Skip to content

Add experimental support for XZ compression. #21

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gouttegd wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Add experimental support for XZ compression. #21

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions cli/src/main/java/org/incenp/obofoundry/sssom/cli/SimpleCLI.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,8 @@
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.tukaani.xz.LZMA2Options;
import org.tukaani.xz.XZOutputStream;

import picocli.CommandLine.ArgGroup;
import picocli.CommandLine.Command;
Expand Down Expand Up @@ -833,6 +835,10 @@ private OutputStream getOutputStream(String filename, CompressionFormat comp)
out = new GZIPOutputStream(out);
break;

case XZ:
out = new XZOutputStream(out, new LZMA2Options());
break;

case NONE:
break;
}
Expand Down
5 changes: 5 additions & 0 deletions ext/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,11 @@
<artifactId>owlapi-distribution</artifactId>
<version>4.5.29</version>
</dependency>
<dependency>
<groupId>org.tukaani</groupId>
<artifactId>xz</artifactId>
<version>1.12</version>
</dependency>
<dependency>
<groupId>io.github.liveontologies</groupId>
<artifactId>elk-owlapi</artifactId>
Expand Down
9 changes: 8 additions & 1 deletion ext/src/main/java/org/incenp/obofoundry/sssom/util/CompressionFormat.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,14 @@ public enum CompressionFormat {
*
* @see <a href="https://www.rfc-editor.org/info/rfc1952/">RFC 1952</a>
*/
GZIP(".gz");
GZIP(".gz"),

/**
* The XZ file format from the XZ Utils project.
*
* @see <a href="https://tukaani.org/xz/xz-file-format.txt">XZ file format</a>
*/
XZ(".xz");

private String extension;

Expand Down
5 changes: 5 additions & 0 deletions ext/src/main/java/org/incenp/obofoundry/sssom/util/ReaderFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
import org.incenp.obofoundry.sssom.TSVReader;
import org.incenp.obofoundry.sssom.TSVReader.SeparatorMode;
import org.incenp.obofoundry.sssom.rdf.RDFReader;
import org.tukaani.xz.XZInputStream;

/**
* A class providing helper methods to obtain SSSOM reader objects.
Expand Down Expand Up @@ -513,6 +514,10 @@ private InputStream getInputStream(String filename, boolean allowStdin, Compress
in = new GZIPInputStream(in);
break;

case XZ:
in = new XZInputStream(in);
break;

case NONE:
break;
}
Expand Down
Loading