Merge remote-tracking branch 'origin/580-dev-phylo-params' into dev

README.md

@@ -189,6 +189,18 @@ From the Backend root folder (haskell-gargantext):
 
 For frontend development and compilation, see the [Frontend Readme.md](https://gitlab.iscpif.fr/gargantext/purescript-gargantext#dev)
 
+### Running tests
+
+From nix shell:
+
+```
+cabal v2-test --test-show-details=streaming
+```
+
+Or, from "outside":
+```
+nix-shell --run "cabal v2-test --test-show-details=streaming"
+```
 ### Working on libraries
 
 When a devlopment is needed on libraries (for instance, the HAL crawler in https://gitlab.iscpif.fr/gargantext/crawlers):

src/Gargantext/Core/Viz/Phylo.hs

@@ -37,6 +37,8 @@ import Data.Vector (Vector)
 import Gargantext.Core.Utils.Prefix (unPrefix)
 import Gargantext.Core.Utils.Prefix (unPrefixSwagger)
 import Gargantext.Prelude
+import Test.QuickCheck
+import Test.QuickCheck.Instances.Text()
 
 ---------------------
 -- | PhyloConfig | --
@@ -678,3 +680,79 @@ instance NFData Sort
 instance NFData Tagger
 instance NFData PhyloLabel
 
+-- Arbitrary instances
+
+instance Arbitrary PhyloConfig where
+  arbitrary = PhyloConfig <$> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary 
+                          <*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary 
+                          <*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary 
+                          <*> vectorOf 10 arbitrary <*> arbitrary <*> vectorOf 10 arbitrary
+
+instance Arbitrary CorpusParser where
+  arbitrary = oneof [ Wos <$> arbitrary
+                    , Csv <$> arbitrary
+                    , Csv' <$> arbitrary
+                    ]
+
+instance Arbitrary ListParser where
+  arbitrary = elements [V3, V4]
+
+instance Arbitrary PhyloSimilarity where
+  arbitrary = oneof [ WeightedLogJaccard <$> arbitrary <*> arbitrary
+                    , WeightedLogSim <$> arbitrary <*> arbitrary
+                    , Hamming <$> arbitrary <*> arbitrary
+                    ]
+
+instance Arbitrary SeaElevation where
+  arbitrary = oneof [ Constante <$> arbitrary <*> arbitrary
+                    , Adaptative <$> arbitrary
+                    , Evolving <$> arbitrary
+                    ]
+
+instance Arbitrary Synchrony where
+  arbitrary = oneof [ ByProximityThreshold <$> arbitrary <*> arbitrary <*> arbitrary <*> arbitrary
+                    , ByProximityDistribution <$> arbitrary <*> arbitrary
+                    ]
+
+instance Arbitrary SynchronyScope where
+  arbitrary = elements [SingleBranch, SiblingBranches, AllBranches]
+
+instance Arbitrary SynchronyStrategy where
+  arbitrary = elements [MergeRegularGroups, MergeAllGroups]
+
+instance Arbitrary Quality where
+  arbitrary = Quality <$> arbitrary <*> arbitrary
+
+instance Arbitrary TimeUnit where
+  arbitrary = oneof [ Epoch <$> arbitrary <*> arbitrary <*> arbitrary
+                    , Year <$> arbitrary <*> arbitrary <*> arbitrary
+                    , Month <$> arbitrary <*> arbitrary <*> arbitrary
+                    , Week <$> arbitrary <*> arbitrary <*> arbitrary
+                    , Day <$> arbitrary <*> arbitrary <*> arbitrary
+                    ]
+
+instance Arbitrary Cluster where
+  arbitrary = oneof [ Fis <$> arbitrary <*> arbitrary
+                    , MaxClique <$> arbitrary <*> arbitrary <*> arbitrary
+                    ]
+
+instance Arbitrary MaxCliqueFilter where
+  arbitrary = elements [ByThreshold, ByNeighbours]
+
+instance Arbitrary PhyloLabel where
+  arbitrary = oneof [ BranchLabel <$> arbitrary <*> arbitrary
+                    , GroupLabel <$> arbitrary <*> arbitrary
+                    ]
+
+instance Arbitrary Tagger where
+  arbitrary = elements [MostInclusive, MostEmergentInclusive, MostEmergentTfIdf]
+
+instance Arbitrary Sort where
+  arbitrary = oneof [ ByBirthDate <$> arbitrary
+                    , ByHierarchy <$> arbitrary]
+
+instance Arbitrary Order where
+  arbitrary = elements [Asc, Desc]
+
+instance Arbitrary Filter where
+  arbitrary = ByBranchSize <$> arbitrary

src/Gargantext/Core/Viz/Phylo/API.hs

@@ -198,7 +198,7 @@ putPhylo = undefined
 -- instance Arbitrary Phylo             where arbitrary     = elements [phylo]
 instance Arbitrary PhyloGroup        where arbitrary     = elements []
 -- instance Arbitrary PhyloView         where arbitrary     = elements [phyloView]
-instance Arbitrary PhyloConfig       where arbitrary     = elements []
+-- instance Arbitrary PhyloConfig       where arbitrary     = elements []
 instance FromHttpApiData DisplayMode where parseUrlPiece = readTextData
 instance FromHttpApiData ExportMode  where parseUrlPiece = readTextData
 instance FromHttpApiData Filiation   where parseUrlPiece = readTextData

test-data/phylo/open_science.json

@@ -1314,5 +1314,73 @@
         "phyloSeaRiseSteps": "0.1"
     },
     "pd_listId": 185785,
-    "pd_corpusId": 185783
+    "pd_corpusId": 185783,
+    "pd_config": {
+        "clique": {
+            "_mcl_filter": "ByThreshold",
+            "_mcl_size": 5,
+            "_mcl_threshold": 1.0e-4,
+            "tag": "MaxClique"
+        },
+        "corpusParser": {
+            "_csv_limit": 150000,
+            "tag": "Csv"
+        },
+        "corpusPath": "corpus.csv",
+        "defaultMode": false,
+        "exportFilter": [
+            {
+                "_branch_size": 3
+            }
+        ],
+        "exportLabel": [
+            {
+                "_branch_labelSize": 2,
+                "_branch_labelTagger": "MostEmergentTfIdf",
+                "tag": "BranchLabel"
+            },
+            {
+                "_group_labelSize": 2,
+                "_group_labelTagger": "MostEmergentInclusive",
+                "tag": "GroupLabel"
+            }
+        ],
+        "exportSort": {
+            "_sort_order": "Desc",
+            "tag": "ByHierarchy"
+        },
+        "findAncestors": true,
+        "listParser": "V4",
+        "listPath": "list.csv",
+        "outputPath": "data/",
+        "phyloName": "Phylo Name",
+        "phyloQuality": {
+            "_qua_granularity": 0.8,
+            "_qua_minBranch": 3
+        },
+        "phyloScale": 2,
+        "phyloSynchrony": {
+            "_bpt_scope": "AllBranches",
+            "_bpt_sensibility": 0,
+            "_bpt_strategy": "MergeAllGroups",
+            "_bpt_threshold": 0.5,
+            "tag": "ByProximityThreshold"
+        },
+        "seaElevation": {
+            "_cons_gap": 0.1,
+            "_cons_start": 0.1,
+            "tag": "Constante"
+        },
+        "similarity": {
+            "_wlj_minSharedNgrams": 2,
+            "_wlj_sensibility": 0.5,
+            "tag": "WeightedLogJaccard"
+        },
+        "timeUnit": {
+            "_year_matchingFrame": 5,
+            "_year_period": 3,
+            "_year_step": 1,
+            "tag": "Year"
+        }
+    }
 }