4cced40b54
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
...
# Conflicts:
# hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
2020-05-05 17:19:32 -04:00
a77aa6a28e
Multitenancy Ticket 2 - #1813 ( #1821 )
...
* Work on multitenancy
* Second ticket started
* More multitenancy work
* Work on tenancy security
* Work on multitenancy
* Test fixes
* Add docs
* cs tweak
* Multitenancy fixes
* Add debug log
* Fix build
* Add headers
* Add partition selection interceptor hook
* Update hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Account for review comments
* Resolve FIXMES
* Work on tests
* Test fixes
* A bit more cleanup
* Work on multitenancy
* Update hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ClientExamples.java
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md
Co-authored-by: Ken Stevens <khstevens@gmail.com>
* Address review comments
* Allow disabling text modifier indexing
* Add changelog
* Docs fixes
* Address review comment
* Resolve merge conflicts
* Merge master
* Compile fix
* Test fix
Co-authored-by: Ken Stevens <khstevens@gmail.com>
2020-05-05 15:12:15 -04:00
0e45db0ba9
More cleanup and test fixes.
2020-04-24 16:23:59 -04:00
4a89860f9b
Additional tests and cleanup.
2020-04-17 17:38:42 -04:00
d03ce6533e
Fixed conflicts after merging latest from Master.
2020-04-13 20:01:34 -04:00
925bbbbcdc
Merge remote-tracking branch 'remotes/origin/master' into im_20200316_lastn_operation_elasticsearch
...
# Conflicts:
# hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
# hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
# hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
# pom.xml
2020-04-13 18:35:15 -04:00
47786660d5
Test fixes
2020-04-07 13:58:24 -04:00
83e673e725
Consolidate changes to Command Line Tool and add/improve tests.
2020-04-03 17:12:04 -04:00
6baf1995c9
Work on subscription cleanup
2020-04-02 20:30:19 -04:00
f819c91530
Initial implementation of lastn operation.
2020-03-31 21:55:57 -04:00
082c201333
Improve debug logging
2020-03-31 11:20:48 -04:00
9d09466c21
Add debug logging to CLI
2020-03-31 10:49:16 -04:00
22413911bf
Validation api changes ( #1719 )
...
* Validation enhancements
* Work on validation api reworking
* Keep working on validation API
* Keep working on new term API
* Work on validation api
* Ongoing work on validation
* Work on integrating validation
* Work on validation API
* Add to validation API
* Work on validation
* Work on API
* Work on validation
* Work on validation API
* Work on validation API
* Work on validation api
* Work on validation API
* Work on validation api
* Validation API changes
* Work on API
* More work on validationo API
* Work on validation API
* FIxes
* WOrk on validation api
* Work on validation API
* Tests passing!
* More cleanup
* More validation API changes
* Fix intermittent test failure
* Package reorg
* Validation API work
* Work on doocumentation
* Work on API
* More work on new validation API
* Fix errorprone-reported error
* Test fixes
* Documentation updates
* Documentation tweaks
* Work on API
* Bean name adjustments
* Build fixes
* Some test fixes
2020-03-17 13:28:59 -04:00
60f16dd91d
Update to 4.3.x core JAR ( #1715 )
...
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Added optionality for adding resource fetcher
* Added coverage that proves invocations
* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences
* Start working on converter
* Account for compile errors
* Test fix
* Work no validator
* Work on getting core working
* Add some test coverage
* Many test fixes
Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
2020-02-17 14:28:29 -05:00
ddc7b601ee
Version bump to 4.3.0-SNAPSHOT
2020-02-16 19:23:22 -05:00
4fd80cfca7
Bump to 4.2.0
2020-02-16 19:00:15 -05:00
4989361922
One more test fix
2020-02-03 21:51:13 -05:00
9c7f5e1b9b
License header updates
2020-01-12 10:15:08 -05:00
0b682eeb1f
Fix broken constructor
2019-12-18 14:28:28 -05:00
68a7613f9e
Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler
...
# Conflicts:
# hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseFlywayMigrateDatabaseCommand.java
2019-12-16 08:58:26 -05:00
e3922d5c01
pre-review cleanup
2019-12-15 08:32:45 -05:00
7c3514fecc
Skip versions tested
2019-12-14 19:00:58 -05:00
4946fffac2
pass test
2019-12-14 17:27:17 -05:00
96003a44cc
Correct issue with CLI
2019-12-13 13:40:40 -05:00
931a41938b
added dry-run output to both Flyway and TaskOnly migrator
...
dry-run only calls TaskOnly migrator now
2019-12-12 14:42:43 -05:00
7c1544d8f3
strip comments from sql before splitting ; (to avoid ; in comments)
2019-12-11 14:02:24 -05:00
176bf657a7
Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler
...
# Conflicts:
# hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
2019-12-10 10:10:41 -05:00
bd1b41ff82
change out-of-order-permitted from environment variablet to flag to work like dont-use-flyway
2019-12-09 16:44:24 -05:00
bfa89483e7
Merge remote-tracking branch 'origin/master' into ks-20191119-scheduler
2019-12-06 18:13:38 -05:00
438ef70fdb
Reuse connections in brute force migrator
2019-12-06 16:52:26 -05:00
6c432733d5
Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler
2019-12-05 18:03:02 -05:00
d91617e923
Account for review changes ( #1623 )
2019-12-05 18:01:45 -05:00
1ce5dca5db
intermittent failure?
2019-12-05 15:32:53 -05:00
69a5266127
Allow non-flyway migration
2019-12-05 10:46:37 -05:00
8c7c4fc56f
configurable table name
2019-11-26 13:40:03 -05:00
01ebe9ae8c
Revert "fix test"
...
This reverts commit 3b35724b
2019-11-26 12:07:31 -05:00
3b35724bdd
fix test
2019-11-26 11:36:25 -05:00
3d00634b16
make migration table name configurable
2019-11-26 09:07:53 -05:00
6543da1470
Merge remote-tracking branch 'remotes/origin/master' into ks-flyway
2019-11-15 09:28:30 -05:00
497a96ae68
Version bump for next round of development
2019-11-12 22:09:21 -05:00
f99ad981b5
Version bump to 4.1.0
2019-11-12 16:08:20 -05:00
30865588e3
pre-review cleanup
2019-11-04 08:36:24 -05:00
5890059362
moar integration tests
2019-11-03 13:46:09 -05:00
de4f909eda
optimize imports
2019-11-02 21:52:35 -04:00
fd9d61018c
FIXME
2019-10-31 17:14:54 -04:00
f95e4d387d
added schema migration validation
2019-10-31 14:56:55 -04:00
d29e112e26
removed old migration command
2019-10-30 17:32:46 -04:00
c8c89d976f
Flyway integration test passes
2019-10-29 14:18:41 -04:00
18e8604494
Merge remote-tracking branch 'remotes/origin/master' into ks-flyway
...
# Conflicts:
# hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
2019-10-27 08:29:52 -04:00
9b94e4e26d
Allow uploading term deltas using CS resource ( #1555 )
...
* Work on accepting codesystem reources for delta operations
* Ongoing work on term uploader
* Restore the ability to use CodeSystem resources for the delta
* Add tests
* Fix NPE
* Test fixes
2019-10-22 17:11:39 -04:00
464c6c5b45
Upgrade dependencies and addess Semmle issues ( #1554 )
...
* Version bumps
* FIx build issues
* Address a few Semmle issues
* Work on tests
* Some test fixes
* Test fix
* Fix deletions
* Test fix
* Fix intermittent test failure
* One more dependency bump
* Add some test logging
* Remove bad import
* Add some tests
* Test updates
2019-10-22 17:10:58 -04:00
12a74e6cbc
Fix term uploads and validate against valueset recalculation ( #1540 )
...
* Start refactoring terminology delta operations
* Work on delta operations
* Work on concept saving
* Split term services into smaller services
* Work on term delta operations
* Work on term svcs
* Work on term operations
* More work on delta uploader
* Add a test
* Wrk on term service
* Fix compile error
* Some refactoring
* Test fix
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Work on delta
* Work on tests#
* Test fixes
* Improve resequencing logic
* Build test
* More testing
* More build testing
* More work on tests
* CHange test logging
* Fix term service PID issue
* Update src/changes/changes.xml
Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>
* Address review comment
* Some cleanup
* Test fix
* Fix some tests
* Work on upload command
* Test fixes
* Work on validation fixes
* Work on validation against pre-expansion
* Work on direct validation
* A bit of cleanup
* Add some javadoc
* Force another build
* Test fixes
* Fix tests
* Fix tests
2019-10-15 21:31:29 -04:00
2725797610
Implement Terminology Delta Operations ( #1536 )
...
* Start refactoring terminology delta operations
* Work on delta operations
* Work on concept saving
* Split term services into smaller services
* Work on term delta operations
* Work on term svcs
* Work on term operations
* More work on delta uploader
* Add a test
* Wrk on term service
* Fix compile error
* Some refactoring
* Test fix
* Test fix
* Test fixes
* Test fix
* Test fixes
* Test fixes
* Work on delta
* Work on tests#
* Test fixes
* Improve resequencing logic
* Build test
* More testing
* More build testing
* More work on tests
* CHange test logging
* Fix term service PID issue
* Update src/changes/changes.xml
Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>
* Address review comment
* Some cleanup
* Test fix
* Fix some tests
* Test fixes
2019-10-14 19:14:41 -04:00
790f655a95
flyway initial implementation (with FIXMEs)
2019-10-06 17:55:10 -04:00
2193a30b45
CodeSystem Delta Uploader ( #1520 )
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* Terminology Delta Uploading
* Add delta operations
* Fix up tests
* Improve test coverage a bit
* Improve test coverage reporting
* fix yaml
* A couple of test enhancements
* FIx intermittent test failure
2019-10-03 07:19:00 -04:00
c8ce07c40e
Deprecate redundant IVersionSpecificBundleProvider method
2019-09-30 09:45:31 -04:00
f5788341f2
Add no-shrink-columns option to migrator ( #1500 )
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* Add no-shrink-columns option to migrator
* Address review comments
2019-09-23 18:44:51 -04:00
8b09b3f3eb
Rename config enum for consistency
2019-09-03 07:01:36 -04:00
1b1d80b850
Test fix
2019-08-29 21:02:19 -04:00
e1b43d811f
Version bump to 4.1.0-SNAPSHOT
2019-08-14 14:06:06 -04:00
3f22456b0f
Bump version to 4.0.0
2019-08-14 11:06:26 -04:00
dd0cb10dbb
validate operation ignores parameter profile ( #1417 )
...
* This should be working now - need to check tests
* Add a changelog and some docs
* One more test fix
* Tests should be passing
* Fix compile
* Test fixes
* Ignore outdated DSTU2 validation test
2019-08-07 15:31:59 -04:00
60eab3ad70
Add support for R5 resources ( #1416 )
...
* Work so far on R5 support
* Add support for R5
* Docs changes
2019-08-06 17:30:31 -04:00
808da73854
Merge pull request #1413 from jamesagnew/ks-migration-tests
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test all migrations to latest version
2019-08-02 16:13:24 -04:00
48c8497086
Changed migration test from derby to h2
...
Added a new test from 340 to latest version.
2019-08-02 16:00:43 -04:00
345ce880ce
Address review comments.
2019-08-02 14:45:59 -04:00
ca01f31ca9
Enable support of DSTU3 for upload-terminology command.
2019-08-02 14:00:56 -04:00
04ce9cfc1a
Add support for uploading custom terminology using the
...
$upload-external-code-system operation
2019-07-30 17:30:18 -04:00
a4ca5374ec
Add terminology delta operations ( #1401 )
...
* Start work on delta operations
* Add changelog
* Some build fixes
* Move upload terminology command to CodeSystem resource
* Updates
* Some test fixes
* Add changelog
* Some test fixes
* More test fixes
* Test fix
* Add additional tests
* Transaction boundary fixes
2019-07-29 17:46:42 -04:00
33531f9010
Add some test logging
2019-07-14 16:56:43 -04:00
7831e8a0ed
Add support for $snapshot generation and validation based on snapshots
2019-07-14 16:15:56 -04:00
120b93f204
Use HL7 FHIR Core Structures ( #1382 )
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* Ongoing work on core structures suport
* Ongoing work on this merge
* Ongoing work to clean up structures
* Credit for #1179
* Address compile issues
* Latest changes
* Work on parallel execution
* Work on getting tests passing
* Add H2 to migrator
* Test fix
2019-07-14 10:16:40 -04:00
dff2fdd3cf
GET RID OF TRAILING LICENSE HEADER SPACES ONCE AND FOR ALL
...
YESSSSSSSSSSSSS
2019-07-05 11:19:51 -04:00
b56f59542a
Move JettyUtil to new module
2019-06-14 18:34:45 -04:00
aab7bb6b64
Issue-1325: Let OS assign random ports to servers during testing, and let tests get the port of the running server once the OS has assigned a port. Delete PortUtil and similar utilities.
2019-06-14 18:34:45 -04:00
aed5bb8955
Resolve #1320 : "import-csv-to-conceptmap is failing unexpectedly." ( #1322 )
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* Reproduced issue in unit test and identified potential solution.
* Fixed using BOMInputStream.
* Added changelog.
* Added a missing word in changelog.
* Added a missing word in changelog. Take two.
2019-06-03 10:53:04 -04:00
c811fe8a2f
One more test fix
2019-05-30 21:57:49 -04:00
50a8c66bf5
Version bump to 4.0.0-SNAPSHOT
2019-05-30 17:13:03 -04:00
73aa53be8f
Release 3.8.0
2019-05-30 16:50:04 -04:00
1aeb54e94e
added all fetchValueSet Implementations
2019-03-30 21:02:24 +01:00
48c10bddc5
Narrative Generator refactoring ( #1219 )
...
* Starting work on this
* Working on narrative templates
* Work on new narrative system
* Account for some failing tests due to refactoring of narrative mode
* Another test fix
* More test fixes
* One more test fix
* Work on searches
* Address review comments
2019-02-27 14:59:57 -05:00
7adb14c754
Make App logging customizable
2019-02-08 17:14:22 -05:00
0f8c8d18e2
Bump version to 3.8.0-SNAPSHOT
2019-02-06 20:02:28 -05:00
207015c3af
Version bump to 3.7.0
2019-02-05 21:36:38 -05:00
d4af1ee2a3
Add tests and license headers
2019-02-04 16:34:39 -05:00
ea84f2c377
Version bump hibernate search
2019-02-02 11:26:19 -05:00
9280cde491
Subscription only registers active ( #1189 )
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* Fixed a bug in standalone subscription subscriber: It was adding REQUESTED subscriptions to the active subscription registry. (Only ACTIVE subscriptions should be added.)
2019-02-01 10:14:46 -05:00
31b8a392b7
Better CLI error handling for unit tests
2019-01-03 12:57:18 -05:00
a0cb7edd08
Version bump a few dependencies
2018-12-22 20:13:03 -05:00
81e8131ffc
Fix broken test
2018-12-09 19:36:03 -05:00
8c7f249a21
Migrator enhancements and adjust reindexer to account for missing
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versions
2018-12-04 17:33:29 -05:00
84acafe3af
Streamline expunge operation
2018-11-15 11:37:16 +01:00
75210d614b
Bump to 3.7.0-SNAPSHOT
2018-11-12 22:37:52 -05:00
bbcbcbf5d6
Don't hardcode commons-compress version
2018-11-12 12:26:17 -05:00
63af04a7b4
Prepare for 3.6.0 release
2018-11-12 05:40:55 -05:00
896568c0f7
License updates
2018-11-04 16:06:53 -05:00
bc72093555
Add reindexing support based on table instead of column
2018-11-04 20:00:27 +01:00
87f90fec47
Correctly handle password promnpt in CLI
2018-10-01 11:59:47 -04:00
3e445faf47
Squashed commit of the following:
...
commit df641506885e09e63f80efc6c658d01a1a3a8142
Author: James Agnew <jamesagnew@gmail.com>
Date: Sat Sep 29 13:47:22 2018 -0400
Shrink validation resources
commit 4c1550eafa26f4235b4b8804741aecc03276b5c6
Author: James Agnew <jamesagnew@gmail.com>
Date: Fri Sep 28 22:45:28 2018 -0400
Updates to get R4 working
commit 8332f15291006691ed9b07ead3e3524b0fc85510
Author: jamesagnew <jamesagnew@gmail.com>
Date: Fri Sep 28 09:02:13 2018 -0400
Ongoing work on gettign R4 working
commit f7146cab7aed937bb625a8aec95744d76db00041
Author: James Agnew <jamesagnew@gmail.com>
Date: Fri Sep 28 05:21:01 2018 -0400
More work on sync
commit f48de4a10b1bab2584fee813017d9b27b237bfa9
Merge: 9e4f3cc722 aacb78b779
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Sep 27 20:11:29 2018 -0400
Merge branch 'sync_r4' of github.com:jamesagnew/hapi-fhir into sync_r4
commit 9e4f3cc722668aae31a77b19bf9b032af3ae01b0
Author: James Agnew <jamesagnew@gmail.com>
Date: Thu Sep 27 20:11:19 2018 -0400
Fix compile error
commit 7ec29e0ceda8f9013cbabb95767cbe15b4b81303
Merge: 23f7517325 002c4b3ff7dfb4de86f1
2018-09-29 13:48:35 -04:00
002c4b3ff7
Add retrigger subscription operation
2018-09-27 20:03:01 -04:00
706e004b9d
Bump to 3.6.0-SNAPSHOT
2018-09-19 10:24:48 -04:00
321e88c811
License header updates
2018-09-14 05:25:07 -04:00
13fc65d6fe
Work on migrator
2018-09-08 09:10:13 +08:00
daef975734
Version bump to 3.5.0
2018-09-08 07:22:21 +08:00
4852b0b60f
Work on migration
2018-09-08 07:14:43 +08:00
f5d567cd00
Work on migrator
2018-09-08 03:30:35 +08:00
fd55aa292c
Allow interactive prompts for credentials from the user
2018-08-19 15:13:06 -04:00
a40b7fe7d3
Add user prompting to BaseCommand
2018-08-18 15:04:14 -04:00
7eb36c3392
Work on subscription
2018-08-11 16:14:53 -04:00
ece0c9defe
Subscription cleanup
2018-08-10 09:07:55 -04:00
43ac912033
Clean up terminology uploading
2018-07-15 15:22:52 -04:00
1ec65d03fb
Merge pull request #969 from rhausam/upload-terminology
...
Fix client upload-terminology for r4.
2018-06-27 10:37:47 -04:00
903df68d2a
978 cli tools for importing exporting terminology mappings need to be fixed ( #988 )
...
* Fixed export issue.
* Fixed import issue.
* Fixed tests.
* Fixed tests.
2018-06-07 10:22:41 -04:00
044fc13b43
Added double quotes to CSV test data to ensure CLI import test still passes.
2018-06-04 13:58:29 -04:00
abcf7852b1
Tests pasing locally
2018-05-31 09:10:34 -04:00
35a827eac3
Support for JDK10 working now
2018-05-30 08:54:16 -04:00
a52805e504
Work on JDK9 support
2018-05-30 05:45:08 -04:00
b29cdc22f3
Fix client upload-terminology for r4.
2018-05-29 22:54:09 -05:00
0e2c57fa60
Bumping version.
2018-05-28 17:44:38 -04:00
2871920734
Preparing release.
2018-05-28 10:45:47 -04:00
49aaa01db8
Fix compile issues
2018-05-23 17:42:48 -04:00
baac934fba
Added QuoteMode.ALL to export-conceptmap-to-csv operation in hapi-fhir-cli.
2018-05-22 15:09:29 -04:00
c588e01a4d
Handle invalid paths in Consent resource
2018-05-16 21:45:23 -04:00
4fd868afae
Credit for #946 and add extensions to the CLI uploader
2018-05-16 19:32:12 -04:00
e187d72a3b
Fix server command
2018-05-16 16:13:16 -04:00
8d6940a70e
Merge branch 'master' of github.com:jamesagnew/hapi-fhir
2018-05-15 07:35:24 -04:00
f9946fee61
Fixes to get the build passing once more
2018-05-15 07:34:44 -04:00
58e231d299
removed duplicated hapi-fhir-igpacks dependency
2018-05-15 11:56:56 +02:00
a3ff08d9ec
Replace phloc with ph for #775 ( #930 )
...
* Replace phloc with ph
* Enable schematron tests
* Make HAPI-FHIR ph-schematron on OSGI
* Work on getting tests passing
* Another test fix
* Fix up transaction handling for DSTU2
* Add changelog
* Avoid double transaction
* Dont use readonly
* One more test fix
* Update to snapshow build
* Resolve a circular dependency
* Try to fix tests
* Solve recurring NPE in DSTU2 tests
* Fix one more test
* Test fix
* More test threading fixes
* One more attempt to get tests passing
* Refactoring for tests
* Refactoring for tests
2018-05-14 17:38:40 -04:00
ccb859fdbe
FIxes to get the synced build working
2018-05-13 08:08:34 -04:00
f1ba0016b2
Improve the error message thrown by JPA server
2018-05-11 17:03:48 -04:00
38e6edf4ae
Command updates for validate command
2018-05-10 17:29:31 -04:00
b17eebd8d2
Squashed commit of the following:
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commit 2be11651c2b3bb5f9052f6b1082ba481a69c265f935938e92c43568a1f8de95894e6439393fb8f4f437f5051e420c51add4f7bf2b0a0e9adc73e75c9
2018-05-10 11:53:32 -04:00
14a070a47e
927 cli tooling is needed for creating and maintaining conceptmaps using csvs ( #934 )
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CLI tooling for import/export of ConceptMaps using CSVs has been implemented.
2018-05-10 11:12:45 -04:00
7c6ba93d9e
Header updates
2018-04-30 16:24:11 -04:00
392feb7082
Refactor CLI to extract commands
2018-04-30 15:04:35 -04:00
ianmarshall
James Agnew
Ken Stevens
Diederik Muylwyk
Stig Rohde Døssing
patrick-werner
Ken Stevens
Rob Hausam