import os, json, requests from getpass import getpass from classes import Header def get_entry_from_elabid(elabid, entryType="items"): ''' Function which returns entrypoint data (as dictionary) from its elabid. ''' header = Header(apikey).dump response = requests.get( headers = header, url = f"{ELABFTW_API_URL}/{entryType}/{elabid}", verify=True ) if response.status_code // 100 in [2,3]: entry_data = response.json() return entry_data else: raise ConnectionError(f"HTTP request failed with status code: {response.status_code}.") class Layer: ''' Layer(layer_data) - where layer_data is a Python dictionary. eLabFTW experiments contain most of the data required by the NeXus file - although every layer is on a different eLab entry; unfortunately, some data like the target's chemical formula must be retrieved through additional HTTP requests. Attributes 'target_elabid', 'rheed_system_elabid' and 'laser_system_elabid' contain elabid's for these resources, which are all items. ''' def __init__(self, layer_data): try: self.extra = layer_data["metadata_decoded"]["extra_fields"] self.target_elabid = self.extra["Target"]["value"] # elabid self.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid self.laser_system_elabid = self.extra["Laser System"]["value"] # elabid self.start_time = layer_data.get("created_at") self.operator = layer_data.get("fullname") self.description = layer_data.get("body") self.deposition_time = self.extra["Duration"]["value"] self.repetition_rate = self.extra["Repetition rate"]["value"] try: self.number_of_pulses = float(self.deposition_time) * float(self.repetition_rate) except ValueError: # Since number_of_pulses is required, if it can't be calculated raise error: raise ValueError(""" Warning: either Duration or Repetition Rate are empty or invalid. If you think this is an error, please edit your eLabFTW entry and retry. Setting Number of Pulses to NoneType. """) # TO-DO: remove trailing space on eLabFTW's template for deposition layers self.temperature = self.extra["Heater temperature "]["value"] # TYPO: trailing space, must fix on elabftw self.process_pressure = self.extra["Process pressure "]["value"] # TYPO: trailing space, must fix on elabftw # self.heating_method = self.extra["Heating Method"]["value"] self.layer_thickness = self.extra["Thickness"]["value"] self.buffer_gas = self.extra["Buffer gas"]["value"] self.heater_target_distance = self.extra["Heater-target distance"]["value"] self.laser_fluence = self.extra["Laser Intensity"]["value"] # here fluence = intensity self.laser_spot_area = self.extra["Spot Area"]["value"] try: self.laser_energy = float(self.laser_fluence) * float(self.laser_spot_area) except ValueError: # Since laser_energy is NOT required, if it can't be calculated warn user but allow the software to continue execution: print(""" Warning: either Laser Intensity or Spot Area are empty or invalid. If you think this is an error, please edit your eLabFTW entry and retry. Setting Laser Energy to NoneType. """) # Placeholder self.laser_energy = None # Laser rasternig section self.laser_rastering_geometry = self.extra["Laser Rastering Geometry"]["value"] self.laser_rastering_positions = self.extra["Laser Rastering Position"]["value"] self.laser_rastering_velocities = self.extra["Laser Rastering Speed"]["value"] # Pre annealing section self.pre_annealing_ambient_gas = self.extra["Buffer gas Pre"]["value"] self.pre_annealing_pressure = self.extra["Process pressure Pre"]["value"] self.pre_annealing_temperature = self.extra["Heater temperature Pre"]["value"] self.pre_annealing_duration = self.extra["Duration Pre"]["value"] # Post annealing section self.post_annealing_ambient_gas = self.extra["Buffer gas PA"]["value"] self.post_annealing_pressure = self.extra["Process pressure PA"]["value"] self.post_annealing_temperature = self.extra["Heater temperature PA"]["value"] self.post_annealing_duration = self.extra["Duration PA"]["value"] # Rejected but suggested by the NeXus standard: #self.laser_rastering_coefficients = None except KeyError as k: # Some keys are not required and can be called through the .get() method - which is permissive and allows null values; # Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program: raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the deposition layer entry on eLabFTW and make sure you used the correct Experiment template.") class Entrypoint: ''' Entrypoint(sample_data) - where sample_data is a Python dictionary. The entrypoint is the starting point of the process of resolving the data chain. The entrypoint must be a dictionary containing the data of a sample, created directly from the JSON of the item endpoint on eLabFTW - which can be done through the function get_entry_from_elabid. ''' def __init__(self, sample_data): try: self.extra = sample_data["metadata_decoded"]["extra_fields"] self.linked_items = sample_data["items_links"] self.batch_elabid = self.extra["Substrate batch"]["value"] self.linked_experiments = sample_data["related_experiments_links"] self.linked_experiments_elabid = [ i["entityid"] for i in self.linked_experiments ] except KeyError as k: # Some keys are not required and can be called through the .get() method - which is permissive and allows null values; # Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program: raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the sample entry on eLabFTW and make sure you used the correct Resource template.") # Non-required attributes: self.name = sample_data.get("title") or None # error prevention is more important than preventing empty fields here class Material: ''' Material(material_data) - where material_data is a Python dictionary. Both a PLD Target and a Substrate are materials made of a certain compound, of which we want to know: * Name and formula; * Shape and dimensions; * Misc. ''' def __init__(self, material_data): try: self.extra = material_data["metadata_decoded"]["extra_fields"] self.compound_elabid = self.extra["Compound"]["value"] except KeyError as k: # Some keys are not required and can be called through the .get() method - which is permissive and allows null values; # Other keys are required so if they can't be called (invalid or null) raise error and stop execution of the program: raise KeyError(f"The provided dictionary lacks a \"{k}\" key. Check the target/substrate entry on eLabFTW and make sure you used the correct Resource template.") def get_compound(self): compound_data = get_entry_from_elabid(self.compound_elabid, entryType="items") formula = compound_data["metadata_decoded"]["extra_fields"].get("Chemical formula") formula_value = formula.get("value") return formula_value 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: ") # TEST. In production the entryType will probably just be "items" since the entrypoint is an item (sample). 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.") pass match eT: case "items" | "i" | "item": entryType = "items" case "experiments" | "e" | "exp" | "experiment": entryType = "experiments" case _: pass # This will probably be reworked in production try: elabid = elabid except NameError: elabid = input("Input elabid here [default = 1108]: ") or 1108 data = 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()) result = item.__dict__ result.pop("extra") print(result) # print(json.dumps(chain.sample_data)) # print(json.dumps(chain.linked_experiments)) # print(chain.batch_elabid)