genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 35)

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Update of /cvsroot/genex/genex-server/site/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv19323

Added Files:
      Tag: Rel-1_0_1-branch
	add_analysis.pl 
Log Message:
Initial draft

--- NEW FILE: add_analysis.pl ---
#!/usr/bin/perl -w

=head1 NAME
 
  act_analysis -  add an analysis to the list of possible analyses

=head1 SYNOPSIS

 ./act_analysis

=head1 DESCRIPTION
  The act_analysis is intended to configure an new analysis for use 
 with in the gene analsys system.  It does the following:
   - adds appropriate records to the database based on the config file
   - puts supplied scripts in appropriate locations
   - verifies syntax and runnability of scripts
   - verifies the existence of documentation

=cut

    use strict;
    use DBI;

    use Getopt::Long 2.13;
    use AppConfig qw(:expand :argcount);
    require "sessionlib.pl";


    my $config = AppConfig->new();
    $config->define('name', {ARGCOUNT => ARGCOUNT_ONE},
        'cmdstr', {ARGCOUNT => ARGCOUNT_ONE},
        'up', { ARGCOUNT => ARGCOUNT_LIST },
        'filetype',{ ARGCOUNT => ARGCOUNT_LIST },
        'sp', { ARGCOUNT => ARGCOUNT_LIST },
        'outputfile', { ARGCOUNT => ARGCOUNT_LIST,},
        'inputfile', { ARGCOUNT => ARGCOUNT_LIST,});
    $config->define('configfile', {ARGCOUNT => ARGCOUNT_ONE},
                    'action', {ARGCOUNT => ARGCOUNT_ONE},
                    'debug', {ARGCOUNT => ARGCOUNT_ONE});
    $config->getopt(\@ARGV);


    my $cfgfile = $config->get('configfile');
    my $debug = $config->get('debug');
    usage() if (!defined $cfgfile);
    $config->file($cfgfile);

    modifyDB($config);

# end main

sub modifyDB
{
    my ($config) = @_;

    my $action = $config->get('action');

    # open handle to database
    my $dbh = new_connection();

    if ($action eq 'insert')
    {
        # insert appropriate values in appropriate tables
        # we need to add filetypes (optional)
        act_filetype($dbh, $config->get('filetype'), $action);    

        # we need to add the analysis
        act_analysis($dbh, $config->get('name'), $config->get('cmdstr'),
             $action);  

        # we need to add the input links to filetypes
        act_file_links($dbh, "input", $config->get('inputfile'), 
            $config->get('name'), $action);    

        # we need to add the output links to filetypes
        act_file_links($dbh, "output", $config->get('outputfile'),
            $config->get('name'), $action);    

        # we need to add the sysparams
        act_sysparams($dbh, $config->get('sp'), $config->get('name'), $action); 

        # we need to add the userparams
        act_userparams($dbh, $config->get('up'), $config->get('name'), $action);    
    }
    elsif ($action eq "remove")
    {
        # note: removing must be done in a somewhat opposite
        # order to adding

        # we need to add the input links to filetypes
        act_file_links($dbh, "input", $config->get('inputfile'), 
            $config->get('name'), $action);    

        # we need to add the output links to filetypes
        act_file_links($dbh, "output", $config->get('outputfile'),
            $config->get('name'), $action);    

        # we need to add the sysparams
        act_sysparams($dbh, $config->get('sp'), $config->get('name'), $action);

        # we need to add the userparams
        act_userparams($dbh, $config->get('up'), $config->get('name'), $action);

        # we need to add the analysis
        act_analysis($dbh, $config->get('name'), $config->get('cmdstr'),
             $action);  
        # insert appropriate values in appropriate tables
        # we need to add filetypes (optional)
        act_filetype($dbh, $config->get('filetype'), $action);    
    } 
    else
    {
        print "Unrecognized action: $action\n";
        usage();
    }   
    $dbh->commit();
    $dbh->disconnect(); 

} # addToDB

sub parse_into_records
{
  my @input = @_;
  my @return = ();
  my %rec = ();

  while (my $element = shift(@input))
  { 
    my ($key, $value) = split(/=/, $element);
    #remove spaces from key
    $key =~ tr/ //d;
    if (exists $rec{$key})
    {
      my %dup = %rec;
      push(@return, \%dup);
      %rec = ();
    }
    $rec{$key} = $value;
  }
  push(@return, \%rec);
  return(@return);
  
} #parse_into_record

sub act_filetype
{

  my ($dbh, $filetype, $action) = @_;
  
  my $stm = "";
  my $record;

  my @records = parse_into_records(@$filetype);

  # TODO - handle spaces in keys
  foreach $record (@records)
  {
    my %rec = %$record;
    my $name = $rec{name};
    my $ext = $rec{extension};
    my $comment = $rec{comment};

    checkValidFields([ "name" ], ["name", "extension", "comment"], $record);

    if ($action eq "remove")
    {
      $stm = "delete from filetypes where name = '$name'";
    }
    else
    {
      $stm = "insert into filetypes (name, extension, comment) " . 
        "values ('$name', '$ext', '$comment');";
    }
    print "$stm\n" if $debug;
    my $sth = $dbh->prepare( $stm ); 
    $sth->execute();
  }
  $dbh->commit();
} # act_filetype    

sub act_analysis
{
  my ($dbh, $name, $cmdstr, $action) = @_; 
  my $stm = "";

  if ($action eq "remove")
  {
    $stm = "delete from analysis where name = '$name'";
  }
  else
  {
    $stm = "insert into analysis (name, cmdstr) values ('$name', '$cmdstr');";
  }

  print "$stm\n" if $debug;
  my $sth = $dbh->prepare( $stm ); 
  $sth->execute();
  $dbh->commit();
} # act_analysis   

sub act_file_links
{
  my ($dbh, $table, $filelist, $name, $action) = @_;    

  my $stm = "";
  my $record;

  $table = "analysis_ft_input_link" if $table eq "input";
  $table = "analysis_ft_output_link" if $table eq "output";

  # select the analysis pk for the analysis
  $stm = $dbh->prepare("select anal_pk from analysis where name = '$name'");
  $stm->execute();

  # get result
  my $an_fk = $stm->fetchrow_array();
  if (!defined $an_fk)
  { 
    warn "Unable to get analysis key value for $name";
    return;
  }
  
  foreach my $rec (@$filelist)
  {
    
    # select the filetypes pk for the filetype
    $stm = $dbh->prepare("select ft_pk from filetypes where name = '$rec'");
    $stm->execute();

    my $ft_fk = $stm->fetchrow_array();
    if (!defined $ft_fk)
    { 
      warn "Unable to get filetypes key value for $rec";
    }
    else
    {
        if ($action eq "remove")
        {
            $stm = "delete from $table where anal_fk = '$an_fk'";
        }
        else
        {
            $stm = "insert into $table (anal_fk, ft_fk) " . 
               "values ('$an_fk', '$ft_fk');";
        }
        print "$stm\n" if $debug;
        my $sth = $dbh->prepare( $stm ); 
        $sth->execute();
    }
  }
} # act_file_links

sub act_sysparams
{
  my ($dbh, $sp, $name, $action) = @_; 
  
  my $stm = "";
  my $record;

  my @records = parse_into_records(@$sp);

  # select the analysis pk for the analysis
  $stm = $dbh->prepare("select anal_pk from analysis where name = '$name'");
  $stm->execute();

  # get result
  my $an_fk = $stm->fetchrow_array();
  if (!defined $an_fk)
  { 
    warn "Unable to get analysis key value for $name";
    return;
  }

  foreach $record (@records)
  {
    my %rec = %$record;

    checkValidFields([ "name" ], ["name", "default"], $record);

    my $name = $rec{name};
    my $default ="NULL";

    $default = "'$rec{default}'" if exists($rec{default});
    if ($action eq "remove")
    {
      $stm = "delete from sys_parameter_names where anal_fk = '$an_fk'";
    }
    else
    {
      $stm = "insert into sys_parameter_names (anal_fk, sp_name, sp_default) values ('$an_fk', '$name', $default);";
    }
    print "$stm\n" if $debug;
    my $sth = $dbh->prepare( $stm ); 
    $sth->execute();
  }

  $dbh->commit();
} # act_sysparams   

sub act_userparams
{
  my ($dbh, $up, $name, $action) = @_; 
  
  my $stm = "";
  my $record;

  my @records = parse_into_records(@$up);

  # select the analysis pk for the analysis
  $stm = $dbh->prepare("select anal_pk from analysis where name = '$name'");
  $stm->execute();

  # get result
  my $an_fk = $stm->fetchrow_array();
  if (!defined $an_fk)
  { 
    warn "Unable to get analysis key value for $name";
    return;
  }

  # TODO - handle spaces in keys
  foreach $record (@records)
  {
    my %rec = %$record;
    my $name = $rec{name};
    my $display_name = $rec{display_name};
    my $type = $rec{type};
    my $default ="NULL";

    $default = "'$rec{default}'" if exists($rec{default});

    checkValidFields([ "name", "display_name", "type" ],
         ["name", "display_name", "type", "default"], $record);
    if ($action eq "remove")
    {
      $stm = "delete from user_parameter_names where anal_fk = '$an_fk'";
    }
    else
    {
      $stm = "insert into user_parameter_names (anal_fk, up_name, up_display_name, up_type, up_default) values ('$an_fk', '$name', '$display_name', '$type', $default);";
    }
    print "$stm\n" if $debug;
    my $sth = $dbh->prepare( $stm ); 
    $sth->execute();
  }
} # act_userparams 

sub checkValidFields
{
    my ($reqref, $fieldsref, $record) = @_;

    my @req = @$reqref;
    my @fields = @$fieldsref;
    my %rec = %$record;

    foreach my $req (@req)
    {
        warn "Incorrect configuration. Sys params requires $req field.\n" 
            if (!exists $rec{$req});
    }

    foreach my $key (keys(%rec))
    {
        my $found = 0;
        foreach my $field (@fields)
        {
            $found = 1 if ($field eq $key);
        }
        if (! $found)
        {
            warn "Invalid sys param field: $key.\n";
            warn "Valid field names are: @fields\n";
        }
    }
} # checkValidFields

sub usage
{
      print "Usage: \n";
      print "./act_analysis.pl --configfile <filename>\n";
} # usage

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genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 35)

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