Merge pull request #136 from Sage-Bionetworks/GEN-1415-update-table-fix

[GEN-1415] Update code to use pandas.concat

scripts/table_updates/README.md

@@ -8,6 +8,7 @@ Installation and Setup
 ### Python version
 Make sure you have Python 3.8 installed
 
+
 ### Install the required packages
     (sudo) pip install -r requirements.txt
 
@@ -17,6 +18,15 @@ Please make sure you have the [.synapseConfig file](https://help.synapse.org/doc
 ### Service catalog instance
 Use a t3.2xlarge ec2 instance for large memory requirement.
 
+Putting it all together.
+
+```
+# 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
+```
+
 Usage
 -----
 ### Prepare the Synapse tables to be updated

scripts/table_updates/update_table_schema.py

@@ -57,7 +57,7 @@ def _update_table_schema(syn, form, curated_data_element, logger, dry_run):
         current_cols = syn.getColumns(row['id'])
         current_cols = pandas.DataFrame(current_cols)
         current_cols['table_id'] = row['id']
-        current_cols_df = current_cols_df.append(current_cols)
+        current_cols_df = pandas.concat([current_cols_df, current_cols])
     # get the table id with the least columns
     tbl_with_least_cols = current_cols_df['table_id'].value_counts()
     tbl_with_least_cols_id = tbl_with_least_cols.idxmin()