<commit_before>/*
 * Copyright 2008-2010 Microarray Informatics Team, EMBL-European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 *
 * For further details of the Gene Expression Atlas project, including source code,
 * downloads and documentation, please see:
 *
 * http://gxa.github.com/gxa
 */

package uk.ac.ebi.gxa.index.builder.service;

import org.apache.solr.client.solrj.SolrServerException;
import uk.ac.ebi.gxa.index.builder.IndexAllCommand;
import uk.ac.ebi.gxa.index.builder.IndexBuilderException;
import uk.ac.ebi.gxa.properties.AtlasProperties;
import uk.ac.ebi.gxa.properties.ResourceFileStorage;

import java.io.IOException;
import java.util.concurrent.Executors;

public class TestGeneAtlasIndexBuilderService extends IndexBuilderServiceTestCase {
    private GeneAtlasIndexBuilderService gaibs;

    public void setUp() throws Exception {
        super.setUp();

        ResourceFileStorage storage = new ResourceFileStorage();
        storage.setResourcePath("atlas.properties");
        AtlasProperties atlasProperties = new AtlasProperties();
        atlasProperties.setStorage(storage);

        gaibs = new GeneAtlasIndexBuilderService();
        gaibs.setAtlasDAO(atlasDAO);
        gaibs.setBioEntityDAO(bioEntityDAO);
        gaibs.setSolrServer(getAtlasSolrServer());
        gaibs.setAtlasProperties(atlasProperties);
        gaibs.setExecutor(Executors.newSingleThreadExecutor());
    }

    public void tearDown() throws Exception {
        super.tearDown();

        gaibs = null;
    }

    public void testCreateIndexDocs() throws IndexBuilderException, IOException, SolrServerException {
        // create the docs
        gaibs.build(new IndexAllCommand(), new IndexBuilderService.ProgressUpdater() {
            public void update(String progress) {
            }
        });
<commit_msg>Mocking AtlasProperties instead of using pre-packaged file<commit_after>/*
 * Copyright 2008-2010 Microarray Informatics Team, EMBL-European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 *
 * For further details of the Gene Expression Atlas project, including source code,
 * downloads and documentation, please see:
 *
 * http://gxa.github.com/gxa
 */

package uk.ac.ebi.gxa.index.builder.service;

import org.apache.solr.client.solrj.SolrServerException;
import uk.ac.ebi.gxa.index.builder.IndexAllCommand;
import uk.ac.ebi.gxa.index.builder.IndexBuilderException;
import uk.ac.ebi.gxa.properties.AtlasProperties;

import java.io.IOException;
import java.util.concurrent.Executors;

import static org.easymock.EasyMock.*;

public class TestGeneAtlasIndexBuilderService extends IndexBuilderServiceTestCase {
    private GeneAtlasIndexBuilderService gaibs;

    public void setUp() throws Exception {
        super.setUp();

        final AtlasProperties atlasProperties = createMock(AtlasProperties.class);
        expect(atlasProperties.getGeneAtlasIndexBuilderChunksize()).andReturn(100);
        expect(atlasProperties.getGeneAtlasIndexBuilderCommitfreq()).andReturn(1000);
        replay(atlasProperties);

        gaibs = new GeneAtlasIndexBuilderService();
        gaibs.setAtlasDAO(atlasDAO);
        gaibs.setBioEntityDAO(bioEntityDAO);
        gaibs.setSolrServer(getAtlasSolrServer());
        gaibs.setAtlasProperties(atlasProperties);
        gaibs.setExecutor(Executors.newSingleThreadExecutor());
    }

    public void tearDown() throws Exception {
        super.tearDown();

        gaibs = null;
    }

    public void testCreateIndexDocs() throws IndexBuilderException, IOException, SolrServerException {
        // create the docs
        gaibs.build(new IndexAllCommand(), new IndexBuilderService.ProgressUpdater() {
            public void update(String progress) {
            }
        });

{'fraction_non_alphanumeric': 0.08458021612635079, 'fraction_numerical': 0.006442227763923524, 'mean_word_length': 3.8420523138832996, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '23157', 'n_tokens_mistral': 1363, 'n_tokens_neox': 1300, 'n_words': 362}