DOESN'T WORK -- Log file created by default for uploads and downloads

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))

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

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
@@ -107,7 +108,19 @@
 @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 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,
+)
 @click.option(
     "--no-prompt", is_flag=True, default=False, help="Run without any interactive features."
 )
@@ -121,7 +134,7 @@
     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.
@@ -138,6 +151,8 @@ def dds_main(click_ctx, verbose, log_file, no_prompt, token_path):
             f"[green]Current user:[/] [red]{username}", highlight=False
         )
 
+    # 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)
@@ -153,20 +168,25 @@ def dds_main(click_ctx, verbose, 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",
-                )
-            )
-            LOG.addHandler(log_fh)
+            # Do not setup log at default location if log_file is specified
+            click_ctx.obj.update({"DEFAULT_LOG": False})
 
-        # Create context object
-        click_ctx.obj = {"NO_PROMPT": no_prompt, "TOKEN_PATH": token_path}
+            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:
+                file_handler = dds_cli.utils.setup_logging_to_file(filename=log_file)
+                LOG.addHandler(file_handler)
+        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})
 
 
 # ************************************************************************************************ #
@@ -1564,12 +1584,12 @@ def data_group_command(_):
 @data_group_command.command(name="put", no_args_is_help=True)
 # Options
 @click.option(
-    "--mount-dir",
-    "-md",
+    "--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."
     ),
 )
@@ -1596,7 +1616,7 @@ def data_group_command(_):
 @click.pass_obj
 def put_data(
     click_ctx,
-    mount_dir,
+    staging_location,
     project,
     source,
     source_path_file,
@@ -1625,9 +1645,21 @@ 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(
-            mount_dir=mount_dir,
+            staging_location=staging_location,
             project=project,
             source=source,
             source_path_file=source_path_file,
@@ -1638,6 +1670,8 @@ 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"),
+            command=click_ctx.get("COMMAND"),
         )
     except (
         dds_cli.exceptions.AuthenticationError,

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,

dds_cli/base.py

@@ -45,11 +45,8 @@ class DDSBaseClass:
     def __init__(
         self,
         project=None,
-        dds_directory: pathlib.Path = None,
-        mount_dir: pathlib.Path = None,
         method: str = None,
         authenticate: bool = True,
-        method_check: bool = True,
         force_renew_token: bool = False,
         totp: str = None,
         no_prompt: bool = False,
@@ -58,37 +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)
-
-            # Use user defined destination if any specified
-            if self.method in DDS_DIR_REQUIRED_METHODS:
-                default_dir = pathlib.Path(
-                    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
-                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
 

dds_cli/data_getter.py

@@ -54,10 +54,19 @@ 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,
             method=method,
             no_prompt=no_prompt,
             token_path=token_path,

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(
-    mount_dir,
+    staging_location,
     project,
     source,
     source_path_file,
@@ -54,11 +55,13 @@ def put(
     no_prompt,
     token_path,
     destination,
+    default_log,
+    command,
 ):
     """Handle upload of data."""
     # Initialize delivery - check user access etc
     with DataPutter(
-        mount_dir=mount_dir,
+        staging_location=staging_location,
         project=project,
         source=source,
         source_path_file=source_path_file,
@@ -68,6 +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(
@@ -201,7 +206,7 @@ class DataPutter(base.DDSBaseClass):
     def __init__(
         self,
         project: str = None,
-        mount_dir: pathlib.Path = None,
+        staging_location: pathlib.Path = None,
         break_on_fail: bool = False,
         overwrite: bool = False,
         source: tuple = (),
@@ -211,12 +216,25 @@ def __init__(
         no_prompt: bool = False,
         token_path: str = None,
         destination: str = None,
+        default_log: bool = True,
+        command: list = [],
     ):
         """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, 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
         super().__init__(
             project=project,
-            mount_dir=mount_dir,
             method=method,
             no_prompt=no_prompt,
             token_path=token_path,