<p>Usage data is collected from the logs of various web services
that the Jalview Desktop contacts through its normal operation.
These are described below:</p>
- <ul>
- <li><em>HTTP logs on the Jalview website</em><br> We
- record IP addresses of machines which access the web site, either
- via the browser when downloading the application, or when the
- Jalview Desktop user interface is launched.<br> <br>
- <ul>
- <li><i>The Jalview Getdown Launcher</i> (Since 2.11.0) examines release
- channels every time Jalview launches to determine if a new
- release is available.</li>
- <li><i>The questionnaire web service at
- www.jalview.org/cgi-bin/questionnaire.pl is checked and a
- unique cookie for the current questionnaire is stored in the
- Jalview properties file.</i></li>
- <li><i>The Jalview web services stack is contacted to
- retrieve the currently available web services. All
- interactions with the public Jalview web services are
- logged, but we delete all job data (input data and results)
- after about two weeks.</i></li>
- </ul> <br></li>
- <li><em>Google Analytics</em><br> Since Jalview 2.4.0b2,
- the Jalview Desktop records usage data with Google Analytics via
- the <a href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
- class.<br> The Google Analytics logs for Jalview version 2.4
- only record the fact that the application was started, but in the
- future, we will use this mechanism to improve the Desktop user
- interface, by tracking which parts of the user interface are being
- used most often.</li>
- </ul>
- </p>
+ <ul>
+ <li><em>HTTP logs on the Jalview website</em><br> We record
+ IP addresses of machines which access the web site, either via the
+ browser when downloading the application, or when the Jalview Desktop
+ user interface is launched.<br> <br>
+ <ul>
+ <li><i>The Jalview Getdown Launcher</i> (Since 2.11.0) examines
+ release channels every time Jalview launches to determine if a new
+ release is available.</li>
+ <li><i>The questionnaire web service at
+ www.jalview.org/cgi-bin/questionnaire.pl is checked and a unique
+ cookie for the current questionnaire is stored in the Jalview
+ properties file.</i></li>
+ <li><i>The Jalview web services stack is contacted to
+ retrieve the currently available web services. All interactions
+ with the public Jalview web services are logged, but we delete all
+ job data (input data and results) after about two weeks.</i></li>
+ </ul> <br></li>
+ <li><em>Usage Analytics</em><br> Since Jalview 2.11.2.7, the
+ Jalview Desktop records usage data with a self-hosted instance of the
+ analytics stack <a href="https://plausible.io">Plausible.io</a> via a
+ custom GPLv3 client developed by Ben Soares. Prior to this, Jalview
+ versions as far back as 2.4 recorded application launches via <a
+ href="http://code.google.com/p/jgoogleanalytics/">JGoogleAnalytics</a>
+ .<br> Usage logs for Jalview record the fact that the
+ application was started, and details about the OS, installed Jalview
+ launcher (if any) and java version used. In the future, we will use
+ this mechanism to improve the Desktop user interface, by tracking
+ which parts of the user interface are being used most often.</li>
+ </ul>
<p>
<strong>Stopping Jalview from calling home</strong><br> If you
run Jalview in 'headless mode' via the command line, then the
--- /dev/null
+---
+version: 2.11.2.7
+date: 2023-06-30
+channel: "release"
+---
+
+## New Features
+- <!-- JAL-4001 --> Jalview now reports usage statistics via Plausible.io
+
+## Issues Resolved
+- <!-- JAL-4116 --> PDB structures slow to view when Jalview Java console is open
+- <!-- JAL-4216 --> chains in PDB or mmCIF files with negative RESNUMs not correctly parsed
---
version: 2.11.3.0
-date: 2023-06-07
+date: 2023-07-19
channel: "release"
---
- <!-- JAL-4089 --> Use selected columns for superposition
- <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
+- <!-- JAL-4221 --> sequence descriptions are updated from database reference sources if not already defined
+
+
### Improved support for working with computationally determined models
- <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
- <!-- JAL-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
- <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
- <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
+- <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
+
### Jalview on the command line
### Other improvements
- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
+- <!-- JAL-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
+- <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
+
+- <!-- JAL-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
+Add a command line option to set Jalview properties for this session only
+Add a command line option to suppress opening the startup file for this session
+
+
+JAL-4187 Powershell launcher script fails when given no arguments with the old ArgsParser
+
+known issue ? <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
+
+
+- <!-- JAL-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
+- <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
## Still in progress (delete on release)
--- /dev/null
+Jalview 2.11.2.7 is a minor patch release - it includes patches affecting efficiency when importing structures and a small revision to the import processing of structures with negative residue numbering.
+
+With this release, Jalview usage statistics are now collected by a jalview.org hosted instance of the open source privacy-preserving analytics stack, Plausible.io.
+
+
The 2.11.3 series includes support for in-depth exploration of predicted alignment error matrices from AlphaFold in the context of multiple alignments, along with support for standard colourschemes for shading models according to their pLDDT.
+We're launching this release at ISMB 2023 - come find us !
+
It also introduces new support for native ARM-based OSX architectures, and a few other goodies!
pdbpos++;
}
- if (allowmismatch || c1 == c2)
+ // ignore case differences
+ if (allowmismatch || (c1 == c2) || (Math.abs(c2-c1)==('a'-'A')))
{
// extend mapping interval
if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
* @param alignment
* the alignment to add them to
* @param selectionGroup
- * current selection group (or null if none)
+ * current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
*/
public static void addReferenceAnnotations(
Map<SequenceI, List<AlignmentAnnotation>> annotations,
* @param seq
* @param ann
* @param selectionGroup
- * - may be null
+ * current selection group - may be null, if provided then any added annotation will be trimmed to just those columns in the selection group
* @return annotation added to {@code seq and {@code alignment}
*/
public static AlignmentAnnotation addReferenceAnnotationTo(
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analytics;
import java.io.BufferedReader;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Random;
import jalview.bin.Cache;
import jalview.bin.Console;
public class Plausible
{
- private static final String USER_AGENT = HttpUtils.getUserAgent(
- MethodHandles.lookup().lookupClass().getCanonicalName());
+ private static final String USER_AGENT;
private static final String JALVIEW_ID = "Jalview Desktop";
private static final String DOMAIN = "jalview.org";
- private static final String CONFIG_API_BASE_URL = "https://www.jalview.org/config/analytics/url";
+ private static final String CONFIG_API_BASE_URL = "https://www.jalview.org/services/config/analytics/url";
- private static final String DEFAULT_API_BASE_URL = "https://plausible.io/api/event";
+ private static final String DEFAULT_API_BASE_URL = "https://analytics.jalview.org/api/event";
private static final String API_BASE_URL;
+ private static final String clientId;
+
public static final String APPLICATION_BASE_URL = "desktop://localhost";
private List<Map.Entry<String, String>> queryStringValues;
// ascertain the API_BASE_URL
API_BASE_URL = getAPIBaseURL();
+
+ // random clientId to make User-Agent unique (to register analytic)
+ clientId = String.format("%08x", new Random().nextInt());
+
+ USER_AGENT = HttpUtils.getUserAgent(
+ MethodHandles.lookup().lookupClass().getCanonicalName() + " "
+ + clientId);
}
private Plausible()
}
return DEFAULT_API_BASE_URL;
}
-}
\ No newline at end of file
+}
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
Console.error("Failed to import and open structure view.");
continue;
}
- while (sv.isBusy())
+ try
{
- try {
+ long tries=1000;
+ while (sv.isBusy() && tries>0)
+ {
Thread.sleep(25);
+ if (sv.isBusy())
+ {
+ tries--;
+ Console.debug(
+ "Waiting for viewer for " + structureFilepath);
+ }
}
- catch (Exception x)
+ if (tries==0 && sv.isBusy())
{
-
+ Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong.");
}
+ } catch (Exception x)
+ {
+ Console.warn("Exception whilst waiting for structure viewer "+structureFilepath,x);
}
-
+ Console.debug("Successfully opened viewer for "+structureFilepath);
String structureImageFilename = ArgParser.getValueFromSubValOrArg(
avm, av, Arg.STRUCTUREIMAGE, subVals);
if (sv != null && structureImageFilename != null)
}
BitmapImageSizing userBis = ImageMaker
.parseScaleWidthHeightStrings(scale, width, height);
+ // TODO MAKE THIS VIEWER INDEPENDENT!!
switch (StructureViewer.getViewerType())
{
case JMOL:
try
{
- Thread.sleep(1000);
+ Thread.sleep(1000); // WHY ???
} catch (InterruptedException e)
{
// TODO Auto-generated catch block
{
AppJmol jmol = (AppJmol) sview;
try {
+ Console.debug("Rendering image to "+structureImageFile);
jmol.makePDBImage(structureImageFile, imageType, renderer,
userBis);
+ Console.debug("Finished Rendering image to "+structureImageFile);
+
}
catch (ImageOutputException ioexc)
{
public static boolean isPrimaryCandidate(String ucversion)
{
+ if (ucversion==null)
+ {
+ // Null/empty version is not a real reference ?
+ return false;
+ }
// tricky - this test really needs to search the sequence's set of dbrefs to
// see if there is a primary reference that derived this reference.
for (int i = allSources.length; --i >= 0;)
transferAnnotation(entry.getDatasetSequence(), mp);
return;
}
+ // transfer from entry to sequence
+ // if entry has a description and sequence doesn't, then transfer
+ if (entry.getDescription()!=null && (description==null || description.trim().length()==0))
+ {
+ description = entry.getDescription();
+ }
+
// transfer any new features from entry onto sequence
if (entry.getSequenceFeatures() != null)
{
{
int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.io.File;
+import java.lang.reflect.InvocationTargetException;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.concurrent.Callable;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.FutureTask;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
};
String view = MessageManager.getString("action.view")
.toLowerCase(Locale.ROOT);
- ImageExporter exporter = new ImageExporter(writer,
+ final ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
- exporter.doExport(file, this, width, height, view, renderer, userBis);
-
+ final Throwable[] exceptions = new Throwable[1];
+ exceptions[0] = null;
+ final AppJmol us = this;
+ try
+ {
+ Thread runner = Executors.defaultThreadFactory().newThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ exporter.doExport(file, us, width, height, view, renderer,
+ userBis);
+ } catch (Throwable t)
+ {
+ exceptions[0] = t;
+ }
+ }
+ });
+ runner.start();
+ do { Thread.sleep(25); } while (runner.isAlive());
+ } catch (Throwable e)
+ {
+ throw new ImageOutputException(
+ "Unexpected error when generating image", e);
+ }
+ if (exceptions[0] != null)
+ {
+ if (exceptions[0] instanceof ImageOutputException)
+ {
+ throw ((ImageOutputException) exceptions[0]);
+ }
+ else
+ {
+ throw new ImageOutputException(
+ "Unexpected error when generating image", exceptions[0]);
+ }
+ }
}
@Override
setKeyBindings(frame);
- desktop.add(frame);
+ // Since the latest FlatLaf patch, we occasionally have problems showing structureViewer frames...
+ int tries=3;
+ boolean shown=false;
+ Exception last=null;
+ do
+ {
+ try
+ {
+ desktop.add(frame);
+ shown=true;
+ } catch (IllegalArgumentException iaex)
+ {
+ last=iaex;
+ tries--;
+ jalview.bin.Console.info(
+ "Squashed IllegalArgument Exception (" + tries + " left) for "+frame.getTitle(),
+ iaex);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException iex)
+ {
+ }
+ ;
+ }
+ } while (!shown && tries > 0);
+ if (!shown)
+ {
+ jalview.bin.Console.error("Serious Problem whilst showing window "+frame.getTitle(),last);
+ }
windowMenu.add(menuItem);
{
Desktop.instance.closeAll_actionPerformed(null);
Desktop.instance.setVisible(false);
- Desktop.instance.dispose();
+ Desktop us = Desktop.instance;
Desktop.instance = null;
+ // call dispose in a separate thread - try to avoid indirect deadlocks
+ new Thread(new Runnable() {
+ @Override
+ public void run()
+ {
+ ExecutorService dex = us.dialogExecutor;
+ if (dex!=null) {
+ dex.shutdownNow();
+ us.dialogExecutor=null;
+ us.block.drainPermits();
+ }
+ us.dispose();
+ }
+ }).start();
}
}
*/
if (file == null && !Jalview.isHeadlessMode())
{
+ if (Desktop.instance.isInBatchMode())
+ {
+ // defensive error report - we could wait for user input.. I guess ?
+ throw(new ImageOutputException("Need an output file to render to when exporting images in batch mode!"));
+ }
JalviewFileChooser chooser = imageType.getFileChooser();
chooser.setFileView(new JalviewFileView());
MessageManager.formatMessage("label.create_image_of",
protected void addReferenceAnnotations_actionPerformed(
Map<SequenceI, List<AlignmentAnnotation>> candidates)
{
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
final AlignmentI alignment = this.ap.getAlignment();
AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
+ null);
refresh();
}
private static final String NOT_OBSERVED = "Not_Observed";
- private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ private static final String SIFTS_SPLIT_FTP_BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/";
private final static String NEWLINE = System.lineSeparator();
pdbId = pdbId.replace(".cif", "");
}
String siftFile = pdbId + ".xml.gz";
- String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
+ String siftsFileFTPURL = getDownloadUrlFor(siftFile);
/*
* Download the file from URL to either
return downloadTo;
}
+ public static String getDownloadUrlFor(String siftFile)
+ {
+ return SIFTS_SPLIT_FTP_BASE_URL +siftFile.substring(1, 3)+"/"+siftFile;
+ }
+
/**
* Delete the SIFTs file for the given PDB Id in the local SIFTs download
* directory
import jalview.gui.JvOptionPane;
import java.io.PrintStream;
+import java.nio.charset.Charset;
+import java.util.Locale;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import com.google.common.base.Charsets;
+
/**
* Test the alignment -> Mapping routines
*
assertEquals(as.getAStr1(), as.getAStr2());
Mapping s1tos2 = as.getMappingFromS1(false);
+ checkMapping(s1tos2,s1,s2);
+ }
+
+ public void checkMapping(Mapping s1tos2,SequenceI _s1,SequenceI _s2)
+ {
System.out.println(s1tos2.getMap().toString());
- for (int i = s2.getStart(); i < s2.getEnd(); i++)
+ for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
{
- System.out.println("Position in s2: " + i
- + " maps to position in s1: " + s1tos2.getPosition(i));
- // TODO fails: getCharAt doesn't allow for the start position??
- // assertEquals(String.valueOf(s2.getCharAt(i)),
- // String.valueOf(s1.getCharAt(s1tos2.getPosition(i))));
+ int p=s1tos2.getPosition(i);
+ char s2c=_s2.getCharAt(i-_s2.getStart());
+ char s1c=_s1.getCharAt(p-_s1.getStart());
+ System.out.println("Position in s2: " + i +s2c
+ + " maps to position in s1: " +p+s1c);
+ assertEquals(s1c,s2c);
}
}
+ @Test(groups = { "Functional" })
+ /**
+ * simple test that mapping from alignment corresponds identical positions.
+ */
+ public void testGetMappingForS1_withLowerCase()
+ {
+ // make one of the sequences lower case
+ SequenceI ns2 = new Sequence(s2);
+ ns2.replace('D', 'd');
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
+ System.out.println("s1: " + as.getAStr1());
+ System.out.println("s2: " + as.getAStr2());
+
+ // aligned results match
+ assertEquals("ASDFA", as.getAStr1());
+ assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
+
+ Mapping s1tos2 = as.getMappingFromS1(false);
+ assertEquals("ASdFA",as.getAStr2());
+ // verify mapping is consistent between original all-caps sequences
+ checkMapping(s1tos2,s1,s2);
+ }
@Test(groups = { "Functional" })
public void testExtractGaps()
import jalview.gui.JvOptionPane;
import jalview.util.ArrayUtils;
-@Test
public class CommandsTest
{
private static final String testfiles = "test/jalview/bin/argparser/testfiles";
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
{
- String[] args = (cmdLine + " --gui").split("\\s+");
- callJalviewMain(args);
- Commands cmds = Jalview.getInstance().getCommands();
- Assert.assertNotNull(cmds);
- Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
- "Commands were not provided in the args");
- Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
- "Overall command parse and operation is false");
+ try
+ {
+ String[] args = (cmdLine + " --gui").split("\\s+");
+ callJalviewMain(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
+ "Commands were not provided in the args");
+ Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
+ "Overall command parse and operation is false");
- Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
- "Wrong number of AlignFrames");
+ Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+ "Wrong number of AlignFrames");
- if (sequences != null)
- {
- Set<String> openedSequenceNames = new HashSet<>();
- AlignFrame[] afs = Desktop.getAlignFrames();
- for (AlignFrame af : afs)
+ if (sequences != null)
{
- openedSequenceNames
- .addAll(af.getViewport().getAlignment().getSequenceNames());
- }
- for (String sequence : sequences)
- {
- Assert.assertTrue(openedSequenceNames.contains(sequence),
- "Sequence '" + sequence
- + "' was not found in opened alignment files: "
- + cmdLine + ".\nOpened sequence names are:\n"
- + String.join("\n", openedSequenceNames));
+ Set<String> openedSequenceNames = new HashSet<>();
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ for (AlignFrame af : afs)
+ {
+ openedSequenceNames.addAll(
+ af.getViewport().getAlignment().getSequenceNames());
+ }
+ for (String sequence : sequences)
+ {
+ Assert.assertTrue(openedSequenceNames.contains(sequence),
+ "Sequence '" + sequence
+ + "' was not found in opened alignment files: "
+ + cmdLine + ".\nOpened sequence names are:\n"
+ + String.join("\n", openedSequenceNames));
+ }
}
- }
- Assert.assertFalse(
- lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ Assert.assertFalse(
+ lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during commandsOpenTest", x);
+ } finally
+ {
+ tearDown();
+
+ }
}
@Test(groups = "Functional", dataProvider = "structureImageOutputFiles")
{
cleanupFiles(filenames);
String[] args = (cmdLine + " --gui").split("\\s+");
- callJalviewMain(args);
- Commands cmds = Jalview.getInstance().getCommands();
- Assert.assertNotNull(cmds);
- File lastFile = null;
- for (String filename : filenames)
+ try
{
- File file = new File(filename);
- Assert.assertTrue(file.exists(), "File '" + filename
- + "' was not created by '" + cmdLine + "'");
- Assert.assertTrue(file.isFile(), "File '" + filename
- + "' is not a file from '" + cmdLine + "'");
- Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
- + "' has no content from '" + cmdLine + "'");
- // make sure the successive output files get bigger!
- if (lastFile != null)
- Assert.assertTrue(
- Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+ callJalviewMain(args);
+ Commands cmds = Jalview.getInstance().getCommands();
+ Assert.assertNotNull(cmds);
+ File lastFile = null;
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ Assert.assertTrue(file.exists(), "File '" + filename
+ + "' was not created by '" + cmdLine + "'");
+ Assert.assertTrue(file.isFile(), "File '" + filename
+ + "' is not a file from '" + cmdLine + "'");
+ Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ + "' has no content from '" + cmdLine + "'");
+ // make sure the successive output files get bigger!
+ if (lastFile != null)
+ Assert.assertTrue(Files.size(file.toPath()) > Files
+ .size(lastFile.toPath()));
+ }
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during structureImageOutputTest",
+ x);
+ } finally
+ {
+ cleanupFiles(filenames);
+ tearDown();
}
- cleanupFiles(filenames);
- tearDown();
}
@Test(groups = "Functional", dataProvider = "argfileOutputFiles")
{
cleanupFiles(filenames);
String[] args = (cmdLine + " --gui").split("\\s+");
+ try {
callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
Assert.assertTrue(
Files.size(file.toPath()) > Files.size(lastFile.toPath()));
}
- cleanupFiles(filenames);
- tearDown();
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during argFilesGlobAndSubstitutions",
+ x);
+ } finally
+ {
+ cleanupFiles(filenames);
+ tearDown();
+ }
}
@DataProvider(name = "structureImageOutputFiles")
{
Sequence origSeq = new Sequence("MYSEQ", "THISISASEQ");
Sequence toSeq = new Sequence("MYSEQ", "THISISASEQ");
+ origSeq.setDescription("DESCRIPTION");
origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
+
+ toSeq.transferAnnotation(origSeq, null);
+ assertEquals("DESCRIPTION",toSeq.getDescription());
+ toSeq = new Sequence("MYSEQ", "THISISASEQ");
+ toSeq.setDescription("unchanged");
toSeq.transferAnnotation(origSeq, null);
+ assertEquals("unchanged",toSeq.getDescription());
+
assertTrue(toSeq.getDBRefs().size() == 1);
assertTrue(toSeq.getDBRefs().get(0).isCanonical());
SiftsSettings.setCacheThresholdInDays("2");
SiftsSettings.setFailSafePIDThreshold("70");
PDBfile pdbFile;
+
pdbFile = new PDBfile(false, false, false,
"test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
+ // TODO: this uses a network connection - we should mock the sifts testPDBId.xml.gz
siftsClient = new SiftsClient(pdbFile);
}
{
siftsClient = null;
}
+
+ @Test(groups= {"Functional"})
+ public void testSIFTsDownloadURL() {
+ String expectedUrl = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/xy/1xyz.sifts.xml.gz";
+ Assert.assertEquals(SiftsClient.getDownloadUrlFor("1xyz.sifts.xml.gz"), expectedUrl);
+ }
@Test(groups = { "Network" })
public void getSIFTsFileTest() throws SiftsException, IOException
long t1 = siftsFile.lastModified();
// re-read file should be returned from cache
- siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ siftsFile = SiftsClient.getSiftsFile(testPDBId);
FileAssert.assertFile(siftsFile);
long t2 = siftsFile.lastModified();
assertEquals(t1, t2);
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
DBRefEntry invalidDBRef = new DBRefEntry();
- invalidDBRef.setAccessionId("BLAR");
+ invalidDBRef.setAccessionId("BLAR"); // note no version is set, so also invalid
invalidTestSeq.addDBRef(invalidDBRef);
siftsClient.getValidSourceDBRef(invalidTestSeq);
}
git://source.jalview.org / jalview.git / commitdiff