syncToSynapse does not work if "the file path in "used" or "executed" of the manifest.tsv uses home directory shortcut "~"

Description

The _sortAndFixProvenance() method actually expands out the home directory ~ while the "path" column in the manifest is not expanded out by readManifestFile(). This causes topological sort to fail
Example:

1 2 3 path parent someAnnotation someOtherAnno executed used ~/sync1.txt syn10165189 anno1 anno2 ~/sync2.txt ~/sync2.txt syn10165189 anno11 anno22

The dataframe ends up looking like:

1 2 3 4 5 6 7 8 path parent someAnnotation someOtherAnno \ 0 ~/sync1.txt syn10165189 anno1 anno2 1 ~/sync2.txt syn10165189 anno11 anno22 executed used 0 [] [C:\Users\Develop/sync2.txt] 1 [] [] 2 [] []

Environment

None

Status

Assignee

Ziming Dong

Reporter

Ziming Dong

Labels

None

Validator

Larsson Omberg

Release Version History

None

Fix versions

Priority

Major