OpenMS 3.1 #697

bernt-matthias · 2022-12-22T15:24:35Z

For preparation .. collecting fixes :)

truncate description to the first line: MSFragger contained a huge disclaimer :(
also GNPSExport has a long description
Fix / improve XMLValidator add mzml-validation tool RECETOX/galaxytools#319
- add xsd to galaxy datatypes [22.05] add xsd datatype galaxyproject/galaxy#15344
- add tests from the above PR to the OpenMS code base
- update file type mapping for xsd .. xsd <-> xsd .. also xml should point to xml not bioml in gxy2oms
try to use remote test data as much as possible
- is it possible to rely on data from OpenMS git as much as possible?

3.1

MapAlignerPoseClustering: out and trafo_out are not OPTIONAL_OUTPUTS .. one needs to be given.
Sirius deprecate all/mostly or support email/password login, but OpenMS likely will drop support anyway SiriusAdapter fails in OpenMS 3.0 OpenMS/OpenMS#7000 (comment)
drop adapters that require 3rd party software not available in conda
- drop NovorAdapter (3rd party software seem not available anymore?)
- MSFragger, MaRaClusterAdapter,MascotAdapter?
add expect_num_outputs
Fix FLASHDecov
- replace command section parts for -out_spec FLASHDeconv_1_spec1.csv FLASHDeconv_1_spec2.csv FLASHDeconv_1_spec3.csv (and analogously for

MSFragger contained a huge disclaimer :(

full message is: ``` Note: This message can also be triggered if you run out of space in your tmp directory or (32bit OMSSA only) OMSSA ran out of RAM because chunking was not used (that's the default) or 'chunk_size' was too large (>30k). Look above! ```

full message in stderr is: ``` Process '/gpfs1/data/galaxy_server/galaxy/database/dependencies/_conda/envs/mulled-v1-4ada2d9266641ecd767c7de738261cde57c65095a0fa06c286e3bc2f08b0cd57/bin/comet' crashed hard (segfault-like). Please check the log. ```

save space when cloning OpenMS

Adapter has been removed

and add test for xsd use in XMLValidator

and remove some code that was needed for tools that are now deprecated

needs login and is therefore difficult to test effort to implement tests would be useless since it will be dropped in next release anyway

won't run at the moment

now provided by OMS

blacklist MaRaClusterAdapter

bernt-matthias · 2024-06-13T14:57:06Z

Linter errors are all: WARNING (TestsMissing): No tests found, most tools should define test cases. which won't be fixed and will be ignored for deployment.

tools/openms/AccurateMassSearch.xml

tools/openms/CometAdapter.xml

tools/openms/FeatureFinderCentroided.xml

bgruening

Nothing scary in here, added 3 small comments, but from my side this is good. Very cool, thanks!

to new aux file locations and remove some unneeded code

otherwise it won't be deployed

bernt-matthias · 2024-06-14T18:30:28Z

Ready :)

bgruening · 2024-06-14T18:40:02Z

🥳🥳🎉🎉

bernt-matthias marked this pull request as draft December 22, 2022 15:24

bernt-matthias mentioned this pull request Jan 20, 2023

add mzml-validation tool RECETOX/galaxytools#319

Merged

bernt-matthias mentioned this pull request Oct 16, 2023

OpenMS tools not updated usegalaxy-eu/usegalaxy-eu-tools#582

Open

bernt-matthias force-pushed the openms2.9 branch from c630ad5 to b02f4f8 Compare October 26, 2023 12:53

bgruening changed the title ~~OpenMS 2.9~~ OpenMS 3.1 Nov 2, 2023

bernt-matthias force-pushed the openms2.9 branch from 6391892 to f59ede2 Compare April 8, 2024 13:41

bernt-matthias referenced this pull request Apr 12, 2024

update testing

55c6ded

bernt-matthias mentioned this pull request Apr 21, 2024

Add Sage (search engine) on usegalaxy.eu galaxyproject/tools-iuc#5960

Closed

bernt-matthias added 22 commits June 4, 2024 11:14

truncate description to the first line

d552f08

MSFragger contained a huge disclaimer :(

Catch OMSSA OOM

30cc402

full message is: ``` Note: This message can also be triggered if you run out of space in your tmp directory or (32bit OMSSA only) OMSSA ran out of RAM because chunking was not used (that's the default) or 'chunk_size' was too large (>30k). Look above! ```

Add Comet OOM

9c64dc5

full message in stderr is: ``` Process '/gpfs1/data/galaxy_server/galaxy/database/dependencies/_conda/envs/mulled-v1-4ada2d9266641ecd767c7de738261cde57c65095a0fa06c286e3bc2f08b0cd57/bin/comet' crashed hard (segfault-like). Please check the log. ```

cnt 3.0

b45b952

towards 3.1

b325f73

openms: improve test-data.sh

d3a0456

save space when cloning OpenMS

remove OMMSA requirement

2b5f852

Adapter has been removed

update requirements

9cb98a7

remove traces of deprecated tools

a6e83e3

and add test for xsd use in XMLValidator

fix xsd file mapping

6b3e38b

hardcode sage_executable

bab0cec

and remove some code that was needed for tools that are now deprecated

generate tests with python

c490657

fix TEST_DATA_LOCATION

c7e79c0

add general stdout assertion to all tests

9b95239

python script linter fixes

9dda0bb

location: fallback needs to be specified via value

8803952

remove location for now

bcdb208

fix python linter errors

12f56c7

remove test params without value

4f220ef

some fixes

9c1fee5

stash

b8e8aed

fix for test generation

8f71324

bernt-matthias added 11 commits June 4, 2024 11:14

drop tests that use Sirius

8ebeb15

needs login and is therefore difficult to test effort to implement tests would be useless since it will be dropped in next release anyway

fix test data generation

5d05d3b

add comment

194bcde

fix tests skipping

7f5ec3b

fix flake

42cf488

skip Dechargers

0dfb2f8

won't run at the moment

fix a test

1e4a1d6

remove manually curated tests for PSMFeatureExtractor

f272f26

now provided by OMS

remove some hardcoded rules

9c0edb2

remove now unused hardcoding

217ad3e

remove some hardcoding for prefix output param

d1be6e4

bernt-matthias force-pushed the openms2.9 branch from d5d2208 to d1be6e4 Compare June 4, 2024 09:14

bernt-matthias added 3 commits June 6, 2024 09:41

OpenSwathFileSplitter: make outdir required

d2e82a6

fix output format for OpenSwathFileSplitter

22b0a33

blacklist MaRaClusterAdapter

cleanup

0a616d8

bernt-matthias marked this pull request as ready for review June 13, 2024 14:56

more cleanup

1c32e81

bgruening reviewed Jun 13, 2024

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bgruening reviewed Jun 13, 2024

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tools/openms/CometAdapter.xml Outdated Show resolved Hide resolved

bgruening reviewed Jun 13, 2024

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bgruening reviewed Jun 13, 2024

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bernt-matthias added 4 commits June 14, 2024 10:11

do dot use checkboxes/radio for selects

39d6e0d

update test data generation

1253e81

to new aux file locations and remove some unneeded code

move test data generation py script to root

fdf6184

otherwise it won't be deployed

omit optional if default

fd81607

bgruening merged commit 5c080b1 into galaxyproteomics:master Jun 14, 2024
12 of 14 checks passed

bernt-matthias deleted the openms2.9 branch June 14, 2024 18:41

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OpenMS 3.1 #697

OpenMS 3.1 #697

bernt-matthias commented Dec 22, 2022 •

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bernt-matthias commented Jun 13, 2024

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bernt-matthias commented Jun 14, 2024

bgruening commented Jun 14, 2024

OpenMS 3.1 #697

OpenMS 3.1 #697

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bernt-matthias commented Dec 22, 2022 • edited Loading

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bernt-matthias commented Jun 14, 2024

bgruening commented Jun 14, 2024

bernt-matthias commented Dec 22, 2022 •

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