Examples with ConsoleProgressBar org.nextprot.api.commons.app.ConsoleProgressBar used on opensource projects

Example 1 with ConsoleProgressBar

use of org.nextprot.api.commons.app.ConsoleProgressBar in project nextprot-api by calipho-sib.

the class OntologyDAGAnalyserTask method readWriteCache.

private void readWriteCache(boolean readCacheForSure) {
    Set<String> allCvTerms = new HashSet<>();
    ConsoleProgressBar pb = ConsoleProgressBar.determinated(((readCacheForSure) ? "read" : "read/write") + " terminology-by-ontology cache", terminologyCvs.length);
    pb.start();
    Instant t = Instant.now();
    for (TerminologyCv ontology : terminologyCvs) {
        allCvTerms.addAll(terminologyService.findCvTermsByOntology(ontology.name()).stream().map(CvTerm::getAccession).collect(Collectors.toSet()));
        pb.incrementValue();
    }
    pb.stop();
    System.out.println("\ttiming 'terminology-by-ontology': " + ChronoUnit.SECONDS.between(t, Instant.now()) + " s");
    pb = ConsoleProgressBar.determinated(((readCacheForSure) ? "read" : "read/write") + " 'ontology-dag' cache", terminologyCvs.length);
    pb.start();
    t = Instant.now();
    for (TerminologyCv ontology : terminologyCvs) {
        cvTermGraphService.findCvTermGraph(ontology);
        pb.incrementValue();
    }
    pb.stop();
    System.out.println("\ttiming 'ontology-dag': " + ChronoUnit.SECONDS.between(t, Instant.now()) + " s");
    pb = ConsoleProgressBar.determinated(((readCacheForSure) ? "read" : "read/write") + " 'terminology-by-accession' cache", allCvTerms.size());
    pb.start();
    t = Instant.now();
    for (String cvTerm : allCvTerms) {
        terminologyService.findCvTermByAccession(cvTerm);
        pb.incrementValue();
    }
    pb.stop();
    System.out.println("\ttiming 'terminology-by-accession': " + ChronoUnit.SECONDS.between(t, Instant.now()) + " s");
}

Example 2 with ConsoleProgressBar

use of org.nextprot.api.commons.app.ConsoleProgressBar in project nextprot-api by calipho-sib.

the class DbXrefAnalyserTask method analyseNextprotEntriesDbXrefs.

private void analyseNextprotEntriesDbXrefs() throws IOException {
    LOGGER.info("**** Analysing dbxrefs from entry accession...");
    ConsoleProgressBar pb;
    try (DbXrefUrlVisitor visitor = new DbXrefUrlVisitor(outputDirectory + "/allentries-xrefs-url.tsv", outputDirectory + "/allentries-xrefs-url.log")) {
        DbXrefService xrefService = getBean(DbXrefService.class);
        Set<String> allEntryAcs = getNextprotEntries();
        pb = ConsoleProgressBar.determinated("analysing dbxrefs (from neXtProt entries)", allEntryAcs.size());
        pb.start();
        for (String entryAc : allEntryAcs) {
            try {
                visitor.visit(entryAc, xrefService.findDbXrefsByMaster(entryAc));
                visitor.flush();
                pb.incrementValue();
            } catch (EntryNotFoundException e) {
                LOGGER.error(e.getMessage() + ": skipping entry " + entryAc);
            }
        }
        visitor.flush();
        visitor.close();
    }
    pb.stop();
}

Example 3 with ConsoleProgressBar

use of org.nextprot.api.commons.app.ConsoleProgressBar in project nextprot-api by calipho-sib.

the class DbXrefAnalyserTask method analyseCvTermsDbXrefs.

private void analyseCvTermsDbXrefs() throws IOException {
    LOGGER.info("**** Analysing dbxrefs from terminology...");
    DbXrefUrlVisitor visitor = new DbXrefUrlVisitor(outputDirectory + "/allterminologies-xrefs-url.tsv", outputDirectory + "/allterminologies-xrefs-url.log");
    TerminologyService terminologyService = getBean(TerminologyService.class);
    List<CvTerm> allCvTerms = terminologyService.findAllCVTerms();
    ConsoleProgressBar pb = ConsoleProgressBar.determinated("analysing dbxrefs (from neXtProt cv terms)", allCvTerms.size());
    pb.start();
    for (CvTerm terminology : allCvTerms) {
        visitor.visit(terminology.getAccession(), terminology.getXrefs());
        visitor.flush();
        pb.incrementValue();
    }
    visitor.flush();
    visitor.close();
    pb.stop();
}

Example 4 with ConsoleProgressBar

use of org.nextprot.api.commons.app.ConsoleProgressBar in project nextprot-api by calipho-sib.

the class PeffServiceValidatorTask method readExpectedIsoformPeffHeaders.

private Map<String, Map<String, Object>> readExpectedIsoformPeffHeaders() throws FileNotFoundException {
    ConsoleProgressBar pb = ConsoleProgressBar.indeterminated("reading expected peff headers from file");
    try {
        ExpectedPeffParser parser = new ExpectedPeffParser();
        pb.run(Files.lines(Paths.get(expectedPeffFilename)).filter(l -> l.startsWith(">nxp:")), parser);
        return parser.isoToPeffHeader;
    } catch (IOException e) {
        throw new IllegalStateException(e.getMessage() + ": cannot open file nextprot_all_updatedTo1.0h.peff");
    }
}

Example 5 with ConsoleProgressBar

use of org.nextprot.api.commons.app.ConsoleProgressBar in project nextprot-api by calipho-sib.

the class PeffServiceValidatorTask method getIsoformPeffHeadersFromAPI.

private Map<String, Map<String, Object>> getIsoformPeffHeadersFromAPI() throws FileNotFoundException {
    Set<String> allEntryAcs = getNextprotEntries();
    ConsoleProgressBar pb = ConsoleProgressBar.determinated("querying peff headers from api", allEntryAcs.size());
    ObservedPeffCollector collector = new ObservedPeffCollector(getBean(IsoformService.class));
    pb.run(allEntryAcs.stream(), collector);
    return collector.map;
}