genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 14)

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Update of /cvsroot/genex/genex-server/Genex/scripts
In directory sc8-pr-cvs1:/tmp/cvs-serv18825/Genex/scripts

Modified Files:
	protocol-insert.pl.in 
Log Message:
* scripts/protocol-insert.pl.in (Repository): 
added ability to add info for a single protocol from the command line

Index: protocol-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/protocol-insert.pl.in,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** protocol-insert.pl.in	11 Oct 2002 02:18:23 -0000	1.8
--- protocol-insert.pl.in	16 Apr 2003 23:25:06 -0000	1.9
***************
*** 4,10 ****
  #    first version Tue Oct 24 14:13:45 MST 2000
  #    script for inserting protocol entries into genex DB
  #
! # author: Jason E. Stewart (je...@nc... || ja...@op...)
! # Copyright 2001-2002 Jason E. Stewart
  # Copyright 2000-2001 NCGR
  #
--- 4,11 ----
  #    first version Tue Oct 24 14:13:45 MST 2000
  #    script for inserting protocol entries into genex DB
+ #    it can take arguments directly from the command line or from and XML file
  #
! # author: Jason E. Stewart (ja...@op...)
! # Copyright 2001-2003 Jason E. Stewart
  # Copyright 2000-2001 NCGR
  #
***************
*** 22,25 ****
--- 23,27 ----
  use Bio::Genex::Protocol;
  use Bio::Genex::Contact;
+ use Bio::Genex::Config;
  use Bio::Genex::GenexAdmin;

***************
*** 31,36 ****
--- 33,47 ----
  my %OPTIONS;
  $OPTIONS{dbname} = $Bio::Genex::Connect::DBNAME;
+ $OPTIONS{ro_groupname} = 'public';
+ $OPTIONS{rw_groupname} = 'superuser';
  my $rc = GetOptions(\%OPTIONS,
  		    'dbname=s',
+ 		    'name=s',
+ 		    'description=s',
+ 		    'uri=s',
+ 		    'ro_groupname=s',
+ 		    'rw_groupname=s',
+ 		    'type=s',
+ 		    'provider=i',
  		    'username=s',
  		    'password=s',
***************
*** 40,60 ****

  my $USAGE = <<"EOU";
! usage: $0 [required flags]
!   required flags:
!     --file=file_name  : the XML file to parse
      --username=name   : the DB username to login as
      --password=word   : the DB password to login with

    optional parameters:
      --dbname=name     : the name of the DB to create
      --debug           : rollback instead of commit
      --help            : print this message
  EOU

! die "Bad option: $rc\n$USAGE" unless $rc;
  die $USAGE if exists $OPTIONS{help};

- die "Must specify --file\n$USAGE" 
-   unless defined $OPTIONS{file};
  die "Must specify --username\n$USAGE"
    unless exists $OPTIONS{username};
--- 51,84 ----

  my $USAGE = <<"EOU";
! usage: $0 [required flags] [options]
!   either --file is specified to read the protocols from an XML file
!   or the information will be specified on the command line
! 
!   required flags (for all uses):
      --username=name   : the DB username to login as
      --password=word   : the DB password to login with

+   required flags (not using --file):
+     --name=name        : the protocol name
+     --description=text : the protocol description
+ 
+   required flags (using --file):
+     --file=file_name  : the XML file to parse
+ 
+ 
    optional parameters:
+     --uri=text        : the protocol information URI
+     --type=name       : the protocol type (fkey)
+     --provider=num    : the protocol provider (fkey)
      --dbname=name     : the name of the DB to create
+     --ro_groupname=name : the name of the read-only group to use
+     --rw_groupname=name : the name of the read-write group to use
      --debug           : rollback instead of commit
      --help            : print this message
  EOU

! die "Bad option\n$USAGE" unless $rc;
  die $USAGE if exists $OPTIONS{help};

  die "Must specify --username\n$USAGE"
    unless exists $OPTIONS{username};
***************
*** 62,70 ****
    unless exists $OPTIONS{password};

- 
- my $PARSER = Bio::Genex::GeneXML::DOMParser->new(validate=>0);
- $PARSER->parse(file=>$OPTIONS{file});
- my $DOC = $PARSER->get_genexml_document();
- 
  # open up a writeable connection
  my $dbh = Bio::Genex::Connect->new(DBNAME=>$OPTIONS{dbname},
--- 86,89 ----
***************
*** 73,118 ****
  				   TRANSACTION => 1,
  				  );
! my $curr_table = 'Protocol';
! my @inserted;
  my @error_args = (caller=>$0);

! my @protocol_list = $DOC->getElementsByTagName('protocol');
! my @protocol_dbs;
! foreach my $protocol_node (@protocol_list) {
!   push(@protocol_dbs,Bio::Genex::Protocol->xml2db(doc=>$DOC,
! 						  dbh=>$dbh,
! 						  resolve_db_xref=>1,
! 						  node=>$protocol_node));
! }

! print STDERR scalar @protocol_list, " Protocol entries to insert\n";
! # now insert the protocol entries
! foreach my $protocol_db (@protocol_dbs) {
!   my $name = $protocol_db->title();
!   $dbh->error(@error_args,
! 	    message=>"Couldn't find name for protocol")
!     unless $name ne '';

!   print STDERR "Inserting protocol $name\n";

!   my $protocol_pk = $protocol_db->insert_db(dbh=>$dbh,
! 					  no_genex_admin=>1);
!   $dbh->error(@error_args,
! 	    message=>"couldn't insert record for protocol: $name")
!     if $dbh->err;
!   push(@inserted,$name);
! }

! print STDERR "Inserting GenexAdmin\n";

! my $ga_db = Bio::Genex::GenexAdmin->new();
! my $description = "upgraded using $0
     Tables affected: $curr_table;
     Entries affected: " . join('; ', @inserted);
! $ga_db->description($description);
! $ga_db->insert_db($dbh);

! $dbh->error(@error_args,message=>"Couldn't insert GenexAdmin record")
!   if $dbh->err;

  print STDERR "Finished\n";
--- 92,195 ----
  				   TRANSACTION => 1,
  				  );
! 
  my @error_args = (caller=>$0);

! if (exists $OPTIONS{file}) {
!   my $PARSER = Bio::Genex::GeneXML::DOMParser->new(validate=>0);
!   $PARSER->parse(file=>$OPTIONS{file});
!   my $DOC = $PARSER->get_genexml_document();

!   my $curr_table = 'Protocol';
!   my @inserted;

!   my @protocol_list = $DOC->getElementsByTagName('protocol');
!   my @protocol_dbs;
!   foreach my $protocol_node (@protocol_list) {
!     push(@protocol_dbs,Bio::Genex::Protocol->xml2db(doc=>$DOC,
! 						    dbh=>$dbh,
! 						    resolve_db_xref=>1,
! 						    node=>$protocol_node));
!   }

!   print STDERR scalar @protocol_list, " Protocol entries to insert\n";
!   # now insert the protocol entries
!   foreach my $protocol_db (@protocol_dbs) {
!     my $name = $protocol_db->title();
!     $dbh->error(@error_args,
! 		message=>"Couldn't find name for protocol")
!       unless $name ne '';

!     print STDERR "Inserting protocol $name\n";

!     my $protocol_pk = $protocol_db->insert_db(dbh=>$dbh,
! 					      no_genex_admin=>1);
!     $dbh->error(@error_args,
! 		message=>"couldn't insert record for protocol: $name")
!       if $dbh->err;
!     push(@inserted,$name);
!   }
! 
!   print STDERR "Inserting GenexAdmin\n";
! 
!   my $ga_db = Bio::Genex::GenexAdmin->new();
!   my $description = "upgraded using $0
     Tables affected: $curr_table;
     Entries affected: " . join('; ', @inserted);
!   $ga_db->description($description);
!   $ga_db->insert_db($dbh);

!   $dbh->error(@error_args,message=>"Couldn't insert GenexAdmin record")
!     if $dbh->err;
! } else {
!   die "Must specify --name\n$USAGE"
!     unless exists $OPTIONS{name};
!   die "Must specify --description\n$USAGE"
!     unless exists $OPTIONS{description};
! 
!   # get all the arguments for a single protocol from the command line
!   my ($ro_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
! 							    column=>'name',
! 							    value=>$OPTIONS{ro_groupname},
! 							   );
!   $dbh->error(@error_args,
! 	      no_errstr=>1,
! 	      message=>"Couldn't locate $OPTIONS{ro_groupname} group")
!     unless defined $ro_group_db;
! 
!   my ($rw_group_db) = Bio::Genex::GroupSec->get_all_objects($dbh,
! 							    column=>'name',
! 							    value=>$OPTIONS{rw_groupname},
! 							   );
!   $dbh->error(@error_args,
! 	      no_errstr=>1,
! 	      message=>"Couldn't locate $OPTIONS{rw_groupname} group")
!     unless defined $rw_group_db;
! 
!   my $proto_db = Bio::Genex::Protocol->new(ro_groupname_obj=>$ro_group_db,
! 					   rw_groupname_obj=>$rw_group_db,
! 					   name=>$OPTIONS{name},
! 					   description=>$OPTIONS{description},
! 
! 					  );
! 
!   # handle the simple optional arguments
!   $proto_db->type($OPTIONS{type})
!     if exists $OPTIONS{type};
!   $proto_db->URI($OPTIONS{uri})
!     if exists $OPTIONS{uri};
! 
!   # if they've specified a provider, we check to ensure that it exists in the DB
!   if (exists $OPTIONS{provider}) {
!     my ($con_db) = Bio::Genex::Contact->get_all_objects($dbh,
! 							column=>'con_pk',
! 							value=>$OPTIONS{provider},
! 						       );
!     $dbh->error(@error_args,
! 		no_errstr=>1,
! 		message=>"Couldn't locate Contact entry for value: $OPTIONS{provider}")
!       unless defined $con_db;
!     $proto_db->provider_con_obj($con_db);
!   }
! }

  print STDERR "Finished\n";

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genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 14)

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