Package: otelib
OTELibOTELib is a small Python library on top of the OTEAPI, that provides a simple and pythonic interface to the REST services.It makes it very simple to configure, set up and run a pipeline based on the pipes and filter design pattern.ContentOverviewHow to use OTELibSessionHow to run the pore fraction exampleLicenseOverviewThe OTEAPI provides a REST API for connecting a sequence of microservices into a pipeline for connecting simulation tools to data sources in a very flexible and reusable way.
OTELib provides a simple Python interface to OTEAPI that makes it easy to utilise OTEAPI from user applications and Python scripts/notebooks as illustrated in the figure below.Figure:Overview showing how the OTELib can be used by user applications to access data and simulation tools via a simple Python interface.OTEAPI utilises thepipes and filtersoftware design pattern to separate the process of connecting to external data resources, mapping it to a common ontology (for interoperability), data processing and running simulations into a set of reusable components.
This design provides a very high degree of flexibility and is easy to maintain due to the modularity, making it well suited for use in EU projects with distributed and loosely coupled teams.
The pipes and filters themselves are implemented as microservices that can be fetched from a docker repository.In OTELib the pipes and filters are represented by classes - one Pipe class and currently 4 generic filter classes.
It uses thestrategysoftware design pattern is used to specify the underlying microservice.Pipe:represent data with a type and connects the output from one filter into the input of another filter.
Apart from connecting filters, pipes may also have some additional features, including (not implemented yet):Provide access to data and querying.Performing authorisation checks.Provide caching to avoid unnecessary repeating previous operations.
In order to avoid unauthorised access to the cache, the cache may utilise access tokens for authorisation.
If needed different caching strategies may be supported.Pipes will be created transparently by OTELib, so as an user, you will normally not interact with pipes.DataResource:is a filter intended to connect to external data resources and allow the user to perform operations like query, read from or write to the resource.
Where it make sense, some data resource filters may implement full CRUD (create, read, update, and delete) support.If the DataResource filter reads from a resource, itsget()method will use a given data model (which may be generated on the fly) and store the content acquired data according to that.
It will return a reference to the internal data representation.Mapping:is a filter intended to map the data model describing the input to concepts in a common ontology.
The mappings themselves may either be provided during configuration of the filter or fetched from a triplestore.DataFilter:is a filter intended for fast data processing, like simple data conversions.
Theget()method will not return before the output is generated.Transformation:is a filter intended for more time-consuming data processing, like simulations or demanding data conversions.
It supports polling and waiting for the transformation to finish.How to use OTELibLets assume that you want to set up a simple pipeline as shown in the following figure.Figure:Generic pipeline connecting three filters, a DataResource filter, a Mapping filter and a Transformation filter via pipes.The DataResource filter connects to a data resource and represents selected content from it using a data model.The Mapping filter maps the data model to ontologies, making the data read from the data resource fully semantically.The Transformation filter performs a transformation of the data, which could involve a simulation.
The result will typically be an instance of another data model.To set up a pipeline, you will first have to connect to a running OTE server using theOTEClient:fromotelibimportOTEClientclient=OTEClient('http://localhost:8080')Then you must configure the instances of the filters you want to use:data_resource=client.create_dataresource(downloadUrl="https://jpeg.org/images/jpegsystems-home.jpg",mediaType="image/jpeg",)mapping=client.create_mapping(mappingType="triples")transformation=client.create_transformation(transformation_type="celery/remote")Before you easily and elegant can combine them into a pipeline:pipeline=data_resource>>mapping>>transformationNote, this also transparently creates the pipes connecting the filters.To execute the pipeline, simply call itsget()method:pipeline.get()which will return a reference to the result of the last transformation.
Note that no data will be read before theget()method of the pipeline is called.A pipeline can be reused and forked:filter2=client.create_filter(filterType="filter/crop",configuration={"crop":[0,0,200,200]},)filter3=client.create_filter(filterType="filter/blur")pipeline2=pipeline>>filter2pipeline3=pipeline>>filter3Note: Thefilter/blurfilter strategy does not exist in the core OTEAPI package.
This strategy should come from another plugin package.As well as merged:pipeline4=pipeline2+pipeline3SessionA pipeline is executed by calling itsget()method which will call theget()method of the last filter, which will call theget()method of its input pipe and so forth.
Hence, a pipeline is executed upstream, from the back to the front, while the data is communicated downstream.The purpose of asessionis to allow the user or downstream filters to provide configurations consumed by filters further upstream.
It is implemented as a common dict shared by all pipes and filters in a pipeline.
If a session is not provided when you call theget()method, a newsessionwill be created and passed upstream.LicenseOTELib is released under theMIT licensewith copyright © SINTEF.AcknowledgmentOTEAPI Core has been supported by the following projects:OntoTrans(2020-2024) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement no. 862136.VIPCOAT(2021-2025) receives funding from the European Union’s Horizon 2020 Research and Innovation Programme - DT-NMBP-11-2020 Open Innovation Platform for Materials Modelling, under Grant Agreement no: 952903.OpenModel(2021-2025) receives funding from the European Union’s Horizon 2020 Research and Innovation Programme - DT-NMBP-11-2020 Open Innovation Platform for Materials Modelling, under Grant Agreement no: 953167.