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sacdallago wants to merge 132 commits intodebbiemarkslab:developdebbiemarkslab/EVcouplings:developfrom sacdallago:staging_protocolsacdallago/EVcouplings:staging_protocolCopy head branch name to clipboard

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Commits on Feb 21, 2018

• move zip file creation to a different stage of the pipeline --> eventually have a protocol to write to db result files

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  1ec0e0d

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• update example configs to account for new step

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  7b3a193

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• avoid circular dependencies

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• newline at end of file

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• adding database upload protocol in management

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Commits on Feb 22, 2018

• final config should be written in pipeline not protocol

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• cleaned up code, this should work --> now results are stored in database

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  775d3df

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• formatting

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  6b8ecf4

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• Merge branch 'master' of github.com:debbiemarkslab/EVcouplings into staging_protocol

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• Merge branch 'develop' of github.com:debbiemarkslab/EVcouplings into staging_protocol

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  7defcdf

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• remove useless logging

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Commits on Feb 23, 2018

• add getting functions

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  5134ca4

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• refactoring

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Commits on Feb 24, 2018

• add prefix to search and remove heavy fields

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• wrong sql filtering --> need to use load_only for column names

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Commits on Feb 26, 2018

• database params are actually flattened + rise exceptions if something is missing, don't just walk away

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  546603e

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• creating abstract dumper claesses

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• creating abstract dumper claesses

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Commits on Feb 27, 2018

• interface should be working

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  547060c

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• remove unnecesaary pass

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  d469957

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• wrote local dumper + wrote azure dumper + writing jobdb interfaces

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  9bd6ac4

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• fixed some inconsistencies

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  9f18de0

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Commits on Mar 1, 2018

• computejob database interfaces

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  32576cf

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• give option to download or just get url

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  f3dad1e

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• update fields and surround by try catch

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  b634a91

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• only CUD operations need try-catch

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  81babae

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• refactor --> folder name = option in config

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  e9b9313

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• refactor factory instantiation and database update jobs

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  130e468

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• minor refactoring

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  40f92a1

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• refactor

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  71a8159

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• stubbed protocol web

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  6ab4cdd

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• backward compativbility

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• python namespaces fix

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• refactor folder name

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Commits on Mar 2, 2018

• naming consistency

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  5708762

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• refactor: didn't use the correct function call

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  f2537db

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• fix no object management exists

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  8a5f893

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• added todo

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• adding recursive overwrite function

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  f838d51

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Commits on Mar 5, 2018

• job name needs to be azure friendly

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  a9bd2bd

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• make search by primary key explicit

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• always close connections

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• add nullPool to kill connections after commit, otherwise: pool augments and hits the limit too soon

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Commits on Mar 9, 2018

• add abstract methods

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Commits on Mar 25, 2018

• add coments, make returns similar, new TODO

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  93df623

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• added comments for dumper + refactored results

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  53e2fe1

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• removed unused abstract property

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Commits on Mar 26, 2018

• remove todo as that would be update and not overwrite

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  6c86057

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• extend function (instead of overwrite)

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  65e301e

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• removed requirement

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Commits on Apr 10, 2018

• merge and resolve conflicts

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  95b8ce5

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• remove management as a stage

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• add properties to normalize output

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Commits on Apr 11, 2018

• added mongo compute job tracker and revamped model

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• reintroduced delete in pipeline

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  a5d2263

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Commits on Apr 13, 2018

• fix filtering

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  1d350a7

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• extend life to month based on updated at

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  1579ac8

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• checked two main implementations

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• local compute_job tracker refactor

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  4d2a190

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• remove unused import

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  80c07a0

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• refactor faulty lines

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  4bfa4ff

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• refactoring

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  423c35a

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• starting to write mongo dumper

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Commits on Apr 16, 2018

• merge conflicts

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• merge conflicts

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  aec2ec4

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• clear bucket, store file(s)

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  eb94980

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• added outconfig parser

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  12dd940

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• add todos

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  2c34f63

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• refactor and add methofs

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  285c9b0

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• remove AzureDumper

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  d84998f

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• refactor + factoid call

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  8fe45bc

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Commits on Apr 17, 2018

• fix datettime call problem

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  0ea6022

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• fix return on no file

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  e3c0efe

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• signature move

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  3afe4be

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• refactoring + integrating in pipeline

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  b4bccdf

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• close connections + other methods

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  21df677

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• close connections

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  9d79693

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• return connection, so it can be closed

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  e87fa73

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• write accessory methods for backend

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  93e37b0

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• add pymongo to requirements, otherwise evcouplings CLI WILL FAIL

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  75a6034

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• prefix is in global

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  2e85589

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• oh well, os was missing

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  f9d5435

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• simplify imports

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Commits on Apr 18, 2018

• After meeting with RC: change default queue

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• [THOMAS CALL] Max depth: 2 (0+1)

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• added warning for clairity

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  d0c3500

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Commits on Apr 19, 2018

• [THOMAS CALL] always create zip, dump zip if in tracked files list

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  e4f22f3

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• [THOMAS CALL] all options flattened out

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  e202449

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• gohsts of future past

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  586bb19

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• clean up default configs

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Commits on Apr 20, 2018

• getters should be static

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  327f203

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Commits on Apr 25, 2018

• refactor

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  f610fb5

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• refactor: get them all

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Commits on Apr 26, 2018

• refactor: move

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  72c9f8c

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• refactor init

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  09dcc88

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• refactor init

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  89a6857

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• refactor: name

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• refactor: use const extensions and refactor done to finished as it was before

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  2b24c7a

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• refactor: too many lines

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  2fb9e1b

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• refactor: null dumper behaviour

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  8c8990b

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• refactor: local dumper behaviour

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  45f9fdb

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• refactor: job_group

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• refactor: add headers

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• refactor: docstring format + doc general style

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• refactor: no assertation, but if/else

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• refactor: mongo as conditional import

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Commits on May 9, 2018

• strange bug: testing remotely

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  7757bfb

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• strange bug: testing remotely

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  2fefc58

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• strange bug: testing remotely

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  2d1a2a1

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• never trust autorefactoring

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Commits on Jun 12, 2018

• NO TT:

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  1345eb8

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• merge conflicts

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Commits on Jun 28, 2018

• Merge branch 'develop' into staging_protocol

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Commits on Jul 9, 2018

• write metadata

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  2ed2940

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• completely get rid of TTL code to avoid confusion

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  69b0076

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• closes debbiemarkslab#122

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• if template doesn't contain field, don't recurse: patch

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• merge

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• compute_job --> metadata_tracker

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• dumper --> results_tracker

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Commits on Jul 10, 2018

• emulated previous DB test with SQL instance

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• Good thing we have tests

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Commits on Aug 14, 2018

• In compare: keys may contain .(dots) because called as aux relative paths with extensions (e.g. something.pdb). Mongo doesn't like ., so change that to underscore

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Commits on Aug 15, 2018

• 817403fed3bed98f457130388638c0fa_b0.2/compare/aux/817403fed3bed98f457130388638c0fa_b0.2_1oxo_B_33.pdb are nested in remapped_pdb_files, so must apply key correction recursively

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• make keys in database for fail/terminate files more explicit

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• add metadata bucket retriever

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Commits on Oct 11, 2018

• Merge branch 'develop' into staging_protocol

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Commits on Oct 25, 2018

• Merge branch 'develop' into staging_protocol

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Commits on Dec 16, 2018

• Merge branch 'develop' into staging_protocol

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Commits on Jan 18, 2019

• Merge branch 'develop' into staging_protocol

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Commits on Jan 21, 2019

• FIX: keyword arguments on NULL tracker

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Commits on Apr 9, 2019

• Merge branch 'develop' into staging_protocol

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