Conversion bruker data #148
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Can you add a "--version" command so we dont have to hardcode the version in workflows everytime and everywhere? |
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…o conversion_bruker_data
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How can you specify that both raw and d are converted to mzml? |
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You mean having a conversion where you have more than one file type? Right now you will only have one file type to another, this is allowed: |
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what if you have multiple file types in the initial design? |
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We don't allow that in quantms or even OpenMS. I guess is a really future use case. |
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It is allowed in quantms. |
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If you only allow one type of raw file, why a mapping at all? |
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Ok, what will be the expected behaviour, something like: raw:mzml Which mean convert the raw to mzml and keep the d as d? |
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Yes exactly. |
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What should happen if the user gives contradictory changes, like d:d and d:raw ? Error? |
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I will put the following behavior: |
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@jpfeuffer the following commit allows multiple file conversions: 9c304a7 |
| @@ -12,17 +12,28 @@ def test_validate_srdf(): | |||
| runner = CliRunner() | |||
| result = runner.invoke(cli, ["validate-sdrf", "--sdrf_file", "testdata/PXD000288.sdrf.tsv", "--check_ms"]) | |||
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| print(result.output) | |||
| assert "ERROR" not in result.output | |||
| print("validate sdrf " + result.output) | |||
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Any particular reason to not use an assert statement here instead of the print? Just reading this test, I don't know what would count as a test failure. Or success. There might be an
assert "ERROR" not in result.output
missing?
| def test_search_mods_by_accession(): | ||
| unimod = UnimodDatabase() | ||
| ptm = unimod.get_by_accession("UNIMOD:21") | ||
| print(ptm.get_name()) | ||
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| def test_search_mods_by_keyword(): | ||
| unimod = UnimodDatabase() | ||
| ptms = unimod.search_mods_by_keyword("Phospho") | ||
| for ptm in ptms: | ||
| print(ptm.to_str()) |
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Again, tests should have an assert. Without they still require human interpretation and the idea is to have the test automated and as little as possible human interpretation/interaction.
| @@ -37,7 +37,7 @@ def verify_content(pname, pvalue, ptype): | |||
| # exit("ERROR: " + pname + " needs to be a numeric value!!") | |||
| elif ptype == "class": | |||
| not_matching = [x for x in pvalue.split(",") if x not in p["value"]] | |||
| if not_matching != []: | |||
| if len(not_matching) != 0: | |||
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Sidenote: This could be just if not_matching:
| @@ -98,7 +98,7 @@ def add_ptms(mods, pname, mod_columns): | |||
| modname = tmod[0] | |||
| modpos = tmod[1] | |||
| found = [x for x in unimod.modifications if modname == x.get_name()] | |||
| if found == []: | |||
| if len(found) == 0: | |||
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Sidenote: I would probably have gone with if not found.
| @@ -35,6 +41,15 @@ def get_name(self): | |||
| def get_accession(self): | |||
| return self._ontology_term.get_accession() | |||
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| def get_delta_mono_mass(self): | |||
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Another option would be to make them properties with the "@Property" decorator. That way the "get_" prefix could be left out and the attributes would still have some protection against overwriting.
extension_convertreflecting discussion in [Pitch] Partial keep raw in OpenMS #145 and PR in quantms Feature/bruker data quantms#275.