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refactor: prefix doi management commands
- prefix all one-off destructive DOI commands with `doi_` - add reset_staging to mint new DOIs on staging using the datacite sandbox, doi_reset_staging -> step 3, doi_mint_parent_codebase_dois - bump deps for datacite schema 4.5 and django cve
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16 changes: 0 additions & 16 deletions
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django/curator/management/commands/curator_register_dois.py
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44
django/curator/management/commands/doi_mint_pending_releases.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| from django.core.management.base import BaseCommand | ||
| from library.doi import DataCiteApi, VERIFICATION_MESSAGE, get_welcome_message | ||
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| import argparse | ||
| import logging | ||
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| logger = logging.getLogger(__name__) | ||
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| def mint_pending_dois(interactive=True, dry_run=True): | ||
| print(get_welcome_message(dry_run)) | ||
| if interactive: | ||
| input( | ||
| "Minting new DOIs for all reviewed releases and parent codebases without DOIs. Press Enter to continue or CTRL+C to quit..." | ||
| ) | ||
| api = DataCiteApi(dry_run) | ||
| api.mint_pending_dois() | ||
| print(VERIFICATION_MESSAGE) | ||
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| class Command(BaseCommand): | ||
| """ | ||
| Syncs metadata for all codebases and releases with Datacite metadata service. | ||
| """ | ||
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| def add_arguments(self, parser): | ||
| parser.add_argument( | ||
| "--interactive", | ||
| action=argparse.BooleanOptionalAction, | ||
| help="Wait for explicit user confirmation to continue.", | ||
| default=True, | ||
| ) | ||
| parser.add_argument( | ||
| "--dry-run", | ||
| action=argparse.BooleanOptionalAction, | ||
| help="Emit what would have happened.", | ||
| default=True, | ||
| ) | ||
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| def handle(self, *args, **options): | ||
| interactive = options["interactive"] | ||
| dry_run = options["dry_run"] | ||
| logger.info("minting new DOIs for reviewed releases without DOIs") | ||
| mint_pending_dois(interactive, dry_run) |
113 changes: 113 additions & 0 deletions
113
django/curator/management/commands/doi_reset_production.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| import argparse | ||
| import csv | ||
| import logging | ||
| import sys | ||
| from django.core.management.base import BaseCommand | ||
| from library.doi import VERIFICATION_MESSAGE, get_welcome_message, DataCiteApi | ||
| from library.models import Codebase, CodebaseRelease | ||
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| logger = logging.getLogger(__name__) | ||
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| def cleanup_existing_dois(interactive=True, dry_run=True): | ||
| print(get_welcome_message(dry_run)) | ||
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| api = DataCiteApi(dry_run=dry_run) | ||
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| # clean up all Codebases with existing DOIs | ||
| codebases_with_dois = Codebase.objects.with_doi() | ||
| logger.info("Removing all Codebase DOIs") | ||
| if interactive and codebases_with_dois.exists(): | ||
| confirm = input( | ||
| "WARNING: this will remove all existing codebase DOIs and is unrecoverable. Type 'DELETE' to continue or Ctrl+C to quit: " | ||
| ) | ||
| if not confirm.lower() == "delete": | ||
| logger.info("Aborting.") | ||
| sys.exit() | ||
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| """ | ||
| assert that all Codebase DOIs have been reset | ||
| """ | ||
| if not dry_run: | ||
| print(VERIFICATION_MESSAGE) | ||
| with open("cleanup_codebases_with_doi.csv", "w") as f: | ||
| writer = csv.writer(f) | ||
| writer.writerow(["Codebase ID", "Codebase DOI"]) | ||
| for codebase in codebases_with_dois: | ||
| writer.writerow([codebase.pk, codebase.doi]) | ||
| codebases_with_dois.update(doi=None) | ||
| assert not Codebase.objects.with_doi().exists() | ||
| logger.info("Success. All existing codebase DOIs deleted.") | ||
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| # clean up unreviewed release DOIs | ||
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| unreviewed_releases_with_dois = CodebaseRelease.objects.unreviewed().with_doi() | ||
| total_unreviewed_releases_with_dois = unreviewed_releases_with_dois.count() | ||
| logger.info( | ||
| "Removing %s unreviewed CodebaseRelease DOIs", | ||
| total_unreviewed_releases_with_dois, | ||
| ) | ||
| if interactive: | ||
| confirm = input( | ||
| f"Deleting all DOIs for {total_unreviewed_releases_with_dois} unreviewed CodebaseReleases. Enter 'DELETE' to continue or CTRL+C to quit: " | ||
| ) | ||
| if not confirm.lower() == "delete": | ||
| logger.debug("Aborting...") | ||
| sys.exit() | ||
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| if not dry_run: | ||
| with open("cleanup_unreviewed_releases_with_doi.csv", "w") as f: | ||
| writer = csv.writer(f) | ||
| writer.writerow(["CodebaseRelease ID", "CodebaseRelease DOI"]) | ||
| for release in unreviewed_releases_with_dois: | ||
| writer.writerow([release.pk, release.doi]) | ||
| unreviewed_releases_with_dois.update(doi=None) | ||
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| # mint DOIs for all public peer reviewed CodebaseReleases without a DOI | ||
| reviewed_releases_without_dois = ( | ||
| CodebaseRelease.objects.reviewed().public().without_doi() | ||
| ) | ||
| invalid_releases = [] | ||
| for release in reviewed_releases_without_dois: | ||
| try: | ||
| log, ok = api.mint_public_doi(release) | ||
| if not ok: | ||
| invalid_releases.append((release, log)) | ||
| except Exception as e: | ||
| logger.error("Error minting DOI for release %s", release) | ||
| invalid_releases.append((release, e)) | ||
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| for release, log in invalid_releases: | ||
| with open("invalid_releases.csv", "w") as f: | ||
| writer = csv.writer(f) | ||
| writer.writerow( | ||
| ["CodebaseRelease ID", "Status Code", "Reason", "Datacite Metadata"] | ||
| ) | ||
| writer.writerow( | ||
| [release.pk, log.status_code, log.message, release.datacite.to_dict()] | ||
| ) | ||
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| class Command(BaseCommand): | ||
| """ | ||
| Removes all existing parent Codebase DOIs and mints new DOIs for all Peer Reviewed CodebaseReleases | ||
| """ | ||
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| def add_arguments(self, parser): | ||
| parser.add_argument( | ||
| "--interactive", | ||
| action=argparse.BooleanOptionalAction, | ||
| help="Wait for user to press enter to continue.", | ||
| default=True, | ||
| ) | ||
| parser.add_argument( | ||
| "--dry-run", | ||
| action=argparse.BooleanOptionalAction, | ||
| help="Output what would have happened.", | ||
| default=False, | ||
| ) | ||
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| def handle(self, *args, **options): | ||
| interactive = options["interactive"] | ||
| dry_run = options["dry_run"] | ||
| cleanup_existing_dois(interactive, dry_run) |
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