Add automatic database creation to install script

The installation script will now automatically install the augur database schemas if prompted by the user. Signed-off-by: Carter Landis <[email protected]>
chaoss · Sep 20, 2019 · 39a481d · 39a481d
1 parent f34241e
commit 39a481d
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diff --git a/.gitignore b/.gitignore
@@ -6,7 +6,8 @@ __pycache__/
 *$py.class
 *.pyc
 augur_venv/
-
+runtime/
+logs/
 
 # C extensions
 *.so

diff --git a/augur/cli/util.py b/augur/cli/util.py
@@ -52,8 +52,9 @@ def upgrade(app, from_directory):
     """
     Print the location of the interpreter that is running this
     """
-    app.log.info(pyrcss.util.self_upgrade(from_directory=from_directory, dry_run=True))
-    pyrcss.util.self_upgrade(from_directory=from_directory)
+    pass
+    # app.log.info(pyrcss.util.self_upgrade(from_directory=from_directory, dry_run=true))
+    # pyrcss.util.self_upgrade(from_directory=from_directory)
 
 
 @cli.command('test', short_help='Test Augur')

diff --git a/augur_localstart.sh b/augur_localstart.sh
@@ -2,6 +2,8 @@
 
 ./augur_localkill.sh
 
+# TODO: make sure the logs/ directory is present
+
 if [[ $(ps x -o pid= -p $(cat logs/augur_backend_pid.txt) | wc -l) -ge 1 ]]; then
     echo "Backend server already running."
 else

diff --git a/logs/augur_backend.err b/logs/augur_backend.err
diff --git a/logs/augur_backend_pid.txt b/logs/augur_backend_pid.txt
diff --git a/logs/augur_backend_pid.txt.orig b/logs/augur_backend_pid.txt.orig
diff --git a/logs/augur_frontend.err b/logs/augur_frontend.err
diff --git a/logs/augur_frontend_pid.txt b/logs/augur_frontend_pid.txt
diff --git a/logs/augur_frontend_pid.txt.orig b/logs/augur_frontend_pid.txt.orig
diff --git a/logs/backend.pid b/logs/backend.pid
diff --git a/util/scripts/install/augurinstall.sh b/util/scripts/install/augurinstall.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
-PS3="Press the number corresponding to your selection.
+PS3="
+Please type the number corresponding to your selection and then press the Enter/Return key.
 Your choice: "
 
 echo
@@ -68,7 +69,7 @@ echo "Checking for virtual environment..."
 echo "**********************************"
 echo
 if [[ -z $VIRTUAL_ENV ]]; then
-  echo "*** We noticed you're not using a virtual environment. It is STRONGLY recommended to install Augur in its own virutal environment. ***"
+  echo "*** We noticed you're not using a virtual environment. It is STRONGLY recommended to install Augur in its own virtual environment. ***"
   echo "*** Would you like to create a virtual environment? ***"
   select choice in "Yes" "No"
   do
@@ -107,115 +108,71 @@ else
   echo "Virtual environment detected under `echo $VIRTUAL_ENV`. Resuming installation..."
 fi
 
-echo
-echo "**********************************"
-echo "Installing backend dependencies..."
-echo "**********************************"
-echo
-
-rm -rf build/*; rm -rf dist/*; rm $VIRTUAL_ENV/bin/*worker*;
-pip install pipreqs sphinx xlsxwriter; 
-pip install -e .; 
-pip install xlsxwriter; 
-pip install ipykernel; 
-python -m ipykernel install --user --name augur --display-name "Python (augur)"; 
-npm install apidoc;
-python setup.py install;
-
-echo
-echo "**********************************"
-echo "Installing workers and their dependencies..."
-echo "**********************************"
-echo
-for OUTPUT in $(ls -d workers/*/)
-do
-    if [[ $OUTPUT == *"_worker"* ]]; then
-        cd $OUTPUT
-        echo "Running setup for $(basename $(pwd))"
-        rm -rf build/*;
-        rm -rf dist/*;
-        python setup.py install;
-        pip install -e .
-        cd ../..
-    fi
-done
-
-echo "Would you like to install Augur's frontend dependencies?"
-select choice in "Yes" "No"
-do
-  case $choice in
-    "Yes" )
-      echo
-      echo "**********************************"
-      echo "Installing frontend dependencies..."
-      echo "**********************************"
-      echo
-      cd frontend/;
-      npm install brunch canvas vega @vue/cli;
-      npm install; 
-      npm run build;
-      cd ../;
-      break
-      ;;
-    "No" )
-      echo "Skipping frontend dependencies..."
-      break
-      ;;
-   esac
-done
+# echo
+# echo "**********************************"
+# echo "Installing backend dependencies..."
+# echo "**********************************"
+# echo
+
+# rm -rf build/*; rm -rf dist/*; rm $VIRTUAL_ENV/bin/*worker*;
+# pip install pipreqs sphinx xlsxwriter; 
+# pip install -e .; 
+# pip install xlsxwriter; 
+# pip install ipykernel; 
+# python -m ipykernel install --user --name augur --display-name "Python (augur)"; 
+# npm install apidoc;
+# python setup.py install;
+
+# echo
+# echo "**********************************"
+# echo "Installing workers and their dependencies..."
+# echo "**********************************"
+# echo
+# for OUTPUT in $(ls -d workers/*/)
+# do
+#     if [[ $OUTPUT == *"_worker"* ]]; then
+#         cd $OUTPUT
+#         echo "Running setup for $(basename $(pwd))"
+#         rm -rf build/*;
+#         rm -rf dist/*;
+#         python setup.py install;
+#         pip install -e .
+#         cd ../..
+#     fi
+# done
+
+# echo "Would you like to install Augur's frontend dependencies?"
+# select choice in "Yes" "No"
+# do
+#   case $choice in
+#     "Yes" )
+#       echo
+#       echo "**********************************"
+#       echo "Installing frontend dependencies..."
+#       echo "**********************************"
+#       echo
+#       cd frontend/;
+#       npm install brunch canvas vega @vue/cli;
+#       npm install; 
+#       npm run build;
+#       cd ../;
+#       break
+#       ;;
+#     "No" )
+#       echo "Skipping frontend dependencies..."
+#       break
+#       ;;
+#    esac
+# done
+
+# echo
+# echo "**********************************"
+# echo "Setting up API documentation..."
+# echo "**********************************"
+# echo
+
+# cd docs && apidoc --debug -f "\.py" -i ../augur/ -o api/; rm -rf ../frontend/public/api_docs; mv api ../frontend/public/api_docs; cd ..
 
-echo
-echo "**********************************"
-echo "Setting up API documentation..."
-echo "**********************************"
-echo
-
-cd docs && apidoc --debug -f "\.py" -i ../augur/ -o api/; rm -rf ../frontend/public/api_docs; mv api ../frontend/public/api_docs; cd ..
-
-echo
-echo "**********************************"
-echo "Setting up the database configuration..."
-echo "**********************************"
-echo
-
-function generate_config_file() {
-  echo
-  echo "**********************************"
-  echo "Generating configuration file..."
-  echo "**********************************"
-  echo
-  python make_config.py
-  rm temp.config.json
-}
-
-function enter_db_credentials() {
-
-  cd util/scripts/install
-
-  read -p "database: " database
-  read -p "host: " host
-  read -p "port: " port
-  read -p "user: " user
-  read -p "password: " password
-  read -p "key: " key
-
-  config="
-  {
-    \"database\": \"$database\",
-    \"host\": \"$host\",
-    \"port\": \"$port\",
-    \"user\": \"$user\",
-    \"password\": \"$password\",
-    \"key\": \"$key\"
-  }"
-
-  rm temp.config.json
-  touch temp.config.json
-  echo $config > temp.config.json
-
-  python make_config.py
-  rm temp.config.json
-}
 
 on_command_line=false
 echo

diff --git a/util/scripts/install/setup_db.sh b/util/scripts/install/setup_db.sh
@@ -1,29 +1,119 @@
+#!/bin/bash
+
+PS3="
+Please type the number corresponding to your selection and then press the Enter/Return key.
+Your choice: "
+
+echo
+echo "**********************************"
+echo "Setting up the database configuration..."
+echo "**********************************"
+echo
+
+function generate_config_file() {
+
+  echo
+  echo "**********************************"
+  echo "Generating configuration file..."
+  echo "**********************************"
+  echo
+
+  INSTALL_SCRIPT_HOME="util/scripts/install"
+  cd $INSTALL_SCRIPT_HOME
+
+  rm temp.config.json
+  touch temp.config.json
+
+  echo $1 > temp.config.json
+
+  python make_config.py
+
+  rm temp.config.json
+
+  cd ../../.. #get back to augur root
+}
+
+function set_remote_db_credentials() {
+
+  read -p "database: " database
+  read -p "host: " host
+  read -p "port: " port
+  read -p "user: " user
+  read -p "password: " password
+  read -p "key: " key
+
+  config="
+  {
+    \"database\": \"$database\",
+    \"host\": \"$host\",
+    \"port\": \"$port\",
+    \"user\": \"$user\",
+    \"password\": \"$password\",
+    \"key\": \"$key\"
+  }"
+
+  # generate_config_file $config
+}
+
+function set_local_db_credentials() {
+
+  read -p "database: " database
+  read -p "user: " user
+  read -p "port: " port
+  read -p "password: " password
+  read -p "key: " key
+
+  config="
+  {
+    \"database\": \"$database\",
+    \"host\": \"localhost\",
+    \"port\": \"$port\",
+    \"user\": \"$augur\",
+    \"password\": \"$password\",
+    \"key\": \"$key\"
+  }"
+
+  # generate_config_file $config
+}
+
 echo "If you need to install Postgres, the downloads can be found here: https://www.postgresql.org/download/"
-installpostgreslocally="Would you like to use a pre-existing Postgres 10 or 11 installation to which you can install the Augur schema?"
-installpostgresremotely="Would you like to use a pre-existing Postgres 10 or 11 installation to which someone else can install the Augur schema?"
-postgresalreadyinstalled="Would you like to use a pre-existing Postgres 10 or 11 installation with the Augur schema already installed? "
+echo
+install_locally="Would you like to use a LOCAL Postgres 10 or 11 installation without the database already installed?"
+install_remotely="Would you like to use a REMOTE Postgres 10 or 11 installation without the database already installed?"
+already_installed="Would you like to use a pre-existing Postgres 10 or 11 installation with the Augur database ALREADY installed? "
 SKIP="Skip this section"
+echo
 
-select haveinstalledpostgres in "$installpostgreslocally" "$installpostgresremotely" "$postgresalreadyinstalled" "$SKIP"
+select install_location in "$install_locally" "$install_remotely" "$already_installed" "$SKIP"
 do
-  case $haveinstalledpostgres in
+  case $install_location in
       $SKIP )
+      echo
       echo "Skipping database configuration..."
+      echo
       break
     ;;
-    $installpostgreslocally )
-        echo "After you have installed the Augur schema to your database, please return to this point in the installation."
-        echo "Please enter the credentials for your database."
-        enter_db_credentials
+    $install_locally )
+        echo "Please set the credentials for your database."
+        set_local_db_credentials
+        psql -c "create database $database;"
+        psql -c "create user $user with encrypted password '$password';"
+        psql -c "alter database $database owner to $user;"
+        psql -c "grant all privileges on database $database to $user;"
+        psql -h "localhost" -d $database -U $user -p $port -a -w -f augur/persistence_schema/0-all.sql
         break
       ;;
-    $installpostgresremotely )
-        echo "Once the Augur schema has been installed on to your database for you, please return to this point in the installation."
-        echo "Please enter the credentials for your database."
-        enter_db_credentials
+    $install_remotely )
+        echo "Please set the credentials for your database."
+        set_remote_db_credentials
+        psql -h $host -p $port -c "create database $database;"
+        psql -h $host -p $port -c "create user $user with encrypted password '$password';"
+        psql -h $host -p $port -c "alter database $database owner to $user;"
+        psql -h $host -p $port -c "grant all privileges on database $database to $user;"
+        psql -h $host -d $database -U $user -p $port -a -w -f augur/persistence_schema/0-all.sql
         break
       ;;
-    $postgresalreadyinstalled )
+    $already_installed )
         echo "Please enter the credentials for your database."
         enter_db_credentials
         break