tricc-oo 1.5.23__tar.gz → 1.5.25__tar.gz

{tricc_oo-1.5.23/tricc_oo.egg-info → tricc_oo-1.5.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tricc-oo
-Version: 1.5.23
+Version: 1.5.25
 Summary: Python library that converts CDSS L2 in L3
 Project-URL: Homepage, https://github.com/SwissTPH/tricc
 Project-URL: Issues, https://github.com/SwissTPH/tricc/issues
@@ -26,7 +26,130 @@ Requires-Dist: beautifulsoup4
 Requires-Dist: ocldev
 Dynamic: license-file
 
-# design  rules tricc_oo
+# TRICC-OO
+
+
+## Strategy
+
+### XLSFormStrategy
+
+to use on OKD and clones,
+
+### XLSFormCDSSStrategy
+
+based on XLSFormStrategy
+to use on OKD and clones, 
+support the CDSS specific behaviour such as Classification management
+
+### XLSFormCHTStrategy
+
+based on XLSFormCDSSStrategy
+to use on medic CHT if the questionnaire is run Patient level
+Support the inputs from patient
+Support the extention libs
+
+### XLSFormCHTHFStrategy
+
+based on XLSFormCHTStrategy
+to use on medic CHT if the questionnaire is run on Health facility level without selecting a patient
+Support inputs from HF
+
+
+### OpenMRSStrategy
+
+(under development)
+
+### FhirStrategy
+
+(UNTESTED)
+
+### HTMLStrategy
+
+(UNTESTED)
+
+## start nodes
+
+### Main start
+
+the flow required at least 1 main start node, but in case of cdss output strategy , several could be used given that they have a 'process' atrribute
+
+here is the list of the CPG process, this will be the execution oder too:
+- **registration**,
+- **triage**,
+- **emergency-care**,
+- **local-urgent-care**,
+- **actue-tertiary-care**,
+- **history-and-physical**,
+- **diagnostic-testing**,
+- **determine-diagnosis**,
+- **provide-counseling**,
+- **dispense-medications**,
+- **monitor-and-follow-up-of-patient**,
+- **alerts-reminders-education**,
+- **discharge-referral-of-patient**,
+- **charge-for-service**,
+- **record-and-report** 
+	
+	
+
+
+# Note
+
+## generation of the expressions 
+
+### add calcualte:
+
+ - Non or No in an egde will generate a negate node
+ - save adds a calcualte
+ - a rhombus will generate a calcualte using the reference (can you the label as a test, either with comparaisin or option selected with [option label])
+
+### for calculate 
+    
+Then we calculate based on the previous nodes: [get_prev_node_expression]
+    - if a "fake" calculate (Rhombus, exclusion) then get the underlying expression (should not depend of Calcualte = true) [get_calculation_terms]
+    - if a Select, manage it as a calculate too (should not depend of Calcualte = true) [get_calculation_terms]
+    - else get the expression via  [get_calculation_terms] [get_prev_node_expression , calculate = False] -> get_node_expression for the prev node
+
+# Running directly
+
+`tricc` is technically a python library, but you can run it directly via the [`build.py` script](./tests/build.py).
+
+## Running with Docker
+
+Alternatively, if you prefer to build/run the project with Docker, you can do the following.
+
+Start by building the Docker image:
+
+```shell
+git clone https://github.com/SwissTPH/tricc.git
+cd tricc
+
+docker build -t tricc .
+```
+
+Once you have the image built you can use it to convert local `.drawio` files by mapping the local directory to the `docker run` command. (Note that `--user` is specified to make sure the current host user has write access to the output files.)
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc --help
+```
+
+This command will convert all `.drawio` files in the current directory:
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj
+```
+
+You can also convert a single file:
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj/demo.drawio -o /proj
+```
+
+Use the `-O` flag to specify the output strategy. For example to generate CHT files:
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj -O XLSFormCHTStrategy
+```
 
 ## Nodes
 
@@ -133,90 +256,8 @@ if not a calculate then relevance will be used unless it is "required" then cond
 the Rhombus act as an AND between its imputs and its reference BUT it is an OR beween the inputs
 (input1 OR input2 OR input3) AND reference
 
-## start nodes
-
-### Main start
-
-the flow required at least 1 main start node, but in case of cdss output strategy , several could be used given that they have a 'process' atrribute
-
-here is the list of the CPG process, this will be the execution oder too:
-- **registration**,
-- **triage**,
-- **emergency-care**,
-- **local-urgent-care**,
-- **actue-tertiary-care**,
-- **history-and-physical**,
-- **diagnostic-testing**,
-- **determine-diagnosis**,
-- **provide-counseling**,
-- **dispense-medications**,
-- **monitor-and-follow-up-of-patient**,
-- **alerts-reminders-education**,
-- **discharge-referral-of-patient**,
-- **charge-for-service**,
-- **record-and-report** 
-	
-	
 # READ Xressource
 https://jgraph.github.io/drawio-tools/tools/convert.html
 
 option can have only incoming edge from images to be placed as option$
 
-
-# Note
-
-## generation of the expressions 
-
-### add calcualte:
-
- - Non or No in an egde will generate a negate node
- - save adds a calcualte
- - a rhombus will generate a calcualte using the reference (can you the label as a test, either with comparaisin or option selected with [option label])
-
-### for calculate 
-    
-Then we calculate based on the previous nodes: [get_prev_node_expression]
-    - if a "fake" calculate (Rhombus, exclusion) then get the underlying expression (should not depend of Calcualte = true) [get_calculation_terms]
-    - if a Select, manage it as a calculate too (should not depend of Calcualte = true) [get_calculation_terms]
-    - else get the expression via  [get_calculation_terms] [get_prev_node_expression , calculate = False] -> get_node_expression for the prev node
-
-# Running directly
-
-`tricc` is technically a python library, but you can run it directly via the [`build.py` script](./tests/build.py).
-
-## Running with Docker
-
-Alternatively, if you prefer to build/run the project with Docker, you can do the following.
-
-Start by building the Docker image:
-
-```shell
-git clone https://github.com/SwissTPH/tricc.git
-cd tricc
-
-docker build -t tricc .
-```
-
-Once you have the image built you can use it to convert local `.drawio` files by mapping the local directory to the `docker run` command. (Note that `--user` is specified to make sure the current host user has write access to the output files.)
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc --help
-```
-
-This command will convert all `.drawio` files in the current directory:
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj
-```
-
-You can also convert a single file:
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj/demo.drawio -o /proj
-```
-
-Use the `-O` flag to specify the output strategy. For example to generate CHT files:
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj -O XLSFormCHTStrategy
-```

{tricc_oo-1.5.23 → tricc_oo-1.5.25}/README.md

@@ -1,4 +1,127 @@
-# design  rules tricc_oo
+# TRICC-OO
+
+
+## Strategy
+
+### XLSFormStrategy
+
+to use on OKD and clones,
+
+### XLSFormCDSSStrategy
+
+based on XLSFormStrategy
+to use on OKD and clones, 
+support the CDSS specific behaviour such as Classification management
+
+### XLSFormCHTStrategy
+
+based on XLSFormCDSSStrategy
+to use on medic CHT if the questionnaire is run Patient level
+Support the inputs from patient
+Support the extention libs
+
+### XLSFormCHTHFStrategy
+
+based on XLSFormCHTStrategy
+to use on medic CHT if the questionnaire is run on Health facility level without selecting a patient
+Support inputs from HF
+
+
+### OpenMRSStrategy
+
+(under development)
+
+### FhirStrategy
+
+(UNTESTED)
+
+### HTMLStrategy
+
+(UNTESTED)
+
+## start nodes
+
+### Main start
+
+the flow required at least 1 main start node, but in case of cdss output strategy , several could be used given that they have a 'process' atrribute
+
+here is the list of the CPG process, this will be the execution oder too:
+- **registration**,
+- **triage**,
+- **emergency-care**,
+- **local-urgent-care**,
+- **actue-tertiary-care**,
+- **history-and-physical**,
+- **diagnostic-testing**,
+- **determine-diagnosis**,
+- **provide-counseling**,
+- **dispense-medications**,
+- **monitor-and-follow-up-of-patient**,
+- **alerts-reminders-education**,
+- **discharge-referral-of-patient**,
+- **charge-for-service**,
+- **record-and-report** 
+	
+	
+
+
+# Note
+
+## generation of the expressions 
+
+### add calcualte:
+
+ - Non or No in an egde will generate a negate node
+ - save adds a calcualte
+ - a rhombus will generate a calcualte using the reference (can you the label as a test, either with comparaisin or option selected with [option label])
+
+### for calculate 
+    
+Then we calculate based on the previous nodes: [get_prev_node_expression]
+    - if a "fake" calculate (Rhombus, exclusion) then get the underlying expression (should not depend of Calcualte = true) [get_calculation_terms]
+    - if a Select, manage it as a calculate too (should not depend of Calcualte = true) [get_calculation_terms]
+    - else get the expression via  [get_calculation_terms] [get_prev_node_expression , calculate = False] -> get_node_expression for the prev node
+
+# Running directly
+
+`tricc` is technically a python library, but you can run it directly via the [`build.py` script](./tests/build.py).
+
+## Running with Docker
+
+Alternatively, if you prefer to build/run the project with Docker, you can do the following.
+
+Start by building the Docker image:
+
+```shell
+git clone https://github.com/SwissTPH/tricc.git
+cd tricc
+
+docker build -t tricc .
+```
+
+Once you have the image built you can use it to convert local `.drawio` files by mapping the local directory to the `docker run` command. (Note that `--user` is specified to make sure the current host user has write access to the output files.)
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc --help
+```
+
+This command will convert all `.drawio` files in the current directory:
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj
+```
+
+You can also convert a single file:
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj/demo.drawio -o /proj
+```
+
+Use the `-O` flag to specify the output strategy. For example to generate CHT files:
+
+```shell
+docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj -O XLSFormCHTStrategy
+```
 
 ## Nodes
 
@@ -105,90 +228,8 @@ if not a calculate then relevance will be used unless it is "required" then cond
 the Rhombus act as an AND between its imputs and its reference BUT it is an OR beween the inputs
 (input1 OR input2 OR input3) AND reference
 
-## start nodes
-
-### Main start
-
-the flow required at least 1 main start node, but in case of cdss output strategy , several could be used given that they have a 'process' atrribute
-
-here is the list of the CPG process, this will be the execution oder too:
-- **registration**,
-- **triage**,
-- **emergency-care**,
-- **local-urgent-care**,
-- **actue-tertiary-care**,
-- **history-and-physical**,
-- **diagnostic-testing**,
-- **determine-diagnosis**,
-- **provide-counseling**,
-- **dispense-medications**,
-- **monitor-and-follow-up-of-patient**,
-- **alerts-reminders-education**,
-- **discharge-referral-of-patient**,
-- **charge-for-service**,
-- **record-and-report** 
-	
-	
 # READ Xressource
 https://jgraph.github.io/drawio-tools/tools/convert.html
 
 option can have only incoming edge from images to be placed as option$
 
-
-# Note
-
-## generation of the expressions 
-
-### add calcualte:
-
- - Non or No in an egde will generate a negate node
- - save adds a calcualte
- - a rhombus will generate a calcualte using the reference (can you the label as a test, either with comparaisin or option selected with [option label])
-
-### for calculate 
-    
-Then we calculate based on the previous nodes: [get_prev_node_expression]
-    - if a "fake" calculate (Rhombus, exclusion) then get the underlying expression (should not depend of Calcualte = true) [get_calculation_terms]
-    - if a Select, manage it as a calculate too (should not depend of Calcualte = true) [get_calculation_terms]
-    - else get the expression via  [get_calculation_terms] [get_prev_node_expression , calculate = False] -> get_node_expression for the prev node
-
-# Running directly
-
-`tricc` is technically a python library, but you can run it directly via the [`build.py` script](./tests/build.py).
-
-## Running with Docker
-
-Alternatively, if you prefer to build/run the project with Docker, you can do the following.
-
-Start by building the Docker image:
-
-```shell
-git clone https://github.com/SwissTPH/tricc.git
-cd tricc
-
-docker build -t tricc .
-```
-
-Once you have the image built you can use it to convert local `.drawio` files by mapping the local directory to the `docker run` command. (Note that `--user` is specified to make sure the current host user has write access to the output files.)
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc --help
-```
-
-This command will convert all `.drawio` files in the current directory:
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj
-```
-
-You can also convert a single file:
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj/demo.drawio -o /proj
-```
-
-Use the `-O` flag to specify the output strategy. For example to generate CHT files:
-
-```shell
-docker run --rm -v "$PWD":/proj --user $(id -u):$(id -g) tricc -i /proj -o /proj -O XLSFormCHTStrategy
-```

{tricc_oo-1.5.23 → tricc_oo-1.5.25}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tricc-oo"
-version = "1.5.23"
+version = "1.5.25"
 description = "Python library that converts CDSS L2 in L3"
 readme = "README.md"
 requires-python = ">=3.8"

{tricc_oo-1.5.23 → tricc_oo-1.5.25}/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):

{tricc_oo-1.5.23 → tricc_oo-1.5.25}/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-1.5.23 → tricc_oo-1.5.25}/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-1.5.25/tricc_oo/converters/tricc_to_xls_form.py

@@ -0,0 +1,86 @@
+import logging
+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, TriccStatic, TriccReference
+
+# from babel import _
+
+# TRICC_SELECT_MULTIPLE_CALC_EXPRESSION = "count-selected(${{{0}}}) - number(selected(${{{0}}},'opt_none'))"
+# TRICC_SELECT_MULTIPLE_CALC_NONE_EXPRESSION = "selected(${{{0}}},'opt_none')"
+# TRICC_CALC_EXPRESSION = "${{{0}}}>0"
+# TRICC_CALC_NOT_EXPRESSION = "${{{0}}}=0"
+# TRICC_EMPTY_EXPRESSION = "coalesce(${{{0}}},'') != ''"
+# TRICC_SELECTED_EXPRESSION = 'selected(${{{0}}}, "{1}")'
+# TRICC_SELECTED_NEGATE_EXPRESSION = 'count-selected(${{{0}}})>0 and not(selected(${{{0}}}, "{1}"))'
+# TRICC_REF_EXPRESSION = "${{{0}}}"
+TRICC_NEGATE = "not({})"
+# TRICC_NUMBER = "number({})"
+# 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")
+
+# gettext language dict {'code':gettext}
+
+
+def get_export_name(node, replace_dots=True):
+    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
+        elif node.last is False:
+            node.export_name = clean_name(
+                node.name + VERSION_SEPARATOR + str(node.version),
+                replace_dots=replace_dots,
+            )
+        elif isinstance(node, TriccNodeInput):
+            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
+
+
+def get_list_names(list):
+    names = []
+    for elm in list:
+        if issubclass(elm.__class__, TriccNodeBaseModel):
+            names.append(get_export_name(elm))
+        elif isinstance(elm, str):
+            names.append(elm)
+    return names

{tricc_oo-1.5.23 → tricc_oo-1.5.25}/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-1.5.23 → tricc_oo-1.5.25}/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