fixed package structures for the following packages: nlp, decision support,...

fixed package structures for the following packages: nlp, decision support, subgroup discovery, bioinformatics.

mothra/settings.py

@@ -171,6 +171,10 @@ if USE_CONCURRENCY:
         'south',
         'workflows',
         'workflows.latino',
+        'workflows.decision_support',
+        'workflows.bioinformatics',
+        'workflows.subgroup_discovery',
+        'workflows.nlp',
         'website',
         'signuplogin',
         'django_extensions',
@@ -190,6 +194,7 @@ else:
         'south',
         'workflows',
         'workflows.latino',
+        'workflows.decision_support',
         'website',
         'signuplogin',
         'django_extensions',

workflows/bioinformatics/settings.py

+import os
+
+package_name = 'bioinformatics'
+
+package_root = os.path.dirname(__file__)
+package_statics = os.path.join(os.path.dirname(__file__), 'static', package_name)
+package_bin = os.path.join(package_root, 'bin')
+
+auto_update_db = True
+create_backups = True
+

workflows/decision_support/settings.py

+import os
+
+package_name = 'decision_support'
+
+package_root = os.path.dirname(__file__)
+package_statics = os.path.join(os.path.dirname(__file__), 'static', package_name)
+package_bin = os.path.join(package_root, 'bin')
+
+auto_update_db = True
+create_backups = True
+

workflows/interaction_views.py

 import sys
 from django.shortcuts import render
-from decision_support.interaction import *
-from subgroup_discovery.interaction import *
 
 from workflows import packageLibImporter
 def setattr_local(name, value, package):

workflows/library.py

 from workflows.security import safeOpen
-import nlp
 import cPickle
 import json
 import sys
-from decision_support.library import *
-from subgroup_discovery.library import *
 
 from workflows import packageLibImporter
 def setattr_local(name, value, package):
@@ -807,47 +804,6 @@ def odt_to_arff(input_dict):
     f = toARFFstring(input_dict['odt'])
     output_dict['arff'] = f.getvalue()
     return output_dict  
-             
-# NLP tools
-
-def merge_sentences(input_dict):
-    """
-    Merges the input sentences in XML according to the specified method.
-    """
-    method = input_dict['method']
-    merged_sen, id_to_sent = set(), {}
-    ids_list = []
-    for sentsXML in input_dict['sentences']:
-        sents = nlp.parse_def_sentences(sentsXML)
-        ids = set(map(lambda x: x['id'], sents))
-        ids_list.append(ids)
-        # Save the map from id to sentence
-        for sent in sents:
-            id_to_sent[sent['id']] = sent
-        if len(merged_sen) == 0:
-            merged_sen = ids
-        if method == 'union':
-            merged_sen = merged_sen | ids
-        elif method == 'intersection':
-            merged_sen = merged_sen & ids
-        elif method == 'intersection_two':
-            for ids_alt in ids_list:
-                merged_sen = merged_sen | (ids_alt & ids)
-    return {'merged_sentences' : nlp.sentences_to_xml([id_to_sent[sid] for sid in merged_sen])}
-
-def load_corpus(input_dict):
-    '''
-    Parses an input file and encodes it in base 64.
-    '''
-    import os.path
-    import base64
-    f = safeOpen(input_dict['file'])
-    fname = os.path.basename(input_dict['file'])
-    data = base64.b64encode(f.read())
-    from services.webservice import WebService
-    ws = WebService('http://bodysnatcher.ijs.si:8092/totale?wsdl', 600)
-    response = ws.client.parseFile(fileName=fname, inFile=data)
-    return {'corpus' : response['parsedFile']}
 
 def string_to_file(input_dict):
     return {}

workflows/nlp/library.py

+import nlp
+import os.path
+import base64
+from services.webservice import WebService
+
+def merge_sentences(input_dict):
+    """
+    Merges the input sentences in XML according to the specified method.
+    """
+    method = input_dict['method']
+    merged_sen, id_to_sent = set(), {}
+    ids_list = []
+    for sentsXML in input_dict['sentences']:
+        sents = nlp.parse_def_sentences(sentsXML)
+        ids = set(map(lambda x: x['id'], sents))
+        ids_list.append(ids)
+        # Save the map from id to sentence
+        for sent in sents:
+            id_to_sent[sent['id']] = sent
+        if len(merged_sen) == 0:
+            merged_sen = ids
+        if method == 'union':
+            merged_sen = merged_sen | ids
+        elif method == 'intersection':
+            merged_sen = merged_sen & ids
+        elif method == 'intersection_two':
+            for ids_alt in ids_list:
+                merged_sen = merged_sen | (ids_alt & ids)
+    return {'merged_sentences' : nlp.sentences_to_xml([id_to_sent[sid] for sid in merged_sen])}
+
+def load_corpus(input_dict):
+    '''
+    Parses an input file and encodes it in base 64.
+    '''
+    f = safeOpen(input_dict['file'])
+    fname = os.path.basename(input_dict['file'])
+    data = base64.b64encode(f.read())
+    ws = WebService('http://bodysnatcher.ijs.si:8092/totale?wsdl', 600)
+    response = ws.client.parseFile(fileName=fname, inFile=data)
+    return {'corpus' : response['parsedFile']}

workflows/nlp/settings.py

+import os
+
+package_name = 'nlp'
+
+package_root = os.path.dirname(__file__)
+package_statics = os.path.join(os.path.dirname(__file__), 'static', package_name)
+package_bin = os.path.join(package_root, 'bin')
+
+auto_update_db = True
+create_backups = True
+