tricc-oo 1.5.23__py3-none-any.whl → 1.5.25__py3-none-any.whl

tests/build.py

@@ -1,16 +1,17 @@
-from tricc_oo.strategies.output.spice import SpiceStrategy
-from tricc_oo.strategies.output.xlsform_cht_hf import XLSFormCHTHFStrategy
-from tricc_oo.strategies.output.xlsform_cht import XLSFormCHTStrategy
-from tricc_oo.strategies.output.xlsform_cdss import XLSFormCDSSStrategy
-from tricc_oo.strategies.output.xls_form import XLSFormStrategy
-from tricc_oo.strategies.input.drawio import DrawioStrategy
+from tricc_oo.strategies.output.spice import SpiceStrategy  # noqa: F401
+from tricc_oo.strategies.output.xlsform_cht_hf import XLSFormCHTHFStrategy  # noqa: F401
+from tricc_oo.strategies.output.xlsform_cht import XLSFormCHTStrategy  # noqa: F401
+from tricc_oo.strategies.output.xlsform_cdss import XLSFormCDSSStrategy  # noqa: F401
+from tricc_oo.strategies.output.xls_form import XLSFormStrategy  # noqa: F401
+from tricc_oo.strategies.output.openmrs_form import OpenMRSStrategy  # noqa: F401
+from tricc_oo.strategies.output.fhir_form import FHIRStrategy  # noqa: F401
+from tricc_oo.strategies.output.html_form import HTMLStrategy  # noqa: F401
+from tricc_oo.strategies.input.drawio import DrawioStrategy  # noqa: F401
 import getopt
-import gettext
 import logging
 import os
 import sys
 import gc
-import shutil
 from pathlib import Path
 
 # set up logging to file
@@ -39,15 +40,15 @@ def setup_logger(
     level=logging.INFO,
     formatting="[%(asctime)s] {%(pathname)s:%(lineno)d} %(levelname)s - %(message)s",
 ):
-    l = logging.getLogger(logger_name)
+    logger = logging.getLogger(logger_name)
     formatter = logging.Formatter(formatting)
     file_handler = logging.FileHandler(log_file, mode="w+")
     file_handler.setFormatter(formatter)
     stream_handler = logging.StreamHandler()
     stream_handler.setFormatter(formatter)
 
-    l.setLevel(level)
-    l.addHandler(file_handler)
+    logger.setLevel(level)
+    logger.addHandler(file_handler)
 
 
 class ColorFormatter(logging.Formatter):

tests/test_cql.py

@@ -53,9 +53,9 @@ class TestCql(unittest.TestCase):
 
     def test_case(self):
         case_cql = """
-        case AgeInMonths() 
-        when 0 then 'newborn' 
-        when 1 then 'newborn' 
+        case AgeInMonths()
+        when 0 then 'newborn'
+        when 1 then 'newborn'
         else 'child' end
         """
         case_operation = transform_cql_to_operation(case_cql)
@@ -72,7 +72,7 @@ class TestCql(unittest.TestCase):
 
     def test_ifs(self):
         case_cql = """
-        case 
+        case
         when AgeInMonths() <= 2 then true
         when AgeInYears() > 5 then true
         else false end

tricc_oo/converters/datadictionnary.py

@@ -6,9 +6,13 @@ from fhir.resources.codesystem import (
 
 from fhir.resources.valueset import ValueSet
 import logging
+import uuid
 
 logger = logging.getLogger("default")
 
+# Namespace for deterministic UUIDs
+UUID_NAMESPACE = uuid.UUID('12345678-1234-5678-9abc-def012345678')
+
 
 def lookup_codesystems_code(codesystems, ref):
     if ref.startswith("final."):
@@ -83,7 +87,8 @@ def check_and_add_concept(code_system: CodeSystem, code: str, display: str, attr
             new_concept = concept
     if not new_concept:
         # Add the new concept if it does not exist
-        new_concept = CodeSystemConcept.construct(code=code, display=display)
+        concept_id = str(uuid.uuid5(UUID_NAMESPACE, display))
+        new_concept = CodeSystemConcept.construct(code=code, display=display, id=concept_id)
         if not hasattr(code_system, "concept"):
             code_system.concept = []
         code_system.concept.append(new_concept)

tricc_oo/converters/tricc_to_xls_form.py

@@ -1,8 +1,9 @@
 import logging
-from tricc_oo.converters.utils import clean_name
-from tricc_oo.models.tricc import TriccNodeSelectOption
+from tricc_oo.converters.utils import clean_name, clean_str
+from tricc_oo.models.tricc import TriccNodeSelectOption, TRICC_TRUE_VALUE, TRICC_FALSE_VALUE
 from tricc_oo.models.calculate import TriccNodeInput
-from tricc_oo.models.base import TriccNodeBaseModel
+from tricc_oo.models.base import TriccNodeBaseModel, TriccStatic, TriccReference
+
 # from babel import _
 
 # TRICC_SELECT_MULTIPLE_CALC_EXPRESSION = "count-selected(${{{0}}}) - number(selected(${{{0}}},'opt_none'))"
@@ -18,6 +19,10 @@ TRICC_NEGATE = "not({})"
 # TRICC_AND_EXPRESSION = '{0} and {1}'
 VERSION_SEPARATOR = "_Vv_"
 INSTANCE_SEPARATOR = "_Ii_"
+BOOLEAN_MAP = {
+    str(TRICC_TRUE_VALUE): 1,
+    str(TRICC_FALSE_VALUE): 0,
+}
 
 
 logger = logging.getLogger("default")
@@ -26,9 +31,36 @@ logger = logging.getLogger("default")
 
 
 def get_export_name(node, replace_dots=True):
-    if isinstance(node, str):
-        return clean_name(node, replace_dots=replace_dots)
-    if node.export_name is None:
+    if hasattr(node, 'export_name') and node.export_name is not None:
+        return node.export_name
+    elif isinstance(node, bool):
+        return BOOLEAN_MAP[str(TRICC_TRUE_VALUE)] if node else BOOLEAN_MAP[str(TRICC_FALSE_VALUE)]
+    elif isinstance(node, TriccReference):
+        logger.warning(f"Reference {node.value} use in export, bad serialiuation probable")
+        return str(node.value)
+    elif isinstance(node, (str, TriccStatic, TriccNodeSelectOption)):
+        if isinstance(node, TriccNodeSelectOption):
+            value = node.name
+        elif isinstance(node, TriccStatic):
+            value = node.value
+        else:
+            value = node
+        if isinstance(value, bool):  # or r.value in ('true', 'false')
+            export_name = BOOLEAN_MAP[str(TRICC_TRUE_VALUE)] if value else BOOLEAN_MAP[str(TRICC_FALSE_VALUE)]
+        elif value == TRICC_TRUE_VALUE:
+            export_name = BOOLEAN_MAP[str(TRICC_TRUE_VALUE)]
+        elif value == TRICC_FALSE_VALUE:
+            export_name = BOOLEAN_MAP[str(TRICC_FALSE_VALUE)]
+        elif isinstance(value, str):
+            export_name = f"'{clean_str(value, replace_dots=replace_dots)}'"
+        else:
+            export_name = str(value)
+        if hasattr(node, 'export_name'):
+            node.export_name = export_name
+        return export_name
+    elif not hasattr(node, 'export_name'):
+        return node
+    else:
         node.gen_name()
         if isinstance(node, TriccNodeSelectOption):
             node.export_name = node.name
@@ -41,8 +73,7 @@ def get_export_name(node, replace_dots=True):
             node.export_name = clean_name("load." + node.name, replace_dots=replace_dots)
         else:
             node.export_name = clean_name(node.name, replace_dots=replace_dots)
-
-    return node.export_name
+        return node.export_name
 
 
 def get_list_names(list):

tricc_oo/converters/utils.py

@@ -23,7 +23,7 @@ def clean_str(name, replace_dots=False):
 
 def clean_name(name, prefix="", replace_dots=False):
     name = clean_str(name, replace_dots)
-    if name[0].isdigit():
+    if name and name[0].isdigit():
         name = "id_" + name
     elif name[0].isdigit() == "_":
         name = name[1:]

tricc_oo/models/tricc.py

@@ -15,6 +15,8 @@ import logging
 
 
 logger = logging.getLogger(__name__)
+TRICC_TRUE_VALUE = "true"
+TRICC_FALSE_VALUE = "false"
 
 
 class TriccNodeCalculateBase(TriccNodeBaseModel):
@@ -404,7 +406,7 @@ class TriccNodeSelectYesNo(TriccNodeSelectOne):
     pass
 
 
-class TriccNodeAcceptDiagnostic(TriccNodeSelectOne):
+class TriccNodeAcceptDiagnostic(TriccNodeSelectYesNo):
     severity: Optional[str] = None
     priority: Union[float, int, None] = None
 

tricc_oo/serializers/xls_form.py

@@ -3,7 +3,7 @@ import hashlib
 
 # from bs4 import BeautifulSoup
 from tricc_oo.converters.tricc_to_xls_form import (
-    get_export_name,
+    get_export_name, BOOLEAN_MAP
 )
 from tricc_oo.models.lang import SingletonLangClass
 from tricc_oo.converters.utils import clean_name, remove_html
@@ -13,7 +13,6 @@ from tricc_oo.models.base import (
 )
 from tricc_oo.models.calculate import (
     TriccNodeDisplayCalculateBase,
-
 )
 from tricc_oo.models.tricc import (
     TriccNodeActivity, TriccNodeBaseModel, TriccNodeSelectMultiple, TriccNodeSelectOption,
@@ -29,8 +28,6 @@ from tricc_oo.visitors.tricc import (
     is_ready_to_process,
     process_reference,
     add_calculate,
-    TRICC_TRUE_VALUE,
-    TRICC_FALSE_VALUE,
     get_applicability_expression,
     get_prev_instance_skip_expression,
     get_process_skip_expression,
@@ -41,11 +38,6 @@ logger = logging.getLogger("default")
 langs = SingletonLangClass()
 TRICC_CALC_EXPRESSION = "${{{0}}}>0"
 
-BOOLEAN_MAP = {
-    str(TRICC_TRUE_VALUE): 1,
-    str(TRICC_FALSE_VALUE): 0,
-}
-
 
 def start_group(
     strategy,

tricc_oo/strategies/input/drawio.py

@@ -3,7 +3,7 @@ import os
 
 from tricc_oo.converters.xml_to_tricc import create_activity
 from tricc_oo.visitors.tricc import (
-    process_calculate,
+    load_calculate,
     set_prev_next_node,
     replace_node,
     stashed_node_func,
@@ -47,7 +47,7 @@ class DrawioStrategy(BaseInputStrategy):
         # add save nodes and merge nodes
         stashed_node_func(
             start_page.root,
-            process_calculate,
+            load_calculate,
             used_calculates=used_calculates,
             calculates=calculates,
             recursive=False,

tricc_oo/strategies/output/base_output_strategy.py

@@ -83,6 +83,7 @@ class BaseOutPutStrategy:
     # node function
     @abc.abstractmethod
     def generate_calculate(self, node, **kwargs):
+        # called to generate the calculates on the project
         pass
 
     @abc.abstractmethod
@@ -91,10 +92,14 @@ class BaseOutPutStrategy:
 
     @abc.abstractmethod
     def generate_relevance(self, node, **kwargs):
+        # called to generate the references on the project
+
         pass
 
     @abc.abstractmethod
     def generate_export(self, node, **kwargs):
+        # called to the project export
+
         pass
 
     @abc.abstractmethod
@@ -102,87 +107,116 @@ class BaseOutPutStrategy:
         pass
 
     def tricc_operation_equal(self, ref_expressions):
+        # r[0] = r[1]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_not_equal(self, ref_expressions):
+        # r[0] != r[1]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_not(self, ref_expressions):
+        # !r[0]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_and(self, ref_expressions):
+        # r[0] and r[1] ... and r[n]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_or(self, ref_expressions):
+        # r[0] or r[1] ... or r[n]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_or_and(self, ref_expressions):
+        # (r[0] or r[1] ... or r[n-1]) and r[n]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_native(self, ref_expressions):
+        # r[0](*r[1:])
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_istrue(self, ref_expressions):
+        # r[0] is true
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_isfalse(self, ref_expressions):
+        # r[0] is false
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_selected(self, ref_expressions):
+        # for choice question (single or multiple) it returns true if the second reference is selected
+        # r[1] in r[0]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_more_or_equal(self, ref_expressions):
+        # r[0] >= r[1]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_less_or_equal(self, ref_expressions):
+        # r[0] <= r[1]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_more(self, ref_expressions):
+        # r[0] > r[1]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_less(self, ref_expressions):
+        # r[0] < r[1]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_between(self, ref_expressions):
+        # r[0] between r[1] and r[2]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_case(self, ref_expressions):
+        # case r[0] when r[1][0] then r[1][1] ...  when r[n-1][0] then r[n-1][1] else (r[n] or None)
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_if(self, ref_expressions):
+        # if r[0][0] then r[0][1] ... elif r[n-1][0] then r[n-1][1] else (r[n] or None)
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_contains(self, ref_expressions):
+        # r[0] contains r[1]
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_exists(self, ref_expressions):
+        # r[0] exists
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_has_qualifier(self, ref_expressions):
+        # r[0] is a class and has r[1] qualifier
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_zscore(self, ref_expressions):
+        # FIXME zscore((gender=r[0], Xfy=r[1], xfY=r[2])
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_datetime_to_decimal(self, ref_expressions):
+        # cast r[0] in decimal
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_round(self, ref_expressions):
+        # round(r[0], r[1])
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_izscore(self, ref_expressions):
+        # FIXME izscore(gender=r[0], Z=r[1], xfY=r[2])
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_age_day(self, ref_expressions):
+        # Patient age in day
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_age_month(self, ref_expressions):
+        # Patient age in Month
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_age_year(self, ref_expressions):
+        # Patient age in Years
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     def tricc_operation_concatenate(self, ref_expressions):
+        # concatenate(*r)
         raise NotImplementedError("This type of opreration  is not supported in this strategy")
 
     # Utils