Examples with BioAssaySet ubic.gemma.model.expression.experiment.BioAssaySet used on opensource projects

Example 6 with BioAssaySet

use of ubic.gemma.model.expression.experiment.BioAssaySet in project Gemma by PavlidisLab.

the class ExpressionExperimentManipulatingCLI method removeTroubledEes.

/**
 * removes EEs that are troubled, or their parent Array design is troubled.
 */
private void removeTroubledEes(Collection<BioAssaySet> ees) {
    if (ees == null || ees.size() == 0) {
        AbstractCLI.log.warn("No experiments to remove troubled from");
        return;
    }
    BioAssaySet theOnlyOne = null;
    if (ees.size() == 1) {
        theOnlyOne = ees.iterator().next();
    }
    int size = ees.size();
    CollectionUtils.filter(ees, new Predicate() {

        @Override
        public boolean evaluate(Object object) {
            return !((ExpressionExperiment) object).getCurationDetails().getTroubled();
        }
    });
    int newSize = ees.size();
    if (newSize != size) {
        assert newSize < size;
        if (size == 1 && theOnlyOne != null) {
            AbstractCLI.log.info(theOnlyOne.getName() + " has an active trouble flag");
        } else {
            AbstractCLI.log.info("Removed " + (size - newSize) + " experiments with 'trouble' flags, leaving " + newSize);
        }
    }
}

Example 7 with BioAssaySet

use of ubic.gemma.model.expression.experiment.BioAssaySet in project Gemma by PavlidisLab.

the class ExpressionExperimentManipulatingCLI method readExpressionExperimentListFile.

/**
 * Load expression experiments based on a list of short names or IDs in a file. Only the first column of the file is
 * used, comments (#) are allowed.
 */
private Set<BioAssaySet> readExpressionExperimentListFile(String fileName) throws IOException {
    Set<BioAssaySet> ees = new HashSet<>();
    for (String eeName : AbstractCLIContextCLI.readListFileToStrings(fileName)) {
        ExpressionExperiment ee = eeService.findByShortName(eeName);
        if (ee == null) {
            try {
                Long id = Long.parseLong(eeName);
                ee = eeService.load(id);
                if (ee == null) {
                    AbstractCLI.log.error("No experiment " + eeName + " found");
                    continue;
                }
            } catch (NumberFormatException e) {
                AbstractCLI.log.error("No experiment " + eeName + " found");
                continue;
            }
        }
        ees.add(ee);
    }
    return ees;
}

Example 8 with BioAssaySet

use of ubic.gemma.model.expression.experiment.BioAssaySet in project Gemma by PavlidisLab.

the class ExpressionExperimentManipulatingCLI method findExpressionExperimentsByQuery.

/**
 * Use the search engine to locate expression experiments.
 */
private Set<BioAssaySet> findExpressionExperimentsByQuery(String query) {
    Set<BioAssaySet> ees = new HashSet<>();
    Collection<SearchResult> eeSearchResults = searchService.search(SearchSettingsImpl.expressionExperimentSearch(query)).get(ExpressionExperiment.class);
    AbstractCLI.log.info(ees.size() + " Expression experiments matched '" + query + "'");
    // Filter out all the ee that are not of correct taxon
    for (SearchResult sr : eeSearchResults) {
        ExpressionExperiment ee = (ExpressionExperiment) sr.getResultObject();
        Taxon t = eeService.getTaxon(ee);
        if (t != null && t.getCommonName().equalsIgnoreCase(taxon.getCommonName())) {
            ees.add(ee);
        }
    }
    return ees;
}

Example 9 with BioAssaySet

use of ubic.gemma.model.expression.experiment.BioAssaySet in project Gemma by PavlidisLab.

the class ExpressionExperimentPrimaryPubCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception err = processCommandLine(args);
    if (err != null)
        return err;
    ExpressionExperimentService ees = this.getBean(ExpressionExperimentService.class);
    Persister ph = this.getPersisterHelper();
    PubMedXMLFetcher fetcher = new PubMedXMLFetcher();
    // collect some statistics
    Collection<String> nullPubCount = new ArrayList<>();
    Collection<String> samePubCount = new ArrayList<>();
    Collection<String> diffPubCount = new ArrayList<>();
    Collection<String> failedEe = new ArrayList<>();
    ExpressionExperimentBibRefFinder finder = new ExpressionExperimentBibRefFinder();
    for (BioAssaySet bioassay : expressionExperiments) {
        if (!(bioassay instanceof ExpressionExperiment)) {
            log.info(bioassay.getName() + " is not an ExpressionExperiment");
            continue;
        }
        ExpressionExperiment experiment = (ExpressionExperiment) bioassay;
        // if ( experiment.getPrimaryPublication() != null ) continue;
        if (experiment.getPrimaryPublication() == null) {
            log.warn(experiment + " has no existing primary publication");
        }
        experiment = ees.thawLite(experiment);
        // get from GEO or get from a file
        BibliographicReference ref = fetcher.retrieveByHTTP(pubmedIds.get(experiment.getShortName()));
        if (ref == null) {
            if (this.pubmedIdFilename != null) {
                log.warn("Pubmed ID for " + experiment.getShortName() + " was not found in " + this.pubmedIdFilename);
            }
            ref = finder.locatePrimaryReference(experiment);
            if (ref == null) {
                log.error("No ref for " + experiment);
                failedEe.add(experiment.getShortName());
                continue;
            }
        }
        // collect some statistics
        if (experiment.getPrimaryPublication() == null) {
            nullPubCount.add(experiment.getShortName());
        } else if (experiment.getPrimaryPublication().getPubAccession().getAccession().equals(pubmedIds.get(experiment.getShortName()).toString())) {
            samePubCount.add(experiment.getShortName());
        } else {
            diffPubCount.add(experiment.getShortName());
        }
        try {
            log.info("Found pubAccession " + ref.getPubAccession().getAccession() + " for " + experiment);
            ref = (BibliographicReference) ph.persist(ref);
            experiment.setPrimaryPublication(ref);
            ees.update(experiment);
        } catch (Exception e) {
            log.error(experiment.getShortName() + " (id=" + experiment.getId() + ") update failed.");
            e.printStackTrace();
        }
    }
    // print statistics
    log.info("\n\n========== Summary ==========");
    log.info("Total number of experiments: " + expressionExperiments.size());
    log.info("Same publication: " + samePubCount.size());
    log.info("Diff publication: " + diffPubCount.size());
    log.info("No initial publication: " + nullPubCount.size());
    log.info("No publications found: " + failedEe.size());
    log.info("\n\n========== Details ==========");
    log.info("Diff publication: " + Arrays.toString(diffPubCount.toArray()));
    log.info("No initial publication: " + Arrays.toString(nullPubCount.toArray()));
    log.info("No publications found: " + Arrays.toString(failedEe.toArray()));
    return null;
}

Example 10 with BioAssaySet

use of ubic.gemma.model.expression.experiment.BioAssaySet in project Gemma by PavlidisLab.

the class MakeExperimentsPublicCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception e = super.processCommandLine(args);
    if (e != null)
        return e;
    SecurityService securityService = this.getBean(SecurityService.class);
    for (BioAssaySet ee : this.expressionExperiments) {
        securityService.makePublic(ee);
        this.auditTrailService.addUpdateEvent(ee, MakePublicEvent.class, "Made public from command line", null);
    }
    return null;
}