Parameterized Advanced Querying System
| dc.contributor.author | Master, Sahal |
| dc.contributor.author | Marchesani, Nicole |
| dc.contributor.other | PEDSnet Data Coordinating Center |
| dc.contributor.other | PCORnet® Query Fulfillment Core |
| dc.date.accessioned | 2026-04-23T13:29:12Z |
| dc.date.created | 2026-04 |
| dc.description | This repository provides scripts for developing PAQS queries. Follow the steps below to set up your local environment, develop and test PAQS queries. <br><br> ##### Build With     ##### Databases Supported<br>      Tested<br>   <br><br> ##### **Prerequisites** Development can be done in the container or natively. However, we recommend to use the container for easier dependency management and portablity of the package. [Ensure you have container management software such as Docker or Podman installed.](https://docs.docker.com/get-started/get-docker/)<br><br> ##### **Clone this Repository** You'll need this base package to start query development from regardless of environment **Note:** Avoid direct edits to the cloned directory to maintain integrity. ```sh git clone https://github.com/Query-Fulfillment/paqs.git ``` <br> ##### **Scripts and Directories** ```sh paqs ├── config_template │ ├── bigquery │ ├── databricks │ ├── duckdb │ ├── mssql_ad │ ├── mssql_db │ ├── oracle │ ├── postgres │ └── snowflake ├── Dockerfile ├── LICENSE.txt ├── package ├── query │ ├── code_sets │ ├── execute_req.R │ ├── results │ └── script │ ├── base │ │ ├── helper.R │ │ └── setup.R │ ├── study │ ├── driver.R │ ├── report.qmd │ └── study ├── README ├── renv.lock ├── results ├── tools │ ├── banner │ ├── build_package.sh │ ├── handler.sh │ ├── parse_log.sh │ ├── PCORnet-logo-resize.png │ └── pcornet-style-sheet.css └── workplan.qmd ``` - **Dockerfile:** Contains the recipe to build a query specific image from a pre-built image and execute the query within the container - **config_template/:** Contains configuration templates for establishing a connection to the database - **query/code_sets/:** Contains codeset files when required to execute the request - **query/results/:** Initially empty. Will store query results in the container which will be mounted to `../results` - **query/script/:** Contains query execution code needed to execute the request - **query/script/base:** Contains query execution code that is standard for all queries [DO NOT EDIT] - **query/script/study:** Empty initially. Should contain query execution code that is specific to the current request [ALWAYS CUSTOM CODE] - **query/script/query:** Contains query execution code that is specific to the query that is being developed [Add new code/scripts in this directory] - **query/execute_req.R:** Contains code to drive query execution using an R function - **tools/:** Contains miscellaneous files required for the query - **results**: Initially empty. This directory will be mounted with the `query/results` directory within the container. Output generated by the query are to be returned via your site’s PCORnet® AWS S3 bucket. These tables consist of aggregate data/output and transfers the minimum information required to answer the analytic question. Please see Step 4 of the Returning Results section of this workplan for information on returning query output generated in this folder.<br><br> ##### **Booting up a Development Environment** Run below command in terminal. Please replace `{home_dir}` with the home directory on your machine and update the tag with the version you want to use. For new query, it's recommended to use the latest version. ```sh docker run --rm -p 8787:8787 -e PASSWORD=pass -e ROOT=TRUE -v {home_dir}:/home/rstudio pcornetqf/qf-r-base-rstudio:2.0.1 ``` Open web browser and go to [localhost:8787](localhost:8787). Log in with `username=rstudio` and `password=pass`. For more details on pre-built docker image see [here](https://github.com/Query-Fulfillment/qf-r-base-image).<br><br> ##### **New request** 1. Navigate to the terminal in R-studio and navigate to the directory where you want to create a new request. 2. Copy and paste the path to new_request.sh, then execute it with a unique identifier for the report, such as: ```sh path/to/new_request.sh fd1000 **Note:** This repository is under active development; the code is subjected to change. |
| dc.description.abstract | Standard repository for development work related to hyperfast and slightly modern querying platform. |
| dc.identifier.uri | https://hdl.handle.net/20.500.14642/1640 |
| dc.provenance | This package was developed to support activities of the PCORnet® Query Fulfillment team as well as to support research conducted within PEDSnet, A Pediatric Clinical Research Network. PCORnet® Query Fulfillment is funded through Patient-Centered Outcomes Research Institute (PCORI®) award RI-CHOP-01-PS2. PEDSnet has been developed with funding from the PCORI®; PEDSnet’s participation in PCORnet® is funded through PCORI® award RI-CHOP-01-PS1. The package and its documentation do not necessarily represent the opinions of PCORI® or other organizations participating in, collaborating with, or funding PCORnet®. |
| dc.publisher | PEDSnet |
| dc.rights | an MPL-2.0 license. |
| dc.subject | R |
| dc.subject | Docker Dependence |
| dc.subject | Postgres Compatible |
| dc.subject | Snowflake Compatible |
| dc.subject | DuckDB Compatible |
| dc.subject | Oracle Compatible |
| dc.subject | Microsoft SQL Server Compatible |
| dc.subject | Quarto |
| dc.subject | Bootstrap |
| dc.title | Parameterized Advanced Querying System |
| dc.title.alternative | PAQS |
| dspace.entity.type | Code |
| local.code.github | https://github.com/Query-Fulfillment/paqs |
| local.code.package | git clone https://github.com/Query-Fulfillment/paqs.git |