/**
* Finds the <code>Syn_GenesDAO</code> identified by <code>
* id_syn_genesTarget</code> by searching the genesDAO's <code>Syn_GenesDAO
* </code> collection. Returns the object if found; null otherwise.
*
* @param genesDAO the <code>GenesDAO</code>containing the <code>Syn_GenesDAO
* </code> collection
* @param id_syn the id_syn to match
* @return The object if found; null otherwise.
*/
public static Syn_GenesDAO findSyn_genesDAO(GenesDAO genesDAO, int id_syn) {
if (genesDAO.getSynonyms() == null) return null;
Iterator<Syn_GenesDAO> syn_genesIterator = genesDAO.getSynonyms().iterator();
while (syn_genesIterator.hasNext()) {
Syn_GenesDAO itSyn_genesDAO = syn_genesIterator.next();
if (itSyn_genesDAO.getId_syn() == id_syn) {
return itSyn_genesDAO;
}
}
return null;
}
/**
* Returns a <code>List<String></code> of distinct gene ids suitable for autocomplete
* sourcing.
*
* @return a <code>List<String></code> of gene ids suitable for autocomplete sourcing.
*/
public List<String> getGeneIds() {
List<GenesDAO> genesDAOList = getGenes();
List<String> targetList = new ArrayList();
if (genesDAOList != null) {
for (GenesDAO genesDAO : genesDAOList) {
String sId_gene = Integer.toString(genesDAO.getId_gene());
targetList.add(Utils.wrap(sId_gene, "\""));
}
}
logger.debug("targetList count = " + targetList.size());
return targetList;
}
/**
* Adds a new synonym to the gene identified by <code>gene</code>.
*
* @param gene the <code>GenesDAO</code> instance to which the new synonym is to be added
* @return the new <code>Syn_GenesDAO</code> instance.
*/
public Syn_GenesDAO addSynonym(GenesDAO gene) {
synchronized (gene) {
Set<Syn_GenesDAO> syn_genesDAOSet = gene.getSynonyms();
if (syn_genesDAOSet == null) {
syn_genesDAOSet = new LinkedHashSet();
gene.setSynonyms(syn_genesDAOSet);
}
Syn_GenesDAO syn_genesDAO = new Syn_GenesDAO();
syn_genesDAO.setLast_change(new Date());
syn_genesDAO.setUsername("EMMA");
syn_genesDAO.setGenes(gene);
gene.getSynonyms().add(syn_genesDAO);
save(gene);
return syn_genesDAO;
}
}
/**
* Saves the given <code>GenesDAO</code> gene
*
* @param gene the <code>GenesDAO</code> to be saved
*/
public void save(GenesDAO gene) {
Session session = factory.getCurrentSession();
Integer centimorgan = Utils.tryParseInt(gene.getCentimorgan());
gene.setCentimorgan(
centimorgan == null
? null
: centimorgan
.toString()); // Centimorgans are numeric, nullable in the database, so re-map any
// non-numeric values to null.
SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
String currentTimestamp = dateFormat.format(new Date());
gene.setLast_change(currentTimestamp);
gene.setUsername("EMMA");
try {
session.beginTransaction();
session.saveOrUpdate(gene);
session.getTransaction().commit();
} catch (HibernateException e) {
session.getTransaction().rollback();
throw e;
}
}
/**
* Deletes the synonym identified by the primary key <code>id_syn</code> from the <code>GenesDAO
* </code> object identified by <code>gene</code>.
*
* @param gene the gene from which the synonym is to be deleted
* @param id_syn the primary key of the synonym to be deleted
*/
public void deleteSynonym(GenesDAO gene, int id_syn) {
Session session = factory.getCurrentSession();
if (gene == null) return;
synchronized (gene) {
Syn_GenesDAO syn_genesDAO = findSyn_genesDAO(gene, id_syn);
if (syn_genesDAO != null) {
gene.getSynonyms().remove(syn_genesDAO);
try {
session.beginTransaction();
session.delete(syn_genesDAO);
session.getTransaction().commit();
} catch (HibernateException e) {
session.getTransaction().rollback();
}
}
}
}
/**
* Remaps null fields to empty strings suitable for use in the client.
*
* @param genesDAO the instance to remap
* @return the same instance, with nulls remapped to empty strings.
*/
private GenesDAO remapNulls(GenesDAO genesDAO) {
// Re-map null fields to empty strings.
if (genesDAO != null) {
if (genesDAO.getCentimorgan() == null) genesDAO.setCentimorgan("");
if (genesDAO.getChromosome() == null) genesDAO.setChromosome("");
if (genesDAO.getCytoband() == null) genesDAO.setCytoband("");
if (genesDAO.getEnsembl_ref() == null) genesDAO.setEnsembl_ref("");
if (genesDAO.getFounder_line_number() == null) genesDAO.setFounder_line_number("");
if (genesDAO.getLast_change() == null) genesDAO.setLast_change("");
if (genesDAO.getMgi_ref() == null) genesDAO.setMgi_ref("");
if (genesDAO.getName() == null) genesDAO.setName("");
if (genesDAO.getPlasmid_construct() == null) genesDAO.setPlasmid_construct("");
if (genesDAO.getPromoter() == null) genesDAO.setPromoter("");
if (genesDAO.getSpecies() == null) genesDAO.setSpecies("");
if (genesDAO.getSymbol() == null) genesDAO.setSymbol("");
if (genesDAO.getUsername() == null) genesDAO.setUsername("");
}
return genesDAO;
}
/**
* Transforms a <code>List<GenesDAO></code> to a JSON string.
*
* @param genesDAOList the list to be transformed
* @return the transformed JSON string
*/
public static String toJSON(List<GenesDAO> genesDAOList) {
JSONArray jsonList = new JSONArray();
for (GenesDAO gene : genesDAOList) {
JSONObject jsonGeneDAO = new JSONObject();
jsonGeneDAO.put("centimorgan", gene.getCentimorgan() == null ? "" : gene.getCentimorgan());
jsonGeneDAO.put("chromosome", gene.getChromosome() == null ? "" : gene.getChromosome());
jsonGeneDAO.put("cytoband", gene.getCytoband() == null ? "" : gene.getCytoband());
jsonGeneDAO.put("ensembl_ref", gene.getEnsembl_ref() == null ? "" : gene.getEnsembl_ref());
jsonGeneDAO.put(
"founder_line_number",
gene.getFounder_line_number() == null ? "" : gene.getFounder_line_number());
jsonGeneDAO.put("id_gene", Integer.toString(gene.getId_gene()));
jsonGeneDAO.put("mgi_ref", gene.getMgi_ref() == null ? "" : gene.getMgi_ref());
jsonGeneDAO.put("name", gene.getName() == null ? "" : gene.getName());
jsonGeneDAO.put(
"plasmid_construct",
gene.getPlasmid_construct() == null ? "" : gene.getPlasmid_construct());
jsonGeneDAO.put("promoter", gene.getPromoter() == null ? "" : gene.getPromoter());
jsonGeneDAO.put("species", gene.getSpecies() == null ? "" : gene.getSpecies());
jsonGeneDAO.put("symbol", gene.getSymbol() == null ? "" : gene.getSymbol());
if ((gene.getSynonyms() != null) && (gene.getSynonyms().size() > 0)) {
JSONArray synonyms = new JSONArray();
Iterator<Syn_GenesDAO> iterator = gene.getSynonyms().iterator();
while (iterator.hasNext()) {
Syn_GenesDAO syn_genesDAO = iterator.next();
JSONObject synonym = new JSONObject();
synonym.put("id_syn", Integer.toString(syn_genesDAO.getId_syn()));
synonym.put("name", syn_genesDAO.getName());
synonym.put("symbol", syn_genesDAO.getSymbol());
synonyms.add(synonym);
}
jsonGeneDAO.put("synonyms", synonyms);
}
jsonList.add(jsonGeneDAO);
}
// Gson dosn't reserve space for fields with null values!!!!
//////// Gson gson = new Gson();
//////// String s = gson.toJson(genesDAOList);
//////// System.out.println(s);
//////// return s;
return jsonList.toString();
}
