pheno
Merge branch 'master' of github.com:cmungall/monarch-app
initial commit of the "modeltype" widget
- added functionality to abbreviate the model names
add phenotype selectors
add phenotype maps
added function initPhenotype(imageDiv, phenotypelist).  This function
allows the user to initialize the widget with an array of phenotypes
objects.  This will eventually pass the call to the OwlSim application
Merge branch 'master' of https://github.com/monarch-initiative/monarch-app.git
refactored fetching genotype and phenotype info from the refactored geno/pheno tables for mgi,zfin,wb,omim.  this included making a generic fetchGenoPheno, which built genotypes in makeGenotype.  there are several species_to_resource maps being utilized for the hardcoding of nif ids.  also, added first trial of api calls to MyGene.info, though doesn't appear to be working yet.
added functionality to fetch the top X models/diseases by querying the NIF precomputed tables.  this is a generic call that can be used for any disease-based comparison.  defaults to fetch the top 25.  also added a mustache template section to accomodate the model table.
docs
limit
resolved
remove evidence form display for now
remove evidence form display for now

Fixes #26.

It turns out that there was some funniness going on in the widgets for
generating a table. genTable(), in widgets.js builds tables from
scratch in bare html, not escaping anything. These tables are then
passed into mustache essentially untouched, as indicated by the triple
curly bracket notation - ie.,

{{{simModelTable}}}

this is a problem for the URL labels that contain characters reserved
in HTML, such as angle brackets.

One approach might be to back away from the triple curlies, and to let
mustache esacpe things. This will not work, as we are sending legal
html of forms like "<A HREF=..." into the template. We can't have this
escaped.

To get around this, I added convChars() to widgets.js, to convert all
escapd characters to an html friendly form - "<" becomes "&lt;",
etc. This is now called for all HREF labels and free text generated in
widgets.js.

One minor complication of this approach. Some calls generate HTML that
has already been escaped. Naive escaping will muck things up- changing
"&lt;" to "&amp lt;", for example. convChars() handles this by
changing the ampersand only if it is not prefixing an already-escaped
character. In other words, "&" will become "&amp;", but "&lt;" will
not be changed.
re-instating accidentally deleted readme
Merge remote-tracking branch 'upstream/master' into sarah_branch

Conflicts:
	keggerator/index.html
	templates/disease.mustache