uk.ac.ebi.phis.service.ChannelService.java Source code

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Here is the source code for uk.ac.ebi.phis.service.ChannelService.java

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/*******************************************************************************
 * Copyright 2015 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.
 *******************************************************************************/
package uk.ac.ebi.phis.service;

import java.io.IOException;
import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.List;

import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.client.solrj.response.FacetField.Count;

import uk.ac.ebi.phis.solrj.dto.ChannelDTO;
import uk.ac.ebi.phis.solrj.dto.ImageDTO;
import uk.ac.ebi.phis.solrj.dto.RoiDTO;
import uk.ac.ebi.phis.utils.web.JSONRestUtil;

public class ChannelService extends BasicService {

    public ChannelService(String solrUrl) {

        super(solrUrl);
    }

    public void deleteAssociatedRoi(RoiDTO roi) {

        String roiId = roi.getId();
        List<String> channelIds = roi.getAssociatedChannel();
        if (channelIds != null) {
            for (String channelId : channelIds) {
                ChannelDTO channel = getChannelBean(channelId);
                while (channel.getAssociatedRoi().contains(roiId)) {
                    channel.getAssociatedRoi().remove(roiId);
                }
                List<ChannelDTO> docs = new ArrayList<>();
                docs.add(channel);
                addBeans(docs);
            }
        }
    }

    public void addAssociatedRoi(RoiDTO roi) {
        String roiId = roi.getId();
        List<String> channelIds = roi.getAssociatedChannel();
        if (channelIds != null) {
            for (String channelId : channelIds) {
                ChannelDTO channel = getChannelBean(channelId);
                channel.addAssociatedRoi(roiId);
                List<ChannelDTO> docs = new ArrayList<>();
                docs.add(channel);
                addBeans(docs);
            }
        }
    }

    public ChannelDTO getChannelBean(String channelId) {
        ChannelDTO channel = null;

        SolrQuery solrQuery = new SolrQuery();
        channelId = handleSpecialCharacters(channelId);
        solrQuery.setQuery(ChannelDTO.ID + ":\"" + channelId + "\"");
        solrQuery.set("wt", "json");
        try {
            QueryResponse result = solr.query(solrQuery);
            if (result.getBeans(ChannelDTO.class).size() > 0) {
                // should have only one anyway as ids are unique
                channel = result.getBeans(ChannelDTO.class).get(0);
            }
        } catch (SolrServerException e) {
            e.printStackTrace();
        }
        return channel;
    }

    public String getChannelAsJsonString(String channelId, Integer resNo) {
        SolrQuery solrQuery = new SolrQuery();
        channelId = handleSpecialCharacters(channelId);
        solrQuery.setQuery(ChannelDTO.ID + ":\"" + channelId + "\"");
        if (resNo != null) {
            solrQuery.setRows(resNo);
        } else {
            solrQuery.setRows(10000);
        }
        solrQuery.set("wt", "json");

        System.out.println("------ ChannelPojo" + getQueryUrl(solrQuery));

        try {
            return JSONRestUtil.getResults(getQueryUrl(solrQuery)).toString();
        } catch (IOException e) {
            e.printStackTrace();
        } catch (URISyntaxException e) {
            e.printStackTrace();
        }

        return "Couldn't get anything back from solr.";
    }

    public String getChannels(String imageId, Integer resNo) {

        SolrQuery solrQuery = new SolrQuery();
        imageId = handleSpecialCharacters(imageId);
        solrQuery.setQuery(ChannelDTO.ASSOCIATED_IMAGE + ":\"" + imageId + "\"");

        if (resNo != null) {
            solrQuery.setRows(resNo);
        } else {
            solrQuery.setRows(10000);
        }
        solrQuery.set("wt", "json");

        try {
            return JSONRestUtil.getResults(getQueryUrl(solrQuery)).toString();
        } catch (IOException e) {
            e.printStackTrace();
        } catch (URISyntaxException e) {
            e.printStackTrace();
        }

        return "getChannels : Couldn't get anything back from solr.";
    }

    public void addBeans(List<ChannelDTO> docs) {

        try {
            solr.addBeans(docs);
            solr.commit();
        } catch (SolrServerException | IOException e) {
            e.printStackTrace();
        }
    }

    public String getQueryUrl(SolrQuery q) {
        return solr.getBaseURL() + "/select?" + q.toString();
    }

    /**
     * Removes all documents from the core
     * 
     * @throws IOException
     * @throws SolrServerException
     */
    public void clear() throws SolrServerException, IOException {

        solr.deleteByQuery("*:*");
        solr.commit();
    }

    /**
     * @since 2015/08/18
     * @return
     * @throws SolrServerException
     */
    public List<String> getGeneIds() throws SolrServerException {

        List<String> geneIds = new ArrayList<>();

        SolrQuery q = new SolrQuery().setQuery("*:*").setRows(0).setFacet(true).addFacetField(ChannelDTO.GENE_ID)
                .setFacetMinCount(1).setFacetLimit(-1);

        QueryResponse res = solr.query(q);
        if (res.getFacetField(ChannelDTO.GENE_ID).getValues() != null) {
            for (Count count : res.getFacetField(ChannelDTO.GENE_ID).getValues()) {
                geneIds.add(count.getName());
            }
        }

        return geneIds;
    }

}