plan_factory.py

# -*- coding: utf-8 -*-
#
# Copyright 2018-2021- 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 a ``PlanFactory`` for tracking workflows."""

import os
import re
import shlex
import time
from contextlib import contextmanager
from itertools import chain
from pathlib import Path
from typing import Any, List, Optional, Set, Tuple

import click
import yaml
from git import Actor

from renku.core import errors
from renku.core.management.command_builder.command import inject
from renku.core.management.config import RENKU_HOME
from renku.core.management.interface.client_dispatcher import IClientDispatcher
from renku.core.management.interface.project_gateway import IProjectGateway
from renku.core.management.workflow.types import PATH_OBJECTS, Directory, File
from renku.core.models.datastructures import DirectoryTree
from renku.core.models.workflow.parameter import (
    DIRECTORY_MIME_TYPE,
    CommandInput,
    CommandOutput,
    CommandParameter,
    MappedIOStream,
)
from renku.core.models.workflow.plan import Plan
from renku.core.utils.git import add_to_git
from renku.core.utils.scm import git_unicode_unescape, safe_path
from renku.version import __version__, version_url

STARTED_AT = int(time.time() * 1000)

RENKU_TMP = "tmp"


class PlanFactory:
    """Factory for creating a plan from a command line call."""

    _RE_SUBCOMMAND = re.compile(r"^[A-Za-z]+(-[A-Za-z]+)?$")

    def __init__(
        self,
        command_line: str,
        explicit_inputs: List[str] = None,
        explicit_outputs: List[str] = None,
        directory: Optional[str] = None,
        working_dir: Optional[str] = None,
        no_input_detection: bool = False,
        no_output_detection: bool = False,
        success_codes: List[int] = None,
        stdin: Optional[str] = None,
        stdout: Optional[str] = None,
        stderr: Optional[str] = None,
    ):
        self.plan_id = Plan.generate_id()

        self.no_input_detection = no_input_detection
        self.no_output_detection = no_output_detection

        if not command_line:
            raise errors.UsageError("Command line can not be empty.")

        if not directory:
            directory = os.getcwd()
        self.directory = Path(directory)
        if not self.directory.exists():
            raise errors.UsageError("Directory must exist.")

        if not working_dir:
            working_dir = os.getcwd()
        self.working_dir = Path(working_dir)
        if not self.working_dir.exists():
            raise errors.UsageError("Working Directory must exist.")

        if isinstance(command_line, (list, tuple)):
            self.command_line = list(command_line)
        else:
            self.command_line = shlex.split(command_line)

        self.success_codes = success_codes or []

        self.explicit_inputs = [Path(os.path.abspath(p)) for p in explicit_inputs] if explicit_inputs else []
        self.explicit_outputs = [Path(os.path.abspath(p)) for p in explicit_outputs] if explicit_outputs else []

        self.stdin = stdin
        self.stdout = stdout
        self.stderr = stderr

        self.base_command, detected_arguments = self.split_command_and_args()
        self.parameters = []
        self.inputs = []
        self.outputs = []

        self.add_inputs_and_parameters(*detected_arguments)

    def split_command_and_args(self):
        """Return tuple with command and args from command line arguments."""
        if self.is_existing_path(self.command_line[0]):
            return [], list(self.command_line)

        cmd = [self.command_line[0]]
        args = list(self.command_line[1:])

        if len(args) < 2:
            # only guess subcommand for more arguments
            return cmd, args

        while args and re.match(self._RE_SUBCOMMAND, args[0]) and not self.is_existing_path(args[0]):
            cmd.append(args.pop(0))

        return cmd, args

    def is_existing_path(self, candidate, ignore=None):
        """Return a path instance if it exists in current directory."""
        if ignore and candidate in ignore:
            return

        candidate = Path(candidate)

        if not candidate.is_absolute():
            candidate = self.directory / candidate

        if candidate.exists() or candidate.is_symlink():
            try:
                path = candidate.resolve()
                path.relative_to(self.directory)
            except ValueError:  # An external file
                return Path(os.path.abspath(candidate))
            else:
                return path

    def add_inputs_and_parameters(self, *arguments):
        """Yield command input parameters."""
        position = 0
        prefix = None

        output_streams = {getattr(self, stream_name) for stream_name in ("stdout", "stderr")}

        for index, argument in enumerate(arguments):

            if prefix:
                if argument.startswith("-"):
                    position += 1
                    self.add_command_parameter(default_value=prefix, position=position)
                    prefix = None

            if argument.startswith("--"):
                if "=" in argument:
                    prefix, default = argument.split("=", 1)
                    prefix += "="
                    default, type = self.guess_type(default, ignore_filenames=output_streams)

                    position += 1
                    if type in PATH_OBJECTS:
                        self.add_command_input(
                            default_value=self._path_relative_to_root(default.path),
                            prefix=prefix,
                            position=position,
                            encoding_format=[DIRECTORY_MIME_TYPE] if type == "Directory" else default.mime_type,
                        )
                    else:
                        self.add_command_parameter(default_value=default, prefix=prefix, position=position)

                    prefix = None
                else:
                    prefix = argument

            elif argument.startswith("-"):
                if len(argument) > 2:
                    if "=" in argument:
                        prefix, default = argument.split("=", 1)
                        prefix += "="
                        default, type = self.guess_type(default, ignore_filenames=output_streams)
                    else:
                        # possibly a flag with value
                        prefix = argument[0:2]
                        default, type = self.guess_type(argument[2:], ignore_filenames=output_streams)

                    position += 1

                    if type in PATH_OBJECTS:
                        self.add_command_input(
                            default_value=self._path_relative_to_root(default.path),
                            prefix=prefix,
                            position=position,
                            encoding_format=[DIRECTORY_MIME_TYPE] if type == "Directory" else default.mime_type,
                        )
                    else:
                        self.add_command_parameter(default_value=default, prefix=prefix, position=position)
                    prefix = None
                else:
                    prefix = argument

            else:
                default, type = self.guess_type(argument, ignore_filenames=output_streams)

                position += 1

                if prefix:
                    prefix = prefix + " "  # NOTE: Make sure prefix is separated from argument by space

                if type in PATH_OBJECTS:
                    self.add_command_input(
                        default_value=self._path_relative_to_root(default.path),
                        prefix=prefix,
                        position=position,
                        encoding_format=[DIRECTORY_MIME_TYPE] if type == "Directory" else default.mime_type,
                    )
                else:
                    self.add_command_parameter(default_value=default, prefix=prefix, position=position)
                prefix = None

        if prefix:
            position += 1
            self.add_command_parameter(default_value=prefix, position=position)

        if self.stdin:
            position += 1
            default, type = self.guess_type(str(self.working_dir / self.stdin), ignore_filenames=output_streams)
            assert isinstance(default, File)
            self.add_command_input(default_value=str(default), encoding_format=default.mime_type, position=position)

    def add_outputs(self, candidates: Set[str]):
        """Yield detected output and changed command input parameter."""
        # TODO what to do with duplicate paths & inputs with same defaults
        tree = DirectoryTree.from_list(candidates)

        input_candidates = {}
        parameter_candidates = {}

        for input in self.inputs:
            # NOTE: Check if an input directory was modified
            input_path = Path(input.default_value)

            if input_path.is_dir() and tree.get(input_path):
                # The directory might exist before running the script
                candidates = self._check_potential_output_directory(input_path, candidates, tree)

            input_candidates[str(input_path)] = input

        for parameter in self.parameters:
            # NOTE: find parameters that might actually be outputs
            try:
                path = self.directory / str(parameter.default_value)
                input_path = Path(os.path.abspath(path)).relative_to(self.working_dir)
            except FileNotFoundError:
                continue

            if input_path.is_dir() and tree.get(input_path):
                # The directory might exist before running the script
                candidates = self._check_potential_output_directory(input_path, candidates, tree)

                parameter_candidates[str(input_path)] = parameter
            parameter_candidates[str(input_path)] = parameter

        for path in candidates:
            candidate = self.is_existing_path(self.working_dir / path)

            if candidate is None:
                raise errors.UsageError('Path "{0}" does not exist.'.format(path))

            glob = str(candidate.relative_to(self.working_dir))

            if glob in input_candidates:
                input = input_candidates[glob]

                self.add_command_output_from_input(input)
            elif glob in parameter_candidates:
                param = parameter_candidates[glob]

                self.add_command_output_from_parameter(param)
            else:
                self.add_command_output(default_value=glob)

    def _check_potential_output_directory(
        self, input_path: Path, candidates: Set[str], tree: DirectoryTree
    ) -> Set[str]:
        """Check an input/parameter for being a potential output directory."""
        subpaths = {str(input_path / path) for path in tree.get(input_path, default=[])}
        absolute_path = os.path.abspath(input_path)
        if Path(absolute_path) not in self.explicit_outputs:
            content = {str(path) for path in input_path.rglob("*") if not path.is_dir() and path.name != ".gitkeep"}
            preexisting_paths = content - subpaths
            if preexisting_paths:
                raise errors.InvalidOutputPath(
                    'The output directory "{0}" is not empty. \n\n'
                    "Delete existing files before running the "
                    "command:"
                    '\n  (use "git rm <file>..." to remove them '
                    "first)"
                    "\n\n".format(input_path)
                    + "\n".join("\t" + click.style(path, fg="yellow") for path in preexisting_paths)
                    + "\n\n"
                    "Once you have removed files that should be used "
                    "as outputs,\n"
                    "you can safely rerun the previous command."
                )

        # Remove files from the input directory
        candidates = {path for path in candidates if path not in subpaths}
        # Include input path in the candidates to check
        candidates.add(str(input_path))

        return candidates

    def _get_mimetype(self, file: Path) -> List[str]:
        """Return the MIME-TYPE of the given file."""
        # TODO: specify the actual mime-type of the file
        return ["application/octet-stream"]

    def guess_type(self, value: str, ignore_filenames: Set[str] = None) -> Tuple[Any, str]:
        """Return new value and CWL parameter type."""
        candidate = self.is_existing_path(value, ignore=ignore_filenames)
        if candidate:
            try:
                if candidate.is_dir():
                    return Directory(path=candidate), "Directory"
                return File(path=candidate, mime_type=self._get_mimetype(candidate)), "File"
            except ValueError:
                # The candidate points to a file outside the working
                # directory
                # TODO suggest that the file should be imported to the repo
                pass

        return value, "string"

    def get_stream_mapping_for_value(self, value: Any):
        """Return a stream mapping if value is a path mapped to a stream."""
        if self.stdin and self.stdin == value:
            return MappedIOStream(id=MappedIOStream.generate_id("stdin"), stream_type="stdin")
        if self.stdout and self.stdout == value:
            return MappedIOStream(id=MappedIOStream.generate_id("stdout"), stream_type="stdout")
        if self.stderr and self.stderr == value:
            return MappedIOStream(id=MappedIOStream.generate_id("stderr"), stream_type="stderr")

    def add_command_input(
        self,
        default_value: Any,
        prefix: Optional[str] = None,
        position: Optional[int] = None,
        postfix: Optional[str] = None,
        encoding_format: List[str] = None,
    ):
        """Create a CommandInput."""
        if self.no_input_detection and Path(default_value).resolve() not in self.explicit_inputs:
            return

        mapped_stream = self.get_stream_mapping_for_value(default_value)

        self.inputs.append(
            CommandInput(
                id=CommandInput.generate_id(
                    plan_id=self.plan_id,
                    position=position,
                    postfix=mapped_stream.stream_type if mapped_stream else postfix,
                ),
                default_value=default_value,
                prefix=prefix,
                position=position,
                mapped_to=mapped_stream,
                encoding_format=encoding_format,
                postfix=postfix,
            )
        )

    def add_command_output(
        self,
        default_value: Any,
        prefix: Optional[str] = None,
        position: Optional[int] = None,
        postfix: Optional[str] = None,
        encoding_format: List[str] = None,
    ):
        """Create a CommandOutput."""
        if self.no_output_detection and Path(default_value).resolve() not in self.explicit_outputs:
            return

        mapped_stream = self.get_stream_mapping_for_value(default_value)

        if mapped_stream and position is None:
            position = (
                max((p.position for p in chain(self.inputs, self.outputs, self.parameters) if p.position), default=0)
                + 1
            )

        self.outputs.append(
            CommandOutput(
                id=CommandOutput.generate_id(
                    plan_id=self.plan_id,
                    position=position,
                    postfix=mapped_stream.stream_type if mapped_stream else postfix,
                ),
                default_value=default_value,
                prefix=prefix,
                position=position,
                mapped_to=mapped_stream,
                encoding_format=encoding_format,
                postfix=postfix,
            )
        )

    def add_command_output_from_input(self, input: CommandInput):
        """Create a CommandOutput from an input."""
        self.inputs.remove(input)
        self.outputs.append(
            CommandOutput(
                id=input.id.replace("/inputs/", "/outputs/"),
                default_value=input.default_value,
                prefix=input.prefix,
                position=input.position,
                mapped_to=input.mapped_to,
                encoding_format=input.encoding_format,
            )
        )

    def add_command_output_from_parameter(self, parameter: CommandParameter):
        """Create a CommandOutput from a parameter."""
        self.parameters.remove(parameter)
        value = Path(self._path_relative_to_root(parameter.default_value))
        encoding_format = [DIRECTORY_MIME_TYPE] if value.resolve().is_dir() else self._get_mimetype(value)
        self.add_command_output(
            default_value=str(value),
            prefix=parameter.prefix,
            position=parameter.position,
            encoding_format=encoding_format,
        )

    def add_command_parameter(
        self,
        default_value: Any,
        prefix: Optional[str] = None,
        position: Optional[int] = None,
        name: Optional[str] = None,
    ):
        """Create a CommandParameter."""
        self.parameters.append(
            CommandParameter(
                id=CommandParameter.generate_id(plan_id=self.plan_id, position=position),
                default_value=default_value,
                prefix=prefix,
                position=position,
                name=name,
            )
        )

    def add_explicit_inputs(self):
        """Add explicit inputs ."""
        input_paths = [input.default_value for input in self.inputs]
        input_id = len(self.inputs) + len(self.parameters)

        for explicit_input in self.explicit_inputs:
            try:
                relative_explicit_input = str(explicit_input.relative_to(self.working_dir))
            except ValueError:
                raise errors.UsageError(
                    "The input file or directory is not in the repository."
                    "\n\n\t" + click.style(str(explicit_input), fg="yellow") + "\n\n"
                )

            if relative_explicit_input in input_paths:
                continue

            input_paths.append(explicit_input)

            if self.is_existing_path(explicit_input) is None:
                raise errors.UsageError(
                    "The input file or directory does not exist."
                    "\n\n\t" + click.style(str(explicit_input), fg="yellow") + "\n\n"
                )
            input_id += 1
            default, type = self.guess_type(explicit_input)
            # Explicit inputs are either File or Directory
            assert type in PATH_OBJECTS
            self.add_command_input(
                default_value=str(default),
                postfix=str(input_id),
                encoding_format=[DIRECTORY_MIME_TYPE] if type == "Directory" else default.mime_type,
            )

    @contextmanager
    @inject.autoparams()
    def watch(self, client_dispatcher: IClientDispatcher, no_output=False):
        """Watch a Renku repository for changes to detect outputs."""
        client = client_dispatcher.current_client
        client.check_external_storage()

        repo = client.repo

        # Remove indirect files list if any
        delete_indirect_files_list(self.working_dir)

        from renku.core.plugins.pluginmanager import get_plugin_manager

        pm = get_plugin_manager()
        pm.hook.pre_run(tool=self)
        self.existing_directories = {str(p.relative_to(client.path)) for p in client.path.glob("**/")}

        yield self

        if repo:
            # Include indirect inputs and outputs before further processing
            self.add_indirect_inputs()
            self.add_indirect_outputs()

            self._include_indirect_parameters()

            # Remove indirect files list if any
            delete_indirect_files_list(self.working_dir)

            # List of all output paths.
            output_paths = []

            inputs = {input.id: input for input in self.inputs}

            # Keep track of unmodified output files.
            unmodified = set()

            candidates = set()

            if not self.no_output_detection:
                # Calculate possible output paths.
                # Capture newly created files through redirects.
                candidates |= {file_ for file_ in repo.untracked_files}

                # Capture modified files through redirects.
                candidates |= {git_unicode_unescape(o.a_path) for o in repo.index.diff(None) if not o.deleted_file}

            # Include explicit outputs
            candidates |= {str(path.relative_to(self.working_dir)) for path in self.explicit_outputs}

            candidates = {path for path in candidates if safe_path(path)}

            self.add_outputs(candidates)

            for stream_name in ("stdout", "stderr"):
                stream = getattr(self, stream_name)
                if stream and stream not in candidates and Path(os.path.abspath(stream)) not in self.explicit_outputs:
                    unmodified.add(stream)
                elif stream:
                    output_paths.append(stream)

            for output in self.outputs:
                if output.default_value not in output_paths:
                    output_paths.append(output.default_value)

            if unmodified:
                raise errors.UnmodifiedOutputs(repo, unmodified)

            if not no_output and not output_paths:
                raise errors.OutputsNotFound(repo, inputs.values())

            if client.check_external_storage():
                client.track_paths_in_storage(*output_paths)

            add_to_git(repo.git, *output_paths)

            if repo.is_dirty():
                commit_msg = f"renku run: committing {len(output_paths)} newly added files"

                committer = Actor("renku {0}".format(__version__), version_url)

                repo.index.commit(commit_msg, committer=committer, skip_hooks=True)

                self._had_changes = True

        results = pm.hook.cmdline_tool_annotations(tool=self)
        self.annotations = [a for r in results for a in r]

    def _path_relative_to_root(self, path) -> str:
        """Make a potentially relative path in a subdirectory relative to the root of the repo."""
        return str((self.directory / path).resolve().relative_to(self.working_dir))

    def _include_indirect_parameters(self):
        run_parameters = read_indirect_parameters(self.working_dir)

        for k, v in run_parameters.items():
            self.add_command_parameter(name=k, default_value=str(v))

    def add_indirect_inputs(self):
        """Read indirect inputs list and add them to explicit inputs."""
        indirect_inputs_list = get_indirect_inputs_path(self.working_dir)

        for indirect_input in self._read_files_list(indirect_inputs_list):
            # treat indirect inputs like explicit inputs
            path = Path(os.path.abspath(indirect_input))
            self.explicit_inputs.append(path)

        # add new explicit inputs (if any) to inputs
        self.add_explicit_inputs()

    def add_indirect_outputs(self):
        """Read indirect outputs list and add them to explicit outputs."""
        indirect_outputs_list = get_indirect_outputs_path(self.working_dir)

        for indirect_output in self._read_files_list(indirect_outputs_list):
            # treat indirect outputs like explicit outputs
            path = Path(os.path.abspath(indirect_output))
            self.explicit_outputs.append(path)

    def iter_input_files(self, basedir):
        """Yield tuples with input id and path."""
        for input_ in self.inputs:
            yield input_.id, os.path.normpath(os.path.join(basedir, input_.default_value))

    @staticmethod
    def _read_files_list(files_list):
        """Read files list where each line is a filepath."""
        try:
            path = str(files_list)
            with open(path, "r") as f:
                for line in f:
                    line = line.strip()
                    if line:
                        yield Path(os.path.abspath(line))
        except FileNotFoundError:
            return

    @inject.autoparams("project_gateway")
    def to_plan(
        self,
        project_gateway: IProjectGateway,
        name: Optional[str] = None,
        description: str = Optional[None],
        keywords: Optional[List[str]] = None,
    ) -> Plan:
        """Return an instance of ``Plan`` based on this factory."""
        return Plan(
            id=self.plan_id,
            name=name,
            description=description,
            keywords=keywords,
            command=" ".join(self.base_command),
            inputs=self.inputs,
            outputs=self.outputs,
            parameters=self.parameters,
            project_id=project_gateway.get_project().id,
            success_codes=self.success_codes,
        )


def delete_indirect_files_list(working_dir):
    """Remove indirect inputs, outputs, and parameters list."""
    paths = [
        get_indirect_inputs_path(working_dir),
        get_indirect_outputs_path(working_dir),
        get_indirect_parameters_path(working_dir),
    ]
    for path in paths:
        try:
            os.remove(path)
        except FileNotFoundError:
            pass


def get_indirect_inputs_path(client_path):
    """Return path to file that contains indirect inputs list."""
    parent = _get_indirect_parent_path(client_path)
    return parent / "inputs.txt"


def get_indirect_outputs_path(client_path):
    """Return path to file that contains indirect outputs list."""
    parent = _get_indirect_parent_path(client_path)
    return parent / "outputs.txt"


def get_indirect_parameters_path(client_path):
    """Return path to file that contains indirect parameters list."""
    parent = _get_indirect_parent_path(client_path)
    return parent / "parameters.yml"


def _get_indirect_parent_path(client_path):
    renku_indirect_path = os.getenv("RENKU_INDIRECT_PATH") or ""

    base = (Path(client_path) / RENKU_HOME / RENKU_TMP).resolve()
    parent = (base / renku_indirect_path).resolve()

    try:
        parent.relative_to(base)
    except ValueError:
        raise errors.InvalidFileOperation(f"Invalid value for RENKU_INDIRECT_PATH env var: {renku_indirect_path}.")

    return parent


def read_indirect_parameters(working_dir):
    """Read and return indirect parameters."""
    path = get_indirect_parameters_path(working_dir)

    if not path.exists():
        return {}

    data = yaml.safe_load(path.read_text())

    if not isinstance(data, dict):
        raise errors.OperationError("Run parameters must be a dictionary.")

    return data


def add_indirect_parameter(working_dir, name, value):
    """Add a parameter to indirect parameters."""
    data = read_indirect_parameters(working_dir)
    data[name] = value

    yaml_data = yaml.dump(data)

    path = get_indirect_parameters_path(working_dir)
    path.parent.mkdir(exist_ok=True, parents=True)
    path.write_text(yaml_data)