Examples with PublicationDirectLink org.nextprot.api.core.domain.publication.PublicationDirectLink used on opensource projects

Example 1 with PublicationDirectLink

use of org.nextprot.api.core.domain.publication.PublicationDirectLink in project nextprot-api by calipho-sib.

the class EntryPublicationTest method testPublicationDirectLinkListOrder.

@Test
public void testPublicationDirectLinkListOrder() {
    EntryPublication p = new EntryPublication("", 12);
    List<String> scopes = Arrays.asList("VARIANT SCA34 PHE-168", "CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS]", "INVOLVEMENT IN SCA34");
    List<String> comments = Arrays.asList("[PDB:1JWU] [Structure]", "[iPTMnet:P04637] [PTM/processing]Phosphorylation", "[GeneRif:3303] S100A4 has opposite roles in Tag7 and Hsp70- mediated tumoricidal mechanisms", "[PRO:PR:000028557] [PTM/processing]P18848-1", "[GAD:125207] [Pathology & Biotech]Associated with CARDIOVASCULAR: pulmonary hypertension; thrombosis, deep vein; pulmonary thromboembolism; HLA-B");
    List<PublicationDirectLink> list = new ArrayList<>();
    scopes.forEach(scope -> list.add(new PublicationDirectLink(188, PublicationProperty.SCOPE, scope)));
    comments.forEach(comment -> list.add(new PublicationDirectLink(188, PublicationProperty.COMMENT, comment)));
    p.setDirectLinks(list);
    Assert.assertEquals(3, p.getDirectLinks(PublicationProperty.SCOPE).size());
    Assert.assertEquals(5, p.getDirectLinks(PublicationProperty.COMMENT).size());
    List<PublicationDirectLink> links = p.getDirectLinks();
    Assert.assertEquals(8, links.size());
    // should be datasource UniProt first, then order by database alpha insensitive, then by label alpha
    Assert.assertEquals(links.get(0).getLabel(), "CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS]");
    Assert.assertEquals(links.get(1).getLabel(), "INVOLVEMENT IN SCA34");
    Assert.assertEquals(links.get(2).getLabel(), "VARIANT SCA34 PHE-168");
    Assert.assertEquals(links.get(3).getLabel(), "[Pathology & Biotech]Associated with CARDIOVASCULAR: pulmonary hypertension; thrombosis, deep vein; pulmonary thromboembolism; HLA-B");
    Assert.assertEquals(links.get(4).getLabel(), "S100A4 has opposite roles in Tag7 and Hsp70- mediated tumoricidal mechanisms");
    Assert.assertEquals(links.get(5).getLabel(), "[PTM/processing]Phosphorylation");
    Assert.assertEquals(links.get(6).getLabel(), "[Structure]");
    Assert.assertEquals(links.get(7).getLabel(), "[PTM/processing]P18848-1");
    Assert.assertEquals(links.get(0).getDatasource(), "Uniprot");
    Assert.assertEquals(links.get(1).getDatasource(), "Uniprot");
    Assert.assertEquals(links.get(2).getDatasource(), "Uniprot");
    Assert.assertEquals(links.get(3).getDatasource(), "PIR");
    Assert.assertEquals(links.get(4).getDatasource(), "PIR");
    Assert.assertEquals(links.get(5).getDatasource(), "PIR");
    Assert.assertEquals(links.get(6).getDatasource(), "PIR");
    Assert.assertEquals(links.get(7).getDatasource(), "PIR");
}