Initial iRODS integration

mikkonie commented 6 years ago

Integrate iRODS operations into the site. Initially support similar functionality to the prototype.

TODO

[x] Add and refactor taskflowbackend app
[x] Add and refactor irodsbackend app
[x] Modify omics_taskflow API to match the current system (see issues/progress in projects)
[x] Modify omics_irods_rest API to match the current system
[x] Modify omics_taskflow for new folder structures
[x] Modify omics_irods_rest for new folder structures
[x] Add and refactor landingzones app
[x] Add new folder linkage behaviour to landingzones
[x] Modify omics_taskflow for new landing zone structures
[x] Make relevant synchronous actions async
[x] Add iRODS liks to samplesheets
[x] Make sure zone status is set to NOT CREATED if a failure is encountered during creation (see also omics_taskflow)
[x] Use domain suffixes with user names in iRODS (see new server)
[x] Deploy and test

Estimate: 1wk/2wk/3wk

mikkonie commented 6 years ago

mentioned in commit 97a016d2fc075963d2ad3906f4e787954b92fcd8

mikkonie commented 6 years ago

marked the task Add and refactor taskflowbackend app as completed

mikkonie commented 6 years ago

marked the task Modify omics_taskflow API to match the current system (see issues/progress in projects) as completed

mikkonie commented 6 years ago

marked the task Make relevant synchronous actions async (e.g. landing zone creation, see existing issues) as completed

mikkonie commented 6 years ago

mentioned in commit ae256909c2edb1ccdd6c80ed48b73eae7613ef36

mikkonie commented 6 years ago

marked the task Modify omics_taskflow for new folder structures as completed

mikkonie commented 6 years ago

mentioned in commit d7b27a47992838eb879786d3320a061a5f9b08ad

mikkonie commented 6 years ago

mentioned in commit 03aa75c89afabab860c57d2411f78ed1f7a4174f

mikkonie commented 6 years ago

mentioned in commit 5cff13f914597608a0e884aa172b292d7c278b97

mikkonie commented 6 years ago

mentioned in commit 4f513676af8654651bf86e4c177b7b74ff9014a6

mikkonie commented 6 years ago

mentioned in commit cec4ba3b491d87c668b1e617c2757f7f5b46c4bd

mikkonie commented 6 years ago

mentioned in commit c2c7e8b2e9c2cc44f6158d483eafeb6300d7c3a6

mikkonie commented 6 years ago

mentioned in commit a7f6e7ec35eed34c5d6ce397207dfd07688fb1a3

mikkonie commented 6 years ago

mentioned in commit e2cade32d96dcf68fd26798d896671679a58a321

mikkonie commented 6 years ago

mentioned in commit c35787b853c7f628487e0f05f2db0e2300cf0ad2

mikkonie commented 6 years ago

marked the task Modify omics_taskflow for new landing zone structures as completed

mikkonie commented 6 years ago

mentioned in commit ab33e55f81cc69bd274b917c5f80aded03b9dcd0

mikkonie commented 6 years ago

mentioned in commit a841a353daf26f0b122e1b2443679b590aef438b

mikkonie commented 6 years ago

mentioned in commit b7a7bb864db9ec5118aa24dcb5a09d2eff7ab47a

mikkonie commented 6 years ago

mentioned in commit 882141ef546fe05e355604fda086d4d9d831bdca

mikkonie commented 6 years ago

marked the task Modify omics_irods_rest API to match the current system as completed

mikkonie commented 6 years ago

marked the task Add and refactor irodsbackend app as completed

mikkonie commented 6 years ago

marked the task Modify omics_irods_rest for new folder structures as completed

mikkonie commented 6 years ago

NOTE: The functionality of omics_irods_rest was integrated into the irodsbackend app. I originally assumed the component to be a lot more complicated. As it is, keeping it as a separate REST service is IMHO not currently justified.

I can change this back in the future if there is a case for it, but this basically gives us the same functionality plus improved access control while making everything a lot easier to use and maintain.

mikkonie commented 6 years ago

mentioned in commit ff79cd5ca1c14a08791752b9f6675c22291187ec

mikkonie commented 6 years ago

mentioned in commit eaf8b37d6057048c162b7ba59e14771ee4a4ce9f

mikkonie commented 6 years ago

mentioned in commit a3655620e535c4ca0dbfabd51c15a564975d8730

mikkonie commented 6 years ago

mentioned in commit bea33fa196cb3073bae92d6106857e4105689571

mikkonie commented 6 years ago

mentioned in commit 1f9f66b73d7506dbd213ff1877adf4bb79ecfa2a

mikkonie commented 6 years ago

marked the task Add and refactor landingzones app as completed

mikkonie commented 6 years ago

marked the task Add new folder linkage behaviour to landingzones as completed

mikkonie commented 6 years ago

marked the task Make sure zone status is set to NOT CREATED if a failure is encountered during creation (see also omics_taskflow) as completed

mikkonie commented 6 years ago

mentioned in commit 199054758a293dc5884679727352b3ae0947b170

mikkonie commented 6 years ago

mentioned in commit b97e9f97db1ed8ede3ed950459531c10ab87eac8

mikkonie commented 6 years ago

mentioned in commit 51e985df19c957e7b1f96b02e362ce6e3d6707bc

mikkonie commented 6 years ago

mentioned in commit 6a3b3c72a0ecdf6aa44058739d2a162ebd27d27c

mikkonie commented 6 years ago

marked the task Add iRODS liks to samplesheets as completed

mikkonie commented 6 years ago

marked the task Use domain suffixes with user names in iRODS (see new server) as completed

mikkonie commented 6 years ago

marked the task Deploy and test as completed

mikkonie commented 6 years ago

Considering this done, but will of course fix bugs as needed :)

mikkonie commented 6 years ago

closed

bihealth / sodar-server

Initial iRODS integration #139

TODO