code cleanup: deletes debug lines from main.py

takes API key and elabid of the "entrypoint" sample as input
returns indented JSON with the reconstructed dataset!
currently lacks instruments_used data (matter of minutes)
and all the layer data (already present in Layer-class objects)

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

@@ -157,6 +157,8 @@ class Target(Material):
             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 ""
 
 
 

src/main.py

@@ -98,71 +98,52 @@ def chain_layer_to_target(layer_object):
     material_object = call_material_from_elabid(target_elabid)
     return material_object
 
-#sample_object = call_entrypoint_from_elabid(elabid)
-#from_entrypoint_to_material(sample_object)
-    
+def make_nexus_schema_dictionary(substrate_object, layers):
+    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": {},
+        },
+    }
+    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
+        }
+    return json.dumps(pld_fabrication, indent=2)
 
 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: ")
     elabid = input("Enter elabid of your starting sample [default= 1111]: ") or 1111
     data = APIHandler(apikey).get_entry_from_elabid(elabid)
     sample = Entrypoint(data)
-    batch = chain_entrypoint_to_batch(sample) # Material-class object
-    bd = batch.__dict__
-    bd.pop("extra")
+    substrate_object = chain_entrypoint_to_batch(sample) # Substrate-class object
     layers = chain_entrypoint_to_layers(sample) # list of Layer-class objects
-    print(f"Sample name:\n{sample.name}\n")
-    print(f"Substrate data:\n{bd}\n")
-    print(f"Layers data:")
-    for layer in layers:
-        ld = layer.__dict__
-        ld.pop("extra")
-        tgt = chain_layer_to_target(layer)
-        td = tgt.__dict__
-        td.pop("extra")
-        print(ld)
-        print(td)
-        print()
-
-    # 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.")
-    #             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)
+    print(make_nexus_schema_dictionary(substrate_object, layers)) # debug