diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index fe1cbc680..0d38b3f7e 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,13 +2,27 @@ name: build on: push: - branches: [ master ] + branches: [ series/3.1.0 ] pull_request: - branches: [ master ] + branches: [ series/3.1.0 ] jobs: - build: + java8: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Java + uses: actions/setup-java@v4 + with: + distribution: 'temurin' + java-version: 8 + cache: maven + - name: Build with Maven + run: mvn -f pom-java8.xml clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Dproject.build.sourceEncoding=UTF-8 -Djunit5.excludeGroups=webservice,mysql + + build: + needs: java8 runs-on: ubuntu-latest steps: diff --git a/CITATION.cff b/CITATION.cff index 76ec07fb0..9c9192b3b 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.0.23 -date-released: '2023-08-07' +version: 3.1.4 +date-released: '2024-12-19' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index 49786071c..fee8fd1b2 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.0.23`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.4`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.0.23 + 3.1.4 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.0.23' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.4' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.0.23' +'org.bridgedb:org.bridgedb.bio:jar:3.1.4' ``` @@ -58,6 +58,8 @@ able to compile with a simple: mvn clean install -Dgpg.skip ``` +When compiling the Java8-compatible components, use the `pom-java8.xml` file instead, with `mvn -f pom-java8.xml`. + You can find the libraries in the folder called "target", in each sublibrary folder (used to be called "dist" in ant). If you want to ignore failing tests, e.g. because you are not online, @@ -127,13 +129,13 @@ Making releases --------------- If it is time for a release, first, update `org.bridgedb/src/main/resources/version.props` (for BridgeDb), -this `README.md` and `CITATION.cff` (for Zenodo). +this `README.md` and `CITATION.cff` (for Zenodo), as well as the `pom-java8.xml`. To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.0.23 +mvn versions:set -DnewVersion=3.1.4 mvn clean deploy ``` @@ -143,7 +145,7 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.0.23-SNAPSHOT +mvn versions:set -DnewVersion=3.1.5-SNAPSHOT mvn clean deploy ``` diff --git a/UPGRADE_NOTES.md b/UPGRADE_NOTES.md index f6b3f5dab..53aa00618 100644 --- a/UPGRADE_NOTES.md +++ b/UPGRADE_NOTES.md @@ -1,35 +1,49 @@ -Upgrade notes to BridgeDb 2.0 +# Upgrade notes to BridgeDb 2.0 -1. Initialing data sources +## 1. Initialing data sources Replace +```java BioDataSource.init(); +``` with +```java DataSourceTxt.init(); +``` -2. Getting DataSource's +## 2. Getting DataSource's Replace +```java DataSource ds = DataSource.getBySystemCode("Ck"); +``` with +```java DataSource ds = DataSource.getExistingBySystemCode("Ck"); +``` Similarly, and more important: +```java DataSource ds = DataSource.getByFullName("PubChem-compound"); +``` with +```java DataSource ds = DataSource.getExistingByFullName("PubChem-compound"); +``` -The latter two new methods throw an IllegalArgumentException if the DataSource does not exist. +The latter two new methods throw an `IllegalArgumentException` if the `DataSource` does not exist. Use one of the following two methods to check first: +```java DataSource.systemCodeExists("Ck"); DataSource.fullNameExists("PubChem-compound"); +``` diff --git a/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java b/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java index 2744b8743..1c9c7a97b 100644 --- a/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java +++ b/benchmarking/src/org/bridgedb/benchmarking/ComparisonScript.java @@ -300,7 +300,7 @@ enum Connector PICR ("picr", "idmapper-picr:"), SYNERGIZER_ENSEMBL ("synergizer(ensembl)", "idmapper-synergizer:authority=ensembl&species=Homo sapiens"), - BRIDGEWEBSERVICE ("BridgeWebservice", "idmapper-bridgerest:http://webservice.bridgedb.org/Human"), + BRIDGEWEBSERVICE ("BridgeWebservice", "idmapper-bridgerest:https://webservice.bridgedb.org/Human"), BRIDGEWEBSERVICE_LOCAL ("BridgeWebservice(local)", "idmapper-bridgerest:http://localhost:8183/Human"), BIOMART ("biomart", "idmapper-biomart:http://www.biomart.org/biomart/martservice?mart=ensembl&dataset=hsapiens_gene_ensembl"), CRONOS ("cronos", "idmapper-cronos:hsa"), diff --git a/benchmarking/test/org/bridgedb/benchmarking/TestAll.java b/benchmarking/test/org/bridgedb/benchmarking/TestAll.java index 5be513373..f1cc3d2e1 100644 --- a/benchmarking/test/org/bridgedb/benchmarking/TestAll.java +++ b/benchmarking/test/org/bridgedb/benchmarking/TestAll.java @@ -74,7 +74,7 @@ public void testBridgeWebservice() throws IDMapperException, ClassNotFoundExcept Class.forName("org.bridgedb.webservice.bridgerest.BridgeRest"); Xref insr1 = new Xref ("ENSG00000171105", DataSource.getBySystemCode("EnHs")); Xref insr2 = new Xref ("3643", DataSource.getBySystemCode("L")); - basicMapperTest (measure, "bridgerest", "idmapper-bridgerest:http://webservice.bridgedb.org/Human", insr1, insr2); + basicMapperTest (measure, "bridgerest", "idmapper-bridgerest:https://webservice.bridgedb.org/Human", insr1, insr2); } public void testFile() throws IDMapperException, ClassNotFoundException diff --git a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl index 42d8576ad..ffbb03311 100755 --- a/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl +++ b/dbbuilder/src/org/bridgedb/extract/Ensembl_ETL_Device_v18_local.pl @@ -743,7 +743,7 @@ %{$GeneTables{CCDS}} = ('NAME' => ['CCDS', 'Cc'], 'SYSTEM' => ["\'Consensus CDS Protein Set (NCBI)\'", "\'$dateArg\'", "\'ID\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", + "\'https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=~&ORGANISM=".$genus_species."\'", "\'\'", "\'ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'PRIMARY KEY (ID)' @@ -863,7 +863,7 @@ %{$GeneTables{RGD}} = ('NAME' => ['RGD', 'R'], 'SYSTEM' => ["\'Rat Genome Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF|Synonyms\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", + "\'https://rgd.mcw.edu/query/query.cgi?id=~\'", "\'\'", "\'ftp://rgd.mcw.edu/pub/\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', @@ -916,8 +916,8 @@ %{$GeneTables{GrameneGenes}} = ('NAME' => ['GrameneGenes', 'Gg'], 'SYSTEM' => ["\'Gramene Genes Database\'", "\'$dateArg\'", "\'ID|Symbol\\\\sBF|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", - "\'http://www.gramene.org\'"], + "\'https://www.gramene.org/db/genes/search_gene?acc=~\'", "\'\'", + "\'https://www.gramene.org\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Symbol VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', @@ -926,8 +926,8 @@ %{$GeneTables{GramenePathway}} = ('NAME' => ['GramenePathway', 'Gm'], 'SYSTEM' => ["\'Gramene Pathway\'", "\'$dateArg\'", "\'ID|Description\\\\BF\|\'", "\'\|$species\|\'", "\'\'", - "\'http://www.gramene.org/pathway\'", "\'\'", - "\'http://www.gramene.org/pathway\'"], + "\'https://www.gramene.org/pathway\'", "\'\'", + "\'https://www.gramene.org/pathway\'"], 'HEADER' => ['ID VARCHAR(128) NOT NULL DEFAULT \'\'', 'Description VARCHAR(255) DEFAULT NULL', 'PRIMARY KEY (ID)' diff --git a/examples/pom.xml b/examples/pom.xml index 1e6f5ed1b..d2a705db1 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 4.0.0 org.bridgedb.examples @@ -65,22 +65,10 @@ wsdl4j wsdl4j - 1.6.2 + 1.6.3 jar runtime - - org.apache.axis - axis - 1.4 - jar - - - org.apache.axis - axis-jaxrpc - 1.4 - jar - diff --git a/examples/src/org/bridgedb/examples/ChebiPubchemExample.java b/examples/src/org/bridgedb/examples/ChebiPubchemExample.java index eadc6a5df..6b507827e 100644 --- a/examples/src/org/bridgedb/examples/ChebiPubchemExample.java +++ b/examples/src/org/bridgedb/examples/ChebiPubchemExample.java @@ -15,7 +15,7 @@ public static void main (String[] args) throws ClassNotFoundException, IDMapperE // We'll use the BridgeRest webservice in this case, as it does compound mapping fairly well. // We'll use the human database, but it doesn't really matter which species we pick. Class.forName ("org.bridgedb.webservice.bridgerest.BridgeRest"); - IDMapper mapper = BridgeDb.connect("idmapper-bridgerest:http://webservice.bridgedb.org/Human"); + IDMapper mapper = BridgeDb.connect("idmapper-bridgerest:https://webservice.bridgedb.org/Human"); DataSourceTxt.init(); // Start with defining the Chebi identifier for diff --git a/examples/src/org/bridgedb/examples/ExHello.java b/examples/src/org/bridgedb/examples/ExHello.java index baf811d6c..35efbd6e2 100644 --- a/examples/src/org/bridgedb/examples/ExHello.java +++ b/examples/src/org/bridgedb/examples/ExHello.java @@ -23,7 +23,7 @@ public static void main(String args[]) throws ClassNotFoundException, IDMapperEx DataSourceTxt.init(); // now we connect to the driver and create a IDMapper instance. - IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human"); + IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:https://webservice.bridgedb.org/Human"); // We create an Xref instance for the identifier that we want to look up. // In this case we want to look up Entrez gene 3643. diff --git a/examples/src/org/bridgedb/examples/ExIDSearch.java b/examples/src/org/bridgedb/examples/ExIDSearch.java index f309b89db..60029a480 100644 --- a/examples/src/org/bridgedb/examples/ExIDSearch.java +++ b/examples/src/org/bridgedb/examples/ExIDSearch.java @@ -20,7 +20,7 @@ public static void main(String args[]) throws ClassNotFoundException, IDMapperEx DataSourceTxt.init(); // now we connect to the driver and create a IDMapper instance. - IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:http://webservice.bridgedb.org/Human"); + IDMapper mapper = BridgeDb.connect ("idmapper-bridgerest:https://webservice.bridgedb.org/Human"); String query = "3643"; diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index d46207678..c0f0be58d 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index d3c029c9f..655878bd4 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -1,21 +1,21 @@ -Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe -Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe +Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe +Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene -BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction -BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway -BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway -BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein -BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite +BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene +BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction +BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway +BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway +BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein +BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite -CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene +CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite -ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite +ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology -Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene -Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene -Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene -Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway -Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene +Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -54,8 +54,7 @@ ICD-11 ICD11 http://www.who.int/classifications/icd/en/ 1A95 unknown Homo sapie Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina illumina.probe probe InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction -InterPro I http://www.ebi.ac.uk/interpro/ http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein -IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein +InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication ISSN issn https://portal.issn.org https://portal.issn.org/resource/ISSN/$id 1776-3045 publication 1 urn:miriam:issn ^\d{4}-\d{3}[\dX]$ ISSN P236 issn publication @@ -77,15 +76,15 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction -miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene NCBI Protein Np http://www.ncbi.nlm.nih.gov/protein http://www.ncbi.nlm.nih.gov/protein/$id CAA71118.1 protein 1 urn:miriam:ncbiprotein ^\w+\d+(\.\d+)?$ NCBI Protein ncbiprotein protein NCI Pathway Interaction Database Pid http://pid.nci.nih.gov/ http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id pi3kcipathway pathway 1 urn:miriam:pid.pathway ^\w+$ NCI Pathway Interaction Database pid.pathway pathway OMIM Om http://omim.org/ http://omim.org/entry/$id 603903 gene 0 urn:miriam:mim ^[*#+%^]?\d{6}$ OMIM P492 omim gene,disease -OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ ensembl gene +OpenTargets Opt https://www.opentargets.org/ https://genetics.opentargets.org/gene/$id ENSG00000169174 gene 1 ^ENS[A-Z]*[FPTG]\d{11}$ gene ORCID orcid https://orcid.org https://orcid.org/$id 0000-0002-5355-2576 other Homo sapiens 1 urn:miriam:orcid ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ ORCID P496 orcid other,author Orphanet On http://www.orpha.net/consor/ https://identifiers.org/orphanet:$id 85163 other Homo sapiens 1 urn:miriam:orphanet ^\d+$ Bio2RDF orphanet other Oryzabase Ob http://www.shigen.nig.ac.jp/rice/oryzabase http://www.shigen.nig.ac.jp/rice/oryzabase/gateway/gatewayAction.do?target=symbol&id=$id 468 gene Oryza sativa 1 Ob Oryzabase oryzabase.gene gene @@ -110,9 +109,9 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene -RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene +RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene +Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein @@ -123,9 +122,9 @@ SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/prote SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki subtiwiki gene SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM supfam protein SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein -SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids swisslipid metabolite +SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology -TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene +TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein @@ -133,7 +132,7 @@ TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser P2576 ucsc gene UMLS CUI Cu https://www.nlm.nih.gov/research/umls/rxnorm/index.html https://www.ncbi.nlm.nih.gov/medgen/{$id} 760050 other Homo sapiens 1 urn:miriam:medgen ^[CN]*\d{4,7}$ MedGen medgen other Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 ^UPA\d{5}$ Unipathway upa pathway -Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein +UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein VMH metabolite VmhM http://www.vmh.life https://www.vmh.life/#metabolite/$id h2o metabolite 1 [a-zA-Z0-9_\(\_\)\[\]]+ VMH Life_Metabolite vmhmetabolite metabolite Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 1-FEH+w3 gene Triticum aestivum 1 Wn Wheat gene names graingenes.symbol gene Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs graingenes.reference gene diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv index f20b733ea..940d8117d 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv @@ -40,9 +40,11 @@ Plasmodium falciparum Malaria parasite Pf 5833 Prymnesium parvum Pp 97485 Populus trichocarpa Western Balsam Poplar Pi 3694 Rattus norvegicus Rat Rn 10116 +Rosmarinus officinalis Rosemary Ro 39367 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index d3c029c9f..4b50c0d78 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -1,21 +1,21 @@ -Affy X http://www.affymetrix.com/ https://www.affymetrix.com/LinkServlet?probeset=$id 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe -Agilent Ag http://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe +Affy X 1851_s_at probe 0 urn:miriam:affy.probeset \d{4,}((_[asx])?_at)? Affymetrix Probeset affy.probeset probe +Agilent Ag https://agilent.com A_24_P98555 probe 0 Ag A_\d+_.+ Agilent agilent.probe probe AOP-Wiki KE AopKe https://aopwiki.org/ https://aopwiki.org/events/$id 3 unknown 1 urn:miriam:aop.events ^\d+$ AOP-Wiki Key Events aop.events unknown,event AOP-Wiki AOP Aop https://aopwiki.org/ https://aopwiki.org/aops/$id 3 pathway 1 urn:miriam:aop ^\d+$ AOP-Wiki Adverse Outcome Pathway aop pathway AOP-Wiki KER AopKer https://aopwiki.org/ https://aopwiki.org/relationships/$id 5 interaction 1 urn:miriam:aop.relationships ^\d+$ AOP-Wiki Key Event Relationships aop.relationships interaction AOP-Wiki Stressor AopS https://aopwiki.org/ https://aopwiki.org/stressors/$id 222 metabolite 1 urn:miriam:aop.stressor ^\d+$ AOP-Wiki Stressor aop.stressor metabolite BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch=$id interaction 1 ^\d+$ BIND interaction -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene -BioGrid Bg http://thebiogrid.org/ http://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction -BioModels Database Bm http://www.ebi.ac.uk/biomodels/ http://www.ebi.ac.uk/biomodels-main/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway -BioSystems Bs http://www.ncbi.nlm.nih.gov/biosystems/ http://www.ncbi.nlm.nih.gov/biosystems/$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway -BRENDA Br http://www.brenda-enzymes.org/ http://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein -BRENDA Ligands Brl http://www.brenda-enzymes.org/ http://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite +BioCyc Bc https://biocyc.org https://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^\w+\:[A-Za-z0-9-]+$ BioCyc biocyc gene +BioGrid Bg https://thebiogrid.org/ https://thebiogrid.org/$id 31623 interaction 1 urn:miriam:biogrid ^\d+$ BioGRID biogrid interaction +BioModels Database Bm https://www.ebi.ac.uk/biomodels/ https://www.ebi.ac.uk/biomodels/$id BIOMD0000000048 pathway 1 urn:miriam:biomodels.db ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BioModels Database biomodels.db pathway +BioSystems Bs https://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:$id 1 pathway 1 urn:miriam:biosystems ^\d+$ BioSystems biosystems pathway +BRENDA Br https://www.brenda-enzymes.org/ https://www.brenda-enzymes.org/enzyme.php?ecno=$id 1.1.1.1 protein 1 urn:miriam:brenda ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ BRENDA brenda protein +BRENDA Ligands Brl https://www.brenda-enzymes.org/ https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$id 278 metabolite 1 Brl ^\d+$ BRENDA Ligands brenda.ligand metabolite CAS Ca https://commonchemistry.cas.org/ https://commonchemistry.cas.org/detail?cas_rn=$id 50-00-0 metabolite 1 urn:miriam:cas ^\d{1,7}\-\d{2}\-\d$ CAS P231 cas metabolite -CCDS Cc http://identifiers.org/ccds/ http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene +CCDS Cc https://identifiers.org/ccds/ https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=$id CCDS33337.1 gene 0 urn:miriam:ccds ^CCDS\d+\.\d+$ Consensus CDS ccds gene ChEMBL compound Cl https://www.ebi.ac.uk/chembldb/ https://www.ebi.ac.uk/chembl/compound/inspect/$id CHEMBL308052 metabolite 1 urn:miriam:chembl.compound ^CHEMBL\d+$ ChEMBL compound P592 chembl.compound metabolite -ChEBI Ce http://www.ebi.ac.uk/chebi/ http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite -Chemspider Cs http://www.chemspider.com/ http://www.chemspider.com/Chemical-Structure.$id.html 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite +ChEBI Ce https://www.ebi.ac.uk/chebi/ https://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id CHEBI:36927 metabolite 1 urn:miriam:chebi ^(CHEBI:)?\d+$ ChEBI P683 chebi metabolite +Chemspider Cs https://www.chemspider.com/ https://www.chemspider.com/$id 56586 metabolite 1 urn:miriam:chemspider ^\d+$ ChemSpider P661 chemspider metabolite CodeLink Ge http://www.appliedmicroarrays.com/ GE86325 probe 0 Ge CodeLink codelink probe Complex Portal Cpx https://www.ebi.ac.uk/complexportal/ https://www.ebi.ac.uk/complexportal/complex/$id CPX-373 complex 1 urn:miriam:complexportal ^CPX-[0-9]+$ Complex Portal complexportal complex Database of Interacting Proteins Dip http://dip.doe-mbi.ucla.edu/ http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id DIP-743N interaction 1 urn:miriam:dip ^DIP[\:\-]\d{3}[EN]$ Database of Interacting Proteins dip interaction @@ -34,12 +34,12 @@ FlyBase F http://flybase.org/ http://flybase.org/reports/$id.html FBgn0011293 ge GenBank G http://www.ncbi.nlm.nih.gov/genbank/ http://www.ncbi.nlm.nih.gov/nuccore/$id NW_004190323 gene 0 urn:miriam:insdc (\w\d{5})|(\w{2}\d{6})|(\w{3}\d{5}) GenBank insdc gene Gene Wiki Gw http://en.wikipedia.org/wiki/Portal:Gene_Wiki http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id 1017 gene 0 urn:miriam:genewiki \d+ Gene Wiki P351 genewiki gene GeneOntology T http://www.ebi.ac.uk/QuickGO/ http://www.ebi.ac.uk/QuickGO/GTerm?id=$id GO:0006915 ontology 0 urn:miriam:go ^GO:\d{7}$ Gene Ontology P686 go ontology -Gramene Arabidopsis EnAt http://www.gramene.org/ http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene -Gramene Genes DB Gg http://www.gramene.org/ http://www.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene -Gramene Literature Gl http://www.gramene.org/ http://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene -Gramene Maize EnZm http://www.ensembl.org http://www.maizesequence.org/Zea_mays/Gene/Summary?g=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene -Gramene Pathway Gp http://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway -Gramene Rice EnOj http://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene +Gramene Arabidopsis EnAt https://www.gramene.org/ https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=$id ATMG01360 gene Arabidopsis thaliana 1 EnAt AT[\dCM]G\d{5} Gramene Arabidopsis gene +Gramene Genes DB Gg https://www.gramene.org/ https://archive.gramene.org/db/genes/search_gene?acc=$id GR:0060184 gene 1 Gg GR:\d+ Gramene Genes gramene.gene gene +Gramene Literature Gl https://www.gramene.org/ https://www.gramene.org/db/literature/pub_search?ref_id=$id 6200 gene 0 Gl Gramene Literature gramene.reference gene +Gramene Maize EnZm https://www.ensembl.org https://ensembl.gramene.org/Zea_mays/Search/Results?q=$id GRMZM2G174107 gene 1 EnZm Gramene Maize gene +Gramene Pathway Gp https://www.gramene.org/pathway AAH72400 pathway 1 Gp Gramene Pathway pathway +Gramene Rice EnOj https://www.gramene.org/ http://plants.ensembl.org/Oryza_sativa/Gene/Summary?db=otherfeatures;g=$id Os05g0113900 gene 1 EnOj Gramene Rice gene Guide to Pharmacology Gpl http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id 1627 gene 1 ^\d+$ Guide to Pharmacology Targets P5458 iuphar.receptor gene Guide to Pharmacology Targets Gpt http://www.guidetopharmacology.org/ https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id 256 metabolite 1 ^\d+$ Guide to Pharmacology P595 iuphar.ligand metabolite HGNC H http://www.genenames.org https://www.genenames.org/data/gene-symbol-report/#!/symbol/$id DAPK1 gene Homo sapiens 1 urn:miriam:hgnc.symbol ^[A-Za-z0-9]+ HGNC Symbol P353 hgnc.symbol gene @@ -54,8 +54,7 @@ ICD-11 ICD11 http://www.who.int/classifications/icd/en/ 1A95 unknown Homo sapie Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina illumina.probe probe InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction -InterPro I http://www.ebi.ac.uk/interpro/ http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein -IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein +InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication ISSN issn https://portal.issn.org https://portal.issn.org/resource/ISSN/$id 1776-3045 publication 1 urn:miriam:issn ^\d{4}-\d{3}[\dX]$ ISSN P236 issn publication @@ -77,8 +76,8 @@ MetaboLights Compounds Ml http://www.ebi.ac.uk/metabolights/ http://www.ebi.ac.u MetaCyc Mc http://www.metacyc.org/ http://www.metacyc.org/META/NEW-IMAGE?type=NIL&object=$id D-GLUTAMATE-OXIDASE-RXN interaction 1 Mc MetaCyc metacyc.reaction interaction MGI M http://www.informatics.jax.org/ http://www.informatics.jax.org/marker/$id MGI:2442292 gene Mus musculus 1 urn:miriam:mgi ^MGI:\d+$ Mouse Genome Database P671 mgi gene MINT Mi http://mint.bio.uniroma2.it/mint/ http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id MINT-10000 interaction 1 urn:miriam:mint ^MINT\-\d{1,5}$ MINT mint interaction -miRBase mature sequence Mbm http://www.mirbase.org/ http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene -miRBase Sequence Mb http://microrna.sanger.ac.uk/ http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene +miRBase mature sequence Mbm https://www.mirbase.org/ https://mirbase.org/mature/$id MIMAT0000001 gene 1 urn:miriam:mirbase.mature MIMAT\d{7} miRBase mature sequence P2871 mirbase.mature gene +miRBase Sequence Mb http://microrna.sanger.ac.uk/ https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id MI0000001 gene 1 urn:miriam:mirbase MI\d{7} miRBase Sequence P2870 mirbase gene Mondo Mo https://mondo.monarchinitiative.org/ https://monarchinitiative.org/disease/$id MONDO:0000001 disease 1 MONDO:\d{7} Mondo Disease Ontology P5270 mondo disease NanoMILE Nmnm https://cordis.europa.eu/project/id/310451 NP00262 material 1 ^NP\d{5}$ material NASC Gene N http://arabidopsis.info/ ATMG00960-TAIR-G gene Arabidopsis thaliana 1 N AT[\dCM]G\d{5}\-TAIR\-G NASC Gene gene @@ -110,9 +109,9 @@ Reactome Re http://www.reactome.org/ https://reactome.org/content/detail/$id R-H RefSeq Q http://www.ncbi.nlm.nih.gov/projects/RefSeq/ https://www.ncbi.nlm.nih.gov/protein/$id NP_012345 gene 1 urn:miriam:refseq ^(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|ZP)_\d+$ RefSeq P656 refseq gene RESID Res http://www.ebi.ac.uk/RESID/ http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] AA0001 protein 1 urn:miriam:resid ^AA\d{4}$ RESID resid protein Rfam Rf https://rfam.org/family/$id RF00066 gene 1 Rf RF\d+ RFAM rfam gene -RGD R http://rgd.mcw.edu/ http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene +RGD R https://rgd.mcw.edu/ https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id 2018 gene Rattus norvegicus 1 urn:miriam:rgd ^\d{4,7}$ Rat Genome Database P3853 rgd gene Rhea Rh http://www.ebi.ac.uk/rhea/ http://www.ebi.ac.uk/rhea/reaction.xhtml?id=$id 12345 interaction 1 urn:miriam:rhea ^\d{5}$ Rhea rhea interaction -Rice Ensembl Gene Os http://www.gramene.org/Oryza_sativa http://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene +Rice Ensembl Gene Os https://www.gramene.org/Oryza_sativa https://www.gramene.org/Oryza_sativa/geneview?gene=$id Os04g54800 gene Oryza sativa 1 Os Rice Ensembl Gene gene SGD D http://www.yeastgenome.org/ http://www.yeastgenome.org/locus/$id S000028457 gene Saccharomyces cerevisiae 1 urn:miriam:sgd ^S\d+$ SGD P3406 sgd gene Small Molecule Pathway Database Sm http://www.smpdb.ca/pathways https://smpdb.ca/view/$id SMP00001 pathway 1 urn:miriam:smpdb ^SMP\d{5}$ Small Molecule Pathway Database smpdb pathway SMART Sma http://smart.embl-heidelberg.de/ http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id SM00015 protein 1 urn:miriam:smart ^SM\d{5}$ SMART P3524 smart protein @@ -123,9 +122,9 @@ SubstrateDB Sdb http://substrate.burnham.org/ http://substrate.burnham.org/prote SubtiWiki Bsu http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id BSU29180 gene Bacillus subtilis 1 urn:miriam:subtiwiki ^BSU\d{5}$ SubtiWiki subtiwiki gene SUPFAM Sf http://supfam.org/SUPERFAMILY/ http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id SSF57615 protein 1 urn:miriam:supfam ^\w+$ SUPFAM supfam protein SWISS-MODEL Sw http://swissmodel.expasy.org/ http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id P23298 protein 1 urn:miriam:swiss-model ^\w+$ SWISS-MODEL swiss-model protein -SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids swisslipid metabolite +SwissLipids Sl http://www.swisslipids.org/ http://www.swisslipids.org/#/entity/$id/ SLM:000048885 metabolite 1 ^SLM:\d+$ SwissLipids slm metabolite Systems Biology Ontology Sbo http://www.ebi.ac.uk/sbo/ http://www.ebi.ac.uk/sbo/main/$id SBO:0000262 ontology 1 urn:miriam:sbo ^SBO:\d{7}$ Systems Biology Ontology sbo ontology -TAIR A http://arabidopsis.org/index.jsp http://arabidopsis.org/servlets/TairObject?type=locus&name=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene +TAIR A https://www.arabidopsis.org/ https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=$id AT1G01030 gene Arabidopsis thaliana 1 urn:miriam:tair.locus ^AT[1-5]G\d{5}$ TAIR Locus tair.locus gene TIGR Ti http://www.jcvi.org/ 12012.t00308 gene 1 Ti TIGR gene TTD Drug Td http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDRUG.asp?ID=$id DAP000773 metabolite 1 urn:miriam:ttd.drug ^DAP\d+$ TTD Drug ttd.drug metabolite TTD Target Tt http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp http://bidd.nus.edu.sg/group/cjttd/ZFTTDDetail.asp?ID=$id TTDS00056 protein 1 urn:miriam:ttd.target ^TTDS\d+$ TTD Target ttd.target protein @@ -133,7 +132,7 @@ TubercuList Tb http://tuberculist.epfl.ch http://tuberculist.epfl.ch/quicksearch UCSC Genome Browser Uc http://genome.ucsc.edu/ http://genome.ucsc.edu/cgi-bin/hgTracks?position=$id uc001tyh.1 gene 1 Uc uc\d{3}[a-z]{3}\.\d UCSC Genome Browser P2576 ucsc gene UMLS CUI Cu https://www.nlm.nih.gov/research/umls/rxnorm/index.html https://www.ncbi.nlm.nih.gov/medgen/{$id} 760050 other Homo sapiens 1 urn:miriam:medgen ^[CN]*\d{4,7}$ MedGen medgen other Unipathway Up http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id UPA00206 pathway 1 ^UPA\d{5}$ Unipathway upa pathway -Uniprot-TrEMBL S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein +UniProtKB S http://www.uniprot.org/ http://www.uniprot.org/uniprot/$id P62158 protein 1 urn:miriam:uniprot ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?|([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])$ UniProtKB/TrEMBL P352 uniprot protein VMH metabolite VmhM http://www.vmh.life https://www.vmh.life/#metabolite/$id h2o metabolite 1 [a-zA-Z0-9_\(\_\)\[\]]+ VMH Life_Metabolite vmhmetabolite metabolite Wheat gene names Wn http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/report?class=gene;name=$id 1-FEH+w3 gene Triticum aestivum 1 Wn Wheat gene names graingenes.symbol gene Wheat gene refs Wr http://wheat.pw.usda.gov/ http://wheat.pw.usda.gov/cgi-bin/graingenes/report.cgi?class=reference&name=$id WGS-95-1333 probe Triticum aestivum 0 Wr Wheat gene refs graingenes.reference gene diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv index f20b733ea..940d8117d 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv @@ -40,9 +40,11 @@ Plasmodium falciparum Malaria parasite Pf 5833 Prymnesium parvum Pp 97485 Populus trichocarpa Western Balsam Poplar Pi 3694 Rattus norvegicus Rat Rn 10116 +Rosmarinus officinalis Rosemary Ro 39367 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java index ca9794406..6825e1a4f 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java @@ -14,6 +14,13 @@ */ package org.bridgedb.bio; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNotSame; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.io.BufferedWriter; import java.io.File; import java.io.FileInputStream; @@ -24,15 +31,10 @@ import java.lang.reflect.Method; import java.util.HashSet; import java.util.Set; -import java.util.regex.Pattern; import org.bridgedb.DataSource; -import org.bridgedb.DataSourcePatterns; -import org.junit.BeforeClass; import org.junit.jupiter.api.BeforeAll; -import static org.junit.jupiter.api.Assertions.*; - /** * @@ -42,9 +44,9 @@ public class DataSourceTxtTest { @BeforeAll public static void setUpSources() { - DataSourceTxt.init(); + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); } - + @org.junit.jupiter.api.Test public void testUniqueSystemCodes() { Set codes = new HashSet(); @@ -131,6 +133,15 @@ public void testMIRIAMFeatures() throws Exception { assertEquals("chebi", chebi.getCompactIdentifierPrefix()); } + @org.junit.jupiter.api.Test + public void testEcoGene() throws Exception { + DataSource ecogene = DataSource.getExistingByFullName("EcoGene"); + assertNotNull(ecogene); + assertEquals("urn:miriam:ecogene:EG10173", ecogene.getMiriamURN("EG10173")); + assertNotNull(DataSource.getByIdentiferOrgBase("http://identifiers.org/ecogene/")); + assertNotNull(DataSource.getByIdentiferOrgBase("https://identifiers.org/ecogene/")); + } + @org.junit.jupiter.api.Test public void testPrefix() throws Exception { DataSource ds = DataSource.getExistingBySystemCode("L"); diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java new file mode 100644 index 000000000..1e639458b --- /dev/null +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java @@ -0,0 +1,58 @@ +/* Copyright (c) 2023 Egon Willighagen + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and limitations under the License. + */ +package org.bridgedb.bio; + +import static org.junit.Assert.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertEquals; + +import org.bridgedb.DataSource; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +public class UniProtKBTest { + + @BeforeAll + public static void setUpSources() { + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); + } + + @Test + public void getBySystemCode() { + DataSource ds1 = DataSource.getExistingBySystemCode("S"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } + + @Test + public void getByFullName_TrEMBL() { + DataSource ds1 = DataSource.getExistingByFullName("Uniprot-TrEMBL"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } + + @Test + public void getByFullName_SwissProt() { + DataSource ds1 = DataSource.getExistingByFullName("Uniprot-SwissProt"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } + + @Test + public void getByFullName_UniProtKB() { + DataSource ds1 = DataSource.getExistingByFullName("UniProtKB"); + assertNotNull(ds1); + assertEquals("S", ds1.getSystemCode()); + assertEquals("UniProtKB", ds1.getFullName()); + } +} diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 95be40a64..3433845a9 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 216267721..6b21739b9 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java b/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java index 4fea80c82..adad8e088 100644 --- a/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java +++ b/org.bridgedb.gui/src/org/bridgedb/gui/BridgeRestParameterModel.java @@ -15,8 +15,8 @@ public class BridgeRestParameterModel extends AbstractParameterModel implements { static final int PARAMETER_NUM = 3; - private Object[] metadata = new Object[] {"http://webservice.bridgedb.org", "80", Collections.emptyList()}; - private Object[] values = new Object[] {"http://webservice.bridgedb.org", "80", null}; + private Object[] metadata = new Object[] {"https://webservice.bridgedb.org", "443", Collections.emptyList()}; + private Object[] values = new Object[] {"https://webservice.bridgedb.org", "443", null}; private String[] labels = new String[] {"Base URL", "Port", "Species"}; /** @@ -68,7 +68,7 @@ public String getHelpHtml() "in advance, and no cross-species mapping is possible. Mapping data is derived from " + "Ensembl and HMDB." + "

maintainer:Gladstone Institute / UCSF and BiGCaT / Maastricht University" + - "

more info:http://webservice.bridgedb.org"; + "

more info:https://webservice.bridgedb.org"; } @Override diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index b1d6bd0d7..026adc09b 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -80,8 +80,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime diff --git a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java index 0d60c7728..3576277d7 100644 --- a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java +++ b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DBConnectorDerbyServer.java @@ -65,11 +65,12 @@ public Connection createConnection(String dbName) throws IDMapperException try { sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString()); - Class.forName("org.apache.derby.jdbc.ClientDriver"); - } - catch (ClassNotFoundException e) - { - throw new IDMapperException (e); + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } } catch (IOException f) { diff --git a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java index 64b7b6788..46b172eb4 100644 --- a/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java +++ b/org.bridgedb.rdb.construct/src/org/bridgedb/rdb/construct/DataDerby.java @@ -123,11 +123,12 @@ public Connection createConnection(String dbName, int props) throws IDMapperExce { sysprop.setProperty("derby.storage.tempDirectory", System.getProperty("java.io.tmpdir")); sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString()); - Class.forName("org.apache.derby.jdbc.ClientDriver"); - } - catch (ClassNotFoundException e) - { - throw new IDMapperException (e); + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } } catch (IOException f) { diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 8b75100f7..fdc996246 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -79,8 +79,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime @@ -108,7 +108,7 @@ org.junit.platform junit-platform-launcher - 1.9.3 + ${junit5.platform.launcher.version} test diff --git a/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java b/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java index ad128adfa..7fb4e2dfd 100644 --- a/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java +++ b/org.bridgedb.rdb/src/org/bridgedb/rdb/IDMapperRdb.java @@ -89,8 +89,13 @@ public IDMapper connect(String location) throws IDMapperException String host = args.containsKey("host") ? args.get("host") : "wikipathways.org"; String port = args.containsKey("port") ? args.get("port") : "1527"; - - Class.forName("org.apache.derby.jdbc.ClientDriver"); + + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } Properties sysprop = System.getProperties(); sysprop.setProperty("derby.storage.tempDirectory", System.getProperty("java.io.tmpdir")); sysprop.setProperty("derby.stream.error.file", File.createTempFile("derby",".log").toString()); @@ -102,10 +107,6 @@ public IDMapper connect(String location) throws IDMapperException { throw new IDMapperException (e); } - catch (ClassNotFoundException e) - { - throw new IDMapperException (e); - } } } diff --git a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java index f9cf6b643..c72f48bf0 100644 --- a/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java +++ b/org.bridgedb.rdb/test/org/bridgedb/rdb/Test.java @@ -61,6 +61,14 @@ public static void setup() { @org.junit.jupiter.api.Test public void testGdbProvider() throws ClassNotFoundException, IDMapperException, IOException{ + // only for Java 11 and higher + String specVersion = System.getProperty("java.specification.version"); + if (specVersion.contains(".")) specVersion = specVersion.substring(0, specVersion.indexOf('.')); + if (Integer.valueOf(specVersion) < 11) { + System.out.print("Only running testGdbProvider() for Java 11 or higher"); + return; + } + Class.forName("org.bridgedb.file.IDMapperText"); ClassLoader classLoader = this.getClass().getClassLoader(); @@ -143,7 +151,6 @@ public void testSimpleGdb() throws ClassNotFoundException, IDMapperException, IO Class.forName("org.bridgedb.file.IDMapperText"); Class.forName("org.bridgedb.rdb.IDMapperRdb"); Class.forName("com.mysql.jdbc.Driver"); - // no longer needed?? Class.forName("org.apache.derby.jdbc.ClientDriver"); String fileName = "yeast_id_mapping"; String fullName = fileName + ".txt"; @@ -173,8 +180,13 @@ public void testDerbyClient() throws IDMapperException, ClassNotFoundException { long start, end, delta; start = System.currentTimeMillis(); Class.forName ("org.bridgedb.rdb.IDMapperRdb"); - Class.forName ("org.apache.derby.jdbc.ClientDriver"); - + try { + Class.forName("org.apache.derby.jdbc.ClientDriver"); // Derby 10.4 + System.out.println("Derby ClientDriver loaded"); + } catch (ClassNotFoundException e) { + // ignore, probably we're running this with Derby 10.14 or higher + } + IDMapper mapper = BridgeDb.connect ("idmapper-derbyclient:Homo sapiens?host=www.wikipathways.org"); end = System.currentTimeMillis(); delta = end - start; diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 40f505e81..e56013aa6 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.rdf/resources/BioDataSource.ttl b/org.bridgedb.rdf/resources/BioDataSource.ttl index 996f91d0c..5b3bc8747 100644 --- a/org.bridgedb.rdf/resources/BioDataSource.ttl +++ b/org.bridgedb.rdf/resources/BioDataSource.ttl @@ -35,7 +35,7 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -45,7 +45,7 @@ bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:fullName "BioGrid" ; bridgeDB:systemCode "Bg" ; - bridgeDB:mainUrl "http://thebiogrid.org/" ; + bridgeDB:mainUrl "https://thebiogrid.org/" ; bridgeDB:idExample "31623" ; bridgeDB:primary "true"^^ ; bridgeDB:type "interaction" ; @@ -55,7 +55,7 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; @@ -105,7 +105,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; @@ -115,7 +115,7 @@ bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; @@ -473,7 +473,7 @@ bridgeDB:DataSource_GeneOntology a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -484,7 +484,7 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -494,7 +494,7 @@ bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; @@ -503,7 +503,7 @@ bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -512,7 +512,7 @@ bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; @@ -521,7 +521,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -780,7 +780,7 @@ bridgeDB:DataSource_MINT a bridgeDB:DataSource ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1032,7 +1032,7 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1053,7 +1053,7 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1175,7 +1175,7 @@ bridgeDB:DataSource_Systems_Biology_Ontology a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -1263,7 +1263,7 @@ bridgeDB:DataSource_Uniprot_SwissProt a bridgeDB:DataSource ; dcterms:alternative "UniProtKB/Swiss-Prot" . bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ; - bridgeDB:fullName "Uniprot-TrEMBL" ; + bridgeDB:fullName "UniProtKB" ; bridgeDB:systemCode "S" ; bridgeDB:mainUrl "http://www.uniprot.org/" ; bridgeDB:idExample "P62158" ; diff --git a/org.bridgedb.rdf/resources/DataSource.ttl b/org.bridgedb.rdf/resources/DataSource.ttl index a786321d8..cd15ae023 100644 --- a/org.bridgedb.rdf/resources/DataSource.ttl +++ b/org.bridgedb.rdf/resources/DataSource.ttl @@ -38,32 +38,32 @@ bridgeDB:DataSource_BIND a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:fullName "BioGrid" ; bridgeDB:systemCode "Bg" ; - bridgeDB:mainUrl "http://thebiogrid.org/" ; + bridgeDB:mainUrl "https://thebiogrid.org/" ; bridgeDB:idExample "31623" ; bridgeDB:primary "true"^^ ; bridgeDB:type "interaction" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . @@ -134,16 +134,16 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:idExample "CCDS43989" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasUriPattern ; #Deprecated bridgeDB:hasIdentifiersOrgPattern . @@ -286,16 +286,16 @@ bridgeDB:DataSource_ChEMBL_target_component a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern . bridgeDB:DataSource_Cint a bridgeDB:DataSource ; bridgeDB:fullName "Cint" ; @@ -366,7 +366,7 @@ bridgeDB:DataSource_drugbankv4Target a bridgeDB:DataSource ; bridgeDB:fullName "Drugbank Target v4" ; bridgeDB:systemCode "drugbankv4.target" ; bridgeDB:idExample "BE0000938" ; - bridgeDB:hasRegexPattern "^BE\\d{7}$" ; + bridgeDB:hasRegexPattern "^BE\\d{7}$" ; bridgeDB:mainUrl "http://www.drugbank.ca/" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; @@ -379,6 +379,7 @@ bridgeDB:DataSource_drugbankDrugs a bridgeDB:DataSource ; bridgeDB:systemCode "Dr" ; bridgeDB:mainUrl "http://www.drugbank.ca/" ; bridgeDB:idExample "DB00001" ; + bridgeDB:hasRegexPattern "^DB\\d{5,7}$" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; bridgeDB:hasPrimaryUriPattern ; @@ -518,45 +519,45 @@ bridgeDB:DataSource_GOA a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_At . bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern . + bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "false"^^ ; bridgeDB:type "pathway" . @@ -564,7 +565,7 @@ bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; @@ -646,7 +647,7 @@ bridgeDB:DataSource_InterPro a bridgeDB:DataSource ; bridgeDB:idExample "IPR000100" ; bridgeDB:primary "true"^^ ; bridgeDB:type "protein" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasUriPattern . @@ -806,11 +807,11 @@ bridgeDB:CodeMapper_MGI a bridgeDB:CodeMapper ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; @@ -821,7 +822,7 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; bridgeDB:idExample "MI0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_NASC_Gene a bridgeDB:DataSource ; @@ -914,7 +915,7 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ; bridgeDB:systemCode "PW" ; bridgeDB:xrefPrefix "PW:"; - bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; @@ -1036,24 +1037,24 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; - bridgeDB:hasUriPattern ; + bridgeDB:hasUriPattern ; bridgeDB:hasUriPattern ; bridgeDB:Organism bridgeDB:Organism_Rn . bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_Os ; bridgeDB:hasRegexUriPattern . @@ -1071,11 +1072,11 @@ bridgeDB:DataSource_SGD a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . bridgeDB:DataSource_TIGR a bridgeDB:DataSource ; @@ -1135,7 +1136,7 @@ bridgeDB:DataSource_Uniprot_Enzyme a bridgeDB:DataSource ; bridgeDB:hasPrimaryUriPattern . bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ; - bridgeDB:fullName "Uniprot-TrEMBL" ; + bridgeDB:fullName "UniProtKB" ; bridgeDB:alternativeFullName "Uniprot/TrEMBL" ; bridgeDB:systemCode "S" ; bridgeDB:mainUrl "http://www.uniprot.org/" ; diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl index ab3092e11..0b72ed5d4 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl @@ -1,4 +1,4 @@ - @prefix bridgeDB: . +@prefix bridgeDB: . @prefix dcat: . @prefix dcterms: . @@ -504,11 +504,11 @@ bridgeDB:DataSource_BioCatalogue a bridgeDB:DataSource ; bridgeDB:DataSource_BioCyc a bridgeDB:DataSource ; bridgeDB:fullName "BioCyc" ; bridgeDB:systemCode "Bc" ; - bridgeDB:mainUrl "http://biocyc.org" ; + bridgeDB:mainUrl "https://biocyc.org" ; bridgeDB:idExample "ECOLI:CYT-D-UBIOX-CPLX" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^[A-Z-0-9]+(? ; bridgeDB:type "interaction" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; @@ -531,11 +531,11 @@ bridgeDB:DataSource_BioGrid a bridgeDB:DataSource ; bridgeDB:DataSource_BioModels_Database a bridgeDB:DataSource ; bridgeDB:fullName "BioModels Database" ; bridgeDB:systemCode "Bm" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/biomodels/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/biomodels/" ; bridgeDB:idExample "BIOMD0000000048" ; bridgeDB:primary "true"^^ ; bridgeDB:type "pathway" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$" ; @@ -832,7 +832,7 @@ bridgeDB:DataSource_CCDS a bridgeDB:DataSource ; bridgeDB:idExample "CCDS43989" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^CCDS\\d+(\\.\\d+)?$" ; @@ -921,11 +921,11 @@ bridgeDB:DataSource_CharProt a bridgeDB:DataSource ; bridgeDB:DataSource_ChEBI a bridgeDB:DataSource ; bridgeDB:fullName "ChEBI" ; bridgeDB:systemCode "Ce" ; - bridgeDB:mainUrl "http://www.ebi.ac.uk/chebi/" ; + bridgeDB:mainUrl "https://www.ebi.ac.uk/chebi/" ; bridgeDB:idExample "CHEBI:36927" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^CHEBI:\\d+$" ; @@ -1055,16 +1055,16 @@ bridgeDB:DataSource_ChemIDplus a bridgeDB:DataSource ; bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" ; dcterms:alternative "ChemSpider" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_Cint a bridgeDB:DataSource ; bridgeDB:fullName "Cint" ; @@ -2515,11 +2515,11 @@ bridgeDB:DataSource_GPCRDB a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Arabidopsis" ; bridgeDB:systemCode "EnAt" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "ATMG01360-TAIR-G" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_At ; bridgeDB:hasRegexPattern "AT[\\dCM]G\\d{5}\\-TAIR\\-G" ; dcterms:alternative "Grameen Arabidopsis" . @@ -2527,11 +2527,11 @@ bridgeDB:DataSource_Gramene_Arabidopsis a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Genes_DB a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Genes DB" ; bridgeDB:systemCode "Gg" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "GR:0060184" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GR\\:\\d+$" ; @@ -2543,36 +2543,36 @@ bridgeDB:DataSource_Gramene_Growth_Stage_Ontology a bridgeDB:DataSource ; bridgeDB:idExample "GRO:0007133" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GRO\\:\\d+$" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_Gramene_Literature a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Literature" ; bridgeDB:systemCode "Gl" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "6200" ; bridgeDB:primary "false"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Literature" . bridgeDB:DataSource_Gramene_Maize a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Maize" ; bridgeDB:systemCode "EnZm" ; - bridgeDB:mainUrl "http://www.ensembl.org" ; + bridgeDB:mainUrl "https://www.ensembl.org" ; bridgeDB:idExample "GRMZM2G174107" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Maize" . bridgeDB:DataSource_Gramene_Pathway a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Pathway" ; bridgeDB:systemCode "Gp" ; - bridgeDB:mainUrl "http://www.gramene.org/pathway" ; + bridgeDB:mainUrl "https://www.gramene.org/pathway" ; bridgeDB:idExample "AAH72400" ; bridgeDB:primary "false"^^ ; bridgeDB:type "pathway" ; @@ -2584,7 +2584,7 @@ bridgeDB:DataSource_Gramene_protein a bridgeDB:DataSource ; bridgeDB:idExample "78073" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -2595,7 +2595,7 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ; bridgeDB:idExample "CQG5" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\w+$" . @@ -2603,11 +2603,11 @@ bridgeDB:DataSource_Gramene_QTL a bridgeDB:DataSource ; bridgeDB:DataSource_Gramene_Rice a bridgeDB:DataSource ; bridgeDB:fullName "Gramene Rice" ; bridgeDB:systemCode "EnOj" ; - bridgeDB:mainUrl "http://www.gramene.org/" ; + bridgeDB:mainUrl "https://www.gramene.org/" ; bridgeDB:idExample "osa-MIR171a" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; dcterms:alternative "Gramene Rice" . bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ; @@ -2616,11 +2616,11 @@ bridgeDB:DataSource_Gramene_Taxonomy a bridgeDB:DataSource ; bridgeDB:idExample "GR_tax:013681" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^GR\\_tax\\:\\d+$" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_GreenGenes a bridgeDB:DataSource ; bridgeDB:fullName "GreenGenes" ; @@ -3029,11 +3029,11 @@ bridgeDB:DataSource_InChI a bridgeDB:DataSource ; bridgeDB:idExample "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^InChI\\=1S\\/[A-Za-z0-9]+(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,]+)+$" ; - bridgeDB:hasUriPattern , , , . + bridgeDB:hasUriPattern , , , . bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:fullName "InChIKey" ; @@ -3045,7 +3045,7 @@ bridgeDB:DataSource_InChIKey a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-N])?" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_IntAct a bridgeDB:DataSource ; bridgeDB:fullName "IntAct" ; @@ -3101,7 +3101,7 @@ bridgeDB:DataSource_InterPro a bridgeDB:DataSource ; bridgeDB:idExample "IPR000100" ; bridgeDB:primary "true"^^ ; bridgeDB:type "protein" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^IPR\\d{6}$" ; @@ -3799,11 +3799,11 @@ bridgeDB:DataSource_MIPModDB a bridgeDB:DataSource ; bridgeDB:DataSource_miRBase_mature_sequence a bridgeDB:DataSource ; bridgeDB:fullName "miRBase mature sequence" ; bridgeDB:systemCode "Mbm" ; - bridgeDB:mainUrl "http://www.mirbase.org/" ; + bridgeDB:mainUrl "https://www.mirbase.org/" ; bridgeDB:idExample "MIMAT0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "MIMAT\\d{7}" ; @@ -3816,12 +3816,12 @@ bridgeDB:DataSource_miRBase_Sequence a bridgeDB:DataSource ; bridgeDB:idExample "MI0000001" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "MI\\d{7}" ; dcterms:alternative "miRBase Sequence" ; - bridgeDB:hasUriPattern . + bridgeDB:hasUriPattern . bridgeDB:DataSource_mirEX a bridgeDB:DataSource ; bridgeDB:fullName "mirEX" ; @@ -4608,7 +4608,7 @@ bridgeDB:DataSource_Pathway_Commons a bridgeDB:DataSource ; bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:fullName "Pathway Ontology" ; bridgeDB:systemCode "PW" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/rgdweb/ontology/search.html" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/rgdweb/ontology/search.html" ; bridgeDB:idExample "PW:0000208" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; @@ -4616,12 +4616,12 @@ bridgeDB:DataSource_Pathway_Ontology a bridgeDB:DataSource ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^PW:\\d{7}$" ; - bridgeDB:hasUriPattern , . + bridgeDB:hasUriPattern , . bridgeDB:CodeMapper_Pathway_Ontology a bridgeDB:CodeMapper ; bridgeDB:systemCode "PW" ; bridgeDB:xrefPrefix "PW:" ; - bridgeDB:hasUriPattern , , , , . + bridgeDB:hasUriPattern , , , , . bridgeDB:DataSource_PATO a bridgeDB:DataSource ; bridgeDB:fullName "PATO" ; @@ -5195,7 +5195,7 @@ bridgeDB:DataSource_Rat_Genome_Database_qTL a bridgeDB:DataSource ; bridgeDB:idExample "1354581" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -5206,7 +5206,7 @@ bridgeDB:DataSource_Rat_Genome_Database_strain a bridgeDB:DataSource ; bridgeDB:idExample "5688061" ; bridgeDB:primary "true"^^ ; bridgeDB:type "unknown" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^\\d+$" . @@ -5290,17 +5290,17 @@ bridgeDB:DataSource_Rfam a bridgeDB:DataSource ; bridgeDB:DataSource_RGD a bridgeDB:DataSource ; bridgeDB:fullName "RGD" ; bridgeDB:systemCode "R" ; - bridgeDB:mainUrl "http://rgd.mcw.edu/" ; + bridgeDB:mainUrl "https://rgd.mcw.edu/" ; bridgeDB:idExample "2018" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:Organism bridgeDB:Organism_Rn ; bridgeDB:hasRegexPattern "^\\d{4,7}$" ; dcterms:alternative "Rat Genome Database" ; - bridgeDB:hasUriPattern , . + bridgeDB:hasUriPattern , . bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:fullName "Rhea" ; @@ -5318,11 +5318,11 @@ bridgeDB:DataSource_Rhea a bridgeDB:DataSource ; bridgeDB:DataSource_Rice_Ensembl_Gene a bridgeDB:DataSource ; bridgeDB:fullName "Rice Ensembl Gene" ; bridgeDB:systemCode "Os" ; - bridgeDB:mainUrl "http://www.gramene.org/Oryza_sativa" ; + bridgeDB:mainUrl "https://www.gramene.org/Oryza_sativa" ; bridgeDB:idExample "LOC_Os04g54800" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:Organism bridgeDB:Organism_Os ; dcterms:alternative "Rice Ensembl Gene" . @@ -5770,11 +5770,11 @@ bridgeDB:DataSource_T3DB a bridgeDB:DataSource ; bridgeDB:DataSource_TAIR a bridgeDB:DataSource ; bridgeDB:fullName "TAIR" ; bridgeDB:systemCode "A" ; - bridgeDB:mainUrl "http://arabidopsis.org/index.jsp" ; + bridgeDB:mainUrl "https://www.arabidopsis.org/" ; bridgeDB:idExample "AT1G01030" ; bridgeDB:primary "true"^^ ; bridgeDB:type "gene" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern ; bridgeDB:hasIdentifiersOrgInfoPattern ; bridgeDB:hasRegexPattern "^AT[1-5]G\\d{5}$" ; @@ -6202,7 +6202,7 @@ bridgeDB:DataSource_Uniprot_SwissProt a bridgeDB:DataSource ; bridgeDB:hasUriPattern . bridgeDB:DataSource_Uniprot_TrEMBL a bridgeDB:DataSource ; - bridgeDB:fullName "Uniprot-TrEMBL" ; + bridgeDB:fullName "UniProtKB" ; bridgeDB:systemCode "S" ; bridgeDB:mainUrl "http://www.uniprot.org/" ; bridgeDB:idExample "P62158" ; @@ -6875,8 +6875,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?accession=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://arabidopsis.org/servlets/TairObject?type=locus&name=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.arabidopsis.org/results?mainType=general&category=genes&searchText=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://arxiv.org/abs/" . @@ -7007,8 +7007,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://bio2rdf.org/uniprot:" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://biocyc.org/getid?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://biocyc.org/getid?id=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=" . @@ -10557,8 +10557,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://mi.caspur.it/PMDB/user/search.php?idsearch=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=" . @@ -10953,23 +10953,23 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://rfam.sanger.ac.uk/family/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/gene/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?orf=" . @@ -11076,8 +11076,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://tgr.pharma.openphacts.com/target/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://thebiogrid.org/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://thebiogrid.org/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://tolweb.org/" . @@ -11292,22 +11292,22 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; bridgeDB:hasPrefix "http://www.cellsignal.com/reference/pathway/" ; bridgeDB:hasPostfix ".html" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".html" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".rdf" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/inchi-resolver/Resolver.aspx?q=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/inchi-resolver/Resolver.aspx?q=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.conceptwiki.org/concept/" . @@ -11347,8 +11347,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/arrayexpress/experiments/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/biomodels-main/" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/biomodels/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/biosamples/browse.html?keywords=" . @@ -11363,11 +11363,11 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "https://www.ebi.ac.uk/chembl/target/inspect/" . @@ -11427,8 +11427,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ebi.ac.uk/interpro/entry/InterPro/" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ebi.ac.uk/interpro/entry/" . @@ -11610,29 +11610,29 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.gpcr.org/7tm/proteins/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Arabidopsis_thaliana/Gene/Summary?g=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/genes/search_gene?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/genes/search_gene?acc=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/literature/pub_search?ref_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/literature/pub_search?ref_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/ontology/search?id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/ontology/search?id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/protein/protein_search?protein_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/protein/protein_search?protein_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.gramene.org/Oryza_sativa/geneview?gene=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.gramene.org/Oryza_sativa/geneview?gene=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" . @@ -11722,7 +11722,7 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=" . - a bridgeDB:UriPattern ; + a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.maizesequence.org/Zea_mays/Gene/Summary?g=" . a bridgeDB:UriPattern ; @@ -11734,11 +11734,11 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://mirbase.org/mature/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=" . @@ -11764,8 +11764,8 @@ bridgeDB:Organism_Zm a bridgeDB:Organism ; a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/biosystems/" . - a bridgeDB:UriPattern ; - bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=" . + a bridgeDB:UriPattern ; + bridgeDB:hasPrefix "https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=" . a bridgeDB:UriPattern ; bridgeDB:hasPrefix "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&%3BDATA=" . diff --git a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt index 3b35ab01a..6b85d16d7 100644 --- a/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt +++ b/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.txt @@ -47,9 +47,9 @@ BIND Bi http://www.bind.ca/ http://www.bind.ca/Action?identifier=bindid&idsearch BindingDB bindingDB http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$id 22360 unknown 1 urn:miriam:bindingDB ^\d+$ BioCarta Pathway biocarta.pathway http://www.biocarta.com/pathfiles/$id.asp h_aktPathway unknown 1 urn:miriam:biocarta.pathway ^([hm]\_)?\w+Pathway$ BioCatalogue biocatalogue.service https://www.biocatalogue.org/services/$id 614 unknown 1 urn:miriam:biocatalogue.service ^\d+$ -BioCyc Bc http://biocyc.org http://biocyc.org/getid?id=$id ECOLI:CYT-D-UBIOX-CPLX gene 1 urn:miriam:biocyc ^[A-Z-0-9]+(? ; "Medical College of Wisconsin, Milwaukee, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -1003,7 +1003,7 @@ Each page contains information about a particular group, with pages linked one t "USA"^^ ; "Medical College of Wisconsin, Milwaukee, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -1313,7 +1313,7 @@ Each page contains information about a particular group, with pages linked one t a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -1329,7 +1329,7 @@ Each page contains information about a particular group, with pages linked one t a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -2236,7 +2236,7 @@ The interactions include direct (physical) and indirect (functional) association a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -3203,7 +3203,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3368,7 +3368,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3781,7 +3781,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -3904,7 +3904,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4134,7 +4134,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -4274,7 +4274,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR)"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4461,7 +4461,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "United Kingdom"^^ ; "European Bioinformatics Institute"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4551,7 +4551,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "United Kingdom"^^ ; "European Bioinformatics Institute"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -4945,7 +4945,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Medical College of Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -5126,7 +5126,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -5431,7 +5431,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "USA"^^ ; "Bioinformatics Research Group, SRI International, California"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "100"^^ ; @@ -5451,7 +5451,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -5510,7 +5510,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -5875,7 +5875,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -6485,7 +6485,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -6555,7 +6555,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7041,7 +7041,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7093,7 +7093,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -7265,7 +7265,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -8447,7 +8447,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Faculty of Life Sciences, University of Manchester"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -8545,7 +8545,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -9346,7 +9346,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "Canada"^^ ; "Ontario Cancer Institute"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "99"^^ ; @@ -9518,7 +9518,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -9925,7 +9925,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -10534,7 +10534,7 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "98"^^ ; @@ -12015,7 +12015,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "UK"^^ ; "Royal Society of Chemistry, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -12342,7 +12342,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "UK"^^ ; "European Bioinformatics Institute, Hinxton, Cambridge"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -12408,7 +12408,7 @@ Note: Currently, direct access to RNA products is restricted. This is expected t "USA"^^ ; "Medical College of Wisconsin, Wisconsin"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:CatalogRecord ; @@ -13094,7 +13094,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -13327,7 +13327,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14443,7 +14443,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14554,7 +14554,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -14576,7 +14576,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from "UK"^^ ; "Faculty of Life Sciences, University of Manchester"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; @@ -14618,7 +14618,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . idot:reliability "100"^^ ; @@ -16492,7 +16492,7 @@ SubtiList provides a complete dataset of DNA and protein sequences derived from a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -17403,7 +17403,7 @@ All content is under the Creative Commons Attribution 3.0 Unported license."""^^ a dcat:Distribution ; - dcat:accessURL ; + dcat:accessURL ; dcat:mediaType "application/xhtml+xml"^^ ; dcat:publisher . @@ -18125,7 +18125,7 @@ All content is under the Creative Commons Attribution 3.0 Unported license."""^^ "USA"^^ ; "Cold Spring Harbor Laboratory, New York"^^ ; - dcat:landingPage . + dcat:landingPage . a dcat:Distribution ; diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java index 3ee58896f..72fa651dd 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/BridgeDBRdfHandler.java @@ -47,9 +47,7 @@ import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; import org.eclipse.rdf4j.model.Value; -import org.eclipse.rdf4j.model.impl.BooleanLiteralImpl; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.Repository; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -86,7 +84,7 @@ private void doParseRdfInputStream(InputStream stream) throws BridgeDBException RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); repositoryConnection.add(stream, DEFAULT_BASE_URI, DEFAULT_FILE_FORMAT); readAllDataSources(repositoryConnection); @@ -216,7 +214,7 @@ public DataSource readDataSource(RepositoryConnection repositoryConnection, Reso private void readCodeMapper(RepositoryConnection repositoryConnection, String systemCode, Pattern regex) throws RepositoryException, BridgeDBException { RepositoryResult statements = - repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(systemCode), true); + repositoryConnection.getStatements(null, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(systemCode), true); // String xrefPrefix = null; Resource codeMapperReseource = null; while (statements.hasNext()) { @@ -321,7 +319,7 @@ public static void writeRdfToFile(File file, SortedSet dataSources) RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); for (DataSource dataSource: dataSources){ writeDataSource(repositoryConnection, dataSource); @@ -341,29 +339,25 @@ private static void writeDataSource(RepositoryConnection repositoryConnection, D repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.DATA_SOURCE_URI); if (dataSource.getFullName() != null){ - repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, new LiteralImpl(dataSource.getFullName())); + repositoryConnection.add(id, BridgeDBConstants.FULL_NAME_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getFullName())); } if (dataSource.getSystemCode() != null && (!dataSource.getSystemCode().trim().isEmpty())){ - repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode())); + repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode())); } if (dataSource.getMainUrl() != null){ - repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, new LiteralImpl(dataSource.getMainUrl())); + repositoryConnection.add(id, BridgeDBConstants.MAIN_URL_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getMainUrl())); } if (dataSource.getExample() != null && dataSource.getExample().getId() != null){ - repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, new LiteralImpl(dataSource.getExample().getId())); + repositoryConnection.add(id, BridgeDBConstants.ID_EXAMPLE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getExample().getId())); } - if (dataSource.isPrimary()){ - repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.TRUE); - } else { - repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, BooleanLiteralImpl.FALSE); - } + repositoryConnection.add(id, BridgeDBConstants.PRIMARY_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.isPrimary())); if (dataSource.getType() != null){ - repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, new LiteralImpl(dataSource.getType())); + repositoryConnection.add(id, BridgeDBConstants.TYPE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getType())); } Pattern regex = DataSourcePatterns.getPatterns().get(dataSource); @@ -391,16 +385,16 @@ private static void writeDataSource(RepositoryConnection repositoryConnection, D Pattern pattern = DataSourcePatterns.getPatterns().get(dataSource); if (pattern != null && !pattern.toString().isEmpty()){ - Value patternValue = new LiteralImpl(pattern.toString()); + Value patternValue = SimpleValueFactory.getInstance().createLiteral(pattern.toString()); repositoryConnection.add(id, BridgeDBConstants.HAS_REGEX_PATTERN_URI, patternValue); } if (dataSource.getAlternative() != null){ - repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, new LiteralImpl(dataSource.getAlternative())); + repositoryConnection.add(id, DCTermsConstants.ALTERNATIVE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getAlternative())); } if (dataSource.getDescription() != null){ - repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, new LiteralImpl(dataSource.getDescription())); + repositoryConnection.add(id, DCatConstants.DESCRIPTION_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getDescription())); } SortedSet sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.dataSourceUriPattern); @@ -421,8 +415,8 @@ private static void writeCodeMapper(RepositoryConnection repositoryConnection, D } Resource id = asCodeMapperResource(dataSource); repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.CODE_MAPPER_URI); - repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, new LiteralImpl(dataSource.getSystemCode())); - Value prefixValue = new LiteralImpl(xrefPrefix); + repositoryConnection.add(id, BridgeDBConstants.SYSTEM_CODE_URI, SimpleValueFactory.getInstance().createLiteral(dataSource.getSystemCode())); + Value prefixValue = SimpleValueFactory.getInstance().createLiteral(xrefPrefix); repositoryConnection.add(id, BridgeDBConstants.XREF_PREFIX_URI, prefixValue); SortedSet sortedPatterns = UriPattern.byCodeAndType(dataSource.getSystemCode(), UriPatternType.codeMapperPattern); @@ -476,17 +470,17 @@ private static RDFFormat getFormat(File file){ protected static Resource asResource(DataSource dataSource) { if (dataSource.getFullName() == null){ - return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); } else { - return new URIImpl(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.DATA_SOURCE1 + "_" + scrub(dataSource.getFullName())); } } protected static Resource asCodeMapperResource(DataSource dataSource) { if (dataSource.getFullName() == null){ - return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_bysysCode_" + scrub(dataSource.getSystemCode())); } else { - return new URIImpl(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName())); + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.CODE_MAPPER1 + "_" + scrub(dataSource.getFullName())); } } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java index 36407e02b..a25752ffa 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/OrganismRdf.java @@ -22,16 +22,16 @@ import java.io.IOException; import java.util.HashMap; import java.util.Set; + import org.bridgedb.bio.Organism; import org.bridgedb.rdf.constants.BridgeDBConstants; import org.bridgedb.rdf.constants.RdfConstants; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; import org.eclipse.rdf4j.rio.RDFHandler; @@ -64,8 +64,8 @@ public static final String getRdfLabel(Organism organism) { return scrub(organism.code()); } - public static final URI getResourceId(Organism organism){ - return new URIImpl(BridgeDBConstants.ORGANISM1 + "_" + getRdfLabel(organism)); + public static final IRI getResourceId(Organism organism){ + return SimpleValueFactory.getInstance().createIRI(BridgeDBConstants.ORGANISM1 + "_" + getRdfLabel(organism)); } public static void addAll(RepositoryConnection repositoryConnection) throws IOException, RepositoryException { @@ -82,11 +82,11 @@ public void addComments(RDFHandler handler) throws RDFHandlerException{ public static void add(RepositoryConnection repositoryConnection, Organism organism) throws IOException, RepositoryException { - URI id = getResourceId(organism); + IRI id = getResourceId(organism); repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.ORGANISM_URI); - repositoryConnection.add(id, BridgeDBConstants.CODE_URI, new LiteralImpl(organism.code())); - repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, new LiteralImpl(organism.shortName())); - repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, new LiteralImpl(organism.latinName())); + repositoryConnection.add(id, BridgeDBConstants.CODE_URI, SimpleValueFactory.getInstance().createLiteral(organism.code())); + repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.shortName())); + repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, SimpleValueFactory.getInstance().createLiteral(organism.latinName())); } public static Object readRdf(Resource organismId, Set allStatements) throws BridgeDBException { diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java index 3c2999eda..11847b3d9 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/RdfBase.java @@ -21,13 +21,14 @@ import java.util.HashSet; import java.util.Set; + import org.apache.log4j.Logger; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.Repository; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -61,7 +62,7 @@ static String convertToShortName(Value value) { return id; } - public static String getSingletonString(RepositoryConnection repositoryConnection, Resource id, URI predicate) + public static String getSingletonString(RepositoryConnection repositoryConnection, Resource id, IRI predicate) throws BridgeDBException, RepositoryException { String result = getPossibleSingletonString(repositoryConnection, id, predicate); if (result == null){ @@ -71,7 +72,7 @@ public static String getSingletonString(RepositoryConnection repositoryConnectio } public static String getPossibleSingletonString(RepositoryConnection repositoryConnection, Resource id, - URI predicate) throws RepositoryException, BridgeDBException { + IRI predicate) throws RepositoryException, BridgeDBException { Value result = getPossibleSingleton(repositoryConnection, id, predicate); if (result == null) { return null; @@ -81,7 +82,7 @@ public static String getPossibleSingletonString(RepositoryConnection repositoryC } static Resource getPossibleSingletonResource(RepositoryConnection repositoryConnection, Resource id, - URI predicate) throws RepositoryException, BridgeDBException { + IRI predicate) throws RepositoryException, BridgeDBException { Value value = getPossibleSingleton(repositoryConnection, id, predicate); return toResource(value); } @@ -92,11 +93,11 @@ private static Resource toResource(Value value){ } else if (value instanceof Resource){ return (Resource)value; } - return new URIImpl(value.stringValue()); + return SimpleValueFactory.getInstance().createIRI(value.stringValue()); } static Value getPossibleSingleton(RepositoryConnection repositoryConnection, Resource id, - URI predicate) throws RepositoryException, BridgeDBException { + IRI predicate) throws RepositoryException, BridgeDBException { RepositoryResult statements = repositoryConnection.getStatements(id, predicate, null, true); if (statements.hasNext()) { @@ -111,7 +112,7 @@ static Value getPossibleSingleton(RepositoryConnection repositoryConnection, Res return null; } - static Set getAllStrings(RepositoryConnection repositoryConnection, Resource id, URI predicate) + static Set getAllStrings(RepositoryConnection repositoryConnection, Resource id, IRI predicate) throws RepositoryException { HashSet results = new HashSet(); RepositoryResult statements = @@ -123,7 +124,7 @@ static Set getAllStrings(RepositoryConnection repositoryConnection, Reso return results; } - static Set getAllResources(RepositoryConnection repositoryConnection, Resource id, URI predicate) + static Set getAllResources(RepositoryConnection repositoryConnection, Resource id, IRI predicate) throws RepositoryException { HashSet results = new HashSet(); RepositoryResult statements = diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java index af615b6c4..f7a62083e 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/UriPattern.java @@ -27,18 +27,17 @@ import java.util.SortedSet; import java.util.TreeSet; import java.util.regex.Pattern; + import org.bridgedb.DataSource; import org.bridgedb.DataSourcePatterns; import org.bridgedb.bio.DataSourceTxt; import org.bridgedb.rdf.constants.BridgeDBConstants; -import org.bridgedb.rdf.constants.IdenitifiersOrgConstants; import org.bridgedb.rdf.constants.RdfConstants; import org.bridgedb.rdf.identifiers.org.IdentifersOrgReader; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -59,7 +58,7 @@ public class UriPattern extends RdfBase implements Comparable{ private static HashMap> byCode = new HashMap>(); static boolean initialized = false; - private static HashSet expectedPredicates = new HashSet(Arrays.asList(new URI[] { + private static HashSet expectedPredicates = new HashSet(Arrays.asList(new IRI[] { BridgeDBConstants.HAS_POSTFIX_URI, BridgeDBConstants.HAS_PREFIX_URI, RdfConstants.TYPE_URI, @@ -96,7 +95,7 @@ public static void refreshUriPatterns() throws BridgeDBException{ if (initialized){ return; } - DataSourceTxt.init(); + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); DataSourceMetaDataProvidor.assumeUnknownsAreBio(); BridgeDBRdfHandler.init(); IdentifersOrgReader.init(); @@ -201,8 +200,8 @@ public static UriPattern existingByPrefixAndPostfix(String prefix, String postfi return existingByPattern(prefix + "$id" + postfix); } - public final URI getResourceId(){ - return new URIImpl(getUriPattern()); + public final IRI getResourceId(){ + return SimpleValueFactory.getInstance().createIRI(getUriPattern()); } public String getUriPattern() { @@ -221,11 +220,11 @@ public static void addAll(RepositoryConnection repositoryConnection) } public void add(RepositoryConnection repositoryConnection) throws RepositoryException{ - URI id = getResourceId(); + IRI id = getResourceId(); repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.URI_PATTERN_URI); - repositoryConnection.add(id, BridgeDBConstants.HAS_PREFIX_URI, new LiteralImpl(prefix)); + repositoryConnection.add(id, BridgeDBConstants.HAS_PREFIX_URI, SimpleValueFactory.getInstance().createLiteral(prefix)); if (!postfix.isEmpty()){ - repositoryConnection.add(id, BridgeDBConstants.HAS_POSTFIX_URI, new LiteralImpl(postfix)); + repositoryConnection.add(id, BridgeDBConstants.HAS_POSTFIX_URI, SimpleValueFactory.getInstance().createLiteral(postfix)); } } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java index b88c61eb1..d0546c091 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/BridgeDBConstants.java @@ -19,14 +19,15 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class BridgeDBConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); public static final String OLD_PREFIX = "http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl#"; public static final String OLD_PREFIX_NAME = "bridgeDB"; @@ -36,92 +37,92 @@ public class BridgeDBConstants { //Types public static final String DATA_SOURCE_LABEL = "DataSource"; public static final String DATA_SOURCE1 = PREFIX + DATA_SOURCE_LABEL; - public static final URI DATA_SOURCE_URI = new URIImpl(PREFIX + DATA_SOURCE_LABEL); + public static final IRI DATA_SOURCE_URI = factory.createIRI(PREFIX + DATA_SOURCE_LABEL); //public static final String URI_MAPPING = "UriMapping"; - //public static final URI URI_MAPPING_URI = new URIImpl(PREFIX + URI_MAPPING); + //public static final IRI URI_MAPPING_URI = factory.createIRI(PREFIX + URI_MAPPING); public static final String URI_PATTERN_LABEL = "UriPattern"; public static final String URI_PATTERN1 = PREFIX + URI_PATTERN_LABEL; - public static final URI URI_PATTERN_URI = new URIImpl(URI_PATTERN1); + public static final IRI URI_PATTERN_URI = factory.createIRI(URI_PATTERN1); //DataSource fields private static final String FULL_NAME = "fullName"; - public static final URI FULL_NAME_URI = new URIImpl(PREFIX + FULL_NAME); + public static final IRI FULL_NAME_URI = factory.createIRI(PREFIX + FULL_NAME); private static final String ID_EXAMPLE = "idExample"; - public static final URI ID_EXAMPLE_URI = new URIImpl(PREFIX + ID_EXAMPLE); + public static final IRI ID_EXAMPLE_URI = factory.createIRI(PREFIX + ID_EXAMPLE); private static final String MAIN_URL = "mainUrl"; - public static final URI MAIN_URL_URI = new URIImpl(PREFIX + MAIN_URL); + public static final IRI MAIN_URL_URI = factory.createIRI(PREFIX + MAIN_URL); public static final String ORGANISM_LABEL = "Organism"; public static final String ORGANISM1 = PREFIX + ORGANISM_LABEL; - public static final URI ORGANISM_URI = new URIImpl(ORGANISM1); + public static final IRI ORGANISM_URI = factory.createIRI(ORGANISM1); public static final String ABOUT_ORGANISM_LABEL = "aboutOrganism"; public static final String ABOUT_ORGANISM1 = PREFIX + ORGANISM_LABEL; - public static final URI ABOUT_ORGANISM_URI = new URIImpl(ORGANISM1); + public static final IRI ABOUT_ORGANISM_URI = factory.createIRI(ORGANISM1); private static final String PRIMARY = "primary"; - public static final URI PRIMARY_URI = new URIImpl(PREFIX + PRIMARY); + public static final IRI PRIMARY_URI = factory.createIRI(PREFIX + PRIMARY); private static final String SYSTEM_CODE = "systemCode"; - public static final URI SYSTEM_CODE_URI = new URIImpl(PREFIX + SYSTEM_CODE); + public static final IRI SYSTEM_CODE_URI = factory.createIRI(PREFIX + SYSTEM_CODE); private static final String TYPE = "type"; - public static final URI TYPE_URI = new URIImpl(PREFIX + TYPE); - public static final URI HAS_DATA_TYPE_URI = new URIImpl(PREFIX + "hasDataType"); + public static final IRI TYPE_URI = factory.createIRI(PREFIX + TYPE); + public static final IRI HAS_DATA_TYPE_URI = factory.createIRI(PREFIX + "hasDataType"); - public static final URI HAS_REGEX_PATTERN_URI = new URIImpl(PREFIX + "hasRegexPattern"); - public static final URI HAS_REGEX_URL_PATTERN_URI = new URIImpl(PREFIX + "hasRegexUrlPattern"); - public static final URI HAS_PRIMARY_URI_PATTERN_URI = new URIImpl(PREFIX + "hasPrimaryUriPattern"); - public static final URI HAS_URI_PATTERN_URI = new URIImpl(PREFIX + "hasUriPattern"); - public static final URI HAS_REGEX_URI_PATTERN_URI = new URIImpl(PREFIX + "hasRegexUriPattern"); - public static final URI IS_DEPRICATED_BY_URI = new URIImpl(PREFIX + "isDepricatedBy"); + public static final IRI HAS_REGEX_PATTERN_URI = factory.createIRI(PREFIX + "hasRegexPattern"); + public static final IRI HAS_REGEX_URL_PATTERN_URI = factory.createIRI(PREFIX + "hasRegexUrlPattern"); + public static final IRI HAS_PRIMARY_URI_PATTERN_URI = factory.createIRI(PREFIX + "hasPrimaryUriPattern"); + public static final IRI HAS_URI_PATTERN_URI = factory.createIRI(PREFIX + "hasUriPattern"); + public static final IRI HAS_REGEX_URI_PATTERN_URI = factory.createIRI(PREFIX + "hasRegexUriPattern"); + public static final IRI IS_DEPRICATED_BY_URI = factory.createIRI(PREFIX + "isDepricatedBy"); public static final String VARIOUS = PREFIX + "various"; //old verions private static final String URN_BASE = "urnBase"; - public static final URI URN_BASE_URI = new URIImpl(PREFIX + URN_BASE); + public static final IRI URN_BASE_URI = factory.createIRI(PREFIX + URN_BASE); //Organism Fields private static final String CODE = "code"; - public static final URI CODE_URI = new URIImpl(PREFIX + CODE); + public static final IRI CODE_URI = factory.createIRI(PREFIX + CODE); private static final String SHORT_NAME = "shortName"; - public static final URI SHORT_NAME_URI = new URIImpl(PREFIX + SHORT_NAME); + public static final IRI SHORT_NAME_URI = factory.createIRI(PREFIX + SHORT_NAME); private static final String LATIN_NAME = "latinName"; - public static final URI LATIN_NAME_URI = new URIImpl(PREFIX + LATIN_NAME); + public static final IRI LATIN_NAME_URI = factory.createIRI(PREFIX + LATIN_NAME); //UriPatternFields private static final String HAS_PREFIX = "hasPrefix"; - public static final URI HAS_PREFIX_URI = new URIImpl(PREFIX + HAS_PREFIX); + public static final IRI HAS_PREFIX_URI = factory.createIRI(PREFIX + HAS_PREFIX); private static final String HAS_POSTFIX = "hasPostfix"; - public static final URI HAS_POSTFIX_URI = new URIImpl(PREFIX + HAS_POSTFIX); + public static final IRI HAS_POSTFIX_URI = factory.createIRI(PREFIX + HAS_POSTFIX); private static final String IDENTIFERS_ORG_PATTERN = "IdentifiersOrgPattern"; - public static final URI HAS_IDENTIFERS_ORG_PATTERN_URI = new URIImpl(PREFIX + "has" + IDENTIFERS_ORG_PATTERN); + public static final IRI HAS_IDENTIFERS_ORG_PATTERN_URI = factory.createIRI(PREFIX + "has" + IDENTIFERS_ORG_PATTERN); private static final String IDENTIFERS_ORG_INFO_PATTERN = "IdentifiersOrgInfoPattern"; - public static final URI HAS_IDENTIFERS_ORG_INFO_PATTERN_URI = new URIImpl(PREFIX + "has" + IDENTIFERS_ORG_INFO_PATTERN); + public static final IRI HAS_IDENTIFERS_ORG_INFO_PATTERN_URI = factory.createIRI(PREFIX + "has" + IDENTIFERS_ORG_INFO_PATTERN); //CodeMapper feilds private static final String CODE_MAPPER = "CodeMapper"; public static final String CODE_MAPPER1 = PREFIX + CODE_MAPPER; - public static final URI CODE_MAPPER_URI = new URIImpl(CODE_MAPPER1); + public static final IRI CODE_MAPPER_URI = factory.createIRI(CODE_MAPPER1); private static final String XREF_PREFIX = "xrefPrefix"; - public static final URI XREF_PREFIX_URI = new URIImpl(PREFIX + XREF_PREFIX); + public static final IRI XREF_PREFIX_URI = factory.createIRI(PREFIX + XREF_PREFIX); - public static final URI HAS_DATA_SOURCE = new URIImpl(PREFIX + "hasDataSource"); - public static final URI IS_URI_PATTERN_OF = new URIImpl(PREFIX + "isUriPatternOf"); + public static final IRI HAS_DATA_SOURCE = factory.createIRI(PREFIX + "hasDataSource"); + public static final IRI IS_URI_PATTERN_OF = factory.createIRI(PREFIX + "isUriPatternOf"); private static final String bdb = "http://www.bridgedb.org/test#"; - public static final URI TEST_PREDICATE = new URIImpl(bdb + "testPredicate"); + public static final IRI TEST_PREDICATE = factory.createIRI(bdb + "testPredicate"); - public static final URI ASSERTION_METHOD = new URIImpl(PREFIX + "assertionMethod "); - public static final URI VIA_URI = new URIImpl(PREFIX + "isTransativeVia"); - public static final URI IS_SYMETRIC = new URIImpl(PREFIX + "isSymetric"); - public static final URI LINKSET_JUSTIFICATION = new URIImpl(PREFIX + "linksetJustification"); - public static final URI SUBJECTS_DATATYPE = new URIImpl(PREFIX + "subjectsDatatype"); - public static final URI OBJECTS_DATATYPE = new URIImpl(PREFIX + "objectsDatatype"); - public static final URI SUBJECTS_SPECIES = new URIImpl(PREFIX + "subjectsSpecies"); - public static final URI OBJECTS_SPECIES = new URIImpl(PREFIX + "objectsSpecies"); - public static final URI FULFILLS_LENS = new URIImpl(PREFIX + "fulfillsLens"); + public static final IRI ASSERTION_METHOD = factory.createIRI(PREFIX + "assertionMethod "); + public static final IRI VIA_URI = factory.createIRI(PREFIX + "isTransativeVia"); + public static final IRI IS_SYMETRIC = factory.createIRI(PREFIX + "isSymetric"); + public static final IRI LINKSET_JUSTIFICATION = factory.createIRI(PREFIX + "linksetJustification"); + public static final IRI SUBJECTS_DATATYPE = factory.createIRI(PREFIX + "subjectsDatatype"); + public static final IRI OBJECTS_DATATYPE = factory.createIRI(PREFIX + "objectsDatatype"); + public static final IRI SUBJECTS_SPECIES = factory.createIRI(PREFIX + "subjectsSpecies"); + public static final IRI OBJECTS_SPECIES = factory.createIRI(PREFIX + "objectsSpecies"); + public static final IRI FULFILLS_LENS = factory.createIRI(PREFIX + "fulfillsLens"); - public static final URI LENS_URI = new URIImpl(PREFIX + "lens"); + public static final IRI LENS_URI = factory.createIRI(PREFIX + "lens"); public static final String TRANSITIVE = PREFIX + "Transitive"; - public static final URI TRANSITIVE_URI = new URIImpl(TRANSITIVE); + public static final IRI TRANSITIVE_URI = factory.createIRI(TRANSITIVE); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java index 43b69f2cf..0d036730a 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/CitoConstants.java @@ -4,8 +4,8 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -16,6 +16,6 @@ public class CitoConstants { public static final String PREFIX_NAME = "cito"; public static final String CITE_AS_AUTHORITY = "citeAsAuthority"; - public static final URI CITE_AS_AUTHORITY_URI = new URIImpl(voidns + CITE_AS_AUTHORITY); + public static final IRI CITE_AS_AUTHORITY_URI = SimpleValueFactory.getInstance().createIRI(voidns + CITE_AS_AUTHORITY); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java index 27be81a10..0da39f63d 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCTermsConstants.java @@ -4,35 +4,37 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class DCTermsConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://purl.org/dc/terms/"; public static final String PREFIX_NAME = "dcterms"; public static final String ACCRUAL_PERIODICITY = "accrualPeriodicity"; - public static final URI ACCRUAL_PERIODICITY_URI = new URIImpl(voidns + ACCRUAL_PERIODICITY); + public static final IRI ACCRUAL_PERIODICITY_URI = factory.createIRI(voidns + ACCRUAL_PERIODICITY); public static final String ALTERNATIVE = "alternative"; - public static final URI ALTERNATIVE_URI = new URIImpl(voidns + ALTERNATIVE); + public static final IRI ALTERNATIVE_URI = factory.createIRI(voidns + ALTERNATIVE); public static final String DESCRIPTION = "description"; - public static final URI DESCRIPTION_URI = new URIImpl(voidns + DESCRIPTION); + public static final IRI DESCRIPTION_URI = factory.createIRI(voidns + DESCRIPTION); public static final String ISSUED = "issued"; - public static final URI ISSUED_URI = new URIImpl(voidns + ISSUED); + public static final IRI ISSUED_URI = factory.createIRI(voidns + ISSUED); public static final String LICENSE = "license"; - public static final URI LICENSE_URI = new URIImpl(voidns + LICENSE); + public static final IRI LICENSE_URI = factory.createIRI(voidns + LICENSE); public static final String PUBLISHER = "publisher"; - public static final URI PUBLISHER_URI = new URIImpl(voidns + PUBLISHER); + public static final IRI PUBLISHER_URI = factory.createIRI(voidns + PUBLISHER); public static final String TITLE = "title"; - public static final URI TITLE_URI = new URIImpl(voidns + TITLE); + public static final IRI TITLE_URI = factory.createIRI(voidns + TITLE); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java index 2e7ee9b89..443f80700 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DCatConstants.java @@ -4,35 +4,37 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class DCatConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://www.w3.org/ns/dcat#"; public static final String PREFIX_NAME = "dcat"; public static final String ACCESS_URL = "accessURL"; - public static final URI ACCESS_URL_URI = new URIImpl(voidns + ACCESS_URL); + public static final IRI ACCESS_URL_URI = factory.createIRI(voidns + ACCESS_URL); public static final String BYTE_SIZE = "byteSize"; - public static final URI BYTE_SIZE_URI = new URIImpl(voidns + BYTE_SIZE); + public static final IRI BYTE_SIZE_URI = factory.createIRI(voidns + BYTE_SIZE); public static final String DESCRIPTION = "description"; - public static final URI DESCRIPTION_URI = new URIImpl(voidns + DESCRIPTION); + public static final IRI DESCRIPTION_URI = factory.createIRI(voidns + DESCRIPTION); public static final String DISTRIBUTION = "distribution"; - public static final URI DISTRIBUTION_URI = new URIImpl(voidns + DISTRIBUTION); + public static final IRI DISTRIBUTION_URI = factory.createIRI(voidns + DISTRIBUTION); public static final String DOWNLOAD = "downloadURL"; - public static final URI DOWNLOAD_URI = new URIImpl(voidns + DOWNLOAD); + public static final IRI DOWNLOAD_URI = factory.createIRI(voidns + DOWNLOAD); public static final String LANDING_PAGE = "landingPage"; - public static final URI LANDING_PAGE_URI = new URIImpl(voidns + LANDING_PAGE); + public static final IRI LANDING_PAGE_URI = factory.createIRI(voidns + LANDING_PAGE); public static final String MEDIA_TYPE = "mediaType "; - public static final URI MEDIA_TYPE_URI = new URIImpl(voidns + MEDIA_TYPE); + public static final IRI MEDIA_TYPE_URI = factory.createIRI(voidns + MEDIA_TYPE); public static final String THEME = "theme"; - public static final URI THEME_URI = new URIImpl(voidns + THEME); + public static final IRI THEME_URI = factory.createIRI(voidns + THEME); public static final String TITLE = "title"; - public static final URI TITLE_URI = new URIImpl(voidns + TITLE); + public static final IRI TITLE_URI = factory.createIRI(voidns + TITLE); diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java index 7d78296fb..ba92aab66 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/DulConstants.java @@ -19,13 +19,13 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; public class DulConstants { public static final String dulns = "http://www.ontologydesignpatterns.org/ont/dul/DUL.owl#"; - public static final URI EXPRESSES = new URIImpl(dulns + "expresses"); + public static final IRI EXPRESSES = SimpleValueFactory.getInstance().createIRI(dulns + "expresses"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java index 0bd87ca78..17a5be926 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/FoafConstants.java @@ -4,21 +4,23 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class FoafConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://xmlns.com/foaf/0.1/"; public static final String PREFIX_NAME = "foaf"; public static final String PAGE = "citeAsAuthority"; - public static final URI PAGE_URI = new URIImpl(voidns + PAGE); + public static final IRI PAGE_URI = factory.createIRI(voidns + PAGE); public static final String PRIMARY_TOPIC = "primaryTopic"; - public static final URI PRIMARY_TOPIC_URI = new URIImpl(voidns + PRIMARY_TOPIC); + public static final IRI PRIMARY_TOPIC_URI = factory.createIRI(voidns + PRIMARY_TOPIC); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java index 7bc37e1c6..c1dec6384 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/IdenitifiersOrgConstants.java @@ -4,22 +4,22 @@ */ package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * * @author Christian */ public class IdenitifiersOrgConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + public static final String voidns = "http://identifiers.org/terms#"; public static final String PREFIX_NAME = "idot:"; public static final String NAMESPACE = "namespace"; - public static final URI NAMESPACE_URI = new URIImpl(voidns + NAMESPACE); + public static final IRI NAMESPACE_URI = factory.createIRI(voidns + NAMESPACE); public static final String REGEX = "idRegexPattern"; - public static final URI REGEX_URI = new URIImpl(voidns + REGEX); - - + public static final IRI REGEX_URI = factory.createIRI(voidns + REGEX); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java index a6dcb8ed3..7ba7bb6a2 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/OWLConstants.java @@ -19,8 +19,8 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -31,7 +31,7 @@ public class OWLConstants { public static final String EQUIVALENT_CLASS = xmlschemans + "equivalentClass"; public static final String SAME_AS = xmlschemans + "sameAs"; - public static final URI SAMEAS_URI = new URIImpl(SAME_AS); + public static final IRI SAMEAS_URI = SimpleValueFactory.getInstance().createIRI(SAME_AS); public static final String THING = "owl:Thing"; } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java index 7fb0909cc..abd85435c 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/PavConstants.java @@ -19,37 +19,38 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * */ public class PavConstants { - + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); + private static final String pavTermns = "http://purl.org/pav/"; - public static final URI SOURCE_ACCESSED_BY = new URIImpl(pavTermns + "sourceAccessedBy"); - public static final URI SOURCE_ACCESSED_FROM = new URIImpl(pavTermns + "sourceAccessedAt"); - public static final URI SOURCE_ACCESSED_ON = new URIImpl(pavTermns + "sourceAccessedOn"); - public static final URI AUTHORED_BY = new URIImpl(pavTermns + "authoredBy"); - public static final URI AUTHORED_ON = new URIImpl(pavTermns + "authoredOn"); - public static final URI CREATED_BY = new URIImpl(pavTermns + "createdBy"); - public static final URI CREATED_ON = new URIImpl(pavTermns + "createdOn"); - public static final URI CREATED_WITH = new URIImpl(pavTermns + "createdWith"); - public static final URI DERIVED_BY = new URIImpl(pavTermns + "derivedBy"); - public static final URI DERIVED_FROM = new URIImpl(pavTermns + "derivedFrom"); - public static final URI DERIVED_ON = new URIImpl(pavTermns + "derivedOn"); - public static final URI IMPORTED_BY = new URIImpl(pavTermns + "importedBy"); - public static final URI IMPORTED_FROM = new URIImpl(pavTermns + "importedFrom"); - public static final URI IMPORTED_ON = new URIImpl(pavTermns + "importedOn"); - public static final URI LAST_REFERSHED_ON = new URIImpl(pavTermns + "lastRefreshedOn"); - public static final URI MODIFIED_ON = new URIImpl(pavTermns + "modified"); - public static final URI PREVIOUS_VERSION = new URIImpl(pavTermns + "previousVersion"); - public static final URI RETRIEVED_BY = new URIImpl(pavTermns + "retrievedBy"); - public static final URI RETRIEVED_ON = new URIImpl(pavTermns + "retrievedOn"); - public static final URI RETRIEVED_FROM = new URIImpl(pavTermns + "retrievedFrom"); - public static final URI VERSION = new URIImpl(pavTermns + "version"); + public static final IRI SOURCE_ACCESSED_BY = factory.createIRI(pavTermns + "sourceAccessedBy"); + public static final IRI SOURCE_ACCESSED_FROM = factory.createIRI(pavTermns + "sourceAccessedAt"); + public static final IRI SOURCE_ACCESSED_ON = factory.createIRI(pavTermns + "sourceAccessedOn"); + public static final IRI AUTHORED_BY = factory.createIRI(pavTermns + "authoredBy"); + public static final IRI AUTHORED_ON = factory.createIRI(pavTermns + "authoredOn"); + public static final IRI CREATED_BY = factory.createIRI(pavTermns + "createdBy"); + public static final IRI CREATED_ON = factory.createIRI(pavTermns + "createdOn"); + public static final IRI CREATED_WITH = factory.createIRI(pavTermns + "createdWith"); + public static final IRI DERIVED_BY = factory.createIRI(pavTermns + "derivedBy"); + public static final IRI DERIVED_FROM = factory.createIRI(pavTermns + "derivedFrom"); + public static final IRI DERIVED_ON = factory.createIRI(pavTermns + "derivedOn"); + public static final IRI IMPORTED_BY = factory.createIRI(pavTermns + "importedBy"); + public static final IRI IMPORTED_FROM = factory.createIRI(pavTermns + "importedFrom"); + public static final IRI IMPORTED_ON = factory.createIRI(pavTermns + "importedOn"); + public static final IRI LAST_REFERSHED_ON = factory.createIRI(pavTermns + "lastRefreshedOn"); + public static final IRI MODIFIED_ON = factory.createIRI(pavTermns + "modified"); + public static final IRI PREVIOUS_VERSION = factory.createIRI(pavTermns + "previousVersion"); + public static final IRI RETRIEVED_BY = factory.createIRI(pavTermns + "retrievedBy"); + public static final IRI RETRIEVED_ON = factory.createIRI(pavTermns + "retrievedOn"); + public static final IRI RETRIEVED_FROM = factory.createIRI(pavTermns + "retrievedFrom"); + public static final IRI VERSION = factory.createIRI(pavTermns + "version"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java index edab7a489..34de791ed 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/RdfConstants.java @@ -19,8 +19,8 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -29,5 +29,5 @@ public class RdfConstants { static final String TYPE = "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"; - public static final URI TYPE_URI = new URIImpl(TYPE); + public static final IRI TYPE_URI = SimpleValueFactory.getInstance().createIRI(TYPE); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java index b250e2925..336663915 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/VoidConstants.java @@ -19,33 +19,34 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * */ public class VoidConstants { + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); public static final String voidns = "http://rdfs.org/ns/void#"; public static final String PREFIX_NAME = "void:"; - public static final URI DATA_DUMP = new URIImpl(voidns + "dataDump"); - public static final URI DATASET = new URIImpl(voidns + "Dataset"); - public static final URI DATASET_DESCRIPTION = new URIImpl(voidns + "DatasetDescription"); - public static final URI EXAMPLE_RESOURCE = new URIImpl(voidns + "exampleResource"); - public static final URI LINK_PREDICATE = new URIImpl(voidns + "linkPredicate"); - public static final URI IN_DATASET = new URIImpl(voidns + "inDataset"); - public static final URI LINKSET = new URIImpl(voidns + "Linkset"); - public static final URI TARGET = new URIImpl(voidns + "target"); - public static final URI TRIPLES = new URIImpl(voidns + "triples"); - public static final URI SUBJECTSTARGET = new URIImpl(voidns + "subjectsTarget"); - public static final URI OBJECTSTARGET = new URIImpl(voidns + "objectsTarget"); - public static final URI SUBSET = new URIImpl(voidns + "subset"); - public static final URI SPARQL_ENDPOINT = new URIImpl(voidns + "sparqlEndpoint"); + public static final IRI DATA_DUMP = factory.createIRI(voidns + "dataDump"); + public static final IRI DATASET = factory.createIRI(voidns + "Dataset"); + public static final IRI DATASET_DESCRIPTION = factory.createIRI(voidns + "DatasetDescription"); + public static final IRI EXAMPLE_RESOURCE = factory.createIRI(voidns + "exampleResource"); + public static final IRI LINK_PREDICATE = factory.createIRI(voidns + "linkPredicate"); + public static final IRI IN_DATASET = factory.createIRI(voidns + "inDataset"); + public static final IRI LINKSET = factory.createIRI(voidns + "Linkset"); + public static final IRI TARGET = factory.createIRI(voidns + "target"); + public static final IRI TRIPLES = factory.createIRI(voidns + "triples"); + public static final IRI SUBJECTSTARGET = factory.createIRI(voidns + "subjectsTarget"); + public static final IRI OBJECTSTARGET = factory.createIRI(voidns + "objectsTarget"); + public static final IRI SUBSET = factory.createIRI(voidns + "subset"); + public static final IRI SPARQL_ENDPOINT = factory.createIRI(voidns + "sparqlEndpoint"); private static final String URI_SPACE = "uriSpace"; public static final String URI_SPACE_SHORT = PREFIX_NAME + URI_SPACE; - public static final URI URI_SPACE_URI = new URIImpl(voidns + URI_SPACE); - public static final URI VOCABULARY = new URIImpl(voidns + "vocabulary"); + public static final IRI URI_SPACE_URI = factory.createIRI(voidns + URI_SPACE); + public static final IRI VOCABULARY = factory.createIRI(voidns + "vocabulary"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java index 2a4103b4e..2b0394c0b 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/constants/XMLSchemaConstants.java @@ -19,37 +19,34 @@ // package org.bridgedb.rdf.constants; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; -/** - * - */ public class XMLSchemaConstants { - + private static final SimpleValueFactory factory = SimpleValueFactory.getInstance(); public static final String PREFIX = "http://www.w3.org/2001/XMLSchema#"; - public static final URI STRING = new URIImpl(PREFIX + "string"); - public static final URI BOOLEAN = new URIImpl(PREFIX + "boolean"); - public static final URI DECIMAL = new URIImpl(PREFIX + "decimal"); - public static final URI FLOAT = new URIImpl(PREFIX + "float"); - public static final URI DOUBLE = new URIImpl(PREFIX + "double"); - public static final URI DURATION = new URIImpl(PREFIX + "duration"); - public static final URI DATE_TIME = new URIImpl(PREFIX + "dateTime"); - public static final URI TIME = new URIImpl(PREFIX + "time"); - public static final URI DATE = new URIImpl(PREFIX + "date"); - public static final URI G_YEAR_MONTH = new URIImpl(PREFIX + "gYearMonth"); - public static final URI G_YEAR = new URIImpl(PREFIX + "gYear"); - public static final URI G_MONTH_DAY = new URIImpl(PREFIX + "gMonthDay"); - public static final URI G_DAY = new URIImpl(PREFIX + "gDay"); - public static final URI G_MONTH = new URIImpl(PREFIX + "gMonth"); - public static final URI HEX_BINARY = new URIImpl(PREFIX + "hexBinary"); - public static final URI BASE_64_BINARY = new URIImpl(PREFIX + "base64Binary"); - public static final URI ANY_URI = new URIImpl(PREFIX + "anyURI"); - public static final URI QNAME = new URIImpl(PREFIX + "QName"); - public static final URI NOTATION = new URIImpl(PREFIX + "NOTATION"); - public static final URI INTEGER = new URIImpl(PREFIX + "integer"); - public static final URI NON_NEGATIVE_INTEGER = new URIImpl(PREFIX + "nonNegativeInteger"); - public static final URI UNISGNED_BYTE = new URIImpl(PREFIX + "unsignedByte"); + public static final IRI STRING = factory.createIRI(PREFIX + "string"); + public static final IRI BOOLEAN = factory.createIRI(PREFIX + "boolean"); + public static final IRI DECIMAL = factory.createIRI(PREFIX + "decimal"); + public static final IRI FLOAT = factory.createIRI(PREFIX + "float"); + public static final IRI DOUBLE = factory.createIRI(PREFIX + "double"); + public static final IRI DURATION = factory.createIRI(PREFIX + "duration"); + public static final IRI DATE_TIME = factory.createIRI(PREFIX + "dateTime"); + public static final IRI TIME = factory.createIRI(PREFIX + "time"); + public static final IRI DATE = factory.createIRI(PREFIX + "date"); + public static final IRI G_YEAR_MONTH = factory.createIRI(PREFIX + "gYearMonth"); + public static final IRI G_YEAR = factory.createIRI(PREFIX + "gYear"); + public static final IRI G_MONTH_DAY = factory.createIRI(PREFIX + "gMonthDay"); + public static final IRI G_DAY = factory.createIRI(PREFIX + "gDay"); + public static final IRI G_MONTH = factory.createIRI(PREFIX + "gMonth"); + public static final IRI HEX_BINARY = factory.createIRI(PREFIX + "hexBinary"); + public static final IRI BASE_64_BINARY = factory.createIRI(PREFIX + "base64Binary"); + public static final IRI ANY_URI = factory.createIRI(PREFIX + "anyURI"); + public static final IRI QNAME = factory.createIRI(PREFIX + "QName"); + public static final IRI NOTATION = factory.createIRI(PREFIX + "NOTATION"); + public static final IRI INTEGER = factory.createIRI(PREFIX + "integer"); + public static final IRI NON_NEGATIVE_INTEGER = factory.createIRI(PREFIX + "nonNegativeInteger"); + public static final IRI UNISGNED_BYTE = factory.createIRI(PREFIX + "unsignedByte"); } diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java index 4fb1e9434..415644f16 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/FormatConvertor.java @@ -76,7 +76,7 @@ public static void convert(File inputFile, File outputFile) throws Exception { RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); repositoryConnection.add(inputFile, DEFAULT_BASE_URI, getFormat(inputFile.getName())); writeRDF(repositoryConnection, outputFile); diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java index b9d25a2cb..29fb8b077 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/create/LinkSetCombiner.java @@ -77,7 +77,7 @@ public static void convert(Collection inputFiles, File outputFile) throws RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); for (File inputFile:inputFiles){ Reporter.println("Parsing " + inputFile.getAbsolutePath()); @@ -96,7 +96,7 @@ public static long count(File inputFile) throws Exception { RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); Reporter.println("Parsing (to count)" + inputFile.getAbsolutePath()); repositoryConnection.add(inputFile, DEFAULT_BASE_URI, getFormat(inputFile.getName())); diff --git a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java index 777b7cdc4..5b7182e60 100644 --- a/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java +++ b/org.bridgedb.rdf/src/org/bridgedb/rdf/identifiers/org/IdentifersOrgReader.java @@ -33,6 +33,7 @@ import java.util.HashSet; import java.util.Set; import java.util.regex.Pattern; + import org.apache.log4j.Logger; import org.bridgedb.DataSource; import org.bridgedb.DataSourcePatterns; @@ -48,10 +49,10 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.repository.Repository; import org.eclipse.rdf4j.repository.RepositoryConnection; import org.eclipse.rdf4j.repository.RepositoryException; @@ -85,13 +86,13 @@ private void doParseRdfInputStream(InputStream stream) throws BridgeDBException RepositoryConnection repositoryConnection = null; try { repository = new SailRepository(new MemoryStore()); - repository.initialize(); + repository.init(); repositoryConnection = repository.getConnection(); repositoryConnection.add(stream, DEFAULT_BASE_URI, DEFAULT_FILE_FORMAT); // for (String multiple:multiples){ // checkMultiple(repositoryConnection, multiple); // } - Reporter.println("Registry read in. Now loading DataSources"); + Reporter.println("Registry read in. Now loading DataSources from the in memory store"); loadData(repositoryConnection); } catch (Exception ex) { throw new BridgeDBException ("Error parsing RDF inputStream: " + ex.getMessage(), ex); @@ -133,7 +134,7 @@ public static void init() throws BridgeDBException{ public static void saveRegister() throws BridgeDBException { try { URL url = new URL(MIRAM_REGISTRY_URI); - Reporter.println("Readng " + url); + Reporter.println("Reading " + url); InputStream inputStream = url.openStream(); InputStreamReader inputReader = new InputStreamReader(inputStream); BufferedReader inputBuffer = new BufferedReader(inputReader); @@ -203,7 +204,7 @@ private DataSource readDataSource(RepositoryConnection repositoryConnection, Res UriPattern.register(identiferOrgBase + "$id", sysCode, UriPatternType.identifiersOrgPatternSimple); String identifersOrgInfoBase = identiferOrgBase.replace("identifiers.org","info.identifiers.org"); UriPattern.register(identifersOrgInfoBase + "$id", sysCode, UriPatternType.identifiersOrgPatternInfo); - + DataSource ds = DataSource.register(sysCode, fullName) .identifiersOrgBase(identiferOrgBase) .asDataSource(); @@ -283,7 +284,7 @@ private void loadUriPatterns(RepositoryConnection repositoryConnection, Resource } private void checkMultiple(RepositoryConnection repositoryConnection, String multiple) throws Exception{ - URI uri = new URIImpl(multiple); + IRI uri = SimpleValueFactory.getInstance().createIRI(multiple); RepositoryResult accessStatements = repositoryConnection.getStatements(null, null, uri, true); while(accessStatements.hasNext()) { diff --git a/org.bridgedb.rdf/test-data/DataSourceMin.ttl b/org.bridgedb.rdf/test-data/DataSourceMin.ttl index 8902f8567..29f328e3c 100644 --- a/org.bridgedb.rdf/test-data/DataSourceMin.ttl +++ b/org.bridgedb.rdf/test-data/DataSourceMin.ttl @@ -3,19 +3,23 @@ bridgeDB:DataSource_Chemspider a bridgeDB:DataSource ; bridgeDB:fullName "Chemspider" ; bridgeDB:systemCode "Cs" ; - bridgeDB:mainUrl "http://www.chemspider.com/" ; + bridgeDB:mainUrl "https://www.chemspider.com/" ; bridgeDB:idExample "56586" ; bridgeDB:primary "true"^^ ; bridgeDB:type "metabolite" ; - bridgeDB:hasPrimaryUriPattern ; + bridgeDB:hasPrimaryUriPattern ; bridgeDB:hasIdentifiersOrgPattern . a bridgeDB:uriPattern ; bridgeDB:hasPrefix "http://identifiers.org/chemspider/" ; bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . - a bridgeDB:uriPattern ; - bridgeDB:hasPrefix "http://www.chemspider.com/Chemical-Structure." ; + a bridgeDB:uriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/Chemical-Structure." ; bridgeDB:hasPostfix ".html" ; bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . + a bridgeDB:uriPattern ; + bridgeDB:hasPrefix "https://www.chemspider.com/" ; + bridgeDB:hasPostfix "" ; + bridgeDB:isUriPatternOf bridgeDB:DataSource_Chemspider . diff --git a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java index 35d3e49c9..2b4e8fa58 100644 --- a/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java +++ b/org.bridgedb.rdf/test/org/bridgedb/rdf/DataSourceComparatorTest.java @@ -16,19 +16,24 @@ package org.bridgedb.rdf; +import static org.hamcrest.Matchers.greaterThan; +import static org.hamcrest.Matchers.hasItem; +import static org.hamcrest.Matchers.lessThan; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertThat; + import java.io.InputStream; import java.util.Set; + import org.bridgedb.DataSource; import org.bridgedb.bio.DataSourceComparator; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; -import static org.hamcrest.Matchers.*; - -import static org.junit.Assert.*; -import org.junit.jupiter.api.*; - import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; +import org.junit.jupiter.api.Test; /** * @@ -46,7 +51,7 @@ public class DataSourceComparatorTest { public void testGetResourceId() { Reporter.println("getResourceId"); DataSource dataSource = DataSource.register("DataSourceUrisTest_testGetResourceId", "DataSourceUrisTest_testGetResourceId").asDataSource(); - Resource expResult = new URIImpl("http://vocabularies.bridgedb.org/ops#DataSource_DataSourceUrisTest_testGetResourceId"); + Resource expResult = SimpleValueFactory.getInstance().createIRI("http://vocabularies.bridgedb.org/ops#DataSource_DataSourceUrisTest_testGetResourceId"); Resource result = BridgeDBRdfHandler.asResource(dataSource); assertEquals(expResult, result); } @@ -95,7 +100,7 @@ public void testGetUriPatterns() throws BridgeDBException{ BridgeDBRdfHandler.parseRdfInputStream(dataSourceStream); Set result = UriPattern.byCodeAndType("Cs", UriPatternType.mainUrlPattern); assertFalse("Could not find main URL pattern for Cs", result.isEmpty()); - UriPattern pattern = UriPattern.existingByPattern("http://www.chemspider.com/Chemical-Structure.$id.html"); + UriPattern pattern = UriPattern.existingByPattern("https://www.chemspider.com/$id"); assertThat (result, hasItem(pattern)); // pattern = UriPattern.existingOrCreateByPattern("http://identifiers.org/chemspider/$id"); // assertThat (result, hasItem(pattern)); diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 111270a52..d8ed5f761 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -47,8 +47,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 89bcf8fac..d65a4d9a3 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.0.23 + 3.1.4 compile org.bridgedb org.bridgedb.bio - 3.0.23 + 3.1.4 compile org.bridgedb org.bridgedb.rdb - 3.0.23 + 3.1.4 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 96afc0d73..91adf6d8c 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index c61438b76..327225eab 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,15 +82,15 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j com.google.guava guava - [32.0.1-jre,) + [32.0.0-jre,) org.apache.derby diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index d20732b63..f195a05c2 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,15 +82,15 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j com.google.guava guava - [30.0-jre,) + [32.0-jre,) org.apache.derby diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index dea13dc22..6f74e8c71 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 635bb5794..867d93212 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java index 1b6c5f380..f799087f0 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinkHandler.java @@ -19,16 +19,17 @@ // package org.bridgedb.uri.loader; +import java.net.URI; + import org.apache.log4j.Logger; -import org.bridgedb.uri.tools.RegexUriPattern; import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; import org.eclipse.rdf4j.rio.RDFHandlerException; -import org.eclipse.rdf4j.rio.helpers.RDFHandlerBase; +import org.eclipse.rdf4j.rio.helpers.AbstractRDFHandler; /** * Reads an RDF linkset file and passes the information on to a RdfLoader. @@ -39,9 +40,9 @@ * * @author Christian */ -public class LinkHandler extends RDFHandlerBase{ +public class LinkHandler extends AbstractRDFHandler { - protected final URI linkPredicate; + protected final IRI linkPredicate; private boolean symetric; protected final UriListener uriListener; @@ -49,13 +50,13 @@ public class LinkHandler extends RDFHandlerBase{ static final Logger logger = Logger.getLogger(LinkHandler.class); - public LinkHandler(UriListener uriListener, URI linkPredicate, boolean symetric){ + public LinkHandler(UriListener uriListener, IRI linkPredicate, boolean symetric){ this.uriListener = uriListener; this.linkPredicate = linkPredicate; this.symetric = symetric; } - public LinkHandler(UriListener uriListener, URI linkPredicate){ + public LinkHandler(UriListener uriListener, IRI linkPredicate){ this (uriListener, linkPredicate, true); } @@ -87,10 +88,10 @@ public void endRDF() throws RDFHandlerException{ private void insertUriMapping(Statement st) throws RDFHandlerException { Resource subject = st.getSubject(); Value object = st.getObject(); - if (!(subject instanceof URI)){ + if (!(subject instanceof IRI)){ throw new RDFHandlerException ("None URI subject in " + st); } - if (!(object instanceof URI)){ + if (!(object instanceof IRI)){ throw new RDFHandlerException ("None URI object in " + st); } String sourceUri = subject.stringValue(); diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java index 5049c2b92..41709c78b 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetHandler.java @@ -25,9 +25,9 @@ import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Resource; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; import org.eclipse.rdf4j.model.Value; import org.eclipse.rdf4j.rio.RDFHandlerException; @@ -46,12 +46,12 @@ public class LinksetHandler extends LinkHandler{ protected final String justification; protected final String backwardJustification; - protected final URI mappingSource; + protected final IRI mappingSource; private int noneLinkStatements; static final Logger logger = Logger.getLogger(LinksetHandler.class); - public LinksetHandler(UriListener uriListener, URI linkPredicate, String justification, URI mappingSource){ + public LinksetHandler(UriListener uriListener, IRI linkPredicate, String justification, IRI mappingSource){ super(uriListener, linkPredicate); this.justification = justification; this.mappingSource = mappingSource; @@ -66,7 +66,7 @@ public LinksetHandler(UriListener uriListener, URI linkPredicate, String justifi * @param mappingSource * @param ignore */ - public LinksetHandler(UriListener uriListener, URI linkPredicate, String justification, URI mappingSource, boolean ignore){ + public LinksetHandler(UriListener uriListener, IRI linkPredicate, String justification, IRI mappingSource, boolean ignore){ this(uriListener, linkPredicate, justification, mappingSource); } @@ -91,17 +91,17 @@ public void handleStatement(Statement st) throws RDFHandlerException { * @throws RDFHandlerException */ private void processFirstStatement(Statement st) throws RDFHandlerException{ - final URI predicate = st.getPredicate(); + final IRI predicate = st.getPredicate(); if (predicate.equals(linkPredicate)) { Resource subject = st.getSubject(); Value object = st.getObject(); try { processingFirstStatement = false; - if (!(subject instanceof URI)){ + if (!(subject instanceof IRI)){ Reporter.error("None URI subject in " + st); return; } - if (!(object instanceof URI)){ + if (!(object instanceof IRI)){ Reporter.error("None URI object in " + st); return; } diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java index 783f7110c..7b29d2f59 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/LinksetListener.java @@ -20,12 +20,12 @@ package org.bridgedb.uri.loader; import java.io.File; -import java.util.Set; +import java.net.URI; + import org.apache.log4j.Logger; import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; -import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.URI; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.rio.RDFHandler; public class LinksetListener { @@ -39,15 +39,15 @@ public LinksetListener(UriListener uriListener){ static final Logger logger = Logger.getLogger(LinksetListener.class); - public int parse(File file, URI linkPredicate, String justification, boolean symetric) throws BridgeDBException{ - URI mappingUri = RdfParser.fileToURL(file); + public int parse(File file, IRI linkPredicate, String justification, boolean symetric) throws BridgeDBException{ + IRI mappingUri = RdfParser.fileToURL(file); LinksetHandler handler = new LinksetHandler(uriListener, linkPredicate, justification, mappingUri, symetric); RdfParser parser = getParser(handler); parser.parse(mappingUri.stringValue(), file); return handler.getMappingsetId(); } - public int parse(File file, URI mappingSource, URI linkPredicate, String justification, + public int parse(File file, IRI mappingSource, IRI linkPredicate, String justification, Boolean symetric) throws BridgeDBException{ LinksetHandler handler = new LinksetHandler(uriListener, linkPredicate, justification, mappingSource, symetric); RdfParser parser = getParser(handler); @@ -55,7 +55,7 @@ public int parse(File file, URI mappingSource, URI linkPredicate, String justifi return handler.getMappingsetId(); } - public int parse(String uri, URI mappingSource, URI linkPredicate, String justification, boolean symetric) + public int parse(String uri, IRI mappingSource, IRI linkPredicate, String justification, boolean symetric) throws BridgeDBException{ LinksetHandler handler = new LinksetHandler(uriListener, linkPredicate, justification, mappingSource, symetric); RdfParser parser = getParser(handler); diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java index d441a645b..679d8f92b 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/RdfParser.java @@ -32,9 +32,9 @@ import org.apache.log4j.Logger; import org.bridgedb.uri.loader.transative.TransativeConfig; import org.bridgedb.utils.BridgeDBException; -import org.eclipse.rdf4j.OpenRDFException; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.common.exception.RDF4JException; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.rio.RDFFormat; import org.eclipse.rdf4j.rio.RDFHandler; import org.eclipse.rdf4j.rio.RDFParser; @@ -66,11 +66,10 @@ public void parse(String baseURI, File file, String rdfFormatName) throws Bridge RDFParser parser = getParser(file.getName(), rdfFormatName); parser.setRDFHandler(handler); parser.setParseErrorListener(new LinksetParserErrorListener()); - parser.setVerifyData(true); parser.parse (reader, baseURI); } catch (IOException ex) { throw new BridgeDBException("Error reading " + file.getAbsolutePath() + " " + ex.getMessage(), ex); - } catch (OpenRDFException ex) { + } catch (RDF4JException ex) { throw new BridgeDBException("Error parsing " + file.getAbsolutePath() + " " + ex.getMessage(), ex); } finally { try { @@ -98,11 +97,10 @@ public void parse(InputStream stream, String mappingSource, String rdfFormatName RDFParser parser = getParser(mappingSource, rdfFormatName); parser.setRDFHandler(handler); parser.setParseErrorListener(new LinksetParserErrorListener()); - parser.setVerifyData(true); parser.parse (stream, mappingSource); } catch (IOException ex) { throw new BridgeDBException("Error reading " + mappingSource + " " + ex.getMessage(), ex); - } catch (OpenRDFException ex) { + } catch (RDF4JException ex) { throw new BridgeDBException("Error parsing " + mappingSource + " " + ex.getMessage(), ex); } finally { try { @@ -128,22 +126,22 @@ public InputStream getInputStream(String uri) throws BridgeDBException { } } - public static URI fileToURL(File file) throws BridgeDBException{ + public static IRI fileToURL(File file) throws BridgeDBException{ String baseURI = TransativeConfig.getTransitiveBaseUri(); if (baseURI == null || baseURI.isEmpty()){ return fileToURI(file); } if (file.getParent().equals(TransativeConfig.getTransativeDirectory())){ - return new URIImpl(baseURI + file.getName()); + return SimpleValueFactory.getInstance().createIRI(baseURI + file.getName()); } else { return RdfParser.fileToURI(file); } } - private static URI fileToURI(File file) throws BridgeDBException{ + private static IRI fileToURI(File file) throws BridgeDBException{ try { String uri = file.toURI().toURL().toExternalForm(); - return new URIImpl(uri); + return SimpleValueFactory.getInstance().createIRI(uri); } catch (MalformedURLException ex) { throw new BridgeDBException("Unable to convert file to URI", ex); } diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java index be84bea78..7382bcf63 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/SetupWithTestData.java @@ -5,12 +5,13 @@ package org.bridgedb.uri.loader; import java.io.File; + import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.uri.lens.Lens; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -20,7 +21,7 @@ public class SetupWithTestData { static final String MAIN_JUSTIFCATION = "http://semanticscience.org/resource/CHEMINF_000059"; static final String LENS_JUSTIFCATION = "http://www.bridgedb.org/test#testJustification"; - static final URI linkPredicate = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + static final IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); private SQLUriMapper uriListener; private LinksetListener instance; diff --git a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java index e76d8743b..c25150890 100644 --- a/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java +++ b/org.bridgedb.uri.loader/src/main/java/org/bridgedb/uri/loader/transative/TransativeCreator.java @@ -10,6 +10,7 @@ import java.sql.Connection; import java.sql.ResultSet; import java.sql.SQLException; + import org.apache.log4j.Logger; import org.bridgedb.DataSource; import org.bridgedb.rdf.UriPattern; @@ -24,10 +25,9 @@ import org.bridgedb.uri.tools.RegexUriPattern; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.StatementImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.rio.RDFHandlerException; import org.eclipse.rdf4j.rio.RDFWriter; import org.eclipse.rdf4j.rio.turtle.TurtleWriter; @@ -42,13 +42,13 @@ public class TransativeCreator { private final UriMapper mapper; protected final MappingSetInfo leftInfo; protected final MappingSetInfo rightInfo; - protected final URI predicate; + protected final IRI predicate; protected final String justification; private final RegexUriPattern sourceRegexUriPattern; private final RegexUriPattern targetRegexUriPattern; private final boolean reflexive; - private static URI GENERATE_PREDICATE = null; + private static IRI GENERATE_PREDICATE = null; static final Logger logger = Logger.getLogger(TransativeCreator.class); @@ -73,7 +73,7 @@ protected TransativeCreator(MappingSetInfo left, MappingSetInfo right) mapper = SQLUriMapper.getExisting(); leftInfo = left; rightInfo = right; - predicate = new URIImpl(LoosePredicateMaker.getInstance().combine(left.getPredicate(), right.getPredicate())); + predicate = SimpleValueFactory.getInstance().createIRI(LoosePredicateMaker.getInstance().combine(left.getPredicate(), right.getPredicate())); justification = OpsJustificationMaker.getInstance().combine(left.getJustification(), right.getJustification()); reflexive = left.getSource().getSysCode().equals(right.getTarget().getSysCode()); UriPattern sourceUriPattern = getUriPattern(left.getSource()); @@ -145,10 +145,10 @@ private boolean getSQL(RDFWriter rdfwriter) throws BridgeDBException, IOExceptio //do nothing as same uri; } else { String sourceUri = sourceRegexUriPattern.getUri(sourceId); - URI sourceURI = new URIImpl(sourceUri); + IRI sourceURI = SimpleValueFactory.getInstance().createIRI(sourceUri); String targetUri = targetRegexUriPattern.getUri(targetId); - URI targetURI = new URIImpl(targetUri); - Statement statment = new StatementImpl(sourceURI, predicate, targetURI); + IRI targetURI = SimpleValueFactory.getInstance().createIRI(targetUri); + Statement statment = SimpleValueFactory.getInstance().createStatement(sourceURI, predicate, targetURI); rdfwriter.handleStatement(statment); found = true; } diff --git a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java index 14181297c..429a4f9ee 100644 --- a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java +++ b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/LinksetListenerTest.java @@ -4,12 +4,14 @@ */ package org.bridgedb.loader; +import static org.hamcrest.MatcherAssert.assertThat; +import static org.hamcrest.Matchers.greaterThanOrEqualTo; + import java.io.File; import java.io.FileOutputStream; import java.io.InputStream; import org.apache.commons.io.IOUtils; -import org.bridgedb.loader.transative.TransativeCreatorTest; import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.sql.TestSqlFactory; import org.bridgedb.statistics.MappingSetInfo; @@ -18,22 +20,18 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; - +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; -import static org.hamcrest.MatcherAssert.assertThat; -import static org.hamcrest.Matchers.*; - /** * * @author Christian */ public class LinksetListenerTest { - static final URI linkPredicate = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + static final IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); static SQLUriMapper uriListener; static LinksetListener instance; diff --git a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java index 36841348f..bfaea772c 100644 --- a/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java +++ b/org.bridgedb.uri.loader/src/test/java/org/bridgedb/loader/transative/TransativeCreatorTest.java @@ -20,7 +20,7 @@ package org.bridgedb.loader.transative; import static org.hamcrest.MatcherAssert.assertThat; -import static org.hamcrest.Matchers.*; +import static org.hamcrest.Matchers.greaterThanOrEqualTo; import java.io.File; import java.io.FileOutputStream; @@ -37,10 +37,10 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; /** * @@ -48,7 +48,7 @@ */ public class TransativeCreatorTest { - static final URI linkPredicate = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + static final IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); static SQLUriMapper uriListener; static LinksetListener instance; diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl index 8b7f06aa8..b83034c73 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops.ttl @@ -30,11 +30,11 @@ pav:createdOn "2014-11-03"^^xsd:date . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl index 43a8723fe..402a2dbae 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cs-ops_lensed.ttl @@ -25,11 +25,11 @@ dcterms:created "2014-11-21"^^xsd:date . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl index 6b66cd9e9..09c540d2a 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs.ttl @@ -29,7 +29,7 @@ void:uriSpace . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl index c5e22fc58..47e9e5701 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/cw-cs_lensed.ttl @@ -29,7 +29,7 @@ void:uriSpace . :chemspider a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl b/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl index 8fde9b3ba..57e7f7dfa 100644 --- a/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl +++ b/org.bridgedb.uri.loader/src/test/resources/test-data/ops-ops_lensed.ttl @@ -25,7 +25,7 @@ dcterms:created "2014-11-21"^^xsd:date . :ops a void:Dataset ; dcterms:title "ChemSpider"^^xsd:string ; - dcterms:license ; + dcterms:license ; void:uriSpace . skos:exactMatch . diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index ce6767b3b..8a83fe0c9 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -64,8 +64,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.uri.sql/resources/graph.properties b/org.bridgedb.uri.sql/resources/graph.properties index c77029660..ab351ded6 100644 --- a/org.bridgedb.uri.sql/resources/graph.properties +++ b/org.bridgedb.uri.sql/resources/graph.properties @@ -80,10 +80,10 @@ context.chebi1.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id context.chebi1.graph http://www.ebi.ac.uk/chebi context.chebi2.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id -context.chebi2.graph http://www.ebi.ac.uk/chebi/direct +context.chebi2.graph https://www.ebi.ac.uk/chebi/direct context.chebi3.pattern.1 http://purl.obolibrary.org/obo/CHEBI_$id -context.chebi3.graph http://www.ebi.ac.uk/chebi/inference +context.chebi3.graph https://www.ebi.ac.uk/chebi/inference context.enzyme1.pattern.1 http://purl.uniprot.org/enzyme/$id context.enzyme1.graph http://purl.uniprot.org/enzyme diff --git a/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java b/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java index f3c442a60..76065ee22 100644 --- a/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java +++ b/org.bridgedb.uri.sql/src/org/bridgedb/sql/SQLUriMapper.java @@ -449,7 +449,7 @@ public IdSysCodePair toIdSysCodePair(String uri) throws BridgeDBException { //Know dulicate prefixes of this type include //http://www.kegg.jp/entry/ //http://www.ebi.ac.uk/ontology-lookup/?termId= - //http://www.gramene.org/db/ontology/search?id= + //https://www.gramene.org/db/ontology/search?id= //http://stke.sciencemag.org/cgi/cm/stkecm; //http://purl.uniprot.org/uniprot/ //http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name= diff --git a/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java b/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java index 746c4d7ec..216873956 100644 --- a/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java +++ b/org.bridgedb.uri.sql/src/org/bridgedb/uri/lens/LensTools.java @@ -26,6 +26,7 @@ import java.util.List; import java.util.Properties; import java.util.Set; + import org.apache.log4j.Logger; import org.bridgedb.rdf.BridgeDBRdfHandler; import org.bridgedb.rdf.constants.BridgeDBConstants; @@ -35,11 +36,9 @@ import org.bridgedb.uri.api.UriMapper; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.LiteralImpl; -import org.eclipse.rdf4j.model.impl.StatementImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.sail.memory.model.CalendarMemLiteral; /** @@ -291,15 +290,15 @@ public static Set getLensAsRdf(String baseUri, String group) throws B public static Set asRdf(Lens lens, String baseUri) { HashSet results = new HashSet(); - URI subject = new URIImpl(lens.toUri(baseUri)); - results.add(new StatementImpl(subject, RdfConstants.TYPE_URI, BridgeDBConstants.LENS_URI)); - results.add(new StatementImpl(subject, DCTermsConstants.TITLE_URI, new LiteralImpl(lens.getName()))); - results.add(new StatementImpl(subject, DCTermsConstants.DESCRIPTION_URI, new LiteralImpl(lens.getDescription()))); - results.add(new StatementImpl(subject, PavConstants.CREATED_BY, new LiteralImpl(lens.getCreatedBy()))); + IRI subject = SimpleValueFactory.getInstance().createIRI(lens.toUri(baseUri)); + results.add(SimpleValueFactory.getInstance().createStatement(subject, RdfConstants.TYPE_URI, BridgeDBConstants.LENS_URI)); + results.add(SimpleValueFactory.getInstance().createStatement(subject, DCTermsConstants.TITLE_URI, SimpleValueFactory.getInstance().createLiteral(lens.getName()))); + results.add(SimpleValueFactory.getInstance().createStatement(subject, DCTermsConstants.DESCRIPTION_URI, SimpleValueFactory.getInstance().createLiteral(lens.getDescription()))); + results.add(SimpleValueFactory.getInstance().createStatement(subject, PavConstants.CREATED_BY, SimpleValueFactory.getInstance().createLiteral(lens.getCreatedBy()))); CalendarMemLiteral createdOnLiteral = new CalendarMemLiteral(lens, lens.getCreatedOn()); - results.add(new StatementImpl(subject, PavConstants.CREATED_ON, createdOnLiteral)); + results.add(SimpleValueFactory.getInstance().createStatement(subject, PavConstants.CREATED_ON, createdOnLiteral)); for (String justification:lens.getJustifications()){ - results.add(new StatementImpl(subject, BridgeDBConstants.LINKSET_JUSTIFICATION, new URIImpl(justification))); + results.add(SimpleValueFactory.getInstance().createStatement(subject, BridgeDBConstants.LINKSET_JUSTIFICATION, SimpleValueFactory.getInstance().createIRI(justification))); } return results; } diff --git a/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java b/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java index 4e1b00c7a..d05e438c3 100644 --- a/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java +++ b/org.bridgedb.uri.sql/src/org/bridgedb/uri/tools/DirectStatementMaker.java @@ -26,11 +26,9 @@ import org.bridgedb.uri.lens.Lens; import org.bridgedb.uri.lens.LensTools; import org.bridgedb.utils.BridgeDBException; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.ContextStatementImpl; -import org.eclipse.rdf4j.model.impl.StatementImpl; -import org.eclipse.rdf4j.model.impl.URIImpl; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; /** * @@ -38,41 +36,41 @@ */ public class DirectStatementMaker implements StatementMaker{ - protected final URI toURI(String text){ + protected final IRI toURI(String text){ try { - return new URIImpl(text); + return SimpleValueFactory.getInstance().createIRI(text); } catch (IllegalArgumentException ex){ - return new URIImpl("<" + text + ">"); + return SimpleValueFactory.getInstance().createIRI("<" + text + ">"); } } private Set asRDF(SetMappings setMappings, String lens, String baseUri, String methodName) throws BridgeDBException { HashSet statements = new HashSet(); - URI setUri; - setUri = new URIImpl(baseUri + methodName + "/" + setMappings.getId()); - URI predicateURI = toURI(setMappings.getPredicate()); - Statement statement = new StatementImpl(setUri, VoidConstants.LINK_PREDICATE, predicateURI); + IRI setUri; + setUri = SimpleValueFactory.getInstance().createIRI(baseUri + methodName + "/" + setMappings.getId()); + IRI predicateURI = toURI(setMappings.getPredicate()); + Statement statement = SimpleValueFactory.getInstance().createStatement(setUri, VoidConstants.LINK_PREDICATE, predicateURI); statements.add(statement); - URI justifcationURI = toURI(setMappings.getJustification()); - statement = new StatementImpl(setUri, DulConstants.EXPRESSES, justifcationURI); + IRI justifcationURI = toURI(setMappings.getJustification()); + statement = SimpleValueFactory.getInstance().createStatement(setUri, DulConstants.EXPRESSES, justifcationURI); statements.add(statement); String source = setMappings.getMappingSource(); if (source != null && !source.isEmpty()){ - URI mappingSourceURI = toURI(setMappings.getMappingSource()); - statement = new StatementImpl(setUri, VoidConstants.DATA_DUMP, mappingSourceURI); + IRI mappingSourceURI = toURI(setMappings.getMappingSource()); + statement = SimpleValueFactory.getInstance().createStatement(setUri, VoidConstants.DATA_DUMP, mappingSourceURI); statements.add(statement); } if (lens != null){ Lens theLens = LensTools.byId(lens); - URI lensUri = new URIImpl(theLens.toUri(baseUri)); - URI hasLensUri = BridgeDBConstants.FULFILLS_LENS; - statement = new StatementImpl(setUri, hasLensUri, lensUri); + IRI lensUri = SimpleValueFactory.getInstance().createIRI(theLens.toUri(baseUri)); + IRI hasLensUri = BridgeDBConstants.FULFILLS_LENS; + statement = SimpleValueFactory.getInstance().createStatement(setUri, hasLensUri, lensUri); statements.add(statement); } for (UriMapping mapping:setMappings.getMappings()){ - URI sourceURI = toURI(mapping.getSourceUri()); - URI targetURI = toURI(mapping.getTargetUri()); - statement = new ContextStatementImpl(sourceURI, predicateURI, targetURI, setUri); + IRI sourceURI = toURI(mapping.getSourceUri()); + IRI targetURI = toURI(mapping.getTargetUri()); + statement = SimpleValueFactory.getInstance().createStatement(sourceURI, predicateURI, targetURI, setUri); statements.add(statement); } return statements; @@ -95,9 +93,9 @@ public Set asRDF(MappingsBySet mappingsBySet, String baseUri, String for (UriMapping mapping:mappingsBySet.getMappings()){ //Inclusion of mapping to self at Antonis request April 2014 //if (!mapping.getSourceUri().equals(mapping.getTargetUri())){ - URI sourceURI = toURI(mapping.getSourceUri()); - URI targetURI = toURI(mapping.getTargetUri()); - Statement statement = new StatementImpl(sourceURI, OWLConstants.SAMEAS_URI, targetURI); + IRI sourceURI = toURI(mapping.getSourceUri()); + IRI targetURI = toURI(mapping.getTargetUri()); + Statement statement = SimpleValueFactory.getInstance().createStatement(sourceURI, OWLConstants.SAMEAS_URI, targetURI); statements.add(statement); //} } @@ -105,7 +103,7 @@ public Set asRDF(MappingsBySet mappingsBySet, String baseUri, String return statements; } - protected URI mappingSetURI(String id, String baseUri, String predicateURI){ + protected IRI mappingSetURI(String id, String baseUri, String predicateURI){ String uriStr = baseUri + UriConstants.MAPPING_SET + UriConstants.RDF + "/" + id; if (predicateURI != null) { String p; @@ -129,28 +127,28 @@ private String encodeWithinQuery(String str) { @Override public Set asRDF(MappingSetInfo info, String baseUri, String contextString) throws BridgeDBException{ HashSet results = new HashSet(); - URI linksetId = mappingSetURI(info.getStringId(), baseUri, null); - URI source = toURI(info.getMappingSource()); - URI context = new URIImpl(contextString); - results.add(new ContextStatementImpl(linksetId, PavConstants.IMPORTED_FROM, source, context)); - URI predicate = toURI(info.getPredicate()); - results.add(new ContextStatementImpl(linksetId, VoidConstants.LINK_PREDICATE, predicate, context)); - URI justification = toURI(info.getJustification()); - results.add(new ContextStatementImpl(linksetId, BridgeDBConstants.LINKSET_JUSTIFICATION, justification, context)); + IRI linksetId = mappingSetURI(info.getStringId(), baseUri, null); + IRI source = toURI(info.getMappingSource()); + IRI context = SimpleValueFactory.getInstance().createIRI(contextString); + results.add(SimpleValueFactory.getInstance().createStatement(linksetId, PavConstants.IMPORTED_FROM, source, context)); + IRI predicate = toURI(info.getPredicate()); + results.add(SimpleValueFactory.getInstance().createStatement(linksetId, VoidConstants.LINK_PREDICATE, predicate, context)); + IRI justification = toURI(info.getJustification()); + results.add(SimpleValueFactory.getInstance().createStatement(linksetId, BridgeDBConstants.LINKSET_JUSTIFICATION, justification, context)); return results; } - private void addMappingsRDF(Set statements, Mapping mapping, URI predicateUri, URI mappingSet) throws BridgeDBException{ + private void addMappingsRDF(Set statements, Mapping mapping, IRI predicateUri, IRI mappingSet) throws BridgeDBException{ for (String source:mapping.getSourceUri()){ - URI sourceUri = new URIImpl(source); + IRI sourceUri = SimpleValueFactory.getInstance().createIRI(source); for (String target: mapping.getTargetUri()){ - URI targetUri = new URIImpl(target); - statements.add(new ContextStatementImpl(sourceUri, predicateUri, targetUri, mappingSet)); + IRI targetUri = SimpleValueFactory.getInstance().createIRI(target); + statements.add(SimpleValueFactory.getInstance().createStatement(sourceUri, predicateUri, targetUri, mappingSet)); } } } - protected void addLinksetInfo(Set statements, Mapping mapping, URI mappingSet) throws BridgeDBException{ + protected void addLinksetInfo(Set statements, Mapping mapping, IRI mappingSet) throws BridgeDBException{ if (mapping.isMappingToSelf()){ //No void for mapping to self at the moment. } else if (mapping.isTransitive()){ @@ -162,26 +160,26 @@ protected void addLinksetInfo(Set statements, Mapping mapping, URI ma } } - protected void addMappingVoid(Set statements, Mapping mapping, URI mappingSet) + protected void addMappingVoid(Set statements, Mapping mapping, IRI mappingSet) throws BridgeDBException { - URI sourceUri = toURI(mapping.getMappingSource()); - statements.add(new ContextStatementImpl(mappingSet, PavConstants.DERIVED_FROM, sourceUri, mappingSet)); + IRI sourceUri = toURI(mapping.getMappingSource()); + statements.add(SimpleValueFactory.getInstance().createStatement(mappingSet, PavConstants.DERIVED_FROM, sourceUri, mappingSet)); } private void addSelfMappingsRDF(Set statements, Mapping mapping, String selfMappingPredicateURI) throws BridgeDBException{ - URI predicate; + IRI predicate; if (selfMappingPredicateURI == null || selfMappingPredicateURI.isEmpty()) { predicate = OWLConstants.SAMEAS_URI; } else { - predicate = new URIImpl(selfMappingPredicateURI); + predicate = SimpleValueFactory.getInstance().createIRI(selfMappingPredicateURI); } for (String source:mapping.getSourceUri()){ - URI sourceUri = new URIImpl(source); + IRI sourceUri = SimpleValueFactory.getInstance().createIRI(source); for (String target: mapping.getTargetUri()){ if (!source.equals(target)){ - URI targetUri = new URIImpl(target); - statements.add(new StatementImpl(sourceUri, predicate, targetUri)); + IRI targetUri = SimpleValueFactory.getInstance().createIRI(target); + statements.add(SimpleValueFactory.getInstance().createStatement(sourceUri, predicate, targetUri)); } } } @@ -200,8 +198,8 @@ public Set asRDF(Set mappings, String baseUri, boolean links } if (predicate != null){ String id = mapping.getMappingSetId(); - URI mappingSet = mappingSetURI(id, baseUri, overridePredicateURI); - URI predicateUri = new URIImpl(predicate); + IRI mappingSet = mappingSetURI(id, baseUri, overridePredicateURI); + IRI predicateUri = SimpleValueFactory.getInstance().createIRI(predicate); addMappingsRDF(statements, mapping, predicateUri, mappingSet); if (linksetInfo){ addLinksetInfo(statements, mapping, mappingSet); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java index 4738159c3..d1eee6396 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/UriMapperRecoverTest.java @@ -21,7 +21,10 @@ package org.bridgedb.mysql; +import static org.junit.jupiter.api.Assertions.assertEquals; + import java.util.Date; + import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.sql.TestSqlFactory; import org.bridgedb.statistics.OverallStatistics; @@ -29,13 +32,10 @@ import org.bridgedb.uri.lens.Lens; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; - -import org.junit.jupiter.api.Test; import org.eclipse.rdf4j.model.Resource; -import org.eclipse.rdf4j.model.impl.URIImpl; - -import static org.junit.jupiter.api.Assertions.assertEquals; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.Test; /** @@ -68,7 +68,7 @@ public void testRecover()throws BridgeDBException{ stats = uriMapper.getOverallStatistics(Lens.ALL_LENS_NAME); assertEquals(12, stats.getNumberOfMappings()); assertEquals(4, stats.getNumberOfMappingSets()); - Resource resource = new URIImpl("http://example.com/1to2Another"); + Resource resource = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2Another"); int mappingSet = listener.registerMappingSet(regexUriPattern1, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern2, resource); assertEquals(5, mappingSet); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java index 557742e5f..b158346fd 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/mysql/transative/TransitiveTest.java @@ -20,7 +20,11 @@ package org.bridgedb.mysql.transative; +import static org.bridgedb.uri.UriListenerTest.SYMETRIC; +import static org.junit.jupiter.api.Assertions.assertEquals; + import java.util.Set; + import org.bridgedb.DataSource; import org.bridgedb.pairs.IdSysCodePair; import org.bridgedb.rdf.UriPattern; @@ -28,9 +32,6 @@ import org.bridgedb.sql.SQLUriMapper; import org.bridgedb.sql.TestSqlFactory; import org.bridgedb.sql.transative.DirectMapping; -import static org.bridgedb.uri.UriListenerTest.SYMETRIC; -import static org.junit.jupiter.api.Assertions.assertEquals; - import org.bridgedb.uri.api.Mapping; import org.bridgedb.uri.lens.Lens; import org.bridgedb.uri.lens.LensTools; @@ -38,11 +39,10 @@ import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.ConfigReader; import org.bridgedb.utils.Reporter; - +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Tag; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; /** * Tests the UriMapper interface (and by loading the UriListener interface) @@ -162,107 +162,107 @@ public static void setupIDMapper() throws BridgeDBException{ public static void loadData() throws BridgeDBException{ - URI source = new URIImpl("http://example.com/TransitiveTest/AtoB"); + IRI source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoB"); mappingSetAB = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternB, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoB2"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoB2"); mappingSetAB2 = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE2, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternB, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoC"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoC"); mappingSetAC = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoD"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoD"); mappingSetAD = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoE"); mappingSetAE = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoF"); mappingSetAF = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoC"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoC"); mappingSetBC = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoC2"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoC2"); mappingSetBC2 = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE2, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoC9"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoC9"); mappingSetBC9 = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, TEST_JUSTIFICATION9, TEST_JUSTIFICATION9, regexUriPatternC, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoD"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoD"); mappingSetBD = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoE"); mappingSetBE = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/BtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/BtoF"); mappingSetBF = sqlUriMapper.registerMappingSet(regexUriPatternB, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoD"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoD"); mappingSetCD = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoD2"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoD2"); mappingSetCD2 = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE2, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoD9"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoD9"); mappingSetCD9 = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, TEST_JUSTIFICATION9, TEST_JUSTIFICATION9, regexUriPatternD, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoE"); mappingSetCE = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoF"); mappingSetCF = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/DtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/DtoE"); mappingSetDE = sqlUriMapper.registerMappingSet(regexUriPatternD, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/DtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/DtoF"); mappingSetDF = sqlUriMapper.registerMappingSet(regexUriPatternD, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/EtoE"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/EtoE"); mappingSetEE = sqlUriMapper.registerMappingSet(regexUriPatternE, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternE, source); - source = new URIImpl("http://example.com/TransitiveTest/EtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/EtoF"); mappingSetEF = sqlUriMapper.registerMappingSet(regexUriPatternE, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/FtoF"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/FtoF"); mappingSetFF = sqlUriMapper.registerMappingSet(regexUriPatternF, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternF, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoX"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoX"); mappingSetAX = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternX, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoX"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoX"); mappingSetCX = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternX, source); - source = new URIImpl("http://example.com/TransitiveTest/AtoY"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/AtoY"); mappingSetAY = sqlUriMapper.registerMappingSet(regexUriPatternA, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternY, source); - source = new URIImpl("http://example.com/TransitiveTest/CtoY"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/TransitiveTest/CtoY"); mappingSetCY = sqlUriMapper.registerMappingSet(regexUriPatternC, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPatternY, source); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java index 441cc3c36..38040182b 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriListenerTest.java @@ -21,8 +21,11 @@ package org.bridgedb.uri; +import static org.junit.jupiter.api.Assertions.assertFalse; + import java.util.Set; import java.util.regex.Pattern; + import org.bridgedb.DataSourcePatterns; import org.bridgedb.Xref; import org.bridgedb.rdf.UriPattern; @@ -33,13 +36,10 @@ import org.bridgedb.uri.tools.UriListener; import org.bridgedb.utils.BridgeDBException; import org.bridgedb.utils.IDMapperTestBase; - +import org.eclipse.rdf4j.model.IRI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Tag; -import org.eclipse.rdf4j.model.URI; -import org.eclipse.rdf4j.model.impl.URIImpl; - -import static org.junit.jupiter.api.Assertions.assertFalse; /** * Base class of all Test using Uris @@ -192,7 +192,7 @@ public static void setupUriPatterns() throws BridgeDBException{ DataSourcePatterns.registerPattern(DataSource2, Pattern.compile("^\\d+$")); uriPattern1 = UriPattern.register(uriSpace1, dataSource1Code, UriPatternType.dataSourceUriPattern); uriPattern2 = UriPattern.register(uriSpace2, dataSource2Code, UriPatternType.dataSourceUriPattern); - uriPattern2 = UriPattern.register("http://www.chemspider.com/Chemical-Structure.$id.html", dataSource2Code, UriPatternType.dataSourceUriPattern); + uriPattern2 = UriPattern.register("https://www.chemspider.com/Chemical-Structure.$id.html", dataSource2Code, UriPatternType.dataSourceUriPattern); UriPattern.register(uriSpace2a + "$id", dataSource2Code, UriPatternType.dataSourceUriPattern); uriPattern3 = UriPattern.register(uriSpace3, dataSource3Code, UriPatternType.dataSourceUriPattern); UriPattern.register(uriSpace3a + "$id", dataSource3Code, UriPatternType.dataSourceUriPattern); @@ -215,14 +215,14 @@ public static void setupUriPatterns() throws BridgeDBException{ */ public static void loadDataPart1() throws BridgeDBException{ - URI source = new URIImpl("http://example.com/1to2"); + IRI source = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2"); mappingSet1to2 = listener.registerMappingSet(regexUriPattern1, TEST_PREDICATE, Lens.getDefaultJustifictaionString(), Lens.getDefaultJustifictaionString(), regexUriPattern2, source); listener.insertUriMapping(map1Uri1, map1Uri2, mappingSet1to2, SYMETRIC); listener.insertUriMapping(map2Uri1, map2Uri2, mappingSet1to2, SYMETRIC); listener.insertUriMapping(map3Uri1, map3Uri2, mappingSet1to2, SYMETRIC); - source = new URIImpl("http://example.com/2to3"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3"); mappingSet2to3 = listener.registerMappingSet(regexUriPattern2, TEST_PREDICATE, Lens.getDefaultJustifictaionString(), Lens.getDefaultJustifictaionString(), regexUriPattern3, source); listener.insertUriMapping(map1Uri2, map1Uri3, mappingSet2to3, SYMETRIC); @@ -232,21 +232,21 @@ public static void loadDataPart1() throws BridgeDBException{ //Close here to test recover listener.closeInput(); - source = new URIImpl("http://example.com/3to3Lensed"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/3to3Lensed"); mappingSet3to3Lensed = listener.registerMappingSet(regexUriPattern3, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern3, source); listener.insertUriMapping(map1Uri3, map1AUri3, mappingSet3to3Lensed, SYMETRIC); listener.insertUriMapping(map2Uri3, map2AUri3, mappingSet3to3Lensed, SYMETRIC); listener.insertUriMapping(map3Uri3, map3AUri3, mappingSet3to3Lensed, SYMETRIC); - source = new URIImpl("http://example.com/1to2lensed"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2lensed"); mappingSet1to2Lensed = listener.registerMappingSet(regexUriPattern1, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern2, source); listener.insertUriMapping(map1AUri1, map1AUri2, mappingSet1to2Lensed, SYMETRIC); listener.insertUriMapping(map2AUri1, map2AUri2, mappingSet1to2Lensed, SYMETRIC); listener.insertUriMapping(map3AUri1, map3AUri2, mappingSet1to2Lensed, SYMETRIC); - source = new URIImpl("http://example.com/2to3"); + source = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3"); mappingSet2to3Lensed = listener.registerMappingSet(regexUriPattern2, TEST_PREDICATE, Lens.getTestJustifictaion(), Lens.getTestJustifictaion(), regexUriPattern3, source); listener.insertUriMapping(map1AUri2, map1AUri3, mappingSet2to3Lensed, SYMETRIC); @@ -267,7 +267,7 @@ public static void loadData() throws BridgeDBException{ * @throws BridgeDBException */ public static void loadData2Way() throws BridgeDBException{ - URI source = new URIImpl("http://example.com/2to3Lensed"); + IRI source = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3Lensed"); int mappingSet = listener.registerMappingSet(regexUriPattern2, TEST_PREDICATE, Lens.getTestJustifictaion() +"Forward", Lens.getTestJustifictaion() +"BackWard", regexUriPattern3, source); listener.insertUriMapping(map1Uri2, map1AUri3, mappingSet, SYMETRIC); diff --git a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java index fd7540036..e1cca43a5 100644 --- a/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java +++ b/org.bridgedb.uri.sql/test/org/bridgedb/uri/UriMapperRdfTest.java @@ -19,6 +19,9 @@ */ package org.bridgedb.uri; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; + import java.util.Set; import org.bridgedb.DataSource; @@ -26,18 +29,16 @@ import org.bridgedb.statistics.MappingSetInfo; import org.bridgedb.uri.api.Mapping; import org.bridgedb.uri.tools.StatementMaker; -import org.junit.jupiter.api.*; +import org.eclipse.rdf4j.model.IRI; import org.eclipse.rdf4j.model.Model; import org.eclipse.rdf4j.model.Statement; -import org.eclipse.rdf4j.model.URI; +import org.eclipse.rdf4j.model.impl.SimpleValueFactory; import org.eclipse.rdf4j.model.impl.TreeModel; -import org.eclipse.rdf4j.model.impl.URIImpl; import org.eclipse.rdf4j.rio.RDFFormat; import org.eclipse.rdf4j.rio.RDFHandlerException; import org.eclipse.rdf4j.rio.Rio; - -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertTrue; +import org.junit.jupiter.api.Tag; +import org.junit.jupiter.api.Test; /** * Tests the UriMapper interface (and by loading the UriListener interface) @@ -57,20 +58,20 @@ public abstract class UriMapperRdfTest extends UriListenerTest{ public static StatementMaker statementMaker; - URI mappingSet1 = new URIImpl("http://example.com/testBasemappingSetRDF/1"); - URI linksetJustification = new URIImpl("http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl#linksetJustification"); - URI inChlKey = new URIImpl("http://semanticscience.org/resource/CHEMINF_000059"); + IRI mappingSet1 = SimpleValueFactory.getInstance().createIRI("http://example.com/testBasemappingSetRDF/1"); + IRI linksetJustification = SimpleValueFactory.getInstance().createIRI("http://openphacts.cs.man.ac.uk:9090/ontology/DataSource.owl#linksetJustification"); + IRI inChlKey = SimpleValueFactory.getInstance().createIRI("http://semanticscience.org/resource/CHEMINF_000059"); - URI importedFrom = new URIImpl("http://purl.org/pav/importedFrom"); - URI derivedFrom = new URIImpl("http://purl.org/pav/derivedFrom"); - URI example1to2 = new URIImpl("http://example.com/1to2"); - URI linkPredicate = new URIImpl("http://rdfs.org/ns/void#linkPredicate"); - URI exactMatch = new URIImpl("http://www.w3.org/2004/02/skos/core#exactMatch"); + IRI importedFrom = SimpleValueFactory.getInstance().createIRI("http://purl.org/pav/importedFrom"); + IRI derivedFrom = SimpleValueFactory.getInstance().createIRI("http://purl.org/pav/derivedFrom"); + IRI example1to2 = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2"); + IRI linkPredicate = SimpleValueFactory.getInstance().createIRI("http://rdfs.org/ns/void#linkPredicate"); + IRI exactMatch = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2004/02/skos/core#exactMatch"); - URI sameAs = new URIImpl("http://www.w3.org/2002/07/owl#sameAs"); - URI concept = new URIImpl("http://www.conceptwiki.org/concept/f25a234e-df03-419f-8504-cde8689a4d1f"); + IRI sameAs = SimpleValueFactory.getInstance().createIRI("http://www.w3.org/2002/07/owl#sameAs"); + IRI concept = SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/f25a234e-df03-419f-8504-cde8689a4d1f"); - URI override = new URIImpl("http://example.com/override"); + IRI override = SimpleValueFactory.getInstance().createIRI("http://example.com/override"); public void checkMapping(Mapping mapping){ if (!mapping.isMappingToSelf()){ @@ -116,22 +117,22 @@ public void testMappingNoLink() throws Exception { Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", false, null); Model m = asModel(rdf); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @@ -143,34 +144,34 @@ public void testMappingNoLinkFixedPredicate() throws Exception { Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", true, "http://example.com/override"); Model m = asModel(rdf); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, override, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); - assertTrue(m.contains(concept, override, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); - URI mapSet1Override = new URIImpl("http://example.com/testContextmappingSetRDF/1?predicate=http%3A%2F%2Fexample.com%2Foverride"); - URI mapSet1_3Override = new URIImpl("http://example.com/testContextmappingSetRDF/1_3?predicate=http%3A%2F%2Fexample.com%2Foverride"); - URI example1to2 = new URIImpl("http://example.com/1to2"); - URI example2to3 = new URIImpl("http://example.com/2to3"); + IRI mapSet1Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1?predicate=http%3A%2F%2Fexample.com%2Foverride"); + IRI mapSet1_3Override = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1_3?predicate=http%3A%2F%2Fexample.com%2Foverride"); + IRI example1to2 = SimpleValueFactory.getInstance().createIRI("http://example.com/1to2"); + IRI example2to3 = SimpleValueFactory.getInstance().createIRI("http://example.com/2to3"); // FIXME: Exactly how should the provenance chains go here? -// URIImpl mapset1 = new URIImpl("http://example.com/testContextmappingSetRDF/1"); +// URIImpl mapset1 = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1"); // assertTrue(m.contains(mapSet1Override, derivedFrom, mapset1)); // assertTrue(m.contains(mapset1, derivedFrom, example1to2)); // -// URIImpl mapset1_3 = new URIImpl("http://example.com/testContextmappingSetRDF/1_3"); +// URIImpl mapset1_3 = SimpleValueFactory.getInstance().createIRI("http://example.com/testContextmappingSetRDF/1_3"); // assertTrue(m.contains(mapSet1_3Override, derivedFrom, mapset1_3)); // assertTrue(m.contains(mapset1_3, derivedFrom, example1to2)); // assertTrue(m.contains(mapset1_3, derivedFrom, example2to3)); @@ -183,22 +184,22 @@ public void testMappingWithLink() throws Exception { Set mappings = uriMapper.mapFull(map1Uri1, null, true, null, null); Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", false, "http://example.com/override"); Model m = asModel(rdf); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - - assertTrue(m.contains(concept, override, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); - - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, override, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); - - assertTrue(m.contains(concept, override, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, override, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); + + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); + + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, override, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } @Test @@ -207,22 +208,22 @@ public void testMappingWithLinkOverride() throws Exception { Set mappings = uriMapper.mapFull(map1Uri1, null, true, null, null); Set rdf = statementMaker.asRDF(mappings, "http://example.com/testContext", false, null); Model m = asModel(rdf); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); - assertTrue(m.contains(concept, sameAs, new URIImpl("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); - - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://identifiers.org/chemspider/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://info.identifiers.org/chemspider/28509384"))); - - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/Compounds/Get/8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc-us.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://ops.rsc.org/OPS8/rdf"))); - - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://rdf.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.html"))); - assertTrue(m.contains(concept, exactMatch, new URIImpl("http://www.chemspider.com/Chemical-Structure.28509384.rdf"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/concept/index/f25a234e-df03-419f-8504-cde8689a4d1f"))); + assertTrue(m.contains(concept, sameAs, SimpleValueFactory.getInstance().createIRI("http://www.conceptwiki.org/web-ws/concept/get?uuid=f25a234e-df03-419f-8504-cde8689a4d1f"))); + + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://identifiers.org/chemspider/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://info.identifiers.org/chemspider/28509384"))); + + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/Compounds/Get/8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc-us.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://ops.rsc.org/OPS8/rdf"))); + + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("http://rdf.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.html"))); + assertTrue(m.contains(concept, exactMatch, SimpleValueFactory.getInstance().createIRI("https://www.chemspider.com/Chemical-Structure.28509384.rdf"))); } } diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 50abcd29a..fcaa82428 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index fc54d5fd5..b39522c77 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index e5ab5c25f..f20a40911 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -21,7 +21,7 @@ org.apache.maven.plugins maven-war-plugin - 2.4 + 3.4.0 BridgeDb diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 910e813f4..2d4066439 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java b/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java index 45d680a78..9646affe0 100644 --- a/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java +++ b/org.bridgedb.utils/src/org/bridgedb/pairs/IdSysCodePair.java @@ -28,7 +28,7 @@ * This is required for xrefs like "ChEBI" * These refs contain "CHEBI:" as part of the id. Such as CHEBI:36927 * Which is fine for URIs like: - * http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36927 or + * https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:36927 or * http://identifiers.org/obo.chebi/CHEBI:36927 * but does not work for others like: * http://purl.org/obo/owl/CHEBI#CHEBI_36927 or diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index 60376e71d..d6b1d7ca5 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 4ddcc92e8..d00d424d7 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -16,24 +16,24 @@ target/classes ${project.artifactId}-${project.version} target/test-classes - src + src/main/java scripts - test + src/test/java - resources + src/main/resources - test-resources + src/test/resources org.apache.felix maven-bundle-plugin - 5.1.1 + ${felix.version} true @@ -57,7 +57,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF @@ -80,5 +80,35 @@ ${project.parent.version} compile + + org.bridgedb + org.bridgedb.bio + ${project.parent.version} + test + + + org.junit.platform + junit-platform-surefire-provider + 1.3.2 + test + + + org.junit.jupiter + junit-jupiter-engine + ${junit5.jupiter.version} + test + + + org.junit.vintage + junit-vintage-engine + ${junit5.jupiter.version} + test + + + org.junit.jupiter + junit-jupiter-api + ${junit5.jupiter.version} + test + diff --git a/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java b/org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java similarity index 99% rename from org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java rename to org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java index 6062dcdc0..8adf39eae 100644 --- a/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java +++ b/org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java @@ -276,7 +276,7 @@ private BufferedReader openReader() throws IOException } /** - * @param baseUrl base Url, e.g. http://webservice.bridgedb.org/Human or + * @param baseUrl base Url, e.g. https://webservice.bridgedb.org/Human or * http://localhost:8182 * @throws IDMapperException when service is unavailable */ diff --git a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java new file mode 100644 index 000000000..645f2e75d --- /dev/null +++ b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java @@ -0,0 +1,49 @@ +// Copyright 2024 Egon Willighagen +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. +// +package org.bridgedb.webservice.bridgerest; + +import static org.junit.Assert.assertNotSame; +import static org.junit.Assert.assertTrue; +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import java.util.Set; + +import org.bridgedb.DataSource; +import org.bridgedb.IDMapperException; +import org.bridgedb.Xref; +import org.bridgedb.bio.DataSourceTxt; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +public class BridgeRestTest { + + private static BridgeRest service; + + @BeforeAll + public static void init() throws IDMapperException { + if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + BridgeRestTest.service = new BridgeRest("https://webservice.bridgedb.org/Human"); + assertNotNull(service); + assertTrue(service.isConnected()); + } + + @Test + public void testMap() throws IDMapperException { + assertNotNull(service); + assertTrue(service.isConnected()); + Set mappings = service.mapID(new Xref("CHEBI:123", DataSource.getExistingBySystemCode("Ce"))); + assertNotSame(0, mappings.size()); + } +} diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index fd1978afb..e98637f25 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 3dde85a80..a4f29eb99 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -80,7 +80,7 @@ org.junit.platform junit-platform-surefire-provider - 1.2.0 + ${junit-platform-surefire-provider} test diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index a7558a2d8..bda968c58 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index abba6a136..15c9a5641 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.0.23 + 3.1.4 @@ -57,7 +57,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -81,7 +81,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java index 355c6cc06..1487399ae 100644 --- a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java +++ b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java @@ -807,6 +807,10 @@ public static DataSource getExistingByFullName(String fullName) { if (byFullName.containsKey(fullName)){ return byFullName.get(fullName); + // the following lines are added on 2023-10 for backwards compatibility + } else if ("Uniprot-TrEMBL".equals(fullName) || + "Uniprot-SwissProt".equals(fullName)) { + return byFullName.get("UniProtKB"); } throw new IllegalArgumentException ("No DataSource known for " + fullName); } @@ -969,10 +973,10 @@ public static DataSource getByMiriamBase(String base) * @return the DataSource for a given base, or null if the base is invalid or unknown. */ public static DataSource getByIdentiferOrgBase(String base) { - if (base == null || !base.startsWith (IDENTIFIERS_ORG_PREFIX)) - { - return null; - } + if (base == null) return null; + // support the HTTPS variant too + base = base.replace("https://identifiers.org", "http://identifiers.org"); + if (!base.startsWith (IDENTIFIERS_ORG_PREFIX)) return null; String key = base.substring(IDENTIFIERS_ORG_PREFIX.length()); if (key.endsWith("/")){ diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 645ae3a65..0da9c3ac6 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.0.23 +bridgedb.version=3.1.3 diff --git a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java index 4eab3aa5c..c782b6a30 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java +++ b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java @@ -375,7 +375,9 @@ public void testBuilders() { .alternative("MetaboLoci Alternative") .asDataSource(); assertEquals("Ecogene",DataSource.getByMiriamBase("urn:miriam:ecogene").toString()); - assertEquals("urn:miriam:ecogene:urn%3Amiriam%3Aecogene",source3.getMiriamURN("urn:miriam:ecogene").toString()); + assertEquals("Ecogene",DataSource.getByIdentiferOrgBase("http://identifiers.org/ecogene/").toString()); + assertEquals("Ecogene",DataSource.getByIdentiferOrgBase("https://identifiers.org/ecogene/").toString()); + assertEquals("urn:miriam:ecogene:EG10173",source3.getMiriamURN("EG10173").toString()); DataSource source4 = DataSource.register("Ect", "EPA CompTox") .urnBase("urn:miriam:Ect") diff --git a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java index 7b1c83849..2d5a4d312 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java +++ b/org.bridgedb/src/test/java/org/bridgedb/IDMapperTestBase.java @@ -71,7 +71,7 @@ public abstract class IDMapperTestBase { protected static String badKey; protected static final String uriSpace1 = "http://www.conceptwiki.org/concept/$id"; - protected static final String uriSpace2 = "http://www.chemspider.com/Chemical-Structure.$id.html"; + protected static final String uriSpace2 = "https://www.chemspider.com/Chemical-Structure.$id.html"; protected static final String uriSpace3 = "http://chemistry.openphacts.org/OPS$id"; @BeforeAll @@ -87,16 +87,16 @@ public abstract class IDMapperTestBase { public static void setupXref() throws IDMapperException{ //If the actual source to be tested does not contain these please overwrite with ones that do exist. dataSource1Code = "ConceptWiki"; - DataSource1 = DataSource.register(dataSource1Code, "ConceptWiki"). urlPattern(uriSpace1) + DataSource1 = DataSource.mock(dataSource1Code, "ConceptWiki"). urlPattern(uriSpace1) .idExample("33a28bb2-35ed-4d94-adfd-3c96053cbaaf").asDataSource(); dataSource2Code = "Cs"; - DataSource2 = DataSource.register(dataSource2Code, "Chemspider").urlPattern(uriSpace2) + DataSource2 = DataSource.mock(dataSource2Code, "Chemspider").urlPattern(uriSpace2) .idExample("56586").asDataSource(); dataSource3Code = "OPS-CRS"; - DataSource3 = DataSource.register(dataSource3Code, "OPS Chemical Registry Service").urlPattern(uriSpace3) + DataSource3 = DataSource.mock(dataSource3Code, "OPS Chemical Registry Service").urlPattern(uriSpace3) .idExample("8").asDataSource(); //This DataSource MUST not be supported - DataSourceBad = DataSource.register("TestDSBad", "TestDSBad") + DataSourceBad = DataSource.mock("TestDSBad", "TestDSBad") .urlPattern("http://www.NotInTheURlMapper.com#$id").asDataSource(); //Set of Xrefs that are expected to map together. diff --git a/pom-java8.xml b/pom-java8.xml index 107aa4116..f0bd47b1a 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.0.22 + 3.1.4 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database @@ -26,19 +26,20 @@ UTF-8 UTF-8 1.2 - 3.2.14 - 2.2 + 3.6.4 + 3.0 1.10 - 2.20.0 - 8.0.33 + 2.22.0 + 9.0.0 Tomcat 3.4 - 3.7.7 + 4.3.8 2.5 - 1.6.4 - 10.15.2.0 + 2.0.9 + 10.4.2.0 1.3.2 - 5.10.0 + 1.11.0 + 5.11.0 mysql @@ -110,4 +111,12 @@ + + + mvnrepository + MVN Repository + https://mvnrepository.com/artifact/ + + + diff --git a/pom.xml b/pom.xml index 8f7867726..d7ab84f33 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.0.23 + 3.1.4 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database @@ -45,19 +45,21 @@ UTF-8 UTF-8 1.2 - 3.2.14 - 2.2 + 3.6.4 + 5.1.9 + 3.0 1.10 - 2.20.0 - 8.0.33 + 2.22.0 + 9.0.0 Tomcat 3.4 - 3.7.7 + 4.3.8 2.5 - 1.6.4 + 2.0.9 10.15.2.0 1.3.2 - 5.10.0 + 1.11.0 + 5.11.0 mysql @@ -150,7 +152,7 @@ 1.6.8 true - ossrh + sso https://oss.sonatype.org/ true @@ -192,11 +194,11 @@ - ossrh + sso https://oss.sonatype.org/service/local/staging/deploy/maven2/ - ossrh + sso https://oss.sonatype.org/content/repositories/snapshots @@ -317,4 +319,11 @@ https://github.com/bridgedb/BridgeDb/issues + + + mvnrepository + https://mvnrepository.com/artifact/ + + +