Diffusion SHRINE MedCo Fork 5c7637a87679

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5c7637a87679
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Authored by Ty <Ty_Coghlan@hms.harvard.edu> on Nov 7 2016, 22:34.

Description

Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine into feature/new-crypto

Details

Committed

Ty <Ty_Coghlan@hms.harvard.edu>

Nov 7 2016, 22:34

Pushed

mickmis

Mar 14 2017, 15:12

Parents

R2664:0a61653e5804: Added net.shrine.steward.CannotStartDsa and net.shrine.dashboard.
R2664:5eed792535e8: rough draft of finished prodcut

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Event Timeline

Ty <Ty_Coghlan@hms.harvard.edu> committed R2664:5c7637a87679: Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine… (authored by Ty <Ty_Coghlan@hms.harvard.edu>).Nov 7 2016, 22:34

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
0a61653e5804	David Walend	Added net.shrine.steward.CannotStartDsa and net.shrine.dashboard.	Nov 7 2016
2f16c2ad8650	David Walend	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Nov 7 2016
0d8852f43324	David Walend	Added net.shrine.steward.CannotStartDsa and net.shrine.dashboard.	Nov 7 2016
a9011f8d43fd	ben-carmen	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Nov 7 2016
ae284ec2d0bb	ben-carmen	added unit tests	Nov 7 2016
94aa08085524	David Walend	Added net.shrine.steward.CannotStartDsa for SHRINE-1745	Nov 7 2016
fcd6d0d4d95f	David Walend	Schema updates for mssql and mysql for SHRINE-1731	Nov 7 2016
c19bd3e6cd74	David Walend	A canonical shrine.conf SHRINE-1742 and SHRINE-1747	Nov 7 2016
bdf5327454db	David Walend	MSSQL and Oracle ddl updates for the user audit table. SHRINE-1741.	Nov 4 2016
fe45ebbc8b03	David Walend	Made the stewardBaseUrl not an option	Nov 4 2016
48efeccdacc4	David Walend	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Nov 4 2016
7067649ad944	David Walend	Delay the email until 6 am, and get the right URL for the DSA.	Nov 4 2016
e4939b0a87db	ben-carmen	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Nov 4 2016
d38f727295a1	ben-carmen	fix of date range not being reflected in term digest	Nov 4 2016
e9108b76a403	David Walend	Added new problems and factored the audit email subsystem into its own package.	Nov 4 2016
8fb6732e9bc5	David Walend	Better words in the DSA email	Nov 3 2016
e7fdb8905e05	David Walend	Wire up the database for SHRINE-1733	Nov 3 2016
3f8d731467bc	David Walend	Way to override default durations in typesafe config. SHRINE-1703	Nov 3 2016
479b81714ae0	David Walend	ExceptionInInitializerError is fatal. Should help catch config problems.	Nov 3 2016
585d0b5d3758	David Walend	Exception trap for missing config	Nov 3 2016
942e871c22c8	David Walend	Why the steward's email config is missing	Nov 3 2016
ab0f136851b4	ben-carmen	fixed the issue of missing userName on graphs bars	Nov 3 2016
ca383631ee19	David Walend	typo	Nov 3 2016
1ce892f5f896	David Walend	Trying for a faster failure when misconfigured	Nov 3 2016
0228c4a3921d	David Walend	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Nov 3 2016
0ec08a5cb1fb	David Walend	Maybe able to send email for SHRINE-1704, SHRINE-1705, SHRINE-1733	Nov 3 2016
168dae2d2d07	ben-carmen	completed style of graph	Nov 2 2016
4b2a21a21731	ben-carmen	fix of term colorization	Nov 2 2016
020cc110b437	ben-carmen	fix of ontology parsing issue	Nov 2 2016
f84adcb53e81	ben-carmen	fix of parsing bug on dev	Nov 2 2016
a3e65229c7ef	ben-carmen	latest version	Nov 2 2016
8465b0bb9fe5	ben-carmen	latest topic filter styles	Nov 2 2016
bf52afbf668f	David Walend	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Nov 2 2016
52e59af218db	ben-carmen	fix for missing zoom in webclient	Nov 2 2016
ea705a1f3ae1	ben-carmen	stylized graphs	Nov 1 2016
1a60a9b136f2	David Walend	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Nov 1 2016
500e03e5557d	ben-carmen	full functionality for demo	Nov 1 2016
f312d79ecb15	ben-carmen	styles for topic filter	Nov 1 2016
d5e5e02e914f	ben-carmen	working filter	Nov 1 2016
33e53ee7d093	ben-carmen	latest version of dropdown	Oct 28 2016
d0a7d7c9ca28	ben-carmen	latest version of tooltip	Oct 27 2016
6c68775695b3	ben-carmen	hover styles	Oct 26 2016
2ba433dbd3be	ben-carmen	added highight styles and tooltip	Oct 26 2016
d1581a6591aa	ben-carmen	added a little more style polish	Oct 26 2016
942258ada6bb	ben-carmen	polished styles for ontology tree	Oct 26 2016
0535b3cf6fe5	David Walend	Merge branch 'develop' of https://open.med.harvard.edu/stash/scm/shrine/shrine…	Oct 26 2016
1698b22eb23d	Ben Carmen	file cleanup	Oct 26 2016
73eade508668	ben-carmen	added more styles	Oct 26 2016
9f8e61807879	ben-carmen	added close button	Oct 26 2016
7b77f583462b	ben-carmen	added an overlay for the query digest.	Oct 25 2016

Changes (108)
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This commit is very large. Load each file individually.

		Path
M		adapter/adapter-service/src/main/sql/adapter.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-war/src/main/resources/reference.conf
M		apps/steward-app/pom.xml
M		apps/steward-app/src/main/js/.jshintrc
A		apps/steward-app/src/main/js/.vscode/launch.json
D		apps/steward-app/src/main/js/Gruntfile.js
A		apps/steward-app/src/main/js/app/assets/css/color-codes.css
M		apps/steward-app/src/main/js/app/assets/css/graphs.css
A		apps/steward-app/src/main/js/app/assets/css/overlay.css
A		apps/steward-app/src/main/js/app/assets/css/query-digest.css
M		apps/steward-app/src/main/js/app/assets/css/shrine.css
A		apps/steward-app/src/main/js/app/assets/css/tooltip.css
A		apps/steward-app/src/main/js/app/assets/css/topic-dropdown.css
D		apps/steward-app/src/main/js/app/client/statistics/directives
D		apps/steward-app/src/main/js/app/client/statistics/directives/ontology-term
V		apps/steward-app/src/main/js/app/client/statistics/{directives/ontology-term → query-digest}/ontology-term.factory.js
V		apps/steward-app/src/main/js/app/client/statistics/{directives/ontology-term → query-digest}/ontology-term.service.js
V		apps/steward-app/src/main/js/app/client/statistics/{directives/ontology-term → query-digest}/ontology-term.service.spec.js
D		apps/steward-app/src/main/js/app/client/statistics/directives/statistics-graph
D		apps/steward-app/src/main/js/app/client/statistics/directives/statistics-graph/bar.tpl.html
D		apps/steward-app/src/main/js/app/client/statistics/directives/statistics-graph/statistics-graph.js
D		apps/steward-app/src/main/js/app/client/statistics/directives/statistics-graph/statistics-graph.service.js
D		apps/steward-app/src/main/js/app/client/statistics/directives/statistics-graph/statistics-graph.service.spec.js
D		apps/steward-app/src/main/js/app/client/statistics/directives/statistics-graph/statistics-graph.tpl.html
A	(dir)	apps/steward-app/src/main/js/app/client/statistics/query-digest/
V		apps/steward-app/src/main/js/app/client/statistics/{query-digest ← directives/ontology-term}/ontology-term.factory.js
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/ontology-term.factory.spec.js
V		apps/steward-app/src/main/js/app/client/statistics/{query-digest ← directives/ontology-term}/ontology-term.service.js
V		apps/steward-app/src/main/js/app/client/statistics/{query-digest ← directives/ontology-term}/ontology-term.service.spec.js
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/query-digest.js
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/query-digest.tpl.html
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/term.js
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/term.service.js
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/term.service.spec.js
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/term.tpl.html
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/topic-dropdown.js
A		apps/steward-app/src/main/js/app/client/statistics/query-digest/topic-dropdown.tpl.html
A	(dir)	apps/steward-app/src/main/js/app/client/statistics/statistics-graph/
A		apps/steward-app/src/main/js/app/client/statistics/statistics-graph/bar.js
A		apps/steward-app/src/main/js/app/client/statistics/statistics-graph/bar.tpl.html
V		apps/steward-app/src/main/js/app/client/{statistics/statistics-graph ← topics/directives}/new-topic.tpl.html
A		apps/steward-app/src/main/js/app/client/statistics/statistics-graph/statistics-graph.js
A		apps/steward-app/src/main/js/app/client/statistics/statistics-graph/statistics-graph.service.js
A		apps/steward-app/src/main/js/app/client/statistics/statistics-graph/statistics-graph.service.spec.js
A		apps/steward-app/src/main/js/app/client/statistics/statistics-graph/statistics-graph.tpl.html
M		apps/steward-app/src/main/js/app/client/statistics/statistics.controller.js
M		apps/steward-app/src/main/js/app/client/statistics/statistics.model.js
D		apps/steward-app/src/main/js/app/client/statistics/statistics.service.js
M		apps/steward-app/src/main/js/app/client/statistics/statistics.tpl.html
V		apps/steward-app/src/main/js/app/client/{topics/directives → statistics/statistics-graph}/new-topic.tpl.html
A	(dir)	apps/steward-app/src/main/js/app/mock/
A	(dir)	apps/steward-app/src/main/js/app/mock/data/
A		apps/steward-app/src/main/js/app/mock/data/query-history.js
A		apps/steward-app/src/main/js/app/mock/data/query-result.js
A		apps/steward-app/src/main/js/app/mock/data/steward-data.js
A		apps/steward-app/src/main/js/app/mock/data/topic.js
A		apps/steward-app/src/main/js/app/mock/query-history-result.js
A		apps/steward-app/src/main/js/app/mock/shrine-mock.service.js
A		apps/steward-app/src/main/js/app/mock/steward-mock.service.js
A		apps/steward-app/src/main/js/app/mock/test.js
A		apps/steward-app/src/main/js/app/sass/color-codes.scss
M		apps/steward-app/src/main/js/app/sass/graphs.scss
A		apps/steward-app/src/main/js/app/sass/overlay.scss
A		apps/steward-app/src/main/js/app/sass/query-digest.scss
M		apps/steward-app/src/main/js/app/sass/shrine.scss
A		apps/steward-app/src/main/js/app/sass/tooltip.scss
A		apps/steward-app/src/main/js/app/sass/topic-dropdown.scss
A	(dir)	apps/steward-app/src/main/js/app/server/
A		apps/steward-app/src/main/js/app/server/package.json
A		apps/steward-app/src/main/js/app/server/steward-api.js
M		apps/steward-app/src/main/js/gulp.config.js
M		apps/steward-app/src/main/js/gulpfile.js
M		apps/steward-app/src/main/js/karma.conf.js
M		apps/steward-app/src/main/js/package.json
P		apps/steward-app/src/main/resources/reference.conf Copied to apps/steward-war/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
A	(dir)	apps/steward-app/src/main/scala/net/shrine/steward/email/
A		apps/steward-app/src/main/scala/net/shrine/steward/email/AuditEmailer.scala
M		apps/steward-app/src/main/sql/mysql.ddl
M		apps/steward-app/src/main/sql/oracle.ddl
M		apps/steward-app/src/main/sql/sqlserver.ddl
M		apps/steward-app/src/test/scala/net/shrine/steward/StewardServiceSpec.scala
A	(dir)	apps/steward-app/src/test/scala/net/shrine/steward/db/
A		apps/steward-app/src/test/scala/net/shrine/steward/db/StewardDbTest.scala
P		apps/steward-war/src/main/resources/reference.conf Copied from apps/steward-app/src/main/resources/reference.conf
M		commons/auth/src/main/scala/net/shrine/authorization/steward/StewardModel.scala
M		commons/config/src/main/scala/net/shrine/config/DurationConfigParser.scala
M		commons/crypto/src/main/scala/net/shrine/crypto/Verifier.scala
M		commons/email/pom.xml
A	(dir)	commons/email/src/main/resources/
A		commons/email/src/main/resources/reference.conf
A		commons/email/src/main/scala/net/shrine/email/ConfiguredMailer.scala
M		commons/email/src/main/scala/net/shrine/email/package.scala
M		commons/email/src/test/scala/net/shrine/email/EmailTest.scala
M		hub/broadcaster-aggregator/src/main/resources/reference.conf
M		install/i2b2-1.7/shrine/sqlserver/adapter.sql
A	(dir)	install/src/main/resources/
A		install/src/main/resources/shrine.conf
M		shrine-webclient/src/main/html/index.html
M		shrine-webclient/src/main/html/js-i2b2/cells/CRC/CRC_ctrlr_QryTool.js
M		shrine-webclient/src/main/html/js-i2b2/cells/CRC/CRC_view_Graphs.js
M		shrine-webclient/src/main/html/js-i2b2/cells/CRC/assets/query_report.css
A	(dir)	tools/js/
A	(dir)	tools/js/i2b2-msg-parser/
A		tools/js/i2b2-msg-parser/SHRINE-1522.xml