v0.6.1

Linking mass spectra and genomic information to discover new chemistry.

• Links MS/MS mass spectra with genome, sample preparation, extraction method and instrumentation method
• Links biosynthetic gene cluster with MS^2 mass spectra

A web application for storing paired omics data projects.

Fixed

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

v0.6.0

Linking mass spectra and genomic information to discover new chemistry.

• Links MS/MS mass spectra with genome, sample preparation, extraction method and instrumentation method
• Links biosynthetic gene cluster with MS^2 mass spectra

A web application for storing paired omics data projects.

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)

v0.5.0

Linking mas spectra and genomic information to discover new chemistry.

• Links MS/MS mass spectra with genome, sample preparation, extraction method and instrumentation method
• Links biosynthetic gene cluster with MS^2 mass spectra

A web application for storing paired omics data projects.

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)

v0.4.0

Linking mas spectra and genomic information to discover new chemistry.

• Links MS/MS mass spectra with genome, sample preparation, extraction method and instrumentation method
• Links biosynthetic gene cluster with MS^2 mass spectra

A web application for storing paired omics data projects.

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

v0.3.0

Linking mas spectra and genomic information to discover new chemistry.

• Links MS/MS mass spectra with genome, sample preparation, extraction method and instrumentation method
• Links biosynthetic gene cluster with MS^2 mass spectra

A web application for storing paired omics data projects.

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)

v0.2.0

Linking mas spectra and genomic information to discover new chemistry.

• Links MS/MS mass spectra with genome, sample preparation, extraction method and instrumentation method
• Links biosynthetic gene cluster with MS^2 mass spectra

A web application for storing paired omics data projects.

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

v0.1.0

Web form for paired data for mapping between genomic and metabolomic (mass spectra) datasets.

Initial release.