removes debug line, writes json to file instead (path: output/)

only lacks units of measurement, then I'll be ready for conversion

.gitignore

@@ -1,6 +1,9 @@
-# ignora log di h5tojson e jsontoh5
+# ignores logs of h5tojson, jsontoh5
 *.log
 
+# ignores output json of main.py
+output/*.json
+
 # ---> Python
 # Byte-compiled / optimized / DLL files
 __pycache__/

src/APIHandler.py

@@ -33,6 +33,8 @@ class APIHandler:
                     raise ConnectionError(f"Invalid API key or authentication method.")
                 case 404:
                     raise ConnectionError(f"404: Not Found. This means there's no resource with this elabid (wrong elabid?) on your eLabFTW (wrong endpoint?).")
+                case 400:
+                    raise ConnectionError(f"400: Bad Request. This means the API endpoint you tried to reach is invalid. Did you tamper with the source code? If not, contact the developer.")
                 case _:
                     raise ConnectionError(f"HTTP request failed with status code: {response.status_code} (NOTE: 4xx means user's fault).")
         else:

src/classes.py

@@ -16,8 +16,9 @@ class Layer:
             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.rheed_system_elabid = self.extra["RHEED System"]["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.start_time = layer_data.get("created_at")
             self.operator = layer_data.get("fullname")
             self.description = layer_data.get("body")
@@ -71,6 +72,16 @@ class Layer:
             # 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.")
+    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")
+        instruments_used = {
+            "laser_system": raw_lasersys_data.get("title") or None,
+            "deposition_chamber": raw_chamber_data.get("title") or None,
+            "rheed_system": raw_rheedsys_data.get("title") or None,
+        }
+        return instruments_used
 
 class Entrypoint:
     '''
@@ -108,8 +119,10 @@ class Material:
     '''
     def __init__(self, material_data):
         try:
+            self.name = material_data["title"] # required
             self.extra = material_data["metadata_decoded"]["extra_fields"]
             self.compound_elabid = self.extra["Compound"]["value"]
+            self.dimensions = self.extra["Size"]["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:
@@ -130,6 +143,34 @@ class Material:
         formula = self.get_compound_data(apikey).get("chemical_formula")
         return formula
 
+class Substrate(Material):
+    def __init__(self, material_data):
+        super().__init__(material_data)
+        try:
+            self.orientation = self.extra["Orientation"]["value"]
+            self.miscut_angle = self.extra["Miscut Angle"]["value"]
+            self.miscut_direction = self.extra["Miscut Direction"]["value"]
+            # Not present (yet) on eLabFTW for Substrates:
+            self.thickness = None #self.extra["Thickness"]["value"]
+            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.")
+
+class Target(Material):
+    def __init__(self, material_data):
+        super().__init__(material_data)
+        try:
+            self.thickness = self.extra["Thickness"]["value"]
+            self.shape = self.extra["shape"]["value"]
+            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.")
+        # Non-required attributes:
+        self.description = material_data.get("body") or ""
+
 
 
 if __name__=="__main__":

src/main.py

@@ -5,6 +5,11 @@ 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":
@@ -15,17 +20,33 @@ def call_entrypoint_from_elabid(elabid):
     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 matching exactly "PLD Target" or "Substrate".
+    Because of an old typo, the value "Subtrate" (second 's' is missing) is also accepted.
+    '''
     try: 
         material_data = APIHandler(apikey).get_entry_from_elabid(elabid, entryType="items")
+        material_category = material_data.get("category_title")
         # TO-DO: correct this typo on elabftw: Subtrate → Substrate.
-        if not sample_data.get("category_title") in ["PLD Target", "Substrate batch", "Subtrate batch"]:
+        if not material_category in ["PLD Target", "Substrate", "Subtrate"]:
+            print(f"Category of the resource: {material_category}.")
             raise ValueError(f"The referenced resource (elabid = {elabid}) is not a material.")
-        material_object = Material(material_data)
+        elif material_category == "PLD Target":
+            material_object = Target(material_data)
+        else:
+            material_object = Substrate(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:
@@ -37,64 +58,158 @@ def call_layers_from_list(elabid_list):
         except ConnectionError as e:
             nums = [ layer.layer_number for layer in list_of_layers ]
             nums.sort()
-            print(f"LISTA DEI LAYER PROCESSATI FINORA (in ordine sparso):\n" + str(nums))
+            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 from_entrypoint_to_material(sample_object):
+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 sample_object, material_object
+    return material_object
 
-sample_object = call_entrypoint_from_elabid(elabid)
+def chain_entrypoint_to_layers(sample_object):
-from_entrypoint_to_material(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
+
+def chain_layer_to_target(layer_object):
+    '''
+    Takes a Layer-class object, looks at its .target_elabid attribute and returns a Material-class object containing data on the PLD target used in the deposition of said layer.
+
+    Dependency: call_material_from_elabid.
+    '''
+    target_elabid = layer_object.target_elabid
+    material_object = call_material_from_elabid(target_elabid)
+    return material_object
+
+def deduplicate_instruments_from_layers(layers):
+    '''
+    Takes a list of Layer-class objects and for each layer gets the instruments used (laser, depo chamber and RHEED), returns deduplicated list. Ideally, the lists should only contain one element.
+    '''
+    lasers = []
+    chambers = []
+    rheeds = []
+    for lyr in layers:
+        instruments = lyr.get_instruments(apikey)
+        lasers.append(instruments["laser_system"])
+        chambers.append(instruments["deposition_chamber"])
+        rheeds.append(instruments["rheed_system"])
+    instruments_used_dict = {
+        "laser_system": list( set( lasers ) ),
+        "deposition_chamber": list( set( chambers ) ),
+        "rheed_system" : list( set( rheeds ) ),
+    }
+    # lasers = { f"layer_{lyr.layer_number}": lyr.laser_system for lyr in layers }
+    # chambers = { f"layer_{lyr.layer_number}": lyr.deposition_chamber for lyr in layers }
+    # rheeds = { f"layer_{lyr.layer_number}": lyr.rheed_system for lyr in layers }
+    # instruments_used_dict = {
+    #     "laser_system": lasers,
+    #     "deposition_chamber": chambers,
+    #     "rheed_system": rheeds,
+    # }
+    return instruments_used_dict
+
+def make_nexus_schema_dictionary(substrate_object, layers):
+    '''
+    Main function, takes all the other functions to reconstruct the full dataset. Takes a Substrate-class object (output of the chain_entrypoint_to_batch() function) and a list of Layer-class objects (output of the chain_entrypoint_to_layers() function), returns dictionary with the same schema as the NeXus standard for PLD fabrications.
+    '''
+    pld_fabrication = {
+        "sample": {
+            "substrate": {
+                "name": substrate_object.name,
+                "chemical_formula" : substrate_object.get_compound_formula(apikey),
+                "orientation" : substrate_object.orientation,
+                "miscut_angle" : substrate_object.miscut_angle,
+                "miscut_direction" : substrate_object.miscut_direction,
+                "thickness" : substrate_object.thickness,
+                "dimensions" : substrate_object.dimensions,
+                "surface_treatment" : substrate_object.surface_treatment,
+                "manufacturer" : substrate_object.manufacturer,
+                "batch_id" : substrate_object.batch_id,
+            },
+            "multilayer": {},
+        },
+        "instruments_used": deduplicate_instruments_from_layers(layers),
+    }
+    multilayer = pld_fabrication["sample"]["multilayer"]
+    for layer in layers:
+        name = "layer_" + layer.layer_number
+        target_object = chain_layer_to_target(layer)
+        target_dict = {
+            "name": target_object.name,
+            "chemical_formula" : target_object.get_compound_formula(apikey),
+            "description" : target_object.description,
+            "shape" : target_object.shape,
+            "dimensions" : target_object.dimensions,
+            "thickness" : target_object.thickness,
+            "solid_form" : target_object.solid_form,
+            "manufacturer" : target_object.manufacturer,
+            # TO-DO: currently not available:
+            # "batch_id" : target_object.batch_id,
+        }
+        multilayer[name] = {
+            "target": target_dict,
+            "start_time": layer.start_time,
+            "operator": layer.operator,
+            "description": layer.description,
+            "number_of_pulses": layer.number_of_pulses,
+            "deposition_time": layer.deposition_time,
+            "temperature": layer.temperature,
+            "heating_method": layer.heating_method,
+            "layer_thickness": layer.layer_thickness,
+            "buffer_gas": layer.buffer_gas,
+            "process_pressure": layer.process_pressure,
+            "heater_target_distance": layer.heater_target_distance,
+            "repetition_rate": layer.repetition_rate,
+            "laser_fluence": layer.laser_fluence,
+            "laser_spot_area": layer.laser_spot_area,
+            "laser_energy": layer.laser_energy,
+            "laser_rastering": {
+                "geometry": layer.laser_rastering_geometry,
+                "positions": layer.laser_rastering_positions,
+                "velocities": layer.laser_rastering_velocities,
+            },
+            "pre_annealing": {
+                "ambient_gas": layer.pre_annealing_ambient_gas,
+                "pressure": layer.pre_annealing_pressure,
+                "temperature": layer.pre_annealing_temperature,
+                "duration": layer.pre_annealing_duration,
+            },
+            "post_annealing": {
+                "ambient_gas": layer.post_annealing_ambient_gas,
+                "pressure": layer.post_annealing_pressure,
+                "temperature": layer.post_annealing_temperature,
+                "duration": layer.post_annealing_duration,
+            },
+        }
+    return pld_fabrication
 
 if __name__=="__main__":
-    print(f"=======================\n===== DEBUG MODE! =====\n=======================\n")
+    # TO-DO: place the API base URL somewhere else. 
     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).
+    elabid = input("Enter elabid of your starting sample [default= 1111]: ") or 1111
-    entryType = None
+    data = APIHandler(apikey).get_entry_from_elabid(elabid)
-    while entryType not in ["items", "experiments"]:
+    sample = Entrypoint(data)
-        eT = input("Enter a valid entry type [items, experiments]: ")
+    substrate_object = chain_entrypoint_to_batch(sample) # Substrate-class object
-        # 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...
+    layers = chain_entrypoint_to_layers(sample) # list of Layer-class objects
-        if eT[0] in ["e", "i"] and eT[-1].isnumeric():
+    result = make_nexus_schema_dictionary(substrate_object, layers)
-            try:
+    # print(make_nexus_schema_dictionary(substrate_object, layers)) # debug
-                elabid = int(eT[1:])
+    with open (f"output/sample-{elabid}.json", "w") as f:
-                eT = eT[0]
+        json.dump(result, f, indent=3)
-            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)

tests/chained_requests.py

@@ -42,6 +42,7 @@ class Layer:
     def __init__(self, layer_data):
         try:
             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.rheed_system_elabid = self.extra["RHEED System"]["value"] # elabid
             self.laser_system_elabid = self.extra["Laser System"]["value"] # elabid
@@ -174,14 +175,14 @@ if __name__=="__main__":
                 eT = eT[0]
             except Exception:
                 print("Usage: i|item|items|i[ELABID] for items, e|experiment|experiments|e[ELABID] for experiments.")
-                pass
+                continue
         match eT:
             case "items" | "i" | "item":
                 entryType = "items"
             case "experiments" | "e" | "exp" | "experiment":
                 entryType = "experiments"
             case _:
-                pass
+                continue
     # This will probably be reworked in production
     try:
         elabid = elabid
@@ -198,10 +199,9 @@ if __name__=="__main__":
             item = Entrypoint(data)
         elif data.get("category_title") in ["PLD Target", "Substrate"]:
             item = Material(data)
-            print(item.get_compound_formula())
+            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)
-    # print(json.dumps(chain.sample_data))
-    # print(json.dumps(chain.linked_experiments))
-    # print(chain.batch_elabid)

tests/layer_A.json

@@ -0,0 +1,480 @@
+{
+	"access_key": null,
+	"body": "",
+	"body_html": "",
+	"canread": "{\"base\": 40, \"teams\": [], \"users\": [], \"teamgroups\": []}",
+	"canread_is_immutable": 0,
+	"canwrite": "{\"base\": 20, \"teams\": [], \"users\": [], \"teamgroups\": []}",
+	"canwrite_is_immutable": 0,
+	"category": 2,
+	"category_color": "8b8d43",
+	"category_title": "PLD Deposition",
+	"comments": [],
+	"compounds": [],
+	"containers": [],
+	"content_type": 1,
+	"created_at": "2026-02-09 09:53:50",
+	"custom_id": null,
+	"date": "2026-02-09",
+	"elabid": "20260209-8ba774f27896bbec37a7cc5eab18747dbac3a4fb",
+	"events_start": null,
+	"events_start_itemid": null,
+	"exclusive_edit_mode": null,
+	"experiments_links": [
+		{
+			"entityid": 59,
+			"title": "Na-26-015 lao on stocazzo",
+			"custom_id": null,
+			"elabid": "20260209-554888c7b8a17efd963fece04426f6ec5722fa8a",
+			"link_state": 1,
+			"page": "experiments.php",
+			"type": "experiments",
+			"category_title": "PLD Deposition",
+			"category_color": "8b8d43",
+			"status_title": null,
+			"status_color": null
+		}
+	],
+	"firstname": "Emiliano",
+	"fullname": "Emiliano Di Gennaro",
+	"id": 58,
+	"is_pinned": 0,
+	"items_links": [
+		{
+			"entityid": 1075,
+			"title": "ETO single crystal",
+			"custom_id": null,
+			"elabid": "20260126-6f77512fa5a3c5803fcfc64797ffa003429094dc",
+			"link_state": 1,
+			"is_bookable": 0,
+			"page": "database.php",
+			"type": "items",
+			"category_title": "PLD Target",
+			"category_color": "1a5fb4",
+			"status_title": null,
+			"status_color": null
+		},
+		{
+			"entityid": 1074,
+			"title": "LAO single crystal",
+			"custom_id": null,
+			"elabid": "20260126-2cef9e71c0ff4aa15062cb6562f64f6ac3a366fb",
+			"link_state": 1,
+			"is_bookable": 0,
+			"page": "database.php",
+			"type": "items",
+			"category_title": "PLD Target",
+			"category_color": "1a5fb4",
+			"status_title": null,
+			"status_color": null
+		},
+		{
+			"entityid": 1099,
+			"title": "Coherent Excimer Laser (KrF 248 nm)",
+			"custom_id": null,
+			"elabid": "20260126-9175c1674aef9947736fbc12447f912c8ea9bc81",
+			"link_state": 1,
+			"is_bookable": 0,
+			"page": "database.php",
+			"type": "items",
+			"category_title": "Process Instrument",
+			"category_color": "a51d2d",
+			"status_title": "Available",
+			"status_color": "6a7753"
+		},
+		{
+			"entityid": 1096,
+			"title": "PLD  Chamber I (small area)",
+			"custom_id": null,
+			"elabid": "20260126-19cf5d06fd119f841383f21db1c29eebfad550c5",
+			"link_state": 1,
+			"is_bookable": 1,
+			"page": "database.php",
+			"type": "items",
+			"category_title": "Process Instrument",
+			"category_color": "a51d2d",
+			"status_title": "Available",
+			"status_color": "6a7753"
+		},
+		{
+			"entityid": 1098,
+			"title": "STAIB RHEED 30",
+			"custom_id": null,
+			"elabid": "20260126-5df7738907b198451c19296ab07e5093d12a3ead",
+			"link_state": 1,
+			"is_bookable": 0,
+			"page": "database.php",
+			"type": "items",
+			"category_title": "Process Instrument",
+			"category_color": "a51d2d",
+			"status_title": "Available",
+			"status_color": "6a7753"
+		},
+		{
+			"entityid": 1111,
+			"title": "Na-26-015",
+			"custom_id": null,
+			"elabid": "20260209-6e19f19795b7ea79594a35d9a11da1896b13453e",
+			"link_state": 1,
+			"is_bookable": 0,
+			"page": "database.php",
+			"type": "items",
+			"category_title": "Sample",
+			"category_color": "ffbe6f",
+			"status_title": null,
+			"status_color": null
+		}
+	],
+	"lastchangeby": 2,
+	"lastname": "Di Gennaro",
+	"locked": 0,
+	"locked_at": null,
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