I'm (hopefully) getting very close to trying a v3.0.0 beta release

2017-09-01 Thread Marshall Schor 
If anyone has things they think are missing or ?? in v3, please speak up soon,
as I'm close to trying to do the beta release :-) .

-Marshall

[jira] [Resolved] (UIMA-5546) uv3 rework iterator use of typeOrder

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5546?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5546.
--
Resolution: Fixed

> uv3 rework iterator use of typeOrder
> 
>
> Key: UIMA-5546
> URL: https://issues.apache.org/jira/browse/UIMA-5546
> Project: UIMA
>  Issue Type: Improvement
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> Simplify the implementation of the feature of the select API to create 
> iterators which can bypass type order.  Make a universal 
> iterator(orderNotNeeded, ignoreType) API, pushing the implementation of these 
> into the iterator framework (instead of subiterator impl). Change subiterator 
> impl to focus on boundaries and iteration styles (strict, unambiguous, etc).  
> Change select API to use new iterator creation apis.



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[jira] [Resolved] (UIMA-5504) uv3 cleanup iterator classes

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5504?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5504.
--
Resolution: Fixed

> uv3 cleanup iterator classes
> 
>
> Key: UIMA-5504
> URL: https://issues.apache.org/jira/browse/UIMA-5504
> Project: UIMA
>  Issue Type: Improvement
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> general iterator refactoring and cleanup, remove duplicate code by 
> refactoring to common spots, make uniform the copy-on-write support across 
> all iterators / indexes as appropriate.



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[jira] [Resolved] (UIMA-5470) ReDo AllFSs to support excluding the merely reachables

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5470?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5470.
--
Resolution: Fixed

> ReDo AllFSs to support excluding the merely reachables
> --
>
> Key: UIMA-5470
> URL: https://issues.apache.org/jira/browse/UIMA-5470
> Project: UIMA
>  Issue Type: Improvement
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> some operations (Comparing 2 CASs) work better when starting from just the 
> set of indexed FSs. Rework the AllFSs class to support this.  Update the 
> callers as needed.



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[jira] [Resolved] (UIMA-5497) uv3 copy on write generation bugs

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5497?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5497.
--
Resolution: Fixed

> uv3 copy on write generation bugs
> -
>
> Key: UIMA-5497
> URL: https://issues.apache.org/jira/browse/UIMA-5497
> Project: UIMA
>  Issue Type: Bug
>Affects Versions: 3.0.0SDK-alpha02
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> Race condition possible in copy on write generation.  Also missing for bag. 
> unify parts with more sharing via refactoring, guarantee no gc of weak ref 
> before can hold on to it.



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[jira] [Resolved] (UIMA-5479) uv3 performance bug - FsIterator_subtypes_ordered not using custom comparator

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5479?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5479.
--
Resolution: Fixed

> uv3 performance bug - FsIterator_subtypes_ordered not using custom comparator
> -
>
> Key: UIMA-5479
> URL: https://issues.apache.org/jira/browse/UIMA-5479
> Project: UIMA
>  Issue Type: Improvement
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> Most uses of Sorted UIMA indexes for comparing FSs make use of custom 
> comparators for Annotation indexes (versus using the general purpose 
> comparator).  But the implementation of FsIterator_subtypes_ordered fails to 
> use this one.  



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[jira] [Resolved] (UIMA-5454) uv3 refactor feature structure compare for wider use cases + more accurate Cas Compare mode

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5454?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5454.
--
Resolution: Fixed

> uv3 refactor feature structure compare for wider use cases + more accurate 
> Cas Compare mode
> ---
>
> Key: UIMA-5454
> URL: https://issues.apache.org/jira/browse/UIMA-5454
> Project: UIMA
>  Issue Type: Task
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> BinaryCasSerDes6 has general CAS compare methods, currently set up for equal 
> / not-equal with error reporting for not-equal (used in testing).  For other 
> uses, it is helpful to be able to "sort" feature structures; so change some 
> parts of this to return -1 0 1 instead of true/false, and allow use without 
> error reporting.  Use this new capability to have a mode for CAS compare that 
> does a more thorough sorting of the FSs for a more accurate compare.



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[jira] [Commented] (UIMA-5544) XmiCasDeserializer test doing invalid cas building - causes error in uv3

2017-09-01 Thread Marshall Schor (JIRA) 

[ 
https://issues.apache.org/jira/browse/UIMA-5544?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16151002#comment-16151002
 ] 

Marshall Schor commented on UIMA-5544:
--

only fixed the test case

> XmiCasDeserializer test doing invalid cas building - causes error in uv3
> 
>
> Key: UIMA-5544
> URL: https://issues.apache.org/jira/browse/UIMA-5544
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta, 2.10.2SDK
>
>
> The XmiCasDeserializerTest does an invalid operation:  It runs two tests 
> sequentially (in the same method), with a cas reset inbetween them.  But the 
> first test creates two FSs which are held in Java local variables, and reused 
> after the CAS has been reset (they were never recreated after the CAS was 
> reset).
> This causes some strange behavior in Uima V3 (in its current state), which 
> trips a runtime check.  The easy fix is to recreate the two FSs after the cas 
> reset.
> Besides fixing the test case, maybe add a (maybe optional) catcher for these 
> kinds of errors: something like detecting if a FS that was created in CAS nnn 
> (where nnn is different for different CASs and different "resets" of the same 
> CAS) is attempted to be set as a reference in another CASnnn.  Or maybe this 
> is overdesign, since no one's complained...



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[jira] [Resolved] (UIMA-5544) XmiCasDeserializer test doing invalid cas building - causes error in uv3

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5544?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5544.
--
Resolution: Fixed

> XmiCasDeserializer test doing invalid cas building - causes error in uv3
> 
>
> Key: UIMA-5544
> URL: https://issues.apache.org/jira/browse/UIMA-5544
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta, 2.10.2SDK
>
>
> The XmiCasDeserializerTest does an invalid operation:  It runs two tests 
> sequentially (in the same method), with a cas reset inbetween them.  But the 
> first test creates two FSs which are held in Java local variables, and reused 
> after the CAS has been reset (they were never recreated after the CAS was 
> reset).
> This causes some strange behavior in Uima V3 (in its current state), which 
> trips a runtime check.  The easy fix is to recreate the two FSs after the cas 
> reset.
> Besides fixing the test case, maybe add a (maybe optional) catcher for these 
> kinds of errors: something like detecting if a FS that was created in CAS nnn 
> (where nnn is different for different CASs and different "resets" of the same 
> CAS) is attempted to be set as a reference in another CASnnn.  Or maybe this 
> is overdesign, since no one's complained...



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[jira] [Resolved] (UIMA-5409) uv3 migrate tool not skipping built-in classes

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5409?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5409.
--
Resolution: Done

lost track of where this got fixed

> uv3 migrate tool not skipping built-in classes
> --
>
> Key: UIMA-5409
> URL: https://issues.apache.org/jira/browse/UIMA-5409
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework, Tools
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> migrate tool not skipping built-in classes, categorizing them in reports 
> incorrectly as a result.



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[jira] [Resolved] (UIMA-5496) uv3 replace FsIndex_set_sorted, apply many fixes to replaced one

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5496?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5496.
--
Resolution: Fixed

> uv3 replace FsIndex_set_sorted, apply many fixes to replaced one
> 
>
> Key: UIMA-5496
> URL: https://issues.apache.org/jira/browse/UIMA-5496
> Project: UIMA
>  Issue Type: Improvement
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> The first implementation of FsIndex_set_sorted assumed the underlying index 
> was implemented by OrderedFsSet_array2.  This did a complex set of tradeoffs 
> that improved insert/remove performance at the expense of more complex 
> iteration. The OrderedFsSet_array2 impl was complex and was buggy (many bugs 
> were removed, though, in this most recent commit).
> This implementation was based on "NavigableSet" apis, which required creation 
> of multiple iterators as direction of iteration was reversed, and was quite 
> complex.
> This change reverts both of these to a simpler more straight forward 
> implementation, closer to how UIMA v2 did this, but with significant 
> improvements in both iteration and insert/remove.  The underlying 
> OrderedFsSet_array keeps the indexed items for one type in a compacted array, 
> with free space possible at the begin and/or end, and rebalancing done as 
> needed.  The iterator implementation removed several layers of indirection 
> and is now implemented directly on top of the OrderedFsSet_array itself.



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[jira] [Resolved] (UIMA-5471) Better CasCompre code, move to own class

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5471?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5471.
--
Resolution: Fixed

change sets 1806955 1806846 1803747 1800335

> Better CasCompre code, move to own class
> 
>
> Key: UIMA-5471
> URL: https://issues.apache.org/jira/browse/UIMA-5471
> Project: UIMA
>  Issue Type: Improvement
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> BinaryCasSerDes6 has a cas compare routine, used more generally.  Break out 
> into its own class, change callers. Make the compare do a better job of 
> comparing, handling not just unequal type systems, but also better handling 
> of FsRefs and arrays.



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[jira] [Resolved] (UIMA-5408) uv3 migrate missing report of duplicates

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5408?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5408.
--
Resolution: Fixed

changed the logic to handle duplicates as duplicates (all instances are 
migrated).

> uv3 migrate missing report of duplicates
> 
>
> Key: UIMA-5408
> URL: https://issues.apache.org/jira/browse/UIMA-5408
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework, Tools
>Reporter: Marshall Schor
>Assignee: Marshall Schor
>Priority: Minor
> Fix For: 3.0.0SDK-beta
>
>
> logic bug stops reports from printing after first one returns false.  Reverse 
> order of && tests to insure subsequent reports run.



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[jira] [Commented] (UIMA-5536) uv3 remove positionUsesType from select api

2017-09-01 Thread Marshall Schor (JIRA) 

[ 
https://issues.apache.org/jira/browse/UIMA-5536?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16150960#comment-16150960
 ] 

Marshall Schor commented on UIMA-5536:
--

went back to the original v2 implementation, for backwards compatibility.  
Removed this from select apis.  

> uv3 remove positionUsesType from select api
> ---
>
> Key: UIMA-5536
> URL: https://issues.apache.org/jira/browse/UIMA-5536
> Project: UIMA
>  Issue Type: Bug
>Affects Versions: 3.0.0SDK-alpha02
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> The select API attempts to combine some of uimaFIT's capability for 
> iterating.  The design included a configuration choice "positionUsesType".  
> This was implemented incorrectly for some cases, and it seems it would be 
> hard to fix.  This Jira suggests removing it altogether.
> What it does: It affects two bits of iterator operation:
> # moveTo(fs) - move to the leftmost item that "matches" fs
> # for bounded iterators: skip the item which is "equal" to the bound.
> Details: The "matches" in 1) is based on the comparator for the index.  For 
> Annotation indexes, this includes the typePriority.  However, the select API 
> framework by default doesn't use type priorities (can be configured though). 
> This means, if the underlying iterator is using type priorities, then doing a 
> moveTo on it will move to a spot which might not be the "left-most" when type 
> priorities are not used.  The correction for this has two flavors: depending 
> on the setting of positionUsesType.  If not specified, the correction worked, 
> and moved to the left-most same-begin-end-ignoring-type.  If specified, the 
> correction was ignoring this, and a fix would need to scan in both directions 
> to find the right type.  Although this could be done, it's complex.  And I 
> think this is designing beyond a real need.  
> Use 2 is for skipping the bounding annotation when iterating (if it is in the 
> index).  The normal mode for skipping is to skip only the item if it is == 
> identical to the bounding annotation.  But (for UIMA v2 bounded iterator 
> compatibility) a mode where the compare is done using the Annotation 
> Comparator is provided.  The positionUsesType would narrow this equal test by 
> also requiring that the types match.  I think this is unnecessarily complex, 
> since I think most uses will be using the == style.
> So I propose to remove positionUsesType from the implementation / 
> documentation.



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[jira] [Resolved] (UIMA-5536) uv3 remove positionUsesType from select api

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5536?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5536.
--
Resolution: Fixed

> uv3 remove positionUsesType from select api
> ---
>
> Key: UIMA-5536
> URL: https://issues.apache.org/jira/browse/UIMA-5536
> Project: UIMA
>  Issue Type: Bug
>Affects Versions: 3.0.0SDK-alpha02
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> The select API attempts to combine some of uimaFIT's capability for 
> iterating.  The design included a configuration choice "positionUsesType".  
> This was implemented incorrectly for some cases, and it seems it would be 
> hard to fix.  This Jira suggests removing it altogether.
> What it does: It affects two bits of iterator operation:
> # moveTo(fs) - move to the leftmost item that "matches" fs
> # for bounded iterators: skip the item which is "equal" to the bound.
> Details: The "matches" in 1) is based on the comparator for the index.  For 
> Annotation indexes, this includes the typePriority.  However, the select API 
> framework by default doesn't use type priorities (can be configured though). 
> This means, if the underlying iterator is using type priorities, then doing a 
> moveTo on it will move to a spot which might not be the "left-most" when type 
> priorities are not used.  The correction for this has two flavors: depending 
> on the setting of positionUsesType.  If not specified, the correction worked, 
> and moved to the left-most same-begin-end-ignoring-type.  If specified, the 
> correction was ignoring this, and a fix would need to scan in both directions 
> to find the right type.  Although this could be done, it's complex.  And I 
> think this is designing beyond a real need.  
> Use 2 is for skipping the bounding annotation when iterating (if it is in the 
> index).  The normal mode for skipping is to skip only the item if it is == 
> identical to the bounding annotation.  But (for UIMA v2 bounded iterator 
> compatibility) a mode where the compare is done using the Annotation 
> Comparator is provided.  The positionUsesType would narrow this equal test by 
> also requiring that the types match.  I think this is unnecessarily complex, 
> since I think most uses will be using the == style.
> So I propose to remove positionUsesType from the implementation / 
> documentation.



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[jira] [Resolved] (UIMA-5534) uv3 subiterator fixups

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5534?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5534.
--
Resolution: Fixed

> uv3 subiterator fixups
> --
>
> Key: UIMA-5534
> URL: https://issues.apache.org/jira/browse/UIMA-5534
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework
>Affects Versions: 3.0.0SDK-alpha02
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> The subiterator impl has lots of small fixups needed.



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[jira] [Resolved] (UIMA-5523) uv3 wrong test in one iterator impl for index becoming non-empty

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5523?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5523.
--
Resolution: Done

lost the details but should be fixed

> uv3 wrong test in one iterator impl for index becoming non-empty
> 
>
> Key: UIMA-5523
> URL: https://issues.apache.org/jira/browse/UIMA-5523
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> a test to see if an empty iterator is no longer empty is mistakenly testing 
> the copy-on-write version. 



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[jira] [Resolved] (UIMA-5519) uv3 clarify use of ll_indexsize - used incorrectly in one spot

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5519?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5519.
--
Resolution: Fixed

fixed in change set 1803725

> uv3 clarify use of ll_indexsize - used incorrectly in one spot
> --
>
> Key: UIMA-5519
> URL: https://issues.apache.org/jira/browse/UIMA-5519
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> Given an iterator, there are two definitions of index size.  One is the size 
> as seen by the iterator, which in v3, may not be the current index size 
> (because iterators iterate over a view of the index at a particular point in 
> time - either the time of iterator creation, or when a moveTo, moveToFirst, 
> or moveToLast operation happens (except for snapshot iterators)).  The other 
> size is the current size of the index (and any sub-type indexes). 
> Change the name of the api to indicate this to reduce mistakes in the future. 
>  Change uses which are incorrect (which need the current index size).



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[jira] [Resolved] (UIMA-5505) uv3 APIs which take a UIMA Type instance, allow JCas class additionally, instead

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5505?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5505.
--
Resolution: Fixed

fixed in change set 1803745

> uv3 APIs which take a UIMA Type instance, allow JCas class additionally, 
> instead
> 
>
> Key: UIMA-5505
> URL: https://issues.apache.org/jira/browse/UIMA-5505
> Project: UIMA
>  Issue Type: Improvement
>  Components: Core Java Framework
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> Some methods which need a UIMA Type can take a Type instance, or the 
> corresponding JCas class.  Extend this feature to more APIs.



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[jira] [Resolved] (UIMA-5453) uv3 select api index not set, causing NPE

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5453?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5453.
--
Resolution: Fixed

fixed in change set 1763809

> uv3 select api index not set, causing NPE
> -
>
> Key: UIMA-5453
> URL: https://issues.apache.org/jira/browse/UIMA-5453
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework
>Affects Versions: 3.0.0SDK-alpha02
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> doing aCas.select("someTypeName").count() causes an NPE, because the index is 
> null in the splititerator impl used to create the stream.



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[jira] [Resolved] (UIMA-5410) uv3 migration tool sorting of reports sometimes throws exception

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5410?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5410.
--
Resolution: Fixed

was fixed in commit 796919 under jira UIMA-5421

> uv3 migration tool sorting of reports sometimes throws exception
> 
>
> Key: UIMA-5410
> URL: https://issues.apache.org/jira/browse/UIMA-5410
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework, Tools
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> The reports does sorting; and the sort compare occasionally fails trying to 
> compare two File System objects. saying they are not compatible, when one of 
> them is a zip file system.  Add work-around for this case.



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[jira] [Resolved] (UIMA-5407) uv3 migrate: throwing array index out of bounds

2017-09-01 Thread Marshall Schor (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-5407?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Marshall Schor resolved UIMA-5407.
--
Resolution: Done

This must have been fixed along the way... didn't record enough info to 
identify further.

> uv3 migrate: throwing array index out of bounds
> ---
>
> Key: UIMA-5407
> URL: https://issues.apache.org/jira/browse/UIMA-5407
> Project: UIMA
>  Issue Type: Bug
>  Components: Core Java Framework, Tools
>Reporter: Marshall Schor
>Assignee: Marshall Schor
> Fix For: 3.0.0SDK-beta
>
>
> Running the migration tool in linux, Burn found a bug - throwing array index 
> out of bounds.  Traced to using an "Optional" value instead of the actual 
> value.



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[jira] [Commented] (UIMA-4810) DUCC Job Driver (JD) C-Groups size not dynamic?

2017-09-01 Thread Burn Lewis (JIRA) 

[ 
https://issues.apache.org/jira/browse/UIMA-4810?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16150902#comment-16150902
 ] 

Burn Lewis commented on UIMA-4810:
--

Alternatively we could add a new argument to complement process_memory_size, 
e.g.

--driver_memory_size [size]
This specifies the maximum amount of RAM in MB to be allocated to the Job 
Driver. This value is used by the Resource Manager to allocate resources.
The default value is specified by jd.share.quantum in ducc.properties

> DUCC Job Driver (JD) C-Groups size not dynamic?
> ---
>
> Key: UIMA-4810
> URL: https://issues.apache.org/jira/browse/UIMA-4810
> Project: UIMA
>  Issue Type: Bug
>  Components: DUCC
>Reporter: Lou DeGenaro
>Assignee: Lou DeGenaro
> Fix For: future-DUCC
>
>
> Updated JD quantum size in ducc.properties to be 800. The next job driver got 
> a cgroup size of 
> 29 Feb 2016 21:50:53,953  INFO Agent.NodeAgent - J[N/A] T[2213] launchCommand 
>  Launching Process - 
> Commandline:/apps/ducc/ducc_runtime/duccling/bin/ducc_ling -u ducc -- 
> /bin/cgset -r memory.limit_in_bytes=734003200 ducc/5752.5752.0 
> the same value as it was when DUCC started: 700 [MB].



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Jenkins build is back to normal : UIMA-v3-sdk #202

2017-09-01 Thread Apache Jenkins Server 
See

Build failed in Jenkins: UIMA-v3-sdk #201

2017-09-01 Thread Apache Jenkins Server 
See 


Changes:

[schor] no Jira - cleanup XmiCompare for general usage, improve javadocs

--
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[jira] [Updated] (UIMA-4772) DUCC Web Server (WS) refresh button breaks sorting (in manual mode)

2017-09-01 Thread Lou DeGenaro (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-4772?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Lou DeGenaro updated UIMA-4772:
---
Summary: DUCC Web Server (WS) refresh button breaks sorting (in manual 
mode)  (was: re)

> DUCC Web Server (WS) refresh button breaks sorting (in manual mode)
> ---
>
> Key: UIMA-4772
> URL: https://issues.apache.org/jira/browse/UIMA-4772
> Project: UIMA
>  Issue Type: Bug
>  Components: DUCC
>Reporter: Lou DeGenaro
>Assignee: Lou DeGenaro
> Fix For: future-DUCC
>
>
> Two complaints (so far):
> 1. When displaying machines page:
> - click on C-Groups column heading several times (sorting works)
> - click on refresh button (two arrows)
> - click on C-Groups column heading several times (sorting doesn't work)
> 2. When displaying Viz page, clicking refresh button results in stale data?



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[jira] [Updated] (UIMA-4772) re

2017-09-01 Thread Lou DeGenaro (JIRA) 

 [ 
https://issues.apache.org/jira/browse/UIMA-4772?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
 ]

Lou DeGenaro updated UIMA-4772:
---
Summary: re  (was: DUCC Web Server (WS) refersh button breaks sorting (in 
manual mode))

> re
> --
>
> Key: UIMA-4772
> URL: https://issues.apache.org/jira/browse/UIMA-4772
> Project: UIMA
>  Issue Type: Bug
>  Components: DUCC
>Reporter: Lou DeGenaro
>Assignee: Lou DeGenaro
> Fix For: future-DUCC
>
>
> Two complaints (so far):
> 1. When displaying machines page:
> - click on C-Groups column heading several times (sorting works)
> - click on refresh button (two arrows)
> - click on C-Groups column heading several times (sorting doesn't work)
> 2. When displaying Viz page, clicking refresh button results in stale data?



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[jira] [Commented] (UIMA-4810) DUCC Job Driver (JD) C-Groups size not dynamic?

2017-09-01 Thread Lou DeGenaro (JIRA) 

[ 
https://issues.apache.org/jira/browse/UIMA-4810?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16150540#comment-16150540
 ] 

Lou DeGenaro commented on UIMA-4810:


For JD's DUCC should:

1. inspect each job's --driver_jvm_args for -Xmx value.
2. if -Xmx is not specified, then use the value specified for jd.share.quantum 
in ducc.properties.
3. dynamically allocate a JD share of the correct size.
4. dynamically assign cgroup size in correspondence with the allocated JD share.



> DUCC Job Driver (JD) C-Groups size not dynamic?
> ---
>
> Key: UIMA-4810
> URL: https://issues.apache.org/jira/browse/UIMA-4810
> Project: UIMA
>  Issue Type: Bug
>  Components: DUCC
>Reporter: Lou DeGenaro
>Assignee: Lou DeGenaro
> Fix For: future-DUCC
>
>
> Updated JD quantum size in ducc.properties to be 800. The next job driver got 
> a cgroup size of 
> 29 Feb 2016 21:50:53,953  INFO Agent.NodeAgent - J[N/A] T[2213] launchCommand 
>  Launching Process - 
> Commandline:/apps/ducc/ducc_runtime/duccling/bin/ducc_ling -u ducc -- 
> /bin/cgset -r memory.limit_in_bytes=734003200 ducc/5752.5752.0 
> the same value as it was when DUCC started: 700 [MB].



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Build failed in Jenkins: UIMA-v3-sdk #200

2017-09-01 Thread Apache Jenkins Server 
See 


Changes:

[schor] no Jira - slight speedup of cas compare

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Build failed in Jenkins: UIMA-v3-sdk #199

2017-09-01 Thread Apache Jenkins Server 
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Changes:

[schor] no Jira, correct 2 compile errors due to ambiguous method inheritance, 
not caught by Eclipse, but complained about by Jenkins.

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