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TASK-5932 - Format filter autocomplete is broken "The results could not be loaded" #2436

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merged 2 commits into from
May 13, 2024
Merged

TASK-5932 - Format filter autocomplete is broken "The results could not be loaded" #2436

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accfa3b
catalog: fix FORMAT and bioformat regex queries, #TASK-5932
pfurio Apr 30, 2024
22b5cac
Merge branch 'release-2.12.x' into TASK-5932
pfurio May 13, 2024
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9 changes: 2 additions & 7 deletions opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/FileMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1479,20 +1479,15 @@ private Bson parseQuery(Query query, Document extraQuery, String user)
addAutoOrQuery(queryParam.key(), queryParam.key(), myQuery, queryParam.type(), andBsonList);
}
break;
case FORMAT:
case BIOFORMAT:
// Replace the value for an uppercase string as we know it will always be in that way
String uppercaseValue = myQuery.getString(queryParam.key()).toUpperCase();
myQuery.put(queryParam.key(), uppercaseValue);
addAutoOrQuery(queryParam.key(), queryParam.key(), myQuery, queryParam.type(), andBsonList);
break;
case UUID:
case EXTERNAL:
case TYPE:
case URI:
case ID:
case PATH:
case RELEASE:
case FORMAT:
case BIOFORMAT:
case TAGS:
case SIZE:
case SOFTWARE_NAME:
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26 changes: 26 additions & 0 deletions opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/FileManagerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -188,6 +188,32 @@ public void testLinkFileWithoutReadPermissions() throws IOException, CatalogExce
fileManager.link(studyFqn, new FileLinkParams().setUri(file.getPath()), false, token);
}

@Test
public void filterByFormatTest() throws CatalogException {
Query query = new Query(FileDBAdaptor.QueryParams.FORMAT.key(), "PLAIN");
OpenCGAResult<File> search = catalogManager.getFileManager().search(studyFqn, query, QueryOptions.empty(), token);
assertEquals(2, search.getNumResults());

query = new Query(FileDBAdaptor.QueryParams.FORMAT.key(), "plain");
search = catalogManager.getFileManager().search(studyFqn, query, QueryOptions.empty(), token);
assertEquals(0, search.getNumResults());

// Case sensitive search in lower case
query = new Query(FileDBAdaptor.QueryParams.FORMAT.key(), "~/^pla/");
search = catalogManager.getFileManager().search(studyFqn, query, QueryOptions.empty(), token);
assertEquals(0, search.getNumResults());

// Case sensitive in upper case
query = new Query(FileDBAdaptor.QueryParams.FORMAT.key(), "~/^PLA/");
search = catalogManager.getFileManager().search(studyFqn, query, QueryOptions.empty(), token);
assertEquals(2, search.getNumResults());

// Case insensitive search
query = new Query(FileDBAdaptor.QueryParams.FORMAT.key(), "~/^pla/i");
search = catalogManager.getFileManager().search(studyFqn, query, QueryOptions.empty(), token);
assertEquals(2, search.getNumResults());
}

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