fixed stupid name issue report keys not found

phac-nml · Nov 12, 2024 · 6ba57b0 · 6ba57b0
1 parent 70d0291
commit 6ba57b0
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Showing 3 changed files with 9 additions and 13 deletions.
diff --git a/bin/report_summaries.py b/bin/report_summaries.py
@@ -264,11 +264,10 @@ def output_indv_json(self, flattened_data):
         """
         updated_items = dict()
         for k, v in flattened_data.items():
-            #out_path = os.path.join(self.output_dir, k + self.flat_sample_string)
             out_key = k
             sample_dir = k
-            if v.get(self.__inx_irida_key) != k:
-                sample_dir = v[self.__inx_irida_key]
+            if dir_name := v.get(self.__inx_irida_key) != k:
+                sample_dir = dir_name
                 #! this field affects the identification of the irida next id being passed out of the pipeline
                 out_key = sample_dir # this field must be overwritten for iridanext to identify the correct metdata field
 

diff --git a/modules/local/report.nf b/modules/local/report.nf
@@ -41,40 +41,38 @@ process REPORT{
         def report_tag = test_in[i+1]
         def report_value = test_in[i+2]
 
+        println meta_data
         if(!sample_data.containsKey(meta_data.sample)){
             // Todo issue grabbing correct tag is here
             sample_data[meta_data.sample] = [:]
             sample_data[meta_data.sample]["meta"] = [:]
         }
 
         update_map_values(sample_data, meta_data, "metagenomic")
-        //update_map_values(sample_data, meta_data, "sample")
-        //update_map_values(sample_data, meta_data, "external_id")
-        //update_map_values(sample_data, meta_data, "id")
+        update_map_values(sample_data, meta_data, "sample")
+        update_map_values(sample_data, meta_data, "external_id")
         update_map_values(sample_data, meta_data, "assembly")
         update_map_values(sample_data, meta_data, "hybrid")
         update_map_values(sample_data, meta_data, "single_end")
         update_map_values(sample_data, meta_data, "merge")
         update_map_values(sample_data, meta_data, "downsampled")
 
-
-        if(!sample_data[meta_data.sample].containsKey(meta_data.id)){
-            sample_data[meta_data.sample][meta_data.id] = [:]
+        if(!sample_data[meta_data.sample].containsKey(meta_data.external_id)){
+            sample_data[meta_data.sample][meta_data.external_id] = [:]
         }
 
         if(report_value instanceof Path){
             def extension = report_value.getExtension()
             if(!check_file_params(report_tag, extension)){
                 continue
             }
-            // TODO pass in report metadata
             def output_data = parse_data(report_value, extension, report_tag, headers_list)
             if(output_data){
                 report_value = output_data
             }
         }
 
-        sample_data[meta_data.sample][meta_data.id][report_tag.report_tag] = report_value
+        sample_data[meta_data.sample][meta_data.external_id][report_tag.report_tag] = report_value
     }
 
 

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
@@ -47,7 +47,6 @@ workflow INPUT_CHECK {
                         meta[0].id = "${meta[0].id}_${meta[0].external_id}"
                     }
                 }
-                println "${meta[0].id} ${meta[0]}"
                 processedIDs << meta[0].id
                 tuple(meta[0].id, meta[0])
         }
@@ -135,7 +134,7 @@ def format_reads(ArrayList sheet_data){
     def error_occured = false
     meta.id = sheet_data[0] // id is first value
     meta.sample = sheet_data[1].external_id
-    meta.external_id = sheet_data[0]
+    meta.external_id = sheet_data[1].external_id
 
     meta.hybrid = false
     meta.assembly = false