From 8ebc04cf9413f9ad4065f5a678984f3fcc5dac32 Mon Sep 17 00:00:00 2001
From: Konstantinos <kostas24061992@yahoo.com>
Date: Mon, 9 Dec 2019 09:53:05 +0200
Subject: [PATCH] Get missing arguments in order to run workflow even if those
missing.KK
On branch dev_merge_middleware
Changes to be committed:
modified: src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
---
.../eu/hbp/mip/controllers/GalaxyAPI.java | 23 +++++++++++++++++++
1 file changed, 23 insertions(+)
diff --git a/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java b/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
index b78b60d34..7ae5cccf8 100644
--- a/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
+++ b/src/main/java/eu/hbp/mip/controllers/GalaxyAPI.java
@@ -5,6 +5,7 @@ import com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory;
import com.github.jmchilton.blend4j.galaxy.WorkflowsClient;
import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
import com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails;
+import com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition;
import com.google.gson.Gson;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
@@ -185,6 +186,28 @@ class GalaxyAPI {
logger.info(LogHelper.logUser(userDetails) + "Put to map: " + key + " : " + value);
allJsonParams.put(key,value);
}
+ final GalaxyInstance instance = GalaxyInstanceFactory.get(url, apiKey);
+ final WorkflowsClient workflowsClient = instance.getWorkflowsClient();
+
+ Workflow matchingWorkflow = null;
+ for(Workflow workflow : workflowsClient.getWorkflows()) {
+ if(workflow.getId().equals(id)) {
+ matchingWorkflow = workflow;
+ }
+ }
+ if(matchingWorkflow == null){
+ logger.error(LogHelper.logUser(userDetails) + "Run workflow could not find workflow with id : " + id + " ,in order to get missing input parameters");
+ return ResponseEntity.notFound().build();
+ }
+ final WorkflowDetails workflowDetails = workflowsClient.showWorkflow(matchingWorkflow.getId());
+ for (Map.Entry<String, WorkflowInputDefinition> entry : workflowDetails.getInputs().entrySet()) {
+ if(!(allJsonParams.containsKey(entry.getValue().getUuid()))) {
+ logger.warn("Find extra value with label:" + entry.getValue().getLabel() + "and uuid:" + entry.getValue().getUuid() + ", that is mandatory to run the workflow. The uuid will be automate add it with empty value in the parameters to run the workflow.");
+ allJsonParams.put(entry.getValue().getUuid(), "");
+ }
+ }
+
+ ////
StringBuffer stringBuffer = new StringBuffer("{\n" +
"\t\"inputs\": {\n");
--
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