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explain EXTERNAL_LINK sample type
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wow-such-code committed Oct 21, 2024
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10 changes: 10 additions & 0 deletions README.md
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Expand Up @@ -263,6 +263,16 @@ The data itself can be transferred and stored in SEEK using the '-d' flag.
To completely exclude some dataset information from being transferred, a file ('--blacklist')
containing dataset codes (from openBIS) can be specified. //TODO do this for samples/sample types

In order to store links to the newly created SEEK objects in the source openBIS instance, the
following sample type is needed:

Sample Type Code: EXTERNAL_LINK
Property: LINK_TYPE (VARCHAR)
Property: URL (VARCHAR)

EXTERNAL_LINK samples are added to transferred experiments and samples and point to their respective
counterparts in SEEK. If the sample type is not available, this will be logged.

### Updating nodes in SEEK based on updates in openBIS

Updating nodes in SEEK uses the same general command, parameters and options. Unless otherwise
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Expand Up @@ -545,7 +545,7 @@ public void createSeekLinks(SeekStructurePostRegistrationInformation postRegInfo
SampleTypeFetchOptions typeOptions = new SampleTypeFetchOptions();
typeOptions.withPropertyAssignments().withPropertyType();
typeOptions.withPropertyAssignments().withEntityType();
if(openBIS.searchSampleTypes(criteria, typeOptions).getObjects().size() == 0) {
if(openBIS.searchSampleTypes(criteria, typeOptions).getObjects().isEmpty()) {
System.out.printf(
"This is where links would be put into openBIS, but EXTERNAL_LINK sample was "
+ "not yet added to openBIS instance.%n");
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