Snakemake report: visualize results with vega - report

I notice that vega is used by snakemake report to generate workflow summaries such as runtime statistics, for example here.
Is it possible for me to also generate vega reports for results of my own?

Once your snakemake workflow has completed successfully, you can generate a report with:
snakemake --report report.html
Read more about the reports feature here: https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html

Related

BERT not showing R shell in console

I have a question regarding to BERT, because it doen't show me the R shell in the console. I only see the 4 scripts (preferences, welcome, excel scripting and functions.r). I also can't execute the script functions.r and excel doesn't recognise BERT when I try to call functions from bert with application.run ( "bert.call"...).
Neža

Dialogflow with Botium Testing : how to generate report file

My botium is running and can already test my dialogflow bot, but it seems i have problem in getting the report to output files like CSV or mochawesome html. Either way the result was shown only in the terminal command line
I write in CLI like this :
botium-cli run csv
OR
botium-cli run mochawesome
I am using dialogflow for LINE BOT and following this tutorial. But it does not say much about generating the test output.
How do I solve this problem?
Botium CLI provides help on the available reporters and options by adding the --help flag (as usual):
botium-cli run --help
will show command line help of the available output formats and other options.

Allure report with robotframework is showing html file without the test run results

I am running tests with robot framework and i want to get allure report. I have been able to successfully install it and i can see that the .xml files are getting created with the test run results. But when i do "Allure serve " it displays a report without any test information in it.
Can someone please help me? I am using AllureReportLibrary in the robotframework
share one lession.
robot --listener allure_robotframework CustomerService.robot
Default output directory is output/allure.
allure generate output --clean
where I use this command to generate report, no testcase in report.
allure generate output/allure --clean
when I change to this dir, it works. So I guess the innermost directory is necessary.

How to load the WEKA pre-preprocessing steps to R?

I have used the WEKA GUI Java here to do the preprocessing of the data. I would like to use the same preprocessing steps now in R.
For example, I want to load the preprocessing of MultiFilter of WEKA GUI to R. I cannot find it in RWeka.
How to load the WEKA prepreprocessing steps to R?
You can load WEKA GUI steps partially with RWeka or with Weka command line tools that are are far more extensive than the available functions in RWeka. So you can extend the RWeka with the command line commands through the system command in R. Luckily, the parameters in WEKA GUI and the WEKA commandline are the same. I recommend extracting the weka-src.jar with jar xf weka-src.jar to read the source.
There exist many functions for the MultiFilter
java weka.filters.MultiFilter --help
java weka.filters.unsupervised.attribute.PartitionedMultiFilter --help
where the second allows you specify the attribute range. Otherwise, they seem to be identical.
Then you can run your first discretize filter with
java weka.filters.unsupervised.attribute.Discretize -F -B 20 -M -1.0 -R 27 -i yourFile.arff
and then direct its output to next Discretize, eventually to NumericTransform and Resample. The command line provides fabulous instructions on the commands in the following way
java weka.filters.unsupervised.attribute.NumericTransform --help
java weka.filters.unsupervised.attribute.Remove --help
java weka.filters.unsupervised.instance.Resample --help
java weka.filters.supervised.instance.Resample --help
and you can check them from the directory structure or the index.
RWeka
RWeka package provides the functions
Discretize()
Normalize()
make_Weka_filter() to create R interfaces to Weka filters
and there is no NumericTransform and Remove functions. You need to use their arguments so not directly just by copy-pasting a java code from WEKA GUI. Perhaps, one solution could be use the system command and execute the Java code with it, without having to need to learn the RWeka itself. There seems to be some gap between the WEKA GUI and the R package.
Running Weka on Commandline
Even though the commands are missing through RWeka interface, you can also use the system commands in R. For example, you can run the remove command
java weka.filters.unsupervised.attribute.Remove -i yourfile.arff
such that
system("java weka.filters.unsupervised.attribute.Remove -i yourfile.arff")
I have the following setup here so we can run Discretize with the following way.
$ cat $WEKAINSTALL/data/iris.arff |tail
6.8,3.2,5.9,2.3,Iris-virginica
6.7,3.3,5.7,2.5,Iris-virginica
6.7,3.0,5.2,2.3,Iris-virginica
6.3,2.5,5.0,1.9,Iris-virginica
6.5,3.0,5.2,2.0,Iris-virginica
6.2,3.4,5.4,2.3,Iris-virginica
5.9,3.0,5.1,1.8,Iris-virginica
%
%
%
$ java weka.filters.unsupervised.attribute.Discretize -i $WEKAINSTALL/data/iris.arff |tail
'\'(6.46-6.82]\'','\'(2.96-3.2]\'','\'(5.13-5.72]\'','\'(2.26-inf)\'',Iris-virginica
'\'(6.82-7.18]\'','\'(2.96-3.2]\'','\'(4.54-5.13]\'','\'(2.26-inf)\'',Iris-virginica
'\'(5.74-6.1]\'','\'(2.48-2.72]\'','\'(4.54-5.13]\'','\'(1.78-2.02]\'',Iris-virginica
'\'(6.46-6.82]\'','\'(2.96-3.2]\'','\'(5.72-6.31]\'','\'(2.26-inf)\'',Iris-virginica
'\'(6.46-6.82]\'','\'(3.2-3.44]\'','\'(5.13-5.72]\'','\'(2.26-inf)\'',Iris-virginica
'\'(6.46-6.82]\'','\'(2.96-3.2]\'','\'(5.13-5.72]\'','\'(2.26-inf)\'',Iris-virginica
'\'(6.1-6.46]\'','\'(2.48-2.72]\'','\'(4.54-5.13]\'','\'(1.78-2.02]\'',Iris-virginica
'\'(6.46-6.82]\'','\'(2.96-3.2]\'','\'(5.13-5.72]\'','\'(1.78-2.02]\'',Iris-virginica
'\'(6.1-6.46]\'','\'(3.2-3.44]\'','\'(5.13-5.72]\'','\'(2.26-inf)\'',Iris-virginica
'\'(5.74-6.1]\'','\'(2.96-3.2]\'','\'(4.54-5.13]\'','\'(1.78-2.02]\'',Iris-virginica
$
Some useful information
Use Weka in your Java code
Download the Linux Developer version, unzip it and read the README with many fabulous examples about using WEKA particularly on command line.
Wiki here
Maybe irrelevant: Generating source code from WEKA classes

build should fail if code coverage Report Percenatge is less

I have written a build.xml for generating Reports through phing.
I have added below command in build.xml to generate code coverage Report ::
<exec command="phpunit --coverage-html ./code_Coverage_Report codecoverage_test/CodeCoverage.php "/>
Now i wanted to add a check in build.xml that if my code coverage Report percentage is less than 85% then the build should automatically fail.
This is not possible with PHPUnit. There was a pull request to implement what you want, but it was rejected.
https://github.com/sebastianbergmann/phpunit/pull/2402
Although not directly possible with PHPUnit, there are alternative open-source packages that will let you do the same such as https://github.com/richardregeer/phpunit-coverage-check

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