tricc-oo 1.5.13__py3-none-any.whl → 1.6.8__py3-none-any.whl

tricc_oo/visitors/utils.py

@@ -1,17 +1,17 @@
 PROCESSES = [
-        "triage",
-        "emergency-care",
-        "registration",
-        "history-and-physical",
-        "local-urgent-care",
-        "acute-tertiary-care",
-        "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",
-    ]
+    "triage",
+    "emergency-care",
+    "registration",
+    "history-and-physical",
+    "local-urgent-care",
+    "acute-tertiary-care",
+    "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",
+]

tricc_oo/visitors/xform_pd.py

@@ -4,15 +4,16 @@ Created on Thu Sep  1 11:21:39 2022
 
 @author: kluera
 
-Make subforms that allow to be releoaded seperately as a 'task' in CHT, 
-allowing to simulate a pause functionality. 
+Make subforms that allow to be releoaded seperately as a 'task' in CHT,
+allowing to simulate a pause functionality.
 """
 
 import pandas as pd
-import json
+
 
 def remove_dots(s):
-     return s.replace('.','_')
+    return s.replace(".", "_")
+
 
 def chf_clean_name(s, remove_dots=False):
     # Check if there is a dot in the string
@@ -24,159 +25,161 @@ def chf_clean_name(s, remove_dots=False):
         # If no dot is present, return None or handle it as needed
         return s
 
+
 # df is the dataframe to be split
 # pausepoint is the index of the row after which the form should pause
 def make_breakpoints(df, pausepoint, calculate_name=None, replace_dots=False):
     """
     Creates a dataframe for a follow-up questionnaire while preserving previous inputs.
-    
+
     Args:
         df: Input dataframe containing the questionnaire
         pausepoint: Point where the questionnaire should pause
         calculate_name: Optional name for calculation fields
     """
-    
+
     # Get data points collected before break
-    if 'input end' not in df['name'].values:
+    if "input end" not in df["name"].values:
         raise ValueError("input end field not found in input dataframe")
-    end_inputs_loc = df.index[df['name'] == 'input end'][0]
-    next_begin_group_loc = min([i for i in df.index[df['type'] == 'begin group'] if i > end_inputs_loc])
-    next_pause_point_begin_group_loc = min([i for i in df.index[df['type'] == 'begin group'] if i > pausepoint])
-    
+    end_inputs_loc = df.index[df["name"] == "input end"][0]
+    next_begin_group_loc = min([i for i in df.index[df["type"] == "begin group"] if i > end_inputs_loc])
+    next_pause_point_begin_group_loc = min([i for i in df.index[df["type"] == "begin group"] if i > pausepoint])
+
     df_input = df.loc[next_begin_group_loc:next_pause_point_begin_group_loc]
-    
+
     # Define field types to handle
-    typesconvert = ['integer', 'decimal', 'select_', 'text']
-    typeskeep = ['hidden', 'calculate', 'string'] 
-    
+    typesconvert = ["integer", "decimal", "select_", "text"]
+    typeskeep = ["hidden", "calculate", "string"]
+
     # Create masks for filtering
-    type_mask = df_input['type'].str.contains('|'.join(typeskeep + typesconvert))
-    optin_mask = ~df_input['name'].str.contains('more_info_optin', na=False)
-    
+    type_mask = df_input["type"].str.contains("|".join(typeskeep + typesconvert))
+    optin_mask = ~df_input["name"].str.contains("more_info_optin", na=False)
+
     # Filter dataframe keeping important fields
     df_input = df_input.loc[type_mask & optin_mask]
-    
+
     # Preserve existing hidden fields and their calculations
-    existing_hidden = df_input[df_input['type'] == 'hidden'].copy()
-    
+    existing_hidden = df_input[df_input["type"] == "hidden"].copy()
+
     # Convert specified types to hidden while preserving their data
-    mask_indices = df_input.index[df_input['type'].str.contains('|'.join(typesconvert))]
+    mask_indices = df_input.index[df_input["type"].str.contains("|".join(typesconvert))]
     # Get hidden field names
 
-    df_input.loc[mask_indices, 'type'] = 'hidden'
-    df_input.loc[mask_indices, 'appearance'] = 'hidden'    
+    df_input.loc[mask_indices, "type"] = "hidden"
+    df_input.loc[mask_indices, "appearance"] = "hidden"
 
     # Handle label columns while preserving existing labels where needed
-    label_cols = [col for col in df.columns if 'label' in col]
-    df_input.loc[mask_indices, label_cols] = 'NO_LABEL'
-    
+    label_cols = [col for col in df.columns if "label" in col]
+    df_input.loc[mask_indices, label_cols] = "NO_LABEL"
+
     # Clear non-essential columns while preserving crucial data
-    essential_cols = ['name', 'type', 'calculation'] + label_cols
+    essential_cols = ["name", "type", "calculation"] + label_cols
     other_cols = df_input.columns.drop(essential_cols)
-    df_input[other_cols] = ''
-    
+    df_input[other_cols] = ""
+
     # Preserve calculations for existing hidden fields
-    df_input.update(existing_hidden[['calculation']])
+    df_input.update(existing_hidden[["calculation"]])
     # SAVE THE INPUT NAMES
-    hidden_names = list(df_input.loc[df_input['type']=='hidden', 'name'])
+    hidden_names = list(df_input.loc[df_input["type"] == "hidden", "name"])
     if replace_dots:
-        df_input['name'] = df_input['name'].map(remove_dots)
+        df_input["name"] = df_input["name"].map(remove_dots)
     # Handle indexing and grouping
     df_input.index = df_input.index.map(str)
-    hidden_ids = df_input.loc[df_input['type']=='hidden'].index
-    inputs_group_index = '0'
-    new_hidden_ids = inputs_group_index + '.' + hidden_ids
-    
+    hidden_ids = df_input.loc[df_input["type"] == "hidden"].index
+    inputs_group_index = "0"
+    new_hidden_ids = inputs_group_index + "." + hidden_ids
+
     # Update indices
     index_map = dict(zip(hidden_ids, new_hidden_ids))
     df_input.rename(index=index_map, inplace=True)
     df_input.sort_index(inplace=True)
     df_input.reset_index(drop=True, inplace=True)
-    
+
     if remove_dots:
         # Precompute replacement dictionary
-        replacement_dict = {f'${old_name}': f'${remove_dots(old_name)}' for old_name in hidden_names if '.' in old_name}
+        replacement_dict = {f"${old_name}": f"${remove_dots(old_name)}" for old_name in hidden_names if "." in old_name}
 
         # Apply replacements to entire DataFrame
         df_input = df_input.astype(str).replace(replacement_dict, regex=False)
-    
 
- 
-    
-    
-# put all together
-    if 'data_load' not in df['name'].values:
+    # put all together
+    if "data_load" not in df["name"].values:
         raise ValueError("data_load field not found in input dataframe")
-    data_load_loc = df.index[df['name'] == 'data_load'][0]
-    
+    data_load_loc = df.index[df["name"] == "data_load"][0]
+
     # Split the dataframe into three parts
     df_before_data_load = df.loc[:data_load_loc]  # Everything up to data_load
-    df_until_begin_group = df.loc[data_load_loc+1:next_begin_group_loc-1]  # From data_load to next begin_group
-    
+    df_until_begin_group = df.loc[data_load_loc + 1: next_begin_group_loc - 1]  # From data_load to next begin_group
+
     # Reset indices for proper concatenation
     df_input = df_input.reset_index(drop=True)
     df_before_data_load = df_before_data_load.reset_index(drop=True)
     df_until_begin_group = df_until_begin_group.reset_index(drop=True)
-    
+
     # Concatenate in the correct order
-    df_combined = pd.concat([
-        df_before_data_load,  # First part until data_load
-        df_input,            # Injected converted fields
-        df_until_begin_group # Remaining part until next begin_group
-    ]).reset_index(drop=True)
-    
+    df_combined = pd.concat(
+        [
+            df_before_data_load,  # First part until data_load
+            df_input,  # Injected converted fields
+            df_until_begin_group,  # Remaining part until next begin_group
+        ]
+    ).reset_index(drop=True)
+
     # Handle post-break section
     df_after = df.loc[next_pause_point_begin_group_loc:].reset_index(drop=True)
 
-    
     # Final concatenation
     final_df = pd.concat([df_combined, df_after])
     if calculate_name:
-        final_df.loc[final_df['name']=='hidden','calculation']='0'
-    
-    final_df.fillna('', inplace=True)
+        final_df.loc[final_df["name"] == "hidden", "calculation"] = "0"
+
+    final_df.fillna("", inplace=True)
     final_df.reset_index(inplace=True, drop=True)
-    
-    return final_df, hidden_names
 
+    return final_df, hidden_names
 
 
 def get_tasksstrings(hidden_names, df_survey):
-    '''This function makes a list of strings of hidden fields that will be loaded into a form that continues the consultation. 
-    This is very handy as this string must be pasted into the tasks.js file in CHT. 
+    """This function makes a list of strings of hidden fields that will be loaded
+    into a form that continues the consultation.
+    This is very handy as this string must be pasted into the tasks.js file in CHT.
     @hidden_names: are the names of the 'hidden' fields in the input group of the follow up form
     @df_survey: is the survey tab of the complete (original) form without breaks, going from A to Z
-    @tasks_strings: is the string that has to be pasted into tasks.js'''
-    
+    @tasks_strings: is the string that has to be pasted into tasks.js"""
+
     task_string_template = "content['{variableName}'] = getField(report, '{full_path}')"
     task_strings = {}
     for s in hidden_names:
-        df_above_s = df_survey.iloc[:df_survey.loc[df_survey['name']==s].index[0]]
-        df_above_s_groups = df_above_s.loc[df_above_s['type'].isin(['begin group', 'end group'])]
+        df_above_s = df_survey.iloc[: df_survey.loc[df_survey["name"] == s].index[0]]
+        df_above_s_groups = df_above_s.loc[df_above_s["type"].isin(["begin group", "end group"])]
         above_s_grouprows = df_above_s_groups.index
         fullpath = []
         for i in above_s_grouprows:
-            if df_above_s.iloc[i]['type']=='begin group':
-                fullpath.append(df_above_s.iloc[i]['name'])
-            else: 
+            if df_above_s.iloc[i]["type"] == "begin group":
+                fullpath.append(df_above_s.iloc[i]["name"])
+            else:
                 fullpath = fullpath[:-1]
-        if len(fullpath)>0:
-            line = task_string_template.format(
-                variableName=s, full_path='.'.join(fullpath) + chf_clean_name(s)
-            )
+        if len(fullpath) > 0:
+            line = task_string_template.format(variableName=s, full_path=".".join(fullpath) + chf_clean_name(s))
         else:
-            line = task_string_template.format(
-                variableName=s, full_path=chf_clean_name(s)
-            )
-        task_strings[s]=line
-    return  list(task_strings.values())
-
-
-def get_task_js(form_id, calculate_name, title, form_types, hidden_names, df_survey, repalce_dots=False, task_title="'id: '+getField(report, 'g_registration.p_id')+'; age: '+getField(report, 'p_age')+getField(report, 'g_registration.p_gender')+' months; '+getField(report, 'p_weight') + 'kg; ' + getField(report, 'g_fever.p_temp')+'°'"):
+            line = task_string_template.format(variableName=s, full_path=chf_clean_name(s))
+        task_strings[s] = line
+    return list(task_strings.values())
+
+
+def get_task_js(
+    form_id,
+    calculate_name,
+    title,
+    form_types,
+    hidden_names,
+    df_survey,
+    repalce_dots=False,
+    task_title="id: '+getField(report, 'g_registration.p_id')+';age: '+getField(report, 'p_age')+getField(report, 'g_registration.p_gender')+' months; '+getField(report, 'p_weight') + 'kg; ' + getField(report, 'g_fever.p_temp')+'°'",  # noqa: E501
+):
     task_name = f"{form_id}"
     task_name_upper = task_name.upper()
 
-    
     return f"""
 /* eslint-disable no-use-before-define */
 /* eslint-disable */
@@ -185,7 +188,7 @@ const {{injectDataFromForm, isFormArrayHasSourceId}} = require('./stph-extras');
 const {{getField}} = require("./nools-extras");
 
 const CASE_DATA = ['{"','".join(hidden_names)}'];
-    
+
 
 const {task_name_upper}_FORMS = ['{"','".join(form_types)}'];
 
@@ -195,7 +198,7 @@ const {task_name_upper}_TASK_FORM = '{form_id}';
 
 const {task_name}Content =  function (content, contact, report){{
 
-  injectDataFromForm(content, '', CASE_DATA, {task_name_upper}_FORMS, [report], {'true' if repalce_dots else  'false'});
+  injectDataFromForm(content, '', CASE_DATA, {task_name_upper}_FORMS, [report], {'true' if repalce_dots else 'false'});
   content['patient_id'] = report.contact._id;
   content['source_id'] = report._id;
   console.log(content);
@@ -230,7 +233,7 @@ module.exports = {{
   {task_name}ResolveIf,
   {task_name}AppliesIf,
 }}
-// 
+//
 //// to be copied in task
 //
 //const {{
@@ -238,7 +241,7 @@ module.exports = {{
 //  {task_name_upper}_FORMS,
 //  {task_name}Content,
 //  {task_name}ContactLabel,
-//  {task_name}ResolveIf, 
+//  {task_name}ResolveIf,
 //  {task_name}AppliesIf, }} = require('./{task_name}');
 //
 //module.exports = [
@@ -270,4 +273,3 @@ module.exports = {{
 //    }}
 //];
 """
-

{tricc_oo-1.5.13.dist-info → tricc_oo-1.6.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tricc-oo
-Version: 1.5.13
+Version: 1.6.8
 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
@@ -9,6 +9,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+License-File: LICENSE
 Requires-Dist: lxml
 Requires-Dist: markdownify
 Requires-Dist: pydantic
@@ -23,8 +24,133 @@ Requires-Dist: antlr4-python3-runtime==4.13.2
 Requires-Dist: antlr4-tools==0.2.1
 Requires-Dist: beautifulsoup4
 Requires-Dist: ocldev
+Requires-Dist: pyxform
+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
 
@@ -131,90 +257,8 @@ 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-1.6.8.dist-info/RECORD

@@ -0,0 +1,52 @@
+tests/build.py,sha256=Qbxvjkj_Wk2nQ-WjaMGiE1FIe3SRmJMRIgeoMoxqlfQ,6748
+tests/test_build.py,sha256=5t8iliPe_0XwoZjSGkHxUbZaNOWBfc6SpIQijh9DLUA,10037
+tests/test_cql.py,sha256=dAsLMqVaS6qxnq62fg5KqTFu6UG6pHO6Ab3NZ1c9T3Y,5248
+tests/to_ocl.py,sha256=4e-i65K3UM6wHgdVcrZcM9AyL1bahIsXJiZTXhhHgQk,2048
+tricc_oo/__init__.py,sha256=oWCE1ubmC_6iqaWOMgTei4eXVQgV202Ia-tXS1NnW_4,139
+tricc_oo/converters/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tricc_oo/converters/codesystem_to_ocl.py,sha256=Fh7Vk73OsxljZKu1k6H9uzYwz334tpQTMZBjWWbamYE,6151
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