Install/upgrade scripts output colorized messages.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@347 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

extras/migrations/001-db-gbinfo-add-created.migration

@@ -8,27 +8,14 @@ Usage:
 """
 
 
-import sys
-import MySQLdb
-
-
-def _connect():
-    try:
-        connection = MySQLdb.connect(host='localhost',
-                                     user='mutalyzer',
-                                     passwd='',
-                                     db='mutalyzer')
-    except MySQLdb.Error, e:
-        print 'Error %d: %s' % (e.args[0], e.args[1])
-        sys.exit(1)
-    return connection
+import migration
 
 
 def check():
     """
     Check if migration is needed.
     """
-    connection = _connect()
+    connection = migration.db_connect('mutalyzer')
     cursor = connection.cursor()
     cursor.execute('SHOW COLUMNS FROM GBInfo WHERE field = "created";')
     has_column = len(cursor.fetchall()) > 0
@@ -36,8 +23,7 @@ def check():
     has_index = len(cursor.fetchall()) > 0
     connection.close()
     if has_column != has_index:
-        print 'Installation is not in a recognizable state. Fix manually.'
-        sys.exit(1)
+        migration.fatal('Installation is not in a recognizable state. Fix manually.')
     return not has_column
 
 
@@ -45,25 +31,17 @@ def migrate():
     """
     Perform migration.
     """
-    connection = _connect()
+    connection = migration.db_connect('mutalyzer')
     cursor = connection.cursor()
     cursor.execute("""
-        ALTER TABLE GBInfo
-        #ADD COLUMN created TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    ALTER TABLE GBInfo
+        ADD COLUMN created TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
         ADD INDEX created (created);""")
     connection.commit()
     connection.close()
-    print 'Added column mutalyzer.GBInfo.created'
-    print 'Added index on mutalyzer.GBInfo.created'
+    migration.info('Added column mutalyzer.GBInfo.created')
+    migration.info('Added index on mutalyzer.GBInfo.created')
 
 
 if __name__ == '__main__':
-    needed = check()
-    if needed:
-        print 'This migration is needed.'
-        if len(sys.argv) > 1 and sys.argv[1] == 'migrate':
-            print 'Performing migration.'
-            migrate()
-            print 'Performed migration.'
-    else:
-        print 'This migration is not needed.'
+    migration.main(check, migrate)

extras/migrations/002-db-map-to-mapping.migration

@@ -20,20 +20,7 @@ The map tables are renamed to map_backup.
 """
 
 
-import sys
-import MySQLdb
-
-
-def _connect(db):
-    try:
-        connection = MySQLdb.connect(host='localhost',
-                                     user='mutalyzer',
-                                     passwd='',
-                                     db=db)
-    except MySQLdb.Error, e:
-        print 'Error %d: %s' % (e.args[0], e.args[1])
-        sys.exit(1)
-    return connection
+import migration
 
 
 def _exon_starts(starts):
@@ -50,7 +37,7 @@ def _exon_stops(stops):
 
 def _check(db):
     # Todo: Also check if 'map' is gone.
-    connection = _connect(db)
+    connection = migration.db_connect(db)
     cursor = connection.cursor()
     cursor.execute('SHOW TABLES LIKE "Mapping";')
     ok = len(cursor.fetchall()) > 0
@@ -59,7 +46,7 @@ def _check(db):
 
 
 def _migrate(db):
-    connection = _connect(db)
+    connection = migration.db_connect(db)
     cursor = connection.cursor()
     cursor.execute("""
         CREATE TABLE Mapping (
@@ -114,13 +101,13 @@ def _migrate(db):
              r['cds_stop'], _exon_starts(r['exon_starts']), _exon_stops(r['exon_stops']),
              r['protein'], r['source']))
 
-    print 'Converted table map to table Mapping on %s (%d entries)' % (db, count)
+    migration.info('Converted table map to table Mapping on %s (%d entries)' % (db, count))
 
     cursor.execute('DROP TABLE IF EXISTS gbStatus, map_cdsBackup, refGene, refLink')
     cursor.execute('RENAME TABLE map TO map_backup')
 
-    print 'Dropped tables gbStatus, map_cdsBackup, refGene, refLink on %s' % db
-    print 'Renamed table map to map_backup on %s' % db
+    migration.info('Dropped tables gbStatus, map_cdsBackup, refGene, refLink on %s' % db)
+    migration.info('Renamed table map to map_backup on %s' % db)
 
     select_cursor.close()
     cursor.close()
@@ -135,8 +122,7 @@ def check():
     hg18_ok = _check('hg18')
     hg19_ok = _check('hg19')
     if hg18_ok != hg19_ok:
-        print 'Installation is not in a recognizable state. Fix manually.'
-        sys.exit(1)
+        migration.fatal('Installation is not in a recognizable state. Fix manually.')
     return not hg18_ok
 
 
@@ -149,12 +135,4 @@ def migrate():
 
 
 if __name__ == '__main__':
-    needed = check()
-    if needed:
-        print 'This migration is needed.'
-        if len(sys.argv) > 1 and sys.argv[1] == 'migrate':
-            print 'Performing migration.'
-            migrate()
-            print 'Performed migration.'
-    else:
-        print 'This migration is not needed.'
+    migration.main(check, migrate)

extras/migrations/003-config-remove-ucsc.migration

@@ -5,11 +5,16 @@
 # Usage:
 #   ./003-config-remove-ucsc.migration [migrate]
 
+COLOR_INFO='\033[92m'
+COLOR_WARNING='\033[93m'
+COLOR_ERROR='\033[91m'
+COLOR_END='\033[0m'
+
 if [ -e /etc/mutalyzer/config ] && $(grep -q 'MySQL username for the UCSC database' /etc/mutalyzer/config); then
-    echo 'This migration is needed.'
+    echo -e "${COLOR_WARNING}This migration is needed.${COLOR_END}"
     if [ "$1" = 'migrate' ]; then
         echo 'Performing migration.'
-        echo 'Copying /etc/mutalyzer/config to /etc/mutalyzer/config.backup'
+        echo -e "${COLOR_INFO}Copying /etc/mutalyzer/config to /etc/mutalyzer/config.backup${COLOR_END}"
         cp /etc/mutalyzer/config /etc/mutalyzer/config.backup
         sed -i '/MySQL username for the UCSC database/d' /etc/mutalyzer/config
         sed -i '/Host name for the UCSC database/d' /etc/mutalyzer/config
@@ -17,9 +22,9 @@ if [ -e /etc/mutalyzer/config ] && $(grep -q 'MySQL username for the UCSC databa
         sed -i '/RemoteMySQLuser =/d' /etc/mutalyzer/config
         sed -i '/^RemoteMySQLhost =/d' /etc/mutalyzer/config
         sed -i '/^UpdateInterval =/d' /etc/mutalyzer/config
-        echo 'Removed all UCSC database configuration values from /etc/mutalyzer/config'
+        echo -e "${COLOR_INFO}Removed all UCSC database configuration values from /etc/mutalyzer/config${COLOR_END}"
         echo 'Performed migration.'
     fi
 else
-    echo 'This migration is not needed.'
+    echo -e "${COLOR_INFO}This migration is not needed.${COLOR_END}"
 fi

extras/migrations/004-cron-ucsc-to-ncbi.migration

@@ -5,20 +5,25 @@
 # Usage:
 #   ./004-cron-ucsc-to-ncbi.migration [migrate]
 
+COLOR_INFO='\033[92m'
+COLOR_WARNING='\033[93m'
+COLOR_ERROR='\033[91m'
+COLOR_END='\033[0m'
+
 if [ -e /etc/cron.d/mutalyzer-ucsc-update ] && $(grep -v -q '^#' /etc/cron.d/mutalyzer-ucsc-update); then
-    echo 'This migration is needed.'
+    echo -e "${COLOR_WARNING}This migration is needed.${COLOR_END}"
     if [ "$1" = 'migrate' ]; then
         echo 'Performing migration.'
         sed -i 's/^/#/' /etc/cron.d/mutalyzer-ucsc-update
-        echo 'Commented all lines in /etc/cron.d/mutalyzer-ucsc-update'
+        echo -e "${COLOR_INFO}Commented all lines in /etc/cron.d/mutalyzer-ucsc-update${COLOR_END}"
         if [ ! -e /etc/cron.d/mutalyzer-mapping-update ]; then
             BIN_MAPPING_UPDATE=$(which mutalyzer-mapping-update)
             cp extras/cron.d/mutalyzer-mapping-update /etc/cron.d/mutalyzer-mapping-update
             sed -i -e "s@<MUTALYZER_BIN_MAPPING_UPDATE>@${BIN_MAPPING_UPDATE}@g" /etc/cron.d/mutalyzer-mapping-update
-            echo 'Installed /etc/cron.d/mutalyzer-mapping-update'
+            echo -e "${COLOR_INFO}Installed /etc/cron.d/mutalyzer-mapping-update${COLOR_END}"
         fi
         echo 'Performed migration.'
     fi
 else
-    echo 'This migration is not needed.'
+    echo -e "${COLOR_INFO}This migration is not needed.${COLOR_END}"
 fi

extras/migrations/migration.py

+"""
+Some utility functions for our simple migrations.
+
+@todo: Perhaps this should be moved to the mutalyzer package.
+"""
+
+
+import sys
+import MySQLdb
+
+
+COLOR_INFO = '\033[92m'
+COLOR_WARNING = '\033[93m'
+COLOR_ERROR = '\033[91m'
+COLOR_END = '\033[0m'
+
+
+def print_color(message, color=None):
+    if color is None:
+        print message
+    else:
+        print color + message + COLOR_END
+
+
+def info(message):
+    print_color(message, COLOR_INFO)
+
+
+def warning(message):
+    print_color(message, COLOR_WARNING)
+
+
+def error(message):
+    print_color(message, COLOR_ERROR)
+
+
+def fatal(message):
+    error(message)
+    sys.exit(1)
+
+
+def db_connect(database):
+    try:
+        connection = MySQLdb.connect(host='localhost',
+                                     user='mutalyzer',
+                                     passwd='',
+                                     db=database)
+    except MySQLdb.Error as e:
+        fatal('Error %d: %s' % (e.args[0], e.args[1]))
+    return connection
+
+
+def main(check, migrate):
+    needed = check()
+    if needed:
+        warning('This migration is needed.')
+        if len(sys.argv) > 1 and sys.argv[1] == 'migrate':
+            print 'Performing migration.'
+            migrate()
+            print 'Performed migration.'
+    else:
+        info('This migration is not needed.')

extras/post-install.sh

@@ -17,6 +17,11 @@
 
 set -e
 
+COLOR_INFO='\033[92m'
+COLOR_WARNING='\033[93m'
+COLOR_ERROR='\033[91m'
+COLOR_END='\033[0m'
+
 # The 'cd /' is a hack to prevent the mutalyzer package under the current
 # directory to be used.
 PACKAGE_ROOT=$(cd / && python -c 'import mutalyzer; print mutalyzer.package_root()')
@@ -27,40 +32,40 @@ BIN_WEBSITE=$(which mutalyzer-website.wsgi)
 BIN_WEBSERVICE=$(which mutalyzer-webservice.wsgi)
 
 if [ ! -e /etc/mutalyzer/config ]; then
-    echo "Creating /etc/mutalyzer/config"
+    echo -e "${COLOR_INFO}Creating /etc/mutalyzer/config${COLOR_END}"
     mkdir -p /etc/mutalyzer
     cp extras/config.example /etc/mutalyzer/config
     chmod -R u=rwX,go=rX /etc/mutalyzer
 else
-    echo "Not touching /etc/mutalyzer/config (it exists)"
+    echo -e "${COLOR_WARNING}Not touching /etc/mutalyzer/config (it exists)${COLOR_END}"
 fi
 
-echo "Touching /var/log/mutalyzer.log"
+echo -e "${COLOR_INFO}Touching /var/log/mutalyzer.log${COLOR_END}"
 touch /var/log/mutalyzer.log
 chown www-data:www-data /var/log/mutalyzer.log
 chmod u=rw,go=r /var/log/mutalyzer.log
 
-echo "Touching /var/cache/mutalyzer"
+echo -e "${COLOR_INFO}Touching /var/cache/mutalyzer${COLOR_END}"
 mkdir -p /var/cache/mutalyzer
 chown -R www-data:www-data /var/cache/mutalyzer
 chmod -R u=rwX,go=rX /var/cache/mutalyzer
 
-echo "Creating /etc/init.d/mutalyzer-batchd"
+echo -e "${COLOR_INFO}Creating /etc/init.d/mutalyzer-batchd${COLOR_INFO}"
 cp extras/init.d/mutalyzer-batchd /etc/init.d/mutalyzer-batchd
 sed -i -e "s@<MUTALYZER_BIN_BATCHD>@${BIN_BATCHD}@g" /etc/init.d/mutalyzer-batchd
 chmod u=rwx,go=rx /etc/init.d/mutalyzer-batchd
 
-echo "Installing init script links"
+echo -e "${COLOR_INFO}Installing init scripts${COLOR_END}"
 update-rc.d -f mutalyzer-batchd remove
 update-rc.d mutalyzer-batchd defaults 98 02
 
-echo "Installing crontab"
+echo -e "${COLOR_INFO}Installing crontab${COLOR_END}"
 cp extras/cron.d/mutalyzer-cache-sync /etc/cron.d/mutalyzer-cache-sync
 sed -i -e "s@<MUTALYZER_BIN_CACHE_SYNC>@${BIN_CACHE_SYNC}@g" /etc/cron.d/mutalyzer-cache-sync
 cp extras/cron.d/mutalyzer-mapping-update /etc/cron.d/mutalyzer-mapping-update
 sed -i -e "s@<MUTALYZER_BIN_MAPPING_UPDATE>@${BIN_MAPPING_UPDATE}@g" /etc/cron.d/mutalyzer-mapping-update
 
-echo "Creating /etc/apache2/conf.d/mutalyzer.conf"
+echo -e "${COLOR_INFO}Creating /etc/apache2/conf.d/mutalyzer.conf${COLOR_END}"
 cp extras/apache/mutalyzer.conf /etc/apache2/conf.d/mutalyzer.conf
 sed -i -e "s@<MUTALYZER_BIN_WEBSITE>@${BIN_WEBSITE}@g" -e "s@<MUTALYZER_BIN_WEBSERVICE>@${BIN_WEBSERVICE}@g" -e "s@<MUTALYZER_BIN_BATCHD>@${BIN_BATCHD}@g" /etc/apache2/conf.d/mutalyzer.conf
 chmod u=rw,go=r /etc/apache2/conf.d/mutalyzer.conf
@@ -199,7 +204,7 @@ EOF
 wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md
 $(BIN_MAPPING_UPDATE hg19 /tmp/seq_gene.md 'GRCh37.p2-Primary Assembly')
 
-echo "Creating tables in mutalyzer database"
+echo -e "${COLOR_INFO}Creating tables in mutalyzer database${COLOR_END}"
 
 # Create mutalyzer tables
 cat << EOF | mysql -u mutalyzer -D mutalyzer
@@ -254,7 +259,7 @@ if [ -e /var/www/mutalyzer/base ]; then
     rm /var/www/mutalyzer/base
 fi
 
-echo "Symlinking /var/www/mutalyzer/base to $PACKAGE_ROOT/templates/base"
+echo -e "${COLOR_INFO}Symlinking /var/www/mutalyzer/base to $PACKAGE_ROOT/templates/base${COLOR_END}"
 ln -s $PACKAGE_ROOT/templates/base /var/www/mutalyzer/base
 
 echo "Restarting Apache"

extras/post-upgrade.sh

@@ -13,6 +13,11 @@
 
 set -e
 
+COLOR_INFO='\033[92m'
+COLOR_WARNING='\033[93m'
+COLOR_ERROR='\033[91m'
+COLOR_END='\033[0m'
+
 # The 'cd /' is a hack to prevent the mutalyzer package under the current
 # directory to be used.
 PACKAGE_ROOT=$(cd / && python -c 'import mutalyzer; print mutalyzer.package_root()')
@@ -26,7 +31,7 @@ if [ -e /var/www/mutalyzer/base ]; then
     rm /var/www/mutalyzer/base
 fi
 
-echo "Symlinking /var/www/mutalyzer/base to $PACKAGE_ROOT/templates/base"
+echo -e "${COLOR_INFO}Symlinking /var/www/mutalyzer/base to $PACKAGE_ROOT/templates/base${COLOR_END}"
 ln -s $PACKAGE_ROOT/templates/base /var/www/mutalyzer/base
 
 echo "Running any needed migrations"

extras/pre-install.sh

@@ -13,7 +13,12 @@
 
 set -e
 
-echo "Installing packages with apt"
+COLOR_INFO='\033[92m'
+COLOR_WARNING='\033[93m'
+COLOR_ERROR='\033[91m'
+COLOR_END='\033[0m'
+
+echo -e "${COLOR_INFO}Installing packages with apt${COLOR_END}"
 
 apt-get install -y \
   mysql-server \
@@ -36,7 +41,7 @@ apt-get install -y \
   python-setuptools \
   git-core
 
-echo "Installing latest soaplib from git master"
+echo -e "${COLOR_INFO}Installing latest soaplib from git master${COLOR_END}"
 
 mkdir -p /tmp/mutalyzer-install
 pushd /tmp/mutalyzer-install
@@ -48,8 +53,6 @@ python setup.py install
 popd
 rm -Rf /tmp/mutalyzer-install
 
-echo "Installing suds using easy_install"
+echo -e "${COLOR_INFO}Installing suds using easy_install${COLOR_END}"
 
 easy_install suds
-
-echo "kthxbye"