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Add explicit "htsget" menu to IGV doesn't have to guess. 99% or more …
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…of urls entered are not going to be htsget endpoints, so we should not be making https requests to try to find out.
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@jrobinso
jrobinso committed Sep 29, 2023
1 parent 396c7e2 commit b8e4abe
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Showing 5 changed files with 56 additions and 69 deletions.
3 changes: 3 additions & 0 deletions src/main/java/org/broad/igv/htsget/HtsgetUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,9 @@ public static Metadata getMetadata(final String url) throws IOException {
return null;
} else {
String format = json.get("htsget").getAsJsonObject().get("format").getAsString();
// if(!(format.toUpperCase().equals("BAM")) || format.toUpperCase().equals("VCF")) {
// throw new RuntimeException(("Format"))
// }
return new Metadata(url, format);
}
}
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105 changes: 38 additions & 67 deletions src/main/java/org/broad/igv/track/TrackLoader.java
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Expand Up @@ -124,6 +124,7 @@ public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadE

log.info("Loading resource: " + (locator.isDataURL() ? "<data url>" : path));
try {

String format = locator.getFormat();

if (format.equals("tbi")) {
Expand All @@ -134,9 +135,23 @@ public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadE
//This list will hold all new tracks created for this locator
List<Track> newTracks = new ArrayList<Track>();


// Determine track type, if possible, and add new tracks
if (locator.isHtsget()) {
tryHtsget(locator, newTracks, genome);
} else if (format.equals("gmt")) {
HtsgetUtils.Metadata htsgetMeta = HtsgetUtils.getMetadata(locator.getPath());
locator.setFormat(htsgetMeta.getFormat().toLowerCase());
if (htsgetMeta.getFormat().equals("VCF")) {
locator.setHtsget(true);
HtsgetVariantSource source = new HtsgetVariantSource(htsgetMeta, genome);
loadVCFWithSource(locator, source, newTracks);
} else if (htsgetMeta.getFormat().equals("BAM") || htsgetMeta.getFormat().equals("CRAM")) {
locator.setHtsget(true);
loadAlignmentsTrack(locator, newTracks, genome);
} else {
throw new RuntimeException("Format: '" + htsgetMeta.getFormat() + "' is not supported for htsget servers.");
}

} else if (format.equals("gmt")) {
loadGMT(locator);
} else if (format.equals("vcf.list")) {
loadVCFListFile(locator, newTracks, genome);
Expand Down Expand Up @@ -208,33 +223,29 @@ public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadE
loadMutFile(locator, newTracks, genome); // Must be tried before ".maf" test below
} else if (format.equals("maf")) {
loadMultipleAlignmentTrack(locator, newTracks, genome);
} else {
//if a url, try htsget
boolean isHtsget = tryHtsget(locator, newTracks, genome);
if (!isHtsget) {

// If the file is too large, give up
// TODO -- ftp test
final int tenMB = 10000000;
long fileLength = ParsingUtils.getContentLength(locator.getPath());
if (fileLength > tenMB) {
MessageUtils.confirm("<html>Cannot determine file type of: " + locator.getPath());
}
} else {
// If the file is too large, give up
// TODO -- ftp test
final int tenMB = 10000000;
long fileLength = ParsingUtils.getContentLength(locator.getPath());
if (fileLength > tenMB) {
MessageUtils.confirm("<html>Cannot determine file type of: " + locator.getPath());
}

// Read file contents and try to sort it out
String contents = FileUtils.getContents(locator.getPath());
BufferedReader reader = new BufferedReader(new StringReader(contents));

if (CytoBandFileParser.isValid(reader, locator.getPath())) {
Track track = new CytobandTrack(locator, new BufferedReader(new StringReader(contents)), genome);
newTracks.add(track);
} else if (AttributeManager.isSampleInfoFile(reader)) {
// This might be a sample information file.
AttributeManager.getInstance().loadSampleInfo(locator);
} else {
MessageUtils.showMessage("<html>Unknown file type: " + path + "<br>Check file extension");
}
// Read file contents and try to sort it out
String contents = FileUtils.getContents(locator.getPath());
BufferedReader reader = new BufferedReader(new StringReader(contents));

if (CytoBandFileParser.isValid(reader, locator.getPath())) {
Track track = new CytobandTrack(locator, new BufferedReader(new StringReader(contents)), genome);
newTracks.add(track);
} else if (AttributeManager.isSampleInfoFile(reader)) {
// This might be a sample information file.
AttributeManager.getInstance().loadSampleInfo(locator);
} else {
MessageUtils.showMessage("<html>Unknown file type: " + path + "<br>Check file extension");
}

}

// Track line
Expand Down Expand Up @@ -275,46 +286,6 @@ public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadE

}

/**
* Try to load as an htsget resource. As most (all?) htsget endpoints use an https:// scheme URL, there is
* no way to detect other than try.
*
* @param locator
* @param newTracks
* @param genome
* @return
*/
private boolean tryHtsget(ResourceLocator locator, List<Track> newTracks, Genome genome) {
boolean isHtsget = false;
if (locator.getPath().startsWith("https://") ||
locator.getPath().startsWith("http://") ||
locator.getPath().startsWith("htsget://")) {
try {
HtsgetUtils.Metadata htsgetMeta = HtsgetUtils.getMetadata(locator.getPath());
if (htsgetMeta != null) {
isHtsget = true;
locator.setFormat(htsgetMeta.getFormat().toLowerCase());
if (htsgetMeta.getFormat().equals("VCF")) {
locator.setHtsget(true);
HtsgetVariantSource source = new HtsgetVariantSource(htsgetMeta, genome);
loadVCFWithSource(locator, source, newTracks);
} else if (htsgetMeta.getFormat().equals("BAM") || htsgetMeta.getFormat().equals("CRAM")) {
locator.setHtsget(true);
loadAlignmentsTrack(locator, newTracks, genome);
} else {
throw new RuntimeException("Format: '" + htsgetMeta.getFormat() + "' is not supported for htsget servers.");
}
}
} catch (IOException e) {
// Not neccessarily an error, might just indicate its not an htsget server. Not sure
// if this should be logged or not, it will be a common and expected occurence when loading
// sample information, which is checked after htsget
return false;
}
}
return isHtsget;
}

public static boolean isAlignmentTrack(String typeString) {
if (typeString == null) {
return false;
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7 changes: 6 additions & 1 deletion src/main/java/org/broad/igv/ui/IGVMenuBar.java
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Original file line number Diff line number Diff line change
Expand Up @@ -284,7 +284,12 @@ JMenu createFileMenu() {
menuAction.setToolTipText(UIConstants.LOAD_TRACKS_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

menuAction = new LoadFromServerAction("Load from Server...", KeyEvent.VK_S, igv);
menuAction = new LoadFromURLMenuAction(LoadFromURLMenuAction.LOAD_FROM_HTSGET, 0, igv);
menuAction.setToolTipText(UIConstants.LOAD_HTSGET_TOOLTOP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));


menuAction = new LoadFromServerAction("Load from IGV Server...", KeyEvent.VK_S, igv);
menuAction.setToolTipText(UIConstants.LOAD_SERVER_DATA_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

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2 changes: 2 additions & 0 deletions src/main/java/org/broad/igv/ui/UIConstants.java
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Expand Up @@ -49,6 +49,8 @@ public class UIConstants {

// Menu tooltips
static final public String LOAD_TRACKS_TOOLTIP = "Load tracks or sample information";

static final public String LOAD_HTSGET_TOOLTOP = "Load BAM or VCF tracks from an htsget server";
static final public String LOAD_SERVER_DATA_TOOLTIP = "Load tracks or sample information from a server";
static final public String SAVE_PNG_IMAGE_TOOLTIP = "Capture and save a PNG image";
static final public String SAVE_SVG_IMAGE_TOOLTIP = "Capture and save an SVG image";
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8 changes: 7 additions & 1 deletion src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,8 @@ public class LoadFromURLMenuAction extends MenuAction {
static Logger log = LogManager.getLogger(LoadFilesMenuAction.class);
public static final String LOAD_FROM_URL = "Load from URL...";
public static final String LOAD_GENOME_FROM_URL = "Load Genome from URL...";

public static final String LOAD_FROM_HTSGET = "Load from htsget server...";
private IGV igv;

public LoadFromURLMenuAction(String label, int mnemonic, IGV igv) {
Expand All @@ -71,7 +73,8 @@ public void actionPerformed(ActionEvent e) {

JPanel ta = new JPanel();
ta.setPreferredSize(new Dimension(600, 20));
if (e.getActionCommand().equalsIgnoreCase(LOAD_FROM_URL)) {
boolean isHtsGet = e.getActionCommand().equalsIgnoreCase(LOAD_FROM_HTSGET);
if (e.getActionCommand().equalsIgnoreCase(LOAD_FROM_URL) || isHtsGet) {

LoadFromURLDialog dlg = new LoadFromURLDialog(IGV.getInstance().getMainFrame());
dlg.setVisible(true);
Expand Down Expand Up @@ -114,6 +117,9 @@ public void actionPerformed(ActionEvent e) {
String indexUrl = indexes[i];
rl.setIndexPath(indexUrl);
}
if(isHtsGet) {
rl.setHtsget(true);
}
locators.add(rl);
}
igv.loadTracks(locators);
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