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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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| import csv | ||
| import logging | ||
| import sys | ||
| from django.conf import settings | ||
| 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 reset_all_dois(interactive=True, dry_run=True): | ||
| print(get_welcome_message(dry_run)) | ||
| if settings.DEPLOY_ENVIRONMENT.is_production: | ||
| logger.error("This command is not allowed in production.") | ||
| sys.exit() | ||
| logger.info("(ENV: %s) Removing all DOIs", settings.DEPLOY_ENVIRONMENT) | ||
| releases_with_dois = CodebaseRelease.objects.with_doi() | ||
| codebases_with_dois = Codebase.objects.with_doi() | ||
| confirm = input( | ||
| "WARNING: this will remove ALL existing DOIs and is unrecoverable. Type 'DELETE' to continue or Ctrl+C to quit: " | ||
| ) | ||
| if confirm.lower() == "delete": | ||
| with open("codebase_dois.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]) | ||
| Codebase.objects.update(doi=None) | ||
| with open("release_doi.csv", "w") as f: | ||
| writer = csv.writer(f) | ||
| writer.writerow(["CodebaseRelease ID", "CodebaseRelease DOI"]) | ||
| for release in releases_with_dois: | ||
| writer.writerow([release.pk, release.doi]) | ||
| CodebaseRelease.objects.update(doi=None) | ||
| else: | ||
| logger.info("Aborting.") | ||
| sys.exit() | ||
|
|
||
| """ | ||
| assert correctness | ||
| """ | ||
| if not dry_run: | ||
| print(VERIFICATION_MESSAGE) | ||
| assert Codebase.objects.with_doi().count() == 0 | ||
| assert CodebaseRelease.objects.with_doi().count() == 0 | ||
| logger.info("Success. All existing codebase DOIs deleted.") | ||
|
|
||
| """ Mint DOIs for all new Peer Reviewed Releases""" | ||
| peer_reviewed_releases = CodebaseRelease.objects.reviewed().public() | ||
| datacite_api = DataCiteApi(dry_run=dry_run) | ||
| invalid_releases = [] | ||
| for release in peer_reviewed_releases: | ||
| try: | ||
| datacite_api.mint_new_doi_for_release(release) | ||
| except Exception as e: | ||
| logger.error("Error minting DOI for release %s", release) | ||
| invalid_releases.append((release, e)) | ||
|
|
||
| for release, error in invalid_releases: | ||
| with open("invalid_releases.csv", "w") as f: | ||
| writer = csv.writer(f) | ||
| writer.writerow(["CodebaseRelease ID", "Reason", "Datacite Metadata"]) | ||
| writer.writerow([release.pk, error, release.datacite.to_dict()]) | ||
|
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|
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| class Command(BaseCommand): | ||
|
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| def add_arguments(self, parser): | ||
| parser.add_argument( | ||
| "--interactive", | ||
| action="store_true", | ||
| help="Wait for user to press enter to continue.", | ||
| default=True, | ||
| ) | ||
| parser.add_argument( | ||
| "--dry-run", action="store_true", help="Output what would have happened." | ||
| ) | ||
|
|
||
| def handle(self, *args, **options): | ||
| interactive = options["interactive"] | ||
| dry_run = options["dry_run"] | ||
| reset_all_dois(interactive, dry_run) |
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96 changes: 96 additions & 0 deletions
96
django/library/migrations/0031_dataciteregistrationlog_and_more.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| # Generated by Django 4.2.16 on 2024-10-29 21:28 | ||
|
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| from django.db import migrations, models | ||
| import django.db.models.deletion | ||
|
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|
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| class Migration(migrations.Migration): | ||
|
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| dependencies = [ | ||
| ("library", "0030_peerreviewinvitation"), | ||
| ] | ||
|
|
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| operations = [ | ||
| migrations.CreateModel( | ||
| name="DataCiteRegistrationLog", | ||
| fields=[ | ||
| ( | ||
| "id", | ||
| models.AutoField( | ||
| auto_created=True, | ||
| primary_key=True, | ||
| serialize=False, | ||
| verbose_name="ID", | ||
| ), | ||
| ), | ||
| ( | ||
| "action", | ||
| models.CharField( | ||
| choices=[ | ||
| ("CREATE_RELEASE_DOI", "create release DOI"), | ||
| ("CREATE_CODEBASE_DOI", "create codebase DOI"), | ||
| ("UPDATE_RELEASE_METADATA", "update release metadata"), | ||
| ("UPDATE_CODEBASE_METADATA", "update codebase metadata"), | ||
| ], | ||
| max_length=50, | ||
| ), | ||
| ), | ||
| ("timestamp", models.DateTimeField(auto_now_add=True)), | ||
| ("http_status", models.IntegerField(default=None, null=True)), | ||
| ("message", models.TextField(default=None, null=True)), | ||
| ("metadata_hash", models.CharField(max_length=255)), | ||
| ("doi", models.CharField(blank=True, max_length=255, null=True)), | ||
| ], | ||
| ), | ||
| migrations.AlterModelOptions( | ||
| name="peerreviewinvitation", | ||
| options={"ordering": ["-date_sent"]}, | ||
| ), | ||
| migrations.RemoveField( | ||
| model_name="contributor", | ||
| name="affiliations", | ||
| ), | ||
| migrations.AlterField( | ||
| model_name="codebase", | ||
| name="date_created", | ||
| field=models.DateTimeField(auto_now_add=True), | ||
| ), | ||
| migrations.AlterField( | ||
| model_name="codebaserelease", | ||
| name="date_created", | ||
| field=models.DateTimeField(auto_now_add=True), | ||
| ), | ||
| migrations.AlterField( | ||
| model_name="codebasereleasedownload", | ||
| name="date_created", | ||
| field=models.DateTimeField(auto_now_add=True), | ||
| ), | ||
| migrations.AlterField( | ||
| model_name="peerreviewinvitation", | ||
| name="date_sent", | ||
| field=models.DateTimeField(auto_now=True), | ||
| ), | ||
| migrations.DeleteModel( | ||
| name="ContributorAffiliation", | ||
| ), | ||
| migrations.AddField( | ||
| model_name="dataciteregistrationlog", | ||
| name="codebase", | ||
| field=models.ForeignKey( | ||
| null=True, | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="datacite_logs", | ||
| to="library.codebase", | ||
| ), | ||
| ), | ||
| migrations.AddField( | ||
| model_name="dataciteregistrationlog", | ||
| name="release", | ||
| field=models.ForeignKey( | ||
| null=True, | ||
| on_delete=django.db.models.deletion.CASCADE, | ||
| related_name="datacite_logs", | ||
| to="library.codebaserelease", | ||
| ), | ||
| ), | ||
| ] |
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