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Issue 50861: Pass around properly encoded WebDav URLs #320

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Merged
labkey-jeckels merged 2 commits into from
Nov 5, 2024
Merged

Issue 50861: Pass around properly encoded WebDav URLs #320

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b375e6e
Issue 50861: Pass around properly encoded WebDav URLs
labkey-jeckels Oct 21, 2024
7fbfb87
Merge branch 'develop' into fb_50861_webdavUrlEncoding
labkey-jeckels Oct 30, 2024
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7 changes: 4 additions & 3 deletions jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
import org.labkey.jbrowse.JBrowseSchema;

import java.io.File;
import java.net.URI;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
Expand Down Expand Up @@ -361,12 +362,12 @@ public static String getAssemblyName(ReferenceGenome rg)
public static JSONObject getIndexedFastaAdapter(ReferenceGenome rg)
{
ExpData d = ExperimentService.get().getExpData(rg.getFastaExpDataId());
String url = d.getWebDavURL(FileContentService.PathType.full);
URI url = d.getWebDavURL(FileContentService.PathType.full);

JSONObject ret = new JSONObject();
ret.put("type", "IndexedFastaAdapter");
ret.put("fastaLocation", new JSONObject(){{
put("uri", url);
put("uri", url.toString());
}});
ret.put("faiLocation", new JSONObject(){{
put("uri", url + ".fai");
Expand All @@ -378,7 +379,7 @@ public static JSONObject getIndexedFastaAdapter(ReferenceGenome rg)
public static JSONObject getBgZippedIndexedFastaAdapter(ReferenceGenome rg)
{
ExpData d = ExperimentService.get().getExpData(rg.getFastaExpDataId());
String url = d.getWebDavURL(FileContentService.PathType.full);
URI url = d.getWebDavURL(FileContentService.PathType.full);

JSONObject ret = new JSONObject();
ret.put("type", "BgzipFastaAdapter");
Expand Down
28 changes: 19 additions & 9 deletions jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@
import org.labkey.api.util.JobRunner;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Path;
import org.labkey.api.util.UnexpectedException;
import org.labkey.api.view.UnauthorizedException;
import org.labkey.jbrowse.JBrowseLuceneSearch;
import org.labkey.jbrowse.JBrowseManager;
Expand All @@ -59,6 +60,8 @@

import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.sql.SQLException;
import java.util.Arrays;
Expand Down Expand Up @@ -512,7 +515,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
put(JBrowseSession.getAssemblyName(rg));
}});

String url = targetFile.getWebDavURL(FileContentService.PathType.full);
URI url = targetFile.getWebDavURL(FileContentService.PathType.full);
if (url == null)
{
log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
Expand All @@ -522,7 +525,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
ret.put("adapter", new JSONObject(){{
put("type", "ExtendedVariantAdapter");
put("vcfGzLocation", new JSONObject(){{
put("uri", url);
put("uri", url.toString());
}});

put("index", new JSONObject(){{
Expand Down Expand Up @@ -596,7 +599,7 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe
put(JBrowseSession.getAssemblyName(rg));
}});

String url = targetFile.getWebDavURL(FileContentService.PathType.full);
URI url = targetFile.getWebDavURL(FileContentService.PathType.full);
if (url == null)
{
log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
Expand All @@ -612,7 +615,7 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe
put("type", type);
put("bamLocation", new JSONObject()
{{
put("uri", url);
put("uri", url.toString());
}});

put("index", new JSONObject()
Expand Down Expand Up @@ -667,7 +670,7 @@ private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenom
put(getCategory());
}});

String url = targetFile.getWebDavURL(FileContentService.PathType.full);
URI url = targetFile.getWebDavURL(FileContentService.PathType.full);
if (url == null)
{
log.info("Unable to create WebDav URL for JBrowse resource with path: " + targetFile.getFile());
Expand All @@ -677,7 +680,7 @@ private JSONObject getBigWigTrack(Logger log, ExpData targetFile, ReferenceGenom
ret.put("adapter", new JSONObject(){{
put("type", "BigWigAdapter");
put("bigWigLocation", new JSONObject(){{
put("uri", url);
put("uri", url.toString());
put("locationType", "UriLocation");
}});
}});
Expand Down Expand Up @@ -747,7 +750,7 @@ private JSONObject getTabixTrack(User u, Logger log, ExpData targetFile, Referen

// if not gzipped, we need to process it:
File gzipped = prepareResource(u, log, true, false);
final String url;
final URI url;
if (!getExpData().getFile().equals(gzipped))
{
url = getWebDavURL(gzipped);
Expand Down Expand Up @@ -1192,7 +1195,7 @@ public File getExpectedLocationOfIndexFile(String extension, boolean throwIfNotF
return ret;
}

private String getWebDavURL(File input)
private URI getWebDavURL(File input)
{
java.nio.file.Path path = input.toPath();
if (getContainerObj() == null)
Expand Down Expand Up @@ -1221,7 +1224,14 @@ private String getWebDavURL(File input)
relPath = Path.parse(FilenameUtils.separatorsToUnix(relPath)).toString();
}

return AppProps.getInstance().getBaseServerUrl() + root.getWebdavURL() + relPath;
try
{
return new URI(AppProps.getInstance().getBaseServerUrl() + root.getWebdavURL() + relPath);
}
catch (URISyntaxException e)
{
throw UnexpectedException.wrap(e);
}
}

return null;
Expand Down