Workflow

The server strategy sends a stage value in each Flower fit configuration. The client reads config["stage"], runs the matching branch, and returns numpy arrays or empty parameters.

Stage overview

Order	Stage	Client action	Server action
1	key_exchange	Generate ECC keypair and send public key.	Collect public keys and check exchange completion.
2	sync	Receive peer public keys, encrypt seed messages for peers, and send ciphertext envelopes.	Forward encrypted seed messages without decrypting them.
3	sync_response	Decrypt peer seed messages and compute or persist the global seed.	Advance after clients have had a round to process forwarded seed messages.
4	local_qc	Run PLINK --mind to filter samples by missingness.	Acknowledge local QC and advance the workflow.
5	global_qc	Compute genotype counts, missingness counts, and thresholds; encrypt typed QC payloads for peers.	Forward encrypted QC messages without decrypting them.
6	global_qc_response	Decrypt peer QC payloads, compute the SNP exclusion list locally, and apply filtering.	Advance after clients have processed QC shares.
7	init_chunks	Receive chunk parameters and create chunks for KING.	Send chunk parameters.
8	iterative_king	Send one encoded PLINK chunk per call and process returned KING partials/maps.	Rebuild chunk files, merge data, run KING, and drain chunks until clients report done.
9	local_lr	Run local PLINK logistic regression and send tokenized insignificant SNPs.	Forward token arrays without resolving SNP identities.
10	local_lr_filter_response	Compute the token intersection locally and filter insignificant SNPs.	Advance after clients filter.
11	init_chunks_lr	Repartition filtered data for final LR.	Send LR chunk parameters.
12	iterative_lr	Send LR chunks and map returned p-values back to local SNP IDs when possible.	Merge chunks, run logistic regression, return p-values, and drain chunks until clients report done.
13	iterative_lr_response	Receive final LR results if the server has stored a last result payload.	Send final LR results and move to done.

State machine

Encoded chunk format

BaseGWASClient._read_chunk_as_array serializes each PLINK chunk into one numpy array:

1. The first 12 bytes contain three uint32 values: bed_size, bim_size, and fam_size.
2. The remaining bytes concatenate bed_data + bim_data + fam_data.
3. Server aggregators split the array by those recorded sizes and rebuild temporary PLINK files.

The same format is consumed by aggregator_king.py and aggregator_lr.py.