tricc-oo 1.0.2__py3-none-any.whl → 1.4.16__py3-none-any.whl

tricc_oo/visitors/utils.py

@@ -0,0 +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",
+    ]

tricc_oo/visitors/xform_pd.py

@@ -0,0 +1,264 @@
+# -*- coding: utf-8 -*-
+"""
+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. 
+"""
+
+import pandas as pd
+import json
+
+def remove_dots(s):
+     return s.replace('.','_')
+
+def chf_clean_name(s, remove_dots=False):
+    # Check if there is a dot in the string
+    if remove_dots:
+        return remove_dots(s)
+    elif "." in s:
+        return f'["{s}"]'
+    else:
+        # 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:
+        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])
+        
+    df_input = df.loc[next_begin_group_loc:pausepoint]
+    
+    # Define field types to handle
+    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)
+    
+    # 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()
+    
+    # Convert specified types to hidden while preserving their data
+    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'    
+
+    # 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'
+    
+    # Clear non-essential columns while preserving crucial data
+    essential_cols = ['name', 'type', 'calculation'] + label_cols
+    other_cols = df_input.columns.drop(essential_cols)
+    df_input[other_cols] = ''
+    
+    # Preserve calculations for existing hidden fields
+    df_input.update(existing_hidden[['calculation']])
+    # SAVE THE INPUT NAMES
+    hidden_names = list(df_input.loc[df_input['type']=='hidden', 'name'])
+    if replace_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
+    
+    # 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}
+
+        # 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:
+        raise ValueError("data_load field not found in input dataframe")
+    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
+    
+    # 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)
+    
+    # Handle post-break section
+    df_after = df.loc[pausepoint+1:].reset_index(drop=True)
+    if df_after.iloc[0,0] == 'end group':
+        df_after = df_after.iloc[1:]
+    
+    # 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.reset_index(inplace=True, drop=True)
+    
+    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. 
+    @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'''
+    
+    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'])]
+        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: 
+                fullpath = fullpath[:-1]
+        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')+'°'"):
+    task_name = f"{form_id}_{calculate_name}"
+    task_name_upper = task_name.upper()
+
+    
+    return f"""
+/* eslint-disable no-use-before-define */
+/* eslint-disable */
+
+const {{injectDataFromForm, isFormArrayHasSourceId}} = require('./stph-extras'); -> isFormArrayHasSourceId was missing from the imports
+
+const CASE_DATA = ['{"','".join(hidden_names)}'];
+    
+const {{injectDataFromForm}} = require('./stph-extras');
+
+const {task_name_upper}_FORMS = ['{"','".join(form_types)}'];
+
+var task_title = "{task_title}"
+
+const {task_name_upper}_TASK_FORM = '{form_id}_{calculate_name}';
+
+const {task_name}Content =  function (content, contact, report){{
+
+  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);
+  console.log(report);
+}};
+//TODO: redirect after task
+/*function navigateToTask() {{
+      Router.navigate(['first'])
+}}*/
+
+
+function {task_name}ContactLabel (){{
+  task_title;
+}}
+
+
+function {task_name}ResolveIf(contact, report, event, dueDate) {{
+  return isFormArrayHasSourceId( report, contact.reports, event, dueDate, {task_name_upper}_TASK_FORMS);
+}}
+
+
+module.exports = {{
+  {task_name_upper}_TASK_FORM,
+  {task_name_upper}_FORMS,
+  {task_name}Content,
+  {task_name}ContactLabel,
+  {task_name}ResolveIf,
+}}
+// 
+//// to be copied in task
+//
+//const {{
+//  {task_name_upper}_TASK_FORM,
+//  {task_name_upper}_FORMS,
+//  {task_name}Content,
+//  {task_name}ContactLabel,
+//  {task_name}ResolveIf, }} = require('./{task_name}');
+//
+//module.exports = [
+//
+//    {{
+//        name: '{task_name}',
+//        icon: 'icon-healthcare-diagnosis',
+//        title: 'diagnostic',
+//        appliesTo: 'reports',
+//        appliesToType: {task_name_upper}_FORMS,
+//        actions: [
+//            {{
+//                type: 'report',
+//                form: {task_name_upper}_TASK_FORM,
+//                modifyContent: {task_name}Content
+//            }}
+//        ],
+//        events: [
+//            {{
+//                id: '{task_name}',
+//                days: 0,
+//                start: 1,
+//                end: 0
+//            }}
+//        ],
+//        resolvedIf: {task_name}ResolveIf
+//    }}
+//];
+"""
+

tricc_oo-1.4.16.dist-info/METADATA

@@ -0,0 +1,219 @@
+Metadata-Version: 2.4
+Name: tricc-oo
+Version: 1.4.16
+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
+Keywords: xlsform,drawio,authoring
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: lxml
+Requires-Dist: markdownify
+Requires-Dist: pydantic
+Requires-Dist: babel
+Requires-Dist: xlsxwriter
+Requires-Dist: pandas
+Requires-Dist: polib
+Requires-Dist: strenum
+Requires-Dist: fhir.resources
+Requires-Dist: antlr4-python3-runtime==4.13.2
+Requires-Dist: antlr4-tools==0.2.1
+Requires-Dist: beautifulsoup4
+Requires-Dist: ocldev
+
+# design  rules tricc_oo
+
+## Nodes
+
+## Node Types and Properties
+
+**Start Node**
+This node type represents the beginning of a process. It requires a label and can have attributes like process, parent, and form_id.
+
+**Activity Start Node**
+Marking the start of an activity, this node type needs both a label and a name. It can have attributes such as parent and instance.
+
+**Note Nodes**
+This node type are used for providing  information. Note nodes require both a label and a name,.
+
+**Selection Nodes**
+There are three types of selection nodes:
+- Select One: For single-choice selections
+- Select Multiple: For multiple-choice selections
+- Select Yes/No: For binary choices
+
+All these nodes require a label, name, and list_name. They can have attributes like required, save, filter, constraint, and constraint_message.
+
+**Numeric Input Nodes**
+Decimal and Integer nodes are used for numeric input. They require a label and name, and can have attributes like min, max, constraint, save, constraint_message, and required. 
+
+**Text and Date Nodes**
+These nodes are for text input and date selection. Both require a label and name.
+
+**Calculation Nodes**
+Add, Count, and Calculate nodes are used for various calculations. They require a label and name, and can have save and expression attributes
+
+**Flow Control Nodes**
+Rhombus and Wait nodes are used for flow control. They require a reference, name, and label, and can have save and expression attributes. 
+
+**Exclusive Node**
+This node type doesn't have any mandatory attributes or specific attributes defined.
+
+**Not Available Node**
+Used to indicate unavailability, this node requires a label, name, and list_name.
+
+**Link Nodes**
+Link Out and Link In nodes are used for creating connections. Link Out requires a reference, label, and name, while Link In only needs a label and name. 
+
+**Go To Node**
+This node is used for navigation. It requires a link, label, and name, and can have an instance attribute. 
+
+**End Nodes**
+End and Activity End nodes mark the conclusion of processes or activities.
+
+**Bridge Node**
+This node can have a label attribute but doesn't have any mandatory attributes. 
+
+**Diagnosis Node**
+Used for diagnostic purposes, this node requires a name and label
+
+### Enrichment
+
+Node can be enriched with message and media, simply add the media on the draw.io andlink them with an edge
+
+**Image Node**
+Used to add image to a question
+
+**Hint Message Node**
+Used to add an hint message to a question, need a label
+
+**Help Message Node**
+Used to add an help message to a question, need a label
+
+## Attributes
+
+**expression**
+replace the calcualte deducted by inputs
+
+**default**
+not supported yet
+
+**save**
+will create a calculate with the same name
+- obs: observation: save the option as a calcualte obs_[name of the option]
+  - can be written obs.[othername].[snomedCode]
+- diag: diagnostic/classification save the option as a calcualte diag_[name of the option]
+- flag: calculate save the option as a calcualte is_[name of the option]
+
+
+## Edges
+
+The edge are in general labeless unless for :
+    - after a select multiple: can setup quick rhombus for the number of choice selected, an opperator is required (<>=) in the edge label
+    - after a yes/no quesiton:  'Yes', 'No', 'Follow' (translation can be added in the code )
+    - before a calculate to put weight: integer only
+
+
+# notes
+
+## advanced interpretation of the edges:
+
+Activity instances: if there is more that 1 instance of a single actity then the 1+ activity will be displayed only if the previous one were not, to do that the GoTO node are replaced by a path and a rombhus, the path got to the activitvy and rhombus and the next node (if any) are attached to the rhombus that is use to wait that the activity
+
+the node following an 1+ activity will be display after the activy OR instead of the activity
+
+Select multiple: if followed by a calculate (rhombus included) the calculate will be equal to the number of selected option BUT opt_none
+if not a calculate then relevance will be used unless it is "required" then condition will be at least 1 selection
+
+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-1.4.16.dist-info/RECORD

@@ -0,0 +1,46 @@
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+tricc_oo/visitors/tricc.py,sha256=rkF2GxTS-GQbo9a9lLv8_mS4bkd5tdmMDGfou1gPFMo,95347
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+tricc_oo-1.4.16.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
+tricc_oo-1.4.16.dist-info/top_level.txt,sha256=NvbfMNAiy9m4b1unBsqpeOQWh4IgA1Xa33BtKA4abxk,15
+tricc_oo-1.4.16.dist-info/RECORD,,

{tricc_oo-1.0.2.dist-info → tricc_oo-1.4.16.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (80.3.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tricc_oo-1.4.16.dist-info/top_level.txt

@@ -0,0 +1,2 @@
+tests
+tricc_oo