Added better messaging

[ptth222]

For some reason the bottom part of the function only logged errors and did not add them to the validator dictionary. They also did not indicate which filename the error was from, so tracking down where the problem is was difficult. This might just be an oversight since the warnings at the top of the function were just fine.

I would also like to bring up an issue with this function. It doesn't seem to be working quite correctly. I have attached an assay from the examples that this function prints errors for. The first error is "(E) Unexpected column heading following Labeled Extract Name column. Found MS Assay Name at offset 3" If I am understanding the code correctly it is trying to make sure that "Labeled Extract Name" is followed by "Label" and then possibly "Term Source REF" and/or "Term Accession Number". The "Labeled Extract Name" column in this file is followed by those columns exactly, but after those "MS Assay Name" is next. I think the issue is where "object_index" is created. It doesn't create a new set of object columns on the "MS Assay Name" column, so that column and the 2 comments that follow it are put into the "Labeled Extract Name" object columns. I think this happens for other columns in the file as well. It looks to me like this function might have been made originally when there were fewer column headers and was then updated at some point, but parts were missed in the update. Someone who understands the possible column headers should probably take a look at what is going on here.

a_proteome.txt

[ptth222]

Incorporated in #551.

[ptth222]

Not everything got incorporated. This latest commit should have it straightened out.

[coveralls]

coverage: 81.212%. remained the same when pulling 682611d1ff87525b7228a2b04010112b0ce3129e on ptth222:load-table-checks-improvement into d7aa0277b8a6a0848094cc8adbc0d5f512899bf5 on ISA-tools:issue-511.