[GEN-1577] Update README.md to help with installation of running the scripts

scripts/table_updates/README.md

@@ -3,42 +3,81 @@ BPC Table Update
 [![automated](https://img.shields.io/docker/cloud/automated/sagebionetworks/genie-bpc-pipeline-table-updates)](https://hub.docker.com/r/sagebionetworks/genie-bpc-pipeline-table-updates)
 ![status](https://img.shields.io/docker/cloud/build/sagebionetworks/genie-bpc-pipeline-table-updates)
 
-Installation and Setup
-----------------------
-### Python version
-Make sure you have Python 3.8 installed
 
+This folder contains multiple scripts to update the tables required for the BPC pipeline.  Note there are two separate update scripts right now
+that may require different synapseclient versions. We encourage using different conda environments for each script.
 
-### Install the required packages
-    (sudo) pip install -r requirements.txt
+# Service catalog instance
+Use a t3.2xlarge ec2 instance for large memory requirement.
 
-### Synapse Credential
+# Synapse Credential
 Please make sure you have the [.synapseConfig file](https://help.synapse.org/docs/Client-Configuration.1985446156.html)
 
-### Service catalog instance
-Use a t3.2xlarge ec2 instance for large memory requirement.
 
-Putting it all together.
+# Update data element catalog + table schema
+
+## Installation and Setup
+
+### Python version
+Make sure you have Python 3.8 and conda installed.
+
+### Install the required packages
+
+> [!NOTE]  
+> Due to this tool using an older version of the python client, until there is bandwidth to update
+> please do `rm -rf ~/.synapseCache/*` to clear the synapse cache to avoid this error
+> ```
+> if cached_time.endswith(".000Z"):
+> AttributeError: 'dict' object has no attribute 'endswith'
+> ```
 
 ```
 # Make sure you have anaconda installed
-conda create -n genie-table-update python=3.8
-conda activate genie-table-update
-pip install -r requirements.txt
+conda create -n genie-table-update-precursor python=3.8
+conda activate genie-table-update-precursor
+pip install 'synapseclient[pandas] == 2.7.2'
 ```
 
-Usage
------
-### Prepare the Synapse tables to be updated
+### Usage
+
+Prepare the Synapse tables to be updated
 > **_NOTE:_** ONLY need to be executed when there is a new version of PRISSMM data dictionary
 
 ##### Step 1. Update the Data Catalog
-    python update_data_element_catalog.py -v [prissmm_version_number]
+
+```
+python update_data_element_catalog.py -v [prissmm_version_number]
+```
+
 ##### Step 2. Update the table schema
-    python update_table_schema.py
 
-### Update the Synapse Tables with data
+```
+python update_table_schema.py
+```
+
+# Update Data Table
+
+The `update_data_table.py` script is used to update the BPC internal tables. 
+
+## Installation and Setup
+
+### Python version
+Make sure you have Python 3.9+ and conda installed.
+
+### Install the required packages
+
+```
+conda create -n genie-table-update python=3.10
+conda activate genie-table-update
+pip install -r requirements.txt
+```
+
+### Usage
+Update the Synapse Tables with data
+
 #### Primary Case Tables
     python update_data_table.py -m [version_comment] primary
 #### IRR Case Tables
     python update_data_table.py -m [version_comment] irr
+
+This is to run the script manually, there is a nextflow workflow associated with this script.