import re
import json
from typing import Optional, Union

from multi_swe_bench.harness.image import Config, File, Image
from multi_swe_bench.harness.instance import Instance, TestResult
from multi_swe_bench.harness.pull_request import PullRequest


class ImageDefault(Image):
    def __init__(self, pr: PullRequest, config: Config):
        self._pr = pr
        self._config = config

    @property
    def pr(self) -> PullRequest:
        return self._pr

    @property
    def config(self) -> Config:
        return self._config

    def dependency(self) -> str:
        return "python:3.9"

    def image_prefix(self) -> str:
        return "envagent"

    def image_tag(self) -> str:
        return f"pr-{self.pr.number}"

    def workdir(self) -> str:
        return f"pr-{self.pr.number}"

    def files(self) -> list[File]:
        repo_name = self.pr.repo
        return [
            File(
                ".",
                "fix.patch",
                f"{self.pr.fix_patch}",
            ),
            File(
                ".",
                "test.patch",
                f"{self.pr.test_patch}",
            ),
            File(
                ".",
                "prepare.sh",
                """ls -la
###ACTION_DELIMITER###
pip install .[test]
###ACTION_DELIMITER###
pip install numpy==1.16.6
###ACTION_DELIMITER###
pip install .[test]
###ACTION_DELIMITER###
echo 'pytest --no-header -rA --tb=no -p no:cacheprovider ./tests' > test_commands.sh
###ACTION_DELIMITER###
cat test_commands.sh
###ACTION_DELIMITER###
bash test_commands.sh
###ACTION_DELIMITER###
python -c "import scvi; print(scvi.__version__)"
###ACTION_DELIMITER###
echo 'pytest --no-header -rA -p no:cacheprovider ./tests' > test_commands.sh
###ACTION_DELIMITER###
bash test_commands.sh
###ACTION_DELIMITER###
pip install anndata
###ACTION_DELIMITER###
bash test_commands.sh
###ACTION_DELIMITER###
pip install llvmlite==0.30.0
###ACTION_DELIMITER###
apt-get update && apt-get install -y llvm-7 llvm-7-dev
###ACTION_DELIMITER###
apt-get install -y llvm
###ACTION_DELIMITER###
wget https://releases.llvm.org/7.0.1/clang+llvm-7.0.1-x86_64-linux-gnu-ubuntu-18.04.tar.xz && tar xvf clang+llvm-7.0.1-x86_64-linux-gnu-ubuntu-18.04.tar.xz && export LLVM_CONFIG=$(pwd)/clang+llvm-7.0.1-x86_64-linux-gnu-ubuntu-18.04/bin/llvm-config && pip install llvmlite==0.30.0
###ACTION_DELIMITER###
apt-get install -y libtinfo5
###ACTION_DELIMITER###
export LLVM_CONFIG=$(pwd)/clang+llvm-7.0.1-x86_64-linux-gnu-ubuntu-18.04/bin/llvm-config && pip install llvmlite==0.30.0
###ACTION_DELIMITER###
apt-get install -y g++-10 && export CXX=g++-10 && pip install llvmlite==0.30.0
###ACTION_DELIMITER###
apt-get install -y clang && export CXX=clang++ && pip install llvmlite==0.30.0
###ACTION_DELIMITER###
bash test_commands.sh
###ACTION_DELIMITER###
pip install numpy==1.16.6 && bash test_commands.sh
###ACTION_DELIMITER###
pip install numpy==1.16.6 scipy==1.5.4 scikit-learn==0.24.2 pandas==1.1.5 matplotlib==3.3.4 h5py==2.10.0 anndata==0.7.8 && bash test_commands.sh
###ACTION_DELIMITER###
apt-get install -y libhdf5-dev && pip install h5py==2.10.0 && bash test_commands.sh
###ACTION_DELIMITER###

###ACTION_DELIMITER###
pip install Cython==0.29.21 && pip install h5py==2.10.0
###ACTION_DELIMITER###
pip install numpy==1.16.6 scipy==1.5.4 scikit-learn==0.24.2 pandas==1.1.5 matplotlib==3.3.4 h5py==2.10.0 anndata==0.7.8 && bash test_commands.sh
###ACTION_DELIMITER###
pip install seaborn==0.11.2 && bash test_commands.sh
###ACTION_DELIMITER###
pip install scanpy python-igraph louvain umap-learn && apt-get install -y mongodb && bash test_commands.sh
###ACTION_DELIMITER###
apt-get install -y mongodb-server && pip install scanpy==1.4.6 && bash test_commands.sh
###ACTION_DELIMITER###
wget -qO - https://www.mongodb.org/static/pgp/server-6.0.asc | apt-key add - && echo 'deb http://repo.mongodb.org/apt/debian bullseye/mongodb-org/6.0 main' > /etc/apt/sources.list.d/mongodb-org-6.0.list && apt-get update && apt-get install -y mongodb-org && pip install numba==0.45.0 && bash test_commands.sh
###ACTION_DELIMITER###
echo 'deb http://deb.debian.org/debian bullseye main' > /etc/apt/sources.list.d/bullseye.list && apt-get update && apt-get install -y libssl1.1 && rm /etc/apt/sources.list.d/bullseye.list && apt-get update && apt-get install -y mongodb-org && pip install numba==0.45.0 && bash test_commands.sh
###ACTION_DELIMITER###
pip install --force-reinstall llvmlite==0.30.0 numba==0.45.0 && bash test_commands.sh
###ACTION_DELIMITER###
pip install numpy==1.16.6 numba==0.45.0 llvmlite==0.30.0 && apt-get install -y libssl1.1 && wget -qO - https://www.mongodb.org/static/pgp/server-5.0.asc | apt-key add - && echo 'deb http://repo.mongodb.org/apt/debian buster/mongodb-org/5.0 main' > /etc/apt/sources.list.d/mongodb-org-5.0.list && apt-get update && apt-get install -y mongodb-org && bash test_commands.sh
###ACTION_DELIMITER###
pip install numpy==1.16.6 numba==0.45.0 llvmlite==0.30.0 scipy==1.5.4 pandas==1.1.5 matplotlib==3.3.4 h5py==2.10.0 anndata==0.7.8 seaborn==0.11.2 scanpy==1.4.6 && apt-get install -y libssl1.1 && wget -qO - https://www.mongodb.org/static/pgp/server-4.2.asc | apt-key add - && echo 'deb http://repo.mongodb.org/apt/debian buster/mongodb-org/4.2 main' > /etc/apt/sources.list.d/mongodb-org-4.2.list && apt-get update && apt-get install -y mongodb-org && service mongod start && bash test_commands.sh
###ACTION_DELIMITER###
apt-get install -y mongodb-server && service mongodb start && pip install scanpy==1.4.6 umap-learn==0.3.10 && bash test_commands.sh
###ACTION_DELIMITER###
echo 'deb http://deb.debian.org/debian bookworm main non-free contrib' > /etc/apt/sources.list && apt-get update && apt-get install -y mongodb && service mongodb start && bash test_commands.sh
###ACTION_DELIMITER###
echo 'pytest --no-header -rA --tb=no -p no:cacheprovider ./tests --ignore=tests/test_notebook.py' > test_commands.sh && bash test_commands.sh""",
            ),
            File(
                ".",
                "run.sh",
                """#!/bin/bash
cd /home/[[REPO_NAME]]
pytest --no-header -rA --tb=no -p no:cacheprovider ./tests --ignore=tests/test_notebook.py

""".replace("[[REPO_NAME]]", repo_name),
            ),
            File(
                ".",
                "test-run.sh",
                """#!/bin/bash
cd /home/[[REPO_NAME]]
if ! git -C /home/[[REPO_NAME]] apply --whitespace=nowarn /home/test.patch; then
    echo "Error: git apply failed" >&2
    exit 1  
fi
pytest --no-header -rA --tb=no -p no:cacheprovider ./tests --ignore=tests/test_notebook.py

""".replace("[[REPO_NAME]]", repo_name),
            ),
            File(
                ".",
                "fix-run.sh",
                """#!/bin/bash
cd /home/[[REPO_NAME]]
if ! git -C /home/[[REPO_NAME]] apply --whitespace=nowarn  /home/test.patch /home/fix.patch; then
    echo "Error: git apply failed" >&2
    exit 1  
fi
pytest --no-header -rA --tb=no -p no:cacheprovider ./tests --ignore=tests/test_notebook.py

""".replace("[[REPO_NAME]]", repo_name),
            ),
        ]

    def dockerfile(self) -> str:
        copy_commands = ""
        for file in self.files():
            copy_commands += f"COPY {file.name} /home/\n"

        dockerfile_content = """
# This is a template for creating a Dockerfile to test patches
# LLM should fill in the appropriate values based on the context

# Choose an appropriate base image based on the project's requirements - replace [base image] with actual base image
# For example: FROM ubuntu:**, FROM python:**, FROM node:**, FROM centos:**, etc.
FROM python:3.9

## Set noninteractive
ENV DEBIAN_FRONTEND=noninteractive

# Install basic requirements
# For example: RUN apt-get update && apt-get install -y git
# For example: RUN yum install -y git
# For example: RUN apk add --no-cache git
RUN apt-get update && apt-get install -y git

# Ensure bash is available
RUN if [ ! -f /bin/bash ]; then         if command -v apk >/dev/null 2>&1; then             apk add --no-cache bash;         elif command -v apt-get >/dev/null 2>&1; then             apt-get update && apt-get install -y bash;         elif command -v yum >/dev/null 2>&1; then             yum install -y bash;         else             exit 1;         fi     fi

WORKDIR /home/
COPY fix.patch /home/
COPY test.patch /home/
RUN git clone https://github.com/scverse/scvi-tools.git /home/scvi-tools

WORKDIR /home/scvi-tools
RUN git reset --hard
RUN git checkout {pr.base.sha}
"""
        dockerfile_content += f"""
{copy_commands}
"""
        return dockerfile_content.format(pr=self.pr)


@Instance.register("scverse", "scvi_tools_521_to_499")
class SCVI_TOOLS_521_TO_499(Instance):
    def __init__(self, pr: PullRequest, config: Config, *args, **kwargs):
        super().__init__()
        self._pr = pr
        self._config = config

    @property
    def pr(self) -> PullRequest:
        return self._pr

    def dependency(self) -> Optional[Image]:
        return ImageDefault(self.pr, self._config)

    def run(self, run_cmd: str = "") -> str:
        if run_cmd:
            return run_cmd

        return "bash /home/run.sh"

    def test_patch_run(self, test_patch_run_cmd: str = "") -> str:
        if test_patch_run_cmd:
            return test_patch_run_cmd

        return "bash /home/test-run.sh"

    def fix_patch_run(self, fix_patch_run_cmd: str = "") -> str:
        if fix_patch_run_cmd:
            return fix_patch_run_cmd

        return "bash /home/fix-run.sh"

    def parse_log(self, log: str) -> TestResult:
        # Parse the log content and extract test execution results.
        passed_tests = set()  # Tests that passed successfully
        failed_tests = set()  # Tests that failed
        skipped_tests = set()  # Tests that were skipped
        import re

        # Extract test names using regular expressions
        passed_tests = set(re.findall(r"^PASSED (\S+)", log, re.MULTILINE))
        failed_tests = set(re.findall(r"^FAILED (\S+)", log, re.MULTILINE))
        skipped_tests = set(re.findall(r"^SKIPPED (\S+)", log, re.MULTILINE))
        parsed_results = {
            "passed_tests": passed_tests,
            "failed_tests": failed_tests,
            "skipped_tests": skipped_tests,
        }

        return TestResult(
            passed_count=len(passed_tests),
            failed_count=len(failed_tests),
            skipped_count=len(skipped_tests),
            passed_tests=passed_tests,
            failed_tests=failed_tests,
            skipped_tests=skipped_tests,
        )
