Clinical data is supported in File, Sample, Cohort, Individual and Family in field called annotationSets. Any of these entities will be able to perform the same operations described below apart from their own particular features.
Clinical data ingestion
In order to add new clinical information to one entity, the user will need to call to the main /update web service of the entity (files/{file}/update, samples/{sample}/update, etc.). These web services accept a list of annotationSets using the format described above. By default, any time the user sends a list of annotationSets without adding any other parameter, those annotationSets containing the clinical information will be added to the already existing annotationSets the entity might contain (if any). However, this behaviour can be altered by changing the value of the annotationSetsActionquery parameter. This parameter accepts 3 possible action values:
- ADD: This is the default behavior, even if the query parameter is not sent. Any annotationSets sent through the main body of the POST operation will be added to the already existing ones (if any).
- SET: Replace the current existing annotationSets (if any) of the entity being updated by the ones sent through the main body of the POST operation.
- REMOVE: Remove the list of annotationSets sent through the main body of the POST operation if they already exist in the entity being updated. In this case, the only field that is necessary and therefore taken into account, will be the annotationSet id.
Updating some values of already stored clinical data
In order to update only a few values (annotations) of an already stored annotationSet, users will need to call to a new web service .../annotationSets/{annotationSetId}/annotations/update present for the different 5 supported entities. This web service accepts a map of key-values that will generally contain the name of the annotation being updated and the new value to be stored. At the moment, there are 5 different actions supported by the action query parameter:
- ADD: Default behavior if the query parameter is not provided. Adds the new value to the annotation. If it already existed, the value will be replaced.
- SET:
This action might be really harmful. It will set the annotations provided in the body of the POST operation and will remove any other annotations the annotationSet might have had stored. - REPLACE: Replace the value of an already existing annotation. Similar to the ADD action but, in this case, If the annotation did not exist, it will not set the new value !!
REMOVE: Empty the values of some stored annotations. To perform this action, the map of the body will need to contain the key 'remove' and a comma separated list containing the annotations to be removed. Example: {"remove": "member.address,member.age"}
- RESET: Reset the values of the annotations defined to their default values defined in the variables of the variableSet. To perform this actiont, he map of the body will need to contain the key 'reset' and a comma separated list containing the annotations to be resetted. Example: {"reset": "member.address"}
Querying by clinical data
- All the annotationset webservices have been deprecated.
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