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2.0 10.0 8.0 3.26 MB

A library of code for parsing (mostly biomedical) data source files and converting their contents to RDF

License: BSD 3-Clause "New" or "Revised" License

Java 99.72% Shell 0.28%

datasource's Issues

datasource-identifiers fails to build, missing src/main/resources

--- maven-resources-plugin:2.6:resources (default-resources) @ datasource-identifiers ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/croeder/git-test/datasource.git/datasource-identifiers/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ datasource-identifiers ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 299 source files to /Users/croeder/git-test/datasource.git/datasource-identifiers/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] datasource ........................................ SUCCESS [0.294s]
[INFO] datasource-identifiers ............................ FAILURE [1.754s]
[INFO] datasource-fileparsers ............................ SKIPPED
[INFO] datasource-rdfizer ................................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------

Unhandled synonym Type exception

Hi, I'm using the edu.ucdenver.ccp.datasource.fileparsers.obo.OntologyUtil to build a conceptmapper dictionary for the NcbiTaxonomy. This raises the following exception

ERROR (OntologyUtil:193) Unhandled synonym type: http://www.geneontology.org/formats/oboInOWL#hasRelatedSynonym

The property value obtained from the OWLAnnotation is
http://www.geneontology.org/formats/**oboInOWL**#hasRelatedSynonym>

while in line 59 of OntologyUtil.java you set it to "http://www.geneontology.org/formats/**oboInOwl**#hasRelatedSynonym"

that fails the matching since the property.equals(RELATED_SYN_PROP) is not case sensitive

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