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org.hl7.fhir.core
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fix rendering of profiles in choice rows

This commit is contained in:
Grahame Grieve 2019-10-29 12:31:58 +11:00
parent 1a789dae9b
commit cc496623a6
4 changed files with 110 additions and 11 deletions
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1
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/R3TEchnicalCorrectionProcessor.java
View File

@ -142,6 +142,7 @@ public class R3TEchnicalCorrectionProcessor {
} else {
dst = new FileOutputStream(Utilities.path(examplesPath, n));
new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(dst, r);
examplesCount++;
if (isCoreResource(r.fhirType())) {
coreCount++;
DomainResource dr = (DomainResource) r;

86
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/importers/Mimic14Importer.java
View File

@ -291,6 +291,7 @@ public class Mimic14Importer {
Item ab = items.get(csv.cell("ab_itemid"));
Observation obs;
boolean isCulture = true;
if (cache.containsKey(cacheId)) {
obs = cache.get(cacheId);
} else {
@ -302,8 +303,37 @@ public class Mimic14Importer {
obs.addCategory().setText("microbiology");
bnd.addEntry().setResource(obs);
// todo: these are all cultures, but the codes state mainly what the culture is on
obs.getCode().setText(csv.cell("spec_itemid"));
obs.getCode().setText(csv.cell("spec_type_desc"));
if ("70012".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("600-7").setDisplay("Bacteria identified in Blood by Culture");
} else if ("70079".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("630-4").setDisplay("Bacteria identified in Urine by Culture");
} else if ("70064".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("625-4").setDisplay("Bacteria identified in Stool by Culture");
} else if ("70053".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("619-7").setDisplay("Bacteria identified in Peritoneal fluid by Culture");
// } else if ("70013".equals(csv.cell("spec_itemid"))) {
// obs.getCode().addCoding().setSystem("http://loinc.org").setCode().setDisplay();
} else if ("70023".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("19128-8").setDisplay("Bacteria identified in Catheter tip by Culture");
} else if ("70046".equals(csv.cell("spec_itemid"))) {
isCulture = false;
obs.getCode().setText("HIV-1 Viral Load/Ultrasensitive");
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("20447-9").setDisplay("HIV 1 RNA [#/volume] (viral load) in Serum or Plasma by NAA with probe detection");
} else if ("70051".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("6463-4").setDisplay("Bacteria identified in Unspecified specimen by Culture");
} else if ("70062".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("6460-0").setDisplay("Bacteria identified in Sputum by Culture");
} else if ("70067".equals(csv.cell("spec_itemid"))) {
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("6462-6").setDisplay("Bacteria identified in Wound by Culture");
} else if ("70070".equals(csv.cell("spec_itemid"))) { // check...
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("6462-6").setDisplay("Bacteria identified in Wound by Culture");
} else if ("70091".equals(csv.cell("spec_itemid"))) { // check...
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("13317-3").setDisplay("Methicillin resistant Staphylococcus aureus [Presence] in Unspecified specimen by Organism specific culture");
} else
throw new Error("Not coded yet: "+csv.cell("spec_itemid"));
obs.getCode().addCoding().setSystem("http://mimic.physionet.org/fhir/TestType").setCode(csv.cell("spec_itemid"));
}
@ -324,9 +354,59 @@ public class Mimic14Importer {
} else {
obs.setValue(new CodeableConcept(new Coding().setSystem("http://mimic.physionet.org/fhir/Organism").setCode(csv.cell("org_itemid"))).setText(csv.cell("org_name")));
}
if (ab != null) {
// todo: make this members not components
if (isCulture && ab != null) {
ObservationComponentComponent oc = obs.addComponent();
oc.setCode(new CodeableConcept(new Coding().setSystem("http://mimic.physionet.org/fhir/Antibiotic").setCode(csv.cell("ab_itemid"))).setText(csv.cell("ab_name")));
if ("90015".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("19000-9").setDisplay("Vancomycin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90012".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18928-2").setDisplay("Gentamicin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90025".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("20629-2").setDisplay("levoFLOXacin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90016".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18961-3").setDisplay("Oxacillin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90011".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18993-6").setDisplay("Tetracycline [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90006".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18919-1").setDisplay("Erythromycin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90002".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18964-7").setDisplay("Penicillin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90004".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18864-9").setDisplay("Ampicillin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90005".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18878-9").setDisplay("ceFAZolin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90007".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18908-4").setDisplay("Clindamycin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90008".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18997-7").setDisplay("Trimethoprim [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90010".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18955-5").setDisplay("Nitrofurantoin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90020".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18932-4").setDisplay("Imipenem [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90021".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18969-6").setDisplay("Piperacillin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90013".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18996-9").setDisplay("Tobramycin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90017".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18893-8").setDisplay("cefTAZidime [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90018".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18895-3").setDisplay("cefTRIAXone [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90019".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18906-8").setDisplay("Ciprofloxacin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90022".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18865-6").setDisplay("Ampicillin+Sulbactam [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90023".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("51724-3").setDisplay("Cefuroxime [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90026".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18969-6").setDisplay("Piperacillin [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90028".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18879-7").setDisplay("Cefepime [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90029".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("18943-1").setDisplay("Meropenem [Susceptibility]")).setText(csv.cell("ab_name")));
} else if ("90031".equals(csv.cell("ab_itemid"))) {
oc.setCode(new CodeableConcept(new Coding().setSystem("http://loinc.org").setCode("29258-1").setDisplay("Linezolid [Susceptibility]")).setText(csv.cell("ab_name")));
} else
throw new Error("Not coded yet: "+csv.cell("ab_itemid"));
if (csv.has("dilution_text")) {
oc.setValue(parseQuantity(csv.cell("dilution_text")));
}

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -2914,6 +2914,9 @@ public class ProfileUtilities extends TranslatingUtilities {
genTargetLink(gen, profileBaseFileName, corePath, c, tr, rt.getValue());
first = false;
}
if (first)
c.getPieces().add(gen.new Piece(null, "Any", null));
if (ADD_REFERENCE_TO_TABLE)
c.getPieces().add(gen.new Piece(null, ")", null));
@ -2939,6 +2942,21 @@ public class ProfileUtilities extends TranslatingUtilities {
choicerow.setIcon("icon_datatype.gif", HierarchicalTableGenerator.TEXT_ICON_DATATYPE);
choicerow.getCells().add(gen.new Cell(null, pkp.getLinkFor(corePath, t), t, null, null));
}
if (tr.hasProfile()) {
Cell typeCell = choicerow.getCells().get(3);
typeCell.addPiece(gen.new Piece(null, "(", null));
boolean first = true;
for (CanonicalType pt : tr.getProfile()) {
if (first) first = false; else typeCell.addPiece(gen.new Piece(null, " | ", null));
StructureDefinition psd = context.fetchResource(StructureDefinition.class, pt.getValue());
if (psd == null)
typeCell.addPiece(gen.new Piece(null, "??", null));
else
typeCell.addPiece(gen.new Piece(psd.getUserString("path"), psd.getName(), psd.present()));
}
typeCell.addPiece(gen.new Piece(null, ")", null));
}
}
choicerow.getCells().add(gen.new Cell());
subRows.add(choicerow);

16
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ElementDefinition.java
View File

@ -2288,11 +2288,11 @@ public class ElementDefinition extends BackboneType implements ICompositeType {
return null;
if (getCodeElement().hasExtension(ToolingExtensions.EXT_XML_TYPE)) {
String s = getCodeElement().getExtensionString(ToolingExtensions.EXT_XML_TYPE);
if ("xsd:gYear OR xsd:gYearMonth OR xsd:date OR xsd:dateTime".equals(s))
if ("xsd:gYear OR xsd:gYearMonth OR xsd:date OR xsd:dateTime".equalsIgnoreCase(s))
return "dateTime";
if ("xsd:gYear OR xsd:gYearMonth OR xsd:date".equals(s))
if ("xsd:gYear OR xsd:gYearMonth OR xsd:date".equalsIgnoreCase(s))
return "date";
if ("xsd:dateTime".equals(s))
if ("xsd:dateTime".equalsIgnoreCase(s))
return "instant";
if ("xsd:token".equals(s))
return "code";
@ -2306,15 +2306,15 @@ public class ElementDefinition extends BackboneType implements ICompositeType {
return "integer";
if ("xsd:decimal OR xsd:double".equals(s))
return "decimal";
if ("xsd:decimal".equals(s))
if ("xsd:decimal".equalsIgnoreCase(s))
return "decimal";
if ("xsd:base64Binary".equals(s))
if ("xsd:base64Binary".equalsIgnoreCase(s))
return "base64Binary";
if ("xsd:positiveInteger".equals(s))
if ("xsd:positiveInteger".equalsIgnoreCase(s))
return "positiveInt";
if ("xsd:nonNegativeInteger".equals(s))
if ("xsd:nonNegativeInteger".equalsIgnoreCase(s))
return "unsignedInt";
if ("xsd:anyURI".equals(s))
if ("xsd:anyURI".equalsIgnoreCase(s))
return "uri";
throw new Error("Unknown xml type '"+s+"'");