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Dictionary: Funders

VAISHALI ARORA edited this page Aug 6, 2020 · 24 revisions

Owner :

Vaishali Arora

Dictionary :

Funders

Find here :

https://github.com/petermr/openVirus/blob/master/dictionaries/funders/funders.xml

Source :

https://github.com/petermr/openVirus/blob/master/dictionaries/funders/funders_dictionary.md

Blocked on :

I need the syntax for converting the SPARQL.xml file to the ami dictionary format.

My SPARQL dictionary funder is committed here : https://raw.githubusercontent.com/petermr/openVirus/master/dictionaries/funders/sparql%20(6)

Attributes in my SPARQL dictionary :

    ` <head>`
	`<variable name='item'/>`
	`<variable name='Crossref_funder_ID'/>`
	`<variable name='Crossref_funder_IDLabel'/>`
	`<variable name='country'/>`
	`<variable name='countryLabel'/>`
	`<variable name='funder'/>`
	`<variable name='funderLabel'/>`
`</head>`

I have tried this syntax to convert SPARQL to ami format:

amidict -vv --dictionary funders --directory dict --input funder.sparql.xml create --informat=wikisparqlxml --sparqlmap wikidata=item,funder_ID=Crossref_funder_ID,name=Crossref_funder_IDLabel,country=country,countryLabel=countryLabel,funder=funder,funderLabel=funderLabel

After running this command, the commanLine says :

Specific values (DictionaryCreationTool) ================================ names [FunderLabel, Country, CountryLabel, instanceofLabel, Funder, crossrefid] results 17480 java.lang.NullPointerException at org.contentmine.ami.tools.dictionary.DictionaryCreationTool.addMappedFieldsToDictionary(DictionaryCreationTool.java:619) at org.contentmine.ami.tools.dictionary.DictionaryCreationTool.addWikidataID(DictionaryCreationTool.java:609) at org.contentmine.ami.tools.dictionary.DictionaryCreationTool.readSparqlXml(DictionaryCreationTool.java:463) at org.contentmine.ami.tools.dictionary.DictionaryCreationTool.createDictionary(DictionaryCreationTool.java:320) at org.contentmine.ami.tools.dictionary.DictionaryCreationTool.runSub(DictionaryCreationTool.java:240) at org.contentmine.ami.tools.AbstractAMIDictTool.runSpecifics(AbstractAMIDictTool.java:423) at org.contentmine.ami.tools.AbstractAMIDictTool.runCommands(AbstractAMIDictTool.java:93) at org.contentmine.ami.tools.AbstractAMIDictTool.call(AbstractAMIDictTool.java:74) at org.contentmine.ami.tools.AbstractAMIDictTool.call(AbstractAMIDictTool.java:55) at picocli.CommandLine.executeUserObject(CommandLine.java:1933) at picocli.CommandLine.access100(CommandLine.java:145)

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