Merge remote-tracking branch 'origin/develop' into fb_exportMetricsFromAudit

Author: labkey-susanh

api/build.gradle

@@ -1132,8 +1132,8 @@ dependencies {
     BuildUtils.addExternalDependency(
         project,
         new ExternalDependency(
-            "org.springframework.ai:spring-ai-advisors-vector-store:${springAiVersion}",
-            "spring-ai-advisors-vector-store",
+            "org.springframework.ai:spring-ai-vector-store:${springAiVersion}",
+            "spring-ai-vector-store",
             "spring-ai",
             "https://github.com/spring-projects/spring-ai",
             ExternalDependency.APACHE_2_LICENSE_NAME,

api/src/org/labkey/api/data/CompareType.java

@@ -560,44 +560,6 @@ public boolean isNewLineSeparatorAllowed()
         }
     };
 
-    public static final CompareType IN_NS = new CompareType("Equals One Of A Member Of A Named Set", "inns", "IN", true, null, OperatorType.IN)
-    {
-        // Each compare type uses CompareClause by default
-        @Override
-        public FilterClause createFilterClause(@NotNull FieldKey fieldKey, Object value)
-        {
-            String namedSet = null;
-            if (value != null && StringUtils.isNotBlank(value.toString()))
-                namedSet = value.toString();
-            return new SimpleFilter.InClause(fieldKey, namedSet, true);
-        }
-
-        @Override
-        public boolean meetsCriteria(ColumnRenderProperties col, Object value, Object[] paramVals)
-        {
-            throw new UnsupportedOperationException("Should be handled inside of " + SimpleFilter.InClause.class);
-        }
-    };
-
-    public static final CompareType NOT_IN_NS = new CompareType("Does Not Equal Any Members Of A Named Set", "notinns", "NOT IN", true, null, OperatorType.NOTIN)
-    {
-        // Each compare type uses CompareClause by default
-        @Override
-        public FilterClause createFilterClause(@NotNull FieldKey fieldKey, Object value)
-        {
-            String namedSet = null;
-            if (value != null && StringUtils.isNotBlank(value.toString()))
-                namedSet = value.toString();
-            return new SimpleFilter.InClause(fieldKey, namedSet, true);
-        }
-
-        @Override
-        public boolean meetsCriteria(ColumnRenderProperties col, Object value, Object[] paramVals)
-        {
-            throw new UnsupportedOperationException("Should be handled inside of " + SimpleFilter.InClause.class);
-        }
-    };
-
     // BETWEEN is inclusive of the begin and end values
     public static final CompareType BETWEEN = new CompareType("Between", "between", "BETWEEN", true, " BETWEEN ? AND ?", OperatorType.BETWEEN)
     {

api/src/org/labkey/api/data/NestedRenderContext.java

@@ -131,7 +131,7 @@ public SimpleFilter buildFilter(TableInfo tinfo, List<ColumnInfo> displayColumns
             fullSQL.append(" ) Limited )");
 
             // Apply a filter that restricts the group ids to the right "page" of data
-            result.addClause(new SimpleFilter.SQLClause(fullSQL.getSQL(), fullSQL.getParamsArray()));
+            result.addClause(new SimpleFilter.SQLClause(fullSQL));
         }
         return result;
     }

api/src/org/labkey/api/data/SimpleFilter.java

@@ -719,11 +719,6 @@ public InClause(FieldKey fieldKey, Collection<?> params, boolean urlClause, bool
             _needsTypeConversion = urlClause;
         }
 
-        public InClause(FieldKey fieldKey, String namedSet, boolean urlClause)
-        {
-            this(fieldKey, QueryService.get().getNamedSet(namedSet), urlClause, false);
-        }
-
         @Override
         public void appendFilterText(StringBuilder sb, ColumnNameFormatter formatter)
         {

api/src/org/labkey/api/mcp/McpService.java

@@ -118,7 +118,7 @@ default User getUser(ToolContext toolContext)
         default void incrementResourceRequestCount(String resource)
         {
             if (!get().isEnabled())
-                throw new RuntimeException("The MCP server is not enabled for external requests. Consider toggling the experimental feature flag.");
+                throw new RuntimeException("The MCP server is not enabled for external requests. Consider toggling the optional feature flag.");
 
             get().incrementResourceRequestCount(resource);
         }

api/src/org/labkey/api/module/Module.java

@@ -24,6 +24,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
+import org.labkey.api.Constants;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbScope;
@@ -444,4 +445,10 @@ default String getBuildTime()
     default void registerMigrationHandlers(@NotNull DatabaseMigrationService service)
     {
     }
+
+    // Override in cases such as a module transitioning from unmanaged to managed
+    default double getEarliestUpgradeVersion()
+    {
+        return Constants.getEarliestUpgradeVersion();
+    }
 }

api/src/org/labkey/api/module/ModuleLoader.java

@@ -633,13 +633,21 @@ private void doInit(Execution execution) throws ServletException
                 .filter(ctx -> ctx.getSchemaVersion() != null)
                 .collect(Collectors.toMap(ModuleContext::getName, ctx->ctx));
 
+            record ModuleAndModuleContext(Module module, ModuleContext context)
+            {
+                boolean isTooOld()
+                {
+                    return context.getInstalledVersion() < module.getEarliestUpgradeVersion();
+                }
+            }
+
             // List of "<name> (<installedSchemaVersion>)" of LabKey-managed modules with schemas where the installed
-            // version is less than "earliest upgrade version"
+            // version is less than the module's earliest upgrade version
             var tooOld = labkeyModules.stream()
-                .map(m -> moduleContextMap.get(m.getName()))
-                .filter(Objects::nonNull)
-                .filter(ctx -> ctx.getInstalledVersion() < Constants.getEarliestUpgradeVersion())
-                .map(UpgradeInfo::new)
+                .map(m -> new ModuleAndModuleContext(m, moduleContextMap.get(m.getName())))
+                .filter(mmc -> mmc.context() != null)
+                .filter(ModuleAndModuleContext::isTooOld)
+                .map(mmc -> new UpgradeInfo(mmc.context()))
                 .toList();
 
             if (!tooOld.isEmpty())
@@ -655,7 +663,7 @@ private void doInit(Execution execution) throws ServletException
 
         // Now that we know if this is a new install...
         setDatabaseMigrationConfiguration(labkeyRoot);
-        boolean coreRequiredUpgrade = upgradeCoreModule(lockFile);
+        upgradeCoreModule(lockFile);
 
         // Issue 40422 - log server and session GUIDs during startup. Do it after the core module has
         // been bootstrapped/upgraded to ensure that AppProps is ready

api/src/org/labkey/api/query/InvalidNamedSetException.java

@@ -42,7 +42,6 @@
 import org.labkey.api.data.Sort;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
-import org.labkey.api.data.TableSelector;
 import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
 import org.labkey.api.module.Module;
@@ -62,7 +61,6 @@
 import org.springframework.web.servlet.mvc.Controller;
 
 import java.io.IOException;
-import java.sql.ResultSet;
 import java.util.Collection;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -504,10 +502,6 @@ interface Hierarchy
      */
     Collection<Hierarchy> getOlapHierarchies(String configId, Container c, String cubeName, String dimension);
 
-    void saveNamedSet(String setName, List<String> setList);
-    void deleteNamedSet(String setName);
-    List<String> getNamedSet(String setName);
-
     /**
      * Add a pass-through method to the allow list for the primary LabKey database type. This enables modules to create
      * and enable custom database functions, for example.

api/src/org/labkey/api/query/QueryService.java

@@ -55,7 +55,6 @@
 import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.RuntimeSQLException;
 import org.labkey.api.data.SQLFragment;
-import org.labkey.api.data.Selector;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.SqlSelector;
@@ -1883,126 +1882,6 @@ public static String getMembershipPathwayHTMLDisplay(Set<List<UserPrincipal>> pa
             sb.append("<BR/>");
         }
         return sb.toString();
-    }    
-
-    // TODO: Redundant with getProjectUsers() -- this approach should be more efficient for simple cases
-    // TODO: Also redundant with getFolderUserids()
-    // TODO: Cache this set
-    public static Set<Integer> getProjectUsersIds(Container c)
-    {
-        SQLFragment sql = getProjectUsersSQL(c.getProject());
-        sql.insert(0, "SELECT DISTINCT members.UserId ");
-
-        Selector selector = new SqlSelector(core.getSchema(), sql);
-        return new HashSet<>(selector.getCollection(Integer.class));
-    }
-
-    // True fragment -- need to prepend SELECT DISTINCT() or IN () for this to be valid SQL
-    public static SQLFragment getProjectUsersSQL(Container c)
-    {
-        return new SQLFragment("FROM " + core.getTableInfoMembers() + " members INNER JOIN " + core.getTableInfoUsers() + " users ON members.UserId = users.UserId\n" +
-                                    "INNER JOIN " + core.getTableInfoPrincipals() + " groups ON members.GroupId = groups.UserId\n" +
-                                    "WHERE (groups.Container = ?)", c);
-    }
-
-    public static @NotNull List<User> getProjectUsers(Container c)
-    {
-        return getProjectUsers(c, false, true);
-    }
-
-    public static @NotNull List<User> getProjectUsers(Container c, boolean includeGlobal, boolean includeInactive)
-    {
-        if (c != null && !c.isProject())
-            c = c.getProject();
-
-        List<Group> groups = getGroups(c, includeGlobal);
-        Set<String> emails = new HashSet<>();
-
-        //get members for each group
-        ArrayList<User> projectUsers = new ArrayList<>();
-        Set<User> members;
-
-        for (Group g : groups)
-        {
-            if (g.isGuests() || g.isUsers())
-                continue;
-
-            // TODO: currently only getting members that are users (no groups). should this be changed to get users of member groups?
-            members = getGroupMembers(g, includeInactive ? MemberType.ACTIVE_AND_INACTIVE_USERS : MemberType.ACTIVE_USERS);
-
-            //add this group's members to hashset
-            if (!members.isEmpty())
-            {
-                //get list of users from email
-                for (UserPrincipal member : members)
-                {
-                    User user = UserManager.getUser(member.getUserId());
-                    if (null != user && emails.add(user.getEmail()))
-                        projectUsers.add(user);
-                }
-            }
-        }
-
-        return projectUsers;
-    }
-
-    public static Collection<Integer> getFolderUserids(Container c)
-    {
-        Container project = (c.isProject() || c.isRoot()) ? c : c.getProject();
-        SecurityPolicy policy = c.getPolicy();
-
-        //don't filter if all site users is playing a role
-        Group allSiteUsers = getGroup(Group.groupUsers);
-        if (policy.getAssignedRoles(allSiteUsers).findAny().isPresent())
-        {
-            // Just select all users
-            SQLFragment sql = new SQLFragment("SELECT u.UserId FROM ");
-            sql.append(core.getTableInfoPrincipals(), "u");
-            sql.append(" WHERE u.type='u'");
-
-            return new SqlSelector(core.getSchema(), sql).getCollection(Integer.class);
-        }
-
-        //users "in the project" consists of:
-        // - users who are members of a project group
-        // - users who belong to a site group that has a role assignment in the policy for the specified folder
-        // - users who have a direct role assignment in the policy for the specified folder
-
-        Set<Integer> userIds = new HashSet<>();
-
-        // Add all project groups
-        Set<Group> groupsToExpand = new HashSet<>(getGroups(project, false));
-
-        // Look for users and site groups that have direct assignment to the container
-        for (RoleAssignment roleAssignment : c.getPolicy().getAssignments())
-        {
-            User user = UserManager.getUser(roleAssignment.getUserId());
-            if (user != null)
-            {
-                userIds.add(user.getUserId());
-            }
-            else
-            {
-                Group assignedGroup = getGroup(roleAssignment.getUserId());
-                if (assignedGroup != null && !assignedGroup.isProjectGroup())
-                {
-                    // Add all site groups
-                    groupsToExpand.add(assignedGroup);
-                }
-            }
-        }
-
-        // Find the users who are members of all the relevant site groups
-        for (Group group : groupsToExpand)
-        {
-            Set<User> groupMembers = getAllGroupMembers(group, MemberType.ACTIVE_AND_INACTIVE_USERS);
-            for (User groupMember : groupMembers)
-            {
-                userIds.add(groupMember.getUserId());
-            }
-        }
-
-        return userIds;
     }
 
     /**