Merge pull request #24 from Australian-Imaging-Service/invalid-hyphens

added hyphen to list of invalid id chars
Australian-Imaging-Service · Oct 23, 2024 · 58d261e · 58d261e
2 parents 8f4877d + 746998c
commit 58d261e
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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]')
Original file line number	Diff line number	Diff line change
Expand Up		@@ -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]')