src/Gargantext/Viz/Phylo.hs

   1 {-|
   2 Module      : Gargantext.Viz.Phylo
   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 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
  25 {-# LANGUAGE DeriveGeneric     #-}
  26 {-# LANGUAGE NoImplicitPrelude #-}
  27 {-# LANGUAGE TemplateHaskell   #-}
  28
  29 module Gargantext.Viz.Phylo where
  30
  31 import Control.Lens (makeLenses)
  32 import Data.Aeson.TH (deriveJSON)
  33 import Data.Maybe   (Maybe)
  34 import Data.Text    (Text)
  35 import Data.Time.Clock.POSIX  (POSIXTime)
  36 import GHC.Generics (Generic)
  37 import Gargantext.Database.Schema.Ngrams (NgramsId)
  38 import Gargantext.Core.Utils.Prefix (unPrefix)
  39 import Gargantext.Prelude
  40
  41 ------------------------------------------------------------------------
  42 data PhyloFormat =
  43      PhyloFormat { _phyloFormat_parm :: PhyloParam
  44                  , _phyloFormat_data :: Phylo
  45      } deriving (Generic)
  46
  47 -- | .phylo parameters
  48 data PhyloParam =
  49      PhyloParam { _phyloParam_version     :: Text -- Double ?
  50                 , _phyloParam_software    :: Software
  51                 , _phyloParam_params      :: Hash
  52      } deriving (Generic)
  53
  54 type Hash = Text
  55
  56 -- | Software
  57 -- TODO move somewhere since it is generic
  58 data Software =
  59      Software { _software_name    :: Text
  60               , _software_version :: Text
  61      } deriving (Generic)
  62
  63 ------------------------------------------------------------------------
  64 -- | Phylo datatype descriptor of a phylomemy
  65 -- Duration : time Segment of the whole phylomemy (start,end)
  66 -- Ngrams   : list of all (possible) terms contained in the phylomemy (with their id)
  67 -- Steps    : list of all steps to build the phylomemy
  68 data Phylo =
  69      Phylo { _phylo_puration :: (Start, End)
  70            , _phylo_ngrams   :: [Ngram]
  71            , _phylo_periods  :: [PhyloPeriod]
  72            }
  73            deriving (Generic)
  74
  75 -- | UTCTime in seconds since UNIX epoch
  76 type Start   = POSIXTime
  77 type End     = POSIXTime
  78
  79 -- | Indexed Ngram
  80 type Ngram   = (NgramsId, Text)
  81
  82 -- | PhyloStep : steps of phylomemy on temporal axis
  83 -- Period: tuple (start date, end date) of the step of the phylomemy
  84 -- Levels: levels of granularity
  85 data PhyloPeriod =
  86      PhyloPeriod { _phylo_periodId     :: PhyloPeriodId
  87                  , _phylo_periodLevels :: [PhyloLevel]
  88                  }
  89                  deriving (Generic)
  90
  91 type PhyloPeriodId = (Start, End)
  92
  93 -- | PhyloLevel : levels of phylomemy on level axis
  94 -- Levels description:
  95 -- Level -1: Ngram equals itself         (by identity) == _phylo_Ngrams
  96 -- Level  0: Group of synonyms           (by stems + by qualitative expert meaning)
  97 -- Level  1: First level of clustering
  98 -- Level  N: Nth   level of clustering
  99 data PhyloLevel =
 100      PhyloLevel { _phylo_levelId     :: PhyloLevelId
 101                 , _phylo_levelGroups :: [PhyloGroup]
 102                 }
 103                 deriving (Generic)
 104
 105 type PhyloLevelId = (PhyloPeriodId, Int)
 106
 107 -- | PhyloGroup : group of ngrams at each level and step
 108 -- Label : maybe has a label as text
 109 -- Ngrams: set of terms that build the group
 110 -- Period Parents|Childs: weighted link to Parents|Childs (Temporal Period   axis)
 111 -- Level  Parents|Childs: weighted link to Parents|Childs (Level Granularity axis)
 112 data PhyloGroup =
 113      PhyloGroup { _phylo_groupId    :: PhyloGroupId
 114                 , _phylo_groupLabel :: Maybe Text
 115                 , _phylo_groupNgrams        :: [NgramsId]
 116
 117                 , _phylo_groupPeriodParents :: [Edge]
 118                 , _phylo_groupPeriodChilds  :: [Edge]
 119
 120                 , _phylo_groupLevelParents  :: [Edge]
 121                 , _phylo_groupLevelChilds   :: [Edge]
 122                 }
 123                 deriving (Generic)
 124
 125 type PhyloGroupId = (PhyloLevelId, Int)
 126 type Edge         = (PhyloGroupId, Weight)
 127 type Weight       = Double
 128
 129 -- | Lenses
 130 makeLenses ''Phylo
 131 makeLenses ''PhyloParam
 132 makeLenses ''PhyloFormat
 133 makeLenses ''Software
 134
 135 -- | JSON instances
 136 $(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       )
 137 $(deriveJSON (unPrefix "_phylo_period" ) ''PhyloPeriod )
 138 $(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
 139 $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
 140 --
 141 $(deriveJSON (unPrefix "_software_"  ) ''Software )
 142 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
 143 $(deriveJSON (unPrefix "_phyloFormat_" ) ''PhyloFormat  )
 144
 145 -- | TODO XML instances
 146