remanifest | R Documentation |
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:
remanifest(scope, file = "manifest.csv", recurse = TRUE, mf = data.table())
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 |
recurse |
Include everything nested within folder scope, default |
mf |
Intermediate manifest to build upon; used when recursive. |
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.
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