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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 --- |
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 --- |
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 $2 |wc -l` \ *************** *** 14,18 **** } ! echo "type files funcs lines bytes" cntstuff www "*.phtml" cntstuff classes "../include/classes/*.php" --- 14,18 ---- } ! echo "type files funcs lines bytes" cntstuff www "*.phtml" cntstuff classes "../include/classes/*.php" *************** *** 22,26 **** cntstuff webinc "../include/web/*.php" cntstuff bin "../bin/*.php" ! cntstuff plotapp "plotapplet/*.phtml" cntstuff total " *.phtml --- 22,26 ---- cntstuff webinc "../include/web/*.php" cntstuff bin "../bin/*.php" ! cntstuff plotapplet "plotapplet/*.phtml" cntstuff total " *.phtml |
From: <tr...@us...> - 2003-02-18 07:49:27
|
Update of /cvsroot/basedb/basedb/www/plotapplet In directory sc8-pr-cvs1:/tmp/cvs-serv17061/www/plotapplet Modified Files: plot_assay.phtml plot_raw.phtml Log Message: began cleanup Index: plot_assay.phtml =================================================================== RCS file: /cvsroot/basedb/basedb/www/plotapplet/plot_assay.phtml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** plot_assay.phtml 3 Feb 2003 20:13:20 -0000 1.2 --- plot_assay.phtml 18 Feb 2003 07:49:24 -0000 1.3 *************** *** 3,7 **** // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ ! // Copyright (C) 2002 Mats Attnäs // // This file is part of BASE. --- 3,7 ---- // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ ! // Copyright (C) 2002, 2003 Mats Attnäs, Carl Troein // // This file is part of BASE. *************** *** 23,38 **** require_once("../getconfig.inc.php"); require_once("init.inc.php"); - require_once("item_common.inc.php"); require_once("misc.inc.php"); ! require_once("raw.inc.php"); ! require_once("mime.inc.php"); verifyAccess(BioAssay::globalRead()); ?> ! <applet code="plotapplet.PlotApplet" archive="plot.jar" width=1100 height=800> ! <param name="dataUrlBase" value="read_data.phtml?i_type=assay&i_id=<?= (int)$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> ! |
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=$id'>HTML plot tool</a>] ". "[<a class=popup target=rawJavaPlot_$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=$id'>HTML plot tool</a>]\n". "[<a class=popup target=rawJavaPlot_$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); ) { |
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 == "") ! $this->addedDate = now(); } |
From: <tr...@us...> - 2003-02-18 07:33:56
|
Update of /cvsroot/basedb/basedb/include/drivers In directory sc8-pr-cvs1:/tmp/cvs-serv8583 Modified Files: pgsql.inc.php Log Message: Undid changes after re-reading bug report Index: pgsql.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/include/drivers/pgsql.inc.php,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** pgsql.inc.php 18 Feb 2003 07:28:37 -0000 1.12 --- pgsql.inc.php 18 Feb 2003 07:33:52 -0000 1.13 *************** *** 487,496 **** { if($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"; } |
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"; } |
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" |
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 |
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"; |
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. + $config["useFlock"] = 1; + // Paths to various parts of BASE. // Note that you can move the "www" directory to wherever you wish, as |
From: <tr...@us...> - 2003-02-16 02:03:52
|
Update of /cvsroot/basedb/basedb/include/web In directory sc8-pr-cvs1:/tmp/cvs-serv9956/include/web Modified Files: newinit.inc.php Log Message: rewrote BaseControl to be much more robust and optionally use flock() Index: newinit.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/include/web/newinit.inc.php,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** newinit.inc.php 13 Feb 2003 12:34:39 -0000 1.5 --- newinit.inc.php 16 Feb 2003 02:03:49 -0000 1.6 *************** *** 3,7 **** // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ ! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. --- 3,7 ---- // // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/ ! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson // // This file is part of BASE. *************** *** 22,27 **** // ! if(!isset($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($config["sessionTimeout"]); --- 55,58 ---- |
From: <tr...@us...> - 2003-02-16 02:03:52
|
Update of /cvsroot/basedb/basedb/include/common In directory sc8-pr-cvs1:/tmp/cvs-serv9956/include/common Modified Files: common.inc.php Log Message: rewrote BaseControl to be much more robust and optionally use flock() Index: common.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/include/common/common.inc.php,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** common.inc.php 13 Feb 2003 08:47:46 -0000 1.19 --- common.inc.php 16 Feb 2003 02:03:49 -0000 1.20 *************** *** 80,84 **** "rootDir", "uploadDir", "tempDir", "jobDir", "rawFileDir", "rawImageDir", "printMapDir", "protocolDir", "logDir", ! "spotImageDir", "umask", "pluginArguments", "useJobRunner"); if(isset($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"; |
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()); |
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]"; |
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"); |
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, $show) ); |
From: <tr...@us...> - 2003-02-15 12:39:30
|
Update of /cvsroot/basedb/basedb/include/web In directory sc8-pr-cvs1:/tmp/cvs-serv9484/include/web Modified Files: gene_common.inc.php Log Message: fixed some table cell rendering stuff Index: gene_common.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/include/web/gene_common.inc.php,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** gene_common.inc.php 11 Feb 2003 14:43:12 -0000 1.10 --- gene_common.inc.php 15 Feb 2003 12:39:26 -0000 1.11 *************** *** 118,121 **** --- 118,127 ---- ">$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(&$element) |
From: <tr...@us...> - 2003-02-15 12:39:04
|
Update of /cvsroot/basedb/basedb/www In directory sc8-pr-cvs1:/tmp/cvs-serv9294/www Modified Files: spotinfo.phtml Log Message: added missing () Index: spotinfo.phtml =================================================================== RCS file: /cvsroot/basedb/basedb/www/spotinfo.phtml,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -d -r1.16 -r1.17 *** spotinfo.phtml 22 Jan 2003 21:47:43 -0000 1.16 --- spotinfo.phtml 15 Feb 2003 12:39:01 -0000 1.17 *************** *** 33,36 **** --- 33,37 ---- require_once("links_common.inc.php"); require_once("htmlinit.inc.php"); + require_once("experiment.inc.php"); verifyAccess(RawBioAssay::globalRead()); *************** *** 159,163 **** <tr><td rowspan=2 width=1 bgcolor=#4080c0><img src="img/1.gif" width=1 height=1></td> ! <th class=subhead>Raw data set <?= html($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> |
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); |
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"; |
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()) ; } |
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 <?= $cellpad ?>> ! <tr><td><input type=button onclick="setGene(1)" value="Explore"> ! <span class=help>or click a gene name.</span> ! <input type=button onclick="exportData(this.form)" value="Export data"> ! <input type=button onclick="doTrans(this.form,1)" ! value="Filter data"> ! <input type=button onclick="doTrans(this.form,0)" ! value="Send to application"> ! <input type=button onclick="makeReporterList(this.form)" ! value="Add as reporter list"></td></tr> <? if($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(" \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: <?= $err ?></td></tr> |
From: <tr...@us...> - 2003-02-15 11:29:10
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Update of /cvsroot/basedb/basedb/include/web In directory sc8-pr-cvs1:/tmp/cvs-serv20384/include/web Modified Files: experiment_common.inc.php item_common.inc.php links_common.inc.php Log Message: Fixed problems that were found while running as non-superuser Index: experiment_common.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/include/web/experiment_common.inc.php,v retrieving revision 1.25 retrieving revision 1.26 diff -C2 -d -r1.25 -r1.26 *** experiment_common.inc.php 11 Feb 2003 14:43:12 -0000 1.25 --- experiment_common.inc.php 15 Feb 2003 11:29:07 -0000 1.26 *************** *** 573,577 **** unset($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=". |