SciCrunch / sparc-curation / 616
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tgbugs 
dev guide python ir example, validate extract step

also supporting changes needed for the extract step

change bids_root to dataset_root, with a note that we can probably do
away with this check now since dataset_description should always be
at the top level of the folder

notes on mapping subjects and samples to folder names
this is going to be a mess, and starting in on it we are likely going
to have to provide significantly restricted rules for how folders must
be named, because at the moment it is impossible to check whether a
folder hierarchy is valid without knowing what is in multiple metadata
files, subjects, samples, and manifests. This is very bad because it
means that we cannot provide low noise error detection when subjects
and samples folder names are mismatched with what is in the metadata
sheet, it is also impossible to tell whether other folders are junk
or not without checking the manifest, because in theory a folder named
subjects could be a legit name for a sample (we've seen a subject
named heart4 so this is not just some crazy brainstorming)

for the template 2.0 we are going to require a subjects file if a
samples file is provided and we are probably going to serverly
restrict the naming and nesting rules for folders, all sample names
must be unique, all subject names must be unique, no more local names
for those, it complicates the implementation way too much and will
make the data very hard to reuse

1985 of 10162 relevant lines covered (19.53%)

0.2 hits per line

Jobs
ID Job ID Ran Files Coverage
2 616.2 (SCIGRAPH_API=https://scicrunch.org/api/1/sparc-scigraph SCICRUNCH_API_KEY=[secure]) 0
19.53
 Travis Job 616.2
Source Files on build 616
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