tricc-oo 1.0.1__py3-none-any.whl → 1.4.15__py3-none-any.whl

tricc/strategies/output/xls_form.py

@@ -1,194 +0,0 @@
-'''
-Strategy to build the skyp logic following the XLSForm way
-
-'''
-
-import datetime
-import logging
-import os
-
-import pandas as pd
-
-from tricc.converters.tricc_to_xls_form import (generate_xls_form_calculate,
-                                                generate_xls_form_condition,
-                                                generate_xls_form_relevance)
-from tricc.models.tricc import (TriccNodeActivity, check_stashed_loop,
-                          walktrhough_tricc_node_processed_stached, TriccGroup)
-from tricc.serializers.xls_form import (CHOICE_MAP, SURVEY_MAP, end_group,
-                                        generate_xls_form_export, start_group)
-from tricc.strategies.output.base_output_strategy import BaseOutPutStrategy
-
-logger = logging.getLogger('default')
-
-
-class XLSFormStrategy(BaseOutPutStrategy):
-
-    df_survey = pd.DataFrame(columns=SURVEY_MAP.keys())
-    df_calculate = pd.DataFrame(columns=SURVEY_MAP.keys())
-    df_choice = pd.DataFrame(columns=CHOICE_MAP.keys())
-    
-    
-            # add save nodes and merge nodes
-    
-    def generate_base(self,node, **kwargs):
-        return generate_xls_form_condition(node, **kwargs)
-            
-    def generate_relevance(self, node, **kwargs):
-        return  generate_xls_form_relevance(node, **kwargs)
-
-    def generate_calculate(self, node, **kwargs):
-        return generate_xls_form_calculate( node, **kwargs)
-
-
-    def __init__(self, output_path):
-        super().__init__( output_path)
-        self.do_clean()
-
-    def do_clean(self, **kwargs):
-        self.calculates= {}
-        self.used_calculates = {}
-        
-    
-    def get_kwargs(self):  
-        return { 
-            'df_survey':self.df_survey, 
-            'df_choice':self.df_choice,
-            'df_calculate':self.df_calculate
-            }  
-
-    def generate_export(self, node, **kwargs):
-        return generate_xls_form_export(node, **kwargs)
-
-    def export(self,start_pages ):
-                
-        if start_pages['main'].root.form_id is not None:
-            form_id= str(start_pages['main'].root.form_id )
-        else:
-            logger.error("form id required in the first start node")
-            exit()
-        title = start_pages['main'].root.label
-        file_name = form_id + ".xlsx"
-        # make a 'settings' tab
-        now = datetime.datetime.now()
-        version=now.strftime('%Y%m%d%H%M')
-        indx=[[1]]
-
-        settings={'form_title':title,'form_id':form_id,'version':version,'default_language':'English (en)','style':'pages'}
-        df_settings=pd.DataFrame(settings,index=indx)
-        df_settings.head()
-        
-        newpath = os.path.join(self.output_path, file_name)
-        #create a Pandas Excel writer using XlsxWriter as the engine
-        writer = pd.ExcelWriter(newpath, engine='xlsxwriter')
-        self.df_survey.to_excel(writer, sheet_name='survey',index=False)
-        self.df_choice.to_excel(writer, sheet_name='choices',index=False)
-        df_settings.to_excel(writer, sheet_name='settings',index=False)
-
-        #close the Pandas Excel writer and output the Excel file
-        #writer.save()
-
-        # run this on a windows python instance because if not then the generated xlsx file remains open
-        writer.close()
-        #writer.handles = None
-    
-    def process_export(self, start_pages,  **kwargs):
-        self.activity_export(start_pages['main'], **kwargs)
-    
-    def activity_export(self, activity, processed_nodes = [], **kwargs):
-        stashed_nodes =  []
-        # The stashed node are all the node that have all their prevnode processed but not from the same group
-        # This logic works only because the prev node are ordered by group/parent .. 
-        skip_header = 0
-        groups= {}
-        cur_group = activity
-        groups[activity.id] = 0
-        path_len = 0
-        # keep the vesrions on the group id, max version
-        start_group( cur_group=cur_group, groups=groups, **self.get_kwargs())
-        walktrhough_tricc_node_processed_stached(activity.root, self.generate_export, processed_nodes, stashed_nodes,path_len , cur_group = activity.root.group, **self.get_kwargs() )
-        end_group( cur_group =activity, groups=groups, **self.get_kwargs())
-        # we save the survey data frame
-        df_survey_final =   pd.DataFrame(columns=SURVEY_MAP.keys())
-        if len(self.df_survey)>(2+skip_header):
-            df_survey_final = self.df_survey
-        ## MANAGE STASHED NODES
-        prev_stashed_nodes = stashed_nodes.copy()
-        loop_count = 0
-        len_prev_processed_nodes = 0
-        while len(stashed_nodes)>0:
-            self.df_survey = pd.DataFrame(columns=SURVEY_MAP.keys())
-            loop_count = check_stashed_loop(stashed_nodes,prev_stashed_nodes, processed_nodes,len_prev_processed_nodes, loop_count)
-            prev_stashed_nodes = stashed_nodes.copy()
-            len_prev_processed_nodes = len(processed_nodes)   
-            if len(stashed_nodes)>0:
-                s_node = stashed_nodes.pop()
-                #while len(stashed_nodes)>0 and isinstance(s_node,TriccGroup):
-                #    s_node = stashed_nodes.pop()
-                if len(s_node.prev_nodes)>0:
-                    path_len = sorted(s_node.prev_nodes, key=lambda p_node:p_node.path_len, reverse=True )[0].path_len+1
-                if s_node.group is None:
-                    logger.error("ERROR group is none for node {}".format(s_node.get_name()))
-                start_group( cur_group =s_node.group, groups=groups, relevance= True,  **self.get_kwargs())
-                # arrange empty group
-                walktrhough_tricc_node_processed_stached(s_node, self.generate_export, processed_nodes, stashed_nodes, path_len, groups=groups,cur_group = s_node.group, **self.get_kwargs() )
-                # add end group if new node where added OR if the previous end group was removed
-                end_group( cur_group =s_node.group, groups=groups, **self.get_kwargs())
-                # if two line then empty grou
-                if len(self.df_survey)>(2+skip_header):
-                    if cur_group == s_node.group:
-                        # drop the end group (to merge)
-                        logger.debug("printing same group {}::{}::{}::{}".format(s_node.group.__class__, s_node.group.get_name(),s_node.id, s_node.group.instance))
-                        df_survey_final.drop(index=df_survey_final.index[-1], axis=0, inplace=True)
-                        self.df_survey = self.df_survey[(1+skip_header):]
-                        df_survey_final=pd.concat([df_survey_final, self.df_survey], ignore_index=True)
-
-                    else:
-                        logger.debug("printing group {}::{}::{}::{}".format(s_node.group.__class__, s_node.group.get_name(),s_node.id,s_node.group.instance))
-                        df_survey_final =pd.concat([df_survey_final, self.df_survey], ignore_index=True)
-                    cur_group = s_node.group
-                    
-
-        # add the calulate
-        
-        self.df_calculate=self.df_calculate.dropna(axis=0, subset=['calculation'])
-        df_empty_calc  = self.df_calculate[self.df_calculate['calculation'] == '']
-        self.df_calculate=self.df_calculate.drop(df_empty_calc.index)
-        self.df_survey = pd.concat([df_survey_final,self.df_calculate], ignore_index=True)
-        df_duplicate = self.df_calculate[self.df_calculate.duplicated(subset=['calculation'], keep='first')]
-        #self.df_survey=self.df_survey.drop_duplicates(subset=['name'])
-        for index, drop_calc in df_duplicate.iterrows():
-            #remove the duplicate
-            replace_name = False
-            #find the actual calcualte 
-            similar_calc =  self.df_survey[(drop_calc['calculation'] == self.df_survey['calculation']) & (self.df_survey['type'] == 'calculate')]
-            same_calc = self.df_survey[self.df_survey['name'] == drop_calc['name']]
-            if len(same_calc) > 1:
-                # check if all calc have the same name
-                if len(same_calc) == len(similar_calc):
-                    # drop all but one
-                    self.df_survey.drop(same_calc.index[1:])
-                elif len(same_calc) < len(similar_calc):
-                    self.df_survey.drop(same_calc.index)
-                    replace_name = True
-            elif len(same_calc) == 1:
-                self.df_survey.drop(similar_calc.index)
-                replace_name = True
-                
-
-            if replace_name:
-                save_calc =  self.df_survey[(drop_calc['calculation'] == self.df_survey['calculation']) & (self.df_survey['type'] == 'calculate')     ]
-                if len(save_calc) >= 1:
-                    save_calc = save_calc.iloc[0]
-                    if save_calc['name']!= drop_calc['name']:
-                        self.df_survey.replace('\$\{'+drop_calc['name']+'\}', '\$\{'+save_calc['name']+'\}', regex=True)
-                else:
-                    logger.error("duplicate reference not found for calculation: {}".format(drop_calc['calculation']))
-        for index, empty_calc in df_empty_calc.iterrows():
-                 self.df_survey.replace('\$\{'+empty_calc['name']+'\}', '1', regex=True)
-    
-        #TODO try to reinject calc to reduce complexity
-        for i,c in self.df_calculate[~self.df_calculate['name'].isin(self.df_survey['name'])].iterrows():
-            real_calc = re.find(r'^number\((.+)\)$',c['calculation'])
-            if real_calc is not None and real_calc != '':
-                self.df_survey[~self.df_survey['name']==c['name']].replace(real_calc, '\$\{'+c['name']+'\}')
-        return processed_nodes

tricc/strategies/output/xlsform_cdss.py

@@ -1,46 +0,0 @@
-from tricc.models.tricc import TriccNodeActivity
-from tricc.serializers.xls_form import (get_diagnostic_add_line,
-                                        get_diagnostic_line,
-                                        get_diagnostic_none_line,
-                                        get_diagnostic_start_group_line,
-                                        get_diagnostic_stop_group_line)
-from tricc.converters.tricc_to_xls_form import get_export_name
-from tricc.strategies.output.xls_form import XLSFormStrategy
-
-
-
-class XLSFormCDSSStrategy(XLSFormStrategy):
-
-            
-    
-    def process_export(self, start_pages,  **kwargs):
-        diags = []
-        self.activity_export(start_pages[self.processes[0]], **kwargs)
-
-        diags += self.export_diag( start_pages[self.processes[0]],  **kwargs)
-
-        # add the diag
-        self.df_survey.loc[len(self.df_survey)] = get_diagnostic_start_group_line()
-        # TODO inject flow driven diag list, the folowing fonction will fill the missing ones
-        
-        if len(diags)>0:
-            for diag in diags:
-                self.df_survey.loc[len(self.df_survey)] = get_diagnostic_line(diag)
-            self.df_survey.loc[len(self.df_survey)] = get_diagnostic_none_line(diags)
-            self.df_survey.loc[len(self.df_survey)] = get_diagnostic_add_line(diags, self.df_choice)
-            
-            self.df_survey.loc[len(self.df_survey)] = get_diagnostic_stop_group_line()
-        #TODO inject the TT flow
-        
-        
-                
-
-    def export_diag(self, activity, diags = [], **kwargs):
-        for node in activity.nodes.values():
-            if isinstance(node, TriccNodeActivity):
-                diags = self.export_diag(node, diags, **kwargs)
-            if hasattr(node, 'name') and node.name is not None:
-                if node.name.startswith('diag') and node.last\
-                    and not any([get_export_name(diag)  == get_export_name(node) for diag in diags]):
-                        diags.append(node)
-        return diags

tricc/strategies/output/xlsform_cht.py

@@ -1,106 +0,0 @@
-import datetime
-import logging
-import os
-import shutil
-
-import pandas as pd
-
-from tricc.models.lang import SingletonLangClass
-from tricc.serializers.xls_form import SURVEY_MAP
-from tricc.strategies.output.xlsform_cdss import XLSFormCDSSStrategy
-
-langs = SingletonLangClass()
-
-class XLSFormCHTStrategy(XLSFormCDSSStrategy):
-    def process_export(self, start_pages,  **kwargs):
-        
-        super().process_export( start_pages,  **kwargs)
-        cht_header = pd.DataFrame(columns=SURVEY_MAP.keys())
-        
-        
-        self.df_survey = pd.concat([self.get_cht_input(),self.df_survey[~self.df_survey['name'].isin(['select_sex','p_age_day','p_age_month','p_age_year','p_name','dob'])],self.get_cht_summary() ], ignore_index=True)
- 
-    def get_cht_input(self):
-        df_input = pd.DataFrame(columns=SURVEY_MAP.keys())
-         #[ #type, '',#name ''#label, '',#hint '',#help '',#default '',#'appearance',  '',#'constraint',  '',#'constraint_message' '',#'relevance' '',#'disabled' '',#'required' '',#'required message' '',#'read only' '',#'expression' '',#'repeat_count' ''#'image' ],
-        df_input.loc[len(df_input)] = [ 'begin group', 'inputs' ,*list(langs.get_trads('Inputs', force_dict = True).values()), *list(langs.get_trads('', force_dict = True).values()), *list(langs.get_trads('', force_dict = True).values()), '',  'field-list',  '', *list(langs.get_trads('', force_dict = True).values()), './source = "user"', '','', *list(langs.get_trads('', force_dict = True).values()) ,'', '', '', '' ]
-        df_input.loc[len(df_input)] = [  'hidden', 'source', *list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '' ]
-        df_input.loc[len(df_input)] = [  'hidden', 'source_id',*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '' ]
-        df_input.loc[len(df_input)] = [  'hidden', 'task_id' ,*list(langs.get_trads('Task ID', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '']
-        df_input.loc[len(df_input)] = [  'begin group	', 'contact' ,*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '' ]
-        df_input.loc[len(df_input)] = [  'db:person', '_id', *list(langs.get_trads('Patient ID', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', 'db-object',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '' ]
-        df_input.loc[len(df_input)] = [  'string', 'patient_id' ,*list(langs.get_trads('Medic ID', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', 'hidden',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '' ]
-        df_input.loc[len(df_input)] = [  'string', 'patient_name',*list(langs.get_trads('Patient Name', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', 'hidden',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '',  '','' ]
-        df_input.loc[len(df_input)] = [  'date', 'date_of_birth',*list(langs.get_trads('Date of birth', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', 'hidden',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '',  '','' ]
-        df_input.loc[len(df_input)] = [  'string', 'sex',*list(langs.get_trads('Patient Sex', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', 'hidden',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '',  '','' ]
-        df_input.loc[len(df_input)] = [  'end group', '' ,*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '']
-        df_input.loc[len(df_input)] = [  'end group', '' ,*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '', '', '' ]
-        df_input.loc[len(df_input)] = [  'calculate', '_id' ,*list(langs.get_trads('label', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '',  '../inputs/contact/_id', '', '' ]
-        df_input.loc[len(df_input)] = [  'calculate', 'patient_uuid' ,*list(langs.get_trads('label', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '',  '../inputs/contact/patient_id', '', '' ]
-        df_input.loc[len(df_input)] = [  'calculate', 'p_name' ,*list(langs.get_trads('label', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '../inputs/contact/patient_name', '', '' ]
-
-        df_input.loc[len(df_input)] = [  'calculate', 'p_age_day' ,*list(langs.get_trads('label', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', 'int((today()-date(${date_of_birth})))', '', '' ]
-        df_input.loc[len(df_input)] = [  'calculate', 'p_age_month' ,*list(langs.get_trads('label', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', 'int(${p_age_day} div 30.4)', '', '' ]
-        df_input.loc[len(df_input)] = [  'calculate', 'p_age_year' ,*list(langs.get_trads('label', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', 'int(${p_age_month} div 12)', '', '' ]
-        df_input.loc[len(df_input)] = [  'calculate', 'select_sex' ,*list(langs.get_trads('label', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', '../inputs/contact/sex', '', '' ]
-        df_input.loc[len(df_input)] = [  'calculate', 'dob',*list(langs.get_trads('Date of birth', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()),*list(langs.get_trads('', force_dict = True).values()), '', '',  '',  *list(langs.get_trads('', force_dict = True).values()), '', '', '', *list(langs.get_trads('', force_dict = True).values()), '', 'date(../inputs/contact/date_of_birth)',  '','' ]
-
-        
-        return df_input
-        
-    def get_cht_summary(self):
-        
-        df_summary = pd.DataFrame(columns=SURVEY_MAP.keys())
-         #[ #type, '',#name ''#label, '',#hint '',#help '',#default '',#'appearance',  '',#'constraint',  '',#'constraint_message' '',#'relevance' '',#'disabled' '',#'required' '',#'required message' '',#'read only' '',#'expression' '',#'repeat_count' ''#'image' ],
-        #df_summary.loc[len(df_summary)] = [  'begin group', 'group_summary' , 'Summary',                                  '', '', '',  'field-list summary',  '', '', '', '', '', '', '', '', '', '' ]
-        #df_summary.loc[len(df_summary)] = [  'note',        'r_patient_info', '**${patient_name}** ID: ${patient_id}',  '', '', '',  '',                    '', '', '', '', '', '', '', '', '', '' ]
-        #df_summary.loc[len(df_summary)] = [  'note',        'r_followup', 'Follow Up <i class=“fa fa-flag”></i>', '', '', '',  '',  '', '','', '', '', '', '', '', '', '' ]
-        #df_summary.loc[len(df_summary)] = [  'note',        'r_followup_note' ,'FOLLOWUP instruction', '', '', '',  '',  '', '', '','', '', '', '', '', '', '' ]
-        #df_summary.loc[len(df_summary)] = [  'end group', '' ,'', '', '', '',  '',  '', '', '', '', '', '', '', '','', '' ]
-        return df_summary
-    
-    def export(self, start_pages):
-        form_id = None
-        if start_pages[self.processes[0]].root.form_id is not None:
-            form_id= str(start_pages[self.processes[0]].root.form_id )
-        else:
-            logger.error("form id required in the first start node")
-            exit()
-        title = start_pages[self.processes[0]].root.label
-        file_name = form_id + ".xlsx"
-        # make a 'settings' tab
-        now = datetime.datetime.now()
-        version=now.strftime('%Y%m%d%H%M')
-        indx=[[1]]
-        # CHT FORCE file name to be equal to id
-        
-        newfilename = form_id + ".xlsx"
-        newpath = os.path.join(self.output_path, newfilename)
-        media_path = os.path.join(self.output_path, form_id + "-media")
-
-        settings={'form_title':title,'form_id':form_id,'version':version,'default_language':'English (en)','style':'pages'}
-        df_settings=pd.DataFrame(settings,index=indx)
-        df_settings.head()
-
-        #create a Pandas Excel writer using XlsxWriter as the engine
-        writer = pd.ExcelWriter(newpath, engine='xlsxwriter')
-        self.df_survey.to_excel(writer, sheet_name='survey',index=False)
-        self.df_choice.to_excel(writer, sheet_name='choices',index=False)
-        df_settings.to_excel(writer, sheet_name='settings',index=False)
-
-        #close the Pandas Excel writer and output the Excel file
-        #writer.save()
-
-        # run this on a windows python instance because if not then the generated xlsx file remains open
-        writer.close()
-        media_path_tmp = os.path.join(self.output_path, 'media-tmp')
-        if (os.path.isdir(media_path_tmp)):
-            if os.path.isdir(media_path): # check if it exists, because if it does, error will be raised 
-                shutil.rmtree(media_path)
-                # (later change to make folder complaint to CHT)
-            os.mkdir(media_path)
-            
-            file_names = os.listdir(media_path_tmp)
-            for file_name in file_names:
-                shutil.move(os.path.join(media_path_tmp, file_name), media_path)
-            shutil.rmtree(media_path_tmp)