Opened 6 years ago
Closed 6 years ago
#1081 closed enhancement (fixed)
The release exporter should export more data
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | major | Milestone: | Reggie v4.21 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description (last modified by )
For existing items we should export more annotations/other data:
- Specimen items:
- If there is an image of the Stained child item with GoodStain=true we should export the image to the release archive. The image should be located in top folder given by external id of the specimen with a filename given by exported HisName annotation + '.jpg' (for example
/S000001/S000001.his.jpg
). If the image exists in earlier releases it should be linked by symbolic links just as other files are. - Remaining quantity
- If there is an image of the Stained child item with GoodStain=true we should export the image to the release archive. The image should be located in top folder given by external id of the specimen with a filename given by exported HisName annotation + '.jpg' (for example
- Lysate items:
- Protocol
- Original and remaining quantity (µl)
- RNA items (and DNA + FlowThrough)
- Protocol
- Original and remaining quantity (in µg for RNA/DNA and µl for FlowThrough)
We should export more types of items. Some (Lysate, Retract, No and NotAsked) have already been added as part of #1075.
- DNA
- FlowThrough
- NoSpecimen
- Blood
- BloodDNA
Change History (20)
comment:1 by , 6 years ago
Status: | new → assigned |
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comment:2 by , 6 years ago
Description: | modified (diff) |
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comment:3 by , 6 years ago
comment:4 by , 6 years ago
(In [5131]) References #1081: The release exporter should export more data
Added writer implementations for DNA and FlowThrough. They both have a single filter: DoNotUse=null
. On the FlowThrough QiacubeBatchNo
is the only annotations. DNA also has the same NanoDrop annotations as RNA but doens't have RNAQC.
comment:5 by , 6 years ago
comment:6 by , 6 years ago
comment:7 by , 6 years ago
(In [5136]) References #1081: The release exporter should export more data
Added NoSpecimenWriter
implementation. Annotations:
- Site
- SamplingDate
- Laterality
The !NameToExternalID mapping has also been updated to allow more item types than specimen. It may not actually be needed for NoSpecimen items that doesn't have any child items.
comment:8 by , 6 years ago
Description: | modified (diff) |
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comment:9 by , 6 years ago
comment:10 by , 6 years ago
comment:11 by , 6 years ago
(In [5142]) References #1081: The release exporter should export more data
Added BloodDnaWriter
implementation. The query filter is DoNotUse=null
and not annotations are currently exported.
This requried a change in the code for converting items names to release ID names since the blood items have '.b' suffix instead of a digit as specimen have. To be on the safe side, the exporter will now throw an exception if it encounters a name that can't be mapped instead of letting the name pass through unchanged. This might complicate things for file names, but this can now be controlled via flag.
comment:12 by , 6 years ago
Description: | modified (diff) |
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comment:13 by , 6 years ago
comment:14 by , 6 years ago
comment:15 by , 6 years ago
comment:16 by , 6 years ago
Description: | modified (diff) |
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comment:17 by , 6 years ago
Description: | modified (diff) |
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comment:18 by , 6 years ago
comment:19 by , 6 years ago
comment:20 by , 6 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
(In [5117]) References #1081: The release exporter should export more data
The
SpecimenWriter
should now export the JPG image that is attached to theStained
item withGoodStain=true
. It will write the image directly to the correct place on the release server. Except, if the same image already exists in an earlier release, it will instead create a symbolic link to it just as the exporter already do for other files.