3 dev 2024 01 17 (#10)

* Make tripal daemon mandatory since it is needed for blast test

* Exit installation if whiptail can't be installed

* Remove creation of pg_trgm extension of psql

I think it is only needed for tripal 4 and not 3

* Minor tweaks

* Remove non-whiptail commands to make code concise

* Remove non-whiptail commands to make code concise

* Minor tweaks

* Instead of setting /var/www/html directly to apache, user DRUPAL_HOME variable

* Separate install-web-server in to install-apache & install-php

* Minor comment tweaks

* Separate drush installation into separate script

* Add system cron job only if successfully disabled drupal cron

* Add executing install-drush.sh to install.sh

* Separate preparation of chado into separate script

* Separate installation of chado into separate script

* Move installing bind9-dnsutils from install-tripal.sh to prepare-chado.sh

* Make install-chado.sh executable

* Move install-chado.sh & prepare-chado.sh from install-tripal.sh to install.sh

* Simplify installation of ncbi-blast+

* Simplify setup of sample blastdb

* Separate install-jbrowse.sh from install-tripal-jbrowse.sh

* Create dependencies.txt and install-dependencies.sh

* Create dependencies.txt and install-dependencies.sh

* Simplify country codes using json file

* Only source funtions otherwise json will get pulled

* Install dependencies before whiptail

* Change directory before installing dependencies

* Move countries.json to components/

* Simplify _input_drupal_country.sh

* Move  libapache2-mod-php from install-apache.sh to install-php.sh

* Rename country variables & thereby fix drupal error - Illegal choice India in Default country element

* Minor tweaks

* Fix - blast_path variable

* Run install-jbrowse.sh before install-tripal-jbrowse.sh

* Not use debian repo version of blast+

* Move blastdb from scripts/ to components/

* Move dependencies.txt from scripts/ to components/

* Move  aboutus.txt from root dir to components/

* Move show-about-us-page.sh from root dir to scripts/

* Refresh repos before installing dependencies

* Specify correct path to show-about-us-page.sh in install.sh

* Rename aboutus.txt -> about-us.txt

* Remove an unneeded space

* Revert "Not use debian repo version of blast+"

This reverts commit ff5f301.

* Fix blast_path variable

* Add success msg after sample blast db setup

* Remove success/fail msg from install-chado.sh

* Fix - pm-enable needs a higher bootstrap level (install-tripal-jbrowse.sh)

* Move field_formatter_settings.patch from scripts/ to components/

* Update some documentation

* Rename DRUPAL_HOME -> WEB_ROOT

* Rename drupalsitedir -> DRUPAL_HOME

* Remove whiptail from _is_internet_available

* Install whiptail before executing other scripts/functions

* Simplify warning msgs in _input_memory_limit

* Simplify warning msgs in _input_drupal_mail

* Add 'does dir exist' check to _input_drupal_dir.sh

* Simplify checking if email is valid

* Add is_dir_name_valid to _input_drupal_dir.sh

* Add is_username_valid to _input_drupal_username.sh

* Add is_username_valid to _input_db_username.sh

* Minor tweaks

* Simplify headers of .log files

* Use -z instead of ! -n

* Double quotes to prevent globbing & splitting

* Correct the use of a variable in printf statement

* 'expr length' has unspecified results. Prefer ${#var}

* Fix - i appears unused in for loops

* Minor tweaks

* Simplify calculation of left padding

* Create _is_db_name_valid.sh

* Remove replacing spaces in dbname since it is taken care of by _is_db_name_valid

* Incorporate _is_db_name_valid into _input_db_name

* Indentation - 4 spaces -> 2 spaces

* Correct the use of _is_db_name_valid in _input_db_name

* Correct the position of _is_db_name_valid in while loop of _input_db_name

* Create _is_variable_empty.sh

* Add return 1 to _is_variable_empty

* Change function _is_variable_empty -> _is_variable_nonempty

* Simplify functions using _is_variable_nonempty

* Minor tweaks

* Minor tweaks

components/countries.json

@@ -0,0 +1,252 @@
+{
+  "AD": "Andorra",
+  "AE": "United Arab Emirates",
+  "AF": "Afghanistan",
+  "AG": "Antigua and Barbuda",
+  "AI": "Anguilla",
+  "AL": "Albania",
+  "AM": "Armenia",
+  "AN": "Netherlands Antilles",
+  "AO": "Angola",
+  "AQ": "Antarctica",
+  "AR": "Argentina",
+  "AS": "American Samoa",
+  "AT": "Austria",
+  "AU": "Australia",
+  "AW": "Aruba",
+  "AX": "Aland Islands",
+  "AZ": "Azerbaijan",
+  "BA": "Bosnia and Herzegovina",
+  "BB": "Barbados",
+  "BD": "Bangladesh",
+  "BE": "Belgium",
+  "BF": "Burkina Faso",
+  "BG": "Bulgaria",
+  "BH": "Bahrain",
+  "BI": "Burundi",
+  "BJ": "Benin",
+  "BL": "Saint Barthélemy",
+  "BM": "Bermuda",
+  "BN": "Brunei",
+  "BO": "Bolivia",
+  "BQ": "Caribbean Netherlands",
+  "BR": "Brazil",
+  "BS": "Bahamas",
+  "BT": "Bhutan",
+  "BV": "Bouvet Island",
+  "BW": "Botswana",
+  "BY": "Belarus",
+  "BZ": "Belize",
+  "CA": "Canada",
+  "CC": "Cocos (Keeling) Islands",
+  "CD": "Congo (Kinshasa)",
+  "CF": "Central African Republic",
+  "CG": "Congo (Brazzaville)",
+  "CH": "Switzerland",
+  "CI": "Ivory Coast",
+  "CK": "Cook Islands",
+  "CL": "Chile",
+  "CM": "Cameroon",
+  "CN": "China",
+  "CO": "Colombia",
+  "CR": "Costa Rica",
+  "CU": "Cuba",
+  "CV": "Cape Verde",
+  "CW": "Curaçao",
+  "CX": "Christmas Island",
+  "CY": "Cyprus",
+  "CZ": "Czech Republic",
+  "DE": "Germany",
+  "DJ": "Djibouti",
+  "DK": "Denmark",
+  "DM": "Dominica",
+  "DO": "Dominican Republic",
+  "DZ": "Algeria",
+  "EC": "Ecuador",
+  "EE": "Estonia",
+  "EG": "Egypt",
+  "EH": "Western Sahara",
+  "ER": "Eritrea",
+  "ES": "Spain",
+  "ET": "Ethiopia",
+  "FI": "Finland",
+  "FJ": "Fiji",
+  "FK": "Falkland Islands",
+  "FM": "Micronesia",
+  "FO": "Faroe Islands",
+  "FR": "France",
+  "GA": "Gabon",
+  "GB": "United Kingdom",
+  "GD": "Grenada",
+  "GE": "Georgia",
+  "GF": "French Guiana",
+  "GG": "Guernsey",
+  "GH": "Ghana",
+  "GI": "Gibraltar",
+  "GL": "Greenland",
+  "GM": "Gambia",
+  "GN": "Guinea",
+  "GP": "Guadeloupe",
+  "GQ": "Equatorial Guinea",
+  "GR": "Greece",
+  "GS": "South Georgia and the South Sandwich Islands",
+  "GT": "Guatemala",
+  "GU": "Guam",
+  "GW": "Guinea-Bissau",
+  "GY": "Guyana",
+  "HK": "Hong Kong S.A.R., China",
+  "HM": "Heard Island and McDonald Islands",
+  "HN": "Honduras",
+  "HR": "Croatia",
+  "HT": "Haiti",
+  "HU": "Hungary",
+  "ID": "Indonesia",
+  "IE": "Ireland",
+  "IL": "Israel",
+  "IM": "Isle of Man",
+  "IN": "India",
+  "IO": "British Indian Ocean Territory",
+  "IQ": "Iraq",
+  "IR": "Iran",
+  "IS": "Iceland",
+  "IT": "Italy",
+  "JE": "Jersey",
+  "JM": "Jamaica",
+  "JO": "Jordan",
+  "JP": "Japan",
+  "KE": "Kenya",
+  "KG": "Kyrgyzstan",
+  "KH": "Cambodia",
+  "KI": "Kiribati",
+  "KM": "Comoros",
+  "KN": "Saint Kitts and Nevis",
+  "KP": "North Korea",
+  "KR": "South Korea",
+  "KW": "Kuwait",
+  "KY": "Cayman Islands",
+  "KZ": "Kazakhstan",
+  "LA": "Laos",
+  "LB": "Lebanon",
+  "LC": "Saint Lucia",
+  "LI": "Liechtenstein",
+  "LK": "Sri Lanka",
+  "LR": "Liberia",
+  "LS": "Lesotho",
+  "LT": "Lithuania",
+  "LU": "Luxembourg",
+  "LV": "Latvia",
+  "LY": "Libya",
+  "MA": "Morocco",
+  "MC": "Monaco",
+  "MD": "Moldova",
+  "ME": "Montenegro",
+  "MF": "Saint Martin (French part)",
+  "MG": "Madagascar",
+  "MH": "Marshall Islands",
+  "MK": "Macedonia",
+  "ML": "Mali",
+  "MM": "Myanmar",
+  "MN": "Mongolia",
+  "MO": "Macao S.A.R., China",
+  "MP": "Northern Mariana Islands",
+  "MQ": "Martinique",
+  "MR": "Mauritania",
+  "MS": "Montserrat",
+  "MT": "Malta",
+  "MU": "Mauritius",
+  "MV": "Maldives",
+  "MW": "Malawi",
+  "MX": "Mexico",
+  "MY": "Malaysia",
+  "MZ": "Mozambique",
+  "NA": "Namibia",
+  "NC": "New Caledonia",
+  "NE": "Niger",
+  "NF": "Norfolk Island",
+  "NG": "Nigeria",
+  "NI": "Nicaragua",
+  "NL": "Netherlands",
+  "NO": "Norway",
+  "NP": "Nepal",
+  "NR": "Nauru",
+  "NU": "Niue",
+  "NZ": "New Zealand",
+  "OM": "Oman",
+  "PA": "Panama",
+  "PE": "Peru",
+  "PF": "French Polynesia",
+  "PG": "Papua New Guinea",
+  "PH": "Philippines",
+  "PK": "Pakistan",
+  "PL": "Poland",
+  "PM": "Saint Pierre and Miquelon",
+  "PN": "Pitcairn",
+  "PR": "Puerto Rico",
+  "PS": "Palestinian Territory",
+  "PT": "Portugal",
+  "PW": "Palau",
+  "PY": "Paraguay",
+  "QA": "Qatar",
+  "RE": "Reunion",
+  "RO": "Romania",
+  "RS": "Serbia",
+  "RU": "Russia",
+  "RW": "Rwanda",
+  "SA": "Saudi Arabia",
+  "SB": "Solomon Islands",
+  "SC": "Seychelles",
+  "SD": "Sudan",
+  "SE": "Sweden",
+  "SG": "Singapore",
+  "SH": "Saint Helena",
+  "SI": "Slovenia",
+  "SJ": "Svalbard and Jan Mayen",
+  "SK": "Slovakia",
+  "SL": "Sierra Leone",
+  "SM": "San Marino",
+  "SN": "Senegal",
+  "SO": "Somalia",
+  "SR": "Suriname",
+  "SS": "South Sudan",
+  "ST": "Sao Tome and Principe",
+  "SV": "El Salvador",
+  "SX": "Sint Maarten",
+  "SY": "Syria",
+  "SZ": "Swaziland",
+  "TC": "Turks and Caicos Islands",
+  "TD": "Chad",
+  "TF": "French Southern Territories",
+  "TG": "Togo",
+  "TH": "Thailand",
+  "TJ": "Tajikistan",
+  "TK": "Tokelau",
+  "TL": "Timor-Leste",
+  "TM": "Turkmenistan",
+  "TN": "Tunisia",
+  "TO": "Tonga",
+  "TR": "Turkey",
+  "TT": "Trinidad and Tobago",
+  "TV": "Tuvalu",
+  "TW": "Taiwan",
+  "TZ": "Tanzania",
+  "UA": "Ukraine",
+  "UG": "Uganda",
+  "UM": "United States Minor Outlying Islands",
+  "US": "United States",
+  "UY": "Uruguay",
+  "UZ": "Uzbekistan",
+  "VA": "Vatican",
+  "VC": "Saint Vincent and the Grenadines",
+  "VE": "Venezuela",
+  "VG": "British Virgin Islands",
+  "VI": "U.S. Virgin Islands",
+  "VN": "Vietnam",
+  "VU": "Vanuatu",
+  "WF": "Wallis and Futuna",
+  "WS": "Samoa",
+  "YE": "Yemen",
+  "YT": "Mayotte",
+  "ZA": "South Africa",
+  "ZM": "Zambia",
+  "ZW": "Zimbabwe"
+}

components/dependencies.txt

@@ -0,0 +1,4 @@
+bind9-dnsutils
+curl
+jq
+wget

functions/_input_db_name.sh

@@ -2,32 +2,30 @@
 
 function _input_db_name {
   while true; do
-    if command -v whiptail > /dev/null; then # Whiptail is installed
-      psqldb=$(whiptail --title "USER INPUT" --inputbox \
-        "\nEnter the name for a new database for our website:\
-        \n\n         (Press ENTER to continue)" \
-        12 47 \
-        "$psqldb" \
-        3>&1 1>&2 2>&3)
-      exitstatus=$?
-      if [ $exitstatus = 1 ]; then
-        exit 1
-      fi
-    else # Whiptail is not installed
-      read -r -p "Enter the name for a new database for our website: " psqldb
+    psqldb=$(whiptail --title "USER INPUT" --inputbox \
+      "\nEnter the name for a new database for our website:\
+      \n\n         (Press ENTER to continue)" \
+      12 47 \
+      "$psqldb" \
+      3>&1 1>&2 2>&3)
+    exitstatus=$?
+    if [ $exitstatus = 1 ]; then
+      exit 1
     fi
 
     # Check if input is empty
-    if [ -n "$psqldb" ]; then
+    if _is_variable_nonempty "$psqldb"; then
+      break
+    fi
+
+    # Check if database name is valid
+    if _is_db_name_valid "$psqldb"; then
       break
     else
-      whiptail --msgbox "   Please enter a value" 7 30
+      continue
     fi
   done
 
-  # Replaces 'spaces' with 'hyphens'
-  psqldb=$(echo "$psqldb" | tr ' ' '-')
-
   # Export variable for use by child scripts
   export psqldb
 }

functions/_input_db_pass.sh

@@ -2,25 +2,19 @@
 
 function _input_db_pass {
   while true; do
-    if command -v whiptail > /dev/null; then
-      PGPASSWORD=$(whiptail --title "USER INPUT" --passwordbox \
-        "\nEnter a password for the new user:\n\n    (Press ENTER to continue)" \
-        11 38 \
-        "$PGPASSWORD" \
-        3>&1 1>&2 2>&3)
-      exitstatus=$?
-      if [ $exitstatus = 1 ]; then
-        exit 1
-      fi
-    else
-      read -r -p "Enter a password for the new user: " PGPASSWORD
+    PGPASSWORD=$(whiptail --title "USER INPUT" --passwordbox \
+      "\nEnter a password for the new user:\n\n    (Press ENTER to continue)" \
+      11 38 \
+      "$PGPASSWORD" \
+      3>&1 1>&2 2>&3)
+    exitstatus=$?
+    if [ $exitstatus = 1 ]; then
+      exit 1
     fi
 
     # Check if input is empty
-    if [ -n "$PGPASSWORD" ]; then
+    if _is_variable_nonempty "$PGPASSWORD"; then
       break
-    else
-      whiptail --msgbox "   Please enter a value" 7 30
     fi
   done
   # Hide PGPASSWORD by replacing characters with *

functions/_input_db_username.sh

@@ -2,29 +2,28 @@
 
 function _input_db_username {
   while true; do
-    if command -v whiptail > /dev/null; then
-      psqluser=$(whiptail --title "USER INPUT" --inputbox \
-        "\nEnter username for a new database user:\n\n       (Press ENTER to continue)" \
-        11 44 \
-        "$psqluser" \
-        3>&1 1>&2 2>&3)
-      exitstatus=$?
-      if [ $exitstatus = 1 ]; then
-        exit 1
-      fi
-    else
-      read -r -p "Enter a new username (role) for postgres: " psqluser
+    psqluser=$(whiptail --title "USER INPUT" --inputbox \
+      "\nEnter username for a new database user:\n\n       (Press ENTER to continue)" \
+      11 44 \
+      "$psqluser" \
+      3>&1 1>&2 2>&3)
+    exitstatus=$?
+    if [ $exitstatus = 1 ]; then
+      exit 1
     fi
 
     # Check if input is empty
-    if [ -n "$psqluser" ]; then
+    if _is_variable_nonempty "$psqluser"; then
+      break
+    fi
+
+    # Check if directory name is valid
+    if _is_username_valid "$psqluser"; then
       break
     else
-      whiptail --msgbox "   Please enter a value" 7 30
+      whiptail --msgbox "Username is invalid. It should only contain alphabets, numbers and underscores & must start with an alphabet." 9 47
     fi
   done
-  # Replaces 'spaces' with 'hyphens'
-  psqluser=$(echo "$psqluser" | tr ' ' '-')
 
   # Export the variable for use by child scripts
   export psqluser