update MIMIC code and reverse testing change (maven said no)
This commit is contained in:
Grahame Grieve
parent
7099f904f5
commit
02791ae21f
File diff suppressed because it is too large
Load Diff
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@ -319,6 +319,25 @@ public class CodeableConcept extends Type implements ICompositeType {
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return super.isEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(coding, text);
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}
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// added from java-adornments.txt:
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public boolean hasCoding(String system, String code) {
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for (Coding c : getCoding()) {
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if (system.equals(c.getSystem()) && code.equals(c.getCode()))
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return true;
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}
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return false;
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}
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public CodeableConcept(Coding code) {
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super();
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addCoding(code);
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}
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// end addition
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}
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@ -31,9 +31,14 @@ import java.io.FileOutputStream;
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import java.io.IOException;
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import java.math.BigDecimal;
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import java.nio.charset.Charset;
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import java.text.DateFormat;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.fhir.ucum.UcumEssenceService;
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@ -53,6 +58,7 @@ import org.hl7.fhir.r4.model.DocumentReference;
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import org.hl7.fhir.r4.model.Encounter;
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import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
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import org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus;
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import org.hl7.fhir.r4.model.InstantType;
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import org.hl7.fhir.r4.model.MedicationRequest;
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import org.hl7.fhir.r4.model.MedicationRequest.MedicationRequestStatus;
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import org.hl7.fhir.r4.model.Observation;
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@ -61,11 +67,15 @@ import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Practitioner;
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import org.hl7.fhir.r4.model.PractitionerRole;
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import org.hl7.fhir.r4.model.Procedure;
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import org.hl7.fhir.r4.model.Procedure.ProcedureStatus;
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import org.hl7.fhir.r4.model.Quantity;
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import org.hl7.fhir.r4.model.Quantity.QuantityComparator;
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import org.hl7.fhir.r4.model.Range;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.Type;
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import org.hl7.fhir.utilities.CSVReader;
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import org.hl7.fhir.utilities.IniFile;
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import org.hl7.fhir.utilities.Utilities;
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public class Mimic14Importer {
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@ -96,9 +106,10 @@ public class Mimic14Importer {
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private Date date;
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private Map<String, LabItem> labItems = new HashMap<>();
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private Map<String, Item> items = new HashMap<>();
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// private Map<String, PractitionerRole> careGivers = new HashMap<>();
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private Map<String, PractitionerRole> careGivers = new HashMap<>();
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private Map<String, Patient> patients = new HashMap<>();
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private Map<String, Encounter> encounters = new HashMap<>();
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private IniFile ini;
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private UcumService ucum;
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@ -116,6 +127,7 @@ public class Mimic14Importer {
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System.out.println("Loading UCUM from "+ucumSrc);
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ucum = new UcumEssenceService(ucumSrc);
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ini = new IniFile(Utilities.path(src, "translations.ini"));
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loadItems(Utilities.path(src, "d_items.csv"));
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loadLabItems(Utilities.path(src, "d_labitems.csv"));
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@ -127,7 +139,11 @@ public class Mimic14Importer {
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processMicroEvents(Utilities.path(src, "microbiologyevents.csv"), Utilities.path(dest, "micro-observations.json"));
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processNoteEvents(Utilities.path(src, "noteevents.csv"), Utilities.path(dest, "notes.json"));
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processDiagnoses(Utilities.path(src, "diagnoses_icd.csv"), Utilities.path(dest, "diagnoses.json"));
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processProcedures(Utilities.path(src, "procedures_icd.csv"), Utilities.path(dest, "procedures.json"));
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processPrescriptions(Utilities.path(src, "prescriptions.csv"), Utilities.path(dest, "prescriptions.json"));
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processProcedureEvents(Utilities.path(src, "procedureevents_mv.csv"), Utilities.path(dest, "procedure-events.json"));
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processOutputEvents(Utilities.path(src, "outputevents.csv"), Utilities.path(dest, "outputs.json"));
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processChartEvents(Utilities.path(src, "chartevents.csv"), Utilities.path(dest, "chartevents.json"));
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System.out.println("saving");
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@ -198,6 +214,7 @@ public class Mimic14Importer {
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t++;
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pr.setId(csv.cell("cgid"));
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pr.addCode().addCoding().setSystem("http://mimic.physionet.org/fhir/CareGiverType").setCode(csv.cell("label")).setDisplay(csv.cell("description"));
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careGivers.put(pr.getId(), pr);
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bnd.addEntry().setResource(pr);
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}
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System.out.println(Integer.toString(t)+" found");
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@ -232,7 +249,7 @@ public class Mimic14Importer {
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obs.setEffective(readDateTime(csv.cell("charttime")));
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if (item != null) {
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if (!Utilities.noString(item.category)) {
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obs.addCategory().setText(item.category);
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obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode(item.category);
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}
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obs.getCode().setText(item.label);
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if (!Utilities.noString(item.fluid)) {
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@ -244,14 +261,7 @@ public class Mimic14Importer {
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}
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if (csv.has("valuenum")) {
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Quantity qty = new Quantity();
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qty.setValue(new BigDecimal(csv.cell("valuenum")));
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String uom = csv.cell("valueuom");
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qty.setUnit(uom);
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if (ucum.validate(uom) == null) {
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qty.setCode(uom);
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qty.setSystem("http://unitsofmeasure.org");
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}
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Quantity qty = parseQuantity(csv.cell("valuenum"), "valueuom");
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obs.setValue(qty);
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} else {
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obs.setValue(new CodeableConcept().setText(csv.cell("value")));
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@ -306,7 +316,7 @@ public class Mimic14Importer {
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cache.put(cacheId, obs);
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obs.setId(csv.cell("row_id"));
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obs.setStatus(ObservationStatus.FINAL);
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obs.addCategory().setText("microbiology");
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obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("microbiology");
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bnd.addEntry().setResource(obs);
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@ -594,6 +604,41 @@ public class Mimic14Importer {
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new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);
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}
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private void processProcedures(String src, String dest) throws FileNotFoundException, IOException {
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System.out.print("Processing Procedures... ");
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CSVReader csv = new CSVReader(new FileInputStream(src));
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Bundle bnd = new Bundle();
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bnd.setId("procedures");
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bnd.setType(BundleType.COLLECTION);
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bnd.setTimestamp(date);
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csv.readHeaders();
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int t = 0;
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while (csv.line()) {
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Procedure prc = new Procedure();
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t++;
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Patient pat = patients.get(csv.cell("subject_id"));
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Encounter enc = encounters.get(csv.cell("hadm_id"));
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prc.setId(csv.cell("row_id"));
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prc.setStatus(ProcedureStatus.UNKNOWN);
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prc.getCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("diagnosis");
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if (pat != null) {
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prc.setSubject(new Reference("Patient/"+pat.getId()));
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}
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if (enc != null) {
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prc.setEncounter(new Reference("Encounter/"+enc.getId()));
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enc.addDiagnosis().setCondition(new Reference("Procedure/"+prc.getId())).setRank(Integer.parseInt(csv.cell("seq_num")));
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}
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prc.setCode(new CodeableConcept(new Coding().setCode(csv.cell("icd9_code")).setSystem("http://hl7.org/fhir/sid/icd-9-cm")));
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bnd.addEntry().setResource(prc);
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}
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System.out.println(Integer.toString(t)+" found");
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csv.close();
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new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);
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}
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private void processPrescriptions(String src, String dest) throws FHIRException, FileNotFoundException, IOException {
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System.out.print("Processing Prescriptions... ");
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CSVReader csv = new CSVReader(new FileInputStream(src));
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@ -618,20 +663,238 @@ public class Mimic14Importer {
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if (enc != null) {
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med.setEncounter(new Reference("Encounter/"+enc.getId()));
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}
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med.getDispenseRequest().getValidityPeriod().setStartElement(readDateTime(csv.cell("startdate")));
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med.getDispenseRequest().getValidityPeriod().setEndElement(readDateTime(csv.cell("enddate")));
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med.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode(csv.cell("drug_type"));
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CodeableConcept cc = new CodeableConcept();
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cc.setText(csv.cell("drug"));
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if (csv.has("formulary_drug_cd")) {
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cc.addCoding().setSystem("http://mimic.physionet.org/fhir/drugs").setCode(csv.cell("formulary_drug_cd"));
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}
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med.setMedication(cc);
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// if (csv.has("gsn")) {
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// cc.addCoding().setSystem("http://hl7.org/fhir/sid/GSN?").setCode(csv.cell("gsn"));
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// }
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if (csv.has("ndc")) {
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cc.addCoding().setSystem("http://hl7.org/fhir/sid/ndc").setCode(csv.cell("ndc"));
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}
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// cnd.setCode(new CodeableConcept(new Coding().setCode(csv.cell("icd9_code")).setSystem("http://hl7.org/fhir/sid/icd-9-cm")));
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//PROD_STRENGTH, DOSE_VAL_RX, DOSE_UNIT_RX - ignore as denomormalizations
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if (csv.has("dose_val_rx")) {
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try {
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med.getDosageInstructionFirstRep().getDoseAndRateFirstRep().setDose(parseQuantityRange(csv.cell("dose_val_rx"), csv.cell("dose_unit_rx")));
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} catch (Exception e) {
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med.getDosageInstructionFirstRep().setText(csv.cell("dose_val_rx"));
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}
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}
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if (csv.has("route")) {
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med.getDosageInstructionFirstRep().getRoute().addCoding().setSystem("http://mimic.physionet.org/fhir/route").setCode(csv.cell("route"));
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}
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bnd.addEntry().setResource(med);
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}
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System.out.println(Integer.toString(t)+" found");
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csv.close();
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new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);
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}
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private Type parseQuantity(String cell) {
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private void processProcedureEvents(String src, String dest) throws FileNotFoundException, IOException {
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System.out.print("Processing Procedure Events... ");
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CSVReader csv = new CSVReader(new FileInputStream(src));
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Bundle bnd = new Bundle();
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bnd.setId("procedure-events");
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bnd.setType(BundleType.COLLECTION);
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bnd.setTimestamp(date);
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csv.readHeaders();
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int t = 0;
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while (csv.line()) {
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Procedure prc = new Procedure();
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t++;
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Patient pat = patients.get(csv.cell("subject_id"));
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Encounter enc = encounters.get(csv.cell("hadm_id"));
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prc.setId(csv.cell("row_id"));
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prc.setStatus(ProcedureStatus.UNKNOWN);
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prc.getCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("diagnosis");
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if (pat != null) {
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prc.setSubject(new Reference("Patient/"+pat.getId()));
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}
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if (enc != null) {
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prc.setEncounter(new Reference("Encounter/"+enc.getId()));
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}
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prc.getPerformedPeriod().setStartElement(readDateTime(csv.cell("starttime")));
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prc.getPerformedPeriod().setEndElement(readDateTime(csv.cell("endtime")));
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Item spec = items.get(csv.cell("itemid"));
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if (spec != null)
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prc.setCode(new CodeableConcept(new Coding().setSystem("http://mimic.physionet.org/fhir/procedures").setCode(csv.cell("itemid")).setDisplay(spec.label)));
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if (csv.has("location"))
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prc.addBodySite().setText(csv.cell("location"));
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bnd.addEntry().setResource(prc);
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}
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System.out.println(Integer.toString(t)+" found");
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csv.close();
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new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);
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}
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private void processOutputEvents(String src, String dest) throws FileNotFoundException, IOException {
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System.out.print("Processing Output Events... ");
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CSVReader csv = new CSVReader(new FileInputStream(src));
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Bundle bnd = new Bundle();
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bnd.setId("output-events");
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bnd.setType(BundleType.COLLECTION);
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bnd.setTimestamp(date);
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csv.readHeaders();
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int t = 0;
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while (csv.line()) {
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t++;
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Patient pat = patients.get(csv.cell("subject_id"));
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Encounter enc = encounters.get(csv.cell("hadm_id"));
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Item spec = items.get(csv.cell("itemid"));
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String loinc = ini.getStringProperty("outputs", csv.cell("itemid"));
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if (loinc != null) {
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if (!loinc.equals("n/a")) {
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String value = null;
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if (loinc.contains(";")) {
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String[] p = loinc.split("\\;");
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value=p[1].trim();
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loinc = p[0];
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}
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Observation obs = new Observation();
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obs.setId(csv.cell("row_id"));
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obs.setStatus(ObservationStatus.FINAL);
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obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("output");
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if (pat != null) {
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obs.setSubject(new Reference("Patient/"+pat.getId()));
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}
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if (enc != null) {
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obs.setEncounter(new Reference("Encounter/"+enc.getId()));
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}
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obs.setEffective(readDateTime(csv.cell("charttime")));
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if (spec != null) {
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obs.setCode(new CodeableConcept(loincCoding(loinc)).setText(spec.label));
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obs.getCode().addCoding().setSystem("http://mimic.physionet.org/fhir/outputs").setCode(csv.cell("itemid"));
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}
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if (value != null) {
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obs.setValue(new CodeableConcept().setText(value));
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} else {
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Quantity qty = parseQuantity(csv.cell("value"), "valueuom");
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obs.setValue(qty);
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}
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obs.setIssuedElement(readInstant(csv.cell("storetime")));
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PractitionerRole prr = careGivers.get(csv.cell("cgid"));
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if (prr != null)
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obs.addPerformer().setReference("PractitionerRole/"+prr.getId());
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bnd.addEntry().setResource(obs);
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}
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} else {
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throw new Error("No LOINC code for output event "+csv.cell("itemid")+" ("+(spec == null ? "n/a" : spec.label)+"="+csv.cell("value")+")");
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}
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}
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System.out.println(Integer.toString(t)+" found");
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csv.close();
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new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);
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}
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private void processChartEvents(String src, String dest) throws FileNotFoundException, IOException {
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System.out.print("Processing Chart Events... ");
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CSVReader csv = new CSVReader(new FileInputStream(src));
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Bundle bnd = new Bundle();
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bnd.setId("chart-events");
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bnd.setType(BundleType.COLLECTION);
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bnd.setTimestamp(date);
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csv.readHeaders();
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int t = 0;
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while (csv.line()) {
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t++;
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Patient pat = patients.get(csv.cell("subject_id"));
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Encounter enc = encounters.get(csv.cell("hadm_id"));
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Item spec = items.get(csv.cell("itemid"));
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if (spec != null) {
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Observation obs = new Observation();
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obs.setId(csv.cell("row_id"));
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obs.setStatus(ObservationStatus.FINAL);
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obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("chart");
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if (pat != null) {
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obs.setSubject(new Reference("Patient/"+pat.getId()));
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}
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if (enc != null) {
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obs.setEncounter(new Reference("Encounter/"+enc.getId()));
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}
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obs.setEffective(readDateTime(csv.cell("charttime")));
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obs.getCode().setText(spec.label).addCoding().setSystem("http://mimic.physionet.org/fhir/outputs").setCode(csv.cell("itemid"));
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String loinc = ini.getStringProperty("chartevents", csv.cell("itemid"));
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String value = null;
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if (!Utilities.noString(loinc)) {
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if (loinc.contains(";")) {
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String[] p = loinc.split("\\;");
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value=p[1].trim();
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loinc = p[0];
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}
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obs.getCode().addCoding(loincCoding(loinc));
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}
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if (value != null) {
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obs.setValue(new CodeableConcept().setText(value));
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} else if (csv.has("valuenum")) {
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Quantity qty = parseQuantity(csv.cell("valuenum"), "valueuom");
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obs.setValue(qty);
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} else {
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obs.setValue(new CodeableConcept().setText(csv.cell("value")));
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}
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obs.setIssuedElement(readInstant(csv.cell("storetime")));
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PractitionerRole prr = careGivers.get(csv.cell("cgid"));
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if (prr != null)
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obs.addPerformer().setReference("PractitionerRole/"+prr.getId());
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bnd.addEntry().setResource(obs);
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}
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}
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System.out.println(Integer.toString(t)+" found");
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csv.close();
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new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);
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}
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|
||||
private Coding loincCoding(String loinc) {
|
||||
Coding c = new Coding();
|
||||
String[] p = loinc.split("\\#");
|
||||
c.setSystem(p[0]);
|
||||
p = p[1].split("\\:");
|
||||
c.setCode(p[0]);
|
||||
c.setDisplay(p[1].trim());
|
||||
return c;
|
||||
}
|
||||
|
||||
private Type parseQuantityRange(String cell, String uom) {
|
||||
if (!Utilities.noString(cell) && cell.contains("-")) {
|
||||
String[] p = cell.split("\\-");
|
||||
Range rng = new Range();
|
||||
rng.setLow(parseQuantity(p[0], uom));
|
||||
rng.setHigh(parseQuantity(p[1], uom));
|
||||
return rng;
|
||||
} else
|
||||
return parseQuantity(cell, uom);
|
||||
}
|
||||
private Quantity parseQuantity(String cell, String uom) {
|
||||
if (Utilities.noString(cell))
|
||||
return null;
|
||||
Quantity qty = parseQuantity(cell);
|
||||
if (!Utilities.noString(uom)) {
|
||||
qty.setUnit(uom);
|
||||
if (ucum.validate(uom) == null) {
|
||||
qty.setCode(uom);
|
||||
qty.setSystem("http://unitsofmeasure.org");
|
||||
}
|
||||
}
|
||||
return qty;
|
||||
}
|
||||
|
||||
private Quantity parseQuantity(String cell) {
|
||||
if (cell.startsWith("<=")) {
|
||||
return new Quantity().setComparator(QuantityComparator.LESS_OR_EQUAL).setValue(new BigDecimal(cell.substring(2)));
|
||||
}
|
||||
|
|
@ -645,7 +908,7 @@ public class Mimic14Importer {
|
|||
return new Quantity().setComparator(QuantityComparator.GREATER_THAN).setValue(new BigDecimal(cell.substring(2)));
|
||||
}
|
||||
if (!Utilities.isDecimal(cell, true)) {
|
||||
throw new Error("Not a valid decimal: "+cell);
|
||||
throw new FHIRException("Not a valid decimal: "+cell);
|
||||
}
|
||||
|
||||
return new Quantity().setValue(new BigDecimal(cell));
|
||||
|
|
@ -734,15 +997,26 @@ public class Mimic14Importer {
|
|||
|
||||
|
||||
private DateType readDate(String cell) {
|
||||
if (Utilities.noString(cell))
|
||||
return null;
|
||||
String src = cell.substring(0, 10);
|
||||
return new DateType(src);
|
||||
}
|
||||
|
||||
private DateTimeType readDateTime(String cell) {
|
||||
if (Utilities.noString(cell))
|
||||
return null;
|
||||
String src = cell.replace(" ", "T");
|
||||
if (src.endsWith("00:00:00"))
|
||||
src = cell.substring(0, 10);
|
||||
return new DateTimeType(src);
|
||||
}
|
||||
|
||||
private InstantType readInstant(String cell) {
|
||||
if (Utilities.noString(cell))
|
||||
return null;
|
||||
String src = cell.replace(" ", "T");
|
||||
return new InstantType(src);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
package org.hl7.fhir.r5.test;
|
||||
package org.hl7.fhir.r5.test.utils;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
|
|
@ -17,6 +17,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
|
|||
import org.hl7.fhir.r5.elementmodel.Manager;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
|
||||
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.FHIRPathEngine;
|
||||
import org.hl7.fhir.utilities.cache.PackageCacheManager;
|
||||
import org.hl7.fhir.utilities.cache.ToolsVersion;
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
|
|||
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
|
||||
import org.hl7.fhir.r5.model.StructureMap;
|
||||
import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@ import org.hl7.fhir.r5.model.Quantity;
|
|||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.model.TypeDetails;
|
||||
import org.hl7.fhir.r5.model.ValueSet;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.FHIRPathEngine;
|
||||
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
|
|
|
|||
|
|
@ -9,6 +9,7 @@ import org.hl7.fhir.r5.model.Bundle;
|
|||
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
|
||||
import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
|
||||
import org.hl7.fhir.r5.model.Bundle.SearchEntryMode;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.model.DomainResource;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.utils.GraphQLEngine;
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@ import java.io.IOException;
|
|||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.graphql.EGraphEngine;
|
||||
|
|
|
|||
|
|
@ -14,6 +14,7 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
|
|||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.LiquidEngine;
|
||||
import org.hl7.fhir.r5.utils.LiquidEngine.ILiquidEngineIcludeResolver;
|
||||
import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import org.hl7.fhir.exceptions.FHIRException;
|
|||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.model.DomainResource;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.EOperationOutcome;
|
||||
import org.hl7.fhir.r5.utils.NarrativeGenerator;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import org.hl7.fhir.r5.formats.JsonParser;
|
|||
import org.hl7.fhir.r5.model.CapabilityStatement;
|
||||
import org.hl7.fhir.r5.openapi.OpenApiGenerator;
|
||||
import org.hl7.fhir.r5.openapi.Writer;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.utilities.xml.XMLUtil;
|
||||
import org.junit.Test;
|
||||
import org.w3c.dom.Document;
|
||||
|
|
|
|||
|
|
@ -16,6 +16,7 @@ import org.hl7.fhir.r5.model.Base;
|
|||
import org.hl7.fhir.r5.model.ElementDefinition;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.EOperationOutcome;
|
||||
import org.hl7.fhir.utilities.CSFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
|
|
|
|||
|
|
@ -19,6 +19,7 @@ import org.hl7.fhir.r5.formats.XmlParser;
|
|||
import org.hl7.fhir.r5.model.Bundle;
|
||||
import org.hl7.fhir.r5.model.DomainResource;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.EOperationOutcome;
|
||||
import org.hl7.fhir.r5.utils.NarrativeGenerator;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ import org.hl7.fhir.r5.conformance.ShExGenerator;
|
|||
import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy;
|
||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.junit.Test;
|
||||
|
||||
|
|
|
|||
|
|
@ -43,6 +43,7 @@ import org.hl7.fhir.r5.model.TestScript.TestActionComponent;
|
|||
import org.hl7.fhir.r5.model.TestScript.TestScriptFixtureComponent;
|
||||
import org.hl7.fhir.r5.model.TestScript.TestScriptTestComponent;
|
||||
import org.hl7.fhir.r5.test.SnapShotGenerationTests.TestFetchMode;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.model.TypeDetails;
|
||||
import org.hl7.fhir.r5.model.ValueSet;
|
||||
import org.hl7.fhir.r5.utils.CodingUtilities;
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
|||
import org.hl7.fhir.r5.model.Base;
|
||||
import org.hl7.fhir.r5.model.Coding;
|
||||
import org.hl7.fhir.r5.model.StructureMap;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.EOperationOutcome;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ package org.hl7.fhir.r5.test;
|
|||
import java.io.FileNotFoundException;
|
||||
import java.io.IOException;
|
||||
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.formats.Turtle;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
|
|||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.test.TestingUtilities;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
|
||||
public class ResourceTest {
|
||||
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ import org.hl7.fhir.exceptions.FHIRException;
|
|||
import org.hl7.fhir.exceptions.FHIRFormatError;
|
||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.model.StructureMap;
|
||||
import org.hl7.fhir.r5.test.TestingUtilities;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.StructureMapUtilities;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@ import com.google.gson.JsonObject;
|
|||
public class PackageHacker {
|
||||
|
||||
public static void main(String[] args) throws FileNotFoundException, IOException {
|
||||
new PackageHacker().edit("C:\\web\\hl7.org\\fhir\\us\\qicore\\STU2\\package.tgz");
|
||||
new PackageHacker().edit("C:\\work\\fhir.org\\web-source\\source\\guides\\argonaut\\questionnaire\\package.tgz");
|
||||
}
|
||||
|
||||
private void edit(String name) throws FileNotFoundException, IOException {
|
||||
|
|
@ -54,8 +54,8 @@ public class PackageHacker {
|
|||
}
|
||||
|
||||
private void change(JsonObject npm, Map<String, byte[]> content) {
|
||||
npm.remove("version");
|
||||
npm.addProperty("version", "2.0.0");
|
||||
npm.remove("name");
|
||||
npm.addProperty("name", "fhir.argonaut.questionnaire");
|
||||
// JsonArray fhirVersions = new JsonArray();
|
||||
// fhirVersions.add("1.9.0");
|
||||
// npm.add("fhirVersions", fhirVersions);
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
package org.hl7.fhir.validation.tests;
|
||||
|
||||
import org.hl7.fhir.r4.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.test.TestingUtilities;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.validation.Validator;
|
||||
import org.hl7.fhir.validation.tests.utilities.TestUtilities;
|
||||
import org.junit.Test;
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
package org.hl7.fhir.validation.tests;
|
||||
|
||||
import org.hl7.fhir.r5.test.TestingUtilities;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.validation.NativeHostServices;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.validation.tests.utilities.TestUtilities;
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ import org.hl7.fhir.r5.model.OperationOutcome;
|
|||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.r5.utils.KeyGenerator;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
|
||||
import org.hl7.fhir.r5.test.TestingUtilities;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.validation.ValidationEngine;
|
||||
import org.hl7.fhir.validation.tests.utilities.TestUtilities;
|
||||
import org.junit.Assert;
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ import org.hl7.fhir.r5.model.FhirPublication;
|
|||
import org.hl7.fhir.r5.model.OperationOutcome;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
|
||||
import org.hl7.fhir.r5.test.TestingUtilities;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.validation.ValidationEngine;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.validation.tests.utilities.TestUtilities;
|
||||
|
|
|
|||
|
|
@ -21,7 +21,7 @@ import org.hl7.fhir.r5.elementmodel.ObjectConverter;
|
|||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.model.*;
|
||||
import org.hl7.fhir.r5.test.TestingUtilities;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
|
||||
import org.hl7.fhir.r5.utils.IResourceValidator;
|
||||
import org.hl7.fhir.r5.utils.IResourceValidator.IValidatorResourceFetcher;
|
||||
|
|
|
|||
Loading…
Reference in New Issue