This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository htsjdk.
commit 72a19ccd3cb274b8b85276481081bb8d51d106a1 Author: Andreas Tille <[email protected]> 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 <[email protected]> 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", "[email protected]"); +- 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", "[email protected]"); +- 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", "[email protected]"); +- 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", "[email protected]"); +- 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", "[email protected]"); +- 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", "[email protected]"); +- 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", "[email protected]"); +- 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()); +- } +- } + } -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
