syncToSynapse does not work if "the file path in "used" or "executed" of the manifest.tsv uses home directory shortcut "~"
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:
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path parent someAnnotation someOtherAnno executed used
~/sync1.txt syn10165189 anno1 anno2 ~/sync2.txt
~/sync2.txt syn10165189 anno11 anno22
The dataframe ends up looking like:
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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 [] []
