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1 #!perl
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2
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3 ## script : downloader_bank_hmdb.pl
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4 #=============================================================================
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5 # Included modules and versions
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6 #=============================================================================
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7 ## Perl modules
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8 use strict ;
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9 use warnings ;
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10 use Carp qw (cluck croak carp) ;
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11
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12 use Data::Dumper ;
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13 use Getopt::Long ;
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14 use File::Basename ;
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15 use FindBin ; ## Allows you to locate the directory of original perl script
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16
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17 ## Specific Perl Modules (PFEM)
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18 use lib $FindBin::Bin.'/lib' ;
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19 my $binPath = $FindBin::Bin ;
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20
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21 ## Dedicate Perl Modules (Home made...)
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22 use hmdb_api qw( :ALL ) ;
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23 use utils qw( :ALL ) ;
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24 use conf qw( :ALL ) ;
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25 use csv qw( :ALL ) ;
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26
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27 ## Initialized values
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28 my $OptHelp ;
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29 my $VERBOSE = 3 ;
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30 my ($bankName, $format, $outTab, $outJson) = (undef, undef, undef, undef) ;
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31
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32 #=============================================================================
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33 # Manage EXCEPTIONS
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34 #=============================================================================
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35 &GetOptions ( "h" => \$OptHelp, # HELP
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36 "bank|b:s" => \$bankName, # bank name to get the rigth url
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37 "format|f:s"=> \$format, # output format
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38 "outTab:s" => \$outTab, # tabular output
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39 "outJson:s" => \$outJson, # Json output
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40 "verbose:i" => \$VERBOSE, # level of scriptt verbose [should be 1 or 3]
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41
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42
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43 ) ;
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44
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45 ## if you put the option -help or -h function help is started
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46 if ( defined($OptHelp) ){ &help ; }
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47
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48 #=============================================================================
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49 # MAIN SCRIPT
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50 #=============================================================================
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51
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52
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53 # get conf informations
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54 my ( $CONF ) = ( undef ) ;
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55 foreach my $conf ( <$binPath/*.cfg> ) {
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56 my $oConf = conf::new() ;
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57 $CONF = $oConf->as_conf($conf) ;
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58 }
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59
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60 # MAIN SCRIPT :
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61
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62 if ( (defined $bankName) ) {
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63
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64 my ( $bankUrl, $bankVersion, $bankSuffixe ) = (undef, undef, undef) ;
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65 my ( $bankOutputTabularFile, $bankOutputJsonFile ) = (undef, undef) ;
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66
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67 print "** Get version information from Wishart server databases (Canada)\n" if $VERBOSE > 1 ;
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68
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69 # get information from conf
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70 if ($CONF->{$bankName.'_URL'}) {
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71 $bankUrl = $CONF->{$bankName.'_URL'} ;
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72 # get version of the http resource
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73 my $oUtils = utils->new() ;
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74 ($bankVersion) = $oUtils->getHttpFileVersion($bankUrl) ;
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75
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76 print "\tThe current version is: $bankVersion\n" if $VERBOSE > 1 ;
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77 }
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78 else {
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79 croak "the given bank name ($bankName) doesn't match with any configuration parameters -- database downloading stopped" ;
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80 }
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81
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82 # manage if needed to download or not the bank (get or not the last version)
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83 my ($bankFileExist, $bankFilePath, $bankFileDir) = (undef, undef, undef) ;
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84
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85 if ($CONF->{$bankName.'_HTTP_FORMAT'}) {
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86 $bankSuffixe = $CONF->{$bankName.'_HTTP_FORMAT'} ;
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87 }
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88 else {
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89 croak "[ERROR] the given bank suffixe doesn't exist! please check your configuration parameters -- database download stopped" ;
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90 }
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91
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92 print "** Manage bank environment\n" if $VERBOSE > 1 ;
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93 my $bankDir = $binPath.'/'.$CONF->{'LOCALBANK_PATH'} ;
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94 if ( !-d $bankDir ) {
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95 print "\tdir creation of $bankDir\n" if $VERBOSE > 1 ;
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96 mkdir $bankDir ;
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97 }
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98
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99
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100 print "** Manage the download of the last version of the bank\n" if $VERBOSE > 1 ;
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101
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102 if ( ( defined $bankUrl ) and ( defined $bankVersion ) ) {
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103 if(-d $binPath.'/'.$CONF->{'LOCALBANK_PATH'}.'/'.$bankName.'_'.$bankVersion) { $bankFileExist = 'TRUE' ; }
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104 else { $bankFileExist = 'FALSE' ; }
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105 # Init the bank file name
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106 $bankFileDir = $binPath.'/'.$CONF->{'LOCALBANK_PATH'}.'/'.$bankName.'_'.$bankVersion ;
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107 $bankFilePath = $bankFileDir.'/'.$bankName.'_'.$bankVersion.'.'.lc($bankSuffixe) ;
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108 # For final files (tabular/json)
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109 $bankOutputTabularFile = $binPath.'/'.$CONF->{'LOCALBANK_PATH'}.'/'.$bankName.'_'.$bankVersion.'/'.$bankName.'_'.$bankVersion.'.tabular' ;
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110 $bankOutputJsonFile = $binPath.'/'.$CONF->{'LOCALBANK_PATH'}.'/'.$bankName.'_'.$bankVersion.'/'.$bankName.'_'.$bankVersion.'.json' ;
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111
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112 print "\tBuilding bank file dir: $bankFileDir\n" if $VERBOSE > 1 ;
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113 print "\tBuilding bank file name: $bankFilePath\n" if $VERBOSE > 1 ;
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114
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115 }
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116 else {
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117 croak "the given bank url ($bankUrl) and the detected version ar undef -- database download stopped" ;
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118 }
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119
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120 my $bankFile = $bankFileDir.'/'.$CONF->{$bankName.'_FILE_NAME'} ;
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121
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122 # dowload the bank if does not exist !
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123 if ( $bankFileExist eq 'FALSE' ) {
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124
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125 print "\t/!\\ The asked bank does not still exist /!\\\n" if $VERBOSE > 1 ;
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126 if (!-d $bankFileDir) {
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127 print "\tdir creation of $bankFileDir\n" if $VERBOSE > 1 ;
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128 mkdir $bankFileDir ;
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129 }
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130
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131 if (-d $bankFileDir) {
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132 print "\tDownload of the asked bank ($bankName)...\n" if $VERBOSE > 1 ;
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133 print "\tFrom...$bankUrl\n" if $VERBOSE > 1 ;
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134 my $oDownloader = utils->new() ;
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135 my ($fileZip) = $oDownloader->getHttpFile($bankUrl, $bankFilePath) ;
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136
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137 print "\tUnzip the download archive ($bankFilePath) and clean env ...\n" if $VERBOSE > 1 ;
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138
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139 my $oUnzip = utils->new() ;
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140 # if archive is a zip
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141 if ($bankSuffixe eq 'ZIP') {
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142 $oUnzip->unzipFile($bankFilePath, $bankFileDir.'/'.$CONF->{$bankName.'_FILE_NAME'}, $CONF->{$bankName.'_FILE_NAME'}) ;
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143 $oUnzip->cleanUnzip($bankFilePath, $bankFileDir.'/'.$CONF->{$bankName.'_FILE_NAME'} ) ;
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144 }
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145 # elsif archive is a gz
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146 elsif ($bankSuffixe eq 'GZ') {
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147 $oUnzip->gunzipFile($bankFilePath, $bankFileDir.'/'.$CONF->{$bankName.'_FILE_NAME'}, $CONF->{$bankName.'_FILE_NAME'}) ;
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148 $oUnzip->cleanUnzip($bankFilePath, $bankFileDir.'/'.$CONF->{$bankName.'_FILE_NAME'} ) ;
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149 }
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150 }
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151 else {
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152 croak "the given bank dir doesn't ($bankFileDir) exist or cannot be created - No download started\n" ;
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153 }
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154 }
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155 else {
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156 print "\t/!\\ $bankName Bank is already present on the disk... /!\\\n" if $VERBOSE > 1 ;
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157 print "\t/!\\ ...in $bankFile /!\\\n" if $VERBOSE > 1 ;
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158 }
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159
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160 ##
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161 if (-e $bankOutputTabularFile) {
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162 # copy the ref file into the user history/session
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163 my $ocsv = csv->new( ) ;
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164 my $csv = $ocsv->get_csv_object("\t") ;
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165 my ($refEntries, $status) = $ocsv->parse_allcsv_object($csv, \$bankOutputTabularFile, 'y') ;
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166 $ocsv->write_csv_from_arrays($csv, $outTab, $refEntries) ;
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167 print "\t/!\\ copy the ref file $bankOutputTabularFile into your session ($outTab)... /!\\\n" if $VERBOSE > 1 ;
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168 }
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169 ## the final tabular file does not exists - need to be created from xml
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170 else {
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171
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172 ## Build a HASH with all metabolites from downloaded xml
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173 my ($handler, $metabolites, $nbEntries) = (undef, undef) ;
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174
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175 if (-e $bankFile) {
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176 my $oHandler = hmdb_api->new ;
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177
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178 # in case the download file is in XML or Metabocard or SDF...
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179 if ($CONF->{$bankName.'_DB_FORMAT'} eq 'XML') {
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180 ($metabolites, $nbEntries) = $oHandler->getMetaboliteFeatures($bankFile) ;
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181 print "\tExtraction of $nbEntries metabolites from $bankName XML file\n" if $VERBOSE > 1 ;
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182 }
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183 elsif ( ($CONF->{$bankName.'_DB_FORMAT'} eq 'CARD') ) {
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184 ($handler, $nbEntries) = $oHandler->cowmetdb_handle($bankFile) ;
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185 ($metabolites) = $oHandler->cowmetdb_hash($handler) ;
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186 print "\tExtraction of $$nbEntries metabolites from $bankName CARD file\n" if $VERBOSE > 1 ;
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187 }
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188 else {
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189 #TODO...
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190 }
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191 }
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192 else {
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193 print "\t/!\\ The bank does not exist: $bankFile\n" if $VERBOSE > 1 ;
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194 }
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195
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196 ## Write outputs !
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197 print "** Write outputs from HMDB in BiH and Json formats\n" if $VERBOSE > 1 ;
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198
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199 if ( (defined $metabolites) and (defined $format) ) {
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200
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201 ## Generation of M+H and M-H masses
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202 my $ometmz = hmdb_api->new ;
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203 my $completedMetabolites = undef ;
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204 $completedMetabolites = $ometmz->setMetaboliteAcurrateMzToModesMz($CONF->{$bankName.'_DB_FORMAT'}, $metabolites, $CONF->{'PROTON_MASS'}, $CONF->{'ELECTRON_MASS'}, 1) ;
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205
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206 # print Dumper $completedMetabolites ;
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207
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208 ## tabular output
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209 if ( ( $format eq 'tabular') and (defined $outTab) ) {
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210 print "\tThe tabular output ($outTab) is created...\n" if $VERBOSE > 1 ;
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211 # print Dumper $metabolites ;
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212 # sort metabolites
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213 my $omet = hmdb_api->new ;
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214 my $sortedMetabolites = undef ;
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215
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216 if ($CONF->{$bankName.'_DB_FORMAT'} eq 'XML') {
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217 $sortedMetabolites = $omet->buildMetabolitesArray($completedMetabolites) ;
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218 }
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219 elsif ( ($CONF->{$bankName.'_DB_FORMAT'} eq 'CARD') ) {
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220 $sortedMetabolites= $omet->cowmetdb_hash_to_inhouse_format($completedMetabolites) ;
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221 }
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222
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223 # print Dumper $sortedMetabolites ;
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224 my $ocsv = csv->new( ) ;
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225 my $csv = $ocsv->get_csv_object("\t") ;
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226 # create the ref file for ./bank repo
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227 $ocsv->write_csv_from_arrays($csv, $bankOutputTabularFile, $sortedMetabolites) ;
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228 # generate also a copy for user history
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229 $ocsv->write_csv_from_arrays($csv, $outTab, $sortedMetabolites) ;
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230
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231 }
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232 elsif ( (defined $format) and (defined $outJson) ) {
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233 #TODO...
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234 }
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235 }
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236 else {
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237 croak "No metabolites are extracted from the $bankName bank file\n" ;
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238 }
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239 ## Clean local envt
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240 unlink $bankFile if (-e $bankFile) ;
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241 }
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242 } ## END IF defined $bankName
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243 else {
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244 &help ;
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245 croak "No bank name and format are defined - Please set one" ;
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246 }
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247
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248 print "\n*************!!End of the job ;-). Thank you for using W4M!!****************\n" if $VERBOSE > 1 ;
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249 ### END of main script
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250
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251
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252
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253
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254
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255 #====================================================================================
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256 # Help subroutine called with -h option
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257 # number of arguments : 0
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258 # Argument(s) :
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259 # Return : 1
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260 #====================================================================================
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261 sub help {
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262 print STDERR "
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263 downloader_bank_hmdb.pl
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264
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265 # downloader_bank_hmdb is a script to export specific tissue/matrix bank from HMDB source.
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266 # Input : N/A
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267 # Author : Franck Giacomoni
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268 # Email : fgiacomoni\@inra.fr
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269 # Version : 1.0
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270 # Created : 21/11/2018
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271 USAGE :
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272 downloader_bank_hmdb.pl -bank [SERUM|URINE|CSF|...] -format [tabular|json] -outTab [tabular file name]
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273
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274 ";
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275 exit(1);
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276 }
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277
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278 ## END of script - F Giacomoni
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279
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280 __END__
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281
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282 =head1 NAME
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283
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284 downloader_bank_hmdb.pl is a script to export specific tissue/matrix bank from HMDB source.
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285
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286 =head1 USAGE
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287
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288 downloader_bank_hmdb.pl -bank [serum|urine|...] -format [tabular|json]
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289 or downloader_bank_hmdb.pl -help
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290
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291 =head1 SYNOPSIS
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292
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293 This script export specific tissue/matrix bank from HMDB source.
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294
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295 =head1 DESCRIPTION
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296
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297 This main program is a galaxy tool (W4M) allowing the export specific tissue/matrix bank from HMDB source in a tabular format.
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298
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299 =over 4
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300
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301 =item B<function01>
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302
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303 =item B<function02>
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304
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305 =back
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306
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307 =head1 AUTHOR
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308
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309 Franck Giacomoni E<lt>franck.giacomoni@inra.frE<gt>
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310
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311 =head1 LICENSE
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312
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313 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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314
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315 =head1 VERSION
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316
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317 version 1 : 21 / 11 / 2018
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318
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319 version 2 : ??
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320
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321 =cut |
