first attempt to refactor the test code into something more elegant

src/classes.py

@@ -1,14 +1,137 @@
-class Header:
+import os, json, requests
+from APIHandler import APIHandler
+
+class Layer:
     '''
-    Class to standardize the format of the headers of our http requests.
+    Layer(layer_data) - where layer_data is a Python dictionary.
+
+    Meant to be used for eLabFTW Experiments of the "PLD Deposition" category.
+
+    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, apikey=""):
-        '''Init method, apikey suggested but not required (empty by default).'''
-        self.auth = {"Authorization" : apikey}
-        self.content = {"Content-Type" : "application/json"}
-        self.dump = {**self.auth, **self.content}
+    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)).__floor__()
+            except ValueError:
+                # Since number_of_pulses is required, if it can't be calculated raise error:
+                raise ValueError("""
+    Fatal: either Duration or Repetition Rate are empty or invalid.
+    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.process_pressure = self.extra["Process pressure"]["value"] # Note: this field used to have a trailing space in its name
+            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)).__round__(3)
+            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.
+
+    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"]
+            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.
+
+    Meant to be used for eLabFTW Resources of either the "PLD Target" or the "Substrate" categories.
+
+    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_data(self, apikey):
+        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 }
+        compound_data = {
+            "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
+
+
 
 if __name__=="__main__":
     head = Header("MyApiKey-123456789abcdef")
-    print(f"Example header: {head.dump()}")
+    print(f"Example header:\n\t{head.dump}\n")
     print("Warning: you're not supposed to be running this as the main program.")