[med-svn] [htsjdk] 01/02: Remove some more tests needing http or ftp connections
Andreas Tille
tille at debian.org
Sun Jul 10 16:55:54 UTC 2016
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in repository htsjdk.
commit 72a19ccd3cb274b8b85276481081bb8d51d106a1
Author: Andreas Tille <tille at debian.org>
Date: Sun Jul 10 18:42:35 2016 +0200
Remove some more tests needing http or ftp connections
---
debian/changelog | 4 +
debian/patches/13-skip_network_tests | 279 +++++++++++++++++++++++++++++++++++
2 files changed, 283 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 34c8d40..21e3c32 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,11 @@
htsjdk (2.5.0+dfsg.2-2) UNRELEASED; urgency=medium
+ [ Vincent Danjean ]
* Tweak build-dependencies
+ [ Andreas Tille ]
+ * Remove some more tests needing http or ftp connections
+
-- Vincent Danjean <vdanjean at debian.org> Thu, 07 Jul 2016 13:54:18 +0200
htsjdk (2.5.0+dfsg.2-1) unstable; urgency=medium
diff --git a/debian/patches/13-skip_network_tests b/debian/patches/13-skip_network_tests
index 2040700..fe62dcd 100644
--- a/debian/patches/13-skip_network_tests
+++ b/debian/patches/13-skip_network_tests
@@ -670,3 +670,282 @@ Last-Updated: 2015-01-06
- }
-
}
+--- a/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
++++ b/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
+@@ -135,27 +135,4 @@ public class TabixReaderTest {
+
+ }
+
+- /**
+- * Test reading a tabix file over http
+- *
+- * @throws java.io.IOException
+- */
+- @Test
+- public void testRemoteQuery() throws IOException {
+- String tabixFile = "http://www.broadinstitute.org/~picard/testdata/igvdata/tabix/trioDup.vcf.gz";
+-
+- TabixReader tabixReader = new TabixReader(tabixFile);
+-
+- TabixIteratorLineReader lineReader = new TabixIteratorLineReader(
+- tabixReader.query(tabixReader.chr2tid("4"), 320, 330));
+-
+- int nRecords = 0;
+- String nextLine;
+- while ((nextLine = lineReader.readLine()) != null) {
+- assertTrue(nextLine.startsWith("4"));
+- nRecords++;
+- }
+- assertTrue(nRecords > 0);
+-
+- }
+ }
+--- a/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
++++ b/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
+@@ -14,18 +14,4 @@ import static org.testng.Assert.assertTr
+ */
+ public class FTPUtilsTest {
+
+- @Test
+- public void testResourceAvailable() throws Exception {
+-
+- URL goodUrl = new URL("ftp://ftp.broadinstitute.org/pub/igv/TEST/test.txt");
+- assertTrue(FTPUtils.resourceAvailable(goodUrl));
+-
+- URL nonExistentURL = new URL("ftp://ftp.broadinstitute.org/pub/igv/TEST/doesntExist");
+- assertFalse(FTPUtils.resourceAvailable(nonExistentURL));
+-
+- URL nonExistentServer = new URL("ftp://noSuchServer/pub/igv/TEST/doesntExist");
+- assertFalse(FTPUtils.resourceAvailable(nonExistentServer));
+-
+-
+- }
+ }
+--- a/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
++++ b/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
+@@ -23,225 +23,4 @@ public class FTPClientTest {
+ static byte[] expectedBytes = "abcdefghijklmnopqrstuvwxyz\n".getBytes();
+ FTPClient client;
+
+- @BeforeMethod
+- public void setUp() throws IOException {
+- client = new FTPClient();
+- FTPReply reply = client.connect(host);
+- Assert.assertTrue(reply.isSuccess(), "connect");
+- }
+-
+- @AfterMethod
+- public void tearDown() {
+- System.out.println("Disconnecting");
+- client.disconnect();
+- }
+-
+- @Test
+- public void testLogin() throws Exception {
+-
+- }
+-
+- @Test
+- public void testPasv() throws Exception {
+- try {
+- FTPReply reply = client.login("anonymous", "igv at broadinstitute.org");
+- Assert.assertTrue(reply.isSuccess(), "login");
+-
+- reply = client.pasv();
+- Assert.assertTrue(reply.isSuccess(), "pasv");
+- } finally {
+- client.closeDataStream();
+- }
+- }
+-
+- @Test
+- public void testSize() throws Exception {
+-
+- FTPReply reply = client.login("anonymous", "igv at broadinstitute.org");
+- Assert.assertTrue(reply.isSuccess());
+-
+- reply = client.binary();
+- Assert.assertTrue(reply.isSuccess(), "binary");
+-
+- reply = client.size(file);
+- String val = reply.getReplyString();
+- int size = Integer.parseInt(val);
+- Assert.assertEquals(fileSize, size, "size");
+- }
+-
+- @Test
+- public void testDownload() throws Exception {
+- try {
+- FTPReply reply = client.login("anonymous", "igv at broadinstitute.org");
+- Assert.assertTrue(reply.isSuccess(), "login");
+-
+- reply = client.binary();
+- Assert.assertTrue(reply.isSuccess(), "binary");
+-
+- reply = client.pasv();
+- Assert.assertTrue(reply.isSuccess(), "pasv");
+-
+- reply = client.retr(file);
+- Assert.assertEquals(reply.getCode(), 150, "retr");
+-
+- InputStream is = client.getDataStream();
+- int idx = 0;
+- int b;
+- while ((b = is.read()) >= 0) {
+- Assert.assertEquals(expectedBytes[idx], (byte) b,"reading from stream");
+- idx++;
+- }
+-
+- } finally {
+- client.closeDataStream();
+- FTPReply reply = client.retr(file);
+- System.out.println(reply.getCode());
+- Assert.assertTrue(reply.isSuccess(), "close");
+- }
+- }
+-
+- @Test
+- public void testRest() throws Exception {
+- try {
+- FTPReply reply = client.login("anonymous", "igv at broadinstitute.org");
+- Assert.assertTrue(reply.isSuccess(), "login");
+-
+- reply = client.binary();
+- Assert.assertTrue(reply.isSuccess(), "binary");
+-
+- reply = client.pasv();
+- Assert.assertTrue(reply.isSuccess(), "pasv");
+-
+- final int restPosition = 5;
+- client.setRestPosition(restPosition);
+-
+- reply = client.retr(file);
+- Assert.assertEquals(reply.getCode(), 150, "retr");
+-
+- InputStream is = client.getDataStream();
+- int idx = restPosition;
+- int b;
+- while ((b = is.read()) >= 0) {
+- Assert.assertEquals(expectedBytes[idx], (byte) b, "reading from stream");
+- idx++;
+- }
+-
+- } finally {
+- client.closeDataStream();
+- FTPReply reply = client.retr(file);
+- System.out.println(reply.getCode());
+- Assert.assertTrue(reply.isSuccess(), "close");
+- }
+- }
+-
+- /**
+- * Test accessing a non-existent file
+- */
+- @Test
+- public void testNonExistentFile() throws Exception {
+-
+- String host = "ftp.broadinstitute.org";
+- String file = "/pub/igv/TEST/fileDoesntExist.txt";
+- FTPClient client = new FTPClient();
+-
+- FTPReply reply = client.connect(host);
+- Assert.assertTrue(reply.isSuccess(), "connect");
+-
+- reply = client.login("anonymous", "igv at broadinstitute.org");
+- Assert.assertTrue(reply.isSuccess(), "login");
+-
+- reply = client.binary();
+- Assert.assertTrue(reply.isSuccess(), "binary");
+-
+- reply = client.executeCommand("size " + file);
+- Assert.assertEquals(550, reply.getCode(), "size");
+-
+- client.disconnect();
+- }
+-
+- /**
+- * Test accessing a non-existent server
+- */
+- @Test
+- public void testNonExistentServer() throws Exception {
+-
+- String host = "ftp.noSuchServer.org";
+- String file = "/pub/igv/TEST/fileDoesntExist.txt";
+- FTPClient client = new FTPClient();
+-
+- FTPReply reply = null;
+- try {
+- reply = client.connect(host);
+- } catch (UnknownHostException e) {
+- // This is expected
+- }
+-
+- client.disconnect();
+- }
+-
+- @Test
+- public void testMultiplePasv() throws Exception {
+-
+- try {
+- FTPReply reply = client.login("anonymous", "igv at broadinstitute.org");
+- Assert.assertTrue(reply.isSuccess(), "login");
+-
+- reply = client.pasv();
+- Assert.assertTrue(reply.isSuccess(), "pasv 1");
+- client.closeDataStream();
+-
+- reply = client.pasv();
+- Assert.assertTrue(reply.isSuccess(), "pasv 2");
+- client.closeDataStream();
+- }
+- finally {
+-
+- }
+- }
+-
+- @Test
+- public void testMultipleRest() throws Exception {
+- FTPReply reply = client.login("anonymous", "igv at broadinstitute.org");
+- Assert.assertTrue(reply.isSuccess(), "login");
+-
+- reply = client.binary();
+- Assert.assertTrue(reply.isSuccess(), "binary");
+-
+- restRetr(5, 10);
+- restRetr(2, 10);
+- restRetr(15, 10);
+- }
+-
+- private void restRetr(int restPosition, int length) throws IOException {
+-
+- try {
+-
+- if (client.getDataStream() == null) {
+- FTPReply reply = client.pasv();
+- Assert.assertTrue(reply.isSuccess(), "pasv");
+- }
+-
+- client.setRestPosition(restPosition);
+-
+- FTPReply reply = client.retr(file);
+- //assertTrue(reply.getCode() == 150);
+-
+- InputStream is = client.getDataStream();
+-
+- byte[] buffer = new byte[length];
+- is.read(buffer);
+-
+- for (int i = 0; i < length; i++) {
+- System.out.print((char) buffer[i]);
+- Assert.assertEquals(expectedBytes[i + restPosition], buffer[i], "reading from stream");
+- }
+- System.out.println();
+- }
+-
+- finally {
+- client.closeDataStream();
+- FTPReply reply = client.getReply(); // <== MUST READ THE REPLY
+- System.out.println(reply.getReplyString());
+- }
+- }
+ }
--
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