Opened 14 years ago

Closed 14 years ago

Last modified 11 years ago

#1152 closed enhancement (fixed)

Improve transaction handling in Base1PluginExecuter

Reported by: Nicklas Nordborg Owned by: Martin Svensson
Priority: major Milestone: BASE 2.9
Component: coreplugins Version:
Keywords: Cc:


The Base1PluginExecuter currently opens and closes transactions in some strange places. The first transactions span the export, execution and data import. It uses a second parallel transaction for attaching files during the data import. A third transaction is then used for some clean-up tasks like removing stdin and stdout.

It is definitely not needed to keep a transaction open during the execution phase. The first transaction should be closed after the data export. A second transaction should be used for data import. If possible things should be rearranged so there is no need for a parallel transaction for the file import or for the third transaction used for clean-up.

Change History (3)

comment:1 Changed 14 years ago by Martin Svensson

Owner: changed from everyone to Martin Svensson
Status: newassigned

comment:2 Changed 14 years ago by Martin Svensson

Resolution: fixed
Status: assignedclosed

(In [4606]) Fixes #1152 Improve transaction handling in Base1PluginExecuter. There is only one transaction open each time and there are three separate transaction now: one for exporting data, one to import files and the last to import data and do some clean-up.

comment:3 Changed 11 years ago by Nicklas Nordborg

(In [5773]) References #1152: Handling short read transcript sequence data

  • Adds a 'Cufflinks' raw data type with five columns: coverage, fpkm, fpkm_lo, fpkm_hi and status
  • Define FPKM_TRACKING file type and MIME type.
  • Adds left(string, index) as a JEP formula so that we can parse out the chromosome from the 'locus' column in the tracking files.
  • Define two new configurations for the raw data importer that parses cufflinks isoform files.
Version 0, edited 11 years ago by Nicklas Nordborg (next)
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