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M2597 Export to Galaxy in data explorer
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51 changes: 51 additions & 0 deletions
51
...-dataexplorer/src/main/java/org/molgenis/dataexplorer/galaxy/GalaxyDataExportRequest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| package org.molgenis.dataexplorer.galaxy; | ||
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| import javax.validation.constraints.NotNull; | ||
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| import org.hibernate.validator.constraints.Length; | ||
| import org.hibernate.validator.constraints.URL; | ||
| import org.molgenis.dataexplorer.controller.DataRequest; | ||
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| public class GalaxyDataExportRequest | ||
| { | ||
| @NotNull | ||
| @URL | ||
| private String galaxyUrl; | ||
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| @NotNull | ||
| @Length(min = 32, max = 32) | ||
| private String galaxyApiKey; | ||
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| @NotNull | ||
| private DataRequest dataRequest; | ||
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| public String getGalaxyUrl() | ||
| { | ||
| return galaxyUrl; | ||
| } | ||
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| public void setGalaxyUrl(String galaxyUrl) | ||
| { | ||
| this.galaxyUrl = galaxyUrl; | ||
| } | ||
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| public String getGalaxyApiKey() | ||
| { | ||
| return galaxyApiKey; | ||
| } | ||
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| public void setGalaxyApiKey(String galaxyApiKey) | ||
| { | ||
| this.galaxyApiKey = galaxyApiKey; | ||
| } | ||
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| public DataRequest getDataRequest() | ||
| { | ||
| return dataRequest; | ||
| } | ||
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| public void setDataRequest(DataRequest dataRequest) | ||
| { | ||
| this.dataRequest = dataRequest; | ||
| } | ||
| } |
65 changes: 65 additions & 0 deletions
65
...s-omx-dataexplorer/src/main/java/org/molgenis/dataexplorer/galaxy/GalaxyDataExporter.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| package org.molgenis.dataexplorer.galaxy; | ||
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| import java.io.File; | ||
| import java.util.List; | ||
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| import com.github.jmchilton.blend4j.galaxy.GalaxyInstance; | ||
| import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory; | ||
| import com.github.jmchilton.blend4j.galaxy.HistoriesClient; | ||
| import com.github.jmchilton.blend4j.galaxy.ToolsClient; | ||
| import com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest; | ||
| import com.github.jmchilton.blend4j.galaxy.ToolsClient.UploadFile; | ||
| import com.github.jmchilton.blend4j.galaxy.beans.History; | ||
| import com.github.jmchilton.blend4j.galaxy.beans.OutputDataset; | ||
| import com.github.jmchilton.blend4j.galaxy.beans.ToolExecution; | ||
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| public class GalaxyDataExporter | ||
| { | ||
| private static final String MOLGENIS_HISTORY_NAME = "MOLGENIS history"; | ||
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| private final GalaxyInstance galaxyInstance; | ||
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| public GalaxyDataExporter(String galaxyUrl, String galaxyApiKey) | ||
| { | ||
| if (galaxyUrl == null) throw new IllegalArgumentException("galaxyUrl is null"); | ||
| if (galaxyApiKey == null) throw new IllegalArgumentException("galaxyApiKey is null"); | ||
| this.galaxyInstance = GalaxyInstanceFactory.get(galaxyUrl, galaxyApiKey); | ||
| } | ||
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| public void export(String dataSetName, File tsvFile) | ||
| { | ||
| export(dataSetName, tsvFile, MOLGENIS_HISTORY_NAME); | ||
| } | ||
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| public void export(String dataSetName, File tsvFile, String historyName) | ||
| { | ||
| // get/create history | ||
| HistoriesClient historiesClient = galaxyInstance.getHistoriesClient(); | ||
| History molgenisHistory = null; | ||
| for (History history : historiesClient.getHistories()) | ||
| { | ||
| if (history.getName().equals(historyName)) | ||
| { | ||
| molgenisHistory = history; | ||
| break; | ||
| } | ||
| } | ||
| if (molgenisHistory == null) | ||
| { | ||
| molgenisHistory = new History(historyName); | ||
| molgenisHistory = historiesClient.create(molgenisHistory); | ||
| } | ||
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| // upload data set file | ||
| ToolsClient toolsClient = galaxyInstance.getToolsClient(); | ||
| UploadFile uploadFile = new UploadFile(tsvFile, dataSetName); | ||
| FileUploadRequest fileUploadRequest = new FileUploadRequest(molgenisHistory.getId(), uploadFile); | ||
| fileUploadRequest.setFileType("tabular"); | ||
| ToolExecution toolsExecution = toolsClient.upload(fileUploadRequest); | ||
| List<OutputDataset> outputDatasets = toolsExecution.getOutputs(); | ||
| if (outputDatasets == null || outputDatasets.size() != 1) | ||
| { | ||
| throw new RuntimeException("Expected one output data set instead of " + outputDatasets.size()); | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -15,10 +15,6 @@ | |
| display: inline; | ||
| } | ||
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| #download-modal-button { | ||
| float: right; | ||
| } | ||
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| #genomebrowser { | ||
| visibility: hidden | ||
| } | ||
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