Overview
We are constantly looking at ways to make it possible (not to mention reliable and easy!) for users and developers to interact with and extend OpenClinica in a programmatic way. This can mean anything from data loading to more meaningful integrations of applications common to the clinical research environment.
As proponents of open, standards-based interoperability here at OpenClinica, our starting point is always to develop interfaces for these interactions based on the most successful, open, and proven methods in the history of technology – namely the protocols that power the World Wide Web (such as HTTP, SSL, XML, OAuth 2.0). They are relatively simple, extensively documented, widely understood, and well-supported out of the box in a large number of programming and IT environments. On top of this foundation, we rely heavily on the wonderful work of CDISC and the CDISC ODM to model and represent the clinical research protocol and clinical data.
This chapter describes a CDISC ODM-based way to interact with OpenClinica using RESTful APIs and OAuth. The REST web services API relies on HTTP, SSL, XML, OAuth 2.0. This architecture makes the ODM study protocol representation for an OpenClinica study available and supports other interactions for study design.
Why REST?
The OpenClinica RESTful architecture was developed to (initially) support one particular use case, but with the intention of becoming more broadly applicable over time. This use case is based on a frequent request of end users: for OpenClinica to support a visual method for designing, editing, and testing “rules” which define edit checks, email notifications, skip pattern definitions, and the like to be used in OpenClinica CRFs. Users have had to learn how to write rules in XML, which can be confusing and have a big learning curve for non-technical individuals. The OpenClinica Rule Designer is an application that allows end users to build cross field edit checks and dynamics within a GUI based application. It is centrally hosted Software as a Service (SaaS) based application available for OpenClinica Enterprise customers at https://designer.openclinica.com.
To support interaction of the centrally hosted rule designer with any instance of OpenClinica Enterprise installed anywhere in the world, we needed to implement a secure protocol and set of API methods to allow exchange of study information between the two systems, and do so in a way where the user experience was as integrated as if these applications were part of the same integrated code base. In doing so, and by adopting the aforementioned web and clinical standards to achieve this, we have built an architecture that can be extended and adapted for a much more diverse set of uses.
This chapter specifies how 3rd party applications can interact with an OpenClinica instance via the REST API and OAuth security, and details the currently supported REST API methods. The currently supported API methods are not comprehensive, and you may get better coverage from our SOAP API. However the OpenClinica team is continuing to expand this API and since it is open source anyone may extend it to add new methods to meet their own purposes. If you do use the API in a meaningful way or if you extend the API with new methods, please let others know on the OpenClinica developers list (developers@openclinica.org), and submit your contributions for inclusion back into the codebase – you’ll get better support, increased QA, and compatibility with future OpenClinica releases.
RESTful Representation, based on ODM
“REST”, an acronym for REpresentational State Transfer, describes an architectural style that allows definition and addressing of resources in a stateless manner, primarily through the use of Uniform Resource Identifiers (URIs) and HTTP.
From Wikipedia: A RESTful web service (also called a RESTful web API) is a simple web service implemented using HTTP and the principles of REST. It is a collection of resources, with three defined aspects:
- the base URI for the web service, such as http://example.com/resources/
- the Internet media type of the data supported by the web service. This is often JSON, XML or YAML but can be any other valid Internet media type.
- the set of operations supported by the web service using HTTP methods (e.g., POST, GET, PUT or DELETE).
REST is also a way of looking at the world, as eloquently articulated by Ryan Tomayko.
In the context of REST for clinical research using OpenClinica, we can conceptually think of an electronic case report form (CRF) as a resource that is essentially a bunch of metadata modeled in CDISC ODM with OpenClinica extensions:
- Some of this metadata (data type, item name, response set, etc) is intrinsic metadata – i.e. tied to the definition of the CRF and its items and mostly unchangeable after it is initially defined.
- Some of this metadata is representation metadata and used only when the CRF is represented as a web-based HTML form (in the OpenClinica database schema we call this form_metadata, but it also can include other things like CRF version information and rules).
An OpenClinica Event CRF is that same bunch of metadata with the corresponding item data, plus references to the study subject, event definition, CRF version, event ordinal, etc that it pertains to.
- The notion of a CRF version pertains to the representation of the CRF. It is not intrinsic to the event CRF (this is debatable but it is how OpenClinica models CRFs). Theoretically you should be able to address and view any Event CRF in any available version of the CRF (i.e. http://oc/RESTpath/StudyA/Subj1234/VisitA/FormB/v1/edit and http://oc/RESTpath/StudyA/Subj1234/VisitA/FormB/v2/edit both show you the same data represented in different versions of the CRF). Of course the audit history needs to clearly show which version/representation of the CRF was used for key events such as data capture, signature, etc.
- Rules are also part of the representation metadata as opposed to intrinsic metadata, even though you don’t need to specify them on a version-by-version basis.
- Anything attached to the actual event CRF object or its item data – discrepancy notes, audit trails, signatures, SDV performance, etc is part of that event data and should be addressable in the same manner (e.g. http://oc/RESTpath/StudyA/Subj1234/VisitA/FormB/v1/GROUPOID/ORDINAL/ITEM…)
In this conceptual view of the world, CRFs (as well as CRF items, studies, study events, etc.) are RESTful resources with core, intrinsic properties and then some other metadata that has to do with how they are presented in a particular representation. We now have a model that allows us a great deal of flexibility and adaptability. We can support multiple modalities, with different representation metadata for rendering the same form, or perhaps the shared representation metadata but applied in a different way. We can address any part of the CRF in an atomic manner. This approach has been successfully applied in the Rule Designer, which takes the ODM study metadata and allows browse of the study CRFs and items, with the ability to drag and drop those resources into rule expressions. Here are some examples of additional future capabilities that could be easily realized on top of this architecture:
- Multiple data entry modalities – a user may need to deploy patient based data entry via web, a tablet, a thick client, or even paper/OCR, each with a very different presentation. Each of these may be part of OpenClinica-web or a separate application altogether, but all will rely on the same resource metadata to represent the CRF (according to the UI + logic appropriate for that modality), and use the same REST-based URL and method for submitting/validating the data.
- Apply a custom view (an XSL or HTML/CSS) to a patient event CRF or full casebook – some uses of this could be to represent as a PDF casebook, show with all audit trails/DNs embedded in line with the CRF data, show a listing of data for that subject, provide (via an XSL mapping) as an XForm or HL7 CCD document for use by another application) – http://oc/RESTpath/StudyA/Subj1234/VisitA/FormB/v1/view?renderer=somemap…
- The same path used in the URLs, eg http://oc/RESTpath/StudyA/Subj1234/VisitA/FormB/v1/GROUPOID/ORDINAL/ITEMOID could be used as the basis for XPath expressions operating on ODM XML representations of CRFs and of event CRF data
- Internationalization – OpenClinica ought to allow our CRF representation metadata to have an additional sub-layer to render the form in different languages, and then automatically show the appropriate language based on client/server HTTP negotiation (like we do with the rest of the app). Currently internationalization of CRFs requires versioning the CRF.
- View CRF & Print CRF – use the same representation metadata (form metadata) but apply slightly different rules on how the presentation works (text values instead of form fields, no buttons, turn drop down lists into text values)
- Discrepancy manager popup – one requested use case would allow a user to update a single event CRF item data value directly from the discrepancy note UI point of view. In this case you could think of just updating that one item as addressing the resource http://oc/RESTpath/StudyA/Subj1234/VisitA/FormB/v1/GROUPOID/ORDINAL/ITEM…. In this model, whatever rules and presentation metadata need to get applied at presentation and save time happen automatically.
- Import of CDISC ODM XML files – imported data would be processed through the same model, but only use the metadata that’s relevant to the data import modality. Same for data coming in as raw ODM XML via a REST web service. A lot of times the import only populates one part of a CRF and the other parts are expected to be finished via data entry. This model would help us manage that process better that the current implementation of ODM data import.
There are many considerations related to user roles and permissions, workflows, and event CRF/item data status attributes that need to be overlaid on top of this REST model, but the model itself is a conceptually useful way to think about clinical trials and the information represented therein. When implemented using CDISC ODM XML syntax it becomes even more powerful. As widespread support for ODM becomes the norm, the barriers to true interoperability – shared, machine readable study protocol definitions, and robust, real-time, ALCOA-compliant exchange of clinical data and metadata that aligns with user’s business processes – get eviscerated.
* This chapter frequently refers to ODM-based representations of study metadata and clinical data in OpenClinica. We strive as much as possible to implement ODM-based representations of OpenClinica metadata and data according to the generic ODM specifications (currently using ODM version 1.3). However, to ensure our representations support the full richness of information used in OpenClinica we often have to rely on ODM’s vendor extensions capability. We have not always made distinctions in this chapter as to where we are using ‘generic’ ODM versus OpenClinica extensions, but that is documented here. It is our goal as ODM matures and supports richer representations of study information to migrate our extensions back into the generic ODM formats.
** Also note the RESTful URL patterns referred to above are conceptual. Refer to the technical subchapters of this REST API specification for the actual URLs.
