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"Join two Datasets" (join1) preserve column headers #4229

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merged 7 commits into from Sep 7, 2017

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commented Jun 26, 2017

Ping @erasche
Related to: #524

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commented Jun 26, 2017

I still have to work on the syntax

@lecorguille lecorguille force-pushed the lecorguille:join_header branch 2 times, most recently from 96fdc10 to 3f2c3df Jun 26, 2017

@lecorguille lecorguille force-pushed the lecorguille:join_header branch from 3f2c3df to 222a750 Jun 26, 2017

@galaxybot galaxybot added the triage label Jun 26, 2017

@galaxybot galaxybot added this to the 17.09 milestone Jun 26, 2017

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commented Jun 26, 2017

@erasche
If you have an idea on this test which fails.
It seems not related to my commits!?

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This looks good to me, though I have not run the code yet. Definitely a big improvement and looks like lots of good planemo linting fixes as well.

out = open( out_filename, 'w+b' )
index = BufferedIndex( filename2, column2, split, buffer, index_depth )
for line1 in open( filename1, 'rb' ):
if keep_headers and not keep_headers_done:

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Isn't there a dataset attribute that tells you the number of header lines? This might be a good alternative to the regex? I don't know, I'd need someone else to comment on this.

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commented Aug 21, 2017

@martenson any ideas on that failed test?

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commented Aug 21, 2017

It is a transiently failing test and unrelated.

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commented Aug 21, 2017

brilliant, then this looks good to me. 👍

@@ -284,7 +285,7 @@ def fill_empty_columns( line, split, fill_values ):
return split.join( filled_columns )


def join_files( filename1, column1, filename2, column2, out_filename, split=None, buffer=1000000, keep_unmatched=False, keep_partial=False, index_depth=3, fill_options=None ):
def join_files( filename1, column1, filename2, column2, out_filename, split=None, buffer=1000000, keep_unmatched=False, keep_partial=False, keep_headers=False, index_depth=3, fill_options=None ):

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this file needs merging against dev so it respects our new whitespace requirements :/

@dannon dannon merged commit 530827f into galaxyproject:dev Sep 7, 2017

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@lecorguille lecorguille deleted the lecorguille:join_header branch Sep 11, 2017

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