REST API for OMICS services

All REST Endpoints

Job Log

The Omics data ingestion job log API provides the latest logs for the ODB data ingestion job in the reverse chronological order by Date. Use this API to get the progress of the data loading. It also provides details of the loading and the status (success or failed).

Loader Job Logs: Method: get
Path: /ohfapi/omics/jobstatus/{jobId}/logs

Job Status

The Job Status RESTful API provides the status of the ODB ingestion job. It informs if the job is still running or completed. It also provides the resource (link) to get the detailed log information for the job. Invoke the Job Log API to get the execution status (success or failed).

Job Status: Method: get
Path: /ohfapi/omics/jobstatus/{jobId}

Reference Loaders

The Reference Loader APIs invoke the Omics Data Bank (ODB) Loader Database procedure that performs the ODB reference data loading.

Add a New Version: Method: post
Path: /ohfapi/omics/reference/versions/{versionType}
ADF Data Loader: Method: post
Path: /ohfapi/omics/reference/adf
Cosmic Loader: Method: post
Path: /ohfapi/omics/reference/cosmic
Ensembl: Method: post
Path: /ohfapi/omics/reference/ensembl
Ensembl GVF Loader: Method: post
Path: /ohfapi/omics/reference/gvf
HGMD Loader: Method: post
Path: /ohfapi/omics/reference/hgmd
Hugo Loader: Method: post
Path: /ohfapi/omics/reference/hugo
List a Version: Method: get
Path: /ohfapi/omics/reference/versions/{versionType}
Pathway: Method: post
Path: /ohfapi/omics/reference/pathway
Prediction Score: Method: post
Path: /ohfapi/omics/reference/predictionscore
Probe Loader: Method: post
Path: /ohfapi/omics/reference/probe
Stage to IOT: Method: post
Path: /ohfapi/omics/reference/stage-iot
SwissProt: Method: post
Path: /ohfapi/omics/reference/sprot

Result Data Loaders

The Result loader resource supports initializing the samples data loading and actual loading of data.
Note:

For all the applicable result loaders, provide the specimen number and specimen vendor.
The "readSize" parameter is an optional parameter. By default, this value is 512 KB. Modify this value if there is a large (structural) variations or many specimens in a file. Using a larger value requires more resources (memory) on the database and hence reduces the performance.

CGI MasterVar: Method: post
Path: /ohfapi/omics/samples/cgi
Copy Number Variation Samples: Method: post
Path: /ohfapi/omics/samples/cnv
Dual Channel Samples: Method: post
Path: /ohfapi/omics/samples/dual-channel
File Lineage Loader: Method: post
Path: /ohfapi/omics/samples/file-lineage
Genomic Test Reference Attributes: Method: post
Path: /ohfapi/omics/samples/genomics-test
MAF Samples: Method: post
Path: /ohfapi/omics/samples/maf
Quality Control Metadata and Genomic Test Transactional Attributes: Method: post
Path: /ohfapi/omics/samples/qcmetadata
RNA-Seq Samples: Method: post
Path: /ohfapi/omics/samples/rna-seq
Single Channel Gene Expression Samples: Method: post
Path: /ohfapi/omics/samples/single-channel-gene-expr
Stage to Target: Method: post
Path: /ohfapi/omics/samples/stage-to-target
VCF Samples: Method: post
Path: /ohfapi/omics/samples/vcf
VCF-CNV: Method: post
Path: /ohfapi/omics/samples/vcf-cnv