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Posted to commits@ctakes.apache.org by ch...@apache.org on 2012/10/10 19:59:45 UTC
svn commit: r1396711 [2/4] - in /incubator/ctakes/trunk:
ctakes-chunker/src/test/ ctakes-chunker/src/test/data/
ctakes-chunker/src/test/data/output/
ctakes-chunker/src/test/data/text-files/ ctakes-chunker/src/test/desc/
ctakes-chunker/src/test/java/ ct...
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/data/unit-test.opennlp.chunks
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/data/unit-test.opennlp.chunks?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/data/unit-test.opennlp.chunks (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/data/unit-test.opennlp.chunks Wed Oct 10 17:59:40 2012
@@ -0,0 +1,1020 @@
+Induction NN B-NP
+of IN B-PP
+NF-KB NN B-NP
+during IN B-PP
+monocyte NN B-NP
+differentiation NN I-NP
+by IN B-PP
+HIV NN B-NP
+type NN I-NP
+1 CD I-NP
+infection NN I-NP
+. . O
+
+The DT B-NP
+production NN I-NP
+of IN B-PP
+human JJ B-NP
+immunodeficiency NN I-NP
+virus NN I-NP
+type NN I-NP
+1 CD I-NP
+( ( O
+HIV-1 NN B-NP
+) ) O
+progeny NN B-NP
+was VBD B-VP
+followed VBN I-VP
+in IN B-PP
+the DT B-NP
+U937 NN I-NP
+promonocytic JJ I-NP
+cell NN I-NP
+line NN I-NP
+after IN B-PP
+stimulation NN B-NP
+either CC B-PP
+with IN I-PP
+retinoic JJ B-NP
+acid NN I-NP
+or CC O
+PMA NN B-NP
+COMMA COMMA O
+and CC O
+in IN B-PP
+purified VBN B-NP
+human JJ I-NP
+monocytes NNS B-NP
+and CC O
+macrophages NNS B-NP
+. . O
+
+Electrophoretic JJ B-NP
+mobility NN I-NP
+shift NN I-NP
+assays NNS I-NP
+and CC O
+Southwestern NN B-NP
+blotting NN I-NP
+experiments NNS I-NP
+were VBD B-VP
+used VBN I-VP
+to TO B-VP
+detect VB I-VP
+the DT B-NP
+binding NN I-NP
+of IN B-PP
+cellular JJ B-NP
+transactivation NN I-NP
+factor NN I-NP
+NF-KB NN I-NP
+to TO B-PP
+the DT B-NP
+double JJ I-NP
+repeat-KB JJ I-NP
+enhancer NN I-NP
+sequence NN I-NP
+located JJ B-ADJP
+in IN B-PP
+the DT B-NP
+long JJ I-NP
+terminal JJ I-NP
+repeat NN I-NP
+. . O
+
+PMA NN B-NP
+treatment NN I-NP
+COMMA COMMA O
+and CC B-CONJP
+not RB I-CONJP
+retinoic JJ B-NP
+acid NN I-NP
+treatment NN I-NP
+of IN B-PP
+the DT B-NP
+U937 NN I-NP
+cells NNS I-NP
+acts VBZ B-VP
+in IN B-PP
+inducing VBG B-VP
+NF-KB NN B-NP
+expression NN I-NP
+in IN B-PP
+the DT B-NP
+nuclei NNS I-NP
+. . O
+
+In IN B-PP
+nuclear JJ B-NP
+extracts NNS I-NP
+from IN B-PP
+monocytes NNS B-NP
+or CC O
+macrophages NNS B-NP
+COMMA COMMA O
+induction NN B-NP
+of IN B-PP
+NF-KB NN B-NP
+occurred VBD B-VP
+only RB B-SBAR
+if IN I-SBAR
+the DT B-NP
+cells NNS I-NP
+were VBD B-VP
+previously RB I-VP
+infected VBN I-VP
+with IN B-PP
+HIV-1 NN B-NP
+. . O
+
+When WRB B-ADVP
+U937 NN B-NP
+cells NNS I-NP
+were VBD B-VP
+infected VBN I-VP
+with IN B-PP
+HIV-1 NN B-NP
+COMMA COMMA O
+no DT B-NP
+induction NN I-NP
+of IN B-PP
+NF-KB NN B-NP
+factor NN I-NP
+was VBD B-VP
+detected VBN I-VP
+COMMA COMMA O
+whereas IN O
+high JJ B-NP
+level NN I-NP
+of IN B-PP
+progeny NN B-NP
+virions NNS I-NP
+was VBD B-VP
+produced VBN I-VP
+COMMA COMMA O
+suggesting VBG B-VP
+that IN B-SBAR
+this DT B-NP
+factor NN I-NP
+was VBD B-VP
+not RB I-VP
+required VBN I-VP
+for IN B-PP
+viral JJ B-NP
+replication NN I-NP
+. . O
+
+These DT B-NP
+results NNS I-NP
+indicate VBP B-VP
+that IN B-SBAR
+in IN B-PP
+monocytic JJ B-NP
+cell NN I-NP
+lineage NN I-NP
+COMMA COMMA O
+HIV-1 NN B-NP
+could MD B-VP
+mimic VB I-VP
+some DT O
+differentiation\/activation JJ B-NP
+stimuli NNS B-NP
+allowing VBG B-VP
+nuclear JJ B-NP
+NF-KB NN I-NP
+expression NN I-NP
+. . O
+
+Positive JJ B-NP
+and CC I-NP
+negative JJ I-NP
+regulation NN I-NP
+of IN B-PP
+immunoglobulin NN B-NP
+gene NN I-NP
+expression NN I-NP
+by IN B-PP
+a DT B-NP
+novel JJ I-NP
+B-cell-specific JJ I-NP
+enhancer NN I-NP
+element NN I-NP
+. . O
+
+A DT B-NP
+new JJ I-NP
+B-cell-specific JJ I-NP
+enhancer NN I-NP
+element NN I-NP
+has VBZ B-VP
+been VBN I-VP
+identified VBN I-VP
+3' JJ B-NP
+of IN B-PP
+E4 NN B-NP
+and CC O
+the DT B-NP
+octamerlike JJ I-NP
+motifs NNS I-NP
+in IN B-PP
+the DT B-NP
+human JJ I-NP
+immunoglobulin NN I-NP
+heavy-chain NN I-NP
+gene NN I-NP
+enhancer NN I-NP
+. . O
+
+Tandem JJ B-NP
+copies NNS I-NP
+of IN B-PP
+this DT B-NP
+67-bp JJ I-NP
+MnlI-AluI NN I-NP
+fragment NN I-NP
+COMMA COMMA O
+when WRB B-ADVP
+fused VBN B-VP
+to TO B-PP
+the DT B-NP
+chloramphenicol JJ I-NP
+acetyltransferase NN I-NP
+gene NN I-NP
+driven VBN B-VP
+by IN B-PP
+the DT B-NP
+conalbumin JJ I-NP
+promoter NN I-NP
+COMMA COMMA O
+stimulated VBD B-VP
+transcription NN B-NP
+in IN B-PP
+B NN B-NP
+cells NNS I-NP
+but CC B-PP
+not RB B-PP
+in IN I-PP
+Jurkat NN B-NP
+T NN I-NP
+cells NNS I-NP
+or CC O
+HeLa NN B-NP
+cells NNS I-NP
+. . O
+
+Footprinting NN B-NP
+analysis NN I-NP
+revealed VBD B-VP
+that IN B-SBAR
+the DT B-NP
+identical JJ I-NP
+sequence NN I-NP
+CCGAAACTGAAAAGG NN I-NP
+COMMA COMMA O
+designated VBN B-VP
+E6 NN B-NP
+COMMA COMMA O
+was VBD B-VP
+protected VBN I-VP
+by IN B-PP
+nuclear JJ B-NP
+extracts NNS I-NP
+from IN B-PP
+B NN B-NP
+cells NNS I-NP
+COMMA COMMA O
+T NN B-NP
+cells NNS I-NP
+COMMA COMMA O
+or CC O
+HeLa NN B-NP
+cells NNS I-NP
+. . O
+
+Gel NN B-NP
+mobility NN I-NP
+shift NN I-NP
+assays NNS I-NP
+using VBG B-VP
+a DT B-NP
+synthetic JJ I-NP
+E6 NN I-NP
+motif NN I-NP
+detected VBD B-VP
+a DT B-NP
+B-cell-specific JJ I-NP
+complex NN I-NP
+in IN B-PP
+addition NN I-PP
+to TO I-PP
+a DT B-NP
+ubiquitous JJ I-NP
+band NN I-NP
+found VBN B-VP
+also RB B-PP
+in IN I-PP
+T NN B-NP
+cells NNS I-NP
+and CC O
+HeLa NN B-NP
+cells NNS I-NP
+. . O
+
+In IN B-PP
+agreement NN I-PP
+with IN I-PP
+the DT B-NP
+results NNS I-NP
+of IN B-PP
+gel NN B-NP
+retardation NN I-NP
+assays NNS I-NP
+COMMA COMMA O
+tandem JJ B-NP
+copies NNS I-NP
+of IN B-PP
+the DT B-NP
+E6 NN I-NP
+motif NN I-NP
+stimulated VBD B-VP
+transcription NN B-NP
+in IN B-PP
+ARH77 NN B-NP
+and CC O
+Raji NN B-NP
+cells NNS B-NP
+but CC B-PP
+not RB B-PP
+in IN I-PP
+Jurkat NN B-NP
+or CC O
+HeLa NN B-NP
+cells NNS B-NP
+. . O
+
+Furthermore RB B-ADVP
+COMMA COMMA O
+a DT B-NP
+mutant JJ I-NP
+E6 NN I-NP
+motif NN I-NP
+lost VBD B-VP
+both CC O
+in FW B-NP
+vitro FW I-NP
+binding NN I-NP
+activity NN I-NP
+and CC B-PP
+in FW B-NP
+vivo FW I-NP
+enhancer NN I-NP
+activity NN I-NP
+. . O
+
+In IN B-PP
+striking JJ B-NP
+contrast NN I-NP
+to TO B-PP
+the DT B-NP
+mouse NN I-NP
+Ig NN I-NP
+heavy-chain JJ I-NP
+enhancer NN I-NP
+COMMA COMMA O
+in IN B-PP
+which WDT B-NP
+the DT B-NP
+octamer NN I-NP
+motif NN I-NP
+acts VBZ B-VP
+as IN B-PP
+a DT B-NP
+B-cell-specific JJ I-NP
+enhancer NN I-NP
+element NN I-NP
+COMMA COMMA O
+the DT B-NP
+human JJ I-NP
+enhancer NN I-NP
+contains VBZ B-VP
+an DT B-NP
+octamerlike JJ I-NP
+sequence NN I-NP
+with IN B-PP
+one CD B-NP
+base NN I-NP
+substitution NN I-NP
+which WDT B-NP
+bound VBD B-VP
+octamer-binding JJ B-NP
+proteins NNS I-NP
+with IN B-PP
+only RB B-NP
+very RB I-NP
+low JJ I-NP
+affinity NN I-NP
+and CC O
+showed VBD B-VP
+no DT B-NP
+enhancer NN I-NP
+activity NN I-NP
+of IN B-PP
+its PRP$ B-NP
+own JJ I-NP
+. . O
+
+Interestingly RB B-ADVP
+COMMA COMMA O
+the DT B-NP
+MnlI-AluI NN I-NP
+fragment NN I-NP
+could MD B-VP
+suppress VB I-VP
+the DT B-NP
+basal-level JJ I-NP
+activity NN I-NP
+of IN B-PP
+the DT B-NP
+conalbumin JJ I-NP
+promoter NN I-NP
+in IN B-PP
+both CC O
+Jurkat NN B-NP
+and CC O
+HeLa NN B-NP
+cells NNS B-NP
+. . O
+
+Moreover RB B-ADVP
+COMMA COMMA O
+simian JJ B-NP
+virus NN I-NP
+40 CD I-NP
+enhancer NN I-NP
+activity NN I-NP
+was VBD B-VP
+blocked VBN I-VP
+by IN B-PP
+the DT B-NP
+MnlI-AluI NN I-NP
+fragment NN I-NP
+in IN B-PP
+HeLa NN B-NP
+cells NNS I-NP
+but CC B-PP
+not RB B-PP
+in IN I-PP
+B NN B-NP
+cells NNS I-NP
+. . O
+
+Thus RB B-ADVP
+COMMA COMMA O
+the DT B-NP
+novel JJ I-NP
+enhancer NN I-NP
+element NN I-NP
+identified VBN B-VP
+in IN B-PP
+this DT B-NP
+study NN I-NP
+is VBZ B-VP
+probably RB B-ADVP
+a DT B-NP
+target NN I-NP
+site NN I-NP
+for IN B-PP
+both CC B-NP
+positive JJ I-NP
+and CC I-NP
+negative JJ I-NP
+factors NNS I-NP
+. . O
+
+The DT B-NP
+NF NN I-NP
+kappa NN I-NP
+B NN I-NP
+independent JJ I-NP
+cis-acting JJ I-NP
+sequences NNS I-NP
+in IN B-PP
+HIV-1 NN B-NP
+LTR NN I-NP
+responsive NN B-ADJP
+to TO B-PP
+T-cell NN B-NP
+activation NN I-NP
+. . O
+
+The DT B-NP
+rate NN I-NP
+of IN B-PP
+transcription NN B-NP
+initiation NN I-NP
+directed VBN B-VP
+by IN B-PP
+the DT B-NP
+long JJ I-NP
+terminal JJ I-NP
+repeat NN I-NP
+( ( O
+LTR NN B-NP
+) ) O
+of IN B-PP
+HIV-1 NN B-NP
+increases VBZ B-VP
+in IN B-PP
+response NN I-PP
+to TO I-PP
+mitogenic JJ B-NP
+stimuli NNS I-NP
+of IN B-PP
+T NN B-NP
+cells NNS I-NP
+. . O
+
+Here RB B-ADVP
+we PRP B-NP
+show VBP B-VP
+that IN B-SBAR
+the DT B-NP
+response NN I-NP
+of IN B-PP
+the DT B-NP
+HIV-1 NN I-NP
+LTR NN I-NP
+may MD B-VP
+be VB I-VP
+governed VBN I-VP
+by IN B-PP
+two CD B-NP
+independent JJ I-NP
+sequences NNS I-NP
+located JJ B-ADJP
+5' JJ B-NP
+to TO B-PP
+the DT B-NP
+site NN I-NP
+of IN B-PP
+transcription NN B-NP
+initiation NN I-NP
+sequences NNS I-NP
+that WDT B-NP
+bind VBP B-VP
+either CC O
+NFAT-1 NN B-NP
+or CC O
+NF NN B-NP
+kappa NN I-NP
+B NN I-NP
+. . O
+
+The DT B-NP
+rate NN I-NP
+of IN B-PP
+LTR-directed JJ B-NP
+gene NN I-NP
+expression NN I-NP
+increased VBD B-VP
+in IN B-PP
+response NN I-PP
+to TO I-PP
+treatment NN B-NP
+with IN B-PP
+either CC O
+a DT B-NP
+phorbol NN I-NP
+ester NN I-NP
+or CC O
+tumor NN B-NP
+necrosis NN I-NP
+factor NN I-NP
+alpha NN I-NP
+if IN B-SBAR
+either CC O
+the DT O
+NFAT-1 NN B-NP
+or CC O
+NF NN B-NP
+kappa NN I-NP
+B NN I-NP
+binding NN B-NP
+sites NNS I-NP
+were VBD B-VP
+deleted VBN I-VP
+COMMA COMMA O
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+failed VBD B-VP
+to TO I-VP
+respond VB I-VP
+to TO B-PP
+these DT B-NP
+mitogenic JJ I-NP
+stimuli NNS I-NP
+if IN B-SBAR
+both DT B-NP
+sequences NNS I-NP
+were VBD B-VP
+absent JJ B-ADJP
+. . O
+
+The DT B-NP
+HIV-1 NN I-NP
+mutant JJ I-NP
+virus NN I-NP
+containing VBG B-VP
+both CC O
+NF NN B-NP
+kappa NN I-NP
+B NN I-NP
+and CC O
+NFAT-1 NN B-NP
+deletion NN B-NP
+was VBD B-VP
+able JJ B-ADJP
+to TO B-VP
+replicate VB I-VP
+although IN B-SBAR
+at IN B-PP
+a DT B-NP
+much JJ I-NP
+decreased VBN I-NP
+growth NN I-NP
+rate NN I-NP
+COMMA COMMA O
+while IN B-SBAR
+the DT B-NP
+deletion NN I-NP
+of IN B-PP
+NFAT-1 NN B-NP
+alone RB B-ADVP
+increased VBD B-VP
+the DT B-NP
+viral JJ I-NP
+growth NN I-NP
+rate NN I-NP
+in IN B-PP
+Jurkat NN B-NP
+cells NNS I-NP
+. . O
+
+Neither CC O
+deletion NN B-NP
+of IN B-PP
+NF NN B-NP
+kappa NN I-NP
+B NN I-NP
+nor CC O
+deletion NN B-NP
+of IN B-PP
+NFAT-1 NN B-NP
+decreased VBD B-VP
+activation NN B-NP
+of IN B-PP
+viral JJ B-NP
+replication NN I-NP
+by IN B-PP
+phorbol NN B-NP
+ester NN I-NP
+. . O
+
+Specific JJ B-NP
+depletion NN I-NP
+of IN B-PP
+the DT B-NP
+B-cell NN I-NP
+population NN I-NP
+induced VBN B-VP
+by IN B-PP
+aberrant JJ B-NP
+expression NN I-NP
+of IN B-PP
+human JJ B-NP
+interferon NN I-NP
+regulatory JJ I-NP
+factor NN I-NP
+1 CD I-NP
+gene NN I-NP
+in IN B-PP
+transgenic JJ B-NP
+mice NNS I-NP
+. . O
+
+Interferons NNS B-NP
+( ( O
+IFNs NNS B-NP
+) ) O
+are VBP B-VP
+well RB I-VP
+known VBN I-VP
+both CC O
+as IN B-PP
+antiviral JJ B-NP
+proteins NNS I-NP
+and CC B-PP
+as IN B-PP
+potent JJ B-NP
+regulators NNS I-NP
+of IN B-PP
+cell NN B-NP
+growth NN B-NP
+and CC O
+differentiation NN B-NP
+. . O
+
+In IN B-PP
+fact NN B-NP
+COMMA COMMA O
+IFNs NNS B-NP
+inhibit VBP B-VP
+growth NN B-NP
+of IN B-PP
+various JJ B-NP
+normal JJ I-NP
+and CC I-NP
+transformed VBN I-NP
+cell NN I-NP
+types NNS I-NP
+. . O
+
+Previously RB B-ADVP
+COMMA COMMA O
+a DT B-NP
+nuclear JJ I-NP
+factor NN I-NP
+COMMA COMMA O
+IRF-1 NN B-NP
+( ( O
+interferon NN B-NP
+regulatory JJ I-NP
+factor NN I-NP
+1 CD I-NP
+) ) O
+COMMA COMMA O
+which WDT B-NP
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+to TO B-PP
+type NN B-NP
+I CD I-NP
+IFN NN I-NP
+and CC O
+some DT B-NP
+IFN-inducible JJ I-NP
+gene NN I-NP
+promoters NNS I-NP
+COMMA COMMA O
+was VBD B-VP
+identified VBN I-VP
+and CC O
+cloned VBN B-VP
+. . O
+
+Since IN B-SBAR
+the DT B-NP
+IRF-1 NN I-NP
+gene NN I-NP
+is VBZ B-VP
+both CC O
+virus NN B-NP
+and CC O
+IFN NN B-NP
+inducible JJ B-ADJP
+COMMA COMMA O
+an DT B-NP
+intriguing JJ I-NP
+issue NN I-NP
+is VBZ B-VP
+raised VBN I-VP
+as IN B-PP
+to TO I-PP
+whether IN B-SBAR
+the DT B-NP
+IRF-1 NN I-NP
+gene NN I-NP
+is VBZ B-VP
+functioning VBG I-VP
+in IN B-PP
+IFN-mediated JJ B-NP
+regulation NN I-NP
+of IN B-PP
+cell NN B-NP
+growth NN B-NP
+and CC O
+differentiation NN B-NP
+. . O
+
+In IN B-PP
+this DT B-NP
+study NN I-NP
+COMMA COMMA O
+we PRP B-NP
+generated VBD B-VP
+transgenic JJ B-NP
+mice NNS I-NP
+carrying VBG B-VP
+the DT B-NP
+human JJ I-NP
+IRF-1 NN I-NP
+gene NN I-NP
+linked VBN B-VP
+to TO B-PP
+the DT B-NP
+human JJ I-NP
+immunoglobulin NN I-NP
+heavy-chain JJ I-NP
+enhancer NN I-NP
+. . O
+
+In IN B-PP
+the DT B-NP
+transgenic JJ I-NP
+mice NNS I-NP
+COMMA COMMA O
+all PDT B-NP
+the DT I-NP
+lymphoid JJ I-NP
+tissues NNS I-NP
+examined VBN B-VP
+showed VBD B-VP
+a DT B-NP
+dramatic JJ I-NP
+reduction NN I-NP
+in IN B-PP
+the DT B-NP
+number NN I-NP
+of IN B-PP
+B NN B-NP
+lymphocytes NNS I-NP
+( ( O
+B NN B-NP
+cells NNS I-NP
+) ) O
+. . O
+
+Preparation NN B-NP
+and CC O
+analysis NN B-NP
+of IN B-PP
+bone NN B-NP
+marrow NN I-NP
+cells NNS I-NP
+from IN B-PP
+the DT B-NP
+chimeric JJ I-NP
+mice NNS I-NP
+indicated VBD B-VP
+that IN B-SBAR
+the DT B-NP
+bone NN I-NP
+marrow NN I-NP
+is VBZ B-VP
+the DT B-NP
+effective JJ I-NP
+site NN I-NP
+for IN B-PP
+specific JJ B-NP
+depletion NN I-NP
+of IN B-PP
+the DT B-NP
+B-cell NN I-NP
+population NN I-NP
+. . O
+
+In IN B-PP
+fact NN B-NP
+COMMA COMMA O
+transgenic JJ B-NP
+bone NN I-NP
+marrow NN I-NP
+cells NNS I-NP
+cocultured VBN B-VP
+with IN B-PP
+a DT B-NP
+bone NN I-NP
+marrow-derived JJ I-NP
+stromal JJ I-NP
+cell NN I-NP
+line NN I-NP
+revealed VBD B-VP
+an DT B-NP
+altered JJ I-NP
+B-cell NN I-NP
+maturation NN I-NP
+pattern NN I-NP
+. . O
+
+Identification NN B-NP
+and CC O
+cloning NN B-NP
+of IN B-PP
+TCF-1 NN B-NP
+COMMA COMMA O
+a DT B-NP
+T NN I-NP
+lymphocyte-specific JJ I-NP
+transcription NN I-NP
+factor NN I-NP
+containing VBG B-VP
+a DT B-NP
+sequence-specific JJ I-NP
+HMG NN I-NP
+box NN I-NP
+. . O
+
+CD3-epsilon NN B-NP
+expression NN I-NP
+is VBZ B-VP
+controlled VBN I-VP
+by IN B-PP
+a DT B-NP
+downstream JJ I-NP
+T NN I-NP
+lymphocyte-specific JJ I-NP
+enhancer NN I-NP
+element NN I-NP
+. . O
+
+We PRP B-NP
+report VBP B-VP
+the DT B-NP
+identification NN I-NP
+of IN B-PP
+a DT B-NP
+T NN I-NP
+cell-specific JJ I-NP
+transcription NN I-NP
+factor NN I-NP
+COMMA COMMA O
+TCF-1 NN B-NP
+COMMA COMMA O
+binding VBG B-VP
+to TO B-PP
+this DT B-NP
+element NN I-NP
+. . O
+
+The DT B-NP
+multimerized JJ I-NP
+recognition NN I-NP
+motif NN I-NP
+of IN B-PP
+TCF-1 NN B-NP
+constituted VBD B-VP
+a DT B-NP
+T NN I-NP
+cell-specific JJ I-NP
+enhancer NN I-NP
+. . O
+
+Subsequent JJ B-NP
+cloning NN I-NP
+of IN B-PP
+TCF-1 NN B-NP
+identified VBD B-VP
+three CD B-NP
+splice NN I-NP
+alternatives NNS I-NP
+. . O
+
+TCF-1 NN B-NP
+contained VBD B-VP
+a DT B-NP
+single JJ I-NP
+DNA-binding JJ I-NP
+HMG NN I-NP
+box NN I-NP
+most RBS B-ADJP
+closely RB I-ADJP
+related JJ I-ADJP
+to TO B-PP
+similar JJ B-NP
+boxes NNS I-NP
+in IN B-PP
+the DT B-NP
+putative JJ I-NP
+mammalian JJ I-NP
+sex-determining JJ I-NP
+gene NN I-NP
+SRY NN I-NP
+and CC B-PP
+in IN B-PP
+the DT B-NP
+Schizosaccharomyces FW I-NP
+pombe FW I-NP
+Mc NN I-NP
+mating NN I-NP
+type NN I-NP
+gene NN I-NP
+. . O
+
+TCF-1 NN B-ADVP
+mRNA NN I-ADVP
+was VBD B-VP
+expressed VBN I-VP
+uniquely RB B-ADVP
+in IN B-PP
+T NN B-NP
+lymphocytes NNS I-NP
+. . O
+
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/data/unit-test.postagger.model.bin.gz
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/data/unit-test.postagger.model.bin.gz?rev=1396711&view=auto
==============================================================================
Binary file - no diff available.
Propchange: incubator/ctakes/trunk/ctakes-chunker/src/test/data/unit-test.postagger.model.bin.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,81 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>Adjust NP in NP PP NP to span all three</name>
+<description></description>
+<version></version>
+<vendor></vendor>
+<configurationParameters>
+<configurationParameter>
+<name>ChunkPattern</name>
+<description>The pattern of Chunks to look for</description>
+<type>String</type>
+<multiValued>true</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+<configurationParameter>
+<name>IndexOfTokenToInclude</name>
+<type>Integer</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>ChunkPattern</name>
+<value>
+<array>
+<string>NP</string>
+<string>PP</string>
+<string>NP</string>
+</array>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>IndexOfTokenToInclude</name>
+<value>
+<integer>2</integer>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<typeSystemDescription/>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs/>
+<outputs/>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<resourceManagerConfiguration/>
+</taeDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkAdjusterAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkAdjusterAggregate.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkAdjusterAggregate.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkAdjusterAggregate.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,150 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>false</primitive>
+<delegateAnalysisEngineSpecifiers>
+<delegateAnalysisEngine key="SimpleSegmentAnnotator">
+<import location="SimpleSegmentAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="ChunkAdjuster">
+<import location="AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="Chunker">
+<import location="Chunker.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="SentenceDetectorAnnotator">
+<import location="SentenceDetectorAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="TokenizerAnnotator">
+<import location="TokenizerAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="POSTagger">
+<import location="POSTagger.xml"/>
+</delegateAnalysisEngine>
+</delegateAnalysisEngineSpecifiers>
+<analysisEngineMetaData>
+<name>Chunker Aggregate</name>
+<description></description>
+<version>1.0</version>
+<vendor></vendor>
+<configurationParameters searchStrategy="language_fallback">
+<configurationParameter>
+<name>PosModelFile</name>
+<description>the file that contains the part-of-speech tagging model</description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>POSTagger/PosModelFile</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>ChunkerModelFile</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>Chunker/ChunkerModelFile</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>PosTagDictionary</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>false</mandatory>
+<overrides>
+<parameter>POSTagger/TagDictionary</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>ChunkCreatorClass</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>Chunker/ChunkCreatorClass</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>CaseSensitive</name>
+<type>Boolean</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>POSTagger/CaseSensitive</parameter>
+</overrides>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>ChunkerModelFile</name>
+<value>
+<string>test/data/unit-test.chunker.model.bin.gz</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>PosModelFile</name>
+<value>
+<string>test/data/unit-test-model.bin.gz</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>ChunkCreatorClass</name>
+<value>
+<string>org.apache.ctakes.chunker.ae.DefaultChunkCreator</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>CaseSensitive</name>
+<value>
+<boolean>true</boolean>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<flowConstraints>
+<fixedFlow>
+<node>SimpleSegmentAnnotator</node>
+<node>TokenizerAnnotator</node>
+<node>SentenceDetectorAnnotator</node>
+<node>POSTagger</node>
+<node>Chunker</node>
+<node>ChunkAdjuster</node>
+</fixedFlow>
+</flowConstraints>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs/>
+<outputs/>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<resourceManagerConfiguration/>
+</analysisEngineDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/Chunker.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/Chunker.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/Chunker.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/Chunker.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>true</primitive>
+ <annotatorImplementationName>org.apache.ctakes.chunker.ae.Chunker</annotatorImplementationName>
+ <analysisEngineMetaData>
+ <name>Chunker</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <configurationParameters>
+ <configurationParameter>
+ <name>ChunkerModelFile</name>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ </configurationParameter>
+ <configurationParameter>
+ <name>ChunkCreatorClass</name>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ </configurationParameter>
+ </configurationParameters>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>ChunkerModelFile</name>
+ <value>
+ <string>CHANGEME</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>ChunkCreatorClass</name>
+ <value>
+ <string>org.apache.ctakes.chunker.ae.DefaultChunkCreator</string>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ <typeSystemDescription>
+ <imports>
+ </imports>
+ </typeSystemDescription>
+ <typePriorities/>
+ <fsIndexCollection/>
+ <capabilities>
+ <capability>
+ <inputs/>
+ <outputs/>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <resourceManagerConfiguration/>
+</analysisEngineDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerAggregate.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerAggregate.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerAggregate.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,146 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>false</primitive>
+<delegateAnalysisEngineSpecifiers>
+<delegateAnalysisEngine key="SimpleSegmentAnnotator">
+<import location="SimpleSegmentAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="Chunker">
+<import location="Chunker.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="SentenceDetectorAnnotator">
+<import location="SentenceDetectorAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="TokenizerAnnotator">
+<import location="TokenizerAnnotator.xml"/>
+</delegateAnalysisEngine>
+<delegateAnalysisEngine key="POSTagger">
+<import location="POSTagger.xml"/>
+</delegateAnalysisEngine>
+</delegateAnalysisEngineSpecifiers>
+<analysisEngineMetaData>
+<name>Chunker Aggregate</name>
+<description></description>
+<version>1.0</version>
+<vendor></vendor>
+<configurationParameters searchStrategy="language_fallback">
+<configurationParameter>
+<name>PosModelFile</name>
+<description>the file that contains the part-of-speech tagging model</description>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>POSTagger/PosModelFile</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>ChunkerModelFile</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>Chunker/ChunkerModelFile</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>PosTagDictionary</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>false</mandatory>
+<overrides>
+<parameter>POSTagger/TagDictionary</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>ChunkCreatorClass</name>
+<type>String</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>Chunker/ChunkCreatorClass</parameter>
+</overrides>
+</configurationParameter>
+<configurationParameter>
+<name>CaseSensitive</name>
+<type>Boolean</type>
+<multiValued>false</multiValued>
+<mandatory>true</mandatory>
+<overrides>
+<parameter>POSTagger/CaseSensitive</parameter>
+</overrides>
+</configurationParameter>
+</configurationParameters>
+<configurationParameterSettings>
+<nameValuePair>
+<name>ChunkerModelFile</name>
+<value>
+<string>test/data/unit-test.chunker.model.bin.gz</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>PosModelFile</name>
+<value>
+<string>test/data/unit-test-model.bin.gz</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>ChunkCreatorClass</name>
+<value>
+<string>org.apache.ctakes.chunker.ae.DefaultChunkCreator</string>
+</value>
+</nameValuePair>
+<nameValuePair>
+<name>CaseSensitive</name>
+<value>
+<boolean>true</boolean>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+<flowConstraints>
+<fixedFlow>
+<node>SimpleSegmentAnnotator</node>
+<node>TokenizerAnnotator</node>
+<node>SentenceDetectorAnnotator</node>
+<node>POSTagger</node>
+<node>Chunker</node>
+</fixedFlow>
+</flowConstraints>
+<typePriorities/>
+<fsIndexCollection/>
+<capabilities>
+<capability>
+<inputs/>
+<outputs/>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<resourceManagerConfiguration/>
+</analysisEngineDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCPE.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCPE.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCPE.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<collectionReader>
+<collectionIterator>
+<descriptor>
+<import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+</descriptor>
+<configurationParameterSettings>
+<nameValuePair>
+<name>InputDirectory</name>
+<value>
+<string>test/data/text-files</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</collectionIterator>
+</collectionReader>
+<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+<casProcessor deployment="integrated" name="Chunker Aggregate">
+<descriptor>
+<import location="ChunkerAggregate.xml"/>
+</descriptor>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+<configurationParameterSettings>
+<nameValuePair>
+<name>PosModelFile</name>
+<value>
+<string>test\data\unit-test.mayo-pos.zip</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</casProcessor>
+<casProcessor deployment="integrated" name="Write CAS to XML file">
+<descriptor>
+<import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
+</descriptor>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+<configurationParameterSettings>
+<nameValuePair>
+<name>outputDir</name>
+<value>
+<string>test\data\output</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</casProcessor>
+</casProcessors>
+<cpeConfig>
+<numToProcess>-1</numToProcess>
+<deployAs>immediate</deployAs>
+<checkpoint batch="0" time="300000ms"/>
+<timerImpl></timerImpl>
+</cpeConfig>
+</cpeDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCpeUsingPosTagDictionary.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCpeUsingPosTagDictionary.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCpeUsingPosTagDictionary.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/ChunkerCpeUsingPosTagDictionary.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<collectionReader>
+<collectionIterator>
+<descriptor>
+<import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+</descriptor>
+<configurationParameterSettings>
+<nameValuePair>
+<name>InputDirectory</name>
+<value>
+<string>test/data/text-files</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</collectionIterator>
+</collectionReader>
+<casProcessors casPoolSize="3" processingUnitThreadCount="1">
+<casProcessor deployment="integrated" name="Chunker Aggregate">
+<descriptor>
+<import location="ChunkerAggregate.xml"/>
+</descriptor>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+<configurationParameterSettings>
+<nameValuePair>
+<name>PosTagDictionary</name>
+<value>
+<string>test\data\unit-test-tag-dictionary.txt</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</casProcessor>
+<casProcessor deployment="integrated" name="Write CAS to XML file">
+<descriptor>
+<import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
+</descriptor>
+<deploymentParameters/>
+<errorHandling>
+<errorRateThreshold action="terminate" value="0/1000"/>
+<maxConsecutiveRestarts action="terminate" value="30"/>
+<timeout max="100000" default="-1"/>
+</errorHandling>
+<checkpoint batch="10000" time="1000ms"/>
+<configurationParameterSettings>
+<nameValuePair>
+<name>outputDir</name>
+<value>
+<string>test\data\output</string>
+</value>
+</nameValuePair>
+</configurationParameterSettings>
+</casProcessor>
+</casProcessors>
+<cpeConfig>
+<numToProcess>-1</numToProcess>
+<deployAs>immediate</deployAs>
+<checkpoint batch="0" time="300000ms"/>
+<timerImpl></timerImpl>
+</cpeConfig>
+</cpeDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/POSTagger.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/POSTagger.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/POSTagger.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/POSTagger.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>true</primitive>
+ <annotatorImplementationName>org.apache.ctakes.postagger.POSTagger</annotatorImplementationName>
+ <analysisEngineMetaData>
+ <name>POSTagger</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <configurationParameters>
+ <configurationParameter>
+ <name>PosModelFile</name>
+ <description>the file that contains the part-of-speech tagging model</description>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ </configurationParameter>
+ <configurationParameter>
+ <name>TagDictionary</name>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>false</mandatory>
+ </configurationParameter>
+ <configurationParameter>
+ <name>CaseSensitive</name>
+ <type>Boolean</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ </configurationParameter>
+ </configurationParameters>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>PosModelFile</name>
+ <value>
+ <string>data/test/unit-test-model.bin.gz</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>CaseSensitive</name>
+ <value>
+ <boolean>true</boolean>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ <typeSystemDescription>
+ <imports>
+ </imports>
+ </typeSystemDescription>
+ <typePriorities/>
+ <fsIndexCollection/>
+ <capabilities>
+ <capability>
+ <inputs>
+ <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+ <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+ </inputs>
+ <outputs>
+ <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+ </outputs>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <resourceManagerConfiguration/>
+</analysisEngineDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/PhraseTypeChunkerAggregate.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/PhraseTypeChunkerAggregate.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/PhraseTypeChunkerAggregate.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/PhraseTypeChunkerAggregate.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,131 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>false</primitive>
+ <delegateAnalysisEngineSpecifiers>
+ <delegateAnalysisEngine key="Chunker">
+ <import location="Chunker.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="TokenizerAnnotator">
+ <import location="TokenizerAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="SentenceDetectorAnnotator">
+ <import location="SentenceDetectorAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="SimpleSegmentAnnotator">
+ <import location="SimpleSegmentAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="POSTagger">
+ <import location="POSTagger.xml"/>
+ </delegateAnalysisEngine>
+ </delegateAnalysisEngineSpecifiers>
+ <analysisEngineMetaData>
+ <name>Chunker Aggregate</name>
+ <description/>
+ <version>1.0</version>
+ <vendor/>
+ <configurationParameters searchStrategy="language_fallback">
+ <configurationParameter>
+ <name>PosModelFile</name>
+ <description>the file that contains the part-of-speech tagging model</description>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ <overrides>
+ <parameter>POSTagger/PosModelFile</parameter>
+ </overrides>
+ </configurationParameter>
+ <configurationParameter>
+ <name>ChunkerModelFile</name>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ <overrides>
+ <parameter>Chunker/ChunkerModelFile</parameter>
+ </overrides>
+ </configurationParameter>
+ <configurationParameter>
+ <name>PosTagDictionary</name>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>false</mandatory>
+ <overrides>
+ <parameter>POSTagger/TagDictionary</parameter>
+ </overrides>
+ </configurationParameter>
+ <configurationParameter>
+ <name>ChunkCreatorClass</name>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ <overrides>
+ <parameter>Chunker/ChunkCreatorClass</parameter>
+ </overrides>
+ </configurationParameter>
+ </configurationParameters>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>ChunkerModelFile</name>
+ <value>
+ <string>test/data/unit-test.chunker.model.bin.gz</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>PosModelFile</name>
+ <value>
+ <string>test/data/unit-test.mayo-pos.zip</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>ChunkCreatorClass</name>
+ <value>
+ <string>org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator</string>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ <flowConstraints>
+ <fixedFlow>
+ <node>SimpleSegmentAnnotator</node>
+ <node>TokenizerAnnotator</node>
+ <node>SentenceDetectorAnnotator</node>
+ <node>POSTagger</node>
+ <node>Chunker</node>
+ </fixedFlow>
+ </flowConstraints>
+ <typePriorities/>
+ <fsIndexCollection/>
+ <capabilities>
+ <capability>
+ <inputs/>
+ <outputs/>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <resourceManagerConfiguration/>
+</analysisEngineDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SentenceDetectorAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SentenceDetectorAnnotator.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SentenceDetectorAnnotator.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SentenceDetectorAnnotator.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+<primitive>true</primitive>
+<annotatorImplementationName>org.apache.ctakes.core.ae.SentenceDetector</annotatorImplementationName>
+<analysisEngineMetaData>
+<name>Sentence Detector annotator</name>
+<description>Discovers sentence boundaries.</description>
+<version>2.1</version>
+<vendor>Mayo Clinic</vendor>
+<configurationParameters/>
+<configurationParameterSettings/>
+<typeSystemDescription>
+<imports>
+</imports>
+</typeSystemDescription>
+<capabilities>
+<capability>
+<inputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+</inputs>
+<outputs>
+<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+</outputs>
+<languagesSupported/>
+</capability>
+</capabilities>
+<operationalProperties>
+<modifiesCas>true</modifiesCas>
+<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+<outputsNewCASes>false</outputsNewCASes>
+</operationalProperties>
+</analysisEngineMetaData>
+<externalResourceDependencies>
+<externalResourceDependency>
+<key>MaxentModel</key>
+<description></description>
+<interfaceName>org.apache.ctakes.core.resource.MaxentModelResource</interfaceName>
+<optional>false</optional>
+</externalResourceDependency>
+</externalResourceDependencies>
+<resourceManagerConfiguration>
+<externalResources>
+<externalResource>
+<name>MaxentModelFile</name>
+<description></description>
+<fileResourceSpecifier>
+<fileUrl>file:sentdetect/sample_sd_included.mod</fileUrl>
+</fileResourceSpecifier>
+<implementationName>org.apache.ctakes.core.resource.SuffixMaxentModelResourceImpl</implementationName>
+</externalResource>
+</externalResources>
+<externalResourceBindings>
+<externalResourceBinding>
+<key>MaxentModel</key>
+<resourceName>MaxentModelFile</resourceName>
+</externalResourceBinding>
+</externalResourceBindings>
+</resourceManagerConfiguration>
+</taeDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SimpleSegmentAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SimpleSegmentAnnotator.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SimpleSegmentAnnotator.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/SimpleSegmentAnnotator.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>true</primitive>
+ <annotatorImplementationName>org.apache.ctakes.core.ae.SimpleSegmentAnnotator</annotatorImplementationName>
+ <analysisEngineMetaData>
+ <name>SimpleSegmentAnnotator</name>
+ <description/>
+ <version>2.1</version>
+ <vendor>Mayo Clinic</vendor>
+ <configurationParameters>
+ <configurationParameter>
+ <name>SegmentID</name>
+ <description/>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>false</mandatory>
+ </configurationParameter>
+ </configurationParameters>
+ <configurationParameterSettings/>
+ <typeSystemDescription>
+ <imports>
+ </imports>
+ </typeSystemDescription>
+ <typePriorities/>
+ <fsIndexCollection/>
+ <capabilities>
+ <capability>
+ <inputs/>
+ <outputs>
+ <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
+ </outputs>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <resourceManagerConfiguration/>
+</taeDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/desc/TokenizerAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/desc/TokenizerAnnotator.xml?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/desc/TokenizerAnnotator.xml (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/desc/TokenizerAnnotator.xml Wed Oct 10 17:59:40 2012
@@ -0,0 +1,110 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>true</primitive>
+ <annotatorImplementationName>org.apache.ctakes.core.ae.TokenizerAnnotator</annotatorImplementationName>
+ <analysisEngineMetaData>
+ <name>TokenizerAnnotator</name>
+ <description>Discovers tokens in the given text. These tokens consist of words, punctuation, etc...</description>
+ <version>2.1</version>
+ <vendor>Mayo Clinic</vendor>
+ <configurationParameters>
+ <configurationParameter>
+ <name>SegmentsToSkip</name>
+ <description>Segments to skip.</description>
+ <type>String</type>
+ <multiValued>true</multiValued>
+ <mandatory>false</mandatory>
+ </configurationParameter>
+ <configurationParameter>
+ <name>FreqCutoff</name>
+ <description>Frequency cutoff for hyphen entries.</description>
+ <type>Integer</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ </configurationParameter>
+ </configurationParameters>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>SegmentsToSkip</name>
+ <value>
+ <array/>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>FreqCutoff</name>
+ <value>
+ <integer>0</integer>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ <typeSystemDescription>
+ <imports>
+ </imports>
+ </typeSystemDescription>
+ <typePriorities/>
+ <fsIndexCollection/>
+ <capabilities>
+ <capability>
+ <inputs>
+ <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Segment</type>
+ </inputs>
+ <outputs>
+ <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+ </outputs>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <externalResourceDependencies>
+ <externalResourceDependency>
+ <key>HyphFreqTable</key>
+ <description/>
+ <interfaceName>org.apache.ctakes.core.resource.StringIntegerMapResource</interfaceName>
+ <optional>true</optional>
+ </externalResourceDependency>
+ </externalResourceDependencies>
+ <resourceManagerConfiguration>
+ <externalResources>
+ <externalResource>
+ <name>HyphFreqFile</name>
+ <description/>
+ <fileResourceSpecifier>
+ <fileUrl>file:tokenizer/hyphenated.txt</fileUrl>
+ </fileResourceSpecifier>
+ <implementationName>org.apache.ctakes.core.resource.StringIntegerMapResourceImpl</implementationName>
+ </externalResource>
+ </externalResources>
+ <externalResourceBindings>
+ <externalResourceBinding>
+ <key>HyphFreqTable</key>
+ <resourceName>HyphFreqFile</resourceName>
+ </externalResourceBinding>
+ </externalResourceBindings>
+ </resourceManagerConfiguration>
+</taeDescription>
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkAdjusterTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkAdjusterTests.java?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkAdjusterTests.java (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkAdjusterTests.java Wed Oct 10 17:59:40 2012
@@ -0,0 +1,100 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.chunker;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.junit.Test;
+
+import org.apache.ctakes.core.TestUtil;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+
+public class ChunkAdjusterTests {
+
+ @Test
+ public void testAdjusterExtendsChunk() throws ResourceInitializationException {
+
+ // new File(String) is rooted under chunker project directory
+ AnalysisEngine ae = TestUtil.getAE(new File("test/desc/ChunkAdjusterAggregate.xml"));
+ // this tests the ChunkAdjuster NP PP NP extending end offset of chunk 0
+ // to match end offset of chunk 2 in the pattern NP PP NP, but with that
+ // process repeated when pattern is repeated.
+ JCas jCas = TestUtil.processAE(ae, "Induction of NF-KB during monocyte differentiation by HIV type 1 infection.");
+
+ // The above should be assigned
+ // NP PP NP PP NP
+
+ // The ChunkAdjuster extends the first NP so it ends up like
+ // NP-----> PP NP
+ // Then the NP is extended again so it ends up like
+ // NP----------->
+
+ Chunk chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 0);
+ assertEquals(0, chunk.getBegin());
+ int chunkEnd = chunk.getEnd();
+ // assertEquals("Induction", chunk.getCoveredText());
+ // assertEquals("NP", chunk.getChunkType());
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 6);
+ assertEquals(chunkEnd, chunk.getEnd());
+ // assertEquals("HIV type 1 infection", chunk.getCoveredText());
+ // assertEquals("NP", chunk.getChunkType());
+
+ }
+
+
+ @Test
+ public void testAdjustDoesNotAlwaysExtend() throws ResourceInitializationException {
+
+ // new File(String) is rooted under chunker project directory
+ AnalysisEngine ae = TestUtil.getAE(new File("test/desc/ChunkAdjusterAggregate.xml"));
+
+ // This tests that no end offsets are changed when the pattern is not matched
+ JCas jCas = TestUtil.processAE(ae, "He prescribed some antibiotics.");
+
+ // The above should be
+ // NP PP NP PP NP
+ // The first NP is extended so it ends up like
+ // NP-----> PP NP
+ // Then the NP is extended again so it ends up like
+ // NP----------->
+
+ Chunk chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 0);
+ assertEquals(0, chunk.getBegin());
+ int chunkEnd = chunk.getEnd();
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 1);
+ assertTrue(chunkEnd < chunk.getEnd());
+ assertTrue(chunkEnd < chunk.getBegin());
+ chunkEnd = chunk.getEnd();
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 2);
+ assertTrue(chunkEnd < chunk.getEnd());
+ assertTrue(chunkEnd < chunk.getBegin());
+
+
+ }
+
+}
Added: incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkerTests.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkerTests.java?rev=1396711&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkerTests.java (added)
+++ incubator/ctakes/trunk/ctakes-chunker/src/test/java/org/apache/ctakes/chunker/ChunkerTests.java Wed Oct 10 17:59:40 2012
@@ -0,0 +1,179 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.ctakes.chunker;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.junit.Test;
+
+import org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator;
+import org.apache.ctakes.typesystem.type.syntax.ADJP;
+import org.apache.ctakes.typesystem.type.syntax.ADVP;
+import org.apache.ctakes.typesystem.type.syntax.CONJP;
+import org.apache.ctakes.typesystem.type.syntax.INTJ;
+import org.apache.ctakes.typesystem.type.syntax.LST;
+import org.apache.ctakes.typesystem.type.syntax.NP;
+import org.apache.ctakes.typesystem.type.syntax.PP;
+import org.apache.ctakes.typesystem.type.syntax.PRT;
+import org.apache.ctakes.typesystem.type.syntax.SBAR;
+import org.apache.ctakes.typesystem.type.syntax.UCP;
+import org.apache.ctakes.typesystem.type.syntax.VP;
+import org.apache.ctakes.core.TestUtil;
+import org.apache.ctakes.typesystem.type.syntax.Chunk;
+
+public class ChunkerTests {
+
+ @Test
+ public void testDefaultChunker() throws ResourceInitializationException {
+
+ // new File(String) is rooted under chunker project directory
+ AnalysisEngine ae = TestUtil.getAE(new File("test/desc/ChunkerAggregate.xml"));
+ //this tests the tagging model with no tag dictionary
+ JCas jCas = TestUtil.processAE(ae, "Induction of NF-KB during monocyte differentiation by HIV type 1 infection.");
+
+ Chunk chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 0);
+ assertEquals(0, chunk.getBegin());
+ assertEquals(9, chunk.getEnd());
+ assertEquals("Induction", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 1);
+ assertEquals("of", chunk.getCoveredText());
+ assertEquals("PP", chunk.getChunkType());
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 2);
+ assertEquals("NF-KB", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 3);
+ assertEquals("during", chunk.getCoveredText());
+ assertEquals("PP", chunk.getChunkType());
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 4);
+ assertEquals("monocyte differentiation", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 5);
+ assertEquals("by", chunk.getCoveredText());
+ assertEquals("PP", chunk.getChunkType());
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 6);
+ assertEquals("HIV type 1 infection", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+
+ }
+
+ @Test
+ public void testPhraseTypeChunker() throws ResourceInitializationException {
+
+ AnalysisEngine ae = TestUtil.getAE(new File("test/desc/PhraseTypeChunkerAggregate.xml"));
+ //this tests the tagging model with no tag dictionary
+ JCas jCas = TestUtil.processAE(ae, "Induction of NF-KB during monocyte differentiation by HIV type 1 infection.");
+
+ Chunk chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 0);
+ assertEquals(0, chunk.getBegin());
+ assertEquals(9, chunk.getEnd());
+ assertEquals("Induction", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+ assertTrue(chunk instanceof NP);
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 1);
+ assertEquals("of", chunk.getCoveredText());
+ assertEquals("PP", chunk.getChunkType());
+ assertTrue(chunk instanceof PP);
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 2);
+ assertEquals("NF-KB", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+ assertTrue(chunk instanceof NP);
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 3);
+ assertEquals("during", chunk.getCoveredText());
+ assertEquals("PP", chunk.getChunkType());
+ assertTrue(chunk instanceof PP);
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 4);
+ assertEquals("monocyte differentiation", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+ assertTrue(chunk instanceof NP);
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 5);
+ assertEquals("by", chunk.getCoveredText());
+ assertEquals("PP", chunk.getChunkType());
+ assertTrue(chunk instanceof PP);
+
+ chunk = TestUtil.getFeatureStructureAtIndex(jCas, Chunk.class, 6);
+ assertEquals("HIV type 1 infection", chunk.getCoveredText());
+ assertEquals("NP", chunk.getChunkType());
+ assertTrue(chunk instanceof NP);
+
+ PhraseTypeChunkCreator chunkCreator = new PhraseTypeChunkCreator();
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "ADJP");
+ assertEquals("ADJP", chunk.getChunkType());
+ assertTrue(chunk instanceof ADJP);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "ADVP");
+ assertEquals("ADVP", chunk.getChunkType());
+ assertTrue(chunk instanceof ADVP);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "CONJP");
+ assertEquals("CONJP", chunk.getChunkType());
+ assertTrue(chunk instanceof CONJP);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "INTJ");
+ assertEquals("INTJ", chunk.getChunkType());
+ assertTrue(chunk instanceof INTJ);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "LST");
+ assertEquals("LST", chunk.getChunkType());
+ assertTrue(chunk instanceof LST);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "NP");
+ assertEquals("NP", chunk.getChunkType());
+ assertTrue(chunk instanceof NP);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "PP");
+ assertEquals("PP", chunk.getChunkType());
+ assertTrue(chunk instanceof PP);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "PRT");
+ assertEquals("PRT", chunk.getChunkType());
+ assertTrue(chunk instanceof PRT);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "SBAR");
+ assertEquals("SBAR", chunk.getChunkType());
+ assertTrue(chunk instanceof SBAR);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "UCP");
+ assertEquals("UCP", chunk.getChunkType());
+ assertTrue(chunk instanceof UCP);
+
+ chunk = (Chunk) chunkCreator.createChunk(jCas, 0, 5, "VP");
+ assertEquals("VP", chunk.getChunkType());
+ assertTrue(chunk instanceof VP);
+
+ }
+
+}
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_pipeline.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_pipeline.launch?rev=1396711&r1=1396710&r2=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_pipeline.launch (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CPE_GUI--clinical_documents_pipeline.launch Wed Oct 10 17:59:40 2012
@@ -1,13 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/ctakes-clinical-pipeline"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx500M"/>
-</launchConfiguration>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-clinical-pipeline"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="4"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx500M"/>
+</launchConfiguration>
Copied: incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/TestUtil.java (from r1395758, incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/test/TestUtil.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/TestUtil.java?p2=incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/TestUtil.java&p1=incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/test/TestUtil.java&r1=1395758&r2=1396711&rev=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/test/TestUtil.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/TestUtil.java Wed Oct 10 17:59:40 2012
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package edu.mayo.bmi.uima.core.test;
+package org.apache.ctakes.core;
import static org.junit.Assert.assertEquals;
Copied: incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java (from r1395758, incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ae/test/SimpleSegmentAnnotatorTests.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java?p2=incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java&p1=incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ae/test/SimpleSegmentAnnotatorTests.java&r1=1395758&r2=1396711&rev=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ae/test/SimpleSegmentAnnotatorTests.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SimpleSegmentAnnotatorTests.java Wed Oct 10 17:59:40 2012
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package org.apache.ctakes.core.ae.test;
+package org.apache.ctakes.core.ae;
import static org.junit.Assert.assertEquals;
@@ -27,7 +27,7 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.junit.Test;
-import edu.mayo.bmi.uima.core.test.TestUtil;
+import org.apache.ctakes.core.TestUtil;
import org.apache.ctakes.typesystem.type.textspan.Segment;
public class SimpleSegmentAnnotatorTests {
Copied: incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java (from r1395758, incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ae/test/TokenizerAnnotatorPTBTests.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java?p2=incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java&p1=incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ae/test/TokenizerAnnotatorPTBTests.java&r1=1395758&r2=1396711&rev=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ae/test/TokenizerAnnotatorPTBTests.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/TokenizerAnnotatorPTBTests.java Wed Oct 10 17:59:40 2012
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package org.apache.ctakes.core.ae.test;
+package org.apache.ctakes.core.ae;
import static org.junit.Assert.assertEquals;
@@ -29,7 +29,7 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.junit.Test;
-import edu.mayo.bmi.uima.core.test.TestUtil;
+import org.apache.ctakes.core.TestUtil;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.ContractionToken;
import org.apache.ctakes.typesystem.type.syntax.NumToken;
Copied: incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ci/HyphenTextModifierImplTests.java (from r1395758, incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ci/test/HyphenTextModifierImplTests.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ci/HyphenTextModifierImplTests.java?p2=incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ci/HyphenTextModifierImplTests.java&p1=incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ci/test/HyphenTextModifierImplTests.java&r1=1395758&r2=1396711&rev=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-core/test/edu/mayo/bmi/uima/core/ci/test/HyphenTextModifierImplTests.java (original)
+++ incubator/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ci/HyphenTextModifierImplTests.java Wed Oct 10 17:59:40 2012
@@ -19,7 +19,7 @@
/**
*
*/
-package org.apache.ctakes.core.ci.test;
+package org.apache.ctakes.core.ci;
import java.util.ArrayList;
Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java (from r1395758, incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForExampleDrugs.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForExampleDrugs.java&r1=1395758&r2=1396711&rev=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForExampleDrugs.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForExampleDrugs.java Wed Oct 10 17:59:40 2012
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package edu.mayo.bmi.dictionarytools;
+package org.apache.ctakes.dictionary.lookup.tools;
/**
* See http://www.onjava.com/pub/a/onjava/2003/01/15/lucene.html?page=1
Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java (from r1395758, incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForSnomedLikeSample.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForSnomedLikeSample.java&r1=1395758&r2=1396711&rev=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForSnomedLikeSample.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexForSnomedLikeSample.java Wed Oct 10 17:59:40 2012
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package edu.mayo.bmi.dictionarytools;
+package org.apache.ctakes.dictionary.lookup.tools;
/**
* See http://www.onjava.com/pub/a/onjava/2003/01/15/lucene.html?page=1
Copied: incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexFromDelimitedFile.java (from r1395758, incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexFromDelimitedFile.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexFromDelimitedFile.java?p2=incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexFromDelimitedFile.java&p1=incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexFromDelimitedFile.java&r1=1395758&r2=1396711&rev=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexFromDelimitedFile.java (original)
+++ incubator/ctakes/trunk/ctakes-dictionary-lookup/scripts/java/org/apache/ctakes/dictionary/lookup/tools/CreateLuceneIndexFromDelimitedFile.java Wed Oct 10 17:59:40 2012
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package edu.mayo.bmi.dictionarytools;
+package org.apache.ctakes.dictionary.lookup.tools;
import java.io.BufferedReader;
import java.io.BufferedWriter;
Modified: incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch?rev=1396711&r1=1396710&r2=1396711&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch (original)
+++ incubator/ctakes/trunk/ctakes-drug-ner/resources/launch/UIMA_CPE_GUI--Drug_NER.launch Wed Oct 10 17:59:40 2012
@@ -1,14 +1,16 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<stringAttribute key="bad_container_name" value="//resources/launch"/>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/ctakes-drug-ner"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-drug-ner"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx1024M"/>
-</launchConfiguration>
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<stringAttribute key="bad_container_name" value="//resources/launch"/>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/ctakes-drug-ner"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="4"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cpm.CpmFrame"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-drug-ner"/>
+<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Xms500M -Xmx1024M"/>
+</launchConfiguration>