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

Fixed

• Periodic Zenodo uploads always went to sandox

0.9.4 - 2022-02-14

Fixed

• Corrupt zip file on Zenodo (#210)

0.9.3 - 2022-02-08

Added

• Linking to proteome and protein

Security

• Severity vulnerability (CVE-2021-44228) for Apache Log4j 2 in Elastic search Docker image

0.9.2 - 2021-03-03

Added

• Conform to Bioschema profile (#177)
• Allow notifications to be disabled with SLACK_TOKEN=false environment variable
• Mention CC BY 4.0 license on add and download page
• Health check API endpoint (#171)

Fixed

• URL in notification message is internal (#168)
• Return 404 http error when path is not /api, a file or part of router paths (#174)

0.9.1 - 2021-01-21

Security

• Axios vulnerability (CVE-2020-28168)
• node-notifier vulnerability (CVE-2020-7789)

0.9.0 - 2020-12-07

Added

• Notify admins on Slack when new project is ready for review (#155)
• Notify admins on Slack when data archive on Zenodo is updated (#163)

0.8.2 - 2020-11-05

Fixed

• Use BioSample DB link to NCBI (#162)

0.8.1 - 2020-09-28

Added

• Links to methods page (#159)

0.8.0 - 2020-09-22

Added

• Column check for uploading of genome links (#154)
• Methods page (#158)

Fixed

• Render publications delimited by spaces (#152)

0.7.0 - 2020-07-10

Added

• SEO optimizations like static sitemap, dynamic sitemap for projects and each project has structured data (#148)

Changed

• Titles synced with draft paper (#146)

Fixed

• Correct title for acetonitrile search example (#141)
• Consistent casing of platform name (#143)
• Smiles render with own optional scrollbar (#147)

0.6.2 - 2020-04-23

Added

• Paging projects (#137)

Changed

• Sort projects moved from web application to elastic search (#138)
• Allow search and filter to be combined

0.6.1 - 2020-04-16

Added

• Added ionization modes to stats page (#132)
• Search query examples (#132)

Fixed

• Enrichments cause Limit of total fields exceeded error in elastic search (#131)

0.6.0 - 2020-04-16

Search functionality using elastic search has been added.

Added

• Full text search functionality (#123)
• Filter projects on statistic functionality (#124)

Changed

• Replaced http with https (#126)

Fixed

• Schema version not constant (#127)

0.5.0 - 2020-04-02

Added

• Mention JSON schema on add form (#115)
• Project list can be sorted by clicking on column header (#117)
• Show software version on about page (#109)
• Download page, shows DOI of dataset archive (#109)

Changed

• Project list sorted on metabolite id (#117)

Fixed

• Submitter email is used where PI email is expected (#118)
• Download button on pending page yields incorrectly formatted json files (#120)

0.4.0 - 2020-03-20

This version requires following migration steps.

• JSON schema changed to version 2. To migrate all projects in data/ dir from 1 to 2 run

  # Backup
  cp -a data/ backup-$(date -I)/
  # Perform migration
  docker-compose exec api npm run migrate
  # Validate projects
  docker-compose exec api npm run validateall
  # Fix any validation errors and rerun validation until all projects are valid
  # For example use VS Code extension https://marketplace.visualstudio.com/items?itemName=tiibun.vscode-docker-ws to edit file in Docker container
  # Edit CTRL-SHIFT-p, select dockerws command, select`paired-data-form_api_1` as Docker container and `/data` as path to open.
  code .
  # Restart api so new updated files are reindexed
  docker-compose restart api

• The enrichment of projects has been improved. To recreate enrichments of all projects run

  # Drop existing enrichment with
  docker-compose exec redis sh
  redis-cli --scan --pattern keyv:enrichment:* | xargs redis-cli del
  exit
  # Recreate all enrichments
  docker-compose exec api npm run enrich

Added

• About page (#86)
• Limit log size of Docker containers (#89)
• Denied projects moved to thrash dir (#95)
• Stats page (#64)
• Fetch species from BioSample, ENA and JGI for each genome
• Download button for pending project in review section (#98)
• Submitter name column to project lists (#101)
• Commands to validate one or all projects (#100)
• Command to perform data migrations (#110)
• Second submitter (#97)
• OpenAPI specification (#112)
• Manual for developers who wish to consume the api

Fixed

• Unable to submit large project (#88)
• Spelling errors (#87)
• Render error when growth medium is not set (#92)
• Unable to download project from add form(#111)

Changed

• Dropped Caddy web server from docker-compose, use nginx from app and external reverse proxy for https
• Download project directly using web service instead of data-url
• BGC number to BGC accession aka 1234 to BGC0001234 (#94)
• Require more fields in Gene cluster - Mass spectra links (#94)
• Increased JSON schema version to 2 due to issue #94

0.3.0 - 2019-12-11

Added

• Confirmation of submission to review (#74)
• Resins field to extraction method (#76)
• erlemeyer flask option to aeration vessel (#76)
• Links to description of fields and check list (#76)
• Warning to not include spaces in urls (#75)

Fixed

• Do validation on labels when selected in links sections (#73)
• Validate uploaded JSON documents (#78)
• GNPS task id link broken (#81)

0.2.0 - 2019-07-05

Added

• Intro page (#45)
• Password protected review section to review pending projects (#45)
• Page with list of projects (#45)
• Page to show single project (#45)
• Web service to store project on disk as JSON documents (#46)
• Task queue to enrich projects (#46)
• Enrich project by fetching organism name based on genome identifier (#46)

Changed

• original form is now for adding a project for review (#45)
• Added metabolights study id to genome (#54)
• Made which fields are required more clear (#42)
• Replaced run command from yarn to docker-compose

0.1.0 - 2019-05-01

Initial release.