Opened 13 years ago

Closed 13 years ago

#1171 closed enhancement (fixed)

Add BioLIMS support to batch importers

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: BASE 2.10
Component: coreplugins Version:
Keywords: Cc:

Description (last modified by Johan Vallon-Christersson)

The batch importers that works with biomaterial items (SampleImporter, ExtractImporter, LabeledExtractImporter) should be extended so that they can also set the location of the biomaterial on a plate. See #979.

Change History (7)

comment:1 Changed 13 years ago by Johan Vallon-Christersson

Description: modified (diff)

comment:2 Changed 13 years ago by Martin Svensson

Owner: changed from everyone to Martin Svensson
Status: newassigned

comment:3 Changed 13 years ago by Martin Svensson

Resolution: fixed
Status: assignedclosed

(In [4736]) Fixes #1171 Add BioLIMS support to batch importers. Also updated the user-role test to place the biomaterials on a bioplate.

comment:4 Changed 13 years ago by Nicklas Nordborg

Resolution: fixed
Status: closedreopened

UserTest? program fails with:

++Entering user test
--Logging in as: user
--Creating bioplate: Bioplate A
--Uploading file: /mouse/genepix.mouse.v4.37k.00h.gpr
--Uploading file: /mouse/genepix.mouse.v4.37k.24h.gpr
--Uploading file: /mouse/genepix.mouse.v4.37k.00h.dyeswap.gpr
--Uploading file: /mouse/genepix.mouse.v4.37k.24h.dyeswap.gpr
--Uploading file: /affymetrix/E-TEST-1.ebi.ac.uk/jos1761.cel.tar.bz2
--Uploading file: /affymetrix/E-TEST-1.ebi.ac.uk/jos1762.cel.tar.bz2
--Uploading file: /affymetrix/E-TEST-1.ebi.ac.uk/jos1763.cel.tar.bz2
--Creating biosource: Biosource A
--Creating sample: Sample A.00h
net.sf.basedb.core.ConnectionClosedException: The connection has been closed.
        at net.sf.basedb.core.DbControl.getItem(DbControl.java:731)
        at net.sf.basedb.core.BioPlate.getBioWell(BioPlate.java:294)
        at net.sf.basedb.test.roles.UserTest.run(UserTest.java:182)
        at net.sf.basedb.test.roles.Run.main(Run.java:70)
++Leaving user test (FAILED)

comment:5 Changed 13 years ago by Nicklas Nordborg

Owner: changed from Martin Svensson to Nicklas Nordborg
Status: reopenednew

comment:6 Changed 13 years ago by Nicklas Nordborg

Status: newassigned

comment:7 Changed 13 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [4751]) Fixes #1171: Add BioLIMS support to batch importers

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