chapmanbe / negex Goto Github PK

What steps will reproduce the problem?
1. Try with input as the phrase "job" in a sentence like "Her job is ruled
out but clearly there is a requirement for her skills".
2. A StringInexOutOfBoundsException occurs in GenNegEx.java


What is the expected output? What do you see instead?
Expected output is the negation of the term "job" as follows:
"Her  [NEGATED]job[NEGATED] [POST]is ruled out[POST] [CONJ]but[CONJ]
clearly there is a requirement for her skills.  negated Her 
[NEGATED]job[NEGATED] [POST]is ruled out"

Got the StringIndexOutOfBoundsException:
java.lang.StringIndexOutOfBoundsException: String index out of range

At the following line in GenNegex.java:
sScope = sentence.substring(startOffset, endOffset);    

What version of the product are you using? On what operating system?
GeneralNegEx.java.v.1.2.05092009.zip

Please provide any additional information below.
Can be fixed by adding another if condition in GenNegEx.java as follows:
if(startOffset > endOffset){
    startOffset = sentence.lastIndexOf("[PSEU]");
}
PFA the modified GenNegEx.java file.

What steps will reproduce the problem?
1.Try to use the function analyzeReport(report, targets, modifiers ) provided 
in the wiki page
2.Define report = "Cardiac examination demonstrated regular rate and rhythm, no 
murmur, rubs, or gallops.", modifiers = 
["DEFINITE_NEGATED_EXISTENCE","probable_existence"], targets = []
3.

What is the expected output? What do you see instead?
  File "C:\Documents and Settings\pyConTextNLP\pyConTextGraph\pyConTextGraph.py", line 293, in markItem
    if(not self.res.has_key(item.getLiteral()) ):
AttributeError: 'str' object has no attribute 'getLiteral'


What version of the product are you using? On what operating system?
pyConTextNLP-0.3.0
Windows XP

Please provide any additional information below.

What steps will reproduce the problem?
1. Open the file negex_triggers.txt file with text editor
2. Search for "patinet" (misspelling of the word "patient")
3. It matches to lines 117, 120, 151

What is the expected output? What do you see instead?
N/A

What version of the product are you using? On what operating system?
N/A

Please provide any additional information below.
It is enough to replace all occurrences of "patinet" to "patient" in the 
negex_triggers.file

What steps will reproduce the problem?
When I try to run my notes for negation detection, I get this error message - 
Traceback (most recent call last):
  File "C:\Users....\Negex\wrapper.py", line 30, in <module>
    if __name__ == '__main__': main()
  File "C:\Users.... \Negex\wrapper.py", line 16, in main
    tagger = negTagger(sentence = report[2], phrases = [report[1]], rules = irules, negP=False)
IndexError: list index out of range
>>> 

What is the expected output? What do you see instead?


What version of the product are you using? On what operating system?
General NegEx Python Implementation v.1.2
On Windows XP

Please provide any additional information below.
I processed the input file to match the demo input

I wasn't sure how else to contact developers for this project...

When inputting a paragraph instead of a sentence, certain paragraphs can
result in an ArrayOutOfBoundsException.  This results from multiple
identifications of various parts ([CONJ], [PREP], etc.) in different
sentences.  If the indexes passed to the substring() function when pulling
out the scope are inverted, the subtracted value is negative.

While this isn't a big issue, I have questions regarding the algorithm
overall.  What is the effect of passing in an entire paragraph as opposed
to a single sentence?

What steps will reproduce the problem?
1. edit wrapper.py testing script on line 16 to set negP=True
2. run wrapper.py

What is the expected output? What do you see instead?
Expected output is negex_output.txt file with entries annotate as "possible" 
"affirmed" or "negated"
Instead, receive error message below:
Traceback (most recent call last):
  File "wrapper.py", line 30, in <module>
    if __name__ == '__main__': main()
  File "wrapper.py", line 16, in main
    tagger = negTagger(sentence = report[2], phrases = [report[1]], rules = irules) #, negP=False)
  File "/Users/grundmeier/svn/negex-read-only/negex.python/negex.py", line 155, in __init__
    sb3 = sb3 + ' ' + sentenceTokens[i]
TypeError: can only concatenate list (not "str") to list

What version of the product are you using? On what operating system?
using revision 170 on Mac OSX 1.6.8 with python 2.6.1

Please provide any additional information below.
Here is the edit I made locally to correct the problem.  I hope it helps!
===================================================================
--- negex.python/negex.py   (revision 170)
+++ negex.python/negex.py   (working copy)
@@ -152,7 +152,7 @@
                     sentenceTokens[i] = sentenceTokens[i].replace('[PHRASE]', '[POSSIBLE]')
                     sentencePortion = sentencePortion + ' ' + sentenceTokens[i]

-                sb3 = sb3 + ' ' + sentenceTokens[i]
+                sb3.append(sentenceTokens[i])

             if sentencePortion.strip():
                 aScopes.append(sentencePortion.strip())