Merge branch 'develop' into fdias-2446-respect-limits-for-shapefile-p…

…rocessing

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/user/AuthenticatedUser.java

@@ -83,7 +83,9 @@ public class AuthenticatedUser implements User, Serializable, JpaEntity<Long> {
     @NotNull
     @Column(nullable = false, unique = true)
     private String email;
+    private String orcid;
     private String affiliation;
+    private String affiliationROR;
     private String position;
 
     @NotBlank(message = "{user.lastName}")
@@ -148,10 +150,18 @@ public String getEmail() {
         return email;
     }
 
+    public String getOrcid() {
+        return orcid;
+    }
+
     public String getAffiliation() {
         return affiliation;
     }
 
+    public String getAffiliationROR() {
+        return affiliationROR;
+    }
+
     public String getPosition() {
         return position;
     }
@@ -214,7 +224,7 @@ public String getIdentifier() {
 
     @Override
     public AuthenticatedUserDisplayInfo getDisplayInfo() {
-        return new AuthenticatedUserDisplayInfo(firstName, lastName, email, affiliation, position);
+        return new AuthenticatedUserDisplayInfo(firstName, lastName, email, orcid, affiliation, affiliationROR, position);
     }
 
     /**
@@ -233,6 +243,12 @@ public void applyDisplayInfo(AuthenticatedUserDisplayInfo inf) {
         if (StringUtils.isNotBlank(inf.getPosition())) {
             setPosition(inf.getPosition());
         }
+        if (StringUtils.isNotBlank(inf.getOrcid())) {
+            setOrcid(inf.getOrcid());
+        }
+        if (StringUtils.isNotBlank(inf.getAffiliationROR())) {
+            setAffiliationROR(inf.getAffiliationROR());
+        }
     }
 
     @Override
@@ -248,12 +264,6 @@ public String getSortByString() {
         return String.format("%s %s %s", getLastName(), getFirstName(), getUserIdentifier());
     }
 
-    public String getOrcidId() {
-        String authProviderId = getAuthenticatedUserLookup().getAuthenticationProviderId();
-        return AuthenticatedUserLookup.ORCID_PROVIDER_ID_PRODUCTION.equals(authProviderId)
-                ? getAuthenticatedUserLookup().getPersistentUserId() : null;
-    }
-
     // -------------------- SETTERS --------------------
 
     public void setDatasetLocks(List<DatasetLock> datasetLocks) {
@@ -277,10 +287,18 @@ public void setEmail(String email) {
         this.email = email.trim();
     }
 
+    public void setOrcid(String orcid) {
+        this.orcid = orcid;
+    }
+
     public void setAffiliation(String affiliation) {
         this.affiliation = affiliation;
     }
 
+    public void setAffiliationROR(String affiliationROR) {
+        this.affiliationROR = affiliationROR;
+    }
+
     public void setPosition(String position) {
         this.position = position;
     }

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/user/AuthenticatedUserDisplayInfo.java

@@ -14,23 +14,35 @@ public class AuthenticatedUserDisplayInfo extends RoleAssigneeDisplayInfo {
     @NotBlank(message = "{user.firstName}")
     private String firstName;
     private String position;
+    private String orcid;
 
     /*
      * @todo Shouldn't we persist the displayName too? It still exists on the
      * authenticateduser table.
      */
-    public AuthenticatedUserDisplayInfo(String firstName, String lastName, String emailAddress, String affiliation, String position) {
-        super(firstName + " " + lastName, emailAddress, affiliation);
+    public AuthenticatedUserDisplayInfo(String firstName, String lastName, String emailAddress,
+                                        String affiliation, String position) {
+        super(firstName + " " + lastName, emailAddress, affiliation, null);
         this.firstName = firstName;
         this.lastName = lastName;
         this.position = position;
     }
 
+    public AuthenticatedUserDisplayInfo(String firstName, String lastName, String emailAddress, String orcid,
+                                        String affiliation, String affiliationROR, String position) {
+        super(firstName + " " + lastName, emailAddress, affiliation, affiliationROR);
+        this.firstName = firstName;
+        this.lastName = lastName;
+        this.position = position;
+        this.orcid = orcid;
+    }
+
     public AuthenticatedUserDisplayInfo() {
-        super("", "", "");
+        super("", "", "", "");
         firstName = "";
         lastName = "";
         position = "";
+        orcid = "";
     }
 
 
@@ -40,7 +52,8 @@ public AuthenticatedUserDisplayInfo() {
      * @param src the display info {@code this} will be a copy of.
      */
     public AuthenticatedUserDisplayInfo(AuthenticatedUserDisplayInfo src) {
-        this(src.getFirstName(), src.getLastName(), src.getEmailAddress(), src.getAffiliation(), src.getPosition());
+        this(src.getFirstName(), src.getLastName(), src.getEmailAddress(), src.getOrcid(), src.getAffiliation(),
+                src.getAffiliationROR(), src.getPosition());
     }
 
     public String getLastName() {
@@ -67,9 +80,18 @@ public void setPosition(String position) {
         this.position = position;
     }
 
+    public String getOrcid() {
+        return orcid;
+    }
+
+    public void setOrcid(String orcid) {
+        this.orcid = orcid;
+    }
+
     @Override
     public String toString() {
-        return "AuthenticatedUserDisplayInfo{firstName=" + firstName + ", lastName=" + lastName + ", position=" + position + ", email=" + getEmailAddress() + '}';
+        return "AuthenticatedUserDisplayInfo{firstName=" + firstName + ", lastName=" + lastName +
+                ", position=" + position + ", email=" + getEmailAddress() + ", orcid=" + getOrcid() + '}';
     }
 
     @Override
@@ -97,7 +119,7 @@ public boolean equals(Object obj) {
         if (!Objects.equals(this.firstName, other.firstName)) {
             return false;
         }
-        return Objects.equals(this.position, other.position) && super.equals(obj);
+        return Objects.equals(this.position, other.position) && Objects.equals(this.orcid, other.orcid) && super.equals(obj);
     }
 
 }

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/user/RoleAssigneeDisplayInfo.java

@@ -13,15 +13,17 @@ public class RoleAssigneeDisplayInfo implements java.io.Serializable {
     private String title;
     private String emailAddress;
     private String affiliation;
+    private String affiliationROR;
 
     public RoleAssigneeDisplayInfo(String title, String emailAddress) {
-        this(title, emailAddress, null);
+        this(title, emailAddress, null, null);
     }
 
-    public RoleAssigneeDisplayInfo(String title, String emailAddress, String anAffiliation) {
+    public RoleAssigneeDisplayInfo(String title, String emailAddress, String anAffiliation, String affiliationROR) {
         this.title = title;
         this.emailAddress = emailAddress;
-        affiliation = anAffiliation;
+        this.affiliation = anAffiliation;
+        this.affiliationROR = affiliationROR;
     }
 
     public String getTitle() {
@@ -36,6 +38,10 @@ public String getAffiliation() {
         return affiliation;
     }
 
+    public String getAffiliationROR() {
+        return affiliationROR;
+    }
+
     public void setTitle(String title) {
         this.title = title;
     }
@@ -48,9 +54,14 @@ public void setAffiliation(String affiliation) {
         this.affiliation = affiliation;
     }
 
+    public void setAffiliationROR(String affiliationROR) {
+        this.affiliationROR = affiliationROR;
+    }
+
     @Override
     public String toString() {
-        return "RoleAssigneeDisplayInfo{" + "title=" + title + ", emailAddress=" + emailAddress + ", affiliation=" + affiliation + '}';
+        return "RoleAssigneeDisplayInfo{" + "title=" + title + ", emailAddress=" + emailAddress +
+                ", affiliation=" + affiliation + ", affiliationROR=" + affiliationROR + '}';
     }
 
     @Override
@@ -78,7 +89,8 @@ public boolean equals(Object obj) {
         if (!Objects.equals(this.emailAddress, other.emailAddress)) {
             return false;
         }
-        return Objects.equals(this.affiliation, other.affiliation);
+        return Objects.equals(this.affiliation, other.affiliation)
+                && Objects.equals(this.affiliationROR, other.affiliationROR);
     }
 
 }

dataverse-persistence/src/main/resources/Bundle_en.properties

@@ -331,7 +331,17 @@ user.lastName=Family Name
 user.lastName.tip=The last name you would like to use for this account.
 user.email.tip=A valid email address you have access to in order to be contacted.
 user.email.taken=This email address is already taken.
+user.orcid=ORCID
+user.orcid.tip=ORCID is an open digital identifier allowing distinction between researchers having the same or similar name and surname.
+user.orcid.invalid.format=Invalid ORCID format.
+user.orcid.invalid.checksum=Invalid ORCID checksum.
 user.affiliation.tip=The organization with which you are affiliated.
+user.affiliationror=Affiliation ROR
+user.affiliationror.tip=ROR identifier of the affiliating institution. The identifier must be provided in its URL form, for instance "https://ror.org/039bjqg32" for the University of Warsaw. You can also enter the name of the institution and select its ROR ID from the list.
+user.affiliationror.suggestionDisplay.valueHeader=ROR
+user.affiliationror.suggestionDisplay.detailsHeader=Institution
+user.affiliationror.ror.invalid.format=Invalid ROR format.
+user.affiliationror.ror.invalid.checksum=Invalid ROR checksum.
 user.position=Position
 user.position.tip=Your role or title at the organization you are affiliated with; such as staff, faculty, student, etc.
 user.notificationsLanguage=E-mail notifications language

dataverse-persistence/src/main/resources/Bundle_pl.properties

@@ -331,7 +331,17 @@ user.lastName=Nazwisko
 user.lastName.tip=Nazwisko, kt\u00F3re chcesz u\u017Cy\u0107 dla tego konta.
 user.email.tip=Aktualny adres e-mail, do kt\u00F3rego posiadasz dost\u0119p i kt\u00F3rego mo\u017Cna u\u017Cy\u0107, by si\u0119 z Tob\u0105 skontaktowa\u0107.
 user.email.taken=Ten adres e-mail jest ju\u017C przypisany do innego konta.
+user.orcid=ORCID
+user.orcid.tip=ORCID to otwarty identyfikator cyfrowy umo\u017Cliwiaj\u0105cy rozr\u00F3\u017Cnienie naukowc\u00F3w o tym samym lub podobnym imieniu i nazwisku.
+user.orcid.invalid.format=Nieprawid\u0142owo zbudowany identyfikator.
+user.orcid.invalid.checksum=Nieprawid\u0142owy identyfikator.
 user.affiliation.tip=Instytucja przy kt\u00F3rej jeste\u015B afiliowana/afiliowany.
+user.affiliationror=ROR instytucji afiliuj\u0105cej
+user.affiliationror.tip=Identyfikator ROR instytucji afiliuj\u0105cej. Identyfikator musi zosta\u0107 podany w formie adresu URL, np. "https://ror.org/039bjqg32" dla Uniwersytetu Warszawskiego. W to pole mo\u017Cesz r\u00F3wnie\u017C wprowadzi\u0107 nazw\u0119 instytucji i wybra\u0107 jej identyfikator ROR z listy.
+user.affiliationror.suggestionDisplay.valueHeader=ROR
+user.affiliationror.suggestionDisplay.detailsHeader=Instytucja
+user.affiliationror.ror.invalid.format=Nieprawid\u0142owo zbudowany identyfikator ROR.
+user.affiliationror.ror.invalid.checksum=Nieprawid\u0142owy identyfikator ROR.
 user.position=Stanowisko
 user.position.tip=Stanowisko lub rola jak\u0105 pe\u0142nisz w instytucji, przy kt\u00F3rej jeste\u015B afiliowana/afiliowany, na przyk\u0142ad "pracownik naukowy", "student", "pracownik administracyjny" itp.
 user.notificationsLanguage=J\u0119zyk powiadomie\u0144 e-mailowych

dataverse-persistence/src/main/resources/db/migration/V72__addUserORCIDAndROR.sql

@@ -0,0 +1 @@
+ALTER TABLE authenticateduser ADD COLUMN orcid TEXT, ADD COLUMN affiliationror TEXT;

dataverse-persistence/src/test/java/edu/harvard/iq/dataverse/persistence/user/AuthenticatedUserTest.java

@@ -45,16 +45,24 @@ public void testGetIdentifier() {
     @Test
     public void testApplyDisplayInfo() {
         System.out.println("applyDisplayInfo");
-        AuthenticatedUserDisplayInfo inf = new AuthenticatedUserDisplayInfo("Homer", "Simpson", "[email protected]", "UnitTester", "In-Memory user");
+        AuthenticatedUserDisplayInfo inf = new AuthenticatedUserDisplayInfo("Homer", "Simpson", "[email protected]",
+                "0000-0001-2345-6789", "UnitTester", "https://ror.org/04k0tth05", "In-Memory user");
         testUser.applyDisplayInfo(inf);
         assertEquals(inf, testUser.getDisplayInfo());
     }
 
     @Test
     public void testGetDisplayInfo() {
         System.out.println("getDisplayInfo");
-        AuthenticatedUserDisplayInfo expResult = new AuthenticatedUserDisplayInfo("Homer", "Simpson", "[email protected]", "UnitTester", "In-Memory user");
+        // given
+        testUser.setOrcid("0000-0001-2345-6789");
+        testUser.setAffiliationROR("https://ror.org/04k0tth05");
+        AuthenticatedUserDisplayInfo expResult = new AuthenticatedUserDisplayInfo("Homer", "Simpson", "[email protected]",
+                "0000-0001-2345-6789", "UnitTester", "https://ror.org/04k0tth05", "In-Memory user");
+        // when
         AuthenticatedUserDisplayInfo result = testUser.getDisplayInfo();
+
+        // then
         assertEquals(expResult, result);
 
     }

dataverse-webapp/pom.xml

@@ -45,6 +45,12 @@
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>fluent-hc</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>commons-logging</groupId>
+                    <artifactId>commons-logging</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
@@ -431,6 +437,12 @@
             <groupId>com.onelogin</groupId>
             <artifactId>java-saml</artifactId>
             <version>2.8.0</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.apache.santuario</groupId>
+                    <artifactId>xmlsec</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
         <!-- OpenID Connect library -->

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java

@@ -23,7 +23,7 @@
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import edu.harvard.iq.dataverse.validation.DatasetFieldValidationService;
-import edu.harvard.iq.dataverse.validation.field.ValidationResult;
+import edu.harvard.iq.dataverse.validation.field.FieldValidationResult;
 import org.swordapp.server.AuthCredentials;
 import org.swordapp.server.Deposit;
 import org.swordapp.server.DepositReceipt;
@@ -322,10 +322,10 @@ DepositReceipt replaceOrAddFiles(String uri, Deposit deposit, AuthCredentials au
                 throw new SwordError(UriRegistry.ERROR_BAD_REQUEST, "Unable to add file(s) to dataset: Unknown error");
             }
             if (!dataFiles.isEmpty()) {
-                List<ValidationResult> validationResults = fieldValidationService.validateFieldsOfDatasetVersion(editVersion);
+                List<FieldValidationResult> fieldValidationResults = fieldValidationService.validateFieldsOfDatasetVersion(editVersion);
                 Set<ConstraintViolation<FileMetadata>> constraintViolations = editVersion.validateFileMetadata();
-                if (!validationResults.isEmpty()) {
-                    ValidationResult firstError = validationResults.get(0);
+                if (!fieldValidationResults.isEmpty()) {
+                    FieldValidationResult firstError = fieldValidationResults.get(0);
                     throw new SwordError(UriRegistry.ERROR_BAD_REQUEST,
                             String.format("Unable to add file(s) to dataset: %s The invalid value was \"%s\".", firstError.getMessage(), firstError.getField().getSingleValue()));
                 } else if (!constraintViolations.isEmpty()) {

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/api/imports/ImportServiceBean.java

@@ -18,7 +18,7 @@
 import edu.harvard.iq.dataverse.search.index.IndexServiceBean;
 import edu.harvard.iq.dataverse.util.json.JsonParseException;
 import edu.harvard.iq.dataverse.validation.DatasetFieldValidationService;
-import edu.harvard.iq.dataverse.validation.field.ValidationResult;
+import edu.harvard.iq.dataverse.validation.field.FieldValidationResult;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
 
@@ -137,10 +137,10 @@ public Dataset doImportHarvestedDataset(DataverseRequest dataverseRequest, Harve
 
             // Check data against validation contraints
             DatasetVersion versionToValidate = ds.getVersions().get(0);
-            List<ValidationResult> validationResults = fieldValidationService.validateFieldsOfDatasetVersion(versionToValidate);
-            if (!validationResults.isEmpty()) {
+            List<FieldValidationResult> fieldValidationResults = fieldValidationService.validateFieldsOfDatasetVersion(versionToValidate);
+            if (!fieldValidationResults.isEmpty()) {
                 // For migration and harvest, add NA for missing required values
-                validationResults.forEach(r -> ((DatasetField) r.getField()).setFieldValue(DatasetField.NA_VALUE));
+                fieldValidationResults.forEach(r -> ((DatasetField) r.getField()).setFieldValue(DatasetField.NA_VALUE));
             }
 
             // A Global ID is required, in order for us to be able to harvest and import

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/authorization/EditableAccountField.java

@@ -9,6 +9,8 @@ public enum EditableAccountField {
     FAMILY_NAME,
     EMAIL,
     AFFILIATION,
+    AFFILIATION_ROR,
     POSITION,
-    NOTIFICATIONS_LANG
+    NOTIFICATIONS_LANG,
+    ORCID
 }

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/authorization/EditableAccountFieldSets.java

@@ -33,7 +33,8 @@ public static Set<EditableAccountField> createAllFieldsSet() {
 
         public static Set<EditableAccountField> createSecondaryFieldsSet() {
             return Collections.unmodifiableSet(
-                    Stream.of(EditableAccountField.AFFILIATION, EditableAccountField.POSITION, EditableAccountField.NOTIFICATIONS_LANG)
+                    Stream.of(EditableAccountField.AFFILIATION, EditableAccountField.POSITION, EditableAccountField.NOTIFICATIONS_LANG,
+                                    EditableAccountField.ORCID, EditableAccountField.AFFILIATION_ROR)
                             .collect(Collectors.toSet()));
         }
 

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java

@@ -8,6 +8,7 @@
 import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
 import edu.harvard.iq.dataverse.authorization.EditableAccountField;
 import edu.harvard.iq.dataverse.authorization.UserRecordIdentifier;
+import edu.harvard.iq.dataverse.authorization.providers.common.BaseUserPage;
 import edu.harvard.iq.dataverse.authorization.providers.shib.ShibAuthenticationProvider;
 import edu.harvard.iq.dataverse.common.BundleUtil;
 import edu.harvard.iq.dataverse.consent.ConsentDto;
@@ -60,7 +61,7 @@
 
 @ViewScoped
 @Named("DataverseUserPage")
-public class DataverseUserPage implements java.io.Serializable {
+public class DataverseUserPage extends BaseUserPage {
 
     private static final Logger logger = Logger.getLogger(DataverseUserPage.class.getCanonicalName());