CHANGELOG.md

Changelog

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.

[Unreleased]

Removed

• BREAKING: Removed lo tasks create-foundation-xml-import. The Foundation XML task-service pipeline was removed (FLE-346, task-service#199). Use the GA4GH replacement flow.

13.9.0 - 2023-01-04

Added

• Added a lo genomics ingestions command set with the following commands
  • lo genomics ingestions list Lists genomic ingestions for a project
  • lo genomics ingestions get Gets a genomic ingestions
  • lo genomics ingestions create-foundation Creates a Foundation ingestion
  • lo genomics ingestions create-caris Creates a Caris ingestion
  • lo genomics ingestions create-foundation-bam Creates a Foundation BAM ingestion
  • lo genomics ingestions create-caris-bam Creates a Caris BAM ingestion

13.8.1 - 2022-07-25

Fixed

• Added maxBodyLength for file uploads

13.8.0 - 2022-05-24

Changed

• lo surveys export-responses now supports an optional query parameter

13.7.0 - 2022-04-06

Changed

• Updated how project is published

13.6.0 - 2021-10-06

Changed

• project is now required for lo fhir list

13.5.0 - 2021-07-22

Added

• Added lo auth -r to support token refresh

13.4.0 - 2021-07-22

Added

• Added --skipPrompts flag to lo setup command to enable unattended scripting of environment changes
  • lo setup -e prod-us --skipPrompts does not give follow up prompts

13.3.0 - 2021-04-05

Added

• Added a new lo ocr get-suggestions command to get suggestions from an OCR document

13.2.0 - 2021-03-18

Changed

• Updated the tool add-version command to use multi-part uploads when the file is larger than 5MB

13.1.0 - 2021-03-15

Changed

• Updated the tool creation command to use multi-part uploads when the file is larger than 5MB

13.0.0 - 2021-03-12

Changed

• Updated creating a cohort to require a subjectId array instead of a dsl query

12.5.0 - 2021-03-02

Added

• Added a command to cancel running data lake queries.
  • data-lake cancel-query Cancels a running data lake query

12.4.0 - 2021-02-17

Added

• Added additional Insights commands to get details of scheduled indexing jobs.
  • lo insights list-jobs Fetches all scheduled Insights indexing jobs in the account
  • lo insights get-job Fetch the details of a single Insights indexing job

12.3.0 - 2021-01-26

Added

• Added support for our upcoming federal government environment

12.2.0 - 2020-12-09

Added

• Added a lo tools command set with the following sub commands:
  • lo tools create Creates a tool in the tool registry
  • lo tools add-version Adds a version to an existing tool
  • lo tools delete Deletes a tool or a specific version of a tool
  • lo tools download Downloads the tool file
  • lo tools get Returns meta data on a tool
  • lo tools list Using optional fitlers, returns a list of tools
• Added two sub commands to lo workflows:
  • lo workflows describe Returns the expected inputs of a workflow and the data type of the input
  • lo workflows run Runs a workflow using a tool in the tool registry

12.1.1 - 2020-11-20

Fixed

• Fixed the genomics list-tests command to list tests by project using the --limit option.

12.1.0 - 2020-11-03

Changed

• Updated the genomics list-tests command to list tests by project by leaving off the [subjectId] parameter.

12.0.0 - 2020-10-08

Changed

• Updated lo ocr sub commands:
  • Removed delete-document, get-document and list-documents. These operations can be performed using fhir and fhir-search commands.
  • Updated create-config to read configuration from JSON file

11.9.0 - 2020-10-02

Changed

• Replaced the pass-filter option in the genomics create-genomic-set command with pass-only.

11.8.1 - 2020-09-22

Fixed

• Fixed issue with 11.8.0 release.

11.8.0 - 2020-09-21

Added

• Added a new lo genomics update-test command to update a genomic test.

11.7.0 - 2020-09-10

Added

• Added an optional argument --output-project-folder to the lo workflows create <datasetId> command that allows for specifying the folder within PHC that the workflow should push all output files.

Fixed

• Corrected the argument workflow-dependencies-file-ids in the lo workflows create <datasetId> to be optional instead of required

11.6.0 - 2020-08-07

Added

• Added a lo tasks retry <taskId> command.

11.5.0 - 2020-08-03

Added

• Added a lo genomics get-test command.
• Addded ablity to read lo fhir sql statement from stdin.

11.4.0 - 2020-07-06

Added

• Added a lo ocr command set with the following sub commands:
  • Configuration:
    • lo ocr create-config Create OCR configuration for a project
    • lo ocr delete-config Delete an OCR configuration
    • lo ocr get-config Fetch configuration information for a project
  • OCR documents:
    • lo ocr create-document Create an OCR-document (starts OCR pipeline)
    • lo ocr delete-document Delete an OCR document
    • lo ocr get-document Fetch OCR document
    • lo ocr list-documents List OCR documents in a project

11.3.0 - 2020-06-25

Added

• Added a lo tasks create-nantomics-bulk-import command.

11.2.0 - 2020-06-22

Added

• Upgraded project dependencies.

11.1.0 - 2020-06-05

Added

• Added a surveys export-responses command to export the responses for a survey in CSV format.

11.0.0 - 2020-05-11

Changed

• Updated the workflows commands sets to use the new workflows api, this includes removing workflows from the command and updating the arguments. Refer to help on the individual commands for more details
• Updated the create-* ingest commands to validate that the optional date provided is in an ISO standard format.

Removed

• The workflow-template and workflow-parameter command sets were removed. This functionality is now covered by the updated workflows commands

10.3.0 - 2020-04-20

Changed

• Replaced TravisCI build with Github Actions.

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