The `google-genomics1_beta2` library allows access to all features of the *Google genomics* service. This documentation was generated from *genomics* crate version *0.1.1+20150303*, where *20150303* is the exact revision of the *genomics:v1beta2* schema built by the [mako](http://www.makotemplates.org/) code generator *v0.1.1*. Everything else about the *genomics* *v1_beta2* API can be found at the [official documentation site](https://developers.google.com/genomics/v1beta2/reference). # Features Handle the following *Resources* with ease from the central [hub](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Genomics.html) ... * [annotation sets](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSet.html) * [*create*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSetCreateCall.html), [*delete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSetDeleteCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSetGetCall.html), [*patch*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSetPatchCall.html), [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSetSearchCall.html) and [*update*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSetUpdateCall.html) * [annotations](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Annotation.html) * [*batch create*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationBatchCreateCall.html), [*create*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationCreateCall.html), [*delete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationDeleteCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationGetCall.html), [*patch*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationPatchCall.html), [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationSearchCall.html) and [*update*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.AnnotationUpdateCall.html) * callsets * [*create*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.CallsetCreateCall.html), [*delete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.CallsetDeleteCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.CallsetGetCall.html), [*patch*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.CallsetPatchCall.html), [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.CallsetSearchCall.html) and [*update*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.CallsetUpdateCall.html) * [datasets](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Dataset.html) * [*create*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.DatasetCreateCall.html), [*delete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.DatasetDeleteCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.DatasetGetCall.html), [*list*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.DatasetListCall.html), [*patch*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.DatasetPatchCall.html), [*undelete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.DatasetUndeleteCall.html) and [*update*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.DatasetUpdateCall.html) * experimental * [*jobs create*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ExperimentalJobCreateCall.html) * [jobs](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Job.html) * [*cancel*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.JobCancelCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.JobGetCall.html) and [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.JobSearchCall.html) * readgroupsets * [*align*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetAlignCall.html), [*call*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetCallCall.html), [*coveragebuckets list*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetCoveragebucketListCall.html), [*delete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetDeleteCall.html), [*export*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetExportCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetGetCall.html), [*import*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetImportCall.html), [*patch*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetPatchCall.html), [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetSearchCall.html) and [*update*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadgroupsetUpdateCall.html) * [reads](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Read.html) * [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReadSearchCall.html) * [references](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Reference.html) * [*bases list*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReferenceBaseListCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReferenceGetCall.html) and [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReferenceSearchCall.html) * referencesets * [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReferencesetGetCall.html) and [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.ReferencesetSearchCall.html) * [variants](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Variant.html) * [*create*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantCreateCall.html), [*delete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantDeleteCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantGetCall.html), [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantSearchCall.html) and [*update*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantUpdateCall.html) * variantsets * [*delete*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetDeleteCall.html), [*export*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetExportCall.html), [*get*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetGetCall.html), [*import variants*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetImportVariantCall.html), [*merge variants*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetMergeVariantCall.html), [*patch*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetPatchCall.html), [*search*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetSearchCall.html) and [*update*](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.VariantsetUpdateCall.html) # Structure of this Library The API is structured into the following primary items: * **[Hub](http://byron.github.io/google-apis-rs/google-genomics1_beta2/struct.Genomics.html)** * a central object to maintain state and allow accessing all *Activities* * **[Resources](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.Resource.html)** * primary types that you can apply *Activities* to * a collection of properties and *Parts* * **[Parts](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.Part.html)** * a collection of properties * never directly used in *Activities* * **[Activities](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.CallBuilder.html)** * operations to apply to *Resources* Generally speaking, you can invoke *Activities* like this: ```Rust,ignore let r = hub.resource().activity(...).doit() ``` Or specifically ... ```ignore let r = hub.annotations().search(...).doit() let r = hub.annotations().patch(...).doit() let r = hub.annotations().create(...).doit() let r = hub.annotations().delete(...).doit() let r = hub.annotations().update(...).doit() let r = hub.annotations().get(...).doit() let r = hub.annotations().batch_create(...).doit() ``` The `resource()` and `activity(...)` calls create [builders][builder-pattern]. The second one dealing with `Activities` supports various methods to configure the impending operation (not shown here). It is made such that all required arguments have to be specified right away (i.e. `(...)`), whereas all optional ones can be [build up][builder-pattern] as desired. The `doit()` method performs the actual communication with the server and returns the respective result. # Usage ## Setting up your Project To use this library, you would put the following lines into your `Cargo.toml` file: ```toml [dependencies] google-genomics1_beta2 = "*" ``` ## A complete example ```Rust extern crate hyper; extern crate "yup-oauth2" as oauth2; extern crate "google-genomics1_beta2" as genomics1_beta2; use genomics1_beta2::Annotation; use genomics1_beta2::Result; use std::default::Default; use oauth2::{Authenticator, DefaultAuthenticatorDelegate, ApplicationSecret, MemoryStorage}; use genomics1_beta2::Genomics; // Get an ApplicationSecret instance by some means. It contains the `client_id` and // `client_secret`, among other things. let secret: ApplicationSecret = Default::default(); // Instantiate the authenticator. It will choose a suitable authentication flow for you, // unless you replace `None` with the desired Flow. // Provide your own `AuthenticatorDelegate` to adjust the way it operates and get feedback about // what's going on. You probably want to bring in your own `TokenStorage` to persist tokens and // retrieve them from storage. let auth = Authenticator::new(&secret, DefaultAuthenticatorDelegate, hyper::Client::new(), ::default(), None); let mut hub = Genomics::new(hyper::Client::new(), auth); // As the method needs a request, you would usually fill it with the desired information // into the respective structure. Some of the parts shown here might not be applicable ! // Values shown here are possibly random and not representative ! let mut req: Annotation = Default::default(); // You can configure optional parameters by calling the respective setters at will, and // execute the final call using `doit()`. // Values shown here are possibly random and not representative ! let result = hub.annotations().patch(&req, "annotationId") .doit(); match result { Result::HttpError(err) => println!("HTTPERROR: {:?}", err), Result::MissingAPIKey => println!("Auth: Missing API Key - used if there are no scopes"), Result::MissingToken => println!("OAuth2: Missing Token"), Result::Cancelled => println!("Operation cancelled by user"), Result::UploadSizeLimitExceeded(size, max_size) => println!("Upload size too big: {} of {}", size, max_size), Result::Failure(_) => println!("General Failure (hyper::client::Response doesn't print)"), Result::FieldClash(clashed_field) => println!("You added custom parameter which is part of builder: {:?}", clashed_field), Result::JsonDecodeError(err) => println!("Couldn't understand server reply - maybe API needs update: {:?}", err), Result::Success(_) => println!("Success (value doesn't print)"), } ``` ## Handling Errors All errors produced by the system are provided either as [Result](http://byron.github.io/google-apis-rs/google-genomics1_beta2/enum.Result.html) enumeration as return value of the doit() methods, or handed as possibly intermediate results to either the [Hub Delegate](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.Delegate.html), or the [Authenticator Delegate](http://byron.github.io/google-apis-rs/google-genomics1_beta2/../yup-oauth2/trait.AuthenticatorDelegate.html). When delegates handle errors or intermediate values, they may have a chance to instruct the system to retry. This makes the system potentially resilient to all kinds of errors. ## Uploads and Downlods If a method supports downloads, the response body, which is part of the [Result](http://byron.github.io/google-apis-rs/google-genomics1_beta2/enum.Result.html), should be read by you to obtain the media. If such a method also supports a [Response Result](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.ResponseResult.html), it will return that by default. You can see it as meta-data for the actual media. To trigger a media download, you will have to set up the builder by making this call: `.param("alt", "media")`. Methods supporting uploads can do so using up to 2 different protocols: *simple* and *resumable*. The distinctiveness of each is represented by customized `doit(...)` methods, which are then named `upload(...)` and `upload_resumable(...)` respectively. ## Customization and Callbacks You may alter the way an `doit()` method is called by providing a [delegate](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.Delegate.html) to the [Method Builder](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.CallBuilder.html) before making the final `doit()` call. Respective methods will be called to provide progress information, as well as determine whether the system should retry on failure. The [delegate trait](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.Delegate.html) is default-implemented, allowing you to customize it with minimal effort. ## Optional Parts in Server-Requests All structures provided by this library are made to be [enocodable](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.RequestValue.html) and [decodable](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.ResponseResult.html) via json. Optionals are used to indicate that partial requests are responses are valid. Most optionals are are considered [Parts](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.Part.html) which are identifyable by name, which will be sent to the server to indicate either the set parts of the request or the desired parts in the response. ## Builder Arguments Using [method builders](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.CallBuilder.html), you are able to prepare an action call by repeatedly calling it's methods. These will always take a single argument, for which the following statements are true. * [PODs][wiki-pod] are handed by copy * strings are passed as `&str` * [request values](http://byron.github.io/google-apis-rs/google-genomics1_beta2/trait.RequestValue.html) are borrowed Arguments will always be copied or cloned into the builder, to make them independent of their original life times. [wiki-pod]: http://en.wikipedia.org/wiki/Plain_old_data_structure [builder-pattern]: http://en.wikipedia.org/wiki/Builder_pattern [google-go-api]: https://github.com/google/google-api-go-client # License The **genomics1_beta2** library was generated by Sebastian Thiel, and is placed under the *MIT* license. You can read the full text at the repository's [license file][repo-license]. [repo-license]: https://github.com/Byron/google-apis-rs/LICENSE.md