Misc datatypes fixes and enhancements #2690
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nsoranzo
commented
Jul 29, 2016
nsoranzo
commented
- Redefine svg datatype as subclass of GenericXml
- Fix some wrong file_ext
- Fix import order and Python3 compatibility
- Specify some classes as abstracts
- Use super() to call superclass methods
- Various semplifications
SVG is XML-based and Python Pillow does not support it.
- Specify some classes are abstracts - Use super() to call superclass methods - Various simplifications
| @@ -72,7 +72,7 @@ def display_peek(self, dataset): | |||
| class ProtXmlReport(Tabular): | |||
| """protxml converted to tabular report""" | |||
| edam_data = "data_2536" | |||
| file_ext = "tsv" | |||
| file_ext = "protxml.tsv" | |||
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I saw you make this comment the other day, and it seemed wrong at the time - that this extension needs to match the datatypes_conf.xml file. I thought file_ext in this file is used for downloads - and that many things with the same file_ext could all have different datatypes_conf.xml keys.
I wouldn't make this change - do you have evidence that it needs to match up?
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@jmchilton The file_ext attribute is not used when downloading a history dataset, in fact if you have a "protxml.tsv" dataset on Galaxy Main and click the disk icon, the downloaded file will have ".protxml.tsv" extension. It is instead used by the guess_ext function in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/sniff.py#L369 .
This PR fixes a problem for the upload of hmm2 and hmm3 files, if you upload a text file starting with HMMER2.0 on Galaxy Main, the sniffer recognizes it as hmm instead of hmm2 because the file_ext attribute was wrong.
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Okay then - I stand quite corrected. Thanks for schooling me.
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@jmchilton I was also assuming it has something do to with the download extension and I think there should be such a reall-ife extension defined in a datatype, isn't it?
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All tests pass after a restart. |
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xref #1715 |
