CLI

Source location - https://github.com/lifeomic/cli/

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

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

10.2.0 - 2020-03-06

Added

  • Added a body-site options to the genomics creat set commands.

10.1.0 - 2020-03-05

Added

  • Added a sequence-id option to the genomics create-genomic-set command.

10.0.2 - 2020-03-04

Fixed

  • Force fsevents dependency bump to avoid node-pregyp error noise on install
  • Fix bin links so lo is available in path after install

10.0.1 - 2020-02-27

Added

  • Support double-click of life-export on MacOS.

10.0.0 - 2020-02-26

Added

  • Created life-export / life-export.exe and added it to the release archive bundles. This command allows a user to extract their LIFE data in one step after authenticating with their credentials.

9.15.0 - 2020-02-18

Added

  • Added storage of ID token from lo auth command.

9.14.3 - 2020-02-12

Added

  • Added fhir me command for getting one's own FHIR Patient records.

9.14.2 - 2020-02-12

Fixed

  • Fixed the alias for the rgel-file option to be f in lo genomics create-rna-quantification-set to keep it from conflicting with other options.

9.14.1 - 2020-02-05

Added

  • Fixed a big in the lo genomics list... commands in which using the -l option was throwing an error
  • Updated help information in the lo genomics list... commands for -l and -n to be more descriptive on limits

9.14.0 - 2020-02-05

Added

  • Added the lo genomics create-readgroup-set command.

9.13.1 - 2020-01-27

Fixed

  • Fixed an issue with lo files mv and trying to rename files in nested folders.

9.13.0 - 2020-01-21

Added

  • Added ability to use auth tokens in the PHC_ACCESS_TOKEN and PHC_REFRESH_TOKEN environment variables.

9.12.0 - 2019-12-09

Added

  • Added missing options to various lo genomics create- commands.

9.11.0 - 2019-12-04

Added

  • Added --strip-path and --remote-path to files upload command.

9.10.0 - 2019-12-04

Added

  • Added the --send-failed-to option to the tasks create-ashion-import, tasks create-foundation-xml-import, and tasks create-nantomics-vcf-import commands.

9.9.0 - 2019-11-14

Added

  • Added the --update-sample option to the lo genomics create-genomic-set command.

9.8.0 - 2019-11-06

Added

  • Added the following commands to fetch data lake table schemas.
  • lo data-lake get-schema Fetch the schema of a single table
  • lo data-lake list-queries Fetch the schema of each table

Updated

  • Updated the query commands to hit the new /v1/analytics/data-lake/query endpoint.

9.7.0 - 2019-10-30

Added

  • Added the following commands to issue and fetch the data of queries against the analytics data lake.
  • lo data-lake query Submits a query to the Lifeomic data-lake API
  • lo data-lake get-query Fetch a single query execution
  • lo data-lake list-queries List the query executions in the project

9.6.0 - 2019-10-16

Added

  • Added the following commands which allow usage of the new workflow api which implements a subset of the Common Workflow Language standard
  • Handling of cwl json templates
    • lo workflows create-template Add the CWL json template
    • lo workflows get-template Returns a CWL json template
    • lo workflows list-templates Returns all CWL json templates belonging to a project
    • lo workflows delete-template Removes the CWL json template from a project
  • Handling of cwl json parameters
    • lo workflows create-parameters Add a CWL json parameter set
    • lo workflows get-parameters Returns a CWL json parameter set
    • lo workflows list-parameters Returns all CWL json parameter sets belonging to a project
    • lo workflows delete-parameters Removes the CWL json parameter set from a project
  • Handling of cwl json parameters
    • lo workflows build-workflow Generates and starts a workflow with a combination of a template and parameter resources
    • lo workflows create-workflow Allows a full CWL JSON template and parameter set to be read into the command directly
    • lo workflows get-workflow Returns a workflow
    • lo workflows list-workflows Returns all workflows belonging to a project
    • lo workflows delete-workflows Removes the workflow from the project

9.5.0 - 2019-10-03

Added

  • Added the following optional argument to the tasks create-ashion-import
    • --re-ingest-file Allows an Ashion file to be re-ingested

9.4.0 - 2019-09-26

Added

  • Added the following optional arguments to the tasks create-ashion-import, create-foundation-xml-import, and create-nantomics-vcf-import
    • --body-site the code indicating the body site of the sample
    • --body-site-system the system from which the body site code is derived
    • --body-site-display a display value for the body site code

9.3.0 - 2019-09-25

Added

  • Added the lo genomics list-tests command to lists genomic tests for a subject
  • Addded the lo genomics delete-test command to delete a test for a subject

9.2.0 - 2019-09-09

Added

  • Added the same arguments to the following genomics commands: list-copy-number-sets, list-readgroup-sets, list-rna-quantification-sets, list-structural-variant-sets and list-variant-sets
  • --missing-patient returns sets that are missing patientIds
  • --missing-sequence returns sets that are missing sequenceIds
  • --missing-samples returns sets that are missing sample names
  • --missing-fhir-sequence returns sets that have no associate FHIR Sequence resource
  • --only-ids causes the return to be only a an array of ids, intended to help with scripting tasks

9.1.0 - 2019-09-06

Added

  • Added the lo tasks create-ashion-import command to ingest Ashion test files

9.0.0 - 2019-09-05

Updated

  • Updated the create-foundation-task and create-nantomics-task commands to make the argument test-type required instead of optional
  • Updated the genomics list commands to allow filtering by sequenceId or patientId

8.3.1 - 2019-08-13

Fixed

  • lo files upload fixed bug with uploading empty files.

8.3.0 - 2019-08-13

Added

  • lo insights schedule-job command to schedule Insights rebuild jobs.

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)

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)
  • lo genomics create-structural-variant-set kicks off the workflow to start indexing of a FNV/structural variant file (#97)
  • lo genomics delete-copy-number-set deletes the copy number genomic set for the provided set id (#97)
  • lo genomics delete-structural-variant-set deletes the structural variant genomic set for the provided set id (#97)
  • lo genomics get-copy-number-set gets the copy number genomic set for the provided set id (#97)
  • lo genomics get-structural-variant-set gets the structural variant genomic set for the provided set id (#97)
  • lo genomics list-copy-number-sets gets the copy number genomic sets for the provided data set id (#97)
  • lo genomics list-structural-variant-sets gets the structural variant genomic set for the provided data set id (#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)
  • 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)

8.0.3 - 2019-06-24

Fixed

  • lo will now no longer colorize YAML output when it is going to a pipe (#93)

8.0.2 - 2019-06-24

Fixed

  • lo auth will only listen on local interfaces. (#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)

8.0.0 - 2019-06-18

Changed

  • lo genomics create-genomic-set has new required parameters. (#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)

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 from @taylordeatri)
  • Added --jsonLine global option to use JSON Line format. (#80 from @taylordeatri)
  • Added --csv option to lo fhir list command to output resources as CSV. (#80 from @taylordeatri)

Fixed

  • Upgraded Axios version to fix issue with proxy support when using https_proxy environment variable. (#80 from @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)

7.2.1 - 2018-05-22

Fixed

  • lo files upload now properly formats the file names when operating on a Windows OS. (#83)

7.2.0 - 2018-05-10

Added

  • lo setup now provides support for providing settings using arguments. (#78 from @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

Last update: March 29, 2020