Upgraded deps due to security issues

Added the MongoDB instance command line options to the output.
Also fixed the spacing in the replicaset section.

CONTRIBUTE.md

@@ -1,149 +1,190 @@
-# Contributing guide
-## How Can I Contribute?
-## Reporting Bugs
-Before creating bug reports, please check this list as you might find out that you don't need to create one. When you create a bug report, please include as many details as possible. You can use this template to structure the information.  
-
-### Before Submitting A Bug Report
-- Ensure you have carefully read the documentation. Percona Toolkit is a mature project with many settings that covers a wide range options.
-- Search for existing bugs in Launchpad to see if the problem has already been reported. If it has, add a comment to the existing issue instead of opening a new one.
-
-### How Do I Submit A (Good) Bug Report?
-- Explain the problem and include additional details to help others reproduce the problem:
-- Use a clear and descriptive title for the issue to identify the problem.
-- Describe the exact steps which reproduce the problem, including as many details as possible. Provide examples of the command you used and include context information like language, OS and database versions.
-Describe the obtained results and the expected results and, if it is possible, provide examples.
-
-## Submiting fixes
-### Create an Issue
-If you find a bug, the first step is to create an issue. Whatever the problem is, you’re likely not the only one experiencing it. Others will find your issue helpful, and other developers might help you find the cause and discuss the best solution for it.
-
-#### Tips for creating an issue
-- Check if there are any existing issues for your problem. By doing this, we can avoid duplicating efforts, since the issue might have been already reported and if not, you might find useful information on older issues related to the same problem.
-- Be clear about what your problem is: which program were you using, what was the expected result and what is the result you are getting. Detail how someone else can reproduce the problem, including examples.
-- Include system details like language version, OS, database details or special configurations, etc.
-- Paste the error output or logs in your issue or in a Gist.
-
-### Pull Requests
-If you fixed a bug or added a new feature – awesome! Open a pull request with the code! Be sure you’ve read any documents on contributing, understand the license and have signed a Contributor Licence Agreement (CLA) if required. Once you’ve submitted a pull request, the maintainers can compare your branch to the existing one and decide whether or not to incorporate (merge) your changes.
-
-### Tips for creating a pull request
-- Fork the repository and clone it locally. Connect your local to the original ‘upstream’ repository by adding it as a remote. Pull in changes from ‘upstream’ often so that you stay up to date so that when you submit your pull request, merge conflicts will be less likely.
-- Create a branch for your code. Usually it is a good practice to name the branch after the issue ID, like issue-12345.
-- Be clear about the problem you fixed or the feature you added. Include explanations and code references to help the maintainers understand what you did.
-- Add useful comments to the code to help others understand it.
-- Write tests. This is an important step. Run your changes against existing tests and create new ones when needed. Whether tests exist or not, make sure your changes don’t break the existing project.
-- Contribute in the style of the project to the best of your abilities. This may mean using indents, semicolons, or comments differently than you would in your own repository, but makes it easier for the maintainer to merge, others to understand and maintain in the future.
-- Keep your changes as small as possible and solve only what's reported in the issue. Mixing fixes might be confusing to others and makes testing harder.
-- Be as explicit as possible. Avoid using special/internal language variables like $_. Use a variable name that clearly represents the value it holds.
-- Write good commit messages. A comment like 'Misc bugfixes' or 'More code added' does not help to understand what's the change about.
-
-### Open Pull Requests
-Once you’ve opened a pull request, a discussion will start around your proposed changes. Other contributors and users may chime in, but ultimately the decision is made by the maintainers. You may be asked to make some changes to your pull request, if so, add more commits to your branch and push them – they’ll automatically go into the existing pull request.
-
-# Licensing
-Along with the pull request, include a message indicating that the submited code is your own creation and it can be distributed under the BSD licence. 
-  
-  
-# Setting up the development environment
-
-#### Setting up the source code
-To start, fork the Percona Toolkit repo to be able to submit pull requests and clone it locally:
-```
-mkdir ${HOME}/perldev
-git clone https://github.com/<your-username>/percona-toolkit.git ${HOME}/perldev/percona-toolkit
-```
-
-For testing, we are going to need to have MySQL with slaves. For that, we already have scripts in the sandbox directory but first we need to download MySQL binaries. Please download the Linux Generic tar file for your distrubution from [https://www.percona.com/downloads/Percona-Server-5.6/](https://www.percona.com/downloads/Percona-Server-5.6/).    
-
-### Set up MySQL sandbox
-In this example, we are going to download Percona Server 5.6.32. Since I am using Ubuntu, according to the documentation [here](https://www.percona.com/doc/percona-server/5.6/installation.html#installing-percona-server-from-a-binary-tarball), I am going to need this tar file: [Percona-Server-5.6.32-rel78.1-Linux.x86_64.ssl100.tar.gz](https://www.percona.com/downloads/Percona-Server-5.6/Percona-Server-5.6.32-78.1/binary/tarball/Percona-Server-5.6.32-rel78.1-Linux.x86_64.ssl100.tar.gz).  
-
-```
-mkdir -p ${HOME}/mysql/percona-server-5.6.32
-```
-```
-wget https://www.percona.com/downloads/Percona-Server-5.6/Percona-Server-5.6.32-78.1/binary/tarball/Percona-Server-5.6.32-rel78.1-Linux.x86_64.ssl100.tar.gz 
-```
-```
-tar xvzf Percona-Server-5.6.32-rel78.1-Linux.x86_64.ssl100.tar.gz --strip 1 -C ${HOME}/mysql/percona-server-5.6.32
-```
-### Set up environment variables
-We need these environment variables to start the MySQL sandbox and to run the tests. Probably it is a good idea to add them to your `.bashrc` file.
-```
-export PERCONA_TOOLKIT_BRANCH=${HOME}/perldev/percona-toolkit
-export PERL5LIB=${HOME}/perldev/percona-toolkit/lib
-export PERCONA_TOOLKIT_SANDBOX=${HOME}/mysql/percona-server-5.6.32
-```
-
-### Check that all needed tools are correctly installed:
-```
-util/check-dev-env
-```
-If not, you will have to either install them via your package manager of preference, or using Perl directly. For example, let's assume that you are missing the `File::Slurp` package (as flagged by a `NA` output from the previous command), you can use:
-```
-sudo perl -MCPAN -e "shell"
-cpan[1]> install File::Slurp
-...
-```
-
-### Starting the sandbox
-```
-cd ${HOME}/perldev/percona-toolkit
-```
-```
-sandbox/test-env start
-```
-To stop the MySQL sandbox: `sandbox/test-env stop`  
-To enable TokuDB (only available in Percona Server 5.7+), run:  
-
-```
-ENABLE_TOKUDB=1 sandbox/test-env start
-```
-
-### Running tests
-```
-cd ${HOME}/perldev/percona-toolkit
-```
-Run all tests for a particular program (pt-stalk in this example):
-```
-prove -v t/pt-stalk/
-```
-You can also add warnings with:
-```
-prove -vw t/pt-stalk/
-```
-or run a specific test:
-```
-prove -v t/pt-stalk/option_sanity.t
-```
-
-# Introducing changes to the toolkit
-
-## Creating a new branch
-
-You should start your own development branch. If you have a JIRA ticket assigned, use its number as reference, and add a short description of what work on this branch will do:
-```
-git checkout -b PT-9999_functionality_name
-```
-The first commit should also have the JIRA reference number as first characters in the commit message (so that JIRA can use the smart tags).
-
-## Running the update-modules tool
-
-Whenever you make changes to libraries under lib/, you should make sure that you run the util/update-modules functionality, to make sure that all tools that use these packages will benefit from the new changes. For example, let's say you changed the lib/bash/collect.sh package, you will need to run:
-```
-cd ${HOME}/perldev/percona-toolkit
-for t in bin/*; do util/update-modules ${t} collect; done
-```
-Or if you changed the lib/NibbleIterator.pm package:
-```
-cd ${HOME}/perldev/percona-toolkit
-for t in bin/*; do util/update-modules ${t} NibbleIterator; done
-```
-
-## Uploading your branch
-
-Finally, after you run another round of tests and everything is ok, you should upload your branch to your GitHub fork:
-```
-git push origin PT-9999_functionality_name
-```
-And then go to the web UI to create the new pull request (PR) based off of this new branch.
+# Contributing Guide
+## How Can I Contribute?
+## Reporting Bugs
+Before creating bug reports, please check [this list](https://jira.percona.com/projects/PT/issues) as you might find out that you don't need to create one. When you create a bug report, please include as many details as possible. You can use [this guide](https://www.percona.com/blog/2019/06/12/report-bugs-improvements-new-feature-requests-for-percona-products/) to structure the information. 
+
+### Before Submitting a Bug Report
+- Ensure you have carefully read the documentation. Percona Toolkit is a mature project with many settings that cover a wide range of options.
+- Search for existing bugs in [Jira](https://jira.percona.com) to see if the problem has already been reported. If it has, add a comment to the existing issue instead of opening a new one. 
+By doing this, we can avoid duplicating efforts, since the issue might have been already reported and if not, you might find useful information on older issues related to the same problem.
+
+### How Do I Submit a (Good) Bug Report?
+- Explain the problem and include additional details to help others to reproduce the problem.
+- Use a clear and descriptive title for the issue. 
+- Be clear about what your problem is: which program you are using, what is the expected result and what is the result you are getting. 
+- Include system details, such as language version, OS, database details or special configurations, etc.
+- Describe the exact steps which reproduce the problem, including as many details as possible. Provide examples of the command you used and include context information like language, OS and database versions.
+- Describe the obtained and the expected results and, if possible, provide examples.
+- Paste the error output or logs into Jira issue or attach them. You may put large files on our SFTP server if needed. Use Jira issue number as a login and password for the [Percona SFTP server](sftp.percona.com). Have Jira issue number in the file name and add a comment, so we can access it.
+
+## Reporting Documentation Issues
+Documentation bugs for Percona Toolkit should be reported at [Percona Jira](https://jira.percona.com/) in the project **PT** and have component **Documentation**.
+
+### Good Documentation Bug Report
+- Contains link to the user manual page where the documentation is wrong
+- Fully explains the problem
+- Optionally explains how documentation should be fixed
+
+## Introducing Changes to the Toolkit
+### Set Up the Source Code
+To start, fork the Percona Toolkit repo to be able to submit pull requests and clone it locally:
+```
+mkdir ${HOME}/perldev
+git clone https://github.com/percona/percona-toolkit.git ${HOME}/perldev/percona-toolkit
+```
+### Create a New Branch
+
+You should start your own development branch. If you have a Jira ticket assigned, use its number as a reference, and add a short description of what work on this branch will do:
+```
+git checkout -b PT-9999_functionality_name
+```
+The first commit should also have the Jira reference number as first characters in the commit message (so that Jiraf can use the smart tags).
+
+### Example Commit Message
+
+```
+PT-12345 - fixed data corruption issue for pt-foo
+
+New check pt-foo-test-env added when pt-foo is going to perform destructive operation.
+If check fails, now pt-foo will stop executing and return an error. 
+```
+
+### Changing Shared Code
+
+Percona Toolkit uses `lib` directory for library code. Once you change it you need to run the `update-modules` tool that will merge module code with the tools. Be careful and **do not modify** anything between the `This package is a copy without comments from the original`  and `End ... package` comments.
+
+### Running the update-modules Tool
+
+Whenever you make changes to libraries under `lib/`, you should make sure that you run the `util/update-modules` functionality, to make sure that all tools that use these packages will benefit from the new changes. For example, let's say you changed the `lib/bash/collect.sh` package, you will need to run:
+```
+cd ${HOME}/perldev/percona-toolkit
+for t in bin/*; do util/update-modules ${t} collect; done
+```
+Or if you changed the `lib/NibbleIterator.pm` package:
+```
+cd ${HOME}/perldev/percona-toolkit
+for t in bin/*; do util/update-modules ${t} NibbleIterator; done
+```
+
+## Uploading Your Branch
+
+Finally, after you run another round of tests and everything is OK, you should upload your branch to your GitHub fork:
+```
+git push origin PT-9999_functionality_name
+```
+And then go to the web UI to create the new pull request (PR) based off of this new branch.
+
+## Submiting Fixes
+### Pull Requests
+Once your fix is ready and you pushed it into the feature branch, open a pull request with the code. Be sure you’ve read any documents on contributing, understand the license and have signed a [Contributor Licence Agreement (CLA)](https://github.com/percona/percona-toolkit/blob/3.x/CONTRIBUTING.md). Once you’ve submitted a pull request, the maintainers can compare your branch to the existing one and decide whether or not to incorporate (merge) your changes.
+
+### Tips for Creating a Pull Request
+- Be clear about the problem you fixed or the feature you added. Include explanations and code references to help the maintainers understand what you did.
+- Add useful comments to the code to help others understand it.
+- Write tests. This is an important step. Run your changes against existing tests and create new ones when needed. Whether tests exist or not, make sure your changes don’t break the existing project.
+- Contribute in the style of the project to the best of your abilities. This may mean using indents, semicolons, or comments differently than you would in your own repository, but makes it easier for the maintainer to merge, others to understand and maintain in the future.
+- Keep your changes as small as possible and solve only what's reported in the issue. Mixing fixes might be confusing to others and makes testing harder.
+- Be as explicit as possible. Avoid using special/internal language variables like `$_`. Use a variable name that clearly represents the value it holds.
+- Write good commit messages. A comment like *'Misc bugfixes'* or *'More code added'* does not help to understand what's the change about.
+- Put Jira issue number into the commit message to automatically link it with the Jira issue.
+
+### Open a Pull Request
+Once you’ve opened a pull request, a discussion will start around your proposed changes. Other contributors and users may chime in, but ultimately the decision is made by the maintainers. You may be asked to make some changes to your pull request, if so, add more commits to your branch and push them – they’ll automatically go into the existing pull request.
+
+## Licensing
+Along with the pull request, include a message indicating that the submited code is your own creation and it can be distributed under the GPL2 licence. 
+  
+  
+## Setting up the Development Environment and Testing
+### Perl and Shell Tools
+For testing, we are going to need to have MySQL with replicas. For that, we already have scripts in the sandbox directory but first we need to download MySQL binaries. Please download the Linux Generic tar file for your distrubution from [https://www.percona.com/downloads/Percona-Server-LATEST/](https://www.percona.com/downloads/Percona-Server-LATEST/). 
+
+#### Set up MySQL Sandbox
+In this example, we are going to download Percona Server 8.0.26-17.
+
+```
+mkdir -p ${HOME}/mysql/percona-server-8.0.26-17
+```
+```
+wget https://downloads.percona.com/downloads/Percona-Server-LATEST/Percona-Server-8.0.26-17/binary/tarball/Percona-Server-8.0.26-17-Linux.x86_64.glibc2.17.tar.gz
+```
+```
+tar xvzf Percona-Server-8.0.26-17-Linux.x86_64.glibc2.17.tar.gz --strip 1 -C ${HOME}/mysql/percona-server-8.0.26-17
+```
+#### Set Up Environment Variables
+We need these environment variables to start the MySQL sandbox and to run the tests. Probably it is a good idea to add them to your `.bashrc` file.
+```
+export PERCONA_TOOLKIT_BRANCH=${HOME}/perldev/percona-toolkit
+export PERL5LIB=${HOME}/perldev/percona-toolkit/lib
+export PERCONA_TOOLKIT_SANDBOX=${HOME}/mysql/percona-server-8.0.26-17
+```
+
+#### Check That All Needed Tools Are Correctly Installed:
+```
+util/check-dev-env
+```
+If not, you will have to either install them via your package manager of preference, or using Perl directly. For example, let's assume that you are missing the `File::Slurp` package (as flagged by a `NA` output from the previous command), you can use:
+```
+sudo perl -MCPAN -e "shell"
+cpan[1]> install File::Slurp
+...
+```
+
+#### Starting the Sandbox
+```
+cd ${HOME}/perldev/percona-toolkit
+```
+```
+sandbox/test-env start
+```
+To stop the MySQL sandbox: `sandbox/test-env stop`  
+To enable TokuDB (only available in Percona Server 5.7+), run:  
+
+```
+ENABLE_TOKUDB=1 sandbox/test-env start
+```
+
+To enable MyRocks (only available in Percona Server 5.7+), run:
+
+```
+ENABLE_ROCKSDB=1 sandbox/test-env start
+```
+
+#### Running Tests
+```
+cd ${HOME}/perldev/percona-toolkit
+```
+Run all tests for a particular program (pt-stalk in this example):
+```
+prove -v t/pt-stalk/
+```
+You can also add warnings with:
+```
+prove -vw t/pt-stalk/
+```
+or run a specific test:
+```
+prove -v t/pt-stalk/option_sanity.t
+```
+
+### Go Tools
+
+Starting from version 3, there are new tools for MongoDB, written in Go language.
+
+To test these tools, first switch to the `src/go` directory, then use command `make`.
+
+#### Starting the Sandbox
+
+Run command `make env-up`. This will start MongoDB container cluster
+
+#### Build Mongo Tools
+
+Run command `make` with your environment as a parameter. For example, `make linux-amd64` will build Mongo tools for Linux AMD64 platform.
+
+#### Running Tests
+
+Run `make test`
+
+#### Stopping the Sandbox
+
+Run `make env-down`

README.md

@@ -33,21 +33,3 @@ are installed in /usr/local/bin.  See the INSTALL file for more information.
 Run `man percona-toolkit` to see a list of installed tools, then `man tool`
 to read the embedded documentation for a specific tool.  You can also read
 the documentation online at [http://www.percona.com/software/percona-toolkit/](http://www.percona.com/software/percona-toolkit/).
-
-## Version 3
-
-Starting from version 3, there are new tools for MongoDB. These tools are written in Go so
-in order to compile these program, this repo must me cloned into the GOPATH directory.  
-Example:  
-
-```
-mkdir ${HOME}/go
-export GOPATH=${HOME}/go
-mkdir -p ${HOME}/go/src/github.com/percona
-cd ${HOME}/go/src/github.com/percona
-git clone https://github.com/percona/percona-toolkit.git
-cd percona-toolkit/src/go
-make
-```
-
-

bin/pt-stalk

@@ -1084,7 +1084,7 @@ open_tables() {
    if [ -n "$open_tables" -a $open_tables -le 1000 ]; then
       $CMD_MYSQL $EXT_ARGV -e 'SHOW OPEN TABLES' &
    else
-      log "Too many open tables: $open_tables"
+      log "Logging disabled due to having over 1000 tables open. Number of tables currently open: $open_tables"
    fi
 }
 

go.mod

@@ -5,59 +5,68 @@ go 1.17
 require (
 	github.com/Masterminds/semver v1.4.2
 	github.com/alecthomas/kingpin v2.2.6+incompatible
-	github.com/go-ini/ini v1.46.0
+	github.com/go-ini/ini v1.66.4
 	github.com/golang/mock v1.4.4
 	github.com/google/uuid v1.3.0
-	github.com/hashicorp/go-version v1.2.1-0.20190424083514-192140e6f3e6
-	github.com/howeyc/gopass v0.0.0-20170109162249-bf9dde6d0d2c
-	github.com/lib/pq v1.2.0
-	github.com/mattn/go-shellwords v1.0.6
-	github.com/montanaflynn/stats v0.0.0-20171201202039-1bf9dbcd8cbe
-	github.com/pborman/getopt v0.0.0-20190409184431-ee0cd42419d3
-	github.com/percona/go-mysql v0.0.0-20190903141930-197f4ad8db8d
+	github.com/hashicorp/go-version v1.4.0
+	github.com/howeyc/gopass v0.0.0-20210920133722-c8aef6fb66ef
+	github.com/lib/pq v1.10.4
+	github.com/mattn/go-shellwords v1.0.12
+	github.com/montanaflynn/stats v0.6.6
+	github.com/pborman/getopt v1.1.0
+	github.com/percona/go-mysql v0.0.0-20210427141028-73d29c6da78c
 	github.com/pkg/errors v0.9.1
-	github.com/shirou/gopsutil v2.20.8+incompatible
-	github.com/sirupsen/logrus v1.6.0
-	github.com/stretchr/testify v1.6.1
-	go.mongodb.org/mongo-driver v1.7.1
-	golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9
+	github.com/shirou/gopsutil v3.21.11+incompatible
+	github.com/sirupsen/logrus v1.8.1
+	github.com/stretchr/testify v1.7.0
+	go.mongodb.org/mongo-driver v1.9.0
+	golang.org/x/crypto v0.0.0-20220331220935-ae2d96664a29
 	gopkg.in/mgo.v2 v2.0.0-20190816093944-a6b53ec6cb22
-	k8s.io/api v0.18.6
+	k8s.io/api v0.23.5
 )
 
 require (
-	github.com/StackExchange/wmi v0.0.0-20180116203802-5d049714c4a6 // indirect
+	github.com/StackExchange/wmi v1.2.1 // indirect
 	github.com/alecthomas/template v0.0.0-20190718012654-fb15b899a751 // indirect
-	github.com/alecthomas/units v0.0.0-20210208195552-ff826a37aa15 // indirect
+	github.com/alecthomas/units v0.0.0-20211218093645-b94a6e3cc137 // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
-	github.com/go-ole/go-ole v1.2.4 // indirect
-	github.com/go-stack/stack v1.8.0 // indirect
-	github.com/gogo/protobuf v1.3.1 // indirect
-	github.com/golang/snappy v0.0.2-0.20190904063534-ff6b7dc882cf // indirect
-	github.com/google/go-cmp v0.5.5 // indirect
-	github.com/google/gofuzz v1.1.0 // indirect
-	github.com/json-iterator/go v1.1.11 // indirect
-	github.com/klauspost/compress v1.10.10 // indirect
+	github.com/go-logr/logr v1.2.3 // indirect
+	github.com/go-ole/go-ole v1.2.6 // indirect
+	github.com/go-stack/stack v1.8.1 // indirect
+	github.com/gogo/protobuf v1.3.2 // indirect
+	github.com/golang/snappy v0.0.4 // indirect
+	github.com/google/go-cmp v0.5.7 // indirect
+	github.com/google/gofuzz v1.2.0 // indirect
+	github.com/json-iterator/go v1.1.12 // indirect
+	github.com/klauspost/compress v1.15.1 // indirect
 	github.com/konsorten/go-windows-terminal-sequences v1.0.3 // indirect
 	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
-	github.com/modern-go/reflect2 v1.0.1 // indirect
+	github.com/modern-go/reflect2 v1.0.2 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/smartystreets/goconvey v1.7.2 // indirect
+	github.com/tklauser/go-sysconf v0.3.10 // indirect
+	github.com/tklauser/numcpus v0.4.0 // indirect
 	github.com/xdg-go/pbkdf2 v1.0.0 // indirect
-	github.com/xdg-go/scram v1.0.2 // indirect
-	github.com/xdg-go/stringprep v1.0.2 // indirect
-	github.com/youmark/pkcs8 v0.0.0-20181117223130-1be2e3e5546d // indirect
-	golang.org/x/net v0.0.0-20210805182204-aaa1db679c0d // indirect
-	golang.org/x/sync v0.0.0-20201207232520-09787c993a3a // indirect
-	golang.org/x/sys v0.0.0-20210603081109-ebe580a85c40 // indirect
-	golang.org/x/text v0.3.6 // indirect
+	github.com/xdg-go/scram v1.1.1 // indirect
+	github.com/xdg-go/stringprep v1.0.3 // indirect
+	github.com/youmark/pkcs8 v0.0.0-20201027041543-1326539a0a0a // indirect
+	github.com/yusufpapurcu/wmi v1.2.2 // indirect
+	golang.org/x/net v0.0.0-20220403103023-749bd193bc2b // indirect
+	golang.org/x/sync v0.0.0-20210220032951-036812b2e83c // indirect
+	golang.org/x/sys v0.0.0-20220406163625-3f8b81556e12 // indirect
+	golang.org/x/term v0.0.0-20210927222741-03fcf44c2211 // indirect
+	golang.org/x/text v0.3.7 // indirect
 	golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1 // indirect
-	gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 // indirect
+	gopkg.in/check.v1 v1.0.0-20200227125254-8fa46927fb4f // indirect
 	gopkg.in/inf.v0 v0.9.1 // indirect
 	gopkg.in/ini.v1 v1.62.0 // indirect
 	gopkg.in/yaml.v2 v2.4.0 // indirect
-	gopkg.in/yaml.v3 v3.0.0-20200615113413-eeeca48fe776 // indirect
-	k8s.io/apimachinery v0.18.6 // indirect
+	gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b // indirect
+	k8s.io/apimachinery v0.23.5 // indirect
 	k8s.io/klog v1.0.0 // indirect
-	sigs.k8s.io/structured-merge-diff/v3 v3.0.0 // indirect
+	k8s.io/klog/v2 v2.60.1 // indirect
+	k8s.io/utils v0.0.0-20220210201930-3a6ce19ff2f9 // indirect
+	sigs.k8s.io/json v0.0.0-20211208200746-9f7c6b3444d2 // indirect
+	sigs.k8s.io/structured-merge-diff/v3 v3.0.1 // indirect
+	sigs.k8s.io/structured-merge-diff/v4 v4.2.1 // indirect
 )

go.sum

@@ -1,37 +1,70 @@
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@@ -58,34 +91,65 @@ github.com/gobuffalo/packr/v2 v2.2.0/go.mod h1:CaAwI0GPIAv+5wKLtv8Afwl+Cm78K/I/V
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 gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/check.v1 v1.0.0-20200227125254-8fa46927fb4f/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI=
 gopkg.in/fsnotify.v1 v1.4.7/go.mod h1:Tz8NjZHkW78fSQdbUxIjBTcgA1z1m8ZHf0WmKUhAMys=
 gopkg.in/inf.v0 v0.9.1 h1:73M5CoZyi3ZLMOyDlQh031Cx6N9NDJ2Vvfl76EDAgDc=
@@ -250,24 +452,52 @@ gopkg.in/mgo.v2 v2.0.0-20190816093944-a6b53ec6cb22/go.mod h1:yeKp02qBN3iKW1OzL3M
 gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7/go.mod h1:dt/ZhP58zS4L8KSrWDmTeBkI65Dw0HsyUHuEVlX15mw=
 gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v2 v2.2.8/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v2 v2.3.0/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
 gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY=
 gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
 gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
 gopkg.in/yaml.v3 v3.0.0-20200615113413-eeeca48fe776 h1:tQIYjPdBoyREyB9XMu+nnTclpTYkz2zFM+lzLJFO4gQ=
 gopkg.in/yaml.v3 v3.0.0-20200615113413-eeeca48fe776/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
+gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
+honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
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 k8s.io/apimachinery v0.18.6 h1:RtFHnfGNfd1N0LeSrKCUznz5xtUP1elRGvHJbL3Ntag=
 k8s.io/apimachinery v0.18.6/go.mod h1:OaXp26zu/5J7p0f92ASynJa1pZo06YlV9fG7BoWbCko=
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 k8s.io/gengo v0.0.0-20190128074634-0689ccc1d7d6/go.mod h1:ezvh/TsK7cY6rbqRK0oQQ8IAqLxYwwyPxAX1Pzy0ii0=
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lib/bash/collect.sh

@@ -382,7 +382,7 @@ open_tables() {
    if [ -n "$open_tables" -a $open_tables -le 1000 ]; then
       $CMD_MYSQL $EXT_ARGV -e 'SHOW OPEN TABLES' &
    else
-      log "Too many open tables: $open_tables"
+      log "Logging disabled due to having over 1000 tables open. Number of tables currently open: $open_tables"
    fi
 }
 

src/go/pt-mongodb-summary/main.go

@@ -93,6 +93,7 @@ type hostInfo struct {
 	ProcCreateTime   time.Time
 	ProcProcessCount int
 
+	CmdlineArgs []string
 	// Server Status
 	ProcessName    string
 	ReplicasetName string
@@ -326,6 +327,11 @@ func formatResults(ci *collectedInfo, format string) ([]byte, error) {
 			return nil, errors.Wrap(err, "cannot parse hosttemplateData section of the output template")
 		}
 
+		t = template.Must(template.New("cmdlineargsa").Parse(templates.CmdlineArgs))
+		if err := t.Execute(buf, ci.HostInfo); err != nil {
+			return nil, errors.Wrap(err, "cannot parse the command line args section of the output template")
+		}
+
 		t = template.Must(template.New("runningOps").Parse(templates.RunningOps))
 		if err := t.Execute(buf, ci.RunningOps); err != nil {
 			return nil, errors.Wrap(err, "cannot parse runningOps section of the output template")
@@ -400,6 +406,7 @@ func getHostInfo(ctx context.Context, client *mongo.Client) (*hostInfo, error) {
 		ProcPath:       pi.Path,
 		ProcUserName:   pi.UserName,
 		ProcCreateTime: pi.CreateTime,
+		CmdlineArgs:    cmdOpts.Argv,
 	}
 	if ss.Repl != nil {
 		i.ReplicasetName = ss.Repl.SetName

src/go/pt-mongodb-summary/templates/cmdline.go

@@ -0,0 +1,8 @@
+package templates
+
+const CmdlineArgs = `
+{{ if . }}
+# Command line arguments
+{{ range .CmdlineArgs -}} {{-  . }} {{ end }}
+{{- end }}				
+`

src/go/pt-mongodb-summary/templates/hostinfo.go

@@ -19,7 +19,7 @@ const HostInfo = `# This host
 {{- end }}
                 Processes | {{.ProcProcessCount}}
              Process Type | {{.NodeType}}
-{{ if .ReplicasetName -}}
+{{- if .ReplicasetName }}
                   ReplSet | {{.ReplicasetName}}
               Repl Status | 
 {{- end -}}

t/pt-stalk/pt-stalk.t

@@ -623,6 +623,57 @@ is(
    "If both options --mysql-only and --system-only are specified only essential collections are triggered"
 );
 
+
+# ###########################################################################
+# Test if open tables are collected if number of open tables <= 1000
+# ###########################################################################
+
+cleanup();
+
+$dbh->do('FLUSH TABLES');
+
+$retval = system("$trunk/bin/pt-stalk --no-stalk --run-time 10 --sleep 2 --dest $dest --pid $pid_file --iterations 1 --prefix test -- --defaults-file=$cnf >$log_file 2>&1");
+
+PerconaTest::wait_until(sub { !-f $pid_file });
+
+$output = `head -n 1 $dest/test-opentables1`;
+
+is(
+  $output,
+  "Database\tTable\tIn_use\tName_locked\n",
+  "If number of open tables is less or equal than 1000, the output of 'SHOW OPEN TABLES' is collected"
+);
+
+# ###########################################################################
+# Test if open tables are not collected if number of open tables > 1000
+# ###########################################################################
+
+cleanup();
+
+$retval = $dbh->do('FLUSH TABLES');
+$retval = $dbh->do('CREATE DATABASE IF NOT EXISTS test_open_tables');
+
+$retval = $dbh->do('SET @old_table_open_cache=@@global.table_open_cache, GLOBAL table_open_cache=1001*@@global.table_open_cache_instances');
+
+for (my $i = 0; $i < 1002; $i++) {
+  $retval = $dbh->do("CREATE TABLE IF NOT EXISTS test_open_tables.t_$i(id int)");
+  $retval = $dbh->do("INSERT INTO test_open_tables.t_$i VALUES($i)");
+}
+
+$retval = system("$trunk/bin/pt-stalk --no-stalk --run-time=10 --dest $dest --pid $pid_file --iterations 1 --prefix test -- --defaults-file=$cnf >$log_file 2>&1");
+
+PerconaTest::wait_until(sub { !-f $pid_file });
+
+$output = `cat $dest/test-opentables1`;
+
+like(
+  $output,
+  qr/Logging disabled due to having over 1000 tables open. Number of tables currently open/,
+  "If number of open tables is greater than 1000, the output of 'SHOW OPEN TABLES' is not collected"
+);
+
+$retval = $dbh->do('SET GLOBAL table_open_cache=@old_table_open_cache');
+$retval = $dbh->do('DROP DATABASE test_open_tables');
 # ###########################################################################
 # Test report about performance schema transactions in MySQL 5.7+
 # ###########################################################################