integrates sub-classes Target and Substrate in main.py

"Substrate" is the title of the category of substrate items
"Substrate batch" is a key in a sample's dictionary

src/classes.py

@@ -108,8 +108,10 @@ 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 +132,32 @@ 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.")
+
 
 
 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 +58,111 @@ 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
+
+#sample_object = call_entrypoint_from_elabid(elabid)
+#from_entrypoint_to_material(sample_object)
     
 
 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).
+    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]: ")
+    batch = chain_entrypoint_to_batch(sample) # Material-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...
+    bd = batch.__dict__
-        if eT[0] in ["e", "i"] and eT[-1].isnumeric():
+    bd.pop("extra")
-            try:
+    layers = chain_entrypoint_to_layers(sample) # list of Layer-class objects
-                elabid = int(eT[1:])
+    print(f"Sample name:\n{sample.name}\n")
-                eT = eT[0]
+    print(f"Substrate data:\n{bd}\n")
-            except Exception:
+    print(f"Layers data:")
-                print("Usage: i|item|items|i[ELABID] for items, e|experiment|experiments|e[ELABID] for experiments.")
+    for layer in layers:
-                continue
+        ld = layer.__dict__
-        match eT:
+        ld.pop("extra")
-            case "items" | "i" | "item":
+        tgt = chain_layer_to_target(layer)
-                entryType = "items"
+        td = tgt.__dict__
-            case "experiments" | "e" | "exp" | "experiment":
+        td.pop("extra")
-                entryType = "experiments"
+        print(ld)
-            case _:
+        print(td)
-                continue
+        print()
-    # This will probably be reworked in production
+
-    try:
+    # entryType = None
-        elabid = elabid
+    # while entryType not in ["items", "experiments"]:
-    except NameError:
+    #     eT = input("Enter a valid entry type [items, experiments]: ")
-        elabid = input("Input elabid here [default = 1111]: ") or 1111
+    #     # 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...
-    data = APIHandler(apikey).get_entry_from_elabid(elabid, entryType)
+    #     if eT[0] in ["e", "i"] and eT[-1].isnumeric():
-    if entryType == "experiments":
+    #         try:
-        layer = Layer(data)
+    #             elabid = int(eT[1:])
-        result = layer.__dict__
+    #             eT = eT[0]
-        result.pop("extra")
+    #         except Exception:
-        print(result)
+    #             print("Usage: i|item|items|i[ELABID] for items, e|experiment|experiments|e[ELABID] for experiments.")
-    elif entryType == "items":
+    #             continue
-        if data.get("category_title") == "Sample":
+    #     match eT:
-            item = Entrypoint(data)
+    #         case "items" | "i" | "item":
-        elif data.get("category_title") in ["PLD Target", "Substrate"]:
+    #             entryType = "items"
-            item = Material(data)
+    #         case "experiments" | "e" | "exp" | "experiment":
-            print(item.get_compound_formula(apikey))
+    #             entryType = "experiments"
-        else:
+    #         case _:
-            raise Exception("The selected item or experiment is not in one of the following categories: [Sample, PLD Target, Substrate, PLD Deposition].")
+    #             continue
-        result = item.__dict__
+    # # This will probably be reworked in production
-        result.pop("extra")
+    # try:
-        print(result)
+    #     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,
+	"lockedby": null,
+	"metadata": "{\"elabftw\": {\"extra_fields_groups\": [{\"id\": 1, \"name\": \"Process\"}, {\"id\": 2, \"name\": \"Laser\"}, {\"id\": 3, \"name\": \"Pre Annealing\"}, {\"id\": 4, \"name\": \"Post Annealing\"}, {\"id\": 5, \"name\": \"Instruments\"}]}, \"extra_fields\": {\"Sample\": {\"type\": \"items\", \"value\": 1111, \"group_id\": 1, \"position\": 0, \"required\": true}, \"Target\": {\"type\": \"items\", \"value\": 1075, \"group_id\": 1, \"position\": 2, \"required\": true}, \"Chamber\": {\"type\": \"items\", \"value\": 1096, \"group_id\": 5, \"position\": 0, \"required\": true}, \"Duration\": {\"type\": \"number\", \"unit\": \"s\", \"units\": [\"s\", \"min\"], \"value\": \"45\", \"group_id\": 1, \"position\": 3, \"required\": true}, \"Spot Area\": {\"type\": \"number\", \"unit\": \"mm^2\", \"units\": [\"mm^2\"], \"value\": \"0.8\", \"group_id\": 2, \"position\": 2}, \"Thickness\": {\"type\": \"number\", \"unit\": \"u.c.\", \"units\": [\"u.c.\", \"nm\"], \"value\": \"3\", \"group_id\": 1, \"position\": 4}, \"Buffer gas\": {\"type\": \"select\", \"value\": \"O2\", \"options\": [\"O2\", \"N2\", \"Ar\", \"\"], \"group_id\": 1, \"position\": 5}, \"Duration PA\": {\"type\": \"number\", \"unit\": \"s\", \"units\": [\"s\", \"min\"], \"value\": \"\", \"group_id\": 4, \"position\": 0}, \"Duration Pre\": {\"type\": \"number\", \"unit\": \"s\", \"units\": [\"s\", \"min\"], \"value\": \"\", \"group_id\": 3, \"position\": 0}, \"Laser System\": {\"type\": \"items\", \"value\": 1099, \"group_id\": 5, \"position\": 1}, \"RHEED System\": {\"type\": \"items\", \"value\": 1098, \"group_id\": 5, \"position\": 2}, \"Buffer gas PA\": {\"type\": \"select\", \"value\": \"O2\", \"options\": [\"O2\", \"N2\", \"Ar\", \"\"], \"group_id\": 4, \"position\": 1}, \"Buffer gas Pre\": {\"type\": \"select\", \"value\": \"O2\", \"options\": [\"O2\", \"N2\", \"Ar\", \"\"], \"group_id\": 3, \"position\": 1}, \"Heating Method\": {\"type\": \"select\", \"value\": \"Radiative Heater\", \"options\": [\"Radiative Heater\", \"Laser Heater\"], \"group_id\": 1, \"position\": 9}, \"Laser Intensity\": {\"type\": \"number\", \"unit\": \"J/(s cm^2)\", \"units\": [\"J/(s cm^2)\"], \"value\": \"1.5\", \"group_id\": 2, \"position\": 0}, \"Repetition rate\": {\"type\": \"number\", \"unit\": \"Hz\", \"units\": [\"Hz\"], \"value\": \"1\", \"group_id\": 2, \"position\": 1}, \"Process pressure\": {\"type\": \"number\", \"unit\": \"mbar\", \"units\": [\"mbar\"], \"value\": \"1e-3\", \"group_id\": 1, \"position\": 6}, \"Heater temperature\": {\"type\": \"number\", \"unit\": \"\u00b0C\", \"units\": [\"\u00b0C\"], \"value\": \"650\", \"group_id\": 1, \"position\": 7}, \"Process pressure PA\": {\"type\": \"number\", \"unit\": \"mbar\", \"units\": [\"mbar\"], \"value\": \"\", \"group_id\": 4, \"position\": 2}, \"Process pressure Pre\": {\"type\": \"number\", \"unit\": \"mbar\", \"units\": [\"mbar\"], \"value\": \"\", \"group_id\": 3, \"position\": 2}, \"Heater temperature PA\": {\"type\": \"number\", \"unit\": \"\u00b0C\", \"units\": [\"\u00b0C\"], \"value\": \"\", \"group_id\": 4, \"position\": 3}, \"Laser Rastering Speed\": {\"type\": \"number\", \"unit\": \"\", \"units\": [], \"value\": \"\", \"group_id\": 2, \"position\": 4}, \"Heater temperature Pre\": {\"type\": \"number\", \"unit\": \"\u00b0C\", \"units\": [\"\u00b0C\"], \"value\": \"\", \"group_id\": 3, \"position\": 3}, \"Heater-target distance\": {\"type\": \"number\", \"unit\": \"mm\", \"units\": [\"mm\"], \"value\": \"45\", \"group_id\": 1, \"position\": 8}, \"Laser Rastering Geometry\": {\"type\": \"select\", \"value\": \"none\", \"options\": [\"none\", \"on a square\", \"on a rectangle\", \"on a line\", \"other\"], \"group_id\": 2, \"position\": 3}, \"Laser Rastering Position\": {\"type\": \"number\", \"unit\": \"\", \"units\": [], \"value\": \"\", \"group_id\": 2, \"position\": 5}, \"Layer Progressive Number\": {\"type\": \"number\", \"unit\": \"\", \"units\": [], \"value\": \"2\", \"group_id\": 1, \"position\": 1, \"required\": true}}}",
+	"metadata_decoded": {
+		"elabftw": {
+			"extra_fields_groups": [
+				{
+					"id": 1,
+					"name": "Process"
+				},
+				{
+					"id": 2,
+					"name": "Laser"
+				},
+				{
+					"id": 3,
+					"name": "Pre Annealing"
+				},
+				{
+					"id": 4,
+					"name": "Post Annealing"
+				},
+				{
+					"id": 5,
+					"name": "Instruments"
+				}
+			]
+		},
+		"extra_fields": {
+			"Sample": {
+				"type": "items",
+				"value": 1111,
+				"group_id": 1,
+				"position": 0,
+				"required": true
+			},
+			"Target": {
+				"type": "items",
+				"value": 1075,
+				"group_id": 1,
+				"position": 2,
+				"required": true
+			},
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+	"timestamped_at": null,
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+	"title": "Na-26-015 eto on lao on sto",
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+}