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haskell-gargantext
haskell-gargantext
Verified Commit 0405e007 authored by Przemyslaw Kaminski's avatar Przemyslaw Kaminski
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Merge branch 'dev' into 224-dev-uniform-ngrams-creation

parents dc21080f fe201115
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.gitignore
View file @ 0405e007
...@@ -4,6 +4,10 @@ ...@@ -4,6 +4,10 @@
# Profiling # Profiling
*.prof *.prof
*.prof.html
*.hp
*.eventlog
*.eventlog.html
profiling profiling
# Stack # Stack
...@@ -39,4 +43,5 @@ data ...@@ -39,4 +43,5 @@ data
devops/docker/js-cache devops/docker/js-cache
cabal.project.local cabal.project.local
\ No newline at end of file gargantext_profile_out.dot
.gitlab-ci.yml
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...@@ -50,7 +50,7 @@ bench: ...@@ -50,7 +50,7 @@ bench:
- .cabal/ - .cabal/
policy: pull-push policy: pull-push
script: script:
- nix-shell --run "./bin/update-project-dependencies $CABAL_STORE_DIR && cabal --store-dir=$CABAL_STORE_DIR v2-bench --ghc-options='-O2 -fclear-plugins'" - nix-shell --run "./bin/update-project-dependencies $CABAL_STORE_DIR && cabal --store-dir=$CABAL_STORE_DIR v2-bench --flags +no-phylo-debug-logs --ghc-options='-O2 -fclear-plugins'"
allow_failure: true allow_failure: true
test: test:
...@@ -84,7 +84,7 @@ test: ...@@ -84,7 +84,7 @@ test:
mkdir -p /builds/gargantext/haskell-gargantext/devops/coreNLP/stanford-corenlp-current mkdir -p /builds/gargantext/haskell-gargantext/devops/coreNLP/stanford-corenlp-current
cp -R /root/devops/coreNLP/stanford-corenlp-${CORENLP}/* /builds/gargantext/haskell-gargantext/devops/coreNLP/stanford-corenlp-current/ cp -R /root/devops/coreNLP/stanford-corenlp-${CORENLP}/* /builds/gargantext/haskell-gargantext/devops/coreNLP/stanford-corenlp-current/
nix-shell --run "chown -R test:test /root/.config/ && su -m test -c \"export PATH=$PATH:$TEST_NIX_PATH && cd /builds/gargantext/haskell-gargantext; $CABAL --store-dir=$CABAL_STORE_DIR v2-test --test-show-details=streaming --flags test-crypto --ghc-options='-O0 -fclear-plugins'\"" nix-shell --run "chown -R test:test /root/.config/ && su -m test -c \"export PATH=$PATH:$TEST_NIX_PATH && cd /builds/gargantext/haskell-gargantext; $CABAL --store-dir=$CABAL_STORE_DIR v2-test --test-show-details=streaming --flags 'test-crypto no-phylo-debug-logs' --ghc-options='-O0 -fclear-plugins'\""
chown -R root:root dist-newstyle/ chown -R root:root dist-newstyle/
chown -R root:root /root/ chown -R root:root /root/
chown -R root:root $CABAL_STORE_DIR chown -R root:root $CABAL_STORE_DIR
......
CHANGELOG.md
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## Version 0.0.6.9.9.9.6.2 [Release Candidate for 007]
* [BACK][FIX][Node stories insertion error (SqlError violates foreign key constraint) (#303)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/303)
* [BACK][DOC][Welcome: Door To enter the project (#177)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/177)
* [BACK][OPTIM][Improve Phylo robustness and performance (#292)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/292)
## Version 0.0.6.9.9.9.6.1 ## Version 0.0.6.9.9.9.6.1
* [BACK][FEAT][Removing Order2_A and Order2_B and use Order2 only instead (#308)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/308) * [BACK][FEAT][Removing Order2_A and Order2_B and use Order2 only instead (#308)](https://gitlab.iscpif.fr/gargantext/haskell-gargantext/issues/308)
......
README.md
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...@@ -199,7 +199,7 @@ See https://www.haskell.org/ghcup/guide/#hls for more details. ...@@ -199,7 +199,7 @@ See https://www.haskell.org/ghcup/guide/#hls for more details.
``` sh ``` sh
# If docker is not installed: # If docker is not installed:
# curl -sSL https://gitlab.iscpif.fr/gargantext/haskell-gargantext/raw/dev/devops/docker/docker-install | sh # curl -sSL https://gitlab.iscpif.fr/gargantext/haskell-gargantext/raw/dev/devops/docker/install_docker | sh
cd devops/docker cd devops/docker
docker compose up docker compose up
``` ```
......
bench-data/phylo/GarganText_DocsList-nodeId-185487.csv 0 → 100644
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This source diff could not be displayed because it is too large. You can view the blob instead.
bench-data/phylo/GarganText_NgramsList-185488.csv 0 → 100644
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status label forms
map %
map % ci
candidate 17α-ethinylestradiol
map 17β-estradiol
candidate 2-ethylhexyl
candidate 4-tert-octylphenol
candidate absence
candidate action
candidate activation
candidate activities activity
candidate activity
map addition
map additional studies
map adsorption
map adult zebrafish
candidate adults
map adverse effect
map adverse effects adverse effect
candidate adverse health effects
map aim
map aim was
candidate algae
map alteration
map alterations alteration
candidate alternatives
map analogs
candidate analogues
map analysis
map androgen receptor
map animal animals
map animal models
map animals
map apoptosis
candidate application applications
candidate applications
candidate aquatic ecosystems
map aquatic environment
candidate aquatic plants
candidate ar
candidate area
candidate areas area
map article is protected
candidate assay
candidate assays assay
candidate association
candidate associations association
map balloon pulmonary angioplasty
candidate basis
map better understanding
candidate beverages
candidate binding affinity
map bioaccumulation potential
candidate biological effects
map birth outcomes
map birth weight
map bisphenol bisphenols
map bisphenol a
map bisphenol a action
map bisphenol a analogues
candidate bisphenol a exposure
candidate bisphenol a.
map bisphenol af
map bisphenol analogues
map bisphenol b
candidate bisphenol compounds
map bisphenol f
map bisphenol s bisphenol-s
candidate bisphenol-a
map bisphenol-s
map bisphenols
candidate bnct
map body weight
map boron neutron capture therapy
map bp bps
map bpa
candidate bpa analogues
map bpa caused
map bpa degradation
candidate bpa did
map bpa disrupts
map bpa exposure
map bpa exposure was
candidate bpa group
candidate bpa had
map bpa increased
map bpa is
candidate bpa leads
candidate bpa replacements
candidate bpa stimulated
map bpa treatment
map bpa was bpa is
candidate bpa was determined
candidate bpa were found
candidate bpa-bnct
candidate bpa-exposed rats
map bpaf
map bpaf was
map bpb
map bpf
map bps
map breast cancer
map c-bisphenol a
candidate caffeine
candidate carbon nanotubes
map case
map cash register receipts
candidate cat
candidate catalase
candidate cck-8
candidate cd
map cell counting kit-8
map cell proliferation
map cell viability
candidate changes
map chemical chemicals
candidate chemical analysis
map chemical exposure
map chemical oxygen demand
map chemicals
candidate chemicals were
candidate children
candidate china
candidate chromosomes
map chronic exposure
map chronic thromboembolic pulmonary hypertension
candidate cm
candidate co
candidate cod
map coexistence
map color developer
candidate combination
candidate common sources
candidate comparison
candidate complications
map compounds
map concentration
map concentration-dependent manner
map concentrations concentration
map concern
map concerns concern
map conclusion
candidate consumer products
candidate contamination
candidate contrast
map control
map control group control groups
map control groups
map controls control
map copyright
candidate cr
map critical period
map critical windows
candidate cross-sectional study
candidate crucial role
candidate cteph
candidate cu
candidate current knowledge
map cyp11a1
map danio rerio
map data
map day
map days day
map dbp
candidate decrease decreases
candidate decreases
candidate degradation
map degradation rate
candidate dehp
candidate deleterious effects
map delivery
map dermal absorption
map dermal exposure
candidate desorption
map desorption time
map detection
candidate detection limit
map determination
map development
map developmental periods
candidate diabetes
map dibutyl phthalate
candidate dietary exposure
candidate different effects
map different products
candidate different regions
map distribution distributions
map distributions
candidate dna damage
map dna methylation
candidate dose
map dose-limiting tissue
candidate doses dose
map drinking water
map e1
map e2
map ecological and human health risk
map edc
map edcs edc
candidate ee2
map effect
map effects effect
map effects are effects were
map effects were
candidate efsa
candidate embryos
map emt
map emt process
candidate endocrine disrupter
candidate endocrine disruption
map endocrine disruptor
map endocrine disruptors endocrine disruptor
map endocrine system
candidate endocrine-disrupting chemical
candidate environment
candidate environmental behaviors
candidate environmental contaminant
candidate environmental endocrine disruptors
map environmental exposure
map environmental remediation
map environmental toxicants
candidate epidemiological studies
map epoxy resins
map er
map er-dependent pathway
candidate erk1/2
map ers er
map estriol
candidate estrogen
map estrogen receptor
map estrogen receptors estrogen receptor
map estrogenic activity
candidate estrogenic properties
candidate estrogens estrogen
map estrone
candidate europe
map european food safety authority
candidate evaluation
candidate evidence
candidate evidence indicates
candidate experimental data
map exposure
map exposure was
map exposures exposure
map expression expressions
map expressions
candidate extent
map extraction
candidate fact
map females
map fetal development
map findings indicate
candidate findings suggest
map first time
candidate fish
map flow rate
map food foods
candidate food packaging
map foods
candidate formation
map fourier transform infrared spectroscopy
candidate freshwater
map freundlich model
candidate ftir
candidate function
map g creatinine
candidate g protein-coupled estrogen receptor
map gene expression
map general population
candidate gestation
candidate glucose homeostasis
map glutathione peroxidase
candidate good linear relationship
map group
map groups group
candidate growth
candidate h
map head circumference
map health effects
candidate high expression
candidate high risk
candidate high sensitivity
candidate high-resolution transmission electron microscopy
map higher bpa levels
candidate higher concentrations
map higher rates
map hippocampus
candidate hong kong
map hormonal regulation
candidate hours
candidate hplc-uv
candidate hrtem
map human exposure
map human health
candidate human plasma
candidate humans
map humans are
map humic acid
map humic acids humic acid
map hydroxyl radicals
candidate hypothalamus
candidate ici
candidate il-6
candidate immune system
candidate impact
candidate impacts impact
candidate impairment
map implantation failure
candidate important role
candidate increase
map induction
candidate influence
candidate inhibition
map initial concentration
map insulin resistance
candidate interaction interactions
candidate interactions
candidate involvement
map john wiley
map juvenile sprague-dawley rats
candidate key role
candidate kg
candidate kinetics
map l
candidate lack
candidate learning
candidate length
map level
map levels level
map limit
candidate limited number
map limits limit
candidate liver
map lod
map lods lod
candidate loq
map low concentrations
candidate low-dose bisphenol a
map low-dose bpa
map low-dose exposure
map ltd.
map major source
map male
map male mice
map male offspring
map males male
candidate manufacture
candidate mapk
candidate mass spectrometry
candidate maternal diet
map matrix effect
map mcf-7 breast cancer cells
map mcf-7 cells
candidate mechanism
candidate mechanisms mechanism
candidate method
map method was
map method was applied
candidate methods method
map mg g
candidate mg kg
candidate mg l
candidate mg/kg
candidate mg/l
candidate mice
map migration
candidate min
map mitogen-activated protein kinase
candidate ml
map mobile phase
candidate modulation
map molecular docking
candidate molecular interactions
candidate motility
map mrna expression
map myelin basic protein
map n
candidate naphthalene
candidate natural waters
map negative effect
candidate neuroendocrine disruption
map new mechanism
candidate ng/l
candidate ni
map nonylphenol
candidate np
candidate number
candidate obesity
candidate objective
candidate objective was
candidate occupational exposure
map occurrence
candidate onset
candidate order
map organic contaminants
map organic pollutants
candidate organisms
map ovarian reserve
map oxidative stress
candidate p
candidate papillary thyroid carcinoma
candidate parabens
candidate part
candidate participants
candidate pathophysiology
candidate pb
candidate pergafast
map perinatal exposure
candidate pfoa
candidate pfos
candidate ph
candidate phenol phenols
candidate phenolic compounds
candidate phenols
candidate phosphate
candidate phosphorylation
map photocatalytic mechanism
map photocatalytic properties
candidate photoluminescence
map phthalate
map phthalates phthalate
candidate physical activity
map physicochemical properties
candidate pl
map plastic industry
map plastic production
candidate plastics
candidate pnd
candidate pnd90
candidate pollutants
map polycarbonate plastic
map polycarbonate plastics polycarbonate plastic
map positive effect
candidate possible effects
map postnatal day
candidate potential
candidate potential applications
candidate potential effects
candidate potential mechanism
candidate potential risk
map potential sources
map pregnancy
candidate preliminary results
candidate prenatal bisphenol a
map prenatal exposure
map presence
map present study
map present study is present study was
map present study was
candidate previous study
map pro-inflammatory cytokines
candidate production
candidate products
candidate proliferation
map protein expression
map protein levels
candidate pseudo-second-order kinetic model
map pubertal development
candidate puberty
candidate quantification
map r
map range
map ranges range
map rat offspring
map reactive oxygen species
candidate regulation
map relation
map relative standard deviations
candidate release
candidate relevant levels
map removal
map removal efficiencies
map removal efficiency removal efficiencies
candidate reproductive development
map reproductive function
map reproductive hormones
candidate response
map result
map results result
candidate results demonstrated
map results indicate
map results indicated results indicate
candidate results revealed
map results show
map results showed results show
map results suggest
candidate review
map rights reserved
map risk
map risk assessment
map risks risk
map role
map ros
candidate s/n
map sample samples
map samples
candidate samples were
map sampling sites showed
candidate scanning electron microscope
map scanning electron microscopy
map sediment
map sediments sediment
candidate sem
map sensitivities
map sensitivity sensitivities
candidate series
candidate serum
map signal-to-noise ratio
map significant decrease
candidate significant differences
map significant increase
map simultaneous determination
map simultaneous removal
candidate soil
map sons
map sorbent
map source
map sources source
map spatial distribution
map spatial memory
candidate species
map stem cells
map structural analogues
candidate structure
map studies study
candidate studies showed
map study
map study aims
map study evaluated
map study investigated
candidate study suggests
map study was
map superoxide dismutase
candidate surface
map surface water surface waters
map surface waters
candidate susceptibility
map synaptic plasticity
map synthesis
candidate t
map taihu lake
candidate tcs
candidate testis
map tetrabromobisphenol a
map thermal paper
map thermal paper contains
candidate thermal paper receipts
map toxicity
map transcriptional activity
candidate treatment
map triclosan
candidate type types
candidate types
candidate ubiquitous endocrine-disrupting chemical
map urinary levels
map urine samples
map urine samples collected
candidate use
map utero development
map utero windows
candidate value
candidate values value
map vi
map visible light irradiation
map wastewater
map water
candidate water sources
candidate water treatment
candidate week weeks
candidate weeks
map wide range
map women
candidate work
map work was
candidate wt %
map x-ray diffraction
candidate xrd
candidate young children
candidate zebrafish
map zebrafish embryos
map μg
map μg kg
candidate μgl
bench-data/phylo/bpa-config.json 0 → 100644
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{
"corpusPath" : "Gargantext_DocsList-nodeId-185487.csv",
"listPath" : "Gargantext_NgramsList-185488.csv",
"outputPath" : "data",
"corpusParser" : {
"tag" : "Csv",
"_csv_limit" : 1500000
},
"listParser" : "V3",
"phyloName" : "bpa",
"phyloScale" : 2,
"similarity" : {
"tag" : "WeightedLogJaccard",
"_wlj_sensibility" : 0.5,
"_wlj_minSharedNgrams" : 1
},
"seaElevation" : {
"tag" : "Evolving",
"_evol_neighborhood" : true
},
"defaultMode" : false,
"findAncestors" : true,
"phyloSynchrony" : {
"tag" : "ByProximityThreshold",
"_bpt_threshold" : 0.6,
"_bpt_sensibility" : 0,
"_bpt_scope" : "AllBranches",
"_bpt_strategy" : "MergeAllGroups"
},
"phyloQuality" : {
"tag" : "Quality",
"_qua_granularity" : 0.1,
"_qua_minBranch" : 2
},
"timeUnit" : {
"tag" : "Week",
"_week_period" : 4,
"_week_step" : 2,
"_week_matchingFrame" : 5
},
"clique" : {
"tag" : "Fis",
"_fis_support" : 3,
"_fis_size" : 1
},
"exportLabel" : [
{
"tag" : "BranchLabel",
"_branch_labelTagger" : "MostEmergentTfIdf",
"_branch_labelSize" : 2
},
{
"tag" : "GroupLabel",
"_group_labelTagger" : "MostEmergentInclusive",
"_group_labelSize" : 2
}
],
"exportSort" : {
"tag" : "ByHierarchy",
"_sort_order" : "Desc"
},
"exportFilter" : [
{
"tag" : "ByBranchSize",
"_branch_size" : 2
}
]
}
bin/gargantext-phylo-profile/Main.hs 0 → 100644
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{-# LANGUAGE OverloadedStrings #-}
module Main where
import Common
import Data.Aeson
import Data.List (nub)
import Gargantext.Core.Viz.Phylo
import Gargantext.Core.Viz.Phylo.API.Tools
import Gargantext.Core.Viz.Phylo.PhyloExport (toPhyloExport, dotToFile)
import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo, toPhyloWithoutLink)
import Gargantext.Core.Viz.Phylo.PhyloTools (printIOMsg, printIOComment, setConfig, toPeriods, getTimePeriod, getTimeStep)
import GHC.IO.Encoding
import GHC.Stack
import Paths_gargantext
import Prelude
import qualified Data.Text as T
import Shelly
import System.Directory
--------------
-- | Main | --
--------------
phyloConfig :: FilePath -> PhyloConfig
phyloConfig outdir = PhyloConfig {
corpusPath = "corpus.csv"
, listPath = "list.csv"
, outputPath = outdir
, corpusParser = Csv {_csv_limit = 150000}
, listParser = V4
, phyloName = "phylo_profile_test"
, phyloScale = 2
, similarity = WeightedLogJaccard {_wlj_sensibility = 0.5, _wlj_minSharedNgrams = 2}
, seaElevation = Constante {_cons_start = 0.1, _cons_gap = 0.1}
, defaultMode = True
, findAncestors = True
, phyloSynchrony = ByProximityThreshold {_bpt_threshold = 0.5, _bpt_sensibility = 0.0, _bpt_scope = AllBranches, _bpt_strategy = MergeAllGroups}
, phyloQuality = Quality {_qua_granularity = 0.8, _qua_minBranch = 3}
, timeUnit = Year {_year_period = 3, _year_step = 1, _year_matchingFrame = 5}
, clique = MaxClique {_mcl_size = 5, _mcl_threshold = 1.0e-4, _mcl_filter = ByThreshold}
, exportLabel = [ BranchLabel {_branch_labelTagger = MostEmergentTfIdf, _branch_labelSize = 2}
, GroupLabel {_group_labelTagger = MostEmergentInclusive, _group_labelSize = 2}
]
, exportSort = ByHierarchy {_sort_order = Desc}
, exportFilter = [ByBranchSize {_branch_size = 3.0}]
}
main :: HasCallStack => IO ()
main = do
shelly $ escaping False $ withTmpDir $ \tdir -> do
curDir <- pwd
let output = curDir <> "/" <> "gargantext_profile_out.dot"
chdir tdir $ do
liftIO $ setLocaleEncoding utf8
bpaConfig <- liftIO $ getDataFileName "bench-data/phylo/bpa-config.json"
corpusPath' <- liftIO $ getDataFileName "bench-data/phylo/GarganText_DocsList-nodeId-185487.csv"
listPath' <- liftIO $ getDataFileName "bench-data/phylo/GarganText_NgramsList-185488.csv"
(Right config) <- fmap (\pcfg -> pcfg { outputPath = tdir
, corpusPath = corpusPath'
, listPath = listPath'
}) <$> liftIO (eitherDecodeFileStrict' bpaConfig)
mapList <- liftIO $ fileToList (listParser config) (listPath config)
corpus <- liftIO $ 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
liftIO $ do
printIOComment (show (length corpus) <> " parsed docs from the corpus")
printIOComment (show (length $ nub $ concat $ map text corpus) <> " Size ngs_coterms")
printIOComment (show (length mapList) <> " Size ngs_terms List Map Ngrams")
printIOMsg "Reconstruct the phylo"
-- check the existing backup files
let backupPhyloWithoutLink = (outputPath config) <> "backupPhyloWithoutLink_" <> (configToSha BackupPhyloWithoutLink config) <> ".json"
let backupPhylo = (outputPath config) <> "backupPhylo_" <> (configToSha BackupPhylo config) <> ".json"
phyloWithoutLinkExists <- doesFileExist backupPhyloWithoutLink
phyloExists <- doesFileExist backupPhylo
-- reconstruct the phylo
phylo <- if phyloExists
then do
printIOMsg "Reconstruct the phylo from an existing file"
readPhylo backupPhylo
else do
if phyloWithoutLinkExists
then do
printIOMsg "Reconstruct the phylo from an existing file without links"
phyloWithoutLink <- readPhylo backupPhyloWithoutLink
writePhylo backupPhyloWithoutLink phyloWithoutLink
pure $ toPhylo (setConfig config phyloWithoutLink)
else do
printIOMsg "Reconstruct the phylo from scratch"
phyloWithoutLink <- pure $ toPhyloWithoutLink corpus config
writePhylo backupPhyloWithoutLink phyloWithoutLink
pure $ toPhylo (setConfig config phyloWithoutLink)
writePhylo backupPhylo phylo
printIOMsg "End of reconstruction, start the export"
let dot = toPhyloExport (setConfig config phylo)
dotToFile output dot
echo "Done."
bin/gargantext-phylo/Main.hs
View file @ 0405e007
...@@ -47,210 +47,7 @@ import Gargantext.Database.Schema.Ngrams (NgramsType(..)) ...@@ -47,210 +47,7 @@ import Gargantext.Database.Schema.Ngrams (NgramsType(..))
import Gargantext.Prelude hiding (hash, replace) import Gargantext.Prelude hiding (hash, replace)
import Prelude qualified import Prelude qualified
import System.Directory (listDirectory,doesFileExist) import System.Directory (listDirectory,doesFileExist)
import Common
data Backup = BackupPhyloWithoutLink | BackupPhylo deriving (Show)
---------------
-- | Tools | --
---------------
-- | To get all the files in a directory or just a file
getFilesFromPath :: FilePath -> IO [FilePath]
getFilesFromPath path = do
if (isSuffixOf "/" path)
then (listDirectory path)
else return [path]
----------------
-- | Parser | --
----------------
-- | To filter the Ngrams of a document based on the termList
termsInText :: Patterns -> Text -> [Text]
termsInText pats txt = nub $ concat $ map (map unwords) $ extractTermsWithList pats txt
-- | To transform a Wos file (or [file]) into a list of Docs
wosToDocs :: Int -> Patterns -> TimeUnit -> FilePath -> IO [Document]
wosToDocs limit patterns time path = do
files <- getFilesFromPath path
take limit
<$> map (\d -> let title = fromJust $ _hd_title d
abstr = if (isJust $ _hd_abstract d)
then fromJust $ _hd_abstract d
else ""
in Document (toPhyloDate
(fromIntegral $ fromJust $ _hd_publication_year d)
(fromJust $ _hd_publication_month d)
(fromJust $ _hd_publication_day d) time)
(toPhyloDate'
(fromIntegral $ fromJust $ _hd_publication_year d)
(fromJust $ _hd_publication_month d)
(fromJust $ _hd_publication_day d) time)
(termsInText patterns $ title <> " " <> abstr) Nothing [] time)
<$> concat
<$> mapConcurrently (\file ->
filter (\d -> (isJust $ _hd_publication_year d)
&& (isJust $ _hd_title d))
<$> fromRight [] <$> parseFile WOS Plain (path <> file) ) files
-- To transform a Csv file into a list of Document
csvToDocs :: CorpusParser -> Patterns -> TimeUnit -> FilePath -> IO [Document]
csvToDocs parser patterns time path =
case parser of
Wos _ -> Prelude.error "csvToDocs: unimplemented"
Csv limit -> Vector.toList
<$> Vector.take limit
<$> Vector.map (\row -> Document (toPhyloDate (Csv.fromMIntOrDec Csv.defaultYear $ csv_publication_year row) (fromMaybe Csv.defaultMonth $ csv_publication_month row) (fromMaybe Csv.defaultDay $ csv_publication_day row) time)
(toPhyloDate' (Csv.fromMIntOrDec Csv.defaultYear $ csv_publication_year row) (fromMaybe Csv.defaultMonth $ csv_publication_month row) (fromMaybe Csv.defaultDay $ csv_publication_day row) time)
(termsInText patterns $ (csv_title row) <> " " <> (csv_abstract row))
Nothing
[]
time
) <$> snd <$> either (\err -> panicTrace $ "CSV error" <> (show err)) identity <$> Csv.readCSVFile path
Csv' limit -> Vector.toList
<$> Vector.take limit
<$> Vector.map (\row -> Document (toPhyloDate (csv'_publication_year row) (csv'_publication_month row) (csv'_publication_day row) time)
(toPhyloDate' (csv'_publication_year row) (csv'_publication_month row) (csv'_publication_day row) time)
(termsInText patterns $ (csv'_title row) <> " " <> (csv'_abstract row))
(Just $ csv'_weight row)
(map (T.strip . pack) $ splitOn ";" (unpack $ (csv'_source row)))
time
) <$> snd <$> Csv.readWeightedCsv path
-- To parse a file into a list of Document
fileToDocsAdvanced :: CorpusParser -> FilePath -> TimeUnit -> TermList -> IO [Document]
fileToDocsAdvanced parser path time lst = do
let patterns = buildPatterns lst
case parser of
Wos limit -> wosToDocs limit 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 panicTrace "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 | --
---------------
-- Config time parameters to label
timeToLabel :: PhyloConfig -> [Char]
timeToLabel config = case (timeUnit config) of
Epoch p s f -> ("time_epochs" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Year p s f -> ("time_years" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Month p s f -> ("time_months" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Week p s f -> ("time_weeks" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Day p s f -> ("time_days" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
seaToLabel :: PhyloConfig -> [Char]
seaToLabel config = case (seaElevation config) of
Constante start step -> ("sea_cst_" <> (show start) <> "_" <> (show step))
Adaptative granularity -> ("sea_adapt" <> (show granularity))
Evolving _ -> ("sea_evolv")
sensToLabel :: PhyloConfig -> [Char]
sensToLabel config = case (similarity config) of
Hamming _ _ -> Prelude.error "sensToLabel: unimplemented"
WeightedLogJaccard s _ -> ("WeightedLogJaccard_" <> show s)
WeightedLogSim s _ -> ( "WeightedLogSim-sens_" <> show s)
cliqueToLabel :: PhyloConfig -> [Char]
cliqueToLabel config = case (clique config) of
Fis s s' -> "fis_" <> (show s) <> "_" <> (show s')
MaxClique s t f -> "clique_" <> (show s)<> "_" <> (show f)<> "_" <> (show t)
syncToLabel :: PhyloConfig -> [Char]
syncToLabel config = case (phyloSynchrony config) of
ByProximityThreshold scl sync_sens scope _ -> ("scale_" <> (show scope) <> "_" <> (show sync_sens) <> "_" <> (show scl))
ByProximityDistribution _ _ -> "syncToLabel: unimplemented"
qualToConfig :: PhyloConfig -> [Char]
qualToConfig config = case (phyloQuality config) of
Quality g m -> "quality_" <> (show g) <> "_" <> (show m)
-- To set up the export file's label from the configuration
configToLabel :: PhyloConfig -> [Char]
configToLabel config = outputPath config
<> (unpack $ phyloName config)
<> "-" <> (timeToLabel config)
<> "-scale_" <> (show (phyloScale config))
<> "-" <> (seaToLabel config)
<> "-" <> (sensToLabel config)
<> "-" <> (cliqueToLabel config)
<> "-level_" <> (show (_qua_granularity $ phyloQuality config))
<> "-" <> (syncToLabel config)
<> ".dot"
-- To write a sha256 from a set of config's parameters
configToSha :: Backup -> PhyloConfig -> [Char]
configToSha stage config = unpack
$ replace "/" "-"
$ T.pack (show (hash $ C8.pack label))
where
label :: [Char]
label = case stage of
BackupPhyloWithoutLink -> (corpusPath config)
<> (listPath config)
<> (timeToLabel config)
<> (cliqueToLabel config)
BackupPhylo -> (corpusPath config)
<> (listPath config)
<> (timeToLabel config)
<> (cliqueToLabel config)
<> (sensToLabel config)
<> (seaToLabel config)
<> (syncToLabel config)
<> (qualToConfig config)
<> (show (phyloScale config))
readListV4 :: [Char] -> IO NgramsList
readListV4 path = do
listJson <- (eitherDecode <$> readJson path) :: IO (Either Prelude.String NgramsList)
case listJson of
Left err -> do
putStrLn err
Prelude.error "readListV4 unimplemented"
Right listV4 -> pure listV4
fileToList :: ListParser -> FilePath -> IO TermList
fileToList parser path =
case parser of
V3 -> csvMapTermList path
V4 -> fromJust
<$> toTermList MapTerm NgramsTerms
<$> readListV4 path
--------------
-- | Main | --
--------------
main :: IO () main :: IO ()
main = do main = do
...@@ -274,7 +71,7 @@ main = do ...@@ -274,7 +71,7 @@ main = do
corpus <- if (defaultMode config) corpus <- if (defaultMode config)
then fileToDocsDefault (corpusParser config) (corpusPath config) [Year 3 1 5,Month 3 1 5,Week 4 2 5] mapList 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 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")
......
bin/gargantext-phylo/Phylo/Common.hs 0 → 100644
View file @ 0405e007
{-# LANGUAGE OverloadedStrings #-}
module Common where
import Control.Concurrent.Async (mapConcurrently)
import Crypto.Hash.SHA256 (hash)
import Data.Aeson
import Data.ByteString.Char8 qualified as C8
import Data.List (nub, tail)
import Data.List.Split
import Data.Maybe (fromJust)
import Data.Text (unpack, replace, pack)
import Data.Text qualified as T
import Data.Vector qualified as Vector
import Gargantext.API.Ngrams.Prelude (toTermList)
import Gargantext.API.Ngrams.Types
import Gargantext.Core.Text.Context (TermList)
import Gargantext.Core.Text.Corpus.Parsers (FileFormat(..), FileType(..), parseFile)
import Gargantext.Core.Text.Corpus.Parsers.CSV (csv_title, csv_abstract, csv_publication_year, csv_publication_month, csv_publication_day, csv'_source, csv'_title, csv'_abstract, csv'_publication_year, csv'_publication_month, csv'_publication_day, csv'_weight)
import Gargantext.Core.Text.Corpus.Parsers.CSV qualified as Csv
import Gargantext.Core.Text.List.Formats.CSV (csvMapTermList)
import Gargantext.Core.Text.Terms.WithList (Patterns, buildPatterns, extractTermsWithList)
import Gargantext.Core.Types.Main (ListType(..))
import Gargantext.Core.Viz.Phylo
import Gargantext.Core.Viz.Phylo.API.Tools
import Gargantext.Core.Viz.Phylo.PhyloTools (toPeriods, getTimePeriod, getTimeStep)
import Gargantext.Database.Admin.Types.Hyperdata (HyperdataDocument(..))
import Gargantext.Database.Schema.Ngrams (NgramsType(..))
import Gargantext.Prelude hiding (hash, replace)
import Prelude qualified
import System.Directory (listDirectory)
data Backup = BackupPhyloWithoutLink | BackupPhylo deriving (Show)
---------------
-- | Tools | --
---------------
-- | To get all the files in a directory or just a file
getFilesFromPath :: FilePath -> IO [FilePath]
getFilesFromPath path = do
if (isSuffixOf "/" path)
then (listDirectory path)
else return [path]
----------------
-- | Parser | --
----------------
-- | To filter the Ngrams of a document based on the termList
termsInText :: Patterns -> Text -> [Text]
termsInText pats txt = nub $ concat $ map (map unwords) $ extractTermsWithList pats txt
-- | To transform a Wos file (or [file]) into a list of Docs
wosToDocs :: Int -> Patterns -> TimeUnit -> FilePath -> IO [Document]
wosToDocs limit patterns time path = do
files <- getFilesFromPath path
take limit
<$> map (\d -> let title = fromJust $ _hd_title d
abstr = if (isJust $ _hd_abstract d)
then fromJust $ _hd_abstract d
else ""
in Document (toPhyloDate
(fromIntegral $ fromJust $ _hd_publication_year d)
(fromJust $ _hd_publication_month d)
(fromJust $ _hd_publication_day d) time)
(toPhyloDate'
(fromIntegral $ fromJust $ _hd_publication_year d)
(fromJust $ _hd_publication_month d)
(fromJust $ _hd_publication_day d) time)
(termsInText patterns $ title <> " " <> abstr) Nothing [] time)
<$> concat
<$> mapConcurrently (\file ->
filter (\d -> (isJust $ _hd_publication_year d)
&& (isJust $ _hd_title d))
<$> fromRight [] <$> parseFile WOS Plain (path <> file) ) files
-- To transform a Csv file into a list of Document
csvToDocs :: CorpusParser -> Patterns -> TimeUnit -> FilePath -> IO [Document]
csvToDocs parser patterns time path =
case parser of
Wos _ -> Prelude.error "csvToDocs: unimplemented"
Csv limit -> Vector.toList
<$> Vector.take limit
<$> Vector.map (\row -> Document (toPhyloDate (Csv.fromMIntOrDec Csv.defaultYear $ csv_publication_year row) (fromMaybe Csv.defaultMonth $ csv_publication_month row) (fromMaybe Csv.defaultDay $ csv_publication_day row) time)
(toPhyloDate' (Csv.fromMIntOrDec Csv.defaultYear $ csv_publication_year row) (fromMaybe Csv.defaultMonth $ csv_publication_month row) (fromMaybe Csv.defaultDay $ csv_publication_day row) time)
(termsInText patterns $ (csv_title row) <> " " <> (csv_abstract row))
Nothing
[]
time
) <$> snd <$> either (\err -> panicTrace $ "CSV error" <> (show err)) identity <$> Csv.readCSVFile path
Csv' limit -> Vector.toList
<$> Vector.take limit
<$> Vector.map (\row -> Document (toPhyloDate (csv'_publication_year row) (csv'_publication_month row) (csv'_publication_day row) time)
(toPhyloDate' (csv'_publication_year row) (csv'_publication_month row) (csv'_publication_day row) time)
(termsInText patterns $ (csv'_title row) <> " " <> (csv'_abstract row))
(Just $ csv'_weight row)
(map (T.strip . pack) $ splitOn ";" (unpack $ (csv'_source row)))
time
) <$> snd <$> Csv.readWeightedCsv path
-- To parse a file into a list of Document
fileToDocsAdvanced :: CorpusParser -> FilePath -> TimeUnit -> TermList -> IO [Document]
fileToDocsAdvanced parser path time lst = do
let patterns = buildPatterns lst
case parser of
Wos limit -> wosToDocs limit 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 panicTrace "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
readListV4 :: [Char] -> IO NgramsList
readListV4 path = do
listJson <- (eitherDecode <$> readJson path) :: IO (Either Prelude.String NgramsList)
case listJson of
Left err -> do
putStrLn err
Prelude.error "readListV4 unimplemented"
Right listV4 -> pure listV4
fileToList :: ListParser -> FilePath -> IO TermList
fileToList parser path =
case parser of
V3 -> csvMapTermList path
V4 -> fromJust
<$> toTermList MapTerm NgramsTerms
<$> readListV4 path
---------------
-- | Label | --
---------------
-- Config time parameters to label
timeToLabel :: PhyloConfig -> [Char]
timeToLabel config = case (timeUnit config) of
Epoch p s f -> ("time_epochs" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Year p s f -> ("time_years" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Month p s f -> ("time_months" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Week p s f -> ("time_weeks" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
Day p s f -> ("time_days" <> "_" <> (show p) <> "_" <> (show s) <> "_" <> (show f))
seaToLabel :: PhyloConfig -> [Char]
seaToLabel config = case (seaElevation config) of
Constante start step -> ("sea_cst_" <> (show start) <> "_" <> (show step))
Adaptative granularity -> ("sea_adapt" <> (show granularity))
Evolving _ -> ("sea_evolv")
sensToLabel :: PhyloConfig -> [Char]
sensToLabel config = case (similarity config) of
Hamming _ _ -> Prelude.error "sensToLabel: unimplemented"
WeightedLogJaccard s _ -> ("WeightedLogJaccard_" <> show s)
WeightedLogSim s _ -> ( "WeightedLogSim-sens_" <> show s)
cliqueToLabel :: PhyloConfig -> [Char]
cliqueToLabel config = case (clique config) of
Fis s s' -> "fis_" <> (show s) <> "_" <> (show s')
MaxClique s t f -> "clique_" <> (show s)<> "_" <> (show f)<> "_" <> (show t)
syncToLabel :: PhyloConfig -> [Char]
syncToLabel config = case (phyloSynchrony config) of
ByProximityThreshold scl sync_sens scope _ -> ("scale_" <> (show scope) <> "_" <> (show sync_sens) <> "_" <> (show scl))
ByProximityDistribution _ _ -> "syncToLabel: unimplemented"
qualToConfig :: PhyloConfig -> [Char]
qualToConfig config = case (phyloQuality config) of
Quality g m -> "quality_" <> (show g) <> "_" <> (show m)
-- To set up the export file's label from the configuration
configToLabel :: PhyloConfig -> [Char]
configToLabel config = outputPath config
<> (unpack $ phyloName config)
<> "-" <> (timeToLabel config)
<> "-scale_" <> (show (phyloScale config))
<> "-" <> (seaToLabel config)
<> "-" <> (sensToLabel config)
<> "-" <> (cliqueToLabel config)
<> "-level_" <> (show (_qua_granularity $ phyloQuality config))
<> "-" <> (syncToLabel config)
<> ".dot"
-- To write a sha256 from a set of config's parameters
configToSha :: Backup -> PhyloConfig -> [Char]
configToSha stage config = unpack
$ replace "/" "-"
$ T.pack (show (hash $ C8.pack label))
where
label :: [Char]
label = case stage of
BackupPhyloWithoutLink -> (corpusPath config)
<> (listPath config)
<> (timeToLabel config)
<> (cliqueToLabel config)
BackupPhylo -> (corpusPath config)
<> (listPath config)
<> (timeToLabel config)
<> (cliqueToLabel config)
<> (sensToLabel config)
<> (seaToLabel config)
<> (syncToLabel config)
<> (qualToConfig config)
<> (show (phyloScale config))
bin/update-project-dependencies
View file @ 0405e007
...@@ -18,8 +18,8 @@ fi ...@@ -18,8 +18,8 @@ fi
# with the `sha256sum` result calculated on the `cabal.project` and # with the `sha256sum` result calculated on the `cabal.project` and
# `cabal.project.freeze`. This ensures the files stay deterministic so that CI # `cabal.project.freeze`. This ensures the files stay deterministic so that CI
# cache can kick in. # cache can kick in.
expected_cabal_project_hash="20253fb02ed59b6e8e72f974aad2aef3409ca6f9d005f7e84bb660812f1a70db" expected_cabal_project_hash="c9fe39301e8b60bfd183e60e7e25a14cd1c9c66d8739bf9041ca3f4db89db7c6"
expected_cabal_project_freeze_hash="745c65c246998cfda4d2a7a22df44a9f1f7fb0927e2afc2f16712861bf552c76" expected_cabal_project_freeze_hash="db24c7d3006167102532e3101e2b49bae13d478003459c7d3f1d66590e57740a"
cabal --store-dir=$STORE_DIR v2-build --dry-run cabal --store-dir=$STORE_DIR v2-build --dry-run
cabal2stack --system-ghc --allow-newer --resolver lts-21.17 --resolver-file devops/stack/lts-21.17.yaml -o stack.yaml cabal2stack --system-ghc --allow-newer --resolver lts-21.17 --resolver-file devops/stack/lts-21.17.yaml -o stack.yaml
......
gargantext.cabal
View file @ 0405e007
...@@ -5,7 +5,7 @@ cabal-version: 3.4 ...@@ -5,7 +5,7 @@ cabal-version: 3.4
-- see: https://github.com/sol/hpack -- see: https://github.com/sol/hpack
name: gargantext name: gargantext
version: 0.0.6.9.9.9.6.1 version: 0.0.6.9.9.9.6.2
synopsis: Search, map, share synopsis: Search, map, share
description: Please see README.md description: Please see README.md
category: Data category: Data
...@@ -17,6 +17,9 @@ license: AGPL-3.0-or-later ...@@ -17,6 +17,9 @@ license: AGPL-3.0-or-later
license-file: LICENSE license-file: LICENSE
build-type: Simple build-type: Simple
data-files: data-files:
bench-data/phylo/bpa-config.json
bench-data/phylo/GarganText_DocsList-nodeId-185487.csv
bench-data/phylo/GarganText_NgramsList-185488.csv
bench-data/phylo/issue-290.json bench-data/phylo/issue-290.json
bench-data/phylo/issue-290-small.json bench-data/phylo/issue-290-small.json
devops/postgres/extensions.sql devops/postgres/extensions.sql
...@@ -82,6 +85,13 @@ flag disable-db-obfuscation-executable ...@@ -82,6 +85,13 @@ flag disable-db-obfuscation-executable
default: False default: False
manual: True manual: True
-- When enabled, it suppresses at compile time the
-- debug output for the phylo code, so that it doesn't
-- hinder its performance.
flag no-phylo-debug-logs
default: False
manual: True
library library
import: import:
defaults defaults
...@@ -431,6 +441,8 @@ library ...@@ -431,6 +441,8 @@ library
src src
if flag(test-crypto) if flag(test-crypto)
cpp-options: -DTEST_CRYPTO cpp-options: -DTEST_CRYPTO
if flag(no-phylo-debug-logs)
cpp-options: -DNO_PHYLO_DEBUG_LOGS
build-depends: build-depends:
HSvm ^>= 0.1.1.3.22 HSvm ^>= 0.1.1.3.22
, KMP ^>= 0.2.0.0 , KMP ^>= 0.2.0.0
...@@ -476,6 +488,7 @@ library ...@@ -476,6 +488,7 @@ library
, data-time-segment ^>= 0.1.0.0 , data-time-segment ^>= 0.1.0.0
, deepseq ^>= 1.4.4.0 , deepseq ^>= 1.4.4.0
, directory ^>= 1.3.6.0 , directory ^>= 1.3.6.0
, discrimination >= 0.5
, duckling ^>= 0.2.0.0 , duckling ^>= 0.2.0.0
, ekg-core ^>= 0.1.1.7 , ekg-core ^>= 0.1.1.7
, ekg-json ^>= 0.1.0.7 , ekg-json ^>= 0.1.0.7
...@@ -745,8 +758,25 @@ executable gargantext-phylo ...@@ -745,8 +758,25 @@ executable gargantext-phylo
main-is: Main.hs main-is: Main.hs
other-modules: other-modules:
Paths_gargantext Paths_gargantext
Common
hs-source-dirs: hs-source-dirs:
bin/gargantext-phylo bin/gargantext-phylo bin/gargantext-phylo/Phylo
default-extensions:
DataKinds
DeriveGeneric
FlexibleContexts
FlexibleInstances
GADTs
GeneralizedNewtypeDeriving
ImportQualifiedPost
MultiParamTypeClasses
NamedFieldPuns
NoImplicitPrelude
OverloadedStrings
RankNTypes
RecordWildCards
StrictData
ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N -O2 -Wmissing-signatures
build-depends: build-depends:
async ^>= 2.2.4 async ^>= 2.2.4
, bytestring ^>= 0.10.12.0 , bytestring ^>= 0.10.12.0
...@@ -1009,4 +1039,26 @@ benchmark garg-bench ...@@ -1009,4 +1039,26 @@ benchmark garg-bench
if impl(ghc >= 8.6) if impl(ghc >= 8.6)
ghc-options: "-with-rtsopts=--nonmoving-gc" ghc-options: "-with-rtsopts=--nonmoving-gc"
executable gargantext-phylo-profile
main-is: Main.hs
other-modules:
Paths_gargantext
Common
hs-source-dirs:
bin/gargantext-phylo-profile bin/gargantext-phylo/Phylo
default-extensions: GHC2021
ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N -O2 -Wmissing-signatures
build-depends:
base
, bytestring
, gargantext
, gargantext-prelude
, shelly
, text
, async
, cryptohash
, aeson
, split
, vector
, directory
default-language: Haskell2010
src/Gargantext/Core/Text/List/Formats/CSV.hs
View file @ 0405e007
...@@ -64,10 +64,11 @@ instance ToNamedRecord CsvList where ...@@ -64,10 +64,11 @@ instance ToNamedRecord CsvList where
] ]
------------------------------------------------------------------------ ------------------------------------------------------------------------
instance FromField CsvListType where instance FromField CsvListType where
parseField "map" = pure CsvMap parseField "map" = pure CsvMap
parseField "main" = pure CsvCandidate parseField "main" = pure CsvCandidate
parseField "stop" = pure CsvStop parseField "candidate" = pure CsvCandidate -- backward compat
parseField _ = mzero parseField "stop" = pure CsvStop
parseField _ = mzero
instance ToField CsvListType where instance ToField CsvListType where
toField CsvMap = "map" toField CsvMap = "map"
......
src/Gargantext/Core/Viz/Phylo/API/Tools.hs
View file @ 0405e007
...@@ -195,7 +195,7 @@ toPhyloDate' y m d _ = pack $ showGregorian $ fromGregorian (toIntege ...@@ -195,7 +195,7 @@ toPhyloDate' y m d _ = pack $ showGregorian $ fromGregorian (toIntege
-- Utils -- Utils
writePhylo :: [Char] -> Phylo -> IO () writePhylo :: HasCallStack => [Char] -> Phylo -> IO ()
writePhylo path phylo = Lazy.writeFile path $ encode phylo writePhylo path phylo = Lazy.writeFile path $ encode phylo
......
src/Gargantext/Core/Viz/Phylo/PhyloExport.hs
View file @ 0405e007
...@@ -702,17 +702,17 @@ toPhyloExport phylo = exportToDot phylo ...@@ -702,17 +702,17 @@ toPhyloExport phylo = exportToDot phylo
traceExportBranches :: [PhyloBranch] -> [PhyloBranch] traceExportBranches :: [PhyloBranch] -> [PhyloBranch]
traceExportBranches branches = traceExportBranches branches =
trace ("\n" tracePhylo ("\n"
<> "-- | Export " <> show(length branches) <> " branches" :: Text) branches <> "-- | Export " <> show(length branches) <> " branches" :: Text) branches
tracePhyloAncestors :: [[PhyloGroup]] -> [[PhyloGroup]] tracePhyloAncestors :: [[PhyloGroup]] -> [[PhyloGroup]]
tracePhyloAncestors groups = tracePhyloAncestors groups =
trace ( "-- | Found " <> show(length $ concat $ map _phylo_groupAncestors $ concat groups) tracePhylo ( "-- | Found " <> show(length $ concat $ map _phylo_groupAncestors $ concat groups)
<> " ancestors" :: Text) groups <> " ancestors" :: Text) groups
tracePhyloInfo :: Phylo -> Phylo tracePhyloInfo :: Phylo -> Phylo
tracePhyloInfo phylo = tracePhyloInfo phylo =
trace ("\n" <> "##########################" <> "\n\n" <> "-- | Phylo with level = " tracePhylo ("\n" <> "##########################" <> "\n\n" <> "-- | Phylo with level = "
<> show(getLevel phylo) <> " applied to " <> show(getLevel phylo) <> " applied to "
<> show(length $ Vector.toList $ getRoots phylo) <> " foundations" :: Text <> show(length $ Vector.toList $ getRoots phylo) <> " foundations" :: Text
) phylo ) phylo
...@@ -720,7 +720,7 @@ tracePhyloInfo phylo = ...@@ -720,7 +720,7 @@ tracePhyloInfo phylo =
traceExportGroups :: [PhyloGroup] -> [PhyloGroup] traceExportGroups :: [PhyloGroup] -> [PhyloGroup]
traceExportGroups groups = traceExportGroups groups =
trace ("\n" <> "-- | Export " tracePhylo ("\n" <> "-- | Export "
<> show(length $ nub $ map (\g -> g ^. phylo_groupBranchId) groups) <> " branches, " <> show(length $ nub $ map (\g -> g ^. phylo_groupBranchId) groups) <> " branches, "
<> show(length groups) <> " groups and " <> show(length groups) <> " groups and "
<> show(length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) groups) <> " terms" :: Text <> show(length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) groups) <> " terms" :: Text
......
src/Gargantext/Core/Viz/Phylo/PhyloMaker.hs
View file @ 0405e007
...@@ -10,19 +10,23 @@ Portability : POSIX ...@@ -10,19 +10,23 @@ Portability : POSIX
{-# OPTIONS_GHC -fno-warn-deprecations #-} {-# OPTIONS_GHC -fno-warn-deprecations #-}
{-# LANGUAGE BangPatterns #-}
module Gargantext.Core.Viz.Phylo.PhyloMaker where module Gargantext.Core.Viz.Phylo.PhyloMaker where
import Control.Lens hiding (Level) import Control.Lens hiding (Level)
import Control.Parallel.Strategies (parList, rdeepseq, using) import Control.Parallel.Strategies (parMap, rpar)
import Data.List (nub, partition, intersect, tail) import Data.Containers.ListUtils (nubOrd)
import Data.Discrimination qualified as D
import Data.List (partition, intersect, tail)
import Data.List qualified as List import Data.List qualified as List
import Data.Map (fromListWith, keys, unionWith, fromList, empty, toList, elems, (!), restrictKeys, insert) import Data.Map (fromListWith, keys, unionWith, fromList, empty, toList, elems, (!), restrictKeys, insert)
import Data.Map qualified as Map import Data.Map qualified as Map
import Data.Set qualified as Set import Data.Set qualified as Set
import Data.Vector (Vector) import Data.Text qualified as T
import Data.Vector qualified as Vector import Data.Vector qualified as Vector
import Data.Vector (Vector)
import Gargantext.Core.Methods.Graph.MaxClique (getMaxCliques) import Gargantext.Core.Methods.Graph.MaxClique (getMaxCliques)
import Gargantext.Core.Methods.Similarities (Similarity(Conditional)) import Gargantext.Core.Methods.Similarities (Similarity(Conditional))
import Gargantext.Core.Text.Metrics.FrequentItemSet (fisWithSizePolyMap, fisWithSizePolyMap', Size(..)) import Gargantext.Core.Text.Metrics.FrequentItemSet (fisWithSizePolyMap, fisWithSizePolyMap', Size(..))
...@@ -131,9 +135,9 @@ evolvSeaLadder nbFdt lambda freq similarities graph = map snd ...@@ -131,9 +135,9 @@ evolvSeaLadder nbFdt lambda freq similarities graph = map snd
-------- --------
-- 1.1) for each measure of similarity, prune the flat phylo, compute the branches and estimate the quality -- 1.1) for each measure of similarity, prune the flat phylo, compute the branches and estimate the quality
qua :: [Double] qua :: [Double]
qua = map (\thr -> qua = parMap rpar (\thr ->
let edges = filter (\edge -> snd edge >= thr) graph let edges = filter (\edge -> snd edge >= thr) graph
nodes = nub $ concat $ map (\((n,n'),_) -> [n,n']) edges nodes = nubOrd $ concat $ map (\((n,n'),_) -> [n,n']) edges
branches = toRelatedComponents nodes edges branches = toRelatedComponents nodes edges
in toPhyloQuality nbFdt lambda freq branches in toPhyloQuality nbFdt lambda freq branches
) $ (Set.toList similarities) ) $ (Set.toList similarities)
...@@ -146,7 +150,7 @@ findSeaLadder :: Phylo -> Phylo ...@@ -146,7 +150,7 @@ findSeaLadder :: Phylo -> Phylo
findSeaLadder phylo = case getSeaElevation phylo of findSeaLadder phylo = case getSeaElevation phylo of
Constante start gap -> phylo & phylo_seaLadder .~ (constSeaLadder start gap Set.empty) Constante start gap -> phylo & phylo_seaLadder .~ (constSeaLadder start gap Set.empty)
Adaptative steps -> phylo & phylo_seaLadder .~ (squareLadder $ adaptSeaLadder steps similarities Set.empty) Adaptative steps -> phylo & phylo_seaLadder .~ (squareLadder $ adaptSeaLadder steps similarities Set.empty)
Evolving _ -> let ladder = evolvSeaLadder Evolving _ -> let !ladder = evolvSeaLadder
(fromIntegral $ Vector.length $ getRoots phylo) (fromIntegral $ Vector.length $ getRoots phylo)
(getLevel phylo) (getLevel phylo)
(getRootsFreq phylo) (getRootsFreq phylo)
...@@ -172,7 +176,7 @@ findSeaLadder phylo = case getSeaElevation phylo of ...@@ -172,7 +176,7 @@ findSeaLadder phylo = case getSeaElevation phylo of
docs = filterDocs (getDocsByDate phylo) ([period] ++ next) docs = filterDocs (getDocsByDate phylo) ([period] ++ next)
diagos = filterDiago (getCoocByDate phylo) ([period] ++ next) diagos = filterDiago (getCoocByDate phylo) ([period] ++ next)
-- 1.2) compute the kinship similarities between pairs of source & target in parallel -- 1.2) compute the kinship similarities between pairs of source & target in parallel
pairs = map (\source -> pairs = parMap rpar (\source ->
let candidates = filter (\target -> (> 2) $ length let candidates = filter (\target -> (> 2) $ length
$ intersect (getGroupNgrams source) (getGroupNgrams target)) targets $ intersect (getGroupNgrams source) (getGroupNgrams target)) targets
in map (\target -> in map (\target ->
...@@ -183,8 +187,7 @@ findSeaLadder phylo = case getSeaElevation phylo of ...@@ -183,8 +187,7 @@ findSeaLadder phylo = case getSeaElevation phylo of
in ((source,target),toSimilarity nbDocs diago (getSimilarity phylo) (getGroupNgrams source) (getGroupNgrams target) (getGroupNgrams target)) in ((source,target),toSimilarity nbDocs diago (getSimilarity phylo) (getGroupNgrams source) (getGroupNgrams target) (getGroupNgrams target))
) candidates ) candidates
) sources ) sources
pairs' = pairs `using` parList rdeepseq in acc ++ (concat pairs)
in acc ++ (concat pairs')
) [] $ keys $ phylo ^. phylo_periods ) [] $ keys $ phylo ^. phylo_periods
appendGroups :: (a -> Period -> (Text,Text) -> Scale -> Int -> [Cooc] -> Map Int Double -> 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
...@@ -311,15 +314,14 @@ filterCliqueBySize thr l = filter (\clq -> (length $ clq ^. clustering_roots) >= ...@@ -311,15 +314,14 @@ filterCliqueBySize thr l = filter (\clq -> (length $ clq ^. clustering_roots) >=
-- To filter nested Fis -- To filter nested Fis
filterCliqueByNested :: Map (Date, Date) [Clustering] -> Map (Date, Date) [Clustering] filterCliqueByNested :: Map (Date, Date) [Clustering] -> Map (Date, Date) [Clustering]
filterCliqueByNested m = filterCliqueByNested m =
let clq = map (\l -> let clq = parMap rpar (\l ->
foldl' (\mem f -> if (any (\f' -> isNested (f' ^. clustering_roots) (f ^. clustering_roots)) mem) foldl (\mem f -> if (any (\f' -> isNested (f' ^. clustering_roots) (f ^. clustering_roots)) mem)
then mem then mem
else else
let fMax = filter (\f' -> not $ isNested (f ^. clustering_roots) (f' ^. clustering_roots)) mem let fMax = filter (\f' -> not $ isNested (f ^. clustering_roots) (f' ^. clustering_roots)) mem
in fMax ++ [f] ) [] l) in fMax ++ [f] ) [] l)
$ elems m $ elems m
clq' = clq `using` parList rdeepseq in fromList $ zip (keys m) clq
in fromList $ zip (keys m) clq'
-- | To transform a time map of docs into a time map of Fis with some filters -- | To transform a time map of docs into a time map of Fis with some filters
...@@ -340,7 +342,7 @@ toSeriesOfClustering phylo phyloDocs = case (clique $ getConfig phylo) of ...@@ -340,7 +342,7 @@ toSeriesOfClustering phylo phyloDocs = case (clique $ getConfig phylo) of
seriesOfClustering :: Map (Date,Date) [Clustering] seriesOfClustering :: Map (Date,Date) [Clustering]
seriesOfClustering = case (clique $ getConfig phylo) of seriesOfClustering = case (clique $ getConfig phylo) of
Fis _ _ -> Fis _ _ ->
let fis = map (\(prd,docs) -> let fis = parMap rpar (\(prd,docs) ->
case (corpusParser $ getConfig phylo) of case (corpusParser $ getConfig phylo) of
Csv' _ -> let lst = toList Csv' _ -> let lst = toList
$ fisWithSizePolyMap' (Segment 1 20) 1 (map (\d -> (ngramsToIdx (text d) (getRoots phylo), (weight d, (sourcesToIdx (sources d) (getSources phylo))))) docs) $ fisWithSizePolyMap' (Segment 1 20) 1 (map (\d -> (ngramsToIdx (text d) (getRoots phylo), (weight d, (sourcesToIdx (sources d) (getSources phylo))))) docs)
...@@ -350,18 +352,16 @@ toSeriesOfClustering phylo phyloDocs = case (clique $ getConfig phylo) of ...@@ -350,18 +352,16 @@ toSeriesOfClustering phylo phyloDocs = case (clique $ getConfig phylo) of
in (prd, map (\f -> Clustering (Set.toList $ fst f) (snd f) prd (Just $ fromIntegral $ snd f) []) lst) in (prd, map (\f -> Clustering (Set.toList $ fst f) (snd f) prd (Just $ fromIntegral $ snd f) []) lst)
) )
$ toList phyloDocs $ toList phyloDocs
fis' = fis `using` parList rdeepseq in fromList fis
in fromList fis'
MaxClique _ thr filterType -> MaxClique _ thr filterType ->
let mcl = map (\(prd,docs) -> let mcl = parMap rpar (\(prd,docs) ->
let cooc = map round let cooc = map round
$ foldl' sumCooc empty $ foldl' sumCooc empty
$ map listToMatrix $ map listToMatrix
$ map (\d -> ngramsToIdx (text d) (getRoots phylo)) docs $ map (\d -> ngramsToIdx (text d) (getRoots phylo)) docs
in (prd, map (\cl -> Clustering cl 0 prd Nothing []) $ getMaxCliques filterType Conditional thr cooc)) in (prd, map (\cl -> Clustering cl 0 prd Nothing []) $ getMaxCliques filterType Conditional thr cooc))
$ toList phyloDocs $ toList phyloDocs
mcl' = mcl `using` parList rdeepseq in fromList mcl
in fromList mcl'
-------------------------------------- --------------------------------------
-- dev viz graph maxClique getMaxClique -- dev viz graph maxClique getMaxClique
...@@ -377,7 +377,7 @@ docsToTimeScaleCooc :: [Document] -> Vector Ngrams -> Map Date Cooc ...@@ -377,7 +377,7 @@ docsToTimeScaleCooc :: [Document] -> Vector Ngrams -> Map Date Cooc
docsToTimeScaleCooc docs fdt = docsToTimeScaleCooc docs fdt =
let mCooc = fromListWith sumCooc let mCooc = fromListWith sumCooc
$ map (\(_d,l) -> (_d, listToMatrix l)) $ map (\(_d,l) -> (_d, listToMatrix l))
$ map (\doc -> (date doc, sort $ ngramsToIdx (text doc) fdt)) docs $ map (\doc -> (date doc, D.sort $ ngramsToIdx (text doc) fdt)) docs
mCooc' = fromList mCooc' = fromList
$ map (\t -> (t,empty)) $ map (\t -> (t,empty))
$ toTimeScale (map date docs) 1 $ toTimeScale (map date docs) 1
...@@ -406,13 +406,12 @@ groupDocsByPeriodRec f prds docs acc = ...@@ -406,13 +406,12 @@ groupDocsByPeriodRec f prds docs acc =
groupDocsByPeriod' :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc] groupDocsByPeriod' :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
groupDocsByPeriod' f pds docs = groupDocsByPeriod' f pds docs =
let docs' = groupBy (\d d' -> f d == f d') $ sortOn f docs let docs' = groupBy (\d d' -> f d == f d') $ sortOn f docs
periods = map (inPeriode f docs') pds periods = parMap rpar (inPeriode f docs') pds
periods' = periods `using` parList rdeepseq
in trace ("\n" <> "-- | Group " in trace ("\n" <> "-- | Group "
<> show(length docs) <> show(length docs)
<> " docs by " <> " docs by "
<> show(length pds) <> " periods" <> "\n" :: Text) <> show(length pds) <> " periods" <> "\n" :: Text)
$ fromList $ zip pds periods' $ fromList $ zip pds periods
where where
-------------------------------------- --------------------------------------
inPeriode :: Ord b => (t -> b) -> [[t]] -> (b, b) -> [t] inPeriode :: Ord b => (t -> b) -> [[t]] -> (b, b) -> [t]
...@@ -425,13 +424,12 @@ groupDocsByPeriod' f pds docs = ...@@ -425,13 +424,12 @@ groupDocsByPeriod' f pds docs =
groupDocsByPeriod :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc] groupDocsByPeriod :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
groupDocsByPeriod _ _ [] = panic "[ERR][Viz.Phylo.PhyloMaker] Empty [Documents] can not have any periods" groupDocsByPeriod _ _ [] = panic "[ERR][Viz.Phylo.PhyloMaker] Empty [Documents] can not have any periods"
groupDocsByPeriod f pds es = groupDocsByPeriod f pds es =
let periods = map (inPeriode f es) pds let periods = parMap rpar (inPeriode f es) pds
periods' = periods `using` parList rdeepseq
in trace ("\n" <> "-- | Group " in trace ("\n" <> "-- | Group "
<> show(length es) <> " docs by " <> show(length es) <> " docs by "
<> show(length pds) <> " periods" <> "\n" :: Text) <> show(length pds) <> " periods" <> "\n" :: Text)
$ fromList $ zip pds periods' $ fromList $ zip pds periods
where where
-------------------------------------- --------------------------------------
inPeriode :: Ord b => (t -> b) -> [t] -> (b, b) -> [t] inPeriode :: Ord b => (t -> b) -> [t] -> (b, b) -> [t]
...@@ -446,7 +444,7 @@ docsToTermFreq docs fdt = ...@@ -446,7 +444,7 @@ docsToTermFreq docs fdt =
freqs = map (/(nbDocs)) freqs = map (/(nbDocs))
$ fromList $ fromList
$ map (\lst -> (head' "docsToTermFreq" lst, fromIntegral $ length lst)) $ map (\lst -> (head' "docsToTermFreq" lst, fromIntegral $ length lst))
$ group $ sort $ concat $ map (\d -> nub $ ngramsToIdx (text d) fdt) docs $ group $ D.sort $ concat $ map (\d -> D.nub $ ngramsToIdx (text d) fdt) docs
sumFreqs = sum $ elems freqs sumFreqs = sum $ elems freqs
in map (/sumFreqs) freqs in map (/sumFreqs) freqs
...@@ -454,28 +452,28 @@ docsToTermFreq docs fdt = ...@@ -454,28 +452,28 @@ docsToTermFreq docs fdt =
docsToTermCount :: [Document] -> Vector Ngrams -> Map Int Double docsToTermCount :: [Document] -> Vector Ngrams -> Map Int Double
docsToTermCount docs roots = fromList docsToTermCount docs roots = fromList
$ map (\lst -> (head' "docsToTermCount" lst, fromIntegral $ length lst)) $ map (\lst -> (head' "docsToTermCount" lst, fromIntegral $ length lst))
$ group $ sort $ concat $ map (\d -> nub $ ngramsToIdx (text d) roots) docs $ group $ D.sort $ concat $ map (\d -> D.nub $ ngramsToIdx (text d) roots) docs
docsToTimeTermCount :: [Document] -> Vector Ngrams -> (Map Date (Map Int Double)) docsToTimeTermCount :: [Document] -> Vector Ngrams -> (Map Date (Map Int Double))
docsToTimeTermCount docs roots = docsToTimeTermCount docs roots =
let docs' = Map.map (\l -> fromList $ map (\lst -> (head' "docsToTimeTermCount" lst, fromIntegral $ length lst)) let docs' = Map.map (\l -> fromList $ map (\lst -> (head' "docsToTimeTermCount" lst, fromIntegral $ length lst))
$ group $ sort l) $ group $ D.sort l)
$ fromListWith (++) $ fromListWith (++)
$ map (\d -> (date d, nub $ ngramsToIdx (text d) roots)) docs $ map (\d -> (date d, D.nub $ ngramsToIdx (text d) roots)) docs
time = fromList $ map (\t -> (t,Map.empty)) $ toTimeScale (keys docs') 1 time = fromList $ map (\t -> (t,Map.empty)) $ toTimeScale (keys docs') 1
in unionWith (Map.union) time docs' 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 $ D.sort $ map date docs
nbDocs = fromIntegral $ length $ filter (\d -> elem (date d) last) docs nbDocs = fromIntegral $ length $ filter (\d -> elem (date d) last) docs
freqs = map (/(nbDocs)) freqs = map (/(nbDocs))
$ fromList $ fromList
$ map (\lst -> (head' "docsToLastTermFreq" lst, fromIntegral $ length lst)) $ map (\lst -> (head' "docsToLastTermFreq" lst, fromIntegral $ length lst))
$ group $ sort $ concat $ map (\d -> nub $ ngramsToIdx (text d) fdt) $ filter (\d -> elem (date d) last) docs $ group $ D.sort $ concat $ map (\d -> D.nub $ ngramsToIdx (text d) fdt) $ filter (\d -> elem (date d) last) docs
sumFreqs = sum $ elems freqs sumFreqs = sum $ elems freqs
in map (/sumFreqs) freqs in map (/sumFreqs) freqs
...@@ -527,10 +525,10 @@ setDefault conf timeScale nbDocs = defaultConfig ...@@ -527,10 +525,10 @@ setDefault conf timeScale nbDocs = defaultConfig
-- --
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 $ D.nubWith T.unpack $ concat $ map text docs
timeScale = head' "initPhylo" $ map docTime 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 $ nubOrd $ 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)) (docsToTimeTermCount docs (foundations ^. foundations_roots))
...@@ -540,7 +538,7 @@ initPhylo docs conf = ...@@ -540,7 +538,7 @@ initPhylo docs conf =
params = if (defaultMode conf) params = if (defaultMode conf)
then defaultPhyloParam { _phyloParam_config = setDefault conf timeScale (length docs) } then defaultPhyloParam { _phyloParam_config = setDefault conf timeScale (length docs) }
else defaultPhyloParam { _phyloParam_config = conf } else defaultPhyloParam { _phyloParam_config = conf }
periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod timeScale) (getTimeStep timeScale) periods = toPeriods (D.sort $ D.nub $ map date docs) (getTimePeriod timeScale) (getTimeStep timeScale)
in trace ("\n" <> "-- | Init a phylo out of " in trace ("\n" <> "-- | Init a phylo out of "
<> show(length docs) <> " docs \n" :: Text) <> show(length docs) <> " docs \n" :: Text)
$ trace ("\n" <> "-- | lambda " $ trace ("\n" <> "-- | lambda "
......
src/Gargantext/Core/Viz/Phylo/PhyloTools.hs
View file @ 0405e007
...@@ -10,7 +10,8 @@ Portability : POSIX ...@@ -10,7 +10,8 @@ Portability : POSIX
{-# OPTIONS_GHC -fno-warn-deprecations #-} {-# OPTIONS_GHC -fno-warn-deprecations #-}
{-# LANGUAGE ViewPatterns #-} {-# LANGUAGE CPP #-}
{-# LANGUAGE ViewPatterns #-}
module Gargantext.Core.Viz.Phylo.PhyloTools where module Gargantext.Core.Viz.Phylo.PhyloTools where
...@@ -232,6 +233,14 @@ keepFilled f thr l = if (null $ f thr l) && (not $ null l) ...@@ -232,6 +233,14 @@ keepFilled f thr l = if (null $ f thr l) && (not $ null l)
then keepFilled f (thr - 1) l then keepFilled f (thr - 1) l
else f thr l else f thr l
-- | General workhorse to use in lieu of /trace/. It decides at compile
-- time whether or not debug logs are enabled.
tracePhylo :: (Print s, IsString s) => s -> a -> a
#if NO_PHYLO_DEBUG_LOGS
tracePhylo _ p = p
#else
tracePhylo msg p = trace msg p
#endif
traceClique :: Map (Date, Date) [Clustering] -> String traceClique :: Map (Date, Date) [Clustering] -> String
traceClique mFis = foldl' (\msg cpt -> msg <> show (countSup cpt cliques) <> " (>" <> show (cpt) <> ") " ) "" [1..6] traceClique mFis = foldl' (\msg cpt -> msg <> show (countSup cpt cliques) <> " (>" <> show (cpt) <> ") " ) "" [1..6]
...@@ -252,7 +261,7 @@ traceSupport mFis = foldl' (\msg cpt -> msg <> show (countSup cpt supports) <> " ...@@ -252,7 +261,7 @@ traceSupport mFis = foldl' (\msg cpt -> msg <> show (countSup cpt supports) <> "
traceFis :: [Char] -> Map (Date, Date) [Clustering] -> Map (Date, Date) [Clustering] traceFis :: [Char] -> Map (Date, Date) [Clustering] -> Map (Date, Date) [Clustering]
traceFis msg mFis = trace ( "\n" <> "-- | " <> msg <> " : " <> show (sum $ map length $ elems mFis) <> "\n" traceFis msg mFis = tracePhylo ( "\n" <> "-- | " <> msg <> " : " <> show (sum $ map length $ elems mFis) <> "\n"
<> "Support : " <> traceSupport mFis <> "\n" <> "Support : " <> traceSupport mFis <> "\n"
<> "Nb Ngrams : " <> traceClique mFis <> "\n" <> "Nb Ngrams : " <> traceClique mFis <> "\n"
) mFis ) mFis
...@@ -636,7 +645,7 @@ updateLevel level phylo = phylo { _phylo_level = level } ...@@ -636,7 +645,7 @@ updateLevel level phylo = phylo { _phylo_level = level }
traceToPhylo :: Scale -> Phylo -> Phylo traceToPhylo :: Scale -> Phylo -> Phylo
traceToPhylo lvl phylo = traceToPhylo lvl phylo =
trace ("\n" <> "-- | End of phylo making at scale " <> show (lvl) <> " with " tracePhylo ("\n" <> "-- | End of phylo making at scale " <> show (lvl) <> " with "
<> show (length $ getGroupsFromScale lvl phylo) <> " groups and " <> show (length $ getGroupsFromScale lvl phylo) <> " groups and "
<> show (length $ nub $ map _phylo_groupBranchId $ getGroupsFromScale lvl phylo) <> show (length $ nub $ map _phylo_groupBranchId $ getGroupsFromScale lvl phylo)
<> " branches" <> "\n" :: Text <> " branches" <> "\n" :: Text
...@@ -702,7 +711,7 @@ toRelatedComponents nodes edges = ...@@ -702,7 +711,7 @@ toRelatedComponents nodes edges =
traceSynchronyEnd :: Phylo -> Phylo traceSynchronyEnd :: Phylo -> Phylo
traceSynchronyEnd phylo = traceSynchronyEnd phylo =
trace ( "-- | End synchronic clustering at scale " <> show (getLastLevel phylo) tracePhylo ( "-- | End synchronic clustering at scale " <> show (getLastLevel phylo)
<> " with " <> show (length $ getGroupsFromScale (getLastLevel phylo) phylo) <> " groups" <> " with " <> show (length $ getGroupsFromScale (getLastLevel phylo) phylo) <> " groups"
<> " and " <> show (length $ nub $ map _phylo_groupBranchId $ getGroupsFromScale (getLastLevel phylo) phylo) <> " and " <> show (length $ nub $ map _phylo_groupBranchId $ getGroupsFromScale (getLastLevel phylo) phylo)
<> " branches" <> "\n" :: Text <> " branches" <> "\n" :: Text
...@@ -710,7 +719,7 @@ traceSynchronyEnd phylo = ...@@ -710,7 +719,7 @@ traceSynchronyEnd phylo =
traceSynchronyStart :: Phylo -> Phylo traceSynchronyStart :: Phylo -> Phylo
traceSynchronyStart phylo = traceSynchronyStart phylo =
trace ( "\n" <> "-- | Start synchronic clustering at scale " <> show (getLastLevel phylo) tracePhylo ( "\n" <> "-- | Start synchronic clustering at scale " <> show (getLastLevel phylo)
<> " with " <> show (length $ getGroupsFromScale (getLastLevel phylo) phylo) <> " groups" <> " with " <> show (length $ getGroupsFromScale (getLastLevel phylo) phylo) <> " groups"
<> " and " <> show (length $ nub $ map _phylo_groupBranchId $ getGroupsFromScale (getLastLevel phylo) phylo) <> " and " <> show (length $ nub $ map _phylo_groupBranchId $ getGroupsFromScale (getLastLevel phylo) phylo)
<> " branches" <> "\n" :: Text <> " branches" <> "\n" :: Text
...@@ -754,7 +763,7 @@ ngramsInBranches branches = nub $ foldl' (\acc g -> acc ++ (g ^. phylo_groupNgra ...@@ -754,7 +763,7 @@ ngramsInBranches branches = nub $ foldl' (\acc g -> acc ++ (g ^. phylo_groupNgra
traceMatchSuccess :: Double -> Double -> Double -> [[[PhyloGroup]]] -> [[[PhyloGroup]]] traceMatchSuccess :: Double -> Double -> Double -> [[[PhyloGroup]]] -> [[[PhyloGroup]]]
traceMatchSuccess thr qua qua' nextBranches = traceMatchSuccess thr qua qua' nextBranches =
trace ( "\n" <> "-- local branches : " tracePhylo ( "\n" <> "-- local branches : "
<> (Text.pack $ init $ show ((init . init . snd) <> (Text.pack $ init $ show ((init . init . snd)
$ (head' "trace" $ head' "trace" $ head' "trace" nextBranches) ^. phylo_groupBranchId)) $ (head' "trace" $ head' "trace" $ head' "trace" nextBranches) ^. phylo_groupBranchId))
<> ",(1.." <> show (length nextBranches) <> ")]" <> ",(1.." <> show (length nextBranches) <> ")]"
...@@ -767,7 +776,7 @@ traceMatchSuccess thr qua qua' nextBranches = ...@@ -767,7 +776,7 @@ traceMatchSuccess thr qua qua' nextBranches =
traceMatchFailure :: Double -> Double -> Double -> [[PhyloGroup]] -> [[PhyloGroup]] traceMatchFailure :: Double -> Double -> Double -> [[PhyloGroup]] -> [[PhyloGroup]]
traceMatchFailure thr qua qua' branches = traceMatchFailure thr qua qua' branches =
trace ( "\n" <> "-- local branches : " tracePhylo ( "\n" <> "-- local branches : "
<> (Text.pack $ init $ show ((init . snd) $ (head' "trace" $ head' "trace" branches) ^. phylo_groupBranchId)) <> (Text.pack $ init $ show ((init . snd) $ (head' "trace" $ head' "trace" branches) ^. phylo_groupBranchId))
<> ",(1.." <> show (length branches) <> ")]" <> ",(1.." <> show (length branches) <> ")]"
<> " | " <> show (length $ concat branches) <> " groups" <> "\n" <> " | " <> show (length $ concat branches) <> " groups" <> "\n"
...@@ -778,7 +787,7 @@ traceMatchFailure thr qua qua' branches = ...@@ -778,7 +787,7 @@ traceMatchFailure thr qua qua' branches =
traceMatchNoSplit :: [[PhyloGroup]] -> [[PhyloGroup]] traceMatchNoSplit :: [[PhyloGroup]] -> [[PhyloGroup]]
traceMatchNoSplit branches = traceMatchNoSplit branches =
trace ( "\n" <> "-- local branches : " tracePhylo ( "\n" <> "-- local branches : "
<> (Text.pack $ init $ show ((init . snd) $ (head' "trace" $ head' "trace" branches) ^. phylo_groupBranchId)) <> (Text.pack $ init $ show ((init . snd) $ (head' "trace" $ head' "trace" branches) ^. phylo_groupBranchId))
<> ",(1.." <> show (length branches) <> ")]" <> ",(1.." <> show (length branches) <> ")]"
<> " | " <> show (length $ concat branches) <> " groups" <> "\n" <> " | " <> show (length $ concat branches) <> " groups" <> "\n"
...@@ -788,7 +797,7 @@ traceMatchNoSplit branches = ...@@ -788,7 +797,7 @@ traceMatchNoSplit branches =
traceMatchLimit :: [[PhyloGroup]] -> [[PhyloGroup]] traceMatchLimit :: [[PhyloGroup]] -> [[PhyloGroup]]
traceMatchLimit branches = traceMatchLimit branches =
trace ( "\n" <> "-- local branches : " tracePhylo ( "\n" <> "-- local branches : "
<> (Text.pack $ init $ show ((init . snd) $ (head' "trace" $ head' "trace" branches) ^. phylo_groupBranchId)) <> (Text.pack $ init $ show ((init . snd) $ (head' "trace" $ head' "trace" branches) ^. phylo_groupBranchId))
<> ",(1.." <> show (length branches) <> ")]" <> ",(1.." <> show (length branches) <> ")]"
<> " | " <> show (length $ concat branches) <> " groups" <> "\n" <> " | " <> show (length $ concat branches) <> " groups" <> "\n"
...@@ -798,15 +807,15 @@ traceMatchLimit branches = ...@@ -798,15 +807,15 @@ traceMatchLimit branches =
traceMatchEnd :: [PhyloGroup] -> [PhyloGroup] traceMatchEnd :: [PhyloGroup] -> [PhyloGroup]
traceMatchEnd groups = traceMatchEnd groups =
trace ("\n" <> "-- | End temporal matching with " <> show (length $ nub $ map (\g -> g ^. phylo_groupBranchId) groups) tracePhylo ("\n" <> "-- | End temporal matching with " <> show (length $ nub $ map (\g -> g ^. phylo_groupBranchId) groups)
<> " branches and " <> show (length groups) <> " groups" <> "\n" :: Text) groups <> " branches and " <> show (length groups) <> " groups" <> "\n" :: Text) groups
traceTemporalMatching :: [PhyloGroup] -> [PhyloGroup] traceTemporalMatching :: [PhyloGroup] -> [PhyloGroup]
traceTemporalMatching groups = traceTemporalMatching groups =
trace ( "\n" <> "-- | Start temporal matching for " <> show(length groups) <> " groups" <> "\n" :: Text ) groups tracePhylo ( "\n" <> "-- | Start temporal matching for " <> show(length groups) <> " groups" <> "\n" :: Text ) groups
traceGroupsProxi :: [Double] -> [Double] traceGroupsProxi :: [Double] -> [Double]
traceGroupsProxi l = traceGroupsProxi l =
trace ( "\n" <> "-- | " <> show(List.length l) <> " computed pairs of groups Similarity" <> "\n" :: Text ) l tracePhylo ( "\n" <> "-- | " <> show(List.length l) <> " computed pairs of groups Similarity" <> "\n" :: Text ) l
src/Gargantext/Core/Viz/Phylo/TemporalMatching.hs
View file @ 0405e007
...@@ -662,7 +662,7 @@ seaLevelRise fdt similarity lambda minBranch frequency ladder rise frame periods ...@@ -662,7 +662,7 @@ seaLevelRise fdt similarity lambda minBranch frequency ladder rise frame periods
else else
-- start breaking up all the possible branches for the current similarity threshold -- start breaking up all the possible branches for the current similarity threshold
let thr = List.head ladder let thr = List.head ladder
branches' = trace ( "threshold = " <> (T.pack $ printf "%.3f" thr) branches' = tracePhylo ( "threshold = " <> (T.pack $ printf "%.3f" thr)
<> " F(λ) = " <> (T.pack $ printf "%.5f" (toPhyloQuality fdt lambda frequency (map fst branches))) <> " F(λ) = " <> (T.pack $ printf "%.5f" (toPhyloQuality fdt lambda frequency (map fst branches)))
<> " ξ = " <> (T.pack $ printf "%.5f" (globalAccuracy frequency (map fst branches))) <> " ξ = " <> (T.pack $ printf "%.5f" (globalAccuracy frequency (map fst branches)))
<> " ρ = " <> (T.pack $ printf "%.5f" (globalRecall frequency (map fst branches))) <> " ρ = " <> (T.pack $ printf "%.5f" (globalRecall frequency (map fst branches)))
......
stack.yaml
View file @ 0405e007
...@@ -324,6 +324,7 @@ flags: ...@@ -324,6 +324,7 @@ flags:
"build-search-demo": false "build-search-demo": false
gargantext: gargantext:
"disable-db-obfuscation-executable": false "disable-db-obfuscation-executable": false
"no-phylo-debug-logs": false
"test-crypto": false "test-crypto": false
"generic-deriving": "generic-deriving":
"base-4-9": true "base-4-9": true
......
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