Updates the way the neuronDB files are found.

Change-Id: I89d245a70f56b12e9d6c32c26c72297c082cfea6

src/synthesis_workflow/circuit.py

@@ -134,6 +134,8 @@ def slice_per_mtype(cells, mtypes):
 
 def slice_n_cells(cells, n_cells, random_state=0):
     """Selects n_cells random cells per mtypes."""
+    if n_cells <= 0:
+        return cells
     sampled_cells = pd.DataFrame()
     for mtype in cells.mtype.unique():
         samples = cells[cells.mtype == mtype].sample(

src/synthesis_workflow/tasks/synthesis.py

@@ -36,6 +36,7 @@
 from synthesis_workflow.tasks.luigi_tools import WorkflowTask
 from synthesis_workflow.tasks.utils import GetSynthesisInputs
 from synthesis_workflow.tools import ensure_dir
+from synthesis_workflow.tools import find_case_insensitive_file
 from synthesis_workflow.tools import load_neurondb_to_dataframe
 
 
@@ -79,11 +80,13 @@ def requires(self):
     def run(self):
         """"""
 
-        L.debug("Build morphology dataframe from %s", self.neurondb_path)
+        neurondb_path = find_case_insensitive_file(self.neurondb_path)
+
+        L.debug("Build morphology dataframe from %s", neurondb_path)
 
         mtype_taxonomy_path = self.input().ppath / self.mtype_taxonomy_path
         morphs_df = load_neurondb_to_dataframe(
-            self.neurondb_path,
+            neurondb_path,
             self.morphology_dirs,
             mtype_taxonomy_path,
             self.apical_points_path,
@@ -323,19 +326,17 @@ class BuildAxonMorphologies(WorkflowTask):
     nb_jobs = luigi.IntParameter(default=20, description="Number of workers.")
     """int: Number of workers."""
 
-    def get_neuron_db_path(self, db_name):
+    def get_neuron_db_path(self, ext):
         """Helper function to fix neuronDB vs neurondb in file names."""
-        return (
-            Path(self.axon_cells_path) / Path(self.neurondb_basename).parent / db_name
-        ).with_suffix(".xml")
+        return (Path(self.axon_cells_path) / self.neurondb_basename).with_suffix(
+            "." + ext
+        )
 
     def requires(self):
         """"""
         tasks = {"circuit": SliceCircuit()}
 
-        neurondb_path = self.get_neuron_db_path("neurondb")
-        if not neurondb_path.exists():
-            neurondb_path = self.get_neuron_db_path("neuronDB")
+        neurondb_path = self.get_neuron_db_path("xml")
 
         tasks["axon_cells"] = BuildAxonMorphsDF(
             neurondb_path=neurondb_path,
@@ -353,9 +354,7 @@ def run(self):
             axon_cells = self.input()["axon_cells"].path
         else:
             axon_cells = None
-            neurondb_path = (
-                Path(self.axon_cells_path) / self.neurondb_basename
-            ).with_suffix(".dat")
+            neurondb_path = find_case_insensitive_file(self.get_neuron_db_path("dat"))
 
         if any(
             [

src/synthesis_workflow/tools.py

@@ -1,4 +1,5 @@
 """utils functions."""
+import glob
 import json
 import logging
 import sys
@@ -20,6 +21,8 @@
 from voxcell import VoxelData
 from voxcell.nexus.voxelbrain import LocalAtlas
 
+L = logging.getLogger(__name__)
+
 
 def add_mtype_taxonomy(morphs_df, mtype_taxonomy):
     """From a dict with mtype to morph_class, fill in the morphs_df dataframe.
@@ -120,6 +123,45 @@ def ensure_dir(file_path):
     Path(file_path).parent.mkdir(parents=True, exist_ok=True)
 
 
+def find_case_insensitive_file(path):
+    """Helper function to find a file ignoring case."""
+
+    def either(c):
+        return "[%s%s]" % (c.lower(), c.upper()) if c.isalpha() else c
+
+    # Return the exact path if it exists
+    exact_path = Path(path)
+    if exact_path.exists():
+        return exact_path
+
+    directory = exact_path.parent
+
+    # Try to find the file ignoring the case
+    pattern = "".join(map(either, exact_path.name))
+    complete_path = (directory / pattern).as_posix()
+
+    all_possible_files = glob.glob(complete_path)
+
+    if len(all_possible_files) == 1:
+        found_file = all_possible_files[0]
+        L.warning(
+            "The file '%s' was not found, using '%s' instead.", exact_path, found_file
+        )
+        return found_file
+    else:
+        if len(all_possible_files) == 0:
+            error_msg = (
+                f"The file '{exact_path.as_posix()}' could not be found even "
+                "ignoring case."
+            )
+        else:
+            error_msg = (
+                f"The file '{exact_path}' could not be found but several files were found "
+                f"ignoring case: {all_possible_files}"
+            )
+        raise ValueError(error_msg)
+
+
 def update_morphs_df(morphs_df_path, new_morphs_df):
     """Updates a morphs_df with new entries to preserve duplicates."""
     return pd.read_csv(morphs_df_path).merge(new_morphs_df, how="left")

src/version.py

@@ -1,2 +1,2 @@
 """Package version."""
-VERSION = "0.0.7"
+VERSION = "0.0.8.dev0"