The release exporter should export more data

[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)

We should export more types of items. Some (Lysate, Retract, No and NotAsked) have already been added as part of #1075.

• DNA
• FlowThrough
• NoSpecimen

[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.

[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.

[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.

[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.

[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.

[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.

[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.

[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.