If the cell represents a composite value then it should not appear fundamentally different from the other cell types.

Can we have an example of a composite value field? Especially since they should not appear fundamentally differently.

in 'Create list of individual items' doesn't do anything.

Get Code not working for anything except XML.

Browser: Firefox
Version: 19.0.2

Also
Browser: Chrome
Version: 25.0.1364.172

Range constraints are cool

The 'view' parameter should be populated with a list of extra view paths. Do this by:

query.getGFF3({views: ["organism.name"]}).done(function(gff3) {
  console.log(gff3);
});

Under the assumption that users typically want data in a consistent format, we should offer to save the current user's export format for future sessions, if possible.

Once you have defined your filter there are two options 'Add Filter' at the bottom right and 'Apply' right underneath. Only 'Apply' works, but I didn't see this box first time through - I automatically clicked 'Add filter'.

[Also, first time I did this there was another box by the 'Apply' button with a 'within' label. This seems to have disappeared now].

See report-widgets for an example of how to do this.

Created a list of exons and selected one of the suggested Tags (based on one of my Filters):

symbol ONE OF yuri,Sam-S,Nhe3,Gpd [ --- all gene names listed on mouse over]

Throws an error:

Failure
Invalid name. Names may only contain letters, numbers, spaces, full stops, hyphens and colons.

Got this after trying to create a list.

the tables should at least offer to remember the user's preferred formats between sessions. This is particularly the case for:

• Export formats
• Code generation formats

These should display fully, but don't extend beyond the edge of the containing modal.

Composite chromosome locations do not collapse when column is hidden.
eg. 2L:10396716-10403206

The user should be able to move this dialogue around

Would be an improvement if one could move the dialog box by dragging on the grey part and not just part of the modal-header?

Download --> json format

Fails with 414 Error : Request-URI Too Large

[Looks to be when lots of filters, sort, column order etc applied as didn't fail when reverting to default view]

the jquery plugin can and should autodetect bootstrap plugin presence, and autoload. It would be nice to automatically find out which plugins are expected (eg: via an expect function).

At the moment dragging is the only way to add to the sort order.

The minus sign for removal does work.

The blue highlighted box spreads outside and for subsequent links stretches all the way across the modal box.

The reference example here is ChromosomeLocation -> chr2:123-456

This should be easy to configure

There is too much stuff in one place, and the separation between what to export, and where to export it, is far from clear.

This can be ameliorated by moving to a wizard interface, with a carousel between definition of content and what to do with that content.

Is the former needed? In the case of Chromosome Location it (for a split second) shows a preview box with some error message.

It seems that the onhover background color for say adding tags interface presents itself as a gradient from dark blue to black, while in Opera and Chrome it is single color light blue.

If someone wanted to theme their Results Table, would/could both colors be the same?

Formatters that take data from subparts, such as the chromosome location formatter, are making redundant requests to the server when they could read the information out of the query results. This massively slows down table performance.

A minor issue as I doubt many would do this: if you click on a reverse reference in the column management it leaves the little box, eg 'Refers back to gene' and you can't get rid of it.

The events are getting unbound, probably at the trail. The solution is to build a new list dialogue for every query update.

The page size should be preserved

The numeric slider allows the values to be changed manually, but the slider interface only allows one end to be changed at a time by dragging.

Users should be able to add new type constraints to references if they do not already have type constraints

The placeholder and normal text color in input boxes is too similar. I am not sure that Description will not be saved as while say Name is prefilled with text, Description is not.

A test query is needed.

It should be possible to get by without bootstrap. The table structure is pretty solid now
and is unlikely to see major changes, so the benefit brought by a rapid prototyping library
are now minimal, and the need to produce a custom set of css hackery is getting in the way of integration.

When removing items from the Manage Columns-->configure sort order

Didn't see the minus sign to the left of the column name so was trying to drag items out of the box to remove them.

It should announce that we are 'building table'

We need a formal specification of what behaviour is expected from the tables.

The modal starts "minimised" but the text says otherwise.

Part of collaboration with the Broad

This breaks downloading, probably code generation as well. Several things:

• Dropdown filter selections should use NONE OF where it would make things smaller.
• Code generation should use post for display.
• We should use the openWindowWithPost hack when the URI gets too large.

The scope machinery works, but is a) a bit hacky, and b) forces any shared code to be public. It should be possible to replace this system with an injected module registry and a require mechanism, into which the code is wrapped at compile time, much the way it is now.

eg:

  class Registry
    _registry_ = {}

    resolve = (obj, path, vivify) ->
      parts = path.split /\./
      while part = parts.shift()
        obj = obj?[part] ? vivify and obj[part] = {}
      obj

    register: (path, mapping) ->
      obj = resolve _registry_, path, true
      for k, v of mapping
        obj[k] = v

    export: (path) ->
      obj = @require path
      throw new Error("Noting to export: #{ path }") unless obj
      dest = resolve window, path, true
      dest[k] = v for k, v of obj

    require: (path) ->
      obj = resolve _registry_,  path, false
      throw new Error("Noting to export: #{ path }") unless obj
      _.extend {}, obj # Don't allow the caller to mutate the object?

  registry = new Registry
  # Then for each code block:

  do ->
   exports = {}
   # ideally this could be autogenerated from the filename, eg
   __SCOPE__ = 'column-header'

   # CODE GOES HERE

   registry.register __SCOPE__, exports

  registry.export 'intermine'

It would be really nice to try and order the code blocks
by dependencies at build time.

I am not sure how the chromosome location column was created but it causes confusion for the column selection under 'Create /Add to list'. This shows 'The chromosome from column 3' which doesn't exist and consequently the column numbers for the subsequent columns are wrong.

There is no longer a link to a new list once it has been created.
[Minor point: box giving details of new list is overlapped a bit by the column icons].

The sub views of a view group are not styled consistently with other view-element styles.

Many of our other tools are being built on framework by Zurb. If we can ween ourselves off bootstrap, then this would be a good basis.

in Opera and IE9 it seems to be at the bottom and in Chrome at a baseline.

vertical-align:top on the checkbox seems to have fixed it in Chrome

This should only happen if there is a problem.

When a subtable has a value that breaks a line (in red), there is only a few (5px) of space to click if I want to get a preview box instead of visiting a Report page.

Perhaps collapse the blue border (in blue) and increase the padding of the inner <td/> (in yellow)?

IE8, IE9 need to use TestModel as it is on the same server.