bin/gargantext-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 Debug.Trace (trace)
  20 import Control.Concurrent.Async (mapConcurrently)
  21 import Crypto.Hash.SHA256 (hash)
  22 import Data.Aeson
  23 import Data.Either (Either(..), fromRight)
  24 import Data.List  (concat, nub, isSuffixOf)
  25 import Data.List.Split
  26 import Data.Maybe (fromMaybe)
  27 import Data.String (String)
  28 import Data.Text  (Text, unwords, unpack, replace, pack)
  29 import GHC.IO (FilePath)
  30 import Gargantext.API.Ngrams.Prelude (toTermList)
  31 import Gargantext.API.Ngrams.Types
  32 import Gargantext.Core.Text.Context (TermList)
  33 import Gargantext.Core.Text.Corpus.Parsers (FileFormat(..), FileType(..), parseFile)
  34 import Gargantext.Core.Text.Corpus.Parsers.CSV (csv_title, csv_abstract, csv_publication_year, csv_publication_month, csv_publication_day, csv'_source, csv'_title, csv'_abstract, csv'_publication_year, csv'_publication_month, csv'_publication_day, csv'_weight)
  35 import Gargantext.Core.Text.List.Formats.CSV (csvMapTermList)
  36 import Gargantext.Core.Text.Terms.WithList (Patterns, buildPatterns, extractTermsWithList)
  37 import Gargantext.Core.Types.Main (ListType(..))
  38 import Gargantext.Core.Viz.Phylo
  39 import Gargantext.Core.Viz.Phylo.API.Tools
  40 import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile)
  41 import Gargantext.Core.Viz.Phylo.PhyloMaker  (toPhylo, toPhyloStep)
  42 import Gargantext.Core.Viz.Phylo.PhyloTools  (printIOMsg, printIOComment, setConfig)
  43 import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
  44 import Gargantext.Database.Schema.Ngrams (NgramsType(..))
  45 import Gargantext.Prelude
  46 import System.Directory (listDirectory,doesFileExist)
  47 import System.Environment
  48 import qualified Data.ByteString.Char8                   as C8
  49 import qualified Data.Text                               as T
  50 import qualified Data.Vector                             as Vector
  51 import qualified Gargantext.Core.Text.Corpus.Parsers.CSV as Csv
  52
  53 data PhyloStage = PhyloWithCliques | PhyloWithLinks deriving (Show)
  54
  55 ---------------
  56 -- | Tools | --
  57 ---------------
  58
  59 -- | To get all the files in a directory or just a file
  60 getFilesFromPath :: FilePath -> IO [FilePath]
  61 getFilesFromPath path = do
  62   if (isSuffixOf "/" path)
  63     then (listDirectory path)
  64     else return [path]
  65
  66 ----------------
  67 -- | Parser | --
  68 ----------------
  69
  70 -- | To filter the Ngrams of a document based on the termList
  71 termsInText :: Patterns -> Text -> [Text]
  72 termsInText pats txt = nub $ concat $ map (map unwords) $ extractTermsWithList pats txt
  73
  74
  75 -- | To transform a Wos file (or [file]) into a list of Docs
  76 wosToDocs :: Int -> Patterns -> TimeUnit -> FilePath -> IO [Document]
  77 wosToDocs limit patterns time path = do
  78       files <- getFilesFromPath path
  79       take limit
  80         <$> map (\d -> let title = fromJust $ _hd_title d
  81                            abstr = if (isJust $ _hd_abstract d)
  82                                    then fromJust $ _hd_abstract d
  83                                    else ""
  84                         in Document (toPhyloDate
  85                                       (fromIntegral $ fromJust $ _hd_publication_year d)
  86                                       (fromJust $ _hd_publication_month d)
  87                                       (fromJust $ _hd_publication_day d) time)
  88                                     (toPhyloDate'
  89                                       (fromIntegral $ fromJust $ _hd_publication_year d)
  90                                       (fromJust $ _hd_publication_month d)
  91                                       (fromJust $ _hd_publication_day d) time)
  92                                     (termsInText patterns $ title <> " " <> abstr) Nothing [])
  93         <$> concat
  94         <$> mapConcurrently (\file ->
  95               filter (\d -> (isJust $ _hd_publication_year d)
  96                          && (isJust $ _hd_title d))
  97                 <$> fromRight [] <$> parseFile WOS Plain (path <> file) ) files
  98
  99
 100 -- To transform a Csv file into a list of Document
 101 csvToDocs :: CorpusParser -> Patterns -> TimeUnit -> FilePath -> IO [Document]
 102 csvToDocs parser patterns time path =
 103   case parser of
 104     Wos  _     -> undefined
 105     Csv  limit -> Vector.toList
 106       <$> Vector.take limit
 107       <$> Vector.map (\row -> Document (toPhyloDate  (Csv.fromMIntOrDec Csv.defaultYear $ csv_publication_year row) (fromMaybe Csv.defaultMonth $ csv_publication_month row) (fromMaybe Csv.defaultDay $ csv_publication_day row) time)
 108                                        (toPhyloDate' (Csv.fromMIntOrDec Csv.defaultYear $ csv_publication_year row) (fromMaybe Csv.defaultMonth $ csv_publication_month row) (fromMaybe Csv.defaultDay $ csv_publication_day row) time)
 109                                        (termsInText patterns $ (csv_title row) <> " " <> (csv_abstract row))
 110                                        Nothing
 111                                        []
 112                      ) <$> snd <$> either (\err -> panic $ cs $ "CSV error" <> (show err)) identity <$> Csv.readCSVFile path
 113     Csv' limit -> Vector.toList
 114       <$> Vector.take limit
 115       <$> Vector.map (\row -> Document (toPhyloDate  (csv'_publication_year row) (csv'_publication_month row) (csv'_publication_day row) time)
 116                                        (toPhyloDate' (csv'_publication_year row) (csv'_publication_month row) (csv'_publication_day row) time)
 117                                        (termsInText patterns $ (csv'_title row) <> " " <> (csv'_abstract row))
 118                                        (Just $ csv'_weight row)
 119                                        (map (T.strip . pack) $ splitOn ";" (unpack $ (csv'_source row)))
 120                      ) <$> snd <$> Csv.readWeightedCsv path
 121
 122
 123 -- To parse a file into a list of Document
 124 fileToDocs' :: CorpusParser -> FilePath -> TimeUnit -> TermList -> IO [Document]
 125 fileToDocs' parser path time lst = do
 126   let patterns = buildPatterns lst
 127   case parser of
 128       Wos limit  -> wosToDocs limit  patterns time path
 129       Csv  _     -> csvToDocs parser patterns time path
 130       Csv' _     -> csvToDocs parser patterns time path
 131
 132
 133 ---------------
 134 -- | Label | --
 135 ---------------
 136
 137
 138 -- Config time parameters to label
 139 timeToLabel :: PhyloConfig -> [Char]
 140 timeToLabel config = case (timeUnit config) of
 141       Epoch p s f -> ("time_epochs" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
 142       Year  p s f -> ("time_years"  <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
 143       Month p s f -> ("time_months" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
 144       Week  p s f -> ("time_weeks"  <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
 145       Day   p s f -> ("time_days"   <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
 146
 147
 148 seaToLabel :: PhyloConfig -> [Char]
 149 seaToLabel config = case (seaElevation config) of
 150       Constante start step   -> ("sea_cst_"  <> (show start) <> "_" <> (show step))
 151       Adaptative granularity -> ("sea_adapt" <> (show granularity))
 152
 153
 154 sensToLabel :: PhyloConfig -> [Char]
 155 sensToLabel config = case (phyloProximity config) of
 156       Hamming _ -> undefined
 157       WeightedLogJaccard s -> ("WeightedLogJaccard_"  <> show s)
 158       WeightedLogSim s -> ( "WeightedLogSim-sens_"  <> show s)
 159
 160
 161 cliqueToLabel :: PhyloConfig -> [Char]
 162 cliqueToLabel config = case (clique config) of
 163       Fis s s' -> "fis_" <> (show s) <> "_" <> (show s')
 164       MaxClique s t f ->  "clique_" <> (show s)<> "_"  <> (show f)<> "_"  <> (show t)
 165
 166
 167 syncToLabel :: PhyloConfig -> [Char]
 168 syncToLabel config = case (phyloSynchrony config) of
 169       ByProximityThreshold scl sync_sens scope _ -> ("scale_" <> (show scope) <> "_" <> (show sync_sens)  <> "_"  <> (show scl))
 170       ByProximityDistribution _ _ -> undefined
 171
 172 qualToConfig :: PhyloConfig -> [Char]
 173 qualToConfig config = case (phyloQuality config) of
 174       Quality g m -> "quality_" <> (show g) <> "_" <> (show m)
 175
 176
 177 -- To set up the export file's label from the configuration
 178 configToLabel :: PhyloConfig -> [Char]
 179 configToLabel config = outputPath config
 180                     <> (unpack $ phyloName config)
 181                     <> "-" <> (timeToLabel config)
 182                     <> "-scale_" <> (show (phyloLevel config))
 183                     <> "-" <> (seaToLabel config)
 184                     <> "-" <> (sensToLabel config)
 185                     <> "-" <> (cliqueToLabel config)
 186                     <> "-level_" <> (show (_qua_granularity $ phyloQuality config))
 187                     <> "-" <> (syncToLabel config)
 188                     <> ".dot"
 189
 190
 191 -- To write a sha256 from a set of config's parameters
 192 configToSha :: PhyloStage -> PhyloConfig -> [Char]
 193 configToSha stage config = unpack
 194                          $ replace "/" "-"
 195                          $ T.pack (show (hash $ C8.pack label))
 196   where
 197     label :: [Char]
 198     label = case stage of
 199       PhyloWithCliques -> (corpusPath    config)
 200                        <> (listPath      config)
 201                        <> (timeToLabel   config)
 202                        <> (cliqueToLabel config)
 203       PhyloWithLinks   -> (corpusPath    config)
 204                        <> (listPath      config)
 205                        <> (timeToLabel   config)
 206                        <> (cliqueToLabel config)
 207                        <> (sensToLabel   config)
 208                        <> (seaToLabel    config)
 209                        <> (syncToLabel   config)
 210                        <> (qualToConfig  config)
 211                        <> (show (phyloLevel config))
 212
 213
 214 readListV4 :: [Char] -> IO NgramsList
 215 readListV4 path = do
 216   listJson <- (eitherDecode <$> readJson path) :: IO (Either String NgramsList)
 217   case listJson of
 218     Left err -> do
 219       putStrLn err
 220       undefined
 221     Right listV4 -> pure listV4
 222
 223
 224 fileToList  :: ListParser -> FilePath -> IO TermList
 225 fileToList parser path =
 226   case parser of
 227     V3 -> csvMapTermList path
 228     V4 -> fromJust
 229       <$> toTermList MapTerm NgramsTerms
 230       <$> readListV4 path
 231
 232
 233 --------------
 234 -- | Main | --
 235 --------------
 236
 237
 238 main :: IO ()
 239 main = do
 240
 241     printIOMsg "Starting the reconstruction"
 242
 243     printIOMsg "Read the configuration file"
 244     [args]   <- getArgs
 245     jsonArgs <- (eitherDecode <$> readJson args) :: IO (Either String PhyloConfig)
 246
 247     case jsonArgs of
 248         Left err     -> putStrLn err
 249         Right config -> do
 250
 251             printIOMsg "Parse the corpus"
 252             mapList <-  fileToList (listParser config) (listPath config)
 253             corpus  <- fileToDocs' (corpusParser config) (corpusPath config) (timeUnit config) mapList
 254             printIOComment (show (length corpus) <> " parsed docs from the corpus")
 255
 256             printIOMsg "Reconstruct the phylo"
 257
 258             let phyloWithCliquesFile =  (outputPath config) <> "phyloWithCliques_" <> (configToSha PhyloWithCliques config) <> ".json"
 259             let phyloWithLinksFile   =  (outputPath config) <> "phyloWithLinks_"   <> (configToSha PhyloWithLinks   config) <> ".json"
 260
 261             phyloWithCliquesExists <- doesFileExist phyloWithCliquesFile
 262             phyloWithLinksExists   <- doesFileExist phyloWithLinksFile
 263
 264             -- phyloStep <- if phyloWithCliquesExists
 265             --                   then do
 266             --                     printIOMsg "Reconstruct the phylo step from an existing file"
 267             --                     readPhylo phyloWithCliquesFile
 268             --                   else do
 269             --                     printIOMsg "Reconstruct the phylo step from scratch"
 270             --                     pure $ toPhyloStep corpus mapList config
 271
 272             -- writePhylo phyloWithCliquesFile phyloStep
 273
 274             -- let phylo = toPhylo (setConfig config phyloStep)
 275
 276             phyloWithLinks <- if phyloWithLinksExists
 277                                   then do
 278                                     printIOMsg "Reconstruct the phylo from an existing file with intertemporal links"
 279                                     readPhylo phyloWithLinksFile
 280                                   else do
 281                                     if phyloWithCliquesExists
 282                                       then do
 283                                         printIOMsg "Reconstruct the phylo from an existing file with cliques"
 284                                         phyloWithCliques <- readPhylo phyloWithCliquesFile
 285                                         writePhylo phyloWithCliquesFile phyloWithCliques
 286                                         pure $ toPhylo (setConfig config phyloWithCliques)
 287                                       else do
 288                                         printIOMsg "Reconstruct the phylo from scratch"
 289                                         phyloWithCliques <- pure $ toPhyloStep corpus mapList config
 290                                         writePhylo phyloWithCliquesFile phyloWithCliques
 291                                         pure $ toPhylo (setConfig config phyloWithCliques)
 292
 293             writePhylo phyloWithLinksFile phyloWithLinks
 294
 295
 296             -- probes
 297
 298             -- writeFile ((outputPath config) <> (unpack $ phyloName config) <> "_synchronic_distance_cumu_jaccard.txt")
 299             --          $ synchronicDistance' phylo 1
 300
 301             -- writeFile ((outputPath config) <> (unpack $ phyloName config) <> "_inflexion_points.txt")
 302             --         $ inflexionPoints phylo 1
 303
 304             printIOMsg "End of reconstruction, start the export"
 305
 306             let dot = toPhyloExport (setConfig config phyloWithLinks)
 307
 308             let output = configToLabel config
 309
 310             dotToFile output dot