test uscdi tag scripts

Healthedata1 · Oct 12, 2023 · 3eccf20 · 3eccf20
1 parent 3523601
commit 3eccf20
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diff --git a/add-add'l-USCDI-extensions.ipynb b/add-add'l-USCDI-extensions.ipynb
@@ -404,7 +404,7 @@
       "----------\n",
       "☞ ☞ ☞ element 16: Patient.telecom\n",
       "❗❗❗add the USCDI extension\n",
-      "❗❗❗add the '𝗔𝗗𝗗'𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
+      "❗❗❗add the short element from the base\n",
       "❗❗❗ done with element\n",
       "----------\n",
       "☞ ☞ ☞ element 17: Patient.telecom.system\n",
@@ -424,7 +424,7 @@
       "----------\n",
       "☞ ☞ ☞ element 22: Patient.deceased[x]\n",
       "❗❗❗add the USCDI extension\n",
-      "❗❗❗add the '𝗔𝗗𝗗'𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
+      "❗❗❗add the short element from the base\n",
       "❗❗❗ done with element\n",
       "----------\n",
       "☞ ☞ ☞ element 23: Patient.address\n",
@@ -454,7 +454,7 @@
       "----------\n",
       "☞ ☞ ☞ element 30: Patient.communication\n",
       "❗❗❗add the USCDI extension\n",
-      "❗❗❗add the '𝗔𝗗𝗗'𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
+      "❗❗❗add the short element from the base\n",
       "❗❗❗ done with element\n",
       "----------\n",
       "☞ ☞ ☞ element 31: Patient.communication.language\n",
@@ -600,9 +600,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "##### DO THIS ONLY when you want to start over with removing all tags ####\n",
+    "##### DO THIS ONLY when you want to start over with removing all tags because it overwrites the original source folder ####\n",
     "\n",
-    "# !cp /Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml-copy/Struct*.yml /Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml"
+    "#!cp /Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml-copy/Struct*.yml /Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml"
    ]
   }
  ],

diff --git a/input/images/additional-uscdi-requirements.csv b/input/images/additional-uscdi-requirements.csv
@@ -0,0 +1,23 @@
+Additional USCDI Requirements,Profile,FHIR Element
+KEEP ME HERE ,KEEP ME HERE ,KEEP ME HERE 
+Contact Detail,[US Core Patient Profile],Patient.telecom
+A Communication Language,[US Core Patient Profile],Patient.communication
+A Race,[US Core Patient Profile],Patient.extension:race
+An Ethnicity,[US Core Patient Profile],Patient.extension:ethnicity
+A Tribal Affiliation,[US Core Patient Profile],Patient.extension:tribalAffiliation
+A Sex,[US Core Patient Profile],Patient.extension:sex
+Gender Identity,[US Core Patient Profile],Patient.extension:genderIdentity
+Date Of Death,[US Core Patient Profile],Patient.deceased[x]
+Previous Address,[US Core Patient Profile],Patient.address.use or Patient.address.period
+Previous Name,[US Core Patient Profile],Patient.name.use or Patient.name.period
+Suffix,[US Core Patient Profile],Patient.name.suffix
+A Reason Or Indication For Referral Or Consultation,[US Core ServiceRequest Profile],ServiceRequest.reasonCode
+A Reason Or Indication For Referral Or Consultation,[US Core ServiceRequest Profile],ServiceRequest.reasonReference
+The Reason Or Indication For The Prescription,[US Core MedicationRequest Profile],MedicationRequest.reasonCode
+The Reason Or Indication For The Prescription,[US Core MedicationRequest Profile],MedicationRequest.reasonReference
+Medication Adherence,[US Core MedicationRequest Profile],MedicationRequest.extension:medicationAdherence
+A Reference To The Request For The Procedure,[US Core Procedure Profile],Procedure.basedOn
+US Core Document Category,[US Core DocumentReference Profile],DocumentReference.category:uscore
+"References To An Associated Survey, Assessment, Or Screening Tool",[US Core Simple Observation Profile],Observation.derivedFrom
+Specimen Source Site,[US Core Specimen Profile],Specimen.collection.bodySite
+Specimen Condition Acceptability,[US Core Specimen Profile],Specimen.condition
diff --git a/input/images/additional-uscdi-requirements.xlsx b/input/images/additional-uscdi-requirements.xlsx
diff --git a/input/images/assessments-valuesets.xlsx b/input/images/assessments-valuesets.xlsx
diff --git a/input/includes/assessment-valueset-table-generator.html b/input/includes/assessment-valueset-table-generator.html
@@ -23,9 +23,9 @@
 <tr>
 <td>{{item["USCDI Data Element"]}}</td>
 <td><a href="{{item["VSAC Link"]}}">{{item["ValueSet Name"]}}</a></td>
-{% if item["Clinical Judgement"] == "TRUE" %}<td style="text-align: center; color:green">&#x2714;</td>{% else %}<td></td>{% endif %}
-{% if item["Panel"] == "TRUE" %}<td style="text-align: center; color:green">&#x2714;</td>{% else %}<td></td>{% endif %}
-{% if item["Panel Item"] == "TRUE" %}<td style="text-align: center; color:green">&#x2714;</td>{% else %}<td></td>{% endif %}
+{% if item["Clinical Judgement"] == "TRUE" %}<td style="text-align:center; color:green">&#x2714;</td>{% else %}<td></td>{% endif %}
+{% if item["Panel"] == "TRUE" %}<td style="text-align:center; color:green">&#x2714;</td>{% else %}<td></td>{% endif %}
+{% if item["Panel Item"] == "TRUE" %}<td style="text-align:center; color:green">&#x2714;</td>{% else %}<td></td>{% endif %}
 <!-- <td><a href="{ {site.data.fhir.path} }terminologies.html#{ {item["Binding Strength"]} }">{ {item["Binding Strength"]} }</a></td> -->
 </tr>
 

diff --git a/input/resources-yaml-copy/StructureDefinition-us-core-patient.yml b/input/resources-yaml-copy/StructureDefinition-us-core-patient.yml
@@ -39,7 +39,6 @@ differential:
     path: Patient.extension
     sliceName: race
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       US Core Race Extension"
     min: 0
     max: '1'
@@ -58,7 +57,6 @@ differential:
     path: Patient.extension
     sliceName: ethnicity
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       US Core ethnicity Extension"
     min: 0
     max: '1'
@@ -77,7 +75,6 @@ differential:
     path: Patient.extension
     sliceName: tribalAffiliation
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Tribal Affiliation Extension"
     min: 0
     max: '*'
@@ -107,7 +104,6 @@ differential:
     path: Patient.extension
     sliceName: sex
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Sex Extension"
     min: 0
     max: '1'
@@ -123,7 +119,6 @@ differential:
     path: Patient.extension
     sliceName: genderIdentity
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       The individual's gender identity"
     min: 0
     max: '*'
@@ -179,7 +174,6 @@ differential:
       valueBoolean: true
     path: Patient.name.use
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       usual | official | temp | nickname | anonymous | old | maiden"
   - id: Patient.name.family
     path: Patient.name.family
@@ -216,7 +210,6 @@ differential:
       valueBoolean: true
     path: Patient.name.period
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Time period when name was/is in use"
     mustSupport: false
     mapping:
@@ -227,9 +220,6 @@ differential:
     - url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-uscdi
       valueBoolean: true
     path: Patient.telecom
-    short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
-      A contact detail for the individual"
     mustSupport: false
     mapping:
     - identity: argonaut-dq-dstu2
@@ -289,9 +279,6 @@ differential:
     - url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-uscdi
       valueBoolean: true
     path: Patient.deceased[x]
-    short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
-      Indicates if the individual is deceased or not"
   - id: Patient.address
     path: Patient.address
     short: An address for the individual
@@ -305,7 +292,6 @@ differential:
       valueBoolean: true
     path: Patient.address.use
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       home | work | temp | old | billing - purpose of this address"
   - id: Patient.address.line
     path: Patient.address.line
@@ -347,7 +333,6 @@ differential:
       valueBoolean: true
     path: Patient.address.period
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Time period when address was/is in use"
     mapping:
     - identity: argonaut-dq-dstu2
@@ -357,10 +342,6 @@ differential:
     - url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-uscdi
       valueBoolean: true
     path: Patient.communication
-    short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
-      A language which may be used to communicate with the patient about his or her
-      health"
     mustSupport: false
     mapping:
     - identity: argonaut-dq-dstu2

diff --git a/input/resources-yaml/StructureDefinition-us-core-patient.yml b/input/resources-yaml/StructureDefinition-us-core-patient.yml
@@ -39,7 +39,6 @@ differential:
     path: Patient.extension
     sliceName: race
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       US Core Race Extension"
     min: 0
     max: '1'
@@ -58,7 +57,6 @@ differential:
     path: Patient.extension
     sliceName: ethnicity
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       US Core ethnicity Extension"
     min: 0
     max: '1'
@@ -77,7 +75,6 @@ differential:
     path: Patient.extension
     sliceName: tribalAffiliation
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Tribal Affiliation Extension"
     min: 0
     max: '*'
@@ -107,7 +104,6 @@ differential:
     path: Patient.extension
     sliceName: sex
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Sex Extension"
     min: 0
     max: '1'
@@ -123,7 +119,6 @@ differential:
     path: Patient.extension
     sliceName: genderIdentity
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       The individual's gender identity"
     min: 0
     max: '*'
@@ -179,7 +174,6 @@ differential:
       valueBoolean: true
     path: Patient.name.use
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       usual | official | temp | nickname | anonymous | old | maiden"
   - id: Patient.name.family
     path: Patient.name.family
@@ -216,7 +210,6 @@ differential:
       valueBoolean: true
     path: Patient.name.period
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Time period when name was/is in use"
     mustSupport: false
     mapping:
@@ -227,9 +220,6 @@ differential:
     - url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-uscdi
       valueBoolean: true
     path: Patient.telecom
-    short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
-      A contact detail for the individual"
     mustSupport: false
     mapping:
     - identity: argonaut-dq-dstu2
@@ -289,9 +279,6 @@ differential:
     - url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-uscdi
       valueBoolean: true
     path: Patient.deceased[x]
-    short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
-      Indicates if the individual is deceased or not"
   - id: Patient.address
     path: Patient.address
     short: An address for the individual
@@ -305,7 +292,6 @@ differential:
       valueBoolean: true
     path: Patient.address.use
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       home | work | temp | old | billing - purpose of this address"
   - id: Patient.address.line
     path: Patient.address.line
@@ -347,7 +333,6 @@ differential:
       valueBoolean: true
     path: Patient.address.period
     short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
       Time period when address was/is in use"
     mapping:
     - identity: argonaut-dq-dstu2
@@ -357,10 +342,6 @@ differential:
     - url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-uscdi
       valueBoolean: true
     path: Patient.communication
-    short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
-      \u2757(\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC)
-      A language which may be used to communicate with the patient about his or her
-      health"
     mustSupport: false
     mapping:
     - identity: argonaut-dq-dstu2