refactor: Fix schema validation when using txt files

dalmolingroup · Mar 30, 2024 · 5893cd2 · 5893cd2
1 parent 252cb8a
commit 5893cd2
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/microview/file_finder.py b/microview/file_finder.py
@@ -96,7 +96,7 @@ def detect_report_type(report_paths: List[Path], console) -> List[Sample]:
           one the report path, the other a string specifying the report type.
     """
     kaiju_validated = [
-        get_validation_dict(report, schema=kaiju_report_schema)
+        get_validation_dict(report, format="tsv", schema=kaiju_report_schema)
         for report in report_paths
     ]
     kaiju_reports = [
@@ -107,7 +107,7 @@ def detect_report_type(report_paths: List[Path], console) -> List[Sample]:
 
     # TODO: Improve Kraken validation
     kraken_validated = [
-        get_validation_dict(report, checks=[checks.table_dimensions(num_fields=6)])
+        get_validation_dict(report, format="tsv", checks=[checks.table_dimensions(num_fields=6)])
         for report in report_paths
     ]
     kraken_reports = [

diff --git a/microview/schemas/kaiju_report.schema.json b/microview/schemas/kaiju_report.schema.json
@@ -10,25 +10,25 @@
       "format": "default",
       "name": "percent",
       "type": "number",
-      "required": false
+      "required": true
     },
     {
       "format": "default",
       "name": "reads",
       "type": "integer",
-      "required": false
+      "required": true
     },
     {
       "format": "default",
       "name": "taxon_id",
       "type": "integer",
-      "required": false
+      "required": true
     },
     {
       "format": "default",
       "name": "taxon_name",
       "type": "string",
-      "required": false
+      "required": true
     }
   ],
   "missingValues": ["NA"]