/** * Get list of returned files. * <p> * Use {@link VariantQueryParam#INCLUDE_FILE} if defined. * If missing, get non negated values from {@link VariantQueryParam#FILE} * <p> * Null for undefined returned files. If null, return ALL files. * Return NONE if empty list * * Does not validate if file names are valid at any study. * * @param query Query with the QueryParams * @param fields Returned fields * @return List of fileIds to return. */ public static List<String> getIncludeFilesList(Query query, Set<VariantField> fields) { List<String> includeFiles; if (!fields.contains(VariantField.STUDIES_FILES)) { includeFiles = Collections.emptyList(); } else { includeFiles = getIncludeFilesList(query); } return includeFiles; }
public static boolean isIncludeFilesDefined(Query query, Set<VariantField> fields) { if (getIncludeFilesList(query, fields) != null) { return true; } return isValidParam(query, SAMPLE, true) || isValidParam(query, INCLUDE_SAMPLE, false) || isValidParam(query, GENOTYPE, false); }
BiFunction<StudyConfiguration, String, T> getSample, Function<StudyConfiguration, T> getStudyId) { List<String> includeFilesList = getIncludeFilesList(query); List<String> includeSamplesList = getIncludeSamplesList(query, options); LinkedHashSet<String> includeSamplesSet = includeSamplesList != null ? new LinkedHashSet<>(includeSamplesList) : null;
List<String> includeFilesList = getIncludeFilesList(query, fields); boolean returnAllFiles = ALL.equals(query.getString(INCLUDE_FILE.key()));
List<String> incFiles = VariantQueryUtils.getIncludeFilesList(query, incFields); if (incFiles == null) {
List<String> includeFiles = getIncludeFilesList(query); if (includeFiles != null) { files = includeFiles.toArray(new String[0]);
List<String> includeFiles = getIncludeFilesList(query); QueryOperation filtersOperation = null; List<String> filterValues = Collections.emptyList();
.collect(Collectors.toList()); } else if (isValidParam(query, INCLUDE_FILE)) { List<String> files = getIncludeFilesList(query); if (files != null) { fileIds = new ArrayList<>(files.size());