new version of verification process,date assignment problem solved

flame/documentation.py

@@ -401,149 +401,146 @@ def dumpYAML (self):
 
         return (yaml_out)
 
-    def dumpExcel (self,oname):
-
-            # openpyxl should be installed in the environment
-            # pip install openpyxl
-
-            from openpyxl import Workbook
-            from openpyxl.styles import Font,NamedStyle,Alignment
-            # from openpyxl.comments import Comment
-
-            wb = Workbook() 
-            ws = wb.active 
-            ws.title = f"Model {self.model} documentation" 
-            alignment_style = Alignment(vertical='top',wrapText=True)
-
-            # Label Style
-            Label = NamedStyle(name="Label")
-            Label.font = Font(name='Calibri',size=11,bold=True)
-            Label.alignment = alignment_style
-
-            ws.column_dimensions['A'].width = 25.10
-            ws.column_dimensions['B'].width = 28.00
-            ws.column_dimensions['C'].width = 60.00
-            ws.column_dimensions['D'].width = 60.00
+    def dumpExcel(self,oname):
+
 
-            # sections of the document, specifying the document keys which will be listed
-            sections = [('General model information',['ID', 'Version', 'Model_title', 'Model_description', 'Keywords', 'Contact', 'Institution', 'Date', 'Endpoint',
-                        'Endpoint_units', 'Interpretation', 'Dependent_variable', 'Species',
-                        'Limits_applicability', 'Experimental_protocol', 'Model_availability',
-                        'Data_info']), 
-                        ('Algorithm and software',['Algorithm', 'Software', 'Descriptors', 'Algorithm_settings',
-                        'AD_method', 'AD_parameters', 'Goodness_of_fit_statistics',
-                        'Internal_validation_1', 'Internal_validation_2', 'External_validation',
-                        'Comments']),
-                        ('Other information',['Other_related_models', 'Date_of_QMRF', 'Date_of_QMRF_updates',
-                        'QMRF_updates', 'References', 'QMRF_same_models', 'Mechanistic_basis', 
-                        'Mechanistic_references', 'Supporting_information', 'Comment_on_the_endpoint',
-                        'Endpoint_data_quality_and_variability', 'Descriptor_selection'])]
+        # openpyxl should be installed in the environment
+        # pip install openpyxl
 
-            #Save the position and name of the label for the first and last section
-            position = []
-            name = [sections[0][1][0],'Other Comments']
-
-            count = 1
-            for isection in sections:
+        from openpyxl import Workbook
+        from openpyxl.styles import Font,NamedStyle,Alignment
 
-                for ik in isection[1]:
-
-                    label_k = ik.replace('_',' ')
+        wb = Workbook()
+        ws = wb.active
+        ws.title = f"Model {self.model} documentation"
+        alignment_style = Alignment(vertical='top',wrapText=True)
 
-                    if label_k == 'Internal validation 2' or label_k == 'External validation':
-                        ws[f"A{count}"] = label_k
-                        ws[f'A{count}'].style = Label
-                    else:
-                        ws[f"B{count}"] = label_k
-                        ws[f"B{count}"].style = Label
-
-                    if ik in self.fields:
-                        # set defaults for value
-                        ivalue= ''
-                        #v is the selected entry in the documentation dictionary
-                        v = self.fields[ik]
+        # Label Style
+        Label = NamedStyle(name="Label")
+        Label.font = Font(name='Calibri',size=11,bold=True)
+        Label.alignment = alignment_style
+
+        ws.column_dimensions['A'].width = 25.10
+        ws.column_dimensions['B'].width = 28.00
+        ws.column_dimensions['C'].width = 60.00
+        ws.column_dimensions['D'].width = 60.00
+
+        # sections of the document, specifying the document keys which will be listed
+        sections = [('General model information',['ID', 'Version', 'Model_title', 'Model_description', 'Keywords', 'Contact', 'Institution', 'Date', 'Endpoint',
+                    'Endpoint_units', 'Interpretation', 'Dependent_variable', 'Species',
+                    'Limits_applicability', 'Experimental_protocol', 'Model_availability',
+                    'Data_info']), 
+                    ('Algorithm and software',['Algorithm', 'Software', 'Descriptors', 'Algorithm_settings',
+                    'AD_method', 'AD_parameters', 'Goodness_of_fit_statistics',
+                    'Internal_validation_1', 'Internal_validation_2', 'External_validation',
+                    'Comments']),
+                    ('Other information',['Other_related_models', 'Date_of_QMRF', 'Date_of_QMRF_updates',
+                    'QMRF_updates', 'References', 'QMRF_same_models', 'Mechanistic_basis', 
+                    'Mechanistic_references', 'Supporting_information', 'Comment_on_the_endpoint',
+                    'Endpoint_data_quality_and_variability', 'Descriptor_selection'])]
+
+        #Save the position and name of the label for the first and last section
+        position = []
+        name = [sections[0][1][0],'Other Comments']
+
+        count = 1
+        for isection in sections:
+
+            for ik in isection[1]:
+
+                label_k = ik.replace('_',' ')
+
+                if label_k in ['Internal validation 2', 'External validation']:
+                    ws[f"A{count}"] = label_k
+                    ws[f'A{count}'].style = Label
+                else:
+                    ws[f"B{count}"] = label_k
+                    ws[f"B{count}"].style = Label
+
+                if ik in self.fields:
+                    # set defaults for value
+                    ivalue= ''
+                    #v is the selected entry in the documentation dictionary
+                    v = self.fields[ik]
                         ## newest parameter formats are extended and contain
                         ## rich metainformation for each entry
-                        if 'value' in v:
-                            ivalue = v['value']
-
-                            if isinstance(ivalue,dict):
+                    if 'value' in v:
+                        ivalue = v['value']
 
-                                ws[f"A{count}"] = label_k
-                                ws[f"A{count}"].style = Label
-
-                                end = (count)+(len(ivalue)-1)
-
-                                for intk in ivalue:
-                                    label_ik = intk.replace('_',' ')
-                                    # label_ik = intk.replace('_f', '').replace('_', ' ')
-                                    ws[f'B{count}'] = label_ik
-                                    ws[f'B{count}'].style = Label
-
-
+                        if isinstance(ivalue,dict):
+
+                            ws[f"A{count}"] = label_k
+                            ws[f"A{count}"].style = Label
+
+                            end = (count)+(len(ivalue)-1)
+
+                            for intk in ivalue:
+                                label_ik = intk.replace('_',' ')
+                                # label_ik = intk.replace('_f', '').replace('_', ' ')
+                                ws[f'B{count}'] = label_ik
+                                ws[f'B{count}'].style = Label
+
+
+                                intv = ivalue[intk]
+                                if not isinstance(intv,dict):
+
+                                    iivalue = intv
+                                    if iivalue is None:
+                                        iivalue = " "
+                                else:
                                     intv = ivalue[intk]
-                                    if not isinstance(intv,dict):
-
-                                        iivalue = intv
-                                        if iivalue is None:
-                                            iivalue = " "
-                                    else:
-                                        intv = ivalue[intk]
+                                    iivalue = ''
+                                    if 'value' in intv:
+                                        iivalue = intv["value"]
+                                    if iivalue is None:
                                         iivalue = ''
-                                        if 'value' in intv:
-                                            iivalue = intv["value"]
-                                        if iivalue is None:
-                                            iivalue = ''
-
-                                        ws[f'D{count}'] = intv['description']
-                                        ws[f'D{count}'].alignment = alignment_style
-
-
-                                    ws[f'C{count}'] = f'{str(iivalue)}'
-                                    ws[f'C{count}'].font = Font(name='Calibri',size=11,color='3465a4')
-                                    ws[f'C{count}'].alignment = alignment_style
-
-                                    ws.merge_cells(f'A{count}:A{end}')
-
-                                    count +=1
-
-                            else:
 
-                                ws[f'D{count}'] = v['description']
-                                ws[f'D{count}'].alignment = alignment_style
+                                    ws[f'D{count}'] = intv['description']
+                                    ws[f'D{count}'].alignment = alignment_style
 
-                                if label_k == 'Experimental protocol' or label_k == 'Comments':
-                                    position.append(count)
-
-                                if ivalue is None:
-                                    ivalue = ''
 
-                                ws[f'C{count}'] = f'{str(ivalue)}'
+                                ws[f'C{count}'] = f'{str(iivalue)}'
                                 ws[f'C{count}'].font = Font(name='Calibri',size=11,color='3465a4')
                                 ws[f'C{count}'].alignment = alignment_style
 
-
-                                count += 1
-
-            itr = 0
-            for i in position:
-                if itr == 0:    
-                    ws[f'A{1}'] = name[itr]
-                    ws[f"A{1}"].style = Label
-                    ws.merge_cells(f'A{1}:A{i}')
-                else:
-                    ws[f'A{i}'] = name[itr]
-                    ws[f"A{i}"].style = Label
-                    ws.merge_cells(f'A{i}:A{count-1}')
+                                ws.merge_cells(f'A{count}:A{end}')
 
-                itr +=1
+                                count +=1
 
-            try:    
-                wb.save(oname)
-            except:
-                return False, f'error saving document as {oname}'
-
-            return True, 'OK'
+                        else:
+
+                            ws[f'D{count}'] = v['description']
+                            ws[f'D{count}'].alignment = alignment_style
+
+                            if label_k in ['Experimental protocol', 'Comments']:
+                                position.append(count)
+
+                            if ivalue is None:
+                                ivalue = ''
+
+                            ws[f'C{count}'] = f'{str(ivalue)}'
+                            ws[f'C{count}'].font = Font(name='Calibri',size=11,color='3465a4')
+                            ws[f'C{count}'].alignment = alignment_style
+
+
+                            count += 1
+
+        for itr, i in enumerate(position):
+            if itr == 0:    
+                ws['A1'] = name[itr]
+                ws['A1'].style = Label
+                ws.merge_cells(f'A1:A{i}')
+            else:
+                ws[f'A{i}'] = name[itr]
+                ws[f"A{i}"].style = Label
+                ws.merge_cells(f'A{i}:A{count-1}')
+
+        try:    
+            wb.save(oname)
+        except:
+            return False, f'error saving document as {oname}'
+
+        return True, 'OK'
 
     def dumpWORD (self, oname):
 
@@ -1069,27 +1066,31 @@ def empty_fields(self):
                         intv = ivalue[intk]
                         if not isinstance(intv,dict):
                             iivalue = intv
-                            if iivalue is None or len(str(iivalue)) is 0:
+                            if iivalue is None or not str(iivalue):
                                 emptyfields.append(intk)
 
                         else:
                             intv = ivalue[intk]
                             iivalue = ''
-                            if intv["value"] is None or len(str(intv["value"])) is 0:
+                            if intv["value"] is None or not str(intv["value"]):
                                 emptyfields.append(intk)
-                  
+
                 else:
-                     if ivalue is None or len(str(ivalue)) is 0:
+                    if ivalue is None or not str(ivalue):
                         emptyfields.append(ik)
-                        
+
         return emptyfields
 
-    def get_mols(self):
+    def get_smiles(self):
+        ''''''
 
-        return dict(zip(self.conveyor.getVal("obj_nam"),self.conveyor.getVal("SMILES")))
-
-
-
+        #dict(zip(self.conveyor.getVal("obj_nam"),self.conveyor.getVal("SMILES")))
+        return self.conveyor.getVal("SMILES")
+
+    def get_names(self):
+        ''''''
+        return self.conveyor.getVal("obj_nam")
+
     def autocomplete_documentation(self):
         """
         Auto complete fields in model documentation
@@ -1101,8 +1102,11 @@ def autocomplete_documentation(self):
         #Date, Date of model development and Date of QMRF.
         today = date.today().strftime("%B %d, %Y")
 
-        self.fields['Date']['value'] = today
-        self.fields['Date_of_QMRF']['value'] = today
+        if not self.fields['Date']['value']:
+            self.fields['Date']['value'] = today
+
+        if not self.fields['Date_of_QMRF']['value']:
+            self.fields['Date_of_QMRF']['value'] = today
 
         #format, Format used(SDF,TSV)
         if self.parameters.getVal('input_type') == 'data':
@@ -1116,10 +1120,7 @@ def autocomplete_documentation(self):
         fieldsapplysoftware = ['model','descriptors','applicability_domain']
 
         for field in fieldsapplysoftware:
-            if field == 'applicability_domain':
-                if self.parameters.getVal('conformal'):
-                    self.fields['Software']['value'][field]['value'] = software
-            else:
+            if field == 'applicability_domain' and self.parameters.getVal('conformal') or field != 'applicability_domain':
                 self.fields['Software']['value'][field]['value'] = software
 
 

flame/util/utils.py

@@ -22,7 +22,7 @@
 
 __modules__ = None
 
-import os
+import os 
 import sys
 import yaml
 import random
@@ -33,8 +33,10 @@
 import codecs
 import string
 import re 
-
 from flame.util import get_logger
+#from knowledgehub.api import KnowledgeHubAPI
+
+
 
 LOG = get_logger(__name__)
 
@@ -463,4 +465,4 @@ def isFingerprint (md):
         if md in fplist:
             return True
 
-    return False 
+    return False