Command to fix mal-formed data paths and update data files

[mbthornton-lbl]

Depends on the output from the find-affected-workflows in

186

Implement a process-affected-files command to

• Fix malformed workflow directories and add symbolic links from the old directory name
• Fix malformed workflow data file names and add symbolic links
• Write out JSON files with updates to be applied to the database via queries:run endpoint

Run on prod and apply updates to DB

• [x] Run process command on production filesystem to update dirs and filenames and get update JSON output files
• [x] Apply the resulting updates to the database via the queries:run endpoint

[mbthornton-lbl]

Blocked by: https://github.com/microbiomedata/nmdc-runtime/issues/575

[aclum]

This is not resolved, we still have 180 assemblies where the paths don't resolve. This is different than the blade issues for EMP500.

[mbthornton-lbl]

This issue can be closed after closing

• [x] #214

[mbthornton-lbl]

159 of 179 data sets processed as of this morning.

[mbthornton-lbl]

{ "ok": 1, "n": 900, "nModified": 900, "upserted": null, "writeErrors": null }