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{-# LANGUAGE OverloadedStrings #-}
import Control.Applicative
import Control.Monad
import Data.Monoid
import Data.Yaml
import Data.List (nub, sort, sortBy)
import Data.Function (on)
import Data.Maybe (catMaybes)
import qualified Data.Text as T
import Data.Text.Encoding (decodeUtf8)
import qualified Data.Aeson as A
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 System.Directory (copyFile)
import Network.URI (isReserved, escapeURIString)
import Lucid
import Paths_comatose
data Protocol = Protocol {
pname :: String
, plongname :: Maybe String
, pdescription :: 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
data JQData = JQData {
jname :: String
, jlongname :: Maybe String
, jdescription :: Maybe String
, jdoi :: Maybe String
, jyear :: Maybe String
, jtitle :: Maybe String
} deriving Show
instance ToJSON JQData where
toJSON d = object [
"name" .= jname d
, "longname" .= jlongname d
, "description" .= jdescription d
, "doi" .= jdoi d
, "year" .= jyear d
, "title" .= jtitle d
]
type FeatureList = M.Map String Feature
instance FromJSON Protocol where
parseJSON (Object v) = Protocol
<$> v .: "name"
<*> v .:? "longname"
<*> v .:? "description"
<*> v .:? "ref" .!= []
<*> v .:? "features" .!= M.empty
parseJSON _ = mzero
instance FromJSON Database where
parseJSON (Object v) = Database
<$> 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
maybeLink :: Html () -> Maybe T.Text -> Html ()
maybeLink text href = maybe text (\x -> a_ [href_ x] text) href
protoentry :: Database -> (String, Protocol) -> Html ()
protoentry db (ident, p) =
let
pubs = protoPublications db p
firstpub = join (head' pubs)
field key = firstpub >>= (return . E.fields) >>= lookup key
jdata = JQData {
jname = pname p
, jlongname = plongname p
, jdescription = pdescription p
, jdoi = field "doi"
, jyear = field "year"
, jtitle = field "title"
}
in
tr_ [
id_ $ T.pack ident
, data_ "proto" ((decodeUtf8 . BS.toStrict . A.encode) jdata)
] $ do
td_ $ maybeLink (toHtml $ pname p) (field "doi" >>= return . T.pack . resolveDoi)
td_ $ maybeToHtml $ plongname p
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)
-- | Try very hard to find an appropriate URL for the bibentry, DOIs are prefered
bibentryurl bib = safeHead $ catMaybes [doi, url]
where
fields = E.fields bib
doi = lookup "doi" fields >>= return . resolveDoi
url = lookup "url" fields
-- | Format bibliography/references item
bibentry :: E.T -> Html ()
bibentry bib = do
let fields = E.fields bib
a_ [href_ $ T.pack $ maybe "" id $ bibentryurl bib] $ maybeToHtml $ lookup "title" fields
", "
maybeToHtml $ lookup "author" fields
", "
maybeToHtml $ lookup "year" fields
-- | References section
references :: [E.T] -> Html ()
references attrib = section_ $ do
h2_ "References"
ol_ $ forM_ attrib (li_ . bibentry)
-- | What is this?!
introduction :: Html ()
introduction = section_ $ do
p_ "The comprehensive MAC taxonomy database (comatose) aims to be …"
-- | The list of protocols
protocols :: Database -> Html ()
protocols db = table_ [id_ "algo", class_ "table table-striped"] $ do
thead_ $ do
tr_ $ do
th_ "Name"
th_ ""
th_ "Year"
th_ "Features"
tbody_ $ forM_ (M.toList $ dalgos db) (protoentry db)
page db attrib = 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"
extcss "style.css"
body_ $ do
div_ [class_ "container"] $ do
div_ [class_ "page-header"] $ do
h1_ "comatose"
introduction
protocols db
references (sortBy (compare `on` lookup "year" . E.fields) attrib)
div_ [id_ "background"] ""
div_ [id_ "popup"] $ do
h2_ ""
p_ [class_ "longname"] ""
ul_ [class_ "ref"] $ do
li_ [class_ "title"] ""
li_ [class_ "year"] ""
li_ $ a_ [class_ "doi"] ""
li_ $ a_ [class_ "scholar"] "Scholar"
p_ [class_ "description"] ""
extjs "script.js"
render f db attribution = renderToFile f (page db attribution)
readAttributions = getDataFileName "data/attribution.bib" >>= parseFromFile file
copyDataFile source dest = getDataFileName source >>= (\x -> copyFile x dest)
main = do
db <- getDataFileName "data/db.yaml" >>= readDb
(Right attribution) <- readAttributions
render "_build/index.html" db attribution
copyDataFile "data/style.css" "_build/style.css"
copyDataFile "data/script.js" "_build/script.js"
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