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[WIP] EBI improvements #1451
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[WIP] EBI improvements #1451
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WIP: ebi-improvements -- initial cleanup
Sync with master
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EBI step 2
Ebi step 3
Ebi improvements pet
…nto next-joy-list
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WIP: Next steps
Solving merge conflicts
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This was referenced Oct 10, 2015
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Make sure that these are done:
lib_strategies = {'metagenome': 'POOLCLONE',
is doing. // This has been coded in step-3 and now is dynamicwrite_xml_file
function. // Modified in cover-some-joy-list-issuesASPERA_SCP_PASS
environment variable should happen when the command is called, not when the command is generated. // fixed in step 4 #1477generate_demultiplexed_fastq
step (hit this edge case while I was writing tests for other sections of the code) // Done in WIP: Next steps #1488Things that are not gonna be done and explanation:
EBISubmission.__init__
as it is getting long and complex. Not really needed. We could split the code in a couple of methods but will not add much clarity + that code is not used anywhere else.ParallelWrapper
class // this is not needed due to how the ebi flow is.For all other updates (where samples are added or removed, or sequence files need to be updated), I believe we cannot actually do the update automatically. However, if we store the proper information in the database (i.e., the EBI aliases for everything that we submit), then we can automatically send an email requesting changes. update EBI study #1487