How to share data#
AiiDA offers two avenues for sharing data with others: archive files and the REST API.
Sharing AiiDA archives#
You have performed your calculations with AiiDA and you would like to share your AiiDA provenance graph, for example to make your scientific study reproducible.
Since AiiDA keeps track of the provenance of every computed result, this step is easy: Tell AiiDA the final results you would like to be reproducible, and AiiDA will automatically include their entire provenance using the Traversal Rules.
Exporting individual nodes#
Let’s say the key results of your study are contained in three AiiDA nodes with PKs
Exporting those results together with their provenance is as easy as:
$ verdi archive create my-calculations.aiida --nodes 12 123 1234
As usual, you can use any identifier (label, PK or UUID) to specify the nodes to be exported.
The resulting archive file
my-calculations.aiida contains all information pertaining to the exported nodes.
The default traversal rules make sure to include the complete provenance of any node specified and should be sufficient for most cases.
verdi archive create --help for ways to modify the traversal rules.
To see what would be exported, before exporting, you can use the
$ verdi archive create --test-run my-calculations.aiida
Please remember to use UUIDs when pointing your colleagues to data inside an AiiDA archive, since UUIDs are guaranteed to be universally unique (while PKs aren’t).
Exporting large numbers of nodes#
If the number of results to be exported is large, for example in a high-throughput study, use the
QueryBuilder to add the corresponding nodes to a group
my-results (see How to group nodes).
Then export the group:
$ verdi archive create my-calculations.aiida --groups my-results
Alternatively, export your entire profile with:
$ verdi archive create my-calculations.aiida --all
Publishing AiiDA archive files#
AiiDA archive files can be published on any research data repository, for example the Materials Cloud Archive, Zenodo, or the Open Science Framework. When publishing AiiDA archives on the Materials Cloud Archive, you also get an interactive EXPLORE section, which allows peers to browse the AiiDA provenance graph directly in the browser.
Inspecting an archive#
In order to get a quick overview of an archive file without importing it into your AiiDA profile, use
verdi archive info:
$ verdi archive info --detailed test.aiida metadata: export_version: main_0001 aiida_version: 2.0.0 key_format: sha256 compression: 6 ctime: '2022-03-06T23:50:57.964429' creation_parameters: entities_starting_set: node: - 6af3f8a0-cf0d-4427-8472-f8907acfc87a include_authinfos: false include_comments: true include_logs: true graph_traversal_rules: input_calc_forward: false input_calc_backward: true create_forward: true create_backward: true return_forward: true return_backward: false input_work_forward: false input_work_backward: true call_calc_forward: true call_calc_backward: true call_work_forward: true call_work_backward: true entities: Users: count: 1 emails: - email@example.com Computers: count: 2 labels: - computer1 - computer2 Nodes: count: 53 node_types: - data.core.array.trajectory.TrajectoryData. - data.core.cif.CifData. - data.core.code.Code. - data.core.dict.Dict. - data.core.folder.FolderData. - data.core.remote.RemoteData. - data.core.singlefile.SinglefileData. - data.core.structure.StructureData. - process.calculation.calcfunction.CalcFunctionNode. - process.calculation.calcjob.CalcJobNode. process_types: - aiida.calculations:codtools.ciffilter - aiida.calculations:quantumespresso.pw Groups: count: 0 type_strings:  Comments: count: 0 Logs: count: 0 Links: count: 59 repository: objects: count: 71
You can also use the Python API to inspect the archive file as a profile, see How to inspect an archive.
Importing an archive#
verdi archive import to import AiiDA archives into your current AiiDA profile.
verdi archive import accepts URLs, e.g.:
$ verdi archive import "https://archive.materialscloud.org/record/file?file_id=2a59c9e7-9752-47a8-8f0e-79bcdb06842c&filename=SSSP_1.1_PBE_efficiency.aiida&record_id=23"
During import, AiiDA will avoid identifier collisions and node duplication based on UUIDs (and email comparisons for
By default, existing entities will be updated with the most recent changes.
Node extras and comments have special modes for determining how to import them - for more details, see
verdi archive import --help.
To see what would be imported, before importing, you can use the
$ verdi archive import --test-run my-calculations.aiida
The AiiDA archive format has evolved over time, but you can still import archives created with previous AiiDA versions. If an outdated archive version is detected during import, the archive file will be automatically migrated to the newest version (within a temporary folder) and the import retried.
You can also use
verdi archive migrate to create updated archive files from existing archive files (or update them in place).
Serving data through the REST API#
The AiiDA REST API allows to query your AiiDA database over HTTP(S) and returns results in JSON format.
As of October 2020, the AiiDA REST API only supports
GET methods (reading); in particular, it does not yet support workflow management.
This feature is, however, part of the AiiDA roadmap.
To ensure that when serving
orm.ArrayData one always obtains a valid JSON compliant with the ECMA-262 standard, any
-np.inf entries will be replaced by
None which will be rendered as
null when getting the array via the API call.
Launching the REST API#
Start serving data from your default AiiDA profile via the REST API:
$ verdi restapi * REST API running on http://127.0.0.1:5000/api/v4 * Serving Flask app "aiida.restapi.run_api" (lazy loading) * Environment: production WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead. * Debug mode: off * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)
The REST API is now running on port
5000 of your local computer.
verdi commands, you can select a different AiiDA profile via the
-p PROFILE option:
verdi -p <another_profile> restapi
REST API version history:
v4. Simplified endpoints; only
aiida-core>= 1.0.0b3, <1.0.0b6:
v3. Development version, never shipped with a stable release.
v2. First API version, with new endpoints added step by step.
Querying the REST API#
A URL to query the REST API consists of:
The base URL, by default:
Querying the base URL returns a list of all available endpoints.
The path defining the requested resource, optionally followed by a more specific endpoint. For example:
/nodes /nodes/page/2 /nodes/projectable_properties /nodes/<uuid> /nodes/<uuid>/links/outgoing
If no endpoint is appended, the API returns a list of objects of that resource. In order to request a specific object of a resource, append its UUID.
As usual, you can use partial UUIDs as long as they are unique.
In order to query by PK you need to use the
idfilter (see below). This also applies to
Users, which don’t have UUIDs (but instead uses email).
(Optional) The query string for filtering, ordering and pagination of results. For example:
?limit=20&offset=35 ?id=200 ?node_type=like="data%"
Here are some examples to try:
http://127.0.0.1:5000/api/v4/users/ http://127.0.0.1:5000/api/v4/computers?scheduler_type="slurm" http://127.0.0.1:5000/api/v4/nodes/?id>45&node_type=like="data%"
The interactive EXPLORE sections on Materials Cloud are all powered by the AiiDA REST API and you can query the underlying API, either using your web browser or using a tool like
$ curl https://aiida-dev.materialscloud.org/2dstructures/api/v4/users
For an extensive user documentation of the endpoints, the query string as well as the format of the responses, see the AiiDA REST API reference.
New in version 2.1.0.
It is possible to allow a request to declare a specific profile for which to run the profile. This makes it possible to use a single REST API to serve the content of all configured profiles. The profile switching functionality is disabled by default but can be enabled through the config:
verdi config set rest_api.profile_switching True
After the REST API is restarted, it will now accept the profile query parameter, for example:
If the specified is already loaded, the REST API functions exactly as without profile switching enabled. If another profile is specified, the REST API will first switch profiles before executing the request.
If the profile parameter is specified in a request and the REST API does not have profile switching enabled, a 400 response is returned.
Deploying a REST API server#
verdi restapi command runs the REST API through the
werkzeug python-based HTTP server.
In order to deploy production instances of the REST API for serving your data to others, we recommend using a fully fledged web server, such as Apache or NGINX, which then runs the REST API python application through the web server gateway interface (WSGI).
One Apache/NGINX server can host multiple instances of the REST APIs, e.g. serving data from different AiiDA profiles.
myprofile-rest.wsgi script for an AiiDA profile
myprofile would look like this:
# -*- coding: utf-8 -*- # wsgi script for AiiDA profile 'myprofile' from aiida.manage.configuration import load_profile from aiida.restapi.run_api import configure_api load_profile('myprofile') api = configure_api() application = api.app
See the documentation of
configure_api() for all available configuration options.
In the following, we explain how to run this wsgi application using Apache on Ubuntu.
Install and enable the
mod_wsgiWSGI module module:
$ sudo apt install libapache2-mod-wsgi-py3 $ sudo a2enmod wsgi
Place the WSGI script in a folder on your server, for example
Configure apache to run the WSGI application using a virtual host configuration similar to:
# Apache virtual host configuration file for AiiDA REST API # Copy to /etc/apache2/sites-enabled/aiida-rest.conf <VirtualHost *:80> LogLevel debug # Let the app do authorization WSGIPassAuthorization On # Require privileges on the wsgi directory <Directory "/home/ubuntu/wsgi"> Require all granted </Directory> # BEGIN SECTION for "myprofile" AiiDA profile # Use 5 threads and "aiida" virtual python environment WSGIDaemonProcess rest-myprofile \ user=ubuntu group=ubuntu \ threads=5 \ python-home=/home/ubuntu/.virtualenvs/aiida \ display-name=aiida-rest-myprofile # REST API will be served on <host>/myprofile/api/v4 WSGIScriptAlias /myprofile /home/ubuntu/wsgi/myprofile-rest.wsgi <Location /myprofile> WSGIProcessGroup myprofile </Location> # END SECTION for "myprofile" AiiDA profile </VirtualHost>
sudo service apache2 restart.
You should now be able to reach your REST API at
localhost/myprofile/api/v4 (Port 80).