Title: Efficient Querying of XML Data Using Structural Joins
1 Efficient Querying of XML Data Using Structural
Joins
2Content
- A quick look at XML query languages
- Lore - an example of a native XML database
- DB2 - an example of RDBMSs support for XML
- On supporting containment queries in RDBMS
- The Tree-Merge and Stack-Tree algorithms
- The StackPath algorithm
3XML
- Replacement for HTML
- Focus is on storing and processing.
- Electronic Data Interchange
- Querying becomes desirable.
- People with many XML documents actually have an
XML database.
4XML query languages
- XML-QL
- Influenced by SQL
- Submitted to W3C (lost favor to XQuery)
- XPath
- used in XSLT
- the basis for path expressions in XQuery
- XQuery
- A W3C working draft (version 1.0)
- Based on Quilt (which in turn was mainly
influenced by XML-QL and Lorel) - No updates, limited IR features
5XPath
- /para
- selects all para grandchildren of the context
node - /doc/chapter5/section2
- selects the second section of the fifth chapter
of the doc - chapter//para
- selects the para element descendants of the
chapter element children of the context node - para_at_type"warning"
- selects all para children of the context node
that have a type attribute with value warning - chaptertitle"Introduction"
- selects the chapter children of the context node
that have one or more title children with
string-value equal to Introduction
6XQuery
- document("books.xml")//chapter/title
- Finds all titles of chapters in document
books.xml - document(bib.xml")//bookpublisher
"Addison-WesleyAND _at_year gt "1991" - Finds all books in document bib.xml published by
Addison-Wesley after 1991 - ltresultsgt
- FOR t IN distinct(document("price
s.xml")/prices/book/title) - LET p avg(document("prices.xml
")/prices/booktitlet/price) - WHERE (document("bib/xml")/bookti
tlet/publisher) "Addison-Wesley" - RETURN
- ltresultgt t ltavggt p
lt/avggt lt/resultgt - lt/resultsgt
- Returns the title and average price of all books
published by Addison-Wesley
7XML documents as trees
- ltbook year2000gt
- lttitlegt XML lt/titlegt
- ltauthorsgt
- ltauthorgt Bill lt/authorgt
- ltauthorgt Jake lt/authorgt
- lt/authorsgt
- ltchaptergt
- ltheadgt History lt/headgt
- ltsectiongt
- ltheadgt lt/headgt
- ltsectiongt lt/sectiongt
- lt/sectiongt
- ltsectiongt lt/sectiongt
- lt/chaptergt
- ltchaptergt lt/chaptergt
- lt/bookgt Order of nodes is important
8XML documents as trees
- ltbook year2000gt
- lttitlegt XML lt/title idid1gt
- ltauthorsgt
- ltauthorgt Bill lt/authorgt
- ltauthorgt Jake lt/authorgt
- lt/authorsgt
- ltchaptergt
- ltheadgt History lt/headgt
- ltsectiongt
- ltheadgt lt/headgt
- ltsectiongt lt/section idrefid1gt
- lt/sectiongt
- ltsectiongt lt/sectiongt
- lt/chaptergt
- ltchaptergt lt/chaptergt
- lt/bookgt Order of nodes is important
book
year
authors
chapter
chapter
title
...
2000
xml
author
head
section
section
author
...
Bill
Jake
History
head
section
...
...
9Executing queries
- How does one execute a complex query
- Parse the query (i.e. break it down to basic
operations). - Let a query optimizer devise a corresponding
physical query plan. - Execute the required basic operations combining
the intermediate results as you go. - The most common basic operations are
- Finding nodes satisfying a given predicate on
their value. - Finding nodes satisfying a given structural
relationship.
10XML databases
- XML is semi-structured data items may have
missing elements or multiple occurrences of the
same element.It may even not have a DTD. - Native semi-structured databases
- X-Hive, Lore
- RDBMS
- Oracle
- SQL-Server
- DB2
- All added support for XML
11Semi-structured XML databases
- There arent many around
- Store XML files plus indexes
- Usually build (and store) most or all of the tree
- Usually solve path expressions by pointer-chasing
12 LOREAn example of a native semi-structured
database
13Lore - sample database
- Select x
- From DBGroup.Member x
- Where exists y in x.age ylt30
14Lore - data model
- Called the Object Exchange Model
- The data model is a graph (though the reference
edges are marked as such). - Each vertex is an object with a unique object
identifier. - Atomic objects have no outgoing edges and contain
values (like strings, gifs, audio etc.) - All other objects may have outgoing edges.
- Tag-Names (labels) are attached to the edges, not
the vertices. - Objects may optionally have aliases (names).
- As is obvious this is just another view of our
XML tree
15Lore - indexes
- Vindex (value index) - implemented as a B-tree
- Supports finding all atomic objects with a given
incoming edge label satisfying a given predicate. - Lindex (label index) - implemented using
extendible hashing - Supports finding all parents of a given object
via an edge with a given label. - Bindex (edge index)
- Supports finding all parent-child pairs connected
via a given label. This is useful for locating
edges with rare labels. - In addition there are some other indexes (not
important to us). - Note that we need more indexes than in a
relational database
16Lore - statistics (partial list)
- For each labeled path p of length lt k (usually
k1) - The total number of instances of p, denoted p
- The total number of distinct objects reachable
via p,denoted pd - The total number of l-labeled edges going out of
p,denoted p l - The total number of l-labeled edges coming into
p,denoted p l
17Lore - path expressions (simplified)
- Simple path expressions
- x.l y
- Path expressions
- an ordered list of simple path expressions
- x.l y, y.l2 z
- Path expressions logical plan
- x.B y, y.C z, z.D v
18Lore - basic physical operators (slightly edited)
- Scan(father, label, son)
- Finds all the sons of a given father (through a
given label). - Does pointer-chasing
- Lindex(father, label, son)
- Finds all the fathers of a given son (through a
given label). - Uses the Lindex
- Bindex(label, father, son)
- Finds all the father-son pairs connected by a
given label. - Uses the Bindex
- Vindex(label, operator, value, atomic-object)
- Finds all the the atomic objects with a given
label incoming label satisfying the given
predicate. - Uses the Vindex
- Name(alias, node)
- Verifies that the specified node has the given
alias.
19Lore - physical path subplans
x and y are unbound
y is bound
x and y are unbound
- The estimated hit-rate (per x) of scan(x, C, y)
is (B C / Bd) - The estimated hit-rate (per y) of Lindex(x, C,
y) is (C B / Cd)
20Lore - sample logical plan
- Select x From DBGroup.Member x Where exists y in
x.age ylt30 - Glue nodes are pivot points, they recursively
evaluate the cost of evaluating their sons in
left-right or right-left order.
21Lore - sample physical subplans
- (a) corresponds to a possible left-right plan of
the top glue - (b) corresponds to a possible left-right plan of
the right glue - (c) corresponds to a possible right-left plan of
the right glue - (d) corresponds to a possible right-left plan of
the top glue, using (c)
22Lore - path expressions strategies
- A higher level view of path expressions solving
- Top-Down
- Look for all Member objects in DBGroup and for
each one look for Age subobjects with a value lt
30. - uses scan
- Bottom-up
- Look for all atomic objects with value lt 30 and
for each one walk up the tree using only
Age-labeled followed by Member-labeled edges. - uses Vindex and then Lindex
- Hybrid
- Do Top-Down part of the way and Bottom-Up part of
the way. - Select x From DBGroup.Member x Where exists y in
x.age ylt30
23Lore - path strategies (continued)
- Top-Down is better when there are few paths
satisfying the required structure, but many
objects satisfying the predicate. - Bottom-Up is better when there are a few objects
satisfying the predicate but many paths
satisfying the required structure. - Hybrid is better when the fan-out degree (going
down), increases at the same time the fan-in
degree (going up) does.
24 DB2An example of a RDBMS support of XML
25DB2 - XML support
- XML column
- An entire XML document is stored as a column in a
table. - may be XMLCLOB, XMLVARCHAR or XMLFile.
- You define which XML elements or attributes
should be extracted to indexed columns in side
tables. - UDFs are provided for inserting, updating and
selecting fragments of a document. - XML collection
- Compose an XML document from existing DB2 tables.
- Decompose an XML document and retrieve some of it
into a set of DB2 tables. - Basically a conversion mechanism.
- Stored procedures automate most of the work.
26DB2 - a nice diagram...
27DB2 - example Data Access Definition
28DB2 - example DAD (continued)
29DB2 - searching XML documents
- Well, whatever is in the side tables is queried
using SQL. - What about things not in any side table?
- A loosely coupled IR engine (part of the DB2 Text
Extender) is called using a UDF to take care of
this. - The UDFs use a syntax compatible with XPath.
30DB2 - conclusions (in a nutshell)
- Pros
- Integrated solution which automates a lot of
work. - We can ask queries that mix data from XML and the
regular database tables (aka web-supported
database queries and database-supported web
queries). - Cons
- One has to manually define the mappings between
the XML documents and the tables. - Is it fast enough?
31 On Supporting Containment Queries in RDBMS
Zhang, Naughton, DeWitt, Luo, Lohman ACM SIGMOD
2001
32Article goals
- Given that a lot of XML data is (and will
probably be) stored in RDBMS which is the best
way to support containment queries? - Using a loosely coupled IR engine?
- OR
- Using the native tables and query mechanisms of
the RDBMS?
33Structural relationships in trees
1
15
2
4
6
11
2
4
9
14
3
5
7
9
12
14
1
3
6
8
11
13
8
10
13
15
5
7
10
12
- Note that x is a descendant of y if and only
ifpreorder(x) gt preorder(y) and postorder(x) lt
postorder(y) - y is the father of x if in addition level(x)
level(y) 1
34Structural relationships in XML
- The previous observations are true even if we
look at any monotone functions of the preorder
and the postorder numbers. - The start and end position of an element in an
XML document are exactly such monotone functions. - In other words we can use a small extension of
the regular - IR inverted-index to also solve structural
relationships! - Note that we have a problem of adapting the
numbers if the document changes.
35The inverted indexes
- An Elements index (E-Index) Holds for each XML
element, the docno, begin, end and level of every
occurrence of that element. - A Text index (T-Index) Holds for each text word,
the docno, wordno and level of every occurrence
of the word.
36Experiment plan
- Compare the following two systems
- An inverted list engine supporting containment
queries on XML data. - The engine was built (due to lack of a commercial
one). - The code was written in C and the
inverted-indexes were stored in a B-tree with
each list stored as a record. - Each list is in ascending order of docno, begin
(or wordno). - An in-house algorithm was developed for
evaluating simple containment queries. - A full RDBMS approach (tried DB2 7.1 and
SQL-Server 7.0) - The E-index and T-index are stored as the
following tables ELEMENTS(term, docno, begin,
end, level)TEXTS(term, docno, wordno, level) - Note that we do not use the IR engine of the
RDBMS.
37Using the inverted indexes tables
- E//"T
- select from ELEMENTS e, TEXTS t
- where e.term E and t.term T
- and e.docno t.docno
- and e.begin lt t.wordno and t.wordno lt e.end
- E"T"
- select from ELEMENTS e, TEXTS t
- where e.term E and t.term T
- and e.docno t.docno
- and e.begin 1 t.wordno and t.wordno 1
e.end - In a similar fashion we solve Elements only
queries, father-son, and words distance queries.
(how will this look for E//E ?)
38Experiment setup
39Experiment setup (continued)
- The queries are all simple queries of the form
E//T, E//E, E/T or E/E
40Experiment results
41Results analysis
- Why did DB2 perform better in QS4, QD4 and QG5?
- Remember that each list in the inverted engine
is stored as one record! - Why did DB2 perform worse in all the other
queries? - Bad optimizer decisions?
- Is I/O more expensive (locking, security, etc.)?
- Other factors?
- It turns out that the queries are CPU-bound!
- Further investigation found out that it was the
merge algorithm.
42DB2 merge algorithms
- When joining on
- a.docno d.docno and a.begin lt d.wordno
and d.wordno lt a.end - Standard Merge-Join only uses the a.docno
d.docno predicate (since it does one comparison,
using one index per table), and applies the rest
of the condition on each matching couple. - Hash-Join only uses the a.docno d.docno
predicate (since it can not handle inequalities
anyway), and thus performs similarly to the
classical merge join. - Index nested-loop join looks, for each row in the
outer table, for all rows in the inner table
index that lie between a start-key and
astop-key. - Assuming the outer table is ELEMENTS and the
inner table is TEXTS - start-key term value and docno outer.docno
and wordno gt outer.begin - end-key term value and docno outer.docno
and wordno lt outer.end
43The Multi-Predicate Merge Join
- begin-desc Dlist-gtfirst node OutputList
NULL - for (a Alist-gtfirstNode a a-gtnextNode)
- d begin_desc
- while (d.docno lt a.docno) d d-gtnextNode
- if (a.docno lt b.docno) continue
- while (d.begin lt a.begin) d d-gtnextNode
- begin_desc d
- while (d.begin lt a.end) // implies d.end lt
a.end - if (a.docno lt b.docno) break
- append (a,d) to OutputList
- d d-gtnextNode
-
44Comparison of the merge algorithms
- It seems like the NLJ algorithm will usually
compare less items, BUT - It has to spend time on index seeks!
- It uses random access so cache utilization is
poor.
45MPMGJN traditional joins - statistics
Note DB2 did not choose NLJ for QG4
46 Structural Joins A Primitive for Efficient XML
Query Pattern Matching
Al-Khalifa, Jagadish, Koudas, Patel, Srivastava,
Wu ICDE 2002
47Structural-Join algorithms
Based on the (docId, startPos, endPos, level)
information of XML elements and attributes. Given
two lists of potential ancestors and potential
descendants, both in ascending order of
docIdstartPos, the following structural join
algorithms are presented
- Tree-Merge-Anc (aka MPMGJN)
- Tree-Merge-Desc
- Stack-Tree-Desc
- Stack-Tree-Anc
- The ?-?-Anc algorithms produce the output sorted
by the ancestors. - The ?-?-Desc algorithms produce the output sorted
by the descendants. - The sorting variant to use depends on the way an
optimizer chooses to compose a complex query.
48Tree-Merge-Anc
- begin-desc Dlist-gtfirst node OutputList
NULL - for (a Alist-gtfirstNode a a-gtnextNode)
- d begin_desc
-
- while (d.startPos lt a.startPos) d
d-gtnextNode - begin_desc d
-
- while (d.startPos lt a.endPos) // implies
d.endPos lt a.endPos - if (a.level 1 ! d.level) continue //
father-son - append (a,d) to OutputList
- d d-gtnextNode
-
-
- Note For ease of exposition, we assume that
Alist and Dlist have the same docId.
49Analysis of Tree-Merge-Anc
- Ancestor-Descendant structural relationships
- O(Alist Dlist OutputList)
- Since first while loop increases d, and second
while loop increases output or a. - Father-Son structural relationships
- O(Alist Dlist)
Can sub-sorting on levelNum help ?
50Tree-Merge-Desc
- begin-anc Alist-gtfirst node OutputList NULL
- for (d Dlist-gtfirstNode d d-gtnextNode)
- a begin_anc
-
- while (a.endPos lt d.startPos) a
a-gtnextNode - begin_anc a
-
- while (a.startPos lt d.startPos)
- if (a.level 1 ! d.level) continue //
father-son - if (d.endPos lt a.endPos) append (a,d) to
OutputList - a a-gtnextNode
-
-
- Note For ease of exposition, we assume that
Alist and Dlist have the same docId.
51Analysis of Tree-Merge-Desc
- Ancestor-Descendant and Father-Son structural
relationships - O(Alist Dlist).
- Works in linear time on most real data.
Dlist
Alist
begin end a0 1 4n2 a1 2 5 a2 6
9 a3 10 13 . . an 4n-2 4n1
begin d1 3 d2 7 d3 11 . . dn 4n-1
a0
a3
a1
a2
an
...
d1
d2
d3
dn
...
52Stack-Tree algorithms
- Motivation
- A depth-first traversal of a tree can be
performed in linear time, using a stack as large
as the height of the tree. - An ancestor-descendant structural relationship is
manifested as the ancestor appearing higher on
the stack than the descendant. - Unfortunately, a depth-first traversal requires
going over all the tree.
53Stack-Tree-Desc
- a Alist-gtfirst node d Dlist-gtfirst node
OutputList NULL - while (lists are not empty)
- e (a.startPos lt d.startPos) ? a d
- while (e.startPos gt stack-gttop.endPos)
stack-gtpop() - if (e a) // remember that e.startPos gt
stack-gttop.startPos - stack-gtpush(a)
- a a-gtnextNode
- else // e d
- for each a in stack // Father-Son If
(stack-gttop.level 1 d.level)
append(stack-gttop, d) - append (a, d) to OutputList
-
- d d-gtnextNode
-
-
- Note For ease of exposition, we assume that
Alist and Dlist have the same docId.
54Stack-Tree-Desc (father-son example)
a1 d1 a2 d2 . . . . an dn dn1 dn2
. . d2n
a1
d1
d2n
a2
d2
d2n-1
a3
an
...
d3
d2n-2
. . .
an
dn
dn1
a2
? e.startPos gt stack-gttop.endPos
a1
(a1,d1)
(a2,d2)
...
(an-1,dn-1)
(an,dn)
(an,dn1)
(an-1,dn2)
...
(a3,d2n-2)
(a2,d2n-1)
(a1,d2n)
55Analysis of Stack-Tree-Dec
- O(Alist Dlist OutputList) for
ancestor-descendant as well as father-son
structural relationships. - Each Alist element is pushed once and popped
once, so stack operations take O(Alist). - The inner for loop outputs a new pair each
time, so its total time is O(OutputList). - When doing father-son structural joins, we do not
even have a for loop. - The algorithm is non-blocking.
- IO complexity is O(Alist/P Dlist/P
OutputList/P) where P is the page size. - Each input page is read just once (and output
sent as soon as it is computed). - The stack is as large as the tree height, so it
is very reasonable to assume that it fits in RAM.
56Stack-Tree-Anc
- a Alist-gtfirst node d Dlist-gtfirst node
OutputList NULL - while (lists are not empty)
- e (a.startPos lt d.startPos) ? a d
- while (e.startPos gt stack-gttop.endPos)
- temp stack-gtpop()
- if (stack-gtisEmpty())
- append temp-gtselfList to OutputList append
temp-gtinheritList to OutputList - else
- append temp-gtinheritList to temp-gtselfList
append temp-gtselfList to stack-gttop-gtinheritList -
-
- if (e a) // remember that e.startPos gt
stack-gttop.startPos - stack-gtpush(a) a a-gtnextNode
- else // e d
- for each a in stack
- if(a stack-gtbottom) append (a, d) to
OutputList - else append (a, d) to selfList associated
with a -
- d d-gtnextNode
57Stack-Tree-Anc (father-son example)
? e.startPos gt stack-gttop.endPos
a1 d1 a2 d2 . . . . an dn dn1 dn2
. . d2n
an
(an,dn)
(an,dn1)
. . .
(an-1,dn-1)
(an,dn), (an,dn1)
. . .
a2
(a2,d2)
(a2,d2n-1)
(a3,d3),(a3,d2n-2)...(an,dn),(an,dn1)
a1
(a1,d1)
(a1,d2n)
(a2,d2),(a2,d2n-1)...(an,dn),(an,dn1)
58Analysis of Stack-Tree-Anc
- O(Alist Dlist OutputList) For
ancestor-descendant as well as father-son
structural relationships. - Assuming the lists are maintained as linked lists
with head and tail pointers. - The algorithm is blocking (but only partially).
- IO complexity is O(Alist/P Dlist/P
OutputList/P) where P is the page size. - We cannot assume that all the lists fit in RAM.
- All that we do with lists (except output) is
appending. - We can page out a list and we need only keep its
tail in RAM. So we need two extra pages in memory
per stack entry - still a reasonable assumption. - We only need to know the address of the head of a
list. - Each list page is thus paged out at most once,
and paged back in only for output.
59Experiment workload
- Experimented with real XML data as well as
synthetic data generated by IBM XML data
generator (with similar results). - Presented the results for the largest data set
6.3 million elements (800Mb of data).
60Experiment results
- Implemented the structural join algorithms, as
well as bottom-up and top-down, on the TIMBER
native XML query engine (built on top of SHORE). - Bottom-up and top-down performed poorly
- Even on 10 of the data it took bottom-up 283.5
seconds to run QS1, and 717.8 seconds for
top-down to do it. - It took less than 15 seconds for any of the join
algorithms to complete QS1 on the full data set!
61Experiment results (continued)
- Implemented the STJ-D as an application program
interfacing to a commercial RDBMS through a set
of cursors. - Also ran the queries using the RDBMS join
mechanisms.
QS1
Combined an index on startPos, endPos
Small up to 10 selectivity, Medium up to 25
62Experiment results (continued)
63 Holistic Twig JoinsOptimal XML Pattern Matching
Bruno, Koudas, Srivastava ACM SIGMOD 2002
64Twig patterns
- booktitle XML AND year 2000
- booktitle XML//authorFn jane AND Ln
doe
book
...
year
authors
chapter
chapter
title
...
2000
XML
author
head
section
section
author
author
...
book
book
...
Ln
title
section
Fn
Ln
Fn
Ln
Fn
title
year
title
author
XML
2000
XML
Ln
Fn
jane
moe
doe
john
john
doe
XML
...
Twig patterns
jane
doe
65Twig pattern matching
- Given a twig pattern Q and an XML database D, a
match is a mapping from nodes in Q to nodes in D,
satisfying - Query node predicates are satisfied by their
images. - The structural relationships between the query
nodes are satisfied by their images. - If Q has k nodes, the result may be represented
by a relation with k columns.
66Twig pattern matching approaches
- Decompose the twig into a series of binary
structural joins, compute each (using STJ-D for
example) and join the results. - Note that one may have intermediate results that
are very big. Consider for example booktitle
XML - Decompose the twig into a series of rooted
path-expressions, compute each one independently
and merge-join the results. - Note that one may have intermediate results that
are very big (but only in different
branches).Consider for example book//authorFn
jane AND Ln doe - Decompose the twig into a series of rooted
path-expressions, compute them simultaneously
taking interdependencies into account, and
merge-join the results.
67PathStack-Desc
- go to start of all lists OutputList NULL
- while (lists are not empty)
- e element with minimum startPos in all lists
- i the list e was taken from advance list i
- for(int j1 j lt numLists j)
- while (e.startPos gt stackj-gttop.endPos)
stackj-gtpop() -
- if (e is not from the leaf list) // remember
that for every stack e.startPos gt
stack-gttop.startPos - stacki-gtpush(a, stacki-1-gttop) // if the
I-1 stack is not empty of course - else // e is the path query leaf
- let (x1, x2, xnumLists-1) be the linked list
whose head is the top of the numLists-1 stack. - For each (y1, y2, ynumLists-1, e) such that
for all j yj is below xj do - append (y1, y2, ynumLists-1, e) to
OutputList -
- Note For ease of exposition, we assume that
all lists have the same docId.
68PathStack-Desc (example)
a1 b1 a2 b2 c1 b3 c2
a2
b2
? e.startPos gt stack-gttop.endPos
a1
b1
b3
(a2,b2,c1) (a1,b2,c1) (a1,b1,c1)
(a1,b3,c2)
69PathStack-Desc experimental results
- Implemented the binary join algorithms, as well
as the StackPath, in C using the file-system as
the storage engine. - Used a synthetic data set made of 1 million nodes
with 6 different labels (A1, A2, A6) uniformly
distributed (no information regarding other
parameters).
70Final remarks
- What we did not do (partial list)
- Look at using B-Trees with the stack algorithms.
- Look at the TwigStack algorithm.
- Look at Kleen-closure evaluation.
- Conclusions
- There is a lot more work to be done by everybody.
71Appendix TwigStack (in a nutshell)
- getNext(q) returns a query node such that the
head of its list satisfies - It has the smallest startPos (L) of all the heads
of its descendant and sibling lists. - It participates in a solution to the sub-query
rooted at that query node. - If it is part of a solution involving its
ancestors they were already read.
72Appendix (continued)
- Note that as long as 09 succeeds we return the
node whose head has the smallest startPos (L) of
all the heads of lists in the sub-tree of q.When
09 fails we float up a node whose list head has
the the smallest startPos (L) of all the heads of
lists in its descendant or sibling lists. - Once a node floats up, its father nodes list
does not contain any more ancestors of its list
head (otherwise 09 would not fail). Applying the
same logic to the father and grandfather etc.
leads us by induction to the conclusion that if
it this nodes list head is part of a solution
involving its ancestors, these ancestors are
already out of their lists.
73Appendix (continued)
- Both used ternary trees.
- Left sub-tree in (a) has only A1A2A3A4 paths.
- Middle sub-tree in (a) has only A1A5A6A7
paths. - Right sub-tree in (a) has solutions. Its size
varies (8 to 24 of the tree). - (b) left has no A2 or A3, middle has no A4 or
A5, right has no A6 or A7.
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