Release v0.4.0 (#57)

* testing

* updated README

* added hourly restart option

* fixed hourly update task

* fixed issue with hourly_restart option

* added check to remove trailing slash from directory variables. update docs

* added monitored_diretories example

* fixed doc, corrected cron_log_folder in Example playbook

* added missing print call

* changed exit to use time vs previous iteration count

* added message for start time

* fixed adding start logging

* adding arguments to control UA logging

* removed waiting period check for incomplete uploads

* updated comment

* fixed optional ua args for logging

* changed hourly restart logic

* corrected novaseq conditional

* added logging for number of tar files and size for this upload

* adding test samples

* updated instructions and test.yml to work directly with run folders in test

* XVG-8595 trigger hourly interrupt when too many modified files are found (#52)

* add comment for XVG-8595

* remove unsused comment

* add more comment

* refactor create_tar_file variable and argument names

* fix 5 hours delay (testing purpose)

typo

bugfix for always true condition

add flag --duration-threshold to gracefully exit the program when the upload duration exceeds the threshold limit

Set --duration-threshold=60 (secs) when args.hourly_restart=False

add e2e docker test

typo make target

update e2e run script

Revert previous additional codes on flag --duration-threshold for dx_sync_directory

revert

add env to cron dev mode

update

update

update

update

update

update

update

update

update

pass envs to subprocess calls

explicitly export env SYNC_DURATION_THRESHOLD for mode=dev

update

update

* Add description for test docker image

* update docker file and minor changes

* typo

* minor updates

update

update

* update base docker image for e2e

* update humanfriendly time log

* update docker image description

* update

* update docs and dockerfiles

* add hourly_restart check

* more comments

* Xvg 8585/do not reupload deleted completed runfolders (#53)

* Do not reupload the Completed Run Folder If the folder was once uploaded already

* minor update

---------

Co-authored-by: Tan Phan <tphan@dnanexus.com>

* XVG-8584 resillient log (#54)

* add comment for XVG-8595

* remove unsused comment

* add more comment

* refactor create_tar_file variable and argument names

* fix 5 hours delay (testing purpose)

typo

bugfix for always true condition

add flag --duration-threshold to gracefully exit the program when the upload duration exceeds the threshold limit

Set --duration-threshold=60 (secs) when args.hourly_restart=False

add e2e docker test

typo make target

update e2e run script

Revert previous additional codes on flag --duration-threshold for dx_sync_directory

revert

add env to cron dev mode

update

update

update

update

update

update

update

update

update

pass envs to subprocess calls

explicitly export env SYNC_DURATION_THRESHOLD for mode=dev

update

update

* Add description for test docker image

* update docker file and minor changes

* typo

* minor updates

update

update

* update base docker image for e2e

* update humanfriendly time log

* update docker image description

* update

* update docs and dockerfiles

* sync log

* add test file

* go to prod

* fix typo

* Update README.md

---------

Co-authored-by: Richard <rle@dnanexus.com>

* print version

* updated version

---------

Co-authored-by: Richard <102358006+truongle1501@users.noreply.github.com>
Co-authored-by: Tan Phan <tphan@dnanexus.com>
Co-authored-by: Tan Phan <ptdtan@gmail.com>
Co-authored-by: Richard <rle@dnanexus.com>