tricc-oo 1.4.7__tar.gz → 1.4.9__tar.gz

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.3
 Name: tricc-oo
-Version: 1.4.7
+Version: 1.4.9
 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
@@ -9,8 +9,9 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
+
 Requires-Dist: lxml
-Requires-Dist: html2text
+Requires-Dist: markdownify
 Requires-Dist: pydantic
 Requires-Dist: babel
 Requires-Dist: xlsxwriter

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tricc-oo"
-version = "1.4.7"
+version = "1.4.9"
 description = "Python library that converts CDSS L2 in L3"
 readme = "README.md"
 license-files = ["LICENSE"]
@@ -16,7 +16,7 @@ classifiers = [
 ]
 dependencies = [
     "lxml",
-    "html2text",
+    "markdownify",
     "pydantic",
     "babel",
     "xlsxwriter",

tricc_oo-1.4.9/tricc_oo/converters/utils.py

@@ -0,0 +1,65 @@
+import logging
+import re
+import random
+import string
+import hashlib
+from markdownify import markdownify as md
+
+
+logger = logging.getLogger("default")
+
+
+def replace_all(text, list_char, replacement):
+    for i in list_char:
+        text = text.replace(i, replacement)
+    return text
+
+
+def clean_str(name, replace_dots=False):
+    replacement_list = ["-", " ", ",", "."] if replace_dots else ["-", " ", ","]
+    return replace_all(name, replacement_list, "_")
+
+
+def clean_name(name, prefix="", replace_dots=False):
+    name = clean_str(name, replace_dots)
+    if name[0].isdigit():
+        name = "id_" + name
+    elif name[0].isdigit() == "_":
+        name = name[1:]
+    return name
+
+
+def generate_id(name=None, length=18):
+    if name:
+        h = hashlib.blake2b(digest_size=length)
+        h.update(name.encode("utf-8") if isinstance(name, str) else name)
+        return h.hexdigest()
+    else:
+        return "".join(
+            random.choices(
+                string.ascii_lowercase + string.digits + string.ascii_uppercase,
+                k=length,
+            )
+        )
+
+
+def get_rand_name(name=None, length=8):
+    return "n" + generate_id(name=name, length=length)
+
+
+# the soup.text strips off the html formatting also
+def remove_html(string):
+    placeholders = {}
+
+    def replace_placeholders(match):
+        key = f"__PLACEHOLDER_{len(placeholders)}__"
+        placeholders[key] = match.group(0)
+        return key
+
+    protected_text = re.sub(r"\${.*?\}", replace_placeholders, string)
+
+    text = md(protected_text, strip=["img", "table", "a"])
+
+    for key, original in placeholders.items():
+        text = text.replace(key, original)
+    return text

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo/converters/xml_to_tricc.py

@@ -29,7 +29,11 @@ TRICC_FOLLOW_LABEL = ["follow", "suivre", "continue"]
 NO_LABEL = "NO_LABEL"
 TRICC_LIST_NAME = "list_{0}"
 import logging
-
+DISPLAY_ATTRIBUTES = [
+    'label',
+    'hint',
+    'help'
+]
 logger = logging.getLogger("default")
 
 
@@ -182,7 +186,7 @@ def process_edges(diagram, media_path, activity, nodes):
             if image is not None:
                 images.append({"file_path": enriched, "image_content": image})
 
-        elif isinstance(nodes[edge.target], (TriccNodeActivityEnd, TriccNodeEnd)):
+        elif isinstance(nodes[edge.target], (TriccNodeActivityEnd)) or (isinstance(nodes[edge.target], (TriccNodeEnd)) and isinstance(activity.root, TriccNodeMainStart )):
             end_found = True
         if (
             edge.target in nodes
@@ -236,7 +240,7 @@ def process_edges(diagram, media_path, activity, nodes):
                     )
                 )
     if not end_found:
-        fake_end = TriccNodeActivityEnd(id=generate_id(), activity=activity, group=activity)
+        fake_end = TriccNodeActivityEnd(id=generate_id(f"e{activity.name}"), activity=activity, group=activity)
         last_nodes = [
             n for n in list(activity.nodes.values())
             if (
@@ -486,8 +490,9 @@ def get_max_named_version(calculates, name):
 
 
 def inject_bridge_path(node, nodes):
-    calc_id = generate_id()
-    calc_name = "path_" + calc_id
+    calc_name = "p" + node.id
+    calc_id = generate_id(calc_name)
+    
     data = {
         "id": calc_id,
         "group": node.group,
@@ -753,10 +758,12 @@ def set_mandatory_attribute(elm, mandatory_attributes, diagram=None):
             exit(1)
         if attributes == "link":
             param[attributes] = clean_link(attribute_value)
-        elif attributes in ("parent", "id", "source", "target"):
-            param[attributes] = attribute_value
+
         elif attribute_value is not None:
-            param[attributes] = remove_html(attribute_value.strip())
+            if attributes in DISPLAY_ATTRIBUTES:
+                param[attributes] = remove_html(attribute_value.strip())
+            else:
+                param[attributes] = attribute_value.strip() if isinstance(attribute_value, str) else attribute_value
     return param
 
 

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo/models/base.py

@@ -116,7 +116,7 @@ class TriccBaseModel(BaseModel):
     def make_instance(self, nb_instance, **kwargs):
         instance = self.copy()
         # change the id to avoid collision of name
-        instance.id = generate_id()
+        instance.id = generate_id(f"{self.id}{nb_instance}")
         instance.instance = int(nb_instance)
         instance.base_instance = self
 
@@ -149,7 +149,7 @@ class TriccBaseModel(BaseModel):
     
     def __init__(self, **data):
         if 'id' not in data:
-            data['id'] = generate_id()
+            data['id'] = generate_id(str(data))
         super().__init__(**data)
 
 
@@ -181,7 +181,7 @@ class TriccGroup(TriccBaseModel):
     def __init__(self, **data):
         super().__init__(**data)
         if self.name is None:
-            self.name = generate_id()
+            self.name = generate_id(str(data))
 
     def get_name(self):
         result = str(super().get_name())

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo/models/calculate.py

@@ -102,7 +102,7 @@ class TriccRhombusMixIn():
                     exit(1)
         instance.reference = reference
         instance.expression_reference = expression_reference
-        instance.name = get_rand_name()
+        instance.name = get_rand_name(self.id)
         return instance
 
 

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo/models/tricc.py

@@ -224,7 +224,7 @@ class TriccNodeActivity(TriccNodeBaseModel):
             TriccNodeEnd,
             TriccNodeActivityEnd,
         )
-        return  list(filter(lambda x:  issubclass(x.__class__, (TriccNodeEnd,TriccNodeActivityEnd)), self.nodes.values()))
+        return  list(filter(lambda x:  isinstance(x, (TriccNodeActivityEnd)) or (isinstance(x, (TriccNodeEnd)) and isinstance(self.root, TriccNodeMainStart )), self.nodes.values()))
 
 
 

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo/strategies/input/base_input_strategy.py

@@ -53,14 +53,14 @@ class BaseInputStrategy:
                     project.start_pages['determine-diagnosis'] = diags_activity
             root_process = sorted_pages[list(sorted_pages.keys())[0]][0].root
             root = TriccNodeMainStart(
-                id=generate_id(),
+                id=generate_id('s-determine-diagnosis'),
                 form_id=root_process.form_id,
                 label=root_process.label
             )
             nodes = {}
             nodes[root.id] = root
             app = TriccNodeActivity(
-                id=generate_id(),
+                id=generate_id('a-determine-diagnosis'),
                 name=root_process.name,
                 root=root,
                 nodes=nodes

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo/visitors/tricc.py

@@ -115,7 +115,8 @@ def process_calculate(node,processed_nodes, stashed_nodes, calculates, used_calc
         ):
             if kwargs.get('warn', True):
                 logger.debug('Processing relevance for node {0}'.format(node.get_name()))
-            last_version = get_last_version(node.name, processed_nodes) if issubclass(node.__class__, (TriccNodeDisplayModel, TriccNodeDisplayCalculateBase)) and not isinstance(node, TriccNodeSelectOption)  else  None
+            node_name = node.name if not isinstance(node, TriccNodeEnd) else 'tricc_end'
+            last_version = get_last_version(node_name, processed_nodes) if issubclass(node.__class__, (TriccNodeDisplayModel, TriccNodeDisplayCalculateBase)) and not isinstance(node, TriccNodeSelectOption)  else  None
             #last_version = processed_nodes.find_prev(node, lambda item: hasattr(item, 'name') and item.name == node.name)
             if last_version:
                 # 0-100 for manually specified instance.  100-200 for auto instance 
@@ -128,9 +129,7 @@ def process_calculate(node,processed_nodes, stashed_nodes, calculates, used_calc
                     if (
                         issubclass(node.__class__, (TriccNodeDisplayCalculateBase )) and node.name is not None
                     ):
-                        node_name = node.name if not isinstance(node, TriccNodeEnd) else 'tricc_end'
-
-                                #logger.debug("set last to false for node {}  and add its link it to next one".format(last_used_calc.get_name()))
+                        #logger.debug("set last to false for node {}  and add its link it to next one".format(last_used_calc.get_name()))
                         if node.prev_nodes:    
                             set_prev_next_node(last_version, node)
                         else:
@@ -163,7 +162,7 @@ def process_calculate(node,processed_nodes, stashed_nodes, calculates, used_calc
                     
                     
                     calc = TriccNodeCalculate(
-                        id=generate_id(),
+                        id=generate_id(f"save{node.id}"),
                         name=node.name,
                         path_len=node.path_len+1,
                         version=last_version.version + 2,
@@ -305,7 +304,7 @@ def get_max_named_version(calculates,name):
     return max
 
 def get_count_node(node):
-    count_id = generate_id()
+    count_id = generate_id(f"count{node.id}")
     count_name = "cnt_"+count_id
     return TriccNodeCount(
         id = count_id,
@@ -332,7 +331,7 @@ def get_activity_wait(prev_nodes, nodes_to_wait, next_nodes, replaced_node = Non
  
     activity = activity or prev_node.activity
     calc_node = TriccNodeWait(
-            id = "ar_"+generate_id(),
+            id = generate_id(f"ar{''.join([x.id for x in nodes_to_wait])}{activity.id}"),
             reference = nodes_to_wait,
             activity = activity,
             group = activity,
@@ -360,7 +359,7 @@ def get_bridge_path(prev_nodes, node=None,edge_only=False):
     p_p_node = next(iterator)    
     if node is None:
         node = p_p_node
-    calc_id  = generate_id()
+    calc_id  = generate_id(f"br{''.join([x.id for x in prev_nodes])}{node.id}")
     calc_name = "path_"+calc_id
     data = {
         'id': calc_id,
@@ -479,7 +478,7 @@ def generate_calculates(node,calculates, used_calculates,processed_nodes):
             calc_node.name=calculate_name
             calc_node.label =  "save select: " +node.get_name()        
         else:
-            calc_id = generate_id()
+            calc_id = generate_id(f"autosave{node.id}")
             calc_node = TriccNodeCalculate(
                 name=calculate_name,
                 id = calc_id,
@@ -736,7 +735,7 @@ def add_used_calculate(node, prev_node, calculates, used_calculates, processed_n
         
 def get_select_not_available_options(node,group,label):
     return {0:TriccNodeSelectOption(
-                id = generate_id(),
+                id = generate_id(f"notavaialble{node.id}"),
                 name="1",
                 label=label,
                 select = node,
@@ -746,7 +745,7 @@ def get_select_not_available_options(node,group,label):
         
 def get_select_yes_no_options(node, group):
     yes = TriccNodeSelectOption(
-                id = generate_id(),
+                id = generate_id(f'yes{node.id}'),
                 name=f"{TRICC_TRUE_VALUE}",
                 label="Yes",
                 select = node,
@@ -754,7 +753,7 @@ def get_select_yes_no_options(node, group):
                 list_name = node.list_name
             )
     no = TriccNodeSelectOption(
-                id = generate_id(),
+                id = generate_id(f'no{node.id}'),
                 name=f"{TRICC_FALSE_VALUE}",
                 label="No",
                 select = node,
@@ -1113,21 +1112,38 @@ def check_stashed_loop(stashed_nodes, prev_stashed_nodes, processed_nodes, len_p
                     logger.critical("Stashed node list was unchanged: loop likely or unresolved dependence")
                     waited, looped =  get_all_dependant(stashed_nodes, stashed_nodes, processed_nodes)               
                     logger.debug(f"{len(looped)} nodes waiting stashed nodes")
-                    logger.info("looped nodes")
-                    for es_node in looped:
+                    logger.info("unresolved reference")
+                    for es_node in [n for n in stashed_nodes if isinstance(n, TriccReference)]:
                         logger.info("Stashed node {}:{}|{} {}".format(
                             es_node.activity.get_name() if hasattr(es_node,'activity') else '' ,
                             es_node.activity.instance if hasattr(es_node,'activity') else '',
                             es_node.__class__, 
                             es_node.get_name()))
+                    logger.info("looped nodes")
+                    for dep_list in looped:
+                        for d in looped[dep_list]:
+                            if d.get_name() == dep_list:
+                                logger.critical("[{}] depends on itself".format(
+                                    dep_list, 
+                                    ))
+                            logger.error("[{}] depends on [{}]".format(
+                                dep_list, str(d)
+                                ))
+                        if dep_list in waited:
+                            for d in waited[dep_list]:
+                                logger.warning("[{}] depends on [{}]".format(
+                                    dep_list, str(d)
+                                    ))
+                        
                         #reverse_walkthrough(es_node, es_node, print_trace, processed_nodes, stashed_nodes)
                     logger.info("waited nodes")
-                    for es_node in waited:
-                        logger.info("Stashed node {}:{}|{} {}".format(
-                            es_node.activity.get_name() if hasattr(es_node,'activity') else '' ,
-                            es_node.activity.instance if hasattr(es_node,'activity') else '',
-                            es_node.__class__, 
-                            es_node.get_name()))
+                    for dep_list in waited:
+                        if dep_list not in looped:
+                            for d in waited[dep_list]:
+                                logger.warning("[{}] depends on [{}]".format(
+                                    dep_list, d.get_name()
+                                    ))
+                            
                     if len(stashed_nodes) == len(prev_stashed_nodes):
                         exit(1)
             else:
@@ -1136,12 +1152,25 @@ def check_stashed_loop(stashed_nodes, prev_stashed_nodes, processed_nodes, len_p
         loop_count = 0
     return loop_count
 
+
+def add_to_tree(tree, n, d):
+    n_str = str(n)
+    if n_str not in tree:
+        tree[n_str] = []
+    if d not in tree[n_str]:
+        tree[n_str].append(d)
+    return tree
+
         
-def get_all_dependant(loop, stashed_nodes, processed_nodes, depth=0, waited=[] , looped=[]):
+def get_all_dependant(loop, stashed_nodes, processed_nodes, depth=0, waited=None , looped=None):
+    if looped is None:
+        looped = {}
+    if waited is None:
+        waited = {}
     for n in loop:
         dependant = OrderedSet()
         i=0
-        logger.critical(f"{i}: {n.__class__}::{n.get_name()}::{getattr(n,'instance','')}::{process_reference(n, processed_nodes, [])}")
+        #logger.critical(f"{i}: {n.__class__}::{n.get_name()}::{getattr(n,'instance','')}::{process_reference(n, processed_nodes, [])}")
         i += 1
         if hasattr(n, 'prev_nodes') and n.prev_nodes:
             dependant =  dependant | n.prev_nodes
@@ -1156,16 +1185,15 @@ def get_all_dependant(loop, stashed_nodes, processed_nodes, depth=0, waited=[] ,
                 if isinstance(d, TriccReference):
                     if not any(n.name == d.value for n in processed_nodes):
                         if not any(n.name == d.value for n in stashed_nodes):
-                            waited.append(d)
+                            waited = add_to_tree(waited, n, d) 
                         else :
-                            looped.append(d)
+                            looped = add_to_tree(looped, n, d)
                 
                 elif d  not in processed_nodes:
-                    
-                    if d not in stashed_nodes:
-                        waited.append(d)
+                    if d in stashed_nodes:
+                        looped = add_to_tree(looped, n, d) 
                     else :
-                        looped.append(d)
+                        waited = add_to_tree(waited, n, d) 
     if depth < MAX_DRILL:
         return get_all_dependant(waited, stashed_nodes, processed_nodes, depth+1, waited , looped)
 
@@ -1556,7 +1584,7 @@ def export_proposed_diags(activity, diags=None, **kwargs):
 
 def get_accept_diagnostic_node(code, display, severity, activity):
     node = TriccNodeAcceptDiagnostic(
-        id=generate_id(),
+        id=generate_id("pre_final." + code),
         name="pre_final." + code,
         label=display,
         list_name="acc_rej",
@@ -1569,7 +1597,7 @@ def get_accept_diagnostic_node(code, display, severity, activity):
 
 def get_diagnostic_node(code, display, severity, activity):
     node = TriccNodeAcceptDiagnostic(
-        id=generate_id(),
+        id=generate_id("final." + code),
         name="final." + code,
         label=display,
         list_name="acc_rej",
@@ -1582,7 +1610,7 @@ def get_diagnostic_node(code, display, severity, activity):
 
 def get_select_accept_reject_options(node, group):
     yes = TriccNodeSelectOption(
-                id = generate_id(),
+                id = generate_id(f'accept{node.id}'),
                 name=f"{TRICC_TRUE_VALUE}",
                 label="Accept",
                 select = node,
@@ -1590,7 +1618,7 @@ def get_select_accept_reject_options(node, group):
                 list_name = node.list_name
             )
     no = TriccNodeSelectOption(
-                id = generate_id(),
+                id = generate_id(f'reject{node.id}'),
                 name=f"{TRICC_FALSE_VALUE}",
                 label="Reject",
                 select = node,
@@ -1601,13 +1629,13 @@ def get_select_accept_reject_options(node, group):
 
 def create_determine_diagnosis_activity(diags):
     start = TriccNodeActivityStart(
-        id=generate_id(),
+        id=generate_id('start.determine-diagnosis'),
         name="start.determine-diagnosis"
     )
 
     
     activity = TriccNodeActivity(
-        id=generate_id(),
+        id=generate_id('activity-determine-diagnosis'),
         name='determine-diagnosis',
         label='Diagnosis',
         root=start,
@@ -1619,7 +1647,7 @@ def create_determine_diagnosis_activity(diags):
     diags_conf = []
     r_diags_conf = []
     end = TriccNodeActivityEnd(
-        id=generate_id(),
+        id=generate_id("end.determine-diagnosis"),
         name="end.determine-diagnosis",
         activity=activity,
         group=activity,
@@ -1629,7 +1657,7 @@ def create_determine_diagnosis_activity(diags):
         d = get_diagnostic_node(proposed.name, proposed.label, proposed.severity, activity)
         diags_conf.append(d)
         r = TriccNodeRhombus(
-            id=generate_id(),
+            id=generate_id(f"proposed-rhombus{proposed.id}"),
             expression_reference=TriccOperation(
                 TriccOperator.ISTRUE,
                 [TriccReference(proposed.name)]

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tricc-oo
-Version: 1.4.7
+Version: 1.4.9
 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
@@ -11,7 +11,7 @@ Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: lxml
-Requires-Dist: html2text
+Requires-Dist: markdownify
 Requires-Dist: pydantic
 Requires-Dist: babel
 Requires-Dist: xlsxwriter

{tricc_oo-1.4.7 → tricc_oo-1.4.9}/tricc_oo.egg-info/requires.txt

@@ -1,5 +1,5 @@
 lxml
-html2text
+markdownify
 pydantic
 babel
 xlsxwriter

tricc_oo-1.4.7/tricc_oo/converters/utils.py

@@ -1,57 +0,0 @@
-import logging
-import random
-import string
-import hashlib
-import html2text
-
-
-
-logger = logging.getLogger("default")
-
-def replace_all(text, list_char, replacement):
-    for i in list_char:
-        text = text.replace(i, replacement)
-    return text
-
-def clean_str(name, replace_dots=False):
-    replacement_list = ['-', ' ', ',', '.'] if replace_dots else ['-', ' ', ',']
-    return replace_all(name, replacement_list,'_')
-
-def clean_name( name, prefix='', replace_dots=False):
-    name = clean_str(name, replace_dots)
-    if name[0].isdigit():
-        name = 'id_' + name
-    elif  name[0].isdigit() == '_':
-        name =  name[1:]
-    return name
-
-def generate_id(name=None, length=18):
-    if name:
-        h = hashlib.blake2b(digest_size=length)
-        h.update(name.encode('utf-8') if isinstance(name, str) else name)
-        return h.hexdigest()
-    else:
-        return ''.join(random.choices(string.ascii_lowercase + string.digits + string.ascii_uppercase, k=length))
-
-
-def get_rand_name(name=None, length=8):
-    return "n" + generate_id(name=name, length=length)
-
-# the soup.text strips off the html formatting also
-def remove_html(string):
-    h = html2text.HTML2Text()
-    h.body_width = 0  # Prevents line wrapping
-    h.ignore_links = True  # Ignores any link processing
-    h.ignore_images = True  # Ignores image processing
-    h.ignore_tables = True  # Ignores table formatting
-    text = h.handle(string).rstrip()  # rstrip()
-    text = text.strip('\n') # get rid of empty lines at the end (and beginning)
-    text = text.split('\n') # split string into a list at new lines
-    text = '\n'.join([i.strip(' ') for i in text if i]) # in each element in that list strip empty space (at the end of line) 
-    # and delete empty lines
-    return text
-
-
-
-
-