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add study and dataset identifiers to folder schema #332

Merged
merged 24 commits into from
Mar 8, 2022
Merged

add study and dataset identifiers to folder schema #332

merged 24 commits into from
Mar 8, 2022

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@blankdots blankdots commented Jan 10, 2022 •
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Description

Related issues

Partly Closes #326

Type of change

  • New feature (non-breaking change which adds functionality)

Changes Made

  1. JSON Schemas adjustments
    • introduce keywords required for Metax in doiInfo
    • dataset description and studyabstract are now mandatory
    • small formatting adjustments
  2. create draft DOIs for Study and Datasets
  3. update DOIs info at Datacite when folder is published
  4. multilevel add patch objects to support /extraInfo/datasetIdentifiers/- which needs dot notation for mongodb to work e.g. extraInfo.datasetIdentifiers
  5. allow inserting only one study in folder, there might some race condition if we try to insert at the same time, however i tried to address that, however if anyone has a better idea, I am open to suggestions
  6. integration and unit tests adjustments
  7. some functions don't need to be async and remove additional check for list when create ids when posting a new object

Testing

  • Unit Tests
  • Integration Tests

Mentions

delete DOI will come in a follow-up PR.

@blankdots blankdots self-assigned this Jan 10, 2022
@blankdots blankdots linked an issue Jan 11, 2022 that may be closed by this pull request
Adjust DOI information so that it can be integrated with Metax/Etsin #326
Closed
@blankdots blankdots force-pushed the feature/doi-workflow branch from 0021331 to 308b958 Compare January 11, 2022 11:05
@blankdots blankdots force-pushed the bugfix/json-messages branch from 1abccca to 7f0ae9d Compare January 12, 2022 16:15
@blankdots blankdots force-pushed the feature/doi-workflow branch from 308b958 to 37990d9 Compare January 12, 2022 16:20
Base automatically changed from bugfix/json-messages to develop January 24, 2022 12:45
@blankdots blankdots force-pushed the feature/doi-workflow branch from 37990d9 to 0d5865a Compare January 25, 2022 08:08
@blankdots blankdots mentioned this pull request Jan 25, 2022
Closed
@blankdots blankdots force-pushed the feature/doi-workflow branch 5 times, most recently from d57eac1 to 04d338d Compare February 15, 2022 12:22
@blankdots blankdots force-pushed the feature/doi-workflow branch from a1712fd to f1d89ab Compare February 16, 2022 14:24
@blankdots blankdots changed the base branch from develop to refactor/patch-object-on-save February 16, 2022 14:25
@blankdots blankdots force-pushed the feature/doi-workflow branch 2 times, most recently from f74bb5a to 7c367fb Compare February 16, 2022 14:30
@genie9 genie9 force-pushed the refactor/patch-object-on-save branch from 135af96 to 2b078c9 Compare February 23, 2022 14:22
@genie9 genie9 mentioned this pull request Feb 23, 2022
Merged
4 tasks
Base automatically changed from refactor/patch-object-on-save to develop February 28, 2022 08:10
@blankdots blankdots added this to the 0.12.0 milestone Feb 28, 2022
@blankdots blankdots changed the base branch from develop to feature/metax-integration February 28, 2022 16:11
@blankdots blankdots force-pushed the feature/doi-workflow branch from a76b1f9 to a2df37c Compare February 28, 2022 16:11
@blankdots blankdots mentioned this pull request Feb 28, 2022
Merged
2 tasks
@blankdots blankdots force-pushed the feature/doi-workflow branch from 0b35a97 to 4a6bf17 Compare March 2, 2022 15:00
blankdots added 14 commits March 7, 2022 08:22
@blankdots
refactor doi in objects to make it easier to test
06a76b0
@blankdots
mock doi API PUT request for publishing DOI
554c08e
@blankdots
publish Study and Dataset when publishing folders
dbcbfa5 
prepare Study and Datasets DOI payload and relationships between them

for now url is omitted till Metax integration is done
@blankdots
integration tests for publishing folder adjusted
e91b222
@blankdots
adjust message logs for integration tests
4dd96db
@blankdots
attempt to curb race condition with study POST
075171d 
we need to use find_one_and_update otherwise the bulkwrite will not be able to accurately catch it.

It is not by far the best solution, and can be improved
@blankdots
not all functions need to be async
504f9c2
@blankdots
create draft dois for study and datasets
8810ed0 
restrict one study per folder.
deprecate creating draft when publishing folder
@blankdots
publish Study and Dataset when publishing folders
a516043 
prepare Study and Datasets DOI payload and relationships between them

for now url is omitted till Metax integration is done
@blankdots
attempt to curb race condition with study POST
4bbc8fa 
we need to use find_one_and_update otherwise the bulkwrite will not be able to accurately catch it.

It is not by far the best solution, and can be improved
@blankdots
check values in set instead of list
3328fc3 
checking a set should be faster than checking a list
@blankdots
add to set instead of extending list
a0390ed
@blankdots
integrating doi with metax
e67d7d1
@blankdots
rebase with metax integrations
d386c7d
@blankdots blankdots force-pushed the feature/doi-workflow branch from 4a6bf17 to d386c7d Compare March 7, 2022 07:22
@genie9 genie9 merged commit d386c7d into feature/metax-integration Mar 8, 2022
@genie9 genie9 deleted the feature/doi-workflow branch March 8, 2022 12:36
blankdots added a commit that referenced this pull request Mar 10, 2022
@blankdots
update changelog with changes from #332
719cfe5
blankdots added a commit that referenced this pull request Mar 10, 2022
@blankdots
update changelog with changes from #332
6f20d1d
genie9 pushed a commit that referenced this pull request Mar 16, 2022
@blankdots @genie9
update changelog with changes from #332
9849b58
genie9 pushed a commit that referenced this pull request Mar 16, 2022
@blankdots @genie9
update changelog with changes from #332
9e90078
genie9 pushed a commit that referenced this pull request Mar 17, 2022
@blankdots @genie9
update changelog with changes from #332
747f06a
genie9 pushed a commit that referenced this pull request Mar 21, 2022
@blankdots @genie9
update changelog with changes from #332
1a4fcce
blankdots added a commit that referenced this pull request Mar 22, 2022
@blankdots
update changelog with changes from #332
5b32530
genie9 pushed a commit that referenced this pull request Mar 29, 2022
@blankdots @genie9
update changelog with changes from #332
0a70787
genie9 pushed a commit that referenced this pull request Mar 31, 2022
@blankdots @genie9
update changelog with changes from #332
d833057
@blankdots blankdots mentioned this pull request Apr 7, 2022
Merged
6 tasks
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Reviewers

@teemukataja teemukataja teemukataja approved these changes

@genie9 genie9 genie9 approved these changes

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Adjust DOI information so that it can be integrated with Metax/Etsin
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@blankdots @genie9 @teemukataja