bin/gargantext-adaptative-phylo/Main.hs

   1 {-|
   2 Module      : Main.hs
   3 Description : Gargantext starter binary with Adaptative Phylo
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 Adaptative Phylo binaries
  11  -}
  12
  13 {-# LANGUAGE StandaloneDeriving #-}
  14 {-# LANGUAGE TypeOperators      #-}
  15 {-# LANGUAGE Strict             #-}
  16
  17 module Main where
  18
  19 import Data.Aeson
  20 import Data.ByteString.Lazy (ByteString)
  21 import Data.Maybe (isJust, fromJust)
  22 import Data.List  (concat, nub, isSuffixOf, take)
  23 import Data.String (String)
  24 import Data.Text  (Text, unwords, unpack)
  25
  26 import Gargantext.Prelude
  27 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
  28 import Gargantext.Core.Text.Context (TermList)
  29 import Gargantext.Core.Text.Corpus.Parsers.CSV (csv_title, csv_abstract, csv_publication_year)
  30 import Gargantext.Core.Text.Corpus.Parsers (FileFormat(..),parseFile)
  31 import Gargantext.Core.Text.List.Formats.CSV (csvMapTermList)
  32 import Gargantext.Core.Text.Terms.WithList (Patterns, buildPatterns, extractTermsWithList)
  33 import Gargantext.Core.Viz.AdaptativePhylo
  34 import Gargantext.Core.Viz.Phylo.PhyloMaker  (toPhylo)
  35 import Gargantext.Core.Viz.Phylo.PhyloTools  (printIOMsg, printIOComment)
  36 import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile)
  37 -- import Gargantext.Core.Viz.Phylo.SynchronicClustering (synchronicDistance')
  38
  39 import GHC.IO (FilePath)
  40 import Prelude (Either(..))
  41 import System.Environment
  42 import System.Directory (listDirectory)
  43 import Control.Concurrent.Async (mapConcurrently)
  44
  45 import qualified Data.ByteString.Lazy as Lazy
  46 import qualified Data.Vector as Vector
  47 import qualified Gargantext.Core.Text.Corpus.Parsers.CSV as Csv
  48
  49
  50 ---------------
  51 -- | Tools | --
  52 ---------------
  53
  54
  55 -- | To get all the files in a directory or just a file
  56 getFilesFromPath :: FilePath -> IO([FilePath])
  57 getFilesFromPath path = do
  58   if (isSuffixOf "/" path)
  59     then (listDirectory path)
  60     else return [path]
  61
  62
  63 --------------
  64 -- | Json | --
  65 --------------
  66
  67
  68 -- | To read and decode a Json file
  69 readJson :: FilePath -> IO ByteString
  70 readJson path = Lazy.readFile path
  71
  72
  73 ----------------
  74 -- | Parser | --
  75 ----------------
  76
  77 -- | To filter the Ngrams of a document based on the termList
  78 filterTerms :: Patterns -> (a, Text) -> (a, [Text])
  79 filterTerms patterns (y,d) = (y,termsInText patterns d)
  80   where
  81     --------------------------------------
  82     termsInText :: Patterns -> Text -> [Text]
  83     termsInText pats txt = nub $ concat $ map (map unwords) $ extractTermsWithList pats txt
  84     --------------------------------------
  85
  86
  87 -- | To transform a Wos file (or [file]) into a readable corpus
  88 wosToCorpus :: Int -> FilePath -> IO ([(Int,Text)])
  89 wosToCorpus limit path = do
  90       files <- getFilesFromPath path
  91       take limit
  92         <$> map (\d -> let date' = fromJust $ _hd_publication_year d
  93                            title = fromJust $ _hd_title d
  94                            abstr = if (isJust $ _hd_abstract d)
  95                                    then fromJust $ _hd_abstract d
  96                                    else ""
  97                         in (date', title <> " " <> abstr))
  98         <$> concat
  99         <$> mapConcurrently (\file ->
 100               filter (\d -> (isJust $ _hd_publication_year d)
 101                          && (isJust $ _hd_title d))
 102                 <$> parseFile WOS (path <> file) ) files
 103
 104
 105 -- | To transform a Csv file into a readable corpus
 106 csvToCorpus :: Int -> FilePath -> IO ([(Int,Text)])
 107 csvToCorpus limit path = Vector.toList
 108     <$> Vector.take limit
 109     <$> Vector.map (\row -> (csv_publication_year row, (csv_title row) <> " " <> (csv_abstract row)))
 110     <$> snd <$> Csv.readFile path
 111
 112
 113 -- | To use the correct parser given a CorpusType
 114 fileToCorpus :: CorpusParser -> FilePath -> IO ([(Int,Text)])
 115 fileToCorpus parser path = case parser of
 116   Wos limit -> wosToCorpus limit path
 117   Csv limit -> csvToCorpus limit path
 118
 119
 120 -- | To parse a file into a list of Document
 121 fileToDocs :: CorpusParser -> FilePath -> TermList -> IO [Document]
 122 fileToDocs parser path lst = do
 123   corpus <- fileToCorpus parser path
 124   let patterns = buildPatterns lst
 125   pure $ map ( (\(y,t) -> Document y t) . filterTerms patterns) corpus
 126
 127
 128 --------------
 129 -- | Main | --
 130 --------------
 131
 132
 133 main :: IO ()
 134 main = do
 135
 136     printIOMsg "Starting the reconstruction"
 137
 138     printIOMsg "Read the configuration file"
 139     [args]   <- getArgs
 140     jsonArgs <- (eitherDecode <$> readJson args) :: IO (Either String Config)
 141
 142     case jsonArgs of
 143         Left err     -> putStrLn err
 144         Right config -> do
 145
 146             printIOMsg "Parse the corpus"
 147             mapList <- csvMapTermList (listPath config)
 148             corpus  <- fileToDocs (corpusParser config) (corpusPath config) mapList
 149             printIOComment (show (length corpus) <> " parsed docs from the corpus")
 150
 151             printIOMsg "Reconstruct the Phylo"
 152
 153             let phylo = toPhylo corpus mapList config
 154
 155             -- | probes
 156
 157             -- writeFile ((outputPath config) <> (unpack $ phyloName config) <> "_synchronic_distance_cumu_jaccard.txt")
 158             --          $ synchronicDistance' phylo 1
 159
 160             -- writeFile ((outputPath config) <> (unpack $ phyloName config) <> "_inflexion_points.txt")
 161             --         $ inflexionPoints phylo 1
 162
 163             printIOMsg "End of reconstruction, start the export"
 164
 165             let dot = toPhyloExport phylo
 166
 167             let clq = case (clique config) of
 168                         Fis s s' -> "fis_" <> (show s) <> "_" <> (show s')
 169                         MaxClique s ->  "clique_" <> (show s)
 170
 171             let sensibility = case (phyloProximity config) of
 172                         Hamming -> undefined
 173                         WeightedLogJaccard s -> (show s)
 174
 175             let sync = case (phyloSynchrony config) of
 176                         ByProximityThreshold t _ _ _ -> (show t)
 177                         ByProximityDistribution _ _ -> undefined
 178
 179             -- to be improved
 180             -- let br_length = case (take 1 $ exportFilter config) of
 181             --             ByBranchSize t -> (show t)
 182
 183
 184             let output = (outputPath config)
 185                       <> (unpack $ phyloName config)
 186                       <> "-" <> clq
 187                       <> "-level_" <> (show (phyloLevel config))
 188                       <> "-sens_" <> sensibility
 189                       -- <> "-lenght_" <> br_length
 190                       <> "-scale_" <> (show (_qua_granularity $ phyloQuality config))
 191                       <> "-sync_" <> sync
 192                       <> ".dot"
 193
 194             dotToFile output dot