genex-cvs-commit — CVS commit messages

[Genex-cvs-commit] genex-server/DTD genexml.dtd,1.1,NONE als.dtd,1.1,NONE ams.dtd,1.1,NONE csf.dtd,1.1,NONE usf.dtd,1.2,NONE

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/DTD
In directory usw-pr-cvs1:/tmp/cvs-serv28884/DTD

Removed Files:
      Tag: Rel-1_0_1-branch
	genexml.dtd als.dtd ams.dtd csf.dtd usf.dtd 
Log Message:
Now that the unused files are archived, I'm deleting the files.


--- genexml.dtd DELETED ---

--- als.dtd DELETED ---

--- ams.dtd DELETED ---

--- csf.dtd DELETED ---

--- usf.dtd DELETED ---

[Genex-cvs-commit] genex-server/RCluster-Demo .cvsignore,1.1,NONE AboutRCluster-Demo.html.in,1.5,NONE RCluster-Demo.html.in,1.9,NONE RCluster-Demos.html.in,1.5,NONE yeast64.rclust.demo.txt,1.1,NONE

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/RCluster-Demo
In directory usw-pr-cvs1:/tmp/cvs-serv28884/RCluster-Demo

Removed Files:
      Tag: Rel-1_0_1-branch
	.cvsignore AboutRCluster-Demo.html.in RCluster-Demo.html.in 
	RCluster-Demos.html.in yeast64.rclust.demo.txt 
Log Message:
Now that the unused files are archived, I'm deleting the files.


--- .cvsignore DELETED ---

--- AboutRCluster-Demo.html.in DELETED ---

--- RCluster-Demo.html.in DELETED ---

--- RCluster-Demos.html.in DELETED ---

--- yeast64.rclust.demo.txt DELETED ---

[Genex-cvs-commit] genex-server/CyberT-dist .cvsignore,1.6.2.1,NONE CTHelp.html.in,1.3.2.2,NONE CTHelp.inc.in,1.3,NONE CTHelp.shtml,1.1,NONE ChangeLog,1.4.2.3,NONE CyberT-6.2.C+E.form.pl.in,1.7,NONE CyberT-6.2.paired.form.pl.in,1.6,NONE CyberT-7.0.form.pl.in,1.2.2.2,NONE CyberT.html.in,1.3,NONE CyberTDB-6.2.C+E.pl.in,1.13,NONE CyberTDB-6.2.paired.pl.in,1.13,NONE CyberTDB-7.0.pl.in,1.5.2.5,NONE CyberT_C+E_DataSet,1.1.1.1,NONE CyberT_Paired_DataSet,1.1.1.1,NONE README,1.5,NONE cyberfilter.pl.in,1.1.2.2,NONE genex_reaper.pl.in,1.6.2.3,NONE hdarray.in,1.6.2.1,NONE index.inc.in,1.6.2.1,NONE index.shtml,1.1.6.1,NONE munge4R.pl.in,1.1,NONE runa.c,1.1.1.1,NONE xgobi.in,1.1,NONE xgobi_1.2-2.tar.gz,1.1.1.1,NONE

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/CyberT-dist
In directory usw-pr-cvs1:/tmp/cvs-serv28884/CyberT-dist

Removed Files:
      Tag: Rel-1_0_1-branch
	.cvsignore CTHelp.html.in CTHelp.inc.in CTHelp.shtml ChangeLog 
	CyberT-6.2.C+E.form.pl.in CyberT-6.2.paired.form.pl.in 
	CyberT-7.0.form.pl.in CyberT.html.in CyberTDB-6.2.C+E.pl.in 
	CyberTDB-6.2.paired.pl.in CyberTDB-7.0.pl.in 
	CyberT_C+E_DataSet CyberT_Paired_DataSet README 
	cyberfilter.pl.in genex_reaper.pl.in hdarray.in index.inc.in 
	index.shtml munge4R.pl.in runa.c xgobi.in xgobi_1.2-2.tar.gz 
Log Message:
Now that the unused files are archived, I'm deleting the files.


--- .cvsignore DELETED ---

--- CTHelp.html.in DELETED ---

--- CTHelp.inc.in DELETED ---

--- CTHelp.shtml DELETED ---

--- ChangeLog DELETED ---

--- CyberT-6.2.C+E.form.pl.in DELETED ---

--- CyberT-6.2.paired.form.pl.in DELETED ---

--- CyberT-7.0.form.pl.in DELETED ---

--- CyberT.html.in DELETED ---

--- CyberTDB-6.2.C+E.pl.in DELETED ---

--- CyberTDB-6.2.paired.pl.in DELETED ---

--- CyberTDB-7.0.pl.in DELETED ---

--- CyberT_C+E_DataSet DELETED ---

--- CyberT_Paired_DataSet DELETED ---

--- README DELETED ---

--- cyberfilter.pl.in DELETED ---

--- genex_reaper.pl.in DELETED ---

--- hdarray.in DELETED ---

--- index.inc.in DELETED ---

--- index.shtml DELETED ---

--- munge4R.pl.in DELETED ---

--- runa.c DELETED ---

--- xgobi.in DELETED ---

--- xgobi_1.2-2.tar.gz DELETED ---

[Genex-cvs-commit] genex-server/CyberT-Demo .cvsignore,1.1,NONE AboutBasic_CyberT_Demo.shtml,1.1,NONE Basic_CyberT_Demo.shtml.in,1.3,NONE CyberT_Demos.html,1.1,NONE CyberT_Demos.shtml,1.1,NONE CyberT_Paired_DataSet,1.1,NONE yeast64.cybert.demo.txt,1.1,NONE

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/CyberT-Demo
In directory usw-pr-cvs1:/tmp/cvs-serv28884/CyberT-Demo

Removed Files:
      Tag: Rel-1_0_1-branch
	.cvsignore AboutBasic_CyberT_Demo.shtml 
	Basic_CyberT_Demo.shtml.in CyberT_Demos.html 
	CyberT_Demos.shtml CyberT_Paired_DataSet 
	yeast64.cybert.demo.txt 
Log Message:
Now that the unused files are archived, I'm deleting the files.


--- .cvsignore DELETED ---

--- AboutBasic_CyberT_Demo.shtml DELETED ---

--- Basic_CyberT_Demo.shtml.in DELETED ---

--- CyberT_Demos.html DELETED ---

--- CyberT_Demos.shtml DELETED ---

--- CyberT_Paired_DataSet DELETED ---

--- yeast64.cybert.demo.txt DELETED ---

[Genex-cvs-commit] genex-server/Bio/Genex .cvsignore,1.2,NONE

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/Bio/Genex
In directory usw-pr-cvs1:/tmp/cvs-serv28884/Bio/Genex

Removed Files:
      Tag: Rel-1_0_1-branch
	.cvsignore 
Log Message:
Now that the unused files are archived, I'm deleting the files.


--- .cvsignore DELETED ---

[Genex-cvs-commit] genex-server/webtools choose_order_curator.html,1.1.2.12,1.1.2.13 edit_study1.html,1.1.2.15,1.1.2.16 edit_study2.pl,1.1.2.19,1.1.2.20

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv5770

Modified Files:
      Tag: Rel-1_0_1-branch
	choose_order_curator.html edit_study1.html edit_study2.pl 
Log Message:
Finished the 'paste' exp. cond feature, fixed duplicate exp. cond name/short name test, fixed duplicate study name test.


Index: choose_order_curator.html
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/choose_order_curator.html,v
retrieving revision 1.1.2.12
retrieving revision 1.1.2.13
diff -C2 -d -r1.1.2.12 -r1.1.2.13
*** choose_order_curator.html	14 Oct 2002 20:13:16 -0000	1.1.2.12
--- choose_order_curator.html	24 Oct 2002 14:44:28 -0000	1.1.2.13
***************
*** 76,80 ****
              </td>
              <td>&nbsp; 
!               <input type="text" name="billing_code" value="{billing_code}">
              </td>
              <td bgcolor="#99FFCC"></td>
--- 76,80 ----
              </td>
              <td>&nbsp; 
!               <input type="text" name="billing_code" value="{billing_code}" maxlength="128">
              </td>
              <td bgcolor="#99FFCC"></td>

Index: edit_study1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study1.html,v
retrieving revision 1.1.2.15
retrieving revision 1.1.2.16
diff -C2 -d -r1.1.2.15 -r1.1.2.16
*** edit_study1.html	23 Oct 2002 18:59:34 -0000	1.1.2.15
--- edit_study1.html	24 Oct 2002 14:44:28 -0000	1.1.2.16
***************
*** 16,24 ****
  <table width="700" border=0 cellpadding=4 cellspacing=0>
  <tr><td valign="top">
! <div align="right">Study Name &nbsp;&nbsp;</div></td><td><input type="text" name="study_name" value="{study_name}">
  </td></tr>
  
  <tr><td valign="top">
! <div align="right">Study Start Date &nbsp;&nbsp;</div></td><td><input type="text" name="start_date" value="{start_date}">
  </td></tr>
  <tr><td>
--- 16,26 ----
  <table width="700" border=0 cellpadding=4 cellspacing=0>
  <tr><td valign="top">
! <div align="right">Study Name &nbsp;&nbsp;</div></td><td>
!         <input type="text" name="study_name" value="{study_name}" maxlength="128">
  </td></tr>
  
  <tr><td valign="top">
! <div align="right">Study Start Date &nbsp;&nbsp;</div></td><td>
!         <input type="text" name="start_date" value="{start_date}" maxlength="128">
  </td></tr>
  <tr><td>
***************
*** 65,69 ****
  <tr>
  <td><div align="right">*Experimental Condition Name &nbsp;&nbsp;</div></td>
! <td><input type="text" name="name" value="{name}" size="60"><br>
  <input type="hidden" name="ec_pk" value="{ec_pk}">
  </td>
--- 67,73 ----
  <tr>
  <td><div align="right">*Experimental Condition Name &nbsp;&nbsp;</div></td>
! <td>
!         <input type="text" name="name" value="{name}" size="60" maxlength="128">
!         <br>
  <input type="hidden" name="ec_pk" value="{ec_pk}">
  </td>
***************
*** 75,79 ****
  <td valign="top"><div align="right">* Short name (5 chars. max) &nbsp;&nbsp;</div></td>
  <td>
! <input type="text" name="abbrev_name" value="{abbrev_name}">
  </td>
  </tr>
--- 79,83 ----
  <td valign="top"><div align="right">* Short name (5 chars. max) &nbsp;&nbsp;</div></td>
  <td>
!         <input type="text" name="abbrev_name" value="{abbrev_name}" size="6" maxlength="5">
  </td>
  </tr>
***************
*** 112,117 ****
  
  <tr>
! <td valign="top"><nobr>*Cell Line/Cell Type <input type=text name="cell_line" value="{cell_line}"></nobr></td>
! <td valign="top">OR &nbsp;&nbsp;&nbsp;*Tissue Type <input type=text name="tissue_type" value="{tissue_type}"></td>
  </tr>
  
--- 116,125 ----
  
  <tr>
! <td valign="top"><nobr>*Cell Line/Cell Type 
!         <input type=text name="cell_line" value="{cell_line}" maxlength="128">
!         </nobr></td>
! <td valign="top">OR &nbsp;&nbsp;&nbsp;*Tissue Type 
!         <input type=text name="tissue_type" value="{tissue_type}" maxlength="128">
!       </td>
  </tr>
  

Index: edit_study2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study2.pl,v
retrieving revision 1.1.2.19
retrieving revision 1.1.2.20
diff -C2 -d -r1.1.2.19 -r1.1.2.20
*** edit_study2.pl	23 Oct 2002 18:59:34 -0000	1.1.2.19
--- edit_study2.pl	24 Oct 2002 14:44:28 -0000	1.1.2.20
***************
*** 36,40 ****
          insert_conditions($dbh, $us_fk, $q);
      }
!     if ($q->param("paste_exp_condition"))
      {
  	# do an insert into the db based on $q->param("paste_ec_fk")
--- 36,42 ----
          insert_conditions($dbh, $us_fk, $q);
      }
!     my $pec = $q->param("paste_exp_condition");
!     write_log("pec: $pec");
!     if ($pec)
      {
  	# do an insert into the db based on $q->param("paste_ec_fk")
***************
*** 70,76 ****
      my $message = "";
      my %ch = $q->Vars();
- 
-     $message .= verify_study($dbh, $us_fk, $ch{sty_pk}, 5, $ch{study_name});
- 
      #
      # Actually, we'll die inside is_writeable() if it fails.
--- 72,75 ----
***************
*** 88,91 ****
--- 87,91 ----
          $sth->finish();
      }
+     $message .= verify_study($dbh, $us_fk, $ch{sty_pk}, 5, $ch{study_name});
      return $message;
  }
***************
*** 318,321 ****
--- 318,322 ----
      {
  	$message = "17m"; # see messages() in sessionlib.pl
+ 	return $message;
      }
  
***************
*** 339,343 ****
              (?,trim(?),trim(?),?,trim(?),trim(?),trim(?),trim(?),trim(?),trim(?))";
      $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
!     $sth->execute($r_hr->{sty_fk},
  		  $r_hr->{name},
  		  $r_hr->{notes},
--- 340,345 ----
              (?,trim(?),trim(?),?,trim(?),trim(?),trim(?),trim(?),trim(?),trim(?))";
      $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
!     # use the sty_pk of the study we are editing, NOT the sty_fk of the exp_cond we are pasting.
!     $sth->execute($ch{sty_pk}, 
  		  $r_hr->{name},
  		  $r_hr->{notes},
***************
*** 350,354 ****
  		  $r_hr->{abbrev_name}) || die "$sql\n$DBI::errstr\n";
      $sth->finish();
!     insert_security($dbh, $us_fk, $us_fk, 0);
      return $message;
  }
--- 352,357 ----
  		  $r_hr->{abbrev_name}) || die "$sql\n$DBI::errstr\n";
      $sth->finish();
!     my $ec_pk = insert_security($dbh, $us_fk, $us_fk, 0);
!     write_log("inserted $ec_pk with sty_fk $r_hr->{sty_fk}");
      return $message;
  }

[Genex-cvs-commit] genex-server/archive - New directory

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/archive
In directory usw-pr-cvs1:/tmp/cvs-serv24412/archive

Log Message:
Directory /cvsroot/genex/genex-server/archive added to the repository
--> Using per-directory sticky tag `Rel-1_0_1-branch'

[Genex-cvs-commit] genex-server/webtools edit_study2.pl,1.1.2.18,1.1.2.19 edit_study1.html,1.1.2.14,1.1.2.15 sessionlib.pl,1.1.2.41,1.1.2.42 edit_study1.pl,1.1.2.15,1.1.2.16

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv18532

Modified Files:
      Tag: Rel-1_0_1-branch
	edit_study2.pl edit_study1.html sessionlib.pl edit_study1.pl 
Log Message:
Finished new feature to paste in an experimental condition from another 
study. Also found and fixed a bug in the dupliate exp. cond. name testing.
The paste feature is necessary for creating an 'analysis study'.


Index: edit_study2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study2.pl,v
retrieving revision 1.1.2.18
retrieving revision 1.1.2.19
diff -C2 -d -r1.1.2.18 -r1.1.2.19
*** edit_study2.pl	23 Oct 2002 15:46:56 -0000	1.1.2.18
--- edit_study2.pl	23 Oct 2002 18:59:34 -0000	1.1.2.19
***************
*** 38,43 ****
      if ($q->param("paste_exp_condition"))
      {
! 	# do an insert into the db based on fields in $ch{paste_ec_fk}
! 	# or maybe $q->param("paste_ec_fk")
      }
      
--- 38,44 ----
      if ($q->param("paste_exp_condition"))
      {
! 	# do an insert into the db based on $q->param("paste_ec_fk")
! 	$iec_flag = 1;
! 	$message .= paste_exp_condition($dbh, $us_fk, $q);
      }
      
***************
*** 214,224 ****
          }
          
-         my $temp = verify_exp($dbh, $us_fk, $all_ch{sty_pk}, 14, $ch{name}, $ch{abbrev_name});
-         if ($temp &&
-             $message !~ m/^$temp|m$temp/)
-         {
-             $message .= "$temp";
-         }
- 
          if (is_writeable($dbh, "exp_condition", "ec_pk", $ch{ec_pk}, $us_fk) == 1)
          {
--- 215,218 ----
***************
*** 237,240 ****
--- 231,258 ----
          }
      }
+     
+     #
+     # Oct 23, 2002 Tom:
+     # This has to come after the write, because the user may have changed values,
+     # and veryify_exp() reads the db, and it can't get a correct answer from that
+     # until ALL the exps have all been written to the db.
+     # 
+     for($xx=0; $xx <= $exp_count; $xx++)
+     {
+         #
+         # Skip deleted entries.
+         # Huh? I thought deleted entries were undef'd above. We should not find any here.
+         #
+         if (! $all_ch{"ec_pk_$xx"})
+         {
+             next;
+         }
+         my $temp = verify_exp($dbh, $us_fk, $all_ch{sty_pk}, 14, $all_ch{"name_$xx"}, $all_ch{"abbrev_name_$xx"});
+         if ($temp &&
+             $message !~ m/^$temp|m$temp/)
+         {
+             $message .= "$temp";
+         }
+     }
      return $message;
  }
***************
*** 274,276 ****
--- 292,354 ----
          }
      }
+ }
+ 
+ sub paste_exp_condition
+ {
+     (my $dbh, my $us_fk, my $q) = @_;
+     my $message = "";
+ 
+     my %ch = $q->Vars();
+     
+     #
+     # There is a top and bottom paste button numbered 1 and 2. The form better
+     # not have just a plain old paste_ec_fk, because we'll overwrite it here.
+     # We need to determine which value the user chose, and if the user chose
+     # both, we will only use the first (1).
+     # 
+     if ($ch{paste_ec_fk1})
+     {
+ 	$ch{paste_ec_fk} = $ch{paste_ec_fk1};
+     }
+     elsif ($ch{paste_ec_fk2})
+     {
+ 	$ch{paste_ec_fk} = $ch{paste_ec_fk2};
+     }
+     else
+     {
+ 	$message = "17m"; # see messages() in sessionlib.pl
+     }
+ 
+     (my $fclause, my $wclause) = read_where_clause("exp_condition", "ec_pk", $us_fk );
+     my $sql = "select * from exp_condition, $fclause where ec_pk=$ch{paste_ec_fk} and $wclause";
+     my $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
+     $sth->execute() || die "$sql\n$DBI::errstr\n";
+     my $rows = $sth->rows();
+     if ($rows != 1)
+     {
+ 	# opps. 
+ 	die "Expecting 1 row, got $rows.\n$sql\n";
+     }
+     # r_hr record hash reference
+     my $r_hr = $sth->fetchrow_hashref();
+     $sth->finish();
+ 
+     $sql = "insert into exp_condition 
+             (sty_fk,name,notes,spc_fk,tissue_type,cell_line,description,sample_treatment,sample_type,abbrev_name) 
+             values 
+             (?,trim(?),trim(?),?,trim(?),trim(?),trim(?),trim(?),trim(?),trim(?))";
+     $sth = $dbh->prepare($sql) || die "$sql\n$DBI::errstr\n";
+     $sth->execute($r_hr->{sty_fk},
+ 		  $r_hr->{name},
+ 		  $r_hr->{notes},
+ 		  $r_hr->{spc_fk},
+ 		  $r_hr->{tissue_type},
+ 		  $r_hr->{cell_line},
+ 		  $r_hr->{description},
+ 		  $r_hr->{sample_treatment},
+ 		  $r_hr->{sample_type},
+ 		  $r_hr->{abbrev_name}) || die "$sql\n$DBI::errstr\n";
+     $sth->finish();
+     insert_security($dbh, $us_fk, $us_fk, 0);
+     return $message;
  }

Index: edit_study1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study1.html,v
retrieving revision 1.1.2.14
retrieving revision 1.1.2.15
diff -C2 -d -r1.1.2.14 -r1.1.2.15
*** edit_study1.html	23 Oct 2002 15:46:56 -0000	1.1.2.14
--- edit_study1.html	23 Oct 2002 18:59:34 -0000	1.1.2.15
***************
*** 36,40 ****
  
    <br>
!   <table width="760" border="1" cellspacing="0" cellpadding="0">
      <tr valign="top"> 
        <td width="306"> Add a blank, empty experimental condition.<br>
--- 36,40 ----
  
    <br>
!   <table width="700" border="1" cellspacing="0" cellpadding="4">
      <tr valign="top"> 
        <td width="306"> Add a blank, empty experimental condition.<br>
***************
*** 43,48 ****
        <td width="448"> Paste in an experimental condition from another study. 
          Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="paste_exp_condition" value="Copy">
!         {exp_select}</td>
      </tr>
    </table>
--- 43,48 ----
        <td width="448"> Paste in an experimental condition from another study. 
          Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="paste_exp_condition" value="Paste">
!         {exp_select1}</td>
      </tr>
    </table>
***************
*** 130,135 ****
        <td width="448"> Paste in an experimental condition from another study. 
          Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="paste_exp_condition" value="Copy">
!         {exp_select}</td>
      </tr>
    </table>
--- 130,135 ----
        <td width="448"> Paste in an experimental condition from another study. 
          Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="paste_exp_condition" value="Paste">
!         {exp_select2}</td>
      </tr>
    </table>

Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.41
retrieving revision 1.1.2.42
diff -C2 -d -r1.1.2.41 -r1.1.2.42
*** sessionlib.pl	23 Oct 2002 15:46:56 -0000	1.1.2.41
--- sessionlib.pl	23 Oct 2002 18:59:34 -0000	1.1.2.42
***************
*** 34,37 ****
--- 34,38 ----
      $messages[15] = "One or more of the samples comes from a study with a duplicate name.<br>\n";
      $messages[16] = "One or more of the samples comes from a study with duplicate experimental condition names or duplicate short names.<br>\n";
+     $messages[17] = "You must choose a study/experimental condition in order to paste in an experimental condition<br>\n";
  
      return $messages[$_[0]];
***************
*** 66,69 ****
--- 67,76 ----
  # Moved select_exp() here from edit_sample1.pl
  # It will also be called from edit_study1.pl.
+ # Oct 23, 2002 Tom:
+ # Default selected item needs a "" value. edit_study1.html has two instances
+ # of this, and since both will return values via CGI, only one of them can be good.
+ # In case of dispute we'll choose the first one, but again, the default value
+ # needs to be "".
+ # 
  #
  sub select_exp
***************
*** 95,98 ****
--- 102,106 ----
      my $study_name;
      my $select = "<select name=\"$field_name\">\n";
+     $select .= "<option value=\"\">Study: Exp. Condition</option>\n";
      while(($ec_pk, $name, $sty_fk, $study_name) = $sth->fetchrow_array())
      {

Index: edit_study1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study1.pl,v
retrieving revision 1.1.2.15
retrieving revision 1.1.2.16
diff -C2 -d -r1.1.2.15 -r1.1.2.16
*** edit_study1.pl	23 Oct 2002 15:46:56 -0000	1.1.2.15
--- edit_study1.pl	23 Oct 2002 18:59:34 -0000	1.1.2.16
***************
*** 52,56 ****
      $ch{message} =~ s/(\d+)m/messages($1)/eg;
  
!     $ch{exp_select} = select_exp($dbh, $us_fk, "paste_ec_fk");
  
      (my $fclause, my $wclause) = write_where_clause("study", "sty_pk", $us_fk );
--- 52,57 ----
      $ch{message} =~ s/(\d+)m/messages($1)/eg;
  
!     $ch{exp_select1} = select_exp($dbh, $us_fk, "paste_ec_fk1");
!     $ch{exp_select2} = select_exp($dbh, $us_fk, "paste_ec_fk2");
  
      (my $fclause, my $wclause) = write_where_clause("study", "sty_pk", $us_fk );

[Genex-cvs-commit] genex-server/webtools edit_study2.pl,1.1.2.17,1.1.2.18 edit_sample1.pl,1.1.2.19,1.1.2.20 edit_study1.pl,1.1.2.14,1.1.2.15 sessionlib.pl,1.1.2.40,1.1.2.41 edit_study1.html,1.1.2.13,1.1.2.14

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv11226

Modified Files:
      Tag: Rel-1_0_1-branch
	edit_study2.pl edit_sample1.pl edit_study1.pl sessionlib.pl 
	edit_study1.html 
Log Message:
first round of code mods for enhanced study creation for 
analysis related studies


Index: edit_study2.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study2.pl,v
retrieving revision 1.1.2.17
retrieving revision 1.1.2.18
diff -C2 -d -r1.1.2.17 -r1.1.2.18
*** edit_study2.pl	14 Oct 2002 21:27:55 -0000	1.1.2.17
--- edit_study2.pl	23 Oct 2002 15:46:56 -0000	1.1.2.18
***************
*** 36,40 ****
          insert_conditions($dbh, $us_fk, $q);
      }
! 
      $dbh->commit;
      $dbh->disconnect;
--- 36,45 ----
          insert_conditions($dbh, $us_fk, $q);
      }
!     if ($q->param("paste_exp_condition"))
!     {
! 	# do an insert into the db based on fields in $ch{paste_ec_fk}
! 	# or maybe $q->param("paste_ec_fk")
!     }
!     
      $dbh->commit;
      $dbh->disconnect;

Index: edit_sample1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_sample1.pl,v
retrieving revision 1.1.2.19
retrieving revision 1.1.2.20
diff -C2 -d -r1.1.2.19 -r1.1.2.20
*** edit_sample1.pl	21 Oct 2002 20:54:09 -0000	1.1.2.19
--- edit_sample1.pl	23 Oct 2002 15:46:56 -0000	1.1.2.20
***************
*** 63,67 ****
      my $sample_count = 0;
      my $key;
!     my $select_exp = select_exp($dbh, $us_fk); # do this only once
      my $select_lab_book_owner = select_lab_book_owner($dbh, $us_fk); # do this only once
      while ($s_hashref = $sth->fetchrow_hashref())
--- 63,67 ----
      my $sample_count = 0;
      my $key;
!     my $select_exp = select_exp($dbh, $us_fk, "ec_fk"); # do this only once
      my $select_lab_book_owner = select_lab_book_owner($dbh, $us_fk); # do this only once
      while ($s_hashref = $sth->fetchrow_hashref())

Index: edit_study1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study1.pl,v
retrieving revision 1.1.2.14
retrieving revision 1.1.2.15
diff -C2 -d -r1.1.2.14 -r1.1.2.15
*** edit_study1.pl	21 Oct 2002 20:54:09 -0000	1.1.2.14
--- edit_study1.pl	23 Oct 2002 15:46:56 -0000	1.1.2.15
***************
*** 52,56 ****
      $ch{message} =~ s/(\d+)m/messages($1)/eg;
  
!     $ch{exp_select} = select_exp($dbh, $us_fk);
  
      (my $fclause, my $wclause) = write_where_clause("study", "sty_pk", $us_fk );
--- 52,56 ----
      $ch{message} =~ s/(\d+)m/messages($1)/eg;
  
!     $ch{exp_select} = select_exp($dbh, $us_fk, "paste_ec_fk");
  
      (my $fclause, my $wclause) = write_where_clause("study", "sty_pk", $us_fk );

Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.40
retrieving revision 1.1.2.41
diff -C2 -d -r1.1.2.40 -r1.1.2.41
*** sessionlib.pl	21 Oct 2002 20:54:09 -0000	1.1.2.40
--- sessionlib.pl	23 Oct 2002 15:46:56 -0000	1.1.2.41
***************
*** 71,74 ****
--- 71,80 ----
      my $dbh = $_[0];
      my $us_fk = $_[1];
+     my $field_name = $_[2];
+ 
+     if (! $field_name)
+     {
+ 	$field_name = "ec_fk";
+     }
  
      #
***************
*** 88,92 ****
      my $sty_fk;
      my $study_name;
!     my $select = "<select name=\"ec_fk\">\n";
      while(($ec_pk, $name, $sty_fk, $study_name) = $sth->fetchrow_array())
      {
--- 94,98 ----
      my $sty_fk;
      my $study_name;
!     my $select = "<select name=\"$field_name\">\n";
      while(($ec_pk, $name, $sty_fk, $study_name) = $sth->fetchrow_array())
      {

Index: edit_study1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study1.html,v
retrieving revision 1.1.2.13
retrieving revision 1.1.2.14
diff -C2 -d -r1.1.2.13 -r1.1.2.14
*** edit_study1.html	21 Oct 2002 20:54:10 -0000	1.1.2.13
--- edit_study1.html	23 Oct 2002 15:46:56 -0000	1.1.2.14
***************
*** 1,151 ****
! <html><head><title>Update Experimental Conditions</title></head>
! <body bgcolor="#FFFFFF">
!   <table width="600" border=0 cellpadding=0 cellspacing=0>
!     <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Experimental Conditions Update<br><br>
!     <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
!     </td>
!   </tr>
!   </table>
! <br>
! <font color="#FF0000">{message}</font>
! <br>
! 
! <form action="edit_study2.pl" method=POST>
! <input type="hidden" name="sty_pk" value="{sty_pk}">
! 
! <table width="700" border=0 cellpadding=4 cellspacing=0>
! <tr><td valign="top">
! <div align="right">Study Name &nbsp;&nbsp;</div></td><td><input type="text" name="study_name" value="{study_name}">
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">Study Start Date &nbsp;&nbsp;</div></td><td><input type="text" name="start_date" value="{start_date}">
! </td></tr>
! <tr><td>
! <div align="right">Study Comments &nbsp;&nbsp;</div></td><td> <textarea name="comments" rows=5 cols=40>{comments}</textarea>
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">No. of Exp. Conditions &nbsp;&nbsp;</div>
!       </td>
! <td valign="top">{number_of_conditions}
! &nbsp;&nbsp;&nbsp;
! </td></tr>
! 
! </table>
! 
!   <br>
!   <table width="760" border="1" cellspacing="0" cellpadding="0">
!     <tr valign="top"> 
!       <td width="306"> Add a blank, empty experimental condition.<br>
!         <input type="submit" name="insert_exp_conditions2" value="Add">
!       </td>
!       <td width="448"> Paste in an experimental condition from another study. 
!         Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="Submit" value="Copy">
!         {exp_select}</td>
!     </tr>
!   </table>
!   <br>
!   <br>
!   <br>
!   <loop> 
!   <table width="700" border="0" cellpadding=4 cellspacing=0>
! <tr bgcolor="#2222FF">
! <td>&nbsp;</td><td>&nbsp;</td>
! </tr>
! 
! <tr>
! <td  valign="top"><div align="right">Delete &nbsp;&nbsp;</div></td>
! <td valign="top"><input type="checkbox" name="delete" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! <tr>
! <td><div align="right">*Experimental Condition Name &nbsp;&nbsp;</div></td>
! <td><input type="text" name="name" value="{name}" size="60"><br>
! <input type="hidden" name="ec_pk" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! 
! <tr>
! <td valign="top"><div align="right">* Short name (5 chars. max) &nbsp;&nbsp;</div></td>
! <td>
! <input type="text" name="abbrev_name" value="{abbrev_name}">
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">Notes &nbsp;&nbsp;</div></td>
! <td>
! <textarea name="notes" rows="5" cols="40">{notes}</textarea>
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">*Species &nbsp;&nbsp;</div></td><td>{species_select}</td>
! </tr>
! 
! <tr>
! <td><div align="right">*Sample Type &nbsp;&nbsp;<br></div></td><td>
! <select name="sample_type">
! <option value="none">Please Select</option>
! <option value="tissue">tissue</option>
! <option value="cells">cells</option>
! <option value="total RNA">total RNA</option>
! </select>
! </td>
! </tr>
! 
! <tr>
! <td width="300" valign="top">
! If your Sample type is cells, please fill in "Cell Line/Cell Type" below.
! </td>
! 
! <td valign="top">
! If your Sample type is tissue, please fill in "Tissue Type" below.
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><nobr>*Cell Line/Cell Type <input type=text name="cell_line" value="{cell_line}"></nobr></td>
! <td valign="top">OR &nbsp;&nbsp;&nbsp;*Tissue Type <input type=text name="tissue_type" value="{tissue_type}"></td>
! </tr>
! 
! <tr>
! <td><div align="right">Description &nbsp;&nbsp;</div></td><td><input type=text name="description" value="{description}" size="60"><br></td>
! </tr>
! 
! </table>
! <br><br>
!   </loop> 
!   <table width="760" border="1" cellspacing="0" cellpadding="0">
!     <tr valign="top"> 
!       <td width="306"> Add a blank, empty experimental condition.<br>
!         <input type="submit" name="insert_exp_conditions22" value="Add">
!       </td>
!       <td width="448"> Paste in an experimental condition from another study. 
!         Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="Submit2" value="Copy">
!         {exp_select}</td>
!     </tr>
!   </table>
!   <br><br>
! <input type=submit name="Finish" value="Finish">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="./">Cancel</a>
! 
! </form>
! <br>
! * Please complete these fields. This information is required before your order 
! is processed by the microarray center. <br>
! <br>
! <table width="700" border=0 cellpadding=0 cellspacing=0>
! <tr><td>
! Study names already in use:
! {sn_list}
! </td></tr></table>
! 
! </body>
! </html>
--- 1,151 ----
! <html><head><title>Update Experimental Conditions</title></head>
! <body bgcolor="#FFFFFF">
!   <table width="600" border=0 cellpadding=0 cellspacing=0>
!     <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Experimental Conditions Update<br><br>
!     <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
!     </td>
!   </tr>
!   </table>
! <br>
! <font color="#FF0000">{message}</font>
! <br>
! 
! <form action="edit_study2.pl" method=POST>
! <input type="hidden" name="sty_pk" value="{sty_pk}">
! 
! <table width="700" border=0 cellpadding=4 cellspacing=0>
! <tr><td valign="top">
! <div align="right">Study Name &nbsp;&nbsp;</div></td><td><input type="text" name="study_name" value="{study_name}">
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">Study Start Date &nbsp;&nbsp;</div></td><td><input type="text" name="start_date" value="{start_date}">
! </td></tr>
! <tr><td>
! <div align="right">Study Comments &nbsp;&nbsp;</div></td><td> <textarea name="comments" rows=5 cols=40>{comments}</textarea>
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">No. of Exp. Conditions &nbsp;&nbsp;</div>
!       </td>
! <td valign="top">{number_of_conditions}
! &nbsp;&nbsp;&nbsp;
! </td></tr>
! 
! </table>
! 
!   <br>
!   <table width="760" border="1" cellspacing="0" cellpadding="0">
!     <tr valign="top"> 
!       <td width="306"> Add a blank, empty experimental condition.<br>
!         <input type="submit" name="insert_exp_conditions" value="Add">
!       </td>
!       <td width="448"> Paste in an experimental condition from another study. 
!         Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="paste_exp_condition" value="Copy">
!         {exp_select}</td>
!     </tr>
!   </table>
!   <br>
!   <br>
!   <br>
!   <loop> 
!   <table width="700" border="0" cellpadding=4 cellspacing=0>
! <tr bgcolor="#2222FF">
! <td>&nbsp;</td><td>&nbsp;</td>
! </tr>
! 
! <tr>
! <td  valign="top"><div align="right">Delete &nbsp;&nbsp;</div></td>
! <td valign="top"><input type="checkbox" name="delete" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! <tr>
! <td><div align="right">*Experimental Condition Name &nbsp;&nbsp;</div></td>
! <td><input type="text" name="name" value="{name}" size="60"><br>
! <input type="hidden" name="ec_pk" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! 
! <tr>
! <td valign="top"><div align="right">* Short name (5 chars. max) &nbsp;&nbsp;</div></td>
! <td>
! <input type="text" name="abbrev_name" value="{abbrev_name}">
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">Notes &nbsp;&nbsp;</div></td>
! <td>
! <textarea name="notes" rows="5" cols="40">{notes}</textarea>
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">*Species &nbsp;&nbsp;</div></td><td>{species_select}</td>
! </tr>
! 
! <tr>
! <td><div align="right">*Sample Type &nbsp;&nbsp;<br></div></td><td>
! <select name="sample_type">
! <option value="none">Please Select</option>
! <option value="tissue">tissue</option>
! <option value="cells">cells</option>
! <option value="total RNA">total RNA</option>
! </select>
! </td>
! </tr>
! 
! <tr>
! <td width="300" valign="top">
! If your Sample type is cells, please fill in "Cell Line/Cell Type" below.
! </td>
! 
! <td valign="top">
! If your Sample type is tissue, please fill in "Tissue Type" below.
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><nobr>*Cell Line/Cell Type <input type=text name="cell_line" value="{cell_line}"></nobr></td>
! <td valign="top">OR &nbsp;&nbsp;&nbsp;*Tissue Type <input type=text name="tissue_type" value="{tissue_type}"></td>
! </tr>
! 
! <tr>
! <td><div align="right">Description &nbsp;&nbsp;</div></td><td><input type=text name="description" value="{description}" size="60"><br></td>
! </tr>
! 
! </table>
! <br><br>
!   </loop> 
!   <table width="760" border="1" cellspacing="0" cellpadding="0">
!     <tr valign="top"> 
!       <td width="306"> Add a blank, empty experimental condition.<br>
!         <input type="submit" name="insert_exp_conditions" value="Add">
!       </td>
!       <td width="448"> Paste in an experimental condition from another study. 
!         Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="paste_exp_condition" value="Copy">
!         {exp_select}</td>
!     </tr>
!   </table>
!   <br><br>
! <input type=submit name="Finish" value="Finish">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="./">Cancel</a>
! 
! </form>
! <br>
! * Please complete these fields. This information is required before your order 
! is processed by the microarray center. <br>
! <br>
! <table width="700" border=0 cellpadding=0 cellspacing=0>
! <tr><td>
! Study names already in use:
! {sn_list}
! </td></tr></table>
! 
! </body>
! </html>

[Genex-cvs-commit] genex-server/G2G/mason generate_group.html.in,NONE,1.1 add_user_to_group.html.in,1.1,1.2 generate_user.html.in,1.1,1.2

[<mwi...@us...>]

Update of /cvsroot/genex/genex-server/G2G/mason
In directory usw-pr-cvs1:/tmp/cvs-serv3865

Modified Files:
	add_user_to_group.html.in generate_user.html.in 
Added Files:
	generate_group.html.in 
Log Message:
added the group creation mason html.  Updated the add user and user-to-group scripts, but the latter is now redundant and should probably be removed.

--- NEW FILE: generate_group.html.in ---
% if (($response_page ne "DONE")) { 
        <center>
        <h1>Create New Genex User</h1>
        <form action="generate_group.html"><br>
        <br>
% if ($response_page eq "BadGroups"){
        <h3><font color="red">You chose an invalid group as having readonly or read/write access</font></h3>
% }
% if ($response_page eq "GroupExists"){
        <h3><font color="red">The group you are trying to create already exists</font></h3>
% }
% if ($response_page eq "BadSUPassword"){
        <h3><font color="red">You entered an incorrect superuser password</font></h3>
% }
        <table cellpadding="2" cellspacing="2" border="0"
         style="width: 70%; text-align: left; margin-left: auto; margin-right: auto;"
         title="Enter the following information for your user"
         summary="information about the new genex user">
          <caption><br>
          </caption>  <tbody>
            <tr>
              <td valign="top">Superuser Password<br>
              </td>
              <td valign="top"><input name="SU_PASSWORD" type="password" width="12" value="<% $SU_PASSWORD %>"></td>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top"><br>
              <br>
              </td>
            </tr>
            <tr>
              <td valign="top">New Genex Group Name<br>
              </td>
              <td valign="top"><input name="groupname" type="text" width="12" value="<% $groupname %>"></td>
              <td valign="top"><br>
              </td>
              <td valign="top"></td>
            </tr>
            <tr>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top"><br>
              <br>
              </td>
            </tr>
            <tr>
              <td valign="top">Details:<br>
              </td>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top"><br>
              <br>
              </td>
            </tr>
            <tr>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top">Readonly By Group<br>
              <br>
              </td>
              <td valign="top">
            <Select name='ro_by'>
% foreach my $group(@group_names) {        
            <option value="<% $group %>"><% $group %>
%}
            </Select>
         </td>
              <td valign="top"><br>
              <br>
              </td>
            </tr>
            <tr>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top">Editable By Group<br>
              </td>
              <td valign="top">
            <Select name='rw_by'>
% foreach my $group(@group_names) {        
            <option value="<% $group %>"><% $group %>
%}
            </Select>
          </td>
              <td valign="top"><br>
              <br>
              </td>
            </tr>
            <tr>
              <td valign="top"><br>
              <br>
              </td>
              <td valign="top">Description of this Group<br>
              </td>
              <td valign="top" colspan="2"><textarea width="40" height="7" name="description"><% $description %></textarea></td>
            </tr>
                                   
          </tbody>
        </table>
        <br>
        <input name="submitted" type="hidden" value="true">
        <input type="submit" name="submit" value="Create This Group"><br>
        <br>
        <br>
        last modified Oct 12, 2002<br>
        </center>
% }

% if ($response_page eq "DONE"){
    
        <div style="text-align: center;">
        <h1>Genex Group Created</h1>
        
% }

<%attr>
  action=>'%%GENEX_WORKSPACE_URL%%/generate_group.html'
  name=>'Create New Genex Group'
  path=>'%%GENEX_WORKSPACE_URL%%/generate_group.html'
</%attr>
<%args>
    $groupname => ""
    $SU_PASSWORD => ""
    $ro_by => ""
    $rw_by => ""
    $description => ""
    $submitted => ""
    $debug => 0
</%args>
<%once>;
</%once>
<%init>;
my $VERSION = '$Id: generate_group.html.in,v 1.1 2002/10/22 16:33:14 mwilkinson Exp $ ';
use Carp;
use Getopt::Long;
use File::Basename;
%%GENEX_EXTRALIBS%%
use Bio::Genex;
use Bio::Genex::Connect;
use Bio::Genex::GroupSec;
use Bio::Genex::Contact;
use Bio::Genex::GroupLink;
my %OPTIONS;
$OPTIONS{ro_groupname} = "public";
$OPTIONS{rw_groupname} = "superuser";
$OPTIONS{SU_USERNAME} = "genex";  # this is now hard coded
$OPTIONS{dbname} = "%%DB_NAME%%";
$response_page;

# get list of all valid groups for various purposes
my @group_names;
my $db=Bio::Genex::Connect->new(
    USER=>$OPTIONS{SU_USERNAME},
    PASSWORD=>$OPTIONS{SU_PASSWORD},
    DBNAME=>$OPTIONS{dbname},
    );
my @testrw = Bio::Genex::GroupSec->get_all_objects($db);
#returns all group objects
foreach (@testrw){
    # get just the names (text) of these groups
    push @group_names, $_->name;  
}

# set predictable default if this variable doesnt exist
$OPTIONS{rw_groupname} = $OPTIONS{rw_groupname}?$OPTIONS{rw_groupname}:"superuser";  

if ($submitted ne "true"){  # this is a fresh load of the page
    $response_page="NEW";
} elsif (!$SU_PASSWORD){    # missing password
    $response_page="BadSUPassword";
} elsif (grep (/$groupname/, @group_names)) {
    $response_page="GroupExists"; # creating a group that already exists
} else {
    my $g = Bio::Genex::GroupSec->new();
    $g->name($groupname);
    my @testro;
    my @testrw;

    @testro = Bio::Genex::GroupSec->get_objects($db,$ro_by);
    @testrw = Bio::Genex::GroupSec->get_objects($db,$rw_by);
    if ($testro[0] && $testrw[0]){
        # this should always be valid if the user is using the HTML page
        $g->ro_groupname_obj($testro[0]);
        $g->rw_groupname_obj($testrw[0]);
        $g->description($description);

        $g->insert_db($db);
        $response_page="DONE";
    } else {
        # but if they are cheating and have created their own CGI page
        $response_page="BadGroups";
    }
}

</%init>

Index: add_user_to_group.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/add_user_to_group.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** add_user_to_group.html.in	17 Oct 2002 00:52:20 -0000	1.1
--- add_user_to_group.html.in	22 Oct 2002 16:33:14 -0000	1.2
***************
*** 10,13 ****
--- 10,20 ----
            <tbody>
              <tr>
+               <td valign="top">Superuser Password:<br>
+               </td>
+               <td valign="top">
+                 <input type = "password" name="SU_PASSWORD">
+               <td valign="top">
+             </tr>
+             <tr>
                <td valign="top">Which User?<br>
                </td>
***************
*** 92,96 ****
  </%once>
  <%init>;
! 
  use Carp;
  use Getopt::Long;
--- 99,103 ----
  </%once>
  <%init>;
! my $VERSION = '$Id$ ';
  use Carp;
  use Getopt::Long;
***************
*** 103,114 ****
  use Bio::Genex::GroupLink;
  
! #my $ro_groupname = %%GENEX_RO_GROUPNAME%%;
! #my $rw_groupname = %%GENEX_RW_GROUPNAME%%;
! my $ro_groupname = "public";
! my $rw_groupname = "superuser";
! my $SU_USERNAME = "genex";  # this is now hard coded
! my $dbname = "%%DB_NAME%%";
  my $response_page;
! my $db=Bio::Genex::Connect->new(USER=>$SU_USERNAME, PASSWORD=>$SU_PASSWORD, DBNAME=>$dbname);
  my @activegroups;  # holds the names of the groups to which this user belongs
  
--- 110,123 ----
  use Bio::Genex::GroupLink;
  
! my $OPTIONS{ro_groupname} = "public";
! my $OPTIONS{rw_groupname} = "superuser";
! my $OPTIONS{SU_USERNAME} = "genex";  # this is now hard coded
! my $OPTIONS{dbname} = "%%DB_NAME%%";
  my $response_page;
! my $db=Bio::Genex::Connect->new(
!     USER=>$OPTIONS{SU_USERNAME},
!     PASSWORD=>$OPTIONS{SU_PASSWORD},
!     DBNAME=>$OPTIONS{dbname},
!     );
  my @activegroups;  # holds the names of the groups to which this user belongs
  
***************
*** 116,149 ****
  my @groupnames;  # holds the names of all groups that exist
  my @usernames;   # holds the names of all users that exist
! my @allgroups = Bio::Genex::GroupSec->get_all_objects($db); #returns objects
  foreach (@allgroups){
      push @groupnames, $_->name;
  }
  my @allusers = Bio::Genex::UserSec->get_all_objects($db);
  foreach (@allusers){
      push @usernames, $_->username;
  }
- my $entered;
- $rw_groupname = $rw_groupname?$rw_groupname:"superuser";  # set predictable default if this variable doesnt exist
  
! if ($submitted ne "true"){  # this is a fresh load of the page
      $response_page="NEW";
! } elsif (!$username || !(grep (/$username/, @usernames))){    # missing or invalid username
      $response_page="BadUsername";
  } elsif ($groupname && !(grep (/$groupname/, @groupnames))) {
      $response_page="BadGroup";
  } elsif (!$modified) {
      my @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
!     @activegroups = map {if ($_->username eq $username){$_->groupname}} @grouplinks;
  }else {
      my @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
!     my @former_groups = map {if ($_->username eq $username){$_->groupname}} @grouplinks;
      foreach my $group(@{$new_group_assoc}){
          next if (grep {/^$group$/} @former_groups);
!         $entered = "yes";
          my $sth = $db->prepare("insert into GroupLink (username, groupname) values ('$username', '$group')");
          $sth->execute;
      }
      
      foreach my $group(@former_groups){
          next if (grep {/^$group$/} @{$new_group_assoc});
--- 125,184 ----
  my @groupnames;  # holds the names of all groups that exist
  my @usernames;   # holds the names of all users that exist
! my @allgroups = Bio::Genex::GroupSec->get_all_objects($db); #objects
  foreach (@allgroups){
+     # get the names of each group in the database
      push @groupnames, $_->name;
  }
  my @allusers = Bio::Genex::UserSec->get_all_objects($db);
  foreach (@allusers){
+     # get the usernames of every user in the database
      push @usernames, $_->username;
  }
  
! # set predictable default if this variable doesnt exist
! $rw_groupname = $rw_groupname?$rw_groupname:"superuser";  
! 
! if ($submitted ne "true"){
!     # this is a fresh load of the page
      $response_page="NEW";
! } elsif (!$username || !(grep (/$username/, @usernames))){
!     # missing or invalid username
      $response_page="BadUsername";
  } elsif ($groupname && !(grep (/$groupname/, @groupnames))) {
+     # missing or invalid group name
      $response_page="BadGroup";
  } elsif (!$modified) {
+     # we have received the username to work with, but have not yet
+     # presented the client with the option to change the group-
+     # association of this user.  We first need to get the current
+     # group association list of this user by:
+     
+     # getting all groups 
      my @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
!     # then checking if that user maps onto that group.
!     @activegroups = map {
!         if ($_->username eq $username){$_->groupname}
!         } @grouplinks;
  }else {
+     # we now have a new list of group associations for this user
+     # again, we have to check what their former state was by retriving
+     # all groups and comparing this username against them
      my @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
!     my @former_groups = map {
!         if ($_->username eq $username){$_->groupname}
!         } @grouplinks;
!         
!     # now go through the list of group associations that were passed
!     # from the CGI
      foreach my $group(@{$new_group_assoc}){
+         # ignore if we already know about this group
          next if (grep {/^$group$/} @former_groups);
!         # otherwise, it must be new, so create the entry
          my $sth = $db->prepare("insert into GroupLink (username, groupname) values ('$username', '$group')");
          $sth->execute;
      }
      
+     # now we have to do the converse, remove this user from any groups
+     # he/she is no longer associated with
      foreach my $group(@former_groups){
          next if (grep {/^$group$/} @{$new_group_assoc});
***************
*** 151,157 ****
      }
      $response_page="DONE";
! 
      @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
!     @activegroups = map {if ($_->username eq $username){$_->groupname}} @grouplinks;
  }
  
--- 186,195 ----
      }
      $response_page="DONE";
!     # refresh out list of current associations and present it back to
!     # the client as a fait d'accompli
      @grouplinks = Bio::Genex::GroupLink->get_all_objects($db);
!     @activegroups = map {
!         if ($_->username eq $username){$_->groupname}
!         } @grouplinks;
  }
  

Index: generate_user.html.in
===================================================================
RCS file: /cvsroot/genex/genex-server/G2G/mason/generate_user.html.in,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** generate_user.html.in	13 Oct 2002 22:23:24 -0000	1.1
--- generate_user.html.in	22 Oct 2002 16:33:14 -0000	1.2
***************
*** 256,260 ****
  </%once>
  <%init>;
! 
  use Carp;
  use Getopt::Long;
--- 256,260 ----
  </%once>
  <%init>;
! my $VERSION = '$Id$ ';
  use Carp;
  use Getopt::Long;
***************
*** 267,304 ****
  use Bio::Genex::GroupLink;
  
! #my $ro_groupname = %%GENEX_RO_GROUPNAME%%;
! #my $rw_groupname = %%GENEX_RW_GROUPNAME%%;
! my $ro_groupname = "public";
! my $rw_groupname = "superuser";
! my $SU_USERNAME = "superuser";
! my $SU_PASSWORD = "superuser";
  
  my $response_page;
- my $dbname = "%%DB_NAME%%";
  
! $SU_USERNAME = "genex";
! $SU_PASSWORD = "genex";
! $rw_groupname = $rw_groupname?$rw_groupname:"superuser";  # set predictable default if this variable doesn't exist;
! 
! 
! unless ($submitted eq "true"){
      $response_page="NEW";
! }
! else {
      if  (((!$username) && (!$password)) || ($password ne $password2)){
!         $response_page="badUP";
      } elsif (!$organization){
!         $response_page="badORG";
      } else {
! 
!         my $db=Bio::Genex::Connect->new(USER=>$SU_USERNAME, PASSWORD=>$SU_PASSWORD, DBNAME=>$dbname);
          my $sth = $db->prepare("create user $username with password '$password' nocreatedb nocreateuser");
!         unless ($sth) {$response_page="badUP";
          } else {
- 
              $sth->execute();
  
!             my $u = Bio::Genex::UserSec->new(dbh=>$db);
!             my $c = Bio::Genex::Contact->new(dbh=>$db);
  
              #okay, start filling in the database
--- 267,302 ----
  use Bio::Genex::GroupLink;
  
! my %OPTIONS;
! $OPTIONS{ro_groupname} = "public";
! $OPTIONS{rw_groupname} = "superuser";
! $OPTIONS{dbname} = "%%DB_NAME%%";
! $OPTIONS{SU_USERNAME} = "genex";
! $OPTIONS{SU_PASSWORD} = "genex";
! $OPTIONS{rw_groupname} = $OPTIONS{rw_groupname}?$OPTIONS{rw_groupname}:"superuser";
! # set predictable default if this variable doesn't exist;
  
  my $response_page;
  
! unless ($submitted eq "true"){ # first time only, never clicked the button
      $response_page="NEW";
! } else {
      if  (((!$username) && (!$password)) || ($password ne $password2)){
!         $response_page="badUP"; # BAD USERNAME/PASSWORD
      } elsif (!$organization){
!         $response_page="badORG"; # BAD ORGANIZATION
      } else {
!         my $db=Bio::Genex::Connect->new(
!             USER=>$OPTIONS{SU_USERNAME},
!             PASSWORD=>$OPTIONS{SU_PASSWORD},
!             DBNAME=>$OPTIONS{dbname},
!             );
          my $sth = $db->prepare("create user $username with password '$password' nocreatedb nocreateuser");
!         unless ($sth) {
!             $response_page="badUP"; # BAD USERNAME AND PASSWORD
          } else {
              $sth->execute();
  
!             my $u = Bio::Genex::UserSec->new();
!             my $c = Bio::Genex::Contact->new();
  
              #okay, start filling in the database

[Genex-cvs-commit] genex-server/webtools edit_study1.pl,1.1.2.13,1.1.2.14 sessionlib.pl,1.1.2.39,1.1.2.40 edit_sample1.pl,1.1.2.18,1.1.2.19 edit_study1.html,1.1.2.12,1.1.2.13

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv18591

Modified Files:
      Tag: Rel-1_0_1-branch
	edit_study1.pl sessionlib.pl edit_sample1.pl edit_study1.html 
Log Message:
adding paste function when adding exp. conds to a study.


Index: edit_study1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study1.pl,v
retrieving revision 1.1.2.13
retrieving revision 1.1.2.14
diff -C2 -d -r1.1.2.13 -r1.1.2.14
*** edit_study1.pl	14 Oct 2002 21:27:55 -0000	1.1.2.13
--- edit_study1.pl	21 Oct 2002 20:54:09 -0000	1.1.2.14
***************
*** 52,55 ****
--- 52,57 ----
      $ch{message} =~ s/(\d+)m/messages($1)/eg;
  
+     $ch{exp_select} = select_exp($dbh, $us_fk);
+ 
      (my $fclause, my $wclause) = write_where_clause("study", "sty_pk", $us_fk );
      my $sql = "select study_name,comments,start_date from study, $fclause where sty_pk=$ch{sty_pk} and $wclause";

Index: sessionlib.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/sessionlib.pl,v
retrieving revision 1.1.2.39
retrieving revision 1.1.2.40
diff -C2 -d -r1.1.2.39 -r1.1.2.40
*** sessionlib.pl	14 Oct 2002 21:27:51 -0000	1.1.2.39
--- sessionlib.pl	21 Oct 2002 20:54:09 -0000	1.1.2.40
***************
*** 62,65 ****
--- 62,101 ----
  }
  
+ #
+ # Oct 21, 2002 Tom:
+ # Moved select_exp() here from edit_sample1.pl
+ # It will also be called from edit_study1.pl.
+ #
+ sub select_exp
+ {
+     my $dbh = $_[0];
+     my $us_fk = $_[1];
+ 
+     #
+     # Get all the ec_pk's I can read.
+     # Maybe later we want to only get ec_pk's that I own.
+     #
+     my $where_clause;
+     my $from_clause;
+     ($from_clause, $where_clause) = read_where_clause("exp_condition", "ec_pk", $us_fk);
+     my $sql = "select ec_pk,exp_condition.name,exp_condition.sty_fk,study_name
+                from study,exp_condition,$from_clause
+                where ($where_clause and exp_condition.sty_fk=study.sty_pk) order by study_name,exp_condition.name";
+     my $sth = $dbh->prepare($sql);
+     $sth->execute() || die "$sql\n$DBI::errstr\n";
+     my $ec_pk;
+     my $name;
+     my $sty_fk;
+     my $study_name;
+     my $select = "<select name=\"ec_fk\">\n";
+     while(($ec_pk, $name, $sty_fk, $study_name) = $sth->fetchrow_array())
+     {
+         $select .= "<option value=\"$ec_pk\">$study_name: $name</option>\n";
+     }
+     $select .= "</select>\n";
+     
+     return $select;
+ }
+ 
  sub verify_exp
  {

Index: edit_sample1.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_sample1.pl,v
retrieving revision 1.1.2.18
retrieving revision 1.1.2.19
diff -C2 -d -r1.1.2.18 -r1.1.2.19
*** edit_sample1.pl	14 Oct 2002 20:20:34 -0000	1.1.2.18
--- edit_sample1.pl	21 Oct 2002 20:54:09 -0000	1.1.2.19
***************
*** 107,141 ****
  }
  
- sub select_exp
- {
-     my $dbh = $_[0];
-     my $us_fk = $_[1];
- 
-     #
-     # Get all the ec_pk's I can read.
-     # Maybe later we want to only get ec_pk's that I own.
-     #
-     my $where_clause;
-     my $from_clause;
-     ($from_clause, $where_clause) = read_where_clause("exp_condition", "ec_pk", $us_fk);
-     my $sql = "select ec_pk,exp_condition.name,exp_condition.sty_fk,study_name
-                from study,exp_condition,$from_clause
-                where ($where_clause and exp_condition.sty_fk=study.sty_pk) order by study_name,exp_condition.name";
-     my $sth = $dbh->prepare($sql);
-     $sth->execute() || die "$sql\n$DBI::errstr\n";
-     my $ec_pk;
-     my $name;
-     my $sty_fk;
-     my $study_name;
-     my $select = "<select name=\"ec_fk\">\n";
-     while(($ec_pk, $name, $sty_fk, $study_name) = $sth->fetchrow_array())
-     {
-         $select .= "<option value=\"$ec_pk\">$study_name: $name</option>\n";
-     }
-     $select .= "</select>\n";
-     
-     return $select;
- }
- 
  sub select_lab_book_owner
  {
--- 107,110 ----

Index: edit_study1.html
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/edit_study1.html,v
retrieving revision 1.1.2.12
retrieving revision 1.1.2.13
diff -C2 -d -r1.1.2.12 -r1.1.2.13
*** edit_study1.html	11 Oct 2002 18:23:24 -0000	1.1.2.12
--- edit_study1.html	21 Oct 2002 20:54:10 -0000	1.1.2.13
***************
*** 1,128 ****
! <html><head><title>Update Experimental Conditions</title></head>
! <body bgcolor="#FFFFFF">
!   <table width="600" border=0 cellpadding=0 cellspacing=0>
!     <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Experimental Conditions Update<br><br>
!     <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
!     </td>
!   </tr>
!   </table>
! <br>
! <font color="#FF0000">{message}</font>
! <br>
! 
! <form action="edit_study2.pl" method=POST>
! <input type="hidden" name="sty_pk" value="{sty_pk}">
! 
! <table width="700" border=0 cellpadding=4 cellspacing=0>
! <tr><td valign="top">
! <div align="right">Study Name &nbsp;&nbsp;</div></td><td><input type="text" name="study_name" value="{study_name}">
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">Study Start Date &nbsp;&nbsp;</div></td><td><input type="text" name="start_date" value="{start_date}">
! </td></tr>
! <tr><td>
! <div align="right">Study Comments &nbsp;&nbsp;</div></td><td> <textarea name="comments" rows=5 cols=40>{comments}</textarea>
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">No. of Exp. Conditions &nbsp;&nbsp;</div><input type="submit" name="insert_exp_conditions" value="Add an Experimental Condition">
! </td>
! <td valign="top">{number_of_conditions}
! &nbsp;&nbsp;&nbsp;
! </td></tr>
! 
! </table>
! 
! <loop>
! 
! <table width="700" border="0" cellpadding=4 cellspacing=0>
! <tr bgcolor="#2222FF">
! <td>&nbsp;</td><td>&nbsp;</td>
! </tr>
! 
! <tr>
! <td  valign="top"><div align="right">Delete &nbsp;&nbsp;</div></td>
! <td valign="top"><input type="checkbox" name="delete" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! <tr>
! <td><div align="right">*Experimental Condition Name &nbsp;&nbsp;</div></td>
! <td><input type="text" name="name" value="{name}" size="60"><br>
! <input type="hidden" name="ec_pk" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! 
! <tr>
! <td valign="top"><div align="right">* Short name (5 chars. max) &nbsp;&nbsp;</div></td>
! <td>
! <input type="text" name="abbrev_name" value="{abbrev_name}">
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">Notes &nbsp;&nbsp;</div></td>
! <td>
! <textarea name="notes" rows="5" cols="40">{notes}</textarea>
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">*Species &nbsp;&nbsp;</div></td><td>{species_select}</td>
! </tr>
! 
! <tr>
! <td><div align="right">*Sample Type &nbsp;&nbsp;<br></div></td><td>
! <select name="sample_type">
! <option value="none">Please Select</option>
! <option value="tissue">tissue</option>
! <option value="cells">cells</option>
! <option value="total RNA">total RNA</option>
! </select>
! </td>
! </tr>
! 
! <tr>
! <td width="300" valign="top">
! If your Sample type is cells, please fill in "Cell Line/Cell Type" below.
! </td>
! 
! <td valign="top">
! If your Sample type is tissue, please fill in "Tissue Type" below.
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><nobr>*Cell Line/Cell Type <input type=text name="cell_line" value="{cell_line}"></nobr></td>
! <td valign="top">OR &nbsp;&nbsp;&nbsp;*Tissue Type <input type=text name="tissue_type" value="{tissue_type}"></td>
! </tr>
! 
! <tr>
! <td><div align="right">Description &nbsp;&nbsp;</div></td><td><input type=text name="description" value="{description}" size="60"><br></td>
! </tr>
! 
! </table>
! <br><br>
! </loop>
! 
! <input type="submit" name="insert_exp_conditions" value="Add an Experimental Condition">
! <br><br>
! <input type=submit name="Finish" value="Finish">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="./">Cancel</a>
! 
! </form>
! <br>
! * Required fields.
! <br>
! <br>
! <table width="700" border=0 cellpadding=0 cellspacing=0>
! <tr><td>
! Study names already in use:
! {sn_list}
! </td></tr></table>
! 
! </body>
! </html>
--- 1,151 ----
! <html><head><title>Update Experimental Conditions</title></head>
! <body bgcolor="#FFFFFF">
!   <table width="600" border=0 cellpadding=0 cellspacing=0>
!     <tr><td align=top><img src="../graphics/genex_logo.jpg" align="left">GeneX Experimental Conditions Update<br><br>
!     <a href="./">Return to Genex Member Home</a><br><br clear=all><br>
!     </td>
!   </tr>
!   </table>
! <br>
! <font color="#FF0000">{message}</font>
! <br>
! 
! <form action="edit_study2.pl" method=POST>
! <input type="hidden" name="sty_pk" value="{sty_pk}">
! 
! <table width="700" border=0 cellpadding=4 cellspacing=0>
! <tr><td valign="top">
! <div align="right">Study Name &nbsp;&nbsp;</div></td><td><input type="text" name="study_name" value="{study_name}">
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">Study Start Date &nbsp;&nbsp;</div></td><td><input type="text" name="start_date" value="{start_date}">
! </td></tr>
! <tr><td>
! <div align="right">Study Comments &nbsp;&nbsp;</div></td><td> <textarea name="comments" rows=5 cols=40>{comments}</textarea>
! </td></tr>
! 
! <tr><td valign="top">
! <div align="right">No. of Exp. Conditions &nbsp;&nbsp;</div>
!       </td>
! <td valign="top">{number_of_conditions}
! &nbsp;&nbsp;&nbsp;
! </td></tr>
! 
! </table>
! 
!   <br>
!   <table width="760" border="1" cellspacing="0" cellpadding="0">
!     <tr valign="top"> 
!       <td width="306"> Add a blank, empty experimental condition.<br>
!         <input type="submit" name="insert_exp_conditions2" value="Add">
!       </td>
!       <td width="448"> Paste in an experimental condition from another study. 
!         Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="Submit" value="Copy">
!         {exp_select}</td>
!     </tr>
!   </table>
!   <br>
!   <br>
!   <br>
!   <loop> 
!   <table width="700" border="0" cellpadding=4 cellspacing=0>
! <tr bgcolor="#2222FF">
! <td>&nbsp;</td><td>&nbsp;</td>
! </tr>
! 
! <tr>
! <td  valign="top"><div align="right">Delete &nbsp;&nbsp;</div></td>
! <td valign="top"><input type="checkbox" name="delete" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! <tr>
! <td><div align="right">*Experimental Condition Name &nbsp;&nbsp;</div></td>
! <td><input type="text" name="name" value="{name}" size="60"><br>
! <input type="hidden" name="ec_pk" value="{ec_pk}">
! </td>
! </tr>
! 
! 
! 
! <tr>
! <td valign="top"><div align="right">* Short name (5 chars. max) &nbsp;&nbsp;</div></td>
! <td>
! <input type="text" name="abbrev_name" value="{abbrev_name}">
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">Notes &nbsp;&nbsp;</div></td>
! <td>
! <textarea name="notes" rows="5" cols="40">{notes}</textarea>
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><div align="right">*Species &nbsp;&nbsp;</div></td><td>{species_select}</td>
! </tr>
! 
! <tr>
! <td><div align="right">*Sample Type &nbsp;&nbsp;<br></div></td><td>
! <select name="sample_type">
! <option value="none">Please Select</option>
! <option value="tissue">tissue</option>
! <option value="cells">cells</option>
! <option value="total RNA">total RNA</option>
! </select>
! </td>
! </tr>
! 
! <tr>
! <td width="300" valign="top">
! If your Sample type is cells, please fill in "Cell Line/Cell Type" below.
! </td>
! 
! <td valign="top">
! If your Sample type is tissue, please fill in "Tissue Type" below.
! </td>
! </tr>
! 
! <tr>
! <td valign="top"><nobr>*Cell Line/Cell Type <input type=text name="cell_line" value="{cell_line}"></nobr></td>
! <td valign="top">OR &nbsp;&nbsp;&nbsp;*Tissue Type <input type=text name="tissue_type" value="{tissue_type}"></td>
! </tr>
! 
! <tr>
! <td><div align="right">Description &nbsp;&nbsp;</div></td><td><input type=text name="description" value="{description}" size="60"><br></td>
! </tr>
! 
! </table>
! <br><br>
!   </loop> 
!   <table width="760" border="1" cellspacing="0" cellpadding="0">
!     <tr valign="top"> 
!       <td width="306"> Add a blank, empty experimental condition.<br>
!         <input type="submit" name="insert_exp_conditions22" value="Add">
!       </td>
!       <td width="448"> Paste in an experimental condition from another study. 
!         Select from the list, then click 'Paste'.<br>
!         <input type="submit" name="Submit2" value="Copy">
!         {exp_select}</td>
!     </tr>
!   </table>
!   <br><br>
! <input type=submit name="Finish" value="Finish">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="./">Cancel</a>
! 
! </form>
! <br>
! * Please complete these fields. This information is required before your order 
! is processed by the microarray center. <br>
! <br>
! <table width="700" border=0 cellpadding=0 cellspacing=0>
! <tr><td>
! Study names already in use:
! {sn_list}
! </td></tr></table>
! 
! </body>
! </html>

[Genex-cvs-commit] genex-server/webtools insert_order.pl,1.1.2.5,1.1.2.6

[<tw...@us...>]

Update of /cvsroot/genex/genex-server/webtools
In directory usw-pr-cvs1:/tmp/cvs-serv17264

Modified Files:
      Tag: Rel-1_0_1-branch
	insert_order.pl 
Log Message:



Index: insert_order.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/webtools/Attic/insert_order.pl,v
retrieving revision 1.1.2.5
retrieving revision 1.1.2.6
diff -C2 -d -r1.1.2.5 -r1.1.2.6
*** insert_order.pl	9 Oct 2002 20:51:20 -0000	1.1.2.5
--- insert_order.pl	21 Oct 2002 18:24:23 -0000	1.1.2.6
***************
*** 20,24 ****
      my $us_fk = get_us_fk($dbh); # also in sessionlib.pl
      
!     my $order_number = generate_order_number($dbh);
      
      my $today = `date`;
--- 20,24 ----
      my $us_fk = get_us_fk($dbh); # also in sessionlib.pl
      
!     my $order_number = generate_order_number($dbh); # see sub below.
      
      my $today = `date`;

[Genex-cvs-commit] genex-www/content genex-server.ssi,1.4,1.5 main.ssi,1.7,1.8

[<jas...@us...>]

Update of /cvsroot/genex/genex-www/content
In directory usw-pr-cvs1:/tmp/cvs-serv30517

Modified Files:
	genex-server.ssi main.ssi 
Log Message:
genex-2.x alpha release info


Index: genex-server.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/genex-server.ssi,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** genex-server.ssi	20 Oct 2002 21:45:20 -0000	1.4
--- genex-server.ssi	20 Oct 2002 22:18:52 -0000	1.5
***************
*** 1,78 ****
! <!-- GeneX Server content -->
! 
!   <table bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>GeneX Server</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	   <tr bgcolor="#FFD78F">
!       <td><h3>October 1, 2002</h3>
! 	  In January of 2002 GeneX development split to two paths. GeneX 1.x 
! development worked on getting a working schema, fully function data 
! repository, and analysis routines, while GeneX 2.x began work on a MAGE 
! compliant schema. This work on GeneX 1.x has primarily been carried out 
! at the University of Virginia. Various versions have been available to 
! the public since March 2002.<br><br>
! Please feel free to download and install the latest version of GeneX 
! 1.x For more info, scroll to the bottom of the page:<br><br>
! 
! <a href="http://genes.med.virginia.edu/">http://genes.med.virginia.edu/</a><br><br>
! 
! CVS checkout instructions are there. Installation is not as mature as 
! we'd like, but we're happy to answer questions. The primary developer 
! is <a href="mailto:tw...@vi...">Tom Laudeman</a><br><br>
! 
! The lastest release is essentially alpha quality. Nearly all features 
! are present and functioning, but the software has not been fully 
! tested.<br><br>
! 
! Version 1.5.7 has a complete security system (owners, groups, row level 
! permissions), data repository for chip spot data and derived data sets, 
! file management and viewing, analysis modules (functional, but not 
! complete), support for Affymetrix MAS4 and MAS5, experimental condition 
! grouping, and some support for the workflow in the microarray chip 
! center. We also support import of DChip data.<br><br>
! 
! Analysis is mostly via R, and we've created an R wrapper to simplify 
! adding new analyses. We are currently working on a comprehensive 
! analysis system with simplified analysis module installation.<br><br>
! 
! All the interfaces for end users are web based, including curation.<br><br>
! 
! Due to certain system constraints, this is essentially Unix only 
! software. It is based on all open source (or free) software such as 
! Perl and PostreSQL, so it could theoretically be ported to Windows. We have 
! installed and tested GeneX 1.x on Red Hat systems.<br><br>
! 
! We anticipate releasing this to our users by mid October. The new 
! analysis package should be complete around the end of October.
! </td></tr>
! <tr bgcolor="#FFD78F"><td>
! 	<h3>GeneX-Server-1.0.4</h3>
! 	<ul>
!           <li>View the 
! 	    <a href="https://sourceforge.net/project/shownotes.php?release_id=55763">
! 	      Release Notes
! 	    </a> to see what's changed.</li>
! 	  <li>Download the complete
! 	    <a href="https://sourceforge.net/project/showfiles.php?group_id=16453&release_id=55763">
! 	      Server Installer
! 	    </a> from here.</li>
! 	</ul>
!       </td>
!     </tr>
!     <tr>
!       <td>
! 	<h3>Supplementary Packages</h3>
! 	<ul>
!           <li>
! 	    <a href="../download/supplementary/perlSGML.2001Jan23.tar.gz">
! 	      Perl::SGML
! 	    </a> This module is needed to create HTML versions of the
! 	    GeneXML DTD</li>
! 	</ul>
!       </td>
!     </tr>
!   </table>
! 
--- 1,120 ----
! <!-- GeneX Server content -->
! 
!   <table bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>GeneX Server</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	<tr bgcolor="#FFD78F">
! 	  <td>
! 	    <h3>GeneX-Server-2.0.0a-2002-10-20</h3>
! 	    <h4>October 20, 2002</h4>
! 	    <p>This is the first developer's alpha release of the
! 	    Genex-2.x series. Don't even think about installing this
! 	    unless you are an experienced Unix administrator.
! 	    </p>
! 	    <p> You can download it from <a
! 	    href="http://prdownloads.sourceforge.net/genex/genex-server-2.0.0a-2002-10-20.tar.gz?download">SourceForge</a>. or you can check it out from CVS using the following:
! 	    </p>
! 	    <p><tt>cvs -d:pserver:ano...@cv...:/cvsroot/genex login
! <br><br>
! cvs -z3 -d:pserver:ano...@cv...:/cvsroot/genex
! co -r 2.0.0a-2002-10-20_1 genex-server
! </tt>
! 	    </p>
! 	    <p>Send all comments and request to the <a
! 	    href="mailto:gen...@li...">development
! 	    list</a>
! 	    </p>	      
! 	  </td>
! 	</tr>
! 	<tr bgcolor="#FFD78F">
! 	  <td>
! 	    <h3>GeneX-Server-1.5.7</h3>
! 	    <h4>October 1, 2002</h4>
! 	    <p>
! 	  In January of 2002 GeneX development split to two paths. GeneX 1.x 
! development worked on getting a working schema, fully function data 
! repository, and analysis routines, while GeneX 2.x began work on a MAGE 
! compliant schema. This work on GeneX 1.x has primarily been carried out 
! at the University of Virginia. Various versions have been available to 
! the public since March 2002.
! 	    </p>
! 	    <p>
! Please feel free to download and install the latest version of GeneX 
! 1.x For more info, scroll to the bottom of the page:
! 	    </p>
! 	    <p>
! <a
! href="http://genes.med.virginia.edu/">http://genes.med.virginia.edu/</a>
! 	    </p>
! 	    <p>
! CVS checkout instructions are there. Installation is not as mature as 
! we'd like, but we're happy to answer questions. The primary developer 
! is <a href="mailto:tw...@vi...">Tom Laudeman</a>
! 	    </p>
! 	    <p>
! 
! The lastest release is essentially alpha quality. Nearly all features 
! are present and functioning, but the software has not been fully 
! tested.
! 	    </p>
! 	    <p>
! 
! Version 1.5.7 has a complete security system (owners, groups, row level 
! permissions), data repository for chip spot data and derived data sets, 
! file management and viewing, analysis modules (functional, but not 
! complete), support for Affymetrix MAS4 and MAS5, experimental condition 
! grouping, and some support for the workflow in the microarray chip 
! center. We also support import of DChip data.
! 	    </p>
! 	    <p>
! Analysis is mostly via R, and we've created an R wrapper to simplify 
! adding new analyses. We are currently working on a comprehensive 
! analysis system with simplified analysis module installation.
! 	    </p>
! 	    <p>
! All the interfaces for end users are web based, including curation.
! 	    </p>
! 	    <p>
! Due to certain system constraints, this is essentially Unix only 
! software. It is based on all open source (or free) software such as 
! Perl and PostreSQL, so it could theoretically be ported to Windows. We have 
! installed and tested GeneX 1.x on Red Hat systems.
! 	    </p>
! 	    <p>
! We anticipate releasing this to our users by mid October. The new 
! analysis package should be complete around the end of October.
! 	    </p>
! 	  </td>
! 	</tr>
! 	<tr bgcolor="#FFD78F">
! 	  <td>
! 	    <h3>GeneX-Server-1.0.4</h3>
! 	    <ul>
! 	      <li>View the 
! 		<a href="https://sourceforge.net/project/shownotes.php?release_id=55763">
! 		  Release Notes
! 		</a> to see what's changed.</li>
! 	      <li>Download the complete
! 		<a href="https://sourceforge.net/project/showfiles.php?group_id=16453&release_id=55763">
! 		  Server Installer
! 		</a> from here.</li>
! 	    </ul>
! 	  </td>
! 	</tr>
! 	<tr>
! 	  <td>
! 	    <h3>Supplementary Packages</h3>
! 	    <ul>
! 	      <li>
! 		<a href="../download/supplementary/perlSGML.2001Jan23.tar.gz">
! 		  Perl::SGML
! 		</a> This module is needed to create HTML versions of the
! 		GeneXML DTD</li>
! 	    </ul>
! 	  </td>
! 	</tr>
!   </table>
! 

Index: main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/main.ssi,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** main.ssi	20 Oct 2002 21:45:20 -0000	1.7
--- main.ssi	20 Oct 2002 22:18:52 -0000	1.8
***************
*** 1,167 ****
! <!--Main content -->
! 
!   <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>Recent News</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	  <p>
! 	  <u>October 1, 2002</u> - GeneX 1.5.7 Released <br>
! 	  This is a more or less stable version. It has the new user interface to 
! manage/import Affymetrix data. There are three analysis routines, but 
! we a preparing for an overhaul of the analysis tools. To learn more go to 
! the <a href="genex-server.shtml">Download</a> page or the <a href="http://genes.med.virginia.edu/">UVa install</a> of GeneX 1.x. 
! 	</p>
! 	<p>
! 	  <u>Aug 29, 2002</u> - Update Genex-2 Schema information can
! 	  be found 
! 	    <A href="genex-2-schema.shtml">
! 	      here
! 	  </A> (now with hyperlinks!!).
! 	</p>
! 	<p>
! 	  <u>Feb 20, 2002</u> - preliminary information now available
! 	  discussing the future directions of GeneX. It includes links
! 	  to 
! 	  <A href="Timelines.shtml">
! 	    timelines and project descriptions
! 	  </A> from the different sources that are currently funding
! 	  GeneX development.
! 	</p>
! 	<p>
! 	  <u>Feb 8, 2002</u> - preliminary
! 	  <A href="G2G.shtml">
! 	    G2G
! 	  </A> information now available.
! 	</p>
! 	<p>
! 	  <u>Feb 6, 2002</u> - Added the 
! 	  <A href="Development.shtml">
! 	    GeneX Development page
! 	  </A> for helping coordinate GeneX developers.
! 	</p>
! 	<p>
! 	  <u>Jan 31, 2002</u> - GeneX and G2G talk given by Jason
! 	  Stewart at the
! 	  <a href="http://conferences.oreilly.com/biocon/">
! 	    O'Reilly Bioinformatics Technology Conference
! 	  </A>. The slides for the talk are available
! 	  <A href="http://prdownloads.sourceforge.net/genex/Oreilly-G2G.ppt">
! 	    here
! 	  </A>.
! 	</P>	  
! 	<P>
! 	  <u>Oct 4, 2001</u> - GeneX Sourceforge Web site is put
! 	  in place, along with user access to the development
! 	  site and CVS repository.</P> 
! 	<P>
! 	  <u>September, 2001</u> - NCGR commits GeneX
! 	  development to a fully Open Source model, enabling GeneX
! 	  to become a truly <b>community supported project</b></P>
! 	<P>
! 	  <u>August, 2001</u> - 
! 	  <a href="genex-server.shtml">
! 	    GeneX-Server-1.0.4
! 	  </a> released</P>
! 	<P>
! 	  <u>Mar 3, 2001</u> -
! 	  DataLoader project started to support large-scale,
! 	  server-side data entry for GeneX.  In Perl. Fewer
! 	  annotation requirements.</P>
! 	<P>
! 	  <u>Jan 20, 2001</u> - Server install seems to be
! 	  user-configurable; no longer need to be root to install the
! 	  GeneX components (but still need root for some other
! 	  components).  (thanks to Micheal Pear for his input!)</P>
! 	<P>
! 	  <u>Jan 16, 2001</u> - Someone outside of NCGR (Michael
! 	  Pear, UCSD) installs GeneX, loads their own data
! 	  set with the Curation Tool and gets data back from a
! 	  query.</P> 
! 	<P>
! 	  <u>Jan 10th, 2001</u> - CyberT paper accepted</P>
!       </td>
!     </tr>
! 
!       <tr bgcolor="#D8E4F7"><th><big>GeneX Description</big></Th></tr>
!       <tr bgcolor="#D8E4F7"><td>
!         GeneX is an Open Source <em>database</em> system.  It is
!         <em>not</em> a commercial-grade, plug and play system for
!         analyzing single sets of gene expression.<br> 
! 	  The GeneX project consists of 4 parts:
!         <ol>
! 	    <li><b>The Data Loader</b> (Perl) to get your data
!           into the database.  
! 	    <li> <b>The Database itself</b> - the          conceptual
! 	    model of the inter-relationships of the data, as
! 	    well as the implementation of that model in a database
! 	    software system.  Currently GeneX is being run on the
! 	    Open Source PostgreSQL database system as it supports the
! 	    SQL92 std and has proven to be reasonably stable and of
! 	    decent performance so far.
! 	    <li> <b>The XML data exchange protocol</b> (the format
! 	    currently used by OpenGenex is called GeneXML, but it will
! 	    be shifting to the new <a
! 	    href="http://mged.sf.net/downloads.shtml">MAGE-ML</a> standard
! 	    shortly.  
! 	    <li><b>The Query and Analytical routines</b> to
! 	    ask for data from the database and perform          some
! 	    useful act on it, hopefully increasing your
! 	    understanding of the biological processes under
! 	    examination. 
!         </ol>       
! 
!         </td></tr>
! 
!       <tr bgcolor="#B9E4B2"><th><big>Open Source aspects of development</big></Th></tr>
!       <tr bgcolor="#B9E4B2"><td>
!         <b>GeneX is an Open Source Project</b>.  It includes a few
!         useful analytical tools as proof of concept, but it is still
!         an evolving system (tho it's now usable) and we encourage you
!         to install it, try to use it, complain about what doesn't
!         work, give us feedback about what you like and don't like.  IF
!         you can give us specific details about an analysis or
!         interface, we'd certainly appreciate that.  If you can give us
!         code that implements it, we'd <em>really</em> like that.
!         <p>
!         If you have programming skills and you're interested in moving
!         the project along in areas where GeneX is lacking, <em>please</em>
!         contact us and we'll try to help you get started.  If you're a
!         biologist in the area of gene expression and you an algorithm
!         implemented or you see a better way of doing something, please
!         let us know and we'll try to address your problem.
!         <p>
!         We are going to attempt to follow one of the precepts of Open
!         Source - release early and release often.  We'll be following
!         the style of Perl and the Linux kernel - there will be
!         'stable' version and a 'development' version.  The stable
!         version will not change very much over time except for bug
!         patches.  All the new stuff will happen with the developement
!         version, and those who want the latest and greatest version
!         will be able to check out the up-to-the-minute code from our
!         anonymous CVS tree.
!         <p>
!         Initially, all the GeneX developers will be NCGR employees
!         or contractors, but we already have one external developer and
!         hope to attract many more as people become aware of the
!         system.  As one who has been collaborating via anonymous CVs
!         for a while, it's a really fun experience to see the code
!         develop and change like a dynamic living thing from day to
!         day.  Bugs get detected, get corrected, and the code gets
!         better.  That's our hope for GeneX and we hope you can get
!         involved as well.
!       </td></tr>
! 
!       <tr><th><big>What features do you want to see?</big></th></tr>
!       <tr><td>
!         OK - here it is.  <a
!         href="mailto:gen...@li..."><b>Please tell
!         us</b></a> what features you desperately need, which would be
!         really neat, even which you'd be willing to pay for (heh heh).
!         Also tell where we've gone wrong (in your humble opinion).
!       </td></tr>
!       
!     </table>
! 
! <!-- End of Content -->
--- 1,174 ----
! <!--Main content -->
! 
!   <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>Recent News</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	  <p>
! 	  <u>Oct 20, 2002</u> - First Beta release of GeneX 2.0.0 <br>
! 	    <b>WARNING</b> This is strictly a developers release. You
! 	    should <em>not</em> attempt to install this package unless
! 	    you are an experienced Unix admin. See the details on the
! 	    <a href="genex-server.shtml">Download</a> page.
! 	</p>
! 	  <p>
! 	  <u>Oct 1, 2002</u> - GeneX 1.5.7 Released <br>
! 	  This is a more or less stable version. It has the new user interface to 
! manage/import Affymetrix data. There are three analysis routines, but 
! we a preparing for an overhaul of the analysis tools. To learn more go to 
! the <a href="genex-server.shtml">Download</a> page or the <a href="http://genes.med.virginia.edu/">UVa install</a> of GeneX 1.x. 
! 	</p>
! 	<p>
! 	  <u>Aug 29, 2002</u> - Update Genex-2 Schema information can
! 	  be found 
! 	    <A href="genex-2-schema.shtml">
! 	      here
! 	  </A> (now with hyperlinks!!).
! 	</p>
! 	<p>
! 	  <u>Feb 20, 2002</u> - preliminary information now available
! 	  discussing the future directions of GeneX. It includes links
! 	  to 
! 	  <A href="Timelines.shtml">
! 	    timelines and project descriptions
! 	  </A> from the different sources that are currently funding
! 	  GeneX development.
! 	</p>
! 	<p>
! 	  <u>Feb 8, 2002</u> - preliminary
! 	  <A href="G2G.shtml">
! 	    G2G
! 	  </A> information now available.
! 	</p>
! 	<p>
! 	  <u>Feb 6, 2002</u> - Added the 
! 	  <A href="Development.shtml">
! 	    GeneX Development page
! 	  </A> for helping coordinate GeneX developers.
! 	</p>
! 	<p>
! 	  <u>Jan 31, 2002</u> - GeneX and G2G talk given by Jason
! 	  Stewart at the
! 	  <a href="http://conferences.oreilly.com/biocon/">
! 	    O'Reilly Bioinformatics Technology Conference
! 	  </A>. The slides for the talk are available
! 	  <A href="http://prdownloads.sourceforge.net/genex/Oreilly-G2G.ppt">
! 	    here
! 	  </A>.
! 	</P>	  
! 	<P>
! 	  <u>Oct 4, 2001</u> - GeneX Sourceforge Web site is put
! 	  in place, along with user access to the development
! 	  site and CVS repository.</P> 
! 	<P>
! 	  <u>September, 2001</u> - NCGR commits GeneX
! 	  development to a fully Open Source model, enabling GeneX
! 	  to become a truly <b>community supported project</b></P>
! 	<P>
! 	  <u>August, 2001</u> - 
! 	  <a href="genex-server.shtml">
! 	    GeneX-Server-1.0.4
! 	  </a> released</P>
! 	<P>
! 	  <u>Mar 3, 2001</u> -
! 	  DataLoader project started to support large-scale,
! 	  server-side data entry for GeneX.  In Perl. Fewer
! 	  annotation requirements.</P>
! 	<P>
! 	  <u>Jan 20, 2001</u> - Server install seems to be
! 	  user-configurable; no longer need to be root to install the
! 	  GeneX components (but still need root for some other
! 	  components).  (thanks to Micheal Pear for his input!)</P>
! 	<P>
! 	  <u>Jan 16, 2001</u> - Someone outside of NCGR (Michael
! 	  Pear, UCSD) installs GeneX, loads their own data
! 	  set with the Curation Tool and gets data back from a
! 	  query.</P> 
! 	<P>
! 	  <u>Jan 10th, 2001</u> - CyberT paper accepted</P>
!       </td>
!     </tr>
! 
!       <tr bgcolor="#D8E4F7"><th><big>GeneX Description</big></Th></tr>
!       <tr bgcolor="#D8E4F7"><td>
!         GeneX is an Open Source <em>database</em> system.  It is
!         <em>not</em> a commercial-grade, plug and play system for
!         analyzing single sets of gene expression.<br> 
! 	  The GeneX project consists of 4 parts:
!         <ol>
! 	    <li><b>The Data Loader</b> The scriptable to get your data
! 	      into the database.  
! 	    <li> <b>The Database itself</b> - the          conceptual
! 	    model of the inter-relationships of the data, as
! 	    well as the implementation of that model in a database
! 	    software system.  Currently GeneX is being run on the
! 	    Open Source PostgreSQL database system as it supports the
! 	    SQL92 std and has proven to be reasonably stable and of
! 	    decent performance so far.
! 	    <li> <b>The XML data exchange protocol</b> (the format
! 	    currently used by Genex is called GeneXML, but it will
! 	    be shifting to the new <a
! 	    href="http://mged.sf.net/">MAGE-ML</a> standard
! 	    shortly.  
! 	    <li><b>The Query and Analytical routines</b> to
! 	    ask for data from the database and perform          some
! 	    useful act on it, hopefully increasing your
! 	    understanding of the biological processes under
! 	    examination. 
!         </ol>       
! 
!         </td></tr>
! 
!       <tr bgcolor="#B9E4B2"><th><big>Open Source aspects of development</big></Th></tr>
!       <tr bgcolor="#B9E4B2"><td>
!         <b>GeneX is an Open Source Project</b>.  It includes a few
!         useful analytical tools as proof of concept, but it is still
!         an evolving system (tho it's now usable) and we encourage you
!         to install it, try to use it, complain about what doesn't
!         work, give us feedback about what you like and don't like.  IF
!         you can give us specific details about an analysis or
!         interface, we'd certainly appreciate that.  If you can give us
!         code that implements it, we'd <em>really</em> like that.
!         <p>
!         If you have programming skills and you're interested in moving
!         the project along in areas where GeneX is lacking, <em>please</em>
!         contact us and we'll try to help you get started.  If you're a
!         biologist in the area of gene expression and you an algorithm
!         implemented or you see a better way of doing something, please
!         let us know and we'll try to address your problem.
!         <p>
!         We are going to attempt to follow one of the precepts of Open
!         Source - release early and release often.  We'll be following
!         the style of Perl and the Linux kernel - there will be
!         'stable' version and a 'development' version.  The stable
!         version will not change very much over time except for bug
!         patches.  All the new stuff will happen with the developement
!         version, and those who want the latest and greatest version
!         will be able to check out the up-to-the-minute code from our
!         anonymous CVS tree.
!         <p>
!         Initially, all the GeneX developers will be NCGR employees
!         or contractors, but we already have one external developer and
!         hope to attract many more as people become aware of the
!         system.  As one who has been collaborating via anonymous CVs
!         for a while, it's a really fun experience to see the code
!         develop and change like a dynamic living thing from day to
!         day.  Bugs get detected, get corrected, and the code gets
!         better.  That's our hope for GeneX and we hope you can get
!         involved as well.
!       </td></tr>
! 
!       <tr><th><big>What features do you want to see?</big></th></tr>
!       <tr><td>
!         OK - here it is.  <a
!         href="mailto:gen...@li..."><b>Please tell
!         us</b></a> what features you desperately need, which would be
!         really neat, even which you'd be willing to pay for (heh heh).
!         Also tell where we've gone wrong (in your humble opinion).
!       </td></tr>
!       
!     </table>
! 
! <!-- End of Content -->

[Genex-cvs-commit] genex-www/content genex-server.ssi,1.3,1.4 main.ssi,1.6,1.7

[<jas...@us...>]

Update of /cvsroot/genex/genex-www/content
In directory usw-pr-cvs1:/tmp/cvs-serv17017/content

Modified Files:
	genex-server.ssi main.ssi 
Log Message:
uncommitted content from Tom

Index: genex-server.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/genex-server.ssi,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** genex-server.ssi	18 Feb 2002 21:25:38 -0000	1.3
--- genex-server.ssi	20 Oct 2002 21:45:20 -0000	1.4
***************
*** 1,35 ****
! <!-- GeneX Server content -->
! 
!   <table bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>GeneX Server</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	<h3>GeneX-Server-1.0.4</h3>
! 	<ul>
!           <li>View the 
! 	    <a href="https://sourceforge.net/project/shownotes.php?release_id=55763">
! 	      Release Notes
! 	    </a> to see what's changed.</li>
! 	  <li>Download the complete
! 	    <a href="https://sourceforge.net/project/showfiles.php?group_id=16453&release_id=55763">
! 	      Server Installer
! 	    </a> from here.</li>
! 	</ul>
!       </td>
!     </tr>
!     <tr>
!       <td>
! 	<h3>Supplementary Packages</h3>
! 	<ul>
!           <li>
! 	    <a href="download/supplementary/perlSGML.2001Jan23.tar.gz">
! 	      Perl::SGML
! 	    </a> This module is needed to create HTML versions of the
! 	    GeneXML DTD</li>
! 	</ul>
!       </td>
!     </tr>
!   </table>
! 
--- 1,78 ----
! <!-- GeneX Server content -->
! 
!   <table bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>GeneX Server</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	   <tr bgcolor="#FFD78F">
!       <td><h3>October 1, 2002</h3>
! 	  In January of 2002 GeneX development split to two paths. GeneX 1.x 
! development worked on getting a working schema, fully function data 
! repository, and analysis routines, while GeneX 2.x began work on a MAGE 
! compliant schema. This work on GeneX 1.x has primarily been carried out 
! at the University of Virginia. Various versions have been available to 
! the public since March 2002.<br><br>
! Please feel free to download and install the latest version of GeneX 
! 1.x For more info, scroll to the bottom of the page:<br><br>
! 
! <a href="http://genes.med.virginia.edu/">http://genes.med.virginia.edu/</a><br><br>
! 
! CVS checkout instructions are there. Installation is not as mature as 
! we'd like, but we're happy to answer questions. The primary developer 
! is <a href="mailto:tw...@vi...">Tom Laudeman</a><br><br>
! 
! The lastest release is essentially alpha quality. Nearly all features 
! are present and functioning, but the software has not been fully 
! tested.<br><br>
! 
! Version 1.5.7 has a complete security system (owners, groups, row level 
! permissions), data repository for chip spot data and derived data sets, 
! file management and viewing, analysis modules (functional, but not 
! complete), support for Affymetrix MAS4 and MAS5, experimental condition 
! grouping, and some support for the workflow in the microarray chip 
! center. We also support import of DChip data.<br><br>
! 
! Analysis is mostly via R, and we've created an R wrapper to simplify 
! adding new analyses. We are currently working on a comprehensive 
! analysis system with simplified analysis module installation.<br><br>
! 
! All the interfaces for end users are web based, including curation.<br><br>
! 
! Due to certain system constraints, this is essentially Unix only 
! software. It is based on all open source (or free) software such as 
! Perl and PostreSQL, so it could theoretically be ported to Windows. We have 
! installed and tested GeneX 1.x on Red Hat systems.<br><br>
! 
! We anticipate releasing this to our users by mid October. The new 
! analysis package should be complete around the end of October.
! </td></tr>
! <tr bgcolor="#FFD78F"><td>
! 	<h3>GeneX-Server-1.0.4</h3>
! 	<ul>
!           <li>View the 
! 	    <a href="https://sourceforge.net/project/shownotes.php?release_id=55763">
! 	      Release Notes
! 	    </a> to see what's changed.</li>
! 	  <li>Download the complete
! 	    <a href="https://sourceforge.net/project/showfiles.php?group_id=16453&release_id=55763">
! 	      Server Installer
! 	    </a> from here.</li>
! 	</ul>
!       </td>
!     </tr>
!     <tr>
!       <td>
! 	<h3>Supplementary Packages</h3>
! 	<ul>
!           <li>
! 	    <a href="../download/supplementary/perlSGML.2001Jan23.tar.gz">
! 	      Perl::SGML
! 	    </a> This module is needed to create HTML versions of the
! 	    GeneXML DTD</li>
! 	</ul>
!       </td>
!     </tr>
!   </table>
! 

Index: main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/content/main.ssi,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** main.ssi	29 Aug 2002 14:05:59 -0000	1.6
--- main.ssi	20 Oct 2002 21:45:20 -0000	1.7
***************
*** 1,160 ****
! <!--Main content -->
! 
!   <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>Recent News</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	<p>
! 	  <u>Aug 29, 2002</u> - Update Genex-2 Schema information can
! 	  be found 
! 	    <A href="genex-2-schema.shtml">
! 	      here
! 	  </A> (now with hyperlinks!!).
! 	</p>
! 	<p>
! 	  <u>Feb 20, 2002</u> - preliminary information now available
! 	  discussing the future directions of GeneX. It includes links
! 	  to 
! 	  <A href="Timelines.shtml">
! 	    timelines and project descriptions
! 	  </A> from the different sources that are currently funding
! 	  GeneX development.
! 	</p>
! 	<p>
! 	  <u>Feb 8, 2002</u> - preliminary
! 	  <A href="G2G.shtml">
! 	    G2G
! 	  </A> information now available.
! 	</p>
! 	<p>
! 	  <u>Feb 6, 2002</u> - Added the 
! 	  <A href="Development.shtml">
! 	    GeneX Development page
! 	  </A> for helping coordinate GeneX developers.
! 	</p>
! 	<p>
! 	  <u>Jan 31, 2002</u> - GeneX and G2G talk given by Jason
! 	  Stewart at the
! 	  <a href="http://conferences.oreilly.com/biocon/">
! 	    O'Reilly Bioinformatics Technology Conference
! 	  </A>. The slides for the talk are available
! 	  <A href="http://prdownloads.sourceforge.net/genex/Oreilly-G2G.ppt">
! 	    here
! 	  </A>.
! 	</P>	  
! 	<P>
! 	  <u>Oct 4, 2001</u> - GeneX Sourceforge Web site is put
! 	  in place, along with user access to the development
! 	  site and CVS repository.</P> 
! 	<P>
! 	  <u>September, 2001</u> - NCGR commits GeneX
! 	  development to a fully Open Source model, enabling GeneX
! 	  to become a truly <b>community supported project</b></P>
! 	<P>
! 	  <u>August, 2001</u> - 
! 	  <a href="genex-server.shtml">
! 	    GeneX-Server-1.0.4
! 	  </a> released</P>
! 	<P>
! 	  <u>Mar 3, 2001</u> -
! 	  DataLoader project started to support large-scale,
! 	  server-side data entry for GeneX.  In Perl. Fewer
! 	  annotation requirements.</P>
! 	<P>
! 	  <u>Jan 20, 2001</u> - Server install seems to be
! 	  user-configurable; no longer need to be root to install the
! 	  GeneX components (but still need root for some other
! 	  components).  (thanks to Micheal Pear for his input!)</P>
! 	<P>
! 	  <u>Jan 16, 2001</u> - Someone outside of NCGR (Michael
! 	  Pear, UCSD) installs GeneX, loads their own data
! 	  set with the Curation Tool and gets data back from a
! 	  query.</P> 
! 	<P>
! 	  <u>Jan 10th, 2001</u> - CyberT paper accepted</P>
!       </td>
!     </tr>
! 
!       <tr bgcolor="#D8E4F7"><th><big>GeneX Description</big></Th></tr>
!       <tr bgcolor="#D8E4F7"><td>
!         GeneX is an Open Source <em>database</em> system.  It is
!         <em>not</em> a commercial-grade, plug and play system for
!         analyzing single sets of gene expression.<br> 
! 	  The GeneX project consists of 4 parts:
!         <ol>
! 	    <li><b>The Data Loader</b> (Perl) to get your data
!           into the database.  
! 	    <li> <b>The Database itself</b> - the          conceptual
! 	    model of the inter-relationships of the data, as
! 	    well as the implementation of that model in a database
! 	    software system.  Currently GeneX is being run on the
! 	    Open Source PostgreSQL database system as it supports the
! 	    SQL92 std and has proven to be reasonably stable and of
! 	    decent performance so far.
! 	    <li> <b>The XML data exchange protocol</b> (the format
! 	    currently used by OpenGenex is called GeneXML, but it will
! 	    be shifting to the new <a
! 	    href="http://mged.sf.net/downloads.shtml">MAGE-ML</a> standard
! 	    shortly.  
! 	    <li><b>The Query and Analytical routines</b> to
! 	    ask for data from the database and perform          some
! 	    useful act on it, hopefully increasing your
! 	    understanding of the biological processes under
! 	    examination. 
!         </ol>       
! 
!         </td></tr>
! 
!       <tr bgcolor="#B9E4B2"><th><big>Open Source aspects of development</big></Th></tr>
!       <tr bgcolor="#B9E4B2"><td>
!         <b>GeneX is an Open Source Project</b>.  It includes a few
!         useful analytical tools as proof of concept, but it is still
!         an evolving system (tho it's now usable) and we encourage you
!         to install it, try to use it, complain about what doesn't
!         work, give us feedback about what you like and don't like.  IF
!         you can give us specific details about an analysis or
!         interface, we'd certainly appreciate that.  If you can give us
!         code that implements it, we'd <em>really</em> like that.
!         <p>
!         If you have programming skills and you're interested in moving
!         the project along in areas where GeneX is lacking, <em>please</em>
!         contact us and we'll try to help you get started.  If you're a
!         biologist in the area of gene expression and you an algorithm
!         implemented or you see a better way of doing something, please
!         let us know and we'll try to address your problem.
!         <p>
!         We are going to attempt to follow one of the precepts of Open
!         Source - release early and release often.  We'll be following
!         the style of Perl and the Linux kernel - there will be
!         'stable' version and a 'development' version.  The stable
!         version will not change very much over time except for bug
!         patches.  All the new stuff will happen with the developement
!         version, and those who want the latest and greatest version
!         will be able to check out the up-to-the-minute code from our
!         anonymous CVS tree.
!         <p>
!         Initially, all the GeneX developers will be NCGR employees
!         or contractors, but we already have one external developer and
!         hope to attract many more as people become aware of the
!         system.  As one who has been collaborating via anonymous CVs
!         for a while, it's a really fun experience to see the code
!         develop and change like a dynamic living thing from day to
!         day.  Bugs get detected, get corrected, and the code gets
!         better.  That's our hope for GeneX and we hope you can get
!         involved as well.
!       </td></tr>
! 
!       <tr><th><big>What features do you want to see?</big></th></tr>
!       <tr><td>
!         OK - here it is.  <a
!         href="mailto:gen...@li..."><b>Please tell
!         us</b></a> what features you desperately need, which would be
!         really neat, even which you'd be willing to pay for (heh heh).
!         Also tell where we've gone wrong (in your humble opinion).
!       </td></tr>
!       
!     </table>
! 
! <!-- End of Content -->
--- 1,167 ----
! <!--Main content -->
! 
!   <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
!     <tr valign="top" bgcolor="#FFD78F">
!       <th><big>Recent News</big></th>
!     </tr>
!     <tr bgcolor="#FFD78F">
!       <td>
! 	  <p>
! 	  <u>October 1, 2002</u> - GeneX 1.5.7 Released <br>
! 	  This is a more or less stable version. It has the new user interface to 
! manage/import Affymetrix data. There are three analysis routines, but 
! we a preparing for an overhaul of the analysis tools. To learn more go to 
! the <a href="genex-server.shtml">Download</a> page or the <a href="http://genes.med.virginia.edu/">UVa install</a> of GeneX 1.x. 
! 	</p>
! 	<p>
! 	  <u>Aug 29, 2002</u> - Update Genex-2 Schema information can
! 	  be found 
! 	    <A href="genex-2-schema.shtml">
! 	      here
! 	  </A> (now with hyperlinks!!).
! 	</p>
! 	<p>
! 	  <u>Feb 20, 2002</u> - preliminary information now available
! 	  discussing the future directions of GeneX. It includes links
! 	  to 
! 	  <A href="Timelines.shtml">
! 	    timelines and project descriptions
! 	  </A> from the different sources that are currently funding
! 	  GeneX development.
! 	</p>
! 	<p>
! 	  <u>Feb 8, 2002</u> - preliminary
! 	  <A href="G2G.shtml">
! 	    G2G
! 	  </A> information now available.
! 	</p>
! 	<p>
! 	  <u>Feb 6, 2002</u> - Added the 
! 	  <A href="Development.shtml">
! 	    GeneX Development page
! 	  </A> for helping coordinate GeneX developers.
! 	</p>
! 	<p>
! 	  <u>Jan 31, 2002</u> - GeneX and G2G talk given by Jason
! 	  Stewart at the
! 	  <a href="http://conferences.oreilly.com/biocon/">
! 	    O'Reilly Bioinformatics Technology Conference
! 	  </A>. The slides for the talk are available
! 	  <A href="http://prdownloads.sourceforge.net/genex/Oreilly-G2G.ppt">
! 	    here
! 	  </A>.
! 	</P>	  
! 	<P>
! 	  <u>Oct 4, 2001</u> - GeneX Sourceforge Web site is put
! 	  in place, along with user access to the development
! 	  site and CVS repository.</P> 
! 	<P>
! 	  <u>September, 2001</u> - NCGR commits GeneX
! 	  development to a fully Open Source model, enabling GeneX
! 	  to become a truly <b>community supported project</b></P>
! 	<P>
! 	  <u>August, 2001</u> - 
! 	  <a href="genex-server.shtml">
! 	    GeneX-Server-1.0.4
! 	  </a> released</P>
! 	<P>
! 	  <u>Mar 3, 2001</u> -
! 	  DataLoader project started to support large-scale,
! 	  server-side data entry for GeneX.  In Perl. Fewer
! 	  annotation requirements.</P>
! 	<P>
! 	  <u>Jan 20, 2001</u> - Server install seems to be
! 	  user-configurable; no longer need to be root to install the
! 	  GeneX components (but still need root for some other
! 	  components).  (thanks to Micheal Pear for his input!)</P>
! 	<P>
! 	  <u>Jan 16, 2001</u> - Someone outside of NCGR (Michael
! 	  Pear, UCSD) installs GeneX, loads their own data
! 	  set with the Curation Tool and gets data back from a
! 	  query.</P> 
! 	<P>
! 	  <u>Jan 10th, 2001</u> - CyberT paper accepted</P>
!       </td>
!     </tr>
! 
!       <tr bgcolor="#D8E4F7"><th><big>GeneX Description</big></Th></tr>
!       <tr bgcolor="#D8E4F7"><td>
!         GeneX is an Open Source <em>database</em> system.  It is
!         <em>not</em> a commercial-grade, plug and play system for
!         analyzing single sets of gene expression.<br> 
! 	  The GeneX project consists of 4 parts:
!         <ol>
! 	    <li><b>The Data Loader</b> (Perl) to get your data
!           into the database.  
! 	    <li> <b>The Database itself</b> - the          conceptual
! 	    model of the inter-relationships of the data, as
! 	    well as the implementation of that model in a database
! 	    software system.  Currently GeneX is being run on the
! 	    Open Source PostgreSQL database system as it supports the
! 	    SQL92 std and has proven to be reasonably stable and of
! 	    decent performance so far.
! 	    <li> <b>The XML data exchange protocol</b> (the format
! 	    currently used by OpenGenex is called GeneXML, but it will
! 	    be shifting to the new <a
! 	    href="http://mged.sf.net/downloads.shtml">MAGE-ML</a> standard
! 	    shortly.  
! 	    <li><b>The Query and Analytical routines</b> to
! 	    ask for data from the database and perform          some
! 	    useful act on it, hopefully increasing your
! 	    understanding of the biological processes under
! 	    examination. 
!         </ol>       
! 
!         </td></tr>
! 
!       <tr bgcolor="#B9E4B2"><th><big>Open Source aspects of development</big></Th></tr>
!       <tr bgcolor="#B9E4B2"><td>
!         <b>GeneX is an Open Source Project</b>.  It includes a few
!         useful analytical tools as proof of concept, but it is still
!         an evolving system (tho it's now usable) and we encourage you
!         to install it, try to use it, complain about what doesn't
!         work, give us feedback about what you like and don't like.  IF
!         you can give us specific details about an analysis or
!         interface, we'd certainly appreciate that.  If you can give us
!         code that implements it, we'd <em>really</em> like that.
!         <p>
!         If you have programming skills and you're interested in moving
!         the project along in areas where GeneX is lacking, <em>please</em>
!         contact us and we'll try to help you get started.  If you're a
!         biologist in the area of gene expression and you an algorithm
!         implemented or you see a better way of doing something, please
!         let us know and we'll try to address your problem.
!         <p>
!         We are going to attempt to follow one of the precepts of Open
!         Source - release early and release often.  We'll be following
!         the style of Perl and the Linux kernel - there will be
!         'stable' version and a 'development' version.  The stable
!         version will not change very much over time except for bug
!         patches.  All the new stuff will happen with the developement
!         version, and those who want the latest and greatest version
!         will be able to check out the up-to-the-minute code from our
!         anonymous CVS tree.
!         <p>
!         Initially, all the GeneX developers will be NCGR employees
!         or contractors, but we already have one external developer and
!         hope to attract many more as people become aware of the
!         system.  As one who has been collaborating via anonymous CVs
!         for a while, it's a really fun experience to see the code
!         develop and change like a dynamic living thing from day to
!         day.  Bugs get detected, get corrected, and the code gets
!         better.  That's our hope for GeneX and we hope you can get
!         involved as well.
!       </td></tr>
! 
!       <tr><th><big>What features do you want to see?</big></th></tr>
!       <tr><td>
!         OK - here it is.  <a
!         href="mailto:gen...@li..."><b>Please tell
!         us</b></a> what features you desperately need, which would be
!         really neat, even which you'd be willing to pay for (heh heh).
!         Also tell where we've gone wrong (in your humble opinion).
!       </td></tr>
!       
!     </table>
! 
! <!-- End of Content -->

[Genex-cvs-commit] genex-server ChangeLog,1.101,1.102

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv8265

Modified Files:
	ChangeLog 
Log Message:
usual


Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.101
retrieving revision 1.102
diff -C2 -d -r1.101 -r1.102
*** ChangeLog	20 Oct 2002 20:02:43 -0000	1.101
--- ChangeLog	20 Oct 2002 21:19:04 -0000	1.102
***************
*** 2,5 ****
--- 2,18 ----
  
  	* db.pl (Repository): 
+ 	give genex user ability to create tables and DB's
+ 
+ 	* Install (Repository): 
+ 	now properly creates the mason data dir
+ 
+ 	* INSTALL (Repository): 
+ 	added Bio::MAGE pre-requisites
+ 
+ 	* Configure (Repository): 
+ 	fixed perl module pre-requisites
+ 	added GENEX_MASON_DATA_DIR
+ 
+ 	* db.pl (Repository): 
  	removed all references to dbi_error()
  	need to disconnect() from template1 before creating new DB

[Genex-cvs-commit] genex-server db.pl,1.5,1.6

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv8192

Modified Files:
	db.pl 
Log Message:
* db.pl (Repository): 
give genex user ability to create tables and DB's


Index: db.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/db.pl,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** db.pl	20 Oct 2002 20:02:22 -0000	1.5
--- db.pl	20 Oct 2002 21:18:51 -0000	1.6
***************
*** 154,158 ****
    $SU_PASS = ask_pass();
  
!   my $sql = "CREATE USER $VARS{GENEX_SU_USER} WITH PASSWORD " . $dbh->quote($SU_PASS);
    $dbh->do($sql);
    die("Couldn't create user $VARS{GENEX_SU_USER}: $DBI::errstr") 
--- 154,158 ----
    $SU_PASS = ask_pass();
  
!   my $sql = "CREATE USER $VARS{GENEX_SU_USER} WITH CREATEUSER CREATEDB PASSWORD " . $dbh->quote($SU_PASS);
    $dbh->do($sql);
    die("Couldn't create user $VARS{GENEX_SU_USER}: $DBI::errstr") 

[Genex-cvs-commit] genex-server Install,1.9,1.10

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv8045

Modified Files:
	Install 
Log Message:
* Install (Repository): 
now properly creates the mason data dir


Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Install	20 Oct 2002 20:00:47 -0000	1.9
--- Install	20 Oct 2002 21:18:13 -0000	1.10
***************
*** 72,76 ****
    $ISO8601_DATE_FORMAT
    $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_DIR $GENEX_WORKSPACE_DIR
!   $GENEX_MASON_URL $GENEX_WORKSPACE_URL
    $GENEX_TEST_USER   $GENEX_TEST_PASSWORD
  );
--- 72,76 ----
    $ISO8601_DATE_FORMAT
    $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_DIR $GENEX_WORKSPACE_DIR
!   $GENEX_MASON_URL $GENEX_WORKSPACE_URL $GENEX_MASON_DATA_DIR
    $GENEX_TEST_USER   $GENEX_TEST_PASSWORD
  );
***************
*** 188,191 ****
--- 188,193 ----
  # the mason data dir needs to be world writable
  $DIR = $VARS{GENEX_MASON_DIR};  # Brevity && Clarity!
+ genex_mkdir($DIR) unless -d $DIR;
+ $DIR = $VARS{GENEX_MASON_DATA_DIR};  # Brevity && Clarity!
  genex_mkdir($DIR) unless -d $DIR;
  genex_system("chmod 777 $DIR");

[Genex-cvs-commit] genex-server INSTALL,1.20,1.21

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv7902

Modified Files:
	INSTALL 
Log Message:
* INSTALL (Repository): 
added Bio::MAGE pre-requisites


Index: INSTALL
===================================================================
RCS file: /cvsroot/genex/genex-server/INSTALL,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** INSTALL	20 Oct 2002 19:59:27 -0000	1.20
--- INSTALL	20 Oct 2002 21:17:37 -0000	1.21
***************
*** 181,184 ****
--- 181,185 ----
  HTML::Mason     - for the new WWW/CGI applications
  Class::ObjectTemplate::DB - used by everything
+ Bio::MAGE       - used for importing and exporting MAGE-ML
  
  Using the CPAN shell to install Perl Modules

[Genex-cvs-commit] genex-server Configure,1.7,1.8

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv7795

Modified Files:
	Configure 
Log Message:
* Configure (Repository): 
fixed perl module pre-requisites
added GENEX_MASON_DATA_DIR


Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Configure	20 Oct 2002 19:58:04 -0000	1.7
--- Configure	20 Oct 2002 21:17:08 -0000	1.8
***************
*** 108,112 ****
    $GENEX_SERVER_INSTALLATION_DATE  $GENEX_SERVER_INSTALLED_BY
    $ISO8601_DATE_FORMAT
!   $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_DIR
    $GENEX_WORKSPACE_DIR   $APACHE_CONF_DIR_DEF
    $GENEX_G2G_DIR $GENEX_MASON_URL $GENEX_WORKSPACE_URL $GENEX_SESSION_PATH
--- 108,112 ----
    $GENEX_SERVER_INSTALLATION_DATE  $GENEX_SERVER_INSTALLED_BY
    $ISO8601_DATE_FORMAT
!   $APACHE_CONF_DIR $MASON_COMP_DATA_ROOT $GENEX_HTMLDIR $GENEX_MASON_DIR $GENEX_MASON_DATA_DIR
    $GENEX_WORKSPACE_DIR   $APACHE_CONF_DIR_DEF
    $GENEX_G2G_DIR $GENEX_MASON_URL $GENEX_WORKSPACE_URL $GENEX_SESSION_PATH
***************
*** 513,522 ****
  EOM
  
!     my @req_modules = qw(DBI
! 			 DBD::Pg
  			 Term::ReadKey
  			 Apache::Session::Postgres
  			 CGI
  			 Digest::MD5
  			 Class::ObjectTemplate::DB);
  
--- 513,524 ----
  EOM
  
!     my @req_modules = qw(DBD::Pg
  			 Term::ReadKey
  			 Apache::Session::Postgres
  			 CGI
  			 Digest::MD5
+ 			 HTML::Mason
+ 			 XML::Xerces
+ 			 Bio::MAGE
  			 Class::ObjectTemplate::DB);
  
***************
*** 1281,1289 ****
  $VARS{GENEX_WORKSPACE_URL} = $GENEX_WORKSPACE_URL = "$GENEX_MASON_URL/workspace";
  $VARS{GENEX_SESSION_PATH} = $GENEX_SESSION_PATH = "/$GENEX_DIR";
  unless (defined $MASON_COMP_DATA_ROOT) {
     # we set up the CompRoot regardless
    $VARS{MASON_COMP_DATA_ROOT} = <<EOT;
  PerlAddVar MasonCompRoot $GENEX_MASON_DIR
! PerlSetVar MasonDataDir  $LOCAL_ROOT/mason
  EOT
  
--- 1283,1292 ----
  $VARS{GENEX_WORKSPACE_URL} = $GENEX_WORKSPACE_URL = "$GENEX_MASON_URL/workspace";
  $VARS{GENEX_SESSION_PATH} = $GENEX_SESSION_PATH = "/$GENEX_DIR";
+ $VARS{GENEX_MASON_DATA_DIR} = $GENEX_MASON_DATA_DIR = "$LOCAL_ROOT/mason";
  unless (defined $MASON_COMP_DATA_ROOT) {
     # we set up the CompRoot regardless
    $VARS{MASON_COMP_DATA_ROOT} = <<EOT;
  PerlAddVar MasonCompRoot $GENEX_MASON_DIR
! PerlSetVar MasonDataDir  $GENEX_MASON_DATA_DIR
  EOT
  

[Genex-cvs-commit] genex-server/Genex ChangeLog,1.115,1.116

[<jas...@us...>]

Update of /cvsroot/genex/genex-server/Genex
In directory usw-pr-cvs1:/tmp/cvs-serv7394/Genex

Modified Files:
	ChangeLog 
Log Message:
usual


Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v
retrieving revision 1.115
retrieving revision 1.116
diff -C2 -d -r1.115 -r1.116
*** ChangeLog	20 Oct 2002 20:02:43 -0000	1.115
--- ChangeLog	20 Oct 2002 21:15:51 -0000	1.116
***************
*** 4,7 ****
--- 4,8 ----
  	* scripts/create_genex_db.pl.in (Repository): 
  	added --admin_db to kludge postgres authentication problem
+ 	corrected permissions on Sessions table
  
  	* scripts/mbad-insert.pl.in (Repository): 

[Genex-cvs-commit] genex-server/Genex/scripts create_genex_db.pl.in,1.4,1.5

[<jas...@us...>]

Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv7311/Genex/scripts

Modified Files:
	create_genex_db.pl.in 
Log Message:
* scripts/create_genex_db.pl.in (Repository): 
corrected permissions on Sessions table



Index: create_genex_db.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_db.pl.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** create_genex_db.pl.in	20 Oct 2002 19:55:24 -0000	1.4
--- create_genex_db.pl.in	20 Oct 2002 21:15:35 -0000	1.5
***************
*** 138,142 ****
  my $sql = $dbh->create_grant_sql(TABLE=>$sessions,
  				 USERS=>['PUBLIC'],
! 				 PERMS=>['SELECT','INSERT','UPDATE'],
  				);
  
--- 138,142 ----
  my $sql = $dbh->create_grant_sql(TABLE=>$sessions,
  				 USERS=>['PUBLIC'],
! 				 PERMS=>['ALL'],
  				);
  

[Genex-cvs-commit] genex-server/Genex ChangeLog,1.114,1.115

[<jas...@us...>]

Update of /cvsroot/genex/genex-server/Genex
In directory usw-pr-cvs1:/tmp/cvs-serv12084/Genex

Modified Files:
	ChangeLog 
Log Message:
usual


Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ChangeLog,v
retrieving revision 1.114
retrieving revision 1.115
diff -C2 -d -r1.114 -r1.115
*** ChangeLog	20 Oct 2002 15:04:14 -0000	1.114
--- ChangeLog	20 Oct 2002 20:02:43 -0000	1.115
***************
*** 1,4 ****
--- 1,8 ----
  2002-10-20  Jason E. Stewart  <ja...@op...>
  
+ 	* scripts/gendb.pl.in (Repository): 
+ 	* scripts/create_genex_db.pl.in (Repository): 
+ 	added --admin_db to kludge postgres authentication problem
+ 
  	* scripts/mbad-insert.pl.in (Repository): 
  	now get data regexes from DB

[Genex-cvs-commit] genex-server ChangeLog,1.100,1.101

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv12084

Modified Files:
	ChangeLog 
Log Message:
usual


Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.100
retrieving revision 1.101
diff -C2 -d -r1.100 -r1.101
*** ChangeLog	20 Oct 2002 15:04:13 -0000	1.100
--- ChangeLog	20 Oct 2002 20:02:43 -0000	1.101
***************
*** 1,4 ****
--- 1,28 ----
  2002-10-20  Jason E. Stewart  <ja...@op...>
  
+ 	* db.pl (Repository): 
+ 	removed all references to dbi_error()
+ 	need to disconnect() from template1 before creating new DB
+ 	added kludge to get around Postgres authentication problem
+ 
+ 	* Install (Repository): 
+ 	doesn't install HTML versions of DTD's if dtd2sgml isn't present
+ 	fixed email addr typo ncgr => sf
+ 
+ 	* INSTALL (Repository): 
+ 	added info about postgres authentication
+ 	added requirement for mod_perl
+ 	update info update using cpan
+ 	indicated which apps were optional and why
+ 	added info about install XML::Xerces
+ 
+ 	* Configure (Repository): 
+ 	updated the URL for SGMLutils
+ 	set GENEX_VOCAB_DIR
+ 	made changes to get_app() to indicate which apps were optional
+ 
+ 	* apache/genex-2.conf.in (Repository): 
+ 	added loadmodule line for mod_perl
+ 
  	* Install (Repository): 
  	added fix for db.pl not being able to run by postgres - was

[Genex-cvs-commit] genex-server db.pl,1.4,1.5

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv11925

Modified Files:
	db.pl 
Log Message:
* db.pl (Repository): 
removed all references to dbi_error()
need to disconnect() from template1 before creating new DB
added kludge to get around Postgres authentication problem


Index: db.pl
===================================================================
RCS file: /cvsroot/genex/genex-server/db.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** db.pl	15 Oct 2002 14:45:28 -0000	1.4
--- db.pl	20 Oct 2002 20:02:22 -0000	1.5
***************
*** 40,44 ****
  
  my $user_ref = $dbh->selectall_arrayref('select usename from pg_shadow');
! dbi_error("Couldn't get users from pg_shadow: $DBI::errstr")
    if $dbh->err;
  
--- 40,44 ----
  
  my $user_ref = $dbh->selectall_arrayref('select usename from pg_shadow');
! die("Couldn't get users from pg_shadow: $DBI::errstr")
    if $dbh->err;
  
***************
*** 78,82 ****
    my $sql = "CREATE USER $VARS{GENEX_TEST_USER} WITH PASSWORD '$VARS{GENEX_TEST_PASSWORD}'";
    $dbh->do($sql);
!   dbi_error("Couldn't create user $VARS{GENEX_TEST_USER}: $DBI::errstr")
      if $dbh->err;
  
--- 78,82 ----
    my $sql = "CREATE USER $VARS{GENEX_TEST_USER} WITH PASSWORD '$VARS{GENEX_TEST_PASSWORD}'";
    $dbh->do($sql);
!   die("Couldn't create user $VARS{GENEX_TEST_USER}: $DBI::errstr")
      if $dbh->err;
  
***************
*** 114,118 ****
    my $sql = "CREATE USER $VARS{GENEX_RO_USER} WITH PASSWORD '$VARS{GENEX_RO_PASSWORD}'";
    $dbh->do($sql);
!   dbi_error("Couldn't create user $VARS{GENEX_RO_USER}: $DBI::errstr")
      if $dbh->err;
  
--- 114,118 ----
    my $sql = "CREATE USER $VARS{GENEX_RO_USER} WITH PASSWORD '$VARS{GENEX_RO_PASSWORD}'";
    $dbh->do($sql);
!   die("Couldn't create user $VARS{GENEX_RO_USER}: $DBI::errstr")
      if $dbh->err;
  
***************
*** 156,160 ****
    my $sql = "CREATE USER $VARS{GENEX_SU_USER} WITH PASSWORD " . $dbh->quote($SU_PASS);
    $dbh->do($sql);
!   dbi_error("Couldn't create user $VARS{GENEX_SU_USER}: $DBI::errstr") 
      if $dbh->err;
  
--- 156,160 ----
    my $sql = "CREATE USER $VARS{GENEX_SU_USER} WITH PASSWORD " . $dbh->quote($SU_PASS);
    $dbh->do($sql);
!   die("Couldn't create user $VARS{GENEX_SU_USER}: $DBI::errstr") 
      if $dbh->err;
  
***************
*** 181,185 ****
  }
  
- $dbh->disconnect();
  
  unless ($continue) {
--- 181,184 ----
***************
*** 189,192 ****
--- 188,192 ----
  
  EOM
+   $dbh->disconnect();
    exit(0);
  }
***************
*** 205,208 ****
--- 205,221 ----
  print STDERR "\tCreating DB and loading test data ...\n\n";
  
+ #
+ # Due to Postgres7.2's lack of user-based security, we have to use
+ #   this kluge to enable user genex to build the DB. We create a
+ #   temporary table for genex to log into instead of template1
+ #
+ my $GENEX_ADMIN_DB = '__genexadmin';
+ my $sql = "CREATE DATABASE $GENEX_ADMIN_DB";
+ $dbh->do($sql);
+ die("Couldn't create temporary DB: $DBI::errstr\nwith SQL=<$sql>")
+   if $dbh->err;
+ 
+ # we have to logout before we can create new DB's
+ $dbh->disconnect();
  
  print STDOUT <<EOM;
***************
*** 213,216 ****
--- 226,230 ----
  my $command = 'Genex/scripts/gendb.pl';
  my @args = ('--db'=>$VARS{DB_NAME},
+ 	    '--admin_db'=>$GENEX_ADMIN_DB,
  	    '--dir'=>'.',
  	    '--user'=>'genex',
***************
*** 220,224 ****
  print STDERR join(' ', $command, @args), "\n";
  system($command,@args);
! die(<<EOE) if $?;
  
    FATAL ERROR
--- 234,251 ----
  print STDERR join(' ', $command, @args), "\n";
  system($command,@args);
! my $fail = $?;
! 
! my $dbh = DBI->connect('dbi:Pg:dbname=template1','','',{PrintError=>0});
! die "Couldn't make connection to Postgres: ", $DBI::errstr
!   unless defined $dbh;
! 
! $sql = "DROP DATABASE $GENEX_ADMIN_DB";
! $dbh->do($sql);
! warn("Couldn't drop temporary DB: $DBI::errstr")
!   if $dbh->err;
! 
! if ($fail) {
!   $dbh->disconnect();
!   die(<<EOE);
  
    FATAL ERROR
***************
*** 228,231 ****
--- 255,259 ----
  
  EOE
+ }
  
  #
***************
*** 239,243 ****
  
  # log in as super user
! my $dbh = Bio::Genex::Connect->new(USER=>$VARS{GENEX_SU_USER},
  				    PASSWORD=>$SU_PASS);
  
--- 267,271 ----
  
  # log in as super user
! $dbh = Bio::Genex::Connect->new(USER=>$VARS{GENEX_SU_USER},
  				    PASSWORD=>$SU_PASS);
  

[Genex-cvs-commit] genex-server Install,1.8,1.9

[<jas...@us...>]

Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv11141

Modified Files:
	Install 
Log Message:
* Install (Repository): 
doesn't install HTML versions of DTD's if dtd2sgml isn't present
fixed email addr typo ncgr => sf


Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Install	20 Oct 2002 15:03:55 -0000	1.8
--- Install	20 Oct 2002 20:00:47 -0000	1.9
***************
*** 337,384 ****
    unless -d $DTD_HTML_DIR;
  
! print STDERR "Preparing to run dtd2html, IGNORE ANY CATALOG WARNINGS\n\n";
! print STDERR "\tRunning dtd2html on genexml.dtd ...\n";
! genex_system("$VARS{DTD2HTML} " .
! 	     " -tree " . 
! 	     " -all genexml-all.html " .
! 	     " -dtd genexml " .
! 	     " -home genexml-home.html " .
! 	     " -out $DTD_HTML_DIR " .
! 	     " -top genexml-top.html " .
! 	     " --treefile genexml-tree.html " .
! 	     " $DIR/genexml.dtd");
  
! print STDERR "\tRunning dtd2html on ams.dtd ...\n";
! genex_system("$VARS{DTD2HTML} " .
! 	     " -tree " . 
! 	     " -all ams-all.html " .
! 	     " -dtd ams " .
! 	     " -home ams-home.html " .
! 	     " -out $DTD_HTML_DIR " .
! 	     " -top ams-top.html " .
! 	     " --treefile ams-tree.html " .
! 	     " $DIR/ams.dtd");
  
! print STDERR "\tRunning dtd2html on als.dtd ...\n";
! genex_system("$VARS{DTD2HTML} " .
! 	     " -tree " . 
! 	     " -all als-all.html " .
! 	     " -dtd als " .
! 	     " -home als-home.html " .
! 	     " -out $DTD_HTML_DIR " .
! 	     " -top als-top.html " .
! 	     " --treefile als-tree.html " .
! 	     " $DIR/als.dtd");
  
! print STDERR "\tRunning dtd2html on usf.dtd ...\n";
! genex_system("$VARS{DTD2HTML} " .
! 	     " -tree " . 
! 	     " -all usf-all.html " .
! 	     " -dtd usf " .
! 	     " -home usf-home.html " .
! 	     " -out $DTD_HTML_DIR " .
! 	     " -top usf-top.html " .
! 	     " --treefile usf-tree.html " .
! 	     " $DIR/usf.dtd");
  
  # make a symlink in the HTML dir for the dtd files
--- 337,389 ----
    unless -d $DTD_HTML_DIR;
  
! if ($VARS{DTD2HTML}) {
  
!   print STDERR "Preparing to run dtd2html, IGNORE ANY CATALOG WARNINGS\n\n";
!   print STDERR "\tRunning dtd2html on genexml.dtd ...\n";
!   genex_system("$VARS{DTD2HTML} " .
! 	       " -tree " . 
! 	       " -all genexml-all.html " .
! 	       " -dtd genexml " .
! 	       " -home genexml-home.html " .
! 	       " -out $DTD_HTML_DIR " .
! 	       " -top genexml-top.html " .
! 	       " --treefile genexml-tree.html " .
! 	       " $DIR/genexml.dtd");
  
!   print STDERR "\tRunning dtd2html on ams.dtd ...\n";
!   genex_system("$VARS{DTD2HTML} " .
! 	       " -tree " . 
! 	       " -all ams-all.html " .
! 	       " -dtd ams " .
! 	       " -home ams-home.html " .
! 	       " -out $DTD_HTML_DIR " .
! 	       " -top ams-top.html " .
! 	       " --treefile ams-tree.html " .
! 	       " $DIR/ams.dtd");
  
!   print STDERR "\tRunning dtd2html on als.dtd ...\n";
!   genex_system("$VARS{DTD2HTML} " .
! 	       " -tree " . 
! 	       " -all als-all.html " .
! 	       " -dtd als " .
! 	       " -home als-home.html " .
! 	       " -out $DTD_HTML_DIR " .
! 	       " -top als-top.html " .
! 	       " --treefile als-tree.html " .
! 	       " $DIR/als.dtd");
! 
!   print STDERR "\tRunning dtd2html on usf.dtd ...\n";
!   genex_system("$VARS{DTD2HTML} " .
! 	       " -tree " . 
! 	       " -all usf-all.html " .
! 	       " -dtd usf " .
! 	       " -home usf-home.html " .
! 	       " -out $DTD_HTML_DIR " .
! 	       " -top usf-top.html " .
! 	       " --treefile usf-tree.html " .
! 	       " $DIR/usf.dtd");
! } else {
!   print STDERR "\tdtd2html not installed, skipping installation of DTD's\n";
! }
  
  # make a symlink in the HTML dir for the dtd files
***************
*** 798,804 ****
  file ($APACHE_CONF_DIR/httpd.conf):
  
- <IfModule mod_perl.c>
    Include $DIR/$file
- </IfModule>
  
  EOT
--- 803,807 ----
***************
*** 880,884 ****
  There were errors in your installation. Please check the file [$ERR_FILE]
  to see more information. Please email the contents of that file, and the 
! file '$REMINDERS' to genex\@ncgr.org so that we can better diagnose the 
  difficulties.
  
--- 883,887 ----
  There were errors in your installation. Please check the file [$ERR_FILE]
  to see more information. Please email the contents of that file, and the 
! file '$REMINDERS' to genex-dev\@lists.sf.net so that we can better diagnose the 
  difficulties.