Tweaks so it runs

src/main/kotlin/me/msoucy/gbat/Analyze.kt

@@ -17,7 +17,8 @@ fun analyze(
     verbose : Boolean = false
 ) : CondensedAnalysis {
     val lineModel = LineModel()
-    val db = Database.connect("jdbc:sqlite:memory:", "org.sqlite.JDBC")
+    val db = Database.connect("jdbc:sqlite::memory:", "org.sqlite.JDBC")
+    return transaction(db) {
         val knowledgeModel = KnowledgeModel(db, createdConstant, riskModel)
         var changesProcessed = 0
 
@@ -32,19 +33,20 @@ fun analyze(
             }
         }
 
-    return condenseAnalysis(
+        condenseAnalysis(
-        historyItem.repoRoot.path,
+            historyItem.repoRoot,
-        historyItem.projectRoot.path,
+            historyItem.projectRoot,
-        historyItem.fname.path,
+            historyItem.fname,
             lineModel,
             knowledgeModel,
             riskModel)
     }
+}
 
 private fun condenseAnalysis(
-    repoRoot : String,
+    repoRoot : File,
-    projectRoot : String,
+    projectRoot : File,
-    fname : String,
+    fname : File,
     lineModel : LineModel,
     knowledgeModel : KnowledgeModel,
     riskModel : RiskModel

src/main/kotlin/me/msoucy/gbat/Main.kt

@@ -136,7 +136,7 @@ fun main(args: Array<String>) = mainBody {
         val riskModel = RiskModel(riskThresh, default_bus_risk, risk_file, departed)
 
         val dbFname = File(outDir, "summary.db")
-        val summaryDb = Database.connect(dbFname.absolutePath, "org.sqlite.JDBC")
+        val summaryDb = Database.connect("jdbc:sqlite:${dbFname.absolutePath}", driver="org.sqlite.JDBC")
         transaction(summaryDb) {
             exec("PRAGMA journal_mode = OFF")
             exec("PRAGMA synchronous = OFF")

src/main/kotlin/me/msoucy/gbat/Repo.kt

@@ -27,12 +27,13 @@ class GitRepo(val projectRoot : File, val git_exe : String) {
             "--show-toplevel"
         )
         val (out, _) = cmd.runCommand(projectRoot)
-        return File(out)
+        return File((out ?: "").trim())
     }
 
     fun log(fname : File) : List<Pair<String, Diff>> {
         val cmd = listOf(
             git_exe,
+            "--no-pager",
             "log",
             "-z", // Null byte separate log entries
             "-w", // Ignore all whitespace
@@ -58,7 +59,7 @@ class GitRepo(val projectRoot : File, val git_exe : String) {
     }
 
     private fun parseAuthor(header : List<String>) : String {
-        val segs = header.getOrNull(1)?.trim()?.split("\\s+")?: listOf()
+        val segs = header.getOrNull(1)?.trim()?.split("\\s+".toRegex())?: listOf()
         return segs.subList(1, segs.size - 2).joinToString(" ")
     }
 

src/main/kotlin/me/msoucy/gbat/Util.kt

@@ -15,7 +15,7 @@ fun List<String>.runCommand(workingDir: File): Pair<String?,String?> {
                 .redirectError(ProcessBuilder.Redirect.PIPE)
                 .start()
 
-        proc.waitFor(60, TimeUnit.MINUTES)
+        proc.waitFor(5, TimeUnit.SECONDS)
         return Pair(proc.inputStream.bufferedReader().readText(),
                     proc.errorStream.bufferedReader().readText())
     } catch(e: IOException) {

src/main/kotlin/me/msoucy/gbat/models/KnowledgeModel.kt

@@ -80,8 +80,8 @@ class KnowledgeModel(val db : Database, val constant : Double, val riskModel : R
         LineKnowledge.select {
             LineKnowledge.linenum eq lineNum
         }.map {
-            Pair(getKnowledgeAcct(it[LineKnowledge.knowledgeacctid]).authors,
+            val acct = getKnowledgeAcct(it[LineKnowledge.knowledgeacctid])
-                 it[LineKnowledge.knowledge])
+            Pair(acct.authors, it[LineKnowledge.knowledge])
         }.sortedBy {
             it.first.joinToString("\n")
         }.copyOf()
@@ -95,7 +95,7 @@ class KnowledgeModel(val db : Database, val constant : Double, val riskModel : R
         }
     }
 
-    private fun getKnowledgeAcct(knowledgeAcctId : Int) = transaction(db) {
+    private fun getKnowledgeAcct(knowledgeAcctId : Int) : KnowledgeAcct = transaction(db) {
         KnowledgeAcctsTable.select {
             KnowledgeAcctsTable.id eq knowledgeAcctId
         }.map {
@@ -104,7 +104,7 @@ class KnowledgeModel(val db : Database, val constant : Double, val riskModel : R
                 it[KnowledgeAcctsTable.authors].split("\n"),
                 it[KnowledgeAcctsTable.authors]
             )
-        }.first()
+        }.firstOrNull() ?: KnowledgeAcct(-1, listOf(), "")
     }
 
     private fun destroyLineKnowledge(knowledgeId : Int, lineNum : Int) = transaction(db) {
@@ -194,9 +194,9 @@ class KnowledgeModel(val db : Database, val constant : Double, val riskModel : R
         val authorStr = authors.sorted().joinToString("\n")
         var newId = KnowledgeAcctsTable.select {
             KnowledgeAcctsTable.authors eq authorStr
-        }.first().let {
+        }.map {
             it[KnowledgeAcctsTable.id]
-        }
+        }.firstOrNull() ?: -1
         if (newId != -1) {
             KnowledgeAcctsTable.insert { 
                 it[KnowledgeAcctsTable.authors] = authorStr
@@ -231,12 +231,14 @@ class KnowledgeModel(val db : Database, val constant : Double, val riskModel : R
     private fun totalLineKnowledge(linenum : Int) = transaction(db) {
         LineKnowledge.select {
             LineKnowledge.linenum eq linenum
-        }.first().let {
+        }.map {
             it[LineKnowledge.knowledge]
-        }
+        }.firstOrNull() ?: 0.0
     }
 
     private fun createTables() = transaction(db) {
+        println ("-- In create tables")
+        SchemaUtils.dropDatabase()
         SchemaUtils.createMissingTablesAndColumns(AuthorsTable, KnowledgeAcctsTable, KnowledgeAuthorsTable, LineKnowledge)
         AuthorsTable.insertIgnore { 
             it[id] = 1

src/main/kotlin/me/msoucy/gbat/models/Models.kt

@@ -1,5 +1,7 @@
 package me.msoucy.gbat.models
 
+import java.io.File
+
 enum class ChangeType {
     Add, Change, Remove
 }
@@ -34,8 +36,8 @@ data class Condensation(
 }
 
 class CondensedAnalysis(
-    var repoRoot : String = "",
+    var repoRoot : File,
-    var projectRoot : String = "",
+    var projectRoot : File,
-    var fileName : String = "",
+    var fileName : File,
     var lineSummaries : MutableList<Pair<String, List<Condensation>>> = mutableListOf()
 )

src/main/kotlin/me/msoucy/gbat/models/RiskModel.kt

@@ -26,7 +26,7 @@ class RiskModel(val threshold : Double,
     fun isDeparted(author : String) = author.trim() in departed
 
     fun jointBusProb(authors : List<String>) =
-        authors.map { this[it] }.reduce { a, b -> a * b }
+        (authors.map { this[it] } + 1.0).reduce { a, b -> a * b }
 
     fun jointBusProbBelowThreshold(authors : List<String>) =
         jointBusProb(authors) <= threshold

src/main/kotlin/me/msoucy/gbat/models/SummaryModel.kt

@@ -97,8 +97,10 @@ class SummaryModel(val db : Database) {
     private val allJoined = (manyJoined leftJoin AuthorsGroupsTable)
 
     fun summarize(ca : CondensedAnalysis) {
-        val fname = adjustFname(File(ca.repoRoot), File(ca.projectRoot), File(ca.fileName))
+        val fname = adjustFname(ca.repoRoot.absoluteFile,
-        val projectId = findOrCreateProject(ca.projectRoot)
+                                ca.projectRoot.absoluteFile,
+                                ca.fileName.absoluteFile)
+        val projectId = findOrCreateProject(ca.projectRoot.absolutePath)
 
         var parentDirId = 0
         splitAllDirs(fname.parentFile).forEach {
@@ -404,7 +406,11 @@ class SummaryModel(val db : Database) {
     private fun splitAllDirs(dirname : File) = dirname.toPath().iterator().asSequence().toList()
 
     private fun adjustFname(repoRoot : File, projectRoot : File, fname : File) : File {
-        var rootDiff = projectRoot.relativeTo(repoRoot)
+        val rootDiff = if(projectRoot.canonicalPath != repoRoot.canonicalPath) {
+            projectRoot.relativeTo(repoRoot)
+        } else {
+            repoRoot
+        }
         return if(rootDiff.toString().length != 0) {
             fname.relativeTo(rootDiff)
         } else {