When createSearcher show No indices found, Where can I get it,Please help me

[xzhou89]

// [private helpers]___________________________________________________
private static Searcher createSearcher(String indexPath) throws IOException {
ArrayList searchers = new ArrayList();
File indices = new File(indexPath);
File[] fileList = indices.listFiles();
if (fileList == null) {
throw new IOException(
String
.format(
"Unable to load indices from path '%s', not a directory or I/O error",
indexPath));
}

	for (File file : fileList) {
		try {
			if (!LuceneMediator.indexExists(file)) {
				continue;
			}
			FSDirectory directory = FSDirectory.open(file);
			searchers.add(new IndexSearcher(directory));
		} catch (IOException e) {
			e.printStackTrace();
		}
	}
	if (searchers.size() == 0) {
		throw new IOException("No indices found");
	}
	return new MultiSearcher(searchers
			.toArray(new Searchable[searchers.size()]));
}

[chrtannus]

Are you trying to run the GeneMANIA website (https://genemania.org/)?

[xzhou89]

I visit the https://genemania.org，It can search gene name, but when i deploy my computer, it not search gene name

Organism organism;
Long organismId;
try {
organismId = sReq.getOrganism();
organism = organismService.findOrganismById(organismId);
params.setOrganism(organism);
} catch (DataStoreException e) {
return new SearchResults(e.getMessage(), SearchResultsErrorCode.DATASTORE);
}

When I tried to perform a search gene name, I couldn't get organism ，by the way geneindexdir this data , where can I get it

[chrtannus]

1. Download the r27.tar.gz file here: http://genemania.org/data/website/
2. Unpack the r27.tar.gz file -- it should contain the lucene_index and network_cache folders inside r27.
3. I suggest you run genemania as a Docker container so, on the Terminal, execute this command to get the latest image from Docker Hub:
   docker pull baderlab/genemania_website
4. Now run the docker container with a command like this:

  sudo docker run -d -v /MY_PATH_TO/GENEMANIA_DATA:/gm/db_build \
      -e GENEMANIA_LUCENE_INDEX_DIR='/gm/db_build/r27/lucene_index' \
      -e GENEMANIA_NETWORK_CACHE_DIR='/gm/db_build/r27/network_cache' \
      -p 8081:8080 \
      --name genemania_website genemania_website

• Replace /MY_PATH_TO/GENEMANIA_DATA with the path that contains the r27 folder from step 2.

5. Wait a few seconds and go to http://localhost:8081/ on your browser.

[chrtannus]

Please let me know if that works for you.

[chrtannus]

And if you want to build your own Docker image, you can use this Dockerfile (remove the ".txt" extension first):
Dockerfile.txt

To build the image, just run this command:

sudo docker build -t genemania_website .

[chrtannus]

You can also download the source files (.txt) for the genemania data here: http://genemania.org/data/website/r27-src.tar.gz

[xzhou89]

Thank you very much. I followed your steps to solve my problem. Genemania is great!