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       deriving (Show,Generic,Eq)
  92
  93
  94 data Quality =
  95      Quality { _qua_relevance :: Double
  96              , _qua_minBranch :: Int }
  97       deriving (Show,Generic,Eq)
  98
  99
 100 data Config =
 101      Config { corpusPath     :: FilePath
 102             , listPath       :: FilePath
 103             , outputPath     :: FilePath
 104             , corpusParser   :: CorpusParser
 105             , phyloName      :: Text
 106             , phyloLevel     :: Int
 107             , phyloProximity :: Proximity
 108             , phyloSynchrony :: Synchrony
 109             , phyloQuality   :: Quality
 110             , timeUnit       :: TimeUnit
 111             , contextualUnit :: ContextualUnit
 112             , exportLabel    :: [PhyloLabel]
 113             , exportSort     :: Sort
 114             , exportFilter   :: [Filter]
 115             } deriving (Show,Generic,Eq)
 116
 117
 118 defaultConfig :: Config
 119 defaultConfig =
 120      Config { corpusPath     = ""
 121             , listPath       = ""
 122             , outputPath     = ""
 123             , corpusParser   = Csv 1000
 124             , phyloName      = pack "Default Phylo"
 125             , phyloLevel     = 2
 126             , phyloProximity = WeightedLogJaccard 10 0 0.1
 127             , phyloSynchrony = ByProximityDistribution 0
 128             , phyloQuality   = Quality 0.5 3
 129             , timeUnit       = Year 3 1 5
 130             , contextualUnit = Fis 1 5
 131             , exportLabel    = [BranchLabel MostInclusive 2, GroupLabel MostEmergentInclusive 2]
 132             , exportSort     = ByHierarchy
 133             , exportFilter   = [ByBranchSize 2]
 134             }
 135
 136 instance FromJSON Config
 137 instance ToJSON Config
 138 instance FromJSON CorpusParser
 139 instance ToJSON CorpusParser
 140 instance FromJSON Proximity
 141 instance ToJSON Proximity
 142 instance FromJSON TimeUnit
 143 instance ToJSON TimeUnit
 144 instance FromJSON ContextualUnit
 145 instance ToJSON ContextualUnit
 146 instance FromJSON PhyloLabel
 147 instance ToJSON PhyloLabel
 148 instance FromJSON Tagger
 149 instance ToJSON Tagger
 150 instance FromJSON Sort
 151 instance ToJSON Sort
 152 instance FromJSON Order
 153 instance ToJSON Order
 154 instance FromJSON Filter
 155 instance ToJSON Filter
 156 instance FromJSON Synchrony
 157 instance ToJSON Synchrony
 158 instance FromJSON Quality
 159 instance ToJSON Quality
 160
 161
 162 -- | Software parameters
 163 data Software =
 164      Software { _software_name    :: Text
 165               , _software_version :: Text
 166      } deriving (Generic, Show, Eq)
 167
 168 defaultSoftware :: Software
 169 defaultSoftware =
 170       Software { _software_name    = pack "Gargantext"
 171                , _software_version = pack "v4" }
 172
 173
 174 -- | Global parameters of a Phylo
 175 data PhyloParam =
 176      PhyloParam { _phyloParam_version  :: Text
 177                 , _phyloParam_software :: Software
 178                 , _phyloParam_config   :: Config
 179      } deriving (Generic, Show, Eq)
 180
 181 defaultPhyloParam :: PhyloParam
 182 defaultPhyloParam =
 183       PhyloParam { _phyloParam_version  = pack "v2.adaptative"
 184                  , _phyloParam_software = defaultSoftware
 185                  , _phyloParam_config   = defaultConfig }
 186
 187
 188 ------------------
 189 -- | Document | --
 190 ------------------
 191
 192
 193 -- | Date : a simple Integer
 194 type Date = Int
 195
 196 -- | Ngrams : a contiguous sequence of n terms
 197 type Ngrams = Text
 198
 199 -- | Document : a piece of Text linked to a Date
 200 data Document = Document
 201       { date :: Date
 202       , text :: [Ngrams]
 203       } deriving (Eq,Show,Generic,NFData)
 204
 205
 206 --------------------
 207 -- | Foundation | --
 208 --------------------
 209
 210
 211 -- | The Foundations of a Phylo created from a given TermList
 212 data PhyloFoundations = PhyloFoundations
 213       { _foundations_roots   :: !(Vector Ngrams)
 214       , _foundations_mapList :: TermList
 215       } deriving (Generic, Show, Eq)
 216
 217
 218 ---------------------------
 219 -- | Coocurency Matrix | --
 220 ---------------------------
 221
 222
 223 -- | Cooc : a coocurency matrix between two ngrams
 224 type Cooc =  Map (Int,Int) Double
 225
 226
 227 -------------------
 228 -- | Phylomemy | --
 229 -------------------
 230
 231
 232 -- | Phylo datatype of a phylomemy
 233 --  foundations : the foundations of the phylo
 234 --  timeCooc : a Map of coocurency by minimal unit of time (ex: by year)
 235 --  timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year)
 236 --  param : the parameters of the phylomemy (with the user's configuration)
 237 --  periods : the temporal steps of a phylomemy
 238 data Phylo =
 239      Phylo { _phylo_foundations :: PhyloFoundations
 240            , _phylo_timeCooc    :: !(Map Date Cooc)
 241            , _phylo_timeDocs    :: !(Map Date Double)
 242            , _phylo_param       :: PhyloParam
 243            , _phylo_periods     :: Map PhyloPeriodId PhyloPeriod
 244            }
 245            deriving (Generic, Show, Eq)
 246
 247
 248 -- | PhyloPeriodId : the id of a given period
 249 type PhyloPeriodId = (Date,Date)
 250
 251 -- | PhyloPeriod : steps of a phylomemy on a temporal axis
 252 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 253 --  levels: levels of granularity
 254 data PhyloPeriod =
 255      PhyloPeriod { _phylo_periodPeriod :: (Date,Date)
 256                  , _phylo_periodLevels :: Map PhyloLevelId PhyloLevel
 257                  } deriving (Generic, Show, Eq)
 258
 259
 260 -- | Level : a level of clustering
 261 type Level = Int
 262
 263 -- | PhyloLevelId : the id of a level of clustering in a given period
 264 type PhyloLevelId  = (PhyloPeriodId,Level)
 265
 266 -- | PhyloLevel : levels of phylomemy on a synchronic axis
 267 -- Levels description:
 268 -- Level 0: The foundations and the base of the phylo
 269 -- Level 1: First level of clustering (the Fis)
 270 -- Level [2..N]: Nth level of synchronic clustering (cluster of Fis)
 271 data PhyloLevel =
 272      PhyloLevel { _phylo_levelPeriod :: (Date,Date)
 273                 , _phylo_levelLevel  :: Level
 274                 , _phylo_levelGroups :: Map PhyloGroupId PhyloGroup
 275                 }
 276                 deriving (Generic, Show, Eq)
 277
 278
 279 type PhyloGroupId  = (PhyloLevelId, Int)
 280
 281 -- | BranchId : (a level, a sequence of branch index)
 282 -- the sequence is a path of heritage from the most to the less specific branch
 283 type PhyloBranchId = (Level, [Int])
 284
 285 -- | PhyloGroup : group of ngrams at each level and period
 286 data PhyloGroup =
 287       PhyloGroup { _phylo_groupPeriod   :: (Date,Date)
 288                  , _phylo_groupLevel    :: Level
 289                  , _phylo_groupIndex    :: Int
 290                  , _phylo_groupLabel    :: Text
 291                  , _phylo_groupSupport  :: Support
 292                  , _phylo_groupNgrams   :: [Int]
 293                  , _phylo_groupCooc     :: !(Cooc)
 294                  , _phylo_groupBranchId :: PhyloBranchId
 295                  , _phylo_groupMeta     :: Map Text [Double]
 296                  , _phylo_groupLevelParents  :: [Pointer]
 297                  , _phylo_groupLevelChilds   :: [Pointer]
 298                  , _phylo_groupPeriodParents :: [Pointer]
 299                  , _phylo_groupPeriodChilds  :: [Pointer]
 300                  }
 301                  deriving (Generic, Show, Eq, NFData)
 302
 303 -- | Weight : A generic mesure that can be associated with an Id
 304 type Weight = Double
 305
 306 -- | Pointer : A weighted pointer to a given PhyloGroup
 307 type Pointer = (PhyloGroupId, Weight)
 308
 309 data Filiation = ToParents | ToChilds deriving (Generic, Show)
 310 data PointerType = TemporalPointer | LevelPointer deriving (Generic, Show)
 311
 312
 313 ---------------------------
 314 -- | Frequent Item Set | --
 315 ---------------------------
 316
 317 -- | Clique : Set of ngrams cooccurring in the same Document
 318 type Clique   = Set Ngrams
 319
 320 -- | Support : Number of Documents where a Clique occurs
 321 type Support  = Int
 322
 323 -- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
 324 data PhyloFis = PhyloFis
 325   { _phyloFis_clique  :: Clique
 326   , _phyloFis_support :: Support
 327   , _phyloFis_period  :: (Date,Date)
 328   } deriving (Generic,NFData,Show,Eq)
 329
 330
 331 ----------------
 332 -- | Export | --
 333 ----------------
 334
 335 type DotId = TextLazy.Text
 336
 337 data EdgeType = GroupToGroup | BranchToGroup | BranchToBranch | PeriodToPeriod deriving (Show,Generic,Eq)
 338
 339 data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 340
 341 data Order = Asc | Desc deriving (Show,Generic,Eq)
 342
 343 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy deriving (Show,Generic,Eq)
 344
 345 data Tagger = MostInclusive | MostEmergentInclusive deriving (Show,Generic,Eq)
 346
 347 data PhyloLabel =
 348       BranchLabel
 349       { _branch_labelTagger :: Tagger
 350       , _branch_labelSize   :: Int }
 351     | GroupLabel
 352       { _group_labelTagger  :: Tagger
 353       , _group_labelSize    :: Int }
 354     deriving (Show,Generic,Eq)
 355
 356 data PhyloBranch =
 357       PhyloBranch
 358       { _branch_id :: PhyloBranchId
 359       , _branch_label   :: Text
 360       , _branch_meta    :: Map Text [Double]
 361       } deriving (Generic, Show)
 362
 363 data PhyloExport =
 364       PhyloExport
 365       { _export_groups   :: [PhyloGroup]
 366       , _export_branches :: [PhyloBranch]
 367       } deriving (Generic, Show)
 368
 369 ----------------
 370 -- | Lenses | --
 371 ----------------
 372
 373 makeLenses ''Config
 374 makeLenses ''Proximity
 375 makeLenses ''Quality
 376 makeLenses ''ContextualUnit
 377 makeLenses ''PhyloLabel
 378 makeLenses ''TimeUnit
 379 makeLenses ''PhyloFoundations
 380 makeLenses ''PhyloFis
 381 makeLenses ''Phylo
 382 makeLenses ''PhyloPeriod
 383 makeLenses ''PhyloLevel
 384 makeLenses ''PhyloGroup
 385 makeLenses ''PhyloParam
 386 makeLenses ''PhyloExport
 387 makeLenses ''PhyloBranch
 388
 389 ------------------------
 390 -- | JSON instances | --
 391 ------------------------
 392
 393
 394 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)