diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
index 1f1e0d2dff1697c5f786bdb7926f4d16cd775284..8d46949ea194fead71a42248edc6e3ccbcc75025 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
@@ -24,7 +24,6 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import java.io.Serializable;
-import java.util.List;
import java.util.Map;
@JsonObject("dss.dto.imaging.ImagingDataSetExport")
@@ -37,18 +36,9 @@ public class ImagingDataSetExport implements Serializable
private Map<String, Serializable> config;
@JsonProperty
- private String format;
-
- @JsonProperty
- private String bytes;
-
- @JsonProperty
- private boolean show;
-
- @JsonProperty
+ @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
private Map<String, String> metaData;
-
@JsonIgnore
public Map<String, Serializable> getConfig()
{
@@ -60,39 +50,6 @@ public class ImagingDataSetExport implements Serializable
this.config = config;
}
- @JsonIgnore
- public String getFormat()
- {
- return format;
- }
-
- public void setFormat(String format)
- {
- this.format = format;
- }
-
- @JsonIgnore
- public String getBytes()
- {
- return bytes;
- }
-
- public void setBytes(String bytes)
- {
- this.bytes = bytes;
- }
-
- @JsonIgnore
- public boolean isShow()
- {
- return show;
- }
-
- public void setShow(boolean show)
- {
- this.show = show;
- }
-
@JsonIgnore
public Map<String, String> getMetaData()
{
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
index 811b5b05ac48b350bce6ac4bf72654f01a508e2e..e726231d0e42141dd27912cffa0dd75b9e6b497c 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
@@ -33,6 +33,9 @@ public class ImagingDataSetImage implements Serializable
@JsonProperty
private List<ImagingDataSetPreview> previews;
+ @JsonProperty
+ private Map<String, Serializable> config;
+
@JsonProperty
private Map<String, String> metaData;
@@ -48,6 +51,16 @@ public class ImagingDataSetImage implements Serializable
this.previews = previews;
}
+ public Map<String, Serializable> getConfig()
+ {
+ return config;
+ }
+
+ public void setConfig(Map<String, Serializable> config)
+ {
+ this.config = config;
+ }
+
@JsonIgnore
public Map<String, String> getMetaData()
{
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetMultiExport.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetMultiExport.java
new file mode 100644
index 0000000000000000000000000000000000000000..d46ced3b5a06b2cbf46a7bb28748ed7f6955d9fd
--- /dev/null
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetMultiExport.java
@@ -0,0 +1,97 @@
+/*
+ * Copyright ETH 2023 Zürich, Scientific IT Services
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
+
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.property.PropertiesDeserializer;
+import ch.systemsx.cisd.base.annotation.JsonObject;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+
+import java.io.Serializable;
+import java.util.List;
+import java.util.Map;
+
+@JsonObject("dss.dto.imaging.ImagingDataSetMultiExport")
+public class ImagingDataSetMultiExport implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ @JsonProperty
+ private String permId;
+ @JsonProperty
+ private int index;
+
+ @JsonProperty
+ @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
+ private Map<String, Serializable> config;
+
+ @JsonProperty
+ @JsonDeserialize(contentUsing = PropertiesDeserializer.class)
+ private Map<String, String> metaData;
+
+ @JsonIgnore
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId) {
+ this.permId = permId;
+ }
+
+ @JsonIgnore
+ public int getIndex()
+ {
+ return index;
+ }
+
+ public void setIndex(int index) {
+ this.index = index;
+ }
+
+ @JsonIgnore
+ public Map<String, Serializable> getConfig()
+ {
+ return config;
+ }
+
+ public void setConfig(Map<String, Serializable> config)
+ {
+ this.config = config;
+ }
+
+ @JsonIgnore
+ public Map<String, String> getMetaData()
+ {
+ return metaData;
+ }
+
+ public void setMetaData(Map<String, String> metaData)
+ {
+ this.metaData = metaData;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "ImagingDataSetMultiExport:" + permId;
+ }
+
+}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingArchiver.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingArchiver.java
new file mode 100644
index 0000000000000000000000000000000000000000..8974f7cccf8ada7dd318ca9711045e5f5c049165
--- /dev/null
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingArchiver.java
@@ -0,0 +1,153 @@
+/*
+ * Copyright ETH 2023 Zürich, Scientific IT Services
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDataSetPackager;
+import ch.systemsx.cisd.openbis.dss.generic.server.TarDataSetPackager;
+import ch.systemsx.cisd.openbis.dss.generic.server.ZipDataSetPackager;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.ISessionWorkspaceProvider;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.Serializable;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Map;
+import java.util.function.Function;
+
+class ImagingArchiver
+{
+ private final String sessionToken;
+ private final String exportDirName;
+ private final String exportArchiveName;
+ private final Function<InputStream, Long> checksumFunction;
+
+
+
+ private ArchiveBuilder archive;
+
+ private final String archiveFormat;
+
+ ImagingArchiver(String sessionToken, Map<String, Serializable> exportConfig) {
+ this.sessionToken = sessionToken;
+ archiveFormat = exportConfig.get("archive-format").toString();
+
+ String currentTimeMs = String.valueOf(System.currentTimeMillis());
+ exportDirName = "imaging_export_" + currentTimeMs;
+
+ if (archiveFormat.equalsIgnoreCase("zip"))
+ {
+ exportArchiveName = "export.zip";
+ checksumFunction = Util::getCRC32Checksum;
+ } else if (archiveFormat.equalsIgnoreCase("tar"))
+ {
+ exportArchiveName = "export.tar.gz";
+ checksumFunction = (x) -> 0L;
+ } else
+ {
+ throw new UserFailureException("Unknown archive format!");
+ }
+
+
+ }
+
+ void prepare() {
+
+// try
+// {
+// Path tempDir = Files.createDirectory(Path.of(tempDirectory.getAbsolutePath(), token));
+// if (archiveFormat.equalsIgnoreCase("zip"))
+// {
+// File archiveFile =
+// Files.createFile(Path.of(tempDir.toAbsolutePath().toString(), "export.zip"))
+// .toFile();
+// checksumFunction = Util::getCRC32Checksum;
+// packager = new ZipDataSetPackager(archiveFile, true, null, null);
+// } else if (archiveFormat.equalsIgnoreCase("tar"))
+// {
+// archiveFile =
+// Files.createFile(
+// Path.of(tempDir.toAbsolutePath().toString(), "export.tar.gz"))
+// .toFile();
+// checksumFunction = (x) -> 0L;
+// packager = new TarDataSetPackager(archiveFile, null, null, DEFAULT_BUFFER_SIZE,
+// 5L * DEFAULT_BUFFER_SIZE);
+// } else
+// {
+// throw new UserFailureException("Unknown archive format!");
+// }
+//
+// } catch (IOException exception)
+// {
+// throw new UserFailureException("Could not export data!", exception);
+// }
+
+
+ }
+
+ ArchiveBuilder newArchive() {
+ archive = new ArchiveBuilder();
+ return archive;
+ }
+
+ ArchiveBuilder addToArchive() {
+ if(archive == null) {
+ newArchive();
+ }
+
+
+// File archiveFile;
+// String token = "export_" + currentTimeMs;
+//
+// ISessionWorkspaceProvider sessionWorkspaceProvider =
+// getSessionWorkspaceProvider(sessionToken);
+// File tempDirectory = sessionWorkspaceProvider.getSessionWorkspace();
+
+ return new ArchiveBuilder("");
+ }
+
+
+ private ISessionWorkspaceProvider getSessionWorkspaceProvider(String sessionToken)
+ {
+ return ServiceProvider.getDataStoreService().getSessionWorkspaceProvider(sessionToken);
+ }
+
+
+ class ArchiveBuilder {
+
+ private AbstractDataSetPackager packager;
+
+ private ArchiveBuilder(String exportArchiveName) {
+ if(exportArchiveName.equalsIgnoreCase("export.zip")) {
+
+ } else if(exportArchiveName.equalsIgnoreCase("export.tar.gz")) {
+
+ }
+ }
+
+ public String build() {
+ return "URL";
+ }
+
+ }
+
+
+}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
index 0beb0960aee4891de964cd7913f3adde04aabff7..9290ddaf4751b14659eacabfd44153fa059f9e06 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
@@ -23,8 +23,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetc
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetConfig;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetImage;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetPreview;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetPropertyConfig;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.CustomDSSServiceExecutionOptions;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.id.ICustomDSSServiceId;
@@ -36,24 +36,28 @@ import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container.ImagingP
import ch.ethz.sis.openbis.generic.dssapi.v3.plugin.service.ICustomDSSServiceExecutor;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.properties.PropertyUtils;
import ch.systemsx.cisd.common.reflection.ClassUtils;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
+import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDataSetPackager;
+import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreServer;
+import ch.systemsx.cisd.openbis.dss.generic.server.TarDataSetPackager;
+import ch.systemsx.cisd.openbis.dss.generic.server.ZipDataSetPackager;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.ISessionWorkspaceProvider;
import ch.systemsx.cisd.openbis.generic.shared.dto.OpenBISSessionHolder;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
import ch.systemsx.cisd.common.logging.LogFactory;
+import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.Serializable;
+import java.io.*;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
import java.util.*;
+import java.util.function.Function;
public class ImagingService implements ICustomDSSServiceExecutor
{
@@ -65,6 +69,9 @@ public class ImagingService implements ICustomDSSServiceExecutor
private static final Logger
operationLog = LogFactory.getLogger(LogCategory.OPERATION, ImagingService.class);
+ private static final int DEFAULT_BUFFER_SIZE = (int) (10 * FileUtils.ONE_MB);
+
+ private static final String IMAGING_CONFIG_PROPERTY_NAME = "$IMAGING_DATA_CONFIG";
public ImagingService(Properties properties)
{
@@ -82,9 +89,15 @@ public class ImagingService implements ICustomDSSServiceExecutor
if (data.getType().equalsIgnoreCase("preview"))
{
return processPreviewFlow(sessionToken, (ImagingPreviewContainer) data);
+ } else if (data.getType().equalsIgnoreCase("export"))
+ {
+ return processExportFlow(sessionToken, (ImagingExportContainer) data);
+ } else if (data.getType().equalsIgnoreCase("multi-export"))
+ {
+ return processMultiExportFlow(sessionToken, (ImagingMultiExportContainer) data);
} else
{
- return processExportFlow(sessionToken, data);
+ throw new UserFailureException("Unknown request type!");
}
} catch (Exception e)
{
@@ -93,61 +106,184 @@ public class ImagingService implements ICustomDSSServiceExecutor
return data;
}
- private ImagingPreviewContainer processPreviewFlow(String sessionToken,
- ImagingPreviewContainer data)
+ private IImagingDataSetAdaptor getAdaptor(ImagingDataSetPropertyConfig config)
{
- DataSet dataSet = getDataSet(sessionToken, data);
-
- ImagingDataSetPropertyConfig config =
- readConfig(dataSet.getJsonProperty("$IMAGING_DATA_CONFIG"), ImagingDataSetPropertyConfig.class);
final String adaptorName = config.getConfig().getAdaptor();
- if(adaptorName == null || adaptorName.isBlank()) {
+ if (adaptorName == null || adaptorName.isBlank())
+ {
throw new UserFailureException("Adaptor name is missing from the config!");
}
-
- IImagingDataSetAdaptor adaptor = null;
try
{
- adaptor = ClassUtils.create(IImagingDataSetAdaptor.class, adaptorName, properties);
- } catch(Exception e) {
+ return ClassUtils.create(IImagingDataSetAdaptor.class, adaptorName, properties);
+ } catch (Exception e)
+ {
throw new UserFailureException("Could not load adapter: " + adaptorName, e);
}
+ }
+
+ private File getRootFile(String sessionToken, DataSet dataSet)
+ {
IHierarchicalContent content =
getHierarchicalContentProvider(sessionToken).asContent(
dataSet.getPermId().getPermId());
IHierarchicalContentNode root = content.getRootNode();
+ return root.getFile();
+ }
+
+ private ImagingPreviewContainer processPreviewFlow(String sessionToken,
+ ImagingPreviewContainer data)
+ {
+ DataSet dataSet = getDataSet(sessionToken, data.getPermId());
+
+ ImagingDataSetPropertyConfig config =
+ Util.readConfig(dataSet.getJsonProperty("$IMAGING_DATA_CONFIG"),
+ ImagingDataSetPropertyConfig.class);
- File rootFile = root.getFile();
+ IImagingDataSetAdaptor adaptor = getAdaptor(config);
+ File rootFile = getRootFile(sessionToken, dataSet);
Map<String, Serializable> previewParams = data.getPreview().getConfig();
Map<String, String> meta = data.getPreview().getMetaData();
String format = data.getPreview().getFormat();
- ImagingServiceContext context = new ImagingServiceContext(sessionToken, getApplicationServerApi(), getDataStoreServerApi());
+ int index = data.getIndex();
+ if (config.getImages().size() <= index)
+ {
+ throw new UserFailureException("There is no image with index:" + index);
+ }
+ Map<String, Serializable> imageConfig = config.getImages().get(index).getConfig();
+
+ if (format == null || format.isBlank())
+ {
+ throw new UserFailureException("Format can not be empty!");
+ }
+
+ previewParams.put("$COMMAND_TYPE", "PREVIEW");
+
+ ImagingServiceContext context =
+ new ImagingServiceContext(sessionToken, getApplicationServerApi(),
+ getDataStoreServerApi());
data.getPreview().setBytes(
adaptor.process(context,
- rootFile, previewParams, meta, format).toString());
+ rootFile, imageConfig, previewParams, meta, format).toString());
return data;
}
- private Serializable processExportFlow(String sessionToken, ImagingDataContainer data)
+
+
+ private Serializable processExportFlow(String sessionToken, ImagingExportContainer data)
{
- DataSet dataSet = getDataSet(sessionToken, data);
- if (data.getType().equalsIgnoreCase("export"))
+ // Get all parameters
+ final DataSet dataSet = getDataSet(sessionToken, data.getPermId());
+ final ImagingDataSetPropertyConfig config =
+ Util.readConfig(dataSet.getJsonProperty(IMAGING_CONFIG_PROPERTY_NAME),
+ ImagingDataSetPropertyConfig.class);
+
+ final File rootFile = getRootFile(sessionToken, dataSet);
+ final int index = data.getIndex();
+ if (config.getImages().size() <= index)
{
- // Single export case
- ImagingExportContainer export = (ImagingExportContainer) data;
+ throw new UserFailureException("There is no image with index:" + index);
+ }
+
+ final ImagingDataSetImage image = config.getImages().get(index);
+
+ Map<String, Serializable> exportConfig = data.getExport().getConfig();
+ Validator.validateExportConfig(exportConfig);
+ String archiveFormat = exportConfig.get("archive-format").toString();
+ Map<String, String> meta = data.getExport().getMetaData();
+ Serializable[] exportTypes = (Serializable[]) exportConfig.get("include");
+ String currentTimeMs = String.valueOf(System.currentTimeMillis());
+ AbstractDataSetPackager packager;
+ Function<InputStream, Long> checksumFunction;
+ File archiveFile;
+ String token = "export_" + currentTimeMs;
+ ISessionWorkspaceProvider sessionWorkspaceProvider = getSessionWorkspaceProvider(sessionToken);
+ File tempDirectory = sessionWorkspaceProvider.getSessionWorkspace();
+ String url = DataStoreServer.getConfigParameters().getDownloadURL() + "/datastore_server/session_workspace_file_download?sessionID=" + sessionToken + "&filePath=";
- } else
+ // Prepare temp directory for archive
+ try
{
- // multi export case
- ImagingMultiExportContainer multiExport = (ImagingMultiExportContainer) data;
+ Path tempDir = Files.createDirectory(Path.of(tempDirectory.getAbsolutePath(), token));
+ if (archiveFormat.equalsIgnoreCase("zip"))
+ {
+ archiveFile = Files.createFile(Path.of(tempDir.toAbsolutePath().toString(), "export.zip")).toFile();
+ checksumFunction = Util::getCRC32Checksum;
+ packager = new ZipDataSetPackager(archiveFile, true, null, null);
+ } else if (archiveFormat.equalsIgnoreCase("tar"))
+ {
+ archiveFile =
+ Files.createFile(Path.of(tempDir.toAbsolutePath().toString(), "export.tar.gz")).toFile();
+ checksumFunction = (x) -> 0L;
+ packager = new TarDataSetPackager(archiveFile, null, null, DEFAULT_BUFFER_SIZE,
+ 5L * DEFAULT_BUFFER_SIZE);
+ } else
+ {
+ throw new UserFailureException("Unknown archive format!");
+ }
+
+ } catch (IOException exception)
+ {
+ throw new UserFailureException("Could not export data!", exception);
+ }
+
+ // For each export type, perform adequate action
+ for (Serializable exportType : exportTypes)
+ {
+ if (exportType.toString().equalsIgnoreCase("image"))
+ {
+ ImagingServiceContext context =
+ new ImagingServiceContext(sessionToken, getApplicationServerApi(),
+ getDataStoreServerApi());
+ IImagingDataSetAdaptor adaptor = getAdaptor(config);
+ archiveImage(context, adaptor, image, exportConfig, packager, rootFile, "", checksumFunction, dataSet);
+ } else if (exportType.toString().equalsIgnoreCase("raw data"))
+ {
+ archiveRawData(packager, rootFile, "", checksumFunction, dataSet);
+ } else
+ {
+ throw new UserFailureException("Unknown export type!");
+ }
+
}
+
+ packager.close();
+ data.setUrl(url + Path.of(token, archiveFile.getName()));
+
return data;
}
+ private Serializable processMultiExportFlow(String sessionToken, ImagingMultiExportContainer data)
+ {
+
+ {
+ // multi export case
+// String archiveFormat;
+// for (ImagingDataSetExport export : data.getExport())
+// {
+// Map<String, Serializable> params = export.getConfig();
+// Map<String, String> meta = export.getMetaData();
+// String fullFormat = export.getFormat();
+//
+// if (fullFormat == null || fullFormat.isBlank())
+// {
+// throw new UserFailureException("Format can not be empty!");
+// }
+// String[] formats = fullFormat.split("/");
+// archiveFormat = formats[0];
+// String otherFormat = formats[1];
+//
+// }
+
+ }
+ return null;
+ }
+
+
private IHierarchicalContentProvider getHierarchicalContentProvider(String sessionToken)
{
if (contentProvider == null)
@@ -169,39 +305,12 @@ public class ImagingService implements ICustomDSSServiceExecutor
return ServiceProvider.getV3DataStoreService();
}
- private ObjectMapper getObjectMapper()
- {
- return ServiceProvider.getObjectMapperV3();
- }
-
- private <T> T readConfig(String val, Class<T> clazz)
- {
- try
- {
- ObjectMapper objectMapper = getObjectMapper();
- return objectMapper.readValue(new ByteArrayInputStream(val.getBytes()),
- clazz);
- } catch (JsonMappingException mappingException) {
- throw new UserFailureException(mappingException.toString(), mappingException);
- } catch (Exception e)
- {
- throw new UserFailureException("Could not read the parameters!", e);
- }
- }
-
- private String mapToJson(Map<String, Object> map)
+ private ISessionWorkspaceProvider getSessionWorkspaceProvider(String sessionToken)
{
- try
- {
- ObjectMapper objectMapper = getObjectMapper();
- return objectMapper.writeValueAsString(map);
- } catch (Exception e)
- {
- throw new UserFailureException("Could not serialize the input parameters!", e);
- }
+ return ServiceProvider.getDataStoreService().getSessionWorkspaceProvider(sessionToken);
}
- private DataSet getDataSet(String sessionToken, ImagingDataContainer data)
+ private DataSet getDataSet(String sessionToken, String permId)
{
DataSetFetchOptions fetchOptions = new DataSetFetchOptions();
fetchOptions.withProperties();
@@ -209,49 +318,78 @@ public class ImagingService implements ICustomDSSServiceExecutor
fetchOptions.withDataStore();
fetchOptions.withPhysicalData();
Map<IDataSetId, DataSet> result = getApplicationServerApi()
- .getDataSets(sessionToken, List.of(new DataSetPermId(data.getPermId())),
+ .getDataSets(sessionToken, List.of(new DataSetPermId(permId)),
fetchOptions);
if (result.isEmpty())
{
- throw new UserFailureException("Could not find Dataset:" + data.getPermId());
+ throw new UserFailureException("Could not find Dataset:" + permId);
}
- return result.get(new DataSetPermId(data.getPermId()));
+ return result.get(new DataSetPermId(permId));
}
- private void validateInputParams(Map<String, Object> params)
- {
- if (!params.containsKey("permId"))
- {
- throw new UserFailureException("Missing dataset permId!");
- }
- if (!params.containsKey("type"))
- {
- throw new UserFailureException("Missing type!");
- }
- if (!params.containsKey("index"))
- {
- throw new UserFailureException("Missing index!");
- }
- }
+
private ImagingDataContainer getDataFromParams(Map<String, Object> params)
{
- validateInputParams(params);
+ Validator.validateInputParams(params);
String type = (String) params.get("type");
- String json = mapToJson(params);
+ String json = Util.mapToJson(params);
switch (type.toLowerCase())
{
case "preview":
- return readConfig(json, ImagingPreviewContainer.class);
+ return Util.readConfig(json, ImagingPreviewContainer.class);
case "export":
- return readConfig(json, ImagingExportContainer.class);
+ return Util.readConfig(json, ImagingExportContainer.class);
case "multi-export":
- return readConfig(json, ImagingMultiExportContainer.class);
+ return Util.readConfig(json, ImagingMultiExportContainer.class);
default:
throw new UserFailureException("Wrong type:" + type);
}
}
+ private void archiveRawData(AbstractDataSetPackager packager, File rootFile, String rootFolderName,
+ Function<InputStream, Long> checksumFunction, DataSet dataSet)
+ {
+ //Add dataset files to archive
+ Util.archiveFiles(packager, rootFile, rootFolderName, checksumFunction);
+ //Add dataset properties to archive
+ Map<String, Serializable> properties = dataSet.getProperties();
+ properties.remove(IMAGING_CONFIG_PROPERTY_NAME);
+ byte[] json = Util.mapToJson(properties).getBytes(StandardCharsets.UTF_8);
+ packager.addEntry("properties.txt",
+ dataSet.getModificationDate().toInstant().toEpochMilli(),
+ json.length,
+ checksumFunction.apply(new ByteArrayInputStream(json)),
+ new ByteArrayInputStream(json));
+ }
+
+
+ private void archiveImage(ImagingServiceContext context, IImagingDataSetAdaptor adaptor,
+ ImagingDataSetImage image, Map<String, Serializable> exportConfig,
+ AbstractDataSetPackager packager, File rootFile, String rootFolderName,
+ Function<InputStream, Long> checksumFunction, DataSet dataSet) {
+
+ String imageFormat = exportConfig.get("image-format").toString();
+ int previewIdx = 0;
+ for(ImagingDataSetPreview preview : image.getPreviews())
+ {
+ Map<String, Serializable> params = preview.getConfig();
+ params.put("resolution", exportConfig.get("resolution"));
+ Serializable img = adaptor.process(context,
+ rootFile, image.getConfig(), params, image.getMetaData(), imageFormat);
+ String imgString = img.toString();
+ byte[] decoded = Base64.getDecoder().decode(imgString);
+ long size = decoded.length;
+ String name = "image" + previewIdx + "." + imageFormat;
+ packager.addEntry(Paths.get(rootFolderName, name).toString(),
+ dataSet.getModificationDate().toInstant().toEpochMilli(),
+ size,
+ checksumFunction.apply(new ByteArrayInputStream(decoded)),
+ new ByteArrayInputStream(decoded));
+ previewIdx++;
+ }
+ }
+
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Util.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Util.java
new file mode 100644
index 0000000000000000000000000000000000000000..f39f10af48cc54037c6bf6f1d10b37d4db0a1283
--- /dev/null
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Util.java
@@ -0,0 +1,137 @@
+/*
+ * Copyright ETH 2023 Zürich, Scientific IT Services
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDataSetPackager;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import java.io.*;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Paths;
+import java.util.AbstractMap;
+import java.util.Deque;
+import java.util.LinkedList;
+import java.util.Map;
+import java.util.function.Function;
+import java.util.zip.CRC32;
+
+class Util
+{
+ private Util() {}
+
+ private static ObjectMapper getObjectMapper()
+ {
+ return ServiceProvider.getObjectMapperV3();
+ }
+
+ static long getCRC32Checksum(InputStream input)
+ {
+ if (input == null)
+ throw new UserFailureException("Can not compute crc32!");
+ CRC32 crc = new CRC32();
+ byte[] buffer = new byte[4096];
+ try
+ {
+ while (true)
+ {
+ int length = input.read(buffer);
+ if (length == -1)
+ break;
+ crc.update(buffer, 0, length);
+ }
+ } catch (Exception ex)
+ {
+ try
+ {
+ input.close();
+ } catch (Exception ignored)
+ {
+ }
+ }
+ return crc.getValue();
+ }
+
+ static <T> T readConfig(String val, Class<T> clazz)
+ {
+ try
+ {
+ ObjectMapper objectMapper = getObjectMapper();
+ return objectMapper.readValue(new ByteArrayInputStream(val.getBytes()),
+ clazz);
+ } catch (JsonMappingException mappingException)
+ {
+ throw new UserFailureException(mappingException.toString(), mappingException);
+ } catch (Exception e)
+ {
+ throw new UserFailureException("Could not read the parameters!", e);
+ }
+ }
+
+ static String mapToJson(Map<String, ?> map)
+ {
+ try
+ {
+ ObjectMapper objectMapper = getObjectMapper();
+ return objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
+ } catch (Exception e)
+ {
+ throw new UserFailureException("Could not serialize the input parameters!", e);
+ }
+ }
+
+
+
+ static void archiveFiles(AbstractDataSetPackager packager, File rootFile, String rootFolderName,
+ Function<InputStream, Long> checksumFunction)
+ {
+ Deque<Map.Entry<String, File>> queue = new LinkedList<>();
+
+ queue.add(new AbstractMap.SimpleImmutableEntry<>(rootFolderName, rootFile));
+ while (!queue.isEmpty())
+ {
+ Map.Entry<String, File> element = queue.pollFirst();
+ String prefixPath = element.getKey();
+ File file = element.getValue();
+ String path = Paths.get(prefixPath, file.getName()).toString();
+ if (file.isDirectory())
+ {
+ for (File f : file.listFiles())
+ {
+ queue.add(new AbstractMap.SimpleImmutableEntry<>(path, f));
+ }
+ packager.addDirectoryEntry(path);
+ } else
+ {
+ try
+ {
+ FileInputStream fileStream = new FileInputStream(file);
+ packager.addEntry(path, file.lastModified(), file.getTotalSpace(),
+ checksumFunction.apply(fileStream), new FileInputStream(file));
+ } catch (IOException exc)
+ {
+ throw new UserFailureException("Failed during export!", exc);
+ }
+ }
+ }
+
+ }
+
+}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Validator.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Validator.java
new file mode 100644
index 0000000000000000000000000000000000000000..6c94cbe70aaa751d1a8134537995171d5bd21ffc
--- /dev/null
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/Validator.java
@@ -0,0 +1,85 @@
+/*
+ * Copyright ETH 2023 Zürich, Scientific IT Services
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+import java.io.Serializable;
+import java.util.Map;
+
+class Validator
+{
+ private Validator() {}
+
+
+ static void validateInputParams(Map<String, Object> params)
+ {
+ if (!params.containsKey("permId"))
+ {
+ throw new UserFailureException("Missing dataset permId!");
+ }
+ if (!params.containsKey("type"))
+ {
+ throw new UserFailureException("Missing type!");
+ }
+ if (!params.containsKey("index"))
+ {
+ throw new UserFailureException("Missing index!");
+ }
+ }
+
+
+ static void validateExportConfig(Map<String, Serializable> exportConfig) {
+ if(exportConfig == null) {
+ throw new UserFailureException("Export config can not be empty!");
+ }
+ validateTag(exportConfig, "include", true);
+ validateTag(exportConfig, "image-format");
+ validateTag(exportConfig, "archive-format");
+ validateTag(exportConfig, "resolution");
+ }
+
+ private static void validateTag(Map<String, Serializable> config, String tagName)
+ {
+ validateTag(config, tagName, false);
+ }
+
+ private static void validateTag(Map<String, Serializable> config, String tagName, boolean isMultiValue)
+ {
+ if(!config.containsKey(tagName)){
+ throw new UserFailureException("Missing '"+tagName+"' in export config!");
+ }
+ Serializable include = config.get(tagName);
+ if(include == null){
+ throw new UserFailureException("'"+tagName+"' tag in export config can not be null!");
+ }
+ if(isMultiValue)
+ {
+ if (!include.getClass().isArray())
+ {
+ throw new UserFailureException("'include' tag in export config must be an array!");
+ }
+ if (((Serializable[]) include).length == 0)
+ {
+ throw new UserFailureException("'include' tag in export config can not be empty!");
+ }
+ }
+ }
+
+
+}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java
index ea3b5ad6e14376c8023db65c17afb38b25bd6ce7..5aaefdeaa94e59057dd0156504dc6242b5349281 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java
@@ -25,7 +25,7 @@ import java.util.Map;
public interface IImagingDataSetAdaptor
{
- Serializable process(ImagingServiceContext context, File rootFile,
+ Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
Map<String, Serializable> previewConfig, Map<String, String> metaData, String format);
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
index e553d1382d09354f6f82fbe4fd8b8341a7b2403d..536f083757128825e389b0966cf809fcc6c77305 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
@@ -38,7 +38,7 @@ public final class ImagingDataSetExampleAdaptor implements IImagingDataSetAdapto
}
@Override
- public Serializable process(ImagingServiceContext context, File rootFile,
+ public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
{
BufferedImage img = new BufferedImage(WIDTH, HEIGHT, BufferedImage.TYPE_INT_ARGB);
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
index 51e5043ba32212f9b7e15a49cf35758776af7552..1a53bcd5c649ef0262d5cb142e1321b7556f82ef 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
@@ -40,7 +40,7 @@ public class ImagingDataSetJythonAdaptor implements IImagingDataSetAdaptor
}
}
@Override
- public Serializable process(ImagingServiceContext context, File rootFile,
+ public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
{
CustomDSSServiceExecutionOptions options = new CustomDSSServiceExecutionOptions();
@@ -48,6 +48,7 @@ public class ImagingDataSetJythonAdaptor implements IImagingDataSetAdaptor
options.withParameter("asApi", context.getAsApi());
options.withParameter("dssApi", context.getDssApi());
options.withParameter("file", rootFile);
+ options.withParameter("imageConfig", imageConfig);
options.withParameter("config", previewConfig);
options.withParameter("metaData", metaData);
IDssServiceScriptRunner
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
index 8c720261064f4fb676f5b798e79e0b274e026fa8..b616666b257ee6a3cae28f082b33c1f052cf1be6 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
@@ -26,55 +26,67 @@ import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
+import java.util.HashMap;
import java.util.Map;
public abstract class ImagingDataSetPythonAdaptor implements IImagingDataSetAdaptor
{
-
protected String pythonPath;
protected String scriptPath;
@Override
- public Serializable process(ImagingServiceContext context, File rootFile,
+ public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
{
ProcessBuilder processBuilder = new ProcessBuilder(pythonPath,
- scriptPath, rootFile.getAbsolutePath(), convertMapToJson(previewConfig), convertMapToJson(metaData), format);
+ scriptPath, rootFile.getAbsolutePath(), convertMapToJson(imageConfig),
+ convertMapToJson(previewConfig), convertMapToJson(metaData), format);
processBuilder.redirectErrorStream(false);
String fullOutput;
- try {
+ try
+ {
Process process = processBuilder.start();
- fullOutput = new String(process.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
+ fullOutput =
+ new String(process.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
int exitCode = process.waitFor();
- if(exitCode != 0) {
- String error = new String(process.getErrorStream().readAllBytes(), StandardCharsets.UTF_8);
+ if (exitCode != 0)
+ {
+ String error =
+ new String(process.getErrorStream().readAllBytes(), StandardCharsets.UTF_8);
throw new UserFailureException("Script evaluation failed: " + error);
}
- } catch (IOException | InterruptedException e) {
+ } catch (IOException | InterruptedException e)
+ {
throw new RuntimeException(e);
}
- if(fullOutput.isBlank()) {
+ if (fullOutput.isBlank())
+ {
throw new UserFailureException("Script produced no results!");
}
String[] resultSplit = fullOutput.split("\n");
- return resultSplit[resultSplit.length-1];
+ return resultSplit[resultSplit.length - 1];
}
- private String convertMapToJson(Map<String,?> map) {
- try {
+ private String convertMapToJson(Map<String, ?> map)
+ {
+ Map<String, ?> mapToConvert = map;
+ if(map == null) {
+ mapToConvert = new HashMap<>();
+ }
+ try
+ {
ObjectMapper objectMapper = new GenericObjectMapper();
- return objectMapper.writeValueAsString(map);
- }catch (Exception e) {
+ return objectMapper.writeValueAsString(mapToConvert);
+ } catch (Exception e)
+ {
throw new UserFailureException("Couldn't convert map to string", e);
}
}
-
-
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisSxmAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisSxmAdaptor.java
index a45e9c496b28c8827fe8b65b3317f6c31d0079a6..4f7601ec881634e0f4cb15aea41424c6d4f6e023 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisSxmAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/NanonisSxmAdaptor.java
@@ -37,7 +37,6 @@ public final class NanonisSxmAdaptor extends ImagingDataSetPythonAdaptor
{
private final String SXM_SCRIPT_PROPERTY = "nanonis-sxm";
-
public NanonisSxmAdaptor(Properties properties)
{
@@ -56,4 +55,24 @@ public final class NanonisSxmAdaptor extends ImagingDataSetPythonAdaptor
this.pythonPath = properties.getProperty("python3-path", "python3");
}
+ @Override
+ public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> imageConfig,
+ Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
+ {
+ Serializable result = super.process(context, rootFile, imageConfig, previewConfig, metaData, format);
+ if (result == null)
+ {
+ return result;
+ }
+ String str = result.toString();
+ if (str.length() > 3)
+ {
+ return str.substring(2, str.length() - 1);
+ } else
+ {
+ return "";
+ }
+
+ }
+
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingDataContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingDataContainer.java
index 3c1252484f38778b256b98e43ad5c70cbd442e1f..7c07d1c0b91e069e1ef724080a415d42e9d85731 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingDataContainer.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingDataContainer.java
@@ -28,12 +28,9 @@ public abstract class ImagingDataContainer implements Serializable
@JsonProperty
private String type;
- @JsonProperty
- private String permId;
+
@JsonProperty
private String error;
- @JsonProperty
- private int index;
@JsonIgnore
public String getType()
@@ -45,16 +42,6 @@ public abstract class ImagingDataContainer implements Serializable
this.type = type;
}
- @JsonIgnore
- public String getPermId()
- {
- return permId;
- }
-
- public void setPermId(String permId) {
- this.permId = permId;
- }
-
@JsonIgnore
public String getError()
{
@@ -66,14 +53,6 @@ public abstract class ImagingDataContainer implements Serializable
this.error = error;
}
- @JsonIgnore
- public int getIndex()
- {
- return index;
- }
- public void setIndex(int index) {
- this.index = index;
- }
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingExportContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingExportContainer.java
index 9041716ddb4ef00770b5993bad01033ac0bc36d4..c1e5fed445dd53bd0180b554737cffabddf1e5eb 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingExportContainer.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingExportContainer.java
@@ -24,9 +24,46 @@ import com.fasterxml.jackson.annotation.JsonProperty;
public final class ImagingExportContainer extends ImagingDataContainer
{
+ @JsonProperty
+ private String permId;
+ @JsonProperty
+ private int index;
+ @JsonProperty
+ private String url;
@JsonProperty
private ImagingDataSetExport export = null;
+ @JsonIgnore
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId) {
+ this.permId = permId;
+ }
+
+ @JsonIgnore
+ public int getIndex()
+ {
+ return index;
+ }
+
+ public void setIndex(int index) {
+ this.index = index;
+ }
+
+ @JsonIgnore
+ public String getUrl()
+ {
+ return url;
+ }
+
+ public void setUrl(String url)
+ {
+ this.url = url;
+ }
+
@JsonIgnore
public ImagingDataSetExport getExport()
{
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingMultiExportContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingMultiExportContainer.java
index c5a342c9b25edbd5829fb70e0ead728bc5441834..183cb54dfd5fb69afa6cd336000f53d1713dc9e7 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingMultiExportContainer.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingMultiExportContainer.java
@@ -17,7 +17,7 @@
package ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.container;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetExport;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetMultiExport;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
@@ -27,16 +27,30 @@ public class ImagingMultiExportContainer extends ImagingDataContainer
{
@JsonProperty
- private List<ImagingDataSetExport> export = null;
+ private String url;
+
+ @JsonProperty
+ private List<ImagingDataSetMultiExport> exports = null;
+
+ @JsonIgnore
+ public String getUrl()
+ {
+ return url;
+ }
+
+ public void setUrl(String url)
+ {
+ this.url = url;
+ }
@JsonIgnore
- public List<ImagingDataSetExport> getExport()
+ public List<ImagingDataSetMultiExport> getExports()
{
- return export;
+ return exports;
}
- public void setExport(List<ImagingDataSetExport> export)
+ public void setExports(List<ImagingDataSetMultiExport> exports)
{
- this.export = export;
+ this.exports = exports;
}
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingPreviewContainer.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingPreviewContainer.java
index 18c75f0c78b02b913f88a91598e8c0667ca441ad..d5d5e23973d6b1a1c328a3a11c96cef27e0687bc 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingPreviewContainer.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/container/ImagingPreviewContainer.java
@@ -24,9 +24,33 @@ import com.fasterxml.jackson.annotation.JsonProperty;
public final class ImagingPreviewContainer extends ImagingDataContainer
{
+ @JsonProperty
+ private String permId;
+ @JsonProperty
+ private int index;
@JsonProperty
private ImagingDataSetPreview preview = null;
+ @JsonIgnore
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId) {
+ this.permId = permId;
+ }
+
+ @JsonIgnore
+ public int getIndex()
+ {
+ return index;
+ }
+
+ public void setIndex(int index) {
+ this.index = index;
+ }
+
@JsonIgnore
public ImagingDataSetPreview getPreview()
{
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
index b8b414bebe5c3972a4f7e5858ad35ccffeb5f75c..6b1c598587aa6ba994e31233e719ccbe49052e67 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
@@ -31,9 +31,10 @@ def get_channel(img, channel_name = 'z'):
file = sys.argv[1]
-params = json.loads(sys.argv[2])
-meta_data = json.loads(sys.argv[3])
-format = sys.argv[4]
+image_params = json.loads(sys.argv[2])
+params = json.loads(sys.argv[3])
+meta_data = json.loads(sys.argv[4])
+format = sys.argv[5]
folder_dir = os.path.join(file, 'original')
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
index 08d5711aab6dd3f9f192a76fd92a5d772c0fbe00..476d27f5a0a1b8e2499b30121a5bbd2aaf7ecc5f 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
@@ -36,14 +36,14 @@ def get_channel(img, channel_name = 'z'):
print("SYS.ARGV:" + str(sys.argv))
file = sys.argv[1]
-params = json.loads(sys.argv[2])
-meta_data = json.loads(sys.argv[3])
-format = sys.argv[4]
+image_params = json.loads(sys.argv[2])
+params = json.loads(sys.argv[3])
+meta_data = json.loads(sys.argv[4])
+format = sys.argv[5]
folder_dir = os.path.join(file, 'original')
file_path = os.path.join(folder_dir, os.listdir(folder_dir)[0])
-# print(file_path)
def generate_random_image(height, width):
@@ -56,90 +56,7 @@ def generate_random_image(height, width):
return encoded
-def get_sxm_image():
- img = load_image(file_path)
- channel = get_channel(img, 'z')
- img_byte_arr = io.BytesIO()
-
- # im = plt.imshow(channel[0])
- # plt.savefig(img_byte_arr, format="png")
- fig = img.plot(show=False, show_params=False)
- fig.frameon=False
- # plt.title(None)
- # plt.axis('off')
- plt.savefig(img_byte_arr, format=format)
-
- # print(img.header)
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
- print_params = img.print_params(show=False).split('\n')
- print_params = {x: y for x, y in (s.split(':') for s in print_params)}
- print_params = json.dumps(print_params)
- print(f'PARAMS={print_params}')
- header = json.dumps(img.header, cls=NumpyEncoder)
- print(f'HEADER={header}')
-
- return encoded
-
-
-def get_sxm_image2():
- img_orig = load_image(file_path)
- channel = get_channel(img_orig, 'z')[0]
-
- min_val = numpy.min(channel)
- max_val = numpy.max(channel)
- scaled_data = (channel - min_val) / (max_val - min_val)
- img = Image.fromarray(numpy.uint8(scaled_data * 255), 'L')
-
- img_byte_arr = io.BytesIO()
- img.save(img_byte_arr, format=format)
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
-
- print_params = img_orig.print_params(show=False).split('\n')
- print_params = {x: y for x, y in (s.split(':') for s in print_params)}
- print_params = json.dumps(print_params)
- print(f'PARAMS={print_params}')
- header = json.dumps(img_orig.header, cls=NumpyEncoder)
- print(f'HEADER={header}')
-
- return encoded
-
-
-def get_sxm_image3(channel_name, scaling, color_scale):
- img = load_image(file_path)
- # channel = get_channel(img, channel_name)
- img_byte_arr = io.BytesIO()
-
- log = False
- if scaling == 'logarithmic':
- log = True
- fig = img.plot(show=False, show_params=False, hide=True, channel=channel_name, log=log)
- fig.frameon=False
- # plt.title('None')
- plt.axis('off')
- plt.savefig(img_byte_arr, format="png", bbox_inches='tight')
-
- pilImg = Image.open(img_byte_arr)
- print(f"SIZE={pilImg.size}")
- im2 = pilImg.crop(pilImg.getbbox())
- print(f"SIZE={im2.size}")
- img_byte_arr = io.BytesIO()
- im2.save(img_byte_arr, format='PNG')
-
- # print(img.header)
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
- print_params = img.print_params(show=False).split('\n')
- print_params = {x: y for x, y in (s.split(':') for s in print_params)}
- print_params = json.dumps(print_params)
- print(f'PARAMS={print_params}')
- header = json.dumps(img.header, cls=NumpyEncoder)
- print(f'HEADER={header}')
-
- return encoded
-
-def get_sxm_image4(channel_name, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling):
+def get_sxm_image(channel_name, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling):
img = load_image(file_path)
img_byte_arr = io.BytesIO()
@@ -161,41 +78,23 @@ def get_sxm_image4(channel_name, x_axis, y_axis, scaling, color_scale, colormap,
return encoded
+def sxm_mode(parameters):
+ channel = parameters['channel']
+ x_axis = [float(x) for x in parameters['x-axis']]
+ y_axis = [float(x) for x in parameters['y-axis']]
+ color_scale = [float(x) for x in parameters['color-scale']]
+ colormap = parameters['colormap']
+ scaling = parameters['scaling']
+ colormap_scaling = False
+ if "colormap_scaling" in parameters:
+ colormap_scaling = parameters['colormap_scaling'].upper() == "TRUE"
+ print(f'{get_sxm_image(channel, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling)}')
+
print(params)
if 'mode' in params:
- if params['mode'] == '1':
- # print(f'IMG={get_sxm_image()}')
- print(f'{get_sxm_image()}')
- elif params['mode'] == '2':
- # print(f'IMG={get_sxm_image2()}')
- print(f'{get_sxm_image2()}')
- elif params['mode'] == '3':
- # print(f'IMG={generate_random_image(320, 320)}')
+ if params['mode'] == '3':
print(f'{generate_random_image(256, 256)}')
- elif params['mode'] == '4':
- channel = params['channel']
- scaling = params['scaling']
- color_scale = [float(x) for x in params['color-scale']]
- print(f'{get_sxm_image3(channel, scaling, color_scale)}')
elif params['mode'] == '5':
- channel = params['channel']
- x_axis = [float(x) for x in params['x-axis']]
- y_axis = [float(x) for x in params['y-axis']]
- color_scale = [float(x) for x in params['color-scale']]
- colormap = params['colormap']
- scaling = params['scaling']
- colormap_scaling = False
- if "colormap_scaling" in params:
- colormap_scaling = params['colormap_scaling'].upper() == "TRUE"
- print(f'{get_sxm_image4(channel, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling)}')
+ sxm_mode(params)
else:
- channel = params['channel']
- x_axis = [float(x) for x in params['x-axis']]
- y_axis = [float(x) for x in params['y-axis']]
- color_scale = [float(x) for x in params['color-scale']]
- colormap = params['colormap']
- scaling = params['scaling']
- colormap_scaling = False
- if "colormap_scaling" in params:
- colormap_scaling = params['colormap_scaling'].upper() == "TRUE"
- print(f'{get_sxm_image4(channel, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling)}')
\ No newline at end of file
+ sxm_mode(params)
\ No newline at end of file