Skip to content

Latest commit

 

History

History
273 lines (206 loc) · 8.68 KB

ENDPOINTS.md

File metadata and controls

273 lines (206 loc) · 8.68 KB

Portal Endpoints

Service Info

LIMS Endpoint

List LIMS entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/lims" | jq

Get a LIMS record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/lims/2866" | jq

Get LIMS record(s) by Subject:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/lims?subject_id=SBJ00700" | jq

Get LIMS record(s) by Sequence Run:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/lims?run=200612_A01052_0017_BH5LYWDSXY" | jq

Search LIMS record(s) by Library ID:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/lims?search=L2000176" | jq

Metadata Endpoint

(aka Lab Metadata)

List Metadata entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/metadata" | jq

Get a Metadata record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/metadata/10" | jq

Get Metadata record(s) by Subject:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/metadata?subject_id=SBJ00700" | jq

Get Metadata record(s) by Subject, Assay Type, Phenotype:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/metadata?phenotype=tumor&type=wgs&subject_id=SBJ00700" | jq

Subjects Endpoint

List Subject entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/subjects" | jq

Get a Subject:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/subjects/SBJ00700" | jq

S3 Endpoint

List S3 object entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/s3" | jq

Get a S3 object record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/s3/309772" | jq

Get PreSigned URL of this S3 object record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/s3/309772/presign" | jq

List S3 object entries belongs to SBJ00700:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/s3?subject=SBJ00700" | jq

Search BAM S3 object entries by SBJ00700:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/s3?subject=SBJ00700&search=.bam$" | jq

GDS Endpoint

List GDS file entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/gds" | jq

Get a GDS file record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/gds/10" | jq

Get PreSigned URL of this GDS file record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/gds/10/presign" | jq

List GDS file entries belongs to Sequence Run:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/gds?run=211125_A00130_0185_AHWC2HDSX2" | jq

Search Fastq GDS files entries by Sequence Run:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/gds?run=211125_A00130_0185_AHWC2HDSX2&search=.fastq.gz$" | jq

Presign Endpoint

(*This is for bulk signing GDS files)

POST payload JSON file that contain list of gds absolute path:

curl -s -X POST -d "@files.json" -H "Content-Type: application/json" -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/presign" | jq

Fastq Endpoint

List Fastq entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/fastq" | jq

Get a Fastq record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/fastq/1388" | jq

Get Fastq record(s) by Sequence Run:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/fastq?run=211014_A00130_0180_BHLGF7DSX2" | jq

Get Fastq record(s) by Sequence Run & Project Owner:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/fastq?run=211014_A00130_0180_BHLGF7DSX2&project_owner=Bedoui" | jq

Get Fastq record(s) by rglb:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/fastq?rglb=L2101106" | jq

Similarly, you can filter request parameters on rgid, rgsm, lane. Additionally, project_owner from metadata.

Sequence Endpoint

List Sequence entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/sequence" | jq

Get a Sequence record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/sequence/2" | jq

Get Sequence record(s) by instrument_run_id:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/sequence?instrument_run_id=211014_A00130_0180_BHLGF7DSX2" | jq

SequenceRun Endpoint

SequenceRun provide BSSH events timeline and transitions

List SequenceRun entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/sequencerun" | jq

Get a SequenceRun record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/sequencerun/570" | jq

Get SequenceRun record(s) by instrument_run_id:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/sequencerun?instrument_run_id=211014_A00130_0180_BHLGF7DSX2" | jq

Similarly, you can filter request parameters on run_id, status.

Workflows Endpoint

List Workflow entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/workflows" | jq

Get a Workflow record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/workflows/800" | jq

Get Workflow by Sequence Run e.g. BCL_CONVERT workflow for a Run:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/workflows?type_name=bcl_convert&sequence_run__instrument_run_id=211129_A00130_0188_BHWCY3DSX2" | jq

Similarly, you can filter request parameters on type_name, end_status.

LibraryRun Endpoint

List LibraryRun entries:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/libraryrun" | jq

Get a LibraryRun record:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/libraryrun/33" | jq

Get LibraryRun record(s) by instrument_run_id:

curl -s -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/libraryrun?instrument_run_id=211014_A00130_0180_BHLGF7DSX2" | jq

Similarly, you can filter request parameters on run_id, lane.

Pairing Endpoint

Create T/N Pairing by SequenceRuns:

curl -s -X POST -d '["220311_A01052_0085_AHGGTWDSX3"]' -H "Content-Type: application/json" -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/pairing" | jq

In iam endpoint with awscurl:

awscurl -X POST -d '["220311_A01052_0085_AHGGTWDSX3"]' -H "Content-Type: application/json" --profile prodops --region ap-southeast-2 "https://api.portal.prod.umccr.org/iam/pairing" | jq

POST payload JSON can also be in file (e.g. pairing.json) as follows:

curl -s -X POST -d "@pairing.json" -H "Content-Type: application/json" -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/pairing/by_sequence_runs" | jq

Create T/N Pairing by Subjects:

curl -s -X POST -d '["SBJ01031", "SBJ01032", "SBJ01033", "SBJ01034"]' -H "Content-Type: application/json" -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/pairing/by_subjects" | jq

Create T/N Pairing by Libraries:

curl -s -X POST -d '["L2200331", "L2200332"]' -H "Content-Type: application/json" -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/pairing/by_libraries" | jq

Create T/N Pairing by Samples:

curl -s -X POST -d '["PRJ220785", "PRJ220786"]' -H "Content-Type: application/json" -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/pairing/by_samples" | jq

Create T/N Pairing by Workflows (WGS QC wfr_id):

curl -s -X POST -d '["wfr.7e52b7b957a140be9b11988355ab6fd1"]' -H "Content-Type: application/json" -H "Authorization: Bearer $PORTAL_TOKEN" "https://api.portal.prod.umccr.org/pairing/by_workflows" | jq