diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
index 12fe9ea91eea4b505af030f87c71316b8c70b480..9b8a4b46d8ea687d8cd0acedcca6de44495b2cec 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
@@ -374,4 +374,10 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
return result;
}
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ //we don't provide example because this annotator is unstable
+ return null;
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
index 919bbde0584c00ecb23c4c03d24d243e3ce0661b..efd4655e13a2ecec421fccda25480bd8adc5b2ee 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
@@ -58,7 +58,7 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
this.setCache(null);
try {
- Collection<MiriamData> mds = new UniprotAnnotator().uniProtToEC(new MiriamData(MiriamType.UNIPROT, "P12345"));
+ Collection<MiriamData> mds = new UniprotAnnotator().uniProtToEC(getExampleValidAnnotation());
status.setStatus(ExternalServiceStatusType.OK);
List<String> ecs = new ArrayList<>();
@@ -139,4 +139,9 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
return Arrays.asList(new AnnotatorOutputParameter(MiriamType.BRENDA));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "P12345");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
index 8a093027246be94944fe8841f868e3afb20ee5b5..b8af336bafb2cc11ece7adea5bd6509d82bcf451 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
@@ -66,7 +66,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
this.setCache(null);
try {
- MiriamData md = uniprotToCazy(new MiriamData(MiriamType.UNIPROT, "Q9SG95"));
+ MiriamData md = uniprotToCazy(getExampleValidAnnotation());
status.setStatus(ExternalServiceStatusType.OK);
if (md == null || !md.getResource().equalsIgnoreCase("GH5_7")) {
@@ -197,4 +197,9 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
return Arrays.asList(new AnnotatorOutputParameter(MiriamType.CAZY));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "Q9SG95");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
index 09d45bfcc84f3a0acad0bc3f441537a94c167b46..c095623c4b45a530b4d7af255c8c43a8f2289671 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
@@ -503,4 +503,9 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
new AnnotatorOutputParameter(BioEntityField.SYNONYMS));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.CHEBI, "CHEBI:15377");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index 38eb3a3c61ff90ae66188f49fe340cacdab18f8a..b75cb06b1e868d7c0558589113cf7b52872711e2 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -675,4 +675,5 @@ public abstract class ElementAnnotator extends CachableInterface {
return result;
}
+ public abstract MiriamData getExampleValidAnnotation();
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index 6e2e95f57937c86b031ee561ae6d0df2d52b87b7..a210054044c054dbbc99706a58b13be1f6888c72 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -91,7 +91,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
try {
GenericProtein proteinAlias = new GenericProtein("mock_id");
- proteinAlias.addMiriamData(new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764"));
+ proteinAlias.addMiriamData(getExampleValidAnnotation());
annotateElement(proteinAlias);
if (proteinAlias.getFullName() == null || proteinAlias.getFullName().isEmpty()) {
@@ -241,4 +241,9 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
new AnnotatorOutputParameter(BioEntityField.SYNONYMS));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
index 88d533adf84717a51e0834d77a2cdfd9fd2a3bf4..9917aa2701c02d1cc03eaceefbf6eb3d1cad2d19 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
@@ -121,8 +121,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
try {
GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias
- .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.ENTREZ, "9999"));
+ proteinAlias.addMiriamData(getExampleValidAnnotation());
annotateElement(proteinAlias);
if (proteinAlias.getFullName() == null || proteinAlias.getFullName().equals("")) {
@@ -336,4 +335,9 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
new AnnotatorOutputParameter(BioEntityField.SYNONYMS));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.ENTREZ, "9999");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index c39be0d4f1a388313f75eede4cc8bafc44402185..f591cbc58c6ad142f77057a470d5f99f3314baaa 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -171,8 +171,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
try {
Compartment compartment = new Compartment("some_id");
- compartment
- .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
+ compartment.addMiriamData(getExampleValidAnnotation());
annotateElement(compartment);
if (compartment.getFullName() == null || compartment.getFullName().equals("")) {
@@ -239,4 +238,9 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
new AnnotatorOutputParameter(BioEntityField.DESCRIPTION));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.GO, "GO:0046902");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index 23ab1ec83bbd0919f93788f070b27d06f1048e4a..33654f8d39dd4c0939ce17d59934f1ac448ef0fc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -21,7 +21,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
@@ -79,8 +78,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
try {
GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias
- .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.HGNC_SYMBOL, "SNCA"));
+ proteinAlias.addMiriamData(getExampleValidAnnotation());
annotateElement(proteinAlias);
if (proteinAlias.getFullName() == null || proteinAlias.getFullName().equals("")) {
@@ -444,4 +442,9 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
new AnnotatorOutputParameter(BioEntityField.FULL_NAME));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
index 15d2607585d0c0868dea6283176a84368965fc5f..eca7c938cf8c4ee785783a4a7f7b3c7e585580a7 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
@@ -85,8 +85,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
try {
Species protein = new GenericProtein("id");
- MiriamData mdEC = new MiriamData(MiriamType.EC, "3.1.2.14");
- protein.addMiriamData(mdEC);
+ protein.addMiriamData(getExampleValidAnnotation());
annotateElement(protein);
status.setStatus(ExternalServiceStatusType.OK);
@@ -252,4 +251,9 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
new AnnotatorOutputParameter(MiriamType.TAIR_LOCUS));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.EC, "3.1.2.14");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
index 94b8f52089729555f6bca5e3a8aca438018aeb8b..5cf529c02cc265eb9f92d260fd9c59fc510b80e4 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -64,7 +64,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
this.setCache(null);
try {
- Collection<Structure> structures = uniProtToPdb(new MiriamData(MiriamType.UNIPROT, "P29373"));
+ Collection<Structure> structures = uniProtToPdb(getExampleValidAnnotation());
if (structures.size() > 0) {
if (structures.iterator().next().getPdbId() != null) { // TODO - is this id?
@@ -246,4 +246,9 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
return Arrays.asList(new AnnotatorOutputParameter(MiriamType.PDB));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "P29373");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index 3b4260c130b8041048e9d1b67aff13f988cabc84..f74ee5d94868e4ee88f14a5b6a0a8a64c3bd3701 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -409,4 +409,11 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
new AnnotatorOutputParameter(BioEntityField.SMILE));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ // we don't provide example because there should be separate example for
+ // reaction and element
+ return null;
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
index 386044dfdc754693429d781f1eadfa91c22ee96d..04923698c98a526364db84c99271daa40bece833 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
@@ -88,11 +88,6 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
}
}
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- return chebiAnnotator.refreshCacheQuery(query);
- }
-
@Override
public String getCommonName() {
return MiriamType.STITCH.getCommonName();
@@ -123,4 +118,9 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
return Arrays.asList(new AnnotatorOutputParameter(MiriamType.EC));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.CHEBI, "CHEBI:35697");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
index c7a4fb3d3e2a787172d97068c91c9abf0cf4cb5e..205fe146cf438214fb730f3d88bf6bbab940ed5f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
@@ -110,4 +110,9 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
return Arrays.asList(new AnnotatorOutputParameter(MiriamType.STRING));
}
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "P53350");
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index a04f0e699e503c646509da05aaa540e0091bf2d9..3f72c60466714059593013083623c9ad4e609dab 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -59,7 +59,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
this.setCache(null);
try {
- Collection<MiriamData> collection = tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+ Collection<MiriamData> collection = tairToUniprot(getExampleValidAnnotation());
status.setStatus(ExternalServiceStatusType.OK);
if (collection.size() == 0) {
@@ -217,4 +217,9 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
return Arrays.asList(new AnnotatorOutputParameter(MiriamType.UNIPROT));
}
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030");
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index e7f6b4206acf09a434fc4099bb58b26d46332a73..a457b65ea0bcb1de32d972ca3aa95ecd77bf1640 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -71,7 +71,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
this.setCache(null);
try {
- MiriamData md = uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, "P37840"));
+ MiriamData md = uniProtToHgnc(getExampleValidAnnotation());
status.setStatus(ExternalServiceStatusType.OK);
if (md == null) {
@@ -280,4 +280,9 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
new AnnotatorOutputParameter(MiriamType.EC),
new AnnotatorOutputParameter(MiriamType.ENTREZ));
}
+
+ @Override
+ public MiriamData getExampleValidAnnotation() {
+ return new MiriamData(MiriamType.UNIPROT, "P37840");
+ }
}