Scripting Galaxy using the API and BioBlend

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# Scripting Galaxy using the API and BioBlend

<div class="contributors-line">
		<a href="/training-material/hall-of-fame/odoppelt/" class="contributor-badge contributor-odoppelt"><img src="https://avatars.githubusercontent.com/odoppelt?s=36" alt="Olivia Doppelt-Azeroual avatar" width="36" class="avatar" />
    Olivia Doppelt-Azeroual</a><a href="/training-material/hall-of-fame/fmareuil/" class="contributor-badge contributor-fmareuil"><img src="https://avatars.githubusercontent.com/fmareuil?s=36" alt="Fabien Mareuil avatar" width="36" class="avatar" />
    Fabien Mareuil</a><a href="/training-material/hall-of-fame/nsoranzo/" class="contributor-badge contributor-nsoranzo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" />
    Nicola Soranzo</a><a href="/training-material/hall-of-fame/dannon/" class="contributor-badge contributor-dannon"><img src="https://avatars.githubusercontent.com/dannon?s=36" alt="Dannon Baker avatar" width="36" class="avatar" />
    Dannon Baker</a>
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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [JupyterLab](https://jupyterlab.readthedocs.io/)

---

### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- What is a REST API?

- How to interact with Galaxy programmatically?

- Why and when should I use BioBlend?

---

## Galaxy API

- **Application Programming Interface (API)**: the protocol defined by a software for how it can be controlled by an external program
- Galaxy provides a rich API:
  - Over the HTTP protocol
  - The Galaxy UI is being migrated on top of the Galaxy API

???

- An Application Programming Interface provides software developers with a definition of the methods to interact with a program or a library.
- When the program is a remote web server like Galaxy, the methods are represented by URIs and the communication is through the HTTP protocol.
- Nowadays, most of the Galaxy user interface makes use of the backend API to implement an asynchronous web application.

---

## Interacting with Galaxy: UI vs. API

- The Galaxy UI is good for:
  - exploring and visualizing data
  - experimenting
  - graphically designing workflows
  - people not comfortable with the command line

- The Galaxy API is good for:
  - interact programmatically with the server
    - complex control: **branching** and **looping** (not yet possible in workflows)
  - automate repetitive tasks
  - integration with external resources

???

- The Galaxy user interface is a better choice for explorative analysis, visualising data and drawing workflows.
- The API instead allows you to automate tasks using Galaxy's capabilities programmatically.
- A typical use case is to upload FASTQ files as soon as your sequencer finishes writing them, and running a quality control workflow.
- Importantly, however you interact with Galaxy, you can equally benefit from features like reproducibility of the analysis and data sharing.
- In fact, all the work done via the API is still accessible when you return to the UI.

---

## Galaxy API functionalities

- Users can:
  - upload and download data
  - run tools and workflows, ...
  - manage histories and datasets

- Admins can also manage:
  - data libraries
  - tools and dependencies
  - users, quotas, roles...

- Source code lives at https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/webapps/galaxy/api/

???

- Most of the operations you would normally perform on the Galaxy UI are available via the API.
- You can for example upload data, run tools and workflows, and manage your histories.
- It is also possible to perform admin tasks, like manage data libraries and install tools.

---

## RESTful API

.left[REpresentational State Transfer (REST) is the architectural style of the World Wide Web:]
- client–server
- API requests:
  - standard HTTP request **methods** (GET, POST, PUT, DELETE,...) and status codes
  - Uniform **Resource** Identifiers (URIs)
  - Query and payload for parameters

???

- The Galaxy API follows the REST model typical of web applications.
- A REST API specifies a protocol for the interaction between a client and a server.
- The client sends requests composed by an HTTP method and a resource.
- The main HTTP methods are: GET (to retrieve a resource); POST (to create); PUT (to replace); and DELETE.
- Resources are identified by Uniform Resource Identifiers.
- Examples of resources in the Galaxy API are: datasets, tools, jobs, histories, libraries, users; essentially anything that is recorded in the Galaxy database.
- The client often need to pass additional parameters or data to specify how a request should be carried out.
- The server replies to the request with a status code (to indicate if there was an error) and usually some data.

---

## API requests

- **HTTP method + URI [+ payload]**

1. `GET https://usegalaxy.org/api/histories?order=name` -> ordered list of histories

- URI parameters: IDs in path, others in the *query* (`?name=value&...`)

???

- Let's see some examples of possible API requests to a Galaxy server.
- In the first example we use the GET method to retrieve a resource, in this case the list of histories.
- The URI starts with the protocol and address of the server, followed by the resource we are interested in: the histories.
- A URI may then include an optional query, preceded by a question mark, containing a sequence of request parameters specified as key-equal-value and separated by ampersands.
- In this example, the query is used to ask that the list of histories is ordered by name.

---

## API requests

- **HTTP method + URI [+ payload]**

1. `GET https://usegalaxy.org/api/histories?order=name` -> ordered list of histories
  2. `POST /api/histories {"name": "New analysis"}` -> create a history named "New analysis"
  3. `PUT /api/histories/<id> {"published": true}` -> publish a history
  4. `DELETE /api/histories/<history_id>/contents/<id>` -> delete a history dataset

- URI parameters: IDs in path, others in the *query* (`?name=value&...`)
- POST/PUT payload as JSON

???

- In the second example, the POST method is used to create a resource on the server, in this case a new history.
- Parameters for the POST request are passed as a payload in JSON format; more on this later.
- In this example the payload contains the new name for the history to be created.
- In the third example, we use the PUT method to update an existing resource, in this case to make a history public.
- The history to modify is indentified by appending its ID to the histories URI.
- The parameters for PUT requests are also passed in a payload.
- In the fourth example, we use the DELETE method to remove a resource from the server.
- In this case, we request the deletion of a particular dataset in a specific history, as indicated in the URI.

---

## JSON format

.left[JavaScript Object Notation https://www.json.org/] <img style="float: right;" height="80" width="80" alt="JSON logo" src="../../images/json160.gif" />
  - Lightweight data-interchange text format
  - Easy to read/write for both humans and machines
  - ECMA-404 open standard (2013), [RFC 8259](https://tools.ietf.org/html/rfc8259) (2017)

```json
{"history_id": "b5731bb49a17bf50",
 "id": "df06cc665d85b6ea",
 "inputs": {"0": {"id": "bbd44e69cb8906b51528b5d606d1fdd0",
                  "src": "hda"}},
 "model_class": "WorkflowInvocation",
 "outputs": ["bbd44e69cb8906b528819eaaff340ecd",
             "0ff30b4e2a4bed9e"],
 "state": "scheduled",
 "update_time": "2015-07-03T19:28:39.544574",
 "workflow_id": "56482e194d798eb6"}
```

???

- Request payloads passed to Galaxy and data returned by the API are encoded in the JSON format.
- JSON is a standard format used to exchange text data and is supported in all major programming languages.
- In JSON, strings are enclosed by double quotes, dictionaries by curly braces, and arrays by square brackets.
- Dictionaries and arrays can be nested at will, as shown in the example.

---

## Status codes and errors

- HTTP status codes:
  - 200 OK, 400 your error, 500 server error, ...<br>
    https://www.iana.org/assignments/http-status-codes/http-status-codes.xhtml
- Galaxy error codes and messages: [`lib/galaxy/exceptions/`](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/exceptions)
  - Still a work in progress

???

- In REST APIs, the server should use the standardised HTTP status codes in its responses to indicate either a successful request or the type of error encountered.
- In the Galaxy API, error status codes and messages are returned to the client by raising specific Python exceptions in the backend.

---

## How to access a REST API

.left[With anything that can communicate over HTTP:]
- Command line:
  - `curl`
- GUI:
  - Browsers: only GET
  - [RESTClient](https://addons.mozilla.org/firefox/addon/restclient/) add-on for Firefox
  - [Advanced REST Client](https://advancedrestclient.com/)
- Software libraries:
  - General HTTP libraries (e.g. [requests](https://requests.readthedocs.io/) for Python)
  - Service-specific libraries (e.g. *BioBlend* to access Galaxy using Python)

???

- A REST API can be accessed via the HTTP protocol. There are 3 main ways to do that.
- On the command line, the curl tool can perform any type of HTTP request; look at its manual for details.
- For graphical user interfaces, you can perform GET requests directly on your browser by simply entering the URI on the address bar.
- For more complex requests, you can use the Advanced REST Client open source app.
- The third and most common way is to write a program.
- All programming languages have some general library to communicate over HTTP.
- For Python, requests is probably the best library to do that.
- Many web services provide dedicated higher-level libraries to access their REST API.
- In particular, BioBlend is a Python library to interact with Galaxy that we will describe later.

---

## Security

- Most API calls require authentication
  - When the UI accesses the API, session auth is used
  - Other callers needs an **API key**: alphanumeric string (32 chars) identifying a registered user<br>
    Keep it secure, it’s the same as a username+password!
- Always use HTTPS:
  - **https**://example.org/api?key=foo is safer due to the encryption of the transmitted data

???

- A note about security.
- When programmatically performing requests that require authentication, the client need to pass an API key.
- An API key is an alphanumeric string uniquely identifying a user on a server.
- Since it is equivalent to the combination of your username and password, keep it secure!
- In particular, always use the HTTPS protocol to make requests, not HTTP which sends data unencrypted.

---

## Advanced Galaxy API config

.left[Options in `config/galaxy.yml`:]
- User impersonation by adding `run_as` in the payload
  ```yaml
  # Optional list of email addresses of API users who can make calls on
  # behalf of other users.
  api_allow_run_as: foo@foo.com
  ```

- Bootstrapping Galaxy

```yaml
  # API key that allows performing some admin actions without actually
  # having a real admin user in the database and config. Only set this
  # if you need to bootstrap Galaxy, in particular to create a real
  # admin user account via API. You should probably not set this on a
  # production server.
  bootstrap_admin_api_key: MASTERLOCK
  ```

This option was called ``master_api_key`` in Galaxy 22.05 and earlier.

???

- There are 2 options in the Galaxy configuration file that are relevant for the API.
- api_allow_run_as allows the specified user to impersonate any other user on the Galaxy instance.
- bootstrap_admin_api_key instead is an optional special API key that can be used to bootstrap a Galaxy instance, in particular to create an initial admin account.

---

## Galaxy API Modernization

.left[Moving to [FastAPI](https://fastapi.tiangolo.com/)]

- Main advantages:
  - [Async requests](https://fastapi.tiangolo.com/async/)
  - Subscriptions via [websockets](https://fastapi.tiangolo.com/advanced/websockets/)
  - Integrated [OpenAPI](https://spec.openapis.org/oas/v3.1.0) interactive documentation, e.g. https://usegalaxy.org/api/docs
  - Reduce maintenance burden
  - Simplify client code generation

???

- The Galaxy API is currently in the process of migrating towards FastAPI, which is a modern framework for building REST APIs in Python with really interesting features.
- For example, FastAPI can serve requests with better performances using asynchronous coroutines.
- Another performance advantage is the ability to avoid inefficient polling by using WebSockets subscriptions.
- In addition to the performance benefits, by using FastAPI in combination with type annotations, the Galaxy API can comply with the OpenAPI standard.
- This standard can greatly enhance interoperability with other systems and reduce the maintenance burden of documentation and client code generation.

---

## Galaxy API pros and cons

- Pros:
  - Integrated with Galaxy
  - Well tested
  - Language agnostic
- Cons:
  - Very low-level

???

- To summarise this first part, Galaxy has an extensive REST API that allows users and admins to interact programmatically with a server.
- It can be accessed with any programming language, but it's also very low level.
- For example, you need to construct complex URIs, encode payloads and decode returned data.

---

## BioBlend

- BioBlend is a **Python library** that wraps the functionality of Galaxy and CloudMan APIs
- Started by Enis Afgan, Nuwan Goonasekera and Clare Sloggett in 2012. Contributions by the Galaxy Team and the community
- Open source (MIT license)
- Available via PyPI and from https://github.com/galaxyproject/bioblend

???

- A Python library called BioBlend was created in 2012 to make it easier to interact with the Galaxy API.
- BioBlend is open source and developed by a community of contributors.
- It is hosted on GitHub and can be installed via pip.

---

## BioBlend features

- Stable procedural API
- Supported under Python >=3.7
- Wraps all main Galaxy API controllers
- Extensive Continuous Integration testing:
  - on Galaxy release_17.09 and later
  - \>240 unit tests
- Well-documented on https://bioblend.readthedocs.io

???

- BioBlend has a very stable procedural API and works on all supported Python versions.
- It provides methods wrapping all the important Galaxy API endpoints.
- The library uses Continuous Integration to perform a large number of tests on a wide range of Galaxy releases.
- The documentation of BioBlend is very well curated and is often more accurate than the corresponding Galaxy API one.

---

## BioBlend limitations

- Python-only (but separate *blend4j* and *blend4php* exist)
- Its methods just deserialize the JSON response
  - No isolation from changes in the Galaxy API
  - Need to extract the entity ID for further processing
- No explicit modeling of Galaxy entities and their relationships
- Complex operations still need many function calls
  - Need for higher-level functionality

???

- Although easier to use than the Galaxy API, BioBlend has some limitations.
- First of all, it's only available for Python.
- There are alternative libraries for Java and PHP, but they are less complete.
- Another limitation of BioBlend is that it doesn't shield the caller from possible changes in responses from the Galaxy API.
- It can also be annoying to have to constantly keep track of entity IDs.
- This happens because BioBlend does not try to model Galaxy entities and how they are connected.

---

## BioBlend.objects

- BioBlend.objects is an extra layer which adds an **object-oriented interface** for the Galaxy API
- Started by Simone Leo, Luca Pireddu and Nicola Soranzo at CRS4 in 2013
- Distributed with BioBlend
- Presently limited to datasets, histories, invocations, jobs, libraries, tools and workflows

???

- To implement this modelling of Galaxy entities, some years ago an object-oriented interface was added on top of BioBlend: BioBlend objects
- This is developed and distributed together with BioBlend itself.
- When using this interface, methods will return objects encapsulating the dictionaries returned by the Galaxy API.
- The user can then invoke further methods on these objects, for example the download method for a Dataset object.
- Only a subset of BioBlend is available through the object interface, but most of the common user functionalities are included.

---

## References

- Galaxy API docs: https://docs.galaxyproject.org/en/master/api_doc.html
- BioBlend docs: https://bioblend.readthedocs.io/
- BioBlend chat: https://matrix.to/#/#galaxyproject_bioblend:gitter.im
- C. Sloggett, N. Goonasekera, E. Afgan. BioBlend: automating pipeline analyses within Galaxy and CloudMan. *Bioinformatics* 29(13), 1685-1686, 2013, doi:[10.1093/bioinformatics/btt199](https://doi.org/10.1093/bioinformatics/btt199)
- S. Leo, L. Pireddu, G. Cuccuru, L. Lianas, N. Soranzo, E. Afgan, G. Zanetti. BioBlend.objects: metacomputing with Galaxy. *Bioinformatics* 30 (19), 2816-2817, 2014, doi:[10.1093/bioinformatics/btu386](https://doi.org/10.1093/bioinformatics/btu386)

???

- Here you can find the links to the documentation of the Galaxy API and of BioBlend.
- We have a dedicated Gitter channel to chat about BioBlend.
- If you use BioBlend or BioBlend objects, please cite these papers.

---
### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points

- The API allows you to use Galaxy's capabilities programmatically.

- BioBlend makes using the Galaxy API from Python easier.

- BioBlend objects is an object-oriented interface for interacting with Galaxy.

---

## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

<div class="contributors-line">
		Authors: <a href="/training-material/hall-of-fame/odoppelt/" class="contributor-badge contributor-odoppelt"><img src="https://avatars.githubusercontent.com/odoppelt?s=36" alt="Olivia Doppelt-Azeroual avatar" width="36" class="avatar" />
    Olivia Doppelt-Azeroual</a><a href="/training-material/hall-of-fame/fmareuil/" class="contributor-badge contributor-fmareuil"><img src="https://avatars.githubusercontent.com/fmareuil?s=36" alt="Fabien Mareuil avatar" width="36" class="avatar" />
    Fabien Mareuil</a><a href="/training-material/hall-of-fame/nsoranzo/" class="contributor-badge contributor-nsoranzo"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" />
    Nicola Soranzo</a><a href="/training-material/hall-of-fame/dannon/" class="contributor-badge contributor-dannon"><img src="https://avatars.githubusercontent.com/dannon?s=36" alt="Dannon Baker avatar" width="36" class="avatar" />
    Dannon Baker</a>
	</div>

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