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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:18:00 UTC
[44/52] [abbrv] incubator-taverna-language git commit: Make several
tests much less chatty, yet more exacting.
Make several tests much less chatty, yet more exacting.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/98b8b237
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/98b8b237
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/98b8b237
Branch: refs/heads/master
Commit: 98b8b237966dfb59105fd30a5055ba075e96eca9
Parents: 7e05272
Author: Donal Fellows <do...@manchester.ac.uk>
Authored: Thu Feb 12 14:43:37 2015 +0000
Committer: Donal Fellows <do...@manchester.ac.uk>
Committed: Thu Feb 12 14:43:37 2015 +0000
----------------------------------------------------------------------
.../taverna/databundle/TestFullExample.java | 77 ++++++++------------
.../apache/taverna/robundle/TestExample.java | 21 ++++--
.../taverna/robundle/manifest/TestManifest.java | 17 +++--
.../robundle/manifest/TestManifestJSON.java | 2 +-
.../manifest/combine/TestCombineManifest.java | 22 +-----
5 files changed, 58 insertions(+), 81 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
----------------------------------------------------------------------
diff --git a/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java b/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
index 1fec071..ca6e1e1 100644
--- a/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
+++ b/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestFullExample.java
@@ -24,17 +24,16 @@ package org.apache.taverna.databundle;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
-import java.awt.Desktop;
-import java.io.IOException;
import java.net.URL;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
-import java.util.NavigableMap;
import java.util.UUID;
import org.apache.taverna.databundle.DataBundles;
@@ -110,67 +109,55 @@ public class TestFullExample {
// NOTE: From now dataBundle and its Path's are CLOSED
// and can no longer be accessed
- System.out.println("Saved to " + zip);
- if (Desktop.isDesktopSupported()) {
- // Open ZIP file for browsing
- Desktop.getDesktop().open(zip.toFile());
- }
+ //System.out.println("Saved to " + zip);
// Loading a data bundle back from disk
try (Bundle dataBundle2 = DataBundles.openBundle(zip)) {
assertEquals(zip, dataBundle2.getSource());
- System.out.println("\n== Inputs");
- printPorts(DataBundles.getInputs(dataBundle2));
- System.out.println("\n== Outputs");
- printPorts(DataBundles.getOutputs(dataBundle2));
+ List<String> s = new ArrayList<>(DataBundles.getPorts(
+ DataBundles.getInputs(dataBundle2)).keySet());
+ Collections.sort(s);
+ assertEquals("[email, sequence]", s.toString());
+ assertEquals(
+ "soiland-reyes@cs.manchester.ac.uk",
+ DataBundles.getStringValue(DataBundles.getPort(
+ DataBundles.getInputs(dataBundle2), "email")));
+ s = new ArrayList<>(DataBundles.getPorts(
+ DataBundles.getOutputs(dataBundle2)).keySet());
+ Collections.sort(s);
+ assertEquals(
+ "[Graphical_output, Workflow16_getStatus_output_status, "
+ + "getResult_3_output_output, getResult_output_output]",
+ s.toString());
+ assertEquals("FINISHED", DataBundles.getStringValue(DataBundles
+ .getPort(DataBundles.getOutputs(dataBundle2),
+ "Workflow16_getStatus_output_status")));
- System.out.println("\n== Intermediates");
UUID uuid = UUID.fromString("1f536bcf-ba43-44ec-a983-b30a45f2b739");
Path intermediate = DataBundles.getIntermediate(dataBundle2, uuid);
String intermediateStr = DataBundles.getStringValue(intermediate);
assertTrue(intermediateStr.contains("<status>RUNNING</status>"));
- System.out.println(uuid + ": " + intermediateStr);
Path prov = DataBundles.getWorkflowRunProvenance(dataBundle2);
List<String> provLines = Files.readAllLines(prov, Charset.forName("UTF8"));
- System.out.println("\n== Provenance");
- for (String line : provLines.subList(13, 18)) {
- // Show a tiny abstract
- System.out.println(line);
- }
+ assertEquals(" prov:startedAtTime \"2013-05-31T11:23:10.463+01:00\"^^xsd:dateTime ;",
+ provLines.get(15));
- System.out.println("\n== Workflow bundle");
WorkflowBundle wfb = DataBundles.getWorkflowBundle(dataBundle2);
- System.out.print(wfb.getName());
- System.out.println(" containing processors: ");
+ assertEquals("EBI_InterproScan_NewServices", wfb.getName());
+ s=new ArrayList<>();
for (Workflow w : wfb.getWorkflows()) {
for (Processor p : w.getProcessors()) {
- System.out.print(p.getName() + " ");
- }
- }
- System.out.println();
-
-
-
- }
- }
-
-
- private void printPorts(Path path) throws IOException {
- NavigableMap<String, Path> ports = DataBundles.getPorts(path);
- for (String portName : ports.keySet()) {
- Path port = ports.get(portName);
- if (DataBundles.isValue(port)) {
- System.out.print(portName + ": ");
- long size = Files.size(port);
- if (size < 1024) {
- // TODO: Detect binaries properly
- System.out.println(DataBundles.getStringValue(port));
- } else {
- System.out.println("(" + size + " bytes) " + port);
+ s.add(p.getName());
}
}
+ Collections.sort(s);
+ assertEquals("[Status, getResult, getResult_graphic, getResult_graphic_input, "
+ + "getResult_graphic_output, getResult_input, getResult_output, getResult_xml, "
+ + "getResult_xml_input, getResult_xml_output, getStatus, getStatus_input, "
+ + "getStatus_output, run, run_input, run_input_2, run_output, text, visual_png, "
+ + "xml]", s.toString());
}
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
index f5efb55..51767f5 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
@@ -21,6 +21,8 @@ package org.apache.taverna.robundle;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import java.io.OutputStream;
import java.net.URI;
@@ -51,14 +53,16 @@ public class TestExample {
Bundles.setStringValue(in1, "Hello");
// And retrieving it
- if (Bundles.isValue(in1)) {
- System.out.println(Bundles.getStringValue(in1));
- }
+ assertTrue(Bundles.isValue(in1));
+ assertEquals("Hello", Bundles.getStringValue(in1));
// Or just use the regular Files methods:
+ int lines = 0;
for (String line : Files.readAllLines(in1, Charset.forName("UTF-8"))) {
- System.out.println(line);
+ assertEquals("Hello", line);
+ lines++;
}
+ assertEquals(1, lines);
// Binaries and large files are done through the Files API
try (OutputStream out = Files.newOutputStream(in1,
@@ -68,17 +72,18 @@ public class TestExample {
// Or Java 7 style
Path localFile = Files.createTempFile("", ".txt");
Files.copy(in1, localFile, StandardCopyOption.REPLACE_EXISTING);
- System.out.println("Written to: " + localFile);
+ //System.out.println("Written to: " + localFile);
Files.copy(localFile, bundle.getRoot().resolve("out1"));
// Representing references
URI ref = URI.create("http://example.com/external.txt");
Path out3 = bundle.getRoot().resolve("out3");
- System.out.println(Bundles.setReference(out3, ref));
+ Bundles.setReference(out3, ref);
if (Bundles.isReference(out3)) {
URI resolved = Bundles.getReference(out3);
- System.out.println(resolved);
+ assertNotNull(resolved);
+ //System.out.println(resolved);
}
// Saving a bundle:
@@ -87,7 +92,7 @@ public class TestExample {
// NOTE: From now "bundle" and its Path's are CLOSED
// and can no longer be accessed
- System.out.println("Saved to " + zip);
+ //System.out.println("Saved to " + zip);
// Loading a bundle back from disk
try (Bundle bundle2 = Bundles.openBundle(zip)) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
index fa30487..3ca4030 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java
@@ -26,6 +26,7 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
+import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URI;
@@ -81,7 +82,7 @@ public class TestManifest {
.replace("uuid:", ""));
assertEquals(s.getCreatedOn(), Files.getLastModifiedTime(path));
}
- System.out.println(uris);
+ //System.out.println(uris);
assertFalse(uris.contains("/mimetype"));
assertFalse(uris.contains("/META-INF"));
assertTrue(uris.remove("/hello.txt"));
@@ -118,7 +119,7 @@ public class TestManifest {
.replace("uuid:", ""));
assertEquals(s.getCreatedOn(), Files.getLastModifiedTime(path));
}
- System.out.println(uris);
+ //System.out.println(uris);
assertFalse(uris.contains("/mimetype"));
assertFalse(uris.contains("/META-INF"));
assertTrue(uris.remove("/hello.txt"));
@@ -152,7 +153,7 @@ public class TestManifest {
jsonld);
assertTrue(Files.exists(jsonld));
String manifestStr = new String(Files.readAllBytes(jsonld), "UTF8");
- System.out.println(manifestStr);
+ //System.out.println(manifestStr);
// Rough and ready that somethings are there
// TODO: Read back and check as JSON structure
@@ -167,8 +168,8 @@ public class TestManifest {
try (InputStream jsonIn = Files.newInputStream(jsonld)) {
URI baseURI = jsonld.toUri();
Model model = RDFToManifest.jsonLdAsJenaModel(jsonIn, baseURI);
- model.write(System.out, "TURTLE", baseURI.toString());
- model.write(System.out, "RDF/XML", baseURI.toString());
+ model.write(new ByteArrayOutputStream(), "TURTLE", baseURI.toString());
+ model.write(new ByteArrayOutputStream(), "RDF/XML", baseURI.toString());
String queryStr = "PREFIX ore: <http://www.openarchives.org/ore/terms/>"
+ "PREFIX bundle: <http://purl.org/wf4ever/bundle#>"
@@ -186,8 +187,8 @@ public class TestManifest {
QuerySolution soln = results.nextSolution();
Resource fileRes = soln.getResource("file");
Resource proxy = soln.getResource("proxy");
- System.out.println("File: " + fileRes);
- System.out.println(asURI(fileRes));
+ //System.out.println("File: " + fileRes);
+ //System.out.println(asURI(fileRes));
Path file = Paths.get(asURI(fileRes));
assertTrue(Files.exists(file));
@@ -231,7 +232,7 @@ public class TestManifest {
// assertNotNull(manifest.getAggregation(
// URI.create("http://example.com/comments.txt")).getProxy());
- System.out.println(manifest.getAnnotations());
+ //System.out.println(manifest.getAnnotations());
assertEquals(3, manifest.getAnnotations().size());
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
index ecab340..efab8a9 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java
@@ -145,7 +145,7 @@ public class TestManifestJSON {
Path jsonPath = bundle.getManifest().writeAsJsonLD();
ObjectMapper objectMapper = new ObjectMapper();
String jsonStr = Bundles.getStringValue(jsonPath);
- System.out.println(jsonStr);
+ //System.out.println(jsonStr);
JsonNode json = objectMapper.readTree(jsonStr);
checkManifestJson(json);
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/98b8b237/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
----------------------------------------------------------------------
diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
index ce2af70..5286d67 100644
--- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
+++ b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java
@@ -28,31 +28,15 @@ import java.net.URI;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardCopyOption;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
import org.apache.taverna.robundle.Bundle;
import org.apache.taverna.robundle.Bundles;
import org.apache.taverna.robundle.manifest.Agent;
import org.apache.taverna.robundle.manifest.Manifest;
import org.apache.taverna.robundle.manifest.PathMetadata;
-import org.junit.BeforeClass;
import org.junit.Test;
public class TestCombineManifest {
-
- @BeforeClass
- public static void setLogging() {
- Logger logger = Logger.getLogger("");
- // logger.setLevel(Level.FINER);
- ConsoleHandler console = new ConsoleHandler();
- console.setLevel(Level.FINEST);
- logger.addHandler(console);
- Logger.getLogger("org.apache.taverna.robundle.manifest.combine")
- .setLevel(Level.FINEST);
- }
-
@Test
public void convertAslanidi() throws Exception {
Path file = Files.createTempFile("aslanidi", ".zip");
@@ -94,7 +78,7 @@ public class TestCombineManifest {
"/combine/Boris.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
- System.out.println(file);
+ //System.out.println(file);
try (Bundle bundle = Bundles.openBundle(file)) {
Manifest manifest = bundle.getManifest();
Path manifestXml = bundle.getRoot().resolve("manifest.xml");
@@ -122,7 +106,7 @@ public class TestCombineManifest {
"/combine/DirectoryMadness.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
- System.out.println(file);
+ //System.out.println(file);
try (Bundle bundle = Bundles.openBundle(file)) {
Manifest manifest = bundle.getManifest();
Path manifestXml = bundle.getRoot().resolve("manifest.xml");
@@ -162,7 +146,7 @@ public class TestCombineManifest {
"/combine/DirectoryMadnessZipped.omex")) {
Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
}
- System.out.println(file);
+ //System.out.println(file);
try (Bundle bundle = Bundles.openBundle(file)) {
}