From 5893cd260bb58c420275bc7bfe100b7e783fb3cd Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Sat, 30 Mar 2024 20:31:01 -0300
Subject: [PATCH] refactor: Fix schema validation when using txt files

---
 microview/file_finder.py                   | 4 ++--
 microview/schemas/kaiju_report.schema.json | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/microview/file_finder.py b/microview/file_finder.py
index 8c2ec55..24d3193 100644
--- 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
index e42a531..7ec9012 100644
--- 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"]