analysis: send token as an environment variable, #TASK-6445

opencb · Nov 12, 2024 · 6a17eec · 6a17eec
1 parent fc9d19b
commit 6a17eec
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Showing 3 changed files with 11 additions and 7 deletions.
diff --git a/...cga-analysis/src/main/java/org/opencb/opencga/analysis/customTool/CustomToolExecutor.java b/...cga-analysis/src/main/java/org/opencb/opencga/analysis/customTool/CustomToolExecutor.java
@@ -14,8 +14,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 
 @Tool(id = CustomToolExecutor.ID, resource = Enums.Resource.JOB, description = CustomToolExecutor.DESCRIPTION)
 public class CustomToolExecutor extends OpenCgaDockerToolScopeStudy {
@@ -60,16 +62,19 @@ protected void check() throws Exception {
         tags.add(this.dockerImage);
         updateJobInformation(tags, toolInfoExecutor);
 
-        StringBuilder cliParamsBuilder = new StringBuilder()
-                .append(" --opencga-token ").append(refreshToken());
+        StringBuilder cliParamsBuilder = new StringBuilder();
         processInputParams(runParams.getCommandLine(), cliParamsBuilder);
         this.cliParams = cliParamsBuilder.toString();
     }
 
     @Override
     protected void run() throws Exception {
         StopWatch stopWatch = StopWatch.createStarted();
-        String cmdline = runDocker(dockerImage, cliParams);
+
+        Map<String, String> dockerParams = new HashMap<>();
+        dockerParams.put("-e", "OPENCGA_TOKEN=" + getExpiringToken());
+        String cmdline = runDocker(dockerImage, null, cliParams, dockerParams);
+
         logger.info("Docker command line: " + cmdline);
         logger.info("Execution time: " + TimeUtils.durationToString(stopWatch));
     }

diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaTool.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/tools/OpenCgaTool.java
@@ -474,7 +474,7 @@ public final ObjectMap getParams() {
         return params;
     }
 
-    public final String refreshToken() throws CatalogException {
+    public final String getExpiringToken() throws CatalogException {
         return catalogManager.getUserManager().refreshToken(token).getToken();
     }
 

diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/workflow/NextFlowExecutor.java
@@ -227,16 +227,15 @@ protected void run() throws Exception {
         if (StringUtils.isNotEmpty(cliParams)) {
             stringBuilder.append(" ").append(cliParams);
         }
-        stringBuilder
-                .append(" --opencga-token ").append(refreshToken())
-                .append(" -with-report ").append(outDirPath).append("/report.html\"");
+        stringBuilder.append(" -with-report ").append(outDirPath).append("/report.html\"");
 
         startTraceFileMonitor();
 
         Map<String, String> dockerParams = new HashMap<>();
         // Set HOME environment variable to the temporal input directory. This is because nextflow creates a hidden folder there and,
         // when nextflow runs on other dockers, we need to store those files in a path shared between the parent docker and the host
         dockerParams.put("-e", "HOME=" + temporalInputDir);
+        dockerParams.put("-e", "OPENCGA_TOKEN=" + getExpiringToken());
 
         // Execute docker image
         StopWatch stopWatch = StopWatch.createStarted();