Merge pull request #149 from intermine/fixes-columns

Fixes column manager and removes infinite loop in open-nodes.

bower.json

@@ -1,6 +1,6 @@
 {
   "name": "imtables",
-  "version": "2.0.0-beta-18",
+  "version": "2.0.0-beta-39",
   "description": "ui widgets for displaying query results in interactive tables",
   "main": [
     "dist/imtables.min.js",

less/active-constraints.less

@@ -1,10 +1,35 @@
+.im-path-finder {
+    overflow: visible;
+}
 .im-filter-manager {
-    .im-path-finder {
+    .im-path-finder.open {
         max-height: 400px;
         overflow-y: auto;
     }
 }
 
+.im-new-constraint {
+    .im-con-overview {
+        .im-name-part {
+            display: none;
+        }
+        .im-name-part:first-child:after {
+            content: '...';
+        }
+       .im-name-part:nth-last-child(-n+4):after {
+            content: "\00bb";
+            margin-left: 0.5em;
+        }
+       .im-name-part:last-child:after {
+           content: '';
+       }
+       .im-name-part:first-child,
+       .im-name-part:nth-last-child(-n+3) {
+           display: inline-block;
+       }
+    }
+}
+
 .im-filter-summary {
     .label-path {
         .im-name-part {
@@ -43,7 +68,6 @@
         position: relative;
 
         .im-slider-marker {
-            position: absolute;
             font-family: @font-family-monospace;
             top: 1em;
 
@@ -86,7 +110,7 @@
             margin-right: 0.2em;
         }
         .label {
-            font-size: 1.25em;
+            font-size: 1.1em;
         }
     }
 

less/main.less

@@ -88,3 +88,12 @@ ul.dropdown-menu {
         margin-left: 0px;
     }
 }
+
+.im-evenly-spaced {
+    display: -webkit-box;
+    display: -moz-box;
+    display: -ms-flexbox;
+    display: -webkit-flex;
+    display: flex;
+    justify-content: space-between;
+}

less/path-chooser.less

@@ -1,4 +1,7 @@
 .im-path-chooser {
+    ul {
+        padding-left: 2em;
+    }
     li {
         list-style-type: none;
         margin-left: 0px;

less/preview.less

@@ -1,5 +1,5 @@
 .popover.item-preview {
-    min-width: 300px;
+    min-width: 385px;
 }
 .im-cell-preview-inner {
 
@@ -18,6 +18,7 @@
         .im-relation {
             padding: 0.1em 1em;
             width: 50%;
+            margin-left: 0;
             .pull-left();
             display: inline-block;
 

less/slider.less

@@ -90,3 +90,9 @@
     .im-ui-default-widget-state;
 }
 
+.im-slider {
+    display: flex;
+    flex-direction: row;
+    justify-content: space-between;
+}
+

less/summary.less

@@ -73,6 +73,13 @@
         }
 
     }
+    .im-item-col {
+        .null-value:after {
+            font-weight: bold;
+            color: @gray-lightish;
+            content: 'NOTHING';
+        }
+    }
     .im-count-col {
         font-weight: bold;
         text-shadow: -1px -1px #fff;

package.json

@@ -1,6 +1,6 @@
 {
   "name": "imtables",
-  "version": "2.0.0-beta-38",
+  "version": "2.0.0-beta-39",
   "description": "UI widgets for displaying query results in interactive tables",
   "config": {
     "port": "9000"

src/main.coffee

@@ -5,6 +5,7 @@ require './shim'
 {Service: {connect}} = require 'imjs'
 {Promise} = require 'es6-promise'
 
+version = require './version'
 Types = require './core/type-assertions'
 Dashboard = require './views/dashboard'
 Table = require './views/table'
@@ -54,6 +55,9 @@ asElement = (e) ->
 
 # Exported top-level API
 
+# The version of this library, see: bin/inject-version.js
+exports.version = version
+
 # Allow end users to configure text.
 exports.setMessages = Messages.set.bind(Messages)
 

src/messages/actions.coffee

@@ -26,6 +26,7 @@ module.exports =
   'export.category.JsonFormat': """
     As <%= (jsonFormat === 'objects') ? 'Objects' : 'Rows' %>
   """
+  'export.category.FastaFormat': 'FASTA options'
   'export.category.ColumnHeaders': """
     <% if (headers) { %>
       <%= {friendly: 'Formatted', path: 'Raw'}[headerType] %>

src/messages/logic.coffee

@@ -0,0 +1,8 @@
+Messages = require '../messages'
+
+Messages.setWithPrefix 'logic',
+  Heading: 'Manage Constraint Logic'
+  Manage: -> Messages.getText 'logic.Heading' # synonymous by default - can be made distinct.
+  ManageShort: 'Constraint Logic'
+  LogicLabel: -> Messages.getText 'logic.ManageShort'
+  ApplyLogic: 'Change logic'

src/mixins/has-typeaheads.coffee

@@ -5,17 +5,26 @@ exports.initTypeaheads = -> @_typeaheads ?= []
 exports.removeTypeAheads = ->
   return unless @_typeaheads?
   while (ta = @_typeaheads.shift())
+    ta.off('typeahead:select')
     ta.off('typeahead:selected')
     ta.off('typeahead:autocompleted')
+    ta.off('typeahead:close')
     ta.typeahead('destroy')
-    ta.remove()
 
 exports.lastTypeahead = -> _.last(@_typeaheads ? [])
 
-exports.activateTypeahead = (input, opts, data, placeholder, cb) ->
+# @param input [jQuery] A jQuery selection to apply a typeahead to.
+# @param opts [Object] The typeahead options (see http://twitter.github.io/typeahead.js/examples/)
+# @param data [(String, ([String]) ->) ->] Data source
+# @param placeholder [String] The new place-holder
+# @param cb [(Event, Object) ->] Suggestion handler
+exports.activateTypeahead = (input, opts, data, placeholder, cb, onChange) ->
   input.attr(placeholder: placeholder).typeahead opts, data
   input.on 'typeahead:selected', cb
+  input.on 'typeahead:select', cb
   input.on 'typeahead:autocompleted', cb
+  if onChange?
+    input.on 'typeahead:close', onChange
 
   # Keep a track of it, so it can be removed.
   @initTypeaheads().push input

src/mixins/runs-query.coffee

@@ -6,7 +6,11 @@ CACHE = {}
 exports.runQuery = (overrides = {}) ->
   params = @getExportParameters overrides
   key = "results:#{ @query.service.root }:#{ JSON.stringify params }"
-  CACHE[key] ?= @query.service.post 'query/results', params
+  endpoint = 'query/results'
+  format = @model.get('format')
+  # Custom formats have custom endpoints.
+  endpoint += "/#{ format.id }" if format.needs?.length
+  CACHE[key] ?= @query.service.post endpoint, params
 
 exports.getEstimatedSize = ->
   q = @getExportQuery()
@@ -40,4 +44,6 @@ exports.getExportParameters = (overrides = {}) ->
   # TODO - this is hacky - the model should reflect the request
   if (data.format is 'json') and ('rows' isnt @model.get 'jsonFormat')
     data.format += @model.get 'jsonFormat'
+  if (data.format is 'fasta') and (@model.get('fastaExtension'))
+    data.extension = @model.get('fastaExtension')
   _.extend data, overrides

src/models/available-columns.coffee

@@ -17,10 +17,13 @@ module.exports = class AvailableColumns extends Collection
 
   model: PathModel
 
+  add: (model) ->
+    returned = super
+    if returned and !returned.collection? then returned.collection = @
+
   initialize: ->
     super
     @on 'change:parts change:displayName', => @sort()
 
   comparator: (a, b) -> # sort by path-length, and then lexically by attribute name.
-    (cmp partsLen, a, b) or (cmp displayName, a, b)
-
+    (cmp partsLen, a, b) or (cmp displayName, a, b)

src/models/export-formats.coffee

@@ -2,7 +2,7 @@ _ = require 'underscore'
 
 class Format
 
-  constructor: ({@id, @group, icon, needs}) ->
+  constructor: ({@id, @group, icon, needs, @maxColumns}) ->
     # Sigh, it's either this or list redundant info.
     ext = if @id is 'tab' then 'tsv' else @id
     EXT = ext.toUpperCase()
@@ -30,7 +30,7 @@ formats = [
   new Format(id: 'csv', group: 'flat'),
   new Format(id: 'xml',  group: 'machine'),
   new Format(id: 'json', group: 'machine'),
-  new Format(id: 'fasta', group: 'bio', icon: 'dna', needs: ['Protein', 'SequenceFeature']),
+  new Format(id: 'fasta', group: 'bio', icon: 'dna', needs: ['Protein', 'SequenceFeature'], maxColumns: 1),
   new Format(id: 'gff3',  group: 'bio', icon: 'dna', needs: ['SequenceFeature']),
   new Format(id: 'bed',   group: 'bio', icon: 'dna', needs: ['SequenceFeature']),
   new Format(id: 'fake',   group: 'fake', icon: 'fake', needs: ['Department'])

src/models/history.coffee

@@ -42,21 +42,26 @@ module.exports = class History extends Collection
     @listenTo q, "change:views", @onChangeViews
     @listenTo q, "change:joins", @onChangeJoins
     @listenTo q, "change:sortorder", @onChangeSortOrder
+    @listenTo q, "change:logic", @onChangeLogic
     @listenTo q, "undo", @popState
 
   # TODO - get rid of labels - they are pointless. Use the query prop instead
 
   onChangeConstraints: ->
-    @onChange 'constraints', 'filter', JSON.stringify
+    @onChange 'constraints', 'filter', (cons) -> _.map cons, JSON.stringify
 
   onChangeViews: ->
     @onChange 'views', 'column'
 
   onChangeJoins: ->
-    @onChange 'joins', 'join', (style, path) -> "#{ path }:#{ style }"
+    @onChange 'joins', 'join', (joins) -> _.map joins, (style, path) -> "#{ path }:#{ style }"
 
   onChangeSortOrder: ->
-    @onChange 'sortOrder', 'sort order element', JSON.stringify
+    @onChange 'sortOrder', 'sort order element', (so) -> _.map so, JSON.stringify
+
+  onChangeLogic: ->
+    @onChange 'constraintLogic', 'constraint logic element', (expr) ->
+      expr?.match(/([A-Z]+)/) ? []
 
   # Inform clients that the current query is different
   triggerChangedCurrent: ->
@@ -67,8 +72,8 @@ module.exports = class History extends Collection
   onChange: ( prop, label, f = (x) -> x ) ->
     query = @currentQuery
     prev = @last().get 'query'
-    xs = _.map prev[prop], f
-    ys = _.map query[prop], f
+    xs = f prev[prop]
+    ys = f query[prop]
     was = xs.length
     now = ys.length
     n = Math.abs was - now

src/models/open-nodes.coffee

@@ -23,10 +23,10 @@ module.exports = class OpenNodes extends UniqItems
 
   # Also removes sub-nodes.
   remove: (path) ->
+    if !path? then return false
     if path instanceof Backbone.Model
       super path
 
     delenda = @filter (node) -> descendsFrom path, node.get('item')
     for delendum in delenda
       super delendum
-

src/utils/calculate-row-template.coffee

@@ -6,17 +6,14 @@ getOJCBelow = (query, p, below) ->
   oj = query.getOuterJoin p
   return null if (not oj) or (oj is below) # not outerjoined, or joined at the target level.
   path = query.makePath(oj)
+  # outer loop variables.
   highest = if path.isCollection() then oj else null
   path = path.getParent()
 
-  while path and (not path.isRoot())
-    next = query.getOuterJoin path
+  while path and (not path.isRoot()) then do (next = query.getOuterJoin path) ->
     nextPath = query.makePath(next) if next?
     highest = next if nextPath?.isCollection() and (next isnt below)
-    if nextPath
-      path = nextPath.getParent()
-    else
-      path = null
+    path = nextPath?.getParent()
 
   return highest
 

src/utils/count-executor.coffee

@@ -2,7 +2,9 @@
 
 CACHE = {}
 
-key = (q) -> "#{ q.root }:#{ q.token }:#{ q.toXML() }"
+# A unique key composed of the service we are connected to and the
+# canonical representation of the query.
+key = (q) -> "#{ q.service.root }:#{ q.service.token }:#{ q.toXML() }"
 
 # Simple caching layer that caches counts.
 exports.count = (q) -> CACHE[key q] ?= q.count()

src/utils/path-suggestions.coffee

@@ -0,0 +1,16 @@
+_ = require 'underscore'
+{Promise} = require 'es6-promise'
+
+# Suggestions can be very large and expensive.
+CACHE = {}
+
+matchPathsToNames = (paths) -> (names) ->
+  ({path, name} for [path, name] in _.zip paths, names)
+
+module.exports = getPathSuggestions = (query, depth) ->
+  key = "#{ query.service.root }:#{ query.root }:#{ depth }"
+  return CACHE[key] if key of CACHE
+  paths = (query.makePath p for p in query.getPossiblePaths depth)
+  paths = paths.filter (p) -> not (p.end?.name is 'id')
+  namings = (p.getDisplayName() for p in paths)
+  CACHE[key] ?= Promise.all(namings).then matchPathsToNames(paths)

src/utils/suggestion-source.coffee

@@ -19,6 +19,8 @@ module.exports = class SuggestionSource
       @tooMany = template icons: Icons, messages: Messages, extra: total - maxSuggestions
 
   suggest: (term, cb) =>
+    if not term? or term is ''
+      return cb(s for s in @suggestions.slice(0, 10))
     parts = (term?.toLowerCase()?.split(' ') ? [])
     matches = ({item}) ->
       item ?= ''

src/views/active-constraint.coffee

@@ -5,6 +5,7 @@ $ = require 'jquery'
 {Query, Model} = require 'imjs'
 
 # Support
+CoreModel = require '../core-model'
 Messages = require '../messages'
 Templates = require '../templates'
 Icons = require '../icons'
@@ -54,9 +55,18 @@ basicEql = (a, b) ->
     same and= (if _.isArray va then aeql va, vb else va is vb)
   return same
 
+class ConstraintModel extends CoreModel
+
+  defaults: ->
+    code: null
+
+  isTypeConstraint: -> not @get('op')?
+
 # Composite view with a summary, and controls for editing the constraint.
 module.exports = class ActiveConstraint extends View
 
+  Model: ConstraintModel
+
   tagName: "div"
 
   className: "im-constraint row-fluid"