From 38f37be611a6fd65622d3a9d694a74e221fad90e Mon Sep 17 00:00:00 2001
From: Nana Mensah <Nana.mensah1@nhs.net>
Date: Mon, 28 Oct 2019 10:59:35 +0000
Subject: [PATCH] Add minumum age option and set default age to 14. Add usage
 to readme.

---
 wscleaner/README.md         | 24 ++++++++++++++++++++++--
 wscleaner/wscleaner/lib.py  |  3 +--
 wscleaner/wscleaner/main.py |  3 ++-
 3 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/wscleaner/README.md b/wscleaner/README.md
index d470659..515e4cb 100644
--- a/wscleaner/README.md
+++ b/wscleaner/README.md
@@ -18,11 +18,31 @@ pip install workstation_housekeeping/wscleaner
 wscleaner --version # Print version number
 ```
 
-## Usage
+## Quickstart
 
 ```bash
 wscleaner --set-key DNA_NEXUS_KEY # Cache dnanexus api key
-wscleaner ROOT_DIRECTORY --logfile LOGFILE_PATH
+wscleaner ROOT_DIRECTORY
+```
+
+## Usage
+
+```
+wscleaner   [-h] [--set-key SET_KEY] [--print-key] [--dry-run]
+            [--logfile LOGFILE] [--min-age MIN_AGE] [--version]
+            root
+
+positional arguments:
+  root               A directory containing runfolders to process
+
+optional arguments:
+  -h, --help         show this help message and exit
+  --set-key SET_KEY  Cache a DNA Nexus API key
+  --print-key        Print the cached DNA Nexus API key
+  --dry-run          Perform a dry run without deleting files
+  --logfile LOGFILE  A path for the application logfile
+  --min-age MIN_AGE  The age (days) a runfolder must be to be deleted
+  --version          Print version
 ```
 
 ## Test
diff --git a/wscleaner/wscleaner/lib.py b/wscleaner/wscleaner/lib.py
index 72c8804..7fc1040 100644
--- a/wscleaner/wscleaner/lib.py
+++ b/wscleaner/wscleaner/lib.py
@@ -174,7 +174,7 @@ def __validate(self, directory):
             self.logger.error(f'Directory does not exist: {directory}', exc_info=True)
             raise
 
-    def find_runfolders(self, min_age=14):
+    def find_runfolders(self, min_age=None):
         """Search the parent directory for subdirectories containing fastq.gz files.
         Args:
             min_age(int): Minimum age in days of runfolders returned.
@@ -211,7 +211,6 @@ def check_logfiles(self, runfolder):
     
     def delete(self, runfolder):
         """Delete the local runfolder from the root directory and append name to self.deleted."""
-        print(self.__dry_run)
         if self.__dry_run:
             self.logger.info(f'DRY RUN DELETE {runfolder.name}')
         else:
diff --git a/wscleaner/wscleaner/main.py b/wscleaner/wscleaner/main.py
index af2110a..cf8a51e 100644
--- a/wscleaner/wscleaner/main.py
+++ b/wscleaner/wscleaner/main.py
@@ -34,6 +34,7 @@ def cli_parser():
     parser.add_argument('--dry-run', help='Perform a dry run without deleting files', action='store_true', default=False)
     parser.add_argument('root', help='A directory containing runfolders to process')
     parser.add_argument('--logfile', help='A path for the application logfile', default='mokaguys_logger.log')
+    parser.add_argument('--min-age', help='The age (days) a runfolder must be to be deleted', type=int, default=14)
     # Get version from setup.py as version CLI response
     version_number = pkg_resources.require("wscleaner")[0].version
     parser.add_argument('--version', help='Print version', action='version', version=f"wscleaner v{version_number}")
@@ -56,7 +57,7 @@ def main():
     # If dry-run CLI flag is given, no directories are deleted by the runfolder manager.
     RFM = RunFolderManager(args.root, dry_run=args.dry_run)
     logger.info(f'Root directory {args.root}')
-    local_runfolders = RFM.find_runfolders(min_age=0)
+    local_runfolders = RFM.find_runfolders(min_age=args.min_age)
     logger.debug(f'Found local runfolders: {[rf.name for rf in local_runfolders]}')
 
     for runfolder in local_runfolders: