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Solaris Install Instructions for Curation Tool User and Developer
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CONTENTS
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I. USER INSTALL
II. DEVELOPER INSTALL
III. RELEASE NOTES
I. USER INSTALL
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The USER package (bundled with the correct JRE) is available from:
http://genex.ncgr.org/genex/download/curation_tool/solaris/
1. Copy the same version of the "....tar.gz" install package and the
"...expand.sh" script to the desired install location on your hard drive.
2a. You can install the "....tar.gz" package by double-clicking in the File
Manager Window on the "...expand.sh" script and passing through the
arguments panel that comes by entering no arguments. This starts a RUN
window. When the install is complete, you can close the RUN window.
2b. You can also install the "....tar.gz" package by opening a terminal
window and typing the name of the "...expand.sh" script.
NOTE1: In both the above cases this results in an install directory being
created at the location of the "...expand.sh" script. The name of this
directory will depend on the version of the Curation Tool and OS platform
(eg. "curtool_033user_sol").
NOTE2: In both the above cases the "...expand.sh" script destroys the
"....tar.gz" install package, so if you want to keep the "....tar.gz"
package, you should make a copy before running the "...expand.sh" script.
3a. You can run the Curation Tool application by double-clicking in the File
Manager Window on the "go.sh" script found in the "bin" subdirectory under
the installed directory. This starts a RUN window. When you exit the
application, you can close the RUN window.
3b. You can also run the Curation Tool application by opening a terminal
window at the "bin" subdirectory under the installed directory and typing
the name of the "go.sh" script found there.
II. DEVELOPER INSTALL
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IMPORTANT! This developer installation package will only work if you
already have Java SDK installed on your computer and have an
environment variable called JAVA_HOME which points to the jdk
directory.
The current version of jdk is:
Java 2 SDK, Standard Edition, Version 1.3.0
You can download it at:
java.sun.com/j2se/1.3/download-solaris.html
You can set JAVA_HOME in your shell startup script:
setenv JAVA_HOME = "your path to jdk"
setenv JAVA_HOME /home/javadk/jdk1.3.0 (in .shrc if you use c shell)
1. Copy the same version of the "....tar.gz" install package and the
"...expand.sh" script to the desired install location on your hard drive.
2a. You can install the "....tar.gz" package by double-clicking in the File
Manager Window on the "...expand.sh" script and passing through the
arguments panel that comes by entering no arguments. This starts a RUN
window. When the install is complete, you can close the RUN window.
2b. You can also install the "....tar.gz" package by opening a terminal
window and typing the name of the "...expand.sh" script.
NOTE1: In both the above cases this results in an install directory being
created at the location of the "...expand.sh" script. The name of this
directory will depend on the version of the Curation Tool (eg.
"curtool_033dev"). Note the developer package has no OS dependency.
NOTE2: In both the above cases the "...expand.sh" script destroys the
"....tar.gz" install package, so if you want to keep the "....tar.gz"
package, you should make a copy before running the "...expand.sh" script.
3a. Now you can build a developer version of the Curation Tool by
double-clicking in the File Manager Window on the "devinstall.sh" script
found in the "package/solaris/scripts" subdirectory under the installed
directory. This starts a RUN window. When the build is complete, you can
close the RUN window.
3b. You can also build a developer version of the Curation Tool application
by opening a terminal window at the "package/solaris/scripts" subdirectory
under the installed directory and typing the name of the "devinstall.sh"
script found there.
4a. You can run the Curation Tool application by double-clicking in the File
Manager Window on the "go.sh" script found in the "bin" subdirectory under
the installed directory. This starts a RUN window. When you exit the
application, you can close the RUN window.
4b. You can also run the Curation Tool application by opening a terminal
window at the "bin" subdirectory under the installed directory and typing
the name of the "go.sh" script found there.
5. Source Changes: You can change the source code by editing any of the
".java" files found in the "java" subdirectory under the installed
directory.
6a. Compiling All Source: Run the "compile.sh" script found in the "bin"
subdirectory under the installed directory to compile all the code.
6b. Compiling One Source File in Curator: To compile a single source file in
the "java/org/ncgr/genex/curator" directory, run the "compilec.sh" script
found in the "bin" subdirectory under the installed directory with the
".java" file name as an argument (eg. compilec.sh Curator.java).
6c. Compiling One Source File in Model: To compile a single source file in
the "java/org/ncgr/genex/model" directory, run the "compilem.sh" script
found in the "bin" subdirectory under the installed directory with the
".java" file name as an argument (eg. compilem.sh DataManager.java).
NOTE: Use either the double-clicking or terminal window approach, as
described above, to compile.
gdc, lxm 8-23-00, 1:13pm MDT
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RELEASE NOTES for Curation Tool v0.90 (02-09-01)
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The following changes have been added since release v0.81:
NOTE: We report all release changes as items RESOLVED from our bug tracking
system, Bugzilla. You will find below a summary list of the bugs RESOLVED
followed by a long format listing for each bug. See
http://sourceforge.net/bugs/?group_id=16453 for additional bug listings.
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SHORT LISTING:
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Here are the bugs that the status changed to "RESOLVED" between 01-17-2001
and 02-10-2001.
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Bug ID Assigned To Short Description Status Changed
1317 tfp@ncgr.org Column File Editor throws exceptions 2001-01-17
06:34:51
1340 tfp@ncgr.org CSFs are obsolete 2001-01-26
15:45:17
1293 tfp@ncgr.org The Use as Template option still does 2001-01-26
not work in the Table Editer, and is 16:00:30
1267 jes@ncgr.org [Genex Anal]: genex.ncgr.org must be 2001-01-29
updated from auto-install 11:29:44
1167 jes@ncgr.org [Query] species need to be listed by 2001-01-29
scientific name 11:30:33
1149 jes@ncgr.org pretty_print() does not preserved 2001-01-31
whitespace in elements 13:01:57
1344 lxm@ncgr.org The array layout spots are not being 2001-02-02
read into an array layout 18:27:58
1345 lxm@ncgr.org cancel doesn't work for missing al 2001-02-02
spot in dialog message 18:30:06
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LONG LISTING:
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Column File Editor throws exceptions
Bug#: 1317 Product: Version: v0.8 Platform:
GeneX-Curation All
OS/Version: All Status: RESOLVED Severity: normal Priority:
P1
Resolution: FIXED Assigned To: Reported By:
tfp@ncgr.org tfp@ncgr.org
Component:
GeneX-Curation
URL:
Summary: Column File Editor throws exceptions
Description:
When the start row is set and then the delimiter, several exceptions are thrown.
------- Additional Comments From tfp@ncgr.org 01/17/01 06:34 -------
Was trying to add column number to combo box before the entire row in the
JTable was populated. The change of the combo box fired events which expected
the row to be populated.
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CSFs are obsolete
Bug#: 1340 Product: Version: v0.8 Platform:
GeneX-Curation All
OS/Version: All Status: RESOLVED Severity: normal Priority:
P1
Resolution: FIXED Assigned To: Reported By:
tfp@ncgr.org tfp@ncgr.org
Component:
GeneX-Curation
URL:
Summary: CSFs are obsolete
Description:
The curation tool should not generate CSFs in XML. If they exist in a previous
control bundle, they should be ignored.
------- Additional Comments From tfp@ncgr.org 01/26/01 15:45 -------
CSF references and functionality removed.
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The Use as Template option still does not work in the Table Editer,
and is
Bug#: 1293 Product: Version: v0.6 Platform:
GeneX-Curation All
OS/Version: All Status: RESOLVED Severity: normal Priority:
P2
Resolution: FIXED Assigned To: Reported By:
tfp@ncgr.org lxm@ncgr.org
Component:
GeneX-Curation
URL:
Summary: The Use as Template option still does not work in the Table
Editer, and is
Description:
The Use as Template option still does not work in the Table Editer, and is
critical to make these screen really usable.
------- Additional Comments From tfp@ncgr.org 01/26/01 16:00 -------
Use As Template buttons now work.
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[Genex Anal]: genex.ncgr.org must be updated from auto-install
Bug#: 1267 Product: Version: v0.5 Platform:
GeneX-Analysis All
OS/Version: All Status: RESOLVED Severity: critical Priority:
P1
Resolution: FIXED Assigned To: Reported By:
jes@ncgr.org jes@ncgr.org
Component:
GeneX-Analysis
URL:
Summary: [Genex Anal]: genex.ncgr.org must be updated from auto-install
Description:
The entire cgi-bin directory on genex is patched to the point of breaking. Once
the installation script is tested on genesoup and verified, genex must be updated.
The major symptom of this problem is that whenever a bug is found in the cgi
scripts, fixing the problem on genex requires hand editing in a terminal window
using vi. This creates more problems than it solves.
------- Additional Comments From jes@ncgr.org 01/29/01 11:29 -------
genex.ncgr.org now runs under auto install
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[Query] species need to be listed by scientific name
Bug#: 1167 Product: GeneX-Query Version: v0.3 Platform: All
OS/Version: All Status: RESOLVED Severity: normal Priority: P2
Resolution: FIXED Assigned To: Reported By:
jes@ncgr.org jes@ncgr.org
Component:
GeneX-Query
URL: http://genex.ncgr.org/cgi-bin/genex/gxquery/gxquery1.pl
Summary: [Query] species need to be listed by scientific name
Description:
The main query page currently lists species by common name. This doesn't work
since some species have no common name in the DB
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pretty_print() does not preserved whitespace in elements
Bug#: 1149 Product: GeneX-GEML Version: v0.4 Platform: All
OS/Version: All Status: RESOLVED Severity: normal Priority: P2
Resolution: FIXED Assigned To: Reported By:
jes@ncgr.org jes@ncgr.org
Component:
GeneX-GEML
URL:
Summary: pretty_print() does not preserved whitespace in elements
Description:
Genex::XMLUtils::pretty_print() is called by db2xml.pl in order to make the XML
output be human readable. The problem is that it's first step is to remove *all*
newlines from the XML. This of course destroys any preformatted text, like
protocols.
Fix it.
------- Additional Comments From jes@ncgr.org 01/31/01 13:01 -------
Fix in CVS. Now whitespace is preserved and elements are indented for easier
reading
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The array layout spots are not being read into an array layout
Bug#: 1344 Product: Version: v0.8 Platform:
GeneX-Curation All
OS/Version: All Status: RESOLVED Severity: critical Priority:
P1
Resolution: FIXED Assigned To: Reported By:
lxm@ncgr.org lxm@ncgr.org
Component:
GeneX-Curation
URL:
Summary: The array layout spots are not being read into an array layout
Description:
The array layout spots are not being read into an array layout for a new
experiment set. Consequently, none of the am spots can be associated with al
spots.
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cancel doesn't work for missing al spot in dialog message
Bug#: 1345 Product: Version: v0.8 Platform:
GeneX-Curation All
OS/Version: All Status: RESOLVED Severity: critical Priority:
P1
Resolution: FIXED Assigned To: Reported By:
lxm@ncgr.org lxm@ncgr.org
Component:
GeneX-Curation
URL:
Summary: cancel doesn't work for missing al spot in dialog message
Description:
When an array layout spot is not found for an array measurement spot, a dialog
appears asking if you want to cancel or continue. If you select cancel, it
contiunues anyway.
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Download Latest Version
genex-server-2003-06-06.tar.gz (2.6 MB)
