From 36269913355334e1ee2a8dade7dbb3120f9fed58 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Thu, 9 Jan 2025 15:02:45 +0800 Subject: [PATCH 01/12] Add new steps --- patchwork/step.py | 44 ++- patchwork/steps/CallCommand/CallCommand.py | 60 ++++ patchwork/steps/CallCommand/__init__.py | 0 patchwork/steps/CallCommand/typed.py | 19 + patchwork/steps/CallSQL/CallSQL.py | 43 +++ patchwork/steps/CallSQL/__init__.py | 0 patchwork/steps/CallSQL/typed.py | 21 ++ poetry.lock | 381 ++++++++++++++++----- pyproject.toml | 3 +- 9 files changed, 460 insertions(+), 111 deletions(-) create mode 100644 patchwork/steps/CallCommand/CallCommand.py create mode 100644 patchwork/steps/CallCommand/__init__.py create mode 100644 patchwork/steps/CallCommand/typed.py create mode 100644 patchwork/steps/CallSQL/CallSQL.py create mode 100644 patchwork/steps/CallSQL/__init__.py create mode 100644 patchwork/steps/CallSQL/typed.py diff --git a/patchwork/step.py b/patchwork/step.py index ae7157af0..b9f343522 100644 --- a/patchwork/step.py +++ b/patchwork/step.py @@ -11,7 +11,16 @@ from enum import Enum -from typing_extensions import Any, Dict, List, Optional, Union, is_typeddict +from typing_extensions import ( + Any, + Collection, + Dict, + List, + Optional, + Type, + Union, + is_typeddict, +) from patchwork.logger import logger @@ -45,10 +54,9 @@ def __init__(self, inputs: DataPoint): """ # check if the inputs have the required keys - if self.__input_class is not None: - missing_keys = self.__input_class.__required_keys__.difference(inputs.keys()) - if len(missing_keys) > 0: - raise ValueError(f"Missing required data: {list(missing_keys)}") + missing_keys = self.find_missing_inputs(inputs) + if len(missing_keys) > 0: + raise ValueError(f"Missing required data: {list(missing_keys)}") # store the inputs self.inputs = inputs @@ -64,19 +72,23 @@ def __init__(self, inputs: DataPoint): self.original_run = self.run self.run = self.__managed_run - def __init_subclass__(cls, **kwargs): - input_class = kwargs.get("input_class", None) or getattr(cls, "input_class", None) - output_class = kwargs.get("output_class", None) or getattr(cls, "output_class", None) + def __init_subclass__(cls, input_class: Optional[Type] = None, output_class: Optional[Type] = None, **kwargs): + input_class = input_class or getattr(cls, "input_class", None) + if input_class is not None and not is_typeddict(input_class): + input_class = None - if input_class is not None and is_typeddict(input_class): - cls.__input_class = input_class - else: - cls.__input_class = None + output_class = output_class or getattr(cls, "output_class", None) + if output_class is not None and not is_typeddict(output_class): + output_class = None - if output_class is not None and is_typeddict(output_class): - cls.__output_class = output_class - else: - cls.__output_class = None + cls.__input_class = input_class + cls.__output_class = output_class + + @classmethod + def find_missing_inputs(cls, inputs: DataPoint) -> Collection: + if getattr(cls, "__input_class", None) is None: + return [] + return cls.__input_class.__required_keys__.difference(inputs.keys()) def __managed_run(self, *args, **kwargs) -> Any: self.debug(self.inputs) diff --git a/patchwork/steps/CallCommand/CallCommand.py b/patchwork/steps/CallCommand/CallCommand.py new file mode 100644 index 000000000..adf6765bf --- /dev/null +++ b/patchwork/steps/CallCommand/CallCommand.py @@ -0,0 +1,60 @@ +from __future__ import annotations + +import shlex +import shutil +import subprocess +from pathlib import Path + +from patchwork.logger import logger +from patchwork.step import Step, StepStatus +from patchwork.steps.CallCommand.typed import CallCommandInputs, CallCommandOutputs + + +class CallCommand(Step, input_class=CallCommandInputs, output_class=CallCommandOutputs): + def __init__(self, inputs: dict): + super().__init__(inputs) + self.command = shutil.which(inputs["command"]) + if self.command is None: + raise ValueError(f"Command `{inputs['command']}` not found in PATH") + self.command_args = shlex.split(inputs.get("command_args", "")) + self.working_dir = inputs.get("working_dir", Path.cwd()) + self.env = self.__parse_env_text(inputs.get("env", "")) + + @staticmethod + def __parse_env_text(env_text: str) -> dict[str, str]: + env_spliter = shlex.shlex(env_text, posix=True) + env_spliter.whitespace_split = True + env_spliter.whitespace += ";" + + env: dict[str, str] = dict() + for env_assign in env_spliter: + env_assign_spliter = shlex.shlex(env_assign, posix=True) + env_assign_spliter.whitespace_split = True + env_assign_spliter.whitespace += "=" + env_parts = list(env_assign_spliter) + if len(env_parts) < 1: + continue + + env_assign_target = env_parts[0] + if len(env_parts) < 2: + logger.error(f"{env_assign_target} is not assigned anything, skipping...") + continue + if len(env_parts) > 2: + logger.error(f"{env_assign_target} has more than 1 assignment, skipping...") + continue + env[env_assign_target] = env_parts[1] + + return env + + def run(self) -> dict: + cmd = [self.command, *self.command_args] + p = subprocess.run(cmd, capture_output=True, text=True, cwd=self.working_dir, env=self.env) + try: + p.check_returncode() + return dict(stdout_output=p.stdout) + except subprocess.CalledProcessError as e: + self.set_status( + StepStatus.FAILED, + f"`{self.command} {self.command_args}` failed with stdout:\n{p.stdout}\nstderr:\n{e.stderr}", + ) + return dict(stdout_output="") diff --git a/patchwork/steps/CallCommand/__init__.py b/patchwork/steps/CallCommand/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/patchwork/steps/CallCommand/typed.py b/patchwork/steps/CallCommand/typed.py new file mode 100644 index 000000000..8cbe4deec --- /dev/null +++ b/patchwork/steps/CallCommand/typed.py @@ -0,0 +1,19 @@ +from __future__ import annotations + +from typing_extensions import Annotated, TypedDict + +from patchwork.common.utils.step_typing import StepTypeConfig + + +class __RequiredCallCommandInputs(TypedDict): + command: str + + +class CallCommandInputs(__RequiredCallCommandInputs, total=False): + command_args: str + working_dir: Annotated[str, StepTypeConfig(is_path=True)] + env: str + + +class CallCommandOutputs(TypedDict): + stdout_output: str diff --git a/patchwork/steps/CallSQL/CallSQL.py b/patchwork/steps/CallSQL/CallSQL.py new file mode 100644 index 000000000..b1d78b583 --- /dev/null +++ b/patchwork/steps/CallSQL/CallSQL.py @@ -0,0 +1,43 @@ +from __future__ import annotations + +from sqlalchemy import URL, create_engine, exc, text + +from patchwork.step import Step, StepStatus +from patchwork.steps.CallSQL.typed import CallSQLInputs, CallSQLOutputs + + +class CallSQL(Step, input_class=CallSQLInputs, output_class=CallSQLOutputs): + def __init__(self, inputs: dict): + super().__init__(inputs) + self.query = inputs["query"] + self.__build_engine(inputs) + + def __build_engine(self, inputs: dict): + dialect = inputs["dialect"] + driver = inputs.get("driver") + dialect_plus_driver = f"{dialect}+{driver}" if driver is not None else dialect + kwargs = dict( + username=inputs["username"], + host=inputs.get("host", "localhost"), + port=inputs.get("port", 5432), + ) + if inputs.get("password") is not None: + kwargs["password"] = inputs.get("password") + connection_url = URL.create( + dialect_plus_driver, + **kwargs, + ) + self.engine = create_engine(connection_url) + with self.engine.connect() as conn: + conn.execute(text("SELECT 1")) + return self.engine + + def run(self) -> dict: + try: + with self.engine.begin() as conn: + cursor = conn.execute(text(self.query)) + result = cursor.fetchall() + return dict(result=result) + except exc.InvalidRequestError as e: + self.set_status(StepStatus.FAILED, f"`{self.query}` failed with message:\n{e}") + return dict(result=[]) diff --git a/patchwork/steps/CallSQL/__init__.py b/patchwork/steps/CallSQL/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/patchwork/steps/CallSQL/typed.py b/patchwork/steps/CallSQL/typed.py new file mode 100644 index 000000000..1593b76a8 --- /dev/null +++ b/patchwork/steps/CallSQL/typed.py @@ -0,0 +1,21 @@ +from __future__ import annotations + +from typing_extensions import Any, TypedDict + + +class __RequiredCallSQLInputs(TypedDict): + dialect: str + username: str + query: str + + +class CallSQLInputs(__RequiredCallSQLInputs, total=False): + driver: str + password: str + host: str + port: int + database: str + + +class CallSQLOutputs(TypedDict): + result: list[dict[str, Any]] diff --git a/poetry.lock b/poetry.lock index dda1bfe67..607134f19 100644 --- a/poetry.lock +++ b/poetry.lock @@ -476,13 +476,13 @@ virtualenv = ["virtualenv (>=20.0.35)"] [[package]] name = "cachecontrol" -version = "0.14.1" +version = "0.14.2" description = "httplib2 caching for requests" optional = false python-versions = ">=3.8" files = [ - {file = "cachecontrol-0.14.1-py3-none-any.whl", hash = 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= "~1.1.0" +sqlalchemy = "~2.0.36" patched-code2prompt = "~0.9.0.dev1" pyyaml = "^6.0.1" packageurl-python = "~0.15.0" From d32edc8254ff617d7fdcc980300fc14f7ad271e2 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Thu, 9 Jan 2025 15:08:46 +0800 Subject: [PATCH 02/12] update init file --- patchwork/steps/__init__.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/patchwork/steps/__init__.py b/patchwork/steps/__init__.py index deef1bffe..dcf124b6d 100644 --- a/patchwork/steps/__init__.py +++ b/patchwork/steps/__init__.py @@ -48,6 +48,8 @@ from patchwork.steps.SimplifiedLLM.SimplifiedLLM import SimplifiedLLM from patchwork.steps.SimplifiedLLMOnce.SimplifiedLLMOnce import SimplifiedLLMOnce from patchwork.steps.SlackMessage.SlackMessage import SlackMessage +from patchwork.steps.CallCommand.CallCommand import CallCommand +from patchwork.steps.CallSQL.CallSQL import CallSQL # Compatibility Aliases JoinListPB = JoinList @@ -61,6 +63,8 @@ "AnalyzeImpact", "CallAPI", "CallCode2Prompt", + "CallCommand", + "CallSQL", "CallLLM", "Combine", "CommitChanges", From 5b4daf78e0865eee1270e5a045b71f21d998c3d6 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Thu, 9 Jan 2025 16:42:16 +0800 Subject: [PATCH 03/12] change command to shell --- patchwork/common/utils/utils.py | 18 +++++++++++++++++ patchwork/steps/CallCommand/typed.py | 19 ------------------ patchwork/steps/CallSQL/CallSQL.py | 4 +++- patchwork/steps/CallSQL/typed.py | 1 + .../CallCommand.py => CallShell/CallShell.py} | 20 ++++++++----------- .../{CallCommand => CallShell}/__init__.py | 0 patchwork/steps/CallShell/typed.py | 19 ++++++++++++++++++ .../steps/PreparePrompt/PreparePrompt.py | 14 ++----------- patchwork/steps/__init__.py | 6 +++--- 9 files changed, 54 insertions(+), 47 deletions(-) delete mode 100644 patchwork/steps/CallCommand/typed.py rename patchwork/steps/{CallCommand/CallCommand.py => CallShell/CallShell.py} (66%) rename patchwork/steps/{CallCommand => CallShell}/__init__.py (100%) create mode 100644 patchwork/steps/CallShell/typed.py diff --git a/patchwork/common/utils/utils.py b/patchwork/common/utils/utils.py index bd5e24fc5..bd1d50082 100644 --- a/patchwork/common/utils/utils.py +++ b/patchwork/common/utils/utils.py @@ -2,10 +2,14 @@ import atexit import dataclasses +import random import signal +import string import tempfile +from collections.abc import Mapping from pathlib import Path +import chevron import tiktoken from chardet.universaldetector import UniversalDetector from git import Head, Repo @@ -19,6 +23,20 @@ _NEWLINES = {"\n", "\r\n", "\r"} +def mustache_render(template: str, data: Mapping) -> str: + if len(data.keys()) < 1: + return template + + chevron.render.__globals__["_html_escape"] = lambda x: x + return chevron.render( + template=template, + data=data, + partials_path=None, + partials_ext="".join(random.choices(string.ascii_uppercase + string.digits, k=32)), + partials_dict=dict(), + ) + + def detect_newline(path: str | Path) -> str | None: with open(path, "r", newline="") as f: lines = f.read().splitlines(keepends=True) diff --git a/patchwork/steps/CallCommand/typed.py b/patchwork/steps/CallCommand/typed.py deleted file mode 100644 index 8cbe4deec..000000000 --- a/patchwork/steps/CallCommand/typed.py +++ /dev/null @@ -1,19 +0,0 @@ -from __future__ import annotations - -from typing_extensions import Annotated, TypedDict - -from patchwork.common.utils.step_typing import StepTypeConfig - - -class __RequiredCallCommandInputs(TypedDict): - command: str - - -class CallCommandInputs(__RequiredCallCommandInputs, total=False): - command_args: str - working_dir: Annotated[str, StepTypeConfig(is_path=True)] - env: str - - -class CallCommandOutputs(TypedDict): - stdout_output: str diff --git a/patchwork/steps/CallSQL/CallSQL.py b/patchwork/steps/CallSQL/CallSQL.py index b1d78b583..5d8273eb2 100644 --- a/patchwork/steps/CallSQL/CallSQL.py +++ b/patchwork/steps/CallSQL/CallSQL.py @@ -2,6 +2,7 @@ from sqlalchemy import URL, create_engine, exc, text +from patchwork.common.utils.utils import mustache_render from patchwork.step import Step, StepStatus from patchwork.steps.CallSQL.typed import CallSQLInputs, CallSQLOutputs @@ -9,7 +10,8 @@ class CallSQL(Step, input_class=CallSQLInputs, output_class=CallSQLOutputs): def __init__(self, inputs: dict): super().__init__(inputs) - self.query = inputs["query"] + query_template_data = inputs.get("query_template_values", {}) + self.query = mustache_render(inputs["query"], query_template_data) self.__build_engine(inputs) def __build_engine(self, inputs: dict): diff --git a/patchwork/steps/CallSQL/typed.py b/patchwork/steps/CallSQL/typed.py index 1593b76a8..9f00e2b6c 100644 --- a/patchwork/steps/CallSQL/typed.py +++ b/patchwork/steps/CallSQL/typed.py @@ -15,6 +15,7 @@ class CallSQLInputs(__RequiredCallSQLInputs, total=False): host: str port: int database: str + query_template_values: dict[str, Any] class CallSQLOutputs(TypedDict): diff --git a/patchwork/steps/CallCommand/CallCommand.py b/patchwork/steps/CallShell/CallShell.py similarity index 66% rename from patchwork/steps/CallCommand/CallCommand.py rename to patchwork/steps/CallShell/CallShell.py index adf6765bf..efc10d1e2 100644 --- a/patchwork/steps/CallCommand/CallCommand.py +++ b/patchwork/steps/CallShell/CallShell.py @@ -1,22 +1,20 @@ from __future__ import annotations import shlex -import shutil import subprocess from pathlib import Path +from patchwork.common.utils.utils import mustache_render from patchwork.logger import logger from patchwork.step import Step, StepStatus -from patchwork.steps.CallCommand.typed import CallCommandInputs, CallCommandOutputs +from patchwork.steps.CallShell.typed import CallShellInputs, CallShellOutputs -class CallCommand(Step, input_class=CallCommandInputs, output_class=CallCommandOutputs): +class CallShell(Step, input_class=CallShellInputs, output_class=CallShellOutputs): def __init__(self, inputs: dict): super().__init__(inputs) - self.command = shutil.which(inputs["command"]) - if self.command is None: - raise ValueError(f"Command `{inputs['command']}` not found in PATH") - self.command_args = shlex.split(inputs.get("command_args", "")) + script_template_values = inputs.get("script_template_values", {}) + self.script = mustache_render(inputs["script"], script_template_values) self.working_dir = inputs.get("working_dir", Path.cwd()) self.env = self.__parse_env_text(inputs.get("env", "")) @@ -47,14 +45,12 @@ def __parse_env_text(env_text: str) -> dict[str, str]: return env def run(self) -> dict: - cmd = [self.command, *self.command_args] - p = subprocess.run(cmd, capture_output=True, text=True, cwd=self.working_dir, env=self.env) + p = subprocess.run(self.script, shell=True, capture_output=True, text=True, cwd=self.working_dir, env=self.env) try: p.check_returncode() - return dict(stdout_output=p.stdout) except subprocess.CalledProcessError as e: self.set_status( StepStatus.FAILED, - f"`{self.command} {self.command_args}` failed with stdout:\n{p.stdout}\nstderr:\n{e.stderr}", + f"script failed with stdout:\n{p.stdout}\nstderr:\n{e.stderr}", ) - return dict(stdout_output="") + return dict(stdout_output=p.stdout, stderr_output=p.stderr) diff --git a/patchwork/steps/CallCommand/__init__.py b/patchwork/steps/CallShell/__init__.py similarity index 100% rename from patchwork/steps/CallCommand/__init__.py rename to patchwork/steps/CallShell/__init__.py diff --git a/patchwork/steps/CallShell/typed.py b/patchwork/steps/CallShell/typed.py new file mode 100644 index 000000000..a8fd050bf --- /dev/null +++ b/patchwork/steps/CallShell/typed.py @@ -0,0 +1,19 @@ +from __future__ import annotations + +from typing_extensions import Annotated, Any, TypedDict + +from patchwork.common.utils.step_typing import StepTypeConfig + + +class __RequiredCallShellInputs(TypedDict): + script: str + + +class CallShellInputs(__RequiredCallShellInputs, total=False): + working_dir: Annotated[str, StepTypeConfig(is_path=True)] + env: str + script_template_values: dict[str, Any] + + +class CallShellOutputs(TypedDict): + stdout_output: str diff --git a/patchwork/steps/PreparePrompt/PreparePrompt.py b/patchwork/steps/PreparePrompt/PreparePrompt.py index a9d78767a..3596ce363 100644 --- a/patchwork/steps/PreparePrompt/PreparePrompt.py +++ b/patchwork/steps/PreparePrompt/PreparePrompt.py @@ -1,13 +1,10 @@ from __future__ import annotations import json -import random -import string from pathlib import Path -import chevron - from patchwork.common.constants import PROMPT_TEMPLATE_FILE_KEY +from patchwork.common.utils.utils import mustache_render from patchwork.logger import logger from patchwork.step import Step, StepStatus @@ -76,7 +73,6 @@ def run(self) -> dict: return dict(prompts=[]) prompts = [] - chevron.render.__globals__["_html_escape"] = lambda string: string for prompt_value in self.prompt_values: dict_value = prompt_value if not isinstance(dict_value, dict): @@ -86,13 +82,7 @@ def run(self) -> dict: for prompt_part in self.prompt_template: prompt_instance = {} for key, value in prompt_part.items(): - new_value = chevron.render( - template=value, - data=dict_value, - partials_path=None, - partials_ext="".join(random.choices(string.ascii_uppercase + string.digits, k=32)), - partials_dict=dict(), - ) + new_value = mustache_render(value, dict_value) prompt_instance[key] = new_value prompt.append(prompt_instance) prompts.append(prompt) diff --git a/patchwork/steps/__init__.py b/patchwork/steps/__init__.py index dcf124b6d..19bca5f94 100644 --- a/patchwork/steps/__init__.py +++ b/patchwork/steps/__init__.py @@ -3,6 +3,8 @@ from patchwork.steps.CallAPI.CallAPI import CallAPI from patchwork.steps.CallCode2Prompt.CallCode2Prompt import CallCode2Prompt from patchwork.steps.CallLLM.CallLLM import CallLLM +from patchwork.steps.CallShell.CallShell import CallShell +from patchwork.steps.CallSQL.CallSQL import CallSQL from patchwork.steps.Combine.Combine import Combine from patchwork.steps.CommitChanges.CommitChanges import CommitChanges from patchwork.steps.CreateIssue.CreateIssue import CreateIssue @@ -48,8 +50,6 @@ from patchwork.steps.SimplifiedLLM.SimplifiedLLM import SimplifiedLLM from patchwork.steps.SimplifiedLLMOnce.SimplifiedLLMOnce import SimplifiedLLMOnce from patchwork.steps.SlackMessage.SlackMessage import SlackMessage -from patchwork.steps.CallCommand.CallCommand import CallCommand -from patchwork.steps.CallSQL.CallSQL import CallSQL # Compatibility Aliases JoinListPB = JoinList @@ -63,7 +63,7 @@ "AnalyzeImpact", "CallAPI", "CallCode2Prompt", - "CallCommand", + "CallShell", "CallSQL", "CallLLM", "Combine", From 07b68d17b4b97d51c85b749c59c6cb9ae2c481d3 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Tue, 14 Jan 2025 14:46:10 +0800 Subject: [PATCH 04/12] bugfixes and changes --- patchwork/steps/CallSQL/CallSQL.py | 33 ++++++++++++++++---------- patchwork/steps/CallSQL/typed.py | 20 ++++++++-------- patchwork/steps/CallShell/CallShell.py | 4 +++- patchwork/steps/__init__.py | 1 - 4 files changed, 34 insertions(+), 24 deletions(-) diff --git a/patchwork/steps/CallSQL/CallSQL.py b/patchwork/steps/CallSQL/CallSQL.py index 5d8273eb2..0b5f6c7c2 100644 --- a/patchwork/steps/CallSQL/CallSQL.py +++ b/patchwork/steps/CallSQL/CallSQL.py @@ -3,6 +3,7 @@ from sqlalchemy import URL, create_engine, exc, text from patchwork.common.utils.utils import mustache_render +from patchwork.logger import logger from patchwork.step import Step, StepStatus from patchwork.steps.CallSQL.typed import CallSQLInputs, CallSQLOutputs @@ -10,21 +11,25 @@ class CallSQL(Step, input_class=CallSQLInputs, output_class=CallSQLOutputs): def __init__(self, inputs: dict): super().__init__(inputs) - query_template_data = inputs.get("query_template_values", {}) - self.query = mustache_render(inputs["query"], query_template_data) + query_template_data = inputs.get("db_query_template_values", {}) + self.query = mustache_render(inputs["db_query"], query_template_data) self.__build_engine(inputs) def __build_engine(self, inputs: dict): - dialect = inputs["dialect"] - driver = inputs.get("driver") + dialect = inputs["db_dialect"] + driver = inputs.get("db_driver") dialect_plus_driver = f"{dialect}+{driver}" if driver is not None else dialect kwargs = dict( - username=inputs["username"], - host=inputs.get("host", "localhost"), - port=inputs.get("port", 5432), + username=inputs["db_username"], + host=inputs.get("db_host", "localhost"), + port=inputs.get("db_port", 5432), ) - if inputs.get("password") is not None: - kwargs["password"] = inputs.get("password") + if inputs.get("db_password") is not None: + kwargs["password"] = inputs.get("db_password") + if inputs.get("db_name") is not None: + kwargs["database"] = inputs.get("db_name") + if inputs.get("db_params") is not None: + kwargs["query"] = inputs.get("db_params") connection_url = URL.create( dialect_plus_driver, **kwargs, @@ -36,10 +41,14 @@ def __build_engine(self, inputs: dict): def run(self) -> dict: try: + rv = [] with self.engine.begin() as conn: cursor = conn.execute(text(self.query)) - result = cursor.fetchall() - return dict(result=result) + for row in cursor: + result = row._asdict() + rv.append(result) + logger.info(f"Retrieved {len(rv)} rows!") + return dict(results=rv) except exc.InvalidRequestError as e: self.set_status(StepStatus.FAILED, f"`{self.query}` failed with message:\n{e}") - return dict(result=[]) + return dict(results=[]) diff --git a/patchwork/steps/CallSQL/typed.py b/patchwork/steps/CallSQL/typed.py index 9f00e2b6c..13b4ab5ed 100644 --- a/patchwork/steps/CallSQL/typed.py +++ b/patchwork/steps/CallSQL/typed.py @@ -4,19 +4,19 @@ class __RequiredCallSQLInputs(TypedDict): - dialect: str - username: str - query: str + db_dialect: str + db_username: str + db_query: str class CallSQLInputs(__RequiredCallSQLInputs, total=False): - driver: str - password: str - host: str - port: int - database: str - query_template_values: dict[str, Any] + db_driver: str + db_password: str + db_host: str + db_port: int + db_name: str + db_query_template_values: dict[str, Any] class CallSQLOutputs(TypedDict): - result: list[dict[str, Any]] + results: list[dict[str, Any]] diff --git a/patchwork/steps/CallShell/CallShell.py b/patchwork/steps/CallShell/CallShell.py index efc10d1e2..d738706e6 100644 --- a/patchwork/steps/CallShell/CallShell.py +++ b/patchwork/steps/CallShell/CallShell.py @@ -51,6 +51,8 @@ def run(self) -> dict: except subprocess.CalledProcessError as e: self.set_status( StepStatus.FAILED, - f"script failed with stdout:\n{p.stdout}\nstderr:\n{e.stderr}", + f"Script failed.", ) + logger.info(f"stdout: \n{p.stdout}") + logger.info(f"stderr:\n{p.stderr}") return dict(stdout_output=p.stdout, stderr_output=p.stderr) diff --git a/patchwork/steps/__init__.py b/patchwork/steps/__init__.py index 19bca5f94..515a3fe14 100644 --- a/patchwork/steps/__init__.py +++ b/patchwork/steps/__init__.py @@ -95,7 +95,6 @@ "ReadPRDiffs", "ReadPRDiffsPB", "ReadPRs", - "ResolveIssue", "ScanDepscan", "ScanSemgrep", "ScanSonar", From 0f95efdf7663bf75bf9fad539698583e1f1d48f4 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Tue, 14 Jan 2025 14:47:26 +0800 Subject: [PATCH 05/12] lock update --- poetry.lock | 606 ++++++++++++++++++++++++++-------------------------- 1 file changed, 307 insertions(+), 299 deletions(-) diff --git a/poetry.lock b/poetry.lock index 607134f19..ac3ebd3b6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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b/patchwork/steps/CallSQL/CallSQL.py index 0b5f6c7c2..dc5bccff8 100644 --- a/patchwork/steps/CallSQL/CallSQL.py +++ b/patchwork/steps/CallSQL/CallSQL.py @@ -34,7 +34,12 @@ def __build_engine(self, inputs: dict): dialect_plus_driver, **kwargs, ) - self.engine = create_engine(connection_url) + + connect_args = None + if inputs.get("db_driver_args") is not None: + connect_args = inputs.get("db_driver_args") + + self.engine = create_engine(connection_url, connect_args=connect_args) with self.engine.connect() as conn: conn.execute(text("SELECT 1")) return self.engine diff --git a/patchwork/steps/CallSQL/typed.py b/patchwork/steps/CallSQL/typed.py index 13b4ab5ed..a4bf26aa4 100644 --- a/patchwork/steps/CallSQL/typed.py +++ b/patchwork/steps/CallSQL/typed.py @@ -15,6 +15,8 @@ class CallSQLInputs(__RequiredCallSQLInputs, total=False): db_host: str db_port: int db_name: str + db_params: dict[str, Any] + db_driver_args: dict[str, Any] db_query_template_values: dict[str, Any] From 1689cd55d88aa4e4495e76a1a6b27f8526357114 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Mon, 20 Jan 2025 11:09:22 +0800 Subject: [PATCH 07/12] make username optional since some dbs take username in connect args instead --- patchwork/steps/CallSQL/typed.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/patchwork/steps/CallSQL/typed.py b/patchwork/steps/CallSQL/typed.py index a4bf26aa4..91e5684a5 100644 --- a/patchwork/steps/CallSQL/typed.py +++ b/patchwork/steps/CallSQL/typed.py @@ -5,12 +5,12 @@ class __RequiredCallSQLInputs(TypedDict): db_dialect: str - db_username: str db_query: str class CallSQLInputs(__RequiredCallSQLInputs, total=False): db_driver: str + db_username: str db_password: str db_host: str db_port: int From 2f4d48674abb46a92c34b26017abcbe96fe823ec Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Mon, 20 Jan 2025 12:02:18 +0800 Subject: [PATCH 08/12] fix test and filter url kwargs by none --- patchwork/step.py | 10 ++++++---- patchwork/steps/CallSQL/CallSQL.py | 13 +++++-------- 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/patchwork/step.py b/patchwork/step.py index b9f343522..62d81fde7 100644 --- a/patchwork/step.py +++ b/patchwork/step.py @@ -73,6 +73,8 @@ def __init__(self, inputs: DataPoint): self.run = self.__managed_run def __init_subclass__(cls, input_class: Optional[Type] = None, output_class: Optional[Type] = None, **kwargs): + if cls.__name__ == "PreparePR": + print(1) input_class = input_class or getattr(cls, "input_class", None) if input_class is not None and not is_typeddict(input_class): input_class = None @@ -81,14 +83,14 @@ def __init_subclass__(cls, input_class: Optional[Type] = None, output_class: Opt if output_class is not None and not is_typeddict(output_class): output_class = None - cls.__input_class = input_class - cls.__output_class = output_class + cls._input_class = input_class + cls._output_class = output_class @classmethod def find_missing_inputs(cls, inputs: DataPoint) -> Collection: - if getattr(cls, "__input_class", None) is None: + if getattr(cls, "_input_class", None) is None: return [] - return cls.__input_class.__required_keys__.difference(inputs.keys()) + return cls._input_class.__required_keys__.difference(inputs.keys()) def __managed_run(self, *args, **kwargs) -> Any: self.debug(self.inputs) diff --git a/patchwork/steps/CallSQL/CallSQL.py b/patchwork/steps/CallSQL/CallSQL.py index dc5bccff8..da69b1f91 100644 --- a/patchwork/steps/CallSQL/CallSQL.py +++ b/patchwork/steps/CallSQL/CallSQL.py @@ -20,19 +20,16 @@ def __build_engine(self, inputs: dict): driver = inputs.get("db_driver") dialect_plus_driver = f"{dialect}+{driver}" if driver is not None else dialect kwargs = dict( - username=inputs["db_username"], + username=inputs.get("db_username"), host=inputs.get("db_host", "localhost"), port=inputs.get("db_port", 5432), + password=inputs.get("db_password"), + database=inputs.get("db_database"), + query=inputs.get("db_params"), ) - if inputs.get("db_password") is not None: - kwargs["password"] = inputs.get("db_password") - if inputs.get("db_name") is not None: - kwargs["database"] = inputs.get("db_name") - if inputs.get("db_params") is not None: - kwargs["query"] = inputs.get("db_params") connection_url = URL.create( dialect_plus_driver, - **kwargs, + **{k: v for k, v in kwargs.items() if v is not None}, ) connect_args = None From ce927c7190976f418027e3436880c1b7fe7e9fe7 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Mon, 20 Jan 2025 15:28:03 +0800 Subject: [PATCH 09/12] auto parse dict inputs --- patchwork/common/utils/input_parsing.py | 21 +++++++++++++++++++++ patchwork/steps/CallSQL/CallSQL.py | 5 +++-- patchwork/steps/ModifyCodeOnce/typed.py | 1 + pyproject.toml | 2 +- 4 files changed, 26 insertions(+), 3 deletions(-) diff --git a/patchwork/common/utils/input_parsing.py b/patchwork/common/utils/input_parsing.py index 0f5318dec..94b5771b7 100644 --- a/patchwork/common/utils/input_parsing.py +++ b/patchwork/common/utils/input_parsing.py @@ -1,6 +1,8 @@ from __future__ import annotations +import json from collections.abc import Iterable, Mapping +from shutil import posix from typing_extensions import AnyStr, Union @@ -69,3 +71,22 @@ def parse_to_list( continue rv.append(stripped_value) return rv + +def parse_to_dict(possible_dict, limit = -1): + if possible_dict is None and limit == 0: + return None + + if isinstance(possible_dict, dict): + new_dict = dict() + for k, v in possible_dict.items(): + new_dict[k] = parse_to_dict(v, limit - 1) + return new_dict + elif isinstance(possible_dict, str): + try: + new_dict = json.loads(possible_dict, strict=False) + except json.JSONDecodeError: + return possible_dict + + return parse_to_dict(new_dict, limit - 1) + else: + return possible_dict diff --git a/patchwork/steps/CallSQL/CallSQL.py b/patchwork/steps/CallSQL/CallSQL.py index da69b1f91..502c76fa0 100644 --- a/patchwork/steps/CallSQL/CallSQL.py +++ b/patchwork/steps/CallSQL/CallSQL.py @@ -2,6 +2,7 @@ from sqlalchemy import URL, create_engine, exc, text +from patchwork.common.utils.input_parsing import parse_to_dict from patchwork.common.utils.utils import mustache_render from patchwork.logger import logger from patchwork.step import Step, StepStatus @@ -25,7 +26,7 @@ def __build_engine(self, inputs: dict): port=inputs.get("db_port", 5432), password=inputs.get("db_password"), database=inputs.get("db_database"), - query=inputs.get("db_params"), + query=parse_to_dict(inputs.get("db_params")), ) connection_url = URL.create( dialect_plus_driver, @@ -34,7 +35,7 @@ def __build_engine(self, inputs: dict): connect_args = None if inputs.get("db_driver_args") is not None: - connect_args = inputs.get("db_driver_args") + connect_args = parse_to_dict(inputs.get("db_driver_args")) self.engine = create_engine(connection_url, connect_args=connect_args) with self.engine.connect() as conn: diff --git a/patchwork/steps/ModifyCodeOnce/typed.py b/patchwork/steps/ModifyCodeOnce/typed.py index 0333aa59a..2df0c676c 100644 --- a/patchwork/steps/ModifyCodeOnce/typed.py +++ b/patchwork/steps/ModifyCodeOnce/typed.py @@ -15,3 +15,4 @@ class ModifyCodeOnceOutputs(TypedDict): path: str start_line: int end_line: int + diff: str diff --git a/pyproject.toml b/pyproject.toml index a50e1bfef..839a1d297 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "patchwork-cli" -version = "0.0.91.dev0" +version = "0.0.92.dev0" description = "" authors = ["patched.codes"] license = "AGPL" From aedaac21127eddbc3720db708a4dc1310e8d69ea Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Tue, 21 Jan 2025 10:10:00 +0800 Subject: [PATCH 10/12] bump version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 839a1d297..d7c5ee356 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "patchwork-cli" -version = "0.0.92.dev0" +version = "0.0.92" description = "" authors = ["patched.codes"] license = "AGPL" From b87eb7e1fdaf03e3a48268352bcb48b69b7494a4 Mon Sep 17 00:00:00 2001 From: TIANYOU CHEN <42710806+CTY-git@users.noreply.github.com> Date: Tue, 21 Jan 2025 10:28:07 +0800 Subject: [PATCH 11/12] lint and update deps --- patchwork/common/utils/input_parsing.py | 4 +- patchwork/steps/FixIssue/FixIssue.py | 16 +- patchwork/steps/FixIssue/typed.py | 8 +- patchwork/steps/ModifyCode/ModifyCode.py | 34 +- patchwork/steps/ModifyCode/typed.py | 5 +- poetry.lock | 628 ++++++++++++----------- pyproject.toml | 32 +- 7 files changed, 373 insertions(+), 354 deletions(-) diff --git a/patchwork/common/utils/input_parsing.py b/patchwork/common/utils/input_parsing.py index 94b5771b7..45c2e9047 100644 --- a/patchwork/common/utils/input_parsing.py +++ b/patchwork/common/utils/input_parsing.py @@ -2,7 +2,6 @@ import json from collections.abc import Iterable, Mapping -from shutil import posix from typing_extensions import AnyStr, Union @@ -72,7 +71,8 @@ def parse_to_list( rv.append(stripped_value) return rv -def parse_to_dict(possible_dict, limit = -1): + +def parse_to_dict(possible_dict, limit=-1): if possible_dict is None and limit == 0: return None diff --git a/patchwork/steps/FixIssue/FixIssue.py b/patchwork/steps/FixIssue/FixIssue.py index bcb81e7a2..0f7d419af 100644 --- a/patchwork/steps/FixIssue/FixIssue.py +++ b/patchwork/steps/FixIssue/FixIssue.py @@ -1,10 +1,8 @@ -import difflib import re from pathlib import Path from typing import Any, Optional -from git import Repo, InvalidGitRepositoryError -from patchwork.logger import logger +from git import InvalidGitRepositoryError, Repo from openai.types.chat import ChatCompletionMessageParam from patchwork.common.client.llm.aio import AioLlmClient @@ -15,6 +13,7 @@ AnalyzeImplementStrategy, ) from patchwork.common.tools import CodeEditTool, Tool +from patchwork.logger import logger from patchwork.step import Step from patchwork.steps.FixIssue.typed import FixIssueInputs, FixIssueOutputs @@ -100,7 +99,7 @@ def is_stop(self, messages: list[ChatCompletionMessageParam]) -> bool: class FixIssue(Step, input_class=FixIssueInputs, output_class=FixIssueOutputs): def __init__(self, inputs): """Initialize the FixIssue step. - + Args: inputs: Dictionary containing input parameters including: - base_path: Optional path to the repository root @@ -145,12 +144,12 @@ def __init__(self, inputs): def run(self): """Execute the FixIssue step. - + This method: 1. Executes the multi-turn LLM conversation to analyze and fix the issue 2. Tracks file modifications made by the CodeEditTool 3. Generates in-memory diffs for all modified files - + Returns: dict: Dictionary containing list of modified files with their diffs """ @@ -162,8 +161,7 @@ def run(self): if not isinstance(tool, CodeEditTool): continue tool_modified_files = [ - dict(path=str(file_path.relative_to(cwd)), diff="") - for file_path in tool.tool_records["modified_files"] + dict(path=str(file_path.relative_to(cwd)), diff="") for file_path in tool.tool_records["modified_files"] ] modified_files.extend(tool_modified_files) @@ -174,7 +172,7 @@ def run(self): file = modified_file["path"] try: # Try to get the diff using git - diff = self.repo.git.diff('HEAD', file) + diff = self.repo.git.diff("HEAD", file) modified_file["diff"] = diff or "" except Exception as e: # Git-specific errors (untracked files, etc) - keep empty diff diff --git a/patchwork/steps/FixIssue/typed.py b/patchwork/steps/FixIssue/typed.py index 2ead5452f..cd0265f40 100644 --- a/patchwork/steps/FixIssue/typed.py +++ b/patchwork/steps/FixIssue/typed.py @@ -1,4 +1,4 @@ -from typing_extensions import Annotated, Dict, List, TypedDict +from typing_extensions import Annotated, List, TypedDict from patchwork.common.constants import TOKEN_URL from patchwork.common.utils.step_typing import StepTypeConfig @@ -37,19 +37,21 @@ class FixIssueInputs(__FixIssueRequiredInputs, total=False): class ModifiedFile(TypedDict): """Represents a file that has been modified by the FixIssue step. - + Attributes: path: The relative path to the modified file from the repository root diff: A unified diff string showing the changes made to the file. Generated using Python's difflib to compare the original and modified file contents in memory. - + Note: The diff is generated by comparing file contents before and after modifications, without relying on version control systems. """ + path: str diff: str + class FixIssueOutputs(TypedDict): modified_files: List[ModifiedFile] diff --git a/patchwork/steps/ModifyCode/ModifyCode.py b/patchwork/steps/ModifyCode/ModifyCode.py index 5f517c1e4..0252431ef 100644 --- a/patchwork/steps/ModifyCode/ModifyCode.py +++ b/patchwork/steps/ModifyCode/ModifyCode.py @@ -9,7 +9,7 @@ def save_file_contents(file_path: str | Path, content: str) -> None: """Utility function to save content to a file. - + Args: file_path: Path to the file to save content to (str or Path) content: Content to write to the file @@ -47,7 +47,7 @@ def replace_code_in_file( new_code: str, ) -> None: """Replace code in a file at the specified line range. - + Args: file_path: Path to the file to modify (str or Path) start_line: Starting line number (1-based) @@ -109,23 +109,25 @@ def run(self) -> dict: try: # Store original content in memory original_content = file_path.read_text() if file_path.exists() else "" - + # Apply the changes replace_code_in_file(file_path, start_line, end_line, new_code) - + # Read modified content current_content = file_path.read_text() if file_path.exists() else "" - + # Generate unified diff fromfile = f"a/{file_path}" tofile = f"b/{file_path}" - diff = "".join(difflib.unified_diff( - original_content.splitlines(keepends=True), - current_content.splitlines(keepends=True), - fromfile=fromfile, - tofile=tofile - )) - + diff = "".join( + difflib.unified_diff( + original_content.splitlines(keepends=True), + current_content.splitlines(keepends=True), + fromfile=fromfile, + tofile=tofile, + ) + ) + if not diff and new_code: # If no diff but we have new code (new file) diff = f"+++ {file_path}\n{new_code}" except (OSError, IOError) as e: @@ -133,14 +135,10 @@ def run(self) -> dict: # Still proceed with the modification even if diff generation fails replace_code_in_file(file_path, start_line, end_line, new_code) diff = f"+++ {file_path}\n{new_code}" # Use new code as diff on error - + # Create the modified code file dictionary modified_code_file = dict( - path=str(file_path), - start_line=start_line, - end_line=end_line, - diff=diff, - **extracted_response + path=str(file_path), start_line=start_line, end_line=end_line, diff=diff, **extracted_response ) modified_code_files.append(modified_code_file) diff --git a/patchwork/steps/ModifyCode/typed.py b/patchwork/steps/ModifyCode/typed.py index 6f26f79b4..3fcffd82e 100644 --- a/patchwork/steps/ModifyCode/typed.py +++ b/patchwork/steps/ModifyCode/typed.py @@ -12,7 +12,7 @@ class ModifyCodeOutputs(TypedDict): class ModifiedCodeFile(TypedDict, total=False): """Represents a file that has been modified by the ModifyCode step. - + Attributes: path: The path to the modified file start_line: The starting line number of the modification (1-based) @@ -20,12 +20,13 @@ class ModifiedCodeFile(TypedDict, total=False): diff: A unified diff string showing the changes made to the file. Generated using Python's difflib for in-memory comparison of original and modified file contents. - + Note: The diff field is generated using difflib.unified_diff() to compare the original and modified file contents in memory, ensuring efficient and secure diff generation. """ + path: str start_line: int end_line: int diff --git a/poetry.lock b/poetry.lock index ac3ebd3b6..afcb0b86c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. [[package]] name = "aiofiles" @@ -1483,19 +1483,22 @@ yaml = ["PyYAML"] [[package]] name = "google-ai-generativelanguage" -version = "0.6.10" +version = "0.6.15" description = "Google Ai Generativelanguage API client library" optional = false python-versions = ">=3.7" files = [ - {file = "google_ai_generativelanguage-0.6.10-py3-none-any.whl", hash = "sha256:854a2bf833d18be05ad5ef13c755567b66a4f4a870f099b62c61fe11bddabcf4"}, - {file = "google_ai_generativelanguage-0.6.10.tar.gz", hash = "sha256:6fa642c964d8728006fe7e8771026fc0b599ae0ebeaf83caf550941e8e693455"}, + {file = "google_ai_generativelanguage-0.6.15-py3-none-any.whl", hash = "sha256:5a03ef86377aa184ffef3662ca28f19eeee158733e45d7947982eb953c6ebb6c"}, + {file = "google_ai_generativelanguage-0.6.15.tar.gz", hash = "sha256:8f6d9dc4c12b065fe2d0289026171acea5183ebf2d0b11cefe12f3821e159ec3"}, ] [package.dependencies] google-api-core = {version = ">=1.34.1,<2.0.dev0 || >=2.11.dev0,<3.0.0dev", extras = ["grpc"]} google-auth = ">=2.14.1,<2.24.0 || >2.24.0,<2.25.0 || >2.25.0,<3.0.0dev" -proto-plus = ">=1.22.3,<2.0.0dev" +proto-plus = [ + {version = ">=1.25.0,<2.0.0dev", markers = "python_version >= \"3.13\""}, + {version = ">=1.22.3,<2.0.0dev", markers = "python_version < \"3.13\""}, +] protobuf = ">=3.20.2,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<6.0.0dev" [[package]] @@ -1535,13 +1538,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"] [[package]] name = "google-api-python-client" -version = "2.158.0" +version = "2.159.0" description = "Google API Client Library for Python" optional = false python-versions = ">=3.7" files = [ - {file = "google_api_python_client-2.158.0-py2.py3-none-any.whl", hash = "sha256:36f8c8d2e79e50f76790ca5946d2f3f8333e210dc8539a6c88e0742416474ad2"}, - {file = "google_api_python_client-2.158.0.tar.gz", hash = "sha256:b6664597a9955e04977a62752e33fe44cb35c580e190c1cb08a041893172bd67"}, + {file = "google_api_python_client-2.159.0-py2.py3-none-any.whl", hash = "sha256:baef0bb631a60a0bd7c0bf12a5499e3a40cd4388484de7ee55c1950bf820a0cf"}, + {file = "google_api_python_client-2.159.0.tar.gz", hash = "sha256:55197f430f25c907394b44fa078545ffef89d33fd4dca501b7db9f0d8e224bd6"}, ] [package.dependencies] @@ -1592,16 +1595,16 @@ httplib2 = ">=0.19.0" [[package]] name = "google-generativeai" -version = "0.8.3" +version = "0.8.4" description = "Google Generative AI High level API client library and tools." optional = false python-versions = ">=3.9" files = [ - {file = "google_generativeai-0.8.3-py3-none-any.whl", hash = "sha256:1108ff89d5b8e59f51e63d1a8bf84701cd84656e17ca28d73aeed745e736d9b7"}, + {file = "google_generativeai-0.8.4-py3-none-any.whl", hash = "sha256:e987b33ea6decde1e69191ddcaec6ef974458864d243de7191db50c21a7c5b82"}, ] [package.dependencies] -google-ai-generativelanguage = "0.6.10" +google-ai-generativelanguage = "0.6.15" google-api-core = "*" google-api-python-client = "*" 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[metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "6c406ed9fa40b8ecda3d7ab91c32a6aaf56aa2ee2ea742f12ad86e443241a923" +content-hash = "5916c662b332b6965befab7f6b97ce7f8f31c09e90333e18b0591be7f9f7add3" diff --git a/pyproject.toml b/pyproject.toml index d7c5ee356..fa687fe0f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,35 +52,35 @@ json-repair = "~0.30.0" # pinning transitive dependencies tree-sitter = "~0.21.3" numpy = [ - { version = "^1.26", python = "^3.12", optional = true}, - { version = "^1.24", python = "^3.9, <=3.11", optional = true} + { version = "^1.26", python = "^3.12", optional = true }, + { version = "^1.24", python = "^3.9, <=3.11", optional = true } ] pandas = [ - { version = "^2.1.4", python = "^3.12", optional = true}, - { version = "^2.0.3", python = "3.9, <=3.11", optional = true} + { version = "^2.1.4", python = "^3.12", optional = true }, + { version = "^2.0.3", python = "3.9, <=3.11", optional = true } ] scipy = [ - { version = 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+++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 patchwork/steps/CallShell/README.md diff --git a/patchwork/steps/CallShell/README.md b/patchwork/steps/CallShell/README.md new file mode 100644 index 000000000..dd337d3ea --- /dev/null +++ b/patchwork/steps/CallShell/README.md @@ -0,0 +1,71 @@ +# Documentation for CallShell Module + +This documentation provides an overview of the `CallShell` module, explaining its purpose, how it can be used, and detailing its input and output parameters. + +## Overview + +The `CallShell` module is part of the `patchwork` library, designed to execute shell scripts from a Python context. It offers a structured way of defining the inputs necessary for running shell commands, handles output capture, and provides error logging. + +This module can be particularly useful in automated pipelines or scenarios where shell interaction within a Python script is needed. + +## Inputs + +### Required Inputs + +- **script** (`str`): The shell script or command to be executed. + +### Optional Inputs + +- **working_dir** (`str`): Specifies the working directory for executing the shell command. It can be provided as a path. +- **env** (`str`): A semi-colon separated string for setting environment variables in `KEY=VALUE` format. +- **script_template_values** (`dict[str, Any]`): A dictionary of values to be used in template rendering the script. + +## Outputs + +- **stdout_output** (`str`): Captures the standard output produced by the shell command. +- **stderr_output** (`str`): Captures the standard error output produced by the shell command. + +Note: While not explicitly defined in `typed.py`, `stderr_output` is captured in the `CallShell` class's `run()` method. + +## Implementation Details + +### Class: `CallShell` + +This class inherits from the `Step` base class, using `CallShellInputs` as the input type and `CallShellOutputs` as the output type. It processes the specified script and runs it within a subprocess. + +#### Methods + +- **`__init__`**: Initializes the `CallShell` instance with given inputs, rendering the script if template values are provided, and preparing the environment. + +- **`__parse_env_text`**: A static method to parse environment variable assignments from a text string. + +- **`run`**: Executes the shell command, logs output and error details, and sets the status based on the execution outcome. Uses Python's `subprocess.run` for executing the command. + +### Utility Imports and Logging + +The module makes use of utility functions like `mustache_render` for template processing and leverages a `logger` for logging standard output and error messages during execution. + +This integration is essential for efficiently managing and debugging shell script executions embedded within Python workflows. + +## Usage + +To use this module: + +1. Instantiate the `CallShell` class with a dictionary of inputs. +2. Invoke the `run` method to execute the shell script. +3. Capture the outputs, particularly `stdout_output` and `stderr_output`, for further processing or analysis. + +```python +inputs = { + "script": "echo Hello World", + "working_dir": "/path/to/dir", + "env": "VAR1=value1;VAR2=value2", + "script_template_values": {"some_placeholder": "some_value"} +} + +call_shell = CallShell(inputs) +outputs = call_shell.run() +print(outputs["stdout_output"]) +``` + +This module provides a robust interface for handling shell commands within Python, ensuring that inputs are properly managed, and outputs are consistently captured and logged.