Releases · CSCfi/metadata-submitter

Added

Submission endpoint update #371
- Adds mandatory query parameter folder for submit endpoint POST
- On actions add and modify object is added or updated to folder(submission) where it belongs with it's accession ID, schema, submission type, title and filename
- Adds metax integration to submit endpoint
Integration with Metax service #356 #387
- Adds new local container for testing against mocked Metax API
- Introduces new env vars: METAX_USER, METAX_PASS, METAX_URL for connection to Metax service
- Introduces new env var DISCOVERY_URL for creating link to dataset inside Fairdata SD catalog
- Adds new key metaxIdentifier to Study and Dataset collections containing metax id returned from Metax API
- Adds new handler MetaxServiceHandler to take care of mapping Submitter metadata to Metax metadata and to connect to Metax API
- Adds new mapper class to adjust incoming metadata to Metax schema
Add patching of folders after object save and update operations #354
- Adds mandatory query parameter folder for objects endpoint POST
- Object is added or updated to folder(submission) where it belongs with it's accession ID, schema, submission type, title and filename in the case of CSV and XML upload
- Adds configuration for mypy linting to VScode devcontainer setup
Templates API #256
- use ujson as default json library
Creating draft Datacite DOI for folders #257 #332
- created a mock web app, which would act similarly to DataCite REST API
- altered publish_folder endpoint so that extraInfo containing the DOI data is added upon publishing
- added datePublished key to folders which takes in the date/time, when folder is published
DOI Publishing and deletion to Datacite #332 #369
- create draft DOIs for both Study and Datasets and add them to the folder extraInfo when published
- delete draft DOIs on object delete
- update DOI info at Datacite when folder is published
VScode Dev environment #287
- Add VS Code development container
- Update docker for development
Docker-compose and docker-compose-tls files changed to use variables from .env file. #301
Add folder querying by name #305
- Add indexing on database initialization
- Add new field text_name to folder collection
- Python scripts for database operations. mongo_indexes.py for collections and indexes creation to be run if the database is destroyed and clean_db.py script with new functionality to only delete documents from collections
- update github actions
Add folder querying by date #308
Add description to JSON schemas #323
- add JSON schema spelling checker to pyspelling github action
- optimise wordlist by adding regex ignore patterns
- added pyspelling to pre-commit hooks (fixed syntax for scripts according to https://github.com/koalaman/shellcheck )
- enum are sorted alphabetically, with the exception of other and unspecified values which are left at the end of the list
- allow for accession key in referenceAlignment & process sequence as array, previously all accession keys were converted to accessionId which is not correct
- add default gender as unknown
Project ownership #346
- added new collection project
- added new key projects to user
- added new key projectId to folder and template-* collections
- new mandatory /userinfo value from AAI at login time sdSubmitProjects
  - user is redirected to an info page by AAI if key is missing
- new mandatory query parameter projectId in GET /folders
- new mandatory JSON key projectId in POST /folders and POST /templates
- new endpoint GET /templates to replace GET /users/current {"templates":[...]}
- new JSON keys index and tags to PATCH /templates/schema/templateId, same values as were previously used in PATCH /user which is now removed
- WARNING: breaking change that requires fresh database, because "project" is new information that did not exist before, and it can't be migrated to existing user-owned hierarchy
Multilevel add patch objects to support /extraInfo/datasetIdentifiers/- which needs dot notation for mongodb to work e.g. extraInfo.datasetIdentifiers #332

Changed

Refactor auth.py package by removing custom OIDC code and replacing it with https://github.com/IdentityPython/JWTConnect-Python-OidcRP. #315
- New mandatory ENV OIDC_URL
- New optional ENVs OIDC_SCOPE, AUTH_METHOD
- Added oidcrp dependency
Use node 16+ #345
VScode Dev environment #287
- Adds requirements-dev.in/txt files. Now pip dependencies can be managed with pip-tools
- README updated with tox command, development build instructions, and prettify Dockerfile.
Update ENA XML and JSON schemas #299
Github actions changed the use of https://git.io/misspell to rojopolis/spellcheck-github-actions #316
Separated most of the handlers to own files inside the handlers folder #319
allow inserting only one study in folder #332
JSON schemas #332
- introduce keywords required for Metax in doiInfo
- dataset description and study studyAbstract are now mandatory
keywords will be comma separated values, that will require splitting when adding to Metax API

Fixed

Coveralls report #267
Typos for functions and tests #279
Fix spelling mistakes for JSON schemas #323
Oidcrp does not allow empty values, prefill them in mockauth so front-end can start #333
Fix development environment #336
- Add env vars OIDC_URL and OIDC_URL_TEST to mock auth container
- Adds logging configs for mock auth
- Updates mock auth api's token endpoint with expiration configs
- Adds config .pre-commit-config.yaml file required by pre-commit library
- Redirect url in docker-compose is now default
- Adds logging for doi mock api

Removed

Removed Authlib dependency #315
Project ownership #346
- deprecated folders and templates keys from GET /users/current
  - as a side effect, deprecated items query parameter from the same endpoint
- deprecated PATCH /user

Deprecated

Deprecated ENVs ISS_URL, AUTH_URL, AUTH_REFERER, JWK_URL #315

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[0.13.1] - 2022-05-30

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Releases: CSCfi/metadata-submitter

v0.13.1

[0.13.1] - 2022-05-30

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v0.13.0

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Deprecated

metadata-submitter v0.11.0

metadata-submitter v0.10.0

metadata-submitter v0.9.0

metadata-submitter v0.8.1

metadata-submitter v0.8.0

metadata-submitter v0.7.1

metadata-submitter v0.7.0

metadata-submitter v0.6.1