Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#1451 closed task (fixed)

Implement BFS importer for spot data

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: BASE 2.15
Component: coreplugins Version:
Keywords: Cc:

Description

The implementation of the plug-in should build on/use the generic parsers that are implemented as part of #1444.

This ticket in itself can also be split in two parts. First, a working import implementation (not a plug-in) is created, then a plug-in is created that uses the importer.

Change History (11)

comment:1 Changed 12 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:2 Changed 12 years ago by Nicklas Nordborg

(In [5227]) References #1451: Implement BFS importer for spot data

First version of the importer. It can import serial/matrix BFS with data in the same datacube. There is code also for remapping position/reporter and parents assays into a new datacube, but the test code needs to be extended with those two cases. I have currently "hijacked" the BASEfile exporter test case for both the BFS export and import tests.

I am thinking that maybe we need a better way to handle complex tests like this since it is rally hard for every test case to setup a complete experiment of it's own.

comment:3 Changed 12 years ago by Nicklas Nordborg

(In [5232]) References #1451: Implement BFS importer for spot data

Do not report progress on every line.

comment:4 Changed 12 years ago by Nicklas Nordborg

(In [5233]) Fixes #1452: Refactor analysis test cases References #1451: Implement BFS importer for spot data

The BFS exporter/importer test case is now moved to a separate class.

comment:5 Changed 12 years ago by Nicklas Nordborg

(In [5236]) References #1451: Implement BFS importer for spot data

Added a test case that merge all assays into one.

comment:6 Changed 12 years ago by Nicklas Nordborg

(In [5237]) References #1451: Implement BFS importer for spot data

Added a test case that merge reporters. It's a fake merge which just merges two data lines, but it should test the code for creating a new reporter->position mapping.

comment:7 Changed 12 years ago by Nicklas Nordborg

(In [5238]) References #1451: Implement BFS importer for spot data

Added support for importing/linking additional files to the child bioassay set.

comment:8 Changed 12 years ago by Nicklas Nordborg

(In [5240]) References #1451: Implement BFS importer for spot data

Added support for specifying the intensity transformation in the metadata file. Useful if the plug-in has transformed non-logged to logged data or the other way around.

comment:9 Changed 12 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

The importer can now import spot data and extra files. Support for other types of data (extra values, reporter lists, etc.) are added when needed by a plug-in use-case. New tickets should be created for this.

comment:10 Changed 12 years ago by Nicklas Nordborg

(In [5284]) References #1451: Implement BFS importer for spot data

Added support for BFS that only includes extra files and no spot data. In this case, only a transformation is created and the extra files are uploaded to BASE and attached to the transformation.

comment:11 Changed 12 years ago by Nicklas Nordborg

(In [5309]) References #1444, #1448, #1451. Added methods for closing BFS parsers and an auto-close feature on the exporter and importer. This was needed since some temporary working files could not be deleted without closing the streams.

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