Phase 2: Use register_dataset for all datasets including built-ins#51
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Phase 2: Use register_dataset for all datasets including built-ins#51
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- Change cf_ids expand default to TRUE - Add 'expanded' attribute to cidlist objects to track resolution state - Add check_expanded() to verify IDs have been resolved before use - cf_partners and cf_meta now check for expanded IDs instead of calling expand_ids - c.cidlist checks inputs are expanded and propagates the attribute - Remove redundant fanc_ids()/banc_ids() calls from .fanc_partners() and .banc_partners() This ensures all query resolution happens in cf_ids, making it the single entry point for ID resolution. Downstream functions receive only resolved numeric IDs, preparing for Phase 3 local cache support.
- Create separate files for each dataset (flywire.R, hemibrain.R, etc.) - Add R/zzz.R with .onLoad() to register all built-in datasets - Simplify get_id_fun(), get_meta_fun() to use registered functions - Simplify cf_partners() dispatch to use registered partnerfun - Use registered shortnames in abbreviate_datasets() Bug fixes: - Fix fafbseg::.flywire_ids -> fafbseg::flywire_ids (exported function) - Fix malevnc::.manc_ids -> malevnc::manc_ids (exported function) - Fix fancorbanc_ids/meta function references in banc.R - Fix fanc_meta/banc_meta -> .fanc_meta/.banc_meta in fancorbanc_ids - Restore neuprint.chunksize parameter for neuprint-based datasets
- Add test helper register_rhubarb() with idfun for expanded ID tests - Update test expectations for new expand=TRUE default - Suppress expected warnings in tests to reduce CI noise - Install malecns in R CMD check workflow
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Summary
Depends on: #50 (Phase 1)
This PR establishes a uniform registration mechanism for all datasets (builtin and external) using
coconat::register_dataset.New files for dataset-specific functions:
R/zzz.R:.onLoad()to register all built-in datasetsR/flywire.R:.flywire_ids,.flywire_meta,.flywire_partnersR/hemibrain.R:.hemibrain_ids,.hemibrain_meta,.hemibrain_partnersR/opticlobe.R:.opticlobe_ids,.opticlobe_meta,.opticlobe_partnersR/malecns.R:.malecns_ids,.malecns_meta,.malecns_partnersR/manc.R:.manc_ids,.manc_meta,.manc_partnersR/banc.R:.banc_ids,.banc_meta,banc_error,.banc_partners,banc_versionR/yakubavnc.R:.yakubavnc_ids,.yakubavnc_meta,.yakubavnc_partnersUpdated R/fanc.R:
.fanc_ids,.fanc_metafanc_versionand.fanc_partnersSimplified dispatch functions:
get_id_fun: now uses only registered functionsget_meta_fun: now uses only registered functionscf_partners: uses registeredpartnerfuninstead of if-else chainabbreviate_datasets: uses only registered shortnameslengthen_datasets: uses only registered shortnamesCleaned up:
R/meta.R: removed functions moved to dataset-specific filesR/partners.R: removed functions moved to dataset-specific filesAll dataset-specific functions now use private naming convention (
.prefix) for consistency.Test plan
cf_datasets('builtin')returns all 8 datasetsabbreviate_datasets(cf_datasets('builtin'))workscf_ids(hemibrain=12345)workscoconat:::dataset_details()cf_metaandcf_partnerswork with all datasets