added ilp package

workflows/ilp/aleph/__init__.py

+from aleph import Aleph
\ No newline at end of file

workflows/ilp/aleph/aleph.py

+#
+# Python interface to Aleph.
+# 
+# author: Anze Vavpetic <anze.vavpetic@ijs.si>, 2011
+#
+import os.path
+import shutil
+import logging
+import re
+import tempfile
+from stat import S_IREAD, S_IEXEC
+from subprocess import Popen, PIPE
+
+DEBUG = True
+
+# Setup a logger
+logger = logging.getLogger("Aleph [Python]")
+logger.setLevel(logging.DEBUG if DEBUG else logging.INFO)
+ch = logging.StreamHandler()
+formatter = logging.Formatter("%(name)s %(levelname)s: %(message)s")
+ch.setFormatter(formatter)
+logger.addHandler(ch)
+
+class Aleph(object):
+    # The aleph source file is presumed to be in the same dir as this file.
+    THIS_DIR = os.path.dirname(__file__) if os.path.dirname(__file__) else '.'
+    ALEPH_FN = 'aleph.pl'
+    YAP = '/usr/local/bin/yap'
+    RULES_SUFFIX = 'Rules'
+    SCRIPT = 'run_aleph.pl'
+    
+    def __init__(self, verbosity=logging.NOTSET):
+        """
+        Creates an Aleph object.
+        
+        @param logging can be DEBUG, INFO or NOTSET (default). This controls the verbosity of the output.
+        """
+        self.tmpdir = tempfile.mkdtemp()
+        self.aleph_script = '%s/%s' % (self.tmpdir, Aleph.ALEPH_FN)
+        self.postGoal = None
+        self.postScript = None
+        # Dictionary of non-default settings
+        self.settings = dict()
+        logger.setLevel(verbosity)
+        
+        shutil.copy("%s/%s" % (Aleph.THIS_DIR, Aleph.ALEPH_FN), self.aleph_script)
+        
+    def set(self, name, value):
+        """
+        Sets the value of setting 'name' to 'value'.
+        """
+        self.settings[name] = value
+
+    def settingsAsFacts(self, settings):
+        """
+        Parses a string of settings in the form set(name1, val1), set(name2, val2)...
+        """
+        pattern = re.compile('set\(([a-zA-Z0-9_]+),(\[a-zA-Z0-9_]+)\)')
+        pairs = pattern.findall(settings)
+        for name, val in pairs:
+            self.set(name, val)
+
+    def setPostScript(self, goal, script):
+        """
+        After learning call the given script using 'goal'.
+        """
+        self.postGoal = goal
+        self.postScript = script
+            
+    def induce(self, mode, pos, neg, b, filestem='default'):
+        """
+        Induce a theory in 'mode'.
+        
+        @param filestem The base name of this experiment.
+        @param mode In which mode to induce rules.
+        @param pos String of positive examples.
+        @param neg String of negative examples.
+        @param b String with background knowledge.
+        """
+        # Write the inputs to appropriate files.
+        self.__prepare(filestem, pos, neg, b)
+
+        # Make a script to run aleph (with appropriate settings, stack/heap sizes, ...).
+        self.__script(mode, filestem)
+
+        logger.info("Running aleph...")
+
+        # Run the aleph script.
+        p = Popen(['./' + Aleph.SCRIPT], cwd=self.tmpdir, stdout=PIPE)
+        stdout_str, stderr_str = p.communicate()
+        
+        logger.debug(stdout_str)
+        logger.debug(stderr_str)
+        
+        logger.info("Done.")
+        
+        # Return the rules written in the output file.
+        rules = open('%s/%s' % (self.tmpdir, filestem + Aleph.RULES_SUFFIX)).read()
+
+        #shutil.copy('%s/%s.py' % (self.tmpdir, filestem), '/home/anzev/programiranje/sdm/results/')
+        
+        # Cleanup.
+        self.__cleanup()
+        
+        return rules
+
+    def __prepare(self, filestem, pos, neg, b):
+        """
+        Prepares the needed files.
+        """
+        posFile = open('%s/%s.f' % (self.tmpdir, filestem), 'w')
+        negFile = open('%s/%s.n' % (self.tmpdir, filestem), 'w')
+        bFile = open('%s/%s.b' % (self.tmpdir, filestem), 'w')
+
+        posFile.write(pos)
+        negFile.write(neg)
+        bFile.write(b)
+        
+        posFile.close()
+        negFile.close()
+        bFile.close()
+        
+    def __cleanup(self):
+        """
+        Cleans up all the temporary files.
+        """
+        try:
+            shutil.rmtree(self.tmpdir)
+        except:
+            logger.info('Problem removing temporary files. The files are probably in use.')
+
+    def __script(self, mode, filestem):
+        """
+        Makes the script file to be run by yap.
+        """
+        scriptPath = '%s/%s' % (self.tmpdir, Aleph.SCRIPT)
+        script = open(scriptPath, 'w')
+        
+        #print scriptPath
+        
+        # Permit the owner to execute and read this script
+        os.chmod(scriptPath, S_IREAD | S_IEXEC)
+        
+        cat = lambda x: script.write(x + '\n')
+        cat("#!%s -L -s50000 -h200000" % Aleph.YAP)
+        cat(":- initialization(run_aleph).")
+        cat("run_aleph :- ")
+        cat("consult(aleph),")
+        cat("read_all('%s')," % filestem)
+        # Cat all the non-default settings
+        for setting, value in self.settings.items():
+            cat("set(%s, %s)," % (setting, value))
+        cat("%s," % mode)
+        cat("write_rules('%s')%s" % (filestem + Aleph.RULES_SUFFIX, ',' if self.postScript else '.'))
+        if self.postScript:
+            cat(self.postGoal + ".")
+            cat(self.postScript)
+        script.close()
\ No newline at end of file

workflows/ilp/db/package_data.json

+[
+  {
+    "pk": 72,
+    "model": "workflows.category",
+    "fields": {
+      "uid": "ed859be5-cc13-46b9-b249-c8f026732c1c",
+      "parent": null,
+      "workflow": null,
+      "user": null,
+      "order": 1,
+      "name": "ILP"
+    }
+  },
+  {
+    "pk": 300,
+    "model": "workflows.abstractwidget",
+    "fields": {
+      "category": 72,
+      "treeview_image": "",
+      "name": "Aleph",
+      "is_streaming": false,
+      "uid": "b8289304-389e-414a-98ab-273b16478cee",
+      "interaction_view": "",
+      "image": "",
+      "package": "ilp",
+      "static_image": "ilp.png",
+      "post_interact_action": "",
+      "user": null,
+      "visualization_view": "",
+      "action": "ilp_aleph",
+      "wsdl_method": "",
+      "wsdl": "",
+      "interactive": false,
+      "has_progress_bar": false,
+      "order": 1,
+      "description": ""
+    }
+  },
+  {
+    "pk": 988,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 300,
+      "name": "settings",
+      "short_name": "set",
+      "uid": "bfe16b08-89b1-4835-875c-6b0302fb1da3",
+      "default": "",
+      "required": false,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "settings",
+      "parameter": false,
+      "order": 1,
+      "description": "settings facts"
+    }
+  },
+  {
+    "pk": 989,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 300,
+      "name": "mode",
+      "short_name": "mod",
+      "uid": "00b174f3-250d-4c47-9a60-b515e5260e0c",
+      "default": "induce",
+      "required": true,
+      "multi": false,
+      "parameter_type": "select",
+      "variable": "mode",
+      "parameter": true,
+      "order": 2,
+      "description": "induction mode"
+    }
+  },
+  {
+    "pk": 101,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "8e5631e5-6497-4720-9e26-5936619caf5c",
+      "abstract_input": 989,
+      "value": "induce",
+      "name": "induce"
+    }
+  },
+  {
+    "pk": 105,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "92f66b17-02fd-4bb6-b4cb-03bb54b403f6",
+      "abstract_input": 989,
+      "value": "induce_constraints",
+      "name": "induce_constraints"
+    }
+  },
+  {
+    "pk": 102,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "ce82b005-81e4-4997-80c3-05731651869a",
+      "abstract_input": 989,
+      "value": "induce_cover",
+      "name": "induce_cover"
+    }
+  },
+  {
+    "pk": 107,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "968d079a-871c-4cae-b15e-c8e7b61f3b8c",
+      "abstract_input": 989,
+      "value": "induce_features",
+      "name": "induce_features"
+    }
+  },
+  {
+    "pk": 103,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "0103c466-0e2e-47fe-b182-0a034beb7eed",
+      "abstract_input": 989,
+      "value": "induce_max",
+      "name": "induce_max"
+    }
+  },
+  {
+    "pk": 106,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "78cb938d-16b8-4c7c-b712-b59e27aa837d",
+      "abstract_input": 989,
+      "value": "induce_modes",
+      "name": "induce_modes"
+    }
+  },
+  {
+    "pk": 104,
+    "model": "workflows.abstractoption",
+    "fields": {
+      "uid": "45f5cc84-b097-439a-9363-d2299c540913",
+      "abstract_input": 989,
+      "value": "induce_tree",
+      "name": "induce_tree"
+    }
+  },
+  {
+    "pk": 990,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 300,
+      "name": "pos",
+      "short_name": "pos",
+      "uid": "03788382-f3b9-4580-8e85-b600874ef643",
+      "default": "",
+      "required": true,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "pos",
+      "parameter": false,
+      "order": 3,
+      "description": "positive examples"
+    }
+  },
+  {
+    "pk": 991,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 300,
+      "name": "neg",
+      "short_name": "neg",
+      "uid": "01529349-3300-41c5-8585-3f7a90175120",
+      "default": "",
+      "required": true,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "neg",
+      "parameter": false,
+      "order": 4,
+      "description": "negative examples"
+    }
+  },
+  {
+    "pk": 992,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 300,
+      "name": "b",
+      "short_name": "b",
+      "uid": "2ec81e9e-d911-46a1-a95d-2eaf349443a8",
+      "default": "",
+      "required": true,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "b",
+      "parameter": false,
+      "order": 5,
+      "description": "background knowledge"
+    }
+  },
+  {
+    "pk": 355,
+    "model": "workflows.abstractoutput",
+    "fields": {
+      "widget": 300,
+      "name": "theory",
+      "short_name": "the",
+      "variable": "theory",
+      "uid": "d1d8839b-a2f1-4b82-b759-7c6c7d7d57e5",
+      "order": 1,
+      "description": "theory"
+    }
+  },
+  {
+    "pk": 301,
+    "model": "workflows.abstractwidget",
+    "fields": {
+      "category": 72,
+      "treeview_image": "",
+      "name": "RSD",
+      "is_streaming": false,
+      "uid": "dabcb4ed-ae86-4f3e-8d3e-bb0306ff11f8",
+      "interaction_view": "",
+      "image": "",
+      "package": "ilp",
+      "static_image": "ilp.png",
+      "post_interact_action": "",
+      "user": null,
+      "visualization_view": "",
+      "action": "ilp_rsd",
+      "wsdl_method": "",
+      "wsdl": "",
+      "interactive": false,
+      "has_progress_bar": false,
+      "order": 1,
+      "description": "Relational subgroup discovery by Zelezny et al."
+    }
+  },
+  {
+    "pk": 993,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 301,
+      "name": "settings",
+      "short_name": "set",
+      "uid": "a1660c9f-952d-4f29-9f23-9b0be5fe8cea",
+      "default": "",
+      "required": false,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "settings",
+      "parameter": false,
+      "order": 1,
+      "description": "settings"
+    }
+  },
+  {
+    "pk": 994,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 301,
+      "name": "pos",
+      "short_name": "pos",
+      "uid": "676ef826-7dd9-415a-8a8a-d82146dcc95a",
+      "default": "",
+      "required": false,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "pos",
+      "parameter": false,
+      "order": 2,
+      "description": "positive examples"
+    }
+  },
+  {
+    "pk": 995,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 301,
+      "name": "neg",
+      "short_name": "neg",
+      "uid": "0b46921d-50fe-46b1-a1e4-67c918160a7f",
+      "default": "",
+      "required": false,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "neg",
+      "parameter": false,
+      "order": 3,
+      "description": "negative examples"
+    }
+  },
+  {
+    "pk": 996,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 301,
+      "name": "examples",
+      "short_name": "ex",
+      "uid": "817a82dc-2264-4181-a31a-6a7ff2b6c882",
+      "default": "",
+      "required": false,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "examples",
+      "parameter": false,
+      "order": 4,
+      "description": "classified examples (pos+neg in one file)"
+    }
+  },
+  {
+    "pk": 997,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 301,
+      "name": "b",
+      "short_name": "b",
+      "uid": "746dac3a-bcf9-4546-b0cb-ccfea866707a",
+      "default": "",
+      "required": true,
+      "multi": false,
+      "parameter_type": null,
+      "variable": "b",
+      "parameter": false,
+      "order": 5,
+      "description": "background knowledge"
+    }
+  },
+  {
+    "pk": 998,
+    "model": "workflows.abstractinput",
+    "fields": {
+      "widget": 301,
+      "name": "subgroups",
+      "short_name": "sg",
+      "uid": "1c982c21-0b97-40d1-a35e-30ba16342b00",
+      "default": "",
+      "required": true,
+      "multi": false,
+      "parameter_type": "checkbox",
+      "variable": "subgroups",
+      "parameter": true,
+      "order": 6,
+      "description": "find subgroups as well"
+    }
+  },
+  {
+    "pk": 356,
+    "model": "workflows.abstractoutput",
+    "fields": {
+      "widget": 301,
+      "name": "features",
+      "short_name": "frs",
+      "variable": "features",
+      "uid": "1097065e-83f9-4dfa-89b8-775d500caa89",
+      "order": 1,
+      "description": "features as prolog facts"
+    }
+  },
+  {
+    "pk": 357,
+    "model": "workflows.abstractoutput",
+    "fields": {
+      "widget": 301,
+      "name": "arff",
+      "short_name": "arf",
+      "variable": "arff",
+      "uid": "20b53049-5a43-46f8-9d1d-b49d8db2b1bc",
+      "order": 2,
+      "description": "arff file of the propositionalized data"
+    }
+  },
+  {
+    "pk": 358,
+    "model": "workflows.abstractoutput",
+    "fields": {
+      "widget": 301,
+      "name": "rules",
+      "short_name": "rul",
+      "variable": "rules",
+      "uid": "3f70b720-fd68-4770-936b-68512046a12e",
+      "order": 3,
+      "description": "rules as prolog facts"
+    }
+  }
+]
\ No newline at end of file

workflows/ilp/interaction_views.py

+from django.shortcuts import render
+

workflows/ilp/library.py

+import re
+from string import ascii_lowercase as chars
+from random import choice
+
+from aleph import Aleph
+from rsd import RSD
+
+def ilp_aleph(input_dict):
+    aleph = Aleph()
+    settings = input_dict['settings']
+    mode = input_dict['mode']
+    pos = input_dict['pos']
+    neg = input_dict['neg']
+    b = input_dict['b']
+    # Parse settings
+    if settings:
+        aleph.settingsAsFacts(settings)
+    # Run aleph
+    theory = aleph.induce(mode, pos, neg, b)
+    return {'theory' : theory}
+
+def ilp_rsd(input_dict):
+    rsd = RSD()
+    settings = input_dict.get('settings',None)
+    pos = input_dict.get('pos', None)
+    neg = input_dict.get('neg', None)
+    examples = input_dict.get('examples', None)
+    b = input_dict['b']
+    subgroups = True if input_dict['subgroups'] == 'true' else False
+    # Parse settings
+    if settings:
+        rsd.settingsAsFacts(settings)
+    # Run rsd
+    features, arff, rules = rsd.induce(b, examples=examples, pos=pos, neg=neg, cn2sd=subgroups)
+    return {'features' : features, 'arff' : arff, 'rules' : rules}

workflows/ilp/rsd/__init__.py

+from rsd import RSD
\ No newline at end of file

workflows/ilp/rsd/example/trains.b

+:-modeh(1,train(+train)).   % main key
+:-modeb(1,hasCar(+train,-car)).
+:-modeb(1,carshape(+car,-car_shape)).
+:-modeb(1,instantiate(+car_shape)). % a constant value should be considered for this var when generating features
+:-modeb(1,carlength(+car,-car_length)).
+:-modeb(1,instantiate(+car_length)). % a constant value should be considered for this var when generating features
+:-modeb(1,has_sides(+car,-sides)).
+:-modeb(1,instantiate(+sides)). % a constant value should be considered for this var when generating features
+:-modeb(1,has_roof(+car,-roof)).
+:-modeb(1,instantiate(+roof)). % a constant value should be considered for this var when generating features
+:-modeb(1,has_wheels(+car,-wheels)).
+:-modeb(1,instantiate(+wheels)). % a constant value should be considered for this var when generating features
+:-modeb(1,has_load(+car,-load)).
+:-modeb(1,loadshape(+load,-load_shape)).
+:-modeb(1,instantiate(+load_shape)).  % a constant value should be considered for this var when generating features
+:-modeb(1,loadnum(+load,-load_num)).
+:-modeb(1,instantiate(+load_num)).  % a constant value should be considered for this var when generating features
+
+%:-modeb(1,notSame(+car,+car)).
+
+% settings considered by "featurize.pl":
+% ... none - all default
+
+% settings considered by "process.pl"
+% ... none - all default
+
+% settings considered by "rules.pl"
+:-set(eval_threshold,0.01).
+:-set(sig_threshold,0).  % chi^2 value threshold does not make sense with 20 train instances -> therefore 0
+
+hasCar(Train,Car):-
+    my_member(Car,Train).
+
+carshape(c(_,S,_,_,_,_,_),S).
+
+carlength(c(_,_,LE,_,_,_,_),LE).
+
+has_sides(c(_,_,_,SD,_,_,_),SD).
+
+has_roof(c(_,_,_,_,R,_,_),R).
+
+has_wheels(c(_,_,_,_,_,W,_),W).
+
+has_load(c(_,_,_,_,_,_,L),L).
+
+loadshape(l(LS,_),LS).
+
+loadnum(l(_,LN),LN).

workflows/ilp/rsd/example/trains.pl

+
+% 20 Eastbound and Westbound trains
+
+train(east,[c(1,rectangle,short,not_double,none,2,l(circle,1)),c(2,rectangle,
+	long,not_double,none,3,l(hexagon,1)),c(3,rectangle,short,
+	not_double,peaked,2,l(triangle,1)),c(4,rectangle,long,
+	not_double,none,2,l(rectangle,3))]).
+train(east,[c(1,rectangle,short,not_double,flat,2,l(circle,2)),c(2,bucket,
+	short,not_double,none,2,l(rectangle,1)),c(3,u_shaped,
+	short,not_double,none,2,l(triangle,1))]).
+train(east,[c(1,rectangle,long,not_double,flat,3,l(utriangle,1)),c(2,hexagon,
+	short,not_double,flat,2,l(triangle,1)),c(3,rectangle,
+	short,not_double,none,2,l(circle,1))]).
+train(east,[c(1,rectangle,short,not_double,none,2,l(rectangle,1)),c(2,ellipse,
+	short,not_double,arc,2,l(diamond,1)),c(3,rectangle,short,
+	double,none,2,l(triangle,1)),c(4,bucket,short,not_double,
+	none,2,l(triangle,1))]).
+train(east,[c(1,rectangle,short,not_double,flat,2,l(circle,1)),c(2,rectangle,
+	long,not_double,flat,3,l(rectangle,1)),c(3,rectangle,
+	short,double,none,2,l(triangle,1))]).
+train(east,[c(1,rectangle,long,not_double,jagged,3,l(rectangle,1)),c(2,hexagon,
+	short,not_double,flat,2,l(circle,1)),c(3,rectangle,short,
+	not_double,none,2,l(triangle,1)),c(4,rectangle,long,not_double,
+	jagged,2,l(rectangle,0))]).
+train(east,[c(1,rectangle,long,not_double,none,2,l(hexagon,1)),c(2,rectangle,
+	short,not_double,none,2,l(rectangle,1)),c(3,rectangle,
+	short,not_double,flat,2,l(triangle,1))]).
+train(east,[c(1,rectangle,short,not_double,peaked,2,l(rectangle,1)),c(2,
+	bucket,short,not_double,none,2,l(rectangle,1)),c(3,rectangle,
+	long,not_double,flat,2,l(circle,1)),c(4,rectangle,short,
+	not_double,none,2,l(rectangle,1))]).
+train(east,[c(1,rectangle,long,not_double,none,2,l(rectangle,3)),c(2,rectangle,
+	short,not_double,none,2,l(circle,1)),c(3,rectangle,long,
+	not_double,jagged,3,l(hexagon,1)),c(4,u_shaped,short,
+	not_double,none,2,l(triangle,1))]).
+train(east,[c(1,bucket,short,not_double,none,2,l(triangle,1)),c(2,u_shaped,
+	short,not_double,none,2,l(circle,1)),c(3,rectangle,short,
+	not_double,none,2,l(triangle,1)),c(4,rectangle,short,
+	not_double,none,2,l(triangle,1))]).
+train(west,[c(1,rectangle,short,not_double,none,2,l(triangle,1)),
+	c(2,rectangle, long,not_double,flat,2,l(circle,3))]).
+train(west,[c(1,rectangle,long,not_double,jagged,2,l(circle,0)),c(2,u_shaped,
+	short,not_double,none,2,l(triangle,1)),c(3,rectangle,short,
+	double,none,2,l(circle,1))]).
+train(west,[c(1,u_shaped,short,not_double,none,2,l(circle,1)),c(2,rectangle,
+	long,not_double,flat,3,l(rectangle,1))]).
+train(west,[c(1,bucket,short,not_double,none,2,l(circle,1)),c(2,rectangle,
+	short,not_double,none,2,l(rectangle,1)),c(3,rectangle,
+	long,not_double,jagged,3,l(rectangle,1)),c(4,bucket,short,
+	not_double,none,2,l(circle,1))]).
+train(west,[c(1,rectangle,long,not_double,none,2,l(rectangle,2)),c(2,u_shaped,
+