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WIP: working to minimize (or at least enumerate) the ways that CCDA generation loses data fidelity #127

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WIP: working to minimize (or at least enumerate) the ways that CCDA generation loses data fidelity #127

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WIP: working to minimize (or at least enumerate) the ways that CCDA g…
sankarravi Mar 2, 2015
5c1eb06
Many fewer data losses in going from JSON -> CCDA -> JSON
sankarravi Apr 4, 2015
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19 changes: 16 additions & 3 deletions lib/core/xml.js
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Original file line number Diff line number Diff line change
Expand Up @@ -144,6 +144,16 @@ Core.XML = (function () {
var elsByTag = function (tag) {
return wrapElement(this.el.getElementsByTagName(tag));
};


var unescapeSpecialChars = function(s) {
if (!s) { return s; }
return s.replace(/&lt;/g, '<')
.replace(/&gt;/g, '>')
.replace(/&amp;/g, '&')
.replace(/&quot;/g, '"')
.replace(/&apos;/g, "'");
};


/*
Expand All @@ -158,7 +168,10 @@ Core.XML = (function () {
var attr = function (attrName) {
if (!this.el) { return null; }
var attrVal = this.el.getAttribute(attrName);
return attrVal || null;
if (attrVal) {
return unescapeSpecialChars(attrVal);
}
return null;
};

/*
Expand Down Expand Up @@ -207,7 +220,7 @@ Core.XML = (function () {
contentId = this.el.childNodes[1].getAttribute('value');

} else {
return textContent;
return unescapeSpecialChars(textContent);
}

if (contentId && contentId[0] === '#') {
Expand All @@ -218,7 +231,7 @@ Core.XML = (function () {
}
}

return textContent;
return unescapeSpecialChars(textContent);
};


Expand Down
83 changes: 64 additions & 19 deletions lib/generators/ccda_template.ejs
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Original file line number Diff line number Diff line change
Expand Up @@ -95,9 +95,13 @@
<%} else { %>
<ethnicGroupCode nullFlavor="NI" />
<%} %>
<% if (codes.reverseRole(bb.demographics.guardian.relationship) && bb.demographics.guardian.name.family) { %>
<% if (bb.demographics.guardian.name.family) { %>
<guardian>
<code code="<%=: codes.reverseRole(bb.demographics.guardian.relationship) %>" displayName="<%= bb.demographics.guardian.relationship %>" codeSystem="2.16.840.1.113883.5.111" codeSystemName="HL7 Role code"/>
<% if (codes.role(bb.demographics.guardian.relationship_code)) { -%>
<code code="<%=: bb.demographics.guardian.relationship_code %>" displayName="<%= bb.demographics.guardian.relationship %>" codeSystem="2.16.840.1.113883.5.111" codeSystemName="HL7 Role code"/>
<% } else if (codes.reverseRole(bb.demographics.guardian.relationship)) { -%>
<code code="<%=: codes.reverseRole(bb.demographics.guardian.relationship) %>" displayName="<%= bb.demographics.guardian.relationship %>" codeSystem="2.16.840.1.113883.5.111" codeSystemName="HL7 Role code"/>
<% } -%>
<addr use="HP">
<!-- HP is "primary home" from codeSystem 2.16.840.1.113883.5.1119 -->
<%-: tagHelpers.addressTags(bb.demographics.guardian.address) %>
Expand Down Expand Up @@ -366,15 +370,17 @@
</playingEntity>
</participantRole>
</participant>
<entryRelationship typeCode="SUBJ" inversionInd="true">
<observation classCode="OBS" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.22.4.28"/>
<!-- Alert status observation template -->
<code code="33999-4" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Status"/>
<statusCode code="completed"/>
<value xsi:type="CE" code="55561003" codeSystem="2.16.840.1.113883.6.96" displayName="<%= bb.allergies[i].status %>"/>
</observation>
</entryRelationship>
<% if (bb.allergies[i].status) { -%>
<entryRelationship typeCode="SUBJ" inversionInd="true">
<observation classCode="OBS" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.22.4.28"/>
<!-- Alert status observation template -->
<code code="33999-4" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Status"/>
<statusCode code="completed"/>
<value xsi:type="CE" code="55561003" codeSystem="2.16.840.1.113883.6.96" displayName="<%= bb.allergies[i].status %>"/>
</observation>
</entryRelationship>
<%} -%>
<entryRelationship typeCode="MFST" inversionInd="true">
<observation classCode="OBS" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.22.4.9"/>
Expand Down Expand Up @@ -757,7 +763,7 @@
</effectiveTime>
<routeCode <%-: bb.visit_medications[i].route | hl7Code %> />
<% if (bb.visit_medications[i].dose_quantity.value) { %>
<doseQuantity value="<%= bb.visit_medications[i].dose_quantity.value %>" unit="<%= bb.visit_medications[i].dose_quantity.unit %>"/>
<doseQuantity value="<%= bb.visit_medications[i].dose_quantity.value %>" <% if (bb.visit_medications[i].dose_quantity.unit) { %> unit="<%= bb.visit_medications[i].dose_quantity.unit %>" <% } %> />
<%} %>
<% if (bb.visit_medications[i].rate_quantity.value) { %>
<rateQuantity value="<%= bb.visit_medications[i].rate_quantity.value %>" unit="<%= bb.visit_medications[i].rate_quantity.unit %>"/>
Expand Down Expand Up @@ -856,7 +862,7 @@
<% } %>
<routeCode <%-: bb.medications[i].route | hl7Code %> />
<% if (bb.medications[i].dose_quantity.value) { %>
<doseQuantity value="<%= bb.medications[i].dose_quantity.value %>" unit="<%= bb.medications[i].dose_quantity.unit %>"/>
<doseQuantity value="<%= bb.medications[i].dose_quantity.value %>" <% if (bb.medications[i].dose_quantity.unit) { %> unit="<%= bb.medications[i].dose_quantity.unit %>" <% } %> />
<%} %>
<% if (bb.medications[i].rate_quantity.value) { %>
<rateQuantity value="<%= bb.medications[i].rate_quantity.value %>" unit="<%= bb.medications[i].rate_quantity.unit %>"/>
Expand All @@ -878,6 +884,18 @@
<manufacturerOrganization/>
</manufacturedProduct>
</consumable>
<% if (bb.medications[i].vehicle.name) { -%>
<participant typeCode="CSM">
<participantRole classCode="MANU">
<templateId root="2.16.840.1.113883.10.20.22.4.24"/>
<code code="412307009" displayName="drug vehicle" codeSystem="2.16.840.1.113883.6.96"/>
<playingEntity classCode="MMAT">
<code <%-: bb.medications[i].vehicle | hl7Code %> />
<name><%= bb.medications[i].vehicle.name %></name>
</playingEntity>
</participantRole>
</participant>
<% } %>
<entryRelationship typeCode="RSON">
<observation classCode="OBS" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.22.4.19"/>
Expand Down Expand Up @@ -993,7 +1011,11 @@
<effectiveTime>
<low <%-: bb.problems[i].date_range.start | hl7Date %> />
</effectiveTime>
<value xsi:type="CD" <%-: bb.problems[i] | hl7Code %> />
<value xsi:type="CD" <%-: bb.problems[i] | hl7Code %> >
<% if (bb.problems[i].translation && bb.problems[i].translation.code) { -%>
<translation <%-: bb.problems[i].translation | hl7Code %> />
<% } -%>
</value>
<entryRelationship typeCode="REFR">
<observation classCode="OBS" moodCode="EVN">
<!-- Problem status observation template -->
Expand All @@ -1003,6 +1025,17 @@
<value xsi:type="CD" code="<%=: codes.reverseProblemStatus(bb.problems[i].status) %>" codeSystem="2.16.840.1.113883.6.96" displayName="<%= bb.problems[i].status %>" codeSystemName="SNOMED CT"/>
</observation>
</entryRelationship>
<% if (bb.problems[i].age) { -%>
<entryRelationship typeCode="SUBJ" inversionInd="true">
<observation classCode="OBS" moodCode="EVN">
<templateId root="2.16.840.1.113883.10.20.22.4.31"/>
<!-- Age observation template -->
<code code="445518008" codeSystem="2.16.840.1.113883.6.96" displayName="Age At Onset"/>
<statusCode code="completed"/>
<value xsi:type="PQ" value="<%= bb.problems[i].age %>" unit="a"/>
</observation>
</entryRelationship>
<% } %>
</observation>
</entryRelationship>
</act>
Expand Down Expand Up @@ -1173,7 +1206,7 @@
<!-- Result organizer template -->
<templateId root="2.16.840.1.113883.10.20.22.4.1"/>
<id root="7d5a02b0-67a4-11db-bd13-0800200c9a66"/>
<code code="<%=bb.results[i].code %>" displayName="<%=bb.results[i].name %>" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT"/>
<code <%-: bb.results[i] | hl7Code %> />
<statusCode code="completed"/>

<% for (var j=0; j<bb.results[i].tests.length; j++) { %>
Expand Down Expand Up @@ -1201,7 +1234,17 @@
<targetSiteCode/>
<referenceRange>
<observationRange>
<text></text>
<% if (bb.results[i].tests[j].reference_range.text) { -%>
<text><%= bb.results[i].tests[j].reference_range.text %></text>
<% } else if (bb.results[i].tests[j].reference_range.low_value &&
bb.results[i].tests[j].reference_range.high_value) { -%>
<value xsi:type="IVL_PQ">
<low value="<%= bb.results[i].tests[j].reference_range.low_value %>"
unit="<%= bb.results[i].tests[j].reference_range.low_unit %>"/>
<high value="<%= bb.results[i].tests[j].reference_range.high_value %>"
unit="<%= bb.results[i].tests[j].reference_range.high_unit %>"/>
</value>
<% } -%>
</observationRange>
</referenceRange>
</observation>
Expand Down Expand Up @@ -1300,7 +1343,7 @@
<!-- Encounter Activities -->
<!-- ******** Encounter activity template ******** -->
<id root="2a620155-9d11-439e-92b3-5d9815ff4de8"/>
<code <%-: bb.encounters[i] | hl7Code %> >
<code <%-: bb.encounters[i] | hl7Code %> <% if (bb.encounters[i].code_system_version) { %>codeSystemVersion="<%= bb.encounters[i].code_system_version %>"<% } %> >
<% if (bb.encounters[i].translation) { -%>
<translation <%-: bb.encounters[i].translation | hl7Code %> />
<% } -%>
Expand Down Expand Up @@ -1413,7 +1456,9 @@
<templateId root="2.16.840.1.113883.10.20.22.4.20"/>
<!-- ** Instructions Template ** -->
<code <%-: bb.immunizations[i].education_type | hl7Code %> />
<text><%= bb.immunizations[i].instructions%></text>
<% if (bb.immunizations[i].instructions) { -%>
<text><%= bb.immunizations[i].instructions%></text>
<% } -%>
<statusCode code="completed"/>
</act>
</entryRelationship>
Expand Down Expand Up @@ -1499,7 +1544,7 @@
<templateId root="2.16.840.1.113883.10.20.22.4.26"/>
<!-- Vital signs organizer template -->
<id root="c6f88320-67ad-11db-bd13-0800200c9a66"/>
<code code="46680005" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED -CT" displayName="Vital signs"/>
<code code="46680005" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Vital signs"/>
<statusCode code="completed"/>
<effectiveTime <%-: bb.vitals[i].date | hl7Date %> />

Expand Down
2 changes: 2 additions & 0 deletions lib/parsers/c32/demographics.js
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Expand Up @@ -40,6 +40,7 @@ Parsers.C32.demographics = function (c32) {

el = patient.tag('guardian');
var guardian_relationship = el.tag('code').attr('displayName'),
guardian_relationship_code = el.tag('code').attr('code'),
guardian_home = el.tag('telecom').attr('value');

el = el.tag('guardianPerson').tag('name');
Expand Down Expand Up @@ -80,6 +81,7 @@ Parsers.C32.demographics = function (c32) {
family: guardian_name_dict.family
},
relationship: guardian_relationship,
relationship_code: guardian_relationship_code,
address: guardian_address_dict,
phone: {
home: guardian_home
Expand Down
13 changes: 9 additions & 4 deletions lib/parsers/c32/medications.js
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Expand Up @@ -95,10 +95,15 @@ Parsers.C32.medications = function (c32) {
route_code_system = el.attr('codeSystem'),
route_code_system_name = el.attr('codeSystemName');

// participant => vehicle
el = entry.tag('participant').tag('code');
var vehicle_name = el.attr('displayName'),
vehicle_code = el.attr('code'),
// participant/playingEntity => vehicle
el = entry.tag('participant').tag('playingEntity');
var vehicle_name = el.tag('name').val();

el = el.tag('code');
// prefer the code vehicle_name but fall back to the non-coded one
// (which for C32s is in fact the primary field for this info)
vehicle_name = el.attr('displayName') || vehicle_name;
var vehicle_code = el.attr('code'),
vehicle_code_system = el.attr('codeSystem'),
vehicle_code_system_name = el.attr('codeSystemName');

Expand Down
2 changes: 2 additions & 0 deletions lib/parsers/ccda/demographics.js
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Expand Up @@ -40,6 +40,7 @@ Parsers.CCDA.demographics = function (ccda) {

el = patient.tag('guardian');
var guardian_relationship = el.tag('code').attr('displayName'),
guardian_relationship_code = el.tag('code').attr('code'),
guardian_home = el.tag('telecom').attr('value');

el = el.tag('guardianPerson').tag('name');
Expand Down Expand Up @@ -81,6 +82,7 @@ Parsers.CCDA.demographics = function (ccda) {
family: guardian_name_dict.family
},
relationship: guardian_relationship,
relationship_code: guardian_relationship_code,
address: guardian_address_dict,
phone: {
home: guardian_home
Expand Down
12 changes: 8 additions & 4 deletions lib/parsers/ccda/medications.js
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Expand Up @@ -82,10 +82,14 @@ Parsers.CCDA.medications = function (ccda) {
route_code_system = el.attr('codeSystem'),
route_code_system_name = el.attr('codeSystemName');

// participant => vehicle
el = entry.tag('participant').tag('code');
var vehicle_name = el.attr('displayName'),
vehicle_code = el.attr('code'),
// participant/playingEntity => vehicle
el = entry.tag('participant').tag('playingEntity');
var vehicle_name = el.tag('name').val();

el = el.tag('code');
// prefer the code vehicle_name but fall back to the non-coded one
vehicle_name = el.attr('displayName') || vehicle_name;
var vehicle_code = el.attr('code'),
vehicle_code_system = el.attr('codeSystem'),
vehicle_code_system_name = el.attr('codeSystemName');

Expand Down
2 changes: 1 addition & 1 deletion lib/parsers/ccda/procedures.js
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Expand Up @@ -39,7 +39,7 @@ Parsers.CCDA.procedures = function (ccda) {
performer_dict.phone = phone;

// participant => device
el = entry.tag('participant').tag('code');
el = entry.template('2.16.840.1.113883.10.20.22.4.37').tag('code');
var device_name = el.attr('displayName'),
device_code = el.attr('code'),
device_code_system = el.attr('codeSystem');
Expand Down
0 spec/javascripts/amd_specs/ccda_spec.js → ...javascripts/amd_specs/ccda_parser_spec.js
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0 spec/javascripts/browser_specs/ccda_spec.js → ...scripts/browser_specs/ccda_parser_spec.js
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