From b8dc95d6629802297cfd42746fce5febf7768e46 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 16 Jan 2018 12:53:37 +0100
Subject: [PATCH] unnecessary method getByNames removed
---
.../services/search/db/IDbSearchService.java | 12 -
.../search/db/chemical/ChemicalService.java | 476 +++++++++---------
.../services/search/db/drug/DrugService.java | 30 +-
.../search/db/mirna/MiRNAService.java | 366 +++++++-------
.../db/chemical/ChemicalServiceTest.java | 32 --
.../search/db/mirna/MiRNAServiceTest.java | 87 ++--
6 files changed, 428 insertions(+), 575 deletions(-)
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java
index bfacf6371b..b3630c46ab 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java
@@ -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.
*
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
index 94eaaef9c4..6ff3510b5a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
@@ -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...");
+ }
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index 275dd76631..c3217f0a99 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -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
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
index a859f321b0..526459bdab 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
@@ -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();
+ }
+ }
+ }
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java
index b0eb8bd661..daecc44c3e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java
@@ -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 {
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/mirna/MiRNAServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/mirna/MiRNAServiceTest.java
index c4bd306e27..f623d5349f 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/mirna/MiRNAServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/mirna/MiRNAServiceTest.java
@@ -1,72 +1,47 @@
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;
+ }
+ }
}
--
GitLab