fix(gravsearch): Prevent duplicate results #1626

loicjaouen · 2020-03-10T10:03:56Z

a simple query in the available anything data set:

PREFIX knora-api: <http://api.knora.org/ontology/knora-api/v2#>
PREFIX anything: <http://0.0.0.0:3333/ontology/0001/anything/v2#>
CONSTRUCT {
    ?thing knora-api:isMainResource true .
    ?thing anything:hasInteger ?int .
} WHERE {
    ?thing a knora-api:Resource .
    ?thing a anything:Thing .
    {
        ?thing anything:hasRichtext ?richtext .
        ?richtext knora-api:valueAsString ?richtextLitteral
        FILTER knora-api:match(?richtextLitteral, "test")

		?thing anything:hasInteger ?int .
		?int knora-api:intValueAsInt 1
    }
    UNION
    {
        ?thing anything:hasText ?text .
        ?text knora-api:valueAsString ?textLitteral
        FILTER knora-api:match(?textLitteral, "test")

		?thing anything:hasInteger ?int .
		?int knora-api:intValueAsInt 1
    }
}
order by (?int)

gives a match count of one with the route: /v2/searchextended/count
gives a result set of two with the route: /v2/searchextended

the in and outs of this have been discussed in the above mentionned #1588

if ever it helps, here are the generated sparql requests, for the count:

SELECT DISTINCT (COUNT(DISTINCT ?thing) AS ?count)
WHERE {
    ?thing <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.knora.org/ontology/knora-base#Resource> .
    GRAPH <http://www.ontotext.com/explicit> {
        ?thing <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
    }
    ?thing <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.knora.org/ontology/0001/anything#Thing> .
    {
        ?thing <http://www.knora.org/ontology/0001/anything#hasRichtext> ?richtext .
        GRAPH <http://www.ontotext.com/explicit> {
            ?richtext <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        ?richtext <http://www.knora.org/ontology/knora-base#valueHasString> ?richtextLitteral .
        ?thing <http://www.knora.org/ontology/0001/anything#hasInteger> ?int .
        GRAPH <http://www.ontotext.com/explicit> {
            ?int <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        ?int <http://www.knora.org/ontology/knora-base#valueHasInteger> "1"^^<http://www.w3.org/2001/XMLSchema#integer> .
        GRAPH <http://www.ontotext.com/explicit> {
            ?richtextLitteral <http://www.ontotext.com/owlim/lucene#fullTextSearchIndex> "test"^^<http://www.w3.org/2001/XMLSchema#string> .
        }
    } UNION {
        ?thing <http://www.knora.org/ontology/0001/anything#hasText> ?text .
        GRAPH <http://www.ontotext.com/explicit> {
            ?text <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        ?text <http://www.knora.org/ontology/knora-base#valueHasString> ?textLitteral .
        ?thing <http://www.knora.org/ontology/0001/anything#hasInteger> ?int .
        GRAPH <http://www.ontotext.com/explicit> {
            ?int <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        ?int <http://www.knora.org/ontology/knora-base#valueHasInteger> "1"^^<http://www.w3.org/2001/XMLSchema#integer> .
        GRAPH <http://www.ontotext.com/explicit> {
            ?textLitteral <http://www.ontotext.com/owlim/lucene#fullTextSearchIndex> "test"^^<http://www.w3.org/2001/XMLSchema#string> .
        }
    }
}
LIMIT 1

for the search:

SELECT DISTINCT ?thing (GROUP_CONCAT(DISTINCT(?text); SEPARATOR='') AS ?text__Concat) (GROUP_CONCAT(DISTINCT(?int); SEPARATOR='') AS ?int__Concat) (GROUP_CONCAT(DISTINCT(?richtext); SEPARATOR='') AS ?richtext__Concat)
WHERE {
    ?thing <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.knora.org/ontology/knora-base#Resource> .
    GRAPH <http://www.ontotext.com/explicit> {
        ?thing <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
    }
    ?thing <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.knora.org/ontology/0001/anything#Thing> .
    {
        ?thing <http://www.knora.org/ontology/0001/anything#hasRichtext> ?richtext .
        GRAPH <http://www.ontotext.com/explicit> {
            ?richtext <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        ?richtext <http://www.knora.org/ontology/knora-base#valueHasString> ?richtextLitteral .
        ?thing <http://www.knora.org/ontology/0001/anything#hasInteger> ?int .
        GRAPH <http://www.ontotext.com/explicit> {
            ?int <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        GRAPH <http://www.ontotext.com/explicit> {
            ?int <http://www.knora.org/ontology/knora-base#valueHasInteger> ?int__valueHasInteger .
        }
        ?int <http://www.knora.org/ontology/knora-base#valueHasInteger> "1"^^<http://www.w3.org/2001/XMLSchema#integer> .
        GRAPH <http://www.ontotext.com/explicit> {
            ?richtextLitteral <http://www.ontotext.com/owlim/lucene#fullTextSearchIndex> "test"^^<http://www.w3.org/2001/XMLSchema#string> .
        }
    } UNION {
        ?thing <http://www.knora.org/ontology/0001/anything#hasText> ?text .
        GRAPH <http://www.ontotext.com/explicit> {
            ?text <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        ?text <http://www.knora.org/ontology/knora-base#valueHasString> ?textLitteral .
        ?thing <http://www.knora.org/ontology/0001/anything#hasInteger> ?int .
        GRAPH <http://www.ontotext.com/explicit> {
            ?int <http://www.knora.org/ontology/knora-base#isDeleted> "false"^^<http://www.w3.org/2001/XMLSchema#boolean> .
        }
        ?int <http://www.knora.org/ontology/knora-base#valueHasInteger> "1"^^<http://www.w3.org/2001/XMLSchema#integer> .
        GRAPH <http://www.ontotext.com/explicit> {
            ?textLitteral <http://www.ontotext.com/owlim/lucene#fullTextSearchIndex> "test"^^<http://www.w3.org/2001/XMLSchema#string> .
        }
    }
}
GROUP BY ?thing ?int__valueHasInteger
ORDER BY ASC(?int__valueHasInteger) ASC(?thing)
LIMIT 25

# Conflicts: # webapi/src/main/scala/org/knora/webapi/util/StringFormatter.scala

loicjaouen · 2020-03-10T10:09:23Z

so for now, this is only the test case demonstrating the bug of the issue #1588

Sorry @benjamingeer, I assign this to you as you are also the assignee on #1588

benjamingeer · 2020-03-10T10:16:03Z

@loicjaouen What would you like to change in the generated SPARQL SELECT?

We need the GROUP_CONCAT for each variable whose values you want to receive in the API response.

tobiasschweizer · 2020-03-19T15:33:44Z

I can confirm that omitting MainQueryResultProcessor.getRequestedValuesFromResultsWithFullGraphPattern before returning the Gravsearch results leads to the presence of knora-api:hasIncomingLinkValue.

This is the simplified JSON for the first resource:

{
  "@graph": [
    {
      "@id": "http://rdfh.ch/0803/2e0252679a35",
      "@type": "knora-api:Region",
      "knora-api:isRegionOfValue": {
        "@id": "http://rdfh.ch/0803/2e0252679a35/values/498d07ec-dddb-4051-bfd1-62626f282fc5",
        "@type": "knora-api:LinkValue",
        "knora-api:linkValueHasTarget": {
          "@id": "http://rdfh.ch/0803/3f89a693a501",
          "@type": "http://0.0.0.0:3333/ontology/0803/incunabula/v2#page",
          "http://0.0.0.0:3333/ontology/0803/incunabula/v2#partOfValue": {
            "@id": "http://rdfh.ch/0803/3f89a693a501/values/133ea4ce-b9a5-4c66-a3ab-38be07ccd201",
            "@type": "knora-api:LinkValue",
            "knora-api:linkValueHasTarget": {
              "@id": "http://rdfh.ch/0803/ff17e5ef9601",
              "@type": "http://0.0.0.0:3333/ontology/0803/incunabula/v2#book",
              "http://0.0.0.0:3333/ontology/0803/incunabula/v2#title": {
                "@id": "http://rdfh.ch/0803/ff17e5ef9601/values/d9a522845006",
                "@type": "knora-api:TextValue",
                "knora-api:valueAsString": "Zeitglöcklein des Lebens und Leidens Christi",
              },
              "knora-api:hasIncomingLinkValue": [
                {
                  "@id": "http://rdfh.ch/0803/6240ce899801/values/e29da7bf-bfa5-4842-a4fc-e455c72dbb0a",
                  "@type": "knora-api:LinkValue",
                  "knora-api:linkValueHasSource": {
                    "@id": "http://rdfh.ch/0803/6240ce899801",
                    "@type": "http://0.0.0.0:3333/ontology/0803/incunabula/v2#page",
                    "http://0.0.0.0:3333/ontology/0803/incunabula/v2#partOfValue": {
                      "@id": "http://rdfh.ch/0803/6240ce899801/values/e29da7bf-bfa5-4842-a4fc-e455c72dbb0a",
                      "@type": "knora-api:LinkValue",
                      "knora-api:linkValueHasTargetIri": {
                        "@id": "http://rdfh.ch/0803/ff17e5ef9601"
                      }
                    },
                    "rdfs:label": "a3v"
                  }
                },
                {
                  "@id": "http://rdfh.ch/0803/c568b7239a01/values/46951e64-8f06-47fb-a07a-c8b19c146447",
                  "@type": "knora-api:LinkValue",
                  "knora-api:linkValueHasSource": {
                    "@id": "http://rdfh.ch/0803/c568b7239a01",
                    "@type": "http://0.0.0.0:3333/ontology/0803/incunabula/v2#page",
                    "http://0.0.0.0:3333/ontology/0803/incunabula/v2#partOfValue": {
                      "@id": "http://rdfh.ch/0803/c568b7239a01/values/46951e64-8f06-47fb-a07a-c8b19c146447",
                      "@type": "knora-api:LinkValue",
                      "knora-api:linkValueHasTargetIri": {
                        "@id": "http://rdfh.ch/0803/ff17e5ef9601"
                      }
                    },
                    "rdfs:label": "a7r"
                  }
                }
              ],
              "rdfs:label": "Zeitglöcklein des Lebens und Leidens Christi"
            }
          },
          "rdfs:label": "d8r"
        }
      },
      "rdfs:label": "DEMOX"
    }
  ],
  "@context": {
    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
    "xsd": "http://www.w3.org/2001/XMLSchema#",
    "knora-api": "http://api.knora.org/ontology/knora-api/v2#"
  }
}

benjamingeer · 2020-03-19T17:04:37Z

After talking with @tobiasschweizer, we decided to handle further refactoring in a separate PR (see issue #1632).

# Conflicts: # webapi/src/main/scala/org/knora/webapi/responders/v2/search/MainQueryResultProcessor.scala

- Simplify Gravsearch paging. - Add design docs.

# Conflicts: # docs/src/paradox/05-internals/design/api-v2/gravsearch.md

# Conflicts: # docs/src/paradox/05-internals/design/api-v2/gravsearch.md # webapi/src/main/scala/org/knora/webapi/responders/v2/SearchResponderV2.scala # webapi/src/main/scala/org/knora/webapi/responders/v2/search/MainQueryResultProcessor.scala # webapi/src/main/scala/org/knora/webapi/responders/v2/search/QueryTraverser.scala # webapi/src/main/scala/org/knora/webapi/responders/v2/search/gravsearch/prequery/AbstractPrequeryGenerator.scala # webapi/src/main/scala/org/knora/webapi/responders/v2/search/gravsearch/prequery/NonTriplestoreSpecificGravsearchToPrequeryGenerator.scala

# Conflicts: # docs/src/paradox/05-internals/design/api-v2/gravsearch.md # webapi/src/main/scala/org/knora/webapi/messages/v2/responder/resourcemessages/ResourceMessagesV2.scala # webapi/src/main/scala/org/knora/webapi/responders/v2/ResourcesResponderV2.scala # webapi/src/main/scala/org/knora/webapi/responders/v2/SearchResponderV2.scala # webapi/src/main/scala/org/knora/webapi/responders/v2/StandoffResponderV2.scala # webapi/src/main/scala/org/knora/webapi/util/ConstructResponseUtilV2.scala # webapi/src/test/scala/org/knora/webapi/util/ConstructResponseUtilV2Spec.scala

…und variables.

tobiasschweizer · 2020-04-09T07:38:02Z

@benjamingeer I will review this PR today in the afternoon.

tobiasschweizer · 2020-04-09T10:06:39Z

Doing this review will also help me understand our own paper :-)

tobiasschweizer

I had a first look, please see my comments. However, I would appreciate if I could talk to you on video chat some time next week to make sure I understand the changes introduced by this PR.

tobiasschweizer · 2020-04-09T13:39:42Z

docs/src/paradox/05-internals/design/api-v2/gravsearch.md

+The prequery's SELECT clause is built by
+`NonTriplestoreSpecificGravsearchToPrequeryTransformer.getSelectColumns`,
+based on the variables used in the input query's `CONSTRUCT` clause.
+The resulting SELECT clause looks as follows:

 ```sparql
 SELECT DISTINCT


I am unaware of the construct (GROUP_CONCAT(DISTINCT(IF(BOUND(?book), STR(?book), "")); SEPARATOR='') AS ?book__Concat) (82f8a55). I presume this means that if the variable is bound, an IRI is returned, otherwise an empty string.

Yes. This is explained in the paragraph starting on line 211:

Each GROUP_CONCAT checks whether the concatenated variable is bound in each result in the group; if a variable is unbound, we concatenate an empty string. This is necessary because, in Apache Jena (and perhaps other triplestores), "If GROUP_CONCAT has an unbound value in the list of values to concat, the overall result is 'error'" (see this Jena issue).

tobiasschweizer · 2020-04-09T13:44:52Z

webapi/src/main/scala/org/knora/webapi/responders/v2/SearchResponderV2.scala

@@ -281,7 +282,8 @@ class SearchResponderV2(responderData: ResponderData) extends ResponderWithStand

            // Create a Select prequery

-            nonTriplestoreSpecificConstructToSelectTransformer: NonTriplestoreSpecificGravsearchToCountPrequeryGenerator = new NonTriplestoreSpecificGravsearchToCountPrequeryGenerator(
+            nonTriplestoreSpecificConstructToSelectTransformer: NonTriplestoreSpecificGravsearchToCountPrequeryTransformer = new NonTriplestoreSpecificGravsearchToCountPrequeryTransformer(
+                constructClause = inputQuery.constructClause,


I assume you need to know about the Construct clause because you only want to return the IRIs of the resources and values that the client asks for.

tobiasschweizer · 2020-04-09T13:47:17Z

.../search/gravsearch/prequery/NonTriplestoreSpecificGravsearchToCountPrequeryTransformer.scala

+ * the search criteria. This query will be used to get resource IRIs for a single page of results. These IRIs will be included in a CONSTRUCT
+ * query to get the actual results for the page.
+ *
+ * @param typeInspectionResult the result of type inspection of the original query.


Could you add all args to the doc string?

Done in 8d4fdfb.

tobiasschweizer · 2020-04-09T13:50:37Z

...rs/v2/search/gravsearch/prequery/NonTriplestoreSpecificGravsearchToPrequeryTransformer.scala

+
+/**
+ * Transforms a preprocessed CONSTRUCT query into a SELECT query that returns only the IRIs and sort order of the main resources that matched
+ * the search criteria. This query will be used to get resource IRIs for a single page of results. These IRIs will be included in a CONSTRUCT


I think the comment should include additional information such as:

Transforms a preprocessed CONSTRUCT query into a SELECT query that returns only the IRIs and sort order of the main resources that matched the search criteria and are requested by client in the input query's WHERE clause.

Done in 8d4fdfb.

tobiasschweizer · 2020-04-09T13:59:43Z

...rs/v2/search/gravsearch/prequery/NonTriplestoreSpecificGravsearchToPrequeryTransformer.scala

@@ -0,0 +1,345 @@
+/*


Has NonTriplestoreSpecificGravsearchToPrequeryGenerator.scala been renamed / moved to NonTriplestoreSpecificGravsearchToPrequeryTransformer? If yes, I don't see a diff (it looks like the files are unrelated) and it's hard for me to see what has changed exactly.

Yes, will attach the diff below.

benjamingeer · 2020-04-09T14:50:51Z

Here's the diff you asked for:

prequery.diff.zip

benjamingeer · 2020-04-09T14:53:25Z

I would appreciate if I could talk to you on video chat some time next week to make sure I understand the changes introduced by this PR.

No problem. I'll take a couple of days of holiday next week. How about we talk on Friday 16 April?

tobiasschweizer · 2020-04-09T14:55:08Z

I would appreciate if I could talk to you on video chat some time next week to make sure I understand the changes introduced by this PR.

No problem. I'll take a couple of days of holiday next week. How about we talk on Friday 16 April?

Works for me. I would prefer to have an online meeting before 12. Would 10 o'clock work for you?

benjamingeer · 2020-04-09T14:56:15Z

Would 10 o'clock work for you?

Perfect!

tobiasschweizer · 2020-04-09T15:00:33Z

Would 10 o'clock work for you?

Perfect!

The appointment you created is on a Thursday, but that's also ok for me.

tobiasschweizer

Thanks for the additional comments and adaptions.

benjamingeer · 2020-04-16T11:39:37Z

Thanks for the review!

Benjamin Geer and others added 22 commits February 19, 2020 18:41

feat(api-v2): Refactor to use ForbiddenResource consistently (ongoing).

3dbb59c

Merge branch 'develop' into wip/1543-forbidden-resource

b6d3cf2

# Conflicts: # webapi/src/main/scala/org/knora/webapi/util/StringFormatter.scala

test: Fix tests.

49f4214

feat(api-v2): Use ForbiddenResource consistently (ongoing).

9171746

Merge branch 'develop' into wip/1543-forbidden-resource

15c3be5

refactor(api-v2): Move ForbiddenResource from triplestore to app.

cae954d

refactor(test): Simplify code.

d6c8fc0

refactor(api-v2): Simplify response processing (ongoing).

7f1d91f

Merge branch 'develop' into wip/1543-forbidden-resource

623630c

feat(api-v2): Add ForbiddenValue (ongoing).

5d1b28e

feat(api-v2): Remove ForbiddenResource (ongoing).

e86b20b

test(api-v2): Fix compile error.

c25808e

feat(api-v2): Get rid of ForbiddenResource (ongoing).

d8d1c38

feat(api-v2): Remove ForbiddenResource (ongoing).

da23fc6

feat(api-v2): Remove ForbiddenResource (ongoing).

baeff8a

feat(api-v2): Remove ForbiddenResource (ongoing).

144863d

refactor(api-v2): Move checkResourceIris into ReadResourcesSequenceV2.

f3ed00c

style(api-v2): Clean up a few things.

5de2b47

docs(gravsearch): Update docs.

ba61578

Merge branch 'develop' into wip/1543-forbidden-resource

8a0c8c6

initial commit of a possible test case

ce602dc

add the count route

9499f85

loicjaouen added API/V2 bug something isn't working Gravsearch labels Mar 10, 2020

loicjaouen assigned benjamingeer Mar 10, 2020

loicjaouen added this to the Backlog milestone Mar 10, 2020

loicjaouen linked an issue Mar 10, 2020 that may be closed by this pull request

Duplicated resources in Gravsearch result #1588

Closed

benjamingeer mentioned this pull request Mar 19, 2020

refactor(gravsearch): Simplify filtering of incoming links #1632

Open

Benjamin Geer added 7 commits March 20, 2020 14:28

docs(gravsearch): Update design docs.

b46c4f0

Merge branch 'wip/1543-forbidden-resource' into wip/1588_duplicates

5232359

# Conflicts: # webapi/src/main/scala/org/knora/webapi/responders/v2/search/MainQueryResultProcessor.scala

docs(gravsearch): Update design docs.

8617571

feat(upgrade): Increment knora-base version.

8e81c67

- Simplify Gravsearch paging. - Add design docs.

Merge branch 'wip/1543-forbidden-resource' into wip/1588_duplicates

c3b19cd

# Conflicts: # docs/src/paradox/05-internals/design/api-v2/gravsearch.md

test(ResourcesResponderV2): Increase timeouts.

9794698

benjamingeer mentioned this pull request Apr 6, 2020

feat(api-v2): Remove ForbiddenResource #1615

Merged

7 tasks

Benjamin Geer added 3 commits April 8, 2020 17:46

fix(gravsearch): Handle empty GROUP_CONCAT values resulting from unbo…

c7b9703

…und variables.

fix(gravsearch): Ignore empty strings in GROUP_CONCAT results.

9f38418

benjamingeer requested review from tobiasschweizer and SepidehAlassi April 8, 2020 18:41

tobiasschweizer reviewed Apr 9, 2020

View reviewed changes

style(gravsearch): Improve comments.

8d4fdfb

refactor(gravsearch): Clarify code after review.

06be757

tobiasschweizer approved these changes Apr 16, 2020

View reviewed changes

benjamingeer merged commit 9313b88 into develop Apr 16, 2020

benjamingeer deleted the wip/1588_duplicates branch April 16, 2020 11:39

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fix(gravsearch): Prevent duplicate results #1626

fix(gravsearch): Prevent duplicate results #1626

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fix(gravsearch): Prevent duplicate results #1626

fix(gravsearch): Prevent duplicate results #1626

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tobiasschweizer Apr 9, 2020 •

edited

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tobiasschweizer commented Apr 9, 2020 •

edited

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