MAJOR: solves problem related to ELABFTW_API_URL variable

if no value was specified for such variable (or .env was missing) EAU would be set to None and get stuck in a prompt loop solved by turning EAU into a required variable in APIHandler (and editing a lot of code through all of src/)
2026-05-14 17:24:02 +02:00
parent 1ce381f341
commit 685d15d55b
3 changed files with 56 additions and 36 deletions
--- a/src/APIHandler.py
+++ b/src/APIHandler.py
@@ -23,11 +23,11 @@ class APIHandler:
    # TO-DO: remove static url.
    def __init__(self, api_key="", ELABFTW_API_URL=None):
        """Init method, api_key suggested but not required (empty by default)."""
-        if not ELABFTW_API_URL:
-            load_dotenv()
-            ELABFTW_API_URL = os.getenv("ELABFTW_API_URL") or input(
-                "Enter a valid eLabFTW API URL (ends with '/api/v2)': "
-            )
+        # if not ELABFTW_API_URL:
+        #    load_dotenv()
+        #    ELABFTW_API_URL = os.getenv("ELABFTW_API_URL") or input(
+        #        "Enter a valid eLabFTW API URL (ends with '/api/v2)': "
+        #    )
        self.api_key = api_key
        self.auth = {"Authorization": api_key}
        self.content = {"Content-Type": "application/json"}
--- a/src/classes.py
+++ b/src/classes.py
@@ -134,7 +134,7 @@ class Layer:
        self.start_time = layer_data.get("created_at") or None
        self.description = layer_data.get("body") or None

-    def get_instruments(self, api_key):
+    def get_instruments(self, api_key, ELABFTW_API_URL):
        """
        Retruns a dictionary of all the instruments used to create the layer.
        The format of the dictionary is:
@@ -144,18 +144,20 @@ class Layer:
                "rheed_system": str
            }

-        Arg: api_key: str:  A valid API key for the eLabFTW instance where the data is stored, with permissions to access the relevant entries.
-                            eLabFTW's API keys are well documented here: https://doc.elabftw.net/docs/usage/api/.
-                            If you don't have an API key and are uncapable of creating one, contact your eLabFTW administrator.
-                            Or RTFM and create one yourself, it's not that hard.
+        Args:
+            api_key: str:           A valid API key for the eLabFTW instance where the data is stored, with permissions to access the relevant entries.
+                                    eLabFTW's API keys are well documented here: https://doc.elabftw.net/docs/usage/api/.
+                                    If you don't have an API key and are uncapable of creating one, contact your eLabFTW administrator.
+                                    Or RTFM and create one yourself, it's not that hard.
+            ELABFTW_API_URL: str:   URL for the API root endpoint of the eLabFTW instance. Ends with '/api/v2' - no trailing slash.
        """
-        raw_lasersys_data = APIHandler(api_key).get_entry_from_elabid(
+        raw_lasersys_data = APIHandler(api_key, ELABFTW_API_URL).get_entry_from_elabid(
            self.laser_system_elabid, entryType="items"
        )
-        raw_chamber_data = APIHandler(api_key).get_entry_from_elabid(
+        raw_chamber_data = APIHandler(api_key, ELABFTW_API_URL).get_entry_from_elabid(
            self.chamber_elabid, entryType="items"
        )
-        raw_rheedsys_data = APIHandler(api_key).get_entry_from_elabid(
+        raw_rheedsys_data = APIHandler(api_key, ELABFTW_API_URL).get_entry_from_elabid(
            self.rheed_system_elabid, entryType="items"
        )
        instruments_used = {
@@ -248,6 +250,7 @@ class Entrypoint:
            * linked_experiments_elabid: list:  List of eLabFTW internal id's of the experiments linked to the entrypoint.
        """
        try:
+            self.name = sample_data["title"]
            self.extra = sample_data["metadata_decoded"]["extra_fields"]
            self.linked_items = sample_data["items_links"]  # dict
            self.batch_elabid = self.extra["Substrate batch"]["value"]  # elabid
@@ -262,11 +265,6 @@ class Entrypoint:
            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
-        # although I don't think it's even possible to fuck up this bad...


 class Material:
@@ -310,7 +308,7 @@ class Material:
                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_data(self, apikey):
+    def get_compound_data(self, apikey, ELABFTW_API_URL):
        """
        Returns a dictionary with the relevant data on the compound of which the material is made.
        The format of the dictionary is:
@@ -320,12 +318,14 @@ class Material:
                "cas_number": str
            }

-        Arg: api_key: str:  A valid API key for the eLabFTW instance where the data is stored, with permissions to access the relevant entries.
-                            eLabFTW's API keys are well documented here: https://doc.elabftw.net/docs/usage/api/.
-                            If you don't have an API key and are uncapable of creating one, contact your eLabFTW administrator.
-                            Or RTFM and create one yourself, it's not that hard.
+        Args:
+            api_key: str:           A valid API key for the eLabFTW instance where the data is stored, with permissions to access the relevant entries.
+                                    eLabFTW's API keys are well documented here: https://doc.elabftw.net/docs/usage/api/.
+                                    If you don't have an API key and are uncapable of creating one, contact your eLabFTW administrator.
+                                    Or RTFM and create one yourself, it's not that hard.
+            ELABFTW_API_URL: str:   URL for the API root endpoint of the eLabFTW instance. Ends with '/api/v2' - no trailing slash.
        """
-        raw_compound_data = APIHandler(apikey).get_entry_from_elabid(
+        raw_compound_data = APIHandler(apikey, ELABFTW_API_URL).get_entry_from_elabid(
            self.compound_elabid, entryType="items"
        )
        name = raw_compound_data["title"]
@@ -339,8 +339,20 @@ class Material:
        }
        return compound_data

-    def get_compound_formula(self, apikey):
-        formula = self.get_compound_data(apikey).get("chemical_formula")
+    def get_compound_formula(self, apikey, ELABFTW_API_URL):
+        """
+        Returns a string with the chemical formula of the compound.
+
+        Args:
+            api_key: str:           A valid API key for the eLabFTW instance where the data is stored, with permissions to access the relevant entries.
+                                    eLabFTW's API keys are well documented here: https://doc.elabftw.net/docs/usage/api/.
+                                    If you don't have an API key and are uncapable of creating one, contact your eLabFTW administrator.
+                                    Or RTFM and create one yourself, it's not that hard.
+            ELABFTW_API_URL: str:   URL for the API root endpoint of the eLabFTW instance. Ends with '/api/v2' - no trailing slash.
+        """
+        formula = self.get_compound_data(apikey, ELABFTW_API_URL).get(
+            "chemical_formula"
+        )
        return formula


@@ -454,7 +466,8 @@ if __name__ == "__main__":
    # print(f"Example header:\n\t{head.header}\n")
    # print("Warning: you're not supposed to be running this as the main program.")
    api_key = getpass("Paste API key here [no echo]: ")
-    handler = APIHandler(api_key=api_key)
+    ELABFTW_API_URL = input("Enter a valid eLabFTW API URL (ends with '/api/v2)': ")
+    handler = APIHandler(api_key, ELABFTW_API_URL)
    exp58 = handler.get_entry_from_elabid(elabid=58, entryType="experiments")
    layer58 = Layer(exp58)
    print(layer58.list_attachments())
--- a/src/main.py
+++ b/src/main.py
@@ -20,7 +20,7 @@ def call_entrypoint_from_elabid(elabid):
    Arg: elabid: int    eLabFTW internal id of the selected resource.
    """
    try:
-        sample_data = APIHandler(api_key).get_entry_from_elabid(
+        sample_data = APIHandler(api_key, ELABFTW_API_URL).get_entry_from_elabid(
            elabid, entryType="items"
        )
        if not sample_data.get("category_title") == "Sample":
@@ -44,7 +44,7 @@ def call_material_from_elabid(elabid):
    arg: elabid: int    eLabFTW internal id of the selected resource.
    """
    try:
-        material_data = APIHandler(api_key).get_entry_from_elabid(
+        material_data = APIHandler(api_key, ELABFTW_API_URL).get_entry_from_elabid(
            elabid, entryType="items"
        )
        material_category = material_data.get("category_title")
@@ -75,7 +75,7 @@ def call_layers_from_list(elabid_list):
    list_of_layers = []
    for elabid in elabid_list:
        try:
-            layer_data = APIHandler(api_key).get_entry_from_elabid(
+            layer_data = APIHandler(api_key, ELABFTW_API_URL).get_entry_from_elabid(
                elabid, entryType="experiments"
            )
            if not layer_data.get("category_title") == "PLD Deposition":
@@ -106,7 +106,7 @@ def call_proposal_from_elabid(elabid):
    Arg: elabid: int    eLabFTW internal id of the selected resource.
    """
    try:
-        proposal_data = APIHandler(api_key).get_entry_from_elabid(
+        proposal_data = APIHandler(api_key, ELABFTW_API_URL).get_entry_from_elabid(
            elabid, entryType="items"
        )
        proposal_category = proposal_data.get("category_title")
@@ -186,7 +186,7 @@ def deduplicate_instruments_from_layers(layers):
    rheeds = []
    elegant_dict = {}
    for lyr in layers:
-        instruments = lyr.get_instruments(api_key)
+        instruments = lyr.get_instruments(api_key, ELABFTW_API_URL)
        lasers.append(instruments["laser_system"])
        chambers.append(instruments["deposition_chamber"])
        rheeds.append(instruments["rheed_system"])
@@ -356,7 +356,9 @@ def make_nexus_schema_dictionary(substrate_object, layers):
        "sample": {
            "substrate": {
                "name": substrate_object.name,
-                "chemical_formula": substrate_object.get_compound_formula(api_key),
+                "chemical_formula": substrate_object.get_compound_formula(
+                    api_key, ELABFTW_API_URL
+                ),
                "orientation": substrate_object.orientation,
                "miscut_angle": {
                    "value": substrate_object.miscut_angle,
@@ -384,7 +386,9 @@ def make_nexus_schema_dictionary(substrate_object, layers):
        target_object = chain_layer_to_target(layer)
        target_dict = {
            "name": target_object.name,
-            "chemical_formula": target_object.get_compound_formula(api_key),
+            "chemical_formula": target_object.get_compound_formula(
+                api_key, ELABFTW_API_URL
+            ),
            "description": target_object.description,
            "shape": target_object.shape,
            "dimensions": target_object.dimensions,
@@ -772,7 +776,7 @@ def build_nexus_file(pld_fabrication, output_path="output/nffa-di_unnamed.h5"):
            n = layer_dict["layer_number"]
            rheed_data_file = layer_dict["data"][0]  # first in the tuple
            rheed_image_file = layer_dict["data"][1]  # second in the tuple
-            handler = APIHandler(api_key)
+            handler = APIHandler(api_key, ELABFTW_API_URL)

            # TO-DO: maybe make a dedicated function???
            data_path = None
@@ -877,7 +881,10 @@ if __name__ == "__main__":
        or input("Enter elabid of your starting sample [default = 1111]: ")
        or 1111
    )
-    handler = APIHandler(api_key)
+    ELABFTW_API_URL = os.getenv("ELABFTW_API_URL") or input(
+        "Enter a valid eLabFTW API URL (ends with '/api/v2)': "
+    )
+    handler = APIHandler(api_key, ELABFTW_API_URL)
    data = handler.get_entry_from_elabid(elabid)
    sample = Entrypoint(data)
    sample_name = sample.name.strip().replace(