From 3b58720828c12e1f90ecaf045abbdba412835bd0 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 23 Sep 2024 21:26:19 +0200 Subject: [PATCH 1/6] Open for development --- bacting-core/pom.xml | 2 +- bundle/pom.xml | 32 +++++++++---------- .../net.bioclipse.managers.biojava/pom.xml | 4 +-- .../net.bioclipse.managers.bridgedb/pom.xml | 6 ++-- .../net.bioclipse.managers.libgpml/pom.xml | 6 ++-- managers-bioinfo/pom.xml | 2 +- .../net.bioclipse.managers.cdk/pom.xml | 6 ++-- .../net.bioclipse.managers.cdkdebug/pom.xml | 4 +-- .../net.bioclipse.managers.chemspider/pom.xml | 6 ++-- .../net.bioclipse.managers.inchi/pom.xml | 6 ++-- .../net.bioclipse.managers.nm/pom.xml | 6 ++-- .../net.bioclipse.managers.opsin/pom.xml | 6 ++-- .../net.bioclipse.managers.oscar/pom.xml | 6 ++-- .../net.bioclipse.managers.pubchem/pom.xml | 10 +++--- managers-cheminfo/pom.xml | 2 +- managers-core/managers-jsoup/pom.xml | 6 ++-- managers-core/managers-ui/pom.xml | 4 +-- managers-core/pom.xml | 2 +- managers-excel/pom.xml | 6 ++-- managers-search/managers-doi/pom.xml | 4 +-- managers-search/managers-find/pom.xml | 6 ++-- managers-search/managers-pubmed/pom.xml | 4 +-- managers-search/managers-zenodo/pom.xml | 4 +-- .../net.bioclipse.managers.duckduckgo/pom.xml | 8 ++--- .../net.bioclipse.managers.mwmbl/pom.xml | 6 ++-- managers-search/pom.xml | 2 +- managers-semweb/managers-rdf/pom.xml | 4 +-- managers-semweb/managers-xml/pom.xml | 6 ++-- .../net.bioclipse.managers.wikidata/pom.xml | 10 +++--- managers-semweb/pom.xml | 2 +- pom.xml | 2 +- 31 files changed, 90 insertions(+), 90 deletions(-) diff --git a/bacting-core/pom.xml b/bacting-core/pom.xml index c19425f1..fbb6d37f 100644 --- a/bacting-core/pom.xml +++ b/bacting-core/pom.xml @@ -4,7 +4,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT bacting-core diff --git a/bundle/pom.xml b/bundle/pom.xml index 4c1f2dc1..deb604f0 100644 --- a/bundle/pom.xml +++ b/bundle/pom.xml @@ -5,7 +5,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT bacting-bundle @@ -15,77 +15,77 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-rdf - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-xml - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting net.bioclipse.managers.wikidata - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-bridgedb - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-biojava - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-cdkdebug - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-chemspider - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-inchi - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-opsin - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-oscar - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-pubchem - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-excel - 1.0.2 + 1.0.3-SNAPSHOT diff --git a/managers-bioinfo/net.bioclipse.managers.biojava/pom.xml b/managers-bioinfo/net.bioclipse.managers.biojava/pom.xml index 74a021f6..ec42e26f 100644 --- a/managers-bioinfo/net.bioclipse.managers.biojava/pom.xml +++ b/managers-bioinfo/net.bioclipse.managers.biojava/pom.xml @@ -4,7 +4,7 @@ managers-bioinfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-biojava @@ -34,7 +34,7 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT org.junit.jupiter diff --git a/managers-bioinfo/net.bioclipse.managers.bridgedb/pom.xml b/managers-bioinfo/net.bioclipse.managers.bridgedb/pom.xml index faace422..cc50fb18 100644 --- a/managers-bioinfo/net.bioclipse.managers.bridgedb/pom.xml +++ b/managers-bioinfo/net.bioclipse.managers.bridgedb/pom.xml @@ -4,7 +4,7 @@ managers-bioinfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-bridgedb @@ -39,7 +39,7 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT org.bridgedb @@ -97,7 +97,7 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT test diff --git a/managers-bioinfo/net.bioclipse.managers.libgpml/pom.xml b/managers-bioinfo/net.bioclipse.managers.libgpml/pom.xml index de85d5d0..495a83ea 100644 --- a/managers-bioinfo/net.bioclipse.managers.libgpml/pom.xml +++ b/managers-bioinfo/net.bioclipse.managers.libgpml/pom.xml @@ -4,7 +4,7 @@ managers-bioinfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-libgpml @@ -34,13 +34,13 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-ui test - 1.0.2 + 1.0.3-SNAPSHOT org.junit.jupiter diff --git a/managers-bioinfo/pom.xml b/managers-bioinfo/pom.xml index 850026ae..3f660260 100644 --- a/managers-bioinfo/pom.xml +++ b/managers-bioinfo/pom.xml @@ -5,7 +5,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-bioinfo diff --git a/managers-cheminfo/net.bioclipse.managers.cdk/pom.xml b/managers-cheminfo/net.bioclipse.managers.cdk/pom.xml index 2c033c38..f8252559 100644 --- a/managers-cheminfo/net.bioclipse.managers.cdk/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.cdk/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-cdk @@ -34,13 +34,13 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-ui test - 1.0.2 + 1.0.3-SNAPSHOT xom diff --git a/managers-cheminfo/net.bioclipse.managers.cdkdebug/pom.xml b/managers-cheminfo/net.bioclipse.managers.cdkdebug/pom.xml index 3ea1964b..0a357707 100644 --- a/managers-cheminfo/net.bioclipse.managers.cdkdebug/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.cdkdebug/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-cdkdebug @@ -34,7 +34,7 @@ io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT org.openscience.cdk diff --git a/managers-cheminfo/net.bioclipse.managers.chemspider/pom.xml b/managers-cheminfo/net.bioclipse.managers.chemspider/pom.xml index 350f2944..eb6d9ac1 100644 --- a/managers-cheminfo/net.bioclipse.managers.chemspider/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.chemspider/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-chemspider @@ -34,12 +34,12 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT org.junit.jupiter diff --git a/managers-cheminfo/net.bioclipse.managers.inchi/pom.xml b/managers-cheminfo/net.bioclipse.managers.inchi/pom.xml index 674c94f6..9d4d4aac 100644 --- a/managers-cheminfo/net.bioclipse.managers.inchi/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.inchi/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-inchi @@ -49,7 +49,7 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting @@ -81,7 +81,7 @@ io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT test diff --git a/managers-cheminfo/net.bioclipse.managers.nm/pom.xml b/managers-cheminfo/net.bioclipse.managers.nm/pom.xml index 638c4bc2..33c0c302 100644 --- a/managers-cheminfo/net.bioclipse.managers.nm/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.nm/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-nm @@ -34,12 +34,12 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw diff --git a/managers-cheminfo/net.bioclipse.managers.opsin/pom.xml b/managers-cheminfo/net.bioclipse.managers.opsin/pom.xml index 7d884405..39cf0732 100644 --- a/managers-cheminfo/net.bioclipse.managers.opsin/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.opsin/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-opsin @@ -34,12 +34,12 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT uk.ac.cam.ch.opsin diff --git a/managers-cheminfo/net.bioclipse.managers.oscar/pom.xml b/managers-cheminfo/net.bioclipse.managers.oscar/pom.xml index 88f2cf62..b5d85145 100644 --- a/managers-cheminfo/net.bioclipse.managers.oscar/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.oscar/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-oscar @@ -34,7 +34,7 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT uk.ac.cam.ch.wwmm.oscar @@ -70,7 +70,7 @@ io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT net.htmlparser.jericho diff --git a/managers-cheminfo/net.bioclipse.managers.pubchem/pom.xml b/managers-cheminfo/net.bioclipse.managers.pubchem/pom.xml index b4db3c3b..50882e5d 100644 --- a/managers-cheminfo/net.bioclipse.managers.pubchem/pom.xml +++ b/managers-cheminfo/net.bioclipse.managers.pubchem/pom.xml @@ -4,7 +4,7 @@ managers-cheminfo io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-pubchem @@ -49,7 +49,7 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting @@ -64,17 +64,17 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-rdf - 1.0.2 + 1.0.3-SNAPSHOT org.openscience.cdk diff --git a/managers-cheminfo/pom.xml b/managers-cheminfo/pom.xml index e946bbd7..61e2891d 100644 --- a/managers-cheminfo/pom.xml +++ b/managers-cheminfo/pom.xml @@ -5,7 +5,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-cheminfo diff --git a/managers-core/managers-jsoup/pom.xml b/managers-core/managers-jsoup/pom.xml index 2f9a4639..dc2e0a63 100644 --- a/managers-core/managers-jsoup/pom.xml +++ b/managers-core/managers-jsoup/pom.xml @@ -4,7 +4,7 @@ managers-core io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT net.bioclipse.managers.jsoup @@ -35,12 +35,12 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT org.jsoup diff --git a/managers-core/managers-ui/pom.xml b/managers-core/managers-ui/pom.xml index 53a8304b..dfc1161b 100644 --- a/managers-core/managers-ui/pom.xml +++ b/managers-core/managers-ui/pom.xml @@ -4,7 +4,7 @@ managers-core io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-ui @@ -35,7 +35,7 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting diff --git a/managers-core/pom.xml b/managers-core/pom.xml index 23effb2e..8e5b9b23 100644 --- a/managers-core/pom.xml +++ b/managers-core/pom.xml @@ -5,7 +5,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-core diff --git a/managers-excel/pom.xml b/managers-excel/pom.xml index 181d5925..85579009 100644 --- a/managers-excel/pom.xml +++ b/managers-excel/pom.xml @@ -4,7 +4,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-excel @@ -35,12 +35,12 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT test diff --git a/managers-search/managers-doi/pom.xml b/managers-search/managers-doi/pom.xml index 4a23346a..257ae907 100644 --- a/managers-search/managers-doi/pom.xml +++ b/managers-search/managers-doi/pom.xml @@ -4,7 +4,7 @@ managers-search io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT net.bioclipse.managers.doi @@ -35,7 +35,7 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT org.json diff --git a/managers-search/managers-find/pom.xml b/managers-search/managers-find/pom.xml index ed4dd7a5..a6bdbfcc 100644 --- a/managers-search/managers-find/pom.xml +++ b/managers-search/managers-find/pom.xml @@ -4,7 +4,7 @@ managers-search io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT net.bioclipse.managers.find @@ -35,7 +35,7 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT org.junit.jupiter @@ -52,7 +52,7 @@ io.github.egonw.bacting managers-xml - 1.0.2 + 1.0.3-SNAPSHOT diff --git a/managers-search/managers-pubmed/pom.xml b/managers-search/managers-pubmed/pom.xml index 4f5fd63d..a0373c45 100644 --- a/managers-search/managers-pubmed/pom.xml +++ b/managers-search/managers-pubmed/pom.xml @@ -4,7 +4,7 @@ managers-search io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT net.bioclipse.managers.pubmed @@ -35,7 +35,7 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT org.json diff --git a/managers-search/managers-zenodo/pom.xml b/managers-search/managers-zenodo/pom.xml index b7fb4d63..c1695eaa 100644 --- a/managers-search/managers-zenodo/pom.xml +++ b/managers-search/managers-zenodo/pom.xml @@ -4,7 +4,7 @@ managers-search io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-zenodo @@ -35,7 +35,7 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT org.json diff --git a/managers-search/net.bioclipse.managers.duckduckgo/pom.xml b/managers-search/net.bioclipse.managers.duckduckgo/pom.xml index e7ecc6a5..0019765e 100644 --- a/managers-search/net.bioclipse.managers.duckduckgo/pom.xml +++ b/managers-search/net.bioclipse.managers.duckduckgo/pom.xml @@ -4,7 +4,7 @@ managers-search io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT net.bioclipse.managers.duckduckgo @@ -35,17 +35,17 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting net.bioclipse.managers.jsoup - 1.0.2 + 1.0.3-SNAPSHOT org.junit.jupiter diff --git a/managers-search/net.bioclipse.managers.mwmbl/pom.xml b/managers-search/net.bioclipse.managers.mwmbl/pom.xml index c9c5bdc4..458223ae 100644 --- a/managers-search/net.bioclipse.managers.mwmbl/pom.xml +++ b/managers-search/net.bioclipse.managers.mwmbl/pom.xml @@ -4,7 +4,7 @@ managers-search io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT net.bioclipse.managers.mwmbl @@ -35,12 +35,12 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT org.json diff --git a/managers-search/pom.xml b/managers-search/pom.xml index aa7f05e6..3840909b 100644 --- a/managers-search/pom.xml +++ b/managers-search/pom.xml @@ -5,7 +5,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-search diff --git a/managers-semweb/managers-rdf/pom.xml b/managers-semweb/managers-rdf/pom.xml index 69017369..eb49cbbc 100644 --- a/managers-semweb/managers-rdf/pom.xml +++ b/managers-semweb/managers-rdf/pom.xml @@ -4,7 +4,7 @@ managers-semweb io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-rdf @@ -99,7 +99,7 @@ io.github.egonw.bacting managers-ui test - 1.0.2 + 1.0.3-SNAPSHOT diff --git a/managers-semweb/managers-xml/pom.xml b/managers-semweb/managers-xml/pom.xml index 9525127e..37279d75 100644 --- a/managers-semweb/managers-xml/pom.xml +++ b/managers-semweb/managers-xml/pom.xml @@ -4,7 +4,7 @@ managers-semweb io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-xml @@ -35,7 +35,7 @@ io.github.egonw.bacting bacting-core - 1.0.2 + 1.0.3-SNAPSHOT xom @@ -73,7 +73,7 @@ io.github.egonw.bacting managers-ui test - 1.0.2 + 1.0.3-SNAPSHOT diff --git a/managers-semweb/net.bioclipse.managers.wikidata/pom.xml b/managers-semweb/net.bioclipse.managers.wikidata/pom.xml index 9b7fae82..9dd81f7e 100644 --- a/managers-semweb/net.bioclipse.managers.wikidata/pom.xml +++ b/managers-semweb/net.bioclipse.managers.wikidata/pom.xml @@ -4,7 +4,7 @@ managers-semweb io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT net.bioclipse.managers.wikidata @@ -40,22 +40,22 @@ io.github.egonw.bacting managers-ui - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-rdf - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-inchi - 1.0.2 + 1.0.3-SNAPSHOT io.github.egonw.bacting managers-cdk - 1.0.2 + 1.0.3-SNAPSHOT org.junit.jupiter diff --git a/managers-semweb/pom.xml b/managers-semweb/pom.xml index 83219918..f8613ace 100644 --- a/managers-semweb/pom.xml +++ b/managers-semweb/pom.xml @@ -5,7 +5,7 @@ bacting io.github.egonw.bacting - 1.0.2 + 1.0.3-SNAPSHOT managers-semweb diff --git a/pom.xml b/pom.xml index d420399c..b67802d5 100644 --- a/pom.xml +++ b/pom.xml @@ -8,7 +8,7 @@ Bacting := acting as the Bioclipse TNG. Bioclipse version that can be used from the command line, e.g. with Groovy. http://www.github.com/egonw/bacting - 1.0.2 + 1.0.3-SNAPSHOT pom From 6e9a4f1360a1fd7afcc361d3ac884342a23ba26b Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 23 Sep 2024 21:26:44 +0200 Subject: [PATCH 2/6] Handle the situation when the query returned no data --- .../src/main/java/net/bioclipse/managers/WikidataManager.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java b/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java index f0896b34..592ced41 100644 --- a/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java +++ b/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java @@ -286,12 +286,12 @@ public List getDOIsForWorksOfAuthor(String author) throws BioclipseExcep "https://query-scholarly.wikidata.org/sparql", query ); IStringMatrix results = rdf.processSPARQLXML(resultRaw, query); - dois = results.getColumn("doi"); + if (results.getRowCount() > 0) dois.addAll(results.getColumn("doi")); resultRaw = bioclipse.sparqlRemote( "https://query-main.wikidata.org/sparql", query ); results = rdf.processSPARQLXML(resultRaw, query); - dois.addAll(results.getColumn("doi")); + if (results.getRowCount() > 0) dois.addAll(results.getColumn("doi")); return dois; } From a49632dba0c0293125b4b7e59bf66c1b56c0467a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 23 Sep 2024 21:44:55 +0200 Subject: [PATCH 3/6] More empty results checking --- .../java/net/bioclipse/managers/WikidataManager.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java b/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java index 592ced41..69e544aa 100644 --- a/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java +++ b/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java @@ -256,12 +256,12 @@ public List getEntityIDsForWorksOfAuthor(String author) throws Bioclipse "https://query-scholarly.wikidata.org/sparql", query ); IStringMatrix results = rdf.processSPARQLXML(resultRaw, query); - entities = results.getColumn("entity"); + if (results.getRowCount() > 0) entities.addAll(results.getColumn("entity")); resultRaw = bioclipse.sparqlRemote( "https://query-main.wikidata.org/sparql", query ); results = rdf.processSPARQLXML(resultRaw, query); - entities.addAll(results.getColumn("entity")); + if (results.getRowCount() > 0) entities.addAll(results.getColumn("entity")); return entities; } @@ -315,12 +315,12 @@ public List getEntityIDsForWorksOfVenue(String venue) throws BioclipseEx "https://query-scholarly.wikidata.org/sparql", query ); IStringMatrix results = rdf.processSPARQLXML(resultRaw, query); - entities = results.getColumn("entity"); + if (results.getRowCount() > 0) entities.addAll(results.getColumn("entity")); resultRaw = bioclipse.sparqlRemote( "https://query-main.wikidata.org/sparql", query ); results = rdf.processSPARQLXML(resultRaw, query); - entities.addAll(results.getColumn("entity")); + if (results.getRowCount() > 0) entities.addAll(results.getColumn("entity")); return entities; } @@ -345,12 +345,12 @@ public List getDOIsForWorksOfVenue(String venue) throws BioclipseExcepti "https://query-scholarly.wikidata.org/sparql", query ); IStringMatrix results = rdf.processSPARQLXML(resultRaw, query); - dois = results.getColumn("doi"); + if (results.getRowCount() > 0) dois.addAll(results.getColumn("doi")); resultRaw = bioclipse.sparqlRemote( "https://query-main.wikidata.org/sparql", query ); results = rdf.processSPARQLXML(resultRaw, query); - dois.addAll(results.getColumn("doi")); + if (results.getRowCount() > 0) dois.addAll(results.getColumn("doi")); return dois; } From 93575b2b032e478a5d0c728fe19e050778b1f8ea Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 11:13:10 +0200 Subject: [PATCH 4/6] Added a method for DOIs/works for a main subject --- .../bioclipse/managers/WikidataManager.java | 59 +++++++++++++++++++ .../managers/WikidataManagerTest.java | 15 +++++ 2 files changed, 74 insertions(+) diff --git a/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java b/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java index 69e544aa..3ffec0a5 100644 --- a/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java +++ b/managers-semweb/net.bioclipse.managers.wikidata/src/main/java/net/bioclipse/managers/WikidataManager.java @@ -354,6 +354,65 @@ public List getDOIsForWorksOfVenue(String venue) throws BioclipseExcepti return dois; } + /** + * Returns the Wikidata entity IDs for works the given topic as main subject (P921). + * + * @param venue identifier of the Wikidata item for the topic + * @return the list of Wikidata identifiers for the works + */ + public List getEntityIDsForWorksForTopic(String venue) throws BioclipseException { + if (!isValidQIdentifier(venue)) throw new BioclipseException("You must give a valid Wikidata identifier, but got " + venue + "."); + String query = + "PREFIX wdt: " + + "SELECT DISTINCT ?entity WHERE {" + + " ?entity wdt:P921 wd:" + venue + " ." + + "}"; + // handle the split Wikidata SPARQL endpoints, as a DOI can be for a scholarly article (first call) + // and for other types, like datasets (second call) + List entities = new ArrayList<>(); + byte[] resultRaw = bioclipse.sparqlRemote( + "https://query-scholarly.wikidata.org/sparql", query + ); + IStringMatrix results = rdf.processSPARQLXML(resultRaw, query); + if (results.getRowCount() > 0) entities.addAll(results.getColumn("entity")); + resultRaw = bioclipse.sparqlRemote( + "https://query-main.wikidata.org/sparql", query + ); + results = rdf.processSPARQLXML(resultRaw, query); + if (results.getRowCount() > 0) entities.addAll(results.getColumn("entity")); + return entities; + } + + /** + * Returns the DOIs for works the given topic as main subject (P921). + * + * @param venue identifier of the Wikidata item for the topic + * @return the list of Wikidata identifiers for the works + */ + public List getDOIsForWorksForTopic(String venue) throws BioclipseException { + if (!isValidQIdentifier(venue)) throw new BioclipseException("You must give a valid Wikidata identifier, but got " + venue + "."); + String query = + "PREFIX wdt: " + + "SELECT DISTINCT ?doi WHERE {" + + " ?entity wdt:P921 wd:" + venue + " ;" + + " wdt:P356 ?doi ." + + "}"; + // handle the split Wikidata SPARQL endpoints, as a DOI can be for a scholarly article (first call) + // and for other types, like datasets (second call) + List dois = new ArrayList<>(); + byte[] resultRaw = bioclipse.sparqlRemote( + "https://query-scholarly.wikidata.org/sparql", query + ); + IStringMatrix results = rdf.processSPARQLXML(resultRaw, query); + if (results.getRowCount() > 0) dois.addAll(results.getColumn("doi")); + resultRaw = bioclipse.sparqlRemote( + "https://query-main.wikidata.org/sparql", query + ); + results = rdf.processSPARQLXML(resultRaw, query); + if (results.getRowCount() > 0) dois.addAll(results.getColumn("doi")); + return dois; + } + /** * Determines if an identifier is a valid Wikidata entity identifier, like Q5. * diff --git a/managers-semweb/net.bioclipse.managers.wikidata/src/test/java/net/bioclipse/managers/WikidataManagerTest.java b/managers-semweb/net.bioclipse.managers.wikidata/src/test/java/net/bioclipse/managers/WikidataManagerTest.java index 5ba5b380..427c2ffa 100644 --- a/managers-semweb/net.bioclipse.managers.wikidata/src/test/java/net/bioclipse/managers/WikidataManagerTest.java +++ b/managers-semweb/net.bioclipse.managers.wikidata/src/test/java/net/bioclipse/managers/WikidataManagerTest.java @@ -258,6 +258,21 @@ public void testGetDOIsForWorksOfVenue() throws Exception { assertTrue(entityIDs.get(0).startsWith("10.")); } + @Test + public void testGetEntityIDsForWorksForTopic() throws Exception { + List entityIDs = wikidata.getEntityIDsForWorksForTopic("Q2383032"); + assertNotNull(entityIDs); + assertTrue(entityIDs.size() > 10); + } + + @Test + public void testGetDOIsForWorksForTopic() throws Exception { + List entityIDs = wikidata.getDOIsForWorksForTopic("Q2383032"); + assertNotNull(entityIDs); + assertTrue(entityIDs.size() > 10); + assertTrue(entityIDs.get(0).startsWith("10.")); + } + @Test public void testGetEntityIDsForType_InvalidType() throws Exception { Exception exception = assertThrows( From c5d33136d9b7c829784748b178ed8075cbbfea2e Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 11:24:16 +0200 Subject: [PATCH 5/6] Release 1.0.3 --- CITATION.cff | 4 ++-- README.md | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index c1a34e7c..297d0abe 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -5,8 +5,8 @@ authors: given-names: Egon orcid: https://orcid.org/0000-0001-7542-0286 title: Bacting -version: 1.0.2 -date-released: 2024-09-23 +version: 1.0.3 +date-released: 2024-10-01 doi: 10.5281/zenodo.2638709 url: "https://github.com/egonw/bacting" preferred-citation: diff --git a/README.md b/README.md index cd6a4a93..ba80ea03 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ If these requirements are fulfilled then the following commands to the job: ```shell export MAVEN_OPTS="--add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.text=ALL-UNNAMED --add-opens=java.desktop/java.awt.font=ALL-UNNAMED" -mvn versions:set -DnewVersion=1.0.2 +mvn versions:set -DnewVersion=1.0.3 git commit -m "New release" -a mvn deploy -P release ``` @@ -55,7 +55,7 @@ mvn deploy -P release ### Making snapshots ```shell -mvn versions:set -DnewVersion=1.0.3-SNAPSHOT +mvn versions:set -DnewVersion=1.0.4-SNAPSHOT mvn deploy ``` @@ -83,7 +83,7 @@ itself), and then converts a [SMILES](https://en.wikipedia.org/wiki/Simplified_m string to a Bioclipse `IMolecule` data object: ```groovy -@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='1.0.2') +@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='1.0.3') workspaceRoot = "." def cdk = new net.bioclipse.managers.CDKManager(workspaceRoot); @@ -117,7 +117,7 @@ The code example looks like: ```python from scyjava import config, jimport -config.add_endpoints('io.github.egonw.bacting:managers-cdk:1.0.2') +config.add_endpoints('io.github.egonw.bacting:managers-cdk:1.0.3') workspaceRoot = "." cdkClass = jimport("net.bioclipse.managers.CDKManager") From 3e969f4e3b32cd2322f96ec4c2297d6087a90ddf Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 11:34:16 +0200 Subject: [PATCH 6/6] Latest BridgeDb --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index b67802d5..37fdf19b 100644 --- a/pom.xml +++ b/pom.xml @@ -49,7 +49,7 @@ 1.3.9 1.9.7 4.10.0 - 3.1.2 + 3.1.3 10.15.2.0 4.5.14 1.5.0