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Commit b8dc95d6 authored by Piotr Gawron's avatar Piotr Gawron
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unnecessary method getByNames removed

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1 merge request!156Resolve "search by chemical names"
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service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java
+ 0
− 12
View file @ b8dc95d6
......@@ -18,18 +18,6 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public interface IDbSearchService<T> {
/**
* Returns list of objects found by list of names.
*
* @param names
* list of object names
* @param searchCriteria
* set of {@link DbSearchCriteria} used for searching (like:
* {@link lcsb.mapviewer.model.map.model.Model Model})
* @return list of objects for given list of names
*/
List<T> getByNames(List<String> names, DbSearchCriteria searchCriteria);
/**
* Returns the drugs found by drug name.
*
......
service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+ 227
− 249
View file @ b8dc95d6
......@@ -31,8 +31,6 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.DbSearchService;
......@@ -45,272 +43,252 @@ import lcsb.mapviewer.services.search.db.DbSearchService;
@Transactional(value = "txManager")
public class ChemicalService extends DbSearchService implements IChemicalService {
/**
* Default class logger.
*/
private Logger logger = Logger.getLogger(ChemicalService.class);
/**
* Default class logger.
*/
private Logger logger = Logger.getLogger(ChemicalService.class);
/**
* List of chemicals pairs of id and name.
*/
private Map<MiriamData, Map<MiriamData, String>> diseases = new HashMap<>();
/**
* List of chemicals pairs of id and name.
*/
private Map<MiriamData, Map<MiriamData, String>> diseases = new HashMap<>();
/**
* Access point and parser for the online ctd database.
*/
@Autowired
private ChemicalParser chemicalParser;
/**
* Access point and parser for the online ctd database.
*/
@Autowired
private ChemicalParser chemicalParser;
/**
* Object used to perform operations on {@link MiriamType#HGNC} annotations.
*/
@Autowired
private HgncAnnotator hgncAnnotator;
/**
* Object used to perform operations on {@link MiriamType#HGNC} annotations.
*/
@Autowired
private HgncAnnotator hgncAnnotator;
/**
* Service that manages search history.
*/
@Autowired
private ISearchHistoryService searchHistoryService;
/**
* Default constructor.
*/
public ChemicalService() {
super();
}
/**
* Default constructor.
*/
public ChemicalService() {
super();
}
/**
* Returns list of {@link Chemical chemicals} for a given disease and list of
* names.
*
* @param diseaseID
* {@link MiriamData} identifying disease; it should be a
* {@link MiriamType#MESH_2012} identifier
* @param names
* list of drug names that we are looking for
* @return list of {@link Chemical chemicals} that were found
*/
protected List<Chemical> getChemicalByName(MiriamData diseaseID, List<String> names) {
if (diseaseID == null || names == null) {
throw new InvalidArgumentException("diseaseID cannot be null");
}
names.removeAll(Collections.singleton(null));
@Override
public List<Chemical> getByNames(List<String> names, DbSearchCriteria criteria) {
if (names == null) {
return null;
}
// Create a map with the each search string and chemical id.
// Remove empty string and special characters.
Map<String, MiriamData> searchNamesMap = new LinkedHashMap<String, MiriamData>();
for (int i = 0; i < names.size(); i++) {
String name = names.get(i).trim().toLowerCase().replaceAll("[^\\w]", "");
if (!name.isEmpty()) {
searchNamesMap.put(name, null);
}
}
try {
if (criteria.getIpAddress() != null && criteria.getModel() != null) {
searchHistoryService.addQuery(names.toString(), SearchType.CHEMICAL, criteria.getIpAddress(), criteria.getModel().getProject().getProjectId());
}
// Search id, name Map for matching records
List<MiriamData> ids = new ArrayList<MiriamData>();
Iterator<Entry<MiriamData, String>> idNameEnteries = getChemicalsByDisease(diseaseID).entrySet().iterator();
int namesFound = 0;
while (idNameEnteries.hasNext() && namesFound < searchNamesMap.size()) {
Map.Entry<MiriamData, String> pair = idNameEnteries.next();
String chemicalName = pair.getValue();
if (chemicalName != null) {
chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
if (nameEntry.getKey().equals(chemicalName)) {
nameEntry.setValue(pair.getKey());
namesFound++;
List<Chemical> chemicals = getChemicalByName(criteria.getDisease(), names);
}
}
return chemicals;
}
}
}
/**
* Returns list of {@link Chemical chemicals} for a given disease and list of
* names.
*
* @param diseaseID
* {@link MiriamData} identifing disease; it should be a
* {@link MiriamType#MESH_2012} identifier
* @param names
* list of drug names that we are looking for
* @return list of {@link Chemical chemicals} that were found
*/
protected List<Chemical> getChemicalByName(MiriamData diseaseID, List<String> names) {
if (diseaseID == null || names == null) {
throw new InvalidArgumentException("diseaseID cannot be null");
}
names.removeAll(Collections.singleton(null));
// Get what all values include null where no matching record is found,
// remove null and look in the database.
ids.addAll(searchNamesMap.values());
ids.removeAll(Collections.singleton(null));
List<Chemical> sortedResult = new ArrayList<Chemical>();
if (!ids.isEmpty()) {
List<Chemical> result = chemicalParser.getChemicals(diseaseID, ids);
// Create a map with the each search string and chemical id.
// Remove empty string and special characters.
Map<String, MiriamData> searchNamesMap = new LinkedHashMap<String, MiriamData>();
for (int i = 0; i < names.size(); i++) {
String name = names.get(i).trim().toLowerCase().replaceAll("[^\\w]", "");
if (!name.isEmpty()) {
searchNamesMap.put(name, null);
}
}
try {
// If the result is not empty and we found chemicals, try to sort as
// by the initial list provided.
Map<MiriamData, Chemical> resultAsMap = new HashMap<MiriamData, Chemical>();
if (result != null && !result.isEmpty()) {
for (Chemical chemo : result) {
resultAsMap.put(chemo.getChemicalId(), chemo);
}
// Search id, name Map for matching records
List<MiriamData> ids = new ArrayList<MiriamData>();
Iterator<Entry<MiriamData, String>> idNameEnteries = getChemicalsByDisease(diseaseID).entrySet().iterator();
int namesFound = 0;
while (idNameEnteries.hasNext() && namesFound < searchNamesMap.size()) {
Map.Entry<MiriamData, String> pair = idNameEnteries.next();
String chemicalName = pair.getValue();
if (chemicalName != null) {
chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
if (nameEntry.getKey().equals(chemicalName)) {
nameEntry.setValue(pair.getKey());
namesFound++;
for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
if (nameEntry.getValue() != null) {
sortedResult.add(resultAsMap.get(nameEntry.getValue()));
}
}
}
}
}
}
return sortedResult;
} catch (ChemicalSearchException e) {
logger.error("Problem with accessing database", e);
return new ArrayList<Chemical>();
}
}
}
}
@Override
public Chemical getByName(String name, DbSearchCriteria searchCriteria) {
if (searchCriteria.getDisease() == null) {
throw new InvalidArgumentException("diseaseID cannot be null");
}
if (name == null || name.isEmpty()) {
return null;
}
MiriamData id = null;
List<Chemical> result = new ArrayList<Chemical>();
name = name.toLowerCase().replaceAll("[^\\w]", "");
try {
Iterator<Entry<MiriamData, String>> mapValues = getChemicalsByDisease(searchCriteria.getDisease()).entrySet()
.iterator();
int shortestName = Integer.MAX_VALUE;
while (mapValues.hasNext()) {
Map.Entry<MiriamData, String> pair = mapValues.next();
String chemicalName = pair.getValue();
if (chemicalName != null) {
chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
if (chemicalName.contains(name) && name.length() < shortestName) {
id = pair.getKey();
shortestName = chemicalName.length();
}
}
}
if (id != null) {
List<MiriamData> chemicalId = new ArrayList<>();
chemicalId.add(id);
result = chemicalParser.getChemicals(searchCriteria.getDisease(), chemicalId);
}
} catch (ChemicalSearchException e) {
logger.error("Problem with accesing database", e);
}
if (result.size() == 0) {
return null;
} else {
// return chemicalViewFactory.create(result.get(0),
// searchCriteria.getModel(), searchCriteria.getColorSet());
return result.get(0);
}
// Get what all values include null where no matching record is found,
// remove null and look in the database.
ids.addAll(searchNamesMap.values());
ids.removeAll(Collections.singleton(null));
List<Chemical> sortedResult = new ArrayList<Chemical>();
if (!ids.isEmpty()) {
List<Chemical> result = chemicalParser.getChemicals(diseaseID, ids);
}
// If the result is not empty and we found chemicals, try to sort as
// by the initial list provided.
Map<MiriamData, Chemical> resultAsMap = new HashMap<MiriamData, Chemical>();
if (result != null && !result.isEmpty()) {
for (Chemical chemo : result) {
resultAsMap.put(chemo.getChemicalId(), chemo);
}
@Override
public List<Chemical> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
List<Chemical> chemicalList = new ArrayList<>();
Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
for (Element alias : targets) {
if (alias instanceof Protein || alias instanceof Gene || alias instanceof Rna) {
boolean hgncFound = false;
for (MiriamData md : alias.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetsMiriam.add(md);
hgncFound = true;
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
// ad also entrez in case of mouse, rat, etc
targetsMiriam.add(md);
}
for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
if (nameEntry.getValue() != null) {
sortedResult.add(resultAsMap.get(nameEntry.getValue()));
}
}
}
}
}
if (!hgncFound) {
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, alias.getName());
try {
if (hgncAnnotator.isValidHgncMiriam(md)) {
targetsMiriam.add(md);
}
} catch (AnnotatorException e) {
logger.error("Problem with accessing HGNC database", e);
}
}
}
}
try {
chemicalList = chemicalParser.getChemicalListByTarget(targetsMiriam, searchCriteria.getDisease());
} catch (ChemicalSearchException e) {
logger.error("Problem with accessing chemical database", e);
}
return sortedResult;
} catch (ChemicalSearchException e) {
logger.error("Problem with accessing database", e);
return new ArrayList<Chemical>();
}
}
Collections.sort(chemicalList, new Chemical.NameComparator());
return chemicalList;
}
@Override
public Chemical getByName(String name, DbSearchCriteria searchCriteria) {
if (searchCriteria.getDisease() == null) {
throw new InvalidArgumentException("diseaseID cannot be null");
}
if (name == null || name.isEmpty()) {
return null;
}
MiriamData id = null;
List<Chemical> result = new ArrayList<Chemical>();
name = name.toLowerCase().replaceAll("[^\\w]", "");
try {
Iterator<Entry<MiriamData, String>> mapValues = getChemicalsByDisease(searchCriteria.getDisease()).entrySet().iterator();
int shortestName = Integer.MAX_VALUE;
while (mapValues.hasNext()) {
Map.Entry<MiriamData, String> pair = mapValues.next();
String chemicalName = pair.getValue();
if (chemicalName != null) {
chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
if (chemicalName.contains(name) && name.length() < shortestName) {
id = pair.getKey();
shortestName = chemicalName.length();
}
}
}
if (id != null) {
List<MiriamData> chemicalId = new ArrayList<>();
chemicalId.add(id);
result = chemicalParser.getChemicals(searchCriteria.getDisease(), chemicalId);
}
} catch (ChemicalSearchException e) {
logger.error("Problem with accesing database", e);
}
if (result.size() == 0) {
return null;
} else {
// return chemicalViewFactory.create(result.get(0),
// searchCriteria.getModel(), searchCriteria.getColorSet());
return result.get(0);
}
/**
* @param disease
* {@link MiriamType#MESH_2012 mesh term} describing disease
*
* @return chemicals related to the disease
* @see #diseases
* @throws ChemicalSearchException
* thrown when there is problem with accessing ctd database
*/
private Map<MiriamData, String> getChemicalsByDisease(MiriamData disease) throws ChemicalSearchException {
if (diseases.get(disease) == null) {
diseases.put(disease, chemicalParser.getChemicalsForDisease(disease));
}
return diseases.get(disease);
}
}
@Override
public List<Chemical> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
List<Chemical> chemicalList = new ArrayList<>();
Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
for (Element alias : targets) {
if (alias instanceof Protein || alias instanceof Gene || alias instanceof Rna) {
boolean hgncFound = false;
for (MiriamData md : alias.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetsMiriam.add(md);
hgncFound = true;
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
// ad also entrez in case of mouse, rat, etc
targetsMiriam.add(md);
}
}
if (!hgncFound) {
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, alias.getName());
try {
if (hgncAnnotator.isValidHgncMiriam(md)) {
targetsMiriam.add(md);
}
} catch (AnnotatorException e) {
logger.error("Problem with accessing HGNC database", e);
}
}
}
}
try {
chemicalList = chemicalParser.getChemicalListByTarget(targetsMiriam, searchCriteria.getDisease());
} catch (ChemicalSearchException e) {
logger.error("Problem with accessing chemical database", e);
}
Collections.sort(chemicalList, new Chemical.NameComparator());
return chemicalList;
}
/**
* @param disease
* {@link MiriamType#MESH_2012 mesh term} describing disease
*
* @return chemicals related to the disease
* @see #diseases
* @throws ChemicalSearchException
* thrown when there is problem with accessing ctd database
*/
private Map<MiriamData, String> getChemicalsByDisease(MiriamData disease) throws ChemicalSearchException {
if (diseases.get(disease) == null) {
diseases.put(disease, chemicalParser.getChemicalsForDisease(disease));
}
return diseases.get(disease);
}
@Override
public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
double progress = 0.0;
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
MiriamData disease = originalModel.getProject().getDisease();
if (disease != null) {
logger.debug("Caching chemical queries...");
Set<MiriamData> targetMiriams = new HashSet<>();
List<Model> models = new ArrayList<>();
models.add(originalModel);
models.addAll(originalModel.getSubmodels());
for (Model model : models) {
for (BioEntity element : model.getBioEntities()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetMiriams.add(md);
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
targetMiriams.add(md);
}
}
}
}
double counter = 0.0;
for (MiriamData md : targetMiriams) {
try {
List<Chemical> chemicalList = chemicalParser.getChemicalListByTarget(md, disease);
for (Chemical chemical : chemicalList) {
cacheMiriamData(chemical);
}
} catch (ChemicalSearchException | AnnotatorException e) {
logger.error("Problem with accessing info about chemical for target: " + md, e);
}
counter += 1;
progress = counter / (double) targetMiriams.size();
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
}
} else {
logger.debug("Caching chemical queries not possible...");
}
}
@Override
public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
double progress = 0.0;
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
MiriamData disease = originalModel.getProject().getDisease();
if (disease != null) {
logger.debug("Caching chemical queries...");
Set<MiriamData> targetMiriams = new HashSet<>();
List<Model> models = new ArrayList<>();
models.add(originalModel);
models.addAll(originalModel.getSubmodels());
for (Model model : models) {
for (BioEntity element : model.getBioEntities()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetMiriams.add(md);
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
targetMiriams.add(md);
}
}
}
}
double counter = 0.0;
for (MiriamData md : targetMiriams) {
try {
List<Chemical> chemicalList = chemicalParser.getChemicalListByTarget(md, disease);
for (Chemical chemical : chemicalList) {
cacheMiriamData(chemical);
}
} catch (ChemicalSearchException | AnnotatorException e) {
logger.error("Problem with accessing info about chemical for target: " + md, e);
}
counter += 1;
progress = counter / (double) targetMiriams.size();
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
}
} else {
logger.debug("Caching chemical queries not possible...");
}
}
}
service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+ 1
− 29
View file @ b8dc95d6
......@@ -72,36 +72,8 @@ public class DrugService extends DbSearchService implements IDrugService {
@Autowired
private ISearchHistoryService searchHistoryService;
@Override
public List<Drug> getByNames(List<String> names, DbSearchCriteria searchCriteria) {
List<Drug> result = new ArrayList<>();
Set<MiriamData> processedDrugIds = new HashSet<>();
int oldSet = searchCriteria.getColorSet();
for (String string : names) {
searchCriteria.colorSet(searchCriteria.getColorSet() + 1);
Drug drug = getByName(string, searchCriteria);
if (drug != null) {
boolean isNewDrug = false;
for (MiriamData id : drug.getSources()) {
if (!processedDrugIds.contains(id)) {
isNewDrug = true;
}
processedDrugIds.add(id);
}
if (isNewDrug) {
result.add(drug);
}
}
}
searchCriteria.colorSet(oldSet);
return result;
}
/**
* Removes targets for unknown orginisms from the drug.
* Removes targets for unknown organisms from the drug.
*
* @param drug
* drug from which we want to remove targets
......
service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
+ 169
− 197
View file @ b8dc95d6
......@@ -28,13 +28,11 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.DbSearchService;
/**
* Implementation of the service that allows access information about che.
* Implementation of the service that allows access information about miRNAs.
*
* @author Ayan Rota
*
......@@ -42,199 +40,173 @@ import lcsb.mapviewer.services.search.db.DbSearchService;
@Transactional(value = "txManager")
public class MiRNAService extends DbSearchService implements IMiRNAService {
/**
* Default class logger.
*/
private Logger logger = Logger.getLogger(MiRNAService.class);
/**
* Access point and parser for the online ctd database.
*/
@Autowired
private MiRNAParser miRNAParser;
/**
* Object used to get information about {@link MiriamType#HGNC} annotations
* and transformations.
*/
@Autowired
private HgncAnnotator hgncAnnotator;
/**
* Service that manages search history.
*/
@Autowired
private ISearchHistoryService searchHistoryService;
/**
* Default constructor.
*/
public MiRNAService() {
super();
}
/**
* Init method called after intialization of spring bean.
*/
@PostConstruct
public void init() {
}
@Override
public List<MiRNA> getByNames(List<String> names, DbSearchCriteria criteria) {
if (names == null) {
return null;
}
if (criteria.getIpAddress() != null && criteria.getModel() != null) {
searchHistoryService.addQuery(names.toString(), SearchType.MI_RNA, criteria.getIpAddress(), criteria.getModel().getProject().getProjectId());
}
List<MiRNA> views = new ArrayList<>();
try {
List<MiRNA> miRNAs = miRNAParser.getMiRnasByNames(names);
for (MiRNA miRNA : miRNAs) {
views.add(miRNA);
}
} catch (MiRNASearchException e) {
logger.error("Problem with accessing mirna database", e);
}
return views;
}
@Override
public MiRNA getByName(String name, DbSearchCriteria searchCriteria) {
if ("".equals(name)) {
return null;
}
try {
List<String> names = new ArrayList<>();
names.add(name);
List<MiRNA> miRNAs = miRNAParser.getMiRnasByNames(names);
if (miRNAs.size() > 0) {
return miRNAs.get(0);
}
return null;
// return miRNAViewFactory.create(miRNAs.get(0),
// searchCriteria.getModel(), searchCriteria.getColorSet());
} catch (MiRNASearchException e) {
logger.error("Problem with accessing mirna database", e);
return null;
}
}
@Override
public List<MiRNA> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
List<MiRNA> mirnaList = new ArrayList<MiRNA>();
Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
for (Element element : targets) {
if (element instanceof Protein || element instanceof Gene || element instanceof Rna) {
boolean hgncFound = false;
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetsMiriam.add(md);
hgncFound = true;
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
// ad also entrez in case of mouse, rat, etc
targetsMiriam.add(md);
}
}
if (!hgncFound) {
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
try {
if (hgncAnnotator.isValidHgncMiriam(md)) {
targetsMiriam.add(md);
}
} catch (AnnotatorException e) {
logger.error("Problem with accessing HGNC database", e);
}
}
}
}
try {
mirnaList = miRNAParser.getMiRnaListByTargets(targetsMiriam);
} catch (MiRNASearchException e) {
logger.error("Problem with accessing mirna database", e);
}
for (MiRNA drug : mirnaList) {
removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
}
Collections.sort(mirnaList, new MiRNA.NameComparator());
return mirnaList;
}
/**
* Removes targets for unknown organisms from the mirna.
*
* @param drug
* drug from which we want to remove targets
* @param organisms
* organisms that should be kept
*/
private void removeUnknownOrganisms(MiRNA drug, List<MiriamData> organisms) {
if (organisms.size() > 0) {
List<Target> toRemove = new ArrayList<Target>();
for (Target target : drug.getTargets()) {
boolean remove = true;
for (MiriamData organism : organisms) {
if (target.getOrganism() == null) {
remove = false;
} else if (target.getOrganism().equals(organism)) {
remove = false;
}
}
if (remove) {
logger.debug("Target " + target.getName() + " removed from list because results are limited to organisms: " + organisms);
toRemove.add(target);
}
}
drug.getTargets().removeAll(toRemove);
}
}
@Override
public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
logger.debug("Caching mirna queries...");
double progress = 0.0;
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
Set<MiriamData> targetMiriams = new HashSet<>();
List<Model> models = new ArrayList<>();
models.add(originalModel);
models.addAll(originalModel.getSubmodels());
for (Model model : models) {
for (BioEntity element : model.getBioEntities()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetMiriams.add(md);
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
targetMiriams.add(md);
}
}
}
}
double counter = 0.0;
int step = Math.max(targetMiriams.size() / 100, 1);
List<MiriamData> currentList = new ArrayList<>();
for (MiriamData md : targetMiriams) {
counter += 1;
currentList.add(md);
if (currentList.size() >= step) {
logger.debug("check mirna target: " + currentList);
try {
List<MiRNA> chemicalList = miRNAParser.getMiRnaListByTargets(currentList);
for (MiRNA chemical : chemicalList) {
cacheMiriamData(chemical);
}
} catch (MiRNASearchException | AnnotatorException e) {
logger.error("Problem with accessing info about mirna for target: " + md, e);
}
progress = counter / (double) targetMiriams.size();
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
currentList.clear();
}
}
}
/**
* Default class logger.
*/
private Logger logger = Logger.getLogger(MiRNAService.class);
/**
* Access point and parser for the online ctd database.
*/
@Autowired
private MiRNAParser miRNAParser;
/**
* Object used to get information about {@link MiriamType#HGNC} annotations and
* transformations.
*/
@Autowired
private HgncAnnotator hgncAnnotator;
/**
* Default constructor.
*/
public MiRNAService() {
super();
}
/**
* Init method called after initialization of spring bean.
*/
@PostConstruct
public void init() {
}
@Override
public MiRNA getByName(String name, DbSearchCriteria searchCriteria) {
if ("".equals(name)) {
return null;
}
try {
List<String> names = new ArrayList<>();
names.add(name);
List<MiRNA> miRNAs = miRNAParser.getMiRnasByNames(names);
if (miRNAs.size() > 0) {
return miRNAs.get(0);
}
return null;
// return miRNAViewFactory.create(miRNAs.get(0),
// searchCriteria.getModel(), searchCriteria.getColorSet());
} catch (MiRNASearchException e) {
logger.error("Problem with accessing mirna database", e);
return null;
}
}
@Override
public List<MiRNA> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
List<MiRNA> mirnaList = new ArrayList<MiRNA>();
Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
for (Element element : targets) {
if (element instanceof Protein || element instanceof Gene || element instanceof Rna) {
boolean hgncFound = false;
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetsMiriam.add(md);
hgncFound = true;
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
// ad also entrez in case of mouse, rat, etc
targetsMiriam.add(md);
}
}
if (!hgncFound) {
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
try {
if (hgncAnnotator.isValidHgncMiriam(md)) {
targetsMiriam.add(md);
}
} catch (AnnotatorException e) {
logger.error("Problem with accessing HGNC database", e);
}
}
}
}
try {
mirnaList = miRNAParser.getMiRnaListByTargets(targetsMiriam);
} catch (MiRNASearchException e) {
logger.error("Problem with accessing mirna database", e);
}
for (MiRNA drug : mirnaList) {
removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
}
Collections.sort(mirnaList, new MiRNA.NameComparator());
return mirnaList;
}
/**
* Removes targets for unknown organisms from the mirna.
*
* @param drug
* drug from which we want to remove targets
* @param organisms
* organisms that should be kept
*/
private void removeUnknownOrganisms(MiRNA drug, List<MiriamData> organisms) {
if (organisms.size() > 0) {
List<Target> toRemove = new ArrayList<Target>();
for (Target target : drug.getTargets()) {
boolean remove = true;
for (MiriamData organism : organisms) {
if (target.getOrganism() == null) {
remove = false;
} else if (target.getOrganism().equals(organism)) {
remove = false;
}
}
if (remove) {
logger.debug("Target " + target.getName() + " removed from list because results are limited to organisms: "
+ organisms);
toRemove.add(target);
}
}
drug.getTargets().removeAll(toRemove);
}
}
@Override
public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
logger.debug("Caching mirna queries...");
double progress = 0.0;
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
Set<MiriamData> targetMiriams = new HashSet<>();
List<Model> models = new ArrayList<>();
models.add(originalModel);
models.addAll(originalModel.getSubmodels());
for (Model model : models) {
for (BioEntity element : model.getBioEntities()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetMiriams.add(md);
} else if (MiriamType.ENTREZ.equals(md.getDataType())) {
targetMiriams.add(md);
}
}
}
}
double counter = 0.0;
int step = Math.max(targetMiriams.size() / 100, 1);
List<MiriamData> currentList = new ArrayList<>();
for (MiriamData md : targetMiriams) {
counter += 1;
currentList.add(md);
if (currentList.size() >= step) {
logger.debug("check mirna target: " + currentList);
try {
List<MiRNA> chemicalList = miRNAParser.getMiRnaListByTargets(currentList);
for (MiRNA chemical : chemicalList) {
cacheMiriamData(chemical);
}
} catch (MiRNASearchException | AnnotatorException e) {
logger.error("Problem with accessing info about mirna for target: " + md, e);
}
progress = counter / (double) targetMiriams.size();
iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
currentList.clear();
}
}
}
}
service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java
+ 0
− 32
View file @ b8dc95d6
......@@ -31,38 +31,6 @@ public class ChemicalServiceTest extends ServiceTestFunctions {
public void tearDown() throws Exception {
}
/**
* @throws Exception
*/
@Test
public void testgetPDChemicalByName() throws Exception {
try {
List<Chemical> result = null;
MiriamData pdDiseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
List<String> names = new ArrayList<String>();
names.add("Dopamine");
names.add("2-(2-furanyl)-7-(2-(4-(4-(2-methoxyethoxy)phenyl)-1-piperazinyl)ethyl)-7H-pyrazolo(4,3-e)(1,2,4)triazolo(1,5-c)pyrimidine-5-amine");
names.add("Anti-Inflammatory Agents, Non-Steroidal");
names.add("2-furanyl");
names.add(null);
result = chemicalService.getByNames(names, new DbSearchCriteria().disease(pdDiseaseID));
assertNotNull(result);
assertTrue(!result.isEmpty());
assertTrue(result.size() == 3);
names.clear();
names.add("2-furanyl");
result = chemicalService.getByNames(names, new DbSearchCriteria().disease(pdDiseaseID));
assertNotNull(result);
assertTrue(result.isEmpty());
assertEquals("No warnings expected.", 0, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testgetPDChemicalByName2() throws Exception {
try {
......
service/src/test/java/lcsb/mapviewer/services/search/db/mirna/MiRNAServiceTest.java
+ 31
− 56
View file @ b8dc95d6
package lcsb.mapviewer.services.search.db.mirna;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.data.MiRNA;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
public class MiRNAServiceTest extends ServiceTestFunctions {
Logger logger = Logger.getLogger(MiRNAServiceTest.class);
@Autowired
protected IMiRNAService miRNAService;
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
@Test
public void testgetMiRNAByID() throws Exception {
try {
List<MiRNA> result = null;
List<String> idStrings = new ArrayList<String>();
idStrings.add("hsa-miR-122-5p");
idStrings.add("hsa-miR-32-5p");
result = miRNAService.getByNames(idStrings, new DbSearchCriteria());
assertNotNull(result);
assertTrue(!result.isEmpty());
assertTrue(result.size() == 2);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testCacheStub() throws Exception {
try {
// CellDesignerXmlParser parser = new CellDesignerXmlParser();
// Model model = parser.createModel(new
// ConverterParams().filename("testFiles/pd_full/PD_130909.xml"));
Model model = new ModelFullIndexed(null);
miRNAService.cacheDataForModel(model, new IProgressUpdater() {
@Override
public void setProgress(double progress) {
logger.debug("Progress: " + progress);
}
});
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
Logger logger = Logger.getLogger(MiRNAServiceTest.class);
@Autowired
protected IMiRNAService miRNAService;
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
@Test
public void testCacheStub() throws Exception {
try {
// CellDesignerXmlParser parser = new CellDesignerXmlParser();
// Model model = parser.createModel(new
// ConverterParams().filename("testFiles/pd_full/PD_130909.xml"));
Model model = new ModelFullIndexed(null);
miRNAService.cacheDataForModel(model, new IProgressUpdater() {
@Override
public void setProgress(double progress) {
logger.debug("Progress: " + progress);
}
});
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
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