org.molgenis.ontology.initializer.OntologyScriptInitializerImpl Maven / Gradle / Ivy

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package org.molgenis.ontology.initializer;

import static java.util.Objects.requireNonNull;
import static org.molgenis.script.core.ScriptMetadata.SCRIPT;
import static org.molgenis.script.core.ScriptParameterMetadata.SCRIPT_PARAMETER;

import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UncheckedIOException;
import java.util.Arrays;
import org.molgenis.data.DataService;
import org.molgenis.data.Entity;
import org.molgenis.data.UnknownEntityException;
import org.molgenis.data.support.QueryImpl;
import org.molgenis.script.core.Script;
import org.molgenis.script.core.ScriptFactory;
import org.molgenis.script.core.ScriptMetadata;
import org.molgenis.script.core.ScriptParameterFactory;
import org.molgenis.script.core.ScriptParameterMetadata;
import org.molgenis.script.core.ScriptTypeMetadata;
import org.molgenis.security.core.runas.RunAsSystem;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.ClassPathResource;
import org.springframework.core.io.Resource;
import org.springframework.stereotype.Service;
import org.springframework.util.FileCopyUtils;

@Service
public class OntologyScriptInitializerImpl implements OntologyScriptInitializer {
  private static final String ROC_CURVE_SCRIPT_NAME = "roc";
  private static final String ROC_CURVE_SCRIPT_PARAMETER = "filePath";
  private static final Logger LOG = LoggerFactory.getLogger(OntologyScriptInitializerImpl.class);

  private final DataService dataService;
  private final ScriptFactory scriptFactory;
  private final ScriptParameterFactory scriptParameterFactory;
  private final ScriptMetadata scriptMetaData;

  public OntologyScriptInitializerImpl(
      DataService dataService,
      ScriptFactory scriptFactory,
      ScriptParameterFactory scriptParameterFactory,
      ScriptMetadata scriptMetaData) {
    this.dataService = requireNonNull(dataService);
    this.scriptFactory = requireNonNull(scriptFactory);
    this.scriptParameterFactory = requireNonNull(scriptParameterFactory);
    this.scriptMetaData = requireNonNull(scriptMetaData);
  }

  @Override
  @RunAsSystem
  public void initialize() {
    Resource resource = new ClassPathResource("roc-curve.R");
    if (resource.exists()) {
      long count =
          dataService.count(
              SCRIPT, new QueryImpl<>().eq(ScriptMetadata.NAME, ROC_CURVE_SCRIPT_NAME));
      if (count == 0) {
        Entity scriptType =
            dataService.findOne(
                ScriptTypeMetadata.SCRIPT_TYPE, new QueryImpl<>().eq(ScriptTypeMetadata.NAME, "R"));

        if (scriptType == null)
          throw new UnknownEntityException(
              scriptMetaData, scriptMetaData.getAttribute(ScriptMetadata.NAME), "R");

        String scriptContent;
        try {
          scriptContent =
              FileCopyUtils.copyToString(new InputStreamReader(resource.getInputStream(), "UTF-8"));

        } catch (IOException e) {
          throw new UncheckedIOException(e);
        }

        if (dataService.count(
                SCRIPT_PARAMETER,
                new QueryImpl<>().eq(ScriptParameterMetadata.NAME, ROC_CURVE_SCRIPT_PARAMETER))
            == 0) {
          dataService.add(
              SCRIPT_PARAMETER,
              scriptParameterFactory.create().setName(ROC_CURVE_SCRIPT_PARAMETER));
        }

        Entity scriptParameterEntity =
            dataService.findOne(
                SCRIPT_PARAMETER,
                new QueryImpl<>().eq(ScriptParameterMetadata.NAME, ROC_CURVE_SCRIPT_PARAMETER));

        Script script = scriptFactory.create();
        script.setName(ROC_CURVE_SCRIPT_NAME);
        script.setGenerateToken(true);
        script.set(ScriptMetadata.TYPE, scriptType);
        script.setResultFileExtension("png");
        script.setContent(scriptContent);
        script.set(ScriptMetadata.PARAMETERS, Arrays.asList(scriptParameterEntity));
        dataService.add(SCRIPT, script);

        LOG.info("Script entity \"roc\" has been added to the database!");
      } else {
        LOG.info("Script entity \"roc\" already exists in the database!");
      }
    } else {
      LOG.info("R script \"roc-curve.R\" does not exist on classpath!");
    }
  }
}