update postgresql jdbc driver to version 42.6.0

[kencho51]

This PR is for the following functionalities:

1. Update postgresql jdbc driver as part of the PR move postUpload logs to user's uploadDir gigadb-website#1318 as described in Problem.

Problem

In production environment, when execute datasetUpload.sh, the java.log would contain the following error:

java.io.FileNotFoundException: time.txt (Permission denied)
org.postgresql.util.PSQLException: The authentication type 10 is not supported. Check that you have configured the pg_hba.conf 
file to include the client's IP address or subnet, and that it is using an authentication scheme supported by the driver.
        at org.postgresql.core.v3.ConnectionFactoryImpl.doAuthentication(ConnectionFactoryImpl.java:403)
        at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:108)
        at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
        at org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:125)
        at org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:30)
        at org.postgresql.jdbc3g.AbstractJdbc3gConnection.<init>(AbstractJdbc3gConnection.java:22)
        at org.postgresql.jdbc4.AbstractJdbc4Connection.<init>(AbstractJdbc4Connection.java:32)
        at org.postgresql.jdbc4.Jdbc4Connection.<init>(Jdbc4Connection.java:24)
        at org.postgresql.Driver.makeConnection(Driver.java:393)
        at org.postgresql.Driver.connect(Driver.java:267)
        at java.sql.DriverManager.getConnection(DriverManager.java:664)
        at java.sql.DriverManager.getConnection(DriverManager.java:247)
        at Database.<init>(Database.java:32)
        at Validation.<init>(Validation.java:80)
        at Main.processExcel(Main.java:121)
        at Main.main(Main.java:168)

How have functionalities been implemented?

Download the latest postgresql jdbc driver from here: https://jdbc.postgresql.org/download/ and replace the current one lib/lib/postgresql-9.1-901.jdbc4.jar.

How to test in staging

# go to tool's dir
% cd gigadb/app/tools/excel-spreadsheet-uploader
# get the latest change of the tool
./setup.sh
# make sure the postgresql jdbc driver has been updated
# then spin up staging gigadb website
% cd /gigadb-website/ops/infrastructure/envs/staging
% ../../../scripts/tf_init.sh --project gigascience/forks/kencho-gigadb-website --env staging
% terraform apply
% terraform refresh
% ../../../scripts/ansible_init.sh --env staging
% TF_KEY_NAME=private_ip ansible-playbook -i ../../inventories webapp_playbook.yml -v
% ansible-playbook -i ../../inventories bastion_playbook.yml -e "backup=latest" -v
# Complete gitlab pipeline, make sure all staging jobs have been deployed.
# log into bastion server
% ssh -i $pem centos@$bastion-ip
# run the datasetUpload.sh
$ ./datasetUpload.sh
# check the logs, and the postgresql error should be gone
$ less logs/java.log 

[rija]

Hi @kencho51,

I see this PR is still in draft yet asking us for review. Is it meant to be switched to ready for review?

[rija]

LGTM!

[pli888]

This the same change I made a month ago where I identified that postgresql-42.6.0.jar was working with PostgreSQL 14 for GigaDB so I approve this PR.