From 9c0f02400171464c6d303600e93b220cc7f75318 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 4 Mar 2025 16:11:20 +0100
Subject: [PATCH 01/39] log file required unless force-no-log

---
 dds_cli/__main__.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 6ed3d471e..c0cf5dd5d 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -39,6 +39,7 @@
 import dds_cli.user
 import dds_cli.utils
 from dds_cli.options import (
+    NotRequiredIf,
     destination_option,
     email_arg,
     email_option,
@@ -107,7 +108,8 @@
 @click.option(
     "-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console."
 )
-@click.option("-l", "--log-file", help="Save a log to a file.", metavar="<filename>")
+@click.option("--force-no-log", help="[NOT RECOMMENDED] Do not save logs to a file.", is_flag=True)
+@click.option("-l", "--log-file", help="Save a log to a file.", metavar="<filename>", required=not bool("--force-no-log" in sys.argv))
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
 )
@@ -121,7 +123,7 @@
     help="List the options of any DDS subcommand and its default settings.",
 )
 @click.pass_context
-def dds_main(click_ctx, verbose, log_file, no_prompt, token_path):
+def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
     """SciLifeLab Data Delivery System (DDS) command line interface.
 
     Access token is saved in a .dds_cli_token file in the home directory.
@@ -165,6 +167,7 @@ def dds_main(click_ctx, verbose, log_file, no_prompt, token_path):
             )
             LOG.addHandler(log_fh)
 
+        sys.exit()
         # Create context object
         click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path}
 

From 8980d25341a0bf34f43364911fcc289d5af65d43 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 4 Mar 2025 16:12:10 +0100
Subject: [PATCH 02/39] remove sys exit

---
 dds_cli/__main__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index c0cf5dd5d..9b0a43abd 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -167,7 +167,6 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             )
             LOG.addHandler(log_fh)
 
-        sys.exit()
         # Create context object
         click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path}
 

From 828dd8a2a5e73f30a57e70646bd991964ccc04cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 4 Mar 2025 16:57:47 +0100
Subject: [PATCH 03/39] Update help info to option

---
 dds_cli/__main__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 9b0a43abd..592aa1afc 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -39,7 +39,6 @@
 import dds_cli.user
 import dds_cli.utils
 from dds_cli.options import (
-    NotRequiredIf,
     destination_option,
     email_arg,
     email_option,
@@ -109,7 +108,7 @@
     "-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console."
 )
 @click.option("--force-no-log", help="[NOT RECOMMENDED] Do not save logs to a file.", is_flag=True)
-@click.option("-l", "--log-file", help="Save a log to a file.", metavar="<filename>", required=not bool("--force-no-log" in sys.argv))
+@click.option("-l", "--log-file", help="Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. We recommend naming it according to this format: <date>_<time>_<command>.log.", metavar="<filename>", required=not bool("--force-no-log" in sys.argv))
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
 )

From 1d355c81473281f3c51349e9a3f1aabc93143031 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 4 Mar 2025 16:58:15 +0100
Subject: [PATCH 04/39] black

---
 dds_cli/__main__.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 592aa1afc..7d3d85da0 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -108,7 +108,13 @@
     "-v", "--verbose", is_flag=True, default=False, help="Print verbose output to the console."
 )
 @click.option("--force-no-log", help="[NOT RECOMMENDED] Do not save logs to a file.", is_flag=True)
-@click.option("-l", "--log-file", help="Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. We recommend naming it according to this format: <date>_<time>_<command>.log.", metavar="<filename>", required=not bool("--force-no-log" in sys.argv))
+@click.option(
+    "-l",
+    "--log-file",
+    help="Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. We recommend naming it according to this format: <date>_<time>_<command>.log.",
+    metavar="<filename>",
+    required=not bool("--force-no-log" in sys.argv),
+)
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
 )

From 0d983c7531de817849b7d6c85a07fcfb60fef8e1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 16:35:34 +0100
Subject: [PATCH 05/39] generate file name if put or get is used

---
 dds_cli/__main__.py | 46 +++++++++++++++++++++++++++++++++------------
 1 file changed, 34 insertions(+), 12 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 7d3d85da0..c9996e68f 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -9,6 +9,8 @@
 import itertools
 import logging
 import sys
+import typing
+from datetime import datetime
 
 # Installed
 import pathlib
@@ -113,7 +115,7 @@
     "--log-file",
     help="Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. We recommend naming it according to this format: <date>_<time>_<command>.log.",
     metavar="<filename>",
-    required=not bool("--force-no-log" in sys.argv),
+    required=False,
 )
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
@@ -160,20 +162,40 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             )
         )
 
-        # Set up logs to a file if we asked for one
-        if log_file:
-            log_fh = logging.FileHandler(log_file, encoding="utf-8")
-            log_fh.setLevel(logging.DEBUG)
-            log_fh.setFormatter(
-                logging.Formatter(
-                    fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
-                    datefmt="%Y-%m-%d %H:%M:%S",
+        # Don't log to file if this flag is used
+        if not force_no_log:
+            
+            # Get command and strip from leading - / --
+            subcommands: typing.List = [i.lstrip("-") for i in sys.argv[1::]]
+
+            # Check if put or get in subcommand 
+            put_or_get: typing.List = [i for i in subcommands if i in ["put", "get"]]
+
+            # Always log to file if uploading or downloading
+            if put_or_get and not log_file:
+                # Create command part of log file name 
+                command_as_string: str = "dds_" + "_".join(subcommands)
+
+                # Get timestamp
+                timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
+                
+                # Full log file path
+                log_file = command_as_string + "_" + timestamp_string + ".log"
+
+            # Set up logs to a file (if chosen, or by default above)
+            if log_file:
+                log_fh = logging.FileHandler(log_file, encoding="utf-8")
+                log_fh.setLevel(logging.DEBUG)
+                log_fh.setFormatter(
+                    logging.Formatter(
+                        fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
+                        datefmt="%Y-%m-%d %H:%M:%S",
+                    )
                 )
-            )
-            LOG.addHandler(log_fh)
+                LOG.addHandler(log_fh)
 
         # Create context object
-        click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path}
+        click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "LOG_FILE": log_file}
 
 
 # ************************************************************************************************ #

From 65bd650ff1e7b77139f4fd2f117738b71af22694 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 16:36:01 +0100
Subject: [PATCH 06/39] black

---
 dds_cli/__main__.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index c9996e68f..de528fe98 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -164,21 +164,21 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
 
         # Don't log to file if this flag is used
         if not force_no_log:
-            
+
             # Get command and strip from leading - / --
             subcommands: typing.List = [i.lstrip("-") for i in sys.argv[1::]]
 
-            # Check if put or get in subcommand 
+            # Check if put or get in subcommand
             put_or_get: typing.List = [i for i in subcommands if i in ["put", "get"]]
 
             # Always log to file if uploading or downloading
             if put_or_get and not log_file:
-                # Create command part of log file name 
+                # Create command part of log file name
                 command_as_string: str = "dds_" + "_".join(subcommands)
 
                 # Get timestamp
                 timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
-                
+
                 # Full log file path
                 log_file = command_as_string + "_" + timestamp_string + ".log"
 

From 0df622f52b5e2702e87fdf016cd4917ddbdda917 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 16:38:30 +0100
Subject: [PATCH 07/39] remove some comments

---
 dds_cli/__main__.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index de528fe98..21b589eae 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -173,13 +173,9 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
 
             # Always log to file if uploading or downloading
             if put_or_get and not log_file:
-                # Create command part of log file name
+                # Format log file path name to contain command and timestamp
                 command_as_string: str = "dds_" + "_".join(subcommands)
-
-                # Get timestamp
                 timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
-
-                # Full log file path
                 log_file = command_as_string + "_" + timestamp_string + ".log"
 
             # Set up logs to a file (if chosen, or by default above)

From 19aeac4ce350110afd78c05ec5a73809e9656347 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 17:10:39 +0100
Subject: [PATCH 08/39] error message if both used because I didn't get the
 mutually exclusive part to work

---
 dds_cli/__main__.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 21b589eae..98ca3c85c 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -104,6 +104,8 @@
             dds_cli.utils.stderr_console.print(f"{motd['Created']} - {motd['Message']} \n")
 
 
+from cloup.constraints import constraint, mutually_exclusive 
+
 # -- dds -- #
 @click.group()
 @click.option(
@@ -117,6 +119,7 @@
     metavar="<filename>",
     required=False,
 )
+@constraint(mutually_exclusive, ['force_no_log', 'log_file'])
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
 )
@@ -162,6 +165,11 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             )
         )
 
+        # Only one can be used 
+        if force_no_log and log_file: 
+            LOG.warning("You can only use '--log-file' or '--force-no-log', not both. Please try again.")
+            sys.exit(1)
+
         # Don't log to file if this flag is used
         if not force_no_log:
 
@@ -190,6 +198,8 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 )
                 LOG.addHandler(log_fh)
 
+        sys.exit()
+
         # Create context object
         click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "LOG_FILE": log_file}
 

From 082249d3a7df5a2e788fd39e36fb80f4c11c0189 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 17:12:21 +0100
Subject: [PATCH 09/39] removed one sys exit

---
 dds_cli/__main__.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 98ca3c85c..30b90d435 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -198,8 +198,6 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 )
                 LOG.addHandler(log_fh)
 
-        sys.exit()
-
         # Create context object
         click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "LOG_FILE": log_file}
 

From 017fc99f73cf30c724d941acd64dc980ea64bdd3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 17:12:37 +0100
Subject: [PATCH 10/39] black

---
 dds_cli/__main__.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 30b90d435..0ae20b7e1 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -104,7 +104,8 @@
             dds_cli.utils.stderr_console.print(f"{motd['Created']} - {motd['Message']} \n")
 
 
-from cloup.constraints import constraint, mutually_exclusive 
+from cloup.constraints import constraint, mutually_exclusive
+
 
 # -- dds -- #
 @click.group()
@@ -119,7 +120,7 @@
     metavar="<filename>",
     required=False,
 )
-@constraint(mutually_exclusive, ['force_no_log', 'log_file'])
+@constraint(mutually_exclusive, ["force_no_log", "log_file"])
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
 )
@@ -165,9 +166,11 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             )
         )
 
-        # Only one can be used 
-        if force_no_log and log_file: 
-            LOG.warning("You can only use '--log-file' or '--force-no-log', not both. Please try again.")
+        # Only one can be used
+        if force_no_log and log_file:
+            LOG.warning(
+                "You can only use '--log-file' or '--force-no-log', not both. Please try again."
+            )
             sys.exit(1)
 
         # Don't log to file if this flag is used

From 601285fd83399095c3cc26fc00ca64a140826937 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 17:13:09 +0100
Subject: [PATCH 11/39] remove cloup

---
 dds_cli/__main__.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 0ae20b7e1..62fe5df09 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -104,9 +104,6 @@
             dds_cli.utils.stderr_console.print(f"{motd['Created']} - {motd['Message']} \n")
 
 
-from cloup.constraints import constraint, mutually_exclusive
-
-
 # -- dds -- #
 @click.group()
 @click.option(
@@ -120,7 +117,6 @@
     metavar="<filename>",
     required=False,
 )
-@constraint(mutually_exclusive, ["force_no_log", "log_file"])
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
 )

From 6e4fb2e641938083bfd3d295646af636753fb0ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 5 Mar 2025 17:16:19 +0100
Subject: [PATCH 12/39] update help message

---
 dds_cli/__main__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 62fe5df09..5118b9d91 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -113,7 +113,7 @@
 @click.option(
     "-l",
     "--log-file",
-    help="Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. We recommend naming it according to this format: <date>_<time>_<command>.log.",
+    help="Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. We recommend naming it according to this format: <command>_<date>_<time>.log.",
     metavar="<filename>",
     required=False,
 )
@@ -165,7 +165,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
         # Only one can be used
         if force_no_log and log_file:
             LOG.warning(
-                "You can only use '--log-file' or '--force-no-log', not both. Please try again."
+                "You have used both the '--log-file' and '--force-no-log' option, you can only use one."
             )
             sys.exit(1)
 

From eb8aad4dea0fd1dc45d4536106a29fc1437a2c71 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:09:21 +0100
Subject: [PATCH 13/39] Create folder to store all automatically generated logs

---
 dds_cli/__main__.py | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 5118b9d91..4f8f53563 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -113,7 +113,10 @@
 @click.option(
     "-l",
     "--log-file",
-    help="Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. We recommend naming it according to this format: <command>_<date>_<time>.log.",
+    help=(
+        "Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. "
+        "We recommend naming it according to this format: <command>_<date>_<time>.log."
+    ),
     metavar="<filename>",
     required=False,
 )
@@ -180,10 +183,21 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
 
             # Always log to file if uploading or downloading
             if put_or_get and not log_file:
+                try:
+                    # Save logs to specific folder in home directory
+                    dds_log_dir: str = pathlib.Path("~/dds-cli_logs/").expanduser()
+                    dds_log_dir.mkdir(exist_ok=True)
+                except Exception as err:
+                    LOG.warning(
+                        f"Could not create log directory '{dds_log_dir}'. Logs will not be saved to file. \nDetails: {err}"
+                    )
+
                 # Format log file path name to contain command and timestamp
                 command_as_string: str = "dds_" + "_".join(subcommands)
                 timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
-                log_file = command_as_string + "_" + timestamp_string + ".log"
+                log_file = str(
+                    dds_log_dir / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")
+                )
 
             # Set up logs to a file (if chosen, or by default above)
             if log_file:
@@ -197,6 +211,8 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 )
                 LOG.addHandler(log_fh)
 
+        sys.exit()
+
         # Create context object
         click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "LOG_FILE": log_file}
 

From a5b87bf4e4be3ccf568187a833c03cb85ecd69e1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:11:21 +0100
Subject: [PATCH 14/39] sprintlog

---
 SPRINTLOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/SPRINTLOG.md b/SPRINTLOG.md
index 61d448cab..bbba2a7fd 100644
--- a/SPRINTLOG.md
+++ b/SPRINTLOG.md
@@ -407,3 +407,7 @@ _Empty sprint_
 # 2025-02-17 – 2025-02-28
 
 - Remove executable for Ubuntu 20.04 and add one for Ubuntu 22.04 ([#733](https://github.com/ScilifelabDataCentre/dds_cli/pull/733)).
+
+# 2025-03-03 - 2025-03-14 
+
+- Generate log file by default ([#737](https://github.com/ScilifelabDataCentre/dds_cli/pull/737))

From 22bbb5096b77fb8827a5e8f6cfeafcd1263cac9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:12:15 +0100
Subject: [PATCH 15/39] new line in warning

---
 dds_cli/__main__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 4f8f53563..530333fa9 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -189,7 +189,8 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                     dds_log_dir.mkdir(exist_ok=True)
                 except Exception as err:
                     LOG.warning(
-                        f"Could not create log directory '{dds_log_dir}'. Logs will not be saved to file. \nDetails: {err}"
+                        f"Could not create log directory '{dds_log_dir}'. "
+                        f"Logs will not be saved to file. \nDetails: {err}"
                     )
 
                 # Format log file path name to contain command and timestamp

From 981fadfe65082475a6587592df182e6d13f141ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:14:17 +0100
Subject: [PATCH 16/39] less general exception

---
 dds_cli/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 530333fa9..d524b8b99 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -187,7 +187,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                     # Save logs to specific folder in home directory
                     dds_log_dir: str = pathlib.Path("~/dds-cli_logs/").expanduser()
                     dds_log_dir.mkdir(exist_ok=True)
-                except Exception as err:
+                except (OSError, RuntimeError) as err:
                     LOG.warning(
                         f"Could not create log directory '{dds_log_dir}'. "
                         f"Logs will not be saved to file. \nDetails: {err}"

From d5360300a4ff5fe824cc3f1d0e83c67215f48bc1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:15:14 +0100
Subject: [PATCH 17/39] lazy logging

---
 dds_cli/__main__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index d524b8b99..8bb777ade 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -189,8 +189,8 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                     dds_log_dir.mkdir(exist_ok=True)
                 except (OSError, RuntimeError) as err:
                     LOG.warning(
-                        f"Could not create log directory '{dds_log_dir}'. "
-                        f"Logs will not be saved to file. \nDetails: {err}"
+                        "Could not create log directory '%s'. "
+                        "Logs will not be saved to file. \nDetails: %s", dds_log_dir, err
                     )
 
                 # Format log file path name to contain command and timestamp

From 6dbdc7fd721aba22da6989526a66d77f5e694c4a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:15:50 +0100
Subject: [PATCH 18/39] remove sys exit

---
 dds_cli/__main__.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 8bb777ade..e3a0404e2 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -212,8 +212,6 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 )
                 LOG.addHandler(log_fh)
 
-        sys.exit()
-
         # Create context object
         click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "LOG_FILE": log_file}
 

From 1bbcfa1430df2b40b6554d6666c1b9b258918c1a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:17:16 +0100
Subject: [PATCH 19/39] black

---
 dds_cli/__main__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index e3a0404e2..fb7ed13cf 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -190,7 +190,9 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 except (OSError, RuntimeError) as err:
                     LOG.warning(
                         "Could not create log directory '%s'. "
-                        "Logs will not be saved to file. \nDetails: %s", dds_log_dir, err
+                        "Logs will not be saved to file. \nDetails: %s",
+                        dds_log_dir,
+                        err,
                     )
 
                 # Format log file path name to contain command and timestamp

From a3e0fb402fb4f84a00a52e09adc4ef95cf54c50a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 6 Mar 2025 15:19:50 +0100
Subject: [PATCH 20/39] prettier

---
 SPRINTLOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SPRINTLOG.md b/SPRINTLOG.md
index bbba2a7fd..0e7d5d6ec 100644
--- a/SPRINTLOG.md
+++ b/SPRINTLOG.md
@@ -408,6 +408,6 @@ _Empty sprint_
 
 - Remove executable for Ubuntu 20.04 and add one for Ubuntu 22.04 ([#733](https://github.com/ScilifelabDataCentre/dds_cli/pull/733)).
 
-# 2025-03-03 - 2025-03-14 
+# 2025-03-03 - 2025-03-14
 
 - Generate log file by default ([#737](https://github.com/ScilifelabDataCentre/dds_cli/pull/737))

From add61b72763771779f2a70965d415391e1729071 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Fri, 7 Mar 2025 16:37:23 +0100
Subject: [PATCH 21/39] replace slash and backslash with _

---
 dds_cli/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index fb7ed13cf..4a82d413f 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -196,7 +196,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                     )
 
                 # Format log file path name to contain command and timestamp
-                command_as_string: str = "dds_" + "_".join(subcommands)
+                command_as_string: str = "dds_" + "_".join(subcommands).replace("/", "_").replace("\\", "_")
                 timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
                 log_file = str(
                     dds_log_dir / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")

From c392ebb780a27795d1d04f2a40d94089a1edd1bc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Fri, 7 Mar 2025 16:42:05 +0100
Subject: [PATCH 22/39] black

---
 dds_cli/__main__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 4a82d413f..e89388df8 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -196,7 +196,9 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                     )
 
                 # Format log file path name to contain command and timestamp
-                command_as_string: str = "dds_" + "_".join(subcommands).replace("/", "_").replace("\\", "_")
+                command_as_string: str = "dds_" + "_".join(subcommands).replace("/", "_").replace(
+                    "\\", "_"
+                )
                 timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
                 log_file = str(
                     dds_log_dir / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")

From b85321e1f250e4f1832250f8c881a49282db048d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 11:50:46 +0100
Subject: [PATCH 23/39] mount_dir to staging_dir

---
 dds_cli/__main__.py    | 79 ++++++++++++++++++++++--------------------
 dds_cli/base.py        |  6 ++--
 dds_cli/data_putter.py |  8 ++---
 3 files changed, 48 insertions(+), 45 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index e89388df8..a661c25fd 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -114,8 +114,10 @@
     "-l",
     "--log-file",
     help=(
-        "Save logs to file. In the case of opening a support ticket regarding the DDS, attach this file. "
-        "We recommend naming it according to this format: <command>_<date>_<time>.log."
+        "Save logs to file. Define a custom path with this option. "
+        "Recommended format: <command>_<date>_<time>.log."
+        "In the case of opening a support ticket regarding the DDS, attach this file. "
+        "Note that a log file will be generated by default for uploads and downloads."
     ),
     metavar="<filename>",
     required=False,
@@ -172,37 +174,37 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             )
             sys.exit(1)
 
-        # Don't log to file if this flag is used
-        if not force_no_log:
-
-            # Get command and strip from leading - / --
-            subcommands: typing.List = [i.lstrip("-") for i in sys.argv[1::]]
-
-            # Check if put or get in subcommand
-            put_or_get: typing.List = [i for i in subcommands if i in ["put", "get"]]
-
-            # Always log to file if uploading or downloading
-            if put_or_get and not log_file:
-                try:
-                    # Save logs to specific folder in home directory
-                    dds_log_dir: str = pathlib.Path("~/dds-cli_logs/").expanduser()
-                    dds_log_dir.mkdir(exist_ok=True)
-                except (OSError, RuntimeError) as err:
-                    LOG.warning(
-                        "Could not create log directory '%s'. "
-                        "Logs will not be saved to file. \nDetails: %s",
-                        dds_log_dir,
-                        err,
-                    )
-
-                # Format log file path name to contain command and timestamp
-                command_as_string: str = "dds_" + "_".join(subcommands).replace("/", "_").replace(
-                    "\\", "_"
-                )
-                timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
-                log_file = str(
-                    dds_log_dir / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")
-                )
+        # # Don't log to file if this flag is used
+        # if not force_no_log:
+
+        #     # Get command and strip from leading - / --
+        #     subcommands: typing.List = [i.lstrip("-") for i in sys.argv[1::]]
+
+        #     # Check if put or get in subcommand
+        #     put_or_get: typing.List = [i for i in subcommands if i in ["put", "get"]]
+
+        #     # Always log to file if uploading or downloading
+        #     if put_or_get and not log_file:
+        #         try:
+        #             # Save logs to specific folder in home directory
+        #             dds_log_dir: str = pathlib.Path("~/dds-cli_logs/").expanduser()
+        #             dds_log_dir.mkdir(exist_ok=True)
+        #         except (OSError, RuntimeError) as err:
+        #             LOG.warning(
+        #                 "Could not create log directory '%s'. "
+        #                 "Logs will not be saved to file. \nDetails: %s",
+        #                 dds_log_dir,
+        #                 err,
+        #             )
+
+        #         # Format log file path name to contain command and timestamp
+        #         command_as_string: str = "dds_" + "_".join(subcommands).replace("/", "_").replace(
+        #             "\\", "_"
+        #         )
+        #         timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
+        #         log_file = str(
+        #             dds_log_dir / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")
+        #         )
 
             # Set up logs to a file (if chosen, or by default above)
             if log_file:
@@ -217,7 +219,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 LOG.addHandler(log_fh)
 
         # Create context object
-        click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "LOG_FILE": log_file}
+        click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "DEFAULT_LOG": log_file != ""}
 
 
 # ************************************************************************************************ #
@@ -1615,8 +1617,8 @@ def data_group_command(_):
 @data_group_command.command(name="put", no_args_is_help=True)
 # Options
 @click.option(
-    "--mount-dir",
-    "-md",
+    "--staging-dir",
+    "-sd",
     required=False,
     type=click_pathlib.Path(exists=False, file_okay=False, dir_okay=True, resolve_path=True),
     help=(
@@ -1647,7 +1649,7 @@ def data_group_command(_):
 @click.pass_obj
 def put_data(
     click_ctx,
-    mount_dir,
+    staging_dir,
     project,
     source,
     source_path_file,
@@ -1678,7 +1680,7 @@ def put_data(
     """
     try:
         dds_cli.data_putter.put(
-            mount_dir=mount_dir,
+            staging_dir=staging_dir,
             project=project,
             source=source,
             source_path_file=source_path_file,
@@ -1689,6 +1691,7 @@ def put_data(
             no_prompt=click_ctx.get("NO_PROMPT", False),
             token_path=click_ctx.get("TOKEN_PATH"),
             destination=destination,
+            default_log=click_ctx.get("DEFAULT_LOG"),
         )
     except (
         dds_cli.exceptions.AuthenticationError,
diff --git a/dds_cli/base.py b/dds_cli/base.py
index 416ba7002..124d127f6 100644
--- a/dds_cli/base.py
+++ b/dds_cli/base.py
@@ -46,7 +46,7 @@ def __init__(
         self,
         project=None,
         dds_directory: pathlib.Path = None,
-        mount_dir: pathlib.Path = None,
+        staging_dir: pathlib.Path = None,
         method: str = None,
         authenticate: bool = True,
         method_check: bool = True,
@@ -75,8 +75,8 @@ def __init__(
                     f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{self.project}_"
                     f"{'upload' if self.method == 'put' else 'download'}"
                 )
-                if mount_dir:
-                    new_directory = mount_dir / default_dir
+                if staging_dir:
+                    new_directory = staging_dir / default_dir
                 elif dds_directory:
                     new_directory = dds_directory
                 else:
diff --git a/dds_cli/data_putter.py b/dds_cli/data_putter.py
index 6fb675c38..01b4592f6 100644
--- a/dds_cli/data_putter.py
+++ b/dds_cli/data_putter.py
@@ -43,7 +43,7 @@
 
 
 def put(
-    mount_dir,
+    staging_dir,
     project,
     source,
     source_path_file,
@@ -58,7 +58,7 @@ def put(
     """Handle upload of data."""
     # Initialize delivery - check user access etc
     with DataPutter(
-        mount_dir=mount_dir,
+        staging_dir=staging_dir,
         project=project,
         source=source,
         source_path_file=source_path_file,
@@ -201,7 +201,7 @@ class DataPutter(base.DDSBaseClass):
     def __init__(
         self,
         project: str = None,
-        mount_dir: pathlib.Path = None,
+        staging_dir: pathlib.Path = None,
         break_on_fail: bool = False,
         overwrite: bool = False,
         source: tuple = (),
@@ -216,7 +216,7 @@ def __init__(
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             project=project,
-            mount_dir=mount_dir,
+            staging_dir=staging_dir,
             method=method,
             no_prompt=no_prompt,
             token_path=token_path,

From 2c776d065fee2ceb5b894c41ff78879d77ddd487 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:03:13 +0100
Subject: [PATCH 24/39] staging location and staging dir created in data_putter

---
 dds_cli/__main__.py    | 14 ++++++++------
 dds_cli/base.py        |  2 +-
 dds_cli/data_putter.py | 21 +++++++++++++++++----
 3 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index a661c25fd..a759831b0 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -26,6 +26,7 @@
 # Own modules
 import dds_cli
 import dds_cli.account_manager
+import dds_cli.timestamp
 import dds_cli.unit_manager
 import dds_cli.motd_manager
 import dds_cli.superadmin_helper
@@ -1617,12 +1618,12 @@ def data_group_command(_):
 @data_group_command.command(name="put", no_args_is_help=True)
 # Options
 @click.option(
-    "--staging-dir",
-    "-sd",
+    "--staging-location",
+    "-sl",
     required=False,
     type=click_pathlib.Path(exists=False, file_okay=False, dir_okay=True, resolve_path=True),
     help=(
-        "New directory where the files will be mounted before upload "
+        "New directory where the files will be staged before upload "
         "and any error log files will be saved for a specific upload."
     ),
 )
@@ -1649,7 +1650,7 @@ def data_group_command(_):
 @click.pass_obj
 def put_data(
     click_ctx,
-    staging_dir,
+    staging_location,
     project,
     source,
     source_path_file,
@@ -1678,9 +1679,10 @@ def put_data(
     delivery to finish. To avoid that a delivery fails because of an expired token, we recommend
     reauthenticating yourself before uploading data.
     """
+    # Run upload
     try:
         dds_cli.data_putter.put(
-            staging_dir=staging_dir,
+            staging_location=staging_location,
             project=project,
             source=source,
             source_path_file=source_path_file,
@@ -1691,7 +1693,7 @@ def put_data(
             no_prompt=click_ctx.get("NO_PROMPT", False),
             token_path=click_ctx.get("TOKEN_PATH"),
             destination=destination,
-            default_log=click_ctx.get("DEFAULT_LOG"),
+            # default_log=click_ctx.get("DEFAULT_LOG"),
         )
     except (
         dds_cli.exceptions.AuthenticationError,
diff --git a/dds_cli/base.py b/dds_cli/base.py
index 124d127f6..1300eb9d0 100644
--- a/dds_cli/base.py
+++ b/dds_cli/base.py
@@ -70,7 +70,7 @@ def __init__(
             LOG.debug("Attempted operation: %s", self.method)
 
             # Use user defined destination if any specified
-            if self.method in DDS_DIR_REQUIRED_METHODS:
+            if self.method == "get":
                 default_dir = pathlib.Path(
                     f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{self.project}_"
                     f"{'upload' if self.method == 'put' else 'download'}"
diff --git a/dds_cli/data_putter.py b/dds_cli/data_putter.py
index 01b4592f6..0e347ed82 100644
--- a/dds_cli/data_putter.py
+++ b/dds_cli/data_putter.py
@@ -29,6 +29,7 @@
 from dds_cli.custom_decorators import verify_proceed, update_status, subpath_required
 
 import dds_cli
+import dds_cli.directory
 import dds_cli.utils
 
 ###############################################################################
@@ -43,7 +44,7 @@
 
 
 def put(
-    staging_dir,
+    staging_location,
     project,
     source,
     source_path_file,
@@ -58,7 +59,7 @@ def put(
     """Handle upload of data."""
     # Initialize delivery - check user access etc
     with DataPutter(
-        staging_dir=staging_dir,
+        staging_location=staging_location,
         project=project,
         source=source,
         source_path_file=source_path_file,
@@ -201,7 +202,7 @@ class DataPutter(base.DDSBaseClass):
     def __init__(
         self,
         project: str = None,
-        staging_dir: pathlib.Path = None,
+        staging_location: pathlib.Path = None,
         break_on_fail: bool = False,
         overwrite: bool = False,
         source: tuple = (),
@@ -213,10 +214,22 @@ def __init__(
         destination: str = None,
     ):
         """Handle actions regarding upload of data."""
+        # Define staging directory path
+        staging_dir: pathlib.Path = pathlib.Path(f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{project}_upload") 
+        if staging_location:
+            staging_dir = staging_location / staging_dir
+        else: 
+            staging_dir = pathlib.Path.cwd() / staging_dir
+
+        # Generate staging directory
+        self.temporary_directory = staging_dir
+        self.dds_directory = dds_cli.directory.DDSDirectory(path=staging_dir)
+        self.failed_delivery_log = self.dds_directory.directories["LOGS"] / pathlib.Path("dds_failed_delivery.json")
+
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             project=project,
-            staging_dir=staging_dir,
+            # staging_dir=staging_dir,
             method=method,
             no_prompt=no_prompt,
             token_path=token_path,

From c2a9dae660ef977a0fdd7d526ca16ff145859bc0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:13:55 +0100
Subject: [PATCH 25/39] staging dir is destination moved to datagetter

---
 dds_cli/base.py        | 38 +++++++++++++++++++-------------------
 dds_cli/data_getter.py | 13 ++++++++++++-
 2 files changed, 31 insertions(+), 20 deletions(-)

diff --git a/dds_cli/base.py b/dds_cli/base.py
index 1300eb9d0..bab3cc919 100644
--- a/dds_cli/base.py
+++ b/dds_cli/base.py
@@ -69,25 +69,25 @@ def __init__(
                 raise exceptions.InvalidMethodError(attempted_method=self.method)
             LOG.debug("Attempted operation: %s", self.method)
 
-            # Use user defined destination if any specified
-            if self.method == "get":
-                default_dir = pathlib.Path(
-                    f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{self.project}_"
-                    f"{'upload' if self.method == 'put' else 'download'}"
-                )
-                if staging_dir:
-                    new_directory = staging_dir / default_dir
-                elif dds_directory:
-                    new_directory = dds_directory
-                else:
-                    new_directory = pathlib.Path.cwd() / default_dir
-
-                self.temporary_directory = new_directory
-
-                self.dds_directory = dds_cli.directory.DDSDirectory(path=new_directory)
-                self.failed_delivery_log = self.dds_directory.directories["LOGS"] / pathlib.Path(
-                    "dds_failed_delivery.json"
-                )
+            # # Use user defined destination if any specified
+            # if self.method == "get":
+            #     default_dir = pathlib.Path(
+            #         f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{self.project}_"
+            #         f"{'upload' if self.method == 'put' else 'download'}"
+            #     )
+            #     if staging_dir:
+            #         new_directory = staging_dir / default_dir
+            #     elif dds_directory:
+            #         new_directory = dds_directory
+            #     else:
+            #         new_directory = pathlib.Path.cwd() / default_dir
+
+            #     self.temporary_directory = new_directory
+
+            #     self.dds_directory = dds_cli.directory.DDSDirectory(path=new_directory)
+            #     self.failed_delivery_log = self.dds_directory.directories["LOGS"] / pathlib.Path(
+            #         "dds_failed_delivery.json"
+            #     )
 
         # Keyboardinterrupt
         self.stop_doing = False
diff --git a/dds_cli/data_getter.py b/dds_cli/data_getter.py
index 78af7c373..0ae58aa04 100644
--- a/dds_cli/data_getter.py
+++ b/dds_cli/data_getter.py
@@ -54,10 +54,21 @@ def __init__(
         token_path: str = None,
     ):
         """Handle actions regarding downloading data."""
+        # Define staging directory path
+        staging_dir: pathlib.Path = pathlib.Path.cwd() / pathlib.Path(f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{project}_download") 
+        if destination:
+            staging_dir = destination
+        
+        # Generate staging directory
+        self.temporary_directory = staging_dir
+        self.dds_directory = dds_cli.directory.DDSDirectory(path=staging_dir)
+        self.failed_delivery_log = self.dds_directory.directories["LOGS"] / pathlib.Path("dds_failed_delivery.json")
+
+
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             project=project,
-            dds_directory=destination,
+            # dds_directory=destination,
             method=method,
             no_prompt=no_prompt,
             token_path=token_path,

From 4763fb0fb5da6eef285217138738c670a462f246 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:14:42 +0100
Subject: [PATCH 26/39] remove duplicate code in base class

---
 dds_cli/base.py | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/dds_cli/base.py b/dds_cli/base.py
index bab3cc919..33748e949 100644
--- a/dds_cli/base.py
+++ b/dds_cli/base.py
@@ -69,26 +69,6 @@ def __init__(
                 raise exceptions.InvalidMethodError(attempted_method=self.method)
             LOG.debug("Attempted operation: %s", self.method)
 
-            # # Use user defined destination if any specified
-            # if self.method == "get":
-            #     default_dir = pathlib.Path(
-            #         f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{self.project}_"
-            #         f"{'upload' if self.method == 'put' else 'download'}"
-            #     )
-            #     if staging_dir:
-            #         new_directory = staging_dir / default_dir
-            #     elif dds_directory:
-            #         new_directory = dds_directory
-            #     else:
-            #         new_directory = pathlib.Path.cwd() / default_dir
-
-            #     self.temporary_directory = new_directory
-
-            #     self.dds_directory = dds_cli.directory.DDSDirectory(path=new_directory)
-            #     self.failed_delivery_log = self.dds_directory.directories["LOGS"] / pathlib.Path(
-            #         "dds_failed_delivery.json"
-            #     )
-
         # Keyboardinterrupt
         self.stop_doing = False
 

From 13c19f5eff700a8e9ddc16598a9a77f8d4f3977b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:15:44 +0100
Subject: [PATCH 27/39] remove unused options

---
 dds_cli/base.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/dds_cli/base.py b/dds_cli/base.py
index 33748e949..a790ed4ed 100644
--- a/dds_cli/base.py
+++ b/dds_cli/base.py
@@ -45,8 +45,6 @@ class DDSBaseClass:
     def __init__(
         self,
         project=None,
-        dds_directory: pathlib.Path = None,
-        staging_dir: pathlib.Path = None,
         method: str = None,
         authenticate: bool = True,
         method_check: bool = True,

From 07507e8a76833175b7a21fc6fd120bb5bc706c70 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:17:37 +0100
Subject: [PATCH 28/39] remove commented option

---
 dds_cli/data_getter.py | 1 -
 dds_cli/data_putter.py | 1 -
 2 files changed, 2 deletions(-)

diff --git a/dds_cli/data_getter.py b/dds_cli/data_getter.py
index 0ae58aa04..6a796b96e 100644
--- a/dds_cli/data_getter.py
+++ b/dds_cli/data_getter.py
@@ -68,7 +68,6 @@ def __init__(
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             project=project,
-            # dds_directory=destination,
             method=method,
             no_prompt=no_prompt,
             token_path=token_path,
diff --git a/dds_cli/data_putter.py b/dds_cli/data_putter.py
index 0e347ed82..d21abbc3b 100644
--- a/dds_cli/data_putter.py
+++ b/dds_cli/data_putter.py
@@ -229,7 +229,6 @@ def __init__(
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             project=project,
-            # staging_dir=staging_dir,
             method=method,
             no_prompt=no_prompt,
             token_path=token_path,

From fdd7c36c51b6d3e5d5630176b62b4a0d18ed28ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:18:16 +0100
Subject: [PATCH 29/39] too many empty lines

---
 dds_cli/data_getter.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dds_cli/data_getter.py b/dds_cli/data_getter.py
index 6a796b96e..b8662f3aa 100644
--- a/dds_cli/data_getter.py
+++ b/dds_cli/data_getter.py
@@ -64,7 +64,6 @@ def __init__(
         self.dds_directory = dds_cli.directory.DDSDirectory(path=staging_dir)
         self.failed_delivery_log = self.dds_directory.directories["LOGS"] / pathlib.Path("dds_failed_delivery.json")
 
-
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             project=project,

From 2294a8f64ca1bf74a3ad5926e2ac42bceb147be8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:25:06 +0100
Subject: [PATCH 30/39] remove method check - unneccesary

---
 dds_cli/auth.py              | 1 -
 dds_cli/base.py              | 8 --------
 dds_cli/project_info.py      | 1 -
 dds_cli/project_status.py    | 2 --
 dds_cli/superadmin_helper.py | 1 -
 5 files changed, 13 deletions(-)

diff --git a/dds_cli/auth.py b/dds_cli/auth.py
index 94c0d4c9f..ee20a8e58 100644
--- a/dds_cli/auth.py
+++ b/dds_cli/auth.py
@@ -41,7 +41,6 @@ def __init__(
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             authenticate=authenticate,
-            method_check=False,
             force_renew_token=force_renew_token,
             token_path=token_path,
             totp=totp,
diff --git a/dds_cli/base.py b/dds_cli/base.py
index a790ed4ed..31bbd3cf3 100644
--- a/dds_cli/base.py
+++ b/dds_cli/base.py
@@ -47,7 +47,6 @@ def __init__(
         project=None,
         method: str = None,
         authenticate: bool = True,
-        method_check: bool = True,
         force_renew_token: bool = False,
         totp: str = None,
         no_prompt: bool = False,
@@ -56,17 +55,10 @@ def __init__(
     ):
         """Initialize Base class for authenticating the user and preparing for DDS action."""
         self.project = project
-        self.method_check = method_check
         self.method = method
         self.no_prompt = no_prompt
         self.token_path = token_path
 
-        if self.method_check:
-            # Get attempted operation e.g. put/ls/rm/get
-            if self.method not in DDS_METHODS:
-                raise exceptions.InvalidMethodError(attempted_method=self.method)
-            LOG.debug("Attempted operation: %s", self.method)
-
         # Keyboardinterrupt
         self.stop_doing = False
 
diff --git a/dds_cli/project_info.py b/dds_cli/project_info.py
index 26abcad68..1ca3677e0 100644
--- a/dds_cli/project_info.py
+++ b/dds_cli/project_info.py
@@ -39,7 +39,6 @@ def __init__(
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             no_prompt=no_prompt,
-            method_check=False,
             token_path=token_path,
         )
         self.project = project
diff --git a/dds_cli/project_status.py b/dds_cli/project_status.py
index 58bd17f2b..7e082ac43 100644
--- a/dds_cli/project_status.py
+++ b/dds_cli/project_status.py
@@ -44,7 +44,6 @@ def __init__(
         super().__init__(
             authenticate=authenticate,
             no_prompt=no_prompt,
-            method_check=False,
             token_path=token_path,
         )
         self.project = project
@@ -274,7 +273,6 @@ def __init__(
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             no_prompt=no_prompt,
-            method_check=False,
             token_path=token_path,
         )
 
diff --git a/dds_cli/superadmin_helper.py b/dds_cli/superadmin_helper.py
index 0961865d7..1ad194d34 100644
--- a/dds_cli/superadmin_helper.py
+++ b/dds_cli/superadmin_helper.py
@@ -45,7 +45,6 @@ def __init__(
         # Initiate DDSBaseClass to authenticate user
         super().__init__(
             authenticate=authenticate,
-            method_check=False,
             no_prompt=no_prompt,
             token_path=token_path,
         )

From 650f7280caff7907e2c7ba10947f3b5e9d67b8e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 13:43:00 +0100
Subject: [PATCH 31/39] clarify default log in context object

---
 dds_cli/__main__.py    | 60 +++++++++++-------------------------------
 dds_cli/data_putter.py |  1 +
 2 files changed, 17 insertions(+), 44 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index a759831b0..5a336e7ae 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -153,6 +153,9 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             f"[green]Current user:[/] [red]{username}", highlight=False
         )
 
+    # Create context object
+    click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path}
+
     if "--help" not in sys.argv:
         # Set the base logger to output DEBUG
         LOG.setLevel(logging.DEBUG)
@@ -168,47 +171,17 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             )
         )
 
-        # Only one can be used
-        if force_no_log and log_file:
-            LOG.warning(
-                "You have used both the '--log-file' and '--force-no-log' option, you can only use one."
-            )
-            sys.exit(1)
+        if log_file:
+            # Do not setup log at default location if log_file is specified
+            click_ctx.obj.update({"DEFAULT_LOG": False})
 
-        # # Don't log to file if this flag is used
-        # if not force_no_log:
-
-        #     # Get command and strip from leading - / --
-        #     subcommands: typing.List = [i.lstrip("-") for i in sys.argv[1::]]
-
-        #     # Check if put or get in subcommand
-        #     put_or_get: typing.List = [i for i in subcommands if i in ["put", "get"]]
-
-        #     # Always log to file if uploading or downloading
-        #     if put_or_get and not log_file:
-        #         try:
-        #             # Save logs to specific folder in home directory
-        #             dds_log_dir: str = pathlib.Path("~/dds-cli_logs/").expanduser()
-        #             dds_log_dir.mkdir(exist_ok=True)
-        #         except (OSError, RuntimeError) as err:
-        #             LOG.warning(
-        #                 "Could not create log directory '%s'. "
-        #                 "Logs will not be saved to file. \nDetails: %s",
-        #                 dds_log_dir,
-        #                 err,
-        #             )
-
-        #         # Format log file path name to contain command and timestamp
-        #         command_as_string: str = "dds_" + "_".join(subcommands).replace("/", "_").replace(
-        #             "\\", "_"
-        #         )
-        #         timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
-        #         log_file = str(
-        #             dds_log_dir / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")
-        #         )
-
-            # Set up logs to a file (if chosen, or by default above)
-            if log_file:
+            if force_no_log:
+                LOG.warning(
+                    "You have used both the '--log-file' and '--force-no-log' option, you can only use one."
+                )
+                sys.exit(1)
+            else:
+                # Set up logging to chosen file
                 log_fh = logging.FileHandler(log_file, encoding="utf-8")
                 log_fh.setLevel(logging.DEBUG)
                 log_fh.setFormatter(
@@ -218,9 +191,8 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                     )
                 )
                 LOG.addHandler(log_fh)
-
-        # Create context object
-        click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "DEFAULT_LOG": log_file != ""}
+        else: 
+            click_ctx.obj.update({"DEFAULT_LOG": True})
 
 
 # ************************************************************************************************ #
@@ -1693,7 +1665,7 @@ def put_data(
             no_prompt=click_ctx.get("NO_PROMPT", False),
             token_path=click_ctx.get("TOKEN_PATH"),
             destination=destination,
-            # default_log=click_ctx.get("DEFAULT_LOG"),
+            default_log=click_ctx.get("DEFAULT_LOG"),
         )
     except (
         dds_cli.exceptions.AuthenticationError,
diff --git a/dds_cli/data_putter.py b/dds_cli/data_putter.py
index d21abbc3b..cd7084ec9 100644
--- a/dds_cli/data_putter.py
+++ b/dds_cli/data_putter.py
@@ -212,6 +212,7 @@ def __init__(
         no_prompt: bool = False,
         token_path: str = None,
         destination: str = None,
+        default_log: str = None,
     ):
         """Handle actions regarding upload of data."""
         # Define staging directory path

From f187ecb7c25e9eac8eebb9ffc48b7c49d3e41308 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Tue, 25 Mar 2025 14:26:54 +0100
Subject: [PATCH 32/39] start logging to deault file

---
 dds_cli/__main__.py    |  4 ++--
 dds_cli/data_putter.py |  9 +++++++--
 dds_cli/directory.py   | 35 ++++++++++++++++++++++++++++++++++-
 3 files changed, 43 insertions(+), 5 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 5a336e7ae..4b39d386f 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -154,8 +154,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
         )
 
     # Create context object
-    click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path}
-
+    click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "COMMAND": [i.lstrip("-") for i in sys.argv[1::]]}
     if "--help" not in sys.argv:
         # Set the base logger to output DEBUG
         LOG.setLevel(logging.DEBUG)
@@ -1666,6 +1665,7 @@ def put_data(
             token_path=click_ctx.get("TOKEN_PATH"),
             destination=destination,
             default_log=click_ctx.get("DEFAULT_LOG"),
+            command=click_ctx.get("COMMAND"),
         )
     except (
         dds_cli.exceptions.AuthenticationError,
diff --git a/dds_cli/data_putter.py b/dds_cli/data_putter.py
index cd7084ec9..b593823a8 100644
--- a/dds_cli/data_putter.py
+++ b/dds_cli/data_putter.py
@@ -55,6 +55,8 @@ def put(
     no_prompt,
     token_path,
     destination,
+    default_log,
+    command,
 ):
     """Handle upload of data."""
     # Initialize delivery - check user access etc
@@ -69,6 +71,8 @@ def put(
         no_prompt=no_prompt,
         token_path=token_path,
         destination=destination,
+        default_log=default_log,
+        command=command,
     ) as putter:
         # Progress object to keep track of progress tasks
         with Progress(
@@ -212,7 +216,8 @@ def __init__(
         no_prompt: bool = False,
         token_path: str = None,
         destination: str = None,
-        default_log: str = None,
+        default_log: bool = True,
+        command: list = [],
     ):
         """Handle actions regarding upload of data."""
         # Define staging directory path
@@ -224,7 +229,7 @@ def __init__(
 
         # Generate staging directory
         self.temporary_directory = staging_dir
-        self.dds_directory = dds_cli.directory.DDSDirectory(path=staging_dir)
+        self.dds_directory = dds_cli.directory.DDSDirectory(path=staging_dir, default_log=default_log, command=command)
         self.failed_delivery_log = self.dds_directory.directories["LOGS"] / pathlib.Path("dds_failed_delivery.json")
 
         # Initiate DDSBaseClass to authenticate user
diff --git a/dds_cli/directory.py b/dds_cli/directory.py
index a82c9500e..1a25619e3 100644
--- a/dds_cli/directory.py
+++ b/dds_cli/directory.py
@@ -9,6 +9,7 @@
 import logging
 import pathlib
 import sys
+from datetime import datetime
 
 # Installed
 import rich.markup
@@ -29,16 +30,19 @@
 class DDSDirectory:
     """Data Delivery System directory class."""
 
-    def __init__(self, path=pathlib.Path, add_file_dir: bool = True):
+    def __init__(self, path=pathlib.Path, add_file_dir: bool = True, default_log: bool = True, command: list = []):
+        # The following subdirs should be included in staging directory
         dirs = {
             "ROOT": path,
             "META": path / pathlib.Path("meta/"),
             "LOGS": path / pathlib.Path("logs/"),
         }
 
+        # files subdir only relevant for some commands 
         if add_file_dir:
             dirs["FILES"] = path / pathlib.Path("files/")
 
+        # Create staging directory and subdirectories
         for directory in dirs.values():
             try:
                 directory.mkdir(parents=True, exist_ok=False)
@@ -54,3 +58,32 @@ def __init__(self, path=pathlib.Path, add_file_dir: bool = True):
                     )
 
         self.directories = dirs
+
+        if default_log:
+            # Include command in log file name
+            if not command:
+                command_as_string = "command_not_found"
+            else:
+                # Format log file path name to contain command and timestamp
+                command_as_string: str = "dds_" + "_".join(command).replace("/", "_").replace(
+                    "\\", "_"
+                )
+            
+            # Include time stamp in file name
+            timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
+
+            # Final log name
+            log_file = str(
+                dirs["LOGS"] / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")
+            )
+
+            # Start logging to file 
+            log_fh = logging.FileHandler(log_file, encoding="utf-8")
+            log_fh.setLevel(logging.DEBUG)
+            log_fh.setFormatter(
+                logging.Formatter(
+                    fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
+                    datefmt="%Y-%m-%d %H:%M:%S",
+                )
+            )
+            LOG.addHandler(log_fh)
\ No newline at end of file

From 73c627efd108789f21a083c07d76506442867460 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Wed, 26 Mar 2025 14:14:44 +0100
Subject: [PATCH 33/39] save command to log file as first item

---
 dds_cli/directory.py | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/dds_cli/directory.py b/dds_cli/directory.py
index 1a25619e3..a43711b05 100644
--- a/dds_cli/directory.py
+++ b/dds_cli/directory.py
@@ -60,21 +60,32 @@ def __init__(self, path=pathlib.Path, add_file_dir: bool = True, default_log: bo
         self.directories = dirs
 
         if default_log:
+            # Do not include source in file name
+            # Could e.g. be a very long file name --> errors
+            command_for_file_name = command.copy()
+            source_options: typing.List = ["-s, --source", "-spf", "--source-path-file"]
+            for s in source_options:
+                index = command_for_file_name.index(s)
+                command_for_file_name[index+1] = "x"
+
             # Include command in log file name
             if not command:
                 command_as_string = "command_not_found"
             else:
                 # Format log file path name to contain command and timestamp
-                command_as_string: str = "dds_" + "_".join(command).replace("/", "_").replace(
+                command_as_string_file: str = "dds_" + "_".join(command_for_file_name).replace("/", "_").replace(
                     "\\", "_"
                 )
-            
+                command_as_string: str = "dds_" + "_".join(command).replace("/", "_").replace(
+                    "\\", "_"
+                )      
+              
             # Include time stamp in file name
             timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
 
             # Final log name
             log_file = str(
-                dirs["LOGS"] / pathlib.Path(command_as_string + "_" + timestamp_string + ".log")
+                dirs["LOGS"] / pathlib.Path(command_as_string_file + "_" + timestamp_string + ".log")
             )
 
             # Start logging to file 
@@ -86,4 +97,6 @@ def __init__(self, path=pathlib.Path, add_file_dir: bool = True, default_log: bo
                     datefmt="%Y-%m-%d %H:%M:%S",
                 )
             )
-            LOG.addHandler(log_fh)
\ No newline at end of file
+            LOG.addHandler(log_fh)
+
+            LOG.info("Command: %s", command_as_string)
\ No newline at end of file

From 93ebdbf44c51134572f87f0c5d9d84aa819ac080 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 27 Mar 2025 08:28:15 +0100
Subject: [PATCH 34/39] remove imports

---
 dds_cli/__main__.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 4b39d386f..40453398b 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -9,8 +9,6 @@
 import itertools
 import logging
 import sys
-import typing
-from datetime import datetime
 
 # Installed
 import pathlib
@@ -26,7 +24,6 @@
 # Own modules
 import dds_cli
 import dds_cli.account_manager
-import dds_cli.timestamp
 import dds_cli.unit_manager
 import dds_cli.motd_manager
 import dds_cli.superadmin_helper

From d47c385a9496dd00f63fd0904e9670cac924446a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 27 Mar 2025 08:32:31 +0100
Subject: [PATCH 35/39] comment regarding command

---
 dds_cli/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 40453398b..483edb72d 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -150,7 +150,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             f"[green]Current user:[/] [red]{username}", highlight=False
         )
 
-    # Create context object
+    # Create context object and save command to context
     click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "COMMAND": [i.lstrip("-") for i in sys.argv[1::]]}
     if "--help" not in sys.argv:
         # Set the base logger to output DEBUG

From bdfe5b4ca2774f18cfeb18276d6d1b11d34d9ee1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 27 Mar 2025 08:33:02 +0100
Subject: [PATCH 36/39] comment regarding command

---
 dds_cli/__main__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 483edb72d..da6bbe99c 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -150,7 +150,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             f"[green]Current user:[/] [red]{username}", highlight=False
         )
 
-    # Create context object and save command to context
+    # Create context object and save command to context - exclude the dds or executable name
     click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "COMMAND": [i.lstrip("-") for i in sys.argv[1::]]}
     if "--help" not in sys.argv:
         # Set the base logger to output DEBUG

From 972bb1573a5912fa5b1a83eaf1ed19307bbed015 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 27 Mar 2025 09:12:06 +0100
Subject: [PATCH 37/39] add utils function for setting up logging to file

---
 dds_cli/__init__.py  |  2 --
 dds_cli/__main__.py  | 17 ++++-------------
 dds_cli/directory.py | 27 ++++++++++++++++-----------
 dds_cli/utils.py     | 12 ++++++++++++
 4 files changed, 32 insertions(+), 26 deletions(-)

diff --git a/dds_cli/__init__.py b/dds_cli/__init__.py
index d7cdafa51..b7b1bcff6 100644
--- a/dds_cli/__init__.py
+++ b/dds_cli/__init__.py
@@ -158,7 +158,6 @@ class FileSegment:
     SEGMENT_SIZE_RAW = 65536  # Size of chunk to read from raw file
     SEGMENT_SIZE_CIPHER = SEGMENT_SIZE_RAW + 16  # Size of chunk to read from encrypted file
 
-
 # Custom styles for questionary
 dds_questionary_styles = prompt_toolkit.styles.Style(
     [
@@ -181,7 +180,6 @@ class FileSegment:
 # Determine if the user is on an old terminal without proper Unicode support
 dds_on_legacy_console = rich.console.detect_legacy_windows()
 
-
 # Required to make the standalone executables build with PyInstaller work.
 if __name__ == "__main__":
     from dds_cli.__main__ import dds_main
diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index da6bbe99c..31a9ad6ac 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -150,8 +150,8 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             f"[green]Current user:[/] [red]{username}", highlight=False
         )
 
-    # Create context object and save command to context - exclude the dds or executable name
-    click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "COMMAND": [i.lstrip("-") for i in sys.argv[1::]]}
+    # Create context object and save command to context
+    click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path, "COMMAND": sys.argv}
     if "--help" not in sys.argv:
         # Set the base logger to output DEBUG
         LOG.setLevel(logging.DEBUG)
@@ -177,20 +177,11 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 )
                 sys.exit(1)
             else:
-                # Set up logging to chosen file
-                log_fh = logging.FileHandler(log_file, encoding="utf-8")
-                log_fh.setLevel(logging.DEBUG)
-                log_fh.setFormatter(
-                    logging.Formatter(
-                        fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
-                        datefmt="%Y-%m-%d %H:%M:%S",
-                    )
-                )
-                LOG.addHandler(log_fh)
+                file_handler = dds_cli.utils.setup_logging_to_file(logger=LOG, filename=log_file)
+                LOG.addHandler(file_handler)
         else: 
             click_ctx.obj.update({"DEFAULT_LOG": True})
 
-
 # ************************************************************************************************ #
 # MAIN DDS COMMANDS ************************************************************ MAIN DDS COMMANDS #
 # ************************************************************************************************ #
diff --git a/dds_cli/directory.py b/dds_cli/directory.py
index a43711b05..1a821f864 100644
--- a/dds_cli/directory.py
+++ b/dds_cli/directory.py
@@ -10,11 +10,13 @@
 import pathlib
 import sys
 from datetime import datetime
+import typing
 
 # Installed
 import rich.markup
 
 # Own modules
+import dds_cli.utils
 
 ###############################################################################
 # START LOGGING CONFIG ################################# START LOGGING CONFIG #
@@ -65,8 +67,9 @@ def __init__(self, path=pathlib.Path, add_file_dir: bool = True, default_log: bo
             command_for_file_name = command.copy()
             source_options: typing.List = ["-s, --source", "-spf", "--source-path-file"]
             for s in source_options:
-                index = command_for_file_name.index(s)
-                command_for_file_name[index+1] = "x"
+                if s in command_for_file_name:
+                    index = command_for_file_name.index(s)
+                    command_for_file_name[index+1] = "x"
 
             # Include command in log file name
             if not command:
@@ -89,14 +92,16 @@ def __init__(self, path=pathlib.Path, add_file_dir: bool = True, default_log: bo
             )
 
             # Start logging to file 
-            log_fh = logging.FileHandler(log_file, encoding="utf-8")
-            log_fh.setLevel(logging.DEBUG)
-            log_fh.setFormatter(
-                logging.Formatter(
-                    fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
-                    datefmt="%Y-%m-%d %H:%M:%S",
-                )
-            )
-            LOG.addHandler(log_fh)
+            file_handler = dds_cli.utils.setup_logging_to_file(logger=LOG, filename=log_file)
+            LOG.addHandler(file_handler)
+            # log_fh = logging.FileHandler(log_file, encoding="utf-8")
+            # log_fh.setLevel(logging.DEBUG)
+            # log_fh.setFormatter(
+            #     logging.Formatter(
+            #         fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
+            #         datefmt="%Y-%m-%d %H:%M:%S",
+            #     )
+            # )
+            # LOG.addHandler(log_fh)
 
             LOG.info("Command: %s", command_as_string)
\ No newline at end of file
diff --git a/dds_cli/utils.py b/dds_cli/utils.py
index 1d6dc4b8c..d6eb069e6 100644
--- a/dds_cli/utils.py
+++ b/dds_cli/utils.py
@@ -5,6 +5,7 @@
 import typing
 import http
 from typing import Dict, List, Union
+import logging
 
 import requests
 import rich.console
@@ -81,6 +82,17 @@ def format(num: Union[int, float], metric: bool = False, precision: int = 1) ->
 
 # Functions
 
+def setup_logging_to_file(logger: logging.Logger, filename: str) -> logging.FileHandler:
+    """Setup logging to specific file."""
+    log_fh = logging.FileHandler(filename=filename, encoding="utf-8")
+    log_fh.setLevel(logging.DEBUG)
+    log_fh.setFormatter(
+        logging.Formatter(
+            fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
+            datefmt="%Y-%m-%d %H:%M:%S",
+        )
+    )
+    return log_fh
 
 def sort_items(items: list, sort_by: str) -> list:
     """Sort list of dicts according to specified key."""

From 065577cab001e50392da9d32894aa3708c3247f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 27 Mar 2025 11:26:50 +0100
Subject: [PATCH 38/39] logging started, but doesn't log from all modules

---
 dds_cli/__main__.py  | 14 ++++++++++-
 dds_cli/directory.py | 55 +++++++++++++++++++-------------------------
 dds_cli/utils.py     |  2 +-
 3 files changed, 38 insertions(+), 33 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 31a9ad6ac..04e5df8bc 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -24,6 +24,7 @@
 # Own modules
 import dds_cli
 import dds_cli.account_manager
+import dds_cli.directory
 import dds_cli.unit_manager
 import dds_cli.motd_manager
 import dds_cli.superadmin_helper
@@ -177,7 +178,7 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 )
                 sys.exit(1)
             else:
-                file_handler = dds_cli.utils.setup_logging_to_file(logger=LOG, filename=log_file)
+                file_handler = dds_cli.utils.setup_logging_to_file(filename=log_file)
                 LOG.addHandler(file_handler)
         else: 
             click_ctx.obj.update({"DEFAULT_LOG": True})
@@ -1638,6 +1639,17 @@ def put_data(
     delivery to finish. To avoid that a delivery fails because of an expired token, we recommend
     reauthenticating yourself before uploading data.
     """
+    # # Setup logging
+    # # Define staging directory path
+    # staging_dir: pathlib.Path = pathlib.Path(f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{project}_upload") 
+    # if staging_location:
+    #     staging_dir = staging_location / staging_dir
+    # else: 
+    #     staging_dir = pathlib.Path.cwd() / staging_dir
+
+    # # Generate staging directory
+    # stag_dir_obj = dds_cli.directory.DDSDirectory(path=staging_dir, default_log=click_ctx.get("DEFAULT_LOG"), command=click_ctx.get("COMMAND"))
+
     # Run upload
     try:
         dds_cli.data_putter.put(
diff --git a/dds_cli/directory.py b/dds_cli/directory.py
index 1a821f864..9450128ec 100644
--- a/dds_cli/directory.py
+++ b/dds_cli/directory.py
@@ -62,46 +62,39 @@ def __init__(self, path=pathlib.Path, add_file_dir: bool = True, default_log: bo
         self.directories = dirs
 
         if default_log:
+            default_log_name = self.get_default_log_name(command=command if command else ["commandnotfound"])
+            
+            # Start logging to file 
+            file_handler = dds_cli.utils.setup_logging_to_file(filename=default_log_name)
+            LOG.addHandler(file_handler)
+            LOG.debug("Command: %s", " ".join(command))
+
+    def get_default_log_name(self, command: list):
+            # Include command in log file name
             # Do not include source in file name
             # Could e.g. be a very long file name --> errors
             command_for_file_name = command.copy()
-            source_options: typing.List = ["-s, --source", "-spf", "--source-path-file"]
+            source_options: typing.List = ["-s", "--source", "-spf", "--source-path-file"]
             for s in source_options:
-                if s in command_for_file_name:
-                    index = command_for_file_name.index(s)
-                    command_for_file_name[index+1] = "x"
+                indexes = [i for i, x in enumerate(command_for_file_name) if x == s]
+                for i in indexes:
+                    command_for_file_name[i+1] = "x"
+
+            # Remove leading - from options
+            command_for_file_name = [i.lstrip("-") for i in command_for_file_name[1::]]
+
+            # Format log file path name to contain command
+            command_for_file_name: str = "dds_" + "_".join(command_for_file_name).replace("/", "_").replace(
+                "\\", "_"
+            )
 
-            # Include command in log file name
-            if not command:
-                command_as_string = "command_not_found"
-            else:
-                # Format log file path name to contain command and timestamp
-                command_as_string_file: str = "dds_" + "_".join(command_for_file_name).replace("/", "_").replace(
-                    "\\", "_"
-                )
-                command_as_string: str = "dds_" + "_".join(command).replace("/", "_").replace(
-                    "\\", "_"
-                )      
-              
             # Include time stamp in file name
             timestamp_string: str = datetime.now().strftime("%Y%m%d-%H%M%S")
 
             # Final log name
             log_file = str(
-                dirs["LOGS"] / pathlib.Path(command_as_string_file + "_" + timestamp_string + ".log")
+                self.directories["LOGS"] / pathlib.Path(command_for_file_name + "_" + timestamp_string + ".log")
             )
 
-            # Start logging to file 
-            file_handler = dds_cli.utils.setup_logging_to_file(logger=LOG, filename=log_file)
-            LOG.addHandler(file_handler)
-            # log_fh = logging.FileHandler(log_file, encoding="utf-8")
-            # log_fh.setLevel(logging.DEBUG)
-            # log_fh.setFormatter(
-            #     logging.Formatter(
-            #         fmt="[%(asctime)s] %(name)-15s %(lineno)-5s [%(levelname)-7s]  %(message)s",
-            #         datefmt="%Y-%m-%d %H:%M:%S",
-            #     )
-            # )
-            # LOG.addHandler(log_fh)
-
-            LOG.info("Command: %s", command_as_string)
\ No newline at end of file
+            return log_file
+    
\ No newline at end of file
diff --git a/dds_cli/utils.py b/dds_cli/utils.py
index d6eb069e6..840600d23 100644
--- a/dds_cli/utils.py
+++ b/dds_cli/utils.py
@@ -82,7 +82,7 @@ def format(num: Union[int, float], metric: bool = False, precision: int = 1) ->
 
 # Functions
 
-def setup_logging_to_file(logger: logging.Logger, filename: str) -> logging.FileHandler:
+def setup_logging_to_file(filename: str) -> logging.FileHandler:
     """Setup logging to specific file."""
     log_fh = logging.FileHandler(filename=filename, encoding="utf-8")
     log_fh.setLevel(logging.DEBUG)

From 0b15ae0edf4ba1a2aff6d77c3f1c36818dd0d3a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?=
 <i-oden@users.noreply.github.com>
Date: Thu, 24 Apr 2025 09:02:17 +0200
Subject: [PATCH 39/39] force-no-log to work on its own

---
 dds_cli/__main__.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py
index 04e5df8bc..16a552bf5 100644
--- a/dds_cli/__main__.py
+++ b/dds_cli/__main__.py
@@ -180,8 +180,14 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
             else:
                 file_handler = dds_cli.utils.setup_logging_to_file(filename=log_file)
                 LOG.addHandler(file_handler)
-        else: 
+        else:
             click_ctx.obj.update({"DEFAULT_LOG": True})
+            if force_no_log:
+                LOG.warning(
+                    "You have chosen the '--force-no-log' option; No log will be generated for this run."
+                )
+                click_ctx.obj.update({"DEFAULT_LOG": False})
+
 
 # ************************************************************************************************ #
 # MAIN DDS COMMANDS ************************************************************ MAIN DDS COMMANDS #
@@ -1641,10 +1647,10 @@ def put_data(
     """
     # # Setup logging
     # # Define staging directory path
-    # staging_dir: pathlib.Path = pathlib.Path(f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{project}_upload") 
+    # staging_dir: pathlib.Path = pathlib.Path(f"DataDelivery_{dds_cli.timestamp.TimeStamp().timestamp}_{project}_upload")
     # if staging_location:
     #     staging_dir = staging_location / staging_dir
-    # else: 
+    # else:
     #     staging_dir = pathlib.Path.cwd() / staging_dir
 
     # # Generate staging directory