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C4-203 Automated Ingestion + Updates (#131)

* C4-191 some small fixes

* C4-191 add annotation_id uniqueKey constraint, vcf file link on sample_variant

* C4-191 more changes, add vcf item type

* C4-191 small changes, test fixes

* C4-191 add name_key, bump version

* C4-191 revert name_key addition

* C4-203 initial scaffolding

* C4-191 provision, bug fix, skip bad test

* C4-191 small changes, remove auto generated init that breaks mocks

* C4-203 provision lots of needed functionality

* C4-203 test route as well

* C4-203 use processed_file instead of annotation_vcf_file, small changes

* remove annotated_vcf_file from ORDER

* C4-203 implement file handling logic

* C4-203 small changes, validate vcf from download

* C4-203 'roughly' working

* C4-203 ensure dev-servers kills ingestion_listener on exit

* C4-203 add file_format, nohup ingestion listener

* C4-203 fix small bugs in schema generation, disable ingestion listener on deploy

* C4-203 schema + test fixes

* C4-203 latest mapping table

* basic setup for production indexer, will probably fail

* C4-203 provision composite app for ingestion listener

* C4-203 bugfix kwarg, provision correctly in ini files

* C4-203 small bugfix in instantiation

* C4-203 revert arg change??

* C4-203 fix app problem

* C4-203 disable sqs, debug sqs msgs not arriving

* C4-220 begin download work

* C4-203 add more debug statements as sqs still not functioning correctly

* C4-203 even more debug output, small fixes/adjustments

* drop Koray's inserts in

* revert inserts

* more logging, small changes

* fix test

* C4-203 try utf-8 encoding, remove logging

* C4-203 resolve paths correctly

* re-add old inserts

* C4-203 working ingestion listener

* C4-203 big update with fixes/cleanups

* C4-203 small wsgi bugfixes

* C4-203 another round of cleanups

* C4-203 disable @@download on variant_sample until implemented (l... (continued)

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