# Copyright Swiss Data Science Center (SDSC). A partnership between
# École Polytechnique Fédérale de Lausanne (EPFL) and
# Eidgenössische Technische Hochschule Zürich (ETHZ).
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Represent run templates."""
import copy
import itertools
import re
from abc import ABC
from datetime import datetime
from typing import Any, List, Optional, Set, Tuple, Union, cast
from uuid import uuid4
import marshmallow
from werkzeug.utils import secure_filename
from renku.core import errors
from renku.core.util import communication
from renku.core.util.datetime8601 import local_now
from renku.domain_model.provenance.agent import Person
from renku.domain_model.provenance.annotation import Annotation
from renku.domain_model.workflow.parameter import (
CommandInput,
CommandOutput,
CommandParameter,
CommandParameterBase,
HiddenInput,
)
from renku.infrastructure.database import Persistent
MAX_GENERATED_NAME_LENGTH = 25
[docs]class AbstractPlan(Persistent, ABC):
"""Abstract base class for all plans."""
date_created: datetime
creators: List[Person] = list()
def __init__(
self,
*,
description: Optional[str] = None,
id: str,
date_created: Optional[datetime] = None,
date_modified: Optional[datetime] = None,
date_removed: Optional[datetime] = None,
keywords: Optional[List[str]] = None,
name: Optional[str] = None,
project_id: Optional[str] = None,
derived_from: Optional[str] = None,
creators: Optional[List[Person]] = None,
):
self.description: Optional[str] = description
self.id: str = id
self.date_created: datetime = date_created or local_now()
self.date_modified: datetime = date_modified or local_now()
self.date_removed: Optional[datetime] = date_removed
self.keywords: List[str] = keywords or []
if creators:
self.creators = creators
self.project_id: Optional[str] = project_id
self.derived_from: Optional[str] = derived_from
if name is None:
self.name: str = self._get_default_name()
else:
self.validate_name(name)
self.name = name
def __repr__(self):
return f"<{self.__class__.__name__} '{self.name}'>"
@property
def deleted(self) -> bool:
"""True if plan is deleted."""
return self.date_removed is not None
[docs] @staticmethod
def generate_id(*, uuid: Optional[str] = None, **_) -> str:
"""Generate an identifier for Plan."""
uuid = uuid or uuid4().hex
return f"/plans/{uuid}"
def _get_default_name(self) -> str:
name = "-".join(str(a).replace(".", "_") for a in self.to_argv())
if not name:
return uuid4().hex[:MAX_GENERATED_NAME_LENGTH]
name = secure_filename(name)
rand_length = 5
return f"{name[:MAX_GENERATED_NAME_LENGTH - rand_length -1]}-{uuid4().hex[:rand_length]}"
[docs] @staticmethod
def validate_name(name: str):
"""Check a name for invalid characters."""
validate_plan_name(name=name)
[docs] def assign_new_id(self, *, uuid: Optional[str] = None) -> str:
"""Assign a new UUID.
This is required only when there is another plan which is exactly the same except the parameters' list.
"""
current_uuid = self._extract_uuid()
new_uuid = uuid or uuid4().hex
self.id = self.id.replace(current_uuid, new_uuid)
# NOTE: We also need to re-assign the _p_oid since identifier has changed
self.reassign_oid()
return new_uuid
def _extract_uuid(self) -> str:
path_start = self.id.find("/plans/")
return self.id[path_start + len("/plans/") :]
[docs] def resolve_mapping_path(self, mapping_path: str) -> Tuple[CommandParameterBase, "Plan"]:
"""Resolve a mapping path to its reference parameter."""
raise NotImplementedError()
[docs] def resolve_direct_reference(self, reference: str) -> CommandParameterBase:
"""Resolve a direct parameter reference."""
raise NotImplementedError()
[docs] def find_parameter(self, parameter: CommandParameterBase) -> bool:
"""Find if a parameter exists on this plan."""
raise NotImplementedError()
[docs] def find_parameter_workflow(self, parameter: CommandParameterBase) -> Optional["AbstractPlan"]:
"""Return the workflow a parameter belongs to."""
raise NotImplementedError()
[docs] def derive(self, creator: Optional[Person] = None) -> "AbstractPlan":
"""Create a new ``AbstractPlan`` that is derived from self."""
raise NotImplementedError()
[docs] def is_derivation(self) -> bool:
"""Return if an ``AbstractPlan`` has correct derived_from."""
raise NotImplementedError()
[docs] def delete(self, when: Optional[datetime] = None):
"""Mark a plan as deleted.
NOTE: Don't call this function for deleting plans since it doesn't delete the whole plan derivatives chain. Use
renku.core.workflow.plan::remove_plan instead.
"""
when = when or local_now()
self.unfreeze()
self.date_removed = when or local_now()
self.freeze()
[docs]class Plan(AbstractPlan):
"""Represent a `renku run` execution template."""
annotations: List[Annotation] = list()
hidden_inputs: List[HiddenInput] = list()
"""Includes a list of dependencies that are defined by Renku and should be hidden from users."""
def __init__(
self,
*,
annotations: Optional[List[Annotation]] = None,
command: str,
creators: Optional[List[Person]] = None,
date_created: Optional[datetime] = None,
date_modified: Optional[datetime] = None,
derived_from: Optional[str] = None,
description: Optional[str] = None,
hidden_inputs: Optional[List[HiddenInput]] = None,
id: str,
inputs: Optional[List[CommandInput]] = None,
date_removed: Optional[datetime] = None,
keywords: Optional[List[str]] = None,
name: Optional[str] = None,
outputs: Optional[List[CommandOutput]] = None,
parameters: Optional[List[CommandParameter]] = None,
project_id: Optional[str] = None,
success_codes: Optional[List[int]] = None,
):
self.annotations: List[Annotation] = annotations or []
self.command: str = command
cmd = self.command.split(" ", 1)[0]
if cmd == "renku" or cmd.endswith("/renku"):
communication.error(
f"Calling the 'renku' executable in workflows is not supported. Occurred in workflow {name}."
)
self.hidden_inputs: List[HiddenInput] = hidden_inputs or []
self.inputs: List[CommandInput] = inputs or []
self.outputs: List[CommandOutput] = outputs or []
self.parameters: List[CommandParameter] = parameters or []
self.success_codes: List[int] = success_codes or []
super().__init__(
id=id,
description=description,
date_created=date_created,
date_modified=date_modified,
date_removed=date_removed,
keywords=keywords,
name=name,
project_id=project_id,
derived_from=derived_from,
creators=creators,
)
# NOTE: Validate plan
duplicates = get_duplicate_arguments_names(plan=self)
if duplicates:
duplicates_string = ", ".join(duplicates)
raise errors.ParameterError(f"Duplicate input, output or parameter names found: {duplicates_string}")
@property
def keywords_csv(self) -> str:
"""Comma-separated list of keywords associated with workflow."""
return ", ".join(self.keywords)
[docs] def is_equal_to(self, other: "Plan") -> bool:
"""Return true if plan hasn't changed from the other plan."""
def are_equal_with_order(values, other_values):
return len(values) == len(other_values) and all(s.is_equal_to(o) for s, o in zip(values, other_values))
def are_equal(values, other_values):
return len(values) == len(other_values) and set(values) == set(other_values)
# TODO: Include ``annotations`` if it is added to the workflow definition file
return (
self.name == other.name
and self.description == other.description
and self.project_id == other.project_id
and self.command == other.command
and are_equal(self.success_codes, other.success_codes)
and are_equal(self.keywords, other.keywords)
and are_equal(self.creators, other.creators)
and are_equal_with_order(self.inputs, other.inputs)
and are_equal_with_order(self.outputs, other.outputs)
and are_equal_with_order(self.parameters, other.parameters)
)
[docs] def resolve_mapping_path(self, mapping_path: str) -> Tuple[CommandParameterBase, "Plan"]:
"""Resolve a mapping path to its reference parameter."""
parts = mapping_path.split(".", maxsplit=1)
if len(parts) > 1:
raise errors.ParameterNotFoundError(mapping_path, self.name)
return self.resolve_direct_reference(parts[0]), self
[docs] def resolve_direct_reference(self, reference: str) -> CommandParameterBase:
"""Resolve a direct parameter reference."""
try:
if reference.startswith("@input"):
return self.inputs[int(reference[6:]) - 1]
elif reference.startswith("@output"):
return self.outputs[int(reference[7:]) - 1]
elif reference.startswith("@param"):
return self.parameters[int(reference[6:]) - 1]
except (ValueError, IndexError):
raise errors.ParameterNotFoundError(reference, self.name)
for parameter in self.inputs + self.outputs + self.parameters: # type: ignore
if parameter.name == reference:
return parameter
raise errors.ParameterNotFoundError(reference, self.name)
[docs] def find_parameter(self, parameter: CommandParameterBase) -> bool:
"""Find if a parameter exists on this plan."""
return any(
parameter.id == p.id and parameter.actual_value == p.actual_value
for p in self.inputs + self.outputs + self.parameters # type: ignore
)
[docs] def get_parameter_path(self, parameter: CommandParameterBase):
"""Get the path to a parameter inside this plan."""
if self.find_parameter(parameter):
return [self]
return None
[docs] def get_parameter_by_id(self, parameter_id: str) -> Optional[CommandParameterBase]:
"""Get a parameter on this plan by id."""
return next(
(p for p in self.inputs + self.outputs + self.parameters if parameter_id == p.id), None # type: ignore
)
[docs] def find_parameter_workflow(self, parameter: CommandParameterBase) -> Optional["Plan"]:
"""Return the workflow a parameter belongs to."""
if self.find_parameter(parameter):
return self
return None
[docs] def assign_new_id(self, *, uuid: Optional[str] = None):
"""Assign a new UUID.
This is required only when there is another plan which is exactly the same except the parameters' list.
"""
new_uuid = super().assign_new_id(uuid=uuid)
current_uuid = self._extract_uuid()
if hasattr(self, "parameters"):
self.parameters = copy.deepcopy(self.parameters)
for a in self.parameters:
a.id = a.id.replace(current_uuid, new_uuid)
[docs] def derive(self, creator: Optional[Person] = None) -> "Plan":
"""Create a new ``Plan`` that is derived from self."""
derived = copy.copy(self)
derived.derived_from = self.id
derived.date_modified = local_now()
derived.parameters = self.parameters.copy()
derived.inputs = self.inputs.copy()
derived.keywords = copy.deepcopy(self.keywords)
derived.outputs = self.outputs.copy()
derived.success_codes = self.success_codes.copy()
derived.creators = self.creators.copy()
derived.assign_new_id()
if creator and hasattr(creator, "email") and not any(c for c in self.creators if c.email == creator.email):
self.creators.append(creator)
return derived
[docs] def is_derivation(self) -> bool:
"""Return if an ``Plan`` has correct derived_from."""
return self.derived_from is not None and self.id != self.derived_from
[docs] def to_argv(self, with_streams: bool = False, quote_string: bool = True) -> List[Any]:
"""Convert a Plan into argv list."""
arguments = itertools.chain(self.inputs, self.outputs, self.parameters)
filtered_arguments = filter(lambda a: a.position is not None and not getattr(a, "mapped_to", None), arguments)
arguments = sorted(filtered_arguments, key=lambda a: a.position) # type: ignore
argv = self.command.split(" ") if self.command else []
argv.extend(e for a in arguments for e in a.to_argv(quote_string=quote_string))
if with_streams:
arguments = itertools.chain(self.inputs, self.outputs, self.parameters)
filtered_arguments = filter(lambda a: a.position is not None and getattr(a, "mapped_to", None), arguments)
argv.extend(a.to_stream_representation() for a in filtered_arguments) # type: ignore
return argv
[docs] def set_parameters_from_strings(self, params_strings: List[str]) -> None:
"""Set parameters by parsing parameters strings."""
for param_string in params_strings:
name, value = param_string.split("=", maxsplit=1)
found = False
for collection in cast(List[List[CommandParameterBase]], [self.inputs, self.outputs, self.parameters]):
for i, param in enumerate(collection):
if param.name == name:
new_param = param.derive(plan_id=self.id)
new_param.default_value = value
collection[i] = new_param
found = True
break
if found:
break
else:
self.parameters.append(
CommandParameter(default_value=value, id=CommandParameter.generate_id(plan_id=self.id), name=name)
)
[docs] def copy(self):
"""Create a copy of this plan.
Required where a plan is used several times in a workflow, but we need to set different values on them.
"""
return copy.deepcopy(self)
[docs] def get_field_by_id(self, id: str) -> Union[CommandInput, CommandOutput, CommandParameter]:
"""Return an in Input/Output/Parameter by its id."""
for field in itertools.chain(self.inputs, self.outputs, self.parameters):
if field.id == id:
return field # type: ignore
raise errors.ParameterError(f"Parameter {id} not found on plan {self.id}.")
[docs]class PlanDetailsJson(marshmallow.Schema):
"""Serialize a plan to a response object."""
name = marshmallow.fields.String(required=True)
full_command = marshmallow.fields.String(data_key="command")
derived_from = marshmallow.fields.String()
description = marshmallow.fields.String()
keywords = marshmallow.fields.List(marshmallow.fields.String())
id = marshmallow.fields.String()
[docs]def get_duplicate_arguments_names(plan: Plan) -> List[str]:
"""Return a list of duplicate inputs/outputs/parameters names in a plan."""
all_names = [p.name for p in itertools.chain(plan.inputs, plan.outputs, plan.parameters) if p.name]
seen: Set[str] = set()
duplicates: List[str] = []
for n in all_names:
if n in seen:
duplicates.append(n)
else:
seen.add(n)
return duplicates
[docs]def validate_plan_name(name: str, extra_valid_characters: str = "_-"):
"""Check a name for invalid characters."""
if not re.match(f"^[a-zA-Z0-9][a-zA-Z0-9{extra_valid_characters}]+$", name):
raise errors.ParameterError(
f"Name '{name}' contains illegal characters. Only English letters, numbers, _ and - are allowed."
)