tricc-oo 1.5.23__tar.gz → 1.5.24__tar.gz

{tricc_oo-1.5.23/tricc_oo.egg-info → tricc_oo-1.5.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tricc-oo
-Version: 1.5.23
+Version: 1.5.24
 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-1.5.24}/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-1.5.24}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tricc-oo"
-version = "1.5.23"
+version = "1.5.24"
 description = "Python library that converts CDSS L2 in L3"
 readme = "README.md"
 requires-python = ">=3.8"

{tricc_oo-1.5.23 → tricc_oo-1.5.24}/tests/build.py

@@ -3,6 +3,10 @@ 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.output.openmrs_form import OpenMRSStrategy
+from tricc_oo.strategies.output.fhir_form import FHIRStrategy
+from tricc_oo.strategies.output.html_form import HTMLStrategy
+
 from tricc_oo.strategies.input.drawio import DrawioStrategy
 import getopt
 import gettext

{tricc_oo-1.5.23 → tricc_oo-1.5.24}/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-1.5.23 → tricc_oo-1.5.24}/tricc_oo/models/tricc.py

@@ -404,7 +404,7 @@ class TriccNodeSelectYesNo(TriccNodeSelectOne):
     pass
 
 
-class TriccNodeAcceptDiagnostic(TriccNodeSelectOne):
+class TriccNodeAcceptDiagnostic(TriccNodeSelectYesNo):
     severity: Optional[str] = None
     priority: Union[float, int, None] = None
 

{tricc_oo-1.5.23 → tricc_oo-1.5.24}/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-1.5.23 → tricc_oo-1.5.24}/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