From 4e5a182b9b0cf41175760117b3080769255bb859 Mon Sep 17 00:00:00 2001
From: Eduardo Pareja-Tobes <eparejatobes@ohnosequences.com>
Date: Tue, 8 Nov 2016 13:00:22 +0100
Subject: [PATCH] add tests for accessing the whole GO data

---
 src/main/scala/go.scala            |  2 +-
 src/main/scala/oboxml/parser.scala |  4 +-
 src/test/scala/Datago.scala        | 16 ------
 src/test/scala/oboxml.scala        | 86 ++++++++++++++++++++++++++++++
 4 files changed, 89 insertions(+), 19 deletions(-)
 delete mode 100644 src/test/scala/Datago.scala
 create mode 100644 src/test/scala/oboxml.scala

diff --git a/src/main/scala/go.scala b/src/main/scala/go.scala
index 9db4754..b0f9190 100644
--- a/src/main/scala/go.scala
+++ b/src/main/scala/go.scala
@@ -18,7 +18,7 @@ trait AnyTerm extends Any {
   def name: String
   def definition: String
   def namespace: String // TODO finite known set of namespaces
-  def comments: String
+  def comments: Seq[String]
 }
 
 sealed trait AnyRel {
diff --git a/src/main/scala/oboxml/parser.scala b/src/main/scala/oboxml/parser.scala
index 4153e4f..cbf4c8f 100644
--- a/src/main/scala/oboxml/parser.scala
+++ b/src/main/scala/oboxml/parser.scala
@@ -33,8 +33,8 @@ case class XmlTerm(val xml: Node) extends AnyVal with AnyTerm {
   def name: String =
     (xml \ "name").head.text
 
-  def comments: String =
-    (xml \ "comment").head.text
+  def comments: Seq[String] =
+    (xml \ "comment") map { _.text }
 
   def namespace: String =
     (xml \ "namespace").head.text
diff --git a/src/test/scala/Datago.scala b/src/test/scala/Datago.scala
deleted file mode 100644
index a1dd53f..0000000
--- a/src/test/scala/Datago.scala
+++ /dev/null
@@ -1,16 +0,0 @@
-package bio4j.datago.test
-
-import org.scalatest.FunSuite
-
-import bio4j.datago._
-
-class DatagoTest extends FunSuite {
-
-  test("Dummy test coming from the template") {
-
-    assert(
-
-      12 === 12
-    )
-  }
-}
diff --git a/src/test/scala/oboxml.scala b/src/test/scala/oboxml.scala
new file mode 100644
index 0000000..996ce7a
--- /dev/null
+++ b/src/test/scala/oboxml.scala
@@ -0,0 +1,86 @@
+package com.bio4j.data.go.test
+
+import org.scalatest.FunSuite
+import com.bio4j.data.go._
+import scala.xml._
+
+class OBOXML extends FunSuite {
+
+  private lazy val MyXML = new factory.XMLLoader[Elem] {
+
+    private lazy val parserFactory = {
+      val f0 = javax.xml.parsers.SAXParserFactory.newInstance()
+      f0.setNamespaceAware(false)
+      f0.setValidating(false)
+      f0.setXIncludeAware(false)
+      f0
+    }
+
+    private lazy val parser0 = parserFactory.newSAXParser()
+
+    override def parser: SAXParser = parser0
+  }
+
+
+  test("parse whole GO oboxml file, access all data") {
+
+    val go = oboxml.GOOBOXML(MyXML.loadFile("go_daily-termdb.obo-xml"))
+
+    val terms = go.terms
+    println { s"number of terms: ${terms.size}" }
+
+    terms foreach { term =>
+
+      val id          = term.ID
+      val name        = term.name
+      val definition  = term.definition
+      val namespace   = term.namespace
+      val comments    = term.comments
+    }
+
+    val isA = go.isA
+    println { s"number of isA: ${isA.size}" }
+
+    isA foreach { rel =>
+
+      val source = rel.sourceID
+      val target = rel.targetID
+    }
+
+    val partOf = go.partOf
+    println { s"number of partOf: ${partOf.size}" }
+
+    partOf foreach { rel =>
+
+      val source = rel.sourceID
+      val target = rel.targetID
+    }
+
+    val regulates = go.regulates
+    println { s"number of regulates: ${regulates.size}" }
+
+    regulates foreach { rel =>
+
+      val source = rel.sourceID
+      val target = rel.targetID
+    }
+
+    val positivelyRegulates = go.positivelyRegulates
+    println { s"number of positivelyRegulates: ${positivelyRegulates.size}" }
+
+    positivelyRegulates foreach { rel =>
+
+      val source = rel.sourceID
+      val target = rel.targetID
+    }
+
+    val negativelyRegulates = go.negativelyRegulates
+    println { s"number of negativelyRegulates: ${negativelyRegulates.size}" }
+
+    negativelyRegulates foreach { rel =>
+
+      val source = rel.sourceID
+      val target = rel.targetID
+    }
+  }
+}