Example 1 with ScanOutputItem
use of org.hl7.fhir.validation.cli.model.ScanOutputItem in project org.hl7.fhir.core by hapifhir.
the class Scanner method validateScan.
public void validateScan(String output, List<String> sources) throws Exception {
if (Utilities.noString(output))
throw new Exception("Output parameter required when scanning");
if (!(new File(output).isDirectory()))
throw new Exception("Output '" + output + "' must be a directory when scanning");
System.out.println(" .. scan " + sources + " against loaded IGs");
Set<String> urls = new HashSet<>();
for (ImplementationGuide ig : getContext().allImplementationGuides()) {
if (ig.getUrl().contains("/ImplementationGuide") && !ig.getUrl().equals("http://hl7.org/fhir/ImplementationGuide/fhir"))
urls.add(ig.getUrl());
}
List<ScanOutputItem> res = validateScan(sources, urls);
genScanOutput(output, res);
System.out.println("Done. output in " + Utilities.path(output, "scan.html"));
}
Also used :
ImplementationGuide(org.hl7.fhir.r5.model.ImplementationGuide)
ScanOutputItem(org.hl7.fhir.validation.cli.model.ScanOutputItem)
TextFile(org.hl7.fhir.utilities.TextFile)
FHIRException(org.hl7.fhir.exceptions.FHIRException)
Example 2 with ScanOutputItem
use of org.hl7.fhir.validation.cli.model.ScanOutputItem in project org.hl7.fhir.core by hapifhir.
the class Scanner method genScanOutput.
protected void genScanOutput(String folder, List<ScanOutputItem> items) throws IOException, FHIRException, EOperationOutcome {
String f = Utilities.path(folder, "comparison.zip");
download("http://fhir.org/archive/comparison.zip", f);
unzip(f, folder);
for (int i = 0; i < items.size(); i++) {
items.get(i).setId("c" + i);
genScanOutputItem(items.get(i), Utilities.path(folder, items.get(i).getId() + ".html"));
}
StringBuilder b = new StringBuilder();
b.append("<html>");
b.append("<head>");
b.append("<title>Implementation Guide Scan</title>");
b.append("<link rel=\"stylesheet\" href=\"fhir.css\"/>\r\n");
b.append("<style>\r\n");
b.append("th \r\n");
b.append("{\r\n");
b.append(" vertical-align: bottom;\r\n");
b.append(" text-align: center;\r\n");
b.append("}\r\n");
b.append("\r\n");
b.append("th span\r\n");
b.append("{\r\n");
b.append(" -ms-writing-mode: tb-rl;\r\n");
b.append(" -webkit-writing-mode: vertical-rl;\r\n");
b.append(" writing-mode: vertical-rl;\r\n");
b.append(" transform: rotate(180deg);\r\n");
b.append(" white-space: nowrap;\r\n");
b.append("}\r\n");
b.append("</style>\r\n");
b.append("</head>");
b.append("<body>");
b.append("<h2>Implementation Guide Scan</h2>");
// organise
Set<String> refs = new HashSet<>();
Set<String> igs = new HashSet<>();
Map<String, Set<String>> profiles = new HashMap<>();
for (ScanOutputItem item : items) {
refs.add(item.getRef());
if (item.getIg() != null) {
igs.add(item.getIg().getUrl());
if (!profiles.containsKey(item.getIg().getUrl())) {
profiles.put(item.getIg().getUrl(), new HashSet<>());
}
if (item.getProfile() != null)
profiles.get(item.getIg().getUrl()).add(item.getProfile().getUrl());
}
}
b.append("<h2>By reference</h2>\r\n");
b.append("<table class=\"grid\">");
b.append("<tr><th></th><th></th>");
for (String s : sort(igs)) {
ImplementationGuide ig = getContext().fetchResource(ImplementationGuide.class, s);
b.append("<th colspan=\"" + Integer.toString(profiles.get(s).size() + 1) + "\"><b title=\"" + s + "\">" + ig.present() + "</b></th>");
}
b.append("</tr>\r\n");
b.append("<tr><th><b>Source</b></th><th><span>Core Spec</span></th>");
for (String s : sort(igs)) {
ImplementationGuide ig = getContext().fetchResource(ImplementationGuide.class, s);
b.append("<th><span>Global</span></th>");
for (String sp : sort(profiles.get(s))) {
StructureDefinition sd = getContext().fetchResource(StructureDefinition.class, sp);
b.append("<th><b title=\"" + sp + "\"><span>" + sd.present() + "</span></b></th>");
}
}
b.append("</tr>\r\n");
for (String s : sort(refs)) {
b.append("<tr>");
b.append("<td>" + s + "</td>");
b.append(genOutcome(items, s, null, null));
for (String si : sort(igs)) {
ImplementationGuide ig = getContext().fetchResource(ImplementationGuide.class, si);
b.append(genOutcome(items, s, si, null));
for (String sp : sort(profiles.get(ig.getUrl()))) {
b.append(genOutcome(items, s, si, sp));
}
}
b.append("</tr>\r\n");
}
b.append("</table>\r\n");
b.append("<h2>By IG</h2>\r\n");
b.append("<table class=\"grid\">");
b.append("<tr><th></th><th></th>");
for (String s : sort(refs)) {
b.append("<th><span>" + s + "</span></th>");
}
b.append("</tr>\r\n");
b.append("<tr><td></td><td>Core Spec</td>");
for (String s : sort(refs)) {
b.append(genOutcome(items, s, null, null));
}
b.append("</tr>\r\n");
for (String si : sort(igs)) {
b.append("<tr>");
ImplementationGuide ig = getContext().fetchResource(ImplementationGuide.class, si);
b.append("<td><b title=\"" + si + "\">" + ig.present() + "</b></td>");
b.append("<td>Global</td>");
for (String s : sort(refs)) {
b.append(genOutcome(items, s, si, null));
}
b.append("</tr>\r\n");
for (String sp : sort(profiles.get(ig.getUrl()))) {
b.append("<tr>");
StructureDefinition sd = getContext().fetchResource(StructureDefinition.class, sp);
b.append("<td></td><td><b title=\"" + sp + "\">" + sd.present() + "</b></td>");
for (String s : sort(refs)) {
b.append(genOutcome(items, s, si, sp));
}
b.append("</tr>\r\n");
}
}
b.append("</table>\r\n");
b.append("</body>");
b.append("</html>");
TextFile.stringToFile(b.toString(), Utilities.path(folder, "scan.html"));
}
Also used :
StructureDefinition(org.hl7.fhir.r5.model.StructureDefinition)
ImplementationGuide(org.hl7.fhir.r5.model.ImplementationGuide)
ScanOutputItem(org.hl7.fhir.validation.cli.model.ScanOutputItem)
Example 3 with ScanOutputItem
use of org.hl7.fhir.validation.cli.model.ScanOutputItem in project org.hl7.fhir.core by hapifhir.
the class Scanner method validateScan.
protected List<ScanOutputItem> validateScan(List<String> sources, Set<String> guides) throws FHIRException, IOException, EOperationOutcome {
List<String> refs = new ArrayList<>();
ValidatorUtils.parseSources(sources, refs, getContext());
List<ScanOutputItem> res = new ArrayList();
for (String ref : refs) {
Content cnt = getIgLoader().loadContent(ref, "validate", false);
List<ValidationMessage> messages = new ArrayList<>();
Element e = null;
try {
System.out.println("Validate " + ref);
messages.clear();
e = getValidator().validate(null, messages, new ByteArrayInputStream(cnt.focus), cnt.cntType);
res.add(new ScanOutputItem(ref, null, null, ValidatorUtils.messagesToOutcome(messages, getContext(), getFhirPathEngine())));
} catch (Exception ex) {
res.add(new ScanOutputItem(ref, null, null, exceptionToOutcome(ex)));
}
if (e != null) {
String rt = e.fhirType();
for (String u : guides) {
ImplementationGuide ig = getContext().fetchResource(ImplementationGuide.class, u);
System.out.println("Check Guide " + ig.getUrl());
String canonical = ig.getUrl().contains("/Impl") ? ig.getUrl().substring(0, ig.getUrl().indexOf("/Impl")) : ig.getUrl();
String url = getGlobal(ig, rt);
if (url != null) {
try {
System.out.println("Validate " + ref + " against " + ig.getUrl());
messages.clear();
getValidator().validate(null, messages, new ByteArrayInputStream(cnt.focus), cnt.cntType, url);
res.add(new ScanOutputItem(ref, ig, null, ValidatorUtils.messagesToOutcome(messages, getContext(), getFhirPathEngine())));
} catch (Exception ex) {
res.add(new ScanOutputItem(ref, ig, null, exceptionToOutcome(ex)));
}
}
Set<String> done = new HashSet<>();
for (StructureDefinition sd : getContext().allStructures()) {
if (!done.contains(sd.getUrl())) {
done.add(sd.getUrl());
if (sd.getUrl().startsWith(canonical) && rt.equals(sd.getType())) {
try {
System.out.println("Validate " + ref + " against " + sd.getUrl());
messages.clear();
validator.validate(null, messages, new ByteArrayInputStream(cnt.focus), cnt.cntType, Collections.singletonList(sd));
res.add(new ScanOutputItem(ref, ig, sd, ValidatorUtils.messagesToOutcome(messages, getContext(), getFhirPathEngine())));
} catch (Exception ex) {
res.add(new ScanOutputItem(ref, ig, sd, exceptionToOutcome(ex)));
}
}
}
}
}
}
}
return res;
}
Also used :
ValidationMessage(org.hl7.fhir.utilities.validation.ValidationMessage)
ImplementationGuide(org.hl7.fhir.r5.model.ImplementationGuide)
Element(org.hl7.fhir.r5.elementmodel.Element)
FHIRException(org.hl7.fhir.exceptions.FHIRException)
StructureDefinition(org.hl7.fhir.r5.model.StructureDefinition)
ScanOutputItem(org.hl7.fhir.validation.cli.model.ScanOutputItem)
Example 4 with ScanOutputItem
use of org.hl7.fhir.validation.cli.model.ScanOutputItem in project org.hl7.fhir.core by hapifhir.
the class Scanner method genScanOutputItem.
protected void genScanOutputItem(ScanOutputItem item, String filename) throws IOException, FHIRException, EOperationOutcome {
RenderingContext rc = new RenderingContext(getContext(), null, null, "http://hl7.org/fhir", "", null, RenderingContext.ResourceRendererMode.END_USER);
rc.setNoSlowLookup(true);
RendererFactory.factory(item.getOutcome(), rc).render(item.getOutcome());
String s = new XhtmlComposer(XhtmlComposer.HTML).compose(item.getOutcome().getText().getDiv());
String title = item.getTitle();
StringBuilder b = new StringBuilder();
b.append("<html>");
b.append("<head>");
b.append("<title>" + title + "</title>");
b.append("<link rel=\"stylesheet\" href=\"fhir.css\"/>\r\n");
b.append("</head>");
b.append("<body>");
b.append("<h2>" + title + "</h2>");
b.append(s);
b.append("</body>");
b.append("</html>");
TextFile.stringToFile(b.toString(), filename);
}
Also used :
RenderingContext(org.hl7.fhir.r5.renderers.utils.RenderingContext)
XhtmlComposer(org.hl7.fhir.utilities.xhtml.XhtmlComposer)
Example 5 with ScanOutputItem
use of org.hl7.fhir.validation.cli.model.ScanOutputItem in project org.hl7.fhir.core by hapifhir.
the class Scanner method genOutcome.
protected String genOutcome(List<ScanOutputItem> items, String src, String ig, String profile) {
ScanOutputItem item = null;
for (ScanOutputItem t : items) {
boolean match = true;
if (!t.getRef().equals(src))
match = false;
if (!((ig == null && t.getIg() == null) || (ig != null && t.getIg() != null && ig.equals(t.getIg().getUrl()))))
match = false;
if (!((profile == null && t.getProfile() == null) || (profile != null && t.getProfile() != null && profile.equals(t.getProfile().getUrl()))))
match = false;
if (match) {
item = t;
break;
}
}
if (item == null)
return "<td></td>";
boolean ok = true;
for (OperationOutcome.OperationOutcomeIssueComponent iss : item.getOutcome().getIssue()) {
if (iss.getSeverity() == OperationOutcome.IssueSeverity.ERROR || iss.getSeverity() == OperationOutcome.IssueSeverity.FATAL) {
ok = false;
}
}
if (ok)
return "<td style=\"background-color: #e6ffe6\"><a href=\"" + item.getId() + ".html\">\u2714</a></td>";
else
return "<td style=\"background-color: #ffe6e6\"><a href=\"" + item.getId() + ".html\">\u2716</a></td>";
}
Also used :
ScanOutputItem(org.hl7.fhir.validation.cli.model.ScanOutputItem)
OperationOutcome(org.hl7.fhir.r5.model.OperationOutcome)
EOperationOutcome(org.hl7.fhir.r5.utils.EOperationOutcome)
Aggregations
ScanOutputItem (org.hl7.fhir.validation.cli.model.ScanOutputItem)4
ImplementationGuide (org.hl7.fhir.r5.model.ImplementationGuide)3
FHIRException (org.hl7.fhir.exceptions.FHIRException)2
StructureDefinition (org.hl7.fhir.r5.model.StructureDefinition)2
Element (org.hl7.fhir.r5.elementmodel.Element)1
OperationOutcome (org.hl7.fhir.r5.model.OperationOutcome)1
RenderingContext (org.hl7.fhir.r5.renderers.utils.RenderingContext)1
EOperationOutcome (org.hl7.fhir.r5.utils.EOperationOutcome)1
TextFile (org.hl7.fhir.utilities.TextFile)1
ValidationMessage (org.hl7.fhir.utilities.validation.ValidationMessage)1
XhtmlComposer (org.hl7.fhir.utilities.xhtml.XhtmlComposer)1
