require groups of regional timepoints (for trace merger) to be named; c…

…lose gerlichlab#383

build.sbt

@@ -77,6 +77,7 @@ lazy val root = (project in file("."))
       gerlibs ++
       logging ++
       Seq( // only for tests
+        catsLaws,
         gerlibTesting,
         ironScalacheck,
         scalaCsv,

project/Dependencies.scala

@@ -2,6 +2,11 @@ import sbt._
 
 /** Dependencies for the project */
 object Dependencies {
+    /** Get a typelevel cats dependency specification. */
+    object Cats {
+        def getModuleId(name: String) = "org.typelevel" %% s"cats-$name" % "2.12.0"
+    }
+
     /** gerlichlab dependency declaration helper */
     object Gerlib {
         def getModuleId(name: String) = groupId %% artifact(name) % version
@@ -37,7 +42,7 @@ object Dependencies {
     lazy val scalatestVersion = "3.2.18"
 
     /* core libraries */
-    lazy val catsCore = "org.typelevel" %% "cats-core" % "2.12.0"
+    lazy val catsCore = Cats.getModuleId("core")
     lazy val gerlibs = Seq(
         "graph",
         "io",
@@ -69,6 +74,7 @@ object Dependencies {
     lazy val uPickle = HaoyiJson.getModuleId("upickle")
 
     /* testing-related dependencies */
+    lazy val catsLaws = Cats.getModuleId("laws")
     lazy val gerlibTesting = Gerlib.getModuleId("testing")
     lazy val scalacheck = "org.scalacheck" %% "scalacheck" % "1.18.0"
     lazy val scalactic = "org.scalactic" %% "scalactic" % scalatestVersion

src/main/scala/ImagingRoundsConfiguration.scala

@@ -520,6 +520,7 @@ object ImagingRoundsConfiguration extends LazyLogging:
 
     /** How to redefine trace IDs and filter ROIs on the basis of proximity to one another */
     final case class TraceIdDefinitionRule(
+        name: String,
         mergeGroup: ProximityGroup[EuclideanDistance.Threshold, ImagingTimepoint],
         requirement: RoiPartnersRequirementType, 
     )
@@ -567,16 +568,17 @@ object ImagingRoundsConfiguration extends LazyLogging:
                         .flatMap{ (strictness, maybeThreshold, maybeRequirementType) => 
                             kvPairs.get(groupsKey)
                                 .toRight(s"Missing key for groups: $groupsKey")
-                                .flatMap(_.arrOpt.toRight(s"Can't parse groups (from '$groupsKey') as array-like"))
-                                .flatMap(_.toList.toNel.toRight(s"Groups (from '$groupsKey') is empty"))
+                                .flatMap(_.objOpt.toRight(s"Can't parse groups (from '$groupsKey') as map-like"))
+                                .flatMap(_.toList.toNel.toRight(s"Data for groups (from '$groupsKey') is empty"))
                                 .leftMap(NonEmptyList.one)
-                                .flatMap(_.nonEmptyTraverse(v => parseGroupMembersSimple(v).leftMap(NonEmptyList.one)))
+                                .flatMap(_.nonEmptyTraverse{ (k, v) => parseGroupMembersSimple(v).bimap(NonEmptyList.one, k -> _) })
                                 .flatMap(groups => (maybeThreshold, maybeRequirementType) match {
                                     case (None, None) => NonEmptyList.one("Missing threshold and requirement type for ROI merge").asLeft
                                     case (Some(threshold), None) => NonEmptyList.one("Missing requirement type for ROI merge").asLeft
                                     case (None, Some(reqType)) => NonEmptyList.one("Missing threshold for ROI merge").asLeft
                                     case (Some(threshold), Some(reqType)) => 
-                                        groups.map{ g => TraceIdDefinitionRule(
+                                        groups.map{ (k, g) => TraceIdDefinitionRule(
+                                            k,
                                             ProximityGroup(threshold, g), 
                                             reqType,
                                             )

src/test/resources/TestImagingRoundsConfiguration/DifferentTimepointRegionalMergeForTracing/bad_example__blank_time_in_tracing_merge_groups.json

@@ -6,7 +6,7 @@
         "discardRoisNotInGroupsOfInterest": true,
         "distanceThreshold": 2000,
         "requirementType": "Conjunctive",
-        "groups": [[0, 7], [8, 9]]
+        "groups": {"A": [0, 7], "B": [8, 9]}
     },
     "imagingRounds": [
         {"time": 0, "name": "pre_image", "isBlank": true},

src/test/resources/TestImagingRoundsConfiguration/DifferentTimepointRegionalMergeForTracing/bad_example__locus_time_in_tracing_merge_groups.json

@@ -6,7 +6,7 @@
         "discardRoisNotInGroupsOfInterest": true,
         "distanceThreshold": 2000,
         "requirementType": "Conjunctive",
-        "groups": [[5, 7], [8, 9]]
+        "groups": {"A": [5, 7], "B": [8, 9]}
     },
     "imagingRounds": [
         {"time": 0, "name": "pre_image", "isBlank": true},

src/test/resources/TestImagingRoundsConfiguration/DifferentTimepointRegionalMergeForTracing/bad_example__overlap_locus_times_for_regional_times_to_merge__384.json

@@ -6,7 +6,7 @@
         "discardRoisNotInGroupsOfInterest": true,
         "distanceThreshold": 2000,
         "requirementType": "Conjunctive",
-        "groups": [[6, 7], [8, 9]]
+        "groups": {"A": [6, 7], "B": [8, 9]}
     },
     "imagingRounds": [
         {"time": 0, "name": "pre_image", "isBlank": true},

src/test/resources/TestImagingRoundsConfiguration/DifferentTimepointRegionalMergeForTracing/good_example__legitimate_tracing_merge_groups.json

@@ -6,7 +6,7 @@
         "discardRoisNotInGroupsOfInterest": true,
         "distanceThreshold": 2000,
         "requirementType": "Conjunctive",
-        "groups": [[6, 7], [8, 9]]
+        "groups": {"A": [6, 7], "B": [8, 9]}
     },
     "imagingRounds": [
         {"time": 0, "name": "pre_image", "isBlank": true},

src/test/resources/TestImagingRoundsConfiguration/DifferentTimepointRegionalMergeForTracing/good_example__locus_time_overlap_prohibition_for_trace_merge_is_only_within_group.json

@@ -6,7 +6,7 @@
         "discardRoisNotInGroupsOfInterest": true,
         "distanceThreshold": 2000,
         "requirementType": "Conjunctive",
-        "groups": [[6, 7], [8, 9]]
+        "groups": {"A": [6, 7], "B": [8, 9]}
     },
     "imagingRounds": [
         {"time": 0, "name": "pre_image", "isBlank": true},

src/test/scala/TestImagingRoundsConfigurationExamplesParsability.scala

@@ -215,14 +215,16 @@ class TestImagingRoundsConfigurationExamplesParsability extends AnyFunSuite with
                 val expDistance = 
                     import io.github.iltotore.iron.autoRefine
                     EuclideanDistance.Threshold(NonnegativeReal(2000))
-                NonEmptyList.of(Set(6, 7), Set(8, 9))
-                    .map(_.map(ImagingTimepoint.unsafe).pipe(AtLeast2.unsafe))
-                    .map{ g => 
-                        TraceIdDefinitionRule(
-                            ProximityGroup(expDistance, g), 
-                            RoiPartnersRequirementType.Conjunctive,
-                        ) 
-                    }
+                NonEmptyList.of(
+                    "A" -> MergeBag.unsafe(Set(6, 7)), 
+                    "B" -> MergeBag.unsafe(Set(8, 9)),
+                ).map{ (k, g) => 
+                    TraceIdDefinitionRule(
+                        k,
+                        ProximityGroup(expDistance, g), 
+                        RoiPartnersRequirementType.Conjunctive,
+                    ) 
+                }
             Table(
                 ("configFileName", "expectedMergeRules"), 
                 ("good_example__legitimate_tracing_merge_groups.json", expRules), 
@@ -287,6 +289,9 @@ class TestImagingRoundsConfigurationExamplesParsability extends AnyFunSuite with
                 }
         }
 
+    object MergeBag:
+        def unsafe = (_: Set[Int]).map(ImagingTimepoint.unsafe).pipe(AtLeast2.unsafe)
+
     private def checkParseFailure(configFile: os.Path, expectedMessage: String, check: (String, String) => Boolean = cats.Eq[String].eqv) = 
         ImagingRoundsConfiguration.fromJsonFile(configFile) match {
             case Left(messages) =>