Check: physical format matches data file format

[eeerika]

Purpose

This check will look to see if the format name listed in the physical section of the metadata matches the data file's format.

Components

• format name from physical section
• file format from data file itself

Result

SUCCESS: if the two formats match
FAILURE: if the two formats do not match
ERROR: on system error or exception in the check code, representing a bug in the check system

[jeanetteclark]

I'm starting to think about this check, and wondering what pieces of information we should actually be checking. The data-format of a file will be recorded in 3 places, potentially:

• the file itself
• sysmeta formatId
• EML dataFormat OR ISO field

I'm envisioning this as a congruency check between the return value of file test.csv (bash, wrapped in an R system call) and either the formatId, metadata field, or both. I see a couple of hurdles though.

1. establishing a mapping between the format name in each location. For example, file test.csv returns "CSV text" which should be "text/csv" in the sysmeta, and in EML could be described in a few ways but probably the most reliably as `physical/dataFormat/textFormat/ with fieldDelimeter set to ","
2. I don't think that any checks currently actually use sysmeta values as part of the check. So need to review how this information could be made available to the R process.

I think the steps needed to implement this check are, in order of difficulty:

• determine how (if?) sysmeta values can be passed to check code in metadig-engine
• add sysmetaXML as an argument to runCheck in metadig-R
• establish mapping between common file types for the output of file commands and DataONE formatIds
• add to the above mapping for EML spec
• add to the above mapping for ISO spec

lmk if you see anything that seems amiss @mbjones @iannesbitt

[jeanetteclark]

The initial version of this check is done, and is in this repo for now (inst/extdata).