CohortExplorer

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lib/CohortExplorer/Application.pm  view on Meta::CPAN

 if ( catch my $e ) {
  throw_app_init_exception( error => $e );
 }
 my $logger = Log::Log4perl->get_logger;

 # Check command history file exists and is readable and writable
 my $command_history_file =
   File::Spec->catfile( File::HomeDir->my_home, ".CohortExplorer_History" );
 if ( !-r $command_history_file || !-w $command_history_file ) {
  throw_app_init_exception( error =>
"'$command_history_file' must exist with RW enabled (i.e. chmod 766) for CohortExplorer"
  );
 }

 # Prompt for password if not provided at command line
 if ( !$opts->{password} ) {
  $app->render("Enter password: ");
  ReadMode 'noecho';
  $opts->{password} = ReadLine(300);
  ReadMode 'normal';
  $app->render("\n");

lib/CohortExplorer/Command/Query.pm  view on Meta::CPAN

 # Untaint and set command history file
 $COMMAND_HISTORY_FILE = $1
 if File::Spec->catfile( File::HomeDir->my_home, ".CohortExplorer_History" ) =~ /^(.+)$/;
 
 my $fh = FileHandle->new(">> $COMMAND_HISTORY_FILE");

 # Throw exception if command history file does not exist or
 # is not readable and writable
 if ( !$fh ) {
  throw_cmd_run_exception( error =>
"'$COMMAND_HISTORY_FILE' must exist with RW enabled (i.e. chmod 766) for CohortExplorer"
  );
 }
 $fh->close;

 # Read command history file
 eval {
  $COMMAND_HISTORY_CONFIG =
    Config::General->new(
                          -ConfigFile            => $COMMAND_HISTORY_FILE,
                          -MergeDuplicateOptions => "false",

lib/CohortExplorer/Command/Query.pm  view on Meta::CPAN

sub validate {
 my ( $self, $opts, @args ) = @_;
 my ( $ds, $csv, $verbose ) = @{ $self->cache->get('cache') }{qw/datasource csv verbose/};
 
 print STDERR "\nValidating command options/arguments ...\n\n" if $verbose;
 
 ##----- VALIDATE ARG LENGTH, EXPORT AND OUT OPTIONS -----##
 if ( !$opts->{out} || !-d $opts->{out} || !-w $opts->{out} ) {
  throw_cmd_validation_exception( error =>
"Option 'out' is required. The directory specified in 'out' option must exist with RWX enabled (i.e. chmod 777) for CohortExplorer"
  );
 }

 
 if ( $opts->{export} && $opts->{export_all} ) {
  throw_cmd_validation_exception( error =>
      'Mutually exclusive options (export and export-all) specified together' );
 }
 if ( @args == 0 || @args > $arg_max ) {
  throw_cmd_validation_exception(

lib/CohortExplorer/Command/Query.pm  view on Meta::CPAN

   $dir = File::Spec->catdir( $1, 'CohortExplorer-' . time . $$ );
  }

  # Create dir to export data
  eval { mkdir $dir };
  if ( catch my $e ) {
   warn $e . "\n";
   $dir = $1;
  }
  else {
   eval { chmod 0777, $dir };
   if ( catch my $e ) {
    warn $e . "\n";
    $dir = $1;
   }
  }
  $self->export( $opts, $rs, $dir, @args );
  
  return {
           headingText => 'summary statistics',
           rows        => $self->summary_stats( $opts, $rs, $dir )

lib/CohortExplorer/Command/Query/Compare.pm  view on Meta::CPAN

       Other variables in arguments/cond (option) must be referenced as <table>.<variable> or <visit>.<table>.<variable>
       where visit can be vAny, vLast, v1, v2, v3 ... vMax. Here vMax is the maximum visit number for which data is
       available.

       Conditions can be imposed using the operators: =, !=, >, <, >=, <=, between, not_between, like, not_like, ilike, in,
       not_in, regexp and not_regexp. The keyword undef can be used to specify null.

       When condition is imposed on variable with no prefix such as vAny, vLast, v1, v2 and v3 the command assumes the
       condition applies to all visits of the variable.

       The directory specified in 'out' option must have RWX enabled (i.e. chmod 777) for CohortExplorer.


     EXAMPLES
       compare --out=/home/user/exports --stats --save-command --cond=v1.CER.Score='>, 20' v1.SC.Date

       compare --out=/home/user/exports --export=CER --cond=SD.Sex='=, Male' v1.CER.Score v3.DIS.Status
 
       compare --out=/home/user/exports --export=CER --cond=v2.CER.Score'!=, undef' vLast.DIS.Status

       compare -o/home/user/exports -Ssa -c vLast.CER.Score='in, 25, 30, 40' DIS.Status 

lib/CohortExplorer/Command/Query/Search.pm  view on Meta::CPAN

         The variables entity_id and visit (if applicable) must not be provided as arguments as they are already part of
         the query-set. However, the user can impose conditions on both variables.

         Other variables in arguments/cond (option) must be referenced as <table>.<variable>.

         The conditions can be imposed using the operators such as =, !=, >, <, >=, <=, between, not_between, like, 
         not_like, ilike, in, not_in, regexp and not_regexp. 

         The keyword undef can be used to search for null values.

         The directory specified in 'out' option must have RWX enabled (i.e. chmod 777) for CohortExplorer.


     EXAMPLES
         search --out=/home/user/exports --stats --save-command --cond=DS.Status='=, CTL, MCI' GDS.Score
                 
         search --out=/home/user/exports --stats --save-command --cond=CER.Score='<=, 30' GDS.Score

         search --out=/home/user/exports --export-all --cond=SD.Sex='=, Male' CER.Score DIS.Status

         search -o/home/user/exports -eDS -eSD -c entity_id='like, DCR%' DIS.Status