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209 lines
16 KiB
Markdown
<!---
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DO NOT EDIT !
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This file was generated automatically from 'src/mako/api/README.md.mako'
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DO NOT EDIT !
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-->
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The `google-genomics1` library allows access to all features of the *Google genomics* service.
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This documentation was generated from *genomics* crate version *1.0.2+20160928*, where *20160928* is the exact revision of the *genomics:v1* schema built by the [mako](http://www.makotemplates.org/) code generator *v1.0.2*.
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Everything else about the *genomics* *v1* API can be found at the
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[official documentation site](https://cloud.google.com/genomics/).
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# Features
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Handle the following *Resources* with ease from the central [hub](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Genomics.html) ...
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* [annotations](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Annotation.html)
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* [*batch create*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationBatchCreateCall.html), [*create*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationCreateCall.html), [*delete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationDeleteCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationGetCall.html), [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationSearchCall.html) and [*update*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationUpdateCall.html)
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* annotationsets
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* [*create*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationsetCreateCall.html), [*delete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationsetDeleteCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationsetGetCall.html), [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationsetSearchCall.html) and [*update*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.AnnotationsetUpdateCall.html)
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* callsets
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* [*create*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.CallsetCreateCall.html), [*delete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.CallsetDeleteCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.CallsetGetCall.html), [*patch*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.CallsetPatchCall.html) and [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.CallsetSearchCall.html)
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* [datasets](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Dataset.html)
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* [*create*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetCreateCall.html), [*delete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetDeleteCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetGetCall.html), [*get iam policy*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetGetIamPolicyCall.html), [*list*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetListCall.html), [*patch*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetPatchCall.html), [*set iam policy*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetSetIamPolicyCall.html), [*test iam permissions*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetTestIamPermissionCall.html) and [*undelete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.DatasetUndeleteCall.html)
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* [operations](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Operation.html)
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* [*cancel*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.OperationCancelCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.OperationGetCall.html) and [*list*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.OperationListCall.html)
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* readgroupsets
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* [*coveragebuckets list*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadgroupsetCoveragebucketListCall.html), [*delete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadgroupsetDeleteCall.html), [*export*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadgroupsetExportCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadgroupsetGetCall.html), [*import*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadgroupsetImportCall.html), [*patch*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadgroupsetPatchCall.html) and [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadgroupsetSearchCall.html)
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* [reads](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Read.html)
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* [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadSearchCall.html) and [*stream*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReadStreamCall.html)
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* [references](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Reference.html)
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* [*bases list*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReferenceBaseListCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReferenceGetCall.html) and [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReferenceSearchCall.html)
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* referencesets
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* [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReferencesetGetCall.html) and [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.ReferencesetSearchCall.html)
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* [variants](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Variant.html)
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* [*create*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantCreateCall.html), [*delete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantDeleteCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantGetCall.html), [*import*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantImportCall.html), [*merge*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantMergeCall.html), [*patch*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantPatchCall.html), [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantSearchCall.html) and [*stream*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantStreamCall.html)
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* variantsets
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* [*create*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantsetCreateCall.html), [*delete*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantsetDeleteCall.html), [*export*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantsetExportCall.html), [*get*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantsetGetCall.html), [*patch*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantsetPatchCall.html) and [*search*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.VariantsetSearchCall.html)
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# Structure of this Library
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The API is structured into the following primary items:
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* **[Hub](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/struct.Genomics.html)**
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* a central object to maintain state and allow accessing all *Activities*
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* creates [*Method Builders*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.MethodsBuilder.html) which in turn
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allow access to individual [*Call Builders*](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.CallBuilder.html)
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* **[Resources](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.Resource.html)**
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* primary types that you can apply *Activities* to
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* a collection of properties and *Parts*
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* **[Parts](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.Part.html)**
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* a collection of properties
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* never directly used in *Activities*
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* **[Activities](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.CallBuilder.html)**
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* operations to apply to *Resources*
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All *structures* are marked with applicable traits to further categorize them and ease browsing.
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Generally speaking, you can invoke *Activities* like this:
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```Rust,ignore
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let r = hub.resource().activity(...).doit()
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```
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Or specifically ...
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```ignore
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let r = hub.datasets().set_iam_policy(...).doit()
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let r = hub.datasets().delete(...).doit()
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let r = hub.datasets().get_iam_policy(...).doit()
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let r = hub.datasets().test_iam_permissions(...).doit()
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let r = hub.datasets().get(...).doit()
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let r = hub.datasets().undelete(...).doit()
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let r = hub.datasets().create(...).doit()
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let r = hub.datasets().patch(...).doit()
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let r = hub.datasets().list(...).doit()
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```
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The `resource()` and `activity(...)` calls create [builders][builder-pattern]. The second one dealing with `Activities`
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supports various methods to configure the impending operation (not shown here). It is made such that all required arguments have to be
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specified right away (i.e. `(...)`), whereas all optional ones can be [build up][builder-pattern] as desired.
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The `doit()` method performs the actual communication with the server and returns the respective result.
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# Usage
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## Setting up your Project
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To use this library, you would put the following lines into your `Cargo.toml` file:
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```toml
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[dependencies]
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google-genomics1 = "*"
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```
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## A complete example
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```Rust
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extern crate hyper;
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extern crate yup_oauth2 as oauth2;
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extern crate google_genomics1 as genomics1;
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use genomics1::Dataset;
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use genomics1::{Result, Error};
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use std::default::Default;
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use oauth2::{Authenticator, DefaultAuthenticatorDelegate, ApplicationSecret, MemoryStorage};
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use genomics1::Genomics;
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// Get an ApplicationSecret instance by some means. It contains the `client_id` and
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// `client_secret`, among other things.
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let secret: ApplicationSecret = Default::default();
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// Instantiate the authenticator. It will choose a suitable authentication flow for you,
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// unless you replace `None` with the desired Flow.
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// Provide your own `AuthenticatorDelegate` to adjust the way it operates and get feedback about
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// what's going on. You probably want to bring in your own `TokenStorage` to persist tokens and
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// retrieve them from storage.
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let auth = Authenticator::new(&secret, DefaultAuthenticatorDelegate,
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hyper::Client::new(),
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<MemoryStorage as Default>::default(), None);
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let mut hub = Genomics::new(hyper::Client::new(), auth);
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// As the method needs a request, you would usually fill it with the desired information
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// into the respective structure. Some of the parts shown here might not be applicable !
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// Values shown here are possibly random and not representative !
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let mut req = Dataset::default();
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// You can configure optional parameters by calling the respective setters at will, and
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// execute the final call using `doit()`.
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// Values shown here are possibly random and not representative !
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let result = hub.datasets().patch(req, "datasetId")
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.update_mask("sit")
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.doit();
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match result {
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Err(e) => match e {
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// The Error enum provides details about what exactly happened.
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// You can also just use its `Debug`, `Display` or `Error` traits
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Error::HttpError(_)
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|Error::MissingAPIKey
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|Error::MissingToken(_)
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|Error::Cancelled
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|Error::UploadSizeLimitExceeded(_, _)
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|Error::Failure(_)
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|Error::BadRequest(_)
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|Error::FieldClash(_)
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|Error::JsonDecodeError(_, _) => println!("{}", e),
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},
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Ok(res) => println!("Success: {:?}", res),
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}
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```
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## Handling Errors
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All errors produced by the system are provided either as [Result](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/enum.Result.html) enumeration as return value of
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the doit() methods, or handed as possibly intermediate results to either the
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[Hub Delegate](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.Delegate.html), or the [Authenticator Delegate](https://docs.rs/yup-oauth2/*/yup_oauth2/trait.AuthenticatorDelegate.html).
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When delegates handle errors or intermediate values, they may have a chance to instruct the system to retry. This
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makes the system potentially resilient to all kinds of errors.
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## Uploads and Downloads
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If a method supports downloads, the response body, which is part of the [Result](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/enum.Result.html), should be
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read by you to obtain the media.
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If such a method also supports a [Response Result](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.ResponseResult.html), it will return that by default.
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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
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this call: `.param("alt", "media")`.
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Methods supporting uploads can do so using up to 2 different protocols:
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*simple* and *resumable*. The distinctiveness of each is represented by customized
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`doit(...)` methods, which are then named `upload(...)` and `upload_resumable(...)` respectively.
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## Customization and Callbacks
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You may alter the way an `doit()` method is called by providing a [delegate](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.Delegate.html) to the
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[Method Builder](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.CallBuilder.html) before making the final `doit()` call.
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Respective methods will be called to provide progress information, as well as determine whether the system should
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retry on failure.
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The [delegate trait](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.Delegate.html) is default-implemented, allowing you to customize it with minimal effort.
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## Optional Parts in Server-Requests
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All structures provided by this library are made to be [enocodable](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.RequestValue.html) and
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[decodable](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.ResponseResult.html) via *json*. Optionals are used to indicate that partial requests are responses
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are valid.
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Most optionals are are considered [Parts](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.Part.html) which are identifiable by name, which will be sent to
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the server to indicate either the set parts of the request or the desired parts in the response.
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## Builder Arguments
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Using [method builders](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.CallBuilder.html), you are able to prepare an action call by repeatedly calling it's methods.
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These will always take a single argument, for which the following statements are true.
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* [PODs][wiki-pod] are handed by copy
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* strings are passed as `&str`
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* [request values](https://docs.rs/google-genomics1/1.0.2+20160928/google_genomics1/trait.RequestValue.html) are moved
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Arguments will always be copied or cloned into the builder, to make them independent of their original life times.
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[wiki-pod]: http://en.wikipedia.org/wiki/Plain_old_data_structure
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[builder-pattern]: http://en.wikipedia.org/wiki/Builder_pattern
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[google-go-api]: https://github.com/google/google-api-go-client
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# License
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The **genomics1** library was generated by Sebastian Thiel, and is placed
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under the *MIT* license.
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You can read the full text at the repository's [license file][repo-license].
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[repo-license]: https://github.com/Byron/google-apis-rsblob/master/LICENSE.md
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