PHIRI APP - WP7 - PHIRI Federated Research Infrastructure (FRI) - D7.1 Small-scale prototype of PHIRI federated infrastructure

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 cases 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.

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") 

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#### 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