INSTALL.txt needs some updating
osbo...@optonline.net
Version 06 beta. In docs/INSTALL.txt we see:
5. Copy dist/cpath.war to [JAKARTA_TOMCAT_DIR]/webapps and restart
Apache Tomcat.
However there's no dist/ directory nor a cpath.war file in the package.
What's the right file or files?
Thanks again,
Brian O.
Ethan Cerami
You are right. The INSTALL.txt file is out of date. For more current
installation instructions, please refer to the Administrator Guide (PDF):
http://cbio.mskcc.org/dev_site/cpath/
http://cbio.mskcc.org/dev_site/cpath/cpath_admin_guide.pdf
Ethan
osbo...@optonline.net wrote:
--
Ethan Cerami
Computational Biology Center
Memorial Sloan-Kettering Cancer Center
http://cbio.mskcc.org
Email: cer...@cbio.mskcc.org
Direct phone: (646) 735-8082
Brian Osborne
Yes, much better. OK, everything's fine up to step 7 (Load a Sample BIOPAX
File), as described in cpath_admin_guide.pdf. At this point I'm trying to
load some PSI MI XML and I see:
219 /usr/local/cpath/bin>./admin.pl -f ../testData/psi_mi/dip_psi.xml import
Using CPATH_HOME /usr/local/cpath
Exception in thread "main" java.lang.NoClassDefFoundError:
org/mskcc/pathdb/tool/Admin
Previous steps appear to have worked, a cpath database has been created and
I can log in to it using tomcat/kitty. This is all on Mac OS 10.6.4, I'm
showing my build.properties file below.
Any thoughts? Yes, I copied those *jar files to ANT_HOME/lib. I should add
that I see the same error when I try to load a Biopax file.
Thanks again,
BIO
# Application Name and Version
app.name=cpath
app.version=0.6
# Database Settings
db.name=cpath
db.user=tomcat
db.password=kitty
db.host=localhost
# Set Location or persistent cache
# If the path is a Java System Property it is replaced by
# its value in the running VM.
# The following properties are translated:
# user.home - User's home directory
# user.dir - User's current working directory
# java.io.tmpdir - Default temp file path
cache.path=user.dir
# Web Administrator Setting
web.admin.user=admin
web.admin.password=cpath
# Set to 0 to disable all web admin functionality
web.admin.active=1
# Web UI Settings
# set to "psi_mi" or "biopax" -->
web.mode=psi_mi
# Tomcat installation directory
catalina.home=/Library/Tomcat/
# Manager webapp username and password
manager.username=tomcat
manager.password=tomcat
# Maven Configuration
maven.username=cerami
Ethan Cerami
OK, there is a missing step in the documentation (another user recently brought this to my attention, but I neglected to update the docs until today).
Missing step:
7. Compile the Code: To do so:
> cd [CPATH_HOME]
> ant
then, load sample data.
The updated admin guide (PDF) (w/ missing step now included) is here: http://cbio.mskcc.org/dev_site/cpath/cpath_admin_guide.pdf
Ethan
Brian Osborne
OK, seems I’m using Java 1.5. I see:
255 /usr/local/cpath>ant
Buildfile: build.xml
prepare:
[copy] Copying 1 file to /usr/local/cpath_beta_06/build/WEB-INF
[replace] Replaced 1 occurrences in 1 files.
[replace] Replaced 1 occurrences in 1 files.
[replace] Replaced 1 occurrences in 1 files.
[replace] Replaced 1 occurrences in 1 files.
[replace] Replaced 1 occurrences in 1 files.
[replace] Replaced 1 occurrences in 1 files.
[replace] Replaced 1 occurrences in 1 files.
[replace] Replaced 1 occurrences in 1 files.
[copy] Copying 1 file to /usr/local/cpath_beta_06/build/WEB-INF/classes
[replace] Replaced 1 occurrences in 1 files.
compile:
[javac] Compiling 276 source files to /usr/local/cpath_beta_06/build/WEB-INF/classes
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:144: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] Enumeration enum = request.getHeaderNames();
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:145: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] while (enum.hasMoreElements()) {
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:146: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] String headerName = (String) enum.nextElement();
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:202: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] Enumeration enum = session.getAttributeNames();
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:203: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] while (enum.hasMoreElements()) {
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:204: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] String name = (String) enum.nextElement();
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:216: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] Enumeration enum = servletContext.getAttributeNames();
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:217: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] while (enum.hasMoreElements()) {
[javac] ^
[javac] /usr/local/cpath_beta_06/src/org/mskcc/pathdb/xdebug/SnoopHttp.java:218: as of release 1.5, 'enum' is a keyword, and may not be used as an identifier
[javac] (try -source 1.4 or lower to use 'enum' as an identifier)
[javac] String name = (String) enum.nextElement();
[javac] ^
[javac] 9 errors
BUILD FAILED
/usr/local/cpath_beta_06/build.xml:98: Compile failed; see the compiler error output for details.
Total time: 5 seconds
Can I modify build.xml to pass “-source 1.4” to javac?
Thanks again,
BIO
On 6/29/06 11:40 AM, "Ethan Cerami" <cer...@cbio.mskcc.org> <mailto:cer...@cbio.mskcc.org> wrote:
Ethan Cerami
Ethan
Brian Osborne
All the errors come from SnoopHttp.java, just rename ‘enum’ there and the ant build works (I changed it to ‘menum’).
BIO
On 6/30/06 11:32 AM, "Ethan Cerami" <cer...@cbio.mskcc.org> wrote:
yes, I think “-source 1.4” will work. let me know, and I'll modify the build.xml file in CVS.
Ethan
Brian Osborne wrote:
Re: INSTALL.txt needs some updating Ethan,
On 6/30/06 10:29 AM, "Ethan Cerami" <cer...@cbio.mskcc.org> <mailto:cer...@cbio.mskcc.org> wrote:
On 6/29/06 11:40 AM, "Ethan Cerami" <cer...@cbio.mskcc.org> <mailto:cer...@cbio.mskcc.org> <mailto:cer...@cbio.mskcc.org> wrote:
Brian Osborne
...and after the successful build the import of the PSI MI file works.
BIO
On 6/30/06 11:32 AM, "Ethan Cerami" <cer...@cbio.mskcc.org> wrote:
yes, I think “-source 1.4” will work. let me know, and I'll modify the build.xml file in CVS.
Ethan
Brian Osborne wrote:
Re: INSTALL.txt needs some updating Ethan,
On 6/30/06 10:29 AM, "Ethan Cerami" <cer...@cbio.mskcc.org> <mailto:cer...@cbio.mskcc.org> wrote:
On 6/29/06 11:40 AM, "Ethan Cerami" <cer...@cbio.mskcc.org> <mailto:cer...@cbio.mskcc.org> <mailto:cer...@cbio.mskcc.org> wrote: