Examples with Rule org.hl7.fhir.utilities.xml.SchematronWriter.Rule used on opensource projects

Example 96 with Rule

use of org.hl7.fhir.utilities.xml.SchematronWriter.Rule in project beneficiary-fhir-data by CMSgov.

the class BeneficiaryTransformerV2Test method shouldIncludeMedicareExtensionIdentifierWithHistory.

@Test
public void shouldIncludeMedicareExtensionIdentifierWithHistory() {
    createPatient(getRHwithIncldIdentityHdr("mbi"));
    List<Identifier> patientIdentList = patient.getIdentifier();
    assertEquals(2, patientIdentList.size());
    ArrayList<Identifier> compareIdentList = new ArrayList<Identifier>();
    Identifier ident = TransformerTestUtilsV2.createIdentifier("https://bluebutton.cms.gov/resources/variables/bene_id", "567834", "http://terminology.hl7.org/CodeSystem/v2-0203", "MB", "Member Number");
    compareIdentList.add(ident);
    Extension extension = new Extension("https://bluebutton.cms.gov/resources/codesystem/identifier-currency", new Coding("https://bluebutton.cms.gov/resources/codesystem/identifier-currency", "current", "Current"));
    Period period = new Period();
    try {
        Date start = (new SimpleDateFormat("yyyy-MM-dd")).parse("2020-07-30");
        period.setStart(start, TemporalPrecisionEnum.DAY);
    } catch (Exception e) {
    }
    ident = new Identifier();
    ident.setValue("3456789").setSystem("http://hl7.org/fhir/sid/us-mbi").setPeriod(period).getType().addCoding().setCode("MC").setSystem("http://terminology.hl7.org/CodeSystem/v2-0203").setDisplay("Patient's Medicare number").addExtension(extension);
    compareIdentList.add(ident);
    /**
     * We have implemented a rule that for a valid MBI history record it has to have an end date; if
     * no end date then the MBI has probably been provided by the CURRENT MBI extension. the
     * following code is therefore commented out until the current Sample_A rif data provides a
     * valid MedicareBeneficiaryIdHistory record.
     */
    /*
    extension =
        new Extension(
            "https://bluebutton.cms.gov/resources/codesystem/identifier-currency",
            new Coding(
                "https://bluebutton.cms.gov/resources/codesystem/identifier-currency",
                "historic",
                "Historic"));

    ident = new Identifier();
    ident
        .setValue("9AB2WW3GR44")
        .setSystem("http://hl7.org/fhir/sid/us-mbi")
        .getType()
        .addCoding()
        .setCode("MC")
        .setSystem("http://terminology.hl7.org/CodeSystem/v2-0203")
        .setDisplay("Patient's Medicare number")
        .addExtension(extension);
    compareIdentList.add(ident);
    */
    assertEquals(compareIdentList.size(), patientIdentList.size());
    for (int i = 0; i < compareIdentList.size(); i++) {
        assertTrue(compareIdentList.get(i).equalsDeep(patientIdentList.get(i)));
    }
}

Example 97 with Rule

use of org.hl7.fhir.utilities.xml.SchematronWriter.Rule in project fhir-bridge by ehrbase.

the class SmartOnFhirAuthorizationInterceptor method addSmartOFPatientRules.

/**
 * Allos read and write access to all Patients resources for a particular patient Id In FHIR
 * terms, if the resource's Patient compartment matches the provided id, then read and write
 * operations can take place.
 *
 * @param pSmartOnFhirPatientId The patient identifier a resource should have to be allowed for
 *     read or write access.
 * @param rules A list of rules to add to. Rules based on the provided patient id will be added to
 *     this collection.
 */
private void addSmartOFPatientRules(String pSmartOnFhirPatientId, List<IAuthRule> rules) {
    // no create rule -> should be done by keycloak registration at the moment
    IdType sofId = new IdType(Patient.class.getSimpleName(), pSmartOnFhirPatientId);
    rules.addAll(buildReadRule("rule_read_own_sof_patient_resource", Patient.class, Patient.class.getSimpleName(), sofId));
    rules.addAll(buildWriteRule("rule_update_own_sof_patient_resource", Patient.class, Patient.class.getSimpleName(), sofId));
}

Example 98 with Rule

use of org.hl7.fhir.utilities.xml.SchematronWriter.Rule in project kindling by HL7.

the class ResourceValidator method check.

// private List<ValidationMessage> check(String n, BindingSpecification cd) throws Exception {
// List<ValidationMessage> errors = new ArrayList<ValidationMessage>();
// check(errors, n, cd);
// return errors;
// }
private void check(List<ValidationMessage> errors, String path, BindingSpecification cd, String sd, ElementDefn e) throws Exception {
    // basic integrity checks
    List<DefinedCode> ac = cd.getAllCodes(definitions.getCodeSystems(), definitions.getValuesets(), false);
    for (DefinedCode c : ac) {
        String d = c.getCode();
        if (Utilities.noString(d))
            d = c.getId();
        if (Utilities.noString(d))
            d = c.getDisplay();
        if (Utilities.noString(d))
            d = c.getDisplay();
        if (Utilities.noString(c.getSystem()))
            warning(errors, IssueType.STRUCTURE, "Binding @ " + path, !Utilities.noString(c.getDefinition()), "Code " + d + " must have a definition");
        rule(errors, IssueType.STRUCTURE, "Binding @ " + path, !(Utilities.noString(c.getId()) && Utilities.noString(c.getSystem())), "Code " + d + " must have a id or a system");
    }
    // trigger processing into a Heirachical set if necessary
    // rule(errors, IssueType.STRUCTURE, "Binding @ "+path, !cd.isHeirachical() || (cd.getChildCodes().size() < cd.getCodes().size()), "Logic error processing Hirachical code set");
    // now, rules for the source
    hint(errors, IssueType.STRUCTURE, "Binding @ " + path, cd.getBinding() != BindingMethod.Unbound, "Need to provide a binding");
    rule(errors, IssueType.STRUCTURE, "Binding @ " + path, Utilities.noString(cd.getDefinition()) || (cd.getDefinition().charAt(0) == cd.getDefinition().toUpperCase().charAt(0)), "Definition cannot start with a lowercase letter");
    if (cd.getBinding() == BindingMethod.CodeList || (cd.getBinding() == BindingMethod.ValueSet && cd.getStrength() == BindingStrength.REQUIRED && ac.size() > 0 && "code".equals(e.typeCode()))) {
        if (path.toLowerCase().endsWith("status")) {
            if (rule(errors, IssueType.STRUCTURE, path, definitions.getStatusCodes().containsKey(path), "Status element not registered in status-codes.xml")) {
                // rule(errors, IssueType.STRUCTURE, path, e.isModifier(), "Status elements that map to status-codes should be labelled as a modifier");
                ArrayList<String> list = definitions.getStatusCodes().get(path);
                for (DefinedCode c : ac) {
                    boolean ok = false;
                    for (String s : list) {
                        String[] parts = s.split("\\,");
                        for (String p : parts) if (p.trim().equals(c.getCode()))
                            ok = true;
                    }
                    rule(errors, IssueType.STRUCTURE, path, ok, "Status element code \"" + c.getCode() + "\" not found in status-codes.xml");
                }
                for (String s : list) {
                    String[] parts = s.split("\\,");
                    for (String p : parts) {
                        List<String> cl = new ArrayList<>();
                        if (!Utilities.noString(p)) {
                            boolean ok = false;
                            for (DefinedCode c : ac) {
                                cl.add(c.getCode());
                                if (p.trim().equals(c.getCode()))
                                    ok = true;
                            }
                            if (!ok)
                                rule(errors, IssueType.STRUCTURE, path, ok, "Status element code \"" + p + "\" found for " + path + " in status-codes.xml but has no matching code in the resource (codes = " + cl + ")");
                        }
                    }
                }
            }
        }
        StringBuilder b = new StringBuilder();
        for (DefinedCode c : ac) {
            if (!c.getAbstract())
                b.append(" | ").append(c.getCode());
        }
        if (sd.equals("*")) {
            e.setShortDefn(b.toString().substring(3));
            sd = b.toString().substring(3);
        }
        if (sd.contains("|")) {
            if (b.length() < 3)
                throw new Error("surprise");
            String esd = b.substring(3);
            rule(errors, IssueType.STRUCTURE, path, sd.startsWith(esd) || (sd.endsWith("+") && b.substring(3).startsWith(sd.substring(0, sd.length() - 1))), "The short description \"" + sd + "\" does not match the expected (\"" + b.substring(3) + "\")");
        } else {
            rule(errors, IssueType.STRUCTURE, path, cd.getStrength() != BindingStrength.REQUIRED || ac.size() > 12 || ac.size() <= 1 || !hasGoodCode(ac) || isExemptFromCodeList(path), "The short description of an element with a code list should have the format code | code | etc (is " + sd.toString() + ") (" + ac.size() + " codes = \"" + b.toString() + "\")");
        }
    }
    boolean isComplex = !e.typeCode().equals("code");
    if (isComplex && cd.getValueSet() != null && hasInternalReference(cd.getValueSet()) && cd.getStrength() != BindingStrength.EXAMPLE) {
        hint(errors, IssueType.BUSINESSRULE, path, false, "The value " + cd.getValueSet().getUrl() + " defines codes, but is used by a Coding/CodeableConcept @ " + path + ", so it should not use FHIR defined codes");
        cd.getValueSet().setUserData("vs-val-warned", true);
    }
    if (cd.getElementType() == ElementType.Unknown) {
        if (isComplex)
            cd.setElementType(ElementType.Complex);
        else
            cd.setElementType(ElementType.Simple);
    } else if (isComplex && !cd.hasMax())
        rule(errors, IssueType.STRUCTURE, path, cd.getElementType() == ElementType.Complex, "Cannot use a binding from both code and Coding/CodeableConcept elements");
    else
        rule(errors, IssueType.STRUCTURE, path, cd.getElementType() == ElementType.Simple, "Cannot use a binding from both code and Coding/CodeableConcept elements");
    if (isComplex && cd.getValueSet() != null) {
        for (ConceptSetComponent inc : cd.getValueSet().getCompose().getInclude()) if (inc.hasSystem())
            txurls.add(inc.getSystem());
    }
    rule(errors, IssueType.STRUCTURE, "Binding @ " + path, (cd.getElementType() != ElementType.Simple || cd.getStrength() == BindingStrength.REQUIRED || cd.hasMax()) || isExemptFromProperBindingRules(path), "Must be a required binding if bound to a code instead of a Coding/CodeableConcept");
    rule(errors, IssueType.STRUCTURE, "Binding @ " + path, cd.getElementType() != ElementType.Simple || cd.getBinding() != BindingMethod.Unbound, "Need to provide a binding for code elements");
    if (!isComplex && !externalException(path)) {
        ValueSet vs = cd.getValueSet();
        if (warning(errors, IssueType.REQUIRED, path, vs != null || cd.hasReference(), "Unable to resolve value set on 'code' Binding")) {
            hint(errors, IssueType.REQUIRED, path, noExternals(vs), "Bindings for code data types should only use internally defined codes (" + vs.getUrl() + ")");
        // don't disable this without discussion on Zulip
        }
    }
}

Example 99 with Rule

use of org.hl7.fhir.utilities.xml.SchematronWriter.Rule in project kindling by HL7.

the class ResourceValidator method check.

public void check(List<ValidationMessage> errors, String name, ResourceDefn rd) throws Exception {
    for (String s : rd.getHints()) hint(errors, IssueType.INFORMATIONAL, rd.getName(), false, s);
    rule(errors, IssueType.STRUCTURE, rd.getName(), !name.equals("Metadata"), "The name 'Metadata' is not a legal name for a resource");
    rule(errors, IssueType.STRUCTURE, rd.getName(), !name.equals("History"), "The name 'History' is not a legal name for a resource");
    rule(errors, IssueType.STRUCTURE, rd.getName(), !name.equals("Tag"), "The name 'Tag' is not a legal name for a resource");
    rule(errors, IssueType.STRUCTURE, rd.getName(), !name.equals("Tags"), "The name 'Tags' is not a legal name for a resource");
    rule(errors, IssueType.STRUCTURE, rd.getName(), !name.equals("MailBox"), "The name 'MailBox' is not a legal name for a resource");
    rule(errors, IssueType.STRUCTURE, rd.getName(), !name.equals("Validation"), "The name 'Validation' is not a legal name for a resource");
    rule(errors, IssueType.REQUIRED, rd.getName(), name.equals("Parameters") || translations.hasTranslation(name), "The name '" + name + "' is not found in the file translations.xml");
    rule(errors, IssueType.STRUCTURE, rd.getName(), name.length() > 1 && Character.isUpperCase(name.charAt(0)), "Resource Name must start with an uppercase alpha character");
    rule(errors, IssueType.STRUCTURE, rd.getName(), !Utilities.noString(rd.getFmmLevel()), "Resource must have a maturity level");
    // too many downstream issues in the parsers, and it would only happen as a transient thing when designing the resources
    rule(errors, IssueType.REQUIRED, rd.getName(), rd.getRoot().getElements().size() > 0, "A resource must have at least one element in it before the build can proceed");
    // too many downstream issues in the parsers, and it would only happen as a transient thing when designing the resources
    rule(errors, IssueType.REQUIRED, rd.getName(), rd.getWg() != null, "A resource must have a designated owner");
    rule(errors, IssueType.REQUIRED, rd.getName(), !Utilities.noString(rd.getRoot().getW5()), "A resource must have a W5 category");
    rd.getRoot().setMinCardinality(0);
    rd.getRoot().setMaxCardinality(Integer.MAX_VALUE);
    // pattern related rules
    buildW5Mappings(rd.getRoot(), true);
    if ((isWorkflowPattern(rd, "Event") || isWorkflowPattern(rd, "Request")) && hasPatient(rd)) {
        rule(errors, IssueType.STRUCTURE, rd.getName(), rd.getSearchParams().containsKey("patient"), "An 'event' or 'request' resource must have a search parameter 'patient'");
    }
    if (suppressedwarning(errors, IssueType.REQUIRED, rd.getName(), hasW5Mappings(rd) || rd.getName().equals("Binary") || rd.getName().equals("OperationOutcome") || rd.getName().equals("Parameters"), "A resource must have w5 mappings")) {
        String w5Order = listW5Elements(rd);
        String w5CorrectOrder = listW5Correct(rd);
        if (!w5Order.equals(w5CorrectOrder)) {
            warning(errors, IssueType.REQUIRED, rd.getName(), false, "Resource elements are out of order. The correct order is '" + w5CorrectOrder + "' but the actual order is '" + w5Order + "'");
        // System.out.println("Resource "+parent.getName()+": elements are out of order. The correct order is '"+w5CorrectOrder+"' but the actual order is '"+w5Order+"'");
        }
        if (!Utilities.noString(rd.getProposedOrder())) {
            w5Order = listW5Elements(rd, rd.getProposedOrder());
            if (!w5Order.equals(w5CorrectOrder)) {
                rule(errors, IssueType.REQUIRED, rd.getName(), false, "Proposed Resource elements are out of order. The correct order is '" + w5CorrectOrder + "' but the proposed order is '" + w5Order + "'");
            } else
                System.out.println("Proposed order for " + rd.getName() + ": build order ok");
        }
    }
    if (Utilities.noString(rd.getEnteredInErrorStatus()))
        if (hasStatus(rd, "entered-in-error"))
            rd.setEnteredInErrorStatus(".status = entered-in-error");
        else if (hasStatus(rd, "retired"))
            rd.setEnteredInErrorStatus(".status = retired");
        else if (hasActivFalse(rd))
            rd.setEnteredInErrorStatus(".active = false");
        else
            // too many downstream issues in the parsers, and it would only happen as a transient thing when designing the resources
            warning(errors, IssueType.REQUIRED, rd.getName(), false, "A resource must have an 'entered in error' status");
    String s = rd.getRoot().getMapping(Definitions.RIM_MAPPING);
    hint(errors, IssueType.REQUIRED, rd.getName(), !Utilities.noString(s), "RIM Mapping is required");
    for (Operation op : rd.getOperations()) {
        warning(errors, IssueType.BUSINESSRULE, rd.getName() + ".$" + op.getName(), hasOpExample(op.getExamples(), false), "Operation must have an example request");
        warning(errors, IssueType.BUSINESSRULE, rd.getName() + ".$" + op.getName(), hasOpExample(op.getExamples(), true), "Operation must have an example response");
    }
    List<String> vsWarns = new ArrayList<String>();
    int vsWarnings = checkElement(errors, rd.getName(), rd.getRoot(), rd, null, s == null || !s.equalsIgnoreCase("n/a"), false, hasSummary(rd.getRoot()), vsWarns, true, rd.getStatus());
    if (!resourceIsTechnical(name)) {
        // these are exempt because identification is tightly managed
        ElementDefn id = rd.getRoot().getElementByName(definitions, "identifier", true, false);
        if (id == null)
            warning(errors, IssueType.STRUCTURE, rd.getName(), false, "All resources should have an identifier");
        else
            rule(errors, IssueType.STRUCTURE, rd.getName(), id.typeCode().equals("Identifier"), "If a resource has an element named identifier, it must have a type 'Identifier'");
    }
    rule(errors, IssueType.STRUCTURE, rd.getName(), rd.getRoot().getElementByName(definitions, "text", true, false) == null, "Element named \"text\" not allowed");
    rule(errors, IssueType.STRUCTURE, rd.getName(), rd.getRoot().getElementByName(definitions, "contained", true, false) == null, "Element named \"contained\" not allowed");
    if (rd.getRoot().getElementByName(definitions, "subject", true, false) != null && rd.getRoot().getElementByName(definitions, "subject", true, false).typeCode().startsWith("Reference"))
        rule(errors, IssueType.STRUCTURE, rd.getName(), rd.getSearchParams().containsKey("subject"), "A resource that contains a subject reference must have a search parameter 'subject'");
    ElementDefn ped = rd.getRoot().getElementByName(definitions, "patient", true, false);
    if (ped != null && ped.typeCode().startsWith("Reference")) {
        SearchParameterDefn spd = rd.getSearchParams().get("patient");
        if (rule(errors, IssueType.STRUCTURE, rd.getName(), spd != null, "A resource that contains a patient reference must have a search parameter 'patient'"))
            rule(errors, IssueType.STRUCTURE, rd.getName(), (spd.getTargets().size() == 1 && spd.getTargets().contains("Patient")) || (ped.getTypes().get(0).getParams().size() == 1 && ped.getTypes().get(0).getParams().get(0).equals("Patient")), "A Patient search parameter must only refer to patient");
    }
    ElementDefn sed = rd.getRoot().getElementByName(definitions, "subject", true, false);
    if (sed != null && sed.typeCode().startsWith("Reference") && sed.typeCode().contains("Patient"))
        warning(errors, IssueType.STRUCTURE, rd.getName(), rd.getSearchParams().containsKey("patient"), "A resource that contains a subject that can be a patient reference must have a search parameter 'patient'");
    if (rd.getRoot().getElementByName(definitions, "identifier", true, false) != null) {
        warning(errors, IssueType.STRUCTURE, rd.getName(), rd.getSearchParams().containsKey("identifier"), "A resource that contains an identifier must have a search parameter 'identifier'");
    }
    if (rd.getRoot().getElementByName(definitions, "status", true, false) != null) {
        // todo: change to a warning post STU3
        hint(errors, IssueType.STRUCTURE, rd.getName(), rd.getSearchParams().containsKey("status"), "A resource that contains a status element must have a search parameter 'status'");
    }
    if (rd.getRoot().getElementByName(definitions, "url", true, false) != null) {
        warning(errors, IssueType.STRUCTURE, rd.getName(), rd.getSearchParams().containsKey("url"), "A resource that contains a url element must have a search parameter 'url'");
    }
    checkSearchParams(errors, rd);
    for (Operation op : rd.getOperations()) {
        rule(errors, IssueType.STRUCTURE, rd.getName() + "/$" + op.getName(), !parentHasOp(rd.getRoot().typeCode(), op.getName()), "Duplicate Operation Name $" + op.getName() + " on " + rd.getName());
    }
    for (Compartment c : definitions.getCompartments()) {
        if (rule(errors, IssueType.STRUCTURE, rd.getName(), name.equals("Parameters") || c.getResources().containsKey(rd), "Resource not entered in resource map for compartment '" + c.getTitle() + "' (compartments.xml)")) {
            String param = c.getResources().get(rd);
            if (!Utilities.noString(param)) {
                // rule(errors, IssueType.STRUCTURE, parent.getName(), param.equals("{def}") || parent.getSearchParams().containsKey(c.getName()), "Resource "+parent.getName()+" in compartment " +c.getName()+" must have a search parameter named "+c.getName().toLowerCase()+")");
                for (String p : param.split("\\|")) {
                    String pn = p.trim();
                    if (pn.contains("."))
                        pn = pn.substring(0, pn.indexOf("."));
                    rule(errors, IssueType.STRUCTURE, rd.getName(), Utilities.noString(pn) || pn.equals("{def}") || rd.getSearchParams().containsKey(pn), "Resource " + rd.getName() + " in compartment " + c.getName() + ": parameter " + param + " was not found (" + pn + ")");
                }
            }
        }
    }
    // Remove suppressed messages
    List<ValidationMessage> suppressed = new ArrayList<ValidationMessage>();
    for (ValidationMessage em : errors) {
        if (isSuppressedMessage(em.getDisplay())) {
            suppressed.add(em);
        }
    }
    errors.removeAll(suppressed);
    // last check: if maturity level is
    int warnings = 0;
    int hints = 0;
    for (ValidationMessage em : errors) {
        if (em.getLevel() == IssueSeverity.WARNING)
            warnings++;
        else if (em.getLevel() == IssueSeverity.INFORMATION)
            hints++;
    }
    boolean ok = warnings == 0 || "0".equals(rd.getFmmLevel());
    if (rule(errors, IssueType.STRUCTURE, rd.getName(), ok, "Resource " + rd.getName() + " (FMM=" + rd.getFmmLevel() + ") cannot have an FMM level >1 (" + rd.getFmmLevel() + ") if it has warnings"))
        rule(errors, IssueType.STRUCTURE, rd.getName(), vsWarnings == 0 || "0".equals(rd.getFmmLevel()), "Resource " + rd.getName() + " (FMM=" + rd.getFmmLevel() + ") cannot have an FMM level >1 (" + rd.getFmmLevel() + ") if it has linked value set warnings (" + vsWarns.toString() + ")");
    ok = hints == 0 || Integer.parseInt(rd.getFmmLevel()) < 3;
    rule(errors, IssueType.STRUCTURE, rd.getName(), ok, "Resource " + rd.getName() + " (FMM=" + rd.getFmmLevel() + ") cannot have an FMM level >2 (" + rd.getFmmLevel() + ") if it has informational hints");
// if (isInterface(rd.getRoot().typeCode())) {
// checkInterface(errors, rd, definitions.getBaseResources().get(rd.getRoot().typeCode()));
// }
}

Example 100 with Rule

use of org.hl7.fhir.utilities.xml.SchematronWriter.Rule in project kindling by HL7.

the class ValueSetValidator method checkCodeCaseDuplicates.

private void checkCodeCaseDuplicates(List<ValidationMessage> errors, String nameForErrors, CodeSystem cs, Set<String> codes, List<ConceptDefinitionComponent> concepts) {
    for (ConceptDefinitionComponent c : concepts) {
        if (c.hasCode()) {
            String cc = c.getCode().toLowerCase();
            rule(errors, IssueType.BUSINESSRULE, getWg(cs) + ":CodeSystem[" + cs.getId() + "].define", !codes.contains(cc), "Value set " + nameForErrors + " (" + cs.getName() + "): Code '" + cc + "' is defined twice, different by case - this is not allowed in a FHIR definition");
            if (c.hasConcept())
                checkCodeCaseDuplicates(errors, nameForErrors, cs, codes, c.getConcept());
        }
    }
}