Examples with EdamUri org.edamontology.edammap.core.edam.EdamUri used on opensource projects

Example 11 with EdamUri

use of org.edamontology.edammap.core.edam.EdamUri in project edammap by edamontology.

the class QueryLoader method edamUriJson.

private static EdamUri edamUriJson(Edam edam, Map<EdamUri, Concept> concepts) {
    if (edam.getUri() != null && !edam.getUri().trim().isEmpty()) {
        EdamUri edamUri = new EdamUri(edam.getUri().trim().toLowerCase(Locale.ROOT), EDAM_PREFIX);
        if (!checkEdamUri(edamUri, concepts))
            return null;
        return edamUri;
    }
    if (edam.getTerm() != null && !edam.getTerm().trim().isEmpty()) {
        String term = edam.getTerm().trim();
        if (concepts != null) {
            for (Entry<EdamUri, Concept> e : concepts.entrySet()) {
                if (e.getValue().getLabel().equals(term))
                    return e.getKey();
            }
            for (Entry<EdamUri, Concept> e : concepts.entrySet()) {
                if (e.getValue().getExactSynonyms().contains(term))
                    return e.getKey();
            }
            for (Entry<EdamUri, Concept> e : concepts.entrySet()) {
                if (e.getValue().getNarrowSynonyms().contains(term))
                    return e.getKey();
                if (e.getValue().getBroadSynonyms().contains(term))
                    return e.getKey();
            }
        }
        logger.warn("Can't find EDAM URI for term {} in JSON", term);
        return null;
    } else {
        logger.warn("An EDAM object is empty in JSON");
        return null;
    }
}