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feat: update core schema v2 for alignments and mesh #273

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merged 68 commits into from
Sep 27, 2024

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Bento007
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@Bento007 Bento007 commented Sep 17, 2024

Description

Update core schema v2 to match the changes in for v1 from chanzuckerberg/cryoet-data-portal#997

  • remove is_portal_standard.

Bento007 and others added 30 commits September 4, 2024 17:59
# Conflicts:
#	ingestion_tools/dataset_configs/template.yaml
#	schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py
- add enums for alignment types and format
…smith/997-ctf-alignment

# Conflicts:
#	ingestion_tools/dataset_configs/template.yaml
#	schema/core/v1.1.0/metadata.yaml
# Conflicts:
#	ingestion_tools/dataset_configs/10003.yaml
#	ingestion_tools/dataset_configs/10006.yaml
#	ingestion_tools/dataset_configs/10436.yaml
#	ingestion_tools/dataset_configs/10439.yaml
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Please run make-build-ingestion-config to update the pydantic models before merging!

@@ -594,6 +612,9 @@ classes:
is_visualization_default:
exact_mappings:
- cdp-common:annotation_source_file_is_visualization_default
is_portal_standard:
exact_mappings:
- cdp-common:annotation_source_file_is_portal_standard
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We had a discussion about the is_portal_standard field the other day and iirc It's only supposed to be present on Tomogram and Alignment

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cc @uermel

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remove from v1 and v2

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Just marking this for changes while we get clarification on the crossreferences/dates fields on tomograms, and the is_portal_standard field on annotations. The rest lgtm!

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Approved once the standardized field is removed from annotations

# Conflicts:
#	ingestion_tools/dataset_configs/10002.yaml
#	ingestion_tools/dataset_configs/10004.yaml
#	ingestion_tools/dataset_configs/10008.yaml
#	ingestion_tools/dataset_configs/10009.yaml
#	ingestion_tools/dataset_configs/10426.yaml
#	ingestion_tools/dataset_configs/10436.yaml
#	ingestion_tools/dataset_configs/10437.yaml
#	ingestion_tools/dataset_configs/10438.yaml
#	ingestion_tools/dataset_configs/10439.yaml
#	ingestion_tools/dataset_configs/deposition_10301.yaml
#	ingestion_tools/dataset_configs/deposition_10303.yaml
#	ingestion_tools/dataset_configs/deposition_10304.yaml
#	ingestion_tools/dataset_configs/deposition_10308.yaml
#	ingestion_tools/scripts/schema_migration/transform_ingestion_configs.py
Base automatically changed from tsmith/997-ctf-alignment to main September 27, 2024 16:28
# Conflicts:
#	ingestion_tools/dataset_configs/10000.yaml
#	ingestion_tools/dataset_configs/10001.yaml
#	ingestion_tools/dataset_configs/10002.yaml
#	ingestion_tools/dataset_configs/10003.yaml
#	ingestion_tools/dataset_configs/10004.yaml
#	ingestion_tools/dataset_configs/10005.yaml
#	ingestion_tools/dataset_configs/10006.yaml
#	ingestion_tools/dataset_configs/10007.yaml
#	ingestion_tools/dataset_configs/10008.yaml
#	ingestion_tools/dataset_configs/10009.yaml
#	ingestion_tools/dataset_configs/10010.yaml
#	ingestion_tools/dataset_configs/10301.yaml
#	ingestion_tools/dataset_configs/10436.yaml
#	ingestion_tools/dataset_configs/10437.yaml
#	ingestion_tools/dataset_configs/10438.yaml
#	ingestion_tools/dataset_configs/10439.yaml
#	ingestion_tools/dataset_configs/deposition_10301.yaml
#	ingestion_tools/dataset_configs/deposition_10302.yaml
#	ingestion_tools/dataset_configs/deposition_10303.yaml
#	ingestion_tools/dataset_configs/deposition_10304.yaml
#	ingestion_tools/dataset_configs/deposition_10305.yaml
#	ingestion_tools/dataset_configs/deposition_10308.yaml
#	ingestion_tools/scripts/schema_migration/migrate_v1_1_0.py
#	schema/core/v1.1.0/codegen/metadata_materialized.yaml
#	schema/core/v1.1.0/codegen/metadata_models.py
#	schema/core/v1.1.0/metadata.yaml
#	schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.py
#	schema/ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json
@Bento007 Bento007 merged commit 61a4a08 into main Sep 27, 2024
7 of 8 checks passed
@Bento007 Bento007 deleted the tsmith/997-ctf-corev2 branch September 27, 2024 18:10
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4 participants