From 7ef5058c541d6cf7209de2bb1f50c7aab8754ad9 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 23 May 2019 20:39:52 +0200
Subject: [PATCH] removed unused test file for wikipathways
---
.../wikipathway/GPMLToModelTest.java | 124 ++-----
pathvisio/testFiles/small/reactions.gpml | 302 ------------------
2 files changed, 18 insertions(+), 408 deletions(-)
delete mode 100644 pathvisio/testFiles/small/reactions.gpml
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 47d83f9847..41becbd5d1 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -5,20 +5,10 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import java.awt.Desktop;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import org.apache.logging.log4j.*;
-import org.junit.Ignore;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.junit.Test;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.PngImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
@@ -40,10 +30,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void DopamineTest() throws Exception {
try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "Dopamine.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/Dopamine.gpml");
assertEquals(22, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -58,10 +45,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void WP1403_75220Test() throws Exception {
try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP1403_75220.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP1403_75220.gpml");
assertEquals(22, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -76,11 +60,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void WP528_76269Test() throws Exception {
try {
-
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP528_76269.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP528_76269.gpml");
assertEquals(15, getWarnings().size());
Model model2 = serializeModelOverCellDesignerParser(model1);
@@ -95,10 +75,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void WP550_73391Test() throws Exception {
try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP550_73391.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP550_73391.gpml");
assertEquals(16, getWarnings().size());
@@ -114,10 +91,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void WP197_69902Test() throws Exception {
try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP197_69902.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP197_69902.gpml");
assertEquals(3, getWarnings().size());
@@ -133,10 +107,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void WP179_70629Test() throws Exception {
try {
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP179_70629.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP179_70629.gpml");
assertEquals(38, getWarnings().size());
@@ -152,11 +123,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void WP306_71714Test() throws Exception {
try {
-
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP306_71714.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP306_71714.gpml");
assertEquals(41, getWarnings().size());
@@ -172,11 +139,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void WP481_72080Test() throws Exception {
try {
-
- String pathToFile = "testFiles/wikipathways/";
- String fileName = "WP481_72080.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/WP481_72080.gpml");
assertEquals(22, getWarnings().size());
@@ -192,11 +155,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testTwoReactants() throws Exception {
try {
-
- String pathToFile = "testFiles/small/";
- String fileName = "two_reactant.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/small/two_reactant.gpml");
assertEquals(0, getWarnings().size());
@@ -212,10 +171,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testTwoPubmeds() throws Exception {
try {
-
- String pathToFile = "testFiles/small/reaction_with_two_pubmeds.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile);
+ Model model1 = new GPMLToModel().getModel("testFiles/small/reaction_with_two_pubmeds.gpml");
assertEquals(2, model1.getReactions().iterator().next().getMiriamData().size());
assertEquals(0, getWarnings().size());
@@ -232,10 +188,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testComment() throws Exception {
try {
-
- String pathToFile = "testFiles/small/comment.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile);
+ Model model1 = new GPMLToModel().getModel("testFiles/small/comment.gpml");
assertTrue(model1.getNotes().contains("Metabolic Process"));
assertEquals(0, getWarnings().size());
@@ -252,10 +205,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testGstp() throws Exception {
try {
-
- String pathToFile = "testFiles/wikipathways/gstp.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile);
+ Model model1 = new GPMLToModel().getModel("testFiles/wikipathways/gstp.gpml");
assertEquals(3, getWarnings().size());
@@ -271,10 +221,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testMissingAliasesInCompartment() throws Exception {
try {
-
- String pathToFile = "testFiles/small/missing_aliases_in_compartment.gpml";
-
- Model model1 = new GPMLToModel().getModel(pathToFile);
+ Model model1 = new GPMLToModel().getModel("testFiles/small/missing_aliases_in_compartment.gpml");
assertEquals(3, getWarnings().size());
@@ -290,9 +237,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testModelLines() throws Exception {
try {
-
- String fileName = "testFiles/small/model_with_line.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model1 = new GPMLToModel().getModel("testFiles/small/model_with_line.gpml");
assertEquals(0, getWarnings().size());
@@ -306,8 +251,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testModelShapes() throws Exception {
try {
- String fileName = "testFiles/small/shapes.gpml";
- new GPMLToModel().getModel(fileName);
+ new GPMLToModel().getModel("testFiles/small/shapes.gpml");
assertEquals(11, getWarnings().size());
@@ -320,8 +264,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
@Test
public void testHypotheticlaComplex() throws Exception {
try {
- String fileName = "testFiles/complex/hypothetical_complex.gpml";
- Model model = new GPMLToModel().getModel(fileName);
+ Model model = new GPMLToModel().getModel("testFiles/complex/hypothetical_complex.gpml");
for (Complex species : model.getComplexList()) {
assertTrue("Complex parsed from gpml should be hypothetical", species.isHypothetical());
}
@@ -382,37 +325,6 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
}
}
- @Test(timeout = 30000)
- @Ignore
- public void test() throws Exception {
- try {
- String fileName = "D:/WP3408_81714.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().model(model1).width(model1.getWidth())
- .height(model1.getHeight());
- PngImageGenerator pig = new PngImageGenerator(params);
- pig.saveToFile("D:/tes1.png");
-
- Desktop.getDesktop().open(new File("D:/tes1.png"));
-
- params = new AbstractImageGenerator.Params().model(model2).width(model2.getWidth()).height(model2.getHeight());
- pig = new PngImageGenerator(params);
- pig.saveToFile("D:/tes2.png");
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testComplexInCompartment() throws Exception {
try {
diff --git a/pathvisio/testFiles/small/reactions.gpml b/pathvisio/testFiles/small/reactions.gpml
deleted file mode 100644
index 7881323aec..0000000000
--- a/pathvisio/testFiles/small/reactions.gpml
+++ /dev/null
@@ -1,302 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="New Pathway" Version="20141030">
- <Graphics BoardWidth="780.5258105729853" BoardHeight="856.5884269130537" />
- <DataNode TextLabel="Protein" GraphId="fb902" Type="Protein">
- <Graphics CenterX="401.39438860121174" CenterY="162.45304091785962" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="bac50" Type="Protein">
- <Graphics CenterX="703.2862896402343" CenterY="163.1299285883508" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="a38b9" Type="Protein">
- <Graphics CenterX="704.4867499238503" CenterY="196.82099705553867" Width="80.0" Height="20.0" ZOrder="32769" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="f3232" Type="Protein">
- <Graphics CenterX="402.59484888482774" CenterY="196.1441093850475" Width="80.0" Height="20.0" ZOrder="32770" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="a48e0" Type="Protein">
- <Graphics CenterX="703.6565471959931" CenterY="230.51206552272654" Width="80.0" Height="20.0" ZOrder="32771" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="e9915" Type="Protein">
- <Graphics CenterX="401.7646461569703" CenterY="229.83517785223538" Width="80.0" Height="20.0" ZOrder="32772" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="efb65" Type="Protein">
- <Graphics CenterX="704.1801198091179" CenterY="263.5262463194233" Width="80.0" Height="20.0" ZOrder="32773" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="a7a77" Type="Protein">
- <Graphics CenterX="402.2882187700952" CenterY="262.84935864893214" Width="80.0" Height="20.0" ZOrder="32774" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="e867e" Type="Protein">
- <Graphics CenterX="705.3805800927336" CenterY="295.8635394456291" Width="80.0" Height="20.0" ZOrder="32775" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="d0104" Type="Protein">
- <Graphics CenterX="403.4886790537111" CenterY="295.18665177513793" Width="80.0" Height="20.0" ZOrder="32776" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="f9cf9" Type="Protein">
- <Graphics CenterX="705.9041527058586" CenterY="328.2008325718346" Width="80.0" Height="20.0" ZOrder="32777" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="e66b6" Type="Protein">
- <Graphics CenterX="404.01225166683605" CenterY="327.52394490134344" Width="80.0" Height="20.0" ZOrder="32778" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="e1f3e" Type="Protein">
- <Graphics CenterX="703.7201746370191" CenterY="358.5074626865673" Width="80.0" Height="20.0" ZOrder="32779" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="e2924" Type="Protein">
- <Graphics CenterX="401.82827359799654" CenterY="357.8305750160761" Width="80.0" Height="20.0" ZOrder="32780" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="f631e" Type="Protein">
- <Graphics CenterX="705.5975225911261" CenterY="394.2291941652282" Width="80.0" Height="20.0" ZOrder="32781" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="f0f96" Type="Protein">
- <Graphics CenterX="403.7056215521036" CenterY="393.552306494737" Width="80.0" Height="20.0" ZOrder="32782" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="ec825" Type="Protein">
- <Graphics CenterX="704.7673198632689" CenterY="425.8895996209428" Width="80.0" Height="20.0" ZOrder="32783" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="f93d1" Type="Protein">
- <Graphics CenterX="402.87541882424625" CenterY="425.21271195045165" Width="80.0" Height="20.0" ZOrder="32784" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="dbf25" Type="Protein">
- <Graphics CenterX="707.3215554878669" CenterY="522.5312214438013" Width="80.0" Height="20.0" ZOrder="32785" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="bdb72" Type="Protein">
- <Graphics CenterX="405.42965444884436" CenterY="521.8543337733101" Width="80.0" Height="20.0" ZOrder="32786" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="da63a" Type="Protein">
- <Graphics CenterX="705.8144650895185" CenterY="553.5147392290248" Width="80.0" Height="20.0" ZOrder="32787" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="dc089" Type="Protein">
- <Graphics CenterX="403.9225640504959" CenterY="552.8378515585337" Width="80.0" Height="20.0" ZOrder="32788" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="e5f32" Type="Protein">
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- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="b86d8" Type="Protein">
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- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="afc1b" Type="Protein">
- <Graphics CenterX="706.1847226452772" CenterY="614.1279994584897" Width="80.0" Height="20.0" ZOrder="32791" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="e38a8" Type="Protein">
- <Graphics CenterX="404.2928216062546" CenterY="613.4511117879986" Width="80.0" Height="20.0" ZOrder="32792" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="ecd1d" Type="Protein">
- <Graphics CenterX="706.0314075879107" CenterY="646.4652925846955" Width="80.0" Height="20.0" ZOrder="32793" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="c977c" Type="Protein">
- <Graphics CenterX="404.1395065488884" CenterY="645.7884049142043" Width="80.0" Height="20.0" ZOrder="32794" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="dda7f" Type="Protein">
- <Graphics CenterX="709.449318035672" CenterY="687.7302179578297" Width="80.0" Height="20.0" ZOrder="32795" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="e4385" Type="Protein">
- <Graphics CenterX="407.5574169966496" CenterY="687.0533302873386" Width="80.0" Height="20.0" ZOrder="32796" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
- </DataNode>
- <DataNode TextLabel="Protein" GraphId="cab71" Type="Protein">
- <Graphics CenterX="710.3989449013436" CenterY="726.5268597488745" Width="80.0" Height="20.0" ZOrder="32797" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="ea814" Type="Protein">
- <Graphics CenterX="408.5070438623212" CenterY="725.8499720783833" Width="80.0" Height="20.0" ZOrder="32798" FontSize="10" Valign="Middle" />
- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="ac370" Type="Protein">
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- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="bb9cc" Type="Protein">
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- <DataNode TextLabel="Protein" GraphId="cdc0b" Type="Protein">
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- <DataNode TextLabel="Protein" GraphId="b6469" Type="Protein">
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- <Xref Database="" ID="" />
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- <Xref Database="" ID="" />
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- <DataNode TextLabel="Protein" GraphId="aaa0d" Type="Protein">
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- <Xref Database="" ID="" />
- </DataNode>
- <Interaction GraphId="idb291cbac">
- <Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="441.39438860121174" Y="162.45304091785962" GraphRef="fb902" RelX="1.0" RelY="0.0" />
- <Point X="663.2862896402343" Y="163.1299285883508" GraphRef="bac50" RelX="-1.0" RelY="0.0" />
- </Graphics>
- <Xref Database="" ID="" />
- </Interaction>
- <Interaction GraphId="idb909b660">
- <Graphics ZOrder="12288" LineThickness="1.0">
- <Point X="442.59484888482774" Y="196.1441093850475" GraphRef="f3232" RelX="1.0" RelY="0.0" />
- <Point X="664.4867499238503" Y="196.82099705553867" GraphRef="a38b9" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" />
- </Graphics>
- <Xref Database="" ID="" />
- </Interaction>
- <Interaction GraphId="id6570f943">
- <Graphics ZOrder="12288" LineStyle="Broken" LineThickness="1.0">
- <Point X="441.7646461569703" Y="229.83517785223538" GraphRef="e9915" RelX="1.0" RelY="0.0" />
- <Point X="663.6565471959931" Y="230.51206552272654" GraphRef="a48e0" RelX="-1.0" RelY="0.0" />
- </Graphics>
- <Xref Database="" ID="" />
- </Interaction>
- <Interaction GraphId="id506a5e94">
- <Graphics ZOrder="12288" LineStyle="Broken" LineThickness="1.0">
- <Point X="442.2882187700952" Y="262.84935864893214" GraphRef="a7a77" RelX="1.0" RelY="0.0" />
- <Point X="664.1801198091179" Y="263.5262463194233" GraphRef="efb65" RelX="-1.0" RelY="0.0" ArrowHead="Arrow" />
- </Graphics>
- <Xref Database="" ID="" />
- </Interaction>
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