Endpoint Tests¶
The endpoint tests here are run against the Progenetix beacon and are also used to demonstrate path & query options as well as response formats.
Standard Beacon Paths¶
We here show examples using the Progenetix instance with its /beacon/ root path.
Base /¶
/filtering_terms/¶
/filtering_terms/ + query¶
/biosamples/ + query¶
/biosamples/{id}/¶
- /biosamples/pgxbs-kftva5c9/
- retrieval of a single biosample
/biosamples/{id}/variants/¶
/biosamples/{id}/analyses/¶
Base /individuals¶
/individuals/ + query¶
/individuals/{id}/¶
/individuals/{id}/variants/¶
Base /variants¶
/variants/ + query¶
- /variants/?referenceName=refseq:NC_000017.11&variantType=DEL&start=7500000&start=7676592&end=7669607&end=7800000
- /variants/?referenceName=refseq:NC_000017.11&variantType=DEL&start=7500000&start=7676592&end=7669607&end=7800000&requestedGranularity=count
- same w/ Boolean response
- /variants/?requestedGranularity=boolean&referenceBases=G&alternateBases=A&referenceName=refseq:NC_000017.11&start=7577120
/variants/{id}/ or /g_variants/{id}/¶
/variants/{id}/biosamples/¶
Base /analyses (or /analyses)¶
/analyses/ + query¶
- /analyses/?filters=cellosaurus:CVCL_0004
- this example retrieves all analyses having an annotation for the Cellosaurus CVCL_0004 identifier (K562)
Non-standard output options &output=...¶
&output=histoplot¶
Beacon Support & Beacon+¶
Phenopackets /biosamples/{id}/phenopackets/ & /individuals/{id}/phenopackets/¶
/aggregator/¶
Query examples¶
Filter use¶
Region query with positive and excluded filter¶
In this example we use a filter negation by having a ! prefixed PATO:0020002
resulting in a