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org.hl7.fhir.core
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Merge remote-tracking branch 'origin/master'

This commit is contained in:
Grahame Grieve 2023-03-19 08:52:55 +11:00
parent 95f3fdd187 bc4a76f1ad
commit e1fed0a8eb
7 changed files with 147 additions and 29 deletions
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7
README.md
View File

@ -74,6 +74,13 @@ _The source contains cached terminology server responses for testing. If the exp
this cache should be cleaned and rebuilt with the above so that subsequent `mvn test` calls will have the most current
responses cached._
To build only the validator_cli jar locally:
```
mvn clean package -Dmaven.test.skip=true --projects org.hl7.fhir.validation.cli --no-transfer-progress
cp org.hl7.fhir.validation.cli/target/org.hl7.fhir.validation.cli*-SNAPSHOT.jar ./validator_cli.jar
```
_This will produce `./validator_cli.jar` in the project root directory._
## Releases

2
master-branch-pipeline.yml
View File

@ -90,6 +90,7 @@ steps:
jdkVersionOption: '1.11'
jdkArchitectureOption: 'x64'
options: '--settings $(System.DefaultWorkingDirectory)/settings.xml -pl "!org.hl7.fhir.report, !org.hl7.fhir.validation.cli" -DdeployToSonatype'
mavenOptions: '-Xmx4096m'
publishJUnitResults: false
# Deploy the SNAPSHOT artifact to GitHub packages.
@ -103,4 +104,5 @@ steps:
jdkVersionOption: '1.11'
jdkArchitectureOption: 'x64'
options: '--settings $(System.DefaultWorkingDirectory)/settings.xml -pl "!org.hl7.fhir.report, !org.hl7.fhir.validation.cli" -Dmaven.test.skip -DdeployToGitHub'
mavenOptions: '-Xmx4096m'
publishJUnitResults: false

129
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/FTPClient.java
View File

@ -1,5 +1,7 @@
package org.hl7.fhir.utilities;
import lombok.AccessLevel;
import lombok.AllArgsConstructor;
import lombok.Getter;
import org.apache.commons.net.ftp.FTP;
import org.apache.commons.net.ftp.FTPReply;
@ -16,6 +18,15 @@ public class FTPClient {
private final org.apache.commons.net.ftp.FTPClient clientImpl;
@Getter
private long createRemotePathIfNotExistsNanos;
@Getter
private long storeFileTimeNanos;
@Getter
private long deleteFileTimeNanos;
@Getter
private final String server;
@ -35,6 +46,20 @@ public class FTPClient {
private final String remoteSeparator;
@AllArgsConstructor(access = AccessLevel.PROTECTED)
private class FTPReplyCodeAndString {
@Getter
private final int replyCode;
@Getter
private final String replyString;
public String toString()
{
return "Reply code: " + replyCode + " Message: " + replyString;
}
}
/**
* Connect to an FTP server
* @param server - the server to connect to (usually just an IP address). It's up to the system to figure out access (VPN etc)
@ -74,27 +99,39 @@ public class FTPClient {
*/
public void connect() throws IOException {
if (port != -1) {
logger.debug("Connecting to : " + server + ":" + port);
clientImpl.connect(server, port);
logger.debug("Connected");
}
else {
logger.debug("Connecting to : " + server);
clientImpl.connect(server);
logger.debug("Connected");
}
clientImpl.login(user, password);
checkForPositiveCompletionAndLogErrors("FTP server could not connect.", true);
throwExceptionForNegativeCompletion("FTP server could not connect.", true);
resetTimers();
logger.debug("Initial Working directory: " + clientImpl.printWorkingDirectory());
clientImpl.changeWorkingDirectory(path);
checkForPositiveCompletionAndLogErrors("FTP server could not establish default working directory", true);
throwExceptionForNegativeCompletion("FTP server could not establish default working directory", true);
resolvedPath = clientImpl.printWorkingDirectory();
logger.debug("Resolved working directory: " + resolvedPath);
}
private void resetTimers() {
this.createRemotePathIfNotExistsNanos = 0;
this.storeFileTimeNanos = 0;
this.deleteFileTimeNanos = 0;
}
/**
* Delete a file on the FTP server
*
@ -103,9 +140,11 @@ public class FTPClient {
public void delete(String path) throws IOException {
String resolvedPath = resolveRemotePath(path);
logger.debug("Deleting remote file: " + resolvedPath);
long startTime = System.nanoTime();
clientImpl.deleteFile(resolvedPath);
checkForPositiveCompletionAndLogErrors("Error deleting file.", false);
logger.debug("Remote file deleted: " + resolvedPath);
this.deleteFileTimeNanos += System.nanoTime() - startTime;
throwExceptionForNegativeCompletion("Error deleting file.", false);
logger.debug("Deleted remote file: " + resolvedPath);
}
/**
@ -114,6 +153,7 @@ public class FTPClient {
* @throws IOException
*/
protected void createRemotePathIfNotExists(String filePath) throws IOException {
long startTime = System.nanoTime();
String[] subPath = filePath.split(remoteSeparator);
try {
for (int i = 0 ; i < subPath.length - 1; i++){
@ -122,16 +162,24 @@ public class FTPClient {
}
boolean exists = clientImpl.changeWorkingDirectory(subPath[i]);
if (!exists) {
logger.debug("Remote directory does not exist: " + clientImpl.printWorkingDirectory() + remoteSeparator + subPath[i]);
logger.debug("Creating non-existent directory: " + clientImpl.printWorkingDirectory() + remoteSeparator + subPath[i] + " Creating");
clientImpl.makeDirectory(subPath[i]);
throwExceptionForNegativeCompletion("Creating directory:", true);
logger.debug("Created directory: " + subPath[i]);
logger.debug("Changing to created directory: " + subPath[i]);
clientImpl.changeWorkingDirectory(subPath[i]);
logger.debug("Made remote directory: " + clientImpl.printWorkingDirectory());
throwExceptionForNegativeCompletion("Changing to directory:", true);
logger.debug("Changed to directory: " + subPath[i]);
}
}} catch (IOException e) {
throw new IOException("Error creating remote path: " + filePath, e);
} finally {
logger.debug("Changing to original directory: " + this.resolvedPath);
clientImpl.changeWorkingDirectory(this.resolvedPath);
logger.debug("Changed to original directory: " + this.resolvedPath);
}
this.createRemotePathIfNotExistsNanos += System.nanoTime() - startTime;
}
protected boolean remotePathExists(String path) throws IOException {
@ -159,32 +207,66 @@ public class FTPClient {
public void upload(String source, String path) throws IOException {
String resolvedPath = resolveRemotePath(path);
logger.debug("Uploading file to remote path: " + resolvedPath);
createRemotePathIfNotExists(path);
FileInputStream localStream = new FileInputStream(source);
clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
clientImpl.enterLocalPassiveMode();
clientImpl.storeFile( resolvedPath, localStream);
localStream.close();
checkForPositiveCompletionAndLogErrors("Error uploading file.", false);
logger.debug("Remote file uploaded: " + resolvedPath);
}
attemptUpload(source, resolvedPath);
private void checkForPositiveCompletionAndLogErrors(String localErrorMessage, boolean disconnectOnError) throws IOException {
int reply = clientImpl.getReplyCode();
if (FTPReply.isPositiveCompletion(reply)) {
FTPReplyCodeAndString reply = getFTPReplyCodeAndString();
if (FTPReply.isPositiveCompletion(reply.replyCode)) {
logger.debug("Uploaded file: " + resolvedPath);
return;
} else if (possibleDirectoryNotExistsCode(reply)) {
logger.debug("Uploading failed with reply: " + reply);
createRemotePathIfNotExists(resolvedPath);
attemptUpload(source, resolvedPath);
throwExceptionForNegativeCompletion("Error uploading file (second attempt).", false);
logger.debug("Uploaded file after path creation: " + resolvedPath);
return;
}
throwExceptionForNegativeCompletion(reply,"Error uploading file.", false);
logger.debug("Remote file uploaded: " + resolvedPath);
}
private boolean possibleDirectoryNotExistsCode(FTPReplyCodeAndString reply) {
/*
Note: This code may be 550 on some servers (IIS) and 553 on others (mockftpserver).
*/
return reply.replyCode == 550 || reply.replyCode == 553;
}
private void attemptUpload(String source, String resolvedPath) throws IOException {
final long startTime = System.nanoTime();
FileInputStream localStream = new FileInputStream(source);
clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
clientImpl.enterLocalPassiveMode();
clientImpl.storeFile(resolvedPath, localStream);
localStream.close();
this.storeFileTimeNanos += System.nanoTime() - startTime;
}
private FTPReplyCodeAndString getFTPReplyCodeAndString() {
final int replyCode = clientImpl.getReplyCode();
final String replyString = clientImpl.getReplyString();
return new FTPReplyCodeAndString(replyCode, replyString);
}
private void throwExceptionForNegativeCompletion(String localErrorMessage, boolean disconnectOnError) throws IOException {
FTPReplyCodeAndString reply = getFTPReplyCodeAndString();
throwExceptionForNegativeCompletion(reply, localErrorMessage, disconnectOnError);
}
private void throwExceptionForNegativeCompletion(FTPReplyCodeAndString reply, String localErrorMessage, boolean disconnectOnError) throws IOException {
if (FTPReply.isPositiveCompletion(reply.replyCode)) {
return;
}
String remoteErrorMessage = clientImpl.getReplyString();
if (disconnectOnError) {
clientImpl.disconnect();
}
throw new IOException(localErrorMessage + " Reply code: " + reply + " Message: " + remoteErrorMessage);
throw new IOException(localErrorMessage + " " + reply);
}
public void disconnect() throws IOException {
@ -199,7 +281,6 @@ public class FTPClient {
ftp.delete("testing/test.xml");
ftp.disconnect();
}
private static String getNamedParam(String[] args, String param) {
boolean found = false;
for (String a : args) {

30
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/FTPClientTest.java
View File

@ -133,11 +133,17 @@ public class FTPClientTest implements ResourceLoaderTests {
client.delete( RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_DELETE);
assertFalse(fakeFtpServer.getFileSystem().exists(deleteFilePath));
assertTrue(client.getDeleteFileTimeNanos() > 0);
assertTrue(client.getStoreFileTimeNanos() == 0);
assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
}
private static FTPClient connectToFTPClient() throws IOException {
private FTPClient connectToFTPClient() throws IOException {
FTPClient client = new FTPClient(LOCALHOST, FAKE_FTP_PORT, RELATIVE_PATH_1, DUMMY_USER, DUMMY_PASSWORD);
client.connect();
assertAllMillisFieldsAreZero(client);
return client;
}
@ -152,6 +158,10 @@ public class FTPClientTest implements ResourceLoaderTests {
client.delete( RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_DELETE);
assertFalse(fakeFtpServer.getFileSystem().exists(deleteFilePath));
client.disconnect();
assertTrue(client.getDeleteFileTimeNanos() > 0);
assertTrue(client.getStoreFileTimeNanos() == 0);
assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
}
@ -166,6 +176,10 @@ public class FTPClientTest implements ResourceLoaderTests {
client.upload(dummyFileToUploadPath.toFile().getAbsolutePath(), RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_UPLOAD);
assertUploadedFileCorrect(uploadFilePath);
assertTrue(client.getDeleteFileTimeNanos() == 0);
assertTrue(client.getStoreFileTimeNanos() > 0);
assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
}
private void assertUploadedFileCorrect(String uploadedFilePath) throws IOException {
@ -193,10 +207,20 @@ public class FTPClientTest implements ResourceLoaderTests {
assertTrue(fakeFtpServer.getFileSystem().exists(newPath1.toFile().getAbsolutePath()));
assertTrue(fakeFtpServer.getFileSystem().exists(newPath2.toFile().getAbsolutePath()));
assertTrue(client.getDeleteFileTimeNanos() == 0);
assertTrue(client.getStoreFileTimeNanos() == 0);
assertTrue(client.getCreateRemotePathIfNotExistsNanos() > 0);
}
private void assertAllMillisFieldsAreZero(FTPClient client) {
assertTrue(client.getDeleteFileTimeNanos() == 0);
assertTrue(client.getStoreFileTimeNanos() == 0);
assertTrue(client.getCreateRemotePathIfNotExistsNanos() == 0);
}
@Test
public void testUploadWherePathDoesntExist() throws IOException {
Path newPath1 = relativePath2.resolve("newPath1");
Path newPath2 = newPath1.resolve("newPath2");
@ -214,5 +238,9 @@ public class FTPClientTest implements ResourceLoaderTests {
assertTrue(fakeFtpServer.getFileSystem().exists(newPath2.toFile().getAbsolutePath()));
assertUploadedFileCorrect(uploadFilePath.toFile().getAbsolutePath());
assertTrue(client.getDeleteFileTimeNanos() == 0);
assertTrue(client.getStoreFileTimeNanos() > 0);
assertTrue(client.getCreateRemotePathIfNotExistsNanos() > 0);
}
}

4
pull-request-pipeline-parameterized.yml
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@ -24,7 +24,7 @@ jobs:
inputs:
mavenPomFile: 'pom.xml'
options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
mavenOptions: '-Xmx3072m'
mavenOptions: '-Xmx4096m'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '${{image.jdkVersion}}'
jdkArchitectureOption: 'x64'
@ -35,7 +35,7 @@ jobs:
- task: Maven@3
inputs:
mavenPomFile: 'pom.xml'
mavenOptions: '-Xmx3072m'
mavenOptions: '-Xmx4096m'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '${{image.jdkVersion}}'
jdkArchitectureOption: 'x64'

2
pull-request-pipeline.yml
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@ -39,7 +39,7 @@ jobs:
inputs:
mavenPomFile: 'pom.xml'
options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
mavenOptions: '-Xmx3072m'
mavenOptions: '-Xmx4096m'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '1.11'
jdkArchitectureOption: 'x64'

2
release-branch-pipeline.yml
View File

@ -127,7 +127,7 @@ jobs:
- task: Maven@3
inputs:
mavenPomFile: 'pom.xml'
mavenOptions: '-Xmx3072m'
mavenOptions: '-Xmx4096m'
javaHomeOption: 'JDKVersion'
jdkVersionOption: '1.11'
jdkArchitectureOption: 'x64'