Fix docs data-preview: column order and label linkification

src/main/scala/org/monarchinitiative/dosdp/cli/Docs.scala

@@ -58,7 +58,8 @@ object Docs {
         axioms <- Generate.renderPattern(dosdp, prefixes, fillers, Some(ontology), true, true, None, false, OboInOwlSource, false, Map(RDFSLabel.getIRI -> variableReadableIdentifiers))
         patternIRI = IRI.create(iri)
         docAxioms = findDocAxioms(patternIRI, axioms, target, config.dataLocationPrefix)
-        data = columns.to(List) :: rows.take(5).map(formatDataRow(_, columns.to(List), prefixes)) ::: Nil
+        entityColumns = dosdp.vars.getOrElse(Map.empty).keySet ++ dosdp.list_vars.getOrElse(Map.empty).keySet + DOSDP.DefinedClassVariable
+        data = columns.to(List) :: rows.take(5).map(formatDataRow(_, columns.to(List), entityColumns, prefixes)) ::: Nil
         markdown <- DocsMarkdown.markdown(compiled, docAxioms, renderer, data)
         _ <- ZIO.attemptBlockingIO(new PrintWriter(target.outputFile, "utf-8")).acquireReleaseWithAuto { writer =>
           ZIO.attemptBlockingIO(writer.print(markdown))
@@ -97,8 +98,16 @@ object Docs {
   }
 
   //TODO better handling for list values?
-  private def formatDataRow(row: Map[String, String], columns: List[String], prefixes: PartialFunction[String, String]): List[String] =
-    columns.map(c => row.getOrElse(c, "")).map(v => Prefixes.idToIRI(v, prefixes).map(iri => s"[$v]($iri)").getOrElse(v))
+  // Only entity-valued columns (pattern vars/list_vars and defined_class) are
+  // linkified. Free-text columns (labels, data_vars) can legitimately contain a
+  // colon, which would otherwise be misparsed as a CURIE and turned into a bogus
+  // OBO link.
+  private[cli] def formatDataRow(row: Map[String, String], columns: List[String], entityColumns: Set[String], prefixes: PartialFunction[String, String]): List[String] =
+    columns.map { c =>
+      val v = row.getOrElse(c, "")
+      if (entityColumns(c)) Prefixes.idToIRI(v, prefixes).map(iri => s"[$v]($iri)").getOrElse(v)
+      else v
+    }
 
   private final case class DocsTarget(templateFile: String, inputFile: String, outputFile: String) {
 

src/main/scala/org/monarchinitiative/dosdp/cli/Generate.scala

@@ -113,16 +113,11 @@ object Generate {
       cleaned <- ZIO.attemptBlockingIO(Source.fromFile(file, StandardCharsets.UTF_8.name())).acquireReleaseWithAuto { source =>
         ZIO.attemptBlockingIO(source.getLines().filterNot(_.trim.isEmpty).mkString("\n"))
       }.flatMapError(e => logError("Unable to read input table", e))
-      columns <- ZIO.succeed(CSVReader.open(new StringReader(cleaned))(sepFormat)).acquireReleaseWithAuto { reader =>
-        ZIO.succeed {
-          val iteratorToCheckColumns = reader.iteratorWithHeaders
-          if (iteratorToCheckColumns.hasNext) iteratorToCheckColumns.next().keys.to(Seq) else Seq.empty[String]
-        }
-      }
-      data <- ZIO.succeed(CSVReader.open(new StringReader(cleaned))(sepFormat)).acquireReleaseWithAuto { reader =>
-        ZIO.succeed(reader.iteratorWithHeaders.toList)
+      columnsAndData <- ZIO.succeed(CSVReader.open(new StringReader(cleaned))(sepFormat)).acquireReleaseWithAuto { reader =>
+        ZIO.succeed(reader.allWithOrderedHeaders())
       }
-    } yield columns -> data
+      (columns, data) = columnsAndData
+    } yield columns.to(Seq) -> data
 
   def axiomsOutputChoice(kind: AxiomKind): (Boolean, Boolean) = kind match {
     case AllAxioms        => (true, true)

src/test/scala/org/monarchinitiative/dosdp/cli/FormatDataRowTest.scala

@@ -0,0 +1,44 @@
+package org.monarchinitiative.dosdp.cli
+
+import org.monarchinitiative.dosdp.{DOSDP, OBOPrefixes}
+import zio.test.Assertion._
+import zio.test._
+
+object FormatDataRowTest extends ZIOSpecDefault {
+
+  private val columns = List("input1", "input1_label", "defined_class", "defined_class_label")
+  private val entityColumns = Set("input1", DOSDP.DefinedClassVariable)
+
+  def spec = suite("Docs.formatDataRow")(
+    test("entity columns are linkified") {
+      val row = Map("input1" -> "CHEBI:15378", DOSDP.DefinedClassVariable -> "GO:0015649")
+      val out = Docs.formatDataRow(row, columns, entityColumns, OBOPrefixes)
+      assert(out)(equalTo(List(
+        "[CHEBI:15378](http://purl.obolibrary.org/obo/CHEBI_15378)",
+        "",
+        "[GO:0015649](http://purl.obolibrary.org/obo/GO_0015649)",
+        ""
+      )))
+    },
+    test("label columns containing a colon are not misparsed as CURIEs") {
+      val row = Map(
+        "input1" -> "CHEBI:15378",
+        "input1_label" -> "hydron",
+        DOSDP.DefinedClassVariable -> "GO:0015649",
+        "defined_class_label" -> "2-keto-3-deoxygluconate:proton symporter activity"
+      )
+      val out = Docs.formatDataRow(row, columns, entityColumns, OBOPrefixes)
+      assert(out)(equalTo(List(
+        "[CHEBI:15378](http://purl.obolibrary.org/obo/CHEBI_15378)",
+        "hydron",
+        "[GO:0015649](http://purl.obolibrary.org/obo/GO_0015649)",
+        "2-keto-3-deoxygluconate:proton symporter activity"
+      )))
+    },
+    test("missing cells render as empty strings") {
+      val out = Docs.formatDataRow(Map.empty, columns, entityColumns, OBOPrefixes)
+      assert(out)(equalTo(List("", "", "", "")))
+    }
+  )
+
+}

src/test/scala/org/monarchinitiative/dosdp/cli/ReadFillersTest.scala

@@ -0,0 +1,37 @@
+package org.monarchinitiative.dosdp.cli
+
+import com.github.tototoshi.csv.TSVFormat
+import zio.test.Assertion._
+import zio.test._
+import zio.{Console => _, _}
+
+import java.io.{File, PrintWriter}
+import java.nio.file.Files
+
+object ReadFillersTest extends ZIOSpecDefault {
+
+  private val header = List("input2", "input1", "input1_label", "input2_label", "defined_class", "defined_class_label")
+
+  private def writeTsv(rows: List[List[String]]): Task[File] =
+    ZIO.attempt {
+      val f = Files.createTempFile("fillers-", ".tsv").toFile
+      f.deleteOnExit()
+      val w = new PrintWriter(f, "utf-8")
+      try rows.foreach(r => w.println(r.mkString("\t")))
+      finally w.close()
+      f
+    }
+
+  def spec = suite("Generate.readFillers")(
+    test("columns are returned in file order") {
+      val dataRow = List("CHEBI:1", "CHEBI:2", "alpha", "beta", "GO:1", "alpha:beta activity")
+      for {
+        file <- writeTsv(List(header, dataRow))
+        result <- Generate.readFillers(file, new TSVFormat {})
+        (columns, rows) = result
+      } yield assert(columns.toList)(equalTo(header)) &&
+        assert(rows)(equalTo(List(header.zip(dataRow).toMap)))
+    }
+  )
+
+}