Merge branch 'dev' of workflow.ijs.si:mothra into dev

mothra/settings.py

@@ -191,6 +191,7 @@ INSTALLED_APPS_WORKFLOWS_SUB = (
     'workflows.subgroup_discovery',
     'workflows.nlp',
     'workflows.nl_toolkit',
+    'workflows.ilp',
     #WORKFLOWS_SUBAPP_PLACEHOLDER
     )
 

workflows/ilp/aleph/__init__.py

+import aleph as __aleph_pkg
+__aleph_pkg.DEBUG = False
+
+# Create an aleph instance
+runner = __aleph_pkg.Aleph()
\ No newline at end of file

workflows/ilp/aleph/aleph.py

+#
+# Python interface to Aleph.
+# 
+# author: Anze Vavpetic <anze.vavpetic@ijs.si>
+#
+import os.path
+import shutil
+import logging
+import re
+import tempfile
+from stat import *
+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 '.'
+    DIR = tempfile.mkdtemp()
+    ALEPH_FN = 'aleph.pl'
+    ALEPH = DIR + '/' + ALEPH_FN
+    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.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), Aleph.ALEPH)
+        
+    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, filestem, pos, neg, b):
+        """
+        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=Aleph.DIR, 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' % (Aleph.DIR, filestem + Aleph.RULES_SUFFIX)).read()
+
+        #shutil.copy('%s/%s.py' % (Aleph.DIR, filestem), '/home/anzev/programiranje/sdm/results/')
+        
+        # Cleanup.
+        self.__cleanup(filestem)
+        
+        return rules
+
+
+    def __prepare(self, filestem, pos, neg, b):
+        """
+        Prepares the needed files.
+        """
+        posFile = open('%s/%s.f' % (Aleph.DIR, filestem), 'w')
+        negFile = open('%s/%s.n' % (Aleph.DIR, filestem), 'w')
+        bFile = open('%s/%s.b' % (Aleph.DIR, filestem), 'w')
+
+        posFile.write(pos)
+        negFile.write(neg)
+        bFile.write(b)
+        
+        posFile.close()
+        negFile.close()
+        bFile.close()
+        
+    def __cleanup(self, filestem):
+        """
+        Cleans up all the temporary files.
+        """
+        try:
+            os.remove('%s/%s.f' % (Aleph.DIR, filestem))
+            os.remove('%s/%s.n' % (Aleph.DIR, filestem))
+            os.remove('%s/%s.b' % (Aleph.DIR, filestem))
+            os.remove('%s/%s' % (Aleph.DIR, filestem + Aleph.RULES_SUFFIX))
+            os.remove('%s/%s' % (Aleph.DIR, Aleph.SCRIPT))
+        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' % (Aleph.DIR, 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()

workflows/ilp/db/package_data.json

+[
+  {
+    "pk": 20, 
+    "model": "workflows.category", 
+    "fields": {
+      "uid": "7aba1e97-0c95-46fb-92a6-47bdf7737393",
+      "parent": null, 
+      "workflow": null, 
+      "user": null, 
+      "order": 1, 
+      "name": "Ilp"
+    }
+  }, 
+  {
+    "pk": 98, 
+    "model": "workflows.abstractwidget", 
+    "fields": {
+      "category": 20, 
+      "treeview_image": "", 
+      "name": "Create Integer List", 
+      "is_streaming": false, 
+      "uid": "fb2d0355-5553-43d8-8da4-58345687d999",
+      "interaction_view": "", 
+      "image": "", 
+      "package": "ilp", 
+      "static_image": "construction_work .png", 
+      "post_interact_action": "", 
+      "user": null, 
+      "visualization_view": "", 
+      "action": "ilp_create_integers", 
+      "wsdl_method": "", 
+      "wsdl": "", 
+      "interactive": false, 
+      "has_progress_bar": false, 
+      "order": 1, 
+      "description": ""
+    }
+  }, 
+  {
+    "pk": 248, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 98, 
+      "name": "Integer List String", 
+      "short_name": "str", 
+      "uid": "2b3923cf-5d05-4c60-8f54-989cc127e5a6",
+      "default": "3\r\n2\r\n1\r\n4", 
+      "required": false, 
+      "multi": false, 
+      "parameter_type": "textarea", 
+      "variable": "intStr", 
+      "parameter": true, 
+      "order": 1, 
+      "description": "Comma or new-line separated list of integers"
+    }
+  }, 
+  {
+    "pk": 253, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 98, 
+      "name": "Sort list", 
+      "short_name": "bol", 
+      "uid": "a8860f91-114d-4b75-996b-d20fc3e604bf",
+      "default": "true", 
+      "required": true, 
+      "multi": false, 
+      "parameter_type": "checkbox", 
+      "variable": "sort", 
+      "parameter": true, 
+      "order": 2, 
+      "description": "Should the list be sorted"
+    }
+  }, 
+  {
+    "pk": 104, 
+    "model": "workflows.abstractoutput", 
+    "fields": {
+      "widget": 98, 
+      "name": "Integer List", 
+      "short_name": "lst", 
+      "variable": "intList", 
+      "uid": "fb7dd14d-0da7-48de-971f-e0f3cc4a1ca3",
+      "order": 1, 
+      "description": "List of integers"
+    }
+  }, 
+  {
+    "pk": 101, 
+    "model": "workflows.abstractwidget", 
+    "fields": {
+      "category": 20, 
+      "treeview_image": "", 
+      "name": "Filter Integers", 
+      "is_streaming": false, 
+      "uid": "efbe15e1-aa17-4ecd-8022-9213a2f23ce0",
+      "interaction_view": "ilp_filter_integers", 
+      "image": "", 
+      "package": "ilp", 
+      "static_image": "construction_work .png", 
+      "post_interact_action": "ilp_post_filter_integers", 
+      "user": null, 
+      "visualization_view": "", 
+      "action": "ilp_pre_filter_integers", 
+      "wsdl_method": "", 
+      "wsdl": "", 
+      "interactive": true, 
+      "has_progress_bar": false, 
+      "order": 2, 
+      "description": ""
+    }
+  }, 
+  {
+    "pk": 250, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 101, 
+      "name": "Integer List", 
+      "short_name": "lst", 
+      "uid": "3eab7307-bb3c-442c-8b0c-e7f02843693c",
+      "default": "", 
+      "required": true, 
+      "multi": false, 
+      "parameter_type": null, 
+      "variable": "intList", 
+      "parameter": false, 
+      "order": 1, 
+      "description": "List of integers"
+    }
+  }, 
+  {
+    "pk": 106, 
+    "model": "workflows.abstractoutput", 
+    "fields": {
+      "widget": 101, 
+      "name": "Filtered Integer List", 
+      "short_name": "lst", 
+      "variable": "intList", 
+      "uid": "4231bb99-97c6-4d49-938d-c36c4d139d50",
+      "order": 1, 
+      "description": "Filtered list of integers"
+    }
+  }, 
+  {
+    "pk": 99, 
+    "model": "workflows.abstractwidget", 
+    "fields": {
+      "category": 20, 
+      "treeview_image": "", 
+      "name": "Sum Integers", 
+      "is_streaming": false, 
+      "uid": "17f89247-5e30-4999-983c-e97e8a1bd5a0",
+      "interaction_view": "", 
+      "image": "", 
+      "package": "ilp", 
+      "static_image": "construction_work .png", 
+      "post_interact_action": "", 
+      "user": null, 
+      "visualization_view": "", 
+      "action": "ilp_sum_integers", 
+      "wsdl_method": "", 
+      "wsdl": "", 
+      "interactive": false, 
+      "has_progress_bar": false, 
+      "order": 3, 
+      "description": ""
+    }
+  }, 
+  {
+    "pk": 249, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 99, 
+      "name": "Integer List", 
+      "short_name": "lst", 
+      "uid": "e6413cd1-61ff-4a15-8953-109139d6e174",
+      "default": "", 
+      "required": true, 
+      "multi": false, 
+      "parameter_type": null, 
+      "variable": "intList", 
+      "parameter": false, 
+      "order": 1, 
+      "description": "List of integers"
+    }
+  }, 
+  {
+    "pk": 105, 
+    "model": "workflows.abstractoutput", 
+    "fields": {
+      "widget": 99, 
+      "name": "Sum", 
+      "short_name": "int", 
+      "variable": "sum", 
+      "uid": "c3b89344-96c8-4e45-8dbb-82bc67ba9c4f",
+      "order": 1, 
+      "description": "Sum of integer list"
+    }
+  }, 
+  {
+    "pk": 100, 
+    "model": "workflows.abstractwidget", 
+    "fields": {
+      "category": 20, 
+      "treeview_image": "", 
+      "name": "Display Summation", 
+      "is_streaming": false, 
+      "uid": "5497f9f3-6eec-4d10-992b-3b809bf2d1dd",
+      "interaction_view": "", 
+      "image": "", 
+      "package": "ilp", 
+      "static_image": "construction_work .png", 
+      "post_interact_action": "", 
+      "user": null, 
+      "visualization_view": "ilp_display_summation", 
+      "action": "ilp_pre_display_summation", 
+      "wsdl_method": "", 
+      "wsdl": "", 
+      "interactive": false, 
+      "has_progress_bar": false, 
+      "order": 4, 
+      "description": ""
+    }
+  }, 
+  {
+    "pk": 251, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 100, 
+      "name": "Integer List", 
+      "short_name": "lst", 
+      "uid": "991d6d0e-c554-48cd-bd72-a1f3b15e139e",
+      "default": "", 
+      "required": false, 
+      "multi": false, 
+      "parameter_type": null, 
+      "variable": "intList", 
+      "parameter": false, 
+      "order": 1, 
+      "description": "List of integers"
+    }
+  }, 
+  {
+    "pk": 252, 
+    "model": "workflows.abstractinput", 
+    "fields": {
+      "widget": 100, 
+      "name": "Sum", 
+      "short_name": "int", 
+      "uid": "1d772dea-3030-4e1b-967c-2a7b221ea893",
+      "default": "", 
+      "required": false, 
+      "multi": false, 
+      "parameter_type": null, 
+      "variable": "sum", 
+      "parameter": false, 
+      "order": 2, 
+      "description": "Sum (possibly correct) of integer list"
+    }
+  }
+]
\ No newline at end of file

workflows/ilp/interaction_views.py

+from django.shortcuts import render
+
+def ilp_filter_integers(request,input_dict,output_dict,widget):
+    return render(request, 'interactions/ilp_filter_integers.html',{'widget':widget,'intList':input_dict['intList']})
\ No newline at end of file

workflows/ilp/library.py

+import re
+
+def ilp_create_integers(input_dict):
+    intStr = input_dict['intStr']
+    intList = []
+    for i in re.findall(r'\w+', intStr):
+        try:
+            intList.append(int(i))
+        except:
+            pass
+    if input_dict['sort'].lower() == "true":
+        intList.sort()
+    return {'intList':intList}
+
+def ilp_sum_integers(input_dict):
+    intList = input_dict['intList']
+    return {'sum':sum(intList)}
+
+def ilp_pre_filter_integers(input_dict):
+    return input_dict
+
+def ilp_post_filter_integers(postdata,input_dict,output_dict):
+    intListOut = postdata['intListOut']
+    intList = []
+    for i in intListOut:
+        try:
+            intList.append(int(i))
+        except:
+            pass
+    return {'intList': intList}
+
+def ilp_pre_display_summation(input_dict):
+    return {}
+
+def ilp_pre_aleph(input_dict):
+    return input_dict
+
+def ilp_post_aleph(postdata, input_dict, output_dict):
+    return {'result' : result}
\ No newline at end of file

workflows/ilp/settings.py

+import os
+
+# === STANDARD PACKAGE SETTINGS ===
+PACKAGE_ROOT = os.path.dirname(__file__)
+
+# === AUTO IMPORT OPTIONS ===
+#If auto_import_package_data is true then given data file is automatically imported when ClowdFlows project is newly deployed or refreshed from git
+AUTO_IMPORT_DB = False
+#For auto_import_package_data_replace_option description see the 'replace' option in workflows/import_package command
+AUTO_IMPORT_DB_REPLACE_OPTION = True
+#If file(s) other than ./db/package_data.json should be imported, auto_import_package_data_files should be corrected
+AUTO_IMPORT_DB_FILES = [os.path.join(PACKAGE_ROOT,'db/package_data.json')]
+

workflows/ilp/templates/interactions/ilp_filter_integers.html

+<div id="widgetinteract-{{widget.pk}}" rel="{{widget.pk}}" class="widgetinteractdialog" title="{{widget.name}} wants your input!">
+<form id="interactionform-{{widget.pk}}" name="interactionform-{{widget.pk}}">
+{% for i in intList %}
+<input type="checkbox" name="intListOut" value="{{i}}" style="display:inline;width:auto;">{{i}}<br>
+{% endfor %}
+<input type="hidden" name="widget_id" value="{{widget.pk}}">
+</form>
+</div>
\ No newline at end of file

workflows/ilp/templates/visualizations/ilp_display_integers.html

+<div id="widgetvisualization-{{widget.pk}}" rel="{{widget.pk}}" class="widgetvisualizationdialog" title="{{widget.name}} visualization">
+<div style="width:400px;font-family:monospace;">
+
+<table style="width:auto; border-collapse:collapse;">
+    {% for i in input_dict.intList %}
+        <tr style="width:auto">
+            <td style="text-align: right; width:auto; line-height: 0.5em;  padding: 2px; padding-bottom: 4px; padding-top: 0; margin:2px;">
+                {% if forloop.first %} {% else %}+{% endif %}
+            </td>
+            <td style="text-align: right; width:auto; line-height: 0.5em;  padding: 2px; padding-bottom: 4px; padding-top: 0; margin:2px;">
+                {{ i }}
+            </td>
+        </tr>
+    {% endfor %}
+    <tr style="width:auto">
+        <td style="text-align: right; width:auto; line-height: 0.5em; border-top: 1px solid black; padding: 2px; padding-top: 4px; margin:2px;">
+            =
+        </td>
+        <td style="text-align: right; width:auto; line-height: 0.5em; border-top: 1px solid black; padding: 2px;margin:2px;">
+            {{ input_dict.sum }}
+        </td>
+    </tr>
+</table>
+<br/>
+{{ check }}
+
+</div>
+</div>
\ No newline at end of file

workflows/ilp/urls.py

+from django.conf.urls.defaults import patterns, include, url
+
+urlpatterns = patterns('',
+    #url(r'^get-adc-index/widget(?P<widget_id>[0-9]+)/nx/Index.html$', 'workflows.latino.views.get_adc_index', name='get adc index'),
+    #url(r'^get-adc-index/widget(?P<widget_id>[0-9]+)/(?P<narrow_doc>n?)x/Index.html$', 'workflows.latino.views.get_adc_index', name='get adc index'),
+    #url(r'^get-adc-index/widget(?P<widget_id>[0-9]+)/(?P<narrow_doc>n?)x/Index(?P<document_id_from>[0-9]+)-(?P<document_id_to>[0-9]+).html$', 'workflows.latino.views.get_adc_index', name='get adc index'),
+    #url(r'^get-adc-index/widget(?P<widget_id>[0-9]+)/(?P<narrow_doc>n?)x/Document(?P<document_id>[0-9]+).html', 'workflows.latino.views.get_adc_page', name='get adc page'),
+)
\ No newline at end of file

workflows/ilp/visualization_views.py

+from django.shortcuts import render
+
+def ilp_display_summation(request,input_dict,output_dict,widget):
+    if sum(input_dict['intList']) == input_dict['sum']:
+        check = 'The calculation appears correct.'
+    else:
+        check = 'The calculation appears incorrect!'
+    return render(request, 'visualizations/ilp_display_integers.html',{'widget':widget,'input_dict':input_dict, 'output_dict':output_dict, 'check':check})