fiddling with click types

Australian-Imaging-Service · Mar 14, 2024 · 1d4690e · 1d4690e
1 parent 0121350
commit 1d4690e
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Showing 3 changed files with 21 additions and 21 deletions.
diff --git a/xnat_ingest/cli/stage.py b/xnat_ingest/cli/stage.py
@@ -60,23 +60,23 @@
 )
 @click.option(
     "--associated-files",
-    type=AssociatedFiles(),
+    type=AssociatedFiles,
     nargs=2,
     default=None,
     envvar="XNAT_INGEST_ASSOCIATED",
     metavar="<glob> <id-pattern>",
     help=(
-        "The \"glob\" arg is a glob pattern by which to detect associated files to be "
+        'The "glob" arg is a glob pattern by which to detect associated files to be '
         "attached to the DICOM sessions. Note that when this pattern corresponds to a "
         "relative path it is considered to be relative to the parent directory containing "
         "the DICOMs for the session NOT the current working directory Can contain string "
         "templates corresponding to DICOM metadata fields, which are substituted before "
         "the glob is called. For example, "
-        '"./associated/{PatientName.given_name}_{PatientName.family_name}/*)\" '
+        '"./associated/{PatientName.given_name}_{PatientName.family_name}/*)" '
         "will find all files under the subdirectory within '/path/to/dicoms/associated' that matches "
         "<GIVEN-NAME>_<FAMILY-NAME>. Will be interpreted as being relative to `dicoms_dir` "
         "if a relative path is provided.\n"
-        "The \"id-pattern\" arg is a regular expression that is used to extract the scan ID & "
+        'The "id-pattern" arg is a regular expression that is used to extract the scan ID & '
         "type/resource from the associated filename. Should be a regular-expression "
         "(Python syntax) with named groups called 'id' and 'type', e.g. "
         r"--assoc-id-pattern '[^\.]+\.[^\.]+\.(?P<id>\d+)\.(?P<type>\w+)\..*'"
@@ -98,7 +98,7 @@
 @click.option(
     "--log-file",
     default=None,
-    type=LogFile(),
+    type=LogFile,
     nargs=2,
     metavar="<path> <loglevel>",
     envvar="XNAT_INGEST_LOGFILE",
@@ -110,7 +110,7 @@
 @click.option(
     "--log-email",
     "log_emails",
-    type=LogEmail(),
+    type=LogEmail,
     nargs=3,
     metavar="<address> <loglevel> <subject-preamble>",
     multiple=True,
@@ -122,7 +122,7 @@
 )
 @click.option(
     "--mail-server",
-    type=MailServer(),
+    type=MailServer,
     nargs=4,
     metavar="<host> <sender-email> <user> <password>",
     default=None,
@@ -142,7 +142,7 @@
     "--deidentify/--dont-deidentify",
     default=False,
     type=bool,
-    help="whether to deidentify the file names and DICOM metadata before staging"
+    help="whether to deidentify the file names and DICOM metadata before staging",
 )
 def stage(
     dicoms_path: str,
@@ -193,7 +193,8 @@ def stage(
                 continue
             # Identify theDeidentify files if necessary and save them to the staging directory
             session.stage(
-                staging_dir, associated_files=associated_files,
+                staging_dir,
+                associated_files=associated_files,
                 remove_original=delete,
                 deidentify=deidentify,
             )

diff --git a/xnat_ingest/cli/transfer.py b/xnat_ingest/cli/transfer.py
@@ -82,7 +82,7 @@ def remove_old_files_on_ssh(remote_store: str, threshold: int):
 @click.argument("remote_store", type=str, envvar="XNAT_INGEST_REMOTE_STORE")
 @click.option(
     "--store-credentials",
-    type=str,
+    type=click.Path(path_type=Path),
     metavar="<access-key> <secret-key>",
     envvar="XNAT_INGEST_STORE_CREDENTIALS",
     default=None,
@@ -99,7 +99,7 @@ def remove_old_files_on_ssh(remote_store: str, threshold: int):
 @click.option(
     "--log-file",
     default=None,
-    type=LogFile(),
+    type=LogFile,
     nargs=2,
     metavar="<path> <loglevel>",
     envvar="XNAT_INGEST_LOGFILE",
@@ -111,7 +111,7 @@ def remove_old_files_on_ssh(remote_store: str, threshold: int):
 @click.option(
     "--log-email",
     "log_emails",
-    type=LogEmail(),
+    type=LogEmail,
     nargs=3,
     metavar="<address> <loglevel> <subject-preamble>",
     multiple=True,
@@ -123,7 +123,7 @@ def remove_old_files_on_ssh(remote_store: str, threshold: int):
 )
 @click.option(
     "--mail-server",
-    type=MailServer(),
+    type=MailServer,
     metavar="<host> <sender-email> <user> <password>",
     default=None,
     envvar="XNAT_INGEST_MAILSERVER",
@@ -161,20 +161,19 @@ def remove_old_files_on_ssh(remote_store: str, threshold: int):
     help="The number of days to keep files in the remote store for",
 )
 def transfer(
-    staging_dir: str,
+    staging_dir: Path,
     remote_store: str,
     credentials: ty.Tuple[str, str],
-    log_file: ty.Tuple[str, str],
+    log_file: LogFile,
     log_level: str,
-    log_emails: ty.List[ty.Tuple[str, str, str]],
-    mail_server: ty.Tuple[str, str, str, str],
+    log_emails: ty.List[LogEmail],
+    mail_server: ty.Tuple[MailServer],
     delete: bool,
     raise_errors: bool,
     xnat_login: ty.Optional[ty.Tuple[str, str, str]],
     clean_up_older_than: int,
 ):
 
-    staging_dir = Path(staging_dir)
     if not staging_dir.exists():
         raise ValueError(f"Staging directory '{staging_dir}' does not exist")
 

diff --git a/xnat_ingest/cli/upload.py b/xnat_ingest/cli/upload.py
@@ -60,7 +60,7 @@
 @click.option(
     "--log-file",
     default=None,
-    type=LogFile(),
+    type=LogFile,
     nargs=2,
     metavar="<path> <loglevel>",
     envvar="XNAT_INGEST_LOGFILE",
@@ -72,7 +72,7 @@
 @click.option(
     "--log-email",
     "log_emails",
-    type=LogEmail(),
+    type=LogEmail,
     nargs=3,
     metavar="<address> <loglevel> <subject-preamble>",
     multiple=True,
@@ -84,7 +84,7 @@
 )
 @click.option(
     "--mail-server",
-    type=MailServer(),
+    type=MailServer,
     metavar="<host> <sender-email> <user> <password>",
     default=None,
     envvar="XNAT_INGEST_MAILSERVER",