Diffusion SHRINE MedCo Fork 5d48cd0ab33d

Merge remote-tracking branch 'origin/develop' into develop
5d48cd0ab33d
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Authored by Ben Carmen <benjamin_carmen@hms.harvard.edu> on Jan 29 2016, 15:39.

Description

Merge remote-tracking branch 'origin/develop' into develop

Conflicts:
apps/dashboard-app/src/main/scala/net/shrine/dashboard/DashboardService.scala

Details

Committed

Ben Carmen <benjamin_carmen@hms.harvard.edu>

Jan 29 2016, 15:39

Pushed

mickmis

Mar 14 2017, 15:12

Parents

R2664:3ef029060a95: Another try at getting akka to run as all-daemon
R2664:8a37f2c00429: Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…

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Ben Carmen <benjamin_carmen@hms.harvard.edu> committed R2664:5d48cd0ab33d: Merge remote-tracking branch 'origin/develop' into develop (authored by Ben Carmen <benjamin_carmen@hms.harvard.edu>).Jan 29 2016, 15:39

Merged Changes

Commit	Author	Details	Committed
3ef029060a95	David Walend	Another try at getting akka to run as all-daemon	Jan 28 2016
6c7bf41ae493	David Walend	Seeing if I can get some control over akka threads and make them daemons via…	Jan 28 2016
d6a2021af428	David Walend	Removed stray columns from previousQueries	Jan 28 2016
85fb775a3a20	David Walend	Added logging to try to find where the message comes in	Jan 28 2016
9a403f61dfab	David Walend	Attempting to track down what happened to the FlagQueryRequest's message	Jan 27 2016
29407c707e89	David Walend	Attempting to track down what happened to the FlagQueryRequest's message	Jan 27 2016
c623fa3f3116	David Walend	Should now handle flag/unflag query requests in the QEP's database	Jan 27 2016
254268658d55	David Walend	Some tests for flagged queries	Jan 27 2016
54645092738b	David Walend	Add flagged query table and use it a little bit	Jan 27 2016
5315849aa994	David Walend	Factored the JDNI/tomcat boilerplate off into its own class	Jan 26 2016
685c37db95eb	David Walend	todo node to check finding the right cert.	Jan 26 2016
3c0dcb5f165c	David Walend	Handling a case where the dashboard's KeyStore just has the right cert in it.	Jan 26 2016
bfad2e33d56b	David Walend	Removing the parts that the QEP uses to ask adapters for previous queries	Jan 26 2016
75b470281df5	David Walend	Renamed mysterious thing that is the heart of the QEP to AbstractQepService…	Jan 26 2016
4eba8153a907	David Walend	Renamed shrine-service to shrine-qep	Jan 26 2016
5b03b448644f	David Walend	Renamed 'service' package to 'qep'	Jan 26 2016
30dd91476f9c	David Walend	Cleaned up dead imports from some ancient refactoring.	Jan 26 2016
bfeaa8acc95a	David Walend	Added test for selecting by user	Jan 26 2016
b3ad90ab2ed9	David Walend	Guess for the right value of queryMasterid	Jan 25 2016
627357bb98ce	David Walend	Trying out reading previous queries from the db	Jan 25 2016
53d591999cb2	David Walend	Some debugs to see what's what	Jan 22 2016
fe5b56ccf246	David Walend	Bill's recommendations for handling the previous query table	Jan 22 2016
ba61dcf294fc	David Walend	Now storing queries locally in the QEP	Jan 22 2016
4a0864cdb8b3	David Walend	Adding mysql.ddl for qepQueryDb. Split out the sql directory into…	Jan 21 2016
87fdce25c99e	David Walend	cleaned up a lot of dead sql code. SHRINE-1263	Jan 20 2016
69fb78df0401	David Walend	Moving sql scripts	Jan 20 2016
adc59d4ba10b	David Walend	Added test for QepQueryDb, fixed a typo	Jan 20 2016
75f57ff39ec6	David Walend	Adding some slick code for the qep db	Jan 19 2016
e59e514d57f6	David Walend	Basics of the QueryInstance db table	Jan 19 2016
270675b52301	David Walend	Make testing work a bit better	Jan 15 2016
def752429556	David Walend	Crap. test.com is a real domain. Changed to bogus.harvard.edu	Jan 15 2016
c59582c7fa5b	David Walend	Remove test of failing to talk to a missing web service	Jan 15 2016
8dc4aedc6b15	David Walend	Trying out trimming the url to save mischief	Jan 15 2016
03430c9da802	David Walend	Cleaning up some suggestions from IDEA	Jan 15 2016
42aa7426ea22	David Walend	Rearranged dashboard-to-dashboard auth, got through IDEAs checks to green	Jan 14 2016
bd59adccfa3c	David Walend	Last of the for comprehension	Jan 14 2016
87ff89e8081d	David Walend	Added more to the for comprehension	Jan 14 2016
9579770dc231	David Walend	Added more to the for comprehension	Jan 14 2016
865dfd959dbe	David Walend	Added more to the for comprehension	Jan 14 2016
7bf1574d5841	David Walend	Started refactoring to a for comprehension	Jan 14 2016
4f5b748e323c	David Walend	Added a null check for the issuer	Jan 14 2016
c2f3e5bc06fd	David Walend	More sensible values for the jwts subject field to help refill the user object…	Jan 14 2016

Changes (137)
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		Path
D		adapter/adapter-service/src/main/resources/adapter-drop-1.13-tables.sql
D		adapter/adapter-service/src/main/resources/adapter-drop.sql
D		adapter/adapter-service/src/main/resources/adapter-migrate-data-to-1.14-tables.sql
D		adapter/adapter-service/src/main/resources/adapter-migrate-schema-to-1.14.sql
D		adapter/adapter-service/src/main/resources/adapter-migrate-schema-to-1.16.sql
D		adapter/adapter-service/src/main/resources/adapter-migrate-schema-to-1.18.sql
D		adapter/adapter-service/src/main/resources/adapter-oracle-drop.sql
D		adapter/adapter-service/src/main/resources/adapter-oracle.sql
V		adapter/adapter-service/src/main/{resources → sql}/adapter.sql
M		adapter/adapter-service/src/main/scala/net/shrine/adapter/audit/AdapterAuditDb.scala
M		adapter/adapter-service/src/main/scala/net/shrine/adapter/dao/model/ShrineQuery.scala
V		adapter/adapter-service/src/main/{sql ← resources}/adapter.sql
D		adapter/adapter-service/src/test/resources/adapter-h2.sql
M		apps/dashboard-app/src/main/resources/reference.conf
M		apps/dashboard-app/src/main/scala/net/shrine/dashboard/Boot.scala
M		apps/dashboard-app/src/main/scala/net/shrine/dashboard/DashboardService.scala
M		apps/dashboard-app/src/main/scala/net/shrine/dashboard/httpclient/HttpClientDirectives.scala
M		apps/dashboard-app/src/main/scala/net/shrine/dashboard/jwtauth/ShrineJwtAuthenticator.scala
M		apps/dashboard-app/src/test/resources/teststatus/configuration
M		apps/dashboard-app/src/test/resources/teststatus/status
M		apps/dashboard-app/src/test/scala/net/shrine/dashboard/DashboardServiceTest.scala
M		apps/dashboard-war/src/main/resources/reference.conf
M		apps/dashboard-war/src/test/resources/dashboard.conf
A		apps/dashboard-war/src/test/resources/shrine.keystore
M		apps/shrine-app/pom.xml
M		apps/shrine-app/src/main/scala/net/shrine/happy/HappyShrineService.scala
M		apps/shrine-app/src/main/scala/net/shrine/wiring/AuthStrategy.scala
M		apps/shrine-app/src/main/scala/net/shrine/wiring/ManuallyWiredShrineJaxrsResources.scala
M		apps/shrine-app/src/main/scala/net/shrine/wiring/ShrineConfig.scala
M		apps/shrine-app/src/test/scala/net/shrine/wiring/AuthStrategyTest.scala
M		apps/steward-app/pom.xml
M		apps/steward-app/src/main/resources/reference.conf
M		apps/steward-app/src/main/scala/net/shrine/steward/Boot.scala
M		apps/steward-app/src/main/scala/net/shrine/steward/db/StewardDatabase.scala
M		apps/steward-war/src/main/resources/reference.conf
M		commons/auth/src/main/scala/net/shrine/authorization/StewardQueryAuthorizationService.scala
A	(dir)	commons/data-commons/src/main/scala/net/shrine/slick/
A		commons/data-commons/src/main/scala/net/shrine/slick/TestableDataSourceCreator.scala
A		commons/data-commons/src/main/scala/net/shrine/slick/package.scala
M		commons/protocol/src/main/scala/net/shrine/protocol/FlagQueryRequest.scala
M		commons/protocol/src/main/scala/net/shrine/protocol/QueryMaster.scala
M		commons/protocol/src/main/scala/net/shrine/protocol/ReadResultOutputTypesResponse.scala
V		hub/broadcaster-aggregator/src/main/{resources → sql}/hub.sql
D		hub/broadcaster-aggregator/src/main/scala/net/shrine/aggregation/ReadPreviousQueriesAggregator.scala
A	(dir)	hub/broadcaster-aggregator/src/main/sql/
V		hub/broadcaster-aggregator/src/main/{sql ← resources}/hub.sql
D		hub/broadcaster-aggregator/src/test/scala/net/shrine/aggregation/ReadPreviousQueriesAggregatorTest.scala
M		integration/pom.xml
A		integration/src/test/resources/shrine.conf
M		integration/src/test/scala/net/shrine/integration/AbstractHubAndSpokesTest.scala
M		integration/src/test/scala/net/shrine/integration/AbstractHubComponent.scala
M		integration/src/test/scala/net/shrine/integration/Hubs.scala
M		integration/src/test/scala/net/shrine/integration/MockAuditDao.scala
M		integration/src/test/scala/net/shrine/integration/NetworkSimulationTest.scala
M		integration/src/test/scala/net/shrine/integration/OneHubTwoSpokesJaxrsTest.scala
M		integration/src/test/scala/net/shrine/integration/OneQepOneHubTwoSpokesJaxrsTest.scala
M		qep/service/pom.xml
V		qep/service/src/main/{resources → sql}/create_broadcaster_audit_table.sql
A	(dir)	qep/service/src/main/scala/net/shrine/qep/
V		qep/service/src/main/scala/net/shrine/{qep/AbstractQepService.scala ← service/AbstractShrineService.scala}
V		qep/service/src/main/scala/net/shrine/{qep ← service}/AllowsAllAuthenticator.scala
V		qep/service/src/main/scala/net/shrine/{qep ← service}/I2b2BroadcastResource.scala
V		qep/service/src/main/scala/net/shrine/{qep/I2b2QepService.scala ← service/I2b2BroadcastService.scala}
V		qep/service/src/main/scala/net/shrine/{qep ← service}/QepConfig.scala
V		qep/service/src/main/scala/net/shrine/{qep ← service}/QepConfigSource.scala
V		qep/service/src/main/scala/net/shrine/{qep/QepService.scala ← service/ShrineService.scala}
V		qep/service/src/main/scala/net/shrine/{qep ← service}/ShrineResource.scala
A	(dir)	qep/service/src/main/scala/net/shrine/qep/audit/
V		qep/service/src/main/scala/net/shrine/{qep ← service}/audit/QepAuditDb.scala
V		qep/service/src/main/scala/net/shrine/{qep ← service}/audit/package.scala
A	(dir)	qep/service/src/main/scala/net/shrine/qep/dao/
V		qep/service/src/main/scala/net/shrine/{qep ← service}/dao/AuditDao.scala
A	(dir)	qep/service/src/main/scala/net/shrine/qep/dao/model/
V		qep/service/src/main/scala/net/shrine/{qep ← service}/dao/model/AuditEntry.scala
A	(dir)	qep/service/src/main/scala/net/shrine/qep/dao/squeryl/
V		qep/service/src/main/scala/net/shrine/{qep ← service}/dao/squeryl/SquerylAuditDao.scala
V		qep/service/src/main/scala/net/shrine/{qep ← service}/dao/squeryl/SquerylEntryPoint.scala
A	(dir)	qep/service/src/main/scala/net/shrine/qep/dao/squeryl/tables/
V		qep/service/src/main/scala/net/shrine/{qep ← service}/dao/squeryl/tables/AuditEntryComponent.scala
A		qep/service/src/main/scala/net/shrine/qep/dao/squeryl/tables/Tables.scala
A	(dir)	qep/service/src/main/scala/net/shrine/qep/queries/
A		qep/service/src/main/scala/net/shrine/qep/queries/QepQueryDb.scala
A		qep/service/src/main/scala/net/shrine/qep/queries/package.scala
D		qep/service/src/main/scala/net/shrine/service
V		qep/service/src/main/scala/net/shrine/{service/AbstractShrineService.scala → qep/AbstractQepService.scala}
V		qep/service/src/main/scala/net/shrine/{service → qep}/AllowsAllAuthenticator.scala
V		qep/service/src/main/scala/net/shrine/{service → qep}/I2b2BroadcastResource.scala
V		qep/service/src/main/scala/net/shrine/{service/I2b2BroadcastService.scala → qep/I2b2QepService.scala}
V		qep/service/src/main/scala/net/shrine/{service → qep}/QepConfig.scala
V		qep/service/src/main/scala/net/shrine/{service → qep}/QepConfigSource.scala
V		qep/service/src/main/scala/net/shrine/{service → qep}/ShrineResource.scala
V		qep/service/src/main/scala/net/shrine/{service/ShrineService.scala → qep/QepService.scala}
D		qep/service/src/main/scala/net/shrine/service/audit
V		qep/service/src/main/scala/net/shrine/{service → qep}/audit/QepAuditDb.scala
V		qep/service/src/main/scala/net/shrine/{service → qep}/audit/package.scala
D		qep/service/src/main/scala/net/shrine/service/dao
V		qep/service/src/main/scala/net/shrine/{service → qep}/dao/AuditDao.scala
D		qep/service/src/main/scala/net/shrine/service/dao/model
V		qep/service/src/main/scala/net/shrine/{service → qep}/dao/model/AuditEntry.scala
D		qep/service/src/main/scala/net/shrine/service/dao/squeryl
V		qep/service/src/main/scala/net/shrine/{service → qep}/dao/squeryl/SquerylAuditDao.scala
V		qep/service/src/main/scala/net/shrine/{service → qep}/dao/squeryl/SquerylEntryPoint.scala
D		qep/service/src/main/scala/net/shrine/service/dao/squeryl/tables
V		qep/service/src/main/scala/net/shrine/{service → qep}/dao/squeryl/tables/AuditEntryComponent.scala
D		qep/service/src/main/scala/net/shrine/service/dao/squeryl/tables/Tables.scala
V		qep/service/src/main/{sql ← resources}/create_broadcaster_audit_table.sql
M		qep/service/src/main/sql/mysql.ddl
V		qep/service/src/main/sql/{mysql_qep_audit.sql ← report.sql}
V		qep/service/src/main/sql/{report.sql → mysql_qep_audit.sql}
A	(dir)	qep/service/src/test/scala/net/shrine/qep/
V		qep/service/src/test/scala/net/shrine/{qep/I2B2QepServiceTest.scala ← service/I2b2BroadcastServiceTest.scala}
V		qep/service/src/test/scala/net/shrine/{qep ← service}/I2b2BroadcastResourceTest.scala
V		qep/service/src/test/scala/net/shrine/{qep ← service}/QepConfigTest.scala
V		qep/service/src/test/scala/net/shrine/{qep/QepServiceTest.scala ← service/ShrineServiceTest.scala}
V		qep/service/src/test/scala/net/shrine/{qep ← service}/ShrineResourceJaxrsTest.scala
V		qep/service/src/test/scala/net/shrine/{qep ← service}/ShrineResourceTest.scala
A	(dir)	qep/service/src/test/scala/net/shrine/qep/audit/
V		qep/service/src/test/scala/net/shrine/{qep ← service}/audit/QepQueryAuditTest.scala
A	(dir)	qep/service/src/test/scala/net/shrine/qep/dao/
V		qep/service/src/test/scala/net/shrine/{qep ← service}/dao/AbstractAuditDaoTest.scala
V		qep/service/src/test/scala/net/shrine/{qep ← service}/dao/AuditDaoTest.scala
V		qep/service/src/test/scala/net/shrine/{qep ← service}/dao/Wiring.scala
A	(dir)	qep/service/src/test/scala/net/shrine/qep/queries/
A		qep/service/src/test/scala/net/shrine/qep/queries/QepQueryDbTest.scala
D		qep/service/src/test/scala/net/shrine/service
V		qep/service/src/test/scala/net/shrine/{service → qep}/I2b2BroadcastResourceTest.scala
V		qep/service/src/test/scala/net/shrine/{service/I2b2BroadcastServiceTest.scala → qep/I2B2QepServiceTest.scala}
V		qep/service/src/test/scala/net/shrine/{service → qep}/QepConfigTest.scala
V		qep/service/src/test/scala/net/shrine/{service → qep}/ShrineResourceJaxrsTest.scala
V		qep/service/src/test/scala/net/shrine/{service → qep}/ShrineResourceTest.scala
V		qep/service/src/test/scala/net/shrine/{service/ShrineServiceTest.scala → qep/QepServiceTest.scala}
D		qep/service/src/test/scala/net/shrine/service/audit
V		qep/service/src/test/scala/net/shrine/{service → qep}/audit/QepQueryAuditTest.scala
D		qep/service/src/test/scala/net/shrine/service/dao
V		qep/service/src/test/scala/net/shrine/{service → qep}/dao/AbstractAuditDaoTest.scala
V		qep/service/src/test/scala/net/shrine/{service → qep}/dao/AuditDaoTest.scala
V		qep/service/src/test/scala/net/shrine/{service → qep}/dao/Wiring.scala