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haskell-gargantext
haskell-gargantext
Commit ef13af01 authored by Alexandre Delanoë's avatar Alexandre Delanoë
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Revert "[MERGE]" 

Test failed, not merging.

This reverts commit 2e77bfa5, reversing
changes made to fe201115.
parent 809b68b9
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Showing with 9 additions and 670 deletions
gargantext.cabal
View file @ ef13af01
......@@ -38,9 +38,6 @@ data-files:
test-data/phylo/bpa_phylo_test.json
test-data/phylo/open_science.json
test-data/phylo/issue-290-small.golden.json
test-data/phylo/small_phylo_docslist.csv
test-data/phylo/small_phylo_ngramslist.csv
test-data/phylo/small-phylo.golden.json
test-data/test_config.ini
gargantext-cors-settings.toml
.clippy.dhall
......@@ -839,7 +836,6 @@ test-suite garg-test-tasty
type: exitcode-stdio-1.0
main-is: drivers/tasty/Main.hs
other-modules:
Common
Test.API.Setup
Test.Core.Text
Test.Core.Text.Corpus.Query
......@@ -872,22 +868,7 @@ test-suite garg-test-tasty
Test.Utils.Jobs
Paths_gargantext
hs-source-dirs:
test bin/gargantext-phylo/Phylo
default-extensions:
DataKinds
DeriveGeneric
FlexibleContexts
FlexibleInstances
GADTs
GeneralizedNewtypeDeriving
ImportQualifiedPost
MultiParamTypeClasses
NamedFieldPuns
NoImplicitPrelude
OverloadedStrings
RankNTypes
RecordWildCards
StrictData
test
ghc-options: -Wall -threaded -rtsopts -with-rtsopts=-N
build-depends:
QuickCheck ^>= 2.14.2
......@@ -900,8 +881,6 @@ test-suite garg-test-tasty
, conduit ^>= 1.3.4.2
, containers ^>= 0.6.5.1
, crawlerArxiv
, cryptohash
, directory
, duckling ^>= 0.2.0.0
, extra ^>= 1.7.9
, fast-logger ^>= 3.0.5
......@@ -939,7 +918,6 @@ test-suite garg-test-tasty
, servant-server
, shelly >= 1.9 && < 2
, stm ^>= 2.5.0.1
, split
, tasty ^>= 1.4.2.1
, tasty-hspec
, tasty-hunit
......@@ -951,7 +929,6 @@ test-suite garg-test-tasty
, tmp-postgres >= 1.34.1 && < 1.35
, unordered-containers ^>= 0.2.16.0
, validity ^>= 0.11.0.1
, vector
, wai
, wai-extra
, warp
......
src/Gargantext/Core/Viz/Phylo/PhyloTools.hs
View file @ ef13af01
......@@ -16,19 +16,18 @@ Portability : POSIX
module Gargantext.Core.Viz.Phylo.PhyloTools where
import Control.Lens hiding (Level)
import Data.Discrimination qualified as D
import Data.List qualified as List
import Data.List (union, nub, init, tail, partition, nubBy, (!!))
import Data.List qualified as List
import Data.Map (elems, empty, fromList, findWithDefault, unionWith, keys, member, (!), filterWithKey, fromListWith, restrictKeys)
import Data.Map qualified as Map
import Data.Maybe (fromJust)
import Data.Set (disjoint)
import Data.Set qualified as Set
import Data.String (String)
import Data.Text qualified as Text
import Data.Text (unpack)
import Data.Vector qualified as Vector
import Data.Text qualified as Text
import Data.Vector (Vector, elemIndex)
import Data.Vector qualified as Vector
import Gargantext.Core.Viz.Phylo
import Gargantext.Prelude hiding (empty)
import Prelude (read)
......@@ -694,13 +693,13 @@ groupsToBranches' groups =
in map (\g -> g & phylo_groupBranchId %~ (\(lvl,_) -> (lvl,bId))) groups') graph
relatedComponents :: (D.Grouping a, Ord a) => [[a]] -> [[a]]
relatedComponents :: Ord a => [[a]] -> [[a]]
relatedComponents graph = foldl' (\branches groups ->
if (null branches)
then branches ++ [groups]
else
let branchPart = partition (\branch -> disjoint (Set.fromList branch) (Set.fromList groups)) branches
in (fst branchPart) ++ [D.nub $ concat $ (snd branchPart) ++ [groups]]) [] graph
in (fst branchPart) ++ [nub $ concat $ (snd branchPart) ++ [groups]]) [] graph
toRelatedComponents :: [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)] -> [[PhyloGroup]]
......
test-data/phylo/small-phylo.golden.json deleted 100644 → 0
View file @ 809b68b9
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Publication Day,Publication Month,Publication Year,Authors,Title,Source,Abstract
31,10,2016,"Shuanglong Lin, Miao Wang, Li Liu, Yinghua Liang, Wenquan Cui, Zisheng Zhang, Nan Yun",Enhanced Visible Light Photocatalytic Degradation of Organic Pollutants over Flower-Like Bi₂O₂CO₃ Dotted with Ag@AgBr.,"Materials (Basel, Switzerland)","A facile and feasible oil-in-water self-assembly approach was developed to synthesize flower-like Ag@AgBr/Bi₂O₂CO₃ micro-composites. The photocatalytic activities of the samples were evaluated through methylene blue degradation under visible light irradiation. Compared to Bi₂O₂CO₃, flower-like Ag@AgBr/Bi₂O₂CO₃ micro-composites show enhanced photocatalytic activities. In addition, results indicate that both the physicochemical properties and associated photocatalytic activities of Ag@AgBr/Bi₂O₂CO₃ composites are shown to be dependent on the loading quantity of Ag@AgBr. The highest photocatalytic performance was achieved at 7 wt % Ag@AgBr, degrading 95.18% methylene blue (MB) after 20 min of irradiation, which is over 1.52 and 3.56 times more efficient than that of pure Ag@AgBr and pure Bi₂O₂CO₃, respectively. Bisphenol A (BPA) was also degraded to further demonstrate the degradation ability of Ag@AgBr/Bi₂O₂CO₃. A photocatalytic mechanism for the degradation of organic compounds over Ag@AgBr/Bi₂O₂CO₃ was proposed. Results from this study illustrate an entirely new approach to fabricate semiconductor composites containing Ag@AgX/bismuth (X = a halogen)."
1,1,2017,"Nasim Mohammadnezhad, Amir Abbas Matin, Naser Samadi, Ashkan Shomali, Hassan Valizadeh",Ionic Liquid-Bonded Fused Silica as a New Solid-Phase Microextraction Fiber for the Liquid Chromatographic Determination of Bisphenol A as an Endocrine Disruptor.,Journal of AOAC International,"Linear ionic liquid bonded to fused silica and its application as a solid-phase microextraction fiber for the extraction of bisphenol A (BPA) from water samples were studied. After optimization of microextraction conditions (15 mL sample volume, extraction time of 40 min, extraction temperature of 30 ± 1°C, 300 μL acetonitrile as the desorption solvent, and desorption time of 7 min), the fiber was used to extract BPA from packed mineral water, followed by HPLC-UV on an XDB-C18 column (150 × 4.6 mm id, 3.5 μm particle) with a mobile phase of acetonitrile-water (45 + 55%, v/v) and flow rate of 1 mL . min-1). A low LOD (0.20 μg . L-1) and good linearity (0.9977) in the calibration graph indicated that the proposed method was suitable for the determination of BPA."
1,1,2017,"L Du, W Sun, X M Li, X Y Li, W Liu, D Chen",DNA methylation and copy number variation analyses of human embryonic stem cell-derived neuroprogenitors after low-dose decabromodiphenyl ether and/or bisphenol A exposure.,Human & experimental toxicology,"The polybrominated diphenyl ether flame retardants decabromodiphenyl ether (BDE-209) and bisphenol A (BPA) are environmental contaminants that can cross the placenta and exert toxicity in the developing fetal nervous system. Copy number variants (CNVs) play a role in a number of genetic disorders and may be implicated in BDE-209/BPA teratogenicity. In this study, we found that BDE-209 and/or BPA exposure decreased neural differentiation efficiency of human embryonic stem cells (hESCs), although there was a >90% induction of neuronal progenitor cells (NPCs) from exposed hESCs. However, the mean of CNV numbers in the NPCs with BDE-209 + BPA treatment was significantly higher compared to the other groups, whereas DNA methylation was lower and DNA methyltransferase(DNMT1 and DNMT3A) expression were significantly decreased in all of the BDE-209 and/or BPA treatment groups compared with the control groups. The number of CNVs in chromosomes 3, 4, 11, 22, and X in NPCs with BDE-209 and/or BPA exposure was higher compared to the control group. In addition, CNVs in chromosomes 7, 8, 14, and 16 were stable in hESCs and hESCs-derived NPCs irrespective of BDE-209/BPA exposure, and CNVs in chromosomes 20 q11.21 and 16 p13.11 might be induced by neural differentiation. Thus, BDE-209/BPA exposure emerges as a potential source of CNVs distinct from neural differentiation by itself. BDE-209 and/or BPA exposure may cause genomic instability in cultured stem cells via reduced activity of DNA methyltransferase, suggesting a new mechanism of human embryonic neurodevelopmental toxicity caused by this class of environmental toxins."
1,1,2017,"La-Or Chailurkit, Pechngam Tengpraettanakorn, Suwannee Chanprasertyotin, Boonsong Ongphiphadhanakul",Is bisphenol A exposure associated with the development of glucose intolerance and increased insulin resistance in Thais?,Nutrition and health,"Bisphenol A (BPA), the monomeric component of polycarbonate plastics, reportedly possesses endocrine-disrupting effects. Exposure to low levels of BPA during more vulnerable periods leads to abnormalities related to sexual development in experimental animals. Moreover, recently a few epidemiological studies in Caucasians have demonstrated the association of BPA exposure with type 2 diabetes. Therefore, in the present study we examined the association of BPA exposure and abnormal glucose tolerance in Thais. This is a cross-sectional study of 240 participants aged at least 50 years, randomly selected by computer-generated random numbers within each glucose tolerance status from an oral glucose tolerance study of 661 participants. There were 80 participants in each group of type 2 diabetes, impaired glucose tolerance (IGT) and normal glucose tolerance (NGT). Serum BPA was measured by competitive ELISA. The detection rate of BPA was significantly higher in participants with IGT compared to those with NGT ( p < 0.05), while no difference was found between participants with type 2 diabetes and NGT. When participants with type 2 diabetes were stratified into those with fasting plasma glucose (FPG) under the diabetic threshold (<126 mg/dL) and those over (≥126 mg/dL), it was found that those with FPG under the diabetic threshold had measurable rates of BPA comparable to those with IGT, and rates significantly higher than the NGT group ( p < 0.05), while those with FPG over the diabetic threshold did not have higher rates of measurable BPA compared with the NGT group. In conclusion, BPA exposure is not uncommon in Thais. There is an association between BPA exposure and IGT, but not type 2 diabetes."
3,1,2017,"Lan Ching Sim, Wei Han Tan, Kah Hon Leong, Mohammed J K Bashir, Pichiah Saravanan, Nur Atiqah Surib",Mechanistic Characteristics of Surface Modified Organic Semiconductor g-C₃N₄ Nanotubes Alloyed with Titania.,"Materials (Basel, Switzerland)","The visible-light-driven photocatalytic degradation of Bisphenol A (BPA) was investigated using the binary composite of alkaline treated g-C₃N₄ (HT-g-C₃N₄) deposited over commercial TiO₂ (Evonik Degussa GmbH, Essen, Germany). The existence and contribution of both TiO₂ and g-C₃N₄/HT-g-C₃N₄ in the composite was confirmed through various analytical techniques including powder X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), field emission scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), ultraviolet-visible diffuse reflectance spectra (UV-vis-DRS), and photoluminescence (PL) analysis. The results showed that the titania in the binary composite exhibited both pure rutile and anatase phases. The morphological analysis indicated that the spongy ""morel-like"" structure of g-C₃N₄ turned to nanotube form after alkaline hydrothermal treatment and thereby decreased the specific surface area of HT-g-C₃N₄. The low surface area of HT-g-C₃N₄ dominates its promising optical property and effective charge transfer, resulting in a deprived degradation efficiency of BPA two times lower than pure g-C₃N₄. The binary composite of HT-g-C₃N₄/TiO₂ exhibited excellent degradation efficiency of BPA with 2.16 times higher than the pure HT-g-C₃N₄. The enhanced photocatalytic activity was mainly due to the promising optical band gap structure with heterojunction interface, favorable specific surface area, and good charge separation."
1,5,2017,"Jennifer A Honeycutt, Jenny Q T Nguyen, Amanda C Kentner, Heather C Brenhouse",Effects of Water Bottle Materials and Filtration on Bisphenol A Content in Laboratory Animal Drinking Water.,Journal of the American Association for Laboratory Animal Science : JAALAS,"Bisphenol A (BPA) is widely used in the polycarbonate plastics and epoxy resins that are found in laboratory animal husbandry materials including cages and water bottles. Concerns about BPA exposure in humans has led to investigations that suggest physiologic health risks including disruptions to the endocrine system and CNS. However, the extent of exposure of laboratory animals to BPA in drinking water is unclear. In the first study, we compared the amount of BPA contamination in water stored in plastic bottles used in research settings with that in glass bottles. The amount of BPA that leached into water was measured across several time points ranging from 24 to 96 h by using a BPA ELISA assay. The results showed that considerable amounts of BPA (approximately 0.15 μg/L) leached from polycarbonate bottles within the first 24 h of storage. In the second study, BPA levels were measured directly from water taken from filtered compared with unfiltered taps. We observed significantly higher BPA levels in water from unfiltered taps (approximately 0.40 μg/L) compared with taps with filtration systems (approximately 0.04 μg/L). Taken together, our findings indicate that the use of different types of water bottles and water sources, combined with the use of different laboratory products (food, caging systems) between laboratories, likely contribute to decreased rigor and reproducibility in research. We suggest that researchers consider reporting the types of water bottles used and that animal care facilities educate staff regarding the importance of flushing nonfiltered water taps when filling animal water bottles."
17,5,2017,"Agostino Di Ciaula, Piero Portincasa",Diet and contaminants: driving the rise to obesity epidemics?,Current medicinal chemistry,"The obesity epidemic is spreading worldwide without reversal trend and despite specific policies oriented to dietary habits and lifestyle, which seem to have modest effects. Genetic factors only partly explain the rise, whereas environmental factors seem to play a key role, mainly by gene-environment interactions through epigenetic mechanisms. A number of animal and human studies point to maternal diet, intestinal microbiota and chemicals introduced as contaminants with food, all factors able to increase the risk of obesity. Widely diffused toxics (mainly BPA, phthalates, pesticides) are able to promote obesity in children and adults, mainly by acting on the differentiation pathway linking multipotent stromal stem cell to mature adipocyte, modulating epigenetic factors and influencing a series of mechanisms finally leading to altered dietary habits, increased adipocyte formation and fat storage. Furthermore, the adipose tissue is an important target for several chemicals (mainly POPs) which represent a threat to metabolic health. In conclusion, besides excessive individual energy intake and inadequate lifestyle, other broadly diffused and modifiable factors (mainly ingestion of toxic chemicals with food) seem to have a critical role in the rapid epidemiological growing of obesity, also considering trans-generational transmission of risk and later development of obesity due to exposure during early life. Further studies are needed, to better assess interactions between cumulative effects of toxic food contaminants and modification of diet and lifestyle, and to verify the efficacy of primary prevention strategies acting on all these factors and potentially able to reverse the continuous rising of the obesity epidemic."
19,5,2017,,Prenatal bisphenol a exposure and dysregulation of infant hypothalamic-pituitary-adrenal axis function: findings from the APrON cohort study.,Environmental health : a global access science source,"Animal models show that prenatal bisphenol A (BPA) exposure leads to sexually dimorphic disruption of the neuroendocrine system in offspring, including the hypothalamic-pituitary-adrenal (HPA) neuroendocrine system, but human data are lacking. In humans, prenatal BPA exposure is associated with sex-specific behavioural problems in children, and HPA axis dysregulation may be a biological mechanism. The objective of the current study was to examine sex differences in associations between prenatal maternal urinary BPA concentration and HPA axis function in 3 month old infants."
25,5,2017,"Y M Wong, R Li, C K F Lee, H T Wan, Chris K C Wong","The measurement of bisphenol A and its analogues, perfluorinated compounds in twenty species of freshwater and marine fishes, a time-trend comparison and human health based assessment.",Marine pollution bulletin,"Our previous study in 2011 reported the detection of BPA and PFAAs in 20 species of marine and freshwater fishes. With an emerging evidence to suggest the metabolic-disrupting effects of BPA/PFAAs in animals, the present study was aimed to provide a time-trend analysis to determine the current concentrations of PFAAs and BPA in 20 commercially available Hong Kong species of fishes. Since the manufacture and use of BPA is being prohibited in most nations, the introduction of BPA alternatives has recently been incorporated in the markets. Therefore, the concentrations of BPB, BPF and BPS were determined. In the present study, all freshwater and seawater fish samples showed quantified concentrations [>Limit of Quantification (LOQ<0.5ng/g)] of BPA. BPF was detected in some marine (yellow seafin, bigeye, goldspotted rabbitfish, snubnose pompano, tongue sole, Bleeker's grouper and orange-spotted grouper) and freshwater fishes (mud carp, crucian carp, tilapia, catfish, mandarin fish, grass carp, grey mullet and spotted snakehead). Two of the compounds, BPS and BPB could only be identified in the marine fishes (snubnose pompano, yellow seafin). In PFAA analysis, PFOA, PFDA, PFOS, PFUdA and PFDoA were found in most of the marine and freshwater fishes. PFOS and PFOA were shown to be the two predominant PFAAs in fishes. On the basis of the measured concentrations of bisphenols, BPs (BPA, BPB, BPF, BPS) and PFAAs, the average daily intake for BPs (20.5-31.5ng/kgb.w./day) and PFAAs (1.17-1.83ng/kgb.w./day) were calculated and found to be lower than values of tolerable daily intake (TDI) established in Europe. However, as compared with our previous study in 2011, the present study revealed an approximate 10-fold increase in the concentrations of BPA in the fish samples. Although the hazard ratio of consuming fishes for BPA and PFAA exposure is expected to remain low, possible additive metabolic-disrupting effect of BPA and its analogues as well PFAAs should be taken into consideration for human health risk assessment."
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status label forms
map %
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candidate 17α-ethinylestradiol
map 17β-estradiol
candidate 2-ethylhexyl
candidate 4-tert-octylphenol
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map body weight
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map bpa
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map bpa degradation
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map bpa exposure was
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map bpa increased
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candidate bpa replacements
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map bpa treatment
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candidate bpa-bnct
candidate bpa-exposed rats
map bpaf
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map bpb
map bpf
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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
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map chemical oxygen demand
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candidate chemicals were
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candidate china
candidate chromosomes
map chronic exposure
map chronic thromboembolic pulmonary hypertension
candidate cm
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candidate cod
map coexistence
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map day
map days day
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candidate deleterious effects
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map dermal exposure
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candidate detection limit
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map developmental periods
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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
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map nonylphenol
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candidate organisms
map ovarian reserve
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candidate papillary thyroid carcinoma
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test/Test/Offline/Phylo.hs
View file @ ef13af01
......@@ -5,18 +5,15 @@
module Test.Offline.Phylo (tests) where
import Data.Aeson
import Gargantext.Core.Viz.Phylo
import Gargantext.Core.Viz.Phylo.API.Tools (readPhylo)
import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo, toPhyloWithoutLink)
import Gargantext.Core.Viz.Phylo.API.Tools (readPhylo, writePhylo)
import Gargantext.Core.Viz.Phylo.PhyloMaker (toPhylo)
import Gargantext.Core.Viz.Phylo.PhyloTools
import Prelude
import Test.Tasty
import Test.Tasty.HUnit
import Test.Tasty.QuickCheck
import Common
import Paths_gargantext
phyloConfig :: PhyloConfig
......@@ -45,52 +42,12 @@ phyloConfig = PhyloConfig {
tests :: TestTree
tests = testGroup "Phylo" [
testGroup "toPhyloWithoutLink" [
testCase "returns expected data" testSmallPhyloWithoutLinkExpectedOutput
]
, testGroup "toPhylo" [
testCase "returns expected data" testSmallPhyloExpectedOutput
]
, testGroup "relatedComponents" [
testCase "finds simple connection" testRelComp_Connected
]
testCase "returns expected data" testSmallPhyloExpectedOutput
]
testSmallPhyloWithoutLinkExpectedOutput :: Assertion
testSmallPhyloWithoutLinkExpectedOutput = do
bpaConfig <- getDataFileName "bench-data/phylo/bpa-config.json"
corpusPath' <- getDataFileName "test-data/phylo/small_phylo_docslist.csv"
listPath' <- getDataFileName "test-data/phylo/small_phylo_ngramslist.csv"
(Right config) <- fmap (\pcfg -> pcfg { corpusPath = corpusPath'
, listPath = listPath'
}) <$> (eitherDecodeFileStrict' bpaConfig)
mapList <- fileToList (listParser config) (listPath config)
corpus <- fileToDocsDefault (corpusParser config)
(corpusPath config)
[Year 3 1 5,Month 3 1 5,Week 4 2 5]
mapList
actual <- pure $ toPhyloWithoutLink corpus config
expected <- readPhylo =<< getDataFileName "test-data/phylo/small-phylo.golden.json"
expected @?= actual
testSmallPhyloExpectedOutput :: Assertion
testSmallPhyloExpectedOutput = do
issue290PhyloSmall <- setConfig phyloConfig <$> (readPhylo =<< getDataFileName "bench-data/phylo/issue-290-small.json")
expected <- readPhylo =<< getDataFileName "test-data/phylo/issue-290-small.golden.json"
let actual = toPhylo issue290PhyloSmall
expected @?= actual
testRelComp_Connected :: Assertion
testRelComp_Connected = do
(relatedComponents @Int) [] @?= []
(relatedComponents @Int) [[]] @?= [[]]
(relatedComponents @Int) [[],[1,2]] @?= [[],[1,2]]
(relatedComponents @Int) [[1,2],[]] @?= [[1,2],[]]
(relatedComponents @Int) [[1,2], [2]] @?= [[1,2]]
(relatedComponents @Int) [[1,2], [2],[2]] @?= [[1,2]]
(relatedComponents @Int) [[1,2], [2],[2,1]] @?= [[1,2]]
(relatedComponents @Int) [[1,2], [2,4]] @?= [[1,2,4]]
(relatedComponents @Int) [[1,2], [3,5], [2,4]] @?= [[3,5], [1,2,4]]
(relatedComponents @Int) [[1,2], [3,5], [2,4],[9,5],[5,4]] @?= [[1,2,4,3,5,9]]
(relatedComponents @Int) [[1,2,5], [4,5,9]] @?= [[1,2,5,4,9]]
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