B2SHARE REST API
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In this hands on session will make use of the scenario demonstrated previously to show how the same results can be achieved programmatically. The ability to use the services via the API are essential to automate the data management process when dealing with large volumes of data, potentially from many different sources. This will require hands on coding (the demonstrations will be given using python but if users are confident they may choose their own language). By the end of this sessions, attendees should be able to understand how to use the B2 services within their own scientific workflows to allow automated data management.
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B2SHARE REST API
- 1. www.eudat.eu EUDAT receives funding from the European Union's Horizon 2020 programme - DG CONNECT e-Infrastructures. Contract No. 654065 B2SHARE REST API hands-on Hans van Piggelen, hans.vanpiggelen@surfsara.nl Thursday July 6th, 2017 This work is licensed under the Creative Commons CC-BY 4.0 licence
- 2. Today’s hands-on Theory: (30 min) The B2SHARE REST API B2SHARE concepts, variables, metadata schemas API: making requests, authentication and payloads Publication workflow Practice: (1 hour) Simple examples Hands-on exercises Next hands-on: B2FIND
- 3. What is the B2SHARE REST API? The B2SHARE REST API is a set of instructions to interact with a B2SHARE service instance The B2SHARE REST API: Allows direct remote interaction with the B2SHARE service without using a graphical user interface Allows integration within application or data processing workflows for automation of publishing tasks Supports any programming language or operating system that supports HTTP requests There is (almost) no limitation on usage and number of calls, even for unregistered users To create new or modify existing content, registration is required
- 4. Why use the B2SHARE REST API? Using the B2SHARE API you can automate: Creation of records Uploading of files Adding/changing metadata Changing publications state Retrieval of object data Enable: Precise replication of metadata into repository Large file uploads Implement publishing in your own workflow or application Direct data ingest Ease administration and overview of your records
- 5. What can I do with the B2SHARE API? List (all) existing records and communities Search for specific records and communities Retrieval of community-specific information Including community metadata schemas Create new draft records Upload files to draft records Add metadata using metadata schemas Publish draft records Modification of the metadata of existing records More to be added in future releases…
- 6. Important concepts of B2SHARE Records: Contain data files and associated metadata Connected to a community which possibly maintains it Metadata: Set of common fixed metadata fields and custom metadata blocks with additional fields Governed by fixed and community metadata schemas Communities: Curate datasets which are part of the scientific domain or a research project Maintain their own metadata schemas and have community administrators States: Current condition of a record, either draft, submitted or published Can be changed through the API 7
- 7. B2SHARE request variables B2SHARE defines several request variables that function as identifiers for objects in B2SHARE Used in most HTTP request addresses as part of the path to access specific objects directly Most important variables: COMMUNITY_ID: identifier of a user community RECORD_ID: identifier for a specific record, in either state FILE_BUCKET_ID: identifier for a set of files of a specific record 8
- 8. Draft records and versioning Draft records: Can be updated with new files and metadata Have publication state ‘draft’ Published records: Cannot have files updated anymore Metadata updates possible but discouraged B2SHARE supports versioning of records: Existing published records can be updated through their draft counterpart Creates new PIDs, bucket IDs, links Draft ✔ New files ✔ New records Published ✗ New files ✗ New records Draft
- 9. Community metadata schemas Every community defines its own metadata schema using a hierarchical JSON Schema-based structure Metadata schemas: Contain descriptions, vocabularies and expected structure and format of every metadata field, including optional fields May contain community-specific fields Definitions are publically available, e.g. EUDAT: 10
- 10. Example metadata field definitions
- 11. Example metadata field definitions
- 12. Example metadata field definitions
- 13. Example metadata field definitions
- 14. Making a request Requests can be made by using a specific application directly or by using a programming language that supports making requests in code Example applications: GUI: any file transfer application or web interface Command line: cURL, wGet Almost all programming languages support making requests over HTTP For more complex operations (like publication), a dedicated interface or command line application is more useful 16
- 15. HTTP requests A specific call to a service through an API using a method with address and parameters An address is a URL: URL = protocol + hostname + port + path Protocol: always http:// or https:// Hostname: base address, e.g. b2share.eudat.eu Port: sometimes required specifically, usually 80 or 443 Path: endpoint specification, e.g. /api/record/1 Optional parameters are additional options given to the request and are added to the URL On success the current state of the requested piece of information is provided The B2SHARE service accepts payloads along with a HTTP request, e.g. text, binary data, files 17
- 16. HTTP request method Different methods have different meaning, but up to service on how to process them Common methods: GET: requests data from a specified resource POST: submits data to be processed to a specified resource PUT: uploads a representation of the specified URI PATCH: modify state of specified resource DELETE: delete a specified resource
- 17. HTTP responses Every request returns a status, header and message body, even when an error occurred Status line: status code and reason Header: information on body content Body: actual response text Status codes: 1xx: Informational – Request received, continuing process 2xx: Success – Action was successfully received, understood, and accepted 3xx: Redirection – Further action must be taken in order to complete the request 4xx: Client Error – Request contains bad syntax or cannot be fulfilled 5xx: Server Error – Server failed to fulfill an apparently valid request HTTP response is pure text, needs interpretation
- 18. HTTP request overview 20 Browser CLI tool Your app or workflow HTTP response: - Header - Status code - Response text HTTP request: - Request method - Header - URL & parameters - Authentication - Payloads Server Client
- 19. Authentication through the API B2SHARE does not accept username and password combination, instead use tokens for authentication! B2SHARE contains open and restricted data: Public: all published records and metadata, most files No access token required Private: your draft records and files in private records Only accessible using your access token as parameter in HTTP request Access tokens: Automatically generated unique string of characters attached to your account in B2SHARE Only known by the owner, do not share with others! 21
- 20. Full B2SHARE publication workflow Publishing in B2SHARE using the API involves multiple steps: Identify a target community for your data Retrieve the metadata schema definition of the community The submitted metadata will have to conform to this schema Create a draft record: Upload files into the draft record (one by one) Add metadata according to schema (possibly in multiple steps) Publish the record 22
- 21. Full publication workflow diagram 23 Create draft Add metadata Add files POST /api/records GET /api/records/RECORD_ID/draft PATCH /api/records/RECORD_ID/draft PUT /api/files/FILE_BUCKET_ID/FILE_NAME Commit Published record PATCH /api/records/RECORD_ID/draft Draft record PID Checksum Needs approval? Submitted record Community Approve NO YES
- 22. Adding metadata Metadata is added to a record using the API: Upon creation of a draft record in a POST request Or by providing so-called JSON patches in a PATCH request Patches modify the current state of the metadata by either changing, adding or removing fields and values The structure of the data provided in the patch request must strictly follow the metadata schema of the community As many patches as necessary can be applied before publishing your draft record 24 Add metadata Draft record
- 23. Adding files Files can be added during the draft phase of your new record using a PUT request Files are uploaded into the file bucket of the draft record, not the draft record itself Use the file bucket ID found in the metadata of the draft record Files are uploaded one-by-one in separate requests As many file upload requests as necessary can be made before publishing your draft record 25 Add files Draft record Checksum
- 24. Publishing your draft record Draft records are published by altering the value of the publication state in the metadata Once your record is published: The included files can not be changed anymore! No new files can be added! Metadata can be changed after publication, but will create a new version of your published record Persistent identifiers are automatically added on commit 26 Commit Draft record Published record PID
- 25. Simple examples Protocol and host: https://trng-b2share.eudat.eu Application: python (using command-line interface) HTTP method: GET Retrieve all existing records: List all communities: Search for specific records of a community: 27 r = requests.get(‘https://trng-b2share.eudat.eu/api/records’) r = requests.get(‘https://trng-b2share.eudat.eu/api/records? q=community:COMMUNITY_ID`) r = requests.get(‘https://trng-b2share.eudat.eu/api/communities’)
- 26. Complex example HTTP method: POST Create draft record ‘My test upload’: header = {‘Content-Type’: 'application/json'} metadata = {"titles": [{"title":"My test upload"}], "community": "e9b9792e-79fb-4b07-b6b4-b9c2bd06d095", "open_access": True} r = requests.post('https://trng-b2share.eudat.eu/api/records/', params=parameters, data=json.dumps(metadata), headers=header) parameters = {'access_token': token}
- 27. JSON patch A set of operations that alter an existing set of metadata fields based on another set of fields Loosely equals the difference between two sets Operations: add, remove, replace, copy, move, test Generated by jsonpatch package Requires PATCH request to apply to record Metadata OLD Metadata NEW Metadata PATCH
- 28. JSON patch example [ { "path": "/community_specific", "value": {}, "op": "add" }, { "path": "/disciplines", "value": [ "EUDAT Summer School" ], "op": "add" } ]
- 29. Today’s hands-on exercises Get and store your API token Retrieve single record information Check metadata and included files Download files and compare checksum Retrieve existing communities Retrieve community metadata schema Investigate metadata schema structure Create a new draft record Upload files and metadata Update and complete metadata Publish record
- 30. General instructions Create an API token on the B2SHARE training website Requirements for each request: Request URL and HTTP method (e.g. GET, PUT) Optional: Object identifiers (e.g. record, community) Additional parameters (e.g. your token) Data payloads (e.g. files or text) Use requests package for HTTP requests Use jsonpatch package to create metadata update patches B2SHARE API endpoint: /api
- 31. General instructions Log in to 145.100.59.156 ssh <user>@145.100.59.156 Use Python or iPython as interface Helpful links: Exercises: https://hdl.handle.net/21.T12996/ESS2017- B2SHARE-API Example image: https://hdl.handle.net/21.T12996/ESS2017-Image.png Backup token: https://hdl.handle.net/21.T12996/token.txt Ask questions anytime!
- 32. Getting your access token Log in on B2SHARE and navigate to profile page: Create a token by entering a new name: Click on ‘New token’
- 33. Saving your token to file Store the token in a file so it can be restored later: Load the token in Python: $ echo “<your token>” > token.txt f = open(‘token.txt’, ‘r’) token = f.read().strip()
- 34. Exercise 1a: single record retrieval Endpoint: /api/records/<RECORD_ID> Method: GET Response status code: 200 RECORD_ID: 47077e3c4b9f4852a40709e338ad4620 Steps: Create the URL Retrieve the object data Parse the response text
- 35. Exercise 1b: process record metadata Use data of previous record Steps: Get the metadata field values Investigate the file(s) contained Check if open access and published Get the file bucket ID, file key(s) and checksum(s)
- 36. Exercise 1c: download file and check Endpoint: /api/files/<FILE_BUCKET_ID>/<FILE_KEY> Method: GET Response status code: 200 Steps: Create the URL Download files Calculate checksum and compare
- 37. Exercise 2a: communities retrieval Endpoint: /api/communities Method: GET Response status code: 200 Steps: Get all communities Parse the response text Locate the EUDAT community and its ID
- 38. Exercise 2b: EUDAT community records Endpoint: /api/records?q=community:<COMMUNITY_ID> Method: GET Response status code: 200 COMMUNITY_ID: <> Steps: Set required parameters for request Determine number of records Show first record
- 39. Exercise 2c: EUDAT community metadata schema Endpoint: /api/communities/<COMMUNITY_ID>/schemas/last Method: GET Response status code: 200 COMMUNITY_ID: <> Steps: Determine number of metadata fields Determine required fields Determine community-specific fields Determine metadata field structure
- 40. Exercise 3a: create draft record Endpoint: /api/records/ Method: POST Response status code: 201 Steps: Prepare header and payloads Get API token Get draft record ID Check publication state Get file bucket ID
- 41. Exercise 3b: add files Endpoint: /api/files/<FILE_BUCKET_ID>/<FILE_KEY> Method: PUT Response status code: 200 FILE_BUCKET_ID: <draft record’s file bucket ID> FILE_KEY: <your file name> Steps: Prepare header Open file handle Send file with request
- 42. Exercise 3c: add metadata Endpoint: /api/records/<RECORD_ID>/draft Method: PATCH Response status code: 200 RECORD_ID: <draft record ID> Steps: Prepare header Prepare JSON patch Send patch with request
- 43. Exercise 3d: publish record Endpoint: /api/records/<RECORD_ID>/draft Method: PATCH Response status code: 200 RECORD_ID: <draft record ID> Steps: Prepare header Prepare JSON patch Send patch with request Check publication state of record Check record in web browser
- 44. For more info: https://eudat.eu/services/b2share B2SHARE User Documentation: https://eudat.eu/services/userdoc/b2share B2SHARE Training presentations: https://www.eudat.eu/b2share-training-suite B2SHARE hands-on training: https://github.com/EUDAT-Training/B2SHARE-Training 46
- 45. www.eudat.eu This work is licensed under the Creative Commons CC-BY 4.0 licence EUDAT receives funding from the European Union's Horizon 2020 programme - DG CONNECT e-Infrastructures. Contract No. 654065 Authors Contributors Hans van Piggelen, SURFsara Thank you!
Editor's Notes
- Who knows what B2SHARE is? Who knows what an API is? Who has used an API before? Who has accessed an API using Python before?
- The next three slides may be common knowledge, so we can skip them if everybody knows about these. API stands for Application Programming Interface, and is a specification of a set of definitions, protocols and tools which allow to interact with a service, possibly from a remote location. An API provides an abstraction layer of the underlying service technologies used by the service itself and external applications to communicate with the technology without exactly knowing how it works. This allows machines to easily interact with the service and correctly handle responses and possible errors. When it comes to APIs for the Internet, communication is done through HTTP requests which return machine-readable structures of data representing the current state of a piece of information. The API can often used to alter information on the server side as well. The returned data is usually provided in specific formats like XML or JSON. In many cases this can be changed upon request. Your own browser is using the same mechanisms to get data from a server and present it to the user.
- B2SHARE has web-based GUI, but it also offers a REST API. The B2SHARE API is a set of instructions to interact with a B2SHARE service instance, for example the one of EUDAT. It provides direct interaction with the service without using a graphical user interface. Instead a command line tool or an application that integrates the communication is used. For example, the tools used in a research workflow might include automatic upload of final data in order to directly publish it. Most programming language have built-in functionality to interact with a remote service using HTTP requests. The B2SHARE REST API can be used by any user without registration and without limitations. The only functionality that requires registration is the creation and modification of records and defined communities.
- Using the B2SHARE API, the user can do several important operations such as listing all existing records and communities that are currently defined in the service. When a user is looking for specific records and/or communities the query functionality can be used and filtered using several parameters. Once a community has been chosen, detailed community-specific information, including community metadata schema definitions and other requirements can be retrieved. New draft records can be created, including the upload of files and the addition of metadata in accordance to the metadata schema defined by a community or project. Once a draft record is completed, it can be published. Furthermore, existing published records can be modified in terms of metadata and published as a new versioned record. The old version will always be available and citable.
- There are several important concepts used in B2SHARE which are relevant to using the API. First there are communities that curate datasets which are part of the scientific domain or a research project. Community administrators maintain the metadata schema of the community. Users have to select the community when creating new records in order to have it connected that community. Records contain data files and associated metadata and are always connected to a specific community. Communities actively curate records that are published under their name. When publishing under the EUDAT general community, this is not the case. Metadata are a set of common fixed metadata fields and custom metadata blocks with additional fields. They are governed by fixed and community metadata schemas. When choosing a specific community, there might be additional metadata fields to be filled in. A state is the current condition of a record, either draft, submitted or published. They can be changed through the API. Only published records are visible in B2SHARE. Draft and submitted records are only visible to the owner and possibly the community administrator under which the record is published.
- B2SHARE defines several request variables that function as identifiers for objects in B2SHARE. They are used in most HTTP request addresses as part of the path to access specific objects directly The most important variables are the community ID which uniquely identifies a community. Record IDs identify specific records, either in draft or published state. The file bucket ID is used to identify a set of files of a specific record
- All records are published under a specific community and have metadata added according to the corresponding community metadata schema in case this is required. Metadata schemas contain the descriptions, vocabularies and expected structure and format of every metadata field in the schema. Furthermore, they define which fields are mandatory to fill in during the creation of new records. Community metadata schema definitions are publically available through the API and on the B2SHARE website.
- To actually make a request, use a designated tool or application, or integrate it into your own application using a programming language which supports this. Examples are GUI applications like file transfer tools or web interfaces on websites. On the command line typical examples are curl and wget. Most programming languages support making requests over HTTP, but often require the inclusion of packages which provide this functionality. For more complex operations (like publication), a dedicated interface or command line application is required and therefore a file transfer tool often doesn’t suffice.
- APIs are used by making HTTP requests. These are specific calls to a service using a supported method with address and parameters. The address is structured as a URL which consists of a protocol, hostname, port (often not necessary) and a path which possibly identifies the piece of information requested. The path is often called the API endpoint. Multiple endpoints can exists for a given service. Parameters are additional options given to the request which can further filter the return information or specify for example the return format. All requests always return a response, provided that the server is available, even when the request is malformed or some other error occurred. Depending on the success, the request contains a HTTP status code and a response text with further information. On success the current state of the requested piece of information is provided.
- We will now look at some examples of using the API. For many requests you need to authenticate yourself. As APIs are often used directly in applications, you don’t want to provide usernames and passwords for every request you make. Instead an access token is generated on the website which uniquely identifies yourself during a request. B2SHARE contains public or open access and restricted data. All open access published records and metadata are public and can be accessed by anyone, this mostly holds for the contained files as well. Therefore no access tokens are required. For privately shared records and your draft records and files an access token is required. Depending on the authorization and community settings, you may or may not be able to access these records. As the access token unique identifies yourself and allows alteration of your published and draft records, do not share it with anyone!
- The full publication workflow using the B2SHARE REST API is as follows: Identify a target community to place your new record under. You need the community ID of that community and depending on the community, only members of that community can publish under their name. Get the metadata schema definition of that community using the community ID. Now you know the required fields for your publication Create a draft record and upload your files and add metadata. This can all be done in multiple separate steps and for files one-by-one. When adding files, checksums will be generated for each file. Finally publish your record. Depending on the community’s settings, your record may need approval of the community before it will be shown in B2SHARE. A persistent identifier is added to the record so that it can be uniquely identified.
- For clarity, here there is a complete overview of the full publication workflow using the B2SHARE REST API in a diagram. For every step (blue boxes) the corresponding request and HTTP method has been added in which the variables need to be filled in. The only exception is the ‘community approve’ step which can’t be done through the API yet. A record can be in three states: draft, submitted or published (red boxes). Draft and submitted records are not visible openly, but only to the user or community. Checksums are calculated for every file added and a PID is added once the draft record is committed (green boxes).
- There are two ways of adding metadata to a record using the API: upon creation of a draft record and by providing so-called JSON patches in a request. This can also be done to already published records, but will create a new version of that record with new PIDs and checksums. JSON patch requests modify the current state of the metadata by either changing, adding or removing fields and values. The structure of the data provided in the patch request must strictly follow the metadata schema of the community. You can make as many patch requests as necessary before publishing your draft record or new published version.
- Files can be added during the draft phase of your new record using a PUT request. Files are uploaded into the file bucket of the draft record, not the draft record itself. Therefore use the file bucket ID found in the metadata of the draft record. All added files have their checksum calculated. Files are uploaded one-by-one in separate requests. You can upload as many files as necessary before publishing your draft record or published version.
- Draft records are published by altering the value of the publication state in the metadata. Once your record is published, the included files can not be changed anymore and no new files can be added! Metadata can be changed after publication, but will create a new version of your published record. After your publication request, the persistent identifiers are automatically added to the record
- Here are some example GET requests using the B2SHARE training instance and the curl application. No access token is necessary yet, as all this information is publically available. Examples: The retrieve all existing records and list all communities examples do not use a variable in the address To search for specific records of a community, use the community ID in the query parameter q. Community IDs can be found in the listing of all communities
- To generate an access token, go to the B2SHARE website, log in and navigate to the profile page. Create new token by entering a name, followed by a click on the new token button. Note that you will not be able to retrieve this token, so store it safely. If you loose your token you can create a new one on this page. You can create as many as you like.
- Have a look at our website for more information regarding B2SHARE User documentation is also available here B2SHARE hands-on training can be found on GitHub. Currently only API access using Python is covered. In the future more modules will be added.
- Thank you!