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Overview
Understanding the URL
The general format of the REST API web services is:
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http://HOST_URL/webservices/rest/{apiVersion}/{resource}/{id(s)}/{endpoint}?{options} |
where HOST_URL is the name of the host machine and the name of Java war file deployed in web server (eg. tomcat) over that server for example http://bioinfo.hpc.cam.ac.uk/opencga-demo/
Entities inside the curly braces { } are the web service parameters, and they are treated as variables. For example the following URL:
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http://bioinfo.hpc.cam.ac.uk/opencga-demoHOST_URL/webservices/rest/v1/userssamples/opencgasample1,sample2/info?study=1000genomes |
As it is explained later in this documentation, this RESTful web service will return the information stored in OpenCGA of the user opencga.
- apiVersion (v1) : indicates OpenCGA version to retrieve information from, data models and API may change between versions.
- resource (userssamples) : specifies the data type of what the user wants to retrieve. This can be one of the resources listed below.
- id (opencgasample1,sample2) : the resource id's we want to query.
- endpoint (info) : these parameters must be specified depending on the nature of your input data. For example, if we want to query all files by a specific study (e.g. 1000genomes) we should use the studies resource and files endpoint. options (passwordinstance, info is used to fetch the information stored in the database regarding the id's passed.
- options (study=1000genomes) : variables in key value pair form, passed as query parameters.
URL parameters
apiVersion
apiVersions are numbered as v1, v2, etc. At this moment we are heading to second stable apiVersion which will be v2.
entityresource
There are several metadata entities resources implemented such as users, samples, individuals, ... see below for more info..
IDs
This is the query parameter and the type matches resources path parameter, this is a unique identifier for the resource we are interactingunique identifier(s) corresponding to the resource we want to interact with. Plural means a comma separated list of IDs can be passed to improve performance with a single REST call separated by commas rather than multiple calls. OpenCGA preserves the order of the results with corresponding IDs. A Boolean variable, silent, can be set to indicate either if user is interested to receive partial results (true) as well or only expects complete set of results or nothing , in case of any a failure (resource doesn't exist, permission denied etc), whether the user is interested in receiving partial results (true) with the information that could be successfully retrieved or just a failure with no results. As a trade off between performance and ease of use a maximum of 100 IDs are allowed in one web service.
options
These query parameters can modify the behaviour of the query (exclude, include, limit, skip and count) or add some filters to some specific endpoints to add useful functionality. The following image shows some typical options for a certain web service.
REST Response
OpenCGA 1.x
Most web services return the results encapsulated in a single QueryResponse object (view data model) consisting of some metadata and a list of QueryResult objects (view data model) called response containing the data and metadata requested. The reason for this two-level response is that some REST web services allow to pass multiple IDs as input parameter, this improves significantly the performance by reducing the number of calls, for instance a calling /info method with three sample IDs will return a QueryResponse object with three QueryResults. Then, each QueryResult can contain multiple results, for instance when getting all samples from an individual or when fetching all variants from a gene.
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The Response object as well as the behaviour regarding the nested lists change in OpenCGA 2.x |
However, most of the web services will return a QueryResponse with one single QueryResult with one or more result. In general the response object looks like:
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{ "apiVersion": "v1", "time": 19, "warning": "", "error": "", "queryOptions": { "metadata": true, "skipCount": false, "limit": 10 }, "response": [ { "id": "search", "dbTime": 18, "numResults": 10, "numTotalResults": 56, "warningMsg": "", "errorMsg": "", "resultType": "", "result": [ { // result 1 }, { // result 2 }, // ... { // result 10 } ] } ] } |
where:
- Line 1: single QueryResponse object
- Lines 2 and 3: show the version and the duration time (ms)
- Lines 4 and 5: show warning and error messages, for instance when having network issues you could get "Catalog database not accessible"
- Line 6: summary of all option parameters provided
- Line 11: list of QueryResults called response. In this example, and in most of calls, there is only one QueryResult.
- Line 14: database duration time (ms) for each QueryResult.
- Line 15 and 16: number of elements returned in the list result (see below) and total number of records found in the database for a given query.
- Line 17 and 18: specific warning and error messages for each QueryResult
- Line 19: type of result such as entity
- Line 20: list of results for this query, this can be samples, variants, ...
OpenCGA 2.x
Most web services return the results encapsulated in a single DataResponse object (view data model) consisting of some metadata and a list of DataResult objects (view data model) called responses containing the data and metadata requested. The first response of the list will always contain the response of the OpenCGA federation being directly queried. Any additional response in the list will belong to other federated servers that could be connected. Each federated response will contain a list of results (DataResults) containing the data that has been queried.
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To be completed with JSON example of DataResponse |
Resources and Endpoints
REST API is organised in into two main groups of web services depending you want , one to work with metadata and permission or a different one to run some analysisanalyses: Catalog and Analysis. See below a description of the web services.
Catalog Web Services
Contains all endpoints for managing and querying metadata and permission.
Entity | Path | Description | Main Endpoints | ||||
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Users | /users | Different methods to work with users | info, create, login, ... | ||||
Projects | /projects | projects Projects are defined for each user and contains studies | info, create, studies, ... | ||||
Studies | /studies | studies Studies are the main component of catalog, the OpenCGA Catalog. They can be shared and contain with other users and are the containers of the data (files, samples and jobs, cohorts, jobs...). | info, create, files, samples, jobs, variants, alignments, groups, ... | ||||
Files | /files | files Files are added to the study and can be indexed to be queried | info, create, index, share, ... | ||||
Jobs | /jobs | jobs are tool executions that can be queuedJobs are used to execute analyses. | info, create, ... | ||||
Families | /families | families are Family is a connected collection of individuals based on their relationship. | info, create, ... | ||||
Individuals | /individuals | samples come from the individualsIndividual is the member from which a sample was taken. | info, create, ... | ||||
Samples | /samples | samples Samples are each of the experiment samples, typically matches a NGS BAM file or VCF sample. | info, create, annotate, share, ... | ||||
Cohorts | /cohorts | these model Cohort is a group of samples that share some common properties, these . These are used for data analysis. | info, create, stats, samples, ... | ||||
Clinical Analysis | /clinical | this This handles creating and search of a clinical analysisanalyses. | info, create, ... | Variable Set | /variableset | variables annotate samples with different information useful for data analysisinfo, crate, ... | |
Meta | /meta | gives the meta Contains basic information about the status of an OpenCGA installation instance. | ping, about, status | ||||
GA4GH | /ga4gh | GA4GH standard web services to search genomics data in OpenCGA | variant search, reads search, responses |
Analysis Web Services
Different endpoint for running the alignment, variant and clinical analysis
Category | Path | Description | Main Endpoints |
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Alignment Analysis | /analysis/alignment | Operations over Read Alignments to facilitate complete analysis with different tools. | index, query, stats, coverage |
Variant Analysis | /analysis/variant | Operations over Genomic Variants to facilitate complete analysis with different tools. | index, stats, query, validate, ibs, facet, samples, metadata |
Clinical Analysis | /analysis/clinical | You can manage Clinical Analysis metadata (e.g create a case, set permissions) or run a genome interpretation | execute |
Swagger
OpenCGA has been documented using Swagger project. Detailed information about resources, endpoints and options is available at:
http://bioinfodevbioinfo.hpc.cam.ac.uk/opencga/webservices/-demo
Client Libraries
Currently OpenCGA implements the following four client libraries:
Deprecation Policy
Certain APIs are deprecated over the period of time as OpenCGA is a live project and continuously improved and new features are implemented. Deprecation cycle consists of a warning period to let make user aware that these services are considered for change and highly likely will be replaced followed by a deprecated message. OpenCGA supports deprecated services for two releases (Deprecated and Next one). Deprecated services are hidden from Swagger in the following release of deprecation and finally completely removed completely in the next releaseone.
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Warning (working) ---> Deprecated (working) ---> Hidden (working) ---> Removed (not working) |
All deprecated web services are clearly marked as deprecated along with a warning help message for user.
Table of Contents:
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