Examples with Summary gov.nih.nci.ctd2.dashboard.util.Summary used on opensource projects

Example 1 with Summary

use of gov.nih.nci.ctd2.dashboard.util.Summary in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method summarizeTotal.

private Summary summarizeTotal() {
    Session session = getSession();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<BigInteger> query = session.createNativeQuery("SELECT COUNT(*) FROM submission" + " JOIN observation_template ON submission.observationTemplate_id=observation_template.id");
    BigInteger submissions = query.getSingleResult();
    String tierQuery = "SELECT tier, COUNT(*) FROM observation" + " JOIN submission ON observation.submission_id=submission.id" + " JOIN observation_template ON submission.observationTemplate_id=observation_template.id" + " GROUP BY tier";
    @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> query2 = session.createNativeQuery(tierQuery);
    int[] tierCount = new int[3];
    List<Object[]> result = query2.list();
    for (Object[] obj : result) {
        Integer tier = (Integer) obj[0];
        BigInteger count = (BigInteger) obj[1];
        tierCount[tier - 1] = count.intValue();
    }
    session.close();
    return new Summary("", submissions.intValue(), tierCount[0], tierCount[1], tierCount[2]);
}

Example 2 with Summary

use of gov.nih.nci.ctd2.dashboard.util.Summary in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method summarizeStories.

private Summary summarizeStories() {
    Session session = getSession();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<BigInteger> query = session.createNativeQuery("SELECT COUNT(*) FROM submission" + " JOIN observation_template ON submission.observationTemplate_id=observation_template.id" + " WHERE isSubmissionStory=True");
    BigInteger submissions = query.getSingleResult();
    String tierQuery = "SELECT tier, COUNT(*) FROM observation" + " JOIN submission ON observation.submission_id=submission.id" + " JOIN observation_template ON submission.observationTemplate_id=observation_template.id" + " WHERE isSubmissionStory=TRUE" + " GROUP BY tier";
    @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> query2 = session.createNativeQuery(tierQuery);
    int[] tierCount = new int[3];
    List<Object[]> result = query2.list();
    for (Object[] obj : result) {
        Integer tier = (Integer) obj[0];
        BigInteger count = (BigInteger) obj[1];
        tierCount[tier - 1] = count.intValue();
    }
    session.close();
    return new Summary("Stories", submissions.intValue(), tierCount[0], tierCount[1], tierCount[2]);
}

Example 3 with Summary

use of gov.nih.nci.ctd2.dashboard.util.Summary in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method summarize.

@Override
public void summarize() {
    findEntities(Summary.class).forEach(s -> delete(s));
    Map<Class<?>, String> summaryClasses = new HashMap<Class<?>, String>();
    summaryClasses.put(AnimalModel.class, "Animal Models");
    summaryClasses.put(CellSample.class, "Cell Lines");
    summaryClasses.put(Compound.class, "Compounds");
    summaryClasses.put(Gene.class, "Genes");
    summaryClasses.put(ShRna.class, "shRNA");
    summaryClasses.put(TissueSample.class, "Disease Contexts (Tissues)");
    summaryClasses.forEach((clazz, label) -> {
        @SuppressWarnings("unchecked") Summary s = summarizePerSubject((Class<? extends Subject>) clazz, label);
        save(s);
    });
    Summary s = summarizeStories();
    save(s);
    Summary eco = summarizeECO();
    save(eco);
    Summary total = summarizeTotal();
    save(total);
}

Example 4 with Summary

use of gov.nih.nci.ctd2.dashboard.util.Summary in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method summarizeECO.

private Summary summarizeECO() {
    Session session = getSession();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<BigInteger> query = session.createNativeQuery("SELECT COUNT(*) FROM submission" + " JOIN observation_template ON submission.observationTemplate_id=observation_template.id" + " WHERE ecoCode <> ''");
    BigInteger submissions = query.getSingleResult();
    String tierQuery = "SELECT tier, COUNT(*) FROM observation" + " JOIN submission ON observation.submission_id=submission.id" + " JOIN observation_template ON submission.observationTemplate_id=observation_template.id" + " WHERE ecoCode <> ''" + " GROUP BY tier";
    @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> query2 = session.createNativeQuery(tierQuery);
    int[] tierCount = new int[3];
    List<Object[]> result = query2.list();
    for (Object[] obj : result) {
        Integer tier = (Integer) obj[0];
        BigInteger count = (BigInteger) obj[1];
        tierCount[tier - 1] = count.intValue();
    }
    session.close();
    return new Summary("Evidence Types", submissions.intValue(), tierCount[0], tierCount[1], tierCount[2]);
}

Example 5 with Summary

use of gov.nih.nci.ctd2.dashboard.util.Summary in project nci-ctd2-dashboard by CBIIT.

the class RssController method generateFeed.

private String generateFeed(List<? extends DashboardEntity> dashboardEntities, String rssTitlePostfix, String rssDescription, String rssLink) {
    String dashboardUrl = context.getScheme() + "://" + context.getServerName() + context.getContextPath() + "/";
    // Set the stage and define metadata on the RSS feed
    SyndFeed feed = new SyndFeedImpl();
    feed.setFeedType("rss_2.0");
    feed.setTitle("CTD^2 Dashboard - " + rssTitlePostfix);
    feed.setDescription(rssDescription);
    feed.setLink(rssLink);
    // We will have two major categories: Subject and Submission
    // and will have subcategories of Subject for each particular subject
    List<SyndCategory> categories = new ArrayList<SyndCategory>();
    SyndCategory subjectCategory = new SyndCategoryImpl();
    subjectCategory.setName("Subject");
    categories.add(subjectCategory);
    SyndCategory submissionCategory = new SyndCategoryImpl();
    submissionCategory.setName("Submission");
    categories.add(submissionCategory);
    feed.setCategories(categories);
    feed.setLanguage("en");
    feed.setManagingEditor("ocg@mail.nih.gov (CTD^2 Network)");
    SyndImage feedImg = new SyndImageImpl();
    feedImg.setTitle("CTD^2 Logo");
    feedImg.setUrl(dashboardUrl + "img/logos/ctd2_overall.png");
    feedImg.setLink(dashboardUrl);
    feed.setImage(feedImg);
    // And prepare the items to be put into the RSS
    List<SyndEntry> rssItems = new ArrayList<SyndEntry>();
    for (DashboardEntity entity : dashboardEntities) {
        if (entity instanceof Subject) {
            Subject subject = (Subject) entity;
            // Collect all role & submission pairs for this particular subject
            Map<Submission, Set<String>> roleMap = new HashMap<Submission, Set<String>>();
            Map<Submission, Set<ObservedSubject>> osMap = new HashMap<Submission, Set<ObservedSubject>>();
            List<ObservedSubject> sObservations = dashboardDao.findObservedSubjectBySubject((Subject) entity);
            for (ObservedSubject sObservation : sObservations) {
                String role = sObservation.getObservedSubjectRole().getSubjectRole().getDisplayName();
                Submission submission = sObservation.getObservation().getSubmission();
                Set<String> roles = roleMap.get(submission);
                if (roles == null) {
                    roles = new HashSet<String>();
                    roleMap.put(submission, roles);
                }
                roles.add(role);
                Set<ObservedSubject> oses = osMap.get(submission);
                if (oses == null) {
                    oses = new HashSet<ObservedSubject>();
                    osMap.put(submission, oses);
                }
                oses.add(sObservation);
            }
            // These will always belong to "Subject"
            List<SyndCategory> sCategories = new ArrayList<SyndCategory>();
            sCategories.add(subjectCategory);
            // and "Subject/<name>" categories
            SyndCategory sCategory = new SyndCategoryImpl();
            sCategory.setName(subjectCategory.getName() + "/" + entity.getDisplayName());
            categories.add(sCategory);
            // Also add this specific category to the global list
            sCategories.add(sCategory);
            // And now combine this information into individual items around submissions/subject
            for (Submission submission : roleMap.keySet()) {
                Set<String> roles = roleMap.get(submission);
                assert roles != null;
                Set<ObservedSubject> oses = osMap.get(submission);
                assert oses != null;
                SyndEntry item = new SyndEntryImpl();
                item.setCategories(sCategories);
                // Construct title
                ObservationTemplate observationTemplate = submission.getObservationTemplate();
                String description = observationTemplate.getDescription();
                Integer tier = observationTemplate.getTier();
                String combinedRoles = StringUtils.join(roles, ", ");
                String name = subject.getDisplayName();
                int noOfObservations = oses.size();
                StringBuilder title = new StringBuilder();
                title.append("Role '").append(combinedRoles).append("'").append(": ").append(description).append(" ").append("(").append("Tier ").append(tier).append(" - ").append(noOfObservations).append(" ").append(noOfObservations > 1 ? "observations" : "observation").append(" on ").append(name).append(")");
                item.setTitle(title.toString());
                String centerName = observationTemplate.getSubmissionCenter().getDisplayName();
                item.setAuthor(centerName);
                item.setPublishedDate(submission.getSubmissionDate());
                String submissionDescription = observationTemplate.getSubmissionDescription();
                StringBuilder itemDescStr = new StringBuilder();
                itemDescStr.append("<b>Project</b>: ").append(observationTemplate.getProject()).append("<br />");
                if (submissionDescription != null && !submissionDescription.isEmpty()) {
                    itemDescStr.append("<b>Summary</b>: ").append(submissionDescription);
                }
                SyndContent itemDesc = new SyndContentImpl();
                itemDesc.setType("text/html");
                itemDesc.setValue(itemDescStr.toString());
                item.setDescription(itemDesc);
                // Create a link to the subject page with filters enabled
                item.setLink(dashboardUrl + "#subject/" + subject.getId() + "/" + combinedRoles + "/" + tier);
                item.setUri(String.format("#ctd2#subject#%s#%d", name, title.hashCode() & Integer.MAX_VALUE));
                rssItems.add(item);
            }
        // End of subject-centered items
        } else if (entity instanceof Submission) {
            Submission submission = (Submission) entity;
            SyndEntry item = new SyndEntryImpl();
            ObservationTemplate observationTemplate = submission.getObservationTemplate();
            int noOfObservations = dashboardDao.findObservationsBySubmission(submission).size();
            StringBuilder title = new StringBuilder();
            Boolean isStory = observationTemplate.getIsSubmissionStory();
            title.append(isStory ? "Story" : "Submission").append(": ");
            title.append(observationTemplate.getDescription().replaceAll("\\.$", "")).append(" (").append("Tier ").append(observationTemplate.getTier()).append(" - ").append(noOfObservations).append(" ").append(noOfObservations > 1 ? "observations" : "observation").append(")");
            item.setTitle(title.toString());
            String submissionDescription = observationTemplate.getSubmissionDescription();
            StringBuilder itemDescStr = new StringBuilder();
            itemDescStr.append("<b>Project</b>: ").append(observationTemplate.getProject()).append("<br />");
            if (submissionDescription != null && !submissionDescription.isEmpty()) {
                itemDescStr.append("<b>Summary</b>: ").append(submissionDescription);
            }
            SyndContent itemDesc = new SyndContentImpl();
            itemDesc.setType("text/html");
            itemDesc.setValue(itemDescStr.toString());
            item.setDescription(itemDesc);
            item.setPublishedDate(submission.getSubmissionDate());
            String centerName = observationTemplate.getSubmissionCenter().getDisplayName();
            item.setAuthor(centerName);
            item.setLink(dashboardUrl + "#submission/" + submission.getId());
            item.setUri(String.format("ctd2#submission#%d", title.hashCode() & Integer.MAX_VALUE));
            rssItems.add(item);
        }
    // End of submission item(s)
    }
    // Add all items into the feed
    feed.setEntries(rssItems);
    // And print the XML/RSS version out
    SyndFeedOutput feedOutput = new SyndFeedOutput();
    String feedStr = null;
    try {
        feedStr = feedOutput.outputString(feed, true);
    } catch (FeedException e) {
        e.printStackTrace();
    }
    return feedStr;
}