#!/bin/bash

# script to admin and import data to SelenoDB. 
# Type "./selenodb_admin -h" for details

# Sergi Castellano, scaste@imim.es

  set +o verbose
  set +o xtrace

### GLOBAL VARIABLES ###

LIB=lib

DB=selenodb

INIT=data/init
META=data/meta
GENE=data/genes
POST=data/post

LOG=logs
LOGF=$(date "+20%y-%m-%d")_selenodb.log
LOGG=genes_imported.log
LOGGG=$(date "+20%y-%m-%d")_genes_imported.log

### FUNCTIONS ###

source $LIB/help.sh
source $LIB/import.sh
source $LIB/admin.sh 


### SHOW IF WRONG COMMAND LINE ###

usage="USAGE $0 -a [create drop dump undump] -i [init meta gene] -d [dir]"

### PICK UP COMMAND LINE OPTIONS ###

while getopts ":a:i:d:h" opt; do

	case $opt in
		a) admin=$OPTARG;;
		i) import=$OPTARG;;
	        d) dir=$OPTARG;;
	        h) help;;
		\?) echo $usage     # to catch invalid options
		    exit 1;;
	esac
done

shift $(($OPTIND -1))

#########
# ADMIN #
#########

#####################
# - DUMP DATABASE - #
#####################

case $admin in
	dump)
	
	echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

# A shorter but less clear syntax is:
# mysql -e 'USE selenodb' 2>/dev/null && dump && fdone || ferror;;

	if mysql -e "USE $DB" 2>/dev/null; then

	    if dump; then fdone

	    else ferror; exit 1 # Dump did not work

	    fi

	else

	    echo -e "### DUMP $DB DATABASE ###\n" | log_tee

	    echo -e "DATABASE does NOT exist. No DUMP is possible!\n" | log_tee  # Database does not exist

	    exit 1

	fi;;

##############
# - UNDUMP - #
##############

     undump)

        echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

# A shorter but less clear syntax is:
#  mysql -e 'USE selenodb' 2>/dev/null && fdone && dump && fdone && undump && fdone && dump || ferror

	if mysql -e "USE $DB" 2>/dev/null; then

	    if dump; then fdone
 
		if undump; then fdone

		    if dump; then fdone

		    else ferror # Dump did not work

		    fi

		else ferror; exit 1 # Undump did not work			 

		fi

	    else ferror; exit 1 # Dump did not work

	    fi

	else

	    echo -e "### UNDUMP $DB DATABASE ###\n" | log_tee

	    echo -e "DATABASE does NOT exist. CREATE it first!\n" | log_tee # Database does not exist

	    exit 1

	fi;;

#####################
# - DROP DATABASE - #
#####################

	drop)

        echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

	if mysql -e "USE $DB" 2>/dev/null; then

	    if dump; then fdone

		if drop; then fdone

		else ferror; exit 1 # Drop did not work

		fi

	    else ferror; exit 1 # Dump did not work

	    fi

	else

	    echo -e "### DROP $DB DATABASE ###\n" | log_tee

	    echo -e "DATABASE does NOT exist. No DROP is possible!\n" | log_tee # Database does not exist

	    exit 1

	fi;;

#######################
# - CREATE DATABASE - #
#######################

	create)

        echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

	if mysql -e "USE $DB" 2>/dev/null; then

	    echo -e "### CREATE $DB DATABASE ###\n" | log_tee

	    echo -e "DATABASE exist. DROP it first!\n" | log_tee

	    exit 1

	else

	    if create; then fdone
	
		if load; then fdone 

		    if dump; then fdone

		    else ferror; exit 1 # Dump did not work

		    fi

		else ferror; exit 1 # Load schema did not work

		fi

	    else ferror; exit 1 # Create did not work

	    fi

	fi;;

# ANY OTHER OPTION

#    *) echo $usage;;

esac

#########################
# - INITIALIZE TABLES - #
#########################

# Imports tables one by one in the right order (there are dependencies!)
# Stops if error and notify erroneous table
# No need to rollback imported tables
# Those tables (files) are tagged as ".imported"
# Retryes again from the unsuccessful table

case $import in
    init)

        echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

	echo -e "### INITIALIZE DATABASE $DB ###\n" | log_tee

	if mysql -e "USE $DB" 2>/dev/null; then # Check DB exists

	    for name in $INIT/*/*/*; do mv $name ${name%.imported}; done # prepare init files

	    if import "$INIT/*/*/*"; then # parameter is a list of files

		echo -e "DATABASE INITIALIZATION DONE!\n" | log_tee

		else 

		echo -e "DATABASE INITIALIZATION ERROR!\n" | log_tee
		
		exit 1

	    fi

	else

	    echo -e "DATABASE does NOT exist: No INITIALIZATION data import is possible\n" | log_tee

	    exit 1

	fi;;

####################################
# - GENE INDEPENDENT (META) DATA - #
####################################

# Imports tables one by one in the right order (there are dependencies!)
# Stops if error and notify erroneous table
# No need to rollback imported tables
# Those tables (files) are tagged as ".imported"
# Retryes again from the unsuccessful table

	meta)

        echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

	echo -e "### IMPORT META DATA ###\n" | log_tee

	if mysql -e "USE $DB" 2>/dev/null; then # Check DB exists

	    for name in $META/*/*/*; do mv $name ${name%.imported}; done # prepare meta files

	  if  import "$META/*/*/*"; then # parameter is a list of files

	      echo -e "META DATA IMPORT DONE!\n" | log_tee

	  else 

	      echo -e "META DATA IMPORT ERROR!\n" | log_tee    
	      
              exit 1

	  fi  

	else

	    echo -e "DATABASE does NOT exist: No META data IMPORT is possible\n" | log_tee

	    exit 1

	fi;;	    


####################################
# - GENE INDEPENDENT (POST) DATA - #
####################################

# Imports tables one by one in the right order (there are dependencies!)
# Stops if error and notify erroneous table
# No need to rollback imported tables
# Those tables (files) are tagged as ".imported"
# Retryes again from the unsuccessful table

	post)

        echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

	echo -e "### IMPORT POST DATA ###\n" | log_tee

	if mysql -e "USE $DB" 2>/dev/null; then # Check DB exists

            for name in $POST/*/*/*; do mv $name ${name%.imported}; done # prepare meta files

	                    if  import "$POST/*/*/*"; then # parameter is a list of files

	                        echo -e "POST DATA IMPORT DONE!\n" | log_tee

	                    else 

	                        echo -e "POST DATA IMPORT ERROR!\n" | log_tee    
	      
                                exit 1

	                    fi

	else

	    echo -e "DATABASE does NOT exist: No META data IMPORT is possible\n" | log_tee

	    exit 1

	fi;;	    



###########################
# - GENE DEPENDENT DATA - #
###########################

# Imports tables one by one in the right order (there are dependencies!)
# Stops if error and notify erroneous table
# Usually, no need to rollback imported tables
# Those tables (files) are tagged as ".imported"
# Retryes again from the unsuccessful table

        gene)

        echo -e "###########################" >> $LOG/$LOGF
	echo -e "### $(date "+%H:%M:%S %m-%d-20%y") ###" >> $LOG/$LOGF
        echo -e "###########################\n" >> $LOG/$LOGF

	echo -e "### IMPORT GENE ANNOTATION DATA ###\n" | log_tee

	echo -e "Gene: $dir\n" | log_tee

	if mysql -e "USE $DB" 2>/dev/null; then # Check DB exists

	    if dump; then

		for name in $GENE/$dir/*/*/*.imported; do mv $name ${name%.imported}; done # prepare gene files

		rm -f $GENE/$dir/*/*/*.tmp # remove tmp files of a previous annotation

		if import "$GENE/$dir/*/*/*"; then # parameter is a list of files

		    if import "$GENE/$dir/*/*/*.tmp"; then # Second round

			if [ -e $GENE/$dir/*/*/*.tmp ]; then

			    if import "$GENE/$dir/*/*/*.tmp"; then # Third round: import protein_release_ext_ref.tmp

				echo -e "GENE ANNOTATION DATA IMPORT DONE!\n" | log_tee

				echo -e "$(date "+%m-%d-20%y"): $dir\n" >> $LOG/$LOGG

				if dump; then

				    fdone

				else ferror

				fi

			    else				

				echo -e "GENE ANNOTATION DATA IMPORT ERROR!\n" | log_tee

				exit 1

			    fi

			else 
			    
			    echo -e "GENE ANNOTATION DATA IMPORT DONE!\n" | log_tee                          

			    echo -e "$(date "+%m-%d-20%y"): $dir\n" >> $LOG/$LOGG

			    if dump; then

				fdone

			    else ferror

			    fi

			fi

		    else

			echo -e "GENE ANNOTATION DATA IMPORT ERROR!\n" | log_tee

			exit 1

		    fi

		else 

		    echo -e "GENE ANNOTATION DATA IMPORT ERROR!\n" | log_tee

		    exit 1

		fi  

	    else ferror; exit 1

	    fi

	else

	    echo -e "DATABASE does NOT exist: No GENE data IMPORT is possible\n" | log_tee

	    exit 1

	    fi;;	    

# ANY OTHER OPTION

#    *) echo $usage;;

esac # end gene

exit 0 # succesful end of program