Create get_cde_permissible_value.py

scripts/get_cde_permissible_value.py

@@ -0,0 +1,88 @@
+import requests
+import copy
+import re
+from datetime import datetime
+
+# CaDSR Variables
+cde_id = "14808227"
+cde_deeplink= "https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=14808227%20and%20ver_nr=1"
+url = "https://cadsrapi.cancer.gov/rad/NCIAPI/1.0/api/DataElement/" + cde_id
+
+# CCDI Federation variables
+enum_name = "LibrarySourceMaterial"
+cde_version = "v1"
+data_type = "sample"
+enum_value_template = """
+    /// `CCDI_TEMPLATE_REPLACE_1`
+    ///
+    /// * **VM Long Name**: CCDI_TEMPLATE_REPLACE_2
+    /// * **VM Public ID**: CCDI_TEMPLATE_REPLACE_3
+    /// * **Concept Code**: CCDI_TEMPLATE_REPLACE_4
+    /// * **Begin Date**:   CCDI_TEMPLATE_REPLACE_5
+    ///
+    /// CCDI_TEMPLATE_REPLACE_6
+    #[serde(rename = "CCDI_TEMPLATE_REPLACE_1")]
+    CCDI_TEMPLATE_REPLACE_7,
+
+"""
+enum_template = """
+/// **`caDSR CDE CCDI_TEMPLATE_REPLACE_1 CCDI_TEMPLATE_REPLACE_2`**
+///
+/// This metadata element is defined by the caDSR as "CCDI_TEMPLATE_REPLACE_3".
+///
+/// Link:
+/// <CCDI_TEMPLATE_REPLACE_4>
+#[derive(Clone, Debug, Deserialize, Eq, PartialEq, Serialize, ToSchema, Introspect)]
+#[schema(as = cde::CCDI_TEMPLATE_REPLACE_5::CCDI_TEMPLATE_REPLACE_6::CCDI_TEMPLATE_REPLACE_7)]
+pub enum CCDI_TEMPLATE_REPLACE_7 {
+CCDI_TEMPLATE_REPLACE_8
+}
+"""
+
+
+
+# Retrieve the data from CaDSR
+payload = {}
+headers = {
+  'accept': 'application/json',
+}
+response = requests.request("GET", url, headers=headers, data=payload)
+# print(response.text)
+response = response.json()
+# print(response["DataElement"]["ValueDomain"]["PermissibleValues"])
+permissible_values = response["DataElement"]["ValueDomain"]["PermissibleValues"]
+
+
+
+
+values = []
+for permissible_value in permissible_values:
+  # print(permissible_value)
+  value = copy.deepcopy(enum_value_template)
+  value = value.replace("CCDI_TEMPLATE_REPLACE_1", permissible_value["value"])
+  value = value.replace("CCDI_TEMPLATE_REPLACE_2", permissible_value["ValueMeaning"]["Concepts"][0]["longName"])
+  value = value.replace("CCDI_TEMPLATE_REPLACE_3",permissible_value["ValueMeaning"]["publicId"])
+  value = value.replace("CCDI_TEMPLATE_REPLACE_4", permissible_value["ValueMeaning"]["Concepts"][0]["conceptCode"])
+  formatted_date = datetime.strptime(permissible_value["ValueMeaning"]["dateModified"], '%Y-%m-%d').strftime('%m/%d/%Y')
+  value = value.replace("CCDI_TEMPLATE_REPLACE_5", formatted_date)
+  value = value.replace("CCDI_TEMPLATE_REPLACE_6", permissible_value["ValueMeaning"]["Concepts"][0]["definition"])
+  formatted_name = ''.join(word.capitalize() for word in permissible_value["value"].split()) 
+  value = value.replace("CCDI_TEMPLATE_REPLACE_7", formatted_name)
+  values.append(value)
+
+combined_values = ''.join(values)
+# print(combined_values)
+
+cde_enum = copy.deepcopy(enum_template)
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_1", response["DataElement"]["publicId"])
+match = re.search(r'v\d+\.\d+$', response["DataElement"]["shortName"])
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_2", match.group())
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_3", response["DataElement"]["definition"])
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_4", cde_deeplink)
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_5", cde_version)
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_6", data_type)
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_7", enum_name)
+cde_enum = cde_enum.replace("CCDI_TEMPLATE_REPLACE_8", combined_values)
+
+print(cde_enum)
+