-}
-{-# LANGUAGE DataKinds #-}
-{-# LANGUAGE DeriveGeneric #-}
-{-# LANGUAGE FlexibleInstances #-}
-{-# LANGUAGE NoImplicitPrelude #-}
-{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE StandaloneDeriving #-}
-{-# LANGUAGE TypeOperators #-}
+{-# LANGUAGE TypeOperators #-}
{-# LANGUAGE Strict #-}
module Main where
+import Control.Concurrent.Async as CCA (mapConcurrently)
+import Control.Monad (mapM)
import Data.Aeson
-import Data.Text (Text, unwords)
+import Data.List ((++),concat)
+import Data.Maybe
+import Data.Text (Text, unwords, unlines)
import GHC.Generics
import GHC.IO (FilePath)
+import Gargantext.Database.Admin.Types.Hyperdata
+import Gargantext.Database.Admin.Types.Node
import Gargantext.Prelude
-import Gargantext.Text.List.CSV (csvGraphTermList)
-import Gargantext.Text.Parsers.CSV (readCsv, csv_title, csv_abstract, csv_publication_year)
-import Gargantext.Text.Parsers (FileFormat(..),parseDocs)
-import Gargantext.Text.Terms.WithList
import Gargantext.Text.Context (TermList)
-
-import System.Environment
-
+import Gargantext.Text.Corpus.Parsers (FileFormat(..),parseFile)
+import Gargantext.Text.Corpus.Parsers.CSV (csv_title, csv_abstract, csv_publication_year)
+import Gargantext.Text.List.CSV (csvMapTermList)
+import Gargantext.Text.Terms.WithList
import Gargantext.Viz.Phylo
-import Gargantext.Viz.Phylo.Tools
import Gargantext.Viz.Phylo.LevelMaker
+import Gargantext.Viz.Phylo.Tools
import Gargantext.Viz.Phylo.View.Export
import Gargantext.Viz.Phylo.View.ViewMaker
-
-
-import Gargantext.Database.Types.Node
-
-import Data.Maybe
-
-
-import qualified Data.Map as DM
-import qualified Data.Vector as DV
+import System.Directory (doesFileExist)
+import System.Environment
+import qualified Data.ByteString.Lazy as L
import qualified Data.List as DL
+import qualified Data.Map as DM
import qualified Data.Text as DT
+import qualified Data.Vector as DV
+import qualified Gargantext.Text.Corpus.Parsers.CSV as CSV
import qualified Prelude as P
-import qualified Data.ByteString.Lazy as L
--------------
type ListPath = FilePath
+type FisPath = FilePath
type CorpusPath = FilePath
data CorpusType = Wos | Csv deriving (Show,Generic)
type Limit = Int
Conf { corpusPath :: CorpusPath
, corpusType :: CorpusType
, listPath :: ListPath
+ , fisPath :: FilePath
, outputPath :: FilePath
, phyloName :: Text
, limit :: Limit
, timeGrain :: Int
, timeStep :: Int
+ , timeFrame :: Int
+ , timeFrameTh :: Double
, timeTh :: Double
, timeSens :: Double
+ , reBranchThr :: Double
+ , reBranchNth :: Int
, clusterTh :: Double
, clusterSens :: Double
, phyloLevel :: Int
, viewLevel :: Int
, fisSupport :: Int
- , fisClique :: Int
+ , fisClique :: Int
+ , minSizeBranch :: Int
} deriving (Show,Generic)
instance FromJSON Conf
instance FromJSON CorpusType
instance ToJSON CorpusType
+
+decoder :: P.Either a b -> b
+decoder (P.Left _) = P.error "Error"
+decoder (P.Right x) = x
+
-- | Get the conf from a Json file
getJson :: FilePath -> IO L.ByteString
getJson path = L.readFile path
where
--------------------------------------
termsInText :: Patterns -> Text -> [Text]
- termsInText pats txt = DL.nub $ DL.concat $ map (map unwords) $ extractTermsWithList pats txt
+ termsInText pats txt = DL.nub
+ $ DL.concat
+ $ map (map unwords)
+ $ extractTermsWithList pats txt
--------------------------------------
-- | To transform a Csv nfile into a readable corpus
csvToCorpus :: Limit -> CorpusPath -> IO ([(Int,Text)])
csvToCorpus limit csv = DV.toList
+ -- . DV.reverse
. DV.take limit
+ -- . DV.reverse
. DV.map (\n -> (csv_publication_year n, (csv_title n) <> " " <> (csv_abstract n)))
- . snd <$> readCsv csv
+ . snd <$> CSV.readFile csv
-- | To transform a Wos nfile into a readable corpus
wosToCorpus :: Limit -> CorpusPath -> IO ([(Int,Text)])
wosToCorpus limit path = DL.take limit
- . map (\d -> ((fromJust $_hyperdataDocument_publication_year d)
- ,(fromJust $_hyperdataDocument_title d) <> " " <> (fromJust $_hyperdataDocument_abstract d)))
- . filter (\d -> (isJust $_hyperdataDocument_publication_year d)
- && (isJust $_hyperdataDocument_title d)
- && (isJust $_hyperdataDocument_abstract d))
- <$> parseDocs WOS path
+ . map (\d -> ((fromJust $_hd_publication_year d)
+ ,(fromJust $_hd_title d) <> " " <> (fromJust $_hd_abstract d)))
+ . filter (\d -> (isJust $_hd_publication_year d)
+ && (isJust $_hd_title d)
+ && (isJust $_hd_abstract d))
+ . concat
+ <$> mapConcurrently (\idx -> parseFile WOS (path <> show(idx) <> ".txt")) [1..20]
-- | To use the correct parser given a CorpusType
pure $ map ( (\(y,t) -> Document y t) . filterTerms patterns) corpus
+-- | To parse an existing Fis file
+parseFis :: FisPath -> Text -> Int -> Int -> Int -> Int -> IO [PhyloFis]
+parseFis path name grain step support clique = do
+ fisExists <- doesFileExist (path <> (DT.unpack name) <> "_" <> show(grain) <> "_" <> show(step) <> "_" <> show(support) <> "_" <> show(clique) <> ".json")
+ if fisExists
+ then do
+ fisJson <- (eitherDecode <$> getJson (path <> (DT.unpack name) <> "_" <> show(grain) <> "_" <> show(step) <> "_" <> show(support) <> "_" <> show(clique) <> ".json")) :: IO (P.Either P.String [PhyloFis])
+ case fisJson of
+ P.Left err -> do
+ putStrLn err
+ pure []
+ P.Right fis -> pure fis
+ else pure []
+
+writeFis :: FisPath -> Text -> Int -> Int -> Int -> Int -> DM.Map (Date,Date) [PhyloFis] -> IO ()
+writeFis path name grain step support clique fis = do
+ let fisPath = path <> (DT.unpack name) <> "_" <> show(grain) <> "_" <> show(step) <> "_" <> show(support) <> "_" <> show(clique) <> ".json"
+ L.writeFile fisPath $ encode (DL.concat $ DM.elems fis)
+
--------------
-- | Main | --
--------------
P.Left err -> putStrLn err
P.Right conf -> do
- termList <- csvGraphTermList (listPath conf)
+ termList <- csvMapTermList (listPath conf)
corpus <- parse (corpusType conf) (limit conf) (corpusPath conf) termList
- let roots = DL.nub $ DL.concat $ map text corpus
+ putStrLn $ ("\n" <> show (length corpus) <> " parsed docs")
- putStrLn $ (show (length corpus) <> " parsed docs")
+ fis <- parseFis (fisPath conf) (phyloName conf) (timeGrain conf) (timeStep conf) (fisSupport conf) (fisClique conf)
+
+ putStrLn $ ("\n" <> show (length fis) <> " parsed fis")
+
+ let fis' = DM.fromListWith (++) $ DL.sortOn (fst . fst) $ map (\f -> (getFisPeriod f,[f])) fis
let query = PhyloQueryBuild (phyloName conf) "" (timeGrain conf) (timeStep conf)
- (Fis $ FisParams True (fisSupport conf) (fisClique conf)) [] [] (WeightedLogJaccard $ WLJParams (timeTh conf) (timeSens conf)) (phyloLevel conf)
+ (Fis $ FisParams True (fisSupport conf) (fisClique conf)) [] [] (WeightedLogJaccard $ WLJParams (timeTh conf) (timeSens conf)) (timeFrame conf) (timeFrameTh conf)
+ (reBranchThr conf) (reBranchNth conf) (phyloLevel conf)
(RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams (clusterTh conf) (clusterSens conf))
- let queryView = PhyloQueryView (viewLevel conf) Merge False 1 [BranchAge] [defaultSmallBranch] [BranchPeakFreq,GroupLabelCooc] (Just (ByBranchAge,Asc)) Json Flat True
+ let queryView = PhyloQueryView (viewLevel conf) Merge False 1 [BranchAge,BranchBirth,BranchGroups] [SizeBranch $ SBParams (minSizeBranch conf)] [GroupLabelIncDyn,BranchPeakInc] (Just (ByBranchBirth,Asc)) Json Flat True
+
+ let phylo = toPhylo query corpus termList fis'
- let phylo = toPhylo query corpus roots termList
+ writeFis (fisPath conf) (phyloName conf) (timeGrain conf) (timeStep conf) (fisSupport conf) (fisClique conf) (getPhyloFis phylo)
let view = toPhyloView queryView phylo