D7.1 Small-scale prototype of PHIRI federated infrastructure (PHIRI app) The PHIRI Federated Research Infrastructure (FRI) is supported by a containerized reproducible solution for data analysis deployed on-premises by each participant partner. This solution is based on the identification of the relevant data sources for each case study (including the demonstration pilot), the development of the common data models and the analytical pipelines, and enables the FAIR reporting of the rapid cycle outputs. The small-scale prototype includes, in this version: - Common data models for both the demonstration pilot and PHIRI use cases A to D (including their respective synthetic datasets) (see links in Additional notes) - Data quality analysis scripts for all use cases - Data analysis scripts for the demonstration pilot and PHIRI Use Cases A, B, C, and D *Rapid-cycle analysis is enabled by participant partners deploying this prototype through continuous data updates. The current technical stack of the PHIRI FLI includes (x2) Docker containers, using: (x1) Server-side (Back-end) Framework: Nest (NestJS) -> TypeScript (https://nestjs.com/) Execution environment: Node.js® >= v14.0.0 (https://nodejs.org/es/) Database management system: SQLite (https://www.sqlite.org/index.html) Data analysis environment: R version 4.0.4 (https://www.r-project.org/) Data wrangling and management: Python (>= Python 3.8.12 (https://www.python.org/)) (x1) Client-side (Front-end Web application) Web server/proxy: Nginx (https://www.nginx.com/) Framework: Vue.js -> HTML, CSS, and JavaScript/TypeScript (https://vuejs.org/) General requirements for installing Docker (support) Server: 1 server (or VM) CPU: 1 CPU minimum (or 2 CPU for VM configuration) GPU: No dedicated GPU required RAM Memory: 4 GB minimum (8 GB recommended) OS: Unix-based (Linux or other) with Docker support Specific PHIRI FDI Docker deployment requirements RAM Memory: 8 GB minimum (16 GB recommended) Links to other deliverables: Common Data Models for the different use cases (included in the PHIRI app): PHIRI - WP7 - Pilot Common Data Model https://doi.org/10.5281/zenodo.5148467 PHIRI - WP6 - Use Case A Common Data Model https://doi.org/10.5281/zenodo.5148014 PHIRI - WP6 - Use Case B Common Data Model https://doi.org/10.5281/zenodo.5148022 PHIRI - WP6 - Use Case C Common Data Model https://doi.org/10.5281/zenodo.5148032 PHIRI - WP6 - Use Case D Common Data Model https://doi.org/10.5281/zenodo.5148040 RMarkdown scripts for analysis of the different use cases (included in the PHIRI app): PHIRI - WP6 - Use Case A scripts for local analyses (R Markdown) https://doi.org/10.5281/zenodo.6377096 PHIRI - WP6 - Use Case B scripts for local analyses (R Markdown) https://doi.org/10.5281/zenodo.6359893 PHIRI - WP6 - Use Case C scripts for local analyses (R Markdown) https://doi.org/10.5281/zenodo.6380734 PHIRI - WP6 - Use Case D scripts for local analyses (R Markdown) https://doi.org/10.5281/zenodo.6377112 Note 1: The PHIRI FRI includes deployment instructions as a PDF document ("deploy_phiri_app.pdf") Note 2: The PHIRI FRI includes virtual machine installation and deployment instructions as a PDF document ("PHIRI_WP7_vm_installation_guide.pdf") ############################################################################################ #### PHIRI app v.2.2.3 changelog #### Fixed RMarkdown analysis scripts related to socio-economic level for use cases A, B and D. Fixed RMarkdown analyses script for use case C to show 0.0 or NA values as empty values. Fixed the data syntax checker during the data mapping process that caused problems in required numeric variables when non-numeric values were present and the error was not reported correctly. Fixed RMarkdown analysis script for use case D, the aggregated function had an unexpected behaviour in periods with null information. Fixed RMarkdown analysis script for use case D to identify anxiety and depression for other ontologies such as ICD9 or SNOMED. Fixed RMarkdown analysis script for use case D to dynamically consider if the dataset contains data from 2021 or not (optional data). Update: Do not set the maximum value of the "period" variable in the mapping and checking script to support successive periods. Update: Do not set the maximum value of the "age" variable in the mapping and checking script. Update: Fixed axes of the graphs (y = 0) Update: Minor change in the visualization of figure legend and axes labels Fixed: Removed the filter that took into account the type of treatment to create the selection of patient #### PHIRI app v.2.2.2 changelog #### Fixed RMarkdown analyses scripts for use cases A, B, and D to handle variables (recommended) with all values missing (empty vars). Updated the RMarkdown analyses scripts to introduce checkpoints before proceeding with the analyses and continue running even if there are not all recommended variables. Removed the 'Actions' icons in the 'Outputs retrieval' menu interface disabled in certain deployment settings. Substituted all 'Actions' icons within the user interface with labelled buttons. Added PHIRI app versioning information in the collapsible menu (left-side) #### PHIRI app v.2.2.1 changelog #### Fixed data syntaxis checker during the data mapping process affecting the expected data model in variables with restricted values when the entire variable is missing #### PHIRI app v.2.2.0 changelog #### Fixed data syntaxis checker during the data mapping process affecting the expected data model for the Demonstration Pilot Improved display of previous analyses in the Outputs. Now outputs are presented sorted by date of generation. Updated Demonstration Pilot analyses Added supplementary methodological notes to the output HTML report Added generation of aggregated data outputs Refactored R code to facilitate maintenance

Disclaimer: Please, note that we provide these scripts as they are, complying with the specifications of the Deliverable 7.1 "Small-scale prototype of PHIRI federated infrastructure" of PHIRI WP7 on "Building a federated research infrastructure for a rapid policy response" for the purposes of achieving the objectives specified in PHIRI WP6 and WP7. Software is provided as-is without further support out of the scope of the partners participating in the Demonstration Pilot or the use cases.