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new a1e1649263 TIKA-4986: remove ISArchiveParser(String location) (#3375)
a1e1649263 is described below
commit a1e16492631e7722b5cd111f1f6bdabc90e85f48
Author: Tim Allison <[email protected]>
AuthorDate: Wed Oct 21 05:43:01 2026 -0400
TIKA-4986: remove ISArchiveParser(String location) (#3375)
The ISA-Tab directory is always the study file's parent directory.
Add CHANGES rows for the per-parse location fix (#3374) and the removal.
Co-Authored-By: Claude Opus 5.5 <[email protected]
---
CHANGES.txt | 8 +++++++
.../apache/tika/parser/isatab/ISArchiveParser.java | 26 +---------------------
.../tika/parser/isatab/ISArchiveParserTest.java | 15 ++++++-------
3 files changed, 16 insertions(+), 33 deletions(-)
diff --git a/CHANGES.txt b/CHANGES.txt
index 24423f0dc6..f09d0be37b 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -1,5 +1,13 @@
Release 4.2.0 - unreleased
+ * ISArchiveParser no longer reads every ISA-Tab document's investigation
and assay files
+ from the directory of the first document it parsed; concurrent parses no
longer share
+ the study file name (TIKA-4986).
+
+ * ISArchiveParser(String location) is removed: the ISA-Tab directory is
always the
+ parent directory of the study file, so pass a file-backed TikaInputStream
+ (TikaInputStream.get(Path)) (TIKA-4986).
+
BREAKING CHANGES AND DEPRECATIONS
* Unpack output is a Frictionless Data Package by default on tika-server
/unpack,
diff --git
a/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/main/java/org/apache/tika/parser/isatab/ISArchiveParser.java
b/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/main/java/org/apache/tika/parser/isatab/ISArchiveParser.java
index 0a363c1ad8..f7581f018e 100644
---
a/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/main/java/org/apache/tika/parser/isatab/ISArchiveParser.java
+++
b/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/main/java/org/apache/tika/parser/isatab/ISArchiveParser.java
@@ -50,26 +50,6 @@ public class ISArchiveParser implements Parser {
private static String studyAssayFileNameField =
ISATabUtils.ISATAB.key("Study Assay File Name");
private final Set<MediaType> SUPPORTED_TYPES =
Collections.singleton(MediaType.application("x-isatab"));
- private final String location;
-
- /**
- * Default constructor.
- */
- public ISArchiveParser() {
- this(null);
- }
-
- /**
- * Constructor that accepts the pathname of ISArchive folder.
- *
- * @param location pathname of ISArchive folder including ISA-Tab files
- */
- public ISArchiveParser(String location) {
- if (location != null && !location.endsWith(File.separator)) {
- location += File.separator;
- }
- this.location = location;
- }
@Override
public Set<MediaType> getSupportedTypes(ParseContext context) {
@@ -83,11 +63,7 @@ public class ISArchiveParser implements Parser {
TemporaryResources tmp = null;
try {
- // the parser is shared across parses: resolve the directory per
document
- String location = this.location;
- if (location == null) {
- location = tis.getFile().getParent() + File.separator;
- }
+ String location = tis.getFile().getParent() + File.separator;
// Use resource name from metadata if available, fall back to file
name
String resourceName =
metadata.get(TikaCoreProperties.RESOURCE_NAME_KEY);
String studyFileName = resourceName != null ? resourceName :
tis.getFile().getName();
diff --git
a/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/test/java/org/apache/tika/parser/isatab/ISArchiveParserTest.java
b/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/test/java/org/apache/tika/parser/isatab/ISArchiveParserTest.java
index 8d20ee20b9..02308159e0 100644
---
a/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/test/java/org/apache/tika/parser/isatab/ISArchiveParserTest.java
+++
b/tika-parsers/tika-parsers-extended/tika-parser-scientific-module/src/test/java/org/apache/tika/parser/isatab/ISArchiveParserTest.java
@@ -24,6 +24,7 @@ import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
+import java.nio.file.Paths;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
@@ -41,18 +42,16 @@ public class ISArchiveParserTest extends TikaTest {
@Test
public void testParseArchive() throws Exception {
- String path = "/test-documents/testISATab_BII-I-1/s_BII-S-1.txt";
-
- Parser parser = new ISArchiveParser(
-
ISArchiveParserTest.class.getResource("/test-documents/testISATab_BII-I-1/").toURI()
- .getPath());
- //Parser parser = new AutoDetectParser();
+ // the parser reads the investigation file next to the study, so open
the file itself
+ Path study = Paths.get(ISArchiveParserTest.class
+
.getResource("/test-documents/testISATab_BII-I-1/s_BII-S-1.txt").toURI());
+ Parser parser = new ISArchiveParser();
ContentHandler handler = new BodyContentHandler();
Metadata metadata = new Metadata();
metadata.set(TikaCoreProperties.RESOURCE_NAME_KEY, "s_BII-S-1.txt");
ParseContext context = new ParseContext();
- try (TikaInputStream tis = getResourceAsStream(path)) {
+ try (TikaInputStream tis = TikaInputStream.get(study)) {
parser.parse(tis, handler, metadata, context);
}
@@ -95,7 +94,7 @@ public class ISArchiveParserTest extends TikaTest {
Path study = isaDir.resolve("s_test.txt");
Files.write(study, "\"Source
Name\"\n\"culture1\"\n".getBytes(StandardCharsets.UTF_8));
- Parser parser = new ISArchiveParser(isaDir.toString());
+ Parser parser = new ISArchiveParser();
ContentHandler handler = new BodyContentHandler();
Metadata metadata = new Metadata();
metadata.set(TikaCoreProperties.RESOURCE_NAME_KEY, "s_test.txt");
