[kepler-dev] [Bug 4926] Examine Kepler for duplicated Ptolemy code

[bugzilla-daemon at ecoinformatics.org]

http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4926

Christopher Brooks <cxh at eecs.berkeley.edu> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |MOVED

--- Comment #5 from Christopher Brooks <cxh at eecs.berkeley.edu> 2012-08-06 17:00:50 PDT ---
To find files that have the same name in both Ptolemy II and Kepler:
Look for duplicate file names:
# Get all the .java files except the ptolemy ones
find . -name "*.java" | grep -v ptolemy/src > /tmp/kjnop

# Get all the ptolemy.java files                                                
find ptolemy/src -name "*.java" > /tmp/pj

# Get the Kepler .java files
awk -F / '{print $NF}' /tmp/kjnop | sort > /tmp/kjnopl

# Get the Ptolemy .java files
awk -F / '{print $NF}' /tmp/pj | sort > /tmp/pjl

# Print any files in common, create a script to find them in the Kepler java
files
comm -12 /tmp/kjnopl /tmp/pjl | awk '{print "grep /" $1 " /tmp/kjnop"}' >
/tmp/doit

# Run the script
sh /tmp/doit | sort

These are to be ignored:

########
./actors/src/org/geon/DatabaseQuery.java
Ignore? Duplicate of ptolemy/src/ptolemy/actor/lib/database/DatabaseQuery.java

########
./actors/src/org/sdm/spa/actors/piw/viz/Sequence.java
Ignore: Undocumented file, seems to construct a gene sequence?

########
./actors/src/org/sdm/spa/Pause.java
Ignore: Name match with: ptolemy/src/ptolemy/domains/coroutine/lib/Pause.java

#####
./build-area/src/org/kepler/build/Branch.java
./build-area/src/org/kepler/build/modules/Node.java
./build-area/src/org/kepler/build/Tag.java
./build-area/src/org/kepler/build/Test.java
./build-area/src/org/kepler/build/util/ExecuteCommands.java
Ignore these, they are part of the build system.

######
./core/src/org/kepler/moml/DocumentationAttribute.java
Ignore.  This is deprecated:
 @deprecated Use ptolemy.vergil.basic.KeplerDocumentationAttribute instead.

######
./core/src/org/kepler/objectmanager/cache/CacheManager.java
./core/src/org/kepler/objectmanager/data/db/Attribute.java
./core/src/org/kepler/objectmanager/data/db/Constraint.java
./core/src/org/kepler/objectmanager/data/db/Entity.java
./core/src/org/kepler/sms/Constants.java

Ignore the above, the names are common enough

######
./gui/src/org/kepler/gui/AboutAction.java
Ignore. Matches
ptolemy/src/ptolemy/backtrack/eclipse/plugin/actions/AboutAction.java

####
./io/src/org/kepler/io/DirectoryListing.java
./outreach/workflows/demos/getting-started/HelloWorld.java
Ignore.

I've submitted separate bugs for the non-ignored duplicates.

I've checked the Kepler tree for code that says Edward is the author
and it looks good:

bash-4.1$ cat /tmp/kjnop | xargs grep "Edward A. Lee" 
./gui/src/org/kepler/gui/KeplerXMLIcon.java: * @author Chad Berkley, based on
XMLIcon by Steve Neuendorffer, John Reekie, Contributor: Edward A. Lee
./gui/src/org/kepler/gui/frame/MultiCompositeGraphFrame.java: @author Daniel
Crawl, Possibly based on CaseGraphFrame by Edward A. Lee.
./gui/src/org/kepler/gui/frame/CaseGraphFrame.java: @author Daniel Crawl, based
on ptolemy.vergil.modal.CaseGraphFrame by Edward A. Lee
./gui/src/org/kepler/gui/frame/CaseGraphTableau.java: @author Daniel Crawl,
based on ptolemy.vergil.modal.CaseGraphFrame by Edward A. Lee
./gui/src/org/kepler/gui/frame/MultiCompositeTableau.java: @author Daniel
Crawl, Possibly based on CaseGraphTableau by Edward A. Lee.
./gui/src/org/kepler/gui/frame/KeplerGraphTableau.java: @author  Based on
GraphTableau by Steve Neuendorffer and Edward A. Lee
./gui/src/org/kepler/gui/KeplerIconLoader.java: * @author Christopher Brooks,
contributor: Edward A. Lee
./actors/src/org/sdm/spa/gui/UserInteractiveShell.java: * This actor code is
adopted from InteractiveShell.java by Edward A. Lee
./actors/src/org/sdm/spa/Pause.java: * ptolemy.actor.lib.Stop actor code by
Edward A. Lee.
./actors/src/org/sdm/spa/Pause.java: * @author Ilkay Altintas, Contributors:
Edward A. Lee and Christopher Brooks.
./actors/src/org/sdm/spa/CommandLineExec.java: *         Contributor: Edward A.
Lee
grep: ./actors/src/org/resurgence/actor/.#FileCopier.java: No such file or
directory
./util/src/util/LineReader.java: * @author Efrat Jaeger, based on LineReader by
Edward A. Lee, Yuhong Xiong


I'm closing this because we have other bugs and opening a new bug for 2.5.0

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