Commit f09cc342 authored by David Tosolini's avatar David Tosolini
Browse files

Update checkfits.sh 

E' stato aggiunto del codice per usare uno script di astropy-pyfits chimato fitscheck.
La modifica scrive in tutti i nuovi files.fits le keywords CHECKSUM e DATASUM
parent ce6b597a

script/checkfits.sh

+361 −216
Original line number Diff line number Diff line
@@ -2,24 +2,35 @@ 


#: Title	: checkfits.sh

#: Date		: 2014/10/28

#: Author	: "Marco De Marco" <demarco@oats.inaf.it>

#: Version	: 1.0

#: Author	:"David Tosolini" david.tosolini@inaf.it /"Marco De Marco"

#: Version	: 2.0

#: Description	: Fits verification and proccessing script



# ===========================================================================



#Tools paths



# --------------------------------------------------------------------------



VERIFY_TOOL="/usr/local/bin/fitsverify"

LISTHEAD_TOOL="/usr/local/bin/listhead"

MODHEAD_TOOL="/usr/local/bin/modhead"

FITSCHECK_TOOL="/usr/bin/fitscheck"



# ===========================================================================



if [ "$1" == "CHECK" ]; then



# --------------------------------------------------------------------------

        #: Section	: CHECK

        #: Parameter	: none

        #: Response	: CHECK OK

        #: 		: CHECK FATAL

        #: Description	: Check availability of script tools

# ===========================================================================



        # 1. Check fitsverify tools



	#Check fitsverify tools

        CHECK_STRING="conform to the FITS format"



        res=$($VERIFY_TOOL 2>&1)
@@ -30,7 +41,9 @@ if [ "$1" == "CHECK" ]; then 
                exit 0

        fi



	#Check listhead tools



        # 2. Check listhead tools



        CHECK_STRING="Usage: listhead filename"



        res=$($LISTHEAD_TOOL 2>&1)
@@ -41,7 +54,9 @@ if [ "$1" == "CHECK" ]; then 
                exit 0

        fi



	#Check modhead tools



        # 3. Check modhead tools



        CHECK_STRING="Usage: modhead filename"



        res=$($MODHEAD_TOOL 2>&1)
@@ -52,16 +67,35 @@ if [ "$1" == "CHECK" ]; then 
                exit 0

        fi





        # 4. Check fitscheck tools

        CHECK_STRING="Usage: fitscheck"



        res=$($FITSCHECK_TOOL 2>&1)



        check=$(echo $res | grep "$CHECK_STRING" | wc | awk '{print $1}')

        if [ "$check" -lt "1" ]; then

             echo "CHECK FATAL"

             exit 0

        fi



        # if 1.2.3.4. are ok then the Section CHECK gives "CHECK OK" output



        echo "CHECK OK"

        exit 0



# ===========================================================================



elif [ "$1" == "VALID" ]; then



# ---------------------------------------------------------------------------

        #: Section	: VALID

        #: Parameter	: file path

        #: Response	: VALID OK

        #: 		: VALID IGNORE

        #: Description	: Check file name compliance

# ===========================================================================





        file=$2

        file_name=${file##*/}
@@ -81,14 +115,19 @@ elif [ "$1" == "VALID" ]; then 
        echo "VALID OK"

        exit 0



# ===========================================================================



elif [ "$1" == "VERIFY" ]; then



# ---------------------------------------------------------------------------

        #: Section	: VERIFY

        #: Parameter	: file path

        #: Response	: VERIFY OK

        #: 		: VERIFY WAIT

        #: 		: VERIFY FATAL

        #: Description	: Check file compliance to fits format

# ===========================================================================





        file=$2
@@ -131,8 +170,12 @@ elif [ "$1" == "VERIFY" ]; then 
        echo "VERIFY OK"

        exit 0



# ===========================================================================



elif [ "$1" == "PREPROCESS" ]; then



# ---------------------------------------------------------------------------



        #: Section	: PREPROCESS

        #: Parameter	: file path

        #: 		: ingestion result [OK, WAIT, FATAL]
@@ -140,25 +183,42 @@ elif [ "$1" == "PREPROCESS" ]; then 
        #: 		: PREPROCESS FATAL

        #: Description	: Apply preprocessing before ingestion





# ===========================================================================



        file=$2

        file_name=${file##*/}



        verified=$3







# ---------------------------------------------------------------------------







        #Check verified parameter value



        if [ "$verified" != "OK" -a "$verified" != "WAIT" -a "$verified" != "FATAL" ]; then

                echo "PREPROCESS FATAL"

                exit 0

        fi





# ---------------------------------------------------------------------------



        #Pre processing for verified OK files



        if [ "$verified" == "OK" ]; then



                #Change file ownership

                /usr/bin/sudo -n /bin/chown controls:controls $file



                #Change file and permission before processing

                /usr/bin/sudo -n /bin/chmod u+rw $file



# ---------------------------------------------------------------------------



                #Check regular expression for luci files

                if [[ "${file_name,,}" =~ ^.*luci.*\.(fits|fit|fts).*$ ]]; then
@@ -174,6 +234,7 @@ elif [ "$1" == "PREPROCESS" ]; then 
                                exit 0

                        fi





                        #if fits file not exists -> fatal

                        if [ ! -f $file ]; then

                                echo "PREPROCESS FATAL : file not exists"
@@ -191,8 +252,11 @@ elif [ "$1" == "PREPROCESS" ]; then 
                        if [[ $gratorde =~ "'not used'/" ]]; then

                                $MODHEAD_TOOL $file GRATORDE 0.0 &>/dev/null

                        fi



                fi #luci files



# ---------------------------------------------------------------------------



                #Check regular expression for irt files

                if [[ "${file_name,,}" =~ ^.*irt.*\.(fits|fit|fts).*$ ]]; then
@@ -208,6 +272,7 @@ elif [ "$1" == "PREPROCESS" ]; then 
                                exit 0

                        fi





                        #if fits file not exists -> fatal

                        if [ ! -f $file ]; then

                                echo "PREPROCESS FATAL : file not exists"
@@ -226,15 +291,80 @@ elif [ "$1" == "PREPROCESS" ]; then 
                                        $MODHEAD_TOOL $file DATE_OBS "'$date_obs'" &>/dev/null

                                fi

                        fi







                fi #irt files





# ---------------------------------------------------------------------------





        fi #verified ok files





# ---------------------------------------------------------------------------



        #: Sub Section	: PREPROCESS - Wright CHECKSUM and DATASUM

        #: Parameter	: file path

        #: Response	: PREPROCESS OK

        #: 		: PREPROCESS FATAL

        #: Description	: Wrighting CHECKSUM and DATASUM in $file before moving it





# ===========================================================================





        file=$2

        file_name=${file##*/}





        #if fitscheck tools exists -> fatal

            if [ ! -x $FITSCHECK_TOOL ]; then

                echo "PREPROCESS FATAL : fitscheck tools not exists"

                exit 0

            fi





        #if listhead tools exists -> fatal

            if [ ! -x $LISTHEAD_TOOL ]; then

                echo "PREPROCESS FATAL : listhead tools not exists"

                exit 0

            fi





        #if fits file not exists -> fatal

            if [ ! -f $file ]; then

                echo "PREPROCESS FATAL : file not exists"

                exit 0

            fi





         new_file=$($FITSCHECK_TOOL -vf  $file )

         datasum=$($LISTHEAD_TOOL $file| grep DATASUM)

         datasum_value=$($LISTHEAD_TOOL $file| grep DATASUM|awk '{print $3}')

         checkdatasum=$(echo $datasum | grep DATASUM | wc | awk '{print $1}')







   if [ "$checkdatasum" -lt "1" ]; then

           echo "DATASUM is NOT recorded in $file"

           exit 0 ; else

           echo "DATASUM is recorded: $datasum_value"

    fi



# ---------------------------------------------------------------------------



        echo "PREPROCESS OK"

        exit 0





# ===========================================================================



elif [ "$1" == "POSTPROCESS" ]; then



# ---------------------------------------------------------------------------



        #: Section	: POSTPROCESS

        #: Parameter	: file path

        #: 		: ingestion result [OK, WAIT, FATAL]
@@ -242,37 +372,52 @@ elif [ "$1" == "POSTPROCESS" ]; then 
        #: 		: POSTPROCESS FATAL

        #: Description	: Apply postprocessing after ingestion



# ===========================================================================



        file=$2

        file_name=${file##*/}



        verified=$3



        #Check verified parameter value



        if [ "$verified" != "OK" -a "$verified" != "WAIT" -a "$verified" != "FATAL" ]; then

                echo "POSTPROCESS FATAL"

                exit 0

        fi



# ---------------------------------------------------------------------------



        #Post process verified WAIT files

        if [ "$verified" == "WAIT" ]; then

                echo "Warning file: $file_name" | mutt -s "Pre process log" -- demarco@oats.inaf.it

        fi



# ---------------------------------------------------------------------------



        #Post process verified FATAL files

        if [ "$verified" == "FATAL" ]; then

                echo "Fatal file: $file_name" | mutt -s "Pre process log" -- demarco@oats.inaf.it

        fi





        echo "POSTPROCESS OK"

        exit 0



# ===========================================================================



else



# ---------------------------------------------------------------------------



        #: Section	: DEFAULT

        #: Parameter	: none

        #: Response	: UNKNOWN



# ===========================================================================



        echo "UNKNOWN"

        exit 0





fi