Split cleanData and add Parquet exports

[AbhirupaGhosh]

Rename the original cleanData to cleanMetaData and add roxygen skeleton. Introduce a writeCompressedParquet helper and export cleaned metadata, AMR phenotype, genome data and original metadata to compressed Parquet files, then create a separate DuckDB (parquet-backed) with views for metadata, amr_phenotype, genome_data and original_metadata. Reintroduce a new cleanData function focused on feature matrices (genes/proteins/domains/etc.) that writes feature tables to Parquet and creates corresponding views; remove duplicated metadata parquet exports from the feature-matrix flow. Minor whitespace and path-handling adjustments to normalize paths and ensure output directories exist.

Description

What kind of change(s) are included?

• Feature (adds or updates new capabilities)
• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (these changes would cause existing functionality to not work as expected).

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[AbhirupaGhosh]

It printed

Initial summary: targets=24421 | AMR genomes=24422 | genome_data genomes=24423
Final summary:
  targets      : 24421
  bac_data     : 24421
  genome_data  : 24423
  amr_phenotype: 24422
  genomes with 0 AMR rows: 2
  e.g.: , genome.genome_id

So I am guessing it is considering column name as genome id!

[epbrenner]

We can strip this out. It was for debugging originally which is why it's messy. Alternatively, if it is useful to keep a summary, I can work on some improvements for it!

[AbhirupaGhosh]

I didn't find any logical impact of this misprinting. We can come back to this later. I have made an issue.

[AbhirupaGhosh]

Suggested change

	message("FTPS pass 1 (30s timeout)")
	future::plan(future::multisession, workers = max(1, workers_first))
	res1 <- future.apply::future_lapply(
	genome_ids,
	function(gid) {
	ok <- .ftpes_download_one(gid, out_dir,
	connect_timeout = 10L, max_time = 30L,
	speed_time = 30L, speed_limit = 2048L
	message("FTPS pass 1 (45s timeout)")
	future::plan(future::multisession, workers = max(1, workers_first))
	res1 <- future.apply::future_lapply(
	genome_ids,
	function(gid) {
	ok <- .ftpes_download_one(gid, out_dir,
	connect_timeout = 10L, max_time = 45L,
	speed_time = 30L, speed_limit = 2048L

[AbhirupaGhosh]

Suggested change

	message("FTPS pass 2 (60s timeout) for failed genomes")
	future::plan(future::multisession, workers = max(1, workers_second))
	res2 <- future.apply::future_lapply(
	fail_ids,
	function(gid) {
	ok <- .ftpes_download_one(gid, out_dir,
	connect_timeout = 10L, max_time = 60L,
	speed_time = 30L, speed_limit = 2048L
	)
	list(gid = gid, ok = ok)
	},
	future.seed = TRUE
	)
	message("FTPS pass 2 (120s timeout) for failed genomes")
	future::plan(future::multisession, workers = max(1, workers_second))
	res2 <- future.apply::future_lapply(
	fail_ids,
	function(gid) {
	ok <- .ftpes_download_one(gid, out_dir,
	connect_timeout = 10L, max_time = 120L,
	speed_time = 30L, speed_limit = 2048L
	)
	list(gid = gid, ok = ok)
	},
	future.seed = TRUE
	)