From a44f929ddff106073e6a5ec1717e0d3ac378704a Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Wed, 26 May 2021 18:02:00 +0200
Subject: [PATCH 01/34] log empty model

---
 src/main/java/eu/tib/service/ResponseService.java | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/main/java/eu/tib/service/ResponseService.java b/src/main/java/eu/tib/service/ResponseService.java
index dbe7ccb..6595cf3 100644
--- a/src/main/java/eu/tib/service/ResponseService.java
+++ b/src/main/java/eu/tib/service/ResponseService.java
@@ -22,23 +22,28 @@ public class ResponseService {
     @Autowired
     private VIVOProperties vivoProperties;
 
-    public ResponseEntity<String> buildResponse(String queryName, Map<String,String> input) {
+    public ResponseEntity<String> buildResponse(String queryName, Map<String, String> input) {
 
         log.info("Starting pipeline for " + queryName);
         GeneratePipeline pipeline = new GeneratePipeline();
         Model result = pipeline.run(queryName, input);
         log.info("Finished pipeline for " + queryName);
 
-        if (vivoProperties.isValid()) {
+        String bodyTxt = "";
+        if (result.isEmpty()) {
+            log.info("No data was generated, Model is empty.");
+            bodyTxt = "{\"status\":\"No data was generated.\"}";
+        } else if (vivoProperties.isValid()) {
             log.info("Found VIVO properties");
             vivoExport.exportData(result, vivoProperties);
-            return ResponseEntity.status(HttpStatus.OK).body("{\"status\":\"SPARQL update accepted.\"}");
+            bodyTxt = "{\"status\":\"SPARQL update accepted.\"}";
         } else {
             log.info("Returning JSON-LD");
             StringWriter stringWriter = new StringWriter();
             result.write(stringWriter, "JSON-LD");
-            String dataJson = stringWriter.toString();
-            return ResponseEntity.status(HttpStatus.OK).body(dataJson);
+            bodyTxt = stringWriter.toString();
         }
+
+        return ResponseEntity.status(HttpStatus.OK).body(bodyTxt);
     }
 }

From cc556ec6e0bbdda26f0eaf69381c7cdc6843637b Mon Sep 17 00:00:00 2001
From: smierz <sandra.mierz@tib.eu>
Date: Wed, 26 May 2021 21:23:15 +0200
Subject: [PATCH 02/34] handle empty model

---
 .../java/eu/tib/service/ResponseService.java  | 24 +++++++++++--------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/src/main/java/eu/tib/service/ResponseService.java b/src/main/java/eu/tib/service/ResponseService.java
index 6595cf3..d879471 100644
--- a/src/main/java/eu/tib/service/ResponseService.java
+++ b/src/main/java/eu/tib/service/ResponseService.java
@@ -29,21 +29,25 @@ public ResponseEntity<String> buildResponse(String queryName, Map<String, String
         Model result = pipeline.run(queryName, input);
         log.info("Finished pipeline for " + queryName);
 
-        String bodyTxt = "";
-        if (result.isEmpty()) {
-            log.info("No data was generated, Model is empty.");
-            bodyTxt = "{\"status\":\"No data was generated.\"}";
-        } else if (vivoProperties.isValid()) {
+        if (vivoProperties.isValid()) {
             log.info("Found VIVO properties");
-            vivoExport.exportData(result, vivoProperties);
-            bodyTxt = "{\"status\":\"SPARQL update accepted.\"}";
+
+            String status = "{\"status\":\"%s\"}";
+            if (result.isEmpty()) {
+                log.info("No data was generated, Model is empty.");
+                status = String.format(status, "No data was generated.");
+            } else {
+                vivoExport.exportData(result, vivoProperties);
+                status = String.format(status, "SPARQL update accepted.");
+            }
+            return ResponseEntity.status(HttpStatus.OK).body(status);
+
         } else {
             log.info("Returning JSON-LD");
             StringWriter stringWriter = new StringWriter();
             result.write(stringWriter, "JSON-LD");
-            bodyTxt = stringWriter.toString();
+            String dataJSON = stringWriter.toString();
+            return ResponseEntity.status(HttpStatus.OK).body(dataJSON);
         }
-
-        return ResponseEntity.status(HttpStatus.OK).body(bodyTxt);
     }
 }

From bfc2a708d57b38e31b370c6f3fb820225d6e48fa Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 27 May 2021 10:56:48 +0200
Subject: [PATCH 03/34] simplify ROR mapping

---
 .../sparqlg/objects/organization.rqg          | 104 ++++++++++++++++++
 .../ror/orga2children/orga2children.rqg       |  16 +--
 .../orga2children/sparql-generate-conf.json   |  32 +-----
 .../sparqlg/ror/organization/orga_mapping.rqg |  36 ++++++
 .../sparqlg/ror/organization/orga_source.rqg  |   6 +-
 .../organization/queryset/orga_acronym.rqg    |   8 --
 .../organization/queryset/orga_address.rqg    |  31 ------
 .../ror/organization/queryset/orga_email.rqg  |  20 ----
 .../queryset/orga_established.rqg             |  20 ----
 .../ror/organization/queryset/orga_geo.rqg    |  24 ----
 .../ror/organization/queryset/orga_labels.rqg |  15 ---
 .../organization/queryset/orga_website.rqg    |  23 ----
 .../organization/queryset/organization.rqg    |  43 --------
 .../organization/sparql-generate-conf.json    |  32 +-----
 14 files changed, 157 insertions(+), 253 deletions(-)
 create mode 100644 src/main/resources/sparqlg/objects/organization.rqg
 create mode 100644 src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/orga_acronym.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/orga_address.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/orga_email.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/orga_established.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/orga_geo.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/orga_labels.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/orga_website.rqg
 delete mode 100644 src/main/resources/sparqlg/ror/organization/queryset/organization.rqg

diff --git a/src/main/resources/sparqlg/objects/organization.rqg b/src/main/resources/sparqlg/objects/organization.rqg
new file mode 100644
index 0000000..886bb2b
--- /dev/null
+++ b/src/main/resources/sparqlg/objects/organization.rqg
@@ -0,0 +1,104 @@
+PREFIX iter: <http://w3id.org/sparql-generate/iter/>
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX vivo: <http://vivoweb.org/ontology/core#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
+
+
+GENERATE <organization>(?parent_id, ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) {
+
+### id, name : basic attributes of an organization
+    <{?id}> a foaf:Organization ;
+        rdfs:label ?name .
+
+
+### parent : TRIPLES TO ADD SUPER-ORGANISATION
+  GENERATE{
+     <{?parent_id}> obo:BFO_0000051 <{?id}> .
+  }
+  WHERE {
+     FILTER( BOUND(?parent_id) ).
+  } .
+
+### established : TRIPLES TO ADD THE DATE THE ORGANIZATION WAS ESTABLISHED
+  GENERATE{
+    <{?id}> vivo:dateTimeInterval <{?id}-dti> .
+
+    <{?id}-dti> a vivo:DateTimeInterval ;
+        vivo:start <{?id}-dtv> .
+
+    <{?id}-dtv> a vivo:DateTimeValue ;
+        vivo:dateTime ?established_dtv ;
+        vivo:dateTimePrecision vivo:yearPrecision .
+  }
+  WHERE {
+     FILTER( BOUND(?established_dtv) ).
+  } .
+
+
+### vcard : TRIPLES TO ADD VCARD
+  GENERATE{
+    <{?id}> obo:ARG_2000028 <{?id}-vcard> .
+
+    <{?id}-vcard> a vcard:Individual ;
+        obo:ARG_2000029 <{?id}> .
+  }
+  WHERE {
+     FILTER( BOUND(?email) || BOUND(?website) || BOUND(?city) || BOUND(?state) || BOUND(?country) || (BOUND(?lat) && BOUND(?lng))).
+  } .
+
+
+### email : TRIPLES TO ADD EMAIL
+  GENERATE{
+    <{?id}-vcard> vcard:hasEmail <{?id}-vcard-email> .
+
+    <{?id}-vcard-email> a vcard:Email ;
+        vcard:email ?email .
+  }
+  WHERE {
+     FILTER( BOUND(?email) ).
+  } .
+
+
+### website : TRIPLES TO ADD WEBSITE
+  GENERATE{
+    <{?id}-vcard> vcard:hasURL <{?id}-vcard-url> .
+
+    <{?id}-vcard-url> a vcard:URL ;
+      vivo:rank 1 ;
+      vcard:url "{?website}"^^xsd:anyURI .
+  }
+  WHERE {
+     FILTER( BOUND(?website) ).
+  } .
+
+
+### address (city, state, country) : TRIPLES TO ADD ADDRESS DATA
+  GENERATE{
+     <{?id}-vcard> vcard:hasAddress <{?id}-vcard-address> .
+
+    <{?id}-vcard-address> a vcard:Address ;
+      vcard:locality ?city ;
+      vcard:region ?state ;
+      vcard:country ?country .
+  }
+  WHERE {
+     FILTER( BOUND(?city) || BOUND(?state) || BOUND(?country) ).
+  } .
+
+
+### geo (lat,lng) : TRIPLES TO ADD LATITUDE & LONGITUDE
+  GENERATE{
+    <{?id}-vcard> vcard:hasGeo <{?id}-vcard-geo> .
+
+    <{?id}-vcard-geo> a vcard:Geo ;
+        vcard:geo "geo:{?lat},{?lng}" .
+  }
+  WHERE {
+     FILTER( BOUND(?lat) && BOUND(?lng)  ).
+  } .
+
+}
diff --git a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
index 8cc4bf7..3feb5a9 100644
--- a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
+++ b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
@@ -1,17 +1,14 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
 
-GENERATE <orga2children>(?ror) {
+GENERATE <orga2children>(?parent_ror, ?ror) {
 
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/organization.rqg>( ?orga ) .
+  ### use the organization mapping already defined in /ror/organization/orga_mapping.rqg
+  GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?parent_ror, ?orga ) .
 
+  ### call this query recursively for all children
   GENERATE {
-    <{?id}> obo:BFO_0000051 <{?child_id}> .
-
-    GENERATE <https://projects.tib.eu/tapir/ror/orga2children/orga2children.rqg>(?child_ror ) .
+    GENERATE <https://projects.tib.eu/tapir/ror/orga2children/orga2children.rqg>(?ror, ?child_ror ) .
   }
   ITERATOR iter:JSONPath(?orga, '$.relationships[*]') AS ?relationships
   WHERE {
@@ -27,6 +24,3 @@ GENERATE <orga2children>(?ror) {
 
 }
 SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga
-WHERE {
-    BIND(REPLACE(fun:JSONPath(?orga, '$.id' ), "https://ror.org/" , "" ) AS ?id)
-}
diff --git a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
index 9bc8d5d..c0665d5 100644
--- a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
@@ -7,36 +7,12 @@
       "path": "orga2children.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/organization.rqg",
-      "path": "../organization/queryset/organization.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg",
+      "path": "../organization/orga_mapping.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_email.rqg",
-      "path": "../organization/queryset/orga_email.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_website.rqg",
-      "path": "../organization/queryset/orga_website.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_geo.rqg",
-      "path": "../organization/queryset/orga_geo.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_labels.rqg",
-      "path": "../organization/queryset/orga_labels.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_established.rqg",
-      "path": "../organization/queryset/orga_established.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_acronym.rqg",
-      "path": "../organization/queryset/orga_acronym.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_address.rqg",
-      "path": "../organization/queryset/orga_address.rqg"
+      "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",
+      "path": "../../objects/organization.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg b/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
new file mode 100644
index 0000000..fd2b3c4
--- /dev/null
+++ b/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
@@ -0,0 +1,36 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+GENERATE <orga_mapping>(?parent_ror, ?orga) {
+
+    ## fill in blanks in organization definition in vivo ontology
+    GENERATE <https://projects.tib.eu/tapir/objects/organization.rqg>(?parent_id, ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
+
+}
+WHERE {
+    ### basic properties of organization
+    BIND(REPLACE(fun:JSONPath(?orga, '$.id' ), "https://ror.org/" , "" ) AS ?id)
+    BIND(fun:JSONPath(?orga, '$.name' ) AS ?name)
+
+    ### super organization
+    BIND(REPLACE(?parent_ror, "https://ror.org/" , "" ) AS ?parent_id)
+
+    ### established
+    BIND(fun:JSONPath(?orga, '$.established' ) AS ?established)
+    BIND(xsd:dateTime(CONCAT(STR(?established), "-01-01T00:00:00"))  AS ?established_dtv)
+
+    ### email
+    BIND(fun:JSONPath(?orga, '$.email_address' ) AS ?email)
+
+    ### website
+    BIND(fun:JSONPath(?orga, '$.links[0]' ) AS ?website)
+
+    ### address (city, state, country, lat, lng)
+    BIND(fun:JSONPath(?orga, '$.country.country_name' ) AS ?country)
+
+    BIND(fun:JSONPath(?orga, '$.addresses[0]' ) AS ?address)
+    BIND(fun:JSONPath(?address, '$.city' ) AS ?city)
+    BIND(fun:JSONPath(?address, '$.geonames_city.geonames_admin1.name' ) AS ?state)
+    BIND(xsd:decimal(fun:JSONPath(?address, '$.lat' )) AS ?lat)
+    BIND(xsd:decimal(fun:JSONPath(?address, '$.lng' )) AS ?lng)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/orga_source.rqg b/src/main/resources/sparqlg/ror/organization/orga_source.rqg
index 04baa6f..3cb00aa 100644
--- a/src/main/resources/sparqlg/ror/organization/orga_source.rqg
+++ b/src/main/resources/sparqlg/ror/organization/orga_source.rqg
@@ -1,4 +1,6 @@
+### query data about organization from ROR
+
 GENERATE <orga_source>(?ror) {
-    GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/organization.rqg>( ?orga ) .
+    GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?undef, ?orga ) .
 }
-SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga
+SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/orga_acronym.rqg b/src/main/resources/sparqlg/ror/organization/queryset/orga_acronym.rqg
deleted file mode 100644
index c5b9f0e..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/orga_acronym.rqg
+++ /dev/null
@@ -1,8 +0,0 @@
-PREFIX iter: <http://w3id.org/sparql-generate/iter/>
-PREFIX vivo: <http://vivoweb.org/ontology/core#>
-
-### acronyms: SUB-QUERY TO ADD ABBREVIATION
-GENERATE <orga_acronym> (?id, ?orga) {
-    <{?id}> vivo:abbreviation ?acronym .
-}
-ITERATOR iter:JSONPath(?orga, '$.acronyms[*]') AS ?acronym
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/orga_address.rqg b/src/main/resources/sparqlg/ror/organization/queryset/orga_address.rqg
deleted file mode 100644
index e18019e..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/orga_address.rqg
+++ /dev/null
@@ -1,31 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-
-### address (city, state, country) : SUB-QUERY TO ADD ADDRESS DATA
-GENERATE <orga_address> (?id, ?orga) {
-  <{?id}> obo:ARG_2000028 <{?id}-vcard> .
-
-  <{?id}-vcard> a vcard:Individual ;
-      obo:ARG_2000029 <{?id}> .
-
-  <{?id}-vcard> vcard:hasAddress <{?id}-vcard-address> .
-
-  <{?id}-vcard-address> a vcard:Address ;
-      vcard:locality ?city_with_tag ;
-      vcard:region ?state_with_tag ;
-      vcard:country ?country_with_tag .
-}
-WHERE {
-  BIND(fun:JSONPath(?orga, '$.country.country_name' ) AS ?country)
-  BIND(STRLANG(?country, "en") AS ?country_with_tag)
-
-  BIND(fun:JSONPath(?orga, '$.addresses[0]' ) AS ?address)
-  BIND(fun:JSONPath(?address, '$.city' ) AS ?city)
-  BIND(STRLANG(?city, "en") AS ?city_with_tag)
-
-  BIND(fun:JSONPath(?address, '$.geonames_city.geonames_admin1.name' ) AS ?state)
-  BIND(STRLANG(?state, "en") AS ?state_with_tag)
-
-  FILTER( BOUND(?city) || BOUND(?city) || BOUND(?state) )
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/orga_email.rqg b/src/main/resources/sparqlg/ror/organization/queryset/orga_email.rqg
deleted file mode 100644
index 49601b6..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/orga_email.rqg
+++ /dev/null
@@ -1,20 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-
-### email_address : SUB-QUERY TO ADD EMAIL
-GENERATE <orga_email> (?id, ?orga) {
-    <{?id}> obo:ARG_2000028 <{?id}-vcard> .
-
-    <{?id}-vcard> a vcard:Individual ;
-        obo:ARG_2000029 <{?id}> .
-
-    <{?id}-vcard> vcard:hasEmail <{?id}-vcard-email> .
-
-    <{?id}-vcard-email> a vcard:Email ;
-        vcard:email ?email .
-}
-  WHERE {
-    BIND(fun:JSONPath(?orga, '$.email_address' ) AS ?email)
-    FILTER( BOUND(?email) )
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/orga_established.rqg b/src/main/resources/sparqlg/ror/organization/queryset/orga_established.rqg
deleted file mode 100644
index f380b94..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/orga_established.rqg
+++ /dev/null
@@ -1,20 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX vivo: <http://vivoweb.org/ontology/core#>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-
-### established : SUB-QUERY TO ADD THE DATE THE ORGANIZATION WAS ESTABLISHED
-GENERATE <orga_established> (?id, ?orga) {
-    <{?id}> vivo:dateTimeInterval <{?id}-dti> .
-
-    <{?id}-dti> a vivo:DateTimeInterval ;
-        vivo:start <{?id}-dtv> .
-
-    <{?id}-dtv> a vivo:DateTimeValue ;
-        vivo:dateTime ?established_dtv ;
-        vivo:dateTimePrecision vivo:yearPrecision .
-}
-WHERE {
-    BIND(fun:JSONPath(?orga, '$.established' ) AS ?established)
-    BIND(xsd:dateTime(CONCAT(STR(?established), "-01-01T00:00:00"))  AS ?established_dtv)
-    FILTER( BOUND(?established) )
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/orga_geo.rqg b/src/main/resources/sparqlg/ror/organization/queryset/orga_geo.rqg
deleted file mode 100644
index b110253..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/orga_geo.rqg
+++ /dev/null
@@ -1,24 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-
-### address (lat,lng) : SUB-QUERY TO ADD LATITUDE & LONGITUDE
-GENERATE  <orga_geo> (?id, ?orga) {
-  <{?id}> obo:ARG_2000028 <{?id}-vcard> .
-
-  <{?id}-vcard> a vcard:Individual ;
-      obo:ARG_2000029 <{?id}> .
-
-  <{?id}-vcard> vcard:hasGeo <{?id}-vcard-geo> .
-
-  <{?id}-vcard-geo> a vcard:Geo ;
-      vcard:geo "geo:{?lat},{?lng}" .
-}
-WHERE {
-  BIND(fun:JSONPath(?orga, '$.addresses[0]' ) AS ?address)
-  BIND(xsd:decimal(fun:JSONPath(?address, '$.lat' )) AS ?lat)
-  BIND(xsd:decimal(fun:JSONPath(?address, '$.lng' )) AS ?lng)
-
-  FILTER( BOUND(?lat) && BOUND(?lng) )
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/orga_labels.rqg b/src/main/resources/sparqlg/ror/organization/queryset/orga_labels.rqg
deleted file mode 100644
index 7203740..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/orga_labels.rqg
+++ /dev/null
@@ -1,15 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX iter: <http://w3id.org/sparql-generate/iter/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-### labels: SUB-QUERY TO ADD NAMES IN DIFFERENT LANGUAGES
-GENERATE  <orga_labels> (?id, ?orga) {
-    <{?id}> rdfs:label ?label_with_tag .
-}
-ITERATOR iter:JSONPath(?orga, '$.labels[*]') AS ?labels
-WHERE {
-    # alternative labels in different languages
-    BIND(fun:JSONPath(?labels, '$.label' ) AS ?label)
-    BIND(fun:JSONPath(?labels, '$.iso639' ) AS ?iso639)
-    BIND(STRLANG(?label, ?iso639) AS ?label_with_tag)
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/orga_website.rqg b/src/main/resources/sparqlg/ror/organization/queryset/orga_website.rqg
deleted file mode 100644
index d398602..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/orga_website.rqg
+++ /dev/null
@@ -1,23 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-PREFIX vivo: <http://vivoweb.org/ontology/core#>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-
-### links : SUB-QUERY TO ADD WEBSITE
-GENERATE <orga_website> (?id, ?orga) {
-  <{?id}> obo:ARG_2000028 <{?id}-vcard> .
-
-  <{?id}-vcard> a vcard:Individual ;
-      obo:ARG_2000029 <{?id}> .
-
-  <{?id}-vcard> vcard:hasURL <{?id}-vcard-url> .
-
-  <{?id}-vcard-url> a vcard:URL ;
-      vivo:rank 1 ;
-      vcard:url "{?url}"^^xsd:anyURI .
-}
-WHERE {
-  BIND(fun:JSONPath(?orga, '$.links[0]' ) AS ?url)
-  FILTER( BOUND(?url) )
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/queryset/organization.rqg b/src/main/resources/sparqlg/ror/organization/queryset/organization.rqg
deleted file mode 100644
index 1f5c02d..0000000
--- a/src/main/resources/sparqlg/ror/organization/queryset/organization.rqg
+++ /dev/null
@@ -1,43 +0,0 @@
-PREFIX iter: <http://w3id.org/sparql-generate/iter/>
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-PREFIX vivo: <http://vivoweb.org/ontology/core#>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-
-
-GENERATE <organization>(?orga) {
-
-    <{?id}> a foaf:Organization ;
-        rdfs:label ?name_with_tag .
-
-### labels: SUB-QUERY TO ADD NAMES IN DIFFERENT LANGUAGES
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/orga_labels.rqg>( ?id, ?orga ) .
-
-### acronyms: SUB-QUERY TO ADD ABBREVIATION
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/orga_acronym.rqg>( ?id, ?orga ) .
-
-### established : SUB-QUERY TO ADD THE DATE THE ORGANIZATION WAS ESTABLISHED
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/orga_established.rqg>( ?id, ?orga ) .
-
-### email_address : SUB-QUERY TO ADD EMAIL
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/orga_email.rqg>( ?id, ?orga ) .
-
-### links : SUB-QUERY TO ADD WEBSITE
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/orga_website.rqg>( ?id, ?orga ) .
-
-### address (city, state, country) : SUB-QUERY TO ADD ADDRESS DATA
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/orga_address.rqg>( ?id, ?orga ) .
-
-### geo (lat,lng) : SUB-QUERY TO ADD LATITUDE & LONGITUDE
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/queryset/orga_geo.rqg>( ?id, ?orga ) .
-
-}
-WHERE {
-    # basic properties of organization
-    BIND(REPLACE(fun:JSONPath(?orga, '$.id' ), "https://ror.org/" , "" ) AS ?id)
-    BIND(fun:JSONPath(?orga, '$.name' ) AS ?name)
-    BIND(STRLANG(?name, "en") AS ?name_with_tag)
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
index 1c3af82..0d32495 100644
--- a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
@@ -3,36 +3,12 @@
   "query": "orga_source.rqg",
   "namedqueries": [
     {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/organization.rqg",
-      "path": "queryset/organization.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg",
+      "path": "orga_mapping.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_email.rqg",
-      "path": "queryset/orga_email.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_website.rqg",
-      "path": "queryset/orga_website.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_geo.rqg",
-      "path": "queryset/orga_geo.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_labels.rqg",
-      "path": "queryset/orga_labels.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_established.rqg",
-      "path": "queryset/orga_established.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_acronym.rqg",
-      "path": "queryset/orga_acronym.rqg"
-    },
-    {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/queryset/orga_address.rqg",
-      "path": "queryset/orga_address.rqg"
+      "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",
+      "path": "../../objects/organization.rqg"
     }
   ]
 }
\ No newline at end of file

From 2f012c4d31cfc1ac1d4bfbd7bfb212a301b19bee Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 27 May 2021 19:21:05 +0200
Subject: [PATCH 04/34] extract orga_id only in one place

---
 .../sparqlg/objects/organization.rqg          | 15 ++++-----------
 .../resources/sparqlg/ror/mapping/orga_id.rqg |  5 +++++
 .../orga_mapping.rqg                          |  9 +++------
 .../ror/orga2children/orga2children.rqg       | 19 ++++++++++++-------
 .../orga2children/sparql-generate-conf.json   |  8 ++++++--
 .../sparqlg/ror/organization/orga_source.rqg  |  2 +-
 .../organization/sparql-generate-conf.json    |  8 ++++++--
 7 files changed, 37 insertions(+), 29 deletions(-)
 create mode 100644 src/main/resources/sparqlg/ror/mapping/orga_id.rqg
 rename src/main/resources/sparqlg/ror/{organization => mapping}/orga_mapping.rqg (76%)

diff --git a/src/main/resources/sparqlg/objects/organization.rqg b/src/main/resources/sparqlg/objects/organization.rqg
index 886bb2b..732d6dd 100644
--- a/src/main/resources/sparqlg/objects/organization.rqg
+++ b/src/main/resources/sparqlg/objects/organization.rqg
@@ -1,5 +1,3 @@
-PREFIX iter: <http://w3id.org/sparql-generate/iter/>
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX foaf: <http://xmlns.com/foaf/0.1/>
 PREFIX vivo: <http://vivoweb.org/ontology/core#>
@@ -8,21 +6,13 @@ PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
 
 
-GENERATE <organization>(?parent_id, ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) {
+GENERATE <organization>(?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) {
 
 ### id, name : basic attributes of an organization
     <{?id}> a foaf:Organization ;
         rdfs:label ?name .
 
 
-### parent : TRIPLES TO ADD SUPER-ORGANISATION
-  GENERATE{
-     <{?parent_id}> obo:BFO_0000051 <{?id}> .
-  }
-  WHERE {
-     FILTER( BOUND(?parent_id) ).
-  } .
-
 ### established : TRIPLES TO ADD THE DATE THE ORGANIZATION WAS ESTABLISHED
   GENERATE{
     <{?id}> vivo:dateTimeInterval <{?id}-dti> .
@@ -102,3 +92,6 @@ GENERATE <organization>(?parent_id, ?id, ?name, ?established_dtv, ?email, ?websi
   } .
 
 }
+WHERE {
+  FILTER( BOUND(?id) ).
+}
diff --git a/src/main/resources/sparqlg/ror/mapping/orga_id.rqg b/src/main/resources/sparqlg/ror/mapping/orga_id.rqg
new file mode 100644
index 0000000..09a1ca9
--- /dev/null
+++ b/src/main/resources/sparqlg/ror/mapping/orga_id.rqg
@@ -0,0 +1,5 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+FUNCTION <func>(?ror_data) {
+    REPLACE(fun:JSONPath(?ror_data, '$.id' ), "https://ror.org/" , "" )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg b/src/main/resources/sparqlg/ror/mapping/orga_mapping.rqg
similarity index 76%
rename from src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
rename to src/main/resources/sparqlg/ror/mapping/orga_mapping.rqg
index fd2b3c4..8a60f51 100644
--- a/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
+++ b/src/main/resources/sparqlg/ror/mapping/orga_mapping.rqg
@@ -1,20 +1,17 @@
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 
-GENERATE <orga_mapping>(?parent_ror, ?orga) {
+GENERATE <orga_mapping>(?orga) {
 
     ## fill in blanks in organization definition in vivo ontology
-    GENERATE <https://projects.tib.eu/tapir/objects/organization.rqg>(?parent_id, ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
+    GENERATE <https://projects.tib.eu/tapir/objects/organization.rqg>( ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
 
 }
 WHERE {
     ### basic properties of organization
-    BIND(REPLACE(fun:JSONPath(?orga, '$.id' ), "https://ror.org/" , "" ) AS ?id)
+    BIND(<https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg>(?orga) AS ?id)
     BIND(fun:JSONPath(?orga, '$.name' ) AS ?name)
 
-    ### super organization
-    BIND(REPLACE(?parent_ror, "https://ror.org/" , "" ) AS ?parent_id)
-
     ### established
     BIND(fun:JSONPath(?orga, '$.established' ) AS ?established)
     BIND(xsd:dateTime(CONCAT(STR(?established), "-01-01T00:00:00"))  AS ?established_dtv)
diff --git a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
index 3feb5a9..02b953e 100644
--- a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
+++ b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
@@ -1,16 +1,18 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
 
-GENERATE <orga2children>(?parent_ror, ?ror) {
+GENERATE <orga2children>(?parent_id, ?ror) {
 
   ### use the organization mapping already defined in /ror/organization/orga_mapping.rqg
-  GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?parent_ror, ?orga ) .
+  GENERATE <https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg>( ?orga_data ) .
+
+  ### connection organization & sub-organization
+  <{?parent_id}> obo:BFO_0000051 <{?id}> .
 
   ### call this query recursively for all children
-  GENERATE {
-    GENERATE <https://projects.tib.eu/tapir/ror/orga2children/orga2children.rqg>(?ror, ?child_ror ) .
-  }
-  ITERATOR iter:JSONPath(?orga, '$.relationships[*]') AS ?relationships
+  GENERATE <https://projects.tib.eu/tapir/ror/orga2children/orga2children.rqg>(?id, ?child_ror )
+  ITERATOR iter:JSONPath(?orga_data, '$.relationships[*]') AS ?relationships
   WHERE {
     BIND(fun:JSONPath(?relationships, '$.label' ) AS ?rel_label)
     BIND(fun:JSONPath(?relationships, '$.type' ) AS ?rel_type)
@@ -23,4 +25,7 @@ GENERATE <orga2children>(?parent_ror, ?ror) {
   }  .
 
 }
-SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga
+SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga_data
+WHERE{
+    BIND(<https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg>(?orga_data) AS ?id)
+}
diff --git a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
index c0665d5..a947a6a 100644
--- a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
@@ -7,8 +7,12 @@
       "path": "orga2children.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg",
-      "path": "../organization/orga_mapping.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg",
+      "path": "../mapping/orga_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg",
+      "path": "../mapping/orga_id.rqg"
     },
     {
       "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",
diff --git a/src/main/resources/sparqlg/ror/organization/orga_source.rqg b/src/main/resources/sparqlg/ror/organization/orga_source.rqg
index 3cb00aa..72ac045 100644
--- a/src/main/resources/sparqlg/ror/organization/orga_source.rqg
+++ b/src/main/resources/sparqlg/ror/organization/orga_source.rqg
@@ -1,6 +1,6 @@
 ### query data about organization from ROR
 
 GENERATE <orga_source>(?ror) {
-    GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?undef, ?orga ) .
+    GENERATE <https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg>( ?orga ) .
 }
 SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
index 0d32495..35a6c2a 100644
--- a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
@@ -3,8 +3,12 @@
   "query": "orga_source.rqg",
   "namedqueries": [
     {
-      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg",
-      "path": "orga_mapping.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg",
+      "path": "../mapping/orga_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg",
+      "path": "../mapping/orga_id.rqg"
     },
     {
       "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",

From 159900af7cc482606ff13ee41a0485de3fb754ac Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 3 Jun 2021 10:48:03 +0200
Subject: [PATCH 05/34] clean up ROR import

---
 .../sparqlg/ror/orga2children/orga2children.rqg  |  6 +++---
 .../ror/orga2children/sparql-generate-conf.json  | 10 +++++-----
 .../ror/{mapping => organization}/orga_id.rqg    |  0
 .../{mapping => organization}/orga_mapping.rqg   | 16 ++++++++--------
 .../sparqlg/ror/organization/orga_source.rqg     |  2 +-
 .../ror/organization/sparql-generate-conf.json   | 10 +++++-----
 .../{objects => vivo-rdf}/organization.rqg       |  0
 7 files changed, 22 insertions(+), 22 deletions(-)
 rename src/main/resources/sparqlg/ror/{mapping => organization}/orga_id.rqg (100%)
 rename src/main/resources/sparqlg/ror/{mapping => organization}/orga_mapping.rqg (62%)
 rename src/main/resources/sparqlg/{objects => vivo-rdf}/organization.rqg (100%)

diff --git a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
index 02b953e..d7e9b34 100644
--- a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
+++ b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
@@ -4,8 +4,8 @@ PREFIX obo: <http://purl.obolibrary.org/obo/>
 
 GENERATE <orga2children>(?parent_id, ?ror) {
 
-  ### use the organization mapping already defined in /ror/organization/orga_mapping.rqg
-  GENERATE <https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg>( ?orga_data ) .
+  ### use the organization mapping already defined in orga_mapping.rqg
+  GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?orga_data ) .
 
   ### connection organization & sub-organization
   <{?parent_id}> obo:BFO_0000051 <{?id}> .
@@ -27,5 +27,5 @@ GENERATE <orga2children>(?parent_id, ?ror) {
 }
 SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga_data
 WHERE{
-    BIND(<https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg>(?orga_data) AS ?id)
+    BIND(<https://projects.tib.eu/tapir/ror/organization/orga_id.rqg>(?orga_data) AS ?id)
 }
diff --git a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
index a947a6a..2e32d28 100644
--- a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
@@ -7,16 +7,16 @@
       "path": "orga2children.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg",
-      "path": "../mapping/orga_mapping.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg",
+      "path": "../organization/orga_mapping.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg",
-      "path": "../mapping/orga_id.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_id.rqg",
+      "path": "../organization/orga_id.rqg"
     },
     {
       "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",
-      "path": "../../objects/organization.rqg"
+      "path": "../../vivo-rdf/organization.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/mapping/orga_id.rqg b/src/main/resources/sparqlg/ror/organization/orga_id.rqg
similarity index 100%
rename from src/main/resources/sparqlg/ror/mapping/orga_id.rqg
rename to src/main/resources/sparqlg/ror/organization/orga_id.rqg
diff --git a/src/main/resources/sparqlg/ror/mapping/orga_mapping.rqg b/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
similarity index 62%
rename from src/main/resources/sparqlg/ror/mapping/orga_mapping.rqg
rename to src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
index 8a60f51..57c1787 100644
--- a/src/main/resources/sparqlg/ror/mapping/orga_mapping.rqg
+++ b/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
@@ -1,7 +1,7 @@
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 
-GENERATE <orga_mapping>(?orga) {
+GENERATE <orga_mapping>(?ror_data) {
 
     ## fill in blanks in organization definition in vivo ontology
     GENERATE <https://projects.tib.eu/tapir/objects/organization.rqg>( ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
@@ -9,23 +9,23 @@ GENERATE <orga_mapping>(?orga) {
 }
 WHERE {
     ### basic properties of organization
-    BIND(<https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg>(?orga) AS ?id)
-    BIND(fun:JSONPath(?orga, '$.name' ) AS ?name)
+    BIND(<https://projects.tib.eu/tapir/ror/organization/orga_id.rqg>(?ror_data) AS ?id)
+    BIND(fun:JSONPath(?ror_data, '$.name' ) AS ?name)
 
     ### established
-    BIND(fun:JSONPath(?orga, '$.established' ) AS ?established)
+    BIND(fun:JSONPath(?ror_data, '$.established' ) AS ?established)
     BIND(xsd:dateTime(CONCAT(STR(?established), "-01-01T00:00:00"))  AS ?established_dtv)
 
     ### email
-    BIND(fun:JSONPath(?orga, '$.email_address' ) AS ?email)
+    BIND(fun:JSONPath(?ror_data, '$.email_address' ) AS ?email)
 
     ### website
-    BIND(fun:JSONPath(?orga, '$.links[0]' ) AS ?website)
+    BIND(fun:JSONPath(?ror_data, '$.links[0]' ) AS ?website)
 
     ### address (city, state, country, lat, lng)
-    BIND(fun:JSONPath(?orga, '$.country.country_name' ) AS ?country)
+    BIND(fun:JSONPath(?ror_data, '$.country.country_name' ) AS ?country)
 
-    BIND(fun:JSONPath(?orga, '$.addresses[0]' ) AS ?address)
+    BIND(fun:JSONPath(?ror_data, '$.addresses[0]' ) AS ?address)
     BIND(fun:JSONPath(?address, '$.city' ) AS ?city)
     BIND(fun:JSONPath(?address, '$.geonames_city.geonames_admin1.name' ) AS ?state)
     BIND(xsd:decimal(fun:JSONPath(?address, '$.lat' )) AS ?lat)
diff --git a/src/main/resources/sparqlg/ror/organization/orga_source.rqg b/src/main/resources/sparqlg/ror/organization/orga_source.rqg
index 72ac045..cb82721 100644
--- a/src/main/resources/sparqlg/ror/organization/orga_source.rqg
+++ b/src/main/resources/sparqlg/ror/organization/orga_source.rqg
@@ -1,6 +1,6 @@
 ### query data about organization from ROR
 
 GENERATE <orga_source>(?ror) {
-    GENERATE <https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg>( ?orga ) .
+    GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?orga ) .
 }
 SOURCE <https://api.ror.org/organizations/{?ror}> AS ?orga
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
index 35a6c2a..b4bb786 100644
--- a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
@@ -3,16 +3,16 @@
   "query": "orga_source.rqg",
   "namedqueries": [
     {
-      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_mapping.rqg",
-      "path": "../mapping/orga_mapping.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg",
+      "path": "orga_mapping.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/ror/mapping/orga_id.rqg",
-      "path": "../mapping/orga_id.rqg"
+      "uri": "https://projects.tib.eu/tapir/ror/organization/orga_id.rqg",
+      "path": "orga_id.rqg"
     },
     {
       "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",
-      "path": "../../objects/organization.rqg"
+      "path": "../../vivo-rdf/organization.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/objects/organization.rqg b/src/main/resources/sparqlg/vivo-rdf/organization.rqg
similarity index 100%
rename from src/main/resources/sparqlg/objects/organization.rqg
rename to src/main/resources/sparqlg/vivo-rdf/organization.rqg

From 13f7ea7474331433fb7c35d954e2da8424fb991c Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 3 Jun 2021 10:56:49 +0200
Subject: [PATCH 06/34] query single person from ORCID

---
 .../eu/tib/controller/OrcidController.java    | 31 ++++++++++++++++---
 .../sparqlg/orcid/person/person_id.rqg        |  5 +++
 .../sparqlg/orcid/person/person_mapping.rqg   | 17 ++++++++++
 .../sparqlg/orcid/person/person_source.rqg    | 15 +++++++++
 .../orcid/person/sparql-generate-conf.json    | 18 +++++++++++
 .../resources/sparqlg/vivo-rdf/person.rqg     |  9 ++++++
 6 files changed, 90 insertions(+), 5 deletions(-)
 create mode 100644 src/main/resources/sparqlg/orcid/person/person_id.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/person/person_mapping.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/person/person_source.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
 create mode 100644 src/main/resources/sparqlg/vivo-rdf/person.rqg

diff --git a/src/main/java/eu/tib/controller/OrcidController.java b/src/main/java/eu/tib/controller/OrcidController.java
index edfc149..fc1bde3 100644
--- a/src/main/java/eu/tib/controller/OrcidController.java
+++ b/src/main/java/eu/tib/controller/OrcidController.java
@@ -27,18 +27,39 @@ public class OrcidController {
     @Autowired
     private ResponseService responseService;
 
+    @PostMapping(value = "/getPerson", produces = "application/json")
+    public ResponseEntity<String> getPerson(
+            @Valid @Pattern(regexp = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{4}")
+            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
+            @RequestParam String orcid) {
+
+        final String id = "sparqlg/orcid/person";
+        log.info("Incoming Request for " + id + " with orcid: " + orcid);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        String orcid_id = orcid.replaceFirst("https://orcid.org/","");
+        ResponseEntity result = responseService.buildResponse(id,
+                Collections.singletonMap("orcid", orcid_id));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+
     @PostMapping(value = "/getCurrentEmployees", produces = "application/json")
     public ResponseEntity<String> getCurrentEmployees(
-            @Valid @Pattern(regexp = "^Q[1-9]\\d*$")
-            @ApiParam("Wikidata id for a research organization starting with Q")
-            @RequestParam String wikidata) {
+            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
 
         final String id = "sparqlg/orcid/employees";
-        log.info("Incoming Request for " + id + " with wikidata: " + wikidata);
+        log.info("Incoming Request for " + id + " with ror: " + ror);
         StopWatch stopWatch = new StopWatch(id);
         stopWatch.start(id);
 
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("wikidata", wikidata));
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
 
         stopWatch.stop();
         log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
diff --git a/src/main/resources/sparqlg/orcid/person/person_id.rqg b/src/main/resources/sparqlg/orcid/person/person_id.rqg
new file mode 100644
index 0000000..90b35f1
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/person/person_id.rqg
@@ -0,0 +1,5 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+FUNCTION <func>(?orcid_data) {
+    fun:JSONPath(?orcid_data, '$.orcid-identifier.path' )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/person/person_mapping.rqg b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
new file mode 100644
index 0000000..97deeae
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
@@ -0,0 +1,17 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+GENERATE <person_mapping>(?orcid_data) {
+
+    ## fill in blanks in person definition in vivo ontology
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?name) .
+
+}
+WHERE {
+    ### extract properties of person
+    BIND(<https://projects.tib.eu/tapir/orcid/person/person_id.rqg>(?orcid_data) AS ?id)
+
+    BIND(fun:JSONPath(?orcid_data, '$.person.name.given-names.value' ) AS ?givenName)
+    BIND(fun:JSONPath(?orcid_data, '$.person.name.family-name.value' ) AS ?familyName)
+    BIND(CONCAT(?familyName, ", ", ?givenName)  AS ?name)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/person/person_source.rqg b/src/main/resources/sparqlg/orcid/person/person_source.rqg
new file mode 100644
index 0000000..8b631a9
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/person/person_source.rqg
@@ -0,0 +1,15 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+### query data about person from ORCID
+GENERATE <person_source>(?orcid) {
+
+    GENERATE <https://projects.tib.eu/tapir/orcid/person/person_mapping.rqg>( ?orcid_data ) .
+
+}
+WHERE {
+    # query person data from ORCID
+    BIND(<https://pub.orcid.org/v3.0/{?orcid}> as ?orcid_url)
+    BIND(  fun:HTTPGet(?orcid_url, "Accept: application/json") AS ?orcid_response )
+    FILTER( fun:HTTPExtractResponseCode( ?orcid_response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?orcid_response ) AS ?orcid_data )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json b/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
new file mode 100644
index 0000000..e6607d0
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
@@ -0,0 +1,18 @@
+{
+  "base": "http://vivo.mydomain.edu/individual/",
+  "query": "person_source.rqg",
+  "namedqueries": [
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/person/person_mapping.rqg",
+      "path": "person_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/person/person_id.rqg",
+      "path": "person_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/person.rqg",
+      "path": "../../vivo-rdf/person.rqg"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/vivo-rdf/person.rqg b/src/main/resources/sparqlg/vivo-rdf/person.rqg
new file mode 100644
index 0000000..f8196ef
--- /dev/null
+++ b/src/main/resources/sparqlg/vivo-rdf/person.rqg
@@ -0,0 +1,9 @@
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+
+GENERATE <person> (?id, ?name){
+
+### id, name : basic attributes of a person
+    <{?id}> a foaf:Person ;
+     rdfs:label ?name .
+}
\ No newline at end of file

From 2c64be28141f7e6ade95aede5fb7466c43f174e5 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Fri, 4 Jun 2021 09:48:17 +0200
Subject: [PATCH 07/34] make get requests and central validation

---
 .../controller/DataciteCommonsController.java | 14 +++----
 .../eu/tib/controller/OrcidController.java    | 39 ++++++++++++++-----
 .../java/eu/tib/controller/RORController.java | 14 +++----
 .../tib/controller/validation/Validator.java  |  6 +++
 4 files changed, 47 insertions(+), 26 deletions(-)
 create mode 100644 src/main/java/eu/tib/controller/validation/Validator.java

diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index f15a256..fe99660 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -1,5 +1,6 @@
 package eu.tib.controller;
 
+import eu.tib.controller.validation.Validator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiParam;
@@ -8,10 +9,7 @@
 import org.springframework.http.ResponseEntity;
 import org.springframework.util.StopWatch;
 import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
 import javax.validation.constraints.Pattern;
@@ -27,9 +25,9 @@ public class DataciteCommonsController {
     @Autowired
     private ResponseService responseService;
 
-    @PostMapping(value = "/getOrganizationPlusPersons", produces = "application/json")
+    @GetMapping(value = "/organizationPlusPersons", produces = "application/json")
     public ResponseEntity<String> getOrganizationPlusPersons(
-            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
+            @Valid @Pattern(regexp = Validator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
@@ -45,9 +43,9 @@ public ResponseEntity<String> getOrganizationPlusPersons(
         return result;
     }
 
-    @PostMapping(value = "/getPersonPlusPublications", produces = "application/json")
+    @GetMapping(value = "/personPlusPublications", produces = "application/json")
     public ResponseEntity<String> getPersonPlusPublications(
-            @Valid @Pattern(regexp = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{4}")
+            @Valid @Pattern(regexp = Validator.orcid)
             @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
             @RequestParam String orcid) {
 
diff --git a/src/main/java/eu/tib/controller/OrcidController.java b/src/main/java/eu/tib/controller/OrcidController.java
index edfc149..d4b53fe 100644
--- a/src/main/java/eu/tib/controller/OrcidController.java
+++ b/src/main/java/eu/tib/controller/OrcidController.java
@@ -1,5 +1,6 @@
 package eu.tib.controller;
 
+import eu.tib.controller.validation.Validator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiParam;
@@ -8,10 +9,7 @@
 import org.springframework.http.ResponseEntity;
 import org.springframework.util.StopWatch;
 import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
 import javax.validation.constraints.Pattern;
@@ -27,18 +25,39 @@ public class OrcidController {
     @Autowired
     private ResponseService responseService;
 
-    @PostMapping(value = "/getCurrentEmployees", produces = "application/json")
+    @GetMapping(value = "/person", produces = "application/json")
+    public ResponseEntity<String> getPerson(
+            @Valid @Pattern(regexp = Validator.orcid)
+            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
+            @RequestParam String orcid) {
+
+        final String id = "sparqlg/orcid/person";
+        log.info("Incoming Request for " + id + " with orcid: " + orcid);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        String orcid_id = orcid.replaceFirst("https://orcid.org/","");
+        ResponseEntity result = responseService.buildResponse(id,
+                Collections.singletonMap("orcid", orcid_id));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+
+    @GetMapping(value = "/currentEmployees", produces = "application/json")
     public ResponseEntity<String> getCurrentEmployees(
-            @Valid @Pattern(regexp = "^Q[1-9]\\d*$")
-            @ApiParam("Wikidata id for a research organization starting with Q")
-            @RequestParam String wikidata) {
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
 
         final String id = "sparqlg/orcid/employees";
-        log.info("Incoming Request for " + id + " with wikidata: " + wikidata);
+        log.info("Incoming Request for " + id + " with ror: " + ror);
         StopWatch stopWatch = new StopWatch(id);
         stopWatch.start(id);
 
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("wikidata", wikidata));
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
 
         stopWatch.stop();
         log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
diff --git a/src/main/java/eu/tib/controller/RORController.java b/src/main/java/eu/tib/controller/RORController.java
index 4cb9fbe..3ad6c23 100644
--- a/src/main/java/eu/tib/controller/RORController.java
+++ b/src/main/java/eu/tib/controller/RORController.java
@@ -1,5 +1,6 @@
 package eu.tib.controller;
 
+import eu.tib.controller.validation.Validator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiParam;
@@ -8,10 +9,7 @@
 import org.springframework.http.ResponseEntity;
 import org.springframework.util.StopWatch;
 import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
 import javax.validation.constraints.Pattern;
@@ -27,9 +25,9 @@ public class RORController {
     @Autowired
     private ResponseService responseService;
 
-    @PostMapping(value = "/getOrganizationPlusChildren", produces = "application/json")
+    @GetMapping(value = "/organizationPlusChildren", produces = "application/json")
     public ResponseEntity<String> getOrganizationPlusChildren(
-            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
+            @Valid @Pattern(regexp = Validator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
@@ -45,9 +43,9 @@ public ResponseEntity<String> getOrganizationPlusChildren(
         return result;
     }
 
-    @PostMapping(value = "/getOrganization", produces = "application/json")
+    @GetMapping(value = "/organization", produces = "application/json")
     public ResponseEntity<String> getOrganization(
-            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
+            @Valid @Pattern(regexp = Validator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
diff --git a/src/main/java/eu/tib/controller/validation/Validator.java b/src/main/java/eu/tib/controller/validation/Validator.java
new file mode 100644
index 0000000..050ad84
--- /dev/null
+++ b/src/main/java/eu/tib/controller/validation/Validator.java
@@ -0,0 +1,6 @@
+package eu.tib.controller.validation;
+
+public class Validator {
+    public static final String ror = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}$";
+    public static final String orcid = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$";
+}

From 15de27414d6ebf060f4d15ed050266172f9dd7f2 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 7 Jun 2021 09:32:58 +0200
Subject: [PATCH 08/34] add pid to objects

---
 .../sparqlg/ror/orga2children/orga2children.rqg   |  3 +--
 .../ror/orga2children/sparql-generate-conf.json   | 10 +++++++++-
 .../sparqlg/ror/organization/orga_mapping.rqg     |  5 ++++-
 .../ror/organization/sparql-generate-conf.json    |  6 +++++-
 src/main/resources/sparqlg/vivo-rdf/agent_pid.rqg | 15 +++++++++++++++
 .../resources/sparqlg/vivo-rdf/orga2suborga.rqg   |  5 +++++
 6 files changed, 39 insertions(+), 5 deletions(-)
 create mode 100644 src/main/resources/sparqlg/vivo-rdf/agent_pid.rqg
 create mode 100644 src/main/resources/sparqlg/vivo-rdf/orga2suborga.rqg

diff --git a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
index d7e9b34..301b270 100644
--- a/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
+++ b/src/main/resources/sparqlg/ror/orga2children/orga2children.rqg
@@ -1,6 +1,5 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
 
 GENERATE <orga2children>(?parent_id, ?ror) {
 
@@ -8,7 +7,7 @@ GENERATE <orga2children>(?parent_id, ?ror) {
   GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?orga_data ) .
 
   ### connection organization & sub-organization
-  <{?parent_id}> obo:BFO_0000051 <{?id}> .
+  GENERATE <https://projects.tib.eu/tapir/vivo-rdf/orga2suborga.rqg>(?parent_id, ?id ) .
 
   ### call this query recursively for all children
   GENERATE <https://projects.tib.eu/tapir/ror/orga2children/orga2children.rqg>(?id, ?child_ror )
diff --git a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
index 2e32d28..8bfb361 100644
--- a/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/orga2children/sparql-generate-conf.json
@@ -15,8 +15,16 @@
       "path": "../organization/orga_id.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
       "path": "../../vivo-rdf/organization.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/orga2suborga.rqg",
+      "path": "../../vivo-rdf/orga2suborga.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg b/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
index 57c1787..2eab358 100644
--- a/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
+++ b/src/main/resources/sparqlg/ror/organization/orga_mapping.rqg
@@ -4,7 +4,10 @@ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 GENERATE <orga_mapping>(?ror_data) {
 
     ## fill in blanks in organization definition in vivo ontology
-    GENERATE <https://projects.tib.eu/tapir/objects/organization.rqg>( ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/organization.rqg>( ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
+
+    ## add ROR as PID
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://ror.org/", ?id) .
 
 }
 WHERE {
diff --git a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
index b4bb786..cb45b7f 100644
--- a/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/ror/organization/sparql-generate-conf.json
@@ -11,8 +11,12 @@
       "path": "orga_id.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/objects/organization.rqg",
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
       "path": "../../vivo-rdf/organization.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/vivo-rdf/agent_pid.rqg b/src/main/resources/sparqlg/vivo-rdf/agent_pid.rqg
new file mode 100644
index 0000000..8c43219
--- /dev/null
+++ b/src/main/resources/sparqlg/vivo-rdf/agent_pid.rqg
@@ -0,0 +1,15 @@
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+
+GENERATE <agent_pid>(?agent_id, ?service_url, ?account_name){
+
+    <{?agent_id}> foaf:holdsAccount <{?service_domain_clean}-{?account_name_clean}> .
+
+    <{?service_domain_clean}-{?account_name_clean}> a foaf:OnlineAccount ;
+       foaf:accountServiceHomePage ?service_url;
+       foaf:accountName ?account_name .
+
+} WHERE {
+    BIND(REPLACE(?service_url, "^(?:.*?://)?(?:.*?@)?([^:]+?)(:\\d+)?((/.*)|$)", "$1") AS ?service_domain)
+    BIND(REPLACE(?service_domain,  "\\W", "", "i") AS ?service_domain_clean)
+    BIND(REPLACE(?account_name,  "\\W", "", "i") AS ?account_name_clean)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/vivo-rdf/orga2suborga.rqg b/src/main/resources/sparqlg/vivo-rdf/orga2suborga.rqg
new file mode 100644
index 0000000..b3e227e
--- /dev/null
+++ b/src/main/resources/sparqlg/vivo-rdf/orga2suborga.rqg
@@ -0,0 +1,5 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+GENERATE <orga2suborga>(?parent_id, ?id){
+    <{?parent_id}> obo:BFO_0000051 <{?id}> .
+}
\ No newline at end of file

From 3525f8f1c8efc4e321a631c786886143f0ee1ecc Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 7 Jun 2021 10:01:29 +0200
Subject: [PATCH 09/34] query orcid for person and employment

---
 .../sparqlg/orcid/employees/README.md         |  3 +-
 .../orcid/employees/currentEmployees.rqg      | 29 -----------
 .../orcid/employees/employees_filter.rqg      | 51 +++++++++++++++++++
 .../orcid/employees/employees_source.rqg      | 29 +++++++++++
 .../orcid/employees/employment_mapping.rqg    | 23 +++++++++
 .../sparqlg/orcid/employees/orga_source.rqg   | 24 ---------
 .../orcid/employees/organization/orga_id.rqg  |  5 ++
 .../organization/orga_placeholder.rqg         | 25 +++++++++
 .../orcid/employees/sparql-generate-conf.json | 42 +++++++++++++--
 .../sparqlg/orcid/person/person_mapping.rqg   |  3 ++
 .../orcid/person/sparql-generate-conf.json    |  4 ++
 .../resources/sparqlg/vivo-rdf/position.rqg   | 47 +++++++++++++++++
 12 files changed, 227 insertions(+), 58 deletions(-)
 delete mode 100644 src/main/resources/sparqlg/orcid/employees/currentEmployees.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/employees/employees_filter.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/employees/employees_source.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/employees/employment_mapping.rqg
 delete mode 100644 src/main/resources/sparqlg/orcid/employees/orga_source.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/employees/organization/orga_id.rqg
 create mode 100644 src/main/resources/sparqlg/orcid/employees/organization/orga_placeholder.rqg
 create mode 100644 src/main/resources/sparqlg/vivo-rdf/position.rqg

diff --git a/src/main/resources/sparqlg/orcid/employees/README.md b/src/main/resources/sparqlg/orcid/employees/README.md
index 072615a..6a0b69c 100644
--- a/src/main/resources/sparqlg/orcid/employees/README.md
+++ b/src/main/resources/sparqlg/orcid/employees/README.md
@@ -2,8 +2,7 @@
 
 This query reengineers the DataciteCommons organization -> people connection, 
 described in https://www.pidforum.org/t/employment-field-always-empty-when-using-connection/1571/12 ,
-skipping the first step ROR->Wikidata and adding a filter at the end to only return ORCIDs 
-affiliated with the organization via Ringgold or Grid-id in their ORCID profile and with an empty end-date.
+adding a filter at the end to only return ORCIDs affiliated with the organization via Ringgold or Grid-id in their ORCID profile and with an empty end-date.
 
 This query is very costly and takes quite some time as you need to call the ORCID API
 x times (x being the number of affiliated employees).
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/currentEmployees.rqg b/src/main/resources/sparqlg/orcid/employees/currentEmployees.rqg
deleted file mode 100644
index bd32b73..0000000
--- a/src/main/resources/sparqlg/orcid/employees/currentEmployees.rqg
+++ /dev/null
@@ -1,29 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX iter: <http://w3id.org/sparql-generate/iter/>
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-GENERATE <currentEmployees>( ?grid_id, ?ringgold_id, ?orcid ) {
-
-    GENERATE {
-        <{?orcid}> a foaf:Person ;
-        rdfs:label ?name.
-    }
-    ITERATOR iter:JSONPath(?body, '$.affiliation-group[*]') AS ?employment
-    WHERE{
-    # filter only employees where orga_id is same as ringgold or grid AND no end-date (=current)
-        BIND(fun:JSONPath(?employment, '$.summaries[0].employment-summary.organization.disambiguated-organization.disambiguated-organization-identifier' ) AS ?orga_id)
-        BIND(fun:JSONPath(?employment, '$.summaries[0].employment-summary.end-date' ) AS ?end_date)
-        FILTER( !BOUND(?end_date) && (?orga_id = ?grid_id || ?orga_id = ?ringgold_id) ).
-
-        BIND(fun:JSONPath(?body, '$.affiliation-group[0].summaries[0].employment-summary.source.source-name.value' ) AS ?name)
-    }.
-
-}
-WHERE{
-    # query employments of orcid for every person
-    BIND(<https://pub.orcid.org/v3.0/{?orcid}/employments> as ?geturl)
-    BIND(  fun:HTTPGet(?geturl, "Accept: application/json") AS ?response )
-    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
-    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/employees_filter.rqg b/src/main/resources/sparqlg/orcid/employees/employees_filter.rqg
new file mode 100644
index 0000000..c69050d
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/employees/employees_filter.rqg
@@ -0,0 +1,51 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX iter: <http://w3id.org/sparql-generate/iter/>
+
+## get all people affiliated with the organization
+GENERATE <employees_filter>(?orga_id, ?ringgold_id, ?grid_id){
+
+    ## get orcid data for each person
+    GENERATE{
+
+        ### for every person check if current employment and if yes, create triples
+        ## current = employees where orga_id is same as ringgold or grid AND no end-date
+        GENERATE {
+            ## create person in vivo ontology, if current employee
+            GENERATE <https://projects.tib.eu/tapir/orcid/person/person_mapping.rqg>(?orcid_data) .
+
+
+            ## connect person to organization via current employment
+            GENERATE <https://projects.tib.eu/tapir/orcid/employees/employment_mapping.rqg>(?person_id, ?orga_id, ?employment) .
+        }
+        ITERATOR iter:JSONPath(?orcid_data, '$.activities-summary.employments.affiliation-group[*]') AS ?employment
+        WHERE{
+            BIND(<https://projects.tib.eu/tapir/orcid/person/person_id.rqg>(?orcid_data) AS ?person_id)
+
+            BIND(fun:JSONPath(?employment, '$.summaries[0].employment-summary.organization.disambiguated-organization.disambiguated-organization-identifier' ) AS ?disamb_orga)
+            BIND(fun:JSONPath(?employment, '$.summaries[0].employment-summary.end-date' ) AS ?end_date)
+            FILTER( !BOUND(?end_date) && (?disamb_orga = ?grid_id || ?disamb_orga = ?ringgold_id) ).
+        }.
+
+    }
+    ITERATOR iter:JSONPath(?orcid_employees, '$.expanded-result[*]') AS ?person
+    WHERE{
+        BIND(fun:JSONPath(?person, '$.orcid-id') AS ?orcid)
+
+        # query person data from ORCID as json
+        BIND(<https://pub.orcid.org/v3.0/{?orcid}> as ?orcid_url)
+        BIND( fun:HTTPGet(?orcid_url, "Accept: application/json" ) AS ?orcid_response )
+        FILTER( fun:HTTPExtractResponseCode( ?orcid_response ) = 200 )
+        BIND( fun:HTTPExtractBody( ?orcid_response ) AS ?orcid_data )
+    } .
+}
+WHERE{
+  ### call orcid with ringgold and grid-id for affiliated employees
+  BIND(IF(BOUND(?ringgold_id) && BOUND(?grid_id), "%20OR%20", "") AS ?connector)
+  BIND(IF(BOUND(?ringgold_id), "ringgold-org-id:{?ringgold_id}", "") AS ?ringgold_search)
+  BIND(IF(BOUND(?grid_id), "grid-org-id:{?grid_id}", "") AS ?grid_search)
+
+  BIND("https://pub.orcid.org/v3.0/expanded-search/?q={?ringgold_search}{?connector}{?grid_search}" as ?orcid_employees_url)
+  BIND(fun:HTTPGet(IRI(?orcid_employees_url), "Accept: application/json") AS ?orcid_employees_response)
+  FILTER(fun:HTTPExtractResponseCode( ?orcid_employees_response ) = 200)
+  BIND(fun:HTTPExtractBody( ?orcid_employees_response ) AS ?orcid_employees)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/employees_source.rqg b/src/main/resources/sparqlg/orcid/employees/employees_source.rqg
new file mode 100644
index 0000000..a329cfa
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/employees/employees_source.rqg
@@ -0,0 +1,29 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX iter: <http://w3id.org/sparql-generate/iter/>
+
+GENERATE <employees_source>(?ror) {
+
+    ### if ROR is included, you could use GENERATE <https://projects.tib.eu/tapir/ror/organization/orga_mapping.rqg>( ?ror_data ) .
+    ### but to keep data sources independent:
+    GENERATE <https://projects.tib.eu/tapir/orcid/employees/organization/orga_placeholder.rqg>( ?ror_data, ?wikidata_id, ?ringgold_id, ?grid_id ) .
+
+    GENERATE <https://projects.tib.eu/tapir/orcid/employees/employees_filter.rqg>(?orga_id, ?ringgold_id, ?grid_id ) .
+
+}
+SOURCE <https://api.ror.org/organizations/{?ror}> AS ?ror_data
+WHERE{
+  ### extract wikidata id from ROR data
+  BIND(fun:JSONPath(?ror_data, '$.external_ids.Wikidata.all[0]' ) AS ?wikidata_id)
+
+  ### call wikidata to get ringgold and grid-id for organization
+  BIND(<https://www.wikidata.org/w/api.php?action=wbgetentities&ids={?wikidata_id}&props=claims&format=json> as ?wikidata_url)
+  BIND(fun:HTTPGet(?wikidata_url, "Accept: application/json") AS ?wikidata_response)
+  FILTER(fun:HTTPExtractResponseCode( ?wikidata_response ) = 200)
+  BIND(fun:HTTPExtractBody( ?wikidata_response ) AS ?wikidata_body)
+
+  BIND(fun:JSONPath(?wikidata_body, '$.entities.{?wikidata_id}.claims.P3500[0].mainsnak.datavalue.value' ) AS ?ringgold_id)
+  BIND(fun:JSONPath(?wikidata_body, '$.entities.{?wikidata_id}.claims.P2427[0].mainsnak.datavalue.value' ) AS ?grid_id)
+
+  # after creating organization, get its id to make the orga-person connection
+  BIND(<https://projects.tib.eu/tapir/orcid/employees/organization/orga_id.rqg>(?ror_data) AS ?orga_id)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/employment_mapping.rqg b/src/main/resources/sparqlg/orcid/employees/employment_mapping.rqg
new file mode 100644
index 0000000..9b6a369
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/employees/employment_mapping.rqg
@@ -0,0 +1,23 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+## extract properties of employment data for mapping
+GENERATE <employment_mapping>(?person_id, ?orga_id, ?employment) {
+
+   GENERATE <https://projects.tib.eu/tapir/vivo-rdf/position.rqg>(?person_id, ?orga_id, ?role, ?start_date, ?end_date) .
+}
+WHERE{
+    BIND(fun:JSONPath(?employment, '$.summaries[0].employment-summary.role-title' ) AS ?role)
+
+    BIND(fun:JSONPath(?employment, '$.summaries[0].employment-summary.start-date' ) AS ?start)
+    BIND(fun:JSONPath(?start, '$.year.value') as ?start_year)
+    BIND(fun:JSONPath(?start, '$.month.value') as ?start_month)
+    BIND(fun:JSONPath(?start, '$.day.value') as ?start_day)
+    BIND(xsd:dateTime(CONCAT(?start_year, "-", ?start_month, "-", ?start_day, "T00:00:00")) as ?start_date)
+
+    BIND(fun:JSONPath(?employment, '$.summaries[0].employment-summary.end-date' ) AS ?end)
+    BIND(fun:JSONPath(?end, '$.year.value') as ?end_year)
+    BIND(fun:JSONPath(?end, '$.month.value') as ?end_month)
+    BIND(fun:JSONPath(?end, '$.day.value') as ?end_day)
+    BIND(xsd:dateTime(CONCAT(?end_year, "-", ?end_month, "-", ?end_day, "T00:00:00")) as ?end_date)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/orga_source.rqg b/src/main/resources/sparqlg/orcid/employees/orga_source.rqg
deleted file mode 100644
index 16a87a2..0000000
--- a/src/main/resources/sparqlg/orcid/employees/orga_source.rqg
+++ /dev/null
@@ -1,24 +0,0 @@
-PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX iter: <http://w3id.org/sparql-generate/iter/>
-
-GENERATE <orga_source>(?wikidata) {
-
-     GENERATE <https://projects.tib.eu/tapir/orcid/employees/currentEmployees.rqg>( ?grid_id, ?ringgold_id, ?orcid )
-     ITERATOR iter:JSONPath(?body, '$.expanded-result[*]') AS ?person
-     WHERE{
-       BIND(fun:JSONPath(?person, '$.orcid-id') AS ?orcid)
-     }.
-
-}
-SOURCE <https://www.wikidata.org/w/api.php?action=wbgetentities&ids={?wikidata}&props=claims&format=json> AS ?orga
-WHERE{
-  # get organization-ids (ringgold & grid) from wikidata
-  BIND(fun:JSONPath(?orga, '$.entities.{?wikidata}.claims.P3500[0].mainsnak.datavalue.value' ) AS ?ringgold_id)
-  BIND(fun:JSONPath(?orga, '$.entities.{?wikidata}.claims.P2427[0].mainsnak.datavalue.value' ) AS ?grid_id)
-
-  # call orcid with ringgold and grid-id for affiliated employees
-  BIND(<https://pub.orcid.org/v3.0/expanded-search/?q=ringgold-org-id:{?ringgold_id}%20OR%20grid-org-id:{?grid_id}> as ?orcid_url)
-  BIND(fun:HTTPGet(?orcid_url, "Accept: application/json") AS ?response)
-  FILTER(fun:HTTPExtractResponseCode( ?response ) = 200)
-  BIND(fun:HTTPExtractBody( ?response ) AS ?body)
-}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/organization/orga_id.rqg b/src/main/resources/sparqlg/orcid/employees/organization/orga_id.rqg
new file mode 100644
index 0000000..09a1ca9
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/employees/organization/orga_id.rqg
@@ -0,0 +1,5 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+FUNCTION <func>(?ror_data) {
+    REPLACE(fun:JSONPath(?ror_data, '$.id' ), "https://ror.org/" , "" )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/organization/orga_placeholder.rqg b/src/main/resources/sparqlg/orcid/employees/organization/orga_placeholder.rqg
new file mode 100644
index 0000000..b6b280c
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/employees/organization/orga_placeholder.rqg
@@ -0,0 +1,25 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+GENERATE <orga_placeholder>( ?ror_data, ?wikidata_id, ?ringgold_id, ?grid_id ) {
+
+    ## fill in blanks in person definition in vivo ontology
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/organization.rqg>(?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
+
+    ## add ROR as PID
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://ror.org/", ?id) .
+
+    ## add Wikidata as PID
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://www.wikidata.org/wiki/", ?wikidata_id) .
+
+    ## add Grid as PID
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://www.grid.ac/institutes/", ?grid_id) .
+
+    ## add Ringgold as PID
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://www.ringgold.com/", ?ringgold_id) .
+}
+WHERE {
+    ### basic properties of organization
+    BIND(<https://projects.tib.eu/tapir/orcid/employees/organization/orga_id.rqg>(?ror_data) AS ?id)
+    BIND(fun:JSONPath(?ror_data, '$.name' ) AS ?name)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json b/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json
index 5163c1a..caafa84 100644
--- a/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json
@@ -1,10 +1,46 @@
 {
   "base": "http://vivo.mydomain.edu/individual/",
-  "query": "orga_source.rqg",
+  "query": "employees_source.rqg",
   "namedqueries": [
     {
-      "uri": "https://projects.tib.eu/tapir/orcid/employees/currentEmployees.rqg",
-      "path": "currentEmployees.rqg"
+      "uri": "https://projects.tib.eu/tapir/orcid/employees/organization/orga_placeholder.rqg",
+      "path": "organization/orga_placeholder.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/employees/organization/orga_id.rqg",
+      "path": "organization/orga_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/employees/employees_filter.rqg",
+      "path": "employees_filter.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/employees/employment_mapping.rqg",
+      "path": "employment_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/person/person_mapping.rqg",
+      "path": "../person/person_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/person/person_id.rqg",
+      "path": "../person/person_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/person.rqg",
+      "path": "../../vivo-rdf/person.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/position.rqg",
+      "path": "../../vivo-rdf/position.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
+      "path": "../../vivo-rdf/organization.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/person/person_mapping.rqg b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
index 97deeae..65aadbf 100644
--- a/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
+++ b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
@@ -6,6 +6,9 @@ GENERATE <person_mapping>(?orcid_data) {
     ## fill in blanks in person definition in vivo ontology
     GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?name) .
 
+    ## add ORCID as data source
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://orcid.org/", ?id) .
+
 }
 WHERE {
     ### extract properties of person
diff --git a/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json b/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
index e6607d0..e389611 100644
--- a/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
@@ -13,6 +13,10 @@
     {
       "uri": "https://projects.tib.eu/tapir/vivo-rdf/person.rqg",
       "path": "../../vivo-rdf/person.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/vivo-rdf/position.rqg b/src/main/resources/sparqlg/vivo-rdf/position.rqg
new file mode 100644
index 0000000..c210083
--- /dev/null
+++ b/src/main/resources/sparqlg/vivo-rdf/position.rqg
@@ -0,0 +1,47 @@
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX vivo: <http://vivoweb.org/ontology/core#>
+
+GENERATE <position> (?person_id, ?orga_id, ?role, ?start_date, ?end_date){
+
+    <{?position_id_clean}> a vivo:Position ;
+        rdfs:label ?role_value ;
+        vivo:relates <{?person_id}> ;
+        vivo:relates <{?orga_id}> .
+
+   GENERATE{
+        <{?position_id_clean}> vivo:dateTimeInterval <{?position_id_clean}-dti> .
+
+        <{?position_id_clean}-dti> a vivo:DateTimeInterval ;
+            vivo:start <{?position_id}-start> ;
+            vivo:end <{?position_id}-end> .
+   }
+   WHERE {
+     FILTER( BOUND(?start_date) || BOUND(?end_date) ).
+   } .
+
+   GENERATE{
+      <{?position_id_clean}-start> a vivo:DateTimeValue ;
+        vivo:dateTime ?start_date ;
+        vivo:dateTimePrecision vivo:yearPrecision .
+   }
+   WHERE {
+     FILTER( BOUND(?start_date) ).
+   } .
+
+  GENERATE{
+    <{?position_id_clean}-end> a vivo:DateTimeValue ;
+        vivo:dateTime ?end_date ;
+        vivo:dateTimePrecision vivo:yearPrecision .
+  }
+  WHERE {
+     FILTER( BOUND(?end_date) ).
+  } .
+
+}
+WHERE {
+    BIND("{?person_id}-{?role}-{?start_date}" AS ?position_id)
+    BIND(REPLACE(?position_id,  "\\W", "", "i") AS ?position_id_clean)
+    BIND(IF(BOUND(?role) && strlen(?role)>0, ?role, "Unknown") AS ?role_value)
+
+    FILTER( BOUND(?person_id) && BOUND(?orga_id) ).
+}
\ No newline at end of file

From 651ce6dfee736a1a0190811a23db48aaa98f8499 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 7 Jun 2021 16:36:32 +0200
Subject: [PATCH 10/34] add dc basic types

---
 .../datacitecommons/organization/orga_id.rqg  |  5 ++
 .../organization/orga_mapping.rqg             | 18 ++++++
 .../organization/orga_source.rqg              | 17 +++++
 .../queryset/organization.graphql             | 10 +++
 .../organization/sparql-generate-conf.json    | 26 ++++++++
 .../datacitecommons/person/person_id.rqg      |  5 ++
 .../datacitecommons/person/person_mapping.rqg | 18 ++++++
 .../datacitecommons/person/person_source.rqg  | 17 +++++
 .../person/queryset/person.graphql            |  7 +++
 .../person/sparql-generate-conf.json          | 26 ++++++++
 .../work/queryset/work.graphql                | 12 ++++
 .../work/sparql-generate-conf.json            | 22 +++++++
 .../sparqlg/datacitecommons/work/work_id.rqg  |  5 ++
 .../datacitecommons/work/work_mapping.rqg     | 62 +++++++++++++++++++
 .../datacitecommons/work/work_source.rqg      | 17 +++++
 .../resources/sparqlg/vivo-rdf/research.rqg   | 19 ++++++
 16 files changed, 286 insertions(+)
 create mode 100644 src/main/resources/sparqlg/datacitecommons/organization/orga_id.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/organization/orga_mapping.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/organization/queryset/organization.graphql
 create mode 100644 src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
 create mode 100644 src/main/resources/sparqlg/datacitecommons/person/person_id.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/person/queryset/person.graphql
 create mode 100644 src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
 create mode 100644 src/main/resources/sparqlg/datacitecommons/work/queryset/work.graphql
 create mode 100644 src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
 create mode 100644 src/main/resources/sparqlg/datacitecommons/work/work_id.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/work/work_mapping.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
 create mode 100644 src/main/resources/sparqlg/vivo-rdf/research.rqg

diff --git a/src/main/resources/sparqlg/datacitecommons/organization/orga_id.rqg b/src/main/resources/sparqlg/datacitecommons/organization/orga_id.rqg
new file mode 100644
index 0000000..8e489cc
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/organization/orga_id.rqg
@@ -0,0 +1,5 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+FUNCTION <func>(?orga_data) {
+    REPLACE(fun:JSONPath(?orga_data, '$.id' ), "https://ror.org/" , "" )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/orga_mapping.rqg b/src/main/resources/sparqlg/datacitecommons/organization/orga_mapping.rqg
new file mode 100644
index 0000000..6a20c7d
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/organization/orga_mapping.rqg
@@ -0,0 +1,18 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+GENERATE <orga_mapping>(?orga_data) {
+    ## fill in blanks in organization definition in vivo ontology
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/organization.rqg>( ?id, ?name, ?established_dtv, ?email, ?website, ?city, ?state, ?country, ?lat, ?lng) .
+
+    ## add ROR as PID
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://ror.org/", ?id) .
+}
+WHERE {
+    ### basic properties of organization
+    BIND(<https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg>(?orga_data) AS ?id)
+    BIND(fun:JSONPath(?orga_data, '$.name' ) AS ?name)
+
+    BIND(xsd:decimal(fun:JSONPath(?orga_data, '$.geolocation.pointLatitude' )) AS ?lat)
+    BIND(xsd:decimal(fun:JSONPath(?orga_data, '$.geolocation.pointLongitude' )) AS ?lng)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg b/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
new file mode 100644
index 0000000..6766a9f
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
@@ -0,0 +1,17 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE <orga_source>(?ror) {
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg>( ?orga_data ) .
+}
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/organization/queryset/organization.graphql> AS ?graphqlquery
+WHERE {
+    # replace whitespace in graphql query (compress message)
+    BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
+    BIND ("""\{"variables":\{"ror":"{?ror}"},"query":"{?graphql}"}""" AS ?postbody)
+
+    # build http post request
+    BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
+    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/queryset/organization.graphql b/src/main/resources/sparqlg/datacitecommons/organization/queryset/organization.graphql
new file mode 100644
index 0000000..2126463
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/organization/queryset/organization.graphql
@@ -0,0 +1,10 @@
+query organization($ror: ID!) {
+    organization(id: $ror) {
+        id
+        name
+        geolocation {
+            pointLatitude
+            pointLongitude
+        }
+    }
+}
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
new file mode 100644
index 0000000..2029d4d
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
@@ -0,0 +1,26 @@
+{
+  "base": "http://vivo.mydomain.edu/individual/",
+  "query": "orga_source.rqg",
+  "namedqueries": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/queryset/organization.graphql",
+      "path": "queryset/organization.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg",
+      "path": "orga_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg",
+      "path": "orga_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
+      "path": "../../vivo-rdf/organization.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/person_id.rqg b/src/main/resources/sparqlg/datacitecommons/person/person_id.rqg
new file mode 100644
index 0000000..e0ff92d
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/person/person_id.rqg
@@ -0,0 +1,5 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+FUNCTION <func>(?person_data) {
+    REPLACE(fun:JSONPath(?person_data, '$.id' ), "https://orcid.org/" , "" )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg b/src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg
new file mode 100644
index 0000000..ca06e58
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg
@@ -0,0 +1,18 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE <person_mapping>(?person_data) {
+
+    ## fill in blanks in person definition in vivo ontology
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?name) .
+
+    ## add ORCID as PID
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://orcid.org/", ?id) .
+}
+WHERE {
+    ### basic properties of organization
+    BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?id)
+
+    BIND(fun:JSONPath(?person_data, '$.givenName' ) AS ?givenName)
+    BIND(fun:JSONPath(?person_data, '$.familyName' ) AS ?familyName)
+    BIND(CONCAT(?familyName, ", ", ?givenName)  AS ?name)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg b/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
new file mode 100644
index 0000000..4f741ba
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
@@ -0,0 +1,17 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE <person_source>(?orcid) {
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg>( ?person_data ) .
+}
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/person/queryset/person.graphql> AS ?graphqlquery
+WHERE {
+    # replace whitespace in graphql query (compress message)
+    BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
+    BIND ("""\{"variables":\{"orcid":"{?orcid}"},"query":"{?graphql}"}""" AS ?postbody)
+
+    # build http post request
+    BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
+    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+    BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person_data )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/queryset/person.graphql b/src/main/resources/sparqlg/datacitecommons/person/queryset/person.graphql
new file mode 100644
index 0000000..21fb92b
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/person/queryset/person.graphql
@@ -0,0 +1,7 @@
+query person($orcid :ID!){
+    person(id: $orcid) {
+        familyName
+        givenName
+        id
+    }
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
new file mode 100644
index 0000000..829839a
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
@@ -0,0 +1,26 @@
+{
+  "base": "http://vivo.mydomain.edu/individual/",
+  "query": "person_source.rqg",
+  "namedqueries": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/queryset/person.graphql",
+      "path": "queryset/person.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg",
+      "path": "person_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg",
+      "path": "person_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/person.rqg",
+      "path": "../../vivo-rdf/person.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/work/queryset/work.graphql b/src/main/resources/sparqlg/datacitecommons/work/queryset/work.graphql
new file mode 100644
index 0000000..80ff97e
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/work/queryset/work.graphql
@@ -0,0 +1,12 @@
+query work($doi :ID!){
+    work(id: $doi) {
+        doi
+        titles {
+            title
+        }
+        publicationYear
+        types {
+            citeproc
+        }
+    }
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
new file mode 100644
index 0000000..40880bc
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
@@ -0,0 +1,22 @@
+{
+  "base": "http://vivo.mydomain.edu/individual/",
+  "query": "work_source.rqg",
+  "namedqueries": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/queryset/work.graphql",
+      "path": "queryset/work.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg",
+      "path": "work_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_id.rqg",
+      "path": "work_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/research.rqg",
+      "path": "../../vivo-rdf/research.rqg"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/work/work_id.rqg b/src/main/resources/sparqlg/datacitecommons/work/work_id.rqg
new file mode 100644
index 0000000..9641838
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/work/work_id.rqg
@@ -0,0 +1,5 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+FUNCTION <func>(?work_data) {
+    REPLACE(fun:JSONPath(?work_data, '$.doi' ),  "\\W", "", "i")
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/work/work_mapping.rqg b/src/main/resources/sparqlg/datacitecommons/work/work_mapping.rqg
new file mode 100644
index 0000000..f8cf9f5
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/work/work_mapping.rqg
@@ -0,0 +1,62 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX bibo: <http://purl.org/ontology/bibo/>
+PREFIX vivo: <http://vivoweb.org/ontology/core#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+GENERATE <work_mapping>(?work_data) {
+
+    ## fill in blanks in work definition in vivo ontology
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/research.rqg> (?id, ?pubtype, ?title, ?doi, ?pubyear_dtv) .
+}
+WHERE {
+    ### basic properties of organization
+    BIND(<https://projects.tib.eu/tapir/datacitecommons/work/work_id.rqg>(?work_data) AS ?id)
+
+    # basic properties of a publication in json
+    BIND(fun:JSONPath(?work_data, '$.doi' ) AS ?doi)
+    BIND(fun:JSONPath(?work_data, '$.titles[0].title' ) AS ?title)
+
+    BIND(fun:JSONPath(?work_data, '$.publicationYear' ) AS ?pubyear)
+    BIND(xsd:dateTime(CONCAT(STR(?pubyear), "-01-01T00:00:00"))  AS ?pubyear_dtv)
+
+    BIND(fun:JSONPath(?work_data, '$.types.citeproc' ) AS ?citeproc)
+    # mapping taken from VIVO (claim DOI functionality)
+    BIND (
+     IRI(COALESCE(
+       IF(?citeproc = "article-journal", bibo:AcademicArticle, 1/0),
+       IF(?citeproc = "article", bibo:Article, 1/0),
+       IF(?citeproc = "book", bibo:Book, 1/0),
+       IF(?citeproc = "chapter", bibo:Chapter, 1/0),
+       IF(?citeproc = "dataset", vivo:Dataset, 1/0),
+       IF(?citeproc = "figure", bibo:Image, 1/0),
+       IF(?citeproc = "graphic", bibo:Image, 1/0),
+       IF(?citeproc = "legal_case", bibo:LegalCaseDocument, 1/0),
+       IF(?citeproc = "legislation", bibo:Legislation, 1/0),
+       IF(?citeproc = "manuscript", bibo:Manuscript, 1/0),
+       IF(?citeproc = "map", bibo:Map, 1/0),
+       IF(?citeproc = "musical_score", vivo:Score, 1/0),
+       IF(?citeproc = "paper-conference", vivo:ConferencePaper, 1/0),
+       IF(?citeproc = "patent", bibo:Patent, 1/0),
+       IF(?citeproc = "personal_communication", bibo:PersonalCommunicationDocument, 1/0),
+       IF(?citeproc = "post-weblog", vivo:BlogPosting, 1/0),
+       IF(?citeproc = "report", bibo:Report, 1/0),
+       IF(?citeproc = "review", vivo:Review, 1/0),
+       IF(?citeproc = "speech", vivo:Speech, 1/0),
+       IF(?citeproc = "thesis", bibo:Thesis, 1/0),
+       IF(?citeproc = "webpage", bibo:Webpage, 1/0),
+
+     # mapping leftover types
+       IF(STRSTARTS(?citeproc, "article"), bibo:Article, 1/0),
+       IF(?citeproc = "bill", bibo:Bill, 1/0),
+       IF(STRSTARTS(?citeproc, "entry"), bibo:DocumentPart, 1/0),
+       IF(?citeproc = "interview", bibo:Interview, 1/0),
+       IF(?citeproc = "motion_picture", bibo:Film, 1/0),
+       IF(?citeproc = "post", vivo:BlogPosting, 1/0),
+       IF(?citeproc = "review-book", vivo:Review, 1/0),
+       IF(?citeproc = "song", bibo:AudioDocument, 1/0),
+       IF(?citeproc = "treaty", bibo:LegalDocument, 1/0),
+
+       bibo:Document  #default if nothing else fits
+     )) AS ?pubtype
+    )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg b/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
new file mode 100644
index 0000000..19bd42c
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
@@ -0,0 +1,17 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE <work_source>(?doi) {
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg>( ?work_data ) .
+}
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/work/queryset/work.graphql> AS ?graphqlquery
+WHERE {
+    # replace whitespace in graphql query (compress message)
+    BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
+    BIND ("""\{"variables":\{"doi":"{?doi}"},"query":"{?graphql}"}""" AS ?postbody)
+
+    # build http post request
+    BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
+    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+    BIND( fun:JSONPath( ?body, "$.data.work" ) AS ?work_data )
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/vivo-rdf/research.rqg b/src/main/resources/sparqlg/vivo-rdf/research.rqg
new file mode 100644
index 0000000..be6cb4a
--- /dev/null
+++ b/src/main/resources/sparqlg/vivo-rdf/research.rqg
@@ -0,0 +1,19 @@
+PREFIX vivo: <http://vivoweb.org/ontology/core#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX bibo: <http://purl.org/ontology/bibo/>
+
+GENERATE <research> (?id, ?pubtype, ?title, ?doi, ?pubyear) {
+
+        <{?id}> a ?pubtype ;
+            rdfs:label ?title ;
+            bibo:doi ?doi ;
+            vivo:dateTimeValue <{?id}-dtv> .
+
+        <{?id}-dtv> a vivo:DateTimeValue ;
+            vivo:dateTime ?pubyear ;
+            vivo:dateTimePrecision vivo:yearPrecision .
+
+}
+WHERE {
+  FILTER( BOUND(?id) && BOUND(?pubtype) ).
+}
\ No newline at end of file

From 540b09cd5c03ba63d0a524e82f35b6e686697074 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 7 Jun 2021 16:43:00 +0200
Subject: [PATCH 11/34] rename documentset

---
 .../{queryset => documentset}/organization.graphql            | 0
 .../sparqlg/datacitecommons/organization/orga_source.rqg      | 2 +-
 .../datacitecommons/organization/sparql-generate-conf.json    | 4 ++--
 .../person/{queryset => documentset}/person.graphql           | 0
 .../sparqlg/datacitecommons/person/person_source.rqg          | 2 +-
 .../sparqlg/datacitecommons/person/sparql-generate-conf.json  | 4 ++--
 .../work/{queryset => documentset}/work.graphql               | 0
 .../sparqlg/datacitecommons/work/sparql-generate-conf.json    | 4 ++--
 .../resources/sparqlg/datacitecommons/work/work_source.rqg    | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)
 rename src/main/resources/sparqlg/datacitecommons/organization/{queryset => documentset}/organization.graphql (100%)
 rename src/main/resources/sparqlg/datacitecommons/person/{queryset => documentset}/person.graphql (100%)
 rename src/main/resources/sparqlg/datacitecommons/work/{queryset => documentset}/work.graphql (100%)

diff --git a/src/main/resources/sparqlg/datacitecommons/organization/queryset/organization.graphql b/src/main/resources/sparqlg/datacitecommons/organization/documentset/organization.graphql
similarity index 100%
rename from src/main/resources/sparqlg/datacitecommons/organization/queryset/organization.graphql
rename to src/main/resources/sparqlg/datacitecommons/organization/documentset/organization.graphql
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg b/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
index 6766a9f..f93662e 100644
--- a/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
@@ -3,7 +3,7 @@ PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 GENERATE <orga_source>(?ror) {
     GENERATE <https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg>( ?orga_data ) .
 }
-SOURCE <https://projects.tib.eu/tapir/datacitecommons/organization/queryset/organization.graphql> AS ?graphqlquery
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql> AS ?graphqlquery
 WHERE {
     # replace whitespace in graphql query (compress message)
     BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
index 2029d4d..d29eb92 100644
--- a/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
@@ -3,8 +3,8 @@
   "query": "orga_source.rqg",
   "namedqueries": [
     {
-      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/queryset/organization.graphql",
-      "path": "queryset/organization.graphql"
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql",
+      "path": "documentset/organization.graphql"
     },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg",
diff --git a/src/main/resources/sparqlg/datacitecommons/person/queryset/person.graphql b/src/main/resources/sparqlg/datacitecommons/person/documentset/person.graphql
similarity index 100%
rename from src/main/resources/sparqlg/datacitecommons/person/queryset/person.graphql
rename to src/main/resources/sparqlg/datacitecommons/person/documentset/person.graphql
diff --git a/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg b/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
index 4f741ba..23dea39 100644
--- a/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
@@ -3,7 +3,7 @@ PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 GENERATE <person_source>(?orcid) {
     GENERATE <https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg>( ?person_data ) .
 }
-SOURCE <https://projects.tib.eu/tapir/datacitecommons/person/queryset/person.graphql> AS ?graphqlquery
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/person/documentset/person.graphql> AS ?graphqlquery
 WHERE {
     # replace whitespace in graphql query (compress message)
     BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
diff --git a/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
index 829839a..294af52 100644
--- a/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
@@ -3,8 +3,8 @@
   "query": "person_source.rqg",
   "namedqueries": [
     {
-      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/queryset/person.graphql",
-      "path": "queryset/person.graphql"
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/documentset/person.graphql",
+      "path": "documentset/person.graphql"
     },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg",
diff --git a/src/main/resources/sparqlg/datacitecommons/work/queryset/work.graphql b/src/main/resources/sparqlg/datacitecommons/work/documentset/work.graphql
similarity index 100%
rename from src/main/resources/sparqlg/datacitecommons/work/queryset/work.graphql
rename to src/main/resources/sparqlg/datacitecommons/work/documentset/work.graphql
diff --git a/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
index 40880bc..707a4b1 100644
--- a/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
@@ -3,8 +3,8 @@
   "query": "work_source.rqg",
   "namedqueries": [
     {
-      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/queryset/work.graphql",
-      "path": "queryset/work.graphql"
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/documentset/work.graphql",
+      "path": "documentset/work.graphql"
     },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg",
diff --git a/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg b/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
index 19bd42c..1f77405 100644
--- a/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
@@ -3,7 +3,7 @@ PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 GENERATE <work_source>(?doi) {
     GENERATE <https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg>( ?work_data ) .
 }
-SOURCE <https://projects.tib.eu/tapir/datacitecommons/work/queryset/work.graphql> AS ?graphqlquery
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/work/documentset/work.graphql> AS ?graphqlquery
 WHERE {
     # replace whitespace in graphql query (compress message)
     BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)

From d864eb5071ec54a20713296c9bffb41530fe1cfa Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 7 Jun 2021 18:25:17 +0200
Subject: [PATCH 12/34] refactor dc orga2person

---
 .../orga2person/orga2person.rqg               | 54 ++++++-------------
 .../orga2person/sparql-generate-conf.json     | 32 +++++++++++
 .../datacitecommons/person/person_mapping.rqg |  4 +-
 .../sparqlg/orcid/person/person_mapping.rqg   |  4 +-
 .../resources/sparqlg/vivo-rdf/person.rqg     | 38 +++++++++++--
 .../resources/sparqlg/vivo-rdf/position.rqg   | 27 ++++++----
 6 files changed, 104 insertions(+), 55 deletions(-)

diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
index bc40b9a..3990c90 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
@@ -9,48 +9,31 @@ PREFIX owl: <http://www.w3.org/2002/07/owl#>
 
 GENERATE  <orga2person>(?ror, ?after) {
 
-    <{?rorid}> a foaf:Organization ;
-               rdfs:label ?name .
+### map organization data
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg>( ?orga_data ) .
 
-    GENERATE {
-        <{?orcidid}-to-{?rorid}> a vivo:Position ;
-            rdfs:label "Unknown" ;
-            vivo:relates <{?orcidid}> ;
-            vivo:relates <{?rorid}> .
-
-        <{?orcidid}> a foaf:Person ;
-            rdfs:label ?completeName ;
-            vivo:orcidId <https://orcid.org/{?orcid}> ;
-            obo:ARG_2000028 <{?orcid}-vcard-dc> .
-
-        <{?orcid}> a owl:Thing ;
-            vivo:confirmedOrcidId <{?orcidid}> .
 
-        <{?orcidid}-vcard> a vcard:Individual ;
-            obo:ARG_2000029 <{?orcidid}> ;
-            vcard:hasName <{?orcidid}-vcard-name> .
+### map person data
+### and for every person: create a connection to organization
+    GENERATE {
+        GENERATE <https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg>( ?person_data ) .
 
-        <{?orcidid}-vcard-name> a vcard:Name ;
-            vcard:familyName ?familyName ;
-            vcard:givenName ?givenName .
+        GENERATE <https://projects.tib.eu/tapir/vivo-rdf/position.rqg>(?person_id, ?orga_id, ?role, ?start_date, ?end_date) .
     }
-    ITERATOR iter:JSONPath(?orga, '$.people.nodes[*]') AS ?person
+    ITERATOR iter:JSONPath(?orga_data, '$.people.nodes[*]') AS ?person_data
     WHERE{
-       # basic properties of a person in json
-      BIND(fun:JSONPath(?person, '$.id' ) AS ?orcid)
-      BIND(REPLACE(?orcid, "https://orcid.org/" , "" ) AS ?orcidid)
-      BIND(fun:JSONPath(?person, '$.givenName' ) AS ?givenName)
-      BIND(fun:JSONPath(?person, '$.familyName' ) AS ?familyName)
-      # processed properties
-      BIND(CONCAT(?familyName, ", ", ?givenName)  AS ?completeName)
-    }.
+        BIND(<https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg>(?orga_data) AS ?orga_id)
+        BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
+    } .
+
 
+############################# call this query again if hasNextPage =true  #############################################
     GENERATE{
       GENERATE <https://projects.tib.eu/tapir/datacitecommons/orga2person/orga2person.rqg>( ?ror, ?cursor ) .
     }
     WHERE{
-      BIND(fun:JSONPath(?orga, '$.people.pageInfo.hasNextPage' ) AS ?hasNextPage)
-      BIND(fun:JSONPath(?orga, '$.people.pageInfo.endCursor' ) AS ?endCursor)
+      BIND(fun:JSONPath(?orga_data, '$.people.pageInfo.hasNextPage' ) AS ?hasNextPage)
+      BIND(fun:JSONPath(?orga_data, '$.people.pageInfo.endCursor' ) AS ?endCursor)
       BIND(IF(STR(?hasNextPage)="true", ?endCursor, ?undef) AS ?cursor )
       FILTER( BOUND(?cursor) ).
      }.
@@ -66,10 +49,5 @@ WHERE {
     BIND(  fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
-    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga )
-
-    # basic properties of organization in json
-    BIND(fun:JSONPath(?orga, '$.id' ) AS ?ror)
-    BIND(REPLACE(?ror, "https://ror.org/" , "" ) AS ?rorid)
-    BIND(fun:JSONPath(?orga, '$.name' ) AS ?name)
+    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
 }
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
index 7d844dc..6c37d32 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
@@ -9,6 +9,38 @@
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person/documentset/orga2person.graphql",
       "path": "documentset/orga2person.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg",
+      "path": "../organization/orga_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg",
+      "path": "../organization/orga_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
+      "path": "../../vivo-rdf/organization.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg",
+      "path": "../person/person_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg",
+      "path": "../person/person_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/person.rqg",
+      "path": "../../vivo-rdf/person.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/position.rqg",
+      "path": "../../vivo-rdf/position.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg b/src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg
index ca06e58..10174d7 100644
--- a/src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/person/person_mapping.rqg
@@ -3,7 +3,7 @@ PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 GENERATE <person_mapping>(?person_data) {
 
     ## fill in blanks in person definition in vivo ontology
-    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?name) .
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?orcid, ?familyName, ?givenName) .
 
     ## add ORCID as PID
     GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://orcid.org/", ?id) .
@@ -11,8 +11,8 @@ GENERATE <person_mapping>(?person_data) {
 WHERE {
     ### basic properties of organization
     BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?id)
+    BIND(?id AS ?orcid)
 
     BIND(fun:JSONPath(?person_data, '$.givenName' ) AS ?givenName)
     BIND(fun:JSONPath(?person_data, '$.familyName' ) AS ?familyName)
-    BIND(CONCAT(?familyName, ", ", ?givenName)  AS ?name)
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/person/person_mapping.rqg b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
index 65aadbf..afa421b 100644
--- a/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
+++ b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
@@ -4,7 +4,7 @@ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 GENERATE <person_mapping>(?orcid_data) {
 
     ## fill in blanks in person definition in vivo ontology
-    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?name) .
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?orcid, ?familyName, ?givenName) .
 
     ## add ORCID as data source
     GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://orcid.org/", ?id) .
@@ -13,8 +13,8 @@ GENERATE <person_mapping>(?orcid_data) {
 WHERE {
     ### extract properties of person
     BIND(<https://projects.tib.eu/tapir/orcid/person/person_id.rqg>(?orcid_data) AS ?id)
+    BIND(?id AS ?orcid)
 
     BIND(fun:JSONPath(?orcid_data, '$.person.name.given-names.value' ) AS ?givenName)
     BIND(fun:JSONPath(?orcid_data, '$.person.name.family-name.value' ) AS ?familyName)
-    BIND(CONCAT(?familyName, ", ", ?givenName)  AS ?name)
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/vivo-rdf/person.rqg b/src/main/resources/sparqlg/vivo-rdf/person.rqg
index f8196ef..5bdef7e 100644
--- a/src/main/resources/sparqlg/vivo-rdf/person.rqg
+++ b/src/main/resources/sparqlg/vivo-rdf/person.rqg
@@ -1,9 +1,41 @@
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX vivo: <http://vivoweb.org/ontology/core#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
 
-GENERATE <person> (?id, ?name){
+GENERATE <person> (?id, ?orcid, ?familyName, ?givenName){
 
-### id, name : basic attributes of a person
     <{?id}> a foaf:Person ;
-     rdfs:label ?name .
+        rdfs:label ?completeName ;
+        vivo:orcidId <https://orcid.org/{?orcid}> .
+
+
+### vcard : TRIPLES TO ADD VCARD
+    GENERATE{
+       <{?id}> obo:ARG_2000028 <{?id}-vcard> .
+
+       <{?id}-vcard> a vcard:Individual ;
+           obo:ARG_2000029 <{?id}> .
+    }
+    WHERE {
+       FILTER( BOUND(?familyName) || BOUND(?givenName)  ).
+    } .
+
+
+### name : TRIPLES TO ADD NAME
+    GENERATE{
+       <{?id}-vcard> vcard:hasName <{?id}-vcard-name> .
+
+       <{?id}-vcard-name> a vcard:Name ;
+           vcard:familyName ?familyName ;
+           vcard:givenName ?givenName .
+    }
+    WHERE {
+       FILTER( BOUND(?familyName) || BOUND(?givenName)  ).
+    } .
+}
+WHERE{
+    BIND(CONCAT(?familyName, ", ", ?givenName)  AS ?completeName)
+    FILTER( BOUND(?id) ).
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/vivo-rdf/position.rqg b/src/main/resources/sparqlg/vivo-rdf/position.rqg
index c210083..50e29e9 100644
--- a/src/main/resources/sparqlg/vivo-rdf/position.rqg
+++ b/src/main/resources/sparqlg/vivo-rdf/position.rqg
@@ -3,24 +3,24 @@ PREFIX vivo: <http://vivoweb.org/ontology/core#>
 
 GENERATE <position> (?person_id, ?orga_id, ?role, ?start_date, ?end_date){
 
-    <{?position_id_clean}> a vivo:Position ;
+    <{?position_id}> a vivo:Position ;
         rdfs:label ?role_value ;
         vivo:relates <{?person_id}> ;
         vivo:relates <{?orga_id}> .
 
-   GENERATE{
-        <{?position_id_clean}> vivo:dateTimeInterval <{?position_id_clean}-dti> .
 
-        <{?position_id_clean}-dti> a vivo:DateTimeInterval ;
-            vivo:start <{?position_id}-start> ;
-            vivo:end <{?position_id}-end> .
+### position dates : TRIPLES FOR POSITION DATES
+   GENERATE{
+        <{?position_id}> vivo:dateTimeInterval <{?position_id}-dti> .
    }
    WHERE {
      FILTER( BOUND(?start_date) || BOUND(?end_date) ).
    } .
 
    GENERATE{
-      <{?position_id_clean}-start> a vivo:DateTimeValue ;
+      <{?position_id}-dti>  vivo:start <{?position_id}-start> .
+
+      <{?position_id}-start> a vivo:DateTimeValue ;
         vivo:dateTime ?start_date ;
         vivo:dateTimePrecision vivo:yearPrecision .
    }
@@ -29,7 +29,9 @@ GENERATE <position> (?person_id, ?orga_id, ?role, ?start_date, ?end_date){
    } .
 
   GENERATE{
-    <{?position_id_clean}-end> a vivo:DateTimeValue ;
+    <{?position_id}-dti> vivo:end <{?position_id}-end> .
+
+    <{?position_id}-end> a vivo:DateTimeValue ;
         vivo:dateTime ?end_date ;
         vivo:dateTimePrecision vivo:yearPrecision .
   }
@@ -39,9 +41,14 @@ GENERATE <position> (?person_id, ?orga_id, ?role, ?start_date, ?end_date){
 
 }
 WHERE {
-    BIND("{?person_id}-{?role}-{?start_date}" AS ?position_id)
-    BIND(REPLACE(?position_id,  "\\W", "", "i") AS ?position_id_clean)
+    # set default values if empty or unbound
     BIND(IF(BOUND(?role) && strlen(?role)>0, ?role, "Unknown") AS ?role_value)
+    BIND(REPLACE(?role_value,  "\\W", "", "i") AS ?role_clean)
+
+    BIND(IF(BOUND(?start_date) && strlen(?start_date)>0, STR(?start_date), "") AS ?start_value)
+
+    # create (hopefully) unique id
+    BIND("{?person_id}-{?role_clean}-{?start_value}" AS ?position_id)
 
     FILTER( BOUND(?person_id) && BOUND(?orga_id) ).
 }
\ No newline at end of file

From 5c0b9ef0c3a80d2ad614d7a0a3e74441f0ee0a97 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 7 Jun 2021 18:49:01 +0200
Subject: [PATCH 13/34] refactor dc person2publication

---
 .../person2publication/person2publication.rqg | 106 ++----------------
 .../sparql-generate-conf.json                 |  36 +++++-
 .../resources/sparqlg/vivo-rdf/authorship.rqg |   9 ++
 3 files changed, 56 insertions(+), 95 deletions(-)
 create mode 100644 src/main/resources/sparqlg/vivo-rdf/authorship.rqg

diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg b/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
index a974f60..3842220 100644
--- a/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
@@ -1,102 +1,27 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-PREFIX vivo: <http://vivoweb.org/ontology/core#>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX bibo: <http://purl.org/ontology/bibo/>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 
 GENERATE  <person2publication>(?orcid, ?after) {
 
-## triples for person
-    <{?orcidid}> a foaf:Person ;
-        rdfs:label ?completeName ;
-        vivo:orcidId <{?orcid}> ;
-        obo:ARG_2000028 <{?orcidid}-vcard> .
-
-    <{?orcid}> a owl:Thing ;
-        vivo:confirmedOrcidId <{?orcidid}> .
-
-    <{?orcidid}-vcard> a vcard:Individual ;
-        obo:ARG_2000029 <{?orcidid}> ;
-        vcard:hasName <{?orcidid}-vcard-name> .
-
-    <{?orcidid}-vcard-name> a vcard:Name ;
-        vcard:familyName ?familyName ;
-        vcard:givenName ?givenName .
+### map person data
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg>( ?person_data ) .
 
 
+### map work data
+### and for every work: create a connection to person
     GENERATE {
-        ## connection person -> publication
-            <{?orcidid}-to-{?doi_clean}> a vivo:Authorship ;
-                vivo:relates <{?orcidid}> ;
-                vivo:relates <{?doi_clean}> .
-
-        ## triples for publication
-            <{?doi_clean}> a ?pubtype ;
-                rdfs:label ?title ;
-                bibo:doi ?doi ;
-                vivo:dateTimeValue <{?doi_clean}-dtv> .
+        GENERATE <https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg>( ?work_data ) .
 
-            <{?doi_clean}-dtv> a vivo:DateTimeValue ;
-                vivo:dateTime ?pubyear_dtv ;
-                vivo:dateTimePrecision vivo:yearPrecision .
+        GENERATE <https://projects.tib.eu/tapir/vivo-rdf/authorship.rqg>(?person_id, ?work_id) .
     }
-    ITERATOR iter:JSONPath(?person, '$.publications.nodes[*][?(!@.versions.nodes[0])]') AS ?pub
+    ITERATOR iter:JSONPath(?person_data, '$.publications.nodes[*][?(!@.versions.nodes[0])]') AS ?work_data
     WHERE{
-       # basic properties of a publication in json
-       BIND(fun:JSONPath(?pub, '$.doi' ) AS ?doi)
-       BIND(REPLACE(?doi,  "\\W", "", "i") AS ?doi_clean)
-       BIND(fun:JSONPath(?pub, '$.titles[0].title' ) AS ?title)
+        BIND(<https://projects.tib.eu/tapir/datacitecommons/work/work_id.rqg>(?work_data) AS ?work_id)
+        BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
+    } .
 
-       BIND(fun:JSONPath(?pub, '$.publicationYear' ) AS ?pubyear)
-       BIND(xsd:dateTime(CONCAT(STR(?pubyear), "-01-01T00:00:00"))  AS ?pubyear_dtv)
-
-       BIND(fun:JSONPath(?pub, '$.types.citeproc' ) AS ?citeproc)
-       # mapping taken from VIVO (claim DOI)
-       BIND (
-         IRI(COALESCE(
-           IF(?citeproc = "article-journal", bibo:AcademicArticle, 1/0),
-           IF(?citeproc = "article", bibo:Article, 1/0),
-           IF(?citeproc = "book", bibo:Book, 1/0),
-           IF(?citeproc = "chapter", bibo:Chapter, 1/0),
-           IF(?citeproc = "dataset", vivo:Dataset, 1/0),
-           IF(?citeproc = "figure", bibo:Image, 1/0),
-           IF(?citeproc = "graphic", bibo:Image, 1/0),
-           IF(?citeproc = "legal_case", bibo:LegalCaseDocument, 1/0),
-           IF(?citeproc = "legislation", bibo:Legislation, 1/0),
-           IF(?citeproc = "manuscript", bibo:Manuscript, 1/0),
-           IF(?citeproc = "map", bibo:Map, 1/0),
-           IF(?citeproc = "musical_score", vivo:Score, 1/0),
-           IF(?citeproc = "paper-conference", vivo:ConferencePaper, 1/0),
-           IF(?citeproc = "patent", bibo:Patent, 1/0),
-           IF(?citeproc = "personal_communication", bibo:PersonalCommunicationDocument, 1/0),
-           IF(?citeproc = "post-weblog", vivo:BlogPosting, 1/0),
-           IF(?citeproc = "report", bibo:Report, 1/0),
-           IF(?citeproc = "review", vivo:Review, 1/0),
-           IF(?citeproc = "speech", vivo:Speech, 1/0),
-           IF(?citeproc = "thesis", bibo:Thesis, 1/0),
-           IF(?citeproc = "webpage", bibo:Webpage, 1/0),
-
-         # mapping leftover types
-           IF(STRSTARTS(?citeproc, "article"), bibo:Article, 1/0),
-           IF(?citeproc = "bill", bibo:Bill, 1/0),
-           IF(STRSTARTS(?citeproc, "entry"), bibo:DocumentPart, 1/0),
-           IF(?citeproc = "interview", bibo:Interview, 1/0),
-           IF(?citeproc = "motion_picture", bibo:Film, 1/0),
-           IF(?citeproc = "post", vivo:BlogPosting, 1/0),
-           IF(?citeproc = "review-book", vivo:Review, 1/0),
-           IF(?citeproc = "song", bibo:AudioDocument, 1/0),
-           IF(?citeproc = "treaty", bibo:LegalDocument, 1/0),
-
-           bibo:Document  #default if nothing else fits
-         )) AS ?pubtype
-       )
-    }.
 
+############################# call this query again if hasNextPage =true  #############################################
     GENERATE{
       GENERATE <https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg>( ?orcid, ?cursor ) .
     }
@@ -119,12 +44,5 @@ WHERE {
     BIND(  fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
-
-    BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person )
-   # basic properties of a person in json
-   BIND(fun:JSONPath(?person, '$.id' ) AS ?orcid)
-   BIND(REPLACE(?orcid, "https://orcid.org/" , "" ) AS ?orcidid)
-   BIND(fun:JSONPath(?person, '$.givenName' ) AS ?givenName)
-   BIND(fun:JSONPath(?person, '$.familyName' ) AS ?familyName)
-   BIND(CONCAT(?familyName, ", ", ?givenName)  AS ?completeName)
+    BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person_data )
 }
diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json
index eb1e635..1391eaa 100644
--- a/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json
@@ -1,11 +1,45 @@
 {
   "base": "http://vivo.mydomain.edu/individual/",
   "query": "person2publication.rqg",
-  "documentset": [
+  "namedqueries": [
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg",
       "path": "person2publication.rqg"
     },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg",
+      "path": "../work/work_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_id.rqg",
+      "path": "../work/work_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/research.rqg",
+      "path": "../../vivo-rdf/research.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg",
+      "path": "../person/person_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg",
+      "path": "../person/person_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/person.rqg",
+      "path": "../../vivo-rdf/person.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/authorship.rqg",
+      "path": "../../vivo-rdf/authorship.rqg"
+    }
+  ],
+  "documentset": [
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/person2publication/documentset/person2publication.graphql",
       "path": "documentset/person2publication.graphql"
diff --git a/src/main/resources/sparqlg/vivo-rdf/authorship.rqg b/src/main/resources/sparqlg/vivo-rdf/authorship.rqg
new file mode 100644
index 0000000..751f072
--- /dev/null
+++ b/src/main/resources/sparqlg/vivo-rdf/authorship.rqg
@@ -0,0 +1,9 @@
+PREFIX vivo: <http://vivoweb.org/ontology/core#>
+
+GENERATE <authorship> (?person_id, ?work_id){
+
+    <{?person_id}-to-{?work_id}> a vivo:Authorship ;
+        vivo:relates <{?person_id}> ;
+        vivo:relates <{?work_id}> .
+
+}
\ No newline at end of file

From e2c88dd5131977fadaeaccb3189d5e2e5b1b35c1 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 7 Jun 2021 18:50:24 +0200
Subject: [PATCH 14/34] namedqueries and rm prefixes

---
 .../datacitecommons/orga2person/orga2person.rqg      |  6 ------
 .../orga2person/sparql-generate-conf.json            | 12 +++++++-----
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
index 3990c90..20049ba 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
@@ -1,11 +1,5 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX foaf: <http://xmlns.com/foaf/0.1/>
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-PREFIX vcard: <http://www.w3.org/2006/vcard/ns#>
-PREFIX vivo: <http://vivoweb.org/ontology/core#>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
 
 GENERATE  <orga2person>(?ror, ?after) {
 
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
index 6c37d32..eedfa4b 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
@@ -1,15 +1,11 @@
 {
   "base": "http://vivo.mydomain.edu/individual/",
   "query": "orga2person.rqg",
-  "documentset": [
+  "namedqueries": [
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person/orga2person.rqg",
       "path": "orga2person.rqg"
     },
-    {
-      "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person/documentset/orga2person.graphql",
-      "path": "documentset/orga2person.graphql"
-    },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg",
       "path": "../organization/orga_mapping.rqg"
@@ -42,5 +38,11 @@
       "uri": "https://projects.tib.eu/tapir/vivo-rdf/position.rqg",
       "path": "../../vivo-rdf/position.rqg"
     }
+  ],
+  "documentset": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person/documentset/orga2person.graphql",
+      "path": "documentset/orga2person.graphql"
+    }
   ]
 }
\ No newline at end of file

From f3e3b5963eaca8c373679a3acd5e25e41c82b32b Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 8 Jun 2021 16:30:58 +0200
Subject: [PATCH 15/34] merge develop

---
 .../controller/DataciteCommonsController.java | 128 ++++++++---------
 .../eu/tib/controller/OrcidController.java    | 134 +++++++++---------
 .../java/eu/tib/controller/RORController.java | 128 ++++++++---------
 .../tib/controller/validation/Validator.java  |   6 +
 4 files changed, 198 insertions(+), 198 deletions(-)
 create mode 100644 src/main/java/eu/tib/controller/validation/Validator.java

diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index f15a256..53c5992 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -1,65 +1,63 @@
-package eu.tib.controller;
-
-import eu.tib.service.ResponseService;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiParam;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.util.StopWatch;
-import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import javax.validation.Valid;
-import javax.validation.constraints.Pattern;
-import java.util.Collections;
-
-@Slf4j
-@Validated
-@RestController
-@RequestMapping(value = "/datacitecommons")
-@Api(value = "Controller", tags = {"datacitecommons"})
-public class DataciteCommonsController {
-
-    @Autowired
-    private ResponseService responseService;
-
-    @PostMapping(value = "/getOrganizationPlusPersons", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusPersons(
-            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/datacitecommons/orga2person";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-
-    @PostMapping(value = "/getPersonPlusPublications", produces = "application/json")
-    public ResponseEntity<String> getPersonPlusPublications(
-            @Valid @Pattern(regexp = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{4}")
-            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
-            @RequestParam String orcid) {
-
-        final String id = "sparqlg/datacitecommons/person2publication";
-        log.info("Incoming Request for " + id + " with orcid: " + orcid);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("orcid", orcid));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-}
+package eu.tib.controller;
+
+import eu.tib.controller.validation.Validator;
+import eu.tib.service.ResponseService;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.StopWatch;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;
+
+import javax.validation.Valid;
+import javax.validation.constraints.Pattern;
+import java.util.Collections;
+
+@Slf4j
+@Validated
+@RestController
+@RequestMapping(value = "/datacitecommons")
+@Api(value = "Controller", tags = {"datacitecommons"})
+public class DataciteCommonsController {
+
+    @Autowired
+    private ResponseService responseService;
+
+    @GetMapping(value = "/organizationPlusPersons", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusPersons(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/datacitecommons/orga2person";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+    @GetMapping(value = "/personPlusPublications", produces = "application/json")
+    public ResponseEntity<String> getPersonPlusPublications(
+            @Valid @Pattern(regexp = Validator.orcid)
+            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
+            @RequestParam String orcid) {
+
+        final String id = "sparqlg/datacitecommons/person2publication";
+        log.info("Incoming Request for " + id + " with orcid: " + orcid);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("orcid", orcid));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+}
diff --git a/src/main/java/eu/tib/controller/OrcidController.java b/src/main/java/eu/tib/controller/OrcidController.java
index fc1bde3..3764202 100644
--- a/src/main/java/eu/tib/controller/OrcidController.java
+++ b/src/main/java/eu/tib/controller/OrcidController.java
@@ -1,68 +1,66 @@
-package eu.tib.controller;
-
-import eu.tib.service.ResponseService;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiParam;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.util.StopWatch;
-import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import javax.validation.Valid;
-import javax.validation.constraints.Pattern;
-import java.util.Collections;
-
-@Slf4j
-@Validated
-@RestController
-@RequestMapping(value = "/orcid")
-@Api(value = "Controller", tags = {"orcid"})
-public class OrcidController {
-
-    @Autowired
-    private ResponseService responseService;
-
-    @PostMapping(value = "/getPerson", produces = "application/json")
-    public ResponseEntity<String> getPerson(
-            @Valid @Pattern(regexp = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{4}")
-            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
-            @RequestParam String orcid) {
-
-        final String id = "sparqlg/orcid/person";
-        log.info("Incoming Request for " + id + " with orcid: " + orcid);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        String orcid_id = orcid.replaceFirst("https://orcid.org/","");
-        ResponseEntity result = responseService.buildResponse(id,
-                Collections.singletonMap("orcid", orcid_id));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-
-
-    @PostMapping(value = "/getCurrentEmployees", produces = "application/json")
-    public ResponseEntity<String> getCurrentEmployees(
-            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/orcid/employees";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-}
+package eu.tib.controller;
+
+import eu.tib.controller.validation.Validator;
+import eu.tib.service.ResponseService;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.StopWatch;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;
+
+import javax.validation.Valid;
+import javax.validation.constraints.Pattern;
+import java.util.Collections;
+
+@Slf4j
+@Validated
+@RestController
+@RequestMapping(value = "/orcid")
+@Api(value = "Controller", tags = {"orcid"})
+public class OrcidController {
+
+    @Autowired
+    private ResponseService responseService;
+
+    @GetMapping(value = "/person", produces = "application/json")
+    public ResponseEntity<String> getPerson(
+            @Valid @Pattern(regexp = Validator.orcid)
+            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
+            @RequestParam String orcid) {
+
+        final String id = "sparqlg/orcid/person";
+        log.info("Incoming Request for " + id + " with orcid: " + orcid);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        String orcid_id = orcid.replaceFirst("https://orcid.org/","");
+        ResponseEntity result = responseService.buildResponse(id,
+                Collections.singletonMap("orcid", orcid_id));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+
+    @GetMapping(value = "/currentEmployees", produces = "application/json")
+    public ResponseEntity<String> getCurrentEmployees(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/orcid/employees";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+}
diff --git a/src/main/java/eu/tib/controller/RORController.java b/src/main/java/eu/tib/controller/RORController.java
index 4cb9fbe..32151b2 100644
--- a/src/main/java/eu/tib/controller/RORController.java
+++ b/src/main/java/eu/tib/controller/RORController.java
@@ -1,65 +1,63 @@
-package eu.tib.controller;
-
-import eu.tib.service.ResponseService;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiParam;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.util.StopWatch;
-import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import javax.validation.Valid;
-import javax.validation.constraints.Pattern;
-import java.util.Collections;
-
-@Slf4j
-@Validated
-@RestController
-@RequestMapping(value = "/ror")
-@Api(value = "Controller", tags = {"ror"})
-public class RORController {
-
-    @Autowired
-    private ResponseService responseService;
-
-    @PostMapping(value = "/getOrganizationPlusChildren", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusChildren(
-            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/ror/orga2children";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-
-    @PostMapping(value = "/getOrganization", produces = "application/json")
-    public ResponseEntity<String> getOrganization(
-            @Valid @Pattern(regexp = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}")
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/ror/organization";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-}
+package eu.tib.controller;
+
+import eu.tib.controller.validation.Validator;
+import eu.tib.service.ResponseService;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.StopWatch;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;
+
+import javax.validation.Valid;
+import javax.validation.constraints.Pattern;
+import java.util.Collections;
+
+@Slf4j
+@Validated
+@RestController
+@RequestMapping(value = "/ror")
+@Api(value = "Controller", tags = {"ror"})
+public class RORController {
+
+    @Autowired
+    private ResponseService responseService;
+
+    @GetMapping(value = "/organizationPlusChildren", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusChildren(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/ror/orga2children";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+    @GetMapping(value = "/organization", produces = "application/json")
+    public ResponseEntity<String> getOrganization(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/ror/organization";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+}
diff --git a/src/main/java/eu/tib/controller/validation/Validator.java b/src/main/java/eu/tib/controller/validation/Validator.java
new file mode 100644
index 0000000..2ca80cd
--- /dev/null
+++ b/src/main/java/eu/tib/controller/validation/Validator.java
@@ -0,0 +1,6 @@
+package eu.tib.controller.validation;
+
+public class Validator {
+    public static final String ror = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}$";
+    public static final String orcid = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$";
+}

From ec89175c4e02e5958ce2b69cea2dfa590c5f325b Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 8 Jun 2021 16:31:55 +0200
Subject: [PATCH 16/34] add person2publication in orcid

---
 .../sparqlg/orcid/person/person_mapping.rqg   | 12 +++++++----
 .../orcid/person/sparql-generate-conf.json    | 12 +++++++++++
 .../orcid/person/work/work_mapping.rqg        | 20 +++++++++++++++++++
 3 files changed, 40 insertions(+), 4 deletions(-)
 create mode 100644 src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg

diff --git a/src/main/resources/sparqlg/orcid/person/person_mapping.rqg b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
index afa421b..d690806 100644
--- a/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
+++ b/src/main/resources/sparqlg/orcid/person/person_mapping.rqg
@@ -1,19 +1,23 @@
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 
 GENERATE <person_mapping>(?orcid_data) {
 
     ## fill in blanks in person definition in vivo ontology
-    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?id, ?orcid, ?familyName, ?givenName) .
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/person.rqg>(?person_id, ?orcid, ?familyName, ?givenName) .
 
     ## add ORCID as data source
-    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?id, "https://orcid.org/", ?id) .
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg>(?person_id, "https://orcid.org/", ?orcid) .
 
+    ## map works
+    GENERATE <https://projects.tib.eu/tapir/orcid/person/work/work_mapping.rqg>(?person_id, ?work_data)
+    ITERATOR iter:JSONPath(?orcid_data, '$.activities-summary.works.group[*]') AS ?work_data .
 }
 WHERE {
     ### extract properties of person
-    BIND(<https://projects.tib.eu/tapir/orcid/person/person_id.rqg>(?orcid_data) AS ?id)
-    BIND(?id AS ?orcid)
+    BIND(<https://projects.tib.eu/tapir/orcid/person/person_id.rqg>(?orcid_data) AS ?person_id)
+    BIND(?person_id AS ?orcid)
 
     BIND(fun:JSONPath(?orcid_data, '$.person.name.given-names.value' ) AS ?givenName)
     BIND(fun:JSONPath(?orcid_data, '$.person.name.family-name.value' ) AS ?familyName)
diff --git a/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json b/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
index e389611..e100be8 100644
--- a/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/orcid/person/sparql-generate-conf.json
@@ -17,6 +17,18 @@
     {
       "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
       "path": "../../vivo-rdf/agent_pid.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/orcid/person/work/work_mapping.rqg",
+      "path": "work/work_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/research.rqg",
+      "path": "../../vivo-rdf/research.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/authorship.rqg",
+      "path": "../../vivo-rdf/authorship.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg b/src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg
new file mode 100644
index 0000000..3dd1798
--- /dev/null
+++ b/src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg
@@ -0,0 +1,20 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+PREFIX bibo: <http://purl.org/ontology/bibo/>
+
+GENERATE <work_mapping>(?person_id, ?work_data) {
+
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/research.rqg> (?work_id, ?pubtype, ?title, ?doi, ?pubyear_dtv) .
+
+    GENERATE <https://projects.tib.eu/tapir/vivo-rdf/authorship.rqg>(?person_id, ?work_id) .
+
+}
+WHERE {
+    BIND(fun:JSONPath(?work_data, '$.work-summary[0]' ) AS ?work_summary)
+    BIND(fun:JSONPath(?work_summary, '$.title.title.value' ) AS ?title)
+    BIND(fun:JSONPath(?work_summary, '$.publication-date.year.value' ) AS ?pubyear)
+    BIND(fun:JSONPath(?work_summary, '$.external-ids.external-id[?(@.external-id-type==\'doi\')]' ) AS ?all_dois)
+    BIND(fun:JSONPath(?all_dois, '$.[0].external-id-value' ) AS ?doi)
+    BIND(bibo:Document AS ?pubtype)
+
+    BIND(REPLACE(?doi,  "\\W", "", "i") AS ?work_id)
+}
\ No newline at end of file

From 3697c0256196794857b512ba2493facc382ee548 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 8 Jun 2021 16:32:14 +0200
Subject: [PATCH 17/34] merge develop

---
 .../controller/DataciteCommonsController.java | 126 ++++++++---------
 .../eu/tib/controller/OrcidController.java    | 132 +++++++++---------
 .../java/eu/tib/controller/RORController.java | 126 ++++++++---------
 .../tib/controller/validation/Validator.java  |  12 +-
 4 files changed, 198 insertions(+), 198 deletions(-)

diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index 53c5992..fe99660 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -1,63 +1,63 @@
-package eu.tib.controller;
-
-import eu.tib.controller.validation.Validator;
-import eu.tib.service.ResponseService;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiParam;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.util.StopWatch;
-import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.*;
-
-import javax.validation.Valid;
-import javax.validation.constraints.Pattern;
-import java.util.Collections;
-
-@Slf4j
-@Validated
-@RestController
-@RequestMapping(value = "/datacitecommons")
-@Api(value = "Controller", tags = {"datacitecommons"})
-public class DataciteCommonsController {
-
-    @Autowired
-    private ResponseService responseService;
-
-    @GetMapping(value = "/organizationPlusPersons", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusPersons(
-            @Valid @Pattern(regexp = Validator.ror)
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/datacitecommons/orga2person";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-
-    @GetMapping(value = "/personPlusPublications", produces = "application/json")
-    public ResponseEntity<String> getPersonPlusPublications(
-            @Valid @Pattern(regexp = Validator.orcid)
-            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
-            @RequestParam String orcid) {
-
-        final String id = "sparqlg/datacitecommons/person2publication";
-        log.info("Incoming Request for " + id + " with orcid: " + orcid);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("orcid", orcid));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-}
+package eu.tib.controller;
+
+import eu.tib.controller.validation.Validator;
+import eu.tib.service.ResponseService;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.StopWatch;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;
+
+import javax.validation.Valid;
+import javax.validation.constraints.Pattern;
+import java.util.Collections;
+
+@Slf4j
+@Validated
+@RestController
+@RequestMapping(value = "/datacitecommons")
+@Api(value = "Controller", tags = {"datacitecommons"})
+public class DataciteCommonsController {
+
+    @Autowired
+    private ResponseService responseService;
+
+    @GetMapping(value = "/organizationPlusPersons", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusPersons(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/datacitecommons/orga2person";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+    @GetMapping(value = "/personPlusPublications", produces = "application/json")
+    public ResponseEntity<String> getPersonPlusPublications(
+            @Valid @Pattern(regexp = Validator.orcid)
+            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
+            @RequestParam String orcid) {
+
+        final String id = "sparqlg/datacitecommons/person2publication";
+        log.info("Incoming Request for " + id + " with orcid: " + orcid);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("orcid", orcid));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+}
diff --git a/src/main/java/eu/tib/controller/OrcidController.java b/src/main/java/eu/tib/controller/OrcidController.java
index 3764202..d4b53fe 100644
--- a/src/main/java/eu/tib/controller/OrcidController.java
+++ b/src/main/java/eu/tib/controller/OrcidController.java
@@ -1,66 +1,66 @@
-package eu.tib.controller;
-
-import eu.tib.controller.validation.Validator;
-import eu.tib.service.ResponseService;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiParam;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.util.StopWatch;
-import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.*;
-
-import javax.validation.Valid;
-import javax.validation.constraints.Pattern;
-import java.util.Collections;
-
-@Slf4j
-@Validated
-@RestController
-@RequestMapping(value = "/orcid")
-@Api(value = "Controller", tags = {"orcid"})
-public class OrcidController {
-
-    @Autowired
-    private ResponseService responseService;
-
-    @GetMapping(value = "/person", produces = "application/json")
-    public ResponseEntity<String> getPerson(
-            @Valid @Pattern(regexp = Validator.orcid)
-            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
-            @RequestParam String orcid) {
-
-        final String id = "sparqlg/orcid/person";
-        log.info("Incoming Request for " + id + " with orcid: " + orcid);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        String orcid_id = orcid.replaceFirst("https://orcid.org/","");
-        ResponseEntity result = responseService.buildResponse(id,
-                Collections.singletonMap("orcid", orcid_id));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-
-
-    @GetMapping(value = "/currentEmployees", produces = "application/json")
-    public ResponseEntity<String> getCurrentEmployees(
-            @Valid @Pattern(regexp = Validator.ror)
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/orcid/employees";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-}
+package eu.tib.controller;
+
+import eu.tib.controller.validation.Validator;
+import eu.tib.service.ResponseService;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.StopWatch;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;
+
+import javax.validation.Valid;
+import javax.validation.constraints.Pattern;
+import java.util.Collections;
+
+@Slf4j
+@Validated
+@RestController
+@RequestMapping(value = "/orcid")
+@Api(value = "Controller", tags = {"orcid"})
+public class OrcidController {
+
+    @Autowired
+    private ResponseService responseService;
+
+    @GetMapping(value = "/person", produces = "application/json")
+    public ResponseEntity<String> getPerson(
+            @Valid @Pattern(regexp = Validator.orcid)
+            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
+            @RequestParam String orcid) {
+
+        final String id = "sparqlg/orcid/person";
+        log.info("Incoming Request for " + id + " with orcid: " + orcid);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        String orcid_id = orcid.replaceFirst("https://orcid.org/","");
+        ResponseEntity result = responseService.buildResponse(id,
+                Collections.singletonMap("orcid", orcid_id));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+
+    @GetMapping(value = "/currentEmployees", produces = "application/json")
+    public ResponseEntity<String> getCurrentEmployees(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/orcid/employees";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+}
diff --git a/src/main/java/eu/tib/controller/RORController.java b/src/main/java/eu/tib/controller/RORController.java
index 32151b2..3ad6c23 100644
--- a/src/main/java/eu/tib/controller/RORController.java
+++ b/src/main/java/eu/tib/controller/RORController.java
@@ -1,63 +1,63 @@
-package eu.tib.controller;
-
-import eu.tib.controller.validation.Validator;
-import eu.tib.service.ResponseService;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiParam;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
-import org.springframework.util.StopWatch;
-import org.springframework.validation.annotation.Validated;
-import org.springframework.web.bind.annotation.*;
-
-import javax.validation.Valid;
-import javax.validation.constraints.Pattern;
-import java.util.Collections;
-
-@Slf4j
-@Validated
-@RestController
-@RequestMapping(value = "/ror")
-@Api(value = "Controller", tags = {"ror"})
-public class RORController {
-
-    @Autowired
-    private ResponseService responseService;
-
-    @GetMapping(value = "/organizationPlusChildren", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusChildren(
-            @Valid @Pattern(regexp = Validator.ror)
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/ror/orga2children";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-
-    @GetMapping(value = "/organization", produces = "application/json")
-    public ResponseEntity<String> getOrganization(
-            @Valid @Pattern(regexp = Validator.ror)
-            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
-            @RequestParam String ror) {
-
-        final String id = "sparqlg/ror/organization";
-        log.info("Incoming Request for " + id + " with ror: " + ror);
-        StopWatch stopWatch = new StopWatch(id);
-        stopWatch.start(id);
-
-        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
-
-        stopWatch.stop();
-        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
-        return result;
-    }
-}
+package eu.tib.controller;
+
+import eu.tib.controller.validation.Validator;
+import eu.tib.service.ResponseService;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.StopWatch;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;
+
+import javax.validation.Valid;
+import javax.validation.constraints.Pattern;
+import java.util.Collections;
+
+@Slf4j
+@Validated
+@RestController
+@RequestMapping(value = "/ror")
+@Api(value = "Controller", tags = {"ror"})
+public class RORController {
+
+    @Autowired
+    private ResponseService responseService;
+
+    @GetMapping(value = "/organizationPlusChildren", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusChildren(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/ror/orga2children";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
+    @GetMapping(value = "/organization", produces = "application/json")
+    public ResponseEntity<String> getOrganization(
+            @Valid @Pattern(regexp = Validator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/ror/organization";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+}
diff --git a/src/main/java/eu/tib/controller/validation/Validator.java b/src/main/java/eu/tib/controller/validation/Validator.java
index 2ca80cd..050ad84 100644
--- a/src/main/java/eu/tib/controller/validation/Validator.java
+++ b/src/main/java/eu/tib/controller/validation/Validator.java
@@ -1,6 +1,6 @@
-package eu.tib.controller.validation;
-
-public class Validator {
-    public static final String ror = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}$";
-    public static final String orcid = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$";
-}
+package eu.tib.controller.validation;
+
+public class Validator {
+    public static final String ror = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}$";
+    public static final String orcid = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$";
+}

From 9031a53e6fc7b6be87277d428fc80f7067416637 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 8 Jun 2021 16:35:58 +0200
Subject: [PATCH 18/34] rename validator for clarity

---
 .../java/eu/tib/controller/DataciteCommonsController.java   | 6 +++---
 src/main/java/eu/tib/controller/OrcidController.java        | 6 +++---
 src/main/java/eu/tib/controller/RORController.java          | 6 +++---
 .../validation/{Validator.java => InputValidator.java}      | 2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)
 rename src/main/java/eu/tib/controller/validation/{Validator.java => InputValidator.java} (88%)

diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index fe99660..d9c61a9 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -1,6 +1,6 @@
 package eu.tib.controller;
 
-import eu.tib.controller.validation.Validator;
+import eu.tib.controller.validation.InputValidator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiParam;
@@ -27,7 +27,7 @@ public class DataciteCommonsController {
 
     @GetMapping(value = "/organizationPlusPersons", produces = "application/json")
     public ResponseEntity<String> getOrganizationPlusPersons(
-            @Valid @Pattern(regexp = Validator.ror)
+            @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
@@ -45,7 +45,7 @@ public ResponseEntity<String> getOrganizationPlusPersons(
 
     @GetMapping(value = "/personPlusPublications", produces = "application/json")
     public ResponseEntity<String> getPersonPlusPublications(
-            @Valid @Pattern(regexp = Validator.orcid)
+            @Valid @Pattern(regexp = InputValidator.orcid)
             @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
             @RequestParam String orcid) {
 
diff --git a/src/main/java/eu/tib/controller/OrcidController.java b/src/main/java/eu/tib/controller/OrcidController.java
index d4b53fe..a110497 100644
--- a/src/main/java/eu/tib/controller/OrcidController.java
+++ b/src/main/java/eu/tib/controller/OrcidController.java
@@ -1,6 +1,6 @@
 package eu.tib.controller;
 
-import eu.tib.controller.validation.Validator;
+import eu.tib.controller.validation.InputValidator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiParam;
@@ -27,7 +27,7 @@ public class OrcidController {
 
     @GetMapping(value = "/person", produces = "application/json")
     public ResponseEntity<String> getPerson(
-            @Valid @Pattern(regexp = Validator.orcid)
+            @Valid @Pattern(regexp = InputValidator.orcid)
             @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
             @RequestParam String orcid) {
 
@@ -48,7 +48,7 @@ public ResponseEntity<String> getPerson(
 
     @GetMapping(value = "/currentEmployees", produces = "application/json")
     public ResponseEntity<String> getCurrentEmployees(
-            @Valid @Pattern(regexp = Validator.ror)
+            @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
diff --git a/src/main/java/eu/tib/controller/RORController.java b/src/main/java/eu/tib/controller/RORController.java
index 3ad6c23..e6623fc 100644
--- a/src/main/java/eu/tib/controller/RORController.java
+++ b/src/main/java/eu/tib/controller/RORController.java
@@ -1,6 +1,6 @@
 package eu.tib.controller;
 
-import eu.tib.controller.validation.Validator;
+import eu.tib.controller.validation.InputValidator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiParam;
@@ -27,7 +27,7 @@ public class RORController {
 
     @GetMapping(value = "/organizationPlusChildren", produces = "application/json")
     public ResponseEntity<String> getOrganizationPlusChildren(
-            @Valid @Pattern(regexp = Validator.ror)
+            @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
@@ -45,7 +45,7 @@ public ResponseEntity<String> getOrganizationPlusChildren(
 
     @GetMapping(value = "/organization", produces = "application/json")
     public ResponseEntity<String> getOrganization(
-            @Valid @Pattern(regexp = Validator.ror)
+            @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
diff --git a/src/main/java/eu/tib/controller/validation/Validator.java b/src/main/java/eu/tib/controller/validation/InputValidator.java
similarity index 88%
rename from src/main/java/eu/tib/controller/validation/Validator.java
rename to src/main/java/eu/tib/controller/validation/InputValidator.java
index 050ad84..e30c176 100644
--- a/src/main/java/eu/tib/controller/validation/Validator.java
+++ b/src/main/java/eu/tib/controller/validation/InputValidator.java
@@ -1,6 +1,6 @@
 package eu.tib.controller.validation;
 
-public class Validator {
+public class InputValidator {
     public static final String ror = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}$";
     public static final String orcid = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$";
 }

From bed0272b52bee091a2e86e55928fc540c83ac7b0 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 8 Jun 2021 16:37:23 +0200
Subject: [PATCH 19/34] document new developments

---
 CHANGELOG.md | 5 ++++-
 pom.xml      | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 44cf8ff..dc0f464 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,10 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 ### Added
-- Query ORCID and filter for current employees.
+- Query ORCID for person and current employees at ROR organization.
+- refactor all queries to follow three steps: source, mapping, vivo-rdf
+- make all Controller use HTTP Get requests
+- centralize input validation
 
 ## [Renamed Project] - 2021-05-25
 As new datsources were integrated and the name datacitecommons2vivo was not reflecting
diff --git a/pom.xml b/pom.xml
index ff8e0a0..2ace1e7 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
 
     <groupId>eu.tib</groupId>
     <artifactId>generate2vivo</artifactId>
-    <version>1.0.0</version>
+    <version>1.1.0-SNAPSHOT</version>
     <description>Data Ingest from different datasources like Datacite Commons or ROR to VIVO</description>
 
     <properties>

From 26cc4932c6fbb484716ca647c28ec6c212352bbc Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 8 Jun 2021 16:56:56 +0200
Subject: [PATCH 20/34] add new datacite objects for querying

---
 .../controller/DataciteCommonsController.java | 54 +++++++++++++++++++
 .../controller/validation/InputValidator.java |  1 +
 2 files changed, 55 insertions(+)

diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index d9c61a9..26ce037 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -25,6 +25,24 @@ public class DataciteCommonsController {
     @Autowired
     private ResponseService responseService;
 
+    @GetMapping(value = "/organization", produces = "application/json")
+    public ResponseEntity<String> getOrganization(
+            @Valid @Pattern(regexp = InputValidator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/datacitecommons/organization";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
     @GetMapping(value = "/organizationPlusPersons", produces = "application/json")
     public ResponseEntity<String> getOrganizationPlusPersons(
             @Valid @Pattern(regexp = InputValidator.ror)
@@ -43,6 +61,24 @@ public ResponseEntity<String> getOrganizationPlusPersons(
         return result;
     }
 
+    @GetMapping(value = "/person", produces = "application/json")
+    public ResponseEntity<String> getPerson(
+            @Valid @Pattern(regexp = InputValidator.orcid)
+            @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
+            @RequestParam String orcid) {
+
+        final String id = "sparqlg/datacitecommons/person";
+        log.info("Incoming Request for " + id + " with orcid: " + orcid);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("orcid", orcid));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
     @GetMapping(value = "/personPlusPublications", produces = "application/json")
     public ResponseEntity<String> getPersonPlusPublications(
             @Valid @Pattern(regexp = InputValidator.orcid)
@@ -60,4 +96,22 @@ public ResponseEntity<String> getPersonPlusPublications(
         log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
         return result;
     }
+
+    @GetMapping(value = "/publications", produces = "application/json")
+    public ResponseEntity<String> getPublications(
+            @Valid @Pattern(regexp = InputValidator.doi)
+            @ApiParam("DOI of the publication")
+            @RequestParam String doi) {
+
+        final String id = "sparqlg/datacitecommons/work";
+        log.info("Incoming Request for " + id + " with doi: " + doi);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("doi", doi));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
 }
diff --git a/src/main/java/eu/tib/controller/validation/InputValidator.java b/src/main/java/eu/tib/controller/validation/InputValidator.java
index e30c176..3b6c334 100644
--- a/src/main/java/eu/tib/controller/validation/InputValidator.java
+++ b/src/main/java/eu/tib/controller/validation/InputValidator.java
@@ -3,4 +3,5 @@
 public class InputValidator {
     public static final String ror = "^https://ror.org/\\d{2}[a-z0-9]{5}\\d{2}$";
     public static final String orcid = "^https://orcid.org/\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$";
+    public static final String doi = "^10\\.[0-9]{4}.*";
 }

From 3ffe5e1c33e7c68d7c43298b44ac117b4bb76990 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 8 Jun 2021 16:57:06 +0200
Subject: [PATCH 21/34] prepare release

---
 src/main/java/eu/tib/swagger/SwaggerConfig.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/eu/tib/swagger/SwaggerConfig.java b/src/main/java/eu/tib/swagger/SwaggerConfig.java
index 34d6b91..1d3976c 100644
--- a/src/main/java/eu/tib/swagger/SwaggerConfig.java
+++ b/src/main/java/eu/tib/swagger/SwaggerConfig.java
@@ -27,7 +27,7 @@ private ApiInfo apiInfo() {
         return new ApiInfoBuilder()
                 .title("generate2vivo")
                 .description("Data Ingest from different datasources like Datacite Commons or ROR to VIVO")
-                .version("1.0.0")
+                .version("1.1.0-SNAPSHOT")
                 .build();
     }
 }

From 8bddc4ea4c630af61f1f7e729b8b437f5e53de51 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Wed, 9 Jun 2021 19:04:17 +0200
Subject: [PATCH 22/34] optimize dc connection queries

---
 .../controller/DataciteCommonsController.java | 18 +++++
 .../documentset/orga2person.graphql           |  5 +-
 .../orga2person/orga2person.rqg               | 11 +--
 .../orga2person/orga_source.rqg               | 23 ++++++
 .../orga2person/sparql-generate-conf.json     | 10 ++-
 .../documentset/orga2person.graphql           | 15 ++++
 .../orga2person2publication.rqg               | 41 ++++++++++
 .../orga2person2publication/orga_source.rqg   | 23 ++++++
 .../sparql-generate-conf.json                 | 76 +++++++++++++++++++
 .../organization/sparql-generate-conf.json    | 10 ++-
 .../person/sparql-generate-conf.json          | 10 ++-
 .../documentset/person2publication.graphql    |  6 +-
 .../person2publication/person2publication.rqg | 11 +--
 .../person2publication/person_source.rqg      | 24 ++++++
 .../sparql-generate-conf.json                 |  6 +-
 .../work/sparql-generate-conf.json            | 10 ++-
 16 files changed, 258 insertions(+), 41 deletions(-)
 create mode 100644 src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/orga2person2publication/documentset/orga2person.graphql
 create mode 100644 src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg
 create mode 100644 src/main/resources/sparqlg/datacitecommons/orga2person2publication/sparql-generate-conf.json
 create mode 100644 src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg

diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index 26ce037..ae8b3fd 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -61,6 +61,24 @@ public ResponseEntity<String> getOrganizationPlusPersons(
         return result;
     }
 
+    @GetMapping(value = "/organizationPlusPersonsPlusPublications", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusPersonsPlusPublications(
+            @Valid @Pattern(regexp = InputValidator.ror)
+            @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
+            @RequestParam String ror) {
+
+        final String id = "sparqlg/datacitecommons/orga2person2publication";
+        log.info("Incoming Request for " + id + " with ror: " + ror);
+        StopWatch stopWatch = new StopWatch(id);
+        stopWatch.start(id);
+
+        ResponseEntity result = responseService.buildResponse(id, Collections.singletonMap("ror", ror));
+
+        stopWatch.stop();
+        log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
+        return result;
+    }
+
     @GetMapping(value = "/person", produces = "application/json")
     public ResponseEntity<String> getPerson(
             @Valid @Pattern(regexp = InputValidator.orcid)
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/documentset/orga2person.graphql b/src/main/resources/sparqlg/datacitecommons/orga2person/documentset/orga2person.graphql
index 0a01754..3292bba 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/documentset/orga2person.graphql
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/documentset/orga2person.graphql
@@ -1,9 +1,6 @@
 query orga2person($ror: ID!, $after: String) {
     organization(id: $ror) {
-        id
-        name
-
-        people(first:100, after: $after) {
+        people(first:1000, after: $after) {
             pageInfo {
                 endCursor
                 hasNextPage
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
index 20049ba..6fb2ac7 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
@@ -1,11 +1,7 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 
-GENERATE  <orga2person>(?ror, ?after) {
-
-### map organization data
-    GENERATE <https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg>( ?orga_data ) .
-
+GENERATE  <orga2person>(?ror, ?orga_id,  ?after) {
 
 ### map person data
 ### and for every person: create a connection to organization
@@ -16,15 +12,12 @@ GENERATE  <orga2person>(?ror, ?after) {
     }
     ITERATOR iter:JSONPath(?orga_data, '$.people.nodes[*]') AS ?person_data
     WHERE{
-        BIND(<https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg>(?orga_data) AS ?orga_id)
         BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
     } .
 
 
 ############################# call this query again if hasNextPage =true  #############################################
-    GENERATE{
-      GENERATE <https://projects.tib.eu/tapir/datacitecommons/orga2person/orga2person.rqg>( ?ror, ?cursor ) .
-    }
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/orga2person/orga2person.rqg>( ?ror, ?orga_id, ?cursor )
     WHERE{
       BIND(fun:JSONPath(?orga_data, '$.people.pageInfo.hasNextPage' ) AS ?hasNextPage)
       BIND(fun:JSONPath(?orga_data, '$.people.pageInfo.endCursor' ) AS ?endCursor)
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg
new file mode 100644
index 0000000..15b3565
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg
@@ -0,0 +1,23 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE <orga_source>(?ror) {
+    # create organization once
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg>( ?orga_data ) .
+
+    # go into loop
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/orga2person/orga2person.rqg>( ?ror, ?orga_id, ?undef ) .
+}
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql> AS ?graphqlquery
+WHERE {
+    # replace whitespace in graphql query (compress message)
+    BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
+    BIND ("""\{"variables":\{"ror":"{?ror}"},"query":"{?graphql}"}""" AS ?postbody)
+
+    # build http post request
+    BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
+    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
+
+    BIND(<https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg>(?orga_data) AS ?orga_id)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
index eedfa4b..8f575cd 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/sparql-generate-conf.json
@@ -1,11 +1,15 @@
 {
   "base": "http://vivo.mydomain.edu/individual/",
-  "query": "orga2person.rqg",
+  "query": "orga_source.rqg",
   "namedqueries": [
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person/orga2person.rqg",
       "path": "orga2person.rqg"
     },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_source.rqg",
+      "path": "../organization/orga_source.rqg"
+    },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg",
       "path": "../organization/orga_mapping.rqg"
@@ -43,6 +47,10 @@
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person/documentset/orga2person.graphql",
       "path": "documentset/orga2person.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql",
+      "path": "../organization/documentset/organization.graphql"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/documentset/orga2person.graphql b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/documentset/orga2person.graphql
new file mode 100644
index 0000000..3292bba
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/documentset/orga2person.graphql
@@ -0,0 +1,15 @@
+query orga2person($ror: ID!, $after: String) {
+    organization(id: $ror) {
+        people(first:1000, after: $after) {
+            pageInfo {
+                endCursor
+                hasNextPage
+            }
+            nodes {
+                id
+                givenName
+                familyName
+            }
+        }
+    }
+}
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg
new file mode 100644
index 0000000..d6ce293
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg
@@ -0,0 +1,41 @@
+PREFIX iter: <http://w3id.org/sparql-generate/iter/>
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE  <orga2person2publication>(?ror, ?orga_id, ?after) {
+
+### map person data
+### and for every person: create a connection to organization
+    GENERATE {
+        GENERATE <https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg>( ?orcid, ?person_id, ?undef ) .
+
+        GENERATE <https://projects.tib.eu/tapir/vivo-rdf/position.rqg>(?person_id, ?orga_id, ?role, ?start_date, ?end_date) .
+    }
+    ITERATOR iter:JSONPath(?orga_data, '$.people.nodes[*]') AS ?person_data
+    WHERE{
+        BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
+        BIND(CONCAT("https://orcid.org/", ?person_id) AS ?orcid)
+    } .
+
+
+############################# call this query again if hasNextPage =true  #############################################
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/orga2person2publication/orga2person2publication.rqg>( ?ror, ?orga_id,?cursor )
+    WHERE{
+      BIND(fun:JSONPath(?orga_data, '$.people.pageInfo.hasNextPage' ) AS ?hasNextPage)
+      BIND(fun:JSONPath(?orga_data, '$.people.pageInfo.endCursor' ) AS ?endCursor)
+      BIND(IF(STR(?hasNextPage)="true", ?endCursor, ?undef) AS ?cursor )
+      FILTER( BOUND(?cursor) ).
+     }.
+}
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/orga2person2publication/documentset/orga2person.graphql> AS ?graphqlquery
+WHERE {
+    # replace whitespace in graphql query (compress message)
+    BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
+    BIND(IF(BOUND(?after), ?after, "") AS ?after)
+    BIND ("""\{"variables":\{"ror":"{?ror}", "after":"{?after}"},"query":"{?graphql}"}""" AS ?postbody)
+
+    # build http post request
+    BIND(  fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
+    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
+}
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg
new file mode 100644
index 0000000..60d9262
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg
@@ -0,0 +1,23 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE <orga_source>(?ror) {
+    # create organization once
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg>( ?orga_data ) .
+
+    # go into loop
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/orga2person2publication/orga2person2publication.rqg>( ?ror, ?orga_id, ?undef ) .
+}
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql> AS ?graphqlquery
+WHERE {
+    # replace whitespace in graphql query (compress message)
+    BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
+    BIND ("""\{"variables":\{"ror":"{?ror}"},"query":"{?graphql}"}""" AS ?postbody)
+
+    # build http post request
+    BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
+    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
+
+    BIND(<https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg>(?orga_data) AS ?orga_id)
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/sparql-generate-conf.json
new file mode 100644
index 0000000..5e132c3
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/sparql-generate-conf.json
@@ -0,0 +1,76 @@
+{
+  "base": "http://vivo.mydomain.edu/individual/",
+  "query": "orga_source.rqg",
+  "namedqueries": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person2publication/orga2person2publication.rqg",
+      "path": "orga2person2publication.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg",
+      "path": "../organization/orga_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg",
+      "path": "../organization/orga_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
+      "path": "../../vivo-rdf/organization.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg",
+      "path": "../person/person_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg",
+      "path": "../person/person_id.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg",
+      "path": "../person2publication/person2publication.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/person.rqg",
+      "path": "../../vivo-rdf/person.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/position.rqg",
+      "path": "../../vivo-rdf/position.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/authorship.rqg",
+      "path": "../../vivo-rdf/authorship.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/research.rqg",
+      "path": "../../vivo-rdf/research.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg",
+      "path": "../work/work_mapping.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_id.rqg",
+      "path": "../work/work_id.rqg"
+    }
+  ],
+  "documentset": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/orga2person2publication/documentset/orga2person.graphql",
+      "path": "documentset/orga2person.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person2publication/documentset/person2publication.graphql",
+      "path": "../person2publication/documentset/person2publication.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql",
+      "path": "../organization/documentset/organization.graphql"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
index d29eb92..2b5ce9f 100644
--- a/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/organization/sparql-generate-conf.json
@@ -2,10 +2,6 @@
   "base": "http://vivo.mydomain.edu/individual/",
   "query": "orga_source.rqg",
   "namedqueries": [
-    {
-      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql",
-      "path": "documentset/organization.graphql"
-    },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/orga_mapping.rqg",
       "path": "orga_mapping.rqg"
@@ -22,5 +18,11 @@
       "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
       "path": "../../vivo-rdf/agent_pid.rqg"
     }
+  ],
+  "documentset": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/organization/documentset/organization.graphql",
+      "path": "documentset/organization.graphql"
+    }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
index 294af52..d78aacf 100644
--- a/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/person/sparql-generate-conf.json
@@ -2,10 +2,6 @@
   "base": "http://vivo.mydomain.edu/individual/",
   "query": "person_source.rqg",
   "namedqueries": [
-    {
-      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/documentset/person.graphql",
-      "path": "documentset/person.graphql"
-    },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg",
       "path": "person_mapping.rqg"
@@ -22,5 +18,11 @@
       "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
       "path": "../../vivo-rdf/agent_pid.rqg"
     }
+  ],
+  "documentset": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/documentset/person.graphql",
+      "path": "documentset/person.graphql"
+    }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/documentset/person2publication.graphql b/src/main/resources/sparqlg/datacitecommons/person2publication/documentset/person2publication.graphql
index a6215b9..ba7fa1b 100644
--- a/src/main/resources/sparqlg/datacitecommons/person2publication/documentset/person2publication.graphql
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/documentset/person2publication.graphql
@@ -1,10 +1,6 @@
 query person($orcid :ID!, $after:String){
     person(id: $orcid) {
-        familyName
-        givenName
-        id
-
-        publications(first:100, after: $after) {
+        publications(first:1000, after: $after) {
             pageInfo {
                 endCursor
                 hasNextPage
diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg b/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
index 3842220..b6bf2af 100644
--- a/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
@@ -1,11 +1,7 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX fun: <http://w3id.org/sparql-generate/fn/>
 
-GENERATE  <person2publication>(?orcid, ?after) {
-
-### map person data
-    GENERATE <https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg>( ?person_data ) .
-
+GENERATE  <person2publication>(?orcid, ?person_id, ?after) {
 
 ### map work data
 ### and for every work: create a connection to person
@@ -17,14 +13,11 @@ GENERATE  <person2publication>(?orcid, ?after) {
     ITERATOR iter:JSONPath(?person_data, '$.publications.nodes[*][?(!@.versions.nodes[0])]') AS ?work_data
     WHERE{
         BIND(<https://projects.tib.eu/tapir/datacitecommons/work/work_id.rqg>(?work_data) AS ?work_id)
-        BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
     } .
 
 
 ############################# call this query again if hasNextPage =true  #############################################
-    GENERATE{
-      GENERATE <https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg>( ?orcid, ?cursor ) .
-    }
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg>( ?orcid, ?person_id, ?cursor )
     WHERE{
       BIND(fun:JSONPath(?person, '$.publications.pageInfo.hasNextPage' ) AS ?hasNextPage)
       BIND(fun:JSONPath(?person, '$.publications.pageInfo.endCursor' ) AS ?endCursor)
diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg b/src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg
new file mode 100644
index 0000000..91392f7
--- /dev/null
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg
@@ -0,0 +1,24 @@
+PREFIX fun: <http://w3id.org/sparql-generate/fn/>
+
+GENERATE <person_source>(?orcid) {
+    # create person once
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/person/person_mapping.rqg>( ?person_data ) .
+
+    # go into loop
+    GENERATE <https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg>( ?orcid, ?person_id, ?undef ) .
+}
+SOURCE <https://projects.tib.eu/tapir/datacitecommons/person/documentset/person.graphql> AS ?graphqlquery
+WHERE {
+    # replace whitespace in graphql query (compress message)
+    BIND(REPLACE(?graphqlquery, "\\s+", " ") AS ?graphql)
+    BIND ("""\{"variables":\{"orcid":"{?orcid}"},"query":"{?graphql}"}""" AS ?postbody)
+
+    # build http post request
+    BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
+    FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
+    BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+    BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person_data )
+
+    BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
+
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json
index 1391eaa..6f4ab92 100644
--- a/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/sparql-generate-conf.json
@@ -1,6 +1,6 @@
 {
   "base": "http://vivo.mydomain.edu/individual/",
-  "query": "person2publication.rqg",
+  "query": "person_source.rqg",
   "namedqueries": [
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/person2publication/person2publication.rqg",
@@ -43,6 +43,10 @@
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/person2publication/documentset/person2publication.graphql",
       "path": "documentset/person2publication.graphql"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/person/documentset/person.graphql",
+      "path": "../person/documentset/person.graphql"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json b/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
index 707a4b1..05446a2 100644
--- a/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/datacitecommons/work/sparql-generate-conf.json
@@ -2,10 +2,6 @@
   "base": "http://vivo.mydomain.edu/individual/",
   "query": "work_source.rqg",
   "namedqueries": [
-    {
-      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/documentset/work.graphql",
-      "path": "documentset/work.graphql"
-    },
     {
       "uri": "https://projects.tib.eu/tapir/datacitecommons/work/work_mapping.rqg",
       "path": "work_mapping.rqg"
@@ -18,5 +14,11 @@
       "uri": "https://projects.tib.eu/tapir/vivo-rdf/research.rqg",
       "path": "../../vivo-rdf/research.rqg"
     }
+  ],
+  "documentset": [
+    {
+      "uri": "https://projects.tib.eu/tapir/datacitecommons/work/documentset/work.graphql",
+      "path": "documentset/work.graphql"
+    }
   ]
 }
\ No newline at end of file

From fc4e48b989159ed332c09e0a3fd53820af9b8ff8 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 10 Jun 2021 10:45:13 +0200
Subject: [PATCH 23/34] fix work reference in orcid employees

---
 .../eu/tib/controller/OrcidController.java    |  8 ++++----
 .../orcid/employees/employees_filter.rqg      |  1 -
 .../orcid/employees/sparql-generate-conf.json | 20 +++++++++++++++----
 .../orcid/person/work/work_mapping.rqg        |  2 +-
 4 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/src/main/java/eu/tib/controller/OrcidController.java b/src/main/java/eu/tib/controller/OrcidController.java
index a110497..afb2d4b 100644
--- a/src/main/java/eu/tib/controller/OrcidController.java
+++ b/src/main/java/eu/tib/controller/OrcidController.java
@@ -25,8 +25,8 @@ public class OrcidController {
     @Autowired
     private ResponseService responseService;
 
-    @GetMapping(value = "/person", produces = "application/json")
-    public ResponseEntity<String> getPerson(
+    @GetMapping(value = "/personPlusPublications", produces = "application/json")
+    public ResponseEntity<String> getPersonPlusPublications(
             @Valid @Pattern(regexp = InputValidator.orcid)
             @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
             @RequestParam String orcid) {
@@ -46,8 +46,8 @@ public ResponseEntity<String> getPerson(
     }
 
 
-    @GetMapping(value = "/currentEmployees", produces = "application/json")
-    public ResponseEntity<String> getCurrentEmployees(
+    @GetMapping(value = "/currentEmployeesPlusPublications", produces = "application/json")
+    public ResponseEntity<String> getCurrentEmployeesPlusPublications(
             @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
diff --git a/src/main/resources/sparqlg/orcid/employees/employees_filter.rqg b/src/main/resources/sparqlg/orcid/employees/employees_filter.rqg
index c69050d..1e0090b 100644
--- a/src/main/resources/sparqlg/orcid/employees/employees_filter.rqg
+++ b/src/main/resources/sparqlg/orcid/employees/employees_filter.rqg
@@ -13,7 +13,6 @@ GENERATE <employees_filter>(?orga_id, ?ringgold_id, ?grid_id){
             ## create person in vivo ontology, if current employee
             GENERATE <https://projects.tib.eu/tapir/orcid/person/person_mapping.rqg>(?orcid_data) .
 
-
             ## connect person to organization via current employment
             GENERATE <https://projects.tib.eu/tapir/orcid/employees/employment_mapping.rqg>(?person_id, ?orga_id, ?employment) .
         }
diff --git a/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json b/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json
index caafa84..4c07a9d 100644
--- a/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json
+++ b/src/main/resources/sparqlg/orcid/employees/sparql-generate-conf.json
@@ -10,6 +10,14 @@
       "uri": "https://projects.tib.eu/tapir/orcid/employees/organization/orga_id.rqg",
       "path": "organization/orga_id.rqg"
     },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
+      "path": "../../vivo-rdf/organization.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
+      "path": "../../vivo-rdf/agent_pid.rqg"
+    },
     {
       "uri": "https://projects.tib.eu/tapir/orcid/employees/employees_filter.rqg",
       "path": "employees_filter.rqg"
@@ -35,12 +43,16 @@
       "path": "../../vivo-rdf/position.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/vivo-rdf/organization.rqg",
-      "path": "../../vivo-rdf/organization.rqg"
+      "uri": "https://projects.tib.eu/tapir/orcid/person/work/work_mapping.rqg",
+      "path": "../person/work/work_mapping.rqg"
     },
     {
-      "uri": "https://projects.tib.eu/tapir/vivo-rdf/agent_pid.rqg",
-      "path": "../../vivo-rdf/agent_pid.rqg"
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/research.rqg",
+      "path": "../../vivo-rdf/research.rqg"
+    },
+    {
+      "uri": "https://projects.tib.eu/tapir/vivo-rdf/authorship.rqg",
+      "path": "../../vivo-rdf/authorship.rqg"
     }
   ]
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg b/src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg
index 3dd1798..d42307a 100644
--- a/src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg
+++ b/src/main/resources/sparqlg/orcid/person/work/work_mapping.rqg
@@ -14,7 +14,7 @@ WHERE {
     BIND(fun:JSONPath(?work_summary, '$.publication-date.year.value' ) AS ?pubyear)
     BIND(fun:JSONPath(?work_summary, '$.external-ids.external-id[?(@.external-id-type==\'doi\')]' ) AS ?all_dois)
     BIND(fun:JSONPath(?all_dois, '$.[0].external-id-value' ) AS ?doi)
-    BIND(bibo:Document AS ?pubtype)
+    BIND(bibo:Article AS ?pubtype)
 
     BIND(REPLACE(?doi,  "\\W", "", "i") AS ?work_id)
 }
\ No newline at end of file

From 6b43eb1680327e4d81da391932e3a4ae5ec7dd33 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 10 Jun 2021 12:24:53 +0200
Subject: [PATCH 24/34] send data in chunks

---
 src/main/java/eu/tib/storage/VIVOExport.java | 26 ++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/main/java/eu/tib/storage/VIVOExport.java b/src/main/java/eu/tib/storage/VIVOExport.java
index f93906e..3b57dc5 100644
--- a/src/main/java/eu/tib/storage/VIVOExport.java
+++ b/src/main/java/eu/tib/storage/VIVOExport.java
@@ -3,6 +3,8 @@
 import eu.tib.exception.VIVOExportException;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.StmtIterator;
 import org.springframework.stereotype.Repository;
 
 import java.io.ByteArrayOutputStream;
@@ -17,8 +19,32 @@
 @Slf4j
 @Repository
 public class VIVOExport {
+    private static final int CHUNK_SIZE = 2500;  // triples per 'chunk'
 
+    /**
+     *  taken from https://github.com/WheatVIVO/datasources/blob/master/datasources/src/main/java/org/wheatinitiative/vivo/datasource/util/sparql/SparqlEndpoint.java
+     *  and modified to send chunk and free it for garbage collection
+     **/
     public void exportData(Model data, VIVOProperties vivo) {
+
+        StmtIterator sit = data.listStatements();
+        int i = 0;
+        Model currentChunk = ModelFactory.createDefaultModel();
+
+        while (sit.hasNext()) {
+            currentChunk.add(sit.nextStatement());
+            i++;
+
+            if (i >= CHUNK_SIZE || !sit.hasNext()) {
+                send2VIVO(currentChunk, vivo);
+                currentChunk = ModelFactory.createDefaultModel();
+                i=0;
+            }
+        }
+    }
+
+    public void send2VIVO(Model data, VIVOProperties vivo) {
+        log.info("Writing " + data.size() + " new statements to VIVO");
         String sparqlInsertQuery = buildInsertQuery(data, vivo.getGraph());
         log.debug("Sparql Insert Query: \n" + sparqlInsertQuery);
 

From 679b58a9e1e38169612644e8e18f045d5377b877 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 10 Jun 2021 12:50:01 +0200
Subject: [PATCH 25/34] check if empty before export

---
 .../java/eu/tib/service/ResponseService.java  | 12 ++----------
 src/main/java/eu/tib/storage/VIVOExport.java  | 19 ++++++++++++++-----
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/main/java/eu/tib/service/ResponseService.java b/src/main/java/eu/tib/service/ResponseService.java
index d879471..4c6bab0 100644
--- a/src/main/java/eu/tib/service/ResponseService.java
+++ b/src/main/java/eu/tib/service/ResponseService.java
@@ -31,17 +31,9 @@ public ResponseEntity<String> buildResponse(String queryName, Map<String, String
 
         if (vivoProperties.isValid()) {
             log.info("Found VIVO properties");
-
-            String status = "{\"status\":\"%s\"}";
-            if (result.isEmpty()) {
-                log.info("No data was generated, Model is empty.");
-                status = String.format(status, "No data was generated.");
-            } else {
-                vivoExport.exportData(result, vivoProperties);
-                status = String.format(status, "SPARQL update accepted.");
-            }
+            vivoExport.exportData(result, vivoProperties);
+            String status = String.format("{\"status\":\"%s\"}", "SPARQL update accepted.");
             return ResponseEntity.status(HttpStatus.OK).body(status);
-
         } else {
             log.info("Returning JSON-LD");
             StringWriter stringWriter = new StringWriter();
diff --git a/src/main/java/eu/tib/storage/VIVOExport.java b/src/main/java/eu/tib/storage/VIVOExport.java
index 3b57dc5..e3d734a 100644
--- a/src/main/java/eu/tib/storage/VIVOExport.java
+++ b/src/main/java/eu/tib/storage/VIVOExport.java
@@ -19,14 +19,22 @@
 @Slf4j
 @Repository
 public class VIVOExport {
+
     private static final int CHUNK_SIZE = 2500;  // triples per 'chunk'
 
-    /**
-     *  taken from https://github.com/WheatVIVO/datasources/blob/master/datasources/src/main/java/org/wheatinitiative/vivo/datasource/util/sparql/SparqlEndpoint.java
-     *  and modified to send chunk and free it for garbage collection
-     **/
     public void exportData(Model data, VIVOProperties vivo) {
+        if (data.isEmpty()) {
+            log.info("No data was generated, Model is empty.");
+        } else {
+            exportInChunks(data, vivo);
+        }
+    }
 
+    /**
+     * taken from https://github.com/WheatVIVO/datasources/blob/master/datasources/src/main/java/org/wheatinitiative/vivo/datasource/util/sparql/SparqlEndpoint.java
+     * and modified to send chunk and free it for garbage collection
+     **/
+    public void exportInChunks(Model data, VIVOProperties vivo) {
         StmtIterator sit = data.listStatements();
         int i = 0;
         Model currentChunk = ModelFactory.createDefaultModel();
@@ -37,8 +45,9 @@ public void exportData(Model data, VIVOProperties vivo) {
 
             if (i >= CHUNK_SIZE || !sit.hasNext()) {
                 send2VIVO(currentChunk, vivo);
+                //reset variables
                 currentChunk = ModelFactory.createDefaultModel();
-                i=0;
+                i = 0;
             }
         }
     }

From 8eb3f65d495473705decd5781d9aa287d987fece Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 10 Jun 2021 12:56:44 +0200
Subject: [PATCH 26/34] merge refactor-queries into develop

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dc0f464..8f8aab7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ All notable changes to this project will be documented in this file.
 - refactor all queries to follow three steps: source, mapping, vivo-rdf
 - make all Controller use HTTP Get requests
 - centralize input validation
+- export to VIVO in chunks
 
 ## [Renamed Project] - 2021-05-25
 As new datsources were integrated and the name datacitecommons2vivo was not reflecting

From b5344d9fa65d7f5f2ca2a6b13525e1eb8ea3e5a4 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Thu, 17 Jun 2021 15:53:27 +0200
Subject: [PATCH 27/34] note changes

---
 CHANGELOG.md                                 | 6 +++---
 src/main/java/eu/tib/storage/VIVOExport.java | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8f8aab7..2c36030 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,9 +3,9 @@ All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
 ### Added
-- Query ORCID for person and current employees at ROR organization.
-- refactor all queries to follow three steps: source, mapping, vivo-rdf
-- make all Controller use HTTP Get requests
+- query ORCID for person and current employees at ROR organization
+- refactor all queries to follow three steps: source, extraction, mapping to vivo-rdf
+- make all controller use HTTP-Get requests
 - centralize input validation
 - export to VIVO in chunks
 
diff --git a/src/main/java/eu/tib/storage/VIVOExport.java b/src/main/java/eu/tib/storage/VIVOExport.java
index e3d734a..9374270 100644
--- a/src/main/java/eu/tib/storage/VIVOExport.java
+++ b/src/main/java/eu/tib/storage/VIVOExport.java
@@ -31,7 +31,7 @@ public void exportData(Model data, VIVOProperties vivo) {
     }
 
     /**
-     * taken from https://github.com/WheatVIVO/datasources/blob/master/datasources/src/main/java/org/wheatinitiative/vivo/datasource/util/sparql/SparqlEndpoint.java
+     * method taken from https://github.com/WheatVIVO/datasources/blob/master/datasources/src/main/java/org/wheatinitiative/vivo/datasource/util/sparql/SparqlEndpoint.java
      * and modified to send chunk and free it for garbage collection
      **/
     public void exportInChunks(Model data, VIVOProperties vivo) {

From 44b23e262c0eba94bc5b0c5878a84334b65eef94 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Fri, 18 Jun 2021 15:34:15 +0200
Subject: [PATCH 28/34] simplify error handling (#21)

* simplify error handling
---
 .../tib/controller/RestExceptionHandler.java  | 141 ------------------
 src/main/java/eu/tib/exception/ApiError.java  |  88 -----------
 .../java/eu/tib/exception/ApiSubError.java    |   5 -
 .../eu/tib/exception/ApiValidationError.java  |  20 ---
 .../tib/exception/ConfigLoadingException.java |  31 ----
 .../java/eu/tib/exception/ErrorResponse.java  |  39 +++++
 .../exception/GeneralExceptionHandler.java    |  69 +++++++++
 .../exception/LowerCaseClassNameResolver.java |  22 ---
 .../exception/SparqlExecutionException.java   |  28 +---
 .../tib/exception/SparqlParsingException.java |  31 ----
 .../tib/exception/StreamManagerException.java |  31 ----
 .../eu/tib/exception/VIVOExportException.java |  28 +---
 .../java/eu/tib/service/GeneratePipeline.java |  21 ++-
 src/main/java/eu/tib/storage/VIVOExport.java  |   9 +-
 .../eu/tib/service/GeneratePipelineTest.java  |   9 +-
 15 files changed, 128 insertions(+), 444 deletions(-)
 delete mode 100644 src/main/java/eu/tib/controller/RestExceptionHandler.java
 delete mode 100644 src/main/java/eu/tib/exception/ApiError.java
 delete mode 100644 src/main/java/eu/tib/exception/ApiSubError.java
 delete mode 100644 src/main/java/eu/tib/exception/ApiValidationError.java
 delete mode 100644 src/main/java/eu/tib/exception/ConfigLoadingException.java
 create mode 100644 src/main/java/eu/tib/exception/ErrorResponse.java
 create mode 100644 src/main/java/eu/tib/exception/GeneralExceptionHandler.java
 delete mode 100644 src/main/java/eu/tib/exception/LowerCaseClassNameResolver.java
 delete mode 100644 src/main/java/eu/tib/exception/SparqlParsingException.java
 delete mode 100644 src/main/java/eu/tib/exception/StreamManagerException.java

diff --git a/src/main/java/eu/tib/controller/RestExceptionHandler.java b/src/main/java/eu/tib/controller/RestExceptionHandler.java
deleted file mode 100644
index bed691c..0000000
--- a/src/main/java/eu/tib/controller/RestExceptionHandler.java
+++ /dev/null
@@ -1,141 +0,0 @@
-package eu.tib.controller;
-
-import eu.tib.exception.*;
-import lombok.extern.slf4j.Slf4j;
-import org.springframework.core.Ordered;
-import org.springframework.core.annotation.Order;
-import org.springframework.http.HttpHeaders;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.http.converter.HttpMessageNotReadableException;
-import org.springframework.http.converter.HttpMessageNotWritableException;
-import org.springframework.web.HttpMediaTypeNotSupportedException;
-import org.springframework.web.bind.MethodArgumentNotValidException;
-import org.springframework.web.bind.MissingServletRequestParameterException;
-import org.springframework.web.bind.annotation.ControllerAdvice;
-import org.springframework.web.bind.annotation.ExceptionHandler;
-import org.springframework.web.context.request.ServletWebRequest;
-import org.springframework.web.context.request.WebRequest;
-import org.springframework.web.method.annotation.MethodArgumentTypeMismatchException;
-import org.springframework.web.servlet.NoHandlerFoundException;
-import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler;
-
-import static org.springframework.http.HttpStatus.*;
-
-@Order(Ordered.HIGHEST_PRECEDENCE)
-@ControllerAdvice
-@Slf4j
-public class RestExceptionHandler extends ResponseEntityExceptionHandler {
-
-    @Override
-    protected ResponseEntity<Object> handleMissingServletRequestParameter(
-            MissingServletRequestParameterException ex, HttpHeaders headers,
-            HttpStatus status, WebRequest request) {
-        String error = ex.getParameterName() + " parameter is missing";
-        return buildResponseEntity(new ApiError(BAD_REQUEST, error, ex));
-    }
-
-    @Override
-    protected ResponseEntity<Object> handleMethodArgumentNotValid(
-            MethodArgumentNotValidException ex,
-            HttpHeaders headers,
-            HttpStatus status,
-            WebRequest request) {
-        ApiError apiError = new ApiError(BAD_REQUEST);
-        apiError.setMessage("Validation error");
-        apiError.addValidationErrors(ex.getBindingResult().getFieldErrors());
-        apiError.addValidationError(ex.getBindingResult().getGlobalErrors());
-        return buildResponseEntity(apiError);
-    }
-
-    @Override
-    protected ResponseEntity<Object> handleHttpMediaTypeNotSupported(
-            HttpMediaTypeNotSupportedException ex,
-            HttpHeaders headers,
-            HttpStatus status,
-            WebRequest request) {
-        StringBuilder builder = new StringBuilder();
-        builder.append(ex.getContentType());
-        builder.append(" media type is not supported. Supported media types are ");
-        ex.getSupportedMediaTypes().forEach(t -> builder.append(t).append(", "));
-        return buildResponseEntity(new ApiError(HttpStatus.UNSUPPORTED_MEDIA_TYPE, builder.substring(0, builder.length() - 2), ex));
-    }
-
-    @ExceptionHandler(VIVOExportException.class)
-    protected ResponseEntity<Object> handleEntityNotFound(
-            VIVOExportException ex) {
-        ApiError apiError = new ApiError(NOT_FOUND);
-        apiError.setMessage(ex.getMessage());
-        return buildResponseEntity(apiError);
-    }
-
-    @ExceptionHandler(SparqlExecutionException.class)
-    protected ResponseEntity<Object> handleEntityNotFound(
-            SparqlExecutionException ex) {
-        ApiError apiError = new ApiError(INTERNAL_SERVER_ERROR);
-        apiError.setMessage(ex.getMessage());
-        return buildResponseEntity(apiError);
-    }
-
-    @ExceptionHandler(SparqlParsingException.class)
-    protected ResponseEntity<Object> handleEntityNotFound(
-            SparqlParsingException ex) {
-        ApiError apiError = new ApiError(INTERNAL_SERVER_ERROR);
-        apiError.setMessage(ex.getMessage());
-        return buildResponseEntity(apiError);
-    }
-
-    @ExceptionHandler(ConfigLoadingException.class)
-    protected ResponseEntity<Object> handleEntityNotFound(
-            ConfigLoadingException ex) {
-        ApiError apiError = new ApiError(INTERNAL_SERVER_ERROR);
-        apiError.setMessage(ex.getMessage());
-        return buildResponseEntity(apiError);
-    }
-
-    @ExceptionHandler(StreamManagerException.class)
-    protected ResponseEntity<Object> handleEntityNotFound(
-            StreamManagerException ex) {
-        ApiError apiError = new ApiError(INTERNAL_SERVER_ERROR);
-        apiError.setMessage(ex.getMessage());
-        return buildResponseEntity(apiError);
-    }
-
-    @Override
-    protected ResponseEntity<Object> handleHttpMessageNotReadable(HttpMessageNotReadableException ex, HttpHeaders headers, HttpStatus status, WebRequest request) {
-        ServletWebRequest servletWebRequest = (ServletWebRequest) request;
-        log.info("{} to {}", servletWebRequest.getHttpMethod(), servletWebRequest.getRequest().getServletPath());
-        String error = "Malformed JSON request";
-        return buildResponseEntity(new ApiError(HttpStatus.BAD_REQUEST, error, ex));
-    }
-
-    @Override
-    protected ResponseEntity<Object> handleHttpMessageNotWritable(HttpMessageNotWritableException ex, HttpHeaders headers, HttpStatus status, WebRequest request) {
-        String error = "Error writing JSON output";
-        return buildResponseEntity(new ApiError(HttpStatus.INTERNAL_SERVER_ERROR, error, ex));
-    }
-
-    @Override
-    protected ResponseEntity<Object> handleNoHandlerFoundException(
-            NoHandlerFoundException ex, HttpHeaders headers, HttpStatus status, WebRequest request) {
-        ApiError apiError = new ApiError(BAD_REQUEST);
-        apiError.setMessage(String.format("Could not find the %s method for URL %s", ex.getHttpMethod(), ex.getRequestURL()));
-        apiError.setDebugMessage(ex.getMessage());
-        return buildResponseEntity(apiError);
-    }
-
-    @ExceptionHandler(MethodArgumentTypeMismatchException.class)
-    protected ResponseEntity<Object> handleMethodArgumentTypeMismatch(MethodArgumentTypeMismatchException ex,
-                                                                      WebRequest request) {
-        ApiError apiError = new ApiError(BAD_REQUEST);
-        apiError.setMessage(String.format("The parameter '%s' of value '%s' could not be converted to type '%s'", ex.getName(), ex.getValue(), ex.getRequiredType().getSimpleName()));
-        apiError.setDebugMessage(ex.getMessage());
-        return buildResponseEntity(apiError);
-    }
-
-
-    private ResponseEntity<Object> buildResponseEntity(ApiError apiError) {
-        return new ResponseEntity<>(apiError, apiError.getStatus());
-    }
-
-}
diff --git a/src/main/java/eu/tib/exception/ApiError.java b/src/main/java/eu/tib/exception/ApiError.java
deleted file mode 100644
index d1ad140..0000000
--- a/src/main/java/eu/tib/exception/ApiError.java
+++ /dev/null
@@ -1,88 +0,0 @@
-package eu.tib.exception;
-
-import com.fasterxml.jackson.annotation.JsonFormat;
-import com.fasterxml.jackson.annotation.JsonTypeInfo;
-import com.fasterxml.jackson.databind.annotation.JsonTypeIdResolver;
-import lombok.Data;
-import org.springframework.http.HttpStatus;
-import org.springframework.validation.FieldError;
-import org.springframework.validation.ObjectError;
-
-import java.time.LocalDateTime;
-import java.util.ArrayList;
-import java.util.List;
-
-@Data
-@JsonTypeInfo(include = JsonTypeInfo.As.WRAPPER_OBJECT, use = JsonTypeInfo.Id.CUSTOM, property = "error", visible = true)
-@JsonTypeIdResolver(LowerCaseClassNameResolver.class)
-public
-class ApiError {
-
-    private HttpStatus status;
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "dd-MM-yyyy hh:mm:ss")
-    private LocalDateTime timestamp;
-    private String message;
-    private String debugMessage;
-    private List<ApiSubError> subErrors;
-
-    private ApiError() {
-        timestamp = LocalDateTime.now();
-    }
-
-    public ApiError(HttpStatus status) {
-        this();
-        this.status = status;
-    }
-
-    public ApiError(HttpStatus status, Throwable ex) {
-        this();
-        this.status = status;
-        this.message = "Unexpected error";
-        this.debugMessage = ex.getLocalizedMessage();
-    }
-
-    public ApiError(HttpStatus status, String message, Throwable ex) {
-        this();
-        this.status = status;
-        this.message = message;
-        this.debugMessage = ex.getLocalizedMessage();
-    }
-
-    private void addSubError(ApiSubError subError) {
-        if (subErrors == null) {
-            subErrors = new ArrayList<>();
-        }
-        subErrors.add(subError);
-    }
-
-    private void addValidationError(String object, String field, Object rejectedValue, String message) {
-        addSubError(new ApiValidationError(object, field, rejectedValue, message));
-    }
-
-    private void addValidationError(String object, String message) {
-        addSubError(new ApiValidationError(object, message));
-    }
-
-    private void addValidationError(FieldError fieldError) {
-        this.addValidationError(
-                fieldError.getObjectName(),
-                fieldError.getField(),
-                fieldError.getRejectedValue(),
-                fieldError.getDefaultMessage());
-    }
-
-    public void addValidationErrors(List<FieldError> fieldErrors) {
-        fieldErrors.forEach(this::addValidationError);
-    }
-
-    private void addValidationError(ObjectError objectError) {
-        this.addValidationError(
-                objectError.getObjectName(),
-                objectError.getDefaultMessage());
-    }
-
-    public void addValidationError(List<ObjectError> globalErrors) {
-        globalErrors.forEach(this::addValidationError);
-    }
-}
-
diff --git a/src/main/java/eu/tib/exception/ApiSubError.java b/src/main/java/eu/tib/exception/ApiSubError.java
deleted file mode 100644
index 0fa9a5c..0000000
--- a/src/main/java/eu/tib/exception/ApiSubError.java
+++ /dev/null
@@ -1,5 +0,0 @@
-package eu.tib.exception;
-
-public abstract class ApiSubError {
-
-}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/ApiValidationError.java b/src/main/java/eu/tib/exception/ApiValidationError.java
deleted file mode 100644
index b4a61fa..0000000
--- a/src/main/java/eu/tib/exception/ApiValidationError.java
+++ /dev/null
@@ -1,20 +0,0 @@
-package eu.tib.exception;
-
-import lombok.AllArgsConstructor;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
-
-@Data
-@EqualsAndHashCode(callSuper = false)
-@AllArgsConstructor
-public class ApiValidationError extends ApiSubError {
-    private String object;
-    private String field;
-    private Object rejectedValue;
-    private String message;
-
-    ApiValidationError(String object, String message) {
-        this.object = object;
-        this.message = message;
-    }
-}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/ConfigLoadingException.java b/src/main/java/eu/tib/exception/ConfigLoadingException.java
deleted file mode 100644
index 90215b1..0000000
--- a/src/main/java/eu/tib/exception/ConfigLoadingException.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package eu.tib.exception;
-
-import org.apache.commons.lang3.StringUtils;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.IntStream;
-
-public class ConfigLoadingException extends RuntimeException {
-
-    public ConfigLoadingException(Class clazz, String... searchParamsMap) {
-        super(ConfigLoadingException.generateMessage(clazz.getSimpleName(), toMap(String.class, String.class, searchParamsMap)));
-    }
-
-    private static String generateMessage(String entity, Map<String, String> searchParams) {
-        return StringUtils.capitalize(entity) +
-                " could not read FileConfigurations for parameters " +
-                searchParams;
-    }
-
-    private static <K, V> Map<K, V> toMap(
-            Class<K> keyType, Class<V> valueType, Object... entries) {
-        if (entries.length % 2 == 1)
-            throw new IllegalArgumentException("Invalid entries");
-        return IntStream.range(0, entries.length / 2).map(i -> i * 2)
-                .collect(HashMap::new,
-                        (m, i) -> m.put(keyType.cast(entries[i]), valueType.cast(entries[i + 1])),
-                        Map::putAll);
-    }
-
-}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/ErrorResponse.java b/src/main/java/eu/tib/exception/ErrorResponse.java
new file mode 100644
index 0000000..6dd77a3
--- /dev/null
+++ b/src/main/java/eu/tib/exception/ErrorResponse.java
@@ -0,0 +1,39 @@
+package eu.tib.exception;
+
+import com.fasterxml.jackson.annotation.JsonFormat;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import lombok.Getter;
+import lombok.RequiredArgsConstructor;
+import lombok.Setter;
+
+import java.time.LocalDateTime;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+
+@Getter
+@Setter
+@RequiredArgsConstructor
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class ErrorResponse {
+    private final int status;
+    private final String message;
+    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "dd-MM-yyyy hh:mm:ss")
+    private LocalDateTime timestamp = LocalDateTime.now();
+    private List<ValidationError> errors;
+
+    public void addValidationError(String field, String message) {
+        if (Objects.isNull(errors)) {
+            errors = new ArrayList<>();
+        }
+        errors.add(new ValidationError(field, message));
+    }
+
+    @Getter
+    @Setter
+    @RequiredArgsConstructor
+    private static class ValidationError {
+        private final String field;
+        private final String message;
+    }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/GeneralExceptionHandler.java b/src/main/java/eu/tib/exception/GeneralExceptionHandler.java
new file mode 100644
index 0000000..0c105d0
--- /dev/null
+++ b/src/main/java/eu/tib/exception/GeneralExceptionHandler.java
@@ -0,0 +1,69 @@
+package eu.tib.exception;
+
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.validation.FieldError;
+import org.springframework.web.bind.MethodArgumentNotValidException;
+import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.bind.annotation.RestControllerAdvice;
+import org.springframework.web.context.request.WebRequest;
+import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler;
+
+@Slf4j
+@RestControllerAdvice
+public class GeneralExceptionHandler extends ResponseEntityExceptionHandler {
+
+    @ExceptionHandler(SparqlExecutionException.class)
+    public ResponseEntity<Object> handleSparqlExecutionException(SparqlExecutionException ex, WebRequest request) {
+        return buildErrorResponse(ex, HttpStatus.INTERNAL_SERVER_ERROR, request);
+    }
+
+    @ExceptionHandler(VIVOExportException.class)
+    public ResponseEntity<Object> handleVIVOExportException(VIVOExportException ex, WebRequest request) {
+        return buildErrorResponse(ex, HttpStatus.SERVICE_UNAVAILABLE, request);
+    }
+
+    @ExceptionHandler(Exception.class)
+    public ResponseEntity<Object> handleAllUncaughtException(Exception exception, WebRequest request) {
+        return buildErrorResponse(exception, "Unknown error occurred", HttpStatus.INTERNAL_SERVER_ERROR, request);
+    }
+
+    private ResponseEntity<Object> buildErrorResponse(Exception exception,
+                                                      HttpStatus httpStatus,
+                                                      WebRequest request) {
+        return buildErrorResponse(exception, exception.getMessage(), httpStatus, request);
+    }
+
+    private ResponseEntity<Object> buildErrorResponse(Exception exception,
+                                                      String message,
+                                                      HttpStatus httpStatus,
+                                                      WebRequest request) {
+        ErrorResponse errorResponse = new ErrorResponse(httpStatus.value(), message);
+        return ResponseEntity.status(httpStatus).body(errorResponse);
+    }
+
+    @Override
+    public ResponseEntity<Object> handleExceptionInternal(
+            Exception ex,
+            Object body,
+            HttpHeaders headers,
+            HttpStatus status,
+            WebRequest request) {
+
+        return buildErrorResponse(ex, status, request);
+    }
+
+    @Override
+    protected ResponseEntity<Object> handleMethodArgumentNotValid(MethodArgumentNotValidException ex,
+                                                                  HttpHeaders headers,
+                                                                  HttpStatus status,
+                                                                  WebRequest request) {
+        ErrorResponse errorResponse = new ErrorResponse(HttpStatus.UNPROCESSABLE_ENTITY.value(), "Validation error. Check 'errors' field for details.");
+        for (FieldError fieldError : ex.getBindingResult().getFieldErrors()) {
+            errorResponse.addValidationError(fieldError.getField(), fieldError.getDefaultMessage());
+        }
+        return ResponseEntity.unprocessableEntity().body(errorResponse);
+    }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/LowerCaseClassNameResolver.java b/src/main/java/eu/tib/exception/LowerCaseClassNameResolver.java
deleted file mode 100644
index 4dcc1f4..0000000
--- a/src/main/java/eu/tib/exception/LowerCaseClassNameResolver.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package eu.tib.exception;
-
-import com.fasterxml.jackson.annotation.JsonTypeInfo;
-import com.fasterxml.jackson.databind.jsontype.impl.TypeIdResolverBase;
-
-public class LowerCaseClassNameResolver extends TypeIdResolverBase {
-
-    @Override
-    public String idFromValue(Object value) {
-        return value.getClass().getSimpleName().toLowerCase();
-    }
-
-    @Override
-    public String idFromValueAndType(Object value, Class<?> suggestedType) {
-        return idFromValue(value);
-    }
-
-    @Override
-    public JsonTypeInfo.Id getMechanism() {
-        return JsonTypeInfo.Id.CUSTOM;
-    }
-}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/SparqlExecutionException.java b/src/main/java/eu/tib/exception/SparqlExecutionException.java
index b7192b5..aa2ead0 100644
--- a/src/main/java/eu/tib/exception/SparqlExecutionException.java
+++ b/src/main/java/eu/tib/exception/SparqlExecutionException.java
@@ -1,31 +1,7 @@
 package eu.tib.exception;
 
-import org.apache.commons.lang3.StringUtils;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.IntStream;
-
 public class SparqlExecutionException extends RuntimeException {
-
-    public SparqlExecutionException(Class clazz, String... searchParamsMap) {
-        super(SparqlExecutionException.generateMessage(clazz.getSimpleName(), toMap(String.class, String.class, searchParamsMap)));
-    }
-
-    private static String generateMessage(String entity, Map<String, String> searchParams) {
-        return StringUtils.capitalize(entity) +
-                " could not execute SparQL-Generate for parameters " +
-                searchParams;
-    }
-
-    private static <K, V> Map<K, V> toMap(
-            Class<K> keyType, Class<V> valueType, Object... entries) {
-        if (entries.length % 2 == 1)
-            throw new IllegalArgumentException("Invalid entries");
-        return IntStream.range(0, entries.length / 2).map(i -> i * 2)
-                .collect(HashMap::new,
-                        (m, i) -> m.put(keyType.cast(entries[i]), valueType.cast(entries[i + 1])),
-                        Map::putAll);
+    public SparqlExecutionException(String message) {
+        super(message);
     }
-
 }
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/SparqlParsingException.java b/src/main/java/eu/tib/exception/SparqlParsingException.java
deleted file mode 100644
index 02a07f2..0000000
--- a/src/main/java/eu/tib/exception/SparqlParsingException.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package eu.tib.exception;
-
-import org.apache.commons.lang3.StringUtils;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.IntStream;
-
-public class SparqlParsingException extends RuntimeException {
-
-    public SparqlParsingException(Class clazz, String... searchParamsMap) {
-        super(SparqlParsingException.generateMessage(clazz.getSimpleName(), toMap(String.class, String.class, searchParamsMap)));
-    }
-
-    private static String generateMessage(String entity, Map<String, String> searchParams) {
-        return StringUtils.capitalize(entity) +
-                " could not execute SparQL-Generate for parameters " +
-                searchParams;
-    }
-
-    private static <K, V> Map<K, V> toMap(
-            Class<K> keyType, Class<V> valueType, Object... entries) {
-        if (entries.length % 2 == 1)
-            throw new IllegalArgumentException("Invalid entries");
-        return IntStream.range(0, entries.length / 2).map(i -> i * 2)
-                .collect(HashMap::new,
-                        (m, i) -> m.put(keyType.cast(entries[i]), valueType.cast(entries[i + 1])),
-                        Map::putAll);
-    }
-
-}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/StreamManagerException.java b/src/main/java/eu/tib/exception/StreamManagerException.java
deleted file mode 100644
index 787657e..0000000
--- a/src/main/java/eu/tib/exception/StreamManagerException.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package eu.tib.exception;
-
-import org.apache.commons.lang3.StringUtils;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.IntStream;
-
-public class StreamManagerException extends RuntimeException {
-
-    public StreamManagerException(Class clazz, String... searchParamsMap) {
-        super(StreamManagerException.generateMessage(clazz.getSimpleName(), toMap(String.class, String.class, searchParamsMap)));
-    }
-
-    private static String generateMessage(String entity, Map<String, String> searchParams) {
-        return StringUtils.capitalize(entity) +
-                " could not create StreamManager properly for parameters " +
-                searchParams;
-    }
-
-    private static <K, V> Map<K, V> toMap(
-            Class<K> keyType, Class<V> valueType, Object... entries) {
-        if (entries.length % 2 == 1)
-            throw new IllegalArgumentException("Invalid entries");
-        return IntStream.range(0, entries.length / 2).map(i -> i * 2)
-                .collect(HashMap::new,
-                        (m, i) -> m.put(keyType.cast(entries[i]), valueType.cast(entries[i + 1])),
-                        Map::putAll);
-    }
-
-}
\ No newline at end of file
diff --git a/src/main/java/eu/tib/exception/VIVOExportException.java b/src/main/java/eu/tib/exception/VIVOExportException.java
index da1c254..3a49753 100644
--- a/src/main/java/eu/tib/exception/VIVOExportException.java
+++ b/src/main/java/eu/tib/exception/VIVOExportException.java
@@ -1,31 +1,7 @@
 package eu.tib.exception;
 
-import org.apache.commons.lang3.StringUtils;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.stream.IntStream;
-
 public class VIVOExportException extends RuntimeException {
-
-    public VIVOExportException(Class clazz, String... searchParamsMap) {
-        super(VIVOExportException.generateMessage(clazz.getSimpleName(), toMap(String.class, String.class, searchParamsMap)));
-    }
-
-    private static String generateMessage(String entity, Map<String, String> searchParams) {
-        return StringUtils.capitalize(entity) +
-                " could not export data to VIVO for parameters " +
-                searchParams;
-    }
-
-    private static <K, V> Map<K, V> toMap(
-            Class<K> keyType, Class<V> valueType, Object... entries) {
-        if (entries.length % 2 == 1)
-            throw new IllegalArgumentException("Invalid entries");
-        return IntStream.range(0, entries.length / 2).map(i -> i * 2)
-                .collect(HashMap::new,
-                        (m, i) -> m.put(keyType.cast(entries[i]), valueType.cast(entries[i + 1])),
-                        Map::putAll);
+    public VIVOExportException(String message) {
+        super(message);
     }
-
 }
\ No newline at end of file
diff --git a/src/main/java/eu/tib/service/GeneratePipeline.java b/src/main/java/eu/tib/service/GeneratePipeline.java
index cdfdc21..2954009 100644
--- a/src/main/java/eu/tib/service/GeneratePipeline.java
+++ b/src/main/java/eu/tib/service/GeneratePipeline.java
@@ -2,10 +2,7 @@
 
 import com.google.gson.Gson;
 import com.google.gson.JsonSyntaxException;
-import eu.tib.exception.ConfigLoadingException;
 import eu.tib.exception.SparqlExecutionException;
-import eu.tib.exception.SparqlParsingException;
-import eu.tib.exception.StreamManagerException;
 import eu.tib.utils.ResourceUtils;
 import fr.mines_stetienne.ci.sparql_generate.FileConfigurations;
 import fr.mines_stetienne.ci.sparql_generate.SPARQLExt;
@@ -69,7 +66,7 @@ public Model run(String confPath, Map<String, String> input) {
             return output;
         } catch (Exception e) {
             log.error("Error while executing SPARQL-Generate.", e);
-            throw new SparqlExecutionException(GeneratePipeline.class);
+            throw new SparqlExecutionException("Error while executing SPARQL-Generate.");
         }
     }
 
@@ -79,8 +76,8 @@ public FileConfigurations readConfig(String confFilePath) {
             FileConfigurations config = (new Gson()).fromJson(conf, FileConfigurations.class);
             return config;
         } catch (IOException | NullPointerException | JsonSyntaxException e) {
-            log.error("Error while reading the config file.", e);
-            throw new ConfigLoadingException(GeneratePipeline.class, "configFile", confFilePath);
+            log.error("Error while reading config file " + confFilePath, e);
+            throw new SparqlExecutionException("Error while reading config file " + confFilePath);
         }
     }
 
@@ -92,10 +89,10 @@ public SPARQLExtQuery parseSparqlGenerateQuery(String queryPath, FileConfigurati
             return q;
         } catch (IOException | NullPointerException e) {
             log.error(String.format("No query file %s was found.", queryPath), e);
-            throw new SparqlParsingException(GeneratePipeline.class, "queryName", queryPath);
+            throw new SparqlExecutionException(String.format("No query file %s was found.", queryPath));
         } catch (QueryException e) {
             log.error(String.format("Query %s could not be parsed.", queryPath), e);
-            throw new SparqlParsingException(GeneratePipeline.class, "queryName", queryPath);
+            throw new SparqlExecutionException(String.format("Query %s could not be parsed.", queryPath));
         }
     }
 
@@ -144,7 +141,7 @@ public SPARQLExtStreamManager prepareStreamManager(String confPath, FileConfigur
                     mapper.addAltEntry(doc.uri, docpath);
                 } catch (Exception e) {
                     log.error(String.format("No named query was found at %s.", docpath), e);
-                    throw new StreamManagerException(GeneratePipeline.class, "namedQuery", docpath);
+                    throw new SparqlExecutionException(String.format("No named query was found at %s.", docpath));
                 }
             });
         }
@@ -156,7 +153,7 @@ public SPARQLExtStreamManager prepareStreamManager(String confPath, FileConfigur
                     mapper.addAltEntry(doc.uri, docpath);
                 } catch (Exception e) {
                     log.error(String.format("No documentset was found at %s.", docpath), e);
-                    throw new StreamManagerException(GeneratePipeline.class, "documentset", docpath);
+                    throw new SparqlExecutionException(String.format("No documentset was found at %s.", docpath));
                 }
             });
         }
@@ -167,8 +164,8 @@ public SPARQLExtStreamManager prepareStreamManager(String confPath, FileConfigur
                 try {
                     mapper.addAltEntry(doc.uri, docpath);
                 } catch (Exception e) {
-                    log.error(String.format("No named graph was found at %s.", docpath), e);
-                    throw new StreamManagerException(GeneratePipeline.class, "namedGraph", docpath);
+                    log.error(String.format("No named graph was found at %s.", docpath),e);
+                    throw new SparqlExecutionException(String.format("No named graph was found at %s.", docpath));
                 }
             });
         }
diff --git a/src/main/java/eu/tib/storage/VIVOExport.java b/src/main/java/eu/tib/storage/VIVOExport.java
index 9374270..cf0d822 100644
--- a/src/main/java/eu/tib/storage/VIVOExport.java
+++ b/src/main/java/eu/tib/storage/VIVOExport.java
@@ -94,15 +94,12 @@ public void send(HttpRequest request) {
             HttpResponse<String> response = client.send(request, HttpResponse.BodyHandlers.ofString());
 
             if (response.statusCode() != 200) {
-                log.info("Error while exporting data to VIVO: " + response.statusCode());
-                log.info(response.body());
-                throw new VIVOExportException(VIVOExport.class, "errorCode", Integer.toString(response.statusCode()),
-                        "errorMessage", response.body());
+                log.error(response.body());
+                throw new VIVOExportException("Error while exporting data to VIVO: " + response.statusCode());
             }
 
         } catch (IOException | InterruptedException e) {
-            log.error("Error while exporting data to VIVO", e);
-            throw new VIVOExportException(VIVOExport.class, "error", e.getClass().getName());
+            throw new VIVOExportException("Error while exporting data to VIVO");
         }
     }
 }
\ No newline at end of file
diff --git a/src/test/java/eu/tib/service/GeneratePipelineTest.java b/src/test/java/eu/tib/service/GeneratePipelineTest.java
index ef0ff67..9e99cd5 100644
--- a/src/test/java/eu/tib/service/GeneratePipelineTest.java
+++ b/src/test/java/eu/tib/service/GeneratePipelineTest.java
@@ -1,7 +1,6 @@
 package eu.tib.service;
 
-import eu.tib.exception.ConfigLoadingException;
-import eu.tib.exception.SparqlParsingException;
+import eu.tib.exception.SparqlExecutionException;
 import fr.mines_stetienne.ci.sparql_generate.FileConfigurations;
 import fr.mines_stetienne.ci.sparql_generate.stream.LocationMapperAccept;
 import fr.mines_stetienne.ci.sparql_generate.stream.LookUpRequest;
@@ -43,7 +42,7 @@ void readConfigTest() {
     @Test
     void failReadConfigTest() {
         String nonExistingPath = "xxxxxxxxx";
-        assertThrows(ConfigLoadingException.class, () -> pip.readConfig(nonExistingPath));
+        assertThrows(SparqlExecutionException.class, () -> pip.readConfig(nonExistingPath));
     }
 
     @Test
@@ -57,9 +56,9 @@ void parseSparqlGenerateQueryTest() {
     @Test
     void failParseSparqlGenerateQueryTest() {
         String nonExistingPath = "xxxxxxxxx";
-        assertThrows(SparqlParsingException.class, () -> pip.parseSparqlGenerateQuery(nonExistingPath, config));
+        assertThrows(SparqlExecutionException.class, () -> pip.parseSparqlGenerateQuery(nonExistingPath, config));
         String notAQueryPath = confPath + File.separator + CONF_FILE;
-        assertThrows(SparqlParsingException.class, () -> pip.parseSparqlGenerateQuery(notAQueryPath, config));
+        assertThrows(SparqlExecutionException.class, () -> pip.parseSparqlGenerateQuery(notAQueryPath, config));
     }
 
     @Test

From 52bc2e6068c0571f54148fe03b41edc233935349 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Fri, 18 Jun 2021 19:22:43 +0200
Subject: [PATCH 29/34] specify jar in docker

---
 DockerfileBuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DockerfileBuild b/DockerfileBuild
index 75f2c97..6b63768 100644
--- a/DockerfileBuild
+++ b/DockerfileBuild
@@ -3,7 +3,7 @@ FROM maven:3.6.3-jdk-11-slim AS build-env
 WORKDIR /app
 COPY ./pom.xml ./pom.xml
 COPY ./src ./src
-RUN mvn clean install -Dmaven.test.skip=true && cp target/*.jar app.jar
+RUN mvn clean install -Dmaven.test.skip=true && cp target/generate2vivo-*.jar app.jar
 
 #-------- NEXT STAGE -----------
 

From 94e3ba052da15a1cf7d467ea80bb2e130c60380b Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Fri, 18 Jun 2021 20:27:52 +0200
Subject: [PATCH 30/34] update documentation

---
 CHANGELOG.md                                  |  2 +
 README.md                                     | 58 +++++++++++--------
 .../controller/DataciteCommonsController.java | 24 +++++---
 .../eu/tib/controller/OrcidController.java    | 11 ++--
 .../java/eu/tib/controller/RORController.java | 15 +++--
 .../java/eu/tib/swagger/SwaggerConfig.java    |  3 +-
 6 files changed, 69 insertions(+), 44 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c36030..6133e68 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@ All notable changes to this project will be documented in this file.
 - make all controller use HTTP-Get requests
 - centralize input validation
 - export to VIVO in chunks
+- simplify error handling
+- document methods in swagger-UI and remove default responses
 
 ## [Renamed Project] - 2021-05-25
 As new datsources were integrated and the name datacitecommons2vivo was not reflecting
diff --git a/README.md b/README.md
index 394f3dd..df2b907 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +1,43 @@
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 
 ## generate2vivo
-generate2vivo is a Data Ingest Tool for the Open-Source-Software VIVO. 
-It queries metadata from the Datacite Commons PID-Graph and the ROR API, 
-maps it to the VIVO ontology using [sparql-generate](https://ci.mines-stetienne.fr/sparql-generate/index.html) and optionally imports it into a VIVO instance.
+generate2vivo is an extensible Data Ingest Tool for the Open-Source-Software VIVO. 
+It currently queries metadata from Datacite Commons, ROR and ORCID
+and maps them to the VIVO ontology using [sparql-generate](https://ci.mines-stetienne.fr/sparql-generate/index.html).
+The resulting RDF data can be exported to a VIVO instance directly or returned in a HTTP response.
 
+- [Available queries](#available-queries)
+  + [Datacite Commons](#datacite-commons)
+  + [ROR](#ror)
+  + [ORCID](#orcid)
 - [Installation](#installation)
-- [Usage](#usage)
-    + [Datacite Commons](#datacite-commons)
-    + [ROR](#ror)
 - [Run in Command Line](#run-in-command-line)
 - [Extensible](#extensible)
 
+### Available queries
+The datasources and queries that are currently available are listed below.
+
+##### Datacite Commons
+For Datacite Commons the following queries are available:
+* `organization` : This method gets data about an organization by passing a ROR id.
+* `organizationPlusPeople`: This method gets data about an organization and its affiliated people by passing a ROR id.
+* `organizationPlusPeoplePlusWorks`:This method gets data about an organization and its affiliated people and their respective works by passing a ROR id.
+* `person`: This method gets data about a person by passing an ORCID id.
+* `personPlusWorks`: This method gets data about a person and their works by passing an ORCID id.
+* `work`: This method gets data about a work by passing an DOI.
+
+##### ROR
+For ROR there are 2 queries available:
+* `organization`: This method gets data about an organization by passing a ROR id.
+* `organizationPlusChildren`: This method gets data about an organization and all their sub-organizations by passing a ROR id.
+
+##### ORCID
+For ORCID the following queries are available:
+* `personPlusWorks`: This method gets data about a person and their works by passing an ORCID id.
+* `currentEmployeesPlusWorks`: This method gets data about an organization's current employees and their works by passing a ROR id.
+
+
+
 ### Installation
 1. Clone the repository to a local folder using `git clone https://github.com/vivo-community/generate2vivo.git`
 2. Change into the folder where the repository has been cloned. 
@@ -33,32 +59,16 @@ maps it to the VIVO ontology using [sparql-generate](https://ci.mines-stetienne.
 
 5. A minimal swagger-ui will be available at `http://localhost:9000/swagger-ui/`.
 
-### Usage
-Go to `http://localhost:9000/swagger-ui/` in your browser and choose Datacite Commons or ROR as a data source. 
-  
-##### Datacite Commons
-For Datacite Commons there are 2 queries available:
-* `getOrganizationPlusPersons`: Queries Datacite Commons for the organization and its affiliated people.
-* `getPersonPlusPublications`: Queries Datacite Commons for the person and its affiliated publications. 
-
-##### ROR
-For ROR there are 2 queries available:
-* `getOrganization`: Queries ROR for the organization.
-* `getOrganizationPlusChildren`: Queries ROR for the organization and all of its sub-organizations recursively.
-
-The program will return a 200 Status, if the data was imported to VIVO or if you chose not to provide your VIVO details,
-it will return the RDF-data as a result in format JSON-LD.
-
 ### Run in Command Line
 Alternatively you can run the queries from the command line using the sparql-generate executable JAR-file.
 All queries are placed in folder `src/main/resources/sparqlg` and come with a `sparql-generate-conf.json`. 
 Its structure and use are explained in detail on the [sparql-generate website](https://ci.mines-stetienne.fr/sparql-generate/language-cli.html).
 
 ### Extensible
-The software is easily extensible, meaning you can add and remove datasources without touching the code.
+The software is easily extensible, meaning you can add and remove datasources.
 
 For example, if you are not interested in using Datacite Commons, just remove the folder from `src/main/resources/sparqlg`
-and the respective controller in the package `eu.tib.controller` and it's gone.
+and the respective controller in the package `eu.tib.controller`.
 
 On the other hand, if you would like to add a datasource:
 * add a folder with your queries under `src/main/resources/sparqlg` and include a `sparql-generate-conf.json` 
diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index ae8b3fd..149d3e2 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -3,6 +3,7 @@
 import eu.tib.controller.validation.InputValidator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiParam;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -25,6 +26,7 @@ public class DataciteCommonsController {
     @Autowired
     private ResponseService responseService;
 
+    @ApiOperation(value = "Retrieve organization data from Datacite Commons", notes = "This method gets data about an organization from Datacite Commons by passing a ROR id.")
     @GetMapping(value = "/organization", produces = "application/json")
     public ResponseEntity<String> getOrganization(
             @Valid @Pattern(regexp = InputValidator.ror)
@@ -43,8 +45,9 @@ public ResponseEntity<String> getOrganization(
         return result;
     }
 
-    @GetMapping(value = "/organizationPlusPersons", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusPersons(
+    @ApiOperation(value = "Retrieve data about an organization and its affiliated people from Datacite Commons", notes = "This method gets data about an organization and its affiliated people from Datacite Commons by passing a ROR id.")
+    @GetMapping(value = "/organizationPlusPeople", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusPeople(
             @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
@@ -60,9 +63,9 @@ public ResponseEntity<String> getOrganizationPlusPersons(
         log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
         return result;
     }
-
-    @GetMapping(value = "/organizationPlusPersonsPlusPublications", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusPersonsPlusPublications(
+    @ApiOperation(value = "Retrieve data about an organization and its affiliated people and their respective works from Datacite Commons", notes = "This method gets data about an organization and its affiliated people and their respective works from Datacite Commons by passing a ROR id.")
+    @GetMapping(value = "/organizationPlusPeoplePlusWorks", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusPeoplePlusWorks(
             @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
@@ -79,6 +82,7 @@ public ResponseEntity<String> getOrganizationPlusPersonsPlusPublications(
         return result;
     }
 
+    @ApiOperation(value = "Retrieve data about a person from Datacite Commons", notes = "This method gets data about a person from Datacite Commons by passing an ORCID id.")
     @GetMapping(value = "/person", produces = "application/json")
     public ResponseEntity<String> getPerson(
             @Valid @Pattern(regexp = InputValidator.orcid)
@@ -97,8 +101,9 @@ public ResponseEntity<String> getPerson(
         return result;
     }
 
-    @GetMapping(value = "/personPlusPublications", produces = "application/json")
-    public ResponseEntity<String> getPersonPlusPublications(
+    @ApiOperation(value = "Retrieve data about a person and their works from Datacite Commons", notes = "This method gets data about a person and their works from Datacite Commons by passing an ORCID id.")
+    @GetMapping(value = "/personPlusWorks", produces = "application/json")
+    public ResponseEntity<String> getPersonPlusWorks(
             @Valid @Pattern(regexp = InputValidator.orcid)
             @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
             @RequestParam String orcid) {
@@ -115,8 +120,9 @@ public ResponseEntity<String> getPersonPlusPublications(
         return result;
     }
 
-    @GetMapping(value = "/publications", produces = "application/json")
-    public ResponseEntity<String> getPublications(
+    @ApiOperation(value = "Retrieve data about a work from Datacite Commons", notes = "This method gets data about a work from Datacite Commons by passing an DOI.")
+    @GetMapping(value = "/work", produces = "application/json")
+    public ResponseEntity<String> getWork(
             @Valid @Pattern(regexp = InputValidator.doi)
             @ApiParam("DOI of the publication")
             @RequestParam String doi) {
diff --git a/src/main/java/eu/tib/controller/OrcidController.java b/src/main/java/eu/tib/controller/OrcidController.java
index afb2d4b..6d9bc0f 100644
--- a/src/main/java/eu/tib/controller/OrcidController.java
+++ b/src/main/java/eu/tib/controller/OrcidController.java
@@ -3,6 +3,7 @@
 import eu.tib.controller.validation.InputValidator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiParam;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -25,8 +26,9 @@ public class OrcidController {
     @Autowired
     private ResponseService responseService;
 
-    @GetMapping(value = "/personPlusPublications", produces = "application/json")
-    public ResponseEntity<String> getPersonPlusPublications(
+    @ApiOperation(value = "Retrieve data about a person and their works from ORCID", notes = "This method gets data about a person and their works from ORCID by passing an ORCID id.")
+    @GetMapping(value = "/personPlusWorks", produces = "application/json")
+    public ResponseEntity<String> getPersonPlusWorks(
             @Valid @Pattern(regexp = InputValidator.orcid)
             @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
             @RequestParam String orcid) {
@@ -46,8 +48,9 @@ public ResponseEntity<String> getPersonPlusPublications(
     }
 
 
-    @GetMapping(value = "/currentEmployeesPlusPublications", produces = "application/json")
-    public ResponseEntity<String> getCurrentEmployeesPlusPublications(
+    @ApiOperation(value = "Retrieve data about an organization's current employees and their works from ORCID", notes = "This method gets data about an organization's current employees and their works from ORCID by passing a ROR id.")
+    @GetMapping(value = "/currentEmployeesPlusWorks", produces = "application/json")
+    public ResponseEntity<String> getCurrentEmployeesPlusWorks(
             @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
diff --git a/src/main/java/eu/tib/controller/RORController.java b/src/main/java/eu/tib/controller/RORController.java
index e6623fc..844f469 100644
--- a/src/main/java/eu/tib/controller/RORController.java
+++ b/src/main/java/eu/tib/controller/RORController.java
@@ -3,6 +3,7 @@
 import eu.tib.controller.validation.InputValidator;
 import eu.tib.service.ResponseService;
 import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiParam;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -25,13 +26,14 @@ public class RORController {
     @Autowired
     private ResponseService responseService;
 
-    @GetMapping(value = "/organizationPlusChildren", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusChildren(
+    @ApiOperation(value = "Retrieve data about an organization from ROR", notes = "This method gets data about an organization from ROR by passing a ROR id.")
+    @GetMapping(value = "/organization", produces = "application/json")
+    public ResponseEntity<String> getOrganization(
             @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
-        final String id = "sparqlg/ror/orga2children";
+        final String id = "sparqlg/ror/organization";
         log.info("Incoming Request for " + id + " with ror: " + ror);
         StopWatch stopWatch = new StopWatch(id);
         stopWatch.start(id);
@@ -43,13 +45,14 @@ public ResponseEntity<String> getOrganizationPlusChildren(
         return result;
     }
 
-    @GetMapping(value = "/organization", produces = "application/json")
-    public ResponseEntity<String> getOrganization(
+    @ApiOperation(value = "Retrieve data about an organization and all their sub-organizations from ROR", notes = "This method gets data about an organization and all their sub-organizations from ROR by passing a ROR id.")
+    @GetMapping(value = "/organizationPlusChildren", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusChildren(
             @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
 
-        final String id = "sparqlg/ror/organization";
+        final String id = "sparqlg/ror/orga2children";
         log.info("Incoming Request for " + id + " with ror: " + ror);
         StopWatch stopWatch = new StopWatch(id);
         stopWatch.start(id);
diff --git a/src/main/java/eu/tib/swagger/SwaggerConfig.java b/src/main/java/eu/tib/swagger/SwaggerConfig.java
index 1d3976c..881b4c0 100644
--- a/src/main/java/eu/tib/swagger/SwaggerConfig.java
+++ b/src/main/java/eu/tib/swagger/SwaggerConfig.java
@@ -19,6 +19,7 @@ public Docket productApi() {
                 .apis( RequestHandlerSelectors.basePackage( "eu.tib" ) )
                 .paths(PathSelectors.any())
                 .build()
+                .useDefaultResponseMessages(false)
                 .pathMapping("/")
                 .apiInfo(apiInfo());
     }
@@ -26,7 +27,7 @@ public Docket productApi() {
     private ApiInfo apiInfo() {
         return new ApiInfoBuilder()
                 .title("generate2vivo")
-                .description("Data Ingest from different datasources like Datacite Commons or ROR to VIVO")
+                .description("Data Ingest from different datasources like Datacite Commons, ROR or ORCID to VIVO.")
                 .version("1.1.0-SNAPSHOT")
                 .build();
     }

From 743dbaea9d53fb46c05b42af513e9d3c37790c22 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 21 Jun 2021 11:41:17 +0200
Subject: [PATCH 31/34] correct docs

---
 README.md                                            |  4 ++--
 pom.xml                                              |  2 +-
 .../eu/tib/controller/DataciteCommonsController.java | 12 ++++++------
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index df2b907..b53af80 100644
--- a/README.md
+++ b/README.md
@@ -21,9 +21,9 @@ The datasources and queries that are currently available are listed below.
 For Datacite Commons the following queries are available:
 * `organization` : This method gets data about an organization by passing a ROR id.
 * `organizationPlusPeople`: This method gets data about an organization and its affiliated people by passing a ROR id.
-* `organizationPlusPeoplePlusWorks`:This method gets data about an organization and its affiliated people and their respective works by passing a ROR id.
+* `organizationPlusPeoplePlusPublications`:This method gets data about an organization and its affiliated people and their respective publications by passing a ROR id.
 * `person`: This method gets data about a person by passing an ORCID id.
-* `personPlusWorks`: This method gets data about a person and their works by passing an ORCID id.
+* `personPlusPublications`: This method gets data about a person and their publications by passing an ORCID id.
 * `work`: This method gets data about a work by passing an DOI.
 
 ##### ROR
diff --git a/pom.xml b/pom.xml
index 2ace1e7..34056ff 100644
--- a/pom.xml
+++ b/pom.xml
@@ -14,7 +14,7 @@
     <groupId>eu.tib</groupId>
     <artifactId>generate2vivo</artifactId>
     <version>1.1.0-SNAPSHOT</version>
-    <description>Data Ingest from different datasources like Datacite Commons or ROR to VIVO</description>
+    <description>Data Ingest from different datasources like Datacite Commons, ROR or ORCID to VIVO</description>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
diff --git a/src/main/java/eu/tib/controller/DataciteCommonsController.java b/src/main/java/eu/tib/controller/DataciteCommonsController.java
index 149d3e2..901bd54 100644
--- a/src/main/java/eu/tib/controller/DataciteCommonsController.java
+++ b/src/main/java/eu/tib/controller/DataciteCommonsController.java
@@ -63,9 +63,9 @@ public ResponseEntity<String> getOrganizationPlusPeople(
         log.info(id + " took " + stopWatch.getTotalTimeSeconds() + "s");
         return result;
     }
-    @ApiOperation(value = "Retrieve data about an organization and its affiliated people and their respective works from Datacite Commons", notes = "This method gets data about an organization and its affiliated people and their respective works from Datacite Commons by passing a ROR id.")
-    @GetMapping(value = "/organizationPlusPeoplePlusWorks", produces = "application/json")
-    public ResponseEntity<String> getOrganizationPlusPeoplePlusWorks(
+    @ApiOperation(value = "Retrieve data about an organization and its affiliated people and their respective publications from Datacite Commons", notes = "This method gets data about an organization and its affiliated people and their respective publications from Datacite Commons by passing a ROR id.")
+    @GetMapping(value = "/organizationPlusPeoplePlusPublications", produces = "application/json")
+    public ResponseEntity<String> getOrganizationPlusPeoplePlusPublications(
             @Valid @Pattern(regexp = InputValidator.ror)
             @ApiParam("Complete ROR URL consisting of https://ror.org/ plus id")
             @RequestParam String ror) {
@@ -101,9 +101,9 @@ public ResponseEntity<String> getPerson(
         return result;
     }
 
-    @ApiOperation(value = "Retrieve data about a person and their works from Datacite Commons", notes = "This method gets data about a person and their works from Datacite Commons by passing an ORCID id.")
-    @GetMapping(value = "/personPlusWorks", produces = "application/json")
-    public ResponseEntity<String> getPersonPlusWorks(
+    @ApiOperation(value = "Retrieve data about a person and their publications from Datacite Commons", notes = "This method gets data about a person and their publications from Datacite Commons by passing an ORCID id.")
+    @GetMapping(value = "/personPlusPublications", produces = "application/json")
+    public ResponseEntity<String> getPersonPlusPublications(
             @Valid @Pattern(regexp = InputValidator.orcid)
             @ApiParam("Complete Orcid URL consisting of https://orcid.org/ plus id")
             @RequestParam String orcid) {

From 631ce4927f8e3048b309929a8700f79298f46978 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 21 Jun 2021 15:16:29 +0200
Subject: [PATCH 32/34] filter graphql error responses

---
 .../sparqlg/datacitecommons/orga2person/orga2person.rqg     | 4 ++++
 .../sparqlg/datacitecommons/orga2person/orga_source.rqg     | 5 ++++-
 .../orga2person2publication/orga2person2publication.rqg     | 6 +++++-
 .../datacitecommons/orga2person2publication/orga_source.rqg | 5 ++++-
 .../sparqlg/datacitecommons/organization/orga_source.rqg    | 4 ++++
 .../sparqlg/datacitecommons/person/person_source.rqg        | 4 ++++
 .../person2publication/person2publication.rqg               | 6 +++++-
 .../datacitecommons/person2publication/person_source.rqg    | 6 ++++--
 .../resources/sparqlg/datacitecommons/work/work_source.rqg  | 4 ++++
 9 files changed, 38 insertions(+), 6 deletions(-)

diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
index 6fb2ac7..f88e743 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/orga2person.rqg
@@ -36,5 +36,9 @@ WHERE {
     BIND(  fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
     BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
 }
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg
index 15b3565..048abbe 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person/orga_source.rqg
@@ -17,7 +17,10 @@ WHERE {
     BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
-    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
 
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
+    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
     BIND(<https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg>(?orga_data) AS ?orga_id)
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg
index d6ce293..d46f8fb 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga2person2publication.rqg
@@ -37,5 +37,9 @@ WHERE {
     BIND(  fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
     BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
-}
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg
index 60d9262..b378fe8 100644
--- a/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/orga2person2publication/orga_source.rqg
@@ -17,7 +17,10 @@ WHERE {
     BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
-    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
 
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
+    BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
     BIND(<https://projects.tib.eu/tapir/datacitecommons/organization/orga_id.rqg>(?orga_data) AS ?orga_id)
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg b/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
index f93662e..32e4e98 100644
--- a/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/organization/orga_source.rqg
@@ -13,5 +13,9 @@ WHERE {
     BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
     BIND( fun:JSONPath( ?body, "$.data.organization" ) AS ?orga_data )
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg b/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
index 23dea39..e0c5cee 100644
--- a/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/person/person_source.rqg
@@ -13,5 +13,9 @@ WHERE {
     BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
     BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person_data )
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg b/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
index b6bf2af..c83b1fb 100644
--- a/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/person2publication.rqg
@@ -37,5 +37,9 @@ WHERE {
     BIND(  fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
     BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person_data )
-}
+}
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg b/src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg
index 91392f7..decfcfa 100644
--- a/src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/person2publication/person_source.rqg
@@ -17,8 +17,10 @@ WHERE {
     BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
-    BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person_data )
 
-    BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
 
+    BIND( fun:JSONPath( ?body, "$.data.person" ) AS ?person_data )
+    BIND(<https://projects.tib.eu/tapir/datacitecommons/person/person_id.rqg>(?person_data) AS ?person_id)
 }
\ No newline at end of file
diff --git a/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg b/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
index 1f77405..0689ea3 100644
--- a/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
+++ b/src/main/resources/sparqlg/datacitecommons/work/work_source.rqg
@@ -13,5 +13,9 @@ WHERE {
     BIND( fun:HTTPPost(<https://api.datacite.org/graphql>, "Content-type: application/json" , ?postbody) AS ?response )
     FILTER( fun:HTTPExtractResponseCode( ?response ) = 200 )
     BIND( fun:HTTPExtractBody( ?response ) AS ?body )
+
+    BIND( fun:JSONPath( ?body, "$.errors" ) AS ?errors )
+    FILTER( !BOUND(?errors) )
+
     BIND( fun:JSONPath( ?body, "$.data.work" ) AS ?work_data )
 }
\ No newline at end of file

From e152b4ed8dc056a9747acf2690325acb5e19fce3 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Mon, 21 Jun 2021 15:19:33 +0200
Subject: [PATCH 33/34] log empty model

---
 src/main/java/eu/tib/service/ResponseService.java | 8 ++++++--
 src/main/java/eu/tib/storage/VIVOExport.java      | 6 +-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/main/java/eu/tib/service/ResponseService.java b/src/main/java/eu/tib/service/ResponseService.java
index 4c6bab0..fe7115b 100644
--- a/src/main/java/eu/tib/service/ResponseService.java
+++ b/src/main/java/eu/tib/service/ResponseService.java
@@ -29,11 +29,15 @@ public ResponseEntity<String> buildResponse(String queryName, Map<String, String
         Model result = pipeline.run(queryName, input);
         log.info("Finished pipeline for " + queryName);
 
+        if (result.isEmpty()) log.info("No data was generated.");
+
         if (vivoProperties.isValid()) {
             log.info("Found VIVO properties");
             vivoExport.exportData(result, vivoProperties);
-            String status = String.format("{\"status\":\"%s\"}", "SPARQL update accepted.");
-            return ResponseEntity.status(HttpStatus.OK).body(status);
+
+            String msg = (result.isEmpty()) ? "No data was generated." : "SPARQL update accepted.";
+            String statusJSON = String.format("{\"status\":\"%s\"}", msg);
+            return ResponseEntity.status(HttpStatus.OK).body(statusJSON);
         } else {
             log.info("Returning JSON-LD");
             StringWriter stringWriter = new StringWriter();
diff --git a/src/main/java/eu/tib/storage/VIVOExport.java b/src/main/java/eu/tib/storage/VIVOExport.java
index cf0d822..e839b4d 100644
--- a/src/main/java/eu/tib/storage/VIVOExport.java
+++ b/src/main/java/eu/tib/storage/VIVOExport.java
@@ -23,11 +23,7 @@ public class VIVOExport {
     private static final int CHUNK_SIZE = 2500;  // triples per 'chunk'
 
     public void exportData(Model data, VIVOProperties vivo) {
-        if (data.isEmpty()) {
-            log.info("No data was generated, Model is empty.");
-        } else {
-            exportInChunks(data, vivo);
-        }
+        if (!data.isEmpty()) exportInChunks(data, vivo);
     }
 
     /**

From 234cbbffcea8eeb1a9cdb85fa2160c79983d2bc6 Mon Sep 17 00:00:00 2001
From: Sandra Mierz <sandra.mierz@tib.eu>
Date: Tue, 22 Jun 2021 15:31:30 +0200
Subject: [PATCH 34/34] release 1.1.0

---
 CHANGELOG.md                                    | 6 +++++-
 pom.xml                                         | 4 ++--
 src/main/java/eu/tib/swagger/SwaggerConfig.java | 4 ++--
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6133e68..ef4b23b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,14 +2,18 @@
 All notable changes to this project will be documented in this file.
 
 ## [Unreleased]
+
+
+## [1.1.0] - 2021-06-22
 ### Added
 - query ORCID for person and current employees at ROR organization
 - refactor all queries to follow three steps: source, extraction, mapping to vivo-rdf
+- check GraphQL queries for response code 200 and additionally if response body contains error messages (no data)
 - make all controller use HTTP-Get requests
 - centralize input validation
 - export to VIVO in chunks
 - simplify error handling
-- document methods in swagger-UI and remove default responses
+- document methods in swagger-UI and remove response section
 
 ## [Renamed Project] - 2021-05-25
 As new datsources were integrated and the name datacitecommons2vivo was not reflecting
diff --git a/pom.xml b/pom.xml
index 34056ff..5120aa2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,8 +13,8 @@
 
     <groupId>eu.tib</groupId>
     <artifactId>generate2vivo</artifactId>
-    <version>1.1.0-SNAPSHOT</version>
-    <description>Data Ingest from different datasources like Datacite Commons, ROR or ORCID to VIVO</description>
+    <version>1.1.0</version>
+    <description>Extensible Data Ingest Tool for VIVO. Contains data sources like Datacite Commons, ORCID and ROR.</description>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
diff --git a/src/main/java/eu/tib/swagger/SwaggerConfig.java b/src/main/java/eu/tib/swagger/SwaggerConfig.java
index 881b4c0..9e4ddb2 100644
--- a/src/main/java/eu/tib/swagger/SwaggerConfig.java
+++ b/src/main/java/eu/tib/swagger/SwaggerConfig.java
@@ -27,8 +27,8 @@ public Docket productApi() {
     private ApiInfo apiInfo() {
         return new ApiInfoBuilder()
                 .title("generate2vivo")
-                .description("Data Ingest from different datasources like Datacite Commons, ROR or ORCID to VIVO.")
-                .version("1.1.0-SNAPSHOT")
+                .description("Extensible Data Ingest Tool for VIVO. Contains data sources like Datacite Commons, ORCID and ROR.")
+                .version("1.1.0")
                 .build();
     }
 }