Task #8675 (closed)
Opened 7 years ago
Closed 7 years ago
BUG: Error on importing image
| Reported by: | rkferguson | Owned by: | |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-4.4 |
| Component: | Import | Version: | n.a. |
| Keywords: | n.a. | Cc: | jburel, cxallan, mlinkert |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | 2012-06-05 (16) |
Description
Description:
- tried to import data
- Insight crashed
- screenshot shows error message
NB: subsequently tried importing after just logging out from within Insight and in again as another user and importing worked fine - i.e. no replication of crash.
Images being imported:
32262-centrosome in a Cetn2-.ome.tiff
32263-centrosome in a Cetn4-.ome.tiff
Error in log:
2012-04-30 11:28:52,013 ERROR [ ome.formats.OMEROMetadataStoreClient] ( Thread-58) Parsing timestamp '2011-01-27 14:11:07.0' failed!
java.text.ParseException: Unparseable date: "2011-01-27 14:11:07.0"
at java.text.DateFormat.parse(DateFormat.java:337)
at ome.formats.OMEROMetadataStoreClient.timestampFromXmlString(OMEROMetadataStoreClient.java:895)
at ome.formats.OMEROMetadataStoreClient.setImageAcquiredDate(OMEROMetadataStoreClient.java:4447)
Parsing timestamp '2011-01-27 14:11:07.0' failed!
java.text.ParseException: Unparseable date: "2011-01-27 14:11:07.0"
at java.text.DateFormat.parse(DateFormat.java:337)
at ome.formats.OMEROMetadataStoreClient.timestampFromXmlString(OMEROMetadataStoreClient.java:895)
at ome.formats.OMEROMetadataStoreClient.setImageAcquiredDate(OMEROMetadataStoreClient.java:4447)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:764)
at loci.formats.FormatReader.setId(FormatReader.java:1091)
at loci.formats.ImageReader.setId(ImageReader.java:682)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:250)
Attachments (3)
Change History (8)
Changed 7 years ago by rkferguson
Changed 7 years ago by rkferguson
Changed 7 years ago by rkferguson
comment:1 Changed 7 years ago by jburel
- Cc jburel cxallan mlinkert-x added
- Component changed from Insight to Import
- Owner jburel deleted
comment:2 Changed 7 years ago by mlinkert
comment:3 Changed 7 years ago by jburel
- Sprint changed from 2012-05-08 (14) to 2012-05-22 (15)
Moved from sprint 2012-05-08 (14)
comment:4 Changed 7 years ago by jburel
- Sprint changed from 2012-05-22 (15) to 2012-06-05 (16)
Moved from sprint 2012-05-22 (15)
comment:5 Changed 7 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
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The problem is that the value of CreationDate? (now AcquiredDate?) in these files really is invalid. Since we're doing some post-processing on the dates in Bio-Formats anyway, I've put a fix for this here: https://github.com/melissalinkert/bioformats/commit/0c04bbb112576d1008d36e39695e565d14c587a7
It looks like these files were exported from JCB, in which case the root of the problem would be generation of AcquiredDate? by the 4.1 server; not sure if that's worth fixing at this point or not.