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Remote upload files - WIP / No Merge (#1670)

* Fix redundant update operation when adding sequence alterations

* started to stub out entry

* creating a stub for uploading

* just coded up a vaery small change

* updated

* removed errant code so that we can add organisms

* Change config name

* add a new strategy for handling remote upload

* Move unzip logic to FileService; add support for zip and tar.gz; make use of Apache Commons Compress library

* Add support for remote upload of flat files via addTrackToOrganism

* added non-persistent DTOs to fix #1663 (#1725)

* set non-defaults better

* preference saving is far better, but it fails to retreive the proper prefernce when switching

* some minor bug-fixes only

* a small change, but not really getting anywhere

* added non-persistent DTOs to fix #1663

* added some small preference classes

* changing sequence seems to work now

* added 2.5.6

* reverting to 2.5.5

* added suer object, but still a problem when changbing

* more bad preference mappings

* added some geb tests

* added geb login

* minor fixes

* switching organisms seems to work now

* cleaned up setting sequence preferences

* a quick name change

* seems to be remembering locations now

* fixing a minor bug

* fixing a minor bug

* is saving to the right location now

* getting the current preference from the organism

* changed saving filter to 5 seconds

* removed unnecessary printlns

* fixed bad debug statement

* cleaned up code

* cleaning up some of the missed queues

* stubbed out integration tests

* added some now failing integration tests

* changes organisms correclty when switching databases

* able to change the database with the help of the database

* verified that we can change organisms and sequences and it we are golden if we use the backing database

* initial stub of the index

* evaluting saves for the token only

* made preferences reproducible

* added another failing commit when adding after adding sequences

* changed to use addTranscript instead

* added some honeybee sequence data and added transcripts at the onset

* added the second failing test

* fixed some of the integration tests, but not clear if this fixes the user tests or the MySQL test instance

* testing out mysql fix

* testing out mysql fix

* added more test constraints

* fixed sorting to use start vs end

* fixed all preference tests I hope

* minor change

* fixed test because of mysql problems

* deleted preference on load

* updated a bit to make preferences sort properly

* again removing the mysql weirdness

* fixed some minor bugs and exposed some breaking tests

* fixed integratino test

* fixed some bugs on startup

* fixed the integration test for switching two organisms twice over

* removing same mysql test fail

* updated changelog

* Fix changes made from merge

* Tidy up

* Update REST API docs

* Add documentation for data loading via web services

* Remove test curl queries

* Update Changelog.md

* Link documentation for data loading via web services

* fixed a minor bug and updated some of the documentation

* updated the bam doc

* updated the remote upload

5354 of 11874 relevant lines covered (45.09%)

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Source Files on job 4605.3 (DB=h2)