NeuroMorpho: Can use neuron names as file names (#27)

morphapi/api/mouselight.py

@@ -17,9 +17,9 @@
 
 
 """
-    Collections of functions to query http://ml-neuronbrowser.janelia.org/ and get data about either the status of the API,
+    Collections of functions to query https://ml-neuronbrowser.janelia.org/ and get data about either the status of the API,
     the brain regions or the neurons available.
-    Queries are sent by sending POST requests to http://ml-neuronbrowser.janelia.org/graphql
+    Queries are sent by sending POST requests to https://ml-neuronbrowser.janelia.org/graphql
     with a string query.
 """
 

morphapi/api/neuromorphorg.py

@@ -129,16 +129,25 @@ def build_filepath(self, neuron_id):
         return os.path.join(self.neuromorphorg_cache, f"{neuron_id}.swc")
 
     def download_neurons(
-        self, neurons, _name=None, load_neurons=True, **kwargs
+        self,
+        neurons,
+        _name=None,
+        load_neurons=True,
+        use_neuron_names=False,
+        **kwargs,
     ):
         """
         Downloads neuronal morphological data and saves it to .swc files.
         It then returns a list of Neuron instances with morphological data for each neuron.
 
         :param neurons: list of neurons metadata (as returned by one of the functions
-                    used to fetch metadata)
+            used to fetch metadata)
         :param _name: used internally to save cached neurons with a different prefix when the
-                class is used to download neurons for other APIs
+            class is used to download neurons for other APIs
+        :param load_neurons: if set to True, the neurons are loaded into a
+            `morphapi.morphology.morphology.Neuron` object and returned
+        :param use_neuron_names: if set to True, the filenames use the names of the neurons instead
+            of their IDs
         """
         if not isinstance(neurons, (list, tuple)):
             neurons = [neurons]
@@ -154,7 +163,12 @@ class is used to download neurons for other APIs
             except KeyError:
                 pass
 
-            filepath = self.build_filepath(neuron["neuron_id"])
+            if use_neuron_names:
+                filepath = self.build_filepath(
+                    neuron.get("neuron_name", neuron["neuron_id"])
+                )
+            else:
+                filepath = self.build_filepath(neuron["neuron_id"])
             load_current_neuron = load_neurons
 
             if not os.path.isfile(filepath):

morphapi/paths_manager.py

@@ -31,7 +31,7 @@ def __init__(self, base_dir=None, **kwargs):
         if base_dir is None:
             self.base_dir = Path.home() / ".morphapi"
         else:
-            self.base_dir = base_dir
+            self.base_dir = Path(base_dir)
 
         self.base_dir.mkdir(exist_ok=True)
 

tests/test_download.py

@@ -1,10 +1,14 @@
+from pathlib import Path
+
 from morphapi.api.allenmorphology import AllenMorphology
 from morphapi.api.mouselight import MouseLightAPI
 from morphapi.api.neuromorphorg import NeuroMorpOrgAPI
 
 
-def test_neuromorpho_download():
-    api = NeuroMorpOrgAPI()
+def test_neuromorpho_download(tmpdir):
+    api = NeuroMorpOrgAPI(base_dir=tmpdir)
+    cache_path = Path(api.neuromorphorg_cache)
+
     metadata, _ = api.get_neurons_metadata(
         size=2,  # Can get the metadata for up to 500 neurons at the time
         species="mouse",
@@ -15,15 +19,34 @@ def test_neuromorpho_download():
     if len(metadata) != 2:
         raise ValueError("Incorrect metadata length")
 
+    assert len(list(cache_path.iterdir())) == 0
     neurons = api.download_neurons(metadata)
 
-    if len(neurons) != len(metadata):
-        raise ValueError
+    assert len(neurons) == len(metadata)
+    assert len(list(cache_path.iterdir())) == 2
 
     neurons = [neuron.create_mesh()[1] for neuron in neurons]
 
     # Test no load
     assert api.download_neurons(metadata, load_neurons=False)[0].points is None
+    assert len(list(cache_path.iterdir())) == 2
+
+    # Test using neuron names
+    assert (
+        api.download_neurons(
+            metadata, load_neurons=False, use_neuron_names=True
+        )[0].points
+        is None
+    )
+    assert len(list(cache_path.iterdir())) == 4
+
+    cache_files = list(cache_path.iterdir())
+    assert sorted([i.name for i in cache_files]) == [
+        "10075.swc",
+        "10076.swc",
+        "C1q-Cell7-40x.swc",
+        "Ctrl-Cell3-40x.swc",
+    ]
 
     # Test failure
     metadata[0]["neuron_id"] = "BAD ID"
@@ -34,8 +57,8 @@ def test_neuromorpho_download():
     assert neurons[0].points is None
 
 
-def test_mouselight_download():
-    mlapi = MouseLightAPI()
+def test_mouselight_download(tmpdir):
+    mlapi = MouseLightAPI(base_dir=tmpdir)
 
     neurons_metadata = mlapi.fetch_neurons_metadata(
         filterby="soma", filter_regions=["MOs"]
@@ -87,8 +110,8 @@ def test_mouselight_download():
     assert filtered_neurons_metadata == filtered_neurons_metadata_atlas
 
 
-def test_allen_morphology_download():
-    am = AllenMorphology()
+def test_allen_morphology_download(tmpdir):
+    am = AllenMorphology(base_dir=tmpdir)
 
     # Select some mouse neurons in the primary visual cortex
     neurons_df = am.neurons.loc[