LegacyPhylo.hs 17.2 KB
Newer Older
qlobbe's avatar
qlobbe committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570
{-|
Module      : Gargantext.Core.Viz.Phylo
Description : Phylomemy definitions and types.
Copyright   : (c) CNRS, 2017-Present
License     : AGPL + CECILL v3
Maintainer  : team@gargantext.org
Stability   : experimental
Portability : POSIX

Specifications of Phylomemy export format.

Phylomemy can be described as a Temporal Graph with different scale of
granularity of group of ngrams (terms and multi-terms).

The main type is Phylo which is synonym of Phylomemy (only difference is
the number of chars).

References:
Chavalarias, D., Cointet, J.-P., 2013. Phylomemetic patterns
in science evolution — the rise and fall of scientific fields. PloS
one 8, e54847.

-}

{-# LANGUAGE DeriveAnyClass   #-}
{-# LANGUAGE TemplateHaskell   #-}

module Gargantext.Core.Viz.LegacyPhylo where

import Control.DeepSeq
import Control.Lens (makeLenses)
import Data.Aeson.TH (deriveJSON,defaultOptions)
import Data.Map     (Map)
import Data.Set     (Set)
import Data.Swagger
import Data.Text    (Text)
import Data.Vector  (Vector)
import GHC.Generics (Generic)
import Gargantext.Core.Utils.Prefix (unPrefix, unPrefixSwagger)
import Gargantext.Prelude
import Gargantext.Core.Text.Context (TermList)

--------------------
-- | PhyloParam | --
--------------------


-- | Global parameters of a Phylo
data PhyloParam =
     PhyloParam { _phyloParam_version  :: !Text -- Double ?
                , _phyloParam_software :: !Software
                , _phyloParam_query    :: !PhyloQueryBuild
     } deriving (Generic, Show, Eq)


-- | Software parameters
data Software =
     Software { _software_name    :: !Text
              , _software_version :: !Text
     } deriving (Generic, Show, Eq)


---------------
-- | Phylo | --
---------------


-- | Phylo datatype of a phylomemy
-- Duration    : time Segment of the whole Phylo
-- Foundations : vector of all the Ngrams contained in a Phylo (build from a list of actants)
-- Periods     : list of all the periods of a Phylo
data Phylo =
     Phylo { _phylo_duration    :: !(Start, End)
           , _phylo_foundations :: !PhyloFoundations
           , _phylo_periods     :: [PhyloPeriod]
           , _phylo_docsByYears :: !(Map Date Double)
           , _phylo_cooc        :: !(Map Date (Map (Int,Int) Double))
           , _phylo_fis         :: !(Map (Date,Date) [PhyloFis])
           , _phylo_param       :: !PhyloParam
           }
           deriving (Generic, Show, Eq)


-- | The foundations of a phylomemy created from a given TermList 
data PhyloFoundations =
  PhyloFoundations { _phylo_foundationsRoots :: !(Vector Ngrams)
                   , _phylo_foundationsTermsList :: !TermList
  } deriving (Generic, Show, Eq)


-- | Date : a simple Integer
type Date = Int

-- | UTCTime in seconds since UNIX epoch
-- type Start   = POSIXTime
-- type End     = POSIXTime
type Start   = Date
type End     = Date


---------------------
-- | PhyloPeriod | --
---------------------


-- | PhyloStep : steps of phylomemy on temporal axis
-- Period: tuple (start date, end date) of the step of the phylomemy
-- Levels: levels of granularity
data PhyloPeriod =
     PhyloPeriod { _phylo_periodId     :: !PhyloPeriodId
                 , _phylo_periodLevels :: ![PhyloLevel]
                 }
                 deriving (Generic, Show, Eq)


--------------------
-- | PhyloLevel | --
--------------------


-- | PhyloLevel : levels of phylomemy on level axis
-- Levels description:
-- Level -1: Ngram equals itself         (by identity) == _phylo_Ngrams
-- Level  0: Group of synonyms           (by stems + by qualitative expert meaning)
-- Level  1: First level of clustering
-- Level  N: Nth   level of clustering
data PhyloLevel =
     PhyloLevel { _phylo_levelId     :: !PhyloLevelId
                , _phylo_levelGroups :: ![PhyloGroup]
                }
                deriving (Generic, Show, Eq)


--------------------
-- | PhyloGroup | --
--------------------


-- | PhyloGroup : group of ngrams at each level and step
-- Label : maybe has a label as text
-- Ngrams: set of terms that build the group
-- Quality : map of measures (support, etc.) that depict some qualitative aspects of a phylo
-- Period Parents|Childs: weighted link to Parents|Childs (Temporal Period   axis)
-- Level  Parents|Childs: weighted link to Parents|Childs (Level Granularity axis)
-- Pointers are directed link from Self to any PhyloGroup (/= Self ?)
data PhyloGroup =
     PhyloGroup { _phylo_groupId            :: !PhyloGroupId
                , _phylo_groupLabel         :: !Text
                , _phylo_groupNgrams        :: ![Int]
                , _phylo_groupNgramsMeta    :: !(Map Text [Double])
                , _phylo_groupMeta          :: !(Map Text Double)
                , _phylo_groupBranchId      :: !(Maybe PhyloBranchId)
                , _phylo_groupCooc          :: !(Map (Int,Int) Double)

                , _phylo_groupPeriodParents :: ![Pointer]
                , _phylo_groupPeriodChilds  :: ![Pointer]

                , _phylo_groupLevelParents  :: ![Pointer]
                , _phylo_groupLevelChilds   :: ![Pointer]
                }
                deriving (Generic, NFData, Show, Eq, Ord)

-- instance NFData PhyloGroup


-- | Level : A level of aggregation (-1 = Txt, 0 = Ngrams, 1 = Fis, [2..] = Cluster)
type Level = Int
-- | Index : A generic index of an element (PhyloGroup, PhyloBranch, etc) in a given List
type Index = Int


type PhyloPeriodId = (Start, End)
type PhyloLevelId  = (PhyloPeriodId, Level)
type PhyloGroupId  = (PhyloLevelId, Index)
type PhyloBranchId = (Level, Index)


-- | Weight : A generic mesure that can be associated with an Id
type Weight = Double
-- | Pointer : A weighted linked with a given PhyloGroup
type Pointer = (PhyloGroupId, Weight)
-- | Ngrams : a contiguous sequence of n terms
type Ngrams = Text


--------------------
-- | Aggregates | --
--------------------


-- | Document : a piece of Text linked to a Date
data Document = Document
      { date :: !Date
      , text :: ![Ngrams]
      } deriving (Show,Generic,NFData)

-- | Clique : Set of ngrams cooccurring in the same Document
type Clique   = Set Ngrams
-- | Support : Number of Documents where a Clique occurs
type Support  = Int
-- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
data PhyloFis = PhyloFis
  { _phyloFis_clique  :: !Clique
  , _phyloFis_support :: !Support
  , _phyloFis_period  :: !(Date,Date)
  } deriving (Generic,NFData,Show,Eq)

-- | A list of clustered PhyloGroup
type PhyloCluster = [PhyloGroup]


-- | A PhyloGroup in a Graph
type GroupNode  = PhyloGroup
-- | A weighted links between two PhyloGroups in a Graph
type GroupEdge  = ((PhyloGroup,PhyloGroup),Weight)
-- | The association as a Graph between a list of Nodes and a list of Edges
type GroupGraph = ([GroupNode],[GroupEdge])


---------------
-- | Error | --
---------------


data PhyloError = LevelDoesNotExist
                | LevelUnassigned
          deriving (Show)


-----------------
-- | Cluster | --
-----------------


-- | Cluster constructors
data Cluster = Fis FisParams
             | RelatedComponents RCParams
             | Louvain LouvainParams
        deriving (Generic, Show, Eq, Read)

-- | Parameters for Fis clustering
data FisParams = FisParams
  { _fis_keepMinorFis :: !Bool
  , _fis_minSupport   :: !Support
  , _fis_minSize      :: !Int
  } deriving (Generic, Show, Eq, Read)

-- | Parameters for RelatedComponents clustering
data RCParams = RCParams
  { _rc_proximity :: !Proximity } deriving (Generic, Show, Eq, Read)

-- | Parameters for Louvain clustering
data LouvainParams = LouvainParams
  { _louvain_proximity :: !Proximity } deriving (Generic, Show, Eq, Read)


-------------------
-- | Proximity | --
-------------------


-- | Proximity constructors
data Proximity = WeightedLogJaccard WLJParams
               | WeightedLogSim WLJParams
               | Hamming HammingParams
               | Filiation
          deriving (Generic, Show, Eq, Read)

-- | Parameters for WeightedLogJaccard and WeightedLogSim proximity
data WLJParams = WLJParams
  { _wlj_threshold   :: !Double
  , _wlj_sensibility :: !Double
  } deriving (Generic, Show, Eq, Read)

-- | Parameters for Hamming proximity
data HammingParams = HammingParams
  { _hamming_threshold :: !Double } deriving (Generic, Show, Eq, Read)


----------------
-- | Filter | --
----------------


-- | Filter constructors
data Filter = LonelyBranch LBParams
            | SizeBranch SBParams
            deriving (Generic, Show, Eq)

-- | Parameters for LonelyBranch filter
data LBParams = LBParams
  { _lb_periodsInf :: !Int
  , _lb_periodsSup :: !Int
  , _lb_minNodes   :: !Int } deriving (Generic, Show, Eq)

-- | Parameters for SizeBranch filter
data SBParams = SBParams
  { _sb_minSize :: !Int } deriving (Generic, Show, Eq)


----------------
-- | Metric | --
----------------


-- | Metric constructors
data Metric = BranchAge | BranchBirth | BranchGroups deriving (Generic, Show, Eq, Read)


----------------
-- | Tagger | --
----------------


-- | Tagger constructors
data Tagger = BranchPeakFreq | BranchPeakCooc | BranchPeakInc
            | GroupLabelCooc | GroupLabelInc  | GroupLabelIncDyn deriving (Show,Generic,Read)


--------------
-- | Sort | --
--------------


-- | Sort constructors
data Sort  = ByBranchAge | ByBranchBirth deriving (Generic, Show, Read, Enum, Bounded)
data Order = Asc | Desc  deriving (Generic, Show, Read)


--------------------
-- | PhyloQuery | --
--------------------


-- | A Phyloquery describes a phylomemic reconstruction
data PhyloQueryBuild = PhyloQueryBuild
    { _q_phyloTitle :: !Text
    , _q_phyloDesc  :: !Text

    -- Grain and Steps for the PhyloPeriods
    , _q_periodGrain :: !Int
    , _q_periodSteps :: !Int

    -- Clustering method for building the contextual unit of Phylo (ie: level 1)
    , _q_contextualUnit :: !Cluster
    , _q_contextualUnitMetrics :: ![Metric]
    , _q_contextualUnitFilters :: ![Filter]

    -- Inter-temporal matching method of the Phylo
    , _q_interTemporalMatching :: !Proximity
    , _q_interTemporalMatchingFrame :: !Int
    , _q_interTemporalMatchingFrameTh :: !Double

    , _q_reBranchThr :: !Double
    , _q_reBranchNth :: !Int

    -- Last level of reconstruction
    , _q_nthLevel   :: !Level
    -- Clustering method used from level 1 to nthLevel
    , _q_nthCluster :: !Cluster
    } deriving (Generic, Show, Eq)

-- | To choose the Phylo edge you want to export : --> <-- <--> <=>
data Filiation = Ascendant | Descendant | Merge | Complete deriving (Generic, Show, Read)
data EdgeType  = PeriodEdge | LevelEdge deriving (Generic, Show, Eq)

-------------------
-- | PhyloView | --
-------------------


-- | A PhyloView is the output type of a Phylo
data PhyloView = PhyloView
  { _pv_param       :: !PhyloParam
  , _pv_title       :: !Text
  , _pv_description :: !Text
  , _pv_filiation   :: !Filiation
  , _pv_level       :: !Level
  , _pv_periods     :: ![PhyloPeriodId]
  , _pv_metrics     :: !(Map Text [Double])
  , _pv_branches    :: ![PhyloBranch]
  , _pv_nodes       :: ![PhyloNode]
  , _pv_edges       :: ![PhyloEdge]
  } deriving (Generic, Show)

-- | A phyloview is made of PhyloBranches, edges and nodes
data PhyloBranch = PhyloBranch
  { _pb_id      :: !PhyloBranchId
  , _pb_peak    :: !Text
  , _pb_metrics :: !(Map Text [Double])
  } deriving (Generic, Show)

data PhyloEdge = PhyloEdge
  { _pe_source :: !PhyloGroupId
  , _pe_target :: !PhyloGroupId
  , _pe_type   :: !EdgeType
  , _pe_weight :: !Weight
  } deriving (Generic, Show)

data PhyloNode = PhyloNode
  { _pn_id      :: !PhyloGroupId
  , _pn_bid     :: !(Maybe PhyloBranchId)
  , _pn_label   :: !Text
  , _pn_idx     :: ![Int]
  , _pn_ngrams  :: !(Maybe [Ngrams])
  , _pn_metrics :: !(Map Text [Double])
  , _pn_cooc    :: !(Map (Int,Int) Double)
  , _pn_parents :: !(Maybe [PhyloGroupId])
  , _pn_childs  :: ![PhyloNode]
  } deriving (Generic, Show)

------------------------
-- | PhyloQueryView | --
------------------------


data ExportMode = Json | Dot | Svg
  deriving (Generic, Show, Read)
data DisplayMode = Flat | Nested
  deriving (Generic, Show, Read)

-- | A PhyloQueryView describes a Phylo as an output view
data PhyloQueryView = PhyloQueryView
  { _qv_lvl    :: !Level

  -- Does the PhyloGraph contain ascendant, descendant or a complete Filiation ? Complet redondant et merge (avec le max)
  , _qv_filiation :: !Filiation

  -- Does the PhyloGraph contain some levelChilds ? How deep must it go ?
  , _qv_levelChilds      :: !Bool
  , _qv_levelChildsDepth :: !Level

  -- Ordered lists of filters, taggers and metrics to be applied to the PhyloGraph
  -- Firstly the metrics, then the filters and the taggers
  , _qv_metrics :: ![Metric]
  , _qv_filters :: ![Filter]
  , _qv_taggers :: ![Tagger]

  -- An asc or desc sort to apply to the PhyloGraph
  , _qv_sort :: !(Maybe (Sort,Order))

  -- A display mode to apply to the PhyloGraph, ie: [Node[Node,Edge],Edge] or [[Node,Node],[Edge,Edge]]
  , _qv_export  :: !ExportMode
  , _qv_display :: !DisplayMode
  , _qv_verbose :: !Bool
  }


----------------
-- | Lenses | --
----------------


makeLenses ''PhyloParam
makeLenses ''Software
--
makeLenses ''Phylo
makeLenses ''PhyloFoundations
makeLenses ''PhyloGroup
makeLenses ''PhyloLevel
makeLenses ''PhyloPeriod
makeLenses ''PhyloFis
--
makeLenses ''Proximity
makeLenses ''Cluster
makeLenses ''Filter
--
makeLenses ''PhyloQueryBuild
makeLenses ''PhyloQueryView
--
makeLenses ''PhyloView
makeLenses ''PhyloBranch
makeLenses ''PhyloNode
makeLenses ''PhyloEdge


------------------------
-- | JSON instances | --
------------------------


$(deriveJSON (unPrefix "_phylo_"       ) ''Phylo       )
$(deriveJSON (unPrefix "_phylo_foundations"  ) ''PhyloFoundations  )
$(deriveJSON (unPrefix "_phylo_period" ) ''PhyloPeriod )
$(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
$(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
$(deriveJSON (unPrefix "_phyloFis_"    ) ''PhyloFis    )
--
$(deriveJSON (unPrefix "_software_"    ) ''Software    )
$(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
--
$(deriveJSON defaultOptions ''Filter    )
$(deriveJSON defaultOptions ''Metric    )
$(deriveJSON defaultOptions ''Cluster   )
$(deriveJSON defaultOptions ''Proximity )
--
$(deriveJSON (unPrefix "_fis_" )     ''FisParams     )
$(deriveJSON (unPrefix "_hamming_" ) ''HammingParams )
$(deriveJSON (unPrefix "_louvain_" ) ''LouvainParams )
$(deriveJSON (unPrefix "_rc_" )      ''RCParams      )
$(deriveJSON (unPrefix "_wlj_" )     ''WLJParams     )
--
$(deriveJSON (unPrefix "_lb_" )      ''LBParams      )
$(deriveJSON (unPrefix "_sb_" )      ''SBParams      )
--
$(deriveJSON (unPrefix "_q_" )  ''PhyloQueryBuild  )
$(deriveJSON (unPrefix "_pv_" ) ''PhyloView   )
$(deriveJSON (unPrefix "_pb_" ) ''PhyloBranch )
$(deriveJSON (unPrefix "_pe_" ) ''PhyloEdge   )
$(deriveJSON (unPrefix "_pn_" ) ''PhyloNode   )

$(deriveJSON defaultOptions ''Filiation )
$(deriveJSON defaultOptions ''EdgeType  )

---------------------------
-- | Swagger instances | --
---------------------------

instance ToSchema Phylo where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
instance ToSchema PhyloFoundations where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_foundations")
instance ToSchema PhyloPeriod where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_period")
instance ToSchema PhyloLevel where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_level")
instance ToSchema PhyloGroup where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_group")
instance ToSchema PhyloFis where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phyloFis_")
instance ToSchema Software where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_software_")
instance ToSchema PhyloParam where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phyloParam_")
instance ToSchema Filter
instance ToSchema Metric
instance ToSchema Cluster
instance ToSchema Proximity where
  declareNamedSchema = genericDeclareNamedSchemaUnrestricted defaultSchemaOptions
instance ToSchema FisParams where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_fis_")
instance ToSchema HammingParams where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_hamming_")
instance ToSchema LouvainParams where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_louvain_")
instance ToSchema RCParams where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_rc_")
instance ToSchema WLJParams where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_wlj_")
instance ToSchema LBParams where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_lb_")
instance ToSchema SBParams where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_sb_")
instance ToSchema PhyloQueryBuild where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_q_")
instance ToSchema PhyloView where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_pv_")
instance ToSchema PhyloBranch where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_pb_")
instance ToSchema PhyloEdge where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_pe_")
instance ToSchema PhyloNode where
  declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_pn_")
instance ToSchema Filiation
instance ToSchema EdgeType

----------------------------
-- | TODO XML instances | --
----------------------------