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@sverhoeven sverhoeven released this 20 Mar 08:21
· 381 commits to master since this release
v0.4.0
b8564fb

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
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