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From: <man...@pr...> - 2002-11-18 04:18:52
|
Update of /cvsroot/genex/genex-server/CyberT-dist
In directory sc8-pr-cvs1:/tmp/cvs-serv17836/CyberT-dist
Modified Files:
ChangeLog
Log Message:
added GeneSpring.notes, updated INSTALL doc
Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/CyberT-dist/ChangeLog,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** ChangeLog 14 Nov 2002 04:19:28 -0000 1.9
--- ChangeLog 18 Nov 2002 04:18:49 -0000 1.10
***************
*** 6,10 ****
(remove CyberTDB-7.0.pl.in, add CyberTDB-7.1.pl.in,
remove CyberT-7.0.form.pl.in add CyberT-7.1.form.pl.in)
! * updated the hdarray files (hdarray0
* added a replacement xgobi file to the tarball.
(remove xgobi, add xgobi.R.in, add xgobi_1.2-7.tar.gz)
--- 6,10 ----
(remove CyberTDB-7.0.pl.in, add CyberTDB-7.1.pl.in,
remove CyberT-7.0.form.pl.in add CyberT-7.1.form.pl.in)
! * updated the hdarray files (hdarray)
* added a replacement xgobi file to the tarball.
(remove xgobi, add xgobi.R.in, add xgobi_1.2-7.tar.gz)
|
|
From: <ki...@us...> - 2002-11-16 01:30:03
|
Update of /cvsroot/genex/genex-www/status/2002/nov
In directory usw-pr-cvs1:/tmp/cvs-serv23489
Modified Files:
status_main.ssi
Log Message:
update
Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/nov/status_main.ssi,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** status_main.ssi 16 Nov 2002 01:14:31 -0000 1.2
--- status_main.ssi 16 Nov 2002 01:29:59 -0000 1.3
***************
*** 74,127 ****
<b>GeneX 2.x Project</b><br>
-----------------<br>
! -ExperimentSet (Prototype Done)<br>
! -ArrayDesign (Prototype Done)<br>
! -Data-loader (Jason) [< 1 week, 75%]<br>
! -Affy File Format --> MAGE-ML (Jason) [< 1 week, 60%]<br>
! -GenePix File Format --> MAGE-ML (Brandon) [< 1 week, 90%]<br>
! -Agilent File Format --> MAGE-ML (?) [ 0.8-1.2 * GenePix task time]<br>
! -QuantArray File Format --> MAGE-ML (done)<br>
! (Requires working data loader and >= 1 working File Format)<br>
! -Data export [0-2 weeks, 80%]<br>
! -Gene Spring Connection (Prototype) [2 d, 60% - 1 wk, 90%]<br>
! -Basic Analysis (Prototype) <br>
! - MLX connection ( Diane | Chris ) [ 3 d, 70% - 1 wk, 95% ]<br>
! - CyberT, Rcluster ( Harry ) [< 1 wk 60% ]<br>
! - OpenDX integration ( Harry ) [ ??? ]<br>
! -User scratch tables for expression values (Jason) [ 2d 50% -1wk, 80%]<br>
! -Basic Analysis (Beta/Final) ( Harry | Jason | Diane | Joe)<br>
[ 2 wk 50% - 4 wk 90%]<br>
! *Quality Control<br>
! *Normalization<br>
! *Filtering<br>
! *Outlier detection<br>
! -Gene Spring Connection (Beta/Final) ( Joe | Diane | Harry )<br>
[ +1d-2d to prototype ]<br>
! -Moving data from scratch table into final expression table (Jason)<br>
[ 2d, 60% - 1 wk 90% ]<br>
! -Annotation Editors ( unknown ) [ ???? ]<br>
! -research DAS, Cartwheel, current art ( unknown ) [ 3d, 70% - 5d, 95% ]<br>
! -implement annotation functionality ( unknown ) [ ???? ]<br>
</p>
<p>
(Requires: Possible now)<br>
! -Define Security Model (Done)<br>
! -Security Model Implementation (Jason) [ 2d, 75% - 1wk 95%]<br>
! -All applications will have to be updated [ ??? ]<br>
! to support the finished model, doesn't prevent<br>
! work from being done on applications.<br>
</p>
<p>
(Requires: Possible now)<br>
! -Updates to Pymerase for GeneX support<br>
! -Python API for Genex (Prototype) (Diane & Brandon) [ 2d, 70% - 3d, 90%]<br>
! -MLX connection through API (Prototype)<br>
! -Python based GUIs & Apps for GeneX (Prototype) [ 2wk,40% - 4 wk,80% ]<br>
</p>
<p>
(Requires: Finished Security Model Implementation)<br>
! -Security model update to Pymerase<br>
! -Python API for GeneX (Beta/Final)<br>
! -MLX connection through API (Beta/Final)<br>
! -Python based GUIs & Apps for GeneX (Beta/Final)<br>
</p>
<hr>
--- 74,127 ----
<b>GeneX 2.x Project</b><br>
-----------------<br>
! *ExperimentSet (Prototype Done)<br>
! *ArrayDesign (Prototype Done)<br>
! **Data-loader (Jason) [< 1 week, 75%]<br>
! **Affy File Format --> MAGE-ML (Jason) [< 1 week, 60%]<br>
! **GenePix File Format --> MAGE-ML (Brandon) [< 1 week, 90%]<br>
! **Agilent File Format --> MAGE-ML (?) [ 0.8-1.2 * GenePix task time]<br>
! **QuantArray File Format --> MAGE-ML (done)<br>
! ***(Requires working data loader and >= 1 working File Format)<br>
! ***Data export [0-2 weeks, 80%]<br>
! ***Gene Spring Connection (Prototype) [2 d, 60% - 1 wk, 90%]<br>
! ***Basic Analysis (Prototype) <br>
! ****MLX connection ( Diane | Chris ) [ 3 d, 70% - 1 wk, 95% ]<br>
! ****CyberT, Rcluster ( Harry ) [< 1 wk 60% ]<br>
! ****OpenDX integration ( Harry ) [ ??? ]<br>
! ***User scratch tables for expression values (Jason) [ 2d 50% -1wk, 80%]<br>
! ****Basic Analysis (Beta/Final) ( Harry | Jason | Diane | Joe)<br>
[ 2 wk 50% - 4 wk 90%]<br>
! *****Quality Control<br>
! *****Normalization<br>
! *****Filtering<br>
! *****Outlier detection<br>
! ****Gene Spring Connection (Beta/Final) ( Joe | Diane | Harry )<br>
[ +1d-2d to prototype ]<br>
! ****Moving data from scratch table into final expression table (Jason)<br>
[ 2d, 60% - 1 wk 90% ]<br>
! *Annotation Editors ( unknown ) [ ???? ]<br>
! **research DAS, Cartwheel, current art ( unknown ) [ 3d, 70% - 5d, 95% ]<br>
! **implement annotation functionality ( unknown ) [ ???? ]<br>
</p>
<p>
(Requires: Possible now)<br>
! *Define Security Model (Done)<br>
! **Security Model Implementation (Jason) [ 2d, 75% - 1wk 95%]<br>
! ***All applications will have to be updated [ ??? ]<br>
! ---to support the finished model, doesn't prevent<br>
! ---work from being done on applications.<br>
</p>
<p>
(Requires: Possible now)<br>
! *Updates to Pymerase for GeneX support<br>
! **Python API for Genex (Prototype) (Diane & Brandon) [ 2d, 70% - 3d, 90%]<br>
! ***MLX connection through API (Prototype)<br>
! ***Python based GUIs & Apps for GeneX (Prototype) [ 2wk,40% - 4 wk,80% ]<br>
</p>
<p>
(Requires: Finished Security Model Implementation)<br>
! *Security model update to Pymerase<br>
! **Python API for GeneX (Beta/Final)<br>
! ***MLX connection through API (Beta/Final)<br>
! ***Python based GUIs & Apps for GeneX (Beta/Final)<br>
</p>
<hr>
***************
*** 160,209 ****
<p>
<b>Summery:</b><br>
! *Created GenePix-GPR-1.0 FeatureExtractionSoftware xml file
! *Found bugs in array-design.html and data-loader.html
! *Worked on task/depandancy outline with Diane
! *Had strategy meeting with Barbara Wold, Jose Luis Riechmann, Eric Mjolsness, and Jennifer Weller
! *Created tasklist, with estimated development times and dependancies (see Diane's status update)
! *Talked about Caltech Deadlines
! *Two-week deadline (now one-week):
! -Expression data imported and exported from GeneX 2.x
! *Christmas deadline:
! -Allow Biologists to easily get data into the database
! -Basic Analysis (Normalization, Quality Control, etc.)
! -GeneSpring Connection
! -Annotation of experiments
! -I think there is more, but I am forgetting what it is... I'll get back to list on this.
! *Talked about having a more standardized format for these summeries.
! -Something like this where it can be easily skimmed for important updates... something like:
! -Summary Section
! -Next Week
! -Problems
! -Future (optional)
! -other notes / sections (optional)
</p>
<p>
! <b>Next Week:</b>
! *Update GeneX 2.x installation with Jason's fixes
! *Test GenePix upload
! *Create Agilent FeatureExtractionSoftware and/or supply data for testing
</p>
<p>
! <b>Problems:</b>
! *ArrayDesign and Data-loader where broken, Jason says they are fixed now.
</p>
<p>
! <b>Future:</b>
! *Discusion of GUI's
! *GUI Widget Auto-generation with Pymerase
</p>
<p>
! <b>New or Changing Priorities:</b>
! *2 New Deadlines
! -Two week (see Summery)
! -Christmas (see Summer)
</p>
--- 160,209 ----
<p>
<b>Summery:</b><br>
! *Created GenePix-GPR-1.0 FeatureExtractionSoftware xml file<br>
! *Found bugs in array-design.html and data-loader.html<br>
! *Worked on task/depandancy outline with Diane<br>
! *Had strategy meeting with Barbara Wold, Jose Luis Riechmann, Eric Mjolsness, and Jennifer Weller<br>
! *Created tasklist, with estimated development times and dependancies (see Diane's status update)<br>
! **Talked about Caltech Deadlines<br>
! ***Two-week deadline (now one-week):<br>
! ****Expression data imported and exported from GeneX 2.x<br>
! ***Christmas deadline:<br>
! ****Allow Biologists to easily get data into the database<br>
! *****Basic Analysis (Normalization, Quality Control, etc.)<br>
! ***GeneSpring Connection<br>
! ***Annotation of experiments<br>
! ***I think there is more, but I am forgetting what it is... I'll get back to list on this.<br>
! ***Talked about having a more standardized format for these summeries.<br>
! ****Something like this where it can be easily skimmed for important updates... something like:<br>
! *****Summary Section<br>
! *****Next Week<br>
! *****Problems<br>
! *****Future (optional)<br>
! *****other notes / sections (optional)<br>
</p>
<p>
! <b>Next Week:</b><br>
! *Update GeneX 2.x installation with Jason's fixes<br>
! *Test GenePix upload<br>
! *Create Agilent FeatureExtractionSoftware and/or supply data for testing<br>
</p>
<p>
! <b>Problems:</b><br>
! *ArrayDesign and Data-loader where broken, Jason says they are fixed now.<br>
</p>
<p>
! <b>Future:</b><br>
! *Discusion of GUI's<br>
! *GUI Widget Auto-generation with Pymerase<br>
</p>
<p>
! <b>New or Changing Priorities:</b><br>
! *2 New Deadlines<br>
! **Two week (see Summery)<br>
! **Christmas (see Summer)<br>
</p>
|
|
From: <ki...@us...> - 2002-11-16 01:14:36
|
Update of /cvsroot/genex/genex-www/status/2002/nov
In directory usw-pr-cvs1:/tmp/cvs-serv17050
Modified Files:
status_main.ssi
Log Message:
weekly status update
Index: status_main.ssi
===================================================================
RCS file: /cvsroot/genex/genex-www/status/2002/nov/status_main.ssi,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** status_main.ssi 9 Nov 2002 05:48:22 -0000 1.1
--- status_main.ssi 16 Nov 2002 01:14:31 -0000 1.2
***************
*** 1,3 ****
--- 1,214 ----
<!--Main content -->
+ <table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
+ <tr valign="top" bgcolor="#D8E4F7">
+ <th><big>November 14th, 2002</big></th>
+ </tr>
+ <tr bgcolor="#D8E4F7">
+ <td>
+ <p>
+ <b><u>Caltech Update - Diane Trout</u></b><br>
+ </p>
+
+ <p>
+ <b>Current accomplishments:</b><br>
+ * connected novosoft reader to pymerase<br>
+ ** Constructs database using UML model<br>
+ ** Constructs object model connected to database<br>
+ </p>
+
+ <p>
+ <b>next week:</b><br>
+ * finish debugging object model to database<br>
+ * work on debs<br>
+ </p>
+
+ <p>
+ <b>problems:</b><br>
+ * just slogging through the code<br>
+ </p>
+
+ <p>
+ as an aside here's a guess at what needs to be done to "finish" GeneX.<br>
+ Brandon came up with the tasks, I estimated how long I thought the<br>
+ tasks would take.<br>
+ </p>
+
+ -----
+ <p>
+ <b>GeneX 2.x Task and Dependancy Outline</b>
+ </p>
+
+ <p>
+ Notes about time, all time comments are in [ ]<br>
+ [< x] implies will take less than x time units<br>
+ [x-y] implies will take between x and y time units<br>
+ [???] means I don't want to guess<br>
+ [x, y%] implies that I am y% confident that the task will be done in x<br>
+ time units<br>
+ [x, y% - m, n%] implies that think there's a y% chance that it will be<br>
+ done in x units, and n% in m units. e.g.<br>
+ [now, 0% - infinity, 99%]<br>
+ [ x-y * T ] implies between x * T and y * T length, where<br>
+ task is the length of time needed to accomplish task T<br>
+ [ +x-y T ] implies x - y time units in addition to completing task T.<br>
+ </p>
+ <p>
+ Note all times are my (diane's) estimates for how long it will take to<br>
+ accomplish task, not how long from now the task will be done.<br>
+ </p>
+ <p>
+ abbrieviations<br>
+ wk = week<br>
+ d = day<br>
+ h = hour<br>
+ m = month<br>
+ </p>
+ <p>
+ Notes about people performing tasks<br>
+ ( x ) means that person x will do task<br>
+ ( x | y ) means that person x or y could do the task<br>
+ ( x & y ) means that person x and y are needed to the task<br>
+ </p>
+
+ <p>
+ <b>GeneX 2.x Project</b><br>
+ -----------------<br>
+ -ExperimentSet (Prototype Done)<br>
+ -ArrayDesign (Prototype Done)<br>
+ -Data-loader (Jason) [< 1 week, 75%]<br>
+ -Affy File Format --> MAGE-ML (Jason) [< 1 week, 60%]<br>
+ -GenePix File Format --> MAGE-ML (Brandon) [< 1 week, 90%]<br>
+ -Agilent File Format --> MAGE-ML (?) [ 0.8-1.2 * GenePix task time]<br>
+ -QuantArray File Format --> MAGE-ML (done)<br>
+ (Requires working data loader and >= 1 working File Format)<br>
+ -Data export [0-2 weeks, 80%]<br>
+ -Gene Spring Connection (Prototype) [2 d, 60% - 1 wk, 90%]<br>
+ -Basic Analysis (Prototype) <br>
+ - MLX connection ( Diane | Chris ) [ 3 d, 70% - 1 wk, 95% ]<br>
+ - CyberT, Rcluster ( Harry ) [< 1 wk 60% ]<br>
+ - OpenDX integration ( Harry ) [ ??? ]<br>
+ -User scratch tables for expression values (Jason) [ 2d 50% -1wk, 80%]<br>
+ -Basic Analysis (Beta/Final) ( Harry | Jason | Diane | Joe)<br>
+ [ 2 wk 50% - 4 wk 90%]<br>
+ *Quality Control<br>
+ *Normalization<br>
+ *Filtering<br>
+ *Outlier detection<br>
+ -Gene Spring Connection (Beta/Final) ( Joe | Diane | Harry )<br>
+ [ +1d-2d to prototype ]<br>
+ -Moving data from scratch table into final expression table (Jason)<br>
+ [ 2d, 60% - 1 wk 90% ]<br>
+ -Annotation Editors ( unknown ) [ ???? ]<br>
+ -research DAS, Cartwheel, current art ( unknown ) [ 3d, 70% - 5d, 95% ]<br>
+ -implement annotation functionality ( unknown ) [ ???? ]<br>
+ </p>
+ <p>
+ (Requires: Possible now)<br>
+ -Define Security Model (Done)<br>
+ -Security Model Implementation (Jason) [ 2d, 75% - 1wk 95%]<br>
+ -All applications will have to be updated [ ??? ]<br>
+ to support the finished model, doesn't prevent<br>
+ work from being done on applications.<br>
+ </p>
+ <p>
+ (Requires: Possible now)<br>
+ -Updates to Pymerase for GeneX support<br>
+ -Python API for Genex (Prototype) (Diane & Brandon) [ 2d, 70% - 3d, 90%]<br>
+ -MLX connection through API (Prototype)<br>
+ -Python based GUIs & Apps for GeneX (Prototype) [ 2wk,40% - 4 wk,80% ]<br>
+ </p>
+ <p>
+ (Requires: Finished Security Model Implementation)<br>
+ -Security model update to Pymerase<br>
+ -Python API for GeneX (Beta/Final)<br>
+ -MLX connection through API (Beta/Final)<br>
+ -Python based GUIs & Apps for GeneX (Beta/Final)<br>
+ </p>
+ <hr>
+ <p>
+ <b><u>UCI Update - Harry Mangalam</u></b><br>
+ </p>
+
+ <p>
+ Most of what I've done over the past week has been related to installs (of Debian Linux, multiple times) and of the GeneX2 database on Debian systems.
+ </p>
+
+ <p>
+ With a fresh Debian system, GeneX2 installs pretty much as described (now) in the INSTALL doc. I collected the .deb requirements (and some more Perl peculiarities) for later installs. Next week, I'll find out just how well I recorded them with a new series of installs at GMU and at the NRL (talk about installing under the gun..).
+ </p>
+
+ <p>
+ Also, I've just about finished figuring out the GeneSpring <-> GeneX 2 intereraction with both JDBC <-> ODBC <-> Postgresql (on Windows clients) and JDBC <-> GeneX (on Linux clients). The former I posted, the latter is being written up.
+ </p>
+
+ <p>
+ What remains is the actual mapping of GeneSpring data columns to GeneX data columns, for which I may need a bit more time to learn the how each is laid out, or (if the financing is OK) Mark Wilkinson may finish it off.
+ </p>
+
+ <p>
+ However, GeneSpring IS talking to GeneX; from sniffing the tcp packets go back and forth, I can see that the only reason data isn't showing up in GeneSpring is because there is a data mismatch (as well as a lack of data).
+ </p>
+
+ <p>
+ I'm off for much of next week to visit Virginia so I'll probably not make the Thursday deadline, but I'll post an update when I get back.
+ </p>
+ <hr>
+ <p>
+ <b><u>Caltech Update - Brandon King</u></b><br>
+ </p>
+
+ <p>
+ <b>Summery:</b><br>
+ *Created GenePix-GPR-1.0 FeatureExtractionSoftware xml file
+ *Found bugs in array-design.html and data-loader.html
+ *Worked on task/depandancy outline with Diane
+ *Had strategy meeting with Barbara Wold, Jose Luis Riechmann, Eric Mjolsness, and Jennifer Weller
+ *Created tasklist, with estimated development times and dependancies (see Diane's status update)
+ *Talked about Caltech Deadlines
+ *Two-week deadline (now one-week):
+ -Expression data imported and exported from GeneX 2.x
+ *Christmas deadline:
+ -Allow Biologists to easily get data into the database
+ -Basic Analysis (Normalization, Quality Control, etc.)
+ -GeneSpring Connection
+ -Annotation of experiments
+ -I think there is more, but I am forgetting what it is... I'll get back to list on this.
+ *Talked about having a more standardized format for these summeries.
+ -Something like this where it can be easily skimmed for important updates... something like:
+ -Summary Section
+ -Next Week
+ -Problems
+ -Future (optional)
+ -other notes / sections (optional)
+ </p>
+
+ <p>
+ <b>Next Week:</b>
+ *Update GeneX 2.x installation with Jason's fixes
+ *Test GenePix upload
+ *Create Agilent FeatureExtractionSoftware and/or supply data for testing
+ </p>
+
+ <p>
+ <b>Problems:</b>
+ *ArrayDesign and Data-loader where broken, Jason says they are fixed now.
+ </p>
+
+ <p>
+ <b>Future:</b>
+ *Discusion of GUI's
+ *GUI Widget Auto-generation with Pymerase
+ </p>
+
+ <p>
+ <b>New or Changing Priorities:</b>
+ *2 New Deadlines
+ -Two week (see Summery)
+ -Christmas (see Summer)
+ </p>
+
+ </td>
+ </tr>
+ </table>
<table border="2" bgcolor="#BFD8D8" width="100%" cellpadding="15" cellspacing="5">
|
|
From: <jas...@us...> - 2002-11-15 22:08:05
|
Update of /cvsroot/genex/genex-server/Genex/ExternalDatabase In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/ExternalDatabase Modified Files: ExternalDatabase.pm Log Message: new Index: ExternalDatabase.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ExternalDatabase/ExternalDatabase.pm,v retrieving revision 1.30 retrieving revision 1.31 diff -C2 -d -r1.30 -r1.31 |
|
From: <jas...@us...> - 2002-11-15 22:08:05
|
Update of /cvsroot/genex/genex-server/Genex/Feature
In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/Feature
Modified Files:
Feature.pm
Log Message:
new
Index: Feature.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Feature/Feature.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** Feature.pm 9 Nov 2002 00:35:36 -0000 1.12
--- Feature.pm 15 Nov 2002 21:55:12 -0000 1.13
***************
*** 1085,1089 ****
# first we ensure that the container instance is really in the DB
my $sql = $dbh->create_select_sql( COLUMNS=>['ad_pk'],
! FROM=>[$table_name],
WHERE=>qq[ad_pk='$lt_pkey'],
);
--- 1085,1089 ----
# first we ensure that the container instance is really in the DB
my $sql = $dbh->create_select_sql( COLUMNS=>['ad_pk'],
! FROM=>[Bio::Genex::ArrayDesign->table_or_viewname($dbh)],
WHERE=>qq[ad_pk='$lt_pkey'],
);
***************
*** 1096,1100 ****
# ok to proceed with insert
my $header = shift @{$matrix};
! push(@{$header},'ad_fk');
$sql = $dbh->create_insert_sql($table_name,
$header,
--- 1096,1110 ----
# ok to proceed with insert
my $header = shift @{$matrix};
! push(@{$header},'ad_fk','feature_pk');
!
! # pre-fetch the next value of the sequence
! my $seq = 'GENEX_ID_SEQ';
! my $seq_sql = qq[SELECT nextval('"$seq"'::text)];
! my $seq_sth = $dbh->prepare($seq_sql)
! or $dbh->error(@error_args,
! sql=>$seq_sql,
! message=>"Couldn't prepare nextval for sequence $seq",
! );
!
$sql = $dbh->create_insert_sql($table_name,
$header,
***************
*** 1105,1112 ****
sql=>$sql);
foreach my $row (@{$matrix}) {
! my $sth = $sth->execute(@{$row},$lt_pkey)
or $dbh->error(@error_args,
message=>"Couldn't execute insert sql with args: "
! . join(',',@{$row}),
sth=>$sth,
sql=>$sql);
--- 1115,1136 ----
sql=>$sql);
foreach my $row (@{$matrix}) {
! $seq_sth->execute()
! or $dbh->error(@error_args,
! message=>"Couldn't execute nextval from sequence $seq",
! sth=>$seq_sth,
! sql=>$seq_sql);
! my $pkey = $seq_sth->fetchrow_arrayref();
! $dbh->error(@error_args,
! message=>"Couldn't fetch nextval from sequence $seq",
! sth=>$seq_sth,
! sql=>$seq_sql)
! unless defined $pkey && $pkey->[0];
!
! # DBI won't re-run the SQL until we finish
! $seq_sth->finish();
! $sth->execute(@{$row},$lt_pkey,$pkey->[0])
or $dbh->error(@error_args,
message=>"Couldn't execute insert sql with args: "
! . join(',',@{$row},$pkey->[0]),
sth=>$sth,
sql=>$sql);
|
|
From: <jas...@us...> - 2002-11-15 22:08:04
|
Update of /cvsroot/genex/genex-server/Genex/FeatureExtractionSoftware In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/FeatureExtractionSoftware Modified Files: FeatureExtractionSoftware.pm Log Message: new Index: FeatureExtractionSoftware.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/FeatureExtractionSoftware/FeatureExtractionSoftware.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 |
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From: <jas...@us...> - 2002-11-15 22:08:02
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Update of /cvsroot/genex/genex-server/Genex/GenexAdmin In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/GenexAdmin Modified Files: GenexAdmin.pm Log Message: new Index: GenexAdmin.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/GenexAdmin/GenexAdmin.pm,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 |
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From: <jas...@us...> - 2002-11-15 22:08:02
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Update of /cvsroot/genex/genex-server/Genex/GroupLink In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/GroupLink Modified Files: GroupLink.pm Log Message: new Index: GroupLink.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/GroupLink/GroupLink.pm,v retrieving revision 1.29 retrieving revision 1.30 diff -C2 -d -r1.29 -r1.30 |
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From: <jas...@us...> - 2002-11-15 22:05:45
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Update of /cvsroot/genex/genex-server In directory usw-pr-cvs1:/tmp/cvs-serv20849 Modified Files: ChangeLog Log Message: usual Index: ChangeLog =================================================================== RCS file: /cvsroot/genex/genex-server/ChangeLog,v retrieving revision 1.106 retrieving revision 1.107 diff -C2 -d -r1.106 -r1.107 *** ChangeLog 14 Nov 2002 21:23:05 -0000 1.106 --- ChangeLog 15 Nov 2002 22:05:41 -0000 1.107 *************** *** 1,2 **** --- 1,11 ---- + 2002-11-15 Jason E. Stewart <ja...@op...> + + * Install (Repository): + use PERLPATH and *not* $^X + + * Configure (Repository): + fixed START_PERL bug + better error printout for Perl misconfiguration + 2002-11-14 Jason E. Stewart <ja...@op...> |
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From: <jas...@us...> - 2002-11-15 22:04:26
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Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv20254
Modified Files:
Install
Log Message:
* Install (Repository):
use PERLPATH and *not* $^X
Index: Install
===================================================================
RCS file: /cvsroot/genex/genex-server/Install,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Install 14 Nov 2002 21:22:52 -0000 1.14
--- Install 15 Nov 2002 22:04:23 -0000 1.15
***************
*** 609,613 ****
if ($continue) {
my $db_init = 'db.pl';
! my $command = "su -c '$^X $MOTHERDIR/$db_init' postgres";
my $run_installer;
--- 609,613 ----
if ($continue) {
my $db_init = 'db.pl';
! my $command = "su -c '$PERLPATH $MOTHERDIR/$db_init' postgres";
my $run_installer;
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From: <jas...@us...> - 2002-11-15 22:03:55
|
Update of /cvsroot/genex/genex-server
In directory usw-pr-cvs1:/tmp/cvs-serv20102
Modified Files:
Configure
Log Message:
* Configure (Repository):
fixed START_PERL bug
better error printout for Perl misconfiguration
Index: Configure
===================================================================
RCS file: /cvsroot/genex/genex-server/Configure,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Configure 9 Nov 2002 00:29:55 -0000 1.10
--- Configure 15 Nov 2002 22:03:52 -0000 1.11
***************
*** 501,505 ****
# this looks strange, but if the user chose the default,
# we still have to check it out, so we assign it to $tmp
! $tmp = $START_PERL unless $tmp;
my ($rc, $reason);
--- 501,509 ----
# this looks strange, but if the user chose the default,
# we still have to check it out, so we assign it to $tmp
! if ($tmp) {
! $START_PERL = $tmp;
! } else {
! $tmp = $START_PERL;
! }
my ($rc, $reason);
***************
*** 542,547 ****
The perl interpreter you told me to use, '$tmp',
! Is missing a module or has the following problem: $reason.
! Please try a different one or load the required modules (see INSTALL)
#### Error ####
--- 546,554 ----
The perl interpreter you told me to use, '$tmp',
! Is missing a module or has the following problem:
!
! $reason
!
! Please try a different one or install the required modules (see INSTALL)
#### Error ####
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From: <jas...@us...> - 2002-11-15 22:03:07
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv19842/Genex/scripts
Modified Files:
qtdim-insert.pl.in
Log Message:
* scripts/qtdim-insert.pl.in (Repository):
made the data table name based on the command line input instead
of info from the MAGE-ML file
Index: qtdim-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/qtdim-insert.pl.in,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** qtdim-insert.pl.in 20 Oct 2002 14:52:53 -0000 1.3
--- qtdim-insert.pl.in 15 Nov 2002 22:03:04 -0000 1.4
***************
*** 171,175 ****
$name =~ tr/-./__/;
$mage_dim->setName($name);
! $table = 'Data_' . $mage_dim->getName();
my @args = (ro_groupname=>$ro_groupname,
rw_groupname=>$rw_groupname,
--- 171,176 ----
$name =~ tr/-./__/;
$mage_dim->setName($name);
! $table = 'Data_' . $OPTIONS{name} . '_' . $OPTIONS{version};
! $table =~ tr/-./__/;
my @args = (ro_groupname=>$ro_groupname,
rw_groupname=>$rw_groupname,
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From: <jas...@us...> - 2002-11-15 22:02:26
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv19613/Genex/scripts
Modified Files:
mbad-insert.pl.in
Log Message:
* scripts/mbad-insert.pl.in (Repository):
use table_or_viewname() for Feature instead of hardcoding
tablename
better error checking on regex's
fixed broken feature identifier string
Index: mbad-insert.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/mbad-insert.pl.in,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** mbad-insert.pl.in 8 Nov 2002 04:51:28 -0000 1.4
--- mbad-insert.pl.in 15 Nov 2002 22:02:23 -0000 1.5
***************
*** 160,164 ****
# pre-fetch feature_identifiers and pkeys
my $sql = $dbh->create_select_sql(COLUMNS=>['feature_identifier','feature_pk'],
! FROM=>['Feature'],
WHERE=>"ad_fk=$OPTIONS{ad_pk}"
);
--- 160,164 ----
# pre-fetch feature_identifiers and pkeys
my $sql = $dbh->create_select_sql(COLUMNS=>['feature_identifier','feature_pk'],
! FROM=>[Bio::Genex::Feature->table_or_viewname($dbh)],
WHERE=>"ad_fk=$OPTIONS{ad_pk}"
);
***************
*** 196,216 ****
$dbh->error(@error_args,
message=>"Couldn't find data_start_regex1 for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
)
! unless defined $fe_sw_db->data_start_regex1();
! my $data_start_regex1 = qr/$fe_sw_db->data_start_regex1/o;
$dbh->error(@error_args,
message=>"Couldn't find data_start_regex2 for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
)
! unless defined $fe_sw_db->data_start_regex2();
! my $data_start_regex2 = qr/$fe_sw_db->data_start_regex2/o;
$dbh->error(@error_args,
message=>"Couldn't find data_end_regex for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
)
! unless defined $fe_sw_db->data_end_regex();
! my $end_regex = qr/$fe_sw_db->end_regex/o;
my $in_data;
--- 196,220 ----
+ my $data_start_regex1 = $fe_sw_db->data_start_regex1();
$dbh->error(@error_args,
message=>"Couldn't find data_start_regex1 for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
)
! unless defined $data_start_regex1;
! $data_start_regex1 = qr/$data_start_regex1/o;
+ my $data_start_regex2 = $fe_sw_db->data_start_regex2();
$dbh->error(@error_args,
message=>"Couldn't find data_start_regex2 for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
)
! unless defined $data_start_regex2;
! $data_start_regex2 = qr/$data_start_regex2/o;
!
+ my $end_regex = $fe_sw_db->data_end_regex();
$dbh->error(@error_args,
message=>"Couldn't find data_end_regex for Feature Extraction Software: " . $fe_sw_db->name() . ':' . $fe_sw_db->version()
)
! unless defined $end_regex;
! $end_regex = qr/$end_regex/o;
my $in_data;
***************
*** 272,276 ****
my @data = split "\t";
! my $id = eval qq["$feature_id_string"];
print STDERR "Found id: <$id>\n" if $OPTIONS{debug};
print STDERR "Found feature: <$features{$id}>\n" if $OPTIONS{debug};
--- 276,280 ----
my @data = split "\t";
! my $id = eval "$feature_id_string";
print STDERR "Found id: <$id>\n" if $OPTIONS{debug};
print STDERR "Found feature: <$features{$id}>\n" if $OPTIONS{debug};
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From: <jas...@us...> - 2002-11-15 22:01:10
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv19131/Genex/scripts
Modified Files:
gendb.pl.in
Log Message:
* scripts/gendb.pl.in (Repository):
quantarray QT dim fixes
Index: gendb.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/gendb.pl.in,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** gendb.pl.in 20 Oct 2002 19:55:24 -0000 1.7
--- gendb.pl.in 15 Nov 2002 22:01:07 -0000 1.8
***************
*** 201,207 ****
'--version=3.0',
'--feat="1.2.3.4"',
! '--data_start_regex1="^Begin\s+Data"',
! '--data_start_regex2="^Number"',
! '--data_end_regex="^End"',
);
print STDERR "Adding example QuantitationTypeDimension ...\n";
--- 201,207 ----
'--version=3.0',
'--feat="1.2.3.4"',
! '--data_start_regex1=^Begin\s+Data',
! '--data_start_regex2=^Number',
! '--data_end_regex=^End',
);
print STDERR "Adding example QuantitationTypeDimension ...\n";
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From: <jas...@us...> - 2002-11-15 22:00:43
|
Update of /cvsroot/genex/genex-server/Genex/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv18890/Genex/scripts
Modified Files:
create_genex_class.pl.in
Log Message:
* scripts/create_genex_class.pl.in (Repository):
insert_matrix() fixes.
Index: create_genex_class.pl.in
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/scripts/create_genex_class.pl.in,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** create_genex_class.pl.in 9 Nov 2002 00:47:18 -0000 1.18
--- create_genex_class.pl.in 15 Nov 2002 22:00:38 -0000 1.19
***************
*** 1260,1264 ****
# first we ensure that the container instance is really in the DB
my \$sql = \$dbh->create_select_sql( COLUMNS=>['$lt_fkey_pkey'],
! FROM=>[\$table_name],
WHERE=>qq[$lt_fkey_pkey='\$lt_pkey'],
);
--- 1260,1264 ----
# first we ensure that the container instance is really in the DB
my \$sql = \$dbh->create_select_sql( COLUMNS=>['$lt_fkey_pkey'],
! FROM=>[$lt_fkey_class_full->table_or_viewname(\$dbh)],
WHERE=>qq[$lt_fkey_pkey='\$lt_pkey'],
);
***************
*** 1271,1275 ****
# ok to proceed with insert
my \$header = shift \@{\$matrix};
! push(\@{\$header},'$lt_fkey');
\$sql = \$dbh->create_insert_sql(\$table_name,
\$header,
--- 1271,1285 ----
# ok to proceed with insert
my \$header = shift \@{\$matrix};
! push(\@{\$header},'$lt_fkey','$PKEY');
!
! # pre-fetch the next value of the sequence
! my \$seq = 'GENEX_ID_SEQ';
! my \$seq_sql = qq[SELECT nextval('"\$seq"'::text)];
! my \$seq_sth = \$dbh->prepare(\$seq_sql)
! or \$dbh->error(\@error_args,
! sql=>\$seq_sql,
! message=>"Couldn't prepare nextval for sequence \$seq",
! );
!
\$sql = \$dbh->create_insert_sql(\$table_name,
\$header,
***************
*** 1280,1287 ****
sql=>\$sql);
foreach my \$row (\@{\$matrix}) {
! my \$sth = \$sth->execute(\@{\$row},\$lt_pkey)
or \$dbh->error(\@error_args,
message=>"Couldn't execute insert sql with args: "
! . join(',',\@{\$row}),
sth=>\$sth,
sql=>\$sql);
--- 1290,1311 ----
sql=>\$sql);
foreach my \$row (\@{\$matrix}) {
! \$seq_sth->execute()
! or \$dbh->error(\@error_args,
! message=>"Couldn't execute nextval from sequence \$seq",
! sth=>\$seq_sth,
! sql=>\$seq_sql);
! my \$pkey = \$seq_sth->fetchrow_arrayref();
! \$dbh->error(\@error_args,
! message=>"Couldn't fetch nextval from sequence \$seq",
! sth=>\$seq_sth,
! sql=>\$seq_sql)
! unless defined \$pkey && \$pkey->[0];
!
! # DBI won't re-run the SQL until we finish
! \$seq_sth->finish();
! \$sth->execute(\@{\$row},\$lt_pkey,\$pkey->[0])
or \$dbh->error(\@error_args,
message=>"Couldn't execute insert sql with args: "
! . join(',',\@{\$row},\$pkey->[0]),
sth=>\$sth,
sql=>\$sql);
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From: <jas...@us...> - 2002-11-15 21:55:45
|
Update of /cvsroot/genex/genex-server/Genex/ExperimentSet In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/ExperimentSet Modified Files: ExperimentSet.pm Log Message: new Index: ExperimentSet.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ExperimentSet/ExperimentSet.pm,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -d -r1.36 -r1.37 |
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From: <jas...@us...> - 2002-11-15 21:55:45
|
Update of /cvsroot/genex/genex-server/Genex/ExperimentFactors In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/ExperimentFactors Modified Files: ExperimentFactors.pm Log Message: new Index: ExperimentFactors.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ExperimentFactors/ExperimentFactors.pm,v retrieving revision 1.30 retrieving revision 1.31 diff -C2 -d -r1.30 -r1.31 |
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From: <jas...@us...> - 2002-11-15 21:55:45
|
Update of /cvsroot/genex/genex-server/Genex/ControlledVocab In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/ControlledVocab Modified Files: ControlledVocab.pm Log Message: new Index: ControlledVocab.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ControlledVocab/ControlledVocab.pm,v retrieving revision 1.29 retrieving revision 1.30 diff -C2 -d -r1.29 -r1.30 |
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From: <jas...@us...> - 2002-11-15 21:55:44
|
Update of /cvsroot/genex/genex-server/Genex/ContactType In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/ContactType Modified Files: ContactType.pm Log Message: new Index: ContactType.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/ContactType/ContactType.pm,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 |
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From: <jas...@us...> - 2002-11-15 21:55:44
|
Update of /cvsroot/genex/genex-server/Genex/Contact In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/Contact Modified Files: Contact.pm Log Message: new Index: Contact.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Contact/Contact.pm,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -d -r1.36 -r1.37 |
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From: <jas...@us...> - 2002-11-15 21:55:44
|
Update of /cvsroot/genex/genex-server/Genex/Citation In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/Citation Modified Files: Citation.pm Log Message: new Index: Citation.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Citation/Citation.pm,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -d -r1.36 -r1.37 |
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From: <jas...@us...> - 2002-11-15 21:55:43
|
Update of /cvsroot/genex/genex-server/Genex/Chromosome In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/Chromosome Modified Files: Chromosome.pm Log Message: new Index: Chromosome.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Chromosome/Chromosome.pm,v retrieving revision 1.40 retrieving revision 1.41 diff -C2 -d -r1.40 -r1.41 |
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From: <jas...@us...> - 2002-11-15 21:55:42
|
Update of /cvsroot/genex/genex-server/Genex/Channel In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/Channel Modified Files: Channel.pm Log Message: new Index: Channel.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Channel/Channel.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 |
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From: <jas...@us...> - 2002-11-15 21:55:42
|
Update of /cvsroot/genex/genex-server/Genex/BlastHits In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/BlastHits Modified Files: BlastHits.pm Log Message: new Index: BlastHits.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/BlastHits/BlastHits.pm,v retrieving revision 1.30 retrieving revision 1.31 diff -C2 -d -r1.30 -r1.31 |
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From: <jas...@us...> - 2002-11-15 21:55:41
|
Update of /cvsroot/genex/genex-server/Genex/Audit In directory usw-pr-cvs1:/tmp/cvs-serv16636/Genex/Audit Modified Files: Audit.pm Log Message: new Index: Audit.pm =================================================================== RCS file: /cvsroot/genex/genex-server/Genex/Audit/Audit.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 |
