NEWS-api-dev.md

In Paradigm4/insight: SciDB REVEAL/Genomics API

(External facing changes are listed here)

Version 0.5

• start using options(scidb.aio=TRUE) across the board

Version 0.5

• rename scidb connection function from gh_connect to rg_connect
• start using options(scidb.aio=TRUE) for downloads where faster aio_save path of not having to apply dimensions can be used
• revamped fusion data implementation leads to modifications in search_fusion function
• for more details, see https://github.com/Paradigm4/revealgenomics/issues/49

Version 0.4

• package name changed from scidb4gh to revealgenomics
• Github repo changed from reveal-genomics to revealgenomics
• for more details, see https://github.com/Paradigm4/revealgenomics/issues/44

Version 0.3

• improved ontology management
• Following terms dropped: REFERENCESET.species_, FEATURE.strand_term, BIOSAMPLE.disease_, INDIVIDUAL.sex_, INDIVIDUAL.species_

At commit 352afe9

Recent changes:

1. The following external-facing API formulates a table containing information about entities in the hierarchy

get_entity_info()
#                  entity               class     search_by_entity     delete_by_entity
# 1               PROJECT            metadata                 <NA>              PROJECT
# 2               DATASET            metadata              PROJECT              DATASET
# ...
# 7     RNAQUANTIFICATION                data       MEASUREMENTSET       MEASUREMENTSET

1. Delete of measurement data is now working as

delete_entity(entity = 'RNAQUANTIFICATION', 
            ids = 2, dataset_version = 1, 
            delete_by_entity = 'MEASUREMENTSET')
# RnaQuantification data can be deleted by the parent MeasurementSet

delete_entity(entity = 'VARIANT', 
            ids = 1, dataset_version = 2, 
            delete_by_entity = 'MEASUREMENTSET')
# Variant data can be deleted by the parent MeasurementSet

# The earlier API for metadata and feature-data continues to work
delete_entity(entity = 'DATASET', id = 1, dataset_version = 2)
delete_entity(entity = 'PROJECT', id = 1)

1. Change in delete_entity() and get_entity() API: parameter ids is now called id (to be consistent with other calls in the API)

2. Two internal API to infer hierarchy and delete preferences

## parent entity by which one would search an entity 
revealgenomics:::get_search_by_entity(entity = 'RNAQUANTIFICATION')
# [1] "MEASUREMENTSET"
revealgenomics:::get_search_by_entity(entity = 'MEASUREMENTSET')
# [1] "DATASET"

## entity by which one would delete an entity 
revealgenomics:::get_delete_by_entity(entity = 'RNAQUANTIFICATION')
# [1] "MEASUREMENTSET"
revealgenomics:::get_delete_by_entity(entity = 'MEASUREMENTSET')
# [1] "MEASUREMENTSET"

1. search_copynumberset(dataset_id = ..) was throwing an error earlier when there were no CopyNumberSets in a dataset. This should be fixed now.

Paradigm4/insight documentation built on April 5, 2020, 1:12 p.m.