Implement file database for indexing and querying #235

hendrikvanantwerpen · 2023-03-24T13:07:13Z

◀️ #249	#248 ▶️

#248 should be merged as soon as possible after this one to prevent CI for other PRs based of main to be broken.

This PR is part of the work to implement an LSP server (#242). This implements file storage for stack graphs and partial paths, allowing separate index and query invocations.

Changes

A storage module in stack-graphs has the reader and writer types for the SQLite database we use. The reader supports piecemeal loading of paths into the runtime structures. It is guarded by the storage Cargo feature.
A new index command replaces the analyze command. It takes a database argument where the results are stored.
A new query command can be used to query the database. It currently has a single subcommand definition to query for definitions.
A new clean command can be used to clean data from the database. It either expects source paths, in which case all descendants of these paths are cleaned, or the --all flag, in which case the whole database is cleaned.
The database can store a tag for each file, which is used to implement incremental indexing. If the file content did not change, the file is not reindexed (unless --force is passed).

Demo

First index

me@localhost:~/src/typeorm/typeorm(master)$ tree-sitter-stack-graphs-typescript index -v --hide-error-details tsconfig.json package.json src/data-source/ src/entity-manager/
/Users/me/src/typeorm/typeorm/tsconfig.json: not supported
/Users/me/src/typeorm/typeorm/package.json: not supported
/Users/me/src/typeorm/typeorm/src/data-source/BaseDataSourceOptions.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/DataSource.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/DataSourceOptions.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/index.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManager.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManagerFactory.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/MongoEntityManager.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/SqljsEntityManager.ts: success

Cached index

me@localhost:~/src/typeorm/typeorm(master)$ tree-sitter-stack-graphs-typescript index -v --hide-error-details tsconfig.json package.json src/data-source/ src/entity-manager/
/Users/me/src/typeorm/typeorm/tsconfig.json: not supported
/Users/me/src/typeorm/typeorm/package.json: not supported
/Users/me/src/typeorm/typeorm/src/data-source/BaseDataSourceOptions.ts: cached
/Users/me/src/typeorm/typeorm/src/data-source/DataSource.ts: cached
/Users/me/src/typeorm/typeorm/src/data-source/DataSourceOptions.ts: cached
/Users/me/src/typeorm/typeorm/src/data-source/index.ts: cached
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManager.ts: cached
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManagerFactory.ts: cached
/Users/me/src/typeorm/typeorm/src/entity-manager/MongoEntityManager.ts: cached
/Users/me/src/typeorm/typeorm/src/entity-manager/SqljsEntityManager.ts: cached

Forced index

me@localhost:~/src/typeorm/typeorm(master)$ tree-sitter-stack-graphs-typescript index -v --hide-error-details --force tsconfig.json package.json src/data-source/ src/entity-manager/
/Users/me/src/typeorm/typeorm/tsconfig.json: not supported
/Users/me/src/typeorm/typeorm/package.json: not supported
/Users/me/src/typeorm/typeorm/src/data-source/BaseDataSourceOptions.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/DataSource.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/DataSourceOptions.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/index.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManager.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManagerFactory.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/MongoEntityManager.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/SqljsEntityManager.ts: success

Clean and re-index

me@localhost:~/src/typeorm/typeorm(master)$ tree-sitter-stack-graphs-typescript clean .

me@localhost:~/src/typeorm/typeorm(master)$ tree-sitter-stack-graphs-typescript index -v --hide-error-details tsconfig.json package.json src/data-source/ src/entity-manager/
/Users/me/src/typeorm/typeorm/tsconfig.json: not supported
/Users/me/src/typeorm/typeorm/package.json: not supported
/Users/me/src/typeorm/typeorm/src/data-source/BaseDataSourceOptions.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/DataSource.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/DataSourceOptions.ts: success
/Users/me/src/typeorm/typeorm/src/data-source/index.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManager.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/EntityManagerFactory.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/MongoEntityManager.ts: success
/Users/me/src/typeorm/typeorm/src/entity-manager/SqljsEntityManager.ts: success

Query definition

me@localhost:~/src/typeorm/typeorm(master)$ tree-sitter-stack-graphs-typescript query definition src/data-source/DataSource.ts 84 23
/Users/me/src/typeorm/typeorm/src/data-source/DataSource.ts:84:23: found definitions:
   0: /Users/me/src/typeorm/typeorm/src/data-source/DataSource.ts:6:10

github-actions · 2023-03-30T11:09:00Z

Performance Summary

Comparing base 6c96fb2 with head b83aea1 on microsoft/TypeScript@v4.9.5. For details see workflow artifacts. Note that performance is tested on the last commits with changes in stack-graphs, not on every commit.

Before

--------------------------------------------------------------------------------
Command:            base/target/release/tree-sitter-stack-graphs-typescript analyze --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 base-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
5.127^                            #                                           
     |                          ::#                                ::     ::  
     |                   ::     ::#                                ::     ::  
     |                   :      ::#                                ::     ::  
     |                   :      ::#                                ::     ::  
     |                   :      ::#                                ::     ::  
     |                  ::    ::::#                              :@::    :::  
     |          @       ::    : ::#        @  :                  :@::    :::  
     |          @       ::    : ::#        @  :                  :@::    :::  
     |         @@      :::   :: ::#       :@  :                 ::@::   ::::  
     |     @@  @@     ::::   :: ::#      ::@  :       : :       ::@::  @::::  
     |     @  @@@ :   ::::   :: ::#   :: ::@ ::      :: :  :   :::@:: :@::::  
   0 +----------------------------------------------------------------------->Gi
     0                                                                   221.5

After

--------------------------------------------------------------------------------
Command:            head/target/release/tree-sitter-stack-graphs-typescript index -D head.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 head-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
1.976^           #                                                            
     |           #                                                            
     |           #                                                            
     |           #                                                            
     |           #                                                            
     |           #                                                            
     |          @#                                                            
     |          @#                                                       :    
     |          @#           :        :                                  :    
     |         @@#       :   :     :  :                                : :    
     |         @@#     : : :::     ::::   : :       ::   :        : :::::::   
     |         @@#  :: ::: :::  :  :: : :::::  ::  @:: : :    :   :@:::: ::   
   0 +----------------------------------------------------------------------->Gi
     0                                                                   190.9

hendrikvanantwerpen · 2023-03-30T11:44:29Z

I am very surprised by the change in memory usage. I don't really know how to explain that 🤔

github-actions · 2023-04-03T13:50:10Z

Performance Summary

Comparing base 6c96fb2 with head 67db2ae on microsoft/TypeScript@v4.9.5. For details see workflow artifacts. Note that performance is tested on the last commits with changes in stack-graphs, not on every commit.

Before

--------------------------------------------------------------------------------
Command:            base/target/release/tree-sitter-stack-graphs-typescript analyze --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 base-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
5.127^                            #                                           
     |                          ::#                                ::     ::  
     |                   ::     ::#                                ::     ::  
     |                   :      ::#                                ::     ::  
     |                   :      ::#                                ::     ::  
     |                   :      ::#                                ::     ::  
     |                  ::    ::::#                              :@::    :::  
     |          @       ::    : ::#        @  :                  :@::    :::  
     |          @       ::    : ::#        @  :                  :@::    :::  
     |         @@      :::   :: ::#       :@  :                 ::@::   ::::  
     |     @@  @@     ::::   :: ::#      ::@  :       : :       ::@::  @::::  
     |     @  @@@ :   ::::   :: ::#   :: ::@ ::      :: :  :   :::@:: :@::::  
   0 +----------------------------------------------------------------------->Gi
     0                                                                   221.5

After

--------------------------------------------------------------------------------
Command:            head/target/release/tree-sitter-stack-graphs-typescript index -D head.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 head-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
3.139^             #                                                          
     |             #                                                          
     |             #                                                          
     |             #                                                          
     |             #                                                          
     |           @@#                                                          
     |           @ #                                                          
     |          @@ #                                                          
     |          @@ #                                                          
     |          @@ #                 ::                                       
     |          @@ #           :     : ::        : :                   :::    
     |     :    @@ #  ::   :::::    :: :  ::     : ::::   @       :: :::::    
   0 +----------------------------------------------------------------------->Gi
     0                                                                   237.3

rnkaufman · 2023-04-13T19:41:17Z

tree-sitter-stack-graphs/src/cli/index.rs

+                        source_root,
+                        &source_path,


Is it intended that only one of these is a reference? Same for lines 128-129

Good question! Both were passed by reference, but source_root was already a reference, while source_path was a value. However, Rick made a nice suggestion above that allows using source_path now.

rewinfrey

I think I have more questions than comments or suggestions 😄, but left a couple minor things for you to consider. I think the SQLite implementation and additional database commands look good to me.

rewinfrey · 2023-04-14T01:30:32Z

tree-sitter-stack-graphs/src/cli/database.rs

+}
+
+impl DatabaseArgs {
+    pub fn default_for_crate(crate_name: &str) -> anyhow::Result<PathBuf> {


Would it be possible to define the Default trait for DatabaseArgs? That would mean callers could use DatabaseArgs::default().

This method is perhaps a bit confusing here, since it does not actually create or act upon DatabaseArgs values. It's an associated method to easily get a default database location for a given crate name. I'll move this to be a module level function instead, so that it's clearer that it does not use DatabaseArgs in any way.

rewinfrey · 2023-04-14T01:36:21Z

tree-sitter-stack-graphs/src/cli/index.rs

        let mut seen_mark = false;
+        let mut db = SQLiteWriter::open(&db_path)?;
        for source_path in &self.source_paths {
+            let source_path = source_path.canonicalize()?;


It looks like source_path is used always as a reference. If that's the intent, could this be updated to let source_path = &source_path.canonicalize()?;

How about that, that works :). That's a bit cleaner!

I thought that the value created by canonicalize() would not live long enough if you immediately take the reference but don't capture the value itself as well. Here it is accepted, although I know sometimes it doesn't work. Now I'm not sure when it is or is not allowed 🤔.

rewinfrey · 2023-04-14T01:45:30Z

stack-graphs/src/assert.rs

+            }
+        }
+        Displayer(self, graph)
+    }


The inner Displayer struct here to close over self and graph is pretty clever!

It makes me think that AssertionSource could hold the graph as an additional field, and I think would let you implement the Display trait for AssertionSource directly, but that further complicates the AssertionSource struct with the graph lifetime, so I'm not sure it'd be worth spilling the complexity across the code base where AssertionSource is used for the sake of a single trait implementation.

You might be right, that we could capture the graph in the AssertionSource itself. Without having looked at all the current uses, I think this might make it a lot less flexible to use, though. As I recall, these are constructed from tests before the graph even exists (and their construction does not need a graph either). So capturing the graph earlier would restrict users quite a bit.

In one of the later following PRs I've dropped the use of AssertionSource in the CLI again, because it requires full LSP positions which require reading the source file to be calculated.

I looked in the source, and it is not exactly as I said. The graph must already exist, because we store a Handle<File> in AssertionSource. But I think my point is still valid, because capturing the graph would e.g. not allow any &mut references as long as the AssertionSource exists. In other words, it would still force a user to have the graph fully constructed before creating AssertionSources.

That's a great point that having a reference to the graph in AssertionSource would complicate &mut references elsewhere. I still think the current solution is 👍 and a nice way to handle this.

rewinfrey · 2023-04-14T01:47:30Z

stack-graphs/src/serde/partial.rs

+    pub(crate) scope_stack_precondition: PartialScopeStack,
+    pub(crate) scope_stack_postcondition: PartialScopeStack,
+    pub(crate) edges: PartialPathEdgeList,
 }


TIL pub(crate) visibility specifier, that's very handy 👍

rewinfrey · 2023-04-14T01:51:49Z

stack-graphs/src/stitching.rs

        graph: &StackGraph,
        partials: &mut PartialPaths,
-        db: &mut Database,
+        _db: &mut Database,


Is this parameter not needed now, or is this required for some other reason?

Initially it was there for consistency with the from_partial_paths method, which did use it. However, that was mostly because the constructors were already doing a bit of work. I've changed that at some point so that the constructor only sets up the stitcher, but doesn't do work until process_next_phase is called. Given that neither of the constructors use db anymore, I think we can remove it.

rewinfrey · 2023-04-14T01:57:42Z

stack-graphs/src/storage.rs

+        Ok(())
+    }
+
+    /// Add a partial path for a file to the database.  Throws an error if the file does not exist in


Small nit: Could this comment be updated to say Returns an error if the file does not exist?

rewinfrey · 2023-04-14T02:01:48Z

stack-graphs/src/storage.rs

+    }
+
+    /// Open a file database.  If the file does not exist, it is automatically created.
+    /// An error is thrown if the database version is not supported.


Small nit: Could this be updated to say An error is returned ... instead of throws?

rewinfrey · 2023-04-14T02:03:18Z

stack-graphs/src/storage.rs

+                "added path {} must start in given file {} or at root",
+                path.display(graph, partials),
+                graph[file].name()
+            );


General question: when a function can panic, should that be indicated in the comment for the function? I'm not sure if there is a Rust convention for that, and this isn't intended to be a suggestion here, it's only a drive-by question.

Good question. I think you're right that it is a good idea to add that in the comment!

…te comments to reflect current behavior

github-actions · 2023-04-14T10:22:52Z

Performance Summary

Comparing base 6c96fb2 with head 2b9e261 on microsoft/TypeScript@v4.9.5. For details see workflow artifacts. Note that performance is tested on the last commits with changes in stack-graphs, not on every commit.

Before

--------------------------------------------------------------------------------
Command:            base/target/release/tree-sitter-stack-graphs-typescript analyze --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 base-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
9.127^                             ##                                         
     |                             #                                          
     |                             #                                          
     |                             #                                          
     |                             #                                          
     |                             #                                          
     |                   :       ::#                                          
     |                   :       ::#                                          
     |                   :       ::#                                          
     |                   :      :::#       :   :                  :::    ::   
     |          @        :    :::::#       :   :                  ::     :    
     |     @@ ::@     :@@:   :: :::#       :   :      ::        ::::   :::    
   0 +----------------------------------------------------------------------->Gi
     0                                                                   217.1

After

--------------------------------------------------------------------------------
Command:            head/target/release/tree-sitter-stack-graphs-typescript index -D head.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 head-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
1.581^           #                                                            
     |           #                                                            
     |           #                                                            
     |           #                                                            
     |           #                                                            
     |          :#                                                            
     |          :#                  ::                                   :    
     |          :#                  ::              :                : : :    
     |          :#   @   :   :      ::              :    @           :::::    
     |     :   @:#   @ :::   :      :: :::          :    @         : :::::    
     |     :   @:#   @ : :   :     @:: ::   :       : :  @    :    :@::::::   
     |     :   @:#  @@ : :  ::     @:: :: : : : :: :: :::@ ::@:  :::@:::::::  
   0 +----------------------------------------------------------------------->Gi
     0                                                                   226.9

github-actions · 2023-04-14T10:31:32Z

Performance Summary

Comparing base 6c96fb2 with head 8a1df24 on microsoft/TypeScript@v4.9.5. For details see workflow artifacts. Note that performance is tested on the last commits with changes in stack-graphs, not on every commit.

Before

--------------------------------------------------------------------------------
Command:            base/target/release/tree-sitter-stack-graphs-typescript analyze --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 base-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
2.814^                            #                                           
     |                     :      #                                 :     :   
     |                     :      #                                 :     :   
     |                     :      #                                 :     :   
     |           @@        :      #                                 :     :   
     |           @         :     :#                                 :     :   
     |           @        ::     :#                                 @    ::   
     |          :@        ::     :#          :        :: ::         @    ::   
     |          :@        ::    ::#          :        :  :         :@   :::   
     |          :@        ::    ::#         ::        :  :         :@   :::   
     |          :@   :  ::::    ::#   :: :: ::        :  :        ::@ ::::: : 
     |      :  ::@   : :: :: :::::#   : :: ::: :    @::  :      ::::@ ::::: : 
   0 +----------------------------------------------------------------------->Gi
     0                                                                   181.1

After

--------------------------------------------------------------------------------
Command:            head/target/release/tree-sitter-stack-graphs-typescript index -D head.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 head-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
1.534^           #                                                            
     |           #                                                            
     |           #                                                            
     |      @@   #                                                            
     |      @    #                                                            
     |      @    #                                                       :    
     |      @    #                  :::                                  :    
     |      @  ::#                  ::              :                    :    
     |      @  : #          @:      ::         : :  :              : : :::    
     |     :@  : #     :    @:     :::  :      : :  :   ::         @ :::::    
     |    @:@  : #:    ::   @:   : ::: @:      : ::::   :      :   @::::::    
     |    @:@  : #:  :::: ::@: ::: ::: @:  @: :::::::  ::  :: :: ::@::::::::: 
   0 +----------------------------------------------------------------------->Gi
     0                                                                   221.9

hendrikvanantwerpen · 2023-04-14T12:20:29Z

@rewinfrey & @rnkaufman, thank you for taking a look at this. I think I addressed all your comments.

I've included one more change, which changes the command-line syntax for queries. Before, a query was query definition PATH LINE COLUMN. Now it is query definition PATH:LINE:COLUMN+.

I've done this for two reasons:

Multiple queries can be combined in one invocation. This is more flexible for the user, and might make it easier to do some automated profiling later.
This format is closer to the format we and many other tools use when printing source locations. This will make copy/pasting easier.

rewinfrey

👍 this looks great to me, thank you for the additional context and the answers 😄

rewinfrey · 2023-04-14T18:10:07Z

stack-graphs/src/assert.rs

+            }
+        }
+        Displayer(self, graph)
+    }


That's a great point that having a reference to the graph in AssertionSource would complicate &mut references elsewhere. I still think the current solution is 👍 and a nice way to handle this.

hendrikvanantwerpen self-assigned this Mar 24, 2023

hendrikvanantwerpen changed the base branch from query-analysis to more-serde March 24, 2023 13:08

hendrikvanantwerpen mentioned this pull request Mar 24, 2023

Add CLI flag to query analysis result #213

Closed

2 tasks

hendrikvanantwerpen marked this pull request as ready for review March 24, 2023 13:36

hendrikvanantwerpen requested a review from a team as a code owner March 24, 2023 13:36

hendrikvanantwerpen force-pushed the analysis-db branch from ec20740 to 308a435 Compare March 24, 2023 13:38

This was referenced Mar 24, 2023

Generate visualization from database #236

Merged

Generate visualization from file database #237

Closed

Implement (de)serialization for paths and database #230

Merged

Add skeleton LSP server and VSCode extension #238

Merged

Base automatically changed from more-serde to main March 29, 2023 07:41

hendrikvanantwerpen force-pushed the analysis-db branch 2 times, most recently from b31f519 to 05a73d2 Compare March 30, 2023 10:43

hendrikvanantwerpen mentioned this pull request Mar 30, 2023

Update performance CI for base branch #248

Merged

Hendrik van Antwerpen added 14 commits April 3, 2023 15:02

Make AsserionSource::*_iter methods public

623f11e

Implement Display for AssertionSource

81cdff4

Build whole project in single graph and database

8d49ca5

Implement CLI flag that allows querying the result of analysis

8a1ff9e

Stick with LSP terminology

97b33ca

Do not start work in the constructor

e30fbd8

Add storage module and basic in-memory implementation

999b6b5

Use storage types for analyze command

e70a10a

Implement storing and loading in memory sqlite database

8b2d51c

Rename analyze to index

c2367d7

Store database in file

285a736

Add flag to force analysis

750f646

Add clean method

1845ddf

Add clean command

69c157f

Hendrik van Antwerpen added 4 commits April 3, 2023 15:24

Add flag to delete database file and report clean results

67db2ae

Ensure different CLIs use different default databases

5df89d1

Reinstate performance CI

432b92d

Update expect message

451ebec

hendrikvanantwerpen changed the base branch from main to nice-tsg-errors April 3, 2023 13:27

hendrikvanantwerpen force-pushed the analysis-db branch from b6f0100 to 451ebec Compare April 3, 2023 13:28

hendrikvanantwerpen mentioned this pull request Apr 6, 2023

Implement indexing in the LSP server #251

Merged

Base automatically changed from nice-tsg-errors to main April 12, 2023 13:29

This was referenced Apr 13, 2023

Refactor clean methods #254

Merged

Introduce status command #255

Merged

Implement LSP Go to Definition #256

Merged

rnkaufman reviewed Apr 13, 2023

View reviewed changes

rewinfrey reviewed Apr 14, 2023

View reviewed changes

Hendrik van Antwerpen added 8 commits April 14, 2023 11:07

Follow common naming convention for iter methods

20dc8ab

Remove unused Database argument from stitcher constructors and upda…

6b355fe

…te comments to reflect current behavior

throws -> returns

845107b

Add some method doc comments

2b9e261

Move unrelated associated function to module

3e022ca

Take reference immediately

49e7bce

Clarify the semantics of SourcePosition::column

98f35a0

Update headers as well

8a1df24

Hendrik van Antwerpen added 2 commits April 14, 2023 14:12

Include expected format in error message

7ecbb2e

Allow multiple reference arguments to query

43f4af1

rewinfrey approved these changes Apr 14, 2023

View reviewed changes

hendrikvanantwerpen merged commit ed017a5 into main Apr 17, 2023

hendrikvanantwerpen deleted the analysis-db branch April 17, 2023 10:00

Implement file database for indexing and querying #235

Implement file database for indexing and querying #235

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hendrikvanantwerpen commented Apr 14, 2023

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hendrikvanantwerpen commented Mar 24, 2023 •

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