src/Gargantext/Viz/AdaptativePhylo.hs

   1 {-|
   2 Module      : Gargantext.Viz.AdaptativePhylo
   3 Description : Phylomemy definitions and types.
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 Specifications of Phylomemy export format.
  11
  12 Phylomemy can be described as a Temporal Graph with different scale of
  13 granularity of group of ngrams (terms and multi-terms).
  14
  15 The main type is Phylo which is synonym of Phylomemy (only difference is
  16 the number of chars).
  17
  18 References:
  19 Chavalarias, D., Cointet, J.-P., 2013. Phylomemetic patterns
  20 in science evolution — the rise and fall of scientific fields. PloS
  21 one 8, e54847.
  22 -}
  23
  24 {-# LANGUAGE DeriveGeneric, DeriveAnyClass #-}
  25 {-# LANGUAGE NoImplicitPrelude #-}
  26 {-# LANGUAGE TemplateHaskell   #-}
  27 {-# LANGUAGE MultiParamTypeClasses #-}
  28
  29 module Gargantext.Viz.AdaptativePhylo where
  30
  31 import Data.Aeson
  32 import Data.Aeson.TH (deriveJSON)
  33 import Data.Text   (Text, pack)
  34 import Data.Vector (Vector)
  35 import Data.Map (Map)
  36 import Data.Set (Set)
  37
  38 import Gargantext.Core.Utils.Prefix (unPrefix)
  39 import Gargantext.Prelude
  40 import Gargantext.Text.Context (TermList)
  41
  42 import GHC.Generics
  43 import GHC.IO (FilePath)
  44 import Control.DeepSeq (NFData)
  45 import Control.Lens (makeLenses)
  46
  47 import qualified Data.Text.Lazy as TextLazy
  48
  49
  50 ----------------
  51 -- | Config | --
  52 ----------------
  53
  54
  55 data CorpusParser =
  56       Wos {_wos_limit :: Int}
  57     | Csv {_csv_limit :: Int}
  58     deriving (Show,Generic,Eq)
  59
  60
  61 data Proximity =
  62       WeightedLogJaccard
  63       { _wlj_sensibility   :: Double
  64       , _wlj_thresholdInit :: Double
  65       , _wlj_thresholdStep :: Double }
  66     | Hamming
  67     deriving (Show,Generic,Eq)
  68
  69
  70 data Synchrony =
  71       ByProximityThreshold
  72       { _bpt_threshold :: Double
  73       , _bpt_sensibility :: Double}
  74     | ByProximityDistribution
  75       { _bpd_sensibility :: Double}
  76     deriving (Show,Generic,Eq)
  77
  78
  79 data TimeUnit =
  80       Year
  81       { _year_period :: Int
  82       , _year_step   :: Int
  83       , _year_matchingFrame :: Int }
  84       deriving (Show,Generic,Eq)
  85
  86
  87 data ContextualUnit =
  88       Fis
  89       { _fis_support :: Int
  90       , _fis_size    :: Int }
  91     | MaxClique
  92       { _clique_size :: Int }
  93       deriving (Show,Generic,Eq)
  94
  95
  96 data Quality =
  97      Quality { _qua_granularity :: Double
  98              , _qua_minBranch   :: Int }
  99       deriving (Show,Generic,Eq)
 100
 101
 102 data Config =
 103      Config { corpusPath     :: FilePath
 104             , listPath       :: FilePath
 105             , outputPath     :: FilePath
 106             , corpusParser   :: CorpusParser
 107             , phyloName      :: Text
 108             , phyloLevel     :: Int
 109             , phyloProximity :: Proximity
 110             , phyloSynchrony :: Synchrony
 111             , phyloQuality   :: Quality
 112             , timeUnit       :: TimeUnit
 113             , contextualUnit :: ContextualUnit
 114             , exportLabel    :: [PhyloLabel]
 115             , exportSort     :: Sort
 116             , exportFilter   :: [Filter]
 117             } deriving (Show,Generic,Eq)
 118
 119
 120 defaultConfig :: Config
 121 defaultConfig =
 122      Config { corpusPath     = ""
 123             , listPath       = ""
 124             , outputPath     = ""
 125             , corpusParser   = Csv 1000
 126             , phyloName      = pack "Default Phylo"
 127             , phyloLevel     = 2
 128             , phyloProximity = WeightedLogJaccard 10 0 0.1
 129             , phyloSynchrony = ByProximityDistribution 0
 130             , phyloQuality   = Quality 0.5 1
 131             , timeUnit       = Year 3 1 5
 132             , contextualUnit = Fis 1 5
 133             , exportLabel    = [BranchLabel MostInclusive 2, GroupLabel MostEmergentInclusive 2]
 134             , exportSort     = ByHierarchy
 135             , exportFilter   = [ByBranchSize 2]
 136             }
 137
 138 instance FromJSON Config
 139 instance ToJSON Config
 140 instance FromJSON CorpusParser
 141 instance ToJSON CorpusParser
 142 instance FromJSON Proximity
 143 instance ToJSON Proximity
 144 instance FromJSON TimeUnit
 145 instance ToJSON TimeUnit
 146 instance FromJSON ContextualUnit
 147 instance ToJSON ContextualUnit
 148 instance FromJSON PhyloLabel
 149 instance ToJSON PhyloLabel
 150 instance FromJSON Tagger
 151 instance ToJSON Tagger
 152 instance FromJSON Sort
 153 instance ToJSON Sort
 154 instance FromJSON Order
 155 instance ToJSON Order
 156 instance FromJSON Filter
 157 instance ToJSON Filter
 158 instance FromJSON Synchrony
 159 instance ToJSON Synchrony
 160 instance FromJSON Quality
 161 instance ToJSON Quality
 162
 163
 164 -- | Software parameters
 165 data Software =
 166      Software { _software_name    :: Text
 167               , _software_version :: Text
 168      } deriving (Generic, Show, Eq)
 169
 170 defaultSoftware :: Software
 171 defaultSoftware =
 172       Software { _software_name    = pack "Gargantext"
 173                , _software_version = pack "v4" }
 174
 175
 176 -- | Global parameters of a Phylo
 177 data PhyloParam =
 178      PhyloParam { _phyloParam_version  :: Text
 179                 , _phyloParam_software :: Software
 180                 , _phyloParam_config   :: Config
 181      } deriving (Generic, Show, Eq)
 182
 183 defaultPhyloParam :: PhyloParam
 184 defaultPhyloParam =
 185       PhyloParam { _phyloParam_version  = pack "v2.adaptative"
 186                  , _phyloParam_software = defaultSoftware
 187                  , _phyloParam_config   = defaultConfig }
 188
 189
 190 ------------------
 191 -- | Document | --
 192 ------------------
 193
 194
 195 -- | Date : a simple Integer
 196 type Date = Int
 197
 198 -- | Ngrams : a contiguous sequence of n terms
 199 type Ngrams = Text
 200
 201 -- | Document : a piece of Text linked to a Date
 202 data Document = Document
 203       { date :: Date
 204       , text :: [Ngrams]
 205       } deriving (Eq,Show,Generic,NFData)
 206
 207
 208 --------------------
 209 -- | Foundation | --
 210 --------------------
 211
 212
 213 -- | The Foundations of a Phylo created from a given TermList
 214 data PhyloFoundations = PhyloFoundations
 215       { _foundations_roots   :: !(Vector Ngrams)
 216       , _foundations_mapList :: TermList
 217       } deriving (Generic, Show, Eq)
 218
 219
 220 ---------------------------
 221 -- | Coocurency Matrix | --
 222 ---------------------------
 223
 224
 225 -- | Cooc : a coocurency matrix between two ngrams
 226 type Cooc =  Map (Int,Int) Double
 227
 228
 229 -------------------
 230 -- | Phylomemy | --
 231 -------------------
 232
 233
 234 -- | Phylo datatype of a phylomemy
 235 --  foundations : the foundations of the phylo
 236 --  timeCooc : a Map of coocurency by minimal unit of time (ex: by year)
 237 --  timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year)
 238 --  param : the parameters of the phylomemy (with the user's configuration)
 239 --  periods : the temporal steps of a phylomemy
 240 data Phylo =
 241      Phylo { _phylo_foundations :: PhyloFoundations
 242            , _phylo_timeCooc    :: !(Map Date Cooc)
 243            , _phylo_timeDocs    :: !(Map Date Double)
 244            , _phylo_termFreq    :: !(Map Int Double)
 245            , _phylo_param       :: PhyloParam
 246            , _phylo_periods     :: Map PhyloPeriodId PhyloPeriod
 247            }
 248            deriving (Generic, Show, Eq)
 249
 250
 251 -- | PhyloPeriodId : the id of a given period
 252 type PhyloPeriodId = (Date,Date)
 253
 254 -- | PhyloPeriod : steps of a phylomemy on a temporal axis
 255 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 256 --  levels: levels of granularity
 257 data PhyloPeriod =
 258      PhyloPeriod { _phylo_periodPeriod :: (Date,Date)
 259                  , _phylo_periodLevels :: Map PhyloLevelId PhyloLevel
 260                  } deriving (Generic, Show, Eq)
 261
 262
 263 -- | Level : a level of clustering
 264 type Level = Int
 265
 266 -- | PhyloLevelId : the id of a level of clustering in a given period
 267 type PhyloLevelId  = (PhyloPeriodId,Level)
 268
 269 -- | PhyloLevel : levels of phylomemy on a synchronic axis
 270 -- Levels description:
 271 -- Level 0: The foundations and the base of the phylo
 272 -- Level 1: First level of clustering (the Fis)
 273 -- Level [2..N]: Nth level of synchronic clustering (cluster of Fis)
 274 data PhyloLevel =
 275      PhyloLevel { _phylo_levelPeriod :: (Date,Date)
 276                 , _phylo_levelLevel  :: Level
 277                 , _phylo_levelGroups :: Map PhyloGroupId PhyloGroup
 278                 }
 279                 deriving (Generic, Show, Eq)
 280
 281
 282 type PhyloGroupId  = (PhyloLevelId, Int)
 283
 284 -- | BranchId : (a level, a sequence of branch index)
 285 -- the sequence is a path of heritage from the most to the less specific branch
 286 type PhyloBranchId = (Level, [Int])
 287
 288 -- | PhyloGroup : group of ngrams at each level and period
 289 data PhyloGroup =
 290       PhyloGroup { _phylo_groupPeriod   :: (Date,Date)
 291                  , _phylo_groupLevel    :: Level
 292                  , _phylo_groupIndex    :: Int
 293                  , _phylo_groupLabel    :: Text
 294                  , _phylo_groupSupport  :: Support
 295                  , _phylo_groupNgrams   :: [Int]
 296                  , _phylo_groupCooc     :: !(Cooc)
 297                  , _phylo_groupBranchId :: PhyloBranchId
 298                  , _phylo_groupMeta     :: Map Text [Double]
 299                  , _phylo_groupLevelParents  :: [Pointer]
 300                  , _phylo_groupLevelChilds   :: [Pointer]
 301                  , _phylo_groupPeriodParents :: [Pointer]
 302                  , _phylo_groupPeriodChilds  :: [Pointer]
 303                  }
 304                  deriving (Generic, Show, Eq, NFData)
 305
 306 -- | Weight : A generic mesure that can be associated with an Id
 307 type Weight = Double
 308
 309 -- | Pointer : A weighted pointer to a given PhyloGroup
 310 type Pointer = (PhyloGroupId, Weight)
 311
 312 data Filiation = ToParents | ToChilds deriving (Generic, Show)
 313 data PointerType = TemporalPointer | LevelPointer deriving (Generic, Show)
 314
 315
 316 ---------------------------
 317 -- | Frequent Item Set | --
 318 ---------------------------
 319
 320 -- | Support : Number of Documents where a Clique occurs
 321 type Support  = Int
 322
 323 data PhyloCUnit = PhyloCUnit
 324   { _phyloCUnit_nodes   :: Set Ngrams
 325   , _phyloCUnit_support :: Support
 326   , _phyloCUnit_period  :: (Date,Date)
 327   } deriving (Generic,NFData,Show,Eq)
 328
 329
 330 ----------------
 331 -- | Export | --
 332 ----------------
 333
 334 type DotId = TextLazy.Text
 335
 336 data EdgeType = GroupToGroup | BranchToGroup | BranchToBranch | PeriodToPeriod deriving (Show,Generic,Eq)
 337
 338 data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 339
 340 data Order = Asc | Desc deriving (Show,Generic,Eq)
 341
 342 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy deriving (Show,Generic,Eq)
 343
 344 data Tagger = MostInclusive | MostEmergentInclusive deriving (Show,Generic,Eq)
 345
 346 data PhyloLabel =
 347       BranchLabel
 348       { _branch_labelTagger :: Tagger
 349       , _branch_labelSize   :: Int }
 350     | GroupLabel
 351       { _group_labelTagger  :: Tagger
 352       , _group_labelSize    :: Int }
 353     deriving (Show,Generic,Eq)
 354
 355 data PhyloBranch =
 356       PhyloBranch
 357       { _branch_id :: PhyloBranchId
 358       , _branch_label   :: Text
 359       , _branch_meta    :: Map Text [Double]
 360       } deriving (Generic, Show)
 361
 362 data PhyloExport =
 363       PhyloExport
 364       { _export_groups   :: [PhyloGroup]
 365       , _export_branches :: [PhyloBranch]
 366       } deriving (Generic, Show)
 367
 368 ----------------
 369 -- | Lenses | --
 370 ----------------
 371
 372 makeLenses ''Config
 373 makeLenses ''Proximity
 374 makeLenses ''Quality
 375 makeLenses ''ContextualUnit
 376 makeLenses ''PhyloLabel
 377 makeLenses ''TimeUnit
 378 makeLenses ''PhyloFoundations
 379 makeLenses ''PhyloCUnit
 380 makeLenses ''Phylo
 381 makeLenses ''PhyloPeriod
 382 makeLenses ''PhyloLevel
 383 makeLenses ''PhyloGroup
 384 makeLenses ''PhyloParam
 385 makeLenses ''PhyloExport
 386 makeLenses ''PhyloBranch
 387
 388 ------------------------
 389 -- | JSON instances | --
 390 ------------------------
 391
 392
 393 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)