(tool, input_source)
self.data_ref = input_source.get("data_ref", None)
[docs] def to_dict(self, trans, other_values=None):
other_values = other_values or {}
d = ToolParameter.to_dict(self, trans)
if target := other_values.get(self.data_ref):
if not is_runtime_value(target):
d["target"] = {
"src": "hdca" if hasattr(target, "collection") else "hda",
"id": trans.app.security.encode_id(target.id),
}
return d
[docs] def validate(self, value, trans=None):
super().validate(value, trans=trans)
if not isinstance(value, MutableMapping):
raise ValueError("No rules specified for rules parameter.")
if "rules" not in value:
raise ValueError("No rules specified for rules parameter")
mappings = value.get("mapping", None)
if not mappings:
raise ValueError("No column definitions defined for rules parameter.")
[docs] def to_text(self, value):
if value:
rule_set = RuleSet(value)
return rule_set.display
else:
return ""
# Code from CWL branch to massage in order to be shared across tools and workflows,
# and for CWL artifacts as well as Galaxy ones.
[docs]def raw_to_galaxy(
app: "MinimalApp", history: "History", as_dict_value: Dict[str, Any], commit: bool = True
) -> "HistoryItem":
object_class = as_dict_value["class"]
if object_class == "File":
# TODO: relative_to = "/"
location = as_dict_value.get("location")
name = (
as_dict_value.get("identifier")
or as_dict_value.get("basename")
or os.path.basename(urllib.parse.urlparse(location).path)
)
extension = as_dict_value.get("format") or "data"
dataset = Dataset()
source = DatasetSource()
source.source_uri = location
# TODO: validate this...
source.transform = as_dict_value.get("transform")
dataset.sources.append(source)
for hash_name in HASH_NAMES:
# TODO: Convert md5 -> MD5 during tool parsing.
if hash_name in as_dict_value:
hash_object = DatasetHash()
hash_object.hash_function = hash_name
hash_object.hash_value = as_dict_value[hash_name]
dataset.hashes.append(hash_object)
if "created_from_basename" in as_dict_value:
dataset.created_from_basename = as_dict_value["created_from_basename"]
dataset.state = Dataset.states.DEFERRED
primary_data = HistoryDatasetAssociation(
name=name,
extension=extension,
metadata_deferred=True,
designation=None,
visible=True,
dbkey="?",
dataset=dataset,
flush=False,
sa_session=app.model.session,
)
primary_data.state = Dataset.states.DEFERRED
permissions = app.security_agent.history_get_default_permissions(history)
app.security_agent.set_all_dataset_permissions(primary_data.dataset, permissions, new=True, flush=False)
app.model.session.add(primary_data)
history.stage_addition(primary_data)
history.add_pending_items()
if commit:
app.model.session.commit()
return primary_data
else:
name = as_dict_value.get("name")
collection_type = as_dict_value.get("collection_type")
collection = DatasetCollection(
collection_type=collection_type,
)
hdca = HistoryDatasetCollectionAssociation(
name=name,
collection=collection,
)
app.model.session.add(hdca)
def write_elements_to_collection(has_elements, collection_builder):
element_dicts = has_elements.get("elements")
for element_dict in element_dicts:
element_class = element_dict["class"]
identifier = element_dict["identifier"]
if element_class == "File":
# Don't commit for inner elements
hda = raw_to_galaxy(app, history, element_dict, commit=False)
collection_builder.add_dataset(identifier, hda)
else:
subcollection_builder = collection_builder.get_level(identifier)
write_elements_to_collection(element_dict, subcollection_builder)
collection_builder = builder.BoundCollectionBuilder(collection)
write_elements_to_collection(as_dict_value, collection_builder)
collection_builder.populate()
history.stage_addition(hdca)
history.add_pending_items()
if commit:
app.model.session.commit()
return hdca
parameter_types = dict(
text=TextToolParameter,
integer=IntegerToolParameter,
float=FloatToolParameter,
boolean=BooleanToolParameter,
genomebuild=GenomeBuildParameter,
select=SelectToolParameter,
color=ColorToolParameter,
group_tag=SelectTagParameter,
data_column=ColumnListParameter,
hidden=HiddenToolParameter,
hidden_data=HiddenDataToolParameter,
baseurl=BaseURLToolParameter,
file=FileToolParameter,
ftpfile=FTPFileToolParameter,
data=DataToolParameter,
data_collection=DataCollectionToolParameter,
rules=RulesListToolParameter,
directory_uri=DirectoryUriToolParameter,
drill_down=DrillDownSelectToolParameter,
)
[docs]def history_item_dict_to_python(value, app, name):
if isinstance(value, MutableMapping) and "src" in value:
if value["src"] not in ("hda", "dce", "ldda", "hdca"):
raise ParameterValueError(f"Invalid value {value}", name)
return src_id_to_item(sa_session=app.model.context, security=app.security, value=value)
[docs]def history_item_to_json(value, app, use_security):
src = None
if isinstance(value, MutableMapping) and "src" in value and "id" in value:
return value
elif isinstance(value, DatasetCollectionElement):
src = "dce"
elif isinstance(value, HistoryDatasetCollectionAssociation):
src = "hdca"
elif isinstance(value, LibraryDatasetDatasetAssociation):
src = "ldda"
elif isinstance(value, HistoryDatasetAssociation) or hasattr(value, "id"):
# hasattr 'id' fires a query on persistent objects after a flush so better
# to do the isinstance check. Not sure we need the hasattr check anymore - it'd be
# nice to drop it.
src = "hda"
if src is not None:
object_id = cached_id(value)
return {"id": app.security.encode_id(object_id) if use_security else object_id, "src": src}