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:
     '''
@@ -157,6 +168,8 @@ 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 +98,118 @@ 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 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: ")
     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)
+    result = make_nexus_schema_dictionary(substrate_object, layers)
+    # print(make_nexus_schema_dictionary(substrate_object, layers)) # debug
+    with open (f"output/sample-{elabid}.json", "w") as f:
+        json.dump(result, f, indent=3)