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Optional websummary download #31

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Optional websummary download #31

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20 changes: 14 additions & 6 deletions src/main/java/org/mskcc/cellranger/controller/CellRangerController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -190,17 +190,25 @@ public Map<String, Object> getCellRangerSample(@RequestParam("project") String p
public Map<String, Object> getCellRangerFile( @RequestParam("project") String project,
@RequestParam("run") String run,
@RequestParam("sample") String sample,
@RequestParam("type") String type) {
@RequestParam("type") String type,
@RequestParam(required = false, defaultValue = "true") Boolean download) {
log.info(String.format("Retrieving cell ranger output file for run: %s, project: %s, sample: %s, type: %s",
run, project, sample, type));
final String webSummaryPath = getCellRangerOutputPath(run, sample, project, type, WEB_SUMMARY_PATH);
final String data = readFile(webSummaryPath);
String status = String.format("File not found: %s", webSummaryPath);
if(data != null){
status = String.format("Retrieved data from %s", webSummaryPath);

File f = new File(webSummaryPath);
if(!f.exists() || f.isDirectory()) {
String errMessage = String.format("File not found: %s (run=%s project=%s sample=%s type=%s)",
webSummaryPath, run, project, sample, type);
return createErrorResponse(errMessage, true);
}

String status = String.format("Retrieved data from %s", webSummaryPath);
Map<String, Object> resp = createSuccessResponse(status);
resp.put(API_DATA, data);
if(download){
final String data = readFile(webSummaryPath);
resp.put(API_DATA, data);
}
return resp;
}

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2 changes: 1 addition & 1 deletion src/test/java/org/mskcc/cellranger/controller/CellRangerControllerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ public void getCellRangerFile_success() {
log.error(String.format("Failed to test %s. Error: %s", type, e.getMessage()));
}

Map<String,Object> response = cellRangerController.getCellRangerFile(PROJECT, RUN, SAMPLE, type.toString());
Map<String,Object> response = cellRangerController.getCellRangerFile(PROJECT, RUN, SAMPLE, type.toString(), true);
assertNotNull(response.get("data"));
}
}
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