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 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
  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.Set     (Set)
  36 import Data.Map     (Map)
  37 import Data.Vector  (Vector)
  38 import Data.Time.Clock.POSIX  (POSIXTime)
  39 import GHC.Generics (Generic)
  40 import Gargantext.Database.Schema.Ngrams (NgramsId)
  41 import Gargantext.Core.Utils.Prefix (unPrefix)
  42 import Gargantext.Prelude
  43
  44 ------------------------------------------------------------------------
  45 data PhyloExport =
  46      PhyloExport { _phyloExport_param :: PhyloParam
  47                  , _phyloExport_data :: Phylo
  48      } deriving (Generic)
  49
  50 -- | .phylo parameters
  51 data PhyloParam =
  52      PhyloParam { _phyloParam_version     :: Text -- Double ?
  53                 , _phyloParam_software    :: Software
  54                 , _phyloParam_params      :: Hash
  55      } deriving (Generic)
  56
  57 type Hash = Text
  58
  59 -- | Software
  60 -- TODO move somewhere since it is generic
  61 data Software =
  62      Software { _software_name    :: Text
  63               , _software_version :: Text
  64      } deriving (Generic)
  65
  66 ------------------------------------------------------------------------
  67 -- | Phylo datatype descriptor of a phylomemy
  68 -- Duration : time Segment of the whole phylomemy (start,end)
  69 -- Ngrams   : list of all (possible) terms contained in the phylomemy (with their id)
  70 -- Steps    : list of all steps to build the phylomemy
  71 data Phylo =
  72      Phylo { _phylo_duration :: (Start, End)
  73            , _phylo_ngrams   :: PhyloNgrams
  74            , _phylo_periods  :: [PhyloPeriod]
  75            }
  76            deriving (Generic, Show)
  77
  78
  79 -- | Date : a simple Integer
  80 type Date = Int
  81
  82 -- | UTCTime in seconds since UNIX epoch
  83 -- type Start   = POSIXTime
  84 -- type End     = POSIXTime
  85 type Start   = Date
  86 type End     = Date
  87
  88 -- | PhyloStep : steps of phylomemy on temporal axis
  89 -- Period: tuple (start date, end date) of the step of the phylomemy
  90 -- Levels: levels of granularity
  91 data PhyloPeriod =
  92      PhyloPeriod { _phylo_periodId     :: PhyloPeriodId
  93                  , _phylo_periodLevels :: [PhyloLevel]
  94                  }
  95                  deriving (Generic, Show)
  96
  97 type PhyloPeriodId = (Start, End)
  98
  99 -- | PhyloLevel : levels of phylomemy on level axis
 100 -- Levels description:
 101 -- Level -1: Ngram equals itself         (by identity) == _phylo_Ngrams
 102 -- Level  0: Group of synonyms           (by stems + by qualitative expert meaning)
 103 -- Level  1: First level of clustering
 104 -- Level  N: Nth   level of clustering
 105 data PhyloLevel =
 106      PhyloLevel { _phylo_levelId     :: PhyloLevelId
 107                 , _phylo_levelGroups :: [PhyloGroup]
 108                 }
 109                 deriving (Generic, Show)
 110
 111 type PhyloLevelId = (PhyloPeriodId, Int)
 112
 113 -- | PhyloGroup : group of ngrams at each level and step
 114 -- Label : maybe has a label as text
 115 -- Ngrams: set of terms that build the group
 116 -- Quality : map of measures (support, etc.) that depict some qualitative aspects of a phylo
 117 -- Period Parents|Childs: weighted link to Parents|Childs (Temporal Period   axis)
 118 -- Level  Parents|Childs: weighted link to Parents|Childs (Level Granularity axis)
 119 -- Pointers are directed link from Self to any PhyloGroup (/= Self ?)
 120 data PhyloGroup =
 121      PhyloGroup { _phylo_groupId            :: PhyloGroupId
 122                 , _phylo_groupLabel         :: Text
 123                 , _phylo_groupNgrams        :: [Int]
 124                 , _phylo_groupQuality       :: Map Text Double
 125
 126                 , _phylo_groupPeriodParents :: [Pointer]
 127                 , _phylo_groupPeriodChilds  :: [Pointer]
 128
 129                 , _phylo_groupLevelParents  :: [Pointer]
 130                 , _phylo_groupLevelChilds   :: [Pointer]
 131                 }
 132                 deriving (Generic, Show, Eq)
 133
 134 type PhyloGroupId = (PhyloLevelId, Int)
 135 type Pointer      = (PhyloGroupId, Weight)
 136 type Weight       = Double
 137
 138
 139
 140 -- | Ngrams : a contiguous sequence of n terms
 141 type Ngrams = Text
 142 -- | PhyloNgrams : Vector of all the Ngrams (PhyloGroup of level -1) used within a Phylo
 143 type PhyloNgrams = Vector Ngrams
 144
 145
 146 -- | Clique : Set of ngrams cooccurring in the same Document
 147 type Clique  = Set Ngrams
 148 -- | Support : Number of Documents where a Clique occurs
 149 type Support = Int
 150 -- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
 151 type Fis = Map Clique Support
 152
 153
 154 -- | Lenses
 155 makeLenses ''Phylo
 156 makeLenses ''PhyloParam
 157 makeLenses ''PhyloExport
 158 makeLenses ''Software
 159 makeLenses ''PhyloGroup
 160 makeLenses ''PhyloLevel
 161 makeLenses ''PhyloPeriod
 162
 163 -- | JSON instances
 164 $(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       )
 165 $(deriveJSON (unPrefix "_phylo_period" ) ''PhyloPeriod )
 166 $(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
 167 $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
 168 --
 169 $(deriveJSON (unPrefix "_software_"    ) ''Software    )
 170 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
 171 $(deriveJSON (unPrefix "_phyloExport_" ) ''PhyloExport )
 172
 173 -- | TODO XML instances
 174