[ARVADOS] updated: 1.3.0-2616-ga3aee2781

Git user git at public.arvados.org
Fri Jun 5 15:05:54 UTC 2020


Summary of changes:
 services/api/app/models/arvados_model.rb           |  11 +-
 services/api/app/models/user.rb                    |  11 +-
 .../db/migrate/20200501150153_permission_table.rb  | 143 +++++------------
 services/api/db/structure.sql                      | 176 +++++++++------------
 services/api/lib/update_permissions.rb             |  40 ++++-
 services/api/test/unit/permission_test.rb          |  77 ++++++---
 services/api/test/unit/user_test.rb                |   9 --
 7 files changed, 212 insertions(+), 255 deletions(-)

       via  a3aee2781cfcd006fa1b7ce3cfeeb1dd2d53c270 (commit)
      from  b879b9cd18ddba6ba87b65f81eba676114478a06 (commit)

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commit a3aee2781cfcd006fa1b7ce3cfeeb1dd2d53c270
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Jun 4 16:58:18 2020 -0400

    16007: Special handing for users with permissions on other users
    
    Revise & simplify permission traversal.  Don't traverse users except
    when starting from the user (origin_uuid = starting_uuid).
    
    This avoids disasterous queries where we re-traverse other users "just
    in case" and end up recomputing the whole database.  As a tradeoff,
    our epic readable_by query gets a touch more epic, as it now has to go
    to the permissions table to check if there are other user permissions
    the current user also is allowed to use.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/services/api/app/models/arvados_model.rb b/services/api/app/models/arvados_model.rb
index cc6f7816a..a27d6aba4 100644
--- a/services/api/app/models/arvados_model.rb
+++ b/services/api/app/models/arvados_model.rb
@@ -324,9 +324,14 @@ class ArvadosModel < ApplicationRecord
       #
       # see issue 13208 for details.
 
+      user_uuids_subquery = %{
+select target_uuid from materialized_permissions where user_uuid in (:user_uuids)
+and target_uuid like '_____-tpzed-_______________' and traverse_owned=true and perm_level >= 1
+}
+
       # Match a direct read permission link from the user to the record uuid
       direct_check = "#{sql_table}.uuid IN (SELECT target_uuid FROM #{PERMISSION_VIEW} "+
-                     "WHERE user_uuid IN (:user_uuids) AND perm_level >= 1 #{trashed_check})"
+                     "WHERE user_uuid IN (#{user_uuids_subquery}) AND perm_level >= 1 #{trashed_check})"
 
       # Match a read permission for the user to the record's
       # owner_uuid.  This is so we can have a permissions table that
@@ -347,7 +352,7 @@ class ArvadosModel < ApplicationRecord
       owner_check = ""
       if sql_table != "api_client_authorizations" and sql_table != "groups" then
         owner_check = "OR #{sql_table}.owner_uuid IN (SELECT target_uuid FROM #{PERMISSION_VIEW} "+
-          "WHERE user_uuid IN (:user_uuids) AND perm_level >= 1 #{trashed_check} AND traverse_owned) "
+          "WHERE user_uuid IN (#{user_uuids_subquery}) AND perm_level >= 1 #{trashed_check} AND traverse_owned) "
       end
 
       links_cond = ""
@@ -356,7 +361,7 @@ class ArvadosModel < ApplicationRecord
         # users some permission _or_ gives anyone else permission to
         # view one of the authorized users.
         links_cond = "OR (#{sql_table}.link_class IN (:permission_link_classes) AND "+
-                       "(#{sql_table}.head_uuid IN (:user_uuids) OR #{sql_table}.tail_uuid IN (:user_uuids)))"
+                       "(#{sql_table}.head_uuid IN (#{user_uuids_subquery}) OR #{sql_table}.tail_uuid IN (#{user_uuids_subquery})))"
       end
 
       sql_conds = "(#{direct_check} #{owner_check} #{links_cond}) #{exclude_trashed_records}"
diff --git a/services/api/app/models/user.rb b/services/api/app/models/user.rb
index cb7efe9cc..869ac88f4 100644
--- a/services/api/app/models/user.rb
+++ b/services/api/app/models/user.rb
@@ -121,10 +121,15 @@ class User < ArvadosModel
 
       target_owner_uuid = target.owner_uuid if target.respond_to? :owner_uuid
 
+      user_uuids_subquery = %{
+select target_uuid from materialized_permissions where user_uuid = $1
+and target_uuid like '_____-tpzed-_______________' and traverse_owned=true and perm_level >= #{VAL_FOR_PERM[action]}
+}
+
       unless ActiveRecord::Base.connection.
         exec_query(%{
 SELECT 1 FROM #{PERMISSION_VIEW}
-  WHERE user_uuid = $1 and
+  WHERE user_uuid in (#{user_uuids_subquery}) and
         ((target_uuid = $2 and perm_level >= $3)
          or (target_uuid = $4 and perm_level >= $3 and traverse_owned))
 },
@@ -438,8 +443,10 @@ update #{PERMISSION_VIEW} set target_uuid=$1 where target_uuid = $2
       end
       skip_check_permissions_against_full_refresh do
         update_permissions self.owner_uuid, self.uuid, 3
+        update_permissions self.uuid, self.uuid, 3
+        update_permissions new_user.owner_uuid, new_user.uuid, 3
       end
-      update_permissions new_user.owner_uuid, new_user.uuid, 3
+      update_permissions new_user.uuid, new_user.uuid, 3
     end
   end
 
diff --git a/services/api/db/migrate/20200501150153_permission_table.rb b/services/api/db/migrate/20200501150153_permission_table.rb
index 77944eb6e..6dd2c29bd 100644
--- a/services/api/db/migrate/20200501150153_permission_table.rb
+++ b/services/api/db/migrate/20200501150153_permission_table.rb
@@ -2,6 +2,8 @@
 #
 # SPDX-License-Identifier: AGPL-3.0
 
+require 'update_permissions'
+
 class PermissionTable < ActiveRecord::Migration[5.0]
   def up
     # This is a major migration.  We are replacing the
@@ -125,6 +127,8 @@ create view permission_graph_edges as
   select groups.owner_uuid as tail_uuid, groups.uuid as head_uuid, (3) as val from groups
 union all
   select users.owner_uuid as tail_uuid, users.uuid as head_uuid, (3) as val from users
+union all
+  select users.uuid as tail_uuid, users.uuid as head_uuid, (3) as val from users
 union all
   select links.tail_uuid,
          links.head_uuid,
@@ -133,69 +137,18 @@ union all
            WHEN links.name = 'can_login'  THEN 1
            WHEN links.name = 'can_write'  THEN 2
            WHEN links.name = 'can_manage' THEN 3
+           ELSE 0
           END as val
       from links
       where links.link_class='permission'
 }
 
-    ActiveRecord::Base.connection.execute %{
-create or replace function search_permission_graph (starting_uuid varchar(27),
-                                                    starting_perm integer,
-                                                    override_edge_tail varchar(27) default null,
-                                                    override_edge_head varchar(27) default null,
-                                                    override_edge_perm integer default null)
-  returns table (target_uuid varchar(27), val integer, traverse_owned bool)
-STABLE
-language SQL
-as $$
-/*
-  From starting_uuid, perform a recursive self-join on the edges
-  to follow chains of permissions.  This is a breadth-first search
-  of the permission graph.  Permission is propagated across edges,
-  which may narrow the permission for subsequent links (eg I start
-  at can_manage but when traversing a can_read link everything
-  touched through that link will only be can_read).
-
-  When revoking a permission, we follow the chain of permissions but
-  with a permissions level of 0.  The update on the permissions table
-  has to happen _before_ the permission is actually removed, because
-  we need to be able to traverse the edge before it goes away.  When
-  we do that, we also need to traverse it at the _new_ permission
-  level - this is what override_edge_tail/head/perm are for.
-
-  Yields the set of objects that are potentially affected, and
-  their permission levels granted by having starting_perm on
-  starting_uuid.
-
-  If starting_uuid is a user, this computes the entire set of
-  permissions for that user (because it returns everything that is
-  reachable by that user).
-
-  Used by the compute_permission_subgraph function.
-*/
-WITH RECURSIVE
-        traverse_graph(target_uuid, val, traverse_owned) as (
-            values (starting_uuid, starting_perm,
-                    should_traverse_owned(starting_uuid, starting_perm))
-          union
-            (select edges.head_uuid,
-                      least(edges.val,
-                            traverse_graph.val,
-                            case traverse_graph.traverse_owned
-                              when true then null
-                              else 0
-                            end,
-                            case (edges.tail_uuid = override_edge_tail AND
-                                  edges.head_uuid = override_edge_head)
-                               when true then override_edge_perm
+    override = %{,
+                            case (edges.tail_uuid = perm_origin_uuid AND
+                                  edges.head_uuid = starting_uuid)
+                               when true then starting_perm
                                else null
-                            end),
-                    should_traverse_owned(edges.head_uuid, edges.val)
-             from permission_graph_edges as edges, traverse_graph
-             where traverse_graph.target_uuid = edges.tail_uuid))
-        select target_uuid, max(val), bool_or(traverse_owned) from traverse_graph
-        group by (target_uuid);
-$$;
+                            end
 }
 
     ActiveRecord::Base.connection.execute %{
@@ -250,12 +203,13 @@ with
      permission change, using search_permission_graph.
   */
   perm_from_start(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-    select perm_origin_uuid, target_uuid, val, traverse_owned
-      from search_permission_graph(starting_uuid,
-                                   starting_perm,
-                                   perm_origin_uuid,
-                                   starting_uuid,
-                                   starting_perm)),
+    #{PERM_QUERY_TEMPLATE % {:base_case => %{
+             values (perm_origin_uuid, starting_uuid, starting_perm,
+                    should_traverse_owned(starting_uuid, starting_perm),
+                    (perm_origin_uuid = starting_uuid or starting_uuid not like '_____-tpzed-_______________'))
+},
+:override => override
+} }),
 
   /* Finds other inbound edges that grant permissions on the objects
      in perm_from_start, and computes permissions that originate from
@@ -267,50 +221,24 @@ with
      ownership.
   */
   additional_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-    select edges.tail_uuid as perm_origin_uuid, ps.target_uuid, ps.val,
-           should_traverse_owned(ps.target_uuid, ps.val)
-      from permission_graph_edges as edges,
-           lateral search_permission_graph(edges.head_uuid,
-                                           edges.val,
-                                           perm_origin_uuid,
-                                           starting_uuid,
-                                           starting_perm) as ps
+    #{PERM_QUERY_TEMPLATE % {:base_case => %{
+    select edges.tail_uuid as origin_uuid, edges.head_uuid as target_uuid, edges.val,
+           should_traverse_owned(edges.head_uuid, edges.val),
+           edges.head_uuid like '_____-j7d0g-_______________'
+      from permission_graph_edges as edges
       where (not (edges.tail_uuid = perm_origin_uuid and
-                 edges.head_uuid = starting_uuid)) and
-            edges.tail_uuid not in (select target_uuid from perm_from_start) and
-            edges.head_uuid in (select target_uuid from perm_from_start)),
+                  edges.head_uuid = starting_uuid)) and
+            edges.tail_uuid not in (select target_uuid from perm_from_start where target_uuid like '_____-j7d0g-_______________') and
+            edges.head_uuid in (select target_uuid from perm_from_start)
+},
+:override => override
+} }),
 
   /* Combines the permissions computed in the first two phases. */
-  partial_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
+  all_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
       select * from perm_from_start
     union all
       select * from additional_perms
-  ),
-
-  /* If there are any users in the set of potentially affected objects
-     and the user's owner was not traversed, recompute permissions for
-     that user.  This is required because users always have permission
-     to themselves (identity property) which would be missing from the
-     permission set if the user was traversed while computing
-     permissions for another object.
-  */
-  user_identity_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-    select users.uuid as perm_origin_uuid, ps.target_uuid, ps.val, ps.traverse_owned
-      from users, lateral search_permission_graph(users.uuid,
-                                                  3,
-                                                  perm_origin_uuid,
-                                                  starting_uuid,
-                                                  starting_perm) as ps
-      where (users.owner_uuid not in (select target_uuid from partial_perms) or
-             users.owner_uuid = users.uuid) and
-      users.uuid in (select target_uuid from partial_perms)
-  ),
-
-  /* Combines all the computed permissions into one table. */
-  all_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-      select * from partial_perms
-    union
-      select * from user_identity_perms
   )
 
   /* The actual query that produces rows to be added or removed
@@ -351,10 +279,11 @@ with
          u.traverse_owned
       from all_perms as u, materialized_permissions as m
            where u.perm_origin_uuid = m.target_uuid AND m.traverse_owned
+           AND (m.user_uuid = m.target_uuid or m.target_uuid not like '_____-tpzed-_______________')
     union all
-      select perm_origin_uuid as user_uuid, target_uuid, val as perm_level, traverse_owned
+      select target_uuid as user_uuid, target_uuid, 3, true
         from all_perms
-        where all_perms.perm_origin_uuid like '_____-tpzed-_______________') as v
+        where all_perms.target_uuid like '_____-tpzed-_______________') as v
     group by v.user_uuid, v.target_uuid
 $$;
      }
@@ -365,8 +294,11 @@ $$;
     #
     ActiveRecord::Base.connection.execute %{
 INSERT INTO materialized_permissions
-select users.uuid, g.target_uuid, g.val, g.traverse_owned
-from users, lateral search_permission_graph(users.uuid, 3) as g where g.val > 0
+    #{PERM_QUERY_TEMPLATE % {:base_case => %{
+        select uuid, uuid, 3, true, true from users
+},
+:override => ''
+} }
 }
   end
 
@@ -376,7 +308,6 @@ from users, lateral search_permission_graph(users.uuid, 3) as g where g.val > 0
 
     ActiveRecord::Base.connection.execute "DROP function project_subtree_with_trash_at (varchar, timestamp);"
     ActiveRecord::Base.connection.execute "DROP function compute_trashed ();"
-    ActiveRecord::Base.connection.execute "DROP function search_permission_graph(varchar, integer, varchar, varchar, integer);"
     ActiveRecord::Base.connection.execute "DROP function compute_permission_subgraph (varchar, varchar, integer);"
     ActiveRecord::Base.connection.execute "DROP function should_traverse_owned(varchar, integer);"
     ActiveRecord::Base.connection.execute "DROP view permission_graph_edges;"
diff --git a/services/api/db/structure.sql b/services/api/db/structure.sql
index eaa3d6299..aa3ffae62 100644
--- a/services/api/db/structure.sql
+++ b/services/api/db/structure.sql
@@ -89,12 +89,35 @@ with
      permission change, using search_permission_graph.
   */
   perm_from_start(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-    select perm_origin_uuid, target_uuid, val, traverse_owned
-      from search_permission_graph(starting_uuid,
-                                   starting_perm,
-                                   perm_origin_uuid,
-                                   starting_uuid,
-                                   starting_perm)),
+    
+WITH RECURSIVE
+        traverse_graph(origin_uuid, target_uuid, val, traverse_owned, starting_set) as (
+            
+             values (perm_origin_uuid, starting_uuid, starting_perm,
+                    should_traverse_owned(starting_uuid, starting_perm),
+                    (perm_origin_uuid = starting_uuid or starting_uuid not like '_____-tpzed-_______________'))
+
+          union
+            (select traverse_graph.origin_uuid,
+                    edges.head_uuid,
+                      least(edges.val,
+                            traverse_graph.val
+                            ,
+                            case (edges.tail_uuid = perm_origin_uuid AND
+                                  edges.head_uuid = starting_uuid)
+                               when true then starting_perm
+                               else null
+                            end
+),
+                    should_traverse_owned(edges.head_uuid, edges.val),
+                    false
+             from permission_graph_edges as edges, traverse_graph
+             where traverse_graph.target_uuid = edges.tail_uuid
+             and (edges.tail_uuid like '_____-j7d0g-_______________' or
+                  traverse_graph.starting_set)))
+        select traverse_graph.origin_uuid, target_uuid, max(val) as val, bool_or(traverse_owned) as traverse_owned from traverse_graph
+        group by (traverse_graph.origin_uuid, target_uuid)
+),
 
   /* Finds other inbound edges that grant permissions on the objects
      in perm_from_start, and computes permissions that originate from
@@ -106,50 +129,46 @@ with
      ownership.
   */
   additional_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-    select edges.tail_uuid as perm_origin_uuid, ps.target_uuid, ps.val,
-           should_traverse_owned(ps.target_uuid, ps.val)
-      from permission_graph_edges as edges,
-           lateral search_permission_graph(edges.head_uuid,
-                                           edges.val,
-                                           perm_origin_uuid,
-                                           starting_uuid,
-                                           starting_perm) as ps
+    
+WITH RECURSIVE
+        traverse_graph(origin_uuid, target_uuid, val, traverse_owned, starting_set) as (
+            
+    select edges.tail_uuid as origin_uuid, edges.head_uuid as target_uuid, edges.val,
+           should_traverse_owned(edges.head_uuid, edges.val),
+           edges.head_uuid like '_____-j7d0g-_______________'
+      from permission_graph_edges as edges
       where (not (edges.tail_uuid = perm_origin_uuid and
-                 edges.head_uuid = starting_uuid)) and
-            edges.tail_uuid not in (select target_uuid from perm_from_start) and
-            edges.head_uuid in (select target_uuid from perm_from_start)),
+                  edges.head_uuid = starting_uuid)) and
+            edges.tail_uuid not in (select target_uuid from perm_from_start where target_uuid like '_____-j7d0g-_______________') and
+            edges.head_uuid in (select target_uuid from perm_from_start)
+
+          union
+            (select traverse_graph.origin_uuid,
+                    edges.head_uuid,
+                      least(edges.val,
+                            traverse_graph.val
+                            ,
+                            case (edges.tail_uuid = perm_origin_uuid AND
+                                  edges.head_uuid = starting_uuid)
+                               when true then starting_perm
+                               else null
+                            end
+),
+                    should_traverse_owned(edges.head_uuid, edges.val),
+                    false
+             from permission_graph_edges as edges, traverse_graph
+             where traverse_graph.target_uuid = edges.tail_uuid
+             and (edges.tail_uuid like '_____-j7d0g-_______________' or
+                  traverse_graph.starting_set)))
+        select traverse_graph.origin_uuid, target_uuid, max(val) as val, bool_or(traverse_owned) as traverse_owned from traverse_graph
+        group by (traverse_graph.origin_uuid, target_uuid)
+),
 
   /* Combines the permissions computed in the first two phases. */
-  partial_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
+  all_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
       select * from perm_from_start
     union all
       select * from additional_perms
-  ),
-
-  /* If there are any users in the set of potentially affected objects
-     and the user's owner was not traversed, recompute permissions for
-     that user.  This is required because users always have permission
-     to themselves (identity property) which would be missing from the
-     permission set if the user was traversed while computing
-     permissions for another object.
-  */
-  user_identity_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-    select users.uuid as perm_origin_uuid, ps.target_uuid, ps.val, ps.traverse_owned
-      from users, lateral search_permission_graph(users.uuid,
-                                                  3,
-                                                  perm_origin_uuid,
-                                                  starting_uuid,
-                                                  starting_perm) as ps
-      where (users.owner_uuid not in (select target_uuid from partial_perms) or
-             users.owner_uuid = users.uuid) and
-      users.uuid in (select target_uuid from partial_perms)
-  ),
-
-  /* Combines all the computed permissions into one table. */
-  all_perms(perm_origin_uuid, target_uuid, val, traverse_owned) as (
-      select * from partial_perms
-    union
-      select * from user_identity_perms
   )
 
   /* The actual query that produces rows to be added or removed
@@ -190,10 +209,11 @@ with
          u.traverse_owned
       from all_perms as u, materialized_permissions as m
            where u.perm_origin_uuid = m.target_uuid AND m.traverse_owned
+           AND (m.user_uuid = m.target_uuid or m.target_uuid not like '_____-tpzed-_______________')
     union all
-      select perm_origin_uuid as user_uuid, target_uuid, val as perm_level, traverse_owned
+      select target_uuid as user_uuid, target_uuid, 3, true
         from all_perms
-        where all_perms.perm_origin_uuid like '_____-tpzed-_______________') as v
+        where all_perms.target_uuid like '_____-tpzed-_______________') as v
     group by v.user_uuid, v.target_uuid
 $$;
 
@@ -242,63 +262,6 @@ WITH RECURSIVE
 $$;
 
 
---
--- Name: search_permission_graph(character varying, integer, character varying, character varying, integer); Type: FUNCTION; Schema: public; Owner: -
---
-
-CREATE FUNCTION public.search_permission_graph(starting_uuid character varying, starting_perm integer, override_edge_tail character varying DEFAULT NULL::character varying, override_edge_head character varying DEFAULT NULL::character varying, override_edge_perm integer DEFAULT NULL::integer) RETURNS TABLE(target_uuid character varying, val integer, traverse_owned boolean)
-    LANGUAGE sql STABLE
-    AS $$
-/*
-  From starting_uuid, perform a recursive self-join on the edges
-  to follow chains of permissions.  This is a breadth-first search
-  of the permission graph.  Permission is propagated across edges,
-  which may narrow the permission for subsequent links (eg I start
-  at can_manage but when traversing a can_read link everything
-  touched through that link will only be can_read).
-
-  When revoking a permission, we follow the chain of permissions but
-  with a permissions level of 0.  The update on the permissions table
-  has to happen _before_ the permission is actually removed, because
-  we need to be able to traverse the edge before it goes away.  When
-  we do that, we also need to traverse it at the _new_ permission
-  level - this is what override_edge_tail/head/perm are for.
-
-  Yields the set of objects that are potentially affected, and
-  their permission levels granted by having starting_perm on
-  starting_uuid.
-
-  If starting_uuid is a user, this computes the entire set of
-  permissions for that user (because it returns everything that is
-  reachable by that user).
-
-  Used by the compute_permission_subgraph function.
-*/
-WITH RECURSIVE
-        traverse_graph(target_uuid, val, traverse_owned) as (
-            values (starting_uuid, starting_perm,
-                    should_traverse_owned(starting_uuid, starting_perm))
-          union
-            (select edges.head_uuid,
-                      least(edges.val,
-                            traverse_graph.val,
-                            case traverse_graph.traverse_owned
-                              when true then null
-                              else 0
-                            end,
-                            case (edges.tail_uuid = override_edge_tail AND
-                                  edges.head_uuid = override_edge_head)
-                               when true then override_edge_perm
-                               else null
-                            end),
-                    should_traverse_owned(edges.head_uuid, edges.val)
-             from permission_graph_edges as edges, traverse_graph
-             where traverse_graph.target_uuid = edges.tail_uuid))
-        select target_uuid, max(val), bool_or(traverse_owned) from traverse_graph
-        group by (target_uuid);
-$$;
-
-
 --
 -- Name: should_traverse_owned(character varying, integer); Type: FUNCTION; Schema: public; Owner: -
 --
@@ -1092,6 +1055,11 @@ UNION ALL
     users.uuid AS head_uuid,
     3 AS val
    FROM public.users
+UNION ALL
+ SELECT users.uuid AS tail_uuid,
+    users.uuid AS head_uuid,
+    3 AS val
+   FROM public.users
 UNION ALL
  SELECT links.tail_uuid,
     links.head_uuid,
@@ -1100,7 +1068,7 @@ UNION ALL
             WHEN ((links.name)::text = 'can_login'::text) THEN 1
             WHEN ((links.name)::text = 'can_write'::text) THEN 2
             WHEN ((links.name)::text = 'can_manage'::text) THEN 3
-            ELSE NULL::integer
+            ELSE 0
         END AS val
    FROM public.links
   WHERE ((links.link_class)::text = 'permission'::text);
diff --git a/services/api/lib/update_permissions.rb b/services/api/lib/update_permissions.rb
index b2cf6595b..33a8d9736 100644
--- a/services/api/lib/update_permissions.rb
+++ b/services/api/lib/update_permissions.rb
@@ -9,12 +9,15 @@ def refresh_permissions
   ActiveRecord::Base.transaction do
     ActiveRecord::Base.connection.execute("LOCK TABLE #{PERMISSION_VIEW}")
     ActiveRecord::Base.connection.execute("DELETE FROM #{PERMISSION_VIEW}")
+
     ActiveRecord::Base.connection.execute %{
-INSERT INTO #{PERMISSION_VIEW}
-select users.uuid, g.target_uuid, g.val, g.traverse_owned
-from users, lateral search_permission_graph(users.uuid, 3) as g where g.val > 0
+INSERT INTO materialized_permissions
+    #{PERM_QUERY_TEMPLATE % {:base_case => %{
+        select uuid, uuid, 3, true, true from users
 },
-                                          "refresh_permission_view.do"
+:override => ''
+} }
+}, "refresh_permission_view.do"
   end
 end
 
@@ -161,9 +164,12 @@ order by user_uuid, target_uuid
 }, "check_permissions_against_full_refresh.permission_table"
 
   q2 = ActiveRecord::Base.connection.exec_query %{
-select users.uuid as user_uuid, g.target_uuid, g.val as perm_level, g.traverse_owned
-from users, lateral search_permission_graph(users.uuid, 3) as g where g.val > 0
-order by users.uuid, target_uuid
+    select pq.origin_uuid as user_uuid, target_uuid, pq.val as perm_level, pq.traverse_owned from (
+    #{PERM_QUERY_TEMPLATE % {:base_case => %{
+        select uuid, uuid, 3, true, true from users
+},
+:override => ''
+} }) as pq order by origin_uuid, target_uuid
 }, "check_permissions_against_full_refresh.full_recompute"
 
   if q1.count != q2.count
@@ -196,3 +202,23 @@ def skip_check_permissions_against_full_refresh
     Thread.current[:no_check_permissions_against_full_refresh] = check_perm_was
   end
 end
+
+PERM_QUERY_TEMPLATE = %{
+WITH RECURSIVE
+        traverse_graph(origin_uuid, target_uuid, val, traverse_owned, starting_set) as (
+            %{base_case}
+          union
+            (select traverse_graph.origin_uuid,
+                    edges.head_uuid,
+                      least(edges.val,
+                            traverse_graph.val
+                            %{override}),
+                    should_traverse_owned(edges.head_uuid, edges.val),
+                    false
+             from permission_graph_edges as edges, traverse_graph
+             where traverse_graph.target_uuid = edges.tail_uuid
+             and (edges.tail_uuid like '_____-j7d0g-_______________' or
+                  traverse_graph.starting_set)))
+        select traverse_graph.origin_uuid, target_uuid, max(val) as val, bool_or(traverse_owned) as traverse_owned from traverse_graph
+        group by (traverse_graph.origin_uuid, target_uuid)
+}
diff --git a/services/api/test/unit/permission_test.rb b/services/api/test/unit/permission_test.rb
index a0478ec54..d9383cf8e 100644
--- a/services/api/test/unit/permission_test.rb
+++ b/services/api/test/unit/permission_test.rb
@@ -10,7 +10,7 @@ class PermissionTest < ActiveSupport::TestCase
   test "Grant permissions on an object I own" do
     set_user_from_auth :active_trustedclient
 
-    ob = Specimen.create
+    ob = Collection.create
     assert ob.save
 
     # Ensure I have permission to manage this group even when its owner changes
@@ -24,7 +24,7 @@ class PermissionTest < ActiveSupport::TestCase
   test "Delete permission links when deleting an object" do
     set_user_from_auth :active_trustedclient
 
-    ob = Specimen.create!
+    ob = Collection.create!
     Link.create!(tail_uuid: users(:active).uuid,
                  head_uuid: ob.uuid,
                  link_class: 'permission',
@@ -37,7 +37,7 @@ class PermissionTest < ActiveSupport::TestCase
 
   test "permission links owned by root" do
     set_user_from_auth :active_trustedclient
-    ob = Specimen.create!
+    ob = Collection.create!
     perm_link = Link.create!(tail_uuid: users(:active).uuid,
                              head_uuid: ob.uuid,
                              link_class: 'permission',
@@ -48,18 +48,18 @@ class PermissionTest < ActiveSupport::TestCase
   test "readable_by" do
     set_user_from_auth :active_trustedclient
 
-    ob = Specimen.create!
+    ob = Collection.create!
     Link.create!(tail_uuid: users(:active).uuid,
                  head_uuid: ob.uuid,
                  link_class: 'permission',
                  name: 'can_read')
-    assert Specimen.readable_by(users(:active)).where(uuid: ob.uuid).any?, "user does not have read permission"
+    assert Collection.readable_by(users(:active)).where(uuid: ob.uuid).any?, "user does not have read permission"
   end
 
   test "writable_by" do
     set_user_from_auth :active_trustedclient
 
-    ob = Specimen.create!
+    ob = Collection.create!
     Link.create!(tail_uuid: users(:active).uuid,
                  head_uuid: ob.uuid,
                  link_class: 'permission',
@@ -67,6 +67,34 @@ class PermissionTest < ActiveSupport::TestCase
     assert ob.writable_by.include?(users(:active).uuid), "user does not have write permission"
   end
 
+  test "update permission link" do
+    set_user_from_auth :admin
+
+    grp = Group.create! name: "blah project", group_class: "project"
+    ob = Collection.create! owner_uuid: grp.uuid
+
+    assert !users(:active).can?(write: ob)
+    assert !users(:active).can?(read: ob)
+
+    l1 = Link.create!(tail_uuid: users(:active).uuid,
+                 head_uuid: grp.uuid,
+                 link_class: 'permission',
+                 name: 'can_write')
+
+    assert users(:active).can?(write: ob)
+    assert users(:active).can?(read: ob)
+
+    l1.update_attributes!(name: 'can_read')
+
+    assert !users(:active).can?(write: ob)
+    assert users(:active).can?(read: ob)
+
+    l1.destroy
+
+    assert !users(:active).can?(write: ob)
+    assert !users(:active).can?(read: ob)
+  end
+
   test "writable_by reports requesting user's own uuid for a writable project" do
     invited_to_write = users(:project_viewer)
     group = groups(:asubproject)
@@ -124,16 +152,16 @@ class PermissionTest < ActiveSupport::TestCase
   test "user owns group, group can_manage object's group, user can add permissions" do
     set_user_from_auth :admin
 
-    owner_grp = Group.create!(owner_uuid: users(:active).uuid)
-
-    sp_grp = Group.create!
-    sp = Specimen.create!(owner_uuid: sp_grp.uuid)
+    owner_grp = Group.create!(owner_uuid: users(:active).uuid, group_class: "role")
+    sp_grp = Group.create!(group_class: "project")
 
     Link.create!(link_class: 'permission',
                  name: 'can_manage',
                  tail_uuid: owner_grp.uuid,
                  head_uuid: sp_grp.uuid)
 
+    sp = Collection.create!(owner_uuid: sp_grp.uuid)
+
     # active user owns owner_grp, which has can_manage permission on sp_grp
     # user should be able to add permissions on sp.
     set_user_from_auth :active_trustedclient
@@ -149,7 +177,7 @@ class PermissionTest < ActiveSupport::TestCase
   skip "can_manage permission on a non-group object" do
     set_user_from_auth :admin
 
-    ob = Specimen.create!
+    ob = Collection.create!
     # grant can_manage permission to active
     perm_link = Link.create!(tail_uuid: users(:active).uuid,
                              head_uuid: ob.uuid,
@@ -170,7 +198,7 @@ class PermissionTest < ActiveSupport::TestCase
   test "user without can_manage permission may not modify permission link" do
     set_user_from_auth :admin
 
-    ob = Specimen.create!
+    ob = Collection.create!
     # grant can_manage permission to active
     perm_link = Link.create!(tail_uuid: users(:active).uuid,
                              head_uuid: ob.uuid,
@@ -192,7 +220,8 @@ class PermissionTest < ActiveSupport::TestCase
     manager = create :active_user, first_name: "Manage", last_name: "Er"
     minion = create :active_user, first_name: "Min", last_name: "Ion"
     minions_specimen = act_as_user minion do
-      Specimen.create!
+      g = Group.create! name: "minon project", group_class: "project"
+      Collection.create! owner_uuid: g.uuid
     end
     # Manager creates a group. (Make sure it doesn't magically give
     # anyone any additional permissions.)
@@ -255,7 +284,7 @@ class PermissionTest < ActiveSupport::TestCase
         create(:permission_link,
                name: 'can_manage', tail_uuid: manager.uuid, head_uuid: minion.uuid)
       end
-      assert_empty(Specimen
+      assert_empty(Collection
                      .readable_by(manager)
                      .where(uuid: minions_specimen.uuid),
                    "manager saw the minion's private stuff")
@@ -273,7 +302,7 @@ class PermissionTest < ActiveSupport::TestCase
 
     act_as_user manager do
       # Now, manager can read and write Minion's stuff.
-      assert_not_empty(Specimen
+      assert_not_empty(Collection
                          .readable_by(manager)
                          .where(uuid: minions_specimen.uuid),
                        "manager could not find minion's specimen by uuid")
@@ -309,12 +338,12 @@ class PermissionTest < ActiveSupport::TestCase
                      "#{a.first_name} should be able to see 'b' in the user list")
 
     a_specimen = act_as_user a do
-      Specimen.create!
+      Collection.create!
     end
-    assert_not_empty(Specimen.readable_by(a).where(uuid: a_specimen.uuid),
-                     "A cannot read own Specimen, following test probably useless.")
-    assert_empty(Specimen.readable_by(b).where(uuid: a_specimen.uuid),
-                 "B can read A's Specimen")
+    assert_not_empty(Collection.readable_by(a).where(uuid: a_specimen.uuid),
+                     "A cannot read own Collection, following test probably useless.")
+    assert_empty(Collection.readable_by(b).where(uuid: a_specimen.uuid),
+                 "B can read A's Collection")
     [a,b].each do |u|
       assert_empty(User.readable_by(u).where(uuid: other.uuid),
                    "#{u.first_name} can see OTHER in the user list")
@@ -341,13 +370,13 @@ class PermissionTest < ActiveSupport::TestCase
   test "cannot create with owner = unwritable user" do
     set_user_from_auth :rominiadmin
     assert_raises ArvadosModel::PermissionDeniedError, "created with owner = unwritable user" do
-      Specimen.create!(owner_uuid: users(:active).uuid)
+      Collection.create!(owner_uuid: users(:active).uuid)
     end
   end
 
   test "cannot change owner to unwritable user" do
     set_user_from_auth :rominiadmin
-    ob = Specimen.create!
+    ob = Collection.create!
     assert_raises ArvadosModel::PermissionDeniedError, "changed owner to unwritable user" do
       ob.update_attributes!(owner_uuid: users(:active).uuid)
     end
@@ -356,13 +385,13 @@ class PermissionTest < ActiveSupport::TestCase
   test "cannot create with owner = unwritable group" do
     set_user_from_auth :rominiadmin
     assert_raises ArvadosModel::PermissionDeniedError, "created with owner = unwritable group" do
-      Specimen.create!(owner_uuid: groups(:aproject).uuid)
+      Collection.create!(owner_uuid: groups(:aproject).uuid)
     end
   end
 
   test "cannot change owner to unwritable group" do
     set_user_from_auth :rominiadmin
-    ob = Specimen.create!
+    ob = Collection.create!
     assert_raises ArvadosModel::PermissionDeniedError, "changed owner to unwritable group" do
       ob.update_attributes!(owner_uuid: groups(:aproject).uuid)
     end
diff --git a/services/api/test/unit/user_test.rb b/services/api/test/unit/user_test.rb
index 596cd415f..7fcd36d70 100644
--- a/services/api/test/unit/user_test.rb
+++ b/services/api/test/unit/user_test.rb
@@ -478,15 +478,6 @@ class UserTest < ActiveSupport::TestCase
 
     vm = VirtualMachine.create
 
-    # Set up the bogus Link
-    bad_uuid = 'zzzzz-tpzed-xyzxyzxyzxyzxyz'
-
-    resp_link = Link.create ({tail_uuid: email, link_class: 'permission',
-        name: 'can_login', head_uuid: bad_uuid})
-    resp_link.save(validate: false)
-
-    verify_link resp_link, 'permission', 'can_login', email, bad_uuid
-
     response = user.setup(repo_name: 'foo/testrepo',
                           vm_uuid: vm.uuid)
 

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