eXParser-PLD/src/main.py

import os, json, requests
from getpass import getpass
from APIHandler import APIHandler
from classes import *


def call_entrypoint_from_elabid(elabid):
    '''
    Calls an entrypoint sample from eLabFTW using its elabid, then returns an object of the Entrypoint class.

    If the entry is not a sample (category_title not matching exactly "Sample") returns ValueError.
    '''
    try: 
        sample_data = APIHandler(apikey).get_entry_from_elabid(elabid, entryType="items")
        if not sample_data.get("category_title") == "Sample":
            raise ValueError("The resource you selected is not a sample, therefore it can't be used as an entrypoint.")
        sample_object = Entrypoint(sample_data)
    except ConnectionError as e:
        raise ConnectionError(e)
    return sample_object # Entrypoint-class object

def call_material_from_elabid(elabid):
    '''
    Calls a material from eLabFTW using its elabid, then returns an object of the Material class.

    If the entry is neither a PLD Target or a Substrate batch returns ValueError. Such entries always have a category_title key with its value either being "PLD Target" or "Substrate batch".
    Because of an old typo, the value "Subtrate batch" (second 's' is missing) is also accepted.
    '''
    try: 
        material_data = APIHandler(apikey).get_entry_from_elabid(elabid, entryType="items")
        # TO-DO: correct this typo on elabftw: Subtrate → Substrate.
        if not sample_data.get("category_title") in ["PLD Target", "Substrate batch", "Subtrate batch"]:
            raise ValueError(f"The referenced resource (elabid = {elabid}) is not a material.")
        material_object = Material(material_data)
    except ConnectionError as e:
        raise ConnectionError(e)
    return material_object # Material-class object

def call_layers_from_list(elabid_list):
    '''
    Calls a list of (PLD deposition) experiments from eLabFTW using their elabid - which means the input must be a list of integers instead of a single one - then returns a list of Layer-class objects.

    If one of the entries is not related to a deposition layer (category_title not matching exactly "PLD Deposition") that entry is skipped, with no error raised.
    '''
    list_of_layers = []
    for elabid in elabid_list:
        try:
            layer_data = APIHandler(apikey).get_entry_from_elabid(elabid, entryType="experiments")
            if not layer_data.get("category_title") == "PLD Deposition":
                continue
            layer_object = Layer(layer_data)
            list_of_layers.append(layer_object)        
        except ConnectionError as e:
            nums = [ layer.layer_number for layer in list_of_layers ]
            nums.sort()
            print(f"LIST OF THE LAYERS PROCESSED (unordered):\n" + str(nums))
            raise ConnectionError(f"An error occurred while fetching the experiment with elabid = {elabid}:\n" +
                str(e) + f"\nPlease solve the problem before retrying." + "\n\n" +
                f"Last resource attempted to call: {ELABFTW_API_URL}/experiments/{elabid}"
            )
    return list_of_layers # list of Layer-class objects

def chain_entrypoint_to_batch(sample_object):
    '''
    Takes an Entrypoint-class object, looks at its .batch_elabid attribute and returns a Material-class object containing data on the substrate batch associated to the starting sample.

    Dependency: call_material_from_elabid.
    '''
    material_elabid = sample_object.batch_elabid
    material_object = call_material_from_elabid(material_elabid)
    return material_object

def chain_entrypoint_to_layers(sample_object):
    '''
    Takes an Entrypoint-class object, looks at its .linked_experiments_elabid attribute (list) and returns a list of Layer-class objects containing data on the deposition layers associated to the starting sample - using the function call_layers_from_list.

    The list is sorted by progressive layer number (layer_number attribute).

    Dependency: call_layers_from_list.
    '''
    linked_experiments_elabid = sample_object.linked_experiments_elabid # list of elabid
    layer_object_list = call_layers_from_list(linked_experiments_elabid)
    layer_object_list.sort(key=lambda x: x.layer_number)
    return layer_object_list



#sample_object = call_entrypoint_from_elabid(elabid)
#from_entrypoint_to_material(sample_object)
    

if __name__=="__main__":
    print(f"=======================\n===== DEBUG MODE! =====\n=======================\n")
    ELABFTW_API_URL = "https://elabftw.fisica.unina.it/api/v2"
    apikey = getpass("Paste API key here: ")
    elabid = input("Enter elabid of your starting sample [default= 1111]: ") or 1111
    data = APIHandler(apikey).get_entry_from_elabid(elabid)
    sample = Entrypoint(data)
    layers = chain_entrypoint_to_layers(sample)
    print(f"Sample name:\n{sample.name}\n")
    print(f"Layers data:")
    for layer in layers:
        ld = layer.__dict__
        ld.pop("extra")
        print(ld)

    # entryType = None
    # while entryType not in ["items", "experiments"]:
    #     eT = input("Enter a valid entry type [items, experiments]: ")
    #     # This allows for a shortcut: instead of prompting the type before and the elabid after I can just prompt both at the same time - e.g. e51 is exp. 51, i1108 is item 1108...
    #     if eT[0] in ["e", "i"] and eT[-1].isnumeric():
    #         try:
    #             elabid = int(eT[1:])
    #             eT = eT[0]
    #         except Exception:
    #             print("Usage: i|item|items|i[ELABID] for items, e|experiment|experiments|e[ELABID] for experiments.")
    #             continue
    #     match eT:
    #         case "items" | "i" | "item":
    #             entryType = "items"
    #         case "experiments" | "e" | "exp" | "experiment":
    #             entryType = "experiments"
    #         case _:
    #             continue
    # # This will probably be reworked in production
    # try:
    #     elabid = elabid
    # except NameError:
    #     elabid = input("Input elabid here [default = 1111]: ") or 1111
    # data = APIHandler(apikey).get_entry_from_elabid(elabid, entryType)
    # if entryType == "experiments":
    #     layer = Layer(data)
    #     result = layer.__dict__
    #     result.pop("extra")
    #     print(result)
    # elif entryType == "items":
    #     if data.get("category_title") == "Sample":
    #         item = Entrypoint(data)
    #     elif data.get("category_title") in ["PLD Target", "Substrate"]:
    #         item = Material(data)
    #         print(item.get_compound_formula(apikey))
    #     else:
    #         raise Exception("The selected item or experiment is not in one of the following categories: [Sample, PLD Target, Substrate, PLD Deposition].")
    #     result = item.__dict__
    #     result.pop("extra")
    #     print(result)