Opened 6 years ago

Closed 5 years ago

#610 closed defect (fixed)

mzML error for MALDI files

Reported by: Rene Ranzinger Owned by: dbrentw
Priority: high Milestone: GRITS - 1.2
Component: MS data management Version: GRITS 1.1.x
Severity: critical Keywords:
Cc: dbrentw

Description

When converting Bruker MALDI files to mzML a file is generated that uses text spectra ids. The mzML reader in GRITS does not support this although it is valid:

...
<spectrum index="0" id="file=_x0031_SRef_x002f_fid" defaultArrayLength="163840">
...
<indexList count="2">

<index name="spectrum">

<offset idRef="file=_x0031_SRef_x002f_fid">3905</offset>

</index>

</indexList>

Change History (7)

comment:1 Changed 6 years ago by Rene Ranzinger

Owner: set to dbrentw
Status: newassigned

comment:2 Changed 6 years ago by dbrentw

Status: assignedaccepted

comment:3 Changed 6 years ago by Rene Ranzinger

Milestone: GRITS - 1.1 SR1GRITS - 1.1 SR2

comment:4 Changed 5 years ago by dbrentw

Resolution: fixed
Status: acceptedreview

Resolved in SVN revision 1974

comment:5 Changed 5 years ago by Rene Ranzinger

Resolution: fixed
Status: reviewassigned

When uploading this file it seems to work fine. However there are still NumberFormatExceptions written to the console. If that exceptions should be recorded they should go into the logfile as debugs. They are not really errors since we know what cases them and "fix" that.

comment:6 Changed 5 years ago by dbrentw

Resolution: fixed
Status: assignedreview

Update again. I think I've resolved the exceptions problem. SVN revision 2091

comment:7 Changed 5 years ago by Rene Ranzinger

Status: reviewclosed
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