From 8de97883083bf2608a084840ab1f3e03f4244e05 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 24 Jan 2022 11:29:22 +0100
Subject: [PATCH] applied fix for avoiding ruling out the invisible (APC)
 records during the graph cleaning

---
 .../oaf/utils/GraphCleaningFunctions.java     |  16 +
 .../clean/GraphCleaningFunctionsTest.java     |  47 +
 .../dhp/oa/graph/clean/result_invisible.json  | 958 ++++++++++++++++++
 .../graph/clean/result_missing_invisible.json | 922 +++++++++++++++++
 4 files changed, 1943 insertions(+)
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
index f49a47c0a..48e35a342 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
@@ -88,6 +88,22 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 	}
 
 	public static <T extends Oaf> boolean filter(T value) {
+		if (Boolean.TRUE
+			.equals(
+				Optional
+					.ofNullable(value)
+					.map(
+						o -> Optional
+							.ofNullable(o.getDataInfo())
+							.map(
+								d -> Optional
+									.ofNullable(d.getInvisible())
+									.orElse(true))
+							.orElse(true))
+					.orElse(true))) {
+			return true;
+		}
+
 		if (value instanceof Datasource) {
 			// nothing to evaluate here
 		} else if (value instanceof Project) {
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
index 0e9efed21..ebd8cb55c 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
@@ -71,6 +71,53 @@ public class GraphCleaningFunctionsTest {
 		}
 	}
 
+	@Test
+	void testFilter_invisible_true() throws Exception {
+
+		assertNotNull(vocabularies);
+		assertNotNull(mapping);
+
+		String json = IOUtils
+			.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"));
+		Publication p_in = MAPPER.readValue(json, Publication.class);
+
+		assertTrue(p_in instanceof Result);
+		assertTrue(p_in instanceof Publication);
+
+		assertEquals(true, GraphCleaningFunctions.filter(p_in));
+	}
+
+	@Test
+	void testFilter_true_nothing_to_filter() throws Exception {
+
+		assertNotNull(vocabularies);
+		assertNotNull(mapping);
+
+		String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
+		Publication p_in = MAPPER.readValue(json, Publication.class);
+
+		assertTrue(p_in instanceof Result);
+		assertTrue(p_in instanceof Publication);
+
+		assertEquals(true, GraphCleaningFunctions.filter(p_in));
+	}
+
+	@Test
+	void testFilter_missing_invisible() throws Exception {
+
+		assertNotNull(vocabularies);
+		assertNotNull(mapping);
+
+		String json = IOUtils
+			.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"));
+		Publication p_in = MAPPER.readValue(json, Publication.class);
+
+		assertTrue(p_in instanceof Result);
+		assertTrue(p_in instanceof Publication);
+
+		assertEquals(true, GraphCleaningFunctions.filter(p_in));
+	}
+
 	@Test
 	void testCleaning() throws Exception {
 
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json
new file mode 100644
index 000000000..ffcb187c1
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json
@@ -0,0 +1,958 @@
+{
+  "author": [
+    {
+      "affiliation": [
+      ],
+      "fullname": "Brien, Tom",
+      "name": "Tom",
+      "pid": [
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferenceprovenance": "",
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:datasetarchive",
+              "classname": "sysimport:crosswalk:datasetarchive",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "ORCID12",
+            "classname": "ORCID12",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "0000-0001-9613-6639"
+        },
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferenceprovenance": "",
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:datasetarchive",
+              "classname": "sysimport:crosswalk:datasetarchive",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "ORCID12",
+            "classname": "ORCID12",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "https://orcid.org/0000-0001-9613-6639"
+        },
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferenceprovenance": "",
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:entityregistry",
+              "classname": "sysimport:crosswalk:entityregistry",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "orcid",
+            "classname": "ORCID12",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "0000-0001-9613-6639"
+        }
+      ],
+      "rank": 1,
+      "surname": "Brien"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Ade, Peter",
+      "name": "Peter",
+      "pid": [
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferenceprovenance": "",
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:datasetarchive",
+              "classname": "sysimport:crosswalk:datasetarchive",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "xyz",
+            "classname": "XYZ",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "qwerty"
+        },
+        {
+          "dataInfo": {
+            "deletedbyinference": false,
+            "inferenceprovenance": "",
+            "inferred": false,
+            "invisible": false,
+            "provenanceaction": {
+              "classid": "sysimport:crosswalk:datasetarchive",
+              "classname": "sysimport:crosswalk:datasetarchive",
+              "schemeid": "dnet:provenanceActions",
+              "schemename": "dnet:provenanceActions"
+            },
+            "trust": "0.9"
+          },
+          "qualifier": {
+            "classid": "ORCID",
+            "classname": "ORCID",
+            "schemeid": "",
+            "schemename": ""
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+          "value": "asdasd"
+        }
+      ],
+      "rank": 2,
+      "surname": "Ade"
+    },
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+      "fullname": "Barry, Peter S.",
+      "name": "Peter S.",
+      "pid": null,
+      "rank": 3,
+      "surname": "Barry"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Dunscombe, Chris J.",
+      "name": "Chris J.",
+      "pid": [
+      ],
+      "rank": 4,
+      "surname": "Dunscombe"
+    },
+    {
+      "affiliation": [
+      ],
+      "fullname": "Leadley, David R.",
+      "name": "David R.",
+      "pid": [
+      ],
+      "rank": 5,
+      "surname": "Leadley"
+    },
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+      "affiliation": [
+      ],
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+      "pid": [
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+      "rank": 6,
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+    },
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+      "name": "Maksym",
+      "pid": [
+      ],
+      "rank": 7,
+      "surname": "Myronov"
+    },
+    {
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+      ],
+      "fullname": "Parker, Evan",
+      "name": "Evan",
+      "pid": [
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+      "rank": 8,
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+      "name": "Mika",
+      "pid": [
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+      "rank": 10,
+      "surname": "Prunnila"
+    },
+    {
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+      "rank": 12,
+      "surname": "Whall"
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+      "name": "",
+      "pid": [
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+      "rank": 13,
+      "surname": ""
+    },
+    {
+      "affiliation": [
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+      "fullname": " P. D. ",
+      "name": "",
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+  "bestaccessright": null,
+  "publisher": {
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+      "value": "VIRTA"
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+  ],
+  "context": [
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+  "contributor": [
+  ],
+  "country": [
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+      "classid": "DE",
+      "classname": "DE",
+      "schemeid": "dnet:countries",
+      "schemename": "dnet:countries"
+    }
+  ],
+  "coverage": [
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+    "inferred": false,
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+      "inferred": false,
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+    "schemename": "dnet:result_typologies"
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+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
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+      "qualifier": {
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+        "classname": "",
+        "schemeid": "",
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+      "value": "infrared detectors"
+    },
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+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
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+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
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+      "qualifier": {
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+        "classname": "",
+        "schemeid": "",
+        "schemename": ""
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+      "value": "lens antennas"
+    },
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+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
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diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json
new file mode 100644
index 000000000..c0b5a959a
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