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Commits on Feb 17, 2017
@cjllanwarne cjllanwarne Merge pull request #1996 from broadinstitute/cjl_simple_cache_hit_met…
…adatum

Bring sanity to the Call Caching metadata. Closes #1994
66ba80c
@Horneth Horneth don't return invalidated cache entries (#2004)
bda6afe
@adamstruck adamstruck tes backend prototype with centuar setup
added -elocaldockertest to centaur command

print TES logs after run

fixed unmarshalling bug

inputs in read-only volume; matched TES case classes to schema

address final PR comments
d7adb19
@geoffjentry geoffjentry hmm
92d62fe
Commits on Feb 18, 2017
@kshakir kshakir Merge pull request #1979 from ohsu-comp-bio/tes_backend_prototype
TES Backend Prototype. Closes #1294
1524f3d
@Horneth Horneth fail file hashing if the file does not exist (#2006) fe4c397
Commits on Feb 19, 2017
@geoffjentry geoffjentry Rm new (#2008)
Updating travis
aad4a2f
Commits on Feb 21, 2017
@kshakir kshakir Minor Tes updates.
Added note to the changelog.
Replaced usages of `cromwell.core.path.Obsolete._`.
Moved travis centaur tes back to using funnel from ohsu.
f2ad4ea
@Horneth Horneth Throw if cache hit copying fails on SFS (#2003)
* throw if cache hit copying fails on SFS

* PR comment
74727a7
Commits on Feb 22, 2017
@kshakir kshakir Merge pull request #2012 from broadinstitute/ks_tes_patch
Minor Tes updates.
9a734c4
@Horneth Horneth Update allow result reuse (#2010)
* update allowResultReuse

* make job attempt nullable

* fix compile

* fix EJEA variable init order

* init in preStart

* fix test

* PR comment

* custom centaur

* centaur develop
996acc2
@Horneth Horneth Evaluate imports file content eagerly. Fixes "workflowName" centaur f… (
#2013)

* Evaluate imports file content eagerly. Fixes "workflowName" centaur failures.

* add retries

* fix compilation
5588e73
@kshakir kshakir Better NPE handling during terminal JES parsing.
c746ab7
@kshakir kshakir Removed MakingABackend.MD
29d181a
@kshakir kshakir Merge pull request #2015 from broadinstitute/ks_1965_harden
Better NPE handling during terminal JES parsing.
2be82c8
@kshakir kshakir Merge pull request #2018 from broadinstitute/ks_2017_edit
Removed MakingABackend.MD
23375c2
Commits on Feb 23, 2017
@kshakir kshakir Changed TES centaur log level from debug to info.
daf7dd0
@kshakir kshakir Merge pull request #2024 from broadinstitute/ks_tes_log_info
Changed TES centaur log level from debug to info.
76f94b7
@Horneth Horneth Docker Hash (#1969)
* Docker Hash
422f9da
Commits on Feb 24, 2017
@kshakir kshakir Updated wdl4s to import patch for glob indexing.
7e183cb
@kshakir kshakir Merge pull request #2014 from broadinstitute/ks_1980_patch
Updated wdl4s to import patch for glob indexing.
f64c16e
Commits on Feb 26, 2017
@kshakir kshakir Updates for memory validations.
Fixed SGE memory parameter in reference.conf.
Split `MemoryDeclarationValidation` out of `DeclarationValidation`.
Added tests for `MemoryDeclarationValidation`.
`OptionalRuntimeAttributesValidation` were not returning the defaults from the underlying `RuntimeAttributesValidation`.
ba56af3
@kshakir kshakir Slightly better abort behavior in standard backend.
Stopped closing a scala `Future` over akka's `context.become`.
Flipped the default for `requestsAbortAndDiesImmediately` from `false` to `true`.
When killing a Standard backend job with rADI false, both the rc and the standard error are required.
Writing the stderr on abort for the SFS backend.
When rADI is true, sending a backend status of `"Aborted"`.
In the engine, set and store the `ExecutionStatus.Aborted`.
e397e25
Commits on Feb 27, 2017
@mcovarr mcovarr add a knob
2e79a25
@kshakir kshakir Merge pull request #2032 from broadinstitute/ks_std_back_abort_patch
Slightly better abort behavior in standard backend.
6fa1a63
@kshakir kshakir Merge pull request #2031 from broadinstitute/ks_memory_declaration_fix
Updates for memory validations.
509ff2d
Commits on Feb 28, 2017
@delocalizer delocalizer * make sure dir that TMPDIR is set to, exists
9f6180f
@mcovarr mcovarr Merge pull request #2040 from delocalizer/crl_mkdir_tmpdir
* make sure dir that TMPDIR is set to, exists. Fixes #2035
335e983
Commits on Mar 02, 2017
@kshakir kshakir Message, not throw, failures in WEA.startRunnableScopes.
Other syntax fixes.
a89ce0a
@kshakir kshakir Merge pull request #2030 from broadinstitute/ks_catch_runnable_scopes
Message, not throw, failures in WEA.startRunnableScopes.
fe2cd43
@cjllanwarne @geoffjentry cjllanwarne + geoffjentry JES API Manager: run creation and retries (#2026)
c152015
@kshakir kshakir Don't fail Travis JES for external users.
006b386
@kshakir kshakir Merge pull request #2045 from broadinstitute/ks_restore_external_tests
Don't fail Travis JES for external users. Closes #1717
5f02244
@kshakir kshakir Config backend wasn't dockerizing script paths.
560b648
@kshakir kshakir Merge pull request #2028 from broadinstitute/ks_dockerize_paths
Config backend wasn't dockerizing script paths.
ef6f0ed
@mcovarr mcovarr Merge pull request #2027 from broadinstitute/mlc_call_caching_perf
add a knob
528fe2c
Commits on Mar 03, 2017
@delocalizer @mcovarr delocalizer + mcovarr Use mktemp to make temporary directory Fixes #2047 (#2049)
* * use mktemp to make the temporary directory

* * more portable invocation of mktemp, works on OSX also
fac784d
@ruchim ruchim update readme examples and list external contributors (#2051)
2e53c6d
@ruchim @ruchim ruchim + ruchim Update Cromwell to use non-SNAP versions for Lenthall/WDL4s 0e9b8bb
@ruchim @ruchim ruchim + ruchim Update Cromwell develop to the next version
e7791be
Commits on Mar 06, 2017
@cjllanwarne cjllanwarne Failure metadata redux
7912d9c
Commits on Mar 07, 2017
@cjllanwarne cjllanwarne Merge pull request #2055 from broadinstitute/cjl_flatten_causedBy_met…
…adata

Failure metadata redux
38bd23e
Commits on Mar 09, 2017
@mcovarr mcovarr temporary directory should be world writeable (#2053)
cf50d9a
Commits on Mar 13, 2017
@Horneth Horneth I/O Actor (#2056)
* I/O Actor
7dd945e
@cjllanwarne cjllanwarne Workflow name length limit
6928043
@cjllanwarne cjllanwarne Merge pull request #2061 from broadinstitute/cjl_workflow_name_limit
Workflow name length limit. Closes #1725
67a022f
Commits on Mar 14, 2017
@geoffjentry geoffjentry Have our config instructions match what we tell people (#2058)
b1039f7
Commits on Mar 17, 2017
@adamstruck @ruchim adamstruck + ruchim stage required config changes for funnel PR #15 (#2070)
ca85733
Commits on Mar 21, 2017
@jainh @geoffjentry jainh + geoffjentry Update README.md (#2043)
* Update README.md for richer doc on spark backend
8f2b036
@Horneth Horneth send token file
bfe0911
@Horneth Horneth WDL and inputs to release cromwell (#2065)
* WDL and inputs to release cromwell
3e57722
Commits on Mar 22, 2017
@ruchim ruchim replace empty cells in custom_labels column with {} (#2076) 15b34cf
@kshakir kshakir Store custom labels.
742942f
@kshakir kshakir Merge pull request #2083 from broadinstitute/ks_store_custom_labels_d…
…evelop

Store custom labels.
8ededf0
Commits on Mar 24, 2017
@kshakir kshakir Report causal exceptions during Google auth failures.
c4fbde7
@kshakir kshakir Merge pull request #2091 from broadinstitute/ks_causal_auth_failures
Report causal exceptions during Google auth failures. Closes #2090
92b76e3
@Horneth Horneth Improve ExecutionStore and WEA performance (#2087)
* Improve ExecutionStore and WEA performance
b878654
Commits on Mar 27, 2017
@Horneth Horneth Some retry improvements (#2080)
* Add a config option for IO attempts

* add to changelog and readme

* PR comment
ddf58e7
Commits on Mar 28, 2017
@Horneth Horneth Wait for metadata to be flushed in SWM Closes #1932 (#2101)
* wait for metadata to be flushed in SWM

* swap onTransitions in WA

* PR comments
e3bb43f
Commits on Mar 29, 2017
@geoffjentry geoffjentry Move lenthall's spray code over here, with slight mods to handle our … (
#2093)

* Move lenthall's spray code over here, with slight mods to handle our extra compiler flags
b80e56b
@Horneth Horneth Update docker lookup (#2077)
* Update docker hash actor and http retry flow

* add IO dispatchers to streams

* PR comment
1eb4e89
@Horneth Horneth Catch namespace load throwables Closes #2066 (#2098)
* catch namespace load throwables

* remove unnecessary try
fc0b2f9
Commits on Mar 30, 2017
@Horneth Horneth Update wdl4s Closes #1982 Closes #1951 (#2097)
* update wdl4s

* update wdl4s

* update cromwell with new dependencies

* fix hard links

* centaur develop

* indentation
d51bb50
Commits on Mar 31, 2017
@Horneth Horneth Adds submitted and aborted status to Metadata (#2114)
* send submitted amd aborted status to MD

* remove unused import
e9d8c62
@mcovarr mcovarr Docker hashing gets its own subproject. (#2099)
8792a93
@buchanae @Horneth buchanae + Horneth Fix funnel test and pin version to git commit (#2116)
d391706
@cjllanwarne cjllanwarne Failure metadata migration
f6575de
@cjllanwarne cjllanwarne Merge pull request #2059 from broadinstitute/cjl_failure_metadata_mig…
…ration

Failure metadata migration. Closes #2037. Closes #2039
c7dc718
Commits on Apr 03, 2017
@cjllanwarne cjllanwarne Bringing in if then else expressions from wdl4s
bbf9983
@cjllanwarne cjllanwarne Merge pull request #2107 from broadinstitute/cjl_if_then_else
Bringing in if then else expressions from wdl4s
223388a
jsotobroad Adding jsotobroad to pullapprover members list
3ed4dcc
@cjllanwarne cjllanwarne Merge pull request #2123 from broadinstitute/js_interloper_pullapprove
Adding jsotobroad to pullapprover members list
a559aea
@cjllanwarne cjllanwarne If then else Changelog
f9e4922
@cjllanwarne cjllanwarne Merge pull request #2122 from broadinstitute/cjl_ifthenelse_changelog
If then else Changelog
fe81755
@Horneth Horneth Shutdown materializer and Http pool (#2118)
* Shutdown materializer and Http pool

* PR comment
83f2ded
@Horneth Horneth Declaration evaluation (#2119)
* Coerce decalarations:

* update wdl4s + custom centaur

* fix dependency

* be more patient..

* centaur develop
caab258
Commits on Apr 05, 2017
@mcovarr mcovarr handling nullable job store simpletons (#2151) 00d2790
@mcovarr mcovarr Recover from database failures when reading the workflow store. (#2150)
88630db
Commits on Apr 06, 2017
@geoffjentry @cjllanwarne geoffjentry + cjllanwarne Engine and JES changes supporting custom retries
3461b16
@cjllanwarne cjllanwarne Merge pull request #2102 from broadinstitute/cjl_backend_retries
Engine and JES changes supporting custom retries. Closes #1925
82b7854
Commits on Apr 11, 2017
@MatthewMah @Horneth MatthewMah + Horneth Backend configuration for SLURM added in beta state. #1750 (#2158)
aa39ed7
@mcovarr mcovarr Knob for script epilogue. (#2160)
65e59ff
@mcovarr mcovarr Unstick abort, log if the store remove fails. (#2154)
78f8853
@ruchim @ruchim ruchim + ruchim Update cromwell version to 26 89ef12a
@ruchim @ruchim ruchim + ruchim Update cromwell version from 26 to 27
fd15a89
Commits on Apr 12, 2017
@kshakir @geoffjentry kshakir + geoffjentry Updated to Slick 3.2. (#2104)
Removed deadlock workaround.
Minimal updates to fix depracated usage.
Old Slick 3.1 style names are still used in scala, ex: `val driver: JdbcProfile`.
Added notes about SQL converters handling empty LOBs.
1906bdf
@geoffjentry geoffjentry EngineWorkflowFinalizationActor only had a single implementation, rem…
…ove layer of indirection (#2155)
91dd653
Commits on Apr 14, 2017
@cjllanwarne cjllanwarne Upgrade test script
7947d4c
@cjllanwarne cjllanwarne Merge pull request #2164 from broadinstitute/cjl_test_upgrade
Test_upgrade script
5a1f768
@ruchim ruchim Config-specified Default runtime attributes (#2121)
grab runtime attribute defaults from reference.conf, add deprecation warnings, introduced the BadDefaultAttribute WdlValue.
9460d47
@Horneth Horneth Enable local docker lookup (#2139)
* Added a docker cli flow.
Changed the default behavior to use the cli (aka local) flow, with an option to add or switch to the remote registry flow.

* Add enable flag for docker hash lookup

* Disable docker lookup if backend doesn't support docker

* changelog

* get ready for merge
9aff9f2
Commits on Apr 18, 2017
@francares francares Initial implementation of HtCondor backend using configurable backend. (
#2141)

Fixed documentation on Native specs.

Generalized memory validation in order to support disk validation based on information unit.

Prettyfing bash scripts.

Updating README.

Changes after rebase.
89d0b9d
Commits on Apr 19, 2017
@katevoss katevoss Removing CLI from the Readme (#2161)
* Removing CLI from the Readme

* making it one line in the TOC

* updating to the published url
6d79d0a
Commits on Apr 20, 2017
@cjllanwarne cjllanwarne Cromwell API client (for Centaur)
6eb104b
@cjllanwarne cjllanwarne Merge pull request #2169 from broadinstitute/cjl_cromwell_api_client
Cromwell API client for Centaur. Closes #2128
0853385
Commits on Apr 21, 2017
@Horneth Horneth Support for docker hash lookup of public quay.io images (#2184)
* add docker hash lookup for public quay.io images

* custom centaur
2033421
@Horneth Horneth centaur develop
229e974
@Horneth Horneth Some Joint Genotyping related improvements (#2180)
* Add 410 as retryable error and rework metadata building a little.

* custom centaur

* add CRDT test for call executions status

* update timing diagram

* eventuallify test

* PR comments

* oops

* centaur develop
d1c8ea0
@cjllanwarne cjllanwarne Publish cromwell-api-client artifact
63d133a
@cjllanwarne cjllanwarne Merge pull request #2192 from broadinstitute/cjl_aggregate_client
Publish cromwell-api-client artifact
3619ba8
@cjllanwarne cjllanwarne Client publish fixup
1ad7716
@cjllanwarne cjllanwarne Merge pull request #2194 from broadinstitute/cjl_client_publish-fixup
Client publish fixup
77b8b1d
Commits on Apr 24, 2017
@cjllanwarne cjllanwarne (Centaur Port) Decode responses
754134b
@cjllanwarne cjllanwarne Remove race conditions from WriteMetadataActorSpec
5b66bf5
@cjllanwarne cjllanwarne Merge pull request #2199 from broadinstitute/cjl_decode_responses
(Centaur Port) Decode responses
9a9745a
@cjllanwarne cjllanwarne Merge pull request #2195 from broadinstitute/cjl_flaky_test_2193
Remove race conditions from WriteMetadataActorSpec. Closes #2193
20f8687
@cjllanwarne cjllanwarne Deprecation errors for DB configs
c81343c
Commits on Apr 25, 2017
@cjllanwarne cjllanwarne Merge pull request #2200 from broadinstitute/cjl_DEPRECATED
Deprecation errors for DB configs. Closes #2186
69a8d21
@cjllanwarne cjllanwarne JES in-command write_lines fixup
8f6ee41
@Horneth Horneth Execution Store and JobPaths optimizations (#2198)
* Limit JobPaths creation and Improve execution store performance

* Fix subworkflow paths

* PR comments
4a49f93
@cjllanwarne cjllanwarne Merge pull request #2191 from broadinstitute/cjl_write_lines_jes
JES in-command write_lines fixup. Closes #1906
05ec820
Commits on Apr 26, 2017
@cjllanwarne cjllanwarne Cromwell's failure is now complete
50375c7
@cjllanwarne cjllanwarne Merge pull request #2203 from broadinstitute/cjl_consistent_failure
Cromwell's failure is now complete (develop edition). Closes #2201
5360704
@Horneth Horneth Tweak retries (#2208)
* tweak retries

* PR comments
cf37252
Commits on Apr 27, 2017
@Horneth Horneth Use io dispatcher (#2206)
* Use io dispatcher

* PR comments
c89c83f
Commits on Apr 28, 2017
@cjllanwarne cjllanwarne Remove unneeded SubWorkflowStoreCompleteSuccess message
336d4f6
Commits on Apr 29, 2017
@Horneth Horneth JSON auth for Google SA (#2213)
* JSON auth for Google SA

* deprecation warning for pem files
e316d8d
@cjllanwarne cjllanwarne Merge pull request #2218 from broadinstitute/cjl_remove_SubWorkflowSt…
…oreCompleteSuccess

Remove unneeded SubWorkflowStoreCompleteSuccess message. Closes #2185
d54c313
Commits on May 01, 2017
@cjllanwarne cjllanwarne Bring in validation messages from WDL4S
ea5f989
@cjllanwarne cjllanwarne Merge pull request #2214 from broadinstitute/cjl_better_validation_me…
…ssages

Bring in validation messages from WDL4S. Closes #2211
fceeedf
Commits on May 02, 2017
@mcovarr @mcovarr mcovarr + mcovarr Batching Job Store simpleton writes. 7263b5e
@cjllanwarne cjllanwarne Removing semicolon from migration query
aaa64d7
@cjllanwarne cjllanwarne Merge pull request #2231 from broadinstitute/cjl_remove_semicolons_de…
…velop

Removing semicolon from migration query (develop edition)
f094129
Commits on May 03, 2017
@danbills @geoffjentry danbills + geoffjentry adding Dan Billings to pull approve list (#2240)
a4d4616
jsotobroad JobStoreSimpletonMigration was putting quotation marks around file va…
…lues which caused the jobs to fail once cromwell recovered after a migration
f999719
@Horneth Horneth use the right failureMode value (#2239)
98e0e6e
Commits on May 04, 2017
@cjllanwarne cjllanwarne Akka HTTP bump
c8e9c94
@cjllanwarne cjllanwarne Merge pull request #2245 from broadinstitute/cjl_akka_http_10.0.6
Akka HTTP bump
834aaa0
Commits on May 05, 2017
@mcovarr @mcovarr mcovarr + mcovarr Batch writes of call caching related data.
46bd6fe
@cjllanwarne cjllanwarne WDL4S bump
b8574c1
@jsotobroad jsotobroad Merge pull request #2242 from broadinstitute/js_job_store_extra_quota…
…tion_develop

JobStoreSimpletonMigration was putting quotation marks around file values which caused the jobs to fail once cromwell recovered after a migration
c3d8f6c
Commits on May 07, 2017
@cjllanwarne cjllanwarne Merge pull request #2247 from broadinstitute/cjl_wdl4s_bump
WDL4S bump
a046dfe
Commits on May 08, 2017
@jsotobroad jsotobroad Double Quoted file inputs cause PipelineAPI workflows to run forever. C…
…loses #2178 (#2251)

* separate between JesApi status/run creation failures and display proper error messages in workflow metadata
496c4f6
Commits on May 10, 2017
@Horneth Horneth Call Caching v3 (#2243)
* Call Caching revamp

* add chahgelog

* fix test + changelog

* update changelog

* custom centaur

* cleanup

* create directories before copy and write on SFS

* tweak runnable calls

* oops

* fix test

* PR comments

* minor migration fix

* PR comments

* fix

* PR comments

* centaur develop
11abb7f
@Horneth Horneth Allow for tag + digest docker images (#2255)
* allow for tag + digest docker images

* PR comments
aab4763
Commits on May 12, 2017
@Horneth Horneth add conf
(cherry picked from commit c14e64d)
1d4e0ab
@jsotobroad jsotobroad Readme Link Fixes (#2259)
Fix a few links in README
1a131c1
Commits on May 15, 2017
@Horneth Horneth update changelog to reflect reality (#2263)
5bb2875
Commits on May 17, 2017
@Horneth Horneth Add task to release wdl to make a github release (#2275)
* Add task to release wdl to make a github release

* add -x

* wrong organization

* shellchecked
199b1d9
Commits on May 18, 2017
@Horneth Horneth update changelog again (#2272)
* update changelog again

* fix space
cd4059b
Commits on May 19, 2017
@antonkulaga @Horneth antonkulaga + Horneth fix for #2256 (#2280)
This PR fixes #2256 by overriding default entry-point with /bin/bash
ddf223d
Commits on May 22, 2017
@danbills danbills tested read lines 4ac640b
Commits on May 23, 2017
@ruchim ruchim Allow customLabels submission to Cromwell Client (#2257)
allow customLabels submission through CromwellClient
693cda5
@ruchim ruchim wow (#2290)
425cde2
@danbills danbills added tests for all read functions
0be7611
@danbills danbills tidy up the read_X code
e34957f
@ruchim ruchim Query using Labels (#2253)
added querying through labels
091ed3b
@jsotobroad jsotobroad validation of input gcs file paths that start with \" (#2271)
* validateworkflow input gcs file paths that start with \"
e79e081
@cjllanwarne cjllanwarne Bringing map to pair coercion and basename from WDL4S
948efa5
Commits on May 24, 2017
@Horneth Horneth Consume http response and re-synchronize token and manifest (#2287)
* consume http response and re-synchronize token and manifest

* remove irrelevant comment

* PR comments
34323f0
@Horneth Horneth Update google nio + small optimization for copy workflow outputs (#2277)
* upgrade gcs nio version

* remove retry settings

* fix up copy workflow outputs

* PR comments
2c64afc
@Horneth Horneth fix
f673cc8
@cjllanwarne cjllanwarne Merge pull request #2274 from broadinstitute/cjl_coerce_map_to_pairs
Bringing map to pair coercion and basename from WDL4S
81d5945
@danbills danbills added ability to configure read X limits 96b33e5
@danbills danbills Merge branch 'develop' into db_read_limits
52c6faa
Commits on May 25, 2017
@Horneth @mcovarr Horneth + mcovarr Workflow Docker Hashing.
38b52a3
@danbills danbills added README and CHANGELOG comments
45ca36d
@danbills danbills formatting
607a1d0
@danbills danbills Merge pull request #2291 from danbills/db_read_limits
added read limits to read_X functions
06d3f11
Commits on May 26, 2017
@Horneth Horneth fix release wdl and custom label summarizing (#2298)
b30a232
Commits on May 30, 2017
@Horneth Horneth Update mysql and jackson-databind dependencies (#2299)
* update mysql and jackson-databind dependencies

* update jackson-module-scala version
1312eb3
@Horneth Horneth Update cromwell version to 27 1b7c65f
@Horneth Horneth Update cromwell version from 27 to 28
4327ca6
Commits on Jun 01, 2017
@ruchim ruchim Preliminary validation of workflow options (#2295)
preliminary validation of wf options before WorkflowID creation
98d766b
@mcovarr @mcovarr mcovarr + mcovarr Purge workflow store entry before job entries.
bb96682
Commits on Jun 05, 2017
@adamstruck @ruchim adamstruck + ruchim catching up backend to the TES schema (#2293)
added google storage support, let TES handle creating the command script, updated funnel commit for centaur tests
44ba3df
Commits on Jun 06, 2017
@Horneth Horneth Add retries to credential validation (#2314)
* works?

* PR comments

* rebase

* oops
6fbeadc
Commits on Jun 08, 2017
@mcovarr @mcovarr mcovarr + mcovarr jfrog
4487a51
Commits on Jun 09, 2017
@Horneth Horneth honor allow result reuse (#2341) (#2349)
(cherry picked from commit 461cff2)
ac3d65e
Commits on Jun 12, 2017
@mcovarr @mcovarr mcovarr + mcovarr First pass of workflow type and version. This takes parameters on RES…
…T endpoints, roundtrips to the workflow store,

and publishes to metadata.  Currently hardcodes type and version for the command line.
ef012a6
@mcovarr @mcovarr mcovarr + mcovarr Remove some user-facing WDL specificity. c0289dc
@mcovarr @mcovarr mcovarr + mcovarr Make workflow type optional in store, remove references to WDL in Swa…
…gger.
6551129
Commits on Jun 13, 2017
@mcovarr mcovarr oops
bf3202d
Commits on Jun 15, 2017
@mcovarr @mcovarr mcovarr + mcovarr Don't implicitly add a library/ repo prefix to Docker images as that …
…breaks 26-era call caches.
f3e04bf
@Horneth Horneth Config option to disable copying of outputs on cache hit for JES (#2347)
* Add support for copyless call caching in JES
46ad512
Commits on Jun 20, 2017
@Horneth Horneth conf fix
151bf05
@Horneth Horneth Call Caching Diff Endpoint (#2363)
* Call Caching Diff Endpoint
3801e14
Commits on Jun 21, 2017
@ruchim ruchim deprecated image (#2370)
1f166d9
Commits on Jun 22, 2017
@Horneth Horneth Add version endpoint to Cromwell client (#2368)
* add version endpoint to Cromwell client

* add version endpoint to Cromwell client
1394bdd
@mcovarr @mcovarr mcovarr + mcovarr only check stderr if failOnStderr is true
90f1e17
Commits on Jun 23, 2017
@mcovarr @mcovarr mcovarr + mcovarr Make an effort to diagnose bad bucket names.
931f62e
Commits on Jun 26, 2017
@mcovarr @mcovarr mcovarr + mcovarr Some magic to work with the new Travis Trusty images.
9660633
Commits on Jun 27, 2017
@ruchim ruchim Gather completed shards (#2376)
* fail slow fixup, and adding scatter collectorkey to ExecutionStoreBenchmark test
c99856a
@ruchim ruchim Add Labels (#2357)
* add label manager actor, prelim tests and swagger updates, changelog updates and docs
65d1849
@Horneth Horneth Return 404 on CC Endpoint for old workflows + cleanup from previous v…
…ersion (#2372)

* update changelog / readme and return 404 for old workflows
f71f598
Commits on Jun 28, 2017
@mcovarr @mcovarr mcovarr + mcovarr Sanify the default metadata batch write size. 477faa4
Commits on Jun 29, 2017
@Horneth Horneth Cromwell restart (#2386)
* Centaur Restart
5fa488e
@jsotobroad jsotobroad add launch integration test capability with cron / build notifications (
#2375)

* add ability to launch integration tests through cron job in travis
* add notification to all builds through slack
7422714
@mcovarr @mcovarr mcovarr + mcovarr Bump to newliney wdl4s, document this user-visible change. 8962b78
@Horneth Horneth fix wdltool release (#2393) 031d9b1
@jsotobroad @Horneth jsotobroad + Horneth add eventually to WorkflowStoreAactorSpec encrypted workflow options …
…test (#2395)
a33f74a
Commits on Jun 30, 2017
@ruchim ruchim Changed Label Formatting (#2389)
Modify Cromwell label expectations
553ab31
@ruchim ruchim travis tweaks (#2397)
* tone down travis slack notifications
e75afe4
@ruchim ruchim 28 Changelog (#2398)
final additions to changelog
3769c06
@Horneth Horneth Update cromwell version to 28 f63a9e6
@Horneth Horneth Update cromwell version from 28 to 29
7c9641c
@Horneth Horneth update release WDL (#2399)
635733c
Commits on Jul 01, 2017
@geoffjentry geoffjentry Migrate Cromwell from Spray to Akka HTTP. Closes #1243 (#2380)
176de92
Commits on Jul 05, 2017
@geoffjentry geoffjentry Scala 2.12 support for Cromwell (#2412)
3e98082
Commits on Jul 06, 2017
@Horneth @geoffjentry Horneth + geoffjentry Rebased (#2406)
a30c701
@mcovarr @mcovarr mcovarr + mcovarr Remove pre-PBE tables.
13691aa
@mcovarr @mcovarr mcovarr + mcovarr Command line parsing redo.
308f087
Commits on Jul 07, 2017
@geoffjentry geoffjentry Only gzip metadata if requested. Closes #2419 (#2427)
* Only gzip metadata if requested. Closes #2419
644967d
Commits on Jul 11, 2017
@mcovarr @mcovarr mcovarr + mcovarr patvars
6d00a45
Commits on Jul 12, 2017
@mcovarr @mcovarr mcovarr + mcovarr make console usable again
1b958d2
@geoffjentry geoffjentry Add restrict-metadata-access (#2435)
Add restrict-metadata-access
2862235
Commits on Jul 14, 2017
@francares francares Fixed issue regarding parsing request body on query POST API. (#2447)
2e32c41
Commits on Jul 17, 2017
@mcovarr @mcovarr mcovarr + mcovarr Separate out retryables from true terminals from the WEA perspective.
8c0f888
@kshakir kshakir Removed /api prefix from /engine.
9e688ec
@cjllanwarne cjllanwarne Preempted to backendStatus in existing metadata.
c5adbf2
Commits on Jul 18, 2017
@kshakir kshakir Merge pull request #2454 from broadinstitute/ks_move_version_endpoint
Removed /api prefix from /engine.
947f8c6
@cjllanwarne cjllanwarne Merge pull request #2443 from broadinstitute/cjl_2438
Preempted to backendStatus in existing metadata. Develop edition
1786ae5
@kshakir kshakir Docker publish develop branch to dev environment.
2e9a96e
@kshakir kshakir Merge pull request #2465 from broadinstitute/ks_docker_tag_caas
Docker publish develop branch to dev environment.
b32a8fe
@mcovarr @mcovarr mcovarr + mcovarr Update to beginning-cromwomified, subprojecty wdl4s. 2708188
@mcovarr @mcovarr mcovarr + mcovarr Updated wdl4s
9620f74
Commits on Jul 19, 2017
@cjllanwarne cjllanwarne Resurrected the unused `Preempted` status
fd05a87
@cjllanwarne cjllanwarne Merge pull request #2462 from broadinstitute/cjl_2455
Resurrected the unused `Preempted` status
9b08454
Commits on Jul 20, 2017
@geoffjentry geoffjentry Assign a dispatcher to services and allow them to be customized (#2470)
eece7ae
@cjllanwarne cjllanwarne Made 'size' accept empty files, Cromwell-side
9cf69ad
@cjllanwarne cjllanwarne Merge pull request #2468 from broadinstitute/cjl_optional_file_size
Made 'size' accept empty files, Cromwell-side
0b92711
@cjllanwarne cjllanwarne Made call cache hash endpoint more JSONic
32841b9
@cjllanwarne cjllanwarne Merge pull request #2471 from broadinstitute/cjl_reformat_ccdiff
Made call cache hash endpoint more JSONic
f1ee2d2
@cjllanwarne cjllanwarne Diff endpoint doc'ing
9225bc5
@cjllanwarne cjllanwarne Merge pull request #2473 from broadinstitute/cjl_diff_docs
Diff endpoint doc'ing
8a8ed40
Commits on Jul 22, 2017
@danbills danbills Pull approve v2 featuring GH review integration (#2477)
bumped pullapprove to v2 and added GH reviews
36a08ec
@kshakir kshakir Switch from travis encrypted files to vault
d5a51c6
Commits on Jul 24, 2017
@kshakir kshakir Merge pull request #2481 from broadinstitute/ks_test_docker_vault
Switch from travis encrypted files to vault. Closes #1296
be6ad40
@geoffjentry geoffjentry Put the binding timeout back to where it was in spray-land (#2478)
11496fc
Commits on Jul 25, 2017
@ruchim ruchim Don't append to lists (#2485) (#2486)
append metadata events to a vector not list
49b59b0
Commits on Jul 26, 2017
@kshakir kshakir Initialize db before serving over HTTP
76f6aae
@kshakir kshakir Merge pull request #2484 from broadinstitute/ks_liquibase_then_bind
Initialize db before serving over HTTP
5b16d61
@Horneth Horneth Handle failed Cromwell requests (#2488)
* Handle failed Cromwell requests in the CromwellAPIClient
27f9f1c
@danbills danbills removed jainh from committers to fix pullapprove (#2491)
219b0c5
@Horneth Horneth Handle null access token from Google Credentials (#2489)
* handle null access token from Google Credentials
645d8b2
Commits on Jul 27, 2017
@cjllanwarne cjllanwarne Additional clienty bits for Cromwell
bdfaf91
@cjllanwarne cjllanwarne Merge pull request #2474 from broadinstitute/cjl_more_clienty_bits
Additional clienty bits for Cromwell
16a7498
@mcovarr @mcovarr mcovarr + mcovarr Updates for subprojected wdl4s. Also remove "dryRun" since that didn'…
…t actually dry run anything.
bb0f6ea
@mcovarr @mcovarr mcovarr + mcovarr search and replace run amok
e648273
Commits on Jul 28, 2017
@geoffjentry geoffjentry Upgrade to scala 2.12.3 (#2502)
42a1dce
@cjllanwarne cjllanwarne Model objects for Cromwell Queries
4d8825d
@cjllanwarne cjllanwarne Merge pull request #2501 from broadinstitute/cjl_query_responses
Model objects for Cromwell Queries
c041402
@cjllanwarne cjllanwarne Allow "AbortedResponse" even when not aborting
350a024
@cjllanwarne cjllanwarne Merge pull request #2503 from broadinstitute/cjl_jes_6_day_limit
Allow "AbortedResponse" even when not aborting
e642a94
Commits on Jul 30, 2017
@geoffjentry geoffjentry Dispatcherizing undispatcherized actors. Trying to standardize on add…
…ing it to the props where appropriate (#2499)
a611db6
Commits on Jul 31, 2017
@kshakir kshakir Replaced use of Future.foreach with error handling
8d3e615
@kshakir kshakir Merge pull request #2500 from broadinstitute/ks_report_bad_inputs
Replaced use of Future.foreach with error handling
0e4d507
Commits on Aug 01, 2017
@Horneth Horneth Graceful Server Shutdown (#2490)
* Graceful shutdown

* Dont overwrite jes auth file
include application.conf in centaur conf files
07a5671
@kshakir kshakir Client only modifies request json when inserting a refresh token.
cf8c228
@kshakir kshakir Merge pull request #2509 from broadinstitute/ks_client_pass_options
Client only modifies request json when inserting  a refresh token.
e97bcc7