--- a/utils.py	Thu Oct 11 03:29:23 2018 -0400
+++ b/utils.py	Sun Dec 30 01:50:39 2018 -0500
@@ -1,21 +1,34 @@
-import sys
+import json
+import numpy as np
 import os
 import pandas
+import pickle
 import re
-import pickle
-import warnings
-import numpy as np
-import xgboost
 import scipy
 import sklearn
+import sys
+import warnings
+import xgboost
+
 from asteval import Interpreter, make_symbol_table
-from sklearn import (cluster, decomposition, ensemble, feature_extraction, feature_selection,
-                    gaussian_process, kernel_approximation, metrics,
+from sklearn import (cluster, compose, decomposition, ensemble, feature_extraction,
+                    feature_selection, gaussian_process, kernel_approximation, metrics,
                     model_selection, naive_bayes, neighbors, pipeline, preprocessing,
                     svm, linear_model, tree, discriminant_analysis)
 
+try:
+    import skrebate
+except ModuleNotFoundError:
+    pass
+
+
 N_JOBS = int(os.environ.get('GALAXY_SLOTS', 1))
 
+try:
+    sk_whitelist
+except NameError:
+    sk_whitelist = None
+
 
 class SafePickler(pickle.Unpickler):
     """
@@ -25,6 +38,13 @@
     """
     def find_class(self, module, name):
 
+        # sk_whitelist could be read from tool
+        global sk_whitelist
+        if not sk_whitelist:
+            whitelist_file = os.path.join(os.path.dirname(__file__), 'sk_whitelist.json')
+            with open(whitelist_file, 'r') as f:
+                sk_whitelist = json.load(f)
+
         bad_names = ('and', 'as', 'assert', 'break', 'class', 'continue',
                     'def', 'del', 'elif', 'else', 'except', 'exec',
                     'finally', 'for', 'from', 'global', 'if', 'import',
@@ -46,13 +66,14 @@
                 or  (   (   module.startswith('sklearn.')
                             or module.startswith('xgboost.')
                             or module.startswith('skrebate.')
+                            or module.startswith('imblearn')
                             or module.startswith('numpy.')
                             or module == 'numpy'
                         )
                         and (name not in bad_names)
                     ):
                 # TODO: replace with a whitelist checker
-                if fullname not in sk_whitelist['SK_NAMES'] + sk_whitelist['SKR_NAMES'] + sk_whitelist['XGB_NAMES'] + sk_whitelist['NUMPY_NAMES'] + good_names:
+                if fullname not in sk_whitelist['SK_NAMES'] + sk_whitelist['SKR_NAMES'] + sk_whitelist['XGB_NAMES'] + sk_whitelist['NUMPY_NAMES'] + sk_whitelist['IMBLEARN_NAMES'] + good_names:
                     print("Warning: global %s is not in pickler whitelist yet and will loss support soon. Contact tool author or leave a message at github.com" % fullname)
                 mod = sys.modules[module]
                 return getattr(mod, name)
@@ -83,44 +104,56 @@
         return y, data
     else:
         return y
-    return y
 
 
 ## generate an instance for one of sklearn.feature_selection classes
 def feature_selector(inputs):
-    selector = inputs["selected_algorithm"]
+    selector = inputs['selected_algorithm']
     selector = getattr(sklearn.feature_selection, selector)
-    options = inputs["options"]
+    options = inputs['options']
 
     if inputs['selected_algorithm'] == 'SelectFromModel':
         if not options['threshold'] or options['threshold'] == 'None':
             options['threshold'] = None
+        else:
+            try:
+                options['threshold'] = float(options['threshold'])
+            except ValueError:
+                pass
         if inputs['model_inputter']['input_mode'] == 'prefitted':
             model_file = inputs['model_inputter']['fitted_estimator']
             with open(model_file, 'rb') as model_handler:
                 fitted_estimator = load_model(model_handler)
             new_selector = selector(fitted_estimator, prefit=True, **options)
         else:
-            estimator_json = inputs['model_inputter']["estimator_selector"]
+            estimator_json = inputs['model_inputter']['estimator_selector']
             estimator = get_estimator(estimator_json)
             new_selector = selector(estimator, **options)
 
     elif inputs['selected_algorithm'] == 'RFE':
-        estimator = get_estimator(inputs["estimator_selector"])
+        estimator = get_estimator(inputs['estimator_selector'])
+        step = options.get('step', None)
+        if step and step >= 1.0:
+            options['step'] = int(step)
         new_selector = selector(estimator, **options)
 
     elif inputs['selected_algorithm'] == 'RFECV':
         options['scoring'] = get_scoring(options['scoring'])
         options['n_jobs'] = N_JOBS
-        options['cv'] = get_cv(options['cv'].strip())
-        estimator = get_estimator(inputs["estimator_selector"])
+        splitter, groups = get_cv(options.pop('cv_selector'))
+        # TODO support group cv splitters
+        options['cv'] = splitter
+        step = options.get('step', None)
+        if step and step >= 1.0:
+            options['step'] = int(step)
+        estimator = get_estimator(inputs['estimator_selector'])
         new_selector = selector(estimator, **options)
 
-    elif inputs['selected_algorithm'] == "VarianceThreshold":
+    elif inputs['selected_algorithm'] == 'VarianceThreshold':
         new_selector = selector(**options)
 
     else:
-        score_func = inputs["score_func"]
+        score_func = inputs['score_func']
         score_func = getattr(sklearn.feature_selection, score_func)
         new_selector = selector(score_func, **options)
 
@@ -128,12 +161,12 @@
 
 
 def get_X_y(params, file1, file2):
-    input_type = params["selected_tasks"]["selected_algorithms"]["input_options"]["selected_input"]
-    if input_type == "tabular":
-        header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header1"] else None
-        column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
-        if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
-            c = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_1"]["col1"]
+    input_type = params['selected_tasks']['selected_algorithms']['input_options']['selected_input']
+    if input_type == 'tabular':
+        header = 'infer' if params['selected_tasks']['selected_algorithms']['input_options']['header1'] else None
+        column_option = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_1']['selected_column_selector_option']
+        if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
+            c = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_1']['col1']
         else:
             c = None
         X = read_columns(
@@ -147,10 +180,10 @@
     else:
         X = mmread(file1)
 
-    header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None
-    column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
-    if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
-        c = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["col2"]
+    header = 'infer' if params['selected_tasks']['selected_algorithms']['input_options']['header2'] else None
+    column_option = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_2']['selected_column_selector_option2']
+    if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
+        c = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_2']['col2']
     else:
         c = None
     y = read_columns(
@@ -167,7 +200,7 @@
 
 class SafeEval(Interpreter):
 
-    def __init__(self, load_scipy=False, load_numpy=False):
+    def __init__(self, load_scipy=False, load_numpy=False, load_estimators=False):
 
         # File opening and other unneeded functions could be dropped
         unwanted = ['open', 'type', 'dir', 'id', 'str', 'repr']
@@ -199,6 +232,30 @@
             for f in from_numpy_random:
                 syms['np_random_' + f] = getattr(np.random, f)
 
+        if load_estimators:
+            estimator_table = {
+                'sklearn_svm' : getattr(sklearn, 'svm'),
+                'sklearn_tree' : getattr(sklearn, 'tree'),
+                'sklearn_ensemble' : getattr(sklearn, 'ensemble'),
+                'sklearn_neighbors' : getattr(sklearn, 'neighbors'),
+                'sklearn_naive_bayes' : getattr(sklearn, 'naive_bayes'),
+                'sklearn_linear_model' : getattr(sklearn, 'linear_model'),
+                'sklearn_cluster' : getattr(sklearn, 'cluster'),
+                'sklearn_decomposition' : getattr(sklearn, 'decomposition'),
+                'sklearn_preprocessing' : getattr(sklearn, 'preprocessing'),
+                'sklearn_feature_selection' : getattr(sklearn, 'feature_selection'),
+                'sklearn_kernel_approximation' : getattr(sklearn, 'kernel_approximation'),
+                'skrebate_ReliefF': getattr(skrebate, 'ReliefF'),
+                'skrebate_SURF': getattr(skrebate, 'SURF'),
+                'skrebate_SURFstar': getattr(skrebate, 'SURFstar'),
+                'skrebate_MultiSURF': getattr(skrebate, 'MultiSURF'),
+                'skrebate_MultiSURFstar': getattr(skrebate, 'MultiSURFstar'),
+                'skrebate_TuRF': getattr(skrebate, 'TuRF'),
+                'xgboost_XGBClassifier' : getattr(xgboost, 'XGBClassifier'),
+                'xgboost_XGBRegressor' : getattr(xgboost, 'XGBRegressor')
+            }
+            syms.update(estimator_table)
+
         for key in unwanted:
             syms.pop(key, None)
 
@@ -209,33 +266,20 @@
                                         no_raise=True, no_print=True)
 
 
-def get_search_params(params_builder):
-    search_params = {}
-    safe_eval = SafeEval(load_scipy=True, load_numpy=True)
-
-    for p in params_builder['param_set']:
-        search_p = p['search_param_selector']['search_p']
-        if search_p.strip() == '':
-            continue
-        param_type = p['search_param_selector']['selected_param_type']
-
-        lst = search_p.split(":")
-        assert (len(lst) == 2), "Error, make sure there is one and only one colon in search parameter input."
-        literal = lst[1].strip()
-        ev = safe_eval(literal)
-        if param_type == "final_estimator_p":
-            search_params["estimator__" + lst[0].strip()] = ev
-        else:
-            search_params["preprocessing_" + param_type[5:6] + "__" + lst[0].strip()] = ev
-
-    return search_params
-
 
 def get_estimator(estimator_json):
+
     estimator_module = estimator_json['selected_module']
+
+    if estimator_module == 'customer_estimator':
+        c_estimator = estimator_json['c_estimator']
+        with open(c_estimator, 'rb') as model_handler:
+            new_model = load_model(model_handler)
+        return new_model
+
     estimator_cls = estimator_json['selected_estimator']
 
-    if estimator_module == "xgboost":
+    if estimator_module == 'xgboost':
         cls = getattr(xgboost, estimator_cls)
     else:
         module = getattr(sklearn, estimator_module)
@@ -244,7 +288,7 @@
     estimator = cls()
 
     estimator_params = estimator_json['text_params'].strip()
-    if estimator_params != "":
+    if estimator_params != '':
         try:
             params = safe_eval('dict(' + estimator_params + ')')
         except ValueError:
@@ -256,32 +300,68 @@
     return estimator
 
 
-def get_cv(literal):
-    safe_eval = SafeEval()
-    if literal == "":
-        return None
-    if literal.isdigit():
-        return int(literal)
-    m = re.match(r'^(?P<method>\w+)\((?P<args>.*)\)$', literal)
-    if m:
-        my_class = getattr(model_selection, m.group('method'))
-        args = safe_eval('dict('+ m.group('args') + ')')
-        return my_class(**args)
-    sys.exit("Unsupported CV input: %s" % literal)
+def get_cv(cv_json):
+    """
+    cv_json:
+            e.g.:
+            {
+                'selected_cv': 'StratifiedKFold',
+                'n_splits': 3,
+                'shuffle': True,
+                'random_state': 0
+            }
+    """
+    cv = cv_json.pop('selected_cv')
+    if cv == 'default':
+        return cv_json['n_splits'], None
+
+    groups = cv_json.pop('groups', None)
+    if groups:
+        groups = groups.strip()
+        if groups != '':
+            if groups.startswith('__ob__'):
+                groups = groups[6:]
+            if groups.endswith('__cb__'):
+                groups = groups[:-6]
+            groups = [int(x.strip()) for x in groups.split(',')]
+
+    for k, v in cv_json.items():
+        if v == '':
+            cv_json[k] = None
+
+    test_fold = cv_json.get('test_fold', None)
+    if test_fold:
+        if test_fold.startswith('__ob__'):
+            test_fold = test_fold[6:]
+        if test_fold.endswith('__cb__'):
+            test_fold = test_fold[:-6]
+        cv_json['test_fold'] = [int(x.strip()) for x in test_fold.split(',')]
+
+    test_size = cv_json.get('test_size', None)
+    if test_size and test_size > 1.0:
+        cv_json['test_size'] = int(test_size)
+
+    cv_class = getattr(model_selection, cv)
+    splitter = cv_class(**cv_json)
+
+    return splitter, groups
+
+
+# needed when sklearn < v0.20
+def balanced_accuracy_score(y_true, y_pred):
+    C = metrics.confusion_matrix(y_true, y_pred)
+    with np.errstate(divide='ignore', invalid='ignore'):
+        per_class = np.diag(C) / C.sum(axis=1)
+    if np.any(np.isnan(per_class)):
+        warnings.warn('y_pred contains classes not in y_true')
+        per_class = per_class[~np.isnan(per_class)]
+    score = np.mean(per_class)
+    return score
 
 
 def get_scoring(scoring_json):
-    def balanced_accuracy_score(y_true, y_pred):
-        C = metrics.confusion_matrix(y_true, y_pred)
-        with np.errstate(divide='ignore', invalid='ignore'):
-            per_class = np.diag(C) / C.sum(axis=1)
-        if np.any(np.isnan(per_class)):
-            warnings.warn('y_pred contains classes not in y_true')
-            per_class = per_class[~np.isnan(per_class)]
-        score = np.mean(per_class)
-        return score
 
-    if scoring_json['primary_scoring'] == "default":
+    if scoring_json['primary_scoring'] == 'default':
         return None
 
     my_scorers = metrics.SCORERS