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Merge remote-tracking branch 'origin/master'

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Grahame Grieve 2023-01-14 09:04:04 +11:00
commit b92e0e2ef0
7 changed files with 130 additions and 101 deletions
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5
RELEASE_NOTES.md
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@ -4,4 +4,7 @@
## Other code changes ## Other code changes
* no changes * Better tracking and reporting of snapshot generation issues
* Inclusion of SAXON dependency for processing XSLT
* Error message spacing correction
* Basic FTPClient implementation

58
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/ResourceType.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.dstu2.model; package org.hl7.fhir.dstu2.model;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
@ -517,7 +517,7 @@ public enum ResourceType {
if ("VisionPrescription".equals(code)) if ("VisionPrescription".equals(code))
return VisionPrescription; return VisionPrescription;
throw new FHIRException("Unknown resource type"+code); throw new FHIRException("Unknown resource type "+code);
} }
} }

58
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/model/ResourceType.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.dstu2016may.model; package org.hl7.fhir.dstu2016may.model;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
@ -612,7 +612,7 @@ public enum ResourceType {
if ("VisionPrescription".equals(code)) if ("VisionPrescription".equals(code))
return VisionPrescription; return VisionPrescription;
throw new FHIRException("Unknown resource type"+code); throw new FHIRException("Unknown resource type "+code);
} }
} }

58
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/ResourceType.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.dstu3.model; package org.hl7.fhir.dstu3.model;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
@ -632,7 +632,7 @@ public enum ResourceType {
if ("VisionPrescription".equals(code)) if ("VisionPrescription".equals(code))
return VisionPrescription; return VisionPrescription;
throw new FHIRException("Unknown resource type"+code); throw new FHIRException("Unknown resource type "+code);
} }
} }

2
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/ResourceType.java
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@ -746,7 +746,7 @@ public enum ResourceType {
if ("VisionPrescription".equals(code)) if ("VisionPrescription".equals(code))
return VisionPrescription; return VisionPrescription;
throw new FHIRException("Unknown resource type"+code); throw new FHIRException("Unknown resource type "+code);
} }
} }

20
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/FTPClient.java
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@ -1,5 +1,6 @@
package org.hl7.fhir.utilities; package org.hl7.fhir.utilities;
import org.apache.commons.net.ftp.FTP;
import org.apache.commons.net.ftp.FTPReply; import org.apache.commons.net.ftp.FTPReply;
@ -52,15 +53,16 @@ public class FTPClient {
else { else {
clientImpl.connect(server); clientImpl.connect(server);
} }
//clientImpl.setFileTransferMode(FTP.BINARY_FILE_TYPE);
clientImpl.login(user, password); clientImpl.login(user, password);
clientImpl.getSystemType();
int reply = clientImpl.getReplyCode(); int reply = clientImpl.getReplyCode();
if(!FTPReply.isPositiveCompletion(reply)) { if(!FTPReply.isPositiveCompletion(reply)) {
clientImpl.disconnect(); clientImpl.disconnect();
throw new IOException("FTP server refused connection."); throw new IOException("FTP server refused connection. Reply code: " + reply);
} }
} }
@ -85,8 +87,20 @@ public class FTPClient {
*/ */
public void upload(String source, String path) throws IOException { public void upload(String source, String path) throws IOException {
String resolvedPath = resolveRemotePath(path); String resolvedPath = resolveRemotePath(path);
FileInputStream localStream = new FileInputStream(new File(source)); FileInputStream localStream = new FileInputStream(source);
clientImpl.setFileType(FTP.BINARY_FILE_TYPE);
clientImpl.storeFile( resolvedPath, localStream); clientImpl.storeFile( resolvedPath, localStream);
localStream.close();
int reply = clientImpl.getReplyCode();
if(!FTPReply.isPositiveCompletion(reply)) {
throw new IOException("Error uploading file. Reply code: " + reply);
}
}
public void disconnect() throws IOException {
clientImpl.disconnect();
} }
} }

30
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/FTPClientTest.java
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@ -1,6 +1,7 @@
package org.hl7.fhir.utilities; package org.hl7.fhir.utilities;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.utilities.tests.ResourceLoaderTests; import org.hl7.fhir.utilities.tests.ResourceLoaderTests;
import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.NotNull;
import org.junit.jupiter.api.AfterAll; import org.junit.jupiter.api.AfterAll;
@ -11,12 +12,14 @@ import org.mockftpserver.fake.FakeFtpServer;
import org.mockftpserver.fake.UserAccount; import org.mockftpserver.fake.UserAccount;
import org.mockftpserver.fake.filesystem.*; import org.mockftpserver.fake.filesystem.*;
import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import static org.junit.jupiter.api.Assertions.assertFalse; import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertTrue;
@TestInstance(TestInstance.Lifecycle.PER_CLASS) @TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class FTPClientTest implements ResourceLoaderTests { public class FTPClientTest implements ResourceLoaderTests {
@ -30,6 +33,7 @@ public class FTPClientTest implements ResourceLoaderTests {
public static final String DUMMY_FILE_TO_UPLOAD = "dummyFileToUpload"; public static final String DUMMY_FILE_TO_UPLOAD = "dummyFileToUpload";
public static final int FAKE_FTP_PORT = 8021; public static final int FAKE_FTP_PORT = 8021;
public static final String DUMMY_FILE_CONTENT = "Dummy file content\nMore content\n";
FakeFtpServer fakeFtpServer; FakeFtpServer fakeFtpServer;
@ -47,6 +51,8 @@ public class FTPClientTest implements ResourceLoaderTests {
Path dummyFileToUploadPath; Path dummyFileToUploadPath;
Path dummyUploadedFilePath; Path dummyUploadedFilePath;
String dummyFileContent;
@BeforeAll @BeforeAll
public void setup() throws IOException { public void setup() throws IOException {
setupDummyFileToUpload(); setupDummyFileToUpload();
@ -55,7 +61,14 @@ public class FTPClientTest implements ResourceLoaderTests {
} }
private void setupDummyFileToUpload() throws IOException { private void setupDummyFileToUpload() throws IOException {
dummyFileContent = createDummyFileContent();
dummyFileToUploadPath = Files.createTempFile("dummyFtpFileToUpload", "dummy"); dummyFileToUploadPath = Files.createTempFile("dummyFtpFileToUpload", "dummy");
Files.write(dummyFileToUploadPath, DUMMY_FILE_CONTENT.getBytes(StandardCharsets.UTF_8));
}
private String createDummyFileContent() {
return DUMMY_FILE_CONTENT;
} }
public void setupFakeFtpServer() throws IOException { public void setupFakeFtpServer() throws IOException {
@ -74,6 +87,7 @@ public class FTPClientTest implements ResourceLoaderTests {
fileSystem.add(new FileEntry(dummyFileToDeletePath.toFile().getAbsolutePath())); fileSystem.add(new FileEntry(dummyFileToDeletePath.toFile().getAbsolutePath()));
//fileSystem.add(new FileEntry("c:\\data\\run.exe")); //fileSystem.add(new FileEntry("c:\\data\\run.exe"));
fakeFtpServer.setFileSystem(fileSystem); fakeFtpServer.setFileSystem(fileSystem);
fakeFtpServer.start(); fakeFtpServer.start();
} }
@ -102,17 +116,11 @@ public class FTPClientTest implements ResourceLoaderTests {
FTPClient client = connectToFTPClient(); FTPClient client = connectToFTPClient();
String deleteFilePath = dummyFileToDeletePath.toFile().getAbsolutePath(); String deleteFilePath = dummyFileToDeletePath.toFile().getAbsolutePath();
assertTrue(fakeFtpServer.getFileSystem().exists(deleteFilePath)); assertTrue(fakeFtpServer.getFileSystem().exists(deleteFilePath));
client.delete( RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_DELETE); client.delete( RELATIVE_PATH_2 + "/" + DUMMY_FILE_TO_DELETE);
assertFalse(fakeFtpServer.getFileSystem().exists(deleteFilePath)); assertFalse(fakeFtpServer.getFileSystem().exists(deleteFilePath));
} }
@NotNull @NotNull
@ -135,6 +143,10 @@ public class FTPClientTest implements ResourceLoaderTests {
assertTrue(fakeFtpServer.getFileSystem().exists(uploadFilePath)); assertTrue(fakeFtpServer.getFileSystem().exists(uploadFilePath));
FileEntry fileEntry= (FileEntry)fakeFtpServer.getFileSystem().getEntry(uploadFilePath);
InputStream inputStream = fileEntry.createInputStream();
byte[] bytes = IOUtils.toByteArray(inputStream);
String actualContent = new String(bytes, StandardCharsets.UTF_8);
assertEquals(DUMMY_FILE_CONTENT,actualContent);
} }
} }