We have a vast amount of tests. We would like infinitest only to choose between tests that have been included in an .xml-file (i.e. a TestNG suite).
We do not want to put the annotation groups = { "shouldbetested" } in every testcase but rather feed the info from our .xml file into infinitest.
Is this possible?
Is it another tool that could do that for us?
you can use a regular expresstion to "not" skip a certain test:
(?!.*YourTest)
Infinitest can filter out the tests you don't want to run using regular expressions in the infinitest.filters file.
The infinitest.filters contains regular expressions (one per line) that match the test classes you want to filter. Put this file in the root of your project (a.k.a. the working directory), and Infinitest will filter those tests out.
Note that the class names include package names, so use .* in front to match any package.
Related
I am running a pipeline and was trying to optimize it by declaring the paths in a config file (config.yaml). The config.yaml file contains the path to find the scripts to run inside the pipeline, but when I expand the wildcard of the path, the pipeline does not run the script. The script itself runs fine.
To explain my problem:
rule with_script:
input: someinput
output: someoutput
script: expand("{script_path}/scriptfile", script_path = config[scriptpath])
input, output or rule all do not contain the script's path wildcard, so here is the first time I'm declaring it. The config.yaml line that contains the path looks like this:
scriptpath: /path/to/the/script
is there a way to maintain the wildcard and config file path (to make it easier for others to make changes if needed) and have the script work? Like this snakemake doesn't even enter the script file. Or maybe it is possible to declare global wildcards outside the rule all?
Thank you for your help!
P.S.: I'm sorry if this question has already been answered, but I couldn't find anything to help me with this.
You cannot define a function like expand() in the script section. Snakemake expects a path to your script.
Like the documentation states:
The script path is always relative to the Snakefile containing the directive (in contrast to the input and output file paths, which are relative to the working directory). It is recommended to put all scripts into a subfolder "scripts"
If you need to define different paths to your scripts, you can always do it in python outside of your rules. Don't forget, all python code outside of rules is executed before building the DAG. Thus, you can define all variables you want and use them in your rules.
SCRIPTSPATH = config["scriptpath"]
rule with_script:
input: someinput
output: someoutput
script: "{SCRIPTSPATH}/scriptfile"
Note:
Do not mix wildcards and "variables". In an expand function as
expand("{script_path}/scriptfile", script_path = config[scriptpath])
{script_path} is not a wildcard but just a placeholder for the values given in the second parameter of the function.
I am currently using Snakemake for a bioinformatics project. Given a human reference genome (hg19) and a bam file, I want to be able to specify that there will be multiple output files with the same name but different extensions. Here is my code
rule gridss_preprocess:
input:
ref=config['ref'],
bam=config['bamdir'] + "{sample}.dedup.downsampled.bam",
bai=config['bamdir'] + "{sample}.dedup.downsampled.bam.bai"
output:
expand(config['bamdir'] + "{sample}.dedup.downsampled.bam{ext}", ext = config['workreq'], sample = "{sample}")
Currently config['workreq'] is a list of extensions that start with "."
For example, I want to be able to use expand to indicate the following files
S1.dedup.downsampled.bam.cigar_metrics
S1.dedup.downsampled.bam.computesamtags.changes.tsv
S1.dedup.downsampled.bam.coverage.blacklist.bed
S1.dedup.downsampled.bam.idsv_metrics
I want to be able to do this for multiple sample files, S_. Currently I am not getting an error when I try to do a dry run. However, I am not sure if this will run properly.
Am I doing this right?
expand() defines a list of files. If you're using two parameters, the cartesian product will be used. Thus, your rule will define as output ALL files with your extension list for ALL samples. Since you define a wildcard in your input, I think that what you want is all files with your extension for ONE sample. And this rule will be executed as many times as the number of samples.
You're mixing up wildcards and placeholders for the expand() function. You can define a wildcard inside an expand() by doubling the brackets:
rule all:
input: expand(config['bamdir'] + "{sample}.dedup.downsampled.bam{ext}", ext = config['workreq'], sample=SAMPLELIST)
rule gridss_preprocess:
input:
ref=config['ref'],
bam=config['bamdir'] + "{sample}.dedup.downsampled.bam",
bai=config['bamdir'] + "{sample}.dedup.downsampled.bam.bai"
output:
expand(config['bamdir'] + "{{sample}}.dedup.downsampled.bam{ext}", ext = config['workreq'])
This expand function will expand in list
{sample}.dedup.downsampled.bam.cigar_metrics
{sample}.dedup.downsampled.bam.computesamtags.changes.tsv
{sample}.dedup.downsampled.bam.coverage.blacklist.bed
{sample}.dedup.downsampled.bam.idsv_metrics
and thus define the wildcard sample to match the files in the input.
I am new to robot framework and wanted to see if i can get any simple code for custom report. I am also fine with answer to my problem. I went through all questions related to report but could not find any specific answer to my problem. currently my report contains log and wanted to see if i can remove log information from reports and save report in specific location. I just want to get PASS/FAIL information in my report. Can any one give me example how i can overcome this problem? I also need to know how i can save my report in different location. Any example would be helpful. Thank you in advance.
There is a tool called Rebot which is part of Robot Framework.
By default, Robot Framework creates XML reports. The XML reports are automatically converted into HTML reports by Rebot.
You can set the location of the output files in the execution by specifying the parameter --outputdir (and thus set a different base directory for outputs).
From the documentaiton:
All output files can be set using an absolute path, in which case they are created to the specified place, but in other cases, the path is considered relative to the output directory. The default output directory is the directory where the execution is started from, but it can be altered with the --outputdir (-d) option. The path set with this option is, again, relative to the execution directory, but can naturally be given also as an absolute path. Regardless of how a path to an individual output file is obtained, its parent directory is created automatically, if it does not exist already.
You can call Rebot yourself to control this conversion.
You can also run Rebot after the test was run in order to create new output on a different location.
See documentation in:
http://robotframework.org/robotframework/latest/RobotFrameworkUserGuide.html#post-processing-outputs
The following example shows how to store the HTML reports in a different location and including only partial data:
rebot --include smoke --name Smoke_Tests c:\results\output.xml --outputdir c:\version1.0\reports
In the example above, we process the file c:\results\output.xml, create a new report called Smoke_Tests that includes only tests with the tag smoke and save it to the output folder c:\version1.0\reports
In addition you can also set the location of the log file (HTML) from the execution.
The command line option --log (-l) determines where log files are created.
The command line option --report (-r) determines where report files are created
Removing log lines can be done a bit differently. If you run rebot --help you'll get the following options:
--removekeywords all|passed|for|wuks|name: * Remove keyword data
from all generated outputs. Keywords containing
warnings are not removed except in `all` mode.
all: remove data from all keywords
passed: remove data only from keywords in passed
test cases and suites
for: remove passed iterations from for loops
wuks: remove all but the last failing keyword
inside `BuiltIn.Wait Until Keyword Succeeds`
name:: remove data from keywords that match
the given pattern. The pattern is matched
against the full name of the keyword (e.g.
'MyLib.Keyword', 'resource.Second Keyword'),
is case, space, and underscore insensitive,
and may contain `*` and `?` as wildcards.
Examples: --removekeywords name:Lib.HugeKw
--removekeywords name:myresource.*
--flattenkeywords for|foritem|name: * Flattens matching keywords
in all generated outputs. Matching keywords get all
log messages from their child keywords and children
are discarded otherwise.
for: flatten for loops fully
foritem: flatten individual for loop iterations
name:: flatten matched keywords using same
matching rules as with
`--removekeywords name:`
I am facing an issue where I need to run script with three features. Let's say we have 3 feature files with tag names as #smoke1, #smoke2 and #smoke3. And I want these to be executed in that sequence.
Issue is that smoke3 is executing first and rest of them afterwards.
This is my script:
#Cucumber.Options(
glue = { "com.abc", "cucumber.runtime.java.spring.hooks" },
features = "classpath:",
format = { "json", "json:target/cucumber.json" },
tags = "#smoke1, #smoke2, #smoke3"
)
public class ex_Test extends AbstractTest { }
Warning: This only works in older versions of Cucumber.
Cucumber feature files are executed in alphabetical order by path and filename. The execution order is not based on tags.
However, if you specifically specify features, they should be run in the order declared.
For example:
#Cucumber.Options(features={"first_smoke.feature", "another_smoke.feature"})
Should run first_smoke and then another_smoke (compared to the default which is to run in the other order.
Ok we got it , We can have multiple tags for a single scenario like this #tag1 #tag2 #tag3.
You can not define the order in way below.
#Cucumber.Options(features={"first_smoke.feature", "another_smoke.feature"})
Cucumber determines the only alphabetical order and even only first letter of the word.
You can have how many tags you want in feature file, if you want to trigger feature file more times, it's not working like you will add tag more time or more tags from feature like:
tags = {"#Reports,#Reports"}
And tests are triggered in alphabetical order, it's checking tags not feature file name.
For me ack is essential kit (its aliased to a and I use it a million times a day). Mostly it has everything I need so I'm figuring that this behavior is covered and I just can't find it.
I'd love to be able to restrict it to specific kinds of files using a type. the problem is that these files have a full filename rather than an extension. For instance I'd like to restrict it to build files for buildr so i can search them with --buildr (Similar would apply for mvn poms). I have the following defined in my .ackrc
--type-set=buildr=buildfile,.rake
The problem is that 'buildfile' is the entire filename, not an extension, and I'd like ack to match completely on this name. However if I look at the types bound to 'buildr' it shows that .buildfile is an extension rather than the whole filename.
--[no]buildr .buildfile .rake
The ability to restrict to a particular filename would be really useful for me as there are numerous xml usecases (e.g. ant build.xml or mvn pom.xml) that it would be perfect for. I do see that binary, Makefiles and Rakefiles have special type configuration and maybe that's the way to go. I'd really like to be able to do it within ack if possible before resorting to custom functions. Anyone know if this is possible?
No, you cannot do it. ack 1.x only uses extensions for detecting file types. ack 2.0 will have much more flexible capabilities, where you'll be able to do stuff like:
# There are four different ways to match
# is: Match the filename exactly
# ext: Match the extension of the filename exactly
# match: Match the filename against a Perl regular expression
# firstlinematch: Match the first 80 characters of the first line
# of text against a Perl regular expression. This is only for
# the --type-add option.
--type-add=make:ext:mk
--type-add=make:ext:mak
--type-add=make:is:makefile
--type-add=make:is:gnumakefile
# Rakefiles http://rake.rubyforge.org/
--type-add=rake:is:Rakefile
# CMake http://www.cmake.org/
--type-add=cmake:is:CMakeLists.txt
--type-add=cmake:ext:cmake
# Perl http://perl.org/
--type-add=perl:ext:pod
--type-add=perl:ext:pl
--type-add=perl:ext:pm
--type-add=perl:firstlinematch:/perl($|\s)/
You can see what development on ack 2.0 is doing at https://github.com/petdance/ack2. I'd love to have your help.