Merge remote-tracking branch 'upstream/main'

# Conflicts:
#	src/main/java/cz/cvut/kbss/study/model/PatientRecord.java

src/main/java/cz/cvut/kbss/study/dto/PatientRecordDto.java

@@ -1,10 +1,7 @@
 package cz.cvut.kbss.study.dto;
 
 import cz.cvut.kbss.jopa.model.annotations.*;
-import cz.cvut.kbss.study.model.AbstractEntity;
-import cz.cvut.kbss.study.model.Institution;
-import cz.cvut.kbss.study.model.User;
-import cz.cvut.kbss.study.model.Vocabulary;
+import cz.cvut.kbss.study.model.*;
 import cz.cvut.kbss.study.model.util.HasOwlKey;
 
 import java.util.Date;
@@ -39,6 +36,10 @@ public class PatientRecordDto extends AbstractEntity implements HasOwlKey {
     @OWLObjectProperty(iri = Vocabulary.s_p_was_treated_at, fetch = FetchType.EAGER)
     private Institution institution;
 
+    @Enumerated(EnumType.OBJECT_ONE_OF)
+    @OWLObjectProperty(iri = Vocabulary.s_p_has_phase)
+    private RecordPhase phase;
+
     @Override
     public String getKey() {
         return key;
@@ -105,12 +106,21 @@ public void setFormTemplate(String formTemplate) {
         this.formTemplate = formTemplate;
     }
 
+    public RecordPhase getPhase() {
+        return phase;
+    }
+
+    public void setPhase(RecordPhase phase) {
+        this.phase = phase;
+    }
+
     @Override
     public String toString() {
         return "PatientRecordDto{" +
                 "localName=" + localName +
                 "dateCreated=" + dateCreated +
                 ", institution=" + institution +
+                ", phase=" + phase +
                 "} " + super.toString();
     }
 }

src/main/java/cz/cvut/kbss/study/model/PatientRecord.java

@@ -1,6 +1,8 @@
 package cz.cvut.kbss.study.model;
 
 import cz.cvut.kbss.jopa.model.annotations.CascadeType;
+import cz.cvut.kbss.jopa.model.annotations.EnumType;
+import cz.cvut.kbss.jopa.model.annotations.Enumerated;
 import cz.cvut.kbss.jopa.model.annotations.FetchType;
 import cz.cvut.kbss.jopa.model.annotations.Id;
 import cz.cvut.kbss.jopa.model.annotations.OWLAnnotationProperty;
@@ -53,6 +55,10 @@ public class PatientRecord implements Serializable, HasOwlKey, HasUri {
                                                                      CascadeType.REMOVE}, fetch = FetchType.EAGER)
     private Question question;
 
+    @Enumerated(EnumType.OBJECT_ONE_OF)
+    @OWLObjectProperty(iri = Vocabulary.s_p_has_phase)
+    private RecordPhase phase;
+
     @Override
     public URI getUri() {
         return uri;
@@ -136,12 +142,21 @@ public void setFormTemplate(String formTemplate) {
         this.formTemplate = formTemplate;
     }
 
+    public RecordPhase getPhase() {
+        return phase;
+    }
+
+    public void setPhase(RecordPhase phase) {
+        this.phase = phase;
+    }
+
     @Override
     public String toString() {
         return "PatientRecord{<" + uri +
                 ">, localName=" + localName +
                 ", dateCreated=" + dateCreated +
                 ", institution=" + institution +
+                ", phase=" + phase +
                 "}";
     }
 }

src/main/java/cz/cvut/kbss/study/model/RecordPhase.java

@@ -0,0 +1,26 @@
+package cz.cvut.kbss.study.model;
+
+import cz.cvut.kbss.jopa.model.annotations.Individual;
+
+public enum RecordPhase {
+    @Individual(iri = Vocabulary.s_c_open_record_phase)
+    open(Vocabulary.s_c_open_record_phase),
+    @Individual(iri = Vocabulary.s_c_valid_record_phase)
+    valid(Vocabulary.s_c_valid_record_phase),
+    @Individual(iri = Vocabulary.s_c_completed_record_phase)
+    completed(Vocabulary.s_c_completed_record_phase),
+    @Individual(iri = Vocabulary.s_c_published_record_phase)
+    published(Vocabulary.s_c_published_record_phase),
+    @Individual(iri = Vocabulary.s_c_rejected_record_phase)
+    rejected(Vocabulary.s_c_rejected_record_phase);
+
+    private final String iri;
+
+    RecordPhase(String iri) {
+        this.iri = iri;
+    }
+
+    public String getIri() {
+        return iri;
+    }
+}

src/main/java/cz/cvut/kbss/study/rest/OidcUserController.java

@@ -3,19 +3,21 @@
 import cz.cvut.kbss.study.exception.NotFoundException;
 import cz.cvut.kbss.study.model.Institution;
 import cz.cvut.kbss.study.model.User;
+import cz.cvut.kbss.study.model.util.HasUri;
+import cz.cvut.kbss.study.rest.exception.BadRequestException;
 import cz.cvut.kbss.study.security.SecurityConstants;
 import cz.cvut.kbss.study.service.InstitutionService;
 import cz.cvut.kbss.study.service.UserService;
 import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PathVariable;
-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 java.net.URI;
 import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
 
 /**
  * API for getting basic user info.
@@ -61,6 +63,48 @@ public List<User> getUsers(@RequestParam(value = "institution", required = false
         return institutionKey != null ? getByInstitution(institutionKey) : userService.findAll();
     }
 
+    @PreAuthorize("hasRole('" + SecurityConstants.ROLE_ADMIN + "') or #username == authentication.name")
+    @PutMapping(value = "/{username}", consumes = MediaType.APPLICATION_JSON_VALUE)
+    @ResponseStatus(HttpStatus.NO_CONTENT)
+    public void updateUser(@PathVariable("username") String username, @RequestBody User user,
+                                      @RequestParam(value = "email", defaultValue = "true") boolean sendEmail) {
+        if (!username.equals(user.getUsername())) {
+            throw new BadRequestException("The passed user's username is different from the specified one.");
+        }
+        final User original = getByUsername(username);
+
+        assert original != null;
+        Institution newInstitution = user.getInstitution();
+        Institution oldInstitution = original.getInstitution();
+        original.setInstitution(newInstitution);
+        userService.update(original, sendEmail, "profileUpdate");
+
+        if (LOG.isTraceEnabled() && ! equals(newInstitution, oldInstitution)) {
+            LOG.trace("Set user institution {} to institution {} successfully.", user, oldInstitution, newInstitution);
+        }
+    }
+
+    /**
+     * Input arguments can be null and getUri can be null.
+     * @param entity1
+     * @param entity2
+     * @return true if the URIs of the input arguments are equal, false otherwise.
+     */
+    private boolean equals(HasUri entity1, HasUri entity2){
+        URI u1 = getURI(entity1);
+        URI u2 = getURI(entity2);
+        return Objects.equals(u1, u2);
+    }
+
+    /**
+     * Retrieves the URI of entity argument. entity can be null.
+     * @param entity
+     * @return the URI of the entity or null if entity is null.
+     */
+    private URI getURI(HasUri entity){
+        return Optional.of(entity).map(HasUri::getUri).orElse(null);
+    }
+
     private List<User> getByInstitution(String institutionKey) {
         assert institutionKey != null;
         final Institution institution = institutionService.findByKey(institutionKey);

src/main/resources/model.ttl

@@ -7,6 +7,7 @@
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 @prefix form: <http://onto.fel.cvut.cz/ontologies/form/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix ufo: <http://onto.fel.cvut.cz/ontologies/ufo/> .
 @base <http://onto.fel.cvut.cz/ontologies/record-manager> .
 
 <http://onto.fel.cvut.cz/ontologies/record-manager> rdf:type owl:Ontology ;
@@ -74,6 +75,11 @@ rm:relates-to rdf:type owl:ObjectProperty .
 rm:was-treated-at rdf:type owl:ObjectProperty ;
                   rdfs:subPropertyOf rm:relates-to .
 
+###  http://onto.fel.cvut.cz/ontologies/record-manager/has-phase
+rm:has-phase rdf:type owl:ObjectProperty ;
+                rdfs:subPropertyOf rdf:type ;
+                rdfs:label "has phase"@en .
+
 
 #################################################################
 #    Data properties
@@ -163,5 +169,34 @@ rm:user rdf:type owl:Class ;
 rm:impersonator rdf:type owl:Class ;
         rdfs:label "Impersonator"@en .
 
+###  http://onto.fel.cvut.cz/ontologies/record-manager/record-phase
+rm:record-phase rdf:type owl:Class ;
+        rdfs:subClassOf ufo:phase ;
+        rdfs:label "record phase"@en .
+
+###  http://onto.fel.cvut.cz/ontologies/record-manager/open-record-phase
+rm:open-record-phase rdf:type owl:Class ;
+        rdfs:subClassOf rm:record-phase ;
+        rdfs:label "open record phase"@en .
+
+###  http://onto.fel.cvut.cz/ontologies/record-manager/valid-record-phase
+rm:valid-record-phase rdf:type owl:Class ;
+        rdfs:subClassOf rm:record-phase ;
+        rdfs:label "valid record phase"@en .
+
+###  http://onto.fel.cvut.cz/ontologies/record-manager/completed-record-phase
+rm:completed-record-phase rdf:type owl:Class ;
+        rdfs:subClassOf rm:record-phase ;
+        rdfs:label "completed record phase"@en .
+
+###  http://onto.fel.cvut.cz/ontologies/record-manager/published-record-phase
+rm:published-record-phase rdf:type owl:Class ;
+        rdfs:subClassOf rm:record-phase ;
+        rdfs:label "published record phase"@en .
+
+###  http://onto.fel.cvut.cz/ontologies/record-manager/rejected-record-phase
+rm:rejected-record-phase rdf:type owl:Class ;
+        rdfs:subClassOf rm:record-phase ;
+        rdfs:label "rejected record phase"@en .
 
 ###  Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi