H5json

[jreadey]

Use h5json package for typing and objids

Important

Migrated HSDS to use the h5json library for core utilities, restructured utility modules, added support for client-provided object IDs and timestamps, and updated dependencies to require Python 3.10+ with h5json 1.0.0+.

Library Migration and Utility Restructuring

• h5json Library Integration: Migrated from local utility modules to h5json library for data type, array, object ID, shape, dataset, filter, link, and time utilities across 30+ files.
• Deleted Utility Modules: Removed hsds/util/idUtil.py, hsds/util/timeUtil.py, hsds/util/hdf5dtype.py, and hsds/util/arrayUtil.py as their functionality is now provided by h5json.
• New Utility Module: Created hsds/util/nodeUtil.py with node ID generation, partitioning, and datanode URL resolution functions.
• Updated Imports: Changed all references from local util modules to h5json equivalents (e.g., util.idUtil â�� h5json.objid, util.timeUtil â�� h5json.time_util).

Object ID and Timestamp Handling

• Client-Provided Object IDs: Added support for creating objects with client-specified IDs in POST_Dataset, POST_Group, POST_Datatype, and related functions in dset_dn.py, group_dn.py, ctype_dn.py, and dset_sn.py.
• Timestamp Validation: Added max_timestamp_drift configuration parameter to validate client-provided timestamps in attr_dn.py, link_dn.py, and related modules, with fallback to server-generated timestamps when skew exceeds threshold.
• Deleted Object Tracking: Added logic to check and remove previously deleted object IDs from deleted_ids set when creating new objects with the same ID.

Configuration and Dependencies

• New Configuration Parameters: Added default_vlen_type_size, predate_maxtime, posix_delay, max_compact_dset_size, and max_timestamp_drift to admin/config/config.yml.
• Updated Dependencies: Modified pyproject.toml to require Python 3.10+, add h5json 1.0.0+, update numpy to 2.0.0+, and constrain numcodecs to â�¤0.15.1.
• Removed Python 3.9: Removed Python 3.9 from CI/CD test matrix in .github/workflows/python-package.yml.

API and Function Refactoring

• Object Creation Functions: Refactored POST_Dataset, POST_Group, and POST_Datatype handlers to support batch creation of multiple objects using new helper functions (createDatasets, createGroups, createDatatypeObjs) and DomainCrawler for writing initial data.
• Layout Handling: Changed getChunkLayout calls to getChunkDims throughout codebase; moved layout from top-level response to nested under creationProperties.
• Link Handling: Changed external link field from h5domain to file in link_dn.py, link_sn.py, and servicenode_lib.py; added per-link timestamp validation in PUT_Links.
• Attribute Initialization: Added support for initializing attributes from request body in POST_Dataset, POST_Group, and POST_Datatype instead of always creating empty objects.

New Functionality

• PostCrawler Class: Added hsds/post_crawl.py with PostCrawler class for asynchronously creating multiple HDF5 objects with configurable worker count and error handling.
• Domain Metadata Consolidation: Added getConsolidatedMetaData function in async_lib.py to create consolidated metadata summaries for all objects in a domain.
• Data Writing: Added put_data method to DomainCrawler for writing one-chunk dataset values; added doPointWrite and doHyperslabWrite functions in dset_lib.py for writing point and hyperslab selections.
• Domain Objects Retrieval: Added getobjs parameter to getDomainResponse function to optionally return domain objects from S3 summary file.

Bug Fixes and Improvements

• Typo Fixes: Fixed multiple typos including "coniguous" â�� "contiguous", "seperated" â�� "separated", "heirarchy" â�� "hierarchy", "inital" â�� "initial", and various attribute/link-related typos.
• Error Handling: Changed error responses from HTTPInternalServerError to HTTPBadRequest for duplicate object IDs and invalid configurations in ctype_dn.py, dset_dn.py, and group_dn.py.
• Logging Improvements: Added debug logging for request bodies, object creation, and metadata processing; updated log message prefixes for consistency.
• POSIX Delay Support: Added posix_delay configuration support to fileClient.py for simulating cloud storage latencies in get_object, put_object, and list_keys methods.
• Version Update: Updated HSDS_VERSION from 0.9.2 to 1.0.0 in basenode.py.

Test Updates

• New Test Methods: Added tests for client-provided object IDs (testPostDatasetWithId, testPostTypeWithId, testPostWithId), attribute initialization (testPostDatasetWithAttributes, testPostWithAttributes), timestamp handling (testUseTimestamp), and batch creation (testPostMulti, testDatasetPostMulti).
• Test Refactoring: Updated tests to access layout from creationProperties instead of top-level; removed CHUNK_MIN/CHUNK_MAX constants and moved them to local scope; updated external link tests to use file field instead of h5domain.
• Removed Tests: Deleted array_util_test.py, hdf5_dtype_test.py, and id_util_test.py as their functionality is now tested through h5json library.
• Import Updates: Updated test imports to use h5json functions (e.g., createObjId, getFilterItem) instead of local utilities.

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[mattjala]

Since we now depend on hdf5-json to do this testing, it might be a good idea to include hdf5-json's tests as a step in the CI

[mattjala]

Besides a few minor comments and questions, this is good to go in. I'll try to get the outstanding PRs on hdf5-json reviewed this week so that we can avoid having HSDS depend on a specific branch.

[mattjala]

This comparison seems backwards. If I understand correctly, the difference between current time and creation time should need to be under the max time, not above it

[mattjala]

@jreadey Should we mark this as draft until it's in a final state for review?