Opened 8 years ago

Closed 7 years ago

#365 closed task (fixed)

Export bioplate information to a file that can be used by the Caliper machine

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v2.4
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

This is related to #364.

When the plate is full it is going to be processed by the Caliper machine. We need to create a data file about the extracts on the plate that can be used by the machine.

Change History (10)

comment:1 Changed 8 years ago by Nicklas Nordborg

It seems like the file format is a simple csv without headers. Each well is represented on one row with following columns:

  • Well label (A1, A2, etc.)
  • Sample name
  • User comment
  • List of expected peak sizes (separated by ;)
  • List of search window size

comment:2 Changed 7 years ago by Nicklas Nordborg

Status: newassigned

comment:3 Changed 7 years ago by Nicklas Nordborg

(In [1544]) References #365: Export bioplate information to a file that can be used by the Caliper machine

Added CaliperSampleNameExporter. It can be used from Reggie or from the Bioplate view page (as an export plug-in).

comment:4 Changed 7 years ago by Nicklas Nordborg

(In [1545]) References #365: Export bioplate information to a file that can be used by the Caliper machine

Should have been included as part of [1544].

comment:5 Changed 7 years ago by Nicklas Nordborg

(In [1548]) References #365: Export bioplate information to a file that can be used by the Caliper machine

  • Fixed an issue with empty wells causing a NPE.
  • Make sure that commas are removed from sample names

comment:6 Changed 7 years ago by Nicklas Nordborg

(In [1550]) References #365: Export bioplate information to a file that can be used by the Caliper machine

Export HiSense? setting in the "User comment" field. Can be moved to be part of the name if that is better, but then the importer also need to be updated since the sample names in the Caliper output files are affected.

Otherwise, the exporter should now be fully working.

comment:7 Changed 7 years ago by Nicklas Nordborg

(In [1557]) References #364, #365 and #366. Added a short note about the new wizards to the README.

comment:8 Changed 7 years ago by Nicklas Nordborg

(In [1570]) References #365 and #370. Added checks in the installation wizard that verify the installation of plug-ins and configurations.

comment:9 Changed 7 years ago by Nicklas Nordborg

(In [1583]) References #364, #365, #366, #370. Show a message and animated 'loading' icon when waiting for JSON request to return data from server

comment:10 Changed 7 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

Worked just fine during the run today.

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