gt:     for (String pmid : pmids) {
context: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program is free software: you can redistribute it and/or modify  *
  *  it under the terms of the GNU General Public License as published by  *
  *  the Free Software Foundation, either version 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program is distributed in the hope that it will be useful,       *
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
  *  GNU General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package act.installer.sequence;
  
  import act.server.MongoDB;
  import act.shared.Organism;
  import act.shared.Reaction;
  import act.shared.Seq;
  import act.shared.helpers.MongoDBToJSON;
  import com.act.biointerpretation.Utils.OrgMinimalPrefixGenerator;
  import com.act.biointerpretation.test.util.MockedMongoDB;
  import com.act.utils.parser.UniprotInterpreter;
  import com.mongodb.DBObject;
  import org.json.JSONArray;
  import org.json.JSONObject;
  import org.junit.Before;
  import org.junit.Test;
  
  import java.io.File;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Collections;
  import java.util.HashMap;
  import java.util.Iterator;
  import java.util.List;
  import java.util.Map;
  
  import static org.junit.Assert.assertEquals;
  
  
  public class UniprotSeqEntryTest {
    private ArrayList<UniprotSeqEntry> seqEntries;
    private ArrayList<String> sequences;
  
    @Before
    public void setUp() throws Exception {
      MockedMongoDB mockAPI = new MockedMongoDB();
  
      Map<Long, String> organismNames = new HashMap<>();
      organismNames.put(4000000399L, "Arabidopsis thaliana");
  
      // manually assemble an Org Iterator since you can't mock DBCollection in getDbIteratorOverOrgs()
      List<Organism> orgs = new ArrayList<>();
      for (Map.Entry<Long, String> orgName : organismNames.entrySet()) {
        orgs.add(new Organism(orgName.getKey(), orgName.getValue()));
      }
  
      Iterator<Organism> orgIterator = orgs.iterator();
  
      OrgMinimalPrefixGenerator prefixGenerator = new OrgMinimalPrefixGenerator(orgIterator);
      Map<String, String> minimalPrefixMapping = prefixGenerator.getMinimalPrefixMapping();
  
      // only information needed for these set of tests is a db with organism id's.
      mockAPI.installMocks(new ArrayList<Reaction>(), new ArrayList<Seq>(), organismNames, new HashMap<>());
  
      MongoDB mockDb = mockAPI.getMockMongoDB();
  
      seqEntries = new ArrayList<>();
      sequences = new ArrayList<>();
  
      UniprotInterpreter upProtein =
          new UniprotInterpreter(new File(this.getClass().getResource("uniprot_test_1.xml").getFile()));
      upProtein.init();
      sequences.add(upProtein.getSequence());
      UniprotSeqEntry seqEntry = new UniprotSeqEntryFactory().createFromDocumentReference(upProtein.getXmlDocument(),
          mockDb, minimalPrefixMapping);
      seqEntries.add(seqEntry);
    }
  
    @Test
    public void testMetadata() {
      ArrayList<DBObject> metadatas = new ArrayList<>();
  
      List<String> uniprotAccessions = Arrays.asList("P06525", "O04080", "O04713", "O04717", "O04868", "O23821", "Q8LA61",
          "Q94AY6", "Q9CAZ2", "Q9CAZ3", "Q9SX08");
  
      List<String> genbankNucleotideAccessions = Arrays.asList("M12196", "X77943", "D84240", "D84241", "D84242", "D84243",
          "D84244", "D84245", "D84246", "D84247", "D84248", "D84249", "D63460", "D63461", "D63462", "D63463", "D63464",
          "AF110456", "AB048394", "AB048395", "AY536888", "AC002291", "CP002684", "AY045612", "AY090330", "AY088010",
          "AF056557");
  
      List<String> genbankProteinAccessions = Arrays.asList("AAA32728", "CAA54911", "BAA19615", "BAA19616", "BAA19617",
          "BAA19618", "BAA19619", "BAA19620", "BAA19621", "BAA19622", "BAA19623", "BAA19624", "BAA22983", "BAA22979",
          "BAA22980", "BAA22981", "BAA22982", "AAF23554", "BAB32568", "BAB32569", "AAS45601", "AAC00625", "AEE35937",
          "AAK73970", "AAL90991", "AAM65556", "AAD41572");
  
      JSONObject accessions = new JSONObject();
      accessions.put(Seq.AccType.uniprot.toString(), new JSONArray(uniprotAccessions));
      accessions.put(Seq.AccType.genbank_nucleotide.toString(), new JSONArray(genbankNucleotideAccessions));
      accessions.put(Seq.AccType.genbank_protein.toString(), new JSONArray(genbankProteinAccessions));
  
      JSONObject obj = new JSONObject();
  
      obj.put("xref", new JSONObject());
      obj.put("name", "ADH1");
      obj.put("synonyms", Collections.singletonList("ADH"));
      obj.put("product_names", Arrays.asList("Alcohol dehydrogenase class-P", "Alc Dehyd"));
      obj.put("accession", accessions);
      obj.put("catalytic_activity", "An alcohol + NAD(+) = an aldehyde or ketone + NADH.");
  
      metadatas.add(MongoDBToJSON.conv(obj));
  
      assertEquals("tests whether metadata is extracted accurately", metadatas.get(0),
          seqEntries.get(0).getMetadata());
    }
  
    @Test
    public void testAccession() {
      List<String> uniprotAccessions = Arrays.asList("P06525", "O04080", "O04713", "O04717", "O04868", "O23821", "Q8LA61",
          "Q94AY6", "Q9CAZ2", "Q9CAZ3", "Q9SX08");
  
      List<String> genbankNucleotideAccessions = Arrays.asList("M12196", "X77943", "D84240", "D84241", "D84242", "D84243",
          "D84244", "D84245", "D84246", "D84247", "D84248", "D84249", "D63460", "D63461", "D63462", "D63463", "D63464",
          "AF110456", "AB048394", "AB048395", "AY536888", "AC002291", "CP002684", "AY045612", "AY090330", "AY088010",
          "AF056557");
  
      List<String> genbankProteinAccessions = Arrays.asList("AAA32728", "CAA54911", "BAA19615", "BAA19616", "BAA19617",
          "BAA19618", "BAA19619", "BAA19620", "BAA19621", "BAA19622", "BAA19623", "BAA19624", "BAA22983", "BAA22979",
          "BAA22980", "BAA22981", "BAA22982", "AAF23554", "BAB32568", "BAB32569", "AAS45601", "AAC00625", "AEE35937",
          "AAK73970", "AAL90991", "AAM65556", "AAD41572");
  
      JSONObject accessions = new JSONObject();
      accessions.put(Seq.AccType.uniprot.toString(), new JSONArray(uniprotAccessions));
      accessions.put(Seq.AccType.genbank_nucleotide.toString(), new JSONArray(genbankNucleotideAccessions));
      accessions.put(Seq.AccType.genbank_protein.toString(), new JSONArray(genbankProteinAccessions));
  
  
      assertEquals("tests whether accession ID is extracted accurately", accessions.toString(),
          seqEntries.get(0).getAccession().toString());
    }
  
    @Test
    public void testGeneName() {
      assertEquals("tests whether gene name is extracted accurately", "ADH1",
          seqEntries.get(0).getGeneName());
    }
  
    @Test
    public void testGeneSynonyms() {
      assertEquals("tests whether gene synonyms are extracted accurately", Collections.singletonList("ADH"),
          seqEntries.get(0).getGeneSynonyms());
    }
  
    @Test
    public void testProductName() {
      assertEquals("tests whether product names are extracted accurately",
          Arrays.asList("Alcohol dehydrogenase class-P", "Alc Dehyd"), seqEntries.get(0).getProductName());
    }
  
    @Test
    public void testCatalyticActivity() {
      assertEquals("tests whether catalytic activity is extracted accurately",
          "An alcohol + NAD(+) = an aldehyde or ketone + NADH.", seqEntries.get(0).getCatalyticActivity());
    }
  
    @Test
    public void testOrgId() {
      assertEquals("tests whether organism ids are extracted accurately", (Long) 4000000399L,
          seqEntries.get(0).getOrgId());
    }
  
    @Test
    public void testOrg() {
      assertEquals("tests whether organism names are extracted accurately", "Arabidopsis thaliana",
          seqEntries.get(0).getOrg());
    }
  
    @Test
    public void testSeq() {
      assertEquals("tests whether sequences are extracted accurately", sequences.get(0),
          seqEntries.get(0).getSeq());
    }
  
    @Test
    public void testEc() {
      assertEquals("tests whether ec_numbers are extracted accurately", "1.1.1.1",
          seqEntries.get(0).getEc());
    }
  
    @Test
    public void testReferences() {
      List<JSONObject> pmidRefs = new ArrayList<>();
  
      List<String> pmids = Arrays.asList("2937058", "7851777", "8844162", "8587508", "11018155", "11158375", "11130712",
          "14593172", "10382288", "3377754", "2277648", "12231733", "8787023", "9522467", "9611167", "9880346",
          "11402191", "11402202", "11987307", "12509334", "12857811", "16055689", "18433157", "18441225", "19245862",
          "20508152", "22223895", "23707506", "24395201", "26566261", "25447145");
  
  