src/Gargantext/Core/Viz/Phylo.hs

   1 {-
   2 Module      : Gargantext.Core.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 DeriveAnyClass   #-}
  25 {-# LANGUAGE TemplateHaskell   #-}
  26
  27 module Gargantext.Core.Viz.Phylo where
  28
  29 import Control.DeepSeq (NFData)
  30 import Control.Lens (makeLenses)
  31 import Data.Aeson
  32 import Data.Aeson.TH (deriveJSON)
  33 import Data.Map (Map)
  34 import Data.Swagger
  35 import Data.Text   (Text, pack)
  36 import Data.Vector (Vector)
  37 import GHC.Generics
  38 import GHC.IO (FilePath)
  39 import Gargantext.Core.Utils.Prefix (unPrefix)
  40 import Gargantext.Core.Utils.Prefix (unPrefixSwagger)
  41 import Gargantext.Prelude
  42 import qualified Data.Text.Lazy as TextLazy
  43
  44 ---------------------
  45 -- | PhyloConfig | --
  46 ---------------------
  47
  48 data CorpusParser =
  49       Wos  {_wos_limit  :: Int}
  50     | Csv  {_csv_limit  :: Int}
  51     | Csv' {_csv'_limit :: Int}
  52     deriving (Show,Generic,Eq)
  53
  54 instance ToSchema CorpusParser where
  55   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
  56
  57
  58 data ListParser = V3 | V4 deriving (Show,Generic,Eq)
  59 instance ToSchema ListParser
  60
  61
  62 data SeaElevation =
  63       Constante
  64       { _cons_start :: Double
  65       , _cons_gap   :: Double }
  66     | Adaptative
  67       { _adap_steps :: Double }
  68     | Evolving
  69       { _evol_neighborhood :: Bool }
  70     deriving (Show,Generic,Eq)
  71
  72 instance ToSchema SeaElevation
  73
  74 data PhyloSimilarity =
  75       WeightedLogJaccard
  76       { _wlj_sensibility     :: Double
  77       , _wlj_minSharedNgrams :: Int }
  78     | WeightedLogSim
  79       { _wls_sensibility     :: Double
  80       , _wls_minSharedNgrams :: Int }
  81     | Hamming
  82       { _hmg_sensibility     :: Double
  83       , _hmg_minSharedNgrams :: Int}
  84
  85     deriving (Show,Generic,Eq)
  86
  87 instance ToSchema PhyloSimilarity where
  88   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
  89
  90
  91 data SynchronyScope = SingleBranch | SiblingBranches | AllBranches
  92   deriving (Show,Generic,Eq, ToSchema)
  93
  94 data SynchronyStrategy = MergeRegularGroups | MergeAllGroups
  95   deriving (Show,Generic,Eq)
  96
  97 instance ToSchema SynchronyStrategy where
  98   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
  99
 100
 101 data Synchrony =
 102       ByProximityThreshold
 103       { _bpt_threshold :: Double
 104       , _bpt_sensibility :: Double
 105       , _bpt_scope :: SynchronyScope
 106       , _bpt_strategy :: SynchronyStrategy }
 107     | ByProximityDistribution
 108       { _bpd_sensibility :: Double
 109       , _bpd_strategy :: SynchronyStrategy }
 110     deriving (Show,Generic,Eq)
 111
 112 instance ToSchema Synchrony where
 113   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 114
 115
 116
 117 data TimeUnit =
 118       Epoch
 119       { _epoch_period :: Int
 120       , _epoch_step   :: Int
 121       , _epoch_matchingFrame :: Int }
 122     | Year
 123       { _year_period :: Int
 124       , _year_step   :: Int
 125       , _year_matchingFrame :: Int }
 126     | Month
 127       { _month_period :: Int
 128       , _month_step   :: Int
 129       , _month_matchingFrame :: Int }
 130     | Week
 131       { _week_period :: Int
 132       , _week_step   :: Int
 133       , _week_matchingFrame :: Int }
 134     | Day
 135       { _day_period :: Int
 136       , _day_step   :: Int
 137       , _day_matchingFrame :: Int }
 138       deriving (Show,Generic,Eq,NFData)
 139
 140 instance ToSchema TimeUnit where
 141   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 142
 143
 144 data MaxCliqueFilter = ByThreshold | ByNeighbours deriving (Show,Generic,Eq)
 145
 146 instance ToSchema MaxCliqueFilter where
 147   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 148
 149
 150
 151 data Cluster =
 152       Fis
 153       { _fis_support :: Int
 154       , _fis_size    :: Int }
 155     | MaxClique
 156       { _mcl_size      :: Int
 157       , _mcl_threshold :: Double
 158       , _mcl_filter    :: MaxCliqueFilter }
 159       deriving (Show,Generic,Eq)
 160
 161 instance ToSchema Cluster where
 162   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 163
 164
 165 data Quality =
 166      Quality { _qua_granularity :: Double
 167              , _qua_minBranch   :: Int }
 168       deriving (Show,Generic,Eq)
 169
 170 instance ToSchema Quality where
 171   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_qua_")
 172
 173
 174 data PhyloConfig =
 175      PhyloConfig { corpusPath     :: FilePath
 176             , listPath       :: FilePath
 177             , outputPath     :: FilePath
 178             , corpusParser   :: CorpusParser
 179             , listParser     :: ListParser
 180             , phyloName      :: Text
 181             , phyloScale     :: Int
 182             , similarity     :: PhyloSimilarity
 183             , seaElevation   :: SeaElevation
 184             , defaultMode    :: Bool
 185             , findAncestors  :: Bool
 186             , phyloSynchrony :: Synchrony
 187             , phyloQuality   :: Quality
 188             , timeUnit       :: TimeUnit
 189             , clique         :: Cluster
 190             , exportLabel    :: [PhyloLabel]
 191             , exportSort     :: Sort
 192             , exportFilter   :: [Filter]
 193             } deriving (Show,Generic,Eq)
 194
 195
 196 --------------------------------
 197 -- | SubConfig API & 1Click | --
 198 --------------------------------
 199
 200 data PhyloSubConfigAPI =
 201   PhyloSubConfigAPI { _sc_phyloProximity :: Double
 202                     , _sc_phyloSynchrony :: Double
 203                     , _sc_phyloQuality   :: Double
 204                     , _sc_timeUnit       :: TimeUnit
 205                     , _sc_clique         :: Cluster
 206                     , _sc_exportFilter   :: Double
 207                     , _sc_defaultMode    :: Bool
 208                     } deriving (Show,Generic,Eq)
 209
 210
 211 subConfigAPI2config :: PhyloSubConfigAPI -> PhyloConfig
 212 subConfigAPI2config subConfig = defaultConfig
 213                                            { similarity     = WeightedLogJaccard (_sc_phyloProximity subConfig) 2
 214                                            , phyloSynchrony = ByProximityThreshold (_sc_phyloSynchrony subConfig) 0 AllBranches MergeAllGroups
 215                                            , phyloQuality   = Quality (_sc_phyloQuality   subConfig) 3
 216                                            , timeUnit       = _sc_timeUnit       subConfig
 217                                            , clique         = _sc_clique         subConfig
 218                                            , defaultMode    = _sc_defaultMode    subConfig
 219                                            , exportFilter   = [ByBranchSize $ _sc_exportFilter   subConfig]
 220                                            }
 221
 222 --------------------------
 223 -- | SubConfig 1Click | --
 224 --------------------------
 225
 226 defaultConfig :: PhyloConfig
 227 defaultConfig =
 228      PhyloConfig { corpusPath = "corpus.csv" -- useful for commandline only
 229             , listPath       = "list.csv"   -- useful for commandline only
 230             , outputPath     = "data/"
 231             , corpusParser   = Csv 150000
 232             , listParser     = V4
 233             , phyloName      = pack "Phylo Name"
 234             , phyloScale     = 2
 235             , similarity     = WeightedLogJaccard 0.5 2
 236             , seaElevation   = Constante 0.1 0.1
 237             , defaultMode    = False
 238             , findAncestors  = True
 239             , phyloSynchrony = ByProximityThreshold 0.6 0 AllBranches MergeAllGroups
 240             , phyloQuality   = Quality 0.5 3
 241             , timeUnit       = Year 3 1 5
 242             , clique         = Fis 2 3
 243             , exportLabel    = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2]
 244             , exportSort     = ByHierarchy Desc
 245             , exportFilter   = [ByBranchSize 3]
 246             }
 247
 248 -- Main Instances
 249 instance ToSchema PhyloConfig
 250 instance ToSchema PhyloSubConfigAPI
 251
 252 instance FromJSON PhyloConfig
 253 instance ToJSON PhyloConfig
 254
 255 instance FromJSON PhyloSubConfigAPI
 256 instance ToJSON PhyloSubConfigAPI
 257
 258 instance FromJSON CorpusParser
 259 instance ToJSON CorpusParser
 260
 261 instance FromJSON ListParser
 262 instance ToJSON ListParser
 263
 264 instance FromJSON PhyloSimilarity
 265 instance ToJSON PhyloSimilarity
 266
 267 instance FromJSON SeaElevation
 268 instance ToJSON SeaElevation
 269
 270 instance FromJSON TimeUnit
 271 instance ToJSON TimeUnit
 272
 273 instance FromJSON MaxCliqueFilter
 274 instance ToJSON MaxCliqueFilter
 275
 276 instance FromJSON Cluster
 277 instance ToJSON Cluster
 278
 279 instance FromJSON PhyloLabel
 280 instance ToJSON PhyloLabel
 281
 282 instance FromJSON Tagger
 283 instance ToJSON Tagger
 284
 285 instance FromJSON Sort
 286 instance ToJSON Sort
 287
 288 instance FromJSON Order
 289 instance ToJSON Order
 290
 291 instance FromJSON Filter
 292 instance ToJSON Filter
 293
 294 instance FromJSON SynchronyScope
 295 instance ToJSON SynchronyScope
 296
 297 instance FromJSON SynchronyStrategy
 298 instance ToJSON SynchronyStrategy
 299
 300 instance FromJSON Synchrony
 301 instance ToJSON Synchrony
 302
 303 instance FromJSON Quality
 304 instance ToJSON Quality
 305
 306
 307 -- | Software parameters
 308 data Software =
 309      Software { _software_name    :: Text
 310               , _software_version :: Text
 311      } deriving (Generic, Show, Eq)
 312
 313 instance ToSchema Software where
 314   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_software_")
 315
 316
 317
 318 defaultSoftware :: Software
 319 defaultSoftware =
 320       Software { _software_name    = pack "GarganText"
 321                , _software_version = pack "v5" }
 322
 323
 324 -- | Global parameters of a Phylo
 325 data PhyloParam =
 326      PhyloParam { _phyloParam_version  :: Text
 327                 , _phyloParam_software :: Software
 328                 , _phyloParam_config   :: PhyloConfig
 329      } deriving (Generic, Show, Eq)
 330
 331 instance ToSchema PhyloParam where
 332   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phyloParam_")
 333
 334
 335
 336 defaultPhyloParam :: PhyloParam
 337 defaultPhyloParam =
 338       PhyloParam { _phyloParam_version  = pack "v3"
 339                  , _phyloParam_software = defaultSoftware
 340                  , _phyloParam_config   = defaultConfig }
 341
 342
 343 ------------------
 344 -- | Document | --
 345 ------------------
 346
 347 -- | Date : a simple Integer
 348 type Date = Int
 349
 350 -- | DateStr : the string version of a Date
 351 type DateStr = Text
 352
 353 -- | Ngrams : a contiguous sequence of n terms
 354 type Ngrams = Text
 355
 356 -- Document : a piece of Text linked to a Date
 357 -- date = computational date; date' = original string date yyyy-mm-dd
 358 -- Export Database to Document
 359 data Document = Document
 360       { date    :: Date   -- datatype Date {unDate :: Int}
 361       , date'   :: DateStr   -- show date
 362       , text    :: [Ngrams]
 363       , weight  :: Maybe Double
 364       , sources :: [Text]
 365       , docTime :: TimeUnit
 366       } deriving (Eq,Show,Generic,NFData)
 367
 368
 369 --------------------
 370 -- | Foundation | --
 371 --------------------
 372
 373
 374 -- | The Foundations of a Phylo created from a given TermList
 375 data PhyloFoundations = PhyloFoundations
 376       { _foundations_roots    :: (Vector Ngrams)
 377       , _foundations_rootsInGroups :: Map Int [PhyloGroupId] -- map of roots associated to groups
 378       } deriving (Generic, Show, Eq)
 379
 380 data PhyloCounts = PhyloCounts
 381       { coocByDate    :: !(Map Date Cooc)
 382       , docsByDate    :: !(Map Date Double)
 383       , rootsCountByDate :: !(Map Date (Map Int Double))
 384       , rootsCount    :: !(Map Int  Double)
 385       , rootsFreq     :: !(Map Int  Double)
 386       , lastRootsFreq :: !(Map Int  Double)
 387       } deriving (Generic, Show, Eq)
 388
 389 data PhyloSources = PhyloSources
 390       { _sources :: !(Vector Text) } deriving (Generic, Show, Eq)
 391
 392 instance ToSchema PhyloFoundations where
 393   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_foundations_")
 394 instance ToSchema PhyloCounts where
 395   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 396 instance ToSchema PhyloSources where
 397   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 398
 399 ---------------------------
 400 -- | Coocurency Matrix | --
 401 ---------------------------
 402
 403
 404 -- | Cooc : a coocurency matrix between two ngrams
 405 type Cooc =  Map (Int,Int) Double
 406
 407
 408 -------------------
 409 -- | Phylomemy | --
 410 -------------------
 411
 412 -- | Period : a tuple of Dates
 413 type Period = (Date,Date)
 414
 415 -- | PeriodStr : a tuple of DateStr
 416 type PeriodStr = (DateStr,DateStr)
 417
 418
 419
 420
 421 -- | Phylo datatype of a phylomemy
 422 --  foundations : the foundations of the phylo
 423 --  timeCooc : a Map of coocurency by minimal unit of time (ex: by year)
 424 --  timeDocs : a Map with the numbers of docs by minimal unit of time (ex: by year)
 425 --  param : the parameters of the phylomemy (with the user's configuration)
 426 --  periods : the temporal steps of a phylomemy
 427 data Phylo =
 428      Phylo { _phylo_foundations  :: PhyloFoundations
 429            , _phylo_sources      :: PhyloSources
 430            , _phylo_counts       :: PhyloCounts
 431            , _phylo_seaLadder    :: [Double]
 432            , _phylo_param        :: PhyloParam
 433            , _phylo_periods      :: Map Period PhyloPeriod
 434            , _phylo_quality      :: Double
 435            , _phylo_level        :: Double
 436            }
 437            deriving (Generic, Show, Eq)
 438
 439 instance ToSchema Phylo where
 440   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 441
 442
 443 ----------------
 444 -- | Period | --
 445 ----------------
 446
 447 -- | PhyloPeriod : steps of a phylomemy on a temporal axis
 448 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 449 --  scales: scales of synchronic description
 450 data PhyloPeriod =
 451      PhyloPeriod { _phylo_periodPeriod    :: Period
 452                  , _phylo_periodPeriodStr :: PeriodStr
 453                  , _phylo_periodScales    :: Map PhyloScaleId PhyloScale
 454                  } deriving (Generic, Show, Eq)
 455
 456 instance ToSchema PhyloPeriod where
 457   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 458
 459 ---------------
 460 -- | Scale | --
 461 ---------------
 462
 463 -- | Scale : a scale of synchronic description
 464 type Scale = Int
 465
 466 -- | PhyloScaleId : the id of a scale of synchronic description
 467 type PhyloScaleId  = (Period,Scale)
 468
 469 -- | PhyloScale : sub-structure of the phylomemy in scale of synchronic description
 470 data PhyloScale =
 471      PhyloScale { _phylo_scalePeriod    :: Period
 472                 , _phylo_scalePeriodStr :: PeriodStr
 473                 , _phylo_scaleScale     :: Scale
 474                 , _phylo_scaleGroups    :: Map PhyloGroupId PhyloGroup
 475                 }
 476                 deriving (Generic, Show, Eq)
 477
 478 instance ToSchema PhyloScale where
 479   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 480
 481
 482 type PhyloGroupId  = (PhyloScaleId, Int)
 483
 484 -- | BranchId : (a scale, a sequence of branch index)
 485 -- the sequence is a path of heritage from the most to the less specific branch
 486 type PhyloBranchId = (Scale, [Int])
 487
 488 -- | PhyloGroup : group of ngrams at each scale and period
 489 data PhyloGroup =
 490       PhyloGroup { _phylo_groupPeriod   :: Period
 491                  , _phylo_groupPeriod'  :: (Text,Text)
 492                  , _phylo_groupScale    :: Scale
 493                  , _phylo_groupIndex    :: Int
 494                  , _phylo_groupLabel    :: Text
 495                  , _phylo_groupSupport  :: Support
 496                  , _phylo_groupWeight   :: Maybe Double
 497                  , _phylo_groupSources  :: [Int]
 498                  , _phylo_groupNgrams   :: [Int]
 499                  , _phylo_groupCooc     :: !(Cooc)
 500                  , _phylo_groupDensity  :: Double
 501                  , _phylo_groupBranchId :: PhyloBranchId
 502                  , _phylo_groupMeta     :: Map Text [Double]
 503                  , _phylo_groupRootsCount    :: Map Int Double
 504                  , _phylo_groupScaleParents  :: [Pointer]
 505                  , _phylo_groupScaleChilds   :: [Pointer]
 506                  , _phylo_groupPeriodParents :: [Pointer]
 507                  , _phylo_groupPeriodChilds  :: [Pointer]
 508                  , _phylo_groupAncestors     :: [Pointer]
 509                  , _phylo_groupPeriodMemoryParents :: [Pointer']
 510                  , _phylo_groupPeriodMemoryChilds  :: [Pointer']
 511                  }
 512                  deriving (Generic, Show, Eq, NFData)
 513
 514 instance ToSchema PhyloGroup where
 515   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_phylo_")
 516
 517
 518 -- | Weight : A generic mesure that can be associated with an Id
 519 type Weight = Double
 520 type Thr = Double
 521
 522 -- | Pointer : A weighted pointer to a given PhyloGroup
 523 type Pointer = (PhyloGroupId, Weight)
 524 -- | Pointer' : A weighted pointer to a given PhyloGroup with a lower bounded threshold
 525 type Pointer' = (PhyloGroupId, (Thr,Weight))
 526
 527 data Filiation = ToParents | ToChilds | ToParentsMemory | ToChildsMemory deriving (Generic, Show)
 528 data PointerType = TemporalPointer | ScalePointer deriving (Generic, Show)
 529
 530
 531 --------------------------
 532 -- | Phylo Clustering | --
 533 --------------------------
 534
 535 -- | Support : Number of Documents where a Cluster occurs
 536 type Support  = Int
 537
 538 data Clustering = Clustering
 539   { _clustering_roots   :: [Int]
 540   , _clustering_support :: Support
 541   , _clustering_period  :: Period
 542   -- additional materials for visualization
 543   , _clustering_visWeighting :: Maybe Double
 544   , _clustering_visFiltering :: [Int]
 545   } deriving (Generic,NFData,Show,Eq)
 546
 547 ----------------
 548 -- | Export | --
 549 ----------------
 550
 551 type DotId = TextLazy.Text
 552
 553 data EdgeType = GroupToGroup | GroupToGroupMemory | BranchToGroup | BranchToBranch | GroupToAncestor | PeriodToPeriod deriving (Show,Generic,Eq)
 554
 555 data Filter = ByBranchSize { _branch_size :: Double } deriving (Show,Generic,Eq)
 556 instance ToSchema Filter where
 557   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 558
 559
 560 data Order = Asc | Desc deriving (Show,Generic,Eq, ToSchema)
 561
 562 data Sort = ByBirthDate { _sort_order :: Order } | ByHierarchy {_sort_order :: Order } deriving (Show,Generic,Eq)
 563 instance ToSchema Sort where
 564   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_sort_")
 565
 566
 567 data Tagger = MostInclusive | MostEmergentInclusive | MostEmergentTfIdf deriving (Show,Generic,Eq)
 568 instance ToSchema Tagger where
 569   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
 570
 571
 572 data PhyloLabel =
 573       BranchLabel
 574       { _branch_labelTagger :: Tagger
 575       , _branch_labelSize   :: Int }
 576     | GroupLabel
 577       { _group_labelTagger  :: Tagger
 578       , _group_labelSize    :: Int }
 579     deriving (Show,Generic,Eq)
 580
 581 instance ToSchema PhyloLabel where
 582   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_")
 583
 584
 585 data PhyloBranch =
 586       PhyloBranch
 587       { _branch_id :: PhyloBranchId
 588       , _branch_canonId  :: [Int]
 589       , _branch_seaLevel :: [Double]
 590       , _branch_x        :: Double
 591       , _branch_y        :: Double
 592       , _branch_w        :: Double
 593       , _branch_t        :: Double
 594       , _branch_label    :: Text
 595       , _branch_meta     :: Map Text [Double]
 596       } deriving (Generic, Show, Eq)
 597
 598 instance ToSchema PhyloBranch where
 599   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_branch_")
 600
 601 data PhyloExport =
 602       PhyloExport
 603       { _export_groups    :: [PhyloGroup]
 604       , _export_branches  :: [PhyloBranch]
 605       } deriving (Generic, Show)
 606 instance ToSchema PhyloExport where
 607   declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_export_")
 608
 609
 610 ----------------
 611 -- | Lenses | --
 612 ----------------
 613
 614 makeLenses ''PhyloConfig
 615 makeLenses ''PhyloSubConfigAPI
 616 makeLenses ''PhyloSimilarity
 617 makeLenses ''SeaElevation
 618 makeLenses ''Quality
 619 makeLenses ''Cluster
 620 makeLenses ''PhyloLabel
 621 makeLenses ''TimeUnit
 622 makeLenses ''PhyloFoundations
 623 makeLenses ''Clustering
 624 makeLenses ''Phylo
 625 makeLenses ''PhyloPeriod
 626 makeLenses ''PhyloScale
 627 makeLenses ''PhyloGroup
 628 makeLenses ''PhyloParam
 629 makeLenses ''PhyloExport
 630 makeLenses ''PhyloBranch
 631
 632 ------------------------
 633 -- | JSON instances | --
 634 ------------------------
 635
 636 instance FromJSON Phylo
 637 instance ToJSON Phylo
 638
 639 instance FromJSON PhyloSources
 640 instance ToJSON PhyloSources
 641
 642 instance FromJSON PhyloParam
 643 instance ToJSON PhyloParam
 644
 645 instance FromJSON PhyloCounts
 646 instance ToJSON PhyloCounts
 647
 648 instance FromJSON PhyloPeriod
 649 instance ToJSON PhyloPeriod
 650
 651 instance FromJSON PhyloScale
 652 instance ToJSON PhyloScale
 653
 654 instance FromJSON Software
 655 instance ToJSON Software
 656
 657 instance FromJSON PhyloGroup
 658 instance ToJSON PhyloGroup
 659
 660 $(deriveJSON (unPrefix "_foundations_"  ) ''PhyloFoundations)