We haven't written detailed documentation of the new build process yet. The goals were to restore module build consistency, ease the creation of new modules (by default, we automatically build new module directories when they appear) and improve efficiency by supporting developer-defined module manifests (instead of ever-growing hard-coded module lists).

The standard.modules file should appear in your /server directory (same place as the main build.xml). If this file doesn't exist then you'll need to fix your enlistment.

You have a few options:

- Modify your local standard.modules file to include just the path to your module. A standard "ant build" will then build only your module, none of the others.
- Create an alternate .modules file (say, "cyto.modules") and invoke "ant build -DmodulesFile=cyto.modules" to build your module
- Create a build.xml file in your module directory that defines a "build_module" target. This target should invoke sub_build_module in the main build.xml (if you want your module to ever be built by the standard build), but you can define whatever other targets you want ("build", etc.). This will restore the previous behavior. The core, query, flow, wiki, et. al modules have build.xml files that you can use as a model.

Adam

Thanks, Adam!

I do not have as can be seen from my listing of the server folder a file called standard.modules. What do you mean by "fix your enlistment"? Where can I get it from?

Well, like I said, the 2nd way does not work for me, it does not seem to build my modules (unless having a standard.modules file is a requirement for that).

I also do not have build.xml in either flow, core, or query module folders! (WTH?)

Keep in mind that I am not on the trunk, as can be seen above...

What to do, what to do?

Sorry, I assumed you were talking about trunk. We haven't made any major build changes on the 13.2 release branch, so you won't see any of these new files there.

You should probably just put your build.xml file back in your module directory and debug why invoking it causes an error. When you move to 13.3, you may need to adjust your build.xml slightly, but you'll be able to continue with this approach if you're comfortable with it.

Adam

I'm now trying to build the latest trunk version: revision 28012

I'm getting an error:

...

clientapi:

api:
     [echo] Build API sources
    [javac] Compiling 1685 source files to /home/ldashevs/Labkey/release/build/modules/api/classes
    [javac] /home/ldashevs/Labkey/release/server/api/src/org/labkey/api/data/LabKeyScope.java:61: error: method does not override or implement a method from a supertype
    [javac] @Override
    [javac] ^
    [javac] /home/ldashevs/Labkey/release/server/api/src/org/labkey/api/data/LabKeyScope.java:74: error: method does not override or implement a method from a supertype
    [javac] @Override
    [javac] ^
    [javac] /home/ldashevs/Labkey/release/server/api/src/org/labkey/api/data/LabKeyScope.java:90: error: method does not override or implement a method from a supertype
    [javac] @Override
    [javac] ^
    [javac] /home/ldashevs/Labkey/release/server/api/src/org/labkey/api/data/LabKeyScope.java:112: error: method loadSchema in class DbScope cannot be applied to given types;
    [javac] DbSchema schema = super.loadSchema(schemaName);
    [javac] ^
    [javac] required: String,DbSchemaType
    [javac] found: String
    [javac] reason: actual and formal argument lists differ in length
    [javac] /home/ldashevs/Labkey/release/server/api/src/org/labkey/api/data/LabKeyScope.java:105: error: method does not override or implement a method from a supertype
    [javac] @Override
    [javac] ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 5 errors

BUILD FAILED
/home/ldashevs/Labkey/release/server/build.xml:1843: The following error occurred while executing this line:
/home/ldashevs/Labkey/release/server/build.xml:664: The following error occurred while executing this line:
/home/ldashevs/Labkey/release/server/build.xml:1499: The following error occurred while executing this line:
/home/ldashevs/Labkey/release/server/build.xml:756: Compile failed; see the compiler error output for details.

What is going on there?
Thanks.

There's something wrong with your enlistment; that file was removed 10 days ago. Did you switch or update only part of the tree?

You'll probably have better results if you checkout the release branch and the trunk to separate folders on your machine.

Hm, well, the folder is just called 'release' it is in fact the trunk. But I did switch back from that other branch above... Let me try and clean things up...

Ok, I compiled a fresh copy of the trunk fine.

1) I am having difficulties starting a debug run from IntelliJ, I get the following error:

/usr/lib/jvm/java-7-oracle/bin/java -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:37362,suspend=y,server=n -ea -Xmx1G -XX:MaxPermSize=512M -Dsun.io.useCanonCaches=false -Djava.endorsed.dirs=/usr/local/tomcat/common/endorsed -classpath /usr/lib/jvm/java-7-oracle/lib/tools.jar;/usr/local/tomcat/bin/bootstrap.jar;/home/ldashevs/Labkey/idea-IU-117.117/lib/idea_rt.jar;./bin/tomcat-juli.jar -Dcatalina.base=/usr/local/tomcat/ -Dcatalina.home=/usr/local/tomcat/ -Djava.io.tmpdir=/usr/local/tomcat/temp -Ddevmode=true -javaagent:/home/ldashevs/Labkey/idea-IU-117.117/plugins/Groovy/lib/agent/gragent.jar -Dfile.encoding=UTF-8 org.apache.catalina.startup.Bootstrap start
Connected to the target VM, address: '127.0.0.1:37362', transport: 'socket'
Error: Could not find or load main class org.apache.catalina.startup.Bootstrap
Disconnected from the target VM, address: '127.0.0.1:37362', transport: 'socket'

Process finished with exit code 1

(I can start the server fine by just starting tomcat, though)


2) I have 3 modules, 2 of them depend on the 3rd one. This third one installed fine, but the other two, even though the build says, that they are built and I can see before firing up the server that <labkey root>/build/deploy/modules contains the *.module files, then when I fire up the server, those *.module files get unzipped into folders, but their folder structure seems incomplete and does not contain actual files, for example, the module folder contains the following: "config lib META-INF schemas web" and 'web' and 'schemas' are empty, 'lib' has <module name>.jar file and 'config' has module.xml file, 'META-INF' contains 'MANIFEST.MF' file -- no queries, reports or views. What's going on and how to fix that?

Thanks.

Ok, so regarding issue number 2:

In the <labkey home>/build/staging/modules folder I have my <module name>.module file.
In it I have besides other 'junk' a folder called 'lib' and in it I have a file called <module name>.jar and inside that archive I have all of my proper module contents!
So, somehow the contents instead of being zipped up into <module name>.module end up int <module name>.module/lib/<module name>.jar

Please, advise, if I have something misconfigured or if this is a bug of some sort?


Still, cannot resolve issue number 1.

Thanks.

Hi Leo,

It sounds like there may be a mismatch between your module source code layout and what the build is expecting. Can you either zip or tar.gz your source module directory and post it here, or just post a recursive file listing?

Thanks,
Josh

~/Labkey/trunk/server/customModules ll OpenCyto* -R

THIS IS THE MODULE THAT BUILDS FINE AND HAS THE "opencyto.modules" file in it with just one line: "server/customModules/OpenCyto*"

OpenCytoPreprocessing:
total 20
-rw-rw-r-- 1 ldashevs ldashevs 143 2013-08-23 17:34 module.properties
-rw-rw-r-- 1 ldashevs ldashevs 1200 2013-08-23 17:34 module.template.xml
-rw-rw-r-- 1 ldashevs ldashevs 32 2013-08-23 17:34 opencyto.modules
-rw-rw-r-- 1 ldashevs ldashevs 141 2013-08-23 17:34 README.md
drwxrwxr-x 8 ldashevs ldashevs 4096 2013-08-23 17:34 resources

OpenCytoPreprocessing/resources:
total 24
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 config
drwxrwxr-x 5 ldashevs ldashevs 4096 2013-08-23 17:34 queries
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 reports
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 schemas
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 views
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-26 10:53 web

OpenCytoPreprocessing/resources/config:
total 4
-rw-rw-r-- 1 ldashevs ldashevs 1340 2013-08-23 17:34 module.xml

OpenCytoPreprocessing/resources/queries:
total 12
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 exp
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 flow
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 opencyto_preprocessing

OpenCytoPreprocessing/resources/queries/exp:
total 8
-rw-rw-r-- 1 ldashevs ldashevs 251 2013-08-23 17:34 Workspaces.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 162 2013-08-23 17:34 Workspaces.sql

OpenCytoPreprocessing/resources/queries/flow:
total 32
-rw-rw-r-- 1 ldashevs ldashevs 242 2013-08-23 17:34 FilePaths.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 113 2013-08-23 17:34 FilePaths.sql
-rw-rw-r-- 1 ldashevs ldashevs 230 2013-08-23 17:34 Files.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 107 2013-08-23 17:34 Files.sql
-rw-rw-r-- 1 ldashevs ldashevs 237 2013-08-23 17:34 Keyword.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 60 2013-08-23 17:34 Keyword.sql
-rw-rw-r-- 1 ldashevs ldashevs 234 2013-08-23 17:34 RootPath.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 131 2013-08-23 17:34 RootPath.sql

OpenCytoPreprocessing/resources/queries/opencyto_preprocessing:
total 16
-rw-rw-r-- 1 ldashevs ldashevs 142 2013-08-23 17:34 GatingSet.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 204 2013-08-23 17:34 GatingSet.sql
-rw-rw-r-- 1 ldashevs ldashevs 143 2013-08-23 17:34 Population.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 171 2013-08-23 17:34 Population.sql

OpenCytoPreprocessing/resources/reports:
total 4
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-27 16:03 schemas

OpenCytoPreprocessing/resources/reports/schemas:
total 28
-rw-rw-r-- 1 ldashevs ldashevs 2795 2013-08-23 17:34 Delete.R
-rw-rw-r-- 1 ldashevs ldashevs 17012 2013-08-27 16:03 OpenCytoPreprocessing.R
-rw-rw-r-- 1 ldashevs ldashevs 2243 2013-08-23 17:34 SampleGroups.R

OpenCytoPreprocessing/resources/schemas:
total 8
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 dbscripts
-rw-rw-r-- 1 ldashevs ldashevs 4074 2013-08-23 17:34 opencyto_preprocessing.xml

OpenCytoPreprocessing/resources/schemas/dbscripts:
total 4
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 postgresql

OpenCytoPreprocessing/resources/schemas/dbscripts/postgresql:
total 4
-rw-rw-r-- 1 ldashevs ldashevs 1862 2013-08-23 17:34 opencyto_preprocessing-0.00-0.01.sql

OpenCytoPreprocessing/resources/views:
total 12
-rw-rw-r-- 1 ldashevs ldashevs 2863 2013-08-23 17:34 begin.html
-rw-rw-r-- 1 ldashevs ldashevs 1540 2013-08-23 17:34 begin.view.xml
-rw-rw-r-- 1 ldashevs ldashevs 118 2013-08-23 17:34 begin.webpart.xml

OpenCytoPreprocessing/resources/web:
total 68
drwxrwxr-x 5 ldashevs ldashevs 4096 2013-08-27 12:08 OpenCyto
-rw-rw-r-- 1 ldashevs ldashevs 63220 2013-08-26 10:53 OpenCytoPreprocessing.js

OpenCytoPreprocessing/resources/web/OpenCyto:
total 80
-rw-rw-r-- 1 ldashevs ldashevs 2198 2013-08-23 17:34 CheckBoxMemory.js
-rw-rw-r-- 1 ldashevs ldashevs 4859 2013-08-23 17:34 ExtendedComboBox.js
-rw-rw-r-- 1 ldashevs ldashevs 10731 2013-08-23 17:34 ExtendedLovCombo.js
-rw-rw-r-- 1 ldashevs ldashevs 4775 2013-08-23 17:34 Ext.ux.tree.TreeFilterX.js
drwxrwxr-x 4 ldashevs ldashevs 4096 2013-08-23 17:34 FancyBox
drwxrwxr-x 6 ldashevs ldashevs 4096 2013-08-23 17:34 gridfilters
-rw-rw-r-- 1 ldashevs ldashevs 2563 2013-08-23 17:34 GridPanelHeaderResize.js
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 images
-rw-rw-r-- 1 ldashevs ldashevs 6111 2013-08-23 17:34 MsgBus.js
-rw-rw-r-- 1 ldashevs ldashevs 7091 2013-08-27 12:08 OpenCyto.css
-rw-rw-r-- 1 ldashevs ldashevs 15190 2013-08-23 17:34 OpenCyto.js

OpenCytoPreprocessing/resources/web/OpenCyto/FancyBox:
total 8
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 lib
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 source

OpenCytoPreprocessing/resources/web/OpenCyto/FancyBox/lib:
total 4
-rw-rw-r-- 1 ldashevs ldashevs 1383 2013-08-23 17:34 jquery.mousewheel-3.0.6.pack.js

OpenCytoPreprocessing/resources/web/OpenCyto/FancyBox/source:
total 80
-rw-rw-r-- 1 ldashevs ldashevs 43 2013-08-23 17:34 blank.gif
-rw-rw-r-- 1 ldashevs ldashevs 13984 2013-08-23 17:34 fancybox_loading@2x.gif
-rw-rw-r-- 1 ldashevs ldashevs 6567 2013-08-23 17:34 fancybox_loading.gif
-rw-rw-r-- 1 ldashevs ldashevs 1003 2013-08-23 17:34 fancybox_overlay.png
-rw-rw-r-- 1 ldashevs ldashevs 6553 2013-08-23 17:34 fancybox_sprite@2x.png
-rw-rw-r-- 1 ldashevs ldashevs 1362 2013-08-23 17:34 fancybox_sprite.png
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 helpers
-rw-rw-r-- 1 ldashevs ldashevs 4895 2013-08-23 17:34 jquery.fancybox.css
-rwxrwxr-x 1 ldashevs ldashevs 23135 2013-08-23 17:34 jquery.fancybox.pack.js

OpenCytoPreprocessing/resources/web/OpenCyto/FancyBox/source/helpers:
total 28
-rw-rw-r-- 1 ldashevs ldashevs 1080 2013-08-23 17:34 fancybox_buttons.png
-rw-rw-r-- 1 ldashevs ldashevs 2447 2013-08-23 17:34 jquery.fancybox-buttons.css
-rw-rw-r-- 1 ldashevs ldashevs 3041 2013-08-23 17:34 jquery.fancybox-buttons.js
-rw-rw-r-- 1 ldashevs ldashevs 5305 2013-08-23 17:34 jquery.fancybox-media.js
-rw-rw-r-- 1 ldashevs ldashevs 735 2013-08-23 17:34 jquery.fancybox-thumbs.css
-rw-rw-r-- 1 ldashevs ldashevs 3836 2013-08-23 17:34 jquery.fancybox-thumbs.js

OpenCytoPreprocessing/resources/web/OpenCyto/gridfilters:
total 40
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 css
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 filter
-rw-rw-r-- 1 ldashevs ldashevs 23908 2013-08-23 17:34 GridFilters.js
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 images
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 menu

OpenCytoPreprocessing/resources/web/OpenCyto/gridfilters/css:
total 8
-rw-rw-r-- 1 ldashevs ldashevs 1134 2013-08-23 17:34 GridFilters.css
-rw-rw-r-- 1 ldashevs ldashevs 401 2013-08-23 17:34 RangeMenu.css

OpenCytoPreprocessing/resources/web/OpenCyto/gridfilters/filter:
total 44
-rw-rw-r-- 1 ldashevs ldashevs 2988 2013-08-23 17:34 BooleanFilter.js
-rw-rw-r-- 1 ldashevs ldashevs 8947 2013-08-23 17:34 DateFilter.js
-rw-rw-r-- 1 ldashevs ldashevs 6024 2013-08-23 17:34 Filter.js
-rw-rw-r-- 1 ldashevs ldashevs 5372 2013-08-23 17:34 ListFilter.js
-rw-rw-r-- 1 ldashevs ldashevs 5524 2013-08-23 17:34 NumericFilter.js
-rw-rw-r-- 1 ldashevs ldashevs 3755 2013-08-23 17:34 StringFilter.js

OpenCytoPreprocessing/resources/web/OpenCyto/gridfilters/images:
total 48
-rw-rw-r-- 1 ldashevs ldashevs 217 2013-08-23 17:34 equals.png
-rw-rw-r-- 1 ldashevs ldashevs 659 2013-08-23 17:34 find.png
-rw-rw-r-- 1 ldashevs ldashevs 359 2013-08-23 17:34 greater_than.png
-rw-rw-r-- 1 ldashevs ldashevs 354 2013-08-23 17:34 less_than.png
-rw-rw-r-- 1 ldashevs ldashevs 13129 2013-08-23 17:34 sort_filtered_asc.gif
-rw-rw-r-- 1 ldashevs ldashevs 13131 2013-08-23 17:34 sort_filtered_desc.gif

OpenCytoPreprocessing/resources/web/OpenCyto/gridfilters/menu:
total 12
-rw-rw-r-- 1 ldashevs ldashevs 5483 2013-08-23 17:34 ListMenu.js
-rw-rw-r-- 1 ldashevs ldashevs 3513 2013-08-23 17:34 RangeMenu.js

OpenCytoPreprocessing/resources/web/OpenCyto/images:
total 20
-rw-rw-r-- 1 ldashevs ldashevs 177 2013-08-23 17:34 arrow-left.gif
-rw-rw-r-- 1 ldashevs ldashevs 180 2013-08-23 17:34 arrow-right.gif
-rw-rw-r-- 1 ldashevs ldashevs 771 2013-08-23 17:34 loading.gif
-rw-rw-r-- 1 ldashevs ldashevs 639 2013-08-23 17:34 reset.png
-rw-rw-r-- 1 ldashevs ldashevs 391 2013-08-23 17:34 scatter_plot.gif


BELOW ARE THE TWO OTHER MODULES THAT DO NOT GET BUILT PROPERLY (SEE ABOVE)

OpenCytoQualityControl:
total 16
-rw-rw-r-- 1 ldashevs ldashevs 161 2013-08-23 17:34 module.properties
-rw-rw-r-- 1 ldashevs ldashevs 1200 2013-08-23 17:34 module.template.xml
-rw-rw-r-- 1 ldashevs ldashevs 98 2013-08-23 17:34 README.md
drwxrwxr-x 8 ldashevs ldashevs 4096 2013-08-23 17:34 resources

OpenCytoQualityControl/resources:
total 24
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-26 12:37 config
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 queries
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 reports
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 schemas
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 views
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 web

OpenCytoQualityControl/resources/config:
total 4
-rw-rw-r-- 1 ldashevs ldashevs 1359 2013-08-26 12:37 module.xml

OpenCytoQualityControl/resources/queries:
total 4
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 opencyto_quality_control

OpenCytoQualityControl/resources/queries/opencyto_quality_control:
total 8
-rw-rw-r-- 1 ldashevs ldashevs 141 2013-08-23 17:34 Summary.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 296 2013-08-23 17:34 Summary.sql

OpenCytoQualityControl/resources/reports:
total 4
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 schemas

OpenCytoQualityControl/resources/reports/schemas:
total 8
-rw-rw-r-- 1 ldashevs ldashevs 3730 2013-08-23 17:34 Preprocess.R
-rw-rw-r-- 1 ldashevs ldashevs 1592 2013-08-23 17:34 QAPlot.R

OpenCytoQualityControl/resources/schemas:
total 8
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 dbscripts
-rw-rw-r-- 1 ldashevs ldashevs 3303 2013-08-23 17:34 opencyto_quality_control.xml

OpenCytoQualityControl/resources/schemas/dbscripts:
total 4
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 postgresql

OpenCytoQualityControl/resources/schemas/dbscripts/postgresql:
total 4
-rw-rw-r-- 1 ldashevs ldashevs 2430 2013-08-23 17:34 opencyto_quality_control-0.00-0.01.sql

OpenCytoQualityControl/resources/views:
total 12
-rw-rw-r-- 1 ldashevs ldashevs 3014 2013-08-23 17:34 begin.html
-rw-rw-r-- 1 ldashevs ldashevs 1478 2013-08-23 17:34 begin.view.xml
-rw-rw-r-- 1 ldashevs ldashevs 120 2013-08-23 17:34 begin.webpart.xml

OpenCytoQualityControl/resources/web:
total 24
-rw-rw-r-- 1 ldashevs ldashevs 23241 2013-08-23 17:34 OpenCytoQualityControl.js

OpenCytoVisualization:
total 20
-rw-rw-r-- 1 ldashevs ldashevs 2148 2013-08-27 15:53 build.xml
-rw-rw-r-- 1 ldashevs ldashevs 160 2013-08-23 17:34 module.properties
-rw-rw-r-- 1 ldashevs ldashevs 1200 2013-08-23 17:34 module.template.xml
-rw-rw-r-- 1 ldashevs ldashevs 190 2013-08-23 17:34 README.md
drwxrwxr-x 7 ldashevs ldashevs 4096 2013-08-23 17:34 src

OpenCytoVisualization/src:
total 20
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-27 15:53 config
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 queries
drwxrwxr-x 3 ldashevs ldashevs 4096 2013-08-23 17:34 reports
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 views
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-28 11:02 web

OpenCytoVisualization/src/config:
total 4
-rw-rw-r-- 1 ldashevs ldashevs 1348 2013-08-27 15:53 module.xml

OpenCytoVisualization/src/queries:
total 4
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-23 17:34 opencyto_preprocessing

OpenCytoVisualization/src/queries/opencyto_preprocessing:
total 32
-rw-rw-r-- 1 ldashevs ldashevs 251 2013-08-23 17:34 AnalysisFiles.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 73 2013-08-23 17:34 AnalysisFiles.sql
-rw-rw-r-- 1 ldashevs ldashevs 137 2013-08-23 17:34 Axes.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 326 2013-08-23 17:34 Axes.sql
-rw-rw-r-- 1 ldashevs ldashevs 148 2013-08-23 17:34 ParentPopulation.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 202 2013-08-23 17:34 ParentPopulation.sql
-rw-rw-r-- 1 ldashevs ldashevs 141 2013-08-23 17:34 StudyVars.query.xml
-rw-rw-r-- 1 ldashevs ldashevs 169 2013-08-23 17:34 StudyVars.sql

OpenCytoVisualization/src/reports:
total 4
drwxrwxr-x 2 ldashevs ldashevs 4096 2013-08-27 10:17 schemas

OpenCytoVisualization/src/reports/schemas:
total 12
-rw-rw-r-- 1 ldashevs ldashevs 1235 2013-08-23 17:34 Load.r
-rw-rw-r-- 1 ldashevs ldashevs 4736 2013-08-27 10:17 Plot.r

OpenCytoVisualization/src/views:
total 24
-rw-rw-r-- 1 ldashevs ldashevs 13974 2013-08-23 17:34 begin.html
-rw-rw-r-- 1 ldashevs ldashevs 1639 2013-08-23 17:34 begin.view.xml
-rw-rw-r-- 1 ldashevs ldashevs 118 2013-08-23 17:34 begin.webpart.xml

OpenCytoVisualization/src/web:
total 56
-rw-rw-r-- 1 ldashevs ldashevs 54617 2013-08-28 11:02 OpenCytoVisualization.js


Thanks!
Let me know if you still need that zipped up file attached!

Any ideas about this? Would an attached zipped up file with the modules help?

Hi Leo,

How are you building these modules? I notice that OpenCytoVisualization has its own build.xml file, while the other don't.

Thanks,
Josh

Josh, well, my hope is to take care of building all of these (and future ones from our suite starting with OpenCyto...) with just that one file opencyto.modules within the OpenCytoPreprocessing module's main folder.

The build.xml within the OpenCytoVisualization module's folder is a temporary solution to deploy that module until this above mechanism is resolved for me...

Thanks.
-Leo

I'm still at a loss here, here is a tar ball with my 3 modules.

So where do I have the "mismatch between module source code layout and what the build is expecting"?

Thanks.
-Leo

Hello, I am still having issues with this.

Is it possible to point me to an example in the trunk's source code, where this is implemented already?

Thanks.
-Leo

I think the problem is that two of the modules have their files under "src" rather than "resources". This may have worked previously, but there was a change recently to be more consistent where we look for files. Note, that in that in a file-based modules where all the files are static resources, the resource directory can be flattened out. I'd probably recommend leaving it for consistency anyway.

see
https://www.labkey.org/wiki/home/Documentation/page.view?name=moduleDirectoryStructures

That seems to have been it - thanks Matt!