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galaxyproject / usegalaxy-playbook

Ansible Playbook for usegalaxy.org
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Test updated vcffilter once installed at main #182

Open jennaj opened 5 years ago

jennaj commented 5 years ago

IUC issue: https://github.com/galaxyproject/tools-iuc/issues/1910

PR fix: https://github.com/galaxyproject/tools-iuc/pull/2209

Test these:

Test history: https://usegalaxy.org:/u/jen/h/test-history-vcffilter-100rc1galaxy1

jennaj commented 5 years ago

@VJalili Hi - looks like the tool is updated in the MTS and ready to get installed on main. Once there, I can do final testing and close this out. Thanks!

1.0.0_rc1+galaxy2: https://toolshed.g2.bx.psu.edu/view/devteam/vcffilter/de885f4afb7f

(Main has 1.0.0_rc1+galaxy1 as of today)

jennaj commented 5 years ago

@VJalili @davebx who will be doing the update? Timeframe? Re: https://github.com/galaxyproject/usegalaxy-playbook/projects/2#card-15677536

jennaj commented 5 years ago

Status? @VJalili @davebx

davebx commented 5 years ago

Updated to 1.0.0_rc1+galaxy2

jennaj commented 5 years ago

Testing

jennaj commented 5 years ago

Good news: Quoted terms are being parsed correctly

Minor bad news: Tool form help is not rendering correctly. Not sure if that is a problem with the wrapper or the new GUI display in 19.01. Has this text inserted:

System Message: ERROR/3 (<string>, line 20)

Unexpected indentation.

Major bad news: Missed that the "invert" (grep -v) functionality is not working (prior version and this one). Needs another ticket at IUC repo.

Some terms will allow a < operator that (sort of) gets around this. Examples: DP > 10 vs DP < 10 (both work)

Mixed operators are problematic:!= and <= and >= -- so no way to do this kind of filtering. Tried ne instead of != but don't think that is expected to work with this tool. Examples: type = ins (works) versus type != ins (fails). DP >= 10(fails). DP != 10(fails)

All tests in the same original test history. I'll create and link back new IUC issue for invert problems and create a new tracking ticket in this repo.

BUT we shouldn't close this one out until the tool help renders correctly (need to figure out why & fix). Updating the form help was one of the changes for the new version. If the tool form needs a change, we should probably fix the invert functionality, then update the wrapper in MTS & main at the same time.

@dannon -- can you tell why the tool help is not rendering? Or who could? Is it the new Galaxy GUI or some problem with the tool form itself?

jennaj commented 5 years ago

OK, more filter cases can be worked around (not using invert) by using multi-terms and logical OR.

DP > 10 OR (using buttons) DP = 10 will filter for DP >= 10

BUT for the filters like these, can't be worked around, only a functional "invert" would work.

type != ins (fails and could be an actual use case). DP != 10(fails but is unlikely to be an actual use case, is just an example)

There might be problems with the Genotype filter -- testing that again next. All in same history w tags.

jennaj commented 5 years ago

Tests pass for current fixes, new issue opened for other problems

VJalili commented 5 years ago

Minor bad news: Tool form help is not rendering correctly. Not sure if that is a problem with the wrapper or the new GUI display in 19.01. Has this text inserted: System Message: ERROR/3 (, line 20) Unexpected indentation.

Fixed; xref: https://github.com/galaxyproject/tools-iuc/pull/2383

jennaj commented 5 years ago

Use this as the tracking ticket for final steps (MTS update, tool installed at .org + .eu, functionality tests)

jennaj commented 5 years ago

Form fixes: https://github.com/galaxyproject/usegalaxy-playbook/issues/216

VJalili commented 5 years ago

@jennaj

Mixed operators are problematic:!= and <= and >=

xref: https://github.com/galaxyproject/tools-iuc/pull/2385 As the tool help form says, the only valid operators as:

=, !, <, >, |, &

The tool does not support mixing them as one filter (e.g, you cannot use "!=", "<="). Instead you would need to leverage composition of filters for operators such as "<=".

VJalili commented 5 years ago

Regarding negation operators:

They work as expected, please check their correct syntax here: https://github.com/galaxyproject/tools-iuc/issues/2300#issuecomment-473043691

Also documented in the tool help form: 

Obtain logical negation through the use of parentheses, e.g. "! ( DP = 10 )"
Please mind the blank space between parentheses and the arguments.

[REF]

jennaj commented 5 years ago

Right -- it is the tool form option for "invert" that is not working (further down the form, not part of the expression itself).

Put details in here https://github.com/galaxyproject/tools-iuc/pull/2385#issuecomment-488872711 (wrong place, I know) but branched off four issues from it, linked below my comment and now in our project list. Doesn't have to all be the same person doing all.

Those should capture all the tool errors I see what this is used. If/when all done, will probably eliminate all bug reports from this tool going forward. And we can tune up other tools with high usage error problems that same way (if it works!).