diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
index 85d4105e01be05a67a1a7dc2fb85f3f9498856ac..b9cdf4c350cef2be50835c5a575c212a2a123644 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
@@ -208,6 +208,21 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testGetUrlForDoi() throws Exception {
+ try {
+ // exclude first cached value
+ MiriamData md = new MiriamData(MiriamType.DOI, "10.1038/npjsba.2016.20");
+
+ String url = miriamConnector.getUrlString(md);
+ assertNotNull(url);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testMiriamDataToUri() throws Exception {
try {
diff --git a/annotation/src/test/resources/log4j.properties b/annotation/src/test/resources/log4j.properties
index 473855faa6b70690575e254c92710b3c8e06fe32..e23927cb8932324e1cb8b40fe1be2b99fb755c69 100644
--- a/annotation/src/test/resources/log4j.properties
+++ b/annotation/src/test/resources/log4j.properties
@@ -14,6 +14,8 @@ log4j.appender.R.File=${catalina.home}/logs/MapViewer.log
log4j.appender.R.layout=org.apache.log4j.PatternLayout
log4j.appender.R.layout.ConversionPattern=%d %5p [%t] (%F:%L) - %m%n
+#Silence miriam debug logs
+log4j.logger.uk.ac.ebi.miriam.lib=warn
log4j.logger.org.springframework=warn
log4j.logger.org.hibernate=warn
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 13c6eb2568020b909c41cc40c8143cb71f373e32..daa4b747f786e615c7d8ab82b4e30dd275732f3b 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -119,7 +119,8 @@ GuiUtils.prototype.createAnnotationLink = function (annotation, showType) {
type = "PUBMED";
name = article.getId();
} else {
- name = annotation.getResource();
+ //replace encoded parts of uri (like %2F - > "/")
+ name = decodeURIComponent(annotation.getResource());
var miriamType = self.getConfiguration().getMiriamTypeByName(annotation.getType());
if (miriamType === null) {
logger.warn("Unknown miriam type: " + annotation.getType());
diff --git a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
index 0b8d3520736d54720a2643a36ed2324a1ec71d13..5d3aa3a65bb5bb07828a255af7625f7770079c10 100644
--- a/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
+++ b/frontend-js/src/test/js/gui/leftPanel/GuiUtils-test.js
@@ -3,6 +3,7 @@
require('../../mocha-config.js');
var Alias = require('../../../../main/js/map/data/Alias');
+var Annotation = require('../../../../main/js/map/data/Annotation');
var GuiUtils = require('../../../../main/js/gui/leftPanel/GuiUtils');
var chai = require('chai');
@@ -11,7 +12,7 @@ var logger = require('../../logger');
describe('GuiUtils', function () {
- it('constructor', function() {
+ it('constructor', function () {
var map = helper.createCustomMap();
helper.createSearchDbOverlay(map);
@@ -21,19 +22,19 @@ describe('GuiUtils', function () {
it('default', function () {
var aliasObj = {
- symbol : "S1_SYMBOL",
- formerSymbols : [],
- modelId : 15781,
- synonyms : [ "syn44" ],
- description : "DESCRIPTION",
- type : "Simple molecule",
- abbreviation : "ABBREVIATION",
- name : "s1",
- bounds : {
- x : 170.0,
- y : 171.5,
- width : 70.0,
- height : 25.0
+ symbol: "S1_SYMBOL",
+ formerSymbols: [],
+ modelId: 15781,
+ synonyms: ["syn44"],
+ description: "DESCRIPTION",
+ type: "Simple molecule",
+ abbreviation: "ABBREVIATION",
+ name: "s1",
+ bounds: {
+ x: 170.0,
+ y: 171.5,
+ width: 70.0,
+ height: 25.0
},
formula: "FORMULA",
id: 380217,
@@ -152,5 +153,21 @@ describe('GuiUtils', function () {
assert.ok(logger.getWarnings().length > 0);
});
});
+ describe('createAnnotationLink', function () {
+ it('with encoded part in resource', function () {
+ // noinspection SpellCheckingInspection
+ var annotation = new Annotation({
+ resource: "10.1038%2Fnpjsba.2016.20",
+ link: "http://doi.org/10.1038%2Fnpjsba.2016.20",
+ id: 1116748,
+ type: "DOI"
+ });
+ var guiUtils = new GuiUtils(helper.getConfiguration());
+ var link = guiUtils.createAnnotationLink(annotation);
+ assert.ok(link);
+ assert.equal(0, logger.getWarnings().length);
+ assert.ok(link.innerHTML.indexOf("%2F") < 0, "url contains encoded %2F part of id");
+ });
+ });
});
diff --git a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
index 0511d724faaed26c89ddcc24ff4dca4fb5f4eaa8..363a62838acc6969b9b792ed50978f9c493c102e 100644
--- a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"modelFormats":[{"handler":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser","extension":"xml","name":"CellDesigner SBML"},{"handler":"lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter","extension":"sbgn","name":"SBGN-ML"}],"elementTypes":[{"name":"Degraded","className":"lcsb.mapviewer.model.map.species.Degraded","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.IonChannelProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.TopSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Ion","className":"lcsb.mapviewer.model.map.species.Ion","parentClass":"lcsb.mapviewer.model.map.species.Chemical"},{"name":"Species","className":"lcsb.mapviewer.model.map.species.Species","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.RightSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Drug","className":"lcsb.mapviewer.model.map.species.Drug","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.Protein","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.TruncatedProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.PathwayCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"RNA","className":"lcsb.mapviewer.model.map.species.Rna","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Chemical","className":"lcsb.mapviewer.model.map.species.Chemical","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.Compartment","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.OvalCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.SquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Unknown","className":"lcsb.mapviewer.model.map.species.Unknown","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Element","className":"lcsb.mapviewer.model.map.species.Element","parentClass":"lcsb.mapviewer.model.map.BioEntity"},{"name":"Phenotype","className":"lcsb.mapviewer.model.map.species.Phenotype","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Complex","className":"lcsb.mapviewer.model.map.species.Complex","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Antisense RNA","className":"lcsb.mapviewer.model.map.species.AntisenseRna","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.ReceptorProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Simple molecule","className":"lcsb.mapviewer.model.map.species.SimpleMolecule","parentClass":"lcsb.mapviewer.model.map.species.Chemical"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.GenericProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Gene","className":"lcsb.mapviewer.model.map.species.Gene","parentClass":"lcsb.mapviewer.model.map.species.Species"}],"modificationStateTypes":{"PHOSPHORYLATED":{"commonName":"phosphorylated","abbreviation":"P"},"METHYLATED":{"commonName":"methylated","abbreviation":"Me"},"PALMYTOYLATED":{"commonName":"palmytoylated","abbreviation":"Pa"},"ACETYLATED":{"commonName":"acetylated","abbreviation":"Ac"},"SULFATED":{"commonName":"sulfated","abbreviation":"S"},"GLYCOSYLATED":{"commonName":"glycosylated","abbreviation":"G"},"PRENYLATED":{"commonName":"prenylated","abbreviation":"Pr"},"UBIQUITINATED":{"commonName":"ubiquitinated","abbreviation":"Ub"},"PROTONATED":{"commonName":"protonated","abbreviation":"H"},"HYDROXYLATED":{"commonName":"hydroxylated","abbreviation":"OH"},"MYRISTOYLATED":{"commonName":"myristoylated","abbreviation":"My"},"UNKNOWN":{"commonName":"unknown","abbreviation":"?"},"EMPTY":{"commonName":"empty","abbreviation":""},"DONT_CARE":{"commonName":"don't care","abbreviation":"*"}},"imageFormats":[{"handler":"lcsb.mapviewer.converter.graphics.PngImageGenerator","extension":"png","name":"PNG image"},{"handler":"lcsb.mapviewer.converter.graphics.PdfImageGenerator","extension":"pdf","name":"PDF"},{"handler":"lcsb.mapviewer.converter.graphics.SvgImageGenerator","extension":"svg","name":"SVG image"}],"plugins":[{"load-on-start":false,"url":"resources/js/plugins/empty.js"}],"annotators":[{"name":"Biocompendium","className":"lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://biocompendium.embl.de/"},{"name":"Chebi","className":"lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Chemical"],"url":"http://www.ebi.ac.uk/chebi/"},{"name":"Uniprot","className":"lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Gene","lcsb.mapviewer.model.map.species.Rna"],"url":"http://www.uniprot.org/"},{"name":"Gene Ontology","className":"lcsb.mapviewer.annotation.services.annotators.GoAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Phenotype","lcsb.mapviewer.model.map.compartment.Compartment","lcsb.mapviewer.model.map.species.Complex"],"url":"http://amigo.geneontology.org/amigo"},{"name":"HGNC","className":"lcsb.mapviewer.annotation.services.annotators.HgncAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"http://www.genenames.org"},{"name":"Protein Data Bank","className":"lcsb.mapviewer.annotation.services.annotators.PdbAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"http://www.pdbe.org/"},{"name":"Recon annotator","className":"lcsb.mapviewer.annotation.services.annotators.ReconAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Chemical","lcsb.mapviewer.model.map.reaction.Reaction"],"url":"http://humanmetabolism.org/"},{"name":"Entrez Gene","className":"lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"http://www.ncbi.nlm.nih.gov/gene"},{"name":"Ensembl","className":"lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator","elementClassNames":["lcsb.mapviewer.model.map.species.Protein","lcsb.mapviewer.model.map.species.Rna","lcsb.mapviewer.model.map.species.Gene"],"url":"www.ensembl.org"}],"buildDate":" 15/11/2017 14:13","reactionTypes":[{"name":"Unknown positive influence","className":"lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Generic Reaction","className":"lcsb.mapviewer.model.map.reaction.Reaction","parentClass":"lcsb.mapviewer.model.map.BioEntity"},{"name":"Reduced physical stimulation","className":"lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Negative influence","className":"lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Known transition omitted","className":"lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced modulation","className":"lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Translation","className":"lcsb.mapviewer.model.map.reaction.type.TranslationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Heterodimer association","className":"lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Transcription","className":"lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced trigger","className":"lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown negative influence","className":"lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Truncation","className":"lcsb.mapviewer.model.map.reaction.type.TruncationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Transport","className":"lcsb.mapviewer.model.map.reaction.type.TransportReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Reduced trigger","className":"lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"State transition","className":"lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Positive influence","className":"lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced physical stimulation","className":"lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Boolean logic gate","className":"lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown reduced modulation","className":"lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Unknown transition","className":"lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"},{"name":"Dissociation","className":"lcsb.mapviewer.model.map.reaction.type.DissociationReaction","parentClass":"lcsb.mapviewer.model.map.reaction.Reaction"}],"version":"11.0.4","mapTypes":[{"name":"Downstream targets","id":"DOWNSTREAM_TARGETS"},{"name":"Pathway","id":"PATHWAY"},{"name":"Unknown","id":"UNKNOWN"}],"miriamTypes":{"CHEMBL_TARGET":{"commonName":"ChEMBL target","uris":["urn:miriam:chembl.target"],"homepage":"https://www.ebi.ac.uk/chembldb/","registryIdentifier":"MIR:00000085"},"UNIPROT":{"commonName":"Uniprot","uris":["urn:miriam:uniprot"],"homepage":"http://www.uniprot.org/","registryIdentifier":"MIR:00000005"},"MI_R_BASE_MATURE_SEQUENCE":{"commonName":"miRBase Mature Sequence Database","uris":["urn:miriam:mirbase.mature"],"homepage":"http://www.mirbase.org/","registryIdentifier":"MIR:00000235"},"PFAM":{"commonName":"Protein Family Database","uris":["urn:miriam:pfam"],"homepage":"http://pfam.xfam.org//","registryIdentifier":"MIR:00000028"},"ENSEMBL_PLANTS":{"commonName":"Ensembl Plants","uris":["urn:miriam:ensembl.plant"],"homepage":"http://plants.ensembl.org/","registryIdentifier":"MIR:00000205"},"WIKIPEDIA":{"commonName":"Wikipedia (English)","uris":["urn:miriam:wikipedia.en"],"homepage":"http://en.wikipedia.org/wiki/Main_Page","registryIdentifier":"MIR:00000384"},"CHEBI":{"commonName":"Chebi","uris":["urn:miriam:obo.chebi","urn:miriam:chebi"],"homepage":"http://www.ebi.ac.uk/chebi/","registryIdentifier":"MIR:00000002"},"WIKIDATA":{"commonName":"Wikidata","uris":["urn:miriam:wikidata"],"homepage":"https://www.wikidata.org/","registryIdentifier":"MIR:00000549"},"REACTOME":{"commonName":"Reactome","uris":["urn:miriam:reactome"],"homepage":"http://www.reactome.org/","registryIdentifier":"MIR:00000018"},"EC":{"commonName":"Enzyme Nomenclature","uris":["urn:miriam:ec-code"],"homepage":"http://www.enzyme-database.org/","registryIdentifier":"MIR:00000004"},"UNIPROT_ISOFORM":{"commonName":"UniProt Isoform","uris":["urn:miriam:uniprot.isoform"],"homepage":"http://www.uniprot.org/","registryIdentifier":"MIR:00000388"},"OMIM":{"commonName":"Online Mendelian Inheritance in Man","uris":["urn:miriam:omim"],"homepage":"http://omim.org/","registryIdentifier":"MIR:00000016"},"DRUGBANK_TARGET_V4":{"commonName":"DrugBank Target v4","uris":["urn:miriam:drugbankv4.target"],"homepage":"http://www.drugbank.ca/targets","registryIdentifier":"MIR:00000528"},"MIR_TAR_BASE_MATURE_SEQUENCE":{"commonName":"miRTarBase Mature Sequence Database","uris":["urn:miriam:mirtarbase"],"homepage":"http://mirtarbase.mbc.nctu.edu.tw/","registryIdentifier":"MIR:00100739"},"CHEMBL_COMPOUND":{"commonName":"ChEMBL","uris":["urn:miriam:chembl.compound"],"homepage":"https://www.ebi.ac.uk/chembldb/","registryIdentifier":"MIR:00000084"},"KEGG_PATHWAY":{"commonName":"Kegg Pathway","uris":["urn:miriam:kegg.pathway"],"homepage":"http://www.genome.jp/kegg/pathway.html","registryIdentifier":"MIR:00000012"},"CAS":{"commonName":"Chemical Abstracts Service","uris":["urn:miriam:cas"],"homepage":"http://commonchemistry.org","registryIdentifier":"MIR:00000237"},"REFSEQ":{"commonName":"RefSeq","uris":["urn:miriam:refseq"],"homepage":"http://www.ncbi.nlm.nih.gov/projects/RefSeq/","registryIdentifier":"MIR:00000039"},"WORM_BASE":{"commonName":"WormBase","uris":["urn:miriam:wormbase"],"homepage":"http://wormbase.bio2rdf.org/fct","registryIdentifier":"MIR:00000027"},"MI_R_BASE_SEQUENCE":{"commonName":"miRBase Sequence Database","uris":["urn:miriam:mirbase"],"homepage":"http://www.mirbase.org/","registryIdentifier":"MIR:00000078"},"TAIR_LOCUS":{"commonName":"TAIR Locus","uris":["urn:miriam:tair.locus"],"homepage":"http://arabidopsis.org/index.jsp","registryIdentifier":"MIR:00000050"},"PHARM":{"commonName":"PharmGKB Pathways","uris":["urn:miriam:pharmgkb.pathways"],"homepage":"http://www.pharmgkb.org/","registryIdentifier":"MIR:00000089"},"PDB":{"commonName":"Protein Data Bank","uris":["urn:miriam:pdb"],"homepage":"http://www.pdbe.org/","registryIdentifier":"MIR:00000020"},"PANTHER":{"commonName":"PANTHER Family","uris":["urn:miriam:panther.family","urn:miriam:panther"],"homepage":"http://www.pantherdb.org/","registryIdentifier":"MIR:00000060"},"TAXONOMY":{"commonName":"Taxonomy","uris":["urn:miriam:taxonomy"],"homepage":"http://www.ncbi.nlm.nih.gov/taxonomy/","registryIdentifier":"MIR:00000006"},"UNIGENE":{"commonName":"UniGene","uris":["urn:miriam:unigene"],"homepage":"http://www.ncbi.nlm.nih.gov/unigene","registryIdentifier":"MIR:00000346"},"HGNC":{"commonName":"HGNC","uris":["urn:miriam:hgnc"],"homepage":"http://www.genenames.org","registryIdentifier":"MIR:00000080"},"HGNC_SYMBOL":{"commonName":"HGNC Symbol","uris":["urn:miriam:hgnc.symbol"],"homepage":"http://www.genenames.org","registryIdentifier":"MIR:00000362"},"COG":{"commonName":"Clusters of Orthologous Groups","uris":["urn:miriam:cogs"],"homepage":"https://www.ncbi.nlm.nih.gov/COG/","registryIdentifier":"MIR:00000296"},"WIKIPATHWAYS":{"commonName":"WikiPathways","uris":["urn:miriam:wikipathways"],"homepage":"http://www.wikipathways.org/","registryIdentifier":"MIR:00000076"},"HMDB":{"commonName":"HMDB","uris":["urn:miriam:hmdb"],"homepage":"http://www.hmdb.ca/","registryIdentifier":"MIR:00000051"},"CHEMSPIDER":{"commonName":"ChemSpider","uris":["urn:miriam:chemspider"],"homepage":"http://www.chemspider.com//","registryIdentifier":"MIR:00000138"},"ENSEMBL":{"commonName":"Ensembl","uris":["urn:miriam:ensembl"],"homepage":"www.ensembl.org","registryIdentifier":"MIR:00000003"},"GO":{"commonName":"Gene Ontology","uris":["urn:miriam:obo.go","urn:miriam:go"],"homepage":"http://amigo.geneontology.org/amigo","registryIdentifier":"MIR:00000022"},"KEGG_REACTION":{"commonName":"Kegg 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Gene","uris":["urn:miriam:ncbigene","urn:miriam:entrez.gene"],"homepage":"http://www.ncbi.nlm.nih.gov/gene","registryIdentifier":"MIR:00000069"},"PUBCHEM_SUBSTANCE":{"commonName":"PubChem-substance","uris":["urn:miriam:pubchem.substance"],"homepage":"http://pubchem.ncbi.nlm.nih.gov/","registryIdentifier":"MIR:00000033"},"CCDS":{"commonName":"Consensus CDS","uris":["urn:miriam:ccds"],"homepage":"http://www.ncbi.nlm.nih.gov/CCDS/","registryIdentifier":"MIR:00000375"},"KEGG_GENES":{"commonName":"Kegg Genes","uris":["urn:miriam:kegg.genes","urn:miriam:kegg.genes:hsa"],"homepage":"http://www.genome.jp/kegg/genes.html","registryIdentifier":"MIR:00000070"},"TOXICOGENOMIC_CHEMICAL":{"commonName":"Toxicogenomic Chemical","uris":["urn:miriam:ctd.chemical"],"homepage":"http://ctdbase.org/","registryIdentifier":"MIR:00000098"},"SGD":{"commonName":"Saccharomyces Genome Database","uris":["urn:miriam:sgd"],"homepage":"http://www.yeastgenome.org/","registryIdentifier":"MIR:00000023"},"KEGG_COMPOUND":{"commonName":"Kegg Compound","uris":["urn:miriam:kegg.compound"],"homepage":"http://www.genome.jp/kegg/ligand.html","registryIdentifier":"MIR:00000013"},"INTERPRO":{"commonName":"InterPro","uris":["urn:miriam:interpro"],"homepage":"http://www.ebi.ac.uk/interpro/","registryIdentifier":"MIR:00000011"},"UNKNOWN":{"commonName":"Unknown","uris":[],"homepage":null,"registryIdentifier":null},"DRUGBANK":{"commonName":"DrugBank","uris":["urn:miriam:drugbank"],"homepage":"http://www.drugbank.ca/","registryIdentifier":"MIR:00000102"},"PUBMED":{"commonName":"PubMed","uris":["urn:miriam:pubmed"],"homepage":"http://www.ncbi.nlm.nih.gov/PubMed/","registryIdentifier":"MIR:00000015"}},"options":[{"idObject":9,"type":"EMAIL_ADDRESS","value":"your.account@domain.com","valueType":"EMAIL","commonName":"E-mail address"},{"idObject":10,"type":"EMAIL_LOGIN","value":"your@l","valueType":"STRING","commonName":"E-mail server login"},{"idObject":11,"type":"EMAIL_PASSWORD","value":"email.secret.password","valueType":"PASSWORD","commonName":"E-mail server password"},{"idObject":13,"type":"EMAIL_IMAP_SERVER","value":"your.imap.domain.com","valueType":"STRING","commonName":"IMAP server"},{"idObject":12,"type":"EMAIL_SMTP_SERVER","value":"your.smtp.domain.com","valueType":"STRING","commonName":"SMTP server"},{"idObject":14,"type":"EMAIL_SMTP_PORT","value":"25","valueType":"INTEGER","commonName":"SMTP port"},{"idObject":6,"type":"DEFAULT_MAP","value":"sample","valueType":"STRING","commonName":"Default Project Id"},{"idObject":4,"type":"LOGO_IMG","value":"udl.png","valueType":"URL","commonName":"Logo icon"},{"idObject":3,"type":"LOGO_LINK","value":"http://wwwen.uni.lu/","valueType":"URL","commonName":"Logo link (after click)"},{"idObject":7,"type":"SEARCH_DISTANCE","value":"10","valueType":"DOUBLE","commonName":"Max distance for clicking on element (px)"},{"idObject":1,"type":"REQUEST_ACCOUNT_EMAIL","value":"your.email@domain.com","valueType":"EMAIL","commonName":"Email used for requesting an account"},{"idObject":8,"type":"SEARCH_RESULT_NUMBER","value":"100","valueType":"INTEGER","commonName":"Max number of results in search box. "},{"idObject":2,"type":"GOOGLE_ANALYTICS_IDENTIFIER","value":"","valueType":"STRING","commonName":"Google Analytics tracking ID used for statistics"},{"idObject":5,"type":"LOGO_TEXT","value":"University of Luxembourg","valueType":"STRING","commonName":"Logo description"},{"idObject":56,"type":"X_FRAME_DOMAIN","value":"http://localhost:8080/","valueType":"URL","commonName":"Domain allowed to connect via x-frame technology"},{"idObject":131,"type":"BIG_FILE_STORAGE_DIR","value":"minerva-big/","valueType":"STRING","commonName":"Path to store big files"},{"idObject":138,"type":"LEGEND_FILE_1","value":"resources/images/legend_a.png","valueType":"URL","commonName":"Legend 1 image file"},{"idObject":139,"type":"LEGEND_FILE_2","value":"resources/images/legend_b.png","valueType":"URL","commonName":"Legend 2 image file"},{"idObject":140,"type":"LEGEND_FILE_3","value":"resources/images/legend_c.png","valueType":"URL","commonName":"Legend 3 image file"},{"idObject":141,"type":"LEGEND_FILE_4","value":"resources/images/legend_d.png","valueType":"URL","commonName":"Legend 4 image file"},{"idObject":142,"type":"USER_MANUAL_FILE","value":"resources/other/user_guide.pdf","valueType":"URL","commonName":"User manual file"},{"idObject":205,"type":"MIN_COLOR_VAL","value":"FF0000","valueType":"COLOR","commonName":"Overlay color for negative values"},{"idObject":206,"type":"MAX_COLOR_VAL","value":"fbff00","valueType":"COLOR","commonName":"Overlay color for postive values"},{"idObject":218,"type":"SIMPLE_COLOR_VAL","value":"00ff40","valueType":"COLOR","commonName":"Overlay color when no values are defined"},{"idObject":239,"type":"NEUTRAL_COLOR_VAL","value":"0400ff","valueType":"COLOR","commonName":"Overlay color for value=0"}],"privilegeTypes":{"VIEW_PROJECT":{"commonName":"View project","valueType":"boolean","objectType":"Project"},"LAYOUT_MANAGEMENT":{"commonName":"Manage layouts","valueType":"boolean","objectType":"Project"},"PROJECT_MANAGEMENT":{"commonName":"Map management","valueType":"boolean","objectType":null},"CUSTOM_LAYOUTS":{"commonName":"Custom layouts","valueType":"int","objectType":null},"ADD_MAP":{"commonName":"Add project","valueType":"boolean","objectType":null},"LAYOUT_VIEW":{"commonName":"View layout","valueType":"boolean","objectType":"Layout"},"MANAGE_GENOMES":{"commonName":"Manage genomes","valueType":"boolean","objectType":null},"EDIT_COMMENTS_PROJECT":{"commonName":"Manage comments","valueType":"boolean","objectType":"Project"},"CONFIGURATION_MANAGE":{"commonName":"Manage configuration","valueType":"boolean","objectType":null},"USER_MANAGEMENT":{"commonName":"User management","valueType":"boolean","objectType":null}},"overlayTypes":[{"name":"GENERIC"},{"name":"GENETIC_VARIANT"}]}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 31fa7c1338738febf5798debcde11f33fafa604a..56e6dd03a066c3e940c16a5af0442ab2cb64a4c6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -22,651 +22,660 @@ import lcsb.mapviewer.model.map.species.Rna;
*/
@SuppressWarnings("unchecked")
public enum MiriamType {
- /**
- * Chemical Abstracts Service database: http://commonchemistry.org.
- */
- CAS("Chemical Abstracts Service", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cas" }, //
- new Class<?>[] {}, "MIR:00000237"), //
-
- /**
- * Consensus CDS: http://identifiers.org/ccds/.
- */
- CCDS("Consensus CDS", //
- "http://www.ncbi.nlm.nih.gov/CCDS/", //
- new String[] { "urn:miriam:ccds" }, //
- new Class<?>[] {}, "MIR:00000375"), //
-
- /**
- * Chebi database:
- * <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
- */
- CHEBI("Chebi", //
- "http://www.ebi.ac.uk/chebi/", //
- new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * ChemSpider database:
- * <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
- */
- CHEMSPIDER("ChemSpider", //
- "http://www.chemspider.com//", //
- new String[] { "urn:miriam:chemspider" }, //
- new Class<?>[] {}, "MIR:00000138"), //
-
- /**
- * Chembl database: https://www.ebi.ac.uk/chembldb/.
- */
- CHEMBL_COMPOUND("ChEMBL", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.compound" }, //
- new Class<?>[] { Drug.class }, "MIR:00000084"), //
-
- /**
- * Target in chembl database: https://www.ebi.ac.uk/chembldb/.
- */
- CHEMBL_TARGET("ChEMBL target", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.target" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
-
- /**
- * Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
- */
- COG("Clusters of Orthologous Groups", //
- "https://www.ncbi.nlm.nih.gov/COG/", //
- new String[] { "urn:miriam:cogs" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000296"), //
-
- /**
- * Drugbank database: http://www.drugbank.ca/.
- */
- DRUGBANK("DrugBank", //
- "http://www.drugbank.ca/", //
- new String[] { "urn:miriam:drugbank" }, //
- new Class<?>[] { Drug.class }, "MIR:00000102"), //
- /**
- * Drugbank tagrets: http://www.drugbank.ca/targets.
- */
- DRUGBANK_TARGET_V4("DrugBank Target v4", //
- "http://www.drugbank.ca/targets", //
- new String[] { "urn:miriam:drugbankv4.target" }, //
- new Class<?>[] {}, "MIR:00000528"), //
-
- /**
- * Enzyme Nomenclature: http://www.enzyme-database.org/.
- */
- EC("Enzyme Nomenclature", //
- "http://www.enzyme-database.org/", //
- new String[] { "urn:miriam:ec-code" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
-
- /**
- * Ensembl: www.ensembl.org.
- */
- ENSEMBL("Ensembl", //
- "www.ensembl.org", //
- new String[] { "urn:miriam:ensembl" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
-
- /**
- * Ensembl Plants: http://plants.ensembl.org/.
- */
- ENSEMBL_PLANTS("Ensembl Plants", //
- "http://plants.ensembl.org/", //
- new String[] { "urn:miriam:ensembl.plant" }, //
- new Class<?>[] {}, "MIR:00000205"), //
-
- /**
- * Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
- */
- ENTREZ("Entrez Gene", //
- "http://www.ncbi.nlm.nih.gov/gene", //
- new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"), //
-
- /**
- * Gene Ontology: http://amigo.geneontology.org/amigo.
- */
- GO("Gene Ontology", //
- "http://amigo.geneontology.org/amigo", //
- new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
-
- /**
- * HGNC: http://www.genenames.org.
- */
- HGNC("HGNC", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
-
- /**
- * HGNC symbol: http://www.genenames.org.
- */
- HGNC_SYMBOL("HGNC Symbol", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc.symbol" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
-
- /**
- * HMDB: http://www.hmdb.ca/.
- */
- HMDB("HMDB", //
- "http://www.hmdb.ca/", //
- "urn:miriam:hmdb", //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
-
- /**
- * InterPro: http://www.ebi.ac.uk/interpro/.
- */
- INTERPRO("InterPro", //
- "http://www.ebi.ac.uk/interpro/", //
- new String[] { "urn:miriam:interpro" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
-
- /**
- * KEGG Compound: http://www.genome.jp/kegg/ligand.html.
- */
- KEGG_COMPOUND("Kegg Compound", //
- "http://www.genome.jp/kegg/ligand.html", //
- "urn:miriam:kegg.compound", //
- new Class<?>[] { Chemical.class }, "MIR:00000013"), //
-
- /**
- * KEGG Genes: http://www.genome.jp/kegg/genes.html.
- */
- KEGG_GENES("Kegg Genes", //
- "http://www.genome.jp/kegg/genes.html", //
- new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
-
- /**
- * KEGG Orthology: http://www.genome.jp/kegg/ko.html.
- */
- KEGG_ORTHOLOGY("KEGG Orthology", //
- "http://www.genome.jp/kegg/ko.html", //
- new String[] { "urn:miriam:kegg.orthology" }, //
- new Class<?>[] {}, "MIR:00000116"), //
-
- /**
- * KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
- */
- KEGG_PATHWAY("Kegg Pathway", //
- "http://www.genome.jp/kegg/pathway.html", //
- "urn:miriam:kegg.pathway", //
- new Class<?>[] { Reaction.class }, "MIR:00000012"), //
-
- /**
- * KEGG Reaction: http://www.genome.jp/kegg/reaction/.
- */
- KEGG_REACTION("Kegg Reaction", //
- "http://www.genome.jp/kegg/reaction/", //
- "urn:miriam:kegg.reaction", //
- new Class<?>[] { Reaction.class }, "MIR:00000014"), //
-
- /**
- * MeSH 2012: http://www.nlm.nih.gov/mesh/.
- */
- MESH_2012("MeSH 2012", //
- "http://www.nlm.nih.gov/mesh/", //
- new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
-
- /**
- * miRBase Sequence: http://www.mirbase.org/.
- */
- MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase" }, //
- new Class<?>[] {}, "MIR:00000078"), //
-
- /**
- * miRBase Mature Sequence: http://www.mirbase.org/.
- */
- MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase.mature" }, //
- new Class<?>[] {}, "MIR:00000235"), //
-
- /**
- * miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
- */
- MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
- "http://mirtarbase.mbc.nctu.edu.tw/", //
- new String[] { "urn:miriam:mirtarbase" }, //
- new Class<?>[] {}, "MIR:00100739"), //
-
- /**
- * Mouse Genome Database: http://www.informatics.jax.org/.
- */
- MGD("Mouse Genome Database", //
- "http://www.informatics.jax.org/", //
- new String[] { "urn:miriam:mgd" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
-
- /**
- * Online Mendelian Inheritance in Man: http://omim.org/.
- */
- OMIM("Online Mendelian Inheritance in Man", //
- "http://omim.org/", //
- new String[] { "urn:miriam:omim" }, //
- new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
-
- /**
- * PANTHER Family: http://www.pantherdb.org/.
- */
- PANTHER("PANTHER Family", //
- "http://www.pantherdb.org/", //
- new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
-
- /**
- * PDB: http://www.pdbe.org/.
- */
- PDB("Protein Data Bank", //
- "http://www.pdbe.org/", //
- "urn:miriam:pdb", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
-
- /**
- * Protein Family Database: http://pfam.xfam.org/.
- */
- PFAM("Protein Family Database", //
- "http://pfam.xfam.org//", //
- "urn:miriam:pfam", //
- new Class<?>[] {}, "MIR:00000028"), //
-
- /**
- * PharmGKB Pathways: http://www.pharmgkb.org/.
- */
- PHARM("PharmGKB Pathways", //
- "http://www.pharmgkb.org/", //
- "urn:miriam:pharmgkb.pathways", //
- new Class<?>[] {}, "MIR:00000089"), //
-
- /**
- * PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
- */
- PUBCHEM("PubChem-compound", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.compound" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000034", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
- */
- PUBCHEM_SUBSTANCE("PubChem-substance", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.substance" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000033", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
- */
- PUBMED("PubMed", //
- "http://www.ncbi.nlm.nih.gov/PubMed/", //
- new String[] { "urn:miriam:pubmed" }, //
- new Class<?>[] { BioEntity.class }, "MIR:00000015", //
- new Class<?>[] { Reaction.class }), //
-
- /**
- * Reactome: http://www.reactome.org/.
- */
- REACTOME("Reactome", //
- "http://www.reactome.org/", //
- "urn:miriam:reactome", //
- new Class<?>[] { Reaction.class }, "MIR:00000018"), //
-
- /**
- * RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
- */
- REFSEQ("RefSeq", //
- "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
- "urn:miriam:refseq", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
-
- /**
- * SGD: http://www.yeastgenome.org/.
- */
- SGD("Saccharomyces Genome Database", //
- "http://www.yeastgenome.org/", //
- "urn:miriam:sgd", //
- new Class<?>[] {}, "MIR:00000023"),
-
- /**
- * The Arabidopsis Information Resource (TAIR) maintains a database of genetic
- * and molecular biology data for the model higher plant Arabidopsis thaliana.
- * The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
- * http://arabidopsis.org/index.jsp.
- */
- TAIR_LOCUS("TAIR Locus", //
- "http://arabidopsis.org/index.jsp", //
- "urn:miriam:tair.locus", //
- new Class<?>[] {}, "MIR:00000050"),
-
- /**
- * Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
- */
- TAXONOMY("Taxonomy", //
- "http://www.ncbi.nlm.nih.gov/taxonomy/", //
- "urn:miriam:taxonomy", //
- new Class<?>[] {}, "MIR:00000006"),
- /**
- * Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
- * http://ctdbase.org/detail.go
- */
- TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
- "http://ctdbase.org/", //
- "urn:miriam:ctd.chemical", //
- new Class<?>[] {}, "MIR:00000098"), //
-
- /**
- * UniGene: http://www.ncbi.nlm.nih.gov/unigene.
- */
- UNIGENE("UniGene", //
- "http://www.ncbi.nlm.nih.gov/unigene", //
- "urn:miriam:unigene", //
- new Class<?>[] {}, "MIR:00000346"),
-
- /**
- * Uniprot: http://www.uniprot.org/.
- */
- UNIPROT("Uniprot", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
-
- /**
- * UniProt Isoform: http://www.uniprot.org/.
- */
- UNIPROT_ISOFORM("UniProt Isoform", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot.isoform", //
- new Class<?>[] { Protein.class }, "MIR:00000388"),
-
- /**
- * Unknown reference type...
- */
- UNKNOWN("Unknown", //
- null, //
- new String[] {}, //
- new Class<?>[] {}, null),
-
- /**
- * Wikidata: https://www.wikidata.org/.
- */
- WIKIDATA("Wikidata", //
- "https://www.wikidata.org/", //
- new String[] { "urn:miriam:wikidata" }, //
- new Class<?>[] {}, "MIR:00000549"), //
-
- /**
- * WikiPathways: http://www.wikipathways.org/.
- */
- WIKIPATHWAYS("WikiPathways", //
- "http://www.wikipathways.org/", //
- new String[] { "urn:miriam:wikipathways" }, //
- new Class<?>[] {}, "MIR:00000076"), //
-
- /**
- * Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
- */
- WIKIPEDIA("Wikipedia (English)", //
- "http://en.wikipedia.org/wiki/Main_Page", // /
- new String[] { "urn:miriam:wikipedia.en" }, //
- new Class<?>[] {}, "MIR:00000384"),
-
- /**
- * WormBase: http://wormbase.bio2rdf.org/fct.
- */
- WORM_BASE("WormBase", //
- "http://wormbase.bio2rdf.org/fct", // /
- new String[] { "urn:miriam:wormbase" }, //
- new Class<?>[] {}, "MIR:00000027");
-
- /**
- * User friendly name.
- */
- private String commonName;
-
- /**
- * url to homepage of given resource type.
- */
- private String dbHomepage;
-
- /**
- * Identifier of the database in miriam registry.
- */
- private String registryIdentifier;
-
- /**
- * Valid uris to this resource.
- */
- private List<String> uris = new ArrayList<String>();
-
- /**
- * Classes that can be annotated by this resource.
- */
- private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
-
- /**
- * When class from this list is marked as "require at least one annotation"
- * then annotation of this type is valid.
- */
- private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uris
- * {@link #uris}
- * @param classes
- * {@link #validClass}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- */
- MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier) {
- this(commonName, dbHomePage, uris, classes, registryIdentifier, new Class<?>[] {});
- }
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uris
- * {@link #uris}
- * @param classes
- * {@link #validClass}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- * @param requiredClasses
- * {@link #requiredClasses}
- */
- MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier, Class<?>[] requiredClasses) {
- this.commonName = commonName;
- this.dbHomepage = dbHomePage;
- for (String string : uris) {
- this.uris.add(string);
- }
- for (Class<?> clazz : classes) {
- this.validClass.add((Class<? extends BioEntity>) clazz);
- }
- for (Class<?> clazz : requiredClasses) {
- this.requiredClass.add((Class<? extends BioEntity>) clazz);
- }
- this.registryIdentifier = registryIdentifier;
- }
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uri
- * one of {@link #uris}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- * @param classes
- * {@link #validClass}
- */
- MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier) {
- this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier);
- }
-
- /**
- *
- * @return {@link #commonName}
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- *
- * @return {@link #uris}
- */
- public List<String> getUris() {
- return uris;
- }
-
- /**
- *
- * @return {@link #validClass}
- */
- public List<Class<? extends BioEntity>> getValidClass() {
- return validClass;
- }
-
- /**
- * Returns {@link MiriamType} associated with parameter uri address.
- *
- * @param uri
- * uri to check
- * @return {@link MiriamType} for given uri
- */
- public static MiriamType getTypeByUri(String uri) {
- for (MiriamType mt : MiriamType.values()) {
- for (String string : mt.getUris()) {
- if (string.equalsIgnoreCase(uri)) {
- return mt;
- }
- }
- }
- return null;
- }
-
- /**
- * @return the dbHomepage
- * @see #dbHomepage
- */
- public String getDbHomepage() {
- return dbHomepage;
- }
-
- /**
- * @return the registryIdentifier
- * @see #registryIdentifier
- */
- public String getRegistryIdentifier() {
- return registryIdentifier;
- }
-
- /**
- * @return the requiredClass
- * @see #requiredClass
- */
- public List<Class<? extends BioEntity>> getRequiredClass() {
- return requiredClass;
- }
-
- /**
- * Returns {@link MiriamType} associated with {@link #commonName}.
- *
- * @param string
- * {@link #commonName}
- * @return {@link MiriamType} for given name
- */
- public static MiriamType getTypeByCommonName(String string) {
- for (MiriamType mt : MiriamType.values()) {
- if (string.equalsIgnoreCase(mt.getCommonName())) {
- return mt;
- }
- }
- return null;
- }
-
- /**
- * Transforms identifier into {@link MiriamData}.
- *
- * @param generalIdentifier
- * identifier in the format NAME:IDENTIFIER. Where NAME is the name
- * from {@link MiriamType#commonName} and IDENTIFIER is reasource
- * identifier.
- * @return {@link MiriamData} representing generalIdentifier, when identifier
- * is invalid InvalidArgumentException is thrown
- */
- public static MiriamData getMiriamDataFromIdentifier(String generalIdentifier) {
- int index = generalIdentifier.indexOf(":");
- if (index < 0) {
- throw new InvalidArgumentException("Identifier doesn't contain type");
- }
- String type = generalIdentifier.substring(0, index);
- String id = generalIdentifier.substring(index + 1);
- for (MiriamType mt : MiriamType.values()) {
- if (mt.getCommonName().equalsIgnoreCase(type)) {
- return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, id);
- }
- }
- throw new InvalidArgumentException("Unknown miriam type: " + type + " (id: " + id + ")");
- }
-
- /**
- * Creates {@link MiriamData} from miriam uri.
- *
- * @param miriamUri
- * miriam uri defining {@link MiriamData}
- * @return {@link MiriamData} from miriam uri
- */
- public static MiriamData getMiriamByUri(String miriamUri) {
- // this hack is due to CellDesigner issue (CellDesigner incorectly handle
- // with identifiers that have ":" inside resource ":" inside resource with
- // "%3A" and also the last ":"
- miriamUri = miriamUri.replace("%3A", ":");
-
- String foundUri = "";
- MiriamType foundType = null;
-
- for (MiriamType type : MiriamType.values()) {
- for (String uri : type.getUris()) {
- if (miriamUri.startsWith(uri + ":")) {
- if (uri.length() > foundUri.length()) {
- foundType = type;
- foundUri = uri;
- }
- }
- }
- }
- if (foundType != null) {
- return new MiriamData(foundType, miriamUri.substring(foundUri.length() + 1));
- }
- throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
- }
+ /**
+ * Chemical Abstracts Service database: http://commonchemistry.org.
+ */
+ CAS("Chemical Abstracts Service", //
+ "http://commonchemistry.org", //
+ new String[] { "urn:miriam:cas" }, //
+ new Class<?>[] {}, "MIR:00000237"), //
+
+ /**
+ * Consensus CDS: http://identifiers.org/ccds/.
+ */
+ CCDS("Consensus CDS", //
+ "http://www.ncbi.nlm.nih.gov/CCDS/", //
+ new String[] { "urn:miriam:ccds" }, //
+ new Class<?>[] {}, "MIR:00000375"), //
+
+ /**
+ * Chebi database:
+ * <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
+ */
+ CHEBI("Chebi", //
+ "http://www.ebi.ac.uk/chebi/", //
+ new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * ChemSpider database:
+ * <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
+ */
+ CHEMSPIDER("ChemSpider", //
+ "http://www.chemspider.com//", //
+ new String[] { "urn:miriam:chemspider" }, //
+ new Class<?>[] {}, "MIR:00000138"), //
+
+ /**
+ * Chembl database: https://www.ebi.ac.uk/chembldb/.
+ */
+ CHEMBL_COMPOUND("ChEMBL", //
+ "https://www.ebi.ac.uk/chembldb/", //
+ new String[] { "urn:miriam:chembl.compound" }, //
+ new Class<?>[] { Drug.class }, "MIR:00000084"), //
+
+ /**
+ * Target in chembl database: https://www.ebi.ac.uk/chembldb/.
+ */
+ CHEMBL_TARGET("ChEMBL target", //
+ "https://www.ebi.ac.uk/chembldb/", //
+ new String[] { "urn:miriam:chembl.target" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
+
+ /**
+ * Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
+ */
+ COG("Clusters of Orthologous Groups", //
+ "https://www.ncbi.nlm.nih.gov/COG/", //
+ new String[] { "urn:miriam:cogs" }, //
+ new Class<?>[] { Reaction.class }, "MIR:00000296"), //
+
+ /**
+ * Digital Object Identifier: http://www.doi.org/.
+ */
+ DOI("Digital Object Identifier", //
+ "http://www.doi.org/", //
+ new String[] { "urn:miriam:doi" }, //
+ new Class<?>[] { Reaction.class }, "MIR:00000019"), //
+
+ /**
+ * Drugbank database: http://www.drugbank.ca/.
+ */
+ DRUGBANK("DrugBank", //
+ "http://www.drugbank.ca/", //
+ new String[] { "urn:miriam:drugbank" }, //
+ new Class<?>[] { Drug.class }, "MIR:00000102"), //
+ /**
+ * Drugbank targets: http://www.drugbank.ca/targets.
+ */
+ DRUGBANK_TARGET_V4("DrugBank Target v4", //
+ "http://www.drugbank.ca/targets", //
+ new String[] { "urn:miriam:drugbankv4.target" }, //
+ new Class<?>[] {}, "MIR:00000528"), //
+
+ /**
+ * Enzyme Nomenclature: http://www.enzyme-database.org/.
+ */
+ EC("Enzyme Nomenclature", //
+ "http://www.enzyme-database.org/", //
+ new String[] { "urn:miriam:ec-code" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
+
+ /**
+ * Ensembl: www.ensembl.org.
+ */
+ ENSEMBL("Ensembl", //
+ "www.ensembl.org", //
+ new String[] { "urn:miriam:ensembl" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
+
+ /**
+ * Ensembl Plants: http://plants.ensembl.org/.
+ */
+ ENSEMBL_PLANTS("Ensembl Plants", //
+ "http://plants.ensembl.org/", //
+ new String[] { "urn:miriam:ensembl.plant" }, //
+ new Class<?>[] {}, "MIR:00000205"), //
+
+ /**
+ * Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
+ */
+ ENTREZ("Entrez Gene", //
+ "http://www.ncbi.nlm.nih.gov/gene", //
+ new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"), //
+
+ /**
+ * Gene Ontology: http://amigo.geneontology.org/amigo.
+ */
+ GO("Gene Ontology", //
+ "http://amigo.geneontology.org/amigo", //
+ new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
+
+ /**
+ * HGNC: http://www.genenames.org.
+ */
+ HGNC("HGNC", //
+ "http://www.genenames.org", //
+ new String[] { "urn:miriam:hgnc" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+
+ /**
+ * HGNC symbol: http://www.genenames.org.
+ */
+ HGNC_SYMBOL("HGNC Symbol", //
+ "http://www.genenames.org", //
+ new String[] { "urn:miriam:hgnc.symbol" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+
+ /**
+ * HMDB: http://www.hmdb.ca/.
+ */
+ HMDB("HMDB", //
+ "http://www.hmdb.ca/", //
+ "urn:miriam:hmdb", //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
+
+ /**
+ * InterPro: http://www.ebi.ac.uk/interpro/.
+ */
+ INTERPRO("InterPro", //
+ "http://www.ebi.ac.uk/interpro/", //
+ new String[] { "urn:miriam:interpro" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
+
+ /**
+ * KEGG Compound: http://www.genome.jp/kegg/ligand.html.
+ */
+ KEGG_COMPOUND("Kegg Compound", //
+ "http://www.genome.jp/kegg/ligand.html", //
+ "urn:miriam:kegg.compound", //
+ new Class<?>[] { Chemical.class }, "MIR:00000013"), //
+
+ /**
+ * KEGG Genes: http://www.genome.jp/kegg/genes.html.
+ */
+ KEGG_GENES("Kegg Genes", //
+ "http://www.genome.jp/kegg/genes.html", //
+ new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
+
+ /**
+ * KEGG Orthology: http://www.genome.jp/kegg/ko.html.
+ */
+ KEGG_ORTHOLOGY("KEGG Orthology", //
+ "http://www.genome.jp/kegg/ko.html", //
+ new String[] { "urn:miriam:kegg.orthology" }, //
+ new Class<?>[] {}, "MIR:00000116"), //
+
+ /**
+ * KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
+ */
+ KEGG_PATHWAY("Kegg Pathway", //
+ "http://www.genome.jp/kegg/pathway.html", //
+ "urn:miriam:kegg.pathway", //
+ new Class<?>[] { Reaction.class }, "MIR:00000012"), //
+
+ /**
+ * KEGG Reaction: http://www.genome.jp/kegg/reaction/.
+ */
+ KEGG_REACTION("Kegg Reaction", //
+ "http://www.genome.jp/kegg/reaction/", //
+ "urn:miriam:kegg.reaction", //
+ new Class<?>[] { Reaction.class }, "MIR:00000014"), //
+
+ /**
+ * MeSH 2012: http://www.nlm.nih.gov/mesh/.
+ */
+ MESH_2012("MeSH 2012", //
+ "http://www.nlm.nih.gov/mesh/", //
+ new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
+
+ /**
+ * miRBase Sequence: http://www.mirbase.org/.
+ */
+ MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
+ "http://www.mirbase.org/", //
+ new String[] { "urn:miriam:mirbase" }, //
+ new Class<?>[] {}, "MIR:00000078"), //
+
+ /**
+ * miRBase Mature Sequence: http://www.mirbase.org/.
+ */
+ MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
+ "http://www.mirbase.org/", //
+ new String[] { "urn:miriam:mirbase.mature" }, //
+ new Class<?>[] {}, "MIR:00000235"), //
+
+ /**
+ * miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
+ */
+ MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
+ "http://mirtarbase.mbc.nctu.edu.tw/", //
+ new String[] { "urn:miriam:mirtarbase" }, //
+ new Class<?>[] {}, "MIR:00100739"), //
+
+ /**
+ * Mouse Genome Database: http://www.informatics.jax.org/.
+ */
+ MGD("Mouse Genome Database", //
+ "http://www.informatics.jax.org/", //
+ new String[] { "urn:miriam:mgd" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
+
+ /**
+ * Online Mendelian Inheritance in Man: http://omim.org/.
+ */
+ OMIM("Online Mendelian Inheritance in Man", //
+ "http://omim.org/", //
+ new String[] { "urn:miriam:omim" }, //
+ new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
+
+ /**
+ * PANTHER Family: http://www.pantherdb.org/.
+ */
+ PANTHER("PANTHER Family", //
+ "http://www.pantherdb.org/", //
+ new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
+
+ /**
+ * PDB: http://www.pdbe.org/.
+ */
+ PDB("Protein Data Bank", //
+ "http://www.pdbe.org/", //
+ "urn:miriam:pdb", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
+
+ /**
+ * Protein Family Database: http://pfam.xfam.org/.
+ */
+ PFAM("Protein Family Database", //
+ "http://pfam.xfam.org//", //
+ "urn:miriam:pfam", //
+ new Class<?>[] {}, "MIR:00000028"), //
+
+ /**
+ * PharmGKB Pathways: http://www.pharmgkb.org/.
+ */
+ PHARM("PharmGKB Pathways", //
+ "http://www.pharmgkb.org/", //
+ "urn:miriam:pharmgkb.pathways", //
+ new Class<?>[] {}, "MIR:00000089"), //
+
+ /**
+ * PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
+ */
+ PUBCHEM("PubChem-compound", //
+ "http://pubchem.ncbi.nlm.nih.gov/", //
+ new String[] { "urn:miriam:pubchem.compound" }, //
+ new Class<?>[] { Chemical.class }, "MIR:00000034", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
+ */
+ PUBCHEM_SUBSTANCE("PubChem-substance", //
+ "http://pubchem.ncbi.nlm.nih.gov/", //
+ new String[] { "urn:miriam:pubchem.substance" }, //
+ new Class<?>[] { Chemical.class }, "MIR:00000033", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
+ */
+ PUBMED("PubMed", //
+ "http://www.ncbi.nlm.nih.gov/PubMed/", //
+ new String[] { "urn:miriam:pubmed" }, //
+ new Class<?>[] { BioEntity.class }, "MIR:00000015", //
+ new Class<?>[] { Reaction.class }), //
+
+ /**
+ * Reactome: http://www.reactome.org/.
+ */
+ REACTOME("Reactome", //
+ "http://www.reactome.org/", //
+ "urn:miriam:reactome", //
+ new Class<?>[] { Reaction.class }, "MIR:00000018"), //
+
+ /**
+ * RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
+ */
+ REFSEQ("RefSeq", //
+ "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
+ "urn:miriam:refseq", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
+
+ /**
+ * SGD: http://www.yeastgenome.org/.
+ */
+ SGD("Saccharomyces Genome Database", //
+ "http://www.yeastgenome.org/", //
+ "urn:miriam:sgd", //
+ new Class<?>[] {}, "MIR:00000023"),
+
+ /**
+ * The Arabidopsis Information Resource (TAIR) maintains a database of genetic
+ * and molecular biology data for the model higher plant Arabidopsis thaliana.
+ * The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
+ * http://arabidopsis.org/index.jsp.
+ */
+ TAIR_LOCUS("TAIR Locus", //
+ "http://arabidopsis.org/index.jsp", //
+ "urn:miriam:tair.locus", //
+ new Class<?>[] {}, "MIR:00000050"),
+
+ /**
+ * Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
+ */
+ TAXONOMY("Taxonomy", //
+ "http://www.ncbi.nlm.nih.gov/taxonomy/", //
+ "urn:miriam:taxonomy", //
+ new Class<?>[] {}, "MIR:00000006"),
+ /**
+ * Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
+ * http://ctdbase.org/detail.go
+ */
+ TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
+ "http://ctdbase.org/", //
+ "urn:miriam:ctd.chemical", //
+ new Class<?>[] {}, "MIR:00000098"), //
+
+ /**
+ * UniGene: http://www.ncbi.nlm.nih.gov/unigene.
+ */
+ UNIGENE("UniGene", //
+ "http://www.ncbi.nlm.nih.gov/unigene", //
+ "urn:miriam:unigene", //
+ new Class<?>[] {}, "MIR:00000346"),
+
+ /**
+ * Uniprot: http://www.uniprot.org/.
+ */
+ UNIPROT("Uniprot", //
+ "http://www.uniprot.org/", //
+ "urn:miriam:uniprot", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
+
+ /**
+ * UniProt Isoform: http://www.uniprot.org/.
+ */
+ UNIPROT_ISOFORM("UniProt Isoform", //
+ "http://www.uniprot.org/", //
+ "urn:miriam:uniprot.isoform", //
+ new Class<?>[] { Protein.class }, "MIR:00000388"),
+
+ /**
+ * Unknown reference type...
+ */
+ UNKNOWN("Unknown", //
+ null, //
+ new String[] {}, //
+ new Class<?>[] {}, null),
+
+ /**
+ * Wikidata: https://www.wikidata.org/.
+ */
+ WIKIDATA("Wikidata", //
+ "https://www.wikidata.org/", //
+ new String[] { "urn:miriam:wikidata" }, //
+ new Class<?>[] {}, "MIR:00000549"), //
+
+ /**
+ * WikiPathways: http://www.wikipathways.org/.
+ */
+ WIKIPATHWAYS("WikiPathways", //
+ "http://www.wikipathways.org/", //
+ new String[] { "urn:miriam:wikipathways" }, //
+ new Class<?>[] {}, "MIR:00000076"), //
+
+ /**
+ * Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
+ */
+ WIKIPEDIA("Wikipedia (English)", //
+ "http://en.wikipedia.org/wiki/Main_Page", // /
+ new String[] { "urn:miriam:wikipedia.en" }, //
+ new Class<?>[] {}, "MIR:00000384"),
+
+ /**
+ * WormBase: http://wormbase.bio2rdf.org/fct.
+ */
+ WORM_BASE("WormBase", //
+ "http://wormbase.bio2rdf.org/fct", // /
+ new String[] { "urn:miriam:wormbase" }, //
+ new Class<?>[] {}, "MIR:00000027");
+
+ /**
+ * User friendly name.
+ */
+ private String commonName;
+
+ /**
+ * url to homepage of given resource type.
+ */
+ private String dbHomepage;
+
+ /**
+ * Identifier of the database in miriam registry.
+ */
+ private String registryIdentifier;
+
+ /**
+ * Valid uris to this resource.
+ */
+ private List<String> uris = new ArrayList<String>();
+
+ /**
+ * Classes that can be annotated by this resource.
+ */
+ private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
+
+ /**
+ * When class from this list is marked as "require at least one annotation" then
+ * annotation of this type is valid.
+ */
+ private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * homepage of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uris
+ * {@link #uris}
+ * @param classes
+ * {@link #validClass}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ */
+ MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier) {
+ this(commonName, dbHomePage, uris, classes, registryIdentifier, new Class<?>[] {});
+ }
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * homepage of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uris
+ * {@link #uris}
+ * @param classes
+ * {@link #validClass}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ * @param requiredClasses
+ * {@link #requiredClasses}
+ */
+ MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier,
+ Class<?>[] requiredClasses) {
+ this.commonName = commonName;
+ this.dbHomepage = dbHomePage;
+ for (String string : uris) {
+ this.uris.add(string);
+ }
+ for (Class<?> clazz : classes) {
+ this.validClass.add((Class<? extends BioEntity>) clazz);
+ }
+ for (Class<?> clazz : requiredClasses) {
+ this.requiredClass.add((Class<? extends BioEntity>) clazz);
+ }
+ this.registryIdentifier = registryIdentifier;
+ }
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * homepage of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uri
+ * one of {@link #uris}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ * @param classes
+ * {@link #validClass}
+ */
+ MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier) {
+ this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier);
+ }
+
+ /**
+ *
+ * @return {@link #commonName}
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ *
+ * @return {@link #uris}
+ */
+ public List<String> getUris() {
+ return uris;
+ }
+
+ /**
+ *
+ * @return {@link #validClass}
+ */
+ public List<Class<? extends BioEntity>> getValidClass() {
+ return validClass;
+ }
+
+ /**
+ * Returns {@link MiriamType} associated with parameter uri address.
+ *
+ * @param uri
+ * uri to check
+ * @return {@link MiriamType} for given uri
+ */
+ public static MiriamType getTypeByUri(String uri) {
+ for (MiriamType mt : MiriamType.values()) {
+ for (String string : mt.getUris()) {
+ if (string.equalsIgnoreCase(uri)) {
+ return mt;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the dbHomepage
+ * @see #dbHomepage
+ */
+ public String getDbHomepage() {
+ return dbHomepage;
+ }
+
+ /**
+ * @return the registryIdentifier
+ * @see #registryIdentifier
+ */
+ public String getRegistryIdentifier() {
+ return registryIdentifier;
+ }
+
+ /**
+ * @return the requiredClass
+ * @see #requiredClass
+ */
+ public List<Class<? extends BioEntity>> getRequiredClass() {
+ return requiredClass;
+ }
+
+ /**
+ * Returns {@link MiriamType} associated with {@link #commonName}.
+ *
+ * @param string
+ * {@link #commonName}
+ * @return {@link MiriamType} for given name
+ */
+ public static MiriamType getTypeByCommonName(String string) {
+ for (MiriamType mt : MiriamType.values()) {
+ if (string.equalsIgnoreCase(mt.getCommonName())) {
+ return mt;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Transforms identifier into {@link MiriamData}.
+ *
+ * @param generalIdentifier
+ * identifier in the format NAME:IDENTIFIER. Where NAME is the name
+ * from {@link MiriamType#commonName} and IDENTIFIER is reasource
+ * identifier.
+ * @return {@link MiriamData} representing generalIdentifier, when identifier is
+ * invalid InvalidArgumentException is thrown
+ */
+ public static MiriamData getMiriamDataFromIdentifier(String generalIdentifier) {
+ int index = generalIdentifier.indexOf(":");
+ if (index < 0) {
+ throw new InvalidArgumentException("Identifier doesn't contain type");
+ }
+ String type = generalIdentifier.substring(0, index);
+ String id = generalIdentifier.substring(index + 1);
+ for (MiriamType mt : MiriamType.values()) {
+ if (mt.getCommonName().equalsIgnoreCase(type)) {
+ return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, id);
+ }
+ }
+ throw new InvalidArgumentException("Unknown miriam type: " + type + " (id: " + id + ")");
+ }
+
+ /**
+ * Creates {@link MiriamData} from miriam uri.
+ *
+ * @param miriamUri
+ * miriam uri defining {@link MiriamData}
+ * @return {@link MiriamData} from miriam uri
+ */
+ public static MiriamData getMiriamByUri(String miriamUri) {
+ // this hack is due to CellDesigner issue (CellDesigner incorectly handle
+ // with identifiers that have ":" inside resource ":" inside resource with
+ // "%3A" and also the last ":"
+ miriamUri = miriamUri.replace("%3A", ":");
+
+ String foundUri = "";
+ MiriamType foundType = null;
+
+ for (MiriamType type : MiriamType.values()) {
+ for (String uri : type.getUris()) {
+ if (miriamUri.startsWith(uri + ":")) {
+ if (uri.length() > foundUri.length()) {
+ foundType = type;
+ foundUri = uri;
+ }
+ }
+ }
+ }
+ if (foundType != null) {
+ return new MiriamData(foundType, miriamUri.substring(foundUri.length() + 1));
+ }
+ throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
+ }
}
diff --git a/web/src/main/webapp/WEB-INF/resources/log4j.properties b/web/src/main/webapp/WEB-INF/resources/log4j.properties
index 2dd44999683a1660220521669ce42700cc847713..cce0380c86937576a3e43eb5c8567cfe25a20c0f 100644
--- a/web/src/main/webapp/WEB-INF/resources/log4j.properties
+++ b/web/src/main/webapp/WEB-INF/resources/log4j.properties
@@ -33,3 +33,6 @@ log4j.logger.lcsb.mapviewer.db.model.map.reaction.ReactionComparator=warn
log4j.logger.lcsb.mapviewer.db.model.map.species.ProteinComparator=warn
log4j.logger.lcsb.mapviewer.db.model.map.layout.alias.ComplexAliasComparator=warn
log4j.logger.lcsb.mapviewer.db.model.map.Element=info
+
+#Silence miriam debug logs
+log4j.logger.uk.ac.ebi.miriam.lib=warn