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ref(migrations): Add copy_tables command #3174

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ref(migrations): Add copy_tables command #3174

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MeredithAnya
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@MeredithAnya MeredithAnya commented Sep 21, 2022 •
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context:
We have some ClickHouse migrations tooling that currently used to run and reverse migrations in addition to list-ing the current status of migrations. This is great for existing datasets where we already have the clusters set up how we want. However, if we want to add a replica or a shard to an existing cluster we cannot easy do so.

add_node today:
There is some prior art which is the current add_node command. This basically runs all the migrations in order for a specific storage set on a new node. The end result is hopefully that the node is now in the same state as all the other nodes in the clusters. This works only in the case where the initial CREATE TABLE statement doesn't differ from what the current schema is.

why it doesn't quite work:
ClickHouse requires the table schema to be same in order to replicate any data. If we have a table that has gone through many schema iterations, the moment we try to run the 0001_add_table... migration, the table on the new node is in a different state than the other nodes in the cluster. When we try to grab parts from ZooKeeper to replicate data we will get some sort of error.

For example, in the case below, the first migration for the generic_metrics actually has multiple SQL operations, first CREATE TABLE, then ADD COLUMN (and then some other add columns/add indexes). But right after we run the first CREATE TABLE, we get an error about the _indexed_tags_hash missing, which makes sense because it hasn't been added yet (that was the next SQL statement).

15:41 $ snuba migrations add-node --type=local --storage-set=generic_metrics_sets --port=9051
migration <snuba.snuba_migrations.generic_metrics.0001_sets_aggregate_table.Migration object at 0x10f8d8790>
Traceback (most recent call last):
  File "/Users/meredith/snuba/snuba/clickhouse/native.py", line 192, in execute
    result_data = query_execute()
  File "/Users/meredith/snuba/.venv/lib/python3.8/site-packages/clickhouse_driver/client.py", line 304, in execute
    rv = self.process_ordinary_query(
  File "/Users/meredith/snuba/.venv/lib/python3.8/site-packages/clickhouse_driver/client.py", line 491, in process_ordinary_query
    return self.receive_result(with_column_types=with_column_types,
  File "/Users/meredith/snuba/.venv/lib/python3.8/site-packages/clickhouse_driver/client.py", line 151, in receive_result
    return result.get_result()
  File "/Users/meredith/snuba/.venv/lib/python3.8/site-packages/clickhouse_driver/result.py", line 50, in get_result
    for packet in self.packet_generator:
  File "/Users/meredith/snuba/.venv/lib/python3.8/site-packages/clickhouse_driver/client.py", line 167, in packet_generator
    packet = self.receive_packet()
  File "/Users/meredith/snuba/.venv/lib/python3.8/site-packages/clickhouse_driver/client.py", line 184, in receive_packet
    raise packet.exception
clickhouse_driver.errors.ServerException: Code: 47.
DB::Exception: Missing columns: '_indexed_tags_hash' while processing query: '_indexed_tags_hash', required columns: '_indexed_tags_hash', source columns: 'value' 'tags.raw_value' 'use_case_id' 'tags.key' 'tags.indexed_value' 'org_id' 'project_id' 'timestamp' 'retention_days' 'granularity' 'metric_id'. Stack trace:

solution
We don't really care about running the migrations in order, since as far as the cluster in concerned, the migrations are up to date (its just the new node that's not). Instead we can copy the current table statement, using SHOW CREATE TABLE, and the use that to create the tables on the new node. This way the schema should be identical to all the other nodes in the cluster, preventing any errors of missing columns, missing indexes etc.

In order to do this we need:

  • access a current node in the cluster to run the SHOW CREATE TABLE command
  • the table names that we actually want to copy over
  • access to the new node to run the collected table statements.

In this PR I've added the option to either pass in the list of table names, or for the command to do that automatically by running the SHOW TABLE command on the node we are copying the table statements from.

lynnagara
lynnagara reviewed Sep 21, 2022
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snuba/migrations/runner.py Outdated
@@ -418,3 +418,69 @@ def add_node(
elif isinstance(migration, CodeMigration):
for python_op in migration.forwards_global():
python_op.execute_new_node(storage_sets)

@classmethod
def create_tables(
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Can we call this copy_tables? To ensure there is no confusion about when to use and to keep it more distinct from the existing create table operation.

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yeah I originally had copy_and_create_tables but that felt too long. copy_tables i think is better

@MeredithAnya MeredithAnya force-pushed the meredith/new-add-node branch from cf02f22 to 3b278dd Compare October 3, 2022 16:44
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Codecov Report

Base: 92.75% // Head: 92.70% // Decreases project coverage by -0.04% ⚠️

Coverage data is based on head (3b278dd) compared to base (8e9f327).
Patch coverage: 10.52% of modified lines in pull request are covered.

Additional details and impacted files 
@@            Coverage Diff             @@
##           master    #3174      +/-   ##
==========================================
- Coverage   92.75%   92.70%   -0.05%     
==========================================
  Files         693      693              
  Lines       31396    31415      +19     
==========================================
+ Hits        29121    29123       +2     
- Misses       2275     2292      +17
Impacted Files Coverage Δ
snuba/migrations/runner.py 84.72% <10.52%> (-7.16%) ⬇️

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@MeredithAnya MeredithAnya changed the title ref(migrations): Add create_tables command ref(migrations): Add copy_tables command Oct 4, 2022
fpacifici
fpacifici reviewed Oct 5, 2022
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snuba/migrations/runner.py
user: str,
password: str,
database: str,
new_port: int,
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What is this for ?

snuba/migrations/runner.py
send_receive_timeout=client_settings.timeout,
)

# TODO: assert that the new node is not in the system.clusters definitions yet
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Did we discuss this before? Not sure why we want to enforce this.
Did you discuss this process with @nikhars and @mwarkentin ?
We want to make the addition of a new node quick, that means having as few manual steps as possible. adding the tables before adding the node to the cluster implies at least three steps: provision node, add tables, then add the node to the cluster.

I think we should ensure we are on the same page on the quickest process to add a node.

snuba/migrations/runner.py
Comment on lines +472 to +474
ch_table_names = [
result[0] for result in clickhouse.execute("SHOW TABLES").results
]
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I think this is going to be a bit fragile. If we trust the content of the tables on another node we should at least validate they are the same you have in the storage set you are trying to deploy on this node.
More in general, how do you expect this script to be used? Is the user going to tell "please duplicate this node" or is the user going to tell "Please create all the tables you should have on this node according to the storage sets on this cluster" ?

snuba/migrations/runner.py
Comment on lines +486 to +487
host_name,
new_port,
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Why are we assuming the host name is going to be the same? In most cases this is not going to be true.

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happened to be true for testing, but yes I should update to have a new_host_name param as well

@MeredithAnya MeredithAnya mentioned this pull request Oct 12, 2022
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Closing in favor of #3241, we may need to come back and add some cli command utility but we can do that in a new PR when the time comes

@MeredithAnya MeredithAnya deleted the meredith/new-add-node branch November 2, 2022 00:43
onkar added a commit that referenced this pull request Nov 1, 2024
@dependabot @onkar
chore(deps): bump urllib3 from 1.26.12 to 2.2.2 (#6036)
7dae163 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.12 to
2.2.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/urllib3/urllib3/releases">urllib3's
releases</a>.</em></p>
<blockquote>
<h2>2.2.2</h2>
<h2>🚀 urllib3 is fundraising for HTTP/2 support</h2>
<p><a
href="https://sethmlarson.dev/urllib3-is-fundraising-for-http2-support">urllib3
is raising ~$40,000 USD</a> to release HTTP/2 support and ensure
long-term sustainable maintenance of the project after a sharp decline
in financial support for 2023. If your company or organization uses
Python and would benefit from HTTP/2 support in Requests, pip, cloud
SDKs, and thousands of other projects <a
href="https://opencollective.com/urllib3">please consider contributing
financially</a> to ensure HTTP/2 support is developed sustainably and
maintained for the long-haul.</p>
<p>Thank you for your support.</p>
<h2>Changes</h2>
<ul>
<li>Added the <code>Proxy-Authorization</code> header to the list of
headers to strip from requests when redirecting to a different host. As
before, different headers can be set via
<code>Retry.remove_headers_on_redirect</code>.</li>
<li>Allowed passing negative integers as <code>amt</code> to read
methods of <code>http.client.HTTPResponse</code> as an alternative to
<code>None</code>. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3122">#3122</a>)</li>
<li>Fixed return types representing copying actions to use
<code>typing.Self</code>. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3363">#3363</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/urllib3/urllib3/compare/2.2.1...2.2.2">https://github.com/urllib3/urllib3/compare/2.2.1...2.2.2</a></p>
<h2>2.2.1</h2>
<h2>🚀 urllib3 is fundraising for HTTP/2 support</h2>
<p><a
href="https://sethmlarson.dev/urllib3-is-fundraising-for-http2-support">urllib3
is raising ~$40,000 USD</a> to release HTTP/2 support and ensure
long-term sustainable maintenance of the project after a sharp decline
in financial support for 2023. If your company or organization uses
Python and would benefit from HTTP/2 support in Requests, pip, cloud
SDKs, and thousands of other projects <a
href="https://opencollective.com/urllib3">please consider contributing
financially</a> to ensure HTTP/2 support is developed sustainably and
maintained for the long-haul.</p>
<p>Thank you for your support.</p>
<h2>Changes</h2>
<ul>
<li>Fixed issue where <code>InsecureRequestWarning</code> was emitted
for HTTPS connections when using Emscripten. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3331">#3331</a>)</li>
<li>Fixed <code>HTTPConnectionPool.urlopen</code> to stop automatically
casting non-proxy headers to <code>HTTPHeaderDict</code>. This change
was premature as it did not apply to proxy headers and
<code>HTTPHeaderDict</code> does not handle byte header values correctly
yet. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3343">#3343</a>)</li>
<li>Changed <code>ProtocolError</code> to
<code>InvalidChunkLength</code> when response terminates before the
chunk length is sent. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/2860">#2860</a>)</li>
<li>Changed <code>ProtocolError</code> to be more verbose on incomplete
reads with excess content. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3261">#3261</a>)</li>
</ul>
<h2>2.2.0</h2>
<h2>🖥️ urllib3 now works in the browser</h2>
<p>:tada: <strong>This release adds experimental support for <a
href="https://urllib3.readthedocs.io/en/stable/reference/contrib/emscripten.html">using
urllib3 in the browser with Pyodide</a>!</strong> 🎉</p>
<p>Thanks to Joe Marshall (<a
href="https://github.com/joemarshall"><code>@​joemarshall</code></a>)
for contributing this feature. This change was possible thanks to work
done in urllib3 v2.0 to detach our API from <code>http.client</code>.
Please report all bugs to the <a
href="https://github.com/urllib3/urllib3/issues">urllib3 issue
tracker</a>.</p>
<h2>🚀 urllib3 is fundraising for HTTP/2 support</h2>
<p><a
href="https://sethmlarson.dev/urllib3-is-fundraising-for-http2-support">urllib3
is raising ~$40,000 USD</a> to release HTTP/2 support and ensure
long-term sustainable maintenance of the project after a sharp decline
in financial support for 2023. If your company or organization uses
Python and would benefit from HTTP/2 support in Requests, pip, cloud
SDKs, and thousands of other projects <a
href="https://opencollective.com/urllib3">please consider contributing
financially</a> to ensure HTTP/2 support is developed sustainably and
maintained for the long-haul.</p>
<p>Thank you for your support.</p>
<h2>Changes</h2>
<ul>
<li>Added support for <a
href="https://urllib3.readthedocs.io/en/latest/reference/contrib/emscripten.html">Emscripten
and Pyodide</a>, including streaming support in cross-origin isolated
browser environments where threading is enabled. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/2951">#2951</a>)</li>
<li>Added support for <code>HTTPResponse.read1()</code> method. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3186">#3186</a>)</li>
<li>Added rudimentary support for HTTP/2. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3284">#3284</a>)</li>
<li>Fixed issue where requests against urls with trailing dots were
failing due to SSL errors
when using proxy. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/2244">#2244</a>)</li>
<li>Fixed <code>HTTPConnection.proxy_is_verified</code> and
<code>HTTPSConnection.proxy_is_verified</code> to be always set to a
boolean after connecting to a proxy. It could be <code>None</code> in
some cases previously. (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3130">#3130</a>)</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/urllib3/urllib3/blob/main/CHANGES.rst">urllib3's
changelog</a>.</em></p>
<blockquote>
<h1>2.2.2 (2024-06-17)</h1>
<ul>
<li>Added the <code>Proxy-Authorization</code> header to the list of
headers to strip from requests when redirecting to a different host. As
before, different headers can be set via
<code>Retry.remove_headers_on_redirect</code>.</li>
<li>Allowed passing negative integers as <code>amt</code> to read
methods of <code>http.client.HTTPResponse</code> as an alternative to
<code>None</code>.
(<code>[#3122](urllib3/urllib3#3122)
&lt;https://github.com/urllib3/urllib3/issues/3122&gt;</code>__)</li>
<li>Fixed return types representing copying actions to use
<code>typing.Self</code>.
(<code>[#3363](urllib3/urllib3#3363)
&lt;https://github.com/urllib3/urllib3/issues/3363&gt;</code>__)</li>
</ul>
<h1>2.2.1 (2024-02-16)</h1>
<ul>
<li>Fixed issue where <code>InsecureRequestWarning</code> was emitted
for HTTPS connections when using Emscripten.
(<code>[#3331](urllib3/urllib3#3331)
&lt;https://github.com/urllib3/urllib3/issues/3331&gt;</code>__)</li>
<li>Fixed <code>HTTPConnectionPool.urlopen</code> to stop automatically
casting non-proxy headers to <code>HTTPHeaderDict</code>. This change
was premature as it did not apply to proxy headers and
<code>HTTPHeaderDict</code> does not handle byte header values correctly
yet. (<code>[#3343](urllib3/urllib3#3343)
&lt;https://github.com/urllib3/urllib3/issues/3343&gt;</code>__)</li>
<li>Changed <code>InvalidChunkLength</code> to
<code>ProtocolError</code> when response terminates before the chunk
length is sent.
(<code>[#2860](urllib3/urllib3#2860)
&lt;https://github.com/urllib3/urllib3/issues/2860&gt;</code>__)</li>
<li>Changed <code>ProtocolError</code> to be more verbose on incomplete
reads with excess content.
(<code>[#3261](urllib3/urllib3#3261)
&lt;https://github.com/urllib3/urllib3/issues/3261&gt;</code>__)</li>
</ul>
<h1>2.2.0 (2024-01-30)</h1>
<ul>
<li>Added support for <code>Emscripten and Pyodide
&lt;https://urllib3.readthedocs.io/en/latest/reference/contrib/emscripten.html&gt;</code><strong>,
including streaming support in cross-origin isolated browser
environments where threading is enabled.
(<code>[#2951](urllib3/urllib3#2951)
&lt;https://github.com/urllib3/urllib3/issues/2951&gt;</code></strong>)</li>
<li>Added support for <code>HTTPResponse.read1()</code> method.
(<code>[#3186](urllib3/urllib3#3186)
&lt;https://github.com/urllib3/urllib3/issues/3186&gt;</code>__)</li>
<li>Added rudimentary support for HTTP/2.
(<code>[#3284](urllib3/urllib3#3284)
&lt;https://github.com/urllib3/urllib3/issues/3284&gt;</code>__)</li>
<li>Fixed issue where requests against urls with trailing dots were
failing due to SSL errors
when using proxy.
(<code>[#2244](urllib3/urllib3#2244)
&lt;https://github.com/urllib3/urllib3/issues/2244&gt;</code>__)</li>
<li>Fixed <code>HTTPConnection.proxy_is_verified</code> and
<code>HTTPSConnection.proxy_is_verified</code>
to be always set to a boolean after connecting to a proxy. It could be
<code>None</code> in some cases previously.
(<code>[#3130](urllib3/urllib3#3130)
&lt;https://github.com/urllib3/urllib3/issues/3130&gt;</code>__)</li>
<li>Fixed an issue where <code>headers</code> passed in a request with
<code>json=</code> would be mutated
(<code>[#3203](urllib3/urllib3#3203)
&lt;https://github.com/urllib3/urllib3/issues/3203&gt;</code>__)</li>
<li>Fixed <code>HTTPSConnection.is_verified</code> to be set to
<code>False</code> when connecting
from a HTTPS proxy to an HTTP target. It was set to <code>True</code>
previously.
(<code>[#3267](urllib3/urllib3#3267)
&lt;https://github.com/urllib3/urllib3/issues/3267&gt;</code>__)</li>
<li>Fixed handling of new error message from OpenSSL 3.2.0 when
configuring an HTTP proxy as HTTPS
(<code>[#3268](urllib3/urllib3#3268)
&lt;https://github.com/urllib3/urllib3/issues/3268&gt;</code>__)</li>
<li>Fixed TLS 1.3 post-handshake auth when the server certificate
validation is disabled
(<code>[#3325](urllib3/urllib3#3325)
&lt;https://github.com/urllib3/urllib3/issues/3325&gt;</code>__)</li>
<li>Note for downstream distributors: To run integration tests, you now
need to run the tests a second
time with the <code>--integration</code> pytest flag.
(<code>[#3181](urllib3/urllib3#3181)
&lt;https://github.com/urllib3/urllib3/issues/3181&gt;</code>__)</li>
</ul>
<h1>2.1.0 (2023-11-13)</h1>
<ul>
<li>Removed support for the deprecated urllib3[secure] extra.
(<code>[#2680](urllib3/urllib3#2680)
&lt;https://github.com/urllib3/urllib3/issues/2680&gt;</code>__)</li>
<li>Removed support for the deprecated SecureTransport TLS
implementation.
(<code>[#2681](urllib3/urllib3#2681)
&lt;https://github.com/urllib3/urllib3/issues/2681&gt;</code>__)</li>
<li>Removed support for the end-of-life Python 3.7.
(<code>[#3143](urllib3/urllib3#3143)
&lt;https://github.com/urllib3/urllib3/issues/3143&gt;</code>__)</li>
<li>Allowed loading CA certificates from memory for proxies.
(<code>[#3065](urllib3/urllib3#3065)
&lt;https://github.com/urllib3/urllib3/issues/3065&gt;</code>__)</li>
<li>Fixed decoding Gzip-encoded responses which specified
<code>x-gzip</code> content-encoding.
(<code>[#3174](urllib3/urllib3#3174)
&lt;https://github.com/urllib3/urllib3/issues/3174&gt;</code>__)</li>
</ul>
<h1>2.0.7 (2023-10-17)</h1>
<ul>
<li>Made body stripped from HTTP requests changing the request method to
GET after HTTP 303 &quot;See Other&quot; redirect responses.</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/urllib3/urllib3/commit/27e2a5c5a7ab6a517252cc8dcef3ffa6ffb8f61a"><code>27e2a5c</code></a>
Release 2.2.2 (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3406">#3406</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/accff72ecc2f6cf5a76d9570198a93ac7c90270e"><code>accff72</code></a>
Merge pull request from GHSA-34jh-p97f-mpxf</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/34be4a57e59eb7365bcc37d52e9f8271b5b8d0d3"><code>34be4a5</code></a>
Pin CFFI to a new release candidate instead of a Git commit (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3398">#3398</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/da410581b6b3df73da976b5ce5eb20a4bd030437"><code>da41058</code></a>
Bump browser-actions/setup-chrome from 1.6.0 to 1.7.1 (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3399">#3399</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/b07a669bd970d69847801148286b726f0570b625"><code>b07a669</code></a>
Bump github/codeql-action from 2.13.4 to 3.25.6 (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3396">#3396</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/b8589ec9f8c4da91511e601b632ac06af7e7c10e"><code>b8589ec</code></a>
Measure coverage with v4 of artifact actions (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3394">#3394</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/f3bdc5585111429e22c81b5fb26c3ec164d98b81"><code>f3bdc55</code></a>
Allow triggering CI manually (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3391">#3391</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/52392654b30183129cf3ec06010306f517d9c146"><code>5239265</code></a>
Fix HTTP version in debug log (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3316">#3316</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/b34619f94ece0c40e691a5aaf1304953d88089de"><code>b34619f</code></a>
Bump actions/checkout to 4.1.4 (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3387">#3387</a>)</li>
<li><a
href="https://github.com/urllib3/urllib3/commit/9961d14de7c920091d42d42ed76d5d479b80064d"><code>9961d14</code></a>
Bump browser-actions/setup-chrome from 1.5.0 to 1.6.0 (<a
href="https://redirect.github.com/urllib3/urllib3/issues/3386">#3386</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/urllib3/urllib3/compare/1.26.12...2.2.2">compare
view</a></li>
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