Add pre-pop queries to value[x] items

packages/structure-def-to-questionnaire/convertTypes.py

@@ -0,0 +1,11 @@
+# Convert structure definition type codes to appropriate questionnaire item types
+def convert_to_appropriate_type(item_type):
+    # convert id to string
+    if item_type == "id":
+        return "string"
+
+    # convert uri to url
+    if item_type == "uri":
+        return "url"
+
+    return item_type

packages/structure-def-to-questionnaire/complexItems.py → packages/structure-def-to-questionnaire/createItems.py

@@ -1,3 +1,15 @@
+def add_required_and_repeats_attribute(element, item):
+    # required
+    if element.get("min", 0) > 0:
+        item["required"] = True
+
+    # repeats
+    if element.get("max", 0) == "*":
+        item["repeats"] = True
+
+    return item
+
+
 def create_item(element, parent_link_id=None):
     link_id = element["id"]
 
@@ -12,13 +24,7 @@ def create_item(element, parent_link_id=None):
         "repeats": False,
     }
 
-    # required
-    if element.get("min", 0) > 0:
-        item["required"] = True
-
-    # repeats
-    if element.get("max", 0) == "*":
-        item["repeats"] = True
+    item = add_required_and_repeats_attribute(element, item)
 
     return item
 

packages/structure-def-to-questionnaire/helperFunctions.py

@@ -38,3 +38,14 @@ def add_launch_context_to_questionnaire(questionnaire, profile_resource_type):
     ]
 
     return questionnaire
+
+
+def get_element_name_without_resource(element, root_level=True):
+    if root_level:
+        return ".".join(element["id"].split(".")[1:])
+
+    if ":" not in element["id"]:
+        return element["id"]
+
+    # if element is not at root level (i.e. it was further obtained via profile resolution), only use the last part of the id
+    return element["id"].split(":")[1]

packages/structure-def-to-questionnaire/initial.py

@@ -0,0 +1,64 @@
+def add_item_initial(item, element):
+    if element.get("fixedUri") is not None and element.get("fixedUri") != "":
+        item["initial"] = [{"valueString": element["fixedUri"]}]
+
+    return item
+
+
+def add_initial_expression(item, element, structure_definition_url=None):
+    # skip adding initial expression if item has item.initial
+    if item.get("initial") is not None:
+        return item
+
+    if item.get("extension", None) is None:
+        item["extension"] = []
+
+    initialExpressionString = ""
+    if element["path"].startswith("Extension") and structure_definition_url is not None:
+        preInitialExpressionExtensionString = (
+            item["linkId"].lower().split("extension")[0].replace(":", ".") + "extension"
+        )
+
+        initialExpressionString = f"%{preInitialExpressionExtensionString}.where(url='{structure_definition_url}').value"
+    else:
+        initialExpressionString = f"%{item['linkId'].lower()}"
+
+    item = add_display_instructions(item, initialExpressionString)
+
+    item["extension"].append(
+        {
+            "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
+            "valueExpression": {
+                "language": "text/fhirpath",
+                "expression": initialExpressionString,
+            },
+        }
+    )
+
+    return item
+
+
+def add_display_instructions(item, displayInstructionString):
+    if item.get("type") != "group":
+        item["item"] = [
+            {
+                "extension": [
+                    {
+                        "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-displayCategory",
+                        "valueCodeableConcept": {
+                            "coding": [
+                                {
+                                    "system": "http://hl7.org/fhir/questionnaire-display-category",
+                                    "code": "instructions",
+                                }
+                            ]
+                        },
+                    }
+                ],
+                "linkId": f"{item['linkId']}-display-instructions",
+                "text": displayInstructionString,
+                "type": "display",
+            }
+        ]
+
+    return item

packages/structure-def-to-questionnaire/readTableElements.py

@@ -23,7 +23,10 @@ def read_table_elements(structure_definition):
 
         # Create a dictionary of element names and URLs
         a_tags_dict = {
-            a_tag.text.strip(): a_tag.get("href")
+            a_tag.text.strip(): {
+                "href": a_tag.get("href", None),
+                "title": a_tag.get("title", None),
+            }
             for a_tag in a_tags
             if a_tag.text.strip() != "" or a_tag.get("href") is not None
         }

packages/structure-def-to-questionnaire/resolveProfiles.py

@@ -0,0 +1,77 @@
+import re
+
+
+def get_all_profile_links(table_element):
+    profile_links = []
+    # get links with 'http' in them
+    for value_i in table_element.values():
+        for value_j in value_i.values():
+            if value_j is not None and "http" in value_j:
+                if value_j.startswith("http"):
+                    profile_links.append(value_j)
+                else:
+                    profile_links.append("http" + value_j.split("http")[-1])
+
+    # clean links that does not start with 'http'
+    return profile_links
+
+
+def get_first_profile_link(table_element):
+    # retrieve links from table element
+    profile_links = get_all_profile_links(table_element)
+
+    # not root level, resolve via appending profie name to end of base url (hardcoded)
+    for link in profile_links:
+        if "extension" in link:
+            return link
+
+        if "StructureDefinition" in link:
+            try:
+                # Split the URL by "StructureDefinition-" and ".html"
+                re_match = re.search(
+                    r"(?:StructureDefinition[/\-])(.*?)(?:\.html|\/|$)", link
+                )
+                if re_match:
+                    profile_name = re_match.group(1)
+
+                    return (
+                        "https://build.fhir.org/ig/hl7au/au-fhir-base/StructureDefinition-"
+                        + profile_name
+                        + ".json"
+                    )
+
+                print("Fail to get profile link ", link)
+                return None
+            except IndexError:
+                print("Fail to get profile link ", link)
+                return None
+
+    return None
+
+
+def is_value_set_link(key, value):
+    if key in value and value[key] is not None and "ValueSet" in value[key]:
+        return True
+
+    return False
+
+
+def get_all_valueset_links(table_element):
+    profile_links = []
+    for value in table_element.values():
+        if is_value_set_link(key="title", value=value):
+            profile_links.append(value["title"])
+        elif is_value_set_link(key="href", value=value):
+            profile_links.append(value["href"])
+
+    return profile_links
+
+
+def get_coding_terminology_binding(table_element):
+    if "Coding" in table_element:
+        valueset_links = get_all_valueset_links(table_element)
+
+        if len(valueset_links) > 0:
+            return valueset_links[0]
+
+    return None