381 update import script to json payload

.gitignore

@@ -2,3 +2,4 @@
 *.pyc
 *.egg-info
 docs/build
+.vscode

README.md

@@ -1,40 +1,56 @@
-DPimport: A command line glob importer for DPdash
-=================================================
+# DPimport: A command line glob importer for DPdash
+
 DPimport is a command line tool for importing files into DPdash using a
-simple [`glob`](https://en.wikipedia.org/wiki/Glob_(programming)) expression.
+simple [`glob`](<https://en.wikipedia.org/wiki/Glob_(programming)>) expression.
 
 ## Table of contents
+
 1. [Installation](#installation)
 2. [Configuration](#configuration)
 3. [Usage](#usage)
-4. [MongoDB](#mongodb)
 
 ## Installation
-Just use `pip`
+
+Option 1: Install via `pip`
+
 
 ```bash
 pip install https://github.com/AMP-SCZ/dpimport.git
 ```
 
+Option 2: Clone the repository and run manually
+
+```bash
+git clone https://github.com/AMP-SCZ/dpimport.git
+cd dpimport
+python -m venv venv
+source venv/bin/activate
+pip install -r requirements.txt
+python scripts/import.py -c config.yml '/PHOENIX/GENERAL/STUDY_A/SUB_001/DATA_TYPE/processed/*.csv'
+```
+
 ## Configuration
+
 DPimport requires a configuration file in YAML format, passed as a command
-line argument with `-c|--config`, for establishing a MongoDB database 
-connection. You will find an example configuration file in the `examples` 
-directory within this repository.
+line argument with `-c|--config`, for connecting with an instance of the DPdash
+application API. The configuration file should contain the following fields:  
+
+api_url - Endpoint for the DPdash API
+api_user - Username for the DPdash API
+api_key - API key for the DPdash API
+verify_ssl - Whether to verify SSL certificates (default: True)
 
 ## Usage
+
 The main command line tool is `import.py`. You can use this tool to import any
-DPdash-compatible CSV files or metadata files using the direct path to a file 
+DPdash-compatible CSV files or metadata files using the direct path to a file
 or a glob expression (use single quotes to avoid shell expansion)
 
 ```bash
 import.py -c config.yml '/PHOENIX/GENERAL/STUDY_A/SUB_001/DATA_TYPE/processed/*.csv'
 import.py -c config.yml '/PHOENIX/GENERAL/STUDY_A/SUB_001/DATA_TYPE/processed/*.csv' -n 8
 ```
 
-`-n 8` is for parallelly importing 8 files. The default is `-n 1`.
-
-
 You may also now use the `**` recursive glob expression, for example:
 
 ```bash
@@ -55,18 +71,9 @@ and so on.
 
 `directory/*/*.csv` matches only `directory/[subdirectory]/[filename].csv`. With a [recursive glob pattern](https://docs.python.org/3/library/glob.html#glob.glob), `directory/**/*.csv` will additionally match:
 
-* `directory/[filename].csv` (no subdirectory)
-* `directory/[subdirectory1]/[subdirectory2]/[filename].csv` (sub-subdirectory)
+- `directory/[filename].csv` (no subdirectory)
+- `directory/[subdirectory1]/[subdirectory2]/[filename].csv` (sub-subdirectory)
 
 and so on, for as many levels deep as exist in the directory tree.
 
 </details>
-
-
-
-## MongoDB
-
-This tool requires MongoDB to be running and accessible with the credentials you
-supply in the `config.yml` file. For tips on MongoDB as it is used in DPdash and DPimport,
-see [the DPdash wiki](https://github.com/PREDICT-DPACC/dpdash/wiki/MongoDB-Tips).
-