Examples with ObservedSubject gov.nih.nci.ctd2.dashboard.model.ObservedSubject used on opensource projects

Example 1 with ObservedSubject

use of gov.nih.nci.ctd2.dashboard.model.ObservedSubject in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method search.

@Override
@Cacheable(value = "searchCache")
public SearchResults search(String queryString) {
    queryString = queryString.trim();
    final String[] searchTerms = parseWords(queryString);
    log.debug("search terms: " + String.join(",", searchTerms));
    Map<Subject, Integer> subjects = new HashMap<Subject, Integer>();
    Map<Submission, Integer> submissions = new HashMap<Submission, Integer>();
    for (String singleTerm : searchTerms) {
        searchSingleTerm(singleTerm, subjects, submissions);
    }
    SearchResults searchResults = new SearchResults();
    searchResults.submission_result = submissions.keySet().stream().map(submission -> {
        ObservationTemplate template = submission.getObservationTemplate();
        return new SearchResults.SubmissionResult(submission.getStableURL(), submission.getSubmissionDate(), template.getDescription(), template.getTier(), template.getSubmissionCenter().getDisplayName(), submission.getId(), findObservationsBySubmission(submission).size(), template.getIsSubmissionStory());
    }).collect(Collectors.toList());
    Map<String, Set<Observation>> observationMap = new HashMap<String, Set<Observation>>();
    List<SubjectResult> subject_result = new ArrayList<SubjectResult>();
    for (Subject subject : subjects.keySet()) {
        Set<Observation> observations = new HashSet<Observation>();
        Set<SubmissionCenter> submissionCenters = new HashSet<SubmissionCenter>();
        Set<String> roles = new HashSet<String>();
        for (ObservedSubject observedSubject : findObservedSubjectBySubject(subject)) {
            Observation observation = observedSubject.getObservation();
            observations.add(observation);
            ObservationTemplate observationTemplate = observation.getSubmission().getObservationTemplate();
            submissionCenters.add(observationTemplate.getSubmissionCenter());
            roles.add(observedSubject.getObservedSubjectRole().getSubjectRole().getDisplayName());
        }
        SubjectResult x = new SubjectResult(subject, observations.size(), submissionCenters.size(), subjects.get(subject), roles);
        Arrays.stream(searchTerms).filter(term -> matchSubject(term, subject)).forEach(term -> {
            Set<Observation> obset = observationMap.get(term);
            if (obset == null) {
                obset = new HashSet<Observation>();
            }
            obset.addAll(observations);
            observationMap.put(term, obset);
        });
        subject_result.add(x);
    }
    /* search ECO terms */
    List<ECOTerm> ecoterms = findECOTerms(queryString);
    for (ECOTerm ecoterm : ecoterms) {
        List<Integer> observationIds = observationIdsForEcoCode(ecoterm.getCode());
        int observationNumber = observationIds.size();
        if (observationNumber == 0)
            continue;
        SubjectResult entity = new SubjectResult(ecoterm, observationNumber, centerCount(ecoterm.getCode()), null, // no matchNumber, no roles
        null);
        subject_result.add(entity);
        Set<Observation> observations = new HashSet<Observation>();
        observationIds.forEach(obid -> observations.add(getEntityById(Observation.class, obid)));
        Arrays.stream(searchTerms).filter(term -> ecoterm.containsTerm(term)).forEach(term -> {
            Set<Observation> obset = observationMap.get(term);
            if (obset == null) {
                obset = new HashSet<Observation>();
            }
            obset.addAll(observations);
            observationMap.put(term, obset);
        });
    }
    /*
         * Limit the size. This should be done more efficiently during the process of
         * builing up of the list.
         * Because the limit needs to be based on 'match number' ranking, which depends
         * on all terms, an efficient algorithm is not obvious.
         * Unfortunately, we also have to do this after processing all results because
         * we need (in fact more often) observation numbers as well in ranking. TODO
         */
    if (subject_result.size() > maxNumberOfSearchResults) {
        searchResults.oversized = subject_result.size();
        subject_result = subject_result.stream().sorted(new SearchResultComparator()).limit(maxNumberOfSearchResults).collect(Collectors.toList());
        log.debug("size after limiting: " + subject_result.size());
    }
    searchResults.subject_result = subject_result;
    if (searchTerms.length <= 1) {
        return searchResults;
    }
    // add intersection of observations
    Set<Observation> set0 = observationMap.get(searchTerms[0]);
    if (set0 == null) {
        log.debug("no observation for " + searchTerms[0]);
        return searchResults;
    }
    log.debug("set0 size=" + set0.size());
    for (int i = 1; i < searchTerms.length; i++) {
        Set<Observation> obset = observationMap.get(searchTerms[i]);
        if (obset == null) {
            log.debug("... no observation for " + searchTerms[i]);
            return searchResults;
        }
        log.debug("set " + i + " size=" + obset.size());
        set0.retainAll(obset);
    }
    // set0 is now the intersection
    if (set0.size() == 0) {
        log.debug("no intersection of observations");
    }
    if (set0.size() > maxNumberOfSearchResults) {
        searchResults.oversized_observations = set0.size();
        // no particular ranking is enforced when limiting
        set0 = set0.stream().limit(maxNumberOfSearchResults).collect(Collectors.toSet());
        log.debug("observation results count after limiting: " + set0.size());
    }
    searchResults.observation_result = new ArrayList<Observation>(set0);
    return searchResults;
}

Example 2 with ObservedSubject

use of gov.nih.nci.ctd2.dashboard.model.ObservedSubject in project nci-ctd2-dashboard by CBIIT.

the class SubjectScorer method scoreAllRoles.

@Transactional
public void scoreAllRoles() {
    log.info("Removing all role-based scores...");
    List<SubjectWithSummaries> oldEntities = dashboardDao.findEntities(SubjectWithSummaries.class);
    for (SubjectWithSummaries subjectWithSummaries : oldEntities) {
        dashboardDao.delete(subjectWithSummaries);
    }
    log.info("Removed " + oldEntities.size() + " old scores.");
    log.info("Re-scoring all roles...");
    List<SubjectWithSummaries> subjectWithSummariesList = new ArrayList<SubjectWithSummaries>();
    List<SubjectRole> entities = dashboardDao.findEntities(SubjectRole.class);
    for (SubjectRole subjectRole : entities) {
        String keyword = subjectRole.getDisplayName();
        log.info("Scoring subject with role: " + keyword);
        HashMap<Subject, SubjectWithSummaries> subjectToSummaries = new HashMap<Subject, SubjectWithSummaries>();
        HashMap<Subject, HashSet<SubmissionCenter>> subjectToCenters = new HashMap<Subject, HashSet<SubmissionCenter>>();
        HashMap<Subject, HashMap<SubmissionCenter, Integer>> centerBasedScores = new HashMap<Subject, HashMap<SubmissionCenter, Integer>>();
        for (ObservedSubject observedSubject : dashboardDao.findObservedSubjectByRole(keyword)) {
            Subject subject = observedSubject.getSubject();
            SubjectWithSummaries withSummaries = subjectToSummaries.get(subject);
            ObservationTemplate observationTemplate = observedSubject.getObservation().getSubmission().getObservationTemplate();
            SubmissionCenter submissionCenter = observationTemplate.getSubmissionCenter();
            Integer tier = observationTemplate.getTier();
            if (withSummaries == null) {
                withSummaries = new SubjectWithSummaries();
                withSummaries.setRole(keyword);
                withSummaries.setSubject(subject);
                withSummaries.setMaxTier(tier);
                withSummaries.setNumberOfObservations(1);
                HashSet<SubmissionCenter> centers = new HashSet<SubmissionCenter>();
                centers.add(submissionCenter);
                withSummaries.setNumberOfSubmissionCenters(1);
                withSummaries.addSubmission(tier, submissionCenter.getId());
                subjectToCenters.put(subject, centers);
                subjectToSummaries.put(subject, withSummaries);
                HashMap<SubmissionCenter, Integer> cScores = new HashMap<>();
                cScores.put(submissionCenter, tier);
                centerBasedScores.put(subject, cScores);
            } else {
                withSummaries.setMaxTier(Math.max(withSummaries.getMaxTier(), tier));
                withSummaries.setNumberOfObservations(withSummaries.getNumberOfObservations() + 1);
                HashSet<SubmissionCenter> submissionCenters = subjectToCenters.get(subject);
                submissionCenters.add(submissionCenter);
                withSummaries.setNumberOfSubmissionCenters(submissionCenters.size());
                withSummaries.addSubmission(tier, submissionCenter.getId());
                HashMap<SubmissionCenter, Integer> cScores = centerBasedScores.get(subject);
                Integer previousScore = cScores.get(submissionCenter);
                cScores.put(submissionCenter, previousScore == null ? tier : Math.max(tier, previousScore));
            }
        }
        Collection<SubjectWithSummaries> perRole = subjectToSummaries.values();
        for (SubjectWithSummaries subjectWithSummaries : perRole) {
            Integer totalScore = 0;
            for (Integer aScore : centerBasedScores.get(subjectWithSummaries.getSubject()).values()) {
                totalScore += aScore;
            }
            subjectWithSummaries.setScore(totalScore);
        }
        subjectWithSummariesList.addAll(perRole);
        log.info("Done scoring role: " + keyword);
    }
    dashboardDao.batchSave(subjectWithSummariesList, 0);
    log.info("Done scoring all roles...");
}

Example 3 with ObservedSubject

use of gov.nih.nci.ctd2.dashboard.model.ObservedSubject in project nci-ctd2-dashboard by CBIIT.

the class ObservationDataWriter method write.

public void write(List<? extends ObservationData> items) throws Exception {
    // calls) (2) there is at least one observation in each call
    if (items.size() == 0) {
        // this might happen when some suject is rejected
        log.debug("no item");
        return;
    }
    final Submission submission = items.get(0).observation.getSubmission();
    final String submissionName = submission.getDisplayName();
    StableURL stableURL = new StableURL();
    synchronized (submission) {
        log.debug("[" + ++counter + "]SUBMISSION " + submissionName + ": " + items.size() + " observation(s)");
        final String submissionCacheKey = submissionName + new SimpleDateFormat("yyyy.MM.dd").format(submission.getSubmissionDate()) + submission.getObservationTemplate().getDisplayName();
        if (!submissionCache.contains(submissionCacheKey)) {
            submission.setStableURL(stableURL.createURLWithPrefix("submission", submissionName));
            dashboardDao.save(submission);
            submissionCache.add(submissionCacheKey);
            observationIndex.put(submissionName, 0);
        }
    }
    List<Observation> observations = new ArrayList<Observation>();
    List<Evidence> evidences = new ArrayList<Evidence>();
    List<ObservedSubject> observedSubjects = new ArrayList<ObservedSubject>();
    List<ObservedEvidence> observedEvidences = new ArrayList<ObservedEvidence>();
    for (ObservationData observationData : items) {
        Observation observation = observationData.observation;
        int index = observationIndex.get(submissionName);
        observation.setStableURL(stableURL.createURLWithPrefix("observation", submissionName) + "-" + index);
        observations.add(observation);
        observationIndex.put(submissionName, index + 1);
        for (DashboardEntity e : observationData.evidence) {
            evidences.add((Evidence) e);
        }
        for (DashboardEntity e : observationData.observedEntities) {
            String className = e.getClass().getName();
            switch(className) {
                case "gov.nih.nci.ctd2.dashboard.impl.ObservedSubjectImpl":
                    observedSubjects.add((ObservedSubject) e);
                    break;
                case "gov.nih.nci.ctd2.dashboard.impl.ObservedEvidenceImpl":
                    observedEvidences.add((ObservedEvidence) e);
                    break;
                default:
                    log.error("unexpected type " + className);
            }
        }
    }
    // use a smaller batch size to prevent 'lock wait timeout'
    int batchSize = 100;
    log.debug("observations to write " + observations.size());
    dashboardDao.batchSave(observations, batchSize);
    log.debug("observedSubjects to write " + observedSubjects.size());
    dashboardDao.batchSave(observedSubjects, batchSize);
    log.debug("evidences to write " + evidences.size());
    dashboardDao.batchSave(evidences, batchSize);
    log.debug("observedEvidences to write " + observedEvidences.size());
    dashboardDao.batchSave(observedEvidences, batchSize);
    log.debug("ALL WRITTEN: " + submissionName);
}

Example 4 with ObservedSubject

use of gov.nih.nci.ctd2.dashboard.model.ObservedSubject 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;
}

Example 5 with ObservedSubject

use of gov.nih.nci.ctd2.dashboard.model.ObservedSubject in project nci-ctd2-dashboard by CBIIT.

the class JSONController method getEntityInJson.

@Transactional
@RequestMapping(value = "{type}/{id}", method = { RequestMethod.GET, RequestMethod.POST }, headers = "Accept=application/json")
public ResponseEntity<String> getEntityInJson(@PathVariable String type, @PathVariable String id) {
    DashboardEntity entityById = null;
    Class<? extends DashboardEntity> clazz = Subject.class;
    if (type.equalsIgnoreCase("subject")) {
        clazz = Subject.class;
    } else if (type.equals("observedsubject")) {
        clazz = ObservedSubject.class;
    }
    HttpHeaders headers = new HttpHeaders();
    headers.add("Content-Type", "application/json; charset=utf-8");
    log.debug("JSONController " + type + " " + id);
    if (typesWithStableURL.contains(type)) {
        String stableURL = type + "/" + id;
        if (type.equals("observedevidence"))
            stableURL = "mra/" + id;
        entityById = dashboardDao.getEntityByStableURL(type, stableURL);
    } else {
        entityById = dashboardDao.getEntityById(clazz, Integer.parseInt(id));
    }
    if (entityById == null) {
        return new ResponseEntity<String>(headers, HttpStatus.NOT_FOUND);
    }
    JSONSerializer jsonSerializer = new JSONSerializer().transform(new ImplTransformer(), Class.class).transform(new DateTransformer(), Date.class);
    return new ResponseEntity<String>(jsonSerializer.deepSerialize(entityById), headers, HttpStatus.OK);
}