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{-# LANGUAGE OverloadedStrings #-}
import Control.Applicative
import Control.Monad
import Data.Monoid
import Data.Yaml
import Data.List (nub, sort)
import Data.Maybe (catMaybes)
import qualified Data.Text as T
import Text.BibTeX.Parse
import Text.BibTeX.Entry as E
import qualified Data.Map as M
import Text.Parsec.Error
import Text.ParserCombinators.Parsec.Prim
import qualified Data.ByteString.Lazy as BS
import System.FilePath ((<.>), splitExtension)
import Network.URI (isReserved, escapeURIString)
import Lucid
import Paths_comatose
data Protocol = Protocol {
pname :: String
, plongname :: Maybe String
, pref :: [String]
, pfeatures :: M.Map String (Maybe String)
} deriving Show
data Database = Database {
dalgos :: M.Map String Protocol
, dfeatures :: M.Map String Feature
, dpublications :: [T]
} deriving Show
data Feature = Feature {
fname :: String
, fdescription :: Maybe String
} deriving Show
type FeatureList = M.Map String Feature
instance FromJSON Protocol where
parseJSON (Object v) = Protocol
<$> v .: "name"
<*> v .:? "longname"
<*> v .:? "ref" .!= []
<*> v .:? "features" .!= M.empty
parseJSON _ = mzero
instance FromJSON Database where
parseJSON (Object v) = Database
<$> v .: "algos"
<*> v .: "features"
<*> pure []
parseJSON _ = mzero
instance FromJSON Feature where
parseJSON (Object v) = Feature
<$> v .: "name"
<*> v .:? "description"
parseJSON _ = mzero
safeHead [] = Nothing
safeHead (x:_) = Just x
findPublication db ident = safeHead $ filter (\x -> ident == E.identifier x) $ dpublications db
-- |Get a list of all publications referenced by proto @p@
protoPublications db p = map (findPublication db) (pref p)
-- |Find all referenced features’ names
referencedFeatures db = nub $ sort $ concat $ map (M.keys . pfeatures) $ M.elems $ dalgos db
readDb :: String -> IO Database
readDb f = do
yamlres <- decodeFileEither f
--print yamlres
let
(Right yamldb) = yamlres
(basename, _) = splitExtension f
bibres <- parseFromFile file (basename <.> "bib")
--print bibres
let (Right bibdb) = bibres
return yamldb { dpublications = bibdb }
maybeToHtml = maybe (toHtml ("" :: String)) toHtml
head' [] = Nothing
head' (x:_) = Just x
scholarSearch q = "http://scholar.google.com/scholar?q=" ++ escapeURIString isReserved q
resolveDoi q = "http://doi.org/" ++ q
protoentry :: Database -> (String, Protocol) -> Html ()
protoentry db (ident, p) = tr_ [id_ $ T.pack ident] $ do
let
pubs = protoPublications db p
firstpub = join (head' pubs)
field key = firstpub >>= (return . E.fields) >>= lookup key
td_ $ toHtml $ pname p
td_ $ maybeToHtml $ plongname p
td_ $ do
maybe "" (\x -> a_ [href_ $ T.pack $ resolveDoi x] "doi") $ field "doi"
" "
maybe "" (\x -> a_ [href_ $ T.pack $ scholarSearch x] "Google") $ field "title"
td_ $ maybeToHtml $ field "year"
td_ [class_ "features"] $ ul_ $ forM_ (sort $ M.keys $ pfeatures p) (\x -> li_ $ toHtml $ maybe ("" :: String) fname $ M.lookup x (dfeatures db))
extcss url = link_ [rel_ "stylesheet", type_ "text/css", href_ url]
extjs :: T.Text -> Html ()
extjs url = script_ [type_ "text/javascript", charset_ "utf8", src_ url] ("" :: T.Text)
page db = doctypehtml_ $ do
head_ $ do
title_ "comatose"
meta_ [charset_ "utf-8"]
extjs "https://code.jquery.com/jquery-1.10.2.min.js"
extcss "https://maxcdn.bootstrapcdn.com/bootstrap/3.3.2/css/bootstrap.min.css"
extcss "https://maxcdn.bootstrapcdn.com/bootstrap/3.3.2/css/bootstrap-theme.min.css"
extjs "https://maxcdn.bootstrapcdn.com/bootstrap/3.3.2/js/bootstrap.min.js"
extcss "https://cdn.datatables.net/1.10.5/css/jquery.dataTables.css"
extjs "https://cdn.datatables.net/1.10.5/js/jquery.dataTables.js"
extcss "https://cdn.datatables.net/plug-ins/f2c75b7247b/integration/bootstrap/3/dataTables.bootstrap.css"
extjs "https://cdn.datatables.net/plug-ins/f2c75b7247b/integration/bootstrap/3/dataTables.bootstrap.js"
style_ "td.features ul { list-style-type: none; margin: 0; padding: 0; }"
body_ $ do
div_ [class_ "container"] $ do
div_ [class_ "page-header"] $ do
h1_ "comatose"
h2_ "COmprehensive MAc TaxonOmy databaSE"
table_ [id_ "algo", class_ "table-striped"] $ do
thead_ $ do
tr_ $ do
th_ "Name"
th_ ""
th_ ""
th_ "Year"
th_ "Features"
tbody_ $ forM_ (M.toList $ dalgos db) (protoentry db)
script_ "$(document).ready( function () { $('#algo').DataTable( { paging: false, \"columnDefs\": [ ] } ); } );"
render f db = renderToFile f (page db)
main = getDataFileName "data/db.yaml" >>= readDb >>= render "comatose.html"
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