consolidated utils into single module

Australian-Imaging-Service · Nov 16, 2023 · ea2bc67 · ea2bc67
1 parent 937bbca
commit ea2bc67
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Showing 5 changed files with 189 additions and 184 deletions.
diff --git a/xnat_ingest/cli/stage.py b/xnat_ingest/cli/stage.py
@@ -4,8 +4,14 @@
 from tqdm import tqdm
 from .base import cli
 from ..session import ImagingSession
-from ..utils import logger
-from .utils import DicomField, LogFile, LogEmail, MailServer, set_logger_handling
+from ..utils import (
+    DicomField,
+    logger,
+    LogFile,
+    LogEmail,
+    MailServer,
+    set_logger_handling,
+)
 
 
 @cli.command(
@@ -84,6 +90,7 @@
     "--log-file",
     default=None,
     type=LogFile,
+    metavar="<path> <loglevel>",
     envvar="XNAT_INGEST_LOGFILE",
     help=(
         'Location to write the output logs to, defaults to "upload-logs" in the '

diff --git a/xnat_ingest/cli/upload.py b/xnat_ingest/cli/upload.py
@@ -10,8 +10,9 @@
 from arcana.xnat import Xnat
 from .base import cli
 from ..session import ImagingSession
-from ..utils import logger, add_exc_note
-from .utils import (
+from ..utils import (
+    logger,
+    add_exc_note,
     LogFile,
     LogEmail,
     MailServer,
@@ -57,6 +58,7 @@
     "--log-file",
     default=None,
     type=LogFile,
+    metavar="<path> <loglevel>",
     envvar="XNAT_INGEST_LOGFILE",
     help=(
         'Location to write the output logs to, defaults to "upload-logs" in the '

diff --git a/xnat_ingest/cli/utils.py b/xnat_ingest/cli/utils.py
diff --git a/xnat_ingest/tests/test_cli.py b/xnat_ingest/tests/test_cli.py
@@ -191,13 +191,14 @@ def test_stage_and_upload(
         [
             str(dicoms_dir),
             str(staging_dir),
-            "--assoc-files-glob",
-            str(associated_files_dir)
-            + "/{PatientName.given_name}_{PatientName.family_name}*.ptd",
+            # "--assoc-files-glob",
+            # str(associated_files_dir)
+            # + "/{PatientName.given_name}_{PatientName.family_name}*.ptd",
             "--log-file",
             str(log_file),
-            "--raise-errors",
-            "--delete",
+            "info",
+            # "--raise-errors",
+            # "--delete",
         ]
     )
 
@@ -209,6 +210,7 @@ def test_stage_and_upload(
             str(staging_dir),
             "--log-file",
             str(log_file),
+            "info",
             "--raise-errors",
             "--include-dicoms",
             "--delete",