adapted to merlin plugin

code/manager.py

@@ -162,8 +162,8 @@ def run(files, taxonomyId, dbs, ontologies, isRest):
 
     if inputCheck in validInputs:
         with open("/".join([submission_path, "params.txt"]), "w") as paramsFile:
-            paramsFile.write(taxonomy)  # write TaxonomyID to file
-            paramsFile.write(dbs)  # write databases to file
+            paramsFile.write(taxonomyId + "\n")  # write TaxonomyID to file
+            paramsFile.write(dbs + "\n")  # write databases to file
             paramsFile.write(ontologies)  # write ontologies to file
 
     else:
@@ -332,7 +332,7 @@ def getWorkersLogs(savePath):
 
             if response.status_code == 200:
                 name = re.sub("https*:", "", host)
-                name = name.replace("/", "")
+                name = name.replace("/", "").replace(":", "_")
                 filesavePath = savePath + name + '.zip'
                 zfile = open(filesavePath, 'wb')
                 zfile.write(response.content)

code/templates/home.html

@@ -106,15 +106,15 @@
                 <br>
                 <br>
 
-                <h3>Filter by common ontologies?</h3>
+                <h3>Override common ontologies filter?</h3>
                 <br>
 
                 <div class="form-group">
                     <div class="input-group">
                         <span class="input-group-addon">Ontologies</span>
                             <select name="ontologies" class="selectpicker form-control">
-                                <option value="yes">Yes</option>
-                                <option value="no">No</option>
+                                <option value="false">False</option>
+                                <option value="true">True</option>
                             </select>
                     </div>
                  </div>

code/workersManager.py

@@ -82,7 +82,7 @@ def run():
 
                 files = {
                     'model': open(processingPath + modelFile, 'rb'),
-                    'params': open(processingPath + 'paramsID.txt', 'rb'),
+                    'params': open(processingPath + 'params.txt', 'rb'),
                     'genome': open(processingPath + 'genome.faa', 'rb')}
 
                 logger.info("Sending request to start to " + str(workerID))