Release 2025.7

What's Changed

• Re-enable /nmdcschema/related_ids API endpoint by @eecavanna in #1033
• Remove personal (and unused) dev environment file by @dwinston in #1037
• Remove unused obsolete test file by @dwinston in #1038
• Delete ensure_data_object_type and its test by @dwinston in #1039
• Include trailing dash (-) in w3id pattern match by @dwinston in #1036
• Make it easier to maintain Swagger/OpenAPI tags by @eecavanna in #1034
• pass fully saturated mongo client to ontology-loader package by @sierra-moxon in #1014
• Unpin Swagger UI version so the Runtime always uses the latest version by @eecavanna in #1041
• Source the feature flag value from an environment variable by @eecavanna in #1046
• Serve Scalar API docs at /scalar (according to feature flag) by @eecavanna in #1003
• Update /data_objects/study/{study_id} to accommodate new format of _type_and_ancestors list by @sujaypatil96 in #1060
• Fix bug where /data_objects/study/{study_id} does not return all related data objects by @eecavanna in #1052
• Add depth units when translating submission records by @pkalita-lbl in #1053
• Update /queries:run API endpoint to return more specific errors by @dwinston in #541
• Add referential integrity check to POST /queries:run API endpoint (for update command) by @eecavanna in #1008
• Bump refscan version from 0.3.0 to 0.3.2 by @eecavanna in #1074
• Implement API endpoint that performs cascading deletes from a WorkflowExecution by @shreddd in #1065
• Get data objects that are results (has_output) of workflow execution processes by @sujaypatil96 in #1061
• Add DOI processing to Submission Portal translator by @JamesTessmer in #1079
• Bump nmdc-schema version from 11.8.0 to 11.9.1 by @eecavanna in #1081
• Add mongosh script to migrate config.was_informed_by in jobs collection by @aclum in #1085
• Use MongoDB Compass syntax instead of Studio 3T syntax by @eecavanna in #1086
• Update ensure_default_api_perms function to include aggregation permission by @hesspnnl in #1091
• Add option to enable/disable filtering on biosamples in GOLD translator by @sujaypatil96 in #1090
• Index type field to speed up Mongo queries involving it by @eecavanna in #1097
• Update WorkflowExecution cascading deletion endpoint to also delete related jobs documents by @shreddd in #1096
• Update related_resources endpoint to account for multiple DataGenerations informing a WorkflowExecution by @eecavanna in #1092
• Update log message in run_script_to_update_insdc_biosample_identifiers() Dagster @op by @sujaypatil96 in #1099
• Fix output type of run_script_to_update_insdc_biosample_identifiers() by @sujaypatil96 in #1100
• Update boot code to ensure jobs collection has index on config.activity_id field by @eecavanna in #1102

Full Changelog: v2.8.0...v2.9.0