Reconstitute a manifest

Quickly "reconstitute" a manifest for files with existing annotations. This is a power-user alternative to schematic's manifest_generate with option useAnnotations = TRUE for certain scenarios:

Usage

remanifest(scope, file = "manifest.csv", recurse = TRUE, mf = data.table())

Arguments

scope

Synapse id of something representing one or more datasets. Can be a folder or Synapse dataset entity.

file

Name of file to be written. Use NULL to return the data.table instead of writing to file.

recurse

Include everything nested within folder scope, default TRUE, or only the immediate files. Not used if dataset is Synapse dataset entity.

mf

Intermediate manifest to build upon; used when recursive.

Details

• Meant to be faster and more convenient for workflows focused on scalable/programmatic annotation/revalidation. Convenience and speed mainly comes from bypassing the schematic API layer and using the Synapse API directly, so manifest is reconstituted directly as R data.table instead of having to download a Googlesheets or Excel intermediate. The result .csv is still intended to be schematic-compatible for validation via manifest_validate.

• Works with both a Synapse dataset entity as well as a folder; schematic currently only handles the latter (the folder concept predates Synapse datasets).

• If folder-scoped, can choose between generating manifest with just immediate files or, like schematic, nested files. This is useful, for example, if the main scope folder is "RNA-seq" and the main files are fastqs, but there is a child folder called "md5" with md5 files, and the manifest is really meant for the fastqs.

• Does not try to download synapse_manifest.csv, which can be useful to regenerate a manifest when ARs have been set.

• Does not require an asset view.

Other developer notes: See also gather_annotations for the under-the-hood workhorse. Intended for further development to be used as part of advanced annotation utils.