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https://issues.apache.org/jira/browse/RYA-416?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16308689#comment-16308689
]
ASF GitHub Bot commented on RYA-416:
------------------------------------
Github user kchilton2 commented on a diff in the pull request:
https://github.com/apache/incubator-rya/pull/254#discussion_r159310844
--- Diff:
dao/mongodb.rya/src/main/java/org/apache/rya/mongodb/aggregation/AggregationPipelineQueryNode.java
---
@@ -0,0 +1,882 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.rya.mongodb.aggregation;
+
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.CONTEXT;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.DOCUMENT_VISIBILITY;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.OBJECT;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.OBJECT_HASH;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.OBJECT_TYPE;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.PREDICATE;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.PREDICATE_HASH;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.STATEMENT_METADATA;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.SUBJECT;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.SUBJECT_HASH;
+import static
org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy.TIMESTAMP;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.NavigableSet;
+import java.util.Set;
+import java.util.UUID;
+import java.util.concurrent.ConcurrentSkipListSet;
+import java.util.function.Function;
+
+import org.apache.rya.api.domain.RyaStatement;
+import org.apache.rya.api.domain.RyaType;
+import org.apache.rya.api.domain.RyaURI;
+import org.apache.rya.api.domain.StatementMetadata;
+import org.apache.rya.api.resolver.RdfToRyaConversions;
+import org.apache.rya.mongodb.MongoDbRdfConstants;
+import org.apache.rya.mongodb.dao.MongoDBStorageStrategy;
+import org.apache.rya.mongodb.dao.SimpleMongoDBStorageStrategy;
+import
org.apache.rya.mongodb.document.operators.query.ConditionalOperators;
+import
org.apache.rya.mongodb.document.visibility.DocumentVisibilityAdapter;
+import org.bson.Document;
+import org.bson.conversions.Bson;
+import org.openrdf.model.Literal;
+import org.openrdf.model.Resource;
+import org.openrdf.model.URI;
+import org.openrdf.model.Value;
+import org.openrdf.model.vocabulary.XMLSchema;
+import org.openrdf.query.BindingSet;
+import org.openrdf.query.QueryEvaluationException;
+import org.openrdf.query.algebra.Compare;
+import org.openrdf.query.algebra.ExtensionElem;
+import org.openrdf.query.algebra.ProjectionElem;
+import org.openrdf.query.algebra.ProjectionElemList;
+import org.openrdf.query.algebra.StatementPattern;
+import org.openrdf.query.algebra.ValueConstant;
+import org.openrdf.query.algebra.ValueExpr;
+import org.openrdf.query.algebra.Var;
+import org.openrdf.query.algebra.evaluation.impl.ExternalSet;
+
+import com.google.common.base.Preconditions;
+import com.google.common.collect.BiMap;
+import com.google.common.collect.HashBiMap;
+import com.mongodb.BasicDBObject;
+import com.mongodb.DBObject;
+import com.mongodb.client.MongoCollection;
+import com.mongodb.client.model.Aggregates;
+import com.mongodb.client.model.BsonField;
+import com.mongodb.client.model.Filters;
+import com.mongodb.client.model.Projections;
+
+import info.aduna.iteration.CloseableIteration;
+
+/**
+ * Represents a portion of a query tree as MongoDB aggregation pipeline.
Should
+ * be built bottom-up: start with a statement pattern implemented as a
$match
+ * step, then add steps to the pipeline to handle higher levels of the
query
+ * tree. Methods are provided to add certain supported query operations to
the
+ * end of the internal pipeline. In some cases, specific arguments may be
+ * unsupported, in which case the pipeline is unchanged and the method
returns
+ * false.
+ */
+public class AggregationPipelineQueryNode extends ExternalSet {
+ /**
+ * An aggregation result corresponding to a solution should map this
key
+ * to an object which itself maps variable names to variable values.
+ */
+ static final String VALUES = "<VALUES>";
+
+ /**
+ * An aggregation result corresponding to a solution should map this
key
+ * to an object which itself maps variable names to the corresponding
hashes
+ * of their values.
+ */
+ static final String HASHES = "<HASHES>";
+
+ /**
+ * An aggregation result corresponding to a solution should map this
key
+ * to an object which itself maps variable names to their datatypes,
if any.
+ */
+ static final String TYPES = "<TYPES>";
+
+ private static final String LEVEL = "derivation_level";
+ private static final String[] FIELDS = { VALUES, HASHES, TYPES, LEVEL,
TIMESTAMP };
+
+ private static final String JOINED_TRIPLE = "<JOINED_TRIPLE>";
+ private static final String FIELDS_MATCH = "<JOIN_FIELDS_MATCH>";
+
+ private static final MongoDBStorageStrategy<RyaStatement> strategy =
new SimpleMongoDBStorageStrategy();
+
+ private static final Bson DEFAULT_TYPE = new Document("$literal",
XMLSchema.ANYURI.stringValue());
+ private static final Bson DEFAULT_CONTEXT = new Document("$literal",
"");
+ private static final Bson DEFAULT_DV =
DocumentVisibilityAdapter.toDBObject(MongoDbRdfConstants.EMPTY_DV);
+ private static final Bson DEFAULT_METADATA = new Document("$literal",
+ StatementMetadata.EMPTY_METADATA.toString());
+
+ private static boolean isValidFieldName(String name) {
+ return !(name == null || name.contains(".") || name.contains("$")
+ || name.equals("_id"));
+ }
+
+ /**
+ * For a given statement pattern, represents a mapping from query
variables
+ * to their corresponding parts of matching triples. If necessary, also
+ * substitute variable names including invalid characters with
temporary
+ * replacements, while producing a map back to the original names.
+ */
+ private static class StatementVarMapping {
+ private final Map<String, String> varToTripleValue = new
HashMap<>();
+ private final Map<String, String> varToTripleHash = new
HashMap<>();
+ private final Map<String, String> varToTripleType = new
HashMap<>();
+ private final BiMap<String, String> varToOriginalName;
+
+ String valueField(String varName) {
+ return varToTripleValue.get(varName);
+ }
+ String hashField(String varName) {
+ return varToTripleHash.get(varName);
+ }
+ String typeField(String varName) {
+ return varToTripleType.get(varName);
+ }
+
+ Set<String> varNames() {
+ return varToTripleValue.keySet();
+ }
+
+ private String replace(String original) {
+ if (varToOriginalName.containsValue(original)) {
+ return varToOriginalName.inverse().get(original);
+ }
+ else {
+ String replacement = "field-" + UUID.randomUUID();
+ varToOriginalName.put(replacement, original);
+ return replacement;
+ }
+ }
+
+ private String sanitize(String name) {
+ if (varToOriginalName.containsValue(name)) {
+ return varToOriginalName.inverse().get(name);
+ }
+ else if (name != null && !isValidFieldName(name)) {
+ return replace(name);
+ }
+ return name;
+ }
+
+ StatementVarMapping(StatementPattern sp, BiMap<String, String>
varToOriginalName) {
+ this.varToOriginalName = varToOriginalName;
+ if (sp.getSubjectVar() != null &&
!sp.getSubjectVar().hasValue()) {
+ String name = sanitize(sp.getSubjectVar().getName());
+ varToTripleValue.put(name, SUBJECT);
+ varToTripleHash.put(name, SUBJECT_HASH);
+ }
+ if (sp.getPredicateVar() != null &&
!sp.getPredicateVar().hasValue()) {
+ String name = sanitize(sp.getPredicateVar().getName());
+ varToTripleValue.put(name, PREDICATE);
+ varToTripleHash.put(name, PREDICATE_HASH);
+ }
+ if (sp.getObjectVar() != null &&
!sp.getObjectVar().hasValue()) {
+ String name = sanitize(sp.getObjectVar().getName());
+ varToTripleValue.put(name, OBJECT);
+ varToTripleHash.put(name, OBJECT_HASH);
+ varToTripleType.put(name, OBJECT_TYPE);
+ }
+ if (sp.getContextVar() != null &&
!sp.getContextVar().hasValue()) {
+ String name = sanitize(sp.getContextVar().getName());
+ varToTripleValue.put(name, CONTEXT);
+ }
+ }
+
+ Bson getProjectExpression() {
+ return getProjectExpression(new LinkedList<>(), str -> "$" +
str);
+ }
+
+ Bson getProjectExpression(Iterable<String> alsoInclude,
+ Function<String, String> getFieldExpr) {
+ Document values = new Document();
+ Document hashes = new Document();
+ Document types = new Document();
+ for (String varName : varNames()) {
+ values.append(varName,
getFieldExpr.apply(valueField(varName)));
+ if (varToTripleHash.containsKey(varName)) {
+ hashes.append(varName,
getFieldExpr.apply(hashField(varName)));
+ }
+ if (varToTripleType.containsKey(varName)) {
+ types.append(varName,
getFieldExpr.apply(typeField(varName)));
+ }
+ }
+ for (String varName : alsoInclude) {
+ values.append(varName, 1);
+ hashes.append(varName, 1);
+ types.append(varName, 1);
+ }
+ List<Bson> fields = new LinkedList<>();
+ fields.add(Projections.excludeId());
+ fields.add(Projections.computed(VALUES, values));
+ fields.add(Projections.computed(HASHES, hashes));
+ if (!types.isEmpty()) {
+ fields.add(Projections.computed(TYPES, types));
+ }
+ fields.add(Projections.computed(LEVEL,
+ maxValueExpr("$" + LEVEL, getFieldExpr.apply(LEVEL),
0)));
+ fields.add(Projections.computed(TIMESTAMP,
+ maxValueExpr("$" + TIMESTAMP,
getFieldExpr.apply(TIMESTAMP), 0)));
+ return Projections.fields(fields);
+ }
+ }
+
+ /**
+ * Generate a projection expression that evaluates to the maximum of
two
+ * fields and a default value.
+ */
+ private static Document maxValueExpr(String field1, String field2,
Object defaultValue) {
+ if (field1.equals(field2)) {
+ return ConditionalOperators.ifNull(field1, defaultValue);
+ }
+ else {
+ Document vars = new Document("x",
ConditionalOperators.ifNull(field1, defaultValue))
+ .append("y", ConditionalOperators.ifNull(field2,
defaultValue));
+ Document gt = new Document("$gt", Arrays.asList("$$x", "$$y"));
+ Document maxExpr = new Document("$cond",
+ new Document("if", gt).append("then",
"$$x").append("else", "$$y"));
+ return new Document("$let", new Document("vars",
vars).append("in", maxExpr));
+ }
+ }
+
+ /**
+ * Given a StatementPattern, generate an object representing the
arguments
+ * to a "$match" command that will find matching triples.
+ * @param sp The StatementPattern to search for
+ * @param path If given, specify the field that should be matched
against
+ * the statement pattern, using an ordered list of field names for a
nested
+ * field. E.g. to match records { "x": { "y": <statement pattern } },
pass
+ * "x" followed by "y".
+ * @return The argument of a "$match" query
+ */
+ private static BasicDBObject getMatchExpression(StatementPattern sp,
String ... path) {
+ final Var subjVar = sp.getSubjectVar();
+ final Var predVar = sp.getPredicateVar();
+ final Var objVar = sp.getObjectVar();
+ final Var contextVar = sp.getContextVar();
+ RyaURI s = null;
+ RyaURI p = null;
+ RyaType o = null;
+ RyaURI c = null;
+ if (subjVar != null && subjVar.getValue() instanceof Resource) {
+ s = RdfToRyaConversions.convertResource((Resource)
subjVar.getValue());
+ }
+ if (predVar != null && predVar.getValue() instanceof URI) {
+ p = RdfToRyaConversions.convertURI((URI) predVar.getValue());
+ }
+ if (objVar != null && objVar.getValue() != null) {
+ o = RdfToRyaConversions.convertValue(objVar.getValue());
+ }
+ if (contextVar != null && contextVar.getValue() instanceof URI) {
+ c = RdfToRyaConversions.convertURI((URI)
contextVar.getValue());
+ }
+ RyaStatement rs = new RyaStatement(s, p, o, c);
+ DBObject obj = strategy.getQuery(rs);
+ // Add path prefix, if given
+ if (path.length > 0) {
+ StringBuilder sb = new StringBuilder();
+ for (String str : path) {
+ sb.append(str).append(".");
+ }
+ String prefix = sb.toString();
+ Set<String> originalKeys = new HashSet<>(obj.keySet());
+ originalKeys.forEach(key -> {
+ Object value = obj.removeField(key);
+ obj.put(prefix + key, value);
+ });
+ }
+ return (BasicDBObject) obj;
+ }
+
+ private static String valueFieldExpr(String varName) {
+ return "$" + VALUES + "." + varName;
+ }
+ private static String hashFieldExpr(String varName) {
+ return "$" + HASHES + "." + varName;
+ }
+ private static String typeFieldExpr(String varName) {
+ return "$" + TYPES + "." + varName;
+ }
+ private static String joinFieldExpr(String triplePart) {
+ return "$" + JOINED_TRIPLE + "." + triplePart;
+ }
+
+ /**
+ * Get an object representing the value field of some value
expression, or
+ * return null if the expression isn't supported.
+ */
+ private Object valueFieldExpr(ValueExpr expr) {
+ if (expr instanceof Var) {
+ return valueFieldExpr(((Var) expr).getName());
+ }
+ else if (expr instanceof ValueConstant) {
+ return new Document("$literal", ((ValueConstant)
expr).getValue().stringValue());
+ }
+ else {
+ return null;
+ }
+ }
+
+ private final List<Bson> pipeline;
+ private final MongoCollection<Document> collection;
+ private final Set<String> assuredBindingNames;
+ private final Set<String> bindingNames;
+ private final BiMap<String, String> varToOriginalName;
+
+ private String replace(String original) {
+ if (varToOriginalName.containsValue(original)) {
+ return varToOriginalName.inverse().get(original);
+ }
+ else {
+ String replacement = "field-" + UUID.randomUUID();
+ varToOriginalName.put(replacement, original);
+ return replacement;
+ }
+ }
+
+ /**
+ * Create a pipeline based on a StatementPattern.
+ * @param baseSP The leaf node in the query tree.
+ */
+ public AggregationPipelineQueryNode(MongoCollection<Document>
collection, StatementPattern baseSP) {
--- End diff --
The documentation of this seems to be out of date since it accepts a
collection.
> Add the ability use the MongoDB aggregation pipeline to evaluate simple
> SPARQL expressions
> ------------------------------------------------------------------------------------------
>
> Key: RYA-416
> URL: https://issues.apache.org/jira/browse/RYA-416
> Project: Rya
> Issue Type: New Feature
> Reporter: Jesse Hatfield
> Assignee: Jesse Hatfield
>
> MongoDB provides the [aggregation pipeline
> framework|https://docs.mongodb.com/manual/core/aggregation-pipeline/] for
> multi-stage data processing. Currently, the query engine invokes this
> framework to apply individual statement patterns (using a "$match" expression
> for each and iterating through the results), then applies higher-level query
> operations (join, filter, select, project, etc) client-side.
> In principle, those high-level query operations could be rewritten as
> aggregation pipeline stages as well ($group, $match, $project, etc). This
> would allow more query evaluation logic to be executed by the MongoDB server
> itself, enabling server-side optimization. This could be used as a general
> query optimization, but would additionally be useful for any tool that only
> needed to write query results back to the server: adding a write step to the
> end of the resulting pipeline could obviate the need to communicate
> individual results to the client at all.
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