Violations processor (Python script).

2 files changed, 955 insertions, 0 deletions

diff --git a/scripts/Violations_processor.py b/scripts/Violations_processor.py
new file mode 100644
index 0000000..62c1ade
--- /dev/null
+++ b/scripts/Violations_processor.py
@@ -0,0 +1,48 @@
+import json
+import argparse
+from os.path import dirname, join
+
+class Cleaner:
+    """Given a violation, it can make it very readable.
+
+    For example from:
+        atLeast(1 <RO_0002110> <FBbt_00003972>)(X) :- <auxiliary#NC36>(X)
+    to:
+        active(X) -> across(X,Y), act(Y)
+    """
+
+    def __init__(self):
+        with open(join(dirname(__file__),'list_of_words.txt'), 'r') as f:
+            self._words = [x.strip() for x in f]
+            self._used_words = 0
+            self._cache = {}
+
+    def clean(self, violation, prefix):
+        j = 0
+        atoms = []
+        for i in range(3):
+            i = violation.find('<', j) + 1
+            j = violation.find('>', i)
+            atom = violation[i:j]
+            if atom not in self._cache:
+                self._cache[atom] = str(prefix) + self._words[self._used_words]
+                self._used_words += 1
+            atoms.append(self._cache[atom])
+        return '%10s(X) -> %10s(X,Y), %10s(Y)' % (atoms[2], atoms[0], atoms[1])
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Transform violations (as output by PAGOdA) into a very readable form.')
+    parser.add_argument('input', help='json file containing violations')
+    args = parser.parse_args()
+
+    cleaner = Cleaner()
+    with open(args.input, 'r') as f:
+        violations_list_list = json.load(f)['violationClauses']
+        clean_rules_list_list = []
+        i = 0
+        for violations_list in violations_list_list:
+            clean_rules_list_list.append(sorted(map(lambda x: cleaner.clean(x, i), violations_list)))
+            i += 1
+    print json.dumps(clean_rules_list_list, indent=2)
+        
diff --git a/scripts/list_of_words.txt b/scripts/list_of_words.txt
new file mode 100644
index 0000000..5ac8658
--- /dev/null
+++ b/scripts/list_of_words.txt
@@ -0,0 +1,907 @@
+across
+act
+active
+activity
+add
+afraid
+age
+ago
+agree
+air
+alone
+along
+already
+always
+amount
+angry
+another
+answer
+anyone
+anything
+anytime
+appear
+apple
+area
+arm
+army
+around
+arrive
+art
+ask
+attack
+aunt
+autumn
+away
+baby
+back
+bad
+bag
+ball
+bank
+base
+basket
+bath
+bean
+bear
+beautiful
+bed
+bedroom
+beer
+behave
+begin
+behind
+bell
+besides
+best
+better
+big
+bird
+birth
+birthday
+bit
+bite
+black
+bleed
+block
+blood
+blow
+blue
+board
+boat
+body
+boil
+bone
+book
+border
+born
+borrow
+bottle
+bottom
+bowl
+box
+boy
+branch
+brave
+bread
+break
+breakfast
+breathe
+bridge
+bright
+bring
+brother
+brown
+brush
+build
+burn
+business
+bus
+busy
+buy
+cake
+call
+can
+candle
+cap
+car
+card
+care
+careful
+careless
+carry
+case
+cat
+catch
+central
+century
+certain
+chair
+chance
+change
+chase
+cheap
+cheese
+chicken
+child
+children
+chocolate
+choice
+choose
+circle
+city
+class
+clever
+clean
+clear
+climb
+clock
+cloth
+clothes
+cloud
+cloudy
+close
+coffee
+coat
+coin
+cold
+collect
+colour
+comb
+comfortable
+common
+compare
+come
+complete
+computer
+condition
+continue
+control
+cook
+cool
+copper
+corn
+corner
+correct
+cost
+contain
+count
+country
+course
+cover
+crash
+cross
+cry
+cup
+cupboard
+cut
+dance
+dangerous
+dark
+daughter
+day
+dead
+decide
+decrease
+deep
+deer
+depend
+desk
+destroy
+develop
+die
+different
+difficult
+dinner
+direction
+dirty
+discover
+dish
+dog
+door
+double
+draw
+dream
+dress
+drink
+drive
+drop
+dry
+duck
+dust
+duty
+ear
+early
+earn
+earth
+east
+easy
+eat
+education
+effect
+egg
+eight
+either
+electric
+elephant
+else
+empty
+end
+enemy
+enjoy
+enough
+enter
+equal
+entrance
+escape
+even
+evening
+event
+ever
+every
+everyone
+exact
+everybody
+examination
+example
+except
+excited
+exercise
+expect
+expensive
+explain
+extremely
+eye
+face
+fact
+fail
+fall
+false
+family
+famous
+far
+farm
+father
+fast
+fat
+fault
+fear
+feed
+feel
+female
+fever
+fight
+fill
+film
+find
+fine
+finger
+finish
+fire
+first
+fish
+fit
+five
+fix
+flag
+flat
+float
+floor
+flour
+flower
+fly
+fold
+food
+fool
+foot
+football
+force
+foreign
+forest
+forget
+forgive
+fork
+form
+fox
+four
+free
+freedom
+freeze
+fresh
+friend
+friendly
+front
+fruit
+full
+fun
+funny
+furniture
+future
+game
+garden
+gate
+general
+gentleman
+get
+gift
+give
+glad
+glass
+go
+goat
+god
+gold
+good
+goodbye
+grandfather
+grandmother
+grass
+grave
+great
+green
+grey
+ground
+group
+grow
+gun
+hair
+half
+hall
+hammer
+hand
+happen
+happy
+hard
+hat
+hate
+head
+healthy
+hear
+heavy
+heart
+heaven
+height
+hello
+help
+hen
+hide
+high
+hill
+hit
+hobby
+hold
+hole
+holiday
+home
+hope
+horse
+hospital
+hot
+hotel
+house
+hundred
+hungry
+hour
+hurry
+husband
+hurt
+I
+ice
+idea
+important
+increase
+inside
+introduce
+invent
+iron
+invite
+island
+jelly
+job
+join
+juice
+jump
+just
+keep
+key
+kill
+kind
+king
+kitchen
+knee
+knife
+knock
+know
+ladder
+lady
+lamp
+land
+large
+last
+late
+lately
+laugh
+lazy
+lead
+leaf
+learn
+leave
+leg
+left
+lend
+length
+less
+lesson
+let
+letter
+library
+lie
+life
+light
+like
+lion
+lip
+list
+listen
+little
+live
+lock
+lonely
+long
+look
+lose
+lot
+love
+low
+lower
+luck
+machine
+main
+make
+male
+man
+many
+map
+mark
+market
+marry
+matter
+may
+meal
+mean
+measure
+meat
+medicine
+meet
+member
+mention
+method
+middle
+milk
+million
+mind
+minute
+miss
+mistake
+mix
+model
+modern
+moment
+money
+monkey
+month
+moon
+morning
+mother
+mountain
+mouth
+move
+much
+music
+must
+name
+narrow
+nation
+nature
+near
+nearly
+neck
+need
+needle
+neighbour
+neither
+net
+never
+new
+news
+newspaper
+next
+nice
+night
+nine
+noble
+noise
+none
+north
+nose
+nothing
+notice
+now
+number
+obey
+object
+ocean
+offer
+office
+often
+oil
+old
+one
+open
+opposite
+orange
+order
+outside
+page
+pain
+paint
+pair
+pan
+paper
+parent
+park
+part
+partner
+party
+pass
+past
+path
+pay
+peace
+pen
+pencil
+people
+pepper
+per
+perfect
+period
+person
+petrol
+photograph
+piano
+pick
+picture
+piece
+pig
+pin
+pink
+place
+plane
+plant
+plastic
+plate
+play
+please
+pleased
+plenty
+pocket
+point
+poison
+police
+polite
+pool
+poor
+popular
+position
+possible
+potato
+pour
+power
+present
+press
+pretty
+prevent
+price
+prince
+prison
+private
+prize
+probably
+problem
+produce
+promise
+proper
+protect
+provide
+public
+pull
+punish
+pupil
+push
+put
+queen
+question
+quick
+quiet
+quite
+radio
+rain
+rainy
+raise
+reach
+read
+ready
+real
+really
+receive
+record
+red
+remember
+remind
+remove
+rent
+repair
+repeat
+reply
+report
+rest
+restaurant
+result
+return
+rice
+rich
+ride
+right
+ring
+rise
+road
+rob
+rock
+room
+round
+rubber
+rude
+rule
+ruler
+run
+rush
+sad
+safe
+sail
+salt
+sand
+save
+say
+school
+science
+scissors
+search
+seat
+second
+see
+seem
+sell
+send
+sentence
+serve
+seven
+several
+sex
+shade
+shadow
+shake
+shape
+share
+sharp
+sheep
+sheet
+shelf
+shine
+ship
+shirt
+shoe
+shoot
+shop
+short
+shoulder
+shout
+show
+sick
+side
+signal
+silence
+silly
+silver
+similar
+simple
+single
+since
+sing
+sink
+sister
+sit
+six
+size
+skill
+skin
+skirt
+sky
+sleep
+slip
+slow
+small
+smell
+smile
+smoke
+snow
+soap
+sock
+soft
+someone
+something
+sometimes
+son
+soon
+sorry
+sound
+soup
+south
+space
+speak
+special
+speed
+spell
+spend
+spoon
+sport
+spread
+spring
+square
+stamp
+stand
+star
+start
+station
+stay
+steal
+steam
+step
+still
+stomach
+stone
+stop
+store
+storm
+story
+strange
+street
+strong
+structure
+student
+study
+stupid
+subject
+substance
+successful
+sudden
+sugar
+suitable
+summer
+sun
+sunny
+support
+sure
+surprise
+sweet
+swim
+sword
+table
+take
+talk
+tall
+taste
+taxi
+tea
+teach
+team
+tear
+telephone
+television
+tell
+ten
+tennis
+terrible
+test
+therefore
+thick
+thin
+thing
+think
+third
+though
+threat
+three
+tidy
+tie
+title
+today
+toe
+together
+tomorrow
+tonight
+tool
+tooth
+top
+total
+touch
+town
+train
+tram
+travel
+tree
+trouble
+true
+trust
+twice
+try
+turn
+type
+ugly
+uncle
+understand
+unit
+use
+useful
+usual
+usually
+vegetable
+village
+voice
+visit
+wait
+wake
+walk
+want
+warm
+wash
+waste
+watch
+water
+way
+weak
+wear
+weather
+wedding
+week
+weight
+welcome
+well
+west
+wet
+wheel
+white
+wide
+wife
+wild
+will
+win
+wind
+window
+wine
+winter
+wire
+wise
+wish
+without
+woman
+wonder
+word
+work
+world
+worry
+yard
+yell
+yesterday
+yet
+young
+zero
+zoo