From 008bcff82675b3ce22caaac8da289c025a9ee832d12ee0fcf857626d0b7f6ba5 Mon Sep 17 00:00:00 2001 From: PioApocalypse Date: Fri, 8 May 2026 18:09:03 +0200 Subject: [PATCH] LazyVim tab fix + new unused Layer-class methods to fetch uploads --- src/classes.py | 183 +++++++++++++++++++++++++++++++++++-------------- 1 file changed, 130 insertions(+), 53 deletions(-) diff --git a/src/classes.py b/src/classes.py index 28a93d5..3706936 100644 --- a/src/classes.py +++ b/src/classes.py @@ -1,8 +1,9 @@ import os, json, requests from APIHandler import APIHandler + class Layer: - ''' + """ Layer(layer_data) - where layer_data is a Python dictionary. Meant to be used for eLabFTW Experiments of the "PLD Deposition" category. @@ -10,22 +11,27 @@ class Layer: 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.operator = layer_data["fullname"] self.extra = layer_data["metadata_decoded"]["extra_fields"] - self.layer_number = self.extra["Layer Progressive Number"]["value"] # integer - self.target_elabid = self.extra["Target"]["value"] # elabid - self.laser_system_elabid = self.extra["Laser System"]["value"] # elabid - self.chamber_elabid = self.extra["Chamber"]["value"] # elabid - self.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid + self.layer_number = self.extra["Layer Progressive Number"][ + "value" + ] # integer + self.target_elabid = self.extra["Target"]["value"] # elabid + self.laser_system_elabid = self.extra["Laser System"]["value"] # elabid + self.chamber_elabid = self.extra["Chamber"]["value"] # elabid + self.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid self.deposition_time = self.extra["Duration"]["value"] self.deposition_time_unit = self.extra["Duration"]["unit"] self.repetition_rate = self.extra["Repetition rate"]["value"] self.repetition_rate_unit = self.extra["Repetition rate"]["unit"] try: - self.number_of_pulses = (float(self.deposition_time) * float(self.repetition_rate)).__floor__() + self.number_of_pulses = ( + float(self.deposition_time) * float(self.repetition_rate) + ).__floor__() except ValueError: # Since number_of_pulses is required, if it can't be calculated raise error: raise ValueError(""" @@ -33,22 +39,32 @@ class Layer: This has to be an error, since these fields are required by the NeXus standard. Please edit your eLabFTW entry and retry. """) - self.temperature = self.extra["Heater temperature"]["value"] # Note: this field used to have a trailing space in its name + self.temperature = self.extra["Heater temperature"][ + "value" + ] # Note: this field used to have a trailing space in its name self.temperature_unit = self.extra["Heater temperature"]["unit"] - self.process_pressure = self.extra["Process pressure"]["value"] # Note: this field used to have a trailing space in its name + self.process_pressure = self.extra["Process pressure"][ + "value" + ] # Note: this field used to have a trailing space in its name self.process_pressure_unit = self.extra["Process pressure"]["unit"] self.heating_method = self.extra["Heating Method"]["value"] self.layer_thickness = self.extra["Thickness"]["value"] self.layer_thickness_unit = self.extra["Thickness"]["unit"] self.buffer_gas = self.extra["Buffer gas"]["value"] self.heater_target_distance = self.extra["Heater-target distance"]["value"] - self.heater_target_distance_unit = self.extra["Heater-target distance"]["unit"] - self.laser_fluence = self.extra["Laser Intensity"]["value"] # here fluence = intensity + self.heater_target_distance_unit = self.extra["Heater-target distance"][ + "unit" + ] + self.laser_fluence = self.extra["Laser Intensity"][ + "value" + ] # here fluence = intensity self.laser_fluence_unit = "J/(s cm^2)" self.laser_spot_area = self.extra["Spot Area"]["value"] self.laser_spot_area_unit = "mm^2" try: - self.laser_energy = ( float(self.laser_fluence) * float(self.laser_spot_area) / 100 ).__round__(3) + self.laser_energy = ( + float(self.laser_fluence) * float(self.laser_spot_area) / 100 + ).__round__(3) self.laser_energy_unit = "J/s" except ValueError: # Since laser_energy is NOT required, if it can't be calculated warn user but allow the software to continue execution: @@ -61,39 +77,66 @@ class Layer: self.laser_energy = "N/A" self.laser_energy_unit = "J/s" # 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"] + 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_temperature = self.extra["Heater temperature Pre"][ + "value" + ] self.pre_annealing_duration = self.extra["Duration Pre"]["value"] - self.pre_annealing_pressure_unit = self.extra["Process pressure Pre"]["unit"] - self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"]["unit"] + self.pre_annealing_pressure_unit = self.extra["Process pressure Pre"][ + "unit" + ] + self.pre_annealing_temperature_unit = self.extra["Heater temperature Pre"][ + "unit" + ] self.pre_annealing_duration_unit = self.extra["Duration Pre"]["unit"] # 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_temperature = self.extra["Heater temperature PA"][ + "value" + ] self.post_annealing_duration = self.extra["Duration PA"]["value"] - self.post_annealing_pressure_unit = self.extra["Process pressure PA"]["unit"] - self.post_annealing_temperature_unit = self.extra["Heater temperature PA"]["unit"] + self.post_annealing_pressure_unit = self.extra["Process pressure PA"][ + "unit" + ] + self.post_annealing_temperature_unit = self.extra["Heater temperature PA"][ + "unit" + ] self.post_annealing_duration_unit = self.extra["Duration PA"]["unit"] # Rejected but suggested by the NeXus standard: - #self.laser_rastering_coefficients = None + # 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.") + 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.' + ) # Optional self.start_time = layer_data.get("created_at") or None self.description = layer_data.get("body") or None + def get_instruments(self, apikey): - raw_lasersys_data = APIHandler(apikey).get_entry_from_elabid(self.laser_system_elabid, entryType="items") - raw_chamber_data = APIHandler(apikey).get_entry_from_elabid(self.chamber_elabid, entryType="items") - raw_rheedsys_data = APIHandler(apikey).get_entry_from_elabid(self.rheed_system_elabid, entryType="items") + raw_lasersys_data = APIHandler(apikey).get_entry_from_elabid( + self.laser_system_elabid, entryType="items" + ) + raw_chamber_data = APIHandler(apikey).get_entry_from_elabid( + self.chamber_elabid, entryType="items" + ) + raw_rheedsys_data = APIHandler(apikey).get_entry_from_elabid( + self.rheed_system_elabid, entryType="items" + ) instruments_used = { "laser_system": raw_lasersys_data.get("title") or None, "deposition_chamber": raw_chamber_data.get("title") or None, @@ -101,31 +144,50 @@ class Layer: } return instruments_used + # Three possible approaches for the next two methods: either return the raw data as retrieved from eLabFTW, + # or process it and return only the relevant information, or even simply return the list of filenames. + # + def fetch_textual_uploads(self, api_key): + """ """ + return + + def fetch_rheed_images(self, api_key): + return + + class Entrypoint: - ''' + """ Entrypoint(sample_data) - where sample_data is a Python dictionary. Meant to be used for eLabFTW Resources of the "Sample" category. 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"] # dict - self.batch_elabid = self.extra["Substrate batch"]["value"] # elabid - self.linked_experiments = sample_data["related_experiments_links"] # dict - self.linked_experiments_elabid = [ i["entityid"] for i in self.linked_experiments ] # list of elabid + self.linked_items = sample_data["items_links"] # dict + self.batch_elabid = self.extra["Substrate batch"]["value"] # elabid + self.linked_experiments = sample_data["related_experiments_links"] # dict + self.linked_experiments_elabid = [ + i["entityid"] for i in self.linked_experiments + ] # list of elabid 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.") + 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 + 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. Meant to be used for eLabFTW Resources of either the "PLD Target" or the "Substrate" categories. @@ -134,13 +196,16 @@ class Material: * Name and formula; * Shape and dimensions; * Misc. - ''' + """ + def __init__(self, material_data): try: - self.name = material_data["title"] # required + self.name = material_data["title"] # required self.extra = material_data["metadata_decoded"]["extra_fields"] self.compound_elabid = self.extra["Compound"]["value"] - self.dimensions = str(self.extra["Size"]["value"]) # strings have a .count() method + self.dimensions = str( + self.extra["Size"]["value"] + ) # strings have a .count() method if self.dimensions.count("mm") == 2: self.dimensions_unit = "mm x mm" elif self.dimensions[-1] == '"': @@ -150,23 +215,30 @@ class Material: 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.") + 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_data(self, apikey): - raw_compound_data = APIHandler(apikey).get_entry_from_elabid(self.compound_elabid, entryType="items") + raw_compound_data = APIHandler(apikey).get_entry_from_elabid( + self.compound_elabid, entryType="items" + ) name = raw_compound_data["title"] extra = raw_compound_data["metadata_decoded"]["extra_fields"] formula = extra.get("Chemical formula") - cas = extra.get("CAS number ") or { "value": None } + cas = extra.get("CAS number ") or {"value": None} compound_data = { - "name" : name, - "chemical_formula" : formula.get("value"), - "cas_number" : cas.get("value") + "name": name, + "chemical_formula": formula.get("value"), + "cas_number": cas.get("value"), } return compound_data + def get_compound_formula(self, apikey): formula = self.get_compound_data(apikey).get("chemical_formula") return formula + class Substrate(Material): def __init__(self, material_data): super().__init__(material_data) @@ -176,13 +248,16 @@ class Substrate(Material): self.miscut_angle_unit = self.extra["Miscut Angle"]["unit"] self.miscut_direction = self.extra["Miscut Direction"]["value"] # Not present (yet) on eLabFTW for Substrates: - self.thickness = "" #self.extra["Thickness"]["value"] - self.thickness_unit = "μm" #self.extra["Thickness"]["unit"] + self.thickness = "" # self.extra["Thickness"]["value"] + self.thickness_unit = "μm" # self.extra["Thickness"]["unit"] self.surface_treatment = self.extra["Surface treatment"]["value"] self.manufacturer = self.extra["Supplier"]["value"] self.batch_id = self.extra["Batch ID"]["value"] except KeyError as k: - raise KeyError(f"The provided dictionary lacks a \"{k}\" key - which is specific for substrates. Check the {self.name} substrate entry on eLabFTW and make sure you used the correct Resource template.") + raise KeyError( + f'The provided dictionary lacks a "{k}" key - which is specific for substrates. Check the {self.name} substrate entry on eLabFTW and make sure you used the correct Resource template.' + ) + class Target(Material): def __init__(self, material_data): @@ -194,13 +269,15 @@ class Target(Material): self.solid_form = self.extra["Solid form"]["value"] self.manufacturer = self.extra["Supplier"]["value"] except KeyError as k: - raise KeyError(f"The provided dictionary lacks a \"{k}\" key - which is specific for PLD targets. Check the {self.name} target entry on eLabFTW and make sure you used the correct Resource template.") + raise KeyError( + f'The provided dictionary lacks a "{k}" key - which is specific for PLD targets. Check the {self.name} target entry on eLabFTW and make sure you used the correct Resource template.' + ) # Non-required attributes: self.description = material_data.get("body") or "" - -if __name__=="__main__": - head = Header("MyApiKey-123456789abcdef") +if __name__ == "__main__": + head = APIHandler("MyApiKey-123456789abcdef") print(f"Example header:\n\t{head.header}\n") - print("Warning: you're not supposed to be running this as the main program.") \ No newline at end of file + print("Warning: you're not supposed to be running this as the main program.") +