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Data submission steps
Prepare clinical data
Registering programs
Ingest clinical data
Prepare genomic data
Ingest genomic data
Troubleshooting
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Architecture
Docker and submods
ingest api
Overview
Operations
Retrieve information about this service
Add credentials for an S3 bucket
get credentials for an S3 bucket
delete credentials for an S3 bucket
List users in role_type
Assign users to role
Is user in this role?
Assign user to role
Remove user from role
List registered programs
Add authorization information for a new program
Get authorization information for a program
ingest_operations.remove_program
Add user access for a dataset
Delete user access for a dataset
Add pending user
List pending users
Approve pending users
Delete pending users
Approve pending user
Reject pending user
List program authorizations
Authorize a program for a user
Get program authorization for a user
Remove a program authorization for a user
Ingest Genomic data
Ingest Clinical data
Check status of ingest
Get a new token
query api
Overview
Operations
Retrieve information about this service
Retrieve patients matching the filters
Retrieve summary statistics on genomic data
Retrieve summary statistics on the metadata for each program, as well as the current site.
Retrieve summary statistics on the metadata for each program that match the given query parameters.
Retrieve the user key (usually the email) for the currently logged-in user
katsu api
Overview
authorized
List Biomarkers
List Comorbidities
Get Donor With Clinical Data
List Donors
List Exposures
List Follow Ups
List Primary Diagnoses
List Programs
Query Donors
List Radiations
List Sample Registrations
List Specimens
List Surgeries
List Systemic Therapies
List Treatments
discovery
Discover Donors
Discover Programs
Discover Sidebar List
overview
Discover Cohort Count
Discover Diagnosis Age Count
Discover Gender Count
Discover Individual Count
Discover Patients Per Cohort
Discover Primary Site Count
Discover Treatment Type Count
explorer
Explorer Donor
ingest
Create Biomarkers
Create Comorbidities
Create Donors
Create Exposures
Create Followups
Create Primary Diagnoses
Create Programs
Create Radiations
Create Sample Registrations
Create Specimens
Create Surgeries
Create Systemic Therapies
Create Treatments
delete
Delete Program
Operations
Service Info
htsget drs api
Overview
Operations
Retrieve information about this service
Add a DrsObject to the db
Delete a DrsObject.
drs_operations.list_cohorts
drs_operations.post_cohort
drs_operations.get_cohort
Delete a cohort.
drs_operations.get_cohort_status
Objects
List all DRS objects
Get info about a DrsObject.
Get a URL for fetching bytes
htsget beacon api
Overview
Informational endpoints
beacon_operations.get_beacon_service_info
GET Endpoints
beacon_operations.get_search
POST Endpoints
beacon_operations.post_search
htsget operations api
Overview
Reads
Get reads service info
Get alignment (reads) file download ticket
Stream alignment file part
Calculate size and checksums for the read object
Verify the integrity of the read object
Variants
Get variants service info
Get variant file download ticket
Index variant file for search
Verify the integrity of the variant object
Stream variant file part
Service Info
Get reads service info
Get variants service info
Streaming
Stream alignment file part
Stream variant file part
Operations
List all available gene names
Get transcript region for genes matching id
List all available gene names
Get transcript region for transcripts matching id
Get metadata about a sample
Get metadata about samples in a cohort
Get metadata about multiple samples
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Check status of ingest
GET
/status/{queue_id}
Return status of ingest operation
Parameters
Path Parameters
queue_id
required
string
Responses
200
Success
Select media type
application/json
object
