Update README.md

Finished README and added logs from testruns

update_metadata_bdc/v1.0.0/README.md

@@ -1,11 +1,14 @@
-# Update File Metadata on BioData Catalyst
+# Generate Metadata Manifest on BioData Catalyst
 
-This Dockerfile sets up an environment for running an Rscript that generates a metadata manifest file based on all of the files found within a specified project on BioData Catalyst (BDC). 
+This Dockerfile sets up an environment for running an Rscript that generates a metadata manifest for all files within a specified project on BioData Catalyst (BDC). 
 
 ## Overview
 
 **Metadata Manifest File**
 
+The metadata manifest file allows for batch updating metadata across multiple files using the BioData Catalyst (BDC) user interface.
+
+A key challenge in the current system is the inability to generate a metadata manifest for all files within a project, especially when the project contains nested subdirectories. This application overcomes this limitation by recursively identifying and extracting metadata for all files within the specified project, regardless of their directory structure. It pulls the existing metadata for each file, consolidates it into a single manifest file, and outputs it in a format ready for updates. Once updated, this manifest file can be uploaded back to the platform via the user interface, enabling seamless and accurate metadata updates across the entire project.
 <br>
 
 ## Usage
@@ -38,8 +41,81 @@ Here's what each part of the command does:
 `.`: The dot at the end of the command indicates that the build context is the current directory, where the Dockerfile is located.
 Running this command will build a Docker image with the name `rtibiocloud/update_metadata_bdc:v1.0.0`. Make sure you are in the directory containing the Dockerfile you want to use for building the image.
 
+## Rscript Inputs
+| Short Flag | Long Flag | Description |
+|:-----:|:--------:|--------------------------------|
+|   -t  |  --token       | Authentication token              |
+|   -p  |  --project_id   | Project ID                  |
+|   -o  |  --output_path   | Path to save the output manifest           |
+|   -h  |  --help      | Display the function usage statement       |
+
+## Rscript Outputs
+
+The output of this application is a CSV formatted manifest file. The manifest file contains 4 required columns for identifying the correct file in the project. The remaining columns are prespecified metadata fields. Details on these fields and the overall metadata schema can be found within the following webpage: https://sb-biodatacatalyst.readme.io/docs/metadata-schema
+
+As mentioned above, this output can be updated and uploaded to BDC, using the user interface, to update metadata fields for files in the specified project.
+
+## Perform a testrun
+
+`docker run -v ${PWD}/:/data -t rtibiocloud/update_metadata_bdc:v1.0.0 /bin/bash  -c "Rscript /opt/generate_metadata_manifest.R -t <insert token> -p <insert projectID> -o ."`
+
+<details>
+
+```
+root@0a407da6d20a:/data# Rscript /opt/generate_metadata_manifest.R -t <insert token> -p <insert projectID> -o .
+
+
+Loading required package: getopt
+Loading required package: dplyr
+
+Attaching package: ‘dplyr’
+
+The following objects are masked from ‘package:stats’:
+
+    filter, lag
+
+The following objects are masked from ‘package:base’:
+
+    intersect, setdiff, setequal, union
+
+Loading required package: httr
+Loading required package: stringr
+Loading required package: lubridate
+
+Attaching package: ‘lubridate’
+
+The following objects are masked from ‘package:base’:
+
+    date, intersect, setdiff, union
+
+Loading required package: sevenbridges2
+Loading required package: jsonlite
+[2024-08-22 18:07:17.506371] - setup - INFO - Setting up recursive file and folder extraction function
+[2024-08-22 18:07:17.513716] - setup - INFO - Starting script and setting up API endpoint and platform URL
+[2024-08-22 18:07:17.513962] - setup - INFO - Authenticating with the API
+[2024-08-22 18:07:17.539544] - get_project - INFO - Retrieving project information
+[2024-08-22 18:07:19.057607] - main - INFO - Starting extraction of files and folders
+[2024-08-22 18:07:19.405385] - extract - INFO - Processing folder: Harmonized_Data
+[2024-08-22 18:07:19.794829] - extract - INFO - Processing folder: RMIP_000_CyTOF
+[2024-08-22 18:07:19.98858] - extract - INFO - Processing file: RMIP_000_001_A_001_A.txt
+[2024-08-22 18:07:19.989302] - extract - INFO - Processing file: RMIP_000_002_A_001_A.txt
+[2024-08-22 18:07:19.989939] - extract - INFO - Processing folder: RMIP_000_scRNA
+[2024-08-22 18:07:20.080253] - extract - INFO - Processing folder: RMIP_000_viability
+[2024-08-22 18:07:20.126575] - extract - INFO - Processing folder: Raw_Data
+[2024-08-22 18:07:20.356785] - extract - INFO - Processing folder: RMIP_000_CyTOF
+[2024-08-22 18:07:20.5892] - extract - INFO - Processing file: RMIP_000_001_A_001_A.txt
+[2024-08-22 18:07:20.590099] - extract - INFO - Processing file: RMIP_000_002_A_001_A.txt
+[2024-08-22 18:07:20.590935] - extract - INFO - Processing folder: RMIP_000_scRNA
+[2024-08-22 18:07:20.639246] - extract - INFO - Processing folder: RMIP_000_viability
+[2024-08-22 18:07:20.729023] - extract - INFO - Processing folder: Study_Documentation
+[2024-08-22 18:07:20.777902] - extract - INFO - Processing folder: Templates
+[2024-08-22 18:07:21.013212] - extract - INFO - Processing file: README.md
+[2024-08-22 18:07:21.222711] - main - INFO - CSV file written to ./manifest_20240822.csv
+[2024-08-22 18:07:21.22298] - main - INFO - Metadata Manifest generated successfully
+
+```
+</details>
 
 ## Contact
 For additional information or assistance, please contact Mike Enger (menger@rti.org).
 
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