Not sure what the Google Sheets add-ons API permits, but @rob-knight pointed out that a frequent problem is that people sometimes sort the rows of their mapping files but accidentally do not select all the columns (resulting in "scrambled" metadata files)

If we can get this to work, Keemei will be less intrusive because it won't have to modify cells' notes.

Improvement Description
Would be ideal to integrate with Ontomaton if possible.

References

1. Ontomaton
2. Ontologies and taxon IDs are available at NCBI (http://bioportal.bioontology.org/search?opt=advanced).

Comments
Suggested by @rob-knight and @ackermag.

Support comments below header, before data starts.

Add an About dialog that contains info about the add-on's functionality and the file formats it validates. This feature was requested in the review performed by Google.

Empty cells are currently marked as invalid for the wrong reasons. Specific checks should be put in place for empty cells.

It'd be really great to see some screenshots, and ultimately demos (e.g., like the examples on the bottom of the Emperor website).

Adding a sidebar that lists the various errors and warnings would be really helpful for larger spreadsheets where it's hard to find all problems simply by looking at the cells. See the sidebar documentation. Would be awesome if clicking an error/warning focused on the offending cell in the spreadsheet.

Required if add-on is accepted for publication in the web store.

Header.gs is pretty messy, and a lot of the code could be refactored to use pieces in Base.gs and Column.gs.

Numeric cells currently throw an error during validation. They need to be cast to strings first.

Required if add-on is accepted for publication in the web store.

Improvement Description
iTOL defines several "dataset" formats for attaching metadata to tree nodes.

References

1. iTOL
2. These formats are defined here.

Current docs are on the repo's wiki. It'd be better to create a dedicated website as the add-on's Help menu will direct users to this site.

Required if add-on is accepted for publication in the web store.

Improvement Description
Would it be possible to abstract out the rules, so that if (for example) we wanted to build a QIIME2-based (i.e., python) validator that could work without google access (e.g., while working on a plane, or somewhere where access to google is blocked such as parts of China or DoD/USDA facilities) we don't have to define these rules twice? Ideally, this could be used for auto-generating documentation as well.

Validation is pretty slow for larger sheets. Look into cutting down the number of Google API calls -- these are what's slowing it down. Profile via View -> Execution transcript.

Improvement Description
@gregcaporaso suggested displaying what the valid characters are for a given cell.

Proposed Behavior
For example, listing valid characters for sample IDs.

@gregcaporaso suggested adding a link to the lab website in the About dialog, along with info about who developed the tool. This info should also be added somewhere on the "website" (currently GitHub wiki) and readme.

Add instructions that show how to install the plugin. Need to cut a release first and make it an real Google Sheets "add-on".

A negative number formatted as a currency is marked as an empty cell. Example: (42.45)

Since we're using a third-party library (SheetConverter) for these conversions, this issue may need to be raised on their issue tracker.

Current Behavior
Right now validation is performed manually via a menu item.

Currently only says whether there are invalid characters in a cell, but not what the offending characters are.

This will perform better than the current approach of coloring/annotating each cell separately.

It'd be helpful to list the location of duplicates cells in each error/warning message. Right now it just states that the cell isn't unique and the user has to search for the duplicates.

Improvement Description
A user may have a column with locations of the form 1846 19th street, 9500 Gilman Drive, etc and may want to create latitude and longitude columns from this information.

Optional if add-on is accepted for publication in the web store.

This format is defined and used by geneGIS (defined here). May be used by other tools as well.

Validation should mark cells with leading/trailing whitespace as a warning.

This is basically QIIME's mapping file format with some additional required columns.

Improvement Description
The particular value might be user-defined, or pre-defined (e.g., NaN)

Ensure barcodes are all the same length unless the user has specified variable-length barcodes.

It will be important for the set of rules that are applied to be customizable. For example, Qiita has different requirements for its sample template and prep template (qiita-spots/qiita#933) than QIIME 1.x has for its mapping files.

What probably makes the most sense for this would be if there were multiple validate functions, which were tool/version-specific (e.g., QIIME 1.9.x, Qiita 0.1.x, ...), and if the user could choose to validate with one or more of these from within the Google Spreadsheets interface.

Required if add-on is accepted for publication in the web store.

There are a number of standards that need to be adhered to for this to become an add-on. These need to be met before submitting the add-on proposal.

LinkerPrimerSequence and ReversePrimer can have multiple primers separated by commas.

Keemei doesn't state whether a message (displayed in a note) is an error or a warning. Instead it relies on the color of the cell to indicate this state. The notes should also include this info to improve accessibility.

This should be able to be re-factored to just return the state that represents that column/row and even per cell. This can then be batched as appropriate.

Initially this will be done by either coloring the column header cell green, or perhaps every valid cell.