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Merge pull request HEAL#5 from ciresiemanym/ciresiemanym-patch-1
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ciresiemanym authored May 18, 2023
2 parents 56ef7ef + 4e99d5c commit 92e3828
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20 changes: 11 additions & 9 deletions docs/vlmd-healdata-utils.md
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Expand Up @@ -23,6 +23,8 @@ We highly recommend installing the HEAL Data Utilities in a virtual environment.

- `mkdir output`

You can now download

### Create Virtual Environment

- `python -m venv venv –upgrade-deps`
Expand All @@ -31,35 +33,35 @@ We highly recommend installing the HEAL Data Utilities in a virtual environment.

#### For MacOS and Linux:

##### `source venv/bin/activate`
`source venv/bin/activate`

#### For Windows:

##### `venv\Scripts\activate.bat`
`venv\Scripts\activate.bat`

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

Now that the HEAL Data Utilities python package has been successfully installed, it can be used to generate a HEAL data dictionary. The command `vlmd` will be used to call the healdata-utils python package.

To confirm installation and to see the different options:

##### `vlmd --help`
`vlmd --help`

![](../imgs/healtdata-utils_options.png/)

Expand All @@ -69,15 +71,15 @@ Here is how you would generate a HEAL Data Dictionary with a data dictionary dow

#### 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:

##### `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`

---

## Summary of Command Line
## Summary of Command Line Prompts

1. `mkdir my_project`
2. `cd my_project`
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