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AMPALS Portal - DAR and Approval Integration

AMPALS Portal - DAR and Approval Integration

Introduction

The ALS Knowledge Portal aggregates content from multiple data repositories, enabling researchers to browse, search, query, and select data from multiple platforms for analysis.

Currently, users who want to access data hosted by the Critical Path Institute must submit a data access request through https://fair.dap.c-path.org. After a request is submitted, the ALS Knowledge Portal calls the FAIR API to check the request approval status. Once approved, the user signs in to RDCA-DAP and accesses the data through their approved workspace.

Purpose

The purpose of this design is to improve the user experience by allowing users to create data access requests directly from the ALS Knowledge Portal instead of signing in to RDCA-DAP. The ALS Knowledge Portal will display the request status. Once a request is approved, users will go to RDCA-DAP to download or query their approved data within the approved workspace.

Data

The C-Path datasets displayed on the ALS Knowledge Portal are governed by a contractual agreement with the Critical Path Institute. Any modifications—such as adding or removing datasets—would require changes to this contract. Currently, only 5 RDCA-DAP datasets are listed on the Portal, and users can submit data access requests exclusively for these 5 datasets.

 

Recommended Approach

Users may submit multiple Data Access Requests (DARs) for C-Path datasets. In the initial release, the ALS Knowledge Portal will display the status of the user's most recent DAR for a given dataset; users can visit RDCA-DAP directly to view their full DAR history. Once a DAR is approved, the user must log in to RDCA-DAP to analyze the data in their approved workspace.

This introduces a new feature for tracking DARs submitted to third-party systems that host restricted data outside of Synapse. FAIR serves as the source of truth for form definitions and DAR status; Portal will handles token exchange, aggregation and response shaping.

Eligibility:

A user is eligible to submit a DAR if they have linked their ALS Knowledge Portal account with RDCA-DAP. In practice, this means the user must have logged in to RDCA-DAP at least once prior to creating a DAR.

 

Form Steps & Grouping Strategy

 

Tabs: Destination (choose dictionaries + choose/create workspace) → Workspace (only if creating a new one) → Project → About → Complete (accept terms). Form data is loaded lazily per step (NOT one bootstrap) because a user may linger on Destination, never create a workspace, or abandon the flow.

 

High level Design Diagram

FrontendApproch.png

 

FAIR API endpoints

Description

FAIR Endpint

Request Body

Response Body

Description

FAIR Endpint

Request Body

Response Body

Request page opens (Destination tab)

GET https://fair.dap.c-path.org/api/datasets/{Dataset code}/dictionaries?page=1&dataExists=false.

GET https://fair.dap.c-path.org/api/datasets/{Dataset code}/workspaces-locations/

GET https://fair.dap.c-path.org/api/datasets/{Dataset code}/workspaces/?location=westeurope

None

"items": [
{
"code": "rdca10012_rdca10012_biodex_strength_11766",
"name": "biodex_strength",
"description": "This table captures information from Biodex isometric strength testing.",
"created_at": "2021-09-14T08:13:19.570Z",
"updated_at": "2021-09-14T08:13:19.570Z",
"id": 5819,
"primary": true
}
]

 

"items": [
{
"id": 19,
"value": "westeurope",
"description": "West Europe",
"organisation": null,
"regional_display_name": "(Europe) West Europe"
},
{
"id": 22,
"value": "northeurope",
"description": "North Europe",
"organisation": null,
"regional_display_name": "(Europe) North Europe"
}
],
"additional": {}
}

 

items": [
{
"uuid": "60212081-018d-42f7-8ca9-0a8e7426527a",
"name": "requested-288",
"url": null,
"location": "westeurope",
"requested": true,
"request_form": "#",
"reference": "er",
"requested_before": false,
"compatibility": []
}
],
"additional": {}
}

Request for existing workspace per location

GET https://fair.dap.c-path.org/api/datasets/{Dataset code}/workspaces/?location=location

None

items": [
{
"uuid": "60212081-018d-42f7-8ca9-0a8e7426527a",
"name": "requested-288",
"url": null,
"location": "westeurope",
"requested": true,
"request_form": "#",
"reference": "er",
"requested_before": false,
"compatibility": []
}
],
"additional": {}
}

User selects "create new workspace"

GET https://fair.dap.c-path.org/api/workspaces-forms/workspace_request

None

"name": "Request a workspace",
"sections": {
"workspace": {
"label": "Details of the workspace being requested:",
"fields": [
{
"name": "project_name",
"type": "string",
"label": "Project name",
"placeholder": "Add the name of the project and project ID if applicable",
"validation": {
"required": true,
"maximum": "250"
}
},
{
"name": "project_description",
"type": "markdown",
"label": "Project description",
"validation": {
"required": true,
"maximum": "4096"
}
},
{
"name": "emails",
"type": "text",
"label": "Additional users",
"placeholder": "Provide email addresses of other users who should be invited to the workspace",
"validation": {
"maximum": "4096"
}
},
{
"name": "region",
"type": "list",
"label": "What hub do you need your workspace to be located?",
"placeholder": "Select Hub location...",
"validation": {
"required": true
},
"options": [
{
"text": "West Europe",
"value": "westeurope",
"description": "(Europe) West Europe"
},
{
"text": "North Europe",
"value": "northeurope",
"description": "(Europe) North Europe"
}
],
"default_options": "westeurope"
},
{
"name": "vm_check",
"type": "label",
"label": "Do you require a virtual machine?"
},
{
"name": "windows_vm",
"type": "boolean",
"label": "Windows Virtual Machine"
},
{
"name": "linux_vm",
"type": "boolean",
"label": "Linux Virtual Machine"
},
{
"name": "interests",
"type": "label",
"label": "What is your area of interest? Check all that apply?"
},
{
"name": "data_science",
"type": "boolean",
"label": "Data science - general"
},
{
"name": "bio_informatics",
"type": "boolean",
"label": "Bioinformatics/BioStatistics"
},
{
"name": "maths",
"type": "boolean",
"label": "Mathematics/Statistics"
},
{
"name": "ai",
"type": "boolean",
"label": "AI/Machine Learning"
}
]
}
}

}`

User advances to Project / About tab

GET https://fair.dap.c-path.org/api/workflows/rdca_access_request

None

{
"code": "rdca_access_request",
"created_at": "2021-09-10T13:42:00.899Z",
"updated_at": "2024-06-12T09:00:46.749Z",
"controls_requests": "workflow",
"workflow": {
"id": "rdca_access_request:45:48bd6eb5-6c90-11f0-91ac-de8d4e31b0a3",
"key": "rdca_access_request",
"version": 45,
"name": "RDCA Access Request",
"description": null
},
"enabled": true,
"sections": {
"about": {
"label": "About",
"fields": [
{
"name": "code",
"type": "string",
"label": "ID",
"validation": {
"maximum": "256",
"identifier": true
},
"placeholder": "Enter a unique ID or leave blank and we will allocate one for you",
"defaultValue": ""
},
{
"name": "name",
"type": "string",
"label": "Request name",
"validation": {
"maximum": "256",
"required": true
},
"placeholder": "Name this request",
"defaultValue": ""
},
{
"name": "applicant_affiliation",
"type": "label",
"label": "Applicant Affiliation"
},
{
"name": "full_name",
"type": "string",
"label": "Applicant name",
"validation": {
"maximum": "256",
"required": true
},
"placeholder": "Your first and last name",
"defaultValue": ""
},
{
"name": "organization",
"type": "string",
"label": "Institution or organization",
"validation": {
"maximum": "256",
"required": true
},
"placeholder": "Add the name of your institution or organization",
"defaultValue": ""
},
{
"name": "org_country",
"type": "string",
"label": "Country of institution or organization",
"validation": {
"maximum": "256",
"required": true
},
"placeholder": "Enter the country of your institution or organization",
"defaultValue": ""
},
{
"name": "org_state",
"type": "string",
"label": "State or Region of institution or organization",
"validation": {
"maximum": "256",
"required": false
},
"placeholder": "Enter the state or region of your institution or organization",
"defaultValue": ""
},
{
"name": "org_address",
"type": "text",
"label": "Street address of institution or organization",
"validation": {
"maximum": "4096",
"required": true
},
"placeholder": "Add the street address of your institution or organization",
"defaultValue": ""
},
{
"name": "sector",
"type": "list",
"label": "Sector",
"options": [
{
"text": "Academia",
"value": "Academia",
"description": ""
},
{
"text": "Pharma",
"value": "Pharma",
"description": "Pharmaceutical"
},
{
"text": "Non-profit",
"value": "Non-profit",
"description": ""
},
{
"text": "Government",
"value": "Government",
"description": ""
},
{
"text": "Other",
"value": "Other",
"description": ""
}
],
"validation": {
"required": true
},
"placeholder": "The sector of the institution or organization"
},
{
"name": "dept",
"type": "string",
"label": "Department",
"validation": {
"maximum": "256",
"required": true
},
"placeholder": "Add the name of your department",
"defaultValue": ""
},
{
"name": "position",
"type": "list",
"label": "Position",
"options": [
{
"text": "Research",
"value": "Research",
"description": ""
},
{
"text": "Faculty",
"value": "Faculty",
"description": ""
},
{
"text": "Postdoc",
"value": "Postdoc",
"description": ""
},
{
"text": "Other",
"value": "Other",
"description": ""
}
],
"validation": {
"required": true
},
"placeholder": "Your position or role"
},
{
"name": "education",
"type": "string",
"label": "Education",
"validation": {
"maximum": "256",
"required": false
},
"placeholder": "Degree(s) and respective college or university",
"defaultValue": ""
},
{
"name": "websites",
"type": "markdown",
"label": "LinkedIn, ResearchGate, or other relevant websites",
"validation": {
"maximum": "4096",
"required": false
},
"defaultValue": ""
},
{
"name": "email",
"type": "string",
"label": "Institutional email address",
"validation": {
"maximum": "256",
"required": true
},
"placeholder": "Add your institutional email address",
"defaultValue": ""
},
{
"name": "phone_number",
"type": "phone",
"label": "Phone number",
"country": "us",
"validation": {
"maximum": "64",
"required": true
},
"placeholder": "",
"defaultValue": "",
"preferredCountries": [
"us",
"gb"
]
},
{
"name": "user_country",
"type": "string",
"label": "Country of residence",
"validation": {
"maximum": "256",
"required": true
},
"placeholder": "Enter your country of residence",
"defaultValue": ""
},
{
"name": "user_state",
"type": "string",
"label": "State or Region of residence",
"validation": {
"maximum": "256",
"required": false
},
"placeholder": "Enter your state or region of residence",
"defaultValue": ""
}
]
},
"project": {
"label": "Project",
"fields": [
{
"name": "project_name",
"type": "string",
"label": "Title of proposed research or study",
"validation": {
"maximum": "250",
"required": true
},
"placeholder": "Add the title of the research plan or study to be made publicly available",
"defaultValue": ""
},
{
"name": "project_synopsis",
"type": "text",
"label": "Synopsis of proposed research or study",
"validation": {
"maximum": "4096",
"required": true
},
"placeholder": "Describe goals, expected milestones, and how RDCA-DAP supports your goals",
"defaultValue": ""
},
{
"name": "results_pub_intent",
"type": "text",
"label": "Results and publication intent",
"validation": {
"maximum": "4096",
"required": true
},
"placeholder": "Describe how results will be used and any publication intentions", "defaultValue": "" }, { "name": "curation_req", "type": "list", "label": "If approved, in what format would you prefer the data?", "options": [ { "text": "Raw", "value": "Raw", "description": "" }, { "text": "Curated OMOP", "value": "Curated OMOP", "description": "" }, { "text": "Curated SDTM", "value": "Curated SDTM", "description": "" } ], "validation": { "required": false }, "placeholder": "The preferred format of the data" }, { "name": "principal_investigator", "type": "string", "label": "Principal Investigator (Name, Title, and Email)", "validation": { "maximum": "250", "required": true }, "placeholder": "Name and email for the PI (if different than the requester)", "defaultValue": "" }, { "name": "check_PI", "type": "boolean", "label": "Have you included the title, name, and email of the PI? *", "validation": { "required": true }, "defaultValue": "" }, { "name": "additional_user_access", "type": "text", "label": "Additional Access (Name, Title, and Email)", "validation": { "maximum": "4096", "required": true }, "placeholder": "List any additional users who will need access (name, title, and email)", "defaultValue": "" }, { "name": "check_users", "type": "boolean", "label": "Have you included the title, name, and email of all users? *", "validation": { "required": true }, "defaultValue": "" }, { "name": "project_signatories", "type": "text", "label": "Authorized Signatories (Name, Title, and Email)", "validation": { "maximum": "4096", "required": true }, "placeholder": "Institutional authorized signatory(s) (name, title, and email)", "defaultValue": "" }, { "name": "check_sig", "type": "boolean", "label": "Have you included the title, name, and email of all signatories? *", "validation": { "required": true }, "defaultValue": "" }, { "name": "project_end_date", "type": "date", "label": "Project end date", "validation": { "minimum": "today", "required": true }, "placeholder": "Anticipated end date of your research or study", "defaultValue": "" } ] } }}`

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