diff --git a/README.md b/README.md index 9a7ef6d..b6ff3e9 100644 --- a/README.md +++ b/README.md @@ -175,7 +175,7 @@ or source {venv_directory}/bin/activate ``` -The `chorus-upload` tool can be run from its source directory as +The `chorus-upload` tool can be run from its source directory FOLLOWING THE GENERAL PATTERN as ``` cd chorus-extract-upload @@ -186,10 +186,11 @@ The `-h` parameter will display help information for the tool or each subcommand Different `config.toml` files can be specified by using the `-c` parameter -The general process is 1. create/update journal, and 2. upload files +### UPLOAD PROCESS +There are 2 steps: 1. create/update Journal, and 2. perform actual upload. -### Create or Update Manifest +### 1. Create or Update Jounral To create or an update journal, the following command can be run. ``` python chorus_upload -c config.toml journal update @@ -210,7 +211,7 @@ The types of data (`OMOP`, `Images`, `Waveforms`) can be specified to restrict u python chorus_upload -c config.toml journal update --modalities OMOP,Images ``` -### Upload files +### 2. Upload files Files can be uploaded using either the integrated, multithreading file upload logic, or via a generated az-cli script. Only files that have been added or modified since the last submission will be added.