From 2a7e7acc2bc3f57fb24956a1d89b0b5ca3a712a4 Mon Sep 17 00:00:00 2001 From: eric <98181083+ciresiemanym@users.noreply.github.com> Date: Thu, 18 May 2023 12:36:08 -0500 Subject: [PATCH] Add files via upload --- docs/vlmd-healdata-utils.md | 34 ++++++++++++++++------------------ 1 file changed, 16 insertions(+), 18 deletions(-) diff --git a/docs/vlmd-healdata-utils.md b/docs/vlmd-healdata-utils.md index aeb8227..0f83b8f 100644 --- a/docs/vlmd-healdata-utils.md +++ b/docs/vlmd-healdata-utils.md @@ -1,5 +1,4 @@ # How to Generate HEAL-compliant Data Dictionaries -Or, Using healdata-utils (or something expressing a utility) to Generate HEAL-compliant Data Dictionaries In order to submit a data dictionary to the Platform, the data dictionary must conform to the HEAL variable-level metadata schema. This page will show you how to use a tool we’ve created (healdata-utils) to help you generate a HEAL-compliant data dictionary. @@ -14,46 +13,45 @@ We highly recommend installing the HEAL Data Utilities in a virtual environment. ### Create a Project Folder -`mkdir my_project/` +- `mkdir my_project/` -`cd my_project ` +- `cd my_project ` ### Create Input and Output Folders -`mkdir input` +- `mkdir input` -`mkdir output` +- `mkdir output` ### Create Virtual Environment -`python -m venv venv –upgrade-deps` +- `python -m venv venv –upgrade-deps` ### Activate Virtual Environment #### For MacOS and Linux: -`source venv/bin/activate` +##### `source venv/bin/activate` #### For Windows: -`venv\Scripts\activate.bat` -If you would like to deactivate your virtual environment at any time, use the command: +##### `venv\Scripts\activate.bat` -`deactivate` +If you would like to deactivate your virtual environment at any time, use the command `deactivate` ## Install the HEAL Data Utilities Now that we’ve created and activated our virtual environment, we can install the HEAL Data Utilities. -`pip install healdata-utils` +##### `pip install healdata-utils` Next, to confirm that the HEAL Data Utilities package was installed correctly: -`which vlmd` +##### `which vlmd` The installation path should look like something like this: -`/Users/my_username/path_to_project_folder/my_project/venv/bin/vlmd` +##### `/Users/my_username/path_to_project_folder/my_project/venv/bin/vlmd` ## Generate a HEAL Data Dictionary @@ -61,7 +59,7 @@ Now that the HEAL Data Utilities python package has been successfully installed, To confirm installation and to see the different options: -`vlmd --help` +##### `vlmd --help` ![](../imgs/healtdata-utils_options.png/) @@ -69,13 +67,13 @@ Note that the only required flag is `--filepath`, the path to the file you want Here is how you would generate a HEAL Data Dictionary with a data dictionary downloaded from RedCap: -For MacOS and Linux: +#### For MacOS and Linux: -`vlmd --filepath ./input/example_redcap_demo.redcap.csv --inputtype redcap.csv --outputdir ./output/heal-vlmd-from-redcap.csv` +##### `vlmd --filepath ./input/example_redcap_demo.redcap.csv --inputtype redcap.csv --outputdir ./output/heal-vlmd-from-redcap.csv` -For Windows: +#### For Windows: -`vlmd --filepath ./input/example_redcap_demo.redcap.csv --inputtype redcap.csv --outputdir ./output/heal-vlmd-from-redcap.csv` +##### `vlmd --filepath ./input/example_redcap_demo.redcap.csv --inputtype redcap.csv --outputdir ./output/heal-vlmd-from-redcap.csv` ---