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Merge pull request #100 from opencb/TASK-7134
TASK-7134 - Re-implement Aggregations Stats for all Catalog Browsers
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228 changes: 228 additions & 0 deletions
228
...main/java/org/opencb/commons/datastore/mongodb/MongoDBDocumentToFacetFieldsConverter.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,228 @@ | ||
| package org.opencb.commons.datastore.mongodb; | ||
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| import org.apache.commons.lang3.StringUtils; | ||
| import org.bson.Document; | ||
| import org.opencb.commons.datastore.core.ComplexTypeConverter; | ||
| import org.opencb.commons.datastore.core.FacetField; | ||
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| import java.math.BigDecimal; | ||
| import java.math.RoundingMode; | ||
| import java.util.*; | ||
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| import static org.opencb.commons.datastore.mongodb.GenericDocumentComplexConverter.TO_REPLACE_DOTS; | ||
| import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.Accumulator.*; | ||
| import static org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.*; | ||
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| public class MongoDBDocumentToFacetFieldsConverter implements ComplexTypeConverter<List<FacetField>, Document> { | ||
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| private static final Map<String, String> MONTH_MAP = new HashMap<>(); | ||
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| static { | ||
| MONTH_MAP.put("01", "Jan"); | ||
| MONTH_MAP.put("02", "Feb"); | ||
| MONTH_MAP.put("03", "Mar"); | ||
| MONTH_MAP.put("04", "Apr"); | ||
| MONTH_MAP.put("05", "May"); | ||
| MONTH_MAP.put("06", "Jun"); | ||
| MONTH_MAP.put("07", "Jul"); | ||
| MONTH_MAP.put("08", "Aug"); | ||
| MONTH_MAP.put("09", "Sep"); | ||
| MONTH_MAP.put("10", "Oct"); | ||
| MONTH_MAP.put("11", "Nov"); | ||
| MONTH_MAP.put("12", "Dec"); | ||
| } | ||
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| @Override | ||
| public List<FacetField> convertToDataModelType(Document document) { | ||
| if (document == null || document.entrySet().size() == 0) { | ||
| return Collections.emptyList(); | ||
| } | ||
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| String facetFieldName; | ||
| List<FacetField> facets = new ArrayList<>(); | ||
| for (Map.Entry<String, Object> entry : document.entrySet()) { | ||
| String key = entry.getKey(); | ||
| List<Document> documentValues = (List<Document>) entry.getValue(); | ||
| if (key.endsWith(COUNTS_SUFFIX) || key.endsWith(FACET_ACC_SUFFIX) || key.endsWith(YEAR_SUFFIX) || key.endsWith(MONTH_SUFFIX) | ||
| || key.endsWith(DAY_SUFFIX)) { | ||
| facetFieldName = key.split(SEPARATOR)[0].replace(TO_REPLACE_DOTS, "."); | ||
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| List<FacetField.Bucket> buckets = new ArrayList<>(documentValues.size()); | ||
| long total = 0; | ||
| for (Document documentValue : documentValues) { | ||
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| long counter = documentValue.getInteger(count.name()); | ||
| String bucketValue = ""; | ||
| Object internalIdValue = documentValue.get(INTERNAL_ID); | ||
| if (internalIdValue instanceof String) { | ||
| bucketValue = (String) internalIdValue; | ||
| } else if (internalIdValue instanceof Boolean | ||
| || internalIdValue instanceof Integer | ||
| || internalIdValue instanceof Long | ||
| || internalIdValue instanceof Double) { | ||
| bucketValue = internalIdValue.toString(); | ||
| } else if (internalIdValue instanceof Document) { | ||
| bucketValue = StringUtils.join(((Document) internalIdValue).values(), SEPARATOR); | ||
| if (key.endsWith(COUNTS_SUFFIX)) { | ||
| facetFieldName = key.substring(0, key.indexOf(COUNTS_SUFFIX)); | ||
| } | ||
| } | ||
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| List<FacetField> bucketFacetFields = null; | ||
| if (key.endsWith(FACET_ACC_SUFFIX)) { | ||
| String[] split = key.split(SEPARATOR); | ||
| String name = split[2]; | ||
| String aggregationName = split[1]; | ||
| Double value; | ||
| if (documentValue.get(aggregationName) instanceof Integer) { | ||
| value = 1.0d * documentValue.getInteger(aggregationName); | ||
| } else if (documentValue.get(aggregationName) instanceof Long) { | ||
| value = 1.0d * documentValue.getLong(aggregationName); | ||
| } else { | ||
| value = documentValue.getDouble(aggregationName); | ||
| } | ||
| List<Double> aggregationValues = Collections.singletonList(value); | ||
| FacetField facetField = new FacetField(name.replace(TO_REPLACE_DOTS, "."), aggregationName, aggregationValues); | ||
| // Perhaps it’s redundant, as it is also set in the bucket | ||
| facetField.setCount(counter); | ||
| bucketFacetFields = Collections.singletonList(facetField); | ||
| } | ||
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| buckets.add(new FacetField.Bucket(bucketValue, counter, bucketFacetFields)); | ||
| total += counter; | ||
| } | ||
| FacetField facetField = new FacetField(facetFieldName, total, buckets); | ||
| facetField.setAggregationName(count.name()); | ||
| if (key.endsWith(YEAR_SUFFIX) || key.endsWith(MONTH_SUFFIX) || key.endsWith(DAY_SUFFIX)) { | ||
| Collections.sort(buckets, Comparator.comparing(FacetField.Bucket::getValue)); | ||
| if (key.endsWith(MONTH_SUFFIX)) { | ||
| for (FacetField.Bucket b : buckets) { | ||
| String[] split = b.getValue().split(SEPARATOR); | ||
| b.setValue(MONTH_MAP.get(split[1]) + " " + split[0]); | ||
| } | ||
| } else if (key.endsWith(DAY_SUFFIX)) { | ||
| for (FacetField.Bucket b : buckets) { | ||
| String[] split = b.getValue().split(SEPARATOR); | ||
| b.setValue(split[2] + " " + MONTH_MAP.get(split[1]) + " " + split[0]); | ||
| } | ||
| } | ||
| // Remove the data field and keep year, month and day | ||
| List<String> labels = new ArrayList<>(Arrays.asList(key.split(SEPARATOR))); | ||
| labels.remove(0); | ||
| facetField.setAggregationName(StringUtils.join(labels, SEPARATOR).toLowerCase(Locale.ROOT)); | ||
| } | ||
| facets.add(facetField); | ||
| } else if (key.endsWith(RANGES_SUFFIX)) { | ||
| List<FacetField.Bucket> buckets = new ArrayList<>(documentValues.size()); | ||
| int total = 0; | ||
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| String[] split = key.split(SEPARATOR); | ||
| double start = Double.parseDouble(split[1].replace(TO_REPLACE_DOTS, ".")); | ||
| double end = Double.parseDouble(split[2].replace(TO_REPLACE_DOTS, ".")); | ||
| double step = Double.parseDouble(split[3].replace(TO_REPLACE_DOTS, ".")); | ||
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| int other = 0; | ||
| for (double i = start; i <= end; i += step) { | ||
| int bucketCount = getBucketCountFromRanges(i, documentValues); | ||
| FacetField.Bucket bucket = new FacetField.Bucket(String.valueOf(roundToTwoSignificantDecimals(i)), bucketCount, null); | ||
| buckets.add(bucket); | ||
| total += bucketCount; | ||
| } | ||
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| for (Document value : documentValues) { | ||
| if (value.get(INTERNAL_ID) instanceof String && OTHER.equals(value.getString(INTERNAL_ID))) { | ||
| other = value.getInteger(count.name()); | ||
| } | ||
| } | ||
| facetFieldName = key.split(SEPARATOR)[0].replace(TO_REPLACE_DOTS, "."); | ||
| if (other > 0) { | ||
| FacetField.Bucket bucket = new FacetField.Bucket("Other", other, null); | ||
| buckets.add(bucket); | ||
| total += bucket.getCount(); | ||
| } | ||
| FacetField facetField = new FacetField(facetFieldName, total, buckets) | ||
| .setStart(start) | ||
| .setEnd(end) | ||
| .setStep(step); | ||
| facets.add(facetField); | ||
| } else { | ||
| Document documentValue = ((List<Document>) entry.getValue()).get(0); | ||
| MongoDBQueryUtils.Accumulator accumulator = getAccumulator(documentValue); | ||
| switch (accumulator) { | ||
| case sum: | ||
| case avg: | ||
| case max: | ||
| case min: | ||
| case stdDevPop: | ||
| case stdDevSamp: { | ||
| List<Double> fieldValues = new ArrayList<>(); | ||
| if (documentValue.get(accumulator.name()) instanceof Integer) { | ||
| fieldValues.add(1.0d * documentValue.getInteger(accumulator.name())); | ||
| } else if (documentValue.get(accumulator.name()) instanceof Long) { | ||
| fieldValues.add(1.0d * documentValue.getLong(accumulator.name())); | ||
| } else if (documentValue.get(accumulator.name()) instanceof List) { | ||
| List<Number> list = (List<Number>) documentValue.get(accumulator.name()); | ||
| for (Number number : list) { | ||
| fieldValues.add(number.doubleValue()); | ||
| } | ||
| } else { | ||
| fieldValues.add(documentValue.getDouble(accumulator.name())); | ||
| } | ||
| long count = 0; | ||
| if (documentValue.containsKey("count")) { | ||
| count = Long.valueOf(documentValue.getInteger("count")); | ||
| } | ||
| facetFieldName = documentValue.getString(INTERNAL_ID).replace(TO_REPLACE_DOTS, "."); | ||
| facets.add(new FacetField(facetFieldName, count, accumulator.name(), fieldValues)); | ||
| break; | ||
| } | ||
| default: { | ||
| // Do nothing, exception is raised | ||
| } | ||
| } | ||
| } | ||
| } | ||
| return facets; | ||
| } | ||
|
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| private MongoDBQueryUtils.Accumulator getAccumulator(Document document) { | ||
| for (Map.Entry<String, Object> entry : document.entrySet()) { | ||
| try { | ||
| MongoDBQueryUtils.Accumulator accumulator = MongoDBQueryUtils.Accumulator.valueOf(entry.getKey()); | ||
| return accumulator; | ||
| } catch (IllegalArgumentException e) { | ||
| // Do nothing | ||
| } | ||
| } | ||
| throw new IllegalArgumentException("No accumulators found in facet document: " + StringUtils.join(document.keySet(), ", ") | ||
| + "Valid accumulator functions: " + StringUtils.join(Arrays.asList(count, sum, max, min, avg, stdDevPop, stdDevSamp), ",")); | ||
| } | ||
|
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| @Override | ||
| public Document convertToStorageType(List<FacetField> facetFields) { | ||
| throw new RuntimeException("Not yet implemented"); | ||
| } | ||
|
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| private static double roundToTwoSignificantDecimals(double value) { | ||
| if (value == 0) { | ||
| return 0; | ||
| } | ||
|
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| BigDecimal bd = new BigDecimal(value); | ||
| int integerDigits = bd.precision() - bd.scale(); | ||
| int scale = Math.max(0, 2 + integerDigits); | ||
| return bd.setScale(scale, RoundingMode.HALF_UP).doubleValue(); | ||
| } | ||
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| private int getBucketCountFromRanges(double inputRange, List<Document> documentValues) { | ||
| for (Document document : documentValues) { | ||
| if (!OTHER.equals(document.get(INTERNAL_ID))) { | ||
| if (inputRange == document.getDouble(INTERNAL_ID)) { | ||
| return document.getInteger(count.name()); | ||
| } | ||
| } | ||
| } | ||
| return 0; | ||
| } | ||
| } |
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