Opened 10 months ago

Closed 8 months ago

#1081 closed enhancement (fixed)

The release exporter should export more data

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.21
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

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
  • 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 Changed 10 months ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 10 months ago by Nicklas Nordborg

Description: modified (diff)

comment:3 Changed 10 months ago by Nicklas Nordborg

(In [5117]) References #1081: The release exporter should export more data

The SpecimenWriter should now export the JPG image that is attached to the Stained item with GoodStain=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.

comment:4 Changed 10 months ago by Nicklas Nordborg

(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 Changed 10 months ago by Nicklas Nordborg

(In [5132]) References #1081: The release exporter should export more data

Changed the DNA and FlowThrough writers to work with specific dao objects instead of generic extracts. This should be safer.

comment:6 Changed 10 months ago by Nicklas Nordborg

(In [5133]) References #1081: The release exporter should export more data

Changed the DNA and FlowThrough writers to work with specific dao objects instead of generic extracts. This should be safer.

comment:7 Changed 10 months ago by Nicklas Nordborg

(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 Changed 10 months ago by Nicklas Nordborg

Description: modified (diff)

comment:9 Changed 10 months ago by Nicklas Nordborg

(In [5138]) References #1081: The release exporter should export more data

Added BloodWriter implementation. The query filter is Consent=Yes and DoNotUse=null. Consent is the only annotation that is exported so far.

comment:10 Changed 10 months ago by Nicklas Nordborg

(In [5140]) References #1081: The release exporter should export more data

Added option to exclude histology images. This would be useful when testing.

comment:11 Changed 10 months ago by Nicklas Nordborg

(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 Changed 10 months ago by Nicklas Nordborg

Description: modified (diff)

comment:13 Changed 10 months ago by Nicklas Nordborg

(In [5165]) References #1081: The release exporter should export more data

The specimen exporter is now exporting the remaining quantity in mg as a project-specific annotation.

comment:14 Changed 10 months ago by Nicklas Nordborg

(In [5166]) References #1081: The release exporter should export more data

The lysate exporter is now exporting protocol, original and remaining volume (µl). The remaining volume is project-specific.

comment:15 Changed 10 months ago by Nicklas Nordborg

(In [5170]) References #1081: The release exporter should export more data

Added protocol, original and remaining quantity to exporters for RNA, DNA and FlowThrough. The original and remaining quantities are specific for each item type since not all have the same unit.

comment:16 Changed 10 months ago by Nicklas Nordborg

Description: modified (diff)

comment:17 Changed 8 months ago by Nicklas Nordborg

Description: modified (diff)

comment:18 Changed 8 months ago by Nicklas Nordborg

(In [5211]) References #1081: The release exporter should export more data

Added original and remaining quanity (µg) and NanoDrop concentration to the BloodDNA exporter.

comment:19 Changed 8 months ago by Nicklas Nordborg

(In [5218]) References #1081: The release exporter should export more data

Added BloodSample annotation on Blood items.

comment:20 Changed 8 months ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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