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rework CPT import

This commit is contained in:
Grahame Grieve 2023-08-08 19:57:55 +10:00
parent f9ef847a35
commit 8094604da0
1 changed files with 20 additions and 16 deletions
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36
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CPTImporter.java
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@ -38,7 +38,6 @@ public class CPTImporter {
}
private Connection con;
private void doImport(String src, String version, String dst) throws FHIRException, FileNotFoundException, IOException, ClassNotFoundException, SQLException {
@ -85,8 +84,15 @@ public class CPTImporter {
System.out.println(k);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs);
produceDB(Utilities.changeFileExt(dst, ".db"), cs);
connect(Utilities.changeFileExt(dst, ".db"));
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "25", "P1"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.changeFileExt(dst, "-fragment.json")), cs);
produceDB(Utilities.changeFileExt(dst, "-fragment.db"), cs);
}
private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException {
Connection con = connect(path);
Statement stmt = con.createStatement();
stmt.execute("insert into Information (name, value) values ('version', "+cs.getVersion()+")");
@ -95,7 +101,7 @@ public class CPTImporter {
stmt.execute("insert into Concepts (code, modifier) values ('"+cc.getCode()+"', "+isModifier(cc)+")");
int i = 0;
if (cc.hasDisplay()) {
stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', 0, 0, '"+Utilities.escapeSql(cc.getDisplay())+"')");
stmt.execute("insert into Designations (code, type, sequence, value) values ('"+cc.getCode()+"', 'display', 0, '"+Utilities.escapeSql(cc.getDisplay())+"')");
i++;
}
for (ConceptDefinitionDesignationComponent d : cc.getDesignation()) {
@ -111,9 +117,7 @@ public class CPTImporter {
}
}
}
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "25"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst+"-fragment"), cs);
}
private String isModifier(ConceptDefinitionComponent cc) {
@ -126,19 +130,19 @@ public class CPTImporter {
}
private void connect(String dest) throws SQLException, ClassNotFoundException {
private Connection connect(String dest) throws SQLException, ClassNotFoundException {
// Class.forName("com.mysql.jdbc.Driver");
// con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd});
new File(dest).delete();
con = DriverManager.getConnection("jdbc:sqlite:"+dest);
makeMetadataTable();
makeConceptsTable();
makeDesignationsTable();
makePropertiesTable();
Connection con = DriverManager.getConnection("jdbc:sqlite:"+dest);
makeMetadataTable(con);
makeConceptsTable(con);
makeDesignationsTable(con);
makePropertiesTable(con);
return con;
}
private void makeDesignationsTable() throws SQLException {
private void makeDesignationsTable(Connection con) throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Designations (\r\n"+
"`code` varchar(15) NOT NULL,\r\n"+
@ -149,7 +153,7 @@ public class CPTImporter {
}
private void makePropertiesTable() throws SQLException {
private void makePropertiesTable(Connection con) throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Properties (\r\n"+
@ -162,7 +166,7 @@ public class CPTImporter {
}
private void makeConceptsTable() throws SQLException {
private void makeConceptsTable(Connection con) throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Concepts (\r\n"+
@ -173,7 +177,7 @@ public class CPTImporter {
}
private void makeMetadataTable() throws SQLException {
private void makeMetadataTable(Connection con) throws SQLException {
Statement stmt = con.createStatement();
stmt.execute("CREATE TABLE Information (\r\n"+