Examples with IdfMake org.edamontology.edammap.core.idf.IdfMake used on opensource projects

Example 1 with IdfMake

use of org.edamontology.edammap.core.idf.IdfMake in project edammap by edamontology.

the class Processor method getProcessedConcepts.

public Map<EdamUri, ConceptProcessed> getProcessedConcepts(Map<EdamUri, Concept> concepts, IdfArgs idfArgs, MultiplierArgs multiplierArgs, PreProcessor preProcessor) {
    Map<EdamUri, ConceptProcessed> processedConcepts = new LinkedHashMap<>();
    IdfMake idfMake = new IdfMake();
    for (Map.Entry<EdamUri, Concept> concept : concepts.entrySet()) {
        processedConcepts.put(concept.getKey(), processConcept(concept.getValue(), idfMake, preProcessor));
    }
    Idf idf = new Idf(idfMake.getIdf());
    for (ConceptProcessed processedConcept : processedConcepts.values()) {
        processConceptIdf(processedConcept, idf);
    }
    for (ConceptProcessed processedConcept : processedConcepts.values()) {
        anonymizeProcessedConcept(processedConcept, idfArgs, multiplierArgs);
    }
    return processedConcepts;
}

Example 2 with IdfMake

use of org.edamontology.edammap.core.idf.IdfMake in project edammap by edamontology.

the class Processor method makeQueryIdf.

public int makeQueryIdf(List<Query> queries, QueryType type, String outputPath, boolean webpagesDocs, boolean fulltext, PreProcessor preProcessor, Idf queryIdf, FetcherArgs fetcherArgs) throws IOException {
    IdfMake idfMake = new IdfMake(outputPath);
    for (Query query : queries) {
        QueryProcessed processedQuery = getProcessedQuery(query, type, preProcessor, queryIdf, fetcherArgs);
        if (processedQuery.getNameTokens() != null) {
            idfMake.addTerms(processedQuery.getNameTokens());
        }
        for (List<String> keywordTokens : processedQuery.getKeywordsTokens()) {
            if (keywordTokens != null)
                idfMake.addTerms(keywordTokens);
        }
        if (processedQuery.getDescriptionTokens() != null) {
            idfMake.addTerms(processedQuery.getDescriptionTokens());
        }
        if (webpagesDocs) {
            for (List<String> webpageTokens : processedQuery.getWebpagesTokens()) {
                if (webpageTokens != null)
                    idfMake.addTerms(webpageTokens);
            }
            for (List<String> docTokens : processedQuery.getDocsTokens()) {
                if (docTokens != null)
                    idfMake.addTerms(docTokens);
            }
        }
        for (PublicationProcessed processedPublication : processedQuery.getProcessedPublications()) {
            if (processedPublication == null)
                continue;
            if (processedPublication.getTitleTokens() != null) {
                idfMake.addTerms(processedPublication.getTitleTokens());
            }
            for (List<String> keywordTokens : processedPublication.getKeywordsTokens()) {
                if (keywordTokens != null)
                    idfMake.addTerms(keywordTokens);
            }
            for (List<String> meshTermTokens : processedPublication.getMeshTermsTokens()) {
                if (meshTermTokens != null)
                    idfMake.addTerms(meshTermTokens);
            }
            for (List<String> efoTermTokens : processedPublication.getEfoTermsTokens()) {
                if (efoTermTokens != null)
                    idfMake.addTerms(efoTermTokens);
            }
            for (List<String> goTermTokens : processedPublication.getGoTermsTokens()) {
                if (goTermTokens != null)
                    idfMake.addTerms(goTermTokens);
            }
            if (processedPublication.getAbstractTokens() != null) {
                idfMake.addTerms(processedPublication.getAbstractTokens());
            }
            if (fulltext) {
                if (processedPublication.getFulltextTokens() != null) {
                    idfMake.addTerms(processedPublication.getFulltextTokens());
                }
            }
        }
        idfMake.endDocument();
    }
    return idfMake.writeOutput();
}