From 746998c552dfa75dc0796f0ed0496da02bacbf96 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Wed, 23 Oct 2024 17:31:58 +1100
Subject: [PATCH] added hyphen to list of invalid id chars

---
 xnat_ingest/cli/stage.py      |  6 +++---
 xnat_ingest/tests/test_cli.py | 11 +++++++----
 xnat_ingest/utils.py          |  2 +-
 3 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/xnat_ingest/cli/stage.py b/xnat_ingest/cli/stage.py
index 08ee319..c54b6e1 100644
--- a/xnat_ingest/cli/stage.py
+++ b/xnat_ingest/cli/stage.py
@@ -36,8 +36,8 @@
 are uploaded to XNAT
 """,
 )
-@click.argument("files_path", type=str, envvar="XINGEST_DICOMS_PATH")
-@click.argument("output_dir", type=click.Path(path_type=Path), envvar="XINGEST_DIR")
+@click.argument("files_path", type=str)
+@click.argument("output_dir", type=click.Path(path_type=Path))
 @click.option(
     "--datatype",
     type=str,
@@ -193,7 +193,7 @@
     default=None,
     metavar="<host> <user> <password>",
     help="The XNAT server to upload to plus the user and password to use",
-    envvar="XNAT_INGEST_TRANSFER_XNAT_LOGIN",
+    envvar="XINGEST_XNAT_LOGIN",
 )
 @click.option(
     "--spaces-to-underscores/--no-spaces-to-underscores",
diff --git a/xnat_ingest/tests/test_cli.py b/xnat_ingest/tests/test_cli.py
index 5d3cdc5..5c781d5 100644
--- a/xnat_ingest/tests/test_cli.py
+++ b/xnat_ingest/tests/test_cli.py
@@ -200,10 +200,10 @@ def test_stage_and_upload(
             str(associated_files_dir)
             + "/{PatientName.family_name}_{PatientName.given_name}*.ptd",
             r".*/[^\.]+.[^\.]+.[^\.]+.(?P<id>\d+)\.[A-Z]+_(?P<resource>[^\.]+).*",
-            "--logger",
-            "file",
-            "info",
-            str(log_file),
+            # "--logger",
+            # "file",
+            # "info",
+            # str(log_file),
             "--additional-logger",
             "xnat",
             "--raise-errors",
@@ -213,6 +213,9 @@ def test_stage_and_upload(
             "admin",
             "admin",
         ],
+        env={
+            "XINGEST_LOGGERS": "file,info,/tmp/logging.log;stream,debug,stdout",
+        },
     )
 
     assert result.exit_code == 0, show_cli_trace(result)
diff --git a/xnat_ingest/utils.py b/xnat_ingest/utils.py
index 1b33e6e..b634b11 100644
--- a/xnat_ingest/utils.py
+++ b/xnat_ingest/utils.py
@@ -371,4 +371,4 @@ def glob_to_re(glob_pattern: str) -> str:
 
 _str_templ_replacement = re.compile(r"\{[\w\.]+\}")
 
-invalid_path_chars_re = re.compile(r'[<>:"/\\|?*\x00-\x1F]')
+invalid_path_chars_re = re.compile(r'[\-<>:"/\\|?*\x00-\x1F]')