huge improvements, read below

* function get_entry_from_elabid moved to the top to be used by classes
* class Layers renamed Layer
* class Layer expanded and completed with all NeXus-needed metadata
* classes improved with "quality" error management
* class Material added, for now it fetches just compound_elabid and
  compund chemical formula (as attribute and method respectively)
* class Material has get_compound() method which needs some commenting
* DEBUG MODE improved to cover all cases: layer, sample, substr. and pld
  target; creates a new shortcut for prompting (read line 147)
* removed herobrine (fuck i'm old aren't i)

src/chained_requests.py

@@ -2,45 +2,6 @@ import os, json, requests
 from getpass import getpass
 from classes import Header
 
-class Layers:
-    '''
-    Layers(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"]
-            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"]
-            self.number_of_pulses = float(self.deposition_time) * float(self.repetition_rate)
-            # TO-DO: remove trailing space on eLabFTW's template for deposition layers
-            self.temperature = self.extra["Heater temperature "]["value"]
-            self.heating_method = self.extra["Heating Method"]["value"]
-        except KeyError as k:
-            raise KeyError(f"The provided dictionary lacks a \"{k}\" key.")
-
-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:
-            raise KeyError(f"The provided dictionary lacks a \"{k}\" key.")
-
-
 def get_entry_from_elabid(elabid, entryType="items"):
     '''
     Function which returns entrypoint data (as dictionary) from its elabid.
@@ -57,13 +18,140 @@ def get_entry_from_elabid(elabid, entryType="items"):
     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
+            # </todo>
+            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("===== DEBUG MODE! =====")
+    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"
@@ -71,16 +159,24 @@ if __name__=="__main__":
                 entryType = "experiments"
             case _:
                 pass
-    elabid = input("Input elabid here [default = 1108]: ") or 1108
+    # 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 = Layers(data)
+        layer = Layer(data)
         result = layer.__dict__
         result.pop("extra")
         print(result)
     elif entryType == "items":
-        sample = Entrypoint(data)
+        if data.get("category_title") == "Sample":
-        result = sample.__dict__
+            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))