Opened 11 years ago

Closed 11 years ago

#239 closed defect (fixed)

BGX reporter/feature importer auto-detection matches any files with at least two sections

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Illumina package v1.4
Component: net.sf.basedb.illumina Keywords:
Cc:

Description

The auto-detection never reaches the stage were the data header regular expression is used. This happens because the standard flat file parser assumes that there is 0 or 1 section only. If the auto-detection parsing ends on an UNKNOWN line the file is not importable, otherwise the file is considered importable. With BGX files the standard auto-detection ends on the second SECTION HEADER and the file is considered importable.

This can easily be tested by creating a file like this:

[SectionA]
[SectionB]

Both the BGX reporter importer and the BGX feature importer will think they can import the file. The solution is to override the isImportable(FlatFileParser) method and continue parsing the BGX file to see if the data header regular expression can be matched.

Change History (2)

comment:1 Changed 11 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 11 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [1146]) Fixes #239: BGX reporter/feature importer auto-detection matches any files with at least two sections

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