Refactor project structure

[kephale]

@zhuowenzhao this is my current refactor. I think it is pretty close to done, but I'm running some tests now.

[zhuowenzhao]

line 291 should be copick_config_path=COPICKLIVE_CONFIG_PATH,

[zhuowenzhao]

Found another bug: the counter_checkpoint_file_path is not passed correctly. Can we define another function that return this path, similar to returning local_dataset.

def get_local_dataset(config_path=None):
    global local_dataset

    if config_path or not local_dataset:
        config = configparser.ConfigParser()

        if config_path:
            config_path = os.path.abspath(config_path)
        else:
            config_path = os.path.join(os.getcwd(), "config.ini")

        if os.path.exists(config_path):
            config.read(config_path)
        else:
            raise FileNotFoundError(f"Config file not found at {config_path}")

        LOCAL_FILE_PATH = config.get("local_picks", "PICK_FILE_PATH", fallback=None)
        if LOCAL_FILE_PATH:
            LOCAL_FILE_PATH = os.path.join(LOCAL_FILE_PATH, "ExperimentRuns/")
        COPICK_TEMPLATE_PATH = config.get("copick_template", "COPICK_TEMPLATE_PATH", fallback=None)

        if not LOCAL_FILE_PATH or not COPICK_TEMPLATE_PATH:
            raise ValueError("Config paths for LocalDataset are not provided and not found in the config file.")

        local_dataset = LocalDataset(local_file_path=LOCAL_FILE_PATH, config_path=COPICK_TEMPLATE_PATH)

    return local_dataset


def get_counter_file_path(config_path=None):
    global COUNTER_FILE_PATH

    if config_path or not COUNTER_FILE_PATH:
        config = configparser.ConfigParser()

        if config_path:
            config_path = os.path.abspath(config_path)
        else:
            config_path = os.path.join(os.getcwd(), "config.ini")

        if os.path.exists(config_path):
            config.read(config_path)
        else:
            raise FileNotFoundError(f"Config file not found at {config_path}")
    
        COUNTER_FILE_PATH = config.get("counter_checkpoint", "COUNTER_FILE_PATH", fallback=None)

        if not COUNTER_FILE_PATH:
            raise ValueError("Config path for COUNTER_FILE_PATH is not provided and not found in the config file.")
    
    return COUNTER_FILE_PATH

[zhuowenzhao]

from copick_live.utils.local_dataset import (
    get_local_dataset,
    get_counter_file_path, 
    dirs, 
    dir2id,  
)

[zhuowenzhao]

Replace download_txt() callback function to

@callback(
    Output("download-txt", "data"),
    Input("btn-download-txt", "n_clicks"),
    #State("username", "value"),
    prevent_initial_call=True,
)
def download_txt(n_clicks):
    counter_checkpoint = get_counter_file_path()
    if counter_checkpoint:
        with open(counter_checkpoint) as f:
            counter = json.load(f)
        
        if counter['repeat'] == 2:
            counter['start'] += counter['tasks_per_person']
            counter['repeat'] = 0

        counter['repeat'] += 1
        task_contents = '\n'.join(dirs[counter['start']:counter['start']+counter['tasks_per_person']])
        print(task_contents)
        task_filename = 'task_recommendation.txt' 

        with open(counter_checkpoint, 'w') as f:
            f.write(json.dumps(counter, indent=4))   
        
        return dict(content=task_contents, filename=task_filename)

[kephale]

the comments have been addressed, but this isn't ready to merge due to the project explorer being a wip.

i made heavy modifications to how configs work, and i have also updated the code to use copick's api more explicitly (e.g. removing directory traversals in favor of using copick to traverse runs)