Merge pull request #2543 from antgonza/split-qiita-cron-job

split qiita cron job

Author: Tomasz

.travis.yml

@@ -73,8 +73,8 @@ script:
   - nosetests $COVER_PACKAGE --with-doctest --with-coverage --with-timer -v --cover-package=$COVER_PACKAGE
   - kill $QIITA_PID
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then test_data_studies/commands.sh ; fi
-  - if [ ${TEST_ADD_STUDIES} == "True" ]; then qiita-cron-job ; fi
-  - flake8 qiita_* setup.py scripts/*
+  - if [ ${TEST_ADD_STUDIES} == "True" ]; then all-qiita-cron-job; fi
+  - flake8 qiita_* setup.py scripts/qiita*
   - qiita pet webserver
 addons:
   postgresql: "9.3"

scripts/all-qiita-cron-job

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+qiita-cron-job empty_trash_upload_folder
+qiita-cron-job generate_biom_and_metadata_release
+qiita-cron-job purge_filepaths
+qiita-cron-job purge_files_from_filesystem
+qiita-cron-job update_redis_stats

scripts/qiita-cron-job

@@ -8,31 +8,56 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
+import click
+
 from qiita_db.util import (
-    purge_filepaths, empty_trash_upload_folder, purge_files_from_filesystem)
+    purge_filepaths as qiita_purge_filepaths,
+    empty_trash_upload_folder as qiita_empty_trash_upload_folder,
+    purge_files_from_filesystem as qiita_purge_files_from_filesystem)
 from qiita_db.meta_util import (
-    update_redis_stats, generate_biom_and_metadata_release)
+    update_redis_stats as qiita_update_redis_stats,
+    generate_biom_and_metadata_release as
+    qiita_generate_biom_and_metadata_release)
 
 
-# This script will perform these jobs:
-# 1. purge_filepaths: remove files from that are leftover in the
-#    qiita.filepath and are present in the filesystem
-# 2. empty_trash_upload_folder: remove files that are present in the trash
-#    of the upload folders
-# 3. update_redis_stats: updates the redis stats information
-# 4. generate public releases of biom tables and metadata
-#
-# Note that is responsability of the Qiita install system admin to add to a
-# cron job this script and responsible to define how often it should run
+@click.group()
+def commands():
+    pass
+
+
+@commands.command()
+@click.option('--remove/--no-remove', default=True,
+              help='remove any filepaths from the qiita.filepath table that '
+              'are not linked to any other table')
+def purge_filepaths(remove):
+    qiita_purge_filepaths(remove)
+
+
+@commands.command()
+@click.option('--remove/--no-remove', default=False,
+              help='check the filesystem mounts and remove files not used in '
+              'the database')
+def purge_files_from_filesystem(remove):
+    qiita_purge_files_from_filesystem(remove)
+
+
+@commands.command()
+@click.option('--remove/--no-remove', default=True,
+              help='remove files from the trash folder within the upload '
+              'folders')
+def empty_trash_upload_folder(remove):
+    qiita_empty_trash_upload_folder(remove)
+
+
+@commands.command()
+def update_redis_stats():
+    qiita_update_redis_stats()
 
 
-def main():
-    purge_filepaths(True)
-    purge_files_from_filesystem(False)
-    empty_trash_upload_folder(True)
-    update_redis_stats()
-    generate_biom_and_metadata_release('public')
+@commands.command()
+def generate_biom_and_metadata_release():
+    qiita_generate_biom_and_metadata_release('public')
 
 
 if __name__ == "__main__":
-    main()
+    commands()