Examples with AncestralGroup uk.ac.ebi.spot.goci.model.AncestralGroup used on opensource projects

Example 1 with AncestralGroup

use of uk.ac.ebi.spot.goci.model.AncestralGroup in project goci by EBISPOT.

the class AncestryMappingService method processAncestries.

public void processAncestries() {
    printOutOntologyContent();
    ;
    List<Ancestry> allAncestries = getAllAncestries();
    for (Ancestry ancestry : allAncestries) {
        Long id = ancestry.getId();
        String coo = null;
        if (ancestry.getCountryOfOrigin() != null) {
            for (Country c : ancestry.getCountryOfOrigin()) {
                if (coo == null) {
                    coo = c.getCountryName();
                } else {
                    coo = coo.concat(", ").concat(c.getCountryName());
                }
            }
        } else {
            coo = "NR";
        }
        String cor = null;
        if (ancestry.getCountryOfRecruitment() != null) {
            for (Country c : ancestry.getCountryOfRecruitment()) {
                if (cor == null) {
                    cor = c.getCountryName();
                } else {
                    cor = cor.concat(", ").concat(c.getCountryName());
                }
            }
        } else {
            cor = "NR";
        }
        String ancestralGroup = null;
        if (ancestry.getAncestralGroups() != null) {
            for (AncestralGroup a : ancestry.getAncestralGroups()) {
                if (ancestralGroup == null) {
                    ancestralGroup = a.getAncestralGroup();
                } else {
                    ancestralGroup = ancestralGroup.concat(", ").concat(a.getAncestralGroup());
                }
            }
        } else {
            ancestralGroup = "NR";
        }
        if (ancestralGroup != null) {
            if (ancestralGroup.contains(",")) {
                String[] groups = ancestralGroup.split(",");
                for (String group : groups) {
                    mapAncestralGroup(id, group.toLowerCase());
                }
            } else {
                mapAncestralGroup(id, ancestralGroup.toLowerCase());
            }
        }
        if (coo != null) {
            if (coo.contains(",")) {
                String[] countries = coo.split(",");
                for (String country : countries) {
                    mapCoO(id, country.toLowerCase());
                }
            } else {
                mapCoO(id, coo.toLowerCase());
            }
        }
        if (cor != null) {
            if (cor.contains(",")) {
                String[] countries = cor.split(",");
                for (String country : countries) {
                    mapCoR(id, country.toLowerCase());
                }
            } else {
                mapCoR(id, cor.toLowerCase());
            }
        }
    }
    getErrors().info("All ancestries processed");
    printResult();
}