Users should git clone the repository to their local machine, and navigate into the top level of the repository (2023-Software-Development-Assessment/)
To run the app for the first time in its docker container, and to run the app every time after that, Users need only run the following code in the top level of the repository:
./panelsearch.sh
This will initiate the panelsearch.sh script. This script will search for evidence that the panelsearch app has previously been installed, and if it does not find it, will proceed with installing the panelsearch app in a docker container. Following this, the app will run.
If at any point the User is prompted for a password, the User should enter their sudo password. If the User does not have Sudo permissions, they will have to run the app locally rather than in a docker container.
If Users encounter unexplained errors, or otherwise suspect that their installation of the panelsearch app may have been faulty, users may remove their previous installation and reinstall the app by running the following code in the top level of the repository:
./reset.sh
Please note that this reinstallation should not remove any User files already saved to the panelsearch_downloads and bed_files directories. Once reinstallation has completed, Users can once again run the app using the following code in the top level of the repostitory:
./panelsearch.sh
If at any point the User is prompted for a password, the User should enter their sudo password. If the User does not have Sudo permissions, they will have to run the app locally rather than in a docker container.
Once the app has begun running, there are several points at which the user is prompted for input.
When prompted for input type, choose option 1 if you know the R-code or option 2 if you would like to search by disease name using keywords.
R-code example::
If you would like to search by R-code, enter 1. If you would like to enter a disease description, enter 2.
> 1
Enter your search term:
> R128
Genetic disease keyword example::
If you would like to search by R-code, enter 1. If you would like to enter a disease description, enter 2.
> 2
Enter your search term:
> Brugada
When prompted for genome build, choose option 1 for the GRCh37 reference genome build or option 2 for the GRCh38::
Which genome build would you like to use? Enter 1 for GRCh37. Enter 2 for GRCh38.
> 1
When prompted choose whether to generate a BED file::
Generate BED file? (Y/N)
> Y
For exon coordinates on transcript, press \'1\'. For genomic coordinates, press \'2\'.
> 1
A bed_files folder will be created and your BED file can be found here.
Finally, it will ask whether you would like to save your results::
Would you like to save this search against a patient ID? (Y/N)
> Y
What patient ID would you like to save this search against?
> Example123
Your search was saved
Thank you for using PanelSearch. Goodbye.
The above is our recommended way to run the app for the smoothest user experience. However, users may install and run the app manually if they wish.
Unlike the setup and rerun scripts, manually building or running the app will not include automated installation of all required programs. Users should expect to have to troubleshoot errors due to missing requirements.
These steps can also be found in docker_setup.sh, and involve creating the SQL database and PanelSearch app within Docker containers. Users must already have installed docker and mysql for these commands to work.
To create the SQL database within a docker container, a network for the two containers to connect via, and a volume for data persistence.
# create docker network for containers to connect via
docker network create panelsearch-network
echo "panelsearch-network created"
# create docker volume for sql data to be stored on
docker volume create panelsearch-volume
echo "panelsearch-volume created"
# create mysql server in the panelsearch-database container
docker run --name panelsearch-database\
--network panelsearch-network \
--volume panelsearch-volume \
-e MYSQL_ROOT_PASSWORD=password \
-d mysql:8
echo "panelsearch-database container created"
# start mysql
#echo "mySQL running"
sudo service mysql start
sudo chmod -R 755 /var/run/mysqld
# create panelsearch database and tables on the mysql server
# Set the maximum number of attempts
max_attempts=100
# Set a counter for the number of attempts
attempt_num=1
# Set a flag to indicate whether the command was successful
success=false
# Loop until the command is successful or the maximum number of attempts is reached
while [ $success = false ] && [ $attempt_num -le $max_attempts ]; do
# Execute the command
docker exec panelsearch-database mysql -uroot -ppassword -e \
"CREATE DATABASE IF NOT EXISTS panelsearch;\
CREATE TABLE IF NOT EXISTS panelsearch.patients( \
id int PRIMARY KEY NOT NULL AUTO_INCREMENT,\
patient_id varchar(50),\
search_id int);\
CREATE TABLE IF NOT EXISTS panelsearch.searches( \
id int KEY AUTO_INCREMENT, \
panel_id int, \
panel_name varchar(500),\
panel_version varchar(50),\
GMS varchar(50),\
gene_number int,\
r_code varchar(5),\
transcript varchar(50),\
genome_build varchar(50),\
bed_file varchar(50),\
UNIQUE (panel_id, panel_name, panel_version, GMS, gene_number, r_code, \
transcript, genome_build, bed_file)\
);"
# Check the exit code of the command
if [ $? -eq 0 ]; then
# The command was successful
success=true
else
# The command was not successful
echo "Attempt $attempt_num failed. Trying again..."
sleep 5
# Increment the attempt counter
attempt_num=$(( attempt_num + 1 ))
fi
done
# Check if the command was successful
if [ $success = true ]; then
# The command was successful
echo "The command was successful after $attempt_num attempts."
else
# The command was not successful
echo "The command failed after $max_attempts attempts."
exit "Setup aborted. Please try again"
fi
echo "panelsearch database created"
echo "database tables 'searches' and 'patients' created"
# make sure user has docker permissions
#sudo groupadd docker
#sudo usermod -aG docker ${USER}
#newgrp docker
#echo "User permissions for docker enabled"
sudo chmod 777 PanelSearch/panel_search.log
echo "permissions enabled"
To build the docker image:
# build the app docker container using the Dockerfile in the repo
docker buildx build -t panelsearch .
echo "panelsearch app container created"
To run the docker container for the first time:
# run the docker container for the first time
echo "running panelsearch app... "
docker run -it --name panelsearch --volume panelsearch-volume \
--network panelsearch-network panelsearch
To run the docker container subsequently:
docker exec -it panelsearch bash -c "python PanelSearch/main.py"
Troubleshooting error messsage: 'docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock:'
sudo groupadd docker
sudo usermod -aG docker $USER
newgrp docker
Troubleshooting error message: 'ERROR: Cannot connect to the Docker daemon at unix://?var/run/docker.sock. Is the docker daemon running?
sudo systemct1 start docker
Troubleshooting error message: 'ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)' * suggested tutorial: https://phoenixnap.com/kb/mysql-server-through-socket-var-run-mysqld-mysqld-sock-2
sudo apt install mysql-server
sudo service mysql start
To run tests make sure you are in the root directory before typing the following into the terminal::
pytest -vv
You should see::
============================================================================================= test session starts =============================================================================================
platform win32 -- Python 3.10.5, pytest-7.4.3, pluggy-1.3.0 -- C:\Users\AppData\Local\Programs\Python\Python310\python.exe
cachedir: .pytest_cache
rootdir: C:\Users\2023-Software-Development-Assessment
collected 35 items
Tests/test_API_to_SQL_cloud.py::test_PK_Parse_Data_to_SQL_cloud_works PASSED [ 2%]
Tests/test_API_to_SQL_cloud.py::test_PK_Parse_Data_to_SQL_cloud_type_errors PASSED [ 5%]
Tests/test_API_to_SQL_cloud.py::test_PK_Parse_Data_to_SQL_cloud_value_errors PASSED [ 8%]
Tests/test_PanelApp_API_Request.py::test_request_data PASSED [ 11%]
Tests/test_PanelApp_API_Request.py::test_pk_search PASSED [ 14%]
Tests/test_PanelApp_API_Request.py::test_r_search_works PASSED [ 17%]
Tests/test_PanelApp_API_Request.py::test_r_search_fails PASSED [ 20%]
Tests/test_PanelApp_Request_Parse.py::test_panelapp_search_parse_works PASSED [ 22%]
Tests/test_PanelApp_Request_Parse.py::test_panelapp_search_parse_fails PASSED [ 25%]
Tests/test_SQL_Cloud_Functions.py::test_docker_or_cloud_works PASSED [ 28%]
Tests/test_SQL_Cloud_Functions.py::test_connect_cloud_db_works PASSED [ 31%]
Tests/test_SQL_Cloud_Functions.py::test_add_new_cloud_record_works PASSED [ 34%]
Tests/test_SQL_Cloud_Functions.py::test_browse_cloud_records_no_id PASSED [ 37%]
Tests/test_SQL_Cloud_Functions.py::test_browse_cloud_records_with_id_and_tables PASSED [ 40%]
Tests/test_SQL_Cloud_Functions.py::test_browse_cloud_records_with_id_only PASSED [ 42%]
Tests/test_SQL_Cloud_Functions.py::test_browse_cloud_records_wrong_id PASSED [ 45%]
Tests/test_SQL_Cloud_Functions.py::test_download_records PASSED [ 48%]
Tests/test_VV_API_Request.py::test_genome_build_convert_GRch37 PASSED [ 51%]
Tests/test_VV_API_Request.py::test_genome_build_convert_fails PASSED [ 54%]
Tests/test_VV_API_Request.py::test_request_data_works PASSED [ 57%]
Tests/test_VV_API_Request.py::test_gene_to_transcripts_works PASSED [ 60%]
Tests/test_VV_Request_Parse.py::test_vv_request_parse PASSED [ 62%]
Tests/test_functional.py::test_main_works PASSED [ 65%]
Tests/test_generate_bed.py::test_parse_panel_data PASSED [ 68%]
Tests/test_generate_bed.py::test_write_bed_file_works PASSED [ 71%]
Tests/test_generate_bed.py::test_write_bed_file_no_filename PASSED [ 74%]
Tests/test_generate_bed.py::test_write_bed_file_no_beds PASSED [ 77%]
Tests/test_main.py::test_get_genome_build_works PASSED [ 80%]
Tests/test_main.py::test_get_genome_build_errors PASSED [ 82%]
Tests/test_main.py::test_get_input_string_type_works PASSED [ 85%]
Tests/test_main.py::test_get_input_string_type_errors PASSED [ 88%]
Tests/test_main.py::test_get_input_string PASSED [ 91%]
Tests/test_main.py::test_create_bed_filename PASSED [ 94%]
Tests/test_select_disease.py::test_find_match_works PASSED [ 97%]
Tests/test_select_disease.py::test_find_match_errors PASSED [100%]
======================================================================================= 35 passed in 164.41s (0:02:44) ========================================================================================
https://www.docker.com/blog/how-to-dockerize-your-python-applications/