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

Example 56 with Entry

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

the class SequenceVariantTest method mockEntry.

public static Entry mockEntry(String accession, Isoform... isoforms) {
    Entry entry = Mockito.mock(Entry.class);
    when(entry.getUniqueName()).thenReturn(accession);
    if (isoforms.length > 0) {
        when(entry.getIsoforms()).thenReturn(Arrays.asList(isoforms));
    }
    return entry;
}

Example 57 with Entry

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

the class FeatureQuerySuccessTest method testOnSuccess.

@Test
public void testOnSuccess() throws FeatureQueryException, ParseException {
    SingleFeatureQuery query = new SingleFeatureQuery("NX_Q9UI33", "SCN11A-p.Leu1158Pro", AnnotationCategory.VARIANT.getApiTypeName());
    SequenceVariant sequenceVariant = new SequenceVariant("SCN11A-p.Leu1158Pro");
    String seqIso1 = "MDDRCYPVIFPDERNFRPFTSDSLAAIEKRIAIQKEKKKSKDQTGEVPQPRPQLDLKASRKLPKLYGDIPRELIGKPLEDLDPFYRNHKTFMVLNRKRTIYRFSAKHALFIFGPFNSIRSLAIRVSVHSLFSMFIIGTVIINCVFMATGPAKNSNSNNTDIAECVFTGIYIFEALIKILARGFILDEFSFLRDPWNWLDSIVIGIAIVSYIPGITIKLLPLRTFRVFRALKAISVVSRLKVIVGALLRSVKKLVNVIILTFFCLSIFALVGQQLFMGSLNLKCISRDCKNISNPEAYDHCFEKKENSPEFKMCGIWMGNSACSIQYECKHTKINPDYNYTNFDNFGWSFLAMFRLMTQDSWEKLYQQTLRTTGLYSVFFFIVVIFLGSFYLINLTLAVVTMAYEEQNKNVAAEIEAKEKMFQEAQQLLKEEKEALVAMGIDRSSLTSLETSYFTPKKRKLFGNKKRKSFFLRESGKDQPPGSDSDEDCQKKPQLLEQTKRLSQNLSLDHFDEHGDPLQRQRALSAVSILTITMKEQEKSQEPCLPCGENLASKYLVWNCCPQWLCVKKVLRTVMTDPFTELAITICIIINTVFLAMEHHKMEASFEKMLNIGNLVFTSIFIAEMCLKIIALDPYHYFRRGWNIFDSIVALLSFADVMNCVLQKRSWPFLRSFRVLRVFKLAKSWPTLNTLIKIIGNSVGALGSLTVVLVIVIFIFSVVGMQLFGRSFNSQKSPKLCNPTGPTVSCLRHWHMGDFWHSFLVVFRILCGEWIENMWECMQEANASSSLCVIVFILITVIGKLVVLNLFIALLLNSFSNEERNGNLEGEARKTKVQLALDRFRRAFCFVRHTLEHFCHKWCRKQNLPQQKEVAGGCAAQSKDIIPLVMEMKRGSETQEELGILTSVPKTLGVRHDWTWLAPLAEEEDDVEFSGEDNAQRITQPEPEQQAYELHQENKKPTSQRVQSVEIDMFSEDEPHLTIQDPRKKSDVTSILSECSTIDLQDGFGWLPEMVPKKQPERCLPKGFGCCFPCCSVDKRKPPWVIWWNLRKTCYQIVKHSWFESFIIFVILLSSGALIFEDVHLENQPKIQELLNCTDIIFTHIFILEMVLKWVAFGFGKYFTSAWCCLDFIIVIVSVTTLINLMELKSFRTLRALRPLRALSQFEGMKVVVNALIGAIPAILNVLLVCLIFWLVFCILGVYFFSGKFGKCINGTDSVINYTIITNKSQCESGNFSWINQKVNFDNVGNAYLALLQVATFKGWMDIIYAAVDSTEKEQQPEFESNSLGYIYFVVFIIFGSFFTLNLFIGVIIDNFNQQQKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNKCQGLVFDIVTSQIFDIIIISLIILNMISMMAESYNQPKAMKSILDHLNWVFVVIFTLECLIKIFALRQYYFTNGWNLFDCVVVLLSIVSTMISTLENQEHIPFPPTLFRIVRLARIGRILRLVRAARGIRTLLFALMMSLPSLFNIGLLLFLIMFIYAILGMNWFSKVNPESGIDDIFNFKTFASSMLCLFQISTSAGWDSLLSPMLRSKESCNSSSENCHLPGIATSYFVSYIIISFLIVVNMYIAVILENFNTATEESEDPLGEDDFDIFYEVWEKFDPEATQFIKYSALSDFADALPEPLRVAKPNKYQFLVMDLPMVSEDRLHCMDILFAFTARVLGGSDGLDSMKAMMEEKFMEANPLKKLYEPIVTTTKRKEEERGAAIIQKAFRKYMMKVTKGDQGDQNDLENGPHSPLQTLCNGDLSSFGVAKGKVHCD";
    String seqIso2 = "MDDRCYPVIFPDERNFRPFTSDSLAAIEKRIAIQKEKKKSKDQTGEVPQPRPQLDLKASRKLPKLYGDIPRELIGKPLEDLDPFYRNHKTFMVLNRKRTIYRFSAKHALFIFGPFNSIRSLAIRVSVHSLFSMFIIGTVIINCVFMATGPAKNSNSNNTDIAECVFTGIYIFEALIKILARGFILDEFSFLRDPWNWLDSIVIGIAIVSYIPGITIKLLPLRTFRVFRALKAISVVSRLKVIVGALLRSVKKLVNVIILTFFCLSIFALVGQQLFMGSLNLKCISRDCKNISNPEAYDHCFEKKENSPEFKMCGIWMGNSACSIQYECKHTKINPDYNYTNFDNFGWSFLAMFRLMTQDSWEKLYQQTLRTTGLYSVFFFIVVIFLGSFYLINLTLAVVTMAYEEQNKNVAAEIEAKEKMFQEAQQLLKEEKEALVAMGIDRSSLTSLETSYFTPKKRKLFGNKKRKSFFLRESGKDQPPGSDSDEDCQKKPQLLEQTKRLSQNLSLDHFDEHGDPLQRQRALSAVSILTITMKEQEKSQEPCLPCGENLASKYLVWNCCPQWLCVKKVLRTVMTDPFTELAITICIIINTVFLAMEHHKMEASFEKMLNIGNLVFTSIFIAEMCLKIIALDPYHYFRRGWNIFDSIVALLSFADVMNCVLQKRSWPFLRSFRVLRVFKLAKSWPTLNTLIKIIGNSVGALGSLTVVLVIVIFIFSVVGMQLFGRSFNSQKSPKLCNPTGPTVSCLRHWHMGDFWHSFLVVFRILCGEWIENMWECMQEANASSSLCVIVFILITVIGKLVVLNLFIALLLNSFSNEERNGNLEGEARKTKVQLALDRFRRAFCFVRHTLEHFCHKWCRKQNLPQQKEVAGGCAAQSKDIIPLVMEMKRGSETQEELGILTSVPKTLGVRHDWTWLAPLAEEEDDVEFSGEDNAQRITQPEPEQQAYELHQENKKPTSQRVQSVEIDMFSEDEPHLTIQDPRKKSDVTSILSECSTIDLQDGFGWLPEMVPKKQPERCLPKGFGCCFPCCSVDKRKPPWVIWWNLRKTCYQIVKHSWFESFIIFVILLSSGALIFEDVHLENQPKIQELLNCTDIIFTHIFILEMVLKWVAFGFGKYFTSAWCCLDFIIVIVSVTTLINLMELKSFRTLRALRPLRALSQFEGMKVVVNALIGAIPAILNVLLVCLIFWLVFCILGVYFFSGKFGKCINGTDSVINYTIITNKSQCESGNFSWINQKVNFDNVGNAYLALLQVATFKGWMDIIYAAVDSTEKEQQPEFESNSLGYIYFVVFIIFGSFFTLNLFIGVIIDNFNQQQKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNKCQGLVFDIVTSQIFDIIIISLIILNMISMMAESYNQPKAMKSILDHLNWVFVVIFTLECLIKIFALRQYYFTNGWNLFDCVVVLLSIVSK";
    String seqIso3 = "MDDRCYPVIFPDERNFRPFTSDSLAAIEKRIAIQKEKKKSKDQTGEVPQPRPQLDLKASRKLPKLYGDIPRELIGKPLEDLDPFYRNHKTFMVLNRKRTIYRFSAKHALFIFGPFNSIRSLAIRVSVHSLFSMFIIGTVIINCVFMATGPAKNSNSNNTDIAECVFTGIYIFEALIKILARGFILDEFSFLRDPWNWLDSIVIGIAIVSYIPGITIKLLPLRTFRVFRALKAISVVSRLKVIVGALLRSVKKLVNVIILTFFCLSIFALVGQQLFMGSLNLKCISRDCKNISNPEAYDHCFEKKENSPEFKMCGIWMGNSACSIQYECKHTKINPDYNYTNFDNFGWSFLAMFRLMTQDSWEKLYQQTLRTTGLYSVFFFIVVIFLGSFYLINLTLAVVTMAYEEQNKNVAAEIEAKEKMFQEAQQLLKEEKEALVAMGIDRSSLTSLETSYFTPKKRKLFGNKKRKSFFLRESGKDQPPGSDSDEDCQKKPQLLEQTKRLSQNLSLDHFDEHGDPLQRQRALSAVSILTITMKEQEKSQEPCLPCGENLASKYLVWNCCPQWLCVKKVLRTVMTDPFTELAITICIIINTVFLAMEHHKMEASFEKMLNIGNLVFTSIFIAEMCLKIIALDPYHYFRRGWNIFDSIVALLSFADVMNCVLQKRSWPFLRSFRVLRVFKLAKSWPTLNTLIKIIGNSVGALGSLTVVLVIVIFIFSVVGMQLFGRSFNSQKSPKLCNPTGPTVSCLRHWHMGDFWHSFLVVFRILCGEWIENMWECMQEANASSSLCVIVFILITVIGKLVVLNLFIALLLNSFSNEERNGNLEGEARKTKVQLALDRFRRAFCFVRHTLEHFCHKWCRKQNLPQQKEVAGGCAAQSKDIIPLVMEMKRGSETQEELGILTSVPKTLGVRHDWTWLAPLAEEEDDVEFSGEDNAQRITQPEPEQQKSDVTSILSECSTIDLQDGFGWLPEMVPKKQPERCLPKGFGCCFPCCSVDKRKPPWVIWWNLRKTCYQIVKHSWFESFIIFVILLSSGALIFEDVHLENQPKIQELLNCTDIIFTHIFILEMVLKWVAFGFGKYFTSAWCCLDFIIVIVSVTTLINLMELKSFRTLRALRPLRALSQFEGMKVVVNALIGAIPAILNVLLVCLIFWLVFCILGVYFFSGKFGKCINGTDSVINYTIITNKSQCESGNFSWINQKVNFDNVGNAYLALLQVATFKGWMDIIYAAVDSTEKEQQPEFESNSLGYIYFVVFIIFGSFFTLNLFIGVIIDNFNQQQKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNKCQGLVFDIVTSQIFDIIIISLIILNMISMMAESYNQPKAMKSILDHLNWVFVVIFTLECLIKIFALRQYYFTNGWNLFDCVVVLLSIVSTMISTLENQEHIPFPPTLFRIVRLARIGRILRLVRAARGIRTLLFALMMSLPSLFNIGLLLFLIMFIYAILGMNWFSKVNPESGIDDIFNFKTFASSMLCLFQISTSAGWDSLLSPMLRSKESCNSSSENCHLPGIATSYFVSYIIISFLIVVNMYIAVILENFNTATEESEDPLGEDDFDIFYEVWEKFDPEATQFIKYSALSDFADALPEPLRVAKPNKYQFLVMDLPMVSEDRLHCMDILFAFTARVLGGSDGLDSMKAMMEEKFMEANPLKKLYEPIVTTTKRKEEERGAAIIQKAFRKYMMKVTKGDQGDQNDLENGPHSPLQTLCNGDLSSFGVAKGKVHCD";
    Isoform iso1 = SequenceVariantTest.mockIsoform("NX_Q9UI33-1", "Iso 1", true, seqIso1);
    Isoform iso2 = SequenceVariantTest.mockIsoform("NX_Q9UI33-2", "Iso 2", false, seqIso2);
    Isoform iso3 = SequenceVariantTest.mockIsoform("NX_Q9UI33-3", "Iso 3", false, seqIso3);
    Entry entry = SequenceVariantTest.mockEntry("NX_Q9UI33", iso1, iso2, iso3);
    SingleFeatureQuerySuccessImpl result = new SingleFeatureQuerySuccessImpl(entry, query, sequenceVariant);
    result.addMappedFeature(iso1, 1158, 1158);
    result.addMappedFeature(iso2, 1158, 1158);
    result.addMappedFeature(iso3, 1120, 1120);
    result.addUnmappedFeature(SequenceVariantTest.mockIsoform("NX_Q9UI33-23", "Iso 23", false, ""));
    Assert.assertEquals("SCN11A-iso1-p.Leu1158Pro", result.getData().get("NX_Q9UI33-1").getIsoSpecificFeature());
    Assert.assertEquals("SCN11A-iso2-p.Leu1158Pro", result.getData().get("NX_Q9UI33-2").getIsoSpecificFeature());
    Assert.assertEquals("SCN11A-iso3-p.Leu1120Pro", result.getData().get("NX_Q9UI33-3").getIsoSpecificFeature());
    Assert.assertNull(result.getData().get("NX_Q9UI33-23").getIsoSpecificFeature());
}

Example 58 with Entry

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

the class EntryJSONStreamWriter method writeEntry.

@Override
protected void writeEntry(String entryName) throws IOException {
    Entry entry = entryBuilderService.build(EntryConfig.newConfig(entryName).with(viewName));
    generator.writeObject(entry);
}

Example 59 with Entry

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

the class EntryPageServiceImpl method hasContentForPageDisplay.

@Cacheable(value = "page-display", key = "#entryName")
@Override
public Map<String, Boolean> hasContentForPageDisplay(@ValidEntry String entryName) {
    Entry entry = entryBuilderService.build(EntryConfig.newConfig(entryName).withEverything());
    Map<String, Boolean> map = new HashMap<>();
    for (PageViewFactory page : PageViewFactory.values()) {
        PageView pv = page.getPageView();
        map.put(pv.getLabel(), pv.doDisplayPage(entry));
    }
    return map;
}

Example 60 with Entry

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

the class SeoTagsServiceImpl method getEntrySeoTags.

@Override
public SeoTags getEntrySeoTags(String url) {
    String[] urlElements = RelativeUrlUtils.getPathElements(url);
    String ac = urlElements[1];
    // default subpage
    String subpage = "function";
    if (urlElements.length > 2)
        subpage = urlElements[2];
    String prettySubpage = getPrettyName(subpage);
    Entry entry = entryBuilderService.build(EntryConfig.newConfig(ac).withOverview().with("function-info"));
    String protName = entry.getOverview().getMainProteinName();
    String geneName = entry.getOverview().getMainGeneName();
    // decision QC 18.08.2016
    if (geneName == null || geneName.isEmpty())
        geneName = ac;
    // decision NPC 15.08.2016
    String title = geneName + " - " + protName + " - " + prettySubpage;
    // decision NPC 15.08.2016
    String h1 = geneName + " - " + prettySubpage;
    // TODO: send something different for each subpage... see with amos
    String descr = ac + " - " + title + ". " + getFirstFunctionInfo(entry);
    return new SeoTags(title, descr, h1);
}