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Recent Releases of paired-data-form

paired-data-form - v0.9.4

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

  • Corrupt zip file on Zenodo (#210)

- TypeScript
Published by sverhoeven over 4 years ago

paired-data-form - v0.9.3

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.

Added

  • Linking to proteome and protein

Security

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

- TypeScript
Published by sverhoeven over 4 years ago

paired-data-form - v0.9.2

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.

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)

- TypeScript
Published by sverhoeven over 5 years ago

paired-data-form - v0.9.1

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.

Security

- TypeScript
Published by sverhoeven over 5 years ago

paired-data-form - v0.9.0

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.

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)

- TypeScript
Published by sverhoeven over 5 years ago

paired-data-form - v0.8.2

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

  • Use BioSample DB link to NCBI (#162)

- TypeScript
Published by sverhoeven over 5 years ago

paired-data-form - v0.8.1

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.

Added

  • Links to methods page (#159)

- TypeScript
Published by sverhoeven over 5 years ago

paired-data-form - v0.8.0

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.

Added

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

Fixed

  • Render publications delimited by spaces (#152)

- TypeScript
Published by sverhoeven over 5 years ago

paired-data-form - v0.7.0

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.

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)

- TypeScript
Published by sverhoeven almost 6 years ago

paired-data-form - v0.6.2

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.

Added

  • Paging projects (#137)

Changed

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

- TypeScript
Published by sverhoeven about 6 years ago

paired-data-form - 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)

- TypeScript
Published by sverhoeven about 6 years ago

paired-data-form - 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)

- TypeScript
Published by sverhoeven about 6 years ago

paired-data-form - 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)

- TypeScript
Published by sverhoeven about 6 years ago

paired-data-form - 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

    ```shell

    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, selectpaired-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

    ```shell

    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

- TypeScript
Published by sverhoeven over 6 years ago

paired-data-form - 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)

- TypeScript
Published by sverhoeven over 6 years ago

paired-data-form - 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

- TypeScript
Published by sverhoeven almost 7 years ago

paired-data-form - v0.1.0

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

Initial release.

- TypeScript
Published by sverhoeven about 7 years ago