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TASK-612 - OpenCGA files/link raises a NullPointExeption if it has no read access to the file #2241

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merged 3 commits into from
Feb 8, 2023
Merged

TASK-612 - OpenCGA files/link raises a NullPointExeption if it has no read access to the file #2241

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215d741
catalog: fix NPE when linking a file without read permissions, #TASK-612
pfurio Jan 18, 2023
2205124
catalog: add supressed exception, #TASK-612
pfurio Jan 18, 2023
6e836ec
Merge branch 'develop' into TASK-612
pfurio Feb 8, 2023
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6 changes: 3 additions & 3 deletions opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FileManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2332,7 +2332,7 @@ public OpenCGAResult<File> link(String studyStr, FileLinkParams params, boolean
auditManager.auditCreate(userId, Enums.Action.LINK, Enums.Resource.FILE, params.getUri(), "",
study.getId(), study.getUuid(), auditParams, new AuditRecord.Status(AuditRecord.Status.Result.ERROR,
new Error(0, "", e2.getMessage())));
throw new CatalogException(e2.getMessage(), e2);
throw e2;
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}
}
}
Expand Down Expand Up @@ -3506,7 +3506,7 @@ public FileVisitResult preVisitDirectory(URI dir, BasicFileAttributes attrs) thr
}
}
} catch (CatalogException e) {
logger.error("An error occurred when trying to create folder {}", dir.toString());
throw new IOException("An error occurred when trying to create folder " + dir, e);
}

return FileVisitResult.CONTINUE;
Expand Down Expand Up @@ -3581,7 +3581,7 @@ public FileVisitResult visitFile(URI fileUri, BasicFileAttributes attrs) throws
+ ". There is already a file in the path " + destinyPath + " with the same name.");
}
} catch (CatalogException e) {
logger.error(e.getMessage());
throw new IOException(e);
}

return FileVisitResult.CONTINUE;
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9 changes: 9 additions & 0 deletions opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java
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Expand Up @@ -170,6 +170,15 @@ public void testLinkUserWithNoWritePermissions() throws CatalogException {
fileManager.link(studyFqn, Paths.get(reference).toUri(), "", null, analystToken).first();
}

@Test
public void testLinkFileWithoutReadPermissions() throws IOException, CatalogException {
java.io.File file = createDebugFile("/tmp/file_" + RandomStringUtils.randomAlphanumeric(5) + ".vcf");
Files.setPosixFilePermissions(Paths.get(file.toURI()), new HashSet<>());
thrown.expect(CatalogIOException.class);
thrown.expectMessage("read VariantSource");
fileManager.link(studyFqn, new FileLinkParams().setUri(file.getPath()), false, token);
}

@Test
public void createDirectoryTest() throws CatalogException {
FileCreateParams params = new FileCreateParams()
Expand Down