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From: <tr...@us...> - 2002-10-17 12:51:15
|
Update of /cvsroot/basedb/basedb/contrib
In directory usw-pr-cvs1:/tmp/cvs-serv31391
Modified Files:
Tag: stable_1_0_6
README
Log Message:
Added plotapplet beta version
Index: README
===================================================================
RCS file: /cvsroot/basedb/basedb/contrib/README,v
retrieving revision 1.2
retrieving revision 1.2.2.1
diff -C2 -d -r1.2 -r1.2.2.1
*** README 24 Jul 2002 20:58:57 -0000 1.2
--- README 17 Oct 2002 12:51:12 -0000 1.2.2.1
***************
*** 19,20 ****
--- 19,23 ----
Grzegorz Uszynski <grz...@ca...>
+ plotapplet/*
+ Beta version of Java applet for plotting RawBioAssays
+ Mats Attnäs <ma...@th...>
|
|
From: <tr...@us...> - 2002-10-17 12:49:50
|
Update of /cvsroot/basedb/basedb/contrib/plotapplet/plotapplet In directory usw-pr-cvs1:/tmp/cvs-serv30933/plotapplet/plotapplet Log Message: Directory /cvsroot/basedb/basedb/contrib/plotapplet/plotapplet added to the repository --> Using per-directory sticky tag `stable_1_0_6' |
|
From: <tr...@us...> - 2002-10-17 12:49:31
|
Update of /cvsroot/basedb/basedb/contrib/plotapplet In directory usw-pr-cvs1:/tmp/cvs-serv30824/plotapplet Log Message: Directory /cvsroot/basedb/basedb/contrib/plotapplet added to the repository --> Using per-directory sticky tag `stable_1_0_6' |
Update of /cvsroot/basedb/basedb/documentation/faq
In directory usw-pr-cvs1:/tmp/cvs-serv2983
Modified Files:
Makefile developer.tex faq.tex firstpage.tex general.tex
installation.tex introduction.tex usage.tex
Log Message:
Index: Makefile
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/Makefile,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile 7 Oct 2002 08:49:03 -0000 1.2
--- Makefile 17 Oct 2002 11:21:48 -0000 1.3
***************
*** 1,4 ****
# $Id$
- # $Revision$
MAIN = faq
--- 1,3 ----
Index: developer.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/developer.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** developer.tex 2 Oct 2002 15:16:21 -0000 1.1
--- developer.tex 17 Oct 2002 11:21:48 -0000 1.2
***************
*** 2,5 ****
--- 2,10 ----
\section{Developer}
+ \begin{htmlonly}
+ \begin{verbatim}
+ $Revision$ $Date$
+ \end{verbatim}
+ \end{htmlonly}
\subsection{How do I write plug-ins?}
Index: faq.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/faq.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** faq.tex 2 Oct 2002 15:16:21 -0000 1.1
--- faq.tex 17 Oct 2002 11:21:48 -0000 1.2
***************
*** 20,23 ****
--- 20,25 ----
\begin{document}
+ \bodytext{bgcolor=#f0f4f4 text=black}
+
\input{firstpage}
\input{introduction}
Index: firstpage.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/firstpage.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** firstpage.tex 2 Oct 2002 15:16:21 -0000 1.1
--- firstpage.tex 17 Oct 2002 11:21:48 -0000 1.2
***************
*** 3,7 ****
\begin{htmlonly}
\begin{verbatim}
! $Date$
\end{verbatim}
\end{htmlonly}
--- 3,7 ----
\begin{htmlonly}
\begin{verbatim}
! $Revision$ $Date$
\end{verbatim}
\end{htmlonly}
Index: general.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/general.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** general.tex 2 Oct 2002 15:16:21 -0000 1.1
--- general.tex 17 Oct 2002 11:21:48 -0000 1.2
***************
*** 4,8 ****
\begin{htmlonly}
\begin{verbatim}
! $Date$
\end{verbatim}
\end{htmlonly}
--- 4,8 ----
\begin{htmlonly}
\begin{verbatim}
! $Revision$ $Date$
\end{verbatim}
\end{htmlonly}
Index: installation.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/installation.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** installation.tex 2 Oct 2002 15:16:21 -0000 1.1
--- installation.tex 17 Oct 2002 11:21:48 -0000 1.2
***************
*** 4,8 ****
\begin{htmlonly}
\begin{verbatim}
! $Date$
\end{verbatim}
\end{htmlonly}
--- 4,8 ----
\begin{htmlonly}
\begin{verbatim}
! $Revision$ $Date$
\end{verbatim}
\end{htmlonly}
***************
*** 14,17 ****
--- 14,33 ----
web server versions. Please use the mailing list if you need
additional help.
+
+ \subsubsection{How do I turn on error logging in BASE?}
+ There are several sources of error for BASE; the web server, PHP,
+ plug-ins ...
+
+ For apache, the error logging is usually on by default. Check for
+ lines containing {\it ErrorLog} or {\it LogLevel} in the {\tt
+ httpf.conf} file, and follow the instruction in the file.
+
+ For PHP error logging you need two things in {\tt php.ini}:
+ \begin{verbatim}
+ error_reporting = E_ALL
+ error_log = path_to_error_log
+ \end{verbatim}
+ You might need to restart your web server for the changes to take
+ effect, and should probably keep a separate error log for PHP.
Index: introduction.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/introduction.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** introduction.tex 2 Oct 2002 15:16:21 -0000 1.1
--- introduction.tex 17 Oct 2002 11:21:48 -0000 1.2
***************
*** 4,8 ****
\begin{htmlonly}
\begin{verbatim}
! $Date$
\end{verbatim}
\end{htmlonly}
--- 4,8 ----
\begin{htmlonly}
\begin{verbatim}
! $Revision$ $Date$
\end{verbatim}
\end{htmlonly}
Index: usage.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/usage.tex,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** usage.tex 2 Oct 2002 15:16:21 -0000 1.1
--- usage.tex 17 Oct 2002 11:21:48 -0000 1.2
***************
*** 4,12 ****
\begin{htmlonly}
\begin{verbatim}
! $Date$
\end{verbatim}
\end{htmlonly}
! \subsubsection{Where can I find user documentation?}
We recommend the novice user read the Quick Start Guide, aka ``BASE
v1.0 instruction manual''. It can be found on the
--- 4,12 ----
\begin{htmlonly}
\begin{verbatim}
! $Revision$ $Date$
\end{verbatim}
\end{htmlonly}
! \subsection{Where can I find user documentation?}
We recommend the novice user read the Quick Start Guide, aka ``BASE
v1.0 instruction manual''. It can be found on the
|
|
From: <tr...@us...> - 2002-10-16 16:48:53
|
Update of /cvsroot/basedb/basedb
In directory usw-pr-cvs1:/tmp/cvs-serv30563
Modified Files:
Tag: stable_1_0_6
base_data.sql
Log Message:
Added PCA plugin definition
Index: base_data.sql
===================================================================
RCS file: /cvsroot/basedb/basedb/base_data.sql,v
retrieving revision 1.1
retrieving revision 1.1.2.1
diff -C2 -d -r1.1 -r1.1.2.1
*** base_data.sql 13 Jul 2002 09:41:34 -0000 1.1
--- base_data.sql 16 Oct 2002 16:48:47 -0000 1.1.2.1
***************
*** 3,6 ****
--- 3,7 ----
INSERT INTO Program VALUES (3,'mds','Multi-dimensional scaling (MDS) is a non-linear way to reduce the dimensionality of a data set. This implementation uses the Pearson correlations between assays as a distance metric.\r\n\r\nMDS info:\r\nKhan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS: Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 1998, 58:5009-5013.\r\n','0000-00-00',1,'Analysis: MDS','position','ratio',1,1,0,'');
INSERT INTO Program VALUES (4,'clusteringscript','Hierarchical clustering, bottom-up.\r\nThe two closest points are merged and the new cluster is represented by an unweighted(median) or weighted(center of mass) average of the two points in gene expression space. Distance metric defines closeness.\r\n','2002-05-31',1,'Analysis: Hierarchical clustering','cloneId','ratio',1,1,0,'');
+ INSERT INTO Program VALUES (5,'pca','This program calculates the PCA of the sample variance-covariance matrix of your data set:\r\n a) Data is parsed from a lowess transformed data set in serial BASE file format.\r\n b) The natural logarithm of the ratio of expression intensity 1 to expression intensity 2 is then calculated.\r\n c) The data matrix of the ln transformed date is then created. Rows correspond to genes and columns correspond to experimental variates.\r\n d) The average value of each column is calcuated and a second matrix, called the average matrix is then created. For each column of the average matrix, the row value is equal to the column average of the corresponding column.\r\n e) The average matrix is then subtracted from the data matrix. This produces the difference matrix.\r\n f) The variance-covariance matrix is calcuated from the product of the transpose of the difference matrix times the difference matrix itself. The resulting marix is a symmetric matrix with all positive real values. Multiplying the entire matrix by ( 1/rows -1 ) yields the final sample variance-covariance matrix.\r\n g) The eigenvalues and eigenvectors of the sample variance-covariance matrix are then calculated. The combination of eigenvalues and eigenvectors for a given matrix can be termed the eignensytem of that matrix. The eigensystem is then sorted by the value of the eigenvalue of the system.\r\n h) The variance-covariance matrix and the eigensystem( which is stored in a linked list) are used to generate the output files, currently: covariance.html, eigensystem.html, Scree.png and CoeffieicentPlot.png. \r\n\r\n','2002-09-20',3,'Analysis: PCA','position molecule','intensity1 intensity2',1,'',1,'http://www.ngelab.org/');
INSERT INTO ProgramParameter VALUES (1,1,'min_I','Use elements with both int >','f','5','100','');
|
|
From: <tr...@us...> - 2002-10-10 10:57:55
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv31718
Modified Files:
Tag: stable_1_0_6
user_edit.phtml
Log Message:
Never commit before testing. :-P
Index: user_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user_edit.phtml,v
retrieving revision 1.13.2.1
retrieving revision 1.13.2.2
diff -C2 -d -r1.13.2.1 -r1.13.2.2
*** user_edit.phtml 10 Oct 2002 10:43:56 -0000 1.13.2.1
--- user_edit.phtml 10 Oct 2002 10:57:52 -0000 1.13.2.2
***************
*** 41,45 ****
{
$user->setAccessMask(BUA_USER);
- $user->setActiveUntil("9999-12-31");
}
--- 41,44 ----
***************
*** 100,103 ****
--- 99,103 ----
{
$user->setAccessMask(BUA_USER);
+ $user->setActiveUntil("9999-12-31");
}
if($edit && !acc(BUA_ADMIN_USER))
|
|
From: <tr...@us...> - 2002-10-10 10:56:38
|
Update of /cvsroot/basedb/basedb/exec/source/pca
In directory usw-pr-cvs1:/tmp/cvs-serv31367
Added Files:
Tag: stable_1_0_6
plugin_pca.base
Log Message:
Added plugin definition so that existing installations can use PCA
--- NEW FILE: plugin_pca.base ---
BASEfile
section plugin
name Analysis: PCA
execName pca
descr This program calculates the PCA of the sample variance-covariance matrix of your data set:\r\n a) Data is parsed from a lowess transformed data set in serial BASE file format.\r\n b) The natural logarithm of the ratio of expression intensity 1 to expression intensity 2 is then calculated.\r\n c) The data matrix of the ln transformed date is then created. Rows correspond to genes and columns correspond to experimental variates.\r\n d) The average value of each column is calcuated and a second matrix, called the average matrix is then created. For each column of the average matrix, the row value is equal to the column average of the corresponding column.\r\n e) The average matrix is then subtracted from the data matrix. This produces the difference matrix.\r\n f) The variance-covariance matrix is calcuated from the product of the transpose of the difference matrix times the difference matrix itself. The resulting marix is a symmetric matrix with all positive real values. Multiplying the entire matrix by ( 1/rows -1 ) yields the final sample variance-covariance matrix.\r\n g) The eigenvalues and eigenvectors of the sample variance-covariance matrix are then calculated. The combination of eigenvalues and eigenvectors for a given matrix can be termed the eignensytem of that matrix. The eigensystem is then sorted by the value of the eigenvalue of the system.\r\n h) The variance-covariance matrix and the eigensystem( which is stored in a linked list) are used to generate the output files, currently: covariance.html, eigensystem.html, Scree.png and CoeffieicentPlot.png. \r\n\r\n
url http://www.ngelab.org/
usedColumns position molecule
usedFields intensity1 intensity2
geneAverages 0
serialFormat 1
columns position name commonName type options defaultValue enumOptions
%
|
|
From: <tr...@us...> - 2002-10-10 10:49:05
|
Update of /cvsroot/basedb/basedb/exec/source/pca
In directory usw-pr-cvs1:/tmp/cvs-serv29470
Added Files:
Tag: stable_1_0_6
.cvsignore
Log Message:
Adding PCA plugin for 1.0.7
--- NEW FILE: .cvsignore ---
pca
|
|
From: <tr...@us...> - 2002-10-10 10:48:49
|
Update of /cvsroot/basedb/basedb/exec/source/pca
In directory usw-pr-cvs1:/tmp/cvs-serv29389
Added Files:
Tag: stable_1_0_6
Makefile PCA_README PCA_v01.c TestBig.txt TestSmall.txt
Log Message:
Adding PCA plugin for 1.0.7
--- NEW FILE: Makefile ---
FILES = pca
FLAGS = -c -O3 -Wall -march=i686 -Ignuplot_i-2.6/src/
C = gcc
CC = g++
LDFLAGS = -lgsl -lgslcblas
SOURCE = PCA_v01.c gnuplot_i-2.6/src/gnuplot_i.c
OBJ_PCA = PCA_v01.o gnuplot_i-2.6/src/gnuplot_i.o
OBJ_ALL = Makedep.rule $(OBJ_PCA)
all: $(FILES)
.cc.o:
$(CC) $(FLAGS) -o $@ $<
.c.o:
$(C) $(FLAGS) -o $@ $<
clean:
rm -f $(OBJ_ALL) $(FILES) *~
touch -d20020101 Makedep.rule
depend:
$(CC) $(FLAGS) -MM $(SOURCE) >Makedep.rule
Makedep.rule: Makefile
@echo "The makefile has changed since the last 'make depend'."
install:
cp $(FILES) ../../apps
# Dependencies for executables
pca: $(OBJ_PCA)
$(C) $(LDFLAGS) -o $@ $+
# Dependencies for object files
include Makedep.rule
--- NEW FILE: PCA_README ---
Principal Components Analysis Plug-In Tool version 0.01 8/26/02
-----------------------------------------------
Contents:
-------
1) Acknowledgement of Support
2) Introduction and Credits
3) Program Outline
4) System Parameters
5) Package List
6) Compilation, Linking Running
5) Test Runs
7) Integration with BASE
8) To Do List
9) References
1) Acknowledgement of Support:
------------------------
[...234 lines suppressed...]
3) Resolve diminishing/truncated reporters list issue.
4) Component vs. Component 2D and 3D output with data.
5) Document use/parsing of stdin.txt
6) SQL script for uploading the plug-in definition
9) References:
-----------
Principles of Multivariate Analysis: A User's Perspective. Krzanowski, WJ. Oxford University Press 1988.
A User's Guide to Principal Components. Jackson, EJ. John Wiley & Sons, Inc. 1991
Principal Components Analysis to Summarize Microarray Experiments: Application to Sporulation Time Series. Raychaudhuri S, Stuart JM, Altman RB. Pacific Symposium on Biocomputing 2000. Honolulu, Hawaii, 452-463, 2000.
--- NEW FILE: PCA_v01.c ---
//
// PCA Plug-In for BioArraySoftware Environment( BASE )
// homepage http://www.ngelab.org
// BASE - homepage http://base.thep.lu.se/
// Copyright (C) 2002 Ron Hart, Greg Voronin(rhgv)
//
// Write to: See Below
// This file is part of PCA_v01, a Principal Components Analysis Plug_In for BASE.
//
// PCA_v01 is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public License
// as published by the Free Software Foundation; either version 2
// of the License, or (at your option) any later version.
//
// PCA_v01 is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
[...926 lines suppressed...]
coefficients[ j ] = gsl_vector_get(eList->eigenvector, j );
}
snprintf( label, size, "Principal Component %d ", count );
gnuplot_cmd( session2, "set output \"CoefficientPlot.png\"");
gnuplot_plot_x( session2, coefficients, cols, label );
count = count + 1;
eList = eList->next;
}
/* close the gnuplot session 2 */
gnuplot_close( session2 );
}
--- NEW FILE: TestBig.txt ---
BASEfile
fit_fraction 0.33
min_x_step 0.1
n_iter 4
section lowess settings
%
section assays
count 3
columns id name Hrs Rx Test Tx
annotationColumns Hrs Rx Test Tx
%
4 Test Set 1
5 Test Set 2
6 Test Set 3
section spots
columns position molecule assayData
assayFields intensity1 intensity2
[...2566 lines suppressed...]
2573 336 239.187 261.954
990 5205 320.577 195.822
597 2074 206.474 304.039
636 2231 260.801 240.736
4270 3451 247.211 253.993
977 3823 282.499 222.359
932 1229 191.449 328.474
150 2255 244.294 257.886
2698 343 249.614 252.838
274 2114 215.69 292.656
3512 3034 292.825 216.129
216 1034 248.059 255.254
547 1841 260.216 243.49
87 4955 238.531 265.626
1566 918 287.291 220.641
898 4502 327.925 193.349
2278 3695 192.366 329.964
1480 2246 256.007 248.055
506 1996 265.489 239.196
3800 2461 283.063 224.459
--- NEW FILE: TestSmall.txt ---
BASEfile
fit_fraction 0.33
min_x_step 0.1
n_iter 4
section lowess settings
%
section assays
count 3
columns id name Hrs Rx Test Tx
annotationColumns Hrs Rx Test Tx
%
4 Test Set 1
5 Test Set 2
6 Test Set 3
section spots
columns position molecule assayData
assayFields intensity1 intensity2
assays 4
%
4705 1876 0.182727772 0.639442747
3361 3490 0.178550103 0.734521416
2017 1092 0.75188986 0.946157646
673 4443 0.52163883 0.425572287
4706 4393 0.226277593 0.75675317
3362 4517 0.483571184 0.284209255
2018 4223 0.363921297 0.430420856
674 1501 0.282386944 0.374558038
4707 4540 0.53350036 0.745814532
3363 3266 0.718361323 0.855847816
section spots
columns position molecule assayData
assayFields intensity1 intensity2
assays 4
%
4705 1876 0.956653582 0.144926138
3361 3490 0.530925839 0.154646906
2017 1092 0.433994784 0.998590057
673 4443 0.474103618 0.36427883
4706 4393 0.382959597 0.793716884
3362 4517 0.257531312 0.304847628
2018 4223 0.426341693 0.119879148
674 1501 0.31309046 0.544443088
4707 4540 0.072738575 0.186893687
3363 3266 0.576870571 0.694229354
section spots
columns position molecule assayData
assayFields intensity1 intensity2
assays 4
%
4705 1876 0.116390925 0.643916614
3361 3490 0.791205844 0.630646561
2017 1092 0.769312628 0.557026574
673 4443 0.986900081 0.447894876
4706 4393 0.755242497 0.031620397
3362 4517 0.133165695 0.222270832
2018 4223 0.533144379 0.171807537
674 1501 0.252414263 0.34161909
4707 4540 0.422475338 0.672763583
3363 3266 0.68490596 0.375773707
|
|
From: <tr...@us...> - 2002-10-10 10:43:59
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv28213
Modified Files:
Tag: stable_1_0_6
user_edit.phtml
Log Message:
New users default to active forever
Index: user_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/user_edit.phtml,v
retrieving revision 1.13
retrieving revision 1.13.2.1
diff -C2 -d -r1.13 -r1.13.2.1
*** user_edit.phtml 5 Aug 2002 11:29:35 -0000 1.13
--- user_edit.phtml 10 Oct 2002 10:43:56 -0000 1.13.2.1
***************
*** 41,44 ****
--- 41,45 ----
{
$user->setAccessMask(BUA_USER);
+ $user->setActiveUntil("9999-12-31");
}
|
|
From: <tr...@us...> - 2002-10-10 10:41:52
|
Update of /cvsroot/basedb/basedb/www/misc
In directory usw-pr-cvs1:/tmp/cvs-serv27667
Modified Files:
Tag: stable_1_0_6
welcome.html
Log Message:
Changed sf.net logo link to point to sf.net rather than project basedb
Index: welcome.html
===================================================================
RCS file: /cvsroot/basedb/basedb/www/misc/welcome.html,v
retrieving revision 1.9.2.2
retrieving revision 1.9.2.3
diff -C2 -d -r1.9.2.2 -r1.9.2.3
*** welcome.html 30 Sep 2002 21:20:35 -0000 1.9.2.2
--- welcome.html 10 Oct 2002 10:41:50 -0000 1.9.2.3
***************
*** 30,34 ****
href="mailto:bas...@th...">bas...@th...</a>.
! <p><a target=_top href="http://sourceforge.net/projects/basedb/"><img
width="88" height="31"
src="http://sourceforge.net/sflogo.php?group_id=54527&type=1"
--- 30,34 ----
href="mailto:bas...@th...">bas...@th...</a>.
! <p><a target=_top href="http://sourceforge.net/"><img
width="88" height="31"
src="http://sourceforge.net/sflogo.php?group_id=54527&type=1"
|
|
From: <tr...@us...> - 2002-10-10 10:40:57
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv27433
Modified Files:
Tag: stable_1_0_6
search.inc.php
Log Message:
Enable LIKE searches for cloneId
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.32
retrieving revision 1.32.2.1
diff -C2 -d -r1.32 -r1.32.2.1
*** search.inc.php 5 Aug 2002 11:29:35 -0000 1.32
--- search.inc.php 10 Oct 2002 10:40:53 -0000 1.32.2.1
***************
*** 987,991 ****
{
$s = (string)$arr[$j];
! $arr[$j] = chr(strlen($s)).$s;
$view[] = $s;
}
--- 987,994 ----
{
$s = (string)$arr[$j];
! if(strpos($s, "*") !== false)
! $arr[$j] = "_".str_replace("*", "%", $s);
! else
! $arr[$j] = chr(strlen($s)).$s;
$view[] = $s;
}
|
|
From: <tr...@us...> - 2002-10-09 08:46:07
|
Update of /cvsroot/basedb/basedb In directory usw-pr-cvs1:/tmp/cvs-serv20552 Modified Files: ChangeLog Log Message: Added stuff Index: ChangeLog =================================================================== RCS file: /cvsroot/basedb/basedb/ChangeLog,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ChangeLog 8 Oct 2002 09:19:03 -0000 1.1 --- ChangeLog 9 Oct 2002 08:46:03 -0000 1.2 *************** *** 1,3 **** --- 1,6 ---- + *** 2002-10-08 + * Added ChangeLog + * Rewrote Wizzzard to use admin-defined columns. *** Changes between 1.0.6 and 2002-10-08 |
|
From: <tr...@us...> - 2002-10-08 17:59:58
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv2997
Modified Files:
wizzzard.inc.php wizzzard_list.phtml wizzzard_new.phtml
Log Message:
Revised wizzzard interface
Index: wizzzard.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/wizzzard.inc.php,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** wizzzard.inc.php 8 Oct 2002 09:05:13 -0000 1.28
--- wizzzard.inc.php 8 Oct 2002 17:59:55 -0000 1.29
***************
*** 34,37 ****
--- 34,38 ----
require_once("item.inc.php");
+ require_once("raw_columns.inc.php");
define("CLEN_WIZZZARD_NAME", 80);
***************
*** 41,45 ****
// The number of lines to consider as data header line candidates.
[...343 lines suppressed...]
! // Strip double quotes, hopefully not too slowly.
for($i = 0; $i < count($arr); $i++)
{
***************
*** 464,469 ****
continue;
}
! if(!is_array($map[$i]))
! $m =& $arr[$map[$i]];
else
{
--- 496,503 ----
continue;
}
! if(is_int($map[$i]))
! $m = $arr[$map[$i]];
! else if(!is_array($map[$i]))
! $m = $map[$i];
else
{
Index: wizzzard_list.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/wizzzard_list.phtml,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** wizzzard_list.phtml 8 Oct 2002 09:05:13 -0000 1.15
--- wizzzard_list.phtml 8 Oct 2002 17:59:55 -0000 1.16
***************
*** 40,44 ****
massDeleteHandle("Wizzzard", $curUser);
! $types = array("plate", "result", "reporter");
if(isset($i_type) && in_array($i_type, $types))
$type = $i_type;
--- 40,44 ----
massDeleteHandle("Wizzzard", $curUser);
! $types = Wizzzard::getTypes();
if(isset($i_type) && in_array($i_type, $types))
$type = $i_type;
Index: wizzzard_new.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/wizzzard_new.phtml,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** wizzzard_new.phtml 10 Sep 2002 23:06:40 -0000 1.24
--- wizzzard_new.phtml 8 Oct 2002 17:59:55 -0000 1.25
***************
*** 27,104 ****
require_once("upload.inc.php");
require_once("wizzzard.inc.php");
setLocation("wizzzard_list.phtml");
- $map = 0;
- $err = "";
$upl = new Upload();
! if(isset($i_fileid) && $i_fileid)
! {
[...540 lines suppressed...]
! $row = fgets($fd, 16384);
$lines[] = explode("\t", $row);
$maxcols = max(count($lines[$line-1]), $maxcols);
--- 334,341 ----
$line = 0;
$maxcols = 1;
! while(!feof($fd) && $line < WIZZZARD_HEADERLINES)
{
$line++;
! $row = fgets($fd, WIZZZARD_LINEBUFFER);
$lines[] = explode("\t", $row);
$maxcols = max(count($lines[$line-1]), $maxcols);
***************
*** 370,373 ****
--- 361,365 ----
echo "</tr>\n";
}
+ fclose($fd);
}
?>
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From: <tr...@us...> - 2002-10-08 17:59:26
|
Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv2787
Modified Files:
upload_common.inc.php
Log Message:
Added flag for no 'delete when done'
Index: upload_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/upload_common.inc.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** upload_common.inc.php 30 Sep 2002 16:57:05 -0000 1.2
--- upload_common.inc.php 8 Oct 2002 17:59:22 -0000 1.3
***************
*** 31,35 ****
// Use $inputid if you need more than one instance in a form.
// Input will be passed in i_file, $i_fileid, $i_filedel, $i_filedescr
! function uploadInput(&$user, $inputid = "")
{
$ups = Upload::getBrief($user);
--- 31,35 ----
// Use $inputid if you need more than one instance in a form.
// Input will be passed in i_file, $i_fileid, $i_filedel, $i_filedescr
! function uploadInput(&$user, $inputid = "", $removable = true)
{
$ups = Upload::getBrief($user);
***************
*** 60,69 ****
if($user->access(BUA_UPLOAD))
{
- $chk = isset($GLOBALS["i_filedel$inputid"]) ? "checked" : "";
?>
<tr><th><?= $pick ?> a file to upload</th>
<td><input type=file name=i_file<?= $inputid ?>>
! <input <?= $chk ?> type=checkbox name=i_filedel<?= $inputid
! ?>>Delete after use</td></tr>
<tr><th>File description</th>
<td><input type=text name=i_filedescr<?= $inputid ?> size=50></td></tr>
--- 60,77 ----
if($user->access(BUA_UPLOAD))
{
?>
<tr><th><?= $pick ?> a file to upload</th>
<td><input type=file name=i_file<?= $inputid ?>>
! <?
! if($removable)
! {
! ?>
! <input <?= isset($GLOBALS["i_filedel$inputid"]) ? "checked" : ""
! ?> type=checkbox name=i_filedel<?= $inputid
! ?>>Delete after use
! <?
! }
! ?>
! </td></tr>
<tr><th>File description</th>
<td><input type=text name=i_filedescr<?= $inputid ?> size=50></td></tr>
|
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From: <tr...@us...> - 2002-10-08 10:52:01
|
Update of /cvsroot/basedb/basedb In directory usw-pr-cvs1:/tmp/cvs-serv11146 Modified Files: base_data.sql Log Message: Revised for 1.1.3 Index: base_data.sql =================================================================== RCS file: /cvsroot/basedb/basedb/base_data.sql,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** base_data.sql 13 Jul 2002 09:41:34 -0000 1.1 --- base_data.sql 8 Oct 2002 10:51:58 -0000 1.2 *************** *** 1,6 **** ! INSERT INTO Program VALUES (1,'medianratio','This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant but the median of their ratios (i1/i2) is shifted to 1.\r\n\r\nThe normalizer lets you exclude a percentage of the highest and lowest intensities as well as all spots with at least one intensity below a fixed value.\r\n','0000-00-00',1,'Normalization: Global median ratio','position molecule','intensity1 intensity2',1,0,1,''); ! INSERT INTO Program VALUES (2,'lowess','This is an efficient C++ implementation by Björn Samuelsson <bj...@th...> of the LOWESS algorithm.\r\nIt provides intensity-based normalization.\r\n\r\nThe window size is the only smoothness parameter available in this implementation. The higher it is, the smoother the function will be.\r\nTweaking the other two parameters allows you to gain performance at the price of a small precision loss. The default values are usually good.\r\n\r\nFor more info on LOWESS:\r\nCleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 1988, 83:596-610.\r\n\r\nYang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.\r\n','0000-00-00',1,'Normalization: Lowess','position molecule','intensity1 intensity2',1,0,1,''); ! INSERT INTO Program VALUES (3,'mds','Multi-dimensional scaling (MDS) is a non-linear way to reduce the dimensionality of a data set. This implementation uses the Pearson correlations between assays as a distance metric.\r\n\r\nMDS info:\r\nKhan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS: Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 1998, 58:5009-5013.\r\n','0000-00-00',1,'Analysis: MDS','position','ratio',1,1,0,''); ! INSERT INTO Program VALUES (4,'clusteringscript','Hierarchical clustering, bottom-up.\r\nThe two closest points are merged and the new cluster is represented by an unweighted(median) or weighted(center of mass) average of the two points in gene expression space. Distance metric defines closeness.\r\n','2002-05-31',1,'Analysis: Hierarchical clustering','cloneId','ratio',1,1,0,''); INSERT INTO ProgramParameter VALUES (1,1,'min_I','Use elements with both int >','f','5','100',''); --- 1,12 ---- ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess) VALUES ! (1,'medianratio','This normalizer scales the intensities in such a way that their geometric mean (sqrt(i1 * i2)) is kept constant but the median of their ratios (i1/i2) is shifted to 1.\r\n\r\nThe normalizer lets you exclude a percentage of the highest and lowest intensities as well as all spots with at least one intensity below a fixed value.\r\n','2002-08-31',1,'Normalization: Global median ratio','position molecule','intensity1 intensity2',1,'',1,'','','','',1); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess) VALUES ! (2,'lowess','This is an efficient C++ implementation by Björn Samuelsson <bj...@th...> of the LOWESS algorithm.\r\nIt provides intensity-based normalization.\r\n\r\nThe window size is the only smoothness parameter available in this implementation. The higher it is, the smoother the function will be.\r\nTweaking the other two parameters allows you to gain performance at the price of a small precision loss. The default values are usually good.\r\n\r\nFor more info on LOWESS:\r\nCleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. J Am Stat Assoc 1988, 83:596-610.\r\n\r\nYang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.\r\n','2002-08-31',1,'Normalization: Lowess','position molecule','intensity1 intensity2',1,'',1,'','','','','1'); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess) VALUES ! (3,'mds','Multi-dimensional scaling (MDS) is a non-linear way to reduce the dimensionality of a data set. This implementation uses the Pearson correlations between assays as a distance metric.\r\n\r\nMDS info:\r\nKhan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS: Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res 1998, 58:5009-5013.\r\n','0000-00-00',1,'Analysis: MDS','position','ratio',1,1,'','','','','','1'); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess) VALUES ! (4,'clusteringscript','Hierarchical clustering, bottom-up.\r\nThe two closest points are merged and the new cluster is represented by an unweighted(median) or weighted(center of mass) average of the two points in gene expression space. Distance metric defines closeness.\r\n','2002-05-31',1,'Analysis: Hierarchical clustering','cloneId','ratio',1,1,'','','','','','1'); ! INSERT INTO Program (id, execName, descr, addedDate, owner, name, usedColumns, usedFields, onServer, geneAverages, serialFormat, url, removed, gid, groupAccess, worldAccess) VALUES ! (5,'pca','This program calculates the PCA of the sample variance-covariance matrix of your data set:\r\n a) Data is parsed from a lowess transformed data set in serial BASE file format.\r\n b) The natural logarithm of the ratio of expression intensity 1 to expression intensity 2 is then calculated.\r\n c) The data matrix of the ln transformed date is then created. Rows correspond to genes and columns correspond to experimental variates.\r\n d) The average value of each column is calcuated and a second matrix, called the average matrix is then created. For each column of the average matrix, the row value is equal to the column average of the corresponding column.\r\n e) The average matrix is then subtracted from the data matrix. This produces the difference matrix.\r\n f) The variance-covariance matrix is calcuated from the product of the transpose of the difference matrix times the difference matrix itself. The resulting marix is a symmetric matrix with all positive real values. Multiplying the entire matrix by ( 1/rows -1 ) yields the final sample variance-covariance matrix.\r\n g) The eigenvalues and eigenvectors of the sample variance-covariance matrix are then calculated. The combination of eigenvalues and eigenvectors for a given matrix can be termed the eignensytem of that matrix. The eigensystem is then sorted by the value of the eigenvalue of the system.\r\n h) The variance-covariance matrix and the eigensystem( which is stored in a linked list) are used to generate the output files, currently: covariance.html, eigensystem.html, Scree.png and CoeffieicentPlot.png. \r\n\r\n','2002-08-31',1,'Analysis: PCA','position molecule','intensity1 intensity2',1,'',1,'http://www.ngelab.org/','','','','1'); INSERT INTO ProgramParameter VALUES (1,1,'min_I','Use elements with both int >','f','5','100',''); *************** *** 40,53 **** INSERT INTO ProtocolType VALUES (6,'Plasmid'); INSERT INTO ProtocolType VALUES (7,'PCR'); - INSERT INTO ProtocolType VALUES (16,'Synthesis'); - INSERT INTO ProtocolType VALUES (15,'Bacteria'); INSERT INTO ProtocolType VALUES (11,'Delivery'); INSERT INTO ProtocolType VALUES (12,'Merge'); INSERT INTO ProtocolType VALUES (13,'Other'); INSERT INTO ProtocolType VALUES (14,'Configuration'); INSERT INTO SampleTissue VALUES (1,0,'Homo sapiens'); ! INSERT INTO SchemaVersion VALUES ('1.0.2','1.0.2','2002-07-13 11:28:09'); ! INSERT INTO Submitter VALUES (1,'root','','','','','','root','d41d8cd98f00b204e9800998ecf8427e',5,0,'9999-12-31',0,0,0,0,0); --- 46,62 ---- INSERT INTO ProtocolType VALUES (6,'Plasmid'); INSERT INTO ProtocolType VALUES (7,'PCR'); INSERT INTO ProtocolType VALUES (11,'Delivery'); INSERT INTO ProtocolType VALUES (12,'Merge'); INSERT INTO ProtocolType VALUES (13,'Other'); INSERT INTO ProtocolType VALUES (14,'Configuration'); + INSERT INTO ProtocolType VALUES (15,'Bacteria'); + INSERT INTO ProtocolType VALUES (16,'Synthesis'); INSERT INTO SampleTissue VALUES (1,0,'Homo sapiens'); ! INSERT INTO SchemaVersion VALUES ('1.1','1.1.3','2002-08-10 11:23:29'); ! INSERT INTO UserGroup (id, name, descr, owner, addedDate, removed, accessMask) VALUES ! (1,'root','',1,NOW(),'',1); ! INSERT INTO UserAccount (userGroup, email, address, phone, fax, realName, md5Pass, activeUntil, lastExperiment, lastExploredSet, lastPlateType, lastPlateTypeCreated) VALUES ! (1,'','','','','root','d41d8cd98f00b204e9800998ecf8427e','9999-12-31','','','',''); |
|
From: <tr...@us...> - 2002-10-08 10:35:43
|
Update of /cvsroot/basedb/basedb
In directory usw-pr-cvs1:/tmp/cvs-serv6932
Modified Files:
base.sql
Log Message:
Database schema 1.1.3
Index: base.sql
===================================================================
RCS file: /cvsroot/basedb/basedb/base.sql,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** base.sql 30 Sep 2002 17:19:36 -0000 1.8
--- base.sql 8 Oct 2002 10:35:40 -0000 1.9
***************
*** 6,27 ****
#
- # Table structure for table 'Array'
- #
-
- CREATE TABLE Array (
- id int(11) NOT NULL auto_increment,
- batch int(11) NOT NULL default '0',
- orderNumber smallint(6) NOT NULL default '0',
- barcode varchar(20) NOT NULL default '',
[...330 lines suppressed...]
--- 1188,1206 ----
id int(11) NOT NULL auto_increment,
owner int(11) NOT NULL default '0',
! formatType enum('result','plate','reporter') NOT NULL default 'result',
! name varchar(80) NOT NULL default '',
! minCols tinyint(4) NOT NULL default '0',
! maxCols tinyint(4) NOT NULL default '0',
dataHeader text NOT NULL,
! typeHeader text NOT NULL,
typeHeaderLine int(11) NOT NULL default '0',
mapping mediumtext NOT NULL,
! descr tinytext NOT NULL,
! addedDate date NOT NULL default '0000-00-00',
! removed tinyint(1) NOT NULL default '0',
! gid int(11) NOT NULL default '0',
! groupAccess tinyint(1) NOT NULL default '0',
! worldAccess tinyint(1) NOT NULL default '0',
! PRIMARY KEY (id)
) TYPE=MyISAM;
|
|
From: <tr...@us...> - 2002-10-08 10:34:57
|
Update of /cvsroot/basedb/basedb/exec/migration_tools
In directory usw-pr-cvs1:/tmp/cvs-serv6667
Modified Files:
dbmigrate.php fixreserved.sql
Added Files:
devchanges_1_1_3.sql
Removed Files:
devchanges.sql
Log Message:
Schema version 1.1.3, plus a couple of minor fixes
--- NEW FILE: devchanges_1_1_3.sql ---
-- This file mostly contains the structural changes (from 1.0.6) that
-- have been done so far.
ALTER TABLE Sample
DROP useCount,
ADD sampleDate DATE not null,
ADD removed TINYINT(1) not null,
ADD gid INT not null ,
ADD groupAccess TINYINT(1) not null,
ADD worldAccess TINYINT(1) not null;
ALTER TABLE Extract
DROP useCount,
ADD removed TINYINT(1) not null,
ADD gid INT not null ,
ADD groupAccess TINYINT(1) not null,
ADD worldAccess TINYINT(1) not null;
ALTER TABLE LabeledExtract
[...281 lines suppressed...]
CHANGE FCh1SD FCh1SD FLOAT,
CHANGE BCh1Median BCh1Median FLOAT,
CHANGE BCh1Mean BCh1Mean FLOAT,
CHANGE BCh1SD BCh1SD FLOAT,
CHANGE FCh2Median FCh2Median FLOAT,
CHANGE FCh2Mean FCh2Mean FLOAT,
CHANGE FCh2SD FCh2SD FLOAT,
CHANGE BCh2Median BCh2Median FLOAT,
CHANGE BCh2Mean BCh2Mean FLOAT,
CHANGE BCh2SD BCh2SD FLOAT,
CHANGE FPixels FPixels SMALLINT,
CHANGE BPixels BPixels SMALLINT;
UPDATE RawBioAssayData SET x2 = x, y2 = y;
ALTER TABLE RawBioAssayData
DROP x,
DROP y,
CHANGE x2 x FLOAT NOT NULL,
CHANGE y2 y FLOAT NOT NULL;
Index: dbmigrate.php
===================================================================
RCS file: /cvsroot/basedb/basedb/exec/migration_tools/dbmigrate.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** dbmigrate.php 7 Sep 2002 11:32:02 -0000 1.9
--- dbmigrate.php 8 Oct 2002 10:34:51 -0000 1.10
***************
*** 40,45 ****
// existing ones.
$versions = array("1.0.1", "1.0.1a", "1.0.1b", "1.0.2", "1.1.1",
! "1.1.2");
! $lastVersion = "1.1.2";
require_once("../getconfig2.inc.php");
--- 40,45 ----
// existing ones.
$versions = array("1.0.1", "1.0.1a", "1.0.1b", "1.0.2", "1.1.1",
! "1.1.2", "1.1.3");
[...240 lines suppressed...]
+ "SET mapping = '".addslashes(implode(",", $newm))."' ".
+ "WHERE id = $id";
+ if(!myquery($query))
+ return "Failed to update Wizzzard $id";
+ }
$query = "UPDATE SchemaVersion
! SET baseVersion = '1.1', schemaVersion = '1.1.3',
lastChanged = NOW()";
if(!myquery($query) || mysql_affected_rows() < 1)
return "Can't update SchemaVersion table";
!
! $version = "1.1.3";
return "";
! }
!
!
!
Index: fixreserved.sql
===================================================================
RCS file: /cvsroot/basedb/basedb/exec/migration_tools/fixreserved.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** fixreserved.sql 29 Aug 2002 16:49:11 -0000 1.1
--- fixreserved.sql 8 Oct 2002 10:34:53 -0000 1.2
***************
*** 1,55 ****
! ALTER TABLE base.ArrayBatch CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.ArrayType CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.BioAssay CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.BioAssaySet CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.Cookie CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.Experiment CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.Extract CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.GeneList CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.Hardware CHANGE user owner INT (11) DEFAULT '0' not null;
! ALTER TABLE base.Hybridization CHANGE user owner INT (11) DEFAULT '0' not null;
[...81 lines suppressed...]
! ALTER TABLE SampleAnnotation CHANGE value annotation TINYTEXT not null;
! ALTER TABLE SearchCriterion CHANGE value searchString TINYTEXT not null;
! ALTER TABLE JobFile CHANGE size fileSize INT (11) DEFAULT '0' not null;
! ALTER TABLE Upload CHANGE size fileSize INT (11) DEFAULT '0' not null;
! ALTER TABLE JobFileSection CHANGE count sectionCount SMALLINT (6) DEFAULT '0' not null;
! ALTER TABLE JobFileSection CHANGE section fileSection INT (11) DEFAULT '0' not null;
! ALTER TABLE PlateType CHANGE prefix namePrefix VARCHAR (20) not null;
! ALTER TABLE BioAssaySetSearch CHANGE type searchType ENUM ('ge_gene','ge_onegene','bioassay') DEFAULT 'ge_gene' not null;
! ALTER TABLE Preset CHANGE type searchType ENUM ('sample','arraytype','extract','hybridization','plate','user','value','labeled','raw','exp','gene','array','molecule','upload') DEFAULT 'sample' not null;
! ALTER TABLE ProgramParameter CHANGE type valueType ENUM ('i','f','t','a','n','h','e') DEFAULT 'i' not null;
! ALTER TABLE SampleAnnotation CHANGE type annotationType INT (11) DEFAULT '0' not null;
! ALTER TABLE SampleAnnotationType CHANGE type valueType ENUM ('i','f','t','e') DEFAULT 'i' not null;
! ALTER TABLE TransformationSearch CHANGE type searchType ENUM ('trans_pre','trans_gene') DEFAULT 'trans_pre' not null;
! ALTER TABLE UserSearch CHANGE type searchType ENUM ('plate','sample','extract','labeled','hybridization','value','arraytype','well','wizzzard','raw','exp','user','gene','genelist','program','news','acq','acq_img','ware','acq_rba','platetype','print','array','molecule','upload') DEFAULT 'plate' not null;
--- devchanges.sql DELETED ---
|
|
From: <tr...@us...> - 2002-10-08 09:19:06
|
Update of /cvsroot/basedb/basedb In directory usw-pr-cvs1:/tmp/cvs-serv18588 Added Files: ChangeLog Log Message: Long overdue, isn't it? --- NEW FILE: ChangeLog --- *** Changes between 1.0.6 and 2002-10-08 * Created database API to handle differences between different RDBMSs, most notably MySQL vs. the rest of them. Implemented for MySQL and PostgreSQL. * Added 'removed' flag to the Item class and most subclasses. * Created new user access system with groups. The Submitter class has gone away, and a lot of rewriting is needed wherever the old system was used (i.e. almost everywhere). * Updated the biomaterial and hybridization parts to use the new features in Item. * Rewrote Protocol as subclass of Item, without Upload for storing files. As a consequence, reworked the interface for protocols. * Adapted the Upload class to the new Item, and unified the handling of file selection/upload. * Changed SearchCriterion fields to strings. * A large number of minor or major fixes and changes. |
|
From: <tr...@us...> - 2002-10-08 09:05:17
|
Update of /cvsroot/basedb/basedb/www In directory usw-pr-cvs1:/tmp/cvs-serv14961 Modified Files: array.inc.php bio.inc.php hyb_image.phtml hyb_result.phtml item.inc.php item_common.inc.php links_common.inc.php raw.inc.php test.phtml wizzzard.inc.php wizzzard_list.phtml Added Files: raw_columns.inc.php Log Message: Towards admin-defined raw columns --- NEW FILE: raw_columns.inc.php --- <? // $Id: raw_columns.inc.php,v 1.1 2002/10/08 09:05:13 troein Exp $ // // This file is part of BASE. // BioArray Software Environment (BASE) - http://base.thep.lu.se/ // Copyright (C) 2002 Carl Troein // // BASE is free software; you can redistribute it and/or // modify it under the terms of the GNU General Public License // as published by the Free Software Foundation; either version 2 // of the License, or (at your option) any later version. // // BASE is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program; if not, write to the Free Software [...187 lines suppressed...] array("FMedianMMedian", "Median FG - Mean(Median BG)", "`FCh1Median`-%%", "AVG(`BCh1Median`)", "`FCh2Median`-%%", "AVG(`BCh2Median`)"), array("FMeanMMean", "Mean FG - Mean(Mean BG)", "`FCh1Mean`-%%", "AVG(`BCh1Mean`)", "`FCh2Mean`-%%", "AVG(`BCh2Mean`)"), array("FMedianMMean", "Median FG - Mean(Mean BG)", "`FCh1Median`-%%", "AVG(`BCh1Mean`)", "`FCh2Median`-%%", "AVG(`BCh2Mean`)"), array("FMeanMMedian", "Mean FG - Mean(Median BG)", "`FCh1Mean`-%%", "AVG(`BCh1Median`)", "`FCh2Mean`-%%", "AVG(`BCh2Median`)"), ); } } ?> Index: array.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/array.inc.php,v retrieving revision 1.42 retrieving revision 1.43 diff -C2 -d -r1.42 -r1.43 *** array.inc.php 3 Oct 2002 18:00:07 -0000 1.42 --- array.inc.php 8 Oct 2002 09:05:12 -0000 1.43 *************** *** 731,735 **** } ! // Returns array(id,name, removed,arrayRead) function getBriefForHyb($hyb, &$user) { --- 731,735 ---- } ! // Returns array(id,name,removed,arrayRead) function getBriefForHyb($hyb, &$user) { Index: bio.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/bio.inc.php,v retrieving revision 1.28 retrieving revision 1.29 diff -C2 -d -r1.28 -r1.29 *** bio.inc.php 30 Sep 2002 08:26:43 -0000 1.28 --- bio.inc.php 8 Oct 2002 09:05:13 -0000 1.29 *************** *** 149,153 **** $ob = $search->makeOrderBy($sortfields); ! $query = "SELECT s.*, ug.name AS `userName` ". "FROM Sample s, UserGroup ug ". "WHERE ug.id = s.owner ". --- 149,153 ---- $ob = $search->makeOrderBy($sortfields); ! $query = "SELECT s.*, ug.name AS `userName` ". "FROM Sample s, UserGroup ug ". "WHERE ug.id = s.owner ". Index: hyb_image.phtml =================================================================== RCS file: /cvsroot/basedb/basedb/www/hyb_image.phtml,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -d -r1.26 -r1.27 *** hyb_image.phtml 30 Sep 2002 16:57:05 -0000 1.26 --- hyb_image.phtml 8 Oct 2002 09:05:13 -0000 1.27 *************** *** 369,411 **** { // RawBioAssays $search = new Search(); $search->readForUser($curUser->getId(), "acq_rba"); ! RawBioAssay::prepareAcquisitionSearch($search, $acqid, 0); ! $raws = RawBioAssay::acquisitionSearch($search); ! $headerfields = array("Name", "Filename", "Spots", ! "Feature extr. software", "F. extr. date"); ! $sortorder = array(1, 1, 1, 1, -1); ! $defsort = 0; [...91 lines suppressed...] - $owns = $acq->getOwner() == $userid; for($i = 0, $odd = 1; $i < count($imgs); $i++, $odd ^= 1) { --- 438,441 ---- *************** *** 434,439 **** $ch = $a["channels"]; ! if(isset($chans[$ch])) $ch = $chans[$ch]; ! if($owns) { $un = $a["removed"]; --- 443,449 ---- $ch = $a["channels"]; ! if(isset($chans[$ch])) ! $ch = $chans[$ch]; ! if(Item::isSharedArray($a, $curUser, 2)) { $un = $a["removed"]; Index: hyb_result.phtml =================================================================== RCS file: /cvsroot/basedb/basedb/www/hyb_result.phtml,v retrieving revision 1.56 retrieving revision 1.57 diff -C2 -d -r1.56 -r1.57 *** hyb_result.phtml 3 Oct 2002 18:00:14 -0000 1.56 --- hyb_result.phtml 8 Oct 2002 09:05:13 -0000 1.57 *************** *** 84,94 **** $ratio = isset($i_ratio) && $i_ratio; - // Try to be smart about deleting files - if a file was just uploaded - // we want the 'delete file' box to be checked. - if(!isset($i_deletefile) && isset($i_fileid) && !$i_fileid) - $i_deletefile = true; - else if(!isset($i_deletefile)) - $i_deletefile = false; - if(isset($i_array) && $i_array != "" && $err == "") [...67 lines suppressed...] *************** *** 661,668 **** $err = "Unable to copy uploaded file to repository"; else if($deletefile) ! $upl->remove(); } ! if($err != "") $raw->remove(); else { --- 655,663 ---- $err = "Unable to copy uploaded file to repository"; else if($deletefile) ! $upl->updateRemoved(true); } ! if($err != "") ! $raw->remove(); else { Index: item.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/item.inc.php,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -d -r1.35 -r1.36 *** item.inc.php 2 Oct 2002 17:50:56 -0000 1.35 --- item.inc.php 8 Oct 2002 09:05:13 -0000 1.36 *************** *** 433,438 **** } ! // Locking functions // Returns true on success. --- 433,453 ---- } + function mayDeleteNoSharing(&$user, $access = false) + { + if($user->access(BUA_SUPERUSER)) + return true; + return ($access !== false || $user->access($access)) + && $this->getOwner() == $user->getId(); + } + function mayEditNoSharing(&$user, $access = false) + { + if($user->access(BUA_SUPERUSER)) + return true; + return ($access !== false || $user->access($access)) + && $this->getOwner() == $user->getId() && !$this->removed; + } ! ! /* // Locking functions // Returns true on success. *************** *** 491,494 **** --- 506,511 ---- return -2; } + */ + } Index: item_common.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/item_common.inc.php,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** item_common.inc.php 1 Oct 2002 17:35:10 -0000 1.6 --- item_common.inc.php 8 Oct 2002 09:05:13 -0000 1.7 *************** *** 282,286 **** } ?> ! </select>with<select name=i_shgacc> <option value=-1>same <? --- 282,286 ---- } ?> ! </select> with <select name=i_shgacc> <option value=-1>same <? *************** *** 292,296 **** } ?> ! </select>access. World: <select name=i_shwacc> --- 292,296 ---- } ?> ! </select> access. World: <select name=i_shwacc> *************** *** 304,308 **** } ?> ! </select> access. <input type=submit name=i_shgo value='Ok'></td></tr> <? --- 304,308 ---- } ?> ! </select> access. <input type=submit name=i_shgo value='Ok'></td></tr> <? *************** *** 315,319 **** // Stuff that has to do with Item.removed ! function handleDelete(&$item, &$user, $access = BUA_BIO_EDIT, $sharing = true) { global $i_delete; --- 315,319 ---- // Stuff that has to do with Item.removed ! function handleDelete(&$item, &$user, $access = BUA_BIO_EDIT) { global $i_delete; *************** *** 325,329 **** if(!$user->access($access)) $err = "Can't $act ".$item->getType().": access denied ($access)"; ! else if($sharing && !$item->mayDelete($user)) $err = "Can't $act someone else's ".$item->getType(); else if($item->getRemoved() && !$undel) --- 325,329 ---- if(!$user->access($access)) $err = "Can't $act ".$item->getType().": access denied ($access)"; ! else if(!$item->mayDelete($user)) $err = "Can't $act someone else's ".$item->getType(); else if($item->getRemoved() && !$undel) Index: links_common.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/links_common.inc.php,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** links_common.inc.php 3 Oct 2002 18:00:15 -0000 1.4 --- links_common.inc.php 8 Oct 2002 09:05:13 -0000 1.5 *************** *** 143,146 **** --- 143,156 ---- } + function wareArrLink($type, &$arr) + { + if(!$arr["${type}wareRead"]) + return html($arr["${type}ware"]).remMark($arr["${type}wareRemoved"]); + return "<a ".href("ware_edit.phtml?i_type=$type&i_w=". + (int)$arr["featureSoftware"], 2).">". + html($arr["${type}ware"])."</a>".remMark($arr["${type}wareRemoved"]); + } + + ?> Index: raw.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/raw.inc.php,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -d -r1.39 -r1.40 *** raw.inc.php 12 Sep 2002 11:45:26 -0000 1.39 --- raw.inc.php 8 Oct 2002 09:05:13 -0000 1.40 *************** *** 24,31 **** // Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. // ! require_once("db.inc.php"); require_once("item.inc.php"); require_once("bio.inc.php"); require_once("acquisition.inc.php"); define("CLEN_RAWBIOASSAY_NAME", 60); --- 24,32 ---- // Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. [...372 lines suppressed...] // Returns an array of arrays with various fields. ! function search(&$search) { // Add more fields here ! $sortfields = array("name", "filename", "`sampleName1`", ! "`sampleName2`", "spots", "`userName`", array("`addedDate`", "id"), ! 0, 0, 0, 0); $ob = $search->makeOrderBy($sortfields); --- 272,281 ---- // Returns an array of arrays with various fields. ! function search(&$search, &$user) { // Add more fields here ! $sortfields = array("name", "`sampleName1`", ! "`sampleName2`", array("`addedDate`", "id"), "`userName`", ! 0, 0, 0, "filename", "spots"); $ob = $search->makeOrderBy($sortfields); Index: test.phtml =================================================================== RCS file: /cvsroot/basedb/basedb/www/test.phtml,v retrieving revision 1.51 retrieving revision 1.52 diff -C2 -d -r1.51 -r1.52 *** test.phtml 1 Oct 2002 17:35:10 -0000 1.51 --- test.phtml 8 Oct 2002 09:05:13 -0000 1.52 *************** *** 26,39 **** header("content-type: text/plain"); - echo "aaa\n"; - - eval("echo(\"bbb\\n\");"); ! echo "ccc\n"; ! eval("function foo(){echo \"ddd\\n\";}"); - foo(); exit; --- 26,56 ---- header("content-type: text/plain"); + function si($x) + { + return max(-32768, min(32767, (int)$x)); + } + echo "-100000: ".si(-100000)."\n"; + echo " -10000: ".si(-10000)."\n"; + echo " -100: ".si(-100)."\n"; + echo " 100: ".si(100)."\n"; + echo " 10000: ".si(10000)."\n"; + echo " 100000: ".si(100000)."\n"; ! /*include("getconfig.inc.php"); ! include("wizzzard.inc.php"); ! $m1 = "foo:\\4\\ nuffe \\3\\,bar:\\\\a\\\\b\\\\c,baz:this\\cis\\ca\\ctest,muu:\\51\\,fuu:aa\\1\\\\c\\2\\d"; ! $ma1 = Wizzzard::mappingStringToArray($m1); ! $m2 = Wizzzard::mappingArrayToString($ma1); ! $ma2 = Wizzzard::mappingStringToArray($m2); ! $m3 = Wizzzard::mappingArrayToString($ma2); ! echo "Before: $m1\n"; ! echo "After: $m2\n"; ! echo "Afterer: $m3\n"; ! print_r($ma1); ! print_r($ma2); ! */ exit; Index: wizzzard.inc.php =================================================================== RCS file: /cvsroot/basedb/basedb/www/wizzzard.inc.php,v retrieving revision 1.27 retrieving revision 1.28 diff -C2 -d -r1.27 -r1.28 *** wizzzard.inc.php 10 Sep 2002 23:06:38 -0000 1.27 --- wizzzard.inc.php 8 Oct 2002 09:05:13 -0000 1.28 *************** *** 24,28 **** // Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. // - require_once("db.inc.php"); // 'A new hat. This one's practically had it.' --- 24,27 ---- *************** *** 34,155 **** // Rincewind sighed. 'Oh, all right. I'll do it.' [...1077 lines suppressed...] --- 761,779 ---- function exists($wizid) { ! return parent::exists("Wizzzard", $wizid); } ! function useWizzzard($wizid, $userid) { $query = "INSERT INTO WizzzardUser (owner, wizzzard) VALUES ". ! "(".(int)$userid.", ".(int)$wizid.")"; query($query); } ! function unuseWizzzard($wizid, $userid) { ! $query = "DELETE FROM WizzzardUser WHERE owner = ".(int)$userid. " AND wizzzard = ".(int)$wizid; query($query); } } Index: wizzzard_list.phtml =================================================================== RCS file: /cvsroot/basedb/basedb/www/wizzzard_list.phtml,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** wizzzard_list.phtml 29 Aug 2002 16:51:34 -0000 1.14 --- wizzzard_list.phtml 8 Oct 2002 09:05:13 -0000 1.15 *************** *** 28,54 **** require_once("search.inc.php"); require_once("searchhtml.inc.php"); ! $err = ""; ! if(isset($i_wizdel)) ! { ! if(!Wizzzard::isOwner($i_wizdel, $curUser->getId())) ! $err = "Error deleting: You have no such file format"; ! else if(!Wizzzard::removeId($i_wizdel)) ! $err = "Unable to delete file format"; [...153 lines suppressed...] + echo "<tr bgcolor=$tdbg[$odd]>". ! "<td>".html($s["name"]).remMark($s["removed"])." ". ! implode(" ", $links)."</td>". "<td>".html($s["userName"])."</td>". ! "<td>".groupAccessCheckbox($s["id"])."</td>". ! "<td>".groupInfo($s, $users)."</td>". ! "<td>".worldInfo($s)."</td>". ! "<td>".$s["maxCols"]."</td>". "</tr>\n"; } + $cols = count($headerfields); if($addlink != "") ! echo "<tr><td colspan=$cols>$addlink</td></tr>\n"; ! ! groupAccessFooter($cols, $curUser); ! massDeleteInput($cols, "plate", showDelValue() !== 0); ! showDelLinks($cols); ?> </table> |
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From: <ku...@us...> - 2002-10-07 08:49:06
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Update of /cvsroot/basedb/basedb/documentation/faq In directory usw-pr-cvs1:/tmp/cvs-serv26241 Modified Files: Makefile Log Message: Index: Makefile =================================================================== RCS file: /cvsroot/basedb/basedb/documentation/faq/Makefile,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Makefile 2 Oct 2002 15:16:20 -0000 1.1 --- Makefile 7 Oct 2002 08:49:03 -0000 1.2 *************** *** 1,3 **** --- 1,4 ---- # $Id$ + # $Revision$ MAIN = faq *************** *** 24,28 **** html: pdf ps ! @(rm -rf $(MAIN) ; latex2html $(MAIN) ; \ mv $(MAIN).pdf $(MAIN)/base_$(MAIN).pdf ; \ mv $(MAIN).ps $(MAIN)/base_$(MAIN).ps) --- 25,29 ---- html: pdf ps ! @(rm -rf $(MAIN) ; latex2html -local_icons -split +1 $(MAIN) ; \ mv $(MAIN).pdf $(MAIN)/base_$(MAIN).pdf ; \ mv $(MAIN).ps $(MAIN)/base_$(MAIN).ps) |
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From: <tr...@us...> - 2002-10-05 10:13:17
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Update of /cvsroot/basedb/basedb/exec/migration_tools In directory usw-pr-cvs1:/tmp/cvs-serv30587 Modified Files: devchanges.sql Log Message: Reordered RawBioAssayData, changed SearchCriterion field to string Index: devchanges.sql =================================================================== RCS file: /cvsroot/basedb/basedb/exec/migration_tools/devchanges.sql,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** devchanges.sql 3 Oct 2002 18:01:19 -0000 1.2 --- devchanges.sql 5 Oct 2002 10:13:14 -0000 1.3 *************** *** 247,248 **** --- 247,284 ---- UPDATE Molecule SET cloneId=SUBSTRING(cloneId,2); + + ALTER TABLE RawBioAssayData + ADD x2 FLOAT NOT NULL AFTER molecule, + ADD y2 FLOAT NOT NULL AFTER x2, + CHANGE dia dia FLOAT, + CHANGE FCh1Median FCh1Median FLOAT, + CHANGE FCh1Mean FCh1Mean FLOAT, + CHANGE FCh1SD FCh1SD FLOAT, + CHANGE BCh1Median BCh1Median FLOAT, + CHANGE BCh1Mean BCh1Mean FLOAT, + CHANGE BCh1SD BCh1SD FLOAT, + CHANGE FCh2Median FCh2Median FLOAT, + CHANGE FCh2Mean FCh2Mean FLOAT, + CHANGE FCh2SD FCh2SD FLOAT, + CHANGE BCh2Median BCh2Median FLOAT, + CHANGE BCh2Mean BCh2Mean FLOAT, + CHANGE BCh2SD BCh2SD FLOAT, + CHANGE FPixels FPixels SMALLINT, + CHANGE BPixels BPixels SMALLINT; + + UPDATE RawBioAssayData SET x2 = x, y2 = y; + + ALTER TABLE RawBioAssayData + DROP x, + DROP y, + CHANGE x2 x FLOAT NOT NULL, + CHANGE y2 y FLOAT NOT NULL; + + ALTER TABLE BioAssaySet + ADD removed TINYINT (1) not null; + + ALTER TABLE BioAssay + ADD removed TINYINT (1) not null; + + ALTER TABLE SearchCriterion + CHANGE field field VARCHAR(40) not null; |
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From: <tr...@us...> - 2002-10-05 10:11:13
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Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv29791
Modified Files:
search.inc.php searchhtml.inc.php
Log Message:
Search change: strings as search field keys in preparation for user-defined RawBA columns
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/search.inc.php,v
retrieving revision 1.43
retrieving revision 1.44
diff -C2 -d -r1.43 -r1.44
*** search.inc.php 30 Sep 2002 21:13:10 -0000 1.43
--- search.inc.php 5 Oct 2002 10:11:09 -0000 1.44
***************
*** 63,67 ****
The makeWhere function, which sets up $where, accepts two arrays.
The first is the list of expressions that criterion->$field refers
! to, and the second maps those field numbers to up to three strings
or arrays, which are sent to addExtraTable(), addExtraWhere(),
addLeftJoin() if there are any criteria with the corresponding
--- 63,67 ----
The makeWhere function, which sets up $where, accepts two arrays.
The first is the list of expressions that criterion->$field refers
! to, and the second maps those fields' keys to up to three strings
or arrays, which are sent to addExtraTable(), addExtraWhere(),
[...88 lines suppressed...]
$this->searchString = $row["searchString"];
--- 829,833 ----
if($row =& db_fetch_assoc($res))
{
! $this->field = $row["field"];
$this->op = (int)$row["op"];
$this->searchString = $row["searchString"];
***************
*** 869,873 ****
function setField($val)
{
! $this->field = (int)$val;
}
function setOp($val)
--- 880,884 ----
function setField($val)
{
! $this->field = $val;
}
function setOp($val)
Index: searchhtml.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/searchhtml.inc.php,v
retrieving revision 1.42
retrieving revision 1.43
diff -C2 -d -r1.42 -r1.43
*** searchhtml.inc.php 30 Sep 2002 21:13:10 -0000 1.42
--- searchhtml.inc.php 5 Oct 2002 10:11:09 -0000 1.43
***************
*** 43,49 ****
// $searchType - a string describing a type of search, from UserSearch.searchType
// (or BioAssaySetSearch etc. depending on $searchItemType).
! // $searchfields - reference to array of id_number => name for the things
! // you can search for. The names are shown on the page and the numbers
! // are used in SearchCriterion objects.
// $fieldType - ref to array from id_number to type, where the types are
// as above.
--- 43,50 ----
// $searchType - a string describing a type of search, from UserSearch.searchType
// (or BioAssaySetSearch etc. depending on $searchItemType).
[...62 lines suppressed...]
echo "</select></td><td><select name='i_op${tableId}[$pos]'>\n";
--- 317,321 ----
if($ttype != $typetype[$j]) continue;
$sel = ($j == $crit->getField()) ? "selected" : "";
! echo "<option value='$j' $sel>$f\n";
}
echo "</select></td><td><select name='i_op${tableId}[$pos]'>\n";
***************
*** 401,405 ****
{
$sel = (isset($i_searchgl) && $j == $f0) ? "selected" : "";
! echo "<option $sel value=$j>$f\n";
}
echo "</select></td><td><select name='i_op${tableId}[0]'>\n";
--- 405,409 ----
{
$sel = (isset($i_searchgl) && $j == $f0) ? "selected" : "";
! echo "<option $sel value='$j'>$f\n";
}
echo "</select></td><td><select name='i_op${tableId}[0]'>\n";
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From: <tr...@us...> - 2002-10-03 18:02:07
|
Update of /cvsroot/basedb/basedb/exec/source
In directory usw-pr-cvs1:/tmp/cvs-serv1708
Modified Files:
assayImporter.cc
Log Message:
Removed filtering of negative intensities
Index: assayImporter.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/exec/source/assayImporter.cc,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** assayImporter.cc 5 Aug 2002 11:37:29 -0000 1.4
--- assayImporter.cc 3 Oct 2002 18:02:04 -0000 1.5
***************
*** 61,73 ****
// Only keep points with positive intensities.
int i1C = baseF + i1Field, i2C = baseF + i2Field;
! if(vals[i1C] > 0 && vals[i2C] > 0)
! {
! cout << assayIds[a] << '\t' <<
! int(vals[posCol]) << '\t' <<
! int(vals[molCol]) << '\t' <<
! vals[i1C] << '\t' <<
! vals[i2C] << '\t' <<
! vals[i1C] / vals[i2C] << '\n';
! }
}
}
--- 61,70 ----
// Only keep points with positive intensities.
int i1C = baseF + i1Field, i2C = baseF + i2Field;
! cout << assayIds[a] << '\t' <<
! int(vals[posCol]) << '\t' <<
! int(vals[molCol]) << '\t' <<
! vals[i1C] << '\t' <<
! vals[i2C] << '\t' <<
! vals[i1C] / vals[i2C] << '\n';
}
}
|
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From: <tr...@us...> - 2002-10-03 18:01:22
|
Update of /cvsroot/basedb/basedb/exec/migration_tools
In directory usw-pr-cvs1:/tmp/cvs-serv1226
Modified Files:
devchanges.sql
Log Message:
Changed and rename Array table, set default owner and world read access on some tables
Index: devchanges.sql
===================================================================
RCS file: /cvsroot/basedb/basedb/exec/migration_tools/devchanges.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** devchanges.sql 30 Sep 2002 17:15:57 -0000 1.1
--- devchanges.sql 3 Oct 2002 18:01:19 -0000 1.2
***************
*** 220,224 ****
--- 220,248 ----
'plate' not null;
+ ALTER TABLE Array
+ CHANGE barcode name VARCHAR (20) not null,
+ ADD owner INT not null,
+ ADD addedDate DATE not null,
+ ADD removed TINYINT(1) not null,
+ ADD gid INT not null ,
+ ADD groupAccess TINYINT(1) not null,
+ ADD worldAccess TINYINT(1) not null;
+
UPDATE Protocol SET worldAccess = 1;
UPDATE SampleAnnotationType SET worldAccess = 1;
UPDATE Program SET worldAccess = 1;
+ UPDATE PlateType SET worldAccess = 1;
+ UPDATE Plate SET worldAccess = 1;
+ UPDATE ArrayBatch SET worldAccess = 1;
+ UPDATE ArrayType SET worldAccess = 1;
+ UPDATE Array SET worldAccess = 1;
+
+ UPDATE SampleAnnotationType SET owner = 1;
+ UPDATE SampleTissue SET owner = 1;
+ UPDATE PlateEventType SET owner = 1;
+ UPDATE Array SET owner = 1;
+
+ RENAME TABLE Array TO ArraySlide;
+
+ UPDATE Molecule SET cloneId=SUBSTRING(cloneId,2);
+
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