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Merge pull request #954 from HL7/Ellipsing
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Ellipsing
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@grahamegrieve
grahamegrieve committed Sep 22, 2024
2 parents 0a6cfef + c8d5aca commit eb8babe
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Showing 3 changed files with 345 additions and 24 deletions.
296 changes: 280 additions & 16 deletions org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/Publisher.java
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,8 @@
import java.util.Set;
import java.util.TreeSet;
import java.util.UUID;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;

Expand Down Expand Up @@ -665,7 +667,24 @@ public Base parseType(Element base) throws FHIRFormatError, IOException, FHIRExc
}
}

public class ElideExceptDetails {
private String base = null;
private String except = null;

public ElideExceptDetails(String except) {
this.except = except;
}

public String getBase() {
return base;
}

public boolean hasBase() { return base != null; }

public void setBase(String base) { this.base = base; }

public String getExcept() { return except; }
}

public enum IGBuildMode { MANUAL, AUTOBUILD, WEBSERVER, PUBLICATION }

Expand Down Expand Up @@ -10485,9 +10504,9 @@ private void generateHtmlOutputs(FetchedFile f, boolean regen, DBBuilder db) thr
f.getOutputNames().add(dst);
Utilities.createDirectory(dst);
} else if (f.getPath().endsWith(".md")) {
checkMakeFile(processSQL(db, stripFrontMatter(f.getSource()), f), dst, f.getOutputNames());
checkMakeFile(processCustomLiquid(db, stripFrontMatter(f.getSource()), f), dst, f.getOutputNames());
} else {
checkMakeFile(processSQL(db, f.getSource(), f), dst, f.getOutputNames());
checkMakeFile(processCustomLiquid(db, f.getSource(), f), dst, f.getOutputNames());
}
} catch (IOException e) {
log("Exception generating page "+dst+" for "+f.getRelativePath()+" in "+tempDir+": "+e.getMessage());
Expand All @@ -10505,7 +10524,7 @@ private void generateHtmlOutputs(FetchedFile f, boolean regen, DBBuilder db) thr
f.getOutputNames().add(dst);
Utilities.createDirectory(dst);
} else
checkMakeFile(processSQL(db, new XSLTransformer(debug).transform(f.getSource(), f.getXslt()), f), dst, f.getOutputNames());
checkMakeFile(processCustomLiquid(db, new XSLTransformer(debug).transform(f.getSource(), f.getXslt()), f), dst, f.getOutputNames());
} catch (Exception e) {
log("Exception generating xslt page "+dst+" for "+f.getRelativePath()+" in "+tempDir+": "+e.getMessage());
}
Expand All @@ -10516,6 +10535,9 @@ private void generateHtmlOutputs(FetchedFile f, boolean regen, DBBuilder db) thr
Map<String, String> vars = makeVars(r);
makeTemplates(f, r, vars);
saveDirectResourceOutputs(f, r, r.getResource(), vars);
/* if (r.getResEntry() != null && r.getResEntry().hasExtension("http://hl7.org/fhir/tools/StructureDefinition/implementationguide-resource-fragment")) {
generateResourceFragments(f, r, System.currentTimeMillis());
}*/
List<StringPair> clist = new ArrayList<>();
if (r.getResource() == null) {
try {
Expand Down Expand Up @@ -10620,27 +10642,200 @@ private void generateHtmlOutputs(FetchedFile f, boolean regen, DBBuilder db) thr
}
}

private byte[] processSQL(DBBuilder db, byte[] content, FetchedFile f) {
private String generateResourceFragment(FetchedFile f, FetchedResource r, String fragExpr, String syntax, List<ElideExceptDetails> excepts, List<String> elides) throws FHIRException {
FHIRPathEngine fpe = new FHIRPathEngine(context);
Base root = r.getElement();
if (r.getLogicalElement()!=null)
root = r.getLogicalElement();

List<Base> fragNodes = new ArrayList<Base>();
if (fragExpr == null)
fragNodes.add(root);
else {
try {
fragNodes = fpe.evaluate(root, fragExpr);
} catch (Exception e) {
e.printStackTrace();
}
if (fragNodes.isEmpty()) {
f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.EXCEPTION, fragExpr, "Unable to resolve expression to fragment within resource", IssueSeverity.ERROR));
return "ERROR Expanding Fragment";

} else if (fragNodes.size() > 1) {
f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.EXCEPTION, fragExpr, "Found multiple occurrences of expression within resource, and only one is allowed when extracting a fragment", IssueSeverity.ERROR));
return "ERROR Expanding Fragment";
}
}
Element e = (Element)fragNodes.get(0);
Element jsonElement = e;

if (!elides.isEmpty() || !excepts.isEmpty()) {
// e = e.copy();
for (ElideExceptDetails elideExceptDetails : excepts) {
List<Base> baseElements = new ArrayList<Base>();
baseElements.add(e);
String elideBaseExpr = null;
if (elideExceptDetails.hasBase()) {
elideBaseExpr = elideExceptDetails.getBase();
baseElements = fpe.evaluate(e, elideBaseExpr);
if (baseElements.isEmpty()) {
f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.EXCEPTION, fragExpr, "Unable to find matching base elements for elideExcept expression " + elideBaseExpr + " within fragment path ", IssueSeverity.ERROR));
return "ERROR Expanding Fragment";
}
}

String elideExceptExpr = elideExceptDetails.getExcept();
boolean foundExclude = false;
for (Base elideElement: baseElements) {
for (Element child: ((Element)elideElement).getChildren()) {
child.setElided(true);
}
List<Base> elideExceptElements = fpe.evaluate(elideElement, elideExceptExpr);
if (!elideExceptElements.isEmpty())
foundExclude = true;
for (Base exclude: elideExceptElements) {
((Element)exclude).setElided(false);
}
}
if (!foundExclude) {
f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.EXCEPTION, fragExpr, "Unable to find matching exclude elements for elideExcept expression " + elideExceptExpr + (elideBaseExpr == null ? "": (" within base" + elideBaseExpr)) + " within fragment path ", IssueSeverity.ERROR));
return "ERROR Expanding Fragment";
}
}

for (String elideExpr : elides) {
List<Base> elideElements = fpe.evaluate(e, elideExpr);
if (elideElements.isEmpty()) {
f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.EXCEPTION, fragExpr, "Unable to find matching elements for elide expression " + elideExpr + " within fragment path ", IssueSeverity.ERROR));
return "ERROR Expanding Fragment";
}
for (Base elideElment: elideElements) {
((Element)elideElment).setElided(true);
}
}

jsonElement = trimElided(e, true);
e = trimElided(e, false);
}

try {
if (syntax.equals("xml")) {
org.hl7.fhir.r5.elementmodel.XmlParser xp = new org.hl7.fhir.r5.elementmodel.XmlParser(context);
XmlXHtmlRenderer x = new XmlXHtmlRenderer();
x.setPrism(true);
xp.setElideElements(true);
xp.setLinkResolver(igpkp);
xp.setShowDecorations(false);
if (suppressId(f, r)) {
xp.setIdPolicy(IdRenderingPolicy.NotRoot);
}
xp.compose(e, x);
return x.toString();

} else if (syntax.equals("json")) {
JsonXhtmlRenderer j = new JsonXhtmlRenderer();
j.setPrism(true);
org.hl7.fhir.r5.elementmodel.JsonParser jp = new org.hl7.fhir.r5.elementmodel.JsonParser(context);
jp.setLinkResolver(igpkp);
jp.setAllowComments(true);
jp.setElideElements(true);
/* if (fragExpr != null || r.getLogicalElement() != null)
jp.setSuppressResourceType(true);*/
if (suppressId(f, r)) {
jp.setIdPolicy(IdRenderingPolicy.NotRoot);
}
jp.compose(jsonElement, j);
return j.toString();

} else if (syntax.equals("ttl")) {
org.hl7.fhir.r5.elementmodel.TurtleParser ttl = new org.hl7.fhir.r5.elementmodel.TurtleParser(context);
ttl.setLinkResolver(igpkp);
Turtle rdf = new Turtle();
if (suppressId(f, r)) {
ttl.setIdPolicy(IdRenderingPolicy.NotRoot);
}
ttl.setStyle(OutputStyle.PRETTY);
ttl.compose(e, rdf, "");
return rdf.toString();
} else
throw new FHIRException("Unrecognized syntax: " + syntax);
} catch (Exception except) {
throw new FHIRException(except);
}
}

/*
Recursively removes consecutive elided elements from children of the element
*/
private Element trimElided(Element e, boolean asJson) {
Element trimmed = (Element)e.copy();
trimElide(trimmed, asJson);
return trimmed;
}

private void trimElide(Element e, boolean asJson) {
if (!e.hasChildren())
return;

boolean inElided = false;
for (int i = 0; i < e.getChildren().size();) {
Element child = e.getChildren().get(i);
if (child.isElided()) {
if (inElided) {
// Check to see if this an elided collection item where the previous item isn't in the collection and the following item is in the collection and isn't elided
if (asJson && i > 0 && i < e.getChildren().size()-1 && !e.getChildren().get(i-1).getName().equals(child.getName()) && !e.getChildren().get(i+1).isElided() && e.getChildren().get(i+1).getName().equals(child.getName())) {
// Do nothing
} else {
e.getChildren().remove(child);
continue;
}
} else
inElided = true;
} else {
inElided = false;
trimElide(child, asJson);
}
i++;
}
}

private byte[] processCustomLiquid(DBBuilder db, byte[] content, FetchedFile f) throws FHIRException {
if (!Utilities.existsInList(Utilities.getFileExtension(f.getPath()), "html", "md", "xml")) {
return content;
}
try {
String src = new String(content);
boolean changed = false;
while (db != null && src.contains("{% sql")) {
int i = src.indexOf("{% sql");
String pfx = src.substring(0, i);
src = src.substring(i + 6);
i = src.indexOf("%}");
String sfx = src.substring(i + 2);
String sql = src.substring(0, i);
String[] keywords = {"sql", "fragment"};
for (String keyword: Arrays.asList(keywords)) {

while (db != null && src.contains("{% " + keyword)) {
int i = src.indexOf("{% " + keyword);
String pfx = src.substring(0, i);
src = src.substring(i + 3 + keyword.length());
i = src.indexOf("%}");
if (i == -1)
throw new FHIRException("No closing '%}' for '{% '" + keyword + " in " + f.getName());
String sfx = src.substring(i + 2);
String arguments = src.substring(0, i).trim();

String substitute = "";
switch (keyword) {
case "sql":
if (arguments.trim().startsWith("ToData ")) {
substitute = processSQLData(db, arguments.substring(arguments.indexOf("ToData ") + 7), f);
} else {
substitute = processSQLCommand(db, arguments, f);
}
break;

if (sql.trim().startsWith("ToData ")) {
src = pfx + processSQLData(db, sql.substring(7), f) + sfx;
} else {
src = pfx + processSQLCommand(db, sql, f) + sfx;
case "fragment":
substitute = processFragment(arguments, f);
}

src = pfx + substitute + sfx;
changed = true;
}
changed = true;
}
while (src.contains("[[[")) {
int i = src.indexOf("[[[");
Expand Down Expand Up @@ -10717,6 +10912,75 @@ private String processSQLCommand(DBBuilder db, String src, FetchedFile f) throws
return "{% include sql-"+i+"-fragment.xhtml %}";
}

private String processFragment(String arguments, FetchedFile f) throws FHIRException {
int firstSpace = arguments.indexOf(" ");
int secondSpace = arguments.indexOf(" ",firstSpace + 1);
if (firstSpace == -1)
throw new FHIRException("Fragment syntax error: syntax must be '[ResourceType]/[id] [syntax] [filters]'. Found: " + arguments + "\r\n in file " + f.getName());
String reference = arguments.substring(0, firstSpace);
String format = (secondSpace == -1) ? arguments.substring(firstSpace) : arguments.substring(firstSpace, secondSpace);
format = format.trim().toLowerCase();
String filters = (secondSpace == -1) ? "" : arguments.substring(secondSpace).trim();
Pattern refPattern = Pattern.compile("^([A-Z][a-z]+)+\\/([A-Za-z0-9\\-\\.]{1,64})$");
Matcher refMatcher = refPattern.matcher(reference);
if (!refMatcher.find())
throw new FHIRException("Fragment syntax error: Referenced instance must be expressed as [ResourceType]/[id]. Found " + reference + " in file " + f.getName());
String type = refMatcher.group(1);
String id = refMatcher.group(2);
FetchedResource r = fetchByResource(type, id);
if (r == null)
throw new FHIRException(("Unable to find fragment resource " + reference + " pointed to in file " + f.getName()));
if (!format.equals("xml") && !format.equals("json") && !format.equals("ttl"))
throw new FHIRException("Unrecognized fragment format " + format + " - expecting 'xml', 'json', or 'ttl' in file " + f.getName());

Pattern filterPattern = Pattern.compile("(BASE:|EXCEPT:|ELIDE:)");
Matcher filterMatcher = filterPattern.matcher(filters);
String remainingFilters = filters;
String base = null;
List<String> elides = new ArrayList<>();
List<String> includes = new ArrayList<>();
List<ElideExceptDetails> excepts = new ArrayList<>();
ElideExceptDetails currentExcept = null;
boolean matches = filterMatcher.find();
if (!matches && !filters.isEmpty())
throw new FHIRException("Unrecognized filters in fragment: " + filters + " in file " + f.getName());
while (matches) {
String filterType = filterMatcher.group(0);
String filterText = "";
int start = remainingFilters.indexOf(filterType) + filterType.length();
matches = filterMatcher.find();
if (matches) {
String nextTag = filterMatcher.group(0);
filterText = remainingFilters.substring(start, remainingFilters.indexOf(nextTag, start)).trim();
remainingFilters = remainingFilters.substring(remainingFilters.indexOf(nextTag, start));
} else {
filterText = remainingFilters.substring(start).trim();
remainingFilters = "";
}
switch (filterType) {
case "BASE:":
if (currentExcept==null) {
if (base != null)
throw new FHIRException("Cannot have more than one BASE: declaration in fragment definition - " + filters + " in file " + f.getName());
base = filterText;
} else {
if (currentExcept.hasBase())
throw new FHIRException("Cannot have more than one BASE: declaration for an Except - " + filters + " in file " + f.getName());
currentExcept.setBase(filterText);
}
break;
case "EXCEPT:":
currentExcept = new ElideExceptDetails(filterText);
excepts.add(currentExcept);
break;
default: // "ELIDE:"
elides.add(filterText);
}
}

return generateResourceFragment(f, r, base, format, excepts, elides);
}

class StringPair {
private String name;
private String value;
Expand Down
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