added prefixes to all env vars used in different cli tools

Australian-Imaging-Service · Mar 15, 2024 · 786fc3a · 786fc3a
1 parent 424f822
commit 786fc3a
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Showing 3 changed files with 35 additions and 34 deletions.
diff --git a/xnat_ingest/cli/stage.py b/xnat_ingest/cli/stage.py
@@ -27,29 +27,29 @@
 are uploaded to XNAT
 """,
 )
-@click.argument("dicoms_path", type=str, envvar="XNAT_INGEST_DICOMS_PATH")
+@click.argument("dicoms_path", type=str, envvar="XNAT_INGEST_STAGE_DICOMS_PATH")
 @click.argument(
-    "staging_dir", type=click.Path(path_type=Path), envvar="XNAT_INGEST_STAGING_DIR"
+    "staging_dir", type=click.Path(path_type=Path), envvar="XNAT_INGEST_STAGE_DIR"
 )
 @click.option(
     "--project-field",
     type=DicomField,
     default="StudyID",
-    envvar="XNAT_INGEST_PROJECT",
+    envvar="XNAT_INGEST_STAGE_PROJECT",
     help=("The keyword or tag of the DICOM field to extract the XNAT project ID from "),
 )
 @click.option(
     "--subject-field",
     type=DicomField,
     default="PatientID",
-    envvar="XNAT_INGEST_SUBJECT",
+    envvar="XNAT_INGEST_STAGE_SUBJECT",
     help=("The keyword or tag of the DICOM field to extract the XNAT subject ID from "),
 )
 @click.option(
     "--visit-field",
     type=DicomField,
     default="AccessionNumber",
-    envvar="XNAT_INGEST_SESSION",
+    envvar="XNAT_INGEST_STAGE_SESSION",
     help=(
         "The keyword or tag of the DICOM field to extract the XNAT imaging session ID from "
     ),
@@ -65,7 +65,7 @@
     type=AssociatedFiles.cli_type,
     nargs=2,
     default=None,
-    envvar="XNAT_INGEST_ASSOCIATED",
+    envvar="XNAT_INGEST_STAGE_ASSOCIATED",
     metavar="<glob> <id-pattern>",
     help=(
         'The "glob" arg is a glob pattern by which to detect associated files to be '
@@ -87,14 +87,14 @@
 @click.option(
     "--delete/--dont-delete",
     default=False,
-    envvar="XNAT_INGEST_DELETE",
+    envvar="XNAT_INGEST_STAGE_DELETE",
     help="Whether to delete the session directories after they have been uploaded or not",
 )
 @click.option(
     "--log-level",
     default="info",
     type=str,
-    envvar="XNAT_INGEST_LOGLEVEL",
+    envvar="XNAT_INGEST_STAGE_LOGLEVEL",
     help=("The level of the logging printed to stdout"),
 )
 @click.option(
@@ -103,7 +103,7 @@
     type=LogFile.cli_type,
     nargs=2,
     metavar="<path> <loglevel>",
-    envvar="XNAT_INGEST_LOGFILE",
+    envvar="XNAT_INGEST_STAGE_LOGFILE",
     help=(
         'Location to write the output logs to, defaults to "upload-logs" in the '
         "export directory"
@@ -116,7 +116,7 @@
     nargs=3,
     metavar="<address> <loglevel> <subject-preamble>",
     multiple=True,
-    envvar="XNAT_INGEST_LOGEMAIL",
+    envvar="XNAT_INGEST_STAGE_LOGEMAIL",
     help=(
         "Email(s) to send logs to. When provided in an environment variable, "
         "mail and log level are delimited by ',' and separate destinations by ';'"
@@ -128,7 +128,7 @@
     nargs=4,
     metavar="<host> <sender-email> <user> <password>",
     default=None,
-    envvar="XNAT_INGEST_MAILSERVER",
+    envvar="XNAT_INGEST_STAGE_MAILSERVER",
     help=(
         "the mail server to send logger emails to. When provided in an environment variable, "
         "args are delimited by ';'"
@@ -144,7 +144,7 @@
     "--deidentify/--dont-deidentify",
     default=False,
     type=bool,
-    envvar="XNAT_INGEST_DEIDENTIFY",
+    envvar="XNAT_INGEST_STAGE_DEIDENTIFY",
     help="whether to deidentify the file names and DICOM metadata before staging",
 )
 def stage(

diff --git a/xnat_ingest/cli/transfer.py b/xnat_ingest/cli/transfer.py
@@ -30,13 +30,13 @@
 an SSH server.
 """,
 )
-@click.argument("staging_dir", type=str)
-@click.argument("remote_store", type=str, envvar="XNAT_INGEST_REMOTE_STORE")
+@click.argument("staging_dir", type=str, envvar="XNAT_INGEST_STAGE_DIR")
+@click.argument("remote_store", type=str, envvar="XNAT_INGEST_TRANSFER_REMOTE_STORE")
 @click.option(
     "--store-credentials",
     type=click.Path(path_type=Path),
     metavar="<access-key> <secret-key>",
-    envvar="XNAT_INGEST_STORE_CREDENTIALS",
+    envvar="XNAT_INGEST_TRANSFER_STORE_CREDENTIALS",
     default=None,
     nargs=2,
     help="Credentials to use to access of data stored in remote stores (e.g. AWS S3)",
@@ -45,7 +45,7 @@
     "--log-level",
     default="info",
     type=str,
-    envvar="XNAT_INGEST_LOGLEVEL",
+    envvar="XNAT_INGEST_TRANSFER_LOGLEVEL",
     help=("The level of the logging printed to stdout"),
 )
 @click.option(
@@ -54,7 +54,7 @@
     type=LogFile.cli_type,
     nargs=2,
     metavar="<path> <loglevel>",
-    envvar="XNAT_INGEST_LOGFILE",
+    envvar="XNAT_INGEST_TRANSFER_LOGFILE",
     help=(
         'Location to write the output logs to, defaults to "upload-logs" in the '
         "export directory"
@@ -67,7 +67,7 @@
     nargs=3,
     metavar="<address> <loglevel> <subject-preamble>",
     multiple=True,
-    envvar="XNAT_INGEST_LOGEMAIL",
+    envvar="XNAT_INGEST_TRANSFER_LOGEMAIL",
     help=(
         "Email(s) to send logs to. When provided in an environment variable, "
         "mail and log level are delimited by ',' and separate destinations by ';'"
@@ -78,7 +78,7 @@
     type=MailServer.cli_type,
     metavar="<host> <sender-email> <user> <password>",
     default=None,
-    envvar="XNAT_INGEST_MAILSERVER",
+    envvar="XNAT_INGEST_TRANSFER_MAILSERVER",
     help=(
         "the mail server to send logger emails to. When provided in an environment variable, "
         "args are delimited by ';'"
@@ -87,7 +87,7 @@
 @click.option(
     "--delete/--dont-delete",
     default=False,
-    envvar="XNAT_INGEST_DELETE",
+    envvar="XNAT_INGEST_TRANSFER_DELETE",
     help="Whether to delete the session directories after they have been uploaded or not",
 )
 @click.option(
@@ -103,7 +103,7 @@
     default=None,
     metavar="<host> <user> <password>",
     help="The XNAT server to upload to plus the user and password to use",
-    envvar="XNAT_INGEST_XNAT_LOGIN",
+    envvar="XNAT_INGEST_TRANSFER_XNAT_LOGIN",
 )
 def transfer(
     staging_dir: Path,

diff --git a/xnat_ingest/cli/upload.py b/xnat_ingest/cli/upload.py
@@ -43,21 +43,21 @@
 PASSWORD is the password for the XNAT user, alternatively "XNAT_INGEST_PASS" env. var
 """,
 )
-@click.argument("staged", type=str)
-@click.argument("server", type=str, envvar="XNAT_INGEST_HOST")
-@click.argument("user", type=str, envvar="XNAT_INGEST_USER")
-@click.argument("password", type=str, envvar="XNAT_INGEST_PASS")
+@click.argument("staged", type=str, envvar="XNAT_INGEST_UPLOAD_STAGED")
+@click.argument("server", type=str, envvar="XNAT_INGEST_UPLOAD_HOST")
+@click.argument("user", type=str, envvar="XNAT_INGEST_UPLOAD_USER")
+@click.argument("password", type=str, envvar="XNAT_INGEST_UPLOAD_PASS")
 @click.option(
     "--delete/--dont-delete",
     default=True,
-    envvar="XNAT_INGEST_DELETE",
+    envvar="XNAT_INGEST_UPLOAD_DELETE",
     help="Whether to delete the session directories after they have been uploaded or not",
 )
 @click.option(
     "--log-level",
     default="info",
     type=str,
-    envvar="XNAT_INGEST_LOGLEVEL",
+    envvar="XNAT_INGEST_UPLOAD_LOGLEVEL",
     help=("The level of the logging printed to stdout"),
 )
 @click.option(
@@ -66,7 +66,7 @@
     type=LogFile.cli_type,
     nargs=2,
     metavar="<path> <loglevel>",
-    envvar="XNAT_INGEST_LOGFILE",
+    envvar="XNAT_INGEST_UPLOAD_LOGFILE",
     help=(
         'Location to write the output logs to, defaults to "upload-logs" in the '
         "export directory"
@@ -79,7 +79,7 @@
     nargs=3,
     metavar="<address> <loglevel> <subject-preamble>",
     multiple=True,
-    envvar="XNAT_INGEST_LOGEMAIL",
+    envvar="XNAT_INGEST_UPLOAD_LOGEMAIL",
     help=(
         "Email(s) to send logs to. When provided in an environment variable, "
         "mail and log level are delimited by ',' and separate destinations by ';'"
@@ -90,7 +90,7 @@
     type=MailServer.cli_type,
     metavar="<host> <sender-email> <user> <password>",
     default=None,
-    envvar="XNAT_INGEST_MAILSERVER",
+    envvar="XNAT_INGEST_UPLOAD_MAILSERVER",
     help=(
         "the mail server to send logger emails to. When provided in an environment variable, "
         "args are delimited by ';'"
@@ -102,7 +102,7 @@
     default=(),
     type=str,
     multiple=True,
-    envvar="XNAT_INGEST_ALWAYSINCLUDE",
+    envvar="XNAT_INGEST_UPLOAD_ALWAYSINCLUDE",
     help=(
         "Scan types to always include in the upload, regardless of whether they are"
         "specified in a column or not. Specified using the scan types IANA mime-type or "
@@ -121,7 +121,7 @@
     "--store-credentials",
     type=str,
     metavar="<access-key> <secret-key>",
-    envvar="XNAT_INGEST_STORE_CREDENTIALS",
+    envvar="XNAT_INGEST_UPLOAD_STORE_CREDENTIALS",
     default=None,
     nargs=2,
     help="Credentials to use to access of data stored in remote stores (e.g. AWS S3)",
@@ -130,13 +130,13 @@
     "--temp-dir",
     type=Path,
     default=None,
-    envvar="XNAT_INGEST_WORKDIR",
+    envvar="XNAT_INGEST_UPLOAD_WORKDIR",
     help="The directory to use for temporary downloads (i.e. from s3)",
 )
 @click.option(
     "--use-manifest/--dont-use-manifest",
     default=None,
-    envvar="XNAT_INGEST_REQUIRE_MANIFEST",
+    envvar="XNAT_INGEST_UPLOAD_REQUIRE_MANIFEST",
     help=(
         "Whether to use the manifest file in the staged sessions to load the "
         "directory structure. By default it is used if present and ignore if not there"
@@ -147,6 +147,7 @@
     "--clean-up-older-than",
     type=int,
     metavar="<days>",
+    envvar="XNAT_INGEST_UPLOAD_CLEANUP_OLDER_THAN",
     default=0,
     help="The number of days to keep files in the remote store for",
 )