Example #1
0
def execute_using_docker(mint_config_file: Path):
    model_path = mint_config_file.parent
    name = model_path.name
    docker_path = model_path / DOCKER_DIR
    try:
        image = build_docker(docker_path, name)
    except APIError as e:
        click.secho("Error building the image", fg="red")
        click.echo(e)
        exit(1)
    except Exception as e:
        click.secho("Error building the image", fg="red")
        click.echo(e)
        exit(1)
    now = datetime.now().timestamp()

    src_dir = create_execution_directory(mint_config_file, model_path)
    try:
        resource = create_model_catalog_resource(mint_config_file)
    except ValueError:
        logging.error(exc_info=True)
        pass
    docker_run(image, resource, src_dir)
    detect_news_file(src_dir, mint_config_file, now)
    write_spec(mint_config_file, LAST_EXECUTION_DIR, str(src_dir.absolute()))
    return src_dir
Example #2
0
def step3(mic_file):
    """
    Create MINT wrapper using the mic.yaml. This command will handle adding inputs and parameters into the run file.

    - You must pass the MIC_FILE (mic.yaml) using the option (-f) or run the command from the same directory as mic.yaml

    Example:
    mic encapsulate step3 -f <mic_file>
    """
    if not Path(mic_file).exists():
        click.secho("Error: {} doesn't exists".format(mic_file), fg="red")
        exit(1)
    mic_config_path = Path(mic_file)
    model_directory_path = mic_config_path.parent
    inputs, parameters, outputs, configs = get_inputs_parameters(
        mic_config_path)
    number_inputs, number_parameters, number_outputs = get_numbers_inputs_parameters(
        mic_config_path)
    run_path = render_run_sh(model_directory_path, inputs, parameters,
                             number_inputs, number_parameters)
    render_io_sh(model_directory_path, inputs, parameters, configs)
    render_output(model_directory_path, [], False)
    write_spec(mic_config_path, STEP_KEY, 3)
    click.echo("The MIC Wrapper has been created at: {}".format(run_path))
    click.secho(
        "Before the next step you must add any (bash) commands needed to run your model between the two "
        "comments in the wrapper file. This file is located in {}/{}".format(
            SRC_DIR, RUN_FILE),
        fg="green")
    click.secho(
        "If your model has a configuration file, you will need to edit the values to match {}\'s parameter "
        "names then run step4. Otherwise you can move on to step5. See the docs for more details"
        "".format(CONFIG_YAML_NAME),
        fg="green")
Example #3
0
def publish_docker(mic_config_path, profile):
    # DOCKER_KEY doesn't have the docker username
    docker_image = get_key_spec(mic_config_path, DOCKER_KEY)
    try:
        docker_image = docker_image.split('/')[-1]
    except:
        pass
    try:
        docker_image = docker_image.split(':')[0]
    except:
        pass
    container_name = get_key_spec(mic_config_path, CONTAINER_NAME_KEY)
    docker_username = get_docker_username(profile)
    version = get_key_spec(mic_config_path, VERSION_KEY)
    docker_image_with_version = f"""{docker_username}/{docker_image}:{version}"""
    docker_container_cmd = f"""docker container commit {container_name} {docker_image_with_version} """
    click.secho(f"Committing the changes into the Docker Image "
                f"Please wait...")
    os.system(docker_container_cmd)
    click.secho("Uploading the Docker Image")
    logging.info("Publish docker image")
    try:
        docker_push_cmd = f"""docker push {docker_image_with_version} """
        os.system(docker_push_cmd)
        write_spec(mic_config_path, DOCKER_KEY, docker_image_with_version)

    except Exception as e:
        raise e
Example #4
0
def outputs(mic_file, custom_outputs):
    """
Describe the outputs of your model using the information obtained by the `trace` command.
To identify  which inputs have been automatically detected, execute `mic pkg outputs -f mic/mic.yaml`
and then inspect the mic.yaml file

- You must pass the MIC_FILE (mic.yaml) as an argument using the (-f) option; or run the
command from the same directory as mic.yaml

- Identify undetected files or directories  in the mic.yaml file and pass them as as arguments to the command

mic pkg outputs -f <mic_file> [undetected files]...

Example:

mic pkg outputs -f mic/mic.yaml output.txt outputs_directory
    """
    # Searches for mic file if user does not provide one
    mic_file = check_mic_path(mic_file)
    log_command(logging,
                "outputs",
                mic_file=mic_file,
                custom_outputs=custom_outputs)

    try:
        info_start_outputs()
        mic_config_file = Path(mic_file)
        user_execution_directory = mic_config_file.parent.parent
        repro_zip_trace_dir = find_dir(REPRO_ZIP_TRACE_DIR,
                                       user_execution_directory)
        repro_zip_trace_dir = Path(repro_zip_trace_dir)
        repro_zip_config_file = repro_zip_trace_dir / REPRO_ZIP_CONFIG_FILE
        spec = get_spec(repro_zip_config_file)
        custom_outputs = [
            str(user_execution_directory /
                Path(i).relative_to(user_execution_directory))
            for i in list(custom_outputs)
        ]
        outputs = get_outputs_reprozip(spec, user_execution_directory)
        logging.debug("Outputs found from reprozip: {}".format(outputs))
        for i in list(custom_outputs):
            if Path(i).is_dir():
                outputs += get_filepaths(i)
            else:
                outputs.append(i)
        for i in outputs:
            click.secho(f"""Output added: {Path(i).name} """, fg="blue")
        info_end_outputs(outputs)
        write_spec(mic_config_file, OUTPUTS_KEY,
                   relative(outputs, user_execution_directory))
        logging.info("outputs done")
    except Exception as e:
        logging.exception(f"Outputs failed: {e}")
        click.secho("Failed", fg="red")
        click.secho(e)
Example #5
0
def step6(mic_file):
    """
    Build and run the Docker image

    Example:
    mic encapsulate step6 -f <mic_file>
    """
    mic_config_path = Path(mic_file)
    execute_using_docker(Path(mic_file))
    write_spec(mic_config_path, STEP_KEY, 6)
    click.secho("Success", fg="green")
Example #6
0
def step7(mic_file, profile):
    """
    Publish your code and MIC wrapper on GitHub and the Docker Image on DockerHub

    Example:
    mic encapsulate step7 -f <mic_file>
    """
    info_step8()
    mic_config_path = Path(mic_file)
    model_dir = mic_config_path.parent
    click.secho("Deleting the executions")
    push(model_dir, mic_config_path, profile)
    publish_docker(mic_config_path, profile)
    write_spec(mic_config_path, STEP_KEY, 7)
Example #7
0
def push(model_directory: Path, mic_config_path: Path, name: str, profile):
    repository_name = name
    _version = new_version()
    write_spec(mic_config_path, VERSION_KEY, _version)
    logging.info("Compressing code")
    click.secho("Compressing your code")
    zip_file = compress_src_dir(model_directory, _version)
    url = upload_file(zip_file, profile, "components")
    write_spec(mic_config_path, MINT_COMPONENT_KEY, url)
    logging.info("Push complete: {}".format({
        'repository': url,
        'version': _version
    }))
    click.secho("Repository: {}".format(url))
    click.secho("Version: {}".format(_version))
Example #8
0
def step5(mic_file):
    """
    Set up Docker Image for model.

    Example:
    mic encapsulate step5 -f <mic_file>
    """
    mic_config_path = Path(mic_file)
    model_dir = mic_config_path.parent
    src_dir_path = model_dir / SRC_DIR
    if not mic_config_path.exists():
        exit(1)
    frameworks = detect_framework(src_dir_path)
    if len(frameworks) > 1:
        click.secho(
            "MIC has detect {} possible framework/language on component: {}".
            format(len(frameworks), ",".join([i.label for i in frameworks])))

        click.secho("Please select the correct option")
        click.secho(
            "This information allows MIC to select the correct Docker Image")
        framework = click.prompt("Select a option ".format(Framework),
                                 show_choices=True,
                                 type=click.Choice(frameworks,
                                                   case_sensitive=False),
                                 value_proc=handle)
    elif len(frameworks) == 1:
        framework = frameworks[0]
    else:
        framework = Framework.GENERIC

    if framework == Framework.GENERIC:
        bin_dir = model_dir / DOCKER_DIR / "bin"
        bin_dir.mkdir(exist_ok=True)
    elif framework == Framework.PYTHON37:
        requirements_file = Path(
            mic_file).parent / DOCKER_DIR / REQUIREMENTS_FILE
        freeze(requirements_file)
        click.echo(
            "Extracting the Python dependencies.\nYou can view or edit the dependencies file {} "
            .format(requirements_file))
    dockerfile = render_dockerfile(model_dir, framework)
    click.secho("Dockerfile has been created: {}".format(dockerfile))
    write_spec(mic_config_path, STEP_KEY, 5)
Example #9
0
def step8(mic_file, profile):
    """
    Publish your model into the Model Catalog

    Example:
    mic encapsulate step8 -f <mic_file>
    """
    mic_config_path = Path(mic_file)
    model_configuration = create_model_catalog_resource(Path(mic_file),
                                                        allow_local_path=False)

    api_response_model, api_response_mc = publish_model_configuration(
        model_configuration, profile)
    click.echo(
        "You can run or see the details using DAME. More info at https://dame-cli.readthedocs.io/en/latest/"
    )
    click.echo("For example, you can run it using:\ndame run {}".format(
        obtain_id(api_response_mc.id)))
    write_spec(mic_config_path, STEP_KEY, 8)
Example #10
0
def step4(mic_file, configuration_files):
    """
    If your model does not use configuration files, you can skip this step

    Specify the inputs and parameters of your model component from configuration file(s)

    - You must pass the MIC_FILE (mic.yaml) using the option (-f) or run the command from the same directory as mic.yaml

    - Pass the configuration files as arguments

    mic encapsulate step4 -f <mic_file> [configuration_files]...

    Example:
    mic encapsulate step4 -f mic.yaml data/example_dir/file1.txt  data/file2.txt
    """
    mic_config_path = Path(mic_file)
    if not mic_config_path.exists():
        click.secho("Error: that configuration path does not exist", fg="red")
        exit(1)

    # loop through configuration_files list
    for cp in configuration_files:
        # The program will crash if the users configuration file is not in the data dir. This checks for that
        if DATA_DIR not in Path(cp).absolute().parts:
            click.secho(
                "Error: Configuration file must be stored within {} directory".
                format(DATA_DIR),
                fg="red")
            click.secho("Bad path input: {}".format(cp))
            exit(1)
    add_configuration_files(mic_config_path, configuration_files)
    model_directory_path = mic_config_path.parent
    inputs, parameters, outputs, configs = get_inputs_parameters(
        mic_config_path)
    number_inputs, number_parameters, number_outputs = get_numbers_inputs_parameters(
        mic_config_path)
    render_run_sh(model_directory_path, inputs, parameters, number_inputs,
                  number_parameters)
    render_io_sh(model_directory_path, inputs, parameters, configs)
    render_output(model_directory_path, [], False)
    write_spec(mic_config_path, STEP_KEY, 4)
Example #11
0
def publish_docker(mic_config_path, profile):
    version = get_key_spec(mic_config_path, VERSION_KEY)
    image_name = get_key_spec(mic_config_path, DOCKER_KEY)
    credentials = get_credentials(profile)
    click.secho("Publishing the Docker Image")

    try:
        client = docker.from_env()
        if DOCKER_USERNAME_KEY not in credentials:
            exit(0)
        username = credentials[DOCKER_USERNAME_KEY]
        image = client.images.get(image_name)
        image_name_without_version = image_name.split("/")[-1].split(':')[0]
        repository = "{}/{}".format(username, image_name_without_version)
        image.tag(repository, version)
        client.images.push(repository, version)
    except Exception as e:
        raise e
    docker_image = "{}:{}".format(repository, version)
    click.secho("Docker Image: {}".format(docker_image))
    write_spec(mic_config_path, DOCKER_KEY, docker_image)
Example #12
0
def push(model_directory: Path, mic_config_path: Path, profile):
    click.secho("Creating the git repository")
    repo = get_or_create_repo(model_directory)
    click.secho("Compressing your code")
    compress_src_dir(model_directory)
    click.secho("Creating a new commit")
    git_commit(repo)
    click.secho("Creating or using the GitHub repository")
    url = check_create_remote_repo(repo, profile, model_directory.name,
                                   model_directory)
    click.secho("Creating a new version")
    _version = git_tag(repo, author)
    click.secho("Pushing your changes to the server")
    git_push(repo, profile, _version)
    repo = get_github_repo(profile, model_directory.name)
    for i in repo.get_contents(""):
        if i.name == "{}.zip".format(MINT_COMPONENT_ZIP):
            file = i
            break

    write_spec(mic_config_path, REPO_KEY, url)
    write_spec(mic_config_path, VERSION_KEY, _version)
    write_spec(mic_config_path, MINT_COMPONENT_KEY, file.download_url)
    click.secho("Repository: {}".format(url))
    click.secho("Version: {}".format(_version))
    remove_temp_files(mic_config_path)
Example #13
0
def step2(mic_file, parameters):
    """
    Fill the MIC configuration file with the information about the parameters and inputs

    MIC is going to detect:
     - the inputs (files and directory) and add them in the MIC configuration file.
     - the parameters and add them in the configuration file

    Example:
    mic encapsulate step2 -f <mic_file> -p <number_of_parameters>
    """
    mic_config_path = Path(mic_file)
    inputs_dir = mic_config_path.parent / DATA_DIRECTORY_NAME
    if not inputs_dir.exists():
        exit(1)
    fill_config_file_yaml(Path(mic_file), inputs_dir, parameters)
    click.secho(
        "MIC has added the parameters and inputs into the {} ({})".format(
            MIC_CONFIG_FILE_NAME, CONFIG_YAML_NAME))
    click.secho("You can see the changes in {}".format(
        Path(mic_file).absolute()),
                fg="green")
    click.secho("Before step3: ", fg="green")
    click.secho(
        "You must add a default value for the \"default-value\" field in {}. Just replace the 0 with your value"
        "".format(CONFIG_YAML_NAME),
        fg="green")
    click.secho(
        "It is recommended you also add a description for each input and parameter in {}"
        .format(CONFIG_YAML_NAME),
        fg="green")
    click.secho(
        "If you use a script to initialize or create visualizations of your model you must copy these into the "
        "src directory",
        fg="green")
    write_spec(mic_config_path, STEP_KEY, 2)
Example #14
0
def upload_component(cwl_document, cwl_values, profile):
    # create a temporal file
    cwl_document_path = Path(cwl_document)
    name = cwl_document_path.stem
    cwl_dir = cwl_document_path.parent
    mic_config_path = create_config_file_yaml(cwl_dir, f"""{name}_mic.yaml""")
    cwl_values_dict = get_spec(Path(cwl_values))
    # get the name from cwl document and write
    write_spec(mic_config_path, NAME_KEY, name)
    # read the CWL document and stored as dict
    cwl_document_dict = get_spec(cwl_document_path)
    # get the input, parameters and outputs from CWL document
    inputs = get_inputs(cwl_document_dict)
    outputs = get_outputs(cwl_document_dict)
    parameters = get_parameters(cwl_document_dict)
    # write then on MIC file
    add_inputs(mic_config_path, inputs, cwl_values_dict)
    add_outputs(mic_config_path, outputs, cwl_values)
    add_parameters(mic_config_path, parameters, cwl_values_dict)

    # obtain the docker image from cwl
    docker_image = get_docker_image(cwl_document_dict)
    write_spec(mic_config_path, DOCKER_KEY, docker_image)

    #obtain cwl command
    write_spec(mic_config_path, CWL_KEY, cwl_document_path)
    # Message publish start
    #info_start_publish(True)
    # push the component
    model_configuration = create_model_catalog_resource_cwl(
        Path(mic_config_path),
        name,
        allow_local_path=False
    )
    api_response_model, api_response_mc, model_id, software_version_id = publish_model_configuration(
        model_configuration, profile)
    # Message publish end
    info_end_publish(obtain_id(model_id),
                     obtain_id(software_version_id),
                     obtain_id(api_response_mc.id),
                     profile
                     )
Example #15
0
def start(user_execution_directory, name, image):
    """
    This step generates a mic.yaml file and the directories (data/, src/, docker/). 

    The argument: `model_configuration_name` is the name of the model component you are defining in MIC
     """
    user_execution_directory = Path(user_execution_directory)
    mic_dir = user_execution_directory / MIC_DIR

    create_base_directories(mic_dir)

    # Cant log the start command until the mic dir has been created. Else mic will think the directory already exists
    if make_log_file():
        log_system_info(get_mic_logger().name)

    log_command(logging, "start", name=name, image=image)

    mic_config_path = create_config_file_yaml(mic_dir)
    custom_image = False

    if image is None:
        framework = detect_framework_main(user_execution_directory)
    else:
        # If a user provides a image, the framework is generic.
        custom_image = True
        framework = Framework.GENERIC
        framework.image = image
        os.system(f"docker pull {framework.image}")

        render_dockerfile(mic_dir, framework)

    # Make sure the name given is valid
    if not name.islower():
        logging.debug(
            "User's model name does not contain all lowercase characters. Setting it to lower"
        )
        click.secho(
            "Model name must be lower case. Mic will replace any uppercase letters",
            fg='yellow')
        name = name.lower()

    os.system(f"docker pull {framework.image}")
    try:
        user_image = build_docker(mic_dir / DOCKER_DIR, name)
    except ValueError:
        click.secho("The extraction of dependencies has failed", fg='red')
        user_image = framework.image

    container_name = f"{name}_{str(uuid.uuid4())[:8]}"
    write_spec(mic_config_path, NAME_KEY, name)
    write_spec(mic_config_path, DOCKER_KEY, user_image)
    write_spec(mic_config_path, FRAMEWORK_KEY, framework.label)
    write_spec(mic_config_path, CONTAINER_NAME_KEY, container_name)

    docker_cmd = f"""docker run -ti \
            --name={container_name} \
            --cap-add=SYS_PTRACE \
            -v \"{user_execution_directory}\":/tmp/mint \
            -w /tmp/mint {user_image} """

    if custom_image:
        click.secho(f"""
You are using a custom image
Installing MIC and some dependencies
        """,
                    fg="green")

    try:
        os.system(docker_cmd)
        logging.info("start done")
    except Exception as e:
        logging.exception(f"Start failed: {e}")
        click.secho("Failed", fg="red")
        click.secho(e)
Example #16
0
def inputs(mic_file, custom_inputs):
    """
Describe the inputs of your model using the information obtained by the `trace` command. To identify  which inputs have
been automatically detected, execute `mic pkg inputs -f mic/mic.yaml` and then inspect the mic.yaml file

- You must pass the MIC_FILE (mic.yaml) as an argument using the (-f) option  or run the
command from the same directory as mic.yaml

- Identify undetected files in or directories in mic.yaml and add them as arguments to the `inputs` command

mic pkg inputs -f <mic_file> [undetected files]...

Usage example:

mic pkg inputs -f mic/mic.yaml input.txt inputs_directory


    """
    # Searches for mic file if user does not provide one
    mic_file = check_mic_path(mic_file)
    log_command(logging,
                "inputs",
                mic_file=mic_file,
                custom_inputs=custom_inputs)

    try:
        info_start_inputs()
        mic_config_file = Path(mic_file)
        mic_directory_path = mic_config_file.parent
        user_execution_directory = mic_config_file.parent.parent
        repro_zip_trace_dir = find_dir(REPRO_ZIP_TRACE_DIR,
                                       user_execution_directory)
        repro_zip_trace_dir = Path(repro_zip_trace_dir)
        repro_zip_config_file = repro_zip_trace_dir / REPRO_ZIP_CONFIG_FILE
        spec = get_spec(repro_zip_config_file)
        custom_inputs = [
            str(user_execution_directory /
                Path(i).relative_to(user_execution_directory))
            for i in list(custom_inputs)
        ]
        inputs_reprozip = get_inputs_outputs_reprozip(
            spec, user_execution_directory)
        logging.debug("Inputs found from reprozip: {}".format(inputs_reprozip))

        # obtain config: if a file is a config cannot be a input
        config_files = get_configs(mic_config_file)
        config_files_list = [
            str(user_execution_directory / item[PATH_KEY])
            for key, item in config_files.items()
        ] if config_files else []

        code_files = find_code_files(spec, inputs_reprozip, config_files_list,
                                     user_execution_directory)
        logging.debug("code files found from reprozip: {}".format(code_files))
        new_inputs = []
        inputs_reprozip += list(custom_inputs)
        data_dir = mic_directory_path.absolute() / DATA_DIR
        if data_dir.exists():
            shutil.rmtree(data_dir)
        data_dir.mkdir()
        _outputs = get_outputs_reprozip(spec, user_execution_directory)
        for _input in inputs_reprozip:
            item = user_execution_directory / _input
            name = Path(_input).name

            if str(item) in config_files_list or str(
                    item) in code_files or str(item) in _outputs:
                logging.info(f"Ignoring the config as an input: {item}")
            else:
                # Deleting the outputs of the inputs.
                if item.is_dir():
                    if sorted([str(i)
                               for i in item.iterdir()]) == sorted(_outputs):
                        logging.info(f"Skipping: {item}")
                    else:
                        logging.info(
                            f"""Compressing the input directory ({name})""")
                        zip_file = compress_directory(
                            item, user_execution_directory)
                        dst_dir = data_dir
                        dst_file = dst_dir / Path(zip_file).name
                        if dst_file.exists():
                            os.remove(dst_file)
                        shutil.move(str(zip_file), str(dst_dir))
                        new_inputs.append(zip_file)
                        click.secho(f"""Input {name} added """, fg="blue")
                        logging.info("Input added: {}".format(name))
                else:
                    new_inputs.append(item)
                    dst_file = mic_directory_path / DATA_DIR / str(item.name)
                    shutil.copy(item, dst_file)
                    click.secho(f"""Input {name} added """, fg="blue")
                    logging.info("Input added: {}".format(name))

        info_end_inputs(new_inputs)
        write_spec(mic_config_file, INPUTS_KEY,
                   relative(new_inputs, user_execution_directory))
        write_spec(mic_config_file, CODE_KEY,
                   relative(code_files, user_execution_directory))
        logging.info("inputs done")

    except Exception as e:
        logging.exception(f"Inputs failed: {e}")
        click.secho("Failed", fg="red")
        click.secho(e)
Example #17
0
def configs(mic_file, configuration_files, auto_param):
    """
    Note: If your model does not use configuration files, you can skip this step

    Specify which parameters of your model component you want to expose from any configuration file.

    - You must pass the MIC_FILE (mic.yaml) as an argument using the (-f) option or run the command from the same
    directory as mic.yaml

    - Pass your model configuration files as arguments

    mic pkg configs -f <mic_file> [configuration_files]...

    If you have manually changed some parameters, the -a option will attempt to recognize the configuration files
    automatically

    Example:

    mic pkg configs -f mic.yaml data/example_dir/file1.txt  data/file2.txt
    """

    # Searches for mic file if user does not provide one
    mic_file = check_mic_path(mic_file)

    log_command(logging,
                "configs",
                mic_file=mic_file,
                configuration_files=configuration_files,
                auto_param=auto_param)

    try:
        mic_config_file = Path(mic_file)
        user_execution_directory = mic_config_file.parent.parent

        if not mic_config_file.exists():
            click.secho("Error: that configuration path does not exist",
                        fg="red")
            logging.error("mic config file does not exist")
            exit(1)
        configuration_files = [
            str(Path(x).absolute()) for x in list(configuration_files)
        ]
        try:
            # Add config file names to yaml
            write_spec(mic_config_file, CONFIG_FILE_KEY,
                       relative(configuration_files, user_execution_directory))
        except Exception as e:
            click.secho("Failed. Error message: {}".format(e), fg="red")
            logging.exception("Failed writing configs: {}".format(e))
        for item in configuration_files:
            click.secho("Added: {} as a configuration file".format(item))
            logging.info("Added config file: {}".format(item))
            if auto_param:
                # Parse parameters from config file(s) and add them to mic.yaml
                add_params_from_config(mic_config_file, item)

        write_spec(mic_config_file, STEP_KEY, 2)
        logging.info("configs done")
    except Exception as e:
        logging.exception(f"Configs failed: {e}")
        click.secho("Failed", fg="red")
        click.secho(e)
Example #18
0
def add_parameters(mic_file, name, value, overwrite, description):
    """
    Add a parameter into the MIC file (mic.yaml).

    - You must pass the MIC file (mic.yaml) as an argument using the (-f) option; or run the command from the
    same directory as the MIC file (mic.yaml)

    Usage example:

    mic pkg parameters -f <mic_file> --name PARAMETER_NAME --value PARAMETER_VALUE
    """
    # Searches for mic file if user does not provide one
    mic_file = check_mic_path(mic_file)
    log_command(logging,
                "add_parameters",
                mic_file=mic_file,
                name=name,
                value=value,
                overwrite=overwrite,
                description=description)

    try:
        path = Path(mic_file)
        spec = get_spec(path)
        if (name or value or description or overwrite) and not (
            (name is not None) and (value is not None)):
            click.secho(
                "Must give name and value to manually add new parameter. Aborting",
                fg="yellow")
            logging.info("Invalid manual parameter given")
            exit(0)

        if PARAMETERS_KEY not in spec:
            spec[PARAMETERS_KEY] = {}

        # Automacically add parameters from trace command. Use heuristic "if item isnt file its a parameter"
        if name is None:
            click.echo("Automatically adding any parameters from trace")
            logging.info("Automatically adding any parameters from trace")
            mic_config_file = Path(mic_file)
            user_execution_directory = mic_config_file.parent.parent

            repro_zip_trace_dir = find_dir(REPRO_ZIP_TRACE_DIR,
                                           user_execution_directory)
            repro_zip_trace_dir = Path(repro_zip_trace_dir)
            repro_zip_config_file = repro_zip_trace_dir / REPRO_ZIP_CONFIG_FILE

            reprozip_spec = get_spec(repro_zip_config_file)

            spec = get_parameters_reprozip(spec, reprozip_spec)

        else:
            if not overwrite and name in spec[PARAMETERS_KEY]:
                click.echo(
                    "The parameter exists. Add the option --overwrite to overwrite it."
                )
                logging.info(
                    "Parameter already exists. aborting because overwrite flag is false"
                )
                exit(1)
            else:

                if description is None:
                    description = ""
                type_value____name__ = type(value).__name__
                click.echo(
                    f"Adding the parameter {name}, value {value} and type {type_value____name__}"
                )
                new_par = {
                    name: {
                        NAME_KEY: name,
                        DEFAULT_VALUE_KEY: value,
                        DATATYPE_KEY: type_value____name__,
                        DEFAULT_DESCRIPTION_KEY: description
                    }
                }
                logging.debug("Adding parameter: {}".format(new_par))
                spec[PARAMETERS_KEY].update(new_par)

        write_spec(path, PARAMETERS_KEY, spec[PARAMETERS_KEY])
        logging.info("add_parameters done")

    except Exception as e:
        logging.exception(f"Add Parameters failed: {e}")
        click.secho("Failed", fg="red")
        click.secho(e)