# Changelog

All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [8.2.1]  - 2019-08-10

### Fixed

- `lo` yaml output will now go deeper rather than cutting off at 3 levels deep

## [8.2.0]  - 2019-07-24

### Added

- `--re-ingest-file` flag to `lo tasks create-foundation-xml-import` and `lo tasks create-nantomics-vcf-import`. This flag will allow re-ingesting of a file even if a sequence already exists for it.  The current files for the sequence will be overwritten.  ([#101](https://github.com/lifeomic/cli/pull/101))

## [8.1.0]  - 2019-07-12

### Added

- `lo genomics create-copy-number-set` kicks off the workflow to start indexing of a CNV/copy number file ([#97](https://github.com/lifeomic/cli/pull/97))
- `lo genomics create-structural-variant-set` kicks off the workflow to start indexing of a FNV/structural variant file ([#97](https://github.com/lifeomic/cli/pull/97))
- `lo genomics delete-copy-number-set` deletes the copy number genomic set for the provided set id ([#97](https://github.com/lifeomic/cli/pull/97))
- `lo genomics delete-structural-variant-set` deletes the structural variant genomic set for the provided set id ([#97](https://github.com/lifeomic/cli/pull/97))
- `lo genomics get-copy-number-set` gets the copy number genomic set for the provided set id ([#97](https://github.com/lifeomic/cli/pull/97))
- `lo genomics get-structural-variant-set` gets the structural variant genomic set for the provided set id ([#97](https://github.com/lifeomic/cli/pull/97))
- `lo genomics list-copy-number-sets` gets the copy number genomic sets for the provided data set id ([#97](https://github.com/lifeomic/cli/pull/97))
- `lo genomics list-structural-variant-sets` gets the structural variant genomic set for the provided data set id ([#97](https://github.com/lifeomic/cli/pull/97))
- `--use-existing-sequence` flag to `lo tasks create-foundation-xml-import` and `lo tasks create-nantomics-vcf-import`. This flag when used with any `--indext-type` besides `all` will attempt to add the currently ingest variant type to an existing sequence.  ([#96](https://github.com/lifeomic/cli/pull/96))
- `lo fhir ingest` now allows for CSV content to be passed to stdin with a `--csv` flag which points to a configuration file. See `examples/csv_input/observations.csv` as an example of input, and `examples/csv_format/csv_observation_input.json` as an example of configuration.  ([#99](https://github.com/lifeomic/cli/pull/99))

## [8.0.3] - 2019-06-24

### Fixed

- `lo` will now no longer colorize YAML output when it is going to a pipe ([#93](https://github.com/lifeomic/cli/pull/93))

## [8.0.2] - 2019-06-24

### Fixed

- `lo auth` will only listen on local interfaces. ([#92](https://github.com/lifeomic/cli/pull/92))

## [8.0.1] - 2019-06-23

### Fixed

- `lo fhir list <type> --json` will once again produce valid JSON (i.e. an array of objects) ([#89](https://github.com/lifeomic/cli/pull/89))

## [8.0.0] - 2019-06-18

### Changed

- `lo genomics create-genomic-set` has new required parameters. ([#88](https://github.com/lifeomic/cli/pull/88))

## [7.6.0] - 2019-05-30

### Added

- `lo files mv <source> <dest>` to allow one to rename a file or a set of files within a project. ([#86](https://github.com/lifeomic/cli/pull/86))

## [7.5.0] - 2019-05-30

### Added

- `lo tasks create-foundation-xml-import` now provides for structural variant ingestion by means of a new value for the `index-type` flag, `fnv`
- `lo tasks create-nantomics-vcf-import` now provides for structural variant ingestion by means of an optional new flag `upload-type` which allows selection of either short variant file or structural variant file

## [7.4.0] - 2018-05-29

### Added

- Added `lo layouts` commands that allow one to manage subject viewer layouts.  ([#80](https://github.com/lifeomic/cli/pull/80) from [@taylordeatri](https://github.com/taylordeatri))
- Added `--jsonLine` global option to use JSON Line format.  ([#80](https://github.com/lifeomic/cli/pull/80) from [@taylordeatri](https://github.com/taylordeatri))
- Added `--csv` option to `lo fhir list` command to output resources as CSV.  ([#80](https://github.com/lifeomic/cli/pull/80) from [@taylordeatri](https://github.com/taylordeatri))

### Fixed

- Upgraded Axios version to fix issue with proxy support when using `https_proxy` environment variable.  ([#80](https://github.com/lifeomic/cli/pull/80) from [@taylordeatri](https://github.com/taylordeatri))

## [7.3.0] - 2018-05-28

### Added

- `lo files download` now provides recrusive download support to allow one to download many files from a project. ([#85](https://github.com/lifeomic/cli/pull/85))

## [7.2.1] - 2018-05-22

### Fixed

- `lo files upload` now properly formats the file names when operating on a Windows OS. ([#83](https://github.com/lifeomic/cli/pull/83))

## [7.2.0] - 2018-05-10

### Added

- `lo setup` now provides support for providing settings using arguments. ([#78](https://github.com/lifeomic/cli/pull/78) from [@bmamlin](https://github.com/bmamlin))

## [7.1.3] - 2018-05-09

### Fixed

- Worked around an issue that was causing `lo auth` to fail when using SAML SSO.

## [7.1.2] - 2018-04-19

### Fixed

- Fixed issue with batching over JSON array type objects with `lo ontologies import`.

## [7.1.1] - 2018-04-18

### Fixed

- Fixed issue with importing JSON array type objects with `lo ontologies import`.

## [7.1.0] - 2018-04-16

### Added

- Added `ontologies import` command for uploading ontologies to a project.

## [7.0.0] - 2018-04-09

### Changed

- Replaced the `page-size` and `next-page-token` options with a `limit` option for the `lo files ls` command.

- Replaced the YAML printer library with one that can handle larger lists

### Added

- Added a `limit` option to the following commands which allows them to fetch as many pages needed to hit the limit:
  `lo files list`, `lo genomics list-variant-sets`, `lo genomics list-readgroup-sets`, and `list-rna-quantification-sets`

## [6.15.5] - 2018-03-29

### Fixed

- Fixed issue with uploading very large files with `lo files upload`.

## [6.15.4] - 2018-03-28

### Fixed

- Added more error checking and request retries around `lo files upload`.

## [6.15.3] - 2018-03-27

### Fixed

- Improved the usability of `lo setup` and `lo auth` by improving some of
  the prompts and available choices to make things more obvious.

## [6.15.2] - 2018-03-22

### Fixed

- Add retries for requests issued with `lo files upload`

## [6.15.1] - 2018-03-14

### Fixed

- `lo fhir list` will now properly handle tag queries using `--query`

## [6.15.0] - 2018-02-28

### Added

- `lo fhir ingest` will now retry HTTP 429 (too many requests) errors

## [6.14.0] - 2018-02-20

### Added

- Added `--indexed-date` option to `genomics create-genomic-set`,
  `create-foundation-xml-import`, and `create-nantomics-vcf-import`

- Added `files ls` command for browsing files within a project with folder
  support

## [6.13.0] - 2018-12-21

### Added

- Added `--move-after-upload` option to `files upload`

## [6.12.0] - 2018-12-03

### Added

- Added `status` options to the genomics commands

## [6.11.0] - 2018-10-25

### Added

- Added `test-type` and `performer-id` options to the genomics commands

## [6.10.0] - 2018-10-25

### Added

- Added Content-MD5 checks for s3 file uploads

### Fixed

- Renamed the `--dataset` option on `lo fhir ingest` to `--project`
  to match the other `fhir` commands.

- Added retries on `5xx` errors to the `fhir` commands.

## [6.9.0] - 2018-10-12

### Added

- Added `--sequence-name` option to `create-foundation-xml-import` command

## [6.8.0] - 2018-10-11

### Added

- Added `--sequence-type` option to `create-genomic-set` command

## [6.7.0] - 2018-10-02

### Added

- Added support for managing and using cohorts

### Fixed

- `lo fhir get` now prints the the FHIR resource rather than `null`

## [6.6.0] - 2018-09-24

### Changed

- `lo tasks create-nantomics-vcf-import` - removed report file name argument
  and replaced with file prefix.

## [6.5.0] - 2018-09-14

### Added

- Added new options for `create-nantomics-vcf-import`

## [6.4.0] - 2018-09-13

### Changed

- `lo tasks create-foundation-xml-import` - removed report file name argument
  and replaced with file id.

## [6.3.0] - 2018-08-24

### Added

- Added `create-nantomics-vcf-import`

## [6.2.0] - 2018-08-24

### Changed

- Project id is now a required argument to the `lo fhir ingest` command.

## [6.1.3] - 2018-08-23

### Fixed

- Fixed `lo accounts list` command.

## [6.1.2] - 2018-08-20

### Fixed

- Properly handle errors for `lo fhir ingest` by stopping the ingest at the
  first error.

## [6.1.1] - 2018-08-17

### Fixed

- Prevent `lo fhir ingest` from doing parallel POST requests and causing rate
  limiting and other issues.

## [6.1.0] - 2018-08-17

### Added

- Added `create-foundation-xml-import`

## [6.0.2] - 2018-08-13

### Fixed

- Fixed `lo setup` to add back missing API key options.

## [6.0.0] - 2018-08-10

### Changed

- This releases changes the entire command structure.  Commands like `lo
  files-list` are now `lo files list`.  You can new view help like so: `lo
  --help`, `lo <command> --help`, `lo <command> <subcommand> --help`.

- `fhir ingest' command supports json-lines and will stream and batch the
  resources so it can support arbitrarily large ingests.

## [5.10.0] - 2018-08-08

### Changed

- FHIR commands now request strict handling which makes the FHIR server do
  strict validation on ingest and searches

## [5.9.1] - 2018-08-06

### Fixed

- Fixed `lo files-upload` to make it work better for larger files.

## [5.9.0] - 2018-08-03

### Added

- Added `api-keys` commands and the ability to use an API key for authentication

- Added `--id` option to file-upload

## [5.8.0] - 2018-07-31

### Added

- Added `--delete-after-upload` option to `files-upload`

### Changed

- Updated `files-upload` to ignore "file already uploaded" errors instead of
  throwing

## [5.7.0] - 2018-07-26

### Added

- Added `lo ga4gh-genomicsets-create`.

## [5.5.0] - 2018-07-25

### Added

- Added option to use SSO when `lo auth` by specifying a custom auth client with
  `lo setup`.

## [5.4.0] - 2018-06-26

### Added

- Added `--reference` option to `ga4gh-variantset-create` and
  `ga4gh-readgroupset-create` commands.

## [5.3.0] - 2018-06-26

### Added

- Added `fhir-search-delete` command for bulk deleting.
- Removed `fhir-delete-all` command.

## [5.2.1] - 2018-06-25

### Added

- Fixed issue with the `auth` action in the Linux executable.

## [5.2.0] - 2018-06-25

### Added

- Added executables to release artifacts.

## [5.1.0] - 2018-06-19

### Added

- Added `auth --set` command option to manually set the access token.

## [5.0.0] - 2018-05-22

### Removed

- Dataset commands

### Added

- Project commands, which replace dataset commands

## 4.2.0 - 2018-04-26

### Fixed

- Use POST based searching for FHIR searches.

## 4.1.0 - 2018-04-05

### Added

- Optimized bulk/batch ingest for fhir-ingest

## 4.0.2 - 2018-03-30

### Fixed

- Better error message when using 'auth' command with client credentials

## 4.0.0 - 2018-03-23

### Added

- Public release

### Fixed

- Better error message when using 'auth' command with client credentials

## 3.2.0 - 2018-03-21

### Added

- Commands for Attribute Based Access Control policies and groups.

## 3.1.0 - 2018-03-12

### Added

- Commands for task resources

## 2.5.1 - 2018-01-19

### Fixed

- The `lo fhir` `--limit` option will not set pageSize when requesting resources

## 2.5.0 - 2018-01-15

### Added

- Commands for FHIR resources

## 2.4.2 - 2018-01-12

### Fixed

- `lo auth -c` now produces an error message if a clip board utility isn't
  installed
- `lo auth` no longer hangs for 1 minute

## 2.4.1 - 2018-01-04

### Fixed

- Changed `files-download` to work with new download response.

## 2.4.0 - 2018-01-04

### Added

- Added support for GA4GH RNA Quantification sets.

## 2.3.1 - 2018-01-03

### Fixed

- Throw a proper error when `setup` has not been performed.

## 2.3.0 - 2018-01-02

### Changed

- The `auth` command was changed to perform authentication using the web login
  view.

## 2.2.0 - 2017-12-21

### Added

- Commands for GA4GH resources

## 2.1.0 - 2017-12-21

### Added

- Support to specify client credential settings in the `setup` command
- Ability to automatically refresh access tokens on expiration

## 2.0.0 - 2017-12-20

### Added

- Added a `--copy` option to the `auth` command to copy the access token to the
  clipboard

### Changed

- Replaced the `defaults` command with a `setup` command

[8.2.0]: https://github.com/lifeomic/cli/compare/v8.1.0...v8.2.0
[8.1.0]: https://github.com/lifeomic/cli/compare/v8.0.3...v8.1.0
[8.0.3]: https://github.com/lifeomic/cli/compare/v8.0.2...v8.0.3
[8.0.2]: https://github.com/lifeomic/cli/compare/v8.0.1...v8.0.2
[8.0.1]: https://github.com/lifeomic/cli/compare/v8.0.0...v8.0.1
[8.0.0]: https://github.com/lifeomic/cli/compare/v7.6.0...v8.0.0
[7.6.0]: https://github.com/lifeomic/cli/compare/v7.5.0...v7.6.0
[7.5.0]: https://github.com/lifeomic/cli/compare/v7.4.0...v7.5.0
[7.4.0]: https://github.com/lifeomic/cli/compare/v7.3.0...v7.4.0
[7.3.0]: https://github.com/lifeomic/cli/compare/v7.2.1...v7.3.0
[7.2.1]: https://github.com/lifeomic/cli/compare/v7.2.0...v7.2.1
[7.2.0]: https://github.com/lifeomic/cli/compare/v7.1.3...v7.2.0
[7.1.3]: https://github.com/lifeomic/cli/compare/v7.1.2...v7.1.3
[7.1.2]: https://github.com/lifeomic/cli/compare/v7.1.1...v7.1.2
[7.1.1]: https://github.com/lifeomic/cli/compare/v7.1.0...v7.1.1
[7.1.0]: https://github.com/lifeomic/cli/compare/v7.0.0...v7.1.0
[7.0.0]: https://github.com/lifeomic/cli/compare/v6.15.5...v7.0.0
[6.15.5]: https://github.com/lifeomic/cli/compare/v6.15.4...v6.15.5
[6.15.4]: https://github.com/lifeomic/cli/compare/v6.15.3...v6.15.4
[6.15.3]: https://github.com/lifeomic/cli/compare/v6.15.2...v6.15.3
[6.15.2]: https://github.com/lifeomic/cli/compare/v6.15.1...v6.15.2
[6.15.1]: https://github.com/lifeomic/cli/compare/v6.15.0...v6.15.1
[6.15.0]: https://github.com/lifeomic/cli/compare/v6.14.0...v6.15.0
[6.14.0]: https://github.com/lifeomic/cli/compare/v6.13.0...v6.14.0
[6.13.0]: https://github.com/lifeomic/cli/compare/v6.12.0...v6.13.0
[6.12.0]: https://github.com/lifeomic/cli/compare/v6.11.0...v6.12.0
[6.11.0]: https://github.com/lifeomic/cli/compare/v6.10.0...v6.11.0
[6.10.0]: https://github.com/lifeomic/cli/compare/v6.9.0...v6.10.0
[6.9.0]: https://github.com/lifeomic/cli/compare/v6.8.0...v6.9.0
[6.8.0]: https://github.com/lifeomic/cli/compare/v6.7.0...v6.8.0
[6.7.0]: https://github.com/lifeomic/cli/compare/v6.6.0...v6.7.0
[6.6.0]: https://github.com/lifeomic/cli/compare/v6.5.0...v6.6.0
[6.5.0]: https://github.com/lifeomic/cli/compare/v6.4.0...v6.5.0
[6.4.0]: https://github.com/lifeomic/cli/compare/v6.3.0...v6.4.0
[6.3.0]: https://github.com/lifeomic/cli/compare/v6.2.0...v6.3.0
[6.2.0]: https://github.com/lifeomic/cli/compare/v6.1.0...v6.2.0
[6.1.3]: https://github.com/lifeomic/cli/compare/v6.1.2...v6.1.3
[6.1.2]: https://github.com/lifeomic/cli/compare/v6.1.1...v6.1.2
[6.1.1]: https://github.com/lifeomic/cli/compare/v6.1.0...v6.1.1
[6.1.0]: https://github.com/lifeomic/cli/compare/v6.0.2...v6.1.0
[6.0.2]: https://github.com/lifeomic/cli/compare/v6.0.0...v6.0.2
[6.0.0]: https://github.com/lifeomic/cli/compare/v5.10.0...v6.0.0
[5.10.0]: https://github.com/lifeomic/cli/compare/v5.9.1...v5.10.0
[5.9.1]: https://github.com/lifeomic/cli/compare/v5.9.0...v5.9.1
[5.9.0]: https://github.com/lifeomic/cli/compare/v5.8.0...v5.9.0
[5.8.0]: https://github.com/lifeomic/cli/compare/v5.7.0...v5.8.0
[5.7.0]: https://github.com/lifeomic/cli/compare/v5.5.0...v5.7.0
[5.5.0]: https://github.com/lifeomic/cli/compare/v5.4.0...v5.5.0
[5.4.0]: https://github.com/lifeomic/cli/compare/v5.3.0...v5.4.0
[5.3.0]: https://github.com/lifeomic/cli/compare/v5.2.1...v5.3.0
[5.2.1]: https://github.com/lifeomic/cli/compare/v5.2.0...v5.2.1
[5.2.0]: https://github.com/lifeomic/cli/compare/v5.1.0...v5.2.0
[5.1.0]: https://github.com/lifeomic/cli/compare/5.0.0...v5.1.0
[5.0.0]: https://github.com/lifeomic/cli/compare/v4.0.0...5.0.0