Include paths for tested wrappers in `planemo test` report

[marehr]

Hi planemo-team!

I have the following tool_test_output.html

My problem is that I don't know why raptor is within my tests, as there aren't any .xml files in my current environment.

(I have a different repository where I created a galaxy raptor port; So I know the tool, but I don't know why it is included in my other environment.)

Could you add the paths to the .xml files that were used to instantiate the test in the report? I think this would help me to figure this out.

Thank you!

[simonbray]

Hi @marehr,

What commands are you running? Are you developing a tool?

What do you mean by environment, a directory?

What do you mean by 'galaxy raptor port' - is this a Galaxy tool wrapper?

Simon

[marehr]

(In the meantime I figured it out, I still think that the test report should include the path to the tool-xml file which added the test case!)

Sorry for the poor information:

Hi @marehr,

What commands are you running?

source ./planemo-venv/bin/activate
planemo test

Are you developing a tool?

Yes, I'm playing around developing a galaxy tool.

What do you mean by environment, a directory?

Yes a directory with two toy example, one fastq_to_fasta.xml converter and one gc_counter.xml.

The directory structure is as follows

> ls -al           
drwxr-xr-x  3 marehr marehr   4096 Sep 29 12:17 app_binary
drwxr-xr-x  4 marehr marehr   4096 Sep 29 12:33 fastq_to_fasta
-rw-r--r--  1 marehr marehr   2291 Jun 24 13:32 fastq_to_fasta.xml
-rw-r--r--  1 marehr marehr   2234 Jun 24 13:42 gc_counter.xml
drwxr-xr-x  7 marehr marehr   4096 Sep 29 11:45 planemo-venv
lrwxrwxrwx  1 marehr marehr     75 Sep 29 12:17 test-data
-rw-r--r--  1 marehr marehr 351542 Sep 29 12:00 tool_test_output.html
-rw-r--r--  1 marehr marehr  10674 Sep 29 12:00 tool_test_output.json

(I omitted other files / folders that are also within that folder)

When I run > planemo test, I got the following result:

I was wondering where the third test (i.e. xml file) came from, as only 2 XML file are in the current directory, and they did not contain any "raptor" stuff. Maybe I should mention that I tried to re-run this after 1 month, and I forgot in the meantime what I did 1 month ago.

It turns out that I had this fastq_to_fasta directory (my previous temporary test folder for shed uploads), that contains the following:

> ls -al fastq_to_fasta

-rw-r--r-- 1 marehr marehr    202 Jul 30 12:23 .shed.yml
-rw-r--r-- 1 marehr marehr   1271 Jul 30 12:19 fastq_to_fasta.xml
-rw-r--r-- 1 marehr marehr   1255 Aug  4 13:24 raptor-build.xml
lrwxrwxrwx 1 marehr marehr     12 Jul 30 12:07 test-data -> ../test-data
-rw-r--r-- 1 marehr marehr 353498 Sep 29 14:38 tool_test_output.html
-rw-r--r-- 1 marehr marehr  13068 Sep 29 14:38 tool_test_output.json

Now I found my culprit :) So I learned two things: It seems planemo test searches recursively in all subdirectories, where it found the following files fastq_to_fasta.xml, gc_counter.xml, fastq_to_fasta/fastq_to_fasta.xml, and fastq_to_fasta/raptor-build.xml and it seems to ignore one of the fastq_to_fasta.xml files as they have the same name.

What do you mean by 'galaxy raptor port' - is this a Galaxy tool wrapper?

It is another tool that I try to make accessible for galaxy. And it seems that I still had a prototype-xml of that in my toy-example galaxy tools.

Simon

Form this experience it would be nice to have something like this

as debug information.

[simonbray]

Okay, glad you were able to find a solution! I can see that including the paths in the test report might be handy.