Add restrictions on names of domains

api/src/org/labkey/api/audit/AuditHandler.java

@@ -11,6 +11,7 @@
 import org.labkey.api.exp.api.ExpMaterial;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.gwt.client.AuditBehaviorType;
+import org.labkey.api.query.QueryKey;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.security.User;
 import org.labkey.api.util.Pair;
@@ -72,11 +73,21 @@ static Pair<Map<String, Object>, Map<String, Object>> getOldAndNewRecordForMerge
                     .orElse(key);
             String lcName = nameFromAlias.toLowerCase();
             // Preserve casing of inputs so we can show the names properly
-            if (!lcName.startsWith(ExpData.DATA_INPUT_PARENT.toLowerCase()) && !lcName.startsWith(ExpMaterial.MATERIAL_INPUT_PARENT.toLowerCase()))
+            boolean isExpInput = false;
+            if (lcName.startsWith(ExpData.DATA_INPUTS_PREFIX.toLowerCase()) || lcName.startsWith(ExpMaterial.MATERIAL_INPUTS_PREFIX.toLowerCase()))
+            {
+                String[] parts = nameFromAlias.split("/", 2);
+                String prefix = parts[0];
+                String dataType = parts[1];
+                // MaterialInputs/datypeTypeEncoded
+                if (row.containsKey(prefix + "/" + QueryKey.encodePart(dataType)))
+                    isExpInput = true;
+            }
+            else
                 nameFromAlias = lcName;
 
             boolean isExtraAuditField = extraFieldsToInclude != null && extraFieldsToInclude.contains(nameFromAlias);
-            if (!excludedFromDetailDiff.contains(nameFromAlias) && row.containsKey(nameFromAlias))
+            if (!excludedFromDetailDiff.contains(nameFromAlias) && (row.containsKey(nameFromAlias) || isExpInput))
             {
                 Object oldValue = entry.getValue();
                 Object newValue = row.get(nameFromAlias);

api/src/org/labkey/api/exp/api/ExperimentService.java

@@ -26,6 +26,7 @@
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbScope;
+import org.labkey.api.data.NameGenerator;
 import org.labkey.api.data.RemapCache;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.TableInfo;
@@ -75,6 +76,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.Pair;
+import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewBackgroundInfo;
@@ -118,6 +120,8 @@ public interface ExperimentService extends ExperimentRunTypeSource
 
     String LINEAGE_DEFAULT_MAXIMUM_DEPTH_PROPERTY_NAME = "lineageDefaultMaximumDepth";
 
+    String ILLEGAL_PARENT_ALIAS_CHARSET = "/:<>$[]{};,`\"~!@#$%^*=|?\\";
+
     int SIMPLE_PROTOCOL_FIRST_STEP_SEQUENCE = 1;
     int SIMPLE_PROTOCOL_CORE_STEP_SEQUENCE = 10;
     int SIMPLE_PROTOCOL_EXTRA_STEP_SEQUENCE = 15;
@@ -539,6 +543,14 @@ static void validateParentAlias(Map<String, String> aliasMap, Set<String> reserv
                 throw new IllegalArgumentException(String.format("Duplicate parent alias header found: %1$s", trimmedKey));
             }
 
+            String legalCharacterCheck = StringUtilsLabKey.validateLegalNames(trimmedKey, ILLEGAL_PARENT_ALIAS_CHARSET, "Parent alias");
+            if (legalCharacterCheck != null)
+                throw new IllegalArgumentException(legalCharacterCheck);
+
+            String nameSyntaxError = NameGenerator.validateFieldKeyConflict(trimmedKey);
+            if (nameSyntaxError != null)
+                throw new IllegalArgumentException("Invalid Parent alias '" + trimmedKey + "'. " + nameSyntaxError);
+
             //Check if parent alias has correct format MaterialInput/<name> or NEW_SAMPLE_TYPE_ALIAS_VALUE, or DataInput/<name> or NEW_DATA_CLASS_ALIAS_VALUE
             if (!ExperimentService.parentAliasHasCorrectFormat(trimmedValue))
                 throw new IllegalArgumentException(String.format("Invalid parent alias header: %1$s", trimmedValue));

api/src/org/labkey/api/exp/api/SampleTypeDomainKind.java

@@ -671,4 +671,10 @@ public boolean supportsPhiLevel()
     {
         return ComplianceService.get().isComplianceSupported();
     }
+
+    @Override
+    public boolean supportsNamingPattern()
+    {
+        return true;
+    }
 }

api/src/org/labkey/api/exp/property/DomainKind.java

@@ -410,4 +410,9 @@ public boolean supportsPhiLevel()
     {
         return false;
     }
+
+    public boolean supportsNamingPattern()
+    {
+        return false;
+    }
 }

api/src/org/labkey/api/exp/property/DomainUtil.java

@@ -32,6 +32,7 @@
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.ContainerService;
+import org.labkey.api.data.NameGenerator;
 import org.labkey.api.data.PHI;
 import org.labkey.api.data.SchemaTableInfo;
 import org.labkey.api.data.SimpleFilter;
@@ -76,6 +77,7 @@
 import org.labkey.api.util.JsonUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.StringExpression;
+import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.data.xml.ColumnType;
 import org.labkey.data.xml.ConditionalFormatFilterType;
@@ -104,6 +106,8 @@
 public class DomainUtil
 {
     private static final Logger LOG = LogManager.getLogger(DomainUtil.class);
+    public static final String ILLEGAL_DOMAIN_NAME_CHARSET = "<>[]{};,`\"~!@#$%^*=|?\\";
+
     private DomainUtil()
     {
     }
@@ -688,10 +692,6 @@ public static Domain createDomain(
     {
         // Create a copy of the GWTDomain to ensure the template's Domain is not modified
         domain = new GWTDomain(domain);
-        if (domainName != null)
-        {
-            domain.setName(domainName);
-        }
 
         DomainKind kind = PropertyService.get().getDomainKindByName(kindName);
         if (kind == null)
@@ -700,6 +700,17 @@ public static Domain createDomain(
         if (!kind.canCreateDefinition(user, container))
             throw new UnauthorizedException("You don't have permission to create a new domain");
 
+
+        if (domainName != null)
+            domain.setName(domainName);
+
+        if (domain.getName() != null)
+        {
+            String domainNameError = validateDomainName(domain.getName(), kind.getKindName(), kind.supportsNamingPattern());
+            if (!StringUtils.isEmpty(domainNameError))
+                throw new IllegalArgumentException(domainNameError);
+        }
+
         // Issue 48810: if not creating from templateInfo, validate reserved field names based on domainKind
         boolean strictFieldValidation = arguments != null ? (Boolean) arguments.getOrDefault("strictFieldValidation", true) : true;
         DomainKind validateDomainKind = templateInfo == null && strictFieldValidation ? kind : null;
@@ -754,10 +765,17 @@ public static ValidationException updateDomainDescriptor(GWTDomain<? extends GWT
             return validationException;
         }
 
-        if (updateDomainName && !d.getName().equals(update.getName()))
+        String updatedName = update.getName();
+        if (updateDomainName && !d.getName().equals(updatedName))
         {
+            String domainNameError = validateDomainName(updatedName, kind.getKindName(), kind.supportsNamingPattern());
+            if (!StringUtils.isEmpty(domainNameError))
+            {
+                validationException.addError(new SimpleValidationError(domainNameError));
+                return validationException;
+            }
             DefaultValueService.get().clearDefaultValues(d.getContainer(), d); // default values exp.objects will be re-created
-            d.setName(update.getName());
+            d.setName(updatedName);
         }
 
         d.setDisabledSystemFields(kind.getDisabledSystemFields(update.getDisabledSystemFields()));
@@ -917,6 +935,31 @@ public static ValidationException updateDomainDescriptor(GWTDomain<? extends GWT
         return validationException;
     }
 
+    public static @Nullable String validateDomainName(@NotNull String domainName, String kindName, boolean supportsNamingPattern)
+    {
+        String prefix = "Invalid " + kindName + " name \"" + domainName + "\". ";
+
+        if (StringUtils.isBlank(domainName))
+            return kindName + " name must not be blank.";
+
+        char start = domainName.charAt(0);
+        if (!Character.isLetterOrDigit(start))
+            return prefix + kindName + " name must start with a letter or a number.";
+
+        String legalCharacterCheck = StringUtilsLabKey.validateLegalNames(domainName, ILLEGAL_DOMAIN_NAME_CHARSET, kindName + " name");
+        if (legalCharacterCheck != null)
+            return prefix + legalCharacterCheck;
+
+        if (supportsNamingPattern)
+        {
+            String invalidPattenError = NameGenerator.validateFieldKeyConflict(domainName);
+            if (invalidPattenError != null)
+                return prefix + invalidPattenError;
+        }
+
+        return null;
+    }
+
     private static String getMissingMandatoryField(List<? extends GWTPropertyDescriptor> updatedFields,
                                                    List<? extends GWTPropertyDescriptor> origFields)
     {
@@ -1333,6 +1376,16 @@ public static ValidationException validateProperties(@Nullable Domain domain, @N
                 continue;
             }
 
+            if (domainKind != null && domainKind.supportsNamingPattern())
+            {
+                String nameSyntaxError = NameGenerator.validateFieldKeyConflict(name);
+                if (nameSyntaxError != null)
+                {
+                    exception.addFieldError(name, nameSyntaxError);
+                    continue;
+                }
+            }
+
             if (namePropertyIdMap.containsKey(name))
             {
                 String errorMsg = getDomainErrorMessage(updates,"The field name '" + name + "' is already taken. Please provide a unique name for each field.");

api/src/org/labkey/api/util/FileUtil.java

@@ -334,20 +334,7 @@ static String isAllowedFileName(String s, boolean checkFileExtension, AppProps a
 
     private static @Nullable String validateFileName(String s)
     {
-        if (StringUtils.isBlank(s))
-            return "Filename must not be blank";
-        if (!ViewServlet.validChars(s))
-            return "Filename must contain only valid unicode characters.";
-        if (StringUtils.containsAny(s, restrictedPrintable))
-            return "Filename may not contain any of these characters: " + restrictedPrintable;
-        if (StringUtils.containsAny(s, "\t\n\r"))
-            return "Filename may not contain 'tab', 'new line', or 'return' characters.";
-        if (StringUtils.contains("-$", s.charAt(0)))
-            return "Filename may not begin with any of these characters: -$";
-        if (Pattern.matches("(.*\\s--[^ ].*)|(.*\\s-[^- ].*)", s))
-            return "Filename may not contain space followed by dash.";
-
-        return null;
+        return StringUtilsLabKey.validateLegalNames(s, restrictedPrintable, "Filename");
     }
 
     private static String checkExtension(String filename, AppProps appProps)

api/src/org/labkey/api/util/StringUtilsLabKey.java

@@ -25,6 +25,7 @@
 import org.junit.Test;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.Identifiable;
+import org.labkey.api.view.ViewServlet;
 
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
@@ -52,6 +53,26 @@ public class StringUtilsLabKey
     private static final Random RANDOM = new Random();
     private static final int MAX_LONG_LENGTH = String.valueOf(Long.MAX_VALUE).length() - 1;
 
+
+
+    public static @Nullable String validateLegalNames(String s, @NotNull String illegalCharset, String type)
+    {
+        if (StringUtils.isBlank(s))
+            return type + " must not be blank.";
+        if (!ViewServlet.validChars(s))
+            return type + " must contain only valid unicode characters.";
+        if (StringUtils.containsAny(s, illegalCharset))
+            return type + " may not contain any of these characters: " + illegalCharset;
+        if (StringUtils.containsAny(s, "\t\n\r"))
+            return type + " may not contain 'tab', 'new line', or 'return' characters.";
+        if (StringUtils.contains("-$", s.charAt(0)))
+            return type + " may not begin with any of these characters: -$";
+        if (Pattern.matches("(.*\\s--[^ ].*)|(.*\\s-[^- ].*)", s))
+            return type + " may not contain space followed by dash.";
+
+        return null;
+    }
+
     public static void append(StringBuilder sb, @Nullable Identifiable identifiable)
     {
         if (null != identifiable)

assay/src/org/labkey/assay/AssayDomainServiceImpl.java

@@ -392,6 +392,10 @@ public GWTProtocol saveChanges(GWTProtocol assay, boolean replaceIfExisting) thr
                     if (AssayManager.get().getAssayProtocolByName(getContainer(), assay.getName()) != null)
                         throw new ValidationException("Assay protocol already exists for this name.");
 
+                    String nameError = DomainUtil.validateDomainName(assay.getName(), "Assay Design", false);
+                    if (nameError != null)
+                        throw new ValidationException(nameError);
+
                     XarContext context = new XarContext("Domains", getContainer(), getUser());
                     context.addSubstitution("AssayName", PageFlowUtil.encode(assay.getName()));
 
@@ -437,6 +441,12 @@ public GWTProtocol saveChanges(GWTProtocol assay, boolean replaceIfExisting) thr
                                 "This assay was created in folder " + protocol.getContainer().getPath());
                     oldAssayName = protocol.getName();
                     hasNameChange = !assay.getName().equals(oldAssayName);
+                    if (hasNameChange)
+                    {
+                        String nameError = DomainUtil.validateDomainName(assay.getName(), "Assay Design", false);
+                        if (nameError != null)
+                            throw new ValidationException(nameError);
+                    }
                     protocol.setName(assay.getName());
                     protocol.setProtocolDescription(assay.getDescription());
                     if (assay.getStatus() != null)

core/package.json

@@ -54,7 +54,7 @@
     }
   },
   "dependencies": {
-    "@labkey/components": "6.4.0",
+    "@labkey/components": "6.5.3",
     "@labkey/themes": "1.4.0"
   },
   "devDependencies": {

experiment/package.json

@@ -13,7 +13,7 @@
     "test-integration": "cross-env NODE_ENV=test jest --ci --runInBand -c test/js/jest.config.integration.js"
   },
   "dependencies": {
-    "@labkey/components": "6.4.0"
+    "@labkey/components": "6.5.3"
   },
   "devDependencies": {
     "@labkey/build": "8.3.0",