Develop to master for sprint 6 #86
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…factored/amended/rebased.
…implementation in Slick.
- Added unique constraints, execpt to WORKFLOW_EXECUTION_AUX that already had one - Fixed unique constraint on SYMBOL issue due to MySQL "feature" https://bugs.mysql.com/bug.php?id=8173 - Moved "decoercion" to a WdlValue.toRawString: Try[String] - Refactored usages of null instead of Option, constants, fully qualified class names, Duration instead of `int secs` - LocalJob now allows null PID / RC - Fixed return type of DataAccess.apply(): DataAccess - More tests for duplicate workflow & output inserts, looking up non-existent workflow
… the constructor of SlickDataAccess. TestSlickDatabase now creates (and closes) its own pool to test the database for optional tests, instead of reaching into a partially created instance of SlickDataAccess. At the moment, don't know if it's possible to pass in the existing pool created by TSD, but the second pool creation only takes a second or two.
Persistence WIP - against develop
…bad interactions with Dockerized components of the build system.
Don't run tests during assembly.
A more thorough Hello World restart test.
Moved mysql dependency to test, and the server actually uses google-api-services-drive at runtime.
Turned on mysql testing on travis.
…ated safely by concurrent workflow actors in the WorkflowManagerActorSpec.
Convert DummyDataAccess to use a TrieMap internally.
Append rather than overwrite allows scoverage to run.
Check return codes from calls and fail calls and workflows appropriately.
…local cd to call directory on Dockerless local backend before running command.
PLEASE MERGE #80 FIRST Use absolute File path to be able to pass files in the Dockerized local backend.
Switched `WorkflowExecutionAux` Slick columns from `String` to `Clob`. Added a test to store/retrieve the 441 char `/3step.wdl` resource paired with a ~10K generated json. Fixed bug where workflow creation was storing `Call`s using `.taskFqn` instead of `.fullyQualifiedName`. Added a set of permuted tests for regression checking fully qualified name inserts and updates. Fixed typo in `to*Worfk*low` utility method. Re-enabling connection pool for main and tests. Switched off command line Hikari info & warning logging via logback.xml.
Slick queries are all compiled. Testing SlickDataAccess failures on null and missing values.
Fixed issue with using wdl source/json >254 chars. DSDEEPB-717
Fix coercion failure handling
DSDEEPB-716 Exit cleanly with bad WDL.
Fixed Symbol doubly qualifying the symbol names. (thx mcovarr/scottfrazer) Added `WdlType.fromRawString`, with test against respective `WdlValue.toRawString`. `DummyDataAccess` replaced with using `DataAccess` instances, with cleanup of connections. When creating in memory databases will create unique `DataAccess` instances, just like Dummy. TestSlickDatabase now prints a warning, instead of an error, when unable to connect to MySql.
Updates to fix coercion errors. DSDEEPB-727
Documentation, some (minor) API changes, SBT version now == sprint number
…rtions can be made to see if the files were actually passed!
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@mcovarr Was this supposed to be merged? |
Fix Docker file-passing test.
geoffjentry
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Jul 13, 2015
Develop to master for sprint 6
mcovarr
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Oct 21, 2017
* update failure metadata path * add missing error message * ignore 2 tests
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