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 {-# LANGUAGE MultiParamTypeClasses #-}
  29
  30 module Gargantext.Viz.Phylo where
  31
  32 import Control.Lens (makeLenses)
  33 import Data.Aeson.TH (deriveJSON)
  34 import Data.Maybe   (Maybe)
  35 import Data.Text    (Text)
  36 import Data.Set     (Set)
  37 import Data.Map     (Map)
  38 import Data.Vector  (Vector)
  39 import Data.Time.Clock.POSIX  (POSIXTime)
  40 import GHC.Generics (Generic)
  41 import Gargantext.Database.Schema.Ngrams (NgramsId)
  42 import Gargantext.Core.Utils.Prefix (unPrefix)
  43 import Gargantext.Prelude
  44
  45 ------------------------------------------------------------------------
  46 data PhyloExport =
  47      PhyloExport { _phyloExport_param :: PhyloParam
  48                  , _phyloExport_data :: Phylo
  49      } deriving (Generic)
  50
  51 -- | .phylo parameters
  52 data PhyloParam =
  53      PhyloParam { _phyloParam_version     :: Text -- Double ?
  54                 , _phyloParam_software    :: Software
  55                 , _phyloParam_params      :: Hash
  56      } deriving (Generic)
  57
  58 type Hash = Text
  59
  60 -- | Software
  61 -- TODO move somewhere since it is generic
  62 data Software =
  63      Software { _software_name    :: Text
  64               , _software_version :: Text
  65      } deriving (Generic)
  66
  67 ------------------------------------------------------------------------
  68
  69 -- | Phylo datatype of a phylomemy
  70 -- Duration    : time Segment of the whole Phylo
  71 -- Foundations : vector of all the Ngrams contained in a Phylo (build from a list of actants)
  72 -- Periods     : list of all the periods of a Phylo
  73 data Phylo =
  74      Phylo { _phylo_duration    :: (Start, End)
  75            , _phylo_foundations :: Vector Ngrams
  76            , _phylo_periods     :: [PhyloPeriod]
  77            }
  78            deriving (Generic, Show)
  79
  80
  81 -- | Date : a simple Integer
  82 type Date = Int
  83
  84 -- | UTCTime in seconds since UNIX epoch
  85 -- type Start   = POSIXTime
  86 -- type End     = POSIXTime
  87 type Start   = Date
  88 type End     = Date
  89
  90 -- | PhyloStep : steps of phylomemy on temporal axis
  91 -- Period: tuple (start date, end date) of the step of the phylomemy
  92 -- Levels: levels of granularity
  93 data PhyloPeriod =
  94      PhyloPeriod { _phylo_periodId     :: PhyloPeriodId
  95                  , _phylo_periodLevels :: [PhyloLevel]
  96                  }
  97                  deriving (Generic, Show)
  98
  99
 100 -- | PhyloLevel : levels of phylomemy on level axis
 101 -- Levels description:
 102 -- Level -1: Ngram equals itself         (by identity) == _phylo_Ngrams
 103 -- Level  0: Group of synonyms           (by stems + by qualitative expert meaning)
 104 -- Level  1: First level of clustering
 105 -- Level  N: Nth   level of clustering
 106 data PhyloLevel =
 107      PhyloLevel { _phylo_levelId     :: PhyloLevelId
 108                 , _phylo_levelGroups :: [PhyloGroup]
 109                 }
 110                 deriving (Generic, Show)
 111
 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                 , _phylo_groupCooc          :: Map (Int, Int) Double
 126
 127                 , _phylo_groupPeriodParents :: [Pointer]
 128                 , _phylo_groupPeriodChilds  :: [Pointer]
 129
 130                 , _phylo_groupLevelParents  :: [Pointer]
 131                 , _phylo_groupLevelChilds   :: [Pointer]
 132                 }
 133                 deriving (Generic, Show, Eq, Ord)
 134
 135 data PhyloBranch =
 136      PhyloBranch { _phylo_branchId     :: (Level,Int)
 137                  , _phylo_branchLabel  :: Text
 138                  , _phylo_branchGroups :: [PhyloGroupId]
 139                  }
 140                  deriving (Generic, Show)
 141
 142
 143 -- | Level : A level of aggregation (-1 = Txt, 0 = Ngrams, 1 = Fis, [2..] = Cluster)
 144 type Level = Int
 145 -- | Index : A generic index of an element (PhyloGroup, PhyloBranch, etc) in a given List
 146 type Index = Int
 147
 148
 149 type PhyloPeriodId = (Start, End)
 150 type PhyloLevelId  = (PhyloPeriodId, Level)
 151 type PhyloGroupId  = (PhyloLevelId, Index)
 152 type PhyloBranchId = (Level, Index)
 153
 154
 155 -- | Weight : A generic mesure that can be associated with an Id
 156 type Weight = Double
 157 -- | Pointer : A weighted linked with a given PhyloGroup
 158 type Pointer = (PhyloGroupId, Weight)
 159 -- | Ngrams : a contiguous sequence of n terms
 160 type Ngrams = Text
 161
 162
 163 -- | Clique : Set of ngrams cooccurring in the same Document
 164 type Clique  = Set Ngrams
 165 -- | Support : Number of Documents where a Clique occurs
 166 type Support = Int
 167 -- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
 168 type Fis = (Clique,Support)
 169
 170
 171 -- | Document : a piece of Text linked to a Date
 172 data Document = Document
 173       { date :: Date
 174       , text :: Text
 175       } deriving (Show)
 176
 177
 178 type Cluster = [PhyloGroup]
 179
 180
 181 -- | A List of PhyloGroup in a PhyloGraph
 182 type PhyloNodes = [PhyloGroup]
 183 -- | A List of weighted links between some PhyloGroups in a PhyloGraph
 184 type PhyloEdges = [((PhyloGroup,PhyloGroup),Weight)]
 185 -- | The association as a Graph between a list of Nodes and a list of Edges
 186 type PhyloGraph = (PhyloNodes,PhyloEdges)
 187
 188
 189 data PhyloError = LevelDoesNotExist
 190                 | LevelUnassigned
 191           deriving (Show)
 192
 193
 194 -- | A List of Proximity mesures or strategies
 195 data Proximity  = WeightedLogJaccard | Hamming | FromPairs
 196 -- | A List of Clustering methods
 197 data Clustering  = Louvain | RelatedComponents
 198
 199 data PairTo = Childs | Parents
 200
 201 -- | Views type
 202
 203 data EdgeType = Directed | UnDirected
 204
 205 data ViewGraph = ViewGraph
 206   { _view_graphParam    :: PhyloParam
 207   , _view_graphLabel    :: Text
 208   , _view_graphEdgeType :: EdgeType
 209   , _view_graphBranches :: [(PhyloBranchId,Text)]
 210   , _view_graphNodes    :: [ViewNode]
 211   , _view_graphEdges    :: [ViewEdge]
 212   }
 213
 214 data ViewEdge = ViewEdge
 215   { _view_edgeSource :: PhyloGroupId
 216   , _view_edgeTarget :: PhyloGroupId
 217   , _view_edgeWeight :: Weight
 218   }
 219
 220 data ViewNode = ViewNode
 221   { _view_nodeId     :: PhyloGroupId
 222   , _view_nodeLabel  :: Text
 223   , _view_nodeNgrams :: [Ngrams]
 224   , _view_nodeMeta   :: Map Text Double
 225   , _view_nodeParent :: PhyloGroupId
 226   }
 227
 228 -- | Lenses
 229 makeLenses ''Phylo
 230 makeLenses ''PhyloParam
 231 makeLenses ''PhyloExport
 232 makeLenses ''Software
 233 makeLenses ''PhyloGroup
 234 makeLenses ''PhyloLevel
 235 makeLenses ''PhyloPeriod
 236 makeLenses ''PhyloBranch
 237
 238 -- | JSON instances
 239 $(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       )
 240 $(deriveJSON (unPrefix "_phylo_period" ) 'PhyloPeriod  )
 241 $(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
 242 $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
 243 $(deriveJSON (unPrefix "_phylo_branch" ) ''PhyloBranch )
 244 --
 245 $(deriveJSON (unPrefix "_software_"    ) ''Software    )
 246 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
 247 $(deriveJSON (unPrefix "_phyloExport_" ) ''PhyloExport )
 248
 249 -- | TODO XML instances
 250