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Cqf-Tooling : NewRefreshIg update (#528)
* Added missing tests * _Added CqlRefresh in order to update cql file before conversion. _Made sure that we have the cql data inside the json library and that it matches the udpated cql _Update tests to verify everything works as expected. * Formatting * Test update * Test path update * Update test files * Update test files 2 * Clean up of test file * Clean up of test file 2 * This one is not a file path * Fix output directory * Move files to same directory * TEST: don't swallow exceptions * Add logging of missing files * Revert previous experiments * Fix casing of folder name * Add path to CQL source information * Add more logging * Fix prefix, fix some level 1.3 warnings * Change build to use info log level for debug purposes * Swap up dependency loading code * Revert to normal logging --------- Co-authored-by: Jonathan Percival <[email protected]>
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tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/CqlRefresh.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| package org.opencds.cqf.tooling.operation.ig; | ||
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| import org.hl7.fhir.instance.model.api.IBaseResource; | ||
| import org.opencds.cqf.tooling.parameter.RefreshIGParameters; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.*; | ||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
| import java.util.stream.Collectors; | ||
| import java.util.stream.Stream; | ||
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| public class CqlRefresh extends Refresh { | ||
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| private static final Logger logger = LoggerFactory.getLogger(CqlRefresh.class); | ||
| private final Pattern VERSION_PATTERN = Pattern.compile("^(library\\s+(\\S+)\\s+version\\s+)'[0-9]+\\.[0-9]+\\.[0-9]+'"); | ||
| private final Pattern INCLUDE_PATTERN = Pattern.compile("^(include\\s+(\\S+)\\s+version\\s+)'([0-9]+\\.[0-9]+\\.[0-9]+)'(\\s+called\\s+(\\S+))?"); | ||
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| public CqlRefresh(IGInfo igInfo) { | ||
| super(igInfo); | ||
| } | ||
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| @Override | ||
| public List<IBaseResource> refresh() { | ||
| return List.of(); | ||
| } | ||
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| public void refreshCql(IGInfo igInfo, RefreshIGParameters params) { | ||
| Map<String, String> updatedLibraries = refreshCqlFile(igInfo.getCqlBinaryPath(), params.updatedVersion); | ||
| updateCqlReferences(igInfo.getCqlBinaryPath(), updatedLibraries); | ||
| } | ||
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| private Map<String, String> refreshCqlFile(String cqlBinaryPath, String updatedVersion) { | ||
| Map<String, String> updatedLibraries = new HashMap<>(); | ||
| try (Stream<Path> paths = Files.walk(Paths.get(cqlBinaryPath))) { | ||
| List<Path> files = paths | ||
| .filter(Files::isRegularFile) | ||
| .filter(path -> path.toString().endsWith(".cql")) | ||
| .collect(Collectors.toList()); | ||
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| for (Path file : files) { | ||
| List<String> lines = Files.readAllLines(file); | ||
| for (int i = 0; i < lines.size(); i++) { | ||
| Matcher matcher = VERSION_PATTERN.matcher(lines.get(i)); | ||
| if (matcher.matches()) { | ||
| String libraryName = matcher.group(2); | ||
| String updatedLine = matcher.replaceFirst("$1'" + updatedVersion + "'"); | ||
| lines.set(i, updatedLine); | ||
| Files.write(file, lines); | ||
| updatedLibraries.put(libraryName, updatedVersion); | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| } catch (IOException e) { | ||
| logger.error("Error updating cql files: {}", e.getMessage()); | ||
| } | ||
| return updatedLibraries; | ||
| } | ||
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| private void updateCqlReferences(String cqlBinaryPath, Map<String, String> updatedLibraries) { | ||
| try (Stream<Path> paths = Files.walk(Paths.get(cqlBinaryPath))) { | ||
| List<Path> files = paths | ||
| .filter(Files::isRegularFile) | ||
| .filter(path -> path.toString().endsWith(".cql")) | ||
| .collect(Collectors.toList()); | ||
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| for (Path file : files) { | ||
| List<String> lines = Files.readAllLines(file); | ||
| boolean fileUpdated = false; | ||
| for (int i = 0; i < lines.size(); i++) { | ||
| Matcher matcher = INCLUDE_PATTERN.matcher(lines.get(i)); | ||
| while (matcher.find()) { | ||
| String libraryName = matcher.group(2); | ||
| String newVersion = updatedLibraries.get(libraryName); | ||
| if (newVersion != null && !matcher.group(3).equals(newVersion)) { | ||
| String calledPart = matcher.group(4) != null ? matcher.group(4) : ""; | ||
| String newLine = matcher.replaceFirst("$1'" + newVersion + "'" + calledPart); | ||
| lines.set(i, newLine); | ||
| fileUpdated = true; | ||
| } | ||
| } | ||
| } | ||
| if (fileUpdated) { | ||
| Files.write(file, lines); | ||
| } | ||
| } | ||
| } catch (IOException e) { | ||
| logger.error("Error updating CQL references: {}", e.getMessage()); | ||
| } | ||
| } | ||
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|
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| } |
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