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23
contributors
This comparison is big! We’re only showing the most recent
250
commits
Commits on Feb 17, 2017
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cjllanwarne |
Merge pull request #1996 from broadinstitute/cjl_simple_cache_hit_met…
…adatum Bring sanity to the Call Caching metadata. Closes #1994 |
66ba80c
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Horneth |
don't return invalidated cache entries (#2004)
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bda6afe
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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
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geoffjentry |
hmm
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92d62fe
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Commits on Feb 18, 2017
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kshakir |
Merge pull request #1979 from ohsu-comp-bio/tes_backend_prototype
TES Backend Prototype. Closes #1294 |
1524f3d
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Horneth |
fail file hashing if the file does not exist (#2006)
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fe4c397
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Commits on Feb 19, 2017
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geoffjentry |
Rm new (#2008)
Updating travis |
aad4a2f
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Commits on Feb 21, 2017
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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. |
All checks have passed4 successful checks |
f2ad4ea
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Horneth |
Throw if cache hit copying fails on SFS (#2003)
* throw if cache hit copying fails on SFS * PR comment |
74727a7
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Commits on Feb 22, 2017
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kshakir |
Merge pull request #2012 from broadinstitute/ks_tes_patch
Minor Tes updates. |
9a734c4
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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
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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
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kshakir |
Better NPE handling during terminal JES parsing.
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All checks have passed4 successful checks |
c746ab7
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kshakir |
Removed MakingABackend.MD
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All checks have passed4 successful checks |
29d181a
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kshakir |
Merge pull request #2015 from broadinstitute/ks_1965_harden
Better NPE handling during terminal JES parsing. |
2be82c8
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kshakir |
Merge pull request #2018 from broadinstitute/ks_2017_edit
Removed MakingABackend.MD |
23375c2
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Commits on Feb 23, 2017
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kshakir |
Changed TES centaur log level from debug to info.
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All checks have passed4 successful checks |
daf7dd0
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kshakir |
Merge pull request #2024 from broadinstitute/ks_tes_log_info
Changed TES centaur log level from debug to info. |
76f94b7
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Horneth |
Docker Hash (#1969)
* Docker Hash |
422f9da
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Commits on Feb 24, 2017
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kshakir |
Updated wdl4s to import patch for glob indexing.
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7e183cb
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kshakir |
Merge pull request #2014 from broadinstitute/ks_1980_patch
Updated wdl4s to import patch for glob indexing. |
f64c16e
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Commits on Feb 26, 2017
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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`. |
All checks have passed4 successful checks |
ba56af3
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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`. |
All checks have passed4 successful checks |
e397e25
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Commits on Feb 27, 2017
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mcovarr |
add a knob
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All checks have passed4 successful checks |
2e79a25
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kshakir |
Merge pull request #2032 from broadinstitute/ks_std_back_abort_patch
Slightly better abort behavior in standard backend. |
6fa1a63
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kshakir |
Merge pull request #2031 from broadinstitute/ks_memory_declaration_fix
Updates for memory validations. |
509ff2d
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Commits on Feb 28, 2017
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delocalizer |
* make sure dir that TMPDIR is set to, exists
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9f6180f
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mcovarr |
Merge pull request #2040 from delocalizer/crl_mkdir_tmpdir
* make sure dir that TMPDIR is set to, exists. Fixes #2035 |
335e983
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Commits on Mar 02, 2017
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kshakir |
Message, not throw, failures in WEA.startRunnableScopes.
Other syntax fixes. |
All checks have passed4 successful checks |
a89ce0a
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kshakir |
Merge pull request #2030 from broadinstitute/ks_catch_runnable_scopes
Message, not throw, failures in WEA.startRunnableScopes. |
fe2cd43
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cjllanwarne + geoffjentry |
JES API Manager: run creation and retries (#2026)
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c152015
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kshakir |
Don't fail Travis JES for external users.
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All checks have passed4 successful checks |
006b386
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kshakir |
Merge pull request #2045 from broadinstitute/ks_restore_external_tests
Don't fail Travis JES for external users. Closes #1717 |
5f02244
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kshakir |
Config backend wasn't dockerizing script paths.
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All checks have passed4 successful checks |
560b648
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kshakir |
Merge pull request #2028 from broadinstitute/ks_dockerize_paths
Config backend wasn't dockerizing script paths. |
ef6f0ed
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mcovarr |
Merge pull request #2027 from broadinstitute/mlc_call_caching_perf
add a knob |
528fe2c
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Commits on Mar 03, 2017
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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
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ruchim |
update readme examples and list external contributors (#2051)
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2e53c6d
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ruchim + ruchim |
Update Cromwell to use non-SNAP versions for Lenthall/WDL4s
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0e9b8bb
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ruchim + ruchim |
Update Cromwell develop to the next version
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e7791be
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Commits on Mar 06, 2017
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cjllanwarne |
Failure metadata redux
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Some checks were not successful2 failing and 2 successful checks |
7912d9c
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Commits on Mar 07, 2017
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cjllanwarne |
Merge pull request #2055 from broadinstitute/cjl_flatten_causedBy_met…
…adata Failure metadata redux |
38bd23e
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Commits on Mar 09, 2017
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mcovarr |
temporary directory should be world writeable (#2053)
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cf50d9a
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Commits on Mar 13, 2017
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Horneth |
I/O Actor (#2056)
* I/O Actor |
7dd945e
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cjllanwarne |
Workflow name length limit
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All checks have passed4 successful checks |
6928043
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cjllanwarne |
Merge pull request #2061 from broadinstitute/cjl_workflow_name_limit
Workflow name length limit. Closes #1725 |
67a022f
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Commits on Mar 14, 2017
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geoffjentry |
Have our config instructions match what we tell people (#2058)
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b1039f7
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Commits on Mar 17, 2017
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adamstruck + ruchim |
stage required config changes for funnel PR #15 (#2070)
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ca85733
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Commits on Mar 21, 2017
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jainh + geoffjentry |
Update README.md (#2043)
* Update README.md for richer doc on spark backend |
8f2b036
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Horneth |
send token file
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bfe0911
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Horneth |
WDL and inputs to release cromwell (#2065)
* WDL and inputs to release cromwell |
3e57722
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Commits on Mar 22, 2017
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ruchim |
replace empty cells in custom_labels column with {} (#2076)
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15b34cf
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kshakir |
Store custom labels.
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All checks have passed4 successful checks |
742942f
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kshakir |
Merge pull request #2083 from broadinstitute/ks_store_custom_labels_d…
…evelop Store custom labels. |
8ededf0
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Commits on Mar 24, 2017
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kshakir |
Report causal exceptions during Google auth failures.
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All checks have passed4 successful checks |
c4fbde7
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kshakir |
Merge pull request #2091 from broadinstitute/ks_causal_auth_failures
Report causal exceptions during Google auth failures. Closes #2090 |
92b76e3
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Horneth |
Improve ExecutionStore and WEA performance (#2087)
* Improve ExecutionStore and WEA performance |
b878654
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Commits on Mar 27, 2017
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Horneth |
Some retry improvements (#2080)
* Add a config option for IO attempts * add to changelog and readme * PR comment |
ddf58e7
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Commits on Mar 28, 2017
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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
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Commits on Mar 29, 2017
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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
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Horneth |
Update docker lookup (#2077)
* Update docker hash actor and http retry flow * add IO dispatchers to streams * PR comment |
1eb4e89
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Horneth |
Catch namespace load throwables Closes #2066 (#2098)
* catch namespace load throwables * remove unnecessary try |
fc0b2f9
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Commits on Mar 30, 2017
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Horneth |
Update wdl4s Closes #1982 Closes #1951 (#2097)
* update wdl4s * update wdl4s * update cromwell with new dependencies * fix hard links * centaur develop * indentation |
d51bb50
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Commits on Mar 31, 2017
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Horneth |
Adds submitted and aborted status to Metadata (#2114)
* send submitted amd aborted status to MD * remove unused import |
e9d8c62
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mcovarr |
Docker hashing gets its own subproject. (#2099)
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8792a93
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buchanae + Horneth |
Fix funnel test and pin version to git commit (#2116)
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d391706
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cjllanwarne |
Failure metadata migration
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All checks have passed4 successful checks |
f6575de
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cjllanwarne |
Merge pull request #2059 from broadinstitute/cjl_failure_metadata_mig…
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c7dc718
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Commits on Apr 03, 2017
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cjllanwarne |
Bringing in if then else expressions from wdl4s
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Some checks were not successful2 errored and 1 pending checks |
bbf9983
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cjllanwarne |
Merge pull request #2107 from broadinstitute/cjl_if_then_else
Bringing in if then else expressions from wdl4s |
223388a
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jsotobroad |
Adding jsotobroad to pullapprover members list
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All checks have passed4 successful checks |
3ed4dcc
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cjllanwarne |
Merge pull request #2123 from broadinstitute/js_interloper_pullapprove
Adding jsotobroad to pullapprover members list |
a559aea
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cjllanwarne |
If then else Changelog
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Some checks were not successful2 errored and 1 successful checks |
f9e4922
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cjllanwarne |
Merge pull request #2122 from broadinstitute/cjl_ifthenelse_changelog
If then else Changelog |
fe81755
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Horneth |
Shutdown materializer and Http pool (#2118)
* Shutdown materializer and Http pool * PR comment |
83f2ded
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Horneth |
Declaration evaluation (#2119)
* Coerce decalarations: * update wdl4s + custom centaur * fix dependency * be more patient.. * centaur develop |
caab258
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Commits on Apr 05, 2017
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mcovarr |
handling nullable job store simpletons (#2151)
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00d2790
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mcovarr |
Recover from database failures when reading the workflow store. (#2150)
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88630db
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Commits on Apr 06, 2017
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geoffjentry + cjllanwarne |
Engine and JES changes supporting custom retries
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All checks have passed4 successful checks |
3461b16
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cjllanwarne |
Merge pull request #2102 from broadinstitute/cjl_backend_retries
Engine and JES changes supporting custom retries. Closes #1925 |
82b7854
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Commits on Apr 11, 2017
Commits on Apr 12, 2017
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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
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geoffjentry |
EngineWorkflowFinalizationActor only had a single implementation, rem…
…ove layer of indirection (#2155) |
91dd653
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Commits on Apr 14, 2017
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cjllanwarne |
Upgrade test script
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Some checks were not successful2 errored and 1 successful checks |
7947d4c
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cjllanwarne |
Merge pull request #2164 from broadinstitute/cjl_test_upgrade
Test_upgrade script |
5a1f768
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ruchim |
Config-specified Default runtime attributes (#2121)
grab runtime attribute defaults from reference.conf, add deprecation warnings, introduced the BadDefaultAttribute WdlValue. |
9460d47
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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
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Commits on Apr 18, 2017
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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
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Commits on Apr 19, 2017
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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
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Commits on Apr 20, 2017
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cjllanwarne |
Cromwell API client (for Centaur)
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All checks have passed4 successful checks |
6eb104b
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cjllanwarne |
Merge pull request #2169 from broadinstitute/cjl_cromwell_api_client
Cromwell API client for Centaur. Closes #2128 |
0853385
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Commits on Apr 21, 2017
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Horneth |
Support for docker hash lookup of public quay.io images (#2184)
* add docker hash lookup for public quay.io images * custom centaur |
2033421
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Horneth |
centaur develop
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229e974
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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
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cjllanwarne |
Publish cromwell-api-client artifact
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Some checks were not successful2 errored and 1 successful checks |
63d133a
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cjllanwarne |
Merge pull request #2192 from broadinstitute/cjl_aggregate_client
Publish cromwell-api-client artifact |
3619ba8
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cjllanwarne |
Client publish fixup
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1ad7716
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cjllanwarne |
Merge pull request #2194 from broadinstitute/cjl_client_publish-fixup
Client publish fixup |
77b8b1d
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Commits on Apr 24, 2017
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cjllanwarne |
(Centaur Port) Decode responses
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Some checks were not successful1 failing and 3 successful checks |
754134b
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cjllanwarne |
Remove race conditions from WriteMetadataActorSpec
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All checks have passed4 successful checks |
5b66bf5
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cjllanwarne |
Merge pull request #2199 from broadinstitute/cjl_decode_responses
(Centaur Port) Decode responses |
9a9745a
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cjllanwarne |
Merge pull request #2195 from broadinstitute/cjl_flaky_test_2193
Remove race conditions from WriteMetadataActorSpec. Closes #2193 |
20f8687
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cjllanwarne |
Deprecation errors for DB configs
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All checks have passed4 successful checks |
c81343c
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Commits on Apr 25, 2017
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cjllanwarne |
Merge pull request #2200 from broadinstitute/cjl_DEPRECATED
Deprecation errors for DB configs. Closes #2186 |
69a8d21
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cjllanwarne |
JES in-command write_lines fixup
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All checks have passed4 successful checks |
8f6ee41
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Horneth |
Execution Store and JobPaths optimizations (#2198)
* Limit JobPaths creation and Improve execution store performance * Fix subworkflow paths * PR comments |
4a49f93
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cjllanwarne |
Merge pull request #2191 from broadinstitute/cjl_write_lines_jes
JES in-command write_lines fixup. Closes #1906 |
05ec820
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Commits on Apr 26, 2017
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cjllanwarne |
Cromwell's failure is now complete
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Some checks were not successful1 failing and 3 successful checks |
50375c7
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cjllanwarne |
Merge pull request #2203 from broadinstitute/cjl_consistent_failure
Cromwell's failure is now complete (develop edition). Closes #2201 |
5360704
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Horneth |
Tweak retries (#2208)
* tweak retries * PR comments |
cf37252
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Commits on Apr 27, 2017
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Horneth |
Use io dispatcher (#2206)
* Use io dispatcher * PR comments |
c89c83f
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Commits on Apr 28, 2017
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cjllanwarne |
Remove unneeded SubWorkflowStoreCompleteSuccess message
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All checks have passed4 successful checks |
336d4f6
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Commits on Apr 29, 2017
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Horneth |
JSON auth for Google SA (#2213)
* JSON auth for Google SA * deprecation warning for pem files |
e316d8d
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cjllanwarne |
Merge pull request #2218 from broadinstitute/cjl_remove_SubWorkflowSt…
…oreCompleteSuccess Remove unneeded SubWorkflowStoreCompleteSuccess message. Closes #2185 |
d54c313
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Commits on May 01, 2017
|
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cjllanwarne |
Bring in validation messages from WDL4S
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All checks have passed4 successful checks |
ea5f989
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||
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cjllanwarne |
Merge pull request #2214 from broadinstitute/cjl_better_validation_me…
…ssages Bring in validation messages from WDL4S. Closes #2211 |
fceeedf
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Commits on May 02, 2017
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mcovarr + mcovarr |
Batching Job Store simpleton writes.
|
7263b5e
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cjllanwarne |
Removing semicolon from migration query
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Some checks were not successful2 errored and 1 pending checks |
aaa64d7
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cjllanwarne |
Merge pull request #2231 from broadinstitute/cjl_remove_semicolons_de…
…velop Removing semicolon from migration query (develop edition) |
f094129
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Commits on May 03, 2017
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danbills + geoffjentry |
adding Dan Billings to pull approve list (#2240)
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a4d4616
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jsotobroad |
JobStoreSimpletonMigration was putting quotation marks around file va…
…lues which caused the jobs to fail once cromwell recovered after a migration |
All checks have passed4 successful checks |
f999719
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Horneth |
use the right failureMode value (#2239)
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98e0e6e
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Commits on May 04, 2017
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cjllanwarne |
Akka HTTP bump
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All checks have passed4 successful checks |
c8e9c94
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cjllanwarne |
Merge pull request #2245 from broadinstitute/cjl_akka_http_10.0.6
Akka HTTP bump |
834aaa0
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Commits on May 05, 2017
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mcovarr + mcovarr |
Batch writes of call caching related data.
|
46bd6fe
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cjllanwarne |
WDL4S bump
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b8574c1
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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
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Commits on May 07, 2017
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cjllanwarne |
Merge pull request #2247 from broadinstitute/cjl_wdl4s_bump
WDL4S bump |
a046dfe
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Commits on May 08, 2017
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jsotobroad |
Double Quoted file inputs cause PipelineAPI workflows to run forever. C…
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496c4f6
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Commits on May 10, 2017
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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
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Horneth |
Allow for tag + digest docker images (#2255)
* allow for tag + digest docker images * PR comments |
aab4763
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Commits on May 12, 2017
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Horneth |
add conf
(cherry picked from commit c14e64d) |
1d4e0ab
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jsotobroad |
Readme Link Fixes (#2259)
Fix a few links in README |
1a131c1
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Commits on May 15, 2017
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Horneth |
update changelog to reflect reality (#2263)
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5bb2875
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Commits on May 17, 2017
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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
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Commits on May 18, 2017
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Horneth |
update changelog again (#2272)
* update changelog again * fix space |
cd4059b
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Commits on May 19, 2017
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antonkulaga + Horneth |
fix for #2256 (#2280)
This PR fixes #2256 by overriding default entry-point with /bin/bash |
ddf223d
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Commits on May 22, 2017
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danbills |
tested read lines
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4ac640b
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Commits on May 23, 2017
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ruchim |
Allow customLabels submission to Cromwell Client (#2257)
allow customLabels submission through CromwellClient |
693cda5
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ruchim |
wow (#2290)
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425cde2
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danbills |
added tests for all read functions
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Some checks were not successful1 failing and 1 pending checks |
0be7611
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danbills |
tidy up the read_X code
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e34957f
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ruchim |
Query using Labels (#2253)
added querying through labels |
091ed3b
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jsotobroad |
validation of input gcs file paths that start with \" (#2271)
* validateworkflow input gcs file paths that start with \" |
e79e081
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cjllanwarne |
Bringing map to pair coercion and basename from WDL4S
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All checks have passed4 successful checks |
948efa5
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Commits on May 24, 2017
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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
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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
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Horneth |
fix
|
f673cc8
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cjllanwarne |
Merge pull request #2274 from broadinstitute/cjl_coerce_map_to_pairs
Bringing map to pair coercion and basename from WDL4S |
81d5945
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danbills |
added ability to configure read X limits
|
96b33e5
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danbills |
Merge branch 'develop' into db_read_limits
|
52c6faa
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Commits on May 25, 2017
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Horneth + mcovarr |
Workflow Docker Hashing.
|
38b52a3
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danbills |
added README and CHANGELOG comments
|
45ca36d
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danbills |
formatting
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607a1d0
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danbills |
Merge pull request #2291 from danbills/db_read_limits
added read limits to read_X functions |
06d3f11
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Commits on May 26, 2017
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Horneth |
fix release wdl and custom label summarizing (#2298)
|
b30a232
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Commits on May 30, 2017
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Horneth |
Update mysql and jackson-databind dependencies (#2299)
* update mysql and jackson-databind dependencies * update jackson-module-scala version |
1312eb3
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Horneth |
Update cromwell version to 27
|
1b7c65f
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Horneth |
Update cromwell version from 27 to 28
|
4327ca6
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Commits on Jun 01, 2017
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ruchim |
Preliminary validation of workflow options (#2295)
preliminary validation of wf options before WorkflowID creation |
98d766b
|
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|
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mcovarr + mcovarr |
Purge workflow store entry before job entries.
|
bb96682
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Commits on Jun 05, 2017
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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
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Commits on Jun 06, 2017
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Horneth |
Add retries to credential validation (#2314)
* works? * PR comments * rebase * oops |
6fbeadc
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Commits on Jun 08, 2017
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mcovarr + mcovarr |
jfrog
|
4487a51
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Commits on Jun 09, 2017
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Horneth |
honor allow result reuse (#2341) (#2349)
(cherry picked from commit 461cff2) |
ac3d65e
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Commits on Jun 12, 2017
|
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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
|
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mcovarr + mcovarr |
Remove some user-facing WDL specificity.
|
c0289dc
|
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|
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mcovarr + mcovarr |
Make workflow type optional in store, remove references to WDL in Swa…
…gger. |
6551129
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Commits on Jun 13, 2017
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mcovarr |
oops
|
bf3202d
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Commits on Jun 15, 2017
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mcovarr + mcovarr |
Don't implicitly add a library/ repo prefix to Docker images as that …
…breaks 26-era call caches. |
f3e04bf
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|
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Horneth |
Config option to disable copying of outputs on cache hit for JES (#2347)
* Add support for copyless call caching in JES |
46ad512
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Commits on Jun 20, 2017
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Horneth |
conf fix
|
151bf05
|
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Horneth |
Call Caching Diff Endpoint (#2363)
* Call Caching Diff Endpoint |
3801e14
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Commits on Jun 21, 2017
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ruchim |
deprecated image (#2370)
|
1f166d9
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Commits on Jun 22, 2017
|
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Horneth |
Add version endpoint to Cromwell client (#2368)
* add version endpoint to Cromwell client * add version endpoint to Cromwell client |
1394bdd
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|||
|
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mcovarr + mcovarr |
only check stderr if failOnStderr is true
|
90f1e17
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Commits on Jun 23, 2017
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mcovarr + mcovarr |
Make an effort to diagnose bad bucket names.
|
931f62e
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Commits on Jun 26, 2017
|
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mcovarr + mcovarr |
Some magic to work with the new Travis Trusty images.
|
9660633
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Commits on Jun 27, 2017
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ruchim |
Gather completed shards (#2376)
* fail slow fixup, and adding scatter collectorkey to ExecutionStoreBenchmark test |
c99856a
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ruchim |
Add Labels (#2357)
* add label manager actor, prelim tests and swagger updates, changelog updates and docs |
65d1849
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|
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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
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Commits on Jun 28, 2017
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mcovarr + mcovarr |
Sanify the default metadata batch write size.
|
477faa4
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Commits on Jun 29, 2017
|
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Horneth |
Cromwell restart (#2386)
* Centaur Restart |
5fa488e
|
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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
|
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mcovarr + mcovarr |
Bump to newliney wdl4s, document this user-visible change.
|
8962b78
|
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Horneth |
fix wdltool release (#2393)
|
031d9b1
|
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|
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jsotobroad + Horneth |
add eventually to WorkflowStoreAactorSpec encrypted workflow options …
…test (#2395) |
a33f74a
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Commits on Jun 30, 2017
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ruchim |
Changed Label Formatting (#2389)
Modify Cromwell label expectations |
553ab31
|
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ruchim |
travis tweaks (#2397)
* tone down travis slack notifications |
e75afe4
|
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ruchim |
28 Changelog (#2398)
final additions to changelog |
3769c06
|
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|
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Horneth |
Update cromwell version to 28
|
f63a9e6
|
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Horneth |
Update cromwell version from 28 to 29
|
7c9641c
|
|||
|
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Horneth |
update release WDL (#2399)
|
635733c
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Commits on Jul 01, 2017
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geoffjentry |
Migrate Cromwell from Spray to Akka HTTP. Closes #1243 (#2380)
|
176de92
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Commits on Jul 05, 2017
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geoffjentry |
Scala 2.12 support for Cromwell (#2412)
|
3e98082
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Commits on Jul 06, 2017
|
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Horneth + geoffjentry |
Rebased (#2406)
|
a30c701
|
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mcovarr + mcovarr |
Remove pre-PBE tables.
|
13691aa
|
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|
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mcovarr + mcovarr |
Command line parsing redo.
|
308f087
|
Commits on Jul 07, 2017
|
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geoffjentry |
Only gzip metadata if requested. Closes #2419 (#2427)
* Only gzip metadata if requested. Closes #2419 |
644967d
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Commits on Jul 11, 2017
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mcovarr + mcovarr |
patvars
|
6d00a45
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Commits on Jul 12, 2017
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mcovarr + mcovarr |
make console usable again
|
1b958d2
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|
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geoffjentry |
Add restrict-metadata-access (#2435)
Add restrict-metadata-access |
2862235
|
Commits on Jul 14, 2017
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|
francares |
Fixed issue regarding parsing request body on query POST API. (#2447)
|
2e32c41
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Commits on Jul 17, 2017
|
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mcovarr + mcovarr |
Separate out retryables from true terminals from the WEA perspective.
|
8c0f888
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kshakir |
Removed /api prefix from /engine.
|
All checks have passed4 successful checks |
9e688ec
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cjllanwarne |
Preempted to backendStatus in existing metadata.
|
c5adbf2
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Commits on Jul 18, 2017
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kshakir |
Merge pull request #2454 from broadinstitute/ks_move_version_endpoint
Removed /api prefix from /engine. |
947f8c6
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cjllanwarne |
Merge pull request #2443 from broadinstitute/cjl_2438
Preempted to backendStatus in existing metadata. Develop edition |
1786ae5
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kshakir |
Docker publish develop branch to dev environment.
|
All checks have passed4 successful checks |
2e9a96e
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kshakir |
Merge pull request #2465 from broadinstitute/ks_docker_tag_caas
Docker publish develop branch to dev environment. |
b32a8fe
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mcovarr + mcovarr |
Update to beginning-cromwomified, subprojecty wdl4s.
|
2708188
|
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mcovarr + mcovarr |
Updated wdl4s
|
9620f74
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Commits on Jul 19, 2017
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cjllanwarne |
Resurrected the unused `Preempted` status
|
All checks have passed4 successful checks |
fd05a87
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||
|
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cjllanwarne |
Merge pull request #2462 from broadinstitute/cjl_2455
Resurrected the unused `Preempted` status |
9b08454
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Commits on Jul 20, 2017
|
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geoffjentry |
Assign a dispatcher to services and allow them to be customized (#2470)
|
eece7ae
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cjllanwarne |
Made 'size' accept empty files, Cromwell-side
|
Some checks were not successful2 errored and 1 successful checks |
9cf69ad
|
||
|
|
cjllanwarne |
Merge pull request #2468 from broadinstitute/cjl_optional_file_size
Made 'size' accept empty files, Cromwell-side |
0b92711
|
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|
cjllanwarne |
Made call cache hash endpoint more JSONic
|
All checks have passed4 successful checks |
32841b9
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cjllanwarne |
Merge pull request #2471 from broadinstitute/cjl_reformat_ccdiff
Made call cache hash endpoint more JSONic |
f1ee2d2
|
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cjllanwarne |
Diff endpoint doc'ing
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All checks have passed4 successful checks |
9225bc5
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cjllanwarne |
Merge pull request #2473 from broadinstitute/cjl_diff_docs
Diff endpoint doc'ing |
8a8ed40
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Commits on Jul 22, 2017
|
|
danbills |
Pull approve v2 featuring GH review integration (#2477)
bumped pullapprove to v2 and added GH reviews |
36a08ec
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|
|
kshakir |
Switch from travis encrypted files to vault
|
All checks have passed4 successful checks |
d5a51c6
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Commits on Jul 24, 2017
|
|
kshakir |
Merge pull request #2481 from broadinstitute/ks_test_docker_vault
Switch from travis encrypted files to vault. Closes #1296 |
be6ad40
|
|||
|
|
geoffjentry |
Put the binding timeout back to where it was in spray-land (#2478)
|
11496fc
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Commits on Jul 25, 2017
|
|
ruchim |
Don't append to lists (#2485) (#2486)
append metadata events to a vector not list |
49b59b0
|
Commits on Jul 26, 2017
|
|
kshakir |
Initialize db before serving over HTTP
|
All checks have passed4 successful checks |
76f6aae
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||
|
|
kshakir |
Merge pull request #2484 from broadinstitute/ks_liquibase_then_bind
Initialize db before serving over HTTP |
5b16d61
|
|||
|
|
Horneth |
Handle failed Cromwell requests (#2488)
* Handle failed Cromwell requests in the CromwellAPIClient |
27f9f1c
|
|||
|
|
danbills |
removed jainh from committers to fix pullapprove (#2491)
|
219b0c5
|
|||
|
|
Horneth |
Handle null access token from Google Credentials (#2489)
* handle null access token from Google Credentials |
645d8b2
|
Commits on Jul 27, 2017
|
|
cjllanwarne |
Additional clienty bits for Cromwell
|
bdfaf91
|
|||
|
|
cjllanwarne |
Merge pull request #2474 from broadinstitute/cjl_more_clienty_bits
Additional clienty bits for Cromwell |
16a7498
|
|||
|
|
mcovarr + mcovarr |
Updates for subprojected wdl4s. Also remove "dryRun" since that didn'…
…t actually dry run anything. |
bb0f6ea
|
|||
|
|
mcovarr + mcovarr |
search and replace run amok
|
e648273
|
Commits on Jul 28, 2017
|
|
geoffjentry |
Upgrade to scala 2.12.3 (#2502)
|
42a1dce
|
|||
|
|
cjllanwarne |
Model objects for Cromwell Queries
|
All checks have passed4 successful checks |
4d8825d
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||
|
|
cjllanwarne |
Merge pull request #2501 from broadinstitute/cjl_query_responses
Model objects for Cromwell Queries |
c041402
|
|||
|
|
cjllanwarne |
Allow "AbortedResponse" even when not aborting
|
All checks have passed4 successful checks |
350a024
|
||
|
|
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 |
Dispatcherizing undispatcherized actors. Trying to standardize on add…
…ing it to the props where appropriate (#2499) |
a611db6
|
Commits on Jul 31, 2017
|
|
kshakir |
Replaced use of Future.foreach with error handling
|
All checks have passed4 successful checks |
8d3e615
|
||
|
|
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 |
Graceful Server Shutdown (#2490)
* Graceful shutdown * Dont overwrite jes auth file include application.conf in centaur conf files |
07a5671
|
|||
|
|
kshakir |
Client only modifies request json when inserting a refresh token.
|
All checks have passed4 successful checks |
cf8c228
|
||
|
|
kshakir |
Merge pull request #2509 from broadinstitute/ks_client_pass_options
Client only modifies request json when inserting a refresh token. |
e97bcc7
|
Unified
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3
.gitattributes
| @@ -1,6 +1,3 @@ | ||
| -# This file can always be added to, line additions should never collide. | ||
| -CHANGELOG.MD merge=union | ||
| - | ||
| # These files are text and should be normalized (Convert crlf => lf) | ||
| *.scala text | ||
| *.MD text | ||
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17
.gitignore
| @@ -1,10 +1,19 @@ | ||
| -.idea | ||
| -log | ||
| -target | ||
| +# common scala config | ||
| +*~ | ||
| +.DS_Store | ||
| .artifactory | ||
| +.idea/* | ||
| +!/.idea/inspectionProfiles/ | ||
| +.idea/inspectionProfiles/* | ||
| +!/.idea/inspectionProfiles/Project_Default.xml | ||
| +target | ||
| + | ||
| +# custom config | ||
| cromwell-executions | ||
| cromwell-test-executions | ||
| -cromwell-workflow-logs | ||
| cromwell-test-workflow-logs | ||
| +cromwell-workflow-logs | ||
| local-cromwell-executions | ||
| +log | ||
| native | ||
| +scripts/docker-compose-mysql/compose/mysql/data |
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6
.idea/inspectionProfiles/Project_Default.xml
| @@ -0,0 +1,6 @@ | ||
| +<component name="InspectionProjectProfileManager"> | ||
| + <profile version="1.0"> | ||
| + <option name="myName" value="Project Default" /> | ||
| + <inspection_tool class="TypeAnnotation" enabled="false" level="WARNING" enabled_by_default="false" /> | ||
| + </profile> | ||
| +</component> |
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34
.pullapprove.yml
| @@ -1,18 +1,28 @@ | ||
| -approve_by_comment: true | ||
| -approve_regex: ':\+1:' | ||
| -reset_on_push: false | ||
| -author_approval: ignored | ||
| -reviewers: | ||
| +# enabling version 2 turns github reviews on by default | ||
| +version: 2 | ||
| +group_defaults: | ||
| + approve_by_comment: | ||
| + enabled: true | ||
| + approve_regex: ':\+1:' | ||
| + reset_on_push: | ||
| + enabled: false | ||
| +groups: | ||
| + reviewers: | ||
| required: 2 | ||
| - members: | ||
| - - cjllanwarne | ||
| + github_reviews: | ||
| + enabled: true | ||
| + author_approval: | ||
| + ignored: true | ||
| + users: | ||
| - Horneth | ||
| - - scottfrazer | ||
| - - mcovarr | ||
| - - geoffjentry | ||
| - - kshakir | ||
| + - cjllanwarne | ||
| - francares | ||
| - gauravs90 | ||
| - - jainh | ||
| + - geoffjentry | ||
| + - jsotobroad | ||
| + - katevoss | ||
| - kcibul | ||
| + - kshakir | ||
| + - mcovarr | ||
| - ruchim | ||
| + - danbills |
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42
.travis.yml
| @@ -1,21 +1,51 @@ | ||
| sudo: required | ||
| dist: trusty | ||
| +services: | ||
| + - docker | ||
| language: scala | ||
| scala: | ||
| - - 2.11.8 | ||
| + - 2.12.2 | ||
| jdk: | ||
| - oraclejdk8 | ||
| +cache: | ||
| + # md5deep - https://github.com/travis-ci/travis-ci/issues/3122 | ||
| + branch: md5deep | ||
| + directories: | ||
| + - $HOME/.ivy2/cache | ||
| + - $HOME/.sbt/boot/ | ||
| +before_cache: | ||
| + # Tricks to avoid unnecessary cache updates | ||
| + - find $HOME/.ivy2 -name "ivydata-*.properties" -delete | ||
| + - find $HOME/.sbt -name "*.lock" -delete | ||
| +before_install: | ||
| + # https://github.com/travis-ci/travis-ci/issues/7940#issuecomment-310759657 | ||
| + - sudo rm -f /etc/boto.cfg | ||
| env: | ||
| - # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked | ||
| - - BUILD_TYPE=sbt | ||
| - - BUILD_TYPE=centaurJes | ||
| - - BUILD_TYPE=centaurLocal | ||
| + global: | ||
| + - CENTAUR_BRANCH=develop | ||
| + - INTEGRATION_TESTS_DIR=src/main/resources/integrationTestCases | ||
| + matrix: | ||
| + # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked | ||
| + - BUILD_TYPE=sbt | ||
| + - BUILD_TYPE=checkPublish | ||
| + - BUILD_TYPE=centaurJes | ||
| + - BUILD_TYPE=centaurLocal | ||
| + - BUILD_TYPE=centaurTes | ||
| script: | ||
| - src/bin/travis/test.sh | ||
| after_success: | ||
| - - src/bin/travis/publishSnapshot.sh | ||
| + - src/bin/travis/afterSuccess.sh | ||
| deploy: | ||
| provider: script | ||
| script: src/bin/travis/publishRelease.sh | ||
| on: | ||
| tags: true | ||
| +notifications: | ||
| + slack: | ||
| + rooms: | ||
| + - secure: B5KYcnhk/ujAUWlHsjzP7ROLm6MtYhaGikdYf6JYINovhMbVKnZCTlZEy7rqT3L2T5uJ25iefD500VQGk1Gn7puQ1sNq50wqjzQaj20PWEiBwoWalcV/nKBcQx1TyFT13LJv8fbFnVPxFCkC3YXoHedx8qAhDs8GH/tT5J8XOC8= | ||
| + template: | ||
| + - "Build <%{build_url}|#%{build_number}> (<%{compare_url}|%{commit}>) of %{repository}@%{branch} by %{author} %{result} in %{duration}" | ||
| + on_success: change | ||
| + on_failure: change | ||
| + on_pull_requests: false |
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