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[basedb-cvs] basedb/include/classes plot.inc.php,1.2,NONE

From: <tr...@us...> - 2003-02-18 07:50:42

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv17689/include/classes

Removed Files:
	plot.inc.php 
Log Message:
removed old incompatible overview plot

--- plot.inc.php DELETED ---

[basedb-cvs] basedb/www assay_plotpage.phtml,1.8,NONE assay_plot.phtml,1.10,NONE

From: <tr...@us...> - 2003-02-18 07:50:42

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv17689/www

Removed Files:
	assay_plotpage.phtml assay_plot.phtml 
Log Message:
removed old incompatible overview plot

--- assay_plotpage.phtml DELETED ---

--- assay_plot.phtml DELETED ---

[basedb-cvs] basedb/www codesize,1.8,1.9

From: <tr...@us...> - 2003-02-18 07:49:51

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv17255/www

Modified Files:
	codesize 
Log Message:
widened column

Index: codesize
===================================================================
RCS file: /cvsroot/basedb/basedb/www/codesize,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** codesize	3 Feb 2003 17:22:05 -0000	1.8
--- codesize	18 Feb 2003 07:49:48 -0000	1.9
***************
*** 3,7 ****
  function cntstuff
  {
! 	printf "%-8s %5d %6d %6d %8d\\n" \
  	"$1" \
  	`ls -1 $2 |wc -l` \
--- 3,7 ----
  function cntstuff
  {
! 	printf "%-12s %5d %6d %6d %8d\\n" \
  	"$1" \
  	`ls -1 $2 |wc -l` \
***************
*** 14,18 ****
  }
  
! echo    "type     files  funcs  lines    bytes"
  cntstuff www "*.phtml"
  cntstuff classes "../include/classes/*.php"
--- 14,18 ----
  }
  
! echo    "type         files  funcs  lines    bytes"
  cntstuff www "*.phtml"
  cntstuff classes "../include/classes/*.php"
***************
*** 22,26 ****
  cntstuff webinc "../include/web/*.php"
  cntstuff bin "../bin/*.php"
! cntstuff plotapp "plotapplet/*.phtml"
  cntstuff total "
  	*.phtml
--- 22,26 ----
  cntstuff webinc "../include/web/*.php"
  cntstuff bin "../bin/*.php"
! cntstuff plotapplet "plotapplet/*.phtml"
  cntstuff total "
  	*.phtml

[basedb-cvs] basedb/www/plotapplet plot_assay.phtml,1.2,1.3 plot_raw.phtml,1.1,1.2

From: <tr...@us...> - 2003-02-18 07:49:27

Update of /cvsroot/basedb/basedb/www/plotapplet
In directory sc8-pr-cvs1:/tmp/cvs-serv17061/www/plotapplet

Modified Files:
	plot_assay.phtml plot_raw.phtml 
Log Message:
began cleanup

Index: plot_assay.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plotapplet/plot_assay.phtml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** plot_assay.phtml	3 Feb 2003 20:13:20 -0000	1.2
--- plot_assay.phtml	18 Feb 2003 07:49:24 -0000	1.3
***************
*** 3,7 ****
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Mats Attnäs
  //
  // This file is part of BASE.
--- 3,7 ----
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002, 2003 Mats Attnäs, Carl Troein
  //
  // This file is part of BASE.
***************
*** 23,38 ****
  	require_once("../getconfig.inc.php");
  	require_once("init.inc.php");
- 	require_once("item_common.inc.php");
  	require_once("misc.inc.php");
! 	require_once("raw.inc.php");
! 	require_once("mime.inc.php");
  
  	verifyAccess(BioAssay::globalRead());
  ?>
  
! <applet code="plotapplet.PlotApplet" archive="plot.jar" width=1100 height=800>
! <param name="dataUrlBase" value="read_data.phtml?i_type=assay&i_id=<?= (int)$i_r ?>">
! <param name="cookies" value="<?= $config["cookieName"] . "=" . $_COOKIE[$config["cookieName"]] ?>">
! <param name="infoUrlBase" value="../spotinfo.phtml?i_r=<?= (int)$i_r ?>&i_pos=">
  <param name="infoIdColumn" value="position">
  <param name="addParameterName" value="i_add">
--- 23,46 ----
  	require_once("../getconfig.inc.php");
  	require_once("init.inc.php");
  	require_once("misc.inc.php");
! 	require_once("bioassay.inc.php");
! 	require_once("htmlinit.inc.php");
  
  	verifyAccess(BioAssay::globalRead());
+ 
+ 	$assid = isset($i_a) ? (int)$i_a : 0;
+ 
+ 	$pageTitle="$config[codename] - Java plot tool (BioAssay)";
+ 	htmlBegin($pageTitle);
  ?>
  
! <applet code="plotapplet.PlotApplet" archive="plot.jar" width=1100
! 	height=800>
! <param name="dataUrlBase"
! 	value="read_data.phtml?i_type=assay&i_id=<?= $assid ?>">
! <param name="cookies" value="<?=
! 	html($config["cookieName"] . "=" . $_COOKIE[$config["cookieName"]], 0)
! 	?>">
! <param name="infoUrlBase" value="../spotinfo.phtml?i_a=<?= $assid ?>&i_pos=">
  <param name="infoIdColumn" value="position">
  <param name="addParameterName" value="i_add">
***************
*** 42,44 ****
  
  </body>
! </html>
\ No newline at end of file
--- 50,53 ----
  
  </body>
! </html>
! 

Index: plot_raw.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plotapplet/plot_raw.phtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** plot_raw.phtml	1 Feb 2003 18:19:12 -0000	1.1
--- plot_raw.phtml	18 Feb 2003 07:49:24 -0000	1.2
***************
*** 3,7 ****
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Mats Attnäs
  //
  // This file is part of BASE.
--- 3,7 ----
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002, 2003 Mats Attnäs, Carl Troein
  //
  // This file is part of BASE.
***************
*** 23,39 ****
  	require_once("../getconfig.inc.php");
  	require_once("init.inc.php");
- 	require_once("item_common.inc.php");
  	require_once("misc.inc.php");
  	require_once("raw.inc.php");
! 	require_once("mime.inc.php");
  
  	verifyAccess(RawBioAssay::globalRead());
- ?>
  
! <applet code="plotapplet.PlotApplet" archive="plot.jar" width=1100 height=800>
! <param name="dataUrlBase" value="read_data.phtml?i_type=raw&i_id=<?= (int)$i_r ?>">
! <param name="cookies" value="<?= $config["cookieName"] . "=" . $_COOKIE[$config["cookieName"]] ?>">
! <param name="infoUrlBase" value="../spotinfo.phtml?i_r=<?= (int)$i_r ?>&i_pos=">
! <param name="infoIdColumn" value="position">
  <param name="addParameterName" value="i_add">
  
--- 23,46 ----
  	require_once("../getconfig.inc.php");
  	require_once("init.inc.php");
  	require_once("misc.inc.php");
  	require_once("raw.inc.php");
! 	require_once("htmlinit.inc.php");
  
  	verifyAccess(RawBioAssay::globalRead());
  
! 	$rawid = isset($i_r) ? (int)$i_r : 0;
! 
! 	$pageTitle="$config[codename] - Java plot tool (raw data)";
! 	htmlBegin($pageTitle);
! ?>
! <applet code="plotapplet.PlotApplet" archive="plot.jar" width=1100
! 	height=800>
! <param name="dataUrlBase"
! 	value="read_data.phtml?i_type=raw&i_id=<?= $rawid ?>">
! <param name="cookies" value="<?=
! 	html($config["cookieName"] . "=" . $_COOKIE[$config["cookieName"]], 0)
! 	?>">
! <param name="infoUrlBase" value="../spotinfo.phtml?i_r=<?= $rawid ?>&i_pos=">
! <param name="infoIdColumn" value="rawPosition">
  <param name="addParameterName" value="i_add">
  
***************
*** 42,44 ****
  
  </body>
! </html>
\ No newline at end of file
--- 49,52 ----
  
  </body>
! </html>
!

[basedb-cvs] basedb/include/web raw_common.inc.php,1.11,1.12 searchhtml.inc.php,1.11,1.12

From: <tr...@us...> - 2003-02-18 07:48:36

Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv16614/include/web

Modified Files:
	raw_common.inc.php searchhtml.inc.php 
Log Message:
Minor improvements to html output

Index: raw_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/raw_common.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** raw_common.inc.php	1 Feb 2003 23:04:15 -0000	1.11
--- raw_common.inc.php	18 Feb 2003 07:48:33 -0000	1.12
***************
*** 48,54 ****
  {
  	$id = (int)$id;
! 	return "[<a ".href("raw_table.phtml?i_r=$id", 2).">Table</a>] ".
  		"[<a class=popup target=rawPlotter_$id ".
! 		"href='raw_plotter.phtml?i_r=$id'>HTML&nbsp;plot&nbsp;tool</a>] ".
  		"[<a class=popup target=rawJavaPlot_$id ".
  		"href='plotapplet/plot_raw.phtml?i_r=$id'>".
--- 48,54 ----
  {
  	$id = (int)$id;
! 	return "[<a ".href("raw_table.phtml?i_r=$id", 2).">Table</a>]\n".
  		"[<a class=popup target=rawPlotter_$id ".
! 		"href='raw_plotter.phtml?i_r=$id'>HTML&nbsp;plot&nbsp;tool</a>]\n".
  		"[<a class=popup target=rawJavaPlot_$id ".
  		"href='plotapplet/plot_raw.phtml?i_r=$id'>".
***************
*** 117,129 ****
  		echo "<tr bgcolor=$tdbg[$odd]>".
  			"<td><a href='raw_edit.phtml?i_r=$id'>".
! 				html($s["name"])."</a>".remMark($s)."</td>".
  			"<td>".htmldate($s["addedDate"])."</td>".
  			"<td>".html($s["userName"])."</td>".
  			"<td>".groupAccessCheckbox($id)."</td>".
  			"<td>".groupInfo($s, $users)."</td>".
! 			"<td>".worldInfo($s)."</td>".
  			"<td>".implode(",\n", $slink)."</td>".
  			"<td>".$s["spots"]."</td>".
! 			"<td>".($s["hasLims"] ? "Yes" : "No")."</td>".
  			"<td>".implode(",\n", $elink)."</td>".
  			"<td>".rawPlotLinks($id)."</td>".
--- 117,129 ----
  		echo "<tr bgcolor=$tdbg[$odd]>".
  			"<td><a href='raw_edit.phtml?i_r=$id'>".
! 				html($s["name"])."</a>".remMark($s)."</td>\n".
  			"<td>".htmldate($s["addedDate"])."</td>".
  			"<td>".html($s["userName"])."</td>".
  			"<td>".groupAccessCheckbox($id)."</td>".
  			"<td>".groupInfo($s, $users)."</td>".
! 			"<td>".worldInfo($s)."</td>\n".
  			"<td>".implode(",\n", $slink)."</td>".
  			"<td>".$s["spots"]."</td>".
! 			"<td>".($s["hasLims"] ? "Yes" : "No")."</td>\n".
  			"<td>".implode(",\n", $elink)."</td>".
  			"<td>".rawPlotLinks($id)."</td>".

Index: searchhtml.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/searchhtml.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** searchhtml.inc.php	23 Jan 2003 22:16:54 -0000	1.11
--- searchhtml.inc.php	18 Feb 2003 07:48:33 -0000	1.12
***************
*** 732,736 ****
  
  	if($headerfields)
! 		echo "<tr>";
  	for(reset($headerfields); list($i, $a) = each($headerfields); )
  	{
--- 732,736 ----
  
  	if($headerfields)
! 		echo "<tr style='white-space: nowrap'>";
  	for(reset($headerfields); list($i, $a) = each($headerfields); )
  	{

[basedb-cvs] basedb/include/classes news.inc.php,1.7,1.8

From: <tr...@us...> - 2003-02-18 07:47:23

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv15923/include/classes

Modified Files:
	news.inc.php 
Log Message:
fixed addedDate bug (nicklas)

Index: news.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/news.inc.php,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** news.inc.php	15 Feb 2003 11:29:07 -0000	1.7
--- news.inc.php	18 Feb 2003 07:47:20 -0000	1.8
***************
*** 31,35 ****
  	{
  		$this->Item("News", $name, $descr, $owner, $addedDate, $id, 0);
! 		$this->addedDate = now();
  	}
  
--- 31,36 ----
  	{
  		$this->Item("News", $name, $descr, $owner, $addedDate, $id, 0);
! 		if($addedDate == "")
! 			$this->addedDate = now();
  	}

[basedb-cvs] basedb/include/drivers pgsql.inc.php,1.12,1.13

From: <tr...@us...> - 2003-02-18 07:33:56

Update of /cvsroot/basedb/basedb/include/drivers
In directory sc8-pr-cvs1:/tmp/cvs-serv8583

Modified Files:
	pgsql.inc.php 
Log Message:
Undid changes after re-reading bug report

Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/drivers/pgsql.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** pgsql.inc.php	18 Feb 2003 07:28:37 -0000	1.12
--- pgsql.inc.php	18 Feb 2003 07:33:52 -0000	1.13
***************
*** 487,496 ****
  {
  	if($base)
! 	{
! 		$e = "(LOG(CASE WHEN $arg > 0. THEN float8($arg) ELSE 1. END)".
! 			"/LOG($base.))";
! 	}
  	else
! 		$e = "LOG(CASE WHEN $arg > 0. THEN float8($arg) ELSE 1. END)";
  	return "CASE WHEN $arg > 0. THEN $e ELSE NULL END";
  }
--- 487,493 ----
  {
  	if($base)
! 		$e = "(LOG(float8($arg))/LOG($base.))";
  	else
! 		$e = "LOG(float8($arg))";
  	return "CASE WHEN $arg > 0. THEN $e ELSE NULL END";
  }
***************
*** 499,504 ****
  function db_func_div($num, $denom)
  {
! 	return "CASE WHEN $denom = 0. THEN NULL ELSE ".
! 		"$num/(CASE WHEN $denom = 0. THEN 1. ELSE $denom END) END";
  }
  
--- 496,500 ----
  function db_func_div($num, $denom)
  {
! 	return "CASE WHEN $denom = 0. THEN NULL ELSE $num/$denom END";
  }

[basedb-cvs] basedb/include/drivers pgsql.inc.php,1.11,1.12

From: <tr...@us...> - 2003-02-18 07:28:40

Update of /cvsroot/basedb/basedb/include/drivers
In directory sc8-pr-cvs1:/tmp/cvs-serv5885

Modified Files:
	pgsql.inc.php 
Log Message:
Attempt to fix problem with division by zero

Index: pgsql.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/drivers/pgsql.inc.php,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** pgsql.inc.php	28 Jan 2003 17:22:54 -0000	1.11
--- pgsql.inc.php	18 Feb 2003 07:28:37 -0000	1.12
***************
*** 487,493 ****
  {
  	if($base)
! 		$e = "(LOG(float8($arg))/LOG($base.))";
  	else
! 		$e = "LOG(float8($arg))";
  	return "CASE WHEN $arg > 0. THEN $e ELSE NULL END";
  }
--- 487,496 ----
  {
  	if($base)
! 	{
! 		$e = "(LOG(CASE WHEN $arg > 0. THEN float8($arg) ELSE 1. END)".
! 			"/LOG($base.))";
! 	}
  	else
! 		$e = "LOG(CASE WHEN $arg > 0. THEN float8($arg) ELSE 1. END)";
  	return "CASE WHEN $arg > 0. THEN $e ELSE NULL END";
  }
***************
*** 496,500 ****
  function db_func_div($num, $denom)
  {
! 	return "CASE WHEN $denom = 0. THEN NULL ELSE $num/$denom END";
  }
  
--- 499,504 ----
  function db_func_div($num, $denom)
  {
! 	return "CASE WHEN $denom = 0. THEN NULL ELSE ".
! 		"$num/(CASE WHEN $denom = 0. THEN 1. ELSE $denom END) END";
  }

[basedb-cvs] basedb/plugins/src/merge_bioassays merge_bioassays.cc,1.2,1.3

From: <tr...@us...> - 2003-02-17 14:05:42

Update of /cvsroot/basedb/basedb/plugins/src/merge_bioassays
In directory sc8-pr-cvs1:/tmp/cvs-serv21133/plugins/src/merge_bioassays

Modified Files:
	merge_bioassays.cc 
Log Message:
added missing include of cstdio

Index: merge_bioassays.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/merge_bioassays/merge_bioassays.cc,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** merge_bioassays.cc	6 Feb 2003 00:43:34 -0000	1.2
--- merge_bioassays.cc	17 Feb 2003 14:05:37 -0000	1.3
***************
*** 1,3 ****
--- 1,4 ----
  #include <iostream>
+ #include <cstdio>
  #include "basefile.h"

[basedb-cvs] basedb README,1.24,1.25

From: <tr...@us...> - 2003-02-17 14:03:02

Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv19381

Modified Files:
	README 
Log Message:
added note about mailing list and what to do to piss me off

Index: README
===================================================================
RCS file: /cvsroot/basedb/basedb/README,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** README	13 Feb 2003 22:22:02 -0000	1.24
--- README	17 Feb 2003 14:02:58 -0000	1.25
***************
*** 8,11 ****
--- 8,23 ----
  *ix experience.
  
+ If you have an installation problem, the BASE mailing list is the place to
+ go. The list archive holds answers to a fair number of recent questions, so
+ do a search there before asking if there's any reason to believe that your
+ problem might not be unique. When asking things on the mailing list, please
+ include enough information: What version of BASE you're dealing with, what
+ you did and what happened, and versions of relevant pieces of software
+ (e.g. the compiler if something doesn't compile). If you're reporting a
+ post-installation problem, also include things logged by BASE and PHP.
+ (By default errors from PHP will end up in the apache error log when PHP
+ is run as an apache module.) And whatever you do, please do NOT send
+ installation questions directly to the developers.
+ 
  BASE 1.2.0RC2 is the second release candidate for BASE 1.2.0, and it's
  significantly more stable than the previous RC. Despite what was said about

[basedb-cvs] basedb/bin baseftpd.php,1.2,1.3 checkDatabase.php,1.1,1.2 jobController.php,1.1,1.2 startBase.php,1.4,1.5 stopBase.php,1.4,1.5

From: <tr...@us...> - 2003-02-16 02:04:20

Update of /cvsroot/basedb/basedb/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv9956/bin

Modified Files:
	baseftpd.php checkDatabase.php jobController.php startBase.php 
	stopBase.php 
Log Message:
rewrote BaseControl to be much more robust and optionally use flock()

Index: baseftpd.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/baseftpd.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** baseftpd.php	4 Feb 2003 18:22:50 -0000	1.2
--- baseftpd.php	16 Feb 2003 02:03:46 -0000	1.3
***************
*** 39,52 ****
  
  $BC = new BaseControl();
- if(!$BC->mayRun())
- 	die("421 BASE has been shut down\n");
  
! // Open database connection
! if(!db_connect($config["dbHost"], $config["dbUser"],
! 	$config["dbPassword"], $config["dbDatabase"]))
  {
! 	die("421 Unable to connect to database\n");
  }
- unset($config["dbPassword"]);
  
  $ftpd = new ftpd($_SERVER["argv"][1], $_SERVER["argv"][2]);
--- 39,53 ----
  
  $BC = new BaseControl();
  
! $start = $BC->startScript();
! if($start == -1)
! 	die("421 Failed to connect to the database.\r\n");
! else if($start < 0)
! 	die("421 Internal error in BASE startup\r\n");
! else if(!$start)
  {
! 	die("421 BASE has been shut down: ".
! 		printable($BC->shutdownMessage())."\r\n");
  }
  
  $ftpd = new ftpd($_SERVER["argv"][1], $_SERVER["argv"][2]);
***************
*** 54,60 ****
--- 55,74 ----
  while(!feof(STDIN))
  {
+ 	$BC->endScript();
+ 
  	$line = rtrim(fgets(STDIN));
  	if($line == "")
  		continue;
+ 
+ 	$start = $BC->startScript();
+ 	if($start == -1)
+ 		die("421 Failed to connect to the database.\r\n");
+ 	else if($start < 0)
+ 		die("421 Internal error in BASE startup\r\n");
+ 	else if(!$start)
+ 	{
+ 		die("421 BASE has been shut down: ".
+ 			printable($BC->shutdownMessage())."\r\n");
+ 	}
  
  	$ftpd->dispatch($line);

Index: checkDatabase.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/checkDatabase.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** checkDatabase.php	1 Feb 2003 12:52:50 -0000	1.1
--- checkDatabase.php	16 Feb 2003 02:03:47 -0000	1.2
***************
*** 41,65 ****
  
  $BC = new BaseControl();
! if($BC->mayRun())
! {
! 	mydie("Error: BASE needs to be shut down for this script to work ".
! 		"properly.\n");
! }
! 
! // Open database connection
! echo "Connecting to database...\n";
! if(!db_connect($config["dbHost"], $config["dbUser"],
! 	$config["dbPassword"], $config["dbDatabase"]))
  {
! 	mydie("Unable to connect to $config[RDBMS].\n");
  }
! unset($config["dbPassword"]);
  
- if(!$BC->testShutdown())
- {
- 	mydie("BASE is not fully shut down, but it has to be for this\n".
- 		"script to work properly.\n");
- }
  
  
  echo "Processing users and groups...\n";
--- 41,59 ----
  
  $BC = new BaseControl();
! $start = $BC->startScript(true);
! if($start == -1)
! 	mydie("Failed to connect to the database.\n");
! if($start == -2)
  {
! 	mydie("Error: BASE needs to be shut down first.\n");
  }
! else if($start < 0)
! 	mydie("Internal error in BASE startup.\n");
! else if(!$start)
! 	mydie("Error: Shutdown hasn't take effect yet.\n");
  
  
+ if($config["RDBMS"] != "mysql")
+ 	mydie("This script only supports MySQL databases for now.\n");
  
  echo "Processing users and groups...\n";

Index: jobController.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/jobController.php,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** jobController.php	1 Feb 2003 12:52:50 -0000	1.1
--- jobController.php	16 Feb 2003 02:03:47 -0000	1.2
***************
*** 37,50 ****
  
  $BC = new BaseControl();
! if(!$BC->mayRun())
  	die("BASE has been shut down\n");
- 
- // Open database connection
- if(!db_connect($config["dbHost"], $config["dbUser"],
- 	$config["dbPassword"], $config["dbDatabase"]))
- {
- 	die("Unable to connect to database\n");
- }
- unset($config["dbPassword"]);
  
  $job = new Job();
--- 37,47 ----
  
  $BC = new BaseControl();
! $start = $BC->startScript();
! if($start == -1)
! 	die("Failed to connect to the database.\n");
! else if($start < 0)
! 	die("Internal error in BASE startup.\n");
! else if(!$start)
  	die("BASE has been shut down\n");
  
  $job = new Job();

Index: startBase.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/startBase.php,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** startBase.php	13 Feb 2003 12:23:56 -0000	1.4
--- startBase.php	16 Feb 2003 02:03:47 -0000	1.5
***************
*** 36,44 ****
  
  if(!verifySetup())
! {
! 	if($BC->mayRun())
! 		mydie("\nBASE is running but misconfigured\n");
! 	mydie("\nBASE has not been started\n");
! }
  
  if(!restartBase())
--- 36,40 ----
  
  if(!verifySetup())
! 	return 1;
  
  if(!restartBase())
***************
*** 55,81 ****
  	global $config, $BC;
  
! 	if($BC->mayRun())
! 	{
! 		mydie("BASE is already running. If you did an unclean shutdown ".
! 			"of BASE\n".
! 			"(without using stopBase.php), you may want to run ".
! 			"checkDatabase.php\n");
! 	}
! 
! 	// Open database connection
! 	if(!db_connect($config["dbHost"], $config["dbUser"],
! 		$config["dbPassword"], $config["dbDatabase"]))
  	{
! 		mydie("Unable to connect to $config[RDBMS].\n");
  	}
! 	unset($config["dbPassword"]);
! 
! 	$state = $BC->getState();
! 	if($state && $state["pendingTransactions"])
  	{
! 		mydie("There are pending transactions according to the database.\n".
! 			"The stopBase.php script may provide more information, or you\n".
! 			"can just update the row in table BaseControl after verifying\n".
! 			"that it's incorrect.\n");
  	}
  
--- 51,77 ----
  	global $config, $BC;
  
! 	$start = $BC->startScript(true);
! 	if($start == -1)
! 		mydie("BASE cannot be started: unable to connect to the database\n");
! 	else if($start == -2)
  	{
! 		if($config["useFlock"])
! 			mydie("BASE is already running.\n");
! 		mydie("BASE is already running. If it claims otherwise, check the\n".
! 			"BaseControl table as described in the documentation.\n");
  	}
! 	else if($start < 0)
! 		mydie("BASE cannot be started: early startup failed ($start)\n");
! 	else if(!$start)
  	{
! 		if($config["useFlock"])
! 		{
! 			mydie("BASE cannot be started: a maintenance script seems to ".
! 				"be running.\n");
! 		}
! 		mydie("BASE cannot be started: a maintenance script seems to ".
! 			"be running,\n".
! 			"or the pendingTransactions counter in the BaseControl table ".
! 			"has been\ncorrupted.\n");
  	}
  
***************
*** 133,137 ****
  		fwrite(STDERR, "Error: The database schema version is $sv,\n".
  			"but this version of BASE requires schema version 1.2.3\n".
! 			"Use the migration scripts in bin to correct this.\n");
  		return 0;
  	}
--- 129,133 ----
  		fwrite(STDERR, "Error: The database schema version is $sv,\n".
  			"but this version of BASE requires schema version 1.2.3\n".
! 			"Use the migration scripts in 'bin' to correct this.\n");
  		return 0;
  	}

Index: stopBase.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/stopBase.php,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** stopBase.php	15 Feb 2003 12:37:38 -0000	1.4
--- stopBase.php	16 Feb 2003 02:03:47 -0000	1.5
***************
*** 33,95 ****
  	mydie("Usage: ".$_SERVER["argv"][0]." \"message\"\n");
  
  return shutdownBase($_SERVER["argv"][1]) ? 0 : 1;
  
  function shutdownBase($msg)
  {
! 	global $config;
! 
! 	$BC = new BaseControl();
! 
[...127 lines suppressed...]
  	if(!$down)
  	{
! 		if($config["useFlock"])
! 		{
! 			mydie("Timed out after $maxwait minutes.\n".
! 				"Manual intervention may be needed to restore referential\n".
! 				"integrity, if the running script(s) are killed\n");
! 		}
! 		else
! 		{
! 			mydie("Timed out after $maxwait minutes.\n".
! 				"Manual intervention may be needed to restore referential\n".
! 				"integrity. There may be running scripts which could\n".
! 				"leave things in an undefined state if killed, or the\n".
! 				"BaseControl table's pendingTransaction column holds the\n".
! 				"wrong value because of crashed scripts or a previous\n".
! 				"unclean shutdown.\n");
! 		}
  	}
  	echo "BASE was successfully shut down.\n";

[basedb-cvs] basedb example_config.inc.php,1.16,1.17

From: <tr...@us...> - 2003-02-16 02:04:19

Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv9956

Modified Files:
	example_config.inc.php 
Log Message:
rewrote BaseControl to be much more robust and optionally use flock()

Index: example_config.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/example_config.inc.php,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** example_config.inc.php	1 Feb 2003 17:18:50 -0000	1.16
--- example_config.inc.php	16 Feb 2003 02:03:46 -0000	1.17
***************
*** 62,65 ****
--- 62,71 ----
  	$config["mime.types"]		= "/usr/local/apache/conf/mime.types";
  
+ 	// Whether to use flock() for the locking needed by BASE. If your
+ 	// tempDir is on NFS or VFAT or some other file system which does
+ 	// not support flock(), you _must_ turn this off. The BaseControl
+ 	// table of the relational database will then be used for locking.
+ 	$config["useFlock"]			= 1;
+ 
  	// Paths to various parts of BASE.
  	// Note that you can move the "www" directory to wherever you wish, as

[basedb-cvs] basedb/include/web newinit.inc.php,1.5,1.6

From: <tr...@us...> - 2003-02-16 02:03:52

Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv9956/include/web

Modified Files:
	newinit.inc.php 
Log Message:
rewrote BaseControl to be much more robust and optionally use flock()

Index: newinit.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/newinit.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** newinit.inc.php	13 Feb 2003 12:34:39 -0000	1.5
--- newinit.inc.php	16 Feb 2003 02:03:49 -0000	1.6
***************
*** 3,7 ****
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson
  //
  // This file is part of BASE.
--- 3,7 ----
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson
  //
  // This file is part of BASE.
***************
*** 22,27 ****
  //
  
! if(!isset($config))
! 	die("Fatal error: newinit.inc.php included without config.inc.php!\n");
  
  	require_once("db.inc.php");
--- 22,27 ----
  //
  
! 	if(!isset($config))
! 		die("Fatal error: newinit.inc.php included without config.inc.php!\n");
  
  	require_once("db.inc.php");
***************
*** 44,48 ****
  
  		$BC = new BaseControl();
! 		if(!$BC->mayRun())
  		{
  			$url = ereg_replace("^$config[urlpath]",
--- 44,53 ----
  
  		$BC = new BaseControl();
! 		$start = $BC->startScript();
! 		if($start == -1)
! 			die("Failed to connect to database. See the error log for details");
! 		else if($start < 0)
! 			die("Script startup failed. See the error log for details");
! 		else if(!$start)
  		{
  			$url = ereg_replace("^$config[urlpath]",
***************
*** 50,60 ****
  			redirect("downtime.phtml?location=".urlencode($url));
  		}
- 
- 		if(!db_connect($config["dbHost"], $config["dbUser"],
- 			$config["dbPassword"], $config["dbDatabase"]))
- 		{
- 			die("Failed to connect to database. See the error log for details");
- 		}
- 		unset($config["dbPassword"]);		// Perfectly normal paranoia
  
  		Session::purgeSessions($config["sessionTimeout"]);
--- 55,58 ----

[basedb-cvs] basedb/include/common common.inc.php,1.19,1.20

From: <tr...@us...> - 2003-02-16 02:03:52

Update of /cvsroot/basedb/basedb/include/common
In directory sc8-pr-cvs1:/tmp/cvs-serv9956/include/common

Modified Files:
	common.inc.php 
Log Message:
rewrote BaseControl to be much more robust and optionally use flock()

Index: common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/common/common.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** common.inc.php	13 Feb 2003 08:47:46 -0000	1.19
--- common.inc.php	16 Feb 2003 02:03:49 -0000	1.20
***************
*** 80,84 ****
  		"rootDir", "uploadDir", "tempDir", "jobDir", "rawFileDir",
  		"rawImageDir", "printMapDir", "protocolDir", "logDir",
! 		"spotImageDir", "umask", "pluginArguments", "useJobRunner");
  	if(isset($cfgvars["RDBMS"]) && $cfgvars["RDBMS"] == "mysql")
  		$cfgvars[] = "mysql.localinfile";
--- 80,85 ----
  		"rootDir", "uploadDir", "tempDir", "jobDir", "rawFileDir",
  		"rawImageDir", "printMapDir", "protocolDir", "logDir",
! 		"spotImageDir", "umask", "pluginArguments", "useJobRunner",
! 		"useFlock");
  	if(isset($cfgvars["RDBMS"]) && $cfgvars["RDBMS"] == "mysql")
  		$cfgvars[] = "mysql.localinfile";

[basedb-cvs] basedb/include/classes basecontrol.inc.php,1.10,1.11 ftpd.inc.php,1.3,1.4 jobhandler.inc.php,1.10,1.11

From: <tr...@us...> - 2003-02-16 02:03:51

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv9956/include/classes

Modified Files:
	basecontrol.inc.php ftpd.inc.php jobhandler.inc.php 
Log Message:
rewrote BaseControl to be much more robust and optionally use flock()

Index: basecontrol.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/basecontrol.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** basecontrol.inc.php	15 Feb 2003 11:31:41 -0000	1.10
--- basecontrol.inc.php	16 Feb 2003 02:03:47 -0000	1.11
***************
*** 40,44 ****
  class BaseControl
  {
! 	var $depth, $iua;
  
  	function BaseControl()
--- 40,44 ----
  class BaseControl
  {
! 	var $depth, $iua, $fd;
  
[...389 lines suppressed...]
  	}
  
! 	// Let BASE get back online. Call this function only after a successful
! 	// startScript(true).
  	function endShutdown()
  	{
  		if(!$this->abortShutdown(false))
  			return false;
  		$query = "UPDATE BaseControl SET `startTime` = NOW()";
  		return (bool)query($query);
+ 	}
+ 
+ 	// Returns an array with shutDown, pendingTransactions, etc.
+ 	function getState()
+ 	{
+ 		$query = "SELECT * FROM BaseControl";
+ 		$res = query($query);
+ 		return db_fetch_assoc($res);
  	}
  

Index: ftpd.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/ftpd.inc.php,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** ftpd.inc.php	10 Feb 2003 08:40:44 -0000	1.3
--- ftpd.inc.php	16 Feb 2003 02:03:48 -0000	1.4
***************
*** 73,83 ****
  	function dispatch($line)
  	{	
- 		global $BC;
- 		if(!$BC->mayRun())
- 		{
- 			echo "421 BASE is shutting down";
- 			exit;
- 		}
- 
  		$arr = explode(" ", $line, 2);
  		$cmd = strtoupper($arr[0]);
--- 73,76 ----

Index: jobhandler.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/jobhandler.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** jobhandler.inc.php	11 Feb 2003 14:43:10 -0000	1.10
--- jobhandler.inc.php	16 Feb 2003 02:03:48 -0000	1.11
***************
*** 126,131 ****
  		$prog =& $this->prog;
  
! 		// Let go or transaction while the job's running.
  		$BC->endTransaction();
  
  		list($u, $s) = explode(" ", microtime());
--- 126,132 ----
  		$prog =& $this->prog;
  
! 		// Let go of everything while the job's running.
  		$BC->endTransaction();
+ 		$BC->endScript();
  
  		list($u, $s) = explode(" ", microtime());

[basedb-cvs] basedb/include/classes bioassayset.inc.php,1.22,1.23

From: <tr...@us...> - 2003-02-16 02:02:53

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv9779/include/classes

Modified Files:
	bioassayset.inc.php 
Log Message:
added backticks

Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassayset.inc.php,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** bioassayset.inc.php	11 Feb 2003 14:43:08 -0000	1.22
--- bioassayset.inc.php	16 Feb 2003 02:02:50 -0000	1.23
***************
*** 965,969 ****
  			$name = $a["name"];
  			$expr[] = array("_xc_".printable($name), $types[$a["valueType"]],
! 				"%%.extraValue", $name);
  			$tname = "baef_$id";
  			$comm = "[Extra]";
--- 965,969 ----
  			$name = $a["name"];
  			$expr[] = array("_xc_".printable($name), $types[$a["valueType"]],
! 				"%%.`extraValue`", $name);
  			$tname = "baef_$id";
  			$comm = "[Extra]";

[basedb-cvs] basedb/www acquisition_list.phtml,1.1,1.2

From: <tr...@us...> - 2003-02-16 02:02:40

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv9742/www

Modified Files:
	acquisition_list.phtml 
Log Message:
added missing include

Index: acquisition_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/acquisition_list.phtml,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** acquisition_list.phtml	13 Feb 2003 08:47:47 -0000	1.1
--- acquisition_list.phtml	16 Feb 2003 02:02:34 -0000	1.2
***************
*** 26,29 ****
--- 26,30 ----
  	require_once("hyb.inc.php");
  	require_once("raw.inc.php");
+ 	require_once("ware.inc.php");
  	require_once("search.inc.php");
  	require_once("searchhtml.inc.php");

[basedb-cvs] basedb/www assay_table.phtml,1.25,1.26 raw_table.phtml,1.4,1.5

From: <tr...@us...> - 2003-02-15 12:39:30

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv9484/www

Modified Files:
	assay_table.phtml raw_table.phtml 
Log Message:
fixed some table cell rendering stuff

Index: assay_table.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/assay_table.phtml,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** assay_table.phtml	11 Feb 2003 14:43:56 -0000	1.25
--- assay_table.phtml	15 Feb 2003 12:39:26 -0000	1.26
***************
*** 294,298 ****
  
  	$cols[] = array("geneName", false, "Reporter name", 1,
! 		1, $show);
  
  	$rep = ReporterColumn::getColumns();
--- 294,298 ----
  
  	$cols[] = array("geneName", false, "Reporter name", 1,
! 		"renderGeneName", $show);
  
  	$rep = ReporterColumn::getColumns();

Index: raw_table.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_table.phtml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** raw_table.phtml	13 Feb 2003 22:29:38 -0000	1.4
--- raw_table.phtml	15 Feb 2003 12:39:26 -0000	1.5
***************
*** 131,135 ****
  
  	$spots = $raw->dataSearch($search);
! 	$cbRaw = $rawid;	// For renderSpot()
  
  	for($i = 0, $odd = 0; $i < count($spots); $i++, $odd ^= 1)
--- 131,135 ----
  
  	$spots = $raw->dataSearch($search);
! 	$cbRaw = $rawid;	// For spot and position rendering
  
  	for($i = 0, $odd = 0; $i < count($spots); $i++, $odd ^= 1)
***************
*** 152,156 ****
  	$gshow = $show && $repLevel < 5 ? 1 : 0;
  	$cols = array(
! 		array("rawPosition", false, "Pos", 1, "renderExplorePosition", $show),
  		array("reporterId", false, "Reporter", 1, 3, $show)
  		);
--- 152,157 ----
  	$gshow = $show && $repLevel < 5 ? 1 : 0;
  	$cols = array(
! 		array("rawPosition", false, "Pos", 1,
! 			"renderExplorePositionRaw", $show),
  		array("reporterId", false, "Reporter", 1, 3, $show)
  		);

[basedb-cvs] basedb/include/web gene_common.inc.php,1.10,1.11

From: <tr...@us...> - 2003-02-15 12:39:30

Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv9484/include/web

Modified Files:
	gene_common.inc.php 
Log Message:
fixed some table cell rendering stuff

Index: gene_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/gene_common.inc.php,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** gene_common.inc.php	11 Feb 2003 14:43:12 -0000	1.10
--- gene_common.inc.php	15 Feb 2003 12:39:26 -0000	1.11
***************
*** 118,121 ****
--- 118,127 ----
  		">$pos</a></td>\n";
  }
+ function renderExplorePositionRaw($pos)
+ {
+ 	global $cbRaw;
+ 	echo "<td><a ".href("spotinfo.phtml?i_r=$cbRaw&i_pos=$pos", 2).
+ 		">$pos</a></td>\n";
+ }
  
  function renderExploreBackend1(&$element)

[basedb-cvs] basedb/www spotinfo.phtml,1.16,1.17

From: <tr...@us...> - 2003-02-15 12:39:04

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv9294/www

Modified Files:
	spotinfo.phtml 
Log Message:
added missing ()

Index: spotinfo.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/spotinfo.phtml,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** spotinfo.phtml	22 Jan 2003 21:47:43 -0000	1.16
--- spotinfo.phtml	15 Feb 2003 12:39:01 -0000	1.17
***************
*** 33,36 ****
--- 33,37 ----
  	require_once("links_common.inc.php");
  	require_once("htmlinit.inc.php");
+ 	require_once("experiment.inc.php");
  
  	verifyAccess(RawBioAssay::globalRead());
***************
*** 159,163 ****
  <tr><td rowspan=2 width=1 bgcolor=#4080c0><img src="img/1.gif"
  	width=1 height=1></td>
! 	<th class=subhead>Raw data set <?= html($raw->getName).remMark($raw)
  	?></th></tr>
  <tr><td class=red>Error: <?= $err ?></td></tr>
--- 160,164 ----
  <tr><td rowspan=2 width=1 bgcolor=#4080c0><img src="img/1.gif"
  	width=1 height=1></td>
! 	<th class=subhead>Raw data set <?= html($raw->getName()).remMark($raw)
  	?></th></tr>
  <tr><td class=red>Error: <?= $err ?></td></tr>

[basedb-cvs] basedb/include/classes bioassay.inc.php,1.33,1.34 user.inc.php,1.25,1.26 reporterlist.inc.php,1.12,1.13

From: <tr...@us...> - 2003-02-15 12:38:44

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv9122/include/classes

Modified Files:
	bioassay.inc.php user.inc.php reporterlist.inc.php 
Log Message:
fixed problems with isShared

Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassay.inc.php,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** bioassay.inc.php	12 Feb 2003 16:16:45 -0000	1.33
--- bioassay.inc.php	15 Feb 2003 12:38:39 -0000	1.34
***************
*** 1448,1451 ****
--- 1448,1456 ----
  		return $gDFPdata;
  	}
+ 
+ 	function isShared(&$user, $write = 0)
+ 	{
+ 		return Experiment::isSharedId($this->experiment, $user, $write);
+ 	}
  }
  

Index: user.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/user.inc.php,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** user.inc.php	15 Feb 2003 11:29:07 -0000	1.25
--- user.inc.php	15 Feb 2003 12:38:40 -0000	1.26
***************
*** 265,269 ****
  
  	// Superusers can edit anyone, but cannot be edited by normal user admins.
! 	function isShared($user, $write = 0)
  	{
  		$acc = (int)$write;
--- 265,269 ----
  
  	// Superusers can edit anyone, but cannot be edited by normal user admins.
! 	function isShared(&$user, $write = 0)
  	{
  		$acc = (int)$write;

Index: reporterlist.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/reporterlist.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** reporterlist.inc.php	15 Feb 2003 11:29:07 -0000	1.12
--- reporterlist.inc.php	15 Feb 2003 12:38:40 -0000	1.13
***************
*** 389,393 ****
  	}
  
! 	function isShared($user, $write = 0)
  	{
  		return Experiment::isSharedId($this->experiment, $user, $write);
--- 389,393 ----
  	}
  
! 	function isShared(&$user, $write = 0)
  	{
  		return Experiment::isSharedId($this->experiment, $user, $write);

[basedb-cvs] basedb/bin stopBase.php,1.3,1.4

From: <tr...@us...> - 2003-02-15 12:37:41

Update of /cvsroot/basedb/basedb/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv8779/bin

Modified Files:
	stopBase.php 
Log Message:
more readable handling of timeout

Index: stopBase.php
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/stopBase.php,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** stopBase.php	10 Feb 2003 08:40:40 -0000	1.3
--- stopBase.php	15 Feb 2003 12:37:38 -0000	1.4
***************
*** 93,103 ****
  		mydie("Unable to initiate shutdown\n");
  
  	ob_implicit_flush(1);
  	$down = $BC->waitForShutdown(10);
  	if(!$down)
  	{
! 		fwrite(STDERR, "Waiting for locks (10 min max): ");
  		// Wait for ten minutes
! 		for($i = 0; !$down && $i < 24; $i++)
  		{
  			fwrite(STDERR, ".");
--- 93,106 ----
  		mydie("Unable to initiate shutdown\n");
  
+ 	$maxwait = 10;
+ 	$maxdots = (int)($maxwait * 60 / 25);
+ 
  	ob_implicit_flush(1);
  	$down = $BC->waitForShutdown(10);
  	if(!$down)
  	{
! 		fwrite(STDERR, "Waiting for locks ($maxwait minutes max): ");
  		// Wait for ten minutes
! 		for($i = 0; !$down && $i < $maxdots; $i++)
  		{
  			fwrite(STDERR, ".");
***************
*** 108,113 ****
  	if(!$down)
  	{
! 		mydie("Timed out after 10 minutes. ".
! 			"Manual intervention will be needed.\n");
  	}
  	echo "BASE was successfully shut down.\n";
--- 111,117 ----
  	if(!$down)
  	{
! 		mydie("Timed out after $maxwait minutes. ".
! 			"Manual intervention may be needed to restore database ".
! 			"integrity.\n");
  	}
  	echo "BASE was successfully shut down.\n";

[basedb-cvs] basedb/include/classes basecontrol.inc.php,1.9,1.10

From: <tr...@us...> - 2003-02-15 11:31:44

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv21219/include/classes

Modified Files:
	basecontrol.inc.php 
Log Message:
very minor fix

Index: basecontrol.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/basecontrol.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** basecontrol.inc.php	10 Feb 2003 08:40:42 -0000	1.9
--- basecontrol.inc.php	15 Feb 2003 11:31:41 -0000	1.10
***************
*** 64,68 ****
  		error_log("Script left hanging BaseControl transactions ".
  			"(depth $this->depth): $_SERVER[REQUEST_URI]");
! 		while($this->endTransaction()) ;
  	}
  
--- 64,68 ----
  		error_log("Script left hanging BaseControl transactions ".
  			"(depth $this->depth): $_SERVER[REQUEST_URI]");
! 		while($this->depth && $this->endTransaction()) ;
  	}

[basedb-cvs] basedb/www gene_explore.phtml,1.73,1.74 hyb_edit.phtml,1.54,1.55 hyb_list.phtml,1.27,1.28 labeled_list.phtml,1.26,1.27 left.phtml,1.68,1.69 raw_edit.phtml,1.34,1.35 trans_create.phtml,1.45,1.46

From: <tr...@us...> - 2003-02-15 11:29:11

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv20384/www

Modified Files:
	gene_explore.phtml hyb_edit.phtml hyb_list.phtml 
	labeled_list.phtml left.phtml raw_edit.phtml 
	trans_create.phtml 
Log Message:
Fixed problems that were found while running as non-superuser

Index: gene_explore.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/gene_explore.phtml,v
retrieving revision 1.73
retrieving revision 1.74
diff -C2 -d -r1.73 -r1.74
*** gene_explore.phtml	13 Feb 2003 22:29:37 -0000	1.73
--- gene_explore.phtml	15 Feb 2003 11:29:07 -0000	1.74
***************
*** 178,182 ****
  		$searchtypes = BioAssaySet::geneSearchTypes();
  		$rlmessage = "";
! 		if(isset($i_replistname) && $i_replistname != "")
  		{
  			// Get search
--- 178,183 ----
  		$searchtypes = BioAssaySet::geneSearchTypes();
  		$rlmessage = "";
! 		if(isset($i_replistname) && $i_replistname != "" &&
! 			$exp->mayEdit($curUser))
  		{
  			// Get search
***************
*** 225,228 ****
--- 226,234 ----
  				$BC->endTransaction();
  		}
+ 		else if(isset($i_replistname) && $i_replistname != "")
+ 		{
+ 			$rlmessage = "<span class=red>Write access to ".
+ 				"experiment denied</span>";
+ 		}
  
  		$search = makeSearchTable($curUser, "gene", "BioAssaySet",
***************
*** 234,248 ****
  			$curDisplay->getHitsPerPage(), true);
  
  ?>
  <p><table <?= $cellpad ?>>
! <tr><td><input type=button onclick="setGene(1)" value="Explore">
! 	<span class=help>or click a gene name.</span> &nbsp;
! 	<input type=button onclick="exportData(this.form)" value="Export data">
! 	&nbsp; <input type=button onclick="doTrans(this.form,1)"
! 	value="Filter data">
! 	&nbsp; <input type=button onclick="doTrans(this.form,0)"
! 	value="Send to application">
! 	&nbsp; <input type=button onclick="makeReporterList(this.form)"
! 	value="Add as reporter list"></td></tr>
  <?
  		if($rlmessage != "")
--- 240,262 ----
  			$curDisplay->getHitsPerPage(), true);
  
+ 		$funcs = array("<input type=button onclick='setGene(1)' ".
+ 				"value='Explore'> <span class=help>or click a gene ".
+ 				"name.</span>",
+ 			"<input type=button onclick='exportData(this.form)' ".
+ 				"value='Export data'>");
+ 		if($exp->mayEdit($curUser))
+ 		{
+ 			$funcs[] = "<input type=button onclick='doTrans(this.form,1)' ".
+ 				"value='Filter data'>";
+ 			$funcs[] = "<input type=button onclick='doTrans(this.form,0)' ".
+ 				"value='Send to application'>";
+ 			$funcs[] = "<input type=button ".
+ 				"onclick='makeReporterList(this.form)' ".
+ 				"value='Add as reporter list'>";
+ 		}
+ 
  ?>
  <p><table <?= $cellpad ?>>
! <tr><td><?= implode(" &nbsp;\n", $funcs) ?></td></tr>
  <?
  		if($rlmessage != "")

Index: hyb_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_edit.phtml,v
retrieving revision 1.54
retrieving revision 1.55
diff -C2 -d -r1.54 -r1.55
*** hyb_edit.phtml	13 Feb 2003 22:29:37 -0000	1.54
--- hyb_edit.phtml	15 Feb 2003 11:29:07 -0000	1.55
***************
*** 25,28 ****
--- 25,29 ----
  	require_once("protocol.inc.php");
  	require_once("labeled.inc.php");
+ 	require_once("label.inc.php");
  	require_once("hyb.inc.php");
  	require_once("array.inc.php");

Index: hyb_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_list.phtml,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** hyb_list.phtml	22 Jan 2003 08:02:05 -0000	1.27
--- hyb_list.phtml	15 Feb 2003 11:29:07 -0000	1.28
***************
*** 25,28 ****
--- 25,29 ----
  	require_once("protocol.inc.php");
  	require_once("labeled.inc.php");
+ 	require_once("label.inc.php");
  	require_once("hyb.inc.php");
  	require_once("search.inc.php");

Index: labeled_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/labeled_list.phtml,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** labeled_list.phtml	22 Jan 2003 08:02:09 -0000	1.26
--- labeled_list.phtml	15 Feb 2003 11:29:07 -0000	1.27
***************
*** 26,29 ****
--- 26,30 ----
  	require_once("protocol.inc.php");
  	require_once("labeled.inc.php");
+ 	require_once("label.inc.php");
  	require_once("hyb.inc.php");
  	require_once("search.inc.php");

Index: left.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/left.phtml,v
retrieving revision 1.68
retrieving revision 1.69
diff -C2 -d -r1.68 -r1.69
*** left.phtml	13 Feb 2003 08:47:48 -0000	1.68
--- left.phtml	15 Feb 2003 11:29:08 -0000	1.69
***************
*** 270,281 ****
  			"</td></tr>\n";
  
! 		$acclink = "user_edit.phtml?i_u=".$curUser->getId()."&location=";
  		if(!acc(BUA_USER_READ)) {}
  		else if($l == "users")
  		{
  			echo "<tr><th class=subheadact><a target=_top ".
! 				"href='index.phtml?l=users&m=".urlencode($acclink)."'>".
  				"Users</a></td></tr>\n";
  
  			echo "<tr><td><a target=main href='$acclink'>".
  				"My account</a></td></tr>\n";
--- 270,287 ----
  			"</td></tr>\n";
  
! 		// By default show user list to admins, account to others
! 		if(acc(BUA_ADMIN_USER))
! 			$ulink = "user_list.phtml";
! 		else
! 			$ulink = "user_edit.phtml?i_u=".$curUser->getId()."&location=";
! 
  		if(!acc(BUA_USER_READ)) {}
  		else if($l == "users")
  		{
  			echo "<tr><th class=subheadact><a target=_top ".
! 				"href='index.phtml?l=users&m=".urlencode($ulink)."'>".
  				"Users</a></td></tr>\n";
  
+ 			$acclink = "user_edit.phtml?i_u=".$curUser->getId()."&location=";
  			echo "<tr><td><a target=main href='$acclink'>".
  				"My account</a></td></tr>\n";
***************
*** 288,292 ****
  		{
  			echo "<tr><th class=subhead><a target=_top href='index.phtml".
! 				"?l=users&m=".urlencode($acclink)."'>Users</a></td></tr>\n";
  		}
  
--- 294,298 ----
  		{
  			echo "<tr><th class=subhead><a target=_top href='index.phtml".
! 				"?l=users&m=".urlencode($ulink)."'>Users</a></td></tr>\n";
  		}
  

Index: raw_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw_edit.phtml,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** raw_edit.phtml	25 Jan 2003 00:46:52 -0000	1.34
--- raw_edit.phtml	15 Feb 2003 11:29:08 -0000	1.35
***************
*** 303,307 ****
  			{
  				echo "<tr><th>Image set</th>".
! 					"<td>".imageAcquisitionArrLink($ainfo)."</td></tr>\n";
  			}
  		}
--- 303,308 ----
  			{
  				echo "<tr><th>Image set</th>".
! 					"<td>".imageAcquisitionArrLink($ainfo, $curUser).
! 					"</td></tr>\n";
  			}
  		}

Index: trans_create.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/trans_create.phtml,v
retrieving revision 1.45
retrieving revision 1.46
diff -C2 -d -r1.45 -r1.46
*** trans_create.phtml	10 Feb 2003 08:40:49 -0000	1.45
--- trans_create.phtml	15 Feb 2003 11:29:08 -0000	1.46
***************
*** 71,75 ****
  ?>
  <table <?= $cellpad ?>>
! <tr><th class=pagehead><?= $pageName ?></th></tr>
  <tr><td class=large><a href="<?= html($location) ?>">Return</a></td></tr>
  <tr><td class=red>Error: <?= $err ?></td></tr>
--- 71,75 ----
  ?>
  <table <?= $cellpad ?>>
! <tr><th class=pagehead>Transformation error</th></tr>
  <tr><td class=large><a href="<?= html($location) ?>">Return</a></td></tr>
  <tr><td class=red>Error: <?= $err ?></td></tr>

[basedb-cvs] basedb/include/web experiment_common.inc.php,1.25,1.26 item_common.inc.php,1.17,1.18 links_common.inc.php,1.14,1.15

From: <tr...@us...> - 2003-02-15 11:29:10

Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv20384/include/web

Modified Files:
	experiment_common.inc.php item_common.inc.php 
	links_common.inc.php 
Log Message:
Fixed problems that were found while running as non-superuser

Index: experiment_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/experiment_common.inc.php,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** experiment_common.inc.php	11 Feb 2003 14:43:12 -0000	1.25
--- experiment_common.inc.php	15 Feb 2003 11:29:07 -0000	1.26
***************
*** 573,577 ****
  		unset($s);
  
! 		if($ass)
  		{
  ?>
--- 573,577 ----
  		unset($s);
  
! 		if($ass && $exp->mayEdit($user))
  		{
  ?>

Index: item_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/item_common.inc.php,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** item_common.inc.php	28 Jan 2003 17:22:55 -0000	1.17
--- item_common.inc.php	15 Feb 2003 11:29:07 -0000	1.18
***************
*** 192,196 ****
  		else
  		{
! 			if($user->getId() == $item->getOwner)
  				$un = html($user->getName());
  			else
--- 192,196 ----
  		else
  		{
! 			if($user->getId() == $item->getOwner())
  				$un = html($user->getName());
  			else

Index: links_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/links_common.inc.php,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** links_common.inc.php	13 Feb 2003 08:47:47 -0000	1.14
--- links_common.inc.php	15 Feb 2003 11:29:07 -0000	1.15
***************
*** 51,55 ****
  	if(!isset($arr["sample"]))
  		return html("");
! 	if(!$arr["sampleRead"])
  		return html($arr["sampleName"]).remMark($arr["sampleRemoved"]);
  	return "<a ".href("sample_edit.phtml?i_samp=".
--- 51,55 ----
  	if(!isset($arr["sample"]))
  		return html("");
! 	if(!acc(Sample::globalRead()) || !$arr["sampleRead"])
  		return html($arr["sampleName"]).remMark($arr["sampleRemoved"]);
[...187 lines suppressed...]
+ 	{
+ 		return html($arr["name"]).remMark($arr["removed"]).
+ 			(isset($arr["isReviewer"]) && $arr["isReviewer"] ?
+ 			" (reviewer)" : "");
+ 	}
  	return "<a ".href("usergroup_edit.phtml?i_ug=".
  		(int)$arr["id"], 2).">".
***************
*** 349,353 ****
  function plateTypeArrLink(&$arr)
  {
! 	if(!$arr["typeRead"])
  		return html($arr["typeName"]).remMark($arr["typeRemoved"]);
  	return "<a ".href("platetype_edit.phtml?i_pt=".
--- 362,366 ----
  function plateTypeArrLink(&$arr)
  {
! 	if(!acc(PlateType::globalRead()) || !$arr["typeRead"])
  		return html($arr["typeName"]).remMark($arr["typeRemoved"]);
  	return "<a ".href("platetype_edit.phtml?i_pt=".

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