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haskell-gargantext
haskell-gargantext
Verified Commit 79d0ea23 authored by Przemyslaw Kaminski's avatar Przemyslaw Kaminski
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Merge branch 'dev' into 571-dev-node-corpus-api-search-fixes-take-2

parents 011a5304 138d2f86
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CHANGELOG.md
View file @ 79d0ea23
## Version 0.0.6.9.9.6.7
* [FRONT][FIX][Node Corpus / API search (#571)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/571)
* [BACK][FIX] PhyloTypes
* [FRONT][FIX][[Node Doc] Annotation: select/add ngram to map terms doesn't seems to sync in frontend render (#563)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/563)
* [FRONT][FIX][[Graph] Rearrange the graph toolbar (#567)](https://gitlab.iscpif.fr/gargantext/purescript-gargantext/issues/567)
## Version 0.0.6.9.9.6.6 ## Version 0.0.6.9.9.6.6
* [BACK|FRONT][WARNING] Button to launch API corpus is broken for now * [BACK|FRONT][WARNING] Button to launch API corpus is broken for now
......
bin/gargantext-phylo/Main.hs
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...@@ -21,7 +21,7 @@ import Control.Concurrent.Async (mapConcurrently) ...@@ -21,7 +21,7 @@ import Control.Concurrent.Async (mapConcurrently)
import Crypto.Hash.SHA256 (hash) import Crypto.Hash.SHA256 (hash)
import Data.Aeson import Data.Aeson
import Data.Either (Either(..), fromRight) import Data.Either (Either(..), fromRight)
import Data.List (concat, nub, isSuffixOf) import Data.List (concat, nub, isSuffixOf,sort,tail)
import Data.List.Split import Data.List.Split
import Data.Maybe (fromMaybe) import Data.Maybe (fromMaybe)
import Data.String (String) import Data.String (String)
...@@ -39,7 +39,7 @@ import Gargantext.Core.Viz.Phylo ...@@ -39,7 +39,7 @@ import Gargantext.Core.Viz.Phylo
import Gargantext.Core.Viz.Phylo.API.Tools import Gargantext.Core.Viz.Phylo.API.Tools
import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile) import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile)
import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo, toPhyloWithoutLink) import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo, toPhyloWithoutLink)
import Gargantext.Core.Viz.Phylo.PhyloTools (printIOMsg, printIOComment, setConfig) import Gargantext.Core.Viz.Phylo.PhyloTools (printIOMsg, printIOComment, setConfig, toPeriods, getTimePeriod, getTimeStep)
import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..)) import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
import Gargantext.Database.Schema.Ngrams (NgramsType(..)) import Gargantext.Database.Schema.Ngrams (NgramsType(..))
import Gargantext.Prelude import Gargantext.Prelude
...@@ -89,7 +89,7 @@ wosToDocs limit patterns time path = do ...@@ -89,7 +89,7 @@ wosToDocs limit patterns time path = do
(fromIntegral $ fromJust $ _hd_publication_year d) (fromIntegral $ fromJust $ _hd_publication_year d)
(fromJust $ _hd_publication_month d) (fromJust $ _hd_publication_month d)
(fromJust $ _hd_publication_day d) time) (fromJust $ _hd_publication_day d) time)
(termsInText patterns $ title <> " " <> abstr) Nothing []) (termsInText patterns $ title <> " " <> abstr) Nothing [] time)
<$> concat <$> concat
<$> mapConcurrently (\file -> <$> mapConcurrently (\file ->
filter (\d -> (isJust $ _hd_publication_year d) filter (\d -> (isJust $ _hd_publication_year d)
...@@ -109,6 +109,7 @@ csvToDocs parser patterns time path = ...@@ -109,6 +109,7 @@ csvToDocs parser patterns time path =
(termsInText patterns $ (csv_title row) <> " " <> (csv_abstract row)) (termsInText patterns $ (csv_title row) <> " " <> (csv_abstract row))
Nothing Nothing
[] []
time
) <$> snd <$> either (\err -> panic $ cs $ "CSV error" <> (show err)) identity <$> Csv.readCSVFile path ) <$> snd <$> either (\err -> panic $ cs $ "CSV error" <> (show err)) identity <$> Csv.readCSVFile path
Csv' limit -> Vector.toList Csv' limit -> Vector.toList
<$> Vector.take limit <$> Vector.take limit
...@@ -117,18 +118,35 @@ csvToDocs parser patterns time path = ...@@ -117,18 +118,35 @@ csvToDocs parser patterns time path =
(termsInText patterns $ (csv'_title row) <> " " <> (csv'_abstract row)) (termsInText patterns $ (csv'_title row) <> " " <> (csv'_abstract row))
(Just $ csv'_weight row) (Just $ csv'_weight row)
(map (T.strip . pack) $ splitOn ";" (unpack $ (csv'_source row))) (map (T.strip . pack) $ splitOn ";" (unpack $ (csv'_source row)))
time
) <$> snd <$> Csv.readWeightedCsv path ) <$> snd <$> Csv.readWeightedCsv path
-- To parse a file into a list of Document -- To parse a file into a list of Document
fileToDocs' :: CorpusParser -> FilePath -> TimeUnit -> TermList -> IO [Document] fileToDocsAdvanced :: CorpusParser -> FilePath -> TimeUnit -> TermList -> IO [Document]
fileToDocs' parser path time lst = do fileToDocsAdvanced parser path time lst = do
let patterns = buildPatterns lst let patterns = buildPatterns lst
case parser of case parser of
Wos limit -> wosToDocs limit patterns time path Wos limit -> wosToDocs limit patterns time path
Csv _ -> csvToDocs parser patterns time path Csv _ -> csvToDocs parser patterns time path
Csv' _ -> csvToDocs parser patterns time path Csv' _ -> csvToDocs parser patterns time path
fileToDocsDefault :: CorpusParser -> FilePath -> [TimeUnit] -> TermList -> IO [Document]
fileToDocsDefault parser path timeUnits lst =
if length timeUnits > 0
then
do
let timeUnit = (head' "fileToDocsDefault" timeUnits)
docs <- fileToDocsAdvanced parser path timeUnit lst
let periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod timeUnit) (getTimeStep timeUnit)
if (length periods < 3)
then fileToDocsDefault parser path (tail timeUnits) lst
else pure docs
else panic "this corpus is incompatible with the phylomemy reconstruction"
-- on passe à passer la time unit dans la conf envoyé au phyloMaker
-- dans le phyloMaker si default est true alors dans le setDefault ou pense à utiliser la TimeUnit de la conf
--------------- ---------------
-- | Label | -- -- | Label | --
...@@ -251,7 +269,11 @@ main = do ...@@ -251,7 +269,11 @@ main = do
printIOMsg "Parse the corpus" printIOMsg "Parse the corpus"
mapList <- fileToList (listParser config) (listPath config) mapList <- fileToList (listParser config) (listPath config)
corpus <- fileToDocs' (corpusParser config) (corpusPath config) (timeUnit config) mapList
corpus <- if (defaultMode config)
then fileToDocsDefault (corpusParser config) (corpusPath config) [Year 3 1 5,Month 3 1 5,Week 4 2 5] mapList
else fileToDocsAdvanced (corpusParser config) (corpusPath config) (timeUnit config) mapList
printIOComment (show (length corpus) <> " parsed docs from the corpus") printIOComment (show (length corpus) <> " parsed docs from the corpus")
printIOComment (show (length $ nub $ concat $ map text corpus) <> " Size ngs_coterms") printIOComment (show (length $ nub $ concat $ map text corpus) <> " Size ngs_coterms")
......
gargantext.cabal
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...@@ -5,7 +5,7 @@ cabal-version: 1.12 ...@@ -5,7 +5,7 @@ cabal-version: 1.12
-- see: https://github.com/sol/hpack -- see: https://github.com/sol/hpack
name: gargantext name: gargantext
version: 0.0.6.9.9.6.6 version: 0.0.6.9.9.6.7
synopsis: Search, map, share synopsis: Search, map, share
description: Please see README.md description: Please see README.md
category: Data category: Data
...@@ -26,6 +26,8 @@ data-files: ...@@ -26,6 +26,8 @@ data-files:
ekg-assets/chart_line_add.png ekg-assets/chart_line_add.png
ekg-assets/cross.png ekg-assets/cross.png
test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
test-data/phylo/bpa_phylo_test.json
test-data/phylo/open_science.json
library library
exposed-modules: exposed-modules:
...@@ -81,6 +83,7 @@ library ...@@ -81,6 +83,7 @@ library
Gargantext.Core.Types.Individu Gargantext.Core.Types.Individu
Gargantext.Core.Types.Main Gargantext.Core.Types.Main
Gargantext.Core.Types.Query Gargantext.Core.Types.Query
Gargantext.Core.Types.Phylo
Gargantext.Core.Utils Gargantext.Core.Utils
Gargantext.Core.Utils.Prefix Gargantext.Core.Utils.Prefix
Gargantext.Core.Viz.Graph Gargantext.Core.Viz.Graph
...@@ -235,7 +238,6 @@ library ...@@ -235,7 +238,6 @@ library
Gargantext.Core.Text.Terms.Multi.PosTagging Gargantext.Core.Text.Terms.Multi.PosTagging
Gargantext.Core.Text.Terms.Multi.PosTagging.Types Gargantext.Core.Text.Terms.Multi.PosTagging.Types
Gargantext.Core.Text.Upload Gargantext.Core.Text.Upload
Gargantext.Core.Types.Phylo
Gargantext.Core.Types.Search Gargantext.Core.Types.Search
Gargantext.Core.Utils.DateUtils Gargantext.Core.Utils.DateUtils
Gargantext.Core.Viz Gargantext.Core.Viz
......
package.yaml
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...@@ -6,7 +6,7 @@ name: gargantext ...@@ -6,7 +6,7 @@ name: gargantext
# | | | +----- Layers * : New versions with API additions # | | | +----- Layers * : New versions with API additions
# | | | | +--- Layers * : New versions without API breaking changes # | | | | +--- Layers * : New versions without API breaking changes
# | | | | | # | | | | |
version: '0.0.6.9.9.6.6' version: '0.0.6.9.9.6.7'
synopsis: Search, map, share synopsis: Search, map, share
description: Please see README.md description: Please see README.md
category: Data category: Data
...@@ -45,6 +45,8 @@ data-files: ...@@ -45,6 +45,8 @@ data-files:
- ekg-assets/chart_line_add.png - ekg-assets/chart_line_add.png
- ekg-assets/cross.png - ekg-assets/cross.png
- test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json - test-data/ngrams/GarganText_NgramsTerms-QuantumComputing.json
- test-data/phylo/bpa_phylo_test.json
- test-data/phylo/open_science.json
library: library:
source-dirs: src source-dirs: src
ghc-options: ghc-options:
...@@ -109,6 +111,7 @@ library: ...@@ -109,6 +111,7 @@ library:
- Gargantext.Core.Types.Individu - Gargantext.Core.Types.Individu
- Gargantext.Core.Types.Main - Gargantext.Core.Types.Main
- Gargantext.Core.Types.Query - Gargantext.Core.Types.Query
- Gargantext.Core.Types.Phylo
- Gargantext.Core.Utils - Gargantext.Core.Utils
- Gargantext.Core.Utils.Prefix - Gargantext.Core.Utils.Prefix
- Gargantext.Core.Viz.Graph - Gargantext.Core.Viz.Graph
......
src-test/Offline/JSON.hs
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...@@ -9,16 +9,21 @@ import Data.Aeson ...@@ -9,16 +9,21 @@ import Data.Aeson
import Data.Either import Data.Either
import Gargantext.API.Node.Corpus.New import Gargantext.API.Node.Corpus.New
import Gargantext.API.Node.Corpus.Types import Gargantext.API.Node.Corpus.Types
import Gargantext.Core.Types.Phylo
import Gargantext.Core.Viz.Phylo.API import Gargantext.Core.Viz.Phylo.API
import Prelude import Prelude
import Test.Tasty import Test.Tasty
import Test.Tasty.HUnit import Test.Tasty.HUnit
import Test.Tasty.QuickCheck import Test.Tasty.QuickCheck
import Text.RawString.QQ import Text.RawString.QQ
import qualified Data.ByteString as B
import qualified Data.ByteString.Lazy.Char8 as C8 import qualified Data.ByteString.Lazy.Char8 as C8
import Paths_gargantext
jsonRoundtrip :: (Show a, FromJSON a, ToJSON a, Eq a) => a -> Property jsonRoundtrip :: (Show a, FromJSON a, ToJSON a, Eq a) => a -> Property
jsonRoundtrip a = eitherDecode (encode a) === Right a jsonRoundtrip a =
counterexample ("Parsed JSON: " <> C8.unpack (encode a)) $ eitherDecode (encode a) === Right a
tests :: TestTree tests :: TestTree
tests = testGroup "JSON" [ tests = testGroup "JSON" [
...@@ -26,7 +31,14 @@ tests = testGroup "JSON" [ ...@@ -26,7 +31,14 @@ tests = testGroup "JSON" [
, testProperty "WithQuery roundtrips" (jsonRoundtrip @WithQuery) , testProperty "WithQuery roundtrips" (jsonRoundtrip @WithQuery)
, testCase "WithQuery frontend compliance" testWithQueryFrontend , testCase "WithQuery frontend compliance" testWithQueryFrontend
, testGroup "Phylo" [ , testGroup "Phylo" [
testProperty "PhyloData" (jsonRoundtrip @PhyloData) testProperty "PeriodToNode" (jsonRoundtrip @PeriodToNodeData)
, testProperty "GraphData" (jsonRoundtrip @GraphData)
, testProperty "GraphDataData" (jsonRoundtrip @GraphDataData)
, testProperty "ObjectData" (jsonRoundtrip @ObjectData)
, testProperty "PhyloData" (jsonRoundtrip @PhyloData)
, testProperty "LayerData" (jsonRoundtrip @LayerData)
, testCase "can parse bpa_phylo_test.json" testParseBpaPhylo
, testCase "can parse open_science.json" testOpenSciencePhylo
] ]
] ]
...@@ -40,3 +52,19 @@ testWithQueryFrontend = do ...@@ -40,3 +52,19 @@ testWithQueryFrontend = do
-- instances, this test would fail, and we will be notified. -- instances, this test would fail, and we will be notified.
cannedWithQueryPayload :: String cannedWithQueryPayload :: String
cannedWithQueryPayload = [r| {"query":"Haskell","node_id":138,"lang":"EN","flowListWith":{"type":"MyListsFirst"},"datafield":"External Arxiv","databases":"Arxiv"} |] cannedWithQueryPayload = [r| {"query":"Haskell","node_id":138,"lang":"EN","flowListWith":{"type":"MyListsFirst"},"datafield":"External Arxiv","databases":"Arxiv"} |]
testParseBpaPhylo :: Assertion
testParseBpaPhylo = do
pth <- getDataFileName "test-data/phylo/bpa_phylo_test.json"
jsonBlob <- B.readFile pth
case eitherDecodeStrict' @GraphData jsonBlob of
Left err -> error err
Right _ -> pure ()
testOpenSciencePhylo :: Assertion
testOpenSciencePhylo = do
pth <- getDataFileName "test-data/phylo/open_science.json"
jsonBlob <- B.readFile pth
case eitherDecodeStrict' @PhyloData jsonBlob of
Left err -> error err
Right _ -> pure ()
src/Gargantext/Core/Types/Phylo.hs
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...@@ -28,9 +28,12 @@ module Gargantext.Core.Types.Phylo where ...@@ -28,9 +28,12 @@ module Gargantext.Core.Types.Phylo where
import Control.Monad.Fail (fail) import Control.Monad.Fail (fail)
import Control.Lens (makeLenses) import Control.Lens (makeLenses)
import Control.Applicative ((<|>))
import Data.Aeson import Data.Aeson
import Data.Aeson.Types
import Data.Aeson.TH (deriveJSON) import Data.Aeson.TH (deriveJSON)
import Data.Maybe
import Data.Monoid import Data.Monoid
import Data.Swagger import Data.Swagger
import Data.Text (Text) import Data.Text (Text)
...@@ -38,6 +41,7 @@ import Data.Time.Clock.POSIX (POSIXTime) ...@@ -38,6 +41,7 @@ import Data.Time.Clock.POSIX (POSIXTime)
import qualified Data.Text as T import qualified Data.Text as T
import Test.QuickCheck import Test.QuickCheck
import Test.QuickCheck.Instances.Text() import Test.QuickCheck.Instances.Text()
import Prelude (Either(..))
import GHC.Generics (Generic) import GHC.Generics (Generic)
...@@ -114,12 +118,319 @@ data GraphData = ...@@ -114,12 +118,319 @@ data GraphData =
, _gd_edges :: [EdgeData] , _gd_edges :: [EdgeData]
, _gd_objects :: [ObjectData] , _gd_objects :: [ObjectData]
, _gd_strict :: Bool , _gd_strict :: Bool
, _gd_data :: GraphDataData
} deriving (Show, Eq, Generic) } deriving (Show, Eq, Generic)
data GraphDataData =
GraphDataData {
_gdd_bb :: Text
, _gdd_color :: Text
, _gdd_fontsize :: Text
, _gdd_label :: Text
, _gdd_labelloc :: Text
, _gdd_lheight :: Text
, _gdd_lp :: Text
, _gdd_lwidth :: Text
, _gdd_name :: Text
, _gdd_nodesep :: Text
, _gdd_overlap :: Text
, _gdd_phyloBranches :: Text
, _gdd_phyloDocs :: Text
, _gdd_phyloFoundations :: Text
, _gdd_phyloGroups :: Text
, _gdd_phyloPeriods :: Text
, _gdd_phyloSources :: Text
, _gdd_phyloTerms :: Text
, _gdd_phyloTimeScale :: Text
, _gdd_rank :: Text
, _gdd_ranksep :: Text
, _gdd_ratio :: Text
, _gdd_splines :: Text
, _gdd_style :: Text
} deriving (Show, Eq, Generic)
instance ToJSON GraphDataData where
toJSON GraphDataData{..} = object [
"bb" .= _gdd_bb
, "color" .= _gdd_color
, "fontsize" .= _gdd_fontsize
, "label" .= _gdd_label
, "labelloc" .= _gdd_labelloc
, "lheight" .= _gdd_lheight
, "lp" .= _gdd_lp
, "lwidth" .= _gdd_lwidth
, "name" .= _gdd_name
, "nodesep" .= _gdd_nodesep
, "overlap" .= _gdd_overlap
, "phyloBranches" .= _gdd_phyloBranches
, "phyloDocs" .= _gdd_phyloDocs
, "phyloFoundations" .= _gdd_phyloFoundations
, "phyloGroups" .= _gdd_phyloGroups
, "phyloPeriods" .= _gdd_phyloPeriods
, "phyloSources" .= _gdd_phyloSources
, "phyloTerms" .= _gdd_phyloTerms
, "phyloTimeScale" .= _gdd_phyloTimeScale
, "rank" .= _gdd_rank
, "ranksep" .= _gdd_ranksep
, "ratio" .= _gdd_ratio
, "splines" .= _gdd_splines
, "style" .= _gdd_style
]
instance FromJSON GraphDataData where
parseJSON = withObject "GraphDataData" $ \o -> do
_gdd_bb <- o .: "bb"
_gdd_color <- o .: "color"
_gdd_fontsize <- o .: "fontsize"
_gdd_label <- o .: "label"
_gdd_labelloc <- o .: "labelloc"
_gdd_lheight <- o .: "lheight"
_gdd_lp <- o .: "lp"
_gdd_lwidth <- o .: "lwidth"
_gdd_name <- o .: "name"
_gdd_nodesep <- o .: "nodesep"
_gdd_overlap <- o .: "overlap"
_gdd_phyloBranches <- o .: "phyloBranches"
_gdd_phyloDocs <- o .: "phyloDocs"
_gdd_phyloFoundations <- o .: "phyloFoundations"
_gdd_phyloGroups <- o .: "phyloGroups"
_gdd_phyloPeriods <- o .: "phyloPeriods"
_gdd_phyloSources <- o .: "phyloSources"
_gdd_phyloTerms <- o .: "phyloTerms"
_gdd_phyloTimeScale <- o .: "phyloTimeScale"
_gdd_rank <- o .: "rank"
_gdd_ranksep <- o .: "ranksep"
_gdd_ratio <- o .: "ratio"
_gdd_splines <- o .: "splines"
_gdd_style <- o .: "style"
pure $ GraphDataData{..}
-- temp placeholder. -- temp placeholder.
newtype ObjectData = ObjectData { _ObjectData :: Value } data ObjectData =
deriving stock (Show, Eq, Generic) GroupToNode !GvId !NodeCommonData !GroupToNodeData
deriving newtype (FromJSON, ToJSON) | BranchToNode !GvId !NodeCommonData !BranchToNodeData
| PeriodToNode !GvId !NodeCommonData !PeriodToNodeData
| Layer !GvId !GraphDataData !LayerData
deriving (Show, Eq, Generic)
instance ToJSON ObjectData where
toJSON = \case
GroupToNode gvid commonData nodeTypeData
-> mkObject gvid (Left commonData) nodeTypeData
BranchToNode gvid commonData nodeTypeData
-> mkObject gvid (Left commonData) nodeTypeData
PeriodToNode gvid commonData nodeTypeData
-> mkObject gvid (Left commonData) nodeTypeData
Layer gvid graphData nodeTypeData
-> mkObject gvid (Right graphData) nodeTypeData
instance FromJSON ObjectData where
parseJSON = withObject "ObjectData" $ \o -> do
_gvid <- o .: "_gvid"
-- try to parse the graph data first. If we succeed, then we are dealing with
-- the 'Layer', otherwise we the rest, but for the rest we can avoid re-parsing
-- the 'NodeCommonData' every time.
case parseMaybe @_ @GraphDataData parseJSON (Object o) of
Nothing
-> do commonData <- parseJSON (Object o)
((GroupToNode <$> pure _gvid <*> pure commonData <*> parseJSON (Object o)) <|>
(BranchToNode <$> pure _gvid <*> pure commonData <*> parseJSON (Object o)) <|>
(PeriodToNode <$> pure _gvid <*> pure commonData <*> parseJSON (Object o)))
Just gd
-> Layer <$> pure _gvid <*> pure gd <*> parseJSON (Object o)
mkObject :: ToJSON a => GvId -> Either NodeCommonData GraphDataData -> a -> Value
mkObject gvid commonData objectTypeData =
let commonDataJSON = either toJSON toJSON commonData
objectTypeDataJSON = toJSON objectTypeData
header = object $ [ "_gvid" .= toJSON gvid ]
in case (commonDataJSON, objectTypeDataJSON, header) of
(Object hdr, Object cdJSON, Object etDataJSON)
-> Object $ hdr <> cdJSON <> etDataJSON
_ -> panic "[Gargantext.Core.Types.Phylo.mkObject] impossible: commonData, header or objectTypeDataJSON didn't convert back to JSON Object."
data GroupToNodeData
= GroupToNodeData
{ _gtn_bId :: Text
, _gtn_branchId :: Text
, _gtn_fontname :: Text
, _gtn_foundation :: Text
, _gtn_frequence :: Text
, _gtn_from :: Text
, _gtn_lbl :: Text
, _gtn_penwidth :: Text
, _gtn_role :: Text
, _gtn_seaLvl :: Maybe Text
, _gtn_source :: Text
, _gtn_strFrom :: Maybe Text
, _gtn_strTo :: Maybe Text
, _gtn_support :: Text
, _gtn_to :: Text
, _gtn_weight :: Text
} deriving (Show, Eq, Generic)
instance ToJSON GroupToNodeData where
toJSON GroupToNodeData{..} = object [
"bId" .= _gtn_bId
, "branchId" .= _gtn_branchId
, "fontname" .= _gtn_fontname
, "foundation" .= _gtn_foundation
, "frequence" .= _gtn_frequence
, "from" .= _gtn_from
, "lbl" .= _gtn_lbl
, "penwidth" .= _gtn_penwidth
, "role" .= _gtn_role
, "seaLvl" .= _gtn_seaLvl
, "source" .= _gtn_source
, "strFrom" .= _gtn_strFrom
, "strTo" .= _gtn_strTo
, "support" .= _gtn_support
, "to" .= _gtn_to
, "weight" .= _gtn_weight
]
instance FromJSON GroupToNodeData where
parseJSON = withObject "GroupToNodeData" $ \o -> do
_gtn_bId <- o .: "bId"
_gtn_branchId <- o .: "branchId"
_gtn_fontname <- o .: "fontname"
_gtn_foundation <- o .: "foundation"
_gtn_frequence <- o .: "frequence"
_gtn_from <- o .: "from"
_gtn_lbl <- o .: "lbl"
_gtn_penwidth <- o .: "penwidth"
_gtn_role <- o .: "role"
_gtn_seaLvl <- o .:? "seaLvl"
_gtn_source <- o .: "source"
_gtn_strFrom <- o .:? "strFrom"
_gtn_strTo <- o .:? "strTo"
_gtn_support <- o .: "support"
_gtn_to <- o .: "to"
_gtn_weight <- o .: "weight"
pure $ GroupToNodeData{..}
data BranchToNodeData
= BranchToNodeData
{ _btn_age :: Text
, _btn_bId :: Text
, _btn_birth :: Text
, _btn_branchId :: Text
, _btn_branch_x :: Text
, _btn_branch_y :: Text
, _btn_fillcolor :: Text
, _btn_fontname :: Text
, _btn_fontsize :: Text
, _btn_size :: Text
, _btn_style :: Text
} deriving (Show, Eq, Generic)
instance ToJSON BranchToNodeData where
toJSON BranchToNodeData{..} = object [
"age" .= _btn_age
, "bId" .= _btn_bId
, "birth" .= _btn_birth
, "branchId" .= _btn_branchId
, "branch_x" .= _btn_branch_x
, "branch_y" .= _btn_branch_y
, "fillcolor" .= _btn_fillcolor
, "fontname" .= _btn_fontname
, "fontsize" .= _btn_fontsize
, "size" .= _btn_size
, "style" .= _btn_style
]
instance FromJSON BranchToNodeData where
parseJSON = withObject "BranchToNodeData" $ \o -> do
_btn_age <- o .: "age"
_btn_bId <- o .: "bId"
_btn_birth <- o .: "birth"
_btn_branchId <- o .: "branchId"
_btn_branch_x <- o .: "branch_x"
_btn_branch_y <- o .: "branch_y"
_btn_fillcolor <- o .: "fillcolor"
_btn_fontname <- o .: "fontname"
_btn_fontsize <- o .: "fontsize"
_btn_size <- o .: "size"
_btn_style <- o .: "style"
pure $ BranchToNodeData{..}
data PeriodToNodeData
= PeriodToNodeData
{ _ptn_fontsize :: Text
, _ptn_from :: Text
, _ptn_strFrom :: Maybe Text
, _ptn_strTo :: Maybe Text
, _ptn_to :: Text
} deriving (Show, Eq, Generic)
instance ToJSON PeriodToNodeData where
toJSON PeriodToNodeData{..} = object [
"fontsize" .= _ptn_fontsize
, "from" .= _ptn_from
, "strFrom" .= _ptn_strFrom
, "strTo" .= _ptn_strTo
, "to" .= _ptn_to
]
instance FromJSON PeriodToNodeData where
parseJSON = withObject "PeriodToNodeData" $ \o -> do
_ptn_fontsize <- o .: "fontsize"
_ptn_from <- o .: "from"
_ptn_strFrom <- o .:? "strFrom"
_ptn_strTo <- o .:? "strTo"
_ptn_to <- o .: "to"
pure $ PeriodToNodeData{..}
data LayerData
= LayerData {
_ld_nodes :: [Int]
} deriving (Show, Eq, Generic)
instance ToJSON LayerData where
toJSON LayerData{..} = object [
"nodes" .= toJSON _ld_nodes
]
instance FromJSON LayerData where
parseJSON = withObject "LayerData" $ \o -> do
_ld_nodes <- fromMaybe mempty <$> (o .:? "nodes")
pure $ LayerData{..}
data NodeCommonData =
NodeCommonData {
_nd_height :: !Text
, _nd_label :: !Text
, _nd_name :: !Text
, _nd_nodeType :: !Text
, _nd_pos :: !Text
, _nd_shape :: !Text
, _nd_width :: !Text
} deriving (Show, Eq, Generic)
instance ToJSON NodeCommonData where
toJSON NodeCommonData{..} = object [
"height" .= _nd_height
, "label" .= _nd_label
, "name" .= _nd_name
, "nodeType" .= _nd_nodeType
, "pos" .= _nd_pos
, "shape" .= _nd_shape
, "width" .= _nd_width
]
instance FromJSON NodeCommonData where
parseJSON = withObject "NodeCommonData" $ \o -> do
_nd_height <- o .: "height"
_nd_label <- o .: "label"
_nd_name <- o .: "name"
_nd_nodeType <- o .: "nodeType"
_nd_pos <- o .: "pos"
_nd_shape <- o .: "shape"
_nd_width <- o .: "width"
pure $ NodeCommonData{..}
data EdgeCommonData = data EdgeCommonData =
EdgeCommonData { EdgeCommonData {
...@@ -137,6 +448,7 @@ data EdgeData ...@@ -137,6 +448,7 @@ data EdgeData
= GroupToAncestor !GvId !EdgeCommonData !GroupToAncestorData = GroupToAncestor !GvId !EdgeCommonData !GroupToAncestorData
| GroupToGroup !GvId !EdgeCommonData !GroupToGroupData | GroupToGroup !GvId !EdgeCommonData !GroupToGroupData
| BranchToGroup !GvId !EdgeCommonData !BranchToGroupData | BranchToGroup !GvId !EdgeCommonData !BranchToGroupData
| PeriodToPeriod !GvId !EdgeCommonData
deriving (Show, Eq, Generic) deriving (Show, Eq, Generic)
data GroupToAncestorData data GroupToAncestorData
...@@ -173,13 +485,20 @@ $(deriveJSON (unPrefix "_phylo_Level" ) ''PhyloLevel ) ...@@ -173,13 +485,20 @@ $(deriveJSON (unPrefix "_phylo_Level" ) ''PhyloLevel )
$(deriveJSON (unPrefix "_phylo_Group" ) ''PhyloGroup ) $(deriveJSON (unPrefix "_phylo_Group" ) ''PhyloGroup )
instance ToJSON GraphData where instance ToJSON GraphData where
toJSON GraphData{..} = object toJSON = mkGraphData
[ "_subgraph_cnt" .= _gd__subgraph_cnt
, "directed" .= _gd_directed mkGraphData :: GraphData -> Value
, "edges" .= _gd_edges mkGraphData GraphData{..} =
, "objects" .= _gd_objects let hdrJSON = object [ "_subgraph_cnt" .= _gd__subgraph_cnt
, "strict" .= _gd_strict , "directed" .= _gd_directed
] , "edges" .= _gd_edges
, "objects" .= _gd_objects
, "strict" .= _gd_strict
]
datJSON = toJSON _gd_data
in case (hdrJSON, datJSON) of
(Object a, Object b) -> Object $ a <> b
_ -> panic "[Gargantext.Core.Types.Phylo.mkGraphData] impossible: header or data didn't convert back to JSON Object."
instance FromJSON GraphData where instance FromJSON GraphData where
parseJSON = withObject "GraphData" $ \o -> do parseJSON = withObject "GraphData" $ \o -> do
...@@ -188,6 +507,7 @@ instance FromJSON GraphData where ...@@ -188,6 +507,7 @@ instance FromJSON GraphData where
_gd_edges <- o .: "edges" _gd_edges <- o .: "edges"
_gd_objects <- o .: "objects" _gd_objects <- o .: "objects"
_gd_strict <- o .: "strict" _gd_strict <- o .: "strict"
_gd_data <- parseJSON (Object o)
pure GraphData{..} pure GraphData{..}
instance ToJSON GvId where instance ToJSON GvId where
...@@ -198,14 +518,16 @@ instance FromJSON GvId where ...@@ -198,14 +518,16 @@ instance FromJSON GvId where
instance ToJSON EdgeData where instance ToJSON EdgeData where
toJSON = \case toJSON = \case
GroupToAncestor gvid commonData edgeTypeData GroupToAncestor gvid commonData edgeTypeData
-> mkNode "ancestorLink" gvid commonData edgeTypeData -> mkEdge (Just "ancestorLink") gvid commonData edgeTypeData
GroupToGroup gvid commonData edgeTypeData GroupToGroup gvid commonData edgeTypeData
-> mkNode "link" gvid commonData edgeTypeData -> mkEdge (Just "link") gvid commonData edgeTypeData
BranchToGroup gvid commonData edgeTypeData BranchToGroup gvid commonData edgeTypeData
-> mkNode "branchLink" gvid commonData edgeTypeData -> mkEdge (Just "branchLink") gvid commonData edgeTypeData
PeriodToPeriod gvid commonData
-> mkEdge Nothing gvid commonData (Object mempty)
mkNode :: ToJSON a => Text -> GvId -> EdgeCommonData -> a -> Value mkEdge :: ToJSON a => Maybe Text -> GvId -> EdgeCommonData -> a -> Value
mkNode edgeType gvid commonData edgeTypeData = mkEdge edgeType gvid commonData edgeTypeData =
let commonDataJSON = toJSON commonData let commonDataJSON = toJSON commonData
edgeTypeDataJSON = toJSON edgeTypeData edgeTypeDataJSON = toJSON edgeTypeData
header = object $ [ "edgeType" .= toJSON edgeType header = object $ [ "edgeType" .= toJSON edgeType
...@@ -214,23 +536,24 @@ mkNode edgeType gvid commonData edgeTypeData = ...@@ -214,23 +536,24 @@ mkNode edgeType gvid commonData edgeTypeData =
in case (commonDataJSON, edgeTypeDataJSON, header) of in case (commonDataJSON, edgeTypeDataJSON, header) of
(Object hdr, Object cdJSON, Object etDataJSON) (Object hdr, Object cdJSON, Object etDataJSON)
-> Object $ hdr <> cdJSON <> etDataJSON -> Object $ hdr <> cdJSON <> etDataJSON
_ -> panic "[Gargantext.Core.Types.Phylo.mkNode] impossible: commonData, header or edgeTypeDataJSON didn't convert back to JSON Object." _ -> panic "[Gargantext.Core.Types.Phylo.mkEdge] impossible: commonData, header or edgeTypeDataJSON didn't convert back to JSON Object."
instance FromJSON EdgeData where instance FromJSON EdgeData where
parseJSON = withObject "EdgeData" $ \o -> do parseJSON = withObject "EdgeData" $ \o -> do
edgeType <- o .: "edgeType" edgeType <- o .:? "edgeType"
gvid <- o .: "_gvid" gvid <- o .: "_gvid"
_ed_color <- o .: "color" _ed_color <- o .: "color"
_ed_head <- o .: "head" _ed_head <- o .: "head"
_ed_pos <- o .: "pos" _ed_pos <- o .: "pos"
_ed_tail <- o .: "tail" _ed_tail <- o .: "tail"
_ed_width <- o .: "width" _ed_width <- o .: "width"
case (edgeType :: Text) of case (edgeType :: Maybe Text) of
"ancestorLink" -> GroupToAncestor <$> pure gvid <*> pure EdgeCommonData{..} <*> parseJSON (Object o) Just "ancestorLink" -> GroupToAncestor <$> pure gvid <*> pure EdgeCommonData{..} <*> parseJSON (Object o)
"link" -> GroupToGroup <$> pure gvid <*> pure EdgeCommonData{..} <*> parseJSON (Object o) Just "link" -> GroupToGroup <$> pure gvid <*> pure EdgeCommonData{..} <*> parseJSON (Object o)
"branchLink" -> BranchToGroup <$> pure gvid <*> pure EdgeCommonData{..} <*> parseJSON (Object o) Just "branchLink" -> BranchToGroup <$> pure gvid <*> pure EdgeCommonData{..} <*> parseJSON (Object o)
_ -> fail $ "EdgeData: unrecognised edgeType for Phylo graph: " <> T.unpack edgeType Just unknownEdgeType -> fail $ "EdgeData: unrecognised edgeType for Phylo graph: " <> T.unpack unknownEdgeType
Nothing -> pure $ PeriodToPeriod gvid EdgeCommonData{..}
instance ToJSON EdgeCommonData where instance ToJSON EdgeCommonData where
toJSON EdgeCommonData{..} = object toJSON EdgeCommonData{..} = object
...@@ -307,10 +630,57 @@ instance ToSchema GvId where ...@@ -307,10 +630,57 @@ instance ToSchema GvId where
declareNamedSchema = genericDeclareNamedSchema defaultSchemaOptions declareNamedSchema = genericDeclareNamedSchema defaultSchemaOptions
instance ToSchema EdgeData where instance ToSchema EdgeData where
declareNamedSchema = genericDeclareNamedSchema defaultSchemaOptions declareNamedSchema = genericDeclareNamedSchema defaultSchemaOptions
instance ToSchema GraphDataData where
declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_gdd_")
instance ToSchema GraphData where instance ToSchema GraphData where
declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_gd_") declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "_gd_")
-- | Arbitrary instances -- | Arbitrary instances
instance Arbitrary LayerData where
arbitrary = LayerData <$> arbitrary
instance Arbitrary NodeCommonData where
arbitrary = NodeCommonData <$> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
instance Arbitrary GroupToNodeData where
arbitrary = GroupToNodeData <$> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
instance Arbitrary BranchToNodeData where
arbitrary = BranchToNodeData <$> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
instance Arbitrary PeriodToNodeData where
arbitrary = PeriodToNodeData <$> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
<*> arbitrary
instance Arbitrary BranchToGroupData where instance Arbitrary BranchToGroupData where
arbitrary = BranchToGroupData <$> arbitrary <*> arbitrary arbitrary = BranchToGroupData <$> arbitrary <*> arbitrary
instance Arbitrary GroupToGroupData where instance Arbitrary GroupToGroupData where
...@@ -329,7 +699,11 @@ instance Arbitrary EdgeCommonData where ...@@ -329,7 +699,11 @@ instance Arbitrary EdgeCommonData where
<*> arbitrary <*> arbitrary
<*> arbitrary <*> arbitrary
instance Arbitrary ObjectData where instance Arbitrary ObjectData where
arbitrary = ObjectData <$> (String <$> arbitrary) -- temporary, it doesn't matter. arbitrary = oneof [ GroupToNode <$> arbitrary <*> arbitrary <*> arbitrary
, BranchToNode <$> arbitrary <*> arbitrary <*> arbitrary
, PeriodToNode <$> arbitrary <*> arbitrary <*> arbitrary
, Layer <$> arbitrary <*> arbitrary <*> arbitrary
]
instance Arbitrary GvId where instance Arbitrary GvId where
arbitrary = GvId <$> arbitrary arbitrary = GvId <$> arbitrary
instance Arbitrary EdgeData where instance Arbitrary EdgeData where
...@@ -338,8 +712,12 @@ instance Arbitrary EdgeData where ...@@ -338,8 +712,12 @@ instance Arbitrary EdgeData where
, BranchToGroup <$> arbitrary <*> arbitrary <*> arbitrary , BranchToGroup <$> arbitrary <*> arbitrary <*> arbitrary
] ]
instance Arbitrary GraphData where instance Arbitrary GraphData where
arbitrary = GraphData <$> arbitrary arbitrary = GraphData <$> arbitrary <*> arbitrary <*> vectorOf 10 arbitrary <*> vectorOf 10 arbitrary
<*> arbitrary <*> arbitrary <*> arbitrary
<*> arbitrary instance Arbitrary GraphDataData where
<*> arbitrary arbitrary = GraphDataData <$> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
<*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
<*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
<*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
<*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
<*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
src/Gargantext/Core/Viz/Phylo.hs
View file @ 79d0ea23
...@@ -135,7 +135,7 @@ data TimeUnit = ...@@ -135,7 +135,7 @@ data TimeUnit =
{ _day_period :: Int { _day_period :: Int
, _day_step :: Int , _day_step :: Int
, _day_matchingFrame :: Int } , _day_matchingFrame :: Int }
deriving (Show,Generic,Eq) deriving (Show,Generic,Eq,NFData)
instance ToSchema TimeUnit where instance ToSchema TimeUnit where
declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "") declareNamedSchema = genericDeclareNamedSchema (unPrefixSwagger "")
...@@ -227,7 +227,7 @@ defaultConfig = ...@@ -227,7 +227,7 @@ defaultConfig =
, phyloScale = 2 , phyloScale = 2
, similarity = WeightedLogJaccard 0.5 1 , similarity = WeightedLogJaccard 0.5 1
, seaElevation = Constante 0.1 0.1 , seaElevation = Constante 0.1 0.1
, defaultMode = True , defaultMode = False
, findAncestors = False , findAncestors = False
, phyloSynchrony = ByProximityThreshold 0.5 0 AllBranches MergeAllGroups , phyloSynchrony = ByProximityThreshold 0.5 0 AllBranches MergeAllGroups
, phyloQuality = Quality 0.5 1 , phyloQuality = Quality 0.5 1
...@@ -355,6 +355,7 @@ data Document = Document ...@@ -355,6 +355,7 @@ data Document = Document
, text :: [Ngrams] , text :: [Ngrams]
, weight :: Maybe Double , weight :: Maybe Double
, sources :: [Text] , sources :: [Text]
, docTime :: TimeUnit
} deriving (Eq,Show,Generic,NFData) } deriving (Eq,Show,Generic,NFData)
...@@ -372,6 +373,7 @@ data PhyloFoundations = PhyloFoundations ...@@ -372,6 +373,7 @@ data PhyloFoundations = PhyloFoundations
data PhyloCounts = PhyloCounts data PhyloCounts = PhyloCounts
{ coocByDate :: !(Map Date Cooc) { coocByDate :: !(Map Date Cooc)
, docsByDate :: !(Map Date Double) , docsByDate :: !(Map Date Double)
, rootsCountByDate :: !(Map Date (Map Int Double))
, rootsCount :: !(Map Int Double) , rootsCount :: !(Map Int Double)
, rootsFreq :: !(Map Int Double) , rootsFreq :: !(Map Int Double)
, lastRootsFreq :: !(Map Int Double) , lastRootsFreq :: !(Map Int Double)
...@@ -487,8 +489,10 @@ data PhyloGroup = ...@@ -487,8 +489,10 @@ data PhyloGroup =
, _phylo_groupSources :: [Int] , _phylo_groupSources :: [Int]
, _phylo_groupNgrams :: [Int] , _phylo_groupNgrams :: [Int]
, _phylo_groupCooc :: !(Cooc) , _phylo_groupCooc :: !(Cooc)
, _phylo_groupDensity :: Double
, _phylo_groupBranchId :: PhyloBranchId , _phylo_groupBranchId :: PhyloBranchId
, _phylo_groupMeta :: Map Text [Double] , _phylo_groupMeta :: Map Text [Double]
, _phylo_groupRootsCount :: Map Int Double
, _phylo_groupScaleParents :: [Pointer] , _phylo_groupScaleParents :: [Pointer]
, _phylo_groupScaleChilds :: [Pointer] , _phylo_groupScaleChilds :: [Pointer]
, _phylo_groupPeriodParents :: [Pointer] , _phylo_groupPeriodParents :: [Pointer]
......
src/Gargantext/Core/Viz/Phylo/API/Tools.hs
View file @ 79d0ea23
...@@ -91,7 +91,9 @@ flowPhyloAPI config cId = do ...@@ -91,7 +91,9 @@ flowPhyloAPI config cId = do
corpus <- corpusIdtoDocuments (timeUnit config) cId corpus <- corpusIdtoDocuments (timeUnit config) cId
let phyloWithCliques = toPhyloWithoutLink corpus config let phyloWithCliques = toPhyloWithoutLink corpus config
-- writePhylo phyloWithCliquesFile phyloWithCliques -- writePhylo phyloWithCliquesFile phyloWithCliques
pure $ toPhylo (setConfig config phyloWithCliques) printDebug "PhyloConfig old: " config
pure $ toPhylo $ setConfig config phyloWithCliques
-------------------------------------------------------------------- --------------------------------------------------------------------
corpusIdtoDocuments :: TimeUnit -> CorpusId -> GargNoServer [Document] corpusIdtoDocuments :: TimeUnit -> CorpusId -> GargNoServer [Document]
...@@ -120,7 +122,7 @@ toPhyloDocs patterns time d = ...@@ -120,7 +122,7 @@ toPhyloDocs patterns time d =
(fromIntegral $ fromMaybe 1 $ _hd_publication_year d) (fromIntegral $ fromMaybe 1 $ _hd_publication_year d)
(fromMaybe 1 $ _hd_publication_month d) (fromMaybe 1 $ _hd_publication_month d)
(fromMaybe 1 $ _hd_publication_day d) time) (fromMaybe 1 $ _hd_publication_day d) time)
(termsInText' patterns $ title <> " " <> abstr) Nothing [] (termsInText' patterns $ title <> " " <> abstr) Nothing [] time
...@@ -138,7 +140,7 @@ context2phyloDocument timeUnit context (ngs_terms, ngs_sources) = do ...@@ -138,7 +140,7 @@ context2phyloDocument timeUnit context (ngs_terms, ngs_sources) = do
text' = maybe [] toText $ Map.lookup contextId ngs_terms text' = maybe [] toText $ Map.lookup contextId ngs_terms
sources' = maybe [] toText $ Map.lookup contextId ngs_sources sources' = maybe [] toText $ Map.lookup contextId ngs_sources
pure $ Document date date' text' Nothing sources' pure $ Document date date' text' Nothing sources' (Year 3 1 5)
-- TODO better default date and log the errors to improve data quality -- TODO better default date and log the errors to improve data quality
......
src/Gargantext/Core/Viz/Phylo/Example.hs
View file @ 79d0ea23
...@@ -111,6 +111,7 @@ docs = map (\(d,t) ...@@ -111,6 +111,7 @@ docs = map (\(d,t)
(filter (\n -> isRoots n (foundations ^. foundations_roots)) $ monoTexts t) (filter (\n -> isRoots n (foundations ^. foundations_roots)) $ monoTexts t)
Nothing Nothing
[] []
(Year 3 1 5)
) corpus ) corpus
......
src/Gargantext/Core/Viz/Phylo/PhyloExport.hs
View file @ 79d0ea23
...@@ -143,29 +143,27 @@ periodToDotNode prd prd' = ...@@ -143,29 +143,27 @@ periodToDotNode prd prd' =
groupToDotNode :: Vector Ngrams -> PhyloGroup -> Int -> Dot DotId groupToDotNode :: Vector Ngrams -> PhyloGroup -> Int -> Dot DotId
groupToDotNode fdt g bId = groupToDotNode fdt g bId =
node (groupIdToDotId $ getGroupId g) node (groupIdToDotId $ getGroupId g)
( [ FontName "Arial" ([FontName "Arial", Shape Square, penWidth 4, toLabel (groupToTable fdt g)]
, Shape Square <> [ toAttr "nodeType" "group"
, penWidth 4 , toAttr "gid" (groupIdToDotId $ getGroupId g)
, toLabel (groupToTable fdt g) ] , toAttr "from" (pack $ show (fst $ g ^. phylo_groupPeriod))
<> [ toAttr "nodeType" "group" , toAttr "to" (pack $ show (snd $ g ^. phylo_groupPeriod))
, toAttr "gid" (groupIdToDotId $ getGroupId g) , toAttr "strFrom" (pack $ show (fst $ g ^. phylo_groupPeriod'))
, toAttr "from" (pack $ show (fst $ g ^. phylo_groupPeriod)) , toAttr "strTo" (pack $ show (snd $ g ^. phylo_groupPeriod'))
, toAttr "to" (pack $ show (snd $ g ^. phylo_groupPeriod)) , toAttr "branchId" (pack $ unwords (init $ map show $ snd $ g ^. phylo_groupBranchId))
, toAttr "strFrom" (pack $ show (fst $ g ^. phylo_groupPeriod')) , toAttr "bId" (pack $ show bId)
, toAttr "strTo" (pack $ show (snd $ g ^. phylo_groupPeriod')) , toAttr "support" (pack $ show (g ^. phylo_groupSupport))
, toAttr "branchId" (pack $ unwords (init $ map show $ snd $ g ^. phylo_groupBranchId)) , toAttr "weight" (pack $ show (g ^. phylo_groupWeight))
, toAttr "bId" (pack $ show bId) , toAttr "source" (pack $ show (nub $ g ^. phylo_groupSources))
, toAttr "support" (pack $ show (g ^. phylo_groupSupport)) , toAttr "sourceFull" (pack $ show (g ^. phylo_groupSources))
, toAttr "weight" (pack $ show (g ^. phylo_groupWeight)) , toAttr "density" (pack $ show (g ^. phylo_groupDensity))
, toAttr "source" (pack $ show (nub $ g ^. phylo_groupSources)) , toAttr "cooc" (pack $ show (g ^. phylo_groupCooc))
, toAttr "sourceFull" (pack $ show (g ^. phylo_groupSources)) , toAttr "lbl" (pack $ show (ngramsToLabel fdt (g ^. phylo_groupNgrams)))
, toAttr "lbl" (pack $ show (ngramsToLabel fdt (g ^. phylo_groupNgrams))) , toAttr "foundation" (pack $ show (idxToLabel (g ^. phylo_groupNgrams)))
, toAttr "foundation" (pack $ show (idxToLabel (g ^. phylo_groupNgrams))) , toAttr "role" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "dynamics")))
, toAttr "role" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "dynamics"))) , toAttr "frequence" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "frequence")))
, toAttr "frequence" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "frequence"))) , toAttr "seaLvl" (pack $ show ((g ^. phylo_groupMeta) ! "seaLevels"))
, toAttr "seaLvl" (pack $ show ((g ^. phylo_groupMeta) ! "seaLevels")) ])
])
toDotEdge' :: DotId -> DotId -> [Char] -> [Char] -> EdgeType -> Dot DotId toDotEdge' :: DotId -> DotId -> [Char] -> [Char] -> EdgeType -> Dot DotId
toDotEdge' source target thr w edgeType = edge source target toDotEdge' source target thr w edgeType = edge source target
...@@ -447,8 +445,10 @@ branchDating export = ...@@ -447,8 +445,10 @@ branchDating export =
else acc ) [] $ export ^. export_groups else acc ) [] $ export ^. export_groups
periods = nub groups periods = nub groups
birth = fst $ head' "birth" groups birth = fst $ head' "birth" groups
age = (snd $ last' "age" groups) - birth death = snd $ last' "death" groups
age = death - birth
in b & branch_meta %~ insert "birth" [fromIntegral birth] in b & branch_meta %~ insert "birth" [fromIntegral birth]
& branch_meta %~ insert "death" [fromIntegral death]
& branch_meta %~ insert "age" [fromIntegral age] & branch_meta %~ insert "age" [fromIntegral age]
& branch_meta %~ insert "size" [fromIntegral $ length periods] ) export & branch_meta %~ insert "size" [fromIntegral $ length periods] ) export
......
src/Gargantext/Core/Viz/Phylo/PhyloMaker.hs
View file @ 79d0ea23
...@@ -34,6 +34,7 @@ import Gargantext.Core.Viz.Phylo.TemporalMatching (toPhyloQuality, temporalMatch ...@@ -34,6 +34,7 @@ import Gargantext.Core.Viz.Phylo.TemporalMatching (toPhyloQuality, temporalMatch
import Gargantext.Prelude import Gargantext.Prelude
import qualified Data.Set as Set import qualified Data.Set as Set
import qualified Data.Map as Map
import qualified Data.List as List import qualified Data.List as List
import qualified Data.Vector as Vector import qualified Data.Vector as Vector
...@@ -191,7 +192,7 @@ findSeaLadder phylo = case getSeaElevation phylo of ...@@ -191,7 +192,7 @@ findSeaLadder phylo = case getSeaElevation phylo of
in acc ++ (concat pairs') in acc ++ (concat pairs')
) [] $ keys $ phylo ^. phylo_periods ) [] $ keys $ phylo ^. phylo_periods
appendGroups :: (a -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] -> PhyloGroup) -> Scale -> Map (Date,Date) [a] -> Phylo -> Phylo appendGroups :: (a -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] -> Map Int Double -> PhyloGroup) -> Scale -> Map (Date,Date) [a] -> Phylo -> Phylo
appendGroups f lvl m phylo = trace ("\n" <> "-- | Append " <> show (length $ concat $ elems m) <> " groups to Level " <> show (lvl) <> "\n") appendGroups f lvl m phylo = trace ("\n" <> "-- | Append " <> show (length $ concat $ elems m) <> " groups to Level " <> show (lvl) <> "\n")
$ over ( phylo_periods $ over ( phylo_periods
. traverse . traverse
...@@ -206,23 +207,28 @@ appendGroups f lvl m phylo = trace ("\n" <> "-- | Append " <> show (length $ co ...@@ -206,23 +207,28 @@ appendGroups f lvl m phylo = trace ("\n" <> "-- | Append " <> show (length $ co
& phylo_scaleGroups .~ (fromList $ foldl (\groups obj -> & phylo_scaleGroups .~ (fromList $ foldl (\groups obj ->
groups ++ [ (((pId,lvl),length groups) groups ++ [ (((pId,lvl),length groups)
, f obj pId pId' lvl (length groups) , f obj pId pId' lvl (length groups)
(elems $ restrictKeys (getCoocByDate phylo) $ periodsToYears [pId])) -- select the cooc of the periods
(elems $ restrictKeys (getCoocByDate phylo) $ periodsToYears [pId])
-- select and merge the roots count of the periods
(foldl (\acc count -> unionWith (+) acc count) empty
$ elems $ restrictKeys (getRootsCountByDate phylo) $ periodsToYears [pId]))
] ) [] phyloCUnit) ] ) [] phyloCUnit)
else else
phyloLvl ) phyloLvl )
phylo phylo
clusterToGroup :: Clustering -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] -> PhyloGroup clusterToGroup :: Clustering -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] -> Map Int Double -> PhyloGroup
clusterToGroup fis pId pId' lvl idx coocs = PhyloGroup pId pId' lvl idx "" clusterToGroup fis pId pId' lvl idx coocs rootsCount = PhyloGroup pId pId' lvl idx ""
(fis ^. clustering_support ) (fis ^. clustering_support )
(fis ^. clustering_visWeighting) (fis ^. clustering_visWeighting)
(fis ^. clustering_visFiltering) (fis ^. clustering_visFiltering)
(fis ^. clustering_roots) (fis ^. clustering_roots)
(ngramsToCooc (fis ^. clustering_roots) coocs) (ngramsToCooc (fis ^. clustering_roots) coocs)
(ngramsToDensity (fis ^. clustering_roots) coocs rootsCount)
(1,[0]) -- branchid (lvl,[path in the branching tree]) (1,[0]) -- branchid (lvl,[path in the branching tree])
(fromList [("breaks",[0]),("seaLevels",[0])]) (fromList [("breaks",[0]),("seaLevels",[0])])
[] [] [] [] [] [] [] rootsCount [] [] [] [] [] [] []
----------------------- -----------------------
...@@ -446,6 +452,16 @@ docsToTermCount docs roots = fromList ...@@ -446,6 +452,16 @@ docsToTermCount docs roots = fromList
docsToTimeTermCount :: [Document] -> Vector Ngrams -> (Map Date (Map Int Double))
docsToTimeTermCount docs roots =
let docs' = Map.map (\l -> fromList $ map (\lst -> (head' "docsToTimeTermCount" lst, fromIntegral $ length lst))
$ group $ sort l)
$ fromListWith (++)
$ map (\d -> (date d, nub $ ngramsToIdx (text d) roots)) docs
time = fromList $ map (\t -> (t,Map.empty)) $ toTimeScale (keys docs') 1
in unionWith (Map.union) time docs'
docsToLastTermFreq :: Int -> [Document] -> Vector Ngrams -> Map Int Double docsToLastTermFreq :: Int -> [Document] -> Vector Ngrams -> Map Int Double
docsToLastTermFreq n docs fdt = docsToLastTermFreq n docs fdt =
let last = take n $ reverse $ sort $ map date docs let last = take n $ reverse $ sort $ map date docs
...@@ -472,15 +488,15 @@ initPhyloScales lvlMax pId = ...@@ -472,15 +488,15 @@ initPhyloScales lvlMax pId =
fromList $ map (\lvl -> ((pId,lvl),PhyloScale pId ("","") lvl empty)) [1..lvlMax] fromList $ map (\lvl -> ((pId,lvl),PhyloScale pId ("","") lvl empty)) [1..lvlMax]
setDefault :: PhyloConfig -> PhyloConfig setDefault :: PhyloConfig -> TimeUnit -> PhyloConfig
setDefault conf = conf { setDefault conf timeScale = conf {
phyloScale = 2, phyloScale = 2,
similarity = WeightedLogJaccard 0.5 2, similarity = WeightedLogJaccard 0.5 2,
findAncestors = True, findAncestors = True,
phyloSynchrony = ByProximityThreshold 0.6 0 SiblingBranches MergeAllGroups, phyloSynchrony = ByProximityThreshold 0.6 0 SiblingBranches MergeAllGroups,
phyloQuality = Quality 0.5 3, phyloQuality = Quality 0.5 3,
timeUnit = Year 3 1 3, timeUnit = timeScale,
clique = MaxClique 5 30 ByNeighbours, clique = Fis 3 5,
exportLabel = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2], exportLabel = [BranchLabel MostEmergentTfIdf 2, GroupLabel MostEmergentInclusive 2],
exportSort = ByHierarchy Desc, exportSort = ByHierarchy Desc,
exportFilter = [ByBranchSize 3] exportFilter = [ByBranchSize 3]
...@@ -492,18 +508,21 @@ setDefault conf = conf { ...@@ -492,18 +508,21 @@ setDefault conf = conf {
initPhylo :: [Document] -> PhyloConfig -> Phylo initPhylo :: [Document] -> PhyloConfig -> Phylo
initPhylo docs conf = initPhylo docs conf =
let roots = Vector.fromList $ nub $ concat $ map text docs let roots = Vector.fromList $ nub $ concat $ map text docs
timeScale = head' "initPhylo" $ map docTime docs
foundations = PhyloFoundations roots empty foundations = PhyloFoundations roots empty
docsSources = PhyloSources (Vector.fromList $ nub $ concat $ map sources docs) docsSources = PhyloSources (Vector.fromList $ nub $ concat $ map sources docs)
docsCounts = PhyloCounts (docsToTimeScaleCooc docs (foundations ^. foundations_roots)) docsCounts = PhyloCounts (docsToTimeScaleCooc docs (foundations ^. foundations_roots))
(docsToTimeScaleNb docs) (docsToTimeScaleNb docs)
(docsToTimeTermCount docs (foundations ^. foundations_roots))
(docsToTermCount docs (foundations ^. foundations_roots)) (docsToTermCount docs (foundations ^. foundations_roots))
(docsToTermFreq docs (foundations ^. foundations_roots)) (docsToTermFreq docs (foundations ^. foundations_roots))
(docsToLastTermFreq (getTimePeriod $ timeUnit conf) docs (foundations ^. foundations_roots)) (docsToLastTermFreq (getTimePeriod timeScale) docs (foundations ^. foundations_roots))
params = if (defaultMode conf) params = if (defaultMode conf)
then defaultPhyloParam { _phyloParam_config = setDefault conf } then defaultPhyloParam { _phyloParam_config = setDefault conf timeScale }
else defaultPhyloParam { _phyloParam_config = conf } else defaultPhyloParam { _phyloParam_config = conf }
periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod $ timeUnit conf) (getTimeStep $ timeUnit conf) periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod timeScale) (getTimeStep timeScale)
in trace ("\n" <> "-- | Init a phylo out of " <> show(length docs) <> " docs \n") in trace ("\n" <> "-- | Init a phylo out of " <> show(length docs) <> " docs \n")
$ trace ("\n" <> "-- | lambda " <> show(_qua_granularity $ phyloQuality $ _phyloParam_config params))
$ Phylo foundations $ Phylo foundations
docsSources docsSources
docsCounts docsCounts
...@@ -511,4 +530,4 @@ initPhylo docs conf = ...@@ -511,4 +530,4 @@ initPhylo docs conf =
params params
(fromList $ map (\prd -> (prd, PhyloPeriod prd ("","") (initPhyloScales 1 prd))) periods) (fromList $ map (\prd -> (prd, PhyloPeriod prd ("","") (initPhyloScales 1 prd))) periods)
0 0
(_qua_granularity $ phyloQuality $ conf) (_qua_granularity $ phyloQuality $ _phyloParam_config params)
src/Gargantext/Core/Viz/Phylo/PhyloTools.hs
View file @ 79d0ea23
...@@ -14,7 +14,7 @@ module Gargantext.Core.Viz.Phylo.PhyloTools where ...@@ -14,7 +14,7 @@ module Gargantext.Core.Viz.Phylo.PhyloTools where
import Control.Lens hiding (Level) import Control.Lens hiding (Level)
import Data.List (sort, concat, null, union, (++), tails, sortOn, nub, init, tail, iterate, transpose, partition, tails, nubBy, group, notElem, (!!)) import Data.List (sort, concat, null, union, (++), tails, sortOn, nub, init, tail, iterate, transpose, partition, tails, nubBy, group, notElem, (!!))
import Data.Map (Map, elems, fromList, unionWith, keys, member, (!), filterWithKey, fromListWith, empty, restrictKeys) import Data.Map (Map, elems, fromList, findWithDefault, unionWith, keys, member, (!), filterWithKey, fromListWith, empty, restrictKeys)
import Data.Set (Set, disjoint) import Data.Set (Set, disjoint)
import Data.String (String) import Data.String (String)
import Data.Text (Text,unpack) import Data.Text (Text,unpack)
...@@ -313,6 +313,27 @@ ngramsToCooc ngrams coocs = ...@@ -313,6 +313,27 @@ ngramsToCooc ngrams coocs =
in filterWithKey (\k _ -> elem k pairs) cooc in filterWithKey (\k _ -> elem k pairs) cooc
-----------------
-- | Density | --
-----------------
-- | To build the density of a phylogroup
-- density is defined in Callon M, Courtial JP, Laville F (1991) Co-word analysis as a tool for describing
-- the network of interaction between basic and technological research: The case of polymer chemistry.
-- Scientometric 22: 155–205.
ngramsToDensity :: [Int] -> [Cooc] -> (Map Int Double) -> Double
ngramsToDensity ngrams coocs rootsCount =
let cooc = foldl (\acc cooc' -> sumCooc acc cooc') empty coocs
pairs = listToCombi' ngrams
density = map (\(i,j) ->
let nij = findWithDefault 0 (i,j) cooc
in (nij * nij) / ((rootsCount ! i) * (rootsCount ! j))) pairs
in (sum density) / (fromIntegral $ length ngrams)
------------------ ------------------
-- | Defaults | -- -- | Defaults | --
------------------ ------------------
...@@ -458,6 +479,9 @@ getPeriodIds phylo = sortOn fst ...@@ -458,6 +479,9 @@ getPeriodIds phylo = sortOn fst
$ keys $ keys
$ phylo ^. phylo_periods $ phylo ^. phylo_periods
getLastDate :: Phylo -> Date
getLastDate phylo = snd $ last' "lastDate" $ getPeriodIds phylo
getLevelParentId :: PhyloGroup -> PhyloGroupId getLevelParentId :: PhyloGroup -> PhyloGroupId
getLevelParentId g = fst $ head' "getLevelParentId" $ g ^. phylo_groupScaleParents getLevelParentId g = fst $ head' "getLevelParentId" $ g ^. phylo_groupScaleParents
...@@ -495,7 +519,7 @@ getConfig :: Phylo -> PhyloConfig ...@@ -495,7 +519,7 @@ getConfig :: Phylo -> PhyloConfig
getConfig phylo = (phylo ^. phylo_param) ^. phyloParam_config getConfig phylo = (phylo ^. phylo_param) ^. phyloParam_config
getLevel :: Phylo -> Double getLevel :: Phylo -> Double
getLevel phylo = _phylo_level phylo getLevel phylo = (phyloQuality (getConfig phylo)) ^. qua_granularity
getLadder :: Phylo -> [Double] getLadder :: Phylo -> [Double]
getLadder phylo = phylo ^. phylo_seaLadder getLadder phylo = phylo ^. phylo_seaLadder
...@@ -503,6 +527,9 @@ getLadder phylo = phylo ^. phylo_seaLadder ...@@ -503,6 +527,9 @@ getLadder phylo = phylo ^. phylo_seaLadder
getCoocByDate :: Phylo -> Map Date Cooc getCoocByDate :: Phylo -> Map Date Cooc
getCoocByDate phylo = coocByDate (phylo ^. phylo_counts) getCoocByDate phylo = coocByDate (phylo ^. phylo_counts)
getRootsCountByDate :: Phylo -> Map Date (Map Int Double)
getRootsCountByDate phylo = rootsCountByDate (phylo ^. phylo_counts)
getDocsByDate :: Phylo -> Map Date Double getDocsByDate :: Phylo -> Map Date Double
getDocsByDate phylo = docsByDate (phylo ^. phylo_counts) getDocsByDate phylo = docsByDate (phylo ^. phylo_counts)
......
src/Gargantext/Core/Viz/Phylo/SynchronicClustering.hs
View file @ 79d0ea23
...@@ -16,7 +16,7 @@ import Control.Lens hiding (Level) ...@@ -16,7 +16,7 @@ import Control.Lens hiding (Level)
import Control.Monad (sequence) import Control.Monad (sequence)
import Control.Parallel.Strategies (parList, rdeepseq, using) import Control.Parallel.Strategies (parList, rdeepseq, using)
import Data.List ((++), null, intersect, nub, concat, sort, sortOn, groupBy) import Data.List ((++), null, intersect, nub, concat, sort, sortOn, groupBy)
import Data.Map (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member) import Data.Map (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member, unionWith)
import Gargantext.Core.Viz.Phylo import Gargantext.Core.Viz.Phylo
import Gargantext.Core.Viz.Phylo.PhyloExport (processDynamics) import Gargantext.Core.Viz.Phylo.PhyloExport (processDynamics)
import Gargantext.Core.Viz.Phylo.PhyloTools import Gargantext.Core.Viz.Phylo.PhyloTools
...@@ -32,6 +32,7 @@ import qualified Data.Map as Map ...@@ -32,6 +32,7 @@ import qualified Data.Map as Map
mergeGroups :: [Cooc] -> PhyloGroupId -> Map PhyloGroupId PhyloGroupId -> [PhyloGroup] -> PhyloGroup mergeGroups :: [Cooc] -> PhyloGroupId -> Map PhyloGroupId PhyloGroupId -> [PhyloGroup] -> PhyloGroup
mergeGroups coocs id mapIds childs = mergeGroups coocs id mapIds childs =
let ngrams = (sort . nub . concat) $ map _phylo_groupNgrams childs let ngrams = (sort . nub . concat) $ map _phylo_groupNgrams childs
counts = foldl (\acc count -> unionWith (+) acc count) empty $ map _phylo_groupRootsCount childs
in PhyloGroup (fst $ fst id) (_phylo_groupPeriod' $ head' "mergeGroups" childs) in PhyloGroup (fst $ fst id) (_phylo_groupPeriod' $ head' "mergeGroups" childs)
(snd $ fst id) (snd id) "" (snd $ fst id) (snd id) ""
(sum $ map _phylo_groupSupport childs) (sum $ map _phylo_groupSupport childs)
...@@ -40,8 +41,12 @@ mergeGroups coocs id mapIds childs = ...@@ -40,8 +41,12 @@ mergeGroups coocs id mapIds childs =
(concat $ map _phylo_groupSources childs) (concat $ map _phylo_groupSources childs)
ngrams ngrams
(ngramsToCooc ngrams coocs) (ngramsToCooc ngrams coocs)
(ngramsToDensity ngrams coocs counts)
-- todo add density here
((snd $ fst id),bId) ((snd $ fst id),bId)
(mergeMeta bId childs) [] (map (\g -> (getGroupId g, 1)) childs) (mergeMeta bId childs)
counts
[] (map (\g -> (getGroupId g, 1)) childs)
(updatePointers $ concat $ map _phylo_groupPeriodParents childs) (updatePointers $ concat $ map _phylo_groupPeriodParents childs)
(updatePointers $ concat $ map _phylo_groupPeriodChilds childs) (updatePointers $ concat $ map _phylo_groupPeriodChilds childs)
(mergeAncestors $ concat $ map _phylo_groupAncestors childs) (mergeAncestors $ concat $ map _phylo_groupAncestors childs)
......
test-data/phylo/bpa_phylo_test.json 0 → 100644
View file @ 79d0ea23
This source diff could not be displayed because it is too large. You can view the blob instead.
test-data/phylo/open_science.json 0 → 100644
View file @ 79d0ea23
{
"pd_data": {
"phyloSources": "[]",
"directed": true,
"phyloTimeScale": "year",
"color": "white",
"strict": false,
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"objects": [
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Branches peaks",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 0,
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20002002",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 1,
"nodes": [
23
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20012003",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 2,
"nodes": [
24
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20022004",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 3,
"nodes": [
25
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20032005",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 4,
"nodes": [
26
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20042006",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 5,
"nodes": [
27
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20052007",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 6,
"nodes": [
28
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20062008",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 7,
"nodes": [
29
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20072009",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 8,
"nodes": [
30
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20082010",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 9,
"nodes": [
31
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20092011",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 10,
"nodes": [
32
],
"label": "Phylo Name",
"rank": "same",
"lp": "142,2918.5",
"style": "filled",
"phyloQuality": "0.2253686608796909",
"bb": "0,0,284,2939",
"overlap": "scale",
"splines": "spline",
"nodesep": "1",
"phyloDocs": "313.0",
"phyloPeriods": "22",
"ranksep": "1",
"phyloBranches": "0",
"phyloSeaRiseStart": "0.1",
"phyloSeaRiseSteps": "0.1"
},
{
"phyloSources": "[]",
"phyloTimeScale": "year",
"color": "white",
"lheight": "0.46",
"fontsize": "30",
"phyloGroups": "0",
"labelloc": "t",
"ratio": "fill",
"phyloTerms": "0",
"name": "Period20102012",
"lwidth": "2.51",
"PhyloScale": "0.2",
"phyloFoundations": "346",
"_gvid": 11,
"nodes": [
33
],
"label": "Phylo Name",
"rank": "same",
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