Merge pull request #1382 from Princeton-LSI-ResearchComputing/study_d…

…ir_empty_fix

Study dir empty fix

DataRepo/loaders/msruns_loader.py

@@ -2337,6 +2337,8 @@ def get_mzxml_files(cls, files=None, dir=None):
             return files
         if dir is None:
             return []
+        if dir == "":
+            dir = os.getcwd()
         return [
             os.path.join(p, fl)
             for p, _, fs in os.walk(dir)

DataRepo/loaders/study_loader.py

@@ -328,9 +328,11 @@ def __init__(self, *args, **kwargs):
 
         # Before the superclass constructor is called, we want to use the file path to get its enclosing directory as a
         # default for the (custom derived class argument:) mzxml_dir
-        study_file = kwargs.get("file")
-        study_dir = None if study_file is None else os.path.dirname(study_file)
-        mzxml_dir = kwargs.pop("mzxml_dir", study_dir)
+        mzxml_dir = kwargs.pop("mzxml_dir", None)
+        if mzxml_dir is None:
+            study_file = kwargs.get("file")
+            study_dir = None if study_file is None else os.path.dirname(study_file)
+            mzxml_dir = study_dir
 
         self.mzxml_files = MSRunsLoader.get_mzxml_files(dir=mzxml_dir)
         self.exclude_sheets = kwargs.pop("exclude_sheets", []) or []

DataRepo/management/commands/export_studies.py

@@ -1,3 +1,5 @@
+import os
+
 from django.core.management import BaseCommand
 
 from DataRepo.utils.studies_exporter import StudiesExporter
@@ -11,7 +13,7 @@ def add_arguments(self, parser):
         parser.add_argument(
             "--outdir",
             required=True,
-            default=".",
+            default=os.getcwd(),
             help="Directory to create and save exported files.",
         )
         parser.add_argument(