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refactor: ♻️ 🔏 🔊 🧑‍💻 Add Environment Variables and Convert Logging to…
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… Use Logwatch (#120)

* refactor: ♻️ transfer validation api to codefair repo (#106)

* 🚚 chore: rename `validator-api` to `validator`

* 👷 ci: add validator deploy

* 👷 ci: add validator healthcheck

* 👷 ci: add validator deploy for prod

* refactor: ♻️ update codefair name

* feat: ✨ Metadata + license validators + bug patches (#107)

* merge: 🔀 merge main to staging

* refactor: ♻️ 🐛 Codefair 3.1.0 (#89)

* fix: 🐛 patch removing pull_request.closed bug on metadata pr merge

* fix: 🐛 don't update firstPublished in the codemeta file + better logs

* fix: 🐛 patch error on reading db entry when it doesn't exist

* chore: 🔊 better log on successful Zenodo publish

* style: 🎨 margins between text and icon

* feat: ✨ links to the list of tools used for codefair in /codefair

* refactor: ✨ ♻️ abstract the license validation fn

* doc: 🔖 update changelog

* feat: ✨ ♻️ abstraction to zenodo workflow

* wip: 🚧 abstracting zenodo workflow

* feat: ✨ add help link in the Zenodo release page

* refactor: ♻️ ✨ abstract out github release functions

* refactor: 🔊 ♻️ improve error tracing in metadata file

* chore: 🔨 remove todo

* refactor: ✨ ♻️ abstracted Zenodo workflow (bot)

* wip: 🚧 save custom license content when no assertion is provided

* ✨ feat: add support for custom licenses (#90)

* ✨ feat: add support for custom licenses

* 🐛 fix: reset citation license field

* 🐛 fix: update zenodo workflow for custom licenses

* fix: 🐛 license is valid with custom license

* feat: ✨ custom license template

* ✨ feat: update codemeta, license and cwl ui paths (#91)

* ✨ feat: update meta paths for consistency

* 🚚 fix: updatel icense request path

* ✨ feat: add support for custom license title (#92)

* refactor: ♻️ ✨ new patches for license, cwl, metadata UI's

* refactor: ✨ ♻️ apply migrations from UI to bot

* feat: ✨ request custom license title from user

* refactor: ♻️ hide message box when custom license title is blank

* refactor: ♻️ issue dashboard requests custom title

* feat: ✨ Saving custom title (#93)

* feat: ✨ save custom title option

* refactor: :recyle: reuse saveLicenseDraft for storing custom license title

* refactor: ♻️ join draft and save title buttons together

* refactor: ♻️ use naive-ui's properties for styling

* chore: 🔨 remove typo

* chore: 🔨 remove unused variables

* feat: ✨ toasts for custom title saved button

* refactor: ♻️ function rename

* feat: ✨ create Zenodo metadata fn handles custom licenses

* feat: ✨ custom license reference for archival workflow

* refactor: ♻️ stop creating identifiers for new db entries

* refactor: ♻️ 🐛 revert allowing custom licenses for zenodo

* refactor: ♻️ Custom License Support (#94)

* refactor: ♻️ ✨ custom title saved updates dashboard, disable create release btn when custom license

* refactor: ♻️ block progress of fair release if license is custom

* feat: ✨ listener for when custom license title is saved through UI

* feat: ✨ prevent fair release if not fair compliant

* refactor: ♻️ improve license validation and update template text for custom licenses

* refactor: ♻️ re-render issue from ui side

* refactor: ♻️ update to message explaining custom licenses

* db calls running in parallel

* fix: 🐛 prevent Zendo section from being seen when the license is custom

* fix: 🐛 trim license content before comparison

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* refactor: ♻️ safety checks for protected middleware

* refacotr: ♻️ update protectRoute to redirect to login when no user or session

* feat: :fix: redirect to login if not signed in

* refactor: ♻️ remove import

* chore: 🔊 🔨 remove logs

* docs: 📝 update changelog

* fix: 🐛 check license content all times

* fix: 🐛 update on zenodo ui page

* feat: ✨ delete branch after pr has been closed/merged

* chore: 🔨 spacing in changelog

* wip: 🚧 individual validation requests for license and metadata

* feat: ✨ license validation endpoint

* wip: 🚧 creating updated metadata validation

* wip: 🚧 patches for metadata revalidation workflow

* wip: 🚧 validation for codemeta

* doc: 🔖 jsdoc comments on fns

* fix: 🐛 template renderer will stop using old links (#99)

* fix: 🐛 rerender template will stop using old links

* doc: 📝 update CHANGELOG

* doc: 📝 update metadata

* fix: 🐛 preserve authors and contributors from codemeta

* feat: ✨ re-validated codemeta from repo dashboard

* fix: 🐛 await metadata validation

* feat: ✨ codemeta validation extended with microservice validator

* refactor: ♻️ update timestamps to be unix format

* feat: ✨ clean privatekey env before use

* refactor: ♻️ update cwl validation endpoint

* wip: 🚧 send validation message to db

* feat: ✨ create migrations for metadata validation messages

* wip: 🚧 creating json schema for codemeta.json validations

* 👷 ci: setup deployment environments (#101)

* 👷 ci: setup for staging env (#103)

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
Co-authored-by: slugb0t <wheresdorian@gmail.com>
fix: 🐛 template renderer will stop using old links (#99)

* fix: 🐛 adjust env variables used after env changes

* 👷 ci: cleanup dockerfile

* feat: ✨ codemeta schema first draft

* 👷 ci: cleanup dockerfile

* 👷 ci: cleanup dockerfile

* 👷 ci: cleanup dockerfile

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: cleanup dockerfile

* 👷 ci: fix staging deploys (#104)

* wip: 🚧 abstracting cwl workflow

* refactor: ♻️ update codemeta schema to validate against the raw codemeta.json files

* refactor: ♻️ update codemeta schema for additional fields

* feat: ✨ validating raw content of codemeta.json file for 3.0

* refactor: ♻️ create required fields for codemeta schema

* wip: 🚧 testing validation responses for db

* handle codemeta.json 3.0 and 2.0 versioning

* fix: 🐛 correct branch watch for staging deployment action

* doc: 🔖 update changelog for 3.2.0 release

* feat: ✨ align bot prisma with ui

* fix: 🐛 bug patch for cwl workflow

* feat: ✨ metadata workflow update

* refactor: ♻️ preserving authors and contributors

* wip: 🚧 update the metadata workflow after discussions

* fix: 🐛 don't create cwlobject twice

* refactor: ♻️ send 200 status when invalid codemeta

* refactor: ♻️ update codemeta validation schema

* refactor: ♻️ do not revalidate metadata files for push events unless metadata files are updated themselves

* wip: 🚧 seperate rerun validation with regather information

* wip: 🚧 remove command from issue dashboard if error occurs (allows retry)

* refactor: ♻️ update the issue body after successful validation (remove the command from the issue body)

* refactor: ♻️ add additional key to codemeta schema

* refactor: ♻️ remove the regather options from the UI as validation is still needed when regathering

* fix: 🐛 pr button updated with new links

* fix: 🐛 patch variable declaration not in scope

* refactor: ♻️ update on the dropdown icons

* refactor: ♻️ update the keys of the cwl object

* refactor: ♻️ update the getcwlfiles function

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* fix: 🐛 use the correct env variable for private key

* fix: 🐛 Codefair v3.2.0 finalization (#113)

* fix: 🐛 correct cwlObject variables in push event

* fix: 🐛 better error message in metadata workflow + collect missing fields from codemeta.json

* fix: 🐛 apply await to async function call

* refactor: ♻️ removed unused imports

* refactor: ♻️ add try catch in then statement of promise

* fix: 🐛 missing fields in codemeta gathering + add error handling for convertCitationForDB fn

* refactor: ♻️ add try catch to renderer to preserve errors

* fix: 🐛 preserve metadata validation results in db

* wip: 🚧 validation results being displayed through the repo dashboard

* wip: 🚧 displaying metadata validation results in seperate pages

* feat: ✨ validation page for codemeta

* fix: 🐛 patch fundingCode not being preserved from codemeta

* wip: 🚧 final design for validation results

* feat: ✨ add view validation results conditionally

* test: ⚗️ ensuring validation progresses accordingly

* feat: ✨ popover messages for metadata badges

* feat: ✨ if metadata file fails to parse then update validation message

* fix: 🐛 update schema to handle 2.0 and 3.0 authors

* style: 🎨 formatting

* fix: 🐛 add releaseNotes key to schema for 3.0 versions

* refactor: ✏️ change wording

* fix: 🐛 validate metadata file that was updated only on push events

* chore: 📝 remove test logs

* fix: 🐛 migrate db during deployment

* fix: 🐛 revert

* fix: 🐛 typo on dockerfile

* refactor: ♻️ use npm instead of yarn for migration

* refactor: ♻️ access db url during prisma build

* refactor: ♻️ apply node env

* 💚 ci: copy package json

* 💚 ci: revert arg

* 💚 ci: add prisma migrate to ci

* 💚 ci: add prisma migrate to ci

* 👷 ci: update dockerfile

* refactor: ♻️ use deployed validator

* fix: 🐛 when license is updated validate metadata files

* fix: 🐛 validation returns codemeta version on errors

* 🐛 fix: add basic logwatch

* fix: 🐛 add @type key for 2.0 codemeta.json files

* refactor: ♻️ updated required fields for codemeta schmea

* 🐛 fix: add logwatch support

* 🐛 fix: add json to logwatch

* fix: 🐛 patch json parse issue

* fix: 🐛 update logging parameters

* refactor: ♻️ point a folder above for codemeta-schema

* refactor: ♻️ update dockerfile to include schema

* fix: 🐛 ensure authors have roles key

* refactor: ♻️ 🔊 convert some consola logs to logwatch

* fix: 🐛 roles are optional in save request

* chore: 🔊 remove dev logs

* doc: 📝 update changelog

* refactor: ♻️ revert roles key being optional

* fix: 🐛 add logwatch.start method

* fix: 🐛 ensure contrib and authros have roles

* fix: 🐛 CWL handles multiple installations

* refactor: ♻️ update log error

* feat: ✨ purge zenodo token when sign in is required

* fix: 🐛 make login fn asyncronous

* refactor: 🎨 update spacing and color of validation results button

* fix: 🐛 bad logwatch call removed

* chore: 🔨 sync main to staging (#118)

* fix: 🐛 Zenodo callback issue resolved with purging token before sign in (#116)

* refactor: ♻️ transfer validation api to codefair repo (#106)

* 🚚 chore: rename `validator-api` to `validator`

* 👷 ci: add validator deploy

* 👷 ci: add validator healthcheck

* 👷 ci: add validator deploy for prod

* refactor: ♻️ update codefair name

* feat: ✨ Metadata + license validators + bug patches (#107)

* merge: 🔀 merge main to staging

* refactor: ♻️ 🐛 Codefair 3.1.0 (#89)

* fix: 🐛 patch removing pull_request.closed bug on metadata pr merge

* fix: 🐛 don't update firstPublished in the codemeta file + better logs

* fix: 🐛 patch error on reading db entry when it doesn't exist

* chore: 🔊 better log on successful Zenodo publish

* style: 🎨 margins between text and icon

* feat: ✨ links to the list of tools used for codefair in /codefair

* refactor: ✨ ♻️ abstract the license validation fn

* doc: 🔖 update changelog

* feat: ✨ ♻️ abstraction to zenodo workflow

* wip: 🚧 abstracting zenodo workflow

* feat: ✨ add help link in the Zenodo release page

* refactor: ♻️ ✨ abstract out github release functions

* refactor: 🔊 ♻️ improve error tracing in metadata file

* chore: 🔨 remove todo

* refactor: ✨ ♻️ abstracted Zenodo workflow (bot)

* wip: 🚧 save custom license content when no assertion is provided

* ✨ feat: add support for custom licenses (#90)

* ✨ feat: add support for custom licenses

* 🐛 fix: reset citation license field

* 🐛 fix: update zenodo workflow for custom licenses

* fix: 🐛 license is valid with custom license

* feat: ✨ custom license template

* ✨ feat: update codemeta, license and cwl ui paths (#91)

* ✨ feat: update meta paths for consistency

* 🚚 fix: updatel icense request path

* ✨ feat: add support for custom license title (#92)

* refactor: ♻️ ✨ new patches for license, cwl, metadata UI's

* refactor: ✨ ♻️ apply migrations from UI to bot

* feat: ✨ request custom license title from user

* refactor: ♻️ hide message box when custom license title is blank

* refactor: ♻️ issue dashboard requests custom title

* feat: ✨ Saving custom title (#93)

* feat: ✨ save custom title option

* refactor: :recyle: reuse saveLicenseDraft for storing custom license title

* refactor: ♻️ join draft and save title buttons together

* refactor: ♻️ use naive-ui's properties for styling

* chore: 🔨 remove typo

* chore: 🔨 remove unused variables

* feat: ✨ toasts for custom title saved button

* refactor: ♻️ function rename

* feat: ✨ create Zenodo metadata fn handles custom licenses

* feat: ✨ custom license reference for archival workflow

* refactor: ♻️ stop creating identifiers for new db entries

* refactor: ♻️ 🐛 revert allowing custom licenses for zenodo

* refactor: ♻️ Custom License Support (#94)

* refactor: ♻️ ✨ custom title saved updates dashboard, disable create release btn when custom license

* refactor: ♻️ block progress of fair release if license is custom

* feat: ✨ listener for when custom license title is saved through UI

* feat: ✨ prevent fair release if not fair compliant

* refactor: ♻️ improve license validation and update template text for custom licenses

* refactor: ♻️ re-render issue from ui side

* refactor: ♻️ update to message explaining custom licenses

* db calls running in parallel

* fix: 🐛 prevent Zendo section from being seen when the license is custom

* fix: 🐛 trim license content before comparison

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* refactor: ♻️ safety checks for protected middleware

* refacotr: ♻️ update protectRoute to redirect to login when no user or session

* feat: :fix: redirect to login if not signed in

* refactor: ♻️ remove import

* chore: 🔊 🔨 remove logs

* docs: 📝 update changelog

* fix: 🐛 check license content all times

* fix: 🐛 update on zenodo ui page

* feat: ✨ delete branch after pr has been closed/merged

* chore: 🔨 spacing in changelog

* wip: 🚧 individual validation requests for license and metadata

* feat: ✨ license validation endpoint

* wip: 🚧 creating updated metadata validation

* wip: 🚧 patches for metadata revalidation workflow

* wip: 🚧 validation for codemeta

* doc: 🔖 jsdoc comments on fns

* fix: 🐛 template renderer will stop using old links (#99)

* fix: 🐛 rerender template will stop using old links

* doc: 📝 update CHANGELOG

* doc: 📝 update metadata

* fix: 🐛 preserve authors and contributors from codemeta

* feat: ✨ re-validated codemeta from repo dashboard

* fix: 🐛 await metadata validation

* feat: ✨ codemeta validation extended with microservice validator

* refactor: ♻️ update timestamps to be unix format

* feat: ✨ clean privatekey env before use

* refactor: ♻️ update cwl validation endpoint

* wip: 🚧 send validation message to db

* feat: ✨ create migrations for metadata validation messages

* wip: 🚧 creating json schema for codemeta.json validations

* 👷 ci: setup deployment environments (#101)

* 👷 ci: setup for staging env (#103)

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
Co-authored-by: slugb0t <wheresdorian@gmail.com>
fix: 🐛 template renderer will stop using old links (#99)

* fix: 🐛 adjust env variables used after env changes

* 👷 ci: cleanup dockerfile

* feat: ✨ codemeta schema first draft

* 👷 ci: cleanup dockerfile

* 👷 ci: cleanup dockerfile

* 👷 ci: cleanup dockerfile

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: cleanup dockerfile

* 👷 ci: fix staging deploys (#104)

* wip: 🚧 abstracting cwl workflow

* refactor: ♻️ update codemeta schema to validate against the raw codemeta.json files

* refactor: ♻️ update codemeta schema for additional fields

* feat: ✨ validating raw content of codemeta.json file for 3.0

* refactor: ♻️ create required fields for codemeta schema

* wip: 🚧 testing validation responses for db

* handle codemeta.json 3.0 and 2.0 versioning

* fix: 🐛 correct branch watch for staging deployment action

* doc: 🔖 update changelog for 3.2.0 release

* feat: ✨ align bot prisma with ui

* fix: 🐛 bug patch for cwl workflow

* feat: ✨ metadata workflow update

* refactor: ♻️ preserving authors and contributors

* wip: 🚧 update the metadata workflow after discussions

* fix: 🐛 don't create cwlobject twice

* refactor: ♻️ send 200 status when invalid codemeta

* refactor: ♻️ update codemeta validation schema

* refactor: ♻️ do not revalidate metadata files for push events unless metadata files are updated themselves

* wip: 🚧 seperate rerun validation with regather information

* wip: 🚧 remove command from issue dashboard if error occurs (allows retry)

* refactor: ♻️ update the issue body after successful validation (remove the command from the issue body)

* refactor: ♻️ add additional key to codemeta schema

* refactor: ♻️ remove the regather options from the UI as validation is still needed when regathering

* fix: 🐛 pr button updated with new links

* fix: 🐛 patch variable declaration not in scope

* refactor: ♻️ update on the dropdown icons

* refactor: ♻️ update the keys of the cwl object

* refactor: ♻️ update the getcwlfiles function

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* fix: 🐛 use the correct env variable for private key

* fix: 🐛 Codefair v3.2.0 finalization (#113)

* fix: 🐛 correct cwlObject variables in push event

* fix: 🐛 better error message in metadata workflow + collect missing fields from codemeta.json

* fix: 🐛 apply await to async function call

* refactor: ♻️ removed unused imports

* refactor: ♻️ add try catch in then statement of promise

* fix: 🐛 missing fields in codemeta gathering + add error handling for convertCitationForDB fn

* refactor: ♻️ add try catch to renderer to preserve errors

* fix: 🐛 preserve metadata validation results in db

* wip: 🚧 validation results being displayed through the repo dashboard

* wip: 🚧 displaying metadata validation results in seperate pages

* feat: ✨ validation page for codemeta

* fix: 🐛 patch fundingCode not being preserved from codemeta

* wip: 🚧 final design for validation results

* feat: ✨ add view validation results conditionally

* test: ⚗️ ensuring validation progresses accordingly

* feat: ✨ popover messages for metadata badges

* feat: ✨ if metadata file fails to parse then update validation message

* fix: 🐛 update schema to handle 2.0 and 3.0 authors

* style: 🎨 formatting

* fix: 🐛 add releaseNotes key to schema for 3.0 versions

* refactor: ✏️ change wording

* fix: 🐛 validate metadata file that was updated only on push events

* chore: 📝 remove test logs

* fix: 🐛 migrate db during deployment

* fix: 🐛 revert

* fix: 🐛 typo on dockerfile

* refactor: ♻️ use npm instead of yarn for migration

* refactor: ♻️ access db url during prisma build

* refactor: ♻️ apply node env

* 💚 ci: copy package json

* 💚 ci: revert arg

* 💚 ci: add prisma migrate to ci

* 💚 ci: add prisma migrate to ci

* 👷 ci: update dockerfile

* refactor: ♻️ use deployed validator

* fix: 🐛 when license is updated validate metadata files

* fix: 🐛 validation returns codemeta version on errors

* 🐛 fix: add basic logwatch

* fix: 🐛 add @type key for 2.0 codemeta.json files

* refactor: ♻️ updated required fields for codemeta schmea

* 🐛 fix: add logwatch support

* 🐛 fix: add json to logwatch

* fix: 🐛 patch json parse issue

* fix: 🐛 update logging parameters

* refactor: ♻️ point a folder above for codemeta-schema

* refactor: ♻️ update dockerfile to include schema

* fix: 🐛 ensure authors have roles key

* refactor: ♻️ 🔊 convert some consola logs to logwatch

* fix: 🐛 roles are optional in save request

* chore: 🔊 remove dev logs

* doc: 📝 update changelog

* refactor: ♻️ revert roles key being optional

* fix: 🐛 add logwatch.start method

* fix: 🐛 ensure contrib and authros have roles

* fix: 🐛 CWL handles multiple installations

* refactor: ♻️ update log error

* feat: ✨ purge zenodo token when sign in is required

* fix: 🐛 make login fn asyncronous

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* refactor: 🎨 update view validation & edit metadata buttons (#117)

* refactor: ♻️ transfer validation api to codefair repo (#106)

* 🚚 chore: rename `validator-api` to `validator`

* 👷 ci: add validator deploy

* 👷 ci: add validator healthcheck

* 👷 ci: add validator deploy for prod

* refactor: ♻️ update codefair name

* feat: ✨ Metadata + license validators + bug patches (#107)

* merge: 🔀 merge main to staging

* refactor: ♻️ 🐛 Codefair 3.1.0 (#89)

* fix: 🐛 patch removing pull_request.closed bug on metadata pr merge

* fix: 🐛 don't update firstPublished in the codemeta file + better logs

* fix: 🐛 patch error on reading db entry when it doesn't exist

* chore: 🔊 better log on successful Zenodo publish

* style: 🎨 margins between text and icon

* feat: ✨ links to the list of tools used for codefair in /codefair

* refactor: ✨ ♻️ abstract the license validation fn

* doc: 🔖 update changelog

* feat: ✨ ♻️ abstraction to zenodo workflow

* wip: 🚧 abstracting zenodo workflow

* feat: ✨ add help link in the Zenodo release page

* refactor: ♻️ ✨ abstract out github release functions

* refactor: 🔊 ♻️ improve error tracing in metadata file

* chore: 🔨 remove todo

* refactor: ✨ ♻️ abstracted Zenodo workflow (bot)

* wip: 🚧 save custom license content when no assertion is provided

* ✨ feat: add support for custom licenses (#90)

* ✨ feat: add support for custom licenses

* 🐛 fix: reset citation license field

* 🐛 fix: update zenodo workflow for custom licenses

* fix: 🐛 license is valid with custom license

* feat: ✨ custom license template

* ✨ feat: update codemeta, license and cwl ui paths (#91)

* ✨ feat: update meta paths for consistency

* 🚚 fix: updatel icense request path

* ✨ feat: add support for custom license title (#92)

* refactor: ♻️ ✨ new patches for license, cwl, metadata UI's

* refactor: ✨ ♻️ apply migrations from UI to bot

* feat: ✨ request custom license title from user

* refactor: ♻️ hide message box when custom license title is blank

* refactor: ♻️ issue dashboard requests custom title

* feat: ✨ Saving custom title (#93)

* feat: ✨ save custom title option

* refactor: :recyle: reuse saveLicenseDraft for storing custom license title

* refactor: ♻️ join draft and save title buttons together

* refactor: ♻️ use naive-ui's properties for styling

* chore: 🔨 remove typo

* chore: 🔨 remove unused variables

* feat: ✨ toasts for custom title saved button

* refactor: ♻️ function rename

* feat: ✨ create Zenodo metadata fn handles custom licenses

* feat: ✨ custom license reference for archival workflow

* refactor: ♻️ stop creating identifiers for new db entries

* refactor: ♻️ 🐛 revert allowing custom licenses for zenodo

* refactor: ♻️ Custom License Support (#94)

* refactor: ♻️ ✨ custom title saved updates dashboard, disable create release btn when custom license

* refactor: ♻️ block progress of fair release if license is custom

* feat: ✨ listener for when custom license title is saved through UI

* feat: ✨ prevent fair release if not fair compliant

* refactor: ♻️ improve license validation and update template text for custom licenses

* refactor: ♻️ re-render issue from ui side

* refactor: ♻️ update to message explaining custom licenses

* db calls running in parallel

* fix: 🐛 prevent Zendo section from being seen when the license is custom

* fix: 🐛 trim license content before comparison

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* refactor: ♻️ safety checks for protected middleware

* refacotr: ♻️ update protectRoute to redirect to login when no user or session

* feat: :fix: redirect to login if not signed in

* refactor: ♻️ remove import

* chore: 🔊 🔨 remove logs

* docs: 📝 update changelog

* fix: 🐛 check license content all times

* fix: 🐛 update on zenodo ui page

* feat: ✨ delete branch after pr has been closed/merged

* chore: 🔨 spacing in changelog

* wip: 🚧 individual validation requests for license and metadata

* feat: ✨ license validation endpoint

* wip: 🚧 creating updated metadata validation

* wip: 🚧 patches for metadata revalidation workflow

* wip: 🚧 validation for codemeta

* doc: 🔖 jsdoc comments on fns

* fix: 🐛 template renderer will stop using old links (#99)

* fix: 🐛 rerender template will stop using old links

* doc: 📝 update CHANGELOG

* doc: 📝 update metadata

* fix: 🐛 preserve authors and contributors from codemeta

* feat: ✨ re-validated codemeta from repo dashboard

* fix: 🐛 await metadata validation

* feat: ✨ codemeta validation extended with microservice validator

* refactor: ♻️ update timestamps to be unix format

* feat: ✨ clean privatekey env before use

* refactor: ♻️ update cwl validation endpoint

* wip: 🚧 send validation message to db

* feat: ✨ create migrations for metadata validation messages

* wip: 🚧 creating json schema for codemeta.json validations

* 👷 ci: setup deployment environments (#101)

* 👷 ci: setup for staging env (#103)

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
Co-authored-by: slugb0t <wheresdorian@gmail.com>
fix: 🐛 template renderer will stop using old links (#99)

* fix: 🐛 adjust env variables used after env changes

* 👷 ci: cleanup dockerfile

* feat: ✨ codemeta schema first draft

* 👷 ci: cleanup dockerfile

* 👷 ci: cleanup dockerfile

* 👷 ci: cleanup dockerfile

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: setup for staging env

* 👷 ci: cleanup dockerfile

* 👷 ci: fix staging deploys (#104)

* wip: 🚧 abstracting cwl workflow

* refactor: ♻️ update codemeta schema to validate against the raw codemeta.json files

* refactor: ♻️ update codemeta schema for additional fields

* feat: ✨ validating raw content of codemeta.json file for 3.0

* refactor: ♻️ create required fields for codemeta schema

* wip: 🚧 testing validation responses for db

* handle codemeta.json 3.0 and 2.0 versioning

* fix: 🐛 correct branch watch for staging deployment action

* doc: 🔖 update changelog for 3.2.0 release

* feat: ✨ align bot prisma with ui

* fix: 🐛 bug patch for cwl workflow

* feat: ✨ metadata workflow update

* refactor: ♻️ preserving authors and contributors

* wip: 🚧 update the metadata workflow after discussions

* fix: 🐛 don't create cwlobject twice

* refactor: ♻️ send 200 status when invalid codemeta

* refactor: ♻️ update codemeta validation schema

* refactor: ♻️ do not revalidate metadata files for push events unless metadata files are updated themselves

* wip: 🚧 seperate rerun validation with regather information

* wip: 🚧 remove command from issue dashboard if error occurs (allows retry)

* refactor: ♻️ update the issue body after successful validation (remove the command from the issue body)

* refactor: ♻️ add additional key to codemeta schema

* refactor: ♻️ remove the regather options from the UI as validation is still needed when regathering

* fix: 🐛 pr button updated with new links

* fix: 🐛 patch variable declaration not in scope

* refactor: ♻️ update on the dropdown icons

* refactor: ♻️ update the keys of the cwl object

* refactor: ♻️ update the getcwlfiles function

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* fix: 🐛 use the correct env variable for private key

* fix: 🐛 Codefair v3.2.0 finalization (#113)

* fix: 🐛 correct cwlObject variables in push event

* fix: 🐛 better error message in metadata workflow + collect missing fields from codemeta.json

* fix: 🐛 apply await to async function call

* refactor: ♻️ removed unused imports

* refactor: ♻️ add try catch in then statement of promise

* fix: 🐛 missing fields in codemeta gathering + add error handling for convertCitationForDB fn

* refactor: ♻️ add try catch to renderer to preserve errors

* fix: 🐛 preserve metadata validation results in db

* wip: 🚧 validation results being displayed through the repo dashboard

* wip: 🚧 displaying metadata validation results in seperate pages

* feat: ✨ validation page for codemeta

* fix: 🐛 patch fundingCode not being preserved from codemeta

* wip: 🚧 final design for validation results

* feat: ✨ add view validation results conditionally

* test: ⚗️ ensuring validation progresses accordingly

* feat: ✨ popover messages for metadata badges

* feat: ✨ if metadata file fails to parse then update validation message

* fix: 🐛 update schema to handle 2.0 and 3.0 authors

* style: 🎨 formatting

* fix: 🐛 add releaseNotes key to schema for 3.0 versions

* refactor: ✏️ change wording

* fix: 🐛 validate metadata file that was updated only on push events

* chore: 📝 remove test logs

* fix: 🐛 migrate db during deployment

* fix: 🐛 revert

* fix: 🐛 typo on dockerfile

* refactor: ♻️ use npm instead of yarn for migration

* refactor: ♻️ access db url during prisma build

* refactor: ♻️ apply node env

* 💚 ci: copy package json

* 💚 ci: revert arg

* 💚 ci: add prisma migrate to ci

* 💚 ci: add prisma migrate to ci

* 👷 ci: update dockerfile

* refactor: ♻️ use deployed validator

* fix: 🐛 when license is updated validate metadata files

* fix: 🐛 validation returns codemeta version on errors

* 🐛 fix: add basic logwatch

* fix: 🐛 add @type key for 2.0 codemeta.json files

* refactor: ♻️ updated required fields for codemeta schmea

* 🐛 fix: add logwatch support

* 🐛 fix: add json to logwatch

* fix: 🐛 patch json parse issue

* fix: 🐛 update logging parameters

* refactor: ♻️ point a folder above for codemeta-schema

* refactor: ♻️ update dockerfile to include schema

* fix: 🐛 ensure authors have roles key

* refactor: ♻️ 🔊 convert some consola logs to logwatch

* fix: 🐛 roles are optional in save request

* chore: 🔊 remove dev logs

* doc: 📝 update changelog

* refactor: ♻️ revert roles key being optional

* fix: 🐛 add logwatch.start method

* fix: 🐛 ensure contrib and authros have roles

* fix: 🐛 CWL handles multiple installations

* refactor: ♻️ update log error

* feat: ✨ purge zenodo token when sign in is required

* fix: 🐛 make login fn asyncronous

* refactor: 🎨 update spacing and color of validation results button

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>

* chore: 📝 Update CITATION.cff with Zenodo identifier

* chore: 📝 Update codemeta.json with Zenodo identifier

* fix: 🐛 bad logwatch calls removed

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
Co-authored-by: codefair-io[bot] <165336008+codefair-io[bot]@users.noreply.github.com>

* refactor: ♻️ 🔏 🔊 🧑‍💻 Add Environment Variables and Convert Logging to Use Logwatch (#119)

* dev: 🧑‍💻 🔐 add env variables for logwatch and validator

* refactor: ♻️ 🔊 replace consola with logwatch

* doc: 📝 update CHANGELOG

---------

Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
Co-authored-by: codefair-io[bot] <165336008+codefair-io[bot]@users.noreply.github.com>
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@slugb0t @megasanjay @codefair-io
3 people authored Dec 12, 2024
1 parent 1892533 commit 696fe3b
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3 changes: 3 additions & 0 deletions .github/workflows/deploy-main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ jobs:
KAMAL_SERVER_IP: ${{ secrets.KAMAL_SERVER_IP }}
KAMAL_BOT_DOMAIN: ${{ secrets.KAMAL_BOT_DOMAIN }}
DATABASE_URL: ${{ secrets.DATABASE_URL }}
BOT_LOGWATCH_URL: ${{ secrets.BOT_LOGWATCH_URL }}
APP_ID: ${{ secrets.APP_ID }}
GH_APP_ID: ${{ secrets.GH_APP_ID }}
GH_APP_NAME: ${{ secrets.GH_APP_NAME }}
Expand All @@ -36,6 +37,7 @@ jobs:
CODEFAIR_APP_DOMAIN: ${{ secrets.CODEFAIR_APP_DOMAIN }}
ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
VALIDATOR_URL: ${{ secrets.VALIDATOR_URL }}

steps:
- uses: actions/checkout@v4
Expand Down Expand Up @@ -99,6 +101,7 @@ jobs:
GH_OAUTH_APP_ID: ${{ secrets.GH_OAUTH_APP_ID }}
GH_OAUTH_CLIENT_ID: ${{ secrets.GH_OAUTH_CLIENT_ID }}
GH_OAUTH_CLIENT_SECRET: ${{ secrets.GH_OAUTH_CLIENT_SECRET }}
UI_LOGWATCH_URL: ${{ secrets.UI_LOGWATCH_URL }}
ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
ZENODO_CLIENT_ID: ${{ secrets.ZENODO_CLIENT_ID }}
Expand Down
3 changes: 3 additions & 0 deletions .github/workflows/deploy-staging.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ jobs:
KAMAL_SERVER_IP: ${{ secrets.KAMAL_SERVER_IP }}
KAMAL_BOT_DOMAIN: ${{ secrets.KAMAL_BOT_DOMAIN }}
DATABASE_URL: ${{ secrets.DATABASE_URL }}
BOT_LOGWATCH_URL: ${{ secrets.BOT_LOGWATCH_URL }}
APP_ID: ${{ secrets.APP_ID }}
GH_APP_ID: ${{ secrets.GH_APP_ID }}
GH_APP_NAME: ${{ secrets.GH_APP_NAME }}
Expand All @@ -36,6 +37,7 @@ jobs:
CODEFAIR_APP_DOMAIN: ${{ secrets.CODEFAIR_APP_DOMAIN }}
ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
VALIDATOR_URL: ${{ secrets.VALIDATOR_URL }}

steps:
- uses: actions/checkout@v4
Expand Down Expand Up @@ -99,6 +101,7 @@ jobs:
GH_OAUTH_APP_ID: ${{ secrets.GH_OAUTH_APP_ID }}
GH_OAUTH_CLIENT_ID: ${{ secrets.GH_OAUTH_CLIENT_ID }}
GH_OAUTH_CLIENT_SECRET: ${{ secrets.GH_OAUTH_CLIENT_SECRET }}
UI_LOGWATCH_URL: ${{ secrets.UI_LOGWATCH_URL }}
ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
ZENODO_CLIENT_ID: ${{ secrets.ZENODO_CLIENT_ID }}
Expand Down
11 changes: 11 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,17 @@ All notable changes the Codefair App will be documented in this file.
The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).

## v3.2.1 - 12-12-2024

### Added

- Convert logging from 'consola' to 'logwatch' for improved log management and consistency across the application.

### Fixed

- Update CI and deployment workflows to include new environment variables 'BOT_LOGWATCH_URL' and 'VALIDATOR_URL'.
- Patch to Zenodo workflow that was causing the user to be notified of a failed Zenodo upload when the upload was successful.

## v3.2.0 - 12-10-2024

### Added
Expand Down
2 changes: 2 additions & 0 deletions bot/.kamal/secrets
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ KAMAL_SERVER_IP=$KAMAL_SERVER_IP
# bot secrets
APP_ID=$APP_ID
DATABASE_URL=$DATABASE_URL
BOT_LOGWATCH_URL=$BOT_LOGWATCH_URL
GH_APP_ID=$GH_APP_ID
GH_APP_NAME=$GH_APP_NAME
GH_APP_CLIENT_ID=$GH_APP_CLIENT_ID
Expand All @@ -24,6 +25,7 @@ WEBHOOK_SECRET=$WEBHOOK_SECRET
CODEFAIR_APP_DOMAIN=$CODEFAIR_APP_DOMAIN
ZENODO_API_ENDPOINT=$ZENODO_API_ENDPOINT
ZENODO_ENDPOINT=$ZENODO_ENDPOINT
VALIDATOR_URL=$VALIDATOR_URL

# Option 2: Read secrets via a command
# RAILS_MASTER_KEY=$(cat config/master.key)
Expand Down
40 changes: 20 additions & 20 deletions bot/archival/index.js
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import dbInstance from '../db.js';
import { consola } from 'consola';
import { logwatch } from '../utils/logwatch.js';
import fs from 'fs';
const licensesJson = JSON.parse(fs.readFileSync('./public/assets/data/licenses.json', 'utf8'));

Expand All @@ -20,7 +21,7 @@ export async function updateGitHubRelease(context, repositoryName, owner, releas
release_id: releaseId,
draft: false,
});
consola.success("Updated release to not be a draft!");
logwatch.success("Updated release to not be a draft!");
} catch (error) {
throw new Error(`Error updating the GitHub release: ${error}`, { cause: error });
}
Expand All @@ -33,7 +34,7 @@ export async function updateGitHubRelease(context, repositoryName, owner, releas
*/
export async function publishZenodoDeposition(zenodoToken, depositionId) {
try {
consola.start("Publishing the Zenodo deposition...", depositionId);
logwatch.start(`Publishing the Zenodo deposition: ${depositionId}`);
const publishDeposition = await fetch(
`${ZENODO_API_ENDPOINT}/deposit/depositions/${depositionId}/actions/publish`,
{
Expand All @@ -50,7 +51,7 @@ export async function publishZenodoDeposition(zenodoToken, depositionId) {
}

const publishedDeposition = await publishDeposition.json();
consola.success("Zenodo deposition published successfully at:", publishedDeposition.links.latest_html);
logwatch.success(`Zenodo deposition published successfully at: ${publishedDeposition.links.latest_html}`);
} catch (error) {
throw new Error(`Error publishing the Zenodo deposition: ${error.message}`, { cause: error });
}
Expand Down Expand Up @@ -251,7 +252,7 @@ export async function createNewVersionOfDeposition(zenodoToken, depositionId) {
const errorText = await zenodoRecord.text();
throw new Error(`Failed to create a new version of Zenodo deposition. Status: ${zenodoRecord.status}: ${zenodoRecord.statusText}.`, { cause: errorText});
}
consola.success("New version of Zenodo deposition created successfully!");
logwatch.success("New version of Zenodo deposition created successfully!");

const responseText = await zenodoRecord.json();

Expand All @@ -265,7 +266,7 @@ export async function createNewVersionOfDeposition(zenodoToken, depositionId) {
});

if (!draftZenodoRecord.ok) {
consola.error("Error fetching the latest draft of Zenodo deposition:", draftZenodoRecord);
logwatch.error({message: "Error fetching the latest draft of Zenodo deposition:", fetchReponse: draftZenodoRecord}, true);
const errorText = await draftZenodoRecord.text();
throw new Error(`Failed to fetch the latest draft of Zenodo deposition. Status: ${draftZenodoRecord.status}: ${draftZenodoRecord.statusText}. Error: ${errorText}`, { cause: errorText });
}
Expand Down Expand Up @@ -295,7 +296,7 @@ export async function getZenodoDepositionInfo(

if (zenodoDepositionInfo.submitted === false){
// Delete the files in the draft
consola.start("Requested deposition is a draft. Deleting the files in the draft...");
logwatch.start("Requested deposition is a draft. Deleting the files in the draft...");
for (const file of zenodoDepositionInfo.files) {
await deleteFileFromZenodo(depositionId, zenodoToken, file.id);
}
Expand All @@ -307,12 +308,12 @@ export async function getZenodoDepositionInfo(

if (newZenodoVersion.files.length > 0) {
for (const file of newZenodoVersion.files) {
consola.start("Deleting file from newly created draft:", file.links.download);
logwatch.start(`Deleting file from newly created draft: ${file.links.download}`);
await deleteFileFromZenodo(newZenodoVersion.id, zenodoToken, file.id);
}
}

consola.success("New draft version of Zenodo deposition created successfully!");
logwatch.success("New draft version of Zenodo deposition created successfully!");
return newZenodoVersion;
}
}
Expand Down Expand Up @@ -354,8 +355,8 @@ export async function createZenodoMetadata(codemetadata, repository) {
});
if (!codeMetaContent.license) {
// fetch from the db
consola.warn(`No license found in the codemeta.json file. Fetching from the database...`);
consola.info(`License found in the database: ${existingLicense?.license_id}`);
logwatch.warn(`No license found in the codemeta.json file. Fetching from the database...`);
logwatch.info(`License found in the database: ${existingLicense?.license_id}`);
codeMetaContent.license = `https://spdx.org/licenses/${existingLicense?.license_id}`;
}
const license = licensesJson.find((license) => license.detailsUrl === `${codeMetaContent.license}.json`);
Expand All @@ -372,7 +373,7 @@ export async function createZenodoMetadata(codemetadata, repository) {
})

if (!zenodoMetadata) {
consola.error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
logwatch.error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
throw new Error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
}

Expand Down Expand Up @@ -440,7 +441,7 @@ export async function updateZenodoMetadata(depositionId, zenodoToken, metadata)
);

const updatedMetadataInfo = await updatedMetadata.json();
consola.success("Zenodo deposition metadata updated successfully!");
logwatch.success("Zenodo deposition metadata updated successfully!");
return updatedMetadataInfo;
} catch (error) {
throw new Error(`Error updating Zenodo metadata: ${error}`, { cause: error });
Expand Down Expand Up @@ -480,7 +481,7 @@ export async function uploadReleaseAssetsToZenodo(
accept: 'application/octet-stream'
}
});
consola.success(`Asset data fetched for ${asset.name}, for the release ${tagVersion}, from the GitHub repository: ${repository.name}`);
logwatch.success(`Asset data fetched for ${asset.name}, for the release ${tagVersion}, from the GitHub repository: ${repository.name}`);

// Upload the file to Zenodo
const uploadAsset = await fetch(`${bucket_url}/${asset.name}`,
Expand All @@ -493,9 +494,9 @@ export async function uploadReleaseAssetsToZenodo(
});

if (!uploadAsset.ok) {
consola.error(`Failed to upload ${asset.name}. Status: ${uploadAsset.statusText}. Error: ${uploadAsset}`);
logwatch.error(`Failed to upload ${asset.name}. Status: ${uploadAsset.statusText}. Error: ${uploadAsset}`);
} else {
consola.success(`${asset.name} successfully uploaded to Zenodo!`);
logwatch.success(`${asset.name} successfully uploaded to Zenodo!`);
}
} catch (error) {
throw new Error(`Error uploading assets to Zenodo: ${error}`, { cause: error });
Expand All @@ -516,13 +517,13 @@ export async function uploadReleaseAssetsToZenodo(
);

if (!uploadZip.ok) {
consola.error(`Failed to upload zip file. Status: ${uploadZip.statusText}`);
logwatch.error(`Failed to upload zip file. Status: ${uploadZip.statusText}`);
throw new Error(`Failed to upload zip file. Status: ${uploadZip.statusText}`);
}

const endTime = performance.now();
consola.info(`Total duration to upload assets and zip to Zenodo deposition: ${(endTime - startTime) / 1000} seconds`);
consola.success("Zip file successfully uploaded to Zenodo!");
logwatch.info(`Total duration to upload assets and zip to Zenodo deposition: ${(endTime - startTime) / 1000} seconds`);
logwatch.success("Zip file successfully uploaded to Zenodo!");
}

/**
Expand All @@ -543,12 +544,11 @@ export async function deleteFileFromZenodo(depositionId, zenodoToken, fileId) {
);

if (!deleteFile.ok) {
consola.error(deleteFile);
const errorText = await deleteFile.text();
throw new Error(`Failed to delete file from Zenodo. Status: ${deleteFile.status}: ${deleteFile.statusText}. Error: ${errorText}`);
}

consola.success("File successfully deleted from Zenodo!");
logwatch.success("File successfully deleted from Zenodo!");
} catch (error) {
throw new Error(`Error deleting file from Zenodo: ${error}`, { cause: error });
}
Expand Down
2 changes: 2 additions & 0 deletions bot/config/deploy.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,8 @@ env:
- CODEFAIR_APP_DOMAIN
- ZENODO_API_ENDPOINT
- ZENODO_ENDPOINT
- VALIDATOR_URL
- BOT_LOGWATCH_URL
clear:
NODE_ENV: production

Expand Down
41 changes: 22 additions & 19 deletions bot/cwl/index.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
* * This file contains the functions to interact with the CWL files in the repository
*/
import { consola } from "consola";
import { logwatch } from "../utils/logwatch.js";
import {
isRepoPrivate,
createId,
Expand All @@ -10,6 +11,7 @@ import {
import dbInstance from "../db.js";

const CODEFAIR_DOMAIN = process.env.CODEFAIR_APP_DOMAIN;
const { VALIDATOR_URL } = process.env;

/**
* * This function gets the CWL files in the repository
Expand All @@ -20,7 +22,7 @@ const CODEFAIR_DOMAIN = process.env.CODEFAIR_APP_DOMAIN;
*/
export function getCWLFiles(context, owner, repository) {
return new Promise((resolve, reject) => {
consola.info("Checking for CWL files in the repository...");
logwatch.info("Checking for CWL files in the repository...");

const cwlFiles = [];
const cwlObject = {
Expand Down Expand Up @@ -51,9 +53,12 @@ export function getCWLFiles(context, owner, repository) {
resolve(cwlObject);
return;
}
consola.error(
"Error finding CWL files throughout the repository:",
error,
logwatch.error(
{
message: "Error finding CWL files throughout the repository:",
error,
},
true
);
reject(error);
}
Expand Down Expand Up @@ -93,7 +98,7 @@ export function getCWLFiles(context, owner, repository) {
*/
export async function validateCWLFile(downloadUrl) {
try {
const response = await fetch("https://cwl-validate.codefair.io/validate-cwl", {
const response = await fetch(`${VALIDATOR_URL}/validate-cwl`, {
body: JSON.stringify({
file_path: downloadUrl,
}),
Expand All @@ -108,15 +113,15 @@ export async function validateCWLFile(downloadUrl) {
return [false, error.error];
}
if (!response.ok && response.status === 500) {
consola.error("Error validating CWL file:", response);
logwatch.error({message: "Error validating CWL file:", validation_response: response}, true);
return [false, "Error validating CWL file"];
}
if (response.ok) {
const data = await response.json();
return [true, data.output];
}
} catch (e) {
consola.error("Error validating CWL file:", e);
logwatch.error({message: "Error validating CWL file:", error: e}, true);
return [false, "Error validating CWL file"];
}
}
Expand Down Expand Up @@ -180,14 +185,14 @@ export async function applyCWLTemplate(
});

if (subjects.cwl.files.length === 0) {
consola.warn(
`No new/modified CWL files found in the repository, ${repository.name}`,
logwatch.warn(
`No CWL files found in the repository, ${repository.name}`,
);
}

consola.start("Validating CWL files for", repository.name);
logwatch.start("Validating CWL files for", repository.name);
// Validate each CWL file from list\
consola.info(`Validating ${JSON.stringify(subjects.cwl)} CWL files`);
logwatch.info(`Validating ${JSON.stringify(subjects.cwl)} CWL files`);
if (subjects.cwl.files.length > 0) {
for (const file of subjects.cwl.files) {
const fileSplit = file.name.split(".");
Expand Down Expand Up @@ -252,7 +257,7 @@ export async function applyCWLTemplate(
// Add the file to the table content of the issue dashboard
tableContent += `| ${file.path} | ${isValidCWL ? "✔️" : "❌"} |\n`;

consola.success(
logwatch.success(
`File: ${file.path} is ${isValidCWL ? "valid" : "invalid"}`,
);
}
Expand All @@ -276,7 +281,7 @@ export async function applyCWLTemplate(
});

if (!cwlFiles.length > 0) {
consola.warn(
logwatch.warn(
`No CWL files found in the repository, ${repository.name}, skipping CWL section`,
);
return baseTemplate;
Expand Down Expand Up @@ -317,15 +322,13 @@ export async function applyCWLTemplate(

if (!newFiles.length > 0) {
// All CWL files were removed from the repository
consola.warn(
"All CWL files were removed from:",
repository.name,
"skipping CWL section",
logwatch.warn(
`All CWL files were removed from: ${repository.name}, skipping CWL section`
);
return baseTemplate;
} else {
// Recreate the table content to include the new and old cwl files
consola.start(
logwatch.start(
"Recreating the table content for the CWL section to include new and old files",
);
tableContent = "";
Expand All @@ -349,6 +352,6 @@ export async function applyCWLTemplate(
const cwlBadge = `[![CWL](https://img.shields.io/badge/View_CWL_Report-0ea5e9.svg)](${url})`;
baseTemplate += `${overallSection}\n\n### CWL Validations ${validOverall ? "✔️" : "❗"}\n\nCodefair has detected that you are following the Common Workflow Language (CWL) standard to describe your command line tool. Codefair ran the [cwltool validator](https://cwltool.readthedocs.io/en/latest/) and ${validOverall ? `all ***${subjects.cwl.files.length}*** CWL file(s) in your repository are valid.` : `***${failedCount}/${subjects.cwl.files.length}*** CWL file(s) in your repository are not valid.`}\n\n<details>\n<summary>Summary of the validation report</summary>\n\n| File | Validation result |\n| :---- | :----: |\n${tableContent}</details>\n\nTo view the full report of each CWL file or to rerun the validation, click the "View CWL Report" button below.\n\n${cwlBadge}`;

consola.success("CWL template section applied");
logwatch.success("CWL template section applied");
return baseTemplate;
}
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