Talk:Dazzle
From BioJava
GAH!!!!
The 'Problems' section below represents a mornings worth of bug reports, all I really needed to do was change the line that reads "ant" to "ant -lib jars" and set $JAVA_HOME ... Easy when you know how eh? Please feel free to ignore the 'Problems' section below. However, the point about the javac.source property being set but not used in build.xml could be useful to someone --Dan Bolser 16:06, 5 January 2009 (UTC)
- Hi Dan, I updated the build.xml in SVN to use 1.5 and to use the third party libraries from the jars directory. Using eclipse most of the time... --Andreas 16:31, 5 January 2009 (UTC)
- Cheers Andreas! --Dan Bolser 09:09, 6 January 2009 (UTC)
Problems
I found some install problems here.
uname -a Linux cricket 2.6.18-92.1.22.el5PAE #1 SMP Tue Dec 16 12:36:25 EST 2008 i686 i686 i386 GNU/Linux more /etc/redhat-release CentOS release 5.2 (Final) java -version java version "1.6.0_07" Java(TM) SE Runtime Environment (build 1.6.0_07-b06) Java HotSpot(TM) Server VM (build 10.0-b23, mixed mode) which java /usr/local/jdk1.6.0_07/bin/java javac -version javac 1.6.0_07 which javac /usr/local/jdk1.6.0_07/bin/javac
Hitting "ant -lib path-to-biojava-and-/servlet" gives:
compile-main:
[javac] Compiling 8 source files to /homes/www-potato/src/dazzle/ant-build/classes/dazzle
[javac] ----------
[javac] 1. ERROR in /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/DASStatus.java (at line 47)
[javac] private static final Map<Integer,String> errorMessages;
[javac] ^^^
[javac] The type Map is not generic; it cannot be parameterized with arguments <Integer, String>
[javac] ----------
[javac] 2. ERROR in /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/DASStatus.java
[javac] (at line 47)
[javac] private static final Map<Integer,String> errorMessages;
[javac] ^^^^^^^^^^^^^^
[javac] Syntax error, parameterized types are only available if source level is 5.0
[javac] ----------
[javac] 3. ERROR in /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/DASStatus.java (at line 50)
[javac] errorMessages = new HashMap<Integer,String>();
[javac] ^^^^^^^^^^^^^
[javac] errorMessages cannot be resolved
[javac] ----------
[javac] 4. ERROR in /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/DASStatus.java (at line 50)
[javac] errorMessages = new HashMap<Integer,String>();
[javac] ^^^^^^^
[javac] The type HashMap is not generic; it cannot be parameterized with arguments <Integer, String>
[javac] ----------
[javac] 5. ERROR in /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/DASStatus.java
[javac] (at line 50)
...
for a total of ~1000 lines of output.
I edited build.xml:
diff -u build.xml~ build.xml
--- build.xml~ 2009-01-05 14:39:34.492678763 +0000
+++ build.xml 2009-01-05 15:05:10.675982562 +0000
@@ -75,7 +75,7 @@
<property name="javac.depend" value="false" />
<property name="javac.debug" value="true" />
<property name="javac.deprecation" value="false" />
- <property name="javac.source" value="1.4" />
+ <property name="javac.source" value="1.5" />
<!-- Javadoc properties -->
<property name="build.dest.docs" value="${build.dir}/docs" />
@@ -142,6 +142,7 @@
depend="${javac.depend}"
deprecation="${javac.deprecation}"
debug="${javac.debug}"
+ source="${javac.source}"
srcdir="${src.dir}">
<classpath>
<pathelement path="${classpath}" />
which reduced the number of errors, but there are still lots!
Hmm... for some reason I needed to set JAVA_HOME (export JAVA_HOME=/usr/local/jdk1.6.0_07), now I just have errors like the following:
compile-main:
[javac] Compiling 7 source files to /homes/www-potato/src/dazzle/ant-build/classes/dazzle
[javac] /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/InteractionHandler.java:39: package de.mpg.mpiinf.ag3.dasmi.model does not exist
[javac] import de.mpg.mpiinf.ag3.dasmi.model.Interaction;
[javac] ^
[javac] /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/InteractionHandler.java:40: package de.mpg.mpiinf.ag3.dasmi.model does not exist
[javac] import de.mpg.mpiinf.ag3.dasmi.model.Participant;
[javac] ^
[javac] /homes/www-potato/src/dazzle/src/org/biojava/servlets/dazzle/InteractionHandler.java:41: package de.mpg.mpiinf.ag3.dasmi.model does not exist
[javac] import de.mpg.mpiinf.ag3.dasmi.model.Interactor;
...
Any clue? --Dan Bolser 15:16, 5 January 2009 (UTC)
- Yes, set "-lib jars" in your ant command. --Dan Bolser 16:13, 5 January 2009 (UTC)
Slight glytch in the default config...
Hi, I set up Dazzle according to the instructions on this (and related) page(s). Everything seems to be working fine using the default (example) setup, however, there are a few glitches. When I visit "http://webservices:9080/das" (my server location), and click "Do a DAS - DSN request", I see a nice table of sources in a page with some links - i.e. HOME | DAS SOURCES | HELP, however, all those links point to "http://webservices:9080/xxx" when they should point to "http://webservices:9080/das/xxx". I did set the mapMaster to "http://webservices:9080/das/test/" as described in the docs. what should I change to correct this? Cheers --Dan Bolser 09:17, 6 January 2009 (UTC)
- Sounds like a bug in the XSL stylesheet that formats the DAS-XML into the table... --Andreas 11:09, 6 January 2009 (UTC)
- Yeah, I found its das.xsl. I was going to post this earlier but the wiki was down. Here is my diff...
--- das.xsl~ 2009-01-05 17:38:09.501760906 +0000
+++ das.xsl 2009-01-06 09:43:39.489185333 +0000
@@ -128,9 +128,9 @@
<div id="release-t"> </div>
<div id="release"><div>Please see <i>page source</i> for the actual XML document. </div></div>
<div id="help"><strong>
- <a href="/">HOME</a> ·
- <a href="/sources">DAS SOURCES</a> ·
- <a href="javascript:void(window.open('/help_index.jsp','help','width=700,height=550,resizable,scrollbars'))" class="blue-button">HELP</a>
+ <a href="/das">HOME</a> ·
+ <a href="/das/sources">DAS SOURCES</a> ·
+ <a href="javascript:void(window.open('/das/help_index.jsp','help','width=700,height=550,resizable,scrollbars'))" class="blue-button">HELP</a>
</strong></div>
</xsl:template>
HTH, and thanks for help! --Dan Bolser 15:02, 6 January 2009 (UTC)
