Add integrityt check utils for R4B integrity
This commit is contained in:
Grahame Grieve
parent
7e9b148837
commit
4927d23273
|
|
@ -0,0 +1,241 @@
|
|||
package org.hl7.fhir.r4.utils;
|
||||
|
||||
import java.io.FileInputStream;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collection;
|
||||
import java.util.Collections;
|
||||
import java.util.Comparator;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import org.hl7.fhir.r4.formats.JsonParser;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
import org.hl7.fhir.r4.model.SearchParameter;
|
||||
import org.hl7.fhir.r4.model.StructureDefinition;
|
||||
import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
|
||||
import org.hl7.fhir.r4.utils.IntegrityChecker.SearchParameterNode;
|
||||
import org.hl7.fhir.r4.utils.IntegrityChecker.SearchParameterNodeSorter;
|
||||
import org.hl7.fhir.r4.utils.IntegrityChecker.SearchParameterParamNode;
|
||||
import org.hl7.fhir.r4.utils.IntegrityChecker.SearchParameterParamNodeSorter;
|
||||
import org.hl7.fhir.r4.utils.IntegrityChecker.StructureDefinitionNode;
|
||||
import org.hl7.fhir.r4.utils.IntegrityChecker.StructureDefinitionNodeComparer;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage;
|
||||
|
||||
public class IntegrityChecker {
|
||||
|
||||
public class SearchParameterNodeSorter implements Comparator<SearchParameterNode> {
|
||||
|
||||
@Override
|
||||
public int compare(SearchParameterNode o1, SearchParameterNode o2) {
|
||||
return o1.name.compareTo(o2.name);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class SearchParameterParamNodeSorter implements Comparator<SearchParameterParamNode> {
|
||||
|
||||
@Override
|
||||
public int compare(SearchParameterParamNode o1, SearchParameterParamNode o2) {
|
||||
return o1.sp.getCode().compareTo(o2.sp.getCode());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class SearchParameterParamNode {
|
||||
SearchParameter sp;
|
||||
boolean only;
|
||||
public SearchParameterParamNode(SearchParameter sp, boolean only) {
|
||||
super();
|
||||
this.sp = sp;
|
||||
this.only = only;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
public class SearchParameterNode {
|
||||
|
||||
private String name;
|
||||
private List<SearchParameterParamNode> params = new ArrayList<>();
|
||||
|
||||
public SearchParameterNode(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class StructureDefinitionNodeComparer implements Comparator<StructureDefinitionNode> {
|
||||
|
||||
@Override
|
||||
public int compare(StructureDefinitionNode arg0, StructureDefinitionNode arg1) {
|
||||
if ( arg0.sd.getType().equals(arg1.sd.getType())) {
|
||||
return arg0.sd.getName().compareTo(arg1.sd.getName());
|
||||
} else {
|
||||
return arg0.sd.getType().compareTo(arg1.sd.getType());
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class StructureDefinitionNode {
|
||||
StructureDefinition sd;
|
||||
List<StructureDefinitionNode> children = new ArrayList<>();
|
||||
|
||||
public StructureDefinitionNode(StructureDefinition sd) {
|
||||
this.sd = sd;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private NpmPackage npm;
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
IntegrityChecker check = new IntegrityChecker();
|
||||
check.load(args[0]);
|
||||
check.check();
|
||||
}
|
||||
|
||||
private void check() throws IOException {
|
||||
checkSD();
|
||||
checkSP();
|
||||
}
|
||||
|
||||
|
||||
private void checkSP() throws IOException {
|
||||
List<SearchParameter> list = new ArrayList<>();
|
||||
for (String sdn : npm.listResources("SearchParameter")) {
|
||||
InputStream s = npm.load(sdn);
|
||||
SearchParameter sp = (SearchParameter) new JsonParser().parse(s);
|
||||
list.add(sp);
|
||||
}
|
||||
msg("Loaded "+list.size()+" resources");
|
||||
Map<String, SearchParameterNode> map = new HashMap<>();
|
||||
for (SearchParameter sp : list) {
|
||||
for (CodeType c : sp.getBase()) {
|
||||
String s = c.primitiveValue();
|
||||
if (!map.containsKey(s)) {
|
||||
map.put(s, new SearchParameterNode(s));
|
||||
}
|
||||
addNode(sp, sp.getBase().size() == 1, map.get(s));
|
||||
}
|
||||
}
|
||||
for (SearchParameterNode node : sort(map.values())) {
|
||||
dump(node);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void dump(SearchParameterNode node) {
|
||||
msg(node.name);
|
||||
for (SearchParameterParamNode p : sortP(node.params)) {
|
||||
String exp = p.sp.getExperimental() ? " **exp!" : "";
|
||||
if (p.only) {
|
||||
msg(" "+p.sp.getCode()+exp);
|
||||
} else {
|
||||
msg(" *"+p.sp.getCode()+exp);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private List<SearchParameterParamNode> sortP(List<SearchParameterParamNode> params) {
|
||||
List<SearchParameterParamNode> res = new ArrayList<>();
|
||||
res.addAll(params);
|
||||
Collections.sort(res, new SearchParameterParamNodeSorter());
|
||||
return res;
|
||||
}
|
||||
|
||||
private List<SearchParameterNode> sort(Collection<SearchParameterNode> values) {
|
||||
List<SearchParameterNode> res = new ArrayList<>();
|
||||
res.addAll(values);
|
||||
Collections.sort(res, new SearchParameterNodeSorter());
|
||||
return res;
|
||||
}
|
||||
|
||||
private void addNode(SearchParameter sp, boolean b, SearchParameterNode node) {
|
||||
node.params.add(new SearchParameterParamNode(sp, b));
|
||||
}
|
||||
|
||||
private void checkSD() throws IOException {
|
||||
Map<String, StructureDefinition> map = new HashMap<>();
|
||||
for (String sdn : npm.listResources("StructureDefinition")) {
|
||||
InputStream s = npm.load(sdn);
|
||||
StructureDefinition sd = (StructureDefinition) new JsonParser().parse(s);
|
||||
map.put(sd.getUrl(), sd);
|
||||
}
|
||||
msg("Loaded "+map.size()+" resources");
|
||||
List<StructureDefinitionNode> roots = new ArrayList<>();
|
||||
for (StructureDefinition sd : map.values()) {
|
||||
if (sd.getBaseDefinition() == null || !map.containsKey(sd.getBaseDefinition())) {
|
||||
StructureDefinitionNode root = new StructureDefinitionNode(sd);
|
||||
roots.add(root);
|
||||
analyse(root, map);
|
||||
}
|
||||
}
|
||||
sort(roots);
|
||||
for (StructureDefinitionNode root : roots) {
|
||||
describe(root, 0);
|
||||
}
|
||||
}
|
||||
|
||||
private void sort(List<StructureDefinitionNode> list) {
|
||||
Collections.sort(list, new StructureDefinitionNodeComparer());
|
||||
|
||||
}
|
||||
|
||||
private void analyse(StructureDefinitionNode node, Map<String, StructureDefinition> map) {
|
||||
for (StructureDefinition sd : map.values()) {
|
||||
if (node.sd.getUrl().equals(sd.getBaseDefinition())) {
|
||||
StructureDefinitionNode c = new StructureDefinitionNode(sd);
|
||||
node.children.add(c);
|
||||
analyse(c, map);
|
||||
}
|
||||
}
|
||||
sort(node.children);
|
||||
}
|
||||
|
||||
private void describe(StructureDefinitionNode node, int level) {
|
||||
describe(node.sd, level);
|
||||
for (StructureDefinitionNode c : node.children) {
|
||||
describe(c, level+1);
|
||||
}
|
||||
}
|
||||
|
||||
private void describe(StructureDefinition sd, int level) {
|
||||
String exp = sd.getExperimental() ? " **exp!" : "";
|
||||
if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
|
||||
msg(Utilities.padLeft("", ' ', level)+sd.getType()+" / "+sd.getName()+" ("+sd.getUrl()+")"+exp);
|
||||
} else {
|
||||
msg(Utilities.padLeft("", ' ', level)+sd.getType()+" : "+sd.getKind()+exp);
|
||||
}
|
||||
}
|
||||
|
||||
// private int analyse(Map<String, StructureDefinition> map, List<StructureDefinition> list, StructureDefinition sd) {
|
||||
// if (!list.contains(sd)) {
|
||||
// int level = 0;
|
||||
// if (sd.hasBaseDefinition()) {
|
||||
// StructureDefinition p = map.get(sd.getBaseDefinition());
|
||||
// if (p == null) {
|
||||
// msg("Can't find parent "+sd.getBaseDefinition()+" for "+sd.getUrl());
|
||||
// } else {
|
||||
// level = analyse(map, list, p) + 1;
|
||||
// }
|
||||
// }
|
||||
// list.add(sd);
|
||||
// sd.setUserData("level", level);
|
||||
// }
|
||||
// }
|
||||
|
||||
private void msg(String string) {
|
||||
System.out.println(string);
|
||||
}
|
||||
|
||||
private void load(String folder) throws IOException {
|
||||
msg("Loading resources from "+folder);
|
||||
npm = NpmPackage.fromFolder(folder);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,300 @@
|
|||
package org.hl7.fhir.r4b.utils;
|
||||
|
||||
import java.io.BufferedOutputStream;
|
||||
import java.io.ByteArrayOutputStream;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collection;
|
||||
import java.util.Collections;
|
||||
import java.util.Comparator;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Map.Entry;
|
||||
import java.util.zip.ZipEntry;
|
||||
import java.util.zip.ZipInputStream;
|
||||
|
||||
import org.hl7.fhir.r4b.model.CodeType;
|
||||
import org.hl7.fhir.r4b.model.SearchParameter;
|
||||
import org.hl7.fhir.r4b.utils.IntegrityChecker.SearchParameterNode;
|
||||
import org.hl7.fhir.r4b.utils.IntegrityChecker.SearchParameterNodeSorter;
|
||||
import org.hl7.fhir.r4b.utils.IntegrityChecker.SearchParameterParamNode;
|
||||
import org.hl7.fhir.r4b.utils.IntegrityChecker.SearchParameterParamNodeSorter;
|
||||
import org.hl7.fhir.r4b.formats.JsonParser;
|
||||
import org.hl7.fhir.r4b.formats.XmlParser;
|
||||
import org.hl7.fhir.r4b.model.StructureDefinition;
|
||||
import org.hl7.fhir.r4b.model.StructureDefinition.TypeDerivationRule;
|
||||
import org.hl7.fhir.r4b.utils.IntegrityChecker.StructureDefinitionNode;
|
||||
import org.hl7.fhir.r4b.utils.IntegrityChecker.StructureDefinitionNodeComparer;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.npm.NpmPackage;
|
||||
|
||||
public class IntegrityChecker {
|
||||
|
||||
public class SearchParameterNodeSorter implements Comparator<SearchParameterNode> {
|
||||
|
||||
@Override
|
||||
public int compare(SearchParameterNode o1, SearchParameterNode o2) {
|
||||
return o1.name.compareTo(o2.name);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class SearchParameterParamNodeSorter implements Comparator<SearchParameterParamNode> {
|
||||
|
||||
@Override
|
||||
public int compare(SearchParameterParamNode o1, SearchParameterParamNode o2) {
|
||||
return o1.sp.getCode().compareTo(o2.sp.getCode());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class SearchParameterParamNode {
|
||||
SearchParameter sp;
|
||||
boolean only;
|
||||
public SearchParameterParamNode(SearchParameter sp, boolean only) {
|
||||
super();
|
||||
this.sp = sp;
|
||||
this.only = only;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
public class SearchParameterNode {
|
||||
|
||||
private String name;
|
||||
private List<SearchParameterParamNode> params = new ArrayList<>();
|
||||
|
||||
public SearchParameterNode(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class StructureDefinitionNodeComparer implements Comparator<StructureDefinitionNode> {
|
||||
|
||||
@Override
|
||||
public int compare(StructureDefinitionNode arg0, StructureDefinitionNode arg1) {
|
||||
if ( arg0.sd.getType().equals(arg1.sd.getType())) {
|
||||
return arg0.sd.getName().compareTo(arg1.sd.getName());
|
||||
} else {
|
||||
return arg0.sd.getType().compareTo(arg1.sd.getType());
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public class StructureDefinitionNode {
|
||||
StructureDefinition sd;
|
||||
List<StructureDefinitionNode> children = new ArrayList<>();
|
||||
|
||||
public StructureDefinitionNode(StructureDefinition sd) {
|
||||
this.sd = sd;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private NpmPackage npm;
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
IntegrityChecker check = new IntegrityChecker();
|
||||
check.load(args[0]);
|
||||
check.check(args[1]);
|
||||
}
|
||||
|
||||
private void check(String dst) throws IOException {
|
||||
checkSD();
|
||||
checkSP();
|
||||
checkExamplesXml(dst);
|
||||
checkExamplesJson(dst);
|
||||
}
|
||||
|
||||
private Map<String, byte[]> loadZip(InputStream stream) throws IOException {
|
||||
Map<String, byte[]> res = new HashMap<String, byte[]>();
|
||||
ZipInputStream zip = new ZipInputStream(stream);
|
||||
ZipEntry ze;
|
||||
while ((ze = zip.getNextEntry()) != null) {
|
||||
int size;
|
||||
byte[] buffer = new byte[2048];
|
||||
|
||||
ByteArrayOutputStream bytes = new ByteArrayOutputStream();
|
||||
BufferedOutputStream bos = new BufferedOutputStream(bytes, buffer.length);
|
||||
|
||||
while ((size = zip.read(buffer, 0, buffer.length)) != -1) {
|
||||
bos.write(buffer, 0, size);
|
||||
}
|
||||
bos.flush();
|
||||
bos.close();
|
||||
res.put(ze.getName(), bytes.toByteArray());
|
||||
|
||||
zip.closeEntry();
|
||||
}
|
||||
zip.close();
|
||||
return res;
|
||||
}
|
||||
|
||||
private void checkExamplesJson(String dst) throws FileNotFoundException, IOException {
|
||||
Map<String, byte[]> files = loadZip(new FileInputStream(Utilities.path(dst, "examples-json.zip")));
|
||||
for (Entry<String, byte[]> t : files.entrySet()) {
|
||||
try {
|
||||
new JsonParser().parse(t.getValue());
|
||||
System.out.print(".");
|
||||
} catch (Exception e) {
|
||||
System.out.println("");
|
||||
System.out.println("Error parsing "+t.getKey()+": "+e.getMessage());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void checkExamplesXml(String dst) throws FileNotFoundException, IOException {
|
||||
Map<String, byte[]> files = loadZip(new FileInputStream(Utilities.path(dst, "examples.zip")));
|
||||
for (Entry<String, byte[]> t : files.entrySet()) {
|
||||
try {
|
||||
new XmlParser().parse(t.getValue());
|
||||
System.out.print(".");
|
||||
} catch (Exception e) {
|
||||
System.out.println("");
|
||||
System.out.println("Error parsing "+t.getKey()+": "+e.getMessage());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private void checkSP() throws IOException {
|
||||
List<SearchParameter> list = new ArrayList<>();
|
||||
for (String sdn : npm.listResources("SearchParameter")) {
|
||||
InputStream s = npm.load(sdn);
|
||||
SearchParameter sp = (SearchParameter) new JsonParser().parse(s);
|
||||
list.add(sp);
|
||||
}
|
||||
msg("Loaded "+list.size()+" resources");
|
||||
Map<String, SearchParameterNode> map = new HashMap<>();
|
||||
for (SearchParameter sp : list) {
|
||||
for (CodeType c : sp.getBase()) {
|
||||
String s = c.primitiveValue();
|
||||
if (!map.containsKey(s)) {
|
||||
map.put(s, new SearchParameterNode(s));
|
||||
}
|
||||
addNode(sp, sp.getBase().size() == 1, map.get(s));
|
||||
}
|
||||
}
|
||||
for (SearchParameterNode node : sort(map.values())) {
|
||||
dump(node);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void dump(SearchParameterNode node) {
|
||||
msg(node.name);
|
||||
for (SearchParameterParamNode p : sortP(node.params)) {
|
||||
String exp = p.sp.getExperimental() ? " **exp!" : "";
|
||||
if (p.only) {
|
||||
msg(" "+p.sp.getCode()+exp);
|
||||
} else {
|
||||
msg(" *"+p.sp.getCode()+exp);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private List<SearchParameterParamNode> sortP(List<SearchParameterParamNode> params) {
|
||||
List<SearchParameterParamNode> res = new ArrayList<>();
|
||||
res.addAll(params);
|
||||
Collections.sort(res, new SearchParameterParamNodeSorter());
|
||||
return res;
|
||||
}
|
||||
|
||||
private List<SearchParameterNode> sort(Collection<SearchParameterNode> values) {
|
||||
List<SearchParameterNode> res = new ArrayList<>();
|
||||
res.addAll(values);
|
||||
Collections.sort(res, new SearchParameterNodeSorter());
|
||||
return res;
|
||||
}
|
||||
|
||||
private void addNode(SearchParameter sp, boolean b, SearchParameterNode node) {
|
||||
node.params.add(new SearchParameterParamNode(sp, b));
|
||||
}
|
||||
|
||||
private void checkSD() throws IOException {
|
||||
Map<String, StructureDefinition> map = new HashMap<>();
|
||||
for (String sdn : npm.listResources("StructureDefinition")) {
|
||||
InputStream s = npm.load(sdn);
|
||||
StructureDefinition sd = (StructureDefinition) new JsonParser().parse(s);
|
||||
map.put(sd.getUrl(), sd);
|
||||
}
|
||||
msg("Loaded "+map.size()+" resources");
|
||||
List<StructureDefinitionNode> roots = new ArrayList<>();
|
||||
for (StructureDefinition sd : map.values()) {
|
||||
if (sd.getBaseDefinition() == null || !map.containsKey(sd.getBaseDefinition())) {
|
||||
StructureDefinitionNode root = new StructureDefinitionNode(sd);
|
||||
roots.add(root);
|
||||
analyse(root, map);
|
||||
}
|
||||
}
|
||||
sort(roots);
|
||||
for (StructureDefinitionNode root : roots) {
|
||||
describe(root, 0);
|
||||
}
|
||||
}
|
||||
|
||||
private void sort(List<StructureDefinitionNode> list) {
|
||||
Collections.sort(list, new StructureDefinitionNodeComparer());
|
||||
|
||||
}
|
||||
|
||||
private void analyse(StructureDefinitionNode node, Map<String, StructureDefinition> map) {
|
||||
for (StructureDefinition sd : map.values()) {
|
||||
if (node.sd.getUrl().equals(sd.getBaseDefinition())) {
|
||||
StructureDefinitionNode c = new StructureDefinitionNode(sd);
|
||||
node.children.add(c);
|
||||
analyse(c, map);
|
||||
}
|
||||
}
|
||||
sort(node.children);
|
||||
}
|
||||
|
||||
private void describe(StructureDefinitionNode node, int level) {
|
||||
describe(node.sd, level);
|
||||
for (StructureDefinitionNode c : node.children) {
|
||||
describe(c, level+1);
|
||||
}
|
||||
}
|
||||
|
||||
private void describe(StructureDefinition sd, int level) {
|
||||
String exp = sd.getExperimental() ? " **exp!" : "";
|
||||
if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
|
||||
msg(Utilities.padLeft("", ' ', level)+sd.getType()+" / "+sd.getName()+" ("+sd.getUrl()+")"+exp);
|
||||
} else {
|
||||
msg(Utilities.padLeft("", ' ', level)+sd.getType()+" : "+sd.getKind()+exp);
|
||||
}
|
||||
}
|
||||
|
||||
// private int analyse(Map<String, StructureDefinition> map, List<StructureDefinition> list, StructureDefinition sd) {
|
||||
// if (!list.contains(sd)) {
|
||||
// int level = 0;
|
||||
// if (sd.hasBaseDefinition()) {
|
||||
// StructureDefinition p = map.get(sd.getBaseDefinition());
|
||||
// if (p == null) {
|
||||
// msg("Can't find parent "+sd.getBaseDefinition()+" for "+sd.getUrl());
|
||||
// } else {
|
||||
// level = analyse(map, list, p) + 1;
|
||||
// }
|
||||
// }
|
||||
// list.add(sd);
|
||||
// sd.setUserData("level", level);
|
||||
// }
|
||||
// }
|
||||
|
||||
private void msg(String string) {
|
||||
System.out.println(string);
|
||||
}
|
||||
|
||||
private void load(String folder) throws IOException {
|
||||
msg("Loading resources from "+folder);
|
||||
npm = NpmPackage.fromFolder(folder);
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue