From c55c576f5c572b9f2da9e00061fb18029acf1b23 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Thu, 5 Sep 2019 14:43:40 +1200
Subject: [PATCH] SED-ML L1V4: updated the way we keep track of / retrieve the
 type of our X and Y axes (#2053).

---
 models/tests/sedml/noble_1962_V_iK.sedml      | 8 ++++----
 models/tests/sedml/noble_1962_V_time.sedml    | 8 ++++----
 models/tests/sedml/noble_1962_gL_time.sedml   | 8 ++++----
 models/tests/sedml/noble_1962_iK_V.sedml      | 8 ++++----
 models/tests/sedml/noble_1962_iK_time.sedml   | 8 ++++----
 models/tests/sedml/noble_1962_remote.sedml    | 6 +++---
 models/tests/sedml/noble_1962_time_V.sedml    | 8 ++++----
 models/tests/sedml/noble_1962_time_gL.sedml   | 8 ++++----
 models/tests/sedml/noble_1962_time_iK.sedml   | 8 ++++----
 models/tests/sedml/noble_1962_time_time.sedml | 8 ++++----
 10 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/models/tests/sedml/noble_1962_V_iK.sedml b/models/tests/sedml/noble_1962_V_iK.sedml
index b2e481c53b..89723d1b7a 100644
--- a/models/tests/sedml/noble_1962_V_iK.sedml
+++ b/models/tests/sedml/noble_1962_V_iK.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_V_time.sedml b/models/tests/sedml/noble_1962_V_time.sedml
index 78fe14fd18..70cef2d8ac 100644
--- a/models/tests/sedml/noble_1962_V_time.sedml
+++ b/models/tests/sedml/noble_1962_V_time.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_gL_time.sedml b/models/tests/sedml/noble_1962_gL_time.sedml
index a0e375d334..76d338c62c 100644
--- a/models/tests/sedml/noble_1962_gL_time.sedml
+++ b/models/tests/sedml/noble_1962_gL_time.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_iK_V.sedml b/models/tests/sedml/noble_1962_iK_V.sedml
index 86dce09545..169e41dae1 100644
--- a/models/tests/sedml/noble_1962_iK_V.sedml
+++ b/models/tests/sedml/noble_1962_iK_V.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_iK_time.sedml b/models/tests/sedml/noble_1962_iK_time.sedml
index bfad90f218..c28c544cfe 100644
--- a/models/tests/sedml/noble_1962_iK_time.sedml
+++ b/models/tests/sedml/noble_1962_iK_time.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_remote.sedml b/models/tests/sedml/noble_1962_remote.sedml
index 492fb865dd..70d314b39e 100644
--- a/models/tests/sedml/noble_1962_remote.sedml
+++ b/models/tests/sedml/noble_1962_remote.sedml
@@ -150,7 +150,7 @@
         </dataGenerator>
     </listOfDataGenerators>
     <listOfOutputs>
-        <plot2D id="plot1">
+        <plot2D id="plot1" name="Membrane potential">
             <annotation>
                 <properties xmlns="http://www.opencor.ws/">
                     <backgroundColor>#13000080</backgroundColor>
@@ -214,7 +214,7 @@
                 </curve>
             </listOfCurves>
         </plot2D>
-        <plot2D id="plot2">
+        <plot2D id="plot2" name="Currents">
             <annotation>
                 <properties xmlns="http://www.opencor.ws/">
                     <backgroundColor>#12108001</backgroundColor>
@@ -318,7 +318,7 @@
                 </curve>
             </listOfCurves>
         </plot2D>
-        <plot2D id="plot3">
+        <plot2D id="plot3" name="Gating variables">
             <annotation>
                 <properties xmlns="http://www.opencor.ws/">
                     <backgroundColor>#13800002</backgroundColor>
diff --git a/models/tests/sedml/noble_1962_time_V.sedml b/models/tests/sedml/noble_1962_time_V.sedml
index bfebd04a73..48df5cc688 100644
--- a/models/tests/sedml/noble_1962_time_V.sedml
+++ b/models/tests/sedml/noble_1962_time_V.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_time_gL.sedml b/models/tests/sedml/noble_1962_time_gL.sedml
index 2724b7b3d3..d66de9e02d 100644
--- a/models/tests/sedml/noble_1962_time_gL.sedml
+++ b/models/tests/sedml/noble_1962_time_gL.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_time_iK.sedml b/models/tests/sedml/noble_1962_time_iK.sedml
index f130b58713..38cbc06b92 100644
--- a/models/tests/sedml/noble_1962_time_iK.sedml
+++ b/models/tests/sedml/noble_1962_time_iK.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>
diff --git a/models/tests/sedml/noble_1962_time_time.sedml b/models/tests/sedml/noble_1962_time_time.sedml
index ac173e0174..5b9ac1b28b 100644
--- a/models/tests/sedml/noble_1962_time_time.sedml
+++ b/models/tests/sedml/noble_1962_time_time.sedml
@@ -205,7 +205,7 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
+            <xAxis type="log10"/>
             <yAxis type="linear"/>
             <listOfCurves>
                 <curve id="curve2_1" xDataReference="xDataGenerator2_1" yDataReference="yDataGenerator2_1">
@@ -270,7 +270,7 @@
                 </properties>
             </annotation>
             <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve3_1" xDataReference="xDataGenerator3_1" yDataReference="yDataGenerator3_1">
                     <annotation>
@@ -333,8 +333,8 @@
                     </zoomRegion>
                 </properties>
             </annotation>
-            <xAxis type="linear"/>
-            <yAxis type="linear"/>
+            <xAxis type="log10"/>
+            <yAxis type="log10"/>
             <listOfCurves>
                 <curve id="curve4_1" xDataReference="xDataGenerator4_1" yDataReference="yDataGenerator4_1">
                     <annotation>