test3.pl

#!/usr/local/bin/perl



# Copyright SRA International
#
# Distributed under the OSI-approved BSD 3-Clause License.
# See http://ncip.github.com/pathway-interaction-database/LICENSE.txt for details.



##
## More options to consider:
##   - save the input config file and allow retrieval
##   - allow uploading a config file
##   - limit to atoms of a given data source (maybe also with NOT)
##   - allow retrieval by template
##   - allow retrieval by degree (on incoming and/or outgoing edge) of
##     separation (but don't follow pruned mols)
##

BEGIN {
  my @path_elems = split("/", $0);
  pop @path_elems;
  push @INC, join("/", @path_elems);
}

use strict;
use Blocks;
use PWAppConfig;
use PWApp;
use Pathway;
use PathwayXML;
use PathParams;
use PWLabel;
use FileHandle;
use ServerSupport;
use URI::Escape;

######################################################################
sub InitializeDatabase {

  InitializeLV();
  InitializeComplex2Component();
  InitializeAtom2Atom();
}


######################################################################
sub GetPwImage {
  my ($base, $id) = @_;

  return GetPwImage_1 ($base, $id);  
}

######################################################################
sub MakeCommandFile {
  my ($base, $graphic_type, $parm_string) = @_;

  $parm_string = uri_unescape($parm_string);
  return MakeCommandFile_1 ($base, $graphic_type, $parm_string);
}

######################################################################
sub PrPath {
  my ($base, $graphic_type, $parm_string) = @_;

  $parm_string = uri_unescape($parm_string);
  return PrPath_1 ($base, $graphic_type, $parm_string);
}

######################################################################
sub MoleculePage {
  my ($base, $molid) = @_;

  return MoleculePage_1($base, $molid);
}

######################################################################
sub MoleculeInstance {
  my ($base, $inst) = @_;

  return MoleculeInstance_1($base, $inst);
}

######################################################################
sub PathwayPage {
  my ($base, $pathid) = @_;

  return PathwayPage_1($base, $pathid);
}

######################################################################
sub ListAllPathways {
  my ($base) = @_;

  return ListAllPathways_1($base);
}

######################################################################
sub MoleculeHeader {
  my ($base, $moleculeName, $source_id, $format) = @_;

  return MoleculeHeader_1($base, $moleculeName, $source_id, $format);
}
######################################################################
sub PathwayHeader {
  my ($base, $pid, $format) = @_;

  return PathwayHeader_1($base, $pid, $format);
}

######################################################################
sub SearchPathwayKeywords {
  my ($base, $word, $format) = @_;

  return SearchPathwayKeywords_1($base, $word, $format);
}

######################################################################
sub Comment {
  my ($base, $name, $email, $organization, $atomid, $molname, $molid,
      $pathname, $pathid, $comment) = @_;

  return Comment_1($base, $name, $email, $organization,
      $atomid, $molname, $molid, $pathname, $pathid, $comment);
}

######################################################################
sub AtomPage {
  my ($base, $atomid) = @_;

  return AtomPage_1($base, $atomid);
}

######################################################################

######################################################################
#
# main
#

SetProgramName($0);

SetSafe(
    "ResetServer",
    "PrPath",
    "GetPwImage",
    "MoleculePage",
    "MoleculeInstance",
    "PathwayPage",
    "ListAllPathways",
    "AtomPage",
    "MakeCommandFile",
    "SearchPathwayKeywords",
    "PathwayHeader",
    "MoleculeHeader",
    "Comment"
);

SetForkable(
    "PrPath",
    "GetPwImage",
    "MoleculePage",
    "MoleculeInstance",
    "PathwayPage",
    "ListAllPathways",
    "AtomPage",
    "MakeCommandFile",
    "SearchPathwayKeywords",
    "PathwayHeader",
    "MoleculeHeader"
###    "Comment"          ##!!! do not make this forkable
);

print "Content-type: text/plain\n\n";

InitializeDatabase();


print PrPath("", "text", join("\n",
  "db_inst	cgdev",
  "db_user	web",
  "db_pass	readonly",
  "db_schema	pid",
  "print	xml",
  "molecule	akt1",
  "molecule	des",
  "molecule	foxa2",
  "molecule	foxo3",
  "molecule	foxo4",
  "molecule	fyn",
  "molecule	nfatc1",
  "molecule	nfatc2",
  "molecule	nfkbia",
  "molecule	nsun2",
  "molecule	ptp4a1",
  "molecule	ptpn1",
  "molecule	rxra",
  "molecule	src",
  "molecule	tp53",
  "molecule	zak",
  "include	complex_uses",
  "include	family_uses",
  "source_id	5"
	    ));
exit();

StartServer(PW_SERVER_PORT, "PWAppServer");


#print PrPath_1("","text", join("\n",
#"db_user\tweb",
#"db_inst\tlpgprod",
#"db_pass\treadonly",
#"db_schema\tcgap2",
#"print\tdot",
#"mol_id\t20035") . "\n");

exit();