HBASE-26614 Refactor code related to "dump"ing ZK nodes

The code starting at ZKUtil.dump(ZKWatcher) is a small mess – it has cyclic dependencies woven
through itself, ZKWatcher and RecoverableZooKeeper. It also initializes a static variable in
ZKUtil through the factory for RecoverableZooKeeper instances. Let's decouple and clean it
up.

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GITHUB PR
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git revision
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compile
https://ci-hadoop.apache.org/job/HBase/job/HBase-PreCommit-GitHub-PR/job/PR-3969/3/artifact/yetus-general-check/output/patch-compile-hbase-zookeeper.txt

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https://ci-hadoop.apache.org/job/HBase/job/HBase-PreCommit-GitHub-PR/job/PR-3969/3/artifact/yetus-general-check/output/patch-compile-hbase-zookeeper.txt

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git revision
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Default Java
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Is the replication unit result in the precommit a repeatable failure?

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Are there any shell scripts which might have called the old dump() static method you removed?

Oh, nice thinking. Yeah, looks like admin.rb.
$ find . -type f ! -iname '*.java' -exec grep -iIn 'ZKUtil' {} \+
./bin/draining_servers.rb:29:java_import org.apache.hadoop.hbase.zookeeper.ZKUtil
./bin/draining_servers.rb:96:      ZKUtil.createAndFailSilent(zkw, node)
./bin/draining_servers.rb:113:      ZKUtil.deleteNodeFailSilent(zkw, node)
./bin/draining_servers.rb:129:    servers = ZKUtil.listChildrenNoWatch(zkw, parentZnode)
./CHANGES.txt:1126:   HBASE-3633  ZKUtil::createSetData should only create a node when it
./hbase-server/target/classes/hbase-webapps/master/zk.jsp:22:  import="org.apache.hadoop.hbase.zookeeper.ZKUtil"
./hbase-server/target/classes/hbase-webapps/master/zk.jsp:41:                    <pre><%= StringEscapeUtils.escapeHtml4(ZKUtil.dump(watcher).trim()) %></pre>
./hbase-server/src/main/resources/hbase-webapps/master/zk.jsp:22:  import="org.apache.hadoop.hbase.zookeeper.ZKUtil"
./hbase-server/src/main/resources/hbase-webapps/master/zk.jsp:41:                    <pre><%= StringEscapeUtils.escapeHtml4(ZKUtil.dump(watcher).trim()) %></pre>
./hbase-archetypes/hbase-client-project/target/classes/log4j2.xml:90:    <Logger name="org.apache.hadoop.hbase.zookeeper.ZKUtil" level="debug"/>
./hbase-archetypes/hbase-client-project/target/build-archetype/src/main/resources/log4j2.xml:90:    <Logger name="org.apache.hadoop.hbase.zookeeper.ZKUtil" level="debug"/>
./hbase-archetypes/hbase-client-project/src/main/resources/log4j2.xml:90:    <Logger name="org.apache.hadoop.hbase.zookeeper.ZKUtil" level="debug"/>
./hbase-archetypes/hbase-shaded-client-project/target/classes/log4j2.xml:90:    <Logger name="org.apache.hadoop.hbase.zookeeper.ZKUtil" level="debug"/>
./hbase-archetypes/hbase-shaded-client-project/target/build-archetype/src/main/resources/log4j2.xml:90:    <Logger name="org.apache.hadoop.hbase.zookeeper.ZKUtil" level="debug"/>
./hbase-archetypes/hbase-shaded-client-project/src/main/resources/log4j2.xml:90:    <Logger name="org.apache.hadoop.hbase.zookeeper.ZKUtil" level="debug"/>
./.git/COMMIT_EDITMSG:3:This refactor reduces the size and scope of the `ZKUtil` class. The core of this refactor is
./.git/COMMIT_EDITMSG:4:moving the `login*` methods from `ZKUtil` into their own class, `ZKAuthentication`. The class
./.git/COMMIT_EDITMSG:26:#      modified:   hbase-zookeeper/src/main/java/org/apache/hadoop/hbase/zookeeper/ZKUtil.java
./.git/COMMIT_EDITMSG:28:#      modified:   hbase-zookeeper/src/test/java/org/apache/hadoop/hbase/zookeeper/TestZKUtilNoServer.java
./conf/log4j2.xml:90:    <Logger name="org.apache.hadoop.hbase.zookeeper.ZKUtil" level="debug"/>
./hbase-shell/target/classes/hbase/admin.rb:480:      org.apache.hadoop.hbase.zookeeper.ZKUtil.dump(@zk_wrapper)
./hbase-shell/src/main/ruby/hbase/admin.rb:480:      org.apache.hadoop.hbase.zookeeper.ZKUtil.dump(@zk_wrapper)

Is it possible to deprecate the old method and have it just call the new location of the utility in the ZKDump class instead?

I could, but why? You want to protect users who are calling into an IA.Private class?

Is the replication unit result in the precommit a repeatable failure?

I don't think so but I don't have logs from the failed test runs. Let's see if it's still there for the next one.

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I think this error prone failure is not related to my change. Mike is working on a fix/upgrade over on #3979

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I think this error prone failure is not related to my change. Mike is working on a fix/upgrade over on #3979

It is related.
You call MetaTableLocator.getMetaRegionLocation in ZKDump but the method has a RestrictedApi annotation which only allow calling from ZKUtil and tests code. Since you just move some code in ZKUtil out to a separated class, you need to change the RestrictedApi annotation in MetaTableLocator.
Thanks.

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I think this error prone failure is not related to my change. Mike is working on a fix/upgrade over on #3979

It is related.
You call MetaTableLocator.getMetaRegionLocation in ZKDump but the method has a RestrictedApi annotation which only allow calling from ZKUtil and tests code. Since you just move some code in ZKUtil out to a separated class, you need to change the RestrictedApi annotation in MetaTableLocator.
Thanks.

Have you seen this comment? @ndimiduk
Please update the RestrictedApi annotation in MetaTableLocator.
Thanks.

Thanks for the mention @Apache9 . I did miss your earlier comment. You are correct in that my patch introduces an ErrorProne violation according to the annotation that you point how. However, I didn't know this because the use of that annotation in out code is not compatible with the version of ErrorProne run by Yetus on pre-commit. I think Mike's patch that upgrades ErrorProne will fix this, but I'll need to do some testing to be sure.
In the mean time, let me progress on this ticket.

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@joshelser do you mind if we address your code comments in a subsequent change? I'd like to keep this one isolated to the relocations only, as much as possible.

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Unit test failure looks like HBASE-26651.

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git revision
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https://github.com/apache/hbase/pull/3969

Optional Tests
javac javadoc unit shadedjars compile

uname
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Argh. Build 9 Jdk11/Hadoop3 failed due to Read-only file system.

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Optional Tests
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uname
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git revision
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javac
https://ci-hadoop.apache.org/job/HBase/job/HBase-PreCommit-GitHub-PR/job/PR-3969/11/artifact/yetus-general-check/output/diff-compile-javac-hbase-zookeeper.txt

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https://github.com/apache/hbase/pull/3969

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RuntimeError: shape '[32, 2, 64, 4096]' is invalid for input of size 26214400

I am getting the RuntimeError: shape '[32, 2, 64, 4096]' is invalid for input of size 26214400 after trying to combine vigogne weights with llama 13B and 30B huggingface models converted. it does work well with the 7B.
And here the RuntimeError from the 30B model -> RuntimeError: shape '[32, 2, 64, 4096]' is invalid for input of size 44302336
Here is the command used to combine weights:
python ../scripts/export_state_dict_checkpoint.py \
--base_model_name_or_path "../../llama-13b-hf"
--lora_model_name_or_path "bofenghuang/vigogne-lora-13b"
--output_dir ./models/13B

Hi @S0mbr3 !
Thanks for pointing this out!
Just pushed the modif which adds config for other checkpoints. Now you can run with:
python ../scripts/export_state_dict_checkpoint.py \
    --base_model_name_or_path "../../llama-13b-hf" \
    --lora_model_name_or_path "bofenghuang/vigogne-lora-13b" \
    --output_dir ./models/13B \
    --checkpoint_size "13b"


ReadME - Mac qt5.4.2 deprecated/EOL

The qt5.4.2 links toward the bottom of the ReadME are broken, due to 5.4.2's deprecation.
5.9.0 is out now.. will it still work?
https://download.qt.io/official_releases/qt/5.9/5.9.0/

@cbake6807 yeah we're going to port webkit for 5.9

yes, it will work if webkit is also compiled along side it.

PR #171 updates the link and version to 5.5 to match the version specified in build.sh


Altered attribute type checking for different Integer types

Changed the flow so that the different integer types Integer16,
Integer32, Integer64 would be handled in a way that non 64-bit
architectures could handle them correctly.
(First open source contribution don't kill me)

Thanks for the PR! And congrats on your first open source contribution :smile:
Left a few comments. Could you please push some fixes and we should be good to merge!

Thanks! :boom:


Spotify not fit in wtm

Hi.  It appears as a floating one.

Problem with spotify, the way it renders it will spawn 2 windows, which breaks tiling on many window managers including hyprland, sway, qtile wayland etc.
What you can do is create a script that will tile the program after a few ms, in other words when the entire hurdurr I spawn window in window bs is over.

Spotify


Adding alternate configuration sources

I'm submitting a...

[x] Feature

Checklist

[x] Commit Messages follow the Conventional Commits pattern

Description
Adding multiple configuration sources. The new behavior is first to read from the command line ng-package file, then read from the default ng-package.json file (if different from the command line file), then read from the ngPackage field from package.json. All configuration sources are merged using lodash in that order. This should lay the groundwork for extending multiple configs, should we want to. The primary motivation for this feature is #167.
Does this PR introduce a breaking change?

[x] No -> Care was taken to ensure the behavior is the same as before, if the feature is not used.

I did most of the feature work, but something isn't quite right that's causing the tests to fail. At first glance, I don't see anything obviously wrong. @dherges, maybe you know what's broken.

Hmpf, first, can you try to git rebase or git reset your branch to the current master of this repo?
The build error on circle is:
BUILD ERROR
ENOENT: no such file or directory, open '/home/ubuntu/ng-packagr/dist/lib/conf/tsconfig.ngc.json'
Error: ENOENT: no such file or directory, open '/home/ubuntu/ng-packagr/dist/lib/conf/tsconfig.ngc.json'

module.js:473
      throw err;
      ^

Error: Cannot find module '/home/ubuntu/ng-packagr/dist/cli/ng-packagr.js'
    at Function.Module._resolveFilename (module.js:527:15)
      ^

So maybe a relative import path is wrong? Or the process.cwd() somehow stopped things from working?

ng-packagr/dist/lib/conf/tsconfig.ngc.json ... is something in the typescript compiler wrong? During the yarn build? Because the postbuild should copy that json file to the dist folder

Please don't merge yet - I'm adding a test.

Ready for review.

Double-checked the changes on a larger project and everything still :green_apple:  !
The only thing is the $schema for the json editing support in IDE. How can we get it to work?


fix(versions): update Activiti/activiti-cloud-full-chart-security versions

UpdateBot pushed helm dependency: activiti-cloud-full-example to: 7.1.138

UpdateBot commands:
updatebot push-version --kind helm activiti-cloud-full-example 7.1.138


[stemcells>3312] syslogd on all VMs has memory leak

We're observing syslogd using an excessive amount of memory on all stemcells >3312 (i.e. 3312.x series). This seems to be related to the version of rsyslogd, which got updated from  8.22.0-0adiscon1trusty1 in 3312 to 8.23.0-0adiscon1trusty1  in 3312.3-3312.8.
This prevents us from using most recent 3312.x stemcells which contain important security fixes.
dpkg_l.txt for 3312 stemcell has:
 ii rsyslog                            8.22.0-0adiscon1trusty1           amd64        a rocket-fast system for log processing
ii  rsyslog-gnutls                     8.22.0-0adiscon1trusty1           amd64        TLS protocol support for rsyslog
ii  rsyslog-mmjsonparse                8.22.0-0adiscon1trusty1           amd64        Parsing/handling of CEE/Lumberjack JSON messages in rsyslog
ii  rsyslog-relp                       8.22.0-0adiscon1trusty1

e.g. 3312.8 has:
ii rsyslog                            8.23.0-0adiscon1trusty1           amd64        a rocket-fast system for log processing
ii  rsyslog-gnutls                     8.23.0-0adiscon1trusty1           amd64        TLS protocol support for rsyslog
ii  rsyslog-mmjsonparse                8.23.0-0adiscon1trusty1           amd64        Parsing/handling of CEE/Lumberjack JSON messages in rsyslog
ii  rsyslog-relp                       8.23.0-0adiscon1trusty1

This update probably happened because the base_os step to install packages on Ubuntu uses a PPA to install rsyslog which just contains 'latest v8 version' of rsyslog.
Here some numbers from random VMs showing that rsyslogd consumes way more memory in version 8.23.0 than it did in version 8.22.0:
version 8.23.0:
# ps -p 17469 -fv
  PID TTY      STAT   TIME  MAJFL   TRS   DRS   RSS %MEM COMMAND
17469 ?        Ssl   22:16     86<PHONE_NUMBER> 3961352 51.7 /usr/sbin/rsyslogd

# rsyslogd -version
rsyslogd 8.23.0, compiled with:
        PLATFORM:                               x86_64-pc-linux-gnu
        PLATFORM (lsb_release -d):
        FEATURE_REGEXP:                         Yes
        GSSAPI Kerberos 5 support:              No
        FEATURE_DEBUG (debug build, slow code): No
        32bit Atomic operations supported:      Yes
        64bit Atomic operations supported:      Yes
        memory allocator:                       system default
        Runtime Instrumentation (slow code):    No
        uuid support:                           Yes
        Number of Bits in RainerScript integers: 64

Version 8.22.0:
# ps -p 2088 -fv
  PID TTY      STAT   TIME  MAJFL   TRS   DRS   RSS %MEM COMMAND
 2088 ?        Ssl    0:06      1   557<PHONE_NUMBER>  0.1 /usr/sbin/rsyslogd

# rsyslogd -version
rsyslogd 8.22.0, compiled with:
        PLATFORM:                               x86_64-pc-linux-gnu
        PLATFORM (lsb_release -d):
        FEATURE_REGEXP:                         Yes
        GSSAPI Kerberos 5 support:              No
        FEATURE_DEBUG (debug build, slow code): No
        32bit Atomic operations supported:      Yes
        64bit Atomic operations supported:      Yes
        memory allocator:                       system default
        Runtime Instrumentation (slow code):    No
        uuid support:                           Yes
        Number of Bits in RainerScript integers: 64

Interestingly enough, most CF components continue to work, there are however other services that don't cope well if co-located with a memory hog.

does the memory usage continue to increase over time? or is it stable, but just much higher than before?
what's the rsyslog.conf file?

Our 00-forwarder.conf contains:
$ModLoad imuxsock                       # local message reception (rsyslog uses a datagram socket)
$MaxMessageSize 10240 # default is 2k
$WorkDirectory /var/vcap/sys/rsyslog/buffered # where messages should be buffered on disk

# Forward vcap messages to the aggregator
#
$ActionResumeRetryCount -1              # Try until the server becomes available
$ActionQueueType LinkedList             # Allocate on-demand
$ActionQueueFileName agg_backlog        # Spill to disk if queue is full
$ActionQueueMaxDiskSpace 32m            # Max size for disk queue
$ActionQueueLowWaterMark 2000           # Num messages. Assuming avg size of 512B, this is 1MiB.
$ActionQueueHighWaterMark 8000          # Num messages. Assuming avg size of 512B, this is 4MiB. (If this is reached, messages will spill to disk until the low watermark is reached).
$ActionQueueTimeoutEnqueue 0            # Discard messages if the queue + disk is full
$ActionQueueSaveOnShutdown on           # Save in-memory data to disk if rsyslog shuts down

# Listen for logs over UDP
#
$ModLoad imudp
$UDPServerAddress <IP_ADDRESS>cd
$UDPServerRun 514

template(name="CfLogTemplate" type="list") {
        constant(value="<")
        property(name="pri")
        constant(value=">")
        property(name="timestamp" dateFormat="rfc3339")

          constant(value=" <IP_ADDRESS> ")

        property(name="programname")
        constant(value=" [job=dummy_z1 index=0] ")
        property(name="msg")
}

*.* @@<IP_ADDRESS>:5514;CfLogTemplate

# Log vcap messages locally, too
#$template VcapComponentLogFile, "/var/log/%programname:6:$%/%programname:6:$%.log"
#$template VcapComponentLogFormat, "%timegenerated% %syslogseverity-text% -- %msg%\n"
#:programname, startswith, "vcap." -?VcapComponentLogFile;VcapComponentLogFormat

# Prevent them from reaching anywhere else
:programname, startswith, "vcap." ~

which is basically what metron agent configures. I.e. we send logs via TCP.
We executed the following script on 2 VMs with stemcell 3312.7 and 3312:
while :
do
  logger $RANDOM'TESTTESTSTESTTEST{"timestamp":1481736578.1486158,"message":"(0.000462s) SELECT * FROM \"apps\" WHERE (\"apps\".\"guid\" = a7887e60-6535-4b27-af62-93b11f3f8701) LIMIT 1","log_level":"info","source":"cc.db","data":{"request_guid":"2f5c02f9-aaae-4052-4106-57dfe0548273::8d753b9f-953c-4613-9b7f-71aa9f0b4b49"},"thread_id":47186750830220,"fiber_id":47186770028100'
done

Additional observation: our remote TCP log endpoint (an ELK) is not stable but seems to reset connections quite often.
Using stemcell 3312.7 (rsyslogd 8.23.0) we see increasing memory consumption and the following message in /var/log/syslog:
Dec 15 14:22:11 localhost rsyslogd: action 'action 0' resumed (module 'builtin:omfwd') [v8.23.0 try http://www.rsyslog.com/e/2359 ]
Dec 15 14:22:11 localhost rsyslogd: action 'action 0' resumed (module 'builtin:omfwd') [v8.23.0 try http://www.rsyslog.com/e/2359 ]
Dec 15 14:22:11 localhost rsyslogd: action 'action 0' resumed (module 'builtin:omfwd') [v8.23.0 try http://www.rsyslog.com/e/2359 ]
Dec 15 14:22:11 localhost rsyslogd: action 'action 0' resumed (module 'builtin:omfwd') [v8.23.0 try http://www.rsyslog.com/e/2359 ]
Dec 15 14:22:11 localhost rsyslogd: action 'action 0' resumed (module 'builtin:omfwd') [v8.23.0 try http://www.rsyslog.com/e/2359 ]

On stemcell 3312 (rsyslogd 8.22.0), memory consumption is stable and we don't see the messages above in /var/log/syslog.
Therefore our conclusion is that there is a memory leak in rsyslog 8.23.0 when the remote syslog endpoint is not stable.

Thank you for this detailed investigation.
We're currently working to build os-images with rsyslog pinned to version 8.22.0-0adiscon1trusty1.
We see that a version 8.24 was recently release, but the Changelog for that version makes no mention of a fix for the issue.

Would it be possible to run, for a test, rsyslog under valgrind control (best in an interactive session)?

@voelzmo do you think you can try valgrind in your environment?

@rgerhards You mean with version 8.23 to get a better understanding of where the memory leak is coming from? I can ask out operations people to take a look at that. Any specific options you would like us to set for valgrind so it is most useful for you?

I attached the output of an experiment with valgrind on rsyslog 8.23 to the issue there.

What I have now to reproduce the problem on bosh-lite:

A bosh deployment of the syslog release 9 with the stemcell 3312.9 and haproxy from the cf release 249, here is the manifest: manifest.yml. Note that it won't deploy cleanly as the haproxy misses a pem file and doesn't start successfully.
Manual reconfiguration of the haproxy, here is the changed /var/vcap/jobs/haproxy/config/haproxy.conf. Start the haproxy manually on the vm with /var/vcap/jobs/haproxy/bin/haproxy_ctl start.

Then on that vm run a command to produce log entries: while : ; do logger hallo $RANDOM ; sleep .5 ; done & and watch the RES size of the rsyslogd increase slowly...

Let me know if this is similar to what you're seeing.
rsyslog is configured to buffer, but in one of our environments, what happens is that rsyslog
vcap      4430  2.5  0.6<PHONE_NUMBER>0 ?        Ssl  17:49   0:00 /usr/sbin/rsyslogd

tries to buffer to /var/vcap/sys/rsyslog/buffered, but it's owned by syslog:adm
6286cb9cbeca:~$ ls -dl /var/vcap/sys/rsyslog/buffered
drwxr-xr-x 2 syslog adm 4096 Jun 27 17:14 /var/vcap/sys/rsyslog/buffered

Resulting in permission errors:
[pid  2840] open("/var/vcap/sys/rsyslog/buffered/agg_backlog.00000001", O_WRONLY|O_CREAT|O_NOCTTY|O_CLOEXEC, 0600) = -1 EACCES (Permission denied)

The way to confirm that this is the case is to validate that the rsyslogd user is vcap, and that the /var/vcap/sys/rsyslog/buffered owner is syslog:adm.

What is the status of this issue?  Has this been resolved?

Syslog was pinned back to 8.22 near after the time of this issue, and has
remained at that version in subsequent stemcell series.
On Tue, Oct 10, 2017 at 1:42 PM Paul Nath<EMAIL_ADDRESS>wrote:

What is the status of this issue? Has this been resolved?
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We'd like to propose releasing said version pin.
We (the team currently maintaining syslog-release need features only present in v8.25 and higher. Since rsyslog's stable version is up to v8.32 now, there's every chance that whatever issue originally provoked the pinning is gone. We attempted the replication described above in order to check, but, unfortunately, have concluded that the replication case is invalid.
The issue is that "slow increase in allocated memory" isn't necessarily a memory leak, especially if the memory allocation:

has bounded growth
is released according to business rules

This is what we believe was actually happening in the replication case using HA Proxy above. HA Proxy without a functioning backend accepts and then quickly kills TCP connections, never actually accepting data. When we ran the replication case for longer than ten minutes, the memory usage stabilized and held steady at around 1.4% of available memory. Rsyslog's configured to enqueue actions that haven't been completed in a linked list. If all the replication shows is the growth of action queues, we'd expect the memory reservation to drop as soon as a single good connection was made - and when we performed that experiment, that's exactly what we saw.
Not only that, but the issue "replicates" exactly the same way using the reported method with both the "before/unaffected" v8.22, the originally reported v8.23, and the latest v8.32. Which is good, since it reflects correct functioning of the program.

loading the impstats module will show you the queue status.
even a short connect/disconnect to haproxy can have rsyslog send some messages
(and with TCP, it won't know that they don't get through, you need to use relp
to be sure of delivery), so this would look very differently with different
volumes of logs being sent.

@mfine30 FYI, the team did some previous investigation in bumping rsyslog on the 3469.x through story #155528288. The intent was to let people test out that stemcell before bumping it everywhere, but I don't think we ended up getting much feedback on it.
For what it's worth, we're still installing this same rsyslog in the Xenial stemcell (which is probably bad)...
$ wget -qO- https://s3.amazonaws.com/bosh-aws-light-stemcells/light-bosh-stemcell-97-aws-xen-hvm-ubuntu-xenial-go_agent.tgz | tar -xOzf- packages.txt | grep rsyslog
ii  rsyslog                               8.22.0-0adiscon1trusty1                    amd64        a rocket-fast system for log processing
ii  rsyslog-gnutls                        8.22.0-0adiscon1trusty1                    amd64        TLS protocol support for rsyslog
ii  rsyslog-mmjsonparse                   8.22.0-0adiscon1trusty1                    amd64        Parsing/handling of CEE/Lumberjack JSON messages in rsyslog
ii  rsyslog-relp                          8.22.0-0adiscon1trusty1                    amd64        RELP protocol support for rsyslog

We may want to consider if this is something we should bump in a minor version, or if it warrants a full new version.

Given that there hasn't been much feedback around rsyslogd in the past (except from our side, afaik), I'd say just bump it in a minor version. However, this is entirely your call. If you feel more comfortable with a major bump, go with that.

In the backlog as Story #159533409

Closing this as we have unblocked the pinning of rsyslog. Please feel free to reopen if the memory leak is still an issue.


Codes vs controlled vocabularies

We currently provide a controlled vocabulary and should also include mappings from that vocabulary to concept codes where appropriate. We describe the use of multiple ontologies that are to be used:
https://github.com/ave-dcd/mave_vocabulary/blob/96d3dcc0f59330ddd1d2ddcbf0b5ef9ff54a5cc4/README.md?plain=1#L101-L112
But our schema only provides the ability for codings to be used for phenotypicAssay.relevance (required; we recommend MONDO) and the phenotypicAssay.modelSystem.identifiers (not required; we recommend the cell line ontology). We should update this section to either state that we provide a controlled vocabulary that maps to an ontology (and provide a SSSOM mapping; easy), or we update our schema to require the use of coding objects (as we do phenotypicAssay.relevance).

I agree with this and think it merits further discussion. We should also revisit this in the context of switching over to LinkML, which was out of scope for our initial version of this work but might be a better fit long term. The LinkML representation seems well-suited to this use case, and is also gaining traction.


NeuromodulatedBistableRecurrentCell' object has no attribute 'append'

Hi !
Thank you very much for the implementation. I was trying to run the code in the Readme shamefully this error is raised:
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-41-0960dd467126> in <module>
     18 # Append cells for subsequent layers keeping in mind
     19 for _ in range(num_layers - 1):
---> 20         nbrc.append(
     21             NeuromodulatedBistableRecurrentCell(inner_input_dimensions, hidden_size)
     22         )

~/anaconda3/lib/python3.7/site-packages/torch/nn/modules/module.py in __getattr__(self, name)
    533                 return modules[name]
    534         raise AttributeError("'{}' object has no attribute '{}'".format(
--> 535             type(self).__name__, name))
    536
    537     def __setattr__(self, name, value):

AttributeError: 'NeuromodulatedBistableRecurrentCell' object has no attribute 'append'

*Edit
I think your code just need:
nbrc = [NeuromodulatedBistableRecurrentCell(input_size, hidden_size)]

*Edit
It seems also that the inner_input_size is not defined, but its a minor inconvenience.

yes, that's true, fixed it :)

thanks !


Someone tried installing this on a debian 12 ?

It's a can of worms.
And yes, I know you point towards the 'new' scripts mentioned in mt forum, but I do not want to have to enter winbox or mikrotik web-ui to see those stats.

OK, I managed to install the python modules using apt. I think. Now I get:
python3[13633]:   File "/opt/MikrotikTrafficMonitor/dbo.py", line 153, in <module>
python3[13633]:     config = read_config()
python3[13633]:              ^^^^^^^^^^^^^
python3[13633]:   File "/opt/MikrotikTrafficMonitor/configuration.py", line 8, in read_config
python3[13633]:     data = yaml.load(f.read())
python3[13633]:            ^^^^^^^^^^^^^^^^^^^
python3[13633]: TypeError: load() missing 1 required positional argument: 'Loader'
systemd[1]: MikrotikTrafficMonitor.service: Main process exited, code=exited, status=1/FAILURE
systemd[1]: MikrotikTrafficMonitor.service: Failed with result 'exit-code'.
systemd[1]: MikrotikTrafficMonitor.service: Consumed 1.232s CPU time.

For the yaml you need to change it to safe_load(f.read()), or specify loader. Due to new PyYAML version.
I'm not sure why you had to install anything through apt. You should be able to do apt install python3-pip or apt install python-pip and pip install -r requirements.txt should work from there. If not you may try using virtual environment:
cd /install/folder/MikroticTrafficMonitor
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
python app.py

You would also need to adjust systemd files to work with venv:
[Service]
Type=simple
ExecStart=/install/folder/MikroticTrafficMonitor/venv/bin/python app.py
WorkingDirectory=/install/folder/MikroticTrafficMonitor
ExecReload=/bin/kill -s HUP $MAINPID
KillMode=mixed
TimeoutStopSec=5
PrivateTmp=true

other parts I think remain the same.
But yeah, Mikrotik kinda lacks in this regard. I think there are other solutions for enterprise use, better network monitoring tools that can connect to mikrotik and get all the data needed or something like that. My usecase was more a casual home use rather than anything serious.
Pretty sure if they focused a bit more on making more user friendly UI and some features like that, even if they increase the price a little, they might just kill a lot of the competition.

PR accepted


DB initialization/DB versioning

not sure if theres a framework we can use but
at the start:
-check tables exist, if they dont exist then create the tables

We can use MySQL's CREATE TABLE IF NOT EXISTS to safely attempt table creation.


Support wildcard event descriptor

closes #155

Awesome! Before I merge this, does this type-check? Let's make sure it doesn't cause compilation errors when TEvent is specified in Machine<...>.

Well, I've run the whole test suite after implementing this - so it has compiled both src and test directories without any errors.


Move stream-related extension methods to StreamGroovyMethods

Now that Java 8 is the minimum, stream methods do not need to be located in the vmplugin hierarchy.  Separate the growing number of stream-based extension methods into their own class.

One thing which we have found in the past when moving DGM methods is that some frameworks like Grails, Micronaut or Spock might use the DGM methods directly. They are public static methods after all even though we regard them as somewhat internal and expose them as methods "only" available through the runtime or when using @CS. So, we adopted the convention of marking old variants with @Deprecated which are ignored when loading DGM methods. Plugin DGM methods might be considered even slightly more internal since in theory they might not be activated on older JVM versions but they are still there as static methods, so it might pay to give them the same treatment. We tend to then delete those deprecated methods after a major version or two. For the same reason, I'd target only Groovy 4 for this change.

Actually, Groovy 4 might be a good time to refine how we deactivate extension methods. Re-purposing @Deprecated has always been a compromise. Perhaps we should add an @Inactive annotation and use that instead. I'll start a discussion on the mailing list, but either way, we'd put back the plugin DGM methods and indicate they are inactive. We often truncate the Javadoc when we make such DGM methods inactive.

I'm fine with deprecated as a way to disable as extension but leave for direct use.  I would be more on board with a way to add extension methods without having to make them public so that they cannot be used outside of the extension mechanism.
So when the v5-v7 vmplugins were combined, was binary compatibility not affected similarly?
https://github.com/apache/groovy/commit/6e10c35b7fdc7c6b213372d7fa771f723ca5906a
I could add the deprecated methods back to PluginDefaultGroovyMethods, if there was a string reason to do so.

You can merge one or both commits

All of the v5-v7 classes exist (but aren't used and are deprecated) on the GROOVY_3_0_X branch but they are removed in master. I'd suggest we do the same thing once Groovy 4 is released and we prepare for Groovy 5.

Merged, thanks!