@lifeomic/cli

# 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