Dynmaps

build.txt

@@ -1 +1 @@
-build =144
+build =671

conf.json

@@ -1,8 +1,8 @@
 {
     "processor":{
-        "inputFile":"/home/delcpa/switchdrive/DHU/DHU Projects/WHO DAK/merged/xls_form_iraq_v1.xlsx",
+        "inputFile":"/home/delcpa/Development/smart-emcare-irq/input/l2/xls_form_iraq_v1.xlsx",
         "manual_content":"/home/delcpa/Development/smart-emcare/manual",
-        "outputPath":"/home/delcpa/Development/smart-emcare/input",
+        "outputPath":"/home/delcpa/Development/smart-emcare-irq/input",
         "cql_translator": "https://fhir.cql-translator.dk.swisstph-mis.ch/cql/translator",
         "mapping_translator": "https://fhir.dk.swisstph-mis.ch/matchbox/fhir/StructureMap",
         "fhirpath_validator":"https://fhirpath.dk.swisstph-mis.ch/validate",
@@ -20,7 +20,7 @@
     },
     "fhir":{
         "version": "4.0.1",
-        "lib_version": "1.0.1.rc12.build.144",
+        "lib_version": "1.0.1.rc12.build.671",
         "canonicalBase" : "https://fhir.dk.swisstph-mis.ch/matchbox/fhir/",
         "guideBase":"http://fhir.org/guides/who/emc-cds/",
         "activity":{

pyfhirsdc/converters/extensionsConverter.py

@@ -403,6 +403,7 @@ def convert_reference_to_fhirpath(expression, df_questions):
     matches = re.findall(pattern = r'(?P<op> *!?<< *| *!?= *)?"(?P<linkid>[^"]+)"(?:\.(?P<sufix>\w+))?(?P<op2> *!= *(?:true|false))?', string = str(expression))
 
     for match in matches:
+        null_or_path = None
         fpath = []
         path = ''
         Iscode = False
@@ -441,7 +442,6 @@ def convert_reference_to_fhirpath(expression, df_questions):
                 for elm in fpath:
                     path= ".repeat(item).where(linkId='{}')".format(elm) +path
                 path += ".answer"
-                null_or_path= None
                 if  len(null_or)>0:
                     null_or_path = path + ".empty() "
                 if sufix not in FHIRPATH_FUNCTION:

pyfhirsdc/converters/libraryConverter.py

@@ -334,7 +334,14 @@ def convert_reference_to_cql(cql_exp, df, list_inputs):
     for match in matches:
         replacement = "ToInteger(Coalesce({},false))".format(match[1])
         logger.debug('rework {0}  to  {1}'.format(match[0],replacement))
-        out = out.replace( match[0], replacement)
+        out = out.replace( match[0], replacement)    
+    matches = re.findall(r"= val\.",out)
+
+    # ~ required to test code against codeableconcept
+    for match in matches:
+        replacement = "~ val."
+        logger.debug('rework = val to ~ val')
+        out = out.replace( match, replacement)
     return out
 
 def get_input(profile,code,valueType,desc=''):
@@ -472,6 +479,8 @@ def writeGetObs(list_inputs):
     return ret
 
 
+
+
 def get_cql_define(name, row, expression_column, df_actions, list_inputs):
     prefix = ROW_EXPRESSIONS[expression_column]['prefix']
     cql_exp_raw = get_cql_raw_action(row['id'], row, expression_column, df_actions )

pyfhirsdc/converters/mapHelpers/custom/mHObservations.py

@@ -32,9 +32,9 @@ def get_obs_valueset_str_rules(df_valueset):
     for index, concept in df_valueset.iterrows():
         rules_main.append(
             MappingRule(
-            expression = "a where value = '{}', a.value as val".format(concept['display']),
+            expression = "a where value = '{}'".format(concept['display']),
             rules = [ MappingRule(
-                expression="val -> tgt.value = create('CodeableConcept') as cc, cc.coding = create('Coding') as c, c.code={}, c.system= '{}', tgt.status = 'final'".format(concept['code'], get_custom_codesystem_url())
+                expression="a -> tgt.value = create('CodeableConcept') as cc, cc.coding = create('Coding') as c, c.code='{}', c.system= '{}', tgt.status = 'final'".format(concept['code'], get_custom_codesystem_url())
             )])
         )
 
@@ -84,6 +84,15 @@ def get_obs_value_rules(question_id, df_questions_item,none_name):
     )])])]
 
 
+def SetObservationCodeObs(mode, profile, question_id,df_questions_item, *args):
+    if mode == 'groups':
+        none_name = args[0] if len(args)>1 else 'none'
+        code =  question_id
+        rule_name = clean_group_name(question_id)
+        return [set_generic_observation_v2( profile, rule_name, code, get_obs_value_rules(code,df_questions_item, none_name))]
+    elif mode == 'docs':
+        return get_base_obs_docs(question_id, 'Boolean', df_questions_item)    
+
 
 
 
@@ -202,26 +211,33 @@ def get_obs_bool_code_rules(question_id, df_questions_item):
  ####### SetObservationMultiple :  works only with valueset, will generate an obs for all, cancelled is not selected but for the one with value none   ###### 
 # args[0] : valueSet name
 def SetObservationMultiple(mode, profile, question_id, df_questions, *args):
-    if len(args)!= 1:
-        logger.error('SetObservation must have 1 parameters')
+    return SetObservationMultipleBase(mode, profile, question_id, df_questions, False, *args)
+
+def SetObservationMultipleConcat(mode, profile, question_id, df_questions, *args):
+    return SetObservationMultipleBase(mode, profile, question_id, df_questions, True, *args)
+
+def SetObservationMultipleBase(mode, profile, question_id, df_questions, concat, *args):   
+    if len(args)!= 1 and  len(args)!= 2 :
+        logger.error('SetObservation must have 1 or 2 parameters')
         return None
-    df_valueset = get_valueset_df(args[0], True)   
+    df_valueset = get_valueset_df(args[0], True)
+    none_code  = args[1] if  len(args) == 2 else None
     if mode == 'rules':
-        return get_base_obs_muli_rules(profile, question_id,df_questions,df_valueset)
+        return get_base_obs_muli_rules(profile, question_id,df_questions,df_valueset, none_code, concat)
     elif mode == 'groups':
-        return get_base_obs_muli_groups(profile, question_id,df_valueset)
+        return get_base_obs_muli_groups(profile, question_id,df_valueset, none_code,concat)
     elif mode == 'docs':
-        return get_docs_obs_muli(question_id,df_valueset,  df_questions)
-    
+        return get_docs_obs_muli(question_id,df_valueset,  df_questions, none_code,concat)
+
 
-def get_docs_obs_muli(question_id,df_valueset, df_questions_item):
+def get_docs_obs_muli(question_id,df_valueset, df_questions_item, none_code, concat = True):
     docs = []
     for index, row in df_valueset.iterrows():
-        if "map" in row and   pd.notna(row["map"]) and row['map'].lower().startswith('obs'):
+        if "map" in row and   pd.notna(row["map"]) and row['map'].lower().startswith('obs') and row['code'] != none_code:
             docs.append(
                 {
                     'type' : 'Observation',
-                    'code' : question_id+ "&" +  row['code'],
+                    'code' : question_id+ "&" +  row['code'] if concat else row['code'],
                     'valueType' : 'boolean',
                     'description': '{}:{}'.format(
                         df_questions_item[df_questions_item.id==question_id].iloc[0]['label'],
@@ -234,44 +250,45 @@ def get_docs_obs_muli(question_id,df_valueset, df_questions_item):
 
 
 
-def get_base_obs_muli_rules(profile, question_id,df_questions,df_valueset):
+def get_base_obs_muli_rules(profile, question_id,df_questions,df_valueset, none_code = None, concat = True):
     rules = []
-
-
+
     for index, row in df_valueset.iterrows():
         if "map" in row and   pd.notna(row["map"]) and row['map'].lower().startswith('obs'):
-            row_id = row['code']
-            code  =question_id+ "&" +  row_id
-            rule_name = clean_group_name( profile + code + 't')
-            rules.append(MappingRule(
-                expression = "src where src.item.where(linkId='{0}').answer.where(value.code = '{1}') ".format(question_id, row_id),
-                rules = [wrapin_entry_create( profile, question_id,df_questions,[MappingRule(expression = 'src then {}(src,tgt)'.format(rule_name) )])]
-            ))
 
-            rule_name = clean_group_name( profile + code+ 'f')
-            rules.append(MappingRule(
-                expression = "src where src.item.where(linkId='{0}').exists() and src.item.where(linkId='{0}').answer.where(value.code = '{1}').empty()  ".format(question_id, row_id),
-                rules = [wrapin_entry_create(profile, question_id,df_questions, [MappingRule(expression = 'src then {}(src,tgt)'.format(rule_name) )])]
-            ))
+            row_id = row['code']
+            if none_code is None or  row_id !=  none_code:
+                code  =question_id+ "&" +  row_id if concat else row_id
+                rule_name = clean_group_name( profile + code + 't')
+                rules.append(MappingRule(
+                    expression = "src where src.item.where(linkId='{0}').answer.where(value.code = '{1}') ".format(question_id, row_id),
+                    rules = [wrapin_entry_create( profile, question_id,df_questions,[MappingRule(expression = 'src then {}(src,tgt)'.format(rule_name) )])]
+                ))
+
+                rule_name = clean_group_name( profile + code+ 'f')
+                rules.append(MappingRule(
+                    expression = "src where src.item.where(linkId='{0}').exists() and src.item.where(linkId='{0}').answer.where(value.code = '{1}').empty()  ".format(question_id, row_id),
+                    rules = [wrapin_entry_create(profile, question_id,df_questions, [MappingRule(expression = 'src then {}(src,tgt)'.format(rule_name) )])]
+                ))
 
     return  rules
 
 
-def get_base_obs_muli_groups(profile, question_id,df):
+def get_base_obs_muli_groups(profile, question_id,df,none_code = None, concat = True):
     groups = []
-
     for index, row in df.iterrows():
         if "map" in row and   pd.notna(row["map"]) and row['map'].lower().startswith('obs'):
             row_id = row['code']
-            code  =question_id+ "&" +  row_id
-            rule_name = clean_group_name( profile + code + 't')
-            groups.append(
-                set_generic_observation_v2(profile, rule_name, code, [MappingRule(expression = "src -> tgt.status = 'final', tgt.value = true")],'t')
-            )
-            rule_name = clean_group_name( profile + code+ 'f')
-            groups.append(
-                set_generic_observation_v2(profile, rule_name, code, [MappingRule(expression = "src -> tgt.status = 'cancelled',tgt.value = false",)],'f')
-            )
+            if none_code is None or  row_id !=  none_code:
+                code  =question_id+ "&" +  row_id if concat else row_id
+                rule_name = clean_group_name( profile + code + 't')
+                groups.append(
+                    set_generic_observation_v2(profile, rule_name, code, [MappingRule(expression = "src -> tgt.status = 'final', tgt.value = true")],'t')
+                )
+                rule_name = clean_group_name( profile + code+ 'f')
+                groups.append(
+                    set_generic_observation_v2(profile, rule_name, code, [MappingRule(expression = "src -> tgt.status = 'cancelled',tgt.value = false",)],'f')
+                )
     return groups        
 
 def set_generic_observation_v2(profile, rule_name, code ,spe_rules, sufix = ''):
@@ -291,4 +308,5 @@ def set_generic_observation_v2(profile, rule_name, code ,spe_rules, sufix = ''):
             MappingRule(name = 'patient', expression = "src.subject as subject -> tgt.subject = subject "),
             *spe_rules
         ]
-    )
+    )
+

test/test_cql.http

@@ -3,7 +3,7 @@
 
 @rootemcare=/home/delcpa/Development/smart-emcare
 
-
+#@host=https://cloud.alphora.com/sandbox/r4/cqm/fhir
 
 POST {{host}} HTTP/1.1
 Content-Type: application/json
@@ -113,7 +113,7 @@ POST {{host}}/Library/emcarecombineddataelements/$evaluate?subject=/Patient/a122
 # emcareb23classification
 #emcareobservation
 @file = emcarebase
-@lib = emcaredt01
+@lib = emcarezscore
 PUT {{host}}/Library/{{lib}}
 content-type: application/json