Switch outdir to a keyward argument instead of positional

UW-GAC · Jan 24, 2024 · c593735 · c593735
1 parent b18d9e6
commit c593735
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Showing 2 changed files with 13 additions and 10 deletions.
diff --git a/primed/cdsa/management/commands/cdsa_records.py b/primed/cdsa/management/commands/cdsa_records.py
@@ -12,8 +12,9 @@ class Command(BaseCommand):
 
     def add_arguments(self, parser):
         parser.add_argument(
-            "outdir",
+            "--outdir",
             help="""Output directory where reports should be written. This directory will be created.""",
+            required=True,
         )
 
     def _export_table(self, table, filename):

diff --git a/primed/cdsa/tests/test_commands.py b/primed/cdsa/tests/test_commands.py
@@ -20,12 +20,12 @@ def setUp(self):
 
     def test_output(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         self.assertIn("generating reports... done!", out.getvalue())
 
     def test_files_created(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         self.assertTrue(isdir(self.outdir))
         self.assertTrue(isfile(os.path.join(self.outdir, "representative_records.tsv")))
         self.assertTrue(isfile(os.path.join(self.outdir, "study_records.tsv")))
@@ -34,7 +34,7 @@ def test_files_created(self):
 
     def test_representative_records_zero(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "representative_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 1)
@@ -44,14 +44,14 @@ def test_representative_records_three(self):
         factories.DataAffiliateAgreementFactory.create()
         factories.NonDataAffiliateAgreementFactory.create()
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "representative_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 4)
 
     def test_study_records_zero(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "study_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 1)
@@ -61,14 +61,14 @@ def test_study_records_one(self):
             signed_agreement__is_primary=True
         )
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "study_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 2)
 
     def test_cdsa_workspace_records_zero(self):
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "workspace_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 1)
@@ -77,7 +77,7 @@ def test_cdsa_workspace_records_one(self):
         agreement = factories.DataAffiliateAgreementFactory.create()
         factories.CDSAWorkspaceFactory.create(study=agreement.study)
         out = StringIO()
-        call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+        call_command("cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out)
         with open(os.path.join(self.outdir, "workspace_records.tsv")) as f:
             lines = f.readlines()
         self.assertEqual(len(lines), 2)
@@ -86,5 +86,7 @@ def test_directory_exists(self):
         os.mkdir(self.outdir)
         out = StringIO()
         with self.assertRaises(CommandError) as e:
-            call_command("cdsa_records", self.outdir, "--no-color", stdout=out)
+            call_command(
+                "cdsa_records", "--outdir", self.outdir, "--no-color", stdout=out
+            )
         self.assertIn("already exists", str(e.exception))